Align deoxynucleoside transporter, ATPase component (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 319 bits (817), Expect = 2e-91 Identities = 193/511 (37%), Positives = 292/511 (57%), Gaps = 18/511 (3%) Query: 12 SQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQ 71 S P L + G+ K F GV AL GV + + G+I+ LLGENG GKSTLIK ++G D G Sbjct: 9 SPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGT 68 Query: 72 LVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRR 131 + +EG A EA I TVYQ+++LLPN+SVAEN+ L GR F Sbjct: 69 VTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFL--------GRQPMRFGLV 120 Query: 132 VLAATAARALEAVGLPGNSEFQSTL-IEQLPLATRQLVAIARAIASEAKFVIMDEPTTSL 190 A RA AV +P T + + +AT+Q+VAIARA+ AK +I+DEPT SL Sbjct: 121 DRGAMRRRA-RAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASL 179 Query: 191 TQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQ 250 +EV L V+ LR++G+ ++FV+H LD+ YA+ + VLR+G+ + + AE + Sbjct: 180 DAQEVAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLD 239 Query: 251 ISELMTGRHLSNERYRESAHAQDIVLDVR-------GFTRAGQFSDVSFKLHGGEILGVT 303 + +M GR L +R + A D D R G+ +A + GE++G+ Sbjct: 240 LVAMMLGRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLA 299 Query: 304 GLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLD 363 GLL SGR E AR + G+ A G+ +DGQ + LR P DA R G+ PEDR EG+ Sbjct: 300 GLLGSGRTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGA 359 Query: 364 KPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRV 423 +R+N+I A+ + + I R R + +A++ ++ L I TP ++P+Q LSGGNQQ+ Sbjct: 360 LSVRENIILAL-QARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKA 418 Query: 424 LIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDR 483 L+ RWLA +PR+LIL PT G+DVG+ I R+++RL G+ ++++S +L E++ R Sbjct: 419 LLARWLATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRR 478 Query: 484 ILMMKKGHVSAEYRADELSEADLYHALLSEA 514 +++++ AE R E++ + A+ SE+ Sbjct: 479 VVVLRDRRHVAELRGGEVAVDRIVAAIASES 509 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: 638 Number of extensions: 31 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: 516 Length adjustment: 35 Effective length of query: 480 Effective length of database: 481 Effective search space: 230880 Effective search space used: 230880 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