Alignments for a candidate for lpd in Novosphingobium aromaticivorans DSM 12444

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Novosphingobium aromaticivorans DSM 12444

Align Dihydrolipoyl dehydrogenase, mitochondrial; Dihydrolipoamide dehydrogenase; Glycine cleavage system L protein; Pyruvate dehydrogenase complex E3 subunit; E3; PDC-E3; EC 1.8.1.4 (characterized)
to candidate WP_011444837.1 SARO_RS05875 dihydrolipoyl dehydrogenase

Query= SwissProt::P31023
         (501 letters)



>NCBI__GCF_000013325.1:WP_011444837.1
          Length = 466

 Score =  504 bits (1298), Expect = e-147
 Identities = 265/466 (56%), Positives = 336/466 (72%), Gaps = 9/466 (1%)

Query: 39  DVVIIGGGPGGYVAAIKAAQLGFKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 98
           DV+ IG GPGGYV AI+ AQLG KT C E R  LGGTCLNVGCIPSKALLH S  + EA+
Sbjct: 7   DVLFIGAGPGGYVGAIRTAQLGLKTACAEGRETLGGTCLNVGCIPSKALLHGSEKFDEAR 66

Query: 99  H-SFANHGVKVSNVEIDLAAMMGQKDKAVSNLTRGIEGLFKKNKVTYVKGYGKFVSPSEI 157
           + +FA++G+K   VE+DL AM  QK  +V +LT GIE LFKKNKVT++KGY  F     +
Sbjct: 67  NGTFASYGIKTGAVELDLDAMQAQKADSVKSLTGGIEFLFKKNKVTWLKGYAAFEDAHTV 126

Query: 158 SVDTIEGENTVVKGKHIIIATGSDVKSLPGVTIDEKK--IVSSTGALALSEIPKKLVVIG 215
              T+ G+   V  K+I+IATGS V  LPGVT+D     IV STGALAL+ +P+ LVVIG
Sbjct: 127 ---TVAGQK--VTAKNIVIATGSSVTPLPGVTVDNDAGVIVDSTGALALNRVPQHLVVIG 181

Query: 216 AGYIGLEMGSVWGRIGSEVTVVEFASEIVPTMDAEIRKQFQRSLEKQGMKFKLKTKVVGV 275
            G IGLE+GSVW R+G++VTVVEF  +++P MD ++RK+  +  +KQGM+ KL TKV GV
Sbjct: 182 GGVIGLELGSVWRRLGAKVTVVEFLDQLLPGMDGDVRKEAAKIFKKQGMELKLGTKVTGV 241

Query: 276 DTSGDGVKLTVEPSAGGEQTIIEADVVLVSAGRTPFTSGLNLDKIGVETDKLGRILVNER 335
             +G    LTVEPS GGE + IEAD VLV+ GR P   GL LDKIG+E +  G+I  +  
Sbjct: 242 AVNGGTATLTVEPSKGGEASTIEADCVLVAIGRRPNVDGLGLDKIGLELNARGQIETDHD 301

Query: 336 FSTNVSGVYAIGDVIPGPMLAHKAEEDGVACVEYLAGKVGHVDYDKVPGVVYTNPEVASV 395
           F+T + GV+AIGDVIPGPMLAHKAE++G+A  E +AG  G V++D +PGVVYT PE A V
Sbjct: 302 FATKIPGVWAIGDVIPGPMLAHKAEDEGIAVAENIAGLTGIVNHDVIPGVVYTMPEFAGV 361

Query: 396 GKTEEQVKETGVEYRVGKFPFMANSRAKAIDNAEGLVKIIAEKETDKILGVHIMAPNAGE 455
           G TEE  KE G E +VGKFP +ANSRAK     +G VK+I++ +TD++LGV  +A  AG 
Sbjct: 362 GLTEEAAKERG-EIKVGKFPMLANSRAKTNHEPDGFVKVISDAKTDRVLGVWCIASVAGT 420

Query: 456 LIHEAAIALQYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHI 501
           +I +AA A+++ A+SEDIA  CHAHPT SEA+KEAAMA   KPIH+
Sbjct: 421 MIAQAAQAMEFGATSEDIAYTCHAHPTHSEALKEAAMAVTGKPIHM 466


Lambda     K      H
   0.315    0.133    0.370 

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: 663
Number of extensions: 34
Number of successful extensions: 5
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: 501
Length of database: 466
Length adjustment: 34
Effective length of query: 467
Effective length of database: 432
Effective search space:   201744
Effective search space used:   201744
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: 42 (22.0 bits)
S2: 52 (24.6 bits)

Align candidate WP_011444837.1 SARO_RS05875 (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.28232.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-166  540.8   7.1   1.5e-166  540.6   7.1    1.0  1  lcl|NCBI__GCF_000013325.1:WP_011444837.1  SARO_RS05875 dihydrolipoyl dehyd


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013325.1:WP_011444837.1  SARO_RS05875 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.6   7.1  1.5e-166  1.5e-166       2     461 .]       6     466 .]       5     466 .] 0.97

  Alignments for each domain:
  == domain 1  score: 540.6 bits;  conditional E-value: 1.5e-166
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke..akelg 67 
                                               ydv+ iG+GpgGYv Air+aqlglk+a+ e  e+lGGtClnvGCiP+KalL+ +e ++e+++  ++++g
  lcl|NCBI__GCF_000013325.1:WP_011444837.1   6 YDVLFIGAGPGGYVGAIRTAQLGLKTACAEGrETLGGTCLNVGCIPSKALLHGSEKFDEARNgtFASYG 74 
                                               9*****************************879****************************9989**** PP

                                 TIGR01350  68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleaknii 136
                                               i++  v+ldl++++++k   vk+l+gG+++L+kknkv+ +kG+a ++d+++v+v+++k    ++akni+
  lcl|NCBI__GCF_000013325.1:WP_011444837.1  75 IKTGAVELDLDAMQAQKADSVKSLTGGIEFLFKKNKVTWLKGYAAFEDAHTVTVAGQK----VTAKNIV 139
                                               *******************************************************998....88***** PP

                                 TIGR01350 137 iAtGseprelplk.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldr 204
                                               iAtGs+++ lp+  +++d  v+++s++al+l++vp++lv++GgGviG+E++s++++lG+kvtv+e+ld+
  lcl|NCBI__GCF_000013325.1:WP_011444837.1 140 IATGSSVTPLPGVtVDNDAGVIVDSTGALALNRVPQHLVVIGGGVIGLELGSVWRRLGAKVTVVEFLDQ 208
                                               ************98999999************************************************* PP

                                 TIGR01350 205 ilpaldaevskvlkkklkkkgvkiltnakvt..evekeedevvveakkk.evetleaekvLvavGrkpn 270
                                               +lp +d +v k+++k +kk+g++++ ++kvt  +v+   ++++ve +k+ e++t+ea+ vLva+Gr+pn
  lcl|NCBI__GCF_000013325.1:WP_011444837.1 209 LLPGMDGDVRKEAAKIFKKQGMELKLGTKVTgvAVNGGTATLTVEPSKGgEASTIEADCVLVAIGRRPN 277
                                               *******************************6556666666778888878******************* PP

                                 TIGR01350 271 leelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidy 339
                                               +++lgl+k+g+el+ rg+i++d+++ t++pg++aiGDvi ++mLAh+A++eg+ +ae+iag +   +++
  lcl|NCBI__GCF_000013325.1:WP_011444837.1 278 VDGLGLDKIGLELNARGQIETDHDFATKIPGVWAIGDVIPGPMLAHKAEDEGIAVAENIAGLTG-IVNH 345
                                               *************************************************************887.9*** PP

                                 TIGR01350 340 kavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahi 408
                                               +++P v+yt Pe a vGltee ake+  e+kvgkfp+ an++a + +e dGfvkvi d kt+++lG+  
  lcl|NCBI__GCF_000013325.1:WP_011444837.1 346 DVIPGVVYTMPEFAGVGLTEEAAKER-GEIKVGKFPMLANSRAKTNHEPDGFVKVISDAKTDRVLGVWC 413
                                               ************************99.79**************************************** PP

                                 TIGR01350 409 vgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               ++  a  +i+++a a+e+++t+e++a t+h+HPt sEa+keaa a++gk+ih+
  lcl|NCBI__GCF_000013325.1:WP_011444837.1 414 IASVAGTMIAQAAQAMEFGATSEDIAYTCHAHPTHSEALKEAAMAVTGKPIHM 466
                                               ****************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (466 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: 7.74
//
[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