Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_076582962.1 BB347_RS13020 dihydrolipoyl dehydrogenase
Query= BRENDA::Q04829 (475 letters) >NCBI__GCF_001971705.1:WP_076582962.1 Length = 487 Score = 634 bits (1634), Expect = 0.0 Identities = 323/488 (66%), Positives = 376/488 (77%), Gaps = 14/488 (2%) Query: 1 MVVGDIATGTELLVIGAGPGGYVAAIRAAQNGIDTTLVEKDAYGGTCLNYGCIPSKALIT 60 MVVGD+ T T++LVIGAGP GYVAAIRA Q +D TLVEK+AYGGTCLN+GCIPSKALIT Sbjct: 1 MVVGDVTTATDVLVIGAGPAGYVAAIRAGQLDLDVTLVEKEAYGGTCLNHGCIPSKALIT 60 Query: 61 GANLAHEAGNAEEMGIHADPVVDMSQLRDWKSGVVDQLTGGVEKLCKANGVNLVEGTARF 120 ++AH A AEEMGIHADP +D+S + WK GVVDQLT GVEKLCKAN V+L+EGTA F Sbjct: 61 ATDVAHGAATAEEMGIHADPAIDLSGMVSWKDGVVDQLTSGVEKLCKANQVSLLEGTATF 120 Query: 121 KDENAVRIAHGGEGQGSETIEFEHCIIATGSRVIQIPGFDFGDEPVWSSRDALEADTVPE 180 DE+ RI+H GEGQGSE++EFEH I+ATGSR I IP F F +PV SR AL D+VP+ Sbjct: 121 VDEHTARISHSGEGQGSESLEFEHAIVATGSRPIAIPDFSFDADPVIDSRQALALDSVPD 180 Query: 181 RLVVVGGGYIGMELSTTFAKLGADVTVVEMLDDILPGYESDVARVVRKRAEELGIDMHLG 240 LVVVG GYIGMEL++ +AKLG DVTVVEMLD ILPGY+ D+ R V++RA +LGI+ Sbjct: 181 SLVVVGAGYIGMELASVYAKLGTDVTVVEMLDSILPGYDDDLKRPVKQRANDLGIEFVFE 240 Query: 241 EGASGWREEDDGIMVTTETEDG-------------EENEYRADKVLVAVGRSPVTDTMDI 287 AS W E D+ I V E DG E E +KVLVAVGR PV+DT+D+ Sbjct: 241 HTASEWYEPDEDIRVVAEPVDGAAANGGSAEAIDEERLELDVEKVLVAVGREPVSDTLDL 300 Query: 288 ENAGLEADDRGFLSVDDRRRTDVEHIYAVGDVVEDTPMLAHVASKEGIVAAEHVAGEPVA 347 E AG+E DDRG + D R RT+V+HI+AVGDV + PMLAH S EG AAE +AGEP A Sbjct: 301 EAAGVETDDRGIIQTDTRARTNVDHIFAVGDVAGE-PMLAHKGSMEGQTAAEVIAGEPAA 359 Query: 348 FDSQAVPAAVFTDPEIGTVGMTEADAEEAGFTPVVGQMPFRASGRALTTNHADGFVRVVA 407 D QA+PA VFTDPEI TVG+TE DAEEAG+ PVVGQ PFRASGRALTT ADGFV++VA Sbjct: 360 IDHQAMPAVVFTDPEIATVGLTETDAEEAGYDPVVGQFPFRASGRALTTGDADGFVKIVA 419 Query: 408 DEESGFVLGAQIVGPEASELIAELAFAIEMGATLEDVASTIHTHPTLAEAVMEAAENALG 467 +E G+VLGA IVGPEASELIAEL AIE+GATLEDVAST+H HPTL+E+VMEAAENALG Sbjct: 420 EESDGYVLGASIVGPEASELIAELCLAIELGATLEDVASTVHAHPTLSESVMEAAENALG 479 Query: 468 QAIHTLNR 475 AIHTLNR Sbjct: 480 HAIHTLNR 487 Lambda K H 0.315 0.134 0.381 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: 881 Number of extensions: 45 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: 475 Length of database: 487 Length adjustment: 34 Effective length of query: 441 Effective length of database: 453 Effective search space: 199773 Effective search space used: 199773 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: 51 (24.3 bits)
Align candidate WP_076582962.1 BB347_RS13020 (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.2899784.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-162 527.0 1.4 2.7e-162 526.6 1.4 1.1 1 NCBI__GCF_001971705.1:WP_076582962.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001971705.1:WP_076582962.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 526.6 1.4 2.7e-162 2.7e-162 2 460 .. 10 483 .. 9 484 .. 0.95 Alignments for each domain: == domain 1 score: 526.6 bits; conditional E-value: 2.7e-162 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 +dv+viG+Gp+GYvaAira+ql l v+lveke +GGtCln GCiP+Kal+++++v++ + +a+e+gi++ + + NCBI__GCF_001971705.1:WP_076582962.1 10 TDVLVIGAGPAGYVAAIRAGQLDLDVTLVEKEAYGGTCLNHGCIPSKALITATDVAHGAATAEEMGIHA-DPA 81 79*****************************************************************65.799 PP TIGR01350 75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke...kkleakniiiAtGsepr 144 +dl+ ++ +k+ vv++l++Gv+ L+k n+v+ ++G+a+++d+++ +++++ + ++le++++i+AtGs+p+ NCBI__GCF_001971705.1:WP_076582962.1 82 IDLSGMVSWKDGVVDQLTSGVEKLCKANQVSLLEGTATFVDEHTARISHSGEGqgsESLEFEHAIVATGSRPI 154 ***********************************************9987556889**************** PP TIGR01350 145 elplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvl 217 ++p +++d + vi+s++al+l++vp+slv+vG+G+iG+E+as++aklG++vtv+e+ld ilp d ++ + + NCBI__GCF_001971705.1:WP_076582962.1 155 AIPD-FSFDADPVIDSRQALALDSVPDSLVVVGAGYIGMELASVYAKLGTDVTVVEMLDSILPGYDDDLKRPV 226 ****.9999999************************************************************* PP TIGR01350 218 kkklkkkgvkiltnakvtevekeedevv...............veakkkevetleaekvLvavGrkpnleelg 275 k++ ++ g++++++++ +e + +++++ +ea ++e +l++ekvLvavGr+p + l+ NCBI__GCF_001971705.1:WP_076582962.1 227 KQRANDLGIEFVFEHTASEWYEPDEDIRvvaepvdgaaanggsAEAIDEERLELDVEKVLVAVGREPVSDTLD 299 *****************987777776665567777765555544445556678999***************** PP TIGR01350 276 leklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviyt 348 le+ gve+d+rg+i++d + rtnv++i+a+GDv+g++mLAh+ s eg aae iag+ + +id++a+P+v++t NCBI__GCF_001971705.1:WP_076582962.1 300 LEAAGVETDDRGIIQTDTRARTNVDHIFAVGDVAGEPMLAHKGSMEGQTAAEVIAGEPA-AIDHQAMPAVVFT 371 ********************************************************776.9************ PP TIGR01350 349 ePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaselisela 421 +Pe+a+vGlte++a e+g++ +vg+fpf+a+g+al+++++dGfvk+++++++g +lGa+ivg+easeli+el NCBI__GCF_001971705.1:WP_076582962.1 372 DPEIATVGLTETDAEEAGYDPVVGQFPFRASGRALTTGDADGFVKIVAEESDGYVLGASIVGPEASELIAELC 444 ************************************************************************* PP TIGR01350 422 laveleltveelaktihpHPtlsEaikeaalaalgkaih 460 la+el++t+e++a+t+h+HPtlsE ++eaa++alg+aih NCBI__GCF_001971705.1:WP_076582962.1 445 LAIELGATLEDVASTVHAHPTLSESVMEAAENALGHAIH 483 **************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (487 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: 15.53 // [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