GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Thiothrix lacustris DSM 21227

Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase

Query= uniprot:A0A4R8NY47
         (263 letters)



>NCBI__GCF_000621325.1:WP_211248857.1
          Length = 255

 Score =  115 bits (288), Expect = 9e-31
 Identities = 79/252 (31%), Positives = 126/252 (50%), Gaps = 6/252 (2%)

Query: 15  RSLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPRFFP 74
           ++LAGK VVITG  SGIG A   AF  +G ++       E  EA+ A+++ A      F 
Sbjct: 7   QNLAGKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEAVAAAIR-ATGGEAVFV 65

Query: 75  CN--LMNLEALRATFTEIETVMGGVDILINNAANDDRHKS-EDVTPAYWDERLAVNLRHQ 131
           C   L   +  R   T ++T  GG+D+L NNA  +    +  + + A +D  +  N+R  
Sbjct: 66  CTDVLQEADIARLVQTALDT-FGGLDVLFNNAGTEGVSSAFTEQSTAEYDFTMNTNVRSV 124

Query: 132 FFCAQAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGV 191
            +  Q  +  M+   GG I+N  SI  H+G  +  LY  +KA + GMT   A ++ + G+
Sbjct: 125 LWGMQHAIRAMQSA-GGAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQGI 183

Query: 192 RVNAIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRVDPHDVAALALFLSSDSGAKCTG 251
           R+NA+ PG   TP    L    +E+   +A         P ++AA  +FL+S + +  +G
Sbjct: 184 RINAVCPGITYTPMSQRLLGGEDEQNAFMATTPAGRTGQPEEIAAAVVFLASGNASYISG 243

Query: 252 REYYVDAGWLGA 263
           +   VD G+  A
Sbjct: 244 QCLNVDGGYTAA 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: 178
Number of extensions: 9
Number of successful extensions: 3
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: 255
Length adjustment: 24
Effective length of query: 239
Effective length of database: 231
Effective search space:    55209
Effective search space used:    55209
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 Apr 09 2024. 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