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= psy1955
(512 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NA3|A Chain A, Mutl Protein Homolog 1 Isoform 1 From Homo Sapiens
Length = 348
Score = 327 bits (839), Expect = 8e-90, Method: Compositional matrix adjust.
Identities = 175/342 (51%), Positives = 223/342 (65%), Gaps = 37/342 (10%)
Query: 7 IKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQDNGTG 66
I++LDETVVNRIAAGEVIQRPANA+KE++EN LDAKSTSIQV VK+GGLKL+QIQDNGTG
Sbjct: 9 IRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTG 68
Query: 67 IRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYR 126
IRKED+DIVCERFTTSKL FEDL SIST+GFRGEALASISHVAH+TI TKT CAYR
Sbjct: 69 IRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYR 128
Query: 127 W-------------CTYXXXXXXXXX------XXXSQYLQRDKEQIGDKEEKQWYRTVEH 167
C + L+ E+ G E +V +
Sbjct: 129 ASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRYSVHN 188
Query: 168 TLVPLMKSQYQPSEKIVERACLLEIASLNNL----------ELLSVEGTDDAFQLKVTGW 217
+ S + E + + L ++++N+ EL+ + D K+ G+
Sbjct: 189 AGISF--SVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAFKMNGY 246
Query: 218 ITNVNFSTKKMTFLLFINN------PIKRMIEQVYSIYLPKGSFPFVYLSLCMDPKNVDV 271
I+N N+S KK FLLFIN+ +++ IE VY+ YLPK + PF+YLSL + P+NVDV
Sbjct: 247 ISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDV 306
Query: 272 NVHPTKHEVHFLHEDTIIERVQSMLEKTLLGSNTSRVFYTQS 313
NVHPTKHEVHFLHE++I+ERVQ +E LLGSN+SR+++TQ+
Sbjct: 307 NVHPTKHEVHFLHEESILERVQQHIESKLLGSNSSRMYFTQT 348
Score = 279 bits (714), Expect = 3e-75, Method: Compositional matrix adjust.
Identities = 134/186 (72%), Positives = 153/186 (82%)
Query: 312 QSTSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGE 371
+STSIQV VK+GGLKL+QIQDNGTGIRKED+DIVCERFTTSKL FEDL SIST+GFRGE
Sbjct: 44 KSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGE 103
Query: 372 ALASISHVAHLTIITKTKTSPCAYRASYIDSKLKDPIKPCAGNQGTQIIAEDLFYNIPTR 431
ALASISHVAH+TI TKT CAYRASY D KLK P KPCAGNQGTQI EDLFYNI TR
Sbjct: 104 ALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIATR 163
Query: 432 RKALKQPSEEYNKIADVVSRYAVHNPHVGFTLKKQNENLADIRTNVNSSHSEVIGNIYGN 491
RKALK PSEEY KI +VV RY+VHN + F++KKQ E +AD+RT N+S + I +I+GN
Sbjct: 164 RKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGN 223
Query: 492 NISRRV 497
+SR +
Sbjct: 224 AVSREL 229
>pdb|1BKN|A Chain A, Crystal Structure Of An N-Terminal 40kd Fragment Of E.
Coli Dna Mismatch Repair Protein Mutl
pdb|1BKN|B Chain B, Crystal Structure Of An N-Terminal 40kd Fragment Of E.
Coli Dna Mismatch Repair Protein Mutl
Length = 352
Score = 143 bits (361), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 107/340 (31%), Positives = 164/340 (48%), Gaps = 54/340 (15%)
Query: 7 IKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQDNGTG 66
I+ L + N+IAAGEV++RPA+ +KEL+ENSLDA +T I + +++GG KL++I+DNG G
Sbjct: 6 IQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCG 65
Query: 67 IRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYR 126
I+K+++ + R TSK+ +DL +I + GFRGEALASIS V+ LT+ ++T A
Sbjct: 66 IKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEA-- 123
Query: 127 WCTYXXXXXXXXXXXXSQYLQRDKEQIGDKEEKQWYRT-VEHTLVPLMKSQYQPSEKIVE 185
W Y + + ++ D +Y T + K+++ ++I+
Sbjct: 124 WQAYAEGRDMNVTVKPAAHPVGTTLEVLDL----FYNTPARRKFLRTEKTEFNHIDEIIR 179
Query: 186 RACLLEIASLNNL---------------------ELLSVEGTDDAF------------QL 212
R L NL L ++ GT AF L
Sbjct: 180 RIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGT--AFLEQALAIEWQHGDL 237
Query: 213 KVTGWITNVNFSTKKMTFL--LFINNPIKR------MIEQVYSIYLPKGSFPFVYLSLCM 264
+ GW+ + N +T + + ++N + R I Q L P L L +
Sbjct: 238 TLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEI 297
Query: 265 DPKNVDVNVHPTKHEVHF----LHEDTIIERVQSMLEKTL 300
DP VDVNVHP KHEV F L D I + V S+L++ L
Sbjct: 298 DPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQQQL 337
Score = 117 bits (292), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 61/167 (36%), Positives = 100/167 (59%), Gaps = 5/167 (2%)
Query: 288 IIERVQSMLEKTLLGSNTSRVFYTQSTSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCE 347
++ER S++++ + S +T I + +++GG KL++I+DNG GI+K+++ +
Sbjct: 22 VVERPASVVKELVENS-----LDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALA 76
Query: 348 RFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYRASYIDSKLKDP 407
R TSK+ +DL +I + GFRGEALASIS V+ LT+ ++T A++A +
Sbjct: 77 RHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVT 136
Query: 408 IKPCAGNQGTQIIAEDLFYNIPTRRKALKQPSEEYNKIADVVSRYAV 454
+KP A GT + DLFYN P RRK L+ E+N I +++ R A+
Sbjct: 137 VKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIAL 183
>pdb|1B62|A Chain A, Mutl Complexed With Adp
Length = 355
Score = 143 bits (361), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 107/340 (31%), Positives = 164/340 (48%), Gaps = 54/340 (15%)
Query: 7 IKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQDNGTG 66
I+ L + N+IAAGEV++RPA+ +KEL+ENSLDA +T I + +++GG KL++I+DNG G
Sbjct: 9 IQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCG 68
Query: 67 IRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYR 126
I+K+++ + R TSK+ +DL +I + GFRGEALASIS V+ LT+ ++T A
Sbjct: 69 IKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEA-- 126
Query: 127 WCTYXXXXXXXXXXXXSQYLQRDKEQIGDKEEKQWYRT-VEHTLVPLMKSQYQPSEKIVE 185
W Y + + ++ D +Y T + K+++ ++I+
Sbjct: 127 WQAYAEGRDMNVTVKPAAHPVGTTLEVLDL----FYNTPARRKFLRTEKTEFNHIDEIIR 182
Query: 186 RACLLEIASLNNL---------------------ELLSVEGTDDAF------------QL 212
R L NL L ++ GT AF L
Sbjct: 183 RIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGT--AFLEQALAIEWQHGDL 240
Query: 213 KVTGWITNVNFSTKKMTFL--LFINNPIKR------MIEQVYSIYLPKGSFPFVYLSLCM 264
+ GW+ + N +T + + ++N + R I Q L P L L +
Sbjct: 241 TLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEI 300
Query: 265 DPKNVDVNVHPTKHEVHF----LHEDTIIERVQSMLEKTL 300
DP VDVNVHP KHEV F L D I + V S+L++ L
Sbjct: 301 DPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQQQL 340
Score = 117 bits (292), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 61/167 (36%), Positives = 100/167 (59%), Gaps = 5/167 (2%)
Query: 288 IIERVQSMLEKTLLGSNTSRVFYTQSTSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCE 347
++ER S++++ + S +T I + +++GG KL++I+DNG GI+K+++ +
Sbjct: 25 VVERPASVVKELVENS-----LDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALA 79
Query: 348 RFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYRASYIDSKLKDP 407
R TSK+ +DL +I + GFRGEALASIS V+ LT+ ++T A++A +
Sbjct: 80 RHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVT 139
Query: 408 IKPCAGNQGTQIIAEDLFYNIPTRRKALKQPSEEYNKIADVVSRYAV 454
+KP A GT + DLFYN P RRK L+ E+N I +++ R A+
Sbjct: 140 VKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIAL 186
>pdb|1B63|A Chain A, Mutl Complexed With Adpnp
pdb|1NHH|A Chain A, Crystal Structure Of N-Terminal 40kd Mutl Protein (Ln40)
Complex With Adpnp And One Rubidium
pdb|1NHI|A Chain A, Crystal Structure Of N-Terminal 40kd Mutl (Ln40) Complex
With Adpnp And One Potassium
Length = 333
Score = 142 bits (357), Expect = 6e-34, Method: Compositional matrix adjust.
Identities = 106/337 (31%), Positives = 162/337 (48%), Gaps = 54/337 (16%)
Query: 7 IKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQDNGTG 66
I+ L + N+IAAGEV++RPA+ +KEL+ENSLDA +T I + +++GG KL++I+DNG G
Sbjct: 5 IQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCG 64
Query: 67 IRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYR 126
I+K+++ + R TSK+ +DL +I + GFRGEALASIS V+ LT+ ++T A
Sbjct: 65 IKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEA-- 122
Query: 127 WCTYXXXXXXXXXXXXSQYLQRDKEQIGDKEEKQWYRT-VEHTLVPLMKSQYQPSEKIVE 185
W Y + + ++ D +Y T + K+++ ++I+
Sbjct: 123 WQAYAEGRDMNVTVKPAAHPVGTTLEVLDL----FYNTPARRKFLRTEKTEFNHIDEIIR 178
Query: 186 RACLLEIASLNNL---------------------ELLSVEGTDDAF------------QL 212
R L NL L ++ GT AF L
Sbjct: 179 RIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGT--AFLEQALAIEWQHGDL 236
Query: 213 KVTGWITNVNFSTKKMTFL--LFINNPIKR------MIEQVYSIYLPKGSFPFVYLSLCM 264
+ GW+ + N +T + + ++N + R I Q L P L L +
Sbjct: 237 TLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEI 296
Query: 265 DPKNVDVNVHPTKHEVHF----LHEDTIIERVQSMLE 297
DP VDVNVHP KHEV F L D I + V S+L+
Sbjct: 297 DPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQ 333
Score = 117 bits (293), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 61/167 (36%), Positives = 100/167 (59%), Gaps = 5/167 (2%)
Query: 288 IIERVQSMLEKTLLGSNTSRVFYTQSTSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCE 347
++ER S++++ + S +T I + +++GG KL++I+DNG GI+K+++ +
Sbjct: 21 VVERPASVVKELVENS-----LDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALA 75
Query: 348 RFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYRASYIDSKLKDP 407
R TSK+ +DL +I + GFRGEALASIS V+ LT+ ++T A++A +
Sbjct: 76 RHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVT 135
Query: 408 IKPCAGNQGTQIIAEDLFYNIPTRRKALKQPSEEYNKIADVVSRYAV 454
+KP A GT + DLFYN P RRK L+ E+N I +++ R A+
Sbjct: 136 VKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIAL 182
>pdb|1NHJ|A Chain A, Crystal Structure Of N-Terminal 40kd MutlA100P MUTANT
PROTEIN COMPLEX With Adpnp And One Sodium
Length = 333
Score = 139 bits (351), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 105/337 (31%), Positives = 161/337 (47%), Gaps = 54/337 (16%)
Query: 7 IKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQDNGTG 66
I+ L + N+IAAGEV++RPA+ +KEL+ENSLDA +T I + +++GG KL++I+DNG G
Sbjct: 5 IQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCG 64
Query: 67 IRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYR 126
I+K+++ + R TSK+ +DL +I + GFRGEAL SIS V+ LT+ ++T A
Sbjct: 65 IKKDELALALARHATSKIASLDDLEAIISLGFRGEALPSISSVSRLTLTSRTAEQQEA-- 122
Query: 127 WCTYXXXXXXXXXXXXSQYLQRDKEQIGDKEEKQWYRT-VEHTLVPLMKSQYQPSEKIVE 185
W Y + + ++ D +Y T + K+++ ++I+
Sbjct: 123 WQAYAEGRDMNVTVKPAAHPVGTTLEVLDL----FYNTPARRKFLRTEKTEFNHIDEIIR 178
Query: 186 RACLLEIASLNNL---------------------ELLSVEGTDDAF------------QL 212
R L NL L ++ GT AF L
Sbjct: 179 RIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGT--AFLEQALAIEWQHGDL 236
Query: 213 KVTGWITNVNFSTKKMTFL--LFINNPIKR------MIEQVYSIYLPKGSFPFVYLSLCM 264
+ GW+ + N +T + + ++N + R I Q L P L L +
Sbjct: 237 TLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEI 296
Query: 265 DPKNVDVNVHPTKHEVHF----LHEDTIIERVQSMLE 297
DP VDVNVHP KHEV F L D I + V S+L+
Sbjct: 297 DPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQ 333
Score = 115 bits (288), Expect = 6e-26, Method: Compositional matrix adjust.
Identities = 60/167 (35%), Positives = 99/167 (59%), Gaps = 5/167 (2%)
Query: 288 IIERVQSMLEKTLLGSNTSRVFYTQSTSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCE 347
++ER S++++ + S +T I + +++GG KL++I+DNG GI+K+++ +
Sbjct: 21 VVERPASVVKELVENS-----LDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALA 75
Query: 348 RFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYRASYIDSKLKDP 407
R TSK+ +DL +I + GFRGEAL SIS V+ LT+ ++T A++A +
Sbjct: 76 RHATSKIASLDDLEAIISLGFRGEALPSISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVT 135
Query: 408 IKPCAGNQGTQIIAEDLFYNIPTRRKALKQPSEEYNKIADVVSRYAV 454
+KP A GT + DLFYN P RRK L+ E+N I +++ R A+
Sbjct: 136 VKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIAL 182
>pdb|1H7S|A Chain A, N-Terminal 40kda Fragment Of Human Pms2
pdb|1H7S|B Chain B, N-Terminal 40kda Fragment Of Human Pms2
Length = 365
Score = 97.8 bits (242), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 48/115 (41%), Positives = 80/115 (69%), Gaps = 1/115 (0%)
Query: 3 QPPK-IKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQ 61
+P K IK +D V++I +G+V+ + A+KEL+ENSLDA +T+I + +K G+ L+++
Sbjct: 10 EPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVS 69
Query: 62 DNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIIT 116
DNG G+ +E+ + + + TSK+ +F DL + TFGFRGEAL+S+ ++ +TI T
Sbjct: 70 DNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTIST 124
Score = 79.3 bits (194), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 50/182 (27%), Positives = 94/182 (51%), Gaps = 4/182 (2%)
Query: 313 STSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEA 372
+T+I + +K G+ L+++ DNG G+ +E+ + + + TSK+ +F DL + TFGFRGEA
Sbjct: 51 ATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEA 110
Query: 373 LASISHVAHLTIITKTKTSPCAYRASYIDSKLKDPIKPCAGNQGTQIIAEDLFYNIPTRR 432
L+S+ ++ +TI T ++ R + + P +GT + + LF +P R
Sbjct: 111 LSSLCALSDVTISTCHASAKVGTRLXFDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRH 170
Query: 433 KALKQP-SEEYNKIADVVSRYAVHNPHVGFTLKK---QNENLADIRTNVNSSHSEVIGNI 488
K ++ +EY K V+ Y + + + + Q + + T + S E IG++
Sbjct: 171 KEFQRNIKKEYAKXVQVLHAYCIISAGIRVSCTNQLGQGKRQPVVCTGGSPSIKENIGSV 230
Query: 489 YG 490
+G
Sbjct: 231 FG 232
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 69/144 (47%), Gaps = 29/144 (20%)
Query: 168 TLVPLMKSQYQPSEKIVERACLLEIASLNNLELLSVEGTDDAFQLKVTGWITNVNFSTKK 227
+L+P + Q PS+ + E L +L+NL ++G+I+ +
Sbjct: 238 SLIPFV--QLPPSDSVCEEYGLSCSDALHNL-------------FYISGFISQCTHGVGR 282
Query: 228 MTF---LLFIN----NPIK--RMIEQVYSIYLPKGSFPFVYLSLCMDPKNVDVNVHPTKH 278
+ FIN +P K R++ +VY Y + +PFV L++ +D + VD+NV P K
Sbjct: 283 SSTDRQFFFINRRPCDPAKVCRLVNEVYHXY-NRHQYPFVVLNISVDSECVDINVTPDKR 341
Query: 279 EVHFLHEDTIIERVQSMLEKTLLG 302
++ E ++ ++L+ +L+G
Sbjct: 342 QILLQEEKLLL----AVLKTSLIG 361
>pdb|1H7U|A Chain A, Hpms2-atpgs
pdb|1H7U|B Chain B, Hpms2-atpgs
Length = 365
Score = 97.8 bits (242), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 48/115 (41%), Positives = 80/115 (69%), Gaps = 1/115 (0%)
Query: 3 QPPK-IKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQ 61
+P K IK +D V++I +G+V+ + A+KEL+ENSLDA +T+I + +K G+ L+++
Sbjct: 10 EPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVS 69
Query: 62 DNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIIT 116
DNG G+ +E+ + + + TSK+ +F DL + TFGFRGEAL+S+ ++ +TI T
Sbjct: 70 DNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTIST 124
Score = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 50/182 (27%), Positives = 95/182 (52%), Gaps = 4/182 (2%)
Query: 313 STSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEA 372
+T+I + +K G+ L+++ DNG G+ +E+ + + + TSK+ +F DL + TFGFRGEA
Sbjct: 51 ATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEA 110
Query: 373 LASISHVAHLTIITKTKTSPCAYRASYIDSKLKDPIKPCAGNQGTQIIAEDLFYNIPTRR 432
L+S+ ++ +TI T ++ R + + P +GT + + LF +P R
Sbjct: 111 LSSLCALSDVTISTCHASAKVGTRLMFDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRH 170
Query: 433 KALKQP-SEEYNKIADVVSRYAVHNPHVGFTLKK---QNENLADIRTNVNSSHSEVIGNI 488
K ++ +EY K+ V+ Y + + + + Q + + T + S E IG++
Sbjct: 171 KEFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQLGQGKRQPVVCTGGSPSIKENIGSV 230
Query: 489 YG 490
+G
Sbjct: 231 FG 232
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 70/144 (48%), Gaps = 29/144 (20%)
Query: 168 TLVPLMKSQYQPSEKIVERACLLEIASLNNLELLSVEGTDDAFQLKVTGWITNVNFSTKK 227
+L+P + Q PS+ + E L +L+NL ++G+I+ +
Sbjct: 238 SLIPFV--QLPPSDSVCEEYGLSCSDALHNL-------------FYISGFISQCTHGVGR 282
Query: 228 MTF---LLFIN----NPIK--RMIEQVYSIYLPKGSFPFVYLSLCMDPKNVDVNVHPTKH 278
+ FIN +P K R++ +VY +Y + +PFV L++ +D + VD+NV P K
Sbjct: 283 SSTDRQFFFINRRPCDPAKVCRLVNEVYHMY-NRHQYPFVVLNISVDSECVDINVTPDKR 341
Query: 279 EVHFLHEDTIIERVQSMLEKTLLG 302
++ E ++ ++L+ +L+G
Sbjct: 342 QILLQEEKLLL----AVLKTSLIG 361
>pdb|1EA6|A Chain A, N-Terminal 40kda Fragment Of Nhpms2 Complexed With Adp
pdb|1EA6|B Chain B, N-Terminal 40kda Fragment Of Nhpms2 Complexed With Adp
Length = 364
Score = 97.8 bits (242), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 48/115 (41%), Positives = 80/115 (69%), Gaps = 1/115 (0%)
Query: 3 QPPK-IKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQ 61
+P K IK +D V++I +G+V+ + A+KEL+ENSLDA +T+I + +K G+ L+++
Sbjct: 10 EPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVS 69
Query: 62 DNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIIT 116
DNG G+ +E+ + + + TSK+ +F DL + TFGFRGEAL+S+ ++ +TI T
Sbjct: 70 DNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTIST 124
Score = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 50/182 (27%), Positives = 95/182 (52%), Gaps = 4/182 (2%)
Query: 313 STSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEA 372
+T+I + +K G+ L+++ DNG G+ +E+ + + + TSK+ +F DL + TFGFRGEA
Sbjct: 51 ATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEA 110
Query: 373 LASISHVAHLTIITKTKTSPCAYRASYIDSKLKDPIKPCAGNQGTQIIAEDLFYNIPTRR 432
L+S+ ++ +TI T ++ R + + P +GT + + LF +P R
Sbjct: 111 LSSLCALSDVTISTCHASAKVGTRLMFDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRH 170
Query: 433 KALKQP-SEEYNKIADVVSRYAVHNPHVGFTLKK---QNENLADIRTNVNSSHSEVIGNI 488
K ++ +EY K+ V+ Y + + + + Q + + T + S E IG++
Sbjct: 171 KEFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQLGQGKRQPVVCTGGSPSIKENIGSV 230
Query: 489 YG 490
+G
Sbjct: 231 FG 232
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 70/144 (48%), Gaps = 29/144 (20%)
Query: 168 TLVPLMKSQYQPSEKIVERACLLEIASLNNLELLSVEGTDDAFQLKVTGWITNVNFSTKK 227
+L+P + Q PS+ + E L +L+NL ++G+I+ +
Sbjct: 238 SLIPFV--QLPPSDSVCEEYGLSCSDALHNL-------------FYISGFISQCTHGVGR 282
Query: 228 MTF---LLFIN----NPIK--RMIEQVYSIYLPKGSFPFVYLSLCMDPKNVDVNVHPTKH 278
+ FIN +P K R++ +VY +Y + +PFV L++ +D + VD+NV P K
Sbjct: 283 SSTDRQFFFINRRPCDPAKVCRLVNEVYHMY-NRHQYPFVVLNISVDSECVDINVTPDKR 341
Query: 279 EVHFLHEDTIIERVQSMLEKTLLG 302
++ E ++ ++L+ +L+G
Sbjct: 342 QILLQEEKLLL----AVLKTSLIG 361
>pdb|3H4L|A Chain A, Crystal Structure Of N Terminal Domain Of A Dna Repair
Prote
pdb|3H4L|B Chain B, Crystal Structure Of N Terminal Domain Of A Dna Repair
Prote
Length = 367
Score = 91.7 bits (226), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 43/113 (38%), Positives = 75/113 (66%)
Query: 6 KIKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQDNGT 65
+I ++++ V+RI +G+VI A+KEL++NS+DA + I++ K GL+ ++ DNG
Sbjct: 5 QIHQINDIDVHRITSGQVITDLTTAVKELVDNSIDANANQIEIIFKDYGLESIECSDNGD 64
Query: 66 GIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKT 118
GI + + + + TSK+ +F+D+ + T GFRGEAL+S+ +A L++IT T
Sbjct: 65 GIDPSNYEFLALKHYTSKIAKFQDVAKVQTLGFRGEALSSLCGIAKLSVITTT 117
Score = 88.2 bits (217), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 59/190 (31%), Positives = 102/190 (53%), Gaps = 21/190 (11%)
Query: 313 STSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEA 372
+ I++ K GL+ ++ DNG GI + + + + TSK+ +F+D+ + T GFRGEA
Sbjct: 42 ANQIEIIFKDYGLESIECSDNGDGIDPSNYEFLALKHYTSKIAKFQDVAKVQTLGFRGEA 101
Query: 373 LASISHVAHLTIITKTKTSPCAYRASY-----IDSKLKDPIKPCAGNQGTQIIAEDLFYN 427
L+S+ +A L++IT T + P A + Y I SK + N+GT ++ LF+N
Sbjct: 102 LSSLCGIAKLSVIT-TTSPPKADKLEYDMVGHITSK-----TTTSRNKGTTVLVSQLFHN 155
Query: 428 IPTRRKAL-KQPSEEYNKIADVVSRYAVHNPHVGFTL------KKQNENLADIRTNVNSS 480
+P R+K K ++ K V+ YA+ N + F++ K+N L+ +R NSS
Sbjct: 156 LPVRQKEFSKTFKRQFTKCLTVIQGYAIINAAIKFSVWNITPKGKKNLILSTMR---NSS 212
Query: 481 HSEVIGNIYG 490
+ I +++G
Sbjct: 213 MRKNISSVFG 222
Score = 31.6 bits (70), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 49/99 (49%), Gaps = 10/99 (10%)
Query: 207 DDAFQLKVTGWITNVNF----STKKMTFLLFINNPIK-----RMIEQVYSIYLPKGSFPF 257
D ++++V G+I+ +F ++K F+ P++ + +VY + FP
Sbjct: 257 DLDYKIRVKGYISQNSFGCGRNSKDRQFIYVNKRPVEYSTLLKCCNEVYKTF-NNVQFPA 315
Query: 258 VYLSLCMDPKNVDVNVHPTKHEVHFLHEDTIIERVQSML 296
V+L+L + +DVNV P K + +E +I+ ++ L
Sbjct: 316 VFLNLELPMSLIDVNVTPDKRVILLHNERAVIDIFKTTL 354
>pdb|4FLN|A Chain A, Crystal Structure Of Plant Protease Deg2
pdb|4FLN|B Chain B, Crystal Structure Of Plant Protease Deg2
pdb|4FLN|C Chain C, Crystal Structure Of Plant Protease Deg2
Length = 539
Score = 36.2 bits (82), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 61/144 (42%), Gaps = 13/144 (9%)
Query: 324 GLKLL-QIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHL 382
GLKLL + + + R E + I+ + +ED+N+ F G + +I H+AHL
Sbjct: 397 GLKLLTKARYSVARFRGEQIVILSQVLANEVNIGYEDMNNQQVLKFNGIPIRNIHHLAHL 456
Query: 383 TIITKTKTSPCAYRASYIDSKLKDPIKPCAGNQGTQIIAEDLFYNIPTRRKA-----LKQ 437
+ K K + +Y+ ++ A N + I +D Y IP+ R A
Sbjct: 457 IDMCKDKYLVFEFEDNYVAVLERE-----ASNSASLCILKD--YGIPSERSADLLEPYVD 509
Query: 438 PSEEYNKIADVVSRYAVHNPHVGF 461
P ++ + + V N +GF
Sbjct: 510 PIDDTQALDQGIGDSPVSNLEIGF 533
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 54 GLKLL-QIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHL 112
GLKLL + + + R E + I+ + +ED+N+ F G + +I H+AHL
Sbjct: 397 GLKLLTKARYSVARFRGEQIVILSQVLANEVNIGYEDMNNQQVLKFNGIPIRNIHHLAHL 456
Query: 113 TIITKTK 119
+ K K
Sbjct: 457 IDMCKDK 463
>pdb|3CXB|A Chain A, Crystal Structure Of Sifa And Skip
pdb|3HW2|A Chain A, Crystal Structure Of The Sifa-skip(ph) Complex
Length = 336
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 42/96 (43%), Gaps = 9/96 (9%)
Query: 403 KLKDPIKPCAGNQGTQIIAEDLFYNIPTRRKALKQPSEEYNKIADVV--SRYAVHNPH-- 458
K+KD + + + E LF R+ L + E ++A R+ VHNPH
Sbjct: 33 KIKDFFFSTGKAKADRCLHEMLFAERAPTRERLTEIFFELKELACASQRDRFQVHNPHEN 92
Query: 459 ---VGFTLKKQNEN--LADIRTNVNSSHSEVIGNIY 489
+ + QNE L I N ++ EV+GN+Y
Sbjct: 93 DATIILRIMDQNEENELLRITQNTDTFSCEVMGNLY 128
>pdb|4A4K|A Chain A, Crystal Structure Of The S. Cerevisiae Ski2 Insertion
Domain
pdb|4A4K|C Chain C, Crystal Structure Of The S. Cerevisiae Ski2 Insertion
Domain
pdb|4A4K|E Chain E, Crystal Structure Of The S. Cerevisiae Ski2 Insertion
Domain
pdb|4A4K|G Chain G, Crystal Structure Of The S. Cerevisiae Ski2 Insertion
Domain
pdb|4A4K|I Chain I, Crystal Structure Of The S. Cerevisiae Ski2 Insertion
Domain
Length = 256
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 21 GEVIQRPANALKEL---LENSLDAKSTSIQVTVKQGGLKLLQIQDNGTGIRKE 70
G+VI++ AL E N LD K+ + +++ GLK+ QI + T IR E
Sbjct: 164 GKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDE 216
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 30.0 bits (66), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 21 GEVIQRPANALKEL---LENSLDAKSTSIQVTVKQGGLKLLQIQDNGTGIRKE 70
G+VI++ AL E N LD K+ + +++ GLK+ QI + T IR E
Sbjct: 703 GKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDE 755
>pdb|2X26|A Chain A, Crystal Structure Of The Periplasmic Aliphatic Sulphonate
Binding Protein Ssua From Escherichia Coli
pdb|2X26|B Chain B, Crystal Structure Of The Periplasmic Aliphatic Sulphonate
Binding Protein Ssua From Escherichia Coli
Length = 308
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 55/126 (43%), Gaps = 12/126 (9%)
Query: 322 QGGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAH 381
QGG+++L+ +GT + + + R K F ++TF +AL
Sbjct: 169 QGGVRVLK---DGTDLNQTGSFYLAARPYAEKNGAFIQ-GVLATFS-EADALTRSQREQS 223
Query: 382 LTIITKTKTSPCAYRASYIDSKLKDPIKPC-AGNQGTQIIAEDLFYN---IPTR---RKA 434
+ ++ KT P ASY+D + IKP A Q DLFY +P + R+
Sbjct: 224 IALLAKTMGLPAPVIASYLDHRPPTTIKPVNAEVAALQQQTADLFYENRLVPKKVDIRQR 283
Query: 435 LKQPSE 440
+ QP++
Sbjct: 284 IWQPTQ 289
>pdb|3D36|A Chain A, How To Switch Off A Histidine Kinase: Crystal Structure Of
Geobacillus Stearothermophilus Kinb With The Inhibitor
Sda
pdb|3D36|B Chain B, How To Switch Off A Histidine Kinase: Crystal Structure Of
Geobacillus Stearothermophilus Kinb With The Inhibitor
Sda
Length = 244
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 29 NALKELLENSLDAKSTSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSK 83
N +K +E + + + V++ G + L++I D G G+ KE ++ + E + T+K
Sbjct: 130 NVMKNAIEAMPNGGTLQVYVSIDNGRV-LIRIADTGVGMTKEQLERLGEPYFTTK 183
>pdb|1GJV|A Chain A, Branched-chain Alpha-ketoacid Dehydrogenase Kinase (bck)
Complxed With Atp-gamma-s
pdb|1GKX|A Chain A, Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck)
pdb|1GKZ|A Chain A, Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck)
Complxed With Adp
Length = 388
Score = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 29 NALKELLENSLDAKST--SIQVTVKQGGLKLL-QIQDNGTGIRKEDMDIVCE-RFTTSK 83
NA++ +E+ LD + +T+ + L+ +I D G GI +D+D V + FTT++
Sbjct: 249 NAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAE 307
>pdb|3VAD|A Chain A, Crystal Structure Of I170f Mutant Branched-chain
Alpha-ketoacid Dehydrogenase Kinase In Complex With
3,6-dichlorobenzo[b]thiophene-2- Carboxylic Acid
Length = 418
Score = 28.9 bits (63), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 29 NALKELLENSLDAKST--SIQVTVKQGGLKLL-QIQDNGTGIRKEDMDIVCE-RFTTSK 83
NA++ +E+ LD + +T+ + L+ +I D G GI +D+D V + FTT++
Sbjct: 279 NAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAE 337
>pdb|3TZ0|A Chain A, Crystal Structure Of Branched-Chain Alpha-Ketoacid
Dehydrogenase KinaseS-Alpha-Chloroisocaproate Complex
pdb|3TZ2|A Chain A, Crystal Structure Of Branched-Chain Alpha-Ketoacid
Dehydrogenase KinasePHENYLBUTYRATE COMPLEX
pdb|3TZ4|A Chain A, Crystal Structure Of Branched-Chain Alpha-Ketoacid
Dehydrogenase KinaseS-Alpha-Chloroisocaproate Complex
With Adp
pdb|3TZ5|A Chain A, Crystal Structure Of Branched-Chain Alpha-Ketoacid
Dehydrogenase KinasePHENYLBUTYRATE COMPLEX WITH ADP
Length = 418
Score = 28.9 bits (63), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 29 NALKELLENSLDAKST--SIQVTVKQGGLKLL-QIQDNGTGIRKEDMDIVCE-RFTTSK 83
NA++ +E+ LD + +T+ + L+ +I D G GI +D+D V + FTT++
Sbjct: 279 NAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAE 337
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
0.317 0.132 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,719,460
Number of Sequences: 62578
Number of extensions: 538996
Number of successful extensions: 1292
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1254
Number of HSP's gapped (non-prelim): 48
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)