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= psy3926
(512 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2OCH|A Chain A, J-domain Of Dnj-12 From Caenorhabditis Elegans
Length = 73
Score = 58.9 bits (141), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 31/70 (44%), Positives = 42/70 (60%), Gaps = 3/70 (4%)
Query: 247 ADIKDLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLL 306
A +K+ Y +L + D S+ +++ AYRK ALK HPDKNPD E F +S+A EVL
Sbjct: 3 AMVKETGYYDVLGVKPDASDNELKKAYRKMALKFHPDKNPD---GAEQFKQISQAYEVLS 59
Query: 307 DKSARAAYDS 316
D+ R YD
Sbjct: 60 DEKKRQIYDQ 69
>pdb|2CTQ|A Chain A, Solution Structure Of J-Domain From Human Dnaj Subfamily C
Menber 12
Length = 112
Score = 58.9 bits (141), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 44/69 (63%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y LL S + I + ++ +AL+CHPDK+P++ KA+ETF L KA E+L ++ +RA
Sbjct: 21 DYYTLLGCDELSSVEQILAEFKVRALECHPDKHPENPKAVETFQKLQKAKEILTNEESRA 80
Query: 313 AYDSVIRRK 321
YD R +
Sbjct: 81 RYDHWRRSQ 89
>pdb|2DMX|A Chain A, Solution Structure Of The J Domain Of Dnaj Homolog
Subfamily B Member 8
Length = 92
Score = 58.5 bits (140), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 31/64 (48%), Positives = 42/64 (65%), Gaps = 1/64 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIE-TFHLLSKAIEVLLDKSAR 311
+ Y +L + S +DI+ AYRK AL+ HPDKNPD+K+ E F L+S+A EVL D R
Sbjct: 10 NYYEVLGVQASASPEDIKKAYRKLALRWHPDKNPDNKEEAEKKFKLVSEAYEVLSDSKKR 69
Query: 312 AAYD 315
+ YD
Sbjct: 70 SLYD 73
>pdb|2LGW|A Chain A, Solution Structure Of The J Domain Of Hsj1a
Length = 99
Score = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 31/66 (46%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 255 YGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIE-TFHLLSKAIEVLLDKSARAA 313
Y +L++ S DI+ AYR+KAL+ HPDKNPD+K+ E F +++A EVL DK R
Sbjct: 5 YEILDVPRSASADDIKKAYRRKALQWHPDKNPDNKEFAEKKFKEVAEAYEVLSDKHKREI 64
Query: 314 YDSVIR 319
YD R
Sbjct: 65 YDRYGR 70
>pdb|1XBL|A Chain A, Nmr Structure Of The J-Domain (Residues 2-76) In The
Escherichia Coli N-Terminal Fragment (Residues 2-108) Of
The Molecular Chaperone Dnaj, 20 Structures
Length = 107
Score = 56.2 bits (134), Expect = 4e-08, Method: Composition-based stats.
Identities = 28/63 (44%), Positives = 40/63 (63%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ E++IR AY++ A+K HPD+N DK+A F + +A EVL D RA
Sbjct: 4 DYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDSQKRA 63
Query: 313 AYD 315
AYD
Sbjct: 64 AYD 66
>pdb|1BQ0|A Chain A, J-Domain (Residues 1-77) Of The Escherichia Coli
N-Terminal Fragment (Residues 1-104) Of The Molecular
Chaperone Dnaj, Nmr, 20 Structures
Length = 103
Score = 55.8 bits (133), Expect = 5e-08, Method: Composition-based stats.
Identities = 28/63 (44%), Positives = 40/63 (63%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ E++IR AY++ A+K HPD+N DK+A F + +A EVL D RA
Sbjct: 4 DYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDSQKRA 63
Query: 313 AYD 315
AYD
Sbjct: 64 AYD 66
>pdb|2CTW|A Chain A, Solution Structure Of J-Domain From Mouse Dnaj Subfamily C
Menber 5
Length = 109
Score = 55.5 bits (132), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 27/62 (43%), Positives = 39/62 (62%)
Query: 254 LYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARAA 313
LY +L L + + DI+ +YRK ALK HPDKNPD+ +A + F ++ A +L D + R
Sbjct: 19 LYHVLGLDKNATSDDIKKSYRKLALKYHPDKNPDNPEAADKFKEINNAHAILTDATKRNI 78
Query: 314 YD 315
YD
Sbjct: 79 YD 80
>pdb|3APO|A Chain A, Crystal Structure Of Full-Length Erdj5
Length = 780
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/65 (43%), Positives = 41/65 (63%)
Query: 251 DLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSA 310
D + Y LL ++ S ++IR A++K ALK HPDKNP++ A F +++A EVL D+
Sbjct: 20 DQNFYSLLGVSKTASSREIRQAFKKLALKLHPDKNPNNPNAHGDFLKINRAYEVLKDEDL 79
Query: 311 RAAYD 315
R YD
Sbjct: 80 RKKYD 84
>pdb|2EJ7|A Chain A, Solution Structure Of The Dnaj Domain Of The Human Protein
Hcg3, A Hypothetical Protein Tmp_locus_21
Length = 82
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/65 (44%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 252 LDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIE-TFHLLSKAIEVLLDKSA 310
+D Y +L++ S + I+ AYRK ALK HPDKNP++K+ E F +++A EVL D
Sbjct: 9 VDYYEVLDVPRQASSEAIKKAYRKLALKWHPDKNPENKEEAERRFKQVAEAYEVLSDAKK 68
Query: 311 RAAYD 315
R YD
Sbjct: 69 RDIYD 73
>pdb|1BQZ|A Chain A, J-Domain (Residues 1-77) Of The Escherichia Coli
N-Terminal Fragment (Residues 1-78) Of The Molecular
Chaperone Dnaj, Nmr, 20 Structures
Length = 77
Score = 53.5 bits (127), Expect = 2e-07, Method: Composition-based stats.
Identities = 28/63 (44%), Positives = 40/63 (63%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ E++IR AY++ A+K HPD+N DK+A F + +A EVL D RA
Sbjct: 4 DYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDSQKRA 63
Query: 313 AYD 315
AYD
Sbjct: 64 AYD 66
>pdb|2DN9|A Chain A, Solution Structure Of J-Domain From The Dnaj Homolog,
Human Tid1 Protein
Length = 79
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/64 (43%), Positives = 40/64 (62%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L + + S+++I+ AY + A K HPD N DD KA E F L++A EVL D+ R
Sbjct: 8 DYYQILGVPRNASQKEIKKAYYQLAKKYHPDTNKDDPKAKEKFSQLAEAYEVLSDEVKRK 67
Query: 313 AYDS 316
YD+
Sbjct: 68 QYDA 71
>pdb|3APQ|A Chain A, Crystal Structure Of J-Trx1 Fragment Of Erdj5
pdb|3APQ|B Chain B, Crystal Structure Of J-Trx1 Fragment Of Erdj5
Length = 210
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 40/63 (63%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
+ Y LL ++ S ++IR A++K ALK HPDKNP++ A F +++A EVL D+ R
Sbjct: 3 NFYSLLGVSKTASSREIRQAFKKLALKLHPDKNPNNPNAHGDFLKINRAYEVLKDEDLRK 62
Query: 313 AYD 315
YD
Sbjct: 63 KYD 65
>pdb|2O37|A Chain A, J-Domain Of Sis1 Protein, Hsp40 Co-Chaperone From
Saccharomyces Cerevisiae
Length = 92
Score = 52.0 bits (123), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 247 ADIKDLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLL 306
A +K+ LY LL ++ +EQ+++ YRK ALK HPDK D E F +S+A E+L
Sbjct: 3 AMVKETKLYDLLGVSPSANEQELKKGYRKAALKYHPDKPTGD---TEKFKEISEAFEILN 59
Query: 307 DKSARAAYD 315
D R YD
Sbjct: 60 DPQKREIYD 68
>pdb|2LO1|A Chain A, Nmr Structure Of The Protein Bc008182, A Dnaj-Like Domain
From Homo Sapiens
Length = 71
Score = 48.5 bits (114), Expect = 9e-06, Method: Composition-based stats.
Identities = 27/67 (40%), Positives = 42/67 (62%), Gaps = 3/67 (4%)
Query: 249 IKDLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDK 308
+K+ Y +L + + ++++++ AYRK ALK HPDKNP++ E F +S+A EVL D
Sbjct: 3 VKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEG---EKFKQISQAYEVLSDA 59
Query: 309 SARAAYD 315
R YD
Sbjct: 60 KKRELYD 66
>pdb|2CUG|A Chain A, Solution Structure Of The J Domain Of The Pseudo Dnaj
Protein, Mouse Hypothetical Mkiaa0962
Length = 88
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 251 DLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSA 310
D D Y +L ++ S+ DI+ AY+K A + HPDKN D A + F +SKA E+L ++
Sbjct: 16 DFDPYRVLGVSRTASQADIKKAYKKLAREWHPDKNK-DPGAEDRFIQISKAYEILSNEEK 74
Query: 311 RAAYD 315
R YD
Sbjct: 75 RTNYD 79
>pdb|2CTP|A Chain A, Solution Structure Of J-Domain From Human Dnaj Subfamily B
Menber 12
Length = 78
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ S++D++ AYR+ ALK HPDKN A E F + A VL + R
Sbjct: 8 DYYEILGVSRGASDEDLKKAYRRLALKFHPDKN-HAPGATEAFKAIGTAYAVLSNPEKRK 66
Query: 313 AYD 315
YD
Sbjct: 67 QYD 69
>pdb|1HDJ|A Chain A, Human Hsp40 (Hdj-1), Nmr
Length = 77
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y L L S+++I+ AYR++AL+ HPDKN + A E F +++A +VL D R
Sbjct: 4 DYYQTLGLARGASDEEIKRAYRRQALRYHPDKNK-EPGAEEKFKEIAEAYDVLSDPRKRE 62
Query: 313 AYD 315
+D
Sbjct: 63 IFD 65
>pdb|2D9O|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj10634
Length = 100
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 39/59 (66%)
Query: 39 YTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLYELGLPNCPLTLNYL 97
Y+++ L ++ KYG++ LV+S KK G+A++EF +A A E+GL + PL +++L
Sbjct: 29 YSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWL 87
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 39/59 (66%)
Query: 427 YTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLYELGLPNCPLTLNYL 485
Y+++ L ++ KYG++ LV+S KK G+A++EF +A A E+GL + PL +++L
Sbjct: 29 YSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWL 87
>pdb|2YUA|A Chain A, Solution Structure Of The Dnaj Domain From Human Williams-
Beuren Syndrome Chromosome Region 18 Protein
Length = 99
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 38/72 (52%)
Query: 254 LYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARAA 313
LY LL + ++ I++AY ++ HPD+N +A E F +S+A VL + R
Sbjct: 19 LYDLLGVPSTATQAQIKAAYYRQCFLYHPDRNSGSAEAAERFTRISQAYVVLGSATLRRK 78
Query: 314 YDSVIRRKEEVK 325
YD + E+++
Sbjct: 79 YDRGLLSDEDLR 90
>pdb|2CTR|A Chain A, Solution Structure Of J-Domain From Human Dnaj Subfamily B
Menber 9
Length = 88
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 254 LYGLLELTIDCSEQDIRSAYRKKALKCHPDKN--PDDKKAIETFHLLSKAIEVLLDKSAR 311
Y +L + SE+ I+ A+ K A+K HPDKN PD A F +++A E L D + R
Sbjct: 9 YYDILGVPKSASERQIKKAFHKLAMKYHPDKNKSPD---AEAKFREIAEAYETLSDANRR 65
Query: 312 AAYDSV 317
YD++
Sbjct: 66 KEYDTL 71
>pdb|3LZ8|A Chain A, Structure Of A Putative Chaperone Dnaj From Klebsiella
Pneumoniae Subsp. Pneumoniae Mgh 78578 At 2.9 A
Resolution.
pdb|3LZ8|B Chain B, Structure Of A Putative Chaperone Dnaj From Klebsiella
Pneumoniae Subsp. Pneumoniae Mgh 78578 At 2.9 A
Resolution
Length = 329
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L + + I++AYR+ A K HPD + ++ A F L++A EVL D+ RA
Sbjct: 29 DYYAILGVQPTDDLKTIKTAYRRLARKYHPDVSKEN-DAEAKFKDLAEAWEVLKDEQRRA 87
Query: 313 AYDSVIRRK 321
YD + + +
Sbjct: 88 EYDQLWQHR 96
>pdb|2KQX|A Chain A, Nmr Structure Of The J-Domain (Residues 2-72) In The
Escherichia Coli Cbpa
Length = 73
Score = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPD--KNPDDKKAIETFHLLSKAIEVLLDKSA 310
D Y ++ + + I++AYR+ A K HPD K PD A F +++A EVL D+
Sbjct: 6 DYYAIMGVKPTDDLKTIKTAYRRLARKYHPDVSKEPD---AEARFKEVAEAWEVLSDEQR 62
Query: 311 RAAYDSVIRRK 321
RA YD + + +
Sbjct: 63 RAEYDQMWQHR 73
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 23 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 82
Query: 97 LNPD 100
D
Sbjct: 83 AKTD 86
Score = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 23 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 82
Query: 485 LNPD 488
D
Sbjct: 83 AKTD 86
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 27 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 86
Query: 97 LNPD 100
D
Sbjct: 87 AKTD 90
Score = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 27 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 86
Query: 485 LNPD 488
D
Sbjct: 87 AKTD 90
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 26 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 85
Query: 97 LNPD 100
D
Sbjct: 86 AKTD 89
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 26 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 85
Query: 485 LNPD 488
D
Sbjct: 86 AKTD 89
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 33.1 bits (74), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 26 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 85
Query: 97 LNPD 100
D
Sbjct: 86 AKTD 89
Score = 33.1 bits (74), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 26 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 85
Query: 485 LNPD 488
D
Sbjct: 86 AKTD 89
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 33.1 bits (74), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 24 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 83
Query: 97 LNPD 100
D
Sbjct: 84 AKTD 87
Score = 33.1 bits (74), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 24 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 83
Query: 485 LNPD 488
D
Sbjct: 84 AKTD 87
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 33.1 bits (74), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 22 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 81
Query: 97 LNPD 100
D
Sbjct: 82 AKTD 85
Score = 33.1 bits (74), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 22 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 81
Query: 485 LNPD 488
D
Sbjct: 82 AKTD 85
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 33.1 bits (74), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 26 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 85
Query: 97 LNPD 100
D
Sbjct: 86 AKTD 89
Score = 33.1 bits (74), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 26 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 85
Query: 485 LNPD 488
D
Sbjct: 86 AKTD 89
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 33.1 bits (74), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 27 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 86
Query: 97 LNPD 100
D
Sbjct: 87 AKTD 90
Score = 33.1 bits (74), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 27 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 86
Query: 485 LNPD 488
D
Sbjct: 87 AKTD 90
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 33.1 bits (74), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 21 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 80
Query: 97 LNPD 100
D
Sbjct: 81 AKTD 84
Score = 33.1 bits (74), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P+ + Y
Sbjct: 21 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 80
Query: 485 LNPD 488
D
Sbjct: 81 AKTD 84
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 33.1 bits (74), Expect = 0.37, Method: Composition-based stats.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 38 VYTRE-SLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAK 81
+YT E L ++FSKYG I + I S + RG A + FE+ D A+ AK
Sbjct: 56 LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Score = 33.1 bits (74), Expect = 0.37, Method: Composition-based stats.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 426 VYTRE-SLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAK 469
+YT E L ++FSKYG I + I S + RG A + FE+ D A+ AK
Sbjct: 56 LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 32.7 bits (73), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 38 VYTRE-SLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAK 81
+YT E L ++FSKYG I + I S + RG A + FE+ D A+ AK
Sbjct: 25 LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Score = 32.7 bits (73), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 426 VYTRE-SLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAK 469
+YT E L ++FSKYG I + I S + RG A + FE+ D A+ AK
Sbjct: 25 LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 38 VYTRE-SLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAK 81
+YT E L ++FSKYG I + I S + RG A + FE+ D A+ AK
Sbjct: 25 LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Score = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 426 VYTRE-SLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAK 469
+YT E L ++FSKYG I + I S + RG A + FE+ D A+ AK
Sbjct: 25 LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
>pdb|2Z1A|A Chain A, Crystal Structure Of 5'-Nucleotidase Precursor From
Thermus Thermophilus Hb8
Length = 552
Score = 32.7 bits (73), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 254 LYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKS-ARA 312
+ GLLE+T D + + AY+ +AL P+ P+D A E ++ + L+ + A A
Sbjct: 280 VVGLLEVTFDAKGELL--AYKGEALLMTPEAAPEDFFAKEALLAYAQPVMALMQQVIAEA 337
Query: 313 AYD-----SVIRRKE 322
D +V+RR+E
Sbjct: 338 KVDLVGERAVVRRRE 352
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 32.7 bits (73), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 38 VYTRE-SLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAK 81
+YT E L ++FSKYG I + I S + RG A + FE+ D A+ AK
Sbjct: 22 LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Score = 32.7 bits (73), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 426 VYTRE-SLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAK 469
+YT E L ++FSKYG I + I S + RG A + FE+ D A+ AK
Sbjct: 22 LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
>pdb|2QSA|A Chain A, Crystal Structure Of J-Domain Of Dnaj Homolog Dnj-2
Precursor From C.Elegans
Length = 109
Score = 32.3 bits (72), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 37/77 (48%), Gaps = 11/77 (14%)
Query: 253 DLYGLLELTIDCSE--------QDIRSAYRKKALKCHPD--KNPDDK-KAIETFHLLSKA 301
+LY LE D E Q + AYR A K HPD KN ++K A E F +++ A
Sbjct: 9 ELYCGLENCYDVLEVNREEFDKQKLAKAYRALARKHHPDRVKNKEEKLLAEERFRVIATA 68
Query: 302 IEVLLDKSARAAYDSVI 318
E L D A+ YD +
Sbjct: 69 YETLKDDEAKTNYDYYL 85
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 32.3 bits (72), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P + Y
Sbjct: 26 KKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQY 85
Query: 97 LNPD 100
D
Sbjct: 86 AKTD 89
Score = 32.3 bits (72), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P + Y
Sbjct: 26 KKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQY 85
Query: 485 LNPD 488
D
Sbjct: 86 AKTD 89
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 32.3 bits (72), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P + Y
Sbjct: 27 KKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQY 86
Query: 97 LNPD 100
D
Sbjct: 87 AKTD 90
Score = 32.3 bits (72), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P + Y
Sbjct: 27 KKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQY 86
Query: 485 LNPD 488
D
Sbjct: 87 AKTD 90
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 32.0 bits (71), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P + Y
Sbjct: 24 KKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQY 83
Query: 97 LNPD 100
D
Sbjct: 84 AKTD 87
Score = 32.0 bits (71), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +ILV S K RG A + F+ SA A G P + P + Y
Sbjct: 24 KKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQY 83
Query: 485 LNPD 488
D
Sbjct: 84 AKTD 87
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 32.0 bits (71), Expect = 0.89, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 29/46 (63%), Gaps = 5/46 (10%)
Query: 42 ESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAKL 82
+SL ++FSKYG+I+ +V+ + + RG + FE+ D A+ A +
Sbjct: 27 QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Score = 32.0 bits (71), Expect = 0.89, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 29/46 (63%), Gaps = 5/46 (10%)
Query: 430 ESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAKL 470
+SL ++FSKYG+I+ +V+ + + RG + FE+ D A+ A +
Sbjct: 27 QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 6/47 (12%)
Query: 40 TRESLTKIFSKYGKINILVISPKK------RGSALLEFEHADSARRA 80
T++ + +IFS YGKI ++ + ++ +G A +EFE+ D A +A
Sbjct: 17 TKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Score = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 6/47 (12%)
Query: 428 TRESLTKIFSKYGKINILVISPKK------RGSALLEFEHADSARRA 468
T++ + +IFS YGKI ++ + ++ +G A +EFE+ D A +A
Sbjct: 17 TKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
>pdb|1WEX|A Chain A, Solution Structure Of Rrm Domain In Protein Bab28521
Length = 104
Score = 30.8 bits (68), Expect = 1.8, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 44 LTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLYELGLP 88
L + K+G I +++ P KR AL+EFE+ DSA+ + +P
Sbjct: 32 LVEALEKFGTICYVMMMPFKR-QALVEFENIDSAKECVTFAADVP 75
Score = 30.8 bits (68), Expect = 1.8, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 432 LTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLYELGLP 476
L + K+G I +++ P KR AL+EFE+ DSA+ + +P
Sbjct: 32 LVEALEKFGTICYVMMMPFKR-QALVEFENIDSAKECVTFAADVP 75
>pdb|2Y4U|A Chain A, Crystal Structure Of Human P58(Ipk) In Space Group P312
Length = 450
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPD---DKKAIETFHLLSKAIEVLLDKS 309
D Y +L + + +Q+I AYRK AL+ HPD + KKA + F ++ A EVL D
Sbjct: 383 DYYKILGVKRNAKKQEIIKAYRKLALQWHPDNFQNEEEKKKAEKKFIDIAAAKEVLSDPE 442
Query: 310 ARAAYD 315
R +D
Sbjct: 443 XRKKFD 448
>pdb|2Y4T|A Chain A, Crystal Structure Of The Human Co-Chaperone P58(Ipk)
pdb|2Y4T|B Chain B, Crystal Structure Of The Human Co-Chaperone P58(Ipk)
pdb|2Y4T|C Chain C, Crystal Structure Of The Human Co-Chaperone P58(Ipk)
Length = 450
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPD---DKKAIETFHLLSKAIEVLLDKS 309
D Y +L + + +Q+I AYRK AL+ HPD + KKA + F ++ A EVL D
Sbjct: 383 DYYKILGVKRNAKKQEIIKAYRKLALQWHPDNFQNEEEKKKAEKKFIDIAAAKEVLSDPE 442
Query: 310 ARAAYD 315
R +D
Sbjct: 443 MRKKFD 448
>pdb|1IUR|A Chain A, Dnaj Domain Of Human Kiaa0730 Protein
Length = 88
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 11/80 (13%)
Query: 240 IPLSSIMADIKDLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKK-AIETFHLL 298
+P SI+ ++ ++E E + + R+ LK HPDKNP++ A E F L
Sbjct: 9 VPRGSILKEVT-----SVVEQAWKLPESERKKIIRRLYLKWHPDKNPENHDIANEVFKHL 63
Query: 299 SKAI-----EVLLDKSARAA 313
I + LD++A A
Sbjct: 64 QNEINRLEKQAFLDQNADRA 83
>pdb|2L6L|A Chain A, Solution Structure Of Human J-Protein Co-Chaperone, Dph4
Length = 155
Score = 28.9 bits (63), Expect = 6.5, Method: Composition-based stats.
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDD------KKAIETFHLLSKAIEVLL 306
D Y +L + D++ Y+K L HPDK D ++ ++ F + +A ++L
Sbjct: 11 DWYSILGADPSANISDLKQKYQKLILMYHPDKQSTDVPAGTVEECVQKFIEIDQAWKILG 70
Query: 307 DKSARAAYD 315
++ + YD
Sbjct: 71 NEETKREYD 79
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
0.311 0.130 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,227,442
Number of Sequences: 62578
Number of extensions: 569323
Number of successful extensions: 1962
Number of sequences better than 100.0: 85
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 58
Number of HSP's that attempted gapping in prelim test: 1892
Number of HSP's gapped (non-prelim): 112
length of query: 512
length of database: 14,973,337
effective HSP length: 103
effective length of query: 409
effective length of database: 8,527,803
effective search space: 3487871427
effective search space used: 3487871427
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (25.4 bits)