Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 215 bits (547), Expect = 4e-60 Identities = 145/485 (29%), Positives = 251/485 (51%), Gaps = 20/485 (4%) Query: 10 PLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDE 69 P P + + G+ KRF V A +SL+ G++ LLGENG GKSTL+ +++G PD Sbjct: 19 PQGIPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDA 78 Query: 70 GQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFD 129 G + ++G P SA +A+ AGI VYQ L+ +M+VAENV L E + + Sbjct: 79 GTIALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEGSFFLN--PKEMR 136 Query: 130 RRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTS 189 RV + L+ + + L + +Q V I + + +++ +I DEPT Sbjct: 137 NRVQELSVRYGLDID--------PAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAV 188 Query: 190 LTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFT-K 248 LT +E +L L + QG +++F+SHKL+E A+ E+ +LR G+ + +E T K Sbjct: 189 LTPRETFHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSK 248 Query: 249 AQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDS 308 A ++ M G+ + E RE+ D VL VR T G D++F LH GE++ V G+ + Sbjct: 249 ADLACRMVGKEVLLEVDREAMPHGDAVLQVRNLTGIG-LEDITFDLHQGEVVAVVGVAGN 307 Query: 309 GRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRD 368 G+ L A+ G+ + + G++ + ++ + Y+PEDRL GL + + Sbjct: 308 GQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRL--GLATCRNL-- 363 Query: 369 NVITAMISSLRDRFGQ---IDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLI 425 N++ ++ + R F + +D+ +A + +K+ I + LSGGN Q+ ++ Sbjct: 364 NLVDNLLLTTRQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVL 423 Query: 426 GRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRIL 485 R L PR+++ PT G+D+ + + ++ + + GI+L++ DL E LQ DR+ Sbjct: 424 ARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAREMA-GILLVTGDLNEALQLADRVA 482 Query: 486 MMKKG 490 ++ +G Sbjct: 483 VIYRG 487 Score = 72.0 bits (175), Expect = 5e-17 Identities = 63/237 (26%), Positives = 113/237 (47%), Gaps = 14/237 (5%) Query: 275 VLDVRGFT-RAGQF---SDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLL 330 ++ ++G T R G+ D+S ++ G + + G +G++ L LAG +G + L Sbjct: 24 LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83 Query: 331 DGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRA 390 DG+ + + DA IG V + + L + +NV+ S ++ R R Sbjct: 84 DGKPVRFSSARDAIEAGIGMVYQHFM---LVESMTVAENVLLGQEGSFFLNPKEM-RNRV 139 Query: 391 QALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSK 450 Q L+ + ++ A V LS G +QRV I + L D RVLI PT + Sbjct: 140 QELSVRYGLDIDPAAR-----VSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRET 194 Query: 451 DIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADEL-SEADL 506 ++ + +++++G I+ IS L E+L D I ++++G + E+ E+ S+ADL Sbjct: 195 FHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADL 251 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: 531 Number of extensions: 27 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 515 Length of database: 514 Length adjustment: 35 Effective length of query: 480 Effective length of database: 479 Effective search space: 229920 Effective search space used: 229920 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