GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Bacteroides thetaiotaomicron VPI-5482

Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; LPD; E3 component of pyruvate complex (uncharacterized)
to candidate 351070 BT1542 putative pyridine nucleotide-disulfide oxidoreductase (NCBI ptt file)

Query= curated2:P72740
         (474 letters)



>FitnessBrowser__Btheta:351070
          Length = 457

 Score =  186 bits (472), Expect = 1e-51
 Identities = 147/472 (31%), Positives = 230/472 (48%), Gaps = 28/472 (5%)

Query: 7   YDLVIIGAGVGGHGAALHAVKCGLKTAIIEAKD--MGGTCVNRGCIPSKALLAASGRVRE 64
           YD +IIG G  G   A      G + A++E  D   GG C N  CIP+K L+  S    E
Sbjct: 4   YDAIIIGFGKAGKTLAAELSNRGWQVAVVEQSDEMYGGACPNVACIPTKTLIHES----E 59

Query: 65  MSDQDHLQQLGIQINGVTFTREAIAAHANDLVSKIQSDLTNSLT-RLKVDTIRGWGKVSG 123
           +S   +      Q N     R+AIA   N L S ++ +    L+ R  V    G G +  
Sbjct: 60  ISTLLYHNDFDKQSN---MYRQAIA-RKNKLTSFLRENNYEKLSKRPNVTIYTGKGSLVS 115

Query: 124 PQEVTVIGDNETRILKAKEIMLCPGSVPFVPP--GIEIDHKTVFTSDEAVKLETLPQWIA 181
              V V    E   L+ KEI +  GS P +P   GI+   + V+TS   ++L+ LP+ + 
Sbjct: 116 ANTVKVALPEEEIELQGKEIFINTGSTPIIPSIEGIQ-QSRNVYTSTTLLELDILPKHLI 174

Query: 182 IIGSGYIGLEFSDVYTALGCEVTMIEALPDLMPGFDPEIAKIAERVLIKSRDIETYTGVF 241
           I+G GYIGLEF+ +Y   G +VT++EA    MP  D +IAK    V+ K + +E    V 
Sbjct: 175 IVGGGYIGLEFASMYAGFGSKVTLLEAGNRFMPRNDSDIAKSVREVMEK-KGVEIRLNVR 233

Query: 242 ATKIKAGSPVEIELTDAKTKEVID-TLEVDACLVATGRIPATKNLGLETVGVETDRRGFI 300
              I   +   + LT + T +     ++ DA L+ATGR P  + L L+  GVE D  G I
Sbjct: 234 TQSIH-DTHDGVTLTYSDTSDGTPYFVDGDAILIATGRKPMIEGLNLQAAGVEVDAHGAI 292

Query: 301 EVNDQMQVIKDGKPVPHLWAVGDATGKMMLAHAASGQGVVAVENICG-RKTEVDYR-AIP 358
            VNDQ+         PH+WA+GD  G     + +     +  + + G +K +++ R  +P
Sbjct: 293 VVNDQLHT-----NAPHIWAMGDVKGGAQFTYVSLDDFRIIRDQLFGDKKRDINDRDPLP 347

Query: 359 AAAFTHPEISYVGLTEAQAKELGEKEGFVVSTAKTYFKGNSKALAEKETDGIAKVVYRQD 418
            A F  P ++++G+TE +A   G    F VS         S+ L  ++TDG+ K +    
Sbjct: 348 YAVFIDPPLAHIGITEEEALRKG--YSFKVSRLPATSVVRSRTL--QQTDGMLKAIINSH 403

Query: 419 TGELLGAHIIGIHASDLIQEAAQAIADRKSVRELAFHVHAHPTLSEVLDEAY 470
           +G+++G  +    A +LI   A A+   ++   L   +  HP++SE L++ +
Sbjct: 404 SGKIMGCTMFCTDAPELINMVAMAMKTGQTSTFLRDFIFTHPSMSEGLNQLF 455


Lambda     K      H
   0.317    0.134    0.384 

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: 453
Number of extensions: 18
Number of successful extensions: 8
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: 474
Length of database: 457
Length adjustment: 33
Effective length of query: 441
Effective length of database: 424
Effective search space:   186984
Effective search space used:   186984
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 (21.6 bits)
S2: 51 (24.3 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