Alignments for a candidate for trpB in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Desulfovibrio vulgaris Hildenborough

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate 209013 DVU0085 tryptophan synthase, beta subunit

Query= uniprot:P50383
         (425 letters)



>MicrobesOnline__882:209013
          Length = 414

 Score =  123 bits (309), Expect = 9e-33
 Identities = 118/373 (31%), Positives = 160/373 (42%), Gaps = 62/373 (16%)

Query: 73  GRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTETG 132
           GR TPLF    L   L   ARIY K E     G+HK+N  I Q   AK  G + V+ ETG
Sbjct: 63  GRATPLFLCSNLTARLGG-ARIYLKREDLNHLGAHKVNNTIGQILLAKRMGKKKVIAETG 121

Query: 133 AGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKIL 192
           AGQ G A A  A++  M+ TI+M     E++ +    M++ GA V  + +     G++ L
Sbjct: 122 AGQHGVATAATAALMGMQCTIYMGAEDMERQKLNVFRMRMMGAEVVPAMS-----GQRTL 176

Query: 193 ETNPQHPGSLGIAMSEAIEYAL------KNEFRYLVGSVLD------VVLLHQSVIGQET 240
           +              EA++ AL       NE  YL+GS +       +V   QSVIG+E 
Sbjct: 177 K--------------EAVDEALAAWVQDANETFYLLGSAVGPHPYPAIVRHFQSVIGREA 222

Query: 241 ITQ-LDLLGEDADILIGCVGGGSNFGGFTYPFIGNK-----------KGKRY---IAVSS 285
             Q L+  G   D  I CVGGGSN  G    F+ +            +G  Y    A   
Sbjct: 223 RAQILEAEGRLPDCCIACVGGGSNAIGLFAEFVPDTSVRLIGVEPAGRGLTYGDHAATLC 282

Query: 286 AEIPKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEG 345
              P    G Y Y   D  G    V  I+ G D            Y GV P  S L    
Sbjct: 283 LGEPGVLHGFYSYMLKDDKGEAAAVYSISAGLD------------YPGVGPEHSHLKDMN 330

Query: 346 IVEWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSG 405
             E+    + E  +A       +GI+PA ES+HA+   +  A    K+    +IV NLSG
Sbjct: 331 RAEYVSVTDVEAVDAFFTLSRAEGIIPALESSHALAHAMKMAPAMPKD---AIIVVNLSG 387

Query: 406 HGLLDLSNYESMM 418
            G  D++  E M+
Sbjct: 388 RGDKDVAQIEEMV 400


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: 363
Number of extensions: 20
Number of successful extensions: 5
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: 414
Length adjustment: 32
Effective length of query: 393
Effective length of database: 382
Effective search space:   150126
Effective search space used:   150126
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 209013 DVU0085 (tryptophan synthase, beta subunit)
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.12731.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.9e-186  605.6   0.1   2.2e-186  605.4   0.1    1.0  1  lcl|MicrobesOnline__882:209013  DVU0085 tryptophan synthase, bet


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209013  DVU0085 tryptophan synthase, beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  605.4   0.1  2.2e-186  2.2e-186       1     383 [.      16     398 ..      16     400 .. 0.99

  Alignments for each domain:
  == domain 1  score: 605.4 bits;  conditional E-value: 2.2e-186
                       TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredllhtG 79 
                                     g+fg++GGq+vp++l + l++l ++++  k+d++f +e++++l +y+gr+tpl+ ++nl+ +lgga+iylkredl+h G
  lcl|MicrobesOnline__882:209013  16 GFFGAYGGQFVPDQLKPILDDLAATFDACKDDPSFIEEFTYYLTRYSGRATPLFLCSNLTARLGGARIYLKREDLNHLG 94 
                                     68***************************************************************************** PP

                       TIGR00263  80 ahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgakvvpvtsGs 158
                                     ahk+nn++gq+llakr+Gkk++iaetGaGqhGvata+ aal+g++c++ymGaed+erqklnvfrm+++ga+vvp  sG+
  lcl|MicrobesOnline__882:209013  95 AHKVNNTIGQILLAKRMGKKKVIAETGAGQHGVATAATAALMGMQCTIYMGAEDMERQKLNVFRMRMMGAEVVPAMSGQ 173
                                     ******************************************************************************* PP

                       TIGR00263 159 ktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviacvGGGsnaiGifa 237
                                     +tlk+av+eal +Wv + ++t+y+lGsavGphP+P+ivr+fqsvig+e+++qile+egrlPd  iacvGGGsnaiG+fa
  lcl|MicrobesOnline__882:209013 174 RTLKEAVDEALAAWVQDANETFYLLGSAVGPHPYPAIVRHFQSVIGREARAQILEAEGRLPDCCIACVGGGSNAIGLFA 252
                                     ******************************************************************************* PP

                       TIGR00263 238 afiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgr 316
                                     +f+ d +v+ligve++G+G+   +haatl  G++GvlhG+++++l+d++G+   ++s+saGldypgvgPeh++l++ +r
  lcl|MicrobesOnline__882:209013 253 EFVPDTSVRLIGVEPAGRGLTYGDHAATLCLGEPGVLHGFYSYMLKDDKGEAAAVYSISAGLDYPGVGPEHSHLKDMNR 331
                                     ******************************************************************************* PP

                       TIGR00263 317 aeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvak 383
                                     aey+++td ea++a+ +ls+ eGiipalesshala+++k+ap+++kd+i+vvnlsGrGdkd++++ +
  lcl|MicrobesOnline__882:209013 332 AEYVSVTDVEAVDAFFTLSRAEGIIPALESSHALAHAMKMAPAMPKDAIIVVNLSGRGDKDVAQIEE 398
                                     ****************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (414 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.88
//
[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