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= 017546
(369 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QKD|A Chain A, Crystal Structure Of Tandem Zpr1 Domains
Length = 404
Score = 246 bits (629), Expect = 1e-65, Method: Compositional matrix adjust.
Identities = 127/327 (38%), Positives = 194/327 (59%), Gaps = 46/327 (14%)
Query: 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLK 89
+ESLCM C NG TR LLT IP FR++++S+F C HCG N E+Q AG IQ +G Y+L
Sbjct: 11 IESLCMNCYRNGTTRLLLTKIPFFREIIVSSFSCEHCGWNNTEIQSAGRIQDQGVRYTLT 70
Query: 90 VPSSDQKMFHRQVVKSESATIKIPELDFEIPPEAQRGSLSTVEGILVRAADELEALQEER 149
V S Q+ +R+VVK++SAT +IPELDFEIP +Q+G+L+TVEG++ RA LE Q R
Sbjct: 71 VRS--QEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTVEGLISRAISGLEQDQPTR 128
Query: 150 KKLDPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSFIENLYAPSPDPSLNIKFYER 209
+ ++ AE ID+F+ KL+ + S FT ++DDP+GNSF+EN +AP D +L I +Y+R
Sbjct: 129 RAVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDR 188
Query: 210 TPEQQALLGYLVDPSQQGESSNVVPSEGLSSTSDKREPRGSVGAVAGHRAIAQSNSAEIA 269
TP+Q +LG + ++ ++
Sbjct: 189 TPQQAEMLG-----------------------------------LQAEAPEEKAEEEDLR 213
Query: 270 DALFRYSAPEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKP 329
+ + +++ + C C A +T M + +IP+F+EVI+MA+ C+ CG+R +E+K
Sbjct: 214 NEVLQFN---------TNCPECNAPAQTNMKLVQIPHFKEVIIMATNCENCGHRTNEVKS 264
Query: 330 GGRIPEKGKRITLFVKNINDLSRDLIK 356
GG + G RITL + + +D++RDL+K
Sbjct: 265 GGAVEPLGTRITLHITDPSDMTRDLLK 291
Score = 120 bits (301), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 65/191 (34%), Positives = 107/191 (56%), Gaps = 9/191 (4%)
Query: 27 LYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNY 86
+ Q + C C T L IPHF++V++ A C +CG R NEV+ G ++P G
Sbjct: 216 VLQFNTNCPECNAPAQTNMKLVQIPHFKEVIIMATNCENCGHRTNEVKSGGAVEPLGTRI 275
Query: 87 SLKVPSSDQKMFHRQVVKSESATIKIPELDFEIPPEAQRGSLSTVEGILVRAADELEALQ 146
+L + +D R ++KSE+ +++IPEL+FE+ G +T+EG+L D E +
Sbjct: 276 TLHI--TDPSDMTRDLLKSETCSVEIPELEFELGMAVLGGKFTTLEGLL---KDIRELVT 330
Query: 147 EERKKL----DPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSFIENLYAPSPDPSL 202
+ L +P +E + +F KL +G FI++DPAGNS+++N+YAP DP +
Sbjct: 331 KNPFTLGDSSNPDQSEKLQEFSQKLGQIIEGKMKAHFIMNDPAGNSYLQNVYAPEDDPEM 390
Query: 203 NIKFYERTPEQ 213
++ Y+RT +Q
Sbjct: 391 KVERYKRTFDQ 401
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 53/127 (41%), Gaps = 18/127 (14%)
Query: 49 LIPHFRKVLLSAFECPHCGERNNEVQF-------------AGEIQPRGCNYSL-KVPSSD 94
L + +K + A CPHCGE+ +++ ++ P L KVP SD
Sbjct: 132 LTEYVKKTAMKAQVCPHCGEKQFKIKLEKPYNFYEERKEGVAKLTPSDIRERLEKVPESD 191
Query: 95 QKMFHRQVVKSESATIKIPELDFEIPPEAQRGSLSTVEGILVRAADELEALQEERKKLDP 154
++ S + + L +PP R S+ GI RA D+L + +++
Sbjct: 192 VEILGYDPTTSRPEWMILTVL--PVPPITIRPSIMIESGI--RAEDDLTHKLVDIVRINE 247
Query: 155 QTAEAID 161
+ E+ID
Sbjct: 248 RLKESID 254
>pdb|3SZE|A Chain A, Crystal Structure Of The Passenger Domain Of The E. Coli
Autotransporter Espp
Length = 968
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 24/34 (70%), Gaps = 1/34 (2%)
Query: 101 QVVKSESATIKIPELDF-EIPPEAQRGSLSTVEG 133
++VK + +T+K+PE+ F + P A +GS +++ G
Sbjct: 31 EIVKKDGSTLKLPEVPFPDFSPVANKGSTTSIGG 64
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 29/127 (22%), Positives = 52/127 (40%), Gaps = 18/127 (14%)
Query: 49 LIPHFRKVLLSAFECPHCGERNNEVQF-------------AGEIQPRGCNYSL-KVPSSD 94
L + +K + A CPHC E+ +++ ++ P L K+P SD
Sbjct: 132 LTEYVKKTAMKAQVCPHCNEKQYKIKLEKPYNFYEERKEGVAKLTPSDIRERLEKIPDSD 191
Query: 95 QKMFHRQVVKSESATIKIPELDFEIPPEAQRGSLSTVEGILVRAADELEALQEERKKLDP 154
++ S + + L +PP R S+ GI RA D+L + +++
Sbjct: 192 VEILGYDPTTSRPEWMILTVL--PVPPITIRPSIMIESGI--RAEDDLTHKLVDIVRINE 247
Query: 155 QTAEAID 161
+ E+ID
Sbjct: 248 RLKESID 254
>pdb|2LCQ|A Chain A, Solution Structure Of The Endonuclease Nob1 From
P.Horikoshii
Length = 165
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 21/44 (47%)
Query: 300 FMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLF 343
F T ++VI C CG + S L PGG P+ G ++ L
Sbjct: 118 FRTLKRGIKKVIKWRYVCIGCGRKFSTLPPGGVCPDCGSKVKLI 161
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
0.317 0.133 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,432,109
Number of Sequences: 62578
Number of extensions: 410616
Number of successful extensions: 974
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 966
Number of HSP's gapped (non-prelim): 8
length of query: 369
length of database: 14,973,337
effective HSP length: 100
effective length of query: 269
effective length of database: 8,715,537
effective search space: 2344479453
effective search space used: 2344479453
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: 52 (24.6 bits)