Align D-lysine oxidase (EC 1.4.3.3) (characterized)
to candidate H281DRAFT_03160 H281DRAFT_03160 D-amino-acid dehydrogenase
Query= metacyc::G1G01-3833-MONOMER (414 letters) >FitnessBrowser__Burk376:H281DRAFT_03160 Length = 413 Score = 415 bits (1066), Expect = e-120 Identities = 216/410 (52%), Positives = 261/410 (63%), Gaps = 5/410 (1%) Query: 5 TLVLGAGIVGVSTALHLQARGRQVILIDRDEPGSGTSHGNAGLIERSSVIPYAFPRQLSA 64 T+VLGAGIVGV A+HLQ RGRQV L+DR PG+ TS GNAGLI+R V PYAFPR L A Sbjct: 8 TVVLGAGIVGVCVAVHLQQRGRQVALVDRKLPGNETSFGNAGLIQREGVYPYAFPRGLGA 67 Query: 65 LLRYGLNRQPDVRYSLAHLPKAAPWLWRYWRQSAPGRLAGAAADMLPLVQRCVDEHDALI 124 LLRY N+ DVRY L AAP+LWRYWR S P + A A L++ C+ EH L Sbjct: 68 LLRYARNQSLDVRYHGDALFHAAPFLWRYWRNSEPAKHAAIAKSYSTLIEHCISEHRELA 127 Query: 125 AAAGLEGLVQAKGWIEVFRDPALFE-QAKTDAKGLSRYGLRFEILECGQLQAREHQLDAT 183 A AG L++ GWI+VFR A + + + + YG+ FE L+ +LQ E LD Sbjct: 128 ANAGASALLRPTGWIKVFRSNAAQDAEIRLAEQWRREYGVEFETLDAARLQQAEPDLDKA 187 Query: 184 VVGGIHWLDPKTVNNPGALTRGYAALFLQRGGQFVHGDARSLRQANGQWRVESRRGPITA 243 + GG+ + +V++P AL YA F GG+ GDA +LR NG W V + G I A Sbjct: 188 LQGGLRYTQADSVSDPNALVTAYAKYFETLGGRIFTGDANTLR--NG-WEVTTDAGTIAA 244 Query: 244 DEVVACLGPQSADLFSGLGYQIPLAIKRGYHMHYSTRDGAQLEHSICDTQGGYVLAPMAR 303 VV LGP S L S LGY +PL +KRGYHMHYS R GA+L H + D + GY+LAPMAR Sbjct: 245 SSVVVALGPWSDVLTSRLGYSLPLGVKRGYHMHYSPRAGARLNHPVLDVENGYLLAPMAR 304 Query: 304 GVRLTTGIEFDAASAPGNQIQLGRCEALARKLFPALGDRLDDTPWLGRRPCLPDMRPVIG 363 G+RLTTG E AP QL E +AR LFP L R+DD PW+G RPC PDM PVIG Sbjct: 305 GIRLTTGAEIALRDAPKTPTQLAAVEPIARTLFP-LDQRVDDQPWMGARPCTPDMMPVIG 363 Query: 364 PAPRHPGLWFNFGHAHHGLTLGPVCGRLLAELLTGEPPFTDPAPYSATRF 413 A +H GLWF FGHAHHGLTLGPV GRL+AE++TGE DP P+ RF Sbjct: 364 RAGKHQGLWFAFGHAHHGLTLGPVTGRLIAEMMTGEQTLVDPRPFRVDRF 413 Lambda K H 0.322 0.140 0.447 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: 540 Number of extensions: 27 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: 414 Length of database: 413 Length adjustment: 31 Effective length of query: 383 Effective length of database: 382 Effective search space: 146306 Effective search space used: 146306 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 (21.9 bits) S2: 50 (23.9 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