GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Dokdonella koreensis DS-123

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_067644904.1 I596_RS04715 enoyl-CoA hydratase

Query= BRENDA::P76082
         (255 letters)



>NCBI__GCF_001632775.1:WP_067644904.1
          Length = 270

 Score =  154 bits (388), Expect = 2e-42
 Identities = 96/245 (39%), Positives = 136/245 (55%), Gaps = 8/245 (3%)

Query: 14  LLTLNRPAARNALNNAL--LMQLVNELEAAATDTSISVCVITGNA-RFFAAGADLNEMAE 70
           ++TL+ P A     ++L  L  LV  L A   D  I   VI G   +FF+AGADL + A+
Sbjct: 27  VVTLSNPPANTWTRDSLAALRDLVRALHA---DRDIYAMVIVGEGEKFFSAGADLKQFAD 83

Query: 71  KDLAATLNDTRP--QLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLP 128
            D A      R   + +  L AF    IAA+NGYA+G G E AL CD+ +A E A+  LP
Sbjct: 84  GDKARAREAARRFGEAFETLSAFRGVSIAAINGYAMGGGLECALACDLRIAEEQAQLALP 143

Query: 129 EITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYAL 188
           E T+G++P AGGTQ L R VG+  A +M+L GE I A  A + GLV +V P    L  AL
Sbjct: 144 EATVGLLPCAGGTQNLPRLVGEGWAKRMILLGERIDAATALRIGLVEEVVPKGQALARAL 203

Query: 189 QLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKR 248
           +   +  + SP ++ A K  ++ ++       L  ER+ F  L  + D+ EG++AFL+KR
Sbjct: 204 EWGRQAGKQSPTSVAACKALVQATRSQPHATALVHEREAFVDLFDSADQVEGVAAFLEKR 263

Query: 249 TPDFK 253
            P +K
Sbjct: 264 APQWK 268


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: 122
Number of extensions: 6
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: 255
Length of database: 270
Length adjustment: 25
Effective length of query: 230
Effective length of database: 245
Effective search space:    56350
Effective search space used:    56350
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 24 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