Alignments for a candidate for lpd in Desulfitobacterium hafniense DCB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Desulfitobacterium hafniense DCB-2

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate WP_005809814.1 DHAF_RS20325 dihydrolipoyl dehydrogenase

Query= SwissProt::P18925
         (477 letters)



>NCBI__GCF_000021925.1:WP_005809814.1
          Length = 461

 Score =  347 bits (890), Expect = e-100
 Identities = 194/471 (41%), Positives = 287/471 (60%), Gaps = 11/471 (2%)

Query: 3   QKFDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYKGKEGKTALGGTCLNVGCIPSKALLD 62
           +++ V ++G GPGGYV A+++AQLGL   L+EK +       LGGTCLN GCIP+K L+ 
Sbjct: 2   EQYQVGILGGGPGGYVCALRAAQLGLSVVLVEKER-------LGGTCLNKGCIPTKTLVK 54

Query: 63  SSYKFHEAHESFKLHGISTGEVAIDVPTMIARKDQIVRNLTGGVASLIKANGVTLFEGHG 122
           S+  + E   + +  GI  G   +  P + ARK ++V  L  G+  L+KA  +T+ +G G
Sbjct: 55  SAELWREIKHAEEF-GIQLGGALLHYPQIAARKKEVVNTLVSGIEQLMKAKKITVLKGWG 113

Query: 123 KLLAGKKVEVTAADGSSQVLDTENVILASGSKPVEIPPAPVDQDVIVDSTGALDFQNVPG 182
           ++    ++EVT   G  + L  EN++LA+GS P +IP   VD   +V S   L+ + +P 
Sbjct: 114 EVKEANRIEVTTETGKVE-LHVENLVLATGSIPTKIPVPGVDLPGVVTSEELLEQETLPD 172

Query: 183 KLGVIGAGVIGLELGSVWARLGAEVTVLEAMDKFLPAVDEQVAKEAQKILTKQGLKILLG 242
            L VIG GVIGLE  S++   G +V+V+E +   LP +DE++ K    +L + GL+IL  
Sbjct: 173 SLVVIGGGVIGLEFASIYHEFGVKVSVVEMLPSLLPNIDEEIPKRLAPLLKRSGLEILTK 232

Query: 243 ARVTGTEVKNKQVTVKFVDAEGEKSQAFDKLIVAVGRRPVTTDLLAADSGVTLDERGFIY 302
           A V   + K + + V   D +G K     ++++A GRRP  + +     G+ LD RG I 
Sbjct: 233 AFVREIKPKEEGLVVIVEDGKGLKELPAQQVLLATGRRPSLSGIHGDALGLELD-RGAIK 291

Query: 303 VDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVVVAERIAGHKAQMNYDLIPAVIYTHPE 362
           V+    TSVP VYA+GDVV GAMLAH AS +G+V AE +AG +  M    IP+ I+T+PE
Sbjct: 292 VNSQMQTSVPKVYALGDVVGGAMLAHVASMQGMVAAEHMAGQQVSMEGRAIPSAIFTYPE 351

Query: 363 IAGVGKTEQALKAEGVAINVGVFPFAASGRAMAANDTAGFVKVIADAKTDRVLGVHVIGP 422
           IA VG+TEQALKA G    V  FPF+A+G+A+A  +  G VK++AD +   V+G  ++GP
Sbjct: 352 IAAVGETEQALKASGQNYKVSKFPFSANGKALALGEIMGLVKLLAD-EEGVVIGASIMGP 410

Query: 423 SAAELVQQGAIAMEFGTSAEDLGMMVFAHPALSEALHEAALAVSGHAIHVA 473
            A+ L+Q+  +A+E    AEDL  ++ AHP L EA+ EAA  +S   +H+A
Sbjct: 411 QASSLIQECVLAVEKKIKAEDLAKIIHAHPTLPEAIMEAAHGISAKPLHLA 461


Lambda     K      H
   0.316    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: 558
Number of extensions: 26
Number of successful extensions: 7
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: 477
Length of database: 461
Length adjustment: 33
Effective length of query: 444
Effective length of database: 428
Effective search space:   190032
Effective search space used:   190032
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)

Align candidate WP_005809814.1 DHAF_RS20325 (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.9983.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-162  527.8   7.4   1.3e-162  527.6   7.4    1.0  1  lcl|NCBI__GCF_000021925.1:WP_005809814.1  DHAF_RS20325 dihydrolipoyl dehyd


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_005809814.1  DHAF_RS20325 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.6   7.4  1.3e-162  1.3e-162       2     460 ..       4     459 ..       3     460 .. 0.97

  Alignments for each domain:
  == domain 1  score: 527.6 bits;  conditional E-value: 1.3e-162
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 
                                               y+v ++GgGpgGYv+A raaqlgl+v+lveke+lGGtCln+GCiPtK+l+ksae+ +e+k+a+e+gi++
  lcl|NCBI__GCF_000021925.1:WP_005809814.1   4 YQVGILGGGPGGYVCALRAAQLGLSVVLVEKERLGGTCLNKGCIPTKTLVKSAELWREIKHAEEFGIQL 72 
                                               8899***************************************************************** PP

                                 TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAt 139
                                                +  l + ++ +rk++vv++lv+G+++L+k +k++v+kG +++++++++ev++e+++ +l+++n+++At
  lcl|NCBI__GCF_000021925.1:WP_005809814.1  73 GGALLHYPQIAARKKEVVNTLVSGIEQLMKAKKITVLKGWGEVKEANRIEVTTETGKVELHVENLVLAT 141
                                               ********************************************************9************ PP

                                 TIGR01350 140 Gseprelplk.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp 207
                                               Gs p+++p++ ++  +  v+tsee le +++p+slv++GgGviG+Efasi++++Gvkv+v+e+l+ +lp
  lcl|NCBI__GCF_000021925.1:WP_005809814.1 142 GSIPTKIPVPgVDLPG--VVTSEELLEQETLPDSLVVIGGGVIGLEFASIYHEFGVKVSVVEMLPSLLP 208
                                               *********8888888..*************************************************** PP

                                 TIGR01350 208 aldaevskvlkkklkkkgvkiltnakvtevekeedevv.veakkkevetleaekvLvavGrkpnleelg 275
                                               ++d+e+ k l+  lk++g++ilt+a v e++ +e+ +v + +++k  ++l a++vL+a Gr+p+l+++ 
  lcl|NCBI__GCF_000021925.1:WP_005809814.1 209 NIDEEIPKRLAPLLKRSGLEILTKAFVREIKPKEEGLVvIVEDGKGLKELPAQQVLLATGRRPSLSGIH 277
                                               *******************************9999988444455589********************** PP

                                 TIGR01350 276 leklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPs 344
                                                ++lg+eld+ gaikv+++++t+vp++ya GDv+g++mLAhvAs +g+vaae++ag++  +++ +a+Ps
  lcl|NCBI__GCF_000021925.1:WP_005809814.1 278 GDALGLELDR-GAIKVNSQMQTSVPKVYALGDVVGGAMLAHVASMQGMVAAEHMAGQQV-SMEGRAIPS 344
                                               ********98.*********************************************765.9******** PP

                                 TIGR01350 345 viytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaea 413
                                               +i+t Pe+a+vG te+ +k++g ++kv+kfpf+angkalal+e  G+vk+++d++ g ++Ga+i+g++a
  lcl|NCBI__GCF_000021925.1:WP_005809814.1 345 AIFTYPEIAAVGETEQALKASGQNYKVSKFPFSANGKALALGEIMGLVKLLADEE-GVVIGASIMGPQA 412
                                               ****************************************************975.89*********** PP

                                 TIGR01350 414 seliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                               s li+e +lave ++++e+lak+ih+HPtl Eai+eaa+ ++ k++h
  lcl|NCBI__GCF_000021925.1:WP_005809814.1 413 SSLIQECVLAVEKKIKAEDLAKIIHAHPTLPEAIMEAAHGISAKPLH 459
                                               ********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (461 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: 8.52
//
[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