GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_2179
          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 (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