GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Nocardiopsis lucentensis DSM 44048

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_017598162.1 D471_RS0108155 3-isopropylmalate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>NCBI__GCF_000341125.1:WP_017598162.1
          Length = 354

 Score =  209 bits (533), Expect = 6e-59
 Identities = 134/318 (42%), Positives = 186/318 (58%), Gaps = 23/318 (7%)

Query: 5   ICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETVEKIL 60
           + +I GDGIG EV+    +VLEA      L +E  E E G + + R G ++P+   +++ 
Sbjct: 8   LAVIPGDGIGPEVVGEGLKVLEAVAPQHDLAIEATEYELGAKLWHRTGETLPDSVEDELR 67

Query: 61  SCHATLFGAATSPTRKVPGFF---GAIRYLRRRLDLYANVRPAK-----SRPVPGSRP-G 111
              A L GA   P+  VP      G +  LR   D Y N+RP +       P+ G  P  
Sbjct: 68  EHEAILLGAVGDPS--VPSGVLERGLLLRLRFDFDHYVNLRPVRLFPGVDSPLAGVSPED 125

Query: 112 VDLVIVRENTEGLY-----VEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRKTL 166
           +D+++VRE TEG Y     V ++    ++A  D+V ++   ER+ R A   A  RPRK L
Sbjct: 126 IDMLVVREGTEGPYAGAGGVLRKGTPHEIATQDSVNTRFGVERVVRYAFAKAAVRPRKKL 185

Query: 167 HIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTNLL 226
            + HK NVL     L+   V+EV  ++P V+V    VD  AM  V +P RFDV+VT NL 
Sbjct: 186 TLVHKDNVLTFAGDLWQRVVREVGAEYPQVSVDYCHVDAAAMFFVNQPARFDVVVTDNLF 245

Query: 227 GDILSDLAAGLVGGLGLAPSGNIG-DTT--AVFEPVHGSAPDIAGKGIANPTAAILSAAM 283
           GDI++D+ A + GG+GLA SGN+  D T  ++FEPVHGSAPDIAG+G A+PTA +LS A 
Sbjct: 246 GDIITDIGAAVTGGIGLAASGNVNPDNTFPSMFEPVHGSAPDIAGQGKADPTATVLSVAT 305

Query: 284 MLDYLGEKEAAKRVEKAV 301
           MLD+LG  EAA+R+E AV
Sbjct: 306 MLDHLGVPEAARRIEGAV 323


Lambda     K      H
   0.319    0.137    0.391 

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: 327
Number of extensions: 16
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: 334
Length of database: 354
Length adjustment: 29
Effective length of query: 305
Effective length of database: 325
Effective search space:    99125
Effective search space used:    99125
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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