Align Na+/glucose cotransporter (characterized, see rationale)
to candidate CA265_RS04220 CA265_RS04220 sodium:solute symporter
Query= uniprot:Q8AAV7 (564 letters) >FitnessBrowser__Pedo557:CA265_RS04220 Length = 550 Score = 328 bits (840), Expect = 4e-94 Identities = 181/573 (31%), Positives = 320/573 (55%), Gaps = 43/573 (7%) Query: 5 DWLVIGVFFLALIGIIVWV-VRQKQND---SADYFLGGRDATWLAIGASIFASNIGSEHL 60 D ++ + L ++ I +W R+K+N+ S +YFL G+ W IG ++FA+NI HL Sbjct: 6 DIVITIAYILFIVTIGLWTGTRKKKNEETTSGEYFLAGKTLKWPMIGLALFATNISCLHL 65 Query: 61 IGLAGAGASSGMAMAHWE-IQGWMILILGWVFVPFYSRSMVYTMPEFLERRYNPQSRTIL 119 + LA +G SG+ ++E + + +++L +F+PFY RS + T+P+FLERRYN R L Sbjct: 66 VSLAQSGFDSGLLNGNFEWMAAFTLILLALLFIPFYIRSGISTLPDFLERRYNRACRDWL 125 Query: 120 SVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFGGMK 179 + IS++S ++ +A + AGG+V + +FGI +++ + + +LT LYTI GG++ Sbjct: 126 AFISILSAIIIHIAFSFLAGGIVLETLFGID-------MYVSIVVIALLTGLYTIIGGLR 178 Query: 180 SVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSNDDA 239 +V+ T +Q+ +L+ G++II + ++GGWD M + + + D ++ + D + Sbjct: 179 AVVVTETIQSLVLITGAIIITYFAWNKVGGWDHMTAI---LQKENAMDKLSMIRPIGDKS 235 Query: 240 NFPWLGALIGSAIIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPVFLFLIPG 299 W+ +G ++G WYWC DQ IVQRVL K+E AR G++F ++K+LPVF+F++PG Sbjct: 236 GMSWIAVFLGYPVLGIWYWCADQTIVQRVLGAKDENHARVGSLFCGFIKILPVFIFVLPG 295 Query: 300 MIAFALHQ---------KYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVC 350 + A+ L++ + +G+ GE L N + ++ +LLP G+ G++V Sbjct: 296 LFAYILYKSGTMDLSSLQTVGSNGETVL--------NTKGIYTLMITQLLPKGLVGILVA 347 Query: 351 GILAALMSSLASLFNSSAMLFTIDFYKRFRPETPEKKLVGIGQIATVVIVILGILWIPIM 410 +L+ LMS +A NS A L + D YKRF+PET +KKLV +G+ + + + + I +P++ Sbjct: 348 ALLSGLMSQIAGALNSIATLSSYDLYKRFKPETSDKKLVSVGRWSAGIALTVSIGLLPLL 407 Query: 411 RSVGDVLYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLTRLGAKVY 470 S + L+ + DV + +AP I FLLG+ WK+ SA+G + L+ G IIG Sbjct: 408 NSY-ESLFNGINDVIAHIAPPITCVFLLGVFWKKASAKGAQYTLLLGSIIGAGVFVVNKV 466 Query: 471 YSNAGEVADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSLATEAPTAEKIQGLVFGTAT 530 Y + F + + ++F C+++ +V S + + L + + Sbjct: 467 YGTETIIGQIPFMMMAF---------YLFCICVLIQVVFSHIYPVKHTAQSETLYWTSIW 517 Query: 531 KEQKAATRASWDHWDIIHTVIILAITGAFYWYF 563 + K+ + ++ + +V++LAI G Y YF Sbjct: 518 EPLKSKGWSGIGNYKFL-SVLLLAIMGVLYVYF 549 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: 913 Number of extensions: 52 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: 550 Length adjustment: 36 Effective length of query: 528 Effective length of database: 514 Effective search space: 271392 Effective search space used: 271392 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 Apr 09 2024. 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