Align deoxynucleoside transporter, ATPase component (characterized)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__Smeli:SM_b20713 Length = 513 Score = 349 bits (895), Expect = e-100 Identities = 186/486 (38%), Positives = 301/486 (61%), Gaps = 7/486 (1%) Query: 8 SAPLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPP 67 + P S+ L GV K F GV AL V +RG ++ L+GENG GKSTL+KI++G P Sbjct: 16 AVPKSEYLLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYP 75 Query: 68 DEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLART 127 D+G++ + G S L+AL GI ++Q+L+L+P M+VAEN+ + E G + Sbjct: 76 DQGEVKLRGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHG 135 Query: 128 FDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPT 187 RR+ A+ E + + + E + + L +A RQ+V IA+A++ E+ +IMDEPT Sbjct: 136 EMRRM----TAKLFERLKIDLDPEIE---VRHLSVANRQMVEIAKAVSYESDVLIMDEPT 188 Query: 188 TSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFT 247 ++LT++EV +L ++ +LR+QG+ +++++HK++E + I E V RDG+ + E T Sbjct: 189 SALTEREVAHLFEIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVT 248 Query: 248 KAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLD 307 + I +M GR ++ +E D+VL V+ T G F DVSF + GEILGV GL+ Sbjct: 249 RDDIIRMMVGREITQMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVG 308 Query: 308 SGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIR 367 SGR+ +A L GV PA SG + +DG+++ + + + A RHR+ ++ EDR + G L I Sbjct: 309 SGRSNVAETLFGVTPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDIL 368 Query: 368 DNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGR 427 +N+ A++ + G + A E+ ++L++ TP + + V++LSGGNQQ+VLIGR Sbjct: 369 ENMQIAVLQDKFVKRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGR 428 Query: 428 WLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMM 487 WL +PR+LIL PT G+DVG+K I+R++ L++ G+ +I+IS ++PE+L DRI++M Sbjct: 429 WLLTNPRILILDEPTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVM 488 Query: 488 KKGHVS 493 +G V+ Sbjct: 489 HEGRVT 494 Score = 77.0 bits (188), Expect = 1e-18 Identities = 58/224 (25%), Positives = 113/224 (50%), Gaps = 8/224 (3%) Query: 289 DVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRI 348 DV FKL G + + G +G++ L + LAG+ G+V L G I L++P DA + I Sbjct: 41 DVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKLRGAGIRLKSPLDALENGI 100 Query: 349 GYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQI-ATPG 407 + ++ LN F+ + +N+ ++RFG +D + + + + L+I P Sbjct: 101 AMIHQE-LNLMPFMT--VAENIWIRR--EPKNRFGFVDHGEMRRMTAKLFERLKIDLDPE 155 Query: 408 VDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGI 467 ++ V+ LS N+Q V I + ++ + VLI+ PT + ++ I++ L +GIGI Sbjct: 156 IE--VRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFEIIRDLRSQGIGI 213 Query: 468 ILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHALL 511 + I+ + EL + D + + G + ++E++ D+ ++ Sbjct: 214 VYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMV 257 Score = 61.6 bits (148), Expect = 6e-14 Identities = 60/247 (24%), Positives = 108/247 (43%), Gaps = 13/247 (5%) Query: 14 PFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLV 73 P +VV K T R VS + G+I + G G G+S + + + G P G + Sbjct: 271 PIGDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNVAETLFGVTPASSGTIA 330 Query: 74 IEGVPHARLSALEALA---AGIETVYQDLSLLPNMSVAEN--VALTSELATHEGRLARTF 128 I+G SA +A+ A + +D L + + EN +A+ + G ++ Sbjct: 331 IDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIAVLQDKFVKRGFVS--- 387 Query: 129 DRRVLAATAARALEA-VGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPT 187 +R V AA + + V P E +E L +Q V I R + + + +I+DEPT Sbjct: 388 EREVTAACEEMSRKLRVKTPNLQE----RVENLSGGNQQKVLIGRWLLTNPRILILDEPT 443 Query: 188 TSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFT 247 + + ++ L GV V+ +S ++ E + ++V+ +G+ AE T Sbjct: 444 RGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGILDRAEAT 503 Query: 248 KAQISEL 254 + ++ EL Sbjct: 504 QIKVMEL 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: 581 Number of extensions: 32 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 515 Length of database: 513 Length adjustment: 35 Effective length of query: 480 Effective length of database: 478 Effective search space: 229440 Effective search space used: 229440 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