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= 023068
(287 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus
Star-Gsg Quaking Protein
Length = 140
Score = 128 bits (322), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 58/126 (46%), Positives = 92/126 (73%), Gaps = 4/126 (3%)
Query: 138 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRG 197
+L +PV YP+FNFVGR+LGPRG + K++EA TGC++ +RGKGS++D K E++ RG
Sbjct: 5 KLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKK----EEQNRG 60
Query: 198 RPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAML 257
+P +EHLN+ LH+LI + N +++L++A E +++LL P E +D +K+ +L ELA+L
Sbjct: 61 KPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAIL 120
Query: 258 NSNFRE 263
N +R+
Sbjct: 121 NGTYRD 126
>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
Rna By Splicing Factor 1
Length = 131
Score = 87.0 bits (214), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 53/131 (40%), Positives = 77/131 (58%), Gaps = 14/131 (10%)
Query: 138 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRG 197
++ IP D YP NFVG L+GPRGN+LK +E ++ IRGKGS+K+ KV + ++
Sbjct: 10 KVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEG-KVGRKDGQM-- 66
Query: 198 RPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLK---PVDESQDYIKRQQLREL 254
PG + +PLH L+ A+ N+ ++A E I +LK E Q+ +++ QLREL
Sbjct: 67 LPGED---EPLHALVTANTMENV-----KKAVEQIRNILKQGIETPEDQNDLRKMQLREL 118
Query: 255 AMLNSNFREDS 265
A LN RED
Sbjct: 119 ARLNGTLREDD 129
>pdb|2YQR|A Chain A, Solution Structure Of The Kh Domain In Kiaa0907 Protein
Length = 119
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 19/95 (20%)
Query: 147 PNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGS-IKDPDKVSTPEDKLRGRPGYEHLN 205
P FN ++ GP + L+ ++ TG +V++RGKGS +P GR +E
Sbjct: 25 PTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPAS---------GREAFE--- 72
Query: 206 DPLHILIEADLPANIVDIRLRQAQEIIEELLKPVD 240
P++I I P L A+++ E LL+ V
Sbjct: 73 -PMYIYISHPKPEG-----LAAAKKLCENLLQTVH 101
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 32.0 bits (71), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSI 182
RI+ ++IPVD +G ++GP+ + +++ TG + I G+I
Sbjct: 598 RIITVKIPVDK------IGEVIGPKRQXINQIQEDTGAEITIEDDGTI 639
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSI 182
RI+ ++IPVD +G ++GP+ + +++ TG + I G+I
Sbjct: 598 RIITVKIPVDK------IGEVIGPKRQMINQIQEDTGAEITIEDDGTI 639
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 31.6 bits (70), Expect = 0.59, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 150 NFVGRLLGPRGNSLKRVEATTGCRVYIRGKG 180
N VG +LG G +L + TGCR+ I KG
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGCRIQISKKG 42
>pdb|1S3I|A Chain A, Crystal Structure Of The N Terminal Hydrolase Domain Of
10- Formyltetrahydrofolate Dehydrogenase
Length = 310
Score = 31.2 bits (69), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 30 QYLSELLAEHQKLGPFTQVLPICSRLLTQEIF 61
Q L E++A++Q LG VLP CS+ + E+
Sbjct: 64 QALPEVVAKYQALGAELNVLPFCSQFIPMEVI 95
>pdb|2BW0|A Chain A, Crystal Structure Of The Hydrolase Domain Of Human 10-
Formyltetrahydrofolate 2 Dehydrogenase
pdb|2CFI|A Chain A, The Hydrolase Domain Of Human 10-Fthfd In Complex With 6-
Formyltetrahydropterin
Length = 329
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 30 QYLSELLAEHQKLGPFTQVLPICSRLLTQEIF 61
Q L +++A++Q LG VLP CS+ + EI
Sbjct: 86 QALPDVVAKYQALGAELNVLPFCSQFIPMEII 117
>pdb|3UOR|A Chain A, The Structure Of The Sugar-Binding Protein Male From The
Phytopathogen Xanthomonas Citri
pdb|3UOR|B Chain B, The Structure Of The Sugar-Binding Protein Male From The
Phytopathogen Xanthomonas Citri
Length = 458
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 12/74 (16%)
Query: 61 FRVSGMMPNQGFGDFDRLRHRSPSPMASSNLMSNVAGTGLGG---------WNGLPQERL 111
FR +G GF +D + + +P S +SNV G WN + + +L
Sbjct: 218 FRGAGFRKALGF--YDNMYQQGWAPKVSETQVSNVWYEFFNGYYAFYLSGPWN-VREFKL 274
Query: 112 GGPPGMTMDWQSAP 125
PPGM +W +AP
Sbjct: 275 RQPPGMEGNWGTAP 288
>pdb|1DU5|A Chain A, The Crystal Structure Of Zeamatin.
pdb|1DU5|B Chain B, The Crystal Structure Of Zeamatin
Length = 206
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 154 RLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPD 186
R+ P G + R+ A TGC+ G+GS + D
Sbjct: 33 RITAPAGTTAARIWARTGCKFDASGRGSCRTGD 65
>pdb|3DLS|A Chain A, Crystal Structure Of Human Pas Kinase Bound To Adp
pdb|3DLS|B Chain B, Crystal Structure Of Human Pas Kinase Bound To Adp
pdb|3DLS|C Chain C, Crystal Structure Of Human Pas Kinase Bound To Adp
pdb|3DLS|D Chain D, Crystal Structure Of Human Pas Kinase Bound To Adp
pdb|3DLS|E Chain E, Crystal Structure Of Human Pas Kinase Bound To Adp
pdb|3DLS|F Chain F, Crystal Structure Of Human Pas Kinase Bound To Adp
Length = 335
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 24/53 (45%)
Query: 30 QYLSELLAEHQKLGPFTQVLPICSRLLTQEIFRVSGMMPNQGFGDFDRLRHRS 82
+ L + E KLG T + I SR+ I +V + NQGF +H S
Sbjct: 61 KVLEDCWIEDPKLGKVTLEIAILSRVEHANIIKVLDIFENQGFFQLVMEKHGS 113
>pdb|2I76|A Chain A, Crystal Structure Of Protein Tm1727 From Thermotoga
Maritima
pdb|2I76|B Chain B, Crystal Structure Of Protein Tm1727 From Thermotoga
Maritima
Length = 276
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 17 PQIRSTPDINIDSQYLSELLAEHQKLGPFTQVLPICSRLLTQEIFRVSG---MMPNQGFG 73
P++ + + +Y+ + +A H LG VL CS L+ EIF+ SG + PN F
Sbjct: 56 PELNGVVFVIVPDRYI-KTVANHLNLGD--AVLVHCSGFLSSEIFKKSGRASIHPNFSFS 112
Query: 74 DFDR 77
++
Sbjct: 113 SLEK 116
>pdb|3VKE|A Chain A, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|B Chain B, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|C Chain C, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|D Chain D, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
Length = 76
Score = 27.7 bits (60), Expect = 7.2, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 152 VGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVST 190
VG ++G +G S+KR+ +G R+ I S P+++ T
Sbjct: 14 VGSIIGKKGESVKRIREESGARINISEGNS---PERIIT 49
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 0.136 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,434,169
Number of Sequences: 62578
Number of extensions: 417925
Number of successful extensions: 877
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 863
Number of HSP's gapped (non-prelim): 19
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
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: 51 (24.3 bits)