Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= uniprot:D8IUD1 (522 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 324 bits (830), Expect = 5e-93 Identities = 198/479 (41%), Positives = 282/479 (58%), Gaps = 11/479 (2%) Query: 13 LLTLSGIGKRYAAPV-LDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMML 71 +L G+GKR+ A + LDG+DL LR G+V AL G+NGAGKSTL K++ G+ G + L Sbjct: 12 VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71 Query: 72 DGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLP--RRFGWIDRKKLAEAA 129 DG+ AP++ +A+ GI V QE+NL P LS+AENL+ + P RR ID +++ + A Sbjct: 72 DGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGA 131 Query: 130 RAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLF 189 R+ + + L ELD P+G + +QMV IAR L S R LILDEPT+ L EV LF Sbjct: 132 RSLLRQLHL-ELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELF 190 Query: 190 SRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGEL 249 I +LR G+AI++++H L+++ ++DRI VLRDG V + LV M G Sbjct: 191 RVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRD 250 Query: 250 TKVDLDAEHRRI----GAPVLRIRGLGRAPVVHPASLALHAGEVLGIAGLIGSGRTELLR 305 A+ R P + +GLG +HP L + GE+LG+ GL+GSGRTEL R Sbjct: 251 LPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELAR 310 Query: 306 LIFGADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLA 365 L+FG DRAE+GE+ IG E ++ P DAV G+A+ E+RK G++ ++ N LA Sbjct: 311 LLFGLDRAERGELRIGG--ERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLA 368 Query: 366 NLGSVSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCP 425 GM A + +A+ V+ L I++ + G LSGGNQQKV++ARWL + Sbjct: 369 LQARQGWRGM-SRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEPR 427 Query: 426 IMLFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIA 484 +++ DEPTRGID+ AK ++ A G +L +S++ EL + CDRIAVM R A Sbjct: 428 LLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKA 486 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: 762 Number of extensions: 45 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: 505 Length adjustment: 35 Effective length of query: 487 Effective length of database: 470 Effective search space: 228890 Effective search space used: 228890 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