GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Methanobacterium lacus AL-21

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)



>NCBI__GCF_000191585.1:WP_013645374.1
          Length = 223

 Score =  130 bits (327), Expect = 2e-35
 Identities = 74/180 (41%), Positives = 108/180 (60%), Gaps = 7/180 (3%)

Query: 23  ALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRV------LLDGAPVEG-P 75
           AL  VD E+   + V+I+GPSG GKSTLL ++ GLD A  G++      L+D + +    
Sbjct: 23  ALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKANEGQISVAGVNLMDNSDLSNFR 82

Query: 76  GAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQ 135
             E G VFQ + L P LT+ +N++  L    + + + +ERA   +  V L       P +
Sbjct: 83  SNEIGFVFQLHNLIPNLTVLENVQIPLLGTDIDDKKMEERALKLLKSVNLENKVDQKPTK 142

Query: 136 LSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHD 195
           LSGG +QR AIARAL N P I+L DEP GALD++T+ ++ +LLL I + E  T++ VTH+
Sbjct: 143 LSGGERQRVAIARALVNHPSIILADEPTGALDSETQEVILKLLLDIHKKENVTLIMVTHE 202


Lambda     K      H
   0.322    0.136    0.394 

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: 131
Number of extensions: 7
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: 259
Length of database: 223
Length adjustment: 23
Effective length of query: 236
Effective length of database: 200
Effective search space:    47200
Effective search space used:    47200
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: 46 (22.3 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