GapMind for catabolism of small carbon sources

 

Aligments for a candidate for icd in Dinoroseobacter shibae DFL-12

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate 3607360 Dshi_0775 tartrate dehydrogenase (RefSeq)

Query= BRENDA::Q5SIJ1
         (334 letters)



>lcl|FitnessBrowser__Dino:3607360 Dshi_0775 tartrate dehydrogenase
           (RefSeq)
          Length = 359

 Score =  220 bits (561), Expect = 4e-62
 Identities = 144/356 (40%), Positives = 199/356 (55%), Gaps = 24/356 (6%)

Query: 2   AYRICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAE-AGWETFERRGTSVPEETV 56
           AYRI +I GDGIG EV+P   +VL A      + LEF   + A    ++  G  +P++  
Sbjct: 5   AYRIAVIPGDGIGTEVVPEGLKVLTAAARKFDIGLEFETHDFASAAYYQAHGQMMPDDWK 64

Query: 57  EKILSCHATLFGAATSPTRKVP---GFFGAIRYLRRRLDLYANVRPAK-----SRPVPGS 108
            +I    A  FGA   P   VP     +G++   RR  D Y N+RP +     + P+ G 
Sbjct: 65  SRIGDSDALYFGAVGWPDM-VPDHVSLWGSLLKFRREFDQYVNLRPVRLMPGVTSPLAGR 123

Query: 109 RPG-VDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIG-----RAALRIAEGRP 162
            PG +D  +VRENTEG Y     R  +    + V+ +    R+G     R A  +A+ RP
Sbjct: 124 APGEIDFWVVRENTEGEYSSIGGRIFEGTERETVMQETVMTRVGVDRVLRFAFELAQSRP 183

Query: 163 RKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVT 222
           +K L  A K+N + +T   + + V E+AK +P V V    +D      V+ P+ FDV+V 
Sbjct: 184 KKHLTSATKSNGISITMPYWDERVVEMAKGYPEVAVDKYHIDILTAHFVLHPDWFDVVVA 243

Query: 223 TNLLGDILSDLAAGLVGGLGLAPSGNIG---DTTAVFEPVHGSAPDIAGKGIANPTAAIL 279
           +NL GDILSDL     G +G+APSGNI    D  ++FEPVHGSAPDIAGKGIANP   + 
Sbjct: 244 SNLFGDILSDLGPACTGTIGIAPSGNINPERDFPSLFEPVHGSAPDIAGKGIANPVGQVW 303

Query: 280 SAAMMLDYLGEKEAAKRVEKAVDLVL-ERGPRTPDLGGDATTEAFTEAVVEALKSL 334
           + AMMLD+LG+ EAA  +  A++ VL +   RT DLGG A T A  +A+V AL+ L
Sbjct: 304 AGAMMLDHLGQGEAAAAIVAALEEVLADPVRRTADLGGQAGTVACGDAIVAALERL 359


Lambda     K      H
   0.319    0.137    0.391 

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: 306
Number of extensions: 18
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: 334
Length of database: 359
Length adjustment: 29
Effective length of query: 305
Effective length of database: 330
Effective search space:   100650
Effective search space used:   100650
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 (21.7 bits)
S2: 49 (23.5 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 preprint 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