GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Azospirillum brasilense Sp245

Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate AZOBR_RS00105 AZOBR_RS00105 ornithine decarboxylase

Query= curated2:O50657
         (393 letters)



>FitnessBrowser__azobra:AZOBR_RS00105
          Length = 378

 Score =  201 bits (511), Expect = 3e-56
 Identities = 128/361 (35%), Positives = 186/361 (51%), Gaps = 15/361 (4%)

Query: 16  KRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAGLGSHFDVASAG 75
           +R  TP LV  LD VE NY  +   LP A +FYA+KANP PEIL LL  LGS FD AS  
Sbjct: 12  QRPQTPCLVVDLDVVEANYHDLEEALPDAKIFYAVKANPAPEILGLLTRLGSAFDTASVP 71

Query: 76  EMEILHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKMAKAVPGADVLV 135
           E++++   G    ++ Y N +K    ++ A +  VR F FD  +E++K+A+A PGA V  
Sbjct: 72  EIQMVLAAGCAPERISYGNTIKKEADIRRAFELGVRLFAFDSEAELEKIARAAPGARVFC 131

Query: 136 RIAVRNNKALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQSLSTAAYEEALL 195
           RI      A   L+ KFG  +  A +LL  A+   +   G+ FHVGSQ      ++ A+ 
Sbjct: 132 RILTSGEGAEWPLSRKFGCDLAMARELLLKAKGMNVVPYGVSFHVGSQQKDLMQWDHAIF 191

Query: 196 VARRLFDEAEEMGMHLTDLDIGGGFPV---PDAKGLNVDLAAMMEAINKQIDRLFPDTAV 252
              +LF E E +G+ L  +++GGGFP     D         A+ E++        P+  V
Sbjct: 192 QVAQLFRELEVLGVDLGMINLGGGFPTRYRTDVPETTAYGQAIFESLRTHFGNRLPEAIV 251

Query: 253 WTEPGRYMCGTAVNLVTSVIGTKTRGE---QPWYILDEGIYGCFSGIMYDHWTYPLHCF- 308
             EPGR M G A  + + V+    +     + W  LD G +   +  M +   YP+    
Sbjct: 252 --EPGRSMVGNAGIIESEVVLVSRKSANDVKRWVYLDIGKFSGLAETMDEAIQYPIQVMG 309

Query: 309 --GKGNKKPSTFGGPSCDGIDVLYR--DFMAP-ELKIGDKVLVTEMGSYTSV-SATRFNG 362
             G+G+ +     GP+CD  DVLY   ++  P +LK GD+V +   G+YT+  SA  FNG
Sbjct: 310 DDGEGDSEAVVLAGPTCDSADVLYERAEYKLPMDLKAGDRVRIHATGAYTTTYSAVCFNG 369

Query: 363 F 363
           F
Sbjct: 370 F 370


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: 408
Number of extensions: 21
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: 378
Length adjustment: 30
Effective length of query: 363
Effective length of database: 348
Effective search space:   126324
Effective search space used:   126324
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