Alignments for a candidate for arcB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Marinobacter adhaerens HP15

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate GFF4047 HP15_3987 ornithine carbamoyltransferase

Query= SwissProt::P08308
         (336 letters)



>FitnessBrowser__Marino:GFF4047
          Length = 333

 Score =  449 bits (1155), Expect = e-131
 Identities = 219/333 (65%), Positives = 268/333 (80%), Gaps = 2/333 (0%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           MAFN+ NR+ L+L   S RE+ +LL LS DLK AKY GTE   L+ K+IALIFEK STRT
Sbjct: 1   MAFNLKNRHFLTLRDFSPREIAFLLKLSADLKTAKYAGTEVPKLEGKDIALIFEKNSTRT 60

Query: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120
           R  FEVAA+DQGA VTY+ P  + IGHKES+KDTARVLGR+YDAIEYRGF Q +V+ELA+
Sbjct: 61  RVGFEVAAFDQGARVTYLGPTGTHIGHKESVKDTARVLGRVYDAIEYRGFGQSVVDELAQ 120

Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180
           +AGVPV+NGLT+E+HPTQ+LAD LTM+EH +KPL D++Y ++GDA NNMG+SLL+ GAK+
Sbjct: 121 YAGVPVYNGLTNEFHPTQILADFLTMQEHVEKPLRDVAYVFIGDAANNMGDSLLIGGAKM 180

Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240
           GMDVR+ APKA WP      + +  A E+GA++T+TED   AV GVDFV+TDVWVSMGEP
Sbjct: 181 GMDVRLCAPKACWPGQAVQEEAQALAAETGARITITEDVDAAVAGVDFVYTDVWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
            E W ERIK L+PYQVN  +M  TGNPRA+FMHCLPAFHN+ET VGK+I E Y    + +
Sbjct: 241 KEKWAERIKLLMPYQVNAALMAKTGNPRARFMHCLPAFHNTETVVGKEIQETYG--IDAM 298

Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTL 333
           EVTE+VFESP +I F+QAENRMHTIKA+LV+TL
Sbjct: 299 EVTEEVFESPASIVFDQAENRMHTIKAVLVATL 331


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: 386
Number of extensions: 6
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: 333
Length adjustment: 28
Effective length of query: 308
Effective length of database: 305
Effective search space:    93940
Effective search space used:    93940
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 GFF4047 HP15_3987 (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.6362.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   9.1e-133  428.1   0.0     1e-132  427.9   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF4047  HP15_3987 ornithine carbamoyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF4047  HP15_3987 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.9   0.0    1e-132    1e-132       1     303 [.       8     331 ..       8     332 .. 0.99

  Alignments for each domain:
  == domain 1  score: 427.9 bits;  conditional E-value: 1e-132
                           TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkee 75 
                                         rh+l+l d+s++e+  ll+l+++lk++k++g+e  kl+gk +aliFek+stRtRv fevaa+++Ga+v+yl++  
  lcl|FitnessBrowser__Marino:GFF4047   8 RHFLTLRDFSPREIAFLLKLSADLKTAKYAGTEVPKLEGKDIALIFEKNSTRTRVGFEVAAFDQGARVTYLGPTG 82 
                                         8************************************************************************** PP

                           TIGR00658  76 lqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg.klkev 149
                                         +++g+kes+kDtarvl+r++dai +R++ ++ v ela+ya+vPv+ngLt+++hP+qilaD+lt++e+++  l +v
  lcl|FitnessBrowser__Marino:GFF4047  83 THIGHKESVKDTARVLGRVYDAIEYRGFGQSVVDELAQYAGVPVYNGLTNEFHPTQILADFLTMQEHVEkPLRDV 157
                                         *********************************************************************99**** PP

                           TIGR00658 150 klvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytD 223
                                          +v++GDa nn+++sll+++ak+G+dv++++P++++p +++ ++a+++a+e+g+++++ted++ av+++d++ytD
  lcl|FitnessBrowser__Marino:GFF4047 158 AYVFIGDAaNNMGDSLLIGGAKMGMDVRLCAPKACWPGQAVQEEAQALAAETGARITITEDVDAAVAGVDFVYTD 232
                                         *******99****************************************************************** PP

                           TIGR00658 224 vwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr.................Geevtdevleg 279
                                         vwvsmGe +ek++er+kll pyqvn  l++ + +p + f+hCLPa++                  +evt+ev+e+
  lcl|FitnessBrowser__Marino:GFF4047 233 VWVSMGEpKEKWAERIKLLMPYQVNAALMAKTgNPRARFMHCLPAFHntetvvgkeiqetygidAMEVTEEVFES 307
                                         *******999********************999****************************9999********** PP

                           TIGR00658 280 easivfdeaenRlhaqkavlkall 303
                                         +asivfd+aenR+h++kavl+a+l
  lcl|FitnessBrowser__Marino:GFF4047 308 PASIVFDQAENRMHTIKAVLVATL 331
                                         *********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (333 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: 9.89
//
[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