Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate H281DRAFT_02331 H281DRAFT_02331 L-arabinose ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Burk376:H281DRAFT_02331 Length = 520 Score = 501 bits (1289), Expect = e-146 Identities = 260/493 (52%), Positives = 336/493 (68%), Gaps = 1/493 (0%) Query: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65 PYL GI FPGV AL +S + G+VH LMGENGAGKSTLLK+LSG P G++ Sbjct: 29 PYLQLDGITVRFPGVLALDQVSLEVRRGEVHGLMGENGAGKSTLLKVLSGVNQPAAGTLS 88 Query: 66 INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAG 125 ++G E F+ T AA+ AGVAIIYQELHLVPE+TVAEN+ LG LP++ G+++ L A Sbjct: 89 LDGVEQQFTTTKAAIAAGVAIIYQELHLVPELTVAENLMLGALPNRFGVLDEKALVARAV 148 Query: 126 LQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRV 185 +L+ LG IDP +K LSIGQ QM+EI KAL R+A++IAFDEPTSSLS+RE LFR+ Sbjct: 149 RELERLGEKIDPSQQVKNLSIGQRQMIEIGKALMRDARVIAFDEPTSSLSSRETTQLFRI 208 Query: 186 IRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDI 245 IR LR EGR I+YV+HRM+E++ L D +TVF+DGR + TF +D D L+ MVGR I Sbjct: 209 IRALRAEGRAIIYVTHRMDEVYELCDRVTVFRDGRRIDTFDAGAGLDRDRLISCMVGRSI 268 Query: 246 GDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGG 305 D+YG++ R G+ +L + + PG+R P + + R GEIVG FGLVGAGRSELMK ++G Sbjct: 269 ADVYGYRTRDVGDVQLDVKGLMGPGLREPATFSARKGEIVGFFGLVGAGRSELMKLIYGA 328 Query: 306 TQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVL 365 + TAG + + + + P A+ AG+ LCPEDRK EGI+ + SV DN+NIS RR H Sbjct: 329 VKPTAGDITLKGKQVRFATPRDAVRAGVALCPEDRKQEGIVSIASVSDNLNISCRR-HFS 387 Query: 366 GGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDE 425 V+N E A I L IKT E I LSGGNQQK IL RWL+E++ V L+DE Sbjct: 388 RFNVLNGRKEAQTAKEFIGKLAIKTRNGETPIGTLSGGNQQKVILSRWLAEDIDVFLMDE 447 Query: 426 PTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQ 485 PTRGIDVGA+ EIY ++Y LA G V+ SSDL EV+GV DR++VM+EG + G+L Q Sbjct: 448 PTRGIDVGARSEIYGLLYGLADAGRTVIVVSSDLAEVIGVTDRVIVMKEGRLVGDLPKAQ 507 Query: 486 ADERQALSLAMPK 498 A + LA+P+ Sbjct: 508 ATPDALIKLALPR 520 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: 732 Number of extensions: 35 Number of successful extensions: 6 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: 520 Length adjustment: 35 Effective length of query: 469 Effective length of database: 485 Effective search space: 227465 Effective search space used: 227465 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