RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9485
(190 letters)
>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor,
cell cycle; 1.98A {Homo sapiens}
Length = 411
Score = 149 bits (377), Expect = 7e-44
Identities = 49/163 (30%), Positives = 83/163 (50%), Gaps = 14/163 (8%)
Query: 31 ATQSISRL-NLLCGRDPNPSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYSAS-GDT 88
+I +L +L PS L F C NP+ I + ++G F + ++ + G
Sbjct: 2 EFNTIQQLMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQG 61
Query: 89 ARDFAEKRLSVAVCLYYKLLESILADEQK-KPAYDFNVLLSLQIFHETLFACCIEIVIFC 147
+ +R + V LYY+++ES+L E++ +F+ LL+ IFH +L AC +E+V+
Sbjct: 62 CVEIGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMAT 121
Query: 148 YNSN-----------SFPWILSVLGIEPYHFYKVIEWLLTPNP 179
Y+ + SFPWIL+VL ++ + FYKVIE +
Sbjct: 122 YSRSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEG 164
>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor
protein, phosphorylation, cell; HET: TPO; 2.70A {Homo
sapiens}
Length = 656
Score = 151 bits (383), Expect = 3e-43
Identities = 56/193 (29%), Positives = 95/193 (49%), Gaps = 15/193 (7%)
Query: 4 TPRTPLTGRHYLSKRDLEYGN-VTPVKTATQSISRLN-LLCGRDPNPSPALTRIFEACNK 61
+ T T R ++ TPV+T +I +L +L PS L F C
Sbjct: 278 SFETQRTPRKSNLDEEVNVIPPHTPVRTVMNTIQQLMMILNSASDQPSENLISYFNNCTV 337
Query: 62 NPQPLIDSVLTNLGDKFTQHYSAS-GDTARDFAEKRLSVAVCLYYKLLESILADEQK-KP 119
NP+ I + ++G F + ++ + G + +R + V LYY+++ES+L E++
Sbjct: 338 NPKESILKRVKDIGYIFKEKFAKAVGQGCVEIGSQRYKLGVRLYYRVMESMLKSEEERLS 397
Query: 120 AYDFNVLLSLQIFHETLFACCIEIVIFCYNSN-----------SFPWILSVLGIEPYHFY 168
+F+ LL+ IFH +L AC +E+V+ Y+ + SFPWIL+VL ++ + FY
Sbjct: 398 IQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQNLDSGTDLSFPWILNVLNLKAFDFY 457
Query: 169 KVIEWLLTPNPEV 181
KVIE + +
Sbjct: 458 KVIESFIKAEGNL 470
>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB;
retinoblastoma protein, E2F displacement, transcription
repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3
PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B
1o9k_B
Length = 347
Score = 142 bits (359), Expect = 9e-42
Identities = 49/160 (30%), Positives = 83/160 (51%), Gaps = 14/160 (8%)
Query: 34 SISRL-NLLCGRDPNPSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYSAS-GDTARD 91
+I +L +L PS L F C NP+ I + ++G F + ++ + G +
Sbjct: 2 TIQQLMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQGCVE 61
Query: 92 FAEKRLSVAVCLYYKLLESILADEQK-KPAYDFNVLLSLQIFHETLFACCIEIVIFCYNS 150
+R + V LYY+++ES+L E++ +F+ LL+ IFH +L AC +E+V+ Y+
Sbjct: 62 IGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSR 121
Query: 151 N-----------SFPWILSVLGIEPYHFYKVIEWLLTPNP 179
+ SFPWIL+VL ++ + FYKVIE +
Sbjct: 122 STSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEG 161
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 40.8 bits (95), Expect = 2e-04
Identities = 42/254 (16%), Positives = 65/254 (25%), Gaps = 94/254 (37%)
Query: 2 AMTPRTPLTGRHYLSKRDLEYGNVT---PVKT-----ATQS----ISRLNL----LCGRD 45
A + R PLT L +G++ V T A+Q L D
Sbjct: 3 AYSTR-PLT---------LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADD 52
Query: 46 PNPSPA--LTR----IFEACNKNPQPLIDSVLTNLGDKFTQHYSASGD----------TA 89
+PA + + + + D VL +F Y D
Sbjct: 53 EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEN 112
Query: 90 RDFAEKRLSVAVCLYY-----------KLLESIL---ADEQKKPAY-------DFNVLLS 128
K + Y K S L E + +
Sbjct: 113 DTTLVKTKELIKN-YITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFE 171
Query: 129 -LQIFHETLFACCIEIVIFCYNSNSFPWI------LSVLGIEP----YHFYK---VIEWL 174
L+ ++T Y+ I LS L F + ++EWL
Sbjct: 172 ELRDLYQT------------YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWL 219
Query: 175 ----LTPNPEVLGS 184
TP+ + L S
Sbjct: 220 ENPSNTPDKDYLLS 233
Score = 37.0 bits (85), Expect = 0.003
Identities = 28/176 (15%), Positives = 50/176 (28%), Gaps = 57/176 (32%)
Query: 25 VTPVKTATQSISRLNLLCGRDPNPSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYSA 84
P + SI +L PSP L + + Q + + +K H A
Sbjct: 313 AYPNTSLPPSILEDSLENNEGV-PSPML-----SISNLTQEQVQDYV----NKTNSHLPA 362
Query: 85 SGDTARDFAEKRLSVA---------VC-----LY--YKLLESILAD----------EQKK 118
K++ ++ V LY L A ++K
Sbjct: 363 ---------GKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERK 413
Query: 119 PAYD--FNVLLSLQI---FHETLFACCIEIVIFCYNSNSFPWILSVLGIEP-YHFY 168
+ F L + FH L +++ N+ + + I P Y +
Sbjct: 414 LKFSNRF-----LPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQI-PVYDTF 463
Score = 30.4 bits (68), Expect = 0.36
Identities = 23/129 (17%), Positives = 43/129 (33%), Gaps = 24/129 (18%)
Query: 69 SVLTNLGDKFTQHYSASGDT-ARDFAEKRLSVAVCLYYKLLESI--LADEQKKPAYDFNV 125
+ + L ++F + + A D ++ + A L K L + L + K +D +
Sbjct: 28 FIASQLQEQFNKILPEPTEGFAAD--DEPTTPAE-LVGKFLGYVSSLVEPSKVGQFDQVL 84
Query: 126 LLSLQIFHETLFACCIEIVIFCYNSNSFPWILSVLGIEPYHFYKVIEWL--------LTP 177
L L F E + +I ++ +L K E + +
Sbjct: 85 NLCLTEF-ENCYLEGNDI-------HAL--AAKLLQENDTTLVKTKELIKNYITARIMAK 134
Query: 178 NPEVLGSNS 186
P SNS
Sbjct: 135 RPFDKKSNS 143
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.5 bits (70), Expect = 0.086
Identities = 6/24 (25%), Positives = 11/24 (45%), Gaps = 7/24 (29%)
Query: 33 QSI----SRLNLLCGRDPNPSPAL 52
Q++ + L L + +PAL
Sbjct: 20 QALKKLQASLKLYA---DDSAPAL 40
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 30.2 bits (67), Expect = 0.41
Identities = 34/183 (18%), Positives = 64/183 (34%), Gaps = 46/183 (25%)
Query: 13 HYL----SKRDLEYGNVTPVKTATQSISRLNLLCGRDPN-PSPALTR-----IFEACNKN 62
H++ + +Y ++ V + N C + P L++ I + K+
Sbjct: 5 HHMDFETGEHQYQYKDILSV--FEDAFVD-NFDCKDVQDMPKSILSKEEIDHIIMS--KD 59
Query: 63 PQPLIDSVLTNLGDKFTQHYSASGDTARDFAEKRLSVAVCLYYKLLESILADEQKKPAYD 122
+ L K + + F E+ L + YK L S + EQ++P+
Sbjct: 60 AVSGTLRLFWTLLSKQEE-------MVQKFVEEVLRIN----YKFLMSPIKTEQRQPSMM 108
Query: 123 FNVLLSLQIFHETLFACCIEIVIFCYNSNS-FPWILSVLGIEPYHFYKVIEWL--LTPNP 179
++ + + YN N F +V ++PY K+ + L L P
Sbjct: 109 -----------TRMYIEQRDRL---YNDNQVFA-KYNVSRLQPYL--KLRQALLELRPAK 151
Query: 180 EVL 182
VL
Sbjct: 152 NVL 154
>3ejf_A Non-structural protein 3; IBV, coronavirus, X-domain, macro domain,
NSP3, ADRP, hydrolase, ribosomal frameshifting; 1.60A
{Avian infectious bronchitis virus} PDB: 3eke_A* 3ewo_A
3ewp_A*
Length = 176
Score = 27.6 bits (62), Expect = 2.1
Identities = 5/33 (15%), Positives = 13/33 (39%)
Query: 121 YDFNVLLSLQIFHETLFACCIEIVIFCYNSNSF 153
+ + +S+ E C I +++F +
Sbjct: 136 FGVDFKMSIDAMREAFEGCTIRVLLFSLSQEHI 168
>4ep1_A Otcase, ornithine carbamoyltransferase; structural genomics,
niaid, national institute of allergy AN infectious
diseases; 3.25A {Bacillus anthracis}
Length = 340
Score = 27.6 bits (62), Expect = 2.7
Identities = 4/20 (20%), Positives = 8/20 (40%)
Query: 1 MAMTPRTPLTGRHYLSKRDL 20
M+ L + L+ +L
Sbjct: 25 MSTVQVPKLNTKDLLTLEEL 44
>1bq0_A DNAJ, HSP40; chaperone, heat shock, protein folding, DNAK; NMR
{Escherichia coli} SCOP: a.2.3.1 PDB: 1xbl_A 1bqz_A
Length = 103
Score = 26.0 bits (58), Expect = 3.4
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 111 ILADEQKKPAYD 122
+L D QK+ AYD
Sbjct: 55 VLTDSQKRAAYD 66
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.321 0.137 0.421
Gapped
Lambda K H
0.267 0.0784 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,867,725
Number of extensions: 153840
Number of successful extensions: 391
Number of sequences better than 10.0: 1
Number of HSP's gapped: 380
Number of HSP's successfully gapped: 12
Length of query: 190
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,244,745
Effective search space: 432963990
Effective search space used: 432963990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.5 bits)