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= 039453
(202 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 = 1e-34, Method: Compositional matrix adjust.
Identities = 74/195 (37%), Positives = 114/195 (58%), Gaps = 7/195 (3%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITH 67
LGAGQEVG+SC+++ G++IM DCG+H P I + ID ++I+H
Sbjct: 17 LGAGQEVGRSCIILEFKGRKIMLDCGIHPGLEGMDALPYIDLIDPA-----EIDLLLISH 71
Query: 68 FHLDHIGALPFFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQFTSDHIAE 127
FHLDH GALP+F + + G +MT+ T+A+ +L DY KV + + +T + E
Sbjct: 72 FHLDHCGALPWFLQKTSFKGRTFMTHATKAIYRWLLSDYVKV-SNISADDMLYTETDLEE 130
Query: 128 CMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDSAMVYTGDYNMTPDRHLG 187
M K+ ++ + +V ++ Y+AGHVLGAAMF ++ ++YTGD++ DRHL
Sbjct: 131 SMDKIETINFHEVKEV-AGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLM 189
Query: 188 AARIDRLQLDLLITE 202
AA I ++ D+LI E
Sbjct: 190 AAEIPNIKPDILIIE 204
>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 = 114 bits (285), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 66/198 (33%), Positives = 109/198 (55%), Gaps = 8/198 (4%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQ-YPDFSRISKSCDFNNAIDCIVIT 66
+G +EVG+SC+ + R++ DCG+++A D + YP + + D ++D ++IT
Sbjct: 185 MGGFREVGRSCLYLQTPNSRVLLDCGVNVAGGDDKNSYPYLNVPEFTLD---SLDAVIIT 241
Query: 67 HFHLDHIGALPFFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQFTSDHIA 126
H HLDH G LP+ GY+GP+Y T PTR L ++ D+ + R E F H+
Sbjct: 242 HAHLDHSGFLPYLYH-YGYDGPVYCTAPTRDLMTLLQLDHIDI-AHREDEPLPFNVKHVK 299
Query: 127 ECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDSA--MVYTGDYNMTPDR 184
+ +K I +D + + D+++ + AGH+LG+AM + +GD MVYTGD+ R
Sbjct: 300 KSVKHTITLDYGEVTDIAPDIRLTLHNAGHILGSAMAHLHIGDGQHNMVYTGDFKYEQSR 359
Query: 185 HLGAARIDRLQLDLLITE 202
L AA +++ L+ E
Sbjct: 360 LLEAAANRFPRIETLVME 377
>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 = 103 bits (257), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 62/197 (31%), Positives = 109/197 (55%), Gaps = 7/197 (3%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITH 67
LG +EVG+SC +++ RI+ DCG+++ +D P + + + N ID +++TH
Sbjct: 189 LGGCKEVGRSCFLLSTPESRILIDCGVNVG-SDENMTP-YLYVPEVFPLNQ-IDAVIVTH 245
Query: 68 FHLDHIGALPFFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQFTSDHIAE 127
HLDH G +P + GY GP+Y T PTR L ++ DY V + G+ + S +A+
Sbjct: 246 AHLDHQGLVPLLFKY-GYEGPVYCTPPTRDLMVLLQLDYIDVAA-KEGKKIPYESGMVAK 303
Query: 128 CMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDS--AMVYTGDYNMTPDRH 185
+K I +D ++ + D+++ + AGH+LG+A+ + +GD +V+TGDY R
Sbjct: 304 TLKHTIPLDYEEVTDIAPDIKLTFHNAGHILGSAISHFHIGDGLHNVVFTGDYKYEKTRL 363
Query: 186 LGAARIDRLQLDLLITE 202
A +++ +I+E
Sbjct: 364 FDPAVNKFPRVETVISE 380
>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 = 100 bits (249), Expect = 5e-22, Method: Composition-based stats.
Identities = 61/204 (29%), Positives = 106/204 (51%), Gaps = 14/204 (6%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAY-ND------HRQYPDFSRISKSCDFNNAI 60
LG +EVG+S ++V + ++ D G+++A ND H P+F + + +
Sbjct: 194 LGGFREVGRSALLVQTDESFVLVDFGVNVAMLNDPYKAFPHFDAPEFQYVLRE----GLL 249
Query: 61 DCIVITHFHLDHIGALPFFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQF 120
D I+ITH HLDH G LP+ ++GPIY T PTR L ++ +D+ ++ G+ +
Sbjct: 250 DAIIITHAHLDHCGMLPYLFRYNLFDGPIYTTPPTRDLMVLLQKDFIEIQ-QSNGQDPLY 308
Query: 121 TSDHIAECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDSA--MVYTGDY 178
I E +K I +D + + D+++ + AGH+LG+A+ + +G+ + TGD+
Sbjct: 309 RPRDIKEVIKHTITLDYGEVRDISPDIRLTLHNAGHILGSAIVHLHIGNGLHNIAITGDF 368
Query: 179 NMTPDRHLGAARIDRLQLDLLITE 202
P R L A +L+ L+ E
Sbjct: 369 KFIPTRLLEPANAKFPRLETLVME 392
>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 = 83.2 bits (204), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 53/171 (30%), Positives = 86/171 (50%), Gaps = 15/171 (8%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITH 67
GA +EV S ++ G+R++ DCGM + R + F K +D +++TH
Sbjct: 6 FGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKE------VDAVLLTH 59
Query: 68 FHLDHIGALP-FFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQFTSDHIA 126
HLDH+G LP F E GY GP+Y T T L I+LED KV+ + F + +
Sbjct: 60 AHLDHVGRLPKLFRE--GYRGPVYATRATVLLMEIVLEDALKVMDE-----PFFGPEDVE 112
Query: 127 ECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDSAMVYTGD 177
E + + ++ + +++ L + AGH+ G+A A+ +VY+GD
Sbjct: 113 EALGHLRPLEYGEWLRLGA-LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGD 162
>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 = 83.2 bits (204), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 53/171 (30%), Positives = 86/171 (50%), Gaps = 15/171 (8%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITH 67
GA +EV S ++ G+R++ DCGM + R + F K +D +++TH
Sbjct: 6 FGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKE------VDAVLLTH 59
Query: 68 FHLDHIGALP-FFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQFTSDHIA 126
HLDH+G LP F E GY GP+Y T T L I+LED KV+ + F + +
Sbjct: 60 AHLDHVGRLPKLFRE--GYRGPVYATRATVLLMEIVLEDALKVMDE-----PFFGPEDVE 112
Query: 127 ECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDSAMVYTGD 177
E + + ++ + +++ L + AGH+ G+A A+ +VY+GD
Sbjct: 113 EALGHLRPLEYGEWLRLGA-LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGD 162
>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 = 83.2 bits (204), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 53/171 (30%), Positives = 86/171 (50%), Gaps = 15/171 (8%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITH 67
GA +EV S ++ G+R++ DCGM + R + F K +D +++TH
Sbjct: 6 FGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKE------VDAVLLTH 59
Query: 68 FHLDHIGALP-FFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQFTSDHIA 126
HLDH+G LP F E GY GP+Y T T L I+LED KV+ + F + +
Sbjct: 60 AHLDHVGRLPKLFRE--GYRGPVYATRATVLLMEIVLEDALKVMDE-----PFFGPEDVE 112
Query: 127 ECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDSAMVYTGD 177
E + + ++ + +++ L + AGH+ G+A A+ +VY+GD
Sbjct: 113 EALGHLRPLEYGEWLRLGA-LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGD 162
>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 = 83.2 bits (204), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 53/171 (30%), Positives = 86/171 (50%), Gaps = 15/171 (8%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITH 67
GA +EV S ++ G+R++ DCGM + R + F K +D +++TH
Sbjct: 6 FGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKE------VDAVLLTH 59
Query: 68 FHLDHIGALP-FFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQFTSDHIA 126
HLDH+G LP F E GY GP+Y T T L I+LED KV+ + F + +
Sbjct: 60 AHLDHVGRLPKLFRE--GYRGPVYATRATVLLMEIVLEDALKVMDE-----PFFGPEDVE 112
Query: 127 ECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDSAMVYTGD 177
E + + ++ + +++ L + AGH+ G+A A+ +VY+GD
Sbjct: 113 EALGHLRPLEYGEWLRLGA-LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGD 162
>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 = 83.2 bits (204), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 53/171 (30%), Positives = 86/171 (50%), Gaps = 15/171 (8%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITH 67
GA +EV S ++ G+R++ DCGM + R + F K +D +++TH
Sbjct: 6 FGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKE------VDAVLLTH 59
Query: 68 FHLDHIGALP-FFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQFTSDHIA 126
HLDH+G LP F E GY GP+Y T T L I+LED KV+ + F + +
Sbjct: 60 AHLDHVGRLPKLFRE--GYRGPVYATRATVLLMEIVLEDALKVMDE-----PFFGPEDVE 112
Query: 127 ECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDSAMVYTGD 177
E + + ++ + +++ L + AGH+ G+A A+ +VY+GD
Sbjct: 113 EALGHLRPLEYGEWLRLGA-LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGD 162
>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 = 80.1 bits (196), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 52/171 (30%), Positives = 84/171 (49%), Gaps = 15/171 (8%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITH 67
GA +EV S ++ G+R++ DCG + R + F K +D +++TH
Sbjct: 6 FGAAREVTGSAHLLLAGGRRVLLDCGXFQGKEEARNHAPFGFDPKE------VDAVLLTH 59
Query: 68 FHLDHIGALP-FFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQFTSDHIA 126
HLDH+G LP F E GY GP+Y T T L I+LED KV + F + +
Sbjct: 60 AHLDHVGRLPKLFRE--GYRGPVYATRATVLLXEIVLEDALKVXDE-----PFFGPEDVE 112
Query: 127 ECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDSAMVYTGD 177
E + + ++ + +++ L + AGH+ G+A A+ +VY+GD
Sbjct: 113 EALGHLRPLEYGEWLRLGA-LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGD 162
>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 = 79.3 bits (194), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 52/171 (30%), Positives = 85/171 (49%), Gaps = 15/171 (8%)
Query: 8 LGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITH 67
GA +EV S ++ G+R++ DCGM + R + F K +D +++TH
Sbjct: 6 FGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKE------VDAVLLTH 59
Query: 68 FHLDHIGALP-FFTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEVEQFTSDHIA 126
LDH+G LP F E GY GP+Y T T L I+LED KV+ + F + +
Sbjct: 60 AALDHVGRLPKLFRE--GYRGPVYATRATVLLMEIVLEDALKVMDE-----PFFGPEDVE 112
Query: 127 ECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVLGAAMFYAKVGDSAMVYTGD 177
E + + ++ + +++ L + AGH+ G+A A+ +VY+GD
Sbjct: 113 EALGHLRPLEYGEWLRLGA-LSLAFGQAGHLPGSAFVVAQGEGRTLVYSGD 162
>pdb|3BK1|A Chain A, Crystal Structure Analysis Of Rnase J
pdb|3BK2|A Chain A, Crystal Structure Analysis Of The Rnase JUMP COMPLEX
Length = 562
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 45/193 (23%), Positives = 77/193 (39%), Gaps = 38/193 (19%)
Query: 3 IDCLVLGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPD---------FSRISKS 53
++ + LG E+GK+ V + + D G+ +P+ R+
Sbjct: 17 VEIIPLGGXGEIGKNITVFRFRDEIFVLDGGL--------AFPEEGXPGVDLLIPRVDYL 68
Query: 54 CDFNNAIDCIVITHFHLDHIGALPF-FTEICGYNGPIYMTYPTRALAPIMLEDYRKVLVD 112
+ + I V+TH H DHIG LPF I G P+ PI R L
Sbjct: 69 IEHRHKIKAWVLTHGHEDHIGGLPFLLPXIFGKESPV----------PIY--GARLTLGL 116
Query: 113 RRGEVEQFTSDHIAECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVL---GAAMFYAKVGD 169
RG++E+F A +K++ D +QV + + + H + + +G
Sbjct: 117 LRGKLEEFGLRPGAFNLKEISPDD---RIQVGRYFTLDLFRXTHSIPDNSGVVIRTPIG- 172
Query: 170 SAMVYTGDYNMTP 182
+V+TGD+ + P
Sbjct: 173 -TIVHTGDFKLDP 184
>pdb|3T3N|A Chain A, Molecular Basis For The Recognition And Cleavage Of Rna
(Uuccgu) By The Bifunctional 5'-3' ExoENDORIBONUCLEASE
RNASE J
pdb|3T3O|A Chain A, Molecular Basis For The Recognition And Cleavage Of Rna
(Cugg) By The Bifunctional 5'-3' ExoENDORIBONUCLEASE
RNASE J
Length = 562
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 45/188 (23%), Positives = 77/188 (40%), Gaps = 28/188 (14%)
Query: 3 IDCLVLGAGQEVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDF----NN 58
++ + LG E+GK+ V + + D G+ A+ + P + D+ +
Sbjct: 18 VEIIPLGGMGEIGKNITVFRFRDEIFVLDGGL--AFPEE-GMPGVDLLIPRVDYLIEHRH 74
Query: 59 AIDCIVITHFHLDHIGALPFFTE-ICGYNGPIYMTYPTRALAPIMLEDYRKVLVDRRGEV 117
I V+TH DHIG LPF I G P+ PI R L RG++
Sbjct: 75 KIKAWVLTHGAEDHIGGLPFLLPMIFGKESPV----------PIY--GARLTLGLLRGKL 122
Query: 118 EQFTSDHIAECMKKVIAVDLKQTVQVDKDLQIRAYYAGHVL---GAAMFYAKVGDSAMVY 174
E+F A +K++ D +QV + + + H + + +G +V+
Sbjct: 123 EEFGLRPGAFNLKEISPDD---RIQVGRYFTLDLFRMTHSIPDNSGVVIRTPIG--TIVH 177
Query: 175 TGDYNMTP 182
TGD+ + P
Sbjct: 178 TGDFKLDP 185
>pdb|3ZQ4|A Chain A, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|C Chain C, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|D Chain D, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|E Chain E, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
Length = 555
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 42/90 (46%), Gaps = 9/90 (10%)
Query: 5 CLVLGAGQEVGKSCVVVTINGKRIMFDCGMHMAYND----HRQYPDFSRISKSCDFNNAI 60
LG E+GK+ V + ++ D G+ ++ PD++ + K+ D I
Sbjct: 11 VFALGGLGEIGKNTYAVQFQDEIVLIDAGIKFPEDELLGIDYVIPDYTYLVKNED---KI 67
Query: 61 DCIVITHFHLDHIGALPFFTEICGYNGPIY 90
+ ITH H DHIG +P+ + N P+Y
Sbjct: 68 KGLFITHGHEDHIGGIPYL--LRQVNIPVY 95
>pdb|3ZWF|A Chain A, Crystal Structure Of Human Trnase Z, Short Form (Elac1).
pdb|3ZWF|B Chain B, Crystal Structure Of Human Trnase Z, Short Form (Elac1)
Length = 368
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 36/93 (38%), Gaps = 11/93 (11%)
Query: 15 GKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITHFHLDHIG 74
G S VV+ G+ +FDCG + RI+K I ITH H DH
Sbjct: 18 GASAVVLRCEGECWLFDCGEGTQTQLMKSQLKAGRITK----------IFITHLHGDHFF 67
Query: 75 ALP-FFTEICGYNGPIYMTYPTRALAPIMLEDY 106
LP I +G + P P+ L D+
Sbjct: 68 GLPGLLCTISLQSGSMVSKQPIEIYGPVGLRDF 100
>pdb|3ADR|A Chain A, The First Crystal Structure Of An Archaeal
Metallo-Beta-Lactamase Superfamily Protein; St1585 From
Sulfolobus Tokodaii
pdb|3ADR|B Chain B, The First Crystal Structure Of An Archaeal
Metallo-Beta-Lactamase Superfamily Protein; St1585 From
Sulfolobus Tokodaii
Length = 261
Score = 34.3 bits (77), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 56 FNNAIDCIVITHFHLDHIGALPFFTEI 82
F + +D IV+TH H+DHIG LP ++
Sbjct: 47 FLDKLDYIVLTHLHIDHIGLLPELLQV 73
>pdb|4AD9|A Chain A, Crystal Structure Of Human Lactb2.
pdb|4AD9|B Chain B, Crystal Structure Of Human Lactb2.
pdb|4AD9|C Chain C, Crystal Structure Of Human Lactb2.
pdb|4AD9|D Chain D, Crystal Structure Of Human Lactb2.
pdb|4AD9|E Chain E, Crystal Structure Of Human Lactb2.
pdb|4AD9|F Chain F, Crystal Structure Of Human Lactb2
Length = 289
Score = 34.3 bits (77), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 15 GKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRISKSC--DFNNAIDCIVITHFHLDH 72
G + +V +RI+ D G P++ K +FN AI IV+TH+H DH
Sbjct: 31 GTNTYLVGTGPRRILIDTG-------EPAIPEYISCLKQALTEFNTAIQEIVVTHWHRDH 83
Query: 73 IGAL 76
G +
Sbjct: 84 SGGI 87
>pdb|1E5D|A Chain A, Rubredoxin Oxygen:oxidoreductase (Roo) From Anaerobe
Desulfovibrio Gigas
pdb|1E5D|B Chain B, Rubredoxin Oxygen:oxidoreductase (Roo) From Anaerobe
Desulfovibrio Gigas
Length = 402
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/24 (58%), Positives = 15/24 (62%)
Query: 60 IDCIVITHFHLDHIGALPFFTEIC 83
ID +VI H LDH GALP E C
Sbjct: 72 IDYLVIQHLELDHAGALPALIEAC 95
>pdb|1ZTC|A Chain A, Crystal Structure Of A Putative Metallo-Beta-Lactamase
(Tm0894) From Thermotoga Maritima At 2.10 A Resolution
pdb|1ZTC|B Chain B, Crystal Structure Of A Putative Metallo-Beta-Lactamase
(Tm0894) From Thermotoga Maritima At 2.10 A Resolution
pdb|1ZTC|C Chain C, Crystal Structure Of A Putative Metallo-Beta-Lactamase
(Tm0894) From Thermotoga Maritima At 2.10 A Resolution
pdb|1ZTC|D Chain D, Crystal Structure Of A Putative Metallo-Beta-Lactamase
(Tm0894) From Thermotoga Maritima At 2.10 A Resolution
Length = 221
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 39/92 (42%), Gaps = 5/92 (5%)
Query: 26 KRIMFDCGMHMAYNDHRQYPDFSRISKSCDFNNAIDCIVITHFHLDHIGALPFFTEICGY 85
+RI+ D G + ++ + FS + S D I ++ TH HLDHI F Y
Sbjct: 45 RRIIIDPGNLSSXDELEE--KFSELGISPD---DITDVLFTHVHLDHIFNSVLFENATFY 99
Query: 86 NGPIYMTYPTRALAPIMLEDYRKVLVDRRGEV 117
+Y T + I+ Y KV+ + V
Sbjct: 100 VHEVYKTKNYLSFGTIVGRIYSKVISSWKNVV 131
>pdb|2BIB|A Chain A, Crystal Structure Of The Complete Modular Teichioic Acid
Phosphorylcholine Esterase Pce (Cbpe) From
Streptococcus Pneumoniae
Length = 547
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 32/81 (39%), Gaps = 16/81 (19%)
Query: 12 QEVGKSCVVVTINGKRIMFDCGMHMAYND--HRQYPDFSRISKSCD-------FN----- 57
QE G +++ NG M D G + D +YP I S F
Sbjct: 14 QEGGSDAIILESNGHFAMVDTGEDYDFPDGSDSRYPWREGIETSYKHVLTDRVFRRLKEL 73
Query: 58 --NAIDCIVITHFHLDHIGAL 76
+D I++TH H DHIG +
Sbjct: 74 SVQKLDFILVTHTHSDHIGNV 94
>pdb|1P9E|A Chain A, Crystal Structure Analysis Of Methyl Parathion Hydrolase
From Pseudomonas Sp Wbc-3
pdb|1P9E|B Chain B, Crystal Structure Analysis Of Methyl Parathion Hydrolase
From Pseudomonas Sp Wbc-3
Length = 331
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 9/68 (13%)
Query: 13 EVGKSCVVVTINGKRIMFDCGMHMAYNDHRQYPDFSRIS---KSCDFN-NAIDCIVITHF 68
E + +V K ++ D G + P R++ K+ + +D I ITH
Sbjct: 94 ETSVTGYLVNTGSKLVLVDTGAAGLFG-----PTLGRLAANLKAAGYQPEQVDEIYITHM 148
Query: 69 HLDHIGAL 76
H DH+G L
Sbjct: 149 HPDHVGGL 156
>pdb|1YCF|A Chain A, Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica
pdb|1YCF|B Chain B, Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica
pdb|1YCF|C Chain C, Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica
pdb|1YCF|D Chain D, Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica
pdb|1YCG|A Chain A, X-Ray Structures Of Moorella Thermoacetica Fpra. Novel
Diiron Site Structure And Mechanistic Insights Into A
Scavenging Nitric Oxide Reductase
pdb|1YCG|B Chain B, X-Ray Structures Of Moorella Thermoacetica Fpra. Novel
Diiron Site Structure And Mechanistic Insights Into A
Scavenging Nitric Oxide Reductase
pdb|1YCG|C Chain C, X-Ray Structures Of Moorella Thermoacetica Fpra. Novel
Diiron Site Structure And Mechanistic Insights Into A
Scavenging Nitric Oxide Reductase
pdb|1YCG|D Chain D, X-Ray Structures Of Moorella Thermoacetica Fpra. Novel
Diiron Site Structure And Mechanistic Insights Into A
Scavenging Nitric Oxide Reductase
pdb|1YCH|A Chain A, X-Ray Crystal Structures Of Moorella Thermoacetica Fpra.
Novel Diiron Site Structure And Mechanistic Insights
Into A Scavenging Nitric Oxide Reductase
pdb|1YCH|B Chain B, X-Ray Crystal Structures Of Moorella Thermoacetica Fpra.
Novel Diiron Site Structure And Mechanistic Insights
Into A Scavenging Nitric Oxide Reductase
pdb|1YCH|C Chain C, X-Ray Crystal Structures Of Moorella Thermoacetica Fpra.
Novel Diiron Site Structure And Mechanistic Insights
Into A Scavenging Nitric Oxide Reductase
pdb|1YCH|D Chain D, X-Ray Crystal Structures Of Moorella Thermoacetica Fpra.
Novel Diiron Site Structure And Mechanistic Insights
Into A Scavenging Nitric Oxide Reductase
Length = 398
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 60 IDCIVITHFHLDHIGALPFFTEIC 83
+D +V+ H DH GA P E+C
Sbjct: 73 LDYLVVNHTESDHAGAFPAIMELC 96
>pdb|1WRA|A Chain A, Crystal Structure Of Phosphorylcholine Esterase Domain
Of The Virulence Factor Choline Binding Protein E From
Streptococcus Pneumoniae
pdb|1WRA|B Chain B, Crystal Structure Of Phosphorylcholine Esterase Domain
Of The Virulence Factor Choline Binding Protein E From
Streptococcus Pneumoniae
Length = 308
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 32/81 (39%), Gaps = 16/81 (19%)
Query: 12 QEVGKSCVVVTINGKRIMFDCGMHMAYND--HRQYPDFSRISKSCD-------FN----- 57
QE G +++ NG M D G + D +YP I S F
Sbjct: 13 QEGGSDAIILESNGHFAMVDTGEDYDFPDGSDSRYPWREGIETSYKHVLTDRVFRRLKEL 72
Query: 58 --NAIDCIVITHFHLDHIGAL 76
+D I++TH H DHIG +
Sbjct: 73 SVQKLDFILVTHTHSDHIGNV 93
>pdb|2NZE|A Chain A, Structure Of Beta-lactamase Ii From Bacillus Cereus.
R121h, C221s Double Mutant. Space Group P3121.
pdb|2NZE|B Chain B, Structure Of Beta-lactamase Ii From Bacillus Cereus.
R121h, C221s Double Mutant. Space Group P3121
Length = 222
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 56 FNNAIDCIVITHFHLDHIGALPFFTE 81
F + ++ITH H DHIG + E
Sbjct: 70 FQKRVTDVIITHAHADHIGGIKTLKE 95
>pdb|2NXA|A Chain A, Structure Of Zn-Dependent Metallo-Beta-Lactamase From
Bacillus Cereus R121h, C221d Double Mutant
pdb|2NYP|A Chain A, Structure Of Beta-Lactamase Ii From Bacillus Cereus.
R121h, C221d Doble Mutant With Two Zinc Ions
Length = 221
Score = 27.7 bits (60), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 56 FNNAIDCIVITHFHLDHIGALPFFTE 81
F + ++ITH H DHIG + E
Sbjct: 69 FQKRVTDVIITHAHADHIGGIKTLKE 94
>pdb|2NZF|A Chain A, Structure Of Beta-Lactamase Ii From Bacillus Cereus.
R121h, C221s Double Mutant. Space Group C2
Length = 221
Score = 27.7 bits (60), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 56 FNNAIDCIVITHFHLDHIGALPFFTE 81
F + ++ITH H DHIG + E
Sbjct: 69 FQKRVTDVIITHAHADHIGGIKTLKE 94
>pdb|3AJ3|A Chain A, Crystal Structure Of Selenomethionine Substituted
4-Pyridoxolactonase From Mesorhizobium Loti
Length = 274
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 60 IDCIVITHFHLDHIGALPFF 79
ID +V +HFH DH G +F
Sbjct: 89 IDVVVNSHFHFDHCGGNKYF 108
>pdb|3AJ0|A Chain A, Crystal Structure Of 4-Pyridoxolactonase From
Mesorhizobium Loti
Length = 268
Score = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 60 IDCIVITHFHLDHIGALPFF 79
ID +V +HFH DH G +F
Sbjct: 89 IDVVVNSHFHFDHCGGNKYF 108
>pdb|3SC0|A Chain A, Crystal Structure Of Mmachc (1-238), A Human B12
Processing Enzyme, Complexed With Methylcobalamin
Length = 241
Score = 26.6 bits (57), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 96 RALAPIMLEDYRKVLVDRRGEVEQFTSDHIAECMKKVIAVDLK----QTVQVDKDLQIRA 151
RAL P + + ++L D V+Q + H+ + + + ++ V ++ +I A
Sbjct: 64 RALKPFLQSCHLRMLTD---PVDQCVAYHLGRVRESLPELQIEIIADYEVHPNRRPKILA 120
Query: 152 YYAGHVLGAAMFYAK 166
A HV GAA +Y +
Sbjct: 121 QTAAHVAGAAYYYQR 135
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
0.327 0.141 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,103,800
Number of Sequences: 62578
Number of extensions: 241880
Number of successful extensions: 788
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 729
Number of HSP's gapped (non-prelim): 30
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)