GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dhaD in Synechococcus elongatus PCC 7942

Align glycerol dehydrogenase (EC 1.1.1.6) (characterized)
to candidate Synpcc7942_1653 Synpcc7942_1653 glycerol dehydrogenase

Query= BRENDA::A0MLR7
         (380 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1653 Synpcc7942_1653 glycerol
           dehydrogenase
          Length = 398

 Score =  265 bits (676), Expect = 2e-75
 Identities = 157/360 (43%), Positives = 211/360 (58%), Gaps = 5/360 (1%)

Query: 16  RIIQSPGKYIQGADVINRLGEYLKPL-AERWLVVGDKFVLGFAQSTVEKSFKDAGLVVEI 74
           R+  SP +YIQG  V+  +G YL  L A+R  ++  +         +    + AG+   +
Sbjct: 24  RVFISPQRYIQGRGVLRSVGRYLSLLQAKRAGLLMSQRSSRNEGDLLLAGLRSAGVDAVV 83

Query: 75  APFGGECSQNEIDRLRGIAETAQCGAILGIGGGKTLDTAKALAHFMGVPVAIAPTIASTD 134
           + F GEC+ +EI          +   ++  GGGK +DT KA+A  +G+PV + PT+AS D
Sbjct: 84  STFQGECTTDEITAHTTAFSKERIDCVIAAGGGKCIDTGKAIAFRLGIPVVVVPTLASND 143

Query: 135 APCSALSVIYTDEGEFDRYLLLPNNPNMVIVDTKIVAGAPARLLAAGIGDALATWFEARA 194
           APCSALSV+Y+ EG        PN+P +V+VDT I+A AP R L AG+GDA+ATW+EA  
Sbjct: 144 APCSALSVLYSPEGISQGVEFYPNSPAIVVVDTDIIAAAPERYLVAGMGDAMATWYEASV 203

Query: 195 CSRS-GATTMAGGKCTQAALALAELCYNTLLEEGEKAMLAAEQHVVTPALERVIEANTYL 253
           C R+  A T  G + T AA A+ E+C +TL +EG  A  A     V  ALE V+EANT L
Sbjct: 204 CLRNPAAVTTVGARPTLAACAIGEVCAHTLFQEGCAAAAAVASKTVNDALESVVEANTLL 263

Query: 254 SGVGFESGGLAAAHAVHNGLTAIPDAH-HYYHGEKVAFGTLTQLVLENAPVEEIETVAAL 312
           SG+GFESGGLA AHAV    TAIP    +Y HGE VA GTL QL++E+ P +E   VA  
Sbjct: 264 SGLGFESGGLAGAHAVAQSYTAIPHVRANYLHGEMVAMGTLAQLMMESRP-KEATRVAEF 322

Query: 313 SHAVGLPITLAQLDIKEDVPAKMRIVAEAACAEGETIHNMPGGATPDQVYAALLVADQYG 372
             AVGLPI L QL +       + IV+EA+      + NMP   TP+ V +A+L A   G
Sbjct: 323 FAAVGLPIHLGQLSLSSSDTQALEIVSEASLG-FPFVGNMPMKITPEFVKSAILDAHHLG 381


Lambda     K      H
   0.318    0.134    0.393 

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: 398
Number of extensions: 22
Number of successful extensions: 6
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: 380
Length of database: 398
Length adjustment: 30
Effective length of query: 350
Effective length of database: 368
Effective search space:   128800
Effective search space used:   128800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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