GapMind for catabolism of small carbon sources

 

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

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_045585058.1 AL072_RS29535 branched-chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>NCBI__GCF_001305595.1:WP_045585058.1
          Length = 366

 Score =  309 bits (791), Expect = 9e-89
 Identities = 157/358 (43%), Positives = 229/358 (63%), Gaps = 10/358 (2%)

Query: 11  LFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQ 70
           L AA+A    ++ +  AD I +A AGP+TG  A +G+  + G   A+  IN AGGV G +
Sbjct: 7   LLAAIAATALSATAAKAD-IAVATAGPITGQYATFGEQMKKGMEQAVADINAAGGVLGQK 65

Query: 71  LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATA 130
           L+  + DDACDPKQAVAVAN++   GVKFV GH CS S+ PA+ +Y +EG+L I+P++T 
Sbjct: 66  LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGMLQISPASTN 125

Query: 131 PEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVE 190
           P++T +G K +FR  G D+ QG +AGK++ E+YK K +A+LHDK  YG+G+A E +K + 
Sbjct: 126 PKLTEQGLKNVFRVCGRDDQQGMIAGKYLLEKYKGKNVAILHDKSAYGKGLADETQKALN 185

Query: 191 DAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFM 250
             G K A++E   AG+KD++AL+SKLK+A V  VY GGYH E GLL RQ K  GL A  +
Sbjct: 186 AGGQKEAIYEAYTAGEKDYSALVSKLKQANVDAVYVGGYHTEAGLLARQMKDQGLKAPIV 245

Query: 251 GPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKN----KALIDAFKAKNQDPSGIFVLP 306
             + +  +E  AI GDA E  + T    F  DP+     KA+++ F+    +P G + L 
Sbjct: 246 SGDALVTNEYWAITGDAGEDTMMT----FGPDPREKADAKAVVEKFRKAGYEPEG-YTLY 300

Query: 307 AYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWH 364
            Y+A+ + A+ +++A   D  KV+E LR  ++ET  G +GFD KGD+ +  +  Y+WH
Sbjct: 301 TYAALQIWAEAVKQAKSTDAAKVSEVLRKGSYETVIGKIGFDAKGDVTSPAYVWYKWH 358


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: 394
Number of extensions: 18
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: 373
Length of database: 366
Length adjustment: 30
Effective length of query: 343
Effective length of database: 336
Effective search space:   115248
Effective search space used:   115248
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.

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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