Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_011651835.1 RL_RS11630 dihydrolipoyl dehydrogenase
Query= BRENDA::P50970 (466 letters) >NCBI__GCF_000009265.1:WP_011651835.1 Length = 482 Score = 509 bits (1311), Expect = e-149 Identities = 256/483 (53%), Positives = 336/483 (69%), Gaps = 20/483 (4%) Query: 1 MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60 MA+ +D+I++G GPGGYVAAIRA+QL LK A+VER H+GGICLNWGCIPTK+LLRSAEV Sbjct: 1 MAESYDVIIIGSGPGGYVAAIRASQLGLKTAIVEREHMGGICLNWGCIPTKALLRSAEVL 60 Query: 61 HEMQNAEAYGLT---SFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLT 117 + + +GL + KPD ++ RSR V+ RL +GV L++KNK+++I G ++T Sbjct: 61 DHANHFKDFGLVLEGTVKPD--AKAVVGRSRAVSARLNAGVGFLMKKNKIDIIWGEAKIT 118 Query: 118 GNQQMLV---------------ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWT 162 +++V + + E AK IIIATGAR R LP + DGK IWT Sbjct: 119 KPGEIVVGKSSKPVVEPQHPLPKNVKSGEGTYTAKHIIIATGARPRALPGIEPDGKLIWT 178 Query: 163 YHHALKPPAMPKKLLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAK 222 Y ALKP +PK L+V+GSGAIGIEFASFY G +V++VE P I+P+EDAE++A K Sbjct: 179 YFEALKPDLLPKSLIVMGSGAIGIEFASFYRSMGVDVTVVEVMPTIMPVEDAEITAIARK 238 Query: 223 AFKKRGIRILTQSALQNLTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLD 282 +KRG++I T + + + VTA + ADGKV + I A+GV N+EN+GL+ Sbjct: 239 QLEKRGLKIFTSAKVSKVDKATNSVTAHVETADGKVQQITADRLISAVGVQGNIENLGLE 298 Query: 283 KLGIKLDRGFIAVDGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPL 342 LG+K DRG + +DG+G+TNV ++AIGDVAG P LAHKA H+GV+ E IAG +VHP Sbjct: 299 ALGVKTDRGCVVIDGYGKTNVAGIYAIGDVAGPPMLAHKAEHEGVVCVEKIAGLPNVHPT 358 Query: 343 NTQNIPGCTYARPQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFD 402 + +PGCTY PQVASVG+TE KA++QG ++++G F F ANGKAIA G G VK +FD Sbjct: 359 DKGKVPGCTYCNPQVASVGITEAKAKEQGRDIRVGRFSFAANGKAIALGEDQGMVKVIFD 418 Query: 403 ADSGALLGAHMVGAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGR 462 +G LLGAHMVGAEVTE+IQG+ VA LETTE E+M TIFPHPT+SE+M E+VL AYGR Sbjct: 419 KKTGELLGAHMVGAEVTELIQGFVVAMNLETTEEELMHTIFPHPTVSESMKEAVLDAYGR 478 Query: 463 ALH 465 L+ Sbjct: 479 VLN 481 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: 677 Number of extensions: 30 Number of successful extensions: 3 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: 482 Length adjustment: 33 Effective length of query: 433 Effective length of database: 449 Effective search space: 194417 Effective search space used: 194417 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 WP_011651835.1 RL_RS11630 (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.19189.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-180 584.3 8.1 1e-179 584.0 8.1 1.0 1 lcl|NCBI__GCF_000009265.1:WP_011651835.1 RL_RS11630 dihydrolipoyl dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009265.1:WP_011651835.1 RL_RS11630 dihydrolipoyl dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 584.0 8.1 1e-179 1e-179 1 459 [. 4 480 .. 4 482 .] 0.98 Alignments for each domain: == domain 1 score: 584.0 bits; conditional E-value: 1e-179 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgie 69 +ydv++iG+GpgGYvaAira+qlglk+a+ve+e++GG+Cln+GCiPtKalL+saev+++++++k++g+ lcl|NCBI__GCF_000009265.1:WP_011651835.1 4 SYDVIIIGSGPGGYVAAIRASQLGLKTAIVEREHMGGICLNWGCIPTKALLRSAEVLDHANHFKDFGLV 72 59******************************************************************* PP TIGR01350 70 ven.vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.......... 127 +e+ vk d ++++ r+++v+ +l++Gv +L+kknk++ i+Geak+++++e+ v k++k lcl|NCBI__GCF_000009265.1:WP_011651835.1 73 LEGtVKPDAKAVVGRSRAVSARLNAGVGFLMKKNKIDIIWGEAKITKPGEIVVGKSSKPvvepqhplpk 141 9999*************************************************999876899999***9 PP TIGR01350 128 ......kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifa 190 +++ak+iiiAtG++pr+lp+ +e d+k+++t+ eal+ + +p+sl+++G+G+iG+Efas+++ lcl|NCBI__GCF_000009265.1:WP_011651835.1 142 nvksgeGTYTAKHIIIATGARPRALPG-IEPDGKLIWTYFEALKPDLLPKSLIVMGSGAIGIEFASFYR 209 9988877899*****************.***************************************** PP TIGR01350 191 klGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetle 257 ++Gv+vtv+e++++i+p++dae++ +++k+l+k+g+ki t+akv++v k ++v+ ve+ +++v++++ lcl|NCBI__GCF_000009265.1:WP_011651835.1 210 SMGVDVTVVEVMPTIMPVEDAEITAIARKQLEKRGLKIFTSAKVSKVDKATNSVTahVETADGKVQQIT 278 *******************************************************888888889***** PP TIGR01350 258 aekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaa 326 a++++ avG++ n+e+lgle+lgv++d+ g++++d + +tnv+giyaiGDv+g++mLAh+A++egvv++ lcl|NCBI__GCF_000009265.1:WP_011651835.1 279 ADRLISAVGVQGNIENLGLEALGVKTDR-GCVVIDGYGKTNVAGIYAIGDVAGPPMLAHKAEHEGVVCV 346 *************************776.**************************************** PP TIGR01350 327 ekiagkeks.eidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkv 394 ekiag + +d+ +vP ++y++P+vasvG+te++ake+g +++vg+f+faangka+al+e++G+vkv lcl|NCBI__GCF_000009265.1:WP_011651835.1 347 EKIAGLPNVhPTDKGKVPGCTYCNPQVASVGITEAKAKEQGRDIRVGRFSFAANGKAIALGEDQGMVKV 415 *****9887799********************************************************* PP TIGR01350 395 ivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkai 459 i+dkktge+lGah+vgae++eli+ +++a++le+t+eel++ti+pHPt+sE +kea+l+a+g+ + lcl|NCBI__GCF_000009265.1:WP_011651835.1 416 IFDKKTGELLGAHMVGAEVTELIQGFVVAMNLETTEEELMHTIFPHPTVSESMKEAVLDAYGRVL 480 ************************************************************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (482 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: 10.84 // [ok]
This GapMind analysis is from Sep 24 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