Align ABC transporter related (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 447 bits (1150), Expect = e-130 Identities = 233/497 (46%), Positives = 334/497 (67%), Gaps = 6/497 (1%) Query: 3 LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62 ++L+ + + K + AL+ V L L AGEVHAL+G+NGAGKSTL+K++TG + D G + Sbjct: 11 VVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVE 70 Query: 63 FLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRR--LGLIHFKKMYAD 120 G +TPM+AQ+ GI TVYQEVNL PNL+VA+NL+ G PRR L +I ++++ Sbjct: 71 LDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDG 130 Query: 121 ARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLF 180 AR++L Q L++DV APL Y +A++Q++AIAR + +SA+VL+LDEPT+SLD EV+ LF Sbjct: 131 ARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELF 190 Query: 181 GILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRS 240 ++ QL+ +G+AI+F+THFLDQVY +SDRITVLR+G +GEY A+LP L+ AM+GR Sbjct: 191 RVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRD 250 Query: 241 LQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEV 300 L V + ER + + + +G + ++L V +G+ +GL GLLGSGR+E+ Sbjct: 251 L--PTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTEL 308 Query: 301 CNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILA 360 +FGLD + G + + G+++ L P DA+ G+ALCPE+RK DGI+ LS+RENI+LA Sbjct: 309 ARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLA 368 Query: 361 LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPI 420 LQAR G WR +S RQ E+A+ + L I D + P+ LSGGNQQKV+LARWL EP Sbjct: 369 LQARQG-WRGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEPR 427 Query: 421 LLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVR 480 LL+LDEPTRGID+ A E++ + GM++L S+E EL + +++ V+R+R Sbjct: 428 LLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKAG 487 Query: 481 ELSGAELTSQHVMQAIA 497 EL G T V+ IA Sbjct: 488 ELPGGS-TEARVLAMIA 503 Lambda K H 0.319 0.136 0.377 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: 656 Number of extensions: 24 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: 499 Length of database: 505 Length adjustment: 34 Effective length of query: 465 Effective length of database: 471 Effective search space: 219015 Effective search space used: 219015 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