Align Probable inositol transporter 2 (characterized)
to candidate AO356_27270 AO356_27270 MFS transporter
Query= SwissProt::Q9C757 (580 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27270 Length = 472 Score = 216 bits (549), Expect = 2e-60 Identities = 115/334 (34%), Positives = 193/334 (57%), Gaps = 15/334 (4%) Query: 27 YVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVAGAIVGAA 86 Y+ ++ + A GGLLFG+DTGVI+GALLY++DD + + + ++ S + GA++GA Sbjct: 27 YLQKITWIATFGGLLFGFDTGVINGALLYMKDD---LGLTPFTEGLVASALLIGAMMGAL 83 Query: 87 IGGWANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTAPLYI 146 G +D GRR IL +F LGA+ A AP +++V R +GL VG AS+ P Y+ Sbjct: 84 FSGRLSDLKGRRRIILFLAVVFFLGALACALAPTLNVMVAARFTLGLAVGGASVVVPAYL 143 Query: 147 SEASPAKIRGALVSTNGFLITGGQFLSYLINLA----FTDVTGTWRWMLGIAGIPALLQF 202 +E +P+ IRG +++ N +I GQFL++ N F+D+ G WRWML +A +PA+ + Sbjct: 144 AEMAPSSIRGRIITRNELMIVTGQFLAFTTNATLGNLFSDLDGVWRWMLALATLPAVALW 203 Query: 203 VLMFTLPESPRWLYRKGREEEAKAILRRIYSAEDVEQEIRALKDSVETE-ILEEGSSEKI 261 + M +PESPRWL KGR E +L+ + + E+ A+ + E +++G + Sbjct: 204 LGMLYMPESPRWLATKGRFREGLEVLKLVREEYYAKAEMEAITQQISNERFIKKGGWRDL 263 Query: 262 NMIKLCKAKTVRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFASNRTALLLSLVTA 321 + K RR + G+G+ V Q G+N++MY+ I+ AG R+AL+ ++V Sbjct: 264 SQ------KGARRIFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGL-EQRSALIANVVNG 316 Query: 322 GLNAFGSIISIYFIDRIGRKKLLIISLFGVIISL 355 ++ + + I +DR+GR+ ++++ G +SL Sbjct: 317 VISIGATFVGIALLDRVGRRPMMLLGFTGTTLSL 350 Score = 79.7 bits (195), Expect = 2e-19 Identities = 41/104 (39%), Positives = 63/104 (60%), Gaps = 3/104 (2%) Query: 456 ALLGLGLYIIFFSPGMGTVP---WIVNSEIYPLRFRGICGGIAATANWISNLIVAQSFLS 512 A+L LG +F + G + W++ +EI+P+R RG C G+A A W++N+++ F S Sbjct: 367 AMLILGAMAMFLASMQGLIGPAFWVLLAEIFPMRIRGGCMGMAIAAFWLTNVMIGMFFPS 426 Query: 513 LTEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIEKML 556 L IG TF +F +++L FV V VPET+G +EEIE+ L Sbjct: 427 LVATIGIGQTFFVFVGAGLLSLTFVAVWVPETRGSTLEEIEQRL 470 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: 32 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: 472 Length adjustment: 35 Effective length of query: 545 Effective length of database: 437 Effective search space: 238165 Effective search space used: 238165 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