Align deoxynucleoside transporter, ATPase component (characterized)
to candidate AO356_00965 AO356_00965 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00965 Length = 517 Score = 300 bits (769), Expect = 6e-86 Identities = 176/481 (36%), Positives = 273/481 (56%), Gaps = 10/481 (2%) Query: 31 LRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAA 90 L ++L+ RG++ L GENG GKSTL KII G P GQ+ +G + S +A Sbjct: 24 LTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQDYRPGSRTQAEEL 83 Query: 91 GIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGLPGNS 150 G+ V Q+L+LLP +SVAEN+ L + L +H G ++R + L A A+ VGL Sbjct: 84 GVRMVMQELNLLPTLSVAENLFLDN-LPSHGGWISR----KQLRKAAIEAMAQVGLDAID 138 Query: 151 EFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGV 210 TL+ +L + +Q+V IAR + + +I+DEPT LT +EV+ L + L+A+GV Sbjct: 139 P--DTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGV 196 Query: 211 TVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTGRHLSNERYRESAH 270 ++++SH+L+E + + VLRDG + P+A + Q+ LM GR L Sbjct: 197 AIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYDSEQLVTLMVGRELGEHIDLGPRQ 256 Query: 271 AQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLL 330 L V+G TR+ + DVSF++ GEI G++GL+ +GR EL R + G PA SG V L Sbjct: 257 IGAPALTVKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADPADSGTVAL 316 Query: 331 DG--QQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRT 388 + +++R+PSDA H I + EDR EGL L + I N+ + + G ++ + Sbjct: 317 GSPARVVSIRSPSDAVAHGIALITEDRKGEGLLLTQSIAANIALGNMPEISSA-GLVNGS 375 Query: 389 RAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVG 448 ALA++ V ++I + + V LSGGNQQ+V+IGRWL D V++ PT G+DVG Sbjct: 376 AELALAQRQVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFDEPTRGIDVG 435 Query: 449 SKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYH 508 +K IY ++ L+++G ++++S DL EL+ CDRI ++ G + + D ++ DL Sbjct: 436 AKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLA 495 Query: 509 A 509 A Sbjct: 496 A 496 Score = 71.6 bits (174), Expect = 6e-17 Identities = 65/221 (29%), Positives = 106/221 (47%), Gaps = 14/221 (6%) Query: 23 KRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARL 82 K T +R VS + G+I+ + G G G++ L+++I GA P D G + + G P AR+ Sbjct: 265 KGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADPADSGTVAL-GSP-ARV 322 Query: 83 ----SALEALAAGIETVYQDL---SLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135 S +A+A GI + +D LL S+A N+AL + E A + A Sbjct: 323 VSIRSPSDAVAHGIALITEDRKGEGLLLTQSIAANIALGN---MPEISSAGLVNGSAELA 379 Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195 A R ++A+ + +S Q L+ +L +Q V I R + + ++ DEPT + Sbjct: 380 LAQRQVDAMRIRSSSPTQ--LVSELSGGNQQKVVIGRWLERDCAVMLFDEPTRGIDVGAK 437 Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQ 236 ++ A+L L QG ++ VS L E I + VL G+ Sbjct: 438 FDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGR 478 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: 596 Number of extensions: 30 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 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