GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Phaeobacter inhibens BS107

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate GFF1117 PGA1_c11320 3-hydroxyacyl-CoA dehydrogenase type-2

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__Phaeo:GFF1117
          Length = 251

 Score =  267 bits (683), Expect = 1e-76
 Identities = 143/248 (57%), Positives = 177/248 (71%), Gaps = 4/248 (1%)

Query: 13  AVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQ 72
           AVITGGASGLG ATA      GA   LLD     G A A ++G +  FA  DVTSE+ V 
Sbjct: 8   AVITGGASGLGEATARHFAANGAQVTLLDRDAERGAAVAAEIGGH--FAQTDVTSEESVA 65

Query: 73  TALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLV 132
            A+ALA  K G+++  VNCAGIA+  KT    +   H L+ +QR +D+NL+GTFNV RL 
Sbjct: 66  AAMALASEKMGKINACVNCAGIALGIKTVG--RDGAHPLDAYQRTIDINLVGTFNVARLA 123

Query: 133 AGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIR 192
           A E+ + +  + G RGVIINTAS+AAF+GQ GQAAY+ASKGG+VGM LP+ARDLA  G+R
Sbjct: 124 AVEIAKCDAAEDGGRGVIINTASIAAFDGQKGQAAYAASKGGVVGMCLPMARDLASSGVR 183

Query: 193 VMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIR 252
           VMTIAPG+F TP+L  LPE+V   LA+ VP P+RLGDPAEY  L   I+E  +LNGEVIR
Sbjct: 184 VMTIAPGIFMTPMLAGLPEEVQQQLAADVPNPARLGDPAEYGRLAGFIVEMGYLNGEVIR 243

Query: 253 LDGAIRMQ 260
           LDGA+RM+
Sbjct: 244 LDGALRMR 251


Lambda     K      H
   0.318    0.135    0.385 

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: 233
Number of extensions: 11
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: 261
Length of database: 251
Length adjustment: 24
Effective length of query: 237
Effective length of database: 227
Effective search space:    53799
Effective search space used:    53799
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 (21.7 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