Align dihydrolipoamide dehydrogenase Dld1; EC 1.8.1.4 (characterized)
to candidate CA265_RS24150 CA265_RS24150 dihydrolipoyl dehydrogenase
Query= CharProtDB::CH_124461 (511 letters) >FitnessBrowser__Pedo557:CA265_RS24150 Length = 468 Score = 480 bits (1235), Expect = e-140 Identities = 244/468 (52%), Positives = 329/468 (70%), Gaps = 4/468 (0%) Query: 45 EYDLCVIGGGPGGYVAAIRGAQLGLKTICVEKRGTLGGTCLNVGCIPSKALLNNSHIYHT 104 +YD+ VIG GPGGYV AIR AQLGLKT VEK T GGTCLNVGCIPSKALL++S +H Sbjct: 2 QYDVVVIGSGPGGYVGAIRCAQLGLKTAVVEKYKTFGGTCLNVGCIPSKALLDSSEHFHN 61 Query: 105 VKHDTKRRGIDVSGVSVNLSQMMKAKDDSVKSLTSGIEYLFKKNKVEYAKGTGSFIDPQT 164 H GI++ + V++ QM+ KDD V T+GI YLFKKNK++ +G GSF+D T Sbjct: 62 AAHTFTTHGINLKDLKVDMKQMIARKDDVVAQNTAGITYLFKKNKIDSFEGVGSFVDKNT 121 Query: 165 LSVKGIDGAADQTIKAKNFIIATGSEVKPFPGVTIDEKKIVSSTGALSLSEVPKKMTVLG 224 + V DG+ + T+ AKN IIATGS+ P + ID+K+I++ST AL++ EVPK M V+G Sbjct: 122 ILVTKADGSTE-TLSAKNVIIATGSKPTALPFLPIDKKRIITSTEALNIKEVPKTMVVIG 180 Query: 225 GGIIGLEMGSVWSRLGAEVTVVEFLPAVGGPMDADISKALSRIISKQ-GIKFKTSTKLLS 283 GG+IGLE+GSV++RLG +V+VVEFLP++ G MDA + K L R++ K G++F K+ Sbjct: 181 GGVIGLELGSVYARLGTKVSVVEFLPSIIGTMDAGLGKELQRVLKKTLGMEFYMGHKVTG 240 Query: 284 AKVNGDSVEVEIENMKNNKRETYQTDVLLVAIGRVPYTEGLGLDKLGISMDKSNRVIMDS 343 A G +V V + K + + D +VA+GR Y+EGLGLDK+GI++++ + I + Sbjct: 241 ATTKGKTVTVTADTPKGESI-SLEADYCIVAVGRTAYSEGLGLDKIGITVEERGKKIPVN 299 Query: 344 EY-RTNIPHIRVIGDATLGPMLAHKAEDEGIAAVEYIAKGQGHVNYNCIPAVMYTHPEVA 402 E+ T++ + IGD G MLAHKAEDEG E IA + H+NYN IP V+YT PEVA Sbjct: 300 EHLETSVKGVYAIGDVITGAMLAHKAEDEGTYVAETIAGQKPHINYNLIPGVVYTWPEVA 359 Query: 403 WVGITEQKAKESGIKYRIGTFPFSANSRAKTNMDADGLVKVIVDAETDRLLGVHMIGPMA 462 VG+TE++ KE G+KY+ G+FPF A+ RAK +MD DG +KV+ DA TD +LGVHMIGP A Sbjct: 360 SVGLTEEQLKEKGVKYKAGSFPFKASGRAKASMDTDGFIKVLADAATDEVLGVHMIGPRA 419 Query: 463 GELIGEATLALEYGASAEDVARVCHAHPTLSEATKEAMMAAWCGKSIH 510 ++I EA +A+E+ ASAED+AR CHAHPT +EA KEA +AA ++IH Sbjct: 420 ADMIAEAVIAMEFRASAEDIARTCHAHPTYTEALKEAALAATDNRAIH 467 Lambda K H 0.316 0.134 0.383 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: 616 Number of extensions: 29 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: 511 Length of database: 468 Length adjustment: 34 Effective length of query: 477 Effective length of database: 434 Effective search space: 207018 Effective search space used: 207018 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: 52 (24.6 bits)
Align candidate CA265_RS24150 CA265_RS24150 (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.22253.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-176 573.6 12.3 1.7e-176 573.4 12.3 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS24150 CA265_RS24150 dihydrolipoyl dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS24150 CA265_RS24150 dihydrolipoyl dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 573.4 12.3 1.7e-176 1.7e-176 1 460 [. 2 467 .. 2 468 .] 0.96 Alignments for each domain: == domain 1 score: 573.4 bits; conditional E-value: 1.7e-176 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akel 66 +ydvvviG+GpgGYv Air+aqlglk+a+vek +++GGtClnvGCiP+KalL s+e ++++ + + ++ lcl|FitnessBrowser__Pedo557:CA265_RS24150 2 QYDVVVIGSGPGGYVGAIRCAQLGLKTAVVEKyKTFGGTCLNVGCIPSKALLDSSEHFHNAAHtFTTH 69 69******************************9*********************************** PP TIGR01350 67 gievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleak 133 gi+++++k+d++++ +rk+ vv + ++G+++L+kknk+++++G ++++dk+++ v+k +++ ++l+ak lcl|FitnessBrowser__Pedo557:CA265_RS24150 70 GINLKDLKVDMKQMIARKDDVVAQNTAGITYLFKKNKIDSFEGVGSFVDKNTILVTKADGStETLSAK 137 ********************************************************9998779***** PP TIGR01350 134 niiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtviel 201 n+iiAtGs+p++lp+ l d+k++its+eal++kevp+++v++GgGviG+E++s++a+lG+kv+v+e+ lcl|FitnessBrowser__Pedo557:CA265_RS24150 138 NVIIATGSKPTALPF-LPIDKKRIITSTEALNIKEVPKTMVVIGGGVIGLELGSVYARLGTKVSVVEF 204 ***************.9999999********************************************* PP TIGR01350 202 ldrilpaldaevskvlkkklkkk.gvkiltnakvtevekeedevvveakkk..evetleaekvLvavG 266 l+ i+ ++da + k+l++ lkk+ g+++++++kvt +++ ++v+v+a+ e +lea++ +vavG lcl|FitnessBrowser__Pedo557:CA265_RS24150 205 LPSIIGTMDAGLGKELQRVLKKTlGMEFYMGHKVTGATTKGKTVTVTADTPkgESISLEADYCIVAVG 272 ********************98747**********99999999985554432488899********** PP TIGR01350 267 rkpnleelgleklgvelderg.aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagke 333 r++ e+lgl+k+g++++erg +i+v+e+l+t+v+g+yaiGDvi ++mLAh+A++eg+++ae+iag++ lcl|FitnessBrowser__Pedo557:CA265_RS24150 273 RTAYSEGLGLDKIGITVEERGkKIPVNEHLETSVKGVYAIGDVITGAMLAHKAEDEGTYVAETIAGQK 340 *******************9746*******************************************99 PP TIGR01350 334 kseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktg 401 + +i+y+++P v+yt PevasvGlteeq+ke+g+++k+g+fpf+a+g+a a+ +tdGf+kv++d t+ lcl|FitnessBrowser__Pedo557:CA265_RS24150 341 P-HINYNLIPGVVYTWPEVASVGLTEEQLKEKGVKYKAGSFPFKASGRAKASMDTDGFIKVLADAATD 407 8.9***************************************************************** PP TIGR01350 402 eilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgk.aih 460 e+lG+h++g++a+++i+e+++a+e+++++e++a+t+h+HPt++Ea+keaalaa+++ aih lcl|FitnessBrowser__Pedo557:CA265_RS24150 408 EVLGVHMIGPRAADMIAEAVIAMEFRASAEDIARTCHAHPTYTEALKEAALAATDNrAIH 467 **************************************************9998651555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (468 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: 8.72 // [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