GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Paraburkholderia bryophila 376MFSha3.1

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate H281DRAFT_05115 H281DRAFT_05115 dihydrolipoamide dehydrogenase

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__Burk376:H281DRAFT_05115
          Length = 476

 Score =  516 bits (1328), Expect = e-151
 Identities = 267/477 (55%), Positives = 346/477 (72%), Gaps = 6/477 (1%)

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

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

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

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

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

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

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

Query: 416 GVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHV 472
           GVH+I  +A++L+ +  +AMEF  ++ED+G +   HP+LSE + EAALAV+  A+++
Sbjct: 420 GVHIISANASDLIAEAVVAMEFKAASEDIGRICHPHPSLSEVMREAALAVDKRALNM 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: 714
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 H281DRAFT_05115 H281DRAFT_05115 (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.7331.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   7.3e-176  571.3   8.5   8.2e-176  571.1   8.5    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05115  H281DRAFT_05115 dihydrolipoamide


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05115  H281DRAFT_05115 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  571.1   8.5  8.2e-176  8.2e-176       1     461 []       4     476 .]       4     476 .] 0.96

  Alignments for each domain:
  == domain 1  score: 571.1 bits;  conditional E-value: 8.2e-176
                                    TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.e......klGGtClnvGCiPtKalLksaevvee 59 
                                                  e+dvvviG+GpgGY+aAiraaqlg+ va++ek +      klGGtClnvGCiP+KalL+s+e +e+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05115   4 EFDVVVIGAGPGGYIAAIRAAQLGKTVACIEKwKnpagtlKLGGTCLNVGCIPSKALLASSEEFEN 69 
                                                  69*****************************96445555569************************ PP

                                    TIGR01350  60 lke.akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkk....eve 120
                                                  +++ ++++gi+venvk+d++k+++rk+ +v+k+++G+++L++knk++ +kG++k+++k+    ++e
  lcl|FitnessBrowser__Burk376:H281DRAFT_05115  70 ASHhLADHGISVENVKVDISKMMARKDGIVEKMTKGIEFLFRKNKITWLKGHGKFTGKTdagvQIE 135
                                                  **99***************************************************99652333688 PP

                                    TIGR01350 121 vkkekkekkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfa 186
                                                  v++e ++++++akn+iiAtGs+ r+lp  + +d+k+v ++e+al+++++p++l+++G+GviG+E++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05115 136 VSGEGETEVVTAKNVIIATGSKARHLPN-IPVDNKIVADNEGALAFDTAPKKLAVIGAGVIGLELG 200
                                                  8888888*********************.************************************* PP

                                    TIGR01350 187 sifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakk 250
                                                  s++++lG++vtv+e+l++ l a d+ ++k+++k++kk+g++i+ + kv ev+++e++v+  ++ k+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05115 201 SVWRRLGAEVTVLEALPEFLGAADQALAKEAAKQFKKQGLDIHVGVKVGEVSTTENSVTinYTDKD 266
                                                  **********************************************************96656666 PP

                                    TIGR01350 251 kevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAh 316
                                                  +++++lea++++v++Gr pn+++lgle++g++ +erg+i vd+++ t vp++yaiGDv++++mLAh
  lcl|FitnessBrowser__Burk376:H281DRAFT_05115 267 GNAQKLEADRLIVSIGRVPNTDNLGLEAIGLKANERGFIDVDDHCATAVPNVYAIGDVVRGPMLAH 332
                                                  699*************************************************************** PP

                                    TIGR01350 317 vAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangka 382
                                                  +A++egv++ae i g+++ +idy+ +P viytePe+a vG+te+q+k+eg evk+g+fpf+ang+a
  lcl|FitnessBrowser__Burk376:H281DRAFT_05115 333 KAEDEGVLVAEIIDGQKP-HIDYNCIPWVIYTEPEIAWVGKTEQQLKAEGREVKTGQFPFMANGRA 397
                                                  ***************998.9********************************************** PP

                                    TIGR01350 383 laleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaik 448
                                                  l ++++dGfvk+i+d kt+e+lG+hi++a+as+li+e+++a+e+++ +e++ +++hpHP+lsE++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05115 398 LGINKADGFVKMIADAKTDELLGVHIISANASDLIAEAVVAMEFKAASEDIGRICHPHPSLSEVMR 463
                                                  ****************************************************************** PP

                                    TIGR01350 449 eaalaalgkaihv 461
                                                  eaala+ ++a+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05115 464 EAALAVDKRALNM 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 5.64
//
[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:

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