GapMind for catabolism of small carbon sources

 

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

Align ABC transporter permease (characterized, see rationale)
to candidate H281DRAFT_00093 H281DRAFT_00093 amino acid/amide ABC transporter membrane protein 1, HAAT family

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__Burk376:H281DRAFT_00093
          Length = 551

 Score =  128 bits (321), Expect = 4e-34
 Identities = 94/292 (32%), Positives = 144/292 (49%), Gaps = 13/292 (4%)

Query: 11  GLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAPGWVIL 70
           GL LGS+  L ALG  + YG+I +IN AHGE LMIGA  ++    + Q   PG   W   
Sbjct: 261 GLSLGSVLLLAALGLAITYGLIGVINMAHGEFLMIGAYATYVVQNLFQRFAPGGFDW-YP 319

Query: 71  LLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMS-ILLQTLAMIIWKPNYKP 129
           L+A   + V AA +  VIE++  + L   P L  L+T  G+S IL+Q   M+    N + 
Sbjct: 320 LVAVPASFVAAALVGIVIERLVLKHLYGRP-LETLLTTFGISLILIQATRMLFGAQNVQV 378

Query: 130 Y-PTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAENPRVAS 188
             P+ +      +    +   ++ IL  + + +     ++  T LG  +RA  +N R+A+
Sbjct: 379 VNPSWMSGGVTVMANLILPYNRLAILAFSLIVVGIAWAVLTKTRLGLFVRAVTQNRRMAA 438

Query: 189 LMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGIGNLA 248
            +GVK   V S  F  GA +A + G    S  G     +G    + +F A V GG+G LA
Sbjct: 439 CVGVKTARVDSYAFAFGAGIAGLGGCA-LSQIGNVGPDLGQSYIIDSFMAVVLGGVGQLA 497

Query: 249 GAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300
           G V+GG  LGL+    S  I    G +L      I   +++++ +  RP G+
Sbjct: 498 GTVIGGFGLGLV----SKAIEPFWGAVLAK----IAVLVLIVLFIQKRPQGM 541


Lambda     K      H
   0.327    0.142    0.419 

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: 282
Number of extensions: 14
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: 309
Length of database: 551
Length adjustment: 31
Effective length of query: 278
Effective length of database: 520
Effective search space:   144560
Effective search space used:   144560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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