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= 002503
(914 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SAF|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAF|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
Length = 428
Score = 194 bits (492), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 117/318 (36%), Positives = 176/318 (55%), Gaps = 28/318 (8%)
Query: 71 EKSSGSHPYELEIT------ALLENPRPEFDFSNVDLDLQRSDSFVWVETKSQLNELANA 124
E+ +HPY+ E+ A+L+ P+P+ + ++ ++ + +L EL
Sbjct: 72 EQDMFAHPYQYELNHFTPADAVLQKPQPQL-YRPIE-----ETPCHFISSLDELVELNEK 125
Query: 125 LSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCK 184
L FAV+ E HS RSFLG T L+QIST ED+++DT+ L ++ IL DP + K
Sbjct: 126 LLNCQEFAVNLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELRSDMYILNESLTDPAIVK 185
Query: 185 VFHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQRED 244
VFHG+D+D+ WLQ+DF +YVVN+FDT +A +L+ + SL +LL+ YC V +NK Q D
Sbjct: 186 VFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLAD 245
Query: 245 WRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQGNENSYCPDDKFNFVLEASRRSNTV 304
WR RPLP EML YA+ D HYLLYI + E+ ++GN + V + RS +
Sbjct: 246 WRIRPLPEEMLSYARDDTHYLLYIYDKMRLEMWERGNGQPV----QLQVVWQ---RSRDI 298
Query: 305 CLQVYTKEIESYPGEAAASSIFFRLLNGQGGVSSISSVTQDLVRRLCAWRDLMARVHDES 364
CL+ + K I + E+ + L Q + +T + L AWRD AR DES
Sbjct: 299 CLKKFIKPI--FTDES-----YLELYRKQKKHLNTQQLTA--FQLLFAWRDKTARREDES 349
Query: 365 LRFVLSDQAIIALANKAP 382
+VL + ++ +A + P
Sbjct: 350 YGYVLPNHMMLKIAEELP 367
>pdb|3SAH|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
pdb|3SAH|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
Length = 428
Score = 192 bits (488), Expect = 7e-49, Method: Compositional matrix adjust.
Identities = 117/318 (36%), Positives = 175/318 (55%), Gaps = 28/318 (8%)
Query: 71 EKSSGSHPYELEIT------ALLENPRPEFDFSNVDLDLQRSDSFVWVETKSQLNELANA 124
E+ +HPY+ E+ A+L+ P+P+ + ++ ++ + +L EL
Sbjct: 72 EQDMFAHPYQYELNHFTPADAVLQKPQPQL-YRPIE-----ETPCHFISSLDELVELNEK 125
Query: 125 LSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCK 184
L FAVD E HS RSFLG T L+QIST ED+++DT+ L ++ IL DP + K
Sbjct: 126 LLNCQEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELRSDMYILNESLTDPAIVK 185
Query: 185 VFHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQRED 244
VFHG+D+D+ WLQ+DF +YVVN+FDT +A +L+ + SL +LL+ YC V +NK Q D
Sbjct: 186 VFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLAD 245
Query: 245 WRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQGNENSYCPDDKFNFVLEASRRSNTV 304
WR RPLP EML A+ D HYLLYI + E+ ++GN + V + RS +
Sbjct: 246 WRIRPLPEEMLSAARDDTHYLLYIYDKMRLEMWERGNGQPV----QLQVVWQ---RSRDI 298
Query: 305 CLQVYTKEIESYPGEAAASSIFFRLLNGQGGVSSISSVTQDLVRRLCAWRDLMARVHDES 364
CL+ + K I + E+ + L Q + +T + L AWRD AR DES
Sbjct: 299 CLKKFIKPI--FTDES-----YLELYRKQKKHLNTQQLTA--FQLLFAWRDKTARREDES 349
Query: 365 LRFVLSDQAIIALANKAP 382
+VL + ++ +A + P
Sbjct: 350 YGYVLPNHMMLKIAEELP 367
>pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain
pdb|2HBK|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn
pdb|2HBL|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Amp
pdb|2HBM|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Ump
Length = 410
Score = 181 bits (459), Expect = 2e-45, Method: Compositional matrix adjust.
Identities = 132/377 (35%), Positives = 175/377 (46%), Gaps = 53/377 (14%)
Query: 48 KPQHNFKRVLADNSYSPFKHANKEKSSG---------------------SHPYELEITAL 86
KPQ FK + ++ PF KEK + HPYE EI
Sbjct: 5 KPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNPSHYPHPYEYEIDHQ 64
Query: 87 LENP-----RPEFDFSNVDLDLQRSDSF-VWVETKSQLNELANALSKEFFFAVDTEQHSL 140
+P R E + D DS +WV+T ++L + L AVD E H
Sbjct: 65 EYSPEILQIREEIPSKSWD------DSVPIWVDTSTELESMLEDLKNTKEIAVDLEHHDY 118
Query: 141 RSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKVFHGSDNDVMWLQRDF 200
RS+ G L+QIST + DYLVDT+ L + + IL F +P + KVFHG+ D++WLQRD
Sbjct: 119 RSYYGIVCLMQISTRERDYLVDTLKLRENLHILNEVFTNPSIVKVFHGAFMDIIWLQRDL 178
Query: 201 HIYVVNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQT 260
+YVV LFDT A + + P+ SLAYLLE + T+K Q DWR RPL M A+
Sbjct: 179 GLYVVGLFDTYHASKAIGLPRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAAARA 238
Query: 261 DAHYLLYIAKCLVAELKQQGNENSYCPDDKFNFVLEASRRSNTVCLQVYTKEIESYPGEA 320
D H+LL I L N +K VL SR + Y+K P
Sbjct: 239 DTHFLLNIYDQL---------RNKLIESNKLAGVLYESRNVAKRRFE-YSKYRPLTPSSE 288
Query: 321 AASSIF----FRLLNGQGGVSSISSVTQDLVRRLCAWRDLMARVHDESLRFVLSDQAIIA 376
S I +++L Q + V LVR L WRDL+AR DES RFV+ +Q + A
Sbjct: 289 VYSPIEKESPWKILMYQYNIPPEREV---LVRELYQWRDLIARRDDESPRFVMPNQLLAA 345
Query: 377 LANKAPANRTDVYTTIA 393
L P TDV ++
Sbjct: 346 LVAYTP---TDVIGVVS 359
>pdb|1YT3|A Chain A, Crystal Structure Of Escherichia Coli Rnase D, An
Exoribonuclease Involved In Structured Rna Processing
Length = 375
Score = 64.3 bits (155), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 49/170 (28%), Positives = 69/170 (40%), Gaps = 2/170 (1%)
Query: 112 VETKSQLNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEIS 171
+ T L L A+ A+DTE R++ LIQ+ + L+D + + D S
Sbjct: 6 ITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITD-WS 64
Query: 172 ILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKPQK-SLAYLLET 230
L+ DP + K H D+ F L DT +P A ++E
Sbjct: 65 PLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEE 124
Query: 231 YCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQG 280
Y GV +K R DW RPL +YA D YLL I L+ E + G
Sbjct: 125 YSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVETEASG 174
>pdb|3CYM|A Chain A, Crystal Structure Of Protein Bad_0989 From Bifidobacterium
Adolescentis
Length = 440
Score = 61.6 bits (148), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 63/245 (25%), Positives = 96/245 (39%), Gaps = 43/245 (17%)
Query: 157 EDYLVDTIALHDEISILQP--FFADPGVCKVFHGSDNDVMWLQRD----------FHIYV 204
ED+LV I +L P A F+ + D +W+ D +
Sbjct: 56 EDWLVQFKRDGAGIGLLDPQALAAAGADWNDFNRAVGDAVWILHDSLQDLPGFDELGMEP 115
Query: 205 VNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHY 264
LFDT A +L + LA + E + G+ K DW RPLP + YA D
Sbjct: 116 QRLFDTEIAARLLGLKRFGLAAVTEHFLGLTLAKEHSAADWSYRPLPRDWRNYAALDVEL 175
Query: 265 LLYIAKCLVAELKQQGNENSYCPDDKFNFVLEASRRSNTVCLQVYTKEIESYPGEAAASS 324
L+ + + AELK+QG ++F++ L+ L +
Sbjct: 176 LIELETKMRAELKRQGKME--WAQEEFDYALKEGLGPRKEHLIPWMH------------- 220
Query: 325 IFFRLLNGQGGVSSISSVTQD-----LVRRLCAWRDLMARVHDESLRFVLSDQAIIALAN 379
VS I+ V +D +VR L RD +AR +D + +LSD +II +A
Sbjct: 221 -----------VSHITEVMRDRQALAIVRALWTRRDELAREYDIAPTLLLSDSSIIEVAK 269
Query: 380 KAPAN 384
+ P N
Sbjct: 270 RKPHN 274
>pdb|3VN3|A Chain A, Fungal Antifreeze Protein Exerts Hyperactivity By
Constructing An Inequable Beta-Helix
pdb|3VN3|B Chain B, Fungal Antifreeze Protein Exerts Hyperactivity By
Constructing An Inequable Beta-Helix
Length = 223
Score = 33.1 bits (74), Expect = 0.69, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 30/55 (54%)
Query: 292 NFVLEASRRSNTVCLQVYTKEIESYPGEAAASSIFFRLLNGQGGVSSISSVTQDL 346
N+V+ AS +TV V T + PG AA+ + F +L+G G S+ S VT L
Sbjct: 13 NYVILASTGVSTVPQSVITGAVGVSPGTAASLTGFSLILSGTGTFSTSSQVTGQL 67
>pdb|2CPR|A Chain A, Solution Structure Of The Hrdc Domain Of Human Exosome
Component 10
Length = 124
Score = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 343 TQDLV--RRLCAWRDLMARVHDESLRFVLSDQAIIALANKAP 382
TQ L + L AWRD AR DES +VL + ++ +A + P
Sbjct: 29 TQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELP 70
>pdb|2FBT|A Chain A, Wrn Exonuclease
pdb|2FBV|A Chain A, Wrn Exonuclease, Mn Complex
pdb|2FBX|A Chain A, Wrn Exonuclease, Mg Complex
pdb|2FBY|A Chain A, Wrn Exonuclease, Eu Complex
pdb|2FC0|A Chain A, Wrn Exonuclease, Mn Dgmp Complex
Length = 205
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 38/137 (27%), Positives = 63/137 (45%), Gaps = 13/137 (9%)
Query: 141 RSFLGFTALIQIS-TEKEDYLVDTIALHDEISILQPFFADPGVCKVFHGSDNDVMWLQRD 199
R LG ALIQ+ +E + YL ++ L+ + V K G + D L RD
Sbjct: 60 RGKLGKVALIQLCVSESKCYLFHVSSMSVFPQGLKMLLENKAVKKAGVGIEGDQWKLLRD 119
Query: 200 FHIYVVNLFDTAKACEVLSKPQK-----SLAYLLETYCG--VATNKFLQREDWRQRPLPA 252
F I + N + +V +K K SL L++ G + +K ++ +W + PL
Sbjct: 120 FDIKLKNFVELT---DVANKKLKCTETWSLNSLVKHLLGKQLLKDKSIRCSNWSKFPLTE 176
Query: 253 EMLQYAQTDAH--YLLY 267
+ YA TDA+ +++Y
Sbjct: 177 DQKLYAATDAYAGFIIY 193
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
0.320 0.134 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,778,804
Number of Sequences: 62578
Number of extensions: 1039696
Number of successful extensions: 2378
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2360
Number of HSP's gapped (non-prelim): 16
length of query: 914
length of database: 14,973,337
effective HSP length: 108
effective length of query: 806
effective length of database: 8,214,913
effective search space: 6621219878
effective search space used: 6621219878
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)