Alignments for a candidate for arcB in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Pseudomonas stutzeri A1501

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_011911898.1 PST_RS03485 ornithine carbamoyltransferase

Query= SwissProt::P08308
         (336 letters)



>NCBI__GCF_000013785.1:WP_011911898.1
          Length = 336

 Score =  640 bits (1650), Expect = 0.0
 Identities = 316/336 (94%), Positives = 324/336 (96%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           MAFNMHNRNLLSLMHHSTRELRYL+DLSRDLKRAKYTGTEQQHL RKNIALIFEKTSTRT
Sbjct: 1   MAFNMHNRNLLSLMHHSTRELRYLIDLSRDLKRAKYTGTEQQHLSRKNIALIFEKTSTRT 60

Query: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120
           RCAFEVAAYDQGANVTYIDP SSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELA 
Sbjct: 61  RCAFEVAAYDQGANVTYIDPGSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAT 120

Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180
           +AGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDI+YAYLGDARNNMGNSLLLIGAKL
Sbjct: 121 YAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDIAYAYLGDARNNMGNSLLLIGAKL 180

Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240
           GMDVRIAAPKALWP  E VA CKKFAEESGA+L LTEDPKEAVKGVDFVHTDVWVSMGEP
Sbjct: 181 GMDVRIAAPKALWPSAEHVAACKKFAEESGARLLLTEDPKEAVKGVDFVHTDVWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
           VEAWGERI+ELLPYQVN EIMKA GNPR KFMHCLPAFHNSETKVGKQIAEQYP+L NGI
Sbjct: 241 VEAWGERIQELLPYQVNAEIMKAAGNPRVKFMHCLPAFHNSETKVGKQIAEQYPHLKNGI 300

Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLADI 336
           EVTEDVFESP+NIAFEQAENRMHTIKAILV+TLADI
Sbjct: 301 EVTEDVFESPWNIAFEQAENRMHTIKAILVATLADI 336


Lambda     K      H
   0.318    0.133    0.387 

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: 499
Number of extensions: 7
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: 336
Length of database: 336
Length adjustment: 28
Effective length of query: 308
Effective length of database: 308
Effective search space:    94864
Effective search space used:    94864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_011911898.1 PST_RS03485 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

# 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/TIGR00658.hmm
# target sequence database:        /tmp/gapView.693638.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00658  [M=304]
Accession:   TIGR00658
Description: orni_carb_tr: ornithine carbamoyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-136  438.8   0.0   5.6e-136  438.6   0.0    1.0  1  NCBI__GCF_000013785.1:WP_011911898.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013785.1:WP_011911898.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.6   0.0  5.6e-136  5.6e-136       1     303 [.       8     333 ..       8     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 438.6 bits;  conditional E-value: 5.6e-136
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 
                                           r+llsl+++s++el++l++l+++lk++k++g+e+++l++k++aliFek+stRtR++fevaay++Ga+v+y+++
  NCBI__GCF_000013785.1:WP_011911898.1   8 RNLLSLMHHSTRELRYLIDLSRDLKRAKYTGTEQQHLSRKNIALIFEKTSTRTRCAFEVAAYDQGANVTYIDP 80 
                                           78*********************************************************************** PP

                             TIGR00658  74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg.k 145
                                            ++q+g+kes+kDtarvl+r++dai +R++k+e+veela ya+vPv+ngLtd+ hP+q+laD+lt++e+ +  
  NCBI__GCF_000013785.1:WP_011911898.1  81 GSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELATYAGVPVFNGLTDEYHPTQMLADVLTMREHSDkP 153
                                           ***********************************************************************99 PP

                             TIGR00658 146 lkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkda 217
                                           l+++ ++y+GDa nn++nslll++aklG+dv++a+P++l+p+ae v  +kk+a+e+g++l ltedpk+avk++
  NCBI__GCF_000013785.1:WP_011911898.1 154 LHDIAYAYLGDArNNMGNSLLLIGAKLGMDVRIAAPKALWPSAEHVAACKKFAEESGARLLLTEDPKEAVKGV 226
                                           ************************************************************************* PP

                             TIGR00658 218 dviytDvwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr...................G 269
                                           d+++tDvwvsmGe  e++ er++ l pyqvn e+++ a +p vkf+hCLPa++                   G
  NCBI__GCF_000013785.1:WP_011911898.1 227 DFVHTDVWVSMGEpVEAWGERIQELLPYQVNAEIMKAAgNPRVKFMHCLPAFHnsetkvgkqiaeqyphlknG 299
                                           *************9999******************************************************** PP

                             TIGR00658 270 eevtdevlegeasivfdeaenRlhaqkavlkall 303
                                            evt++v+e++ +i f++aenR+h++ka+l+a+l
  NCBI__GCF_000013785.1:WP_011911898.1 300 IEVTEDVFESPWNIAFEQAENRMHTIKAILVATL 333
                                           *******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (336 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: 22.87
//
[ok]

This GapMind analysis is from Sep 24 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