Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate 8499887 DvMF_0652 Agmatine deiminase (RefSeq)
Query= BRENDA::O86509 (339 letters) >FitnessBrowser__Miya:8499887 Length = 370 Score = 289 bits (740), Expect = 7e-83 Identities = 157/342 (45%), Positives = 199/342 (58%), Gaps = 17/342 (4%) Query: 5 MPPEWAPHERTWMAWPGPNATFTDAEELAGARAAWASVARAVRRFEPVTMVHGPGQAATA 64 MP EW+PH WMAWP P+ DA L R ++A V RA+ RFEPVT++ P A A Sbjct: 29 MPAEWSPHAGCWMAWPCPDPLLEDA--LDTVRTSFAGVVRAIARFEPVTLLARPEDAEVA 86 Query: 65 RELLGPDVDLVERELDDAWMRDIGPTFVTDGRGGLAAVDWVFNGWGAQDWARWEHDAEIA 124 L GP V +V + DAWMRD GPTFV DG GG+A VDW+FN WG + HD ++A Sbjct: 87 AALCGPGVQVVPAPITDAWMRDFGPTFVVDGAGGVAGVDWMFNSWG-HTYDEPTHDDDVA 145 Query: 125 RHVADLAAAPVLSSPLVNEGGAIHVDGEGTVLLTDTVQLGSGRNPGWSREEVEAEIHAKL 184 + + ++P + EGG+IHVDG+GT++ T+ L RN G ++ + E A L Sbjct: 146 QLILSRLGMRRYAAPFILEGGSIHVDGQGTLMTTEQCLLDPRRNAGMTKADFEELFAAYL 205 Query: 185 GTTTAIWLPHGLAGDYGRYGTQGHVDIVAAFARPGTVVVHSQRDPRHPDHERSQLYLEIL 244 G IWL GL GD T GHVDIV+ FARPG V++H DP P+H Q L L Sbjct: 206 GVRKVIWLGEGLEGD----DTHGHVDIVSCFARPGVVLLHRCDDPEDPNHAVYQDNLRRL 261 Query: 245 RGRTDARGRRLEVVEVPAPTVLKDEEGEWADYSYINHYVCNGGVVLCAFGDPN------- 297 + TDA G+ LE+V + P + G+ D SYIN YV NGG+V+ AFG P Sbjct: 262 QLATDADGKPLEIVTIDQPN-RAEHGGKRMDLSYINFYVANGGIVMSAFGAPGGGADSQG 320 Query: 298 --DELAAGIFRRLFPERTVTLVDARTIFAGGGGIHCITQQQP 337 D +A RR+FPER V V + IF GGGGIHCITQQQP Sbjct: 321 ALDRVAFETLRRVFPEREVVQVHSLDIFRGGGGIHCITQQQP 362 Lambda K H 0.319 0.137 0.443 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: 499 Number of extensions: 32 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: 339 Length of database: 370 Length adjustment: 29 Effective length of query: 310 Effective length of database: 341 Effective search space: 105710 Effective search space used: 105710 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 (21.8 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