GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Epibacterium ulvae U95

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 WP_090220500.1 CV091_RS17260 isocitrate/isopropylmalate dehydrogenase family protein

Query= SwissProt::Q58130
         (333 letters)



>NCBI__GCF_002796795.1:WP_090220500.1
          Length = 362

 Score =  219 bits (559), Expect = 6e-62
 Identities = 140/356 (39%), Positives = 200/356 (56%), Gaps = 31/356 (8%)

Query: 4   ICVIEGDGIGKEVVPATIQVLEATGLPFE-----FVYAEAGDEVYKRTGKALPEETIETA 58
           I V +GDGIG E+   T+ +L+      +     F+ A AG   Y+ TG + P+ ++  A
Sbjct: 7   IAVFQGDGIGPEITAPTVSILKTLAAASDDYGLNFIDAPAGAAHYRDTGTSFPDASMAIA 66

Query: 59  LDCDAVLFGAAG--------ETAADVIVKLRHILDTYANIRPVKAYKGVKC-----LRPD 105
            + DA+L  A G         T     + LR  L  +A +RPV    G           +
Sbjct: 67  TNADAILLSAMGLPDVRYPDGTEISPQIDLRKRLGLFAGVRPVTVRTGQTTPLNLPANKE 126

Query: 106 IDYVIVRENTEGLY--KGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGK-E 162
           ID+V++RE+TEGL+  +G   E+       T +IT +  E++FRFAF LA  RK  G+  
Sbjct: 127 IDFVLIRESTEGLFHTQGC-GEVSADEARETLLITREVSEKLFRFAFQLAHGRKAAGRGS 185

Query: 163 GKVTCAHKANVLKLTDGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTS 222
           G+VTC  KANV +     F+++F   A+ + D+ A+  Y+DA  ++++ KP  FDV+VT 
Sbjct: 186 GRVTCVDKANVFRAF-AFFREMFDAEAKNHPDLTADHAYVDATALWMVQKPWEFDVLVTE 244

Query: 223 NLFGDILSDGAAGTVGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVL 282
           N+FGDILSD  AG +GGLGLAPSA+IG  + +F+P HGSAPDIAG+ +ANP A ILSA +
Sbjct: 245 NMFGDILSDLGAGLMGGLGLAPSADIGLNNAVFQPCHGSAPDIAGQGVANPFAMILSAAM 304

Query: 283 MLRYLGEYEA-------ADKVEKALEEVLALGLT-TPDLGGNLNTFEMAEEVAKRV 330
           ML +LG           A ++  A+E V+A   T T DLGG   T   A+ V   V
Sbjct: 305 MLEWLGTSHKIAALSRDAARLRTAVEHVVADESTLTRDLGGTAGTEAAAKAVLNAV 360


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: 300
Number of extensions: 15
Number of successful extensions: 5
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: 362
Length adjustment: 29
Effective length of query: 304
Effective length of database: 333
Effective search space:   101232
Effective search space used:   101232
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 Jul 26 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