GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Marinobacter adhaerens HP15

Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate GFF3372 HP15_3314 N-acetyllutamate synthase

Query= curated2:Q3MFQ8
         (297 letters)



>FitnessBrowser__Marino:GFF3372
          Length = 435

 Score =  134 bits (337), Expect = 4e-36
 Identities = 95/285 (33%), Positives = 149/285 (52%), Gaps = 24/285 (8%)

Query: 25  PYIQQFAGRTVVVKYGGAAMKDSHLKDQVIRDIVFLSCVGLRPILVHGGGPEINSWLDKL 84
           PYI    GRTVV+   G A++  +  + +I DI  LS +G+R ++  G  P+I + LD  
Sbjct: 15  PYINAHRGRTVVLTIPGDAIEHGNFIN-IIHDIALLSSLGVRLVVAFGARPQIQTRLDAA 73

Query: 85  GIEAQFKNGLRVTDAPTMDVVEMVLVGRVNKEIVSLINQAGGLAVGLCGKD--------- 135
           GIE+ F  GLR+T    + +V M  VG +   + S       L++GL             
Sbjct: 74  GIESSFSKGLRITPQEHLSMV-MEAVGGLRAYLES------HLSMGLVNSPMHNARIRVS 126

Query: 136 -GNLITARPQGQ-EGIGF--VGEVSNVNIKILETLASNGYIPVVSSVAADDSGQAYNINA 191
            GN + A+P G  +GI F   G+V  V++  +E L   G+I ++  +    +G A+N++ 
Sbjct: 127 GGNYVAAKPVGVLDGIDFGHTGKVRRVDVAGIEKLLELGHIVLLPPMGYSPTGDAFNLSY 186

Query: 192 DTVAGEIAAALGAEKLILLTDTRGILKDYKDPGTLIPKVDIREARELINGGVVSGGMIPK 251
           + V  ++AAAL AEKL++  D  G+    ++ GTLI ++  R+A E +  G V+G     
Sbjct: 187 EDVGSQVAAALQAEKLMVFIDDPGL---QEEDGTLIRELSARQASERLAAGAVTGHDADL 243

Query: 252 VTCCVRSLAQGVRAAHIIDGRIPHALLLEIFTDVGIGTMILGSQY 296
           +     +  +GVR AHII      ALL E+FT  G GT++ G  Y
Sbjct: 244 LRAACDACVKGVRRAHIISYVDDGALLKELFTRDGAGTLVSGDHY 288


Lambda     K      H
   0.320    0.139    0.395 

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: 306
Number of extensions: 18
Number of successful extensions: 4
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: 297
Length of database: 435
Length adjustment: 29
Effective length of query: 268
Effective length of database: 406
Effective search space:   108808
Effective search space used:   108808
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: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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