GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Caulobacter crescentus NA1000

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate CCNA_03229 CCNA_03229 FAD dependent oxidoreductase

Query= reanno::pseudo5_N2C3_1:AO356_21495
         (427 letters)



>FitnessBrowser__Caulo:CCNA_03229
          Length = 429

 Score =  268 bits (684), Expect = 3e-76
 Identities = 163/430 (37%), Positives = 227/430 (52%), Gaps = 17/430 (3%)

Query: 5   PYPESY-----YAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLE 59
           PYP  Y     YA +   VP  P L  DV  +VC+IGAG+TGL +AL L   G +  VLE
Sbjct: 8   PYPSPYGRGNWYADTVTDVPASPPLDGDVAAEVCIIGAGFTGLGAALAL---GSRAVVLE 64

Query: 60  AAKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQ 119
           A ++G  ASGRNGGQ+     RD   +E++VG   A  L  +A E        V    I 
Sbjct: 65  AGRIGCAASGRNGGQVHTGQRRDQAWLEKTVGRDDALALWRLAEEARAHFASLVTA--ID 122

Query: 120 CDLKDGGVFAALTAKQMGHLESQKRLW---ERFGHTQLELLDQRRIREVVACEEYVGGML 176
           CD + G + A    K  G  E    L    +R+G+ QLEL+ +  +   +  + Y GG+ 
Sbjct: 123 CDWRPGMIHAR--HKPGGEAEDADYLALMADRYGYDQLELIGETALAHELGTDVYHGGLA 180

Query: 177 DMSGGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQGKVRAKFIIVA 235
           D  GGH+HPL LA G AA   + G VI+E + A    R G   VV T  G+V    +I++
Sbjct: 181 DHGGGHVHPLKLAQGMAAQARAAGAVIHENTRADAWRREGGKIVVETGGGRVTCDQLILS 240

Query: 236 GNAYLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDK 295
           G+  L  +     A+ MP    +  T PLG  LA  ++  +  V D  ++++Y+R T D 
Sbjct: 241 GDGLLNRMAGPAQARVMPINNFIAVTAPLG-ALADEIIRSNAAVSDSRFVVNYFRKTPDG 299

Query: 296 RLIFGGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLG 355
           RL+FGGG  Y    P +I  ++R  + K +P+L DV+I +AW G   +T SR+P VG + 
Sbjct: 300 RLLFGGGENYRPGFPHDIAGLVRKNLAKIYPRLADVEITHAWGGTLGITFSRMPFVGEVA 359

Query: 356 DNIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMG 415
             +  + G SG GV      GK+LAEA  G+    D  + LP  PFPGG+LLR P    G
Sbjct: 360 QGVRVAAGYSGQGVMLAPYVGKLLAEAALGETGPVDLLSRLPTPPFPGGRLLRWPLTVAG 419

Query: 416 AWYYGLRDKL 425
             +Y LRD+L
Sbjct: 420 LSWYALRDRL 429


Lambda     K      H
   0.320    0.139    0.421 

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: 614
Number of extensions: 34
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: 427
Length of database: 429
Length adjustment: 32
Effective length of query: 395
Effective length of database: 397
Effective search space:   156815
Effective search space used:   156815
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: 51 (24.3 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