Alignments for a candidate for arcB in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Pseudomonas fluorescens FW300-N2C3

Align Ornithine carbamoyltransferase 1, anabolic; OTCase 1; Ornithine carbamoyltransferase 1, phaseolotoxin-sensitive; SOCT; EC 2.1.3.3 (characterized)
to candidate AO356_18275 AO356_18275 ornithine carbamoyltransferase

Query= SwissProt::Q02047
         (306 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_18275
          Length = 306

 Score =  533 bits (1373), Expect = e-156
 Identities = 266/306 (86%), 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  EAGMIQLGGQAIFLSPRDTQLGRGEPIGDCAIVMSSMLDAVMIRTFAHSTLTEFAAHSRV 120

Query: 121 PVINGLSDDLHPCQLLADMQTFLEHRGSIKGKTVAWIGDGNNMCNSYIEAAIQFDFQLRV 180
           PVINGLSDDLHPCQLLADMQTFLEHRGSI+GKTVAWIGDGNNMCNSYIEAA+QFDFQLRV
Sbjct: 121 PVINGLSDDLHPCQLLADMQTFLEHRGSIQGKTVAWIGDGNNMCNSYIEAAMQFDFQLRV 180

Query: 181 ACPAGYEPNPEFLALAGERVTIVRDPKAAVAGAHLVSTDVWTSMGQEEETARRMALFAPF 240
           ACP G++PN E LA AG+RV+IVRDPK AVAGAHLVSTDVWTSMGQEEETARR+ LFAP 
Sbjct: 181 ACPEGFDPNAELLAKAGDRVSIVRDPKLAVAGAHLVSTDVWTSMGQEEETARRLELFAPL 240

Query: 241 QVTRASLDLAEKDVLFMHCLPAHRGEEISVDLLDDSRSVAWDQAENRLHAQKALLEFLVA 300
           QV RA LDLA+ DVLFMHCLPAHRGEEIS+DLLDD RSVAWDQAENRLHAQKALLEFLV 
Sbjct: 241 QVNRALLDLADADVLFMHCLPAHRGEEISMDLLDDPRSVAWDQAENRLHAQKALLEFLVE 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: 383
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 AO356_18275 AO356_18275 (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.8206.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   3.6e-115  370.3   0.0     4e-115  370.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18275  AO356_18275 ornithine carbamoylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18275  AO356_18275 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.1   0.0    4e-115    4e-115       1     303 [.       4     299 ..       4     300 .. 0.99

  Alignments for each domain:
  == domain 1  score: 370.1 bits;  conditional E-value: 4e-115
                                       TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaaye 63 
                                                     rh+lsl+d++++el  ++ ++ +lk  +++g+  + lk++ l++iFek+stRtR+sfe+++++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18275   4 RHFLSLMDFTPDELLGVIRRGVELKDLRNRGVLFEPLKNRVLGMIFEKSSTRTRISFEAGMIQ 66 
                                                     8************************************************************** PP

                                       TIGR00658  64 lGaqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdl 126
                                                     lG+q+++l++ ++qlgr+e+i D a v+s+++da+++R+++h++++e+a ++ vPvingL+d 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18275  67 LGGQAIFLSPRDTQLGRGEPIGDCAIVMSSMLDAVMIRTFAHSTLTEFAAHSRVPVINGLSDD 129
                                                     *************************************************************** PP

                                       TIGR00658 127 ehPcqilaDlltikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaei 189
                                                      hPcq+laD++t  e+ g++++ +++++GD+nn++ns + aa+++ ++++va+Peg++p+ae+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18275 130 LHPCQLLADMQTFLEHRGSIQGKTVAWIGDGNNMCNSYIEAAMQFDFQLRVACPEGFDPNAEL 192
                                                     *************************************************************** PP

                                       TIGR00658 190 vkkakkiakenggkleltedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneelle 252
                                                     + ka       g ++++++dpk av++a+++ tDvw+smG+ee+++ rl+l+ p qvn+ ll+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18275 193 LAKA-------GDRVSIVRDPKLAVAGAHLVSTDVWTSMGQEEETARRLELFAPLQVNRALLD 248
                                                     9988.......88************************************************** PP

                                       TIGR00658 253 lakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                                     la+ +v f+hCLPa+rGee++ + l+ ++s+ +d+aenRlhaqka+l++l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18275 249 LADADVLFMHCLPAHRGEEISMDLLDDPRSVAWDQAENRLHAQKALLEFLV 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: 10.33
//
[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