Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate PP_5366 PP_5366 dihydrolipoyl dehydrogenase
Query= BRENDA::A0A0H2ZHZ0 (467 letters) >FitnessBrowser__Putida:PP_5366 Length = 466 Score = 714 bits (1844), Expect = 0.0 Identities = 349/465 (75%), Positives = 402/465 (86%) Query: 2 MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61 M+SYDV++IG GPGGYNAAIRAGQLGL VACVEGR TLGGTCLNVGCMPSKALLHASELY Sbjct: 1 MKSYDVVIIGGGPGGYNAAIRAGQLGLSVACVEGRSTLGGTCLNVGCMPSKALLHASELY 60 Query: 62 AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121 AASG EFA LGI V P L+LAQMMKQKDESV LT+G+E+LFRK+KV+WIKGW RL G Sbjct: 61 EAASGDEFAHLGIEVKPTLNLAQMMKQKDESVTGLTKGIEYLFRKNKVEWIKGWGRLDGI 120 Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181 G+V V DG L+A+DIVIATGSEP PLPGV VDNQRI+DSTGAL L +VP+HLVVI Sbjct: 121 GKVVVKAEDGSETALQAKDIVIATGSEPTPLPGVTVDNQRIIDSTGALSLPQVPKHLVVI 180 Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241 GAGVIGLELGSVWRRLG+QVTV+EYL+RICPG D ETA+TLQ+AL +QGM F+LG++V Sbjct: 181 GAGVIGLELGSVWRRLGSQVTVIEYLDRICPGTDTETAKTLQKALAKQGMVFKLGSKVTQ 240 Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301 A +G GV L L+PAAGG ESLQADYVLVAIGRRPYT+GL LE+VGL +D+RGML N+ Sbjct: 241 ATAGADGVSLTLEPAAGGTAESLQADYVLVAIGRRPYTKGLNLESVGLEADKRGMLNNEH 300 Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361 R++ PGVWVIGDVTSGPMLAHKAE+EA+ CIERIAG E+N +IP VIYT+PE+A+V Sbjct: 301 HRTSVPGVWVIGDVTSGPMLAHKAEDEAVACIERIAGKPHEVNYNLIPGVIYTRPEMATV 360 Query: 362 GLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVSE 421 G EEQL+A R YKVG+FPF+ANSRAKINHE+EGF K+++DA +D+VLGVH++GP VSE Sbjct: 361 GKTEEQLKAEGRAYKVGKFPFTANSRAKINHETEGFAKVIADAETDEVLGVHLVGPSVSE 420 Query: 422 MIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGRAMQ 466 MIGE CVAMEFSASAED+ALTCHPHPTRSEALRQAAM+V G AMQ Sbjct: 421 MIGEFCVAMEFSASAEDIALTCHPHPTRSEALRQAAMNVDGMAMQ 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: 782 Number of extensions: 23 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 PP_5366 PP_5366 (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.6618.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-169 549.2 1.9 4.1e-169 549.0 1.9 1.0 1 lcl|FitnessBrowser__Putida:PP_5366 PP_5366 dihydrolipoyl dehydrogen Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_5366 PP_5366 dihydrolipoyl dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 549.0 1.9 4.1e-169 4.1e-169 1 459 [. 3 464 .. 3 466 .] 0.96 Alignments for each domain: == domain 1 score: 549.0 bits; conditional E-value: 4.1e-169 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke..akelgieven 72 +ydvv+iGgGpgGY aAira+qlgl+va+ve ++lGGtClnvGC+P+KalL+++e++e ++ +++lgiev + lcl|FitnessBrowser__Putida:PP_5366 3 SYDVVIIGGGPGGYNAAIRAGQLGLSVACVEGrSTLGGTCLNVGCMPSKALLHASELYEAASGdeFAHLGIEV-K 76 59*****************************8799************************99755699****98.7 PP TIGR01350 73 vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprel 146 +l+l++++++k++ v+ l++G+++L++knkve ikG ++l + ++v vk+e+++ + l+ak+i+iAtGsep+ l lcl|FitnessBrowser__Putida:PP_5366 77 PTLNLAQMMKQKDESVTGLTKGIEYLFRKNKVEWIKGWGRLDGIGKVVVKAEDGSeTALQAKDIVIATGSEPTPL 151 89*************************************************99886789**************** PP TIGR01350 147 plkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkkl 221 p+ + +d++++i+s++al+l++vp++lv++G+GviG+E++s++++lG++vtvie+ldri+p +d+e +k+l+k+l lcl|FitnessBrowser__Putida:PP_5366 152 PG-VTVDNQRIIDSTGALSLPQVPKHLVVIGAGVIGLELGSVWRRLGSQVTVIEYLDRICPGTDTETAKTLQKAL 225 **.9999999***************************************************************** PP TIGR01350 222 kkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvde 293 k+g+ ++ ++kvt+ ++ +d v+ +e + ++e+l+a++vLva+Gr+p +++l+le++g+e d+rg+++ +e lcl|FitnessBrowser__Putida:PP_5366 226 AKQGMVFKLGSKVTQATAGADGVSltLEPAAGgTAESLQADYVLVAIGRRPYTKGLNLESVGLEADKRGMLN-NE 299 *********************99955444444589**********************************665.99 PP TIGR01350 294 elrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegie 368 + rt+vpg+++iGDv++++mLAh+A++e+v ++e+iagk + e++y+++P viyt+Pe+a+vG+teeq+k+eg + lcl|FitnessBrowser__Putida:PP_5366 300 HHRTSVPGVWVIGDVTSGPMLAHKAEDEAVACIERIAGKPH-EVNYNLIPGVIYTRPEMATVGKTEEQLKAEGRA 373 **************************************776.9******************************** PP TIGR01350 369 vkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtl 443 +kvgkfpf+an++a + +et+Gf+kvi+d +t+e+lG+h+vg+++se+i e+ +a+e+ +++e++a t+hpHPt lcl|FitnessBrowser__Putida:PP_5366 374 YKVGKFPFTANSRAKINHETEGFAKVIADAETDEVLGVHLVGPSVSEMIGEFCVAMEFSASAEDIALTCHPHPTR 448 *************************************************************************** PP TIGR01350 444 sEaikeaalaalgkai 459 sEa+ +aa ++ g+a+ lcl|FitnessBrowser__Putida:PP_5366 449 SEALRQAAMNVDGMAM 464 *********9998876 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.61 // [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