GapMind for catabolism of small carbon sources

 

Aligments for a candidate for odc in Shewanella sp. ANA-3

Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate 7026539 Shewana3_3682 ornithine decarboxylase (RefSeq)

Query= curated2:O50657
         (393 letters)



>lcl|FitnessBrowser__ANA3:7026539 Shewana3_3682 ornithine
           decarboxylase (RefSeq)
          Length = 391

 Score =  172 bits (436), Expect = 1e-47
 Identities = 115/366 (31%), Positives = 181/366 (49%), Gaps = 12/366 (3%)

Query: 9   KEVKTLAKRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAGLGSH 68
           K ++  AK   TPF+V     + + Y  M    P A V+YA+KANP  EIL+LL   GS+
Sbjct: 19  KRIEEFAKDKATPFVVIDTSIIAKQYDDMVNSFPYADVYYAVKANPAAEILTLLKNKGSN 78

Query: 69  FDVASAGEMEILHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKMAKAV 128
           FD+AS  E++++  +GV   ++ Y N +K  + ++A  +  VR +  D  +++  +A+  
Sbjct: 79  FDIASIYELDMVTNVGVTPDRVSYGNTIKKRQDVRAFYERGVRMYASDSEADLRMIAEEA 138

Query: 129 PGADVLVRIAVR-NNKALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQSLST 187
           PG+ + VRI     + A   L+ KFG   E A +LL  A + GL   GI FHVGSQ    
Sbjct: 139 PGSRIYVRILTEGTDTADWPLSRKFGCQNEMAYELLVLANELGLEPFGISFHVGSQQRDI 198

Query: 188 AAYEEALLVARRLFDE-AEEMGMHLTDLDIGGGFPVPDAKGLNVDLAAMMEAINKQIDRL 246
            A++ A+   + +FD   +E  + L  +++GGGFP       N  L    E I   +   
Sbjct: 199 GAWDSAIGKVKSIFDRLRDEHNIVLKMINMGGGFPANYIDKTN-QLGVYAEQITHFLKED 257

Query: 247 FPD--TAVWTEPGRYMCGTAVNLVTSVIGTKTRGE---QPWYILDEGIYGCFSGIMYDHW 301
           F D    +  EPGR +   A  LV+ V+    +     + W   D G +      M +  
Sbjct: 258 FGDDLPQIILEPGRSLISNAGVLVSEVVLISKKSYTALERWVFTDVGKFSGLIETMDEAI 317

Query: 302 TYPLHCFGKGNKKPSTFGGPSCDGIDVLYRDF---MAPELKIGDKVLVTEMGSYTSV-SA 357
            +P+    +G        GP+CD  D++Y  +   +  +L IGD++     G+YT+  SA
Sbjct: 318 KFPIFTHKQGELDKCVIAGPTCDSADIMYEHYSYGLPNDLAIGDRMYWLTAGAYTTTYSA 377

Query: 358 TRFNGF 363
             FNGF
Sbjct: 378 VCFNGF 383


Lambda     K      H
   0.320    0.137    0.407 

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: 387
Number of extensions: 14
Number of successful extensions: 3
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: 393
Length of database: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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: 50 (23.9 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 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, the preprint on GapMind for carbon sources, 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