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 H281DRAFT_01223 H281DRAFT_01223 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Burk376:H281DRAFT_01223 Length = 509 Score = 434 bits (1116), Expect = e-126 Identities = 243/494 (49%), Positives = 327/494 (66%), Gaps = 10/494 (2%) Query: 4 LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63 L++ SKSF VRAL DL + GEVHALLGENGAGKSTL+KIL+ H D+G + Sbjct: 11 LELRHASKSFGRVRALSDGDLSLWPGEVHALLGENGAGKSTLVKILAGVHQPDSGELLVD 70 Query: 64 GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREP-RRLGLVDWSRLRADAQ 122 G V P + + G+A IYQE LF +LS+AEN+++GR+P R G + + +R + Sbjct: 71 G-VARRFATPAQARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRFGRIQYDAMRREVD 129 Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 LL LG+ L D VRGL++A+QQ++EIAKA++LNA ++IMDEPTAALS EV+RL AI Sbjct: 130 GLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLTEVERLFAI 189 Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242 + L+ R V++++++HRL EV A+ R T+MRDG V G AD+ +V MVGR +E Sbjct: 190 VRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGMTADLNTDAIVSKMVGRDLE 249 Query: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLA 302 K RPPG L V G+T G + +SF R GEIV LAGLVGAGR+++A Sbjct: 250 TFYPKAERPPGEARLSVRGLTRV-------GVFKDISFDVRAGEIVALAGLVGAGRSEVA 302 Query: 303 RLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPS 362 R IFG DP+ AG++ + KPL SP A++AG+ LVPEDR+QQG L+ SI RN S+ Sbjct: 303 RAIFGIDPLDAGQIQIGGKPLADGSPAAAVRAGLALVPEDRRQQGLALELSIARNASMTV 362 Query: 363 LKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422 L L G + R+E L + +LR+K D +G LSGGNQQKV+LG+ +A PK Sbjct: 363 LGRLVRHG-LITTRSETQLANQWGTRLRLKAGDPNAPVGMLSGGNQQKVVLGKWLATNPK 421 Query: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482 VLI+DEPTRGID+GAKAEV+ L++L G+AV++ISSEL EV+ ++DR++V EG I A Sbjct: 422 VLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISA 481 Query: 483 DLDAQTATEEGLMA 496 D+ A EE +MA Sbjct: 482 DIARAEADEERIMA 495 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: 753 Number of extensions: 43 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 515 Length of database: 509 Length adjustment: 35 Effective length of query: 480 Effective length of database: 474 Effective search space: 227520 Effective search space used: 227520 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