RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 026316
(240 letters)
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 243
Score = 296 bits (760), Expect = e-102
Identities = 185/241 (76%), Positives = 195/241 (80%), Gaps = 9/241 (3%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
MA QISKKRKFVADG+F AELNE LTRELAEDGYSGVEVRVTP RTEIII ATRTQNVLG
Sbjct: 1 MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG 60
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACY 120
EKGRRIRELT+VVQKRF FPE SVELYAEKV RGLCAIAQAESLRYKLLGGLAVRRACY
Sbjct: 61 EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY 120
Query: 121 GVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDSAV 180
GVLRFIMESGAKGC +V+VSGKLR QRAKSMKF DG MI SG PVN Y+D+AV
Sbjct: 121 GVLRFIMESGAKGC--------EVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAV 172
Query: 181 RHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEEV-YVAPATATSIELPV 239
RHVLLRQGVLGIKVKIML WD GK GP PLPD V+I K+E+ P + P
Sbjct: 173 RHVLLRQGVLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPE 232
Query: 240 A 240
Sbjct: 233 P 233
>3iz6_B 40S ribosomal protein S3 (S3P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
1s1h_C 3jyv_C*
Length = 227
Score = 295 bits (758), Expect = e-102
Identities = 201/235 (85%), Positives = 212/235 (90%), Gaps = 8/235 (3%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
MATQISKK+KFV+DGVF+AELNE+LTRELAEDGYSGVEVRVTP+RTEIIIRATRTQNVLG
Sbjct: 1 MATQISKKKKFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG 60
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACY 120
EKGRRIRELTSVVQKRF F EN VELYAEKV NRGLCAIAQAESLRYKLLGGLAVRRACY
Sbjct: 61 EKGRRIRELTSVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACY 120
Query: 121 GVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDSAV 180
GVLRF+MESGAKGC +VIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYID+AV
Sbjct: 121 GVLRFVMESGAKGC--------EVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAV 172
Query: 181 RHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEEVYVAPATATSI 235
RHVLLRQGVLGIKVKIML+WD KGK GPTTPLPDLVTIHP KEE + P +
Sbjct: 173 RHVLLRQGVLGIKVKIMLDWDPKGKLGPTTPLPDLVTIHPPKEENELRPPALVEV 227
>2xzm_C KH domain containing protein; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_C
Length = 243
Score = 295 bits (756), Expect = e-102
Identities = 113/241 (46%), Positives = 164/241 (68%), Gaps = 11/241 (4%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
I+KK+KFVADGVF AEL+ ++ L + GY+G+EVR TP +TEI I+AT+ Q V+G
Sbjct: 4 TTRAINKKKKFVADGVFNAELHSFFSKSLQDAGYAGIEVRRTPTKTEIRIKATKPQQVIG 63
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACY 120
+G++ +ELT +QKRF + ++ ++++AE + +GLCA AQ E++ YKLL + VR A
Sbjct: 64 VEGKKHKELTQFLQKRFGYSDDQIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVRLAAN 123
Query: 121 GVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDSAV 180
+++ +++ GAKGC ++I+SGKL+ QRAK+MKFK GYMI +GQP N+YID AV
Sbjct: 124 YIIKSVIQDGAKGC--------EIIISGKLKQQRAKTMKFKQGYMICTGQPKNDYIDVAV 175
Query: 181 RHVLLRQGVLGIKVKIMLEWD--QKGKQGPTTPLPDLVTIHPLKEE-VYVAPATATSIEL 237
RHV +QG++G+KVKIML ++ K G TP+PD V IHP K+ TA +
Sbjct: 176 RHVFFKQGIMGVKVKIMLPYEPNPAKKFGVKTPIPDNVIIHPPKQITDDKEIRTAVEQQQ 235
Query: 238 P 238
P
Sbjct: 236 P 236
>3u5c_D RP13, YS3, 40S ribosomal protein S3; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_B 3o30_C 3o2z_C 3u5g_D 1s1h_C
3jyv_C*
Length = 240
Score = 289 bits (741), Expect = e-100
Identities = 149/236 (63%), Positives = 180/236 (76%), Gaps = 10/236 (4%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
M ISKKRK VADGVF+AELNE TRELAE+GYSGVEVRVTP +TE+IIRATRTQ+VLG
Sbjct: 1 MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG 60
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACY 120
E GRRI ELT +VQKRFK+ ++ LYAE+V +RGL A+AQAES+++KLL GLA+RRA Y
Sbjct: 61 ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAY 120
Query: 121 GVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDSAV 180
GV+R++MESGAKGC +V+VSGKLRA RAK+MKF DG++I SGQPVN++ID+A
Sbjct: 121 GVVRYVMESGAKGC--------EVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTAT 172
Query: 181 RHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEEVYVAPATATSIE 236
RHVL+RQGVLGIKVKIM D + LPD VTI KEE + +
Sbjct: 173 RHVLMRQGVLGIKVKIM--RDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDYR 226
>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI,
ribosome; NMR {Homo sapiens} SCOP: d.52.3.1
Length = 92
Score = 132 bits (333), Expect = 5e-40
Identities = 70/89 (78%), Positives = 72/89 (80%)
Query: 12 VADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTS 71
F AELNE LTRELAEDGYSGVEVRVTP RTEIII ATRTQNVLGEKGRRIRELT+
Sbjct: 3 SGSSGFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTA 62
Query: 72 VVQKRFKFPENSVELYAEKVNNRGLCAIA 100
VVQKRF FPE SVELYAEKV RG +
Sbjct: 63 VVQKRFGFPEGSVELYAEKVATRGSGPSS 91
>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 = 45.8 bits (108), Expect = 7e-06
Identities = 38/257 (14%), Positives = 65/257 (25%), Gaps = 106/257 (41%)
Query: 25 LTRELAEDGYSGVEV---RVTPVRTEIIIRA-----TRTQN--------------VLGEK 62
+ E DG E + T R+ + TQ L K
Sbjct: 1691 MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSK 1750
Query: 63 GRR-------------------------IRELTSVVQKRFKFPENSVELYAEKVNNRGLC 97
G I L VV R + +V +N G+
Sbjct: 1751 GLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMI 1810
Query: 98 AIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKG----CE---FNFLVSSKVIV-SGK 149
AI G L++++E K E +N V ++ V +G
Sbjct: 1811 AIN----------PGRVAASFSQEALQYVVERVGKRTGWLVEIVNYN--VENQQYVAAGD 1858
Query: 150 LRAQRAKSMKFKDGYMISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPT 209
LRA +D+ VL + I +
Sbjct: 1859 LRA-----------------------LDTVTN-VLNFIKLQKIDII-------------- 1880
Query: 210 TPLPDLVTIHPLKEEVY 226
L +++ ++ ++
Sbjct: 1881 -ELQKSLSLEEVEGHLF 1896
Score = 45.0 bits (106), Expect = 1e-05
Identities = 44/236 (18%), Positives = 71/236 (30%), Gaps = 98/236 (41%)
Query: 13 ADGVFFAELNEVLTRELAEDGYSGVE-VRVTPVRTEIIIRATRTQNVLGEKGRRIRELTS 71
AD F G+S ++ V P + I GEKG+RIRE S
Sbjct: 1649 ADNHFKDTY-----------GFSILDIVINNP--VNLTIHFG------GEKGKRIRENYS 1689
Query: 72 V----------VQKRFKFPE-----NSVELYAEKVNNRGLC---AIAQ-AESLRYKLLGG 112
++ F E S +EK GL Q A L
Sbjct: 1690 AMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEK----GLLSATQFTQPA--L------- 1736
Query: 113 LAVRRACYGVLR--FIMESGAK------GCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGY 164
+ +A + L+ ++ + A G E+ L S A M +
Sbjct: 1737 TLMEKAAFEDLKSKGLIPADATFAGHSLG-EYAALASL------------ADVMSIES-- 1781
Query: 165 MISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHP 220
V V R G+ +++ + D+ G+ ++ I+P
Sbjct: 1782 --------------LVEVVFYR----GMTMQVAVPRDELGRSN-----YGMIAINP 1814
Score = 31.2 bits (70), Expect = 0.36
Identities = 27/175 (15%), Positives = 55/175 (31%), Gaps = 62/175 (35%)
Query: 8 KRKFVADGVF------F-----AELNEVLTRELAEDG--YSGVEVRVTPVRTEIIIRATR 54
+RK F F ++++ ++L ++ ++ ++++ PV T
Sbjct: 411 ERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQI-PVY------DTF 463
Query: 55 TQNVLGEKGRRIRELTSVVQKR-----FKFP---ENSVELYAEKVNNRGLCAIAQAESLR 106
G +R L+ + +R + P E + + A + + G + L
Sbjct: 464 D-------GSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLT 516
Query: 107 YKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFK 161
++ G VR VIV+G L FK
Sbjct: 517 HRNKDGTGVR---------------------------VIVAGTLDINPDDDYGFK 544
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 218
Score = 44.5 bits (106), Expect = 7e-06
Identities = 30/192 (15%), Positives = 72/192 (37%), Gaps = 22/192 (11%)
Query: 7 KKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
K R + + + +G + +E++ ++II + ++ + + +
Sbjct: 38 KIRDCI-----KNYVQKNTKTSSGVEGIARIEIQKRIDLIQVIIHMGFPKLLIENRPQGV 92
Query: 67 RELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFI 126
+L VQK + + ++ AE + +L ++ R+A +
Sbjct: 93 EDLKINVQKELNCVNRKLNIAITRIAKPYGDPNILAEFIAGQLKSRVSFRKAMKKAIELT 152
Query: 127 MESGAKGCEFNFLVSSKVIVSGKLR-AQRAKSMKFKDGYMISSGQPVNEY---IDSAVRH 182
++ KG ++ ++G++ + A+ ++G + P+ ID
Sbjct: 153 EQADTKGI--------QIQIAGRIDGKEIARIEWIREGRV-----PLQTIRAKIDYCAYT 199
Query: 183 VLLRQGVLGIKV 194
V GVLGIK+
Sbjct: 200 VRTIYGVLGIKI 211
>3r8n_C 30S ribosomal protein S3; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2gyb_C 2gy9_C* 2ykr_C 3fih_C* 2wwl_C 3oar_C
3oaq_C 3ofb_C 3ofa_C 3ofp_C 3ofx_C 3ofy_C 3ofo_C 3r8o_C
4a2i_C
Length = 206
Score = 43.7 bits (104), Expect = 1e-05
Identities = 47/179 (26%), Positives = 78/179 (43%), Gaps = 20/179 (11%)
Query: 23 EVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPEN 82
+ LT+ELA+ S + + + I R V+G+KG + +L VV
Sbjct: 40 QYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAG---V 96
Query: 83 SVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSS 142
++ +V L A A+S+ +L + RRA ++ M GAKG
Sbjct: 97 PAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGI-------- 148
Query: 143 KVIVSGKLR-AQRAKSMKFKDGYMISSGQPVNEY---IDSAVRHVLLRQGVLGIKVKIM 197
KV VSG+L A+ A++ +++G + P++ ID GV+G+KV I
Sbjct: 149 KVEVSGRLGGAEIARTEWYREGRV-----PLHTLRADIDYNTSEAHTTYGVIGVKVWIF 202
>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C
3i1q_C 3i1s_C 3i1z_C 3i21_C 3izv_G* 3izw_G* 3kc4_C
3or9_C 3ora_C 3sfs_C* 3uoq_C* 2qal_C* 1p6g_C 1p87_C
2aw7_C ...
Length = 233
Score = 43.0 bits (102), Expect = 2e-05
Identities = 47/179 (26%), Positives = 78/179 (43%), Gaps = 20/179 (11%)
Query: 23 EVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPEN 82
+ LT+ELA+ S + + + I R V+G+KG + +L VV
Sbjct: 41 QYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAG---V 97
Query: 83 SVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSS 142
++ +V L A A+S+ +L + RRA ++ M GAKG
Sbjct: 98 PAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGI-------- 149
Query: 143 KVIVSGKLR-AQRAKSMKFKDGYMISSGQPVNEY---IDSAVRHVLLRQGVLGIKVKIM 197
KV VSG+L A+ A++ +++G + P++ ID GV+G+KV I
Sbjct: 150 KVEVSGRLGGAEIARTEWYREGRV-----PLHTLRADIDYNTSEAHTTYGVIGVKVWIF 203
>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C*
1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F*
1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C
1xmo_C* 1xmq_C* 1xnq_C* ...
Length = 239
Score = 43.0 bits (102), Expect = 2e-05
Identities = 50/179 (27%), Positives = 80/179 (44%), Gaps = 20/179 (11%)
Query: 23 EVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPEN 82
+L +EL G + V++ + + + V+G G RIR L + K
Sbjct: 41 GLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTG---K 97
Query: 83 SVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSS 142
+V L ++V N L A A+ + ++ AVRRA ++ +MESGAKG
Sbjct: 98 NVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGA-------- 149
Query: 143 KVIVSGKLR-AQRAKSMKFKDGYMISSGQPVNEY---IDSAVRHVLLRQGVLGIKVKIM 197
KVIVSG++ A++A++ G + P++ ID GVLG+K I
Sbjct: 150 KVIVSGRIGGAEQARTEWAAQGRV-----PLHTLRANIDYGFALARTTYGVLGVKAYIF 203
>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 = 32.6 bits (73), Expect = 0.046
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 15/44 (34%)
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAI-AQAE 103
EK + +++L + S++LYA+ + L AI A E
Sbjct: 18 EK-QALKKL-----------QASLKLYADD-SAPAL-AIKATME 47
Score = 28.4 bits (62), Expect = 1.3
Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 7/21 (33%)
Query: 221 LKEEVYV---APATA--TSIE 236
LK +Y APA A ++E
Sbjct: 29 LK--LYADDSAPALAIKATME 47
>4e4f_A Mannonate dehydratase; magnesium binding, enzyme function
initiative, isomerase; 2.00A {Pectobacterium carotovorum
subsp}
Length = 426
Score = 28.7 bits (65), Expect = 1.7
Identities = 17/109 (15%), Positives = 29/109 (26%), Gaps = 18/109 (16%)
Query: 107 YKLLGGLAVRRA--CYG------------VLRFIMESGAKGCEFNFLVSSKVIVSGKLRA 152
Y+LLGG A R Y + G K V G +
Sbjct: 128 YQLLGG-ASRTGVMVYCHTTGHSIDEVLDDYAKHRDQGFKAIRVQCGVPGMETTYGMAKG 186
Query: 153 QRAKSMKFKDGYMISSGQPV-NEYIDSAVRHV-LLRQGVLGIKVKIMLE 199
+ G + +Y+D + +R G ++ +
Sbjct: 187 KGLAYEPATKGSLPEEQLWSTEKYLDFTPKLFEAVRDKF-GFNEHLLHD 234
>1wpw_A 3-isopropylmalate dehydrogenase; oxidoreductase; 2.80A {Sulfolobus
tokodaii} SCOP: c.77.1.1
Length = 336
Score = 27.9 bits (63), Expect = 2.7
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 6/43 (13%)
Query: 24 VLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
++ RE ED Y G E V+ + TR RI
Sbjct: 113 LIVRENTEDLYKGFEHIVSDGVAVGMKIITR------FASERI 149
>1r0m_A N-acylamino acid racemase; isomerase; 1.30A {Deinococcus
radiodurans} SCOP: c.1.11.2 d.54.1.1 PDB: 1xpy_A* 1xs2_A
2ggj_A 2ggi_A 2ggh_A* 2ggg_A* 2fkp_A
Length = 375
Score = 28.0 bits (63), Expect = 3.2
Identities = 13/39 (33%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 163 GYMISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWD 201
G + +D RHV QG IK+KI WD
Sbjct: 140 GVSLGIQADEQATVDLVRRHV--EQGYRRIKLKIKPGWD 176
>1wuf_A Hypothetical protein LIN2664; structural genomics, unknown
function, nysgxrc target T2186, superfamily, protein
structure initiative, PSI; 2.90A {Listeria innocua}
SCOP: c.1.11.2 d.54.1.1
Length = 393
Score = 27.7 bits (62), Expect = 3.3
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 163 GYMISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWD 201
G I Q V + ++V QG +K+KI D
Sbjct: 153 GVSIGLQQNVETLLQLVNQYV--DQGYERVKLKIAPNKD 189
>1sjd_A N-acylamino acid racemase; lyase, isomerase; HET: NPG; 1.87A
{Amycolatopsis SP} SCOP: c.1.11.2 d.54.1.1 PDB: 1sja_A*
1sjb_A* 1sjc_A*
Length = 368
Score = 27.6 bits (62), Expect = 3.3
Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 163 GYMISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWD 201
G + + + +D ++ +G + IK+KI WD
Sbjct: 133 GVSVGIMDTIPQLLDVVGGYL--DEGYVRIKLKIEPGWD 169
>1wue_A Mandelate racemase/muconate lactonizing enzyme FA protein;
structural genomics, unknown function, nysgxrc target
T2185; 2.10A {Enterococcus faecalis} SCOP: c.1.11.2
d.54.1.1
Length = 386
Score = 27.6 bits (62), Expect = 3.4
Identities = 7/39 (17%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 163 GYMISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWD 201
G + + + + + V +G +K+KI +D
Sbjct: 153 GISLGIQEDLPQLLKQVQLAV--EKGYQRVKLKIRPGYD 189
>2ab1_A Hypothetical protein; HS.95870, DUF498, structural genomics,
protein structure INI PSI, center for eukaryotic
structural genomics, CESG; 2.59A {Homo sapiens} SCOP:
c.103.1.1 PDB: 2q4q_A
Length = 122
Score = 26.0 bits (57), Expect = 6.6
Identities = 8/31 (25%), Positives = 12/31 (38%), Gaps = 7/31 (22%)
Query: 36 GVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
V V T +A + N L +G R+
Sbjct: 91 DVRVLQTE-------QAVKEYNALVAQGVRV 114
>3blx_A Isocitrate dehydrogenase [NAD] subunit 1; TCA cycle, oxidative
metabolism, allostery, decarboxylase, allosteric enzyme,
magnesium; 2.70A {Saccharomyces cerevisiae} PDB: 3blw_A
3blv_A*
Length = 349
Score = 26.8 bits (60), Expect = 7.0
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 6/43 (13%)
Query: 24 VLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
++ RE E +SG+E P E + TR K RI
Sbjct: 126 IVIRENTEGEFSGLEHESVPGVVESLKVMTR------PKTERI 162
>3mkc_A Racemase; metabolic process, PSI2, NYSGXRC, structu genomics,
protein structure initiative, NEW YORK SGX resear for
structural genomics; 1.77A {Pseudovibrio SP} PDB: 3nzg_A
Length = 394
Score = 26.5 bits (59), Expect = 8.0
Identities = 15/96 (15%), Positives = 29/96 (30%), Gaps = 14/96 (14%)
Query: 107 YKLLGGLAVRRA--CYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGY 164
Y+LLGG + Y L + A I ++AK+
Sbjct: 127 YQLLGG-TNKDKVHPYLTLYPAIPVDA--------SLDVAIKGYAPLLEKAKAHNI-RAV 176
Query: 165 MISSGQPVNEYIDSAVRHV-LLRQGVLGIKVKIMLE 199
+ + ++ LR + G +M++
Sbjct: 177 KVCVPIKADWSTKEVAYYLRELRGIL-GHDTDMMVD 211
>3stp_A Galactonate dehydratase, putative; PSI biology, structural
genomics, NEW YORK structural genomi research
consortium; 1.88A {Labrenzia aggregata iam 12614} PDB:
3sqs_A 3ssz_A
Length = 412
Score = 26.5 bits (59), Expect = 9.1
Identities = 20/98 (20%), Positives = 35/98 (35%), Gaps = 23/98 (23%)
Query: 107 YKLLGGLAVR---RA-CYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKD 162
+KLLGG + + +E+ K E + K+ K +
Sbjct: 157 FKLLGG-RTKDRIPVYYSKLYAGSIEAMQKEAE-------------EAMKGGYKAFKSRF 202
Query: 163 GYMISSGQPVNEYIDSAVRHV-LLRQGVLGIKVKIMLE 199
GY G + ++ V +R+ V+G +MLE
Sbjct: 203 GYGPKDGM---PGMRENLKRVEAVRE-VIGYDNDLMLE 236
>1wyu_A Glycine dehydrogenase (decarboxylating) subunit 1; alpha(2)beta(2)
tetramer, riken structural genomics/proteomi initiative,
RSGI; HET: PLP; 2.10A {Thermus thermophilus} SCOP:
c.67.1.7 PDB: 1wyt_A* 1wyv_A*
Length = 438
Score = 26.4 bits (59), Expect = 9.2
Identities = 8/61 (13%), Positives = 17/61 (27%), Gaps = 5/61 (8%)
Query: 1 MATQISKKRKFVADGVFFAELNEVL-TRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVL 59
+A + + + + E VL E G ++ P+ + V
Sbjct: 143 LALRETGRMGVLVSQGVHPEYRAVLRAY--LE--AVGAKLLTLPLEGGRTPLPEVGEEVG 198
Query: 60 G 60
Sbjct: 199 A 199
>2zc8_A N-acylamino acid racemase; octamer, TIM beta/alpha-barrel,
metal-binding, metal binding; 1.95A {Thermus
thermophilus}
Length = 369
Score = 26.5 bits (59), Expect = 9.8
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 163 GYMISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWD 201
G + V + + RH+ +G IK+KI WD
Sbjct: 133 GVSLGIQPSVEDTLRVVERHL--EEGYRRIKLKIKPGWD 169
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 0.380
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,637,169
Number of extensions: 221330
Number of successful extensions: 500
Number of sequences better than 10.0: 1
Number of HSP's gapped: 484
Number of HSP's successfully gapped: 38
Length of query: 240
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 149
Effective length of database: 4,160,982
Effective search space: 619986318
Effective search space used: 619986318
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: 56 (25.3 bits)