Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate SMc01035 SMc01035 dihydrolipoamide dehydrogenase
Query= BRENDA::P50970 (466 letters) >FitnessBrowser__Smeli:SMc01035 Length = 481 Score = 513 bits (1321), Expect = e-150 Identities = 264/480 (55%), Positives = 334/480 (69%), Gaps = 15/480 (3%) Query: 1 MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60 MA+++D+IV+G GPGGYV AIR+AQL LK A+VER HLGGICLNWGCIPTK+LLRSAE+ Sbjct: 1 MAENYDVIVVGSGPGGYVTAIRSAQLGLKTAIVEREHLGGICLNWGCIPTKALLRSAEIL 60 Query: 61 HEMQNAEAYGLT-SFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGN 119 +A+ YGLT K ++ ++ARSR V+ RL GV L++KNKV+VI G +LT Sbjct: 61 DHANHAKNYGLTLEGKITANVKDVVARSRGVSARLNGGVAFLMKKNKVDVIWGEAKLTKP 120 Query: 120 QQMLVETTEGE--------------EKILEAKDIIIATGARARQLPNVHSDGKHIWTYHH 165 +++V E AK II+ATGAR R LP + DGK IWTY Sbjct: 121 GEIVVGAPSKPAVQPQNPVPKGVKGEGTYTAKHIIVATGARPRALPGIEPDGKLIWTYFE 180 Query: 166 ALKPPAMPKKLLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFK 225 A+KP PK LLV+GSGAIGIEFASFY G +V++VE PQI+P+EDAE+SA+ K + Sbjct: 181 AMKPEEFPKSLLVMGSGAIGIEFASFYRSMGVDVTVVELLPQIMPVEDAEISAFARKQLE 240 Query: 226 KRGIRILTQSALQNLTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLG 285 KRG++I+T + + + VTA + DGKVT + I A+GV N+EN+GL+ LG Sbjct: 241 KRGLKIITDAKVTKVEKGANDVTAHVETKDGKVTPIKADRLISAVGVQGNIENLGLEALG 300 Query: 286 IKLDRGFIAVDGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQ 345 +K DRG I DG+G+TNV ++AIGDVAG P LAHKA H+GVI E IAG VH L+ Sbjct: 301 VKTDRGCIVTDGYGKTNVAGIYAIGDVAGPPMLAHKAEHEGVICVEKIAGVPGVHALDKG 360 Query: 346 NIPGCTYARPQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADS 405 IPGCTY PQVASVGLTE KA++ G ++++G + F ANGKAIA G G +KT+FD + Sbjct: 361 KIPGCTYCDPQVASVGLTEAKAKELGRDIRVGRYSFGANGKAIALGEDQGLIKTIFDKKT 420 Query: 406 GALLGAHMVGAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465 G L+GAHMVGAEVTE+IQG+ VA LETTE E+M T+FPHPTLSE M ESVL AYGR L+ Sbjct: 421 GELIGAHMVGAEVTELIQGFVVAMNLETTEEELMHTVFPHPTLSEMMKESVLDAYGRVLN 480 Lambda K H 0.319 0.135 0.393 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: 31 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: 466 Length of database: 481 Length adjustment: 33 Effective length of query: 433 Effective length of database: 448 Effective search space: 193984 Effective search space used: 193984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate SMc01035 SMc01035 (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.28034.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-180 585.8 6.6 3.3e-180 585.6 6.6 1.0 1 lcl|FitnessBrowser__Smeli:SMc01035 SMc01035 dihydrolipoamide dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc01035 SMc01035 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 585.6 6.6 3.3e-180 3.3e-180 1 459 [. 4 479 .. 4 481 .] 0.97 Alignments for each domain: == domain 1 score: 585.6 bits; conditional E-value: 3.3e-180 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgieven.vk 74 +ydv+v+G+GpgGYv+Air+aqlglk+a+ve+e+lGG+Cln+GCiPtKalL+sae+++++++ak++g+++e+ ++ lcl|FitnessBrowser__Smeli:SMc01035 4 NYDVIVVGSGPGGYVTAIRSAQLGLKTAIVEREHLGGICLNWGCIPTKALLRSAEILDHANHAKNYGLTLEGkIT 78 69*******************************************************************9999** PP TIGR01350 75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke...............kkleakn 134 +++++++r++ v+ +l+gGv++L+kknkv+vi+Geakl++++e+ v + +k +++ak+ lcl|FitnessBrowser__Smeli:SMc01035 79 ANVKDVVARSRGVSARLNGGVAFLMKKNKVDVIWGEAKLTKPGEIVVGAPSKPavqpqnpvpkgvkgeGTYTAKH 153 ***********************************************8877556889999999998878899*** PP TIGR01350 135 iiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpal 209 ii+AtG++pr+lp+ +e d+k+++t+ ea++ +e+p+sl+++G+G+iG+Efas+++++Gv+vtv+ell++i+p++ lcl|FitnessBrowser__Smeli:SMc01035 154 IIVATGARPRALPG-IEPDGKLIWTYFEAMKPEEFPKSLLVMGSGAIGIEFASFYRSMGVDVTVVELLPQIMPVE 227 **************.************************************************************ PP TIGR01350 210 daevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgve 282 dae+s +++k+l+k+g+ki+t+akvt+vek +++v+ ve+k+++v+ ++a++++ avG++ n+e+lgle+lgv+ lcl|FitnessBrowser__Smeli:SMc01035 228 DAEISAFARKQLEKRGLKIITDAKVTKVEKGANDVTahVETKDGKVTPIKADRLISAVGVQGNIENLGLEALGVK 302 ************************************888888889****************************** PP TIGR01350 283 ldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPsviytePevasvG 356 +d+ g+i++d + +tnv+giyaiGDv+g++mLAh+A++egv+++ekiag ++d+ ++P ++y++P+vasvG lcl|FitnessBrowser__Smeli:SMc01035 303 TDR-GCIVTDGYGKTNVAGIYAIGDVAGPPMLAHKAEHEGVICVEKIAGVPGVhALDKGKIPGCTYCDPQVASVG 376 776.*********************************************9988799******************* PP TIGR01350 357 lteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltve 431 lte++ake g +++vg+++f angka+al+e++G++k+i+dkktge++Gah+vgae++eli+ +++a++le+t+e lcl|FitnessBrowser__Smeli:SMc01035 377 LTEAKAKELGRDIRVGRYSFGANGKAIALGEDQGLIKTIFDKKTGELIGAHMVGAEVTELIQGFVVAMNLETTEE 451 *************************************************************************** PP TIGR01350 432 elaktihpHPtlsEaikeaalaalgkai 459 el++t++pHPtlsE++ke++l+a+g+ + lcl|FitnessBrowser__Smeli:SMc01035 452 ELMHTVFPHPTLSEMMKESVLDAYGRVL 479 ***********************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (481 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: 00:00:00.03 # Mc/sec: 7.29 // [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