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 branched-chain alpha-keto acid dehydrogenase complex; LPD-Val (uncharacterized)
to candidate H281DRAFT_02737 H281DRAFT_02737 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component

Query= curated2:P54533
         (474 letters)



>FitnessBrowser__Burk376:H281DRAFT_02737
          Length = 465

 Score =  225 bits (573), Expect = 3e-63
 Identities = 145/460 (31%), Positives = 236/460 (51%), Gaps = 15/460 (3%)

Query: 5   YDVVILGGGTGGYVAAIRAAQLGLKTAVVEKEKLGGTCLHKGCIPSKALLRSAEVYRTAR 64
           +D +ILG G GG + A    + G + AVVE++ +GG+C    C+PSK  + SA V   AR
Sbjct: 7   FDTLILGSGQGGKLLAWHLGRSGQRVAVVERQWVGGSCPAVACLPSKNEIWSARVAHLAR 66

Query: 65  EADQFGVETAGVSLNFEKVQQRKQAVVDKLAAGVNHLMKKGKIDVYTGYGRILGPSIFSP 124
            A  FG  T  ++++  KV++RK+ ++++ AA           ++  G GR +GP     
Sbjct: 67  HAGDFGTTTGPIAVDMAKVRERKRGMIEREAAFHVQAYASSGAELIMGSGRFIGPK---- 122

Query: 125 LPGTISVERGNGEENDMLIPKQVIIATGSRPRM--LPGLEVDGKSVLTSDEALQMEELPQ 182
              TI+V+  +G     L   QV++  G+   +  +PGL   G   LT   AL ++  P 
Sbjct: 123 ---TIAVQLNDGGTR-TLAGDQVVVNVGTHAAIPDVPGLLAAGP--LTHIGALDLDYAPA 176

Query: 183 SIIIVGGGVIGIEWASMLHDFGVKVTVIEYADRILPTEDLEISKEMESLLKKKGIQFITG 242
            ++++GGG IGIE A     FG +VT++E   R++  ED++IS+EM  +L  +GI  +TG
Sbjct: 177 HLVVLGGGYIGIEMAQAYRRFGSRVTIVERGARLMAREDVDISEEMRGILSNEGIDIVTG 236

Query: 243 AKVLPDTMTKTSDDISIQAEKDGETVTYSAEKMLVSIGRQANIEGIGLENTDI-VTENGM 301
           A+ +       +    +     GE V   ++ +LV+ GR  N  GIGLE   I + E G 
Sbjct: 237 AETVRVEGRSGTQVRVVLRTASGERVIEGSD-ILVAAGRVPNTAGIGLEQAGIELDERGY 295

Query: 302 ISVNESCQTKESHIYAIGDVIGGLQLAHVASHEGIIAVEHFAGLNPHPLDPTLVPKCIYS 361
           I VN+  Q     ++AIG+V G  Q  HV+  +  I  ++ AG +       LVP  +++
Sbjct: 296 IRVNDRLQASAPGVWAIGEVAGSPQFTHVSVDDFRIVRDNLAGTD-RTTTGRLVPYTLFT 354

Query: 362 SPEAASVGLTEDEAKANGHNVKIGKFPFMAIGKALVYGESDGFVKIVADRDTDDILGVHM 421
            P  A VGL E +A   G  V++   P   + +     E+ GF+K++ D   D ILG  M
Sbjct: 355 DPPLARVGLNERDALRYGIAVRVATLPMSNVLRTEATDETQGFMKVLVDAKDDRILGFSM 414

Query: 422 IGPHVTDMISEAGLAKVLDATPWEVGQTIHPHPTLSEAIG 461
           IGP   ++++    A + +    ++   +  H T +E +G
Sbjct: 415 IGPEAGEVMASVQTAMIAELPYPKLRDAVISHLTFAEGLG 454


Lambda     K      H
   0.315    0.135    0.382 

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: 484
Number of extensions: 31
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: 474
Length of database: 465
Length adjustment: 33
Effective length of query: 441
Effective length of database: 432
Effective search space:   190512
Effective search space used:   190512
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: 42 (22.0 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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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