GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Dyella japonica UNC79MFTsu3.2

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate N515DRAFT_2155 N515DRAFT_2155 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2155
          Length = 594

 Score =  766 bits (1977), Expect = 0.0
 Identities = 399/602 (66%), Positives = 481/602 (79%), Gaps = 19/602 (3%)

Query: 2   SVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKV 61
           + IEVKVPDIG  D+V VIEVLVKAGD+V  +QSLI LESDKA+M++PSSAAG + EVKV
Sbjct: 3   NTIEVKVPDIGGHDSVPVIEVLVKAGDSVTKDQSLITLESDKATMEIPSSAAGTIKEVKV 62

Query: 62  KVGDKVGQGAVICTIEAQQAAAAPAP-------AQAPAPAQAPAPAAAAPAPAPAAASHS 114
           KVGD++ +GAVI  +E    AAAPA        A APAPA APAPA AA APAP AA  S
Sbjct: 63  KVGDELSEGAVIVILEVSGDAAAPAAEAPKAAAAPAPAPASAPAPAKAA-APAPQAAGAS 121

Query: 115 GG-ADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHN 173
           G  ADI+C+++VLG+GPGGY+AAFRAADLG++TVLVERY+TLGGVCLNVGCIPSKALLH 
Sbjct: 122 GRTADIECKLVVLGSGPGGYTAAFRAADLGVDTVLVERYATLGGVCLNVGCIPSKALLHA 181

Query: 174 AAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNF 233
           AAVIDEA+A+AAHG+ FG+ K+DLD LR +KN+VVG+LTGGLAGM++ RKV+ V+G+G+F
Sbjct: 182 AAVIDEAEAMAAHGVSFGKPKLDLDKLRSFKNKVVGQLTGGLAGMSRQRKVRTVQGVGSF 241

Query: 234 LDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIP-EDPRIVDSTGALEL 292
           + PH +EVE  EG        K ++RFE AIIAAGSQ+VKLP  P +D R++DSTGALEL
Sbjct: 242 VSPHELEVETAEG--------KKLVRFEHAIIAAGSQSVKLPAFPWDDERVMDSTGALEL 293

Query: 293 PEVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFG 352
            +VP K+LV+GGGIIGLEMATVY+ LG+++ VVE +D L+ GAD DL+K   K+   +  
Sbjct: 294 KDVPGKLLVVGGGIIGLEMATVYAALGSEVTVVEFMDQLIPGADADLIKPLAKRLGGKLK 353

Query: 353 KVMLKTKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVS 412
            V LKTK    +A   GI V +EG++ P E + +D VLV+VGRSPNG +I A+KAGVAV+
Sbjct: 354 GVHLKTKVTEAKATKKGIEVAYEGDSIP-ETKLFDRVLVAVGRSPNGGKIGADKAGVAVT 412

Query: 413 ERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSV 472
           ERGFINVD QMRTNVPHIFAIGD+VGQPMLAHKA HEA VAAE   G K++FDA+ IPSV
Sbjct: 413 ERGFINVDTQMRTNVPHIFAIGDLVGQPMLAHKATHEARVAAEVVAGMKSHFDARVIPSV 472

Query: 473 AFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIG 532
           AFTDPEVAW G+TE E KEKG+K   G FPWAASGRAI   R EGFTKLIFDEETHRV+G
Sbjct: 473 AFTDPEVAWVGVTEREAKEKGLKIGVGKFPWAASGRAIGIDRTEGFTKLIFDEETHRVVG 532

Query: 533 GGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPR 592
           G IVG HAGDLI+E+  AIEMG++A DIG TIHPHPTL ES+GMAAE+YEGT TD+  P+
Sbjct: 533 GAIVGPHAGDLIAEITHAIEMGSEAADIGLTIHPHPTLSESVGMAAEVYEGTITDLYMPK 592

Query: 593 KR 594
           ++
Sbjct: 593 RK 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: 1014
Number of extensions: 48
Number of successful extensions: 6
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 N515DRAFT_2155 N515DRAFT_2155 (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.1620.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     3e-154  500.0   4.3   3.8e-154  499.7   4.3    1.1  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2155  N515DRAFT_2155 dihydrolipoamide 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2155  N515DRAFT_2155 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  499.7   4.3  3.8e-154  3.8e-154       3     455 ..     130     582 ..     128     587 .. 0.97

  Alignments for each domain:
  == domain 1  score: 499.7 bits;  conditional E-value: 3.8e-154
                                    TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelg 67 
                                                   +vv+G+GpgGY+aA raa lg  ++lve+  +lGG+ClnvGCiP+KalL++a v++e++ ++ +g
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 130 KLVVLGSGPGGYTAAFRAADLGVDTVLVERyATLGGVCLNVGCIPSKALLHAAAVIDEAEAMAAHG 195
                                                  68****************************99********************************** PP

                                    TIGR01350  68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleak 133
                                                  ++  + kldl+kl   k+kvv +l+gG++++ ++ kv +++G +++++++e+ev++ +++k ++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 196 VSFGKPKLDLDKLRSFKNKVVGQLTGGLAGMSRQRKVRTVQGVGSFVSPHELEVETAEGKKLVRFE 261
                                                  ****************************************************************** PP

                                    TIGR01350 134 niiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvi 199
                                                  ++iiA Gs+  +lp  +  d ++v++s++alelk vp +l++vGgG+iG+E+a+++a lG++vtv+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 262 HAIIAAGSQSVKLPA-FPWDDERVMDSTGALELKDVPGKLLVVGGGIIGLEMATVYAALGSEVTVV 326
                                                  ***************.999999******************************************** PP

                                    TIGR01350 200 elldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLva 264
                                                  e++d+++p  da++ k l+k+l  k   ++ ++kvte +++++ ++v  +++   et   ++vLva
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 327 EFMDQLIPGADADLIKPLAKRLGGKLKGVHLKTKVTEAKATKKGIEVAYEGDsIPETKLFDRVLVA 392
                                                  ***********************9999999****************99999944577779****** PP

                                    TIGR01350 265 vGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekia 330
                                                  vGr+pn  ++g +k gv ++erg+i+vd ++rtnvp+i+aiGD++g++mLAh+A++e+ vaae +a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 393 VGRSPNGGKIGADKAGVAVTERGFINVDTQMRTNVPHIFAIGDLVGQPMLAHKATHEARVAAEVVA 458
                                                  ****************************************************************** PP

                                    TIGR01350 331 gkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkviv 396
                                                  g ++ ++d++++Psv +t+Peva vG+te++ake+g ++ vgkfp aa+g+a+ ++ t+Gf k+i+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 459 GMKS-HFDARVIPSVAFTDPEVAWVGVTEREAKEKGLKIGVGKFPWAASGRAIGIDRTEGFTKLIF 523
                                                  *665.9************************************************************ PP

                                    TIGR01350 397 dkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaal 455
                                                  d++t++++G  ivg++a +li+e++ a+e++ ++ ++  tihpHPtlsE +  aa+   
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 524 DEETHRVVGGAIVGPHAGDLIAEITHAIEMGSEAADIGLTIHPHPTLSESVGMAAEVYE 582
                                                  ***************************************************99998765 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: 13.10
//
[ok]

This GapMind analysis is from Sep 17 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