GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6938535
          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.

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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