GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Bacteroides thetaiotaomicron VPI-5482

Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate 354038 BT4512 putative zinc-type alcohol dehydrogenase (NCBI ptt file)

Query= SwissProt::Q0KDL6
         (366 letters)



>lcl|FitnessBrowser__Btheta:354038 BT4512 putative zinc-type alcohol
           dehydrogenase (NCBI ptt file)
          Length = 350

 Score =  184 bits (466), Expect = 4e-51
 Identities = 121/371 (32%), Positives = 185/371 (49%), Gaps = 41/371 (11%)

Query: 5   MKAAVFVEPGRIELADKPIPDI-GPNDALVRITTTTICGTDVHILKGEYPVA-KGLTVGH 62
           M A  ++E G+ EL +KP P I    DA+VR+T  +IC +D+HI  G  P A  G+TVGH
Sbjct: 1   MLAYTYIEHGKFELREKPEPKITDARDAIVRVTLGSICTSDLHIKHGSVPRAVPGITVGH 60

Query: 63  EPVGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMASGQCGC--HG 120
           E VG++E++G+ VT  R G RV       N  ++                 G+C    HG
Sbjct: 61  EMVGVVEEVGAEVTSVRPGDRVTV-----NVETFC----------------GECFFCHHG 99

Query: 121 Y-----KATAGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTGFKG 175
           Y         GW  G  IDG QAEYV VP A   L  IPD ++DEQ L   D+++TGF  
Sbjct: 100 YVNNCTDPNGGWALGCRIDGGQAEYVRVPYADQGLNRIPDTVSDEQALFVGDVLATGFWA 159

Query: 176 AENANIRIGDTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADVVLNF 235
              + I   DT+ +   GP G+C    + L     II  + +  R++  R+   DV++  
Sbjct: 160 TRISEITEKDTILLIGAGPTGICTLLCSMLKNPKRIIVCEKSPERIQFVREHYPDVLITT 219

Query: 236 -RNCDVVDEVMKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTIPLS 294
             NC   + V++ +   G D  +E  GT+ +F  +    +P   ++ + +Y   L  PL 
Sbjct: 220 PENCK--EFVLQNSDHSGADVVLEVAGTEDSFRMAWDCARPNAIVTIVALYDKPLLFPLP 277

Query: 295 AFAAGLGDHKINTALCPGGKE--RMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLFA 352
                   +  N     GG +      ++++IE G++D   L+TH+  L++I  AY +F 
Sbjct: 278 EM------YGKNLTFKTGGVDGCDCAEILSLIEEGKIDTTPLITHRCSLNEIEEAYRIFE 331

Query: 353 NQRDGVLKIAI 363
           N+ DGV+K+AI
Sbjct: 332 NKLDGVIKVAI 342


Lambda     K      H
   0.320    0.138    0.408 

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: 342
Number of extensions: 18
Number of successful extensions: 7
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: 366
Length of database: 350
Length adjustment: 29
Effective length of query: 337
Effective length of database: 321
Effective search space:   108177
Effective search space used:   108177
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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