GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Bacteroides clarus YIT 12056

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_087412571.1 BUB52_RS05180 phosphate ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_900129655.1:WP_087412571.1
          Length = 250

 Score = 98.6 bits (244), Expect = 1e-25
 Identities = 77/251 (30%), Positives = 130/251 (51%), Gaps = 21/251 (8%)

Query: 6   LEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTT---VFNCLTGFYQPTG--G 60
           +E   +   +G   A+ G+++ + EK VV+ IGP+G GK+T   + N +      T   G
Sbjct: 4   IETRDVNFWYGDFHALKGISMDIAEKSVVAFIGPSGCGKSTFLRLLNRMNDLIPDTRLTG 63

Query: 61  LIRLDGEEI--QGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLF 118
            I +DG++I  +G+   ++ RK V   FQ    F + +  EN  VA    +N     G+ 
Sbjct: 64  EILIDGQDIYKKGVQVDEL-RKNVGMVFQRPNPFPK-SIFEN--VAYGLRVN-----GVT 114

Query: 119 KTPAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLD 178
                RR   E ++ AA W E   + +    SA  L+ GQQ+RL IAR M   P +L++D
Sbjct: 115 DNAFIRRRVEETLKGAALWDE---VKDKLKVSAYALSGGQQQRLCIARAMAVSPSVLLMD 171

Query: 179 EPAAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTP 238
           EPA+ L+P  T  ++ LI +L+ ++  T++++ H+M+    +SD       G  +  G  
Sbjct: 172 EPASALDPISTAKVEELIHELKKQY--TIVIVTHNMQQAARVSDSTAFFYMGEMVEFGDT 229

Query: 239 EQIRDNPDVIK 249
           ++I  NPD ++
Sbjct: 230 KKIFTNPDKVE 240


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: 134
Number of extensions: 10
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: 255
Length of database: 250
Length adjustment: 24
Effective length of query: 231
Effective length of database: 226
Effective search space:    52206
Effective search space used:    52206
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 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