Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate GFF1561 HP15_1523 dihydrolipoamide dehydrogenase
Query= SwissProt::P14218 (478 letters) >FitnessBrowser__Marino:GFF1561 Length = 480 Score = 679 bits (1753), Expect = 0.0 Identities = 334/479 (69%), Positives = 403/479 (84%), Gaps = 1/479 (0%) Query: 1 MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKV-ALGGTCLNVGCIPSKA 59 MS K+DV+VIGAGPGGYVAAI+AAQLGLKTAC+E + ++GK LGGTCLNVGCIPSKA Sbjct: 1 MSDKYDVIVIGAGPGGYVAAIKAAQLGLKTACVESWTSEDGKAQVLGGTCLNVGCIPSKA 60 Query: 60 LLDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFE 119 LL+ S+K+ E+ F++ GI AK V +D+ M+ RK+ IVK LTGGIA LFK+NGVTS Sbjct: 61 LLEISHKFEESSHDFEMQGIIAKDVKMDIGKMMERKSGIVKQLTGGIAGLFKSNGVTSIH 120 Query: 120 GHGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQA 179 GHGKLLAN++VEVT DGK++ EAEN+I+A+GS+P++IPPAP + IVDS GALEF Sbjct: 121 GHGKLLANRKVEVTDKDGKSKTYEAENIILATGSKPIQIPPAPFDGEYIVDSEGALEFTE 180 Query: 180 VPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNI 239 VPK+LGVIGAGVIGLELGSVWARLGAEVTVLEA D FLPA D+Q+AK+ALK KQGLNI Sbjct: 181 VPKRLGVIGAGVIGLELGSVWARLGAEVTVLEAQDTFLPAVDQQVAKDALKQFQKQGLNI 240 Query: 240 RLGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERG 299 +GAR+T +EVK+K V V + D+ G+ + FDKLIVAVGRRP T +LL+ DSGV +DERG Sbjct: 241 VMGARMTGAEVKRKLVNVNYEDSKGKHEAKFDKLIVAVGRRPYTDNLLSEDSGVQMDERG 300 Query: 300 FIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYT 359 FI+VDD+CKT PGV+AIGDVVRG MLAHKASEEG+MVAERIAGHK Q+NYD IP+V+YT Sbjct: 301 FIFVDDNCKTEAPGVWAIGDVVRGPMLAHKASEEGIMVAERIAGHKPQVNYDCIPNVVYT 360 Query: 360 HPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHV 419 PE+AWVGKTE+ +KAEG E NVGTFPFAA+GRAMAAN +GLVK+IADAKTDR++G HV Sbjct: 361 FPEVAWVGKTEEQMKAEGEEYNVGTFPFAANGRAMAANSASGLVKIIADAKTDRIVGFHV 420 Query: 420 IGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIANRKKR 478 +GP A+E+V QG I MEFG+SAEDL + F+HPTLSE++HEAALAV G AIHIANR+K+ Sbjct: 421 VGPQASEIVAQGVIAMEFGSSAEDLALTCFAHPTLSESVHEAALAVGGGAIHIANRRKK 479 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: 791 Number of extensions: 29 Number of successful extensions: 2 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: 480 Length adjustment: 34 Effective length of query: 444 Effective length of database: 446 Effective search space: 198024 Effective search space used: 198024 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 GFF1561 HP15_1523 (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.28282.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-169 548.4 6.5 7.1e-169 548.2 6.5 1.0 1 lcl|FitnessBrowser__Marino:GFF1561 HP15_1523 dihydrolipoamide dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1561 HP15_1523 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 548.2 6.5 7.1e-169 7.1e-169 1 461 [] 4 473 .. 4 473 .. 0.96 Alignments for each domain: == domain 1 score: 548.2 bits; conditional E-value: 7.1e-169 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalve.......k.eklGGtClnvGCiPtKalLksaevveelke.akel 66 +ydv+viG+GpgGYvaAi+aaqlglk+a+ve k + lGGtClnvGCiP+KalL+ ++ +ee ++ ++ lcl|FitnessBrowser__Marino:GFF1561 4 KYDVIVIGAGPGGYVAAIKAAQLGLKTACVEswtsedgKaQVLGGTCLNVGCIPSKALLEISHKFEESSHdFEMQ 78 59****************************9555544433569***************************9**** PP TIGR01350 67 gievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtG 140 gi +++vk+d+ k++erk+ +vk+l+gG+++L+k+n+v++i+G++kll +++vev++++++ k++ea+nii+AtG lcl|FitnessBrowser__Marino:GFF1561 79 GIIAKDVKMDIGKMMERKSGIVKQLTGGIAGLFKSNGVTSIHGHGKLLANRKVEVTDKDGKsKTYEAENIILATG 153 **9999***************************************************998889************ PP TIGR01350 141 seprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevsk 215 s+p+++p +d++++++se+ale++evp++l ++G+GviG+E++s++a+lG++vtv+e++d+ lpa+d++v+k lcl|FitnessBrowser__Marino:GFF1561 154 SKPIQIPP-APFDGEYIVDSEGALEFTEVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEAQDTFLPAVDQQVAK 227 *******9.8999999*********************************************************** PP TIGR01350 216 vlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergai 289 + k+++k+g++i+++a++t e +++ v v+ +++ +++ + +k++vavGr+p +++l e gv++derg+i lcl|FitnessBrowser__Marino:GFF1561 228 DALKQFQKQGLNIVMGARMTGAEVKRKLVNVNYEDSkGKHEAKFDKLIVAVGRRPYTDNLLSEDSGVQMDERGFI 302 ********************8888888888766666567999********************************* PP TIGR01350 290 kvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqake 364 vd++++t++pg++aiGDv++++mLAh+As+eg+++ae+iag+++ +++y+ +P+v+yt Peva vG+teeq+k+ lcl|FitnessBrowser__Marino:GFF1561 303 FVDDNCKTEAPGVWAIGDVVRGPMLAHKASEEGIMVAERIAGHKP-QVNYDCIPNVVYTFPEVAWVGKTEEQMKA 376 ******************************************888.9**************************** PP TIGR01350 365 egievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihp 439 eg e++vg fpfaang+a+a++ ++G+vk+i+d kt++i+G+h+vg++ase++++ ++a+e++ ++e+la t+++ lcl|FitnessBrowser__Marino:GFF1561 377 EGEEYNVGTFPFAANGRAMAANSASGLVKIIADAKTDRIVGFHVVGPQASEIVAQGVIAMEFGSSAEDLALTCFA 451 *************************************************************************** PP TIGR01350 440 HPtlsEaikeaalaalgkaihv 461 HPtlsE ++eaala+ g aih+ lcl|FitnessBrowser__Marino:GFF1561 452 HPTLSESVHEAALAVGGGAIHI 473 *****************99995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (480 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: 9.07 // [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