RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1414
(551 letters)
>3ksy_A SOS-1, SON of sevenless homolog 1; RAS, RAS activator, disease
mutation, guanine-nucleotide releasing factor, signaling
protein; 3.18A {Homo sapiens} PDB: 1xd4_A 1xdv_A 1q9c_A
Length = 1049
Score = 245 bits (626), Expect = 4e-71
Identities = 120/234 (51%), Positives = 164/234 (70%), Gaps = 4/234 (1%)
Query: 51 VLQQVHPTLTAREDACLYVESLVLKILAMLCSKPSPHTTSDVEERVRRQFPTPIDKWAMH 110
V QVHPTL + +DA YVE L+L++L MLC P + SDVEERV++ FP PIDKWA+
Sbjct: 30 VQGQVHPTLESNDDALQYVEELILQLLNMLCQ-AQPRSASDVEERVQKSFPHPIDKWAIA 88
Query: 111 EAKEAIEKSKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAG 170
+A+ AIEK K++ + L LPVEKIH LL K+VL YK++ VS+YI AVLEYISADILKL G
Sbjct: 89 DAQSAIEKRKRR-NPLSLPVEKIHPLL-KEVLGYKIDHQVSVYIVAVLEYISADILKLVG 146
Query: 171 NYVKNIRHVEVAQQDIKVAMYADKVLMDMFYQDEHTSDSGSIVHSVSETTSSELTYEEIV 230
NYV+NIRH E+ +QDIKVAM ADKVLMDMF+QD + S+ +TS E TY ++V
Sbjct: 147 NYVRNIRHYEITKQDIKVAMCADKVLMDMFHQDVEDINILSLTDE-EPSTSGEQTYYDLV 205
Query: 231 HDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSLNF 284
+ + +Q++R+L++I KVF E V +++ +F+ ++DI+E S+
Sbjct: 206 KAFMAEIRQYIRELNLIIKVFREPFVSNSKLFSANDVENIFSRIVDIHELSVKL 259
Score = 170 bits (432), Expect = 3e-45
Identities = 78/274 (28%), Positives = 129/274 (47%), Gaps = 32/274 (11%)
Query: 274 LMDIYEFSLNFKTPPDPLFIHETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIV 333
LMD++ + +TS E TY ++V + + +Q++R+L++I KVF E V
Sbjct: 172 LMDMFHQDVEDINILSLTDEEPSTSGEQTYYDLVKAFMAEIRQYIRELNLIIKVFREPFV 231
Query: 334 KLIPPGKCKELDQMFANLMDIYEFSCNLVGILEDNLEMCNEAS-NVVIGSCLEELAEAAE 392
+++ +F+ ++DI+E S L+G +ED +EM +E S + ++GSC E+LAE
Sbjct: 232 SNSKLFSANDVENIFSRIVDIHELSVKLLGHIEDTVEMTDEGSPHPLVGSCFEDLAEELA 291
Query: 393 FDVYSRYAKDITYYKCPEKLLEELKNPEVSIPLQSDCCAKDITYYKCPEKLLEELKNPEV 452
FD Y YA+DI ++ L +L P ++ LQS
Sbjct: 292 FDPYESYARDILRPGFHDRFLSQLSKPGAALYLQSIG----------------------- 328
Query: 453 SIPLQSGGQGFKEAVKYYLPKLFLHPLWHCFLYFDYIRILRGLSPDKEDRESLIQVEGLL 512
+GFKEAV+Y LP+L L P++HC YF+ ++ L S D+ED+E L Q L
Sbjct: 329 --------EGFKEAVQYVLPRLLLAPVYHCLHYFELLKQLEEKSEDQEDKECLKQAITAL 380
Query: 513 KALQVDLSDSLQNYPRNGRDTGIRALIDATLRRS 546
+Q + R + + +
Sbjct: 381 LNVQSGMEKICSKSLAKRRLSESACRFYSQQMKG 414
>1dbh_A Protein (human SOS 1); guanine nucleotide exchange factor, gene
regulation; 2.30A {Homo sapiens} SCOP: a.87.1.1 b.55.1.1
PDB: 1pms_A 1awe_A
Length = 354
Score = 123 bits (311), Expect = 2e-31
Identities = 72/248 (29%), Positives = 120/248 (48%), Gaps = 32/248 (12%)
Query: 300 ELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSC 359
E TY ++V + + +Q++R+L++I KVF E V +++ +F+ ++DI+E S
Sbjct: 1 EQTYYDLVKAFMAEIRQYIRELNLIIKVFREPFVSNSKLFSANDVENIFSRIVDIHELSV 60
Query: 360 NLVGILEDNLEMCNE-ASNVVIGSCLEELAEAAEFDVYSRYAKDITYYKCPEKLLEELKN 418
L+G +ED +EM +E + + ++GSC E+LAE FD Y YA+DI ++ L +L
Sbjct: 61 KLLGHIEDTVEMTDEGSPHPLVGSCFEDLAEELAFDPYESYARDILRPGFHDRFLSQLSK 120
Query: 419 PEVSIPLQSDCCAKDITYYKCPEKLLEELKNPEVSIPLQSGGQGFKEAVKYYLPKLFLHP 478
P ++ LQS +GFKEAV+Y LP+L L P
Sbjct: 121 PGAALYLQSIG-------------------------------EGFKEAVQYVLPRLLLAP 149
Query: 479 LWHCFLYFDYIRILRGLSPDKEDRESLIQVEGLLKALQVDLSDSLQNYPRNGRDTGIRAL 538
++HC YF+ ++ L S D+ED+E L Q L +Q + R +
Sbjct: 150 VYHCLHYFELLKQLEEKSEDQEDKECLKQAITALLNVQSGMEKICSKSLAKRRLSESACR 209
Query: 539 IDATLRRS 546
+ +
Sbjct: 210 FYSQQMKG 217
Score = 58.8 bits (142), Expect = 2e-09
Identities = 18/62 (29%), Positives = 37/62 (59%)
Query: 223 ELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSL 282
E TY ++V + + +Q++R+L++I KVF E V +++ +F+ ++DI+E S+
Sbjct: 1 EQTYYDLVKAFMAEIRQYIRELNLIIKVFREPFVSNSKLFSANDVENIFSRIVDIHELSV 60
Query: 283 NF 284
Sbjct: 61 KL 62
>2jss_A Chimera of histone H2B.1 and histone H2A.Z; histone/chaperone
complex, intrinsically unfolded protein,
chaperone/structural protein complex; NMR {Saccharomyces
cerevisiae} SCOP: a.22.1.1 a.22.1.1
Length = 192
Score = 75.2 bits (183), Expect = 7e-16
Identities = 43/168 (25%), Positives = 78/168 (46%), Gaps = 18/168 (10%)
Query: 51 VLQQVHPTLTAREDACLYVESLVLKILAMLC---------SKPSPHTTSDVEERVRRQFP 101
VL+Q HP + + + S V I + +K S + +++ VR P
Sbjct: 12 VLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILP 71
Query: 102 TPIDKWAMHEAKEAIEK--------SKKKISCLVLPVEKIHYLLSKDVL-QYKVEMNVSI 152
+ K A+ E A+ K S + L PV +I L + + +V +I
Sbjct: 72 GELAKHAVSEGTRAVTKYSSSTQAQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAI 131
Query: 153 YITAVLEYISADILKLAGNYVKNIRHVEVAQQDIKVAMYADKVLMDMF 200
Y+TAVLEY++A++L+LAGN K+++ + + +++A+ D L +
Sbjct: 132 YLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDDELDSLI 179
>2dfk_A Collybistin II; DH domain, PH domain, cell cycle; 2.15A {Rattus
norvegicus} SCOP: a.87.1.1 b.55.1.1
Length = 402
Score = 72.6 bits (178), Expect = 6e-14
Identities = 25/129 (19%), Positives = 56/129 (43%), Gaps = 5/129 (3%)
Query: 294 HETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMD 353
+ + +++++++ E+ +++ L I + +L++ K ++L +F N+ D
Sbjct: 33 RPLQNRDQMRANVINEIMSTERHYIKHLKDICEGYLKQCRKRRDMFSDEQLKVIFGNIED 92
Query: 354 IYEFSCNLVGILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYAKDITYYKCPEKLL 413
IY F V LE ++ IG C E + F +YS Y + + +L
Sbjct: 93 IYRFQMGFVRDLEKQYNN-DDPHLSEIGPCFLEHQD--GFWIYSEYCNN--HLDACMELS 147
Query: 414 EELKNPEVS 422
+ +K+
Sbjct: 148 KLMKDSRYQ 156
Score = 52.2 bits (125), Expect = 2e-07
Identities = 15/83 (18%), Positives = 40/83 (48%)
Query: 202 QDEHTSDSGSIVHSVSETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPP 261
Q+ H + + + + +++++++ E+ +++ L I + +L++ K
Sbjct: 18 QNGHLDPNSDCLCLGRPLQNRDQMRANVINEIMSTERHYIKHLKDICEGYLKQCRKRRDM 77
Query: 262 GKCKELDQMFANLMDIYEFSLNF 284
++L +F N+ DIY F + F
Sbjct: 78 FSDEQLKVIFGNIEDIYRFQMGF 100
>2f8n_K Histone H2A type 1; nucleosome, NCP, macroh2A, histone variant,
chromatin, X- RAY structure, crystallography, structural
protein/DNA complex; 2.90A {Mus musculus} SCOP: a.22.1.1
Length = 149
Score = 65.7 bits (159), Expect = 5e-13
Identities = 25/83 (30%), Positives = 48/83 (57%)
Query: 118 KSKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAGNYVKNIR 177
K++ + L PV ++H LL K +V +Y+ AVLEY++A+IL+LAGN ++ +
Sbjct: 35 KTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNK 94
Query: 178 HVEVAQQDIKVAMYADKVLMDMF 200
+ + +++A+ D+ L +
Sbjct: 95 KTRIIPRHLQLAIRNDEELNKLL 117
>1tzy_A Histone H2A-IV; histone-fold, tetramer-dimer-dimer, DNA binding
protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB:
1eqz_A 1hq3_A 2aro_A 2hio_A 3c9k_A 3azg_C 3a6n_C 3an2_C
3av1_C 3av2_C 3ayw_C 3aze_C 3azf_C 3afa_C 3azh_C 3azi_C
3azj_C 3azk_C 3azl_C 3azm_C ...
Length = 129
Score = 63.7 bits (154), Expect = 2e-12
Identities = 26/83 (31%), Positives = 48/83 (57%)
Query: 118 KSKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAGNYVKNIR 177
KS+ + L PV ++H LL K +V +Y+ AVLEY++A+IL+LAGN ++ +
Sbjct: 16 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNK 75
Query: 178 HVEVAQQDIKVAMYADKVLMDMF 200
+ + +++A+ D+ L +
Sbjct: 76 KTRIIPRHLQLAIRNDEELNKLL 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 = 67.8 bits (165), Expect = 7e-12
Identities = 66/369 (17%), Positives = 122/369 (33%), Gaps = 92/369 (24%)
Query: 210 GSIVHSVSETTS-----SELTYEEIVHDLVTDEKQHLRD------LHMINKVFLEEIVKL 258
GS+ H + T+ S+L E+ L + D ++ K FL + L
Sbjct: 14 GSLEHVLLVPTASFFIASQL-QEQFNKILPEPTEGFAADDEPTTPAELVGK-FLGYVSSL 71
Query: 259 IPPGKCKELDQMFANLMDIYEFSLNFKTPPDPLFIHETTSSELTYEEIVHDLVTDEKQHL 318
+ P K + DQ+ + EF + D IH + L+ + L
Sbjct: 72 VEPSKVGQFDQVLNLCLT--EFENCYLEGND---IHA----------LAAKLLQENDTTL 116
Query: 319 RDLHMINKVFLE-EIVKLIPPGKCKE---LDQMFANLMDIYEFSCNLV----GILEDNLE 370
+ K ++ I+ P K + + + G +D
Sbjct: 117 VKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV-----AIFGGQGNTDD--- 168
Query: 371 MCNEASNVVIGSCLEELAEAAEFDVYSRYAKDITYYKCPEKLLEELKNPEVSIPLQSDCC 430
EEL + + Y D+ E L E ++ + + +
Sbjct: 169 ------------YFEELRDL--YQTYHVLVGDLIK-FSAETLSELIRTTLDAEKVFTQGL 213
Query: 431 AKDITYYKCPEKLLEELKNPEVSIPLQSGGQGFKEAVKYYLPKLFLHPLWHCFLYFDYIR 490
+I LE L+NP + P + + ++ P + + L H Y +
Sbjct: 214 --NI---------LEWLENPS-NTP----DKDYLLSIPISCPLIGVIQLAH---YVVTAK 254
Query: 491 ILRGLSPDKEDRESL----IQVEGLLKALQVDLSDSLQNYPRNGRDT-------GIRALI 539
+L G +P E R L +GL+ A+ + +DS +++ + R G+R
Sbjct: 255 LL-GFTP-GELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCY- 311
Query: 540 DATLRRSLS 548
+A SL
Sbjct: 312 EAYPNTSLP 320
Score = 54.3 bits (130), Expect = 8e-08
Identities = 79/529 (14%), Positives = 148/529 (27%), Gaps = 195/529 (36%)
Query: 71 SLVLKILAMLCSKPSPHTTSDVEERVRRQF----PTPIDKWAMHEAKEAIEKSKKKISCL 126
L L ++ P + + +++ QF P P + +A +
Sbjct: 8 PLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTT----------- 56
Query: 127 VLPVEKIHYLLSKDVLQY---KVE-MNVSIY---ITAVLEYISADILK------LAGNYV 173
P E L+ K L Y VE V + + L L+ LA +
Sbjct: 57 --PAE----LVGK-FLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLL 109
Query: 174 KNIRHVEVAQQDIKVAMYADKVLMDMFYQDEHTS------DSGSI-VHSV------SETT 220
+ V +++ +++ + + S G+ + ++ ++
Sbjct: 110 QENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDY 169
Query: 221 SSEL-----TYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLM 275
EL TY +V DL+ + L +L + +++ F +
Sbjct: 170 FEELRDLYQTYHVLVGDLIKFSAETLSEL-------------IRTTLDAEKV---FTQGL 213
Query: 276 DIYEFSLNF--KTPPDPLFIHETTS---SELTYEEIVHDLVTDEKQHLRDLHMINKVFLE 330
+I E+ L TP + S + ++ H +VT
Sbjct: 214 NILEW-LENPSNTPDKDYLLSIPISCPLIGVI--QLAHYVVT------------------ 252
Query: 331 EIVKLIPPGKCKELDQMFANLMDIYEFSCNLVGILEDNLEMCNEASNVVIGSCLEELAEA 390
K L L L G ++ +V + E
Sbjct: 253 ----------AKLLGFTPGELRSY------LKGAT-----GHSQG--LVTAVAIAETDSW 289
Query: 391 AEFDVYSRYAKDITY-----YKCPEKLLEELKNPEVSIPLQSDCCAKDITYYKCPEKLLE 445
F + K IT +C E P S+P P L +
Sbjct: 290 ESF--FVSVRKAITVLFFIGVRCYEAY------PNTSLP---------------PSILED 326
Query: 446 ELKNPEVSIPLQSGGQGFKEAVKYYLPKLFLHPLWHCFLYFDYIRILRGLSPDKEDRESL 505
L+N +G +P L + L+ +
Sbjct: 327 SLEN----------NEG--------VPSPMLS--------------ISNLTQE------- 347
Query: 506 IQVEGLLKALQVDLSD------SLQNYPRNGRDTG-IRAL--IDATLRR 545
QV+ + L SL N +N +G ++L ++ TLR+
Sbjct: 348 -QVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRK 395
Score = 37.0 bits (85), Expect = 0.022
Identities = 38/284 (13%), Positives = 64/284 (22%), Gaps = 116/284 (40%)
Query: 261 PGKCKEL-----------DQMFANLMDIYEFSLN--FKTPPDPLFIHETTSSELT----Y 303
G +L ++ + D Y FS+ P L IH Y
Sbjct: 1629 QGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENY 1688
Query: 304 EEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQ-------MFA------N 350
++ + + D K I K E + L +
Sbjct: 1689 SAMIFETIVDGKLKTEK---IFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFE 1745
Query: 351 LM--------DIY-------EFS--------------CNLV---GIL-----------ED 367
+ D E++ +V G+
Sbjct: 1746 DLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRS 1805
Query: 368 NLEMCNEASN---VVIGSCLEELAEAAEFDVYSRYAKDITY------YKCP--------- 409
N M A N V E L E R K + Y
Sbjct: 1806 NYGMI--AINPGRVAASFSQEALQYVVE-----RVGKRTGWLVEIVNYNVENQQYVAAGD 1858
Query: 410 ----EKLLEELKNPEVSIPLQSDCCAKDITYYKCPEKL-LEELK 448
+ + L ++ + I + + L LEE++
Sbjct: 1859 LRALDTVTNVLNFIKL----------QKIDIIELQKSLSLEEVE 1892
Score = 33.5 bits (76), Expect = 0.24
Identities = 31/214 (14%), Positives = 60/214 (28%), Gaps = 92/214 (42%)
Query: 24 ISLAILE-LQEKGTIQM--------L--YDKWWKNT-----GDVLQQVHPTLTAREDACL 67
+ A E L+ KG I L Y DV+ ++ E
Sbjct: 1739 MEKAAFEDLKSKGLIPADATFAGHSLGEY------AALASLADVM-----SI---ESLV- 1783
Query: 68 YVESLVLKILAMLCSKPSPHTTSDVEERVRRQFPTPIDKWAMHEAKEAIEKSKKKISCLV 127
+V R M A E + +
Sbjct: 1784 ---EVV---------------------FYRGM--------TMQVAVPRDELGRSNYGMIA 1811
Query: 128 LPVEKIHYLLSKDVLQYKVEM--------------NVS--IYITA----VLEYISADILK 167
+ ++ S++ LQY VE NV Y+ A L+ ++ ++L
Sbjct: 1812 INPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVT-NVLN 1870
Query: 168 LAGNYVKNIRHVEVAQQDIKVAMYADKVLMDMFY 201
++ I +E+ + ++ ++V +
Sbjct: 1871 FIK--LQKIDIIEL-----QKSLSLEEV-EGHLF 1896
Score = 30.0 bits (67), Expect = 2.6
Identities = 14/84 (16%), Positives = 27/84 (32%), Gaps = 17/84 (20%)
Query: 8 LSIVSRHL-IGSPW-----RDRISLAILELQEKGTIQMLYDKWWKNTGDVLQ-QVHPTLT 60
L +R L + SP+ L +L + + +Q V+ T
Sbjct: 414 LKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNV------SFNAKD---IQIPVYDTFD 464
Query: 61 AREDACLYVESLVLKILAMLCSKP 84
D + S+ +I+ + P
Sbjct: 465 G-SDLRVLSGSISERIVDCIIRLP 487
>2pz1_A RHO guanine nucleotide exchange factor 4; helical bundle, beta
barrel, beta sandwich, signaling protei; 2.25A {Homo
sapiens} PDB: 2dx1_A 3nmz_D 3nmx_D
Length = 466
Score = 65.8 bits (160), Expect = 2e-11
Identities = 25/141 (17%), Positives = 56/141 (39%), Gaps = 5/141 (3%)
Query: 281 SLNFKTPPDPLFIHETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGK 340
L + + +S + +++++++ E+ +++ L I + ++ + K
Sbjct: 97 PLAGNSGAEDGGAEAQSSKDQMRTNVINEILSTERDYIKHLRDICEGYVRQCRKRADMFS 156
Query: 341 CKELDQMFANLMDIYEFSCNLVGILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYA 400
++L +F N+ DIY V LE +G+C L A+F +YS Y
Sbjct: 157 EEQLRTIFGNIEDIYRCQKAFVKALEQRFNR-ERPHLSELGACF--LEHQADFQIYSEYC 213
Query: 401 KDITYYKCPEKLLEELKNPEV 421
+ + +L K +
Sbjct: 214 NN--HPNACVELSRLTKLSKY 232
Score = 50.0 bits (119), Expect = 1e-06
Identities = 14/78 (17%), Positives = 37/78 (47%)
Query: 207 SDSGSIVHSVSETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKE 266
+SG+ +S + +++++++ E+ +++ L I + ++ + K ++
Sbjct: 100 GNSGAEDGGAEAQSSKDQMRTNVINEILSTERDYIKHLRDICEGYVRQCRKRADMFSEEQ 159
Query: 267 LDQMFANLMDIYEFSLNF 284
L +F N+ DIY F
Sbjct: 160 LRTIFGNIEDIYRCQKAF 177
>2nqb_C Histone H2A; nucleosome, NCP, chromatin, structural protein/DNA
complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_C*
Length = 123
Score = 60.3 bits (145), Expect = 2e-11
Identities = 25/86 (29%), Positives = 48/86 (55%)
Query: 117 EKSKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAGNYVKNI 176
KS+ + L PV +IH LL K +V +Y+ AV+EY++A++L+LAGN ++
Sbjct: 13 AKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN 72
Query: 177 RHVEVAQQDIKVAMYADKVLMDMFYQ 202
+ + + +++A+ D+ L +
Sbjct: 73 KKTRIIPRHLQLAIRNDEELNKLLSG 98
>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 = 65.6 bits (159), Expect = 2e-11
Identities = 63/455 (13%), Positives = 134/455 (29%), Gaps = 132/455 (29%)
Query: 25 SLAILELQEKGTIQMLYDK-WWKNTG------DVLQ-------QVHPTLTAREDAC---- 66
+A+ + K +W N VL+ Q+ P T+R D
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK 224
Query: 67 LYVESLVLKILAMLCSKPSPH-------------------------TTSD------VEER 95
L + S+ ++ +L SKP + TT +
Sbjct: 225 LRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAA 284
Query: 96 VRRQFPTPIDKWAMHEAKEAIEKSKKKISCLV--LPVE--KIHYLL-------------- 137
+ E K + C LP E +
Sbjct: 285 TTTHISLDHHSMTLTPD-EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343
Query: 138 SKDVLQYKVEMNVSIYITAVLEYISADILKLAGNYVKNIRHVEVAQQDIKVAMYADKVLM 197
+ + ++ I + L + + + + + V + +L
Sbjct: 344 WDNWKHVNCD-KLTTIIESSLNVLEPAEYR--KMFDR----LSVFPPSAHIPT---ILLS 393
Query: 198 DMFYQDEHTSDSGSIVH-----SVSETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFL 252
+ + D SD +V+ S+ E E T + + + K L + + +++ +
Sbjct: 394 -LIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS--IPSIYLELKVKLENEYALHRSIV 450
Query: 253 E--EIVK------LIPPG-------------KCKELDQMFANLMDIYEFSLNFKTPPDPL 291
+ I K LIPP K E + ++ L+F+
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF---LDFR------ 501
Query: 292 FIH---ETTSSELTYEEIVHDLVTDE---KQHLRDLHMINKVFLEEIVKLIPPGKCKELD 345
F+ S+ + + + K ++ D + + I+ +P K +E
Sbjct: 502 FLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLP--KIEE-- 557
Query: 346 QMFANLMDIYEFSCNL-VGILEDNLEMCNEASNVV 379
NL+ +++ L + ++ ++ + EA V
Sbjct: 558 ----NLI-CSKYTDLLRIALMAEDEAIFEEAHKQV 587
Score = 52.5 bits (125), Expect = 3e-07
Identities = 60/392 (15%), Positives = 122/392 (31%), Gaps = 120/392 (30%)
Query: 214 HSVSETTSSELTYEEIVHDLVTD-----EKQHLRDL--HMINKVFLEEIVKLIPPGKCKE 266
H ET + Y++I+ + + ++D+ +++K ++ I+
Sbjct: 6 HMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMS--KDAVSG 63
Query: 267 LDQMFANLMD----IYEFSLNFKTPPDPLFIHETTSSELTYEEIVHDLVTDEKQHLRD-L 321
++F L+ + + + + F+ S + E+ ++T RD L
Sbjct: 64 TLRLFWTLLSKQEEMVQKFVEEVLRINYKFL----MSPIKTEQRQPSMMTRMYIEQRDRL 119
Query: 322 HMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSCNLVGILEDNLEMCNEASNVVI- 380
+ N+VF + V + P L L A NV+I
Sbjct: 120 YNDNQVFAKYNVSRLQP-----------------------YLKLRQALLELRPAKNVLID 156
Query: 381 G------SCL-------EELAEAAEFDVYSRYAKDITYYKCPEKLLEELKNPEVSIPLQS 427
G + + ++ +F ++ + + PE +LE L+
Sbjct: 157 GVLGSGKTWVALDVCLSYKVQCKMDFKIF--WLN-LKNCNSPETVLEMLQK--------- 204
Query: 428 DCCAKDITYYKCPEKLLEELKNPEVSIPLQSGGQGFKEAVKYYLPKLFLH-PLWHCFL-- 484
Y+ + +I L+ +++ L +L P +C L
Sbjct: 205 -------LLYQIDPNWTSRSDHSS-NIKLRI------HSIQAELRRLLKSKPYENCLLVL 250
Query: 485 ----------YFD----------YIRILRGLSPDKEDRESLI---------QVEGLL-KA 514
F+ + ++ LS SL +V+ LL K
Sbjct: 251 LNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY 310
Query: 515 LQVDLSDSLQNYPRNGRDTGIR--ALIDATLR 544
L D PR T R ++I ++R
Sbjct: 311 LDCRPQDL----PREVLTTNPRRLSIIAESIR 338
>3jv3_A Intersectin-1; SH3 domain, DH domain, guanine nucleotide exchange
factor, autoinhibition, domain-swapped, cell junction,
cell project endocytosis; 2.40A {Mus musculus} PDB:
3gf9_A
Length = 283
Score = 61.7 bits (150), Expect = 9e-11
Identities = 25/135 (18%), Positives = 56/135 (41%), Gaps = 11/135 (8%)
Query: 287 PPDPLFIHETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKEL 344
D + T +E + +H+L+ E+ ++ DL ++ ++F + + + L+ KE+
Sbjct: 67 CSDLHLLDMLTPTERKRQGYIHELIVTEENYVNDLQLVTEIFQKPLTESELLTE---KEV 123
Query: 345 DQMFANLMDIYEFSCNLVGILEDNLEMCNEASNV-VIGSCLEELAEAAEFDVYSRYAKDI 403
+F N ++ + L+ L +M E V +IG L Y R+
Sbjct: 124 AMIFVNWKELIMCNIKLLKALRVRKKMSGEKMPVKMIGDILSAQLP--HMQPYIRF---C 178
Query: 404 TYYKCPEKLLEELKN 418
+ L+++ +
Sbjct: 179 SCQLNGAALIQQKTD 193
Score = 45.9 bits (109), Expect = 1e-05
Identities = 15/85 (17%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 202 QDEHTSDSGSIVHSVSETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LI 259
+ + S +H + T +E + +H+L+ E+ ++ DL ++ ++F + + + L+
Sbjct: 59 DMDPSQQWCSDLHLLDMLTPTERKRQGYIHELIVTEENYVNDLQLVTEIFQKPLTESELL 118
Query: 260 PPGKCKELDQMFANLMDIYEFSLNF 284
KE+ +F N ++ ++
Sbjct: 119 TE---KEVAMIFVNWKELIMCNIKL 140
>1id3_C Histone H2A.1; nucleosome core particle, chromatin, protein/DNA
interaction, nucleoprotein, supercoiled DNA; 3.10A
{Saccharomyces cerevisiae} SCOP: a.22.1.1
Length = 131
Score = 58.8 bits (141), Expect = 9e-11
Identities = 24/85 (28%), Positives = 48/85 (56%)
Query: 118 KSKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAGNYVKNIR 177
+S+ + L PV ++H LL + ++ +Y+TAVLEY++A+IL+LAGN ++ +
Sbjct: 16 QSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNK 75
Query: 178 HVEVAQQDIKVAMYADKVLMDMFYQ 202
+ + +++A+ D L +
Sbjct: 76 KTRIIPRHLQLAIRNDDELNKLLGN 100
>2vrw_B P95VAV, VAV1, proto-oncogene VAV; lipoprotein, GTP-binding,
metal-binding, phosphoprotein, exchange factor, RAC,
GTPase, membrane domain; 1.85A {Mus musculus} PDB:
3bji_A 1f5x_A
Length = 406
Score = 62.2 bits (151), Expect = 1e-10
Identities = 21/126 (16%), Positives = 53/126 (42%), Gaps = 12/126 (9%)
Query: 276 DIYEFSLNFKTPPDPLFIHETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVKL 335
+IYE + ++ P P + + ++ E+++ L I + F++ + +
Sbjct: 3 EIYEDLMRLESVPTP----PKMTEYDKRCCCLREIQQTEEKYTDTLGSIQQHFMKPLQRF 58
Query: 336 IPPGKCKELDQMFANLMDIYEFSCNLVGILEDNLEMCNEASNVVIGSCLEELAEAAEFDV 395
+ P ++++ +F N+ +++ + + L+D L + + + E F V
Sbjct: 59 LKP---QDMETIFVNIEELFSVHTHFLKELKDALAGPGATT---LYQVFIKYKE--RFLV 110
Query: 396 YSRYAK 401
Y RY
Sbjct: 111 YGRYCS 116
Score = 46.0 bits (109), Expect = 2e-05
Identities = 8/58 (13%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 227 EEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSLNF 284
+ ++ E+++ L I + F++ + + + P ++++ +F N+ +++ +F
Sbjct: 27 CCCLREIQQTEEKYTDTLGSIQQHFMKPLQRFLKP---QDMETIFVNIEELFSVHTHF 81
>3ky9_A Proto-oncogene VAV; calponin homology domain, DBL homology domain,
pleckst homology domain, C1 domain, guanine-nucleotide
releasing FA metal-binding; 2.73A {Homo sapiens} PDB:
2d86_A
Length = 587
Score = 60.1 bits (145), Expect = 9e-10
Identities = 25/153 (16%), Positives = 60/153 (39%), Gaps = 18/153 (11%)
Query: 259 IPPGKCKELDQMFANLMDIYEFSLNFKTPPDPLFIHETTSSELTY----------EEIVH 308
I G ++D D+Y+ N + D ++ S ++ +
Sbjct: 144 IYSGLSDQIDDTVEEDEDLYDCVENEEAEGDEIYEDLMRSEPVSMPPKMTEYDKRCCCLR 203
Query: 309 DLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSCNLVGILEDN 368
++ E+++ L I + FL+ + + + P ++++ +F N+ D+ + + +++
Sbjct: 204 EIQQTEEKYTDTLGSIQQHFLKPLQRFLKP---QDIEIIFINIEDLLRVHTHFLKEMKEA 260
Query: 369 LEMCNEASNVVIGSCLEELAEAAEFDVYSRYAK 401
L A+ + + E F VY RY
Sbjct: 261 LGTPGAAN---LYQVFIKYKE--RFLVYGRYCS 288
Score = 46.2 bits (109), Expect = 2e-05
Identities = 18/108 (16%), Positives = 46/108 (42%), Gaps = 9/108 (8%)
Query: 183 QQDIKVAMYADKVLMDMFYQDEHTSDSG--SIVHSVSETTSSELTYEE----IVHDLVTD 236
I + D+ L D +E D ++ S + ++T + + ++
Sbjct: 149 SDQIDDTVEEDEDLYDCVENEEAEGDEIYEDLMRSEPVSMPPKMTEYDKRCCCLREIQQT 208
Query: 237 EKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSLNF 284
E+++ L I + FL+ + + + P ++++ +F N+ D+ +F
Sbjct: 209 EEKYTDTLGSIQQHFLKPLQRFLKP---QDIEIIFINIEDLLRVHTHF 253
>3g3k_A Glutamate receptor, ionotropic kainate 2; membrane protein, cell
junction, cell membrane, glycoprotein, ION transport,
ionic channel, membrane; HET: GLU IPA; 1.24A {Rattus
norvegicus} PDB: 3g3j_A* 3g3i_A* 2i0b_A* 3g3h_A* 3g3g_A*
3g3f_A* 1s7y_A* 1s9t_A* 1sd3_A* 1tt1_A* 1s50_A* 2xxr_A*
2xxt_A* 2xxx_A* 2xxw_A* 2xxy_A* 2xxu_A* 2xxv_A* 3qxm_A*
2i0c_A* ...
Length = 259
Score = 57.3 bits (138), Expect = 2e-09
Identities = 19/33 (57%), Positives = 28/33 (84%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKWWKNTG 49
GSP+RD+I+LAIL+LQE+G + M+ +KWW+ G
Sbjct: 224 GSPYRDKITLAILKLQEQGKLHMMKEKWWRGNG 256
>3jzy_A Intersectin 2; C2 domain, structural genomics consortium (SGC),
endocytosis; 1.56A {Homo sapiens} PDB: 3qbv_B* 1ki1_B
Length = 510
Score = 58.9 bits (142), Expect = 2e-09
Identities = 21/117 (17%), Positives = 48/117 (41%), Gaps = 11/117 (9%)
Query: 305 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSCNLV 362
+H+L+ E++++ DL ++ +VF + + + + E+ +F N ++ + L+
Sbjct: 30 GYIHELIQTEERYMADLQLVVEVFQKRMAESGFLTE---GEMALIFVNWKELIMSNTKLL 86
Query: 363 GILEDNLEMCNEASNV-VIGSCLEELAEAAEFDVYSRYAKDITYYKCPEKLLEELKN 418
L + E V +IG L Y R+ + LL++ +
Sbjct: 87 KALRVRKKTGGEKMPVQMIGDILAAELS--HMQAYIRF---CSCQLNGAALLQQKTD 138
Score = 49.6 bits (118), Expect = 2e-06
Identities = 14/88 (15%), Positives = 38/88 (43%), Gaps = 5/88 (5%)
Query: 199 MFYQDEHTSDSGSIVHSVSETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVK- 257
M + H+S ++ E + +H+L+ E++++ DL ++ +VF + + +
Sbjct: 1 MHHHHHHSSGRENLYFQGDTMQPIERKRQGYIHELIQTEERYMADLQLVVEVFQKRMAES 60
Query: 258 -LIPPGKCKELDQMFANLMDIYEFSLNF 284
+ E+ +F N ++ +
Sbjct: 61 GFLTE---GEMALIFVNWKELIMSNTKL 85
>2z0q_A XPLN, RHO guanine nucleotide exchange factor 3; DH-PH domain,
alternative splicing, cytoplasm, guanine- nucleotide
releasing factor; 1.79A {Mus musculus} PDB: 3eo2_A
Length = 346
Score = 57.5 bits (139), Expect = 4e-09
Identities = 23/120 (19%), Positives = 47/120 (39%), Gaps = 13/120 (10%)
Query: 305 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSCNLV 362
E + +L E+ + DL + K + + ++K ++ +EL+Q+F L + L+
Sbjct: 22 EAIFELSQGEEDLIEDLKLAKKAYHDPMLKLSIMTE---QELNQIFGTLDSLIPLHEELL 78
Query: 363 GILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYAKDITYYKCPEKLLEEL-KNPEV 421
L D + + S +G L Y Y + + LL+ ++ V
Sbjct: 79 SQLRDVRK--PDGSTEHVGPILVGWLP--CLSSYDSY---CSNQVAAKALLDHKKQDHRV 131
Score = 43.2 bits (102), Expect = 2e-04
Identities = 12/59 (20%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 228 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSLNF 284
E + +L E+ + DL + K + + ++K ++ +EL+Q+F L +
Sbjct: 22 EAIFELSQGEEDLIEDLKLAKKAYHDPMLKLSIMTE---QELNQIFGTLDSLIPLHEEL 77
>2f8n_G Core histone macro-H2A.1; nucleosome, NCP, macroh2A, histone
variant, chromatin, X- RAY structure, crystallography,
structural protein/DNA complex; 2.90A {Homo sapiens}
SCOP: a.22.1.1 PDB: 1u35_C
Length = 120
Score = 53.3 bits (127), Expect = 6e-09
Identities = 22/83 (26%), Positives = 47/83 (56%)
Query: 118 KSKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAGNYVKNIR 177
S+ + ++ PV ++ + K +Y++ + +Y+ AVLEY++A+IL+LA N ++ +
Sbjct: 13 TSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNK 72
Query: 178 HVEVAQQDIKVAMYADKVLMDMF 200
V + I +A+ D+ L +
Sbjct: 73 KGRVTPRHILLAVANDEELNQLL 95
>1yae_A Glutamate receptor, ionotropic kainate 2; kainate receptor,
membrane protein; HET: NAG FUC DOQ; 3.11A {Rattus
norvegicus} SCOP: c.94.1.1
Length = 312
Score = 56.7 bits (136), Expect = 6e-09
Identities = 18/33 (54%), Positives = 28/33 (84%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKWWKNTG 49
GSP+RD+I++AIL+LQE+G + M+ +KWW+ G
Sbjct: 258 GSPYRDKITIAILQLQEEGKLHMMKEKWWRGNG 290
>2v3u_A Glutamate receptor delta-2 subunit; postsynaptic membrane,
ionotropic glutamate receptors, transmembrane, membrane
protein; 1.74A {Rattus norvegicus} PDB: 2v3t_A
Length = 265
Score = 55.4 bits (133), Expect = 1e-08
Identities = 17/33 (51%), Positives = 21/33 (63%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKWWKNTG 49
GSP+RD S ILELQ+ G + +L KWW G
Sbjct: 229 GSPYRDVFSQRILELQQSGDMDILKHKWWPKNG 261
>1mqi_A Glutamate receptor 2; GLUR2, ligand binding core, S1S2, partial
agonist, WILLARDIINES, fluoro-WILLARDIINE, membrane
protein; HET: FWD; 1.35A {Rattus norvegicus} SCOP:
c.94.1.1 PDB: 1ftj_A* 1ftl_A* 1fto_A 1fw0_A* 1m5b_A*
1ftm_A* 1m5c_A* 1mm6_A* 1mm7_A* 1mqg_A* 1m5e_A* 1mqj_A*
1ms7_A* 1mxu_A* 1mxv_A 1mxw_A 1mxx_A 1mxy_A 1mxz_A
1my0_A ...
Length = 263
Score = 55.0 bits (132), Expect = 1e-08
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKWWKNTGD 50
GS + ++LA+L+L E+G + L +KWW + G+
Sbjct: 227 GSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGE 260
>3kg2_A Glutamate receptor 2; ION channel, membrane protein, cell membrane,
glycoprotein, transport, membrane, postsynaptic cell
membrane, editing; HET: ZK1 NAG BMA; 3.60A {Rattus
norvegicus}
Length = 823
Score = 56.7 bits (136), Expect = 1e-08
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKWWKNTGD 50
GS ++LA+L+L E+G + L +KWW + G+
Sbjct: 730 GSSLGTPVNLAVLKLSEQGLLDKLKNKWWYDKGE 763
>1by1_A Protein (PIX); RHO-GTPase exchange factor, transport protein; NMR
{Homo sapiens} SCOP: a.87.1.1
Length = 209
Score = 53.8 bits (130), Expect = 2e-08
Identities = 19/108 (17%), Positives = 43/108 (39%), Gaps = 9/108 (8%)
Query: 295 ETTSSELTY-EEIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANL 351
+TT+ +Y ++ +++ E ++ ++L + +L + + + + NL
Sbjct: 5 DTTAINKSYYNVVLQNILETENEYSKELQTVLSTYLRPLQTSEKLSSA---NISYLMGNL 61
Query: 352 MDIYEFSCNLVGILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRY 399
+I F LV LE+ ++ +G C L +Y Y
Sbjct: 62 EEICSFQQMLVQSLEECTKLPEAQQR--VGGCFLNLMPQM-KTLYLTY 106
Score = 41.9 bits (99), Expect = 2e-04
Identities = 10/70 (14%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 218 ETTSSELTY-EEIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANL 274
+TT+ +Y ++ +++ E ++ ++L + +L + + + + NL
Sbjct: 5 DTTAINKSYYNVVLQNILETENEYSKELQTVLSTYLRPLQTSEKLSSA---NISYLMGNL 61
Query: 275 MDIYEFSLNF 284
+I F
Sbjct: 62 EEICSFQQML 71
>3mpx_A FYVE, rhogef and PH domain-containing protein 5; structural
genomics consortium, DH domain, SGC, L binding protein;
2.80A {Homo sapiens}
Length = 434
Score = 53.8 bits (129), Expect = 7e-08
Identities = 17/104 (16%), Positives = 39/104 (37%), Gaps = 12/104 (11%)
Query: 306 IVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCK--------ELDQMFANLMDIYEF 357
I +L++ EK ++ L +N F +++ + + EL Q + L I++
Sbjct: 26 IAQELLSSEKAYVEMLQHLNLDFHGAVMRALDDMDHEGRDTLAREELRQGLSELPAIHDL 85
Query: 358 SCNLVGILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYAK 401
++ LE+ L + + FD ++ +
Sbjct: 86 HQGILEELEERLSNWESQQK--VADVFLAREQ--GFDHHATHIL 125
Score = 39.2 bits (91), Expect = 0.003
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 8/64 (12%)
Query: 229 IVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCK--------ELDQMFANLMDIYEF 280
I +L++ EK ++ L +N F +++ + + EL Q + L I++
Sbjct: 26 IAQELLSSEKAYVEMLQHLNLDFHGAVMRALDDMDHEGRDTLAREELRQGLSELPAIHDL 85
Query: 281 SLNF 284
Sbjct: 86 HQGI 89
>1xcg_A PDZ-rhogef, RHO guanine nucleotide exchange factor 11; X-RAY
crystallography, regulation of RHOA GTPase, protein
complex; 2.50A {Homo sapiens} SCOP: a.87.1.1 b.55.1.1
PDB: 3kz1_A*
Length = 368
Score = 52.9 bits (127), Expect = 1e-07
Identities = 22/120 (18%), Positives = 51/120 (42%), Gaps = 14/120 (11%)
Query: 305 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSCNLV 362
E++++L E HLR L +++ +F + + K L+P +EL ++F NL ++ E +
Sbjct: 24 EVINELFVTEASHLRTLRVLDLIFYQRMKKENLMPR---EELARLFPNLPELIEIHNSWC 80
Query: 363 GILEDNLEMCNEASNVVIGSCLEELAEAAE----FDVYSRYAKDITYYKCPEKLLEELKN 418
++ E I + + V +++ +Y +L++ +
Sbjct: 81 EAMKKLRE--EGPIIKEISDLMLARFDGPAREELQQVAAQF---CSYQSIALELIKTKQR 135
Score = 44.4 bits (105), Expect = 6e-05
Identities = 17/59 (28%), Positives = 35/59 (59%), Gaps = 5/59 (8%)
Query: 228 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSLNF 284
E++++L E HLR L +++ +F + + K L+P +EL ++F NL ++ E ++
Sbjct: 24 EVINELFVTEASHLRTLRVLDLIFYQRMKKENLMPR---EELARLFPNLPELIEIHNSW 79
>1txd_A RHO guanine nucleotide exchange factor 12; helical bundle (DH),
beta sandwich (PH), signaling protein; 2.13A {Homo
sapiens} SCOP: a.87.1.1 b.55.1.1 PDB: 1x86_A
Length = 385
Score = 52.6 bits (126), Expect = 1e-07
Identities = 21/120 (17%), Positives = 52/120 (43%), Gaps = 12/120 (10%)
Query: 305 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSCNLV 362
E++++L E+ H+R L ++++VF + + + ++ P EL ++F+NL DI + L
Sbjct: 27 EVINELFYTERAHVRTLKVLDQVFYQRVSREGILSP---SELRKIFSNLEDILQLHIGLN 83
Query: 363 GILEDNLEMCNEASNVVIGSCLEEL----AEAAEFDVYSRYAKDITYYKCPEKLLEELKN 418
++ + + IG L E + + + ++++ +
Sbjct: 84 EQMKAVRKRNETSVIDQIGEDLLTWFSGPGEEKLKHAAATF---CSNQPFALEMIKSRQK 140
Score = 44.1 bits (104), Expect = 8e-05
Identities = 16/59 (27%), Positives = 36/59 (61%), Gaps = 5/59 (8%)
Query: 228 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSLNF 284
E++++L E+ H+R L ++++VF + + + ++ P EL ++F+NL DI + +
Sbjct: 27 EVINELFYTERAHVRTLKVLDQVFYQRVSREGILSP---SELRKIFSNLEDILQLHIGL 82
>1foe_A T-lymphoma invasion and metastasis inducing protein 1; DBL homology
domain, pleckstrin homology domain, GTPase, guanine
nucleotide exchange factor; 2.80A {Mus musculus} SCOP:
a.87.1.1 b.55.1.1
Length = 377
Score = 51.9 bits (124), Expect = 3e-07
Identities = 25/132 (18%), Positives = 58/132 (43%), Gaps = 20/132 (15%)
Query: 304 EEIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSCNL 361
+++ +L+ E+ +++DL+ + + +L+ + K + ELD +F NL ++ EF
Sbjct: 13 RKVICELLETERTYVKDLNCLMERYLKPLQKETFLTQ---DELDVLFGNLTEMVEFQVEF 69
Query: 362 VGILEDNLEMCNEASNVV-----------IGSCLEELAEAAEFDVYSRYAKDITYYKCPE 410
+ LED + + + + +G A+ F +YS + + K P+
Sbjct: 70 LKTLEDGVRLVPDLEKLEKVDQFKKVLFSLGGSFLYYAD--RFKLYSAFCAS--HTKVPK 125
Query: 411 KLLEELKNPEVS 422
L++ +
Sbjct: 126 VLVKAKTDTAFK 137
Score = 40.4 bits (94), Expect = 0.001
Identities = 16/72 (22%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 215 SVSETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFA 272
++ S +++ +L+ E+ +++DL+ + + +L+ + K + ELD +F
Sbjct: 1 AMGRQLSDADKLRKVICELLETERTYVKDLNCLMERYLKPLQKETFLTQ---DELDVLFG 57
Query: 273 NLMDIYEFSLNF 284
NL ++ EF + F
Sbjct: 58 NLTEMVEFQVEF 69
>3t06_A PDZ-rhogef, RHO guanine nucleotide exchange factor 11; DH-PH RHOA
complex, pdzrhogef, guanine nucleotide exchange F RHOA,
signaling protein; 2.84A {Homo sapiens}
Length = 418
Score = 51.8 bits (124), Expect = 3e-07
Identities = 22/120 (18%), Positives = 51/120 (42%), Gaps = 14/120 (11%)
Query: 305 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSCNLV 362
E++++L E HLR L +++ +F + + K L+P +EL ++F NL ++ E +
Sbjct: 66 EVINELFVTEASHLRTLRVLDLIFYQRMKKENLMPR---EELARLFPNLPELIEIHNSWC 122
Query: 363 GILEDNLEMCNEASNVVIGSCLEELAEAAE----FDVYSRYAKDITYYKCPEKLLEELKN 418
++ E I + + V +++ +Y +L++ +
Sbjct: 123 EAMKKLRE--EGPIIKEISDLMLARFDGPAREELQQVAAQF---CSYQSIALELIKTKQR 177
Score = 44.9 bits (106), Expect = 5e-05
Identities = 24/95 (25%), Positives = 47/95 (49%), Gaps = 10/95 (10%)
Query: 197 MDMFYQDEHTSDSGSIVHSVSETTSSELTYEEI-----VHDLVTDEKQHLRDLHMINKVF 251
+ E D+ + H+V + + LT EI +++L E HLR L +++ +F
Sbjct: 30 LGQLSDLEPEPDAQNWQHTVGKDVVAGLTQREIDRQEVINELFVTEASHLRTLRVLDLIF 89
Query: 252 LEEIVK--LIPPGKCKELDQMFANLMDIYEFSLNF 284
+ + K L+P +EL ++F NL ++ E ++
Sbjct: 90 YQRMKKENLMPR---EELARLFPNLPELIEIHNSW 121
>3odw_A RHO guanine nucleotide exchange factor 1; regulation of RHOA
GTPase, rhogef, DH, PH, signaling PR; 3.20A {Homo
sapiens} PDB: 3odx_A
Length = 536
Score = 51.6 bits (123), Expect = 4e-07
Identities = 26/139 (18%), Positives = 60/139 (43%), Gaps = 17/139 (12%)
Query: 288 PDPLFIHETTSSELTYEEIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELD 345
P +H S++ +E++ +L+ E H+R L +++ +F + + + P +EL
Sbjct: 166 VPPDTLHSLPKSQVKRQEVISELLVTEAAHVRMLRVLHDLFFQPMAECLFFPL---EELQ 222
Query: 346 QMFANLMDIYEFSCNLVGILEDNLEMCNEASNVV--IGSCLEELAEAAE----FDVYSRY 399
+F +L ++ E L+ ++ E+ ++ IG L + AE + SR+
Sbjct: 223 NIFPSLDELIEVHSLF---LDRLMKRRQESGYLIEEIGDVLLARFDGAEGSWFQKISSRF 279
Query: 400 AKDITYYKCPEKLLEELKN 418
+ + L+ +
Sbjct: 280 ---CSRQSFALEQLKAKQR 295
Score = 45.4 bits (107), Expect = 4e-05
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 228 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSLNF 284
E++ +L+ E H+R L +++ +F + + + P +EL +F +L ++ E F
Sbjct: 183 EVISELLVTEAAHVRMLRVLHDLFFQPMAECLFFPL---EELQNIFPSLDELIEVHSLF 238
>1nty_A Triple functional domain protein; DBL, pleckstrin, GEF, RHO,
GTPase, guanine-nucleotide releas factor,
phosphorylation, signaling protein; 1.70A {Homo sapiens}
SCOP: a.87.1.1 b.55.1.1 PDB: 2nz8_B 2kr9_A
Length = 311
Score = 50.6 bits (121), Expect = 5e-07
Identities = 31/101 (30%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 304 EEIVHDLVTDEKQHLRDLHMINKVFLEEIVK---LIPPGKCKELDQMFANLMDIYEFSCN 360
E I+ +L+ EK ++RDL +L E+ IPPG + +F N+ +IYEF N
Sbjct: 11 EFIMAELIQTEKAYVRDLRECMDTYLWEMTSGVEEIPPGIVNKELIIFGNMQEIYEFHNN 70
Query: 361 LVGILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYAK 401
I LE + +G C A+ +F +Y Y K
Sbjct: 71 ---IFLKELEKYEQLPE-DVGHCFVTWAD--KFQMYVTYCK 105
Score = 40.2 bits (94), Expect = 0.001
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 227 EEIVHDLVTDEKQHLRDLHMINKVFLEEIVK---LIPPGKCKELDQMFANLMDIYEF 280
E I+ +L+ EK ++RDL +L E+ IPPG + +F N+ +IYEF
Sbjct: 11 EFIMAELIQTEKAYVRDLRECMDTYLWEMTSGVEEIPPGIVNKELIIFGNMQEIYEF 67
>2rgn_B RHOA/RAC/CDC42 exchange factor; heterotrimeric G-protein, small
molecular weight G-protein, complex, protein-protein
complex, rhogef, galphaq; HET: GDP; 3.50A {Homo sapiens}
Length = 354
Score = 50.6 bits (121), Expect = 5e-07
Identities = 20/116 (17%), Positives = 44/116 (37%), Gaps = 10/116 (8%)
Query: 304 EEIVHDLVTDEKQHLRDLHMINKVFLEEIVK-LIPPGKCKELDQMFANLMDIYEFSCNLV 362
++ +LV EK ++ DL I + ++ + +P +F N+ IYE+ +
Sbjct: 14 MYVLSELVETEKMYVDDLGQIVEGYMATMAAQGVPESLRGRDRIVFGNIQQIYEWHRDY- 72
Query: 363 GILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYAKDITYYKCPEKLLEELKN 418
L+ C + + + +Y Y ++ K E ++ E +
Sbjct: 73 --FLQELQRCLK-DPDWLAQLF--IKHERRLHMYVVYCQN--KPKS-EHVVSEFGD 120
Score = 41.4 bits (97), Expect = 5e-04
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 227 EEIVHDLVTDEKQHLRDLHMINKVFLEEIVK-LIPPGKCKELDQMFANLMDIYEFSLNF 284
++ +LV EK ++ DL I + ++ + +P +F N+ IYE+ ++
Sbjct: 14 MYVLSELVETEKMYVDDLGQIVEGYMATMAAQGVPESLRGRDRIVFGNIQQIYEWHRDY 72
>1kz7_A Guanine nucleotide exchange factor DBS; guanine nucleotide exchange
factor (GEF), small G-protein, signaling protein; 2.40A
{Mus musculus} SCOP: a.87.1.1 b.55.1.1 PDB: 1lb1_A
1kzg_A 1rj2_A
Length = 353
Score = 50.3 bits (120), Expect = 8e-07
Identities = 27/134 (20%), Positives = 55/134 (41%), Gaps = 14/134 (10%)
Query: 304 EEIVHDLVTDEKQHLRDLHMINKVFLEEI-----VKLIPPGKCKELDQMFANLMDIYEFS 358
++++L+ E+ ++ +L + + + E+ LI G + + +F N+ +IY F
Sbjct: 13 RHVMNELLDTERAYVEELLCVLEGYAAEMDNPLMAHLISTGLQNKKNILFGNMEEIYHFH 72
Query: 359 CNLVGILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYAKDITYYKCPEKLLEELKN 418
+ LE C + ++G C E E EF +Y +Y ++ E L + +
Sbjct: 73 NRI---FLRELESCID-CPELVGRCFLERME--EFQIYEKYCQN---KPRSESLWRQCSD 123
Query: 419 PEVSIPLQSDCCAK 432
Q K
Sbjct: 124 CPFFQECQKKLDHK 137
Score = 37.6 bits (87), Expect = 0.009
Identities = 12/63 (19%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 227 EEIVHDLVTDEKQHLRDLHMINKVFLEEI-----VKLIPPGKCKELDQMFANLMDIYEFS 281
++++L+ E+ ++ +L + + + E+ LI G + + +F N+ +IY F
Sbjct: 13 RHVMNELLDTERAYVEELLCVLEGYAAEMDNPLMAHLISTGLQNKKNILFGNMEEIYHFH 72
Query: 282 LNF 284
Sbjct: 73 NRI 75
>3p6a_A RHO guanine nucleotide exchange factor 1; regulation of RHOA
GTPase, rhogef, DH, PH, signaling PR; 2.50A {Homo
sapiens} PDB: 3odo_A
Length = 377
Score = 49.9 bits (119), Expect = 1e-06
Identities = 22/120 (18%), Positives = 48/120 (40%), Gaps = 13/120 (10%)
Query: 305 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSCNLV 362
E++ +L+ E H+R L +++ +F + + + P +EL +F +L ++ E +
Sbjct: 30 EVISELLVTEAAHVRMLRVLHDLFFQPMAECLFFPL---EELQNIFPSLDELIEVHSLFL 86
Query: 363 GILEDNLEMCNEASNVVIGSCLEELAEAAE----FDVYSRYAKDITYYKCPEKLLEELKN 418
L + IG L + AE + SR+ + + L+ +
Sbjct: 87 DRLMKRRQESGYLIE-EIGDVLLARFDGAEGSWFQKISSRF---CSRQSFALEQLKAKQR 142
Score = 44.1 bits (104), Expect = 8e-05
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 228 EIVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSLNF 284
E++ +L+ E H+R L +++ +F + + + P +EL +F +L ++ E F
Sbjct: 30 EVISELLVTEAAHVRMLRVLHDLFFQPMAECLFFPL---EELQNIFPSLDELIEVHSLF 85
>1pb7_A N-methyl-D-aspartate receptor subunit 1; ligand binding receptor,
NR1, ligand binding protein; 1.35A {Rattus norvegicus}
SCOP: c.94.1.1 PDB: 1pbq_A* 1y1m_A 1y1z_A 1y20_A 2a5t_A*
1pb8_A 1pb9_A
Length = 292
Score = 45.0 bits (106), Expect = 3e-05
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKWWKNT 48
SPW+ +SL+IL+ E G ++ L W +
Sbjct: 257 DSPWKQNVSLSILKSHENGFMEDLDKTWVRYQ 288
>2a5s_A N-methyl-D-aspartate receptor nmdar2A subunit, NMDA receptor
nmdar2A; protein-ligand complex, metal
transport,membrane protein; HET: GLU; 1.70A {Rattus
norvegicus} SCOP: c.94.1.1 PDB: 2a5t_B* 3oen_A* 3oel_A*
3oem_A* 3oek_A*
Length = 284
Score = 43.5 bits (102), Expect = 9e-05
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKWWKNT 48
GSPW+ +I LA+L+ G ++ L W
Sbjct: 250 GSPWKRQIDLALLQFVGDGEMEELETLWLTGI 281
>2rc8_A Glutamate [NMDA] receptor subunit 3A; membrane protein, cell
junction, glycoprotein, ION transport channel,
magnesium; 1.45A {Rattus norvegicus} PDB: 2rc7_A 2rc9_A
2rca_A 2rcb_A
Length = 294
Score = 41.2 bits (96), Expect = 5e-04
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKWWK 46
SP IS I + + G + +L+DKW+K
Sbjct: 259 NSPLTSNISELISQYKSHGFMDVLHDKWYK 288
>1jfi_A Transcription regulator NC2 alpha chain; histone, H2A/H2B,
tata-DNA, transcription initiation, NC2, negative
cofactor, structural genomics, PSI; 2.62A {Homo sapiens}
SCOP: a.22.1.3
Length = 98
Score = 31.8 bits (72), Expect = 0.13
Identities = 17/75 (22%), Positives = 29/75 (38%)
Query: 119 SKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAGNYVKNIRH 178
SKKK P +I ++ D KV V + I+ LE +LK A ++
Sbjct: 3 SKKKKYNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNA 62
Query: 179 VEVAQQDIKVAMYAD 193
+ +K + +
Sbjct: 63 KTMTTSHLKQCIELE 77
>3kbr_A Cyclohexadienyl dehydratase; pseudomonas aeruginos structural
genomics, PSI-2, protein structure initiative; HET: EPE;
1.66A {Pseudomonas aeruginosa}
Length = 239
Score = 32.3 bits (74), Expect = 0.27
Identities = 2/31 (6%), Positives = 12/31 (38%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKWWKN 47
++ + + ++ G ++ + W +
Sbjct: 208 DEAFKRYVDQWLHIAEQSGLLRQRMEHWLEY 238
>1ii5_A SLR1257 protein; membrane protein; HET: GLU; 1.60A {Synechocystis
SP} SCOP: c.94.1.1 PDB: 1iit_A 1iiw_A
Length = 233
Score = 31.9 bits (73), Expect = 0.42
Identities = 7/28 (25%), Positives = 13/28 (46%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKW 44
SP + I++ +L L I ++W
Sbjct: 197 NSPLQKTINVEMLNLLYSRVIAEFTERW 224
>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand
binding domain, transport protein; HET: GLU; 2.10A
{Nostoc punctiforme}
Length = 228
Score = 31.1 bits (71), Expect = 0.67
Identities = 16/28 (57%), Positives = 20/28 (71%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKW 44
SP+R I+ A+L L+E GT Q LYDKW
Sbjct: 193 NSPYRKPINQALLNLKENGTYQSLYDKW 220
>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 = 30.3 bits (67), Expect = 0.81
Identities = 9/31 (29%), Positives = 12/31 (38%), Gaps = 8/31 (25%)
Query: 237 EKQHLRDLHMINKVFLEEIVKLIPPGKCKEL 267
EKQ L+ K L+ +KL L
Sbjct: 18 EKQALK------K--LQASLKLYADDSAPAL 40
Score = 30.3 bits (67), Expect = 0.81
Identities = 9/31 (29%), Positives = 12/31 (38%), Gaps = 8/31 (25%)
Query: 314 EKQHLRDLHMINKVFLEEIVKLIPPGKCKEL 344
EKQ L+ K L+ +KL L
Sbjct: 18 EKQALK------K--LQASLKLYADDSAPAL 40
Score = 29.9 bits (66), Expect = 1.1
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 16/44 (36%)
Query: 501 DRESLIQVEGLLKALQVDLSDSLQNYPRNGRDTGIRAL-IDATL 543
++++L +++ LK L D DS P AL I AT+
Sbjct: 18 EKQALKKLQASLK-LYAD--DSA---P---------ALAIKATM 46
>4f3p_A Glutamine-binding periplasmic protein; ssgcid, structural genomics,
GLUT seattle structural genomics center for infectious
disease; 2.40A {Burkholderia pseudomallei}
Length = 249
Score = 30.3 bits (69), Expect = 1.5
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKW 44
GSP +++ + ++ G +Y KW
Sbjct: 213 GSPLVAKVNAELARMKADGRYAKIYKKW 240
>1dkq_A Phytase; histidine acid phosphatase fold, hydrolase; HET: IHP;
2.05A {Escherichia coli} SCOP: c.60.1.2 PDB: 1dkp_A*
1dkm_A 1dkn_A 1dko_A 1dkl_A
Length = 410
Score = 30.3 bits (67), Expect = 1.6
Identities = 27/182 (14%), Positives = 57/182 (31%), Gaps = 16/182 (8%)
Query: 288 PDPLFIHETTSSELTYEEIVHDLVTDEKQHLRDL-HMINKVFLEEIVKLIPPGKCKELDQ 346
P+P + T S + +H+ Q ++ L+ I + P ++
Sbjct: 230 PEPGWGRITDSHQWNTLLSLHNAQFYLLQRTPEVARSRATPLLDLIKTALTPHPPQKQAY 289
Query: 347 MFANLMDIYEFSC------NLVGILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYA 400
+ + NL G LE N + + N G L S++
Sbjct: 290 GVTLPTSVLFIAGHDTNLANLGGALELNWTLPGQPDNTPPGGELV-FERWRRLSDNSQWI 348
Query: 401 KDITYYKCPEKL----LEELKNPEVSIPLQSDCCAKDITYYKCP----EKLLEELKNPEV 452
+ ++ +++ L P + L C + C +++ E + P
Sbjct: 349 QVSLVFQTLQQMRDKTPLSLNTPPGEVKLTLAGCEERNAQGMCSLAGFTQIVNEARIPAC 408
Query: 453 SI 454
S+
Sbjct: 409 SL 410
>2vha_A Periplasmic binding transport protein; periplasmic binding protein,
ligand binding, ultrahigh resolution; HET: GLU; 1.00A
{Shigella flexneri} PDB: 2ia4_A*
Length = 287
Score = 30.0 bits (68), Expect = 1.7
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 20 WRDRISLAILELQEKGTIQMLYDKW 44
++ + I ++Q G + +DKW
Sbjct: 222 FKKLMDDTIAQVQTSGEAEKWFDKW 246
>3k4u_A Binding component of ABC transporter; structural genomics, protein
structure INI NEW YORK structural genomix research
consortium, nysgxrc; HET: LYS; 2.62A {Wolinella
succinogenes}
Length = 245
Score = 29.2 bits (66), Expect = 3.4
Identities = 6/36 (16%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 20 WRDRISLAILELQEKGTIQMLYDKWWKNTGDVLQQV 55
+ + ++ + +++ G+ LY++W+ +T L+++
Sbjct: 202 FLNWLNHFLAQIKHDGSYDELYERWFVDT-KWLEKI 236
>3tql_A Arginine-binding protein; transport and binding proteins, transport
protein; HET: MSE ARG; 1.59A {Coxiella burnetii}
Length = 227
Score = 29.1 bits (66), Expect = 3.5
Identities = 3/24 (12%), Positives = 11/24 (45%)
Query: 21 RDRISLAILELQEKGTIQMLYDKW 44
+++ A+ ++ G + K+
Sbjct: 203 LLKLNKALAAIKANGVYAAIVQKY 226
>1xt8_A Putative amino-acid transporter periplasmic solut protein; ABC
transport, cysteine uptake; 2.00A {Campylobacter jejuni}
SCOP: c.94.1.1
Length = 292
Score = 29.3 bits (66), Expect = 3.5
Identities = 6/27 (22%), Positives = 13/27 (48%)
Query: 20 WRDRISLAILELQEKGTIQMLYDKWWK 46
++ I I++L ++ YD+ K
Sbjct: 239 LKEFIDNLIIKLGQEQFFHKAYDETLK 265
>1b78_A Pyrophosphatase; structural genomics, hyperthermal protein; 2.20A
{Methanocaldococcus jannaschii} SCOP: c.51.4.1 PDB:
2mjp_A*
Length = 193
Score = 28.2 bits (64), Expect = 4.9
Identities = 17/100 (17%), Positives = 34/100 (34%), Gaps = 25/100 (25%)
Query: 338 PGKCKELDQMFANL--MDIYEFSCNLV---GILEDN-LEMCNEASNVVIGSCLEE---LA 388
P K KE + + +L ++I + + G LE+ N++ + E
Sbjct: 18 PNKIKEANIILKDLKDVEIEQIKISYPEIQGTLEEVAEFGAKWVYNILKKPVIVEDSGF- 76
Query: 389 EAAEFD-------VYS-RYAKDITYYKCPEKLLEELKNPE 420
+ YS + I E +L+ L+ +
Sbjct: 77 ---FVEALNGFPGTYSKFVQETIG----NEGILKLLEGKD 109
>3opb_A SWI5-dependent HO expression protein 4; heat and arm fold, myosin
folding and function, myosin bindi protein, protein
binding; 2.90A {Saccharomyces cerevisiae}
Length = 778
Score = 29.0 bits (64), Expect = 5.5
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 488 YIRILRGLSPDKEDRESLIQVEGLLKALQVDLSDSLQNYPRNGRDTGIRAL 538
+RI+ ++ K L Q +G +K + ++ + Q+ R G RAL
Sbjct: 477 VVRIIYNITRSKNFIPQLAQ-QGAVKII-LEYLANKQDIGEPIRILGCRAL 525
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 28.2 bits (62), Expect = 5.8
Identities = 7/35 (20%), Positives = 12/35 (34%), Gaps = 5/35 (14%)
Query: 93 EERVRRQFPTPIDKWAMH-----EAKEAIEKSKKK 122
+ Q P I KW + +A K ++
Sbjct: 76 QADRLTQEPESIRKWREEQRKRLQELDAASKVMEQ 110
>2y7i_A STM4351; arginine-binding protein; HET: ARG; 1.90A {Salmonella
enterica subsp}
Length = 229
Score = 28.3 bits (64), Expect = 6.0
Identities = 4/24 (16%), Positives = 11/24 (45%)
Query: 21 RDRISLAILELQEKGTIQMLYDKW 44
I+ A+ +++ + +KW
Sbjct: 203 LQEINAALDKVKASPEYAQMQEKW 226
>1tlq_A Hypothetical protein YPJQ; structural genomics, NYSGXRC, T1519
protein structure initiative, NEW YORK SGX research
center structural genomics; 2.40A {Bacillus subtilis}
SCOP: a.195.1.1
Length = 189
Score = 27.9 bits (62), Expect = 6.1
Identities = 7/39 (17%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 384 LEELAEAAEFDVYSRYAKDITYYKCPEKLLEELKNPEVS 422
+E++A + +Y ++ C E + + L E+
Sbjct: 26 IEDIARIV-QKLQEKYNPNLPLSVCMENVEKVLNKREII 63
>2pvu_A ARTJ; basic amino acid binding protein, ABC transport system, THER
bacterium, transport protein; HET: LYS; 1.79A
{Geobacillus stearothermophilus} PDB: 2q2a_A* 2q2c_A*
Length = 272
Score = 28.1 bits (63), Expect = 6.4
Identities = 6/28 (21%), Positives = 12/28 (42%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKW 44
S + ++ A+ + G +Y KW
Sbjct: 233 NSELKAKVDEALKNVINSGKYTEIYKKW 260
>3qax_A Probable ABC transporter arginine-binding protein; periplasmic,
transport PR; HET: ARG; 2.00A {Chlamydophila pneumoniae}
PDB: 3g41_A* 3n26_A*
Length = 268
Score = 28.1 bits (63), Expect = 6.7
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 21 RDRISLAILELQEKGTIQMLYDKW 44
I AI +L+ +G IQ L KW
Sbjct: 228 IQTIQQAITDLKSEGVIQSLTKKW 251
>1lst_A Lysine, arginine, ornithine-binding protein; amino-acid binding
protein; HET: LYS; 1.80A {Salmonella typhimurium} SCOP:
c.94.1.1 PDB: 2lao_A 1lag_E* 1lah_E 1laf_E 1hsl_A*
1hpb_P*
Length = 239
Score = 28.0 bits (63), Expect = 6.9
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 21 RDRISLAILELQEKGTIQMLYDKW 44
+ A+ EL++ GT + K+
Sbjct: 207 KAAFDKALTELRQDGTYDKMAKKY 230
>3i6v_A Periplasmic His/Glu/Gln/Arg/opine family-binding; structural
genomics, transporter, PSI-2, protein structure
initiative; HET: LYS; 2.00A {Silicibacter pomeroyi}
Length = 232
Score = 27.9 bits (63), Expect = 7.4
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 21 RDRISLAILELQEKGTIQMLYDKW 44
R + AI ++E GT+ + KW
Sbjct: 192 RGKFDAAITSMKEDGTLNTMIKKW 215
>3del_B Arginine binding protein; alpha and beta protein (A/B), periplasmic
protein, arginine protein binding, transport protein;
1.92A {Chlamydia trachomatis}
Length = 242
Score = 27.6 bits (62), Expect = 9.0
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 21 RDRISLAILELQEKGTIQMLYDKW 44
+I A+ E++++G + L KW
Sbjct: 207 ALKIEAAVQEIRKEGVLAELEQKW 230
>1vp2_A Putative xanthosine triphosphate pyrophosphatase/ protein homolog;
structural genomics, joint center for structural
genomics, JCSG; 1.78A {Thermotoga maritima} SCOP:
c.51.4.1
Length = 208
Score = 27.5 bits (62), Expect = 9.2
Identities = 6/27 (22%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 395 VYS-RYAKDITYYKCPEKLLEELKNPE 420
V S R+ ++ +Y + +L+ L+ +
Sbjct: 94 VMSARFMEEHSYKEKMRTILKMLEGKD 120
>3kzg_A Arginine 3RD transport system periplasmic binding protein; arginine
transport system, protein structure initiative II(PSI
II); 2.06A {Legionella pneumophila subsp}
Length = 237
Score = 27.6 bits (62), Expect = 9.3
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 21 RDRISLAILELQEKGTIQMLYDKW 44
+I+ +LE++ GT LY ++
Sbjct: 205 IKKINKILLEMEADGTYLRLYSEY 228
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
0.320 0.136 0.398
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,616,140
Number of extensions: 536228
Number of successful extensions: 1214
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1147
Number of HSP's successfully gapped: 103
Length of query: 551
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 453
Effective length of database: 3,965,535
Effective search space: 1796387355
Effective search space used: 1796387355
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 (21.8 bits)
S2: 60 (26.8 bits)