Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__WCS417:GFF2162 Length = 500 Score = 582 bits (1501), Expect = e-171 Identities = 296/491 (60%), Positives = 370/491 (75%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 L F GIGKTFPGVKAL ISF + GQVHALMGENGAGKSTLLKIL G Y P +G++ I Sbjct: 6 LRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSGTLHIG 65 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127 Q M+F ++ +GVA+I+QELHLVPEM+VAEN++LG LP + G+VNR LL +A Sbjct: 66 EQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLPSRFGVVNRGLLRKQALAC 125 Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187 LK L +IDP L LS+GQ Q+VEIAKAL+R A +IAFDEPTSSLSAREID L +I Sbjct: 126 LKGLADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIA 185 Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247 LR EG+V+LYVSHRMEE+F + +A+TVFKDGRYV+TF DM + HD LV MVGRDI D Sbjct: 186 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALTHDQLVTCMVGRDIQD 245 Query: 248 IYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQ 307 IY ++PR +GE L++D + PG+R P+S VR GEI+GLFGLVGAGR+EL + + G + Sbjct: 246 IYDYRPREHGEVALKVDGLLGPGLREPVSFNVRKGEILGLFGLVGAGRTELFRLLSGLER 305 Query: 308 ITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGG 367 +AGQ+ + +P+ ++ P AIAAG++LCPEDRK EGIIP+ SV +NINISAR H G Sbjct: 306 ASAGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHSTFG 365 Query: 368 CVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPT 427 ++ GWE+ NAD I ++ +KTP A Q IM LSGGNQQK+ILGRWLS MKV+LLDEPT Sbjct: 366 WLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLLLDEPT 425 Query: 428 RGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQAD 487 RGID+GAK EIY +I+ LAAQG+AV+ SSDL EV+G+ADRI+V+ EG + GE E A Sbjct: 426 RGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTREHAT 485 Query: 488 ERQALSLAMPK 498 E L LA+P+ Sbjct: 486 ESNLLQLALPR 496 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: 751 Number of extensions: 34 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: 500 Length adjustment: 34 Effective length of query: 470 Effective length of database: 466 Effective search space: 219020 Effective search space used: 219020 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