GapMind for catabolism of small carbon sources

 

Aligments for a candidate for odc in Dinoroseobacter shibae DFL-12

Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate 3607967 Dshi_1375 Ornithine decarboxylase (RefSeq)

Query= curated2:O50657
         (393 letters)



>lcl|FitnessBrowser__Dino:3607967 Dshi_1375 Ornithine decarboxylase
           (RefSeq)
          Length = 398

 Score =  157 bits (398), Expect = 4e-43
 Identities = 111/352 (31%), Positives = 162/352 (46%), Gaps = 10/352 (2%)

Query: 21  PFLVASLDKVEENYQFMRRHLPRAG-VFYAMKANPTPEILSLLAGLGSHFDVASAGEMEI 79
           P LV   D V   Y  +   L +   + YAMKANP PEIL  LA  G  FD AS GE+E+
Sbjct: 40  PTLVLDCDAVVAKYHALAHGLGQGTLIHYAMKANPAPEILRALAAEGCGFDAASRGEIEL 99

Query: 80  LHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKMAKAVPGADVLVRIAV 139
               G   +++ + N +K    +  A  + +  F  D  +E+DK+A   PGA V +R+ V
Sbjct: 100 ALAAGATAARISFGNTIKRPSDIAFAHAHGIDLFAADAEAELDKIAAHAPGARVFLRVLV 159

Query: 140 RNNKALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQSLSTAAYEEALLVARR 199
               A   L+ KFG   + AL L+  A   GL  +G+ FHVGSQ+     + + L     
Sbjct: 160 GATGADWPLSRKFGCAPDTALRLMDRAAFLGLRPVGLSFHVGSQTRDPGMWSDTLDQMAE 219

Query: 200 LFDEAEEMGMHLTDLDIGGGFPVPDAKGLNVDLAAMMEAINKQIDRLFPDTAVWTEPGRY 259
           ++      G  L  ++IGGGFP      + ++       +   +   F D  V  EPGR 
Sbjct: 220 IWHAGRARGHDLNLINIGGGFPAFYGDPI-LEAETYAGRVGALVRARFGDATVMAEPGRG 278

Query: 260 MCGTAVNLVTSVIGTKTRGEQP---WYILDEGIYGCFSGIMYDHWTYP-LHCFGKGNKKP 315
           +   A  +V  V+    + E     W  LD G +   +  M +   Y  +     G   P
Sbjct: 279 LVAEAGMIVAEVLLVSRKSEDDLCRWVYLDIGKFSGLAETMEEAIRYQFVTPHDGGETGP 338

Query: 316 STFGGPSCDGIDVLYRD---FMAPELKIGDKVLVTEMGSYTSV-SATRFNGF 363
               GPSCD  DVLY      +   L+ GD++L+   G+YT+  S+  FNGF
Sbjct: 339 CIMAGPSCDSADVLYEQRPVHLPMALQSGDRILIKATGAYTTTYSSVGFNGF 390


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: 371
Number of extensions: 20
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: 398
Length adjustment: 31
Effective length of query: 362
Effective length of database: 367
Effective search space:   132854
Effective search space used:   132854
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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