GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Klebsiella michiganensis M5al

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate BWI76_RS26685 BWI76_RS26685 glutathione-disulfide reductase

Query= CharProtDB::CH_004665
         (470 letters)



>FitnessBrowser__Koxy:BWI76_RS26685
          Length = 450

 Score =  216 bits (551), Expect = 1e-60
 Identities = 143/448 (31%), Positives = 225/448 (50%), Gaps = 15/448 (3%)

Query: 11  DTLVIGAGPGGYVAAIRAAQLGQKVTVVEKATLGGVCLNVGCIPSKALINAGHRYENAK- 69
           D + IG G GG  +  RAA  GQK  ++E   LGG C+NVGC+P K + +A    E    
Sbjct: 6   DYIAIGGGSGGIASINRAAMHGQKCALIEAKDLGGTCVNVGCVPKKVMWHAAQIREAIHL 65

Query: 70  HSDDMGITAENVTVDFTKVQEWKASVVNKLTGGVAGLLKGNKVDVVKGEAYFVDSNSVRV 129
           +  D G        D+ K+   +++ ++++      +L  NKVDV+KG A FVD+ ++ V
Sbjct: 66  YGPDYGFDTTINHFDWDKLVASRSAYIDRIHTSYDNVLGKNKVDVIKGFARFVDAKTIEV 125

Query: 130 MDENSAQTYTFKNAIIATGSRPIELPNFKYSERVLNSTGALALKEIPKKLVVIGGGYIGT 189
               + +T T  + +IATG RP   PN    E  ++S G   L  +PK++ V+G GYI  
Sbjct: 126 ----NGETITADHILIATGGRPSH-PNIPGVEYGIDSDGFFELPALPKRVAVVGAGYIAV 180

Query: 190 ELGTAYANFGTELVILEGGDEILPGFEKQMSSLVTRRLKKKGNVEIHTNAMAKGVEERPD 249
           EL       G E  +       L  F+  +   +   +  +G  ++HTNA+ + V +  D
Sbjct: 181 ELAGVINGLGAETHLFVRKHAPLRSFDPLIVETLVEVMNAEG-PQLHTNAIPQAVVKNAD 239

Query: 250 GVTVTFEVK-GEEKTVDADYVLITVGRRPNTDELGLEQVGIEMTDRGIVKTDKQCRTNVP 308
           G ++T E++ G  +TVD   ++  +GR P TD   L   G++  D+G +  DK   TNVP
Sbjct: 240 G-SLTLELEDGRSQTVDC--LIWAIGREPATDNFNLAATGVKTNDKGYIVVDKFQNTNVP 296

Query: 309 NIYAIGDIIEGPPLAHKASYEGKIAAEAIAGEPAE--IDYLGIPAVVFSEPELASVGYTE 366
            IYA+GD      L   A   G+  +E +     +  +DY  IP VVFS P + +VG TE
Sbjct: 297 GIYAVGDNTGAVELTPVAVAAGRRLSERLFNNKPDEHLDYSNIPTVVFSHPPIGTVGLTE 356

Query: 367 AQAKEEGLD--IVAAKFPFAANGRALSLNETDGFMKLITRKEDGLVIGAQIAGASASDMI 424
            QA+E+  D  +   K  F A   A++ +     MKL+    +  ++G    G    +M+
Sbjct: 357 PQAREQYGDEAVKVYKSSFTAMYTAVTSHRQPCRMKLVCVGPEEKIVGIHGIGFGMDEML 416

Query: 425 SELSLAIEGGMTAEDIAMTIHAHPTLGE 452
              ++A++ G T +D   T+  HPT  E
Sbjct: 417 QGFAVALKMGATKKDFDNTVAIHPTAAE 444


Lambda     K      H
   0.314    0.134    0.372 

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: 546
Number of extensions: 26
Number of successful extensions: 9
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: 470
Length of database: 450
Length adjustment: 33
Effective length of query: 437
Effective length of database: 417
Effective search space:   182229
Effective search space used:   182229
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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