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= 004964
(721 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 = 142 bits (358), Expect = 7e-34, Method: Compositional matrix adjust.
Identities = 97/365 (26%), Positives = 185/365 (50%), Gaps = 30/365 (8%)
Query: 22 LVSIDGFNFLIDCGWNDHFDPSLLQPLSKVA--STIDAVLLSHPDTLHLGALPYAMKQLG 79
++ G ++DCG + + P + + ID +L+SH H GALP+ +++
Sbjct: 29 ILEFKGRKIMLDCGIHPGLEGMDALPYIDLIDPAEIDLLLISHFHLDHCGALPWFLQKTS 88
Query: 80 LSAPVF---STEPVYRLGLLTMYDQYLSRRSVTRLTYSQ-------------NYHLSGKG 123
F +T+ +YR LL+ Y + +S S + Y++ N+H +
Sbjct: 89 FKGRTFMTHATKAIYRW-LLSDYVK-VSNISADDMLYTETDLEESMDKIETINFHEVKEV 146
Query: 124 EGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLNGTVLESFVRPAVLITDA 183
GI + AGH+LG ++ I G ++Y D++R++++HL + + ++P +LI ++
Sbjct: 147 AGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPN-IKPDILIIES 205
Query: 184 YNALHNQPPRQQREM-FQDAISKTLRAGGNVLLPVDSAGRVLELLLILEDYWAEHS--LN 240
H R++RE F + + + GG L+PV + GR ELLLIL++YW H +
Sbjct: 206 TYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHPELHD 265
Query: 241 YPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFLLKHVTLLINKSELDNAPDG 300
PIY+ + ++ + ++++ M D I K +N F+ KH++ L + D+ G
Sbjct: 266 IPIYYASSLAKKCMAVYQTYVNAMNDKIRKQINI--NNPFVFKHISNLKSMDHFDDI--G 321
Query: 301 PKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARMLQADPPPKAVKVTMS 360
P +V+AS +++G S ++F W +D +N V+ GTLA+ + ++ P+ +
Sbjct: 322 PSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHIMSE--PEEITTMSG 379
Query: 361 RRVPL 365
+++PL
Sbjct: 380 QKLPL 384
>pdb|2I7X|A Chain A, Structure Of Yeast Cpsf-100 (Ydh1p)
Length = 717
Score = 123 bits (308), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 163/706 (23%), Positives = 265/706 (37%), Gaps = 166/706 (23%)
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-PVFSTEPVYRLGLLTMYDQY--------------------LSRRSVTRL 111
Y +S V++T PV LG ++ D Y +S + L
Sbjct: 75 YNFTSHFISRIQVYATLPVINLGRVSTIDSYASAGVIGPYDTNKLDLEDIEISFDHIVPL 134
Query: 112 TYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLN----- 166
YSQ L + +G+ + + AG GG++W I+ E ++YA +N ++ LN
Sbjct: 135 KYSQLVDLRSRYDGLTLLAYNAGVCPGGSIWCISTYSEKLVYAKRWNHTRDNILNAASIL 194
Query: 167 ---GTVLESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRV 223
G L + +RP+ +IT +QP +++ ++F+D + K L + G+V++PVD +G+
Sbjct: 195 DATGKPLSTLMRPSAIITTLDRFGSSQPFKKRSKIFKDTLKKGLSSDGSVIIPVDMSGKF 254
Query: 224 LELL-----LILEDYWAEHSLNYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDN 278
L+L L+ E P+ L+Y T+ Y KS LEW+ S+ K++E +R+N
Sbjct: 255 LDLFTQVHELLFESTKINAHTQVPVLILSYARGRTLTYAKSMLEWLSPSLLKTWE-NRNN 313
Query: 279 A--FLLKHVTLLINKSELDNAPDGPKLVLASMA------------------------SLE 312
F + +I +EL P G K+ S S E
Sbjct: 314 TSPFEIGSRIKIIAPNELSKYP-GSKICFVSEVGALINEVIIKVGNSEKTTLILTKPSFE 372
Query: 313 AGFSHDIFVEWA-SDVKNLVLFTERGQFGTLARMLQADPPPKAVKVTMSRRVPLVGEELI 371
S D +E D +N F E G+ + D + PL EE
Sbjct: 373 CASSLDKILEIVEQDERNWKTFPEDGKSFLCDNYISID---------TIKEEPLSKEETE 423
Query: 372 AYEEEQTRLKKEEALKASLVKEEESKASLGPD--NNLSGDPMVIDXXXXXXSADVVEP-- 427
A++ + K++ K LVK E K + G ++ +G+ + + + + V P
Sbjct: 424 AFKVQLKEKKRDRNKKILLVKRESKKLANGNAIIDDTNGERAMRNQDILVENVNGVPPID 483
Query: 428 --HGG---------------------------RYRDILIDGFVPPS-TSVAPMFPFYENN 457
GG + ++ +D + PS S MFPF
Sbjct: 484 HIMGGDEDDDEEEENDNLLNLLKDNSEKSAAKKNTEVPVDIIIQPSAASKHKMFPFNPAK 543
Query: 458 SEWDDFGEVIN-----PDD-----------------------------------YIIKDE 477
+ DD+G V++ PDD Y + D
Sbjct: 544 IKKDDYGTVVDFTMFLPDDSDNVNQNSRKRPLKDGAKTTSPVNEEDNKNEEEDGYNMSDP 603
Query: 478 DMDQAAMHIGGDDGKLDEGSAS-------LILDAKPSKVVSNELTVQVKCLLIFIDYEGR 530
++ G G A L +D SK + + VQ+KC ++ ++ +
Sbjct: 604 ISKRSKHRASRYSGFSGTGEAENFDNLDYLKIDKTLSKRTISTVNVQLKCSVVILNLQSL 663
Query: 531 ADGRSIKTILSHVAPLKLVLVHGSAEATEHLKQHCLKHVCPHVYTP 576
D RS I + K+VL E + +K V P
Sbjct: 664 VDQRSASIIWPSLKSRKIVLSAPKQIQNEEITAKLIKKNIEVVNMP 709
>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 = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 100/402 (24%), Positives = 169/402 (42%), Gaps = 54/402 (13%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCGWN-----------DHFDPSLLQPLSKVAS 53
+++T L G + LV D L+D G N HFD Q + +
Sbjct: 189 IRITGLGGFREVGRSALLVQTDESFVLVDFGVNVAMLNDPYKAFPHFDAPEFQYVLR-EG 247
Query: 54 TIDAVLLSHPDTLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYD------------Q 101
+DA++++H H G LPY + P+++T P L +L D
Sbjct: 248 LLDAIIITHAHLDHCGMLPYLFRYNLFDGPIYTTPPTRDLMVLLQKDFIEIQQSNGQDPL 307
Query: 102 YLSR--RSVTRLTYSQNY-HLSGKGEGIVVAPHVAGHLLGGTV--WKITKDGEDVIYAVD 156
Y R + V + T + +Y + I + H AGH+LG + I ++ D
Sbjct: 308 YRPRDIKEVIKHTITLDYGEVRDISPDIRLTLHNAGHILGSAIVHLHIGNGLHNIAITGD 367
Query: 157 YNRRKEKHLNGTVLE----SFVRPAVLITDAYNALHN--QPPRQQRE-MFQDAISKTLRA 209
+ K + +LE F R L+ ++ N Q PR++ E + I T++
Sbjct: 368 F-----KFIPTRLLEPANAKFPRLETLVMESTYGGANDIQMPREEAEKRLIEVIHNTIKR 422
Query: 210 GGNVLLPVDSAGRVLELLLILEDYWAEHSLNYPIYFLTYVSSSTIDYVKSFLEWMGDSIT 269
GG VL+P + GR E++++LE+Y + PIY + +T + ++ E++ +
Sbjct: 423 GGKVLIPAMAVGRAQEVMMVLEEYARIGGIEVPIYLDGMIWEATAIHT-AYPEYLSRRLR 481
Query: 270 KSFETSRDNAFLLKHVTLLINKSELDNAPDG--PKLVLASMASLEAGFSHDIFVEWASDV 327
+ N FL + + N E + D P +++AS L G S + F + A D
Sbjct: 482 EQIFKEGYNPFLSEIFHPVANSRERQDIIDSNEPAIIIASSGMLVGGPSVEYFKQLAPDP 541
Query: 328 KNLVLFTERGQFGTLARMLQADPPPKAVKVTMSRRVPLVGEE 369
KN ++F GTL R +Q+ R +P+VGEE
Sbjct: 542 KNSIIFVSYQAEGTLGRQVQSG----------IREIPMVGEE 573
>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 = 84.3 bits (207), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 90/371 (24%), Positives = 157/371 (42%), Gaps = 32/371 (8%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCGWN----DHFDPSLLQPLSKVASTIDAVLL 60
V+VT L G +L+S LIDCG N ++ P L P + IDAV++
Sbjct: 184 VRVTALGGCKEVGRSCFLLSTPESRILIDCGVNVGSDENMTPYLYVPEVFPLNQIDAVIV 243
Query: 61 SHPDTLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQY-LSRRSVTRLTYSQNY-- 117
+H H G +P K G PV+ T P L +L D ++ + ++ Y
Sbjct: 244 THAHLDHQGLVPLLFK-YGYEGPVYCTPPTRDLMVLLQLDYIDVAAKEGKKIPYESGMVA 302
Query: 118 ------------HLSGKGEGIVVAPHVAGHLLGGTV--WKITKDGEDVIYAVDYNRRKEK 163
++ I + H AGH+LG + + I +V++ DY K +
Sbjct: 303 KTLKHTIPLDYEEVTDIAPDIKLTFHNAGHILGSAISHFHIGDGLHNVVFTGDYKYEKTR 362
Query: 164 HLNGTVLESFVRPAVLITDAY--NALHNQPPRQQREM-FQDAISKTLRAGGNVLLPVDSA 220
+ V F R +I++A NA QP + E Q + T+ GG ++P +
Sbjct: 363 LFDPAV-NKFPRVETVISEATYGNANAFQPALKDAEKHLQMVVKNTIERGGIAVIPAFAV 421
Query: 221 GRVLELLLILEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNA 279
GR E++++LE+ + + P+Y + +T + + E++ + + K N
Sbjct: 422 GRSQEVMIVLEESIRKGLIPEVPVYLDGMIWEATAIHA-THPEYLNNDLRKLIFQKGQNP 480
Query: 280 FL---LKHVTLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTER 336
FL K V + ++ P P ++LA+ + G + F +A D +N ++F
Sbjct: 481 FLSECFKPVDSHEARQKIIQNPQ-PCVILATSGMMNGGPVMEYFKAFAEDPRNTLVFVGY 539
Query: 337 GQFGTLARMLQ 347
GT+ R +Q
Sbjct: 540 QADGTIGRRIQ 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 = 78.2 bits (191), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 90/358 (25%), Positives = 148/358 (41%), Gaps = 58/358 (16%)
Query: 31 LIDCGWN-----DHFDPSLLQPLSKVASTIDAVLLSHPDTLHLGALPYAMKQLGLSAPVF 85
L+DCG N D L ++DAV+++H H G LPY + G PV+
Sbjct: 206 LLDCGVNVAGGDDKNSYPYLNVPEFTLDSLDAVIITHAHLDHSGFLPY-LYHYGYDGPVY 264
Query: 86 STEPVYRLGLLTMYDQY-LSRR-------SVTRLTYSQNYHLS-GKGEGIVVAP------ 130
T P L L D ++ R +V + S + ++ GE +AP
Sbjct: 265 CTAPTRDLMTLLQLDHIDIAHREDEPLPFNVKHVKKSVKHTITLDYGEVTDIAPDIRLTL 324
Query: 131 HVAGHLLGGTVWKI-TKDGE-DVIYAVDYNRRKEKHLNGTVLESFVRPAVLITDAYNALH 188
H AGH+LG + + DG+ +++Y D+ + + L F R L+ ++ H
Sbjct: 325 HNAGHILGSAMAHLHIGDGQHNMVYTGDFKYEQSRLLEAAA-NRFPRIETLVMESTYGGH 383
Query: 189 N--QPPRQQREM-FQDAISKTLRAGGNVLLPVDSAGRVLELLLILEDYWAEHSLNYPIYF 245
QP R + E I TLR GG +L+PV + GR EL+++LE+
Sbjct: 384 EDVQPSRNRAEKELVKTIYSTLRRGGKILIPVFAVGRAQELMIVLEE------------- 430
Query: 246 LTYVSSSTIDYVKSFLE---WMGDSITKSF-----ETSRDNAFLLKHVTLLINKSELDNA 297
Y+ + ID V +++ W ++I + + RD F + H + + N
Sbjct: 431 --YIRTGIIDEVPVYIDGMIWEANAIHTARPEYLSKDLRDQIFHMGHNPFISDIFHKVNG 488
Query: 298 PD--------GPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARMLQ 347
D P ++L++ L G S + F D N ++F G+L R +Q
Sbjct: 489 MDERREIVEGEPSIILSTSGMLTGGNSLEYFKWLCEDPDNSLVFVGYQAEGSLGRRIQ 546
>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 = 76.3 bits (186), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 95/380 (25%), Positives = 150/380 (39%), Gaps = 32/380 (8%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFST-------EPVYRLGLLTMYDQYLSRRSVTR------ 110
H+G LP ++ G PV++T E V L M + + V
Sbjct: 61 HLDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDALKVMDEPFFGPEDVEEALGHLR 119
Query: 111 -LTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLNGTV 169
L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 120 PLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVLPDPS 175
Query: 170 LESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLELLLI 229
L VL Y ++P R+ F + + KTL GG VL+P + R E+L +
Sbjct: 176 LPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQEILYV 234
Query: 230 LEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL---LKHV 285
L Y H L PIY + ++ + + + + + F + N F L+ V
Sbjct: 235 L--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAGLEVV 291
Query: 286 TLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARM 345
L+ AP GP +VLA L G SD +N ++F G L
Sbjct: 292 EHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAE 350
Query: 346 LQADPPPKAVKVTMSRRVPL 365
+ A PP AV++ + VPL
Sbjct: 351 IIARPP--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 = 76.3 bits (186), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 95/380 (25%), Positives = 150/380 (39%), Gaps = 32/380 (8%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFST-------EPVYRLGLLTMYDQYLSRRSVTR------ 110
H+G LP ++ G PV++T E V L M + + V
Sbjct: 61 HLDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDALKVMDEPFFGPEDVEEALGHLR 119
Query: 111 -LTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLNGTV 169
L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 120 PLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVLPDPS 175
Query: 170 LESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLELLLI 229
L VL Y ++P R+ F + + KTL GG VL+P + R E+L +
Sbjct: 176 LPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQEILYV 234
Query: 230 LEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL---LKHV 285
L Y H L PIY + ++ + + + + + F + N F L+ V
Sbjct: 235 L--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAGLEVV 291
Query: 286 TLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARM 345
L+ AP GP +VLA L G SD +N ++F G L
Sbjct: 292 EHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAE 350
Query: 346 LQADPPPKAVKVTMSRRVPL 365
+ A PP AV++ + VPL
Sbjct: 351 IIARPP--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 = 76.3 bits (186), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 95/380 (25%), Positives = 150/380 (39%), Gaps = 32/380 (8%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFST-------EPVYRLGLLTMYDQYLSRRSVTR------ 110
H+G LP ++ G PV++T E V L M + + V
Sbjct: 61 HLDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDALKVMDEPFFGPEDVEEALGHLR 119
Query: 111 -LTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLNGTV 169
L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 120 PLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVLPDPS 175
Query: 170 LESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLELLLI 229
L VL Y ++P R+ F + + KTL GG VL+P + R E+L +
Sbjct: 176 LPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQEILYV 234
Query: 230 LEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL---LKHV 285
L Y H L PIY + ++ + + + + + F + N F L+ V
Sbjct: 235 L--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAGLEVV 291
Query: 286 TLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARM 345
L+ AP GP +VLA L G SD +N ++F G L
Sbjct: 292 EHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAE 350
Query: 346 LQADPPPKAVKVTMSRRVPL 365
+ A PP AV++ + VPL
Sbjct: 351 IIARPP--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 = 76.3 bits (186), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 95/380 (25%), Positives = 150/380 (39%), Gaps = 32/380 (8%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFST-------EPVYRLGLLTMYDQYLSRRSVTR------ 110
H+G LP ++ G PV++T E V L M + + V
Sbjct: 61 HLDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDALKVMDEPFFGPEDVEEALGHLR 119
Query: 111 -LTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLNGTV 169
L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 120 PLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVLPDPS 175
Query: 170 LESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLELLLI 229
L VL Y ++P R+ F + + KTL GG VL+P + R E+L +
Sbjct: 176 LPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQEILYV 234
Query: 230 LEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL---LKHV 285
L Y H L PIY + ++ + + + + + F + N F L+ V
Sbjct: 235 L--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAGLEVV 291
Query: 286 TLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARM 345
L+ AP GP +VLA L G SD +N ++F G L
Sbjct: 292 EHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAE 350
Query: 346 LQADPPPKAVKVTMSRRVPL 365
+ A PP AV++ + VPL
Sbjct: 351 IIARPP--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 = 76.3 bits (186), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 95/380 (25%), Positives = 150/380 (39%), Gaps = 32/380 (8%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFST-------EPVYRLGLLTMYDQYLSRRSVTR------ 110
H+G LP ++ G PV++T E V L M + + V
Sbjct: 61 ALDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDALKVMDEPFFGPEDVEEALGHLR 119
Query: 111 -LTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLNGTV 169
L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 120 PLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVLPDPS 175
Query: 170 LESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLELLLI 229
L VL Y ++P R+ F + + KTL GG VL+P + R E+L +
Sbjct: 176 LPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQEILYV 234
Query: 230 LEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL---LKHV 285
L Y H L PIY + ++ + + + + + F + N F L+ V
Sbjct: 235 L--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAGLEVV 291
Query: 286 TLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARM 345
L+ AP GP +VLA L G SD +N ++F G L
Sbjct: 292 EHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAE 350
Query: 346 LQADPPPKAVKVTMSRRVPL 365
+ A PP AV++ + VPL
Sbjct: 351 IIARPP--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 = 76.3 bits (186), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 95/380 (25%), Positives = 150/380 (39%), Gaps = 32/380 (8%)
Query: 5 VQVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHP 63
+++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 1 MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHA 60
Query: 64 DTLHLGALPYAMKQLGLSAPVFST-------EPVYRLGLLTMYDQYLSRRSVTR------ 110
H+G LP ++ G PV++T E V L M + + V
Sbjct: 61 HLDHVGRLPKLFRE-GYRGPVYATRATVLLMEIVLEDALKVMDEPFFGPEDVEEALGHLR 119
Query: 111 -LTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLNGTV 169
L Y + L + +A AGHL G +G ++Y+ D R++ L
Sbjct: 120 PLEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVLPDPS 175
Query: 170 LESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLELLLI 229
L VL Y ++P R+ F + + KTL GG VL+P + R E+L +
Sbjct: 176 LPPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQEILYV 234
Query: 230 LEDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL---LKHV 285
L Y H L PIY + ++ + + + + + F + N F L+ V
Sbjct: 235 L--YTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAGLEVV 291
Query: 286 TLLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARM 345
L+ AP GP +VLA L G SD +N ++F G L
Sbjct: 292 EHTEASKALNRAP-GPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAE 350
Query: 346 LQADPPPKAVKVTMSRRVPL 365
+ A PP AV++ + VPL
Sbjct: 351 IIARPP--AVRI-LGEEVPL 367
>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 = 75.5 bits (184), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 93/379 (24%), Positives = 147/379 (38%), Gaps = 32/379 (8%)
Query: 6 QVTPLSGVFNENPLSYLVSIDGFNFLIDCG-WNDHFDPSLLQPLSKVASTIDAVLLSHPD 64
++ P ++L+ G L+DCG + + P +DAVLL+H
Sbjct: 2 RIVPFGAAREVTGSAHLLLAGGRRVLLDCGXFQGKEEARNHAPFGFDPKEVDAVLLTHAH 61
Query: 65 TLHLGALPYAMKQLGLSAPVFSTEPVYRLGLLTMYDQ-------YLSRRSVTR------- 110
H+G LP ++ G PV++T L + + D + V
Sbjct: 62 LDHVGRLPKLFRE-GYRGPVYATRATVLLXEIVLEDALKVXDEPFFGPEDVEEALGHLRP 120
Query: 111 LTYSQNYHLSGKGEGIVVAPHVAGHLLGGTVWKITKDGEDVIYAVDYNRRKEKHLNGTVL 170
L Y + L + +A AGHL G +G ++Y+ D R++ L L
Sbjct: 121 LEYGEWLRLGA----LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVLPDPSL 176
Query: 171 ESFVRPAVLITDAYNALHNQPPRQQREMFQDAISKTLRAGGNVLLPVDSAGRVLELLLIL 230
VL Y ++P R+ F + + KTL GG VL+P + R E+L +L
Sbjct: 177 PPLAD-LVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQEILYVL 235
Query: 231 EDYWAEHSL-NYPIYFLTYVSSSTIDYVKSFLEWMGDSITKSFETSRDNAFL---LKHVT 286
Y H L PIY + + + + + + + F + N F L+ V
Sbjct: 236 --YTHGHRLPRAPIYLDSPXAGRVLSLYPRLVRYFSEEVQAHFLQGK-NPFRPAGLEVVE 292
Query: 287 LLINKSELDNAPDGPKLVLASMASLEAGFSHDIFVEWASDVKNLVLFTERGQFGTLARML 346
L+ AP GP +VLA L G SD +N ++F G L +
Sbjct: 293 HTEASKALNRAP-GPXVVLAGSGXLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAEI 351
Query: 347 QADPPPKAVKVTMSRRVPL 365
A PP AV++ + VPL
Sbjct: 352 IARPP--AVRI-LGEEVPL 367
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/113 (25%), Positives = 53/113 (46%), Gaps = 8/113 (7%)
Query: 20 SYLVSIDGFNFLIDCGWNDHFDPSLLQPLSKVA--STIDAVLLSHPDTLHLGALPYAMKQ 77
+YLV ++G N LID GW ++ + LSK+ I ++++H + H G+LP +K
Sbjct: 54 AYLVKLNGANVLID-GWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDHSGSLPATLKT 112
Query: 78 LGLSAPVFSTEPVYRLGLLTMYDQYLSRRSVTRLTYSQNYHLSGKGEGIVVAP 130
+G + ++ RL + + + VT + + + GK V P
Sbjct: 113 IGHDVEIIASNFGKRL-----LEGFYGIKDVTVVKDGEEREIGGKKFKFVXTP 160
>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 = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/113 (24%), Positives = 54/113 (47%), Gaps = 8/113 (7%)
Query: 20 SYLVSIDGFNFLIDCGWNDHFDPSLLQPLSKVA--STIDAVLLSHPDTLHLGALPYAMKQ 77
+YLV ++G N LID GW ++ + LSK+ I ++++H + + G+LP +K
Sbjct: 54 AYLVKLNGANVLID-GWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDNSGSLPATLKT 112
Query: 78 LGLSAPVFSTEPVYRLGLLTMYDQYLSRRSVTRLTYSQNYHLSGKGEGIVVAP 130
+G + ++ RL + + + VT + + + GK V+ P
Sbjct: 113 IGHDVEIIASNFGKRL-----LEGFYGIKDVTVVKDGEEREIGGKKFKFVMTP 160
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/113 (24%), Positives = 53/113 (46%), Gaps = 8/113 (7%)
Query: 20 SYLVSIDGFNFLIDCGWNDHFDPSLLQPLSKVA--STIDAVLLSHPDTLHLGALPYAMKQ 77
+YLV ++G N LID GW ++ + LSK+ I ++++H + G+LP +K
Sbjct: 54 AYLVKLNGANVLID-GWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDASGSLPATLKT 112
Query: 78 LGLSAPVFSTEPVYRLGLLTMYDQYLSRRSVTRLTYSQNYHLSGKGEGIVVAP 130
+G + ++ RL + + + VT + + + GK V+ P
Sbjct: 113 IGHDVEIIASNFGKRL-----LEGFYGIKDVTVVKDGEEREIGGKKFKFVMTP 160
>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 = 0.44, 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
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 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,284,143
Number of Sequences: 62578
Number of extensions: 960107
Number of successful extensions: 2278
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2234
Number of HSP's gapped (non-prelim): 23
length of query: 721
length of database: 14,973,337
effective HSP length: 106
effective length of query: 615
effective length of database: 8,340,069
effective search space: 5129142435
effective search space used: 5129142435
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: 55 (25.8 bits)