Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_099019200.1 CCS90_RS08975 dihydrolipoyl dehydrogenase
Query= SwissProt::P14218 (478 letters) >NCBI__GCF_002591915.1:WP_099019200.1 Length = 473 Score = 513 bits (1320), Expect = e-150 Identities = 264/475 (55%), Positives = 345/475 (72%), Gaps = 3/475 (0%) Query: 1 MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60 M +K+DVVVIG GP GYVAAIRAAQ+G T C++++ GK+GK +LGGTCLNVGCIPSKAL Sbjct: 1 MMEKYDVVVIGGGPAGYVAAIRAAQMGFNTLCVDRFKGKDGKYSLGGTCLNVGCIPSKAL 60 Query: 61 LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120 LDSS + ++ VHGI +DV M+ARK IVK LTGGIA LFKAN V G Sbjct: 61 LDSSKHFDHMNHSYDVHGISFDNPKMDVATMIARKDKIVKQLTGGIAQLFKANKVKYIGG 120 Query: 121 HGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAV 180 GKLL ++QVE+ +G +QV++ E++I+ASGS P+ IP + ++ I+D+ GAL+ AV Sbjct: 121 SGKLLKDRQVEINNDEG-SQVVQGEHIILASGSVPISIPNVEIDNEYILDNAGALDINAV 179 Query: 181 PKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIR 240 P+KLGVIG GVIGLELGSVW RLG++V V EA+D FL A D+ IAK A + KQGL+I Sbjct: 180 PEKLGVIGGGVIGLELGSVWNRLGSKVKVFEAMDTFLAACDQGIAKMAARTFKKQGLDIH 239 Query: 241 LGARVTASEVKKKQVTVTFTDANGEQ-KETFDKLIVAVGRRPVTTDLLAADSGVTLDERG 299 L V ++ +K +V V ++ NGE+ E FDKL+VAVGR+ T LLA D G+ L ERG Sbjct: 240 LSTFVKSATIKDGKVEVV-SETNGEKTTEIFDKLLVAVGRKAETDGLLADDCGIKLTERG 298 Query: 300 FIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYT 359 I V+D C+TSVP V+AIGD VRG MLAHK SEEG VAERIAG ++++ +P VIYT Sbjct: 299 QIDVNDDCQTSVPNVWAIGDAVRGPMLAHKGSEEGSAVAERIAGQHGHVDFNTVPFVIYT 358 Query: 360 HPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHV 419 PE+AWVGKTE+ LK G++ VG+FP AA+GRA+A N+ TG+VK++ADA+TD +LG H+ Sbjct: 359 EPELAWVGKTEEQLKEAGIDYKVGSFPMAANGRALAMNEPTGMVKILADAETDELLGAHI 418 Query: 420 IGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIAN 474 +AA+L+ + + MEF AEDL ++ +HPTLSEA+ EAA+ V+ AIH AN Sbjct: 419 FSANAADLLSECVVTMEFKGCAEDLSRIIHAHPTLSEAVFEAAMNVDKRAIHKAN 473 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: 629 Number of extensions: 23 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: 478 Length of database: 473 Length adjustment: 33 Effective length of query: 445 Effective length of database: 440 Effective search space: 195800 Effective search space used: 195800 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_099019200.1 CCS90_RS08975 (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.1854001.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-164 533.4 4.7 2.6e-164 533.2 4.7 1.0 1 NCBI__GCF_002591915.1:WP_099019200.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002591915.1:WP_099019200.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 533.2 4.7 2.6e-164 2.6e-164 1 460 [. 4 470 .. 4 471 .. 0.97 Alignments for each domain: == domain 1 score: 533.2 bits; conditional E-value: 2.6e-164 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalve.......keklGGtClnvGCiPtKalLksaevveelke.ake 65 +ydvvviGgGp+GYvaAiraaq+g+++++v+ k +lGGtClnvGCiP+KalL s++ ++++++ + NCBI__GCF_002591915.1:WP_099019200.1 4 KYDVVVIGGGPAGYVAAIRAAQMGFNTLCVDrfkgkdgKYSLGGTCLNVGCIPSKALLDSSKHFDHMNHsYDV 76 59****************************944333333479***************************999* PP TIGR01350 66 lgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiA 138 +gi+ +n k+d++++ +rk+k+vk+l+gG+++L+k nkv+ i G++kll++++ve+++++++++++ ++ii+A NCBI__GCF_002591915.1:WP_099019200.1 77 HGISFDNPKMDVATMIARKDKIVKQLTGGIAQLFKANKVKYIGGSGKLLKDRQVEINNDEGSQVVQGEHIILA 149 ************************************************************************* PP TIGR01350 139 tGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpalda 211 +Gs p+++p +e d+++++++ +al ++ vpe+l ++GgGviG+E++s++++lG+kv v+e++d+ l+a d+ NCBI__GCF_002591915.1:WP_099019200.1 150 SGSVPISIPN-VEIDNEYILDNAGALDINAVPEKLGVIGGGVIGLELGSVWNRLGSKVKVFEAMDTFLAACDQ 221 **********.************************************************************** PP TIGR01350 212 evskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgvel 283 ++k++++++kk+g++i+ ++ v++ + ++ +v+v + + e++t +k+LvavGrk+++++l + g++l NCBI__GCF_002591915.1:WP_099019200.1 222 GIAKMAARTFKKQGLDIHLSTFVKSATIKDGKVEVVSETNgEKTTEIFDKLLVAVGRKAETDGLLADDCGIKL 294 ************************999999999955555547888899************************* PP TIGR01350 284 dergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvG 356 +erg+i v+++++t+vp+++aiGD+++++mLAh+ s+eg +ae+iag++ ++d ++vP viytePe+a vG NCBI__GCF_002591915.1:WP_099019200.1 295 TERGQIDVNDDCQTSVPNVWAIGDAVRGPMLAHKGSEEGSAVAERIAGQHG-HVDFNTVPFVIYTEPELAWVG 366 ************************************************998.9******************** PP TIGR01350 357 lteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalavelelt 429 +teeq+ke+gi++kvg+fp+aang+ala++e +G+vk+++d +t+e+lGahi +a+a++l+se ++ +e+++ NCBI__GCF_002591915.1:WP_099019200.1 367 KTEEQLKEAGIDYKVGSFPMAANGRALAMNEPTGMVKILADAETDELLGAHIFSANAADLLSECVVTMEFKGC 439 ************************************************************************* PP TIGR01350 430 veelaktihpHPtlsEaikeaalaalgkaih 460 +e+l+++ih+HPtlsEa+ eaa ++ ++aih NCBI__GCF_002591915.1:WP_099019200.1 440 AEDLSRIIHAHPTLSEAVFEAAMNVDKRAIH 470 *****************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (473 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 27.16 // [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