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 AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23205 Length = 517 Score = 378 bits (970), Expect = e-109 Identities = 214/494 (43%), Positives = 309/494 (62%), Gaps = 10/494 (2%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL+V VSK FPGV AL V L V G V AL+GENGAGKSTL+KI++ + DAG + Sbjct: 26 LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR-LGLVDWSRLRADA 121 G+ + D PL Q GIA I+QE NL P +S+AEN+++GRE L +VD + Sbjct: 86 RGKPVT-FDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCT 144 Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 LL L + L+P+ V L++AE+QMVEIAKA++ ++ ++IMDEPT+A++ EV L + Sbjct: 145 ARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFS 204 Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 IIA LK++ +IY++H++ EV A+ D V RDG ++ ++ ++ +MVGR + Sbjct: 205 IIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 264 Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301 R +P G +VL V LS G + VSF GEI+G+AGL+G+GRT++ Sbjct: 265 SQLFPVREQPIGELVLSVRD-------LSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNV 317 Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361 A IFG P G + +D +P+R+ P AI+ G L+ EDRK G F S+ N+ + Sbjct: 318 AEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMA 377 Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421 L G ++ ++A R L E +KLR+K E I LSGGNQQK LL R + P Sbjct: 378 VLPHYVGNG-FIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNP 436 Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481 ++LI+DEPTRGID+GAKAE+++++S LA G+AV++ISSEL EV+ +SDR++V EG ++ Sbjct: 437 RILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLM 496 Query: 482 ADLDAQTATEEGLM 495 LD AT+E +M Sbjct: 497 GTLDRSEATQERVM 510 Score = 95.1 bits (235), Expect = 5e-24 Identities = 70/244 (28%), Positives = 123/244 (50%), Gaps = 11/244 (4%) Query: 256 VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGR 315 +L+V V+ P + A L V R G ++ L G GAG++ L ++I G AG Sbjct: 26 LLEVVNVSKGFPGVVA---LSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGE 82 Query: 316 VLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH-SIRRNLSLPSLKALSALGQWVD 374 + + KP+ +P A+QAGI ++ ++ + H SI N+ + + L+ L VD Sbjct: 83 LRLRGKPVTFDTPLAALQAGIAMIHQELN----LMPHMSIAENIWI-GREQLNGL-HMVD 136 Query: 375 ERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGID 434 ++LRIK+ D E +G LS +Q V + +A++ +LI+DEPT I Sbjct: 137 HGEMHRCTARLLERLRIKL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAIT 195 Query: 435 IGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGL 494 A + +++DL G ++ I+ ++ EV A++D + VFR+G + A + + L Sbjct: 196 ETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSL 255 Query: 495 MAYM 498 ++ M Sbjct: 256 ISMM 259 Score = 70.1 bits (170), Expect = 2e-16 Identities = 58/220 (26%), Positives = 102/220 (46%), Gaps = 15/220 (6%) Query: 29 GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIYQE- 87 GE+ + G G+G++ + + + + G + GQ + D P + G A + ++ Sbjct: 301 GEILGIAGLMGSGRTNVAEAIFGVTPSTGGEIRLDGQPVRISD-PHMAIEKGFALLTEDR 359 Query: 88 --FNLFPELSVAENMYLGREPRRLG--LVDWSRLRADAQALLNDLGLPLNPDAP-----V 138 LFP LSV ENM + P +G + LRA L D+ L P + Sbjct: 360 KLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRA----LCEDMCKKLRVKTPSLEQCI 415 Query: 139 RGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSH 198 L+ QQ +A+ + N R++I+DEPT + ++ +I+ L + ++VI +S Sbjct: 416 DTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISS 475 Query: 199 RLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238 L EV M DR VM +G + + D ++ +++L G Sbjct: 476 ELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 515 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: 661 Number of extensions: 36 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 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