Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate GFF2119 HP15_2073 peptidyl-arginine deiminase family protein
Query= BRENDA::Q9PAQ3 (363 letters) >FitnessBrowser__Marino:GFF2119 Length = 332 Score = 295 bits (756), Expect = 9e-85 Identities = 158/338 (46%), Positives = 205/338 (60%), Gaps = 17/338 (5%) Query: 36 LIAWPHANTDWSAHLADVEETYIALVAAITRFQMVIICV--------LDDDLQTYTEARL 87 ++ WPH TDW+ + +VE ++ + A+ + ++I L+ DL Y E Sbjct: 1 MLTWPHPGTDWAGLIDEVEPVFLDIAKAVLPHEHLVISCEHVVRLQELERDLNRYAEDNG 60 Query: 88 RSASVAMQQVRFTVASYNDTWLRDSGPITLIGTNRDFRLLDFRFTGWGGKFEAKADDQLV 147 +VR A NDTW RD GPIT++ T+ LLDFRF WGGKF + DD L Sbjct: 61 FPG-----RVRSVPAPANDTWARDHGPITIL-TDEGPTLLDFRFNAWGGKFPWEKDDALN 114 Query: 148 SVLHANGLFKNTQMHSINFALEGGAIETDGAGTLLTTWRCL--HERHPQRTRKTLDANLT 205 + L G+F T+M + F LEGG+ E+DG GTLLTT CL R+P R ++ L+ Sbjct: 115 NHLFNAGVFGTTRMQQVGFVLEGGSFESDGQGTLLTTSECLLTPTRNPAMDRTAIEQLLS 174 Query: 206 AWLAQNRVLWLEHGYLEGDDTDAHIDTLARFASTDSIVYQSCDNTTDSHYAELQAMANEL 265 L R+LWL HGYL GDDTD+HIDTLARF + D I Y +C + D HY+ L AM EL Sbjct: 175 EVLGIRRILWLNHGYLAGDDTDSHIDTLARFCAPDHICYVTCPDVADEHYSALAAMEEEL 234 Query: 266 TALRTTEGRAYRLFPLPWTKPILDQD-RRLPASYANFLIIEGAVLMPTYDDPADTIAQSV 324 R +G Y+L PLPW I D+D RLPA+YANFLII AVL+P Y D A +V Sbjct: 235 QEFRQADGAPYKLTPLPWPDAIHDEDGERLPATYANFLIINEAVLLPVYGVDQDQDAIAV 294 Query: 325 LAEAFPTREIVPVPCRPLIWQNGSLHCITMQIPAGLLA 362 + E FPTR IVP+ CRPLI Q+GSLHC+TMQIPAG+++ Sbjct: 295 MKEIFPTRAIVPINCRPLIRQHGSLHCVTMQIPAGVVS 332 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: 414 Number of extensions: 14 Number of successful extensions: 5 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: 332 Length adjustment: 29 Effective length of query: 334 Effective length of database: 303 Effective search space: 101202 Effective search space used: 101202 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