RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13670
(380 letters)
>3kdg_A DNA mismatch repair protein MUTL; endonuclease, DNA damage, DNA
repair, hydrolase; HET: DNA; 2.00A {Bacillus subtilis}
PDB: 3gab_A* 3kdk_A*
Length = 197
Score = 106 bits (268), Expect = 1e-27
Identities = 32/173 (18%), Positives = 74/173 (42%), Gaps = 11/173 (6%)
Query: 209 FEKMKIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQK---TTLIKSQKLVVPQNL 265
M +GQ + +I+ + ++ L+IIDQHA E+ +E ++ + Q+++VP
Sbjct: 6 VPIMYPIGQMHGTYILAQNENGLYIIDQHAAQERIKYEYFREKVGEVEPEVQEMIVPLTF 65
Query: 266 HLTKINQCILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLF-ML 324
H + I++ + G +S + ++ P + + EL+ ++
Sbjct: 66 HYSTNEALIIEQHKQELESVGVF--LESFGSNSYIVRCHP----AWFPKGEEAELIEEII 119
Query: 325 QHTNSTEHCRPSRIR-AMFASRACRKSVMIGRALSVGEMTGLVRNMGRIDQPW 376
Q +++ ++R +C+ S+ R L E+ L+ ++ P+
Sbjct: 120 QQVLDSKNIDIKKLREEAAIMMSCKGSIKANRHLRNDEIKALLDDLRSTSDPF 172
>3ncv_A DNA mismatch repair protein MUTL; endonuclease, dimer, hydrolase;
HET: DNA; 2.40A {Neisseria gonorrhoeae}
Length = 220
Score = 103 bits (260), Expect = 3e-26
Identities = 37/172 (21%), Positives = 69/172 (40%), Gaps = 13/172 (7%)
Query: 212 MKIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETL----QKTTLIKSQKLVVPQNLHL 267
+ Q +I+ + + L +ID HA E+ N+E + Q+ ++SQ L++P
Sbjct: 30 GFAIAQLLGIYILAQAEDSLLLIDMHAAAERVNYEKMKRQRQENGNLQSQHLLIPVTFAA 89
Query: 268 TKINQCILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLF-MLQH 326
+ L D+ G E + + + P LG+ D+ L +L
Sbjct: 90 SHEECAALADHAETLAGFGLEL--SDMGGNTLAVRAAP----VMLGKSDVVSLARDVLGE 143
Query: 327 TNSTEHCRP--SRIRAMFASRACRKSVMIGRALSVGEMTGLVRNMGRIDQPW 376
+ S + A+ +C S+ GR L++ EM L+R+M +
Sbjct: 144 LAQVGSSQTIASHENRILATMSCHGSIRAGRRLTLPEMNALLRDMENTPRSN 195
>3h4l_A DNA mismatch repair protein PMS1; ATP binding, DNA repair, DNA
damage, nucleus, phosphop DNA binding protein, protein
binding; HET: DNA ANP; 2.50A {Saccharomyces cerevisiae}
Length = 367
Score = 87.6 bits (218), Expect = 2e-19
Identities = 27/61 (44%), Positives = 39/61 (63%)
Query: 2 KLVNEVYHQFNNHQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSY 61
K NEVY FNN Q+P + LN+E+ +DVNVTPDKR I + +E+ ++ K ++D Y
Sbjct: 299 KCCNEVYKTFNNVQFPAVFLNLELPMSLIDVNVTPDKRVILLHNERAVIDIFKTTLSDYY 358
Query: 62 A 62
Sbjct: 359 N 359
>1h7s_A PMS1 protein homolog 2; DNA repair, GHL ATPase, mismatch repair,
HNPCC; 1.95A {Homo sapiens} SCOP: d.14.1.3 d.122.1.2
PDB: 1h7u_A* 1ea6_A*
Length = 365
Score = 86.5 bits (215), Expect = 5e-19
Identities = 34/60 (56%), Positives = 45/60 (75%)
Query: 2 KLVNEVYHQFNNHQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSY 61
+LVNEVYH +N HQYPF++LNI + + VD+NVTPDKRQI + EKLLLA +K + +
Sbjct: 304 RLVNEVYHMYNRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLIGMF 363
>1x9z_A DNA mismatch repair protein MUTL; alpha-beta fold, dimer,
replication, signaling protein; HET: DNA MSE; 2.10A
{Escherichia coli} SCOP: d.292.1.1
Length = 188
Score = 82.0 bits (203), Expect = 1e-18
Identities = 21/167 (12%), Positives = 63/167 (37%), Gaps = 13/167 (7%)
Query: 213 KIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQK-TTLIKSQKLVVPQNLHLTKIN 271
+++ + +++ D ++ ++ + L + +Q L++P L ++
Sbjct: 10 RVLTIVHSDCALLERDGNISLLSLPVAERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEE 69
Query: 272 QCILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLF-MLQHTNST 330
+ L+ + G +F D +V + ++P L +++++ L+ ++ +
Sbjct: 70 KSALEKAQSALAELGIDFQS---DAQHVTIRAVP----LPLRQQNLQILIPELIGYLAKQ 122
Query: 331 EHCRPSRIRAMFASRACRKSVMIGRALSVGEMTGLVRNMGRIDQPWV 377
P I A + S+ + L+ ++ R+ V
Sbjct: 123 SVFEPGNIAQWIARNLMSEH----AQWSMAQAITLLADVERLCPQLV 165
>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 = 54.1 bits (129), Expect = 5e-08
Identities = 55/447 (12%), Positives = 121/447 (27%), Gaps = 175/447 (39%)
Query: 1 MKLVNEVYHQF--NNHQYPFIILNIEMSRDSVDVNVTPDKRQIFM--DHEKLLLATVKVH 56
++++ ++ +Q N NI++ S+ + R++ +E LL
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ----AELRRLLKSKPYENCLL------ 248
Query: 57 ITDSYAIGFTVDGNNMNQSMEQDPSSDVDMEKIQRSNSEEVEH-----ETIPVPSEDNSN 111
+ +V N++ + + + +
Sbjct: 249 VLL-----------------------NV-------QNAKAWNAFNLSCKIL-LTTRFKQV 277
Query: 112 FSHEANLQQSPETVEPD----TPDETIEV--------IDDMPR--LQGSYRQSTPVTLSL 157
+ + +++ TPDE + D+PR L + P L
Sbjct: 278 TDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN-----P--RRL 330
Query: 158 DIIQDQLKARYAR----------RTVQAQDRCVEN--------RF--------HANIDPS 191
II + ++ A + + + F A+I P+
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI-PT 389
Query: 192 K----------NKEAESELNRVIKKSMFEK---------------------------MKI 214
+ +N++ K S+ EK I
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI 449
Query: 215 VGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTLIKSQKLVVPQNLHLTKINQCI 274
V +N I +DSD I ++Y + + HL I
Sbjct: 450 VDHYN---IPKTFDSDDLIPPY---LDQYFYSHI---------------GHHLKNIEHPE 488
Query: 275 LKDNLPVFYKNGFEF----------SFDSSDDGNVLLTSLP-----MSKNTTLGREDIEE 319
+ + + F F ++++S L L + N +
Sbjct: 489 RMTLFRMVFLD-FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNA 547
Query: 320 LL-FMLQHTNSTEHCRPSRI--RAMFA 343
+L F+ + + + + + A+ A
Sbjct: 548 ILDFLPKIEENLICSKYTDLLRIALMA 574
Score = 37.9 bits (87), Expect = 0.006
Identities = 41/323 (12%), Positives = 91/323 (28%), Gaps = 99/323 (30%)
Query: 83 DVDMEKIQRSNSEEVEHETIPVPSEDNSNFSHEANLQQSPETVEPDTPDETIEVIDDMP- 141
D + + Q + + V + F + + + + E I+ I
Sbjct: 8 DFETGEHQYQYKD-----ILSVFEDA---FVDNFDCKDVQDMPKSILSKEEIDHIIMSKD 59
Query: 142 RLQGSYRQSTPVTLSLDIIQDQLKARYAR--RTVQAQD-RCVENRFHA-NIDPSKNKEA- 196
+ G+ R + + + + V + + + + PS
Sbjct: 60 AVSGTLRL-------FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMY 112
Query: 197 ESELNRVIKKSMFEKMKIVGQFNLGFIIVKYDSDLFIIDQHATDEKYN------FETLQK 250
+ +R+ +N D+ +F KYN + L++
Sbjct: 113 IEQRDRL--------------YN--------DNQVFA--------KYNVSRLQPYLKLRQ 142
Query: 251 TTL-IKSQKLVVPQNLH---------LTK--INQCILKDNLP--VFYKNGFEFSFDSSDD 296
L ++ K V+ + + ++ + +F+ N +S +
Sbjct: 143 ALLELRPAKNVL---IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN---LKNCNSPE 196
Query: 297 G------NVLLTSLPM-------SKNTTLGREDIEELLFMLQHTNSTEHC-------RPS 336
+L P S N L I+ L L + E+C + +
Sbjct: 197 TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNA 256
Query: 337 RIRAMFASRACRKSVMIGRALSV 359
+ F C K ++ R V
Sbjct: 257 KAWNAFNLS-C-KILLTTRFKQV 277
>3na3_A DNA mismatch repair protein MLH1; MUTL protein homolog 1, DNA damag
repair, structural genomics consortium, SGC, protein
bindin; HET: DNA ATP; 2.50A {Homo sapiens}
Length = 348
Score = 44.4 bits (106), Expect = 3e-05
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 4 VNEVYHQF-NNHQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDS 60
+ VY + + +PF+ L++E+S +VDVNV P K ++ HE+ +L V+ HI
Sbjct: 277 IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIESK 334
>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 = 44.3 bits (104), Expect = 7e-05
Identities = 22/176 (12%), Positives = 49/176 (27%), Gaps = 62/176 (35%)
Query: 206 KSMFEKMKIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTLIKSQKLVVPQNL 265
+ ++ + + GF I+ I+ + + +F K +++
Sbjct: 1643 QDVWNRADNHFKDTYGFSILD------IVINNPVNLTIHF------GGEKGKRI------ 1684
Query: 266 HLTKINQCILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMSKNTTLGR---EDIEELLF 322
+N F++ DG + + N + LL
Sbjct: 1685 -----------------RENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLL- 1726
Query: 323 MLQHTNSTEHCRPSRIRAMFA-SRAC-----------RKSVMIGRALSVGEMTGLV 366
++T+ +P A+ +A + G S+GE L
Sbjct: 1727 -----SATQFTQP----ALTLMEKAAFEDLKSKGLIPADATFAG--HSLGEYAALA 1771
Score = 42.7 bits (100), Expect = 2e-04
Identities = 32/224 (14%), Positives = 57/224 (25%), Gaps = 89/224 (39%)
Query: 144 QGSYRQSTPVTLSLDIIQDQLKARYARRTVQAQDRCVENRFHANIDPSKNKEAESELNRV 203
GS V + I QL+ ++ + + + F A+ +P+ +EL
Sbjct: 13 HGSLEHVLLVPTASFFIASQLQEQFNKILPEPTE-----GFAADDEPT----TPAEL--- 60
Query: 204 IKKSMFEKMKIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTLIKSQKLVVPQ 263
VG+F LG++ + D+
Sbjct: 61 -----------VGKF-LGYVSSLVEPS----KVGQFDQ---------------------- 82
Query: 264 NLHLTKINQCILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLFM 323
+L L FE + +D + L L +TTL +
Sbjct: 83 ----------VLNLCL-----TEFENCYLEGNDIHALAAKLLQENDTTLVK--------- 118
Query: 324 LQHTNSTEHCRPSRIRAMFASRACRKSVMIGRALSVGEMTGLVR 367
I+ +R R + L R
Sbjct: 119 ----------TKELIKNYITARIM-----AKRPFDKKSNSALFR 147
Score = 37.0 bits (85), Expect = 0.010
Identities = 28/157 (17%), Positives = 53/157 (33%), Gaps = 49/157 (31%)
Query: 20 ILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSYAIGFTVDGNNMNQSMEQD 79
+++IE V+V V R + M +Y + ++ + S Q+
Sbjct: 1776 VMSIE---SLVEV-VF--YRGMTMQVA----VPRDELGRSNYGM-IAINPGRVAASFSQE 1824
Query: 80 PSSDVDMEKIQRSNSEEVEHETIPVPSEDNSNFSHEANL--QQSPETV---EPDTPDETI 134
V +E++ + VE V N+ N+ QQ V + D
Sbjct: 1825 ALQYV-VERVGKRTGWLVE----IV------NY----NVENQQ---YVAAGDLRALDTVT 1866
Query: 135 EVID-------DMPRLQGSYRQSTPVTLSLDIIQDQL 164
V++ D+ L +LSL+ ++ L
Sbjct: 1867 NVLNFIKLQKIDIIEL--------QKSLSLEEVEGHL 1895
Score = 33.9 bits (77), Expect = 0.11
Identities = 37/190 (19%), Positives = 63/190 (33%), Gaps = 60/190 (31%)
Query: 14 HQ-YPFIILNIEMSRDSVDVNV---TP-------DKRQIFMDHEKL---LLATVKVHITD 59
++ YP L + DS++ N +P + Q+ K L A +V I
Sbjct: 311 YEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI-- 368
Query: 60 SYAIG---FTVDGN-----NMNQSME-QDPSSDVDMEKI---QRSNSEEVEHETIPV--P 105
S G V G +N ++ S +D +I +R + + +PV P
Sbjct: 369 SLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSER--KLKFSNRFLPVASP 426
Query: 106 SEDNSNFSHEANLQQSPETVEPDTPDETIE---------VID-----DMPRLQGSYRQST 151
F H L + + + D + V D D+ L GS
Sbjct: 427 ------F-HSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGS----- 474
Query: 152 PVTLSL-DII 160
++ + D I
Sbjct: 475 -ISERIVDCI 483
>1b63_A MUTL; DNA mismatch repair, ATPase; HET: ANP; 1.90A {Escherichia
coli K12} SCOP: d.14.1.3 d.122.1.2 PDB: 1nhh_A* 1nhi_A*
1bkn_A 1nhj_A* 1b62_A*
Length = 333
Score = 35.5 bits (83), Expect = 0.024
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 4 VNEVYHQF-NNHQYPFIILNIEMSRDSVDVNVTPDKRQI 41
+ + Q P +L +E+ VDVNV P K ++
Sbjct: 274 IRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEV 312
>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 = 33.4 bits (75), Expect = 0.048
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 8/35 (22%)
Query: 37 DKRQIFMDHEKLLLATVKVHITDS---YAIGFTVD 68
+K+ + K L A++K++ DS AI T++
Sbjct: 18 EKQAL-----KKLQASLKLYADDSAPALAIKATME 47
Score = 28.4 bits (62), Expect = 2.2
Identities = 7/23 (30%), Positives = 10/23 (43%), Gaps = 5/23 (21%)
Query: 118 LQQSPETVEPDT-P----DETIE 135
LQ S + D+ P T+E
Sbjct: 25 LQASLKLYADDSAPALAIKATME 47
>1tz9_A Mannonate dehydratase; alpha-beta protein, structural genomics,
PSI, protein struct initiative, northeast structural
genomics consortium; 2.90A {Enterococcus faecalis} SCOP:
c.1.15.6
Length = 367
Score = 31.4 bits (70), Expect = 0.47
Identities = 14/55 (25%), Positives = 23/55 (41%)
Query: 313 GREDIEELLFMLQHTNSTEHCRPSRIRAMFASRACRKSVMIGRALSVGEMTGLVR 367
G D+ EL+ L RP RA++ +A + RA+ + + GL
Sbjct: 304 GSLDMAELMQALVDVGYEGVIRPDHGRAIWDEKAMPGYGLYDRAMGLTYIQGLYE 358
>1kny_A Kntase, kanamycin nucleotidyltransferase; antibiotic resistance,
plasmid; HET: APC KAN; 2.50A {Staphylococcus aureus}
SCOP: a.24.16.1 d.218.1.1 PDB: 1kan_A
Length = 253
Score = 28.7 bits (63), Expect = 3.3
Identities = 15/54 (27%), Positives = 20/54 (37%)
Query: 77 EQDPSSDVDMEKIQRSNSEEVEHETIPVPSEDNSNFSHEANLQQSPETVEPDTP 130
P SD++M + + E HE + NF E L VE D P
Sbjct: 44 TDGPYSDIEMMCVMSTEEAEFSHEWTTGEWKVEVNFYSEEILLDYASQVESDWP 97
>3bdk_A D-mannonate dehydratase; xylose isomerase-like TIM barrel, lyase;
HET: DNO; 2.50A {Streptococcus suis} PDB: 3ban_A*
3dbn_A* 3fvm_A
Length = 386
Score = 27.9 bits (61), Expect = 5.9
Identities = 15/90 (16%), Positives = 28/90 (31%), Gaps = 17/90 (18%)
Query: 283 YKNGFEFSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLFMLQHTNSTEHCRPSRIRAMF 342
GF+ + S G++ D+ ++ +L + RP R ++
Sbjct: 293 GAWGFQETAHLSQAGDI----------------DMNAVVKLLVDYDWQGSLRPDHGRRIW 336
Query: 343 ASRACR-KSVMIGRALSVGEMTGLVRNMGR 371
+ + RAL GL R
Sbjct: 337 GDQTKTPGYGLYDRALGATYFNGLYEANMR 366
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.0 bits (59), Expect = 7.2
Identities = 13/84 (15%), Positives = 31/84 (36%), Gaps = 15/84 (17%)
Query: 113 SHEANLQQSPETVEP--DTPDETIEVIDDMPRLQGSYRQSTPVTLSLDIIQDQLKARYAR 170
+ L Q PE++ + + ++ +D ++ Q + + L+ R
Sbjct: 75 AQADRLTQEPESIRKWREEQRKRLQELDAASKVM---EQEW-----REKAKKDLEEWNQR 126
Query: 171 RTVQAQDRCVENR-----FHANID 189
++ Q + + NR F+ D
Sbjct: 127 QSEQVEKNKINNRIADKAFYQQPD 150
>2a9d_A Sulfite oxidase; molybdopterin, molybdenum, oxidoreductase; HET:
MTE; 1.70A {Gallus gallus} SCOP: b.1.18.6 d.176.1.1 PDB:
2a9a_A* 2a99_A* 2a9b_A* 2a9c_A*
Length = 372
Score = 27.3 bits (61), Expect = 9.2
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 151 TPVTLSLDIIQDQLKARYARRTVQAQDRCVENR 183
++LSL +L++R+ + V A +C NR
Sbjct: 67 RTLSLSLA----ELRSRFPKHEVTATLQCAGNR 95
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
0.317 0.132 0.372
Gapped
Lambda K H
0.267 0.0537 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,511,192
Number of extensions: 319297
Number of successful extensions: 640
Number of sequences better than 10.0: 1
Number of HSP's gapped: 630
Number of HSP's successfully gapped: 24
Length of query: 380
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 285
Effective length of database: 4,049,298
Effective search space: 1154049930
Effective search space used: 1154049930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.6 bits)