Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate BWI76_RS14145 BWI76_RS14145 dihydrolipoyl dehydrogenase
Query= BRENDA::P50970 (466 letters) >FitnessBrowser__Koxy:BWI76_RS14145 Length = 465 Score = 520 bits (1338), Expect = e-152 Identities = 259/465 (55%), Positives = 334/465 (71%), Gaps = 1/465 (0%) Query: 1 MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60 M D +D++++GGGPGGYVAAIRA QL L+ ALVE+ HLGGICLNWGCIPTK+LL AEV Sbjct: 1 MHDKYDVLIIGGGPGGYVAAIRAGQLGLRTALVEKQHLGGICLNWGCIPTKALLHGAEVA 60 Query: 61 HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120 H + +A+ G + + FDL K++ SR V+ +L GV+ LL+KN V VI+G +L G Sbjct: 61 HTIAHADRLGFSLSEVSFDLQKLVQFSRAVSQQLTGGVEYLLKKNGVTVIAGTARLRGKG 120 Query: 121 QMLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIG 180 Q+ V +GEE+ A +I+ATGAR R LP V DG+ IWTY AL+P +P+ LL+IG Sbjct: 121 QVTVADPQGEERDYRADHVILATGARPRALPGVEPDGERIWTYFEALQPERLPESLLIIG 180 Query: 181 SGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNL 240 SGAIG+EFAS Y D G+ V++VE A QILP+EDAEVSA V K+F++RGI + +Q+ L + Sbjct: 181 SGAIGVEFASLYNDLGSNVTLVEQAAQILPVEDAEVSATVRKSFERRGIHVHSQTLLTQV 240 Query: 241 TPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGR 300 D GV + + T E ++A GV NVE +GL+ LG++LDRGFI D R Sbjct: 241 KRTDTGVRCALKTTGAEQTLE-VERVLLAAGVQPNVEGLGLEALGVELDRGFIKTDAACR 299 Query: 301 TNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASV 360 TNV ++AIGDVAG PCLAHKASH+GVI E +AG + V PLN +PGCTYARPQVAS+ Sbjct: 300 TNVFGLYAIGDVAGPPCLAHKASHEGVICVETLAGVEGVRPLNCDYVPGCTYARPQVASL 359 Query: 361 GLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTE 420 GLTE KAR+ G +K+G F + NGKA+A G T+GFVKT+FDA++G LLGAHMVG +VTE Sbjct: 360 GLTEAKARETGRPIKVGKFAYQGNGKALASGETEGFVKTIFDAETGELLGAHMVGEQVTE 419 Query: 421 MIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465 IQG+ +A LE T+ ++ IF HPTLSEAMHES+LAA G+ LH Sbjct: 420 QIQGFGIAHHLEATDESLLSMIFAHPTLSEAMHESILAASGQPLH 464 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: 643 Number of extensions: 24 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: 466 Length of database: 465 Length adjustment: 33 Effective length of query: 433 Effective length of database: 432 Effective search space: 187056 Effective search space used: 187056 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 BWI76_RS14145 BWI76_RS14145 (dihydrolipoyl 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.1455.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-172 560.6 0.0 1.5e-172 560.4 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS14145 BWI76_RS14145 dihydrolipoyl dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS14145 BWI76_RS14145 dihydrolipoyl dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 560.4 0.0 1.5e-172 1.5e-172 1 460 [. 4 464 .. 4 465 .] 0.98 Alignments for each domain: == domain 1 score: 560.4 bits; conditional E-value: 1.5e-172 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgieve 71 +ydv++iGgGpgGYvaAira+qlgl++alvek++lGG+Cln+GCiPtKalL+ aev++++ +a++lg++++ lcl|FitnessBrowser__Koxy:BWI76_RS14145 4 KYDVLIIGGGPGGYVAAIRAGQLGLRTALVEKQHLGGICLNWGCIPTKALLHGAEVAHTIAHADRLGFSLS 74 59********************************************************************* PP TIGR01350 72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGs 141 +v++dl+kl++ +++v+++l+gGv++Llkkn+v+vi G+a+l++k++v+v++ ++e + ++a+++i+AtG+ lcl|FitnessBrowser__Koxy:BWI76_RS14145 75 EVSFDLQKLVQFSRAVSQQLTGGVEYLLKKNGVTVIAGTARLRGKGQVTVADPQGEeRDYRADHVILATGA 145 ***************************************************99888689************ PP TIGR01350 142 eprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldae 212 +pr+lp+ +e d+++++t+ eal+ +++pesl+i+G+G+iGvEfas++++lG++vt++e + +ilp++dae lcl|FitnessBrowser__Koxy:BWI76_RS14145 146 RPRALPG-VEPDGERIWTYFEALQPERLPESLLIIGSGAIGVEFASLYNDLGSNVTLVEQAAQILPVEDAE 215 *******.*************************************************************** PP TIGR01350 213 vskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgve 282 vs +++k+++++g+++++++ +t+v++++ v++ k + ++tle+e+vL+a G++pn+e+lgle+lgve lcl|FitnessBrowser__Koxy:BWI76_RS14145 216 VSATVRKSFERRGIHVHSQTLLTQVKRTDTGVRCALKTTgAEQTLEVERVLLAAGVQPNVEGLGLEALGVE 286 *********************************7777776779**************************** PP TIGR01350 283 ldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPsviytePev 352 ld+ g+ik+d+ +rtnv g+yaiGDv+g++ LAh+As+egv+++e++ag e ++ ++vP ++y++P+v lcl|FitnessBrowser__Koxy:BWI76_RS14145 287 LDR-GFIKTDAACRTNVFGLYAIGDVAGPPCLAHKASHEGVICVETLAGVEGVrPLNCDYVPGCTYARPQV 356 *98.*********************************************999889**************** PP TIGR01350 353 asvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselala 423 as+Glte++a+e g +kvgkf ++ ngkala++et+Gfvk+i+d +tge+lGah+vg++++e i+ + +a lcl|FitnessBrowser__Koxy:BWI76_RS14145 357 ASLGLTEAKARETGRPIKVGKFAYQGNGKALASGETEGFVKTIFDAETGELLGAHMVGEQVTEQIQGFGIA 427 *********************************************************************** PP TIGR01350 424 veleltveelaktihpHPtlsEaikeaalaalgkaih 460 +le+t e+l ++i++HPtlsEa++e++laa+g+++h lcl|FitnessBrowser__Koxy:BWI76_RS14145 428 HHLEATDESLLSMIFAHPTLSEAMHESILAASGQPLH 464 ***********************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (465 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: 00:00:00.02 # Mc/sec: 10.67 // [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