GapMind for catabolism of small carbon sources

 

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

Align N-carbamoylputrescine amidase; EC 3.5.1.53 (characterized)
to candidate Pf1N1B4_2504 5-aminopentanamidase (EC 3.5.1.30)

Query= SwissProt::Q9XGI9
         (300 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2504
          Length = 264

 Score = 95.9 bits (237), Expect = 9e-25
 Identities = 83/269 (30%), Positives = 128/269 (47%), Gaps = 25/269 (9%)

Query: 20  DVSTNVATAERLVRAAHQKGANIILIQELFEGYYFCQAQKEEFFHRAKPYPGHPTIVRMQ 79
           DV+ N+    +L  A   KGA+++++ E+F   Y            A+ + G  +  ++ 
Sbjct: 14  DVAGNLQRLHQL--ALEAKGADLLVLPEMFLTGYNIGIDAVSVL--AEVHNGE-SAQQIA 68

Query: 80  NLAKELGVVIPVSFFEEANNAH-YNSVAIIDADGTDLGLYRKSHIPDGPGYQEKYYFNPG 138
            +AK  G+ I   + E   +   YN+V +IDA+G  L  YRK+H+    G  +   F+PG
Sbjct: 69  RIAKTTGIAILYGYPERTEDGQIYNAVQLIDANGERLCNYRKTHLF---GDLDHSMFSPG 125

Query: 139 DTGFKVFQTKYAKIGVAICWDQWFPEAARAMALQGAEVLFYPTAIGSEPQDDGLDSRDHW 198
              F + +    K+G  IC+D  FPE AR +AL GAE++  PTA    P D   D     
Sbjct: 126 PDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTA-NMIPYDFIADV---- 180

Query: 199 RRVMQGHAGANVVPLVASNRIGKEIIETEHGNSEITFYGYSFIAGPTGELVAAAGDKEEA 258
              ++  A  N   +  +N  G E         EI + G S IA P G  +A AG  +EA
Sbjct: 181 --TVRARAFENQCYVAYANYCGHE--------GEIQYCGQSSIAAPDGSRIAQAG-LDEA 229

Query: 259 VLVAQFDLDKIKSKRHGWGVYRDRRPDLY 287
           ++V + D   +   R     + DRRP+LY
Sbjct: 230 LIVGELDRQLMIDSRAANRYFLDRRPELY 258


Lambda     K      H
   0.319    0.137    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: 220
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: 300
Length of database: 264
Length adjustment: 26
Effective length of query: 274
Effective length of database: 238
Effective search space:    65212
Effective search space used:    65212
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: 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