Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate AO356_11880 AO356_11880 dihydrolipoamide dehydrogenase
Query= BRENDA::A0A0H2ZHZ0 (467 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_11880 Length = 466 Score = 711 bits (1836), Expect = 0.0 Identities = 346/465 (74%), Positives = 402/465 (86%) Query: 2 MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61 M +YDV+++G GPGGYNAAIRAGQLGLK ACVEGR TLGGTCLNVGCMPSKALLHASELY Sbjct: 1 MSNYDVVILGGGPGGYNAAIRAGQLGLKAACVEGRATLGGTCLNVGCMPSKALLHASELY 60 Query: 62 AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121 AA+G EFA LGI VSP L+LAQMMKQKDESV LT+G+EFLFRK+KV WIKGW + G Sbjct: 61 EAATGTEFANLGIEVSPTLNLAQMMKQKDESVTGLTKGIEFLFRKNKVDWIKGWGHIDGP 120 Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181 G+V V DG +L A+DIVIATGSEP PLPGV +DNQRILDSTGAL L+EVPRHLVVI Sbjct: 121 GKVTVTGDDGSKTELTAKDIVIATGSEPMPLPGVTIDNQRILDSTGALSLSEVPRHLVVI 180 Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241 GAGVIGLELGSVWRRLGAQVTV+EYL+RICPG+DGE +TLQRAL +QG++F+L ++V Sbjct: 181 GAGVIGLELGSVWRRLGAQVTVVEYLDRICPGVDGEAGKTLQRALAKQGIQFKLSSKVTG 240 Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301 A + GV+L ++PAAGG + L ADYVLVAIGRRPYT+GLGLE VGL++D+RGML NQ Sbjct: 241 ATTSASGVQLQIEPAAGGEAQILDADYVLVAIGRRPYTQGLGLENVGLSTDKRGMLANQH 300 Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361 R+ APGVWVIGDVT+GPMLAHKAE+EA+ CIE+IAG AAE+N +IPSVIYT+PE+ASV Sbjct: 301 HRTEAPGVWVIGDVTAGPMLAHKAEDEAMACIEQIAGKAAEVNYALIPSVIYTRPELASV 360 Query: 362 GLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVSE 421 G EEQL+A R YKVG+FPF+ANSRAKINHE+EGF K+L+D R+D++LGVH++GP VSE Sbjct: 361 GQTEEQLKAEGRAYKVGKFPFTANSRAKINHETEGFAKVLADERTDEILGVHLVGPSVSE 420 Query: 422 MIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGRAMQ 466 MIGE CVAMEFSASAED+ALTCHPHPTRSEALRQAAM+V G A Q Sbjct: 421 MIGEYCVAMEFSASAEDIALTCHPHPTRSEALRQAAMNVEGMATQ 465 Lambda K H 0.318 0.135 0.390 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: 793 Number of extensions: 27 Number of successful extensions: 1 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: 467 Length of database: 466 Length adjustment: 33 Effective length of query: 434 Effective length of database: 433 Effective search space: 187922 Effective search space used: 187922 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: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate AO356_11880 AO356_11880 (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.16192.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-167 543.5 1.1 2.1e-167 543.4 1.1 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 AO356_11880 dihydrolipoamide deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 AO356_11880 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 543.4 1.1 2.1e-167 2.1e-167 1 460 [. 3 465 .. 3 466 .] 0.96 Alignments for each domain: == domain 1 score: 543.4 bits; conditional E-value: 2.1e-167 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke 62 +ydvv++GgGpgGY aAira+qlglk a+ve +lGGtClnvGC+P+KalL+++e++e ++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 3 NYDVVILGGGPGGYNAAIRAGQLGLKAACVEGrATLGGTCLNVGCMPSKALLHASELYEAATG 65 69*****************************8799************************9875 PP TIGR01350 63 ..akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkk 123 +++lgiev + +l+l++++++k++ v+ l++G+++L++knkv+ ikG +++ ++++v+v++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 66 teFANLGIEV-SPTLNLAQMMKQKDESVTGLTKGIEFLFRKNKVDWIKGWGHIDGPGKVTVTG 127 5699****88.789************************************************9 PP TIGR01350 124 ekke.kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEf 185 ++++ ++l+ak+i+iAtGsep lp+ + d++++++s++al+l+evp++lv++G+GviG+E+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 128 DDGSkTELTAKDIVIATGSEPMPLPG-VTIDNQRILDSTGALSLSEVPRHLVVIGAGVIGLEL 189 998867899*****************.9999999***************************** PP TIGR01350 186 asifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..v 246 +s++++lG++vtv+e+ldri+p +d e k+l+++l k+g++++ ++kvt ++++ v+ + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 190 GSVWRRLGAQVTVVEYLDRICPGVDGEAGKTLQRALAKQGIQFKLSSKVTGATTSASGVQlqI 252 **************************************************7777777777335 PP TIGR01350 247 eakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDv 308 e + e++ l+a++vLva+Gr+p +++lgle++g+++d+rg + +++ rt++pg+++iGDv lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 253 EPAAGgEAQILDADYVLVAIGRRPYTQGLGLENVGLSTDKRG-MLANQHHRTEAPGVWVIGDV 314 5555569*********************************99.567***************** PP TIGR01350 309 igklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkv 371 ++++mLAh+A++e++ ++e+iagk++ e++y ++Psviyt+Pe+asvG teeq+k+eg ++kv lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 315 TAGPMLAHKAEDEAMACIEQIAGKAA-EVNYALIPSVIYTRPELASVGQTEEQLKAEGRAYKV 376 ***********************887.9*********************************** PP TIGR01350 372 gkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveela 434 gkfpf+an++a + +et+Gf+kv++d+ t+eilG+h+vg+++se+i e +a+e+ +++e++a lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 377 GKFPFTANSRAKINHETEGFAKVLADERTDEILGVHLVGPSVSEMIGEYCVAMEFSASAEDIA 439 *************************************************************** PP TIGR01350 435 ktihpHPtlsEaikeaalaalgkaih 460 t+hpHPt sEa+ +aa ++ g+a + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 440 LTCHPHPTRSEALRQAAMNVEGMATQ 465 ******************99988765 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 7.23 // [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