GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Nocardiopsis lucentensis DSM 44048

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_017598162.1 D471_RS0108155 3-isopropylmalate dehydrogenase

Query= SwissProt::P9WKK9
         (336 letters)



>NCBI__GCF_000341125.1:WP_017598162.1
          Length = 354

 Score =  420 bits (1079), Expect = e-122
 Identities = 220/343 (64%), Positives = 258/343 (75%), Gaps = 9/343 (2%)

Query: 1   MKLAIIAGDGIGPEVTAEAVKVLDAVVP----GVQKTSYDLGARRFHATGEVLPDSVVAE 56
           + LA+I GDGIGPEV  E +KVL+AV P     ++ T Y+LGA+ +H TGE LPDSV  E
Sbjct: 6   VNLAVIPGDGIGPEVVGEGLKVLEAVAPQHDLAIEATEYELGAKLWHRTGETLPDSVEDE 65

Query: 57  LRNHDAILLGAIGDPSVPSGVLERGLLLRLRFELDHHINLRPARLYPGVASPLSG--NPG 114
           LR H+AILLGA+GDPSVPSGVLERGLLLRLRF+ DH++NLRP RL+PGV SPL+G     
Sbjct: 66  LREHEAILLGAVGDPSVPSGVLERGLLLRLRFDFDHYVNLRPVRLFPGVDSPLAGVSPED 125

Query: 115 IDFVVVREGTEGPYTGNGGAIRVGTPNEVATEVSVNTAFGVRRVVADAFERAR-RRRKHL 173
           ID +VVREGTEGPY G GG +R GTP+E+AT+ SVNT FGV RVV  AF +A  R RK L
Sbjct: 126 IDMLVVREGTEGPYAGAGGVLRKGTPHEIATQDSVNTRFGVERVVRYAFAKAAVRPRKKL 185

Query: 174 TLVHKTNVLTFAGGLWLRTVDEVGECYPDVEVAYQHVDAATIHMITDPGRFDVIVTDNLF 233
           TLVHK NVLTFAG LW R V EVG  YP V V Y HVDAA +  +  P RFDV+VTDNLF
Sbjct: 186 TLVHKDNVLTFAGDLWQRVVREVGAEYPQVSVDYCHVDAAAMFFVNQPARFDVVVTDNLF 245

Query: 234 GDIITDLAAAVCGGIGLAASGNIDATRANPSMFEPVHGSAPDIAGQGIADPTAAIMSVAL 293
           GDIITD+ AAV GGIGLAASGN++     PSMFEPVHGSAPDIAGQG ADPTA ++SVA 
Sbjct: 246 GDIITDIGAAVTGGIGLAASGNVNPDNTFPSMFEPVHGSAPDIAGQGKADPTATVLSVAT 305

Query: 294 LLSHLGEHDAAARVDRAVEAHLATR--GSERLATSDVGERIAA 334
           +L HLG  +AA R++ AV A L TR  G    +TS +G+ +AA
Sbjct: 306 MLDHLGVPEAARRIEGAVAADLKTRAQGGAARSTSQIGDDLAA 348


Lambda     K      H
   0.319    0.137    0.398 

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: 415
Number of extensions: 19
Number of successful extensions: 4
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: 336
Length of database: 354
Length adjustment: 29
Effective length of query: 307
Effective length of database: 325
Effective search space:    99775
Effective search space used:    99775
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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