Align deoxynucleoside transporter, ATPase component (characterized)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 326 bits (835), Expect = 1e-93 Identities = 175/503 (34%), Positives = 308/503 (61%), Gaps = 11/503 (2%) Query: 14 PFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLV 73 P E+ G+ K F GV AL VS + G+++ LLGENG GKS+L+K++ G D G+ Sbjct: 9 PLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFY 68 Query: 74 IEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVL 133 +G P A S + + GI ++Q+ SL+P + +A+N+ L E GR+ + D + Sbjct: 69 HDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGRE---PRGRIPGSVDAARM 125 Query: 134 AATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQK 193 A A R L+ +G+ ++ T + +L +A +Q+V IA+A++ A+ +++DEPT +L+ + Sbjct: 126 HAEARRILDILGMEVSTR---TPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDR 182 Query: 194 EVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISE 253 E + L AV+A L+A GV+++++SH++ E +A+G + +LRDG+K+ + T ++ Sbjct: 183 ETEKLFAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVA 242 Query: 254 LMTGRHLSNERYRE-SAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNE 312 M GR + RE SA ++ LDVR + +D++ ++ GEI+G+ GL+ SGR+E Sbjct: 243 RMVGRKVDMSYSRERSAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSE 302 Query: 313 LARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVIT 372 +ARA+ G P + G++ + G+++ P A+ +PE R +EGL L + +RDN++ Sbjct: 303 VARAVFGADPIRQGEIYIFGKRLT-GGPDRARELGAALIPESRKSEGLALIRTVRDNLLL 361 Query: 373 AMIS-SLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAI 431 A + + R+ + D+ A+ALAE+ + L+IATP ++ Q LSGGNQQ+++IG+WL Sbjct: 362 AGLRRAFPARWYRADK--AEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVA 419 Query: 432 DPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGH 491 + ++ I PT G+DVG+K I+ ++ L ++G G++LIS +LPE++ CDR +M+ G Sbjct: 420 EAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGR 479 Query: 492 VSAEYRADELSEADLYHALLSEA 514 ++ E E++E + +++A Sbjct: 480 IAGEVAHAEMTEERILQLGMNDA 502 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: 609 Number of extensions: 31 Number of successful extensions: 9 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: 502 Length adjustment: 34 Effective length of query: 481 Effective length of database: 468 Effective search space: 225108 Effective search space used: 225108 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