Alignments for a candidate for astA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Shewanella oneidensis MR-1

Align Arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate 199806 SO0618 arginine N-succinyltransferase (NCBI ptt file)

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



>FitnessBrowser__MR1:199806
          Length = 339

 Score =  638 bits (1645), Expect = 0.0
 Identities = 319/339 (94%), Positives = 330/339 (97%)

Query: 1   MLIIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDKPFDEGYL 60
           MLIIRPI+AGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKV+DKPFDEGYL
Sbjct: 1   MLIIRPIRAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVVDKPFDEGYL 60

Query: 61  MVLEDTATREVVGTCAIEAAVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGA 120
           MVLEDT TREVVGTCAIEAAVGMEDAFYHYRLGTEVY+SEQIEVRNEVETLTLCHDYTGA
Sbjct: 61  MVLEDTETREVVGTCAIEAAVGMEDAFYHYRLGTEVYYSEQIEVRNEVETLTLCHDYTGA 120

Query: 121 AELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSDSDGNSPFYCWL 180
           AELCTLFLRE YRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSD+DG+SPFY WL
Sbjct: 121 AELCTLFLREPYRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSDADGHSPFYGWL 180

Query: 181 QKNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL 240
           QKNFLGIDF+QADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL
Sbjct: 181 QKNFLGIDFVQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL 240

Query: 241 QAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESDKQFIVSNTQLANY 300
           QAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIG+MPESDKQFIVSNTQLANY
Sbjct: 241 QAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGDMPESDKQFIVSNTQLANY 300

Query: 301 RATSACLAVDDKTEQVVISPELAEGLLLAKGDQIRILAM 339
           RATSA L +++K +QVVIS ELAE LLL KGDQIRILAM
Sbjct: 301 RATSAYLCIEEKADQVVISAELAEELLLVKGDQIRILAM 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: 511
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 199806 SO0618 (arginine N-succinyltransferase (NCBI ptt file))
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.1877.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.5e-141  456.3   0.0   2.9e-141  456.1   0.0    1.0  1  lcl|FitnessBrowser__MR1:199806  SO0618 arginine N-succinyltransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199806  SO0618 arginine N-succinyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.1   0.0  2.9e-141  2.9e-141       1     335 [.       3     338 ..       3     339 .] 0.98

  Alignments for each domain:
  == domain 1  score: 456.1 bits;  conditional E-value: 2.9e-141
                       TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfagele.raeegylfvledtetgkvvGvsaieaav 78 
                                     i+rp++  d+++l+++a+e+G+G+tslp+n +ll+++i+rae sf + ++ + +egyl+vledtet +vvG++aieaav
  lcl|FitnessBrowser__MR1:199806   3 IIRPIRAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVVDkPFDEGYLMVLEDTETREVVGTCAIEAAV 81 
                                     79*********************************************9651679************************* PP

                       TIGR03244  79 GleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrkelnGkllskarflflaefkerfskki 157
                                     G+e++fy+yr+g+ v  s+++++ +++etl+l++d+tga+elCtlfl+e yrk++nG++ls++rflfla++ +rf++++
  lcl|FitnessBrowser__MR1:199806  82 GMEDAFYHYRLGTEVYYSEQIEVRNEVETLTLCHDYTGAAELCTLFLREPYRKGNNGRMLSRSRFLFLAQHAKRFGETV 160
                                     ******************************************************************************* PP

                       TIGR03244 158 iaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPiyvdllskeaqdvigkvhektkPalal 236
                                     iaemrGvsd +G+sPf+ +l+k+f  +df +adylsg+Gkkaf+ae+mP+ P+yv+ll++eaq+vig+vh++t+Pal l
  lcl|FitnessBrowser__MR1:199806 161 IAEMRGVSDADGHSPFYGWLQKNFLGIDFVQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSL 239
                                     ******************************************************************************* PP

                       TIGR03244 237 leseGlryqgyvdifdaGptleaevakiravresklvevavaesaaedeaepylvanekledfrvvlvess..ldaeel 313
                                     l++eG+r +gyvdifd+Gpt+e+++++iravres+l++v +++  ++d  ++++v+n++l+++r++ + +    +a+++
  lcl|FitnessBrowser__MR1:199806 240 LQAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGDMPESD--KQFIVSNTQLANYRATSAYLCieEKADQV 316
                                     ********************************************9999..99*************9987654489**** PP

                       TIGR03244 314 vlsaeeakalkveeGdkvrvva 335
                                     v+sae a++l + +Gd++r++a
  lcl|FitnessBrowser__MR1:199806 317 VISAELAEELLLVKGDQIRILA 338
                                     ********************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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.69
//
[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