Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate WP_110205669.1 DNK54_RS04295 arginine deiminase
Query= BRENDA::P13981 (418 letters) >NCBI__GCF_003194585.1:WP_110205669.1 Length = 414 Score = 528 bits (1359), Expect = e-154 Identities = 248/407 (60%), Positives = 315/407 (77%), Gaps = 2/407 (0%) Query: 9 GVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGID 68 GVHSE G LRKV+VC+PGLAH RLTPSNCD+LLFDDV+WV A+RDH +F+ M RGI+ Sbjct: 7 GVHSEVGTLRKVLVCAPGLAHARLTPSNCDDLLFDDVMWVQNAQRDHAEFMELMSGRGIE 66 Query: 69 VLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVA 128 VLE H LL+ET+Q PEA W+LDRK+TA+ VGLGL + R++LE+L +LA YL+GG+A Sbjct: 67 VLEFHQLLSETLQQPEARSWLLDRKVTANQVGLGLVDDTRAFLEALVAEELARYLVGGLA 126 Query: 129 ADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQE 188 DLP + L + R G +LLPPLPN +TRDTTCWI G+TLNP++WPAR E Sbjct: 127 VADLPDEHRTDYLALARGSRGVHEYLLPPLPNMLYTRDTTCWIGDGMTLNPLHWPARHDE 186 Query: 189 TLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQA 248 TLL A+Y FHP FA+A +W+GDP+ G +TLEGGDVMP+GNGVVL+GM ER+SRQA Sbjct: 187 TLLYKALYSFHPAFADAGIPVWWGDPEVSWGQATLEGGDVMPLGNGVVLVGMSERTSRQA 246 Query: 249 IGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFSLRP 308 I Q+A LF GAAE+V+VAG+PK R+AMHLDTV +F DRD+VT + +VV + PF+LRP Sbjct: 247 ITQLAARLFEGGAAEQVVVAGMPKMRSAMHLDTVLTFADRDVVTAYRDVVDHLAPFTLRP 306 Query: 309 DPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNVVCLEPGV 368 G+++ E + +VVA++LG+ +RV+ETGG+ +A+ER+QWD GNNVV LEPGV Sbjct: 307 GVGG--GVHVTAERRHLTDVVAKALGIDGIRVIETGGDVYASERQQWDSGNNVVALEPGV 364 Query: 369 VVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDP 415 VVGYDRNT+TN LL AG+EV+TI +ELGRGRGGGHCMTCP++RDP Sbjct: 365 VVGYDRNTHTNALLEAAGIEVLTIVGAELGRGRGGGHCMTCPLLRDP 411 Lambda K H 0.319 0.137 0.414 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: 592 Number of extensions: 22 Number of successful extensions: 2 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: 418 Length of database: 414 Length adjustment: 31 Effective length of query: 387 Effective length of database: 383 Effective search space: 148221 Effective search space used: 148221 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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