Alignments for a candidate for catA in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Klebsiella variicola At-22

Align Catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate WP_012968101.1 KVAR_RS12095 catechol 1,2-dioxygenase

Query= reanno::pseudo3_N2E3:AO353_23525
         (309 letters)



>NCBI__GCF_000025465.1:WP_012968101.1
          Length = 308

 Score =  377 bits (968), Expect = e-109
 Identities = 182/299 (60%), Positives = 224/299 (74%)

Query: 10  SAQKFLEEASGLLNDAGNPRAKALIYRILRDSVNIIEDLEVTPEEFWKAVNYLNELGARQ 69
           + QK L E +GL    GN R KA+++R+L +   +I+D  VT EEFW AVNYL+ELG RQ
Sbjct: 10  AVQKLLREGAGLNVPGGNERFKAIVHRLLENICTLIDDYNVTEEEFWHAVNYLHELGGRQ 69

Query: 70  EAGLLVAGLGLEHYLDLLMDAEDAQAGKTGGTPRTIEGPLYVAGAPLSNGEARLDDGVDP 129
           EA LL AGLGLEH+LDL  DA DA A +  GTPRTIEGPLYVA APL++  AR+DDG D 
Sbjct: 70  EAALLAAGLGLEHFLDLRQDAIDAAARRETGTPRTIEGPLYVANAPLADSHARMDDGTDA 129

Query: 130 GVVLFMQGQVKNTDGKPLAGAVVDVWHANTGGTYSYFDGSQSEFNLRRRIVTDAEGRYRF 189
           G V+++ GQVK+  G+P+A A+VD+WHANT G YS+FD SQS++NLRRRI T A+GRY  
Sbjct: 130 GEVMWLHGQVKDNQGQPIANAIVDIWHANTLGNYSFFDKSQSDYNLRRRIRTGADGRYSV 189

Query: 190 RSIVPSGYGCPPDGPTQQLLDQLGRHGQRPAHIHFFISADDHRHLTTQINLDGDKYLHDD 249
           RSI+PSGYGCPPDGPTQ+LLDQLGRHG RPAHIHFF+SA  H+HLT+QINL GDKYL DD
Sbjct: 190 RSIMPSGYGCPPDGPTQKLLDQLGRHGNRPAHIHFFVSAPGHKHLTSQINLSGDKYLWDD 249

Query: 250 FAYATRDELIAKITFSDDQQRAREHGVSGRFAEIEFDFTLQSSAQPEEQHRHERVRALE 308
           FA+ATRD LIA      D++   +  + G   E+ FDFTL  +   +E+HR  R+RA E
Sbjct: 250 FAFATRDGLIADPVKVTDRETIAQRDLEGEHTEVCFDFTLCKALNADEEHRGTRLRAKE 308


Lambda     K      H
   0.317    0.136    0.401 

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: 343
Number of extensions: 10
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: 309
Length of database: 308
Length adjustment: 27
Effective length of query: 282
Effective length of database: 281
Effective search space:    79242
Effective search space used:    79242
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 WP_012968101.1 KVAR_RS12095 (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.967903.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-139  450.0   0.1   1.5e-139  449.8   0.1    1.0  1  NCBI__GCF_000025465.1:WP_012968101.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_012968101.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.8   0.1  1.5e-139  1.5e-139       2     285 .]       8     289 ..       7     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 449.8 bits;  conditional E-value: 1.5e-139
                             TIGR02439   2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgllaaGlGl 74 
                                           ++ vq+ll++ agl+  ggn+r+k iv+r+l+++  +i+d+++te+efw+av+yl +lG ++e++llaaGlGl
  NCBI__GCF_000025465.1:WP_012968101.1   8 QEAVQKLLREGAGLNVPGGNERFKAIVHRLLENICTLIDDYNVTEEEFWHAVNYLHELGGRQEAALLAAGLGL 80 
                                           5789********************************************************************* PP

                             TIGR02439  75 ehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvldaeGkpiagak 147
                                           ehfldlr+da+da+a +e gtPrtieGPlyva ap+++ +ar+ddg+  d +e+++l+Gqv d++G+pia+a+
  NCBI__GCF_000025465.1:WP_012968101.1  81 EHFLDLRQDAIDAAARRETGTPRTIEGPLYVANAPLADSHARMDDGT--DAGEVMWLHGQVKDNQGQPIANAI 151
                                           ***********************************************..668********************* PP

                             TIGR02439 148 vevwhanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnllGrhGerPahvhf 220
                                           v++whan+ Gnysffdksqs++nlrr+i+t+a+G+y++rs++P+Gyg+pp+gptq+ll++lGrhG+rPah+hf
  NCBI__GCF_000025465.1:WP_012968101.1 152 VDIWHANTLGNYSFFDKSQSDYNLRRRIRTGADGRYSVRSIMPSGYGCPPDGPTQKLLDQLGRHGNRPAHIHF 224
                                           ************************************************************************* PP

                             TIGR02439 221 fvsapgyrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgvegrfaeiefdlel 285
                                           fvsapg+++lt+qinl+gdkyl+ddfafatr+gl+a+  +v+d +++++r++eg+++e+ fd++l
  NCBI__GCF_000025465.1:WP_012968101.1 225 FVSAPGHKHLTSQINLSGDKYLWDDFAFATRDGLIADPVKVTDRETIAQRDLEGEHTEVCFDFTL 289
                                           ***************************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (308 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: 17.19
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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