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= 035699
(633 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp
pdb|3KX2|A Chain A, Crystal Structure Of Prp43p In Complex With Adp
Length = 767
Score = 300 bits (769), Expect = 1e-81, Method: Compositional matrix adjust.
Identities = 165/340 (48%), Positives = 211/340 (62%), Gaps = 36/340 (10%)
Query: 326 RKTLPIYPFREELLQAVSEYPVLVIVGETGSGKTTQIPQYLY--EAGYTKQGKIGCTQLX 383
R+ LP++ R+E L+ ++V VGETGSGKTTQIPQ++ E + + ++ CTQ
Sbjct: 90 RRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPR 149
Query: 384 XXXXXXXXXXXXQEMGVKLGHEVGYSIRFEDCTSDKTVLKYMTDGMLLREIVLEPSLESY 443
+EM VKLG EVGYSIRFE+ TS+KT+LKYMTDGMLLRE + + L Y
Sbjct: 150 RVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMEDHDLSRY 209
Query: 444 SVLI-------------------DLINYRPDLKLLISSATLDAENFSDYFGSAPIFKIPR 484
S +I ++ RPDLK++I SATLDAE F YF AP+ +P
Sbjct: 210 SCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLLAVPG 269
Query: 485 RRYHVELFYTKAPEADYIEAAIVTALQIHVNEPIGDILVFLTGQDQFETAEEILKQ---- 540
R Y VEL+YT + DY+++AI T LQIH E GDIL+FLTG+D+ E A +
Sbjct: 270 RTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQ 329
Query: 541 --RTRGLGTKIAELIICPIYGNLPTELQAKIFEPTPEG-----ARKVVLATNIAETSLTI 593
R G G L + P+YG+LP Q +IFEP PE RKVV++TNIAETSLTI
Sbjct: 330 LVREEGCGP----LSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTI 385
Query: 594 DGIKYVIDPGFAKVKSYNPKTGMESLLVNPISKASANQRT 633
DGI YV+DPGF+K K YNP+ +ESLLV+PISKASA QR
Sbjct: 386 DGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRA 425
>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
pdb|2XAU|B Chain B, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
Length = 773
Score = 300 bits (769), Expect = 1e-81, Method: Compositional matrix adjust.
Identities = 165/340 (48%), Positives = 211/340 (62%), Gaps = 36/340 (10%)
Query: 326 RKTLPIYPFREELLQAVSEYPVLVIVGETGSGKTTQIPQYLY--EAGYTKQGKIGCTQLX 383
R+ LP++ R+E L+ ++V VGETGSGKTTQIPQ++ E + + ++ CTQ
Sbjct: 90 RRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPR 149
Query: 384 XXXXXXXXXXXXQEMGVKLGHEVGYSIRFEDCTSDKTVLKYMTDGMLLREIVLEPSLESY 443
+EM VKLG EVGYSIRFE+ TS+KT+LKYMTDGMLLRE + + L Y
Sbjct: 150 RVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMEDHDLSRY 209
Query: 444 SVLI-------------------DLINYRPDLKLLISSATLDAENFSDYFGSAPIFKIPR 484
S +I ++ RPDLK++I SATLDAE F YF AP+ +P
Sbjct: 210 SCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLLAVPG 269
Query: 485 RRYHVELFYTKAPEADYIEAAIVTALQIHVNEPIGDILVFLTGQDQFETAEEILKQ---- 540
R Y VEL+YT + DY+++AI T LQIH E GDIL+FLTG+D+ E A +
Sbjct: 270 RTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQ 329
Query: 541 --RTRGLGTKIAELIICPIYGNLPTELQAKIFEPTPEG-----ARKVVLATNIAETSLTI 593
R G G L + P+YG+LP Q +IFEP PE RKVV++TNIAETSLTI
Sbjct: 330 LVREEGCGP----LSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTI 385
Query: 594 DGIKYVIDPGFAKVKSYNPKTGMESLLVNPISKASANQRT 633
DGI YV+DPGF+K K YNP+ +ESLLV+PISKASA QR
Sbjct: 386 DGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRA 425
>pdb|3LLM|A Chain A, Crystal Structure Analysis Of A Rna Helicase
pdb|3LLM|B Chain B, Crystal Structure Analysis Of A Rna Helicase
Length = 235
Score = 85.1 bits (209), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 55/188 (29%), Positives = 91/188 (48%), Gaps = 26/188 (13%)
Query: 319 LEMLQEERKTLPIYPFREELLQAVSEYPVLVIVGETGSGKTTQIPQYLY----EAGYTKQ 374
L+ + +ER+ LP+ F E+L+A+S+ V++I G TG GKTTQ+PQ++ + +
Sbjct: 50 LQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAE 109
Query: 375 GKIGCTQLXXXXXXXXXXXXXQEMGVKLGHEVGYSIRFEDCTS-DKTVLKYMTDGMLLRE 433
I TQ E G + G GYS+RFE + + T G+LLR+
Sbjct: 110 CNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASIXFCTVGVLLRK 169
Query: 434 IVLEPSLESYS-------------------VLIDLINYRPDLKLLISSATLDAENFSDYF 474
LE + S VL D++ P++++++ SAT+D F +YF
Sbjct: 170 --LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLXSATIDTSXFCEYF 227
Query: 475 GSAPIFKI 482
+ PI ++
Sbjct: 228 FNCPIIEV 235
>pdb|1EO1|A Chain A, Solution Structure Of Hypothetical Protein Mth1175 From
Methanobacterium Thermoautotrophicum
Length = 124
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 29/109 (26%), Positives = 48/109 (44%), Gaps = 3/109 (2%)
Query: 456 LKLLISSATLD-AENFSDYFGSAPIFKIPR-RRYHVELF-YTKAPEADYIEAAIVTALQI 512
+K+ I+S+ D S +FG AP F I ++ ++E + P A A + QI
Sbjct: 1 MKIAIASSGTDLGSEVSRFFGRAPYFMIVEMKKGNIESSEVIENPSASASGGAGIRTAQI 60
Query: 513 HVNEPIGDILVFLTGQDQFETAEEILKQRTRGLGTKIAELIICPIYGNL 561
N + ++ G + FE E+ + R GT + E + GNL
Sbjct: 61 IANNGVKAVIASSPGPNAFEVLNELGIKIYRATGTSVEENLKLFTEGNL 109
>pdb|3ZVM|A Chain A, The Structural Basis For Substrate Recognition By
Mammalian Polynucleotide Kinase 3' Phosphatase
pdb|3ZVM|B Chain B, The Structural Basis For Substrate Recognition By
Mammalian Polynucleotide Kinase 3' Phosphatase
Length = 416
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 330 PIY-PFREELLQAVSEYPVLVIVGETGSGKTTQIPQYLYEAGYT 372
P+Y P LL E V+V VG G+GK+T I ++L AGY
Sbjct: 244 PLYLPESSSLLSPNPE--VVVAVGFPGAGKSTFIQEHLVSAGYV 285
>pdb|3ZVL|A Chain A, The Structural Basis For Substrate Recognition By
Mammalian Polynucleotide Kinase 3' Phosphatase
Length = 416
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 330 PIY-PFREELLQAVSEYPVLVIVGETGSGKTTQIPQYLYEAGYT 372
P+Y P LL E V+V VG G+GK+T I ++L AGY
Sbjct: 244 PLYLPESSSLLSPNPE--VVVAVGFPGAGKSTFIQEHLVSAGYV 285
>pdb|3ZVN|A Chain A, The Structural Basis For Substrate Recognition By
Mammalian Polynucleotide Kinase 3' Phosphatase
Length = 416
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 330 PIY-PFREELLQAVSEYPVLVIVGETGSGKTTQIPQYLYEAGYT 372
P+Y P LL E V+V VG G+GK+T I ++L AGY
Sbjct: 244 PLYLPESSSLLSPNPE--VVVAVGFPGAGKSTFIQEHLVSAGYV 285
>pdb|3U7G|A Chain A, Crystal Structure Of Mpnkp Catalytic Fragment (D170a)
Bound To Single- Stranded Dna (Tcctap)
Length = 379
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 330 PIY-PFREELLQAVSEYPVLVIVGETGSGKTTQIPQYLYEAGYT 372
P+Y P LL E V+V VG G+GK+T I ++L AGY
Sbjct: 207 PLYLPESSSLLSPNPE--VVVAVGFPGAGKSTFIQEHLVSAGYV 248
>pdb|1YJ5|A Chain A, Molecular Architecture Of Mammalian Polynucleotide Kinase,
A Dna Repair Enzyme
pdb|1YJ5|B Chain B, Molecular Architecture Of Mammalian Polynucleotide Kinase,
A Dna Repair Enzyme
Length = 383
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 330 PIY-PFREELLQAVSEYPVLVIVGETGSGKTTQIPQYLYEAGYT 372
P+Y P LL E V+V VG G+GK+T I ++L AGY
Sbjct: 211 PLYLPESSSLLSPNPE--VVVAVGFPGAGKSTFIQEHLVSAGYV 252
>pdb|3U7E|B Chain B, Crystal Structure Of Mpnkp Catalytic Fragment (D170a)
pdb|3U7F|B Chain B, Crystal Structure Of Mpnkp Catalytic Fragment (D170a)
Bound To Single- Stranded Dna (Tcctcp)
pdb|3U7H|B Chain B, Crystal Structure Of Mpnkp Catalytic Fragment (D170a)
Bound To Single- Stranded Dna (Tccttp)
Length = 381
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 330 PIY-PFREELLQAVSEYPVLVIVGETGSGKTTQIPQYLYEAGYT 372
P+Y P LL E V+V VG G+GK+T I ++L AGY
Sbjct: 209 PLYLPESSSLLSPNPE--VVVAVGFPGAGKSTFIQEHLVSAGYV 250
>pdb|2GZA|A Chain A, Crystal Structure Of The Virb11 Atpase From The Brucella
Suis Type Iv Secretion System In Complex With Sulphate
pdb|2GZA|B Chain B, Crystal Structure Of The Virb11 Atpase From The Brucella
Suis Type Iv Secretion System In Complex With Sulphate
pdb|2GZA|C Chain C, Crystal Structure Of The Virb11 Atpase From The Brucella
Suis Type Iv Secretion System In Complex With Sulphate
Length = 361
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 13/57 (22%)
Query: 331 IYPFREELL-------------QAVSEYPVLVIVGETGSGKTTQIPQYLYEAGYTKQ 374
+ PF +ELL +AV V+V+ GETGSGKTT + + E + ++
Sbjct: 148 LTPFEQELLALKEAGDYMSFLRRAVQLERVIVVAGETGSGKTTLMKALMQEIPFDQR 204
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 29.3 bits (64), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 335 REELLQAVSEYPVLVIVGETGSGKTTQIPQYLYEAGYTKQG-KIGCT 380
+E +L A+S+ + +I G G+GKTT + + + +A KQG K+ C
Sbjct: 195 KEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQA--VKQGLKVLCC 239
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 335 REELLQAVSEYPVLVIVGETGSGKTTQIPQYLYEAGYTKQG-KIGCT 380
+E +L A+S+ + +I G G+GKTT + + + +A KQG K+ C
Sbjct: 195 KEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQA--VKQGLKVLCC 239
>pdb|4GQV|A Chain A, Crystal Structure Of Cbs-pair Protein, Cbsx1 From
Arabidopsis Thaliana
Length = 166
Score = 29.3 bits (64), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 313 SAVKSALEMLQEERKT-LPIYPFREELLQAVSEYPVLVIVGETGSGKT 359
+ V ALE+L E R T P+ +L+ VS+Y +L + +GSG+T
Sbjct: 24 TTVDEALELLVENRITGFPVIDEDWKLVGLVSDYDLLALDSISGSGRT 71
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
0.314 0.133 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,799,841
Number of Sequences: 62578
Number of extensions: 664605
Number of successful extensions: 1848
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1824
Number of HSP's gapped (non-prelim): 34
length of query: 633
length of database: 14,973,337
effective HSP length: 105
effective length of query: 528
effective length of database: 8,402,647
effective search space: 4436597616
effective search space used: 4436597616
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)