GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysZ in Hyphomicrobium sulfonivorans WDL6

Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_068459661.1 APY04_RS03310 acetylglutamate kinase

Query= curated2:A9A1K7
         (267 letters)



>NCBI__GCF_001541235.1:WP_068459661.1
          Length = 305

 Score =  119 bits (298), Expect = 8e-32
 Identities = 83/253 (32%), Positives = 138/253 (54%), Gaps = 14/253 (5%)

Query: 2   ITIKIGGSVVDD--LHPSTIADIKKIAESEGV--ILVHGGGKEVTKVCEQLGKEPKFVTS 57
           + IK GG  + D  L  +   D+  + +S GV  I+VHGGG ++  + ++L  +  FV  
Sbjct: 32  VIIKFGGHAMGDAALADAFAKDVVYLKQS-GVNPIVVHGGGPQIAAMLKKLEIKSDFVHG 90

Query: 58  PSGIKSRYTDKETAEIFTMVMSGRINKTIVQMLQKNGINAIGLSGVDAKVIEADRKKKLL 117
                 R TDK T E+  MV+SG INK IV  + + G  A+G+SG DA ++ A R  ++ 
Sbjct: 91  -----LRVTDKPTVEVVEMVLSGLINKDIVSAINRQGGKAVGISGKDANLMIASRITEMP 145

Query: 118 IVNEKGRKQAIDGGYTGKIREVNASFIKSLLDQGLTPVISPIAISEESEFLNVDGDRAAA 177
              +    QA+D GY G   EVN   +  +    + PVI+P+A S + E LN++ D  A+
Sbjct: 146 DP-QSNLMQAVDIGYVGDPVEVNPHIVDVISKSDIIPVIAPVAASRDGETLNINADSFAS 204

Query: 178 YVAGKVGSDKVLFITNVDGLL-MDDKVVPKLTLAEAKEI--RPKIGPGMEKKILASTEAL 234
            +A ++ + ++L +T+V G+L    +++ +LT+ EA+ +     I  GM  KI    E +
Sbjct: 205 ALAARMKAKRLLLLTDVAGVLDKSGELISQLTIEEARGLIKDGTISGGMIPKIEGCIEVV 264

Query: 235 DMGVTTALIANGQ 247
           + GV   +I +G+
Sbjct: 265 EAGVEAVVIIDGR 277


Lambda     K      H
   0.313    0.133    0.360 

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: 185
Number of extensions: 10
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: 267
Length of database: 305
Length adjustment: 26
Effective length of query: 241
Effective length of database: 279
Effective search space:    67239
Effective search space used:    67239
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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