RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14236
(290 letters)
>1d8j_A General transcription factor TFIIE-beta; winged helix-turn-helix,
riken structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Homo sapiens} SCOP: a.4.5.18
PDB: 1d8k_A
Length = 81
Score = 133 bits (335), Expect = 8e-40
Identities = 57/82 (69%), Positives = 66/82 (80%), Gaps = 1/82 (1%)
Query: 64 SMSGSSQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQ 123
++SGSS YKFGVLAKIV +MK RHQ GD HPLT+DEILDET LD+G K K WL TEAL
Sbjct: 1 ALSGSSGYKFGVLAKIVNYMKTRHQRGDTHPLTLDEILDETQHLDIGLKQKQWLMTEALV 60
Query: 124 NNPKIEVIEGNKYIFKPVFKIK 145
NNPKIEVI+G KY FKP + ++
Sbjct: 61 NNPKIEVIDG-KYAFKPKYNVR 81
>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 = 52.0 bits (124), Expect = 1e-07
Identities = 44/250 (17%), Positives = 82/250 (32%), Gaps = 87/250 (34%)
Query: 49 SLSSSLGSSNNMAYKSMS-----GS-SQYKFGVLAKIVKHMKQRHQDGDDHP-------- 94
+ + S S K+++ G + + ++ ++ + P
Sbjct: 284 AETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN 343
Query: 95 LTIDEI---LDETNQ-LDVGNKVKIWLSTEALQNNPKIEVIEGNKYIFKPVFKIKDRKGL 150
LT +++ +++TN L G +V+I +L N K V+ G P
Sbjct: 344 LTQEQVQDYVNKTNSHLPAGKQVEI-----SLVNGAKNLVVSGP-----PQ--------- 384
Query: 151 LKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYVTRPADKRKVMFYND--- 207
L G L +R+ KA L Q+ I P +RK+ F N
Sbjct: 385 -------SLYG----LNLTLRK-----AKAPSGLD-QSRI-----PFSERKLKFSNRFLP 422
Query: 208 ----------KSAQLDLDEDFQK---LWRS----ISV----DGMDNDKIKEYLEKQGIRP 246
A +++D K + + I V DG D + + ++ +
Sbjct: 423 VASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDC 482
Query: 247 IQDHGFKKPV 256
I + PV
Sbjct: 483 I----IRLPV 488
>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 = 44.8 bits (105), Expect = 2e-05
Identities = 41/341 (12%), Positives = 89/341 (26%), Gaps = 94/341 (27%)
Query: 1 MDPALLRERDLFKKKALSTPTVEKRKAETS--KDEPWKAKKAKTSSSSSSSLSSSLGSSN 58
A+ LF + ++ E + + KT S ++
Sbjct: 57 SKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQR 116
Query: 59 NMAYKSMSGSSQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKV----- 113
+ Y +Q K+ R Q ++ +L V
Sbjct: 117 DRLY----NDNQ-------VFAKYNVSRLQ-------PYLKLRQALLELRPAKNVLIDGV 158
Query: 114 ----KIWLSTEALQNNPKIEVIEGNKY--------------------------------- 136
K W++ + + ++ +
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218
Query: 137 ----IFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIY 192
I + I+ L +LLK + ++L +V+ + KA +L +I+
Sbjct: 219 HSSNIKLRIHSIQAE--LRRLLKSKPYE-NCLLVLLNVQNA-----KAWNAFNLSCKILL 270
Query: 193 VTR--------PADKRKVMFYNDKSAQLDLDEDFQKLWRSISVDGMDNDKIKEYLEKQGI 244
TR A + + S L DE L + + + E
Sbjct: 271 TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL---DCRPQDLPR--EVLTT 325
Query: 245 RPIQDHGFKKPVLPGRKKNM-NRKKQFKKPRDNEHLADVLE 284
P + ++ ++ +K + + L ++E
Sbjct: 326 NP-----RRLSIIAESIRDGLATWDNWKHV-NCDKLTTIIE 360
Score = 44.5 bits (104), Expect = 3e-05
Identities = 46/320 (14%), Positives = 91/320 (28%), Gaps = 116/320 (36%)
Query: 2 DPALLRERDLFKKKALSTPTVEKRKAETSKDEP-WKAKKAKTSSSSSSSLSSSLGSSNNM 60
P+++ + ++ L K S+ +P K ++A L L + N+
Sbjct: 104 QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQA---------LLE-LRPAKNV 153
Query: 61 AYKSMSGSSQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLS-- 118
+ G G K + +D L Q + K+ WL+
Sbjct: 154 LIDGVLG-----SG---KTW--------------VALDVCLSYKVQCKMDFKI-FWLNLK 190
Query: 119 --------TEALQN------NPKIEVIEGNKYIFKPVFKIKDRKGLLKLLKQHDLKGIGG 164
E LQ + + I + I+ L +LLK +
Sbjct: 191 NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE--LRRLLKSKPYE-NCL 247
Query: 165 ILLDDVRESLPHCEKALKHLSLQNEIIYVTR----------------PADKRKVMFYNDK 208
++L +V+ + KA +L +I+ TR D + D+
Sbjct: 248 LVLLNVQNA-----KAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE 302
Query: 209 SAQL---DLDEDFQKL----------------------------WR-----------SIS 226
L LD Q L W+ S
Sbjct: 303 VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS 362
Query: 227 VDGMDNDKIKEYLEKQGIRP 246
++ ++ + ++ ++ + P
Sbjct: 363 LNVLEPAEYRKMFDRLSVFP 382
Score = 31.4 bits (70), Expect = 0.46
Identities = 39/262 (14%), Positives = 74/262 (28%), Gaps = 105/262 (40%)
Query: 82 HM-----KQRHQDGD-------------------DHPLTI------DEILDETNQLD--- 108
HM + ++Q D D P +I D I+ + +
Sbjct: 6 HMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTL 65
Query: 109 -----------------VGNKVKI---WLSTEALQNNPKIEVIEGNKYI----------- 137
V ++I +L ++ + + YI
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEVLRINYKFL-MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ 124
Query: 138 ---------FKPVFKIKDRKGLLKLLKQ-----HDLKGIG-GILLDDVRESLPHCEKALK 182
+P K+ R+ LL+L + G G + DV C
Sbjct: 125 VFAKYNVSRLQPYLKL--RQALLELRPAKNVLIDGVLGSGKTWVALDV------CLSYKV 176
Query: 183 HLSLQNEIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKLWRSIS------VDGMDNDKIK 236
+ +I ++ N S + L E QKL I D N K++
Sbjct: 177 QCKMDFKIFWLN---------LKNCNSPETVL-EMLQKLLYQIDPNWTSRSDHSSNIKLR 226
Query: 237 EYLEKQGIRP-IQDHGFKKPVL 257
+ + +R ++ ++ +L
Sbjct: 227 IHSIQAELRRLLKSKPYENCLL 248
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 31.8 bits (72), Expect = 0.32
Identities = 27/122 (22%), Positives = 42/122 (34%), Gaps = 41/122 (33%)
Query: 158 DLKGIGGILLDDVRESLPHCEKALKHLSLQNEII-YVTRPADKRKV---------MFYND 207
+L+ I R L + + + + Q TRPA +V F D
Sbjct: 581 ELEHIDSKSEFAHRIMLTNILRMMGCVKKQKSARGIETRPA---QVILPMSPNHGTFGGD 637
Query: 208 ------KSAQLDLDEDFQKLWRS------ISVDG-----------M-DNDKIKEYLEKQG 243
K + L+ F + W S ++V G M N+ I E +EK G
Sbjct: 638 GMYSESKLS---LETLFNR-WHSESWANQLTVCGAIIGWTRGTGLMSANNIIAEGIEKMG 693
Query: 244 IR 245
+R
Sbjct: 694 VR 695
>2x3l_A ORN/Lys/Arg decarboxylase family protein; lyase; HET: LLP; 2.00A
{Staphylococcus aureus}
Length = 446
Score = 30.2 bits (68), Expect = 0.80
Identities = 9/70 (12%), Positives = 22/70 (31%), Gaps = 4/70 (5%)
Query: 177 CEKALKHLSLQNEIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKLWRSISVDGMDNDKIK 236
E A + + ++ KR + ++ ++ + L I +G I+
Sbjct: 254 LESAAQFYKTYDSTLF----FAKRAQLIECLENKGFEMLQVDDPLKLLIKYEGFTGHDIQ 309
Query: 237 EYLEKQGIRP 246
+ I
Sbjct: 310 NWFMNAHIYL 319
>1wmd_A Protease; alpha-beta hydrolase fold, jelly-roll beta-barrel,
hydrolase; 1.30A {Bacillus SP} SCOP: b.18.1.20 c.41.1.1
PDB: 1wme_A 1wmf_A
Length = 434
Score = 29.5 bits (66), Expect = 1.5
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 42 TSSSSSSSLSSSLGSSNNMAYKSMSGSSQ 70
S+ SS + SS ++++ Y M G+S
Sbjct: 228 LSARSSLAPDSSFWANHDSKYAYMGGTSM 256
>2qx5_A Nucleoporin NIC96; mRNA transport, nuclear pore complex, nucleus,
protein transport, translocation, transport, transport
protein; 2.50A {Saccharomyces cerevisiae} PDB: 2rfo_A
Length = 661
Score = 28.9 bits (64), Expect = 2.3
Identities = 16/100 (16%), Positives = 37/100 (37%), Gaps = 2/100 (2%)
Query: 42 TSSSSSSSLSSSLGSSNNMAYKSMSGSSQYKFGVLAKIVKHMKQRHQDGDDHPL--TIDE 99
+ + ++ L S+ + + + + KF A+IV Q + +
Sbjct: 3 SEFELGNKGNNILNSNESRLNVNENNILREKFENYARIVFQFNNSRQANGNFDIANEFIS 62
Query: 100 ILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKYIFK 139
IL N ++ W E++++ V G +Y+ +
Sbjct: 63 ILSSANGTRNAQLLESWKILESMKSKDINIVEVGKQYLEQ 102
>2rbk_A Putative uncharacterized protein; HAD-like phosphatase, unknown
function; 1.00A {Bacteroides thetaiotaomicron} SCOP:
c.108.1.10 PDB: 1ymq_A 2rb5_A 2rav_A 2rar_A
Length = 261
Score = 27.1 bits (61), Expect = 7.2
Identities = 13/132 (9%), Positives = 39/132 (29%), Gaps = 16/132 (12%)
Query: 130 VIEGNKYIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNE 189
G + I+K ++ K + ++ + + ++ P+ +
Sbjct: 73 CFVGEEVIYKSAIPQEEVKAMAAFCEKKGV-PCIFVEEHNISVCQPNEMVKKIFYDFLHV 131
Query: 190 IIYVTRPADKR------KVMFYNDKSAQLDLDEDFQKL----WRSISVDGM--DNDK--- 234
+ T ++ ++ + + + ++ W D + K
Sbjct: 132 NVIPTVSFEEASNKEVIQMTPFITEEEEKEVLPSIPTCEIGRWYPAFADVTAKGDTKQKG 191
Query: 235 IKEYLEKQGIRP 246
I E + GI+
Sbjct: 192 IDEIIRHFGIKL 203
>2f5g_A Transposase, putative; dimer, stem-loop binding, gene regulation;
1.70A {Sulfolobus solfataricus} SCOP: d.58.57.1 PDB:
2f4f_A 2ec2_A
Length = 133
Score = 26.2 bits (56), Expect = 9.5
Identities = 16/115 (13%), Positives = 35/115 (30%), Gaps = 6/115 (5%)
Query: 141 VFKIKDRKGLLKLLKQHDLKGIGGILLDD--VRESLPHCEKALKHLSLQNEIIYVTRPAD 198
V+ K R+ L K + + ++ HL + Y
Sbjct: 18 VWIPKHRRNTLVNEIAEYTKEVLKSIAEELGCEIIALEVMPDHIHLFVNCPPRYAPSYLA 77
Query: 199 KRKVMFYNDKSAQLDLDEDFQKLWR----SISVDGMDNDKIKEYLEKQGIRPIQD 249
+ + KLW + + ++ IK+Y+E+Q + ++
Sbjct: 78 NYFKGKSARLILKKFPQLNKGKLWTRSYFVATAGNVSSEVIKKYIEEQWRKEGEE 132
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
0.313 0.131 0.369
Gapped
Lambda K H
0.267 0.0567 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,305,111
Number of extensions: 254030
Number of successful extensions: 643
Number of sequences better than 10.0: 1
Number of HSP's gapped: 638
Number of HSP's successfully gapped: 29
Length of query: 290
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 197
Effective length of database: 4,105,140
Effective search space: 808712580
Effective search space used: 808712580
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (26.1 bits)