GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dpkA in Burkholderia phytofirmans PsJN

Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; EC 1.5.1.1 (characterized)
to candidate BPHYT_RS24365 BPHYT_RS24365 ornithine cyclodeaminase

Query= SwissProt::V5YW53
         (311 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS24365 BPHYT_RS24365 ornithine
           cyclodeaminase
          Length = 311

 Score =  339 bits (869), Expect = 6e-98
 Identities = 179/301 (59%), Positives = 212/301 (70%), Gaps = 4/301 (1%)

Query: 10  FDAADTAALLAYPALLATLGQAVADYAAGEIVSPERLVVPLQAGGVMLSMPSSARDLATH 69
           FDAA T  L+ Y AL+  L +A  DYA   I SPERLVVPL   G+MLSMP++A DLA H
Sbjct: 9   FDAAATTRLIPYAALVDALKRATIDYAQRRIASPERLVVPLNEDGIMLSMPATAPDLAIH 68

Query: 70  KLVNVCPGNGARGLPTILGQVTAYDASTGEMRFALDGPTVTGRRTAAVTALGIQALHGAA 129
           KLVNVCP N ARGLPTI G+V A+DA TGE  F LDGPTVTGRRTAA++ LG+     A 
Sbjct: 69  KLVNVCPANRARGLPTIHGKVMAFDADTGETLFILDGPTVTGRRTAAISMLGVDTFAAAT 128

Query: 130 PRDILLIGTGKQAANHAEALAAIFPEARLHVRGTSADSAAAFCAAHRAQAPRLVPLD--G 187
           PR+ LLIGTG QA NH EA+  +FP AR+ V+G++   A AFCAAH+ +A  L PL   G
Sbjct: 129 PREFLLIGTGTQALNHLEAIGELFPSARVWVKGSAPARAEAFCAAHQGKAHDLRPLTQAG 188

Query: 188 DAIPDAIDVVVTLTTSRTPVYREAAREGRLVVGVGAFTADAAEIDANTVRASRLVVDDPA 247
             IPD++DVV+ LTTSR PVY EAAR  RLV+GVGAFT    EI A T+  S L VDD A
Sbjct: 189 ATIPDSVDVVIALTTSRQPVYDEAARAERLVIGVGAFTPAMVEIGARTLGESALFVDDEA 248

Query: 248 GARHEAGDLIVAQVDWQHVASLADVLG--GTFDRSGPLLFKSVGCAAWDLAACRTARDAL 305
           GARHEAGD I A VDW  V  +A VL       +  P++FK+VGCAAWDLAACR AR++L
Sbjct: 249 GARHEAGDFIQAGVDWAQVGGIASVLDNPALLPQKKPIVFKTVGCAAWDLAACRVARESL 308

Query: 306 A 306
           +
Sbjct: 309 S 309


Lambda     K      H
   0.320    0.133    0.386 

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: 252
Number of extensions: 8
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: 311
Length of database: 311
Length adjustment: 27
Effective length of query: 284
Effective length of database: 284
Effective search space:    80656
Effective search space used:    80656
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: 48 (23.1 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 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