GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aguA in Desulfovibrio vulgaris Miyazaki F

Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate 8499887 DvMF_0652 Agmatine deiminase (RefSeq)

Query= BRENDA::O86509
         (339 letters)



>lcl|FitnessBrowser__Miya:8499887 DvMF_0652 Agmatine deiminase
           (RefSeq)
          Length = 370

 Score =  289 bits (740), Expect = 7e-83
 Identities = 157/342 (45%), Positives = 199/342 (58%), Gaps = 17/342 (4%)

Query: 5   MPPEWAPHERTWMAWPGPNATFTDAEELAGARAAWASVARAVRRFEPVTMVHGPGQAATA 64
           MP EW+PH   WMAWP P+    DA  L   R ++A V RA+ RFEPVT++  P  A  A
Sbjct: 29  MPAEWSPHAGCWMAWPCPDPLLEDA--LDTVRTSFAGVVRAIARFEPVTLLARPEDAEVA 86

Query: 65  RELLGPDVDLVERELDDAWMRDIGPTFVTDGRGGLAAVDWVFNGWGAQDWARWEHDAEIA 124
             L GP V +V   + DAWMRD GPTFV DG GG+A VDW+FN WG   +    HD ++A
Sbjct: 87  AALCGPGVQVVPAPITDAWMRDFGPTFVVDGAGGVAGVDWMFNSWG-HTYDEPTHDDDVA 145

Query: 125 RHVADLAAAPVLSSPLVNEGGAIHVDGEGTVLLTDTVQLGSGRNPGWSREEVEAEIHAKL 184
           + +         ++P + EGG+IHVDG+GT++ T+   L   RN G ++ + E    A L
Sbjct: 146 QLILSRLGMRRYAAPFILEGGSIHVDGQGTLMTTEQCLLDPRRNAGMTKADFEELFAAYL 205

Query: 185 GTTTAIWLPHGLAGDYGRYGTQGHVDIVAAFARPGTVVVHSQRDPRHPDHERSQLYLEIL 244
           G    IWL  GL GD     T GHVDIV+ FARPG V++H   DP  P+H   Q  L  L
Sbjct: 206 GVRKVIWLGEGLEGD----DTHGHVDIVSCFARPGVVLLHRCDDPEDPNHAVYQDNLRRL 261

Query: 245 RGRTDARGRRLEVVEVPAPTVLKDEEGEWADYSYINHYVCNGGVVLCAFGDPN------- 297
           +  TDA G+ LE+V +  P    +  G+  D SYIN YV NGG+V+ AFG P        
Sbjct: 262 QLATDADGKPLEIVTIDQPN-RAEHGGKRMDLSYINFYVANGGIVMSAFGAPGGGADSQG 320

Query: 298 --DELAAGIFRRLFPERTVTLVDARTIFAGGGGIHCITQQQP 337
             D +A    RR+FPER V  V +  IF GGGGIHCITQQQP
Sbjct: 321 ALDRVAFETLRRVFPEREVVQVHSLDIFRGGGGIHCITQQQP 362


Lambda     K      H
   0.319    0.137    0.443 

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: 499
Number of extensions: 32
Number of successful extensions: 6
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: 339
Length of database: 370
Length adjustment: 29
Effective length of query: 310
Effective length of database: 341
Effective search space:   105710
Effective search space used:   105710
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, the preprint 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