GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruF in Chromobacterium vaccinii MWU205

Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate WP_046157873.1 VL52_RS15520 arginine/ornithine succinyltransferase subunit alpha

Query= CharProtDB::CH_107315
         (338 letters)



>NCBI__GCF_000971335.1:WP_046157873.1
          Length = 339

 Score =  293 bits (751), Expect = 3e-84
 Identities = 153/340 (45%), Positives = 219/340 (64%), Gaps = 6/340 (1%)

Query: 1   MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60
           M  +RP + +DLP ++RLA  S +GVTSLP + E+L ++I  S ++F  E +      Y+
Sbjct: 1   MFTVRPVRTSDLPAIERLAQASGIGVTSLPSNREKLFERIQQSVSAFEHEATGEASRDYY 60

Query: 61  -FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTG 119
            F LE    G +VG ++I ASAGF EPFYS+R+ET VHASR+L ++N++HVL++CHDLTG
Sbjct: 61  MFALEQG--GAVVGTASICASAGFDEPFYSYRSETAVHASRALKVNNRVHVLNICHDLTG 118

Query: 120 NSLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNA 179
              L  F+V   L  ++  EL SR RLLF+A   ERF   ++ E+ G  D+ G+SPFWNA
Sbjct: 119 TVQLCGFFVDSGL-DAIAGELMSRARLLFIAGERERFGRRIIAEMQGVHDDAGQSPFWNA 177

Query: 180 VGRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDI 239
           +GR FF+L++++ E+     S+TF+AELMP YPIYVPLLPD AQ+++GQ+HP  +    +
Sbjct: 178 IGRRFFNLDFLQVEQAFVSHSKTFIAELMPSYPIYVPLLPDEAQQAIGQIHPHFERVCQL 237

Query: 240 LMREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKI-GEAPKSGRPYLVTNGQLQ 298
           L +EGFE DNY+DIFDGG  L A    ++++  SR  PV+I    P      LV+N +L 
Sbjct: 238 LCKEGFEADNYLDIFDGGAVLTAELDRLKTVEHSRAYPVEIQASLPAQASLQLVSNQRLA 297

Query: 299 DFRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338
            F A    +    G    ++ +AA+ALGV  G  VR+  +
Sbjct: 298 GFAATAARVAVVDG-VAFINPDAAKALGVSSGDRVRVAGL 336


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: 305
Number of extensions: 11
Number of successful extensions: 3
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: 339
Length adjustment: 28
Effective length of query: 310
Effective length of database: 311
Effective search space:    96410
Effective search space used:    96410
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 24 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