GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Marinobacter adhaerens HP15

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate GFF838 HP15_817 3-isopropylmalate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>FitnessBrowser__Marino:GFF838
          Length = 384

 Score =  167 bits (423), Expect = 4e-46
 Identities = 125/344 (36%), Positives = 178/344 (51%), Gaps = 57/344 (16%)

Query: 4   RICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVE---AEAGWETFERRGTSVPEETV 56
           RI +  GDGIG EV+  A R LE      GL LE+         W   E  G S+P + +
Sbjct: 6   RIAVTPGDGIGPEVVAEAVRCLETLRAKHGLDLEWTRFPWPSHAWH--EEHGESMPADAL 63

Query: 57  EKILSCHATLFGAATSPTRK-------VPGFFGAIRYL--RRRLDLYANVRPAKSRPVPG 107
            ++    A L GA   P          +P        L  R+  D +   RPA  R +PG
Sbjct: 64  AQLQKYDAILLGALGDPGPMDDPDRYLLPDSISLAPLLDMRKGFDQWVCERPA--RLLPG 121

Query: 108 SRP--------GVDLVIVRENTEGLYVEQERRYL-----DVAIADAVISKKASERI---- 150
           +R          +D++++REN+EG YV Q  R       +VA    V ++KA++RI    
Sbjct: 122 ARQYLADERAKDIDMLVIRENSEGEYVSQGGRLRKGTPDEVATQMEVFTRKATDRIIRYG 181

Query: 151 -----GRAALRIAEGRPR--KTLH---------IAHKANVLPLTQGLFLDTVKEVAKDFP 194
                 RAA R++EGR R  +TL          +  K N L     ++ +   E++K++P
Sbjct: 182 FEQARNRAADRVSEGRTRTFRTLDGRTCESQVCLVTKRNALRYWGDMYTEAFDEISKEYP 241

Query: 195 LVNVQDIIVDNCAMQLVMRPERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIG---- 250
            V     +VD   M+ V  P  FDV+V +NL GDIL+DLAA L GG+G+APS N+     
Sbjct: 242 DVATHHELVDAACMKFVQSPWAFDVVVASNLQGDILTDLAAVLSGGMGVAPSCNLNPTDP 301

Query: 251 DTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAA 294
           D  ++FEP HGSAPDIAG+G+A+PTA + +AA ML++LG K+ A
Sbjct: 302 DMPSMFEPTHGSAPDIAGQGLADPTAMLFTAARMLEWLGRKDPA 345


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: 299
Number of extensions: 17
Number of successful extensions: 5
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: 384
Length adjustment: 29
Effective length of query: 305
Effective length of database: 355
Effective search space:   108275
Effective search space used:   108275
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 Aug 03 2021. The underlying query database was built on Aug 03 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