GapMind for catabolism of small carbon sources

 

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

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_036138918.1 N800_RS12045 dihydrolipoyl dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>NCBI__GCF_000768355.1:WP_036138918.1
          Length = 614

 Score =  703 bits (1814), Expect = 0.0
 Identities = 378/623 (60%), Positives = 453/623 (72%), Gaps = 38/623 (6%)

Query: 1   MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60
           M  IE+KVPDIG +D V VIE+LV  GDTV  +Q L+ LESDKA+M+VP+S AG + E+K
Sbjct: 1   MPTIEIKVPDIGGYDDVPVIELLVAVGDTVAKDQGLVTLESDKATMEVPASHAGVIRELK 60

Query: 61  VKVGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPAPA------------- 107
           VK+GD V +G+VI  IEA+   AAPA   A APA APA AA A  PA             
Sbjct: 61  VKLGDAVSEGSVIALIEAEGEGAAPAATPATAPAAAPASAAPAATPAATGAASAPIAPVA 120

Query: 108 ----------PAAASHSGGA-DIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLG 156
                     PA A+ SG   DI+C MLVLGAGPGGY+AAFR+ADLGM+TVL+ERY++LG
Sbjct: 121 PVAQPASPAGPAPAAASGRKPDIECRMLVLGAGPGGYTAAFRSADLGMDTVLIERYASLG 180

Query: 157 GVCLNVGCIPSKALLHNAAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLA 216
           GVCLNVGCIPSKALLH AAVIDEA     +GI FG+ KI LD LR YK +VVG+LT GL+
Sbjct: 181 GVCLNVGCIPSKALLHAAAVIDEAAHAKDYGIDFGKPKITLDALRAYKEKVVGQLTKGLS 240

Query: 217 GMAKARKVQVVRGIGNFLDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPF 276
           GMAK RKV+VV G+G F+ PH +EV    G          +IRFE+ IIAAGSQAVKLP 
Sbjct: 241 GMAKQRKVRVVEGVGKFVSPHEVEVAGPNGT--------QLIRFEQCIIAAGSQAVKLPG 292

Query: 277 IP-EDPRIVDSTGALELPEVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGA 335
            P  D R++DST ALEL EVP ++LV+GGGIIGLEMATVY  LG+++ VVE  D +M GA
Sbjct: 293 FPWGDARVMDSTDALELAEVPKRLLVVGGGIIGLEMATVYRALGSEVTVVEFADQIMPGA 352

Query: 336 DRDLVKVWEKKNKDRFGKVMLKTKTVGVEAKPDGIYVKFE----GEAAPAEPQRYDLVLV 391
           D DL+K    + K +   V  K K  G EA   G+ V+FE    G +AP EPQ +D VLV
Sbjct: 353 DTDLIKPLADRLKKQGVIVHTKVKAAGTEALKGGLKVRFEPAQEGGSAP-EPQTFDRVLV 411

Query: 392 SVGRSPNGKRISAEKAGVAVSERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAH 451
           +VGRSPNG ++ A KAGV+V++RGFI VD+QMRTNVPHIFAIGD+VGQPMLAHKA HE  
Sbjct: 412 AVGRSPNGGKLDANKAGVSVTDRGFIPVDRQMRTNVPHIFAIGDLVGQPMLAHKATHEGK 471

Query: 452 VAAEAAHGEKAYFDAKQIPSVAFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIA 511
           +AAE A GEK  + A+ IPSVA+TDPE+AW G+TE E K KG+K   G FPWAASGRAI 
Sbjct: 472 LAAEVAFGEKKEWVARVIPSVAYTDPEIAWVGVTETEAKAKGLKVGVGKFPWAASGRAIG 531

Query: 512 NGRDEGFTKLIFDEETHRVIGGGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLG 571
            GR EGFTKL+FDE THR+IGGGIVG HAGDLI+E+ LAIEMG +  DIG TIHPHPTL 
Sbjct: 532 LGRTEGFTKLVFDEATHRIIGGGIVGVHAGDLIAEIGLAIEMGCEVHDIGATIHPHPTLS 591

Query: 572 ESIGMAAEIYEGTCTDVPPPRKR 594
           ES+GMAAE+Y+GT TD+  P+K+
Sbjct: 592 ESVGMAAEVYDGTITDLYLPKKK 614


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: 1051
Number of extensions: 49
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: 614
Length adjustment: 37
Effective length of query: 557
Effective length of database: 577
Effective search space:   321389
Effective search space used:   321389
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 WP_036138918.1 N800_RS12045 (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.2166604.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-154  501.2   1.3   1.7e-154  500.8   1.3    1.1  1  NCBI__GCF_000768355.1:WP_036138918.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000768355.1:WP_036138918.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  500.8   1.3  1.7e-154  1.7e-154       3     454 ..     146     601 ..     144     607 .. 0.96

  Alignments for each domain:
  == domain 1  score: 500.8 bits;  conditional E-value: 1.7e-154
                             TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 
                                            ++v+G+GpgGY+aA r+a lg+ ++l+e+  +lGG+ClnvGCiP+KalL++a v++e+ +ak++gi+  + k
  NCBI__GCF_000768355.1:WP_036138918.1 146 RMLVLGAGPGGYTAAFRSADLGMDTVLIERyASLGGVCLNVGCIPSKALLHAAAVIDEAAHAKDYGIDFGKPK 218
                                           578***************************99***************************************** PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147
                                           + l++l + kekvv +l++G++++ k+ kv v++G +k+++++evev++ ++++ ++++++iiA Gs+  +lp
  NCBI__GCF_000768355.1:WP_036138918.1 219 ITLDALRAYKEKVVGQLTKGLSGMAKQRKVRVVEGVGKFVSPHEVEVAGPNGTQLIRFEQCIIAAGSQAVKLP 291
                                           ************************************************************************* PP

                             TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220
                                           + +     +v++s++alel evp++l++vGgG+iG+E+a++++ lG++vtv+e++d+i+p  d+++ k l+++
  NCBI__GCF_000768355.1:WP_036138918.1 292 G-FPWGDARVMDSTDALELAEVPKRLLVVGGGIIGLEMATVYRALGSEVTVVEFADQIMPGADTDLIKPLADR 363
                                           *.9999999**************************************************************** PP

                             TIGR01350 221 lkkkgvkiltnakvtevekeedevv.....veakkkevetleaekvLvavGrkpnleelgleklgvelderga 288
                                           lkk+gv ++t+ k   +e+ +  ++     +++ ++  e  + ++vLvavGr+pn  +l+ +k gv++++rg+
  NCBI__GCF_000768355.1:WP_036138918.1 364 LKKQGVIVHTKVKAAGTEALKGGLKvrfepAQEGGSAPEPQTFDRVLVAVGRSPNGGKLDANKAGVSVTDRGF 436
                                           ***********999966666665553355444444477899******************************** PP

                             TIGR01350 289 ikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeq 361
                                           i+vd+++rtnvp+i+aiGD++g++mLAh+A++eg +aae ++g++k e  ++++Psv yt+Pe+a vG+te++
  NCBI__GCF_000768355.1:WP_036138918.1 437 IPVDRQMRTNVPHIFAIGDLVGQPMLAHKATHEGKLAAEVAFGEKK-EWVARVIPSVAYTDPEIAWVGVTETE 508
                                           *******************************************887.899*********************** PP

                             TIGR01350 362 akeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveela 434
                                           ak++g +v vgkfp aa+g+a+ l+ t+Gf k+++d+ t++i+G  ivg +a +li+e+ la+e++ +v+++ 
  NCBI__GCF_000768355.1:WP_036138918.1 509 AKAKGLKVGVGKFPWAASGRAIGLGRTEGFTKLVFDEATHRIIGGGIVGVHAGDLIAEIGLAIEMGCEVHDIG 581
                                           ************************************************************************* PP

                             TIGR01350 435 ktihpHPtlsEaikeaalaa 454
                                           +tihpHPtlsE +  aa+  
  NCBI__GCF_000768355.1:WP_036138918.1 582 ATIHPHPTLSESVGMAAEVY 601
                                           *************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (614 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 40.43
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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