GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Echinicola vietnamensis KMM 6221, DSM 17526

Align Homoisocitrate dehydrogenase; HICDH; Homo(2)-isocitrate/homo(3)-isocitrate dehydrogenase; Isohomocitrate dehydrogenase; IHDH; NAD-dependent threo-isohomocitrate dehydrogenase; EC 1.1.1.87; EC 1.1.1.- (characterized)
to candidate Echvi_2062 Echvi_2062 3-isopropylmalate dehydrogenase

Query= SwissProt::Q58991
         (347 letters)



>FitnessBrowser__Cola:Echvi_2062
          Length = 353

 Score =  210 bits (534), Expect = 5e-59
 Identities = 135/361 (37%), Positives = 204/361 (56%), Gaps = 28/361 (7%)

Query: 2   MKVCVIEGDGIGKEVIPEAIKILNELGEF--------EIIKGEAGLECLKKYGNALPEDT 53
           M + ++ GDGIG EVI + +K++  +G+         E + G A ++     GN  P++T
Sbjct: 1   MNIALLPGDGIGPEVIEQTVKVVKAVGKKFGHTITFKEAVVGAAAIDAT---GNPYPDET 57

Query: 54  IEKAKEADIILFGAITSPK----PGEVKNYKSPIITLRKMFHLYANVRPINNFGIGQLIG 109
            E   +AD +LFGAI  PK    P      +  ++ +RK   L++NVRP   F    LI 
Sbjct: 58  HEICLQADAVLFGAIGDPKYDNDPKAKVRPEQGLLAMRKKLGLFSNVRP--TFTFPSLIH 115

Query: 110 KIADYEFLNAKNIDIVIIRENTEDLYVGRERLENDT---AIAERVITRKGSERIIRFAFE 166
           K +  +    +  D+V +RE T  +Y G  R  N+    A    V T++   R+ R  FE
Sbjct: 116 K-SPLKKERIEGTDLVFLRELTGGIYFGEPRGRNEQGTKAFDTNVYTKEEITRLARMGFE 174

Query: 167 YAIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEK 225
           +A K  RK ++C+ KANVL  T  L+ E   E++  Y +++ +   VD+ AM LI+ P+ 
Sbjct: 175 FAQKR-RKLLTCVDKANVLA-TSRLWRETVQELEPEYPDVKVEYEFVDAVAMRLIQWPKA 232

Query: 226 FDVIVTTNMFGDILSDEASALIGGLGLAPSANIGDDKALFEPVHGSAPDIAGKGIANPMA 285
           +DV++T N+FGDIL+DEAS + G +GL PSA++G D  LFEP+HGS P  AGK IANP+A
Sbjct: 233 YDVLITENLFGDILTDEASVISGSMGLMPSASLGTDVKLFEPIHGSYPQAAGKDIANPLA 292

Query: 286 SILSIAMLFDYIGE-KEKGDLIREAVKYCLINKKVTPDLGGD---LKTKDVGDEILNYIR 341
           ++LS AM+F+Y  + K++   I + V   L    VT D+  +    KT +VGD +   I 
Sbjct: 293 TVLSAAMMFEYAFDLKDEAKAISDVVNLSLAEGVVTEDIAEESKPSKTSEVGDWLAAQIL 352

Query: 342 K 342
           K
Sbjct: 353 K 353


Lambda     K      H
   0.319    0.140    0.397 

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: 325
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: 347
Length of database: 353
Length adjustment: 29
Effective length of query: 318
Effective length of database: 324
Effective search space:   103032
Effective search space used:   103032
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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