GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aguA in Caulobacter crescentus NA1000

Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate CCNA_00211 CCNA_00211 Porphyromonas-type peptidyl-arginine deiminase

Query= BRENDA::Q9ABL6
         (370 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00211 CCNA_00211 Porphyromonas-type
           peptidyl-arginine deiminase
          Length = 335

 Score =  679 bits (1752), Expect = 0.0
 Identities = 335/335 (100%), Positives = 335/335 (100%)

Query: 36  MTVTVPAEWAPHRAMWVGFPSHAELWQEDLEQAQQEVADLARALAGPGAERVRLMVVGDE 95
           MTVTVPAEWAPHRAMWVGFPSHAELWQEDLEQAQQEVADLARALAGPGAERVRLMVVGDE
Sbjct: 1   MTVTVPAEWAPHRAMWVGFPSHAELWQEDLEQAQQEVADLARALAGPGAERVRLMVVGDE 60

Query: 96  AEAAARALLSDTTVEIVRGQFGDIWLRDTGPIFVDDAGKAVAAGFKFNGWGGKYSLEGDD 155
           AEAAARALLSDTTVEIVRGQFGDIWLRDTGPIFVDDAGKAVAAGFKFNGWGGKYSLEGDD
Sbjct: 61  AEAAARALLSDTTVEIVRGQFGDIWLRDTGPIFVDDAGKAVAAGFKFNGWGGKYSLEGDD 120

Query: 156 IVAEQIAAASGAPLVRNDFILEGGALDHDGNGTILTTRQCLLNDNRNPGWDEATANAALT 215
           IVAEQIAAASGAPLVRNDFILEGGALDHDGNGTILTTRQCLLNDNRNPGWDEATANAALT
Sbjct: 121 IVAEQIAAASGAPLVRNDFILEGGALDHDGNGTILTTRQCLLNDNRNPGWDEATANAALT 180

Query: 216 EALGAKKVLWLGKGLKNDHTDGHVDNLARFVAPGVVACPMGYGLDDPNADIYGDTAKMLA 275
           EALGAKKVLWLGKGLKNDHTDGHVDNLARFVAPGVVACPMGYGLDDPNADIYGDTAKMLA
Sbjct: 181 EALGAKKVLWLGKGLKNDHTDGHVDNLARFVAPGVVACPMGYGLDDPNADIYGDTAKMLA 240

Query: 276 GMTDSRGSPLQVVRIPSPGKLLDEDGEPIPASHMNFLIANEAVIVPIYAEESGAFAVEVI 335
           GMTDSRGSPLQVVRIPSPGKLLDEDGEPIPASHMNFLIANEAVIVPIYAEESGAFAVEVI
Sbjct: 241 GMTDSRGSPLQVVRIPSPGKLLDEDGEPIPASHMNFLIANEAVIVPIYAEESGAFAVEVI 300

Query: 336 KGLFPERQVIGLPSTAILTGGGSFHCISQQEPETA 370
           KGLFPERQVIGLPSTAILTGGGSFHCISQQEPETA
Sbjct: 301 KGLFPERQVIGLPSTAILTGGGSFHCISQQEPETA 335


Lambda     K      H
   0.318    0.136    0.418 

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: 637
Number of extensions: 21
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: 370
Length of database: 335
Length adjustment: 29
Effective length of query: 341
Effective length of database: 306
Effective search space:   104346
Effective search space used:   104346
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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