Align Probable inositol transporter 2 (characterized)
to candidate WP_057508163.1 ABB28_RS08195 MFS transporter
Query= SwissProt::Q9C757 (580 letters) >NCBI__GCF_001431535.1:WP_057508163.1 Length = 474 Score = 199 bits (505), Expect = 3e-55 Identities = 121/348 (34%), Positives = 186/348 (53%), Gaps = 21/348 (6%) Query: 27 YVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVAGAIVGAA 86 +++ ++ A IGG LFG+D+GVI+G + +R F S + + V+ + G +GA Sbjct: 18 FIVLISCVATIGGFLFGFDSGVINGTVDGLRTAFNSSEAALGFE---VASMLLGCAIGAF 74 Query: 87 IGGWANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTAPLYI 146 + G D LGRRS ++++ LFLL A+ AA L V RV G VG AS+ AP YI Sbjct: 75 LAGRLGDLLGRRSVLIISAVLFLLSALGAGAAHASWLFVAARVIGGFAVGAASVMAPAYI 134 Query: 147 SEASPAKIRGALVSTNGFLITGGQFLSYLINLAFTDVTG-----------TWRWMLGIAG 195 +E + A+ RG L + I G F ++L N G WRWM + Sbjct: 135 AEVASARYRGKLATVQQIAIISGLFAAFLSNYLLARAAGASTEVLWLGQEAWRWMFWMQA 194 Query: 196 IPALLQFVLMFTLPESPRWLYRKGREEEAKAILRRIYSAEDVEQEIRALKDSVETEILEE 255 IP+LL L+ +PESPR+L KGR EA A+L R+Y A + + ++ ++ S+ Sbjct: 195 IPSLLFLALLLVIPESPRFLVVKGRRAEASAVLTRLYGAVEAQAKLGEIEHSLAQHQHRP 254 Query: 256 GSSEKINMIKLCKAKTVRRGLI-AGVGLQVFQQFVGINTVMYYSPTIVQLAGFASNRTAL 314 ++ + KA RG++ G+GL V QQ VGIN V YY + Q GF+ N AL Sbjct: 255 SFADLKD-----KASGKLRGIVWVGIGLAVLQQLVGINVVFYYGAVLWQAVGFSEN-DAL 308 Query: 315 LLSLVTAGLNAFGSIISIYFIDRIGRKKLLIISLFGVIISLGILTGVF 362 L+++++ L+ ++++ IDRIGRK LL + G+ I+L ++ F Sbjct: 309 LINVLSGALSIGACLVTVVLIDRIGRKPLLWVGSVGMAIALALMVVAF 356 Score = 71.6 bits (174), Expect = 7e-17 Identities = 33/101 (32%), Positives = 57/101 (56%) Query: 453 GWFALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFRGICGGIAATANWISNLIVAQSFLS 512 G AL+ +Y++FF+ G V W++ E++P + RG +A A W SN + +F Sbjct: 373 GRLALVAANVYVVFFNMSWGPVMWVMLGEMFPNQIRGSALAVAGAAQWTSNFAITVTFPI 432 Query: 513 LTEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIE 553 L IG + + I+ V + +++ FV+ V ETKG +E++E Sbjct: 433 LLAGIGLAGAYSIYAVAAFLSIFFVIRYVRETKGKELEQME 473 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: 641 Number of extensions: 28 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: 474 Length adjustment: 35 Effective length of query: 545 Effective length of database: 439 Effective search space: 239255 Effective search space used: 239255 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