Align Inositol transport ATP-binding protein IatA, 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 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 332 bits (852), Expect = 1e-95 Identities = 197/501 (39%), Positives = 299/501 (59%), Gaps = 16/501 (3%) Query: 4 LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63 +D+ ++K + GV ALD VD V GE L GENG+GKSTLIKI+S A AGTV A Sbjct: 10 IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69 Query: 64 GQ---VLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENM-YLGREPRRLGLVDWSRLRA 119 GQ L+PR + G+ I+Q+F+LFP LSVAEN+ + + R L + +R Sbjct: 70 GQEHVTLNPRISAAA----GVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRD 125 Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179 A+A L+ +G+ ++ DA V L VA++Q+V I +A+ A+LIIMDEPT AL+ +EV RL Sbjct: 126 IARAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRL 185 Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239 II LK V+VI+VSH+L EV + ++ V+R+G+ VA G ++ + + M GR Sbjct: 186 QGIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGR 245 Query: 240 HVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRT 299 V +++V+G+ A G +SF R GE++G+ GL+G GRT Sbjct: 246 DVPEVPPSDVAAGAQTLMQVQGLGKA-------GSFSDISFDLRTGEVLGITGLLGCGRT 298 Query: 300 DLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359 +A+ +FG AG +LVD P+ L P+ A A I VPEDR +G FL SI RN++ Sbjct: 299 SVAKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVA 358 Query: 360 LPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419 + L A ++ G ++D + ++L++K D E + LSGGNQQ+V L R ++ Sbjct: 359 VGRLDAHTS-GGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSR 417 Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479 P+VLI++ P+ G+D+G+KA++H ++ +LA G+ V+VIS +L E++A R++V REG Sbjct: 418 APRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGR 477 Query: 480 IVADLDAQTATEEGLMAYMAT 500 I+ L+ TE+ L +A+ Sbjct: 478 IIDALEGTALTEDDLAHRLAS 498 Lambda K H 0.320 0.136 0.380 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: 583 Number of extensions: 23 Number of successful extensions: 9 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: 515 Length of database: 498 Length adjustment: 34 Effective length of query: 481 Effective length of database: 464 Effective search space: 223184 Effective search space used: 223184 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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