GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Gracilibacillus halophilus YIM-C55.5

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_003470113.1 J416_RS10100 iron-containing alcohol dehydrogenase

Query= BRENDA::A4ISB9
         (387 letters)



>NCBI__GCF_000359605.1:WP_003470113.1
          Length = 388

 Score =  539 bits (1389), Expect = e-158
 Identities = 253/388 (65%), Positives = 316/388 (81%), Gaps = 1/388 (0%)

Query: 1   MQNFTFRNPTKLIFGRGQIEQLKEEVPKYGKKVLLVYGGGSIKRNGLYDEVMSLLTDIGA 60
           M+NF F NPTKL FG  QIEQLK E+ +YG+ +L+VYGGGSIKRNGLYDEV ++L D G 
Sbjct: 1   MENFAFYNPTKLYFGSDQIEQLKHEIEQYGQNILMVYGGGSIKRNGLYDEVTNILKDAGK 60

Query: 61  EVVELPGVEPNPRLSTVKKGVDICRREGIEFLLAVGGGSVIDCTKAIAAGAKFDGDPWEF 120
            + EL GVEPNPR++T +KG+++C+ E I+F+LAVGGGS IDCTKAIAAGA  D D W+ 
Sbjct: 61  HIFELSGVEPNPRVTTARKGIELCKSENIDFILAVGGGSTIDCTKAIAAGAVTDADIWDI 120

Query: 121 ITKKATVTEALPFGTVLTLAATGSEMNAGSVITNWETKEKYGWGSPVTFPQFSILDPTYT 180
           +TKK   T +LPFGT+LTLAATGSEMNAGSVITNWETKEK+GWGSP +FP FSILDP YT
Sbjct: 121 VTKKEQATGSLPFGTILTLAATGSEMNAGSVITNWETKEKHGWGSPYSFPAFSILDPAYT 180

Query: 181 MTVPKDHTVYGIVDMMSHVFEQYFHHTPNTPLQDRMCEAVLKTVIEAAPKLVDDLENYEL 240
            +VP+  TVYG+VD+MSH  E YFHH  NT LQDRM E +L+TVIE APKL++DLEN   
Sbjct: 181 KSVPEHQTVYGMVDIMSHALEHYFHHEENTLLQDRMVEGILQTVIETAPKLLEDLENETH 240

Query: 241 RETIMYSGTIALNGFLQMGVRGDWATHDIEHAVSAVYDIPHAGGLAILFPNWMKHVLDEN 300
           R TI+Y+GT+ALNG + MG +GDWATH++EHAVSAV+DIPH GGLAILFP+WM++ +DEN
Sbjct: 241 RATILYNGTMALNGMVNMGYKGDWATHNLEHAVSAVHDIPHGGGLAILFPHWMEYAIDEN 300

Query: 301 VSRFAQLAVRVFDVDPTGKTERDVALEGIERLRAFWSSLGAPSRLADYGIGEENLELMAD 360
           V RF QLAVRVFDVD  GK+++++ LEGI++LR FW+SLGAPS L DY I E+++  MAD
Sbjct: 301 VDRFKQLAVRVFDVDTEGKSDKEIGLEGIQKLRDFWNSLGAPSSLGDYDITEDSIPEMAD 360

Query: 361 K-AMAFGEFGRFKTLNRDDVLAILRASL 387
           +  +A  +FG FK+LNR+D +AI + +L
Sbjct: 361 RTVIARDQFGNFKSLNREDAVAIYQKAL 388


Lambda     K      H
   0.320    0.138    0.412 

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: 569
Number of extensions: 14
Number of successful extensions: 2
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: 387
Length of database: 388
Length adjustment: 30
Effective length of query: 357
Effective length of database: 358
Effective search space:   127806
Effective search space used:   127806
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 (21.8 bits)
S2: 50 (23.9 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