GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Neptunomonas antarctica S3-22

Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate WP_054343403.1 Nant_RS19780 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase

Query= BRENDA::C7R702
         (374 letters)



>NCBI__GCF_001305295.1:WP_054343403.1
          Length = 376

 Score =  685 bits (1767), Expect = 0.0
 Identities = 327/374 (87%), Positives = 355/374 (94%)

Query: 1   MSNEVIKCKAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDPEGV 60
           M+N+ IK KAA+AW   +PLSIEEV+V PPQKGEVRV+IVA+GVCHTDAFTLSGDDPEG+
Sbjct: 1   MNNKTIKSKAAIAWGPNQPLSIEEVDVMPPQKGEVRVRIVASGVCHTDAFTLSGDDPEGI 60

Query: 61  FPSILGHEGGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLCQKIRETQGK 120
           FP+ILGHEG GIVES+GEGVTSV  GDHVIPLYTPECG+CKFC SGKTNLCQKIRETQGK
Sbjct: 61  FPAILGHEGAGIVESIGEGVTSVAVGDHVIPLYTPECGECKFCKSGKTNLCQKIRETQGK 120

Query: 121 GLMPDGTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVTTGM 180
           GLMPDGTTRF  +G+PI+HYMG STFSEYTVLPEISLAKVN  APLEE+CLLGCGVTTGM
Sbjct: 121 GLMPDGTTRFHKDGQPIFHYMGCSTFSEYTVLPEISLAKVNKDAPLEEICLLGCGVTTGM 180

Query: 181 GAVMNTAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGATDC 240
           GAVMNTAKVEEGATVAIFG+GGIGLSA+IGA MAKASRIIAIDINESKFELA+KLGATDC
Sbjct: 181 GAVMNTAKVEEGATVAIFGIGGIGLSAIIGATMAKASRIIAIDINESKFELARKLGATDC 240

Query: 241 VNPKDYDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQE 300
           +NPKDYDKPIQ+VIVE+TDGGVDYSFECIGNVNVMRSALECCHKGWGESV+IGVAGAGQE
Sbjct: 241 INPKDYDKPIQDVIVELTDGGVDYSFECIGNVNVMRSALECCHKGWGESVVIGVAGAGQE 300

Query: 301 ISTRPFQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKINDAFD 360
           ISTRPFQLVTGRVW+G+AFGGVKGRSELPD+VERY+ GEFKLDDFITHTM LE+IN AFD
Sbjct: 301 ISTRPFQLVTGRVWRGSAFGGVKGRSELPDFVERYMKGEFKLDDFITHTMTLEEINTAFD 360

Query: 361 LMHEGKSIRSVIHY 374
           LMHEGKSIRSVIH+
Sbjct: 361 LMHEGKSIRSVIHF 374


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: 653
Number of extensions: 16
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: 374
Length of database: 376
Length adjustment: 30
Effective length of query: 344
Effective length of database: 346
Effective search space:   119024
Effective search space used:   119024
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: 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