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= psy4844
(254 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
Length = 977
Score = 152 bits (385), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 93/254 (36%), Positives = 145/254 (57%), Gaps = 13/254 (5%)
Query: 6 VQSSVWLVMKIVREHYLRDDLSCGSELCLACDTKEAILDKIPTSSKAILDKIPTSSSKKY 65
V+S KIVREHYLR D+ C S C C + + D K IL P S
Sbjct: 1 VRSRNGGATKIVREHYLRSDIPCLSRSCTKC-PQIVVPDAQNELPKFILSDSPLELSAP- 58
Query: 66 MEPHYLLLDTNIILEQIDILEEPT-LCNVILVQTILQEVKHRSSSVYKRLKDLI--SNPS 122
+ HY++LDTN++L+ ID+LE P +VI+ Q +L EV+++S VY RL+ L S+
Sbjct: 59 IGKHYVVLDTNVVLQAIDLLENPNCFFDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDH 118
Query: 123 RKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLES-AVRVILLSEDVRNR 181
++F VF NE T+VE+ P E++NDRNDRA+R+ WY EHL+ + V+L++ D NR
Sbjct: 119 KRFIVFHNEFSEHTFVERLPNETINDRNDRAIRKTCQWYSEHLKPYDINVVLVTNDRLNR 178
Query: 182 DLAT---QSGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDSL----YPLHATPS 234
+ AT +S ++T S+ YI L N + + D + + ++ + +D+ +P + + +
Sbjct: 179 EAATKEVESNIITKSLVQYIELLPNADDIRDSIPQMDSFDKDLERDTFSDFTFPEYYSTA 238
Query: 235 EIHAGIKNQSLLQG 248
+ G+KN L QG
Sbjct: 239 RVMGGLKNGVLYQG 252
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 1003
Score = 151 bits (381), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 92/254 (36%), Positives = 145/254 (57%), Gaps = 13/254 (5%)
Query: 6 VQSSVWLVMKIVREHYLRDDLSCGSELCLACDTKEAILDKIPTSSKAILDKIPTSSSKKY 65
V+S KIVREHYLR D+ C S C C + + D K IL P S
Sbjct: 27 VRSRNGGATKIVREHYLRSDIPCLSRSCTKC-PQIVVPDAQNELPKFILSDSPLELSAP- 84
Query: 66 MEPHYLLLDTNIILEQIDILEEPT-LCNVILVQTILQEVKHRSSSVYKRLKDLI--SNPS 122
+ HY++LDTN++L+ ID+LE P +VI+ Q +L EV+++S VY RL+ L S+
Sbjct: 85 IGKHYVVLDTNVVLQAIDLLENPNCFFDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDH 144
Query: 123 RKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLES-AVRVILLSEDVRNR 181
++F VF NE T+VE+ P E++NDRN+RA+R+ WY EHL+ + V+L++ D NR
Sbjct: 145 KRFIVFHNEFSEHTFVERLPNETINDRNNRAIRKTCQWYSEHLKPYDINVVLVTNDRLNR 204
Query: 182 DLAT---QSGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDSL----YPLHATPS 234
+ AT +S ++T S+ YI L N + + D + + ++ + +D+ +P + + +
Sbjct: 205 EAATKEVESNIITKSLVQYIELLPNADDIRDSIPQMDSFDKDLERDTFSDFTFPEYYSTA 264
Query: 235 EIHAGIKNQSLLQG 248
+ G+KN L QG
Sbjct: 265 RVMGGLKNGVLYQG 278
>pdb|1Z68|A Chain A, Crystal Structure Of Human Fibroblast Activation Protein
Alpha
pdb|1Z68|B Chain B, Crystal Structure Of Human Fibroblast Activation Protein
Alpha
Length = 719
Score = 30.4 bits (67), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 31/128 (24%), Positives = 53/128 (41%), Gaps = 20/128 (15%)
Query: 122 SRKFYVFVNEHHYETYVEQEPGE-----SVNDRNDRALRRVATW-YEEHLESAVRVILLS 175
S+ YV+ N Y++Q PG+ + N R ++ + W YEE + + + S
Sbjct: 122 SKLAYVYQNN----IYLKQRPGDPPFQITFNGRENKIFNGIPDWVYEEEMLATKYALWWS 177
Query: 176 EDVRNRDLA----TQSGLLTSSIEG---YISTLSNGEPLLDKLSKKEAVVETSVKDSLYP 228
+ + A T ++ S G Y T++ P K K VV + D+ YP
Sbjct: 178 PNGKFLAYAEFNDTDIPVIAYSYYGDEQYPRTINIPYP---KAGAKNPVVRIFIIDTTYP 234
Query: 229 LHATPSEI 236
+ P E+
Sbjct: 235 AYVGPQEV 242
>pdb|1LJ2|A Chain A, Recognition Of Eif4g By Rotavirus Nsp3 Reveals A Basis For
Mrna Circularization
pdb|1LJ2|B Chain B, Recognition Of Eif4g By Rotavirus Nsp3 Reveals A Basis For
Mrna Circularization
Length = 110
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 181 RDLATQSGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDSLYPLHA 231
RDL + G LTSSIE Y+ ++ LD K + + + D++ PLHA
Sbjct: 27 RDLQNKIGSLTSSIEWYLRSME-----LDPEIKADIEQQINSIDAINPLHA 72
>pdb|2DUT|A Chain A, Crystal Structure Of A M-Loop Deletion Variant Of Ment In
The Native Conformation
pdb|2DUT|B Chain B, Crystal Structure Of A M-Loop Deletion Variant Of Ment In
The Native Conformation
pdb|2DUT|C Chain C, Crystal Structure Of A M-Loop Deletion Variant Of Ment In
The Native Conformation
pdb|2DUT|D Chain D, Crystal Structure Of A M-Loop Deletion Variant Of Ment In
The Native Conformation
Length = 423
Score = 27.3 bits (59), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 137 YVEQEPGESVNDRN--DRALRRVATWYEEHLESAVRVILLSEDVR 179
Y + EP + VN + +++ + + TW E+ ES ++ +L S+DV+
Sbjct: 152 YYKAEP-QKVNFKTAPEQSRKEINTWVEKQTESKIKNLLSSDDVK 195
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 0.132 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,084,632
Number of Sequences: 62578
Number of extensions: 267085
Number of successful extensions: 856
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 848
Number of HSP's gapped (non-prelim): 20
length of query: 254
length of database: 14,973,337
effective HSP length: 97
effective length of query: 157
effective length of database: 8,903,271
effective search space: 1397813547
effective search space used: 1397813547
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: 50 (23.9 bits)