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_085126169.1 B9O00_RS28465 multiple monosaccharide ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_900177295.1:WP_085126169.1 Length = 509 Score = 350 bits (897), Expect = e-101 Identities = 205/500 (41%), Positives = 307/500 (61%), Gaps = 8/500 (1%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAAD--AGTV 60 +L++ ++K+FPGV ALD V+L V GE+HAL GENGAGKSTL+KILS + G + Sbjct: 4 ILEMRDITKTFPGVVALDNVNLQVRQGEIHALAGENGAGKSTLMKILSGVYPYGDYQGDI 63 Query: 61 TFAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRAD 120 + G+V R + GI I+QE L PELS+AEN++LG E R G++DW Sbjct: 64 VYEGEVKKFRGIADSEAE-GIVIIHQELALVPELSIAENIFLGNEIARFGVIDWHATNEL 122 Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180 A L +GL +P V+ L + +QQ+VEIAKA++ +L+I+DEPT++L+ ++ L Sbjct: 123 AADHLKWVGLKESPRTKVQDLGLGKQQLVEIAKALSKEVKLLILDEPTSSLNEQDSAALL 182 Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVA--DMVRLMVG 238 ++A + R +S I +SH+L E+ + D TV+RDG V++ D A ++ D++R MVG Sbjct: 183 KLLAEFRERGISSILISHKLNEISQVADSITVLRDGTTVSTLDCAAASISEDDIIRDMVG 242 Query: 239 RHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGR 298 R + R G ++L+VE + P+ ++ SF R GE+VGLAGL+GAGR Sbjct: 243 RSLSDRFPPRHPKIGELLLEVEHWSVRHPQHLDRRVVKDASFTVRRGEVVGLAGLMGAGR 302 Query: 299 TDLARLIFGADPIA--AGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRR 356 T+LA +FG A AG V + K + + + AI AG+ EDRK G LD ++ Sbjct: 303 TELAMSLFGRSYGADIAGEVRIRGKAVDVSTVERAIAAGLCYATEDRKSYGLVLDDIVKH 362 Query: 357 NLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRA 416 NL+L +L+ + A G +D E + E YR++L IK + LSGGNQQKV+LG+ Sbjct: 363 NLTLANLEGV-ANGPVIDHAREIRVAEDYRRRLNIKTSSIAQKTLNLSGGNQQKVVLGKW 421 Query: 417 MALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFR 476 + P+VLI+DEPTRGID+GAK E++ +++DLA G ++VISSE+ E++ + DRI V Sbjct: 422 LFADPEVLILDEPTRGIDVGAKYEIYSIITDLAAAGKGILVISSEMPELLGICDRIYVMN 481 Query: 477 EGVIVADLDAQTATEEGLMA 496 G +V +L A A++E +M+ Sbjct: 482 AGRLVGELPAAEASQEKIMS 501 Score = 53.9 bits (128), Expect = 1e-11 Identities = 56/229 (24%), Positives = 100/229 (43%), Gaps = 9/229 (3%) Query: 17 RALDQVDLVVGVGEVHALLGENGAGKSTL-IKILSAAHAAD-AGTVTFAGQVLDPRDAPL 74 R + V GEV L G GAG++ L + + ++ AD AG V G+ +D Sbjct: 277 RVVKDASFTVRRGEVVGLAGLMGAGRTELAMSLFGRSYGADIAGEVRIRGKAVDVSTVE- 335 Query: 75 RRQQLGIATIYQE---FNLFPELSVAENMYLGR-EPRRLG-LVDWSRLRADAQALLNDLG 129 R G+ ++ + L + V N+ L E G ++D +R A+ L Sbjct: 336 RAIAAGLCYATEDRKSYGLVLDDIVKHNLTLANLEGVANGPVIDHAREIRVAEDYRRRLN 395 Query: 130 LPLNPDAP-VRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188 + + A L+ QQ V + K + + ++I+DEPT + +++II L A Sbjct: 396 IKTSSIAQKTLNLSGGNQQKVVLGKWLFADPEVLILDEPTRGIDVGAKYEIYSIITDLAA 455 Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237 ++ +S + E+ +CDR VM GR V A+ ++ +++ Sbjct: 456 AGKGILVISSEMPELLGICDRIYVMNAGRLVGELPAAEASQEKIMSMII 504 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: 680 Number of extensions: 34 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: 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 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