Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate GFF1715 PGA1_c17390 dihydrolipoyl dehydrogenase LpdA
Query= BRENDA::P50970 (466 letters) >FitnessBrowser__Phaeo:GFF1715 Length = 464 Score = 541 bits (1393), Expect = e-158 Identities = 268/464 (57%), Positives = 350/464 (75%), Gaps = 3/464 (0%) Query: 2 ADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYH 61 A+ +D+IV+G GPGGYVAAIRAAQL LK +VER H+GGICLNWGCIPTK+LLRS+EV+H Sbjct: 3 AETYDVIVIGAGPGGYVAAIRAAQLGLKTCIVEREHMGGICLNWGCIPTKALLRSSEVFH 62 Query: 62 EMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQ 121 M+ A+ +GL + +DLD ++ RSR VA +L+SG+ L++KNK+ V+ G L + Sbjct: 63 LMERAKDFGLKADNIGYDLDAVVKRSRGVAKQLSSGIGHLMKKNKIAVVMGEATLPAKGK 122 Query: 122 MLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGS 181 + V+T +G ++ L AK+I++ATGARAR+LP + +DG +WTY HAL P MPKKLLVIGS Sbjct: 123 VSVKTEKGTQE-LAAKNIVLATGARARELPGLEADGDLVWTYKHALDPVRMPKKLLVIGS 181 Query: 182 GAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLT 241 GAIGIEFASFY GA+ ++VE ++LP+EDAE+SA+ KAF K+G++I+ ++ ++ L Sbjct: 182 GAIGIEFASFYNTLGADTTVVEVMDRVLPVEDAEISAFAKKAFVKQGMKIMEKAMVKQLD 241 Query: 242 PDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRT 301 VTA I GKV K+ F I A+G+V NVE +GLD LG+K+DR + D + RT Sbjct: 242 RGKGKVTAHIE-VGGKVEKQEFDTVISAVGIVGNVEGLGLDGLGVKVDRTHVVTDEYCRT 300 Query: 302 NVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVG 361 VD ++AIGD+AGAP LAHKASH+GV+ AE IAG H H + ++I GCTY +PQVASVG Sbjct: 301 GVDGLYAIGDIAGAPWLAHKASHEGVMVAELIAG-KHAHAVKPESIAGCTYCQPQVASVG 359 Query: 362 LTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEM 421 TE KA++ GY++K+G FPFI NGKAIA G +G VKT+FDA +G LLGAHMVGAEVTEM Sbjct: 360 YTEAKAKELGYDIKVGRFPFIGNGKAIALGEAEGMVKTIFDAKTGELLGAHMVGAEVTEM 419 Query: 422 IQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465 IQGY V R LETTE ++M T+FPHPTLSE MHESVL A+ R +H Sbjct: 420 IQGYVVGRQLETTEEDLMNTVFPHPTLSEMMHESVLDAFDRVIH 463 Lambda K H 0.319 0.135 0.393 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: 671 Number of extensions: 35 Number of successful extensions: 4 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: 466 Length of database: 464 Length adjustment: 33 Effective length of query: 433 Effective length of database: 431 Effective search space: 186623 Effective search space used: 186623 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate GFF1715 PGA1_c17390 (dihydrolipoyl dehydrogenase LpdA)
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.23860.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-174 564.4 10.8 1e-173 564.2 10.8 1.0 1 lcl|FitnessBrowser__Phaeo:GFF1715 PGA1_c17390 dihydrolipoyl dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF1715 PGA1_c17390 dihydrolipoyl dehydrogenase LpdA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 564.2 10.8 1e-173 1e-173 2 461 .] 6 464 .] 5 464 .] 0.99 Alignments for each domain: == domain 1 score: 564.2 bits; conditional E-value: 1e-173 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldl 77 ydv+viG+GpgGYvaAiraaqlglk+ +ve+e++GG+Cln+GCiPtKalL+s+ev++ ++ ak++g++++n+ +dl lcl|FitnessBrowser__Phaeo:GFF1715 6 YDVIVIGAGPGGYVAAIRAAQLGLKTCIVEREHMGGICLNWGCIPTKALLRSSEVFHLMERAKDFGLKADNIGYDL 81 9*************************************************************************** PP TIGR01350 78 ekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplkleed 153 +++++r++ v k+l++G+ +L+kknk+ v++Gea+l k++v+vk+ek++++l akni++AtG++ relp+ le+d lcl|FitnessBrowser__Phaeo:GFF1715 82 DAVVKRSRGVAKQLSSGIGHLMKKNKIAVVMGEATLPAKGKVSVKTEKGTQELAAKNIVLATGARARELPG-LEAD 156 ***********************************************************************.**** PP TIGR01350 154 ekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkil 229 +++v+t+++al ++p++l+++G+G+iG+Efas++++lG++ tv+e++dr+lp++dae+s ++kk++ k+g+ki+ lcl|FitnessBrowser__Phaeo:GFF1715 157 GDLVWTYKHALDPVRMPKKLLVIGSGAIGIEFASFYNTLGADTTVVEVMDRVLPVEDAEISAFAKKAFVKQGMKIM 232 **************************************************************************** PP TIGR01350 230 tnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiya 304 ++a+v+++ + + +v+++++ + +ve+ e + v+ avG n+e+lgl+ lgv++d+ +++de++rt v+g+ya lcl|FitnessBrowser__Phaeo:GFF1715 233 EKAMVKQLDRGKGKVTAHIEVGgKVEKQEFDTVISAVGIVGNVEGLGLDGLGVKVDR-THVVTDEYCRTGVDGLYA 307 ****************77766668******************************999.77**************** PP TIGR01350 305 iGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaang 380 iGD++g + LAh+As+egv++ae iagk++++++ + + ++y++P+vasvG+te++ake g+++kvg+fpf ng lcl|FitnessBrowser__Phaeo:GFF1715 308 IGDIAGAPWLAHKASHEGVMVAELIAGKHAHAVKPESIAGCTYCQPQVASVGYTEAKAKELGYDIKVGRFPFIGNG 383 **************************************************************************** PP TIGR01350 381 kalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalg 456 ka+al+e++G+vk+i+d ktge+lGah+vgae++e+i+ ++ +le+t+e+l++t++pHPtlsE+++e++l+a++ lcl|FitnessBrowser__Phaeo:GFF1715 384 KAIALGEAEGMVKTIFDAKTGELLGAHMVGAEVTEMIQGYVVGRQLETTEEDLMNTVFPHPTLSEMMHESVLDAFD 459 **************************************************************************** PP TIGR01350 457 kaihv 461 + ih+ lcl|FitnessBrowser__Phaeo:GFF1715 460 RVIHM 464 ***97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (464 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.49 // [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