Align deoxynucleoside transporter, ATPase component (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 417 bits (1073), Expect = e-121 Identities = 227/498 (45%), Positives = 320/498 (64%), Gaps = 8/498 (1%) Query: 15 FLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVI 74 F+++ + KR+ GV AL V + Q G+ L GENG GKSTLIKIISG +P G + I Sbjct: 9 FIDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQI 68 Query: 75 EGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLA 134 G H L+ + AAG+ ++QD SL PN+SVAEN+A T++L+T + R F R + Sbjct: 69 AGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQ----RLFKFRAVR 124 Query: 135 ATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKE 194 A AL+ +G+ + + + +E LP+A +QLVAI RA+AS+A+ +IMDEPTT+LT+KE Sbjct: 125 DIARAALDRIGVQIDLDAR---VETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKE 181 Query: 195 VDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISEL 254 V L ++ L+ +GV V+FVSHKL E + +V+VLR+G+K+A+GP +EF ++ Sbjct: 182 VRRLQGIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYH 241 Query: 255 MTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELA 314 MTGR + + A ++ V+G +AG FSD+SF L GE+LG+TGLL GR +A Sbjct: 242 MTGRDVPEVPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVA 301 Query: 315 RALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAM 374 +AL G+ +G +L+DG + L P A RIGYVPEDRL EGLFL + I NV Sbjct: 302 KALFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGR 361 Query: 375 ISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPR 434 + + G +D T A ++ L++ P V+ PVQSLSGGNQQRV + RWL+ PR Sbjct: 362 LDA-HTSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPR 420 Query: 435 VLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSA 494 VLIL+GP+VGVDVGSK I+ I++ L++ GIG+I+ISDDLPELL C R+L+M++G + Sbjct: 421 VLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIID 480 Query: 495 EYRADELSEADLYHALLS 512 L+E DL H L S Sbjct: 481 ALEGTALTEDDLAHRLAS 498 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: 593 Number of extensions: 21 Number of successful extensions: 6 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: 498 Length adjustment: 34 Effective length of query: 481 Effective length of database: 464 Effective search space: 223184 Effective search space used: 223184 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