Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate BWI76_RS26735 BWI76_RS26735 MFS transporter
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Koxy:BWI76_RS26735 Length = 440 Score = 253 bits (645), Expect = 1e-71 Identities = 146/429 (34%), Positives = 236/429 (55%), Gaps = 17/429 (3%) Query: 26 KAITAAALGNAMEWFDFGVYGFVAYAL-GQVFFPGADPGVQMIAALATFSVPFLIRPLGG 84 K + A+ +G A+E+FDF +Y A + +FFP DP + +LATF++ F+ RP+G Sbjct: 22 KVVVASLIGTAIEFFDFYIYATAAVIVFPHIFFPQGDPAAATLQSLATFAIAFIARPIGS 81 Query: 85 VFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVGG 144 FG GD+ GR+ L +++ M IST IGL+P YE IGI AP+LL LA+ QG +GG Sbjct: 82 AVFGHFGDRVGRKTTLVASLLTMGISTVVIGLLPGYETIGIMAPVLLALARFGQGLGLGG 141 Query: 145 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRLP 204 E+ GA++ E +P RKR GS+ G+ GF G +L+S L+ +Q F+ WGWR+P Sbjct: 142 EWGGAALLATENAPPRKRALYGSFPQLGAPIGFFFANGTFLLLSWLLTDQQFMEWGWRMP 201 Query: 205 FFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLLV 264 F + L +IGLY+R +L E+P F + +Q + + T H + ++ Sbjct: 202 FIFSAVLVIIGLYVRVSLHESPVFAKVAAAKKQ---------VKIPLGTLLTKHVRVTVL 252 Query: 265 CIGLVIATNVTYYMLLTYMPSYLSHS----LHYSENHGVLIIIAIMIGMLFVQPVMGLLS 320 +++AT +Y++ Y ++ + + L N + +++ +IG + PV GLL+ Sbjct: 253 GTFIMLATYTLFYIMTVYSMTFSTAAAPIGLGLPRNEVLWMLMMAVIGFGVMVPVAGLLA 312 Query: 321 DRFG-RKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMASTLPA 379 D FG RK VVI ++ + F L+ S L+F LL+ ++ G M + LP Sbjct: 313 DAFGRRKSMVVITTLIILFALFAFKPLLGSGNPLLVFAFLLIGLSLMGLTFGPMGALLPE 372 Query: 380 LFPTHIRYSALASAFNI-SVLIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTGLF 438 LFPT +RY+ + ++N+ S+L A + P +AAWL + + L YL +A + ++ L Sbjct: 373 LFPTEVRYTGASFSYNVSSILGASVAPYIAAWL-QGNYGLPAVGLYLAAMAALTMIALLL 431 Query: 439 MKETANKPL 447 ET ++ L Sbjct: 432 THETRHQSL 440 Lambda K H 0.327 0.142 0.427 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: 536 Number of extensions: 24 Number of successful extensions: 5 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: 501 Length of database: 440 Length adjustment: 33 Effective length of query: 468 Effective length of database: 407 Effective search space: 190476 Effective search space used: 190476 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: 51 (24.3 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