GapMind for catabolism of small carbon sources

 

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

Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate 3606773 Dshi_0204 acyl-CoA dehydrogenase domain protein (RefSeq)

Query= SwissProt::P81140
         (408 letters)



>FitnessBrowser__Dino:3606773
          Length = 564

 Score =  129 bits (325), Expect = 2e-34
 Identities = 115/388 (29%), Positives = 179/388 (46%), Gaps = 23/388 (5%)

Query: 32  DEI-LIRDTFRTYCQEHLMPRIVLAN-RNEVFHREIISEMGELGVLGPTI-KGYGCAGVS 88
           DE+ +IR+ FR +  + + P     + ++E+   EII E+ E+GV G TI + YG  G+S
Sbjct: 181 DELEMIREQFRRFSVDKVEPHAHEWHLKDELIPMEIIEELAEMGVFGLTIPEEYGGFGLS 240

Query: 89  SVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQQQQKYLPRLAKGELLGCFG 148
             +  +++ EL R   G  S +  +S +    I   G+EEQ+Q K+LPRLA  E L    
Sbjct: 241 KASMCVVSEELSRGYIGVGS-LGTRSEIAAELIICGGTEEQKQ-KWLPRLASAETLPTAV 298

Query: 149 LTEPNHGSDPGSMETRALHNPSNRSYTLNGAKTWITNSPVADLFVVWARCEDNCI--RG- 205
            TEPN GSD G++ TRA+ +  N  + + G KTWIT++    +  + AR + +    RG 
Sbjct: 299 FTEPNTGSDLGALRTRAVQD-ENGDWKVTGNKTWITHAARTHVMTLLARTKPDTTDHRGL 357

Query: 206 --FLLEK---------GMRGLSAPKIEGKFSLRASATGMIIMDDVEVPEENVL--PKASS 252
             FL EK            G++  +IE     R      +  D+  V  EN+L   +   
Sbjct: 358 SMFLAEKTPGTDEAPFPTEGMTGGEIE-VLGYRGMKEYELAFDNFHVKGENLLGGEEGKG 416

Query: 253 LAVPFGCLNNARYGISWGVLGAAEFCLHTARQYTLDRIQFGVPLAKNQLIQRKLADMLTE 312
                    +AR   +   +G A+  L  + QY +DR QFG  L     +  KLA M  E
Sbjct: 417 FKQLMETFESARIQTAARAIGVAQSALDVSMQYAIDRKQFGKSLINFPRVSGKLAMMAVE 476

Query: 313 ITLGLHACLQLGRLKDQDKVTPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIR 372
           I +           KD+ +       + K      A   A     + GGNG + EY + R
Sbjct: 477 IMVARQLTYFSAFEKDEGRRCDVEAGMAKLLGARVAWAAADNGLQIHGGNGFALEYGISR 536

Query: 373 HAMNLEAVNTYEGTHDIHALILGRAITG 400
              +   +N +EG  +I A ++ R + G
Sbjct: 537 ILCDARILNIFEGAAEIQAQVIARRLLG 564


Lambda     K      H
   0.319    0.136    0.404 

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: 32
Number of successful extensions: 4
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: 408
Length of database: 564
Length adjustment: 34
Effective length of query: 374
Effective length of database: 530
Effective search space:   198220
Effective search space used:   198220
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: 51 (24.3 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