GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Pandoraea thiooxydans ATSB16

Align NADH-dependent aldehyde reductase (EC 1.1.1.77; EC 1.1.1.244; EC 1.1.1.1) (characterized)
to candidate WP_047214240.1 PATSB16_RS11390 SDR family oxidoreductase

Query= metacyc::G3O-32155-MONOMER
         (298 letters)



>NCBI__GCF_001931675.1:WP_047214240.1
          Length = 330

 Score =  220 bits (560), Expect = 4e-62
 Identities = 131/317 (41%), Positives = 179/317 (56%), Gaps = 25/317 (7%)

Query: 1   MKVFITGASGFIGSAVLSELISSGHEVVGLARSDEAAAKIKSIDPAAKILRGDLKDLEIL 60
           M+VF+TGASGFIG AV+ EL+++GHEV GLARS  AAAK+ +    A + RG ++DL  L
Sbjct: 1   MRVFVTGASGFIGFAVVRELVAAGHEVTGLARSAAAAAKLAAT--GATVQRGSIEDLGTL 58

Query: 61  KKGATESDGVIHLGFVHDFKN----------------------FEQCCEIDRQATVAMLE 98
           ++ A+++DGVIH  F H F                             E DR A   +  
Sbjct: 59  REAASKADGVIHTAFFHAFSQAGFGTRMRVMLGGMPTGLVRRFMVAAVEADRLAIDTLGH 118

Query: 99  SLKGSNKPFLYTNGTLSLRPNKVANEQDGIDEDSKI-LRAVTEQVALSYKDKGVSARIVR 157
           +L+   +P +    T+++R  + A E D  D D+   LRA  E+ AL+    GV A ++R
Sbjct: 119 ALRAQARPLVIAFPTMAMRQGRPAVETDFADPDAVGGLRARCEKAALALAGCGVDATVIR 178

Query: 158 LPFSVHGKGDKAFVPILMNIAKAAGKSGYVGQGTNAWAAVHRLDTAPLFRLVLEKGKTGQ 217
           LP SVH +  +  V  L+ IA+    S YVG G N WAAVHRLD + LFRL LE GK G 
Sbjct: 179 LPPSVHDQTRQGLVTQLVAIARKKRVSAYVGDGQNRWAAVHRLDASHLFRLALEDGKAGA 238

Query: 218 VYHCVGEQGIPFKDIARVIGEILNVPVASIPVDDAESHFGFLTCFVTRDGPVSSEGTRKE 277
            YH V E+GI   ++A  IG+ L V   S+   +A  HFG+L  FV  D PVSS  TR++
Sbjct: 239 RYHAVAEEGITLSELAGAIGQHLGVRTVSLTPVEAVRHFGWLAPFVGADNPVSSRATREQ 298

Query: 278 LGWQPQQIGLLEDIRAN 294
           L WQP +  L+ D+ A+
Sbjct: 299 LHWQPTRPSLMTDLAAS 315


Lambda     K      H
   0.318    0.136    0.393 

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: 241
Number of extensions: 8
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: 298
Length of database: 330
Length adjustment: 27
Effective length of query: 271
Effective length of database: 303
Effective search space:    82113
Effective search space used:    82113
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: 48 (23.1 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