Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IUD1 (522 letters) >NCBI__GCF_900177295.1:WP_085124759.1 Length = 518 Score = 315 bits (806), Expect = 3e-90 Identities = 188/496 (37%), Positives = 281/496 (56%), Gaps = 7/496 (1%) Query: 11 SPLLTLSGIGKRYAAPV-LDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGM 69 +PLL L G+ +R+ + LD +D LRPG+V L GENGAGKST+ +I G + S G Sbjct: 21 APLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEF 80 Query: 70 MLDGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFGWIDRKKLAEAA 129 G+P S A GLGI V QE +L+P +++ ENLFL R G +DR+ L + A Sbjct: 81 RFRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDRA 140 Query: 130 RAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLF 189 A ++ +G L P V L QQMVEIA+ LILDEPTA LT RE LF Sbjct: 141 DAILKRLGF-PLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLF 199 Query: 190 SRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGEL 249 IE+++A+GV +IYI+HRL E++RI DRI VLRDG+ V D +LV+LM G + Sbjct: 200 KLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTGRV 259 Query: 250 TKVDLDAEHRRIGAPVLRIRGLGRAP-VVHPASLALHAGEVLGIAGLIGSGRTELLRLIF 308 + G +L + L A V ASL++ AGE++G+AGL+GSG++E+ R F Sbjct: 260 YDELFPKVRFKPGRELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACF 319 Query: 309 GADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLAN-- 366 G ++ +G + + E + PK +K G V DR+ +GL++ + + N SL + Sbjct: 320 GLEKIAEGHVRL--KGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLT 377 Query: 367 LGSVSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPI 426 L G +LD E+ + ++L ++ + +A SGGNQQKV++A+ R + Sbjct: 378 LAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQV 437 Query: 427 MLFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIADT 486 FDEPT G+D+G + IY +L G G+L++SSDL E++ + +R V GR+ Sbjct: 438 FAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQAE 497 Query: 487 FSRDDWSQERILAAAF 502 + D+ ++E++L+ F Sbjct: 498 LAGDEITEEKVLSHFF 513 Lambda K H 0.320 0.137 0.390 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: 645 Number of extensions: 37 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: 522 Length of database: 518 Length adjustment: 35 Effective length of query: 487 Effective length of database: 483 Effective search space: 235221 Effective search space used: 235221 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 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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