GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Pseudomonas simiae WCS417

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate GFF3026 PS417_15485 amino acid ABC transporter permease

Query= reanno::acidovorax_3H11:Ac3H11_2554
         (222 letters)



>FitnessBrowser__WCS417:GFF3026
          Length = 222

 Score =  160 bits (405), Expect = 2e-44
 Identities = 86/213 (40%), Positives = 135/213 (63%), Gaps = 7/213 (3%)

Query: 3   LDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAA 62
           LDF P+      LL GA VT++IT  S LL   +GL++ + +L+P R + +   T  +  
Sbjct: 11  LDFLPI------LLQGAWVTIQITVLSFLLSSALGLVLALIKLSPIRALSWTASTI-INV 63

Query: 63  IRGTPLLVQLFILFFGLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEA 122
           IRG P++VQLF ++F LP  G+ L AF  GVIG+GI   AY +E  R  I ++++GQ EA
Sbjct: 64  IRGLPIIVQLFYIYFVLPDMGVHLTAFYAGVIGMGIAYSAYQAENFRTGIIAVEQGQREA 123

Query: 123 ARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISV 182
           A ++GM S L MR V+LPQA    +PP GN  + ++K+S+LVS +T+ ++  +GQ I S 
Sbjct: 124 AEALGMRSALMMRRVILPQAFRIALPPYGNTLVMMLKDSSLVSTITVAEMTRQGQLIASS 183

Query: 183 SYRSLEVYLAIAVVYFILTGATTLVLRRIELRL 215
           +++++ VY  +A++Y +++      LRR+E  L
Sbjct: 184 TFQNMTVYTLVALLYLLMSLPLVYGLRRMEQHL 216


Lambda     K      H
   0.328    0.143    0.412 

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: 135
Number of extensions: 5
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: 222
Length of database: 222
Length adjustment: 22
Effective length of query: 200
Effective length of database: 200
Effective search space:    40000
Effective search space used:    40000
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 (21.8 bits)
S2: 45 (21.9 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