Align Facilitated trehalose transporter Tret1; BmTRET1 (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter
Query= SwissProt::A9ZSY3 (505 letters) >FitnessBrowser__Dyella79:N515DRAFT_1228 Length = 463 Score = 215 bits (547), Expect = 3e-60 Identities = 147/457 (32%), Positives = 237/457 (51%), Gaps = 16/457 (3%) Query: 48 LWTQLLAAFAVSVGSMNVGFSSGYTSPAVLTMNITLDITKEEITWVGGLMPLAALVGGIV 107 ++T +LAA A + +++G SG A + I+ I W+ M A VG + Sbjct: 18 IYTCVLAALAGLMFGLDIGVISG----ASQFIKAEFAISDHTIEWIVSSMMFGAAVGALG 73 Query: 108 GGPLIEYLGRKKTIMGTAVPFTIGWMLIANAINVVMVFAGRVICGVCVGIVSLAFPVYIG 167 G L +LGRK++++ A+ F IG +L A + + A RVI G+ +GI + P+Y+ Sbjct: 74 AGWLSSHLGRKRSLILGAILFVIGSLLCGLAWSPETLIAARVILGLAIGIATFTAPLYLA 133 Query: 168 ETIQPEVRGALGLLPTAFGNTGILLAFLVGSYLDWSNLA--FFGA-AIPVPFFLLMIL-T 223 E +RGA+ GIL+AFL + L + G AIP FLL +L Sbjct: 134 EVAPEHIRGAMISTYQLMITIGILVAFLSDTALSYHGAWRWMLGVIAIPGALFLLGVLGL 193 Query: 224 PETPRWYVSKARVQEARKSLRWLRGKNVNIEKEMRDLTISQTESDRTGGNAFKQLFSKRY 283 P++PRW + + R EA LR LRG V + +E D+ Q ++ + G + F + + + Sbjct: 194 PDSPRWLMMRGRRDEAIDVLRRLRGDEVVVAREAADIE-EQLKTPQRGWDLFAE--NPNF 250 Query: 284 LPAVMISLGLMLFQQLTGINAVIFYAASIFQMSGSSVDENL-ASIIIGVVNFISTFIATM 342 +V + L + QQ TG+N V++YA IFQ G + + ++G+ N ++TFIA Sbjct: 251 RRSVFLGALLQIMQQFTGMNVVMYYAPRIFQEMGYDTAAQMWFTALVGLTNVLATFIAIA 310 Query: 343 LIDRLGRKVLLYISSVAMITTLLALGAYFYLKQNHIDVTAYGWLPLACLVIYVLGFSIGF 402 LIDR GRK +LY M L +GA L I+ + +A L+ +++GF++ Sbjct: 311 LIDRWGRKPILYTGFAVMAVGLGVVGA---LMNGGINGQTEQYTCVAMLLFFIVGFAMSA 367 Query: 403 GPIPWLMLGEILPSKIRGTAASLATGFNWTCTFIVTKTFQNIIDAIYMHGTLWLFAVICI 462 GP+ W + EI P K R ++T NW +V TF ++++ I T WL+A + Sbjct: 368 GPLVWTLCSEIQPLKGRDFGIGVSTFTNWITNMVVGFTFLSLLNTIGNASTFWLYAALNA 427 Query: 463 GGLLFVIFFVPETKGKSLEEIEMKLTSGSRRVRNISK 499 ++ + VPETKG +LE+IE L +G +R+R+I + Sbjct: 428 VFIVLTFWLVPETKGVTLEQIERNLMAG-KRLRDIGR 463 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: 651 Number of extensions: 44 Number of successful extensions: 6 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: 505 Length of database: 463 Length adjustment: 34 Effective length of query: 471 Effective length of database: 429 Effective search space: 202059 Effective search space used: 202059 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