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_RS05320 HSERO_RS05320 ribonucleotide-diphosphate reductase subunit alpha
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__HerbieS:HSERO_RS05320 Length = 502 Score = 369 bits (948), Expect = e-106 Identities = 217/512 (42%), Positives = 312/512 (60%), Gaps = 17/512 (3%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 +L ++ + K+F V L VDL V GEVHALLGENGAGKSTL+KIL DAG + Sbjct: 1 MLQLTGIKKNFGPVTVLRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPDAGEIRI 60 Query: 63 AGQV--LDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRA 119 GQ D A + G+ ++QEF+L P L +NM+L RE R R G + + +R Sbjct: 61 DGQPCRFDSYRAAIAG---GVGVVFQEFSLIPYLDAVDNMFLARELRSRWGWLQRAAMRR 117 Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179 AQ ++ LG+ + D PV L+VA+QQ VEIAKA+ L+AR++++DEPTA L+ EV+ L Sbjct: 118 RAQEIIGQLGVAIPLDVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPAEVEHL 177 Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239 A++ L+A+ V++I++SH L E+ +CDR TV+RDG +VA+ A+V+ A +V +MVGR Sbjct: 178 FAVMRSLRAQGVAIIFISHHLEEIFEICDRITVLRDGAYVATCATAEVDQARLVEMMVGR 237 Query: 240 HVEF----ERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVG 295 +E + K G VVL+V + R AP F R GEI+G AGLVG Sbjct: 238 RIENCFPPKPAKGGEGEGEVVLEVHALQL---RRQAP----VSQFQLRRGEILGFAGLVG 290 Query: 296 AGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIR 355 +GRT+ + GA + ++ + PLR P A+QAGI L+PE RK+QG SI Sbjct: 291 SGRTETVLAMLGAHAALSCKLSMHGVPLRFADPAQALQAGIGLLPESRKEQGLITSFSIL 350 Query: 356 RNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGR 415 N+SL + G ++D R E+ E Q++R+K A+ + LSGGNQQKV++ R Sbjct: 351 HNVSLNNYGKYRLGGLFLDRRREQQATEAAMQRVRVKAPGAQVRVDTLSGGNQQKVVIAR 410 Query: 416 AMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF 475 + KVLI DEPTRGID+GAK+E++Q++ + G ++++ISSEL EV+ ++DR+ VF Sbjct: 411 WINHAMKVLIFDEPTRGIDVGAKSEIYQLMREFTAQGYSILMISSELPEVVGMADRVCVF 470 Query: 476 REGVIVADLDAQTATEEGLMAYMATGTDRVAA 507 R G IVA L+ + E +M + TG R AA Sbjct: 471 RGGGIVATLEGEAVNAEEIMTHATTGRIRHAA 502 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: 652 Number of extensions: 39 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: 502 Length adjustment: 34 Effective length of query: 481 Effective length of database: 468 Effective search space: 225108 Effective search space used: 225108 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