GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Crocosphaera subtropica ATCC 51142

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_009545830.1 CCE_RS09615 LPS export ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_000017845.1:WP_009545830.1
          Length = 238

 Score =  124 bits (311), Expect = 2e-33
 Identities = 78/236 (33%), Positives = 132/236 (55%), Gaps = 19/236 (8%)

Query: 21  VNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLDGEEIQGLPGHKIARK 80
           VN VNLKV   ++V ++GPNGAGKTT F   TG  +P  G + L+ +E+  LP +K AR 
Sbjct: 18  VNRVNLKVAPGEIVGLLGPNGAGKTTTFYIATGLIKPNKGRVWLNQQEVTRLPLNKRARL 77

Query: 81  GVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRRSEREAMEYAAHWLEE 140
           G+    Q   +F+ ++  EN+ VA  +   TN        P  +R +R         L+E
Sbjct: 78  GIGYMTQQPSIFRHLSVAENIQVALEQ---TN-------VPFRQRPQR-----LHTLLKE 122

Query: 141 VNLTEFANRSAGTLAYGQQRRLEIARCM---MTRPRILMLDEPAAGLNPKETDDLKALIA 197
             L + A+     ++ G++RR E+AR +      P  L+LDEP AG++P    +++ +IA
Sbjct: 123 FRLEKIAHTKGSQVSGGERRRTELARSLAVGQQGPDFLLLDEPFAGVDPIAVSEIQTMIA 182

Query: 198 KLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDNPDVIKAYLG 253
           +L  +  + +L+ +H+++  ++I++   ++  G  LA G+ E+I +NP V + YLG
Sbjct: 183 QL-CDRQMGILITDHNVQATLAITNRAYIMRDGQILAAGSAEEIYNNPLVRQYYLG 237


Lambda     K      H
   0.320    0.137    0.391 

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: 140
Number of extensions: 7
Number of successful extensions: 4
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: 255
Length of database: 238
Length adjustment: 24
Effective length of query: 231
Effective length of database: 214
Effective search space:    49434
Effective search space used:    49434
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 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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