GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Paraburkholderia bryophila 376MFSha3.1

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate H281DRAFT_00221 H281DRAFT_00221 amino acid ABC transporter ATP-binding protein, PAAT family

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__Burk376:H281DRAFT_00221
          Length = 259

 Score =  260 bits (665), Expect = 2e-74
 Identities = 140/245 (57%), Positives = 178/245 (72%), Gaps = 9/245 (3%)

Query: 12  DQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVD 71
           D+L K +G  +VL+GVT +    DVIS+IG SG GKST LRC+N LE  + GR+ V G +
Sbjct: 11  DELHKQYGDNEVLKGVTLKANAGDVISVIGSSGSGKSTMLRCINFLEQPNAGRIFVDGEE 70

Query: 72  L------SGAK--IDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEA 123
           +      +GA    D K L+++R ++ MVFQHFNL+ H+ VL+N++ AP  VL +   EA
Sbjct: 71  VRTQIAKNGALRVSDPKQLQRVRTKLSMVFQHFNLWSHMNVLENIVEAPVNVLGLKRKEA 130

Query: 124 KDRALTYLDKVGLGTKADN-YPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELV 182
           +DRA  YL+KVGL  + +  YP  LSGGQ+QRVAIAR L M P+++LFDEPTSALDPELV
Sbjct: 131 EDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMHPDVMLFDEPTSALDPELV 190

Query: 183 GEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRL 242
           GEVL VM+ LAEEG TM VVTHEM FAR VSN V F +QG +EEEG P+EVFRN +S+RL
Sbjct: 191 GEVLKVMQTLAEEGRTMIVVTHEMAFARNVSNHVMFLHQGRVEEEGHPDEVFRNTRSERL 250

Query: 243 RAFLS 247
           + FLS
Sbjct: 251 KQFLS 255


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: 214
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: 259
Length adjustment: 24
Effective length of query: 228
Effective length of database: 235
Effective search space:    53580
Effective search space used:    53580
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: 47 (22.7 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