Align Arginase; EC 3.5.3.1 (characterized)
to candidate BWI76_RS21925 BWI76_RS21925 agmatinase
Query= SwissProt::P53608 (299 letters) >FitnessBrowser__Koxy:BWI76_RS21925 Length = 323 Score = 115 bits (289), Expect = 1e-30 Identities = 93/300 (31%), Positives = 139/300 (46%), Gaps = 40/300 (13%) Query: 4 ISIIGVPMDLGQTRR-GVDMGPSAMRYAGVIERLERLH-------YDIEDLGDIPIGKAE 55 I I+GVP D G T R G GP +R A + R R+H YD +GD+ Sbjct: 40 IGIVGVPWDGGTTNRAGTRHGPRELRNASSLVR--RIHQTTRRSPYDYARVGDL------ 91 Query: 56 RLHEQGDSRLRNLKAVAEANEKLAAAVDQVVQRGRFPLVLGGDHSIAIGTLAGVAKHYER 115 GD R+ N + ++ ++ A + ++ PL GGDH + L + + + Sbjct: 92 -----GDVRI-NPVDMQDSLARIEAWYRALAEQQVMPLTAGGDHLTTLPILRALGRD-KP 144 Query: 116 LGVIWYDAHGDVNTAETSPSGNIHGMPLAASLGFGHPALTQIGGYSPKIKPEHVVLIGVR 175 LG+I +DAH D N + HG P ++ G + P V IG+R Sbjct: 145 LGMIHFDAHSDTNDSYFGGERFTHGTPFRRAVEEG------------VLDPRRTVQIGIR 192 Query: 176 S--LDEGEKKFIREKGIKIYTMHEVDRLGMTRVMEETIAYLKERTDGVHLSLDLDGLDPS 233 E + E GI I M +VD LG+ +VM+ A + E+ ++S D+D LDP Sbjct: 193 GALFSADEHCWAEENGITIIRMEQVDELGIDKVMQRARAIVGEQP--TYISFDIDVLDPV 250 Query: 234 DAPGVGTPVIGGLTYRESHLAMEMLAEAQIITSAEFVEVNPILDERNKTASVAVALMGSL 293 APG GTP IGG+T ++ + LA +I A+ VEV+P D+ N T+ +M L Sbjct: 251 YAPGTGTPEIGGMTTLQAQRCVRQLAGLNLI-GADVVEVSPPFDQGNLTSLTGATMMFEL 309 Lambda K H 0.318 0.138 0.393 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: 244 Number of extensions: 18 Number of successful extensions: 4 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: 299 Length of database: 323 Length adjustment: 27 Effective length of query: 272 Effective length of database: 296 Effective search space: 80512 Effective search space used: 80512 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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