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= psy10677
(317 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 105 bits (262), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 59/167 (35%), Positives = 86/167 (51%), Gaps = 25/167 (14%)
Query: 106 LQGKTKEEIDSFRKEHNITLIGQNIPKPVKTLDETNIPSYILGPMXXXXXXXXXXXXXXX 165
L +T +E++++R+ IT+ G N PKPV E N P+ ++ +
Sbjct: 14 LARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIA-------------- 59
Query: 166 XCGDKESKNWTIPLNFQAKKFISVLQK-----KAEVQSRSVFTYILPALYHILKMPKLEE 220
+N+T P QA+ + L A+ S +Y+LPA+ HI P LE
Sbjct: 60 ------RQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLER 113
Query: 221 GDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQV 267
GDGPI LVLAPTRELAQQ+Q V + + R R++ C+YGG K Q+
Sbjct: 114 GDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQI 160
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 16/28 (57%), Positives = 25/28 (89%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGS 28
MWSATWP+E+++LA++FL D I +N+G+
Sbjct: 226 MWSATWPKEVRQLAEDFLKDYIHINIGA 253
>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I
In Complex With Adp
pdb|3FE2|B Chain B, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I
In Complex With Adp
Length = 242
Score = 105 bits (261), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 58/164 (35%), Positives = 85/164 (51%), Gaps = 25/164 (15%)
Query: 109 KTKEEIDSFRKEHNITLIGQNIPKPVKTLDETNIPSYILGPMXXXXXXXXXXXXXXXXCG 168
+T +E++++R+ IT+ G N PKPV E N P+ ++ +
Sbjct: 3 RTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIA----------------- 45
Query: 169 DKESKNWTIPLNFQAKKFISVLQK-----KAEVQSRSVFTYILPALYHILKMPKLEEGDG 223
+N+T P QA+ + L A+ S +Y+LPA+ HI P LE GDG
Sbjct: 46 ---RQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDG 102
Query: 224 PIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQV 267
PI LVLAPTRELAQQ+Q V + + R R++ C+YGG K Q+
Sbjct: 103 PICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQI 146
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 26/31 (83%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANL 31
MWSATWP+E+++LA++FL D I +N+G+ L
Sbjct: 212 MWSATWPKEVRQLAEDFLKDYIHINIGALEL 242
>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain
pdb|3IUY|B Chain B, Crystal Structure Of Ddx53 Dead-Box Domain
Length = 228
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 31/98 (31%), Positives = 51/98 (52%), Gaps = 8/98 (8%)
Query: 171 ESKNWTIPLNFQAKKFISVLQKKAEVQSRSVFTYILPALYHILKMP-KLEEGDGPIALVL 229
+S+ W P+ Q I V A+ + +Y++P H+ P E+ +GP LVL
Sbjct: 47 QSQAW--PIILQGIDLIVV----AQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVL 100
Query: 230 APTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQV 267
PTRELA ++A S +S ++ C+YGG ++ Q+
Sbjct: 101 TPTRELALHVEAECSKYSYK-GLKSICIYGGRNRNGQI 137
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 1 MWSATWPREIQKLAKEFLSDPI 22
M SATWP +++LA +L DP+
Sbjct: 203 MTSATWPDTVRQLALSYLKDPM 224
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 31/94 (32%), Positives = 43/94 (45%), Gaps = 9/94 (9%)
Query: 177 IPLNFQAKKFISVLQKKAEVQSRSVFTYILPALYHILKMPKLEEGDGPIALVLAPTRELA 236
IPL Q + I + AE S + LP L +L+ P+ ALVL PTRELA
Sbjct: 74 IPLALQGRDIIGL----AETGSGKTGAFALPILNALLETPQR-----LFALVLTPTRELA 124
Query: 237 QQIQAVISIFSRTMRIRHACLYGGTSKMYQVILL 270
QI ++ ++ A + GG M Q + L
Sbjct: 125 FQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL 158
>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSO|B Chain B, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|B Chain B, Crystal Structure Of A Translation Initiation Complex
Length = 395
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/41 (58%), Positives = 29/41 (70%), Gaps = 2/41 (4%)
Query: 223 GPIALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
P AL+LAPTRELA QIQ V+ + M I+ HAC+ GGTS
Sbjct: 90 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACI-GGTS 129
>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation
Initiation Factor 4a From Saccharomyces Cerevisiae-The
Prototype Of The Dead Box Protein Family
Length = 224
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/41 (58%), Positives = 29/41 (70%), Gaps = 2/41 (4%)
Query: 223 GPIALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
P AL+LAPTRELA QIQ V+ + M I+ HAC+ GGTS
Sbjct: 82 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACI-GGTS 121
>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain
Length = 223
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/41 (58%), Positives = 29/41 (70%), Gaps = 2/41 (4%)
Query: 223 GPIALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
P AL+LAPTRELA QIQ V+ + M I+ HAC+ GGTS
Sbjct: 89 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACI-GGTS 128
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/44 (50%), Positives = 26/44 (59%)
Query: 224 PIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQV 267
PI+LVLAPTRELA QI FS R+R +YGG Q+
Sbjct: 102 PISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQI 145
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEKPAKWWDSNNGH 60
M+SAT+P+EIQ LA++FL + I L VG + + NI Q V E +K + D N
Sbjct: 215 MFSATFPKEIQMLARDFLDEYIFLAVGRVG-STSENITQKVVWVEESDKRSFLLDLLNAT 273
Query: 61 YPKSVRFVL 69
S+ V
Sbjct: 274 GKDSLTLVF 282
>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic
Initiation Factor 4a, Eif4a
pdb|2G9N|B Chain B, Structure Of The Dead Domain Of Human Eukaryotic
Initiation Factor 4a, Eif4a
Length = 221
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/48 (52%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTSKMYQVILLRI 272
ALVLAPTRELAQQIQ V+ M HAC+ GGT+ +V L++
Sbjct: 86 ALVLAPTRELAQQIQXVVMALGDYMGASCHACI-GGTNVRAEVQXLQM 132
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/43 (55%), Positives = 28/43 (65%), Gaps = 2/43 (4%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTSKMYQV 267
ALVLAPTRELAQQIQ V+ M HAC+ GGT+ +V
Sbjct: 111 ALVLAPTRELAQQIQKVVMALGDYMGASCHACI-GGTNVRAEV 152
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF 40
+ SAT P ++ ++ K+F+ DPI++ V L I+QF
Sbjct: 219 LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE-GIRQF 257
>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|C Chain C, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|D Chain D, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|F Chain F, Crystal Structure Of The Eif4a-Pdcd4 Complex
Length = 388
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/38 (60%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
ALVLAPTRELAQQIQ V+ M HAC+ GGT+
Sbjct: 85 ALVLAPTRELAQQIQKVVMALGDYMGASCHACI-GGTN 121
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF 40
+ SAT P ++ ++ K+F+ DPI++ V L I+QF
Sbjct: 193 LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE-GIRQF 231
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/41 (56%), Positives = 27/41 (65%), Gaps = 2/41 (4%)
Query: 223 GPIALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
P AL LAPTRELA QIQ V+ + I+ HAC+ GGTS
Sbjct: 89 APQALXLAPTRELALQIQKVVXALAFHXDIKVHACI-GGTS 128
>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation
Initiation Factor 4a-2
Length = 237
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/38 (63%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
ALVLAPTRELAQQIQ VI M HAC+ GGT+
Sbjct: 101 ALVLAPTRELAQQIQKVILALGDYMGATCHACI-GGTN 137
>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWJ|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWK|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWK|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWL|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3MWL|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3NBF|A Chain A, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|B Chain B, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|C Chain C, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|D Chain D, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NEJ|A Chain A, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
pdb|3NEJ|B Chain B, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
Length = 207
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 8/86 (9%)
Query: 177 IPLNFQAKKFISVLQKKAEVQSRSVFTYILPALYHILKMPKLEEGDGPIALVLAPTRELA 236
+PL + K I +A + + LP + P E G P ALVL PTRELA
Sbjct: 32 LPLALEGKDLIG----QARTGTGKTLAFALPIAERL--APSQERGRKPRALVLTPTRELA 85
Query: 237 QQIQAVISIFSRTMRIRHACLYGGTS 262
Q+ + ++ + +++ +YGGT
Sbjct: 86 LQVASELTAVAPHLKV--VAVYGGTG 109
>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1
pdb|2GXS|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXS|B Chain B, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXU|A Chain A, Hera N-Terminal Domain In Complex With Orthophosphate,
Crystal Form 1
Length = 207
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 8/86 (9%)
Query: 177 IPLNFQAKKFISVLQKKAEVQSRSVFTYILPALYHILKMPKLEEGDGPIALVLAPTRELA 236
+PL + K I +A + + LP + P E G P ALVL PTRELA
Sbjct: 32 LPLALEGKDLIG----QARTGTGKTLAFALPIAERL--APSQERGRKPRALVLTPTRELA 85
Query: 237 QQIQAVISIFSRTMRIRHACLYGGTS 262
Q+ + ++ + +++ +YGGT
Sbjct: 86 LQVASELTAVAPHLKV--VAVYGGTG 109
>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|B Chain B, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|C Chain C, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|D Chain D, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
Length = 434
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 37/148 (25%), Positives = 68/148 (45%), Gaps = 17/148 (11%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEKPAKWWDSNNGH 60
M+SAT+P EIQ++A EFL + + + +G A + ++KQ + ++Y K +K + +
Sbjct: 241 MFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACS-DVKQTIYEVNKYAKRSKLIEILSEQ 299
Query: 61 YPKSVRFVLGTAGFLLSAVSFSLPFRDDKTSVVTVPSYPDPSV--NHLQGKTKEEIDSFR 118
++ FV G F F +K +P S+ + LQ + ++ + F+
Sbjct: 300 ADGTIVFVETKRG-----ADFLASFLSEK-------EFPTTSIHGDRLQSQREQALRDFK 347
Query: 119 KEHNITLIGQNIPKPVKTLDETNIPSYI 146
LI ++ + LD NI I
Sbjct: 348 NGSMKVLIATSVAS--RGLDIKNIKHVI 373
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%)
Query: 190 LQKKAEVQSRSVFTYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRT 249
L A+ S ++LP L +L+ P E P ++++PTRELA QI F+
Sbjct: 96 LMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFE 155
Query: 250 MRIRHACLYGGTSKMYQ 266
++ +YGGTS +Q
Sbjct: 156 SYLKIGIVYGGTSFRHQ 172
>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
pdb|1WRB|B Chain B, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
Length = 253
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 194 AEVQSRSVFTYILPALYHI----LKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRT 249
A+ S +++P + H+ L + + P L+LAPTRELA QI + FS
Sbjct: 67 AQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLN 126
Query: 250 MRIRHACLYGGTSKMYQV 267
+R +YGG Q+
Sbjct: 127 TPLRSCVVYGGADTHSQI 144
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/39 (48%), Positives = 28/39 (71%), Gaps = 1/39 (2%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQ 39
M+SAT+P+EIQKLA +FL + I + VG + + +IKQ
Sbjct: 214 MFSATFPKEIQKLAADFLYNYIFMTVGRVG-STSDSIKQ 251
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 30/101 (29%), Positives = 46/101 (45%), Gaps = 15/101 (14%)
Query: 171 ESKNWTIPLNFQAKKFISVLQKKAEVQSRSVFTYILPALYHILKMPKLEEGDGPIALVLA 230
E ++ TIPL Q K + +A+ S Y +P L +K +LV+
Sbjct: 19 EVQSKTIPLMLQGKNVVV----RAKTGSGKTAAYAIPILELGMK-----------SLVVT 63
Query: 231 PTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
PTREL +Q+ + I R M + A +YGG Q+ +R
Sbjct: 64 PTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR 104
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 24/33 (72%), Gaps = 2/33 (6%)
Query: 1 MWSATWPREIQKLAKEFLS--DPIQLNVGSANL 31
++SAT P EI+K+ K+F++ + I+ +G AN+
Sbjct: 165 LFSATIPEEIRKVVKDFITNYEEIEACIGLANV 197
>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|B Chain B, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|C Chain C, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|D Chain D, Crystal Structure Of Human Apo-Eif4aiii
Length = 391
Score = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/38 (52%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
AL+LAPTRELA QIQ + M ++ HAC+ GGT+
Sbjct: 87 ALILAPTRELAVQIQKGLLALGDYMNVQCHACI-GGTN 123
Score = 31.6 bits (70), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF 40
+ SAT P EI ++ +F++DPI++ V L IKQF
Sbjct: 194 LISATLPHEILEMTNKFMTDPIRILVKRDELTLE-GIKQF 232
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/38 (52%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
AL+LAPTRELA QIQ + M ++ HAC+ GGT+
Sbjct: 109 ALILAPTRELAVQIQKGLLALGDYMNVQCHACI-GGTN 145
Score = 31.6 bits (70), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF 40
+ SAT P EI ++ +F++DPI++ V L IKQF
Sbjct: 216 LISATLPHEILEMTNKFMTDPIRILVKRDELTLE-GIKQF 254
>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|B Chain B, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0S|A Chain A, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 410
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/38 (52%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
AL+LAPTRELA QIQ + M ++ HAC+ GGT+
Sbjct: 108 ALILAPTRELAVQIQKGLLALGDYMNVQCHACI-GGTN 144
Score = 31.6 bits (70), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF 40
+ SAT P EI ++ +F++DPI++ V L IKQF
Sbjct: 215 LISATLPHEILEMTNKFMTDPIRILVKRDELTLE-GIKQF 253
>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|X Chain X, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 411
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/38 (52%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
AL+LAPTRELA QIQ + M ++ HAC+ GGT+
Sbjct: 109 ALILAPTRELAVQIQKGLLALGDYMNVQCHACI-GGTN 145
Score = 31.6 bits (70), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF 40
+ SAT P EI ++ +F++DPI++ V L IKQF
Sbjct: 216 LISATLPHEILEMTNKFMTDPIRILVKRDELTLE-GIKQF 254
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 35.4 bits (80), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
AL+LAPTRELA Q+Q + M ++ HAC+ GGT+
Sbjct: 72 ALILAPTRELAVQVQKGLLALGDYMNVQSHACI-GGTN 108
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF 40
+ SAT P E+ ++ +F++DPI++ V L IKQF
Sbjct: 179 LISATLPHEVLEMTNKFMTDPIRILVKRDELTLE-GIKQF 217
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTS 262
AL+LAPTRELA Q+Q + M ++ HAC+ GGT+
Sbjct: 72 ALILAPTRELAVQVQKGLLALGDYMNVQCHACI-GGTN 108
Score = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF 40
+ SAT P EI ++ +F++DPI++ V L IKQF
Sbjct: 179 LISATLPHEILEMTNKFMTDPIRILVKRDELTLE-GIKQF 217
>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
pdb|1HV8|B Chain B, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
Length = 367
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 29/54 (53%)
Query: 218 LEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
+ E +G A++L PTRELA Q+ I ++ A +YGG + Q+ L+
Sbjct: 69 VNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK 122
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 1 MWSATWPREIQKLAKEFLSD------PIQLNVGSANLAANPNIKQFVEICH 45
++SAT PREI LAK++ D I N+ + + N N ++F +C
Sbjct: 183 LFSATXPREILNLAKKYXGDYSFIKAKINANIEQSYVEVNEN-ERFEALCR 232
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 11/73 (15%)
Query: 190 LQKKAEVQSRSVFTYILPALYHILK---MPKLEEGDGPIALVLAPTRELAQQIQAVISIF 246
L A+ S +++PA+ I+K MP+ +G L+L+PTRELA Q V+
Sbjct: 94 LLAAAKTGSGKTLAFLIPAVELIVKLRFMPR----NGTGVLILSPTRELAMQTFGVL--- 146
Query: 247 SRTMRIRHACLYG 259
+ + H YG
Sbjct: 147 -KELMTHHVHTYG 158
>pdb|1ECE|A Chain A, Acidothermus Cellulolyticus Endocellulase E1 Catalytic
Domain In Complex With A Cellotetraose
pdb|1ECE|B Chain B, Acidothermus Cellulolyticus Endocellulase E1 Catalytic
Domain In Complex With A Cellotetraose
Length = 358
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 33/90 (36%), Gaps = 31/90 (34%)
Query: 4 ATWPREIQKLAKEFLSDPIQLN----------------------------VGSANLAANP 35
ATW ++Q LA+ + +P + G+A L+ NP
Sbjct: 135 ATWISDLQALAQRYKGNPTVVGFDLHNEPHDPACWGCGDPSIDWRLAAERAGNAVLSVNP 194
Query: 36 NIKQFVEICHEYEKPAKWWDSN---NGHYP 62
N+ FVE Y + WW N G YP
Sbjct: 195 NLLIFVEGVQSYNGDSYWWGGNLQGAGQYP 224
>pdb|1VRX|A Chain A, Endocellulase E1 From Acidothermus Cellulolyticus Mutant
Y245g
pdb|1VRX|B Chain B, Endocellulase E1 From Acidothermus Cellulolyticus Mutant
Y245g
Length = 358
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 33/90 (36%), Gaps = 31/90 (34%)
Query: 4 ATWPREIQKLAKEFLSDPIQLN----------------------------VGSANLAANP 35
ATW ++Q LA+ + +P + G+A L+ NP
Sbjct: 135 ATWISDLQALAQRYKGNPTVVGFDLHNEPHDPACWGCGDPSIDWRLAAERAGNAVLSVNP 194
Query: 36 NIKQFVEICHEYEKPAKWWDSN---NGHYP 62
N+ FVE Y + WW N G YP
Sbjct: 195 NLLIFVEGVQSYNGDSYWWGGNLQGAGQYP 224
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEKPAKWWD 55
M+SAT +EI+ + ++F+ DP+++ V ++Q+ + EK K +D
Sbjct: 189 MFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFD 243
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 21/122 (17%)
Query: 208 ALYHILKMPKLEEGDGPIA-LVLAPTRELAQQIQAVISIFSRTM-RIRHACLYGGTS-KM 264
A++ + + +LE G ++ LV+ TRELA QI FS+ M ++ A +GG S K
Sbjct: 60 AVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKK 119
Query: 265 YQVILL------------RILTSATNTSLGI------YLQQNDAHSPCLSVWRRLQDILG 306
+ +L RIL A N SL + L + D L + R +Q+I
Sbjct: 120 DEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFR 179
Query: 307 LT 308
+T
Sbjct: 180 MT 181
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEKPAKWWD 55
M+SAT +EI+ + ++F+ DP+++ V ++Q+ + EK K +D
Sbjct: 189 MFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFD 243
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 21/122 (17%)
Query: 208 ALYHILKMPKLEEGDGPIA-LVLAPTRELAQQIQAVISIFSRTM-RIRHACLYGGTS-KM 264
A++ + + +LE G ++ LV+ TRELA QI FS+ M ++ A +GG S K
Sbjct: 60 AVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKK 119
Query: 265 YQVILL------------RILTSATNTSLGI------YLQQNDAHSPCLSVWRRLQDILG 306
+ +L RIL A N SL + L + D L + R +Q+I
Sbjct: 120 DEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFR 179
Query: 307 LT 308
+T
Sbjct: 180 MT 181
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 21/122 (17%)
Query: 208 ALYHILKMPKLEEGDGPIA-LVLAPTRELAQQIQAVISIFSRTM-RIRHACLYGGTS-KM 264
A++ + + +LE G ++ LV+ TRELA QI FS+ M ++ A +GG S K
Sbjct: 59 AVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKK 118
Query: 265 YQVILL------------RILTSATNTSLGI------YLQQNDAHSPCLSVWRRLQDILG 306
+ +L RIL A N SL + L + D L + R +Q+I
Sbjct: 119 DEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFR 178
Query: 307 LT 308
+T
Sbjct: 179 MT 180
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEKPAKWWD 55
M+SAT +EI+ + ++F+ DP+++ V ++Q+ + EK K +D
Sbjct: 188 MFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFD 242
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 193 KAEVQSRSVFTYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQA-VISIFSRTMR 251
+A+ + F +++P H++ K + A+++APTR+LA QI+A V I
Sbjct: 66 RAKTGTGKTFAFLIPIFQHLINT-KFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYG 124
Query: 252 I-RHAC--LYGGT 261
+ ++AC L GGT
Sbjct: 125 LKKYACVSLVGGT 137
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 32.7 bits (73), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 193 KAEVQSRSVFTYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQA-VISIFSRTMR 251
+A+ + F +++P H++ K + A+++APTR+LA QI+A V I
Sbjct: 117 RAKTGTGKTFAFLIPIFQHLINT-KFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYG 175
Query: 252 I-RHAC--LYGGTS 262
+ ++AC L GGT
Sbjct: 176 LKKYACVSLVGGTD 189
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 193 KAEVQSRSVFTYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQA-VISIFSRTMR 251
+A+ + F +++P H++ K + A+++APTR+LA QI+A V I
Sbjct: 66 RAKTGTGKTFAFLIPIFQHLINT-KFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYG 124
Query: 252 I-RHAC--LYGGTS 262
+ ++AC L GGT
Sbjct: 125 LKKYACVSLVGGTD 138
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 5/90 (5%)
Query: 171 ESKNWTIPLNFQAKKFISVLQKKAEVQSRSVFTYILPALYHILKMPKLEEGDGPIALVLA 230
E + TI L Q K + A+ S +++P L + ++ + DG L+++
Sbjct: 50 EIQKQTIGLALQGKDVLGA----AKTGSGKTLAFLVPVLEALYRL-QWTSTDGLGVLIIS 104
Query: 231 PTRELAQQIQAVISIFSRTMRIRHACLYGG 260
PTRELA Q V+ + + GG
Sbjct: 105 PTRELAYQTFEVLRKVGKNHDFSAGLIIGG 134
>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56
pdb|1T6N|B Chain B, Crystal Structure Of The N-Terminal Domain Of Human Uap56
Length = 220
Score = 32.0 bits (71), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 21/122 (17%)
Query: 208 ALYHILKMPKLEEGDGPIA-LVLAPTRELAQQIQAVISIFSRTM-RIRHACLYGGTS-KM 264
A++ + + +LE G ++ LV+ TRELA QI FS+ M ++ A +GG S K
Sbjct: 66 AVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKK 125
Query: 265 YQVILL------------RILTSATNTSLGI------YLQQNDAHSPCLSVWRRLQDILG 306
+ +L RIL A N SL + L + D L + R +Q+I
Sbjct: 126 DEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFR 185
Query: 307 LT 308
+T
Sbjct: 186 MT 187
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 224 PIALVLAPTRELAQQIQAVISIFSRTMRIRHA 255
P A+ LAP+RELA+QI V++ + ++ A
Sbjct: 190 PQAICLAPSRELARQIMDVVTEMGKYTEVKTA 221
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 204 YILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTS 262
+++P L + PKL + AL++ PTRELA Q V+ + I GGT+
Sbjct: 75 FVIPTLEKV--KPKLNKIQ---ALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTN 128
>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex
With Adp
pdb|2OXC|B Chain B, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex
With Adp
pdb|3B7G|A Chain A, Human Dead-Box Rna Helicase Ddx20, Conserved Domain I
(Dead) In Complex With Amppnp
(Adenosine-(Beta,Gamma)-Imidotriphosphate)
pdb|3B7G|B Chain B, Human Dead-Box Rna Helicase Ddx20, Conserved Domain I
(Dead) In Complex With Amppnp
(Adenosine-(Beta,Gamma)-Imidotriphosphate)
Length = 230
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 227 LVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQ 266
L+LAPTRE+A QI +VI+ M ++ G + + Q
Sbjct: 96 LILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQ 135
>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain
pdb|1Q0U|B Chain B, Crystal Structure Of The Bstdead N-Terminal Domain
Length = 219
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 226 ALVLAPTRELAQQIQ----AVISIFSRTMRIRHACLYGGTSK 263
A++ APTRELA QI + + I CL GGT K
Sbjct: 75 AVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDK 116
>pdb|3FY4|A Chain A, (6-4) Photolyase Crystal Structure
pdb|3FY4|B Chain B, (6-4) Photolyase Crystal Structure
pdb|3FY4|C Chain C, (6-4) Photolyase Crystal Structure
Length = 537
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 9 EIQKLAKEFLSDPI--QLNVGSANLAANPNIKQFVEICHEYEKPAKWWDSNNGHYPKSVR 66
++++L E+ +DP L+V + A++ ++ F + H PA + N G P S +
Sbjct: 103 KVKRLCFEYDTDPYYQALDVKVKDYASSTGVEVFSPVSHTLFNPAHIIEKNGGKPPLSYQ 162
Query: 67 FVLGTAG 73
L AG
Sbjct: 163 SFLKVAG 169
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
0.319 0.134 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,817,831
Number of Sequences: 62578
Number of extensions: 335062
Number of successful extensions: 996
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 932
Number of HSP's gapped (non-prelim): 71
length of query: 317
length of database: 14,973,337
effective HSP length: 99
effective length of query: 218
effective length of database: 8,778,115
effective search space: 1913629070
effective search space used: 1913629070
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)