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= 003295
(833 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 45/207 (21%), Positives = 77/207 (37%), Gaps = 26/207 (12%)
Query: 542 CCKDGKPEEGFKLKEDMIKRGIQPDNYTYNLLLHGLCSLGKMEEAIELWEECKRTVFGPD 601
C K G E +L ++ + G+Q Y YN+LL+ +CSL E + P
Sbjct: 36 CSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLA---------EAATESSPNPG 85
Query: 602 IYTYGVMIDGFCKADKIEEGETLFNEMISKKMELNPVVYNTLIRAYCKIGNTTAAFRLSN 661
+ G +F +MI K+ N + R + AF +
Sbjct: 86 L----------------SRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVK 129
Query: 662 DMKSRGILPTSVTYSSLIHGLCNIGLIEDAKCLFDEMRKEGLLPNVACYTALIGGYCKLG 721
MK+ GI P +Y + G C G + A + M + ++P AL+
Sbjct: 130 QMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTK 189
Query: 722 QMDEAESVLQEMASINIHPNKITYTIM 748
D+ LQ + + +K T+ ++
Sbjct: 190 NADKVYKTLQRLRDLVRQVSKSTFDMI 216
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 39/202 (19%), Positives = 85/202 (42%), Gaps = 18/202 (8%)
Query: 249 SPDVFLFSTAINAFCKRGRIEDAIGLFTKMEELGIAPNVVTYNNIIHGLCR--------- 299
SP+ L ++ K+G + +A+ L+ + G+ + YN +++ +C
Sbjct: 24 SPEALL-KQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESS 81
Query: 300 -NGRLYEAFHLKEKMVLREVEPSLITYSILINGLIKLEKFDDANF---VLKEMSVRGFVP 355
N L F + ++M++ +V P+ T++ NG DD ++K+M G P
Sbjct: 82 PNPGLSRGFDIFKQMIVDKVVPNEATFT---NGARLAVAKDDPEMAFDMVKQMKAFGIQP 138
Query: 356 NYVVYNTLIDGYCKKGNISEALKIRDDMVSKGMSPNSVTFNSLIHGFCKSGQMDNAENAL 415
Y + G+C+KG+ +A ++ MV + P +L+ + D L
Sbjct: 139 RLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTL 198
Query: 416 EEMLSRGLSINQGAYTSVIKWL 437
+ + +++ + + +W
Sbjct: 199 QRLRDLVRQVSKSTFDMIEEWF 220
Score = 36.6 bits (83), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 234 VQKGIEVFETM-CRGVSPDVFLFSTAINAFCKRGRIEDAIGLFTKMEELGIAPNVVTYNN 292
+ +G ++F+ M V P+ F+ + E A + +M+ GI P + +Y
Sbjct: 86 LSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGP 145
Query: 293 IIHGLCRNGRLYEAFHLKEKM 313
+ G CR G +A+ + M
Sbjct: 146 ALFGFCRKGDADKAYEVDAHM 166
Score = 36.2 bits (82), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 37/194 (19%), Positives = 83/194 (42%), Gaps = 16/194 (8%)
Query: 649 KIGNTTAAFRLSNDMKSRGILPTSVTYSSLIHGLCNIGLIEDAKC----------LFDEM 698
K G+ A RL ++ + G+ + Y+ L++ +C++ +F +M
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFDIFKQM 96
Query: 699 RKEGLLPNVACYTALIGGYCKLGQMDE--AESVLQEMASINIHPNKITYTIMIGGYCKLG 756
+ ++PN A +T G + + D A ++++M + I P +Y + G+C+ G
Sbjct: 97 IVDKVVPNEATFTN--GARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG 154
Query: 757 DMKEAAKLLNVMAEKGISPDSITYNVFMDGHCKGGNVEEAFKVCDRMLSEGLSLDEITYT 816
D +A ++ M E + P+ + N ++ +K R+ + + T+
Sbjct: 155 DADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTF- 213
Query: 817 TLIDGWQSSTITNQ 830
+I+ W S + +
Sbjct: 214 DMIEEWFKSEVATK 227
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 526 RGLILDKVTYNTLI------LGCCKDGKPEEGFKLKEDMIKRGIQPDNYTYNLLLHGLCS 579
+ +I+DKV N L KD PE F + + M GIQP +Y L G C
Sbjct: 94 KQMIVDKVVPNEATFTNGARLAVAKDD-PEMAFDMVKQMKAFGIQPRLRSYGPALFGFCR 152
Query: 580 LGKMEEAIEL 589
G ++A E+
Sbjct: 153 KGDADKAYEV 162
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 37.4 bits (85), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 43/188 (22%), Positives = 69/188 (36%), Gaps = 33/188 (17%)
Query: 505 HGMCEAGNL-KEAGKLLMEMLQRGLILDKVTYNTLILGCCKDGKPEEGFKLKEDMIKRGI 563
H + NL ++A K ++ L+ K+ C K G E +L ++ + G+
Sbjct: 4 HXASPSENLSRKAKKKAIQQSPEALLKQKLDX------CSKKGDVLEALRLYDEARRNGV 57
Query: 564 QPDNYTYNLLLHGLCSLGKMEEAIELWEECKRTVFGPDIYTYGVMIDGFCKADKIEEGET 623
Q Y YN+LL+ +CSL E A E + P + G
Sbjct: 58 QLSQYHYNVLLY-VCSLA--EAATE-------SSPNPG----------------LSRGFD 91
Query: 624 LFNEMISKKMELNPVVYNTLIRAYCKIGNTTAAFRLSNDMKSRGILPTSVTYSSLIHGLC 683
+F + I K+ N + R + AF K+ GI P +Y + G C
Sbjct: 92 IFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFC 151
Query: 684 NIGLIEDA 691
G + A
Sbjct: 152 RKGDADKA 159
Score = 33.1 bits (74), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 27/141 (19%), Positives = 63/141 (44%), Gaps = 12/141 (8%)
Query: 249 SPDVFLFSTAINAFCKRGRIEDAIGLFTKMEELGIAPNVVTYNNIIHGLCR--------- 299
SP+ L ++ K+G + +A+ L+ + G+ + YN +++ +C
Sbjct: 24 SPEALL-KQKLDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESS 81
Query: 300 -NGRLYEAFHLKEKMVLREVEPSLITYSILINGLIKLEKFDDANFVLKEMSVRGFVPNYV 358
N L F + ++ ++ +V P+ T++ + + + A +K+ G P
Sbjct: 82 PNPGLSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLR 141
Query: 359 VYNTLIDGYCKKGNISEALKI 379
Y + G+C+KG+ +A ++
Sbjct: 142 SYGPALFGFCRKGDADKAYEV 162
Score = 33.1 bits (74), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 31/122 (25%), Positives = 51/122 (41%), Gaps = 12/122 (9%)
Query: 511 GNLKEAGKLLMEMLQRGLILDKVTYNTLILGC-----CKDGKPEEGFKLKEDMIKRGIQ- 564
G++ EA +L E + G+ L + YN L+ C + P G D+ K+ I
Sbjct: 40 GDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXIVD 99
Query: 565 ---PDNYTYNLLLHGLCSLGKMEEAIELWEECKRTVFGPDIYTYGVMIDGFCK---ADKI 618
P+ T+ + E A + ++ K P + +YG + GFC+ ADK
Sbjct: 100 KVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKA 159
Query: 619 EE 620
E
Sbjct: 160 YE 161
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 1/77 (1%)
Query: 234 VQKGIEVF-ETMCRGVSPDVFLFSTAINAFCKRGRIEDAIGLFTKMEELGIAPNVVTYNN 292
+ +G ++F + + V P+ F+ + E A + + GI P + +Y
Sbjct: 86 LSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGP 145
Query: 293 IIHGLCRNGRLYEAFHL 309
+ G CR G +A+ +
Sbjct: 146 ALFGFCRKGDADKAYEV 162
Score = 30.0 bits (66), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 25/125 (20%), Positives = 54/125 (43%), Gaps = 15/125 (12%)
Query: 649 KIGNTTAAFRLSNDMKSRGILPTSVTYSSLIHGLCNIGLIEDAKC----------LFDEM 698
K G+ A RL ++ + G+ + Y+ L++ +C++ +F +
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFDIFKQX 96
Query: 699 RKEGLLPNVACYTALIGGYCKLGQMDE--AESVLQEMASINIHPNKITYTIMIGGYCKLG 756
+ ++PN A +T G + + D A +++ + I P +Y + G+C+ G
Sbjct: 97 IVDKVVPNEATFTN--GARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKG 154
Query: 757 DMKEA 761
D +A
Sbjct: 155 DADKA 159
Score = 29.6 bits (65), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 27/124 (21%), Positives = 51/124 (41%), Gaps = 11/124 (8%)
Query: 686 GLIEDAKCLFDEMRKEGLLPNVACYTALIGGYCKLGQMDEAES----------VLQEMAS 735
G + +A L+DE R+ G+ + Y L+ C L + S + ++
Sbjct: 40 GDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFDIFKQXIV 98
Query: 736 INIHPNKITYTIMIGGYCKLGDMKEAAKLLNVMAEKGISPDSITYNVFMDGHCKGGNVEE 795
+ PN+ T+T D + A + GI P +Y + G C+ G+ ++
Sbjct: 99 DKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADK 158
Query: 796 AFKV 799
A++V
Sbjct: 159 AYEV 162
>pdb|3P26|A Chain A, Crystal Structure Of S. Cerevisiae Hbs1 Protein
(Apo-Form), A Translational Gtpase Involved In Rna
Quality Control Pathways And Interacting With
Dom34PELOTA
pdb|3P26|B Chain B, Crystal Structure Of S. Cerevisiae Hbs1 Protein
(Apo-Form), A Translational Gtpase Involved In Rna
Quality Control Pathways And Interacting With
Dom34PELOTA
Length = 483
Score = 32.7 bits (73), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 44/208 (21%), Positives = 85/208 (40%), Gaps = 17/208 (8%)
Query: 341 ANFVLKEM-SVRGFVPNYVVYNTLIDGY-----CKKGNISEALKIRDDMVSKGMSPNSVT 394
ANF + + R FVPN ++ + D C + + +S+
Sbjct: 111 ANFTIVDAPGHRDFVPNAIMGISQADMAILCVDCSTNAFESGFDLDGQTKEHMLLASSLG 170
Query: 395 FNSLIHGFCKSGQMDNAENALEEMLSRGLS--INQGAYTSVIKWLCINSRFNSALH---F 449
++LI K +D ++ EE+ S+ L ++ G + I W+ I+ ++ +
Sbjct: 171 IHNLIIAMNKMDNVDWSQQRFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKIEY 230
Query: 450 TKEMLLRNLRPGDGLLTLLVSGLCKNGKQAEATE----LCFRLFEKGFTVNTVTSNALIH 505
T E +R G L++ L + K K+ E F + E + T AL+
Sbjct: 231 TDE--VRQWYNGPNLMSTLENAAFKISKENEGINKDDPFLFSVLEIIPSKKTSNDLALVS 288
Query: 506 GMCEAGNLKEAGKLLMEMLQRGLILDKV 533
G E+G+++ L + ++ I+DK+
Sbjct: 289 GKLESGSIQPGESLTIYPSEQSCIVDKI 316
>pdb|3IZQ|1 Chain 1, Structure Of The Dom34-Hbs1-Gdpnp Complex Bound To A
Translating Ribosome
Length = 611
Score = 32.7 bits (73), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 44/208 (21%), Positives = 85/208 (40%), Gaps = 17/208 (8%)
Query: 341 ANFVLKEM-SVRGFVPNYVVYNTLIDGY-----CKKGNISEALKIRDDMVSKGMSPNSVT 394
ANF + + R FVPN ++ + D C + + +S+
Sbjct: 245 ANFTIVDAPGHRDFVPNAIMGISQADMAILCVDCSTNAFESGFDLDGQTKEHMLLASSLG 304
Query: 395 FNSLIHGFCKSGQMDNAENALEEMLSRGLS--INQGAYTSVIKWLCINSRFNSALH---F 449
++LI K +D ++ EE+ S+ L ++ G + I W+ I+ ++ +
Sbjct: 305 IHNLIIAMNKMDNVDWSQQRFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKIEY 364
Query: 450 TKEMLLRNLRPGDGLLTLLVSGLCKNGKQAEATE----LCFRLFEKGFTVNTVTSNALIH 505
T E +R G L++ L + K K+ E F + E + T AL+
Sbjct: 365 TDE--VRQWYNGPNLMSTLENAAFKISKENEGINKDDPFLFSVLEIIPSKKTSNDLALVS 422
Query: 506 GMCEAGNLKEAGKLLMEMLQRGLILDKV 533
G E+G+++ L + ++ I+DK+
Sbjct: 423 GKLESGSIQPGESLTIYPSEQSCIVDKI 450
>pdb|3P27|A Chain A, Crystal Structure Of S. Cerevisiae Hbs1 Protein (Gdp-Bound
Form), A Translational Gtpase Involved In Rna Quality
Control Pathways And Interacting With Dom34PELOTA
pdb|3P27|B Chain B, Crystal Structure Of S. Cerevisiae Hbs1 Protein (Gdp-Bound
Form), A Translational Gtpase Involved In Rna Quality
Control Pathways And Interacting With Dom34PELOTA
Length = 483
Score = 32.7 bits (73), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 44/208 (21%), Positives = 83/208 (39%), Gaps = 17/208 (8%)
Query: 341 ANFVLKEM-SVRGFVPNYVVYNTLIDGY-----CKKGNISEALKIRDDMVSKGMSPNSVT 394
ANF + + R FVPN + + D C + + +S+
Sbjct: 111 ANFTIVDAPGHRDFVPNAIXGISQADXAILCVDCSTNAFESGFDLDGQTKEHXLLASSLG 170
Query: 395 FNSLIHGFCKSGQMDNAENALEEMLSRGLS--INQGAYTSVIKWLCINSRFNSALH---F 449
++LI K +D ++ EE+ S+ L ++ G + I W+ I+ ++ +
Sbjct: 171 IHNLIIAXNKXDNVDWSQQRFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKIEY 230
Query: 450 TKEMLLRNLRPGDGLLTLLVSGLCKNGKQAEATE----LCFRLFEKGFTVNTVTSNALIH 505
T E+ R G L + L + K K+ E F + E + T AL+
Sbjct: 231 TDEV--RQWYNGPNLXSTLENAAFKISKENEGINKDDPFLFSVLEIIPSKKTSNDLALVS 288
Query: 506 GMCEAGNLKEAGKLLMEMLQRGLILDKV 533
G E+G+++ L + ++ I+DK+
Sbjct: 289 GKLESGSIQPGESLTIYPSEQSCIVDKI 316
>pdb|1QOU|A Chain A, Cen (Centroradialis) Protein From Antirrhinum
pdb|1QOU|B Chain B, Cen (Centroradialis) Protein From Antirrhinum
Length = 181
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 147 KMPVLYASNPSIRHIEIASQMVDLNVTSEPALGVQIADL 185
KM V+Y SN SI+H+ ++ VTS P + V D+
Sbjct: 28 KMSVIYNSNNSIKHVYNGHELFPSAVTSTPRVEVHGGDM 66
>pdb|2V3C|C Chain C, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna Complex
Of M. Jannaschii
pdb|2V3C|D Chain D, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna Complex
Of M. Jannaschii
Length = 432
Score = 29.6 bits (65), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 630 SKKMELNPVVYNTLIRAYCK-IGNTTAAFRLSNDMKSRGILPTSVTYSS 677
+KK+ELNP N ++ + G TT A +L+ ++ RG+ P + +
Sbjct: 89 AKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADT 137
>pdb|3NDB|B Chain B, Crystal Structure Of A Signal Sequence Bound To The Signal
Recognition Particle
Length = 454
Score = 29.6 bits (65), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 630 SKKMELNPVVYNTLIRAYCK-IGNTTAAFRLSNDMKSRGILPTSVTYSS 677
+KK+ELNP N ++ + G TT A +L+ ++ RG+ P + +
Sbjct: 89 AKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADT 137
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
0.321 0.138 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,439,921
Number of Sequences: 62578
Number of extensions: 897516
Number of successful extensions: 1932
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1904
Number of HSP's gapped (non-prelim): 28
length of query: 833
length of database: 14,973,337
effective HSP length: 107
effective length of query: 726
effective length of database: 8,277,491
effective search space: 6009458466
effective search space used: 6009458466
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)