Align Probable inositol transporter 2 (characterized)
to candidate WP_084936573.1 HA51_RS21365 sugar porter family MFS transporter
Query= SwissProt::Q9C757 (580 letters) >NCBI__GCF_002095475.1:WP_084936573.1 Length = 464 Score = 233 bits (594), Expect = 1e-65 Identities = 133/341 (39%), Positives = 203/341 (59%), Gaps = 15/341 (4%) Query: 20 SLTWKNPYVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVA 79 S T L + F A + GLLFG D GVI+GAL +I DF QE IVS + Sbjct: 8 SRTSNKMMTLFVCFLAALAGLLFGLDIGVIAGALPFIAKDFNVTAHQ---QEWIVSSMMF 64 Query: 80 GAIVGAAIGGWANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMAS 139 GA VGA GW + +LGR+ +++ LF++G++ A A +P +L+ RV +GL VG+AS Sbjct: 65 GAAVGAVGSGWMSSRLGRKKSLMAGAILFVIGSLWSAMATSPDMLIAARVVLGLAVGVAS 124 Query: 140 MTAPLYISEASPAKIRGALVSTNGFLITGGQFLSYLINLAFTDVTGTWRWMLGIAGIPAL 199 TAPLY+SE +P KIRG+++S +IT G +YL + AF+D G WRWMLG+ IPA+ Sbjct: 125 YTAPLYLSEIAPEKIRGSMISLYQLMITIGILAAYLSDTAFSD-AGAWRWMLGVITIPAI 183 Query: 200 LQFVLMFTLPESPRWLYRKGREEEAKAILRRIY-SAEDVEQEIRALKDSVETEILEEGSS 258 L + +F LP SPRWL KG A+ +L R+ ++E ++E+ +++S++ Sbjct: 184 LLLIGVFFLPNSPRWLAAKGDFRSAQRVLDRLRDTSEQAKRELDEIRESLKI-------- 235 Query: 259 EKINMIKLCKAKT-VRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFASNRTALLLS 317 K + +L ++ + RR + GV LQV QQF G+N +MYY+P I ++AGFA+ + + Sbjct: 236 -KQSGWQLFQSNSHFRRAVYLGVLLQVMQQFTGMNVIMYYAPKIFEIAGFANTTQQMWGT 294 Query: 318 LVTAGLNAFGSIISIYFIDRIGRKKLLIISLFGVIISLGIL 358 ++ +N + I+I +DR GRK L++ + +GIL Sbjct: 295 VIVGLVNVLATFIAIGLVDRWGRKPTLVLGFIVMAAGMGIL 335 Score = 74.7 bits (182), Expect = 8e-18 Identities = 34/103 (33%), Positives = 64/103 (62%) Query: 454 WFALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFRGICGGIAATANWISNLIVAQSFLSL 513 +FA+ L ++I+ F+ G + W++ SEI PL+ R ++ NWI+N+IV +FL++ Sbjct: 350 YFAVAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITVSTATNWIANMIVGATFLTM 409 Query: 514 TEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIEKML 556 ++G + TF ++ ++V +L + +PETK + +E IE+ L Sbjct: 410 LNSLGNAPTFWVYAGLNVFFILLTVALIPETKNVSLEHIERNL 452 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: 679 Number of extensions: 36 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 580 Length of database: 464 Length adjustment: 35 Effective length of query: 545 Effective length of database: 429 Effective search space: 233805 Effective search space used: 233805 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 24 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