Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate BPHYT_RS07705 BPHYT_RS07705 arginine succinyltransferase
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__BFirm:BPHYT_RS07705 Length = 346 Score = 260 bits (664), Expect = 4e-74 Identities = 143/340 (42%), Positives = 202/340 (59%), Gaps = 8/340 (2%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60 ++VR V D+ AL+ LA+ TG GLTT + L RV A + +AE +A Y FV Sbjct: 2 IVVRVVQRGDVDALMRLAQETGPGLTTFKPDRDALAARVERARRTMEDKAEAHEAGYFFV 61 Query: 61 LED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSE 119 +ED D G V G+ I AVGL++P+YNYRV V ASQ+L I + L +++DLTG +E Sbjct: 62 MEDTDTGDVAGVCGIETAVGLQQPFYNYRVSTVVHASQDLGIWTRMRALNISHDLTGYAE 121 Query: 120 LCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGR 179 +CSLFL +R+ G LLSR+RF+F+A+FR F +L AE+RG D EG SPFW ++G Sbjct: 122 VCSLFLSPRYRTSGVGGLLSRSRFMFLAQFRERFPQRLCAELRGHFDAEGTSPFWRAVGS 181 Query: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKA 239 HF++++F+ ADYL+ G KAF+AELMP++P+Y L EEA+ +G H +T PA ML++ Sbjct: 182 HFYQIDFNAADYLSSHGRKAFLAELMPRYPVYVELLPEEAQQCVGLTHNDTIPARRMLES 241 Query: 240 EGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVL------AVGTPGDDAEPYLIHNRK 293 EG Y+ +VDIFDAGP +E +R + ES + + A G P D ++ N Sbjct: 242 EGLRYENHVDIFDAGPVLECHIADLRTVRESVVVPVEIAPSSASGAP-QDGPKSMVSNTS 300 Query: 294 REDCRITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVP 333 D R+ G + A L + AG VR +P Sbjct: 301 LGDFRVGVVAGVPQDGVFRLSATEAAALDVKAGDLVRVLP 340 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: 292 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: 340 Length of database: 346 Length adjustment: 29 Effective length of query: 311 Effective length of database: 317 Effective search space: 98587 Effective search space used: 98587 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