GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lpd in Burkholderia phytofirmans PsJN

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate BPHYT_RS08120 BPHYT_RS08120 dihydrolipoamide dehydrogenase

Query= CharProtDB::CH_015561
         (478 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS08120 BPHYT_RS08120
           dihydrolipoamide dehydrogenase
          Length = 476

 Score =  512 bits (1318), Expect = e-149
 Identities = 263/477 (55%), Positives = 344/477 (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   V +D+A M+ RK GIV+ +T G+  LF+ N +T ++G
Sbjct: 61  LASSEEFENASHHLADHGISVENVSVDIAKMMARKEGIVEKMTKGIEFLFRKNKITWLKG 120

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

Query: 177 FQAVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQG 236
           F++ PK+L VIGAGVIGLELGSVW RLGA+VTVLEAL  FL AAD A++KEA K   KQG
Sbjct: 180 FESTPKKLAVIGAGVIGLELGSVWRRLGADVTVLEALPEFLGAADQALAKEAAKQFKKQG 239

Query: 237 LDIKLGARVTGSKVNGNEVEVTYTNAEGE-QKITFDKLIVAVGRRPVTTDLLAADSGVTI 295
           LDI +G +V       N V V YT+ +G  QK+  D+LIV++GR P T +L     G+  
Sbjct: 240 LDIHVGVKVGEVTTTDNSVTVNYTDKDGNAQKLEADRLIVSIGRVPNTDNLGLEAIGLKA 299

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

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

Query: 416 GVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHV 472
           GVH+I   A++L+ +  +AMEF  ++ED+G +   HP+LSE + EAALAV+  A+++
Sbjct: 420 GVHIIAADASDLIAEAVVAMEFKAASEDIGRICHPHPSLSEVMREAALAVDKRALNM 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: 721
Number of extensions: 29
Number of successful extensions: 4
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 BPHYT_RS08120 BPHYT_RS08120 (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.12647.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   9.4e-176  570.9   9.6   1.1e-175  570.8   9.6    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS08120  BPHYT_RS08120 dihydrolipoamide d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS08120  BPHYT_RS08120 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  570.8   9.6  1.1e-175  1.1e-175       1     461 []       4     476 .]       4     476 .] 0.96

  Alignments for each domain:
  == domain 1  score: 570.8 bits;  conditional E-value: 1.1e-175
                                TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.e......klGGtClnvGCiPtKalLksaevveelke. 62 
                                              e+dvvviG+GpgGY+aAiraaqlg+ va++ek +      klGGtClnvGCiP+KalL+s+e +e++++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS08120   4 EFDVVVIGAGPGGYIAAIRAAQLGKTVACIEKwKnpagalKLGGTCLNVGCIPSKALLASSEEFENASHh 73 
                                              69*****************************96445555569**************************99 PP

                                TIGR01350  63 akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkk....evevkkekkek 128
                                              ++++gi+venv++d++k+++rke +v+k+++G+++L++knk++ +kG++k+++k+    ++ev++e +++
  lcl|FitnessBrowser__BFirm:BPHYT_RS08120  74 LADHGISVENVSVDIAKMMARKEGIVEKMTKGIEFLFRKNKITWLKGHGKFTGKTdagvQIEVSGEGETE 143
                                              ***************************************************996523336888888888* PP

                                TIGR01350 129 kleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtv 198
                                              +++akn+iiAtGs+ r+lp  + +d+k+v ++e+al+++++p++l+++G+GviG+E++s++++lG++vtv
  lcl|FitnessBrowser__BFirm:BPHYT_RS08120 144 TVTAKNVIIATGSKARHLPN-VPVDNKIVADNEGALSFESTPKKLAVIGAGVIGLELGSVWRRLGADVTV 212
                                              ********************.************************************************* PP

                                TIGR01350 199 ielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavG 266
                                              +e+l++ l a d+ ++k+++k++kk+g++i+ + kv ev++++++v+  ++ k++++++lea++++v++G
  lcl|FitnessBrowser__BFirm:BPHYT_RS08120 213 LEALPEFLGAADQALAKEAAKQFKKQGLDIHVGVKVGEVTTTDNSVTvnYTDKDGNAQKLEADRLIVSIG 282
                                              *********************************************995555566699************* PP

                                TIGR01350 267 rkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekse 336
                                              r pn+++lgle++g++ +erg+i vd+++ t vp++yaiGDv++++mLAh+A++egv++ae i g+++ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS08120 283 RVPNTDNLGLEAIGLKANERGFIDVDDHCATAVPNVYAIGDVVRGPMLAHKAEDEGVLVAEIIDGQKP-H 351
                                              *****************************************************************998.9 PP

                                TIGR01350 337 idykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGa 406
                                              idy+ vP viytePe+a vG+te+q+k+eg e+k+g+fp++ang+al +++++Gfvk+i+d kt+eilG+
  lcl|FitnessBrowser__BFirm:BPHYT_RS08120 352 IDYNCVPWVIYTEPEIAWVGKTEQQLKAEGREIKTGQFPMMANGRALGINKAEGFVKMIADAKTDEILGV 421
                                              ********************************************************************** PP

                                TIGR01350 407 hivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                              hi++a+as+li+e+++a+e+++ +e++ +++hpHP+lsE++ eaala+ ++a+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS08120 422 HIIAADASDLIAEAVVAMEFKAASEDIGRICHPHPSLSEVMREAALAVDKRALNM 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 6.90
//
[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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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