GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gbamidase in Pseudomonas fluorescens GW456-L13

Align 4-guanidinobutyramide hydrolase; SubName: Full=Carbon-nitrogen hydrolase (characterized, see rationale)
to candidate PfGW456L13_2675 5-aminopentanamidase (EC 3.5.1.30)

Query= uniprot:A0A291T0X0
         (265 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2675
          Length = 279

 Score = 99.8 bits (247), Expect = 6e-26
 Identities = 91/260 (35%), Positives = 127/260 (48%), Gaps = 18/260 (6%)

Query: 16  GDPAGNLKVLDEAAARAAADGAGLLVTAEMFLTGYAIGGGVR--DLAEPADGPSGRAVAD 73
           GD A N  + + A  +AA  GA ++V  E+  +GY          LAE  DGP+ +    
Sbjct: 19  GDLAYNRTLTERAIRQAAFQGAQVVVLPELVQSGYLFADRFEALGLAETVDGPTLQLWQT 78

Query: 74  IAAAHGLAILYGYPER-HAGAVHNSARLVGADGTELANYRKTHLYGCFERASFTPGETP- 131
           +A    L I+ G+ ER  A  + NSA ++ A+G   A YRK HL+   E+  FT G+ P 
Sbjct: 79  LARELNLVIVGGFCERLPADELANSAAMIDANGLR-AVYRKAHLWDA-EKDIFTAGDAPP 136

Query: 132 -VVQATVGELTVGILVCYDVEFPENVRAHALAGTDLLLVPT----AQMHPFEFVAESL-I 185
            VV+   G L  G+L+CYD+EFPE VR  ALAG +LL  P           E  AE L +
Sbjct: 137 PVVETLHGRL--GMLICYDLEFPEWVRLAALAGAELLCAPVNWPDGPRPQTERPAEVLRV 194

Query: 186 PVRAFESQMYIAYVNRSGPEGEFDFVGLSCLAGPDGATCLRAGR--GEELLLGDVDPKLL 243
              A  ++M+IA  +R G E    +V  S +   DG          GE++LL  ++    
Sbjct: 195 QANASVNRMFIAACDRYGHERGVGWVQGSVIVDADGYPLAGPAEQGGEQMLLATLNLAEA 254

Query: 244 TTSR--RINPYLRDRRPGLY 261
              R    N   +DRRP LY
Sbjct: 255 RNKRISARNDLHQDRRPQLY 274


Lambda     K      H
   0.319    0.138    0.414 

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: 177
Number of extensions: 11
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: 265
Length of database: 279
Length adjustment: 25
Effective length of query: 240
Effective length of database: 254
Effective search space:    60960
Effective search space used:    60960
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