GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Nitratiruptor tergarcus DSM 16512

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_084275692.1 B8779_RS06295 3-isopropylmalate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>NCBI__GCF_900176045.1:WP_084275692.1
          Length = 356

 Score =  235 bits (600), Expect = 1e-66
 Identities = 153/348 (43%), Positives = 206/348 (59%), Gaps = 22/348 (6%)

Query: 3   YRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETVEK 58
           Y + LI+GDGIG E+I  A +VL+A     G  + + EA  G    +  G  +PEET+E 
Sbjct: 4   YTVALIKGDGIGPEIIDEAVKVLDAVSVKEGFEITYKEALLGGAAIDVTGEPIPEETIEI 63

Query: 59  ILSCHATLFGAATSPT-----RKVPGFFGAIRYLRRRLDLYANVRPAK--------SRPV 105
             S  A LFGA   P      R      G ++ LR+ L+++AN+RP          S   
Sbjct: 64  AKSADAVLFGAIGGPQWDDLPRDKRPETGLLK-LRKALEVFANLRPVTVYDELVNASTLK 122

Query: 106 PGSRPGVDLVIVRENTEGLYVEQERRYL-DVAIADAVISKKASERIGRAALRIAEGRPRK 164
           P    G DL++VRE   G+Y  Q R Y  D A    V +K+   RI +    IA  R +K
Sbjct: 123 PEVIQGTDLMVVRELIGGIYFGQPRAYEGDRAYNTMVYTKQEVYRIAKVGFEIAMKRNKK 182

Query: 165 TLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTN 224
            + +  KANVL ++Q L+ DTV EVAK++P V+V+ + VDN AMQLV  P++FDVI+T N
Sbjct: 183 LVSV-DKANVLEVSQ-LWRDTVNEVAKEYPEVSVEHMYVDNAAMQLVRDPKQFDVILTGN 240

Query: 225 LLGDILSDLAAGLVGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMM 284
           + GDILSD A+ L G +GL PS +IG+   ++EP+HGSAPDIAG+GIANP A I SAAMM
Sbjct: 241 IFGDILSDEASMLSGSIGLLPSASIGEKYGLYEPIHGSAPDIAGQGIANPIATIASAAMM 300

Query: 285 LDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331
           L Y  GE+ AAKR+E A+  VL+ G RT DL      E  T + + +L
Sbjct: 301 LRYQFGEESAAKRIEDAIKRVLKEGYRTKDLSSFDAKEVVTTSEMGSL 348


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: 281
Number of extensions: 14
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: 356
Length adjustment: 29
Effective length of query: 305
Effective length of database: 327
Effective search space:    99735
Effective search space used:    99735
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 Jul 25 2024. The underlying query database was built on Jul 25 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