Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate GFF2444 Psest_2492 dihydrolipoamide dehydrogenase
Query= SwissProt::P18925 (477 letters) >FitnessBrowser__psRCH2:GFF2444 Length = 478 Score = 819 bits (2115), Expect = 0.0 Identities = 411/477 (86%), Positives = 447/477 (93%) Query: 1 MSQKFDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYKGKEGKTALGGTCLNVGCIPSKAL 60 MSQKFDV+VIGAGPGGYVAAI++AQLGLKTA IEKY+GK+GKTALGGTCLNVGCIPSKAL Sbjct: 1 MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYQGKDGKTALGGTCLNVGCIPSKAL 60 Query: 61 LDSSYKFHEAHESFKLHGISTGEVAIDVPTMIARKDQIVRNLTGGVASLIKANGVTLFEG 120 LDSSYKFHEAHESFK+HGISTGEVA+DVPTM+ARKDQIV+NLTGGV++L+KANGVT+FEG Sbjct: 61 LDSSYKFHEAHESFKVHGISTGEVAMDVPTMVARKDQIVKNLTGGVSALLKANGVTVFEG 120 Query: 121 HGKLLAGKKVEVTAADGSSQVLDTENVILASGSKPVEIPPAPVDQDVIVDSTGALDFQNV 180 HGKLLAGK+VEVT DG+ Q L ENVILASGS PV IPPAPVDQ VIVDSTGALDFQ V Sbjct: 121 HGKLLAGKQVEVTGLDGNVQTLAAENVILASGSTPVNIPPAPVDQKVIVDSTGALDFQGV 180 Query: 181 PGKLGVIGAGVIGLELGSVWARLGAEVTVLEAMDKFLPAVDEQVAKEAQKILTKQGLKIL 240 PGKLGVIGAGVIGLELGSVWARLGAEVTV+EAMDKFLPA DEQ++KEA KIL+KQGLKIL Sbjct: 181 PGKLGVIGAGVIGLELGSVWARLGAEVTVIEAMDKFLPAADEQISKEAFKILSKQGLKIL 240 Query: 241 LGARVTGTEVKNKQVTVKFVDAEGEKSQAFDKLIVAVGRRPVTTDLLAADSGVTLDERGF 300 LGAR+TG+EVK QVTV F AEGE+ FDKLIVAVGRRPVT++LLAAD+GV +DERGF Sbjct: 241 LGARLTGSEVKGDQVTVSFTSAEGEQQMTFDKLIVAVGRRPVTSELLAADTGVDMDERGF 300 Query: 301 IYVDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVVVAERIAGHKAQMNYDLIPAVIYTH 360 I+VDDYCATSVPGVYAIGDVVRGAMLAHKASEEGV+VAERIAGHK QMNYDLIP+VIYTH Sbjct: 301 IFVDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVMVAERIAGHKTQMNYDLIPSVIYTH 360 Query: 361 PEIAGVGKTEQALKAEGVAINVGVFPFAASGRAMAANDTAGFVKVIADAKTDRVLGVHVI 420 PEIA VGK+EQ LKAEGV +NVG FPFAASGRAMAANDTAG VKVIADAKTDRVLGVHV+ Sbjct: 361 PEIAWVGKSEQVLKAEGVEVNVGTFPFAASGRAMAANDTAGLVKVIADAKTDRVLGVHVM 420 Query: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFAHPALSEALHEAALAVSGHAIHVANRKK 477 GPSAAELVQQGAI MEFGTSAEDLGMMVF+HP +SEALHEAALAV+GHAIH+ANRKK Sbjct: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTMSEALHEAALAVNGHAIHIANRKK 477 Lambda K H 0.316 0.134 0.372 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: 839 Number of extensions: 29 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: 477 Length of database: 478 Length adjustment: 34 Effective length of query: 443 Effective length of database: 444 Effective search space: 196692 Effective search space used: 196692 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 GFF2444 Psest_2492 (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.11030.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-167 542.9 10.9 3.4e-167 542.7 10.9 1.0 1 lcl|FitnessBrowser__psRCH2:GFF2444 Psest_2492 dihydrolipoamide dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF2444 Psest_2492 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 542.7 10.9 3.4e-167 3.4e-167 1 461 [] 4 472 .. 4 472 .. 0.97 Alignments for each domain: == domain 1 score: 542.7 bits; conditional E-value: 3.4e-167 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvek.e......klGGtClnvGCiPtKalLksaevveelke.akelg 67 ++dvvviG+GpgGYvaAiraaqlglk+a++ek + lGGtClnvGCiP+KalL s+ ++e++e +k +g lcl|FitnessBrowser__psRCH2:GFF2444 4 KFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKyQgkdgktALGGTCLNVGCIPSKALLDSSYKFHEAHEsFKVHG 78 59*****************************74222333369***************************9***** PP TIGR01350 68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGs 141 i++ +v++d+ ++++rk+++vk+l+gGv+aLlk n+v+v++G++kll k+vev++ +++ ++l a+n+i+A+Gs lcl|FitnessBrowser__psRCH2:GFF2444 79 ISTGEVAMDVPTMVARKDQIVKNLTGGVSALLKANGVTVFEGHGKLLAGKQVEVTGLDGNvQTLAAENVILASGS 153 ********************************************************998889************* PP TIGR01350 142 eprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskv 216 +p ++p +d+kv+++s++al ++ vp +l ++G+GviG+E++s++a+lG++vtvie++d+ lpa d+++sk+ lcl|FitnessBrowser__psRCH2:GFF2444 154 TPVNIPP-APVDQKVIVDSTGALDFQGVPGKLGVIGAGVIGLELGSVWARLGAEVTVIEAMDKFLPAADEQISKE 227 ******9.9999999************************************************************ PP TIGR01350 217 lkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaik 290 + k l+k+g+kil +a++t e + d+v+v+ + +++++ +k++vavGr+p ++el + +gv++derg+i lcl|FitnessBrowser__psRCH2:GFF2444 228 AFKILSKQGLKILLGARLTGSEVKGDQVTVSFTSAeGEQQMTFDKLIVAVGRRPVTSELLAADTGVDMDERGFIF 302 *******************9999*****988777756799*********************************** PP TIGR01350 291 vdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakee 365 vd+++ t+vpg+yaiGDv++++mLAh+As+egv++ae+iag+++ +++y+++Psviyt+Pe+a vG++e+ +k+e lcl|FitnessBrowser__psRCH2:GFF2444 303 VDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVMVAERIAGHKT-QMNYDLIPSVIYTHPEIAWVGKSEQVLKAE 376 *****************************************666.9***************************** PP TIGR01350 366 gievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpH 440 g+ev+vg fpfaa+g+a+a+++t G+vkvi+d kt+++lG+h++g++a+el+++ a+ +e+++++e+l ++++ H lcl|FitnessBrowser__psRCH2:GFF2444 377 GVEVNVGTFPFAASGRAMAANDTAGLVKVIADAKTDRVLGVHVMGPSAAELVQQGAIGMEFGTSAEDLGMMVFSH 451 *************************************************************************** PP TIGR01350 441 PtlsEaikeaalaalgkaihv 461 Pt+sEa++eaala++g+aih+ lcl|FitnessBrowser__psRCH2:GFF2444 452 PTMSEALHEAALAVNGHAIHI 472 *******************96 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.33 // [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