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 SM_b21344 SM_b21344 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Smeli:SM_b21344 Length = 497 Score = 397 bits (1020), Expect = e-115 Identities = 238/498 (47%), Positives = 309/498 (62%), Gaps = 7/498 (1%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL + + KSF G+ AL L VG EV AL+G+NGAGKSTLIKIL+ A+ D G V F Sbjct: 2 LLSMQGICKSFNGIPALRAASLEVGEAEVMALVGQNGAGKSTLIKILTGAYRRDEGAVVF 61 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 AG+ + P Q GIATIYQE NL P+ SVAEN+YL REPRR GL+D +R A Sbjct: 62 AGEGVS-FSMPAESQARGIATIYQEINLAPQRSVAENIYLSREPRRFGLIDRRAMRDGAA 120 Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 A+L L ++ D PV G + A +QMV IA+A+T ARL+IMDEPT++L REV L Sbjct: 121 AVLRAFNLEIDVDQPVAGFSAATRQMVAIARAVTQKARLVIMDEPTSSLDEREVGILFDT 180 Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV- 241 I LK VSV+++ HRL E+ +CDR T+MRDG+ VA+ +AD+ +VR M+G+ + Sbjct: 181 IRTLKRGGVSVVFIGHRLEELYRICDRVTIMRDGKTVATAAMADMPKLALVRHMLGKELA 240 Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301 FE + GA V + A +R VS R GEI GLAGL+G+GRT+ Sbjct: 241 AFEAIAKDADEGA----QRPVRLSVRNAGAGVRVRDVSLTVREGEISGLAGLLGSGRTET 296 Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361 A LIFGAD + G + + + R P DAI GI LV EDRK G D SIR N++L Sbjct: 297 ANLIFGADRLQRGEIRYNGEARAYRQPADAIADGIGLVAEDRKVDGIIPDMSIRENMTLA 356 Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421 L L+ G VD + ++VE Y L IK + I +LSGGNQQKVLLGR + P Sbjct: 357 LLPKLARAG-IVDRARQDEIVERYITALAIKCTSPDQPIKELSGGNQQKVLLGRWLCTDP 415 Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481 K+LIVDEPTRGIDIGAK+E+ ++L LAD G+ V++ISSEL E++A +DR+ V +G V Sbjct: 416 KLLIVDEPTRGIDIGAKSEILRLLRRLADEGLGVLMISSELEELLAAADRVTVLSDGTSV 475 Query: 482 ADLDAQTATEEGLMAYMA 499 A L + +E L A MA Sbjct: 476 AVLPRKELSEAALFAAMA 493 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: 659 Number of extensions: 34 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: 497 Length adjustment: 34 Effective length of query: 481 Effective length of database: 463 Effective search space: 222703 Effective search space used: 222703 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