Align Facilitated trehalose transporter Tret1; BmTRET1 (characterized)
to candidate 353923 BT4397 xylose/H+ symporter (NCBI ptt file)
Query= SwissProt::A9ZSY3 (505 letters) >FitnessBrowser__Btheta:353923 Length = 460 Score = 189 bits (479), Expect = 2e-52 Identities = 127/412 (30%), Positives = 214/412 (51%), Gaps = 35/412 (8%) Query: 99 LAALVGGIVGGPLIEYLGRKKTIMGTAVPFTIGWMLIANAINVVMVF-AGRVICGVCVGI 157 L L+G +V G + + GRK ++ +A F + A +V F A R + G+ +GI Sbjct: 59 LGCLIGAMVAGMMADRYGRKPLLLISAFIF-LSSAYATGAFSVFSWFLAARFLGGIGIGI 117 Query: 158 VSLAFPVYIGETIQPEVRG---ALGLLPTAFGNTGILLA-FLVGSYL-----------DW 202 S P+YI E +RG +L L G G +A +L+ + W Sbjct: 118 ASGLSPMYIAEVAPTSIRGKLVSLNQLTIVLGILGAQIANWLIAEPIPADFTPADICASW 177 Query: 203 SNLA-----FFGAAIPVPFFLLMI-LTPETPRWYVSKARVQEARKSLRWLRGKNVNIEKE 256 + F+GAA P FLL+ PE+PRW K + ++A L + G N E+E Sbjct: 178 NGQMGWRWMFWGAAFPAAVFLLLACFIPESPRWLAMKGKREKAWSVLSRIGG-NRYAEQE 236 Query: 257 MRDLTISQTESDRTGGNAFKQLFSKRYLPAVMISLGLMLFQQLTGINAVIFYAASIFQMS 316 ++ + QT + ++ G K LFS+ + +++ + + +FQQ G N + YA IFQ + Sbjct: 237 LQ--MVEQTSASKSEGG-LKLLFSRPFRKVLVLGVIVAVFQQWCGTNVIFNYAQEIFQSA 293 Query: 317 GSSVDENLASIII-GVVNFISTFIATMLIDRLGRKVLLYISSVAMITTLLALGAYFYLKQ 375 G S+ + L +I++ GV N I TF+A ++RLGR+ L+ + + + L LG ++ + Sbjct: 294 GYSLGDVLFNIVVTGVANVIFTFVAIYTVERLGRRALMLLGAGGLAGIYLVLGTCYFFQV 353 Query: 376 NHIDVTAYGWLPLACLVIYVLGFSIGFGPIPWLMLGEILPSKIRGTAASLATGFNWTCTF 435 + G+ + +V+ + +++ GPI W++L EI P+++RG A + T W +F Sbjct: 354 S-------GFFMVVLVVLAIACYAMSLGPITWVLLAEIFPNRVRGVAMATCTFALWVGSF 406 Query: 436 IVTKTFQNIIDAIYMHGTLWLFAVICIGGLLFVIFFVPETKGKSLEEIEMKL 487 +T TF + A+ +GT W+++ IC+ G LF + +PETKGKSLE +E L Sbjct: 407 TLTYTFPLLNTALGSYGTFWIYSAICVFGFLFFLRALPETKGKSLETLEKDL 458 Score = 44.7 bits (104), Expect = 7e-09 Identities = 33/113 (29%), Positives = 53/113 (46%), Gaps = 12/113 (10%) Query: 313 FQMSGSSVDENLASIIIGVVNFISTFIATMLIDRLGRKVLLYISSVAMITTLLALGAYFY 372 F ++ S + LA + + I +A M+ DR GRK LL IS+ +++ A GA+ Sbjct: 41 FGIADSPTMQGLAMSVALLGCLIGAMVAGMMADRYGRKPLLLISAFIFLSSAYATGAF-- 98 Query: 373 LKQNHIDVTAYGWLPLACLVIYVLGFSIGFGPIPWLMLGEILPSKIRGTAASL 425 + + W LA + +G I G P + + E+ P+ IRG SL Sbjct: 99 --------SVFSWF-LAARFLGGIGIGIASGLSP-MYIAEVAPTSIRGKLVSL 141 Lambda K H 0.325 0.140 0.420 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: 615 Number of extensions: 35 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 505 Length of database: 460 Length adjustment: 34 Effective length of query: 471 Effective length of database: 426 Effective search space: 200646 Effective search space used: 200646 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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