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= 009000
(547 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2E6L|A Chain A, Structure Of Mouse Wrn Exonuclease Domain
pdb|2E6M|A Chain A, Structure Of Mouse Werner Exonuclease Domain
Length = 208
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 50/168 (29%), Positives = 82/168 (48%), Gaps = 15/168 (8%)
Query: 346 VVGIDCEWKPNYVKGCKMNKVSIMQI-ASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSP 404
VVG D EW P Y G K ++V+++Q+ S+ ++F + ++ V L +L++
Sbjct: 42 VVGFDMEWPPIYKPG-KRSRVAVIQLCVSESKCYLFHISSMS-----VFPQGLKMLLENK 95
Query: 405 GILKLGYNFQCDIKQLAHSYG-ELECFKHYEMLLDIQN--VFKEPKGGLSGLAEKILGAG 461
I K G + D +L + +LE F L D+ N + L+GL + +LG
Sbjct: 96 SIKKAGVGIEGDQWKLLRDFDVKLESFVE---LTDVANEKLKCAETWSLNGLVKHVLGKQ 152
Query: 462 L--NKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDV 507
L +K+ R SNW PL+++Q YAA DA L I+ + + V
Sbjct: 153 LLKDKSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQKLGNLGDTVQV 200
>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 = 55.1 bits (131), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 47/160 (29%), Positives = 85/160 (53%), Gaps = 17/160 (10%)
Query: 346 VVGIDCEWKPNYVKGCKMNKVSIMQI-ASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSP 404
VVG D EW P Y +G K+ KV+++Q+ S+ ++F + ++ V L +L++
Sbjct: 47 VVGFDMEWPPLYNRG-KLGKVALIQLCVSESKCYLFHVSSMS-----VFPQGLKMLLENK 100
Query: 405 GILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFKEPK----GGLSGLAEKILGA 460
+ K G + D +L + +++ K++ L D+ N K+ K L+ L + +LG
Sbjct: 101 AVKKAGVGIEGDQWKLLRDF-DIK-LKNFVELTDVAN--KKLKCTETWSLNSLVKHLLGK 156
Query: 461 GL--NKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHV 498
L +K+ R SNW + PL+++Q YAA DA I+ ++
Sbjct: 157 QLLKDKSIRCSNWSKFPLTEDQKLYAATDAYAGFIIYRNL 196
>pdb|1YT3|A Chain A, Crystal Structure Of Escherichia Coli Rnase D, An
Exoribonuclease Involved In Structured Rna Processing
Length = 375
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 35/134 (26%), Positives = 64/134 (47%), Gaps = 15/134 (11%)
Query: 365 KVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSY 424
++ ++Q+ E + + D + + + P L IL+ P I K + D++ + +
Sbjct: 40 QLGLIQLFDGEHLALIDPLGITDWSP------LKAILRDPSITKFLHAGSEDLEVFLNVF 93
Query: 425 GELECFKHYEMLLDIQNVF----KEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQ 480
GEL + L+D Q + + G + + E+ G L+K+ ++W RPL++ Q
Sbjct: 94 GELP-----QPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQ 148
Query: 481 LEYAALDAVVLLQI 494
EYAA D LL I
Sbjct: 149 CEYAAADVWYLLPI 162
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/138 (26%), Positives = 61/138 (44%), Gaps = 13/138 (9%)
Query: 366 VSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYG 425
V +MQI++ E ++ D +KL E++ L + +P I+K+ + DI L G
Sbjct: 125 VCLMQISTRERDYLVDTLKLRENL-----HILNEVFTNPSIVKVFHGAFMDIIWLQRDLG 179
Query: 426 ELECFKHYEMLLDIQNVFKE---PKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLE 482
+ L D + K P+ L+ L E +K + ++W RPLS+
Sbjct: 180 -----LYVVGLFDTYHASKAIGLPRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTA 234
Query: 483 YAALDAVVLLQIFHHVRS 500
A D LL I+ +R+
Sbjct: 235 AARADTHFLLNIYDQLRN 252
>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 = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 37/141 (26%), Positives = 60/141 (42%), Gaps = 25/141 (17%)
Query: 368 IMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGEL 427
+MQI++ FI D ++L D+ +L+ LT P I+K+ + DI+ L +G
Sbjct: 150 LMQISTRTEDFIIDTLELRSDM-YILNESLT----DPAIVKVFHGADSDIEWLQKDFG-- 202
Query: 428 ECFKHYEMLLDIQNVFKEPKGG---------LSGLAEKILGAGLNKTRRNSNWEQRPLSQ 478
L + N+F + L L + NK + ++W RPL +
Sbjct: 203 ---------LYVVNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPE 253
Query: 479 NQLEYAALDAVVLLQIFHHVR 499
L YA D LL I+ +R
Sbjct: 254 EMLSYARDDTHYLLYIYDKMR 274
>pdb|3CYM|A Chain A, Crystal Structure Of Protein Bad_0989 From Bifidobacterium
Adolescentis
Length = 440
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%)
Query: 449 GLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRS 500
GL+ + E LG L K ++W RPL ++ YAALD +L+++ +R+
Sbjct: 134 GLAAVTEHFLGLTLAKEHSAADWSYRPLPRDWRNYAALDVELLIELETKMRA 185
>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 = 35.4 bits (80), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 59/141 (41%), Gaps = 25/141 (17%)
Query: 368 IMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGEL 427
+MQI++ FI D ++L D+ +L+ LT P I+K+ + DI+ L +G
Sbjct: 150 LMQISTRTEDFIIDTLELRSDM-YILNESLT----DPAIVKVFHGADSDIEWLQKDFG-- 202
Query: 428 ECFKHYEMLLDIQNVFKEPKGG---------LSGLAEKILGAGLNKTRRNSNWEQRPLSQ 478
L + N+F + L L + NK + ++W RPL +
Sbjct: 203 ---------LYVVNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPE 253
Query: 479 NQLEYAALDAVVLLQIFHHVR 499
L A D LL I+ +R
Sbjct: 254 EMLSAARDDTHYLLYIYDKMR 274
>pdb|4DLQ|A Chain A, Crystal Structure Of The Gain And Hormr Domains Of Cirl
1LATROPHILIN 1 (Cl1)
Length = 381
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 40/187 (21%), Positives = 80/187 (42%), Gaps = 18/187 (9%)
Query: 65 RKFRALQQQVSQA--LCNSPEP----GPATFIVRCLYVLPIFGVYSEGFSHLI---ISAL 115
R+ R +Q +Q L P P G A+F +CL L ++ S+ ++ +
Sbjct: 27 REVRRVQWPATQQGMLVERPCPKGTRGIASF--QCLPALGLWNPRGPDLSNCTSPWVNQV 84
Query: 116 RRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAITQL 175
+ K+ N+A+ A E+A + I G V KLM ++L+ D +L + +
Sbjct: 85 AQKIKSGENAANI--ASELARHTRGSIYAGDVSSSVKLMEQLLDILDAQLQALRPIERES 142
Query: 176 KAQNEHRFDTAKTVIEQYIFAMIDSQSYMTAVSLLEHFSIRQSGE-----SFLLKMIQNK 230
+N ++ + + YI A++++ + LE + + E + LL +++
Sbjct: 143 AGKNYNKMHKRERTCKDYIKAVVETVDNLLRPEALESWKDMNATEQVHTATMLLDVLEEG 202
Query: 231 EFKAAEK 237
F A+
Sbjct: 203 AFLLADN 209
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
0.322 0.136 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,205,159
Number of Sequences: 62578
Number of extensions: 583755
Number of successful extensions: 1162
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1152
Number of HSP's gapped (non-prelim): 9
length of query: 547
length of database: 14,973,337
effective HSP length: 104
effective length of query: 443
effective length of database: 8,465,225
effective search space: 3750094675
effective search space used: 3750094675
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)