GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Miya:8499887
          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 (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