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_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 216 bits (549), Expect = 2e-60 Identities = 156/503 (31%), Positives = 257/503 (51%), Gaps = 29/503 (5%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 L+ + ++K F V A D + L + G V ALLGENGAGKSTL+ +L+ + DAGT+ Sbjct: 24 LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83 Query: 63 AGQVL---DPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119 G+ + RDA + GI +YQ F L ++VAEN+ LG+E ++ +R Sbjct: 84 DGKPVRFSSARDAI----EAGIGMVYQHFMLVESMTVAENVLLGQEGSFF--LNPKEMRN 137 Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179 Q L GL ++P A V L++ E+Q VEI K + ++R++I DEPTA L+ RE L Sbjct: 138 RVQELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHL 197 Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEV---ADMVRLM 236 + + + S++++SH+L EV A+ D ++R GR G+ ++ EV AD+ M Sbjct: 198 FEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRI--EGEFSESEVTSKADLACRM 255 Query: 237 VGRHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGA 296 VG+ V E + P G VL+V +T L ++F GE+V + G+ G Sbjct: 256 VGKEVLLEVDREAMPHGDAVLQVRNLTGIG--------LEDITFDLHQGEVVAVVGVAGN 307 Query: 297 GRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRR 356 G+ L I G + + K R + + + + +PEDR + ++ Sbjct: 308 GQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVD 367 Query: 357 NLSLPSLKALSALGQWVD-ERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGR 415 NL L + + A G W+D ++A RD E + K I+ +LSGGN QK +L R Sbjct: 368 NLLLTTRQGF-ARGPWLDKKKAARDTTELIK-KFDIRPGRIAALAWQLSGGNLQKSVLAR 425 Query: 416 AMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF 475 + P++++ ++PT+G+DI A +V L ++ +++++ +L E + ++DR+ V Sbjct: 426 ELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAREM-AGILLVTGDLNEALQLADRVAVI 484 Query: 476 REG---VIVADLDAQTATEEGLM 495 G + + D Q GLM Sbjct: 485 YRGRFMDVFSVSDKQKVNRIGLM 507 Score = 89.4 bits (220), Expect = 3e-22 Identities = 71/274 (25%), Positives = 131/274 (47%), Gaps = 15/274 (5%) Query: 242 EFERRKRRRPP-GAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300 + +R KR PP G ++ ++G+T ++ A +S G + L G GAG++ Sbjct: 9 QLDRSKRDVPPQGIPLVSIKGLTKRFGKVVAND---DISLNIYPGRVKALLGENGAGKST 65 Query: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360 L ++ G AG + +D KP+R S RDAI+AGI +V + + ++++ Sbjct: 66 LMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGIGMV---------YQHFMLVESMTV 116 Query: 361 PSLKALSALGQW-VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419 L G + ++ + R+ V+ + + + D + LS G +Q+V + + + Sbjct: 117 AENVLLGQEGSFFLNPKEMRNRVQELSVRYGLDI-DPAARVSDLSMGEKQRVEILKLLYR 175 Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479 +VLI DEPT + + + L +A+ G ++V IS +L EV+AV+D I + R+G Sbjct: 176 DSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGR 235 Query: 480 IVADLDAQTATEEGLMAYMATGTDRVAAPDMERL 513 I + T + +A G + + D E + Sbjct: 236 IEGEFSESEVTSKADLACRMVGKEVLLEVDREAM 269 Score = 41.2 bits (95), Expect = 9e-08 Identities = 53/232 (22%), Positives = 97/232 (41%), Gaps = 22/232 (9%) Query: 19 LDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRD------- 71 L+ + + GEV A++G G G+ L++ + T+ G+ RD Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRW--RDFYAKPSW 343 Query: 72 ----APLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLND 127 A + +LG+AT + NL L + R P +D + D L+ Sbjct: 344 KNSLAYIPEDRLGLATC-RNLNLVDNLLLTTRQGFARGP----WLDKKKAARDTTELIKK 398 Query: 128 LGL-PLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGL 186 + P A L+ Q +A+ + RLI+ ++PT L +++ + L Sbjct: 399 FDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHL--L 456 Query: 187 KARSVS-VIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237 AR ++ ++ V+ L E + DR V+ GRF+ V+D + + + LM+ Sbjct: 457 AAREMAGILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMM 508 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: 578 Number of extensions: 33 Number of successful extensions: 8 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: 514 Length adjustment: 35 Effective length of query: 480 Effective length of database: 479 Effective search space: 229920 Effective search space used: 229920 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 Apr 09 2024. 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