Align Facilitated trehalose transporter Tret1; BmTRET1 (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter
Query= SwissProt::A9ZSY3 (505 letters) >FitnessBrowser__Koxy:BWI76_RS03110 Length = 499 Score = 193 bits (491), Expect = 1e-53 Identities = 132/444 (29%), Positives = 223/444 (50%), Gaps = 13/444 (2%) Query: 53 LAAFAVSVGSMNVGFSSGYTSPAVLTMNITLDITKEEITWVGGLMPLAALVGGIVGGPLI 112 + A ++G + G+ +G S A+L M L +T V + A G ++ G L Sbjct: 27 VVALIATLGGLLFGYDTGVISGALLFMGTELHLTPFTTGLVTSSLLFGAAFGALLSGNLA 86 Query: 113 EYLGRKKTIMGTAVPFTIGWMLIANAINVVMVFAGRVICGVCVGIVSLAFPVYIGETIQP 172 GRKK I+ AV F IG + + A +V + R+I GV VG + PVYI E Sbjct: 87 NAAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIFFRLILGVAVGGAAATVPVYIAEIAPA 146 Query: 173 EVRGALGLLPTAFGNTGILLAFLVGSYLD--W---SNLAFFGAAIPVPFFLL---MILTP 224 RG L L +G LLA++ + W S + A +P LL M+ P Sbjct: 147 NKRGQLVTLQELMIVSGQLLAYISNATFHEVWGGESTWRWMLAVATLPAVLLWFGMMFMP 206 Query: 225 ETPRWYVSKARVQEARKSLRWLRGKNVNIEKEMRDLTISQTESDRTGGNAFKQLFSKRYL 284 ++PRWY K R+ EAR+ L R K+ ++E E+ ++T + E G F ++ + Sbjct: 207 DSPRWYAMKGRLAEARRVLERTRHKD-DVEWELLEITETLDEQRNLGKPRFSEIMTPWLF 265 Query: 285 PAVMISLGLMLFQQLTGINAVIFYAASIFQMSGSSVDENL-ASIIIGVVNFISTFIATML 343 MI +G+ + QQLTG+N +++YA ++ G + + L A+I GVV+ + TF+ + Sbjct: 266 KLFMIGIGIAVIQQLTGVNTIMYYAPTVLTSVGMTDNAALFATIANGVVSVLMTFVGIWM 325 Query: 344 IDRLGRKVLLYISSVAMITTLLALGAYFYLKQNHIDV---TAYGWLPLACLVIYVLGFSI 400 + ++GR+ + I L+ +GA YL ++ ++ LA +++++ Sbjct: 326 LGKIGRRPMTMIGQFGCTACLVFIGAVSYLLPETVNGQPDALRAYMVLAGMLLFLSFQQG 385 Query: 401 GFGPIPWLMLGEILPSKIRGTAASLATGFNWTCTFIVTKTFQNIIDAIYMHGTLWLFAVI 460 P+ WL++ EI P+++RG A W F+++ F ++ + + GT ++FA I Sbjct: 386 ALSPVTWLLMSEIFPTRLRGIFMGGAVFSMWIANFLISLFFPILLAWLGLSGTFFIFAGI 445 Query: 461 CIGGLLFVIFFVPETKGKSLEEIE 484 + G +FVI VPET+ +SLE+IE Sbjct: 446 GVFGAIFVIKCVPETRHRSLEQIE 469 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: 701 Number of extensions: 38 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: 505 Length of database: 499 Length adjustment: 34 Effective length of query: 471 Effective length of database: 465 Effective search space: 219015 Effective search space used: 219015 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