GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Shewanella loihica PV-4

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate 5211244 Shew_3660 glutathione reductase (RefSeq)

Query= CharProtDB::CH_004665
         (470 letters)



>FitnessBrowser__PV4:5211244
          Length = 451

 Score =  211 bits (536), Expect = 5e-59
 Identities = 143/454 (31%), Positives = 235/454 (51%), Gaps = 26/454 (5%)

Query: 11  DTLVIGAGPGGYVAAIRAAQLGQKVTVVEKATLGGVCLNVGCIPSKALINAGHRYENAKH 70
           D + +GAG GG  +A RAA  G KV ++E   LGG C+NVGC+P K +   G +   A H
Sbjct: 6   DYICLGAGSGGIASANRAAMRGAKVLLIEAKALGGTCVNVGCVPKKVMWY-GAQVAEAMH 64

Query: 71  --SDDMGITAENVTVDFTKVQEWKASVVNKLTGGVAGLLKGNKVDVVKGEAYFVDSNSVR 128
             + D G        D++K+ E + + + ++ G     L  N V +V+G   FVD+N++ 
Sbjct: 65  LYAKDYGFDVSVNKFDWSKLVESREAYIERIHGAYDRGLDSNGVTLVRGYGQFVDNNTIE 124

Query: 129 VMDENSAQTYTFKNAIIATGSRPIELPNFKYSERVLNSTGALALKEIPKKLVVIGGGYIG 188
           V  E+    Y+  + +IATG  P  +PN   +E  ++S G  AL E PK++ V+G GYI 
Sbjct: 125 VNGEH----YSADHILIATGGTPT-IPNIPGAEYGIDSDGFFALNEQPKRVAVVGAGYIA 179

Query: 189 TELGTAYANFGTELVILEGGDEILPGFEKQMSSLVTRRLKKKGNVEIHTNAMAKGVEERP 248
            EL       G+E  +       L  F+  +S  +   +   G   +HT+++ + V +  
Sbjct: 180 VELAGVLHALGSETHLFVRKHAPLRSFDPMLSEALMESMATDGP-SLHTHSIPESVTKNA 238

Query: 249 DGVTVTFEVKGEEKTVDADYVLITVGRRPNTDELGLEQVGIEMTDRGIVKTDKQCRTNVP 308
           DG ++T +++  E + + D ++  +GRRP+TD++GLE   +++ D+G V  D Q  T   
Sbjct: 239 DG-SLTLKLENGE-SYEIDTLIWAIGRRPSTDKIGLENTDVKLNDKGYVVVDAQQNTTAK 296

Query: 309 NIYAIGDIIEG----PPLAHKASYEGKIAAEAIAG--EPAEIDYLGIPAVVFSEPELASV 362
            IY +GDIIEG     P+A KA   G++ +E +      A++DY  +P VVFS P + ++
Sbjct: 297 GIYCVGDIIEGGIELTPVAVKA---GRLLSEHLFNGMTDAKMDYSLVPTVVFSHPAIGTM 353

Query: 363 GYTE----AQAKEEGLDIVAAKFPFAANGRALSLNETDGFMKLITRKEDGLVIGAQIAGA 418
           G TE    AQ  EE + +  +   F +   A++ +     MKL+   ++  V+G    G 
Sbjct: 354 GLTEPEAIAQYGEENVKVYNS--GFTSMYTAVTAHRQACKMKLVCAGKEEKVVGIHGIGY 411

Query: 419 SASDMISELSLAIEGGMTAEDIAMTIHAHPTLGE 452
              +++    +AI+ G T  D    +  HPT  E
Sbjct: 412 GMDEILQGFGVAIKMGATKADFDAVVAIHPTGAE 445


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: 528
Number of extensions: 27
Number of successful extensions: 6
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: 451
Length adjustment: 33
Effective length of query: 437
Effective length of database: 418
Effective search space:   182666
Effective search space used:   182666
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