Alignments for a candidate for arcB in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Pseudomonas fluorescens FW300-N1B4

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate Pf1N1B4_616 Ornithine carbamoyltransferase (EC 2.1.3.3)

Query= SwissProt::P08308
         (336 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616
          Length = 336

 Score =  601 bits (1550), Expect = e-177
 Identities = 292/336 (86%), Positives = 317/336 (94%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           MAFNM NR+LLSLMHH+TREL YLLDLSRDLKRAKYTGTE+ HL+ KNIALIFEKTSTRT
Sbjct: 1   MAFNMRNRSLLSLMHHTTRELNYLLDLSRDLKRAKYTGTERPHLQGKNIALIFEKTSTRT 60

Query: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120
           RCAFEVAA+DQGA+VTYIDP SSQIGHKESMKDTARVLGRM+DAIEYRGF+QEIVEELAK
Sbjct: 61  RCAFEVAAHDQGAHVTYIDPVSSQIGHKESMKDTARVLGRMFDAIEYRGFEQEIVEELAK 120

Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180
           FAGVPVFNGLT E+HPTQM+AD LTMREHSDKPLHDISYAYLGDAR NMGNSLL+IGAKL
Sbjct: 121 FAGVPVFNGLTAEFHPTQMIADTLTMREHSDKPLHDISYAYLGDARYNMGNSLLMIGAKL 180

Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240
           GMDVRIAAPKALWPH +F+ QCK FAEESGA++T+TEDPKEAVK VDF+HTD+WVSMGEP
Sbjct: 181 GMDVRIAAPKALWPHQDFIDQCKAFAEESGARITITEDPKEAVKDVDFIHTDIWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
           VEAW ERI++LLPYQVN E+MKA+GNPR KFMHCLPAFHNSETKVGK IA +YP+LANG+
Sbjct: 241 VEAWDERIEQLLPYQVNAEMMKASGNPRVKFMHCLPAFHNSETKVGKDIAARYPHLANGV 300

Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLADI 336
           EVTEDVFESP NIAFEQAENRMHTIKAILVS LADI
Sbjct: 301 EVTEDVFESPANIAFEQAENRMHTIKAILVSALADI 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: 490
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 Pf1N1B4_616 (Ornithine carbamoyltransferase (EC 2.1.3.3))
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.9347.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   4.6e-133  429.0   0.0   5.2e-133  428.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616  Ornithine carbamoyltransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616  Ornithine carbamoyltransferase (EC 2.1.3.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.9   0.0  5.2e-133  5.2e-133       1     303 [.       8     333 ..       8     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 428.9 bits;  conditional E-value: 5.2e-133
                                     TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelG 65 
                                                   r+llsl++++++el++ll+l+++lk++k++g+e+ +l+gk++aliFek+stRtR++fevaa ++G
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616   8 RSLLSLMHHTTRELNYLLDLSRDLKRAKYTGTERPHLQGKNIALIFEKTSTRTRCAFEVAAHDQG 72 
                                                   78*************************************************************** PP

                                     TIGR00658  66 aqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPc 130
                                                   a+v+y+++ ++q+g+kes+kDtarvl+r++dai +R++++e+veelak+a+vPv+ngLt ++hP+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616  73 AHVTYIDPVSSQIGHKESMKDTARVLGRMFDAIEYRGFEQEIVEELAKFAGVPVFNGLTAEFHPT 137
                                                   ***************************************************************** PP

                                     TIGR00658 131 qilaDlltikeklg.klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkka 193
                                                   q++aD lt++e+ +  l++++++y+GDa  n++nsll+++aklG+dv++a+P++l+p+++ ++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 138 QMIADTLTMREHSDkPLHDISYAYLGDArYNMGNSLLMIGAKLGMDVRIAAPKALWPHQDFIDQC 202
                                                   **************99************99*********************************** PP

                                     TIGR00658 194 kkiakenggkleltedpkkavkdadviytDvwvsmGe.eekkeerlkllkpyqvneellela.kp 256
                                                   k++a+e+g+++++tedpk+avkd+d+i+tD+wvsmGe  e+++er+++l pyqvn e+++ + +p
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 203 KAFAEESGARITITEDPKEAVKDVDFIHTDIWVSMGEpVEAWDERIEQLLPYQVNAEMMKASgNP 267
                                                   *************************************9999********************99** PP

                                     TIGR00658 257 evkflhCLPavr...................GeevtdevlegeasivfdeaenRlhaqkavlkal 302
                                                    vkf+hCLPa++                   G evt++v+e++a+i f++aenR+h++ka+l+  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 268 RVKFMHCLPAFHnsetkvgkdiaaryphlanGVEVTEDVFESPANIAFEQAENRMHTIKAILVSA 332
                                                   *************************************************************9976 PP

                                     TIGR00658 303 l 303
                                                   l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 333 L 333
                                                   6 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.29
//
[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