RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13810
(386 letters)
>3dom_A RNA polymerase II transcription factor B subunit; protein-protein
complex, heterodimer, beta-alpha-beta split, strand
addition; 2.60A {Saccharomyces cerevisiae}
Length = 108
Score = 121 bits (304), Expect = 6e-34
Identities = 40/103 (38%), Positives = 60/103 (58%), Gaps = 4/103 (3%)
Query: 285 AAQIIGFLRLHALPSVSCP---LPPVVSDQIRLWEGERERLTTSEGVLYSQFVSQADFEK 341
A + + +L P+ P LPP V DQIRLW+ E +R+ T EG LYS F + ++
Sbjct: 7 AEEKLEK-KLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNL 65
Query: 342 LRDYAQDLGVLTWQNEKKRTVVVTKQGHSDIKKFWVNHQKGSQ 384
L YAQD+GVL W+++KK+ ++K+G+S + F K Q
Sbjct: 66 LSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLKKKQ 108
>3dgp_A RNA polymerase II transcription factor B subunit; protein-protein
complex, beta-alpha-beta spilt, heterodimer, damage, DNA
excision; 1.80A {Saccharomyces cerevisiae}
Length = 80
Score = 114 bits (288), Expect = 6e-32
Identities = 34/79 (43%), Positives = 50/79 (63%)
Query: 306 PVVSDQIRLWEGERERLTTSEGVLYSQFVSQADFEKLRDYAQDLGVLTWQNEKKRTVVVT 365
P V DQIRLW+ E +R+ T EG LYS F + ++ L YAQD+GVL W+++KK+ ++
Sbjct: 2 PTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFIS 61
Query: 366 KQGHSDIKKFWVNHQKGSQ 384
K+G+S + F K Q
Sbjct: 62 KEGNSQVLDFAKRKLKKKQ 80
>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 = 55.6 bits (133), Expect = 2e-08
Identities = 83/475 (17%), Positives = 134/475 (28%), Gaps = 146/475 (30%)
Query: 1 ELSEIAKHY-----VIRLLFVE-------QPVPQAVIASWLSKTHAKEHKEATDTLTELR 48
E E Y V FV+ Q +P+++ LSK + D ++
Sbjct: 10 ETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSI----LSKEEIDHIIMSKDAVSGTL 65
Query: 49 RNAKVALLGGGKPWSMSAKLEVDSKARDLDFLNQYALERWECILRFMVGSQQTEGISADA 108
R L K M K + + FL + +TE
Sbjct: 66 RLFWTLLS---KQEEMVQKFVEEVLRINYKFL----MSPI-----------KTEQRQPSM 107
Query: 109 VRTLFNEGAE-----NPVITKDG---------FQFLLLE-TPAQVWYFIL-------KYL 146
+ ++ E + N V K + LLE PA+ ++ K
Sbjct: 108 MTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAK--NVLIDGVLGSGK-- 163
Query: 147 ETVESKGLDLVECLTFLFQLKFS------TFGTDYSTEGMSDKLQVFLQHLREFGLVYQR 200
T + L CL++ Q K S E + + LQ L +
Sbjct: 164 -TW----VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP-----NW 213
Query: 201 KRKAGRFYPTKLALNMAT---RGTLKQIREPGFLIVETNFRVYAYTDSNLKVALIGLFCE 257
++ KL ++ R LK L+V N V ++ L C+
Sbjct: 214 TSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN--VQ---NAKA-WNAFNLSCK 267
Query: 258 LMYRFPNLTVGVLTRD-SVRAAL-------------RSGITAAQIIGFL------RLHAL 297
++ + TR V L +T ++ L R L
Sbjct: 268 IL---------LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL 318
Query: 298 PSVSCPLPPVVSDQIRLWEGERERLTTSEGVLY----------SQFVSQADFEKLRDYAQ 347
P P I E R+ L T + + ++ + + R
Sbjct: 319 PREVLTTNPRRLSII--AESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD 376
Query: 348 DLGV-------------LTWQNEKKRTV--VVTK-QGHSDIKKFWVNHQKGSQHS 386
L V L W + K V VV K +S ++K K S S
Sbjct: 377 RLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEK----QPKESTIS 427
>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 = 43.9 bits (103), Expect = 9e-05
Identities = 51/331 (15%), Positives = 98/331 (29%), Gaps = 106/331 (32%)
Query: 104 ISADAVRTLFNEGAENPVITKDGFQFLLLETPAQVWY--------FILKYLETVESKGLD 155
+ A + R L ++ + +LL P ++ F E E D
Sbjct: 1 MDAYSTRPL--------TLSHGSLEHVLL-VPTASFFIASQLQEQFNKILPEPTEGFAAD 51
Query: 156 -----LVECLTFLFQLKFSTFGTDYSTEGMSDK-LQVFLQHL-REF-------GLVYQ-- 199
E L F L + + + S G D+ L + L + L +
Sbjct: 52 DEPTTPAE-LVGKF-LGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLL 109
Query: 200 --------RKRKAGRFYPTKLALNMATRGTLKQIREPGFL--IVETNFRVYA-------- 241
+ ++ + Y + + + + + E N ++ A
Sbjct: 110 QENDTTLVKTKELIKNY---ITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNT 166
Query: 242 ----------YTDSNLKVALIGLFCELMYRFPNLTVGVLTRDSVRAALRSGITAAQIIGF 291
Y + L+G + L+ + T G+ I+ +
Sbjct: 167 DDYFEELRDLYQTYH---VLVGDLIKFS--AETLSELIRTTLDAEKVFTQGL---NILEW 218
Query: 292 LR-LHALPS--------VSCPLPPVVSDQI-------RLWE---GE-RERL----TTSEG 327
L P +SCPL V+ Q+ +L GE R L S+G
Sbjct: 219 LENPSNTPDKDYLLSIPISCPLIGVI--QLAHYVVTAKLLGFTPGELRSYLKGATGHSQG 276
Query: 328 VLYSQFVSQAD----FEKLRDYAQDLGVLTW 354
++ + +++ D F A + VL +
Sbjct: 277 LVTAVAIAETDSWESFFVSVRKA--ITVLFF 305
Score = 39.3 bits (91), Expect = 0.002
Identities = 66/378 (17%), Positives = 103/378 (27%), Gaps = 142/378 (37%)
Query: 19 PVPQA--VIASWLSKTHAKEHKEATDTLTELRRNAKVALLGGGKPWSMSAKLEVDSKARD 76
VP A IAS L + K E T+ +P + E+ +
Sbjct: 21 LVPTASFFIASQLQEQFNKILPEPTEGFA-----------ADDEP---TTPAEL--VGKF 64
Query: 77 LDFLNQYALERWECILRFMVGSQQTEGISADAVRTLFNEGAENPVITKDGF--QFL---- 130
L +++ G + E F +L
Sbjct: 65 LGYVSSLV-------------EPSKVGQFDQVLNLCLTE-----------FENCYLEGND 100
Query: 131 -------LLE----TPAQVWYFILKYLETVESKGLDLVECLT-FLFQLK-------FSTF 171
LL+ T + I Y+ + LF+ + F
Sbjct: 101 IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF 160
Query: 172 G-----TDYSTEGMSDKLQVFLQHLREFGLVYQRKRKAGRFYPTKLA-LNMATRGTLKQ- 224
G DY E LR+ +YQ Y + L + TL +
Sbjct: 161 GGQGNTDDYFEE------------LRD---LYQT-------YHVLVGDLIKFSAETLSEL 198
Query: 225 IREP---------GFLIVE-----TNFRVYAYTDSNLKVA--LIGL--------FC---- 256
IR G I+E +N Y S ++ LIG+
Sbjct: 199 IRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIP-ISCPLIGVIQLAHYVVTAKLLG 257
Query: 257 ----ELMYRFPNLTV---GVL---------TRDSVRAALRSGITAAQIIGFLRLHALPSV 300
EL T G++ + +S ++R IT IG A P+
Sbjct: 258 FTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNT 317
Query: 301 SCPLPPVVSDQIRLWEGE 318
S P P ++ D + EG
Sbjct: 318 SLP-PSILEDSLENNEGV 334
>1vqq_A Saupbp2A, penicillin-binding protein MECA, low-affinity;
beta-lactam, D- transpeptidase, D-carboxypeptidase,
biosynthetic protein; 1.80A {Staphylococcus aureus}
SCOP: d.17.4.5 d.175.1.1 e.3.1.1 PDB: 1mwu_A* 1mwr_A
1mws_A* 1mwt_A*
Length = 646
Score = 33.1 bits (76), Expect = 0.16
Identities = 10/72 (13%), Positives = 24/72 (33%), Gaps = 3/72 (4%)
Query: 174 DYSTEGMSDKLQVFLQHLREFGLVYQRKRKAGRFYPTKLALNMATRGTLKQIREPGFLIV 233
+ ++ +L + ++++ + Q + F P K M ++
Sbjct: 158 KKDYKAIAKELSISEDYIKQQ--MDQNWVQDDTFVPLKTVKKMDEY-LSDFAKKFHLTTN 214
Query: 234 ETNFRVYAYTDS 245
ET R Y +
Sbjct: 215 ETESRNYPLEKA 226
>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 = 29.9 bits (66), Expect = 0.77
Identities = 7/30 (23%), Positives = 17/30 (56%), Gaps = 7/30 (23%)
Query: 223 KQ-IREPGFLIVETNFRVYAYTDSNLKVAL 251
KQ +++ ++ + ++YA DS +A+
Sbjct: 19 KQALKK-----LQASLKLYA-DDSAPALAI 42
>2paj_A Putative cytosine/guanine deaminase; NYSGXRC, PSI-II,
amidohydrolase, sargasso SEA, enviro sample, structural
genomics; 2.70A {Unidentified} SCOP: b.92.1.4 c.1.9.9
Length = 492
Score = 30.0 bits (68), Expect = 1.3
Identities = 17/113 (15%), Positives = 29/113 (25%), Gaps = 17/113 (15%)
Query: 255 FCELMYRFPNLTVGVLTRDSVRAALRSGITAAQIIGFLRLHALPSVSCPLPPVV------ 308
+ Y + + A + G+ + G P
Sbjct: 134 VADHNYVYYPGMPFDSSAILFEEAEKLGLRFVLLRGGATQTRQLEADLPTALRPETLDAY 193
Query: 309 -SDQIRLWE-----GERERLTTSEG---VLYSQFVSQADFEKLRDYAQDLGVL 352
+D RL R VLYS +S + + A+ LG+
Sbjct: 194 VADIERLAARYHDASPRAMRRVVMAPTTVLYS--ISPREMRETAAVARRLGLR 244
>3ls9_A Triazine hydrolase; atrazine chlorohydrolase TRZN; 1.40A
{Arthrobacter aurescens} PDB: 3lsc_A* 3lsb_A*
Length = 456
Score = 28.4 bits (64), Expect = 4.4
Identities = 16/111 (14%), Positives = 24/111 (21%), Gaps = 15/111 (13%)
Query: 255 FCELMYRFPNLTVGVLTRDSVRAALRSGITAAQIIGFLRLHALPSVSCPLPPVVSDQIRL 314
+ FP T ++ AA GI + L C V +
Sbjct: 126 VADQHLFFPGATADSYIDATIEAATDLGIRFHAARSSMTLGKSEGGFCDDLFVEPVDRVV 185
Query: 315 WEGER-----------ERLTTSEG--VLYSQFVSQADFEKLRDYAQDLGVL 352
+ + G + FE A D V
Sbjct: 186 QHCLGLIDQYHEPEPFGMVRIALGPCGVPY--DKPELFEAFAQMAADYDVR 234
>3tm0_A Aminoglycoside 3'-phosphotransferase; protein kinase,
phosphorylation, transferase-antibiotic COMP; HET: ANP
B31; 2.10A {Enterococcus faecalis} PDB: 2b0q_A* 1l8t_A*
3q2j_A* 1j7i_A* 1j7u_A* 3h8p_A* 1j7l_A* 2bkk_A*
Length = 263
Score = 27.7 bits (61), Expect = 5.6
Identities = 7/55 (12%), Positives = 15/55 (27%), Gaps = 1/55 (1%)
Query: 268 GVLTRDSVRAALRSGITAAQIIGFLR-LHALPSVSCPLPPVVSDQIRLWEGERER 321
GVL + +R H++ CP + ++ +
Sbjct: 94 GVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNN 148
>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex,
separation-OF-function helix-hairpin-helix, DNA repair;
HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A*
1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A*
1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A
1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ...
Length = 360
Score = 27.8 bits (61), Expect = 6.7
Identities = 6/51 (11%), Positives = 14/51 (27%), Gaps = 1/51 (1%)
Query: 88 WECILRFMVGSQQTEGISADAVRTLFNEGAENPVITKDGFQFLLLETPAQV 138
EC+ F+ S + + +I D + + +
Sbjct: 153 IECLFSFIC-SSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQAL 202
>3p2c_A Putative glycosyl hydrolase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-biology; HET: MSE PGE; 1.60A {Bacteroides ovatus}
PDB: 3on6_A*
Length = 463
Score = 27.6 bits (61), Expect = 7.4
Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 21/83 (25%)
Query: 60 KPWSMSAKLEVDSKA-------------RDLDFLNQYALERWECILRFMVGSQQTEGISA 106
KP K E+DS D N+ ++ +L+ Q+ +G+
Sbjct: 152 KPELHERKWEIDSLCYPLRLAYHYWKTTGDASIFNEEWIQAITNVLKTFKEQQRKDGVGP 211
Query: 107 D--------AVRTLFNEGAENPV 121
A+ T+ N+G PV
Sbjct: 212 YKFQRKTERALDTVSNDGLGAPV 234
>1p1m_A Hypothetical protein TM0936; putative metal dependent hydrolase,
PSI, protein structure initiative; 1.50A {Thermotoga
maritima} SCOP: b.92.1.4 c.1.9.9 PDB: 2plm_A* 1j6p_A
Length = 406
Score = 27.5 bits (62), Expect = 8.8
Identities = 16/102 (15%), Positives = 28/102 (27%), Gaps = 27/102 (26%)
Query: 259 MYRFPNLTVGVLTRDSVRAALRSGITAAQIIGFLRLH-ALPSVSCPLPP--VVSDQIRL- 314
MY +A G+ R V + + ++L
Sbjct: 114 MYFHEE--------WIAKAVRDFGM---------RALLTRGLVDSNGDDGGRLEENLKLY 156
Query: 315 --WEGERERLTTSEGV--LYSQFVSQADFEKLRDYAQDLGVL 352
W G R+ G Y S+ +++ D A+ L
Sbjct: 157 NEWNGFEGRIFVGFGPHSPYL--CSEEYLKRVFDTAKSLNAP 196
>2yl5_A Beta-N-acetylhexosaminidase; hydrolase; 2.15A {Streptococcus
pneumoniae} PDB: 2yla_A* 2yl9_A*
Length = 442
Score = 27.6 bits (61), Expect = 8.9
Identities = 6/39 (15%), Positives = 15/39 (38%)
Query: 313 RLWEGERERLTTSEGVLYSQFVSQADFEKLRDYAQDLGV 351
+ + E ++QA+ +L +YA+ +
Sbjct: 71 DVKKAIIEGTKAYYDDPNGTALTQAEVTELIEYAKSKDI 109
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 0.136 0.401
Gapped
Lambda K H
0.267 0.0548 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,762,323
Number of extensions: 340305
Number of successful extensions: 1006
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1004
Number of HSP's successfully gapped: 25
Length of query: 386
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 291
Effective length of database: 4,049,298
Effective search space: 1178345718
Effective search space used: 1178345718
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 (21.9 bits)
S2: 58 (26.5 bits)