GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Paenisporosarcina indica PN2

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_075617952.1 GY23_RS04320 glutathione-dependent formaldehyde dehydrogenase

Query= BRENDA::B2ZRE3
         (347 letters)



>NCBI__GCF_001939075.1:WP_075617952.1
          Length = 378

 Score =  217 bits (552), Expect = 4e-61
 Identities = 132/376 (35%), Positives = 194/376 (51%), Gaps = 33/376 (8%)

Query: 1   MRAVVFENKERVAVKEVNAPRLQHPLDALVRVHLAGICGSDLHLYHGKIPVLPGS-VLGH 59
           M+AV F+  + V VK V  P +Q   D +V++    ICGSDLHL HG IP L    V+GH
Sbjct: 1   MKAVTFQGVKNVQVKNVKDPSIQKADDIIVKLTTTAICGSDLHLIHGMIPNLGEDYVIGH 60

Query: 60  EFVGQVEAVGEGIQDLQPGDWVVGPFHIACGTCPYCRRHQYNLC-------ERGGVYGYG 112
           E +G VE VG+ +  ++ GD V+ PF+IACG C YC     + C       E G  +GY 
Sbjct: 61  EPMGIVEEVGKDVTKVKKGDRVIIPFNIACGQCWYCNHELESQCDNANENGEMGAYFGYS 120

Query: 113 PMFGNLQGAQAEILRVPFSNVNLRKLPPN--LSPERAIFAGDILSTAYGGLIQGQLRPGD 170
              G   G QAE +RVP++N    K+P N  ++ E  +   D  STA+  +    ++ GD
Sbjct: 121 DTTGGFPGGQAEFMRVPYANFTPFKIPENSEVADESLVLLADAASTAFWSVDNAGVKAGD 180

Query: 171 SVAVIGAGPVGLMAIEVAQVLGASKILAIDRIPERLERAASLGAIPI-NAEQENPVRRVR 229
           +V ++G GPVGL+A + A + GA +++A+D +  RL+ A     + I N E         
Sbjct: 181 TVVILGCGPVGLLAQKFAWLKGAKRVIAVDYVGYRLKHAKRTNKVEIVNFEDHENCGEYL 240

Query: 230 SETNDEGPDLVLEAVG--------------------GAATLSLALEMVRPGGRVSAVGVD 269
            E    G D+V++ VG                        L +A + VR GG +   GV 
Sbjct: 241 REITQGGADVVIDCVGMSGKMTPLEFLASGLKLQGGAMGALVIASQAVRKGGTIQITGVY 300

Query: 270 NAPSFPFPLASGLVKDLTFRIGLANVHLYIDAVLALLASGRLQPERIVSHYLPLEEAPRG 329
            A    FPL     +++  R G A V  Y+  +  L+A G++ P  IV+H LPL++A  G
Sbjct: 301 GARYNAFPLGDIFQRNVNIRTGQAPVIHYMQHLYNLIAEGKVDPSDIVTHVLPLDQAKHG 360

Query: 330 YELFDRK--EALKVLL 343
           YE+FD K  + +KV+L
Sbjct: 361 YEVFDTKMEDCIKVVL 376


Lambda     K      H
   0.321    0.141    0.420 

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: 373
Number of extensions: 19
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: 347
Length of database: 378
Length adjustment: 29
Effective length of query: 318
Effective length of database: 349
Effective search space:   110982
Effective search space used:   110982
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