GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dpkA in Azospirillum brasilense Sp245

Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H] (EC 1.5.1.1) (characterized)
to candidate AZOBR_RS03120 AZOBR_RS03120 ornithine cyclodeaminase

Query= BRENDA::Q485R8
         (316 letters)



>FitnessBrowser__azobra:AZOBR_RS03120
          Length = 318

 Score =  200 bits (508), Expect = 4e-56
 Identities = 117/313 (37%), Positives = 175/313 (55%), Gaps = 5/313 (1%)

Query: 1   MKIISAEQVHQNLNFEELIPLLKQSFSRPFSMPQRQVYSLAPEQSENHDAFALLPSWN-E 59
           M+ ++  ++   L+F  LI  ++Q+F     +P R  +++     ++     L+P+W   
Sbjct: 1   MRTVTGAELKSVLHFRMLIERMRQTFRAGVEVPMRHHHTVET-YGQSDGTLLLMPAWQVN 59

Query: 60  EVIGNKAFTYFPDNAKKHDLPGLFSKIMLFKRQTGEPLALVDGTSVTYWRTAAISALASQ 119
           + IG K  T FPDN  K DLP +    +L   +TG P A++DGT++T  RTAA SALA+ 
Sbjct: 60  QSIGVKVVTVFPDNGAK-DLPAVQGLYLLMDGKTGMPQAVLDGTALTKRRTAAASALAAS 118

Query: 120 LLSRKNSQHLMLFGTGNLASYLVKAHLTVRDIKQVTLWGRNAKKVSKLIADFSILYPAVT 179
            L+R +S+ L++ GTG LA  L++A  TV  IK V +WGR+ +K  K+ + F    P   
Sbjct: 119 YLARPDSERLLMVGTGALAPELIEAFATVLPIKHVLVWGRSLEKAKKVASRFH--RPKFR 176

Query: 180 FKTSVDVNAEVASADIICCATGAKTPLFDGNSVSAGCHIDCLGNHMTDARECDTTTILRA 239
            + + D+   V  A +I CAT AK PL  G  +  G H+D +G    + RE D   I R+
Sbjct: 177 IEATADLEGAVRGAQVISCATLAKEPLIRGEWLQPGAHLDLVGGFTPEMREADDDCIRRS 236

Query: 240 RVFVDSLTNTLNEAGELLIPMAEDAFNKDEIVGELADMCKTPSMLRQSSDEITLFKSVGT 299
           RVFVD+      EAG+++ PM        +I G+L D+ +     R+  D+ITLFKSVGT
Sbjct: 237 RVFVDTREGACKEAGDIVQPMKAGILTDADIAGDLYDLTRGQRAGRRFYDQITLFKSVGT 296

Query: 300 AISDLVAAHSVVE 312
           A+ DL AA   VE
Sbjct: 297 ALEDLCAAQLAVE 309


Lambda     K      H
   0.318    0.131    0.379 

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: 201
Number of extensions: 12
Number of successful extensions: 4
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: 316
Length of database: 318
Length adjustment: 27
Effective length of query: 289
Effective length of database: 291
Effective search space:    84099
Effective search space used:    84099
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: 48 (23.1 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