GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Paraburkholderia bryophila 376MFSha3.1

Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex (uncharacterized)
to candidate H281DRAFT_00438 H281DRAFT_00438 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component

Query= curated2:O84561
         (465 letters)



>FitnessBrowser__Burk376:H281DRAFT_00438
          Length = 466

 Score =  239 bits (609), Expect = 2e-67
 Identities = 146/456 (32%), Positives = 230/456 (50%), Gaps = 13/456 (2%)

Query: 1   MNEAFDCVVIGAGPGGYVAAITAAQAGLKTALIEKREAGGTCLNRGCIPSKALLAGAEVV 60
           M + FD VVIG G GG   A+   ++G +TA+IE+   GGTC+N GC P+KA +A A   
Sbjct: 1   MAQHFDAVVIGTGQGGAPLAVRLGKSGRRTAVIERAAFGGTCVNVGCTPTKAYVASARAA 60

Query: 61  TQIRHADQFGIHVEG-FSINYPAMVQRKDSVVRSIRDGLNGLIR-SNKITVFSGRGSLIS 118
              RHA + G+H+ G   ++  A+  RKD +V    DG+   +R +  +TVF+G      
Sbjct: 61  HVARHAARLGVHIGGAVGVDMAAVKARKDKIVGQSHDGVEAWLRGARNLTVFTGHARFTG 120

Query: 119 STEVKILGENPSV---IKAHSIILATGSEPRAFPGIPFSAESPRILCSTGVLNLKEIPQK 175
              + + G + +V   + A  I L TG+  RA        E  R   ++ +L + E+P +
Sbjct: 121 PHTLAVSGPDGAVLHELSADEIFLNTGT--RAVVPPLEGIERARYYTNSSLLEITELPSR 178

Query: 176 MAIIGGGVIGCEFASLFHTLGSEVSVIEASSQILALNNPDISKTMFDKFTRQGLRFVLEA 235
           + I+GG  I  EFA +F   GSEV+V+    ++L   + D ++++     R+G+ F    
Sbjct: 179 LVIVGGSYIALEFAQVFRRFGSEVTVLVRGDRVLTREDADFAESVQSVLAREGVEFRFGV 238

Query: 236 SVSNIEDIGDR---VRLTINGNVE--EYDYVLVSIGRRLNTENIGLDKAGVICDERGVIP 290
             S +E    R   V +    NV   E  ++L + GR+ NT+++GL  AG+  D  G IP
Sbjct: 239 QPSRVEPHPHRENEVCIGFEQNVPALEASHLLFATGRKPNTDDLGLAAAGIETDRHGTIP 298

Query: 291 TDATMRTNVPNIYAIGDITGKWQLAHVA-SHQGIIAARNIAGHKEEIDYSAVPSVIFTFP 349
            D  +RTNVP ++AIGDI G+    H +     I+AA    G    +D   +   +F  P
Sbjct: 299 VDGQLRTNVPGVWAIGDINGRGAFTHTSYDDYQIVAANLFDGGTRTVDKRIMAYAVFVDP 358

Query: 350 EVASVGLSPTAAQQQKIPVKVTKFPFRAIGKAVAMGEADGFAAIISHETTQQILGAYVIG 409
            +A VGLS    ++      +   P   +G+A   GE DGF  +++   T+QILGA + G
Sbjct: 359 PLARVGLSEDDVRKSGRDALIATMPMSRVGRARERGETDGFMKVLADPHTRQILGAAIHG 418

Query: 410 PHASSLISEITLAVRNELTLPCIYETIHAHPTLAEV 445
                 I  I   +      P +   +H HPT++E+
Sbjct: 419 IEGDEAIHTIIDIMTAGAPYPTLQYAMHIHPTISEL 454


Lambda     K      H
   0.319    0.135    0.388 

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: 508
Number of extensions: 21
Number of successful extensions: 5
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: 465
Length of database: 466
Length adjustment: 33
Effective length of query: 432
Effective length of database: 433
Effective search space:   187056
Effective search space used:   187056
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 (21.7 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