GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Pseudomonas simiae WCS417

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate GFF4128 PS417_21145 oxidoreductase

Query= reanno::HerbieS:HSERO_RS05210
         (261 letters)



>FitnessBrowser__WCS417:GFF4128
          Length = 248

 Score =  117 bits (294), Expect = 2e-31
 Identities = 92/252 (36%), Positives = 125/252 (49%), Gaps = 16/252 (6%)

Query: 15  SLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEA-SEALCNEVAAAGHPKPLFR 73
           +L GK   I GG  GIGAAIV+  A QGA VAF  +++ A +E L N V + G  K L  
Sbjct: 5   NLSGKVALIQGGSRGIGAAIVKRLAAQGAAVAFTYVSSVAKAEELQNSVISEG-GKALAI 63

Query: 74  HCDLRDIPAFQATIAELQAQLGDFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQRPSFF 133
           H D  D  A +  +       G  D+LVNNA       LE+  LE ++  +AIN R  F 
Sbjct: 64  HADSADAGAIRNAVNATVEAFGRLDILVNNAGVLAIAPLEDFKLEDFDQTLAINVRSVFI 123

Query: 134 AVQSVVEGMKRRGGGSIINFSSISWHQS--GGGFPVYTTAKASTLGLTRGLARDLGPHKI 191
           A Q   + M    GG +IN  S +  +   GGG P Y  +KA+ +GLT+GLARDLGP  I
Sbjct: 124 ATQEAAKHM--ADGGRVINIGSTNAERMPFGGGGP-YAMSKAALVGLTKGLARDLGPRGI 180

Query: 192 RVNTVTPGWVMTERQIKLWLDEE---GKKAIARNQCLQGDLLPWHLARMVLFLAADDSAM 248
            +N V PG V T+         E   G  A+ R   ++       +A  V +LA  ++  
Sbjct: 181 TINNVQPGPVDTDMNPANSDFAESLIGLMAVGRYGHVE------EIASFVAYLAGPEAGY 234

Query: 249 CTAQEFIVDAGW 260
            T     +D G+
Sbjct: 235 ITGASLTIDGGF 246


Lambda     K      H
   0.321    0.134    0.411 

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: 123
Number of extensions: 6
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: 261
Length of database: 248
Length adjustment: 24
Effective length of query: 237
Effective length of database: 224
Effective search space:    53088
Effective search space used:    53088
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 (21.9 bits)
S2: 47 (22.7 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