GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Shewanella amazonensis SB2B

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 6937298 Sama_1468 putative macrolide efflux ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__SB2B:6937298
          Length = 230

 Score =  140 bits (354), Expect = 2e-38
 Identities = 89/232 (38%), Positives = 134/232 (57%), Gaps = 11/232 (4%)

Query: 8   LISFDQLQKNF----GALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGG 63
           +IS   L K+F      +Q LRGV   I   + ++I+GPSG GKST +  +  L+  + G
Sbjct: 1   MISLQALTKSFRMGDAEVQALRGVDIHIRQNEFVAIMGPSGSGKSTLMNIIGCLDRPTSG 60

Query: 64  RLEVAGVDLSGAKIDQKHLRQLRVR-VGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAE 122
              + G  + G   D   L  +R R +G VFQ F+L P L+ L N+LL P +    P  +
Sbjct: 61  NYLLNGSAVGGLSDDA--LSAVRNREIGFVFQSFHLLPRLSALDNVLL-PLRFSETPRGD 117

Query: 123 AKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELV 182
            +  A+  L++VGLG + D+ P+QLSGGQ+QRVAIAR L  +P +LL DEPT ALD +  
Sbjct: 118 -RQHAIELLERVGLGQRLDHRPNQLSGGQRQRVAIARALVNRPTLLLADEPTGALDSKTS 176

Query: 183 GEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGD-PNEV 233
            E++ +  +L   G T+ +VTHE + A E + R+     G+++++   P EV
Sbjct: 177 VEIMALFDELHLSGQTIVLVTHEEEVA-ECAGRIIRMRDGVVQQDKQKPREV 227


Lambda     K      H
   0.321    0.139    0.397 

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: 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: 252
Length of database: 230
Length adjustment: 23
Effective length of query: 229
Effective length of database: 207
Effective search space:    47403
Effective search space used:    47403
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 Sep 17 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