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_01057 H281DRAFT_01057 monosaccharide ABC transporter ATP-binding protein, CUT2 family (TC 3.A.1.2.-)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Burk376:H281DRAFT_01057 Length = 517 Score = 387 bits (994), Expect = e-112 Identities = 222/505 (43%), Positives = 321/505 (63%), Gaps = 12/505 (2%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL+V +++K FPGV++LDQV L V GE+HAL+GENGAGKSTL KI++ +A D+G + F Sbjct: 12 LLEVIRITKEFPGVKSLDQVSLGVRAGEIHALVGENGAGKSTLTKIMAGVYAPDSGEIRF 71 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRADA 121 AGQ L + A ++ GI I+QE LFP+ +VAEN++ G EPR R+G++D R+ DA Sbjct: 72 AGQPLQWKSAADAKRH-GIHVIHQELVLFPQSTVAENIFAGAEPRTRIGVLDHGRMNRDA 130 Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 QALL +LG+ L+ V L+VA+QQMVEIAKAM R++I+DEPTA ++G+EV L A Sbjct: 131 QALLGELGVRLDSRERVGNLSVADQQMVEIAKAMAGETRVLILDEPTAVIAGKEVQLLFA 190 Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 + L+A+ V+++Y+SHRL E+ +CDR TVM+DGR VA+ VA+ +VRLMVGR + Sbjct: 191 RVRALRAKGVAIVYISHRLDEIFELCDRVTVMKDGRKVATQSVANTTRDQLVRLMVGREM 250 Query: 242 E--FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRT 299 + + + P VL+V G L + S R GEIVG+AG+VG+GRT Sbjct: 251 KDIYPDKPILAPGVPNVLEVNG-------LCVGNRVVDASLTVRAGEIVGIAGMVGSGRT 303 Query: 300 DLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359 +LA IFGA G V + +PR AI+ G+ V EDRK QG + + +N++ Sbjct: 304 ELAAGIFGALRAHRGTVDIGGTRRTRMTPRTAIRLGLGFVTEDRKSQGLLMLLDVAQNVT 363 Query: 360 LPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419 +L +S G + ER + + RI A + LSGGNQQKVL+ R + + Sbjct: 364 ATTLAQVSRFG-LMRPALERAAAQAAINEYRIAGAHPAGGVATLSGGNQQKVLISRWVRV 422 Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479 +VLI+DEPTRG+D+GAKAE+++V+ +L G+ +++ISSEL EV+ +SDR++V REG Sbjct: 423 CKRVLILDEPTRGVDVGAKAEIYRVMRELTSRGLGILMISSELQEVIGMSDRVLVMREGR 482 Query: 480 IVADLDAQTATEEGLMAYMATGTDR 504 I ++ + TE +M T T + Sbjct: 483 INGEVSGEQMTEHDIMRLATTETSQ 507 Score = 85.5 bits (210), Expect = 4e-21 Identities = 75/257 (29%), Positives = 125/257 (48%), Gaps = 15/257 (5%) Query: 256 VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGR 315 +L+V +T P + + L QVS R GEI L G GAG++ L +++ G +G Sbjct: 12 LLEVIRITKEFPGVKS---LDQVSLGVRAGEIHALVGENGAGKSTLTKIMAGVYAPDSGE 68 Query: 316 VLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDE 375 + +PL+ +S DA + GI ++ ++ F ++ N+ + + +G Sbjct: 69 IRFAGQPLQWKSAADAKRHGIHVIHQELV---LFPQSTVAENI-FAGAEPRTRIGVLDHG 124 Query: 376 RAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDI 435 R RD + +L +++ D+ +G LS +QQ V + +AMA +VLI+DEPT I Sbjct: 125 RMNRD-AQALLGELGVRL-DSRERVGNLSVADQQMVEIAKAMAGETRVLILDEPTAVI-- 180 Query: 436 GAKAEVHQVLSDLADL---GVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEE 492 A EV + + + L GVA+V IS L E+ + DR+ V ++G VA T + Sbjct: 181 -AGKEVQLLFARVRALRAKGVAIVYISHRLDEIFELCDRVTVMKDGRKVATQSVANTTRD 239 Query: 493 GLMAYMATGTDRVAAPD 509 L+ M + PD Sbjct: 240 QLVRLMVGREMKDIYPD 256 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: 700 Number of extensions: 39 Number of successful extensions: 10 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: 517 Length adjustment: 35 Effective length of query: 480 Effective length of database: 482 Effective search space: 231360 Effective search space used: 231360 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