GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aruG in Klebsiella michiganensis M5al

Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate BWI76_RS11675 BWI76_RS11675 arginine N-succinyltransferase

Query= BRENDA::P80358
         (340 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS11675 BWI76_RS11675 arginine
           N-succinyltransferase
          Length = 344

 Score =  335 bits (858), Expect = 1e-96
 Identities = 177/341 (51%), Positives = 226/341 (66%), Gaps = 2/341 (0%)

Query: 1   MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60
           M++RPV   DLP L+ LA  TG GLT+LPA+E  L  R+  ++  +RGE  + +  Y+FV
Sbjct: 2   MVIRPVEKGDLPGLLTLAGETGGGLTSLPADEATLAARIERSQMTWRGELPKSEQGYVFV 61

Query: 61  LEDDA-GKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSE 119
           LED A G V GI AI  AVGL +PWYNYRVG  V AS+ELN++  +PTLFL+ND TG+SE
Sbjct: 62  LEDCASGAVAGICAIEVAVGLNDPWYNYRVGTQVHASKELNVYNALPTLFLSNDHTGSSE 121

Query: 120 LCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGR 179
           LC+LFL    R   NG LLS++RFLF+A FR  F +K++AEMRG+ DE G SPFWESLG+
Sbjct: 122 LCTLFLDPKWRKEGNGYLLSKSRFLFMAAFRERFNEKVVAEMRGVIDEHGYSPFWESLGK 181

Query: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKA 239
            FF MEFS+ADYL G G KAFIA LMPK PLY  FLS+EAR VIG VHP T PA A+L+ 
Sbjct: 182 RFFAMEFSRADYLCGTGQKAFIAALMPKHPLYIDFLSDEARAVIGEVHPQTAPARAVLEK 241

Query: 240 EGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEP-YLIHNRKREDCR 298
           EGF Y  YVDIFD GP +E E D++RAI +S+ + +A G P     P  L+ N + +  R
Sbjct: 242 EGFRYLNYVDIFDGGPTLECEIDRVRAIRKSRLVTVAEGQPVQGEWPACLVANEQYQQFR 301

Query: 299 ITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPLSAQKR 339
                A   +  LV+       L+   G  +R V L  +++
Sbjct: 302 AMLVHADPESDRLVLSARELDALKCHPGDQIRLVRLCPEEK 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: 348
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: 344
Length adjustment: 29
Effective length of query: 311
Effective length of database: 315
Effective search space:    97965
Effective search space used:    97965
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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