GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas simiae WCS417

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate GFF4186 PS417_21440 3-ketoacyl-ACP reductase

Query= SwissProt::Q9NKW1
         (441 letters)



>FitnessBrowser__WCS417:GFF4186
          Length = 247

 Score =  109 bits (273), Expect = 8e-29
 Identities = 81/260 (31%), Positives = 123/260 (47%), Gaps = 21/260 (8%)

Query: 3   LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKA 62
           ++ + KV +VTGA  GIG+  ALE  ++GA V+         G  +S+  A+++   +K 
Sbjct: 1   MSLQGKVALVTGASRGIGQAIALELGRQGAVVI---------GTATSASGAERIAATLKE 51

Query: 63  AG--GTAVA-NYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYR 119
            G  GT +  N  S E    ++      FG   IL+NNAGI RD    +M D +W  V  
Sbjct: 52  NGVQGTGLELNVTSDESVAAVLAEITAQFGAPAILVNNAGITRDNLMMRMKDDEWYDVVD 111

Query: 120 VHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQE 179
            +    ++LS+     M +  +GRII   S  G  GN GQ NY S K  L G S  LA+E
Sbjct: 112 TNLNSLFRLSKGVLRGMTKARWGRIINIGSVVGAMGNAGQVNYASAKAGLEGFSRALARE 171

Query: 180 GKSKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEV-- 237
             S++I  N++AP       ++ M  E+ E  +   +  + L    Q   E   V     
Sbjct: 172 VGSRSITVNSVAP----GFIDTDMTRELPEAQREALLTQIPLGRLGQ-AQEIANVVTFLA 226

Query: 238 --GAGWVSKVRLQRSAGVYM 255
             GA +V+   +  + G+YM
Sbjct: 227 SDGAAYVTGATIPVNGGMYM 246



 Score = 29.6 bits (65), Expect = 1e-04
 Identities = 22/101 (21%), Positives = 45/101 (44%), Gaps = 7/101 (6%)

Query: 328 GYNASKIFTTIQGNIGAKGAELVKKINGIY----LINIKKGTNTQAWALDLKNGSGS--- 380
           G   + +  T     GA+      K NG+      +N+    +  A   ++    G+   
Sbjct: 26  GRQGAVVIGTATSASGAERIAATLKENGVQGTGLELNVTSDESVAAVLAEITAQFGAPAI 85

Query: 381 IVVGAGSTKPNVTITVSDEDFVDIMTGKLNAQSAFTKGKLK 421
           +V  AG T+ N+ + + D+++ D++   LN+    +KG L+
Sbjct: 86  LVNNAGITRDNLMMRMKDDEWYDVVDTNLNSLFRLSKGVLR 126


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: 250
Number of extensions: 11
Number of successful extensions: 3
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: 247
Length adjustment: 28
Effective length of query: 413
Effective length of database: 219
Effective search space:    90447
Effective search space used:    90447
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 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