Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate BPHYT_RS08120 BPHYT_RS08120 dihydrolipoamide dehydrogenase
Query= CharProtDB::CH_015561 (478 letters) >FitnessBrowser__BFirm:BPHYT_RS08120 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.25043.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12.38 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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