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_085124750.1 B9O00_RS21270 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_900177295.1:WP_085124750.1 Length = 500 Score = 379 bits (973), Expect = e-109 Identities = 222/499 (44%), Positives = 313/499 (62%), Gaps = 18/499 (3%) Query: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68 +SK+F GV ALD+VD + GEVHALLGENGAGKSTLIKI++ A AADAG + G+ + Sbjct: 14 ISKAFAGVPALDRVDFTLHPGEVHALLGENGAGKSTLIKIMTGALAADAGEMRLDGRAVA 73 Query: 69 PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128 R LGI+T+YQE NL P LSVA N+ LGREPRR GL+ W R A+A L L Sbjct: 74 VGSTAEARA-LGISTVYQEVNLVPTLSVARNVTLGREPRRFGLISWRAAREKARARLKRL 132 Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188 L ++ + + VA QQ+V IA+A+ ++R++++DEPTA+L +E L I+ LKA Sbjct: 133 SLEIDVERALGSFPVAVQQLVAIARALEEDSRVLVLDEPTASLDAQETRLLFRILRDLKA 192 Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE-FERRK 247 + ++V+++SH L +V + DR +V+R+GR V S A + +++ LM+GR +E E+R Sbjct: 193 QGMAVVFISHFLDQVYEISDRISVLRNGRLVGSAATAALPQRELITLMLGRELERVEQRA 252 Query: 248 RRRP--PGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLI 305 P GA VL AA +L ++ R GE +GLAGL+G+GRT+ A+LI Sbjct: 253 AAAPKAAGAPVL-------AAEKLGRRRWIEPFDLVLRAGEAIGLAGLLGSGRTETAKLI 305 Query: 306 FGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKA 365 FGA +GR+ +D PL SPR A++ GI PEDRK +G LD S+R N+ L A Sbjct: 306 FGAVRADSGRLTLDGAPLGHASPRRALRRGIAFCPEDRKAEGLVLDLSVRENI----LLA 361 Query: 366 LSALGQW---VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422 L W + +R L E + L I +DAE +G+LSGGNQQKV+L RA+A P+ Sbjct: 362 LQTKRGWLRPLPRDEQRRLAEAMIEALGIATSDAEKPVGQLSGGNQQKVVLARALASKPR 421 Query: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482 VL++DEPTRGID+GA AE+ ++ L G+A++V SSEL E++AVSDR+ V R+ IV Sbjct: 422 VLVLDEPTRGIDVGAHAEIVALVRRLCAEGLALLVASSELDEIVAVSDRVAVLRDRRIVG 481 Query: 483 DLDAQTATEEGLMAYMATG 501 ++ T E ++ +A G Sbjct: 482 EIAGAEITRETIIELIAGG 500 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: 659 Number of extensions: 39 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 515 Length of database: 500 Length adjustment: 34 Effective length of query: 481 Effective length of database: 466 Effective search space: 224146 Effective search space used: 224146 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