Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A165ZSX8 (514 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20820 Length = 517 Score = 361 bits (926), Expect = e-104 Identities = 209/500 (41%), Positives = 297/500 (59%), Gaps = 6/500 (1%) Query: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 L +GIGK++ L I G+V AL GENGAGKSTL KI+GG P++G +Q Sbjct: 10 LSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQ 68 Query: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTL 135 + + G+ ++ QEL+L+P ++VAENLFL +LP+ G ++R LR+ A+ Sbjct: 69 GRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNGGWISRKQLRKAAIAA 128 Query: 136 LKGLA-DEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 + + D IDP VG L +G +Q+VEIA+ L HV+ DEPT+ L+ARE++ L I Sbjct: 129 MAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQI 188 Query: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254 RL+ G ++Y+SHR+EE+ R+ + V +DG V E M+ +QLV MVGR++ Sbjct: 189 TRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLV-CVEPMANYNSEQLVNLMVGRELG 247 Query: 255 DIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314 + D PR G AL VKGL VSF+V GEI G+ GL+GAGRTELLRL+ G + Sbjct: 248 EHIDLGPRHIGAPALTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGAD 307 Query: 315 RQREGSLVLHD--KELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHS 372 G++ L + + +RSP DA+ G+ L EDRK EG++ S+ NI + P S Sbjct: 308 AADSGTVALGSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMPVIS 367 Query: 373 TLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 432 + G + GD E A +QI ++++++ + Q + LSGGNQQK ++GRWL VLL D Sbjct: 368 SGGIVNSGD-EMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERECSVLLFD 426 Query: 433 EPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRD 492 EPTRGID+GAK +IY ++ L G A++VVSSDL E+M I DRI VL G + RD Sbjct: 427 EPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERD 486 Query: 493 QANESNLLQLALPRQRVADA 512 + +LL A + DA Sbjct: 487 SWTQDDLLAAAFAGYQKRDA 506 Lambda K H 0.320 0.138 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: 699 Number of extensions: 43 Number of successful extensions: 11 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: 514 Length of database: 517 Length adjustment: 35 Effective length of query: 479 Effective length of database: 482 Effective search space: 230878 Effective search space used: 230878 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 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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