RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13975
(415 letters)
>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 = 56.0 bits (134), Expect = 2e-08
Identities = 47/368 (12%), Positives = 105/368 (28%), Gaps = 102/368 (27%)
Query: 7 DVFVLRFNDGSVIGNILLISDNSSGKT-----TLIAKLQGIDSPEKGLALEYAYIN---- 57
V F + +I L +S T +L+ K +D + L E N
Sbjct: 274 FKQVTDFLSAATTTHISLD-HHSMTLTPDEVKSLLLKY--LDCRPQDLPREVLTTNPRRL 330
Query: 58 --VSDEYREDHTRLGVWILDGEPAHSNLLRFALNQ----------ETL----------PH 95
+++ R+ W + ++ +LN + L
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTI 390
Query: 96 TMVMLVVSMTT--PWNIIDELHNWASVLQDHIDSLNIGAHDYQAGRCCKLLTFARLRAHL 153
+ ++ + ++++LH S+++ I KL L +
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLHK-YSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI 449
Query: 154 IELLSFYLFYSSVSVIPGEGILERNLGVDIVVVVTKTDY--------MSTLEKDFYYKEE 205
++ Y+ + ++ L D Y + +E
Sbjct: 450 VD------HYNIPKTFDSDDLIPPYL--D--------QYFYSHIGHHLKNIEHPERMTLF 493
Query: 206 H-----FDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRLYGFPFRTSALIVE 260
F F++Q IR + A + + L Y + I +
Sbjct: 494 RMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQ-----LKFYKPY------------ICD 536
Query: 261 KDAVLIPSGWDNMKKIGILYENMQSIKPDDY---YTDVITKPIVRKPISREQDTLVEDEQ 317
D + + + + + I+ + YTD ++R + E + + E+
Sbjct: 537 NDP-------KYERLVNAILDFLPKIEENLICSKYTD-----LLRIALMAEDEAIFEEA- 583
Query: 318 SFLARQLA 325
+Q+
Sbjct: 584 ---HKQVQ 588
Score = 49.5 bits (117), Expect = 2e-06
Identities = 38/320 (11%), Positives = 88/320 (27%), Gaps = 107/320 (33%)
Query: 30 SGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDGEPAHSNLLRFALN 89
SGKT + + + + + ++N+ T L E L + N
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLK-NCNSPETVL-------EMLQKLLYQIDPN 212
Query: 90 QETLPHTMVMLVVSMTTPWNIIDELHNWAS----------------VLQD-----HIDSL 128
+ NI +H+ + VL + ++
Sbjct: 213 WTSRSDHSS----------NIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF 262
Query: 129 NIGAHDYQAGRCCKLLTFARLRAHLIELLSFYLFYSSVSVIP---------GEGILERNL 179
N+ CK+L R + + + LS + +S+ + +L + L
Sbjct: 263 NLS---------CKILLTTRFKQ-VTDFLSAAT-TTHISLDHHSMTLTPDEVKSLLLKYL 311
Query: 180 GVDI----------------VVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGA 223
++ + D ++T + +K + D + I + L
Sbjct: 312 DCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD---NWKHVNCDKLTT-IIESSLNV-- 365
Query: 224 GLFYTSAKEDKNCDLLYKYLAHRLYGFPFRTSALIVEKDAVLIPSGWDNMKKIGILYENM 283
L E + + L+ + IP+ + +++ ++
Sbjct: 366 -L---EPAEYRKM---FDRLS-------------VFPPS-AHIPT-----ILLSLIWFDV 399
Query: 284 QSIKPDDYYTDVITKPIVRK 303
+ +V K
Sbjct: 400 IKSDVMVVVNKLHKYSLVEK 419
Score = 35.2 bits (80), Expect = 0.040
Identities = 30/156 (19%), Positives = 50/156 (32%), Gaps = 34/156 (21%)
Query: 197 EKDFYYKEEHFDFVQQYIRKF-C---LKFGAGLFYTSAKEDKNCDLLYKY-----LAHRL 247
E + YK+ F ++ F C + S +E D + RL
Sbjct: 13 EHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSIL--SKEE---IDHIIMSKDAVSGTLRL 67
Query: 248 YGFPFRTSALIVEK--DAVLIPS-GWDNMKKIGILYENMQSIKPDDYYTDVITK------ 298
+ +V+K + VL + + M I E Q Y + +
Sbjct: 68 FWTLLSKQEEMVQKFVEEVLRINYKF-LMSPIK--TEQRQPSMMTRMYIEQRDRLYNDNQ 124
Query: 299 PIVRKPISREQDTLVEDEQSFLARQLALLQQNPAAN 334
+ +SR Q +L + ALL+ PA N
Sbjct: 125 VFAKYNVSRLQP--------YLKLRQALLELRPAKN 152
>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 = 3e-07
Identities = 69/366 (18%), Positives = 111/366 (30%), Gaps = 132/366 (36%)
Query: 79 AHSNLLR-FALNQETLPHTMVMLVVSMTTPWNIIDELHNWASVLQDH-IDSL-----NIG 131
A+S R L+ +L H + LV P AS LQ+ L
Sbjct: 3 AYS--TRPLTLSHGSLEHVL--LV-----PTA----SFFIASQLQEQFNKILPEPTEGFA 49
Query: 132 AHDYQAGRCCKLLTFARLRAHLIELLSFYLFYSSVSVIPGEGILERNLGVDIVVVVTKTD 191
A D EL+ +L Y S V P +
Sbjct: 50 ADDEP--------------TTPAELVGKFLGYVSSLVEPSK----------------VGQ 79
Query: 192 YMSTLEKDFYYKEEHFDFVQQYIRKFCLK------FGAGLFYTS-AKEDKNCDLL--YKY 242
+ L F+ + L+ A L + K +L+ Y
Sbjct: 80 FDQVLNLCL----TEFE------NCY-LEGNDIHALAAKLLQENDTTLVKTKELIKNY-I 127
Query: 243 LAHRLYGFPFR---TSAL---IVEKDAVLIP--SG-------WDNMKKIGILYENMQSIK 287
A + PF SAL + E +A L+ G ++ ++ LY+
Sbjct: 128 TARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRD---LYQ------ 178
Query: 288 PDDYYTDVITKPIVRKPISREQDTLVE------DEQSFLARQLALLQ--QNPAANPTTRQ 339
Y +V I +TL E D + + L +L+ +NP+ P +
Sbjct: 179 --TY------HVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPD--K 228
Query: 340 DN------SLPQIRTPVGV-QKTGDRRLSNSPAMQGGGANSPKKMIDPTKVGATTPGGEG 392
D S P I GV Q L++ +P ++ K GAT +G
Sbjct: 229 DYLLSIPISCPLI----GVIQ------LAHYVVTAKLLGFTPGELRSYLK-GATGH-SQG 276
Query: 393 VLASFF 398
++ +
Sbjct: 277 LVTAVA 282
Score = 35.0 bits (80), Expect = 0.055
Identities = 28/170 (16%), Positives = 49/170 (28%), Gaps = 40/170 (23%)
Query: 7 DVF-----VLRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDE 61
DV+ + G I +I + +N T EKG + Y + E
Sbjct: 1644 DVWNRADNHFKDTYGFSILDI--VINNPVNLTIHF-------GGEKGKRIRENYSAMIFE 1694
Query: 62 YREDHTRLGVWILDGEPAHSNLLRFALNQETLPHTMV----MLVVSMTTPWNIIDELHNW 117
D I HS F + L T + ++ ++L +
Sbjct: 1695 TIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKA----AFEDLKSK 1750
Query: 118 ASVLQD-----HIDSLNIGAHDYQAGRCC-KLLTFA------RLRAHLIE 155
+ D H SL G +Y A +++ R ++
Sbjct: 1751 GLIPADATFAGH--SL--G--EYAALASLADVMSIESLVEVVFYRGMTMQ 1794
Score = 34.6 bits (79), Expect = 0.066
Identities = 29/148 (19%), Positives = 53/148 (35%), Gaps = 45/148 (30%)
Query: 76 GEPAHSNLLRFA---LNQETLPHTMVMLVVSMTTP-WNIIDELHNWASVLQDHIDSLNIG 131
P HS+LL A +N++ + + + + P ++ D S L+ S+
Sbjct: 424 ASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFD-----GSDLRVLSGSI--- 475
Query: 132 AHDYQAGRCCKLLTFARLRAHLIELLSFYLFYSSVSVI---PGE----GIL-ERNL---G 180
+ R + RL F + ++ PG G+L RN G
Sbjct: 476 -----SERIVDCII--RLPVKWETTTQF----KATHILDFGPGGASGLGVLTHRNKDGTG 524
Query: 181 VDIVVVVTKTDYMSTLEK----DFYYKE 204
V ++V TL+ D+ +K+
Sbjct: 525 VRVIVA-------GTLDINPDDDYGFKQ 545
Score = 31.9 bits (72), Expect = 0.42
Identities = 54/330 (16%), Positives = 100/330 (30%), Gaps = 139/330 (42%)
Query: 24 LISDNSSGKTT--LIAKLQGIDSPEKGL--ALEYAYINVSDE----YREDHTRLGV--WI 73
+++ G T L + L+G +GL A I +D + + V +I
Sbjct: 250 VVTAKLLGFTPGELRSYLKGATGHSQGLVTA---VAIAETDSWESFFVSVRKAITVLFFI 306
Query: 74 LDGEPAHSNLLRFALNQETLPHTMV------------------MLVVSMTTPWNIIDELH 115
G +R E P+T + ML +S T
Sbjct: 307 --G-------VRC---YEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQ-------- 346
Query: 116 NWASVLQDHIDSLNIGAHDYQAGRCCKLLTFARL--RAHLIELLSFYLFYSSVSVIPGEG 173
+QD+++ N + L + +S++
Sbjct: 347 ---EQVQDYVNKTN-----------------SHLPAGKQV-----------EISLV---- 371
Query: 174 ILERNLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAK-- 231
N G +VV + +L + +RK K +GL +
Sbjct: 372 ----N-GAKNLVV---SGPPQSLYG-----------LNLTLRK--AKAPSGLDQSRIPFS 410
Query: 232 EDKNCDLLYKYLAHRLYGF-----PFRTSAL-----IVEKDAVLIPSGWDNMKKIGI-LY 280
E K ++R F PF + L ++ KD V ++ K I I +Y
Sbjct: 411 ERK------LKFSNR---FLPVASPFHSHLLVPASDLINKDLVKNNVSFNA-KDIQIPVY 460
Query: 281 -----ENMQSIKPDDYYTDVITKPIVRKPI 305
+++ + ++ I I+R P+
Sbjct: 461 DTFDGSDLRVLSGSI--SERIVDCIIRLPV 488
>3dpu_A RAB family protein; roccor, G-domain, COR, GTP-binding,
nucleotide-binding, SIGN protein; 2.90A {Chlorobaculum
tepidum}
Length = 535
Score = 34.2 bits (78), Expect = 0.074
Identities = 11/75 (14%), Positives = 23/75 (30%), Gaps = 11/75 (14%)
Query: 174 ILERNLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKED 233
I + ++VV+ K D + ++ Q+ I + S K
Sbjct: 144 IEKYGGKSPVIVVMNKID-----------ENPSYNIEQKKINERFPAIENRFHRISCKNG 192
Query: 234 KNCDLLYKYLAHRLY 248
+ + K L +
Sbjct: 193 DGVESIAKSLKSAVL 207
>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA,
30S ribosome ASSE GTP-binding, nucleotide-binding; HET:
GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*
Length = 308
Score = 32.8 bits (76), Expect = 0.15
Identities = 15/93 (16%), Positives = 30/93 (32%), Gaps = 15/93 (16%)
Query: 161 LFYSSVSVIPGEG---ILERNL---GVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYI 214
LF + I + + ++VV+ K D + + + +
Sbjct: 97 LFMIDATEGWRPRDEEIYQNFIKPLNKPVIVVINKIDKIGP-------AKNVLPLIDEIH 149
Query: 215 RKFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRL 247
+K + + SA + N D L K + L
Sbjct: 150 KKHP-EL-TEIVPISALKGANLDELVKTILKYL 180
>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation,
GTP-binding domain, maturation enzyme, oxidoreductase;
2.99A {Thermotoga neapolitana}
Length = 423
Score = 33.1 bits (76), Expect = 0.15
Identities = 22/111 (19%), Positives = 43/111 (38%), Gaps = 18/111 (16%)
Query: 161 LFYSSVSVIPGEG-ILE--RNLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKF 217
+ + + P E ++ + + + VVVV K D + + K E + +
Sbjct: 118 ILVTDSAPTPYEDDVVNLFKEMEIPFVVVVNKID----VLGE---KAEELKGLYE----- 165
Query: 218 CLKFGAGLFYTSAKEDKNCDLLYKYLAHRLYGFPFRT--SALIVEKDAVLI 266
++ A + SA + K D + K ++ L G LI D V++
Sbjct: 166 -SRYEAKVLLVSALQKKGFDDIGKTISEILPGDEEIPYLGDLIDGGDLVIL 215
>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur
cluster, adenosine diphosphate, nucleotide-binding; HET:
ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*
Length = 607
Score = 31.5 bits (72), Expect = 0.57
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 7 DVFVLRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
+V G VIG ++ N GKTT + L G++ P +G
Sbjct: 373 EVEPGEIRKGEVIG---IVGPNGIGKTTFVKMLAGVEEPTEG 411
>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis,
hydrolyase/translation complex; HET: ADP; 1.90A
{Pyrococcus furiosus}
Length = 538
Score = 31.1 bits (71), Expect = 0.63
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
G VIG ++ N GKTT + L G++ P +G
Sbjct: 307 GEIKKGEVIG---IVGPNGIGKTTFVKMLAGVEEPTEG 341
>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase,
translation; HET: ADP; 2.05A {Sulfolobus solfataricus}
Length = 538
Score = 31.1 bits (71), Expect = 0.78
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
+G +IG ++ N GKTT L G + ++G
Sbjct: 289 GEAKEGEIIG---ILGPNGIGKTTFARILVGEITADEG 323
>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt
transport, TM02 hydrolase, inner membrane, membrane,
nucleotide-binding; 2.30A {Thermotoga maritima}
Length = 266
Score = 30.3 bits (69), Expect = 0.91
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
L N+G + + + SGK+TL+ + G+ P G
Sbjct: 28 LVINEGECLL---VAGNTGSGKSTLLQIVAGLIEPTSG 62
>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like,
hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8
d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X
Length = 301
Score = 30.5 bits (70), Expect = 1.0
Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 12/78 (15%)
Query: 172 EGILER--NLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTS 229
E +L + +++ V K D + K + +Q + F + S
Sbjct: 106 EMVLNKLREGKAPVILAVNKVDNVQE-------KADLLPHLQFLASQM--NF-LDIVPIS 155
Query: 230 AKEDKNCDLLYKYLAHRL 247
A+ N D + + L
Sbjct: 156 AETGLNVDTIAAIVRKHL 173
>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET:
ATP; NMR {Saccharomyces cerevisiae}
Length = 608
Score = 30.8 bits (70), Expect = 1.0
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 5 YYDVFVLR-----FNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
FVL F+D ++ ++ +N +GKTTLI L G P++G
Sbjct: 362 TQGDFVLNVEEGEFSDSEILV---MMGENGTGKTTLIKLLAGALKPDEG 407
>3ugj_A Phosphoribosylformylglycinamidine synthase; amidotransferase,
glutaminase, thioester intermediate, ligas; HET: ADP;
1.78A {Salmonella enterica subsp} PDB: 1t3t_A* 3ujn_A*
3umm_A*
Length = 1303
Score = 30.0 bits (67), Expect = 1.6
Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 11/86 (12%)
Query: 35 LIAKLQGIDSPEKGLALEYAY-INVSDEY-REDHTRLGVWILDGEPAHSNLLRFALNQET 92
L+A+ Q + + EY + +++ + +L +L PA + +
Sbjct: 27 LLARFQAANLQVHNIYAEYVHFADLNAPLNDSEQAQL-TRLLQYGPA------LSSHTPA 79
Query: 93 LPHTMVMLVVSMTTPW--NIIDELHN 116
+V +PW D HN
Sbjct: 80 GKLLLVTPRPGTISPWSSKATDIAHN 105
>4djt_A GTP-binding nuclear protein GSP1; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid, RAN family; HET: GDP; 1.80A {Encephalitozoon
cuniculi}
Length = 218
Score = 29.6 bits (67), Expect = 1.6
Identities = 22/122 (18%), Positives = 39/122 (31%), Gaps = 19/122 (15%)
Query: 175 LERNLGVDIVVVVT--KTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFY--TSA 230
+ +G + +VV K D + + K+ + ++ Y SA
Sbjct: 110 FQAVVGNEAPIVVCANKIDIKNRQKIS---KKLVMEVLKGK----------NYEYFEISA 156
Query: 231 KEDKNCDLLYKYLAHRLYGFP--FRTSALIVEKDAVLIPSGWDNMKKIGILYENMQSIKP 288
K N L + +LA G P S + +E V K E + P
Sbjct: 157 KTAHNFGLPFLHLARIFTGRPDLIFVSNVNLEPTEVNYDYHSPEESKYIDYMEQASKMAP 216
Query: 289 DD 290
++
Sbjct: 217 EE 218
>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome
condensation, condensin, SMC, N subunit, ABC-type
ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus
ducreyi} PDB: 3euk_A*
Length = 483
Score = 29.9 bits (66), Expect = 1.7
Identities = 17/145 (11%), Positives = 43/145 (29%), Gaps = 5/145 (3%)
Query: 23 LLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDGEPAHSN 82
L N +GK+T +A P+ L + N ++ +R +
Sbjct: 33 TLSGGNGAGKSTTMAGFVTALIPDLTLL---NFRNTTEAGSTSSSRDKGLYGKLKAGVCY 89
Query: 83 LLRFALNQETLPHTMVMLVVSMTTPWNIIDELHNWASVLQDHIDSLNIGAHDYQAGRCCK 142
+ +N + + + +D + +++ +
Sbjct: 90 AVLETVNSRAQRIITGVRLQQIAGRDKKVDIRPFSLQNVPMTDSVISLFTEQVANKA--R 147
Query: 143 LLTFARLRAHLIELLSFYLFYSSVS 167
+L+ L+ E + Y S++
Sbjct: 148 VLSLNDLKEKFEETAVTFKPYHSIT 172
>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding,
hydrolase, nucleotide-binding; HET: GDP; 2.25A
{Salmonella typhimurium} PDB: 2ykr_W 4a2i_V
Length = 358
Score = 29.5 bits (67), Expect = 1.8
Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 10/69 (14%)
Query: 178 NLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCD 237
L V+ ++V+ K D L +E DFV + + + G + S+
Sbjct: 158 TLQVEPLIVLNKID----L-----LDDEGMDFVNEQMDIY-RNIGYRVLMVSSHTQDGLK 207
Query: 238 LLYKYLAHR 246
L + L R
Sbjct: 208 PLEEALTGR 216
>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics,
cell membrane, cobalt transport, hydrolase, ION
transport; 2.30A {Clostridium perfringens atcc 13124}
Length = 275
Score = 29.4 bits (67), Expect = 1.9
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
+ G V ++ N GK+TL GI P G
Sbjct: 29 MNIKRGEVTA---ILGGNGVGKSTLFQNFNGILKPSSG 63
>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET:
G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*
Length = 178
Score = 29.0 bits (66), Expect = 1.9
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 215 RKFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRLYG 249
+FC + G + SAK + L ++ +A + G
Sbjct: 139 LRFCQENGFSSHFVSAKTGDSVFLCFQKVAAEILG 173
>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative
iron chelatin ABC transporter, nucleotide binding
domain; 2.40A {Haemophilus influenzae}
Length = 253
Score = 29.5 bits (67), Expect = 2.0
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG---LALEYAYI 56
N G ++ ++ N GK+TL+ L GI P +G + ++
Sbjct: 26 FDLNKGDILA---VLGQNGCGKSTLLDLLLGIHRPIQGKIEVYQSIGFV 71
>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer,
immunology, signaling protein; HET: GDP; 1.95A {Mus
musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A*
1tq2_A*
Length = 413
Score = 29.3 bits (65), Expect = 2.2
Identities = 25/136 (18%), Positives = 39/136 (28%), Gaps = 12/136 (8%)
Query: 124 HIDSLNIGAHDYQAGRCCKLLTFARLRAHLIELLSFYLFYSSVSVIPGEGILERNL---G 180
H + N+ D L F++ S+ + + + +
Sbjct: 116 HPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISMMK 175
Query: 181 VDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGL-------FYTSAKED 233
+ V TK D T E D + + V Q IR C+ F S K
Sbjct: 176 KEFYFVRTKVDSDITNEADGEPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNV 235
Query: 234 KNCDL--LYKYLAHRL 247
+ D L L L
Sbjct: 236 CHYDFPVLMDKLISDL 251
>3gj0_A GTP-binding nuclear protein RAN; G protein, GDP, acetylation,
cytoplasm, HOST- virus interaction, nucleotide-binding,
nucleus, phosphoprotein; HET: GDP; 1.48A {Homo sapiens}
PDB: 3gj3_A* 3gj5_A* 3gj4_A* 3gj6_A* 3gj7_A* 3gj8_A*
1i2m_A 1a2k_C 1ibr_A* 1k5d_A* 1k5g_A* 1qbk_C* 3a6p_C*
3ch5_A* 1qg4_A* 3ea5_A* 1qg2_A* 1byu_A* 3ran_A* 3gjx_C*
...
Length = 221
Score = 28.8 bits (65), Expect = 2.4
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 216 KFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRLYGFP 251
F K + SAK + N + + +LA +L G P
Sbjct: 142 VFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDP 177
>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A
{Sulfolobus acidocaldarius} SCOP: c.37.1.1
Length = 194
Score = 28.5 bits (63), Expect = 3.5
Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 3/83 (3%)
Query: 30 SGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDGEPAHSNLLRFALN 89
GK+T++AK++ I + + IN D +LG E ++ +
Sbjct: 12 VGKSTVLAKVKEILDNQG---INNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKL 68
Query: 90 QETLPHTMVMLVVSMTTPWNIID 112
Q + + + ID
Sbjct: 69 QIDAAKGIAEEARAGGEGYLFID 91
>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein
biosynthesis, nucleotide-binding, phosphorylation, RNA-
binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces
cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A
Length = 986
Score = 29.2 bits (65), Expect = 3.5
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 4 PYYDVFVLRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
P + + S I +I N +GK+TLI L G P G
Sbjct: 687 PQITDINFQCSLSSRIA---VIGPNGAGKSTLINVLTGELLPTSG 728
Score = 27.7 bits (61), Expect = 8.9
Identities = 8/35 (22%), Positives = 12/35 (34%), Gaps = 3/35 (8%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSP 45
LR G + N GK+TL+ +
Sbjct: 456 LRLKRARRYG---ICGPNGCGKSTLMRAIANGQVD 487
>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking,
protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP:
c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*
Length = 170
Score = 28.2 bits (64), Expect = 3.6
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 215 RKFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRLY 248
+ GA ++TSAK++K + L+ L R+
Sbjct: 135 ESYAESVGAKHYHTSAKQNKGIEELFLDLCKRMI 168
>1xzp_A Probable tRNA modification GTPase TRME; GTP-binding, THF-binding,
hydrolase; 2.30A {Thermotoga maritima} SCOP: a.24.25.1
c.37.1.8 d.250.1.2 PDB: 1xzq_A* 1xzp_B 1xzq_B*
Length = 482
Score = 28.7 bits (65), Expect = 3.9
Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 14/86 (16%)
Query: 174 ILERNLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKED 233
ILER +VV+ K D + + ++ + L + SA +
Sbjct: 344 ILERIKNKRYLVVINKVDVVEKINEEEIKNK--------------LGTDRHMVKISALKG 389
Query: 234 KNCDLLYKYLAHRLYGFPFRTSALIV 259
+ + L + + R S ++
Sbjct: 390 EGLEKLEESIYRETQEIFERGSDSLI 415
>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis,
YPT/RAB protein, endocytosis, hydrolase,
endocytosis/exocytosis complex; HET: GDP; 1.35A
{Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*
Length = 182
Score = 27.9 bits (63), Expect = 4.0
Identities = 8/35 (22%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 215 RKFCLKFGAGLFY-TSAKEDKNCDLLYKYLAHRLY 248
++ G + TSAK N D ++ +A
Sbjct: 143 QELAKSLGDIPLFLTSAKNAINVDTAFEEIARSAL 177
>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote
initiative, RSGI, structural genomics, hydrolase; HET:
GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8
d.52.3.1
Length = 301
Score = 28.2 bits (64), Expect = 4.6
Identities = 11/65 (16%), Positives = 18/65 (27%), Gaps = 13/65 (20%)
Query: 183 IVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLYKY 242
I++V K D E+ E A SA +++ L
Sbjct: 120 ILLVGNKLDAAKYPEEAMKAYHELLPE-------------AEPRMLSALDERQVAELKAD 166
Query: 243 LAHRL 247
L +
Sbjct: 167 LLALM 171
>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA,
national P protein structural and functional analyses;
HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8
Length = 190
Score = 27.7 bits (62), Expect = 5.1
Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 7/71 (9%)
Query: 177 RNLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNC 236
R L + +V V K D ++ +E +F+ + + SAK N
Sbjct: 119 RELDIPTIVAVNKLD---KIKN----VQEVINFLAEKFEVPLSEIDKVFIPISAKFGDNI 171
Query: 237 DLLYKYLAHRL 247
+ L + +
Sbjct: 172 ERLKNRIFEVI 182
>2efe_A Similarity to vacuolar protein sorting-associated VPS9; GEF,
GTPase, VPS9, nucleotide, transport protein; HET: GNH;
2.08A {Arabidopsis thaliana} PDB: 2efd_A 2efc_A* 2efh_A*
Length = 267
Score = 28.1 bits (62), Expect = 5.1
Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 3/79 (3%)
Query: 191 DYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLY---KYLAHRL 247
++ + + E+ VQ++ K F A ++ E++ KY+ +L
Sbjct: 33 SFIVSFSNNAPDPEKDCAMVQEFFSKMEAAFRAHPLWSGCSEEELDSAGDGLEKYVMTKL 92
Query: 248 YGFPFRTSALIVEKDAVLI 266
+ F ++ V D L
Sbjct: 93 FTRVFASNTEEVIADEKLF 111
>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein
transport, biosynthetic protein; HET: GNP; 3.00A
{Bacillus subtilis} PDB: 2px3_A* 3syn_A*
Length = 296
Score = 28.1 bits (63), Expect = 5.3
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 22 ILLISDNSSGKTTLIAKL 39
I+L +GKTT +AKL
Sbjct: 108 IVLFGSTGAGKTTTLAKL 125
>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR
complex, HMR, HML, TELO AAA+ domain, structural,
nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}
Length = 318
Score = 28.0 bits (61), Expect = 5.7
Identities = 12/104 (11%), Positives = 34/104 (32%), Gaps = 10/104 (9%)
Query: 9 FVLRFNDGSVIGNILLISDNSSGKTTL----IAKLQGIDSPEKGLALEYAYIN------V 58
+ S + + + S K L + +L + ++ +Y +I+ +
Sbjct: 35 PIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGM 94
Query: 59 SDEYREDHTRLGVWILDGEPAHSNLLRFALNQETLPHTMVMLVV 102
Y + + L G+ + L + N ++++
Sbjct: 95 DALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILI 138
>1af7_A Chemotaxis receptor methyltransferase CHER; chemotaxis receptor
methylation; HET: SAH; 2.00A {Salmonella typhimurium}
SCOP: a.58.1.1 c.66.1.8 PDB: 1bc5_A*
Length = 274
Score = 27.9 bits (63), Expect = 5.9
Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 9/55 (16%)
Query: 193 MSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRL 247
+ + + + HF + Q I + G+ K D++Y L RL
Sbjct: 3 LLQMTQRLALSDAHFRRICQLIYQRA-----GIVLADHKR----DMVYNRLVRRL 48
>2ot3_A RAB5 GDP/GTP exchange factor; rabex-5, VPS9 domain, vesicular
traffic, protein transport; 2.10A {Homo sapiens} SCOP:
a.222.1.1 PDB: 1txu_A
Length = 274
Score = 27.8 bits (61), Expect = 7.1
Identities = 15/93 (16%), Positives = 34/93 (36%), Gaps = 5/93 (5%)
Query: 204 EEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRLYGFPF-RTSALIVEKD 262
EE + Q + + + +K D + KY+ RLY + F + +KD
Sbjct: 53 EEQSECAQDFYHNVAERMQTRGKVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKD 112
Query: 263 AVLIPSGWDNMKKIGILYENMQSIKPDDYYTDV 295
+ ++ + + M + ++ +V
Sbjct: 113 LAI----QKRIRALRWVTPQMLCVPVNEDIPEV 141
>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking,
protein transport; HET: GDP; 1.90A {Mus musculus} SCOP:
c.37.1.8 PDB: 1z22_A*
Length = 168
Score = 27.1 bits (61), Expect = 7.3
Identities = 10/34 (29%), Positives = 15/34 (44%)
Query: 215 RKFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRLY 248
+ + TS KED N ++KYLA +
Sbjct: 133 EGLAKRLKLRFYRTSVKEDLNVSEVFKYLAEKHL 166
>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein
transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A
Length = 320
Score = 27.5 bits (62), Expect = 7.4
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 22 ILLISDNSSGKTTLIAKL 39
+L+ N +GKTT +AK+
Sbjct: 108 FMLVGVNGTGKTTSLAKM 125
>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase,
protein-targeting, transport protein; HET: GDP; 1.97A
{Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*
Length = 328
Score = 27.6 bits (62), Expect = 8.1
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 22 ILLISDNSSGKTTLIAKL 39
I+ + N SGKTT IAKL
Sbjct: 132 IMFVGFNGSGKTTTIAKL 149
>1g6h_A High-affinity branched-chain amino acid transport ATP-binding
protein; beta-core domain; HET: ADP; 1.60A
{Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB:
1gaj_A 1g9x_A*
Length = 257
Score = 27.5 bits (62), Expect = 8.2
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 7 DVFVLRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
D + N G V +I N SGK+TLI + G ++G
Sbjct: 24 DGVSISVNKGDVTL---IIGPNGSGKSTLINVITGFLKADEG 62
>2ged_A SR-beta, signal recognition particle receptor beta subunit;
protein transport, G protein, proline isomerization,
circular permutation; 2.20A {Saccharomyces cerevisiae}
Length = 193
Score = 27.0 bits (60), Expect = 8.4
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 21 NILLISDNSSGKTTLIAKLQG 41
+I++ +SGKT+L+ L
Sbjct: 50 SIIIAGPQNSGKTSLLTLLTT 70
>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292;
mixed alpha-beta protein, rossman fold, signaling
protein, transferase; 1.40A {Aquifex aeolicus} SCOP:
c.37.1.11
Length = 178
Score = 26.9 bits (59), Expect = 9.3
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 21 NILLISDNSSGKTTLIAKL 39
I++ + GKTTL+ K+
Sbjct: 2 KIIITGEPGVGKTTLVKKI 20
>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting,
simibi class GTPase, GTP-BIND membrane,
nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A
2xxa_B* 1fts_A
Length = 503
Score = 27.5 bits (61), Expect = 9.6
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 22 ILLISDNSSGKTTLIAKL 39
IL++ N GKTT I KL
Sbjct: 296 ILMVGVNGVGKTTTIGKL 313
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 0.136 0.401
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,376,352
Number of extensions: 390626
Number of successful extensions: 994
Number of sequences better than 10.0: 1
Number of HSP's gapped: 983
Number of HSP's successfully gapped: 59
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: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.1 bits)