Alignments for a candidate for lpd in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Thauera aminoaromatica S2

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_004324186.1 C665_RS17245 dihydrolipoyl dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>NCBI__GCF_000310185.1:WP_004324186.1
          Length = 474

 Score =  511 bits (1317), Expect = e-149
 Identities = 272/478 (56%), Positives = 338/478 (70%), Gaps = 12/478 (2%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEK--YIGKEGKVALGGTCLNVGCIPSK 58
           MS++FDV+VIG GPGGYVAAIRAAQLG KTAC E   Y   +G+  LGGTCLNVGCIPSK
Sbjct: 1   MSKEFDVLVIGGGPGGYVAAIRAAQLGFKTACCESNPYADPKGEPRLGGTCLNVGCIPSK 60

Query: 59  ALLDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSF 118
           ALL +S+ + EA  AF+  GI      IDVP M+ARK+ IV  LTGGI  LFK N VT  
Sbjct: 61  ALLHTSHLFEEAGHAFEGQGISVGTPKIDVPKMIARKSGIVDQLTGGIKGLFKKNKVTLL 120

Query: 119 EGHGKLL----ANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGA 174
            GHG  +    A  QV+V       +++ A+ VI+A+GS P  +P  P+ + I+ D+ GA
Sbjct: 121 NGHGAFVGKGDAGWQVQVG-----EELVTAKQVIVATGSAPRHLPGVPVDNKIVCDNVGA 175

Query: 175 LEFQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTK 234
           L+  AVPKKL VIGAGVIGLE+GSVW RLGAEVTVLEA+ +FL  AD+ +AKEALKV TK
Sbjct: 176 LDLDAVPKKLAVIGAGVIGLEMGSVWRRLGAEVTVLEAMPEFLSLADQDVAKEALKVFTK 235

Query: 235 QGLNIRLGARVTASEVKKKQVTVTFTDANG-EQKETFDKLIVAVGRRPVTTDLLAADSGV 293
           QGL   LG  +   +V KK V++ + D +G EQK   D+LIV+VGR P T  L A   G+
Sbjct: 236 QGLKFSLGVTIGEVKVGKKGVSIAYKDKDGAEQKLEADRLIVSVGRVPNTQGLNAEAVGL 295

Query: 294 TLDERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLI 353
            L+ERG I VDDHCKT++PGV+A+GDVVRG MLAHKA EE VMVAE +AG     N+D +
Sbjct: 296 KLNERGQIEVDDHCKTNLPGVWAVGDVVRGPMLAHKAMEEAVMVAELMAGQAGHCNFDTV 355

Query: 354 PSVIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDR 413
           P V+YT PEIAWVGKTEQ LKA GV   VG  PF A+GRA+   D+TG VK++ADA TDR
Sbjct: 356 PWVLYTSPEIAWVGKTEQQLKAAGVAYKVGKIPFLANGRALGMGDSTGFVKMLADATTDR 415

Query: 414 VLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIH 471
           +LGVH+IG +A+EL+ +  + MEF   +EDL  +  +HPTLSE +HEAALA +   +H
Sbjct: 416 ILGVHIIGANASELISEAVVAMEFAGCSEDLARICHAHPTLSEVVHEAALACDKRPLH 473


Lambda     K      H
   0.316    0.134    0.375 

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: 668
Number of extensions: 31
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: 478
Length of database: 474
Length adjustment: 33
Effective length of query: 445
Effective length of database: 441
Effective search space:   196245
Effective search space used:   196245
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_004324186.1 C665_RS17245 (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.13089.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.6e-166  538.7   2.2   6.4e-166  538.5   2.2    1.0  1  lcl|NCBI__GCF_000310185.1:WP_004324186.1  C665_RS17245 dihydrolipoyl dehyd


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_004324186.1  C665_RS17245 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  538.5   2.2  6.4e-166  6.4e-166       1     461 []       4     474 .]       4     474 .] 0.96

  Alignments for each domain:
  == domain 1  score: 538.5 bits;  conditional E-value: 6.4e-166
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalveke.........klGGtClnvGCiPtKalLksaevveel 60 
                                               e+dv+viGgGpgGYvaAiraaqlg+k+a+ e +         +lGGtClnvGCiP+KalL++++++ee+
  lcl|NCBI__GCF_000310185.1:WP_004324186.1   4 EFDVLVIGGGPGGYVAAIRAAQLGFKTACCESNpyadpkgepRLGGTCLNVGCIPSKALLHTSHLFEEA 72 
                                               69*****************************6533333333369************************* PP

                                 TIGR01350  61 ke.akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkek 128
                                                + ++  gi+v + k+d+ k+ +rk+ +v++l+gG+k+L+kknkv+ ++G++ +++k+    + + +e+
  lcl|NCBI__GCF_000310185.1:WP_004324186.1  73 GHaFEGQGISVGTPKIDVPKMIARKSGIVDQLTGGIKGLFKKNKVTLLNGHGAFVGKGDAGWQVQVGEE 141
                                               **99*****************************************************999988888889 PP

                                 TIGR01350 129 kleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvt 197
                                                ++ak++i+AtGs pr+lp+ + +d+k+v+++ +al l+ vp++l+++G+GviG+E++s++++lG++vt
  lcl|NCBI__GCF_000310185.1:WP_004324186.1 142 LVTAKQVIVATGSAPRHLPG-VPVDNKIVCDNVGALDLDAVPKKLAVIGAGVIGLEMGSVWRRLGAEVT 209
                                               ********************.************************************************ PP

                                 TIGR01350 198 vielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLva 264
                                               v+e++++ l   d++v+k++ k ++k+g+k+  + ++ ev+  ++ v+  ++ k++ +++lea++++v+
  lcl|NCBI__GCF_000310185.1:WP_004324186.1 210 VLEAMPEFLSLADQDVAKEALKVFTKQGLKFSLGVTIGEVKVGKKGVSiaYKDKDGAEQKLEADRLIVS 278
                                               **************************************99999999885566666688*********** PP

                                 TIGR01350 265 vGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagke 333
                                               vGr pn+++l+ e++g++l+erg+i+vd++++tn+pg++a+GDv++++mLAh+A++e+v++ae +ag++
  lcl|NCBI__GCF_000310185.1:WP_004324186.1 279 VGRVPNTQGLNAEAVGLKLNERGQIEVDDHCKTNLPGVWAVGDVVRGPMLAHKAMEEAVMVAELMAGQA 347
                                               *******************************************************************99 PP

                                 TIGR01350 334 kseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktge 402
                                                 +++ ++vP v yt+Pe+a vG+te+q+k++g+++kvgk+pf ang+al +++++Gfvk+++d +t++
  lcl|NCBI__GCF_000310185.1:WP_004324186.1 348 G-HCNFDTVPWVLYTSPEIAWVGKTEQQLKAAGVAYKVGKIPFLANGRALGMGDSTGFVKMLADATTDR 415
                                               8.9****************************************************************** PP

                                 TIGR01350 403 ilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               ilG+hi+ga+aselise+++a+e+ + +e+la+++h+HPtlsE+++eaala  ++++h+
  lcl|NCBI__GCF_000310185.1:WP_004324186.1 416 ILGVHIIGANASELISEAVVAMEFAGCSEDLARICHAHPTLSEVVHEAALACDKRPLHF 474
                                               *****************************************************999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (474 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: 00:00:00.03
# Mc/sec: 7.20
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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