Alignments for a candidate for lpd in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudovibrio axinellae Ad2

Align Dihydrolipoyl dehydrogenase, mitochondrial; Dihydrolipoamide dehydrogenase; Glycine cleavage system L protein; Pyruvate dehydrogenase complex E3 subunit; E3; PDC-E3; EC 1.8.1.4 (characterized)
to candidate WP_068004348.1 PsAD2_RS06985 dihydrolipoyl dehydrogenase

Query= SwissProt::P31023
         (501 letters)



>NCBI__GCF_001623255.1:WP_068004348.1
          Length = 467

 Score =  550 bits (1417), Expect = e-161
 Identities = 268/464 (57%), Positives = 347/464 (74%), Gaps = 1/464 (0%)

Query: 39  DVVIIGGGPGGYVAAIKAAQLGFKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 98
           D+V+IG GPGGYV AIKAAQLG K   +EKR   GGTCLNVGCIPSKALLH+S M+ EA 
Sbjct: 4   DLVVIGTGPGGYVCAIKAAQLGMKVAVVEKRKTHGGTCLNVGCIPSKALLHASEMFEEAN 63

Query: 99  HSFANHGVKVSNVEIDLAAMMGQKDKAVSNLTRGIEGLFKKNKVTYVKGYGKFVSPSEIS 158
           H+F   G+K S  ++D  AM G K K V     GI+ LFKKNK+    G G+ +    + 
Sbjct: 64  HNFETLGIKTSKPKVDWKAMQGHKAKVVDGNVSGIDYLFKKNKIDVHTGVGRVLGAGRVE 123

Query: 159 VDTIEGENTVVKGKHIIIATGSDVKSLPGVTIDEKKIVSSTGALALSEIPKKLVVIGAGY 218
           V   +G  ++V+  +I+IATGSDV  LPG+ IDEK IVSSTGAL L ++P ++VV+GAG 
Sbjct: 124 VKAEDGSTSIVETTNIVIATGSDVMPLPGIEIDEKTIVSSTGALELEKVPNRMVVVGAGV 183

Query: 219 IGLEMGSVWGRIGSEVTVVEFASEIVPTMDAEIRKQFQRSLEKQGMKFKLKTKVVGVDTS 278
           IGLE+GSV+ R+G++VTVVEF  +I+  MDA++ KQFQR L+KQGM FKL +KV GV   
Sbjct: 184 IGLELGSVYARLGAQVTVVEFMDKILGPMDADVSKQFQRMLKKQGMTFKLSSKVTGVQKK 243

Query: 279 GDGVKLTVEPSAG-GEQTIIEADVVLVSAGRTPFTSGLNLDKIGVETDKLGRILVNERFS 337
           G  +++TVEP+AG      ++ADVVLV+ GR P+T GL L + GVE D+ GR+  +  + 
Sbjct: 244 GRALEVTVEPAAGEAAAETMDADVVLVAIGRRPYTEGLGLAETGVELDERGRVKTDAHYK 303

Query: 338 TNVSGVYAIGDVIPGPMLAHKAEEDGVACVEYLAGKVGHVDYDKVPGVVYTNPEVASVGK 397
           TNV G+YAIGDVI GPMLAHKAE++GVA  E ++G+ GHV+YD +PGVVYT+PEVASVGK
Sbjct: 304 TNVDGIYAIGDVIVGPMLAHKAEDEGVALAEIISGQAGHVNYDVIPGVVYTSPEVASVGK 363

Query: 398 TEEQVKETGVEYRVGKFPFMANSRAKAIDNAEGLVKIIAEKETDKILGVHIMAPNAGELI 457
           TEE++K  GV+Y+ GKFPF AN RAKA+ + +G VK++A+ ETD++LGVHI+   AGELI
Sbjct: 364 TEEELKAAGVKYKSGKFPFSANGRAKAMLHTDGFVKVLADAETDRVLGVHILGHGAGELI 423

Query: 458 HEAAIALQYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHI 501
           HEA + +++  SSED+ R CHAHPTMSEA+KEAAMAT  KPIH+
Sbjct: 424 HEACVLMEFGGSSEDLGRTCHAHPTMSEAVKEAAMATAGKPIHM 467


Lambda     K      H
   0.315    0.133    0.370 

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: 704
Number of extensions: 25
Number of successful extensions: 3
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: 501
Length of database: 467
Length adjustment: 34
Effective length of query: 467
Effective length of database: 433
Effective search space:   202211
Effective search space used:   202211
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: 52 (24.6 bits)

Align candidate WP_068004348.1 PsAD2_RS06985 (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.2978440.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-181  590.2  15.3   1.5e-181  590.0  15.3    1.0  1  NCBI__GCF_001623255.1:WP_068004348.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001623255.1:WP_068004348.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.0  15.3  1.5e-181  1.5e-181       1     461 []       2     467 .]       2     467 .] 0.97

  Alignments for each domain:
  == domain 1  score: 590.0 bits;  conditional E-value: 1.5e-181
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgieve 71 
                                           +yd+vviG+GpgGYv+Ai+aaqlg+kva+vek ++ GGtClnvGCiP+KalL+++e++ee+++ +++lgi+++
  NCBI__GCF_001623255.1:WP_068004348.1   2 SYDLVVIGTGPGGYVCAIKAAQLGMKVAVVEKrKTHGGTCLNVGCIPSKALLHASEMFEEANHnFETLGIKTS 74 
                                           59******************************8999************************************* PP

                             TIGR01350  72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsep 143
                                           + k+d+++++ +k kvv+  v+G+++L+kknk++v++G +++l++++vevk+e+++ + +e+ ni+iAtGs++
  NCBI__GCF_001623255.1:WP_068004348.1  75 KPKVDWKAMQGHKAKVVDGNVSGIDYLFKKNKIDVHTGVGRVLGAGRVEVKAEDGStSIVETTNIVIATGSDV 147
                                           *****************************************************98878899************ PP

                             TIGR01350 144 relplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskv 216
                                             lp+ +e dek++++s++alel++vp+++v+vG+GviG+E++s++a+lG++vtv+e++d+il  +da+vsk+
  NCBI__GCF_001623255.1:WP_068004348.1 148 MPLPG-IEIDEKTIVSSTGALELEKVPNRMVVVGAGVIGLELGSVYARLGAQVTVVEFMDKILGPMDADVSKQ 219
                                           *****.******************************************************************* PP

                             TIGR01350 217 lkkklkkkgvkiltnakvtevekeedevv..veak.kk.evetleaekvLvavGrkpnleelgleklgvelde 285
                                            +++lkk+g++++ ++kvt v+k+ ++++  ve   ++  +et++a+ vLva+Gr+p +e+lgl+++gvelde
  NCBI__GCF_001623255.1:WP_068004348.1 220 FQRMLKKQGMTFKLSSKVTGVQKKGRALEvtVEPAaGEaAAETMDADVVLVAIGRRPYTEGLGLAETGVELDE 292
                                           *******************99999998884444331335789******************************* PP

                             TIGR01350 286 rgaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlt 358
                                           rg++k+d++++tnv+giyaiGDvi ++mLAh+A++egv  ae i g++  +++y+++P v+yt+PevasvG+t
  NCBI__GCF_001623255.1:WP_068004348.1 293 RGRVKTDAHYKTNVDGIYAIGDVIVGPMLAHKAEDEGVALAEIISGQAG-HVNYDVIPGVVYTSPEVASVGKT 364
                                           **********************************************998.9********************** PP

                             TIGR01350 359 eeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltve 431
                                           ee++k++g+++k+gkfpf+ang+a a+ +tdGfvkv++d +t+++lG+hi+g  a eli+e+ +++e+++++e
  NCBI__GCF_001623255.1:WP_068004348.1 365 EEELKAAGVKYKSGKFPFSANGRAKAMLHTDGFVKVLADAETDRVLGVHILGHGAGELIHEACVLMEFGGSSE 437
                                           ************************************************************************* PP

                             TIGR01350 432 elaktihpHPtlsEaikeaalaalgkaihv 461
                                           +l +t+h+HPt+sEa+keaa a+ gk+ih+
  NCBI__GCF_001623255.1:WP_068004348.1 438 DLGRTCHAHPTMSEAVKEAAMATAGKPIHM 467
                                           *****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (467 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.58
//
[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