Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate AZOBR_RS08825 AZOBR_RS08825 agmatine deiminase
Query= BRENDA::Q9I6J9 (368 letters) >FitnessBrowser__azobra:AZOBR_RS08825 Length = 338 Score = 315 bits (806), Expect = 1e-90 Identities = 165/360 (45%), Positives = 219/360 (60%), Gaps = 25/360 (6%) Query: 6 STPRADGFRMPAEWEPHEQTWMVWPERPDNWRNGG-KPAQAAFAAVAKAIARFEPVTVCA 64 +TP A+GF MP EWE H + WM WP RP+ W G A AA+ VA+AI+RFEPVT+ Sbjct: 2 TTPAAEGFTMPGEWERHTRCWMAWPCRPETWPEGAFDAAAAAYTDVARAISRFEPVTMVC 61 Query: 65 SAGQYENARARLDDGNIRVVEISSDDAWVRDTGPTFVIDDKGDVRGVDWGFNAWGGFEGG 124 ++ G + ++ + D+W+RDTGP+FV D KG V GV W FNAWGG Sbjct: 62 DPADVADSSLACGPG-VEILPLPISDSWIRDTGPSFVTDGKGQVAGVHWRFNAWGGN--- 117 Query: 125 LYFPWQRDDQVARKILEIERRARYRTDDFVLEGGSIHVDGEGTLITTEECLLNHNRNPHL 184 Y +D QV R +LE R+ V+EGGS HVDGEGTL+TTE+CLLN NRNP+L Sbjct: 118 -YPDSAKDQQVGRLMLEHLGLRRFEAP-LVMEGGSFHVDGEGTLLTTEQCLLNPNRNPNL 175 Query: 185 SQAEIERTLRDYLAVESIIWLPNGLYNDETDGHVDNFCCYARPGEVLLAWTDDQDDPNYL 244 +AEIE L+++L + S+IWL G +DETDGH+D + +PG V+ TDD D N+ Sbjct: 176 GKAEIEALLKEHLGISSVIWLGEGYQDDETDGHIDEIALFVKPGVVMAITTDDPGDANFK 235 Query: 245 RCQAALRVLEESRDAKGRKLVVHKMPIPGPLYATQEECDGVDIVEGSQPRDPSIRLAGSY 304 Q L L+ +RDA+GR+L V +P+ P ++ + +RL SY Sbjct: 236 AFQDNLDRLKRARDAQGRELEV--IPVRQP----------------ARRDENGVRLTLSY 277 Query: 305 VNFLIVNGGIIAPSFDDPKDAEARAILQRVFPEHEVVMVPGREILLGGGNIHCITQQQPA 364 N I NGGI+ P+F+D D EA I++R FP+ EVV VP +I+ GGG IHCITQQQPA Sbjct: 278 TNLYIANGGIVMPAFEDSADDEAFRIVRRAFPDREVVQVPALDIVRGGGGIHCITQQQPA 337 Lambda K H 0.319 0.138 0.439 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: 519 Number of extensions: 25 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: 368 Length of database: 338 Length adjustment: 29 Effective length of query: 339 Effective length of database: 309 Effective search space: 104751 Effective search space used: 104751 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 (21.7 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