Align Facilitated trehalose transporter Tret1; AmTRET1 (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter
Query= SwissProt::A9ZSY2 (502 letters) >FitnessBrowser__Koxy:BWI76_RS24055 Length = 464 Score = 223 bits (567), Expect = 1e-62 Identities = 141/456 (30%), Positives = 243/456 (53%), Gaps = 20/456 (4%) Query: 33 KRSPMRYTMQLLAALAVSMASLMIGYSSSYTSPALVSMRDNTTATFEVTMDMAMWIGSIM 92 K+ TM ++A L+ G + AL + + F+++ W+ S M Sbjct: 6 KQGRSNKTMTFFVCFLAALAGLLFGLDIGVIAGALPFIANE----FQISAHTQEWVVSSM 61 Query: 93 PLSALIGGIIGGPCIEYIGRRNTILSTALPFLAGWLFIALATNVAMILVGRSICGFCVGV 152 A +G + G +GR+ +++ A+ F+AG LF A A NV ++L+ R + G VGV Sbjct: 62 MFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISRVLLGLAVGV 121 Query: 153 ASLSLPVYLGESIQPEVRGSLGLLPTVFGNSGILMCF---TAGMYL-AWRNLALLGACI- 207 AS + P+YL E ++RGS+ + + GIL + TA Y AWR +LG I Sbjct: 122 ASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYSGAWR--WMLGVIII 179 Query: 208 -PIIFLILMFLIPETPRWYISKGKIKEARKSLQWLRGKTADISEELDSIQKMHIESERIA 266 ++ LI + +P++PRW+ +K + +A + L LR +A+ ELD I+ ES ++ Sbjct: 180 PAVLLLIGVVFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIR----ESLKVK 235 Query: 267 TEGALIELFRKNHIKPVFISLGLMFFQQFSGINAVIFYTVQIFKDSG--STVDENLSTII 324 G + N + VF+ + L QQF+G+N +++Y +IF+ +G +T ++ T+I Sbjct: 236 QSGWSLFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTTEQMWGTVI 295 Query: 325 VGLVNFISTFVAAMIIDRLGRKMLLYISSILMCITLFTFGTFFYVKELMDVTAFGWIPLM 384 VGL N ++TF+A ++DR GRK L + I+M + + G+ ++ + TA + LM Sbjct: 296 VGLTNVLATFIAIGLVDRWGRKPTLILGFIVMALGMGILGSMMHIG-IHSATAQYFAVLM 354 Query: 385 SLIVYVIGFSFGFGPIPWLMMGEILPVKIRGTAASVATAFNWSCTFVVTKTYEDLVLHIG 444 L+++++GF+ GP+ W++ EI P+K R + +TA NW +V T+ ++ +G Sbjct: 355 -LLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNSLG 413 Query: 445 PYGTFWLFGTLVAVAFIFVIICVPETRGRSLEEIER 480 TFW++G L + + +PET+ SLE IER Sbjct: 414 SANTFWVYGGLNILFIFLTLWLIPETKNVSLEHIER 449 Lambda K H 0.327 0.141 0.425 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: 635 Number of extensions: 34 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: 502 Length of database: 464 Length adjustment: 34 Effective length of query: 468 Effective length of database: 430 Effective search space: 201240 Effective search space used: 201240 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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