RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9880
(280 letters)
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 118 bits (296), Expect = 2e-32
Identities = 20/108 (18%), Positives = 34/108 (31%), Gaps = 19/108 (17%)
Query: 156 GQQSLLFQVDYPEIADDVFPRHRFMSAYSLLFQVDYPEIADDVFPRHRFMSAYEQRIEPP 215
G + QV+Y + + V P R +S E
Sbjct: 114 GSVGMAIQVNYSSEVKE---------------NSVDSDDKAKVPPLIRIVSGLELSDTKQ 158
Query: 216 DRKWQYLLFAAEPYETIAFKVSDR---TGLYERITSGLVLVDHVKLTC 260
K ++L+ A EP+E IA ++ + + VD + C
Sbjct: 159 KGK-KFLVIAYEPFENIAIELPPNEILFSENNDMDNNNDGVDELNKKC 205
>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 = 45.4 bits (107), Expect = 2e-05
Identities = 46/280 (16%), Positives = 76/280 (27%), Gaps = 102/280 (36%)
Query: 30 LRQLALETIDLNKDPYFMKNHLGSYECKLCLTLHNNEGSYLAHTQGKKH-QANLARRAAK 88
R L L +H GS E L S+ +Q ++ L
Sbjct: 6 TRPLTL-------------SH-GSLEH----VLLVPTASFFIASQLQEQFNKILPEPTEG 47
Query: 89 EAKDAPQQSCDELL---------LTSDAVYTHKDSILISTLD-------WG--------- 123
A D + EL+ L + D +L L G
Sbjct: 48 FAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAK 107
Query: 124 -PPAPEKPRVEPKKFVKIGRPGY---RVTKQRDPSNGQQSLLFQVDYPEIADDVFPRHRF 179
+ V+ K+ +K Y R+ +R S LF+ + +
Sbjct: 108 LLQENDTTLVKTKELIKN----YITARIMAKRPFDKKSNSALFRA-----VGE--GNAQL 156
Query: 180 MSAYSLLF--Q---VDY-PEIADDVFPRHRFMSAYEQRIEPPDRKWQYLLFAAEPYETIA 233
+ +F Q DY E+ R + Y + + F+AE +
Sbjct: 157 V----AIFGGQGNTDDYFEEL------RDLY-QTYHVLVGD------LIKFSAETLSELI 199
Query: 234 FKVSDRTGLYERITSGLVLVDHVKLTCQNQIRLLNIQQWL 273
D ++ + G LNI +WL
Sbjct: 200 RTTLDAEKVFTQ---G-----------------LNILEWL 219
>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 = 39.1 bits (90), Expect = 0.001
Identities = 39/278 (14%), Positives = 79/278 (28%), Gaps = 65/278 (23%)
Query: 22 SNRDRRERLRQLALETIDLNKDPYFMKNHLGSYECKLCLTL-HNNEGSYLAHTQGKKHQA 80
+D ++ D K+ L E + G+ Q
Sbjct: 17 QYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQE 76
Query: 81 NLARRAAKEA--------KDAPQQSCDELLLTSDAVYTHKDSILISTLDWGPPAPEK--P 130
+ ++ +E + + + + +Y + L + +
Sbjct: 77 EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR-MYIEQRDRLYND---NQVFAKYNVS 132
Query: 131 RVEPKKFVKIG----RPGYRVTKQRDPSNGQQSLLFQV--DYP---EIADDVF------- 174
R++P ++ RP V +G+ + V Y ++ +F
Sbjct: 133 RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNC 192
Query: 175 --PRHRFMSAYSLLFQVDYPEIADDVFPRHRFMSAYEQRIEPPDRKWQYLLFAAEPYETI 232
P LL+Q+D + R S + RI + + L ++PYE
Sbjct: 193 NSPETVLEMLQKLLYQIDPNWTS-----RSDHSSNIKLRIHSIQAELRR-LLKSKPYE-- 244
Query: 233 AFKVSDRTGLYERITSGLVLVDHVK---------LTCQ 261
L LVL +V+ L+C+
Sbjct: 245 -------NCL-------LVL-LNVQNAKAWNAFNLSCK 267
Score = 32.5 bits (73), Expect = 0.16
Identities = 46/276 (16%), Positives = 84/276 (30%), Gaps = 74/276 (26%)
Query: 19 WSESNRDRRERLRQLALETID--LNKDPY-----FMKNHLGSYECKLCLTLHNNEGSYLA 71
W N D+ + + +L ++ + + F + L L + S +
Sbjct: 347 WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL-LSLIWFDVIKSDVM 405
Query: 72 HTQGKKHQANLARRAAKEAKDAPQQSCDELLLTSDAVYTHKDSILISTLDWGPPAPEKPR 131
K H+ +L + KE+ + SI L+ +
Sbjct: 406 VVVNKLHKYSLVEKQPKEST----------------ISIP--SIY---LELKVKLENEYA 444
Query: 132 VEPKKFVKIGRPGYRVTKQRDPSNGQQSLLFQVDYPEIADDVFPRHRFMSAYSLLFQVDY 191
+ + V Y + K D + L Q Y I H L +++
Sbjct: 445 LH-RSIVD----HYNIPKTFDSDDLIPPYLDQYFYSHIG-----HH--------LKNIEH 486
Query: 192 PEIADDVFPR----HRFMSAYEQRIEPPDRKWQY------LLFAAEPYETIAFKVSDRTG 241
PE +F RF+ EQ+I W L + Y+ + D
Sbjct: 487 PE-RMTLFRMVFLDFRFL---EQKIRHDSTAWNASGSILNTLQQLKFYKP---YICDNDP 539
Query: 242 LYERITSGLV---------LVDHVKLTCQNQIRLLN 268
YER+ + ++ L+ K T +I L+
Sbjct: 540 KYERLVNAILDFLPKIEENLICS-KYTDLLRIALMA 574
>1zu1_A DSRBP-ZFA, RNA binding protein ZFA; zinc finger protein,
helix-loop-helix, helix-turn-helix; NMR {Xenopus
laevis} SCOP: g.37.1.4 g.37.1.4
Length = 127
Score = 36.1 bits (82), Expect = 0.003
Identities = 13/59 (22%), Positives = 23/59 (38%)
Query: 39 DLNKDPYFMKNHLGSYECKLCLTLHNNEGSYLAHTQGKKHQANLARRAAKEAKDAPQQS 97
+N + +CK+C + +E LAH Q +KH + R A + +
Sbjct: 18 AVNSLIRENSHIFSDTQCKVCSAVLISESQKLAHYQSRKHANKVRRYMAINQGEDSVPA 76
Score = 30.3 bits (67), Expect = 0.33
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 56 CKLCLTLHNNEGSYLAHTQGKKHQANLARR 85
C +C ++ +H GK H NL R
Sbjct: 96 CPVCNMTFSSPVVAESHYIGKTHIKNLRLR 125
>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding,
nucleotide-binding, nucleotidyltransferase, tRNA
processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A
3crr_A
Length = 323
Score = 30.6 bits (70), Expect = 0.54
Identities = 10/44 (22%), Positives = 14/44 (31%), Gaps = 2/44 (4%)
Query: 205 MSAYEQRIEPPDRKWQYLLFAAEPYET--IAFKVSDRTGLYERI 246
MS +R + PY +A R L+ RI
Sbjct: 177 MSDLRRRQSAEKADFDASGRNQLPYTVAQLAIAPEQRQVLHARI 220
>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta
protein, structural genomics, PSI-2, protein structure
initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A
Length = 322
Score = 30.6 bits (70), Expect = 0.59
Identities = 16/113 (14%), Positives = 36/113 (31%), Gaps = 34/113 (30%)
Query: 158 QSLLFQVDYPEIADDVFPRHRFMSA---------YSLLFQVDYPEIADDVFPRHRF---- 204
+++ Q + +I D RH + + L ++D P+ A + P +
Sbjct: 106 NAVIHQFNLGDIRADEDYRHELEAFVNSYGVQALHDKLSKID-PKAAAAIHPNNYRRVIR 164
Query: 205 -----------MSAYEQRIEPPDRKWQYLLFAAEPYETIAFKVSDRTGLYERI 246
++ + E + ++ +R LY+RI
Sbjct: 165 ALEIIKLTGKTVTEQARHEEETPSPYNLVMIGLTM---------ERDVLYDRI 208
>4dgw_A PRE-mRNA-splicing factor PRP9; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 402
Score = 30.2 bits (67), Expect = 0.66
Identities = 9/60 (15%), Positives = 20/60 (33%)
Query: 28 ERLRQLALETIDLNKDPYFMKNHLGSYECKLCLTLHNNEGSYLAHTQGKKHQANLARRAA 87
+ L + + +++ C C + +H GK H+ N ++R
Sbjct: 267 AAVENLIKSDFEHSYCRGSLRSEAKGIYCPFCSRWFKTSSVFESHLVGKIHKKNESKRRN 326
>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation,
ATP-binding, cytoplasm, mitochondrion,
nucleotide-binding, nucleus; 2.95A {Saccharomyces
cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*
Length = 409
Score = 30.0 bits (68), Expect = 0.97
Identities = 12/83 (14%), Positives = 28/83 (33%), Gaps = 6/83 (7%)
Query: 16 VASWSESNRDRRERLRQLALETIDLNKDPYFMKNHLGSYECKLCLTLHNN------EGSY 69
+ + ++ER + E + + + Y C +C E +
Sbjct: 323 SNDFISNRPIKQERAPKALEELLSKGETTMKKLDDWTHYTCNVCRNADGKNVVAIGEKYW 382
Query: 70 LAHTQGKKHQANLARRAAKEAKD 92
H ++H++NL R + +
Sbjct: 383 KIHLGSRRHKSNLKRNTRQADFE 405
Score = 28.4 bits (64), Expect = 2.4
Identities = 15/112 (13%), Positives = 30/112 (26%), Gaps = 34/112 (30%)
Query: 158 QSLLFQVDYPEIADDVFPRHRFMSA---------YSLLFQVDYPEIADDVFP--RHRFMS 206
Q+L + + ++ + + Y+ L + D P+IA P R
Sbjct: 105 QTLFNKRVDTKSSERKL-TRKQLDILESTDPDVIYNTLVKCD-PDIATKYHPNDYRRVQR 162
Query: 207 AYE------------QRIEPPDRKWQYLLFAAEPYETIAFKVSDRTGLYERI 246
E + K+ L L++R+
Sbjct: 163 MLEIYYKTGKKPSETFNEQKITLKFDTLFLWLYS---------KPEPLFQRL 205
>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta
protein, structural genomics, PSI-2; 2.70A
{Staphylococcus epidermidis atcc 12228}
Length = 340
Score = 29.5 bits (67), Expect = 1.1
Identities = 22/115 (19%), Positives = 35/115 (30%), Gaps = 36/115 (31%)
Query: 158 QSLLFQVDYPEIADDVFPRHRFMSA------------YSLLFQVDYPEIADDVFP--RHR 203
QSLL+ + + + + + L D E A D+ P R R
Sbjct: 110 QSLLYNYAFEDESISEDKMKQVKLKLKELEHLNNNKLHEYLASFD-KESAKDIHPNNRKR 168
Query: 204 FMSAYE------------QRIEPPDRKWQYLLFAAEPYETIAFKVSDRTGLYERI 246
+ A E ++++ + LL E R LY RI
Sbjct: 169 VLRAIEYYLKTKKLLSSRKKVQQFTENYDTLLIGIEM---------SRETLYLRI 214
>1zr9_A Zinc finger protein 593; DNA binding, structural genomics, PSI,
protein structure initiative, center for eukaryotic
structural genomics, CESG; NMR {Homo sapiens} SCOP:
g.37.1.4
Length = 124
Score = 27.7 bits (61), Expect = 2.3
Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 5/44 (11%)
Query: 51 LGSYECKLCLTLHNNEGSYLAHTQGKKHQANLARRAAKEAKDAP 94
G + C C + + H + K H ++ K+ P
Sbjct: 48 GGLHRCLACARYFIDSTNLKTHFRSKDH-----KKRLKQLSVEP 86
>2dk4_A PRE-mRNA-splicing factor 18; SFM domain, HPRP18, structural
NPPSFA, national project on protein structural and
function analyses; NMR {Homo sapiens} SCOP: a.140.6.1
Length = 76
Score = 25.9 bits (56), Expect = 4.1
Identities = 8/23 (34%), Positives = 16/23 (69%)
Query: 20 SESNRDRRERLRQLALETIDLNK 42
E++ D +RLR++ + T ++NK
Sbjct: 47 GETDYDAFQRLRKIEILTPEVNK 69
>1dl2_A Class I alpha-1,2-mannosidase; alpha-alpha helix barrel, hydrolase;
HET: NAG NDG BMA MAN; 1.54A {Saccharomyces cerevisiae}
SCOP: a.102.2.1 PDB: 1g6i_A*
Length = 511
Score = 27.7 bits (61), Expect = 4.6
Identities = 13/81 (16%), Positives = 22/81 (27%)
Query: 66 EGSYLAHTQGKKHQANLARRAAKEAKDAPQQSCDELLLTSDAVYTHKDSILISTLDWGPP 125
E YLA+ G + L R + L + ST+ +G
Sbjct: 181 EFKYLAYLTGNRTYWELVERVYEPLYKNNDLLNTYDGLVPIYTFPDTGKFGASTIRFGSR 240
Query: 126 APEKPRVEPKKFVKIGRPGYR 146
K+++ Y
Sbjct: 241 GDSFYEYLLKQYLLTHETLYY 261
>2bjf_A Choloylglycine hydrolase; amidohydrolase, NTN-hydrolase, bIle
acids, BSH; HET: DXC; 1.67A {Clostridium perfringens}
PDB: 2bjg_A 2rlc_A* 2rf8_A 2rg2_A
Length = 329
Score = 27.5 bits (60), Expect = 5.6
Identities = 13/98 (13%), Positives = 30/98 (30%), Gaps = 4/98 (4%)
Query: 105 SDAVYTHKDSILIS--TLDWGPPAPEKPRVEPKKFVKIGRPGYRVTKQRDPSNGQQSLLF 162
+ KD + + +D + P+ F + + + + G +
Sbjct: 3 TGLALETKDGLHLFGRNMDIEYSFNQSIIFIPRNFKCVNKSNKKELTTKYAVLGMGT--I 60
Query: 163 QVDYPEIADDVFPRHRFMSAYSLLFQVDYPEIADDVFP 200
DYP AD + + + + V Y + +
Sbjct: 61 FDDYPTFADGMNEKGLGCAGLNFPVYVSYSKEDIEGKT 98
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
0.319 0.135 0.412
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,350,734
Number of extensions: 253568
Number of successful extensions: 500
Number of sequences better than 10.0: 1
Number of HSP's gapped: 493
Number of HSP's successfully gapped: 19
Length of query: 280
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 188
Effective length of database: 4,133,061
Effective search space: 777015468
Effective search space used: 777015468
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 (21.7 bits)
S2: 57 (26.2 bits)