Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate CCNA_01805 CCNA_01805 dihydrolipoamide dehydrogenase
Query= BRENDA::P50970 (466 letters) >FitnessBrowser__Caulo:CCNA_01805 Length = 466 Score = 484 bits (1245), Expect = e-141 Identities = 252/470 (53%), Positives = 328/470 (69%), Gaps = 10/470 (2%) Query: 1 MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60 M+ FD++V+G GPGGYVAAIRA+QL L A++ER +LGGICLNWGCIPTK+LL+S EVY Sbjct: 1 MSTEFDVVVIGAGPGGYVAAIRASQLGLNTAIIERENLGGICLNWGCIPTKALLKSGEVY 60 Query: 61 HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120 ++ + YGL+ K FD KII RSR VA ++ G+ L++K+K+EVI G +L Sbjct: 61 EQLSHLGGYGLSVEKASFDFGKIIERSRGVAKNMSGGIAFLMKKHKIEVIEGEAKLEKGA 120 Query: 121 ---QMLVETTEGEEKILEAKDIIIATGARARQLPNVH--SDGKHIWTYHHALKPPAMPKK 175 +++V G + ++AK++I+A+GARAR++P + SDG IWTY AL P +MPK Sbjct: 121 PAPKVVVALKAGGSRTVQAKNVILASGARAREIPAIGAVSDGDKIWTYRDALAPKSMPKS 180 Query: 176 LLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQS 235 L+VIGSGAIGIEFASFY GAEV++VE +I+P+ED EVS KAF+KRGI+ + Sbjct: 181 LVVIGSGAIGIEFASFYRALGAEVTVVEAIDRIMPVEDEEVSKAAQKAFEKRGIKFRVGA 240 Query: 236 ALQNLTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAV 295 + + +GV + A GK+ + IVA+G+ N N GL+ LG+ LDRG + Sbjct: 241 KVSKIEKTKDGVAVTVE-AGGKIEQLTAEKCIVAVGIAPN--NDGLEALGVSLDRGHVVT 297 Query: 296 DGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARP 355 D RTNV ++AIGD+AGAP LAHKASH+G+ AAEAIAG + L+ IPGCTYA P Sbjct: 298 DKHCRTNVPGLYAIGDIAGAPWLAHKASHEGIHAAEAIAGYKTPNVLSP--IPGCTYANP 355 Query: 356 QVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVG 415 QVASVG TE A+ G VK G FPF NGKA+A G T+GFVKTVFDA +GAL+GAHM+G Sbjct: 356 QVASVGYTEAGAKAAGIEVKAGRFPFRVNGKAVASGETEGFVKTVFDAKTGALIGAHMIG 415 Query: 416 AEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465 EVTEMIQG+ A TLE TE ++ ++ HPT+SEAMHE+ L AYGR LH Sbjct: 416 HEVTEMIQGFVTAITLEATEEDLHGVVYAHPTMSEAMHEAALDAYGRVLH 465 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: 654 Number of extensions: 33 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: 466 Length of database: 466 Length adjustment: 33 Effective length of query: 433 Effective length of database: 433 Effective search space: 187489 Effective search space used: 187489 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 CCNA_01805 CCNA_01805 (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.5270.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-170 551.5 10.9 8.1e-170 551.3 10.9 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_01805 CCNA_01805 dihydrolipoamide dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_01805 CCNA_01805 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 551.3 10.9 8.1e-170 8.1e-170 1 460 [. 4 465 .. 4 466 .] 0.97 Alignments for each domain: == domain 1 score: 551.3 bits; conditional E-value: 8.1e-170 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 e+dvvviG+GpgGYvaAira+qlgl++a++e+e+lGG+Cln+GCiPtKalLks+ev+e+l+++ +g++ve+ lcl|FitnessBrowser__Caulo:CCNA_01805 4 EFDVVVIGAGPGGYVAAIRASQLGLNTAIIERENLGGICLNWGCIPTKALLKSGEVYEQLSHLGGYGLSVEKA 76 69*********************************************************************** PP TIGR01350 74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld...kkevevkkekke.kkleakniiiAtGse 142 ++d+ k+ er++ v k+++gG+++L+kk+k+evi+Geakl++ + +v v+ +++ ++++akn+i+A+G++ lcl|FitnessBrowser__Caulo:CCNA_01805 77 SFDFGKIIERSRGVAKNMSGGIAFLMKKHKIEVIEGEAKLEKgapAPKVVVALKAGGsRTVQAKNVILASGAR 149 *****************************************977755677766655459************** PP TIGR01350 143 prelplk.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevs 214 re+p +d++ ++t+++al+ k++p+slv++G+G+iG+Efas+++ lG++vtv+e+ dri+p++d+evs lcl|FitnessBrowser__Caulo:CCNA_01805 150 AREIPAIgAVSDGDKIWTYRDALAPKSMPKSLVVIGSGAIGIEFASFYRALGAEVTVVEAIDRIMPVEDEEVS 222 ******987777789********************************************************** PP TIGR01350 215 kvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgvelder 286 k+++k+++k+g+k+ +akv+++ek++d v v+ + + ++e+l+aek +vavG pn + gle+lgv+ld+ lcl|FitnessBrowser__Caulo:CCNA_01805 223 KAAQKAFEKRGIKFRVGAKVSKIEKTKDGVAVTVEAGgKIEQLTAEKCIVAVGIAPNND--GLEALGVSLDR- 292 *******************************88887779********************..*********98. PP TIGR01350 287 gaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlte 359 g +++d+++rtnvpg+yaiGD++g + LAh+As+eg+ aae+iag ++ + +P ++y++P+vasvG+te lcl|FitnessBrowser__Caulo:CCNA_01805 293 GHVVTDKHCRTNVPGLYAIGDIAGAPWLAHKASHEGIHAAEAIAGYKT-PNVLSPIPGCTYANPQVASVGYTE 364 *********************************************776.78899******************* PP TIGR01350 360 eqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltvee 432 + ak++gievk+g+fpf+ ngka+a++et+Gfvk+++d ktg+++Gah++g e++e+i+ ++ a++le+t+e+ lcl|FitnessBrowser__Caulo:CCNA_01805 365 AGAKAAGIEVKAGRFPFRVNGKAVASGETEGFVKTVFDAKTGALIGAHMIGHEVTEMIQGFVTAITLEATEED 437 ************************************************************************* PP TIGR01350 433 laktihpHPtlsEaikeaalaalgkaih 460 l+ ++++HPt+sEa++eaal+a+g+ +h lcl|FitnessBrowser__Caulo:CCNA_01805 438 LHGVVYAHPTMSEAMHEAALDAYGRVLH 465 ************************9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (466 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: 00:00:00.01 # Mc/sec: 11.84 // [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