GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aguA in Marinobacter adhaerens HP15

Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate GFF2119 HP15_2073 peptidyl-arginine deiminase family protein

Query= BRENDA::Q9PAQ3
         (363 letters)



>FitnessBrowser__Marino:GFF2119
          Length = 332

 Score =  295 bits (756), Expect = 9e-85
 Identities = 158/338 (46%), Positives = 205/338 (60%), Gaps = 17/338 (5%)

Query: 36  LIAWPHANTDWSAHLADVEETYIALVAAITRFQMVIICV--------LDDDLQTYTEARL 87
           ++ WPH  TDW+  + +VE  ++ +  A+   + ++I          L+ DL  Y E   
Sbjct: 1   MLTWPHPGTDWAGLIDEVEPVFLDIAKAVLPHEHLVISCEHVVRLQELERDLNRYAEDNG 60

Query: 88  RSASVAMQQVRFTVASYNDTWLRDSGPITLIGTNRDFRLLDFRFTGWGGKFEAKADDQLV 147
                   +VR   A  NDTW RD GPIT++ T+    LLDFRF  WGGKF  + DD L 
Sbjct: 61  FPG-----RVRSVPAPANDTWARDHGPITIL-TDEGPTLLDFRFNAWGGKFPWEKDDALN 114

Query: 148 SVLHANGLFKNTQMHSINFALEGGAIETDGAGTLLTTWRCL--HERHPQRTRKTLDANLT 205
           + L   G+F  T+M  + F LEGG+ E+DG GTLLTT  CL    R+P   R  ++  L+
Sbjct: 115 NHLFNAGVFGTTRMQQVGFVLEGGSFESDGQGTLLTTSECLLTPTRNPAMDRTAIEQLLS 174

Query: 206 AWLAQNRVLWLEHGYLEGDDTDAHIDTLARFASTDSIVYQSCDNTTDSHYAELQAMANEL 265
             L   R+LWL HGYL GDDTD+HIDTLARF + D I Y +C +  D HY+ L AM  EL
Sbjct: 175 EVLGIRRILWLNHGYLAGDDTDSHIDTLARFCAPDHICYVTCPDVADEHYSALAAMEEEL 234

Query: 266 TALRTTEGRAYRLFPLPWTKPILDQD-RRLPASYANFLIIEGAVLMPTYDDPADTIAQSV 324
              R  +G  Y+L PLPW   I D+D  RLPA+YANFLII  AVL+P Y    D  A +V
Sbjct: 235 QEFRQADGAPYKLTPLPWPDAIHDEDGERLPATYANFLIINEAVLLPVYGVDQDQDAIAV 294

Query: 325 LAEAFPTREIVPVPCRPLIWQNGSLHCITMQIPAGLLA 362
           + E FPTR IVP+ CRPLI Q+GSLHC+TMQIPAG+++
Sbjct: 295 MKEIFPTRAIVPINCRPLIRQHGSLHCVTMQIPAGVVS 332


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: 414
Number of extensions: 14
Number of successful extensions: 5
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: 332
Length adjustment: 29
Effective length of query: 334
Effective length of database: 303
Effective search space:   101202
Effective search space used:   101202
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