GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6937936
          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.

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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