Alignments for a candidate for metA in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for metA in Shewanella loihica PV-4

Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate 5210107 Shew_2551 homoserine O-succinyltransferase (RefSeq)

Query= SwissProt::A6WLE9
         (313 letters)



>FitnessBrowser__PV4:5210107
          Length = 321

 Score =  565 bits (1457), Expect = e-166
 Identities = 266/311 (85%), Positives = 289/311 (92%)

Query: 1   MPVRIPDHLPAAEVLESENIFVMSETRAANQDIRPMKVLILNLMPNKIETETQLLRLLGN 60
           MPV+IPD+LPAAE+LESENIFVMSETRAANQDIRPMKVLILNLMPNKIETETQLLRLLGN
Sbjct: 1   MPVKIPDNLPAAEILESENIFVMSETRAANQDIRPMKVLILNLMPNKIETETQLLRLLGN 60

Query: 61  TPLQVDVDLLRIHDKESKHTSIDHMNTFYRDFEAVRHKNYDGLIITGAPLGQIDFEDVVY 120
           TPLQVDVDLLRIHDK SKHTSIDHMN FYRDFEAVRHKNYDGLIITGAPLGQI+FE+V Y
Sbjct: 61  TPLQVDVDLLRIHDKVSKHTSIDHMNNFYRDFEAVRHKNYDGLIITGAPLGQIEFEEVTY 120

Query: 121 WDHIREIIDWSQEHVTSVLFLCWAAHAGLYHLYGLNRKILQQKRSGVFVHRRTSQHFPLL 180
           WDHIREIIDWSQ HVTSVLFLCWAAHA LYHLYGL RK+L  KRSGVF H+RT +HFPLL
Sbjct: 121 WDHIREIIDWSQHHVTSVLFLCWAAHAALYHLYGLQRKLLSAKRSGVFNHQRTHKHFPLL 180

Query: 181 RGFDDEFFAPHSRFAEMDVEEIRQHPQLQLLAESDEAGAYLVLSRNNRNLFVMGHPEYQK 240
           RGFDDEFFAPHSRFAEM+V +++ H +LQ+LAESDEAGAYLVLSRNNRNLFVMGHPEYQK
Sbjct: 181 RGFDDEFFAPHSRFAEMEVADLKAHKELQVLAESDEAGAYLVLSRNNRNLFVMGHPEYQK 240

Query: 241 STLNEEYQRDLSQGLDPNVPQNYYRNDDPKADAIARWHSHGSLLVSNWLNYYVYQLTPYD 300
           STL +EYQRDL++GL+P VP+NY+R DDP    +ARWH HGSLLVSNWLNYYVYQLTPYD
Sbjct: 241 STLKDEYQRDLAEGLNPRVPKNYFRGDDPSQAPVARWHGHGSLLVSNWLNYYVYQLTPYD 300

Query: 301 LSDMTAMTPWE 311
           L DM+A+TPWE
Sbjct: 301 LHDMSAITPWE 311


Lambda     K      H
   0.321    0.136    0.419 

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: 463
Number of extensions: 11
Number of successful extensions: 1
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: 313
Length of database: 321
Length adjustment: 27
Effective length of query: 286
Effective length of database: 294
Effective search space:    84084
Effective search space used:    84084
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate 5210107 Shew_2551 (homoserine O-succinyltransferase (RefSeq))
to HMM TIGR01001 (metA: homoserine O-succinyltransferase (EC 2.3.1.46))

# 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/TIGR01001.hmm
# target sequence database:        /tmp/gapView.3470041.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01001  [M=301]
Accession:   TIGR01001
Description: metA: homoserine O-succinyltransferase
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-143  463.8   0.4   1.8e-143  463.6   0.4    1.0  1  FitnessBrowser__PV4:5210107  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__PV4:5210107  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.6   0.4  1.8e-143  1.8e-143       1     300 [.       1     301 [.       1     302 [. 0.99

  Alignments for each domain:
  == domain 1  score: 463.6 bits;  conditional E-value: 1.8e-143
                    TIGR01001   1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditllridsrkskntpi 82 
                                  mp+++pd+lpa e+l+ enifvm+e ra +qdirp++vlilnlmp+kiete+qllrll+n+plqvd++llri++++sk+t i
  FitnessBrowser__PV4:5210107   1 MPVKIPDNLPAAEILESENIFVMSETRAANQDIRPMKVLILNLMPNKIETETQLLRLLGNTPLQVDVDLLRIHDKVSKHTSI 82 
                                  9********************************************************************************* PP

                    TIGR01001  83 ehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtstlyicwaaqaalkllygipkrtleekl 164
                                  +h+++fy+++e+v+++++dGli+tGap++++efe+v yw++++ei++ws+++vts l++cwaa+aal+ lyg++++ l+ k 
  FitnessBrowser__PV4:5210107  83 DHMNNFYRDFEAVRHKNYDGLIITGAPLGQIEFEEVTYWDHIREIIDWSQHHVTSVLFLCWAAHAALYHLYGLQRKLLSAKR 164
                                  ********************************************************************************** PP

                    TIGR01001 165 sGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltdleilaesdeagvylaaskdernifvtGhpeydketlrqe 245
                                  sGv++h+ + k+ +llrgfdd+f+aphsr+a+++ ++++++++l++laesdeag+yl++s+++rn+fv+Ghpey+k tl++e
  FitnessBrowser__PV4:5210107 165 SGVFNHQRThKHFPLLRGFDDEFFAPHSRFAEMEVADLKAHKELQVLAESDEAGAYLVLSRNNRNLFVMGHPEYQKSTLKDE 246
                                  ******98868999******************************************************************** PP

                    TIGR01001 246 yvrdvgeglkvdipknyypkddpektpiaswrshanllfanwlnyavyqktpydl 300
                                  y rd+ egl++ +pkny+  ddp++ p+a w+ h+ ll +nwlny+vyq tpydl
  FitnessBrowser__PV4:5210107 247 YQRDLAEGLNPRVPKNYFRGDDPSQAPVARWHGHGSLLVSNWLNYYVYQLTPYDL 301
                                  ******************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (301 nodes)
Target sequences:                          1  (321 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: 00:00:00.00
# Mc/sec: 13.94
//
[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 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