Align deoxynucleoside transporter, ATPase component (characterized)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__Putida:PP_2759 Length = 512 Score = 317 bits (811), Expect = 9e-91 Identities = 179/493 (36%), Positives = 283/493 (57%), Gaps = 14/493 (2%) Query: 11 LSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEG 70 +S P LE+ G+ K F AL G SL G ++ L+GENG GKSTLIK+++G PD G Sbjct: 1 MSTPVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAG 60 Query: 71 QLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDR 130 L+++G PH S + GI ++Q+ L +V E + HE R DR Sbjct: 61 SLLLDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFG-----HERRFGPLLDR 115 Query: 131 RVLAATAARALE---AVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPT 187 R AAR L+ + LP N+ LI +L A +Q+V I RA+ + + ++ DEP+ Sbjct: 116 RSQQREAARLLDDYFGLRLPANA-----LIGELSSAEQQMVQIVRALLIKPRVLVFDEPS 170 Query: 188 TSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFT 247 +L Q+EV+ L+ ++ LR G+ ++++SH L E A+ V VLR+G+ +A+ + Sbjct: 171 VALVQREVERLLRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTS 230 Query: 248 KAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLD 307 QI+ LM R + + + A ++LDVRG RA + + ++ GEI+G+TGL+ Sbjct: 231 LEQITRLMVNREVGELYPKVAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVG 290 Query: 308 SGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIR 367 SG EL R+L G+AP SG+V LDGQ ++LR+P +A + +PE+R +G+ LD ++ Sbjct: 291 SGAKELLRSLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQ 350 Query: 368 DNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGR 427 +N A +S R G + R + + ++ L+I G V+ LSGGNQQ+V + + Sbjct: 351 ENTTLAALSRF-VRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAK 409 Query: 428 WLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMM 487 W A + +L P+VG+DVG+K IYR++ L + G G++++S DLPEL+ CDRI +M Sbjct: 410 WFARCSSLYLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVM 469 Query: 488 KKGHVSAEYRADE 500 +G ++A + A E Sbjct: 470 HRGAIAARFAAGE 482 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: 623 Number of extensions: 30 Number of successful extensions: 6 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: 512 Length adjustment: 35 Effective length of query: 480 Effective length of database: 477 Effective search space: 228960 Effective search space used: 228960 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