RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2632
(374 letters)
>3pqv_A RCL1 protein; RTC-like, cyclase-like, modular, alpha-beta, anion
pocket, R biogenesis, unknown function; HET: TAR; 2.61A
{Kluyveromyces lactis}
Length = 365
Score = 299 bits (766), Expect = e-100
Identities = 73/355 (20%), Positives = 137/355 (38%), Gaps = 12/355 (3%)
Query: 21 GGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQGRLENAHIGST 80
G + R+ +V + L + I + IR+ + PGL ++ L + + + G T
Sbjct: 13 GSRNFRLRVVMATLSGKAIKIEKIRSDDLNPGLKDYEVSFLRLMEAVTNGSSIEISYTGT 72
Query: 81 EIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGGTNADMAPPIDY 140
+IF PG IT G++ + V + L L FS + ++ +G T++ ID
Sbjct: 73 TVIFRPGIITGGSYTHQCPNSKPVGYFAEPMLYLAPFSKKKFSILFRGITSSHNDAGIDA 132
Query: 141 YIHLWRPVFCHFFNFNIDIHDVRRGFFPKGGGEVNVDVTPVQY-IRPIELTQRGELTAVW 199
P+ F +H ++RG P GGGEV++ V + + + ++++
Sbjct: 133 IKWGLMPIMEKFGVRECALHTLKRGSPPLGGGEVHLVVDSLIAQPITMHALDKTMISSIR 192
Query: 200 GHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITT-YQLSSDKAIGNGSGVYIFA 258
G ++ V + M D A L + + + IT + G G+ + A
Sbjct: 193 GVSYST-RVSPSLVNRMIDGAKKVLKSASCE----VNITADVWRGENSGKSPGWGLTLVA 247
Query: 259 ATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQDQLIVMMALAK--- 315
G R G P + G + A L + ++ + I+ M + K
Sbjct: 248 ENKQGWRIFSEAIGDAGDVPEDIGASVAYHLLEEISKSGVVGRNQLPLTILYMIIGKEDI 307
Query: 316 GTSRVRVGQISLHTRTAIHIAELMTSAKFNIIEHEDKS--CIIECQGMGFVNKNW 368
G R+ QI + + + + + +D + I +G+GF N N
Sbjct: 308 GRLRITKDQIDERFVWLLRDIKKVFGTEILLKPVDDNTTDLIATIKGIGFTNTNK 362
>3tut_A RNA 3'-terminal phosphate cyclase; cyclase family, cyclization of
RNA 3'-phosphate ENDS, transf; HET: ATP; 1.58A
{Escherichia coli} PDB: 3tux_A* 3tv1_A* 3tw3_A* 3kgd_A*
1qmh_A* 1qmi_A
Length = 358
Score = 294 bits (754), Expect = 4e-98
Identities = 105/352 (29%), Positives = 163/352 (46%), Gaps = 15/352 (4%)
Query: 8 PDVLNIDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDI 67
++ +DG+ EGGGQILR A+ S + +P + +IRAGR KPGL QHL + A +I
Sbjct: 22 KRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEI 81
Query: 68 CQGRLENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVK 127
C +E A +GS ++F PG + G++ +AGS TL++Q LP L F+ G S++ V
Sbjct: 82 CGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVS 141
Query: 128 GGTNADMAPPIDYYIHLWRPVFCHFFNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPI 187
GGT+ APP D+ + P+ + +R GF+P GGG V +V+PV +
Sbjct: 142 GGTDNPSAPPADFIRRVLEPLLAK-IGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTL 200
Query: 188 ELTQRGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKA 247
+L +RG + + G +A GV + A+ T + + L D+
Sbjct: 201 QLGERGNIVQMRGEVLLA-GVPRHVAEREIATLAGSFSLHEQNI--------HNLPRDQG 251
Query: 248 IGNGSGVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQDQL 307
GN + S G R S KE+ L E+ DQL
Sbjct: 252 PGNTVSLE---VESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQL 308
Query: 308 IVMMALAKGTSRVRVGQISLHTRTAIHIAELMTSAKFNIIEHEDKSCIIECQ 359
++ MALA G V S + T I + E +F++IE + + + +
Sbjct: 309 VLPMALA-GAGEFTVAHPSSNLLTNIAVVERFLPVRFSLIETDGVT-RVSIE 358
>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 = 37.7 bits (87), Expect = 0.007
Identities = 66/387 (17%), Positives = 111/387 (28%), Gaps = 151/387 (39%)
Query: 23 QILRMAMV-F-SGLLH-RPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQ---------G 70
Q+L + + F + L IH A + L ++ L+ K++ +
Sbjct: 82 QVLNLCLTEFENCYLEGNDIHAL---AAK----LLQENDTTLVKTKELIKNYITARIMAK 134
Query: 71 R----------LENAHIGSTEI--IFYPGNITSGN----------FYADSKTAGSVTLIM 108
R G+ ++ IF G GN Y V ++
Sbjct: 135 RPFDKKSNSALFRAVGEGNAQLVAIF-GGQ---GNTDDYFEELRDLYQTYHVL--VGDLI 188
Query: 109 QVALPLL------------LFSSGQSQLIVKGGTNADMAPPIDYYIHLWRPV-------- 148
+ + L +F+ G + I++ N P DY + + P+
Sbjct: 189 KFSAETLSELIRTTLDAEKVFTQGLN--ILEWLENPSNTPDKDYLLSI--PISCPLIGVI 244
Query: 149 -FCHFFNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQRGELTAVWGHAFVAGG 207
H+ K G P EL R L GH G
Sbjct: 245 QLAHYVV------------TAKLLG-----------FTPGEL--RSYLKGATGH--SQGL 277
Query: 208 VKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKAIGNGSGVYIFAATSTGARYS 267
V TA +A S+ F + KAI +F G R
Sbjct: 278 V---TAVAIA------ETDSWESF--------FVS-VRKAI-----TVLF---FIGVR-- 309
Query: 268 GGCNGS-PRTSPGECGLNAAKELWSSLCENICFDEHTQDQLIVMMALAKGTSRVRVGQI- 325
C + P TS L SL E+ + M+++ ++ +V
Sbjct: 310 --CYEAYPNTSL------PPSILEDSL-------ENNEGVPSPMLSI-SNLTQEQVQDYV 353
Query: 326 -----SLHTRTAIHIAELMTSAKFNII 347
L + I+ L+ AK ++
Sbjct: 354 NKTNSHLPAGKQVEIS-LVNGAKNLVV 379
>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 = 35.6 bits (81), Expect = 0.026
Identities = 45/315 (14%), Positives = 90/315 (28%), Gaps = 102/315 (32%)
Query: 12 NIDGSVLEGGGQILRMAMVFSGLLH-RPIHVFNI--RAGRVKPGL-----AAQHLNGLIV 63
N +VLE + ++ R H NI R ++ L + + N L+V
Sbjct: 193 NSPETVLE---MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV 249
Query: 64 AKDICQGRLENA-HIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQS 122
++ + NA ++ ++ T D +A + T I + + +
Sbjct: 250 LLNVQNAKAWNAFNLSCKILL-----TTRFKQVTDFLSAATTTHISLDHHS-MTLTPDEV 303
Query: 123 -QLIVKG-GTNADMAPP-----------------------IDYYIHLWRPVFCHFFNFNI 157
L++K P D + H+ ++
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL 363
Query: 158 DI---HDVRRGF-----FPKGGGEVNVDVTPVQYIRPIELTQRGELTAVWGHAFVAGGVK 209
++ + R+ F FP + + P L L+ +W V
Sbjct: 364 NVLEPAEYRKMFDRLSVFPP-----SAHI-------PTIL-----LSLIW------FDVI 400
Query: 210 MNTAQTMADTAYDY-LVK--------SYPD--FKTKLK-----------ITTYQL----- 242
+ + + + Y LV+ S P + K+K + Y +
Sbjct: 401 KSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD 460
Query: 243 SSDKAIGNGSGVYIF 257
S D Y +
Sbjct: 461 SDDLIPPYLDQ-YFY 474
Score = 33.7 bits (76), Expect = 0.12
Identities = 27/169 (15%), Positives = 49/169 (28%), Gaps = 57/169 (33%)
Query: 140 YYIH-LWRPVFCHFFNFNIDIH-------DVRRGFFPKGGGEVNVDVTPVQYI------- 184
I ++ + N +H ++ + F +D QY
Sbjct: 426 ISIPSIYLELKVKLEN-EYALHRSIVDHYNIPKTFDSDDLIPPYLD----QYFYSHIGHH 480
Query: 185 -RPIELTQRGELTAVW--------------GHAFVAGGVKMNTAQ---------TMADTA 220
+ IE +R L + A+ A G +NT Q D
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPK 540
Query: 221 YDYLVKSYPDF----KTKLKITTY----QLSSDKAIGN-GSGVYIFAAT 260
Y+ LV + DF + L + Y ++ A+ ++ A
Sbjct: 541 YERLVNAILDFLPKIEENLICSKYTDLLRI----ALMAEDEAIFEEAHK 585
>2fkb_A Putative nudix hydrolase YFCD; putative protein, MAD, structural
genomics, escherichia coli putative nudix hydrolase,
PSI; HET: MSE; 2.00A {Escherichia coli K12} SCOP:
d.113.1.2
Length = 180
Score = 31.6 bits (72), Expect = 0.22
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 9 DVLNIDGSVLEGGGQILRMAMVFSGLLHRPIHVF 42
D++N + V+ Q R M L HR ++
Sbjct: 13 DIVNEENEVI---AQASREQMRAQCLRHRATYIV 43
>1q27_A Putative nudix hydrolase DR0079; radiation resistance; NMR
{Deinococcus radiodurans} SCOP: d.113.1.2 PDB: 2o5f_A
Length = 171
Score = 30.8 bits (70), Expect = 0.44
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 9 DVLNIDGSVLEGGGQILRMAMVFSGLLHRPIHVF 42
D++N V+ GQILR R ++ F
Sbjct: 10 DLVNERDEVV---GQILRTDPALRWERVRVVNAF 40
>3npi_A TETR family regulatory protein; structural genomics, joint center
for structural genomics, J protein structure initiative,
PSI; 2.96A {Corynebacterium diphtheriae}
Length = 251
Score = 30.9 bits (70), Expect = 0.48
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 44 IRAGRVKPGLAAQHLNGLIVAKDICQGRLENAHIGST 80
AG +PG++AQ + LI + I R+ +
Sbjct: 151 QDAGAFRPGISAQDVFTLIAS--IAVFRINSRSTTLN 185
>2pz9_A Putative regulatory protein; structural genomics, transcriptional
regulator, PSI, protein structure initiative; 2.80A
{Streptomyces coelicolor A3}
Length = 226
Score = 30.3 bits (68), Expect = 0.70
Identities = 7/36 (19%), Positives = 10/36 (27%), Gaps = 2/36 (5%)
Query: 44 IRAGRVKPGLAAQHLNGLIVAKDICQGRLENAHIGS 79
R G + P + LI I I +
Sbjct: 154 QRIGLLDPAWDPVDVLALINQ--IAMTWAGQPEIAA 187
>4fqd_A NIKO protein; beta/alpha inverse barrel, enolpyruvyl transferase,
fosfomyc binding, transferase; 2.50A {Streptomyces
tendae}
Length = 479
Score = 28.7 bits (65), Expect = 3.2
Identities = 6/47 (12%), Positives = 15/47 (31%), Gaps = 17/47 (36%)
Query: 304 QDQLIVMMALAKGTSRV----------------RVG-QISLHTRTAI 333
Q L ++ A A+G + + +G + ++
Sbjct: 344 QPFLALLGAYAEGPTYIREAVWEHRFGFAPELEALGIRTAVDDTVLR 390
>2yvw_A UDP-N-acetylglucosamine 1-carboxyvinyltransferase; peptidoglycan,
structu genomics, NPPSFA; HET: EPU; 1.81A {Aquifex
aeolicus} PDB: 3swg_A*
Length = 425
Score = 28.6 bits (65), Expect = 3.2
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 17/47 (36%)
Query: 304 QDQLIVMMALAKGTSRV----------------RVG-QISLHTRTAI 333
Q Q + ++++AKG SR+ R+G I++ TA
Sbjct: 313 QAQFMALLSVAKGKSRIKENIFEHRFHHAQELNRLGANITVRGNTAY 359
>3r38_A UDP-N-acetylglucosamine 1-carboxyvinyltransferase; biosynthesis and
degradation of murein sacculus and peptidog infectious
diseases; 2.23A {Listeria monocytogenes} PDB: 3sg1_A*
Length = 454
Score = 28.6 bits (65), Expect = 3.5
Identities = 9/47 (19%), Positives = 19/47 (40%), Gaps = 17/47 (36%)
Query: 304 QDQLIVMMALAKGTSRV----------------RVG-QISLHTRTAI 333
Q Q++V+ L++GTS + R+ + + + I
Sbjct: 331 QSQMMVIQMLSEGTSIMTETVFENRFMHVEEMRRMNADMKIEGHSVI 377
>1ejd_A MURA, EPT, UDP-N-acetylglucosamine enolpyruvyltransferase;
inside-OUT alpha/beta barrel; 1.55A {Enterobacter
cloacae} SCOP: d.68.2.2 PDB: 1ejc_A 1eyn_A* 1ybg_A*
3kqa_A* 3lth_A* 3spb_A 3swq_A* 3upk_A* 1naw_A 1dlg_A
1ryw_A* 1q3g_A* 3su9_A* 3swi_A* 3v4t_A* 3v5v_A* 3swa_A*
1uae_A* 3kqj_A* 3kr6_A* ...
Length = 419
Score = 28.6 bits (65), Expect = 3.6
Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 17/47 (36%)
Query: 304 QDQLIVMMALAKGTSRV----------------RVG-QISLHTRTAI 333
Q Q ++ +A+GT + R+G + + T I
Sbjct: 307 QAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVI 353
>2cki_A Ulilysin; metalloprotease, hydrolase; HET: ARG; 1.7A
{Methanosarcina acetivorans} PDB: 2j83_A* 3lum_A*
3lun_A*
Length = 262
Score = 27.7 bits (60), Expect = 6.1
Identities = 10/53 (18%), Positives = 15/53 (28%)
Query: 260 TSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQDQLIVMMA 312
T A + G P S + ++ C TQ Q + A
Sbjct: 199 TPNQADPNFGAPSYPHVSCSNGPNGDMFMNYMDYVDDKCMVMFTQGQATRVNA 251
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
0.322 0.138 0.421
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,752,594
Number of extensions: 347485
Number of successful extensions: 589
Number of sequences better than 10.0: 1
Number of HSP's gapped: 582
Number of HSP's successfully gapped: 14
Length of query: 374
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 279
Effective length of database: 4,049,298
Effective search space: 1129754142
Effective search space used: 1129754142
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 (21.9 bits)
S2: 58 (26.0 bits)