Align Polyol (xylitol):H+ symporter, PLT4 (characterized)
to candidate CA265_RS01275 CA265_RS01275 hypothetical protein
Query= TCDB::Q1XF07 (519 letters) >FitnessBrowser__Pedo557:CA265_RS01275 Length = 462 Score = 204 bits (519), Expect = 6e-57 Identities = 147/486 (30%), Positives = 233/486 (47%), Gaps = 52/486 (10%) Query: 25 KKPKRNKYAFACAMLASMTSILLGYDIGVMSGAAIYIKRDLKVSDVKIEILLGIINLYSL 84 +K N + F ++A++ L G+D+ V+SG +K +S + + + L + Sbjct: 2 RKQGANYFIFLITLIAALGGFLFGFDMAVVSGIIEPLKSQYGLSSAQEGLFVSCALLGCI 61 Query: 85 IGSGLAGRTSDWIGRRYTIVFAGAIFFVGALLMGFSPNYWFLMFGRFIAGIGIGYALMIA 144 +G +G SD +GRR + A +F V A+ FS Y L+F R +AG+G+G A ++ Sbjct: 62 VGVSFSGYLSDKVGRRKVLFLAAILFLVSAVGFAFSVAYPVLIFFRVLAGMGVGVASNVS 121 Query: 145 PVYTAEVSPASSRGFLTSFPEVFINGGILLGYISNFAFSK---------------LSLKV 189 P+Y +EV+P+ RG L F ++ I GIL YISN + L ++ Sbjct: 122 PLYISEVAPSQKRGRLVVFYQLAITIGILAAYISNLFLQRYATVHAGAGEGILHWLFVEN 181 Query: 190 GWRMMLGVGALPSVILGVGVLAMPESPRWLVMRGRLGDAIKVLNKTSDSPEEAQLRLADI 249 WR M VG +P+ + +L +PESPRWLV GR +A+ L K + + E +L L I Sbjct: 182 VWRGMFIVGVVPAAAFCLLLLIVPESPRWLVQYGRNEEALNTLIKINGA-ETGRLELDSI 240 Query: 250 KRAAGIPESCTDDVVEVSKRSTGEGVWKELFLYPTPAIRHIVIAALGIHFFQQASGIDAV 309 K A S G +KEL P + ++ A + Q SGI+ V Sbjct: 241 KEMA----------------SQKSGGYKELMRLP---LSKLLALATILTALSQFSGINGV 281 Query: 310 VLYSPTIFEKAGIKSDTDKLLATVAVGFVKTCFILVATFMLDRIGRRPLL----LTSVGG 365 + Y PTI + AGI + +D L V +G F +A +D GRRPL L + G Sbjct: 282 IFYGPTILKSAGIVT-SDALFYQVILGSANVLFTFIAISKVDTWGRRPLYIIGSLCAAGA 340 Query: 366 MVLSLLTLGTSLTIIDRSDTKVTWAVGLSIATVLSYVATFSIGAGPITWVYSSEIFPLRL 425 + L+ +T W + SI L + F+ GP+ +V S+EIFP + Sbjct: 341 LALTGFCFLMDIT---------GWFMLFSIILFLLF---FAFSLGPLKFVISTEIFPTHI 388 Query: 426 RAQGCAMGVVVNRVTSGVISMTFLSLSKGITIGGAFFLFGGIAICGWIFFYTMLPETRGK 485 R +M ++ V+ V++M F + G+ I FF+F I +++ L ET+GK Sbjct: 389 RGTALSMCIMTMWVSDWVVNMLFPIMRDGLGIATTFFIFSFFCILSFLYAKKKLFETKGK 448 Query: 486 TLEDME 491 +LE++E Sbjct: 449 SLEEIE 454 Lambda K H 0.323 0.140 0.414 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: 618 Number of extensions: 35 Number of successful extensions: 4 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: 519 Length of database: 462 Length adjustment: 34 Effective length of query: 485 Effective length of database: 428 Effective search space: 207580 Effective search space used: 207580 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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