GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__PV4:5211244 Shew_3660 glutathione reductase
           (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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