Align Na+/glucose cotransporter (characterized, see rationale)
to candidate 5209833 Shew_2286 SSS family solute/sodium (Na+) symporter (RefSeq)
Query= uniprot:Q8AAV7 (564 letters) >FitnessBrowser__PV4:5209833 Length = 519 Score = 270 bits (690), Expect = 1e-76 Identities = 159/519 (30%), Positives = 286/519 (55%), Gaps = 52/519 (10%) Query: 1 MEALDWLVIGVFFLALIGIIVWVVRQK---QNDSADYFLGGRDATWLAIGASIFASNIGS 57 +E LD ++ V+ L L+G+ +W+ RQ + D+ DYFL G+ W AIGAS+ ASNI + Sbjct: 2 LETLDIGILLVYALGLLGLALWISRQDKRHERDTKDYFLAGKALPWWAIGASLIASNISA 61 Query: 58 EHLIGLAGAGASSGMAMAHWEIQGWMILIL-GWVFVPFYSRSMVYTMPEFLERRYNPQSR 116 E +IG++G+G + G+A+A +E + LIL G +P + ++ +YTMP++LE+R++ + + Sbjct: 62 EQIIGMSGSGYAIGLAIASYEWMAAITLILVGKYMLPIFIKNEIYTMPQYLEQRFDKRVK 121 Query: 117 TILSVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFG 176 T L++ L Y+L + ++ GGL + V GI L+G+ F L + + Y+++G Sbjct: 122 TTLALFWLSVYILVNLTAVLWLGGLAIETVAGIDWLYGMVF-------LALFSLAYSLYG 174 Query: 177 GMKSVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSN 236 G+K+V YT ++Q +L+ G L++ L + D + G ++ +I S Sbjct: 175 GLKAVAYTDIIQVVLLIFGGLLLSYLALDRVA--DGQGVLAGFDRLSSALPEHFEMILSQ 232 Query: 237 DDANF---PWLGALIGSA-IIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPV 292 + ++ P + L+G I+ YW +Q+I+QR L+ K+ EA++G F AYLKLL Sbjct: 233 SNPHYMSLPGISVLVGGLWIMNISYWGFNQYIIQRALAAKSVAEAQKGIAFAAYLKLLMP 292 Query: 293 FLFLIPGMIAFALHQKYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVCGI 352 + ++PG+ A L+ G + D A+P+++A L+PAGVKGLV + Sbjct: 293 LIVVLPGIAAVLLYP----------------GLESPDQAYPSMMA-LMPAGVKGLVFAAL 335 Query: 353 LAALMSSLASLFNSSAMLFTIDFYKRFRPETPEKKLVGIGQIATVVIVILGILWIPIMRS 412 +AA++SSLAS+ NS + +FT+D Y RP E V +G++++++ +++ ++ + Sbjct: 336 VAAIVSSLASMTNSISTIFTMDIYAMLRPAKSEGHYVLVGRLSSLISLLIALVMAQPLLG 395 Query: 413 VGDVLYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLTRLGAKVYYS 472 + + Y+Q+ V PGI FL G+ W+R ++QG + + I G + Y+ Sbjct: 396 EFEQAFQYIQEFTGVFTPGIVVIFLTGMFWRRATSQGALAAALGSAIFS---FGLRFYWP 452 Query: 473 NAGEVADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSL 511 ++ ++ G +FL C+ + ++VSL Sbjct: 453 ---------------ELPFMDRIGLVFLLCLALSVLVSL 476 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: 868 Number of extensions: 45 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: 519 Length adjustment: 35 Effective length of query: 529 Effective length of database: 484 Effective search space: 256036 Effective search space used: 256036 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