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= psy423
(255 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ODH|A Chain A, Structure Of The Gcm Domain Bound To Dna
Length = 174
Score = 180 bits (456), Expect = 8e-46, Method: Compositional matrix adjust.
Identities = 83/139 (59%), Positives = 102/139 (73%), Gaps = 2/139 (1%)
Query: 92 WQEWADGHCRFVYPASSEEAKRHASGWAMRNTNNHNVHILKKSCLGVLVCSRRCVLPSGD 151
+QEW D + + +Y + A+RH S WAMRNTNNHN ILKKSCLGV+VCSR C G
Sbjct: 33 FQEWPDSYVKHIYSSDDRNAQRHLSSWAMRNTNNHNSRILKKSCLGVVVCSRDCSTEEGR 92
Query: 152 SVHLRPAICDKARKKQTGKPCPNRKCTGRLEIMPCRGHCGYPVTHFWRHTDYGIFFQAKG 211
++LRPAICDKAR+KQ K CPN C G L+++PCRGH G+PVT+FWRH IFFQ+KG
Sbjct: 93 KIYLRPAICDKARQKQQRKSCPN--CNGPLKLIPCRGHGGFPVTNFWRHDGRFIFFQSKG 150
Query: 212 VHDHLRPEAKSTSEARRSL 230
HDH RPE K +EARR++
Sbjct: 151 EHDHPRPETKLEAEARRAM 169
>pdb|1FPN|1 Chain 1, Human Rhinovirus Serotype 2 (Hrv2)
pdb|1V9U|1 Chain 1, Human Rhinovirus 2 Bound To A Fragment Of Its Cellular
Receptor Protein
pdb|3DPR|A Chain A, Human Rhinovirus 2 Bound To A Concatamer Of The Vldl
Receptor Module V3
pdb|3TN9|1 Chain 1, X-Ray Structure Of The Hrv2 Empty Capsid (B-Particle)
Length = 289
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 57/159 (35%), Gaps = 18/159 (11%)
Query: 31 WDINDSVIPRAGRRFELLTFERLPERLILEDGKVVNMSTLGHAQ---MVIHPGNRVLLVT 87
W IN + + R+FEL T+ R + L +GH M + PG V
Sbjct: 97 WAINLQEMAQIRRKFELFTYTRFDSEITLVPCISALSQDIGHITMQYMYVPPGAPVPNSR 156
Query: 88 EFNSWQE-------WADGHCRFVYPASSEEAKRHASGWAM----RNTNNHNVHILKKSCL 136
+ +WQ W G YP S AS + M + + N + +
Sbjct: 157 DDYAWQSGTNASVFWQHGQA---YPRFSLPFLSVASAYYMFYDGYDEQDQNYGTANTNNM 213
Query: 137 GVLVCSRRCVLPSGDSVHLRPAICDKARKKQTGKPCPNR 175
G L CSR VH+ I KA+ + P P R
Sbjct: 214 GSL-CSRIVTEKHIHKVHIMTRIYHKAKHVKAWCPRPPR 251
>pdb|3VDD|A Chain A, Structure Of Hrv2 Capsid Complexed With Antiviral Compound
Bta798
Length = 283
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 57/159 (35%), Gaps = 18/159 (11%)
Query: 31 WDINDSVIPRAGRRFELLTFERLPERLILEDGKVVNMSTLGHAQ---MVIHPGNRVLLVT 87
W IN + + R+FEL T+ R + L +GH M + PG V
Sbjct: 97 WAINLQEMAQIRRKFELFTYTRFDSEITLVPCISALSQDIGHITMQYMYVPPGAPVPNSR 156
Query: 88 EFNSWQE-------WADGHCRFVYPASSEEAKRHASGWAM----RNTNNHNVHILKKSCL 136
+ +WQ W G YP S AS + M + + N + +
Sbjct: 157 DDYAWQSGTNASVFWQHGQA---YPRFSLPFLSVASAYYMFYDGYDEQDQNYGTANTNNM 213
Query: 137 GVLVCSRRCVLPSGDSVHLRPAICDKARKKQTGKPCPNR 175
G L CSR VH+ I KA+ + P P R
Sbjct: 214 GSL-CSRIVTEKHIHKVHIMTRIYHKAKHVKAWCPRPPR 251
>pdb|1AYN|1 Chain 1, Human Rhinovirus 16 Coat Protein
pdb|1AYM|1 Chain 1, Human Rhinovirus 16 Coat Protein At High Resolution
pdb|1QJU|1 Chain 1, Human Rhinovirus 16 Coat Protein In Complex With Antiviral
Compound Vp61209
pdb|1QJX|1 Chain 1, Human Rhinovirus 16 Coat Protein In Complex With Antiviral
Compound Win68934
pdb|1QJY|1 Chain 1, Human Rhinovirus 16 Coat Protein In Complex With Antiviral
Compound Vp65099
pdb|1C8M|1 Chain 1, Refined Crystal Structure Of Human Rhinovirus 16 Complexed
With Vp63843 (Pleconaril), An Anti-Picornaviral Drug
Currently In Clinical Trials
pdb|1NCR|A Chain A, The Structure Of Rhinovirus 16 When Complexed With
Pleconaril, An Antiviral Compound
pdb|1ND2|A Chain A, The Structure Of Rhinovirus 16
pdb|1ND3|A Chain A, The Structure Of Hrv16, When Complexed With Pleconaril, An
Antiviral Compound
Length = 285
Score = 31.6 bits (70), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 13 VMKSVLPYSPRSFRHTADWDINDSVIPRAGRRFELLTFERLPERLILEDGKVVNMSTLGH 72
V+ V Y+ +SF W+IN + + R+FE+ T+ R + + +GH
Sbjct: 81 VLDIVDNYNDQSF---TKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGH 137
Query: 73 ---AQMVIHPGNRVLLVTEFNSWQ 93
M + PG + + +WQ
Sbjct: 138 IVMQYMYVPPGAPIPTTRDDYAWQ 161
>pdb|1D3E|1 Chain 1, Cryo-Em Structure Of Human Rhinovirus 16 (Hrv16) Complexed
With A Two-Domain Fragment Of Its Cellular Receptor,
Intercellular Adhesion Molecule-1 (D1d2-Icam-1).
Implications For Virus-Receptor Interactions. Alpha
Carbons Only
Length = 285
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 13 VMKSVLPYSPRSFRHTADWDINDSVIPRAGRRFELLTFERLPERLILEDGKVVNMSTLGH 72
V+ V Y+ +SF W+IN + + R+FE+ T+ R + + +GH
Sbjct: 81 VLDIVDNYNDQSF---TKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGH 137
Query: 73 ---AQMVIHPGNRVLLVTEFNSWQ 93
M + PG + + +WQ
Sbjct: 138 IVMQYMYVPPGAPIPTTRDDYAWQ 161
>pdb|2Y9M|B Chain B, Pex4p-Pex22p Structure
pdb|2Y9O|B Chain B, Pex4p-Pex22p Mutant I Structure
pdb|2Y9P|B Chain B, Pex4p-Pex22p Mutant Ii Structure
Length = 130
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 92 WQEWADGHCRFVYPAS-SEEAKRHASGWAMRNTNNHNVHILKKSCLGVLVCSRR-----C 145
W+E+A + P S ++ + + A G A R T N + I S G+ C RR C
Sbjct: 27 WEEYAADEVVLLVPTSHTDGSMKQAIGDAFRKTKNEHKIIYCDSMDGLWSCVRRLGKFQC 86
Query: 146 VLPSGD 151
+L S D
Sbjct: 87 ILNSRD 92
>pdb|1U08|A Chain A, Crystal Structure And Reactivity Of Ybdl From Escherichia
Coli Identify A Methionine Aminotransferase Function.
pdb|1U08|B Chain B, Crystal Structure And Reactivity Of Ybdl From Escherichia
Coli Identify A Methionine Aminotransferase Function
Length = 386
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 47/133 (35%), Gaps = 31/133 (23%)
Query: 65 VNMSTLGHAQMVIHPG--NRVLLVTEFNSWQE---WADGHCRFVYPASSEEAKRHASGWA 119
+N S GHA ++ HP R + V+ F W G+C P S+E K H
Sbjct: 208 INFSQQGHASVLAHPQLRERAVAVSSFGKTYHMTGWKVGYCVAPAPISAEIRKVHQYLTF 267
Query: 120 MRNTNNHNVHILKKSCLGVLVCSRRCVLPSGDSVHLRP----AICDKARKKQTGKPCPNR 175
NT L D + P A+ D R+K+ N
Sbjct: 268 SVNTPAQ--------------------LALADMLRAEPEHYLALPDFYRQKR--DILVNA 305
Query: 176 KCTGRLEIMPCRG 188
RLEI+PC G
Sbjct: 306 LNESRLEILPCEG 318
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 0.137 0.444
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,179,574
Number of Sequences: 62578
Number of extensions: 338509
Number of successful extensions: 648
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 645
Number of HSP's gapped (non-prelim): 8
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
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: 50 (23.9 bits)