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 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 231 bits (588), Expect = 6e-65 Identities = 161/498 (32%), Positives = 255/498 (51%), Gaps = 23/498 (4%) Query: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68 + KSF VRA + L + G + ALLGENGAGKSTL+ ILS A D G + G+ + Sbjct: 40 IGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVR 99 Query: 69 PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128 R +P + GI +YQ F L ++VAEN+ LG+ L V SR+ A+ A Sbjct: 100 FR-SPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSGAWLSPVHMSRVVAELAARY--- 155 Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188 GL ++P A V L++ E+Q VEI K + ++R++I+DEPTA L+ E ++L + + Sbjct: 156 GLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAE 215 Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVE-VADMVRLMVGRHVEFERRK 247 +++++SH++ EV A+ D ++R G V ++V A++ MVGR V E Sbjct: 216 NGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVILEVAA 275 Query: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307 PG VL V+G+ A L+ +SF R GE+ +AG+ G G+ +L + G Sbjct: 276 EPLEPGDRVLHVDGL--------AGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVECVTG 327 Query: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367 A G V + P R + Q G+ +PEDR+ L + N L + + Sbjct: 328 LRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLL-TARGCF 386 Query: 368 ALGQWVDER----AERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKV 423 G ++D + A RD++ Y ++ AE LSGGN QK+++GR P + Sbjct: 387 TRGPFLDRKSADAAARDILAEY----NVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSL 442 Query: 424 LIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVAD 483 ++ + PT+G+DI A EV L ++ V+++S +L EV+A++DR+ V G + Sbjct: 443 IVAENPTQGLDIAATEEVWARLLEVRS-HAGVLLVSGDLNEVLALADRVAVMYRGCFIGL 501 Query: 484 LDAQTATEEGLMAYMATG 501 LD + + M G Sbjct: 502 LDRSDTNKVDAIGLMMAG 519 Score = 82.8 bits (203), Expect = 3e-20 Identities = 64/234 (27%), Positives = 110/234 (47%), Gaps = 21/234 (8%) Query: 285 GEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRK 344 G I L G GAG++ L ++ G G + VD + +R RSP+DA++AGI +V Sbjct: 60 GRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGIGMV----- 114 Query: 345 QQGCFLDHSIRRNLSLPSLKALSALGQWVD----ERAERDLVETYRQKLRIKMADAETAI 400 + + ++++ L G W+ R +L Y + D + Sbjct: 115 ----YQHFMLVDSMTVAENVLLGQSGAWLSPVHMSRVVAELAARYGLDI-----DPAARV 165 Query: 401 GKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISS 460 LS G +Q+V + + + +VLI+DEPT + G ++ + L +A+ G A+V IS Sbjct: 166 CDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENGKAIVFISH 225 Query: 461 ELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYMATGTD---RVAAPDME 511 ++ EV+A++D I + R G +V + E +A G + VAA +E Sbjct: 226 KMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVILEVAAEPLE 279 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: 694 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: 524 Length adjustment: 35 Effective length of query: 480 Effective length of database: 489 Effective search space: 234720 Effective search space used: 234720 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