Alignments for a candidate for arcB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Burkholderia phytofirmans PsJN

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate BPHYT_RS27685 BPHYT_RS27685 ornithine carbamoyltransferase

Query= SwissProt::P08308
         (336 letters)



>FitnessBrowser__BFirm:BPHYT_RS27685
          Length = 332

 Score =  454 bits (1168), Expect = e-132
 Identities = 218/334 (65%), Positives = 271/334 (81%), Gaps = 2/334 (0%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           MAFN+HNR+LL++   S R++ +LLDL+ +LKRAKY G E   L  KN+ALIFEKTSTRT
Sbjct: 1   MAFNLHNRSLLNMQDFSPRDIGFLLDLAAELKRAKYAGNEVPRLNGKNVALIFEKTSTRT 60

Query: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120
           RCAFEVA +DQG +VTYID  SSQ+G KES+KDTARVLGR+YD IEYRGF Q +VE+LA 
Sbjct: 61  RCAFEVAVHDQGGHVTYIDSASSQLGRKESLKDTARVLGRLYDGIEYRGFHQSVVEDLAA 120

Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180
           ++ VPV+NGLTDE+HPTQ+LAD+LTMRE  +KPLH++S+ YLGDAR NMGNSLL+ G ++
Sbjct: 121 YSHVPVWNGLTDEFHPTQVLADLLTMREFGEKPLHELSFCYLGDARFNMGNSLLIGGVQM 180

Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240
           GMDVRIAAP+ LWPHDE V Q +  AE +GA +T+ EDP   V G DFV+TDVWVSMGEP
Sbjct: 181 GMDVRIAAPRELWPHDELVQQMRHLAERTGASVTIVEDPVAGVGGADFVYTDVWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
           +EAWG RI  LLPYQVN  +MKATG  R +FMHCLPA+HN ET +G+Q+ E++    + +
Sbjct: 241 MEAWGPRIDLLLPYQVNAALMKATGKSRTRFMHCLPAYHNLETDIGRQLHERFG--LSEL 298

Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLA 334
           EV+++VFES  +I F QAENRMHTIKA+LV+TLA
Sbjct: 299 EVSDEVFESNASIVFSQAENRMHTIKAVLVATLA 332


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: 403
Number of extensions: 10
Number of successful extensions: 2
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: 332
Length adjustment: 28
Effective length of query: 308
Effective length of database: 304
Effective search space:    93632
Effective search space used:    93632
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 BPHYT_RS27685 BPHYT_RS27685 (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.9533.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.9e-125  403.4   0.0   3.2e-125  403.3   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS27685  BPHYT_RS27685 ornithine carbamoy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS27685  BPHYT_RS27685 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.3   0.0  3.2e-125  3.2e-125       1     303 [.       8     331 ..       8     332 .] 0.99

  Alignments for each domain:
  == domain 1  score: 403.3 bits;  conditional E-value: 3.2e-125
                                TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvly 70 
                                              r+ll+++d+s++++  ll+la++lk++k++g+e  +l+gk++aliFek+stRtR++feva+ ++G++v+y
  lcl|FitnessBrowser__BFirm:BPHYT_RS27685   8 RSLLNMQDFSPRDIGFLLDLAAELKRAKYAGNEVPRLNGKNVALIFEKTSTRTRCAFEVAVHDQGGHVTY 77 
                                              78******************************************************************** PP

                                TIGR00658  71 lnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltik 140
                                              +++ ++qlgrkes+kDtarvl+r++d+i +R+++++ ve+la y+ vPv+ngLtd++hP+q+laDllt++
  lcl|FitnessBrowser__BFirm:BPHYT_RS27685  78 IDSASSQLGRKESLKDTARVLGRLYDGIEYRGFHQSVVEDLAAYSHVPVWNGLTDEFHPTQVLADLLTMR 147
                                              ********************************************************************** PP

                                TIGR00658 141 eklg.klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelte 208
                                              e  +  l+e+++ y+GDa  n++nsll++++++G+dv++a+P++l+p+ e+v++ +++a+++g++++++e
  lcl|FitnessBrowser__BFirm:BPHYT_RS27685 148 EFGEkPLHELSFCYLGDArFNMGNSLLIGGVQMGMDVRIAAPRELWPHDELVQQMRHLAERTGASVTIVE 217
                                              *99989************99************************************************** PP

                                TIGR00658 209 dpkkavkdadviytDvwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr........ 268
                                              dp+ +v +ad++ytDvwvsmGe  e++  r++ll pyqvn  l++ + k+ + f+hCLPa +        
  lcl|FitnessBrowser__BFirm:BPHYT_RS27685 218 DPVAGVGGADFVYTDVWVSMGEpMEAWGPRIDLLLPYQVNAALMKATgKSRTRFMHCLPAYHnletdigr 287
                                              **********************9999*********************9********************** PP

                                TIGR00658 269 .........GeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                                         ev+dev+e++asivf +aenR+h++kavl+a+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS27685 288 qlherfglsELEVSDEVFESNASIVFSQAENRMHTIKAVLVATL 331
                                              ******99889******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (332 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.99
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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