Alignments for a candidate for trpA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpA in Dinoroseobacter shibae DFL-12

Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate 3607540 Dshi_0952 tryptophan synthase, alpha subunit (RefSeq)

Query= uniprot:H0BV16
         (269 letters)



>FitnessBrowser__Dino:3607540
          Length = 272

 Score =  209 bits (532), Expect = 5e-59
 Identities = 107/260 (41%), Positives = 162/260 (62%), Gaps = 7/260 (2%)

Query: 1   MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60
           M+RI  TF+ L+A+G+KA + YV  G P  D +  ++ G+  AG D+IELG+PF+DPMAD
Sbjct: 10  MTRIDETFARLRAEGKKAFVAYVMGGDPDYDTSLEIVRGLPAAGVDIIELGMPFTDPMAD 69

Query: 61  GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120
           GP IQ AG++AL  G  + + LD  R  R+ ++ TP+V+MGY NP+       G   F+ 
Sbjct: 70  GPTIQLAGQRALEAGQTLDKTLDLARALRETDDATPIVMMGYYNPI----YSRGVDRFLA 125

Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180
           D+  AG+DG+++VD PPEE        +A G++ I L  PT+ D R+ +V +  SG+VYY
Sbjct: 126 DAKDAGIDGLIVVDLPPEEDSELCIPAQAAGLNFIRLATPTTDDARLPKVLQNTSGFVYY 185

Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240
           VS+ G+TG+     + V   + RI+    +PV VGFG++    A++I  VAD  V+GS I
Sbjct: 186 VSITGITGAAQAQASDVAPEVARIKSATDLPVIVGFGVKTPELAESIAGVADGTVVGSAI 245

Query: 241 IQLIEDQEHAKVVPLTIDFL 260
           ++++ED    K VP  + F+
Sbjct: 246 VKMVED---GKPVPEILGFV 262


Lambda     K      H
   0.321    0.137    0.389 

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: 241
Number of extensions: 9
Number of successful extensions: 2
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: 269
Length of database: 272
Length adjustment: 25
Effective length of query: 244
Effective length of database: 247
Effective search space:    60268
Effective search space used:    60268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate 3607540 Dshi_0952 (tryptophan synthase, alpha subunit (RefSeq))
to HMM TIGR00262 (trpA: tryptophan synthase, alpha 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/TIGR00262.hmm
# target sequence database:        /tmp/gapView.1128.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00262  [M=256]
Accession:   TIGR00262
Description: trpA: tryptophan synthase, alpha 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.6e-82  262.3   0.0    1.8e-82  262.0   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607540  Dshi_0952 tryptophan synthase, a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607540  Dshi_0952 tryptophan synthase, alpha subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.0   0.0   1.8e-82   1.8e-82       1     237 [.      17     252 ..      17     266 .. 0.98

  Alignments for each domain:
  == domain 1  score: 262.0 bits;  conditional E-value: 1.8e-82
                         TIGR00262   1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalel 77 
                                       f+ l+++++kafv++v  gdPd+++slei++ l  aG+d++ElG+pf DP+aDGptiq a +RAl+ag +++k+l+l
  lcl|FitnessBrowser__Dino:3607540  17 FARLRAEGKKAFVAYVMGGDPDYDTSLEIVRGLPAAGVDIIELGMPFTDPMADGPTIQLAGQRALEAGQTLDKTLDL 93 
                                       78899************************************************************************ PP

                         TIGR00262  78 lkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeee 154
                                       ++++re+  + Piv++ yyn+i+++gv+ F+a ak+ag+dg++v+DlP ee ++l   a+  g++ i l++Pt+++ 
  lcl|FitnessBrowser__Dino:3607540  94 ARALRETDDATPIVMMGYYNPIYSRGVDRFLADAKDAGIDGLIVVDLPPEEDSELCIPAQAAGLNFIRLATPTTDDA 170
                                       ***************************************************************************** PP

                         TIGR00262 155 rlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlv 231
                                       rl k+ ++++GfvY vs +G+tga +  +++v   ++++k+ ++ Pv+vGFG+  +e ++++  + adg +vGsA+v
  lcl|FitnessBrowser__Dino:3607540 171 RLPKVLQNTSGFVYYVSITGITGAAQAQASDVAPEVARIKSATDLPVIVGFGVKTPELAESIAGV-ADGTVVGSAIV 246
                                       ***************************************************************99.99********* PP

                         TIGR00262 232 kiieek 237
                                       k++e+ 
  lcl|FitnessBrowser__Dino:3607540 247 KMVEDG 252
                                       ***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (272 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: 9.88
//
[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