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.6980.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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.01
//
[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:

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:

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:

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:

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