Align Probable inositol transporter 2 (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter
Query= SwissProt::Q9C757 (580 letters) >FitnessBrowser__Koxy:BWI76_RS24055 Length = 464 Score = 230 bits (586), Expect = 1e-64 Identities = 135/335 (40%), Positives = 210/335 (62%), Gaps = 15/335 (4%) Query: 31 LAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVAGAIVGAAIGGW 90 + F A + GLLFG D GVI+GAL +I ++F+ + +T QE +VS + GA VGA GW Sbjct: 18 VCFLAALAGLLFGLDIGVIAGALPFIANEFQ-ISAHT--QEWVVSSMMFGAAVGAVGSGW 74 Query: 91 ANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTAPLYISEAS 150 + KLGR+ ++++ LF+ G++ AAAPN +L++ RV +GL VG+AS TAPLY+SE + Sbjct: 75 LSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISRVLLGLAVGVASYTAPLYLSEIA 134 Query: 151 PAKIRGALVSTNGFLITGGQFLSYLINLAFTDVTGTWRWMLGIAGIPALLQFVLMFTLPE 210 P KIRG+++S +IT G +YL + AF+ +G WRWMLG+ IPA+L + + LP+ Sbjct: 135 PEKIRGSMISMYQLMITIGILGAYLSDTAFS-YSGAWRWMLGVIIIPAVLLLIGVVFLPD 193 Query: 211 SPRWLYRKGREEEAKAILRRIY-SAEDVEQEIRALKDSVETEILEEGSSEKINMIKLCKA 269 SPRW K R +A+ +L R+ ++ + ++E+ +++S+ ++ + G S + K + Sbjct: 194 SPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESL--KVKQSGWS----LFK--EN 245 Query: 270 KTVRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFASNRTALLLSLVTAGL-NAFGS 328 RR + GV LQV QQF G+N +MYY+P I +LAG+A N T + V GL N + Sbjct: 246 SNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYA-NTTEQMWGTVIVGLTNVLAT 304 Query: 329 IISIYFIDRIGRKKLLIISLFGVIISLGILTGVFY 363 I+I +DR GRK LI+ + + +GIL + + Sbjct: 305 FIAIGLVDRWGRKPTLILGFIVMALGMGILGSMMH 339 Score = 75.9 bits (185), Expect = 3e-18 Identities = 34/103 (33%), Positives = 66/103 (64%) Query: 454 WFALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFRGICGGIAATANWISNLIVAQSFLSL 513 +FA+L L ++I+ F+ G + W++ SEI PL+ R + NWI+N+IV +FL++ Sbjct: 349 YFAVLMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTM 408 Query: 514 TEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIEKML 556 ++G++ TF ++G ++++ + + +PETK + +E IE+ L Sbjct: 409 LNSLGSANTFWVYGGLNILFIFLTLWLIPETKNVSLEHIERNL 451 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: 681 Number of extensions: 35 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: 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 Apr 09 2024. 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