GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Caldicellulosiruptor hydrothermalis 108

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_013402459.1 CALHY_RS02575 SDR family oxidoreductase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_000166355.1:WP_013402459.1
          Length = 255

 Score =  124 bits (311), Expect = 2e-33
 Identities = 91/267 (34%), Positives = 134/267 (50%), Gaps = 35/267 (13%)

Query: 9   KGLVAVITGGASGLGLATAERLVGQGASAVL----LDLPNSGGEA--QAKKLGNNCVFAP 62
           K  V +ITG  SG+G  TA      GA   +    L+   +G     + +K+G  C+F  
Sbjct: 4   KDKVVLITGATSGIGRTTAVLYAKYGAKVAVNGRELNKDKNGETTIDEIRKIGGECIFIQ 63

Query: 63  ADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNL 122
            DV+   D Q  +     K+G++D+ VN AGI +  +  N+ +      EDF + + VN+
Sbjct: 64  GDVSKNDDAQRIVMETVEKYGKIDILVNNAGIVLPGRVDNMSE------EDFDKTMAVNV 117

Query: 123 MGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPI 182
            G F V +    +M +    QG  +GVI+N ASVAA +G   ++AYSASKG IV +T  +
Sbjct: 118 KGAFLVSKYAVLQMKK----QG--KGVIVNVASVAALKGHTDRSAYSASKGAIVSLTKAM 171

Query: 183 ARDLAPIGIRVMTIAPGLFGTPLLTSLPEKVCN----------FLASQVPFPSRLGDPAE 232
           A D     IRV  + P   GT L  ++ EK+ N          F+A Q     RLG P E
Sbjct: 172 AADYVKDNIRVNCVCP---GTTLTPAVEEKIVNAPDPEAMRAAFIARQP--MGRLGRPEE 226

Query: 233 --YAHLVQAIIENPFLNGEVIRLDGAI 257
             +A L  +  E  F+NG +I +DG +
Sbjct: 227 IAFAILFASCDEAEFMNGSIIVIDGGM 253


Lambda     K      H
   0.318    0.135    0.385 

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: 184
Number of extensions: 12
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: 261
Length of database: 255
Length adjustment: 24
Effective length of query: 237
Effective length of database: 231
Effective search space:    54747
Effective search space used:    54747
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: 41 (21.7 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