Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)
Query= TCDB::E1WAV3 (456 letters) >FitnessBrowser__Btheta:350322 Length = 484 Score = 294 bits (752), Expect = 5e-84 Identities = 157/474 (33%), Positives = 271/474 (57%), Gaps = 53/474 (11%) Query: 1 MGGILFGYDTAVISGAIGSLTSYFHLSPAET-------GWAVSCVVVGCVIGSFSAGYLS 53 +GG+LFGYDTAVISGA L ++F LS ++ G S ++GCV+G +G + Sbjct: 22 LGGLLFGYDTAVISGAEKGLEAFF-LSASDFQYNKVMHGITSSSALIGCVLGGALSGVFA 80 Query: 54 KRFGRKKSLMVSALLFTISAVGTSLSYTFTH------------FVIYRIIGGLAVGLAAT 101 R GR+ SL ++A+LF +SA+G+ F +YR++GG+ VGLA+ Sbjct: 81 SRLGRRNSLRLAAVLFFLSALGSYYPEVLFFEYGKPNMDLLIAFNLYRVLGGIGVGLASA 140 Query: 102 VSPMYMSEVSPKNMRGRALSMQQFAIVFGQILIFYVNYKI------------------AS 143 V PMY++E++P N+RG +S QFAI+FG +++++VNY I S Sbjct: 141 VCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIMGDHQNPIILKDAAGVLSVS 200 Query: 144 IAADTWLIELGWRYMFAAGIIPCILFCILVFLIPESPRWMMMIGREEETLKILTKISNEE 203 +D W ++ GWRYMF + P F +L+F +P++PR+++++ +EE+ IL KI+ ++ Sbjct: 201 AESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYLVLVQQEEKAYTILEKINGKK 260 Query: 204 HARHLLADIKTSLQNDQLNAHQKLNYRDGNVRFILILGCMIAMLQQVTGVNVMMYYAPIV 263 A+ +L DIK + Q +KL + G ++++G ++++ QQ G+N ++YYAP + Sbjct: 261 KAQEILNDIKATAQEKT----EKL-FTYGVT--VIVIGILLSVFQQAIGINAVLYYAPRI 313 Query: 264 LKDVTGSAQEALFQTIWIGVIQLIGSIIGAMIMDKMGRLSLMRKGTIGSIIGLLLTSWAL 323 ++ G+ + QT+ +G++ +I +++ +D+ GR L+ G+IG +G + Sbjct: 314 FENA-GAEGGGMMQTVIMGIVNIIFTLVAIFTVDRFGRKPLLIIGSIGMAVGAFAVAMCD 372 Query: 324 YSQATGYFALFGMLFFMIFYALSWGVGAWVLISEIFPNRMRSQGMSISVGFMWMANFLVS 383 G + ++ + F+ +SWG WVLISEIFPN +R + ++I+V F W+ N++VS Sbjct: 373 SMAIKGVLPVLSIIVYAAFFMMSWGPICWVLISEIFPNTIRGKAVAIAVAFQWIFNYIVS 432 Query: 384 QFFPMINENPYLLSHFHGAFPMWIFAICCIFSYFFICRYLPETKGISLEKMESV 437 FP + + F F ++ I C+ + F+ R++PETKG +LE M + Sbjct: 433 STFPALYD-------FSPMFAYSLYGIICVAAAIFVWRWVPETKGKTLEDMSKL 479 Lambda K H 0.329 0.141 0.436 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: 644 Number of extensions: 40 Number of successful extensions: 7 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: 456 Length of database: 484 Length adjustment: 33 Effective length of query: 423 Effective length of database: 451 Effective search space: 190773 Effective search space used: 190773 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 (21.8 bits) S2: 51 (24.3 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