Alignments for a candidate for kynB in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for kynB in Pseudomonas fluorescens FW300-N2E3

Align Kynurenine formamidase, bacterial (EC 3.5.1.9) (characterized)
to candidate AO353_05975 AO353_05975 kynurenine formamidase

Query= reanno::pseudo3_N2E3:AO353_05975
         (221 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05975
          Length = 221

 Score =  456 bits (1174), Expect = e-133
 Identities = 221/221 (100%), Positives = 221/221 (100%)

Query: 1   MKKTMSWWDISPPLSTATPTWPGDTPFQEERVWTFGPECPVNVGRITLSPHTGAHVDAPL 60
           MKKTMSWWDISPPLSTATPTWPGDTPFQEERVWTFGPECPVNVGRITLSPHTGAHVDAPL
Sbjct: 1   MKKTMSWWDISPPLSTATPTWPGDTPFQEERVWTFGPECPVNVGRITLSPHTGAHVDAPL 60

Query: 61  HYSADGAAIGDVSLDVYIGPCRVLHCLDSGRLVQPEQLEGRLADLPERVLLRTYQQAPLT 120
           HYSADGAAIGDVSLDVYIGPCRVLHCLDSGRLVQPEQLEGRLADLPERVLLRTYQQAPLT
Sbjct: 61  HYSADGAAIGDVSLDVYIGPCRVLHCLDSGRLVQPEQLEGRLADLPERVLLRTYQQAPLT 120

Query: 121 AWDPDFTAVAKETVDLLSSLGVRLIGIDTPSLDPQQSKTMDSHNAVARHGMAILEGIVLD 180
           AWDPDFTAVAKETVDLLSSLGVRLIGIDTPSLDPQQSKTMDSHNAVARHGMAILEGIVLD
Sbjct: 121 AWDPDFTAVAKETVDLLSSLGVRLIGIDTPSLDPQQSKTMDSHNAVARHGMAILEGIVLD 180

Query: 181 DVPEGDYELIALPLRFANLDASPVRAILRPLNKPPLEEPAQ 221
           DVPEGDYELIALPLRFANLDASPVRAILRPLNKPPLEEPAQ
Sbjct: 181 DVPEGDYELIALPLRFANLDASPVRAILRPLNKPPLEEPAQ 221


Lambda     K      H
   0.318    0.137    0.427 

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: 365
Number of extensions: 11
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: 221
Length of database: 221
Length adjustment: 22
Effective length of query: 199
Effective length of database: 199
Effective search space:    39601
Effective search space used:    39601
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)

Align candidate AO353_05975 AO353_05975 (kynurenine formamidase)
to HMM TIGR03035 (kynB: arylformamidase (EC 3.5.1.9))

# 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/TIGR03035.hmm
# target sequence database:        /tmp/gapView.8984.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03035  [M=206]
Accession:   TIGR03035
Description: trp_arylform: arylformamidase
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-107  343.0   0.0   4.1e-107  342.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05975  AO353_05975 kynurenine formamida


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05975  AO353_05975 kynurenine formamidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.8   0.0  4.1e-107  4.1e-107       2     206 .]       7     211 ..       6     211 .. 0.99

  Alignments for each domain:
  == domain 1  score: 342.8 bits;  conditional E-value: 4.1e-107
                                     TIGR03035   2 lidisqplnedlatwPGdtpfsqelavsleeegsvnvgritlsvhtGahvdaPlhykndgakigd 66 
                                                   ++dis+pl+++++twPGdtpf++e+++++ +e++vnvgritls+htGahvdaPlhy++dga+igd
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05975   7 WWDISPPLSTATPTWPGDTPFQEERVWTFGPECPVNVGRITLSPHTGAHVDAPLHYSADGAAIGD 71 
                                                   9**************************************************************** PP

                                     TIGR03035  67 veldvylGpcrvidclsalekiekealksaleeapervllrtaekakaeafdediaavapdtiel 131
                                                   v+ldvy+Gpcrv++cl++ +++++e+l+ +l+++pervllrt+++a+ +a+d d++ava +t++l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05975  72 VSLDVYIGPCRVLHCLDSGRLVQPEQLEGRLADLPERVLLRTYQQAPLTAWDPDFTAVAKETVDL 136
                                                   ***************************************************************** PP

                                     TIGR03035 132 laekGvrliGvdtpsvdPleskeldahhalakhdlailenlvldevaeGdyelialPlklaelda 196
                                                   l++ GvrliG+dtps+dP++sk++d+h+a+a+h++aile++vld+v eGdyelialPl++a+lda
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05975 137 LSSLGVRLIGIDTPSLDPQQSKTMDSHNAVARHGMAILEGIVLDDVPEGDYELIALPLRFANLDA 201
                                                   ***************************************************************** PP

                                     TIGR03035 197 spvravlral 206
                                                   spvra+lr+l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05975 202 SPVRAILRPL 211
                                                   ********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (206 nodes)
Target sequences:                          1  (221 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 8.08
//
[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