"Robert E. Bruccoleri" wrote:
You can try starting postmaster with the "-o -fs" option. This will disable sequential
scans if there is an index. There is also an environment variable you can set, prior
to the operation. I have run into this same problem.
> Dear Tom,
> I am writing to you because you are the maintainer of the
> query optimizer and planner.
> I have found a very significant performance degradation
> between PostgreSQL 6.5.3 and 7.1beta3, which will severely impact two
> large applications that I have developed and maintain for several
> clients. The performance difference is seen with the use of indices in
> SELECT statements, whereby the current release does not make effective
> use of the indices and 6.5.3 does. All of these tests were run on a SGI
> R10000 Indigo2 system running Irix 6.5. All the regression tests passed
> as expected for both versions.
> I have followed the discussion in pgsql-hackers over the previous
> months and others have noted some performance problems, and the response
> has typically been to VACUUM the tables. Unfortunately, this is not a
> practical option for my applications. They are very large -- I have one
> table that is 17GB in length, and the applications are used frequently.
> More importantly, PostgreSQL 6.5.3 works very, very well without
> VACUUM'ing.
> In order to assist you to diagnosing and correcting this
> problem, I have prepared a test database that shows the problems. I
> will attach three files; the test script, the log from running it on
> version 6.5.3, and the log from running it on version 7.1beta3. In
> addition, I have setup an anonymous FTP directory on
> ftp.congen.com:/pub/pg_perf which contains all of these files as well
> as the compressed table dumps used to build the test database. (When
> you have finished copying the files, please let me know.)
> The test script creates the database including the necessary
> indexing, and then runs EXPLAIN on each of the queries followed by
> actually executing the queries with "timex" commands to report elapsed
> times. The striking difference in the query plans is that 7.1 uses
> only sequential searches for the SELECT's whereas 6.5.3 uses index
> scans. As a result, 7.1 is almost two orders of magnitude slower than
> 6.5.3 with exactly the same data, schema, and queries.
>
> I plead with you to revisit this question of performance and
> fix PostgreSQL 7.1 to work as well as PostgreSQL 6.5.3 does. I depend
> upon PostgreSQL for much of my work, and I do not want to abandon it
> because of this performance problem which arose only recently. Thank
> you.
>
> +----------------------------------+------------------------------------+
> | Robert E. Bruccoleri, Ph.D. | Phone: 609 737 6383 |
> | President, Congenomics, Inc. | Fax: 609 737 7528 |
> | 114 W Franklin Ave, Suite K1,4,5 | email: [EMAIL PROTECTED] |
> | P.O. Box 314 | URL: http://www.congen.com/~bruc |
> | Pennington, NJ 08534 | |
> +----------------------------------+------------------------------------+
>
> ------------------------------------------------------------------------
> #!/bin/csh
>
> createdb perf_test
>
> gunzip <proteins.dmp.gz | timex psql -e perf_test
> gunzip <comparisons_4.dmp.gz | timex psql -e perf_test
> gunzip <concordance_91.dmp.gz | timex psql -e perf_test
>
> psql -e perf_test <<EOF
> explain select * from comparisons_4 where name1 = 'HI0001';
> explain select count(*) from comparisons_4 where code = 80003;
> explain select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 =
>'HI0003' and c.name2 = p.name;
> explain select c.target_name, c.matched_name, c.score, p.purpose from concordance_91
>c, proteins p where c.matched_name = p.name;
> EOF
>
> timex psql -e -c "select * from comparisons_4 where name1 = 'HI0001'" perf_test
> timex psql -e -c "select count(*) from comparisons_4 where code = 80003" perf_test
> timex psql -e -c "select p.name, p.purpose from comparisons_4 c, proteins p where
>c.name1 = 'HI0003' and c.name2 = p.name" perf_test
> timex psql -e -c "select c.target_name, c.matched_name, c.score, p.purpose from
>concordance_91 c, proteins p where c.matched_name = p.name" perf_test
>
> ------------------------------------------------------------------------
> CREATE TABLE "proteins" (
> "name" character varying(16),
> "organism" text,
> "start_position" int4,
> "last_position" int4,
> "seq" text,
> "purpose" text,
> "alternate_key" character varying(16),
> "comment" text,
> "compared" bool,
> "complement" bool,
> "chromosome" character varying(4),
> "essentiality" float8);
> QUERY: CREATE TABLE "proteins" (
> "name" character varying(16),
> "organism" text,
> "start_position" int4,
> "last_position" int4,
> "seq" text,
> "purpose" text,
> "alternate_key" character varying(16),
> "comment" text,
> "compared" bool,
> "complement" bool,
> "chromosome" character varying(4),
> "essentiality" float8);
> COPY "proteins" FROM stdin;
> QUERY: COPY "proteins" FROM stdin;
> CREATE INDEX "protein_names" on "proteins" using btree ( "name" "varchar_ops" );
> QUERY: CREATE INDEX "protein_names" on "proteins" using btree ( "name"
>"varchar_ops" );
> CREATE INDEX "protein_organism" on "proteins" using btree ( "organism" "text_ops" );
> QUERY: CREATE INDEX "protein_organism" on "proteins" using btree ( "organism"
>"text_ops" );
> CREATE
> CREATE
> CREATE
> EOF
>
> real 1:11.42
> user 3.15
> sys 0.53
>
> CREATE TABLE "comparisons_4" (
> "name1" character varying(16),
> "name2" character varying(16),
> "z_score" float8,
> "expected" float8,
> "local_overlap_ratio" float8,
> "local_overlap_count" int4,
> "overlap_ratio" float8,
> "code" int4);
> QUERY: CREATE TABLE "comparisons_4" (
> "name1" character varying(16),
> "name2" character varying(16),
> "z_score" float8,
> "expected" float8,
> "local_overlap_ratio" float8,
> "local_overlap_count" int4,
> "overlap_ratio" float8,
> "code" int4);
> COPY "comparisons_4" FROM stdin;
> QUERY: COPY "comparisons_4" FROM stdin;
> CREATE INDEX "comparisons_4_name1" on "comparisons_4" using btree ( "name1"
>"varchar_ops" );
> QUERY: CREATE INDEX "comparisons_4_name1" on "comparisons_4" using btree ( "name1"
>"varchar_ops" );
> CREATE INDEX "comparisons_4_name2" on "comparisons_4" using btree ( "name2"
>"varchar_ops" );
> QUERY: CREATE INDEX "comparisons_4_name2" on "comparisons_4" using btree ( "name2"
>"varchar_ops" );
> CREATE INDEX "comparisons_4_code" on "comparisons_4" using btree ( "code"
>"int4_ops" );
> QUERY: CREATE INDEX "comparisons_4_code" on "comparisons_4" using btree ( "code"
>"int4_ops" );
> CREATE
> CREATE
> CREATE
> CREATE
> EOF
>
> real 16:42.13
> user 5.86
> sys 0.96
>
> CREATE TABLE "concordance_91" (
> "target_name" character varying(16),
> "matched_name" character varying(16),
> "score" text);
> QUERY: CREATE TABLE "concordance_91" (
> "target_name" character varying(16),
> "matched_name" character varying(16),
> "score" text);
> REVOKE ALL on "concordance_91" from PUBLIC;
> QUERY: REVOKE ALL on "concordance_91" from PUBLIC;
> GRANT ALL on "concordance_91" to PUBLIC;
> QUERY: GRANT ALL on "concordance_91" to PUBLIC;
> COPY "concordance_91" FROM stdin;
> QUERY: COPY "concordance_91" FROM stdin;
> CREATE
> CHANGE
> CHANGE
> EOF
>
> real 0.30
> user 0.02
> sys 0.04
>
> explain select * from comparisons_4 where name1 = 'HI0001';
> QUERY: explain select * from comparisons_4 where name1 = 'HI0001';
> NOTICE: QUERY PLAN:
>
> Index Scan using comparisons_4_name1 on comparisons_4 (cost=2.05 rows=1 width=64)
>
> explain select count(*) from comparisons_4 where code = 80003;
> QUERY: explain select count(*) from comparisons_4 where code = 80003;
> NOTICE: QUERY PLAN:
>
> Aggregate (cost=2.05 rows=1 width=12)
> -> Index Scan using comparisons_4_code on comparisons_4 (cost=2.05 rows=1
>width=12)
>
> explain select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 =
>'HI0003' and c.name2 = p.name;
> QUERY: explain select p.name, p.purpose from comparisons_4 c, proteins p where
>c.name1 = 'HI0003' and c.name2 = p.name;
> NOTICE: QUERY PLAN:
>
> Nested Loop (cost=4.10 rows=1 width=36)
> -> Index Scan using comparisons_4_name1 on comparisons_4 c (cost=2.05 rows=1
>width=12)
> -> Index Scan using protein_names on proteins p (cost=2.05 rows=36840 width=24)
>
> explain select c.target_name, c.matched_name, c.score, p.purpose from concordance_91
>c, proteins p where c.matched_name = p.name;
> QUERY: explain select c.target_name, c.matched_name, c.score, p.purpose from
>concordance_91 c, proteins p where c.matched_name = p.name;
> NOTICE: QUERY PLAN:
>
> Nested Loop (cost=2093.00 rows=36840 width=60)
> -> Seq Scan on concordance_91 c (cost=43.00 rows=1000 width=36)
> -> Index Scan using protein_names on proteins p (cost=2.05 rows=36840 width=24)
>
> EXPLAIN
> EXPLAIN
> EXPLAIN
> EXPLAIN
> EOF
> QUERY: select * from comparisons_4 where name1 = 'HI0001'
> name1 |name2
>|z_score|expected|local_overlap_ratio|local_overlap_count|overlap_ratio| code
>
>------+---------------+-------+--------+-------------------+-------------------+-------------+-----
> HI0001|PDB2DBV_O | 1217.4| 0| 0.56716| 335|
>0.560468|30012
> HI0001|PDB4DBV_O | 1207| 0| 0.56418| 335|
>0.557523|30012
> HI0001|PDB2GD1_P | 1226.4| 0| 0.57015| 335|
>0.563423|30012
> HI0001|PDB1GAE_O | 1861.8| 0| 0.83133| 332|
>0.814164|30012
> HI0001|PDB4GPD_1 | 1357.8| 0| 0.64865| 333|
>0.637169|30012
> HI0001|HP1346 | 850.3| 6.9e-41| 0.39222| 334|
>0.386435|30005
> HI0001|TP0844 | 780.3| 5.8e-37| 0.46307| 352|
>0.465716|30014
> HI0001|PDB1HDG_O | 1020.4| 0| 0.48024| 329|
>0.466074|30012
> HI0001|SCPIR-DEBYG1 | 1405.2| 0| 0.6497| 334|
>0.640117|30000
> HI0001|Rv1436 | 970.4| 0| 0.49558| 339|
> 0.49558|30010
> HI0001|PDB1CER_O | 949.7| 0| 0.47734| 331|
>0.466075|30012
> HI0001|PDB1NLH_ | 935.1| 0| 0.46847| 333|
>0.458825|30012
> HI0001|PDB1GGA_A | 918| 0| 0.52125| 353|
> 0.51397|30012
> HI0001|PDB1GAD_O | 1869.5| 0| 0.83434| 332|
>0.817112|30012
> HI0001|PDB1GYP_A | 900.1| 0| 0.51275| 353|
>0.505589|30012
> HI0001|MG301 | 866.7| 0| 0.43155| 336|
>0.427731|30004
> HI0001|SCSW-G3P1_YEAST| 1425.3| 0| 0.65868| 334|
>0.648965|30000
> HI0001|ScTDH1 | 1424.6| 0| 0.65868| 334|
>0.648965|30013
> HI0001|ScTDH2 | 1405.2| 0| 0.6497| 334|
>0.640117|30013
> HI0001|SCSW-G3P3_YEAST| 1417.5| 0| 0.65868| 334|
>0.648965|30000
> HI0001|ScTDH3 | 1416.8| 0| 0.65868| 334|
>0.648965|30013
> HI0001|SCGP-3720 | 1416.8| 0| 0.66168| 334|
>0.651921|30000
> HI0001|SCGP-E243731 | 1416.8| 0| 0.65868| 334|
>0.648965|30000
> HI0001|SCSW-G3P2_YEAST| 1405.9| 0| 0.6497| 334|
>0.640117|30000
> HI0001|SCGP-1008189 | 1424.6| 0| 0.65868| 334|
>0.648965|30000
> HI0001|SCGP-3726 | 1398.7| 0| 0.6497| 334|
>0.640117|30000
> HI0001|PDB3GPD_R | 1432.2| 0| 0.63772| 334|
>0.628314|30012
> HI0001|HP0921 | 762.6| 5.6e-36| 0.40407| 344|
> 0.41003|30005
> HI0001|MJ1146 | 124.7| 1.9| 0.25094| 267|
>0.195338|30007
> HI0001|SCGP-3724 | 1371.5| 0| 0.63772| 334|
>0.628314|30000
> (30 rows)
>
> real 0.18
> user 0.02
> sys 0.03
>
> QUERY: select count(*) from comparisons_4 where code = 80003
> count
> -----
> 3231
> (1 row)
>
> real 0.34
> user 0.02
> sys 0.03
>
> QUERY: select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 =
>'HI0003' and c.name2 = p.name
> name |purpose
>
>-------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> MG263 |hypothetical protein
> HP0652 |phosphoserine phosphatase
> MJ1594 |phosphoserine phosphatase
> MG125 |hypothetical protein
> TP0290 |conserved hypothetical protein
> HI1033 |phosphoserine phosphatase (o-phosphoserine phosphohydrolase)
> HI0597 |hypothetical protein
> Rv3813c|(MTCY409.17), len: 273. Unknown, similar to many hypothetical proteins eg.
>YXEH_BACSU P54947 hypothetical 30.2 kd protein in idh-deor (270 aa), fasta results;
>opt: 329 z-score: 456.0 E(): 2.2e-18, 32.2% identity in 267 aa overlap
> Rv3042c|(MTV012.57c), len: 409. The C-terminal domain (150-409) is highly similar to
>several SerB proteins e.g. P06862|SERB_ECOLI. N-terminus (1-150) shows no similarity,
>FASTA score: sp|P06862|SERB_ECOLI PHOSPHOSERINE PHOSPHATASE (EC 3.1 (322 aa) opt: 628
>z-score: 753.3 E(): 0; 46.8%identity in 235 aa overlap. TBparse score is 0.884
> MG265 |hypothetical protein
> (10 rows)
>
> real 0.24
> user 0.02
> sys 0.03
>
> QUERY: select c.target_name, c.matched_name, c.score, p.purpose from concordance_91
>c, proteins p where c.matched_name = p.name
> target_name|matched_name| score|purpose
>
>-----------+------------+--------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> ECinfA |BSInfA |0.680556|initiation factor IF-1
> ECinfA |HI0548 | 0.80952|initiation factor IF-1
> ECinfA |HP1298 | 0.61111|translation initiation factor EF-1
> ECinfA |Rv3462c |0.684936|(MTCY13E12.15c), len: 73 aa. infA. Probable
>initiation factor IF-1. FASTA results: identical to IF1_MYCBO P45957 initiation
>factor if-1 (72 aa)
> ECrpmA |BB0780 |0.635297|ribosomal protein L27
> ECrpmA |HI0879 | 0.87059|ribosomal protein L27
> ECrpmA |HP0297 |0.613632|ribosomal protein L27
> ECrpmA |Rv2441c |0.616278|(MTCY428.05), len: 86. Probable rpmA, similar to
>eg RL27_ECOLI P02427 50s ribosomal protein l27, (84 aa), fasta scores, opt: 328, E():
>7.1e-17, (64.2% identity in 81 aa overlap); contains PS00831 Ribosomal protein L27
>signature
> (8 rows)
>
> real 0.17
> user 0.02
> sys 0.03
>
> ------------------------------------------------------------------------
> CREATE DATABASE
> CREATE TABLE "proteins" (
> "name" character varying(16),
> "organism" text,
> "start_position" int4,
> "last_position" int4,
> "seq" text,
> "purpose" text,
> "alternate_key" character varying(16),
> "comment" text,
> "compared" bool,
> "complement" bool,
> "chromosome" character varying(4),
> "essentiality" float8);
> CREATE
> COPY "proteins" FROM stdin;
> CREATE INDEX "protein_names" on "proteins" using btree ( "name" "varchar_ops" );
> CREATE
> CREATE INDEX "protein_organism" on "proteins" using btree ( "organism" "text_ops" );
> CREATE
>
> real 1:04.49
> user 3.14
> sys 0.57
>
> CREATE TABLE "comparisons_4" (
> "name1" character varying(16),
> "name2" character varying(16),
> "z_score" float8,
> "expected" float8,
> "local_overlap_ratio" float8,
> "local_overlap_count" int4,
> "overlap_ratio" float8,
> "code" int4);
> CREATE
> COPY "comparisons_4" FROM stdin;
> CREATE INDEX "comparisons_4_name1" on "comparisons_4" using btree ( "name1"
>"varchar_ops" );
> CREATE
> CREATE INDEX "comparisons_4_name2" on "comparisons_4" using btree ( "name2"
>"varchar_ops" );
> CREATE
> CREATE INDEX "comparisons_4_code" on "comparisons_4" using btree ( "code"
>"int4_ops" );
> CREATE
>
> real 7:04.43
> user 5.87
> sys 1.03
>
> CREATE TABLE "concordance_91" (
> "target_name" character varying(16),
> "matched_name" character varying(16),
> "score" text);
> CREATE
> REVOKE ALL on "concordance_91" from PUBLIC;
> CHANGE
> GRANT ALL on "concordance_91" to PUBLIC;
> CHANGE
> COPY "concordance_91" FROM stdin;
>
> real 0.60
> user 0.01
> sys 0.03
>
> explain select * from comparisons_4 where name1 = 'HI0001';
> NOTICE: QUERY PLAN:
>
> Seq Scan on comparisons_4 (cost=0.00..15640.81 rows=5918 width=64)
>
> EXPLAIN
> explain select count(*) from comparisons_4 where code = 80003;
> NOTICE: QUERY PLAN:
>
> Aggregate (cost=15655.61..15655.61 rows=1 width=0)
> -> Seq Scan on comparisons_4 (cost=0.00..15640.81 rows=5918 width=0)
>
> EXPLAIN
> explain select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 =
>'HI0003' and c.name2 = p.name;
> NOTICE: QUERY PLAN:
>
> Merge Join (cost=22495.22..23029.70 rows=2180283 width=36)
> -> Sort (cost=16011.62..16011.62 rows=5918 width=12)
> -> Seq Scan on comparisons_4 c (cost=0.00..15640.81 rows=5918 width=12)
> -> Sort (cost=6483.60..6483.60 rows=36840 width=24)
> -> Seq Scan on proteins p (cost=0.00..3247.40 rows=36840 width=24)
>
> EXPLAIN
> explain select c.target_name, c.matched_name, c.score, p.purpose from concordance_91
>c, proteins p where c.matched_name = p.name;
> NOTICE: QUERY PLAN:
>
> Merge Join (cost=6553.43..7026.43 rows=368400 width=60)
> -> Sort (cost=69.83..69.83 rows=1000 width=36)
> -> Seq Scan on concordance_91 c (cost=0.00..20.00 rows=1000 width=36)
> -> Sort (cost=6483.60..6483.60 rows=36840 width=24)
> -> Seq Scan on proteins p (cost=0.00..3247.40 rows=36840 width=24)
>
> EXPLAIN
> select * from comparisons_4 where name1 = 'HI0001'
> name1 | name2 | z_score | expected | local_overlap_ratio |
>local_overlap_count | overlap_ratio | code
>
>--------+-----------------+---------+----------+---------------------+---------------------+---------------+-------
> HI0001 | PDB1GAD_O | 1869.5 | 0 | 0.83434 |
> 332 | 0.817112 | 30012
> HI0001 | PDB1GAE_O | 1861.8 | 0 | 0.83133 |
> 332 | 0.814164 | 30012
> HI0001 | PDB3GPD_R | 1432.2 | 0 | 0.63772 |
> 334 | 0.628314 | 30012
> HI0001 | SCSW-G3P1_YEAST | 1425.3 | 0 | 0.65868 |
> 334 | 0.648965 | 30000
> HI0001 | SCGP-1008189 | 1424.6 | 0 | 0.65868 |
> 334 | 0.648965 | 30000
> HI0001 | ScTDH1 | 1424.6 | 0 | 0.65868 |
> 334 | 0.648965 | 30013
> HI0001 | SCSW-G3P3_YEAST | 1417.5 | 0 | 0.65868 |
> 334 | 0.648965 | 30000
> HI0001 | ScTDH3 | 1416.8 | 0 | 0.65868 |
> 334 | 0.648965 | 30013
> HI0001 | SCGP-3720 | 1416.8 | 0 | 0.66168 |
> 334 | 0.651921 | 30000
> HI0001 | SCGP-E243731 | 1416.8 | 0 | 0.65868 |
> 334 | 0.648965 | 30000
> HI0001 | SCSW-G3P2_YEAST | 1405.9 | 0 | 0.6497 |
> 334 | 0.640117 | 30000
> HI0001 | ScTDH2 | 1405.2 | 0 | 0.6497 |
> 334 | 0.640117 | 30013
> HI0001 | SCPIR-DEBYG1 | 1405.2 | 0 | 0.6497 |
> 334 | 0.640117 | 30000
> HI0001 | SCGP-3726 | 1398.7 | 0 | 0.6497 |
> 334 | 0.640117 | 30000
> HI0001 | SCGP-3724 | 1371.5 | 0 | 0.63772 |
> 334 | 0.628314 | 30000
> HI0001 | PDB4GPD_1 | 1357.8 | 0 | 0.64865 |
> 333 | 0.637169 | 30012
> HI0001 | PDB2GD1_P | 1226.4 | 0 | 0.57015 |
> 335 | 0.563423 | 30012
> HI0001 | PDB2DBV_O | 1217.4 | 0 | 0.56716 |
> 335 | 0.560468 | 30012
> HI0001 | PDB4DBV_O | 1207 | 0 | 0.56418 |
> 335 | 0.557523 | 30012
> HI0001 | PDB1HDG_O | 1020.4 | 0 | 0.48024 |
> 329 | 0.466074 | 30012
> HI0001 | Rv1436 | 970.4 | 0 | 0.49558 |
> 339 | 0.49558 | 30010
> HI0001 | PDB1CER_O | 949.7 | 0 | 0.47734 |
> 331 | 0.466075 | 30012
> HI0001 | PDB1NLH_ | 935.1 | 0 | 0.46847 |
> 333 | 0.458825 | 30012
> HI0001 | PDB1GGA_A | 918 | 0 | 0.52125 |
> 353 | 0.51397 | 30012
> HI0001 | PDB1GYP_A | 900.1 | 0 | 0.51275 |
> 353 | 0.505589 | 30012
> HI0001 | MG301 | 866.7 | 0 | 0.43155 |
> 336 | 0.427731 | 30004
> HI0001 | HP1346 | 850.3 | 6.9e-41 | 0.39222 |
> 334 | 0.386435 | 30005
> HI0001 | TP0844 | 780.3 | 5.8e-37 | 0.46307 |
> 352 | 0.465716 | 30014
> HI0001 | HP0921 | 762.6 | 5.6e-36 | 0.40407 |
> 344 | 0.41003 | 30005
> HI0001 | MJ1146 | 124.7 | 1.9 | 0.25094 |
> 267 | 0.195338 | 30007
> (30 rows)
>
> real 22.68
> user 0.01
> sys 0.03
>
> select count(*) from comparisons_4 where code = 80003
> count
> -------
> 3231
> (1 row)
>
> real 21.49
> user 0.01
> sys 0.03
>
> select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 = 'HI0003'
>and c.name2 = p.name
> name |
>
>purpose
>
>---------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> HI0597 | hypothetical protein
> HI1033 | phosphoserine phosphatase (o-phosphoserine phosphohydrolase)
> HP0652 | phosphoserine phosphatase
> MG125 | hypothetical protein
> MG263 | hypothetical protein
> MG265 | hypothetical protein
> MJ1594 | phosphoserine phosphatase
> Rv3042c | (MTV012.57c), len: 409. The C-terminal domain (150-409) is highly similar
>to several SerB proteins e.g. P06862|SERB_ECOLI. N-terminus (1-150) shows no
>similarity, FASTA score: sp|P06862|SERB_ECOLI PHOSPHOSERINE PHOSPHATASE (EC 3.1 (322
>aa) opt: 628 z-score: 753.3 E(): 0; 46.8%identity in 235 aa overlap. TBparse score is
>0.884
> Rv3813c | (MTCY409.17), len: 273. Unknown, similar to many hypothetical proteins
>eg. YXEH_BACSU P54947 hypothetical 30.2 kd protein in idh-deor (270 aa), fasta
>results; opt: 329 z-score: 456.0 E(): 2.2e-18, 32.2% identity in 267 aa overlap
> TP0290 | conserved hypothetical protein
> (10 rows)
>
> real 23.13
> user 0.01
> sys 0.03
>
> select c.target_name, c.matched_name, c.score, p.purpose from concordance_91 c,
>proteins p where c.matched_name = p.name
> target_name | matched_name | score |
> purpose
>
>-------------+--------------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> ECrpmA | BB0780 | 0.635297 | ribosomal protein L27
> ECinfA | BSInfA | 0.680556 | initiation factor IF-1
> ECinfA | HI0548 | 0.80952 | initiation factor IF-1
> ECrpmA | HI0879 | 0.87059 | ribosomal protein L27
> ECrpmA | HP0297 | 0.613632 | ribosomal protein L27
> ECinfA | HP1298 | 0.61111 | translation initiation factor EF-1
> ECrpmA | Rv2441c | 0.616278 | (MTCY428.05), len: 86. Probable rpmA,
>similar to eg RL27_ECOLI P02427 50s ribosomal protein l27, (84 aa), fasta scores,
>opt: 328, E(): 7.1e-17, (64.2% identity in 81 aa overlap); contains PS00831 Ribosomal
>protein L27 signature
> ECinfA | Rv3462c | 0.684936 | (MTCY13E12.15c), len: 73 aa. infA. Probable
>initiation factor IF-1. FASTA results: identical to IF1_MYCBO P45957 initiation
>factor if-1 (72 aa)
> (8 rows)
>
> real 11.16
> user 0.01
> sys 0.03
