Alignments for a candidate for arcB in Methanosarcina mazei Go1

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Methanosarcina mazei Go1

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_011032099.1 MM_RS00775 ornithine carbamoyltransferase

Query= BRENDA::O93656
         (317 letters)



>NCBI__GCF_000007065.1:WP_011032099.1
          Length = 302

 Score =  335 bits (859), Expect = 8e-97
 Identities = 167/303 (55%), Positives = 218/303 (71%), Gaps = 4/303 (1%)

Query: 8   RDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEVA 67
           RD+L + D + EEI+ +LE+A  LK  +K G+P   L+ K+L MIF+K STRTRVSFEVA
Sbjct: 3   RDVLSITDLSREEIYELLESAADLKKKRKAGEPTEYLKHKSLGMIFEKSSTRTRVSFEVA 62

Query: 68  MAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYASVPVI 127
           M+  GGHALYLN++D+Q+ RGETI DTAR LS Y+  IMARV  H  VE LA+++++PVI
Sbjct: 63  MSDFGGHALYLNSRDIQVGRGETIEDTARTLSGYLHGIMARVMSHDTVEKLARFSTIPVI 122

Query: 128 NGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGDGNNVAHSLMIAGTKLGADVVVATP 187
           N LSD  HPCQ L D+MTI E K   +G+K  ++GDGNNV +S ++    +G + V+A P
Sbjct: 123 NALSDREHPCQILGDFMTIMEYKNRFEGLKFAWIGDGNNVCNSALLGSAIMGMEFVIACP 182

Query: 188 EGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEAEERRKI 247
           EGYEP  + +    + A   GG F +  DP  A KDAD+IYTDVW SMG EAE E+R K 
Sbjct: 183 EGYEPGAEFL----EKAKALGGKFSITDDPKTAAKDADIIYTDVWVSMGDEAEQEKRLKD 238

Query: 248 FRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDEAENRLHAQKAVLA 307
           F  FQVN +L+  AKPD + MHCLPA RG E+TD+V+D PNSV+++EAENRLHAQKA++ 
Sbjct: 239 FGSFQVNTELLGVAKPDVIVMHCLPARRGLEITDEVMDGPNSVIFEEAENRLHAQKALIL 298

Query: 308 LLL 310
            L+
Sbjct: 299 KLM 301


Lambda     K      H
   0.319    0.134    0.400 

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: 290
Number of extensions: 9
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: 317
Length of database: 302
Length adjustment: 27
Effective length of query: 290
Effective length of database: 275
Effective search space:    79750
Effective search space used:    79750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_011032099.1 MM_RS00775 (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.2324759.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.5e-135  434.7   0.0   9.5e-135  434.6   0.0    1.0  1  NCBI__GCF_000007065.1:WP_011032099.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007065.1:WP_011032099.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.6   0.0  9.5e-135  9.5e-135       1     303 [.       3     301 ..       3     302 .] 0.99

  Alignments for each domain:
  == domain 1  score: 434.6 bits;  conditional E-value: 9.5e-135
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 
                                           r++ls++dls+ee+ elle a++lkk++k+g+ +++lk k+l++iFek+stRtRvsfeva+ ++G+++lyln+
  NCBI__GCF_000007065.1:WP_011032099.1   3 RDVLSITDLSREEIYELLESAADLKKKRKAGEPTEYLKHKSLGMIFEKSSTRTRVSFEVAMSDFGGHALYLNS 75 
                                           799********************************************************************** PP

                             TIGR00658  74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146
                                            ++q+gr+e+i+Dtar+ls y+++i++Rv++h++ve+la+++++Pvin+L+d ehPcqil D++ti+e+++++
  NCBI__GCF_000007065.1:WP_011032099.1  76 RDIQVGRGETIEDTARTLSGYLHGIMARVMSHDTVEKLARFSTIPVINALSDREHPCQILGDFMTIMEYKNRF 148
                                           ************************************************************************* PP

                             TIGR00658 147 kevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219
                                           +++k++++GD+nnv+ns ll++a +G+++v+a+Peg+ep ae ++kak    + ggk+++t+dpk a+kdad+
  NCBI__GCF_000007065.1:WP_011032099.1 149 EGLKFAWIGDGNNVCNSALLGSAIMGMEFVIACPEGYEPGAEFLEKAK----ALGGKFSITDDPKTAAKDADI 217
                                           **********************************************95....58******************* PP

                             TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRl 292
                                           iytDvwvsmG+e+++e+rlk +  +qvn+ell +akp+v+++hCLPa rG e+tdev++g++s++f+eaenRl
  NCBI__GCF_000007065.1:WP_011032099.1 218 IYTDVWVSMGDEAEQEKRLKDFGSFQVNTELLGVAKPDVIVMHCLPARRGLEITDEVMDGPNSVIFEEAENRL 290
                                           ************************************************************************* PP

                             TIGR00658 293 haqkavlkall 303
                                           haqka++  l+
  NCBI__GCF_000007065.1:WP_011032099.1 291 HAQKALILKLM 301
                                           *****998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (302 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: 15.64
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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

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