Align Na+/glucose cotransporter (characterized, see rationale)
to candidate 349869 BT0341 Na+/glucose cotransporter (NCBI ptt file)
Query= uniprot:Q8AAV7 (564 letters) >FitnessBrowser__Btheta:349869 Length = 523 Score = 279 bits (713), Expect = 2e-79 Identities = 158/465 (33%), Positives = 270/465 (58%), Gaps = 35/465 (7%) Query: 1 MEALDWLVIGVFFLALIGIIVWVVRQKQNDSADYFLGGRDATWLAIGASIFASNIGSEHL 60 ++ LDW ++ +FL LI I +W +++ S+ FL W IG S++ +N+G L Sbjct: 6 LDTLDWGILIAYFLILIAIGIWASSKRKKGSS-LFLAEHSLRWHHIGFSMWGTNVGPSML 64 Query: 61 IGLAGAGASSGMAMAHWEIQGWM-ILILGWVFVPFYSRSMVYTMPEFLERRYNPQSRTIL 119 I A AG ++G+ ++ ++ I +L +VF P Y S V T+PEF+ +R+ +R IL Sbjct: 65 IASASAGFTTGIVSGNYAWYAFVFICLLAFVFAPRYLGSRVSTLPEFMGKRFGQSTRNIL 124 Query: 120 SVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFGGMK 179 + ++V+ +++ +A+T++AGG++ +QVF I W +A+ L++++A +T+ GG+K Sbjct: 125 AWYTIVTILISWLALTLFAGGVLIRQVFDIP-------MWQSALILLIISAFFTMLGGLK 177 Query: 180 SVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSNDDA 239 +V YT+V Q +L+L S + ++G ++GG + + AV + + NL R NDD Sbjct: 178 AVAYTNVYQMILLILVSAALAIVGIYKVGG---ISALTDAVPADFW-----NLFRPNDDT 229 Query: 240 NFPWLGALIGSAIIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPVFLFLIPG 299 FPWL ++G ++G W+WCTDQ +VQ VL+ K+ KE + GT F +LK+L V L+++PG Sbjct: 230 AFPWLPIILGYPVMGVWFWCTDQSMVQPVLAAKSLKEGQLGTNFTGWLKILDVPLYILPG 289 Query: 300 MIAFALHQKYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVCGILAALMSS 359 +I AL P L N D A+ T+V L P G+ GLV+ + AAL+S+ Sbjct: 290 IICLAL------------FPQL----ENPDEAYMTMVTHLFPVGMVGLVLAVLTAALVST 333 Query: 360 LASLFNSSAMLFTIDFY-KRFRPETPEKKLVGIGQIATVVIVILGILWIPIMRSV-GDVL 417 + S N+ + +FT+D Y K+ RP+ +K+++ +GQ+ TV ++ ++ + S+ G L Sbjct: 334 IGSALNALSTVFTMDIYVKKIRPQAKQKEIIRVGQVVTVAGALISVIITIAIDSIHGLNL 393 Query: 418 YTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGL 462 + Q V +AP +AA FL G+ WKRT+ L G + + Sbjct: 394 FNVFQSVLGFIAPPMAAVFLFGVFWKRTTTLAANAALTVGTVFSI 438 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: 908 Number of extensions: 55 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: 523 Length adjustment: 35 Effective length of query: 529 Effective length of database: 488 Effective search space: 258152 Effective search space used: 258152 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