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 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 228 bits (581), Expect = 4e-64 Identities = 162/497 (32%), Positives = 249/497 (50%), Gaps = 20/497 (4%) Query: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQ--- 65 + KSF VRA + L + G + ALLGENGAGKSTL+ IL+ DAGT+ G Sbjct: 35 ICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVVDGVPTV 94 Query: 66 VLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALL 125 PRDA + GI +YQ F L ++VAEN+ LG+ P L + +R+R + AL Sbjct: 95 FASPRDA----LRAGIGMVYQHFMLVDSMTVAENVLLGQSPDML--LRPARMRDEVAALA 148 Query: 126 NDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAG 185 GL ++P A V GL++ E+Q VEI K + ++R++I+DEPTA L+ RE D+L + Sbjct: 149 ERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAMWR 208 Query: 186 LKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADV-EVADMVRLMVGRHVEFE 244 + + +++++SH+L EV + D ++R G V ADV + MVGR V + Sbjct: 209 MADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDVVLQ 268 Query: 245 RRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARL 304 +R P VL VE ++ A L VS R GEIV +AG+ G G+ +L Sbjct: 269 VDAKRLTPVDTVLSVEHLSGAG--------LSDVSLQVRRGEIVAIAGVAGNGQKELVEA 320 Query: 305 IFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLK 364 I G AG V + +P R + G+ +PEDR+ + N L + Sbjct: 321 ICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRN 380 Query: 365 ALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVL 424 A G ++D + V+ + ++ D LSGGN QK+++GR P+V+ Sbjct: 381 QF-AKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVI 439 Query: 425 IVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADL 484 + + PT+G+DI A EV L + V++++ +L E + ++DRI V G + Sbjct: 440 VAENPTQGLDISATEEVWGRLLEARSTS-GVLLVTGDLNEALELADRIAVMYRGRFIDVF 498 Query: 485 DAQTATEEGLMAYMATG 501 D + + M G Sbjct: 499 DKDDTAKVQAIGLMMAG 515 Score = 89.4 bits (220), Expect = 3e-22 Identities = 77/261 (29%), Positives = 127/261 (48%), Gaps = 16/261 (6%) Query: 256 VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGR 315 V++++G+ + ++ A ++ R G I L G GAG++ L ++ G AG Sbjct: 29 VVRLDGICKSFGKVRAN---HDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGT 85 Query: 316 VLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH-SIRRNLSL-PSLKALSALGQWV 373 ++VD P SPRDA++AGI +V Q +D ++ N+ L S L + Sbjct: 86 IVVDGVPTVFASPRDALRAGIGMV----YQHFMLVDSMTVAENVLLGQSPDMLLRPARMR 141 Query: 374 DERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGI 433 DE A L E Y + D +G LS G +Q+V + + + +VLI+DEPT + Sbjct: 142 DEVAA--LAERYGLAV-----DPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVL 194 Query: 434 DIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEG 493 ++ + + +AD G A+V IS +L EV+ V+D I + R G +V + + Sbjct: 195 TPRETDQLFEAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQT 254 Query: 494 LMAYMATGTDRVAAPDMERLT 514 ++A G D V D +RLT Sbjct: 255 VLANRMVGRDVVLQVDAKRLT 275 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: 42 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: 537 Length adjustment: 35 Effective length of query: 480 Effective length of database: 502 Effective search space: 240960 Effective search space used: 240960 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