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_RS12930 RR42_RS12930 dihydrolipoamide dehydrogenase

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__Cup4G11:RR42_RS12930
          Length = 478

 Score =  494 bits (1272), Expect = e-144
 Identities = 262/473 (55%), Positives = 340/473 (71%), Gaps = 8/473 (1%)

Query: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIE--KYTDAEGKLALGGTCLNVGCIPSK 58
           M+++FDV+VIGAGPGGY+AAI+A QLGL  AC E   Y D + +  LGGTCLNVGCIPSK
Sbjct: 1   MSKQFDVLVIGAGPGGYIAAIRAGQLGLNVACCEGNAYDDPKDEPRLGGTCLNVGCIPSK 60

Query: 59  ALLDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSI 118
           ALL SS +++  +     HGI+ G+VK+DVA M+ RK  IV  +T G+  LF+ N VT +
Sbjct: 61  ALLASSEEFENVQHHLGDHGITVGDVKVDVAKMLKRKDDIVGKMTKGIEFLFRKNKVTLL 120

Query: 119 QGHGKLLA----GKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGA 174
           +G+GK +     G +VE+    GT EV+ A+ VI+A+GS+   +P   VD  ++ D+ GA
Sbjct: 121 KGYGKFVGKTAEGFQVEIAGKAGT-EVVTAKQVIVATGSKARHLPGIAVDNVLVSDNEGA 179

Query: 175 LEFQAVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTK 234
           L+F  VPK+LGVIGAGVIGLELGSVW RLGAEVTVLEAL +FL AAD  V+KEAQK LTK
Sbjct: 180 LKFAGVPKKLGVIGAGVIGLELGSVWRRLGAEVTVLEALPSFLGAADEGVAKEAQKLLTK 239

Query: 235 QGLDIKLGARVTGSKVNGNEVEVTYTNAEGE-QKITFDKLIVAVGRRPVTTDLLAADSGV 293
           QGL   LG +V   K   + V V+YT+ +G  Q +  D+LIV+VGR P T +L     G+
Sbjct: 240 QGLKFSLGVKVNEVKTGKDNVTVSYTDKDGAAQTLEVDRLIVSVGRVPNTDNLGLDAIGL 299

Query: 294 TIDERGYIFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLI 353
             D+RG+I VDD+CATSVPG++AIGDVVRG MLAHKA +EG+ V ERI G K  ++Y+ I
Sbjct: 300 AADQRGFIEVDDHCATSVPGLWAIGDVVRGPMLAHKAEDEGVAVAERIAGQKPHIDYNCI 359

Query: 354 PSVIYTHPEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDR 413
           P VIYT PEIAWVGKTEQ LKAEG E   G FPF A+GRA+    + GFVK++ADAKTD 
Sbjct: 360 PWVIYTFPEIAWVGKTEQQLKAEGREYKSGQFPFMANGRALGMGHSEGFVKMLADAKTDE 419

Query: 414 VLGVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVN 466
           +LGVHV+  +A++L+ +  +AMEF  ++ED+G     HP++SE + EAALAV+
Sbjct: 420 ILGVHVVAANASDLIAEAVVAMEFKAASEDIGRTCHPHPSMSEVMREAALAVD 472


Lambda     K      H
   0.316    0.133    0.374 

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: 714
Number of extensions: 33
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: 478
Length of database: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
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: 51 (24.3 bits)

Align candidate RR42_RS12930 RR42_RS12930 (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.8711.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-169  550.6   3.7   1.6e-169  550.4   3.7    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS12930  RR42_RS12930 dihydrolipoamide de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS12930  RR42_RS12930 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  550.4   3.7  1.6e-169  1.6e-169       1     461 []       4     478 .]       4     478 .] 0.96

  Alignments for each domain:
  == domain 1  score: 550.4 bits;  conditional E-value: 1.6e-169
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalve.........keklGGtClnvGCiPtKalLksaevveel 60 
                                               ++dv+viG+GpgGY+aAira+qlgl+va+ e         + +lGGtClnvGCiP+KalL+s+e +e++
  lcl|FitnessBrowser__Cup4G11:RR42_RS12930   4 QFDVLVIGAGPGGYIAAIRAGQLGLNVACCEgnayddpkdEPRLGGTCLNVGCIPSKALLASSEEFENV 72 
                                               59****************************94444444223469************************* PP

                                 TIGR01350  61 ke.akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkk....evevkke 124
                                               ++ + ++gi+v +vk+d++k+l+rk+ +v k+++G+++L++knkv+ +kG++k+++k+    +ve++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS12930  73 QHhLGDHGITVGDVKVDVAKMLKRKDDIVGKMTKGIEFLFRKNKVTLLKGYGKFVGKTaegfQVEIAGK 141
                                               **9***************************************************996533448****** PP

                                 TIGR01350 125 kkekkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklG 193
                                               +++++++ak++i+AtGs+ r+lp+ +++d+ +v ++e+al++  vp++l ++G+GviG+E++s++++lG
  lcl|FitnessBrowser__Cup4G11:RR42_RS12930 142 AGTEVVTAKQVIVATGSKARHLPG-IAVDNVLVSDNEGALKFAGVPKKLGVIGAGVIGLELGSVWRRLG 209
                                               ************************.999999************************************** PP

                                 TIGR01350 194 vkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaek 260
                                               ++vtv+e+l+  l a d+ v+k+++k l+k+g+k+  + kv+ev++ +d+v+  ++ k++ ++tle+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS12930 210 AEVTVLEALPSFLGAADEGVAKEAQKLLTKQGLKFSLGVKVNEVKTGKDNVTvsYTDKDGAAQTLEVDR 278
                                               **************************************************995555555589******* PP

                                 TIGR01350 261 vLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaeki 329
                                               ++v+vGr pn+++lgl+++g+  d+rg+i+vd+++ t+vpg++aiGDv++++mLAh+A++egv +ae+i
  lcl|FitnessBrowser__Cup4G11:RR42_RS12930 279 LIVSVGRVPNTDNLGLDAIGLAADQRGFIEVDDHCATSVPGLWAIGDVVRGPMLAHKAEDEGVAVAERI 347
                                               ********************************************************************* PP

                                 TIGR01350 330 agkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdk 398
                                               ag+++ +idy+ +P viyt Pe+a vG+te+q+k+eg e+k+g+fpf+ang+al +++++Gfvk+++d 
  lcl|FitnessBrowser__Cup4G11:RR42_RS12930 348 AGQKP-HIDYNCIPWVIYTFPEIAWVGKTEQQLKAEGREYKSGQFPFMANGRALGMGHSEGFVKMLADA 415
                                               **998.9************************************************************** PP

                                 TIGR01350 399 ktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               kt+eilG+h+v+a+as+li+e+++a+e+++ +e++ +t+hpHP++sE++ eaala+ ++++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS12930 416 KTDEILGVHVVAANASDLIAEAVVAMEFKAASEDIGRTCHPHPSMSEVMREAALAVDKRQLNM 478
                                               *******************************************************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (478 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 10.53
//
[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