GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Pseudomonas fluorescens FW300-N1B4

Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate Pf1N1B4_3108 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)

Query= BRENDA::C7R702
         (374 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3108
           S-(hydroxymethyl)glutathione dehydrogenase (EC
           1.1.1.284)
          Length = 370

 Score =  611 bits (1576), Expect = e-180
 Identities = 295/370 (79%), Positives = 333/370 (90%)

Query: 5   VIKCKAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDPEGVFPSI 64
           +IK +AAVA+EA KPL I EV+V  P+ GEV +++VA+GVCHTDA+TLSG DPEG+FPSI
Sbjct: 1   MIKSRAAVAFEAKKPLEIVEVDVAMPKAGEVLLRVVASGVCHTDAYTLSGADPEGIFPSI 60

Query: 65  LGHEGGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLCQKIRETQGKGLMP 124
           LGHEGG +VE++GEGVTSV  GDHVIPLYTPECG CKFCLSGKTNLCQ IR TQGKGLMP
Sbjct: 61  LGHEGGAVVEAIGEGVTSVAVGDHVIPLYTPECGKCKFCLSGKTNLCQAIRATQGKGLMP 120

Query: 125 DGTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVTTGMGAVM 184
           DGT+RFS  G+ I+HYMGTSTFSEYTVLPEIS+AK+  +APLE+VCLLGCGVTTG+GAV+
Sbjct: 121 DGTSRFSYKGETIFHYMGTSTFSEYTVLPEISVAKIPKEAPLEKVCLLGCGVTTGIGAVI 180

Query: 185 NTAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGATDCVNPK 244
           NTAKV+ G TVAIFGLGGIGLSAVIGAV AKA RIIAIDIN +KFE+AK+LGATDCVNPK
Sbjct: 181 NTAKVKPGDTVAIFGLGGIGLSAVIGAVKAKAGRIIAIDINPAKFEIAKQLGATDCVNPK 240

Query: 245 DYDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQEISTR 304
           D+D+PIQEVIV+MTDGGVD+SFECIGNV +MR+ALECCHKGWGESVIIGVAGAGQEISTR
Sbjct: 241 DFDRPIQEVIVDMTDGGVDFSFECIGNVQLMRAALECCHKGWGESVIIGVAGAGQEISTR 300

Query: 305 PFQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKINDAFDLMHE 364
           PFQLVTGRVW+G+AFGGV+GR+ELP YVE    GE  LD FITHTM LE IN AFDLMHE
Sbjct: 301 PFQLVTGRVWRGSAFGGVRGRTELPSYVEMAQTGEIPLDTFITHTMGLEDINKAFDLMHE 360

Query: 365 GKSIRSVIHY 374
           GKSIRSVIH+
Sbjct: 361 GKSIRSVIHF 370


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: 598
Number of extensions: 18
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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