Alignments for a candidate for trpB in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Caulobacter crescentus NA1000

Align tryptophan synthase (EC 4.2.1.20) (characterized)
to candidate CCNA_03658 CCNA_03658 tryptophan synthase beta chain

Query= BRENDA::Q97TX6
         (429 letters)



>FitnessBrowser__Caulo:CCNA_03658
          Length = 406

 Score =  137 bits (344), Expect = 8e-37
 Identities = 115/367 (31%), Positives = 165/367 (44%), Gaps = 45/367 (12%)

Query: 76  GRPTPIIRAKRLEEYLGNNIKIYLKMESYTYTGSHKINSALAHVYYAKLDNAKFVTTETG 135
           GRP+P+  A+RL E+ G   KIY K +   +TGSHKIN+AL  +  A       +  ETG
Sbjct: 65  GRPSPLYFAERLTEHFGG-AKIYFKRDELNHTGSHKINNALGQILLAMRMGKTRIIAETG 123

Query: 136 AGQWGSSVALASALFRMKAHIFMVRTSYYAKPYRKYMMQMYGAEVHPSPSDLTEFGRQLL 195
           AGQ G + A   A F +   ++M  T    +    + M + GAEV P  S     G   L
Sbjct: 124 AGQHGVATATVCARFGLPCVVYMGATDVERQKPNVFRMNLLGAEVRPVSS-----GTGTL 178

Query: 196 AKDSNHPGSLGIAISDAVEYAHKNGGKYVVGSVVNS---DIM---FKTIAGMEAKKQ-ME 248
               N       A+ D V   H     Y++G+        +M   F+++ G EA++Q +E
Sbjct: 179 KDAMNE------AMRDWVTNVHDT--YYLIGTAAGPHPYPVMVRDFQSVIGAEAREQILE 230

Query: 249 LIGEDPDYIIGVVGGGSNYAALAYPFLGDE---------LRSGKVRRKYIASGSSEVPKM 299
           + G  PD ++  +GGGSN   L +PFLGDE            G    K+ AS +   P +
Sbjct: 231 MEGRLPDAVVACIGGGSNAIGLFHPFLGDEGVRLIGVEAAGHGVSTDKHAASLTGGRPGV 290

Query: 300 TKGVYKYDYPDTAKLLPMLKMYTIGSDFVPPPVYAGGLRYHGVAPTLSLLISKGIVQARD 359
             G   Y   D                 +     + GL Y G+ P  S L   G  +   
Sbjct: 291 LHGNRTYLLQDD------------DGQIIDAHSISAGLDYPGIGPEHSFLHDIGRAEYVS 338

Query: 360 YSQEESFKWAKLFSELEGYIPAPETSHALPILAEIAEEAKKSGERKTVLVSFSGHGLLDL 419
            +  E+ +  KL S LEG IPA E +HAL  + EIA+E    G+ K V+++  G G  D+
Sbjct: 339 TTDTEALEAFKLCSTLEGIIPALEPAHALARVGEIAQEL---GKGKIVVMNLCGRGDKDI 395

Query: 420 GNYASVL 426
              A  L
Sbjct: 396 FTVAEAL 402


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: 419
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: 406
Length adjustment: 32
Effective length of query: 397
Effective length of database: 374
Effective search space:   148478
Effective search space used:   148478
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 CCNA_03658 CCNA_03658 (tryptophan synthase beta chain)
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.24438.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-196  637.4   0.0   4.9e-196  637.2   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03658  CCNA_03658 tryptophan synthase b


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03658  CCNA_03658 tryptophan synthase beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  637.2   0.0  4.9e-196  4.9e-196       1     384 [.      18     401 ..      18     402 .. 1.00

  Alignments for each domain:
  == domain 1  score: 637.2 bits;  conditional E-value: 4.9e-196
                             TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 
                                           g+fg fGG+yv+e+l++ + +l kay +ak+d+ef+++l+++  +yagrp+pl+fa++l+++ ggakiy+kr+
  lcl|FitnessBrowser__Caulo:CCNA_03658  18 GRFGGFGGRYVAETLMPLVLDLGKAYADAKADPEFQAQLKSYNTHYAGRPSPLYFAERLTEHFGGAKIYFKRD 90 
                                           78*********************************************************************** PP

                             TIGR00263  74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146
                                           +l+htG+hkinnalgq+lla r+Gk+riiaetGaGqhGvatat++a++gl c+vymGa+dverqk+nvfrm+l
  lcl|FitnessBrowser__Caulo:CCNA_03658  91 ELNHTGSHKINNALGQILLAMRMGKTRIIAETGAGQHGVATATVCARFGLPCVVYMGATDVERQKPNVFRMNL 163
                                           ************************************************************************* PP

                             TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219
                                           lga+v pv+sG+ tlkda+nea+rdWvt+v+dt+y++G+a+GphP+P +vr+fqsvig+e++eqile+egrlP
  lcl|FitnessBrowser__Caulo:CCNA_03658 164 LGAEVRPVSSGTGTLKDAMNEAMRDWVTNVHDTYYLIGTAAGPHPYPVMVRDFQSVIGAEAREQILEMEGRLP 236
                                           ************************************************************************* PP

                             TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieea 292
                                           dav+ac+GGGsnaiG+f++f+ de v+ligvea+G+G++t+khaa+l+ G++GvlhG++t+llqd+dGqi +a
  lcl|FitnessBrowser__Caulo:CCNA_03658 237 DAVVACIGGGSNAIGLFHPFLGDEGVRLIGVEAAGHGVSTDKHAASLTGGRPGVLHGNRTYLLQDDDGQIIDA 309
                                           ************************************************************************* PP

                             TIGR00263 293 hsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdei 365
                                           hs+saGldypg+gPeh++l+++graey++ td+ealea+kl+s  eGiipale +hala + ++a++l k +i
  lcl|FitnessBrowser__Caulo:CCNA_03658 310 HSISAGLDYPGIGPEHSFLHDIGRAEYVSTTDTEALEAFKLCSTLEGIIPALEPAHALARVGEIAQELGKGKI 382
                                           ************************************************************************* PP

                             TIGR00263 366 vvvnlsGrGdkdletvaka 384
                                           vv+nl+GrGdkd++tva+a
  lcl|FitnessBrowser__Caulo:CCNA_03658 383 VVMNLCGRGDKDIFTVAEA 401
                                           ****************986 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.02
//
[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