GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Shewanella sp. ANA-3

Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate 7024897 Shewana3_2071 short-chain dehydrogenase/reductase SDR (RefSeq)

Query= uniprot:A0A4R8NY47
         (263 letters)



>FitnessBrowser__ANA3:7024897
          Length = 256

 Score =  223 bits (567), Expect = 4e-63
 Identities = 110/250 (44%), Positives = 153/250 (61%), Gaps = 2/250 (0%)

Query: 14  YRSLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAA--VAPR 71
           Y SL GK + I+GG +GIGA LV AF+ QGA+V F+DI  E S  LVA LK      +  
Sbjct: 7   YPSLQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVT 66

Query: 72  FFPCNLMNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQ 131
           F+ C+L+++ AL+    ++E  +G + +LINNAA D RH  ++VTP YWD+ L  NLRH 
Sbjct: 67  FYHCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHY 126

Query: 132 FFCAQAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGV 191
           FF  QAV P M+   GG ++N GS+SWH     +  Y  +KAG  G+T G+A D G+D +
Sbjct: 127 FFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKI 186

Query: 192 RVNAIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRVDPHDVAALALFLSSDSGAKCTG 251
           R+N + PG + T RQ   W   +    I   QC+   V P D+AA+ALFL++D    CT 
Sbjct: 187 RINTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTA 246

Query: 252 REYYVDAGWL 261
           + + VD GW+
Sbjct: 247 QNFIVDGGWI 256


Lambda     K      H
   0.322    0.137    0.417 

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: 199
Number of extensions: 5
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: 263
Length of database: 256
Length adjustment: 24
Effective length of query: 239
Effective length of database: 232
Effective search space:    55448
Effective search space used:    55448
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