Align Na+/glucose cotransporter (characterized, see rationale)
to candidate CA265_RS06755 CA265_RS06755 sodium transporter
Query= uniprot:Q8AAV7 (564 letters) >FitnessBrowser__Pedo557:CA265_RS06755 Length = 542 Score = 272 bits (696), Expect = 2e-77 Identities = 194/583 (33%), Positives = 306/583 (52%), Gaps = 63/583 (10%) Query: 1 MEALDWLVIGVFFLALIGIIVWVVR---QKQNDSADYFLGGRDATWLAIGASIFASNIGS 57 + A D+ V ++F+ + WV R +K+ D+ DYFL TW AIGASI ASNI + Sbjct: 4 LSAFDYAVFLMYFVIVSAYGYWVYRSKKKKRTDTKDYFLAEGSLTWWAIGASIIASNISA 63 Query: 58 EHLIGLAGAGASSGMAMAHWEIQGWM----ILILGWVFVPFYSRSMVYTMPEFLERRYNP 113 EH IG++G+G + G+A+A +E WM ++I+ F+P Y ++ +YTMP+FL RYN Sbjct: 64 EHFIGMSGSGFAMGLAIASYE---WMAAATLIIVAIFFLPIYIKNKIYTMPQFLSNRYNN 120 Query: 114 QSRTILSVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYT 173 T+++V L+ YV + + G + + + G+ F I I L + +A+ T Sbjct: 121 TVSTLMAVFWLLVYVFVNLTSIFFLGAIAIETITGVP-------FNICIIFLAIFSAIIT 173 Query: 174 IFGGMKSVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTV--NDYGDTMTN 231 + GGMK + YT V+Q +L+ G LI + K + + V ++ + ++ D Sbjct: 174 L-GGMKVIGYTDVIQVFVLVAGGLITCYMALKLVSEKLDAPSVLASLPLLRSEASDHFHM 232 Query: 232 LIRSNDD--ANFPWLGALIGSAIIGFW-----YWCTDQFIVQRVLSGKNEKEARRGTIFG 284 + D P + L+G G W YW +Q+IVQR L G + K R G IF Sbjct: 233 IFSKGDKFYNELPGIAVLVG----GLWINNLNYWGCNQYIVQRAL-GADLKTGRNGLIFA 287 Query: 285 AYLKLLPVFLFLIPGMIAFALHQKYIGAGGEGFLPML-ANGTANADAAFPTLVAKLLPAG 343 A+LKLL + +IPG+ A+ L+Q+ G ML A G D A+P L+ LLPAG Sbjct: 288 AFLKLLIPVIVVIPGIAAYVLYQR-----GYFHSEMLDAAGVVKPDHAYPVLM-NLLPAG 341 Query: 344 VKGLVVCGILAALMSSLASLFNSSAMLFTIDFYKRF-RPETPEKKLVGIGQIATVVIVIL 402 +KGL + AA+++SLA NS A +FT+D YK+F +PE E +LV +G+ + V+ ++ Sbjct: 342 IKGLAFAALTAAIVASLAGKCNSIATIFTLDIYKKFIKPEASETRLVSVGRWSVVIASLI 401 Query: 403 GILWIPIMRSVGDVLYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGL 462 I+ P +RS D +Y ++Q+ ++PG+ A FLLG WK+T+++ + + + I L Sbjct: 402 AIIIAPALRSF-DQVYQFIQEYVGFISPGVFAIFLLGFFWKKTTSRAALTAAL--LTIPL 458 Query: 463 TRLGAKVYYSNAGEVADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSLATEAPTAEKIQ 522 + L + G +A F L W+F+ I ++IVV+L T+ + + Q Sbjct: 459 STLFKFLPAVTNGAIAPIPF---------LNRMSWVFMIIIGLMIVVTL-TDPKSKDNPQ 508 Query: 523 GL-VFGTATKEQKAATRASWDHWDIIHTVIILAITGAFYWYFW 564 GL + + K A T AS V+I I A Y FW Sbjct: 509 GLEIDSSMFKVTPAFTIAS---------VMICGILAALYTVFW 542 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: 855 Number of extensions: 45 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: 542 Length adjustment: 36 Effective length of query: 528 Effective length of database: 506 Effective search space: 267168 Effective search space used: 267168 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