GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Dehalococcoides mccartyi 195

Align Histidine transport system permease protein HisM (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease

Query= SwissProt::P0AEU3
         (238 letters)



>NCBI__GCF_000011905.1:WP_010936196.1
          Length = 273

 Score =  117 bits (292), Expect = 3e-31
 Identities = 69/221 (31%), Positives = 118/221 (53%), Gaps = 4/221 (1%)

Query: 11  PLLWTDGYRFTGVAITLWLLILSVVIGGVLALFLAIGRVSSNKYIQFPIWLFTYIFRGTP 70
           P L    Y + G+ IT+ + ++S  +  +L +F A+GR+S N  ++     +  I RG P
Sbjct: 48  PFLDIFKYVWVGIGITVLVAVVSYFLMLILGMFGALGRLSKNTILRGLATFYVEIVRGIP 107

Query: 71  LYVQLLVFYSGMYTL--EIVKGTEF--LNAFFRSGLNCTVLALTLNTCAYTTEIFAGAIR 126
           L VQL+ +Y     +   I +G  F  +  +  + +   +  +T    AY +EI+   I+
Sbjct: 108 LLVQLIWWYFAFPVIIQSIGQGLNFGPMMNYQANPIVMAIWGMTFCYGAYMSEIYRAGIQ 167

Query: 127 SVPHGEIEAARAYGFSTFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLL 186
           S+P G++EAAR+ G S  +  R +ILP ALR+ LP   NE I +L  T+L  T  V D++
Sbjct: 168 SIPKGQMEAARSLGMSHTQAMRYVILPQALRVVLPPMGNEFIALLKDTSLVSTVAVADMV 227

Query: 187 KIARDINAATYQPFTAFGIAAVLYLIISYVLISLFRRAEKR 227
           ++ R+  A  + P   + +  +LYLI++ +   L    EK+
Sbjct: 228 RLGREFTATNFNPIEVWTMIGLLYLILTLLSSRLINYIEKK 268


Lambda     K      H
   0.330    0.142    0.438 

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: 143
Number of extensions: 9
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: 238
Length of database: 273
Length adjustment: 24
Effective length of query: 214
Effective length of database: 249
Effective search space:    53286
Effective search space used:    53286
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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