Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate Ga0059261_1981 Ga0059261_1981 Peptidylarginine deiminase and related enzymes
Query= BRENDA::Q9ABL6 (370 letters) >FitnessBrowser__Korea:Ga0059261_1981 Length = 321 Score = 299 bits (766), Expect = 6e-86 Identities = 163/333 (48%), Positives = 208/333 (62%), Gaps = 12/333 (3%) Query: 36 MTVTVPAEWAPHRAMWVGFPSHAELWQEDLEQAQQEVADLARALAGPGAERVRLMVVGDE 95 M T P EWA H+A+W+GFPSH ELW E L A+ EVA ARA+ GA L+V DE Sbjct: 1 MKATPPPEWAKHKAVWIGFPSHPELW-ESLNAARAEVAAFARAVHADGAGEQVLLVAADE 59 Query: 96 AEAAARALLSDTTVEIVRGQFGDIWLRDTGPIFVDDAGKAVAAGFKFNGWGGKYSLEGDD 155 A A LL+ ++V FGDIWLRDTG + VD+ G V F+FNGWGGKY EGD Sbjct: 60 EAATAARLLAGDAAKVVVAPFGDIWLRDTG-VIVDNRG--VGHDFEFNGWGGKYHYEGDV 116 Query: 156 IVAEQIAAASGAPLVRNDFILEGGALDHDGNGTILTTRQCLLNDNRNPGWDEATANAALT 215 V +A + +D++LEGG++D DG G ++TT QCLLN NRNP + A L Sbjct: 117 EVGALLADKRRMEVQPHDWVLEGGSIDWDGTGLVVTTEQCLLNRNRNPTLSQREAEERLY 176 Query: 216 EALGAKKVLWLGKGLKNDHTDGHVDNLARFVAPGVVACPMGYGLDDPNADIYGDTAKMLA 275 LG +VLWLG GL DHTDGHVDNLARFV +A P+ +DPN +Y D + Sbjct: 177 TDLGFDRVLWLGNGLAMDHTDGHVDNLARFVGENRLAIPVPEE-NDPNWLVYADARRR-- 233 Query: 276 GMTDSRGSPLQVVRIPSPGKLLDEDGEPIPASHMNFLIANEAVIVPIYAEESGAFAVEVI 335 + ++VV IPSPG+++ D E +PAS+MNF I N AV++P+Y + + AVE I Sbjct: 234 ----AEAFGVEVVPIPSPGRVIHGD-EVVPASYMNFYIGNAAVVIPVYGQPNDRKAVETI 288 Query: 336 KGLFPERQVIGLPSTAILTGGGSFHCISQQEPE 368 LFP R+ +GL + ILTGGGSFHCISQQ P+ Sbjct: 289 GALFPGREAVGLRADHILTGGGSFHCISQQIPK 321 Lambda K H 0.318 0.136 0.418 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: 433 Number of extensions: 25 Number of successful extensions: 6 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: 370 Length of database: 321 Length adjustment: 29 Effective length of query: 341 Effective length of database: 292 Effective search space: 99572 Effective search space used: 99572 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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