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= 005253
(706 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2I7T|A Chain A, Structure Of Human Cpsf-73
pdb|2I7V|A Chain A, Structure Of Human Cpsf-73
Length = 459
Score = 147 bits (370), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 98/371 (26%), Positives = 188/371 (50%), Gaps = 24/371 (6%)
Query: 22 LVSIDGFNFLIDCGWNDHFDPSLLQPLSKVA--STIDAVLLSHPDTLHLGALPYAMKQLG 79
++ G ++DCG + + P + + ID +L+SH H GALP+ +++
Sbjct: 29 ILEFKGRKIMLDCGIHPGLEGMDALPYIDLIDPAEIDLLLISHFHLDHCGALPWFLQKTS 88
Query: 80 LSAPVF---STEPVYRLGLLTMYDQYLSRRQVSEFD-LFTLDDIDSAFQSVTRLTYSQNY 135
F +T+ +YR L Y+ +S D L+T D++ + + + N+
Sbjct: 89 FKGRTFMTHATKAIYRWLL----SDYVKVSNISADDMLYTETDLEESMDKIETI----NF 140
Query: 136 HLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLNGTVLESFVRPA 195
H + GI + AGH+LG ++ I G ++Y D++R++++HL + + ++P
Sbjct: 141 HEVKEVAGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPN-IKPD 199
Query: 196 VLITDAYNALHNQPPRQQREM-FQDAISKTLRAGGNVLLPVDSAGRVLELLLILEDYWAE 254
+LI ++ H R++RE F + + + GG L+PV + GR ELLLIL++YW
Sbjct: 200 ILIIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQN 259
Query: 255 HS--LNYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFLLKHVTLLINKSEL 312
H + PIY+ + ++ + ++++ M D I K +N F+ KH++ L +
Sbjct: 260 HPELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQINI--NNPFVFKHISNLKSMDHF 317
Query: 313 DNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARMLQADPPPKA 372
D+ GP +V+AS +++G S ++F W +D +N V+ GTLA+ + ++ P+
Sbjct: 318 DDI--GPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHIMSE--PEE 373
Query: 373 VKVTMSRRVPL 383
+ +++PL
Sbjct: 374 ITTMSGQKLPL 384
>pdb|2I7X|A Chain A, Structure Of Yeast Cpsf-100 (Ydh1p)
Length = 717
Score = 140 bits (352), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 135/494 (27%), Positives = 211/494 (42%), Gaps = 85/494 (17%)
Query: 22 LVSIDGFNFLIDCGWNDHFDPS------LLQPLSKVASTIDAVLLSHPDTLHLGA---LP 72
+V D LID GWN PS ++ KV ID ++LS P LGA L
Sbjct: 19 VVRFDNVTLLIDPGWN----PSKVSYEQCIKYWEKVIPEIDVIILSQPTIECLGAHSLLY 74
Query: 73 YAMKQLGLSA-PVFSTEPVYRLGLLTMYDQYLSRRQVSEFDLFTLD--DIDSAFQSVTRL 129
Y +S V++T PV LG ++ D Y S + +D LD DI+ +F + L
Sbjct: 75 YNFTSHFISRIQVYATLPVINLGRVSTIDSYASAGVIGPYDTNKLDLEDIEISFDHIVPL 134
Query: 130 TYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLN----- 184
YSQ L + +G+ + + AG GG++W I+ E ++YA +N ++ LN
Sbjct: 135 KYSQLVDLRSRYDGLTLLAYNAGVCPGGSIWCISTYSEKLVYAKRWNHTRDNILNAASIL 194
Query: 185 ---GTVLESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRV 241
G L + +RP+ +IT +QP +++ ++F+D + K L + G+V++PVD +G+
Sbjct: 195 DATGKPLSTLMRPSAIITTLDRFGSSQPFKKRSKIFKDTLKKGLSSDGSVIIPVDMSGKF 254
Query: 242 LELL-----LILEDYWAEHSLNYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDN 296
L+L L+ E P+ L+Y T+ Y KS LEW+ S+ K++E +R+N
Sbjct: 255 LDLFTQVHELLFESTKINAHTQVPVLILSYARGRTLTYAKSMLEWLSPSLLKTWE-NRNN 313
Query: 297 A--FLLKHVTLLINKSELDNAPDGPKLVLASMA------------------------SLE 330
F + +I +EL P G K+ S S E
Sbjct: 314 TSPFEIGSRIKIIAPNELSKYP-GSKICFVSEVGALINEVIIKVGNSEKTTLILTKPSFE 372
Query: 331 AGFSHDIFVEWA-SDVKNLVLFTERGQFGTLARMLQADPPPKAVKVTMSRRVPLVGEELI 389
S D +E D +N F E G+ + D + PL EE
Sbjct: 373 CASSLDKILEIVEQDERNWKTFPEDGKSFLCDNYISID---------TIKEEPLSKEETE 423
Query: 390 AYEEEQTRLKKEEALKASLVKEEESKASLGPDNNLSGDPMVIDXXXXXXSADVVEPHGGR 449
A++ + K++ K LVK E K L+ +ID D R
Sbjct: 424 AFKVQLKEKKRDRNKKILLVKRESKK--------LANGNAIID--------DTNGERAMR 467
Query: 450 YRDILIDGF--VPP 461
+DIL++ VPP
Sbjct: 468 NQDILVENVNGVPP 481
>pdb|3AF5|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii
pdb|3AF6|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii Complexed With Rna-Analog
Length = 651
Score = 103 bits (256), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 101/405 (24%), Positives = 172/405 (42%), Gaps = 42/405 (10%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCGWN-----------DHFDPSLLQPLSKVAS 53
+++T L G + LV D L+D G N HFD Q + +
Sbjct: 189 IRITGLGGFREVGRSALLVQTDESFVLVDFGVNVAMLNDPYKAFPHFDAPEFQYVLR-EG 247
Query: 54 TIDAVLLSHPDTLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQYLSRRQVSEFDL 113
+DA++++H H G LPY + P+++T P L +L D ++ + L
Sbjct: 248 LLDAIIITHAHLDHCGMLPYLFRYNLFDGPIYTTPPTRDLMVLLQKDFIEIQQSNGQDPL 307
Query: 114 FTLDDIDSAFQSVTRLTYSQNYHLSGKGEGIVVAPHVAGHLLGGTV--WKITKDGEDVIY 171
+ DI + L Y + +S I + H AGH+LG + I ++
Sbjct: 308 YRPRDIKEVIKHTITLDYGEVRDIS---PDIRLTLHNAGHILGSAIVHLHIGNGLHNIAI 364
Query: 172 AVDYNRRKEKHLNGTVLE----SFVRPAVLITDAYNALHN--QPPRQQRE-MFQDAISKT 224
D+ K + +LE F R L+ ++ N Q PR++ E + I T
Sbjct: 365 TGDF-----KFIPTRLLEPANAKFPRLETLVMESTYGGANDIQMPREEAEKRLIEVIHNT 419
Query: 225 LRAGGNVLLPVDSAGRVLELLLILEDYWAEHSLNYPIYFLTYVSSSTIDYVKSFLEWMGD 284
++ GG VL+P + GR E++++LE+Y + PIY + +T + ++ E++
Sbjct: 420 IKRGGKVLIPAMAVGRAQEVMMVLEEYARIGGIEVPIYLDGMIWEATAIHT-AYPEYLSR 478
Query: 285 SITKSFETSRDNAFLLKHVTLLINKSELDNAPDG--PKLVLASMASLEAGFSHDIFVEWA 342
+ + N FL + + N E + D P +++AS L G S + F + A
Sbjct: 479 RLREQIFKEGYNPFLSEIFHPVANSRERQDIIDSNEPAIIIASSGMLVGGPSVEYFKQLA 538
Query: 343 SDVKNLVLFTERGQFGTLARMLQADPPPKAVKVTMSRRVPLVGEE 387
D KN ++F GTL R +Q+ R +P+VGEE
Sbjct: 539 PDPKNSIIFVSYQAEGTLGRQVQSG----------IREIPMVGEE 573
>pdb|2DKF|A Chain A, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8, A Rna Degradation Protein Of The
Metallo-Beta-Lactamase Superfamily
pdb|2DKF|B Chain B, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8, A Rna Degradation Protein Of The
Metallo-Beta-Lactamase Superfamily
pdb|2DKF|C Chain C, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8, A Rna Degradation Protein Of The
Metallo-Beta-Lactamase Superfamily
pdb|2DKF|D Chain D, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8, A Rna Degradation Protein Of The
Metallo-Beta-Lactamase Superfamily
Length = 431
Score = 88.6 bits (218), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 96/383 (25%), Positives = 155/383 (40%), Gaps = 22/383 (5%)
Query: 6 QVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHPD 64
++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 2 RIVPFGAAREVTGSAHLLLAGGRRVLLDCGXFQGKEEARNHAPFGFDPKEVDAVLLTHAH 61
Query: 65 TLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQYLSRRQVSEFDLFTLDDIDSAFQ 124
H+G LP ++ G PV++T L + + D +V + F +D++ A
Sbjct: 62 LDHVGRLPKLFRE-GYRGPVYATRATVLLXEIVLEDAL----KVXDEPFFGPEDVEEALG 116
Query: 125 SVTRLTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLN 184
+ L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 117 HLRPLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVLP 172
Query: 185 GTVLESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLEL 244
L VL Y ++P R+ F + + KTL GG VL+P + R E+
Sbjct: 173 DPSLPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQEI 231
Query: 245 LLILEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL---L 300
L +L Y H L PIY + + + + + + + F + N F L
Sbjct: 232 LYVL--YTHGHRLPRAPIYLDSPXAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAGL 288
Query: 301 KHVTLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTL 360
+ V L+ AP GP +VLA L G SD +N ++F G L
Sbjct: 289 EVVEHTEASKALNRAP-GPXVVLAGSGXLAGGRILHHLKHGLSDPRNALVFVGYQPQGGL 347
Query: 361 ARMLQADPPPKAVKVTMSRRVPL 383
+ A PP AV++ + VPL
Sbjct: 348 GAEIIARPP--AVRI-LGEEVPL 367
>pdb|3IDZ|A Chain A, Crystal Structure Of S378q Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IDZ|B Chain B, Crystal Structure Of S378q Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IDZ|C Chain C, Crystal Structure Of S378q Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IDZ|D Chain D, Crystal Structure Of S378q Mutant Ttha0252 From Thermus
Thermophilus Hb8
Length = 431
Score = 87.8 bits (216), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 96/384 (25%), Positives = 157/384 (40%), Gaps = 22/384 (5%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQYLSRRQVSEFDLFTLDDIDSAF 123
H+G LP ++ G PV++T L + + D +V + F +D++ A
Sbjct: 61 HLDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDAL----KVMDEPFFGPEDVEEAL 115
Query: 124 QSVTRLTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHL 183
+ L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 116 GHLRPLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVL 171
Query: 184 NGTVLESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLE 243
L VL Y ++P R+ F + + KTL GG VL+P + R E
Sbjct: 172 PDPSLPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQE 230
Query: 244 LLLILEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL--- 299
+L +L Y H L PIY + ++ + + + + + F + N F
Sbjct: 231 ILYVL--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAG 287
Query: 300 LKHVTLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGT 359
L+ V L+ AP GP +VLA L G SD +N ++F G
Sbjct: 288 LEVVEHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGG 346
Query: 360 LARMLQADPPPKAVKVTMSRRVPL 383
L + A PP AV++ + VPL
Sbjct: 347 LGAEIIARPP--AVRI-LGEEVPL 367
>pdb|3IEK|A Chain A, Crystal Structure Of Native Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IEK|B Chain B, Crystal Structure Of Native Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IEK|C Chain C, Crystal Structure Of Native Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IEK|D Chain D, Crystal Structure Of Native Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IEL|A Chain A, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Ump
pdb|3IEL|B Chain B, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Ump
pdb|3IEL|C Chain C, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Ump
pdb|3IEL|D Chain D, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Ump
pdb|3IEM|A Chain A, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Rna Analog
pdb|3IEM|B Chain B, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Rna Analog
pdb|3IEM|C Chain C, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Rna Analog
pdb|3IEM|D Chain D, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Rna Analog
Length = 431
Score = 87.8 bits (216), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 96/384 (25%), Positives = 157/384 (40%), Gaps = 22/384 (5%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQYLSRRQVSEFDLFTLDDIDSAF 123
H+G LP ++ G PV++T L + + D +V + F +D++ A
Sbjct: 61 HLDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDAL----KVMDEPFFGPEDVEEAL 115
Query: 124 QSVTRLTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHL 183
+ L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 116 GHLRPLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVL 171
Query: 184 NGTVLESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLE 243
L VL Y ++P R+ F + + KTL GG VL+P + R E
Sbjct: 172 PDPSLPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQE 230
Query: 244 LLLILEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL--- 299
+L +L Y H L PIY + ++ + + + + + F + N F
Sbjct: 231 ILYVL--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAG 287
Query: 300 LKHVTLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGT 359
L+ V L+ AP GP +VLA L G SD +N ++F G
Sbjct: 288 LEVVEHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGG 346
Query: 360 LARMLQADPPPKAVKVTMSRRVPL 383
L + A PP AV++ + VPL
Sbjct: 347 LGAEIIARPP--AVRI-LGEEVPL 367
>pdb|3IE1|A Chain A, Crystal Structure Of H380a Mutant Ttha0252 From Thermus
Thermophilus Hb8 Complexed With Rna
pdb|3IE1|B Chain B, Crystal Structure Of H380a Mutant Ttha0252 From Thermus
Thermophilus Hb8 Complexed With Rna
pdb|3IE1|C Chain C, Crystal Structure Of H380a Mutant Ttha0252 From Thermus
Thermophilus Hb8 Complexed With Rna
pdb|3IE1|D Chain D, Crystal Structure Of H380a Mutant Ttha0252 From Thermus
Thermophilus Hb8 Complexed With Rna
Length = 431
Score = 87.8 bits (216), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 96/384 (25%), Positives = 157/384 (40%), Gaps = 22/384 (5%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQYLSRRQVSEFDLFTLDDIDSAF 123
H+G LP ++ G PV++T L + + D +V + F +D++ A
Sbjct: 61 HLDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDAL----KVMDEPFFGPEDVEEAL 115
Query: 124 QSVTRLTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHL 183
+ L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 116 GHLRPLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVL 171
Query: 184 NGTVLESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLE 243
L VL Y ++P R+ F + + KTL GG VL+P + R E
Sbjct: 172 PDPSLPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQE 230
Query: 244 LLLILEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL--- 299
+L +L Y H L PIY + ++ + + + + + F + N F
Sbjct: 231 ILYVL--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAG 287
Query: 300 LKHVTLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGT 359
L+ V L+ AP GP +VLA L G SD +N ++F G
Sbjct: 288 LEVVEHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGG 346
Query: 360 LARMLQADPPPKAVKVTMSRRVPL 383
L + A PP AV++ + VPL
Sbjct: 347 LGAEIIARPP--AVRI-LGEEVPL 367
>pdb|3IE0|A Chain A, Crystal Structure Of S378y Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE0|B Chain B, Crystal Structure Of S378y Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE0|C Chain C, Crystal Structure Of S378y Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE0|D Chain D, Crystal Structure Of S378y Mutant Ttha0252 From Thermus
Thermophilus Hb8
Length = 431
Score = 87.8 bits (216), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 96/384 (25%), Positives = 157/384 (40%), Gaps = 22/384 (5%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQYLSRRQVSEFDLFTLDDIDSAF 123
H+G LP ++ G PV++T L + + D +V + F +D++ A
Sbjct: 61 HLDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDAL----KVMDEPFFGPEDVEEAL 115
Query: 124 QSVTRLTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHL 183
+ L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 116 GHLRPLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVL 171
Query: 184 NGTVLESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLE 243
L VL Y ++P R+ F + + KTL GG VL+P + R E
Sbjct: 172 PDPSLPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQE 230
Query: 244 LLLILEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL--- 299
+L +L Y H L PIY + ++ + + + + + F + N F
Sbjct: 231 ILYVL--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAG 287
Query: 300 LKHVTLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGT 359
L+ V L+ AP GP +VLA L G SD +N ++F G
Sbjct: 288 LEVVEHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGG 346
Query: 360 LARMLQADPPPKAVKVTMSRRVPL 383
L + A PP AV++ + VPL
Sbjct: 347 LGAEIIARPP--AVRI-LGEEVPL 367
>pdb|3IE2|A Chain A, Crystal Structure Of H400v Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE2|B Chain B, Crystal Structure Of H400v Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE2|C Chain C, Crystal Structure Of H400v Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE2|D Chain D, Crystal Structure Of H400v Mutant Ttha0252 From Thermus
Thermophilus Hb8
Length = 431
Score = 87.8 bits (216), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 96/384 (25%), Positives = 157/384 (40%), Gaps = 22/384 (5%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQYLSRRQVSEFDLFTLDDIDSAF 123
H+G LP ++ G PV++T L + + D +V + F +D++ A
Sbjct: 61 HLDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDAL----KVMDEPFFGPEDVEEAL 115
Query: 124 QSVTRLTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHL 183
+ L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 116 GHLRPLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVL 171
Query: 184 NGTVLESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLE 243
L VL Y ++P R+ F + + KTL GG VL+P + R E
Sbjct: 172 PDPSLPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQE 230
Query: 244 LLLILEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL--- 299
+L +L Y H L PIY + ++ + + + + + F + N F
Sbjct: 231 ILYVL--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAG 287
Query: 300 LKHVTLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGT 359
L+ V L+ AP GP +VLA L G SD +N ++F G
Sbjct: 288 LEVVEHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGG 346
Query: 360 LARMLQADPPPKAVKVTMSRRVPL 383
L + A PP AV++ + VPL
Sbjct: 347 LGAEIIARPP--AVRI-LGEEVPL 367
>pdb|3A4Y|A Chain A, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3A4Y|B Chain B, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3A4Y|C Chain C, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3A4Y|D Chain D, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
Length = 431
Score = 87.4 bits (215), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 96/384 (25%), Positives = 157/384 (40%), Gaps = 22/384 (5%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQYLSRRQVSEFDLFTLDDIDSAF 123
H+G LP ++ G PV++T L + + D +V + F +D++ A
Sbjct: 61 ALDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDAL----KVMDEPFFGPEDVEEAL 115
Query: 124 QSVTRLTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHL 183
+ L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 116 GHLRPLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVL 171
Query: 184 NGTVLESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLE 243
L VL Y ++P R+ F + + KTL GG VL+P + R E
Sbjct: 172 PDPSLPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQE 230
Query: 244 LLLILEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL--- 299
+L +L Y H L PIY + ++ + + + + + F + N F
Sbjct: 231 ILYVL--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAG 287
Query: 300 LKHVTLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGT 359
L+ V L+ AP GP +VLA L G SD +N ++F G
Sbjct: 288 LEVVEHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGG 346
Query: 360 LARMLQADPPPKAVKVTMSRRVPL 383
L + A PP AV++ + VPL
Sbjct: 347 LGAEIIARPP--AVRI-LGEEVPL 367
>pdb|2XR1|A Chain A, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
pdb|2XR1|B Chain B, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
Length = 640
Score = 85.5 bits (210), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 91/374 (24%), Positives = 159/374 (42%), Gaps = 20/374 (5%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCGWN----DHFDPSLLQPLSKVASTIDAVLL 60
V+VT L G +L+S LIDCG N ++ P L P + IDAV++
Sbjct: 184 VRVTALGGCKEVGRSCFLLSTPESRILIDCGVNVGSDENMTPYLYVPEVFPLNQIDAVIV 243
Query: 61 SHPDTLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQYLSRRQVSEFDLFTLDDID 120
+H H G +P K G PV+ T P L +L D + + + +
Sbjct: 244 THAHLDHQGLVPLLFK-YGYEGPVYCTPPTRDLMVLLQLDYIDVAAKEGKKIPYESGMVA 302
Query: 121 SAFQSVTRLTYSQNYHLSGKGEGIVVAPHVAGHLLGGTV--WKITKDGEDVIYAVDYNRR 178
+ L Y + ++ I + H AGH+LG + + I +V++ DY
Sbjct: 303 KTLKHTIPLDYEE---VTDIAPDIKLTFHNAGHILGSAISHFHIGDGLHNVVFTGDYKYE 359
Query: 179 KEKHLNGTVLESFVRPAVLITDAY--NALHNQPPRQQREM-FQDAISKTLRAGGNVLLPV 235
K + + V F R +I++A NA QP + E Q + T+ GG ++P
Sbjct: 360 KTRLFDPAV-NKFPRVETVISEATYGNANAFQPALKDAEKHLQMVVKNTIERGGIAVIPA 418
Query: 236 DSAGRVLELLLILEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSR 294
+ GR E++++LE+ + + P+Y + +T + + E++ + + K
Sbjct: 419 FAVGRSQEVMIVLEESIRKGLIPEVPVYLDGMIWEATAIHA-THPEYLNNDLRKLIFQKG 477
Query: 295 DNAFL---LKHVTLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLF 351
N FL K V + ++ P P ++LA+ + G + F +A D +N ++F
Sbjct: 478 QNPFLSECFKPVDSHEARQKIIQNPQ-PCVILATSGMMNGGPVMEYFKAFAEDPRNTLVF 536
Query: 352 TERGQFGTLARMLQ 365
GT+ R +Q
Sbjct: 537 VGYQADGTIGRRIQ 550
>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
Length = 636
Score = 82.8 bits (203), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 88/361 (24%), Positives = 147/361 (40%), Gaps = 46/361 (12%)
Query: 31 LIDCGWN-----DHFDPSLLQPLSKVASTIDAVLLSHPDTLHLGALPYAMKQLGLSAPVF 85
L+DCG N D L ++DAV+++H H G LPY + G PV+
Sbjct: 206 LLDCGVNVAGGDDKNSYPYLNVPEFTLDSLDAVIITHAHLDHSGFLPY-LYHYGYDGPVY 264
Query: 86 STEPVYRLGLLTMYDQYLSRRQVSEFDLFTLDDIDSAFQSVTRLTYSQNYHLSGKGEGIV 145
T P L L D + E F + + + + L Y + ++ I
Sbjct: 265 CTAPTRDLMTLLQLDHIDIAHREDEPLPFNVKHVKKSVKHTITLDYGE---VTDIAPDIR 321
Query: 146 VAPHVAGHLLGGTVWKI-TKDGE-DVIYAVDYNRRKEKHLNGTVLESFVRPAVLITDAYN 203
+ H AGH+LG + + DG+ +++Y D+ + + L F R L+ ++
Sbjct: 322 LTLHNAGHILGSAMAHLHIGDGQHNMVYTGDFKYEQSRLLEAAA-NRFPRIETLVMESTY 380
Query: 204 ALHN--QPPRQQREM-FQDAISKTLRAGGNVLLPVDSAGRVLELLLILEDYWAEHSLNYP 260
H QP R + E I TLR GG +L+PV + GR EL+++LE+
Sbjct: 381 GGHEDVQPSRNRAEKELVKTIYSTLRRGGKILIPVFAVGRAQELMIVLEE---------- 430
Query: 261 IYFLTYVSSSTIDYVKSFLE---WMGDSITKSF-----ETSRDNAFLLKHVTLLINKSEL 312
Y+ + ID V +++ W ++I + + RD F + H + +
Sbjct: 431 -----YIRTGIIDEVPVYIDGMIWEANAIHTARPEYLSKDLRDQIFHMGHNPFISDIFHK 485
Query: 313 DNAPD--------GPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARML 364
N D P ++L++ L G S + F D N ++F G+L R +
Sbjct: 486 VNGMDERREIVEGEPSIILSTSGMLTGGNSLEYFKWLCEDPDNSLVFVGYQAEGSLGRRI 545
Query: 365 Q 365
Q
Sbjct: 546 Q 546
>pdb|1VME|A Chain A, Crystal Structure Of Flavoprotein (Tm0755) From Thermotoga
Maritima At 1.80 A Resolution
pdb|1VME|B Chain B, Crystal Structure Of Flavoprotein (Tm0755) From Thermotoga
Maritima At 1.80 A Resolution
Length = 410
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 20 SYLVSIDGFNFLIDCGWNDHFDPSLLQPLSKVA--STIDAVLLSHPDTLHLGALPYAMKQ 77
+YLV ++G N LID GW ++ + LSK+ I ++++H + H G+LP +K
Sbjct: 54 AYLVKLNGANVLID-GWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDHSGSLPATLKT 112
Query: 78 LGLSAPVFSTEPVYRL 93
+G + ++ RL
Sbjct: 113 IGHDVEIIASNFGKRL 128
>pdb|4DIL|A Chain A, Flavo Di-Iron Protein H90n Mutant From Thermotoga Maritima
pdb|4DIL|B Chain B, Flavo Di-Iron Protein H90n Mutant From Thermotoga Maritima
Length = 410
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 20 SYLVSIDGFNFLIDCGWNDHFDPSLLQPLSKVA--STIDAVLLSHPDTLHLGALPYAMKQ 77
+YLV ++G N LID GW ++ + LSK+ I ++++H + + G+LP +K
Sbjct: 54 AYLVKLNGANVLID-GWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDNSGSLPATLKT 112
Query: 78 LGLSAPVFSTEPVYRL 93
+G + ++ RL
Sbjct: 113 IGHDVEIIASNFGKRL 128
>pdb|4DIK|A Chain A, Flavo Di-Iron Protein H90a Mutant From Thermotoga Maritima
pdb|4DIK|B Chain B, Flavo Di-Iron Protein H90a Mutant From Thermotoga Maritima
Length = 410
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 20 SYLVSIDGFNFLIDCGWNDHFDPSLLQPLSKVA--STIDAVLLSHPDTLHLGALPYAMKQ 77
+YLV ++G N LID GW ++ + LSK+ I ++++H + G+LP +K
Sbjct: 54 AYLVKLNGANVLID-GWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDASGSLPATLKT 112
Query: 78 LGLSAPVFSTEPVYRL 93
+G + ++ RL
Sbjct: 113 IGHDVEIIASNFGKRL 128
>pdb|1ZKP|A Chain A, 1.5a Resolution Crystal Structure Of A Metallo Beta
Lactamase Family Protein, The Elac Homolgue Of Bacillus
Anthracis, A Putative Ribonuclease
pdb|1ZKP|B Chain B, 1.5a Resolution Crystal Structure Of A Metallo Beta
Lactamase Family Protein, The Elac Homolgue Of Bacillus
Anthracis, A Putative Ribonuclease
pdb|1ZKP|C Chain C, 1.5a Resolution Crystal Structure Of A Metallo Beta
Lactamase Family Protein, The Elac Homolgue Of Bacillus
Anthracis, A Putative Ribonuclease
pdb|1ZKP|D Chain D, 1.5a Resolution Crystal Structure Of A Metallo Beta
Lactamase Family Protein, The Elac Homolgue Of Bacillus
Anthracis, A Putative Ribonuclease
Length = 268
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 25/59 (42%), Positives = 29/59 (49%), Gaps = 11/59 (18%)
Query: 21 YLVSIDGFNFLIDCGWNDHFDPSLLQPLSK--VASTIDAVLLSHPDTLH---LGALPYA 74
YL DGF L+DCG +L L K S IDAV+LSH H +G L YA
Sbjct: 46 YLFEHDGFRLLVDCG------SGVLAQLQKYITPSDIDAVVLSHYHHDHVADIGVLQYA 98
>pdb|4H9Q|C Chain C, Complex Structure 4 Of Daxx(E225a)H3.3(SUB5)H4
pdb|4H9R|C Chain C, Complex Structure 5 Of Daxx(E225a)H3.3(SUB5,G90A)H4
Length = 212
Score = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 16/35 (45%), Positives = 19/35 (54%)
Query: 95 LLTMYDQYLSRRQVSEFDLFTLDDIDSAFQSVTRL 129
LL +Y + R Q E DL LDD DSA+ RL
Sbjct: 17 LLALYVAEIRRLQEKELDLSELDDPDSAYLQAARL 51
>pdb|4H9S|E Chain E, Complex Structure 6 Of DaxxH3.3(SUB7)H4
pdb|4H9S|F Chain F, Complex Structure 6 Of DaxxH3.3(SUB7)H4
Length = 216
Score = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 16/35 (45%), Positives = 19/35 (54%)
Query: 95 LLTMYDQYLSRRQVSEFDLFTLDDIDSAFQSVTRL 129
LL +Y + R Q E DL LDD DSA+ RL
Sbjct: 12 LLALYVAEIRRLQEKELDLSELDDPDSAYLQEARL 46
>pdb|4H9N|C Chain C, Complex Structure 1 Of DaxxH3.3(SUB5)H4
pdb|4H9O|C Chain C, Complex Structure 2 Of DaxxH3.3(SUB5,G90M)H4
pdb|4H9P|C Chain C, Complex Structure 3 Of DaxxH3.3(SUB5,G90A)H4
Length = 212
Score = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 16/35 (45%), Positives = 19/35 (54%)
Query: 95 LLTMYDQYLSRRQVSEFDLFTLDDIDSAFQSVTRL 129
LL +Y + R Q E DL LDD DSA+ RL
Sbjct: 17 LLALYVAEIRRLQEKELDLSELDDPDSAYLQEARL 51
>pdb|4HGA|A Chain A, Structure Of The Variant Histone H3.3-H4 Heterodimer In
Complex With Its Chaperone Daxx
Length = 213
Score = 30.4 bits (67), Expect = 3.9, Method: Composition-based stats.
Identities = 16/35 (45%), Positives = 19/35 (54%)
Query: 95 LLTMYDQYLSRRQVSEFDLFTLDDIDSAFQSVTRL 129
LL +Y + R Q E DL LDD DSA+ RL
Sbjct: 17 LLALYVAEIRRLQEKELDLSELDDPDSAYLQEARL 51
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
0.317 0.136 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,819,386
Number of Sequences: 62578
Number of extensions: 937384
Number of successful extensions: 2255
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2209
Number of HSP's gapped (non-prelim): 25
length of query: 706
length of database: 14,973,337
effective HSP length: 106
effective length of query: 600
effective length of database: 8,340,069
effective search space: 5004041400
effective search space used: 5004041400
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)