GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cadA in Pseudomonas simiae WCS417

Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate GFF788 PS417_04005 ornithine decarboxylase

Query= curated2:O50657
         (393 letters)



>FitnessBrowser__WCS417:GFF788
          Length = 387

 Score =  180 bits (457), Expect = 5e-50
 Identities = 122/370 (32%), Positives = 190/370 (51%), Gaps = 12/370 (3%)

Query: 5   RLSEKEVKTLAKRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAG 64
           R +  ++K  A +  TPF+V     + + Y  +R     A V+YA+KANP  EI+ LL  
Sbjct: 11  RATFDKMKAFADKQETPFVVIDTAMISQAYDDLRAGFEFAKVYYAVKANPAVEIIDLLKE 70

Query: 65  LGSHFDVASAGEMEILHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKM 124
            GS FD+AS  E++ + + GV   ++ Y N +K ++ ++   +  VR F+ D  +++  +
Sbjct: 71  KGSSFDIASIYELDKVMDRGVSADRISYGNTIKKSKDIRYFYEKGVRLFSTDSEADLRNI 130

Query: 125 AKAVPGADVLVRIAVR-NNKALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQ 183
           AKA PG+ V VRI    +  A   L+ KFG   + A+DLL  A+D GL   GI FHVGSQ
Sbjct: 131 AKAAPGSKVYVRILTEGSTTADWPLSRKFGCQTDMAMDLLILARDLGLVPYGISFHVGSQ 190

Query: 184 SLSTAAYEEALLVARRLFDE-AEEMGMHLTDLDIGGGFPVPDAKGLNVDLAAMMEAINKQ 242
               + ++ A+   + +F+   EE G+HL  +++GGGFP       N  L    E I + 
Sbjct: 191 QRDISVWDAAIAKVKVIFERLKEEDGIHLKLINMGGGFPANYITRTN-SLETYAEEIIRF 249

Query: 243 IDRLFPD--TAVWTEPGRYMCGTAVNLVTSV--IGTKTR-GEQPWYILDEGIYGCFSGIM 297
           +   F D    +  EPGR +   A  LV+ V  +  K+R   + W   D G +      M
Sbjct: 250 LKEDFGDDLPEIILEPGRSLIANAGILVSEVVLVARKSRTAVERWVYTDVGKFSGLIETM 309

Query: 298 YDHWTYPLHCFGKGNKKPSTFGGPSCDGIDVLYRDF---MAPELKIGDKVLVTEMGSY-T 353
            +   +P+    KG  +     GP+CD  D++Y ++   +   L IGD++     G+Y T
Sbjct: 310 DEAIKFPIWTEKKGEMEEVVIAGPTCDSADIMYENYKYGLPLNLAIGDRLYWLSTGAYTT 369

Query: 354 SVSATRFNGF 363
           S SA  FNGF
Sbjct: 370 SYSAVEFNGF 379


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: 398
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: 387
Length adjustment: 31
Effective length of query: 362
Effective length of database: 356
Effective search space:   128872
Effective search space used:   128872
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 (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