Alignments for a candidate for trpB in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Sinorhizobium meliloti 1021

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate SMc02766 SMc02766 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__Smeli:SMc02766
          Length = 406

 Score =  130 bits (326), Expect = 1e-34
 Identities = 112/363 (30%), Positives = 166/363 (45%), Gaps = 54/363 (14%)

Query: 72  IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131
           IGRP+PL+ A+RL   L   A+IYFK E    TGSHKIN  I Q   AK  G   ++ ET
Sbjct: 64  IGRPSPLYFAERLTAELGG-AKIYFKREELNHTGSHKINNCIGQILLAKRMGKTRIIAET 122

Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191
           GAGQ G A A  A+ + +   ++M     E++      M+L GA V           + +
Sbjct: 123 GAGQHGVASATVAARFGLPCVVYMGATDVERQAPNVFRMKLLGAEV-----------KPV 171

Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVL------DVVLLHQSVIGQETITQ 243
              N    G+L  AM+EA+   + N     YL+G+        ++V   Q+VIG+E   Q
Sbjct: 172 TAGN----GTLKDAMNEALRDWVTNVDSTYYLIGTAAGPHPYPEMVRDFQAVIGEEAKQQ 227

Query: 244 -LDLLGEDADILIGCVGGGSNFGGFTYPFIGNK--------------KGKRYIAVSSAEI 288
            L+  G   D+++  VGGGSN  G  + F+ ++               G  + A  +A  
Sbjct: 228 ILEAEGRLPDLVVAAVGGGSNAIGIFHSFLDDEGVRIVGVEAGGKGLDGDEHCASLTAGS 287

Query: 289 PKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVE 348
           P    G   Y   D  G +     I+ G D            Y G+ P  + L   G VE
Sbjct: 288 PGVLHGNRTYLLQDGDGQIKEGHSISAGLD------------YPGIGPEHAWLNDIGRVE 335

Query: 349 WREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGL 408
           +    + E  EA +     +GI+PA E +HA+  V+  A +  K+   ++I+ NLSG G 
Sbjct: 336 YVPIMDHEALEAFQTLTRLEGIIPALEPSHALAEVIKRAPKMGKD---EIILMNLSGRGD 392

Query: 409 LDL 411
            D+
Sbjct: 393 KDI 395


Lambda     K      H
   0.318    0.138    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 383
Number of extensions: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 425
Length of database: 406
Length adjustment: 31
Effective length of query: 394
Effective length of database: 375
Effective search space:   147750
Effective search space used:   147750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate SMc02766 SMc02766 (tryptophan synthase subunit beta)
to HMM TIGR00263 (trpB: tryptophan synthase, beta subunit (EC 4.2.1.20))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00263.hmm
# target sequence database:        /tmp/gapView.21058.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00263  [M=385]
Accession:   TIGR00263
Description: trpB: tryptophan synthase, beta subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-195  636.1   0.0   1.2e-195  636.0   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02766  SMc02766 tryptophan synthase sub


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02766  SMc02766 tryptophan synthase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  636.0   0.0  1.2e-195  1.2e-195       1     383 [.      18     400 ..      18     402 .. 0.99

  Alignments for each domain:
  == domain 1  score: 636.0 bits;  conditional E-value: 1.2e-195
                           TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredl 75 
                                         g+fg fGG++v+e+l++ + +l++++ +ak+d++fk+ele+l  +y grp+pl+fa++l+ +lggakiy+kre+l
  lcl|FitnessBrowser__Smeli:SMc02766  18 GRFGIFGGRFVAETLMPLILDLQDEWARAKNDPAFKAELENLGTHYIGRPSPLYFAERLTAELGGAKIYFKREEL 92 
                                         78************************************************************************* PP

                           TIGR00263  76 lhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgak 150
                                         +htG+hkinn +gq+llakr+Gk+riiaetGaGqhGva+at+aa++gl c+vymGa+dverq++nvfrm+llga+
  lcl|FitnessBrowser__Smeli:SMc02766  93 NHTGSHKINNCIGQILLAKRMGKTRIIAETGAGQHGVASATVAARFGLPCVVYMGATDVERQAPNVFRMKLLGAE 167
                                         *************************************************************************** PP

                           TIGR00263 151 vvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviac 225
                                         v+pvt G+ tlkda+nealrdWvt+v++t+y++G+a+GphP+Pe+vr+fq+vigee+k+qile+egrlPd v+a+
  lcl|FitnessBrowser__Smeli:SMc02766 168 VKPVTAGNGTLKDAMNEALRDWVTNVDSTYYLIGTAAGPHPYPEMVRDFQAVIGEEAKQQILEAEGRLPDLVVAA 242
                                         *************************************************************************** PP

                           TIGR00263 226 vGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGld 300
                                         vGGGsnaiGif++f++de v+++gveagGkG+d ++h+a+l++G++GvlhG++t+llqd dGqi+e hs+saGld
  lcl|FitnessBrowser__Smeli:SMc02766 243 VGGGSNAIGIFHSFLDDEGVRIVGVEAGGKGLDGDEHCASLTAGSPGVLHGNRTYLLQDGDGQIKEGHSISAGLD 317
                                         *************************************************************************** PP

                           TIGR00263 301 ypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGd 375
                                         ypg+gPeha+l+++gr+ey+ i d+ealea+++l++ eGiipale shala ++k apk+ kdei+++nlsGrGd
  lcl|FitnessBrowser__Smeli:SMc02766 318 YPGIGPEHAWLNDIGRVEYVPIMDHEALEAFQTLTRLEGIIPALEPSHALAEVIKRAPKMGKDEIILMNLSGRGD 392
                                         *************************************************************************** PP

                           TIGR00263 376 kdletvak 383
                                         kd++tv k
  lcl|FitnessBrowser__Smeli:SMc02766 393 KDIFTVGK 400
                                         *****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (406 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.50
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis