GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruF in Pseudomonas fluorescens FW300-N2C3

Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate AO356_01530 AO356_01530 arginine N-succinyltransferase

Query= CharProtDB::CH_107315
         (338 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_01530
          Length = 344

 Score =  206 bits (525), Expect = 5e-58
 Identities = 119/337 (35%), Positives = 192/337 (56%), Gaps = 3/337 (0%)

Query: 2   LVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYFF 61
           +++RP    DLP +  LA  +  G TSLP + ERL  ++  ++ +FA +V    +  Y F
Sbjct: 1   MIVRPVALTDLPALLDLARCAGPGFTSLPANEERLAHRVRWAQRTFAGQVE-RADADYLF 59

Query: 62  VLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGNS 121
           VLED    ++VG SA+  + G  EP+Y++R    V ++  L I  +I  L L ++++G S
Sbjct: 60  VLEDD-DRQVVGISALTGAVGLREPWYNYRVGVTVSSAPELGIQRQIPTLFLNNEMSGQS 118

Query: 122 LLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAVG 181
            + S ++  +        L S  RLLF+A   + F + ++ E+ G++DEQG SPFW+++G
Sbjct: 119 EICSLFLHPEQRHGHNGRLLSLARLLFVAEFSQLFGEKLIAELRGHADEQGCSPFWDSLG 178

Query: 182 RNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDILM 241
           R+FF  ++  A++LSG+ +++F+AELMP  P+Y  LL + AQ  +G+ HP  +    IL 
Sbjct: 179 RHFFQKDFSYADQLSGMGNKSFIAELMPRQPLYTCLLTEQAQAVIGKAHPNTEPALKILS 238

Query: 242 REGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQDFR 301
            EGF    YIDIFDGGP + A  S IRS+  S+ + + IG   +    +L+ N +L++ R
Sbjct: 239 AEGFSHRGYIDIFDGGPVIEAPVSKIRSVRDSQTLTLAIGTPDEQAPVWLIHNRRLENCR 298

Query: 302 AVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338
            V        G  + +    A+ L V  G +VR VA+
Sbjct: 299 -VTSARARLHGNSLLVDRLTAKRLQVQPGDTVRAVAL 334


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: 287
Number of extensions: 19
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