Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate BPHYT_RS19720 BPHYT_RS19720 arabinose ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__BFirm:BPHYT_RS19720 Length = 515 Score = 496 bits (1278), Expect = e-145 Identities = 260/498 (52%), Positives = 337/498 (67%), Gaps = 1/498 (0%) Query: 1 MQQSTPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPT 60 + + PYL GI FPGV AL +S + G+VH LMGENGAGKSTLLK+LSG P Sbjct: 19 LASTEPYLRLDGITVRFPGVLALDQVSLEVRRGEVHGLMGENGAGKSTLLKVLSGVNQPA 78 Query: 61 TGSVVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLL 120 G++ ++G E F T AA+ AGVAIIYQELHLVPE+TVAEN+ LG LP++ GI++ L Sbjct: 79 AGTLSLDGVEQQFITTKAAIAAGVAIIYQELHLVPELTVAENLMLGALPNRFGILDEKAL 138 Query: 121 NYEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREID 180 A +L+ LG IDP +K LSIGQ QM+EI KAL R+A++IAFDEPTSSLS+RE Sbjct: 139 VARAVRELERLGEKIDPSQQVKNLSIGQRQMIEIGKALMRDARVIAFDEPTSSLSSRETT 198 Query: 181 NLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAM 240 LFR+IR L+ EGR I+YV+HRM+E++ L D +TVF+DGR + TF + +D D L+ M Sbjct: 199 QLFRIIRALKAEGRAIIYVTHRMDEVYELCDRVTVFRDGRRIDTFEAGEGLDRDRLISCM 258 Query: 241 VGRDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMK 300 VGR I D+YG++ R G+ +L + + G+R P S R GEIVG FGLVGAGRSELMK Sbjct: 259 VGRSIADVYGYRSRDLGDVQLDVKEMMGRGLREPASFTARKGEIVGFFGLVGAGRSELMK 318 Query: 301 GMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISAR 360 ++G + AG++ + + + P A+ AG+ LCPEDRK EGI+ + SV DN+NIS R Sbjct: 319 LIYGAVKPDAGEIALKGKRVRFATPRDAVRAGVALCPEDRKQEGIVSIASVSDNLNISCR 378 Query: 361 RKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKV 420 R H V+N E A I L IKT + I LSGGNQQK IL RWL+E++ V Sbjct: 379 R-HFSRFNVLNGRKEAQTAKEFIGKLAIKTRNGDTPIGTLSGGNQQKVILSRWLAEDIDV 437 Query: 421 ILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGE 480 L+DEPTRGIDVGA+ EIY ++Y LA G V+ SSDL EV+GVADR++VM+EG I G+ Sbjct: 438 FLMDEPTRGIDVGARSEIYGLLYGLAEAGRTVIVVSSDLAEVIGVADRVIVMKEGRIVGD 497 Query: 481 LLHEQADERQALSLAMPK 498 L QA + LA+P+ Sbjct: 498 LPKAQATPDALIKLALPR 515 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: 713 Number of extensions: 31 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: 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