GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aguB in Marinobacter adhaerens HP15

Align N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) (characterized)
to candidate GFF2120 HP15_2074 carbon-nitrogen hydrolase family protein

Query= metacyc::MONOMER-17350
         (290 letters)



>FitnessBrowser__Marino:GFF2120
          Length = 307

 Score =  344 bits (882), Expect = 2e-99
 Identities = 171/298 (57%), Positives = 215/298 (72%), Gaps = 8/298 (2%)

Query: 1   MKIALIQQKFHSNKEQTIKKTCEFIEEASKQGAELICLGELHQSEYFCQSENVDFFDYAN 60
           + +A+IQQ   S+K  ++  T + + EA   GA L+ L ELH + YFCQ+E    F+ A 
Sbjct: 10  INVAVIQQACSSDKAASLATTEKLVREAVASGANLVILQELHATLYFCQTEETSVFELAE 69

Query: 61  DYEKDV-KFWANIARKNQIVLITSLFEKRSAGLYHNTAVVFEKDGSIAGKYRKMHIPDDP 119
                  K  +++AR+  IVL+ S+FE+R  G+YHNTAVVFEKDGS+AG YRKMHIPDDP
Sbjct: 70  PIPGPTSKRLSDLARELGIVLVGSIFERRMNGVYHNTAVVFEKDGSLAGLYRKMHIPDDP 129

Query: 120 CFYEKFYFTPGDL-------GFEPINTSLGKLGVLICWDQWYPEAARIMALKGAEILIYP 172
            FYEKFYFTPGD        GF PI+TS+G+LGVL+CWDQWYPEAAR+MAL GAEILIYP
Sbjct: 130 GFYEKFYFTPGDAQFNDGRSGFTPIDTSVGRLGVLVCWDQWYPEAARLMALAGAEILIYP 189

Query: 173 TAIGWFDKDKDEEKQRQLNAWLGVQKGHAIANGLYVVAINRVGFEKDVSGVEEGIRFWGN 232
           TAIGW   D  +E+ RQL+AW+ VQ+GHA+AN L VVA NRVG E D SG  +GIRFWGN
Sbjct: 190 TAIGWDVTDDPDEQARQLDAWVTVQRGHAVANNLPVVAPNRVGTEPDPSGHSDGIRFWGN 249

Query: 233 SFVFGPQGEELCLLDSQNECVKIIEIDKKRSENVRRWWPFLRDRRIEYFADLTKRFID 290
           SF+ GPQGE L   D  +EC+  + +D+ RSE+VRR WP+LRDRRI+ + D+ KR  D
Sbjct: 250 SFICGPQGELLARGDDSSECILAVTLDRSRSESVRRIWPYLRDRRIDAYGDILKRVRD 307


Lambda     K      H
   0.322    0.140    0.438 

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: 297
Number of extensions: 14
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: 290
Length of database: 307
Length adjustment: 27
Effective length of query: 263
Effective length of database: 280
Effective search space:    73640
Effective search space used:    73640
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 (21.9 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:

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