GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Herbaspirillum aquaticum IEH 4430

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_088755389.1 CEJ45_RS12295 branched-chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>NCBI__GCF_002213425.1:WP_088755389.1
          Length = 381

 Score =  206 bits (525), Expect = 7e-58
 Identities = 127/366 (34%), Positives = 188/366 (51%), Gaps = 10/366 (2%)

Query: 13  AAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG---GVNGA 69
           A +A   FA  + A + IKI    P+TGP A  G     GA MA++++N  G   G    
Sbjct: 12  ALVAAFSFAGAAQAQEVIKIGHVAPLTGPNAHIGKDNENGARMAVDELNAKGFEIGGKKV 71

Query: 70  QLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSAT 129
             + V  DDA DPKQA  VA  +V+  VK VVGH+ S +T PA+ IY D G+  I+PSAT
Sbjct: 72  TFQLVPQDDASDPKQATTVAQALVDAKVKGVVGHMNSGTTIPASKIYYDAGIPQISPSAT 131

Query: 130 APEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTV 189
            P+ T +G+   FR +  D   G V G++     K K +AV+ D+  YG+G+A E +K+ 
Sbjct: 132 NPKYTQQGFNTAFRVVANDGQLGGVLGRYAVNELKGKNVAVIDDRTAYGQGVAEEFRKSA 191

Query: 190 EDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARF 249
             AG  +   +       DFNA+++ +K      V+FGG     G +LRQ  Q G+ A+F
Sbjct: 192 LAAGATIVATQYTTDKATDFNAILTSVKSKKPDLVFFGGMDAVAGPMLRQMDQLGVAAKF 251

Query: 250 MGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAK-----NQDPSGIFV 304
           MG +G+  +E+ ++AG   +        A       K  ++ FKA      NQD   I+ 
Sbjct: 252 MGGDGICTTELPSLAGAGLKDSEVVCAEAGGVTEAGKKPLEDFKAAYKKKFNQDVV-IYA 310

Query: 305 LPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWH 364
              Y A+  +A  +++AG +DP+     L     +  TG + FD KGD+ N   T+Y  +
Sbjct: 311 PYTYDALMTLADAMKQAGSSDPKVYLPVLAKIKHKGVTGEIAFDAKGDILNGTLTLYT-Y 369

Query: 365 KDATRT 370
           K   RT
Sbjct: 370 KGGKRT 375


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: 369
Number of extensions: 21
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: 381
Length adjustment: 30
Effective length of query: 343
Effective length of database: 351
Effective search space:   120393
Effective search space used:   120393
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 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