GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Leptospirillum ferrooxidans C2-3

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_014448976.1 LFE_RS03940 isocitrate/isopropylmalate dehydrogenase family protein

Query= SwissProt::Q58130
         (333 letters)



>NCBI__GCF_000284315.1:WP_014448976.1
          Length = 336

 Score =  239 bits (610), Expect = 7e-68
 Identities = 138/332 (41%), Positives = 190/332 (57%), Gaps = 9/332 (2%)

Query: 2   HKICVIEGDGIGKEVVPATIQVLEATGLPFEFVYAEAGDEVYKRTGKALPEETIETALDC 61
           H I ++ G+G G E+  A  +V++ +G+   + Y E G +  K  G  LPE+TI++    
Sbjct: 4   HVITMLPGEGTGPEICEAVRRVIDHSGVDITWEYEEIGLDCLKEHGTLLPEKTIKSIAKN 63

Query: 62  DAVLFGAA----GETAADVIVKLRHILDTYANIRPVKAYKGVKCLRPDIDYVIVRENTEG 117
              + G      G       V LR + D YAN+RP K    +K     ID +  RENTE 
Sbjct: 64  KIAIKGPTTTPVGTGHKSANVTLRKMFDLYANVRPAKLIPVLKRPWDKIDILSFRENTED 123

Query: 118 LYKGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKANVLKLT 177
            Y  IE  + + +    +VIT     RI  FAF  AR   +     K+ C HKAN++K+T
Sbjct: 124 SYAAIEHMVSDEVAQCLKVITWPGSIRIAEFAFKWARANNRK----KMQCVHKANIMKMT 179

Query: 178 DGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTV 237
           DGLF + F +VA+ Y DI AED  +D  +M ++  P  FD +V  NL+GDILSD  AG V
Sbjct: 180 DGLFLEAFREVAKNYPDIVAEDIIVDNCSMQLVRNPGQFDCLVLPNLYGDILSDLCAGLV 239

Query: 238 GGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVE 297
           GGLG AP ANIGD   +FE VHGSAP  AG K  NP+A +LS V+ML++L E+EAA ++E
Sbjct: 240 GGLGFAPGANIGDNCSIFEAVHGSAPKYAGMKKVNPSAVLLSGVMMLKWLNEHEAATRIE 299

Query: 298 KALEEVLALGL-TTPDLGGNLNTFEMAEEVAK 328
           K +++VLA     T D GG  +T E A+ + K
Sbjct: 300 KGVDKVLAEAKHLTYDAGGTASTDEYADAIIK 331


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: 304
Number of extensions: 13
Number of successful extensions: 3
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: 336
Length adjustment: 28
Effective length of query: 305
Effective length of database: 308
Effective search space:    93940
Effective search space used:    93940
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 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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