GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysZ in Dechlorosoma suillum PS

Align [LysW]-aminoadipate kinase; EC 2.7.2.- (characterized)
to candidate Dsui_1309 Dsui_1309 acetylglutamate kinase

Query= SwissProt::O50147
         (269 letters)



>FitnessBrowser__PS:Dsui_1309
          Length = 293

 Score =  122 bits (306), Expect = 9e-33
 Identities = 85/274 (31%), Positives = 141/274 (51%), Gaps = 16/274 (5%)

Query: 2   IVVKVGGAEGINY---EAVAKDAASLWKEGVKLLLVHGGSAETNKVAEALGHPPRFLTHP 58
           IVVK GG    +    +  A+D   L   G+ +++VHGG  +   +   +G    F+   
Sbjct: 28  IVVKYGGNAMTDEHLKQCFARDVVLLKLVGMNVVVVHGGGPQIENMLGRVGKKGEFI--- 84

Query: 59  GGQVSRLTDRKTLEIFEMVYCGLVNKRLVELLQKEGANAIGLSGLDGRLFVGRRKTAVKY 118
             Q  R+TD +T+E+ EMV  G VNK +V L+ + G  A+GL+G DG + +  +K  +  
Sbjct: 85  --QGMRVTDAETMEVVEMVLGGQVNKDVVNLINRAGGKAVGLTGKDGGM-IRAKKLLLPN 141

Query: 119 VENGKVKVHRGDYTGTVEEVNKALLDLLLQAGYLPVLTPPALSYENEAINTDGDQIAALL 178
            EN    +  G   G + +++ +L+  L  AG++PV+ P  +  + E  N + D +A  +
Sbjct: 142 KENPDDLIDVGQ-VGDIVQIDPSLIGNLEGAGFIPVIAPIGVGKDGETYNINADVVAGKV 200

Query: 179 ATLYGAEALVYLSNVPGLLARYPDEASLVREIPVERIEDPEYLALAQGRMKRKVMGAVEA 238
           A +  AE LV L+N PG+L +      L+  I  ++I+D        G M  K+  A++A
Sbjct: 201 AEVLKAEKLVLLTNTPGVLDK---AGQLITGITPKQIDDMVEDGTLSGGMLPKISSALDA 257

Query: 239 VRGGVKRVVFADARVENPIRRAL---SGEGTVVR 269
            R GVK V   D RVE+ +   +    G GT+++
Sbjct: 258 ARNGVKSVHIIDGRVEHALLLEILTDHGVGTMIK 291


Lambda     K      H
   0.317    0.137    0.385 

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: 231
Number of extensions: 22
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: 269
Length of database: 293
Length adjustment: 26
Effective length of query: 243
Effective length of database: 267
Effective search space:    64881
Effective search space used:    64881
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 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