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= 011028
(495 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3LZC|A Chain A, Crystal Structure Of Dph2 From Pyrococcus Horikoshii
pdb|3LZC|B Chain B, Crystal Structure Of Dph2 From Pyrococcus Horikoshii
pdb|3LZD|A Chain A, Crystal Structure Of Dph2 From Pyrococcus Horikoshii With
4fe-4s Cluster
pdb|3LZD|B Chain B, Crystal Structure Of Dph2 From Pyrococcus Horikoshii With
4fe-4s Cluster
Length = 378
Score = 66.2 bits (160), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 72/312 (23%), Positives = 126/312 (40%), Gaps = 47/312 (15%)
Query: 59 VDDKDIGLFVMADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTSTLPAFFVFGKASIN 118
+++ +I +F+ + YG+C + A V D +IH GH+ + +P FV A ++
Sbjct: 77 LEENNIEVFLHGEINYGACDPADREAKLVGCDALIHLGHSYMKLPLEVPTIFVPAFARVS 136
Query: 119 TSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASSSYGSGLKLEINFADVMC 178
++ G+ I+V ++ H + +E ++ G ++ I D
Sbjct: 137 VVEALKENIGEIKKLGRKIIVTTTAQHIHQLKEAKEFLE------SEGFEVSIGRGDSRI 190
Query: 179 TVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFN 238
S G GC N K E +LF IGS F + L
Sbjct: 191 ----------SWPGQVLGC----------NYSVAKVRGEGILF-IGS--GIFHPLGLAV- 226
Query: 239 GCEIVRYDATEERLLT--------DVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAG 290
AT +++L P + +++R+ + KA DA GV+V
Sbjct: 227 --------ATRKKVLAIDPYTKAFSWIDPERFIRKRWAQIAKAMDAKKFGVIVSIKKGQL 278
Query: 291 YLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAP 350
L ++ +L+ K G++A +VM N KL FP + ++ V+C + L D + P
Sbjct: 279 RLAEAKRIVKLLKKHGREARLIVMNDVNYHKLEGFP-FEAYVVVACPRVPLDDYGAWRKP 337
Query: 351 VITPFEAMLAFG 362
V+TP E + G
Sbjct: 338 VLTPKEVEILLG 349
>pdb|3RR5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sp. 1519
Length = 570
Score = 32.0 bits (71), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 43/167 (25%), Positives = 68/167 (40%), Gaps = 18/167 (10%)
Query: 12 TADFIYSRKFTRVALQFPDNLLKDSIRIVRALRAKLGSLRSSDGERGVDDKDIGLFVMAD 71
T+DF Y K + L+ + L K SI+I + +R L +S E ++ +G +
Sbjct: 204 TSDFGYVAKVAK--LEGNEGLSKVSIQIGKPIRPMLAQNAASVKEALIE---MGGEAAFE 258
Query: 72 TTYGSCCVDEVGASHVDADCVIHYGHTCLSPTSTLPAFFVFGKASINTSNCIENLSKHAL 131
Y V H D D VI Y + T ++P KAS+ S I A+
Sbjct: 259 IKYDGARVQ----VHRDGDRVIIYSRRLENVTRSIPEIVEAVKASLKPSKVIVEGELVAV 314
Query: 132 -TNGKPILVLYGLEYAHAIPHIREAVKVASSSYGSGLKLEINFADVM 177
NG+P Y L +I E ++ + LE+N D++
Sbjct: 315 GENGRPRPFQYVLRRFRRKYNIDEMIE--------KIPLELNLFDIL 353
>pdb|2I0E|A Chain A, Structure Of Catalytic Domain Of Human Protein Kinase C
Beta Ii Complexed With A Bisindolylmaleimide Inhibitor
pdb|2I0E|B Chain B, Structure Of Catalytic Domain Of Human Protein Kinase C
Beta Ii Complexed With A Bisindolylmaleimide Inhibitor
Length = 353
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 321 KLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMS 380
K+A+F C I + +++AP I ++ +G+ W V+ + L
Sbjct: 161 KIADFGMCKENIWDGVTTKXFCGTPDYIAPEIIAYQP---YGKSVDWWAFGVLLYEMLAG 217
Query: 381 SSPVEGSDQAE 391
+P EG D+ E
Sbjct: 218 QAPFEGEDEDE 228
>pdb|3PFQ|A Chain A, Crystal Structure And Allosteric Activation Of Protein
Kinase C Beta Ii
Length = 674
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 321 KLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMS 380
K+A+F C I + +++AP I ++ +G+ W V+ + L
Sbjct: 482 KIADFGMCKENIWDGVTTKXFCGTPDYIAPEIIAYQP---YGKSVDWWAFGVLLYEMLAG 538
Query: 381 SSPVEGSDQAE 391
+P EG D+ E
Sbjct: 539 QAPFEGEDEDE 549
>pdb|1Z3G|L Chain L, Crystal Structure Of Complex Between Pvs25 And Fab
Fragment Of Malaria Transmission Blocking Antibody 2a8
pdb|1Z3G|M Chain M, Crystal Structure Of Complex Between Pvs25 And Fab
Fragment Of Malaria Transmission Blocking Antibody 2a8
Length = 213
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 138 LVLYGLEYAHAIPHIREAVKVASSSYGSGLKLEINFADVMCTV 180
L + G+E A + + ++GSG KLEIN AD TV
Sbjct: 72 LTISGMEAEDAATYYCQQWSSNPPTFGSGTKLEINRADTAPTV 114
>pdb|3OE0|A Chain A, Crystal Structure Of The Cxcr4 Chemokine Receptor In
Complex With A Cyclic Peptide Antagonist Cvx15
pdb|3OE9|A Chain A, Crystal Structure Of The Chemokine Cxcr4 Receptor In
Complex With A Small Molecule Antagonist It1t In P1
Spacegroup
pdb|3OE9|B Chain B, Crystal Structure Of The Chemokine Cxcr4 Receptor In
Complex With A Small Molecule Antagonist It1t In P1
Spacegroup
Length = 499
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 11/75 (14%)
Query: 67 FVMADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTSTLPAFFVFGKASINTSNCIENL 126
F++ + C + + + + H CL+P + F A TS
Sbjct: 435 FILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPI-----LYAFLGAKFKTS------ 483
Query: 127 SKHALTNGKPILVLY 141
++HALT+G+P+ VL+
Sbjct: 484 AQHALTSGRPLEVLF 498
>pdb|3ODU|A Chain A, The 2.5 A Structure Of The Cxcr4 Chemokine Receptor In
Complex With Small Molecule Antagonist It1t
pdb|3ODU|B Chain B, The 2.5 A Structure Of The Cxcr4 Chemokine Receptor In
Complex With Small Molecule Antagonist It1t
pdb|3OE8|A Chain A, Crystal Structure Of The Cxcr4 Chemokine Receptor In
Complex With A Small Molecule Antagonist It1t In P1
Spacegroup
pdb|3OE8|B Chain B, Crystal Structure Of The Cxcr4 Chemokine Receptor In
Complex With A Small Molecule Antagonist It1t In P1
Spacegroup
pdb|3OE8|C Chain C, Crystal Structure Of The Cxcr4 Chemokine Receptor In
Complex With A Small Molecule Antagonist It1t In P1
Spacegroup
Length = 502
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 11/75 (14%)
Query: 67 FVMADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTSTLPAFFVFGKASINTSNCIENL 126
F++ + C + + + + H CL+P + F A TS
Sbjct: 438 FILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPI-----LYAFLGAKFKTS------ 486
Query: 127 SKHALTNGKPILVLY 141
++HALT+G+P+ VL+
Sbjct: 487 AQHALTSGRPLEVLF 501
>pdb|3OKA|A Chain A, Crystal Structure Of Corynebacterium Glutamicum Pimb' In
Complex With Gdp-Man (Triclinic Crystal Form)
pdb|3OKA|B Chain B, Crystal Structure Of Corynebacterium Glutamicum Pimb' In
Complex With Gdp-Man (Triclinic Crystal Form)
Length = 381
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 244 RYDATEERLLTDVSQPLKILKRRYY--LVEKAKDANIIGVLVGTLG 287
RY++T RL TDVSQ +K L R Y ++ A+I + T G
Sbjct: 239 RYESTLRRLATDVSQNVKFLGRLEYQDMINTLAAADIFAMPARTRG 284
>pdb|3OKC|A Chain A, Crystal Structure Of Corynebacterium Glutamicum Pimb'
Bound To Gdp (Orthorhombic Crystal Form)
pdb|3OKP|A Chain A, Crystal Structure Of Corynebacterium Glutamicum Pimb'
Bound To Gdp-Man (Orthorhombic Crystal Form)
Length = 394
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 244 RYDATEERLLTDVSQPLKILKRRYY--LVEKAKDANIIGVLVGTLG 287
RY++T RL TDVSQ +K L R Y ++ A+I + T G
Sbjct: 239 RYESTLRRLATDVSQNVKFLGRLEYQDMINTLAAADIFAMPARTRG 284
>pdb|1SY6|L Chain L, Crystal Structure Of Cd3gammaepsilon Heterodimer In
Complex With Okt3 Fab Fragment
Length = 213
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 138 LVLYGLEYAHAIPHIREAVKVASSSYGSGLKLEINFADVMCTV 180
L + G+E A + + ++GSG KLEIN AD TV
Sbjct: 72 LTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEINRADTAPTV 114
>pdb|3IW4|A Chain A, Crystal Structure Of Pkc Alpha In Complex With Nvp-Aeb071
pdb|3IW4|B Chain B, Crystal Structure Of Pkc Alpha In Complex With Nvp-Aeb071
pdb|3IW4|C Chain C, Crystal Structure Of Pkc Alpha In Complex With Nvp-Aeb071
Length = 360
Score = 28.9 bits (63), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 3/71 (4%)
Query: 321 KLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMS 380
K+A+F C + + +++AP I ++ +G+ W V+ + L
Sbjct: 160 KIADFGMCKEHMMDGVTTREFCGTPDYIAPEIIAYQP---YGKSVDWWAYGVLLYEMLAG 216
Query: 381 SSPVEGSDQAE 391
P +G D+ E
Sbjct: 217 QPPFDGEDEDE 227
>pdb|3PG5|A Chain A, Crystal Structure Of Protein Dip2308 From Corynebacterium
Diphtheriae, Northeast Structural Genomics Consortium
Target Cdr78
pdb|3PG5|B Chain B, Crystal Structure Of Protein Dip2308 From Corynebacterium
Diphtheriae, Northeast Structural Genomics Consortium
Target Cdr78
pdb|3PG5|C Chain C, Crystal Structure Of Protein Dip2308 From Corynebacterium
Diphtheriae, Northeast Structural Genomics Consortium
Target Cdr78
pdb|3PG5|D Chain D, Crystal Structure Of Protein Dip2308 From Corynebacterium
Diphtheriae, Northeast Structural Genomics Consortium
Target Cdr78
Length = 361
Score = 28.5 bits (62), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 23/48 (47%)
Query: 338 QTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSSSPVE 385
+T LL F+ P T + AFG +W A+V ++ ++ + E
Sbjct: 170 RTVLLGCDAFVTPTATDLFSFHAFGNLARWFDAWVTQYAEIHEGNXAE 217
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
0.319 0.135 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,343,877
Number of Sequences: 62578
Number of extensions: 581888
Number of successful extensions: 1722
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1716
Number of HSP's gapped (non-prelim): 16
length of query: 495
length of database: 14,973,337
effective HSP length: 103
effective length of query: 392
effective length of database: 8,527,803
effective search space: 3342898776
effective search space used: 3342898776
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)