GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Halococcus hamelinensis 100A6

Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate WP_007690519.1 C447_RS02350 fumarylacetoacetate hydrolase family protein

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



>NCBI__GCF_000336675.1:WP_007690519.1
          Length = 242

 Score =  163 bits (412), Expect = 4e-45
 Identities = 85/208 (40%), Positives = 127/208 (61%), Gaps = 11/208 (5%)

Query: 67  KIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEVVLPKNSTHGDWEVELGVVI 126
           KIV IGLNY DHA E  + +P  P++F+K  ++++G  D V LP+     + E EL VVI
Sbjct: 45  KIVCIGLNYADHAEEEGMDLPDRPLLFLKPPNAVSGHGDTVTLPEGKEKVEHEAELAVVI 104

Query: 127 GETCRFVSEDEALSKVAGYVLVNDVSERFNQKQRGTQWSKGKGHDTFCPVGPWLVTPDEV 186
           GE CR V+ D+A+  VAG+   +DVS R +Q+     W +GK  D  CP+GP L  P++V
Sbjct: 105 GEQCRNVAADDAMDVVAGFTCADDVSNRDDQRVE-QNWVRGKAFDNACPLGPVLADPEDV 163

Query: 187 GDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPPGVGEGK 246
             P D  + L +NG  +Q+ +    +F+V +LI  +++Y+TL  GD++ITGTP GVGE  
Sbjct: 164 --PDDASVELRLNGETVQSSSRAEFVFSVPELIEEITQYMTLEAGDVIITGTPAGVGE-- 219

Query: 247 KPQAIYLKAGDVMELGIEKLGTQRQQVS 274
                 L+ GD +E+ +E +GT    V+
Sbjct: 220 ------LEDGDEVEVEVEGVGTLEHTVA 241


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: 232
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: 285
Length of database: 242
Length adjustment: 25
Effective length of query: 260
Effective length of database: 217
Effective search space:    56420
Effective search space used:    56420
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