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_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 388 bits (997), Expect = e-112 Identities = 223/496 (44%), Positives = 322/496 (64%), Gaps = 7/496 (1%) Query: 4 LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAAD-AGTVTF 62 L++ +S++FPGV+ALD+V+L + GEV AL GENGAGKSTL+KIL+ +A D GT+ Sbjct: 10 LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRADA 121 GQ + D+ R LG+ IYQE + L+V EN++L REPR RLGL+D R+ +A Sbjct: 70 EGQEVALADSHHART-LGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREA 128 Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 + +L + + ++P V L+V +QQM+EIAKA+ ++ IIMDEPTA+LS E L Sbjct: 129 REVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLG 188 Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 I+ L+ R+++V+Y+SHRL E+ + DR TV+RDGR V + +AD+ +VRLMV R + Sbjct: 189 IVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVAREL 248 Query: 242 -EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300 E + VL+V ++ R + P +R +SF GE++G+AGLVG+GRT+ Sbjct: 249 SELYGEPQSHASRDPVLEVRALSLKPVRKAEPR-IRDISFTLHRGEVLGIAGLVGSGRTE 307 Query: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360 + +IFG G V ++ KP+ +R+P DAI++GI V EDRK QG L ++R N SL Sbjct: 308 IMEMIFGMRA-CTGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRENFSL 366 Query: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420 L+ S Q+V ER+ + + L IK E + LSGGNQQK+++ + +A + Sbjct: 367 THLERYSPF-QFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVARS 425 Query: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480 PKVLIVDEPTRGID+GAKAEVH +++ LA G+ V+VISS+L EV+AVSDRI+ REG I Sbjct: 426 PKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREGRI 485 Query: 481 VADLDAQTATEEGLMA 496 +L A++E +MA Sbjct: 486 SGELSRAQASQEKVMA 501 Score = 80.9 bits (198), Expect = 1e-19 Identities = 65/254 (25%), Positives = 114/254 (44%), Gaps = 24/254 (9%) Query: 253 GAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGA-DPI 311 G L++ ++ P + A L +V+ R GE++ LAG GAG++ L +++ G P Sbjct: 6 GVPFLEMRNISRTFPGVKA---LDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPD 62 Query: 312 AAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQG-------CFLDHSIRRNLSLPSLK 364 G +LV+ + + L A G+ ++ ++ G FL R L L Sbjct: 63 PGGTILVEGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRP 122 Query: 365 ALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVL 424 + R R+++ T + D T + +LS G QQ + + +A+ K + Sbjct: 123 RMY--------REAREVLATIDMDI-----DPATRVSELSVGQQQMIEIAKALCARSKAI 169 Query: 425 IVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADL 484 I+DEPT + + + ++ L + +AVV IS L E+ ++DR+ V R+G V Sbjct: 170 IMDEPTASLSHHETSVLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTA 229 Query: 485 DAQTATEEGLMAYM 498 T E L+ M Sbjct: 230 PIADMTRETLVRLM 243 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: 672 Number of extensions: 35 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: 505 Length adjustment: 34 Effective length of query: 481 Effective length of database: 471 Effective search space: 226551 Effective search space used: 226551 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