Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Pf6N2E2_5969 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5969 Length = 514 Score = 570 bits (1469), Expect = e-167 Identities = 289/491 (58%), Positives = 368/491 (74%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 L F GIGK+FPGV+AL +ISF + GQVHALMGENGAGKSTLLKIL G Y P++G + I Sbjct: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127 Q M+F T ++ +GVA+I+QELHLVPEMTVAEN++LG LP + G+VNR +L +A Sbjct: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTL 135 Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187 LK L +IDP + LS+GQ Q+VEIAKAL+R A +IAFDEPTSSLSAREID L +I Sbjct: 136 LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIG 195 Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247 LR EG+V+LYVSHRMEE+F + +A+TVFKDGRYV+TF +M ++ HD LV MVGRDI D Sbjct: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQD 255 Query: 248 IYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQ 307 IY ++PR G+ L++ + PG+ P+S V GEI+GLFGLVGAGR+EL++ + G + Sbjct: 256 IYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLER 315 Query: 308 ITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGG 367 G + + + + +R P AIAAG++LCPEDRK EGIIP+ SV +NINISAR H G Sbjct: 316 QREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLG 375 Query: 368 CVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPT 427 C++ WE NAD I+SL +KTP A Q IM LSGGNQQKAILGRWLS MKV+LLDEPT Sbjct: 376 CLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPT 435 Query: 428 RGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQAD 487 RGID+GAK EIY +I+ LAA G+AV+ SSDL EV+G++DRI+V+ EG + GEL +QA+ Sbjct: 436 RGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQAN 495 Query: 488 ERQALSLAMPK 498 E L LA+P+ Sbjct: 496 ESNLLQLALPR 506 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: 764 Number of extensions: 30 Number of successful extensions: 5 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: 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 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