GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Marinicella litoralis KMM 3900

Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate WP_099020037.1 CCS90_RS13170 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase

Query= BRENDA::C7R702
         (374 letters)



>NCBI__GCF_002591915.1:WP_099020037.1
          Length = 370

 Score =  588 bits (1517), Expect = e-173
 Identities = 271/369 (73%), Positives = 326/369 (88%)

Query: 6   IKCKAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDPEGVFPSIL 65
           +K +AAVAWEAG+PLSIE +++Q P+ GEV +K+VATGVCHTDAFTLSG DPEG+FPS+L
Sbjct: 1   MKIRAAVAWEAGQPLSIETLDIQGPKAGEVMIKMVATGVCHTDAFTLSGADPEGIFPSVL 60

Query: 66  GHEGGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLCQKIRETQGKGLMPD 125
           GHEGG IV  +G GVTSV   DHVIPLYTPECG+C FC SGKTNLCQ IR TQG+GLMPD
Sbjct: 61  GHEGGAIVVEIGAGVTSVAVDDHVIPLYTPECGECNFCTSGKTNLCQAIRATQGQGLMPD 120

Query: 126 GTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVTTGMGAVMN 185
           GT+R S NG+ IYHYMGTSTF+EY V+PEI+LAK+N  APL++VCLLGCG+TTG+GAV+N
Sbjct: 121 GTSRLSFNGQTIYHYMGTSTFAEYAVVPEIALAKINRHAPLDKVCLLGCGITTGVGAVLN 180

Query: 186 TAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGATDCVNPKD 245
           TAKVE G+TVA+FGLGGIG   + GAVMA ASRII +DIN  KFE AK++GAT+ VNPKD
Sbjct: 181 TAKVEAGSTVAVFGLGGIGCGVIQGAVMAGASRIIGVDINPDKFEFAKQMGATEFVNPKD 240

Query: 246 YDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQEISTRP 305
           ++ PIQ+V++++TDGGVDYSFEC+GNV +MRSALECCHKGWGESVIIGVAGAGQEI+TRP
Sbjct: 241 HELPIQDVLIDLTDGGVDYSFECVGNVELMRSALECCHKGWGESVIIGVAGAGQEIATRP 300

Query: 306 FQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKINDAFDLMHEG 365
           FQLVTGRVW+G+AFGGVKGRS+LP  V++Y+AGE K+D+F++HTMPL+KIN+AFDLMH G
Sbjct: 301 FQLVTGRVWRGSAFGGVKGRSQLPGMVDQYMAGELKVDEFVSHTMPLDKINEAFDLMHAG 360

Query: 366 KSIRSVIHY 374
             IRSVI +
Sbjct: 361 NGIRSVITF 369


Lambda     K      H
   0.317    0.137    0.413 

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: 562
Number of extensions: 15
Number of successful extensions: 1
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: 374
Length of database: 370
Length adjustment: 30
Effective length of query: 344
Effective length of database: 340
Effective search space:   116960
Effective search space used:   116960
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 (21.6 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