Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate H281DRAFT_01650 H281DRAFT_01650 metabolite-proton symporter
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Burk376:H281DRAFT_01650 Length = 435 Score = 268 bits (686), Expect = 2e-76 Identities = 158/438 (36%), Positives = 249/438 (56%), Gaps = 33/438 (7%) Query: 21 DGRLRKAITAAALGNAMEWFDFGVYGFVA-YALGQVFFPG-ADPGVQMIAALATFSVPFL 78 D L++ + A+ GNAMEW+DF VYG A GQ+FFP ADP + + A A F++ F+ Sbjct: 18 DRALKRIVVASVAGNAMEWYDFFVYGTAAALVFGQLFFPANADPLIGTLGAFAAFAMGFV 77 Query: 79 IRPLGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQ 138 RPLGG+ FG +GD+YGR+ L T++IM +TF IGL+P+Y+ +G+WAP L+ ++ Q Sbjct: 78 ARPLGGIVFGHIGDRYGRRASLVWTLLIMGFATFGIGLLPTYDHVGLWAPAALVALRLLQ 137 Query: 139 GFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLA 198 G + GGE+ G + ++E +P KRG+ +W G GFVL + + + L +Q F++ Sbjct: 138 GIASGGEWGGGVLMISESAPPEKRGYYAAWSQLGVGGGFVLSSAAFLGVQALPHDQ-FVS 196 Query: 199 WGWRLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHH 258 WGWRLPF ++ + +G+Y+RH L E+ F E D+ G A V E+ H Sbjct: 197 WGWRLPFLASILIFALGVYIRHNLPESRDF-------ENADKAGKTAHMPVV--EVIKRH 247 Query: 259 WKSLLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGV---LIIIAIMIGMLFVQPV 315 K +L+ +GL +A N Y+ +L+ SL Y + G+ ++ +M+ M+ Sbjct: 248 PKEILMAMGLRVAENGGAYI-------FLAFSLVYGKYAGIPSSTMLTGVMLAMVVEMVA 300 Query: 316 M---GLLSDRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGV 372 M G LSDR GRKP +IG++++ +A P F L+N+ LI+L L++ + + G Sbjct: 301 MLLWGKLSDRIGRKPVYMIGAISLVAMAFPFFWLLNTHSTPLIWLALVLGTAVCH---GA 357 Query: 373 MASTLPA----LFPTHIRYSALASAFNI-SVLIAGLTPTVAAWLVESSQNLYMPAYYLMV 427 M TLPA LF T +RYS +A + S+ GL+P +A L+ + A +L+V Sbjct: 358 MIGTLPALVGELFSTEVRYSGVALGHEVASIFAGGLSPLIATALLAHYHAYWPVAVFLIV 417 Query: 428 IAVIGLLTGLFMKETANK 445 + +I ++T F ET + Sbjct: 418 LGLITVVTLRFTHETRQR 435 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: 531 Number of extensions: 30 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: 435 Length adjustment: 33 Effective length of query: 468 Effective length of database: 402 Effective search space: 188136 Effective search space used: 188136 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