RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy876
(179 letters)
>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase,
nucleotide excision repair,; 2.20A {Thermoplasma
acidophilum} PDB: 2vsf_A*
Length = 620
Score = 70.9 bits (174), Expect = 5e-15
Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 8/87 (9%)
Query: 61 ADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQ 120
+D+ + + + + CL+ + ++E I SGTL P D +
Sbjct: 340 SDQDEEKYAAILSPEDGG-----YMQAACLDPSGILEVLKE--SKTIHMSGTLDPFDFYS 392
Query: 121 SELGTQFPIKLEANHVIDKDQVFIGVL 147
G + P + + + +I
Sbjct: 393 DITGFEIPF-KKIGEIFPPENRYIAYY 418
Score = 32.0 bits (73), Expect = 0.090
Identities = 9/71 (12%), Positives = 18/71 (25%), Gaps = 8/71 (11%)
Query: 1 MTILSSRKHTCINDEVLKAK-----ENINDLCQELKETEGESNRW---YRKDRTPMRGIE 52
+ R + CI ++ E++ C K N Y + +
Sbjct: 82 AIPMQGRVNMCILYRMVDDLHEINAESLAKFCNMKKREVMAGNEAACPYFNFKIRSDETK 141
Query: 53 PVVSQGPHADE 63
+ E
Sbjct: 142 RFLFDELPTAE 152
>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}
Length = 540
Score = 57.7 bits (139), Expect = 2e-10
Identities = 7/68 (10%), Positives = 16/68 (23%)
Query: 70 RWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPI 129
++ + +L + + D +L SGTL + +
Sbjct: 286 KFVEMKGDLYNCNGSLVKVPSDVNQLIEDALNVKTFKVLMSGTLPESLTLTNSYKIVVNE 345
Query: 130 KLEANHVI 137
Sbjct: 346 SYGRGEYY 353
Score = 29.2 bits (65), Expect = 0.73
Identities = 7/32 (21%), Positives = 13/32 (40%)
Query: 1 MTILSSRKHTCINDEVLKAKENINDLCQELKE 32
L + +CI + + + IN LK+
Sbjct: 78 TGFLIGKSASCIYAQGDEEPDEINCSKCRLKD 109
>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer
aging, hydrolase; HET: FLC; 2.00A {Sulfolobus
acidocaldarius} PDB: 3crw_1*
Length = 551
Score = 52.7 bits (126), Expect = 9e-09
Identities = 18/95 (18%), Positives = 29/95 (30%), Gaps = 1/95 (1%)
Query: 60 HADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSF 119
H + P S L + + ++ S+IL SGTL P +
Sbjct: 272 HIGSILRFFSLLSIGSFIPFSYSKRLVIKNPEISYYLNLLNDNELSIILMSGTLPPREYM 331
Query: 120 QSELGTQFP-IKLEANHVIDKDQVFIGVLGQGQKV 153
+ G + + L+ I K G V
Sbjct: 332 EKVWGIKRNMLYLDVEREIQKRVSGSYECYIGVDV 366
Score = 31.1 bits (70), Expect = 0.19
Identities = 9/58 (15%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 1 MTILSSRKHTCINDEVLKAKENINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQG 58
+ L + +C+ E E+I C+ + + D +P+ ++ + G
Sbjct: 78 FSFLVGKPSSCLYAEKGAESEDIP--CKYCELKGSIVE--VKTDDSPLSLVKKLKKDG 131
>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 = 42.3 bits (99), Expect = 4e-05
Identities = 35/170 (20%), Positives = 57/170 (33%), Gaps = 54/170 (31%)
Query: 26 LCQELKETEGESNRWYRKDRTPMRGIEPVVSQG------P-HADEYQGESNRWYRKDRTP 78
L L++ + S + R P + S P H+ ++ KD
Sbjct: 389 LNLTLRKAKAPSG--LDQSRIPFSERKLKFSNRFLPVASPFHSH-LLVPASDLINKDLVK 445
Query: 79 MSIKYT---LHF--WCLNSGLVFSDIRESARSV-------ILTSGTLAPVDSFQSELGTQ 126
++ + + + G SD+R + S+ I+ PV E TQ
Sbjct: 446 NNVSFNAKDIQIPVYDTFDG---SDLRVLSGSISERIVDCIIRL----PVKW---ETTTQ 495
Query: 127 FPIKLEANHVIDKDQVF-------IGVL------GQGQKVFI-GVLGQGP 162
F A H++D F +GVL G G +V + G L P
Sbjct: 496 FK----ATHILD----FGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINP 537
Score = 37.7 bits (87), Expect = 0.001
Identities = 31/145 (21%), Positives = 51/145 (35%), Gaps = 43/145 (29%)
Query: 19 AKENINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQGP--HADEYQGESNRWYRKDR 76
A++ N K+T G S I +V P + GE + R++
Sbjct: 1642 AQDVWNRADNHFKDTYGFS-------------ILDIVINNPVNLTIHFGGEKGKRIRENY 1688
Query: 77 TPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELG----TQF--P-I 129
+ M + + L + +F +I E + S F+SE G TQF P +
Sbjct: 1689 SAMIFETIVDG-KLKTEKIFKEINEHSTSYT-----------FRSEKGLLSATQFTQPAL 1736
Query: 130 ---------KLEANHVIDKDQVFIG 145
L++ +I D F G
Sbjct: 1737 TLMEKAAFEDLKSKGLIPADATFAG 1761
Score = 35.8 bits (82), Expect = 0.006
Identities = 35/222 (15%), Positives = 66/222 (29%), Gaps = 94/222 (42%)
Query: 21 ENINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQGPHADEYQGESNRWYRK-DRTPM 79
+ + EL T ++ + + + G+ + W TP
Sbjct: 189 KFSAETLSELIRTTLDAEKVFTQ------GLNIL---------------EWLENPSNTP- 226
Query: 80 SIKYTL---------------HFW--CLNSGLVFSDIRESARSV------ILTSGTLAPV 116
Y L H+ G ++R + ++T+ +A
Sbjct: 227 DKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAET 286
Query: 117 DSFQSE-------------LGTQ----FP-IKLEANHVID-------------------K 139
DS++S +G + +P L + + D +
Sbjct: 287 DSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQ 346
Query: 140 DQVFIGV------LGQGQKVFIGVLGQGPQNI----PLQALY 171
+QV V L G++V I L G +N+ P Q+LY
Sbjct: 347 EQVQDYVNKTNSHLPAGKQVEIS-LVNGAKNLVVSGPPQSLY 387
Score = 26.9 bits (59), Expect = 4.6
Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 7/39 (17%)
Query: 102 SARSVILTSGTLA-----PVDSFQ--SELGTQFPIKLEA 133
S R + L+ G+L P SF S+L QF L
Sbjct: 5 STRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPE 43
>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 = 36.4 bits (83), Expect = 0.004
Identities = 25/177 (14%), Positives = 57/177 (32%), Gaps = 39/177 (22%)
Query: 24 NDLCQELKETEGESNR--W--YRKDRTPMRGIEPV-----------VSQGPHADEYQGES 68
D+C K + W + +P +E + S+ H+ +
Sbjct: 168 LDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI 227
Query: 69 NRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRES---------ARSVILTSGTLAPVDSF 119
+ + R + K + CL LV +++ + + ++LT+ D
Sbjct: 228 HSIQAELRRLLKSK--PYENCL---LVLLNVQNAKAWNAFNLSCK-ILLTTRFKQVTDFL 281
Query: 120 QSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLV 176
+ T + + + D+ + + + L PQ++P + L N
Sbjct: 282 SAATTTHISLD-HHSMTLTPDE--------VKSLLLKYLDCRPQDLPREVLTTNPRR 329
>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 = 34.5 bits (78), Expect = 0.008
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 28 QELKETEGESNRWYRKDRTPMRGIEPVV 55
Q LK+ + S + Y D P I+ +
Sbjct: 20 QALKKLQA-SLKLYADDSAPALAIKATM 46
>3rfz_B Outer membrane usher protein, type 1 fimbrial SYN; beta-barrel,
pilus assembly, outer-membrane, cell adhesion-T
protein-chaperone complex; 2.80A {Escherichia coli} PDB:
3ohn_A 1zdv_A
Length = 843
Score = 29.9 bits (67), Expect = 0.43
Identities = 11/66 (16%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 98 DIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANH--------VIDKDQVFIGVLGQ 149
D+ + +V+ T G + + F++ +G + + L N+ V + G++
Sbjct: 725 DLDNAVANVVPTRGAIVRAE-FKARVGIKLLMTLTHNNKPLPFGAMVTSESSQSSGIVAD 783
Query: 150 GQKVFI 155
+V++
Sbjct: 784 NGQVYL 789
>3htk_A Structural maintenance of chromosomes protein 5; SUMO E3 ligase,
SPL-ring, ring, ATP-binding, chromosomal protein,
coiled coil, DNA damage; 2.31A {Saccharomyces
cerevisiae}
Length = 60
Score = 26.7 bits (58), Expect = 1.1
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 6/36 (16%)
Query: 13 NDEVLKAKENINDLCQELKETEGE------SNRWYR 42
DE LKAKE IN++ ++L E N +YR
Sbjct: 25 TDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEYYR 60
>3cf4_A Acetyl-COA decarboxylase/synthase alpha subunit; methanomicrobia,
iron-nikel-sulfur, 4Fe-NI-4S, oxidoreductas; 2.00A
{Methanosarcina barkeri}
Length = 807
Score = 27.8 bits (61), Expect = 2.1
Identities = 8/42 (19%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 108 LTSGTLAPVDSFQSELGTQFPIKLEAN-HVIDKDQVFIGVLG 148
+ + V ++ +E IDK + F+ V+G
Sbjct: 208 MEISDIVQVAAYDFPKADPEAPLVEIGMGTIDKSKPFLCVIG 249
>3dmk_A DOWN syndrome cell adhesion molecule (dscam) ISOF 1.30.30,
N-terminal eight IG domains...; immunoglobulin domain;
HET: NAG NDG; 4.19A {Drosophila melanogaster}
Length = 816
Score = 28.0 bits (62), Expect = 2.3
Identities = 9/43 (20%), Positives = 13/43 (30%)
Query: 70 RWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGT 112
W R D T + L + LVF R + +
Sbjct: 72 IWIRSDGTAVGDVPGLRQISSDGKLVFPPFRAEDYRQEVHAQV 114
>1e5x_A Threonine synthase; threonine biosynthesis, PLP enzyme,
S-adenosyl-methionine, allostery; 2.25A {Arabidopsis
thaliana} SCOP: c.79.1.1 PDB: 2c2b_A* 2c2g_A*
Length = 486
Score = 26.7 bits (59), Expect = 4.5
Identities = 10/54 (18%), Positives = 14/54 (25%)
Query: 44 DRTPMRGIEPVVSQGPHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFS 97
+ V D + E+ R P S KY S +S
Sbjct: 4 NNIKAPIETAVKPPHRTEDNIRDEARRNRSNAVNPFSAKYVPFNAAPGSTESYS 57
>1ze3_H FIMH protein; soluble domain, ternary complex with chaperone and
pilus subunit; 1.84A {Escherichia coli} SCOP: b.2.3.2
Length = 122
Score = 25.9 bits (57), Expect = 5.1
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 150 GQKVFIGVLGQGPQNIPLQALYKNT 174
V +G +G ++ L A Y T
Sbjct: 78 NNTVSLGAVGTSAVSLGLTANYART 102
>2efr_A General control protein GCN4 and tropomyosin 1 Al; destabilizing
cluster, hydrophobic core, contractIle protein; 1.80A
{Saccharomyces cerevisiae} PDB: 2efs_A 2d3e_A
Length = 155
Score = 25.7 bits (56), Expect = 7.9
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 12 INDEVLKAKENINDLCQELKETEGE 36
+ DE+ K + +E+K+ E +
Sbjct: 110 LEDELYAQKLKYKAISEEMKQLEDK 134
>3jwn_H FIMH protein; fimbria, cell adhesion, FIMC, FIMF,FIMG, chaperone,
FI immunoglobulin domain, fimbrium, periplasm, disulfide
bond; 2.69A {Escherichia coli} PDB: 1klf_B* 1qun_B
1kiu_B* 3rfz_A 3mcy_A*
Length = 279
Score = 25.9 bits (56), Expect = 8.0
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 145 GVLGQGQKVFIGVLGQGPQNIPLQALYKNT 174
++ V +G +G ++ L A Y T
Sbjct: 230 TIIPANNTVSLGAVGTSAVSLGLTANYART 259
>3ces_A MNMG, tRNA uridine 5-carboxymethylaminomethyl modificat GIDA, GIDA;
tRNA modification, FAD binding domain, structural
genomics; 2.41A {Escherichia coli} PDB: 3cp2_A 3g05_A
Length = 651
Score = 25.9 bits (58), Expect = 9.7
Identities = 9/23 (39%), Positives = 12/23 (52%), Gaps = 5/23 (21%)
Query: 90 LNSGLVFSDIRESARSVILTSGT 112
GL F A++V+LT GT
Sbjct: 162 TQMGLKFR-----AKAVVLTVGT 179
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
0.317 0.135 0.405
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,557,134
Number of extensions: 135699
Number of successful extensions: 247
Number of sequences better than 10.0: 1
Number of HSP's gapped: 245
Number of HSP's successfully gapped: 25
Length of query: 179
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 92
Effective length of database: 4,272,666
Effective search space: 393085272
Effective search space used: 393085272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.7 bits)