GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Caldicellulosiruptor hydrothermalis 108

Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate WP_013404244.1 CALHY_RS12190 SDR family oxidoreductase

Query= uniprot:A0A4R8NY47
         (263 letters)



>NCBI__GCF_000166355.1:WP_013404244.1
          Length = 264

 Score =  105 bits (262), Expect = 1e-27
 Identities = 79/244 (32%), Positives = 114/244 (46%), Gaps = 5/244 (2%)

Query: 19  GKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPR-FFPCNL 77
           GK VVITG   GIG     +F+  GA V  +D   E  E  +    D       FF C+L
Sbjct: 14  GKNVVITGAAQGIGLVTALSFLENGATVFAIDNDREAIEDALQDFFDKFKNKIIFFECDL 73

Query: 78  MNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQFFCAQA 137
           ++ + +     +I    G +D+LINNAA       E+ +   WD+ + +NLR  +   + 
Sbjct: 74  VDAKEIELVCHKIGEKAGKIDVLINNAAISSTKWIEERSVDEWDKVININLRAPYLMVKF 133

Query: 138 VLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGVRVNAII 197
           +LP ++E  G  I+N  S    +  P+   Y  +K GI  +TH +A       +RVNAI 
Sbjct: 134 LLPYLKE--GASIVNIASTRALMSEPNTEPYSASKGGILALTHSLALSLSLKKIRVNAIS 191

Query: 198 PGAIRTPRQTLLWHTPEEEAKILAAQCLPV-RVD-PHDVAALALFLSSDSGAKCTGREYY 255
           PG I T R        E + + +     P  RV  P D+A   LFLSS+  +  TG    
Sbjct: 192 PGWIETSRYKKRKCRKEPQLREIDHLQHPAGRVGMPEDIANAILFLSSEKSSFITGTNLI 251

Query: 256 VDAG 259
           VD G
Sbjct: 252 VDGG 255


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: 161
Number of extensions: 12
Number of successful extensions: 4
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: 264
Length adjustment: 25
Effective length of query: 238
Effective length of database: 239
Effective search space:    56882
Effective search space used:    56882
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 24 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