Align Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11 (characterized)
to candidate Echvi_1680 Echvi_1680 transporter, SSS family
Query= SwissProt::Q8WWX8 (675 letters) >FitnessBrowser__Cola:Echvi_1680 Length = 528 Score = 288 bits (736), Expect = 6e-82 Identities = 176/540 (32%), Positives = 285/540 (52%), Gaps = 45/540 (8%) Query: 24 LEPGDIAVLVLYFLFVLAVGLWSTVKTKRDTVKGYFLAGGDMVWWPVGASLFASNVGSGH 83 L+P D AVL LY + ++ +G W + K KRD + FLAG + W +G +++ +NVG Sbjct: 7 LQPLDFAVLGLYLVTLIGIGYWVSFKKKRDADENLFLAGNSLGWPSIGFTMWGTNVGPSM 66 Query: 84 FIGLAGSGAATGISVSAYELNGLFSVLMLAWIFLPIYIAGQVTTMPEYLRKRFGGIRIPI 143 I A G TG+ + + +LA +F P Y+ +V T+PE++ KRFG Sbjct: 67 LIASASIGYTTGVVAGNFAWYAFIFIFLLAVVFAPRYLGARVQTLPEFMGKRFGS-STQN 125 Query: 144 ILAVLYLFIYIFTKISVDMYAGAIFIQQSLHLDLYLAIVGLLAITAVYTVAGGLAAVIYT 203 ILA + + + +S+ ++AG I I+Q L L L+L++V L+ I A +T+AGGL A+ YT Sbjct: 126 ILAWYTIVTVLISWLSLTLFAGGILIRQILDLPLWLSVVILILIAAFFTIAGGLKAIAYT 185 Query: 204 DALQTLIMLIGALTLMGYSFAAVGGMEGLKEKYFLALASNRSENSSCGLPREDAFHIFRD 263 + Q +++++ +L L VGG+ L +A+ E + LP +D Sbjct: 186 NVFQMVLLIVVSLALTLTGLYKVGGVGEL-------IANTPGEYWNLLLPADD------- 231 Query: 264 PLTSDLPWPGVLFGMSIPSLWYWCTDQVIVQRTLAAKNLSHAKGGALMAAYLKVLPLFIM 323 + PW + G + +W+WCTDQ +VQ L AKNL + GA +LK+L + + Sbjct: 232 ---PNYPWVAIALGYPVMGVWFWCTDQSMVQSVLGAKNLKEGQLGANFTGWLKILDVALF 288 Query: 324 VFPGMVSRILFPDQVACADPEICQKICSNPSGCSDIAYPKLVLELLPTGLRGLMMAVMVA 383 + PG++ +LFPD NP D AY +V +L P G+ GL+MAV++A Sbjct: 289 IIPGIICYVLFPD-------------LDNP----DEAYMTMVTKLFPVGMTGLVMAVLIA 331 Query: 384 ALMSSLTSIFNSASTIFTMDLW-NHLRPRASEKELMIVGRVFVLLLVLVSILWIPVVQAS 442 AL+S++ S N+ ST+FTMD++ +P A++K+++ +GRV +L +++I + + Sbjct: 332 ALVSTIDSALNALSTVFTMDIYVKKYKPEATQKQIVTIGRVVTVLGAVIAIFLTLAIDSI 391 Query: 443 QGGQLFIYIQSISSYLQPPVAVVFIMGCFWKRTNEKGAFWGLISGLLLGLVRLVLDFIYV 502 +G LF QSI ++ PP++VVF+ G WK+T K A L+ G +L L VL +++V Sbjct: 392 KGLNLFDVFQSILGFIAPPMSVVFLFGVLWKKTTTKAANTVLLFGTILSLGIGVL-YLWV 450 Query: 503 QPRCDQPDERPVLVKSIHYLYFSMILSTVTL--------ITVSTVSWFTEPPSKEMVSHL 554 P + L+ S + F L V + VST+ + T P V L Sbjct: 451 FPNAEYAFWPHFLLLSFYIFVFLAALIVVISYVERNRKDLHVSTLDYGTIPKLPNKVKWL 510 Lambda K H 0.325 0.139 0.427 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: 847 Number of extensions: 30 Number of successful extensions: 5 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: 675 Length of database: 528 Length adjustment: 37 Effective length of query: 638 Effective length of database: 491 Effective search space: 313258 Effective search space used: 313258 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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