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 Ac3H11_1109 ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1109 Length = 513 Score = 273 bits (699), Expect = 8e-78 Identities = 174/493 (35%), Positives = 275/493 (55%), Gaps = 11/493 (2%) Query: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68 ++K +P V A V L V GE+HA+LGENGAGKSTL+KI+ + D G+V F GQ + Sbjct: 3 ITKRYPAVVANSGVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQAVQ 62 Query: 69 PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128 R+ P + LGIA ++Q F+LF L+VAEN++LG + + L L + ++ R A+A + Sbjct: 63 VRN-PQEARALGIAMVFQHFSLFDTLTVAENVWLGLD-KSLTLAEVTQ-RISAKAA--EY 117 Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188 GL ++P PV L+V E Q VEI +A+ N +++I+DEPT+ L+ + V++L ++ L + Sbjct: 118 GLDIDPLRPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKLAS 177 Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVEFERRKR 248 S++Y+SH+L E++A+C TV+R G+ + ++ A + RLM+G R Sbjct: 178 EGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAEPP-ALEHR 236 Query: 249 RRPPGAVVLKVEGVTPAAPRLSAPGY-LRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307 GA VL+V+G+ + PR G L + F + GE+VG+AG+ G G+ +L + G Sbjct: 237 AVQTGATVLRVKGL--SLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLYALSG 294 Query: 308 ADPIA-AGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKAL 366 D A + V + P G+ VPE+R +G + NL L A+ Sbjct: 295 EDQRAEPASIQVTGQNAGRMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTRKNAV 354 Query: 367 SALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIV 426 G W+ A + E Q+ +K +A LSGGN QK ++GR + PK+LIV Sbjct: 355 GGSG-WIKVGALQKHAEDIIQRFNVKAGGPHSAAKSLSGGNLQKFIVGREIDANPKLLIV 413 Query: 427 DEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDA 486 +PT G+D+GA A++ + L D G AV+V+S EL E+ + DR+ V +G + + Sbjct: 414 SQPTWGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSPSVQR 473 Query: 487 QTATEEGLMAYMA 499 AT E + +M+ Sbjct: 474 AEATVERIGEWMS 486 Score = 60.1 bits (144), Expect = 2e-13 Identities = 61/247 (24%), Positives = 109/247 (44%), Gaps = 12/247 (4%) Query: 2 TLLDVSQVSKSFPGVRALDQVDLV--VGVGEVHALLGENGAGKSTLIKILSAA-HAADAG 58 T+L V +S +D +DL V GEV + G +G G+ L+ LS A+ Sbjct: 243 TVLRVKGLSLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLYALSGEDQRAEPA 302 Query: 59 TVTFAGQVLDPRDAPLRRQQLGIATIYQEF---NLFPELSVAENMYLGREPRRLGLVDWS 115 ++ GQ R P +R+ LG+ + +E P + +A N+ L R+ +G W Sbjct: 303 SIQVTGQNAG-RMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTRK-NAVGGSGWI 360 Query: 116 R---LRADAQALLNDLGLPLN-PDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAAL 171 + L+ A+ ++ + P + + L+ Q + + + N +L+I+ +PT + Sbjct: 361 KVGALQKHAEDIIQRFNVKAGGPHSAAKSLSGGNLQKFIVGREIDANPKLLIVSQPTWGV 420 Query: 172 SGREVDRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVAD 231 ++ I L+ +V+ VS L E+ +CDR V+ GR S A+ V Sbjct: 421 DVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSPSVQRAEATVER 480 Query: 232 MVRLMVG 238 + M G Sbjct: 481 IGEWMSG 487 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: 607 Number of extensions: 32 Number of successful extensions: 10 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: 513 Length adjustment: 35 Effective length of query: 480 Effective length of database: 478 Effective search space: 229440 Effective search space used: 229440 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