GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Caldicellulosiruptor hydrothermalis 108

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_013402600.1 CALHY_RS03340 3-isopropylmalate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>NCBI__GCF_000166355.1:WP_013402600.1
          Length = 355

 Score =  208 bits (529), Expect = 2e-58
 Identities = 138/337 (40%), Positives = 197/337 (58%), Gaps = 29/337 (8%)

Query: 3   YRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETVEK 58
           +RI +I GDGIG EVI  A  VL+      G+  E++  +AG    ++ G  + EE +E 
Sbjct: 2   HRIAVIPGDGIGPEVIEQALIVLDKISSKFGVKFEYIFIDAGGCAIDKYGVPIREEDLEL 61

Query: 59  ILSCHATLFGAATSPTRKVPGFFGAIR------YLRRRLDLYANVRPA-------KSRPV 105
           +  C ATL GA   P  K  G  G +R       LR  L +YAN+RPA        S P+
Sbjct: 62  VKKCEATLLGAVGGP--KWDGLPGNLRPEQALLKLRGGLKVYANLRPAVLYDELKDSSPL 119

Query: 106 PGS--RPGVDLVIVRENTEGLYVEQERRYL----DVAIADAVISKKASERIGRAALRIAE 159
                  G+D+++VRE   G+Y   + R +    +VA    V SK    RI + A   A 
Sbjct: 120 KKEIVDKGIDILVVRELIGGMYFGPKGREVKDGDEVAYDTEVYSKSEVRRIAKVAFEAAR 179

Query: 160 GRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDV 219
            R +K   +  KAN+L  ++ L+ +TV+EVAKD+P V +  + VDN +MQLV  P +FDV
Sbjct: 180 KRKKKVTSV-DKANILESSR-LWRETVEEVAKDYPDVELSHMYVDNASMQLVKDPSQFDV 237

Query: 220 IVTTNLLGDILSDLAAGLVGGLGLAPSGNIGD-TTAVFEPVHGSAPDIAGKGIANPTAAI 278
           I+T+N+ GDILSD A+ +VG +G+  S ++G+    ++EP+HG+APDIAG+ +ANP A I
Sbjct: 238 ILTSNMFGDILSDEASMIVGSIGMLASASLGEGRVGLYEPIHGTAPDIAGQDLANPIATI 297

Query: 279 LSAAMMLDYLGEKE-AAKRVEKAVDLVLERGPRTPDL 314
           LSAAMML Y  + E AAK +E AV + L+ G RT D+
Sbjct: 298 LSAAMMLRYSFDMEDAAKAIENAVKIALKEGYRTRDI 334


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: 278
Number of extensions: 15
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: 334
Length of database: 355
Length adjustment: 29
Effective length of query: 305
Effective length of database: 326
Effective search space:    99430
Effective search space used:    99430
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 Sep 24 2021. 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