GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Acidovorax sp. GW101-3H11

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate Ac3H11_4615 Mercuric ion reductase (EC 1.16.1.1)

Query= SwissProt::P11959
         (470 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4615
          Length = 561

 Score =  228 bits (580), Expect = 5e-64
 Identities = 153/456 (33%), Positives = 241/456 (52%), Gaps = 12/456 (2%)

Query: 9   ETETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQA 68
           + +  V+G+G     AA++A + G  VT++E+G +GG C+N+GC+PSK +I A+H     
Sbjct: 98  QLQIAVIGSGGAAMAAALKAVEQGAHVTLIERGTIGGTCVNIGCVPSKIMIRAAHIAHLR 157

Query: 69  KHSE-EMGIKAENVTIDFAKVQEWKASVVKKLTGG-VEGLLKGNK-VEIVKGEAYFVDAN 125
           + S  + GI A    ID +K+   + ++V +L     EG+L  N  + ++ GEA F D  
Sbjct: 158 RESPFDGGITATVPAIDRSKLLAQQQALVDELRHAKYEGILDSNSAITVLHGEARFKDDQ 217

Query: 126 TVRV-VNGDSAQTYTFKNAIIATGSRPI--ELPNFKFSNRILDSTGALNLGEVPKSLVVI 182
           +V V +N    +   F   ++ATG+ P    +P  K S     ST AL    VP+ L VI
Sbjct: 218 SVVVRLNEGGERVVMFDRCLVATGASPAVPPIPGLKESP-YWTSTEALVSETVPERLAVI 276

Query: 183 GGGYIGIELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKG 242
           G   + +EL  A+A  G++VTIL     +    +  +   +    + +G+ V+ +  A  
Sbjct: 277 GSSVVALELAQAFARLGSQVTIL-ARRTLFFREDPAIGEAVTDAFRAEGITVLEHTQASQ 335

Query: 243 AEEREDGVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQC 302
                    +T   +GE   I AD +LV  GR PNT  L L+  G+ +  +G I +D+  
Sbjct: 336 VAHVNREFVLT-TGHGE---IRADKLLVATGRTPNTRSLALDAAGVTVNAQGAIVIDKGM 391

Query: 303 RTSVPNIFAIGDIVPGPALAHKASYEGKVAAEAIAGHPSAVDYVAIPAVVFSDPECASVG 362
           RTS P+I+A GD    P   + A+  G  AA  + G  +A+D  A+PAVVF+DP+ A+VG
Sbjct: 392 RTSTPHIYAAGDCADQPQFVYVAAAAGTRAAINMTGGDAALDLTAMPAVVFTDPQVATVG 451

Query: 363 YFEQQAKDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASDM 422
           Y E +A  +GI+  +         RALA  DT GF+KLV+ +  G +IG Q + P A ++
Sbjct: 452 YSEAEAHHDGIETDSRTLTLDNVPRALANFDTRGFIKLVIEEGSGRLIGVQAVAPEAGEL 511

Query: 423 IAELGLAIEAGMTAEDIALTIHAHPTLGEIAMEAAE 458
           I    LAI   MT +++A  +  + T+ E    AA+
Sbjct: 512 IQTAVLAIRNRMTVQELADQLFPYLTMVEGLKLAAQ 547


Lambda     K      H
   0.316    0.135    0.376 

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: 569
Number of extensions: 30
Number of successful extensions: 3
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: 561
Length adjustment: 35
Effective length of query: 435
Effective length of database: 526
Effective search space:   228810
Effective search space used:   228810
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: 41 (21.6 bits)
S2: 52 (24.6 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