Align Dihydrolipoyl dehydrogenase 1, mitochondrial; AtmLPD1; mtLPD1; Dihydrolipoamide dehydrogenase 1; Glycine cleavage system L protein 1; Pyruvate dehydrogenase complex E3 subunit 1; E3-1; PDC-E3 1; EC 1.8.1.4 (characterized)
to candidate 3609502 Dshi_2886 dihydrolipoamide dehydrogenase (RefSeq)
Query= SwissProt::Q9M5K3 (507 letters) >FitnessBrowser__Dino:3609502 Length = 464 Score = 523 bits (1348), Expect = e-153 Identities = 259/464 (55%), Positives = 340/464 (73%), Gaps = 7/464 (1%) Query: 45 DVVIIGGGPGGYVAAIKASQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104 DV+IIG GPGGYV AI+ +QLGLKT C+E R LGGTCLNVGCIPSKALLH+SH HEA+ Sbjct: 5 DVIIIGSGPGGYVGAIRCAQLGLKTACVEGRDTLGGTCLNVGCIPSKALLHASHQVHEAE 64 Query: 105 HSFANHGIKVSSVEVDLPAMLAQKDNAVKNLTRGIEGLFKKNKVTYVKGYGKFISPNEVS 164 H+F GIKV + ++D MLA KD+ + T+GIE LFKKNKV ++KG+ +V Sbjct: 65 HNFEKMGIKVPAPKIDWKTMLAYKDDVIGQNTKGIEFLFKKNKVDWLKGWASIPEAGKVK 124 Query: 165 VETIDGGNTIVKGKHIIVATGSDVKSLPG--ITIDEKKIVSSTGALSLSEVPKKLIVIGA 222 V G+ + KHII+A+GS+ S+PG + IDEK +V+STGAL L ++PK+++V+G Sbjct: 125 V-----GDETHEAKHIIIASGSEPASIPGAEVEIDEKVVVTSTGALELGKIPKRMVVVGG 179 Query: 223 GYIGLEMGSVWGRLGSEVTVVEFAGDIVPSMDGEIRKQFQRSLEKQKMKFMLKTKVVSVD 282 G IGLE+GSV+ RLG+EV+V+EF I P D E+ +QFQ+ L KQ +KF+ V V Sbjct: 180 GVIGLELGSVYARLGTEVSVIEFMDGITPGQDLEVARQFQKILTKQGLKFITGAAVQKVA 239 Query: 283 SSSDGVKLTVEPAEGGEQSILEADVVLVSAGRTPFTSGLDLEKIGVETDKAGRILVNDRF 342 ++ K+T + + + LEAD+VLVS GR PFT GL L+ +GV+ + G+I + + Sbjct: 240 ATKSKAKVTYKMRKDDSEDSLEADIVLVSTGRKPFTEGLGLDALGVKMTERGQIATDGSY 299 Query: 343 LSNVPGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTHPEVASVG 402 +NVPGVYAIGDVI GPMLAHKAE++G+A E IAG+H HV+Y +PGV+YTHPEVASVG Sbjct: 300 RTNVPGVYAIGDVIEGPMLAHKAEDEGMAVAEMIAGQHPHVNYGVIPGVIYTHPEVASVG 359 Query: 403 KTEEQLKKEGVSYRVGKFPFMANSRAKAIDNAEGLVKILADKETDKILGVHIMAPNAGEL 462 KTEEQLK EGV+Y+VGKF FM N RAKA A+G VK+LADK TD+ILG H++ P AG+L Sbjct: 360 KTEEQLKAEGVAYKVGKFSFMGNGRAKANFAADGFVKLLADKATDRILGAHVIGPMAGDL 419 Query: 463 IHEAVLAINYDASSEDIARVCHAHPTMSEALKEAAMATYDKPIH 506 IHE +A+ + A++ED+AR CHAHPT SEA++EAA+A D IH Sbjct: 420 IHEVCVAMEFGAAAEDLARTCHAHPTYSEAMREAALACGDGAIH 463 Lambda K H 0.315 0.133 0.375 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: 725 Number of extensions: 28 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: 507 Length of database: 464 Length adjustment: 34 Effective length of query: 473 Effective length of database: 430 Effective search space: 203390 Effective search space used: 203390 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: 42 (22.0 bits) S2: 52 (24.6 bits)
Align candidate 3609502 Dshi_2886 (dihydrolipoamide dehydrogenase (RefSeq))
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.11215.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-177 576.4 8.8 2.3e-177 576.2 8.8 1.0 1 lcl|FitnessBrowser__Dino:3609502 Dshi_2886 dihydrolipoamide dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609502 Dshi_2886 dihydrolipoamide dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 576.2 8.8 2.3e-177 2.3e-177 1 460 [. 3 463 .. 3 464 .] 0.98 Alignments for each domain: == domain 1 score: 576.2 bits; conditional E-value: 2.3e-177 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgievenvkl 75 +ydv++iG+GpgGYv Air+aqlglk+a+ve ++lGGtClnvGCiP+KalL++++ v+e+++ ++++gi+v k+ lcl|FitnessBrowser__Dino:3609502 3 SYDVIIIGSGPGGYVGAIRCAQLGLKTACVEGrDTLGGTCLNVGCIPSKALLHASHQVHEAEHnFEKMGIKVPAPKI 79 59*****************************879******************************************* PP TIGR01350 76 dlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplk.le 151 d++++l+ k+ v+ + ++G+++L+kknkv+ +kG a++ ++++v+v +e++ eak+iiiA+Gsep+++p++ +e lcl|FitnessBrowser__Dino:3609502 80 DWKTMLAYKDDVIGQNTKGIEFLFKKNKVDWLKGWASIPEAGKVKVGDETH----EAKHIIIASGSEPASIPGAeVE 152 ***********************************************9985....6*****************99** PP TIGR01350 152 edekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvki 228 dekvv+ts++alel ++p+++v+vGgGviG+E++s++a+lG++v+vie++d i p d ev+++ +k l+k+g+k+ lcl|FitnessBrowser__Dino:3609502 153 IDEKVVVTSTGALELGKIPKRMVVVGGGVIGLELGSVYARLGTEVSVIEFMDGITPGQDLEVARQFQKILTKQGLKF 229 ***************************************************************************** PP TIGR01350 229 ltnakvt..evekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgi 302 +t+a v+ + +k++++v+++++k+ +++lea+ vLv+ Grkp +e+lgl++lgv+++erg+i +d ++rtnvpg+ lcl|FitnessBrowser__Dino:3609502 230 ITGAAVQkvAATKSKAKVTYKMRKDdSEDSLEADIVLVSTGRKPFTEGLGLDALGVKMTERGQIATDGSYRTNVPGV 306 *******5445677788889988887789************************************************ PP TIGR01350 303 yaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaan 379 yaiGDvi+++mLAh+A++eg+ +ae iag+++ +++y ++P viyt+PevasvG+teeq+k+eg+++kvgkf+f+ n lcl|FitnessBrowser__Dino:3609502 307 YAIGDVIEGPMLAHKAEDEGMAVAEMIAGQHP-HVNYGVIPGVIYTHPEVASVGKTEEQLKAEGVAYKVGKFSFMGN 382 *****************************999.9******************************************* PP TIGR01350 380 gkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalg 456 g+a a +dGfvk+++dk t++ilGah++g+ a +li+e+ +a+e+++ +e+la+t+h+HPt+sEa+ eaala + lcl|FitnessBrowser__Dino:3609502 383 GRAKANFAADGFVKLLADKATDRILGAHVIGPMAGDLIHEVCVAMEFGAAAEDLARTCHAHPTYSEAMREAALACGD 459 **************************************************************************999 PP TIGR01350 457 kaih 460 aih lcl|FitnessBrowser__Dino:3609502 460 GAIH 463 9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (464 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: 00:00:00.03 # Mc/sec: 6.83 // [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