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 WP_004129793.1 RHSP_RS32525 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_000359745.1:WP_004129793.1 Length = 527 Score = 365 bits (938), Expect = e-105 Identities = 208/482 (43%), Positives = 305/482 (63%), Gaps = 15/482 (3%) Query: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68 V KSF GV AL V L + G +HAL+GENGAGKSTL+KIL G++ G+ + Sbjct: 18 VRKSFGGVHALRGVSLTIQPGTIHALVGENGAGKSTLLKILQGVVTPTEGSIEVFGEHMS 77 Query: 69 PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLG-LVDWSRLRADAQALLND 127 +P ++LGI I+Q+ +L P L+VA+N++L REPRRL LVD R A A ++ Sbjct: 78 S-SSPENSRRLGIEMIFQDLSLIPTLTVAQNIFLNREPRRLSILVDERREIAQAAEIIGQ 136 Query: 128 LGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLK 187 L L ++P PV L+ + Q+ EIAKA+ +AR++I+DEPT++LS +E D L ++ L Sbjct: 137 LNLRVDPRTPVFELSPGQAQLTEIAKAIHQDARILILDEPTSSLSAQEADTLFGMLKKLT 196 Query: 188 ARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV---EFE 244 A +VIYVSHR+ E+ + D T++RDG+ V SG ++ + +V+ MVG+ V +++ Sbjct: 197 AAGTAVIYVSHRMSEIMTIADEITILRDGQNVTSGKTSEFTLDSIVQHMVGKRVTGFQYQ 256 Query: 245 RRKRRRPPGAVVLKVEGVTPAAPRLSAP-GYLRQVSFAARGGEIVGLAGLVGAGRTDLAR 303 R R G L V G LS P G VSF GEIVG+AGL+GAGR++LAR Sbjct: 257 ARAIDRS-GKPALSVRG-------LSGPSGKPSDVSFDVHRGEIVGIAGLMGAGRSELAR 308 Query: 304 LIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSL 363 L+FG D AG V + D + +SP DAI+AGI+LVPE R ++G ++HS+ NL LP + Sbjct: 309 LLFGVDKKTAGTVELGDTAVEFKSPSDAIKAGIVLVPESRHEEGLVVEHSVGDNLGLPQI 368 Query: 364 KALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKV 423 L G ++D R E L ++LRIK A+ + LSGGNQQK+++ + +A+ P V Sbjct: 369 GQL-VRGPFIDRRREGTLTSDLIKQLRIKTPSADNKVRNLSGGNQQKIVIAKWLAIDPSV 427 Query: 424 LIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVAD 483 +I+DEPT G+DIG+KAE+ +++ +A G +V+VISSE AE++A SDRI+V G + + Sbjct: 428 VILDEPTAGVDIGSKAEIVELIRSVASSGKSVIVISSEPAELLATSDRILVMNNGRLARE 487 Query: 484 LD 485 ++ Sbjct: 488 IE 489 Score = 77.0 bits (188), Expect = 2e-18 Identities = 62/231 (26%), Positives = 106/231 (45%), Gaps = 20/231 (8%) Query: 275 LRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQA 334 LR VS + G I L G GAG++ L +++ G G + V + + SP ++ + Sbjct: 28 LRGVSLTIQPGTIHALVGENGAGKSTLLKILQGVVTPTEGSIEVFGEHMSSSSPENSRRL 87 Query: 335 GIMLVPEDRK-------QQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQ 387 GI ++ +D Q FL+ RR LS L VDER E Sbjct: 88 GIEMIFQDLSLIPTLTVAQNIFLNREPRR---------LSIL---VDERREIAQAAEIIG 135 Query: 388 KLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSD 447 +L +++ D T + +LS G Q + +A+ ++LI+DEPT + + +L Sbjct: 136 QLNLRV-DPRTPVFELSPGQAQLTEIAKAIHQDARILILDEPTSSLSAQEADTLFGMLKK 194 Query: 448 LADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYM 498 L G AV+ +S ++E+M ++D I + R+G V T + ++ +M Sbjct: 195 LTAAGTAVIYVSHRMSEIMTIADEITILRDGQNVTSGKTSEFTLDSIVQHM 245 Score = 65.9 bits (159), Expect = 4e-15 Identities = 57/206 (27%), Positives = 96/206 (46%), Gaps = 7/206 (3%) Query: 29 GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIYQ-- 86 GE+ + G GAG+S L ++L AGTV ++ + +P + GI + + Sbjct: 290 GEIVGIAGLMGAGRSELARLLFGVDKKTAGTVELGDTAVEFK-SPSDAIKAGIVLVPESR 348 Query: 87 -EFNLFPELSVAENMYLGREPR--RLGLVDWSRLRADAQALLNDLGLPL-NPDAPVRGLT 142 E L E SV +N+ L + + R +D R L+ L + + D VR L+ Sbjct: 349 HEEGLVVEHSVGDNLGLPQIGQLVRGPFIDRRREGTLTSDLIKQLRIKTPSADNKVRNLS 408 Query: 143 VAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHRLGE 202 QQ + IAK + ++ ++I+DEPTA + + +I + + SVI +S E Sbjct: 409 GGNQQKIVIAKWLAIDPSVVILDEPTAGVDIGSKAEIVELIRSVASSGKSVIVISSEPAE 468 Query: 203 VKAMCDRYTVMRDGRFVASGDVADVE 228 + A DR VM +GR + ++E Sbjct: 469 LLATSDRILVMNNGRLAREIERDEIE 494 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: 658 Number of extensions: 38 Number of successful extensions: 9 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: 527 Length adjustment: 35 Effective length of query: 480 Effective length of database: 492 Effective search space: 236160 Effective search space used: 236160 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 24 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