Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 325 bits (833), Expect = 3e-93 Identities = 210/519 (40%), Positives = 294/519 (56%), Gaps = 24/519 (4%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADP-GGEC 71 L +R I K+F GV+AL ++L AGE L GENGAGKSTLMK+LSG Y GE Sbjct: 7 LFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEI 66 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 GQ ++ + + G+ +I+QEL L P LSVAENI+LG + R G D + A Sbjct: 67 LWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAMYAK 126 Query: 132 APTLAR-LGA-DFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRL 189 A L + LG D + A +QL EIA+A+ +A++L++DEPT+ L++ ET+ L Sbjct: 127 ADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEVL 186 Query: 190 FALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249 ++ L+ G+A +YISH++ E++ + D V V+RDG + T L L+ +MVGR Sbjct: 187 LGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMVGR 246 Query: 250 DLSGFYTKTHGQAVEREVMLSVRDVA-------DGRRVKGCSFDLRAGEVLGLAGLVGAG 302 L Y + + EV+ R +RV SF LR GE+LG+AGLVGAG Sbjct: 247 KLENLYPRI--EHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGAG 304 Query: 303 RTELARLVFGA-DARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLF 361 RTEL +FGA ++ E+ + L P AI AG+ + EDRK G+ Sbjct: 305 RTELVSAIFGAYTGKSSVELFLEGRP-------LKIRSPADAIRAGLGMVPEDRKRHGIV 357 Query: 362 LDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQ 421 V +NI L A G ++R I ++ A + + LSGGNQQ Sbjct: 358 PLLGVGDNITLATLDHYAHA-GHIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQ 416 Query: 422 KVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLC 481 K +L+++L +P+VLILDEPTRGVD+GAK+EIYRLI LA GVAI+++SSE+PEV+G+ Sbjct: 417 KAVLAKMLLARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMA 476 Query: 482 DRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAA 520 DRVLVM EG L G+ G TQE+++A A +A A Sbjct: 477 DRVLVMGEGRLRGDFPNQGL---TQEQVLAAAIDTSARA 512 Lambda K H 0.320 0.136 0.382 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: 632 Number of extensions: 23 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: 540 Length of database: 513 Length adjustment: 35 Effective length of query: 505 Effective length of database: 478 Effective search space: 241390 Effective search space used: 241390 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