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= 041882
(491 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DIV|S Chain S, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
pdb|4DIV|T Chain T, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
pdb|4DIV|U Chain U, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
pdb|4DIV|V Chain V, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
pdb|4DIV|W Chain W, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
pdb|4DIV|X Chain X, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
Length = 253
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 8/87 (9%)
Query: 286 LVNFGVLMSDLGKRGKIEEAKSLLSEMKKRQYKPDVVTYNILI--------NYLCKEDRA 337
+ +F VL SD K GKI+ K+ + E+ KPD +++ +L NY K +A
Sbjct: 135 ISSFTVLCSDPFKHGKIQSVKNKVIEVLPYPVKPDKLSFKLLTEGLLATDGNYRLKSSQA 194
Query: 338 AEAYKVLTEMQIGGCKPNAATYRMMVD 364
+ + + Q G N ++D
Sbjct: 195 KKGDFLEFDFQTGDTFLNGKVNNNLLD 221
>pdb|3MKR|A Chain A, Crystal Structure Of Yeast AlphaEPSILON-Cop Subcomplex Of
The Copi Vesicular Coat
Length = 291
Score = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 28/110 (25%), Positives = 49/110 (44%), Gaps = 6/110 (5%)
Query: 127 VDKAIEVFNRMTSFDCVRTL-QSFNSLLDILVDNDRVDDAKRMFDD-ADKMGFRPNLISF 184
+D A + +M D TL Q + + + +++ DA +F + ADK P L+
Sbjct: 146 LDLARKELKKMQDQDEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCS--PTLLLL 203
Query: 185 NVMIKGRLKKGEWEEASRVFDEMLEREV--PPTVVTYNSLIGFLCRTGEM 232
N + +G WE A V E L+++ P T++ L L + E+
Sbjct: 204 NGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEV 253
>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 = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 30/127 (23%), Positives = 56/127 (44%), Gaps = 9/127 (7%)
Query: 153 LDILVDNDRVDDAKRMFDDADKMGFRPNLISFNVMIK-GRLKKGEWEEA-----SRVFD- 205
LD+ V +A R++D+A + G + + +NV++ L + E + SR FD
Sbjct: 33 LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 206 --EMLEREVPPTVVTYNSLIGFLCRTGEMGKAKGLFEDMIKKGTYPNAVTYALLMEGLCF 263
+M+ +V P T+ + + A + + M G P +Y + G C
Sbjct: 93 FKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCR 152
Query: 264 KGEYNEA 270
KG+ ++A
Sbjct: 153 KGDADKA 159
>pdb|1JMS|A Chain A, Crystal Structure Of The Catalytic Core Of Murine Terminal
Deoxynucleotidyl Transferase
Length = 381
Score = 29.3 bits (64), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 56/121 (46%), Gaps = 17/121 (14%)
Query: 257 LMEGLCFKGEYNEAKKMMFDMAYRGCKPQLVNFGVLMSD------LGKR--GKIEEAKSL 308
++EG+ GE +EAK ++ D Y+ K FGV + +G R KI+ KSL
Sbjct: 95 IIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSL 154
Query: 309 -LSEMKKRQYKPDVVTYNILINYLCKEDRAAEAYKVLTEMQIGGCKPNAATYRMMVDGFL 367
++M+K + + Y L++ C AEA +L + + P+A M GF
Sbjct: 155 RFTQMQKAGF----LYYEDLVS--CVNRPEAEAVSMLVKEAVVTFLPDALV--TMTGGFR 206
Query: 368 R 368
R
Sbjct: 207 R 207
>pdb|1KDH|A Chain A, Binary Complex Of Murine Terminal Deoxynucleotidyl
Transferase With A Primer Single Stranded Dna
pdb|1KEJ|A Chain A, Crystal Structure Of Murine Terminal Deoxynucleotidyl
Transferase Complexed With Ddatp
Length = 363
Score = 28.9 bits (63), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 56/121 (46%), Gaps = 17/121 (14%)
Query: 257 LMEGLCFKGEYNEAKKMMFDMAYRGCKPQLVNFGVLMSD------LGKR--GKIEEAKSL 308
++EG+ GE +EAK ++ D Y+ K FGV + +G R KI+ KSL
Sbjct: 77 IIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSL 136
Query: 309 -LSEMKKRQYKPDVVTYNILINYLCKEDRAAEAYKVLTEMQIGGCKPNAATYRMMVDGFL 367
++M+K + + Y L++ C AEA +L + + P+A M GF
Sbjct: 137 RFTQMQKAGF----LYYEDLVS--CVNRPEAEAVSMLVKEAVVTFLPDALV--TMTGGFR 188
Query: 368 R 368
R
Sbjct: 189 R 189
>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 = 28.9 bits (63), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 29/123 (23%), Positives = 52/123 (42%), Gaps = 11/123 (8%)
Query: 193 KKGEWEEASRVFDEMLEREVPPTVVTYNSLIGFLCRTGEM--------GKAKG--LFEDM 242
KKG+ EA R++DE V + YN L+ ++C E G ++G +F+
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQX 96
Query: 243 IKKGTYPNAVTYALLMEGLCFKGEYNEAKKMMFDMAYRGCKPQLVNFGVLMSDLGKRGKI 302
I PN T+ K + A + G +P+L ++G + ++G
Sbjct: 97 IVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDA 156
Query: 303 EEA 305
++A
Sbjct: 157 DKA 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
0.323 0.138 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,501,889
Number of Sequences: 62578
Number of extensions: 518337
Number of successful extensions: 1139
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1126
Number of HSP's gapped (non-prelim): 15
length of query: 491
length of database: 14,973,337
effective HSP length: 103
effective length of query: 388
effective length of database: 8,527,803
effective search space: 3308787564
effective search space used: 3308787564
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)