Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate Pf1N1B4_4328 Agmatine deiminase (EC 3.5.3.12)
Query= BRENDA::O86509 (339 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4328 Length = 374 Score = 234 bits (597), Expect = 3e-66 Identities = 138/344 (40%), Positives = 193/344 (56%), Gaps = 18/344 (5%) Query: 3 FRMPPEWAPHERTWMAWPGPNATFTDAEELAGARAAWASVARAVRRFEPVTMVHGPGQAA 62 +RMP E H R ++A+ A + D + A +AR + +EPVT+ + Sbjct: 40 WRMPDEGDKHRRAFVAFGAQEAIWEDFTP--DVQEAIGLIARTIAHYEPVTVFCRSNERG 97 Query: 63 TARELLGP-DVDLVERELDDAWMRDIGPTFVTDGRGGLAAVDWVFNGWGAQDWARWEHDA 121 A E G ++ V ELDD WMRDIG FV DG GGL AVD+ FNGWG + ++ DA Sbjct: 98 LAEEHCGTTNITYVTTELDDVWMRDIGANFVIDGAGGLGAVDFNFNGWGNKQ--QYSKDA 155 Query: 122 EIARHVADLAAAPVLSSPLVNEGGAIHVDGEGTVLLTDTVQLGSGRNPGWSREEVEAEIH 181 ++A VAD A + S LV EGG I VDG GT ++T++ + S RNP WS+ EVE E+ Sbjct: 156 QVAALVADTVDADHIRSELVGEGGGIEVDGHGTGIMTESSWINSNRNPDWSKAEVEQELK 215 Query: 182 AKLGTTTAIWLPHGLAGDYGRYGTQGHVDIVAAFARPGTVVVHSQRDPRHPDHERSQLYL 241 A+LG IWLP G G+ T HVD A F +PG V+ + DP D + + +L Sbjct: 216 ARLGLRKIIWLP----GIKGKDITDAHVDFYARFVKPGVVIANLDNDPESYDRKVTLAHL 271 Query: 242 EILRGRTDARGRRLEVVEVPAPTVLKDEEGEWA----DYS--YINHYVCNGGVVLCAFGD 295 EIL+ TDA GR+L+V V P L + +++ D++ YIN++V NG ++ FGD Sbjct: 272 EILKQATDADGRKLQVHTVSPP--LNPRKSKFSRNNPDFAAGYINYFVINGAIIAPEFGD 329 Query: 296 -PNDELAAGIFRRLFPERTVTLVDARTIFAGGGGIHCITQQQPR 338 D A + L+P+R V ++ I AGGGGIHC+T QP+ Sbjct: 330 KAADTRAFDLLSELYPDREVVQLNIDAIAAGGGGIHCVTSHQPQ 373 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: 410 Number of extensions: 26 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: 374 Length adjustment: 29 Effective length of query: 310 Effective length of database: 345 Effective search space: 106950 Effective search space used: 106950 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