Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate 350404 BT0876 conserved hypothetical protein (NCBI ptt file)
Query= BRENDA::Q9ZN18 (330 letters) >FitnessBrowser__Btheta:350404 Length = 371 Score = 300 bits (769), Expect = 3e-86 Identities = 159/328 (48%), Positives = 211/328 (64%), Gaps = 6/328 (1%) Query: 6 AEFEKIQAILMAFPHEFGDWAYCIEEARESFLHIIQTIAKHAKVLVCVHTNDTIGYETLK 65 AE+ I + +PH DWAY ++E +E F++I + IAK +L+ + + + + Sbjct: 38 AEWHLQSGIQLTWPHAGTDWAYMLKEVQECFVNIAREIAKRELLLIVTPEPEEVKKQIVA 97 Query: 66 --NLPGVEIARIDTNDTWARDFGAISVENHGVLECLDFGFNGWGLKYPSNLDNQVNFKLK 123 N+ V R +TNDTWARD GAI++ + G LDF FNGWGLK+ S LDN + + Sbjct: 98 TVNMDNVRFLRCETNDTWARDHGAITMIDTGNPSLLDFTFNGWGLKFASELDNLITGQAV 157 Query: 124 HLGFLKHP-LKTMPYILEGGSIESDGAGSILTNTQCLLEKNRNPHLNQNGIETMLKKELG 182 G LK + + ++LEGGSIESDG G++LT T+CLL +RN LNQ IE LK Sbjct: 158 KAGALKGQYIDCLDFVLEGGSIESDGMGTLLTTTECLLSPHRNGKLNQVEIEEYLKSTFH 217 Query: 183 AKQVLWYSYGYLKGDDTDSHTDTLARFLNKDTIVYSACEDENDEHYTALKKMQEELKTFK 242 ++VLW +GYL GDDTDSH DTLARF + DTI Y C++ DEHY AL M+E+LKTF+ Sbjct: 218 LQKVLWLDHGYLAGDDTDSHIDTLARFCSTDTIAYVKCDNTEDEHYEALHAMEEQLKTFR 277 Query: 243 KLDGTPYKLIPLEIPKAVYNENQQRLPATYVNFLLCNNALIVPTYNDP-NDTLILETLRQ 301 L G PY+L+ L + V E+ +RLPATY NFL+ N+A++ PTY P ND E L+Q Sbjct: 278 TLAGEPYRLLALPMADKV-EEDGERLPATYANFLIMNDAILYPTYQQPDNDRKAGEVLQQ 336 Query: 302 HTPL-EVIGVDCNTLIKQHGSLHCVTMQ 328 P +VIG+DC LIKQHGSLHCVTMQ Sbjct: 337 AFPKHQVIGIDCRALIKQHGSLHCVTMQ 364 Lambda K H 0.319 0.137 0.418 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: 440 Number of extensions: 34 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: 330 Length of database: 371 Length adjustment: 29 Effective length of query: 301 Effective length of database: 342 Effective search space: 102942 Effective search space used: 102942 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