Alignments for a candidate for lpd in Marinomonas arctica 328

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Marinomonas arctica 328

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_111605733.1 DK187_RS02350 dihydrolipoyl dehydrogenase

Query= BRENDA::P0A9P0
         (474 letters)



>NCBI__GCF_003259225.1:WP_111605733.1
          Length = 472

 Score =  515 bits (1326), Expect = e-150
 Identities = 259/463 (55%), Positives = 341/463 (73%), Gaps = 2/463 (0%)

Query: 9   VVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVAKVIEEAKA 68
           +VVLG+GP GY+AAFR ADLGL   ++ER+NTLGGVCLNVGCIPSKALLHVA  I  A+ 
Sbjct: 5   LVVLGSGPGGYAAAFRAADLGLSVAMIERHNTLGGVCLNVGCIPSKALLHVAGKILMAEE 64

Query: 69  LAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANTLEVE 128
            A HG+ F +P  +++ IR  ++  ++ LTGGL  MAKGRKV V++G G F   N++ V 
Sbjct: 65  PA-HGVQFAKPTINLEDIRQHRQSTVDTLTGGLTMMAKGRKVTVIHGEGTFDSTNSITVT 123

Query: 129 GENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLVMGGGIIGL 188
            +     ++F NAIIA GSR I+LPF+P++DPRI D+T AL+L+ +PE LLV+GGGIIG+
Sbjct: 124 KDGQSQQVDFKNAIIAVGSRAIKLPFVPYDDPRILDATSALQLERIPEHLLVLGGGIIGV 183

Query: 189 EMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTAVEAKEDGI 248
           EM TVY ALG++I V E+ +Q++  ADKD+V+VF +    + + + +T+VT +EA  + +
Sbjct: 184 EMATVYQALGAKITVAELGEQIMTGADKDLVRVFEQVNKDRMSFLTKTQVTNIEATPEAL 243

Query: 249 YVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQLRTNVPHI 308
            VTM+ K         DAVLVA+GR PNGK       GV++D+RGF+  +++ +T+VP+I
Sbjct: 244 NVTMQDKDGERSLS-VDAVLVAVGRSPNGKTAGISDIGVKLDERGFVLTNEKCQTSVPNI 302

Query: 309 FAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWVGLTEKEAK 368
           +AIGD+   PMLAHK  H+GH AAEVIAG K  F P  IPSIAYT PEVAWVGLTE EAK
Sbjct: 303 YAIGDVTHGPMLAHKASHQGHTAAEVIAGHKVDFQPLAIPSIAYTFPEVAWVGLTETEAK 362

Query: 369 EKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGELLGEIGLA 428
           ++ I+ +TA FPW ASGRAIAS    G TKLI+D+ + RV+G  +VG++ GELLGE+ LA
Sbjct: 363 KQNIAIKTAVFPWTASGRAIASGVTQGKTKLIYDEATERVLGAGVVGSHAGELLGELTLA 422

Query: 429 IEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKA 471
           IE G   EDIALTIHAHP+LHE+VGLAAE+  G+ITD+PN KA
Sbjct: 423 IEFGATLEDIALTIHAHPSLHETVGLAAELGAGTITDMPNKKA 465


Lambda     K      H
   0.317    0.137    0.396 

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: 611
Number of extensions: 18
Number of successful extensions: 3
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: 474
Length of database: 472
Length adjustment: 33
Effective length of query: 441
Effective length of database: 439
Effective search space:   193599
Effective search space used:   193599
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: 51 (24.3 bits)

Align candidate WP_111605733.1 DK187_RS02350 (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.3527174.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.2e-152  492.4   6.3   6.9e-152  492.2   6.3    1.0  1  NCBI__GCF_003259225.1:WP_111605733.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003259225.1:WP_111605733.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.2   6.3  6.9e-152  6.9e-152       2     453 ..       3     452 ..       2     460 .. 0.97

  Alignments for each domain:
  == domain 1  score: 492.2 bits;  conditional E-value: 6.9e-152
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                           yd+vv+G+GpgGY aA raa lgl+va++e+ ++lGG+ClnvGCiP+KalL+ a  +  + e   +g++ ++ 
  NCBI__GCF_003259225.1:WP_111605733.1   3 YDLVVLGSGPGGYAAAFRAADLGLSVAMIERhNTLGGVCLNVGCIPSKALLHVAGKIL-MAEEPAHGVQFAKP 74 
                                           9******************************999**********************99.5677889******* PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprel 146
                                           +++le++ ++++++v++l+gG++++ k  kv+vi+Ge+++ + ++++v+k+ +++++++kn+iiA Gs+ ++l
  NCBI__GCF_003259225.1:WP_111605733.1  75 TINLEDIRQHRQSTVDTLTGGLTMMAKGRKVTVIHGEGTFDSTNSITVTKDGQSQQVDFKNAIIAVGSRAIKL 147
                                           ****************************************************99******************* PP

                             TIGR01350 147 plkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkk 219
                                           p+ + +d  ++++ ++al+l+++pe+l+++GgG+iGvE+a++++ lG+k+tv el ++i+   d+++ +v  +
  NCBI__GCF_003259225.1:WP_111605733.1 148 PF-VPYDDPRILDATSALQLERIPEHLLVLGGGIIGVEMATVYQALGAKITVAELGEQIMTGADKDLVRVF-E 218
                                           **.999999***********************************************************976.5 PP

                             TIGR01350 220 klkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikv 291
                                           +++k+ +++lt+++vt++e++ +++ v++++k  +++l++++vLvavGr+pn + +g+  +gv+lderg++ +
  NCBI__GCF_003259225.1:WP_111605733.1 219 QVNKDRMSFLTKTQVTNIEATPEALNVTMQDKdGERSLSVDAVLVAVGRSPNGKTAGISDIGVKLDERGFVLT 291
                                           78999******************9998887776789************************************* PP

                             TIGR01350 292 deelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqake 364
                                           +e+++t+vp+iyaiGDv++++mLAh+As++g  aae iag +k  ++  a+Ps+ yt Peva vGlte++ak+
  NCBI__GCF_003259225.1:WP_111605733.1 292 NEKCQTSVPNIYAIGDVTHGPMLAHKASHQGHTAAEVIAG-HKVDFQPLAIPSIAYTFPEVAWVGLTETEAKK 363
                                           ****************************************.5569**************************** PP

                             TIGR01350 365 egievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelakti 437
                                           ++i++k++ fp +a+g+a+a++ t+G  k+i+d+ t+++lGa +vg +a el+ el+la+e+++t+e++a ti
  NCBI__GCF_003259225.1:WP_111605733.1 364 QNIAIKTAVFPWTASGRAIASGVTQGKTKLIYDEATERVLGAGVVGSHAGELLGELTLAIEFGATLEDIALTI 436
                                           ************************************************************************* PP

                             TIGR01350 438 hpHPtlsEaikeaala 453
                                           h+HP+l E++  aa+ 
  NCBI__GCF_003259225.1:WP_111605733.1 437 HAHPSLHETVGLAAEL 452
                                           *********9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (472 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.19
//
[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