GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Dinoroseobacter shibae DFL-12

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate 3608967 Dshi_2357 acyl-CoA dehydrogenase domain protein (RefSeq)

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>FitnessBrowser__Dino:3608967
          Length = 406

 Score =  555 bits (1430), Expect = e-163
 Identities = 276/391 (70%), Positives = 313/391 (80%), Gaps = 2/391 (0%)

Query: 5   ASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGL 64
           A F+W DPL L+ QL+EEERM+RD    FA DKLAPRV++A+R     P IF EMG  GL
Sbjct: 16  AGFDWPDPLRLEDQLSEEERMLRDGGAAFAADKLAPRVIDAYREATVAPEIFSEMGAAGL 75

Query: 65  LGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKY 124
           LG T+PE YGG G +YV YGL+ARE+ERIDSGYRSMMSVQSSLVM PI+ +GTE Q+QKY
Sbjct: 76  LGITVPEAYGGLGGSYVAYGLVAREIERIDSGYRSMMSVQSSLVMYPIHAYGTEEQRQKY 135

Query: 125 LPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWA 184
           LP LA+G  IGCFGLTEP+ GSDP  M TRA K   GYRLTGSKMWI+NSPIADVFVVWA
Sbjct: 136 LPGLAAGTLIGCFGLTEPDAGSDPAGMKTRAEKTPTGYRLTGSKMWISNSPIADVFVVWA 195

Query: 185 KDDA--GDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLK 242
           K +A  G IRGFVL+KG  GLSAP + GK+ LRAS+TGEIVMD V V E+ + P V GLK
Sbjct: 196 KSEAHGGKIRGFVLDKGTPGLSAPKVGGKLSLRASVTGEIVMDGVEVGEDALLPGVEGLK 255

Query: 243 GPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEIT 302
           GPF CLN ARYGI WG +GA+E CWH ARQY LDR QF RPLA  QL QKKLADMQTEI 
Sbjct: 256 GPFGCLNRARYGIGWGVMGASEFCWHAARQYGLDRHQFKRPLAQTQLFQKKLADMQTEIA 315

Query: 303 LALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHL 362
           L LQ  LR+GR+ DEG AA E+ S++KRN+CGKAL+IAR ARDM GGNGIS+EF V RH+
Sbjct: 316 LGLQAALRVGRLMDEGRAAPEMISLLKRNNCGKALEIARAARDMHGGNGISEEFQVMRHM 375

Query: 363 VNLEVVNTYEGTHDVHALILGRAQTGIQAFY 393
           VNLE VNTYEGTHDVHALILGRAQTG+QAF+
Sbjct: 376 VNLETVNTYEGTHDVHALILGRAQTGLQAFF 406


Lambda     K      H
   0.320    0.137    0.413 

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: 550
Number of extensions: 20
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: 393
Length of database: 406
Length adjustment: 31
Effective length of query: 362
Effective length of database: 375
Effective search space:   135750
Effective search space used:   135750
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