GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Sphingomonas koreensis DSMZ 15582

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate Ga0059261_2164 Ga0059261_2164 Acyl-CoA dehydrogenases

Query= BRENDA::B0EVL5
         (395 letters)



>FitnessBrowser__Korea:Ga0059261_2164
          Length = 394

 Score =  573 bits (1477), Expect = e-168
 Identities = 284/388 (73%), Positives = 322/388 (82%), Gaps = 2/388 (0%)

Query: 8   FDWADPLYLDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLG 67
           FDWADP  LD+QLTD ERMVRD+ARAY+QERLLPRV  AF  E  DR I +EMG+LGLLG
Sbjct: 7   FDWADPFALDAQLTDEERMVRDAARAYAQERLLPRVTRAFLDENFDREIMSEMGQLGLLG 66

Query: 68  ATIPEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLP 127
            TIPE YGG+G+ YV YGL+AREVE VDSGYRS MSVQSSLVM PIN +G+EE K+KYLP
Sbjct: 67  PTIPETYGGAGLGYVAYGLVAREVEAVDSGYRSAMSVQSSLVMHPINAYGTEEQKRKYLP 126

Query: 128 KLATGEWVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKD 187
           KL +GEWVGCFGLTEP+ GSDPGSM TRA K+DGGY ++G+KMWITNSPIADVFVVWAK 
Sbjct: 127 KLLSGEWVGCFGLTEPDAGSDPGSMRTRAEKIDGGYRITGSKMWITNSPIADVFVVWAKS 186

Query: 188 DA--GDIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVRGLKGP 245
           DA  G I+GFVLEKG KGLSAP I GK+ LRASITGEIVMD V   E+   P V+GLKGP
Sbjct: 187 DAHGGGIKGFVLEKGMKGLSAPKIEGKLSLRASITGEIVMDGVEVSEDALLPEVQGLKGP 246

Query: 246 FTCLNSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLG 305
           F CLN ARYGIAWG++GAAEAC+  ARQYT+DR+QFGRPLAA QL+Q KLA+M TEI LG
Sbjct: 247 FGCLNRARYGIAWGSMGAAEACFHAARQYTLDRQQFGRPLAATQLVQLKLANMETEIALG 306

Query: 306 LQGCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVN 365
           LQ  LR GR+ D+G    E  SI+KRN+CGK+L+IARVARDM GGNGIS EF + RH +N
Sbjct: 307 LQAALRAGRMFDQGELAPEAISIIKRNNCGKALEIARVARDMHGGNGISAEFHVMRHAIN 366

Query: 366 LEVVNTYEGTHDIHALILGRAITGLAAF 393
           LE VNTYEGTHD+H LILGRAITG+AAF
Sbjct: 367 LETVNTYEGTHDVHGLILGRAITGIAAF 394


Lambda     K      H
   0.319    0.136    0.409 

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: 529
Number of extensions: 15
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: 395
Length of database: 394
Length adjustment: 31
Effective length of query: 364
Effective length of database: 363
Effective search space:   132132
Effective search space used:   132132
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