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 BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__BFirm:BPHYT_RS28215 Length = 509 Score = 424 bits (1089), Expect = e-123 Identities = 236/493 (47%), Positives = 321/493 (65%), Gaps = 10/493 (2%) Query: 4 LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63 L++ SKSF VRAL DL + GEVHALLGENGAGKST++KIL+ H D G + Sbjct: 11 LELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDTGELVVD 70 Query: 64 GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREP-RRLGLVDWSRLRADAQ 122 G+ P + G+A IYQE LF +LS+AEN+++GR+P R+G + + +R + Sbjct: 71 GEARRFA-TPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQYDAMRREVD 129 Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 LL LG+ L D VRGL++A+QQ++EIAKA++LNA ++IMDEPTAALS EV+RL I Sbjct: 130 GLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLFTI 189 Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242 + L+ R V++++++HRL EV A+ R T+MRDG V G D+ +V MVGR +E Sbjct: 190 VRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIVAKMVGRDLE 249 Query: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLA 302 K RPPG V L V G+T G + +SF R GEIV LAGLVGAGR+++A Sbjct: 250 TFYPKAERPPGEVRLSVRGLTRV-------GVFKDISFDVRAGEIVALAGLVGAGRSEVA 302 Query: 303 RLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPS 362 R IFG DP+ +G + + K L P A++AG+ LVPEDR+QQG L+ SI RN S+ Sbjct: 303 RAIFGIDPLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASMTV 362 Query: 363 LKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422 L L G + R+E L + +LR+K D +G LSGGNQQKV+LG+ +A PK Sbjct: 363 LGRLVKHG-LISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPK 421 Query: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482 VLI+DEPTRGID+GAKAEV+ L++L G+AV++ISSEL EV+ ++DR++V EG I A Sbjct: 422 VLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISA 481 Query: 483 DLDAQTATEEGLM 495 D+ A EE +M Sbjct: 482 DIARADADEERIM 494 Score = 80.9 bits (198), Expect = 1e-19 Identities = 68/259 (26%), Positives = 122/259 (47%), Gaps = 15/259 (5%) Query: 263 TPAAPRLSAP------GYLRQVS---FAARGGEIVGLAGLVGAGRTDLARLIFGADPIAA 313 T A PRL G +R +S A GE+ L G GAG++ + +++ G Sbjct: 5 TSAVPRLELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDT 64 Query: 314 GRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWV 373 G ++VD + R +P +A AG+ ++ ++ F D SI N+ + + + +G+ + Sbjct: 65 GELVVDGEARRFATPAEARDAGLAVIYQEPT---LFFDLSIAENIFM-GRQPVDRIGR-I 119 Query: 374 DERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGI 433 A R V+ L + + A+ + LS +QQ + + +A++L VLI+DEPT + Sbjct: 120 QYDAMRREVDGLLASLGVDLR-ADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAAL 178 Query: 434 DIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEG 493 + + ++ L + VA++ I+ L EV A++ R+ + R+G V D E Sbjct: 179 SLPEVERLFTIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEA 238 Query: 494 LMAYMATGTDRVAAPDMER 512 ++A M P ER Sbjct: 239 IVAKMVGRDLETFYPKAER 257 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: 762 Number of extensions: 47 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: 509 Length adjustment: 35 Effective length of query: 480 Effective length of database: 474 Effective search space: 227520 Effective search space used: 227520 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