Align deoxynucleoside transporter, ATPase component (characterized)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20820 Length = 517 Score = 297 bits (760), Expect = 7e-85 Identities = 179/497 (36%), Positives = 280/497 (56%), Gaps = 13/497 (2%) Query: 16 LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75 L V G+ K + L G+ L+ RG++ L GENG GKSTL KII G P GQ+ + Sbjct: 10 LSVSGIGKTYAQP-VLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQ 68 Query: 76 GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRV-LA 134 G + S +A GI V Q+L+LLP +SVAEN+ L + L ++ G ++R R+ +A Sbjct: 69 GRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDN-LPSNGGWISRKQLRKAAIA 127 Query: 135 ATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKE 194 A A L+A+ TL+ +L + +Q+V IAR + + +I+DEPT LT +E Sbjct: 128 AMAQVGLDAID-------PDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE 180 Query: 195 VDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISEL 254 V+ L + L+A+GV ++++SH+L+E + + VLRDG + P+A + Q+ L Sbjct: 181 VEMLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNL 240 Query: 255 MTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELA 314 M GR L H L V+G +R+ + DVSF++ GEI G++GL+ +GR EL Sbjct: 241 MVGRELGEHIDLGPRHIGAPALTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTELL 300 Query: 315 RALAGVAPAQSGDVLL--DGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVIT 372 R + G A SG V L Q +++R+P+DA H I + EDR EGL L + I N+ Sbjct: 301 RLIFGADAADSGTVALGSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIAL 360 Query: 373 AMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAID 432 + + G ++ ALA++ + ++I + + V LSGGNQQ+V+IGRWL + Sbjct: 361 GNMPVISSG-GIVNSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERE 419 Query: 433 PRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHV 492 VL+ PT G+DVG+K IY ++ L+++G ++++S DL EL+ CDRI ++ G + Sbjct: 420 CSVLLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRL 479 Query: 493 SAEYRADELSEADLYHA 509 + D ++ DL A Sbjct: 480 IDTFERDSWTQDDLLAA 496 Lambda K H 0.319 0.135 0.376 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: 594 Number of extensions: 33 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: 515 Length of database: 517 Length adjustment: 35 Effective length of query: 480 Effective length of database: 482 Effective search space: 231360 Effective search space used: 231360 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 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