GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Acidovorax sp. GW101-3H11

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate Ac3H11_4169 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4169
          Length = 383

 Score =  179 bits (455), Expect = 9e-50
 Identities = 117/364 (32%), Positives = 185/364 (50%), Gaps = 13/364 (3%)

Query: 13  AAMAIAGFASYSMAAD-TIKIALAGPVTGPVAQYGDMQRAGALMAIEQIN-KAGGVNGAQ 70
           AA+ +AG A ++ A +  IKI  +GP++GP A  G     G  +A+E++N K   V G  
Sbjct: 17  AALLLAGHAPHASAQEQVIKIGHSGPLSGPNAFAGKDNENGVRLAVEELNAKKIVVEGKA 76

Query: 71  L--EGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSA 128
           L  E V  DD CD +  V+VA K+V+ GVKFV+G  CS    PA+ +Y D G  M++   
Sbjct: 77  LKFELVSEDDQCDARTGVSVAQKLVDSGVKFVMGPYCSGVAIPASRVYNDGGA-MVSTVG 135

Query: 129 TAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKT 188
           T P++T  GYK +FR I  D   G     + A+  K K +AV+ D+  +G+G+A +  K 
Sbjct: 136 TNPKVTEGGYKNLFRIIASDTQIGSNMAVYAAQVLKVKQVAVIDDRTAFGQGVAEQFTKE 195

Query: 189 VEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDAR 248
            +  G+ V   E       DF ++++ LK    Q ++FGGY P+   + RQ KQ GL A+
Sbjct: 196 AKKQGLTVVGQEFTTDKATDFLSILTSLKAKQPQAIFFGGYAPQAAPMARQMKQLGLTAK 255

Query: 249 FMGPEGVGNSEITAIAGDASEGML-----ATLPRAFEQDPKNKALIDAFKAKNQDPSGIF 303
            +G + + + E+  + GDA    +      T+       P  KA    +KA+ +  +  +
Sbjct: 256 LLGGDTLCSPEVGKLGGDAVNDTVFCAQGGTMLDKVANGPAFKA---KYKARFKLDADAY 312

Query: 304 VLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363
               Y  V  +A  ++KA    P KV   +  ++ +   G   +D+KG+LK    TV  +
Sbjct: 313 AASYYDQVMFMANAMQKANSTQPAKVGAQMLQSSHQGVAGTYAYDDKGNLKQAPITVLTF 372

Query: 364 HKDA 367
              A
Sbjct: 373 RNAA 376


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: 368
Number of extensions: 19
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: 373
Length of database: 383
Length adjustment: 30
Effective length of query: 343
Effective length of database: 353
Effective search space:   121079
Effective search space used:   121079
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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