GapMind for catabolism of small carbon sources

 

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

Align 4-guanidinobutyramide hydrolase; SubName: Full=Carbon-nitrogen hydrolase (characterized, see rationale)
to candidate Pf1N1B4_2504 5-aminopentanamidase (EC 3.5.1.30)

Query= uniprot:A0A291T0X0
         (265 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2504
          Length = 264

 Score =  229 bits (583), Expect = 6e-65
 Identities = 129/265 (48%), Positives = 170/265 (64%), Gaps = 8/265 (3%)

Query: 4   LRTALLQNSGHPGDPAGNLKVLDEAAARAAADGAGLLVTAEMFLTGYAIG-GGVRDLAEP 62
           +R AL Q    P D AGNL+ L + A  A   GA LLV  EMFLTGY IG   V  LAE 
Sbjct: 1   MRVALYQCPPLPLDVAGNLQRLHQLALEAK--GADLLVLPEMFLTGYNIGIDAVSVLAEV 58

Query: 63  ADGPSGRAVADIAAAHGLAILYGYPER-HAGAVHNSARLVGADGTELANYRKTHLYGCFE 121
            +G S + +A IA   G+AILYGYPER   G ++N+ +L+ A+G  L NYRKTHL+G  +
Sbjct: 59  HNGESAQQIARIAKTTGIAILYGYPERTEDGQIYNAVQLIDANGERLCNYRKTHLFGDLD 118

Query: 122 RASFTPG--ETPVVQATVGELTVGILVCYDVEFPENVRAHALAGTDLLLVPTAQMHPFEF 179
            + F+PG  E P+V+    +L  G L+CYD+EFPEN R  ALAG +L+LVPTA M P++F
Sbjct: 119 HSMFSPGPDEFPLVELNGWKL--GFLICYDLEFPENARRLALAGAELILVPTANMIPYDF 176

Query: 180 VAESLIPVRAFESQMYIAYVNRSGPEGEFDFVGLSCLAGPDGATCLRAGRGEELLLGDVD 239
           +A+  +  RAFE+Q Y+AY N  G EGE  + G S +A PDG+   +AG  E L++G++D
Sbjct: 177 IADVTVRARAFENQCYVAYANYCGHEGEIQYCGQSSIAAPDGSRIAQAGLDEALIVGELD 236

Query: 240 PKLLTTSRRINPYLRDRRPGLYTSL 264
            +L+  SR  N Y  DRRP LY  L
Sbjct: 237 RQLMIDSRAANRYFLDRRPELYGEL 261


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: 216
Number of extensions: 12
Number of successful extensions: 3
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: 264
Length adjustment: 25
Effective length of query: 240
Effective length of database: 239
Effective search space:    57360
Effective search space used:    57360
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