GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Erythrobacter gangjinensis K7-2

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_047005555.1 AAW01_RS01220 3-oxoacyl-[acyl-carrier-protein] reductase

Query= SwissProt::Q9NKW1
         (441 letters)



>NCBI__GCF_001010925.1:WP_047005555.1
          Length = 254

 Score =  116 bits (291), Expect = 7e-31
 Identities = 72/195 (36%), Positives = 106/195 (54%), Gaps = 6/195 (3%)

Query: 11  IVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGTA--V 68
           +VTGA GGIG   A   AK+GA++ ++   G           AD    E   AG      
Sbjct: 10  LVTGASGGIGSSIAYALAKQGARLALSGSNGDKLRAFREQLIADCGSPE---AGDHVEIT 66

Query: 69  ANYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAKGAYKL 128
            N       E+++  A+D+ GG+DIL+NNAGI RD    +M D +W+ V +V+ +  ++L
Sbjct: 67  CNLSDTTQVEELIPAAIDTLGGLDILVNNAGITRDNLAMRMKDEEWEQVIQVNLEAVFRL 126

Query: 129 SRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKSKNIHCN 188
            RA+   M +  FGRII  +S  G  GN GQ NY + K  +VG+S +LAQE  ++ I  N
Sbjct: 127 MRASARPMMKARFGRIINITSVVGTTGNPGQMNYCAAKAGVVGMSKSLAQELAARGITVN 186

Query: 189 TIAP-IAASRLTESV 202
            +AP    S +TE++
Sbjct: 187 CVAPGFIRSAMTEAL 201



 Score = 25.8 bits (55), Expect = 0.002
 Identities = 12/41 (29%), Positives = 22/41 (53%)

Query: 371 ALDLKNGSGSIVVGAGSTKPNVTITVSDEDFVDIMTGKLNA 411
           A+D   G   +V  AG T+ N+ + + DE++  ++   L A
Sbjct: 82  AIDTLGGLDILVNNAGITRDNLAMRMKDEEWEQVIQVNLEA 122


Lambda     K      H
   0.313    0.131    0.371 

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: 248
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 441
Length of database: 254
Length adjustment: 28
Effective length of query: 413
Effective length of database: 226
Effective search space:    93338
Effective search space used:    93338
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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