Alignments for a candidate for arcB in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Pseudomonas stutzeri RCH2

Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate GFF1258 Psest_1291 ornithine carbamoyltransferase

Query= SwissProt::P11724
         (305 letters)



>FitnessBrowser__psRCH2:GFF1258
          Length = 306

 Score =  520 bits (1340), Expect = e-152
 Identities = 253/304 (83%), Positives = 279/304 (91%)

Query: 1   MSVRHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSF 60
           MS RHFLS MD +P+EL  L+RRG ELKDLR RGVL+EPLK+RVLGM+FEKASTRTRLSF
Sbjct: 1   MSARHFLSLMDCTPQELNSLVRRGIELKDLRKRGVLFEPLKNRVLGMIFEKASTRTRLSF 60

Query: 61  EAGMIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKV 120
           EAGMIQLGGQAIFLSPRDTQLGRGEPI DSA VMSRMLD VMIRTFAH+TLT+FAA+S V
Sbjct: 61  EAGMIQLGGQAIFLSPRDTQLGRGEPISDSAIVMSRMLDAVMIRTFAHSTLTDFAANSSV 120

Query: 121 PVINGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRV 180
           PVINGLSDDLHPCQL+ADMQTFHEHRGSI GKTVAWIGDGNNMCN+YIEAA++FDFQL+V
Sbjct: 121 PVINGLSDDLHPCQLMADMQTFHEHRGSIAGKTVAWIGDGNNMCNTYIEAAIQFDFQLKV 180

Query: 181 ACPEGYEPKAEFVALAGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240
           ACPEGYEP AE +  AGDR++++RDPREA AGAHL+STDVWASMGQEDEAAAR+A FRPY
Sbjct: 181 ACPEGYEPNAELMGRAGDRVQILRDPREAAAGAHLISTDVWASMGQEDEAAARLATFRPY 240

Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLELLIE 300
           QV+ ALLD AA DVLFMHCLPAHRGEEIS +LLDDPRSVAWDQAENRLH QKALLE L+E
Sbjct: 241 QVDRALLDCAAADVLFMHCLPAHRGEEISHDLLDDPRSVAWDQAENRLHVQKALLEFLVE 300

Query: 301 HAHY 304
            A++
Sbjct: 301 PAYH 304


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: 379
Number of extensions: 9
Number of successful extensions: 1
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: 306
Length adjustment: 27
Effective length of query: 278
Effective length of database: 279
Effective search space:    77562
Effective search space used:    77562
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 GFF1258 Psest_1291 (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.30070.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     2e-117  377.7   0.0   2.2e-117  377.5   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1258  Psest_1291 ornithine carbamoyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1258  Psest_1291 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.5   0.0  2.2e-117  2.2e-117       1     303 [.       4     299 ..       4     300 .. 0.99

  Alignments for each domain:
  == domain 1  score: 377.5 bits;  conditional E-value: 2.2e-117
                           TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkee 75 
                                         rh+lsl+d +++el++l+ ++ +lk  +k+g+  + lk++ l++iFek+stRtR+sfe+++++lG+q+++l++ +
  lcl|FitnessBrowser__psRCH2:GFF1258   4 RHFLSLMDCTPQELNSLVRRGIELKDLRKRGVLFEPLKNRVLGMIFEKASTRTRLSFEAGMIQLGGQAIFLSPRD 78 
                                         8************************************************************************** PP

                           TIGR00658  76 lqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevk 150
                                         +qlgr+e+i+D a v+sr++da+++R+++h++++++a ++svPvingL+d  hPcq++aD++t +e+ g++ + +
  lcl|FitnessBrowser__psRCH2:GFF1258  79 TQLGRGEPISDSAIVMSRMLDAVMIRTFAHSTLTDFAANSSVPVINGLSDDLHPCQLMADMQTFHEHRGSIAGKT 153
                                         *************************************************************************** PP

                           TIGR00658 151 lvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvw 225
                                         ++++GD+nn++n+ + aa ++ ++++va+Peg+ep+ae++ +a       g ++++++dp +a+++a++i tDvw
  lcl|FitnessBrowser__psRCH2:GFF1258 154 VAWIGDGNNMCNTYIEAAIQFDFQLKVACPEGYEPNAELMGRA-------GDRVQILRDPREAAAGAHLISTDVW 221
                                         ***************************************9988.......88*********************** PP

                           TIGR00658 226 vsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlk 300
                                         +smG+e+++++rl+ ++pyqv++ ll++a  +v f+hCLPa+rGee++++ l+ ++s+ +d+aenRlh+qka+l+
  lcl|FitnessBrowser__psRCH2:GFF1258 222 ASMGQEDEAAARLATFRPYQVDRALLDCAAADVLFMHCLPAHRGEEISHDLLDDPRSVAWDQAENRLHVQKALLE 296
                                         **************************************************************************9 PP

                           TIGR00658 301 all 303
                                         +l+
  lcl|FitnessBrowser__psRCH2:GFF1258 297 FLV 299
                                         987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (306 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: 00:00:00.01
# Mc/sec: 6.70
//
[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