Alignments for a candidate for catA in Sphingomonas histidinilytica UM2

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Sphingomonas histidinilytica UM2

Align Catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate WP_079647405.1 B5X82_RS06945 catechol 1,2-dioxygenase

Query= reanno::WCS417:GFF4624
         (309 letters)



>NCBI__GCF_900167915.1:WP_079647405.1
          Length = 310

 Score =  342 bits (878), Expect = 5e-99
 Identities = 168/306 (54%), Positives = 216/306 (70%), Gaps = 2/306 (0%)

Query: 1   MSIRLSQTAHAQQFLEEASGNLNDGGNPRTKALVYRILRDTVNIIEDLEVTPEEFWKAVN 60
           M+  L Q+   Q +L+  SG    GG+ R K ++ RI+ D    I+D +V+ EEFW A++
Sbjct: 1   MASELVQSPEIQAYLDRISGLDQPGGDQRMKQILRRIVSDLFTTIDDFDVSAEEFWAALH 60

Query: 61  YLNELGKHQEAGLLAAGLGLEHYLDLLMDAADEKAGKSGGTPRTIEGPLYVAGAPLSKYE 120
           ++ +     E GL+A GLG +H+LD+ MD AD+KAG +GGTPRTIEGPLY+ GAP+ K  
Sbjct: 61  FMQQGAP--EFGLIAPGLGFDHFLDVRMDIADKKAGTTGGTPRTIEGPLYIPGAPIEKGR 118

Query: 121 ARLDDGKDDAVPLFMRGQVRDTEGKPLAGAIVDVWQANTAGTYSWFDPTQSEFNLRRRIE 180
           ARLDDG+D    L MRG V+D +GKP+AGAIVDVW ANT G YS FDP+Q  +N RRRIE
Sbjct: 119 ARLDDGEDTGEVLIMRGTVKDLDGKPIAGAIVDVWHANTKGGYSGFDPSQKPYNNRRRIE 178

Query: 181 TDAQGNYRFRSIVPSGYGCPPSGPTQQLLDQLGRHGQRPAHIHFFISAPGHRHLTTQINL 240
           T A G+Y FRS+VPSGY  PP G T +LL  +GRHG RPAHIHFF+SAPG+RHLTTQIN+
Sbjct: 179 TAADGSYVFRSVVPSGYSVPPQGSTDRLLQSVGRHGNRPAHIHFFVSAPGYRHLTTQINI 238

Query: 241 SDDPYLHDDFAYATRDELIAQIRFSDDPQLAREFGVEGRFAQIDFDFELQVADAPVEQKR 300
             DPYLHDDFA+AT ++LI ++   +DP+  R   + G F+QIDFDF LQ A    + + 
Sbjct: 239 DGDPYLHDDFAFATHNDLIPEVVRQEDPEQIRAEQLNGPFSQIDFDFTLQKAADAADTEV 298

Query: 301 MQRVRA 306
           M R RA
Sbjct: 299 MARNRA 304


Lambda     K      H
   0.318    0.137    0.408 

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: 358
Number of extensions: 20
Number of successful extensions: 2
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: 310
Length adjustment: 27
Effective length of query: 282
Effective length of database: 283
Effective search space:    79806
Effective search space used:    79806
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: 48 (23.1 bits)

Align candidate WP_079647405.1 B5X82_RS06945 (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.1670842.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.7e-130  417.8   0.0     1e-129  417.6   0.0    1.0  1  NCBI__GCF_900167915.1:WP_079647405.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167915.1:WP_079647405.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.6   0.0    1e-129    1e-129       3     285 .]       9     287 ..       7     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 417.6 bits;  conditional E-value: 1e-129
                             TIGR02439   3 kevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgllaaGlGle 75 
                                           +e+qa+l +++gl+q gg++r+kqi+ r++sdlf +i+d+d++++efwaa++++++   a e+gl+a+GlG++
  NCBI__GCF_900167915.1:WP_079647405.1   9 PEIQAYLDRISGLDQPGGDQRMKQILRRIVSDLFTTIDDFDVSAEEFWAALHFMQQ--GAPEFGLIAPGLGFD 79 
                                           79***************************************************987..4689*********** PP

                             TIGR02439  76 hfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvldaeGkpiagakv 148
                                           hfld+r+d ad+kag +ggtPrtieGPly+ Gap+ +G arlddg+  d++e+l+++G+v d +Gkpiaga+v
  NCBI__GCF_900167915.1:WP_079647405.1  80 HFLDVRMDIADKKAGTTGGTPRTIEGPLYIPGAPIEKGRARLDDGE--DTGEVLIMRGTVKDLDGKPIAGAIV 150
                                           *********************************************9..669********************** PP

                             TIGR02439 149 evwhanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnllGrhGerPahvhff 221
                                           +vwhan+kG ys fd+sq ++n rr+i t a+G y +rsvvP+Gy+vppqg+t++ll+ +GrhG+rPah+hff
  NCBI__GCF_900167915.1:WP_079647405.1 151 DVWHANTKGGYSGFDPSQKPYNNRRRIETAADGSYVFRSVVPSGYSVPPQGSTDRLLQSVGRHGNRPAHIHFF 223
                                           ************************************************************************* PP

                             TIGR02439 222 vsapgyrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgvegrfaeiefdlel 285
                                           vsapgyr+lttqin++gd+yl+ddfafat ++l++ev ++ed +++++++++g+f++i+fd++l
  NCBI__GCF_900167915.1:WP_079647405.1 224 VSAPGYRHLTTQINIDGDPYLHDDFAFATHNDLIPEVVRQEDPEQIRAEQLNGPFSQIDFDFTL 287
                                           **************************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (310 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: 18.87
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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SQLite3 databases

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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