GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuB in Shewanella amazonensis SB2B

Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate 6937936 Sama_2077 oxidoreductase (RefSeq)

Query= SwissProt::P37906
         (426 letters)



>lcl|FitnessBrowser__SB2B:6937936 Sama_2077 oxidoreductase (RefSeq)
          Length = 429

 Score =  307 bits (787), Expect = 4e-88
 Identities = 167/430 (38%), Positives = 248/430 (57%), Gaps = 9/430 (2%)

Query: 1   MTEHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASR 60
           M     SYY A+      +  L E+I  DV V+GGG+TG+++AL LAE G+ VV+LEA++
Sbjct: 1   MQARCGSYYNATIKHETDYPRLTEAIQADVAVIGGGFTGVNTALELAEQGYKVVLLEANK 60

Query: 61  IGFGASGRNGGQLVNSYSRDIDV---IEKSYGMDTARMLGSMMFEGGEIIRERIKRYQID 117
           I +GA+GRNGGQ+  S S D  +   +    G +    + ++ + G +II+ R+ +Y ID
Sbjct: 61  IAWGATGRNGGQVTGSLSGDQAMTKQLRNRIGAEAEDYVWALRWRGHDIIKNRVAKYNID 120

Query: 118 CDYRPGGLFVAMNDKQLATLEEQKENWERYGNKQL-ELLDANAIRREVASDRYTGALLDH 176
           CD R G L  A     +  L+   +  +R G   L  L++ + + + + S  Y G LL+ 
Sbjct: 121 CDLRHGHLHTAYKPAHMNELKSMLDEAQRKGMGDLVSLVEKDEMPQYLESPLYHGGLLNK 180

Query: 177 SGGHIHPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNA 236
              H+H +NL IGEA A    G R++E + V  I      VV+TA G VTA  V++AGNA
Sbjct: 181 KNMHLHSVNLCIGEARAAESLGVRIFEDTQVLDIVEGPRPVVKTAFGSVTANKVLIAGNA 240

Query: 237 Y--LGDKVEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADN 294
           Y  LG    P+L     P       T RLS+++A ++ P N  V DC ++LDYYRLTADN
Sbjct: 241 YHKLG---RPKLRGMLFPASLGNCATVRLSDEVASAINPHNLAVYDCRFVLDYYRLTADN 297

Query: 295 RLLYGGGVVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLD 354
           RL++GGG  Y  RDP +V   + P + +TFP+LKGV+I++ W G   + ++R+PQ G++ 
Sbjct: 298 RLMFGGGTNYSGRDPKNVAEELRPAIERTFPRLKGVEIEFAWAGMAGIVINRIPQLGKVS 357

Query: 355 TNIYYMQGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMG 414
            ++YY QGYSGHGV  +H+   ++A+ + GD   F  FA + H+  P          A+G
Sbjct: 358 EHVYYCQGYSGHGVATSHIMSEIMAKAIDGDLREFGLFAGMKHWRIPLNEWFGNQALAIG 417

Query: 415 AAYYSLRDRL 424
             YY LR+ L
Sbjct: 418 MLYYQLRESL 427


Lambda     K      H
   0.320    0.138    0.411 

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: 519
Number of extensions: 26
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: 426
Length of database: 429
Length adjustment: 32
Effective length of query: 394
Effective length of database: 397
Effective search space:   156418
Effective search space used:   156418
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