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_RS00275 BWI76_RS00275 ribose ABC transporter ATP-binding protein RbsA
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Koxy:BWI76_RS00275 Length = 501 Score = 392 bits (1006), Expect = e-113 Identities = 208/504 (41%), Positives = 323/504 (64%), Gaps = 10/504 (1%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL + + K+FPGV+AL L V G V AL+GENGAGKST++K+L+ +A DAG++ + Sbjct: 4 LLQLKGIDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGSLLW 63 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGRE-PRRLGLVDWSRLRADA 121 G+ + P Q+ GI I+QE NL P+L++AEN++LGRE R G +DW + A+A Sbjct: 64 LGKETT-FNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEA 122 Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 LL L L N V L++ +QQMVEIAK ++ +++IIMDEPT AL+ E + L Sbjct: 123 DKLLAKLNLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182 Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 +I LK++ ++Y+SHR+ E+ +CD TV RDG+F+A +VA ++ ++ +MVGR + Sbjct: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLDEDLLIEMMVGRKL 242 Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301 E + + + PGAV LKV+ + + + +SF R GEI+G+AGL+GAGRT+L Sbjct: 243 EDQYPRLDKAPGAVRLKVDNLCGSG--------VENISFILRQGEILGVAGLMGAGRTEL 294 Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361 ++++GA P ++G V +D + + RSP+D + GI+ + EDRK+ G L S++ N+SL Sbjct: 295 MKVLYGALPRSSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLT 354 Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421 +L+ S G + + E+ V + + +K E AIG LSGGNQQKV + R + P Sbjct: 355 ALRYFSRGGGSLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRP 414 Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481 KVLI+DEPTRG+D+GAK E++Q+++ G++++++SSE+ EV+ +SDRI+V EG + Sbjct: 415 KVLILDEPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLG 474 Query: 482 ADLDAQTATEEGLMAYMATGTDRV 505 + + AT+E LMA +RV Sbjct: 475 GEFTREQATQEVLMAAAVGKLNRV 498 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: 616 Number of extensions: 35 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: 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