GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Flavobacterium sp. LM5

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_078210577.1 BXU11_RS00155 acyl-CoA dehydrogenase

Query= BRENDA::B0EVL5
         (395 letters)



>NCBI__GCF_002017945.1:WP_078210577.1
          Length = 392

 Score =  399 bits (1024), Expect = e-115
 Identities = 200/386 (51%), Positives = 266/386 (68%)

Query: 8   FDWADPLYLDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLG 67
           F   D   LD  LT+  ++VRD+ARA+ +  + P +++  +  +  + I   +GE+G  G
Sbjct: 6   FQSPDYYNLDDLLTEEHKLVRDAARAWVKREVSPIIEDYAQKAEFPKQIIKGLGEIGGFG 65

Query: 68  ATIPEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLP 127
             IP +YGG+G++ + YGLI +E+ER DSG RS  SVQSSLVM PI ++G+EE + KYLP
Sbjct: 66  PYIPVEYGGAGLDQISYGLIMQEIERGDSGVRSTSSVQSSLVMYPIWKYGNEEQRMKYLP 125

Query: 128 KLATGEWVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKD 187
           KLATGE++GCFGLTEP+HGS+PG M T  +     Y L+GAKMWI+N+P AD+ VVWAK+
Sbjct: 126 KLATGEFMGCFGLTEPDHGSNPGGMTTNFKDKGDHYLLNGAKMWISNAPFADIAVVWAKN 185

Query: 188 DAGDIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVRGLKGPFT 247
           + G I G ++E+G +G + P  H K  LRAS TGE++ D V  P+EN  P   GL  P  
Sbjct: 186 EEGRIHGLIVERGMEGFTTPETHNKWSLRASATGELIFDNVKVPKENLLPNKSGLGAPLG 245

Query: 248 CLNSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQ 307
           CL+SARYGIAWGA+GAA  CY+TA +Y  +R QF +P+A  QL QKKLA+M+TEIT    
Sbjct: 246 CLDSARYGIAWGAIGAAMDCYDTALRYAKERIQFDKPIAGTQLQQKKLAEMITEITKAQL 305

Query: 308 GCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLE 367
              RLG L++EG A     S+ KRN+   ++ IAR AR MLGG GI+ E+ I RH++NLE
Sbjct: 306 LTWRLGVLRNEGRATSAQISMAKRNNVDMAIHIAREARQMLGGMGITGEYSIMRHMMNLE 365

Query: 368 VVNTYEGTHDIHALILGRAITGLAAF 393
            V TYEGTHDIH LI G  ITG++AF
Sbjct: 366 SVITYEGTHDIHLLITGMDITGISAF 391


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: 431
Number of extensions: 8
Number of successful extensions: 1
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: 392
Length adjustment: 31
Effective length of query: 364
Effective length of database: 361
Effective search space:   131404
Effective search space used:   131404
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