Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate N515DRAFT_1539 N515DRAFT_1539 Agmatine/peptidylarginine deiminase
Query= BRENDA::Q9PAQ3 (363 letters) >FitnessBrowser__Dyella79:N515DRAFT_1539 Length = 345 Score = 426 bits (1096), Expect = e-124 Identities = 201/337 (59%), Positives = 253/337 (75%) Query: 24 RFPAEWEPQSAILIAWPHANTDWSAHLADVEETYIALVAAITRFQMVIICVLDDDLQTYT 83 R PAEWEPQSA+LIAWPHA+TDW+ LA+VE TY+AL AA+TRF+ +I+ V D +L+ + Sbjct: 7 RLPAEWEPQSAVLIAWPHADTDWADRLAEVETTYVALAAAVTRFEPLIVVVADAELRAHV 66 Query: 84 EARLRSASVAMQQVRFTVASYNDTWLRDSGPITLIGTNRDFRLLDFRFTGWGGKFEAKAD 143 E +LR A V + +VR Y+DTWLRDSGPITL F+L DFRFTGWGGKF A+ D Sbjct: 67 EGKLREAGVDLGRVRLIELPYDDTWLRDSGPITLKDDRGAFQLTDFRFTGWGGKFGAEQD 126 Query: 144 DQLVSVLHANGLFKNTQMHSINFALEGGAIETDGAGTLLTTWRCLHERHPQRTRKTLDAN 203 D LV+ L G+F I++ALEGG IE+DGAGT+LTTWRCL +RHP+++R+ + A Sbjct: 127 DALVAGLVKAGVFGRAAHRRIDWALEGGGIESDGAGTVLTTWRCLVQRHPEQSREEMSAI 186 Query: 204 LTAWLAQNRVLWLEHGYLEGDDTDAHIDTLARFASTDSIVYQSCDNTTDSHYAELQAMAN 263 L L +R+LWL++GYLEGDDTDAHIDTLARFA IV+Q+CD+ D+H+ EL MA Sbjct: 187 LRDGLHASRILWLDYGYLEGDDTDAHIDTLARFAPDGRIVFQACDDLDDAHHDELSRMAG 246 Query: 264 ELTALRTTEGRAYRLFPLPWTKPILDQDRRLPASYANFLIIEGAVLMPTYDDPADTIAQS 323 EL AL +G+ Y L+PLPW KPI+D+ RRL ASYAN+LI+ G VL+P Y DPAD A Sbjct: 247 ELAALCMADGKPYELYPLPWAKPIVDEGRRLAASYANYLIVNGGVLVPAYGDPADDEAAR 306 Query: 324 VLAEAFPTREIVPVPCRPLIWQNGSLHCITMQIPAGL 360 ++ A P RE+V VPCRPLIWQNGSLHCITMQ+PAG+ Sbjct: 307 IIGAAHPGREVVQVPCRPLIWQNGSLHCITMQLPAGI 343 Lambda K H 0.322 0.134 0.423 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: 493 Number of extensions: 20 Number of successful extensions: 1 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: 363 Length of database: 345 Length adjustment: 29 Effective length of query: 334 Effective length of database: 316 Effective search space: 105544 Effective search space used: 105544 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: 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