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= 004620
(741 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NOY|A Chain A, Crystal Structure Of Ispg (Gcpe)
pdb|3NOY|B Chain B, Crystal Structure Of Ispg (Gcpe)
pdb|3NOY|C Chain C, Crystal Structure Of Ispg (Gcpe)
pdb|3NOY|D Chain D, Crystal Structure Of Ispg (Gcpe)
Length = 366
Score = 167 bits (423), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 110/285 (38%), Positives = 157/285 (55%), Gaps = 35/285 (12%)
Query: 85 RRKTRTVMVGNVAIGSEHPIRVQTMTTNDTKDVAGTVEEVMRIADQGADLVRITVQGKRE 144
+RKTR + VGNV IG + PI VQ+MT+ T DV T+ ++ R+ + G ++VR+ V K +
Sbjct: 13 KRKTRQIRVGNVKIGGDAPIVVQSMTSTKTHDVEATLNQIKRLYEAGCEIVRVAVPHKED 72
Query: 145 ADACFEIKNSLVQKNYNIPLVADIHFAPSVA-LRVAECFDKIRVNPGNFADRRAQFEQLE 203
+A EI K +P++ADIHFAPS A L + + IR+NPGN E +E
Sbjct: 73 VEALEEI-----VKKSPMPVIADIHFAPSYAFLSMEKGVHGIRINPGNIGKEEIVREIVE 127
Query: 204 YTDDEYQKELQHIEEVFSPLVEKCKKYGRAVRIGTNHGSLSDRIMSYYG-DSPRGMVESA 262
+ K+ G AVRIG N GSL ++ YG S + ESA
Sbjct: 128 ----------------------EAKRRGVAVRIGVNSGSLEKDLLEKYGYPSAEALAESA 165
Query: 263 FEFARICRKLDFHNFLFSMKASNPVVMVQAYRLLVAEMYVHGWDYPLHLGVTEAGEGEDG 322
++ K F N+ S+K S+ + V+A L+ AE D PLH+G+TEAG G G
Sbjct: 166 LRWSEKFEKWGFTNYKVSIKGSDVLQNVRA-NLIFAERT----DVPLHIGITEAGMGTKG 220
Query: 323 RMKSAIGIGTLLQDGLGDTIRVSLTEPPEKEIDPCRR-LANLGMR 366
+KS++GIG LL G+GDT+RVSLT+ P E++ L +LG+R
Sbjct: 221 IIKSSVGIGILLYMGIGDTVRVSLTDDPVVEVETAYEILKSLGLR 265
Score = 62.8 bits (151), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 46/75 (61%), Gaps = 1/75 (1%)
Query: 624 DTSFNLLQGCRMRNTKTEYVSCPSCGRTLFDLQEISAEIREKTSHLPG-VSIAIMGCIVN 682
+T++ +L+ +R E V+CP+CGR DL ++ E++EK S + + +A+MGC+VN
Sbjct: 253 ETAYEILKSLGLRRRGVEIVACPTCGRIEVDLPKVVKEVQEKLSGVKTPLKVAVMGCVVN 312
Query: 683 GPGEMADADFGYVGG 697
GE +AD G G
Sbjct: 313 AIGEAREADIGLACG 327
>pdb|2Y0F|A Chain A, Structure Of Gcpe (Ispg) From Thermus Thermophilus Hb27
pdb|2Y0F|B Chain B, Structure Of Gcpe (Ispg) From Thermus Thermophilus Hb27
pdb|2Y0F|C Chain C, Structure Of Gcpe (Ispg) From Thermus Thermophilus Hb27
pdb|2Y0F|D Chain D, Structure Of Gcpe (Ispg) From Thermus Thermophilus Hb27
pdb|4G9P|A Chain A, Structure Of The Gcpe-Mecpp (Ispg) Complex From Thermus
Thermophilus
Length = 406
Score = 143 bits (360), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 111/309 (35%), Positives = 150/309 (48%), Gaps = 48/309 (15%)
Query: 84 VRRKTRTVMVGNVAIGSEHPIRVQTMTTNDTKDVAGTVEEVMRIADQGADLVRITVQGKR 143
+RR T TV VG V IG HPI VQ+MT T+DV T +V+ + G+++VR+TV +
Sbjct: 4 MRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLELHRAGSEIVRLTVNDEE 63
Query: 144 EADACFEIKNSLVQKNYNIPLVADIHFAPSVALR----VAECFDKIRVNPGNFADRRAQF 199
A A EIK L+ + +PLV D HF + LR +AE DK R+NPG R
Sbjct: 64 AAKAVPEIKRRLLAEGVEVPLVGDFHFNGHLLLRKYPKMAEALDKFRINPGTLGRGR--- 120
Query: 200 EQLEYTDDEYQKELQHIEEVFSPLVEKCKKYGRAVRIGTNHGSLSDRIMSYYGD------ 253
H +E F+ ++ G+ VRIG N GSL +++ D
Sbjct: 121 ---------------HKDEHFAEMIRIAMDLGKPVRIGANWGSLDPALLTELMDRNASRP 165
Query: 254 SPR--------GMVESAFEF--ARICRKLDFHNFLFSMKASNPVVMVQAYRLLVAEMYVH 303
P+ +VESA A + L + S K S +V YR L
Sbjct: 166 EPKSAHEVVLEALVESAVRAYEAALEMGLGEDKLVLSAKVSKARDLVWVYRELARRT--- 222
Query: 304 GWDYPLHLGVTEAGEGEDGRMKSAIGIGTLLQDGLGDTIRVSLT----EPPEKEIDPCRR 359
PLHLG+TEAG G G + SA + LL +G+GDTIRVSLT EP KE++ +
Sbjct: 223 --QAPLHLGLTEAGMGVKGIVASAAALAPLLLEGIGDTIRVSLTPSPKEPRTKEVEVAQE 280
Query: 360 -LANLGMRA 367
L LG+RA
Sbjct: 281 ILQALGLRA 289
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/127 (33%), Positives = 63/127 (49%), Gaps = 24/127 (18%)
Query: 624 DTSFNLLQGCRMRNTKTEYVSCPSCGRTLFDL-----QEISAEIREKT----SHLPGV-- 672
+ + +LQ +R E SCP CGRT +E+S ++E+ + PGV
Sbjct: 276 EVAQEILQALGLRAFAPEVTSCPGCGRTTSTFFQELAEEVSRRLKERLPEWRARYPGVEE 335
Query: 673 -SIAIMGCIVNGPGEMADADFGYV---GGAPGKIDLYV-GK--TVVK-RGIAMEQATDAL 724
+A+MGC+VNGPGE A G G K +Y GK T++K GIA E
Sbjct: 336 LKVAVMGCVVNGPGESKHAHIGISLPGAGEEPKAPVYADGKLLTILKGEGIAEE-----F 390
Query: 725 IQLIKDH 731
++L++D+
Sbjct: 391 LRLVEDY 397
>pdb|3RCW|A Chain A, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|B Chain B, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|C Chain C, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|D Chain D, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|E Chain E, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|F Chain F, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|G Chain G, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|H Chain H, Crystal Structure Of The Bromodomain Of Human Brd1
Length = 135
Score = 30.0 bits (66), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 170 FAPSVALR-VAECFDKIRVNPGNFADRRAQFEQLEYTDDEYQKELQHIEEVFSPLVEKCK 228
FA V+L+ V + D I+ +P +FA R + E Y K L EE F +++ C
Sbjct: 34 FAQPVSLKEVPDYLDHIK-HPMDFATMRKRLEAQGY------KNLHEFEEDFDLIIDNCM 86
Query: 229 KYG 231
KY
Sbjct: 87 KYN 89
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
0.320 0.137 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,582,618
Number of Sequences: 62578
Number of extensions: 896911
Number of successful extensions: 2067
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 2055
Number of HSP's gapped (non-prelim): 9
length of query: 741
length of database: 14,973,337
effective HSP length: 106
effective length of query: 635
effective length of database: 8,340,069
effective search space: 5295943815
effective search space used: 5295943815
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: 55 (25.8 bits)