GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Caldicellulosiruptor hydrothermalis 108

Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate WP_013402451.1 CALHY_RS02540 fumarylacetoacetate hydrolase family protein

Query= metacyc::MONOMER-16233
         (285 letters)



>NCBI__GCF_000166355.1:WP_013402451.1
          Length = 253

 Score =  164 bits (415), Expect = 2e-45
 Identities = 99/273 (36%), Positives = 147/273 (53%), Gaps = 29/273 (10%)

Query: 3   FCRFGQRGQEKPGIIDADGKIRDLSGVVPELTIEALAAAKGAD--VASLPLVEGEPRYGV 60
           FCRF           + D KI    G+V +  ++++      D  V +   + GE +   
Sbjct: 4   FCRF-----------EKDNKIN--YGIVKDNIVQSIEGNIFGDWKVGNESYLLGEVKLLP 50

Query: 61  PVKGIGKIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEVVLPKNSTHGDWEV 120
           PV+   KIV +GLNY       N  +P EP++F+K  S++ G  D ++ P +     +EV
Sbjct: 51  PVEP-SKIVCVGLNYHSTIKRLNAAVPEEPVIFLKPPSAIIGDGDNIIFPSDVKELGYEV 109

Query: 121 ELGVVIGETCRFVSEDEALSKVAGYVLVNDVSERFNQKQRGTQWSKGKGHDTFCPVGPWL 180
           EL V+I +  + V+ +EAL  V GY + ND++ +   K  G  W+K K +DTF P+GPW+
Sbjct: 110 ELAVIIKDKIKSVNYNEALKHVFGYTIANDLTAK--DKMTGGPWTKAKSYDTFLPLGPWI 167

Query: 181 VTPDEVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPP 240
            T     DP +  + + +NG   Q GNT  M+F+VA LISY+S+ +TL PGD++ITGTPP
Sbjct: 168 ATDL---DPNNAKLEMYINGNMTQNGNTSDMVFDVAYLISYISKIMTLCPGDVIITGTPP 224

Query: 241 GVGEGKKPQAIYLKAGDVMELGIEKLGTQRQQV 273
           G G         L  GD +E  IE +G  R  V
Sbjct: 225 GAG--------LLNPGDYVEAKIEGIGVLRNYV 249


Lambda     K      H
   0.316    0.137    0.411 

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: 266
Number of extensions: 14
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: 285
Length of database: 253
Length adjustment: 25
Effective length of query: 260
Effective length of database: 228
Effective search space:    59280
Effective search space used:    59280
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: 42 (22.0 bits)
S2: 47 (22.7 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