GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:354038
          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 (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