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= 006632
(637 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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/162 (22%), Positives = 73/162 (45%), Gaps = 10/162 (6%)
Query: 195 ESVKLLDLMSREGNVKPNLRTYNVLVRAWCNEKNITEA---------WNVMHKMAASGMK 245
E+++L D R G V+ + YNVL+ + TE+ +++ +M +
Sbjct: 44 EALRLYDEARRNG-VQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVV 102
Query: 246 PDVVTYNTIATAYAQNGEADQAEEVIVEMEHNGVQPNGRTCGIIISGYCKEGKIKEALRF 305
P+ T+ A + + A +++ +M+ G+QP R+ G + G+C++G +A
Sbjct: 103 PNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
Query: 306 ARTMKEYGVHPNLVIFNLLIKGFVEIMDRDGVDEVLALMKEF 347
M E V P L+K ++ + D V + L +++
Sbjct: 163 DAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDL 204
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 49/216 (22%), Positives = 86/216 (39%), Gaps = 26/216 (12%)
Query: 295 KEGKIKEALRFARTMKEYGVHPNLVIFNLLIKGFVEIMDRDGVDEVLALMKEFRVNPDVI 354
K+G + EALR + GV + +N+L+ V + E NP +
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLY----------VCSLAEAATESSPNPGL- 86
Query: 355 TYSTIMNAWSTAGFMDKCKEIFDDMGKAGIKPDAHAYSILAKGYVREQEPEKAEELLMTM 414
+ GF +IF M + P+ ++ A+ V + +PE A +++ M
Sbjct: 87 ----------SRGF-----DIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQM 131
Query: 415 IESGFHPNVVIFTTIISGWCSDGSMDRAIEVFDKMCEHGVSPNLKTFETLMWGYSEARQP 474
G P + + + G+C G D+A EV M E V P L+ + +
Sbjct: 132 KAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNA 191
Query: 475 WRAEEILQIMKAFGVHPQKSTFLLLAEARRATGLTK 510
+ + LQ ++ KSTF ++ E ++ TK
Sbjct: 192 DKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEVATK 227
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 40/162 (24%), Positives = 65/162 (40%), Gaps = 14/162 (8%)
Query: 185 KGYGIAGKPEESVKL-LDLMSREGNVKPNLRTYNVLVRAWCNEKNITE-AWNVMHKMAAS 242
K I PE +K LD+ S++G+V LR Y+ R N +++ +NV+
Sbjct: 17 KKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARR---NGVQLSQYHYNVLLY---- 69
Query: 243 GMKPDVVTYNTIATAYAQNGEADQAEEVIVEMEHNGVQPNGRTCGIIISGYCKEGKIKEA 302
V + AT + N + ++ +M + V PN T + + A
Sbjct: 70 -----VCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMA 124
Query: 303 LRFARTMKEYGVHPNLVIFNLLIKGFVEIMDRDGVDEVLALM 344
+ MK +G+ P L + + GF D D EV A M
Sbjct: 125 FDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHM 166
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 27/125 (21%), Positives = 58/125 (46%), Gaps = 11/125 (8%)
Query: 144 FFNAVINAFSESGNMEEAMDTFWKMKESGLTPTTSTYNTLIKGYGIAGKPEESV-KLLDL 202
+NAV+ ++ G +E + + +K++GLTP +Y ++ G + ++ + L+
Sbjct: 167 MYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQ 226
Query: 203 MSREGNVKPNLRTYNVLVRAWCNEKNITEAWNVMHKMAAS-----GMKPDVVTYNTIATA 257
MS+EG L+ + +E++ +HK+ + + P V T +
Sbjct: 227 MSQEG-----LKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDV 281
Query: 258 YAQNG 262
YA++G
Sbjct: 282 YAKDG 286
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 1/81 (1%)
Query: 212 NLRTYNVLVRAWCNEKNITEAWNVMHKMAASGMKPDVVTYNTIATAYA-QNGEADQAEEV 270
L YN ++ W + E V+ + +G+ PD+++Y Q+ +A E
Sbjct: 164 TLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERC 223
Query: 271 IVEMEHNGVQPNGRTCGIIIS 291
+ +M G++ +++S
Sbjct: 224 LEQMSQEGLKLQALFTAVLLS 244
>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 = 35.4 bits (80), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 28/130 (21%), Positives = 60/130 (46%), Gaps = 8/130 (6%)
Query: 149 INAFSESGNMEEAMDTFWKMKESGLTPTTSTYNTLIKGYGIAGKPEES------VKLLDL 202
++ S+ G++ EA+ + + + +G+ + YN L+ +A ES + D+
Sbjct: 33 LDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 203 MSRE--GNVKPNLRTYNVLVRAWCNEKNITEAWNVMHKMAASGMKPDVVTYNTIATAYAQ 260
+ V PN T+ R + + A++ + + A G++P + +Y + +
Sbjct: 93 FKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCR 152
Query: 261 NGEADQAEEV 270
G+AD+A EV
Sbjct: 153 KGDADKAYEV 162
Score = 33.5 bits (75), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 30/125 (24%), Positives = 53/125 (42%), Gaps = 9/125 (7%)
Query: 295 KEGKIKEALRFARTMKEYGVHPNLVIFNLLI------KGFVEIMDRDGVDEVLALMKEFR 348
K+G + EALR + GV + +N+L+ + E G+ + K+
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXI 97
Query: 349 VNPDVITYSTIMNAWSTAGFMDKCKEIFDDMGKA---GIKPDAHAYSILAKGYVREQEPE 405
V+ V +T N A D + FD + + GI+P +Y G+ R+ + +
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 406 KAEEL 410
KA E+
Sbjct: 158 KAYEV 162
Score = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 25/117 (21%), Positives = 53/117 (45%), Gaps = 10/117 (8%)
Query: 195 ESVKLLDLMSREGNVKPNLRTYNVLVRAWCNEKNITEA---------WNVMHKMAASGMK 245
E+++L D R G V+ + YNVL+ + TE+ +++ + +
Sbjct: 44 EALRLYDEARRNG-VQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXIVDKVV 102
Query: 246 PDVVTYNTIATAYAQNGEADQAEEVIVEMEHNGVQPNGRTCGIIISGYCKEGKIKEA 302
P+ T+ A + + A + + + + G+QP R+ G + G+C++G +A
Sbjct: 103 PNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKA 159
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
0.316 0.131 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,376,668
Number of Sequences: 62578
Number of extensions: 751997
Number of successful extensions: 2305
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 2283
Number of HSP's gapped (non-prelim): 16
length of query: 637
length of database: 14,973,337
effective HSP length: 105
effective length of query: 532
effective length of database: 8,402,647
effective search space: 4470208204
effective search space used: 4470208204
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)