GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Caldicellulosiruptor hydrothermalis 108

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_013403450.1 CALHY_RS07950 methionine ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_000166355.1:WP_013403450.1
          Length = 343

 Score =  141 bits (355), Expect = 3e-38
 Identities = 87/241 (36%), Positives = 132/241 (54%), Gaps = 12/241 (4%)

Query: 15  DVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPPAQ 74
           D+K L N+NL+I++G++   +GPSG GKSTL+R I  LEK T G++EIDG  +  + P +
Sbjct: 17  DIKALDNVNLNIEKGDIFGIIGPSGAGKSTLIRCINMLEKPTHGSIEIDGVEMTKLSPTE 76

Query: 75  -----RGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDR 129
                + + ++FQ + L    TV+ N++F L+IA   +  ID  V+   E + L    D 
Sbjct: 77  LKEMRKKVGIIFQHFNLLSSRTVKGNVAFPLEIAGLDKKTIDNRVKELLELVGLTNKTDS 136

Query: 130 LPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQ-LKEAMPE--S 186
            P  LSGGQ+QRV I R++  +PKV L DE  S LD      T L I   LKE   E   
Sbjct: 137 YPSQLSGGQKQRVGIARALANNPKVLLCDEATSALDP----ETTLSILNLLKEINREFGI 192

Query: 187 TMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGK 246
           T+V VTH+      +  ++ V+  G I + G   E++  P+ +    F+ S   + LP +
Sbjct: 193 TIVVVTHEMNVVKQICNKVAVMEKGQIVEQGLLTEIFANPKTKIAQNFLRSLTFSELPEE 252

Query: 247 I 247
           +
Sbjct: 253 L 253


Lambda     K      H
   0.316    0.135    0.379 

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: 289
Number of extensions: 14
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: 373
Length of database: 343
Length adjustment: 29
Effective length of query: 344
Effective length of database: 314
Effective search space:   108016
Effective search space used:   108016
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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