GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS11675
          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 (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