GapMind for catabolism of small carbon sources

 

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

Align Isocitrate--homoisocitrate dehydrogenase; HICDH; Beta-decarboxylating dehydrogenase; EC 1.1.1.286 (characterized)
to candidate Echvi_2062 Echvi_2062 3-isopropylmalate dehydrogenase

Query= SwissProt::O59394
         (345 letters)



>FitnessBrowser__Cola:Echvi_2062
          Length = 353

 Score =  184 bits (467), Expect = 3e-51
 Identities = 123/351 (35%), Positives = 196/351 (55%), Gaps = 33/351 (9%)

Query: 4   VAVIKGDGIGPEVIDAAIRVVKSVTDK----IKFYEFEGGLSVFKKYGVPIREEDLEEIR 59
           +A++ GDGIGPEVI+  ++VVK+V  K    I F E   G +     G P  +E  E   
Sbjct: 3   IALLPGDGIGPEVIEQTVKVVKAVGKKFGHTITFKEAVVGAAAIDATGNPYPDETHEICL 62

Query: 60  KMDAILFGATTTP-FDVP-----RYKSLIITLRKELDLYANLR-------IIPNFKLRKE 106
           + DA+LFGA   P +D       R +  ++ +RK+L L++N+R       +I    L+KE
Sbjct: 63  QADAVLFGAIGDPKYDNDPKAKVRPEQGLLAMRKKLGLFSNVRPTFTFPSLIHKSPLKKE 122

Query: 107 ------IIIVRENSEGLYSGEGA---YDSNKVVDFRIITRKGAERIAKFAVKLAKDRSTF 157
                 ++ +RE + G+Y GE         K  D  + T++   R+A+   + A+ R   
Sbjct: 123 RIEGTDLVFLRELTGGIYFGEPRGRNEQGTKAFDTNVYTKEEITRLARMGFEFAQKRRKL 182

Query: 158 LTFVHKANILESDRFFRKIVLDIARK-EDVKVREEIVDSFTIKLVKDPWNLGIILSENMF 216
           LT V KAN+L + R +R+ V ++  +  DVKV  E VD+  ++L++ P    ++++EN+F
Sbjct: 183 LTCVDKANVLATSRLWRETVQELEPEYPDVKVEYEFVDAVAMRLIQWPKAYDVLITENLF 242

Query: 217 GDILSDLATIHAGSIGIVPSGNYGEDIALFEPIHGSAPDIAGKGIANPIGAILSAAMMLD 276
           GDIL+D A++ +GS+G++PS + G D+ LFEPIHGS P  AGK IANP+  +LSAAMM +
Sbjct: 243 GDILTDEASVISGSMGLMPSASLGTDVKLFEPIHGSYPQAAGKDIANPLATVLSAAMMFE 302

Query: 277 Y---LGLDGSIIWKAVGRYVRRGNLTPDMEGR---ATTLEVTNGIISEIYR 321
           Y   L  +   I   V   +  G +T D+      + T EV + + ++I +
Sbjct: 303 YAFDLKDEAKAISDVVNLSLAEGVVTEDIAEESKPSKTSEVGDWLAAQILK 353


Lambda     K      H
   0.321    0.142    0.403 

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: 313
Number of extensions: 17
Number of successful extensions: 4
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: 345
Length of database: 353
Length adjustment: 29
Effective length of query: 316
Effective length of database: 324
Effective search space:   102384
Effective search space used:   102384
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 (21.8 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