Alignments for a candidate for lpd in Actinomyces timonensis 7400942

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Actinomyces timonensis 7400942

Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of branched-chain alpha-keto acid dehydrogenase complex; LPD-Val (uncharacterized)
to candidate WP_017178730.1 A1QA_RS0109790 dihydrolipoyl dehydrogenase

Query= curated2:P54533
         (474 letters)



>NCBI__GCF_000295095.1:WP_017178730.1
          Length = 457

 Score =  311 bits (796), Expect = 4e-89
 Identities = 176/473 (37%), Positives = 281/473 (59%), Gaps = 24/473 (5%)

Query: 3   TEYDVVILGGGTGGYVAAIRAAQLGLKTAVVEKEKLGGTCLHKGCIPSKALLRSAEVYRT 62
           T YD+VILG G+GGY AA+R AQLGLK A++E +K+GGTCLH+GC+P+KA+L +AE   T
Sbjct: 4   TVYDMVILGAGSGGYAAALRGAQLGLKVALIEADKVGGTCLHRGCVPTKAILHAAETADT 63

Query: 63  AREADQFGVETAGVSLNFEKVQQRKQAVVDKLAAGVNHLMKKGKIDVYTGYGRILGPSIF 122
            REA   G+  A   ++   V+  K  ++ ++  G+  L+    ID+  G+GR++ P   
Sbjct: 64  VREASALGIRAALEGIDMPAVKAYKDGIISRMHKGLQGLVASRGIDLIQGWGRLVAPD-- 121

Query: 123 SPLPGTISVERGNGEENDMLIPKQVIIATGSRPRMLPGLEVDGKSVLTSDEALQMEELPQ 182
                  +VE     +   +  K VI+A+GS  + + G E+ G  V+TS++AL+++ +P 
Sbjct: 122 -------AVE----VDGRRITGKNVILASGSYSKDI-GQEISG-PVMTSEQALELDHVPA 168

Query: 183 SIIIVGGGVIGIEWASMLHDFGVKVTVIEYADRILPTEDLEISKEMESLLKKKGIQFITG 242
           S +I+GGGVIG+E+AS     G +VT+IE   R++P ED  ISK++E   +K+ I F T 
Sbjct: 169 SAVILGGGVIGVEFASAWASLGCQVTIIEGLPRLVPNEDEAISKQLERAFRKRKIAFRT- 227

Query: 243 AKVLPDTMTKTSDDISIQAEKDGETVTYSAEKMLVSIGRQANIEGIGLENTDIVTENGMI 302
              + +++ +  D ++++A    +  TY AE +L+++GR      +G E   +  + G +
Sbjct: 228 -STMFESVERHEDSVTVRA---ADGTTYYAEVLLIAVGRGPATANLGYEEVGVSMDRGFV 283

Query: 303 SVNESCQTKESHIYAIGDVIGGLQLAHVASHEGIIAVEHFAGLNPHPLDPTLVPKCIYSS 362
             +E  +T    ++A+GD++ G+QLAH    +GI+  E  AGL+P P+D  LVPK  +  
Sbjct: 284 LADEYGRTSVPGVWAVGDIVPGVQLAHRGFAQGIVVAEKIAGLDPTPVDDVLVPKVTFCE 343

Query: 363 PEAASVGLTEDEAK-ANGHN-VKIGKFPFMAIGKALVYGESDGFVKIVADRDTDDILGVH 420
           PE ASVGL+E  AK  +G + +   +F      K+ + G + GFVK+V+ +D   ILG H
Sbjct: 344 PEIASVGLSEAAAKELHGEDAITTAEFNVAGNAKSQILG-TQGFVKLVSLKD-GPILGFH 401

Query: 421 MIGPHVTDMISEAGLAKVLDATPWEVGQTIHPHPTLSEAIGEAALAADGKAIH 473
            IG  + + + E  L    +A   +V   +H HPT +E +GEAA+A  GK +H
Sbjct: 402 AIGARMGEQVGEGQLMVSWEADADDVASLVHAHPTQNETLGEAAMALAGKPLH 454


Lambda     K      H
   0.315    0.135    0.382 

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: 562
Number of extensions: 29
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: 474
Length of database: 457
Length adjustment: 33
Effective length of query: 441
Effective length of database: 424
Effective search space:   186984
Effective search space used:   186984
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_017178730.1 A1QA_RS0109790 (dihydrolipoyl dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01350.hmm
# target sequence database:        /tmp/gapView.1645372.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01350  [M=461]
Accession:   TIGR01350
Description: lipoamide_DH: dihydrolipoyl dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-136  440.3   1.7   4.6e-136  440.1   1.7    1.0  1  NCBI__GCF_000295095.1:WP_017178730.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000295095.1:WP_017178730.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.1   1.7  4.6e-136  4.6e-136       2     460 ..       6     454 ..       5     455 .. 0.96

  Alignments for each domain:
  == domain 1  score: 440.1 bits;  conditional E-value: 4.6e-136
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 
                                           yd+v++G+G gGY aA r aqlglkval+e +k+GGtCl++GC+PtKa+L++ae++++++ea+ lgi+++   
  NCBI__GCF_000295095.1:WP_017178730.1   6 YDMVILGAGSGGYAAALRGAQLGLKVALIEADKVGGTCLHRGCVPTKAILHAAETADTVREASALGIRAALEG 78 
                                           9*******************************************************************999** PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147
                                           +d+ ++++ k+ +++++ +G+++L+ + +++ i+G ++l+ ++ vev++++    ++ kn+i+A+Gs  + + 
  NCBI__GCF_000295095.1:WP_017178730.1  79 IDMPAVKAYKDGIISRMHKGLQGLVASRGIDLIQGWGRLVAPDAVEVDGRR----ITGKNVILASGSYSKDIG 147
                                           ************************************************998....89***************9 PP

                             TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220
                                              e ++  v+tse+alel++vp s vi+GgGviGvEfas++a+lG++vt+ie l+r++p++d+ +sk+l+++
  NCBI__GCF_000295095.1:WP_017178730.1 148 Q--EISG-PVMTSEQALELDHVPASAVILGGGVIGVEFASAWASLGCQVTIIEGLPRLVPNEDEAISKQLERA 217
                                           9..6776.59*************************************************************** PP

                             TIGR01350 221 lkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvde 293
                                           ++k+++ + t+++ ++ve++ed+v+v+a ++  +t+ ae +L+avGr p + +lg e++gv++d+ g++  de
  NCBI__GCF_000295095.1:WP_017178730.1 218 FRKRKIAFRTSTMFESVERHEDSVTVRAADG--TTYYAEVLLIAVGRGPATANLGYEEVGVSMDR-GFVLADE 287
                                           **************************99888..79***************************998.******* PP

                             TIGR01350 294 elrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeeg 366
                                           + rt+vpg++a+GD++ +++LAh+ +++g+v+aekiag  ++ +d  +vP+v+++ePe+asvGl+e+ ake +
  NCBI__GCF_000295095.1:WP_017178730.1 288 YGRTSVPGVWAVGDIVPGVQLAHRGFAQGIVVAEKIAGLDPTPVDDVLVPKVTFCEPEIASVGLSEAAAKELH 360
                                           ***********************************************************************98 PP

                             TIGR01350 367 ievkvgkfpfaangkala.leetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktih 438
                                            e +++  +f+  g a + +  t+Gfvk++   k+g ilG+h +ga+  e + e  l+v++e+ ++++a+++h
  NCBI__GCF_000295095.1:WP_017178730.1 361 GEDAITTAEFNVAGNAKSqILGTQGFVKLVSL-KDGPILGFHAIGARMGEQVGEGQLMVSWEADADDVASLVH 432
                                           76666655555555554314569*****9976.5799************************************ PP

                             TIGR01350 439 pHPtlsEaikeaalaalgkaih 460
                                           +HPt +E++ eaa a+ gk++h
  NCBI__GCF_000295095.1:WP_017178730.1 433 AHPTQNETLGEAAMALAGKPLH 454
                                           *******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (457 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 19.59
//
[ok]

This GapMind analysis is from Sep 24 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources