GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Desulfovibrio vulgaris Miyazaki F

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 8502075 DvMF_2788 ABC transporter related (RefSeq)

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__Miya:8502075
          Length = 243

 Score =  262 bits (669), Expect = 5e-75
 Identities = 136/243 (55%), Positives = 173/243 (71%), Gaps = 4/243 (1%)

Query: 8   LISFDQLQKNFGA-LQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLE 66
           +I FD + K + + L VL+ +T EI   +V+ I GPSG GKST +RC+N+LEPI  G + 
Sbjct: 1   MIKFDHVHKWYASGLHVLQDITLEIKQGEVVVICGPSGSGKSTLIRCINKLEPIQKGHIV 60

Query: 67  VAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDR 126
           V GVD++  + +   L  LR  VG VFQ FNL+PH+TVL+N+ LAP  V   P AEA+  
Sbjct: 61  VDGVDINDPRTN---LTMLRAEVGFVFQQFNLYPHMTVLENITLAPLLVRNTPRAEAEKT 117

Query: 127 ALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVL 186
           A+  L+KV +  KA  YP QLSGGQ+QRVAIARGL MKP I+LFDEPTSALDPE++ EVL
Sbjct: 118 AMELLEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALDPEMINEVL 177

Query: 187 NVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFL 246
           +VM+QLA EGMTM  VTHEM FAREV++RV F +QG++ EE  P   F NP  DR + FL
Sbjct: 178 DVMRQLAREGMTMVCVTHEMGFAREVADRVIFMDQGVMVEENTPEAFFSNPVHDRTKEFL 237

Query: 247 SRI 249
           S+I
Sbjct: 238 SKI 240


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: 192
Number of extensions: 2
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: 252
Length of database: 243
Length adjustment: 24
Effective length of query: 228
Effective length of database: 219
Effective search space:    49932
Effective search space used:    49932
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