Align Na+/glucose cotransporter (characterized, see rationale)
to candidate 3610525 Dshi_3906 SSS sodium solute transporter superfamily (RefSeq)
Query= uniprot:Q8AAV7 (564 letters) >FitnessBrowser__Dino:3610525 Length = 533 Score = 279 bits (714), Expect = 2e-79 Identities = 172/569 (30%), Positives = 289/569 (50%), Gaps = 54/569 (9%) Query: 4 LDWLVIGVFFLALIGIIVWVVRQKQNDSADYFLGGRDATWLAIGASIFASNIGSEHLIGL 63 +D+ ++ ++F+ +I V+V R+ + + YFL GR W IG S+FASN+ +GL Sbjct: 11 IDYAIVVIYFIGVIAHGVYVSRKNEEGADGYFLAGRSLPWYLIGFSLFASNMSGSSFVGL 70 Query: 64 AGAGASSGMAMAHWEIQGWMILILGWVFV-PFYSRSMVYTMPEFLERRYNPQSRTILSVI 122 G ++G+ + ++E ++LIL +FV P + ++ + T+PEFLE+RY+ +SR S+ Sbjct: 71 MGGAYANGIVIFNYEWTAALVLILFAIFVLPSFLKAKISTVPEFLEQRYDVRSRRAFSIF 130 Query: 123 SLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFGGMKSVL 182 ++++ + A +YAGGLV V G LW A L ++ +YTI GG+ +V+ Sbjct: 131 TILAILFIDTAGALYAGGLVISNVTGYLNLW------TAVAVLALVAGIYTILGGLSAVV 184 Query: 183 YTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSNDDANFP 242 T +Q +L++G+ I+ LG E+GGW+++ D + LI DD P Sbjct: 185 VTDTVQAILLIIGAAILFWLGLDEIGGWEQLFV--------DIPEGHDQLILPADDDFLP 236 Query: 243 WLGALIGSAIIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPVFLFLIPGMIA 302 W G L G ++GF+YW +QF+VQR L KN KE + G +F +LKL +FL +IPG+IA Sbjct: 237 WTG-LWGVVLLGFYYWTINQFVVQRTLGAKNLKEGQIGALFAGFLKLPNIFLMIIPGVIA 295 Query: 303 FALHQKYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVCGILAALMSSLAS 362 L+ + D AFPTL +L+P GV+GL++ ++AA+MSSL S Sbjct: 296 LKLYPE----------------LETPDLAFPTLAFELMPIGVRGLIMAALIAAIMSSLDS 339 Query: 363 LFNSSAMLFTIDFYKRFRPETPEKKLVGIGQIATVVIVILGILWIPIMRSVGDVLYTYLQ 422 NS++ L DF + E E K V IG++ T +++ G ++ P + + L++Y Q Sbjct: 340 AMNSASTLVVKDFVEPIW-EVDEGKQVWIGRLVTGAVMVFGAIYAPSIAGF-ESLFSYFQ 397 Query: 423 DVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLTRLGAKVYYSNAGEVADSTF 482 S + P I +++G+ + G W +I G+++G+ K EV Sbjct: 398 SSLSYIIPTIVVVYIVGLFVPWLNGNGAFWTIILGLVVGIPLFIMK-------EVTGVWA 450 Query: 483 KYLFYDMNWLFFCGWMFLFCIIVVIVVSLATEAPTAEKIQGLVFGTATKEQKAATRASWD 542 ++++ M + +S T E I+ LV+ A T+A + Sbjct: 451 GMGLPEIHYTIMSTLMMCLGLATHFGISALTRKADKENIEDLVWSAAD------TKAIFT 504 Query: 543 HWD-------IIHTVIILAITGAFYWYFW 564 W+ I +++ T F +FW Sbjct: 505 QWEEPLWQDRTIWAGLLILSTIGFVAWFW 533 Lambda K H 0.328 0.142 0.454 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: 1008 Number of extensions: 56 Number of successful extensions: 8 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: 564 Length of database: 533 Length adjustment: 36 Effective length of query: 528 Effective length of database: 497 Effective search space: 262416 Effective search space used: 262416 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: 53 (25.0 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