Alignments for a candidate for trpB in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Sinorhizobium fredii NGR234

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate YP_002827861.1 NGR_c33780 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_000018545.1:YP_002827861.1
          Length = 406

 Score =  131 bits (330), Expect = 3e-35
 Identities = 116/363 (31%), Positives = 164/363 (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   P          
Sbjct: 123 GAGQHGVASATVAARFGLPCVVYMGATDVERQAPNVFRMKLLGAEV--KPVTAGH----- 175

Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVL------DVVLLHQSVIGQETITQ 243
                   G+L  AM+EA+   + N     YL+G+        ++V   Q+VIGQE   Q
Sbjct: 176 --------GTLKDAMNEALRDWVTNVDSTYYLIGTAAGPHPYPEMVRDFQAVIGQEAKEQ 227

Query: 244 -LDLLGEDADILIGCVGGGSNFGGFTYPFI------------GNK--KGKRYIAVSSAEI 288
            L   G   D+++  VGGGSN  G  +PF+            G K   G  + A  +A  
Sbjct: 228 LLAAEGRLPDLVVAAVGGGSNAIGIFHPFLDDDGVRIVGVEAGGKGLDGDEHCASITAGS 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: 373
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 YP_002827861.1 NGR_c33780 (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.23279.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-195  634.1   0.0   4.9e-195  634.0   0.0    1.0  1  lcl|NCBI__GCF_000018545.1:YP_002827861.1  NGR_c33780 tryptophan synthase s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002827861.1  NGR_c33780 tryptophan synthase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  634.0   0.0  4.9e-195  4.9e-195       1     383 [.      18     400 ..      18     402 .. 0.99

  Alignments for each domain:
  == domain 1  score: 634.0 bits;  conditional E-value: 4.9e-195
                                 TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 
                                               g+fg fGG++v+e+l++ + +l+++++kak+d+ fk+ele+l  +y grp+pl+fa++l+ +lggakiy
  lcl|NCBI__GCF_000018545.1:YP_002827861.1  18 GRFGIFGGRFVAETLMPLILDLQDEWNKAKNDPVFKAELEKLGAHYIGRPSPLYFAERLTAELGGAKIY 86 
                                               78******************************************************************* PP

                                 TIGR00263  70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138
                                               +kre+l+htG+hkinn +gq+llakr+Gk+riiaetGaGqhGva+at+aa++gl c+vymGa+dverq+
  lcl|NCBI__GCF_000018545.1:YP_002827861.1  87 FKREELNHTGSHKINNCIGQILLAKRMGKTRIIAETGAGQHGVASATVAARFGLPCVVYMGATDVERQA 155
                                               ********************************************************************* PP

                                 TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207
                                               +nvfrm+llga+v+pvt G+ tlkda+nealrdWvt+v++t+y++G+a+GphP+Pe+vr+fq+vig+e+
  lcl|NCBI__GCF_000018545.1:YP_002827861.1 156 PNVFRMKLLGAEVKPVTAGHGTLKDAMNEALRDWVTNVDSTYYLIGTAAGPHPYPEMVRDFQAVIGQEA 224
                                               ********************************************************************* PP

                                 TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276
                                               keq+l++egrlPd v+a+vGGGsnaiGif++f++d+ v+++gveagGkG+d ++h+a++++G++GvlhG
  lcl|NCBI__GCF_000018545.1:YP_002827861.1 225 KEQLLAAEGRLPDLVVAAVGGGSNAIGIFHPFLDDDGVRIVGVEAGGKGLDGDEHCASITAGSPGVLHG 293
                                               ********************************************************************* PP

                                 TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345
                                               ++t+llqd dGqi+e hs+saGldypg+gPeha+l+++gr+ey+ i d+ealea+++l++ eGiipale
  lcl|NCBI__GCF_000018545.1:YP_002827861.1 294 NRTYLLQDGDGQIKEGHSISAGLDYPGIGPEHAWLNDIGRVEYVPIMDHEALEAFQTLTRLEGIIPALE 362
                                               ********************************************************************* PP

                                 TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvak 383
                                                shala ++k apk+ kdei+++nlsGrGdkd++tv k
  lcl|NCBI__GCF_000018545.1:YP_002827861.1 363 PSHALAEVIKRAPKMGKDEIILMNLSGRGDKDIFTVGK 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: 00:00:00.02
# Mc/sec: 7.47
//
[ok]

This GapMind analysis is from Apr 10 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