GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Dyella japonica UNC79MFTsu3.2

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate N515DRAFT_3763 N515DRAFT_3763 N-acetylornithine carbamoyltransferase

Query= BRENDA::O93656
         (317 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3763
          Length = 335

 Score =  176 bits (445), Expect = 9e-49
 Identities = 125/342 (36%), Positives = 175/342 (51%), Gaps = 50/342 (14%)

Query: 8   RDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEVA 67
           R  L  QDY+  EI  +LE A   K   +     + L GK++A++F  PS RTR SFE+ 
Sbjct: 4   RHFLTTQDYSRAEIDALLEQAAAFKRSPR----GQQLAGKSVALLFFNPSMRTRTSFELG 59

Query: 68  MAHLGGHALYL----NAQDLQLRRG--------ETIADTARVLSRYVDAIMARVY----- 110
             HLGGHA+ L    +A  ++   G        E IA+ ARVLSRYVD I  R +     
Sbjct: 60  AFHLGGHAIVLAPGKDAWPIEFDVGTVMDGDTEEHIAEVARVLSRYVDLIAVRAFPKFQD 119

Query: 111 ---DHKD--VEDLAKYASVPVINGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGD-- 163
              D +D  ++  A+YASVPVIN +   +HPCQ LA  + + E  G+++  K V      
Sbjct: 120 WTVDREDRVIKAFAQYASVPVIN-METITHPCQELAHALAMQEHLGSLQNKKYVLTWTYH 178

Query: 164 ----GNNVAHSLMIAGTKLGADVVVATPE-GYEPDEKVIKWAEQNAAESGGSFELLHDPV 218
                  VA+S ++  TK+G DV +  P   Y  D++ ++    NA  +GGS  + HD  
Sbjct: 179 PKPLNTAVANSALLIATKMGMDVTLLCPTPDYVLDDRYMQAGYANAQANGGSLRISHDID 238

Query: 219 KAVKDADVIYTDVWASMGQEAEAEERRKIFRPFQVNKDLVKHAKPDY---------MFMH 269
           +A   ADV+Y   W ++      E+ + I       +D  KH   D          +F H
Sbjct: 239 EAYSGADVVYAKSWGALPFFGRWEQEKPI-------RDAHKHFIVDERKMALTNNGLFSH 291

Query: 270 CLPAHRGEEVTDDVIDSPNSVVWDEAENRLHAQKAVLALLLG 311
           CLP  R  + TD V+D+P  +  DEAENRLH QKAV+A LLG
Sbjct: 292 CLPLRRNVKATDAVMDAPYCIAIDEAENRLHVQKAVMATLLG 333


Lambda     K      H
   0.319    0.134    0.400 

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: 273
Number of extensions: 18
Number of successful extensions: 8
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: 317
Length of database: 335
Length adjustment: 28
Effective length of query: 289
Effective length of database: 307
Effective search space:    88723
Effective search space used:    88723
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 (21.7 bits)
S2: 48 (23.1 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