GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate AO353_12325 AO353_12325 ABC transporter permease

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



>FitnessBrowser__pseudo3_N2E3:AO353_12325
          Length = 319

 Score =  155 bits (393), Expect = 6e-43
 Identities = 86/209 (41%), Positives = 136/209 (65%), Gaps = 7/209 (3%)

Query: 9   WAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRL--NPKRRVVYALCTAYVAAIRGT 66
           WA  P LL G   T+ ++  S +LG ++GL  G+ RL  NP  R    L T Y+  +RGT
Sbjct: 112 WAAGP-LLWGLWTTLWLSLVSGVLGLLIGLATGLCRLSNNPTLR---DLSTVYIELVRGT 167

Query: 67  PLLVQLFILFFGLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSI 126
           PLLVQ+FI +F +     L   F  G+  L +++GAYV+E++R  +QSI +GQ EAARS+
Sbjct: 168 PLLVQIFIFYFFIGTVLNLSREFA-GIAALSLFTGAYVAEIIRSGVQSIARGQNEAARSL 226

Query: 127 GMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRS 186
           G+S+G +MR VVLPQA  R++PPL  +FI+L+K+++LVS++ I +L+  G+++I+ S+  
Sbjct: 227 GLSAGQSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGREVITTSFSP 286

Query: 187 LEVYLAIAVVYFILTGATTLVLRRIELRL 215
            E+   +A +Y ++    + +  R+E RL
Sbjct: 287 FEILFCVAGLYLLINLPLSKIASRLERRL 315


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: 177
Number of extensions: 11
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: 222
Length of database: 319
Length adjustment: 25
Effective length of query: 197
Effective length of database: 294
Effective search space:    57918
Effective search space used:    57918
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: 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