Align DUF1624 domain-containing protein (characterized, see rationale)
to candidate N515DRAFT_0596 N515DRAFT_0596 Predicted acyltransferase
Query= uniprot:L0FVP4 (369 letters) >FitnessBrowser__Dyella79:N515DRAFT_0596 Length = 357 Score = 236 bits (603), Expect = 5e-67 Identities = 145/377 (38%), Positives = 211/377 (55%), Gaps = 36/377 (9%) Query: 4 QRILALDVFRGITIFAMILVNNPGSWSHVYAPLLHAKWHGCTPTDLIFPFFLFIVGVAIE 63 +R+ ++D RG T+ AM+LVN+PG WSHVY PL HA+WHGCTPTDL+FPFFLF+VGV++ Sbjct: 6 RRLASVDALRGCTVAAMLLVNDPGDWSHVYWPLEHAQWHGCTPTDLVFPFFLFVVGVSVA 65 Query: 64 LSLGGQLKKGTPKGFLLRKSLIRALKLIGLGLLLTAIPYFDL--AHLRFPGVLQRIGLVY 121 L++ ++++G +G L+R +L+RAL+++GLGLL+ A L AH+R PGVLQRIG+ + Sbjct: 66 LAIAPRMEQGADRGALMRAALVRALRIVGLGLLINAAAALILPDAHMRIPGVLQRIGICF 125 Query: 122 FISTVMYLYWSPKALVFSSGILLIGYWLCMTFIPVPGIGPANLEPGTNLAAWIDQQVLTG 181 + LY + + + LL GY + LEP N+ + D V G Sbjct: 126 AAAAAFQLYANGRVQWSAIAALLAGYAGLLAL-------GGTLEPFQNIVSRTDTTVF-G 177 Query: 182 HMW-----SQTKTWDPEGLFSTLPAIVTCLLGVACGKILTGNSSHKARLTKWGIAGVTLV 236 H + DPEGL TLP+I T LLG+ G L +A L ++GV V Sbjct: 178 HFAYRYFPATGLGHDPEGLLGTLPSIATSLLGLRAGHWLR-RDDRRALL----LSGVAYV 232 Query: 237 FGGLAWSLFFPLNKALWTSSFVLYTAGWAFLGLAACYWILDVKGWKKWSLPFVIYGMNAI 296 G WSL PLNK LWT SFVL+TAGWA L L A + ++D++GW F G+NA+ Sbjct: 233 LLGAMWSLLQPLNKNLWTPSFVLWTAGWATLALLAFHLLVDLRGWPALGRRF---GVNAV 289 Query: 297 TVFFLSGVIAKLFGLIKVNWEGTRVSLKLFLQEALFNGWLAPKD----ASLCGAILMMII 352 + S + L + ++ L ++F GW+ P ASL A+ + + Sbjct: 290 AAYAGSEFMQILL---------PGLGIQDPLYRSVFAGWITPLAGPYVASLAFAVTFVAV 340 Query: 353 LFIPAYFMWKRNIIIKV 369 + + M +R I +K+ Sbjct: 341 WWAIVWAMDRRRIYLKL 357 Lambda K H 0.329 0.145 0.486 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: 488 Number of extensions: 29 Number of successful extensions: 4 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: 369 Length of database: 357 Length adjustment: 29 Effective length of query: 340 Effective length of database: 328 Effective search space: 111520 Effective search space used: 111520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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