GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Desulfovibrio vulgaris Miyazaki F

Align 3-isopropylmalate/3-methylmalate dehydrogenase; 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; IPMDH; Beta-IPM dehydrogenase; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.85; EC 1.1.1.n5; EC 1.1.1.83 (characterized)
to candidate 8501002 DvMF_1739 isocitrate/isopropylmalate dehydrogenase (RefSeq)

Query= SwissProt::Q58130
         (333 letters)



>FitnessBrowser__Miya:8501002
          Length = 382

 Score =  176 bits (446), Expect = 8e-49
 Identities = 118/360 (32%), Positives = 176/360 (48%), Gaps = 53/360 (14%)

Query: 7   IEGDGIGKEVVPATIQVLEAT-------GLPFEFVYAEAGDEVYKRTGKALPEETIETAL 59
           IEGDGIG +V  A   V++A            E+    AG++ Y  TG+ LPE T++   
Sbjct: 8   IEGDGIGPDVWKAARPVIDAAVAKTYGDARSIEWKELLAGEKAYAATGEYLPEATMQALR 67

Query: 60  DCDAVLFGAAGETAA----DVIVKLRHILDTYANIRPVKAYKGVKC--LRPD-IDYVIVR 112
             +  + G  G         + V LR  LD YA IRP++ ++G+     RPD +D V+ R
Sbjct: 68  GAELAIKGPLGTPVGKGFRSLNVTLRQTLDLYACIRPIRYFEGIMSPVKRPDLVDMVVFR 127

Query: 113 ENTEGLYKGIE--------------------AEIDEGITIATRVITEKACERIFRFAFNL 152
           ENTE +Y GIE                    A +D    +  + +T +  +R+ R A + 
Sbjct: 128 ENTEDVYAGIEYKAGTPEAKRLIDFLRNELGANVDPESAVGIKPMTARGSKRLVRRAMDF 187

Query: 153 ARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVA-EEYDD--------------IKA 197
           A  +K+      +T  HK N++K T+G F++  Y+V  +E+ D              +  
Sbjct: 188 AVAQKR----SSLTLVHKGNIMKFTEGGFREWGYEVVRDEFADAAVLEADAGGAAGKVVV 243

Query: 198 EDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSANIGDEHGLFEP 257
           +D   DAM   ++ +P  + V+ TSNL GD LSD  A  VGGLGLAP  N+ D    FE 
Sbjct: 244 KDRIADAMFQEVLIRPDQYSVIATSNLNGDYLSDALAAQVGGLGLAPGVNMSDSLAFFEA 303

Query: 258 VHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLALGLTTPDLGGNL 317
            HG+AP IAG+  ANP + IL   LML ++G  +AA ++  A+   +     T DL   +
Sbjct: 304 THGTAPTIAGQDKANPGSLILCGALMLEHMGWNDAATRIYNAINTTIGKRTVTVDLASQM 363


Lambda     K      H
   0.318    0.138    0.390 

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: 293
Number of extensions: 22
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: 333
Length of database: 382
Length adjustment: 29
Effective length of query: 304
Effective length of database: 353
Effective search space:   107312
Effective search space used:   107312
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: 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