GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Amantichitinum ursilacus IGB-41

Align ABC transporter related (characterized, see rationale)
to candidate WP_053938863.1 WG78_RS16125 amino acid ABC transporter ATP-binding protein

Query= uniprot:B2TBJ9
         (263 letters)



>NCBI__GCF_001294205.1:WP_053938863.1
          Length = 246

 Score =  243 bits (619), Expect = 4e-69
 Identities = 123/242 (50%), Positives = 173/242 (71%), Gaps = 12/242 (4%)

Query: 14  IHKSFG-DHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLAGEEL 72
           ++K +G DHHVLK ISL+  QG+V+ + G SGSGKST +R +N LE  +DG + + G ++
Sbjct: 7   VNKWYGRDHHVLKNISLEVKQGEVVVVCGPSGSGKSTLIRTINQLEPVNDGEIWVDGVQV 66

Query: 73  KMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSRAESV 132
                         R  ++R+R ++G VFQ+FNL+ H++VL+N+   P++V+K S+A++ 
Sbjct: 67  N-----------HPRTNINRLREEVGFVFQHFNLYPHLSVLQNITLAPVKVRKMSQADAD 115

Query: 133 EEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPELVGE 192
           +    LL +VGL+ KR  YP+ LSGGQQQRVAIAR LAM PKVMLFDEPTSALDPE++GE
Sbjct: 116 QRGMELLERVGLSNKRDAYPSQLSGGQQQRVAIARGLAMQPKVMLFDEPTSALDPEMIGE 175

Query: 193 VLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSDRFRQ 252
           VL+VM++LAE G TM+VVTHEMGFAR V++RV+FL  G++     P + F   + DR +Q
Sbjct: 176 VLKVMQNLAESGMTMMVVTHEMGFAREVADRVVFLDHGEILEQAAPAQFFNNPQCDRAQQ 235

Query: 253 FV 254
           F+
Sbjct: 236 FL 237


Lambda     K      H
   0.318    0.133    0.377 

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: 207
Number of extensions: 8
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: 263
Length of database: 246
Length adjustment: 24
Effective length of query: 239
Effective length of database: 222
Effective search space:    53058
Effective search space used:    53058
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 (21.7 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