Align N-succinylarginine dihydrolase; EC 3.5.3.23 (characterized)
to candidate CCNA_00619 CCNA_00619 succinylarginine dihydrolase
Query= CharProtDB::CH_002938 (447 letters) >FitnessBrowser__Caulo:CCNA_00619 Length = 426 Score = 375 bits (962), Expect = e-108 Identities = 206/432 (47%), Positives = 271/432 (62%), Gaps = 9/432 (2%) Query: 5 EVNFDGLVGLTHHYAGLSFGNEASTRHRFQVSNPRLAAKQGLLKMKALADAGFPQAVIPP 64 E+NFDGL+G TH+YAGLS GN AS + VS+PR AA QGL KM+ L D G Q +PP Sbjct: 4 EINFDGLIGPTHNYAGLSLGNIASHSNAGAVSSPRAAALQGLTKMRTLLDLGLTQGFLPP 63 Query: 65 HERPFIPVLRQLGFSGSDEQVLEKVARQAPHWLSSVSSASPMWVANAATIAPSADTLDGK 124 RP VLR+LGF GSD+ VL +VA + L + SSAS MW ANAAT+ + DT DG+ Sbjct: 64 PPRPAAHVLRRLGFKGSDQAVLAQVADEDLDLLRAASSASSMWTANAATVLAAPDTADGR 123 Query: 125 VHLTVANLNNKFHRSLEAPVTESLLKAIFNDEEKFSVHSALPQVALLGDEGAANHNRLGG 184 VHL ANL HRSLEA T + L+ +F+ E F+VH+ LP A LGDEGAANH RL Sbjct: 124 VHLVTANLGTMLHRSLEADDTYATLRRVFSG-EAFAVHAPLPFAAHLGDEGAANHMRLAA 182 Query: 185 HYGEPGMQLFVYGREEGNDTRPSRYPARQTREASEAVARLNQVNPQQVIFAQQNPDVIDQ 244 ++G G+ +FV+G G R+P RQ AS+A ARL V P +FA Q+ + I Sbjct: 183 NHGARGVNVFVHGAPRG-----GRFPERQALRASQAAARLAGVQP-TALFAMQSAEAIKA 236 Query: 245 GVFHNDVIAVSNRQVLFCHQQAFARQSQLLANLRARVNGFMAIEVPATQVSVSDTVSTYL 304 G FHNDV+AV+N VL H QAFA + LLA L AR+ G + IE +S+ D V++YL Sbjct: 237 GAFHNDVVAVANANVLLAHPQAFATRPDLLAELSARLPGLVVIE--TRDLSLEDAVASYL 294 Query: 305 FNSQLLSRDDGSMMLVLPQECREHAGVWGYLNELLAADNPISELKVFDLRESMANGGGPA 364 FNSQL+S DG M L++P E R++A W + +LAADNP++++KV DLR+SM+NGGGPA Sbjct: 295 FNSQLVSLPDGYMALIVPVEARDNAAAWREIQTILAADNPVTKVKVVDLRQSMSNGGGPA 354 Query: 365 CLRLRVVLTEEERRAVNPAVMMNDTLFNALNDWVDRYYRDRLTAADLADPQLLREGREAL 424 CLRLRV + R +NPA +++ + L V+ ++ + +DL DP L A Sbjct: 355 CLRLRVPVAAAARDQINPAFLLDHARLDRLTRLVETWWPRAIAPSDLTDPALWEAAMVAH 414 Query: 425 DVLSQLLNLGSV 436 L L +V Sbjct: 415 AALETFLTAPTV 426 Lambda K H 0.318 0.133 0.391 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: 453 Number of extensions: 14 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: 447 Length of database: 426 Length adjustment: 32 Effective length of query: 415 Effective length of database: 394 Effective search space: 163510 Effective search space used: 163510 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 (21.7 bits) S2: 51 (24.3 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