GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Sinorhizobium fredii NGR234

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_164924450.1 NGR_RS23860 FAD-binding oxidoreductase

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



>NCBI__GCF_000018545.1:WP_164924450.1
          Length = 437

 Score =  486 bits (1252), Expect = e-142
 Identities = 224/423 (52%), Positives = 308/423 (72%), Gaps = 1/423 (0%)

Query: 6   YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65
           YPESYYAAS N +     L+  VETD+CV+GAGYTGL++A+ L E G+KV V+E A+VG+
Sbjct: 15  YPESYYAASRNVIRTPVKLKGRVETDICVVGAGYTGLATAIHLAEKGYKVAVIEGAQVGW 74

Query: 66  GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125
           GASGRNGGQ+VN  +  +  I+R  G   A+ +G +  EGGRI+R  V+ Y+I CDLK G
Sbjct: 75  GASGRNGGQVVNGLNASLSTIQRRFGEDAARFIGGLVQEGGRILRRIVSHYRIDCDLKSG 134

Query: 126 GVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHP 185
            ++AA T   M  LE+++ LW ++G     +LD+  +R++V  E Y GGMLD++GGH+HP
Sbjct: 135 NIYAAYTGAHMKDLEAKQALWRKYGMDDHLMLDRDALRKLVNSEAYCGGMLDITGGHMHP 194

Query: 186 LNLALGEAAAVESLGGVIYEQSPAVRIE-RGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244
           LNL LGEA A ESLGG+I+E SP  R++ R A P V+T +G+V A+ +++ GNAYLG+ V
Sbjct: 195 LNLVLGEARAFESLGGIIHEMSPVTRVDHRAARPTVYTREGEVSARIVVLCGNAYLGDAV 254

Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304
           PEL ++ MP  TQ+I T PLG+ELA  L+P D CVED  Y+LDY+RL+ DKR++FGGG V
Sbjct: 255 PELVSRVMPVSTQMITTAPLGEELADMLIPSDMCVEDVRYILDYFRLSADKRMVFGGGTV 314

Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGC 364
           YG  DPA++ A +RP + K FP+LK VKIDYAW+GNF L+ +R+PQ+GR+G N Y++ G 
Sbjct: 315 YGGTDPADVVAKLRPNLEKVFPRLKGVKIDYAWSGNFALSFTRVPQMGRIGANTYFAHGY 374

Query: 365 SGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRDK 424
           SGHGVT +HL G+ LAEA+ G   RFD F  LP YPFPGG++ R  ++ +G+W+Y  +D 
Sbjct: 375 SGHGVTGSHLFGRTLAEAIDGDQSRFDMFEKLPWYPFPGGRIFRAQYSTIGSWWYSFKDA 434

Query: 425 LGF 427
           +G+
Sbjct: 435 VGW 437


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: 685
Number of extensions: 33
Number of successful extensions: 2
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: 437
Length adjustment: 32
Effective length of query: 395
Effective length of database: 405
Effective search space:   159975
Effective search space used:   159975
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 Apr 09 2024. 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