Align deoxynucleoside transporter, ATPase component (characterized)
to candidate SM_b20317 SM_b20317 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__Smeli:SM_b20317 Length = 516 Score = 580 bits (1494), Expect = e-170 Identities = 299/502 (59%), Positives = 381/502 (75%), Gaps = 1/502 (0%) Query: 12 SQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQ 71 + PFLEV + KRF GV AL+GVS + +RG+ YHL+GENGCGKSTLIKIISGAQP D G+ Sbjct: 10 TMPFLEVRDLEKRFGGVRALKGVSFTIERGRTYHLMGENGCGKSTLIKIISGAQPADGGE 69 Query: 72 LVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRR 131 L I G L+ + ALAAGIETVYQDLSLLPN+SV ENVALT +L G LAR D + Sbjct: 70 LTINGKKVEGLTPIGALAAGIETVYQDLSLLPNLSVEENVALTQQLVASNGSLARRLDLK 129 Query: 132 VLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLT 191 L TA RAL+ VGLP F ST +E+LP+ATRQL+AIARAIAS+A VIMDEPTT+LT Sbjct: 130 GLRETAVRALKDVGLPTEPAFLSTPVEELPIATRQLIAIARAIASDAGLVIMDEPTTALT 189 Query: 192 QKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQI 251 ++EVDNLI V+ L A+GV+VLFV+HKLDEC AIGG+ I++RDG K+A+ +A +K ++ Sbjct: 190 RREVDNLIRVVHGLHAKGVSVLFVTHKLDECKAIGGQAIIMRDGLKVAECDVATQSKTEL 249 Query: 252 SELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRN 311 MTG++L + RYR H + +L V AG F DVSF + GEI G+TGLLDSGRN Sbjct: 250 GFWMTGKNLDDTRYRVDTHGDETLLSVERLGGAG-FDDVSFTVSKGEIFGITGLLDSGRN 308 Query: 312 ELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVI 371 ELA +LAGV A+ G VLL G++ L +P+ A IGYVPEDRL+EGLFL K IR+N++ Sbjct: 309 ELALSLAGVESARRGSVLLAGRRADLSSPASAIEAGIGYVPEDRLSEGLFLGKSIRENIV 368 Query: 372 TAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAI 431 A++ LR FG +D RA+ALA++TV +LQ+ATP +D PV SLSGGNQQRVLIGRWL I Sbjct: 369 MAVLDRLRGAFGLLDSRRAKALAQKTVDDLQVATPDIDNPVMSLSGGNQQRVLIGRWLTI 428 Query: 432 DPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGH 491 +P +LILHGPTVGVDVGSKD I+RI+QRL+ G+ +++ISDDLPELLQNCDR+++M+KG Sbjct: 429 EPSLLILHGPTVGVDVGSKDTIFRIIQRLAGDGMSVVIISDDLPELLQNCDRVMVMRKGR 488 Query: 492 VSAEYRADELSEADLYHALLSE 513 V+ + A+ L E +Y ++++E Sbjct: 489 VADIFPAEGLEEDAIYKSMMAE 510 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: 674 Number of extensions: 26 Number of successful extensions: 4 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