Align Na+/glucose cotransporter (characterized, see rationale)
to candidate 3610523 Dshi_3904 SSS sodium solute transporter superfamily (RefSeq)
Query= uniprot:Q8AAV7 (564 letters) >FitnessBrowser__Dino:3610523 Length = 526 Score = 271 bits (694), Expect = 4e-77 Identities = 153/460 (33%), Positives = 250/460 (54%), Gaps = 32/460 (6%) Query: 4 LDWLVIGVFFLALIGIIVWVVRQKQNDSADYFLGGRDATWLAIGASIFASNIGSEHLIGL 63 LD+ VI V+ +I I VWV R K D FL GR W AIG S+FASNI + L+GL Sbjct: 12 LDYGVIAVYLAIVIAIGVWVAR-KTRTGEDLFLAGRSLGWAAIGFSLFASNISTSTLVGL 70 Query: 64 AGAGASSGMAMAHWE-IQGWMILILGWVFVPFYSRSMVYTMPEFLERRYNPQSRTILSVI 122 G+ + G+ ++ +E + G +L + ++F P + +S + T PE+LE RY+ + R S + Sbjct: 71 TGSAYTGGLTVSSYEWMAGIPLLFMAFIFAPVFLKSRISTTPEYLENRYSRRVRLYFSGL 130 Query: 123 SLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFGGMKSVL 182 ++V V+ A +YAG +V + F ++W ++ + + + +YT GG+++V+ Sbjct: 131 TIVFTVIVDTAGGLYAGAVVLKVFFPDLDIW------MSCVAIGLFAGIYTATGGLRAVV 184 Query: 183 YTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSNDDANFP 242 YT +LQ +L+ G+ + L ++ + E +R + + ++++ DD P Sbjct: 185 YTDILQAVVLICGTGLTAFLMYQSVDFSWESVR-------SQVPEGHLSIVQPIDDDTLP 237 Query: 243 WLGALIGSAIIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPVFLFLIPGMIA 302 W G G ++GFWYW T+Q+IVQRVL K+ A+ G I G LK+LP F ++PG++A Sbjct: 238 WPGLFTGVWLLGFWYWVTNQYIVQRVLGAKDLSNAQWGAILGGILKILPTFFIILPGVMA 297 Query: 303 FALHQKYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVCGILAALMSSLAS 362 LP + N+D FP ++ ++LP+G+ GLV+ G++AA+MS++ S Sbjct: 298 LVT------------LPDI----QNSDQVFPIIITEVLPSGLTGLVMAGLIAAIMSTVDS 341 Query: 363 LFNSSAMLFTIDFYKRFRPETPEKKLVGIGQIATVVIVILGILWIPIMRSVGDVLYTYLQ 422 NSS+ L DF R E + G +AT+ +++ I W P+++ G L+ Y+Q Sbjct: 342 TLNSSSTLLINDFLTRPEKEPDPETAKKWGMMATLGFMVIAIAWAPLIQYFGG-LWAYIQ 400 Query: 423 DVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGL 462 SVL P + F LG W R + W LI G +GL Sbjct: 401 QAFSVLVPPLVVCFTLGALWSRGTENAAFWTLIIGHTLGL 440 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: 898 Number of extensions: 48 Number of successful extensions: 7 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: 526 Length adjustment: 35 Effective length of query: 529 Effective length of database: 491 Effective search space: 259739 Effective search space used: 259739 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 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