GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Sphingomonas indica Dd16

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_085219040.1 B9N75_RS12195 acyl-CoA dehydrogenase

Query= BRENDA::B0EVL5
         (395 letters)



>NCBI__GCF_900177405.1:WP_085219040.1
          Length = 396

 Score =  568 bits (1463), Expect = e-166
 Identities = 283/396 (71%), Positives = 326/396 (82%), Gaps = 3/396 (0%)

Query: 1   MATNRVT-FDWADPLYLDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNE 59
           M   R+T FDWADP  LD+QLTD ERMVRD+A  Y+QE+L PRV +A+ +E  DR I NE
Sbjct: 1   MTEPRITSFDWADPFGLDAQLTDEERMVRDTAEGYAQEKLQPRVTKAYLNEDFDREIMNE 60

Query: 60  MGELGLLGATIPEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSE 119
           +G LGL+GATI  +YGG+G+ YV YGLIAR VERVDSGYRS MSVQSSLVM PIN +G+E
Sbjct: 61  LGALGLIGATIAPEYGGAGLGYVSYGLIARAVERVDSGYRSAMSVQSSLVMHPINAYGTE 120

Query: 120 ETKQKYLPKLATGEWVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIAD 179
           E ++KYLPKLA+GEWVGCFGLTEP+ GSDPGSM TRA+K+DGGY LSGAKMWITNSPIAD
Sbjct: 121 EQRKKYLPKLASGEWVGCFGLTEPDAGSDPGSMRTRAQKIDGGYRLSGAKMWITNSPIAD 180

Query: 180 VFVVWAKDDA--GDIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFP 237
           VFVVWAK +A  G I+GFVLEKG KGL+AP +  K+ LRASITGEIVMD V  PEEN  P
Sbjct: 181 VFVVWAKSEAHDGKIKGFVLEKGMKGLTAPKVKEKLSLRASITGEIVMDGVEIPEENLLP 240

Query: 238 TVRGLKGPFTCLNSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLAD 297
            V GLKGPF CLN ARYGIAWG++GAAEAC+  AR YT+DRKQFGRPLAA QL+Q KLA+
Sbjct: 241 NVEGLKGPFGCLNRARYGIAWGSMGAAEACFHAARLYTLDRKQFGRPLAATQLVQMKLAN 300

Query: 298 MLTEITLGLQGCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEF 357
           MLT+I+LGLQ  LR+GR  DEG    E  S++KRN+CGK+LDIAR+ARDM GGNGIS EF
Sbjct: 301 MLTDISLGLQAALRVGRRMDEGVLIPETISLIKRNNCGKALDIARIARDMHGGNGISAEF 360

Query: 358 CIARHLVNLEVVNTYEGTHDIHALILGRAITGLAAF 393
            + RH  NLE VNTYEGTHD+H LILGRAITG+AAF
Sbjct: 361 QVMRHAANLETVNTYEGTHDVHGLILGRAITGIAAF 396


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: 513
Number of extensions: 16
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: 396
Length adjustment: 31
Effective length of query: 364
Effective length of database: 365
Effective search space:   132860
Effective search space used:   132860
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 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