Align Na+/glucose cotransporter (characterized, see rationale)
to candidate Echvi_1680 Echvi_1680 transporter, SSS family
Query= uniprot:Q8AAV7 (564 letters) >FitnessBrowser__Cola:Echvi_1680 Length = 528 Score = 283 bits (724), Expect = 1e-80 Identities = 169/535 (31%), Positives = 302/535 (56%), Gaps = 43/535 (8%) Query: 1 MEALDWLVIGVFFLALIGIIVWVVRQKQNDSAD-YFLGGRDATWLAIGASIFASNIGSEH 59 ++ LD+ V+G++ + LIGI WV +K+ D+ + FL G W +IG +++ +N+G Sbjct: 7 LQPLDFAVLGLYLVTLIGIGYWVSFKKKRDADENLFLAGNSLGWPSIGFTMWGTNVGPSM 66 Query: 60 LIGLAGAGASSGMAMAHWEIQGWM-ILILGWVFVPFYSRSMVYTMPEFLERRYNPQSRTI 118 LI A G ++G+ ++ ++ I +L VF P Y + V T+PEF+ +R+ ++ I Sbjct: 67 LIASASIGYTTGVVAGNFAWYAFIFIFLLAVVFAPRYLGARVQTLPEFMGKRFGSSTQNI 126 Query: 119 LSVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFGGM 178 L+ ++V+ +++ +++T++AGG++ +Q+ + W++ + L+++ A +TI GG+ Sbjct: 127 LAWYTIVTVLISWLSLTLFAGGILIRQILDLP-------LWLSVVILILIAAFFTIAGGL 179 Query: 179 KSVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSNDD 238 K++ YT+V Q +L++ SL + + G ++GG E++ A T +Y NL+ DD Sbjct: 180 KAIAYTNVFQMVLLIVVSLALTLTGLYKVGGVGELI----ANTPGEYW----NLLLPADD 231 Query: 239 ANFPWLGALIGSAIIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPVFLFLIP 298 N+PW+ +G ++G W+WCTDQ +VQ VL KN KE + G F +LK+L V LF+IP Sbjct: 232 PNYPWVAIALGYPVMGVWFWCTDQSMVQSVLGAKNLKEGQLGANFTGWLKILDVALFIIP 291 Query: 299 GMIAFALHQKYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVCGILAALMS 358 G+I + L P L N D A+ T+V KL P G+ GLV+ ++AAL+S Sbjct: 292 GIICYVL------------FPDL----DNPDEAYMTMVTKLFPVGMTGLVMAVLIAALVS 335 Query: 359 SLASLFNSSAMLFTIDFY-KRFRPETPEKKLVGIGQIATVVIVILGI-LWIPIMRSVGDV 416 ++ S N+ + +FT+D Y K+++PE +K++V IG++ TV+ ++ I L + I G Sbjct: 336 TIDSALNALSTVFTMDIYVKKYKPEATQKQIVTIGRVVTVLGAVIAIFLTLAIDSIKGLN 395 Query: 417 LYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLTRLGAKVYYSNAGE 476 L+ Q + +AP ++ FL G+ WK+T+ + L+ G I+ LG V Y Sbjct: 396 LFDVFQSILGFIAPPMSVVFLFGVLWKKTTTKAANTVLLFGTILS---LGIGVLYLWVFP 452 Query: 477 VADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSLATEAPTAEKIQGLVFGTATK 531 A+ Y F+ ++L ++F+F +++V+S + L +GT K Sbjct: 453 NAE----YAFWP-HFLLLSFYIFVFLAALIVVISYVERNRKDLHVSTLDYGTIPK 502 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: 928 Number of extensions: 48 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: 528 Length adjustment: 35 Effective length of query: 529 Effective length of database: 493 Effective search space: 260797 Effective search space used: 260797 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