Align DUF1624 domain-containing protein (characterized, see rationale)
to candidate WP_009121798.1 BUB52_RS13780 DUF1624 domain-containing protein
Query= uniprot:L0FVP4 (369 letters) >NCBI__GCF_900129655.1:WP_009121798.1 Length = 396 Score = 226 bits (575), Expect = 1e-63 Identities = 148/397 (37%), Positives = 218/397 (54%), Gaps = 40/397 (10%) Query: 4 QRILALDVFRGITIFAMILVNNPGSWSHVYAPLLHAKWHGCTPTDLIFPFFLFIVGVAIE 63 +RILALD+ RG+TI MI+VNNPG+W+H+YAPL HA+W+G TPTDL+FPFF+FI+G++ Sbjct: 9 KRILALDILRGVTIAGMIMVNNPGTWAHIYAPLRHAEWNGLTPTDLVFPFFMFIMGISTY 68 Query: 64 LSL-----------GGQLKKGTPKGFLLRKSLIRALKL----------IGLGLLL-TAIP 101 +SL G ++ K T FL+ ++ K I G L ++ Sbjct: 69 ISLKKYNFEFSRAVGMKILKRTILIFLIGMAIGWFSKFCYYWTSPTEGISFGAQLWESVW 128 Query: 102 YFDLAHLRFPGVLQRIGLVYFISTVMYLYWSPKALVFSSGILLIGYWLCMTFIPVPGIGP 161 FD +R GV+QR+ L Y + ++ L + + + LL GY++ + V G G Sbjct: 129 TFD--RIRILGVMQRLALCYGATAIIALTVKHRNIPYLIATLLTGYFILL----VCGNGF 182 Query: 162 ANLEPGTNLAAWIDQQVLT-GHMWSQTKTWDPEGLFSTLPAIVTCLLGVACGKILTGN-- 218 A + TN+ + ID+ +LT HM+ DPEGL ST+P+I LLG G+++ N Sbjct: 183 AYND--TNILSVIDRTILTPAHMYKDNGI-DPEGLLSTIPSIAHVLLGFCVGRMMLENGK 239 Query: 219 ------SSHKARLTKWGIAGVTLVFGGLAWSLFFPLNKALWTSSFVLYTAGWAFLGLAAC 272 S + L K +AG L F G S P+NK +W+ +FVL T G A LA Sbjct: 240 ANEDRESMLNSHLIKLFLAGTILTFSGFLLSYGCPINKKIWSPTFVLTTCGLASSFLALL 299 Query: 273 YWILDVKGWKKWSLPFVIYGMNAITVFFLSGVIAKLFGLIKVNWEGTRVSLKLFLQEALF 332 WI+DVKG+KKWSL F +G+N + ++ L GV++ LFG I W + +S+ FL + L Sbjct: 300 IWIIDVKGYKKWSLFFESFGVNPLFMYVLGGVLSILFGSISFPWGASSISIHGFLYKILL 359 Query: 333 NGWLAPKDASLCGAILMMIILFIPAYFMWKRNIIIKV 369 SL A+L + I + Y ++KR I IK+ Sbjct: 360 MPVFGETGGSLAYALLFVGINWCIGYQLYKRKIYIKL 396 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: 547 Number of extensions: 38 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: 396 Length adjustment: 30 Effective length of query: 339 Effective length of database: 366 Effective search space: 124074 Effective search space used: 124074 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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