Alignments for a candidate for trpB in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Methanosarcina acetivorans C2A

Align tryptophan synthase (EC 4.2.1.20) (characterized)
to candidate WP_011022931.1 MA_RS15685 tryptophan synthase subunit beta

Query= BRENDA::Q97TX6
         (429 letters)



>NCBI__GCF_000007345.1:WP_011022931.1
          Length = 403

 Score =  134 bits (338), Expect = 4e-36
 Identities = 125/405 (30%), Positives = 184/405 (45%), Gaps = 46/405 (11%)

Query: 41  ELLKEVLPSKVLELEFAKERYVKIPDEV--LERYLQ--VGRPTPIIRAKRLEEYLGNNIK 96
           + + EVL   + EL+   E+Y   P+ +  L+ YL+   GR TP+  A+ L +  G   K
Sbjct: 21  QYVPEVLMPALEELDVGYEKYKNDPESLAELDHYLRDFAGRETPLYFARNLSKKYGT--K 78

Query: 97  IYLKMESYTYTGSHKINSALAHVYYAKLDNAKFVTTETGAGQWGSSVALASALFRMKAHI 156
           +YLK E   + G+HK+N+AL     AK      +  ETGAGQ G++ A+  A    +  +
Sbjct: 79  VYLKREDLVHGGAHKLNNALGQALLAKFMGKTRLIAETGAGQHGTATAMVGATLGFETIV 138

Query: 157 FMVRTSYYAKPYRKYMMQMYGAEVHPSPSDLTEFGRQLLAKDSNHPGSLGIAISDAVE-- 214
           +M       +    Y M++ G EV        E G + L KD         AI++A+   
Sbjct: 139 YMGAKDIKRQQMNAYRMELMGTEVR-----AVETGSKTL-KD---------AINEAMRDW 183

Query: 215 YAHKNGGKYVVGSVVNSDIM------FKTIAGMEAKKQ-MELIGEDPDYIIGVVGGGSNY 267
             +     Y++GSVV           F+++ G E K+Q ME  G  PD II   GGGSN 
Sbjct: 184 VTNIENTHYLIGSVVGPHPYPMIVRDFQSVIGKEVKEQAMEKEGRLPDSIIACAGGGSNA 243

Query: 268 AALAYPFLGDE------LRSGKVRRKYIASGSSEVPKMTKGVYKYDYPDTAKLLPMLKMY 321
               +PF+ D       + +G    K     +     +  G     +    K+L      
Sbjct: 244 MGTFHPFIEDREVKLIAVEAGGKGLKCTEKAALHSASLCIGEEGILHGARTKILQDKNGQ 303

Query: 322 TIGSDFVPPPVYAGGLRYHGVAPTLSLLISKGIVQARDYSQEESFKWAKLFSELEGYIPA 381
            + S+ V     + GL Y GV P L+ L   G V AR  + +E+       S LEG IPA
Sbjct: 304 ILESESV-----SAGLDYSGVGPELAYLSESGRVTARYVTDDEALDAFNELSRLEGIIPA 358

Query: 382 PETSHALPILAEIAEEAKKSGE-RKTVLVSFSGHGLLDLGNYASV 425
            E+SHAL  L + AE    SGE  + V+V+ SG G  DL    S+
Sbjct: 359 LESSHALAYLKKAAE----SGELGEFVVVNLSGRGDKDLETVLSL 399


Lambda     K      H
   0.316    0.135    0.392 

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: 439
Number of extensions: 26
Number of successful extensions: 3
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: 429
Length of database: 403
Length adjustment: 31
Effective length of query: 398
Effective length of database: 372
Effective search space:   148056
Effective search space used:   148056
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_011022931.1 MA_RS15685 (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.678712.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-187  607.4   0.4   6.6e-187  607.2   0.4    1.0  1  NCBI__GCF_000007345.1:WP_011022931.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007345.1:WP_011022931.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.2   0.4  6.6e-187  6.6e-187       1     382 [.      13     397 ..      13     400 .. 0.98

  Alignments for each domain:
  == domain 1  score: 607.2 bits;  conditional E-value: 6.6e-187
                             TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 
                                           gk+g++GGqyvpevl++aleel+  yek+k+d+e  +el+++l+++agr+tpl+fa+nlskk+g +k+ylkre
  NCBI__GCF_000007345.1:WP_011022931.1  13 GKYGKYGGQYVPEVLMPALEELDVGYEKYKNDPESLAELDHYLRDFAGRETPLYFARNLSKKYG-TKVYLKRE 84 
                                           78*************************************************************8.******** PP

                             TIGR00263  74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146
                                           dl h+Gahk+nnalgqallak +Gk+r+iaetGaGqhG+ata+++a+lg+e  vymGa+d++rq++n +rmel
  NCBI__GCF_000007345.1:WP_011022931.1  85 DLVHGGAHKLNNALGQALLAKFMGKTRLIAETGAGQHGTATAMVGATLGFETIVYMGAKDIKRQQMNAYRMEL 157
                                           ************************************************************************* PP

                             TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219
                                           +g++v +v++Gsktlkda+nea+rdWvt++e+thy++Gs+vGphP+P ivr+fqsvig+evkeq +ekegrlP
  NCBI__GCF_000007345.1:WP_011022931.1 158 MGTEVRAVETGSKTLKDAINEAMRDWVTNIENTHYLIGSVVGPHPYPMIVRDFQSVIGKEVKEQAMEKEGRLP 230
                                           ************************************************************************* PP

                             TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidt....ekhaatlskGkeGvlhGaktkllqdedGq 288
                                           d +iac+GGGsna+G+f++fied ev+li+veagGkG++     + h+a+l  G+eG+lhGa+tk+lqd++Gq
  NCBI__GCF_000007345.1:WP_011022931.1 231 DSIIACAGGGSNAMGTFHPFIEDREVKLIAVEAGGKGLKCtekaALHSASLCIGEEGILHGARTKILQDKNGQ 303
                                           *************************************987444567999************************ PP

                             TIGR00263 289 ieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklk 361
                                           i e+ svsaGldy+gvgPe+a+l e+gr++ + +td+eal+a++ ls+ eGiipalesshala+l+k a++ +
  NCBI__GCF_000007345.1:WP_011022931.1 304 ILESESVSAGLDYSGVGPELAYLSESGRVTARYVTDDEALDAFNELSRLEGIIPALESSHALAYLKKAAESGE 376
                                           ************************************************************************* PP

                             TIGR00263 362 kdeivvvnlsGrGdkdletva 382
                                             e vvvnlsGrGdkdletv 
  NCBI__GCF_000007345.1:WP_011022931.1 377 LGEFVVVNLSGRGDKDLETVL 397
                                           *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (403 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.22
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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