GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuD in Pseudomonas putida KT2440

Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate PP_2179 PP_2179 glutamine amidotransferase

Query= reanno::pseudo6_N2E2:Pf6N2E2_4510
         (258 letters)



>lcl|FitnessBrowser__Putida:PP_2179 PP_2179 glutamine
           amidotransferase
          Length = 257

 Score =  349 bits (896), Expect = e-101
 Identities = 162/250 (64%), Positives = 197/250 (78%)

Query: 1   MSRLPLIGVTTCSRQIGLHAYHISGEKYSRAVATAAKGLPVLIPSLADLFPPSDILDALD 60
           M R+P+IG+T C+  I LHA     EKY+RA A AA GLP++IPSL +L   +DILD +D
Sbjct: 1   MPRVPVIGITACTSMIELHATQTISEKYARAAAKAACGLPIVIPSLGELMDSADILDVVD 60

Query: 61  GILLTGSPSNVEPFHYQGPASAPGTAHDPARDATTLPLIRAAVDAGIPVLGICRGFQEMN 120
           G++ TGSPSN+EP+HY GPASA GT HD  RDATTLPL+RAA+ AG+PVLGICRGFQEMN
Sbjct: 61  GLIFTGSPSNIEPYHYNGPASAAGTHHDQLRDATTLPLMRAAIAAGVPVLGICRGFQEMN 120

Query: 121 VAFGGSLHQKVHEVGTFIDHREDDTQAVDVQYGPAHAVHIQPGGVLAGLGLPQRIEVNSI 180
           VA GG+LHQKVHE G F+DHRE   + +D QYGP H +H++PGG+L  +GLP   +VNSI
Sbjct: 121 VALGGTLHQKVHETGVFMDHREGKDEPLDKQYGPRHTLHVEPGGMLDRMGLPAIFDVNSI 180

Query: 181 HSQGIERLAPGLRAEAVAPDGLIEAVSVPGGKAFALGVQWHPEWEVSSNPHYLAIFQAFG 240
           H QGI+ LAPGLR EA+APDGL+EA+SV   K FALGVQWHPE++V  NPHYLAIFQ+FG
Sbjct: 181 HGQGIDVLAPGLRVEALAPDGLVEAISVESSKGFALGVQWHPEFQVMDNPHYLAIFQSFG 240

Query: 241 DACRARAAQR 250
            ACR R+  R
Sbjct: 241 KACRHRSVLR 250


Lambda     K      H
   0.319    0.136    0.413 

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: 291
Number of extensions: 10
Number of successful extensions: 1
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: 258
Length of database: 257
Length adjustment: 24
Effective length of query: 234
Effective length of database: 233
Effective search space:    54522
Effective search space used:    54522
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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