Alignments for a candidate for catA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Burkholderia phytofirmans PsJN

Align catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate BPHYT_RS07850 BPHYT_RS07850 catechol 1,2-dioxygenase

Query= BRENDA::Q8GAY6
         (311 letters)



>FitnessBrowser__BFirm:BPHYT_RS07850
          Length = 311

 Score =  579 bits (1493), Expect = e-170
 Identities = 281/311 (90%), Positives = 294/311 (94%)

Query: 1   MSVKVFDTKEVQDLLKAAANMGSEDGSARAKQIVNRLLGDLFKAIDDLDMTPDEIWAGVH 60
           MSVKVFDTKEVQDLLKAAAN+GS+DG ARAKQIVNRLLGDLFKAIDDLDMTPDEIWAGVH
Sbjct: 1   MSVKVFDTKEVQDLLKAAANVGSQDGGARAKQIVNRLLGDLFKAIDDLDMTPDEIWAGVH 60

Query: 61  YFNKLGQDGEAALLAAGLGLEKFLDIRMDAEDKAAEITGGTPRTIEGPLYVAGAPVRDGI 120
           YFNKLGQDGEAALLAAGLGLEK+LDIRMDAEDKAAEITGGTPRTIEGPLYVAGAPVR+G+
Sbjct: 61  YFNKLGQDGEAALLAAGLGLEKYLDIRMDAEDKAAEITGGTPRTIEGPLYVAGAPVREGV 120

Query: 121 SKIDVNPDEGAGPLVIRGTVTGPDGKPVANALVECWHANSKGFYSHFDPTGAQSEFNLRG 180
           S+ID++PDE AGPLVIRGTVTGPDGKPVA ALVECWHANSKGFYSHFDPT  QSEFNLRG
Sbjct: 121 SRIDIDPDEDAGPLVIRGTVTGPDGKPVAGALVECWHANSKGFYSHFDPTSKQSEFNLRG 180

Query: 181 AVSTDVDGKYEFRTLMPVGYGCPPHGATQQLLNVLARHGNRPAHVHFFVTTDKYRKLTTQ 240
           AVST  DGKYEFRTLMPVGYGCPPHGATQQLL+VL RHGNRPAHVHFFVT DK RKLTTQ
Sbjct: 181 AVSTGADGKYEFRTLMPVGYGCPPHGATQQLLDVLGRHGNRPAHVHFFVTADKSRKLTTQ 240

Query: 241 INIEGDPLIWDDFAYATREDLIPHVVEKTGGTPLGMKADTYKEIEFNIELTPLVHGKDNQ 300
           INIEGDPLIWDDFAYATREDLIPHVVEKTGGT LGMK D YKEI+F+IELTPL+ GKDNQ
Sbjct: 241 INIEGDPLIWDDFAYATREDLIPHVVEKTGGTALGMKTDAYKEIQFDIELTPLIQGKDNQ 300

Query: 301 LVSRLRASVTA 311
           LV R R SV+A
Sbjct: 301 LVHRPRVSVSA 311


Lambda     K      H
   0.317    0.137    0.409 

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: 502
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: 311
Length of database: 311
Length adjustment: 27
Effective length of query: 284
Effective length of database: 284
Effective search space:    80656
Effective search space used:    80656
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate BPHYT_RS07850 BPHYT_RS07850 (catechol 1,2-dioxygenase)
to HMM TIGR02439 (catA: catechol 1,2-dioxygenase (EC 1.13.11.1))

# 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/TIGR02439.hmm
# target sequence database:        /tmp/gapView.19688.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02439  [M=285]
Accession:   TIGR02439
Description: catechol_proteo: catechol 1,2-dioxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   8.1e-139  447.4   0.0   9.2e-139  447.2   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07850  BPHYT_RS07850 catechol 1,2-dioxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07850  BPHYT_RS07850 catechol 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.2   0.0  9.2e-139  9.2e-139       1     285 []       7     290 ..       7     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: 447.2 bits;  conditional E-value: 9.2e-139
                                TIGR02439   1 dtkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgllaa 70 
                                              dtkevq+llk++a+  +++g ar+kqiv+r+l dlfkai+dld+t+de+wa+v+y+nklGq++e++llaa
  lcl|FitnessBrowser__BFirm:BPHYT_RS07850   7 DTKEVQDLLKAAANVGSQDGGARAKQIVNRLLGDLFKAIDDLDMTPDEIWAGVHYFNKLGQDGEAALLAA 76 
                                              689******************************************************************* PP

                                TIGR02439  71 GlGlehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvldaeG 140
                                              GlGle++ld+r+da d++a+++ggtPrtieGPlyvaGapv eG++r+d ++++d a +lv++G+v+  +G
  lcl|FitnessBrowser__BFirm:BPHYT_RS07850  77 GLGLEKYLDIRMDAEDKAAEITGGTPRTIEGPLYVAGAPVREGVSRIDIDPDED-AGPLVIRGTVTGPDG 145
                                              ***************************************************766.99************* PP

                                TIGR02439 141 kpiagakvevwhanskGnysffdks..qsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnll 208
                                              kp+aga ve+whanskG+ys+fd++  qsefnlr+++ t+a+Gky++r+++PvGyg+pp+g+tqqll++l
  lcl|FitnessBrowser__BFirm:BPHYT_RS07850 146 KPVAGALVECWHANSKGFYSHFDPTskQSEFNLRGAVSTGADGKYEFRTLMPVGYGCPPHGATQQLLDVL 215
                                              ************************999******************************************* PP

                                TIGR02439 209 GrhGerPahvhffvsapgyrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgvegrfae 278
                                              GrhG+rPahvhffv+a+  rklttqin+egd++++ddfa+atre+l+++v e+++ +a     + + ++e
  lcl|FitnessBrowser__BFirm:BPHYT_RS07850 216 GRHGNRPAHVHFFVTADKSRKLTTQINIEGDPLIWDDFAYATREDLIPHVVEKTGGTALG--MKTDAYKE 283
                                              **********************************************************99..7789**** PP

                                TIGR02439 279 iefdlel 285
                                              i+fd+el
  lcl|FitnessBrowser__BFirm:BPHYT_RS07850 284 IQFDIEL 290
                                              *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (311 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: 00:00:00.00
# Mc/sec: 9.88
//
[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