Align Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 180 bits (457), Expect = 1e-49 Identities = 123/329 (37%), Positives = 184/329 (55%), Gaps = 13/329 (3%) Query: 1 MTAPSSPA-PLATDKPRFDLLAFARKHRTILFLLL-LVAVFGAANERFLTARNALNILSE 58 M AP++PA P AT + + +L +L +VA+F + +E F +A + I +E Sbjct: 563 MNAPTAPAAPAATPSSASVWRSQLGTYLGLLAVLAGMVALFSSLSEYFWSAETFITIANE 622 Query: 59 VSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLI 118 + ++AVGMTFV++I GID++VGS++A A+ +A + PA +AL + Sbjct: 623 IPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAAAILQWGWTVPAAAALALATGLVC 682 Query: 119 GLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGS---GE 175 G G + +V W +P+FIV+LG + RG+ ++ D DA W + G Sbjct: 683 GTITGAI---SVAW-RLPSFIVSLGMLEAVRGSAYVVTDSRT-QYVGDAISWLSAPFFGG 737 Query: 176 ILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIG 235 I F + V+ +VA + L T +GR V +G N EA RL+GV+ I V+A+ G Sbjct: 738 ISFAFLLAVVLVVVA---QLVLSRTVFGRCVVGIGTNEEAMRLAGVDPRPIRVIVFAMTG 794 Query: 236 ALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVL 295 LAGL+G + SARL +A+ AGTG EL+VIA+VVIGG SL GG G V T G L+I VL Sbjct: 795 LLAGLAGLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGSVVNTAFGVLIIAVL 854 Query: 296 SNGLVMLHVTSYVQQVVIGLIIVAAVAFD 324 GL + + ++++ G +IVAAV D Sbjct: 855 EAGLAQVGASEPSKRIITGFVIVAAVIVD 883 Lambda K H 0.325 0.140 0.413 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: 579 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 332 Length of database: 892 Length adjustment: 35 Effective length of query: 297 Effective length of database: 857 Effective search space: 254529 Effective search space used: 254529 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 (21.6 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