Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_022530418.1 L248_RS11555 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >NCBI__GCF_000469325.1:WP_022530418.1 Length = 508 Score = 282 bits (722), Expect = 2e-80 Identities = 166/502 (33%), Positives = 279/502 (55%), Gaps = 20/502 (3%) Query: 21 VHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHA 80 + K F GV AL V L + G+++ L+GENG GKSTLIK+++G G + + G Sbjct: 19 IAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVTLHGQDIN 78 Query: 81 RLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTF---DRRVLAATA 137 + EA GI TVYQ+++L PN+SVAENV + GR F D + A A Sbjct: 79 PKTPQEAQDLGISTVYQEVNLCPNLSVAENVYI--------GRQPMRFGQIDWHRMNADA 130 Query: 138 ARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDN 197 + LE++ + + + TL + ++ +Q++AIARA+ A +I+DEPT+SL EV Sbjct: 131 VKLLESLDI--HVDVTKTL-DSYSVSVQQMIAIARAVDMSAGVLILDEPTSSLDSNEVAQ 187 Query: 198 LIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257 L A++ +LR Q + +LFV+H +D+ YAI + VLR+G+ + + + + + M G Sbjct: 188 LFAIIRHLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELDLVTKMIG 247 Query: 258 RHLSNERYRESAHAQDI----VLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNEL 313 + + + ++D + + ++ G D S + GE+LG+ GLL SGR E+ Sbjct: 248 QKFVDANTQAHRPSKDYSTVRFVRMEDISKRGLVHDFSMAVRAGEVLGLAGLLGSGRTEV 307 Query: 314 ARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITA 373 A L GV G + + ++ P A ++GY EDR G+ D IR+N++ + Sbjct: 308 AELLFGVTHFDDGVIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLS 367 Query: 374 MISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDP 433 + + +I + Q +A++ + L I TP ++K + LSGGNQQ+VL+ RWLA DP Sbjct: 368 L--QAKKGLRRIPLKKQQEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLATDP 425 Query: 434 RVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVS 493 ++LIL PT G+D+ +K I ++ +LS++G+ II IS + E+++ CDRI++++ H Sbjct: 426 KLLILDEPTRGIDINTKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVLRDRHAV 485 Query: 494 AEYRADELSEADLYHALLSEAA 515 E +++S+ ++ + A Sbjct: 486 GELTDNQISQDNIMKVIAGGVA 507 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: 558 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: 508 Length adjustment: 35 Effective length of query: 480 Effective length of database: 473 Effective search space: 227040 Effective search space used: 227040 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 24 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