GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aguA in Dyella japonica UNC79MFTsu3.2

Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate N515DRAFT_1539 N515DRAFT_1539 Agmatine/peptidylarginine deiminase

Query= BRENDA::Q9PAQ3
         (363 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1539
          Length = 345

 Score =  426 bits (1096), Expect = e-124
 Identities = 201/337 (59%), Positives = 253/337 (75%)

Query: 24  RFPAEWEPQSAILIAWPHANTDWSAHLADVEETYIALVAAITRFQMVIICVLDDDLQTYT 83
           R PAEWEPQSA+LIAWPHA+TDW+  LA+VE TY+AL AA+TRF+ +I+ V D +L+ + 
Sbjct: 7   RLPAEWEPQSAVLIAWPHADTDWADRLAEVETTYVALAAAVTRFEPLIVVVADAELRAHV 66

Query: 84  EARLRSASVAMQQVRFTVASYNDTWLRDSGPITLIGTNRDFRLLDFRFTGWGGKFEAKAD 143
           E +LR A V + +VR     Y+DTWLRDSGPITL      F+L DFRFTGWGGKF A+ D
Sbjct: 67  EGKLREAGVDLGRVRLIELPYDDTWLRDSGPITLKDDRGAFQLTDFRFTGWGGKFGAEQD 126

Query: 144 DQLVSVLHANGLFKNTQMHSINFALEGGAIETDGAGTLLTTWRCLHERHPQRTRKTLDAN 203
           D LV+ L   G+F       I++ALEGG IE+DGAGT+LTTWRCL +RHP+++R+ + A 
Sbjct: 127 DALVAGLVKAGVFGRAAHRRIDWALEGGGIESDGAGTVLTTWRCLVQRHPEQSREEMSAI 186

Query: 204 LTAWLAQNRVLWLEHGYLEGDDTDAHIDTLARFASTDSIVYQSCDNTTDSHYAELQAMAN 263
           L   L  +R+LWL++GYLEGDDTDAHIDTLARFA    IV+Q+CD+  D+H+ EL  MA 
Sbjct: 187 LRDGLHASRILWLDYGYLEGDDTDAHIDTLARFAPDGRIVFQACDDLDDAHHDELSRMAG 246

Query: 264 ELTALRTTEGRAYRLFPLPWTKPILDQDRRLPASYANFLIIEGAVLMPTYDDPADTIAQS 323
           EL AL   +G+ Y L+PLPW KPI+D+ RRL ASYAN+LI+ G VL+P Y DPAD  A  
Sbjct: 247 ELAALCMADGKPYELYPLPWAKPIVDEGRRLAASYANYLIVNGGVLVPAYGDPADDEAAR 306

Query: 324 VLAEAFPTREIVPVPCRPLIWQNGSLHCITMQIPAGL 360
           ++  A P RE+V VPCRPLIWQNGSLHCITMQ+PAG+
Sbjct: 307 IIGAAHPGREVVQVPCRPLIWQNGSLHCITMQLPAGI 343


Lambda     K      H
   0.322    0.134    0.423 

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: 493
Number of extensions: 20
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: 363
Length of database: 345
Length adjustment: 29
Effective length of query: 334
Effective length of database: 316
Effective search space:   105544
Effective search space used:   105544
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 (21.9 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