GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cadA in Shewanella loihica PV-4

Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate 5210966 Shew_3392 ornithine decarboxylase (RefSeq)

Query= curated2:O50657
         (393 letters)



>FitnessBrowser__PV4:5210966
          Length = 391

 Score =  181 bits (458), Expect = 4e-50
 Identities = 114/366 (31%), Positives = 188/366 (51%), Gaps = 12/366 (3%)

Query: 9   KEVKTLAKRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAGLGSH 68
           + +K  A+  PTPF+V     + + Y  M  + P A ++YA+KANP  E+L+LL   G++
Sbjct: 19  ERIKAFAQDKPTPFVVIDTKIIAKQYDDMVHNFPYASIYYAVKANPAKEVLTLLRDRGAN 78

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

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

Query: 188 AAYEEALLVARRLFDE-AEEMGMHLTDLDIGGGFPVPDAKGLNVDLAAMMEAINKQIDRL 246
            A++ A+   + +F+   EE G+ L  +++GGGFP       N +L    E I   +   
Sbjct: 199 GAWDSAIAKVKSIFERLREEHGIELKMINLGGGFPANYLDKTN-ELGTYAEQITHFLKED 257

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

Query: 302 TYPLHCFGKGNKKPSTFGGPSCDGIDVLYRDF---MAPELKIGDKVLVTEMGSYTSV-SA 357
            +P++   +G        GP+CD  D++Y  +   +  +L IGD++     G+YT+  SA
Sbjct: 318 KFPIYTERQGELDRCVIAGPTCDSADIMYEHYSYGLPLDLAIGDRMYWLTAGAYTTTYSA 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: 381
Number of extensions: 19
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: 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.

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 (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