Alignments for a candidate for argI in Maridesulfovibrio bastinii DSM 16055

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Maridesulfovibrio bastinii DSM 16055

Align ornithine carbamoyltransferase (EC 2.1.3.3); putrescine carbamoyltransferase (EC 2.1.3.6) (characterized)
to candidate WP_027178477.1 G496_RS0105960 ornithine carbamoyltransferase

Query= BRENDA::Q837U7
         (339 letters)



>NCBI__GCF_000429985.1:WP_027178477.1
          Length = 349

 Score =  270 bits (691), Expect = 3e-77
 Identities = 141/326 (43%), Positives = 203/326 (62%), Gaps = 2/326 (0%)

Query: 3   RDYVTTETYTKEEMHYLVDLSLKIKEAIKNGYYPQLLKNKSLGMIFQQSSTRTRVSFETA 62
           R  V+ + +T EEM  +++L   +KEA K+   P L K+KS+ MIF+  STRTR+SFE A
Sbjct: 17  RHMVSMKDFTTEEMDNMMELMSMLKEARKDNAIPHLFKDKSVAMIFEAGSTRTRISFEVA 76

Query: 63  MEQLGGHGEYLAPGQIQLG-GHETIEDTSRVLSRLVDILMARVERHHSIVDLANCATIPV 121
              LGGHG +L+P  I LG G E+I+DT+RVLSR+ DI+MAR     +I  L   +T+PV
Sbjct: 77  ATLLGGHGLFLSPKDIHLGSGKESIDDTARVLSRMCDIVMARTNSPDTIDALCRMSTVPV 136

Query: 122 INGMSDYNHPTQELGDLCTMVEHLPEGKKLEDCKVVFVGDATQVCFSLGLITTKMGMNFV 181
           ING+    HPTQ L DL T+ EH+ +G+KL D  + F+GDAT VC SL L  TK GMNF 
Sbjct: 137 INGLDTRFHPTQMLADLFTIKEHITDGRKLSDLTLAFMGDATDVCRSLLLTCTKYGMNFK 196

Query: 182 HFGPEGFQLNEEHQAKLAKNCEVSGGSFLVTDDASSVEGADFLYTDVWYGLYEAELSEEE 241
             GP+ +Q+ +E      + C+ SG S+ +TDD   +   D +Y D +Y + + +  ++E
Sbjct: 197 QIGPKKYQMQQEWLDMADEFCKESGASYEITDDVEKISECDVVYGDSFYWVTQLD-EKKE 255

Query: 242 RMKVFYPKYQVNQEMMDRAGANCKFMHCLPATRGEEVTDEVIDGKNSICFDEAENRLTSI 301
           R+  F P Y + +E+M +A      +HCLPA   EEVT E ++G  S+ FDEAENRLT+ 
Sbjct: 256 RLAAFMPDYVITEELMSKAKPGALLLHCLPANDKEEVTREALEGPQSVAFDEAENRLTAQ 315

Query: 302 RGLLVYLMNDYEAKNPYDLIKQAEAK 327
             +LVY  + +  +   ++ K+ E K
Sbjct: 316 MAILVYFTHKFSKEPTEEVKKEHETK 341


Lambda     K      H
   0.318    0.134    0.390 

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: 317
Number of extensions: 14
Number of successful extensions: 4
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: 339
Length of database: 349
Length adjustment: 29
Effective length of query: 310
Effective length of database: 320
Effective search space:    99200
Effective search space used:    99200
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_027178477.1 G496_RS0105960 (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.1223822.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-103  331.4   0.2   2.8e-103  331.2   0.2    1.0  1  NCBI__GCF_000429985.1:WP_027178477.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000429985.1:WP_027178477.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.2   0.2  2.8e-103  2.8e-103       1     302 [.      17     322 ..      17     324 .. 0.97

  Alignments for each domain:
  == domain 1  score: 331.2 bits;  conditional E-value: 2.8e-103
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 
                                           rh++s++d+++ee+ +++el ++lk+++k +   + +k k++a+iFe  stRtR+sfevaa+ lG++ l+l++
  NCBI__GCF_000429985.1:WP_027178477.1  17 RHMVSMKDFTTEEMDNMMELMSMLKEARKDNAIPHLFKDKSVAMIFEAGSTRTRISFEVAATLLGGHGLFLSP 89 
                                           89*********************************************************************** PP

                             TIGR00658  74 eelqlgr.kesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg. 144
                                           ++++lg  kesi Dtarvlsr+ d++++R+++ +++ +l++ ++vPvingL   +hP+q+laDl+tike++  
  NCBI__GCF_000429985.1:WP_027178477.1  90 KDIHLGSgKESIDDTARVLSRMCDIVMARTNSPDTIDALCRMSTVPVINGLDTRFHPTQMLADLFTIKEHITd 162
                                           *****9747*************************************************************977 PP

                             TIGR00658 145 ..klkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavk 215
                                             kl++++l+++GDa +v+ slll+++k G++++  +P+++++++e +++a ++ ke+g++ e+t+d++k ++
  NCBI__GCF_000429985.1:WP_027178477.1 163 grKLSDLTLAFMGDATDVCRSLLLTCTKYGMNFKQIGPKKYQMQQEWLDMADEFCKESGASYEITDDVEK-IS 234
                                           799**************************************************************99877.77 PP

                             TIGR00658 216 dadviytDvwvsmGeeekkeerlkllkp.yqvneellelakpevkflhCLPavrGeevtdevlegeasivfde 287
                                           + dv+y D +  + + ++k+erl+++ p y ++eel++ akp + +lhCLPa+  eevt e leg++s+ fde
  NCBI__GCF_000429985.1:WP_027178477.1 235 ECDVVYGDSFYWVTQLDEKKERLAAFMPdYVITEELMSKAKPGALLLHCLPANDKEEVTREALEGPQSVAFDE 307
                                           9**********************999765******************************************** PP

                             TIGR00658 288 aenRlhaqkavlkal 302
                                           aenRl aq+a+l+++
  NCBI__GCF_000429985.1:WP_027178477.1 308 AENRLTAQMAILVYF 322
                                           ***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (349 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: 00:00:00.00
# Mc/sec: 18.08
//
[ok]

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

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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 2024 update 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 original 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