Align Probable inositol transporter 2 (characterized)
to candidate Echvi_2805 Echvi_2805 MFS transporter, sugar porter (SP) family
Query= SwissProt::Q9C757 (580 letters) >FitnessBrowser__Cola:Echvi_2805 Length = 448 Score = 210 bits (535), Expect = 9e-59 Identities = 128/341 (37%), Positives = 199/341 (58%), Gaps = 19/341 (5%) Query: 27 YVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVAGAIVGAA 86 YV+ L+ A +GG LFG+DT VISGA +I++ ++ D W M V++A+ G ++GA Sbjct: 6 YVIFLSIVAALGGFLFGFDTAVISGAERFIQEKWQLSD---WTHGMAVAIALYGTVIGAL 62 Query: 87 IGGWANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTAPLYI 146 GG DK GR++++L L+ + A+ A AP+ + R GLGVG +S+ AP+YI Sbjct: 63 FGGIPADKYGRKTSLLWIGVLYFISALGSALAPDVYSFMFFRFIGGLGVGASSVVAPMYI 122 Query: 147 SEASPAKIRGALVSTNGFLITGGQFLSYLIN--LAFTDVTGTWRWMLGIAGIPALLQFVL 204 SE +PAK RG LV+ F I G ++Y N + D+ +WRWM+G+ IPAL+ +L Sbjct: 123 SEIAPAKNRGVLVALYQFNIVFGILMAYFSNYLIEMADLNESWRWMMGMEAIPALIYTLL 182 Query: 205 MFTLPESPRWLY-RKGREEEAKAILRRIYSAEDVEQEIRALKDSVETEILEEGSSEKINM 263 +P+SPRWL + EEA ILR+ E V++ I +EE + EKI + Sbjct: 183 SIRVPKSPRWLIAHHNKVEEATQILRKT-DPEGVDEAIHL--------AIEERNREKIKV 233 Query: 264 --IKLCKAKTVRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFASNRTALLLSLVTA 321 L K ++ L+A + + +F Q GIN ++Y++P + ++AG ++ALL ++ Sbjct: 234 GFAVLFKHSHLKTTLLA-IMIALFNQLSGINAIIYFAPRVFEMAGI-DQKSALLSTIGIG 291 Query: 322 GLNAFGSIISIYFIDRIGRKKLLIISLFGVIISLGILTGVF 362 +N ++I +Y IDRIGRKKL++I G IISL ++ F Sbjct: 292 VVNMIATMIGLYLIDRIGRKKLMVIGSIGYIISLLLMAYSF 332 Score = 58.5 bits (140), Expect = 5e-13 Identities = 33/107 (30%), Positives = 56/107 (52%), Gaps = 1/107 (0%) Query: 451 NFGWFALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFRGICGGIAATANWISNLIVAQSF 510 N G+ L + ++I + G G+V W+ SE++P R I +WI ++A F Sbjct: 338 NSGYLPLF-VFVFIASHAVGQGSVIWVFISEVFPNETRAFGQSIGCFTHWILAAVIANVF 396 Query: 511 LSLTEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIEKMLE 557 + G + F F V+ + LL+V+ +PETKG +EEI++ L+ Sbjct: 397 PFFANSFGPASIFGFFAVMMGLQLLWVLTKMPETKGRSLEEIQQDLK 443 Lambda K H 0.324 0.139 0.425 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: 665 Number of extensions: 43 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 580 Length of database: 448 Length adjustment: 34 Effective length of query: 546 Effective length of database: 414 Effective search space: 226044 Effective search space used: 226044 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 (21.5 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