GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2561 in Burkholderia phytofirmans PsJN

Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate BPHYT_RS02465 BPHYT_RS02465 taurine ABC transporter permease

Query= reanno::acidovorax_3H11:Ac3H11_2561
         (252 letters)



>FitnessBrowser__BFirm:BPHYT_RS02465
          Length = 289

 Score =  149 bits (376), Expect = 6e-41
 Identities = 81/239 (33%), Positives = 130/239 (54%), Gaps = 13/239 (5%)

Query: 19  AVWAFFTLGGFVSPTFLASPITMAKEGWLLFTE--YGFIKD-------IGMTIWRVVGGF 69
           A+W   T   ++ P FL +P  +    W  F +  +G I+        +  +  RV G F
Sbjct: 51  ALWWLATHLHWLPPLFLPTPEAV----WTAFLDAWHGRIQGGLPLSQHLAWSALRVFGAF 106

Query: 70  VLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGEAQKILVIFI 129
            LAA+ AVP+GI MG  +      +P + F R LP  A++PL+++W GI E  KI+VI++
Sbjct: 107 ALAALTAVPVGILMGVSRVARGLLDPPLEFYRPLPPLAYLPLVVIWFGIDETAKIVVIYL 166

Query: 130 GSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPEIAETLRLVLGWAW 189
                I +     V  A  + + AAY+LG     IV  V++P A PEI   LR+ +G+ W
Sbjct: 167 ACFAPIAMAARAGVRSATIEQIHAAYSLGGRFSQIVRHVVLPAALPEILTGLRIAIGFGW 226

Query: 190 TYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKALNHRLFAW 248
           T ++ AE++ +++G+G M+ ++ S L T  ++ GI++IGLI  + D   + L  RL  W
Sbjct: 227 TTLVAAEMVAATAGLGQMVLNASSFLRTDVVVMGIVLIGLIAWLFDLGMRVLERRLVPW 285


Lambda     K      H
   0.331    0.145    0.456 

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: 199
Number of extensions: 9
Number of successful extensions: 1
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: 252
Length of database: 289
Length adjustment: 25
Effective length of query: 227
Effective length of database: 264
Effective search space:    59928
Effective search space used:    59928
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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