Align arginine oxidase (EC 1.4.3.25) (characterized)
to candidate WP_046157805.1 VL52_RS15120 FAD-dependent oxidoreductase
Query= metacyc::MONOMER-11561 (589 letters) >NCBI__GCF_000971335.1:WP_046157805.1 Length = 539 Score = 284 bits (726), Expect = 7e-81 Identities = 203/564 (35%), Positives = 286/564 (50%), Gaps = 86/564 (15%) Query: 8 DVAIIGGGVSGTYSAWRLQEAQGDHQRIQLFEYSDRIGGRLFSINLPGLPNVVAEVGGMR 67 D+AI+GGGVSG Y AWRL++ Q+I +FE SD IGGRL S+ P +P++VAE+GGMR Sbjct: 7 DIAIVGGGVSGVYCAWRLKQTNPG-QKIAVFEASDHIGGRLLSVRPPDIPDMVAELGGMR 65 Query: 68 WMPATDDNTGGHVMVDKLVGELKLESKNFPMGSNLP-EKDPVGAKDNLFYLRGERFRLRD 126 +PA +V KL+ EL E P + K PV N+ +LRG RL D Sbjct: 66 ILPAVQP------LVTKLITELNQE---LPADEQITLYKFPVDEPQNIAFLRGVYLRLAD 116 Query: 127 FTEAPDKIPYKLAWSERGFGPEDLQVKVMNNIYPGFDKLSLAEQMQ------VKVFGKEI 180 FT PD +PY+L + + G ++ V + I PG +L E+ + + G + Sbjct: 117 FTNDPDIVPYQLNFIDHGQSAGEVIVNAIEQIVPGITNPNLNEEQRREMAQSAEFGGVPL 176 Query: 181 WRYGFWDLLYRVLSNEGYQFMKDAGGYEANVANASAVTQLP--ATEYSDKTIFLTLKKGF 238 ++ GFW++L RV++ E Y + +D GGY++ + N +A +P +++ ++ GF Sbjct: 177 YKQGFWNVLLRVITGEAYHYAEDVGGYDSTLCNWNAADAIPWYLSDFGVSPEYMGFCNGF 236 Query: 239 QALPLTLAQRFAEVPGGLVPGEQRIRMNRRLASVQFSDDTEYPYRLHF-QATRTIDGKTS 297 Q +PL+LAQ F E GG V RLAS H T DG Sbjct: 237 QQVPLSLAQLF-EKSGGDV----------RLAS-------------HISHITLQGDGFAF 272 Query: 298 DVPGAEEIVHARQVILALPRRSLELI--QSPLFDDPWLKENIDSVLVQSAFKLFLAYEQP 355 V G+ A+++ILA+PRRSLEL+ SP D + I +V + FKLF Y+ P Sbjct: 273 QVNGS--AATAKKLILAMPRRSLELLTATSPALQDAKTQALISTVTPRPLFKLFTTYDSP 330 Query: 356 WWRSQG--------------LVAGRSVTDLPIRQCYYMGTECEQDGGEKTL-NSLLMASY 400 WWR+ G + AGRSVTDLP+RQ YY + DG T +++L+ASY Sbjct: 331 WWRNTGYSSTDAKGEPIYVAVQAGRSVTDLPVRQTYYWP---KSDGTAATEGHAMLLASY 387 Query: 401 NDIGTVPFWKGLEDGAPFEGYQPKSLLGR-----------VDAN---EVVPKMQYQISEE 446 +D FW DG + QP++ LGR VD N + + QY+ Sbjct: 388 DDGDNTGFW----DGLRAKRRQPRA-LGRDVAPLADPFIGVDDNVQRDELEWHQYKAPRM 442 Query: 447 MVRIAQRQVTSLHDQIELPAPYSAVYHAWDADPFGGGWHEWKANYRLDLIIQRMRHPVQE 506 M RQ+T +H P +A Y W DPFGGGW+ W + + + P + Sbjct: 443 MTEEVTRQLTVMHSLNYTPKVRNAAYRDWGDDPFGGGWNSWNIGVKSWEVKHAVVQPT-D 501 Query: 507 QEVYIVGEAYSYGQGWVEGALTTA 530 +YI GEAYS QGWVEGAL TA Sbjct: 502 LPLYICGEAYSDAQGWVEGALQTA 525 Lambda K H 0.319 0.137 0.422 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: 938 Number of extensions: 59 Number of successful extensions: 11 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: 589 Length of database: 539 Length adjustment: 36 Effective length of query: 553 Effective length of database: 503 Effective search space: 278159 Effective search space used: 278159 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: 53 (25.0 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