Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 377 bits (968), Expect = e-109 Identities = 213/484 (44%), Positives = 306/484 (63%), Gaps = 9/484 (1%) Query: 13 IGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMS 72 + K+FPGV+AL + G+VHAL+GENGAGKSTL+KILS +A G+V GQ + Sbjct: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68 Query: 73 FSDTTAALNA-GVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQLKHL 131 D G+A IYQE +L PE++VAEN+YLG+ P + G+V+ S L +A L L Sbjct: 69 PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128 Query: 132 GMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRK 191 G+ ++PD P++ L++ + QMVEIAKA+ NA++I DEPT++LS RE+D L +I L+ Sbjct: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188 Query: 192 EGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGDIYGW 251 ++YVSHR+ E+ A+ D TV +DGR+V + D+ V+ +V+ MVGR + Sbjct: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVAS-GDVADVEVADMVRLMVGRHVEFERRK 247 Query: 252 QPRSYGEERLRLDAV-------KAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFG 304 + R G L+++ V APG +S A R GEIVGL GLVGAGR++L + +FG Sbjct: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307 Query: 305 GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364 I AG+V +D +P+ +R P AI AG+ML PEDRK +G HS+R N+++ + + Sbjct: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367 Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424 G ++ E + + + + L IK AE I LSGGNQQK +LGR ++ KV+++D Sbjct: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVD 427 Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHE 484 EPTRGID+GAK E++ V+ LA GVAV+ SS+L EV+ V+DRIVV REG I +L + Sbjct: 428 EPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQ 487 Query: 485 QADE 488 A E Sbjct: 488 TATE 491 Score = 71.6 bits (174), Expect = 6e-17 Identities = 59/247 (23%), Positives = 110/247 (44%), Gaps = 19/247 (7%) Query: 8 LSFRGIGKTFPGVKA---LTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 L G+ P + A L +SF G++ L G GAG++ L +++ G G V Sbjct: 257 LKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRV 316 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELH---LVPEMTVAENIYLGQLPHKGGI------- 114 +++ + + A+ AG+ ++ ++ + ++ N+ L L + Sbjct: 317 LVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDER 376 Query: 115 VNRSLLN-YEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSS 173 R L+ Y L++K D +T + LS G Q V + +A+A K++ DEPT Sbjct: 377 AERDLVETYRQKLRIKMA----DAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRG 432 Query: 174 LSAREIDNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDH 233 + + +V+ +L G ++ +S + E+ A+SD I VF++G V D Q Sbjct: 433 IDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADL-DAQTATE 491 Query: 234 DALVQAM 240 + L+ M Sbjct: 492 EGLMAYM 498 Lambda K H 0.319 0.136 0.391 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: 729 Number of extensions: 38 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: 504 Length of database: 515 Length adjustment: 34 Effective length of query: 470 Effective length of database: 481 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 (21.7 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