GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Jannaschia aquimarina GSW-M26

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043920380.1 jaqu_RS17910 alcohol dehydrogenase catalytic domain-containing protein

Query= BRENDA::D4GSN2
         (353 letters)



>NCBI__GCF_000877395.1:WP_043920380.1
          Length = 344

 Score =  271 bits (692), Expect = 2e-77
 Identities = 157/351 (44%), Positives = 204/351 (58%), Gaps = 12/351 (3%)

Query: 1   MRAAVLREHGEPLDVTEVPDPTCDADGVVVEVEACGICRSDWHSWMGHGEWADDAVPSGQ 60
           MRAA+LR + EPL + +VP P C  DGVV++V ACG+CRSDWH W+G        V  GQ
Sbjct: 1   MRAAILRTYHEPLAIEDVPHPDCPPDGVVLKVLACGVCRSDWHGWVGE----HPRVKPGQ 56

Query: 61  ILGHEPAGRVVEAGDRVETIREGDRVALPFNLACGSCGYCQTGHGNVCTGDHPHALGFEP 120
           I GHE  G VVEAG +  T   GD +  PF LACG+C  C++G  N C          EP
Sbjct: 57  IGGHEYCGEVVEAGPQA-THAVGDLLIAPFILACGTCPQCRSGAQNTCLDQRLPGF-IEP 114

Query: 121 AAQGAFAELVHLPSADYNAIQLPEDVLPTDVAALGCRFMTAYNALDARAGLRAGQWVAVH 180
              GAFAE V +P  D+N  +LPE + PT  AALGCR  TA++AL  RA L  G+W+AVH
Sbjct: 115 ---GAFAEYVAVPR-DHNLARLPEGMAPTLAAALGCRVTTAWHALTGRAALAGGEWLAVH 170

Query: 181 GCGGVGLSTIQVANVLGARVVAVDVRESALDAAADLGADAVVDGSAEDPVDAIRGLTDGG 240
           G GG+GLS   +   LGARVV VDV +  LD A  LG D+ V  + ED    IR +T GG
Sbjct: 171 GTGGIGLSAALLGRALGARVVVVDVVQEKLDHALSLGIDSAV-MAGEDTAARIREITGGG 229

Query: 241 AHVSLDALGVAETCRNSVRSVRPRGSHVQVGLTTEAEKGNVSLPTDWMTRHEVSFLGARG 300
           AHVS++ALG+  T   S+  +RP G HVQVG+        + +    + +  ++  G RG
Sbjct: 230 AHVSVEALGIPATVNASLECLRPLGRHVQVGMPV-GHTARMEVDMSAVYQGNLALFGTRG 288

Query: 301 MPPTNADDLLSLLASDAVDPGSLVTKTVSLDEVPERLAAMTDYDTVGVEVM 351
           MP      LL+L+ S AVD   ++ + V+L +V   LAA       GV V+
Sbjct: 289 MPSWRYSSLLALIESGAVDLAPMIAREVALSDVSAELAAFDGPTPPGVAVI 339


Lambda     K      H
   0.317    0.134    0.412 

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: 442
Number of extensions: 27
Number of successful extensions: 6
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: 353
Length of database: 344
Length adjustment: 29
Effective length of query: 324
Effective length of database: 315
Effective search space:   102060
Effective search space used:   102060
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 (21.7 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