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 Pf6N2E2_5969 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5969 Length = 514 Score = 377 bits (969), Expect = e-109 Identities = 220/499 (44%), Positives = 314/499 (62%), Gaps = 10/499 (2%) Query: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68 + KSFPGV+AL + V G+VHAL+GENGAGKSTL+KIL A+ +G + Q + Sbjct: 21 IGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIGEQTMA 80 Query: 69 PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128 + G+A I+QE +L PE++VAEN++LG P R GLV+ LR A LL L Sbjct: 81 FKGTADSIAS-GVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTLLKGL 139 Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188 ++P V L++ ++Q+VEIAKA++ A +I DEPT++LS RE+DRL AII L+ Sbjct: 140 ADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRD 199 Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGD-VADVEVADMVRLMVGRHVEFERRK 247 V+YVSHR+ EV +C+ TV +DGR+V + + ++++ +V MVGR ++ Sbjct: 200 EGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQDIYDY 259 Query: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307 R R G V L+V+G L PG VSF GEI+GL GLVGAGRT+L RL+ G Sbjct: 260 RPRERGDVALQVKG-------LLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSG 312 Query: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367 + G +++ DK L+LRSPRDAI AG++L PEDRK++G S+ N+++ + + S Sbjct: 313 LERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHS 372 Query: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVD 427 LG + ER + + L++K A I LSGGNQQK +LGR +++ KVL++D Sbjct: 373 TLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 432 Query: 428 EPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQ 487 EPTRGIDIGAKAE++Q++ +LA G+AV+V+SS+L EVM +SDRI+V EG + +L Sbjct: 433 EPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRD 492 Query: 488 TATEEGLMAYMATGTDRVA 506 A E L+ +A RVA Sbjct: 493 QANESNLL-QLALPRQRVA 510 Score = 65.1 bits (157), Expect = 6e-15 Identities = 60/220 (27%), Positives = 99/220 (45%), Gaps = 10/220 (4%) Query: 5 DVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAG 64 DV+ K G + V V GE+ L G GAG++ L+++LS G++ Sbjct: 266 DVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHD 325 Query: 65 QVL---DPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR--LGLV---DWSR 116 + L PRDA + L ++ + P SV EN+ + P LG + DW R Sbjct: 326 KELKLRSPRDA-IAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWER 384 Query: 117 LRADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREV 176 AD Q + P + L+ QQ + + +++ +++++DEPT + Sbjct: 385 GNADKQIKSLKVKTP-TAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAK 443 Query: 177 DRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDG 216 ++ II L A ++VI VS L EV + DR V+ +G Sbjct: 444 AEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEG 483 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: 688 Number of extensions: 34 Number of successful extensions: 8 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: 514 Length adjustment: 35 Effective length of query: 480 Effective length of database: 479 Effective search space: 229920 Effective search space used: 229920 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