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 3609577 Dshi_2961 ABC transporter related (RefSeq)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Dino:3609577 Length = 511 Score = 281 bits (719), Expect = 4e-80 Identities = 182/511 (35%), Positives = 279/511 (54%), Gaps = 16/511 (3%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL V+ ++K++PGV A D V + GEVHALLGENGAGKSTL+K++ D+GT+TF Sbjct: 4 LLRVAGLTKAYPGVVANDDVSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTF 63 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGRE--PRRLGLVDWSRLRAD 120 G P + P + G+A ++Q F+LF L+VAEN+ LG E P+ L +R+ Sbjct: 64 GGVPFAPPE-PRAARSAGVAMVFQHFSLFEALTVAENIALGMEDPPKMRDLA--ARITQV 120 Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180 +QA GLPL+P V L+ E+Q VEI + + +L+IMDEPT+ L+ +EVD L Sbjct: 121 SQAY----GLPLDPSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQEVDILF 176 Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRH 240 A + L+ +++Y+SH+L E++A+CD T++R G+ VA+ D + ++ +MVG+ Sbjct: 177 ATLRKLRDEGTAILYISHKLEEIRALCDSATILRLGKVVATCDPREKSARELAEMMVGKT 236 Query: 241 VEFERRKRRRPPGAVVLKVEGVT-PAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRT 299 ++ + + GA VL++ G++ PA P LR +S R GE++G+ G+ G G+ Sbjct: 237 LQ-QTKSAGNAFGAPVLELRGLSQPATTPFGTP--LRDISLEVRAGEVLGIGGVAGNGQD 293 Query: 300 DLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359 +L I G + A + + P+ P Q G++ PE+R D S+ N Sbjct: 294 ELLSAISG-ERRAEDAIFLHGTPISKIGPAARRQLGVLSGPEERLGHAAAPDMSLTENAL 352 Query: 360 LP-SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418 L S++ ++D R E + ++ E A LSGGN QK ++GR + Sbjct: 353 LTGSVREKLTRNGFLDWAKTRAFAERIIETFDVRTPGPEAAARALSGGNLQKFVIGREVL 412 Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREG 478 P+VLIV++PT G+D A A + Q L DLA G AVVVIS +L E+M +SD G Sbjct: 413 QRPEVLIVNQPTWGVDASAAAAIRQALLDLAAGGTAVVVISQDLDELMEISDTFAALNGG 472 Query: 479 VIVADLDAQTATEEGLMAYMATGTDRVAAPD 509 + + A T E + M G + PD Sbjct: 473 RLSGKVPAAGLTVEQI-GLMLGGAHDMDLPD 502 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: 630 Number of extensions: 32 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: 511 Length adjustment: 35 Effective length of query: 480 Effective length of database: 476 Effective search space: 228480 Effective search space used: 228480 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