GapMind for catabolism of small carbon sources

 

Alignments for a candidate for catA in Cupriavidus basilensis 4G11

Align Catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate RR42_RS34685 RR42_RS34685 catechol 1,2-dioxygenase

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



>FitnessBrowser__Cup4G11:RR42_RS34685
          Length = 288

 Score =  166 bits (421), Expect = 5e-46
 Identities = 100/275 (36%), Positives = 144/275 (52%), Gaps = 13/275 (4%)

Query: 22  LNDGGNPRTKALVYRILRDTVNIIEDLEVTPEEFWKAVNYLNELGK-----HQEAGLLAA 76
           + D  +PR + +V  ++      +  +  + EEF   + ++  LG      + E  L A 
Sbjct: 9   MRDTTDPRLREVVEALVDHLHAFLRQVRPSDEEFEAGLRFVAALGHATHATNNEVVLAAD 68

Query: 77  GLGLEHYLDLLMDAADEKAGKSGG-TPRTIEGPLYVAGAPLSKYEARLDDGKDDAVPLFM 135
            LGL   + L+ +      G +GG TP  + GP Y  GAP       +  G+   +PLF+
Sbjct: 69  VLGLSTLVTLMNN------GITGGRTPGALLGPFYRGGAPSYACGDCVVQGETPGLPLFV 122

Query: 136 RGQVRDTEGKPLAGAIVDVWQANTAGTYSWFDPTQSEFNLRRRIETDAQGNYRFRSIVPS 195
           RGQVR+T G+PLAGA+V+ WQA+  G Y   DP+Q + NLR     DAQG + FRS+ P+
Sbjct: 123 RGQVRNTAGEPLAGALVEAWQASPVGLYDNQDPSQPDKNLRGAFRADAQGRFHFRSVRPA 182

Query: 196 GYGCPPSGPTQQLLDQLGRHGQRPAHIHFFISAPGHRHLTTQINLSDDPYLHDDFAYATR 255
           GY  P  GP  QLL +  RH  RPAHIHF  +APG+R L TQ+   D  +L  D  +   
Sbjct: 183 GYPVPTGGPVGQLLAEQNRHPYRPAHIHFIAAAPGYRTLVTQVFADDSEHLESDVTFGVH 242

Query: 256 DELIAQIRFSDDPQLAREFGVEGRFAQIDFDFELQ 290
            EL+   R  D+   +   G    F  +DF+F L+
Sbjct: 243 RELVGHFRRVDE-GTSPWGGFPAPFYTLDFNFVLE 276


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: 278
Number of extensions: 15
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: 288
Length adjustment: 27
Effective length of query: 282
Effective length of database: 261
Effective search space:    73602
Effective search space used:    73602
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)

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:

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:

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:

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:

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