GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Pseudomonas fluorescens FW300-N2E2

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Pf6N2E2_1834 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1834
          Length = 256

 Score =  210 bits (535), Expect = 2e-59
 Identities = 114/251 (45%), Positives = 160/251 (63%)

Query: 4   LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGA 63
           ++V R   V +L LNR   RNAL+ ++ + + + ++    D+ ++V VITG    FAAGA
Sbjct: 5   VVVERNGAVAILRLNRVEKRNALDLSMRVAIASAMQELERDSGVAVIVITGGDSVFAAGA 64

Query: 64  DLNEMAEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENA 123
           DLN + +K           Q WA +    KPLIAAV+G+ALGAGCELA++CD++VA  +A
Sbjct: 65  DLNLLVDKGAQQVAELDLGQYWAPVAKSQKPLIAAVSGFALGAGCELAMMCDILVADNSA 124

Query: 124 RFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLT 183
           RFG PE  +GIMPGAGGTQRL+R+VGK +AS M+L+GE ++A++A Q GLVS++      
Sbjct: 125 RFGQPEARVGIMPGAGGTQRLLRAVGKPVASLMLLAGELLSAERASQLGLVSELVTEGSA 184

Query: 184 LEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISA 243
           L  A+ LA   A   P AL+A K+ L    + +L   LA E + F LL  T+D+ EG+ A
Sbjct: 185 LARAIVLAQATATMPPKALRAIKRVLALGADQSLDLALALENREFLLLFDTQDKTEGMRA 244

Query: 244 FLQKRTPDFKG 254
           FL KR P + G
Sbjct: 245 FLDKRPPRYTG 255


Lambda     K      H
   0.318    0.130    0.356 

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: 103
Number of extensions: 1
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: 255
Length of database: 256
Length adjustment: 24
Effective length of query: 231
Effective length of database: 232
Effective search space:    53592
Effective search space used:    53592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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