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.
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:
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