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 HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 383 bits (984), Expect = e-111 Identities = 215/511 (42%), Positives = 326/511 (63%), Gaps = 18/511 (3%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 ++ + V K FPGV ALD + GEVHAL+GENGAGKSTL+KILS + D+G + Sbjct: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR-LGL-VDWSRLRAD 120 G+ ++ + P + Q LGI I+QE NL LS A+N+++GREPR+ +GL +D L Sbjct: 82 DGKPVEITE-PRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140 Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180 A A+ + L ++P PV LTVA QQMVEIAKA++ ++R++IMDEPTAAL+ E+ L Sbjct: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200 Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRH 240 II L+A+ V ++Y+SH++ E++ + DR +VMRDG+++A+ + + + ++ +MVGR Sbjct: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260 Query: 241 VEFERRKRRRPPGA----VVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGA 296 ++ E +R PP VVL+V G L+ +R VSF R GEI+G AGL+GA Sbjct: 261 LDGE---QRIPPDTSRNDVVLEVRG-------LNRGRAIRDVSFTLRKGEILGFAGLMGA 310 Query: 297 GRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRR 356 GRT++AR IFGADP+ AG +++ ++SP DA+ GI + EDRK G + ++ Sbjct: 311 GRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQA 370 Query: 357 NLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRA 416 N++L S+ + +G ++D+RA R+ + Y ++L IK E LSGGNQQK+++ + Sbjct: 371 NIALSSMGRFTRVG-FMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKW 429 Query: 417 MALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFR 476 + +L DEPTRGID+GAK+E++++L LA+ G A+V+ISSEL EV+ +S R++V Sbjct: 430 LLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMC 489 Query: 477 EGVIVADLDAQTATEEGLMAYMATGTDRVAA 507 EG I +L AT+E +M VA+ Sbjct: 490 EGRITGELARADATQEKIMQLATQRESAVAS 520 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: 654 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: 520 Length adjustment: 35 Effective length of query: 480 Effective length of database: 485 Effective search space: 232800 Effective search space used: 232800 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