Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate N515DRAFT_1367 N515DRAFT_1367 Predicted arabinose efflux permease, MFS family
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Dyella79:N515DRAFT_1367 Length = 437 Score = 217 bits (553), Expect = 6e-61 Identities = 139/424 (32%), Positives = 231/424 (54%), Gaps = 24/424 (5%) Query: 26 KAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPG-VQMIAALATFSVPFLIRPLGG 84 + + AALG A+E++DF V+ F ALGQ+FFP P + + F+ +L RPLGG Sbjct: 24 RTLALAALGGALEFYDFVVFVFFTKALGQLFFPADMPEWLAQVQVYGIFAAGYLARPLGG 83 Query: 85 VFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVGG 144 + GD+ GR+++ +++ +M++ T CIGL+P+Y ++G++AP+LLLL ++ QG ++GG Sbjct: 84 IVMAHFGDRTGRKRMFTLSVFLMALPTLCIGLLPTYAQLGVFAPMLLLLLRVVQGVAIGG 143 Query: 145 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRLP 204 E GA +FVAE++P + GF + L G AG ++G+ V + T +G + LA+GWRLP Sbjct: 144 EVPGAWVFVAEHAPPGRVGFACASLTSGLTAGILIGSLVAAGV-TGMGAEKMLAYGWRLP 202 Query: 205 FFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLLV 264 F L G ++LR L ETP F + E+ E LK + T H +L+ Sbjct: 203 FILGGVFGFFAVWLRRWLSETPVFAELRERKELASELPLK--------RVMTGHLGGVLL 254 Query: 265 CIGLVIATNVTYYMLLTYMPSYLSHSLHYSEN---HG-VLIIIAIMIGMLFVQPVMGLLS 320 + + +++ P+ + S H + HG L + + G + G+ Sbjct: 255 SMLVTWMLTAAVVVVILMTPTLVQSSFHLPQKLAFHGNSLAALMLCFGCI----AGGVAV 310 Query: 321 DRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGL-IFLGLLMLAVILNAFTGVMASTLPA 379 DRFGR +++GSVA L V +++L G F+ L LA + GV+ + + A Sbjct: 311 DRFGRGWSLLVGSVA---LLVTTYLLYRDLGQGAEHFMLLYALAGLCVGVVGVVPAVMVA 367 Query: 380 LFPTHIRYSALASAFNISVLIAG-LTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTGLF 438 FP +R+S L+ ++NI+ + G +TP + A+L + PA+Y+ V A IG+L ++ Sbjct: 368 AFPPAVRFSGLSFSYNIAYAVFGAITPPLIAYLA-AKLGPMAPAHYVAVTAAIGVLCAVY 426 Query: 439 MKET 442 + T Sbjct: 427 LLTT 430 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: 582 Number of extensions: 37 Number of successful extensions: 6 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: 437 Length adjustment: 33 Effective length of query: 468 Effective length of database: 404 Effective search space: 189072 Effective search space used: 189072 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