Alignments for a candidate for lpd in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Halomonas desiderata SP1

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_086511849.1 BZY95_RS21050 dihydrolipoyl dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>NCBI__GCF_002151265.1:WP_086511849.1
          Length = 701

 Score =  873 bits (2256), Expect = 0.0
 Identities = 442/590 (74%), Positives = 494/590 (83%), Gaps = 7/590 (1%)

Query: 5   EVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVKVG 64
           EV+VPDIGDF  V VIEVLV+ GDT+  E SLI LESDKA+MDVP+  AG+V EV V VG
Sbjct: 119 EVRVPDIGDFGDVPVIEVLVRPGDTIRAEDSLITLESDKAAMDVPAPKAGRVAEVLVTVG 178

Query: 65  DKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPAPAPAAASHSGGADIQCEML 124
           DKV QG+ I  +EA+ +A A APAQ    A  PAP      PAP AAS+ GGAD++C ML
Sbjct: 179 DKVSQGSPILMLEAEGSAHAAAPAQV---AGQPAPVT----PAPKAASYGGGADLECAML 231

Query: 125 VLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVIDEAKALA 184
           VLGAGPGGYSAAFRAADLGM TVLVERY+TLGGVCLNVGCIPSKALLH AAV D A A+A
Sbjct: 232 VLGAGPGGYSAAFRAADLGMKTVLVERYATLGGVCLNVGCIPSKALLHVAAVTDAANAMA 291

Query: 185 AHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPHHMEVELT 244
            HGI FG+ KIDLD LR +K +VV KLTGGLAGMAKARKV+VVRG+G FLDPHH+EV LT
Sbjct: 292 DHGIAFGKPKIDLDKLRGWKEKVVDKLTGGLAGMAKARKVEVVRGVGTFLDPHHLEVALT 351

Query: 245 EGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPNKMLVIGG 304
            G+G+  TG K VI+F K IIAAGSQ+VKLPFIP+DPR+VDSTGAL+L  +P +MLVIGG
Sbjct: 352 GGDGQEPTGAKQVIKFGKCIIAAGSQSVKLPFIPDDPRVVDSTGALKLTTIPKRMLVIGG 411

Query: 305 GIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLKTKTVGVE 364
           GIIGLEMATVYSTLG  IDVVEMLDGLM GADRDLVKVWEK N+ RF KVML T+T  V+
Sbjct: 412 GIIGLEMATVYSTLGTRIDVVEMLDGLMAGADRDLVKVWEKVNQPRFDKVMLNTRTTAVK 471

Query: 365 AKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFINVDKQMR 424
           A+ +G+ V FEGE APAEPQ YD++L +VGRSPNG +I AE AGVAV ERGFI  DKQMR
Sbjct: 472 AQKNGLKVSFEGEGAPAEPQLYDMILQAVGRSPNGHKIGAENAGVAVDERGFIATDKQMR 531

Query: 425 TNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDPEVAWAGL 484
           TNV HIFAIGDIVGQPMLAHKAVHEAHVAAEAA G K++FDA+Q PSVA+TDPEVAWAG 
Sbjct: 532 TNVGHIFAIGDIVGQPMLAHKAVHEAHVAAEAAAGHKSFFDARQNPSVAYTDPEVAWAGK 591

Query: 485 TEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGTHAGDLI 544
           TE ECK +GIKY K VFPWAASGRAIANGRDEGFTKLIFDEETHR+IGG IVGT AGDLI
Sbjct: 592 TEAECKAEGIKYGKAVFPWAASGRAIANGRDEGFTKLIFDEETHRIIGGAIVGTQAGDLI 651

Query: 545 SEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
            E+CLAIEMG D VDIGKTIHPHPTLGES+GMAAE++EG CTD+PP +KR
Sbjct: 652 GELCLAIEMGCDPVDIGKTIHPHPTLGESVGMAAELFEGVCTDLPPQKKR 701



 Score =  102 bits (255), Expect = 4e-26
 Identities = 56/121 (46%), Positives = 74/121 (61%), Gaps = 12/121 (9%)

Query: 2   SVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKV 61
           + IEVKVPDIGDF  VE+IEVLVK GD ++++  LI LE+DKASMDVPS  +G V  ++V
Sbjct: 3   NAIEVKVPDIGDFKDVEIIEVLVKPGDAIDIDTPLITLETDKASMDVPSPVSGTVAALRV 62

Query: 62  KVGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAP-----AAAAPAPAPAAASHSGG 116
           K GD+V +G++I  +E       PA A +      P P        +PAP  A   + GG
Sbjct: 63  KEGDRVSEGSLILMLE-------PAEAGSRVMDHEPQPVVHERGVGSPAPGDAGGGYGGG 115

Query: 117 A 117
           A
Sbjct: 116 A 116


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: 1277
Number of extensions: 53
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 594
Length of database: 701
Length adjustment: 38
Effective length of query: 556
Effective length of database: 663
Effective search space:   368628
Effective search space used:   368628
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: 54 (25.4 bits)

Align candidate WP_086511849.1 BZY95_RS21050 (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.12803.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.1e-142  459.2   2.0   9.1e-142  458.9   2.0    1.1  1  lcl|NCBI__GCF_002151265.1:WP_086511849.1  BZY95_RS21050 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511849.1  BZY95_RS21050 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.9   2.0  9.1e-142  9.1e-142       4     453 ..     230     687 ..     227     693 .. 0.96

  Alignments for each domain:
  == domain 1  score: 458.9 bits;  conditional E-value: 9.1e-142
                                 TIGR01350   4 vvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgieve 71 
                                               ++v+G+GpgGY aA raa lg+k++lve+  +lGG+ClnvGCiP+KalL+ a v + ++ ++++gi   
  lcl|NCBI__GCF_002151265.1:WP_086511849.1 230 MLVLGAGPGGYSAAFRAADLGMKTVLVERyATLGGVCLNVGCIPSKALLHVAAVTDAANAMADHGIAFG 298
                                               68***************************99************************************** PP

                                 TIGR01350  72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke........kklea 132
                                               + k+dl+kl  +kekvv+kl+gG++++ k  kvev+ G +++ld++++ev+ + +         +++++
  lcl|NCBI__GCF_002151265.1:WP_086511849.1 299 KPKIDLDKLRGWKEKVVDKLTGGLAGMAKARKVEVVRGVGTFLDPHHLEVALTGGDgqeptgakQVIKF 367
                                               ***********************************************9998776656689999999*** PP

                                 TIGR01350 133 kniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtviel 201
                                                ++iiA Gs+  +lp+ +  d  +v++s++al+l+++p++++++GgG+iG+E+a+++++lG+ + v+e+
  lcl|NCBI__GCF_002151265.1:WP_086511849.1 368 GKCIIAAGSQSVKLPF-IPDDP-RVVDSTGALKLTTIPKRMLVIGGGIIGLEMATVYSTLGTRIDVVEM 434
                                               ****************.55554.7********************************************* PP

                                 TIGR01350 202 ldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrk 268
                                               ld +++  d+++ kv +k  + +  k++ n++ t+v+++++ ++v+ +++   +e   ++ +L avGr+
  lcl|NCBI__GCF_002151265.1:WP_086511849.1 435 LDGLMAGADRDLVKVWEKVNQPRFDKVMLNTRTTAVKAQKNGLKVSFEGEgaPAEPQLYDMILQAVGRS 503
                                               ******************9999999999999999999998888877666644778899*********** PP

                                 TIGR01350 269 pnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeksei 337
                                               pn +++g e+ gv +derg+i +d+++rtnv +i+aiGD++g++mLAh+A++e+ vaae++ag++ s +
  lcl|NCBI__GCF_002151265.1:WP_086511849.1 504 PNGHKIGAENAGVAVDERGFIATDKQMRTNVGHIFAIGDIVGQPMLAHKAVHEAHVAAEAAAGHK-SFF 571
                                               ***************************************************************55.59* PP

                                 TIGR01350 338 dykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGa 406
                                               d+++ Psv yt+Peva  G+te+++k+egi++  + fp aa+g+a+a + ++Gf k+i+d++t++i+G 
  lcl|NCBI__GCF_002151265.1:WP_086511849.1 572 DARQNPSVAYTDPEVAWAGKTEAECKAEGIKYGKAVFPWAASGRAIANGRDEGFTKLIFDEETHRIIGG 640
                                               ********************************************************************* PP

                                 TIGR01350 407 hivgaeaseliselalaveleltveelaktihpHPtlsEaikeaala 453
                                                ivg++a +li el la+e++    ++ ktihpHPtl+E +  aa+ 
  lcl|NCBI__GCF_002151265.1:WP_086511849.1 641 AIVGTQAGDLIGELCLAIEMGCDPVDIGKTIHPHPTLGESVGMAAEL 687
                                               ****************************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (701 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: 16.45
//
[ok]

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

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Protein sequences (fasta format)
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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