GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pedobacter sp. GW460-11-11-14-LB5

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate CA265_RS09630 CA265_RS09630 acyl-CoA dehydrogenase

Query= BRENDA::B0EVL5
         (395 letters)



>FitnessBrowser__Pedo557:CA265_RS09630
          Length = 396

 Score =  418 bits (1074), Expect = e-121
 Identities = 207/386 (53%), Positives = 271/386 (70%)

Query: 8   FDWADPLYLDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLG 67
           ++  D   LD  LTD  +++R +AR + ++ + P +++  +  +  + +   + ++G  G
Sbjct: 10  YEAPDYYLLDELLTDEHKLIRATARDWVKKEVSPIIEDYAQKAEFPKHLIKGLADIGAFG 69

Query: 68  ATIPEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLP 127
            TIP +YGG+G++Y  YG++ +E+ER DSG RS  SVQ SLVM PI  +GSEE ++KYLP
Sbjct: 70  PTIPVEYGGAGLDYTAYGILMQEIERGDSGIRSTASVQGSLVMYPIYAYGSEEQRKKYLP 129

Query: 128 KLATGEWVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKD 187
           KLA+GE +GCFGLTEP+HGS+PG MVT  +     Y L+GAKMWI+N+P AD+ VVWAKD
Sbjct: 130 KLASGEMMGCFGLTEPDHGSNPGGMVTNIKDAGSHYILNGAKMWISNAPFADIAVVWAKD 189

Query: 188 DAGDIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVRGLKGPFT 247
           ++G IRG ++E+G +G S P  H K  LRAS TGE+V D V  P+EN FP + GLKGP  
Sbjct: 190 ESGKIRGLIVERGMEGFSTPETHHKWSLRASATGELVFDNVKVPKENIFPEISGLKGPLG 249

Query: 248 CLNSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQ 307
           CLN ARYGIAWGALGAA  CY+TA +Y+ +R QFG+P+   QL QKKLA+M+TEIT G  
Sbjct: 250 CLNQARYGIAWGALGAAMDCYDTALRYSKERVQFGKPIGGFQLQQKKLAEMVTEITKGQL 309

Query: 308 GCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLE 367
              RLG LK E  A  E  S+ KRNS   +LDIAR AR MLGG GI+ E+ I RH++NLE
Sbjct: 310 LVWRLGVLKSENRASAEQISMAKRNSVEIALDIARNARQMLGGMGITGEYSIMRHMMNLE 369

Query: 368 VVNTYEGTHDIHALILGRAITGLAAF 393
            V TYEGTHDIH LI G  +TGL AF
Sbjct: 370 SVVTYEGTHDIHLLITGMDVTGLNAF 395


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: 442
Number of extensions: 17
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: 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 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