Align Minor myo-inositol transporter, IolT2, of 478 aas (characterized)
to candidate WP_084932306.1 HA51_RS04265 sugar porter family MFS transporter
Query= TCDB::E1WAV4 (478 letters) >NCBI__GCF_002095475.1:WP_084932306.1 Length = 476 Score = 532 bits (1370), Expect = e-155 Identities = 254/468 (54%), Positives = 348/468 (74%), Gaps = 6/468 (1%) Query: 1 MSQRSKYNSAYVYVLCCIAALAGLMFGYSTAVITGVVLPLQQYYQLTPTETGWAVSSIVI 60 MS + ++N+ YVY+LC AA G MFGYS VI + +++ + L ETGWAVSSI+ Sbjct: 1 MSYQHRFNARYVYMLCLAAAAGGFMFGYSEGVIAATLESIKKSFGLNSMETGWAVSSIIF 60 Query: 61 GCIIGALVGGKIADKLGRKPALLIIAIIFIASSLGAAMSESFMIFSLSRIVCGFAVGMAG 120 G +IGAL GK+ADK GRK +L+ AI+F+ +S +A+++SF +F+ +R++CG AVG+A Sbjct: 61 GGVIGALAAGKMADKTGRKLVMLLSAILFVITSYLSAVADSFTLFTGARLICGIAVGLAA 120 Query: 121 TASTMYMSELAPAEIRGKALGIYNISVVSGQVIVFIVNYLIAKGMPADVLVSQGWKTMLF 180 T + MY+SE++PA++RGKA G Y++S+V+G + VF VNYLIA+GMP +V GW+TM+ Sbjct: 121 TVTPMYISEISPAKMRGKATGTYDLSIVAGVLAVFTVNYLIARGMPQAWMVETGWRTMMA 180 Query: 181 AQVVPSIAMLAITLFLPESPAWCARNNRSEARSIKVLTRIYSGLTATDVAAIFDSMKETV 240 Q+VPS+AML + + +PESP WC R+NR E ++IKVL+RIY + +F Sbjct: 181 VQLVPSVAMLVLIILVPESPHWCIRHNRGE-QAIKVLSRIYPEFNQEEARQLFQLPSSAA 239 Query: 241 RSQDNVAGGERTNLKSSPVLRYILLVGCCIAVLQQFTGVNVMNYYAPLVLQN--SSTEVV 298 + G + +PVLRYIL+VG IAVLQQFTG+NV+NYY P++L+ S+ +++ Sbjct: 240 KKSTTARKGV---MPENPVLRYILVVGVAIAVLQQFTGINVINYYTPMMLEGTTSNKDII 296 Query: 299 MFQTIFIAVCNVVGSFIGMILFDRYGRIPIMKIGTIGSIVGLLIASYGLYTHDTGYITIF 358 F+TIF+A+ N VG+FIGM LFD YGR+PIMKIGT+G+I+GLLIAS+GLYT+D GYI I Sbjct: 297 FFETIFVALLNGVGAFIGMHLFDHYGRLPIMKIGTVGAIIGLLIASWGLYTNDVGYIAIS 356 Query: 359 GILFFMLLFAVSWSVGAWVLISEVFPEKIKGFGMGLAVSLMWIANFLISLLFPVINDNAW 418 GIL F L F + W GAWV+ISE+FP++I+ MGLAV LMW+ NFLI+L+FP++NDNAW Sbjct: 357 GILIFTLFFGMGWGAGAWVMISEIFPDRIRESSMGLAVGLMWVTNFLITLVFPLVNDNAW 416 Query: 419 LQETFGGAFSMWIFVVFNLVCYVFISRYVPETKGVPLTEIERLAENKL 466 LQE F GAFSMWIFVVFN CY F+SRYVPET+GV L +IE++AE K+ Sbjct: 417 LQEQFHGAFSMWIFVVFNAFCYWFLSRYVPETRGVALEDIEKVAEAKM 464 Lambda K H 0.327 0.140 0.419 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: 728 Number of extensions: 23 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 478 Length of database: 476 Length adjustment: 33 Effective length of query: 445 Effective length of database: 443 Effective search space: 197135 Effective search space used: 197135 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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