Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate PfGW456L13_698 Dihydrolipoamide dehydrogenase (EC 1.8.1.4)
Query= BRENDA::A0A0H2ZHZ0 (467 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 Length = 466 Score = 698 bits (1801), Expect = 0.0 Identities = 337/465 (72%), Positives = 399/465 (85%) Query: 2 MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61 M +YDV+++G GPGGYNAAIRAGQLGLK ACVEGR TLGGTCLNVGCMPSKALLHASELY Sbjct: 1 MSTYDVVILGGGPGGYNAAIRAGQLGLKAACVEGRATLGGTCLNVGCMPSKALLHASELY 60 Query: 62 AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121 AA G EFA LGI V P L+L QMMKQKDESV LT+G+EFLFRK+KV WI+GW + G Sbjct: 61 DAAKGAEFANLGIEVKPVLNLNQMMKQKDESVTGLTKGIEFLFRKNKVDWIRGWGHIDGP 120 Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181 G+V V + GG +L ARDI+IATGSEP PLPGV +DN+RILDSTGAL L EVP+HLVVI Sbjct: 121 GKVTVTDSAGGKTELSARDIIIATGSEPTPLPGVDIDNKRILDSTGALALTEVPKHLVVI 180 Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241 GAGVIGLELGSVWRRLGAQVTV+E+L+RICPG+D E +TLQR+L++QG+ F+L ++V + Sbjct: 181 GAGVIGLELGSVWRRLGAQVTVVEFLDRICPGVDIEAGKTLQRSLSKQGLSFKLSSKVTS 240 Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301 A + GV+L ++PAAGGA E L+ADYVLVAIGRRPYT+GLGLE VGLA+D+RGML N+G Sbjct: 241 ATTSATGVQLSIEPAAGGAAELLEADYVLVAIGRRPYTQGLGLENVGLATDKRGMLANKG 300 Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361 R+ A GVWVIGDVTSGPMLAHKAE+EA+ C+E++ G A E+N +IPSV+YT+PE+ASV Sbjct: 301 HRTEAVGVWVIGDVTSGPMLAHKAEDEAMACVEQMVGKAGEVNYNLIPSVVYTKPELASV 360 Query: 362 GLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVSE 421 G EEQL+A R YKVG+FPF+ANSRAKINHE+EGF K+L+D R+D+VLGVH++GP VSE Sbjct: 361 GKTEEQLKAEGRAYKVGKFPFTANSRAKINHETEGFAKVLADERTDEVLGVHLVGPSVSE 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: 776 Number of extensions: 26 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 PfGW456L13_698 (Dihydrolipoamide dehydrogenase (EC 1.8.1.4))
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.19995.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-164 532.2 1.2 5.8e-164 532.1 1.2 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 Dihydrolipoamide dehydrogenase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 Dihydrolipoamide dehydrogenase (EC 1.8.1.4) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 532.1 1.2 5.8e-164 5.8e-164 2 460 .. 4 465 .. 3 466 .] 0.96 Alignments for each domain: == domain 1 score: 532.1 bits; conditional E-value: 5.8e-164 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaev 56 ydvv++GgGpgGY aAira+qlglk a+ve +lGGtClnvGC+P+KalL+++e+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 4 YDVVILGGGPGGYNAAIRAGQLGLKAACVEGrATLGGTCLNVGCMPSKALLHASEL 59 9*****************************8799********************** PP TIGR01350 57 veelke..akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGe 110 ++ +k +++lgiev+ l+l++++++k++ v+ l++G+++L++knkv+ i G lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 60 YDAAKGaeFANLGIEVK-PVLNLNQMMKQKDESVTGLTKGIEFLFRKNKVDWIRGW 114 ***99756899999985.679*********************************** PP TIGR01350 111 aklldkkevevkkekke.kkleakniiiAtGseprelplkleedekvvitseeale 165 +++ ++++v+v+++++ ++l+a +iiiAtGsep+ lp+ ++ d+k++++s++al+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 115 GHIDGPGKVTVTDSAGGkTELSARDIIIATGSEPTPLPG-VDIDNKRILDSTGALA 169 *************997757899*****************.**************** PP TIGR01350 166 lkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkkl 221 l+evp++lv++G+GviG+E++s++++lG++vtv+e+ldri+p +d e k+l+++l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 170 LTEVPKHLVVIGAGVIGLELGSVWRRLGAQVTVVEFLDRICPGVDIEAGKTLQRSL 225 ******************************************************** PP TIGR01350 222 kkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleel 274 +k+g++++ ++kvt+ ++++ v+ +e + +e lea++vLva+Gr+p +++l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 226 SKQGLSFKLSSKVTSATTSATGVQlsIEPAAGgAAELLEADYVLVAIGRRPYTQGL 281 **************888888888844555555589********************* PP TIGR01350 275 gleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekia 330 gle++g+ +d+rg+ ++ rt++ g+++iGDv++++mLAh+A++e++ ++e+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 282 GLENVGLATDKRGM-LANKGHRTEAVGVWVIGDVTSGPMLAHKAEDEAMACVEQMV 336 ***********995.57999************************************ PP TIGR01350 331 gkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalale 386 gk+ e++y+++Psv+yt+Pe+asvG+teeq+k+eg ++kvgkfpf+an++a + + lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 337 GKAG-EVNYNLIPSVVYTKPELASVGKTEEQLKAEGRAYKVGKFPFTANSRAKINH 391 *998.9************************************************** PP TIGR01350 387 etdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPt 442 et+Gf+kv++d+ t+e+lG+h+vg+++se+i e +a+e+ +++e++a t+hpHPt lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 392 ETEGFAKVLADERTDEVLGVHLVGPSVSEMIGEYCVAMEFSASAEDIALTCHPHPT 447 ******************************************************** PP TIGR01350 443 lsEaikeaalaalgkaih 460 sEa+ +aa ++ g+a + lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 448 RSEALRQAAMNVEGMATQ 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.94 // [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