BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 019880
(334 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1AUA|A Chain A, Phosphatidylinositol Transfer Protein Sec14p From
Saccharomyces Cerevisiae
Length = 296
Score = 86.3 bits (212), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 69/253 (27%), Positives = 122/253 (48%), Gaps = 40/253 (15%)
Query: 2 AHQEEIKQFQTLMED------LDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKML 55
A ++ + + + L+ED LDDS TL+RFL+AR ++V A +M
Sbjct: 29 AQEKALAELRKLLEDAGFIERLDDS---------------TLLRFLRARKFDVQLAKEMF 73
Query: 56 VDCLRWRIENDIDNIL------AKPIL----PAELYRAVRDSQLVGVSGYSKEGLPVIAV 105
+C +WR + D IL KP++ P ++ +D + V Y +E V
Sbjct: 74 ENCEKWRKDYGTDTILQDFHYDEKPLIAKFYPQYYHKTDKDGRPV----YFEELGAVNLH 129
Query: 106 GVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLS-AL 164
+ T ++ + V + + +YR LP+ S+ G + TS ++D+ G+ +S A
Sbjct: 130 EMNKVTSEERMLKNLVWEYESVVQYR----LPACSRAAGHLVETSCTIMDLKGISISSAY 185
Query: 165 NQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGR 224
+ + + + I YPE+ +YI+NAP+ FS +++ KP L T K+ +L + +
Sbjct: 186 SVMSYVREASYISQNYYPERMGKFYIINAPFGFSTAFRLFKPFLDPVTVSKIFILGSSYQ 245
Query: 225 DELLKIMDYASLP 237
ELLK + +LP
Sbjct: 246 KELLKQIPAENLP 258
>pdb|3Q8G|A Chain A, Resurrection Of A Functional Phosphatidylinositol Transfer
Protein From A Pseudo-Sec14 Scaffold By Directed
Evolution
Length = 320
Score = 85.9 bits (211), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 69/254 (27%), Positives = 127/254 (50%), Gaps = 38/254 (14%)
Query: 3 HQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVDCLRWR 62
+E + QF++++ L+ + KE + TL+RFL+AR ++++ + +M V+ RWR
Sbjct: 39 QEEALLQFRSIL--LEKNYKERLDD-------STLLRFLRARKFDINASVEMFVETERWR 89
Query: 63 IENDIDNILAKPILPAELYRAVRDSQLVGVSGY--------SKEGLPVIAV---GVGLS- 110
E + I+ E + D + + ++ K+G P+ G+ L
Sbjct: 90 EEYGANTIIED----YENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFAELGGINLKK 145
Query: 111 ----THDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQ 166
T +K + V+ + YR +P+ S++ G I TS VLD+ G+ LS N
Sbjct: 146 MYKITTEKQMLRNLVKEYELFATYR----VPACSRRAGYLIETSCTVLDLKGISLS--NA 199
Query: 167 IKLMTVITTIDDLN---YPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNG 223
+++ I + D++ YPE+ +YI+++P+ FS +K+VKP L T K+ +L +
Sbjct: 200 YHVLSYIKDVADISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSY 259
Query: 224 RDELLKIMDYASLP 237
+ ELLK + +LP
Sbjct: 260 KKELLKQIPIENLP 273
>pdb|3B74|A Chain A, Crystal Structure Of Yeast Sec14 Homolog Sfh1 In Complex
With Phosphatidylethanolamine
pdb|3B7N|A Chain A, Crystal Structure Of Yeast Sec14 Homolog Sfh1 In Complex
With Phosphatidylinositol
pdb|3B7Q|A Chain A, Crystal Structure Of Yeast Sec14 Homolog Sfh1 In Complex
With Phosphatidylcholine
pdb|3B7Q|B Chain B, Crystal Structure Of Yeast Sec14 Homolog Sfh1 In Complex
With Phosphatidylcholine
pdb|3B7Z|A Chain A, Crystal Structure Of Yeast Sec14 Homolog Sfh1 In Complex
With Phosphatidylcholine Or Phosphatidylinositol
Length = 320
Score = 84.7 bits (208), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 69/254 (27%), Positives = 127/254 (50%), Gaps = 38/254 (14%)
Query: 3 HQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVDCLRWR 62
+E + QF++++ L+ + KE + TL+RFL+AR ++++ + +M V+ RWR
Sbjct: 39 QEEALLQFRSIL--LEKNYKERLDD-------STLLRFLRARKFDINASVEMFVETERWR 89
Query: 63 IENDIDNILAKPILPAELYRAVRDSQLVGVSGY--------SKEGLPVIAV---GVGLS- 110
E + I+ E + D + + ++ K+G P+ G+ L
Sbjct: 90 EEYGANTIIED----YENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFEELGGINLKK 145
Query: 111 ----THDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQ 166
T +K + V+ + YR +P+ S++ G I TS VLD+ G+ LS N
Sbjct: 146 MYKITTEKQMLRNLVKEYELFATYR----VPACSRRAGYLIETSCTVLDLKGISLS--NA 199
Query: 167 IKLMTVITTIDDLN---YPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNG 223
+++ I + D++ YPE+ +YI+++P+ FS +K+VKP L T K+ +L +
Sbjct: 200 YHVLSYIKDVADISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSY 259
Query: 224 RDELLKIMDYASLP 237
+ ELLK + +LP
Sbjct: 260 KKELLKQIPIENLP 273
>pdb|1OLM|E Chain E, Supernatant Protein Factor In Complex With
Rrr-Alpha-Tocopherylquinone: A Link Between Oxidized
Vitamin E And Cholesterol Biosynthesis
Length = 403
Score = 76.3 bits (186), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 72/270 (26%), Positives = 125/270 (46%), Gaps = 19/270 (7%)
Query: 32 NPTDT-LVRFLKARDWNVSKAHKMLVDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
NP D L+R+L+AR +++ K+ ML + +R + DIDNI++ P E+ +
Sbjct: 32 NPDDYFLLRWLRARSFDLQKSEAMLRKHVEFRKQKDIDNIIS--WQPPEVIQQYLSG--- 86
Query: 91 GVSGYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSAS---KKHGRYI 147
G+ GY +G PV +G + Q ++ ++L + K GR +
Sbjct: 87 GMCGYDLDGCPVWYDIIGPLDAKGLLFSASKQDLLRTKMRECELLLQECAHQTTKLGRKV 146
Query: 148 GTSLKVLDMTGLKLSALNQ--IKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVK 205
T + D GL L L + ++ + + NYPE + ++V AP +F + ++K
Sbjct: 147 ETITIIYDCEGLGLKHLWKPAVEAYGEFLCMFEENYPETLKRLFVVKAPKLFPVAYNLIK 206
Query: 206 PLLQERTRRKMQVLQGNGRDELLKIMDYASLPHFCRKEGSGSSRHIGNGTTENCFSLDHA 265
P L E TR+K+ VL N ++ LLK + +P + G + GN ++ +
Sbjct: 207 PFLSEDTRKKIMVLGANWKEVLLKHISPDQVP---VEYGGTMTDPDGNPKCKSKINYGGD 263
Query: 266 FHQRLY--NYIKQQAVLTESVVPIRQGSFH 293
++ Y + +KQQ E V I +GS H
Sbjct: 264 IPRKYYVRDQVKQQ---YEHSVQISRGSSH 290
>pdb|1OLM|A Chain A, Supernatant Protein Factor In Complex With
Rrr-Alpha-Tocopherylquinone: A Link Between Oxidized
Vitamin E And Cholesterol Biosynthesis
pdb|1OLM|C Chain C, Supernatant Protein Factor In Complex With
Rrr-Alpha-Tocopherylquinone: A Link Between Oxidized
Vitamin E And Cholesterol Biosynthesis
Length = 403
Score = 76.3 bits (186), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 72/270 (26%), Positives = 125/270 (46%), Gaps = 19/270 (7%)
Query: 32 NPTDT-LVRFLKARDWNVSKAHKMLVDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
NP D L+R+L+AR +++ K+ ML + +R + DIDNI++ P E+ +
Sbjct: 32 NPDDYFLLRWLRARSFDLQKSEAMLRKHVEFRKQKDIDNIIS--WQPPEVIQQYLSG--- 86
Query: 91 GVSGYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSAS---KKHGRYI 147
G+ GY +G PV +G + Q ++ ++L + K GR +
Sbjct: 87 GMCGYDLDGCPVWYDIIGPLDAKGLLFSASKQDLLRTKMRECELLLQECAHQTTKLGRKV 146
Query: 148 GTSLKVLDMTGLKLSALNQ--IKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVK 205
T + D GL L L + ++ + + NYPE + ++V AP +F + ++K
Sbjct: 147 ETITIIYDCEGLGLKHLWKPAVEAYGEFLCMFEENYPETLKRLFVVKAPKLFPVAYNLIK 206
Query: 206 PLLQERTRRKMQVLQGNGRDELLKIMDYASLPHFCRKEGSGSSRHIGNGTTENCFSLDHA 265
P L E TR+K+ VL N ++ LLK + +P + G + GN ++ +
Sbjct: 207 PFLSEDTRKKIMVLGANWKEVLLKHISPDQVP---VEYGGTMTDPDGNPKCKSKINYGGD 263
Query: 266 FHQRLY--NYIKQQAVLTESVVPIRQGSFH 293
++ Y + +KQQ E V I +GS H
Sbjct: 264 IPRKYYVRDQVKQQ---YEHSVQISRGSSH 290
>pdb|1O6U|A Chain A, The Crystal Structure Of Human Supernatant Protein Factor
pdb|1O6U|C Chain C, The Crystal Structure Of Human Supernatant Protein Factor
pdb|1O6U|E Chain E, The Crystal Structure Of Human Supernatant Protein Factor
Length = 403
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 71/270 (26%), Positives = 122/270 (45%), Gaps = 19/270 (7%)
Query: 32 NPTDT-LVRFLKARDWNVSKAHKMLVDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
NP D L+R+L+AR +++ K+ L + +R + DIDNI++ P E+ +
Sbjct: 32 NPDDYFLLRWLRARSFDLQKSEAXLRKHVEFRKQKDIDNIIS--WQPPEVIQQYLSG--- 86
Query: 91 GVSGYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSAS---KKHGRYI 147
G GY +G PV +G + Q ++ ++L + K GR +
Sbjct: 87 GXCGYDLDGCPVWYDIIGPLDAKGLLFSASKQDLLRTKXRECELLLQECAHQTTKLGRKV 146
Query: 148 GTSLKVLDMTGLKLSALNQ--IKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVK 205
T + D GL L L + ++ + NYPE + ++V AP +F + ++K
Sbjct: 147 ETITIIYDCEGLGLKHLWKPAVEAYGEFLCXFEENYPETLKRLFVVKAPKLFPVAYNLIK 206
Query: 206 PLLQERTRRKMQVLQGNGRDELLKIMDYASLPHFCRKEGSGSSRHIGNGTTENCFSLDHA 265
P L E TR+K+ VL N ++ LLK + +P + G + GN ++ +
Sbjct: 207 PFLSEDTRKKIXVLGANWKEVLLKHISPDQVP---VEYGGTXTDPDGNPKCKSKINYGGD 263
Query: 266 FHQRLY--NYIKQQAVLTESVVPIRQGSFH 293
++ Y + +KQQ E V I +GS H
Sbjct: 264 IPRKYYVRDQVKQQ---YEHSVQISRGSSH 290
>pdb|1OIP|A Chain A, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-tocopherol Transfer Protein
pdb|1OIZ|A Chain A, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-Tocopherol Transfer Protein
pdb|1OIZ|B Chain B, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-Tocopherol Transfer Protein
Length = 278
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 47/206 (22%), Positives = 95/206 (46%), Gaps = 28/206 (13%)
Query: 34 TDT-LVRFLKARDWNVSKAHKMLVDCLRWRIENDIDNILAKPILPAELY-RAVRDSQLVG 91
TD+ L+RFL+ARD+++ A ++L + +WR E P + A+L+ R++ G
Sbjct: 48 TDSFLLRFLRARDFDLDLAWRLLKNYYKWRAEC--------PEISADLHPRSIIGLLKAG 99
Query: 92 VSGYSKEGLPVIA--VGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGT 149
G + P + + ++ D Y + + + +V ++++G
Sbjct: 100 YHGVLRSRDPTGSKVLIYRIAHWDPKVFTAYDVFRVSLIT-SELIVQEVETQRNGIK--- 155
Query: 150 SLKVLDMTGLKLSALNQI------KLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKV 203
+ D+ G + S QI K+ V+T ++P K +++N P IF A + +
Sbjct: 156 --AIFDLEGWQFSHAFQITPSVAKKIAAVLTD----SFPLKVRGIHLINEPVIFHAVFSM 209
Query: 204 VKPLLQERTRRKMQVLQGNGRDELLK 229
+KP L E+ + ++ + N + LL+
Sbjct: 210 IKPFLTEKIKERIHMHGNNYKQSLLQ 235
>pdb|1R5L|A Chain A, Crystal Structure Of Human Alpha-tocopherol Transfer
Protein Bound To Its Ligand
Length = 262
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 47/206 (22%), Positives = 93/206 (45%), Gaps = 28/206 (13%)
Query: 34 TDT-LVRFLKARDWNVSKAHKMLVDCLRWRIENDIDNILAKPILPAELY-RAVRDSQLVG 91
TD+ L+RFL+ARD+++ A ++L + +WR E P + A+L+ R++ G
Sbjct: 32 TDSFLLRFLRARDFDLDLAWRLLKNYYKWRAEC--------PEISADLHPRSIIGLLKAG 83
Query: 92 VSGYSKEGLPVIA--VGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGT 149
G + P + + ++ D Y + + + +V ++++G
Sbjct: 84 YHGVLRSRDPTGSKVLIYRIAHWDPKVFTAYDVFRVSLIT-SELIVQEVETQRNGIK--- 139
Query: 150 SLKVLDMTGLKLSALNQI------KLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKV 203
+ D+ G + S QI K+ V+T ++P K +++N P IF A +
Sbjct: 140 --AIFDLEGWQFSHAFQITPSVAKKIAAVLTD----SFPLKVRGIHLINEPVIFHAVFSX 193
Query: 204 VKPLLQERTRRKMQVLQGNGRDELLK 229
+KP L E+ + ++ N + LL+
Sbjct: 194 IKPFLTEKIKERIHXHGNNYKQSLLQ 219
>pdb|3HY5|A Chain A, Crystal Structure Of Cralbp
Length = 316
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 36/178 (20%), Positives = 85/178 (47%), Gaps = 15/178 (8%)
Query: 37 LVRFLKARDWNVSKAHKMLVDCLRWRIEND--IDNILAKPILPAELYRAVRDSQLVGV-S 93
+RF++AR +NV +A+++L + +R++ D+ L E R ++ GV S
Sbjct: 95 FLRFIRARKFNVGRAYELLRGYVNFRLQYPELFDS------LSPEAVRCTIEAGYPGVLS 148
Query: 94 GYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKV 153
K G V+ + + + + +Q++ + E +++ ++ +G I + K
Sbjct: 149 SRDKYGRVVMLFNIENWQSQEITFDEILQAYCFILE---KLLENEETQINGFCIIENFKG 205
Query: 154 LDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQER 211
M + ++L L ++ + D ++P + + + ++ P+ F+ + VVKP L+ +
Sbjct: 206 FTMQ--QAASLRTSDLRKMVDMLQD-SFPARFKAIHFIHQPWYFTTTYNVVKPFLKSK 260
>pdb|3HX3|A Chain A, Crystal Structure Of Cralbp Mutant R234w
Length = 316
Score = 34.7 bits (78), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 36/178 (20%), Positives = 82/178 (46%), Gaps = 15/178 (8%)
Query: 37 LVRFLKARDWNVSKAHKMLVDCLRWRIEND--IDNILAKPILPAELYRAVRDSQLVGV-S 93
+RF++AR +NV +A+++L + +R++ D+ L E R ++ GV S
Sbjct: 95 FLRFIRARKFNVGRAYELLRGYVNFRLQYPELFDS------LSPEAVRCTIEAGYPGVLS 148
Query: 94 GYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKV 153
K G V + + + + +Q++ + E +++ ++ +G I + K
Sbjct: 149 SRDKYGRVVXLFNIENWQSQEITFDEILQAYCFILE---KLLENEETQINGFCIIENFK- 204
Query: 154 LDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQER 211
T + ++L L + + D ++P + + ++ P+ F+ + VVKP L+ +
Sbjct: 205 -GFTXQQAASLRTSDLRKXVDXLQD-SFPAWFKAIHFIHQPWYFTTTYNVVKPFLKSK 260
>pdb|3KMU|A Chain A, Crystal Structure Of The IlkALPHA-Parvin Core Complex
(Apo)
Length = 271
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 6 EIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVDCLRWRI 63
+ KQ L + ++ E +K QGN D +V+ LK RDW+ K+ +C R RI
Sbjct: 8 DFKQLNFLTKLNENHSGELWKGRWQGN--DIVVKVLKVRDWSTRKSRDFNEECPRLRI 63
>pdb|3KMW|A Chain A, Crystal Structure Of The IlkALPHA-Parvin Core Complex
(Mgatp)
pdb|3REP|A Chain A, Crystal Structure Of The IlkALPHA-Parvin Core Complex
(Mnatp)
Length = 271
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 6 EIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVDCLRWRI 63
+ KQ L + ++ E +K QGN D +V+ LK RDW+ K+ +C R RI
Sbjct: 8 DFKQLNFLTKLNENHSGELWKGRWQGN--DIVVKVLKVRDWSTRKSRDFNEECPRLRI 63
>pdb|2GB7|A Chain A, Metal-Depleted Ecl18ki In Complex With Uncleaved, Modified
Dna
pdb|2GB7|B Chain B, Metal-Depleted Ecl18ki In Complex With Uncleaved, Modified
Dna
pdb|2GB7|C Chain C, Metal-Depleted Ecl18ki In Complex With Uncleaved, Modified
Dna
pdb|2GB7|D Chain D, Metal-Depleted Ecl18ki In Complex With Uncleaved, Modified
Dna
pdb|2FQZ|A Chain A, Metal-Depleted Ecl18ki In Complex With Uncleaved Dna
pdb|2FQZ|B Chain B, Metal-Depleted Ecl18ki In Complex With Uncleaved Dna
pdb|2FQZ|C Chain C, Metal-Depleted Ecl18ki In Complex With Uncleaved Dna
pdb|2FQZ|D Chain D, Metal-Depleted Ecl18ki In Complex With Uncleaved Dna
Length = 305
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 172 VITTIDDLNYPEKTETYYIVN-APYIFSA---CWKVVKPLLQERTRRKMQVL 219
V T DL Y +K Y++ N + YI + CWK +P +E T R + L
Sbjct: 28 VYKTFCDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYL 79
>pdb|2XAF|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (+)-Cis-2-Phenylcyclopropyl-1-Amine
pdb|2XAG|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (-)-Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAH|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With (+)-
Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAJ|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
(-)-Trans- 2-Phenylcyclopropyl-1-Amine
pdb|2XAQ|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2584, 13b)
pdb|2XAS|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2580, 14e)
Length = 852
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 11/95 (11%)
Query: 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGN----PTDTLVRFL---KARDWN-VSKAHKML 55
QEE+K+ M +L + +KE + + + P D FL K RD + K + L
Sbjct: 438 QEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDEL 497
Query: 56 VDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
+ + ++E + + A P P+++Y + RD Q++
Sbjct: 498 AET-QGKLEEKLQELEANP--PSDVYLSSRDRQIL 529
>pdb|1WSR|A Chain A, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
pdb|1WSR|B Chain B, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
pdb|1WSV|A Chain A, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
pdb|1WSV|B Chain B, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
Length = 375
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 9/62 (14%)
Query: 176 IDDLNYPEKTETY-YIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKIMDYA 234
+DDL +E + Y+V+ + CW+ L+Q++ R LQ GRD L+++D A
Sbjct: 99 LDDLIVTNTSEGHLYVVSN----AGCWEKDLALMQDKVRE----LQNQGRDVGLEVLDNA 150
Query: 235 SL 236
L
Sbjct: 151 LL 152
>pdb|2C1W|A Chain A, The Structure Of Xendou: A Splicing Independent Snorna
Processing Endoribonuclease
pdb|2C1W|B Chain B, The Structure Of Xendou: A Splicing Independent Snorna
Processing Endoribonuclease
pdb|2C1W|C Chain C, The Structure Of Xendou: A Splicing Independent Snorna
Processing Endoribonuclease
Length = 292
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 12/68 (17%)
Query: 87 SQLVGVSGYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRY 146
S +GVS + L I V L++ +K S + +++ EY ++V+ +HGRY
Sbjct: 228 SSFIGVSPEFEFALYTI---VFLASQEKMS-----REVVRLEEYELQIVV----NRHGRY 275
Query: 147 IGTSLKVL 154
IGT+ VL
Sbjct: 276 IGTAYPVL 283
>pdb|2H94|A Chain A, Crystal Structure And Mechanism Of Human Lysine-Specific
Demethylase-1
Length = 664
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 11/95 (11%)
Query: 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGN----PTDTLVRFL---KARDWN-VSKAHKML 55
QEE+K+ M +L + +KE + + + P D FL K RD + K + L
Sbjct: 267 QEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDEL 326
Query: 56 VDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
+ + ++E + + A P P+++Y + RD Q++
Sbjct: 327 AET-QGKLEEKLQELEANP--PSDVYLSSRDRQIL 358
>pdb|2IW5|A Chain A, Structural Basis For Corest-dependent Demethylation Of
Nucleosomes By The Human Lsd1 Histone Demethylase
pdb|2UXN|A Chain A, Structural Basis Of Histone Demethylation By Lsd1 Revealed
By Suicide Inactivation
pdb|2UXX|A Chain A, Human Lsd1 Histone Demethylase-Corest In Complex With An
Fad-Tranylcypromine Adduct
Length = 666
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 11/95 (11%)
Query: 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGN----PTDTLVRFL---KARDWN-VSKAHKML 55
QEE+K+ M +L + +KE + + + P D FL K RD + K + L
Sbjct: 268 QEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDEL 327
Query: 56 VDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
+ + ++E + + A P P+++Y + RD Q++
Sbjct: 328 AET-QGKLEEKLQELEANP--PSDVYLSSRDRQIL 359
>pdb|2HKO|A Chain A, Crystal Structure Of Lsd1
Length = 664
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 11/95 (11%)
Query: 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGN----PTDTLVRFL---KARDWN-VSKAHKML 55
QEE+K+ M +L + +KE + + + P D FL K RD + K + L
Sbjct: 267 QEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDEL 326
Query: 56 VDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
+ + ++E + + A P P+++Y + RD Q++
Sbjct: 327 AET-QGKLEEKLQELEANP--PSDVYLSSRDRQIL 358
>pdb|2DW4|A Chain A, Crystal Structure Of Human Lsd1 At 2.3 A Resolution
Length = 660
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 11/95 (11%)
Query: 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGN----PTDTLVRFL---KARDWN-VSKAHKML 55
QEE+K+ M +L + +KE + + + P D FL K RD + K + L
Sbjct: 267 QEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDEL 326
Query: 56 VDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
+ + ++E + + A P P+++Y + RD Q++
Sbjct: 327 AET-QGKLEEKLQELEANP--PSDVYLSSRDRQIL 358
>pdb|2EJR|A Chain A, Lsd1-Tranylcypromine Complex
pdb|2Z3Y|A Chain A, Crystal Structure Of Lysine-Specific Demethylase1
pdb|2Z5U|A Chain A, Crystal Structure Of Lysine-Specific Histone Demethylase 1
pdb|3ABT|A Chain A, Crystal Structure Of Lsd1 In Complex With Trans-2-
Pentafluorophenylcyclopropylamine
pdb|3ABU|A Chain A, Crystal Structure Of Lsd1 In Complex With A 2-Pcpa
Derivative, S1201
Length = 662
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 11/95 (11%)
Query: 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGN----PTDTLVRFL---KARDWN-VSKAHKML 55
QEE+K+ M +L + +KE + + + P D FL K RD + K + L
Sbjct: 267 QEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDEL 326
Query: 56 VDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
+ + ++E + + A P P+++Y + RD Q++
Sbjct: 327 AET-QGKLEEKLQELEANP--PSDVYLSSRDRQIL 358
>pdb|2X0L|A Chain A, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 734
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 11/95 (11%)
Query: 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGN----PTDTLVRFL---KARDWN-VSKAHKML 55
QEE+K+ M +L + +KE + + + P D FL K RD + K + L
Sbjct: 320 QEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDEL 379
Query: 56 VDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
+ + ++E + + A P P+++Y + RD Q++
Sbjct: 380 AET-QGKLEEKLQELEANP--PSDVYLSSRDRQIL 411
>pdb|2V1D|A Chain A, Structural Basis Of Lsd1-Corest Selectivity In Histone H3
Recognition
pdb|2Y48|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A N-
Terminal Snail Peptide
Length = 730
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 11/95 (11%)
Query: 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGN----PTDTLVRFL---KARDWN-VSKAHKML 55
QEE+K+ M +L + +KE + + + P D FL K RD + K + L
Sbjct: 316 QEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDEL 375
Query: 56 VDCLRWRIENDIDNILAKPILPAELYRAVRDSQLV 90
+ + ++E + + A P P+++Y + RD Q++
Sbjct: 376 AET-QGKLEEKLQELEANP--PSDVYLSSRDRQIL 407
>pdb|2DVV|A Chain A, Crystal Structure Of The Second Bromodomain Of The Human
Brd2 Protein
pdb|2E3K|A Chain A, Crystal Structure Of The Human Brd2 Second Bromodomain In
Complexed With The Acetylated Histone H4 Peptide
pdb|2E3K|B Chain B, Crystal Structure Of The Human Brd2 Second Bromodomain In
Complexed With The Acetylated Histone H4 Peptide
pdb|2E3K|C Chain C, Crystal Structure Of The Human Brd2 Second Bromodomain In
Complexed With The Acetylated Histone H4 Peptide
pdb|2E3K|D Chain D, Crystal Structure Of The Human Brd2 Second Bromodomain In
Complexed With The Acetylated Histone H4 Peptide
Length = 112
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 123 SHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQI-----KLMTVITTID 177
SH++ ++ + ++ SKKH Y K +D + L L + I L TV ++
Sbjct: 2 SHMEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKME 61
Query: 178 DLNYPEKTETYYIVNAPYIFSACWKVVKP 206
+ +Y + E + + +FS C+K P
Sbjct: 62 NRDYRDAQE--FAADVRLMFSNCYKYNPP 88
>pdb|1LI5|A Chain A, Crystal Structure Of Cysteinyl-Trna Synthetase
pdb|1LI5|B Chain B, Crystal Structure Of Cysteinyl-Trna Synthetase
pdb|1LI7|A Chain A, Crystal Structure Of Cysteinyl-Trna Synthetase With
Cysteine Substrate Bound
pdb|1LI7|B Chain B, Crystal Structure Of Cysteinyl-Trna Synthetase With
Cysteine Substrate Bound
pdb|1U0B|B Chain B, Crystal Structure Of Cysteinyl-Trna Synthetase Binary
Complex With Trnacys
Length = 461
Score = 27.7 bits (60), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKAR--DWNVSKAHKMLVDCLR 60
+E +KQ + +E L +L+ T K V RF++A D+N +A+ +L D R
Sbjct: 306 EENLKQARAALERLYTALRGTDKTVAPAGGEAFEARFIEAMDDDFNTPEAYSVLFDMAR 364
>pdb|3ZEN|D Chain D, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|3ZEN|E Chain E, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|3ZEN|F Chain F, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|4B3Y|A Chain A, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|4B3Y|B Chain B, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|4B3Y|C Chain C, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
Length = 3089
Score = 27.7 bits (60), Expect = 9.3, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 1/56 (1%)
Query: 46 WNVSKAHKMLVDCLR-WRIENDIDNILAKPILPAELYRAVRDSQLVGVSGYSKEGL 100
W +S +D + W I +D L+ P EL R V SQ+ G G+
Sbjct: 2634 WGISPDMASSIDRVALWNIVATVDAFLSSGFTPTELMRWVHPSQVASTQGTGMGGM 2689
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.135 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,066,377
Number of Sequences: 62578
Number of extensions: 420785
Number of successful extensions: 1015
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 992
Number of HSP's gapped (non-prelim): 34
length of query: 334
length of database: 14,973,337
effective HSP length: 99
effective length of query: 235
effective length of database: 8,778,115
effective search space: 2062857025
effective search space used: 2062857025
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)