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_075619871.1 GY23_RS14175 glutathione-dependent formaldehyde dehydrogenase

Query= BRENDA::B2ZRE3
         (347 letters)



>NCBI__GCF_001939075.1:WP_075619871.1
          Length = 379

 Score =  212 bits (539), Expect = 1e-59
 Identities = 125/377 (33%), Positives = 198/377 (52%), Gaps = 34/377 (9%)

Query: 1   MRAVVFENKERVAVKEVNAPRLQHPLDALVRVHLAGICGSDLHLYHGKIPVLPGSVLGHE 60
           M+AV F+  + V VKEV   +L+   D +VR+    ICGSDLH+Y G +P     V+GHE
Sbjct: 1   MKAVTFQGAKDVKVKEVPDAKLEKKDDIIVRITSTAICGSDLHIYRGALPAKKDYVIGHE 60

Query: 61  FVGQVEAVGEGIQDLQPGDWVVGPFHIACGTCPYCRRHQYNLCER---------GGVYGY 111
            +G VE VG  +  ++ GD VV PF+++CG C YC     + C+          GG +G+
Sbjct: 61  PMGIVEEVGPEVTKVKKGDRVVLPFNVSCGDCYYCNHDLESQCDNSNDNPTVDTGGYFGF 120

Query: 112 GPMFGNLQGAQAEILRVPFSNVNLRKLPPN--LSPERAIFAGDILSTAYGGLIQGQLRPG 169
              +GN  G QAE LRVP+ N     +PP+  L  E  +F  D+L TAY  +    ++ G
Sbjct: 121 TERYGNYAGGQAEFLRVPYGNFMPFVIPPSCELEDESLLFLSDVLPTAYWSVESSGMKAG 180

Query: 170 DSVAVIGAGPVGLMAIEVAQVLGASKILAIDRIPERLERAASLGAI-PINAEQENPVRRV 228
           D+VAV+G+GPVGLMA + A + GA +++A+D +P RL+ A  +  +   N ++ + +   
Sbjct: 181 DTVAVLGSGPVGLMAQKFAWMKGAKRVIAVDHLPYRLKHAIKMNNVEAFNFDEYDDMGAH 240

Query: 229 RSETNDEGPDLVLEAVGGAATLS--------------------LALEMVRPGGRVSAVGV 268
             E  + G D+V++ VG    LS                    + L  VR  G +   GV
Sbjct: 241 IKEITNGGVDVVIDCVGMDGKLSAIEKVEQKLKLQGGTLSAIDIGLNSVRKFGTIQLTGV 300

Query: 269 DNAPSFPFPLASGLVKDLTFRIGLANVHLYIDAVLALLASGRLQPERIVSHYLPLEEAPR 328
             +    FPL +   +++T ++G A V  Y+  +   +  G   P  I++H +PL++A +
Sbjct: 301 YGSLYNMFPLGNIFERNVTLKMGQAPVIHYMPLLFDKITKGEFDPTEIITHKVPLDQASK 360

Query: 329 GYELF--DRKEALKVLL 343
            Y+ F     E++K +L
Sbjct: 361 AYQTFHDHEDESIKFIL 377


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: 356
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 347
Length of database: 379
Length adjustment: 29
Effective length of query: 318
Effective length of database: 350
Effective search space:   111300
Effective search space used:   111300
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