Alignments for a candidate for lpd in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Paraburkholderia phymatum STM815

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_041763846.1 BPHY_RS07480 dihydrolipoyl dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>NCBI__GCF_000020045.1:WP_041763846.1
          Length = 580

 Score =  914 bits (2363), Expect = 0.0
 Identities = 461/590 (78%), Positives = 513/590 (86%), Gaps = 12/590 (2%)

Query: 5   EVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVKVG 64
           E+KVPDIGD+  V VIEV VK GD VE EQSL+ LESDKA+MDVPS AAG V E+KVKVG
Sbjct: 3   EIKVPDIGDYKDVPVIEVAVKVGDRVEKEQSLVTLESDKATMDVPSPAAGVVKELKVKVG 62

Query: 65  DKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPAPAPAAASHSGGADIQCEML 124
           D V +G+V+  +E + AAAAPAP +A APA +PA   AAP PAP A S+SG  DI+C+ML
Sbjct: 63  DNVSEGSVLLLLEGEGAAAAPAP-KAAAPAPSPA---AAPTPAPQAGSYSGSTDIECDML 118

Query: 125 VLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVIDEAKALA 184
           VLGAGPGGYSAAFR+ADLGM TVLVERYSTLGGVCLNVGCIPSKALLH A VIDEA+AL 
Sbjct: 119 VLGAGPGGYSAAFRSADLGMKTVLVERYSTLGGVCLNVGCIPSKALLHTALVIDEAEALG 178

Query: 185 AHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPHHMEVELT 244
           +HGI FG+ +IDLD LR +K+ VV KLTGGLAGMAKARKV+VV G+G F+DP+HMEV+  
Sbjct: 179 SHGISFGKPQIDLDKLRDFKSGVVKKLTGGLAGMAKARKVEVVTGVGTFVDPYHMEVQGE 238

Query: 245 EGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPNKMLVIGG 304
            G        K +++F++AIIAAGSQAVKLPFIPEDPR+VDSTGALEL ++P +MLVIGG
Sbjct: 239 NG--------KKIVKFKQAIIAAGSQAVKLPFIPEDPRVVDSTGALELRQLPKRMLVIGG 290

Query: 305 GIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLKTKTVGVE 364
           GIIGLEMATVY+TLGA IDVVEMLDGLM GADRDLVKVWEK N  RF  VMLKTKT G E
Sbjct: 291 GIIGLEMATVYATLGAQIDVVEMLDGLMAGADRDLVKVWEKFNSKRFTNVMLKTKTTGAE 350

Query: 365 AKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFINVDKQMR 424
           AKPDGIYV FEGE APAEPQRYDLVLV+VGRSPNGK+I A+KAGVAV++RGFI VDKQMR
Sbjct: 351 AKPDGIYVTFEGEKAPAEPQRYDLVLVAVGRSPNGKKIGADKAGVAVTDRGFIEVDKQMR 410

Query: 425 TNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDPEVAWAGL 484
           TNVPHIFAIGD+VGQPMLAHKAVHE HVAAEAAHGEKAYFDA QIPSVA+TDPEVAWAG 
Sbjct: 411 TNVPHIFAIGDVVGQPMLAHKAVHEGHVAAEAAHGEKAYFDAMQIPSVAYTDPEVAWAGK 470

Query: 485 TEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGTHAGDLI 544
           TED+CK +GIKY K VFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVG +AGDLI
Sbjct: 471 TEDQCKAEGIKYGKAVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGLNAGDLI 530

Query: 545 SEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
           SEVCLA+EMGADA DIGKTIHPHPTLGESIGMAAE+YEG CTD+PP +K+
Sbjct: 531 SEVCLAVEMGADATDIGKTIHPHPTLGESIGMAAELYEGVCTDLPPQKKK 580


Lambda     K      H
   0.316    0.134    0.387 

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: 1107
Number of extensions: 35
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: 594
Length of database: 580
Length adjustment: 37
Effective length of query: 557
Effective length of database: 543
Effective search space:   302451
Effective search space used:   302451
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: 53 (25.0 bits)

Align candidate WP_041763846.1 BPHY_RS07480 (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.2183280.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.7e-149  482.9   2.6   5.8e-149  482.6   2.6    1.0  1  NCBI__GCF_000020045.1:WP_041763846.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020045.1:WP_041763846.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.6   2.6  5.8e-149  5.8e-149       2     453 ..     115     566 ..     114     572 .. 0.97

  Alignments for each domain:
  == domain 1  score: 482.6 bits;  conditional E-value: 5.8e-149
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                            d++v+G+GpgGY aA r+a lg+k++lve+ ++lGG+ClnvGCiP+KalL++a v++e++ + ++gi+  + 
  NCBI__GCF_000020045.1:WP_041763846.1 115 CDMLVLGAGPGGYSAAFRSADLGMKTVLVERySTLGGVCLNVGCIPSKALLHTALVIDEAEALGSHGISFGKP 187
                                           699****************************99**************************************** PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprel 146
                                           ++dl+kl + k+ vvkkl+gG++++ k  kvev++G ++++d+ ++ev++e+++k +++k++iiA Gs+  +l
  NCBI__GCF_000020045.1:WP_041763846.1 188 QIDLDKLRDFKSGVVKKLTGGLAGMAKARKVEVVTGVGTFVDPYHMEVQGENGKKIVKFKQAIIAAGSQAVKL 260
                                           ************************************************************************* PP

                             TIGR01350 147 plkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkk 219
                                           p+ + ed  +v++s++alel+++p++++++GgG+iG+E+a+++a+lG+++ v+e+ld +++  d+++ kv +k
  NCBI__GCF_000020045.1:WP_041763846.1 261 PF-IPEDP-RVVDSTGALELRQLPKRMLVIGGGIIGLEMATVYATLGAQIDVVEMLDGLMAGADRDLVKVWEK 331
                                           **.77776.7*************************************************************** PP

                             TIGR01350 220 klkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgveldergaik 290
                                             +k+  +++ ++k t  e++ d + v+ +++   +e  +++ vLvavGr+pn +++g +k gv +++rg+i+
  NCBI__GCF_000020045.1:WP_041763846.1 332 FNSKRFTNVMLKTKTTGAEAKPDGIYVTFEGEkaPAEPQRYDLVLVAVGRSPNGKKIGADKAGVAVTDRGFIE 404
                                           *****9**********999999988866666633679999********************************* PP

                             TIGR01350 291 vdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqak 363
                                           vd+++rtnvp+i+aiGDv+g++mLAh+A++eg vaae++ g+++  +d++++Psv yt+Peva  G+te+q+k
  NCBI__GCF_000020045.1:WP_041763846.1 405 VDKQMRTNVPHIFAIGDVVGQPMLAHKAVHEGHVAAEAAHGEKA-YFDAMQIPSVAYTDPEVAWAGKTEDQCK 476
                                           *****************************************776.9*************************** PP

                             TIGR01350 364 eegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelakt 436
                                           +egi++  + fp aa+g+a+a + ++Gf k+i+d++t++++G  ivg +a +lise+ lave+++ ++++ kt
  NCBI__GCF_000020045.1:WP_041763846.1 477 AEGIKYGKAVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGLNAGDLISEVCLAVEMGADATDIGKT 549
                                           ************************************************************************* PP

                             TIGR01350 437 ihpHPtlsEaikeaala 453
                                           ihpHPtl+E i  aa+ 
  NCBI__GCF_000020045.1:WP_041763846.1 550 IHPHPTLGESIGMAAEL 566
                                           ***********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (580 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 26.53
//
[ok]

This GapMind analysis is from Apr 09 2024. 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