Align deoxynucleoside transporter, ATPase component (characterized)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 Length = 514 Score = 288 bits (737), Expect = 3e-82 Identities = 179/497 (36%), Positives = 279/497 (56%), Gaps = 17/497 (3%) Query: 20 GVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPH 79 G+ K F GV AL +S GQ++ L+GENG GKSTL+KI+ GA P G L I Sbjct: 20 GIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIGERTM 79 Query: 80 ARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTF---DRRVLAAT 136 S +++ +G+ ++Q+L L+P M+VAEN+ L G L +F +R L Sbjct: 80 DFKSTADSIGSGVAVIHQELHLVPEMTVAENLFL--------GHLPASFGLINRSTLRQQ 131 Query: 137 AARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVD 196 A L+ GL + Q + +L L RQLV IA+A++ A + DEPT+SL+ +E+D Sbjct: 132 ALACLK--GLADEIDPQEK-VGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREID 188 Query: 197 NLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQ-GPIAEFTKAQISELM 255 L+A++ LR +G VL+VSH+++E + I V V +DG+ + +++ T Q+ M Sbjct: 189 RLMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCM 248 Query: 256 TGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELAR 315 GR + + + L V G G VSF++H GEILG+ GL+ +GR EL R Sbjct: 249 VGRDIQDIYDYRPRQRGAVALKVDGLLGPGLREPVSFEVHKGEILGLFGLVGAGRTELLR 308 Query: 316 ALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMI 375 L+G+A +G + L G ++ LR+P DA I PEDR EG+ + +N I Sbjct: 309 LLSGLARHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAEN-INISA 367 Query: 376 SSLRDRFGQIDRTRAQA-LAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPR 434 FG + R + AEQ +K L++ TP + + LSGGNQQ+ ++GRWL++ + Sbjct: 368 RGAHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMK 427 Query: 435 VLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSA 494 VL+L PT G+D+G+K IY+I+ L+ GI +I++S DL E++ DRIL++ +G + Sbjct: 428 VLLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRG 487 Query: 495 EYRADELSEADLYHALL 511 E ++ +E++L L Sbjct: 488 ELSREQANESNLLQLAL 504 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: 599 Number of extensions: 33 Number of successful extensions: 8 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: 514 Length adjustment: 35 Effective length of query: 480 Effective length of database: 479 Effective search space: 229920 Effective search space used: 229920 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