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

GapMind for catabolism of small carbon sources

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

Align Arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate 5208067 Shew_0579 arginine N-succinyltransferase (RefSeq)

Query= reanno::SB2B:6938907
         (339 letters)



>FitnessBrowser__PV4:5208067
          Length = 339

 Score =  577 bits (1488), Expect = e-169
 Identities = 284/339 (83%), Positives = 311/339 (91%)

Query: 1   MLIIRPIRASDFDALYRIAVESGHGFTSLPVNEDLLRRKIARSEASFQKVVETPYDEGYL 60
           MLIIRPIR+SDFDALY+IA+ESGHGFTSLPVNE+LLR KIAR EASF K +E P+DEGYL
Sbjct: 1   MLIIRPIRSSDFDALYQIAIESGHGFTSLPVNEELLRNKIARVEASFVKEIEKPFDEGYL 60

Query: 61  MVLEDTQTQEVVGTCALEAAVGMEDAFYHYRLGTEVYHSQQINVRNEVETLTLCHDYTGA 120
           MVLEDT+T EVVGTC LEAAVGM DAFYHYRLGTEVY+S+QI+VRNEVETLTLCHDYTGA
Sbjct: 61  MVLEDTETGEVVGTCGLEAAVGMVDAFYHYRLGTEVYYSEQIDVRNEVETLTLCHDYTGA 120

Query: 121 AELCTLFLRGAYRKDNNGRMLSRSRFLFLAQHANRFGETVIAEMRGVSDENGNSPFYGWL 180
           AELCTLFLR  YRK+NNGRMLSRSRFLFLAQHA RFG+TVIAEMRG SD  GNSPFYGWL
Sbjct: 121 AELCTLFLRDTYRKNNNGRMLSRSRFLFLAQHAERFGDTVIAEMRGESDAEGNSPFYGWL 180

Query: 181 QKHFLGIDFVEADYLSGLGRKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL 240
           QK+FLGIDFV+ADYLSGLG+KAFMAEMMP+N VYVCLLPEEAQKVIGEVHTNTRPAL+LL
Sbjct: 181 QKNFLGIDFVQADYLSGLGQKAFMAEMMPKNSVYVCLLPEEAQKVIGEVHTNTRPALNLL 240

Query: 241 RAEGFRCRGYVDIFDGGPTVECNLQDIRGVRESRLLTVRIGEMPASDDSFILSNTQLVDY 300
           +AEGFRCRGYVDIFDGGPTVECNL DIR VRESRLLTV++GEMP S  SFI+SNT L  Y
Sbjct: 241 QAEGFRCRGYVDIFDGGPTVECNLNDIRSVRESRLLTVKVGEMPVSSSSFIISNTLLAGY 300

Query: 301 RATSVELMVSSDSDEVILSPELAAGLLVSDGEQVRVLAI 339
           RATS  LMVS ++DEVILSPELA  LLV++GEQ+RVLA+
Sbjct: 301 RATSANLMVSDETDEVILSPELAGALLVAEGEQIRVLAM 339


Lambda     K      H
   0.321    0.137    0.397 

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: 450
Number of extensions: 8
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 5208067 Shew_0579 (arginine N-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.23788.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   9.7e-140  451.1   0.0   1.1e-139  450.9   0.0    1.0  1  lcl|FitnessBrowser__PV4:5208067  Shew_0579 arginine N-succinyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208067  Shew_0579 arginine N-succinyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.9   0.0  1.1e-139  1.1e-139       1     335 [.       3     338 ..       3     339 .] 0.97

  Alignments for each domain:
  == domain 1  score: 450.9 bits;  conditional E-value: 1.1e-139
                        TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfage.leraeegylfvledtetgkvvGvsaieaa 77 
                                      i+rp+++sd+dal+++a e+G+G+tslp+neell+++i+r e sf +e  ++ +egyl+vledtetg+vvG++++eaa
  lcl|FitnessBrowser__PV4:5208067   3 IIRPIRSSDFDALYQIAIESGHGFTSLPVNEELLRNKIARVEASFVKEiEKPFDEGYLMVLEDTETGEVVGTCGLEAA 80 
                                      79**********************************************44567************************* PP

                        TIGR03244  78 vGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrkelnGkllskarflflaefkerfsk 155
                                      vG+ ++fy+yr+g+ v  s+++++ +++etl+l++d+tga+elCtlfl+++yrk++nG++ls++rflfla++ erf++
  lcl|FitnessBrowser__PV4:5208067  81 VGMVDAFYHYRLGTEVYYSEQIDVRNEVETLTLCHDYTGAAELCTLFLRDTYRKNNNGRMLSRSRFLFLAQHAERFGD 158
                                      ****************************************************************************** PP

                        TIGR03244 156 kiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPiyvdllskeaqdvigkvhektkPa 233
                                      ++iaemrG sd eG+sPf+ +l+k+f  +df +adylsg+G+kaf+ae+mPk  +yv+ll++eaq+vig+vh++t+Pa
  lcl|FitnessBrowser__PV4:5208067 159 TVIAEMRGESDAEGNSPFYGWLQKNFLGIDFVQADYLSGLGQKAFMAEMMPKNSVYVCLLPEEAQKVIGEVHTNTRPA 236
                                      ****************************************************************************** PP

                        TIGR03244 234 lalleseGlryqgyvdifdaGptleaevakiravresklvevavaesaaedeaepylvanekledfrvvlvess..ld 309
                                      l+ll++eG+r +gyvdifd+Gpt+e+++++ir+vres+l++v+v+e   +   ++++++n+ l+ +r++ +++    +
  lcl|FitnessBrowser__PV4:5208067 237 LNLLQAEGFRCRGYVDIFDGGPTVECNLNDIRSVRESRLLTVKVGEMPVSS--SSFIISNTLLAGYRATSANLMvsDE 312
                                      *********************************************988877..89**************998764478 PP

                        TIGR03244 310 aeelvlsaeeakalkveeGdkvrvva 335
                                      ++e++ls+e a al v eG+++rv+a
  lcl|FitnessBrowser__PV4:5208067 313 TDEVILSPELAGALLVAEGEQIRVLA 338
                                      99**********************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.16
//
[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