Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_106713881.1 CU102_RS25520 sugar ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >NCBI__GCF_003010955.1:WP_106713881.1 Length = 512 Score = 361 bits (927), Expect = e-104 Identities = 207/493 (41%), Positives = 298/493 (60%), Gaps = 9/493 (1%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 LS GI K F G+ AL+ SF G+VHAL+G+NGAGKSTL+K+L+G Y G V + Sbjct: 7 LSMTGIDKRFAGIPALSGASFAVGRGEVHALIGQNGAGKSTLIKVLTGYYRRDAGDVAFD 66 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127 G+ A +G++ IYQE++LVP ++ ENI LG+ G+++ ++ EA Sbjct: 67 GKPFEVFSPQLAQASGISTIYQEINLVPYRSITENICLGREARHYGLLDWKRMHKEAETL 126 Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187 L+ + +D D PL + QMV IA+A+ +AK++ DEPTSSL RE+ LF VIR Sbjct: 127 LRRFNVRVDVDRPLMEFNTATQQMVAIARAIGFSAKLVVMDEPTSSLDDREVTVLFDVIR 186 Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247 +L++EG +++VSH+++E++ + D +T+ +DGR VKT M ++D LV +M+GR I Sbjct: 187 QLKQEGVSVVFVSHKLDELYEVCDRVTIMRDGRTVKT-AAMTEIDKIGLVSSMLGRTINR 245 Query: 248 IYGW-------QPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMK 300 G + G+ L + +S VRSGEI G GL+GAGR+E + Sbjct: 246 AEGHATAFSDRDEKKIGKVLLSAQNLSINRTVQDVSFDVRSGEIAGFAGLLGAGRTETAR 305 Query: 301 GMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISAR 360 +FG + AG ++ D Q D R P+ AIAAGM C EDRK+EGI+P SV +N+ ++ Sbjct: 306 LVFGIDRPRAGIMHYDGQQFDPRSPADAIAAGMGFCTEDRKSEGIVPEMSVAENMMLALM 365 Query: 361 RKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKV 420 K G VI+ + + IR L+IK G +Q + LSGGNQQK +LGRWL+ + Sbjct: 366 PKVSKSG-VIDEKAQRKIVERFIRQLDIKCSGPDQKVRELSGGNQQKVLLGRWLAMNPTL 424 Query: 421 ILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGE 480 ++LDEPTRGIDVGAK EI ++I +LA +G+AVL SS+L EV+ ADR+ V+REG E Sbjct: 425 LILDEPTRGIDVGAKGEIQSLIKSLADRGLAVLMISSELEEVIEGADRVFVLREGITVAE 484 Query: 481 LLHEQADERQALS 493 QA E +S Sbjct: 485 FDRNQATEDVLMS 497 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: 619 Number of extensions: 31 Number of successful extensions: 9 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: 512 Length adjustment: 34 Effective length of query: 470 Effective length of database: 478 Effective search space: 224660 Effective search space used: 224660 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 24 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