GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Desulfovibrio vulgaris Hildenborough

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 209413 DVU0477 isocitrate dehydrogenase, NADP-dependent

Query= SwissProt::Q58130
         (333 letters)



>MicrobesOnline__882:209413
          Length = 380

 Score =  191 bits (485), Expect = 3e-53
 Identities = 126/368 (34%), Positives = 187/368 (50%), Gaps = 51/368 (13%)

Query: 7   IEGDGIGKEVVPATIQVLEAT-------GLPFEFVYAEAGDEVYKRTGKALPEETIETAL 59
           IEGDGIG EV  A   V++A            E+    AG++ ++ TG+ LP+ T++T  
Sbjct: 8   IEGDGIGPEVWKAARPVIDAAVEKSYGDSRSIEWKELLAGEKAHRETGEYLPQSTLDTLA 67

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

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

Query: 153 ARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVA-EEYDDIKA------------ED 199
           A ++K+      +T  HK N++K T+G F++  Y+VA +E+ D+              +D
Sbjct: 188 AIDQKRPN----LTLVHKGNIMKFTEGGFREWGYEVARDEFADLTTTETEGTAGRLVVKD 243

Query: 200 YYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSANIGDEHGLFEPVH 259
              DAM   ++ +PQ + V+ TSNL GD +SD  A  VGGLGLAP  N+ D    FE  H
Sbjct: 244 RIADAMFQEVLIRPQQYSVIATSNLNGDYISDALAAQVGGLGLAPGVNMSDSLAFFEATH 303

Query: 260 GSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLALGLTTPDLGGNLNT 319
           G+AP IAG+  ANP + IL   LML ++G  EAA+++ KA+ E +A    T DL   +  
Sbjct: 304 GTAPTIAGQDKANPGSLILCGALMLEHMGWNEAAERIYKAVNEAIASRRVTVDLATQMEN 363

Query: 320 FEMAEEVA 327
                 VA
Sbjct: 364 ATTVGTVA 371


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: 272
Number of extensions: 16
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: 380
Length adjustment: 29
Effective length of query: 304
Effective length of database: 351
Effective search space:   106704
Effective search space used:   106704
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