GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Dechlorosoma suillum PS

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate Dsui_3198 Dsui_3198 3-isopropylmalate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>FitnessBrowser__PS:Dsui_3198
          Length = 354

 Score =  200 bits (508), Expect = 5e-56
 Identities = 141/355 (39%), Positives = 192/355 (54%), Gaps = 33/355 (9%)

Query: 4   RICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVEKILSCH 63
           +IC++ GDGIG E++  A RVLEA  L  E   A  G    +  G   PE + +   +  
Sbjct: 2   KICVLPGDGIGPEIMAEAVRVLEALNLGFEMETALLGGCAVDATGNPYPEASQKLAQAAD 61

Query: 64  ATLFGAATSPT--------RKVPGFFGAIRYLRRRLDLYANVRPAKSRPV--------PG 107
           A L GA   P         R   G  G    +R++L+L+AN+RPA   P         P 
Sbjct: 62  AVLLGAVGGPQWDTLPREQRPERGLLG----IRKQLNLFANLRPAILYPELANASTLKPE 117

Query: 108 SRPGVDLVIVRENTEGLYVEQ----ERRYLD-----VAIADAVISKKASERIGRAALRIA 158
              G+D++IVRE T  +Y  Q    E R +D             S+    RI R A   A
Sbjct: 118 VVAGLDILIVRELTGDIYFGQPRGIEEREIDGQKQRFGFNTMHYSESEIRRILRVAFEAA 177

Query: 159 EGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFD 218
             R +K   +  K NVL  TQ L+ D   E+A ++P V +  ++VDN AMQLV  P++FD
Sbjct: 178 RKRNKKLCSV-DKMNVLETTQ-LWRDIANELAPEYPDVELSHMLVDNAAMQLVRNPKQFD 235

Query: 219 VIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGKGIANPTAA 277
           V+VT N+ GDILSD A+ L G +G+ PS ++  +   ++EP HGSAPDIAGKG+ANP A 
Sbjct: 236 VMVTGNMFGDILSDEASMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGKGVANPLAT 295

Query: 278 ILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331
           ILSAAMML Y    +EAA +VE AV  VL +G RT D+    TT+  T  + +A+
Sbjct: 296 ILSAAMMLRYTFNMEEAAVKVENAVKKVLAQGYRTGDIYEPGTTKVGTRQMGDAV 350


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: 307
Number of extensions: 15
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: 354
Length adjustment: 29
Effective length of query: 305
Effective length of database: 325
Effective search space:    99125
Effective search space used:    99125
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:

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