Alignments for a candidate for argI in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Pseudomonas simiae WCS417

Align Ornithine carbamoyltransferase 1, anabolic; OTCase 1; Ornithine carbamoyltransferase 1, phaseolotoxin-sensitive; SOCT; EC 2.1.3.3 (characterized)
to candidate GFF1103 PS417_05595 ornithine carbamoyltransferase

Query= SwissProt::Q02047
         (306 letters)



>FitnessBrowser__WCS417:GFF1103
          Length = 306

 Score =  534 bits (1375), Expect = e-156
 Identities = 265/306 (86%), Positives = 285/306 (93%)

Query: 1   MNARHFLSMMDYTPDELLGLIRRGVELKDLRIRGELFEPLKNRVLGMIFEKSSTRTRLSF 60
           M+ARHFLS+MD TP+EL+ +IRRG+ELKDLR RG LFEPLKNRVLGMIFEKSSTRTR+SF
Sbjct: 1   MSARHFLSLMDCTPEELVSVIRRGIELKDLRNRGVLFEPLKNRVLGMIFEKSSTRTRVSF 60

Query: 61  EAGMIQLGGQAIFLSHRDTQLGRGEPIADSAKVMSRMLDAVMIRTYAHSNLTEFAANSRV 120
           EAGMIQLGGQAIFLS RDTQLGRGEPIADSAKVMS MLDAVMIRT+AHS +TEF+ANSRV
Sbjct: 61  EAGMIQLGGQAIFLSSRDTQLGRGEPIADSAKVMSSMLDAVMIRTFAHSTVTEFSANSRV 120

Query: 121 PVINGLSDDLHPCQLLADMQTFLEHRGSIKGKTVAWIGDGNNMCNSYIEAAIQFDFQLRV 180
           PVINGLSDDLHPCQLLADMQTFLEHRGSI+GKTVAWIGDGNNMCNSYIEAAIQFDFQLRV
Sbjct: 121 PVINGLSDDLHPCQLLADMQTFLEHRGSIQGKTVAWIGDGNNMCNSYIEAAIQFDFQLRV 180

Query: 181 ACPAGYEPNPEFLALAGERVTIVRDPKAAVAGAHLVSTDVWTSMGQEEETARRMALFAPF 240
           ACP GYEP+  FLA AG+RVT+VRDP+ AV GAHLVSTDVWTSMGQE+ETA+R+ALFAP+
Sbjct: 181 ACPEGYEPDARFLAQAGDRVTLVRDPRDAVIGAHLVSTDVWTSMGQEDETAKRLALFAPY 240

Query: 241 QVTRASLDLAEKDVLFMHCLPAHRGEEISVDLLDDSRSVAWDQAENRLHAQKALLEFLVA 300
           QVTRA LDLA  DVLFMHCLPAHRGEEIS DLLDD RSVAWDQAENRLHAQKALLEFLV 
Sbjct: 241 QVTRALLDLAAPDVLFMHCLPAHRGEEISTDLLDDPRSVAWDQAENRLHAQKALLEFLVP 300

Query: 301 PSHQRA 306
           PS+  A
Sbjct: 301 PSYHHA 306


Lambda     K      H
   0.322    0.135    0.397 

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: 376
Number of extensions: 4
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: 306
Length of database: 306
Length adjustment: 27
Effective length of query: 279
Effective length of database: 279
Effective search space:    77841
Effective search space used:    77841
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 GFF1103 PS417_05595 (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.4142.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.5e-118  380.2   0.0   3.9e-118  380.0   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF1103  PS417_05595 ornithine carbamoylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1103  PS417_05595 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.0   0.0  3.9e-118  3.9e-118       1     303 [.       4     299 ..       4     300 .. 0.99

  Alignments for each domain:
  == domain 1  score: 380.0 bits;  conditional E-value: 3.9e-118
                           TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkee 75 
                                         rh+lsl+d ++eel++++ ++ +lk  +++g+  + lk++ l++iFek+stRtRvsfe+++++lG+q+++l++ +
  lcl|FitnessBrowser__WCS417:GFF1103   4 RHFLSLMDCTPEELVSVIRRGIELKDLRNRGVLFEPLKNRVLGMIFEKSSTRTRVSFEAGMIQLGGQAIFLSSRD 78 
                                         8************************************************************************** PP

                           TIGR00658  76 lqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevk 150
                                         +qlgr+e+i+D a+v+s+++da+++R+++h++v+e++ ++ vPvingL+d  hPcq+laD++t  e+ g++++ +
  lcl|FitnessBrowser__WCS417:GFF1103  79 TQLGRGEPIADSAKVMSSMLDAVMIRTFAHSTVTEFSANSRVPVINGLSDDLHPCQLLADMQTFLEHRGSIQGKT 153
                                         *************************************************************************** PP

                           TIGR00658 151 lvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvw 225
                                         ++++GD+nn++ns + aa ++ ++++va+Peg+ep+a+ + +a       g +++l++dp +av +a+++ tDvw
  lcl|FitnessBrowser__WCS417:GFF1103 154 VAWIGDGNNMCNSYIEAAIQFDFQLRVACPEGYEPDARFLAQA-------GDRVTLVRDPRDAVIGAHLVSTDVW 221
                                         *************************************998877.......88*********************** PP

                           TIGR00658 226 vsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlk 300
                                         +smG+e+++++rl+l+ pyqv++ ll+la p+v f+hCLPa+rGee++ + l+ ++s+ +d+aenRlhaqka+l+
  lcl|FitnessBrowser__WCS417:GFF1103 222 TSMGQEDETAKRLALFAPYQVTRALLDLAAPDVLFMHCLPAHRGEEISTDLLDDPRSVAWDQAENRLHAQKALLE 296
                                         **************************************************************************9 PP

                           TIGR00658 301 all 303
                                         +l+
  lcl|FitnessBrowser__WCS417:GFF1103 297 FLV 299
                                         975 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: 7.01
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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 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 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