Align deoxynucleoside transporter, ATPase component (characterized)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 302 bits (773), Expect = 2e-86 Identities = 191/516 (37%), Positives = 296/516 (57%), Gaps = 26/516 (5%) Query: 11 LSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPD-- 68 L+ P LE+ G+ K F GV AL V+LS + G+I+ L+GENG GKSTL+K++SG P Sbjct: 1 LAMPILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSF 60 Query: 69 EGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTF 128 +G++ G P A ++ GI ++Q+L+L+P +S+ EN+ L +E A+ Sbjct: 61 DGEIRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQAS--------- 111 Query: 129 DRRVLAATAA--RALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEP 186 R V+ AA RA E + L G + TLI + + +QLV IA+A++ E K +I+DEP Sbjct: 112 -RGVIDWDAATLRARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEP 170 Query: 187 TTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEF 246 T SL + + D L+ +L +A+G+ + +SHKL+E + V +LRDG + E Sbjct: 171 TASLNESDSDALLELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREA 230 Query: 247 TKAQ--ISELMTGRHLSNERYRESAHAQDIVLDVRGFT-----RAGQ--FSDVSFKLHGG 297 +Q I M GR LS+ R + D++ +V+G++ G+ DV+ + G Sbjct: 231 VVSQDRIIRGMVGRALSDRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRG 290 Query: 298 EILGVTGLLDSGRNELARALAGVAPAQS--GDVLLDGQQIALRTPSDAKRHRIGYVPEDR 355 E++G+ GL+ +GR E A +L G + ++ G LDG++I + T S A + + Y EDR Sbjct: 291 EVVGIAGLMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDR 350 Query: 356 LNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSL 415 + GL LD IR NV A + + R+ ID R +AE+ + L+I V + +L Sbjct: 351 KHLGLVLDNDIRHNVTLANLRGVAKRW-VIDHEREVQVAEEFRRRLRIRCADVFQETVNL 409 Query: 416 SGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLP 475 SGGNQQ+V++ +WL DP+VLIL PT G+DVG+K IY I+ +L G G++LIS ++P Sbjct: 410 SGGNQQKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMP 469 Query: 476 ELLQNCDRILMMKKGHVSAEYRADELSEADLYHALL 511 ELL DRI +M G + AE A E S+ + A++ Sbjct: 470 ELLGVADRIYVMNAGEMVAEMPAAEASQEKIMGAIM 505 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: 598 Number of extensions: 31 Number of successful extensions: 11 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: 518 Length adjustment: 35 Effective length of query: 480 Effective length of database: 483 Effective search space: 231840 Effective search space used: 231840 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