GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aruG in Pseudomonas fluorescens GW456-L13

Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate PfGW456L13_1973 Arginine N-succinyltransferase (EC 2.3.1.109)

Query= BRENDA::P80358
         (340 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973 Arginine
           N-succinyltransferase (EC 2.3.1.109)
          Length = 341

 Score =  587 bits (1514), Expect = e-172
 Identities = 292/338 (86%), Positives = 316/338 (93%)

Query: 1   MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60
           MIVRPV S+DLPALI+LARSTGTGLTTLPANE+RL HRV WAEK FRGEA RGDADYLFV
Sbjct: 1   MIVRPVRSSDLPALIDLARSTGTGLTTLPANEERLAHRVGWAEKTFRGEAGRGDADYLFV 60

Query: 61  LEDDAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSEL 120
           LEDD G+VVGISAIAGAVGLREPWYN+RVGLTVSASQELNI+REIPTLFLANDLTGNSEL
Sbjct: 61  LEDDDGRVVGISAIAGAVGLREPWYNFRVGLTVSASQELNIYREIPTLFLANDLTGNSEL 120

Query: 121 CSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGRH 180
           CSLFLHAD+RSGLNG++LS+AR LFIAEF  LFG+K+IAEMRG+SDE GRSPFWESLGRH
Sbjct: 121 CSLFLHADYRSGLNGRMLSKARMLFIAEFPQLFGNKIIAEMRGVSDEAGRSPFWESLGRH 180

Query: 181 FFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKAE 240
           FFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLS +AR VIG+VHP+TEPALAMLK+E
Sbjct: 181 FFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSPDARNVIGQVHPDTEPALAMLKSE 240

Query: 241 GFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKREDCRIT 300
           GFSYQGYVDIFDAGPAIE ET KIRA+ +SQ LVLAVGTPGDDA P++IHNRKREDCRIT
Sbjct: 241 GFSYQGYVDIFDAGPAIECETGKIRAVRDSQALVLAVGTPGDDATPFIIHNRKREDCRIT 300

Query: 301 AAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPLSAQK 338
           AAPAR AAGTLVVDPLTAKRL+L+AG  VRAV LSA +
Sbjct: 301 AAPARLAAGTLVVDPLTAKRLQLNAGDQVRAVALSAAR 338


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: 486
Number of extensions: 15
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: 341
Length adjustment: 28
Effective length of query: 312
Effective length of database: 313
Effective search space:    97656
Effective search space used:    97656
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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