GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruG 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= BRENDA::P80358
         (340 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_01530
          Length = 344

 Score =  456 bits (1174), Expect = e-133
 Identities = 219/337 (64%), Positives = 273/337 (81%)

Query: 1   MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60
           MIVRPV   DLPAL++LAR  G G T+LPANE+RL HRV WA++ F G+ ER DADYLFV
Sbjct: 1   MIVRPVALTDLPALLDLARCAGPGFTSLPANEERLAHRVRWAQRTFAGQVERADADYLFV 60

Query: 61  LEDDAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSEL 120
           LEDD  +VVGISA+ GAVGLREPWYNYRVG+TVS++ EL I R+IPTLFL N+++G SE+
Sbjct: 61  LEDDDRQVVGISALTGAVGLREPWYNYRVGVTVSSAPELGIQRQIPTLFLNNEMSGQSEI 120

Query: 121 CSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGRH 180
           CSLFLH + R G NG+LLS AR LF+AEF  LFG+KLIAE+RG +DE+G SPFW+SLGRH
Sbjct: 121 CSLFLHPEQRHGHNGRLLSLARLLFVAEFSQLFGEKLIAELRGHADEQGCSPFWDSLGRH 180

Query: 181 FFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKAE 240
           FF+ +FS AD L+G+GNK+FIAELMP+ PLYTC L+E+A+ VIG+ HPNTEPAL +L AE
Sbjct: 181 FFQKDFSYADQLSGMGNKSFIAELMPRQPLYTCLLTEQAQAVIGKAHPNTEPALKILSAE 240

Query: 241 GFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKREDCRIT 300
           GFS++GY+DIFD GP IEA   KIR++ +SQ L LA+GTP + A  +LIHNR+ E+CR+T
Sbjct: 241 GFSHRGYIDIFDGGPVIEAPVSKIRSVRDSQTLTLAIGTPDEQAPVWLIHNRRLENCRVT 300

Query: 301 AAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPLSAQ 337
           +A AR    +L+VD LTAKRL++  G +VRAV LS Q
Sbjct: 301 SARARLHGNSLLVDRLTAKRLQVQPGDTVRAVALSRQ 337


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: 379
Number of extensions: 12
Number of successful extensions: 1
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