Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate CCNA_01678 CCNA_01678 arginine N-succinyltransferase, beta chain
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__Caulo:CCNA_01678 Length = 334 Score = 201 bits (512), Expect = 2e-56 Identities = 120/337 (35%), Positives = 185/337 (54%), Gaps = 3/337 (0%) Query: 1 MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 MLV+RPA +AD + LA S G TSLP+D LR ++ SEASF A V+ E Y Sbjct: 1 MLVVRPAGSADFEALMELAVLSGRGFTSLPEDEPTLRSRLALSEASFQAGVA-PPEAWYT 59 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 +LED +G + G + + A G PF+SFR T +S +L + L L ++ G Sbjct: 60 LMLEDLETGTVEGVAGVKAGVGLKRPFFSFRVVTLAQSSPTLEMRFDHKALVLVNECAGW 119 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 S + S +++ + + L ++ R + + P+RFA+ V+ E+ G+ DE G PFW V Sbjct: 120 SEVGSLFLRPEKRKGGAGRLLAQSRYMLIGIEPQRFAEMVLAELRGWFDEDGRCPFWEHV 179 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 FF L++ +A+ +S F+ +L P +PIY LLP+ A++ +G+VH + +L Sbjct: 180 SHKFFRLDFDQADLMSASTDGQFILDLAPRHPIYTELLPEEARDVIGRVHRDGEAARAML 239 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQDF 300 REGF +D+FD GPT+ IR++ +R + VK+GE G L++ G++ F Sbjct: 240 EREGFRYQGLVDLFDAGPTVACPRDDIRTVRDARRLRVKVGE-DAYGEEALISTGEVSRF 298 Query: 301 RAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVA 337 RAV + G+ L +A +ALGVGEG VR+ A Sbjct: 299 RAVRAPV-LIDGETAILGRDAMDALGVGEGEVVRVKA 334 Lambda K H 0.319 0.135 0.387 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: 265 Number of extensions: 11 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: 338 Length of database: 334 Length adjustment: 28 Effective length of query: 310 Effective length of database: 306 Effective search space: 94860 Effective search space used: 94860 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 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