Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate 3609759 Dshi_3142 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::BFirm:BPHYT_RS16105 (291 letters) >FitnessBrowser__Dino:3609759 Length = 275 Score = 159 bits (401), Expect = 9e-44 Identities = 82/260 (31%), Positives = 155/260 (59%), Gaps = 3/260 (1%) Query: 33 VIAWLVALLLFFPIFWMTITAFKTEQQAYASSLFFIPTLDSFREVFARSNYFSFA-WNSI 91 +IA + +L+ PI W+ + AFK+ Y LFF PTL++F VF +NS Sbjct: 18 IIAAMFVMLV--PILWIFLAAFKSHVDVYQLKLFFTPTLENFGTVFDDPYRLGEKLFNST 75 Query: 92 LISAGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLLWKNSGL 151 +++ ++ + +A AAY+ + F +L+ +L+T+ +P+V +++P ++++++ GL Sbjct: 76 VVALVTVVIAIPIATLAAYSFSRFRLVGETAMLVVILATQFLPAVVIILPFFIMFRDIGL 135 Query: 152 LDSVSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVYLLMPMSLPG 211 LD+ GL++V I +P A+WM + IP D EA +DG++ Q I +++PM+ PG Sbjct: 136 LDTRLGLILVNLAIVMPFAIWMIKGFIDGIPLDTEEAAMVDGSSRLQVIWNIVLPMAAPG 195 Query: 212 LASTALLLVILSWNEAFWSINLSSSNAAPLTVFIASYSSPEGLFWAKLSAASLLAVAPIL 271 L ++ + I++WNE +++ L++ +A L + +A + EG W LSAA ++ +AP+ Sbjct: 196 LLTSGIFCFIIAWNEFLFALILTNKDAVTLPIGLALFKGEEGDLWNLLSAAGIIIMAPMF 255 Query: 272 IVGWLSQKQLVRGLTFGAVK 291 ++ + +K V+G+T GAV+ Sbjct: 256 VLALMIRKYFVQGMTMGAVR 275 Lambda K H 0.326 0.136 0.421 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: 268 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 291 Length of database: 275 Length adjustment: 26 Effective length of query: 265 Effective length of database: 249 Effective search space: 65985 Effective search space used: 65985 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. 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