GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudarthrobacter sulfonivorans Ar51

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_205630569.1 AU252_RS12475 SDR family oxidoreductase

Query= SwissProt::Q9NKW1
         (441 letters)



>NCBI__GCF_001484605.1:WP_205630569.1
          Length = 315

 Score =  178 bits (451), Expect = 2e-49
 Identities = 114/309 (36%), Positives = 174/309 (56%), Gaps = 17/309 (5%)

Query: 3   LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKA 62
           L +  +V IVTGAG G+G+ +AL  A+RGAKVVVNDLGGS  G+G+ +  A+ VV+EI A
Sbjct: 8   LRYDGRVAIVTGAGRGLGRAHALLLAERGAKVVVNDLGGSKEGEGNDAGPANDVVQEIIA 67

Query: 63  AGGTAVANYDSV--EDG-EKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYR 119
           AGG AVA+ ++V  EDG   IV+TA+  FG +DI++NNAGI R  +F +    + +    
Sbjct: 68  AGGEAVADTNNVGSEDGCHSIVETAVKEFGRIDIVVNNAGISRWATFPEADADNLERTLD 127

Query: 120 VHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQE 179
           VH +G +  +RAAW +M E+ +GR+I T+S  G+ G      Y + K AL+G + +LA  
Sbjct: 128 VHLRGTWHTTRAAWPYMEEQGYGRVITTTS-TGMLGLADNLAYATAKGALIGFTRSLAVA 186

Query: 180 GKSKNIHCNTIAPIAASRLTESVMPPEI----------LEQMKPDYIVPLVLYLCHQDTT 229
              K I  N IAP A +R +ES   P I          ++ M   ++ P+V YL H+   
Sbjct: 187 AAPKGILVNCIAPNAVTRPSESATKPNIVTATAVDKARMQAMDTAHVSPMVAYLAHESCQ 246

Query: 230 ETGGVFEVGAGWVSKVRLQRSAG-VYMKD-LTP-EKIKDNWAQIESFDNPSYPTSASESV 286
             G +   G G  ++  L  + G V+  D + P E + ++W +I    +   P S  +  
Sbjct: 247 VNGEILVAGGGRFARWFLGITPGWVHEGDGVAPLEAVVEHWDEINDDADYYIPASLHDWA 306

Query: 287 SGILAAVNS 295
           S  +  +++
Sbjct: 307 SNFMGHLSA 315


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: 352
Number of extensions: 18
Number of successful extensions: 4
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: 441
Length of database: 315
Length adjustment: 30
Effective length of query: 411
Effective length of database: 285
Effective search space:   117135
Effective search space used:   117135
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 Apr 09 2024. 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