RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5919
(387 letters)
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A
{Human herpesvirus 1} PDB: 1dml_B*
Length = 1193
Score = 128 bits (322), Expect = 2e-32
Identities = 29/203 (14%), Positives = 67/203 (33%), Gaps = 13/203 (6%)
Query: 65 FHHEPITETIVHSELRNLVIQKVPVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHH--EPI 122
H + H+ + + VI + G EG + V V+G Y Y+ +
Sbjct: 115 EHAYGMRAAQFHARFMDAITPTGTVITLLGLTPEGHRVAVHVYGTRQYFYMNKEEVDRHL 174
Query: 123 TETMLQQLAASIDKALNIALG--YKDSVQHVFHISICKKFPMYGYHADERTFLKILLYEP 180
+ L + AL + G ++ F + ++ +Y Y F ++ +
Sbjct: 175 QCRAPRDLCERMAAALRESPGASFRGISADHFEAEVVERTDVYYYETRPALFYRVYVRSG 234
Query: 181 YHMSKLEDLLLNGAVFNERFQPYESHIPYILQFCIDYNLY-GMSNIEFNMVKF--RSDSE 237
+S L D + YE + +F +D + + +
Sbjct: 235 RVLSYLCDNFCPA------IKKYEGGVDATTRFILDNPGFVTFGWYRLKPGRNNTLAQPR 288
Query: 238 TSLPKLSHCQLEADVKAESIVVD 260
+ + +E + A+++ ++
Sbjct: 289 APMAFGTSSDVEFNCTADNLAIE 311
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA
replication, DNA-BI DNA-directed DNA polymerase,
exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A
{Saccharomyces cerevisiae}
Length = 919
Score = 120 bits (303), Expect = 6e-30
Identities = 43/210 (20%), Positives = 75/210 (35%), Gaps = 17/210 (8%)
Query: 63 IPFHHEPITETIVHSELRNLVIQKVPVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHHEPI 122
I F +++++ V+R FG EG V G YLY+P
Sbjct: 47 ISFQQIDAEQSVLNGIKDE---NTSTVVRFFGVTSEGHSVLCNVTGFKNYLYVP-APNSS 102
Query: 123 TETMLQQLAASIDKALNIALGYKDSVQHVFHISICKKFPMYGYHAD-ERTFLKILLYEPY 181
+Q+ + + + I + K ++GY D + F KI + P+
Sbjct: 103 DANDQEQINKFVHYLN------ETFDHAIDSIEVVSKQSIWGYSGDTKLPFWKIYVTYPH 156
Query: 182 HMSKLEDLLLNGAVFNER----FQPYESHIPYILQFCIDYNLYGMSNIEFNMVKFRSDSE 237
++KL G + +I Y L+ +D + GMS I K+
Sbjct: 157 MVNKLRTAFERGHLSFNSWFSNGTTTYDNIAYTLRLMVDCGIVGMSWITLPKGKYSMIEP 216
Query: 238 TSLPKLSHCQLEADVKAESIVVDMAANDSD 267
++S CQLE + +++ A D
Sbjct: 217 N--NRVSSCQLEVSINYRNLIAHPAEGDWS 244
>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B
polymer alpha family polymerase, transferase; 2.10A
{Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A
2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A*
4ail_C* 3a2f_A* 2jgu_A* 1d5a_A
Length = 775
Score = 82.5 bits (204), Expect = 4e-17
Identities = 30/165 (18%), Positives = 47/165 (28%), Gaps = 22/165 (13%)
Query: 83 VIQKVPVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIAL 142
PVIRVF G+ + PY Y + E + + A
Sbjct: 9 TENGKPVIRVFKKE-NGEFKIEYDRTFEPYFYALLKDDSAIEDVKKVTAK---------- 57
Query: 143 GYKDSVQHVFHISICKKFPMYGYHADERTFLKILLYEPYHMSKLEDLLLNGAVFNERFQP 202
+V V +K + K+ P + + D +
Sbjct: 58 -RHGTVVKVKRAEKVQK----KFLGRPIEVWKLYFNHPQDVPAIRDRIRAH---PAVVDI 109
Query: 203 YESHIPYILQFCIDYNLYGMSNI-EFNMVKFRSDSETSLPKLSHC 246
YE IP+ ++ ID L M E M+ F T +
Sbjct: 110 YEYDIPFAKRYLIDKGLIPMEGDEELTMLAF--AIATLYHEGEEF 152
Score = 46.3 bits (110), Expect = 1e-05
Identities = 11/65 (16%), Positives = 21/65 (32%), Gaps = 5/65 (7%)
Query: 31 VIQKVPVIRVFGNNIEGKKTCVFVHGVFPYLYIP----FHHEPITETIVHSELRNLVIQK 86
PVIRVF G+ + PY Y E + + + +++
Sbjct: 9 TENGKPVIRVFKKE-NGEFKIEYDRTFEPYFYALLKDDSAIEDVKKVTAKRHGTVVKVKR 67
Query: 87 VPVIR 91
++
Sbjct: 68 AEKVQ 72
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET:
DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5
e.8.1.1
Length = 847
Score = 79.5 bits (196), Expect = 4e-16
Identities = 28/180 (15%), Positives = 53/180 (29%), Gaps = 29/180 (16%)
Query: 86 KVPVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGYK 145
V ++F + G PY + + + I K +
Sbjct: 28 GKAVCKLFDKETQKIYALYDNTGHKPYFLVDLEPDKV---------GKIPKIVR------ 72
Query: 146 DSVQHVFHISICKKFPMYGYHADERTFLKILLYEPYHMSKLEDLLLNGAVFNERFQPYES 205
HI K Y ++ + KI++ +P + +L + + + YE+
Sbjct: 73 --DPSFDHIETVSKIDPYTWN--KFKLTKIVVRDPLAVRRLRNDV---------PKAYEA 119
Query: 206 HIPYILQFCIDYNLYGMSNIEFNMVKFRSDSETSLPKLSHCQLEADVKAESIVVDMAAND 265
HI Y + D L K S SL + +++ + A D
Sbjct: 120 HIKYFNNYMYDIGLIPGMPYVVKNGKLES-VYLSLDEKDVEEIKKAFADSDEMTRQMAVD 178
Score = 42.2 bits (99), Expect = 3e-04
Identities = 6/54 (11%), Positives = 16/54 (29%), Gaps = 2/54 (3%)
Query: 34 KVPVIRVFGNNIEGKKTCVFVHGVFPYLYIPFHHEPITETIVHSELRNLVIQKV 87
V ++F + G PY + + + + +R+ +
Sbjct: 28 GKAVCKLFDKETQKIYALYDNTGHKPYFLVDLEPDKVGKIP--KIVRDPSFDHI 79
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA
repair, DNA-binding; HET: DNA DOC DCP; 1.92A
{Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A*
3k5n_A* 3k5o_A* 3maq_A* 1q8i_A*
Length = 786
Score = 52.8 bits (127), Expect = 1e-07
Identities = 18/164 (10%), Positives = 41/164 (25%), Gaps = 39/164 (23%)
Query: 88 PVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGYKDS 147
+ + G V + +IP P + +LQ L +
Sbjct: 22 TEVSFWLATDNGP-LQVTLAPQESVAFIPADQVPRAQHILQGEQGFRLTPLAL------- 73
Query: 148 VQHVFHISICKKFPMYGYHADERTFLKILLYEPYHMSKLEDLLLNGAVFNERFQPYESHI 207
K F + + + E L G YE+ +
Sbjct: 74 ----------KDF-------HRQPVYGLYCRAHRQLMNYEKRLREGG-----VTVYEADV 111
Query: 208 PYILQFCIDYNLYGMSNIEFNMVKFRSDSETSLPKLSHCQLEAD 251
++ ++ + +E +M + + +L+
Sbjct: 112 RPPERYLMERFITSPVWVEGDMHNGT---------IVNARLKPH 146
Score = 32.4 bits (74), Expect = 0.30
Identities = 9/67 (13%), Positives = 19/67 (28%), Gaps = 2/67 (2%)
Query: 36 PVIRVFGNNIEGKKTCVFVHGVFPYLYIPFHHEPITETIVHSELRNLVIQKVPVIRVFGN 95
+ + G V + +IP P + I+ E + + + +
Sbjct: 22 TEVSFWLATDNGP-LQVTLAPQESVAFIPADQVPRAQHILQGE-QGFRLTPLALKDFHRQ 79
Query: 96 NVEGKKT 102
V G
Sbjct: 80 PVYGLYC 86
>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 = 46.0 bits (108), Expect = 2e-05
Identities = 39/232 (16%), Positives = 74/232 (31%), Gaps = 51/232 (21%)
Query: 108 GVFPY-LYIPFH------HEPITETMLQQLAASIDKALNIALGYKDSVQHVFHISICKKF 160
VFP +IP + I ++ + +L + K+S + I + K
Sbjct: 379 SVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL-VEKQPKESTISIPSIYLELKV 437
Query: 161 PMYGYHADERTFLKILLYEPYHMSKLEDLLLNGAVFNERFQPYESHIPYILQFCIDYNLY 220
+ L + + Y++ K D ++ PY Y I ++L
Sbjct: 438 -----KLENEYALHRSIVDHYNIPKTFDS-------DDLIPPYLDQ--YFYSH-IGHHLK 482
Query: 221 GMSNIE----FNMV---------KFRSDSETSLPKLSHCQLEADVKA-ESIVVDMAANDS 266
+ + E F MV K R DS S +K + + D ND
Sbjct: 483 NIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICD---NDP 539
Query: 267 DVATSGGITRYLSDVLLNSMRAILLGQEPHLLMDPDVYSMQDLLDVKSGALY 318
R ++ +L + E +L+ ++ L + A++
Sbjct: 540 K------YERLVNAILDFLPKI-----EENLICSKYTDLLRIALMAEDEAIF 580
Score = 44.1 bits (103), Expect = 8e-05
Identities = 63/456 (13%), Positives = 123/456 (26%), Gaps = 136/456 (29%)
Query: 23 VH-------SELRNLVIQKVPVIRVFGNNIE----GKKTC----------VFVHGVFPYL 61
+ + + V V I + +
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214
Query: 62 YIPFHHEPITETI--VHSELRNLVIQK--------------VPVIRVFGNNVEGKKTCV- 104
H I I + +ELR L+ K F + K +
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC---KILLT 271
Query: 105 --------FVHGVFP-YLYIPFHHEPITETMLQQLAASIDKALNIALGYKDSVQ----HV 151
F+ ++ + H +T ++ L K L+ + +
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL---KYLDCRPQ-DLPREVLTTNP 327
Query: 152 FHISIC-----------KKFPMYGYHADERT---FLKILLYEPYHMSKL-EDLLLNGAVF 196
+SI + L +L EP K+ + L +VF
Sbjct: 328 RRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL--EPAEYRKMFDRL----SVF 381
Query: 197 NERFQPYESHIPY-----------------ILQFCIDYNLYGMSNIEFNMVKFRSDSETS 239
P +HIP ++ Y+L + K +S S
Sbjct: 382 -----PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL---------VEKQPKESTIS 427
Query: 240 LPKL---SHCQLEADVKAESIVVD----MAANDSDVATSGGITRYLSDVLLNSMRAILLG 292
+P + +LE + +VD DSD + +Y + + ++ I
Sbjct: 428 IPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHP 487
Query: 293 QEPHLLMDPDVYSMQDLLDVKSGALYLKLKDLVSACSIFRMRAILLGQEPHLLMDPDVYS 352
+ L V+ LD + +L+ K + + + +L + L Y
Sbjct: 488 ERMTLF--RMVF-----LDFR----FLEQK-IRHDSTAWNASGSIL----NTLQQLKFYK 531
Query: 353 --MQDLLDVKSGALYLKLKDLVSACSSHVYNCEPTN 386
+ D D K L + D + ++ + T+
Sbjct: 532 PYICDN-DPKYERLVNAILDFLPKIEENLICSKYTD 566
Score = 39.8 bits (92), Expect = 0.002
Identities = 46/352 (13%), Positives = 112/352 (31%), Gaps = 114/352 (32%)
Query: 72 ETIVHSELRNLVIQKVPVIRV---FGNNVEGKKTCV--FVHGV----FPYLYIPFHHEPI 122
+ E+ ++++ K V F + ++ V FV V + +L P E
Sbjct: 44 SILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR 103
Query: 123 TETMLQQLAASIDKALNIALGYKDSVQHVFHISICKKFPMYGYHADERTFLKILLYEPYH 182
+M+ + MY D R + ++ Y+
Sbjct: 104 QPSMMTR--------------------------------MYIEQRD-RLYNDNQVFAKYN 130
Query: 183 MSKLEDLL-LNGAVFNERFQPYESHIPYILQFCIDYNLYGM------------------- 222
+S+L+ L L A+ R +L + G+
Sbjct: 131 VSRLQPYLKLRQALLELR------PAKNVL-------IDGVLGSGKTWVALDVCLSYKVQ 177
Query: 223 SNIEFNM--VKFRSDSETS-----LPKLSHCQLEADVKAESIVVDMAANDSDVATSGGIT 275
++F + + ++ + L KL + Q++ + + S D ++N
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLY-QIDPNWTSRS---DHSSN----------I 223
Query: 276 RYLSDVLLNSMRAILLGQEPH----LLMDPDVYSMQ--DLLDVKSGALYLKLKDLVSACS 329
+ + +R LL +P+ L++ +V + + + ++ K L++
Sbjct: 224 KLRIHSIQAELR-RLLKSKPYENCLLVLL-NVQNAKAWNAFNLSC-------KILLTTRF 274
Query: 330 IFRMRAILLGQEPHLLMD--PDVYSMQDLLDVKSGALYLKLKDL-VSACSSH 378
+ H+ +D + ++ + L + +DL +++
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN 326
>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 = 0.006
Identities = 38/250 (15%), Positives = 74/250 (29%), Gaps = 93/250 (37%)
Query: 107 HGVFPYLYIPF--------HHEPITETML-------QQLAASIDKA---------LNIAL 142
+ +P +P ++E + ML +Q+ ++K + I+L
Sbjct: 311 YEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISL 370
Query: 143 ----------GYKDSVQHVFHISICK----------KFPMYGYHADER------TFLKIL 176
G S+ ++++ K + P ER FL +
Sbjct: 371 VNGAKNLVVSGPPQSLYG-LNLTLRKAKAPSGLDQSRIPF-----SERKLKFSNRFLPV- 423
Query: 177 LYEPYHMSKLED----LLLNGAVFNERFQPYESHIPYILQFCIDYNLYGMSNIEFNMVKF 232
P+H L + + N F + IP Y+ + S++
Sbjct: 424 -ASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV-------YDTFDGSDL------- 468
Query: 233 RSDSETSLPKLSHCQLEADVKAESIVVDMAANDSDVAT------SGGITR--YLSDVLLN 284
R S + ++ C + V AT GG + L+ +
Sbjct: 469 RVLSGSISERIVDCIIRL-------PVKWETTTQFKATHILDFGPGGASGLGVLTHRNKD 521
Query: 285 --SMRAILLG 292
+R I+ G
Sbjct: 522 GTGVRVIVAG 531
Score = 35.8 bits (82), Expect = 0.031
Identities = 29/169 (17%), Positives = 44/169 (26%), Gaps = 75/169 (44%)
Query: 15 KPIAH--FDPV----HSELRNLVIQKVPVIRVFGNNIEGKKTCVFVHGVFPYLYIPFHHE 68
K F PV HS L + + NN+ + IP +
Sbjct: 413 KLKFSNRFLPVASPFHSHLLVPASDLINK-DLVKNNVSFNA---------KDIQIPVYD- 461
Query: 69 PITET------IVHSELRNLV--IQKVPV------------IRVFG------------NN 96
T + S +V I ++PV I FG N
Sbjct: 462 --TFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRN 519
Query: 97 VEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGYK 145
+G GV I +A ++D + G+K
Sbjct: 520 KDGT-------GV----------RVI-------VAGTLDINPDDDYGFK 544
Score = 32.3 bits (73), Expect = 0.32
Identities = 31/198 (15%), Positives = 54/198 (27%), Gaps = 58/198 (29%)
Query: 237 ETSL--PKLSHC---QLEAD-VKAESIVVDMAANDSDVATSGG-ITRYLS---------- 279
E L P S QL+ K + A D + T + ++L
Sbjct: 17 EHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSK 76
Query: 280 -----DVLLNSM----RAILLGQEPHLLMDPDVYSMQDLLDVKSGALYLKLKDLVSACSI 330
VL + L G + H L + D +K+ ++A +
Sbjct: 77 VGQFDQVLNLCLTEFENCYLEGNDIHAL----AAKLLQENDTTLVKTKELIKNYITARIM 132
Query: 331 FRMRAILLGQEPHLLM-----------------DPDVYSMQDLLDVKSGALY----LKLK 369
+ R L + D Y ++L D LY + +
Sbjct: 133 AK-RPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDY-FEELRD-----LYQTYHVLVG 185
Query: 370 DLVSACSSHVYNCEPTNA 387
DL+ + + T
Sbjct: 186 DLIKFSAETLSELIRTTL 203
>2eaq_A LIM domain only protein 7; conserved hypothetical protein,
structural genomics, NPPSFA; 1.46A {Homo sapiens}
Length = 90
Score = 27.4 bits (61), Expect = 2.3
Identities = 9/35 (25%), Positives = 14/35 (40%)
Query: 25 SELRNLVIQKVPVIRVFGNNIEGKKTCVFVHGVFP 59
S++R + Q FG I+ +FV V
Sbjct: 3 SDMRISINQTPGKSLDFGFTIKWDIPGIFVASVEA 37
Score = 27.0 bits (60), Expect = 3.9
Identities = 8/35 (22%), Positives = 14/35 (40%)
Query: 77 SELRNLVIQKVPVIRVFGNNVEGKKTCVFVHGVFP 111
S++R + Q FG ++ +FV V
Sbjct: 3 SDMRISINQTPGKSLDFGFTIKWDIPGIFVASVEA 37
>1a3w_A Pyruvate kinase; allosteric regulation, tranferase, transfer; HET:
FBP; 3.00A {Saccharomyces cerevisiae} SCOP: b.58.1.1
c.1.12.1 c.49.1.1 PDB: 1a3x_A
Length = 500
Score = 28.0 bits (63), Expect = 5.8
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 108 GVFPYLYIPFHHEPITETMLQQLAASIDKAL 138
GVFP+++ T+ + ++ I+KA
Sbjct: 438 GVFPFVFEKEPVSDWTDDVEARINFGIEKAK 468
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
0.325 0.140 0.418
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,002,694
Number of extensions: 361173
Number of successful extensions: 887
Number of sequences better than 10.0: 1
Number of HSP's gapped: 867
Number of HSP's successfully gapped: 25
Length of query: 387
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 292
Effective length of database: 4,049,298
Effective search space: 1182395016
Effective search space used: 1182395016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.1 bits)