GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Sphingomonas koreensis DSMZ 15582

Align Isovaleryl-CoA dehydrogenase, mitochondrial; IVD; Isovaleryl-CoA dehydrogenase 2; St-IVD2; EC 1.3.8.4 (characterized)
to candidate Ga0059261_2164 Ga0059261_2164 Acyl-CoA dehydrogenases

Query= SwissProt::Q9FS87
         (412 letters)



>FitnessBrowser__Korea:Ga0059261_2164
          Length = 394

 Score =  216 bits (549), Expect = 1e-60
 Identities = 125/381 (32%), Positives = 199/381 (52%), Gaps = 5/381 (1%)

Query: 28  FSTSLLFDDTQKQFKESVAQFAQENIAPHAEKIDRTNYFPQDVNLWKLMGNFNLLGITVP 87
           F+      D ++  +++   +AQE + P   +      F +++     MG   LLG T+P
Sbjct: 13  FALDAQLTDEERMVRDAARAYAQERLLPRVTRAFLDENFDREI--MSEMGQLGLLGPTIP 70

Query: 88  EEYGGLGLGYLYHCIAMEEISRASGSVGLSYGAHTNLCINQLVRNGTHEQKQKYLPKLIS 147
           E YGG GLGY+ + +   E+         +    ++L ++ +   GT EQK+KYLPKL+S
Sbjct: 71  ETYGGAGLGYVAYGLVAREVEAVDSGYRSAMSVQSSLVMHPINAYGTEEQKRKYLPKLLS 130

Query: 148 GEHVGALAMSEPNAGSDVVSMKCKADRVEGGYVLNGNKMWCTNGPTAQTLVVYAKTDVTA 207
           GE VG   ++EP+AGSD  SM+ +A++++GGY + G+KMW TN P A   VV+AK+D   
Sbjct: 131 GEWVGCFGLTEPDAGSDPGSMRTRAEKIDGGYRITGSKMWITNSPIADVFVVWAKSDAHG 190

Query: 208 GSKGITAFIIEKGMTGFSTAQKLDKLGMRGSDTCELVFENCFVPEENVLGQVGRGVYVLM 267
           G  GI  F++EKGM G S  +   KL +R S T E+V +   V E+ +L +V +G+    
Sbjct: 191 G--GIKGFVLEKGMKGLSAPKIEGKLSLRASITGEIVMDGVEVSEDALLPEV-QGLKGPF 247

Query: 268 SGLDLERLVLASGPVGIMQACLDVVLPYVKQREQFGRPIGEFQFVQGKVADMYTSMQSSR 327
             L+  R  +A G +G  +AC      Y   R+QFGRP+   Q VQ K+A+M T +    
Sbjct: 248 GCLNRARYGIAWGSMGAAEACFHAARQYTLDRQQFGRPLAATQLVQLKLANMETEIALGL 307

Query: 328 SYLYSVARECDSGTINTKDCAGVILSAAERATQVALQAIQCLGGNGYVNEYPTGRFLRDA 387
                  R  D G +  +  + +  +   +A ++A  A    GGNG   E+   R   + 
Sbjct: 308 QAALRAGRMFDQGELAPEAISIIKRNNCGKALEIARVARDMHGGNGISAEFHVMRHAINL 367

Query: 388 KLYEIGAGTSEIRRMIIGREL 408
           +      GT ++  +I+GR +
Sbjct: 368 ETVNTYEGTHDVHGLILGRAI 388


Lambda     K      H
   0.319    0.135    0.396 

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: 357
Number of extensions: 14
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: 412
Length of database: 394
Length adjustment: 31
Effective length of query: 381
Effective length of database: 363
Effective search space:   138303
Effective search space used:   138303
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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