Alignments for a candidate for lpd in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Desulfacinum infernum DSM 9756

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_084075849.1 BUB04_RS01350 dihydrolipoyl dehydrogenase

Query= BRENDA::P0A9P0
         (474 letters)



>NCBI__GCF_900129305.1:WP_084075849.1
          Length = 474

 Score =  419 bits (1078), Expect = e-122
 Identities = 216/468 (46%), Positives = 308/468 (65%), Gaps = 6/468 (1%)

Query: 6   KTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVAKVIEE 65
           +T+V V+G GP GY+AAFR ADLGLE  ++E    LGG CL  GCIPSKALL  A+++ +
Sbjct: 9   ETEVAVIGGGPGGYAAAFRAADLGLEVTLIEAEARLGGTCLLRGCIPSKALLQTAEIVWD 68

Query: 66  AKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANTL 125
           A   +E G+ F  P+ D+ K+R+WKE V+++L GGL+ +A+ R V+V+     F    TL
Sbjct: 69  ALHASERGVDFRPPQVDLHKLRSWKESVVDKLCGGLSKLAQRRGVQVLKARAVFEDERTL 128

Query: 126 EVEGENGKTVINFDNAIIAAGSRPIQLPFIPHE-DPRIWDSTDALELKEVPERLLVMGGG 184
            ++G +  T + F +A++A GS P  LP        RI DS+ AL+L ++P+RLLV+GGG
Sbjct: 129 RLDGSD-VTHLKFRHAVVATGSEPAALPDAAFRVGGRIMDSSAALDLDDLPQRLLVIGGG 187

Query: 185 IIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFN-LMLETKVTAVEA 243
            IGLE+G+ Y  LGS++ +V   ++++   D D+ +   KR+++ F  + L+++ T +  
Sbjct: 188 YIGLELGSAYAVLGSRVTLVHRGERLLGGVDPDLTRPLEKRLAQVFEKIHLQSEATEISE 247

Query: 244 KEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQLRT 303
           +EDG+ VT+     P +  R+  VLVA+GR P    L    AGV +  RG+I  D+Q RT
Sbjct: 248 EEDGVAVTLRTPDGPVQ-DRFHKVLVAVGRRPRSAGLGLEAAGVRIGARGYIETDEQCRT 306

Query: 304 NVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWVGLT 363
           +VP IFA+GD+ G PMLAHK + EG VAAE IAG    +D + +P++ YT+P+VAW GLT
Sbjct: 307 SVPTIFAVGDVAGDPMLAHKAMREGKVAAEAIAGLPSAYDVRAVPAVVYTDPQVAWAGLT 366

Query: 364 EKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGELLG 423
           E EA++KG+  + A FPW ASGRA+  + A+G+TK++ D +S RV+G  IVG     L+ 
Sbjct: 367 ETEARQKGLRVKVARFPWGASGRALTMEAAEGLTKMVLDPDSGRVLGMGIVGRGAETLIA 426

Query: 424 EIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDL--PNP 469
           E  LAIEM   AED+AL+IHAHPTL E+ G AAEVF GS T L  P P
Sbjct: 427 EGVLAIEMAATAEDVALSIHAHPTLSETEGEAAEVFLGSATHLFVPGP 474


Lambda     K      H
   0.317    0.137    0.396 

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: 594
Number of extensions: 21
Number of successful extensions: 4
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: 474
Length adjustment: 33
Effective length of query: 441
Effective length of database: 441
Effective search space:   194481
Effective search space used:   194481
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_084075849.1 BUB04_RS01350 (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.24503.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-145  471.6   0.0   1.4e-145  471.4   0.0    1.0  1  lcl|NCBI__GCF_900129305.1:WP_084075849.1  BUB04_RS01350 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_084075849.1  BUB04_RS01350 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  471.4   0.0  1.4e-145  1.4e-145       2     460 ..      10     468 ..       9     469 .. 0.97

  Alignments for each domain:
  == domain 1  score: 471.4 bits;  conditional E-value: 1.4e-145
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgie 69 
                                               ++v viGgGpgGY aA raa lgl+v+l+e   +lGGtCl +GCiP+KalL++ae+v ++ +a+e g++
  lcl|NCBI__GCF_900129305.1:WP_084075849.1  10 TEVAVIGGGPGGYAAAFRAADLGLEVTLIEAeARLGGTCLLRGCIPSKALLQTAEIVWDALHASERGVD 78 
                                               6899**************************9789*********************************** PP

                                 TIGR01350  70 venvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiA 138
                                                +  ++dl+kl  +ke+vv+kl gG++ L ++ +v+v+k +a ++d++++++++++ + +l++ ++++A
  lcl|NCBI__GCF_900129305.1:WP_084075849.1  79 FRPPQVDLHKLRSWKESVVDKLCGGLSKLAQRRGVQVLKARAVFEDERTLRLDGSDVT-HLKFRHAVVA 146
                                               *******************************************************965.********** PP

                                 TIGR01350 139 tGseprelplk.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldril 206
                                               tGsep++lp + + + + ++++s+ al l+ +p++l+++GgG+iG+E++s++a lG+ vt++   +r+l
  lcl|NCBI__GCF_900129305.1:WP_084075849.1 147 TGSEPAALPDAaFRVGG-RIMDSSAALDLDDLPQRLLVIGGGYIGLELGSAYAVLGSRVTLVHRGERLL 214
                                               *********98777777.8************************************************** PP

                                 TIGR01350 207 paldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleel 274
                                                 +d ++++ l+k+l +   ki+ +++ te+++eed v v+ +      + +  kvLvavGr+p+  +l
  lcl|NCBI__GCF_900129305.1:WP_084075849.1 215 GGVDPDLTRPLEKRLAQVFEKIHLQSEATEISEEEDGVAVTLRTPdGPVQDRFHKVLVAVGRRPRSAGL 283
                                               **************************************9887776445667889*************** PP

                                 TIGR01350 275 gleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavP 343
                                               gle+ gv++  rg+i++de++rt+vp i+a+GDv+g +mLAh+A++eg vaae+iag   s++d +avP
  lcl|NCBI__GCF_900129305.1:WP_084075849.1 284 GLEAAGVRIGARGYIETDEQCRTSVPTIFAVGDVAGDPMLAHKAMREGKVAAEAIAGLP-SAYDVRAVP 351
                                               *********************************************************66.59******* PP

                                 TIGR01350 344 sviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgae 412
                                               +v+yt+P+va  Glte++a+++g +vkv++fp  a+g+al++e ++G+ k+++d+++g++lG+ ivg  
  lcl|NCBI__GCF_900129305.1:WP_084075849.1 352 AVVYTDPQVAWAGLTETEARQKGLRVKVARFPWGASGRALTMEAAEGLTKMVLDPDSGRVLGMGIVGRG 420
                                               ********************************************************************* PP

                                 TIGR01350 413 aseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                               a  li+e +la+e+ +t+e++a +ih+HPtlsE+  eaa+  lg+a h
  lcl|NCBI__GCF_900129305.1:WP_084075849.1 421 AETLIAEGVLAIEMAATAEDVALSIHAHPTLSETEGEAAEVFLGSATH 468
                                               ******************************************999988 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.76
//
[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