Align Probable inositol transporter 2 (characterized)
to candidate CCNA_00857 CCNA_00857 glucose/fructose transport protein
Query= SwissProt::Q9C757 (580 letters) >FitnessBrowser__Caulo:CCNA_00857 Length = 478 Score = 190 bits (482), Expect = 1e-52 Identities = 119/356 (33%), Positives = 193/356 (54%), Gaps = 28/356 (7%) Query: 27 YVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVAGAIVGAA 86 +V + A IGG +FGYD+GVI+G + F L ++ + V ++G A Sbjct: 24 FVAAIVAVATIGGFMFGYDSGVINGTQEGLESAFN-------LSKLGTGLNVGAILIGCA 76 Query: 87 IGGWANDKL----GRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTA 142 IG +A +L GRR+ ++++ LF++ AI AA + + ++ R+ GLGVG AS+ Sbjct: 77 IGAFAAGRLADVWGRRTVMIISALLFVISAIGTGAAESSIVFIIFRLIGGLGVGAASVLC 136 Query: 143 PLYISEASPAKIRGALVSTNGFLITGGQFLSYLINLAFTDVTGT-----------WRWML 191 P+YISE +PA IRG L S +I G +++ N A G+ WRWM Sbjct: 137 PVYISEVTPANIRGRLSSVQQIMIITGLTGAFVANYALAHTAGSSTAEFWLGLPAWRWMF 196 Query: 192 GIAGIPALLQFVLMFTLPESPRWLYRKGREEEAKAILRRIYSAEDVEQEIRALKDSVETE 251 + IPA + F+ + +PESPR+L KG++ +A+AIL R++ A +++ ++ S+ + Sbjct: 197 WMQIIPAGVFFLCLLGIPESPRYLVAKGKDAQAEAILSRLFGAGQGAKKVEEIRASLSAD 256 Query: 252 ILEEGSSEKINMIKLCKAKTVRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFASNR 311 + + K +R L AG+ L VFQQ VGIN V YY + Q GF + Sbjct: 257 -----HKPTFSDLLDPTTKKLRVILWAGLVLAVFQQLVGINIVFYYGSVLWQSVGFTED- 310 Query: 312 TALLLSLVTAGLNAFGSIISIYFIDRIGRKKLLIISLFGVIISLGILTGVFYEAAT 367 +L +++++ L+ +++I ID+IGRK LL+I G+ ++LG+LT F A T Sbjct: 311 DSLKINILSGTLSILACLLAIGLIDKIGRKPLLLIGSAGMAVTLGVLTWCFSTATT 366 Score = 61.2 bits (147), Expect = 9e-14 Identities = 31/101 (30%), Positives = 54/101 (53%), Gaps = 1/101 (0%) Query: 453 GWFALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFRGICGGIAATANWISNLIVAQSFLS 512 G AL+ LY+IFF+ G V W++ E++P + RG + A WI+N ++ SF + Sbjct: 378 GLTALIAANLYVIFFNLSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWIANFAISVSFPA 437 Query: 513 LTEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIE 553 L A T+ + + +V++ V V ET+G +E ++ Sbjct: 438 LA-AASLPMTYGFYALSAVVSFFLVQKLVHETRGKELEAMQ 477 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: 682 Number of extensions: 31 Number of successful extensions: 6 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: 478 Length adjustment: 35 Effective length of query: 545 Effective length of database: 443 Effective search space: 241435 Effective search space used: 241435 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