GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruG in Burkholderia phytofirmans PsJN

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.

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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