GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Paraburkholderia bryophila 376MFSha3.1

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate H281DRAFT_01585 H281DRAFT_01585 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__Burk376:H281DRAFT_01585
          Length = 237

 Score =  190 bits (482), Expect = 2e-53
 Identities = 99/232 (42%), Positives = 145/232 (62%), Gaps = 1/232 (0%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           MLKV+G++ FYG    L  V +E+G GE+V+L+G NGAGKST +  + G    R G + F
Sbjct: 5   MLKVAGLNAFYGRAHILFDVGLEVGRGEVVALMGRNGAGKSTTMKAVMGLLPRRQGEVIF 64

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLF 120
            GQ+I  +  Y++ R+G+   PE RR+F  ++V+ENL  G    + G+     E++  LF
Sbjct: 65  RGQNIAALAPYKIARMGMGFVPEDRRVFADLTVMENLDTGRQPPREGAPQWTPEKLFRLF 124

Query: 121 PRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDIN 180
           P L E   +  G MSGGEQQML + R LM  P L+LLDEPS G+AP++V+Q+   + ++ 
Sbjct: 125 PNLGEMPKRPGGQMSGGEQQMLTVSRTLMGNPYLVLLDEPSEGVAPVIVEQMANMILELK 184

Query: 181 REQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232
           RE  +++ + EQN   A  ++ R YV+  G++  SGT  EL +NE VR AYL
Sbjct: 185 RE-GLSILLSEQNLHFAELVSDRAYVLEKGQIRFSGTIGELASNETVRRAYL 235


Lambda     K      H
   0.320    0.136    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: 171
Number of extensions: 8
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: 236
Length of database: 237
Length adjustment: 23
Effective length of query: 213
Effective length of database: 214
Effective search space:    45582
Effective search space used:    45582
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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