Alignments for a candidate for dapE in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Pseudomonas putida KT2440

Align Predicted dapE by GapMind curators (no experimental data)
to candidate PP_2704 PP_2704 Peptidase, M20/M25/M40 family

Query= predicted:L0FXC2
         (397 letters)



>FitnessBrowser__Putida:PP_2704
          Length = 394

 Score =  200 bits (509), Expect = 5e-56
 Identities = 130/375 (34%), Positives = 202/375 (53%), Gaps = 6/375 (1%)

Query: 10  AADQLNQTIAIRRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRKANTGLVALIEGKN 69
           +A +L++ + +RR IHA PE+  +   T A V   LQ +G    +     G+V +++   
Sbjct: 12  SAAELDEFVMLRRQIHAAPEIGGDTPDTSALVADKLQALGYEVHRNVGGHGVVGVLK-VG 70

Query: 70  PSKKVIALRADMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASILHAVKDQFE 129
            S + I LRADMDALP+ E+N   + S   G MHACGHD HT+ LL AA+ L A + QF 
Sbjct: 71  DSPRSIGLRADMDALPMGEKNAFAHASKIPGRMHACGHDGHTAILLAAAAQLAATR-QFN 129

Query: 130 GTVKLIFQPGEEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGFRKGMYMASA 189
           GT+ +IFQP EE +  GA  MI D   E      +   H MP +  G    + G  MAS+
Sbjct: 130 GTLNVIFQPDEEGL-AGAKAMIDDGLFERFPCDSVYALHNMPGLPVGTCVVQAGPTMASS 188

Query: 190 DELYLKVIGKGGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLSFGRIEALGA 249
           + + +++ GKGGHGAMPE  VDPV+  + +I  +Q + SRN S +  +V+S G I+A   
Sbjct: 189 ERVSIRITGKGGHGAMPELSVDPVMALNSLISGIQTIKSRNLSVEDYAVISIGMIQAGTV 248

Query: 250 TNVIPNEVNIQGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKGYPFLQNAPE 309
            N+IP+E  +  + RT     + + + ++  +A+G AE  G  +D +  +  P L N+  
Sbjct: 249 YNIIPDEACMLLSVRTDTAQTQQKINSRIDALAKGHAESYGVEIDVQFTQLAPALCNSDH 308

Query: 310 LTDRAYKAAQAYLGEENVEDL--DIWMAAEDFSYYTQEMDGCFYRLGIRNEEKGITSGVH 367
            +     + +    +  + D      M  EDF+Y  Q   GC++ LG    E    S VH
Sbjct: 309 ESTLLRDSLRPLFADGALLDKMPKKVMGTEDFAYMLQARPGCYFMLGNGTGEFHGCS-VH 367

Query: 368 TPTFDIDESALEVGA 382
            P +D +++ +++GA
Sbjct: 368 NPHYDFNDALVKIGA 382


Lambda     K      H
   0.317    0.134    0.387 

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: 394
Number of extensions: 21
Number of successful extensions: 6
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: 397
Length of database: 394
Length adjustment: 31
Effective length of query: 366
Effective length of database: 363
Effective search space:   132858
Effective search space used:   132858
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

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

GapMind for Amino acid biosynthesis