GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Pseudomonas fluorescens FW300-N2E2

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate Pf6N2E2_2909 Ornithine carbamoyltransferase (EC 2.1.3.3)

Query= SwissProt::P08308
         (336 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2909
          Length = 336

 Score =  597 bits (1539), Expect = e-175
 Identities = 289/336 (86%), Positives = 315/336 (93%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           MAFNM NR+LLSLMHH+ REL +LLDLSRDLKRAKYTGTEQ HLK KNIALIFEKTSTRT
Sbjct: 1   MAFNMRNRSLLSLMHHTNRELHFLLDLSRDLKRAKYTGTEQPHLKGKNIALIFEKTSTRT 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
           GMDVRI APKALWPH +F+ QC+ FA ESGA++T+TEDPKEAVKGVDF+HTD+WVSMGEP
Sbjct: 181 GMDVRIGAPKALWPHQDFIDQCQAFAVESGARITITEDPKEAVKGVDFIHTDIWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
           VEAW ERI++LLPYQVN ++MKA+GNPR KFMHCLPAFHNSETKVGK IA +YPNLANG+
Sbjct: 241 VEAWDERIEQLLPYQVNAQMMKASGNPRVKFMHCLPAFHNSETKVGKDIAARYPNLANGV 300

Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLADI 336
           EVTE+VFESP NIAFEQAENRMHTIKAILVS LADI
Sbjct: 301 EVTEEVFESPANIAFEQAENRMHTIKAILVSALADI 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: 487
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 Pf6N2E2_2909 (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.23750.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.7e-131  423.9   0.0   1.9e-131  423.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2909  Ornithine carbamoyltransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2909  Ornithine carbamoyltransferase (EC 2.1.3.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.7   0.0  1.9e-131  1.9e-131       1     303 [.       8     333 ..       8     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 423.7 bits;  conditional E-value: 1.9e-131
                                      TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayel 64 
                                                    r+llsl++++++el+ ll+l+++lk++k++g+e+ +lkgk++aliFek+stRtR++fevaa ++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2909   8 RSLLSLMHHTNRELHFLLDLSRDLKRAKYTGTEQPHLKGKNIALIFEKTSTRTRCAFEVAAHDQ 71 
                                                    78************************************************************** PP

                                      TIGR00658  65 GaqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdleh 128
                                                    Ga+v+y+++ ++q+g+kes+kDtarvl+r++dai +R++++e+veelak+a+vPv+ngLt ++h
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2909  72 GAHVTYIDPVSSQIGHKESMKDTARVLGRMFDAIEYRGFEQEIVEELAKFAGVPVFNGLTAEFH 135
                                                    **************************************************************** PP

                                      TIGR00658 129 PcqilaDlltikeklg.klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeiv 190
                                                    P+q++aD lt++e+ +  l++++++y+GDa  n++nsll+++aklG+dv++ +P++l+p+++ +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2909 136 PTQMIADTLTMREHSDkPLHDISYAYLGDArYNMGNSLLMIGAKLGMDVRIGAPKALWPHQDFI 199
                                                    ****************99************99******************************** PP

                                      TIGR00658 191 kkakkiakenggkleltedpkkavkdadviytDvwvsmGe.eekkeerlkllkpyqvneellel 253
                                                    ++++++a e+g+++++tedpk+avk++d+i+tD+wvsmGe  e+++er+++l pyqvn ++++ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2909 200 DQCQAFAVESGARITITEDPKEAVKGVDFIHTDIWVSMGEpVEAWDERIEQLLPYQVNAQMMKA 263
                                                    ****************************************9999******************** PP

                                      TIGR00658 254 a.kpevkflhCLPavr...................GeevtdevlegeasivfdeaenRlhaqka 297
                                                    + +p vkf+hCLPa++                   G evt+ev+e++a+i f++aenR+h++ka
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2909 264 SgNPRVKFMHCLPAFHnsetkvgkdiaarypnlanGVEVTEEVFESPANIAFEQAENRMHTIKA 327
                                                    99************************************************************** PP

                                      TIGR00658 298 vlkall 303
                                                    +l+  l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2909 328 ILVSAL 333
                                                    *99766 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.52
//
[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:

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:

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:

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:

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