GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Paraburkholderia bryophila 376MFSha3.1

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate H281DRAFT_02161 H281DRAFT_02161 amino acid/amide ABC transporter substrate-binding protein, HAAT family

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__Burk376:H281DRAFT_02161
          Length = 381

 Score =  211 bits (537), Expect = 3e-59
 Identities = 123/363 (33%), Positives = 195/363 (53%), Gaps = 5/363 (1%)

Query: 6   QRLSRLFAAMAIAGFASYSMAADTI-KIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG 64
           Q+L  + AA  +    + S AADT+ KI    P+TG +A  G     GA +A+E+IN  G
Sbjct: 6   QKLLPISAAAMLFATLATSAAADTVVKIGHVAPLTGGIAHLGKDNENGARLAVEEINAKG 65

Query: 65  GVNGAQ---LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGV 121
              G Q   L+    DDA DP+ A  VA K+V+D V  VVGH+ S ++ PA+ IY D G+
Sbjct: 66  LTIGGQKITLQLDAQDDAADPRTATQVAQKLVDDKVVAVVGHLNSGTSIPASKIYSDAGI 125

Query: 122 LMITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGI 181
           + I+PSAT P  T +G+K  +R +  D  QGP    + A+  K K++A++ D   YG+G+
Sbjct: 126 VQISPSATNPAYTQQGFKTTYRVVATDAQQGPALANYAAKGLKVKSVAIVDDSTAYGQGL 185

Query: 182 ATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAK 241
           A E +KT +  G+ V   +  N    DF A+++K+K      + +GG     G   +QAK
Sbjct: 186 ANEFEKTAKSLGLNVMSHDATNDKAVDFRAILTKIKGENPDAIMYGGMDATGGPFAKQAK 245

Query: 242 QAGLDARFMGPEGVGNSEITAIAGDASEGMLAT-LPRAFEQDPKNKALIDAFKAKNQDPS 300
           Q GL A+ +  +GV   +++ +AGDA++ ++ +    A E+     A    +  +   P 
Sbjct: 246 QLGLRAKVLAGDGVCTDKLSDLAGDATDNIVCSEAGMALEKMEGGPAFQAKYLKRFGQPI 305

Query: 301 GIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTV 360
            I+    Y AV +I   +++AG  DP K+  A+    ++   G   FD KGDLK+   ++
Sbjct: 306 QIYAPFTYDAVYIIVDAMKRAGSTDPAKILAAMPNTDYKGVIGQTTFDSKGDLKHGVISL 365

Query: 361 YEW 363
           Y +
Sbjct: 366 YNY 368


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: 400
Number of extensions: 20
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 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