GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Pseudomonas putida KT2440

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate PP_3571 PP_3571 putative Acetylornithine deacetylase

Query= curated2:Q2W0E7
         (379 letters)



>FitnessBrowser__Putida:PP_3571
          Length = 391

 Score =  102 bits (254), Expect = 2e-26
 Identities = 112/364 (30%), Positives = 154/364 (42%), Gaps = 43/364 (11%)

Query: 34  LEELGFACHHIRSATGGPEIRNLYARLGT-EAPNLCFAGHTDVVP-PGKGWTVEPFAAGI 91
           L ELG  C    +  G     NL+A +G  +   +  +GHTDVVP  G+ WTVEPFA   
Sbjct: 40  LAELGVECELFHNPEGTKA--NLFATVGPRDVGGVVLSGHTDVVPVDGQAWTVEPFALSE 97

Query: 92  DQGRLFGRGSADMKGAIACFVAAVARLLEDGAPKGSLSLLITGDEEGPAVDGTVKVLDWL 151
             GRL+GRG+ADMKG IA  +AAV   L     +  + L  + DEE   + G   +L  L
Sbjct: 98  RDGRLYGRGTADMKGFIASVLAAVPAFLAQPL-RMPVHLAFSYDEEVGCL-GVRSMLAAL 155

Query: 152 AARGERIDCCIVGEPTNPRKLGDMMKIGRRGSLNCRLTVFGTQGHSAYPHLADNPIPRLL 211
             R  +   C++GEPT  + +     +G +G L  R  V G   HSAY     N I    
Sbjct: 156 QQRPCKPRLCLIGEPTELKPV-----LGHKGKLAMRCQVQGAACHSAYAPYGVNAIEYAA 210

Query: 212 DILRRLTEAPLDEGTP--HFQASTLALTTVDV----GNPATNVIPAEARAGFNIRFNDLH 265
            ++ +L E       P  H +      +TV      G  A N++P E    F +R     
Sbjct: 211 KLIGKLGEIGEALALPVHHDERFDPPFSTVQAGVIKGGRALNIVPDECEFDFEVR----- 265

Query: 266 SGASLERWIRDTVA---QAGGEVEI-----KVEVSGESFLTP----PGALSDALAEAAFE 313
              +L  +    VA   Q   E E+     KV  +    L P    PG  +   +EAA  
Sbjct: 266 ---ALPGFEAQAVADQLQTYAEAELLPRMRKVNTASAIRLAPLSAYPGLATPEDSEAA-R 321

Query: 314 VTGLRPELSTSG----GTSDARFIKNHCPVVEFGLVGQTM-HKSDEHVSVADMEALTEIY 368
           +  L     T G    GT    F +   P V  G       HK DE VSV  +     + 
Sbjct: 322 LVALLSGSDTFGTVAFGTEGGLFDQAGIPTVVCGPGSMDQGHKPDEFVSVEQLRGCDAML 381

Query: 369 RRVL 372
            R++
Sbjct: 382 LRLV 385


Lambda     K      H
   0.319    0.137    0.412 

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: 370
Number of extensions: 21
Number of successful extensions: 2
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: 379
Length of database: 391
Length adjustment: 30
Effective length of query: 349
Effective length of database: 361
Effective search space:   125989
Effective search space used:   125989
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: 50 (23.9 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