Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate PfGW456L13_2706 Agmatine deiminase (EC 3.5.3.12)
Query= BRENDA::Q9I6J9 (368 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2706 Length = 374 Score = 212 bits (539), Expect = 2e-59 Identities = 122/350 (34%), Positives = 177/350 (50%), Gaps = 20/350 (5%) Query: 15 MPAEWEPHEQTWMVWPERPDNWRNGGKPAQAAFAAVAKAIARFEPVTVCASAGQYENARA 74 MP E + H++ ++ + + W + Q A +A++IA EPVTV + A Sbjct: 42 MPDEGDKHQRAFIAFGAQAAIWEDFTPHVQDALGRIARSIAEHEPVTVFCRQSERRLAEV 101 Query: 75 RLDDGNIRVVEISSDDAWVRDTGPTFVIDDKGDVRGVDWGFNAWGGFEGGLYFPWQRDDQ 134 + N V DD W+RD G FV+D G + VD+ FN WG + DD Sbjct: 102 KCGSHNTTFVITELDDIWMRDIGANFVVDGSGGLAAVDFNFNGWGNKQQ------HADDA 155 Query: 135 VARKILEIERRARYRTDDFVLEGGSIHVDGEGTLITTEECLLNHNRNPHLSQAEIERTLR 194 ++ +A Y+ + V EGG I VDG GT I TE +N NRNP S+AE+E L+ Sbjct: 156 QLAALVAENAKADYQRSELVGEGGGIEVDGHGTGIMTESSWINRNRNPDWSKAEVEAELK 215 Query: 195 DYLAVESIIWLPNGLYNDETDGHVDNFCCYARPGEVLLAWTDDQDDPNYLRCQAALRVLE 254 + L + IIWLP D TD HVD + + +PG V+ +D + +Y +A L++LE Sbjct: 216 ERLGLRKIIWLPGIKGKDITDAHVDFYARFVKPGVVIANLDNDPESYDYKVTRAHLQILE 275 Query: 255 ESRDAKGRKLVVHKMPIPGPLYATQEECDGVDIVEGSQPRDPSIRLAGSYVNFLIVNGGI 314 + DA GRKL VH + P ++ D D G Y+N+ ++NG I Sbjct: 276 NATDADGRKLQVHTVSPPLNPRNSRFSNDNPDFAAG-------------YINYFVINGAI 322 Query: 315 IAPSF-DDPKDAEARAILQRVFPEHEVVMVPGREILLGGGNIHCITQQQP 363 IAP F D+ DA+A +L ++P+ EVV + I GGG IHC+T QP Sbjct: 323 IAPQFGDEEADAKAFDLLSELYPDREVVQLDIDAISAGGGGIHCVTSHQP 372 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: 452 Number of extensions: 23 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: 368 Length of database: 374 Length adjustment: 30 Effective length of query: 338 Effective length of database: 344 Effective search space: 116272 Effective search space used: 116272 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