Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_108358556.1 B9Z44_RS13620 dihydrolipoyl dehydrogenase
Query= SwissProt::P14218 (478 letters) >NCBI__GCF_003063475.1:WP_108358556.1 Length = 475 Score = 490 bits (1262), Expect = e-143 Identities = 265/474 (55%), Positives = 324/474 (68%), Gaps = 3/474 (0%) Query: 1 MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60 MS++FDVVVIG GPGGY+AAIRAAQLG + ACI+++ G A GGTC NVGCIPSKAL Sbjct: 1 MSKQFDVVVIGGGPGGYIAAIRAAQLGFQVACIDEWKNAAGGPAPGGTCTNVGCIPSKAL 60 Query: 61 LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120 L SS + A F HGI AK V +DV M+ARK N+VK GI LFK N VT F G Sbjct: 61 LQSSEHFDHANHHFAEHGISAKDVKMDVAKMIARKDNVVKQNNDGILYLFKKNKVTFFHG 120 Query: 121 HGKLLANKQVEVT-GLDGKTQV-LEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQ 178 G + T + GKT+ + A+ VIIA+GS +P P + ++ + GAL Sbjct: 121 RGSFAGKAEGGYTVNVAGKTEESITAKQVIIATGSNARALPGTPFDEVNVLSNDGALRVG 180 Query: 179 AVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLN 238 AVPKKL +IG+GVIGLE+GSVW RLGA+VT+LE L FL A DEQIAKEA K KQGL Sbjct: 181 AVPKKLALIGSGVIGLEMGSVWRRLGADVTILEGLPTFLGAVDEQIAKEAKKAFDKQGLK 240 Query: 239 IRLGARVTASEVKKKQVTVTFTDANGEQKET-FDKLIVAVGRRPVTTDLLAADSGVTLDE 297 I LG +V KK VTV +T+A GE DKLIV++GR P T L A G+ +DE Sbjct: 241 IELGVKVGEIVNGKKGVTVNYTNAKGEAIVLEADKLIVSIGRVPNTIGLNAEAIGLAVDE 300 Query: 298 RGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVI 357 RG I VD CKT+VPGV+A+GDVVRG MLAHKA EEGV VAERIAG +N++ IP VI Sbjct: 301 RGAIVVDGDCKTNVPGVWAVGDVVRGPMLAHKAEEEGVAVAERIAGQHGHVNFNTIPWVI 360 Query: 358 YTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGV 417 YT PEIAWVG+TEQ LKA+GV GTFPF A+GRA A DTTG+VK +ADA TD +LGV Sbjct: 361 YTSPEIAWVGRTEQQLKADGVAYKAGTFPFLANGRARALGDTTGMVKFLADATTDEILGV 420 Query: 418 HVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIH 471 H++GP +EL+ + + MEF SAED+ + +HP+LSEA EAALAV+ ++ Sbjct: 421 HMVGPQVSELISEAVVAMEFKASAEDIARICHAHPSLSEATKEAALAVDKRTLN 474 Lambda K H 0.316 0.134 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: 684 Number of extensions: 31 Number of successful extensions: 5 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: 478 Length of database: 475 Length adjustment: 33 Effective length of query: 445 Effective length of database: 442 Effective search space: 196690 Effective search space used: 196690 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 (21.6 bits) S2: 51 (24.3 bits)
Align candidate WP_108358556.1 B9Z44_RS13620 (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.2788997.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-164 531.4 7.5 1e-163 531.3 7.5 1.0 1 NCBI__GCF_003063475.1:WP_108358556.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003063475.1:WP_108358556.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 531.3 7.5 1e-163 1e-163 1 459 [. 4 473 .. 4 475 .] 0.95 Alignments for each domain: == domain 1 score: 531.3 bits; conditional E-value: 1e-163 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvek.ek.l.....GGtClnvGCiPtKalLksaevveelke.ake 65 ++dvvviGgGpgGY+aAiraaqlg++va++++ ++ GGtC+nvGCiP+KalL+s+e ++++++ ++e NCBI__GCF_003063475.1:WP_108358556.1 4 QFDVVVIGGGPGGYIAAIRAAQLGFQVACIDEwKNaAggpapGGTCTNVGCIPSKALLQSSEHFDHANHhFAE 76 59****************************98643223333389************************99*** PP TIGR01350 66 lgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld....kkevevkkekkekkleakn 134 +gi++++vk+d++k+ +rk++vvk+ ++G+ +L+kknkv+ ++G++++ + +v+v++++ e++++ak+ NCBI__GCF_003063475.1:WP_108358556.1 77 HGISAKDVKMDVAKMIARKDNVVKQNNDGILYLFKKNKVTFFHGRGSFAGkaegGYTVNVAGKT-EESITAKQ 148 **********************************************99883333458****998.57****** PP TIGR01350 135 iiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp 207 +iiAtGs+ r+lp+ +de v+++++al++ vp++l+++G+GviG+E++s++++lG++vt++e l++ l NCBI__GCF_003063475.1:WP_108358556.1 149 VIIATGSNARALPG-TPFDEVNVLSNDGALRVGAVPKKLALIGSGVIGLEMGSVWRRLGADVTILEGLPTFLG 220 **************.6667667*************************************************** PP TIGR01350 208 aldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelglek 278 a+d++++k++kk++ k+g+ki + kv e+ + ++ v+ +++ k+e+ +lea+k++v++Gr pn+ +l+ e+ NCBI__GCF_003063475.1:WP_108358556.1 221 AVDEQIAKEAKKAFDKQGLKIELGVKVGEIVNGKKGVTvnYTNAKGEAIVLEADKLIVSIGRVPNTIGLNAEA 293 ***********************************99965666666999************************ PP TIGR01350 279 lgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePe 351 +g+ +dergai+vd +++tnvpg++a+GDv++++mLAh+A++egv +ae+iag++ +++ +++P viyt+Pe NCBI__GCF_003063475.1:WP_108358556.1 294 IGLAVDERGAIVVDGDCKTNVPGVWAVGDVVRGPMLAHKAEEEGVAVAERIAGQHG-HVNFNTIPWVIYTSPE 365 *****************************************************998.9*************** PP TIGR01350 352 vasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalav 424 +a vG te+q+k++g+++k+g fpf ang+a+al++t+G+vk ++d +t+eilG+h+vg+++selise+++a+ NCBI__GCF_003063475.1:WP_108358556.1 366 IAWVGRTEQQLKADGVAYKAGTFPFLANGRARALGDTTGMVKFLADATTDEILGVHMVGPQVSELISEAVVAM 438 ************************************************************************* PP TIGR01350 425 eleltveelaktihpHPtlsEaikeaalaalgkai 459 e+++++e++a+++h+HP+lsEa+keaala+ ++++ NCBI__GCF_003063475.1:WP_108358556.1 439 EFKASAEDIARICHAHPSLSEATKEAALAVDKRTL 473 ****************************9988876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (475 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 15.20 // [ok]
This GapMind analysis is from Sep 24 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