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 GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__WCS417:GFF2162 Length = 500 Score = 384 bits (987), Expect = e-111 Identities = 218/488 (44%), Positives = 316/488 (64%), Gaps = 9/488 (1%) Query: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68 + K+FPGV+ALD + G+VHAL+GENGAGKSTL+KIL A+ ++GT+ QV+ Sbjct: 11 IGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSGTLHIGEQVMA 70 Query: 69 PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128 + A G+A I+QE +L PE+SVAEN++LG P R G+V+ LR A A L L Sbjct: 71 FKSAADSIAS-GVAVIHQELHLVPEMSVAENLFLGHLPSRFGVVNRGLLRKQALACLKGL 129 Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188 ++P + L++ ++Q+VEIAKA++ A +I DEPT++LS RE+DRL AIIA L+ Sbjct: 130 ADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIARLRD 189 Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVAS-GDVADVEVADMVRLMVGRHVEFERRK 247 V+YVSHR+ EV +C+ TV +DGR+V + D++ + +V MVGR ++ Sbjct: 190 EGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALTHDQLVTCMVGRDIQDIYDY 249 Query: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307 R R G V LKV+G L PG VSF R GEI+GL GLVGAGRT+L RL+ G Sbjct: 250 RPREHGEVALKVDG-------LLGPGLREPVSFNVRKGEILGLFGLVGAGRTELFRLLSG 302 Query: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367 + +AG++ + +PL L+SPRDAI AG++L PEDRK++G S+ N+++ + A S Sbjct: 303 LERASAGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHS 362 Query: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVD 427 G + E E+ + +++K +A I LSGGNQQK +LGR +++ KVL++D Sbjct: 363 TFGWLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLLLD 422 Query: 428 EPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQ 487 EPTRGIDIGAKAE++Q++ +LA G+AV+V+SS+L EVM ++DRI+V EG + + + Sbjct: 423 EPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTRE 482 Query: 488 TATEEGLM 495 ATE L+ Sbjct: 483 HATESNLL 490 Score = 79.3 bits (194), Expect = 3e-19 Identities = 65/261 (24%), Positives = 115/261 (44%), Gaps = 32/261 (12%) Query: 254 AVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAA 313 A L+ +G+ P + A L +SF+A G++ L G GAG++ L +++ GA + Sbjct: 3 AAALRFDGIGKTFPGVKA---LDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNS 59 Query: 314 GRVLVDDKPLRLRSPRDAIQAGIM-------LVPEDRKQQGCFLDHSIRR----NLSLPS 362 G + + ++ + +S D+I +G+ LVPE + FL H R N L Sbjct: 60 GTLHIGEQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLPSRFGVVNRGLLR 119 Query: 363 LKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422 +AL+ L DE D +G+LS G +Q V + +A++ Sbjct: 120 KQALACLKGLADE------------------IDPAEKLGRLSLGQRQLVEIAKALSRGAH 161 Query: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482 V+ DEPT + + +++ L D G V+ +S + EV + + + VF++G V Sbjct: 162 VIAFDEPTSSLSAREIDRLMAIIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVR 221 Query: 483 DLDAQTATEEGLMAYMATGTD 503 + +A + G D Sbjct: 222 TFEDMSALTHDQLVTCMVGRD 242 Score = 68.9 bits (167), Expect = 4e-16 Identities = 63/236 (26%), Positives = 107/236 (45%), Gaps = 12/236 (5%) Query: 14 PGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVL---DPR 70 PG+R + V V GE+ L G GAG++ L ++LS A AG + G+ L PR Sbjct: 267 PGLR--EPVSFNVRKGEILGLFGLVGAGRTELFRLLSGLERASAGQLELCGEPLHLQSPR 324 Query: 71 DAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR-----LGLVDWSRLRADAQALL 125 DA + L ++ + P SVAEN+ + L W + AD Q Sbjct: 325 DA-IAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHSTFGWLLREGWEKGNADQQINA 383 Query: 126 NDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAG 185 + P N + L+ QQ + + +++ +++++DEPT + ++ II Sbjct: 384 MKVKTP-NAAQKIMYLSGGNQQKSILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHN 442 Query: 186 LKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 L A+ ++VI VS L EV + DR V+ +G +++++L + R V Sbjct: 443 LAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTREHATESNLLQLALPRSV 498 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: 674 Number of extensions: 30 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 515 Length of database: 500 Length adjustment: 34 Effective length of query: 481 Effective length of database: 466 Effective search space: 224146 Effective search space used: 224146 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