Alignments for a candidate for astA in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Shewanella sp. ANA-3

Align Arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate 7023381 Shewana3_0611 arginine succinyltransferase (RefSeq)

Query= reanno::ANA3:7023381
         (339 letters)



>FitnessBrowser__ANA3:7023381
          Length = 339

 Score =  676 bits (1745), Expect = 0.0
 Identities = 339/339 (100%), Positives = 339/339 (100%)

Query: 1   MLIIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDKPFDEGYL 60
           MLIIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDKPFDEGYL
Sbjct: 1   MLIIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDKPFDEGYL 60

Query: 61  MVLEDTATREVVGTCAIEAAVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGA 120
           MVLEDTATREVVGTCAIEAAVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGA
Sbjct: 61  MVLEDTATREVVGTCAIEAAVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGA 120

Query: 121 AELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSDSDGNSPFYCWL 180
           AELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSDSDGNSPFYCWL
Sbjct: 121 AELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSDSDGNSPFYCWL 180

Query: 181 QKNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL 240
           QKNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL
Sbjct: 181 QKNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL 240

Query: 241 QAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESDKQFIVSNTQLANY 300
           QAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESDKQFIVSNTQLANY
Sbjct: 241 QAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESDKQFIVSNTQLANY 300

Query: 301 RATSACLAVDDKTEQVVISPELAEGLLLAKGDQIRILAM 339
           RATSACLAVDDKTEQVVISPELAEGLLLAKGDQIRILAM
Sbjct: 301 RATSACLAVDDKTEQVVISPELAEGLLLAKGDQIRILAM 339


Lambda     K      H
   0.322    0.138    0.401 

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: 539
Number of extensions: 9
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: 339
Length of database: 339
Length adjustment: 28
Effective length of query: 311
Effective length of database: 311
Effective search space:    96721
Effective search space used:    96721
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: 49 (23.5 bits)

Align candidate 7023381 Shewana3_0611 (arginine succinyltransferase (RefSeq))
to HMM TIGR03244 (astA: arginine N-succinyltransferase (EC 2.3.1.109))

# 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.carbon/TIGR03244.hmm
# target sequence database:        /tmp/gapView.18581.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03244  [M=336]
Accession:   TIGR03244
Description: arg_catab_AstA: arginine N-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.6e-141  455.4   0.0   5.2e-141  455.3   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7023381  Shewana3_0611 arginine succinylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023381  Shewana3_0611 arginine succinyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.3   0.0  5.2e-141  5.2e-141       1     335 [.       3     338 ..       3     339 .] 0.97

  Alignments for each domain:
  == domain 1  score: 455.3 bits;  conditional E-value: 5.2e-141
                         TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfagele.raeegylfvledtetgkvvGvsaiea 76 
                                       i+rp++  d+++l+++a+e+G+G+tslp+n +ll+++i+rae sf + ++ + +egyl+vledt+t +vvG++aiea
  lcl|FitnessBrowser__ANA3:7023381   3 IIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDkPFDEGYLMVLEDTATREVVGTCAIEA 79 
                                       79*********************************************9651579*********************** PP

                         TIGR03244  77 avGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrkelnGkllskarflflaefkerf 153
                                       avG+e++fy+yr+g+ v +s+++++ +++etl+l++d+tga+elCtlfl+e yrk++nG++ls++rflfla++ +rf
  lcl|FitnessBrowser__ANA3:7023381  80 AVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGAAELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRF 156
                                       ***************************************************************************** PP

                         TIGR03244 154 skkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPiyvdllskeaqdvigkvhekt 230
                                       ++++iaemrGvsd +G+sPf+ +l+k+f  +df +adylsg+Gkkaf+ae+mP+ P+yv+ll++eaq+vig+vh++t
  lcl|FitnessBrowser__ANA3:7023381 157 GETVIAEMRGVSDSDGNSPFYCWLQKNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNT 233
                                       ***************************************************************************** PP

                         TIGR03244 231 kPalalleseGlryqgyvdifdaGptleaevakiravresklvevavaesaaedeaepylvanekledfrvvlvess 307
                                       +Pal ll++eG+r +gyvdifd+Gpt+e+++++iravres+l++v ++e  ++d  ++++v+n++l+++r++ + ++
  lcl|FitnessBrowser__ANA3:7023381 234 RPALSLLQAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESD--KQFIVSNTQLANYRATSACLA 308
                                       **************************************************9999..99*************986554 PP

                         TIGR03244 308 ..ldaeelvlsaeeakalkveeGdkvrvva 335
                                          ++e++v+s+e a+ l + +Gd++r++a
  lcl|FitnessBrowser__ANA3:7023381 309 vdDKTEQVVISPELAEGLLLAKGDQIRILA 338
                                       33889***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (336 nodes)
Target sequences:                          1  (339 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: 00:00:00.01
# Mc/sec: 10.86
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources