Alignments for a candidate for arcB in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Desulfovibrio vulgaris Miyazaki F

Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate 8499267 DvMF_0046 ornithine carbamoyltransferase (RefSeq)

Query= SwissProt::P11724
         (305 letters)



>FitnessBrowser__Miya:8499267
          Length = 300

 Score =  295 bits (754), Expect = 1e-84
 Identities = 147/296 (49%), Positives = 204/296 (68%), Gaps = 6/296 (2%)

Query: 4   RHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSFEAG 63
           RHF    D   E    L++R  E+KD  +RG + E  K+ +L  +FEKASTRTR+SFE  
Sbjct: 3   RHFTRIRDLGYEGAWKLLQRAKEMKDTAHRGKIMEG-KTAIL--IFEKASTRTRVSFEMA 59

Query: 64  MIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKVPVI 123
           +  LGG  IF++P ++QLGR EP+ D+ARV+SR  D +++RTF  + +TE A +  +PVI
Sbjct: 60  VRHLGGSTIFMTPAESQLGRSEPLRDTARVLSRYADCMVVRTFGQSKITELAEYGSIPVI 119

Query: 124 NGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRVACP 183
           N L+D+ HPCQ++ D+ T +E    +    VAW+GDGNNM NS+IEAA+ F F+L +A P
Sbjct: 120 NALTDEGHPCQVMGDVLTMYERTPDLSTVRVAWVGDGNNMANSWIEAAVYFPFELFMAFP 179

Query: 184 EGYEPKAEFVAL---AGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240
           EGYEP  + +     AG ++ +  DPR AV GAH V+TDVWASMGQE+E   R A F+ Y
Sbjct: 180 EGYEPDRDLLGYALNAGAKIFLTHDPRMAVEGAHYVNTDVWASMGQEEEQKKREAAFKGY 239

Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLE 296
            ++  ++  AA D  FMHCLPAHRGEE+++E+++ P S+ +DQAENRLH QKA+LE
Sbjct: 240 CIDTEMMALAAPDAKFMHCLPAHRGEEVTDEVMESPASIIFDQAENRLHIQKAILE 295


Lambda     K      H
   0.322    0.136    0.404 

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: 258
Number of extensions: 13
Number of successful extensions: 3
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: 305
Length of database: 300
Length adjustment: 27
Effective length of query: 278
Effective length of database: 273
Effective search space:    75894
Effective search space used:    75894
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate 8499267 DvMF_0046 (ornithine carbamoyltransferase (RefSeq))
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.21687.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.9e-117  376.4   0.0   5.5e-117  376.2   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499267  DvMF_0046 ornithine carbamoyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499267  DvMF_0046 ornithine carbamoyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.2   0.0  5.5e-117  5.5e-117       1     303 [.       3     298 ..       3     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 376.2 bits;  conditional E-value: 5.5e-117
                         TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelq 77 
                                       rh+  + dl  e  ++ll++ak++k + ++    k+++gkt  liFek+stRtRvsfe+a+ +lG+ ++++ + e+q
  lcl|FitnessBrowser__Miya:8499267   3 RHFTRIRDLGYEGAWKLLQRAKEMKDTAHR---GKIMEGKTAILIFEKASTRTRVSFEMAVRHLGGSTIFMTPAESQ 76 
                                       7999**********************9999...5899**************************************** PP

                         TIGR00658  78 lgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklvyv 154
                                       lgr e+++Dtarvlsry d++vvR++ +++++ela+y s+Pvin+Ltd+ hPcq++ D+lt++e++ +l+ v++++v
  lcl|FitnessBrowser__Miya:8499267  77 LGRSEPLRDTARVLSRYADCMVVRTFGQSKITELAEYGSIPVINALTDEGHPCQVMGDVLTMYERTPDLSTVRVAWV 153
                                       ***************************************************************************** PP

                         TIGR00658 155 GDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGee 231
                                       GD+nn+ans + aa+ + +++ +a Peg+ep+ +++  a     + g+k+ lt+dp  av++a+ + tDvw+smG+e
  lcl|FitnessBrowser__Miya:8499267 154 GDGNNMANSWIEAAVYFPFELFMAFPEGYEPDRDLLGYAL----NAGAKIFLTHDPRMAVEGAHYVNTDVWASMGQE 226
                                       ************************************9985....59******************************* PP

                         TIGR00658 232 ekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                       e++++r +++k+y +++e+++la p++kf+hCLPa+rGeevtdev+e++asi+fd+aenRlh qka+l++ +
  lcl|FitnessBrowser__Miya:8499267 227 EEQKKREAAFKGYCIDTEMMALAAPDAKFMHCLPAHRGEEVTDEVMESPASIIFDQAENRLHIQKAILEWAF 298
                                       ********************************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (300 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.81
//
[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