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 SMc02337 SMc02337 ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Smeli:SMc02337 Length = 501 Score = 392 bits (1006), Expect = e-113 Identities = 225/506 (44%), Positives = 322/506 (63%), Gaps = 19/506 (3%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 L+ +S +SK+F GV+AL VD + GEVHAL+GENGAGKSTL+++L+ +GTV+ Sbjct: 4 LVSLSGISKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGTVSI 63 Query: 63 AGQVLD---PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119 G+ + PR A R GI+ I+QE L P+L+VAEN++LGR PR +V+ RLR Sbjct: 64 HGETMQHSGPRGAAGR----GISVIHQELALAPDLTVAENIFLGRLPR---IVNHRRLRK 116 Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179 A +L LG ++P LTVA QQ+VEIAKA++ AR+I+ DEPTA L+ + +RL Sbjct: 117 AASEILERLGFDIDPAIHAGRLTVAHQQVVEIAKALSNRARIIVFDEPTAVLANTDAERL 176 Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239 AII L+A +Y+SHRL EV + DR TVM+DG V + + + +V ++ MVGR Sbjct: 177 LAIIRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLETSATDVDAVIARMVGR 236 Query: 240 HVE-FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGR 298 + K R PG VV++V V+ +R VSF+ R GE+VGL GLVG+GR Sbjct: 237 QMSALFPSKAGRVPGEVVVRVRNVSRGRK-------VRDVSFSVRAGEVVGLGGLVGSGR 289 Query: 299 TDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNL 358 T++ARL+FGAD + +G V ++ KPL L SPR+A++A I LVPEDRKQQG LD IR N Sbjct: 290 TEVARLVFGADKMDSGTVELNGKPLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINT 349 Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418 +L ++++S LG ++D ER + ++R+K + + + LSGGNQQKV L + Sbjct: 350 TLAKIRSISRLG-FLDAGKERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWFH 408 Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREG 478 +LI+DEPTRG+D+GAK E++ +++DLA G A++VISSE E+ + DR++V EG Sbjct: 409 ADCDLLILDEPTRGVDVGAKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEG 468 Query: 479 VIVADLDAQTATEEGLMAYMATGTDR 504 IV +L TE+ L+ T + R Sbjct: 469 AIVGELTESKFTEQQLLTLAMTRSAR 494 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: 703 Number of extensions: 36 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: 501 Length adjustment: 34 Effective length of query: 481 Effective length of database: 467 Effective search space: 224627 Effective search space used: 224627 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