GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruF in Klebsiella michiganensis M5al

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

Query= CharProtDB::CH_107315
         (338 letters)



>FitnessBrowser__Koxy:BWI76_RS11675
          Length = 344

 Score =  231 bits (589), Expect = 2e-65
 Identities = 131/337 (38%), Positives = 196/337 (58%), Gaps = 3/337 (0%)

Query: 1   MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60
           M+V+RP +  DLP +  LA ++  G+TSLP D   L  +I  S+ ++  E+    E+ Y 
Sbjct: 1   MMVIRPVEKGDLPGLLTLAGETGGGLTSLPADEATLAARIERSQMTWRGELP-KSEQGYV 59

Query: 61  FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120
           FVLED ASG + G  AI  + G ++P+Y++R  T VHAS+ L+++N +  L L +D TG+
Sbjct: 60  FVLEDCASGAVAGICAIEVAVGLNDPWYNYRVGTQVHASKELNVYNALPTLFLSNDHTGS 119

Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180
           S L + ++     +     L S+ R LFMA+  ERF + VV E+ G  DE G SPFW ++
Sbjct: 120 SELCTLFLDPKWRKEGNGYLLSKSRFLFMAAFRERFNEKVVAEMRGVIDEHGYSPFWESL 179

Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240
           G+ FF + +  A+ L G   + F+A LMP +P+Y+  L D A+  +G+VHP+      +L
Sbjct: 180 GKRFFAMEFSRADYLCGTGQKAFIAALMPKHPLYIDFLSDEARAVIGEVHPQTAPARAVL 239

Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRP-YLVTNGQLQD 299
            +EGF   NY+DIFDGGPTL      +R+I +SR+V V  G+  +   P  LV N Q Q 
Sbjct: 240 EKEGFRYLNYVDIFDGGPTLECEIDRVRAIRKSRLVTVAEGQPVQGEWPACLVANEQYQQ 299

Query: 300 FRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLV 336
           FRA+++  D      + LS    +AL    G  +RLV
Sbjct: 300 FRAMLVHAD-PESDRLVLSARELDALKCHPGDQIRLV 335


Lambda     K      H
   0.319    0.135    0.387 

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: 277
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: 338
Length of database: 344
Length adjustment: 29
Effective length of query: 309
Effective length of database: 315
Effective search space:    97335
Effective search space used:    97335
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