Alignments for a candidate for arcB in Methanobacterium arcticum M2

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Methanobacterium arcticum M2

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_048082016.1 EI99_RS10890 ornithine carbamoyltransferase

Query= BRENDA::Q51742
         (315 letters)



>NCBI__GCF_000746075.1:WP_048082016.1
          Length = 302

 Score =  308 bits (788), Expect = 1e-88
 Identities = 158/302 (52%), Positives = 213/302 (70%), Gaps = 5/302 (1%)

Query: 10  LLCLQDYTAEEIWTILETAKMFKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEVAMA 69
           LL ++D   + +  IL+ +K FK  +  G+P   L  KTLAM+F+K STRTR+SFEV M 
Sbjct: 4   LLSMED-ARDHVNEILDLSKKFKNGEIPGEP---LAKKTLAMVFEKASTRTRISFEVGMY 59

Query: 70  HLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYATVPVING 129
            LGG+ALYL+ +DLQL RGE + DTARV+SRYVD IM R  +H DV + ++Y+ VPVING
Sbjct: 60  QLGGNALYLSREDLQLGRGEIVEDTARVMSRYVDGIMIRAKEHDDVLEFSRYSDVPVING 119

Query: 130 LSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGDGNNVAHSLMIAGTKLGADVVVATPEG 189
           L++  HPCQA AD +TI+EKK +   VK+ +VGDGNNV +SL+ A   +G D+ V  P G
Sbjct: 120 LTNKEHPCQAFADLLTIYEKKNSFD-VKLAFVGDGNNVCNSLLFASAFVGMDMDVVCPPG 178

Query: 190 YEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEAEERRKIFR 249
           YEPD ++ K A++ A E+G   ++++D    V+ AD +YTDVW SMG E EA +R   F 
Sbjct: 179 YEPDAEIFKKAKKYAEETGAELKIVNDIEAGVEGADAVYTDVWISMGDEEEASKRLNAFA 238

Query: 250 PFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDQAENRLHAQKAVLALV 309
            +QVNKDL+  A  D + +HCLPA RG+E+T D+++S  S VWDQAENRLHAQKAVL  +
Sbjct: 239 DYQVNKDLMGPANEDAIILHCLPAIRGQEITADMLNSTQSAVWDQAENRLHAQKAVLYKL 298

Query: 310 MG 311
           +G
Sbjct: 299 LG 300


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: 286
Number of extensions: 13
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: 315
Length of database: 302
Length adjustment: 27
Effective length of query: 288
Effective length of database: 275
Effective search space:    79200
Effective search space used:    79200
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_048082016.1 EI99_RS10890 (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.3346540.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     7e-132  425.2   0.0   7.9e-132  425.0   0.0    1.0  1  NCBI__GCF_000746075.1:WP_048082016.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000746075.1:WP_048082016.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.0   0.0  7.9e-132  7.9e-132       2     303 ..       3     299 ..       2     300 .. 0.98

  Alignments for each domain:
  == domain 1  score: 425.0 bits;  conditional E-value: 7.9e-132
                             TIGR00658   2 hllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnke 74 
                                           hlls+ d   + ++e+l+l+kk+k+ +      + l +ktla++Fek+stRtR+sfev++y+lG+++lyl++e
  NCBI__GCF_000746075.1:WP_048082016.1   3 HLLSMEDAR-DHVNEILDLSKKFKNGEIP---GEPLAKKTLAMVFEKASTRTRISFEVGMYQLGGNALYLSRE 71 
                                           99***9987.89**************999...589************************************** PP

                             TIGR00658  75 elqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklk 147
                                           +lqlgr+e ++Dtarv+sryvd+i++R+ +h+dv e+++y+ vPvingLt++ehPcq++aDllti+ek+++++
  NCBI__GCF_000746075.1:WP_048082016.1  72 DLQLGRGEIVEDTARVMSRYVDGIMIRAKEHDDVLEFSRYSDVPVINGLTNKEHPCQAFADLLTIYEKKNSFD 144
                                           ************************************************************************6 PP

                             TIGR00658 148 evklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadvi 220
                                            vkl++vGD+nnv+nsll a+a +G+d+ v++P+g+ep+aei+kkakk a+e+g++l++++d++ +v++ad +
  NCBI__GCF_000746075.1:WP_048082016.1 145 -VKLAFVGDGNNVCNSLLFASAFVGMDMDVVCPPGYEPDAEIFKKAKKYAEETGAELKIVNDIEAGVEGADAV 216
                                           .7*********************************************************************** PP

                             TIGR00658 221 ytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlh 293
                                           ytDvw+smG+ee++++rl+++ +yqvn++l+  a++++++lhCLPa rG+e+t ++l++ +s v+d+aenRlh
  NCBI__GCF_000746075.1:WP_048082016.1 217 YTDVWISMGDEEEASKRLNAFADYQVNKDLMGPANEDAIILHCLPAIRGQEITADMLNSTQSAVWDQAENRLH 289
                                           ************************************************************************* PP

                             TIGR00658 294 aqkavlkall 303
                                           aqkavl  ll
  NCBI__GCF_000746075.1:WP_048082016.1 290 AQKAVLYKLL 299
                                           ******9887 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: 21.35
//
[ok]

This GapMind analysis is from Sep 24 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 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