Alignments for a candidate for lpd in Thermomonospora curvata DSM 43183

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Thermomonospora curvata DSM 43183

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_012853418.1 TCUR_RS15235 dihydrolipoyl dehydrogenase

Query= curated2:P54533
         (474 letters)



>NCBI__GCF_000024385.1:WP_012853418.1
          Length = 463

 Score =  351 bits (901), Expect = e-101
 Identities = 192/472 (40%), Positives = 285/472 (60%), Gaps = 22/472 (4%)

Query: 5   YDVVILGGGTGGYVAAIRAAQLGLKTAVVEKEKLGGTCLHKGCIPSKALLRSAEVYRTAR 64
           +DVV+LGGG+GGY  A+RAA+LG++ A++E++ LGGTCL++GCIP+KALL +AEV  TAR
Sbjct: 8   FDVVVLGGGSGGYACALRAAELGMRVALIERDTLGGTCLNRGCIPTKALLHAAEVAETAR 67

Query: 65  EADQFGVETAGVSLNFEKVQQRKQAVVDKLAAGVNHLMKKGKIDVYTGYGRILGPS---I 121
            A +FGV  +   ++   V   K  VV     G+  L++   + +  G GR+ GP+   +
Sbjct: 68  RAARFGVRASFEGVDMPAVHAYKDKVVSGTVKGLTGLLRAKGVTIVEGEGRLAGPTAVQV 127

Query: 122 FSPLPGTISVERGNGEENDMLIPKQVIIATGSRPRMLPGLEVDGKSVLTSDEALQMEELP 181
            +P  G +  E            + +++ATGS PR LPGL VDG+ V+ SD+AL ++ +P
Sbjct: 128 ATP-AGPVRCE-----------GRHLVLATGSAPRSLPGLPVDGERVIFSDQALTLQRVP 175

Query: 182 QSIIIVGGGVIGIEWASMLHDFGVKVTVIEYADRILPTEDLEISKEMESLLKKKGIQFIT 241
            S+I++GGGVIG+E+AS+   FG +VT++E    +LP E+   S+ +E   +K+GI F  
Sbjct: 176 ASVIVLGGGVIGVEFASIWRSFGAEVTIVEALPHLLPMEEPSSSRRLERAFRKRGIAFEL 235

Query: 242 GAKVLPDTMTKTSDDISIQAEKDGETVTYSAEKMLVSIGRQANIEGIGLENTDIVTENGM 301
           GA+V     T+T   +++   +     T +AE +LV++GR     G+GL    + TE G 
Sbjct: 236 GARVEGVKTTETGVTVTLAGGR-----TLAAELLLVAVGRAPCSAGLGLAEAGVRTERGF 290

Query: 302 ISVNESCQTKESHIYAIGDVIGGLQLAHVASHEGIIAVEHFAGLNPHPLDPTLVPKCIYS 361
           + V+  C+T    I A+GD+I   QLAHV   EGI+  E   GL+P P+D   VP+  Y 
Sbjct: 291 VEVDRYCRTSVPTISAVGDLIATPQLAHVGFAEGILVAERLGGLSPAPIDYDGVPRIAYC 350

Query: 362 SPEAASVGLTEDEAKANGHNVKIGKFPFMAIGKALVYGESDGFVKIVADRDTDDILGVHM 421
            PE ASVGLT  +A   GH +    +      K+ + G + G VK++A+R    +LG+HM
Sbjct: 351 DPEVASVGLTSAQAAERGHQIMQVTYDLAGNPKSKILG-TQGEVKVIAERG-GRVLGIHM 408

Query: 422 IGPHVTDMISEAGLAKVLDATPWEVGQTIHPHPTLSEAIGEAALAADGKAIH 473
           +G  V ++I+E  L    +A P EV Q IHPHPT SEA+GEA LA  GK +H
Sbjct: 409 VGARVGELITEGQLIYNWEALPSEVAQLIHPHPTQSEAVGEAHLALAGKPLH 460


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: 588
Number of extensions: 33
Number of successful extensions: 5
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: 463
Length adjustment: 33
Effective length of query: 441
Effective length of database: 430
Effective search space:   189630
Effective search space used:   189630
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_012853418.1 TCUR_RS15235 (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.6816.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-146  475.2   0.0   1.2e-146  475.0   0.0    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012853418.1  TCUR_RS15235 dihydrolipoyl dehyd


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012853418.1  TCUR_RS15235 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.0   0.0  1.2e-146  1.2e-146       2     461 .]       8     461 ..       7     461 .. 0.98

  Alignments for each domain:
  == domain 1  score: 475.0 bits;  conditional E-value: 1.2e-146
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 
                                               +dvvv+GgG gGY +A raa+lg++val+e+++lGGtCln+GCiPtKalL++aev+e+++ a+++g+++
  lcl|NCBI__GCF_000024385.1:WP_012853418.1   8 FDVVVLGGGSGGYACALRAAELGMRVALIERDTLGGTCLNRGCIPTKALLHAAEVAETARRAARFGVRA 76 
                                               8******************************************************************99 PP

                                 TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAt 139
                                               +   +d+ ++++ k+kvv+  v+G+++Ll+ ++v+ ++Ge++l +++ v+v++ ++   +e  ++++At
  lcl|NCBI__GCF_000024385.1:WP_012853418.1  77 SFEGVDMPAVHAYKDKVVSGTVKGLTGLLRAKGVTIVEGEGRLAGPTAVQVATPAGPVRCEGRHLVLAT 145
                                               9999***************************************************999*********** PP

                                 TIGR01350 140 GseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpa 208
                                               Gs pr+lp+ l +d+++vi s++al+l++vp s++++GgGviGvEfasi++++G++vt++e+l+++lp+
  lcl|NCBI__GCF_000024385.1:WP_012853418.1 146 GSAPRSLPG-LPVDGERVIFSDQALTLQRVPASVIVLGGGVIGVEFASIWRSFGAEVTIVEALPHLLPM 213
                                               *********.9999999**************************************************** PP

                                 TIGR01350 209 ldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgle 277
                                               ++   s+ l+++++k+g+ +  +a+v+ v+++e  v+v+  ++  +tl ae +LvavGr p   +lgl+
  lcl|NCBI__GCF_000024385.1:WP_012853418.1 214 EEPSSSRRLERAFRKRGIAFELGARVEGVKTTETGVTVTLAGG--RTLAAELLLVAVGRAPCSAGLGLA 280
                                               ***************************************9999..8*********************** PP

                                 TIGR01350 278 klgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsvi 346
                                               + gv+ +erg+++vd+++rt+vp i a+GD+i++++LAhv ++eg+++ae++ g +++ idy+ vP++ 
  lcl|NCBI__GCF_000024385.1:WP_012853418.1 281 EAGVR-TERGFVEVDRYCRTSVPTISAVGDLIATPQLAHVGFAEGILVAERLGGLSPAPIDYDGVPRIA 348
                                               *****.556************************************************************ PP

                                 TIGR01350 347 ytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaease 415
                                               y++PevasvGlt +qa e+g+++  + +++a n k+ +l+ t+G vkvi+++  g++lG+h+vga++ e
  lcl|NCBI__GCF_000024385.1:WP_012853418.1 349 YCDPEVASVGLTSAQAAERGHQIMQVTYDLAGNPKSKILG-TQGEVKVIAER-GGRVLGIHMVGARVGE 415
                                               ************************************9875.89******987.699************* PP

                                 TIGR01350 416 liselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               li+e  l+ ++e+  +e+a++ihpHPt sEa+ ea la+ gk++hv
  lcl|NCBI__GCF_000024385.1:WP_012853418.1 416 LITEGQLIYNWEALPSEVAQLIHPHPTQSEAVGEAHLALAGKPLHV 461
                                               *******************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (463 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.44
//
[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 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