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

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.25742.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: 00:00:00.03
# Mc/sec: 8.96
//
[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