GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Brucella inopinata BO1

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_008507473.1 BIBO1_RS12225 branched-chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>NCBI__GCF_000182725.1:WP_008507473.1
          Length = 371

 Score =  303 bits (775), Expect = 7e-87
 Identities = 156/359 (43%), Positives = 231/359 (64%), Gaps = 3/359 (0%)

Query: 11  LFAAMAIAGFASYSMAA-DTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGA 69
           LF+ +A+A   ++  +A   + + +  PVTGP A YG   + GA  AI+++N AGG+NG 
Sbjct: 5   LFSGVALAAMIAFGGSAWADVLVGIGIPVTGPNAVYGAQIQKGAEAAIKEVNDAGGINGE 64

Query: 70  QLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSAT 129
           ++   I DD  DPKQ ++VANK   DGVKFV+GH  S  T PA+ +Y + G+L I+P AT
Sbjct: 65  KIAITIGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVTIPASQVYAENGILEISPGAT 124

Query: 130 APEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTV 189
            P+ T +G    FRT G D+ QG VAG++I + +KD  IAV+HDK  YG+G+A E KK +
Sbjct: 125 NPQYTEQGLWNTFRTCGRDDQQGTVAGQYIFDHFKDAKIAVIHDKTPYGQGLADETKKKL 184

Query: 190 EDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARF 249
            + G K  ++EG+N G+KDF+ALI+KLK+AGV  VY+GG HPE GL++RQ    GL A+F
Sbjct: 185 NELGTKEVLYEGVNVGEKDFSALIAKLKQAGVNVVYWGGLHPEAGLIIRQMADQGLKAQF 244

Query: 250 MGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYS 309
           +  +G+ ++E+ +IAG A EG L T       +P N  L+  F+    +P   + L +Y+
Sbjct: 245 ISGDGIVSNELASIAGPAVEGTLNTFGPDPRNNPDNAELVKKFRDAGFEPEA-YTLYSYA 303

Query: 310 AVTVIAKGIEKAGEADPEKVAEALR-ANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDA 367
           AV  +A+  + AG  DP++VA+A++    F+T  G+L +DEKGD K   + +Y+W K A
Sbjct: 304 AVQSLAQAAKAAGSNDPQEVAKAMKEKGPFKTVLGDLSYDEKGDPKLPGYVMYKWEKGA 362


Lambda     K      H
   0.316    0.133    0.377 

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: 432
Number of extensions: 16
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: 373
Length of database: 371
Length adjustment: 30
Effective length of query: 343
Effective length of database: 341
Effective search space:   116963
Effective search space used:   116963
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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