GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Sinorhizobium fredii NGR234

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate WP_012709425.1 NGR_RS25770 ornithine/lysine decarboxylase

Query= SwissProt::Q5HG20
         (421 letters)



>NCBI__GCF_000018545.1:WP_012709425.1
          Length = 377

 Score =  130 bits (328), Expect = 5e-35
 Identities = 112/362 (30%), Positives = 178/362 (49%), Gaps = 32/362 (8%)

Query: 28  PTIVYDELQIREQMRRYHRAFKDSGLKYNISYASKAFTCIQMVKLVAEEDLQLDVVSEGE 87
           P +V D   +R+  + +  A  DS     I YA KA    ++++L+A      D  S  E
Sbjct: 18  PCLVVDLDIVRDNFKAFRHALPDSA----IYYAVKANPAPEILRLLAGLGSNFDCASVAE 73

Query: 88  LYTALEAGFEPSRIHFHGNNKTKHEIRYALENNIGYFVIDSLEEIELIDRYANDTVQVVL 147
           +  ALEAG  PSRI +    K + +I  A    I  F +DS EE+E + R A        
Sbjct: 74  IEMALEAGATPSRISYGNTIKKERDIARAHALGINLFAVDSHEEVEKVARAA-------- 125

Query: 148 RVNPGVEAHTHEFIQTGQEDSKFGLSIQYG-LAKKAIDKVQQSKHLKL--KGVHCHIGSQ 204
              PG        + T  E +++ LS ++G + + A+D +  +  L L   GV  H+GSQ
Sbjct: 126 ---PGARVFCR--VLTDGEGAEWPLSRKFGCVPQMAVDVLVYAHQLGLVSYGVSFHVGSQ 180

Query: 205 ---IEGTEAFIETAKIVLRWLKEQGIQVELLNLGGGFGIKYVEGDESFPIESGIKDITDA 261
              ++  +A +  AK V   L +QGI+++++N+GGGF  KY+    S   E+  + I  A
Sbjct: 181 MTKLDAWDAALADAKRVFGQLDKQGIELKMVNMGGGFPTKYLRDVPS--AEAYGQAIFGA 238

Query: 262 IKSEIKVLGIDAPEIGIEPGRSIVGEAGVTLYEVGTI--KEIPEINKYVSIDGGMSDHIR 319
           +K   K  G + PE  IEPGR +VG AGV   EV  +  K   + +++V +D G    + 
Sbjct: 239 LK---KHFGNNIPETIIEPGRGMVGNAGVIKAEVVLVSKKSDNDSHRWVFLDIGKFGGLA 295

Query: 320 TALYDAKYQALLVNRNEEADDSVTIAGKLCESGDIIIKD--AKLPSSVKRGDYLAILSTG 377
             + +A    +   R+ +  +   +AG  C+S D++ +     LP S+  GD + I  TG
Sbjct: 296 ETMDEAIRYPIRTARDADEMEPCVLAGPTCDSADVLYEKNMYPLPISLTIGDEVLIEGTG 355

Query: 378 AY 379
           AY
Sbjct: 356 AY 357


Lambda     K      H
   0.316    0.136    0.378 

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: 363
Number of extensions: 17
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 421
Length of database: 377
Length adjustment: 31
Effective length of query: 390
Effective length of database: 346
Effective search space:   134940
Effective search space used:   134940
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: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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