Align Agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate PfGW456L13_2703 Agmatine deiminase (EC 3.5.3.12)
Query= reanno::pseudo5_N2C3_1:AO356_10030 (368 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2703 Length = 350 Score = 239 bits (611), Expect = 6e-68 Identities = 144/360 (40%), Positives = 190/360 (52%), Gaps = 31/360 (8%) Query: 12 GFHMPAEWATQTQVWMIWPERPDNWRLGGK----PAQAAHVAVAKAIARFEPVTVAVSAA 67 G+ MPAEW T WM+WP W G + Q VA AIARFEPV + V + Sbjct: 10 GWTMPAEWVTHAATWMVWPHNKTLWESGWRVTLPQVQEDFARVANAIARFEPVKLVVDPS 69 Query: 68 QYENARARLDVPNIRLVEMSSDDAWVRDTGPTFVINDSGEVRGVDWDFNAWGGFDGGLYA 127 +A+A L PNI L+E++ +D+W RD+GP+FV + + GV W FNAWGG + Sbjct: 70 AIASAKA-LCGPNIELIELAVNDSWCRDSGPSFVCHPQQGLAGVSWRFNAWGG-----KS 123 Query: 128 PWNRDSQVASKVLEIERSPRYRTEGFVLEGGSIHVDGEGTVITTEECLLNRNRNPHMSRE 187 + D +A + L + T EGG+IHVDGEGT+ITTE LLN NRNP +S+ Sbjct: 124 AHDLDESLARRALNHLGLECFGT-ALSNEGGAIHVDGEGTLITTESVLLNPNRNPGVSKA 182 Query: 188 QIEAVLSAQLAVDKVIWL---PDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQNPNYT 244 +IE + + L V K IWL PD + D TDGHVD C + RPG +L+ T D Q+ Sbjct: 183 EIEEIFTRLLGVKKTIWLPGDPDYVTGDMTDGHVDGVCAFARPGVLLVDATHDKQSVYAE 242 Query: 245 RCHAAMDVLQNSTDAKGRPFTVHKMPIPGPMYATEEECAGVDAVEGSQERNPTVRLAGSY 304 L+ +TDA+GR F + ++ DAV+ E SY Sbjct: 243 VARENRRALELATDAQGRQFELIEL------------FEATDAVDTEAE-----VFCASY 285 Query: 305 VNFLIVNGGIIAPSFDDPLDAPARDILQNLFPQHEVVMVPGRELLLGGGNIHCLTQQQPA 364 NF I NG II P++ D A ++L FP EVV V L GGG +HC+TQQQPA Sbjct: 286 TNFYIANGAIIMPAYGIDADKVAAEVLAQAFPGREVVPVRINHLAHGGGGVHCITQQQPA 345 Lambda K H 0.318 0.136 0.431 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: 404 Number of extensions: 21 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: 368 Length of database: 350 Length adjustment: 29 Effective length of query: 339 Effective length of database: 321 Effective search space: 108819 Effective search space used: 108819 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