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 GFF2770 PGA1_c28130 ABC transporter, ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Phaeo:GFF2770 Length = 505 Score = 269 bits (687), Expect = 2e-76 Identities = 177/507 (34%), Positives = 274/507 (54%), Gaps = 16/507 (3%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL + ++K++PGV A D V +G GEVHALLGENGAGKSTL+K++ D+G + Sbjct: 5 LLSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKMLL 64 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGRE-PRRLGLVDWSRLRADA 121 G+ P + P + + GIA ++Q F+LF L+VAEN+ LG E P L L Sbjct: 65 HGEPYTPGE-PRQARADGIAMVFQHFSLFDALNVAENIALGMETPPAL-----RDLATQI 118 Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 + + GLPL+P V L+ E+Q VEI + + + +L+IMDEPT+ L+ +EV+ L Sbjct: 119 RKVSETYGLPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFQ 178 Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 + L++ S++Y+SH+L E++ +CD T++R G+ V ++ DM +MVG + Sbjct: 179 TLQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARDMAEMMVGTAL 238 Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPG-YLRQVSFAARGGEIVGLAGLVGAGRTD 300 + R R G V L + G++ AP SA G L+ V R GEI+G+ G+ G G+ + Sbjct: 239 QTPERS-GRALGDVALDISGLSVPAP--SAFGTALKNVHMTVRKGEILGVGGVAGNGQDE 295 Query: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRN--L 358 L ++ G AA V +D P+ P + GI+ PE+R D S+ N L Sbjct: 296 LLGVLSGETTTAADAVTLDGAPIGNLGPVARRRLGILAAPEERLGHAAAPDMSLTENAML 355 Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418 + + + L++ G ++ ++ E + ++ E A LSGGN QK ++GR + Sbjct: 356 TAATREGLASRG-FLKWGLAQEFAEKVIKSFDVRTPGPENAARSLSGGNLQKFVIGREVL 414 Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREG 478 P VL+V++PT G+D A A + Q L DLA G AV+ IS +L E+M ++D EG Sbjct: 415 QRPDVLVVNQPTWGVDAAAAAAIRQSLLDLAAGGTAVICISQDLDELMEIADSFAALNEG 474 Query: 479 VIVADLDAQ--TATEEGLMAYMATGTD 503 + A + E GLM A G + Sbjct: 475 RLSAPRPTAGLSVDEIGLMMGGAHGME 501 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: 618 Number of extensions: 40 Number of successful extensions: 9 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: 505 Length adjustment: 34 Effective length of query: 481 Effective length of database: 471 Effective search space: 226551 Effective search space used: 226551 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