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_022529220.1 L248_RS05900 ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_000469325.1:WP_022529220.1 Length = 516 Score = 265 bits (676), Expect = 4e-75 Identities = 168/502 (33%), Positives = 265/502 (52%), Gaps = 7/502 (1%) Query: 4 LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63 ++V ++K F A D + + + GEVH LLGENGAGK+T++ +LS +G + Sbjct: 8 IEVRGLTKRFGDFVANDHISMQIRSGEVHGLLGENGAGKTTMMNMLSGILQPTSGEILVH 67 Query: 64 GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLG-REPRRLGLVDWSRLRADAQ 122 GQ + A +LGI ++Q F L +V EN+ LG E + LG+++ R Sbjct: 68 GQPVHLASAK-DATRLGIGMVHQHFMLVENFTVLENIMLGVEETKGLGVLNRRAARDKVM 126 Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 AL GL ++PDA V ++V QQ EI K + NA ++I DEPTA L+ +E+ L AI Sbjct: 127 ALSKQYGLAVDPDAKVGDISVGMQQRAEILKVLYRNADILIFDEPTAVLTPQEIKELLAI 186 Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242 L +VI +SH+L E++A+ T++R G+ + + D + LMVGRHV Sbjct: 187 FQRLAQEGKAVILISHKLNELQAVAKVTTIIRRGKVIDTVDTKATSTEKLAELMVGRHVT 246 Query: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLA 302 F+R + P G +LK+ + + + GGEIVGLAG+ G G+++L Sbjct: 247 FQRDRVPMPAGPEILKISHLQVVDNQKVT--RVHDFDLTIHGGEIVGLAGIDGNGQSELV 304 Query: 303 RLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP- 361 R I G P A G+V + + +PR ++G+ +PEDR++ G L S+ N+SL Sbjct: 305 RAITGLMPTAGGQVTIAGQDRTGATPRQITRSGVGHIPEDRQRYGLILPMSLVDNMSLQV 364 Query: 362 -SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420 ++ S G ++++A E + ++ + G LSGGNQQK+++ R ++ Sbjct: 365 YTVAPYSHHGV-LNQKAMVTTTEQLLDQYDVRHSSIMEPAGALSGGNQQKLIIARELSRE 423 Query: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480 P++LI PTRG+D+GA +H L G A+++IS EL E+ +SDR+ V +G I Sbjct: 424 PQLLIAVNPTRGLDVGAIEFIHSQLLAARAAGHAILLISYELDEIRQLSDRVAVIHQGTI 483 Query: 481 VADLDAQTATEEGLMAYMATGT 502 V +E + MA T Sbjct: 484 VGQAKTSDLSESEIGLLMAGET 505 Score = 71.6 bits (174), Expect = 6e-17 Identities = 57/235 (24%), Positives = 108/235 (45%), Gaps = 11/235 (4%) Query: 16 VRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDA-PL 74 V + DL + GE+ L G +G G+S L++ ++ G VT AGQ D A P Sbjct: 274 VTRVHDFDLTIHGGEIVGLAGIDGNGQSELVRAITGLMPTAGGQVTIAGQ--DRTGATPR 331 Query: 75 RRQQLGIATI---YQEFNLFPELSVAENM----YLGREPRRLGLVDWSRLRADAQALLND 127 + + G+ I Q + L +S+ +NM Y G+++ + + LL+ Sbjct: 332 QITRSGVGHIPEDRQRYGLILPMSLVDNMSLQVYTVAPYSHHGVLNQKAMVTTTEQLLDQ 391 Query: 128 LGLPLNPDA-PVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGL 186 + + P L+ QQ + IA+ ++ +L+I PT L ++ +H+ + Sbjct: 392 YDVRHSSIMEPAGALSGGNQQKLIIARELSREPQLLIAVNPTRGLDVGAIEFIHSQLLAA 451 Query: 187 KARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 +A +++ +S+ L E++ + DR V+ G V +D+ +++ LM G V Sbjct: 452 RAAGHAILLISYELDEIRQLSDRVAVIHQGTIVGQAKTSDLSESEIGLLMAGETV 506 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: 596 Number of extensions: 32 Number of successful extensions: 9 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: 516 Length adjustment: 35 Effective length of query: 480 Effective length of database: 481 Effective search space: 230880 Effective search space used: 230880 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