RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy18090
(421 letters)
>4acj_A WU\:FB25H12 protein,; immune system; 0.97A {Danio rerio}
Length = 167
Score = 110 bits (276), Expect = 4e-29
Identities = 54/173 (31%), Positives = 79/173 (45%), Gaps = 10/173 (5%)
Query: 204 SFTMSILDYSHIMFLNLNLMPEFQ-KQWRLLFSSQFQGESFTRLM-ACAINQGPLLVLVK 261
+ +L+ I L +L P W L FS+ G S L A P+L+++K
Sbjct: 2 NEPSDLLEAEQIEKLAKHLPPRTIGYPWNLAFSTSKHGMSIKTLYRAMQDQDSPMLLVIK 61
Query: 262 DDKANIFGAYASTNLTLCPKFYGDQNSFLFTLKPDMKVFNSSGFNENFIYLNSNQQTLPN 321
D IFGA AS + FYG +FLFT P+ + + +G N FI + +
Sbjct: 62 DSDGQIFGALASEPFKVSEGFYGTGETFLFTFYPEFEAYKWTGDNLFFIKGD------MD 115
Query: 322 GLGFGGQFEYWGLWIDSEYGQGECNKTCSTFKDYQMLSHDKHFKIMHIELWGV 374
L FGG +GLW+D + G + +C TF MLS + F + IE+W
Sbjct: 116 SLAFGGGSGEFGLWLDGDLYHGRNH-SCKTF-GNPMLSMKEDFFVQDIEIWSF 166
>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 = 53.7 bits (128), Expect = 7e-08
Identities = 49/361 (13%), Positives = 103/361 (28%), Gaps = 109/361 (30%)
Query: 17 KNLSRKIKPEDVKKIKSLTNGKDVLTK---VDVFELW-SMEIKD-------------SLI 59
K ++ + I SL + LT + + +D S+I
Sbjct: 275 KQVTDFLSAATTTHI-SLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSII 333
Query: 60 -----------NFYLKYYFPDKTEKIDLS-------TFISLYYEL----DGSNIDRKVEI 97
+ + T I+ S + ++ L ++I +
Sbjct: 334 AESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLS 393
Query: 98 LLCFIGSYGDLINYVQALLNSCLFIYQSRDDKELWSSLNIDSDKGSLIVYANYLCM-GDC 156
L+ F D++ V L L + + ++ + + YL +
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYSL--------------VEKQPKESTISIPSIYLELKVKL 439
Query: 157 NNEIT--------FDSLQKW----LSTTHEIAYLHKYVLSHMFGFNTSQRIIPTPVYNPS 204
NE ++ + + L + Y + ++ H+ +R+
Sbjct: 440 ENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERM-------TL 492
Query: 205 FTMSILDYSHIMFLNLNLMPEFQKQWRLLFSSQFQGESFTRLMACAIN-QGPLLVLVKDD 263
F M LD+ FL QK R + A N G +L ++
Sbjct: 493 FRMVFLDFR---FLE-------QK---------------IRHDSTAWNASGSILNTLQQL 527
Query: 264 KANIFGAYASTNLTLCPKFYGDQNSFLFTLK------PDMKVFNSSGFNEN-FIYLNSNQ 316
K + Y N + FL ++ + + E+ I+ +++
Sbjct: 528 K--FYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHK 585
Query: 317 Q 317
Q
Sbjct: 586 Q 586
Score = 41.4 bits (96), Expect = 5e-04
Identities = 61/427 (14%), Positives = 116/427 (27%), Gaps = 148/427 (34%)
Query: 3 NEHSNKKQGSGSL--KKNLSRKIKPEDVKKIKS-LTN---------------GKDVLTKV 44
E ++ + K N+SR + K++ L GK +
Sbjct: 113 IEQRDRLYNDNQVFAKYNVSR---LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL- 168
Query: 45 DVFELWSMEIKDSLINFYLKYYFPDKTEKIDLSTFISLYYELDGSNIDRKVEILLCFIGS 104
D +++ ++ K +++ L+ N +
Sbjct: 169 -----------DVCLSYKVQCKMDFK-----------IFW-LNLKNCNSP---------- 195
Query: 105 YGDLINYVQALLNSCLFIYQSRDDKELWSSLNIDSDKGSLI------VYANYLCMGD--C 156
++ +Q LL + SR D L I S + L Y N L +
Sbjct: 196 -ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254
Query: 157 NNEI--TFDSLQ-KWLSTTHEIAYLHKYVLSHMFGFNTSQRII--PTPVYNPSFTMSILD 211
N + F+ L K L TT K V + T+ + + P S+L
Sbjct: 255 NAKAWNAFN-LSCKILLTTRF-----KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL- 307
Query: 212 YSHIMFLNLNL--MPEFQKQWRLLFSSQFQGESFTRLMACAINQGPLLV-----LVKDDK 264
+ +L+ +P E N P + ++D
Sbjct: 308 ---LKYLDCRPQDLPR---------------E------VLTTN--PRRLSIIAESIRDGL 341
Query: 265 ANIFGAYASTNLTLCPKFYGDQNSFLFTLKPDM--KVFNSSG-FNENFIYLNSNQQTLPN 321
+ + N C K S L L+P K+F+ F + + L
Sbjct: 342 -ATWDNWKHVN---CDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS---AHIPTILLSL 394
Query: 322 GLGFGGQFEYWGLWIDSEYGQ-----GECNKTCSTFKDYQMLS---HDKHFKI------- 366
+W D + +K K + + + ++
Sbjct: 395 ------------IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENE 442
Query: 367 --MHIEL 371
+H +
Sbjct: 443 YALHRSI 449
Score = 32.9 bits (74), Expect = 0.21
Identities = 38/282 (13%), Positives = 67/282 (23%), Gaps = 90/282 (31%)
Query: 85 ELDGSNIDRKVEILLCFIGSY-GDL-INYVQALLNSCL------FIYQSRDDKE-----L 131
E D IL F ++ + VQ + S L I S+D
Sbjct: 13 EHQYQYKD----ILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLF 68
Query: 132 WSSLNIDSDKGSLIVYANYLCMGDCNNEITF--DSLQK---WLSTTHEIAYLHK------ 180
W+ L K +V F + L+ +L + +
Sbjct: 69 WTLL----SKQEEMVQK-------------FVEEVLRINYKFLMSPIKTEQRQPSMMTRM 111
Query: 181 YVLSHMFGFNTSQRIIPTPVYNPSFTMSI----LDYSHIMFLNLNLMPEFQKQWRLLFSS 236
Y+ +N +Q V + + L+ + ++ + K W +
Sbjct: 112 YIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW--VALD 169
Query: 237 QFQGESFTRLMACAINQGPLLVLVKDDKANIF----GAYASTNLTLCPKFYGDQNSFLFT 292
M IF S L L+
Sbjct: 170 VCLSYKVQCKMDF----------------KIFWLNLKNCNSPETVLEM-----LQKLLYQ 208
Query: 293 LKPDMKVFNSSGFNENFIYLNSN-----------QQTLPNGL 323
+ P+ + N I L + + N L
Sbjct: 209 IDPNWTSRSDHSSN---IKLRIHSIQAELRRLLKSKPYENCL 247
>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 = 45.0 bits (106), Expect = 5e-05
Identities = 53/328 (16%), Positives = 103/328 (31%), Gaps = 86/328 (26%)
Query: 31 IKSLTNGKDVLTKVD----VFELWSMEIKDSLINFYLKY--YFPDKTE--------KIDL 76
K L + D EL +L Y + ++ + L
Sbjct: 38 NKILPEPTEGFAADDEPTTPAELVGK---------FLGYVSSLVEPSKVGQFDQVLNLCL 88
Query: 77 STFISLYYELDGSNIDRKVEILLCF----IGSYGDLI-NYVQALLNSCLFIYQSRDDKEL 131
+ F + Y L+G++I LL + +LI NY+ A + + + DK+
Sbjct: 89 TEFENCY--LEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMA-----KRPFDKKS 141
Query: 132 WSSLNIDSDKGSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIAYLHKYVLSHMFGFNT 191
S+L +G+ + A + G N + F+ L+ L T+ + + T
Sbjct: 142 NSALFRAVGEGNAQLVA--IFGGQGNTDDYFEELRD-LYQTYH-VLVGDLIKFS---AET 194
Query: 192 SQRIIPTPVYNPSFTMSILDYSHIMFLNLNLMPEFQKQWRLLFSSQFQGESFTRLMACAI 251
+I T + ++ LN++ +W L S + + L++ I
Sbjct: 195 LSELIRTTLDAEKV------FTQ----GLNIL-----EW-LENPSNTPDKDY--LLSIPI 236
Query: 252 NQGPLLVLVKDDKANIFGAYAST--NLTLCPKFYGDQNSFLFTLKPDM---KVFNSSG-- 304
+ PL+ +++ Y T L P + +
Sbjct: 237 S-CPLIGVIQ------LAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSW 289
Query: 305 --FNEN---------FIYLNSNQQTLPN 321
F + FI + + PN
Sbjct: 290 ESFFVSVRKAITVLFFIGVRC-YEAYPN 316
Score = 28.1 bits (62), Expect = 7.6
Identities = 33/195 (16%), Positives = 62/195 (31%), Gaps = 64/195 (32%)
Query: 169 LSTTH---EIAYLHKYVLSHMFGFNTSQ------RIIPTPVYN------PSFTMSILDY- 212
L+ +H E L + F SQ +I+P P P+ + +
Sbjct: 9 LTLSHGSLEHVLL----VPTASFFIASQLQEQFNKILPEPTEGFAADDEPT---TPAELV 61
Query: 213 -SHIMFLNLNLMPEFQKQW-RLL------FSSQF-QGE---SFTRLMACAINQGPLLVLV 260
+ +++ + P Q+ ++L F + + +G + A + Q LV
Sbjct: 62 GKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHAL----AAKLLQENDTTLV 117
Query: 261 KDDKANIFGAYASTNLTLCPKFYGDQNSFLFTLKPDMKVFNSSGFNENFIYLNSNQQTLP 320
K + Y + + F NS LF + G + +
Sbjct: 118 K--TKELIKNYITARIMAKRPFDKKSNSALF---------RAVGEGNAQLV------AI- 159
Query: 321 NGLGFGGQ---FEYW 332
FGGQ +Y+
Sbjct: 160 ----FGGQGNTDDYF 170
>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport;
HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB:
1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*
Length = 207
Score = 28.8 bits (65), Expect = 2.3
Identities = 6/29 (20%), Positives = 10/29 (34%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
++V+ D TF +L W
Sbjct: 83 CCVLVF-------DVTAPNTFKTLDSWRD 104
>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural
genomics, SGC, structural genomics consortium, signaling
protein; HET: GDP; 2.15A {Homo sapiens}
Length = 199
Score = 28.8 bits (65), Expect = 2.4
Identities = 8/35 (22%), Positives = 17/35 (48%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G L++Y D E +F ++++W+ + A
Sbjct: 103 GVLLLY-------DVTCEKSFLNIREWVDMIEDAA 130
>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 = 28.7 bits (65), Expect = 2.7
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G L+VY D N +F++L+ W + +++
Sbjct: 82 GVLLVY-------DITNYQSFENLEDWYTVVKKVS 109
>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural
genomics, structural genomics consortium, SGC, unknown
function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8
Length = 180
Score = 28.3 bits (64), Expect = 3.3
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
L++Y D N+ +FD++Q WL+ HE A
Sbjct: 86 ALLLLY-------DVTNKASFDNIQAWLTEIHEYA 113
>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein,
endocytosis/exocytosis complex; HET: GDP; 1.80A
{Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A*
2ocy_C 2eqb_A
Length = 170
Score = 28.3 bits (64), Expect = 3.3
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G ++VY D +E TF ++++W T +E A
Sbjct: 78 GIILVY-------DITDERTFTNIKQWFKTVNEHA 105
>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular
trafficking, protein transport; HET: GDP; 2.15A {Homo
sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*
Length = 179
Score = 28.3 bits (64), Expect = 3.4
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G+L+VY D T++ L WL+ +
Sbjct: 90 GALMVY-------DITRRSTYNHLSSWLTDARNLT 117
>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 = 28.3 bits (64), Expect = 3.9
Identities = 6/29 (20%), Positives = 13/29 (44%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
++VY D N +F++++ W
Sbjct: 84 CCVLVY-------DVTNASSFENIKSWRD 105
>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT
complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C
Length = 208
Score = 28.4 bits (64), Expect = 3.9
Identities = 5/29 (17%), Positives = 14/29 (48%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
+++V+ D ++ +F+S + W
Sbjct: 99 YAILVF-------DVSSMESFESCKAWFE 120
>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular
trafficking, protein transport; HET: GNP; 1.81A {Mus
musculus} SCOP: c.37.1.8 PDB: 2g77_B*
Length = 189
Score = 27.9 bits (63), Expect = 4.1
Identities = 8/29 (27%), Positives = 11/29 (37%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
+ VY D N +F SL W+
Sbjct: 96 AVVFVY-------DMTNMASFHSLPAWIE 117
>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural
genomics, structural genomics consortium, SGC, protein
transport; HET: GDP; 2.30A {Homo sapiens}
Length = 193
Score = 28.0 bits (63), Expect = 4.2
Identities = 8/35 (22%), Positives = 17/35 (48%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G+L+V+ D T+ +++WL ++ A
Sbjct: 100 GALLVF-------DLTKHQTYAVVERWLKELYDHA 127
>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics,
structural genomics consortium, SGC, protein transport;
HET: GDP; 2.20A {Homo sapiens}
Length = 200
Score = 28.0 bits (63), Expect = 4.3
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G+L+VY D + T++SL WL+ +A
Sbjct: 100 GALLVY-------DITSRETYNSLAAWLTDARTLA 127
>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase,
geranylgeranylation, vesicular transport, protein
transport; HET: GDP GER; 1.48A {Saccharomyces
cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A*
3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*
Length = 206
Score = 28.0 bits (63), Expect = 4.4
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G +IVY D ++ +F+ ++ WL A
Sbjct: 83 GIIIVY-------DVTDQESFNGVKMWLQEIDRYA 110
>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular
transport, acetylation, golgi apparatus, lipoprotein,
membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}
Length = 223
Score = 28.1 bits (63), Expect = 4.4
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G+LIVY D + ++++ WLS E A
Sbjct: 88 GALIVY-------DISKSSSYENCNHWLSELRENA 115
>1euv_A ULP1 protease; SUMO hydrolase, ubiquitin-like protease 1, SMT3
hydrolase desumoylating enzyme, cysteine protease; 1.60A
{Saccharomyces cerevisiae} SCOP: d.3.1.7 PDB: 2hkp_A
2hl8_A 2hl9_A
Length = 221
Score = 28.2 bits (62), Expect = 4.5
Identities = 28/166 (16%), Positives = 56/166 (33%), Gaps = 23/166 (13%)
Query: 13 GSLKKNLSRKIKPEDVKKIKS-------LTNGKDVLTKVDVFELWSME-IKDSLINFYLK 64
GSL L+ K + V+K + + +T D L + D++I F++K
Sbjct: 1 GSLVPELNEKDDDQ-VQKALASRENTQLMNRDNIEITVRDFKTLAPRRWLNDTIIEFFMK 59
Query: 65 Y-YFPDKTEKIDLSTFISLYYELDGSNIDRKVEILLCFIGSYGDLINYVQALLNSCLFIY 123
Y S F + E + R ++ I + + +N
Sbjct: 60 YIEKSTPNTVAFNSFFYTNLSERGYQGVRRWMKRKKTQIDKL----DKIFTPIN------ 109
Query: 124 QSRDDKELWSSLNIDSDKGSLIVYANYLCMGDCNNEITFDSLQKWL 169
++ W+ ID K ++ + + + LQK++
Sbjct: 110 ---LNQSHWALGIIDLKKKTIGYVDSLSNGPNAMSFAILTDLQKYV 152
>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular
transport, endocytosis, prenylation, protein transport,
transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8
PDB: 2bmd_A* 1yu9_A* 1z0k_A*
Length = 186
Score = 27.9 bits (63), Expect = 4.5
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G+L+VY D + T+++L WL+ +A
Sbjct: 85 GALLVY-------DITSRETYNALTNWLTDARMLA 112
>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase
nucleotide free complex; 2.00A {Mus musculus} SCOP:
c.37.1.8 PDB: 3qbt_A* 3tnf_A*
Length = 183
Score = 27.9 bits (63), Expect = 4.6
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G ++VY D NE +FD+++ W+ E A
Sbjct: 83 GIMLVY-------DITNEKSFDNIRNWIRNIEEHA 110
>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport;
HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB:
1s8f_A* 1yzl_A* 2ocb_A*
Length = 177
Score = 27.9 bits (63), Expect = 4.7
Identities = 4/29 (13%), Positives = 10/29 (34%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
L+ + ++ +F +L W
Sbjct: 82 CCLLTF-------SVDDSQSFQNLSNWKK 103
>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 = 27.8 bits (63), Expect = 4.7
Identities = 3/29 (10%), Positives = 11/29 (37%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
++V+ + +F+++ W
Sbjct: 80 ACVLVF-------STTDRESFEAISSWRE 101
>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics,
structural genomics consortium, SGC, protein transport;
HET: GDP; 2.10A {Homo sapiens}
Length = 192
Score = 28.0 bits (63), Expect = 4.8
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G ++VY D + TFD L KW+ + A
Sbjct: 101 GIILVY-------DITKKETFDDLPKWMKMIDKYA 128
>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics,
structural genomics consortium, SGC, signaling protein;
HET: GDP; 2.05A {Homo sapiens}
Length = 201
Score = 28.0 bits (63), Expect = 5.1
Identities = 7/35 (20%), Positives = 14/35 (40%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G+++ Y D +F S+ W+ + A
Sbjct: 104 GAILAY-------DITKRSSFLSVPHWIEDVRKYA 131
>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein,
GDPNP, SLP2A, exophil GTP-binding, lipoprotein,
membrane, methylation; HET: GNP; 1.80A {Mus musculus}
PDB: 2iey_A* 2if0_A* 2zet_A*
Length = 195
Score = 28.0 bits (63), Expect = 5.2
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
G L+++ D NE +F +++ W+S
Sbjct: 96 GFLLLF-------DLTNEQSFLNVRNWIS 117
>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics,
structural genomics consortium, SGC, protein transport;
HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*
Length = 189
Score = 28.0 bits (63), Expect = 5.2
Identities = 8/29 (27%), Positives = 15/29 (51%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
G L++Y D N+ +F ++Q W +
Sbjct: 97 GFLLMY-------DIANQESFAAVQDWAT 118
>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle
transport, hydrolase; HET: GDP; 1.55A {Homo sapiens}
SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A*
2gzh_A* 2d7c_A* 3bfk_A*
Length = 199
Score = 27.6 bits (62), Expect = 5.3
Identities = 9/35 (25%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G+L+VY D +T++++++WL + A
Sbjct: 80 GALLVY-------DIAKHLTYENVERWLKELRDHA 107
>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics,
structural genomics consortium, SGC, signaling protein;
HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB:
2iez_A*
Length = 217
Score = 28.1 bits (63), Expect = 5.3
Identities = 6/29 (20%), Positives = 16/29 (55%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
G L+++ D ++ +F +++ W+S
Sbjct: 110 GFLLMF-------DLTSQQSFLNVRNWMS 131
>2isb_A Fumarase, FUM-1; NP_069927.1, fumarase of FUM-1, structural
genomics, PSI-2, structure initiative, joint center for
structural genomics; HET: MSE; 1.66A {Archaeoglobus
fulgidus} SCOP: c.8.9.1
Length = 192
Score = 27.8 bits (62), Expect = 5.6
Identities = 5/32 (15%), Positives = 14/32 (43%)
Query: 1 MGNEHSNKKQGSGSLKKNLSRKIKPEDVKKIK 32
MG++ + ++ L + + + K+K
Sbjct: 1 MGSDKIHHHHHHMVMEYELRTPLVKDQILKLK 32
>1oix_A RAS-related protein RAB-11A; small G protein, intracellular
trafficking, GTP-binding, lipoprotein, prenylation,
protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP:
c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*
Length = 191
Score = 27.6 bits (62), Expect = 5.8
Identities = 8/29 (27%), Positives = 17/29 (58%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
G+L+VY D +T++++++WL
Sbjct: 104 GALLVY-------DIAKHLTYENVERWLK 125
>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein
transport-protein binding compl; HET: GTP; 2.18A {Homo
sapiens}
Length = 196
Score = 27.6 bits (62), Expect = 5.9
Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G ++VY D ++ +F+++++WL A
Sbjct: 91 GIIVVY-------DVTDQESFNNVKQWLQEIDRYA 118
>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine
exchange factor; 2.10A {Homo sapiens}
Length = 181
Score = 27.5 bits (62), Expect = 6.0
Identities = 7/35 (20%), Positives = 17/35 (48%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G ++VY D + +F ++++WL ++
Sbjct: 84 GVIVVY-------DVTSAESFVNVKRWLHEINQNC 111
>3l0i_B RAS-related protein RAB-1A; GEF-GDF-RAB complex, GTP-binding,
guanine-nucleotide exchang GDI-displacement factor;
2.85A {Homo sapiens}
Length = 199
Score = 27.6 bits (62), Expect = 6.2
Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G ++VY D ++ +F+++++WL A
Sbjct: 108 GIIVVY-------DVTDQESFNNVKQWLQEIDRYA 135
>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics,
GTP-binding, nucleotide-binding, signaling protein; HET:
GDP; 1.89A {Plasmodium falciparum}
Length = 208
Score = 27.5 bits (61), Expect = 6.4
Identities = 6/29 (20%), Positives = 14/29 (48%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
+++V+ D +N T D + W++
Sbjct: 119 CAIVVF-------DISNSNTLDRAKTWVN 140
>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide,
transport protein; HET: GNH; 2.08A {Arabidopsis
thaliana} PDB: 2efd_B 2efc_B* 2efh_B*
Length = 181
Score = 27.5 bits (62), Expect = 6.4
Identities = 7/35 (20%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
++IV+ D N+ +F+ +KW+
Sbjct: 87 AAIIVF-------DVTNQASFERAKKWVQELQAQG 114
>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular
transport, cytoplasm, cytoplasmic vesicle, exocytosis,
GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae}
SCOP: c.37.1.8
Length = 213
Score = 27.7 bits (62), Expect = 6.5
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G ++VY D +E TF ++++W T +E A
Sbjct: 95 GIILVY-------DVTDERTFTNIKQWFKTVNEHA 122
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 27.8 bits (61), Expect = 6.9
Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 20 SRKIKPEDVKKIKSLTNGKDVLTKVDVFELWSMEIKDSLINFYLKYYFPDKTEK 73
+I + + + +G D L K W K +Y++++F K +
Sbjct: 180 PNEILFSENNDMDNNNDGVDELNKK--CTFWDAISKL----YYVQFFF--KQAE 225
>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB
protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus}
SCOP: c.37.1.8
Length = 203
Score = 27.6 bits (62), Expect = 7.0
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
G +++Y D NE +F+++Q W +
Sbjct: 83 GFILMY-------DITNEESFNAVQDWST 104
>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; HET: GNP; 1.32A {Homo sapiens}
SCOP: c.37.1.8
Length = 195
Score = 27.2 bits (61), Expect = 7.1
Identities = 9/35 (25%), Positives = 12/35 (34%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G ++VY D TF L WL+
Sbjct: 90 GVILVY-------DVTRRDTFVKLDNWLNELETYC 117
>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural
genomics, structural genomics consortium, SGC, protein
transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8
PDB: 1z0a_A*
Length = 191
Score = 27.2 bits (61), Expect = 7.4
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G+L+VY D TF+ L WL + +
Sbjct: 96 GALLVY-------DITRRETFNHLTSWLEDARQHS 123
>3g23_A Peptidase U61, LD-carboxypeptidase A; flavodoxin-like fold,
catalytic triad, merops S66 unassigned peptidases
family; HET: MSE; 1.89A {Novosphingobium
aromaticivorans}
Length = 274
Score = 27.6 bits (61), Expect = 7.5
Identities = 16/155 (10%), Positives = 34/155 (21%), Gaps = 20/155 (12%)
Query: 92 DRKVEILLCFIGSYG-----DLINYVQALLNSCLFIYQSRDDKELWSSLNIDSDKGSLIV 146
D E + G YG + S D L ++L
Sbjct: 66 DDAFEAVWFVRGGYGANRIAEDALARLGRAASAKQYLGYSDAGTLLAALY---AHRIGRS 122
Query: 147 YANYLCMGDCNNEI--TFDSLQKWLSTTHEIAYLHKYVLSHMFGFN-TSQRIIPTPVYNP 203
+ + E WL+ E + FN + ++ P
Sbjct: 123 VHAPMPVDIRRPEGESAVRRTLGWLAGAREGLEPTLGAGAPAVAFNLMTLAMLCGTRLLP 182
Query: 204 SFTMSILDYSHI---------MFLNLNLMPEFQKQ 229
+ ++ + + ++
Sbjct: 183 DLSGHVVMIEEVAEHHYAVDRLLFHVTSCLADAGI 217
>2fbd_A Lysozyme 1; digestive lysozime, hydrolase; HET: PEG; 1.90A {Musca
domestica} PDB: 2h5z_A* 3cb7_A
Length = 122
Score = 26.9 bits (59), Expect = 7.6
Identities = 9/52 (17%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 299 VFNSSGFNENFIYLNSNQQTLPNGLGFGGQFEYWGLWIDSEYGQGECNKTCS 350
+ S + N + ++ + G+ F YW + + EC+ +C
Sbjct: 29 AEHESSYRTNVVGPTNSNGSNDYGI-FQINNYYWCQPSNGRFSYNECHLSCD 79
>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural
genomics, structural genomics consortium, SGC, signaling
protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8
Length = 201
Score = 27.2 bits (61), Expect = 7.7
Identities = 8/35 (22%), Positives = 13/35 (37%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
++ Y D E +F L +WL + A
Sbjct: 101 ALILTY-------DITCEESFRCLPEWLREIEQYA 128
>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 = 27.1 bits (61), Expect = 7.8
Identities = 7/35 (20%), Positives = 17/35 (48%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G+++VY D +E +F ++ W+ ++
Sbjct: 81 GAILVY-------DITDEDSFQKVKNWVKELRKML 108
>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein
transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8
PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A*
1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A*
2hei_A* 1z07_A*
Length = 170
Score = 27.1 bits (61), Expect = 7.8
Identities = 8/35 (22%), Positives = 14/35 (40%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
+++VY D NE +F + W+ A
Sbjct: 81 AAIVVY-------DITNEESFARAKNWVKELQRQA 108
>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 = 27.3 bits (61), Expect = 7.8
Identities = 4/28 (14%), Positives = 13/28 (46%), Gaps = 7/28 (25%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWL 169
++I++ D + +T+ ++ W
Sbjct: 90 CAIIMF-------DVTSRVTYKNVPNWH 110
>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase,
rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus
musculus} SCOP: c.37.1.8 PDB: 1yvd_A*
Length = 170
Score = 27.1 bits (61), Expect = 7.9
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
++IVY D E TF +L+ W+
Sbjct: 81 AAIIVY-------DITKEETFSTLKNWVR 102
>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue,
structural genomics, structural genomics consortium,
SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens}
SCOP: c.37.1.8
Length = 192
Score = 27.2 bits (61), Expect = 8.6
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
++IVY D + +F +L+KW+ E
Sbjct: 98 AAVIVY-------DITKQDSFYTLKKWVKELKEHG 125
>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics
consortium, SGC, cell GTP-binding, lipoprotein,
membrane, methylation; HET: GDP; 1.90A {Homo sapiens}
Length = 191
Score = 26.8 bits (60), Expect = 9.8
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
G +++Y D NE +F+++Q W +
Sbjct: 98 GFILMY-------DITNEESFNAVQDWAT 119
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 0.137 0.415
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: 6,309,860
Number of extensions: 370544
Number of successful extensions: 743
Number of sequences better than 10.0: 1
Number of HSP's gapped: 737
Number of HSP's successfully gapped: 65
Length of query: 421
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 325
Effective length of database: 4,021,377
Effective search space: 1306947525
Effective search space used: 1306947525
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: 59 (26.5 bits)