Alignments for a candidate for lpd in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Cupriavidus basilensis 4G11

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate RR42_RS07380 RR42_RS07380 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__Cup4G11:RR42_RS07380
          Length = 594

 Score = 1058 bits (2737), Expect = 0.0
 Identities = 535/597 (89%), Positives = 562/597 (94%), Gaps = 6/597 (1%)

Query: 1   MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60
           MSVIEV+VPDIGDFDAVEVIEVLVKAGDTVE EQSLIVLESDKASMDVPSSAAGKVVEV+
Sbjct: 1   MSVIEVQVPDIGDFDAVEVIEVLVKAGDTVEQEQSLIVLESDKASMDVPSSAAGKVVEVR 60

Query: 61  VKVGDKVGQGAVICTIEAQQAA---AAPAPAQAPAPAQAPAPAAAAPAPAPAAASHSGGA 117
           +KVGDKV +GAVICT+E++ AA   AAP  A APAPAQ  APAAA   PAP AA+H+G A
Sbjct: 61  IKVGDKVAKGAVICTLESEAAAKPAAAPVSAPAPAPAQVSAPAAA---PAPVAAAHAGSA 117

Query: 118 DIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVI 177
           DI C+MLVLGAGPGGYSAAFR+ADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVI
Sbjct: 118 DITCDMLVLGAGPGGYSAAFRSADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVI 177

Query: 178 DEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPH 237
           DEAKALAAHGILFGEAKIDLDGLRHYK  VVGKLTGGLAGMAKARKVQVVRGIG FLDPH
Sbjct: 178 DEAKALAAHGILFGEAKIDLDGLRHYKETVVGKLTGGLAGMAKARKVQVVRGIGTFLDPH 237

Query: 238 HMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPN 297
           H+EV+ TEG+ K +TGKKTVIRFEKA+IAAGSQAVKLPFIPEDPRIVDSTGALELPEVPN
Sbjct: 238 HLEVQETEGDAKATTGKKTVIRFEKAVIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPN 297

Query: 298 KMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLK 357
           KMLVIGGGIIGLEMATVYSTLGA IDVVEMLDGLM GADRDLVKVW+K NK RF KVMLK
Sbjct: 298 KMLVIGGGIIGLEMATVYSTLGASIDVVEMLDGLMQGADRDLVKVWDKMNKKRFDKVMLK 357

Query: 358 TKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFI 417
           TKTVGVEAKPDGIYVKFEGE APAEPQRYDLVLVSVGR PNGKRI AEKAGVAV++RGFI
Sbjct: 358 TKTVGVEAKPDGIYVKFEGEQAPAEPQRYDLVLVSVGRVPNGKRIGAEKAGVAVTDRGFI 417

Query: 418 NVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDP 477
           +VDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFD KQIPSVA+TDP
Sbjct: 418 DVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDVKQIPSVAYTDP 477

Query: 478 EVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVG 537
           EVAWAG+TED+C+ +GIKYSK VFPWAASGRAIANGRDEGFTKLIFDEETHR+IGGGIVG
Sbjct: 478 EVAWAGVTEDQCRAQGIKYSKSVFPWAASGRAIANGRDEGFTKLIFDEETHRIIGGGIVG 537

Query: 538 THAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
           THAGDLISEVCLA+EMGADAVDIGKTIHPHPTLGESIGMAAEIYEG CTDVPPPRKR
Sbjct: 538 THAGDLISEVCLAVEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGVCTDVPPPRKR 594


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: 1224
Number of extensions: 34
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: 594
Length of database: 594
Length adjustment: 37
Effective length of query: 557
Effective length of database: 557
Effective search space:   310249
Effective search space used:   310249
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 RR42_RS07380 RR42_RS07380 (dihydrolipoamide 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.32693.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-146  472.8   4.7   6.8e-146  472.5   4.7    1.1  1  lcl|FitnessBrowser__Cup4G11:RR42_RS07380  RR42_RS07380 dihydrolipoamide de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS07380  RR42_RS07380 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.5   4.7  6.8e-146  6.8e-146       2     452 ..     121     579 ..     120     586 .. 0.97

  Alignments for each domain:
  == domain 1  score: 472.5 bits;  conditional E-value: 6.8e-146
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgie 69 
                                                d++v+G+GpgGY aA r+a lg++++lve+ ++lGG+ClnvGCiP+KalL++a v++e+k ++ +gi 
  lcl|FitnessBrowser__Cup4G11:RR42_RS07380 121 CDMLVLGAGPGGYSAAFRSADLGMNTVLVERySTLGGVCLNVGCIPSKALLHNAAVIDEAKALAAHGIL 189
                                               699****************************99************************************ PP

                                 TIGR01350  70 venvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke........kkl 130
                                                 + k+dl+ l + ke+vv kl+gG++++ k  kv+v+ G +++ld++++ev+++++         +++
  lcl|FitnessBrowser__Cup4G11:RR42_RS07380 190 FGEAKIDLDGLRHYKETVVGKLTGGLAGMAKARKVQVVRGIGTFLDPHHLEVQETEGDakattgkkTVI 258
                                               *****************************************************9998788889987788 PP

                                 TIGR01350 131 eakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvi 199
                                               ++++++iA Gs+  +lp+ + ed  ++++s++alel+evp++++++GgG+iG+E+a+++++lG+ + v+
  lcl|FitnessBrowser__Cup4G11:RR42_RS07380 259 RFEKAVIAAGSQAVKLPF-IPEDP-RIVDSTGALELPEVPNKMLVIGGGIIGLEMATVYSTLGASIDVV 325
                                               9*****************.77776.7******************************************* PP

                                 TIGR01350 200 elldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavG 266
                                               e+ld +++  d+++ kv  k+ kk+  k++ ++k   ve++ d + v+ +++   +e  +++ vLv+vG
  lcl|FitnessBrowser__Cup4G11:RR42_RS07380 326 EMLDGLMQGADRDLVKVWDKMNKKRFDKVMLKTKTVGVEAKPDGIYVKFEGEqaPAEPQRYDLVLVSVG 394
                                               ********************************************9988888744678999********* PP

                                 TIGR01350 267 rkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks 335
                                               r pn + +g ek gv +++rg+i vd+++rtnvp+i+aiGD++g++mLAh+A++e+ vaae++ g+++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS07380 395 RVPNGKRIGAEKAGVAVTDRGFIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKA- 462
                                               *****************************************************************776. PP

                                 TIGR01350 336 eidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeil 404
                                                +d k++Psv yt+Peva  G+te+q++++gi++  + fp aa+g+a+a + ++Gf k+i+d++t++i+
  lcl|FitnessBrowser__Cup4G11:RR42_RS07380 463 YFDVKQIPSVAYTDPEVAWAGVTEDQCRAQGIKYSKSVFPWAASGRAIANGRDEGFTKLIFDEETHRII 531
                                               9******************************************************************** PP

                                 TIGR01350 405 GahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaal 452
                                               G  ivg++a +lise+ lave+++ + ++ ktihpHPtl+E i  aa+
  lcl|FitnessBrowser__Cup4G11:RR42_RS07380 532 GGGIVGTHAGDLISEVCLAVEMGADAVDIGKTIHPHPTLGESIGMAAE 579
                                               ******************************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (594 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: 00:00:00.01
# Mc/sec: 14.17
//
[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