Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate GFF3097 HP15_3040 arginine N-succinyltransferase subunit beta
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__Marino:GFF3097 Length = 366 Score = 300 bits (768), Expect = 4e-86 Identities = 158/341 (46%), Positives = 215/341 (63%), Gaps = 7/341 (2%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60 +++RP+ DL L +A+S G GLTTLPA+ + LQ +++ A + F YLF Sbjct: 2 LVIRPLQENDLDDLYAMAQSAGKGLTTLPADRELLQKKINHARETFNQRIAPEAGLYLFA 61 Query: 61 LED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSE 119 LED + K VGIS I VGL E +YNYR+ +TV+AS+EL +H PTL L+ND+T SE Sbjct: 62 LEDTERKKTVGISGIQARVGLDEVFYNYRLSVTVNASKELGVHVRTPTLHLSNDMTDTSE 121 Query: 120 LCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGR 179 +CSL L +++ G +G LLSR RF+++ EFR F +K+ AEMRG+SD GRSP W++LG Sbjct: 122 ICSLLLSDEYKGGGSGLLLSRCRFMYLDEFRKHFSEKIFAEMRGVSDANGRSPLWDALGT 181 Query: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKA 239 FF MEFS+AD L+G+GNK+FIAELMPK+P+Y L + AR VIGRVH NT PAL ML++ Sbjct: 182 KFFDMEFSEADMLSGLGNKSFIAELMPKYPIYLSMLPDSARAVIGRVHDNTAPALRMLQS 241 Query: 240 EGFSYQGYVDIFDAGPAIEAETDKIRAIAESQN-----LVLAVGTPGDDAEPYLIHNRKR 294 EGF++ G VDIFD GP +EA +R + E N V E ++ NR Sbjct: 242 EGFNFNGLVDIFDGGPVVEAFVHNVRTVREGMNRHAMVTRKPVNLDVPSEERVMVSNRSF 301 Query: 295 EDCRITAAPARA-AAGTLVVDPLTAKRLRLSAGASVRAVPL 334 D R+T P T+ + P A+ L++ +G VR PL Sbjct: 302 RDFRVTTVPIDCIGPDTVSLPPEVAEALQIESGDPVRLAPL 342 Lambda K H 0.320 0.136 0.398 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: 322 Number of extensions: 17 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: 340 Length of database: 366 Length adjustment: 29 Effective length of query: 311 Effective length of database: 337 Effective search space: 104807 Effective search space used: 104807 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