Align deoxynucleoside transporter, ATPase component (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 306 bits (785), Expect = 9e-88 Identities = 179/504 (35%), Positives = 290/504 (57%), Gaps = 21/504 (4%) Query: 16 LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75 LE+ + K + GV AL VSL G+++ LLGENG GKSTL+K+++GAQ D G ++ Sbjct: 5 LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL 64 Query: 76 GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135 G P + ++A AGI TVYQ+++L+PN++VA+N+ L +E R + + A Sbjct: 65 GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLG-----YEPRRLGLIHFKKMYA 119 Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195 A L L + S + +A +QL+AIAR +A AK +++DEPT SL KEV Sbjct: 120 DARAVLTQFKLDIDV---SAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEV 176 Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255 L +L L+A+GV ++F++H LD+ Y I + VLR+GQ + + AE + ++ E M Sbjct: 177 QVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAM 236 Query: 256 TGRHLSN------ERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSG 309 GR L E+ R A+ ++L + + G ++ + G+ +G+ GLL SG Sbjct: 237 LGRSLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSG 296 Query: 310 RNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDN 369 R+E+ A+ G+ SG + L GQ++ L P DA I PEDR +G+ IR+N Sbjct: 297 RSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIREN 356 Query: 370 VITAMISSLRDRFG---QIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIG 426 +I A L+ R G + TR Q +A+ + +LQIATP DKP++ LSGGNQQ+V++ Sbjct: 357 IILA----LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILA 412 Query: 427 RWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILM 486 RWLAI+P +L+L PT G+D+G+ I ++++ L G+ +++ S +L EL+ +++++ Sbjct: 413 RWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVV 472 Query: 487 MKKGHVSAEYRADELSEADLYHAL 510 ++ + E EL+ + A+ Sbjct: 473 LRDRYAVRELSGAELTSQHVMQAI 496 Score = 89.0 bits (219), Expect = 4e-22 Identities = 61/233 (26%), Positives = 105/233 (45%), Gaps = 21/233 (9%) Query: 289 DVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKR--- 345 DVS +L GE+ + G +G++ L + + G GD+L G+ TP DA++ Sbjct: 22 DVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDAQKAGI 81 Query: 346 ----HRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKEL 401 + VP + + LFL R R G I + A A + + Sbjct: 82 STVYQEVNLVPNLTVAQNLFLGYEPR-------------RLGLIHFKKMYADARAVLTQF 128 Query: 402 QIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLS 461 ++ V P+ S QQ + I R +A+ +VL+L PT +D +++ I+ +L Sbjct: 129 KLDID-VSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLK 187 Query: 462 QRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHALLSEA 514 +G+ I+ I+ L ++ Q DRI +++ G EY EL + L A+L + Sbjct: 188 AKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRS 240 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: 591 Number of extensions: 36 Number of successful extensions: 8 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: 499 Length adjustment: 34 Effective length of query: 481 Effective length of database: 465 Effective search space: 223665 Effective search space used: 223665 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