GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuD in Pseudomonas fluorescens FW300-N1B4

Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate Pf1N1B4_4353 Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)

Query= reanno::pseudo3_N2E3:AO353_29305
         (253 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4353
          Length = 253

 Score =  495 bits (1274), Expect = e-145
 Identities = 241/253 (95%), Positives = 249/253 (98%)

Query: 1   MALKPLIGVTACVKQIGLHPYHVSGDKYLRAVSVAALGLPVVIPSLGELTEIDELLAHLD 60
           MA KPLIGVTAC+KQIGLHPYHVSGDKYLRAVSVAALGLPVVIPSLGELTEID+LLA LD
Sbjct: 1   MAFKPLIGVTACIKQIGLHPYHVSGDKYLRAVSVAALGLPVVIPSLGELTEIDDLLAQLD 60

Query: 61  GLLLTGSPSNVEPFHYQGPASAPGTDHDPARDSTTLPLLRAAIAAGVPVLGICRGFQEMN 120
           GLLLTGSPSNVEPFHYQGPASAPGTDHDP RD+TTLPLLRAAIAAGVPVLGICRGFQEMN
Sbjct: 61  GLLLTGSPSNVEPFHYQGPASAPGTDHDPQRDATTLPLLRAAIAAGVPVLGICRGFQEMN 120

Query: 121 VAFGGSLHQKVHELPGMLDHREADHPDLAVQYAPAHAVSVQPGGVFQALELPPVFQVNSI 180
           VAFGGSLHQKVHELPGMLDHREADHPDLAVQYAPAHAVSVQPGGVF+AL+LP VFQVNSI
Sbjct: 121 VAFGGSLHQKVHELPGMLDHREADHPDLAVQYAPAHAVSVQPGGVFEALDLPQVFQVNSI 180

Query: 181 HSQGIDRLAPGLRAEAIAPDGLIEAISVEHSKAFALGVQWHPEWQVLANPPYLSIFQAFG 240
           HSQGIDRLAPGLRAEA+APDGLIEAISVEHSKAFA+GVQWHPEWQVL+NPPYLSIFQAFG
Sbjct: 181 HSQGIDRLAPGLRAEAVAPDGLIEAISVEHSKAFAVGVQWHPEWQVLSNPPYLSIFQAFG 240

Query: 241 DACRQRAALRNTR 253
           DACRQRAALRNTR
Sbjct: 241 DACRQRAALRNTR 253


Lambda     K      H
   0.320    0.138    0.419 

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: 433
Number of extensions: 19
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: 253
Length of database: 253
Length adjustment: 24
Effective length of query: 229
Effective length of database: 229
Effective search space:    52441
Effective search space used:    52441
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 (21.8 bits)
S2: 46 (22.3 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