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 16017 b1900 fused L-arabinose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Keio:16017 Length = 504 Score = 377 bits (968), Expect = e-109 Identities = 213/484 (44%), Positives = 306/484 (63%), Gaps = 9/484 (1%) Query: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68 + K+FPGV+AL + G+VHAL+GENGAGKSTL+KILS +A G+V GQ + Sbjct: 13 IGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMS 72 Query: 69 PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128 D G+A IYQE +L PE++VAEN+YLG+ P + G+V+ S L +A L L Sbjct: 73 FSDTTAALNA-GVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQLKHL 131 Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188 G+ ++PD P++ L++ + QMVEIAKA+ NA++I DEPT++LS RE+D L +I L+ Sbjct: 132 GMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRK 191 Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVAS-GDVADVEVADMVRLMVGRHVEFERRK 247 ++YVSHR+ E+ A+ D TV +DGR+V + D+ V+ +V+ MVGR + Sbjct: 192 EGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGDIYGW 251 Query: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307 + R G L+++ V APG +S A R GEIVGL GLVGAGR++L + +FG Sbjct: 252 QPRSYGEERLRLDAV-------KAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFG 304 Query: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367 I AG+V +D +P+ +R P AI AG+ML PEDRK +G HS+R N+++ + + Sbjct: 305 GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364 Query: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVD 427 G ++ E + + + + L IK AE I LSGGNQQK +LGR ++ KV+++D Sbjct: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424 Query: 428 EPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQ 487 EPTRGID+GAK E++ V+ LA GVAV+ SS+L EV+ V+DRIVV REG I +L + Sbjct: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHE 484 Query: 488 TATE 491 A E Sbjct: 485 QADE 488 Score = 71.6 bits (174), Expect = 6e-17 Identities = 59/247 (23%), Positives = 110/247 (44%), Gaps = 19/247 (7%) Query: 257 LKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRV 316 L G+ P + A L +SF G++ L G GAG++ L +++ G G V Sbjct: 8 LSFRGIGKTFPGVKA---LTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 Query: 317 LVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDER 376 +++ + + A+ AG+ ++ ++ + ++ N+ L L + Sbjct: 65 VINGQEMSFSDTTAALNAGVAIIYQELH---LVPEMTVAENIYLGQLPHKGGI------- 114 Query: 377 AERDLVETYRQKLRIKMA----DAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRG 432 R L+ Y L++K D +T + LS G Q V + +A+A K++ DEPT Sbjct: 115 VNRSLLN-YEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSS 173 Query: 433 IDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADL-DAQTATE 491 + + +V+ +L G ++ +S + E+ A+SD I VF++G V D Q Sbjct: 174 LSAREIDNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDH 233 Query: 492 EGLMAYM 498 + L+ M Sbjct: 234 DALVQAM 240 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: 7 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: 504 Length adjustment: 34 Effective length of query: 481 Effective length of database: 470 Effective search space: 226070 Effective search space used: 226070 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