Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate RR42_RS21770 RR42_RS21770 dihydrolipoamide dehydrogenase
Query= BRENDA::P50970 (466 letters) >FitnessBrowser__Cup4G11:RR42_RS21770 Length = 466 Score = 531 bits (1367), Expect = e-155 Identities = 264/461 (57%), Positives = 344/461 (74%), Gaps = 1/461 (0%) Query: 5 FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64 FDLIV+GGGPGGYVAAIRA QL +K ALVE+ HLGGICLNWGCIPTK+LLRSA+V ++ Sbjct: 6 FDLIVVGGGPGGYVAAIRATQLGMKTALVEKAHLGGICLNWGCIPTKALLRSADVLRLVK 65 Query: 65 NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124 +A AYG+ + P DL ++ARSR VA +L GV L++KN V V++G G+L G ++ V Sbjct: 66 DAAAYGVHAAPPTADLPAMVARSRAVAAQLNKGVAHLMKKNGVTVLNGHGRLAGKGKLEV 125 Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184 T+G+ +I+ + I++ATGARARQLP + +DGK +WTY AL PP +PK++L++G+GAI Sbjct: 126 TATDGKTRIVSSAHILLATGARARQLPALPADGKTVWTYRDALAPPVVPKRMLIVGAGAI 185 Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPDD 244 GIEFASFY GAEV++VE A +ILP+EDA++ A VA + + GI + T + +Q+ Sbjct: 186 GIEFASFYRAVGAEVTVVEMAQRILPVEDADICAQVASSLTREGIVLHTGTGIQSAERKG 245 Query: 245 EGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNVD 304 +G + E+ G + +VA G+V NVE++GL++ +K+++ I DGFGRT+ Sbjct: 246 QGWSIELQGGKSGGARVDVDVVLVAAGIVGNVEDLGLERTAVKVEKTHIVTDGFGRTDEP 305 Query: 305 HVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLTE 364 V+AIGDVAG P LAHKASH+GVI E IAG H H L+ IP CTY+ PQVASVGLTE Sbjct: 306 GVYAIGDVAGPPWLAHKASHEGVICVERIAGL-HPHALDATRIPACTYSHPQVASVGLTE 364 Query: 365 EKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQG 424 +AR++G+ VK+G FPF NGKAIA G+T G VK VFDA SG LLGAHMVG EVTEMIQG Sbjct: 365 AQARERGHPVKVGKFPFAGNGKAIAMGSTAGLVKVVFDAGSGELLGAHMVGDEVTEMIQG 424 Query: 425 YTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465 Y +A+TLETTEA++M + PHPT+SEAMHE+VLAAYGRALH Sbjct: 425 YAIAQTLETTEADLMAAVLPHPTMSEAMHEAVLAAYGRALH 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: 630 Number of extensions: 18 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: 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 RR42_RS21770 RR42_RS21770 (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.12146.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-165 535.5 3.6 5.7e-165 535.4 3.6 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS21770 RR42_RS21770 dihydrolipoamide de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS21770 RR42_RS21770 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 535.4 3.6 5.7e-165 5.7e-165 2 461 .] 6 466 .] 5 466 .] 0.98 Alignments for each domain: == domain 1 score: 535.4 bits; conditional E-value: 5.7e-165 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 +d++v+GgGpgGYvaAira qlg+k+alvek +lGG+Cln+GCiPtKalL+sa+v++ +k+a+ +g+++ lcl|FitnessBrowser__Cup4G11:RR42_RS21770 6 FDLIVVGGGPGGYVAAIRATQLGMKTALVEKAHLGGICLNWGCIPTKALLRSADVLRLVKDAAAYGVHA 74 8******************************************************************** PP TIGR01350 71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiA 138 + + dl ++++r+++v +l++Gv++L+kkn+v+v++G+++l +k+++ev++++++ + ++ +i++A lcl|FitnessBrowser__Cup4G11:RR42_RS21770 75 APPTADLPAMVARSRAVAAQLNKGVAHLMKKNGVTVLNGHGRLAGKGKLEVTATDGKtRIVSSAHILLA 143 ****************************************************99987688899****** PP TIGR01350 139 tGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp 207 tG++ r+lp l +d+k+v+t+++al+ + vp++++ivG+G+iG+Efas+++ +G++vtv+e+++rilp lcl|FitnessBrowser__Cup4G11:RR42_RS21770 144 TGARARQLPA-LPADGKTVWTYRDALAPPVVPKRMLIVGAGAIGIEFASFYRAVGAEVTVVEMAQRILP 211 **********.********************************************************** PP TIGR01350 208 aldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleel 274 ++da+++ +++++l+++g+ ++t++ +++ e++ + ++e +++ ++++ vLva G n+e+l lcl|FitnessBrowser__Cup4G11:RR42_RS21770 212 VEDADICAQVASSLTREGIVLHTGTGIQSAERKGQGWSIELQGGksGGARVDVDVVLVAAGIVGNVEDL 280 ****************************99999999998877763356899****************** PP TIGR01350 275 gleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavP 343 gle++ v++++ i++d rt pg+yaiGDv+g++ LAh+As+egv+++e+iag +++++d++ +P lcl|FitnessBrowser__Cup4G11:RR42_RS21770 281 GLERTAVKVEK-THIVTDGFGRTDEPGVYAIGDVAGPPWLAHKASHEGVICVERIAGLHPHALDATRIP 348 *********99.77******************************************************* PP TIGR01350 344 sviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgae 412 +++y++P+vasvGlte+qa+e+g+ vkvgkfpfa ngka+a++ t G+vkv++d +ge+lGah+vg e lcl|FitnessBrowser__Cup4G11:RR42_RS21770 349 ACTYSHPQVASVGLTEAQARERGHPVKVGKFPFAGNGKAIAMGSTAGLVKVVFDAGSGELLGAHMVGDE 417 ********************************************************************* PP TIGR01350 413 aseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461 ++e+i+ a+a +le+t+ +l++++ pHPt+sEa++ea+laa+g+a+h+ lcl|FitnessBrowser__Cup4G11:RR42_RS21770 418 VTEMIQGYAIAQTLETTEADLMAAVLPHPTMSEAMHEAVLAAYGRALHI 466 *********************************************9995 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9.32 // [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