Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 355 bits (911), Expect = e-102 Identities = 199/497 (40%), Positives = 301/497 (60%), Gaps = 13/497 (2%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNY--APTTGSVV 65 L R I KTFPGV AL ++ AG++HA++GENGAGKSTL+K+LSG Y +G ++ Sbjct: 3 LEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQIL 62 Query: 66 INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAG 125 +GQE F+ + + G+ II+QEL LVP +++AENI+LG + G+++ + A Sbjct: 63 FDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARHGVIDWMAAHSRAQ 122 Query: 126 LQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRV 185 L +G+ PDTP+ L +G+ Q+VEIAKAL+R +++ DEPT+SL+ + L + Sbjct: 123 ALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALLDL 182 Query: 186 IRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQ-QVDHDALVQAMVGRD 244 + EL+ +G + +SH++ EI ++DAITV +DG V+ + V D ++QAMVGR+ Sbjct: 183 LLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMVGRE 242 Query: 245 IGDIYGWQPRSYGEERLRLDAVKAPGVRTP-------ISLAVRSGEIVGLFGLVGAGRSE 297 + D Y + GE + +A + I L VR GEIVG+ GL+GAGR+E Sbjct: 243 MSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGAGRTE 302 Query: 298 LMKGMFGGT--QITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNI 355 L +FG + Q +G+V + QPID+ A++ G+ EDRK G++ ++ N Sbjct: 303 LAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDIQFNT 362 Query: 356 NISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLS 415 ++ A V VI++G E A + L I+ G +Q +NLSGGNQQK +L +WL Sbjct: 363 SL-ANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSKWLF 421 Query: 416 EEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREG 475 +V++LDEPTRGIDVGAK+EIY +I LAA+G V+ SS++PE+LG+ DRI VM EG Sbjct: 422 TSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVMNEG 481 Query: 476 EIAGELLHEQADERQAL 492 E+ +A + + + Sbjct: 482 RFVAEMPTSEASQEKIM 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: 689 Number of extensions: 35 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 504 Length of database: 505 Length adjustment: 34 Effective length of query: 470 Effective length of database: 471 Effective search space: 221370 Effective search space used: 221370 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