RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8080
(415 letters)
>4ds1_A Dynein light chain 1, cytoplasmic; dynein light chain fold, peptide
binding, nucle structural protein-transport protein
complex; 1.85A {Saccharomyces cerevisiae}
Length = 97
Score = 105 bits (263), Expect = 5e-28
Identities = 30/82 (36%), Positives = 52/82 (63%), Gaps = 1/82 (1%)
Query: 151 KVALIKETTMEKDMQETAVNAAKEGLEKYNIEREVAGHVKQHFDNTYGPYWQCTVGRNFG 210
++K + + ++E + +K+ L+KY +ER++AG VK+ D YG W VG+NFG
Sbjct: 12 STPIVKASDITDKLKEDILTISKDALDKYQLERDIAGTVKKQLDVKYGNTWHVIVGKNFG 71
Query: 211 SYVSYD-DFYTYFYLGKVAILL 231
SYV+++ + YFY+G +A L+
Sbjct: 72 SYVTHEKGHFVYFYIGPLAFLV 93
>1yo3_A Dynein light chain 1; structural genomics consortium, microtub
malaria, SGC, transport protein; 1.65A {Plasmodium
falciparum} PDB: 1f3c_A 1f95_A 1f96_A 1rhw_A 2p1k_A
2p2t_A 3bri_A 3e2b_A 3fm7_E 3glw_A 3dvt_A 2pg1_A 3p8m_A
1pwj_A 2xqq_A 3brl_A 1re6_A 1cmi_A 3dvh_A 3dvp_A ...
Length = 102
Score = 103 bits (259), Expect = 3e-27
Identities = 39/98 (39%), Positives = 62/98 (63%), Gaps = 2/98 (2%)
Query: 135 GAPPPPPEENYLKAENKVALIKETTMEKDMQETAVNAAKEGLEKYNIEREVAGHVKQHFD 194
G+ + +++K M ++MQ A++ A + L+KYN+E+++A H+K+ FD
Sbjct: 2 GSSHHHHHHSSGLVPRG-SVVKNVDMTEEMQIDAIDCANQALQKYNVEKDIAAHIKKEFD 60
Query: 195 NTYGPYWQCTVGRNFGSYVSYD-DFYTYFYLGKVAILL 231
Y P W C VGRNFGSYV+++ + YFY+G+VAILL
Sbjct: 61 RKYDPTWHCVVGRNFGSYVTHETKNFIYFYIGQVAILL 98
>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 = 36.6 bits (84), Expect = 0.016
Identities = 65/352 (18%), Positives = 100/352 (28%), Gaps = 139/352 (39%)
Query: 22 YYLVSAFDPQNKWNLWWKKYITQLQLV------RVL---PGFGFRSSEQ------MELVV 66
YL+S P + L I +QL ++L PG RS + LV
Sbjct: 229 DYLLSI--PIS-CPL-----IGVIQLAHYVVTAKLLGFTPG-ELRSYLKGATGHSQGLVT 279
Query: 67 EEVHHSATTG------LETYLKFQFIICGIHCTIQLCSSNCKYPQFMLYFGLSQDIFMFF 120
+ + + F I G+ C YP L + +D
Sbjct: 280 AVAIAETDSWESFFVSVRKAITVLFFI-GVRC--YEA-----YPNTSLPPSILED----- 326
Query: 121 LFFDFYKKTYWSKG-GAPPP-------PPE--ENYLKAENK---------VALI------ 155
G P P E ++Y+ N ++L+
Sbjct: 327 ---------SLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNL 377
Query: 156 -----------KETTMEKDMQETAVNAAKEGLEKYNI---EREVAGHVKQHFDNTYGPYW 201
T+ K A GL++ I ER K F N + P
Sbjct: 378 VVSGPPQSLYGLNLTLRK-------AKAPSGLDQSRIPFSER------KLKFSNRFLP-- 422
Query: 202 QCTVGRNFGSYVSYDDFYTYFYLGKVAILLLQWFSGDPIRFTCME----VDYSDTPLG-- 255
V F S+ L + L+ + + + F + V Y DT G
Sbjct: 423 ---VASPFHSH----------LLVPASDLINKDLVKNNVSFNAKDIQIPV-Y-DTFDGSD 467
Query: 256 -RSRAGAVWLFFFSRVLDLVDTKDSQVTFLHVYHHTAVVMFAWLAVKFVPGG 306
R +G++ +VD + L V T A + F PGG
Sbjct: 468 LRVLSGSI-------SERIVD----CIIRLPVKWETTTQFKATHILDFGPGG 508
>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 = 0.018
Identities = 51/434 (11%), Positives = 107/434 (24%), Gaps = 160/434 (36%)
Query: 58 SSEQMELVVEEVHHSATTGLETYLKFQFIICGIHCTIQLCSSNCK-YPQFMLYFGLSQDI 116
S E+++ ++ + F L S + +F+ L +
Sbjct: 47 SKEEIDHIIMSKDA------VSGTLRLFWT--------LLSKQEEMVQKFVEE-VLRIN- 90
Query: 117 FMFFLFFDFYKKTYWSKGGAPPPPPEENYLKAENKVALIKETTMEKDMQ---------ET 167
+ F + P Y++ ++ + D Q
Sbjct: 91 ------YKFLM-SPIKTEQRQPSMMTRMYIEQRDR--------LYNDNQVFAKYNVSRLQ 135
Query: 168 AVNAAKEGLEKYNIEREVAGH-------------------VKQHFDNTYGPYWQCTVGRN 208
++ L + + V V+ D +W N
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF--KIFWL-----N 188
Query: 209 FGSYVSYDDFYTYFYLGKVAILLLQWFSGDPIRFTCMEVDYSDTPLGRSRAGAVWL--FF 266
+ S + + +L + DP D+S R + L
Sbjct: 189 LKNCNSPETV--------LEMLQKLLYQIDPN--WTSRSDHSSNIKLRIHSIQAELRRLL 238
Query: 267 FSR-------VLD-----------------LVDTKDSQVT-FLHVYHHTAVVM------- 294
S+ VL L+ T+ QVT FL T + +
Sbjct: 239 KSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298
Query: 295 --------FA-WLAVKF------VPGGHGVFFGTINCFIHVVMYSYYSLTLYNPEYKNVW 339
+L + V + I I + W
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIR--------------DGLATW 344
Query: 340 --WKKYLTQIQMMQFVAVGLHAI-----------LALLTPNCNYPKSLIII----ALPQD 382
WK ++ + L+ + L++ P+ + P L+ + + D
Sbjct: 345 DNWKHVNCD-KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403
Query: 383 IFMFVLFADFYRKT 396
+ + V ++ +
Sbjct: 404 VMVVV--NKLHKYS 415
Score = 28.3 bits (62), Expect = 6.1
Identities = 13/65 (20%), Positives = 22/65 (33%), Gaps = 23/65 (35%)
Query: 161 EKDMQETAVNAAKEGLEKYNIEREVAGHVKQHFDNTYGPYWQCTVGRNFGSYVSYDDFYT 220
K E A++ + ++ YNI + FD+ Y D Y
Sbjct: 437 VKLENEYALH--RSIVDHYNIPKT--------FDSDDLI-------------PPYLDQYF 473
Query: 221 YFYLG 225
Y ++G
Sbjct: 474 YSHIG 478
>1dzl_A Late major capsid protein L1; icosahedral; 3.50A {Human
papillomavirus type 16} SCOP: b.121.6.1
Length = 505
Score = 33.3 bits (76), Expect = 0.15
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 9/61 (14%)
Query: 96 LCSSNCKYPQFMLYFGLSQDIFMFFLFF-----DFYKKTYWSKGGAP-PPPPEENYLKAE 149
+C+S CKYP ++ + + + LFF + + +++ G P++ Y+K
Sbjct: 224 ICTSICKYPDYI---KMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKGS 280
Query: 150 N 150
Sbjct: 281 G 281
>3iyj_F Major capsid protein L1; bovine papillomavirus BPV1, single
cryo-EM, high resolution, late protein, VIR virus; 4.20A
{Bovine papillomavirus type 1}
Length = 495
Score = 33.2 bits (76), Expect = 0.17
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 9/61 (14%)
Query: 96 LCSSNCKYPQFMLYFGLSQDIFMFFLFF-----DFYKKTYWSKGGAPP-PPPEENYLKAE 149
+ + C YP ++ +++D +FF Y + W++GG+ P + YLK
Sbjct: 220 IQNEICLYPDYL---KMAEDAAGNSMFFFARKEQVYVRHIWTRGGSEKEAPTTDFYLKNN 276
Query: 150 N 150
Sbjct: 277 K 277
>3oae_A Late major capsid protein L1; jelly roll, receptor HSPG, virus
capsid, VIR protein; HET: JHM IDS; 2.80A {Human
papillomavirus} PDB: 2r5h_A 2r5j_A 2r5k_A
Length = 428
Score = 32.8 bits (75), Expect = 0.18
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 9/61 (14%)
Query: 96 LCSSNCKYPQFMLYFGLSQDIFMFFLFF-----DFYKKTYWSKGGAP-PPPPEENYLKAE 149
+C+S CKYP ++ + + + LFF + + +++ G P++ Y+K
Sbjct: 207 ICTSICKYPDYI---KMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKGS 263
Query: 150 N 150
Sbjct: 264 G 264
>2r5i_A L1 protein; HPV18, pentamer, structure, type specific epitope,
capsid, capsid protein, virion; 3.40A {Human
papillomavirus type 18} PDB: 3ofl_A*
Length = 428
Score = 32.4 bits (74), Expect = 0.26
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 9/61 (14%)
Query: 96 LCSSNCKYPQFMLYFGLSQDIFMFFLFF-----DFYKKTYWSKGGAP-PPPPEENYLKAE 149
+C S CKYP ++ +S D + +FF + + +W++ G P+ Y+K
Sbjct: 205 ICQSICKYPDYL---QMSADPYGDSMFFCLRREQLFARHFWNRAGTMGDTVPQSLYIKGT 261
Query: 150 N 150
Sbjct: 262 G 262
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.5 bits (68), Expect = 0.66
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 147 KAENKVAL-IKETTMEKDMQETAVNAAKEGLEKYNIERE 184
+ E + L + + QE A K+ LE++N +
Sbjct: 91 REEQRKRLQELDAASKVMEQEWREKAKKD-LEEWNQRQS 128
>3udf_A Penicillin-binding protein 1A; transglycosylase, transpeptidase;
HET: MES; 1.70A {Acinetobacter baumannii} PDB: 3udi_A*
3udx_A* 3ue0_A* 3ue1_A*
Length = 731
Score = 30.4 bits (69), Expect = 1.2
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 158 TTMEKDMQETAVNAAKEGLEKY 179
TT+ Q A A ++GLE Y
Sbjct: 262 TTINAKRQAIAEKAVQDGLEAY 283
>2rdy_A BH0842 protein; PSI-II, structural genomics, protein structure
initiative, NEW YORK SGX research center for structural
genomics; 2.03A {Bacillus halodurans c-125}
Length = 803
Score = 27.5 bits (60), Expect = 9.3
Identities = 16/127 (12%), Positives = 41/127 (32%), Gaps = 5/127 (3%)
Query: 114 QDIFMFFLFFDFYKKTYWSKGGAPPPPPEENYLKAENKVALIKETTMEKDMQETAVNAAK 173
++ +F L + + + P PE+ + E A+ TTM+ + +
Sbjct: 479 KEAALFCLDWLIENEAGYLVTS-PSTSPEQRFRIGEKGYAVSSATTMDLSLIAECFDNCI 537
Query: 174 EGLEKYNIEREVAGHVKQHFDNTYGPYWQCTVGRNFGSYVSYDDFYTYFYLGKVAILLLQ 233
+ ++ +I+ + + S D+ + ++ L+
Sbjct: 538 QAAKRLSIDEDFVKALSDAKQRLLPLQIGKRGQLQEWSNDFEDEDVHHRHV----SHLVG 593
Query: 234 WFSGDPI 240
+ G I
Sbjct: 594 IYPGRLI 600
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
0.326 0.140 0.454
Gapped
Lambda K H
0.267 0.0669 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,731,871
Number of extensions: 399991
Number of successful extensions: 1011
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1002
Number of HSP's successfully gapped: 24
Length of query: 415
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 319
Effective length of database: 4,021,377
Effective search space: 1282819263
Effective search space used: 1282819263
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 58 (26.2 bits)