GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuB in Shewanella amazonensis SB2B

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 6938535 Sama_2638 putative oxidoreductase (RefSeq)

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



>lcl|FitnessBrowser__SB2B:6938535 Sama_2638 putative oxidoreductase
           (RefSeq)
          Length = 428

 Score =  660 bits (1703), Expect = 0.0
 Identities = 319/427 (74%), Positives = 366/427 (85%), Gaps = 1/427 (0%)

Query: 1   MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60
           M+ TP+ ESYYAASAN    RP L++ +ETDVCVIGAGYTGLSSAL LLE+GFKV VLEA
Sbjct: 1   MSATPHTESYYAASANDTRIRPRLEEHLETDVCVIGAGYTGLSSALHLLESGFKVVVLEA 60

Query: 61  AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQC 120
           A++G+GASGRNGGQIVNSYSRDIDVIE++VG ++ +L G MAFEGGRIIR+R+AKY I C
Sbjct: 61  ARIGWGASGRNGGQIVNSYSRDIDVIEKTVGKEKGKLFGEMAFEGGRIIRDRIAKYNIDC 120

Query: 121 DLKDGGVFAALTAKQMGHLESQKRLWERFGHT-QLELLDQRRIREVVACEEYVGGMLDMS 179
           DLK+GGVFAAL  KQMGHL++QK LWE  GHT QLE+LD+  IR VV  E YVGGMLD S
Sbjct: 121 DLKNGGVFAALNQKQMGHLKAQKALWEAHGHTNQLEILDEAGIRNVVNTERYVGGMLDKS 180

Query: 180 GGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAY 239
           GGHIHPLNLALGEA AVESLGG I+E S  + +  G   +V T  G+V+A+F++VAGNAY
Sbjct: 181 GGHIHPLNLALGEARAVESLGGKIFEDSAVLDVVEGEPAIVKTEFGQVKARFVVVAGNAY 240

Query: 240 LGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIF 299
           LG L+PEL AKSMPCGTQVI TEPL DE+A+SLLPQDYCVEDCNYLLDY+RL+GDKRLI+
Sbjct: 241 LGKLMPELMAKSMPCGTQVITTEPLSDEMANSLLPQDYCVEDCNYLLDYFRLSGDKRLIY 300

Query: 300 GGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIY 359
           GGGVVYGARDP NI++II PKML+ FPQLK V+IDY WTGNFLLTLSRLPQVGR+G NIY
Sbjct: 301 GGGVVYGARDPDNIKSIILPKMLETFPQLKGVRIDYTWTGNFLLTLSRLPQVGRIGKNIY 360

Query: 360 YSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYY 419
           YSQGCSGHGVTYTHLAGK++AE L GQA RFD FA+LPHYPFPGG  LR PF+A+GAWYY
Sbjct: 361 YSQGCSGHGVTYTHLAGKLIAEVLNGQATRFDVFAELPHYPFPGGHALRVPFSAIGAWYY 420

Query: 420 GLRDKLG 426
            +RDKLG
Sbjct: 421 TMRDKLG 427


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: 734
Number of extensions: 23
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: 428
Length adjustment: 32
Effective length of query: 395
Effective length of database: 396
Effective search space:   156420
Effective search space used:   156420
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.

Links

Downloads

Related tools

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, 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