Alignments for a candidate for kynB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for kynB in Burkholderia phytofirmans PsJN

Align Kynurenine formamidase, bacterial (EC 3.5.1.9) (characterized)
to candidate BPHYT_RS16025 BPHYT_RS16025 kynurenine formamidase

Query= reanno::BFirm:BPHYT_RS16025
         (212 letters)



>FitnessBrowser__BFirm:BPHYT_RS16025
          Length = 212

 Score =  434 bits (1115), Expect = e-127
 Identities = 212/212 (100%), Positives = 212/212 (100%)

Query: 1   MPTLWDITPAVDTATPVWPGDTPVGIERVWRMEAGSPVNVARLTLSPHTGAHTDAPLHYD 60
           MPTLWDITPAVDTATPVWPGDTPVGIERVWRMEAGSPVNVARLTLSPHTGAHTDAPLHYD
Sbjct: 1   MPTLWDITPAVDTATPVWPGDTPVGIERVWRMEAGSPVNVARLTLSPHTGAHTDAPLHYD 60

Query: 61  AEGVAIGEVPLDAYLGRCRVIHCIGASPVVTPQHLSGSLDDLPPRVLLRTYRNAPTAAWD 120
           AEGVAIGEVPLDAYLGRCRVIHCIGASPVVTPQHLSGSLDDLPPRVLLRTYRNAPTAAWD
Sbjct: 61  AEGVAIGEVPLDAYLGRCRVIHCIGASPVVTPQHLSGSLDDLPPRVLLRTYRNAPTAAWD 120

Query: 121 SAFCAVAPDTIDLLAARGVKLIGIDTPSLDPQESKTMDAHHRIRTHRMAILEGIVLDDVA 180
           SAFCAVAPDTIDLLAARGVKLIGIDTPSLDPQESKTMDAHHRIRTHRMAILEGIVLDDVA
Sbjct: 121 SAFCAVAPDTIDLLAARGVKLIGIDTPSLDPQESKTMDAHHRIRTHRMAILEGIVLDDVA 180

Query: 181 PGDYELIALPLKLTTLDASPVRAILRALPESQ 212
           PGDYELIALPLKLTTLDASPVRAILRALPESQ
Sbjct: 181 PGDYELIALPLKLTTLDASPVRAILRALPESQ 212


Lambda     K      H
   0.320    0.137    0.426 

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: 388
Number of extensions: 19
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: 212
Length of database: 212
Length adjustment: 21
Effective length of query: 191
Effective length of database: 191
Effective search space:    36481
Effective search space used:    36481
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 (21.8 bits)
S2: 45 (21.9 bits)

Align candidate BPHYT_RS16025 BPHYT_RS16025 (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.8806.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.4e-102  327.3   0.1   2.7e-102  327.1   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS16025  BPHYT_RS16025 kynurenine formami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS16025  BPHYT_RS16025 kynurenine formamidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.1   0.1  2.7e-102  2.7e-102       2     206 .]       4     208 ..       3     208 .. 0.99

  Alignments for each domain:
  == domain 1  score: 327.1 bits;  conditional E-value: 2.7e-102
                                TIGR03035   2 lidisqplnedlatwPGdtpfsqelavsleeegsvnvgritlsvhtGahvdaPlhykndgakigdveldv 71 
                                              l+di++++++++++wPGdtp+ +e+++++e+ ++vnv+r+tls+htGah daPlhy+++g +ig+v+ld+
  lcl|FitnessBrowser__BFirm:BPHYT_RS16025   4 LWDITPAVDTATPVWPGDTPVGIERVWRMEAGSPVNVARLTLSPHTGAHTDAPLHYDAEGVAIGEVPLDA 73 
                                              8********************************************************************* PP

                                TIGR03035  72 ylGpcrvidclsalekiekealksaleeapervllrtaekakaeafdediaavapdtiellaekGvrliG 141
                                              ylG+crvi+c++a + +++++l   l+++p+rvllrt+++a++ a+d++++avapdti+lla++Gv+liG
  lcl|FitnessBrowser__BFirm:BPHYT_RS16025  74 YLGRCRVIHCIGASPVVTPQHLSGSLDDLPPRVLLRTYRNAPTAAWDSAFCAVAPDTIDLLAARGVKLIG 143
                                              ********************************************************************** PP

                                TIGR03035 142 vdtpsvdPleskeldahhalakhdlailenlvldevaeGdyelialPlklaeldaspvravlral 206
                                              +dtps+dP+esk++dahh+++ h++aile++vld+va GdyelialPlkl++ldaspvra+lral
  lcl|FitnessBrowser__BFirm:BPHYT_RS16025 144 IDTPSLDPQESKTMDAHHRIRTHRMAILEGIVLDDVAPGDYELIALPLKLTTLDASPVRAILRAL 208
                                              ***************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (206 nodes)
Target sequences:                          1  (212 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: 9.47
//
[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