Alignments for a candidate for lpd in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Acidovorax sp. GW101-3H11

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Ac3H11_4091 Dihydrolipoamide dehydrogenase of pyruvate dehydrogenase complex (EC 1.8.1.4)

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4091
          Length = 616

 Score =  808 bits (2088), Expect = 0.0
 Identities = 416/617 (67%), Positives = 495/617 (80%), Gaps = 25/617 (4%)

Query: 1   MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60
           M++I++KVPDIGDF  V +IEVLVK GDT++ EQSLI +ESDKASM++PSS AG V E+K
Sbjct: 1   MAIIDIKVPDIGDFAEVAIIEVLVKPGDTIKAEQSLITVESDKASMEIPSSHAGVVKELK 60

Query: 61  VKVGDKVGQGAVICTIEAQQA-AAAPAPAQAPAPAQAPAPAAAAP------APAPAAASH 113
           VK+GDK+ +G+V+ T+E Q A AAAPAPA APAPA +    A+AP      A  P A+S 
Sbjct: 61  VKLGDKIAEGSVVLTLEVQGAGAAAPAPAAAPAPAVSEQKTASAPVQQAQVAINPVASSF 120

Query: 114 SGGADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHN 173
           +G AD+ C++LVLG GPGGYSAAFRAADLG+  V+VERY+TLGGVCLNVGCIPSKALLH 
Sbjct: 121 AGTADLDCDVLVLGGGPGGYSAAFRAADLGLKVVIVERYATLGGVCLNVGCIPSKALLHV 180

Query: 174 AAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNF 233
           AAV+DE   +A  G+ FG   +++D LR +K +V+GKLTGGLA MAK RKV  VRG G F
Sbjct: 181 AAVMDEVSHMADLGVDFGAPAVNIDKLRGHKEKVIGKLTGGLAAMAKMRKVTTVRGYGAF 240

Query: 234 LDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELP 293
           +  +H+EVE T G  +  TG K VI F++AIIAAGSQAV+LPF+P+DPR+VDSTGAL L 
Sbjct: 241 VGANHLEVEETTGTAQEKTGTKKVIAFKRAIIAAGSQAVRLPFMPDDPRVVDSTGALALK 300

Query: 294 EVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGK 353
           EVP +ML++GGGIIGLEM TVYSTLGA +DVVEM+DGLM GADRDLVK+W+K N  RF  
Sbjct: 301 EVPKRMLILGGGIIGLEMGTVYSTLGARLDVVEMMDGLMQGADRDLVKIWQKMNAKRFDN 360

Query: 354 VMLKTKTVGVEAKPDGIYVKF----EGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGV 409
           +MLKTKTVG +A P+GI V F    EG  APA PQ YDLVL +VGR+PNGK+I+A+KAGV
Sbjct: 361 IMLKTKTVGAKATPEGIEVTFAAAEEGGTAPA-PQTYDLVLQAVGRTPNGKKIAADKAGV 419

Query: 410 AVSERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGE--------K 461
           AV++RGFINVD QMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAE   GE         
Sbjct: 420 AVTDRGFINVDIQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEVIAGELQGNKELAA 479

Query: 462 AYFDAKQIPSVAFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKL 521
           A F+A+ IPSVA+TDPEVAW GLTED+ K +GIK  KG+FPW ASGRAIANGRDEG TKL
Sbjct: 480 AAFNARVIPSVAYTDPEVAWVGLTEDQAKAQGIKVKKGLFPWTASGRAIANGRDEGVTKL 539

Query: 522 IFDE--ETH---RVIGGGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGM 576
           +FD+  E H   +++GGG+VGTHAGD+I E+ LAIEMGADAVDIGKTIHPHPTLGESIGM
Sbjct: 540 LFDDSPEAHGHGKILGGGMVGTHAGDMIGEIALAIEMGADAVDIGKTIHPHPTLGESIGM 599

Query: 577 AAEIYEGTCTDVPPPRK 593
           AAEI  G+CTDVPP +K
Sbjct: 600 AAEIAHGSCTDVPPQKK 616


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: 1068
Number of extensions: 44
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: 594
Length of database: 616
Length adjustment: 37
Effective length of query: 557
Effective length of database: 579
Effective search space:   322503
Effective search space used:   322503
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 Ac3H11_4091 (Dihydrolipoamide dehydrogenase of pyruvate dehydrogenase complex (EC 1.8.1.4))
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.25442.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.8e-140  454.0   9.2   3.5e-140  453.7   9.2    1.1  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4091  Dihydrolipoamide dehydrogenase o


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4091  Dihydrolipoamide dehydrogenase of pyruvate dehydrogenase complex (EC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.7   9.2  3.5e-140  3.5e-140       2     456 ..     128     606 ..     127     611 .. 0.93

  Alignments for each domain:
  == domain 1  score: 453.7 bits;  conditional E-value: 3.5e-140
                                        TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke 62 
                                                       dv+v+GgGpgGY aA raa lglkv++ve+  +lGG+ClnvGCiP+KalL+ a v++e+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4091 128 CDVLVLGGGPGGYSAAFRAADLGLKVVIVERyATLGGVCLNVGCIPSKALLHVAAVMDEVSH 189
                                                      69*****************************99***************************** PP

                                        TIGR01350  63 akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkke 124
                                                      +++lg++    +++++kl  +kekv+ kl+gG++a+ k  kv+++ G++ +++++++ev+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4091 190 MADLGVDFGAPAVNIDKLRGHKEKVIGKLTGGLAAMAKMRKVTTVRGYGAFVGANHLEVEET 251
                                                      ************************************************************99 PP

                                        TIGR01350 125 kke........kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGg 178
                                                      +++        k++ +k++iiA Gs+  +lp+ +  d  +v++s++al+lkevp++++i+Gg
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4091 252 TGTaqektgtkKVIAFKRAIIAAGSQAVRLPF-MPDDP-RVVDSTGALALKEVPKRMLILGG 311
                                                      887888999988999*****************.65554.7********************** PP

                                        TIGR01350 179 GviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvteveke 240
                                                      G+iG+E+++++++lG+ + v+e++d +++  d+++ k+ +k+  k+  +i+ ++k    +++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4091 312 GIIGLEMGTVYSTLGARLDVVEMMDGLMQGADRDLVKIWQKMNAKRFDNIMLKTKTVGAKAT 373
                                                      ******************************************99999888888888866665 PP

                                        TIGR01350 241 edevv....veakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrt 297
                                                       + ++    + ++++      +++ vL avGr+pn +++  +k gv +++rg+i+vd ++rt
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4091 374 PEGIEvtfaAAEEGGtAPAPQTYDLVLQAVGRTPNGKKIAADKAGVAVTDRGFINVDIQMRT 435
                                                      5555533542333333556789**************************************** PP

                                        TIGR01350 298 nvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.......eidykavPsviytePev 352
                                                      nvp+i+aiGD++g++mLAh+A++e+ vaae iag+ +        +++++++Psv yt+Pev
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4091 436 NVPHIFAIGDIVGQPMLAHKAVHEAHVAAEVIAGELQGnkelaaaAFNARVIPSVAYTDPEV 497
                                                      *********************************98766678999999*************** PP

                                        TIGR01350 353 asvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkk.....tgeilGahiv 409
                                                      a vGlte+qak++gi+vk g fp +a+g+a+a + ++G+ k+++d +      g+ilG  +v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4091 498 AWVGLTEDQAKAQGIKVKKGLFPWTASGRAIANGRDEGVTKLLFDDSpeahgHGKILGGGMV 559
                                                      ********************************************97633333689******* PP

                                        TIGR01350 410 gaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalg 456
                                                      g++a ++i e+ala+e+++ + ++ ktihpHPtl+E i  aa+ a g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4091 560 GTHAGDMIGEIALAIEMGADAVDIGKTIHPHPTLGESIGMAAEIAHG 606
                                                      ***************************************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (616 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 13.07
//
[ok]

This GapMind analysis is from Sep 17 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