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 BWI76_RS00660 BWI76_RS00660 ABC transporter
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Koxy:BWI76_RS00660 Length = 503 Score = 370 bits (949), Expect = e-107 Identities = 208/510 (40%), Positives = 323/510 (63%), Gaps = 18/510 (3%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL + ++K FPGVRAL+ V L + G+V AL+GENGAGKSTL+K+++ + + G + + Sbjct: 7 LLSLKGITKVFPGVRALENVQLDLWPGKVTALIGENGAGKSTLVKVMTGIYQPEEGEILY 66 Query: 63 AG---QVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGR--EPRRLGLVDWSRL 117 Q+ +P A ++GI I+QE LF ELSV EN+++G+ L +DW + Sbjct: 67 KAIPIQLPNPESA----HKVGITAIHQETVLFDELSVTENIFVGQYLHTGLLKKLDWPAM 122 Query: 118 RADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVD 177 A +L L + ++P A ++ L++A++ MV IA+A++ A+++I+DEPTAALS E+ Sbjct: 123 HRKASEILTRLEVQIDPRATLKTLSIAQRHMVAIARALSFEAQVVILDEPTAALSQHEIL 182 Query: 178 RLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237 + I+ LK +++++SH+ E+ + D YT++RDG +V+SG + D+ MV +MV Sbjct: 183 EFYQIVERLKQDGKAILFISHKFDEIFELADYYTILRDGVYVSSGAINDITEERMVAMMV 242 Query: 238 GRHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAG 297 GR + K PG VL+V+ L P +SF+ R GEI+G GLVGAG Sbjct: 243 GRAITQTYPKVDCIPGETVLEVKD-------LCHPTEFAHISFSLRKGEILGFYGLVGAG 295 Query: 298 RTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRN 357 RT+L + + G ++G +++ KP+R R P DAI AGI+ VPE+R++QG + I +N Sbjct: 296 RTELMQALSGVSHPSSGDIVLKGKPMRFRQPADAISAGIVCVPEERQKQGAIIALPIAQN 355 Query: 358 LSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAM 417 +SLP L L+ G D R R L + Y +L++K A+ LSGGNQQKV++G+ + Sbjct: 356 ISLPQLSKLNPGGVLNDAREWR-LADEYASRLQVKAFSWRQAVETLSGGNQQKVVIGKWL 414 Query: 418 ALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFRE 477 A P+V+I+DEPT+GIDIG+KA VHQ +S+L G+AV+++SSEL EVM ++DRI+V E Sbjct: 415 ATHPEVIILDEPTKGIDIGSKAAVHQFMSELVSQGLAVIMVSSELPEVMGMADRIIVMHE 474 Query: 478 GVIVADLDAQTATEEGLMAYMATGTDRVAA 507 G++VA+ A AT E +++ A+G + AA Sbjct: 475 GLMVAEYRAGEATAETIVS-AASGIGQEAA 503 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: 556 Number of extensions: 36 Number of successful extensions: 8 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: 503 Length adjustment: 34 Effective length of query: 481 Effective length of database: 469 Effective search space: 225589 Effective search space used: 225589 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