GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Sphingopyxis indica DS15

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_089216565.1 CHB69_RS13635 Zn-dependent alcohol dehydrogenase

Query= BRENDA::P00326
         (375 letters)



>NCBI__GCF_900188185.1:WP_089216565.1
          Length = 363

 Score =  261 bits (667), Expect = 2e-74
 Identities = 149/367 (40%), Positives = 207/367 (56%), Gaps = 10/367 (2%)

Query: 11  KAAVLWELKKPFSIEEVEVAPPKAHEVRIKMVAAGICRSDEHVVSGNLVTPLPVILGHEA 70
           KAAVL E  KP  +EEV V  P  HEVRI+  A G+C SD H + G    PLP I GHEA
Sbjct: 3   KAAVLIEPGKPLIVEEVVVDKPGPHEVRIRTAACGLCHSDLHFIDGAYPHPLPAIPGHEA 62

Query: 71  AGIVESVGEGVTTVKPGDKVIPLFTPQCGKCRICKNPESNYCLKNDLGNPRGTLQDGTRR 130
           AGIVE+VG  V TVKPGD V+   +  CG C  C     + C+  D     G     TR 
Sbjct: 63  AGIVEAVGSEVRTVKPGDAVVTCLSAFCGHCEFCVTGRMSLCMGGDTRRAPGEPPRITRP 122

Query: 131 FTCSGKPIHHFVGVSTFSQYTVVDENAVAKIDAASPLEKVCLIGCGFSTGYGSAVKVAKV 190
               G  ++  + +S FS+  +V E+A   ID   PL++  +IGC  +TG G+     K+
Sbjct: 123 ---DGSVVNQMLNLSAFSEVMLVHEHACVAIDPDMPLDRAAVIGCAVTTGAGTIFNACKL 179

Query: 191 TPGSTCAVFGLGGVGLSVVMGCKAAGAARIIAVDINKDKFAKAKELGATECIN--PQDYK 248
           TPG T AV G GGVGL+ +   K AGA RIIA D   +K A A++LGAT+ ++    D  
Sbjct: 180 TPGETVAVVGCGGVGLATINAAKIAGAGRIIAADPVPEKRALAEKLGATDTVDALADDAA 239

Query: 249 KPIQEVLKEMTDGGVDFSFEVIGRLDTMMASLLCCHEACGTSVIVGVPPDSQNLSINPML 308
           K I     EMT GGVD + E +GR  +   ++       GT+ I+G+ P ++ + +  M 
Sbjct: 240 KQI----VEMTRGGVDHAIEAVGRPASASLAVASLRRG-GTATILGMMPLAEKVGLGAMD 294

Query: 309 LLTGRTWKGAIFGGFKSKESVPKLVADFMAKKFSLDALITNILPFEKINEGFDLLRSGKS 368
           LL+G+  +GAI GG +    +P+LV  ++     LD+++   +P EKINEGFD ++ G S
Sbjct: 295 LLSGKKLQGAIMGGNRFPVDIPRLVDFYLRGLLDLDSIVAETIPLEKINEGFDKMKKGDS 354

Query: 369 IRTVLTF 375
            R+V+ F
Sbjct: 355 ARSVIVF 361


Lambda     K      H
   0.320    0.137    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: 376
Number of extensions: 20
Number of successful extensions: 5
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: 375
Length of database: 363
Length adjustment: 30
Effective length of query: 345
Effective length of database: 333
Effective search space:   114885
Effective search space used:   114885
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: 49 (23.5 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