Alignments for a candidate for argI in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Pseudomonas fluorescens FW300-N2E2

Align Ornithine carbamoyltransferase 1, anabolic; OTCase 1; Ornithine carbamoyltransferase 1, phaseolotoxin-sensitive; SOCT; EC 2.1.3.3 (characterized)
to candidate Pf6N2E2_5579 Ornithine carbamoyltransferase (EC 2.1.3.3)

Query= SwissProt::Q02047
         (306 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5579
          Length = 306

 Score =  535 bits (1379), Expect = e-157
 Identities = 267/306 (87%), Positives = 284/306 (92%)

Query: 1   MNARHFLSMMDYTPDELLGLIRRGVELKDLRIRGELFEPLKNRVLGMIFEKSSTRTRLSF 60
           M+ARHFLS+MD+TPDELLG+IRRGVELKDLR RG LFEPLKNRVLGMIFEKSSTRTR+SF
Sbjct: 1   MSARHFLSLMDFTPDELLGVIRRGVELKDLRNRGVLFEPLKNRVLGMIFEKSSTRTRISF 60

Query: 61  EAGMIQLGGQAIFLSHRDTQLGRGEPIADSAKVMSRMLDAVMIRTYAHSNLTEFAANSRV 120
           EAGMIQLGGQAIFLS RDTQLGRGEPI+D A VMS MLDAVMIRT+AHS LTEFAA+SRV
Sbjct: 61  EAGMIQLGGQAIFLSPRDTQLGRGEPISDCAIVMSGMLDAVMIRTFAHSTLTEFAAHSRV 120

Query: 121 PVINGLSDDLHPCQLLADMQTFLEHRGSIKGKTVAWIGDGNNMCNSYIEAAIQFDFQLRV 180
           PVINGLSDDLHPCQLLADMQTFLEHRGSI+GKTVAWIGDGNNMCNSYIEAA+QFDFQLR+
Sbjct: 121 PVINGLSDDLHPCQLLADMQTFLEHRGSIQGKTVAWIGDGNNMCNSYIEAALQFDFQLRI 180

Query: 181 ACPAGYEPNPEFLALAGERVTIVRDPKAAVAGAHLVSTDVWTSMGQEEETARRMALFAPF 240
           ACP GY+PN E LA AGERVTIVRDPK AVAGAHLVSTDVWTSMGQEEETA+R+ LFAP 
Sbjct: 181 ACPEGYDPNAELLAKAGERVTIVRDPKQAVAGAHLVSTDVWTSMGQEEETAKRLELFAPL 240

Query: 241 QVTRASLDLAEKDVLFMHCLPAHRGEEISVDLLDDSRSVAWDQAENRLHAQKALLEFLVA 300
           QV RA LDLA+ DVLFMHCLPAHRGEEIS DLLDD RSVAWDQAENRLHAQKALLEFLV 
Sbjct: 241 QVNRALLDLADADVLFMHCLPAHRGEEISFDLLDDPRSVAWDQAENRLHAQKALLEFLVE 300

Query: 301 PSHQRA 306
           P++  A
Sbjct: 301 PAYHHA 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: 391
Number of extensions: 8
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 Pf6N2E2_5579 (Ornithine carbamoyltransferase (EC 2.1.3.3))
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.18394.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.5e-116  374.1   0.0   2.8e-116  373.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5579  Ornithine carbamoyltransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5579  Ornithine carbamoyltransferase (EC 2.1.3.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.9   0.0  2.8e-116  2.8e-116       1     303 [.       4     299 ..       4     300 .. 0.99

  Alignments for each domain:
  == domain 1  score: 373.9 bits;  conditional E-value: 2.8e-116
                                      TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayel 64 
                                                    rh+lsl+d++++el  ++ ++ +lk  +++g+  + lk++ l++iFek+stRtR+sfe+++++l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5579   4 RHFLSLMDFTPDELLGVIRRGVELKDLRNRGVLFEPLKNRVLGMIFEKSSTRTRISFEAGMIQL 67 
                                                    8*************************************************************** PP

                                      TIGR00658  65 GaqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdleh 128
                                                    G+q+++l++ ++qlgr+e+i+D a v+s ++da+++R+++h++++e+a ++ vPvingL+d  h
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5579  68 GGQAIFLSPRDTQLGRGEPISDCAIVMSGMLDAVMIRTFAHSTLTEFAAHSRVPVINGLSDDLH 131
                                                    **************************************************************** PP

                                      TIGR00658 129 PcqilaDlltikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkk 192
                                                    Pcq+laD++t  e+ g++++ +++++GD+nn++ns + aa+++ +++++a+Peg++p+ae++ k
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5579 132 PCQLLADMQTFLEHRGSIQGKTVAWIGDGNNMCNSYIEAALQFDFQLRIACPEGYDPNAELLAK 195
                                                    *************************************************************999 PP

                                      TIGR00658 193 akkiakenggkleltedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakp 256
                                                    a       g ++++++dpk+av++a+++ tDvw+smG+ee++++rl+l+ p qvn+ ll+la+ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5579 196 A-------GERVTIVRDPKQAVAGAHLVSTDVWTSMGQEEETAKRLELFAPLQVNRALLDLADA 252
                                                    8.......77****************************************************** PP

                                      TIGR00658 257 evkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                                    +v f+hCLPa+rGee++ + l+ ++s+ +d+aenRlhaqka+l++l+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5579 253 DVLFMHCLPAHRGEEISFDLLDDPRSVAWDQAENRLHAQKALLEFLV 299
                                                    *******************************************9987 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.14
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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