Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_086510769.1 BZY95_RS15335 dihydrolipoyl dehydrogenase
Query= SwissProt::P14218 (478 letters) >NCBI__GCF_002151265.1:WP_086510769.1 Length = 478 Score = 639 bits (1648), Expect = 0.0 Identities = 316/478 (66%), Positives = 388/478 (81%) Query: 1 MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60 M+ KFDV+VIGAGPGGYVAAIRAAQLGLKTAC+EK++ KEGK GGTCLNVGCIPSKAL Sbjct: 1 MADKFDVIVIGAGPGGYVAAIRAAQLGLKTACVEKWVNKEGKTVHGGTCLNVGCIPSKAL 60 Query: 61 LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120 L++S+K+ EA++ F GI+ + +V M+ K +++ GGI+ LFKANGVT+ +G Sbjct: 61 LETSHKFVEARDHFAEIGIDLEPPKANVAKMLEFKNSVIAKNVGGISALFKANGVTAIDG 120 Query: 121 HGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAV 180 GK++A KQVEVT DG EA+N++IA+GS PVEIPP PL +DI+V STGALEF V Sbjct: 121 TGKVVAAKQVEVTDHDGGKTTYEADNIVIAAGSVPVEIPPTPLHEDIVVTSTGALEFTEV 180 Query: 181 PKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIR 240 PK+LGVIGAGVIGLELGSVW+RLGAEVTVLEA+D FLP D IAKE K+L KQGL+I+ Sbjct: 181 PKRLGVIGAGVIGLELGSVWSRLGAEVTVLEAMDTFLPMVDTAIAKETQKLLKKQGLDIK 240 Query: 241 LGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERGF 300 LGARVT SEVK +VTV ++D NGEQ++TFDKLIV VGRRP T ++ + GV LDERGF Sbjct: 241 LGARVTGSEVKGNEVTVKYSDGNGEQEQTFDKLIVCVGRRPYTKGVVDENVGVGLDERGF 300 Query: 301 IYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYTH 360 I+VDD C+TSVPG++AIGD VRG MLAHKASEEGVMVA+ IAGHKA+MNYD IPSVIYT Sbjct: 301 IHVDDQCRTSVPGIYAIGDCVRGPMLAHKASEEGVMVADIIAGHKAEMNYDAIPSVIYTS 360 Query: 361 PEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHVI 420 PE+AWVG EQ KA+G++V G+FPF+A+GRA+A N G+ KVIADA+TDR+LG+H++ Sbjct: 361 PEVAWVGMNEQEAKAKGIKVKTGSFPFSANGRALANNAPEGMAKVIADAETDRILGMHIV 420 Query: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIANRKKR 478 A EL+ QG I MEFG+SAEDL + ++HP+ SEA+HEAALAV+GHAIH+ANRKKR Sbjct: 421 SQHAGELIAQGVIAMEFGSSAEDLALTCYAHPSTSEAIHEAALAVDGHAIHMANRKKR 478 Lambda K H 0.316 0.134 0.375 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: 790 Number of extensions: 35 Number of successful extensions: 1 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: 478 Length adjustment: 34 Effective length of query: 444 Effective length of database: 444 Effective search space: 197136 Effective search space used: 197136 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_086510769.1 BZY95_RS15335 (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.31633.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-168 545.1 12.0 7.2e-168 544.9 12.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510769.1 BZY95_RS15335 dihydrolipoyl dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510769.1 BZY95_RS15335 dihydrolipoyl dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 544.9 12.0 7.2e-168 7.2e-168 1 461 [] 4 472 .. 4 472 .. 0.96 Alignments for each domain: == domain 1 score: 544.9 bits; conditional E-value: 7.2e-168 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvek..ek.....lGGtClnvGCiPtKalLksaevveelke 62 ++dv+viG+GpgGYvaAiraaqlglk+a+vek +k GGtClnvGCiP+KalL++++ + e+++ lcl|NCBI__GCF_002151265.1:WP_086510769.1 4 KFDVIVIGAGPGGYVAAIRAAQLGLKTACVEKwvNKegktvHGGTCLNVGCIPSKALLETSHKFVEARD 72 59****************************9765332333379*********************99999 PP TIGR01350 63 .akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kk 129 ++e+gi++e k +++k+le k++v+ k vgG++aL+k n+v+ i G++k++ +k+vev+++++ ++ lcl|NCBI__GCF_002151265.1:WP_086510769.1 73 hFAEIGIDLEPPKANVAKMLEFKNSVIAKNVGGISALFKANGVTAIDGTGKVVAAKQVEVTDHDGGkTT 141 8************************************************************99876589 PP TIGR01350 130 leakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtv 198 +ea+ni+iA Gs p e+p +e++v+ts++ale++evp++l ++G+GviG+E++s++++lG++vtv lcl|NCBI__GCF_002151265.1:WP_086510769.1 142 YEADNIVIAAGSVPVEIPP-TPLHEDIVVTSTGALEFTEVPKRLGVIGAGVIGLELGSVWSRLGAEVTV 209 9*****************9.7777778****************************************** PP TIGR01350 199 ielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavG 266 +e++d+ lp++d+ ++k+ +k lkk+g++i+ +a+vt e + +ev+v+ +++ +++ + +k++v+vG lcl|NCBI__GCF_002151265.1:WP_086510769.1 210 LEAMDTFLPMVDTAIAKETQKLLKKQGLDIKLGARVTGSEVKGNEVTVKYSDGnGEQEQTFDKLIVCVG 278 *************************************88888888887766665679999********* PP TIGR01350 267 rkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks 335 r+p ++++ e++gv lderg+i+vd+++rt+vpgiyaiGD+++++mLAh+As+egv++a+ iag+++ lcl|NCBI__GCF_002151265.1:WP_086510769.1 279 RRPYTKGVVDENVGVGLDERGFIHVDDQCRTSVPGIYAIGDCVRGPMLAHKASEEGVMVADIIAGHKA- 346 *****************************************************************665. PP TIGR01350 336 eidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeil 404 e++y+a+Psviyt+Peva vG++e++ak++gi+vk+g+fpf+ang+ala + +G++kvi+d +t++il lcl|NCBI__GCF_002151265.1:WP_086510769.1 347 EMNYDAIPSVIYTSPEVAWVGMNEQEAKAKGIKVKTGSFPFSANGRALANNAPEGMAKVIADAETDRIL 415 9******************************************************************** PP TIGR01350 405 GahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461 G+hiv+++a eli++ ++a+e++ ++e+la t+++HP+ sEai+eaala+ g+aih+ lcl|NCBI__GCF_002151265.1:WP_086510769.1 416 GMHIVSQHAGELIAQGVIAMEFGSSAEDLALTCYAHPSTSEAIHEAALAVDGHAIHM 472 ********************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (478 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: 00:00:00.02 # Mc/sec: 7.65 // [ok]
This GapMind analysis is from Sep 24 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