Align arginase (EC 3.5.3.1) (characterized)
to candidate WP_011841097.1 RSPH17029_RS07860 agmatinase
Query= BRENDA::U6BQJ3 (347 letters) >NCBI__GCF_000015985.1:WP_011841097.1 Length = 321 Score = 87.4 bits (215), Expect = 4e-22 Identities = 88/305 (28%), Positives = 131/305 (42%), Gaps = 53/305 (17%) Query: 26 VAIVGAPFSKG-QKRRGVEHGPKAIRDAGLV-----------DRLRSLENAVHDFGDLRF 73 +A+ G F + R G GP+AIR+A + D L L V D+GDL F Sbjct: 48 LAVTGVAFDQAVTNRTGTRFGPRAIREASTLQPYDRPFGWGFDPLEEL--TVVDYGDLAF 105 Query: 74 EHPQEDNRFMNVPYPRTVGRANEILSDAISRAVGAGHTTVMLGGDHSLAIGSVAGHAQHH 133 ++ + +P L+ ++ + AG + LGGDHS+ + + HA Sbjct: 106 DYAR------TAEFPAR-------LTAHVAGILAAGAGALTLGGDHSITLPILRAHAAVF 152 Query: 134 PELCLIWVDAHADINTPMTSPSGNLHGQPVAFMLKELQDKMPVVPGFSWTKPFLAAKDLV 193 L ++ DAH+D+ P HG FM K +++ + V P S V Sbjct: 153 GPLSVVQFDAHSDLWVD-DDPGRIDHG---TFMYKAVKEGL-VDPARS-----------V 196 Query: 194 YIGLRDVDPGEHVILKSLGIQCFSMRDIDRMGMQRVMEVTLDHLLARKQRPIHLSFDIDA 253 +G+R P LG+ R + G V H + P +L+FDIDA Sbjct: 197 QVGIRTDTPDW------LGMNVIDARTVHEQGPAAVAARV--HAIVG-HHPTYLTFDIDA 247 Query: 254 FDPTLAPATGTPVNGGLTYREGIYITEEIHNTGLLSVMDLVEVNPALGASAEAVEATAGL 313 DP APATGTPV GGL + I ++ L+ D+VEV+P S A A + Sbjct: 248 LDPAFAPATGTPVWGGLASWQAAAILRDLAGLNLVG-GDVVEVSPPYDPSGITAVAGAHV 306 Query: 314 AVDVI 318 A ++I Sbjct: 307 AYELI 311 Lambda K H 0.320 0.136 0.401 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: 325 Number of extensions: 20 Number of successful extensions: 3 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: 347 Length of database: 321 Length adjustment: 28 Effective length of query: 319 Effective length of database: 293 Effective search space: 93467 Effective search space used: 93467 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 Apr 10 2024. 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