Alignments for a candidate for argI in Roseburia faecis M72

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Roseburia faecis M72

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_055067583.1 M72_RS06160 ornithine carbamoyltransferase

Query= metacyc::ORNCARBAMTRANSFERST-MONOMER
         (332 letters)



>NCBI__GCF_001406815.1:WP_055067583.1
          Length = 329

 Score =  390 bits (1002), Expect = e-113
 Identities = 202/331 (61%), Positives = 248/331 (74%), Gaps = 4/331 (1%)

Query: 3   VSLKGRSFLTLKHFTPEEINYLLDLSADLKAKKRAGIKGNLLEGKNVVLLFEKTSTRTRC 62
           ++LKGR+ L +  FTPEEI YL+DLSA+LK KK  GI  + L GKN+ L+FEKTSTRTRC
Sbjct: 1   MTLKGRNLLKMMDFTPEEILYLVDLSAELKEKKHQGIMHDSLVGKNIALIFEKTSTRTRC 60

Query: 63  AFEVGVLDEGGHVTFLGSGDSQMGKKESIEDTAKVLGRFYDGIEFRGFKQETVEILAANA 122
           +FEV   D G HVT+L    SQ+GKKESI DTA+VLGR +DGIE+RG+ QE VE LA  A
Sbjct: 61  SFEVAAHDLGMHVTYLDPSGSQIGKKESIPDTARVLGRMFDGIEYRGYGQEIVEELAKYA 120

Query: 123 GVPVWNGLTDLYHPTQILADFLTIKEHVAKPLNKVKFVYAGDARNNMGNSLMIGAAKMGM 182
           GVPVWNGLT+  HPTQ++AD LTIKEH+ K L  VKFVY GDAR NMGNSLM+  AK+GM
Sbjct: 121 GVPVWNGLTNESHPTQMIADMLTIKEHLGK-LKGVKFVYMGDARYNMGNSLMVTCAKLGM 179

Query: 183 EFWGLAPKELWPSEELVAEMKEVAKETGASINFSENV-DDVKNADVIYTDVWVSMGE-EA 240
            F      + +P ++LV    +VA  TGASI  +++V +  ++ADVIYTDVWVSMGE E 
Sbjct: 180 HFVACTNPKYYPDKKLVDYCVDVASTTGASITLTDSVAEATRDADVIYTDVWVSMGEPEE 239

Query: 241 MFEERIKQLKPYQVNMDMIKKTENPDVLFLHCLPAFHDLNTTVGKDIYEKFGLESMEVTD 300
           ++ ERI  LKPYQVN D  K  ++   +F+HCLPAFHDL TT+GK +YEKFGL  +EVTD
Sbjct: 240 VWAERINDLKPYQVNADAFKNAKD-SAIFMHCLPAFHDLKTTIGKQVYEKFGLSELEVTD 298

Query: 301 EVFRSRHSKVFDEAENRMHTIKAVMVATIGN 331
           EVF S  S VFDEAENRMH+IKA+M AT+ +
Sbjct: 299 EVFESERSVVFDEAENRMHSIKAIMKATLSD 329


Lambda     K      H
   0.317    0.135    0.389 

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: 373
Number of extensions: 17
Number of successful extensions: 5
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: 332
Length of database: 329
Length adjustment: 28
Effective length of query: 304
Effective length of database: 301
Effective search space:    91504
Effective search space used:    91504
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_055067583.1 M72_RS06160 (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.aa/TIGR00658.hmm
# target sequence database:        /tmp/gapView.1172070.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-134  431.8   0.1   7.3e-134  431.7   0.1    1.0  1  NCBI__GCF_001406815.1:WP_055067583.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001406815.1:WP_055067583.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.7   0.1  7.3e-134  7.3e-134       1     303 [.       6     327 ..       6     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 431.7 bits;  conditional E-value: 7.3e-134
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 
                                           r+ll+++d+++ee+ +l++l+++lk++k++g  ++ l gk++aliFek+stRtR+sfevaa +lG +v+yl++
  NCBI__GCF_001406815.1:WP_055067583.1   6 RNLLKMMDFTPEEILYLVDLSAELKEKKHQGIMHDSLVGKNIALIFEKTSTRTRCSFEVAAHDLGMHVTYLDP 78 
                                           78*********************************************************************** PP

                             TIGR00658  74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146
                                           + +q+g+kesi Dtarvl+r++d+i +R+y +e+veelakya+vPv+ngLt+++hP+q++aD+ltike+lgkl
  NCBI__GCF_001406815.1:WP_055067583.1  79 SGSQIGKKESIPDTARVLGRMFDGIEYRGYGQEIVEELAKYAGVPVWNGLTNESHPTQMIADMLTIKEHLGKL 151
                                           ************************************************************************* PP

                             TIGR00658 147 kevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdad 218
                                           k+vk+vy+GDa  n++nsl++++aklG+++v +t +++ p++++v+ + ++a+ +g++++lt+ +++a++dad
  NCBI__GCF_001406815.1:WP_055067583.1 152 KGVKFVYMGDArYNMGNSLMVTCAKLGMHFVACTNPKYYPDKKLVDYCVDVASTTGASITLTDSVAEATRDAD 224
                                           ***********99************************************************************ PP

                             TIGR00658 219 viytDvwvsmGe.eekkeerlkllkpyqvneellelakpevkflhCLPavr.................Geevt 273
                                           viytDvwvsmGe ee ++er++ lkpyqvn + ++ ak++++f+hCLPa++                   evt
  NCBI__GCF_001406815.1:WP_055067583.1 225 VIYTDVWVSMGEpEEVWAERINDLKPYQVNADAFKNAKDSAIFMHCLPAFHdlkttigkqvyekfglsELEVT 297
                                           ************9999*************************************************99889*** PP

                             TIGR00658 274 devlegeasivfdeaenRlhaqkavlkall 303
                                           dev+e+e+s+vfdeaenR+h++ka++ka+l
  NCBI__GCF_001406815.1:WP_055067583.1 298 DEVFESERSVVFDEAENRMHSIKAIMKATL 327
                                           ***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (329 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: 25.15
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis