GapMind for Amino acid biosynthesis

 

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

Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate Echvi_4068 Echvi_4068 isocitrate dehydrogenase

Query= BRENDA::Q945K7
         (374 letters)



>FitnessBrowser__Cola:Echvi_4068
          Length = 487

 Score =  259 bits (662), Expect = 1e-73
 Identities = 146/336 (43%), Positives = 214/336 (63%), Gaps = 10/336 (2%)

Query: 47  TLFPGDGIGPEIAESVKKVFTTAGVPIEWEEHYVGTEIDPR-TQSFLTWESLESVRRNKV 105
           T+  GDGIGPEI ++  ++   AG  IE E   +G ++  +   S +  ++ +S+R  K+
Sbjct: 8   TVAYGDGIGPEIMKATLEILEAAGAQIEPEVIEIGEQVYLKGISSGIEPKAWDSLRETKI 67

Query: 106 GLKGPMATPIGKGHRSLNLTLRKELNLYANVRPCYSLPGY-KTRYDDVDLITIRENTEGE 164
            LK P+ TP G G +SLN+T RK L LYANVRPC +   Y +T + + D++ +REN E  
Sbjct: 68  FLKSPITTPQGGGFKSLNVTTRKTLGLYANVRPCKAYSPYIRTHFPETDMVIVRENEEDL 127

Query: 165 YSGLEHQVVRGVVESLKIITRQASLRVAEYAFLYAKTHGRERVSAIHKANIMQKTDGLFL 224
           Y+G+EH+    V + LK+I+R  S ++  YAF YAK + R++V+ + K NIM+  DGLF 
Sbjct: 128 YAGIEHRQTDDVYQCLKLISRPGSEKIIRYAFEYAKKYNRKKVTCMTKDNIMKLADGLFH 187

Query: 225 KCCREVAEKYPEITYEEVVIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCAGLVGGLGL 284
           K   +VA++YPEI  +  +ID    ++   P +FDV+V  NLYGDIISD+ A + G +GL
Sbjct: 188 KVFNDVAKEYPEIEADHKIIDIGTALIADKPEMFDVIVTLNLYGDIISDVAAQITGSVGL 247

Query: 285 TPSCNIGEDGVALAEAVHGSAPDIAGKNLANPTALLLSGVMMLRHLKFNEQAEQIHSAII 344
             S N+GED VA+ EA+HGSAPDIAG+N+ANP+ LL   +MML H+   E AE++ +A +
Sbjct: 248 GGSSNVGED-VAMFEAIHGSAPDIAGQNIANPSGLLNGAIMMLVHIGQPEVAEKVSNAWM 306

Query: 345 NTIAEGKYRTADL---GGSST---TTEFTKAICDHL 374
            T+ +G   T D+   G SS    T EF +A+ D L
Sbjct: 307 KTLEDG-IHTGDIYQEGVSSQLVGTKEFAQAVIDRL 341


Lambda     K      H
   0.318    0.134    0.389 

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: 415
Number of extensions: 19
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: 374
Length of database: 487
Length adjustment: 32
Effective length of query: 342
Effective length of database: 455
Effective search space:   155610
Effective search space used:   155610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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