Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 199618 SO0426 pyruvate dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI ptt file)
Query= BRENDA::P0A9P0 (474 letters) >FitnessBrowser__MR1:199618 Length = 475 Score = 825 bits (2132), Expect = 0.0 Identities = 408/475 (85%), Positives = 448/475 (94%), Gaps = 1/475 (0%) Query: 1 MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60 MS EIKTQVVVLGAGPAGYSAAFR ADLGLETVIVER++TLGGVCLNVGCIPSKALLHVA Sbjct: 1 MSNEIKTQVVVLGAGPAGYSAAFRAADLGLETVIVERFSTLGGVCLNVGCIPSKALLHVA 60 Query: 61 KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120 KVIEEAKA+A HG+VFGEP D+DK+R++K+KVI+QLTGGL GM+K RKV VVNG GKF+ Sbjct: 61 KVIEEAKAVAAHGVVFGEPTIDLDKLRSFKQKVISQLTGGLGGMSKMRKVNVVNGFGKFS 120 Query: 121 GANTLEVEGENGK-TVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLL 179 G N+LEV E+G TV+ FD AIIAAGSRPI+LPFIPHEDPRIWDSTDALELKEVP +LL Sbjct: 121 GPNSLEVTAEDGTVTVVKFDQAIIAAGSRPIKLPFIPHEDPRIWDSTDALELKEVPGKLL 180 Query: 180 VMGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVT 239 VMGGGIIGLEMGTVY +LGS+IDVVEMFDQVIPAADKD+V+VFTK+I KKFNL+LETKVT Sbjct: 181 VMGGGIIGLEMGTVYSSLGSEIDVVEMFDQVIPAADKDVVRVFTKQIKKKFNLILETKVT 240 Query: 240 AVEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDK 299 AVEA+EDGIYV+MEGK APAEP RYDAVLVAIGR PNGK +DA KAGV++D+RGFI VDK Sbjct: 241 AVEAREDGIYVSMEGKSAPAEPVRYDAVLVAIGRTPNGKLIDAEKAGVKIDERGFINVDK 300 Query: 300 QLRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAW 359 QLRTNVPHI+AIGDIVGQPMLAHKGVHEGHVAAEVIAG KHYFDPKVIPSIAYT+PEVAW Sbjct: 301 QLRTNVPHIYAIGDIVGQPMLAHKGVHEGHVAAEVIAGMKHYFDPKVIPSIAYTDPEVAW 360 Query: 360 VGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGG 419 VGLTEKEAKE+GI+YETATFPWAASGRAIASDC++GMTKLIFDK++HRVIGGAIVG NGG Sbjct: 361 VGLTEKEAKEQGIAYETATFPWAASGRAIASDCSEGMTKLIFDKDTHRVIGGAIVGVNGG 420 Query: 420 ELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474 ELLGEIGLAIEMGCDAED+ALTIHAHPTLHESVGLAAE++EGSITDLPNPKAKKK Sbjct: 421 ELLGEIGLAIEMGCDAEDLALTIHAHPTLHESVGLAAEIYEGSITDLPNPKAKKK 475 Lambda K H 0.317 0.137 0.396 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: 829 Number of extensions: 24 Number of successful extensions: 5 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: 474 Length of database: 475 Length adjustment: 33 Effective length of query: 441 Effective length of database: 442 Effective search space: 194922 Effective search space used: 194922 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 199618 SO0426 (pyruvate dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI ptt file))
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.12246.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-153 496.0 5.1 6e-153 495.7 5.1 1.0 1 lcl|FitnessBrowser__MR1:199618 SO0426 pyruvate dehydrogenase co Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:199618 SO0426 pyruvate dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI pt # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 495.7 5.1 6e-153 6e-153 2 453 .. 7 459 .. 6 466 .. 0.97 Alignments for each domain: == domain 1 score: 495.7 bits; conditional E-value: 6e-153 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldlek 79 ++vvv+G+Gp+GY aA raa lgl++++ve+ ++lGG+ClnvGCiP+KalL+ a+v+ee+k ++ +g+ + ++dl+k lcl|FitnessBrowser__MR1:199618 7 TQVVVLGAGPAGYSAAFRAADLGLETVIVERfSTLGGVCLNVGCIPSKALLHVAKVIEEAKAVAAHGVVFGEPTIDLDK 85 579**************************************************************************** PP TIGR01350 80 llerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprelplkleedekvv 157 l k+kv+++l+gG+ ++ k kv+v++G +k+++++++ev++e+++ ++++++++iiA Gs+p++lp+ + ++ ++ lcl|FitnessBrowser__MR1:199618 86 LRSFKQKVISQLTGGLGGMSKMRKVNVVNGFGKFSGPNSLEVTAEDGTvTVVKFDQAIIAAGSRPIKLPF-IPHEDPRI 163 **********************************************998999******************.8888889* PP TIGR01350 158 itseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvte 236 ++s++alelkevp +l+++GgG+iG+E+++++++lG+++ v+e+ d+++pa d++v +v +k++kk + +++ ++kvt+ lcl|FitnessBrowser__MR1:199618 164 WDSTDALELKEVPGKLLVMGGGIIGLEMGTVYSSLGSEIDVVEMFDQVIPAADKDVVRVFTKQIKK-KFNLILETKVTA 241 ***************************************************************976.689********* PP TIGR01350 237 vekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklm 313 ve++ed + v++++k +e +++++vLva+Gr+pn + ++ ek gv++derg+i+vd++lrtnvp+iyaiGD++g++m lcl|FitnessBrowser__MR1:199618 242 VEAREDGIYVSMEGKsaPAEPVRYDAVLVAIGRTPNGKLIDAEKAGVKIDERGFINVDKQLRTNVPHIYAIGDIVGQPM 320 *********999988656899********************************************************** PP TIGR01350 314 LAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfv 392 LAh+ ++eg vaae iag ++ +d k++Ps+ yt+Peva vGlte++ake+gi+++++ fp aa+g+a+a++ ++G+ lcl|FitnessBrowser__MR1:199618 321 LAHKGVHEGHVAAEVIAGMKH-YFDPKVIPSIAYTDPEVAWVGLTEKEAKEQGIAYETATFPWAASGRAIASDCSEGMT 398 ******************665.9******************************************************** PP TIGR01350 393 kvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaala 453 k+i+dk+t++++G ivg + el+ e+ la+e++ +e+la tih+HPtl E + aa+ lcl|FitnessBrowser__MR1:199618 399 KLIFDKDTHRVIGGAIVGVNGGELLGEIGLAIEMGCDAEDLALTIHAHPTLHESVGLAAEI 459 *****************************************************99888775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (475 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: 00:00:00.02 # Mc/sec: 9.62 // [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