Alignments for a candidate for lpd in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Paraburkholderia phymatum STM815

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_012401111.1 BPHY_RS08755 dihydrolipoyl dehydrogenase

Query= CharProtDB::CH_015561
         (478 letters)



>NCBI__GCF_000020045.1:WP_012401111.1
          Length = 476

 Score =  520 bits (1338), Expect = e-152
 Identities = 268/477 (56%), Positives = 348/477 (72%), Gaps = 6/477 (1%)

Query: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60
           M+++FDVVVIGAGPGGY+AAI+AAQLG   ACIEK+ +  G L LGGTCLNVGCIPSKAL
Sbjct: 1   MSKEFDVVVIGAGPGGYIAAIRAAQLGKTVACIEKWKNPAGALKLGGTCLNVGCIPSKAL 60

Query: 61  LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120
           L SS +++ A      HGIS   VK+D+A M+ RK GIV+ +T G+  LF+ N +T ++G
Sbjct: 61  LASSEEFENASHHLADHGISVENVKVDIAKMLARKEGIVEKMTKGIEFLFRKNKITWLKG 120

Query: 121 HGKLL----AGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALE 176
           HGK      AG ++EV+  +G TEV+ A+NVI+A+GS+   +P  PVD  ++ D+ GAL 
Sbjct: 121 HGKFTGKTDAGVQIEVS-GEGETEVVTAKNVIIATGSKARHLPNVPVDNKIVADNEGALS 179

Query: 177 FQAVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQG 236
           F  VPK+L VIGAGVIGLELGSVW RLGAEVTVLEAL  FL AAD A++KEA K   KQG
Sbjct: 180 FTEVPKKLAVIGAGVIGLELGSVWRRLGAEVTVLEALPEFLGAADQALAKEAAKQFKKQG 239

Query: 237 LDIKLGARVTGSKVNGNEVEVTYTNAEGEQK-ITFDKLIVAVGRRPVTTDLLAADSGVTI 295
           LDI +G +V   K   N V ++YT+ +G  K +  D+LIV++GR P T +L     G+  
Sbjct: 240 LDIHVGVKVGEVKTTANSVSISYTDKDGNAKTLDADRLIVSIGRVPNTDNLGLEAIGLKA 299

Query: 296 DERGYIFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPS 355
           +ERG+I VDD+CATSVP VYAIGDVVRG MLAHKA +EG++V E I G K  ++Y+ +P 
Sbjct: 300 NERGFIDVDDHCATSVPNVYAIGDVVRGPMLAHKAEDEGVLVAEVIDGQKPHIDYNCVPW 359

Query: 356 VIYTHPEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVL 415
           VIYT PEIAWVGKTEQ LKAEG E+  G FPF A+GRA+  N   GFVK+IADAKTD +L
Sbjct: 360 VIYTEPEIAWVGKTEQQLKAEGREIKSGQFPFMANGRALGINKADGFVKMIADAKTDELL 419

Query: 416 GVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHV 472
           GVH+I  +A++L+ +  +AMEF  ++ED+G +   HP+LSE + EAALAV+  A+++
Sbjct: 420 GVHIIAANASDLIAEAVVAMEFKAASEDIGRICHPHPSLSEVMREAALAVDKRALNM 476


Lambda     K      H
   0.316    0.133    0.374 

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: 708
Number of extensions: 28
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: 478
Length of database: 476
Length adjustment: 33
Effective length of query: 445
Effective length of database: 443
Effective search space:   197135
Effective search space used:   197135
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_012401111.1 BPHY_RS08755 (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.1693426.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-176  572.8   8.6   2.8e-176  572.6   8.6    1.0  1  NCBI__GCF_000020045.1:WP_012401111.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020045.1:WP_012401111.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.6   8.6  2.8e-176  2.8e-176       1     461 []       4     476 .]       4     476 .] 0.96

  Alignments for each domain:
  == domain 1  score: 572.6 bits;  conditional E-value: 2.8e-176
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.e......klGGtClnvGCiPtKalLksaevveelke.ake 65 
                                           e+dvvviG+GpgGY+aAiraaqlg+ va++ek +      klGGtClnvGCiP+KalL+s+e +e++++ +++
  NCBI__GCF_000020045.1:WP_012401111.1   4 EFDVVVIGAGPGGYIAAIRAAQLGKTVACIEKwKnpagalKLGGTCLNVGCIPSKALLASSEEFENASHhLAD 76 
                                           69*****************************96445555569**************************99*** PP

                             TIGR01350  66 lgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkk....evevkkekkekkleakn 134
                                           +gi+venvk+d++k+l+rke +v+k+++G+++L++knk++ +kG++k+++k+    ++ev++e ++++++akn
  NCBI__GCF_000020045.1:WP_012401111.1  77 HGISVENVKVDIAKMLARKEGIVEKMTKGIEFLFRKNKITWLKGHGKFTGKTdagvQIEVSGEGETEVVTAKN 149
                                           ************************************************996523336888888888******* PP

                             TIGR01350 135 iiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp 207
                                           +iiAtGs+ r+lp  + +d+k+v ++e+al+++evp++l+++G+GviG+E++s++++lG++vtv+e+l++ l 
  NCBI__GCF_000020045.1:WP_012401111.1 150 VIIATGSKARHLPN-VPVDNKIVADNEGALSFTEVPKKLAVIGAGVIGLELGSVWRRLGAEVTVLEALPEFLG 221
                                           **************.********************************************************** PP

                             TIGR01350 208 aldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelglek 278
                                           a d+ ++k+++k++kk+g++i+ + kv ev++++++v+  ++ k+++++tl+a++++v++Gr pn+++lgle+
  NCBI__GCF_000020045.1:WP_012401111.1 222 AADQALAKEAAKQFKKQGLDIHVGVKVGEVKTTANSVSisYTDKDGNAKTLDADRLIVSIGRVPNTDNLGLEA 294
                                           ******************************999999995556666699************************* PP

                             TIGR01350 279 lgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePe 351
                                           +g++ +erg+i vd+++ t+vp++yaiGDv++++mLAh+A++egv++ae i g+++ +idy+ vP viytePe
  NCBI__GCF_000020045.1:WP_012401111.1 295 IGLKANERGFIDVDDHCATSVPNVYAIGDVVRGPMLAHKAEDEGVLVAEVIDGQKP-HIDYNCVPWVIYTEPE 366
                                           *****************************************************998.9*************** PP

                             TIGR01350 352 vasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalav 424
                                           +a vG+te+q+k+eg e+k+g+fpf+ang+al ++++dGfvk+i+d kt+e+lG+hi++a+as+li+e+++a+
  NCBI__GCF_000020045.1:WP_012401111.1 367 IAWVGKTEQQLKAEGREIKSGQFPFMANGRALGINKADGFVKMIADAKTDELLGVHIIAANASDLIAEAVVAM 439
                                           ************************************************************************* PP

                             TIGR01350 425 eleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                           e+++ +e++ +++hpHP+lsE++ eaala+ ++a+++
  NCBI__GCF_000020045.1:WP_012401111.1 440 EFKAASEDIGRICHPHPSLSEVMREAALAVDKRALNM 476
                                           ******************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (476 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: 20.90
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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