Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Synpcc7942_1198 Synpcc7942_1198 dihydrolipoamide dehydrogenase
Query= BRENDA::A0A0K9R8G5 (565 letters) >FitnessBrowser__SynE:Synpcc7942_1198 Length = 479 Score = 556 bits (1434), Expect = e-163 Identities = 284/474 (59%), Positives = 358/474 (75%), Gaps = 9/474 (1%) Query: 81 FDYDLLIIGAGVGGHGAALHAVEKGLKTAIIEGDVMGGTCVNRGCVPSKALLAVSGRMRE 140 FDYD+++IGAG GG AA HA EKGLKTAI+E +GGTCVNRGCVPSKALLA SGR+RE Sbjct: 5 FDYDVIVIGAGYGGFDAAKHACEKGLKTAIVEARDLGGTCVNRGCVPSKALLAASGRVRE 64 Query: 141 LQNEQHLKSFGIQVGAANYDRQGVADHASNLASKIRGNLTNSLKALGVDILTGFGTILGP 200 + + HL++FGIQV ++DRQ +ADHA+NL +R NL N+LK LG +IL G G + G Sbjct: 65 ITDTDHLQNFGIQVQGVSFDRQAIADHAANLVDTVRTNLGNTLKRLGAEILMGRGRLAGS 124 Query: 201 QKVQF----GKDNIVTAKDIIIATGSVPFVPRGIEVDGKTVITSDHALKLESVPDWIAIV 256 Q+V G + +A+D+I+ATGS PFVP GIE+DGKTV TSD ALKLE++P WIAI+ Sbjct: 125 QRVTVTAADGTEKTYSARDVILATGSDPFVPPGIEIDGKTVFTSDDALKLETLPQWIAII 184 Query: 257 GSGYIGLEFSDVYTALGSEVTFIEALDQLMPGFDPEVSKLAQRILINPRKIDYHTGVFAT 316 GSGYIGLEFSDVYTALG EVT IEALD+L+P FDP+V+K+AQR L++ R I+ TGV A Sbjct: 185 GSGYIGLEFSDVYTALGCEVTMIEALDRLLPTFDPDVAKVAQRSLLDGRDIETRTGVLAR 244 Query: 317 KITPAKDGKPVTIELTDAKTKEHKDTLEVDAALIATGRAPYTQGLGLESINV-VTQRGFV 375 KITP G PV IEL D +TKE + LEVDA L+ATGR P T+ LGLE++ V V +RGF+ Sbjct: 245 KITP---GSPVVIELADFETKELVEVLEVDACLVATGRIPSTKNLGLETVAVEVDRRGFI 301 Query: 376 PVDDRMRVIDANGKLVPNLYCIGDANGKMMLAHAASAQGISVVEQVTGRDHVLNHLSIPA 435 PVDD MRV+ + K VP+L+ +GDA GK+MLAHAA+AQG+ +E +TG +++ SIPA Sbjct: 302 PVDDGMRVL-RDSKPVPHLFAVGDATGKLMLAHAAAAQGVVAIENITGHPRSVDYRSIPA 360 Query: 436 ACFTHPEISMVGLTEPQAREKAEKEGFPVSVAKTSFKANSKALAENEAEGIAKLIYRPDN 495 A FTHPEIS VGL+E A+ +EGF V ++ FKANSKALAE +A+G AK+++R D Sbjct: 361 ATFTHPEISSVGLSEADAKALGGQEGFEVGSVRSYFKANSKALAEADADGFAKVLFRKDT 420 Query: 496 GEILGVHIFGLHAADLIHEASNAIAMGTPIQDLKLAVHAHPTLSEVLDELYKAA 549 GE+LG HIFGLHAADLI E +NAIA +++L VH HPTLSEV++ YK A Sbjct: 421 GEVLGAHIFGLHAADLIQEVANAIARRQSVKELAFEVHTHPTLSEVIESAYKQA 474 Lambda K H 0.316 0.133 0.377 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: 709 Number of extensions: 28 Number of successful extensions: 6 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: 565 Length of database: 479 Length adjustment: 35 Effective length of query: 530 Effective length of database: 444 Effective search space: 235320 Effective search space used: 235320 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 Synpcc7942_1198 Synpcc7942_1198 (dihydrolipoamide 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.17123.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-135 435.8 0.1 1e-134 435.6 0.1 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1198 Synpcc7942_1198 dihydrolipoamide Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1198 Synpcc7942_1198 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.6 0.1 1e-134 1e-134 2 456 .. 7 476 .. 6 479 .] 0.92 Alignments for each domain: == domain 1 score: 435.6 bits; conditional E-value: 1e-134 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke...akelg 67 ydv+viG+G gG+ aA +a ++glk+a+ve ++lGGtC+n+GC+P+KalL+++ v+e+++ ++++g lcl|FitnessBrowser__SynE:Synpcc7942_1198 7 YDVIVIGAGYGGFDAAKHACEKGLKTAIVEARDLGGTCVNRGCVPSKALLAASGRVREITDtdhLQNFG 75 9****************************************************99998864334899** PP TIGR01350 68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakni 135 i+v++v++d +++ ++ + v+++++ + lk+ + e ++G+++l ++++v+v++ +++ k+++a ++ lcl|FitnessBrowser__SynE:Synpcc7942_1198 76 IQVQGVSFDRQAIADHAANLVDTVRTNLGNTLKRLGAEILMGRGRLAGSQRVTVTAADGTeKTYSARDV 144 *******************************************************999877999***** PP TIGR01350 136 iiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldr 204 i+AtGs+p +p+ +e d+k+v ts++al+l+++p+ ++i+G+G+iG+Ef+ +++ lG++vt+ie+ldr lcl|FitnessBrowser__SynE:Synpcc7942_1198 145 ILATGSDPFVPPG-IEIDGKTVFTSDDALKLETLPQWIAIIGSGYIGLEFSDVYTALGCEVTMIEALDR 212 *************.******************************************************* PP TIGR01350 205 ilpaldaevskvlkkklkk.kgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkp 269 +lp++d +v+kv++++l + + ++ t+ +++ + v + + k ve+le+++ Lva Gr p lcl|FitnessBrowser__SynE:Synpcc7942_1198 213 LLPTFDPDVAKVAQRSLLDgRDIETRTGVLARKITPGSPVVIelADFETKeLVEVLEVDACLVATGRIP 281 **************9986514466666666667777777666774444443589*************** PP TIGR01350 270 nleelgleklgveldergaikvdeelrt.....nvpgiyaiGDvigklmLAhvAskegvvaaekiagke 333 ++++lgle++ ve+d+rg+i+vd+ +r+ vp+++a+GD++gklmLAh A ++gvva+e+i+g+ lcl|FitnessBrowser__SynE:Synpcc7942_1198 282 STKNLGLETVAVEVDRRGFIPVDDGMRVlrdskPVPHLFAVGDATGKLMLAHAAAAQGVVAIENITGHP 350 **************************98433334899******************************66 PP TIGR01350 334 kseidykavPsviytePevasvGlteeqak....eegievkvgkfpfaangkalaleetdGfvkvivdk 398 + ++dy+ +P++++t+Pe++svGl+e++ak +eg ev +++ f+an+kala ++dGf+kv++ k lcl|FitnessBrowser__SynE:Synpcc7942_1198 351 R-SVDYRSIPAATFTHPEISSVGLSEADAKalggQEGFEVGSVRSYFKANSKALAEADADGFAKVLFRK 418 6.9***************************33333568999999************************* PP TIGR01350 399 ktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalg 456 +tge+lGahi g +a++li+e+a a++ +++v+ela +h+HPtlsE+i+ a ++a + lcl|FitnessBrowser__SynE:Synpcc7942_1198 419 DTGEVLGAHIFGLHAADLIQEVANAIARRQSVKELAFEVHTHPTLSEVIESAYKQAAT 476 ****************************************************999865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (479 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: 9.55 // [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