Alignments for a candidate for trpB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Pedobacter sp. GW460-11-11-14-LB5

Align tryptophan synthase (EC 4.2.1.20) (characterized)
to candidate CA265_RS05020 CA265_RS05020 tryptophan synthase subunit beta

Query= BRENDA::Q97TX6
         (429 letters)



>FitnessBrowser__Pedo557:CA265_RS05020
          Length = 393

 Score =  138 bits (347), Expect = 3e-37
 Identities = 130/400 (32%), Positives = 190/400 (47%), Gaps = 51/400 (12%)

Query: 43  LKEVLPSKVLELEFAKERYVKIPDE---------VLERYLQVGRPTPIIRAKRLEEYLGN 93
           + E+L   V EL   ++ Y+KI D+         +L+ Y  VGRP+P+  AKR  E  G 
Sbjct: 19  IPEMLYPNVEEL---RQNYLKIIDDADFQKEFHQLLKDY--VGRPSPLYLAKRYSERYGA 73

Query: 94  NIKIYLKMESYTYTGSHKINSALAHVYYAKLDNAKFVTTETGAGQWGSSVALASALFRMK 153
           NI  +LK E   +TG+HKIN+ +  +  A+    K +  ETGAGQ G + A   AL  ++
Sbjct: 74  NI--FLKREDLNHTGAHKINNTIGQILLAEKLGKKRIIAETGAGQHGVATATVCALRNLE 131

Query: 154 AHIFMVRTSYYAKPYRKYMMQMYGAEVHPSPSDLTEFGRQLLAKDSNHPGSLGIAISDAV 213
             I+M       +      M+M GA+V P+ S     G + L   +N       A+ D +
Sbjct: 132 CVIYMGEVDIERQAPNVARMKMLGAKVVPASS-----GSKTLKDATNE------AMRDWI 180

Query: 214 EYAHKNGGKYVVGSVVNSD------IMFKTIAGMEAKKQ-MELIGED-PDYIIGVVGGGS 265
              +     Y++GSVV          +F++I   E KKQ +E  G D PDY++  VGGGS
Sbjct: 181 N--NPVDTHYIIGSVVGPHPYPDMVAIFQSIISEETKKQLLEQTGSDQPDYVLACVGGGS 238

Query: 266 NYAALAYPFLGDE---LRSGKVRRKYIASGSSEVPKMTKGVYKYDYPDTAKLLPMLKMYT 322
           N   + Y F+ DE   L + +   K ++SG S     T  + K      ++    + M T
Sbjct: 239 NAMGMFYHFMDDENVKLIAVEAAGKGVSSGFSAA---TTYLGKEGVLHGSR---SILMQT 292

Query: 323 IGSDFVPPPVYAGGLRYHGVAPTLSLLISKGIVQARDYSQEESFKWAKLFSELEGYIPAP 382
                V P   + GL Y G+ P  + L   G  Q    + EES     L ++LEG IPA 
Sbjct: 293 EDGQVVEPHSVSAGLDYPGIGPQHAHLFKTGRGQYVSITDEESLDAGLLCTQLEGIIPAI 352

Query: 383 ETSHALPILAEIAEEAKKSGERKTVLVSFSGHGLLDLGNY 422
           E++HAL  L ++     K GE   V+V  SG G  DL  Y
Sbjct: 353 ESAHALAYLEKM---EFKGGE--NVVVCLSGRGDKDLDTY 387


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: 449
Number of extensions: 25
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: 429
Length of database: 393
Length adjustment: 31
Effective length of query: 398
Effective length of database: 362
Effective search space:   144076
Effective search space used:   144076
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 CA265_RS05020 CA265_RS05020 (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.1046.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   6.6e-181  587.4   0.1   7.5e-181  587.2   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS05020  CA265_RS05020 tryptophan synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS05020  CA265_RS05020 tryptophan synthase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.2   0.1  7.5e-181  7.5e-181       1     383 [.       9     389 ..       9     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 587.2 bits;  conditional E-value: 7.5e-181
                                  TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggaki 68 
                                                g++g+fGG+y+pe+l +++eel+++y k+ +d +f+ke+++llk+y+grp+pl+ ak++s+++g a+i
  lcl|FitnessBrowser__Pedo557:CA265_RS05020   9 GYYGDFGGAYIPEMLYPNVEELRQNYLKIIDDADFQKEFHQLLKDYVGRPSPLYLAKRYSERYG-ANI 75 
                                                79*************************************************************8.*** PP

                                  TIGR00263  69 ylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedver 136
                                                +lkredl+htGahkinn++gq+lla++lGkkriiaetGaGqhGvatat++al +lec++ymG+ d+er
  lcl|FitnessBrowser__Pedo557:CA265_RS05020  76 FLKREDLNHTGAHKINNTIGQILLAEKLGKKRIIAETGAGQHGVATATVCALRNLECVIYMGEVDIER 143
                                                ******************************************************************** PP

                                  TIGR00263 137 qklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvig 204
                                                q++nv rm++lgakvvp +sGsktlkda+nea+rdW+ +  dthy++Gs+vGphP+P++v  fqs+i+
  lcl|FitnessBrowser__Pedo557:CA265_RS05020 144 QAPNVARMKMLGAKVVPASSGSKTLKDATNEAMRDWINNPVDTHYIIGSVVGPHPYPDMVAIFQSIIS 211
                                                ******************************************************************** PP

                                  TIGR00263 205 eevkeqileke.grlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGke 271
                                                ee+k+q+le+     Pd+v+acvGGGsna+G+f++f++de+v+li+vea+GkG+++   aat   Gke
  lcl|FitnessBrowser__Pedo557:CA265_RS05020 212 EETKKQLLEQTgSDQPDYVLACVGGGSNAMGMFYHFMDDENVKLIAVEAAGKGVSSGFSAATTYLGKE 279
                                                *********996789***************************************************** PP

                                  TIGR00263 272 GvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeG 339
                                                GvlhG+++ l+q+edGq+ e hsvsaGldypg+gP+ha+l +tgr +y++itdee+l+a  l+++ eG
  lcl|FitnessBrowser__Pedo557:CA265_RS05020 280 GVLHGSRSILMQTEDGQVVEPHSVSAGLDYPGIGPQHAHLFKTGRGQYVSITDEESLDAGLLCTQLEG 347
                                                ******************************************************************** PP

                                  TIGR00263 340 iipalesshalaaleklapklkkdeivvvnlsGrGdkdletvak 383
                                                iipa+es+hala+lek+    k  e vvv lsGrGdkdl+t +k
  lcl|FitnessBrowser__Pedo557:CA265_RS05020 348 IIPAIESAHALAYLEKMEF--KGGENVVVCLSGRGDKDLDTYIK 389
                                                ****************987..7788999***********99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 7.86
//
[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