Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 349837 BT0309 Dihydrolipoamide dehydrogenase (NCBI ptt file)
Query= BRENDA::Q8VPK7 (567 letters) >FitnessBrowser__Btheta:349837 Length = 447 Score = 298 bits (762), Expect = 4e-85 Identities = 180/451 (39%), Positives = 259/451 (57%), Gaps = 14/451 (3%) Query: 112 FDIVVIGGGPAGYVAAIKAAQFGGKVALVEKSELGGTCLNRGCIPTKTYLHNAEIIENIG 171 FDI +IGGGPAGY AA +A G + L EK +GG CLN GCIPTKT L++A+I+++I Sbjct: 3 FDIAIIGGGPAGYTAAERAGANGLRAVLFEKKAIGGVCLNEGCIPTKTLLYSAKILDSIK 62 Query: 172 HAANRGIVIENPNFTVDMEKLLETKSKVVNTLVGGVAGLLRSYGVTVHKGIGTITKDKNV 231 A+ GI E+P+F D+ K++ K K V L GGV + SYGVT+ + I ++N Sbjct: 63 SASKYGISAESPSF--DLTKIMSRKEKTVKMLTGGVKMTVNSYGVTIVEKEAFIEGEENG 120 Query: 232 LVN---GSELLETKKIILAGGSKVNKINVPGMESPLVMTSDDILEMNEVPESLVIIGGGV 288 L+ E E K +++ GS +PG+ TS + LE+ E+PE+LV+IGGGV Sbjct: 121 LIRIICDGERYEVKYLLVCTGSDTVIPPIPGLSEVSYWTSKEALEIKELPETLVVIGGGV 180 Query: 289 VGIELGQAFMTFGSKVTVIEMMDRIVPAMDVEVSKNLRLILERKGMTILTGTKLQEIIEE 348 +G+E F + G KV V+EMM I+ MD E S LR+ ++G+T TK+ E+ + Sbjct: 181 IGMEFASFFNSMGVKVHVVEMMPEILGVMDKETSSMLRMEYAKRGVTFYLNTKVIEVKPD 240 Query: 349 NGQLRIKVEGKDDII-ASKALLSIGRMPDLEGIG--EVEFELDRGCIKVTEYMETSVPGI 405 + I+ +GK I K LLS+GR ++ +G ++ EL R +KV EY++TS PG+ Sbjct: 241 G--VVIEKDGKASTIKTEKILLSVGRKANITNVGLDKLNIELHRNGVKVDEYLQTSHPGV 298 Query: 406 YAPGDINGTKMLAHAAFRMGEVSAENALKGNHAVAKLNLTPAAIYTLPEVAAVGLTEEQ- 464 YA GDI G +LAH A R EV A N + G N P +YT PEVA VG TEE+ Sbjct: 299 YACGDITGYSLLAHTAIREAEV-AINHILGVEDRMNYNSVPGVVYTNPEVAGVGKTEEEL 357 Query: 465 AREKYDVAIGKFNFAANGRAIA-SDAAQGFVKVIADKKYGEILGVHIIGPAAAELINEAS 523 ++ + K A +GR +A ++ G K+I D+ I+G H++G A+ELI A Sbjct: 358 TKQGIPYRVTKLPMAYSGRFVAENEQVNGICKLILDEA-DHIIGCHMLGNPASELIVIAG 416 Query: 524 SIIEMEITVEEMLKTIHGHPTYSEVMYEAFA 554 I+ TVEE K + HPT E+ +E + Sbjct: 417 IAIQKGYTVEEFQKNVFPHPTVGEIYHEVLS 447 Lambda K H 0.314 0.135 0.370 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: 622 Number of extensions: 32 Number of successful extensions: 8 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: 567 Length of database: 447 Length adjustment: 34 Effective length of query: 533 Effective length of database: 413 Effective search space: 220129 Effective search space used: 220129 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: 42 (21.9 bits) S2: 52 (24.6 bits)
Align candidate 349837 BT0309 (Dihydrolipoamide 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.3843.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-142 459.3 8.4 7.9e-142 459.1 8.4 1.0 1 lcl|FitnessBrowser__Btheta:349837 BT0309 Dihydrolipoamide dehydrog Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:349837 BT0309 Dihydrolipoamide dehydrogenase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.1 8.4 7.9e-142 7.9e-142 1 451 [. 2 446 .. 2 447 .] 0.96 Alignments for each domain: == domain 1 score: 459.1 bits; conditional E-value: 7.9e-142 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvkld 76 ++d+ +iGgGp+GY+aA ra+ +gl+ +l ek+ +GG+Cln+GCiPtK+lL sa++++++k a+++gi++e+ ++d lcl|FitnessBrowser__Btheta:349837 2 NFDIAIIGGGPAGYTAAERAGANGLRAVLFEKKAIGGVCLNEGCIPTKTLLYSAKILDSIKSASKYGISAESPSFD 77 59************************************************************************** PP TIGR01350 77 lekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplk.le 151 l+k++ rkek+vk+l+gGvk+ +++++v+ ++ ea ++++++ ++ + + +e+k +++ tGs+ +p++ l+ lcl|FitnessBrowser__Btheta:349837 78 LTKIMSRKEKTVKMLTGGVKMTVNSYGVTIVEKEAFIEGEENGLIRIICDGERYEVKYLLVCTGSDTVIPPIPgLS 153 **************************************999877777776689****************9998643 PP TIGR01350 152 edekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvk 227 e + +ts+eale+ke+pe+lv++GgGviG+Efas+f+++Gvkv v+e++++il ++d+e s++l+ ++ k+gv+ lcl|FitnessBrowser__Btheta:349837 154 EVS--YWTSKEALEIKELPETLVVIGGGVIGMEFASFFNSMGVKVHVVEMMPEILGVMDKETSSMLRMEYAKRGVT 227 333..6********************************************************************** PP TIGR01350 228 iltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiy 303 ++ n+kv e + d vv+e+++k ++t+++ek+L++vGrk+n++++gl+kl++el+++g +kvde+l+t+ pg+y lcl|FitnessBrowser__Btheta:349837 228 FYLNTKVI--EVKPDGVVIEKDGK-ASTIKTEKILLSVGRKANITNVGLDKLNIELHRNG-VKVDEYLQTSHPGVY 299 *******9..77899999998777.89*****************************9977.*************** PP TIGR01350 304 aiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaan 379 a+GD++g LAh+A +e+ va+++i+g e+ ++y+ vP v+yt+Peva vG+tee++ ++gi ++v+k+p+a + lcl|FitnessBrowser__Btheta:349837 300 ACGDITGYSLLAHTAIREAEVAINHILGVED-RMNYNSVPGVVYTNPEVAGVGKTEEELTKQGIPYRVTKLPMAYS 374 ****************************776.9******************************************* PP TIGR01350 380 gkalalee.tdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaa 451 g+ +a +e +G+ k+i+d+ ++i+G+h++g+ aseli + +a++ + tvee +k ++pHPt++E+ +e++ lcl|FitnessBrowser__Btheta:349837 375 GRFVAENEqVNGICKLILDE-ADHIIGCHMLGNPASELIVIAGIAIQKGYTVEEFQKNVFPHPTVGEIYHEVL 446 *****998579*******97.578**********************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (447 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: 9.97 // [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