GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Azospirillum thiophilum BV-S

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_045582841.1 AL072_RS18480 amino acid ABC transporter ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_001305595.1:WP_045582841.1
          Length = 251

 Score =  247 bits (630), Expect = 2e-70
 Identities = 130/245 (53%), Positives = 170/245 (69%), Gaps = 1/245 (0%)

Query: 5   TAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGR 64
           +AP I    + K+FG+  VL+GVT  +    V+ IIGPSG GKST LRC+N L  I  G 
Sbjct: 7   SAPFIEMRDVYKSFGSTAVLKGVTLSVRDGGVVCIIGPSGSGKSTILRCINGLMTIDRGT 66

Query: 65  LEVAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAK 124
           + V    +   K D K L  LR +V MVFQ +NLFPH TVLQNL +AP +VL    A  +
Sbjct: 67  IRVGSFAVETLKSD-KQLVPLRHQVAMVFQQYNLFPHRTVLQNLTMAPVQVLGENPAAVR 125

Query: 125 DRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGE 184
           +RAL  L KV L  K D+YP +LSGGQ+QRVAIAR L M+P+++LFDE T+ALDPE+V E
Sbjct: 126 ERALALLAKVRLTGKQDSYPGELSGGQQQRVAIARALAMQPKVILFDEVTAALDPEMVSE 185

Query: 185 VLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRA 244
           VLNV++ LA EGMT  +VTHEM+FA+EV++ VFF ++G+I E G P  +F+NP   RL+A
Sbjct: 186 VLNVIRDLAREGMTCVLVTHEMRFAQEVADEVFFTDRGVIVEHGPPGTIFQNPTDPRLKA 245

Query: 245 FLSRI 249
           FL ++
Sbjct: 246 FLDKV 250


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: 206
Number of extensions: 7
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: 251
Length adjustment: 24
Effective length of query: 228
Effective length of database: 227
Effective search space:    51756
Effective search space used:    51756
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 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