GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Lysobacter daejeonensis GH1-9

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_036136112.1 N800_RS06360 dihydrolipoyl dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>NCBI__GCF_000768355.1:WP_036136112.1
          Length = 480

 Score =  536 bits (1381), Expect = e-157
 Identities = 284/476 (59%), Positives = 348/476 (73%), Gaps = 4/476 (0%)

Query: 3   QKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKALLD 62
           Q FDVVVIG GP GY AAIRAAQLGLKTACI+  +GK+GK ALGGTCL VGCIPSKALLD
Sbjct: 5   QNFDVVVIGGGPAGYHAAIRAAQLGLKTACIDAALGKDGKPALGGTCLRVGCIPSKALLD 64

Query: 63  SSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEGHG 122
           SS ++      F  HGI  +   IDV  MVARK  IVK  TGGIA+LFKAN V +F G G
Sbjct: 65  SSRQFWNMGHIFDQHGISFEKPAIDVKKMVARKDGIVKQFTGGIASLFKANKVAAFYGFG 124

Query: 123 KLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAVPK 182
           +L     V+VT  DG    L+  NVIIA+GS  +E+P A    + IVD+ G L+F+AVP+
Sbjct: 125 QLQPGNVVKVTQHDGSVVELKGTNVIIAAGSDSIELPFAKFDGECIVDNVGGLDFEAVPE 184

Query: 183 KLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIRLG 242
           +LGVIGAGVIGLELGSVW RLGA+VT+LEAL  FL AAD ++ K + +   KQGL+I+LG
Sbjct: 185 RLGVIGAGVIGLELGSVWNRLGAKVTILEALPGFLSAADAEVGKVSAREFKKQGLDIKLG 244

Query: 243 ARVTASEV----KKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDER 298
           A+V+ +EV    KKK+V +T+TDA GEQ    DKL+VAVGRR  T  LLA  +GV ++ER
Sbjct: 245 AKVSKAEVKGKGKKKEVELTYTDAAGEQTLVVDKLLVAVGRRAATKGLLAEGTGVRVNER 304

Query: 299 GFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIY 358
           G I VD+HC T V GV+A+GD VRG MLAHK  EEG+ VAE IAG    +N+D IP VIY
Sbjct: 305 GQIEVDEHCHTGVDGVWAVGDCVRGPMLAHKGFEEGIAVAELIAGLPGHVNFDTIPWVIY 364

Query: 359 THPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVH 418
           T PEIAWVGKTE+ LKAEGV    G+FPFAA GRA+A  +  G VKVIA A+TDRVLG+H
Sbjct: 365 TEPEIAWVGKTEEQLKAEGVPYKAGSFPFAAVGRAVAMAEPAGFVKVIAHAETDRVLGMH 424

Query: 419 VIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIAN 474
           ++G + +ELV +G + MEF  SA+DL  +  +HP+LSEA+H+AA+AV+  AIH AN
Sbjct: 425 LVGANVSELVHEGVLTMEFSGSADDLARICHAHPSLSEAVHDAAMAVHKRAIHKAN 480


Lambda     K      H
   0.316    0.134    0.375 

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: 712
Number of extensions: 28
Number of successful extensions: 2
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: 480
Length adjustment: 34
Effective length of query: 444
Effective length of database: 446
Effective search space:   198024
Effective search space used:   198024
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 WP_036136112.1 N800_RS06360 (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.2834393.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-153  497.1   4.0   2.6e-153  496.9   4.0    1.0  1  NCBI__GCF_000768355.1:WP_036136112.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000768355.1:WP_036136112.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.9   4.0  2.6e-153  2.6e-153       1     460 [.       6     477 ..       6     478 .. 0.95

  Alignments for each domain:
  == domain 1  score: 496.9 bits;  conditional E-value: 2.6e-153
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalve.......keklGGtClnvGCiPtKalLksaevveelke.ake 65 
                                           ++dvvviGgGp+GY aAiraaqlglk+a+++       k  lGGtCl vGCiP+KalL s+  + ++ + +++
  NCBI__GCF_000768355.1:WP_036136112.1   6 NFDVVVIGGGPAGYHAAIRAAQLGLKTACIDaalgkdgKPALGGTCLRVGCIPSKALLDSSRQFWNMGHiFDQ 78 
                                           69****************************85555444568******************************** PP

                             TIGR01350  66 lgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniii 137
                                           +gi+ e+ ++d++k+++rk+ +vk+ +gG++ L+k nkv  + G ++l+  + v+v++++++  +l+  n+ii
  NCBI__GCF_000768355.1:WP_036136112.1  79 HGISFEKPAIDVKKMVARKDGIVKQFTGGIASLFKANKVAAFYGFGQLQPGNVVKVTQHDGSvVELKGTNVII 151
                                           ***********************************************************9887788899**** PP

                             TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpald 210
                                           A Gs+ +elp+  ++d+++++++ + l ++ vpe+l ++G+GviG+E++s++++lG+kvt++e+l+  l a d
  NCBI__GCF_000768355.1:WP_036136112.1 152 AAGSDSIELPF-AKFDGECIVDNVGGLDFEAVPERLGVIGAGVIGLELGSVWNRLGAKVTILEALPGFLSAAD 223
                                           ***********.99*********************************************************** PP

                             TIGR01350 211 aevskvlkkklkkkgvkiltnakvt..eve..keedevvveakkk.evetleaekvLvavGrkpnleelglek 278
                                           aev kv ++++kk+g++i+ +akv+  ev+   +++ev+++  +   ++tl ++k+LvavGr++ +++l  e 
  NCBI__GCF_000768355.1:WP_036136112.1 224 AEVGKVSAREFKKQGLDIKLGAKVSkaEVKgkGKKKEVELTYTDAaGEQTLVVDKLLVAVGRRAATKGLLAEG 296
                                           ************************9553331134455554444444679************************ PP

                             TIGR01350 279 lgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePe 351
                                           +gv+++erg+i+vde+++t v+g++a+GD+++++mLAh+ ++eg+ +ae iag    +++ +++P viytePe
  NCBI__GCF_000768355.1:WP_036136112.1 297 TGVRVNERGQIEVDEHCHTGVDGVWAVGDCVRGPMLAHKGFEEGIAVAELIAGLPG-HVNFDTIPWVIYTEPE 368
                                           *****************************************************777.9*************** PP

                             TIGR01350 352 vasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalav 424
                                           +a vG+teeq+k+eg+ +k+g+fpfaa+g+a+a+ e  Gfvkvi++ +t+++lG+h+vga++sel++e +l +
  NCBI__GCF_000768355.1:WP_036136112.1 369 IAWVGKTEEQLKAEGVPYKAGSFPFAAVGRAVAMAEPAGFVKVIAHAETDRVLGMHLVGANVSELVHEGVLTM 441
                                           ************************************************************************* PP

                             TIGR01350 425 eleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                           e+ +++++la+++h+HP+lsEa+++aa a+ ++aih
  NCBI__GCF_000768355.1:WP_036136112.1 442 EFSGSADDLARICHAHPSLSEAVHDAAMAVHKRAIH 477
                                           **********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (480 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: 15.21
//
[ok]

This GapMind analysis is from Sep 24 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