GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Methanococcus aeolicus Nankai-3

Align ATPase (characterized, see rationale)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>NCBI__GCF_000017185.1:WP_011974043.1
          Length = 238

 Score =  155 bits (391), Expect = 1e-42
 Identities = 92/223 (41%), Positives = 140/223 (62%), Gaps = 8/223 (3%)

Query: 21  MIYAEGVEKWYGN---QFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRG 77
           +I A+ + K YG    +   L G++L ++ GE V +MGPSG GKST L  L  L+   +G
Sbjct: 17  LIEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKG 76

Query: 78  EIWIEGHRLS-HDRRDIATIRQEV-GMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAE 135
            ++I+G + +     D A  R+++ G +FQQFNL   LT L+N+ L P+ +         
Sbjct: 77  MVYIKGKKTTMFSENDRAVFRRKISGFIFQQFNLINTLTALENVEL-PLVLDEKNKNYRI 135

Query: 136 ATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVRE 195
             A++LL+ + +  + + YP QLSGGQQQRVAIARAL+  P+I+  DEPT  LD +  RE
Sbjct: 136 KKAKKLLKIINLGHRENYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGNLDSKNSRE 195

Query: 196 VLDVMRDL-ASEGMTMLVATHEVGFAREVADRVVLMADGQIVE 237
           V+D++++L   EG+T+++ THE  FA+  A R++ M DG+IVE
Sbjct: 196 VMDILKELNEKEGITVIMVTHEPEFAK-YASRIINMKDGEIVE 237


Lambda     K      H
   0.321    0.134    0.387 

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: 151
Number of extensions: 8
Number of successful extensions: 5
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: 261
Length of database: 238
Length adjustment: 24
Effective length of query: 237
Effective length of database: 214
Effective search space:    50718
Effective search space used:    50718
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