Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_106713889.1 CU102_RS25570 sugar ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >NCBI__GCF_003010955.1:WP_106713889.1 Length = 506 Score = 358 bits (918), Expect = e-103 Identities = 193/476 (40%), Positives = 301/476 (63%), Gaps = 3/476 (0%) Query: 5 TPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 TP L RGI K+FPGVKAL D++ YAG+V AL+GENGAGKSTL+KIL+G Y G + Sbjct: 13 TPLLEMRGISKSFPGVKALNDVNIALYAGKVTALIGENGAGKSTLVKILTGIYQSDEGEI 72 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPH-KGGIVNRSLLNYE 123 ++G ++F++ A++ GV I+QE L E++VAENI+LG P + G VN +N Sbjct: 73 HVDGSPVAFANAQDAIDFGVTAIHQETVLFDELSVAENIFLGHAPKTRLGFVNWKAVNAR 132 Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183 A L L +IDP T LK LSI Q +V IA+AL+ +A+I+ DEPT++LS +E+D+LF Sbjct: 133 ALALLHSLESNIDPRTRLKDLSIAQRHLVAIARALSVDARIVIMDEPTAALSRKEVDDLF 192 Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243 ++++ L+ G+ IL++SH+ +E++ ++D VF+DG+ V + + V D +V+ MVGR Sbjct: 193 QIVKRLKSHGKAILFISHKFDEVYEIADNFAVFRDGKAVGSGV-LAGVAQDEIVRLMVGR 251 Query: 244 DIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMF 303 I + GE L ++ P I+ A++ GEI G++GLVGAGRSE+ + +F Sbjct: 252 SIEHAFPKVAIPLGEAVLSVENYTHPTEFRDITFALKKGEIFGIYGLVGAGRSEICQSLF 311 Query: 304 GGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKH 363 G T+ + G + +D + I IR P AI AG++ PE+R G + + NI++ + + Sbjct: 312 GVTRPSGGTLKLDGKEIVIRSPGDAIKAGIVYVPEERGRHGAVLQLPIYQNISLPSLVRT 371 Query: 364 VLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILL 423 G + E A + +++ + LSGGNQQK ++G+WL+ K+++L Sbjct: 372 SRSG-FLRAAEEFALARKYAERFDLRAAALSVPVGTLSGGNQQKVVIGKWLATHPKILIL 430 Query: 424 DEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAG 479 DEPT+GID+G+K ++ I LA +G++++ SS+LPE+LG++DR++VMREG AG Sbjct: 431 DEPTKGIDIGSKAAVHAFISELAGEGLSIIMVSSELPEILGMSDRVLVMREGLSAG 486 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: 668 Number of extensions: 34 Number of successful extensions: 8 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: 506 Length adjustment: 34 Effective length of query: 470 Effective length of database: 472 Effective search space: 221840 Effective search space used: 221840 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