GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruG in Paraburkholderia bryophila 376MFSha3.1

Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate H281DRAFT_06479 H281DRAFT_06479 arginine succinyltransferase

Query= BRENDA::P80358
         (340 letters)



>FitnessBrowser__Burk376:H281DRAFT_06479
          Length = 352

 Score =  197 bits (500), Expect = 4e-55
 Identities = 117/339 (34%), Positives = 187/339 (55%), Gaps = 6/339 (1%)

Query: 1   MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAE-RGDADYLF 59
           + VRP   ADL AL  +AR+    L +LP + + L+ RV+ +E +FR E +  G+  YLF
Sbjct: 2   LFVRPGRLADLDALEHMARTAQPVLHSLPHDRRALEARVALSEDSFRAEVDFPGEEFYLF 61

Query: 60  VLED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118
           VLED ++GK++G ++I  A G  +P+Y +R    + AS+EL+++R+I  L ++++LTG S
Sbjct: 62  VLEDSESGKLMGTASIVAAAGYSDPFYAFRNDALIHASRELHVNRKIHALTMSHELTGKS 121

Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178
            L   ++    R      L+SRAR ++IA  R  F  ++ + + G++DE G SPFWE++G
Sbjct: 122 RLAGYYIDPSLRGDAAAHLMSRARMMYIAANRKRFTPEVFSLLLGVTDENGVSPFWEAVG 181

Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238
           R FF   F+  +  +G  ++ FIAE+MP +P+Y   L E A+ V+G        A  +  
Sbjct: 182 RKFFGRNFADIEIESGGRSRTFIAEVMPTYPIYVPLLPEAAQRVLGEPDSKALLAYEIHL 241

Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKRED-- 296
            EGF    ++DIFDAGP + A+ D+   +  ++  V      G +   YLI +   +   
Sbjct: 242 EEGFETDRFIDIFDAGPVLTAQVDRSACVTLNETRVAHEAAAGANGSTYLIAHNGADGQF 301

Query: 297 -CRITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPL 334
            C +   P     G  +  P  A  L +  G +VR VPL
Sbjct: 302 RCVLGELPTARNEGAPLAQPARA-ALGVQDGDTVRCVPL 339


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: 289
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: 352
Length adjustment: 29
Effective length of query: 311
Effective length of database: 323
Effective search space:   100453
Effective search space used:   100453
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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