Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 240 bits (613), Expect = 8e-68 Identities = 152/481 (31%), Positives = 264/481 (54%), Gaps = 21/481 (4%) Query: 3 QSTPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTG 62 Q P +S +G+ K F V A DIS + Y G+V AL+GENGAGKSTL+ +L+G Y P G Sbjct: 20 QGIPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAG 79 Query: 63 SVVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGG--IVNRSLL 120 ++ ++G+ + FS A+ AG+ ++YQ LV MTVAEN+ LGQ +G + + + Sbjct: 80 TIALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQ---EGSFFLNPKEMR 136 Query: 121 NYEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREID 180 N L +++ G+DIDP + LS+G+ Q VEI K L R+++++ FDEPT+ L+ RE Sbjct: 137 NRVQELSVRY-GLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETF 195 Query: 181 NLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAM 240 +LF + ++ ++G+ I+++SH++EE+ A++D I + + GR F++ + L M Sbjct: 196 HLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRM 255 Query: 241 VGRDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMK 300 VG+++ + +G+ L++ + G+ I+ + GE+V + G+ G G+ L++ Sbjct: 256 VGKEVLLEVDREAMPHGDAVLQVRNLTGIGLE-DITFDLHQGEVVAVVGVAGNGQKALVE 314 Query: 301 GMFG------GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDN 354 + G T G+ + D KPS + PEDR ++ DN Sbjct: 315 AICGLRKPPVDTMFIMGKRWRD----FYAKPSW--KNSLAYIPEDRLGLATCRNLNLVDN 368 Query: 355 INISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWL 414 + ++ R+ G ++ + I+ +I+ L LSGGN QK++L R L Sbjct: 369 LLLTTRQGFARGPW-LDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLAREL 427 Query: 415 SEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMRE 474 ++I+ ++PT+G+D+ A +++N + A A + +L + DL E L +ADR+ V+ Sbjct: 428 YRCPRLIVAEQPTQGLDIAATEQVWNHLLA-AREMAGILLVTGDLNEALQLADRVAVIYR 486 Query: 475 G 475 G Sbjct: 487 G 487 Score = 85.5 bits (210), Expect = 4e-21 Identities = 61/222 (27%), Positives = 108/222 (48%), Gaps = 9/222 (4%) Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMM 334 ISL + G + L G GAG+S LM + G Q AG + +D +P+ AI AG+ Sbjct: 43 ISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGIG 102 Query: 335 LCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAE 394 + + ++ +V +N+ + L + N +E + + L+I P A Sbjct: 103 MVYQHFM---LVESMTVAENVLLGQEGSFFLNPKEMRNRVQELSVRY---GLDID-PAAR 155 Query: 395 QLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLF 454 + +LS G +Q+ + + L + +V++ DEPT + ++ ++ +A QG +++F Sbjct: 156 --VSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVF 213 Query: 455 ASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSLAM 496 S L EVL VAD I ++R+G I GE + + L+ M Sbjct: 214 ISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRM 255 Score = 52.0 bits (123), Expect = 5e-11 Identities = 53/230 (23%), Positives = 104/230 (45%), Gaps = 9/230 (3%) Query: 23 LTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMSFSDTTAALNA 82 L DI+FD + G+V A++G G G+ L++ + G P ++ I G+ + Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345 Query: 83 GVAIIYQE---LHLVPEMTVAENIYLG--QLPHKGGIVNRSLLNYEAGLQLKHLGMDIDP 137 +A I ++ L + + +N+ L Q +G +++ + +K + Sbjct: 346 SLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFARGPWLDKKKAARDTTELIKKFDIRPGR 405 Query: 138 DTPLKY-LSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEGRVI 196 L + LS G Q +A+ L R ++I ++PT L + ++ + R+ ++ Sbjct: 406 IAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAREMAGIL 465 Query: 197 LYVSHRMEEIFALSDAITVFKDGRYVKTF--TDMQQVDHDALVQAMVGRD 244 L V+ + E L+D + V GR++ F +D Q+V+ L+ A V D Sbjct: 466 L-VTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMMAGVEED 514 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: 582 Number of extensions: 30 Number of successful extensions: 7 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: 504 Length of database: 514 Length adjustment: 34 Effective length of query: 470 Effective length of database: 480 Effective search space: 225600 Effective search space used: 225600 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 Apr 09 2024. 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