GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Marinobacter adhaerens HP15

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate GFF194 HP15_194 mercuric ion reductase

Query= SwissProt::P11959
         (470 letters)



>FitnessBrowser__Marino:GFF194
          Length = 468

 Score =  244 bits (623), Expect = 4e-69
 Identities = 150/443 (33%), Positives = 243/443 (54%), Gaps = 11/443 (2%)

Query: 14  VVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQAKHSE- 72
           V+G+G     AA++A + G +VT++E+G +GG C+NVGC+PSK +I A+H     K S  
Sbjct: 11  VIGSGGAAMAAALKATERGARVTLIERGTVGGTCVNVGCVPSKIMIRAAHIAHLRKESPF 70

Query: 73  EMGIKAENVTIDFAKVQEWKASVVKKLTGG-VEGLLKGNK-VEIVKGEAYFVDANTVRVV 130
           + GI A    +D AK+ + + + V++L     E +L+ +K + ++ GEA F+D N++ V 
Sbjct: 71  DAGISAAAPEVDRAKLLQQQLARVEELRDTKYEKILREHKDITVLNGEARFLDTNSLLVT 130

Query: 131 NGDSAQTYT-FKNAIIATGSRPIELPNFKFSNR-ILDSTGALNLGEVPKSLVVIGGGYIG 188
             +  +    F  A I TG+RP E P    ++   L ST AL L   PK L+VIG G++ 
Sbjct: 131 LAEGGEKPVHFDRAFIGTGARPAEPPITGLADTPYLTSTSALTLDTGPKRLIVIGAGFVA 190

Query: 189 IELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAEERED 248
           +EL  A+A  G+KVT+L     +LS  +  +   I     ++G+EV++  L    +  ++
Sbjct: 191 LELAQAFARLGSKVTVL-ARSRVLSSEDPAIGEAIAGAFNREGIEVLSQTLPSNVDYSDN 249

Query: 249 GVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQCRTSVPN 308
              V   A     T+ AD +LV  GR PNT+ L L  IG++ T+R  I+VD+  +T+VP 
Sbjct: 250 EFIVETPAG----TLRADQLLVATGRTPNTEALNLASIGVE-TSRDAIQVDEHLQTTVPG 304

Query: 309 IFAIGDIVPGPALAHKASYEGKVAAEAIAGHPSAVDYVAIPAVVFSDPECASVGYFEQQA 368
           I+A GD    P   + A+  G  AA  +    + +D+ A+P V+F+DP+ A+VG  E +A
Sbjct: 305 IYAAGDCTNQPQFVYVAAAGGSRAAINMTEGEAKLDFSAMPGVMFTDPQVATVGLSEAEA 364

Query: 369 KDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASDMIAELGL 428
              G  V           RAL   DT GF+K+V  +  G ++G QI+     ++I    +
Sbjct: 365 VARGYSVDTRLLDLENVPRALVNFDTQGFIKMVAERNSGRLLGVQIVAAEGGEIIQTAVM 424

Query: 429 AIEAGMTAEDIALTIHAHPTLGE 451
           A+ AG+T ++I   +  + T+ E
Sbjct: 425 ALRAGLTVQEIGDDLFPYLTMVE 447


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: 492
Number of extensions: 30
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 470
Length of database: 468
Length adjustment: 33
Effective length of query: 437
Effective length of database: 435
Effective search space:   190095
Effective search space used:   190095
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: 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