RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8633
(327 letters)
>3e0j_A DNA polymerase subunit delta-2; DNA polymerase delta, P66 subunit,
P50 subunit, human, DNA replication, DNA-directed DNA
polymerase; HET: DNA; 3.00A {Homo sapiens}
Length = 476
Score = 219 bits (558), Expect = 5e-68
Identities = 88/163 (53%), Positives = 117/163 (71%)
Query: 156 SSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQ 215
+S+ VD+MPGEFDP N TLPQQPLHPC+FP A+ YST VTNPY ++G +GTSGQ
Sbjct: 295 ASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQ 354
Query: 216 PVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQ 275
VSDI ++S++ + L+ILE+TLR H++PTAPDTL CYPFY DP I CP VYF GN
Sbjct: 355 NVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNT 414
Query: 276 SKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECHSL 318
F +K I +D+ V L++VPDF +++T ++NL +L C +
Sbjct: 415 PSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSLACQPI 457
Score = 116 bits (292), Expect = 2e-29
Identities = 54/140 (38%), Positives = 79/140 (56%), Gaps = 2/140 (1%)
Query: 21 KTIEIEKGKSVSVLKLSDLNETDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHT 80
+ G V V KL +L E+C ++GTLFK L+P+IL+E+SEE L+PQP +
Sbjct: 74 NRAQQHWGSGVGVKKLCELQPE--EKCCVVGTLFKAMPLQPSILREVSEEHNLLPQPPRS 131
Query: 81 HFVSDSDELILEDELQRIPLHGNIDIHNQVTGVVVAIKGTPVGNGKFKVSDVCYATPVFN 140
++ DEL+LEDELQRI L G ID+ VTG V+A+ G+ +GKF V D C+A
Sbjct: 132 KYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFADLAPQ 191
Query: 141 PRTTLSNNENKYVNHSSIEV 160
+ + + S + +
Sbjct: 192 KPAPPLDTDRFVLLVSGLGL 211
Score = 46.3 bits (109), Expect = 7e-06
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 1 MIIESCPDVYFTGNQSKFETKTIEIEKGKSVSVLKLSDLNETDTEECVIIGTL 53
I CP VYF GN F +K I + ++V ++ + D + T T V + +L
Sbjct: 400 FIFPECPHVYFCGNTPSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSL 452
>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 = 56.6 bits (136), Expect = 6e-09
Identities = 52/266 (19%), Positives = 76/266 (28%), Gaps = 74/266 (27%)
Query: 39 LNETDTEECVIIGT-LFKH-QQLK---PNILKEISEELKLVPQPQHT--------HFVSD 85
L+ E +++ T F QL+ IL E +E +P +VS
Sbjct: 11 LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSS 70
Query: 86 SDE--------LILE---DELQRIPLHGNIDIHNQVTGVVVAIKGTPVGNGKFKVSDVCY 134
E +L E + L GN DIH + ++ T + K + Y
Sbjct: 71 LVEPSKVGQFDQVLNLCLTEFENCYLEGN-DIHA-LAAKLLQENDTTLVKTKELIK--NY 126
Query: 135 ATPVFNPRTTLSNNENKYVNHSSIEVDLMPGEFDPANTTLPQQPLHPCL---------FP 185
R +K +S L F L F
Sbjct: 127 ----ITARIMAKRPFDK--KSNSA---L----FRAVGE--GNAQLVAIFGGQGNTDDYFE 171
Query: 186 E-ASKYSTFHPVTNPYIFEMEGKLLMGTSGQPVSDIAKFSNLSNPLDILEYTLRCGHVAP 244
E Y T+H + I + L + F + L+ILE+ L P
Sbjct: 172 ELRDLYQTYHVLVGDLIKFS-AETLSELIRTTLDAEKVF---TQGLNILEW-LE----NP 222
Query: 245 -TAPDT--LACYPFYDNDPMIIESCP 267
PD L P SCP
Sbjct: 223 SNTPDKDYLLSIPI---------SCP 239
Score = 37.7 bits (87), Expect = 0.005
Identities = 49/226 (21%), Positives = 78/226 (34%), Gaps = 74/226 (32%)
Query: 127 FKVSDVCYATPVFNPRTTLSNNENK----YVNHSSIEVDLMPGEFDPANTTLPQQPLHPC 182
F + D+ P T+ K N+S++ + + D T
Sbjct: 1659 FSILDIVINNP---VNLTIHFGGEKGKRIRENYSAMIFETIV---DGKLKTEK------- 1705
Query: 183 LFPEASKYSTFHPVTNPYIFEMEGKLLMGTSG-QP----VSDIAKFSNLSN----PLDIL 233
+F E +++ST Y F E LL T QP + A F +L + P D
Sbjct: 1706 IFKEINEHST------SYTFRSEKGLLSATQFTQPALTLME-KAAFEDLKSKGLIPADAT 1758
Query: 234 -------EYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPD-VYFTGNQSKFETKTIEI 285
EY A LA D M IES + V++ G T + +
Sbjct: 1759 FAGHSLGEYA------A------LASL----ADVMSIESLVEVVFYRG-----MTMQVAV 1797
Query: 286 EKDK----NVRLISV-PDFFSSRTVAILNLSTLECHSLVVEDLTEE 326
+D+ N +I++ P R A + L+ VVE + +
Sbjct: 1798 PRDELGRSNYGMIAINP----GRVAASFSQEALQ---YVVERVGKR 1836
Score = 35.8 bits (82), Expect = 0.022
Identities = 18/143 (12%), Positives = 38/143 (26%), Gaps = 53/143 (37%)
Query: 55 KHQQLKPNILKE---ISEELKLVPQPQHTHFVSDSDELILEDELQRIPLHGNIDIHNQVT 111
+ K ++ P H+H + + +LI +D L + +
Sbjct: 408 PFSERKLKFSNRFLPVAS-------PFHSHLLVPASDLINKD-LVKNNV----------- 448
Query: 112 GVVVAIKGTPVGNGKFKVSDVCYATPVFNPRTTLSNNENKYVNHSSIEVDLMPGEFDPAN 171
F D+ PV++ + V SI ++
Sbjct: 449 --------------SFNAKDI--QIPVYDTFD----GSDLRVLSGSISERIV-----DCI 483
Query: 172 TTLPQQPLHPCLFPEASKYSTFH 194
L P + +++ H
Sbjct: 484 IRL------PVKWETTTQFKATH 500
Score = 29.6 bits (66), Expect = 2.0
Identities = 10/44 (22%), Positives = 15/44 (34%), Gaps = 5/44 (11%)
Query: 13 GNQSKFETKTIEIEKGKSVSVLKLSDLNETDTEECVIIGTLFKH 56
G S T + G V V+ L+ ++ G FK
Sbjct: 507 GGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDD---YG--FKQ 545
>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 = 55.6 bits (133), Expect = 1e-08
Identities = 74/434 (17%), Positives = 122/434 (28%), Gaps = 135/434 (31%)
Query: 6 CPDV--YFTGNQSKFETKTIEIEKGKSVSVLKLSDLNETDTEECVIIGTLFKHQQLKPN- 62
C DV SK E I + K L+L + EE V F + L+ N
Sbjct: 35 CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMV---QKFVEEVLRINY 91
Query: 63 --ILKEISEELKLVPQPQHTHFVSDSDEL------ILEDELQRIPLHGNIDIH----NQV 110
++ I E + P ++ D L + + R+ + +
Sbjct: 92 KFLMSPIKTEQR-QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPA 150
Query: 111 TGVVVAIKGTPVGNGK-FKVSDVCYATPVFNPRTTLSNNENK--YVN---HSSIEVDLMP 164
V++ G G+GK + DVC + V + K ++N +S E L
Sbjct: 151 KNVLI--DGVL-GSGKTWVALDVCLSYKV------QCKMDFKIFWLNLKNCNSPETVLEM 201
Query: 165 GE-----FDPANTTLPQQPLHPCLFPEASKY-------STFHP--------VTNPYI--- 201
+ DP T+ + L + + S + V N
Sbjct: 202 LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA 261
Query: 202 FEMEGKLLMGTSGQPVSDIAKFSN---------------------LSNPLDILEYTLR-- 238
F + K+L+ T + V+D + L LD L
Sbjct: 262 FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPRE 321
Query: 239 -CGHVAPTA-----------PDTLACYPFYDNDPM--IIESC-----PDVY--------- 270
P T + + D + IIES P Y
Sbjct: 322 VLT-TNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380
Query: 271 FTGNQSKFETKTIEI-----------------------EKDKNVRLISVPDFFSSRTVAI 307
F + + T + + EK IS+P + V +
Sbjct: 381 FPPS-AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL 439
Query: 308 LNLSTLECHSLVVE 321
N L H +V+
Sbjct: 440 ENEYAL--HRSIVD 451
Score = 31.4 bits (70), Expect = 0.55
Identities = 31/249 (12%), Positives = 73/249 (29%), Gaps = 69/249 (27%)
Query: 57 QQLKPNILKEISEELKLVPQ----PQHT------HFVSDSDELILEDELQRIPLHGNIDI 106
L+P +++ + L + P P + +++ ++L + L ++
Sbjct: 364 NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV-NKLHKYSL---VEK 419
Query: 107 HNQVTGVVVAIKGTPVGNGKFKVSDVCYATPVFNPRTTLSNNENKYVNHSS-IEVDLMPG 165
+ + + Y EN+Y H S ++ +P
Sbjct: 420 QPK--------------ESTISIPSI-Y-------LELKVKLENEYALHRSIVDHYNIPK 457
Query: 166 EFDPANTTLPQQ--------PLHPCLFPEASKYSTFHPVTNPYIFEMEGKL-LMGTSGQP 216
FD + P H + + F V + F +E K+ T+
Sbjct: 458 TFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRF-LEQKIRHDSTAWNA 516
Query: 217 VSDIA----------KFSNLSNPL------DILEYTLRCGHVAPTAPDT----LACYPFY 256
I + ++P IL++ + + T +A
Sbjct: 517 SGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIAL--MA 574
Query: 257 DNDPMIIES 265
+++ + E+
Sbjct: 575 EDEAIFEEA 583
>2cua_A Protein (CUA); CUA center, electron transport; 1.60A {Thermus
thermophilus} SCOP: b.6.1.2 PDB: 2fwl_B*
Length = 135
Score = 29.3 bits (66), Expect = 0.89
Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 240 GHVAPTAPDTL-ACYPFYDNDPMIIESCPD---VYFTGNQSKFETKTIEIEKDKNVRLI 294
G + P T+ P+ D ++++ P+ VY ++ IE+ + +
Sbjct: 15 GKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFK 73
>3flo_A DNA polymerase alpha subunit B; protein-protein complex,
phosphoesterase fold, OB fold, zinc-binding motif, DNA
replication; HET: DNA; 2.50A {Saccharomyces cerevisiae}
Length = 460
Score = 28.2 bits (62), Expect = 4.0
Identities = 35/207 (16%), Positives = 69/207 (33%), Gaps = 20/207 (9%)
Query: 96 QRIPL-HGNIDIHNQVTGVVVAIKGTPVGNGKFKVSDVCYATPVFNPRTTLSNNE--NKY 152
+R+ L ++ + G +VA KG F V+ + +P +T +
Sbjct: 83 RRVRLDLSQVNELSFFLGQIVAFKGKNANGDYFTVNSILPLPYPNSPVSTSQELQEFQAN 142
Query: 153 VNHSSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYST--------FHPVTNPYIFEM 204
+ SS++V + G + + + L + ++ F +T+P I
Sbjct: 143 LEGSSLKVIVTCGPYFAND-NFSLELLQEFIDSINNEVKPHVLIMFGPFIDITHPLIASG 201
Query: 205 EGKLLMGTSGQPVSDIAKFSNLSNPLDILEYTLRCGHVA--PTAPDTLACYPFYDNDPMI 262
+ QP + F L P IL+ P+ D ++ + Y +I
Sbjct: 202 KLPNFPQFKTQPKTLDELFLKLFTP--ILKTISPHIQTVLIPSTKDAISNHAAYPQASLI 259
Query: 263 IE----SCPDVYFTGNQSKFETKTIEI 285
+ + N S F+ I
Sbjct: 260 RKALQLPKRNFKCMANPSSFQINEIYF 286
>3s8f_B Cytochrome C oxidase subunit 2; complex IV, respiratory chain,
lipid cubic phase, monoolein, peroxide, electron
transport, proton pump; HET: HEM HAS OLC; 1.80A {Thermus
thermophilus} PDB: 1ehk_B* 2qpd_B* 3qjq_B* 3qjr_B*
3qju_B* 3qjv_B* 1xme_B* 3s8g_B* 4esl_B* 3qjs_B* 3bvd_B*
2qpe_B* 3qjt_B* 3eh5_B* 3eh3_B* 3eh4_B*
Length = 168
Score = 27.5 bits (61), Expect = 4.9
Identities = 7/45 (15%), Positives = 17/45 (37%), Gaps = 3/45 (6%)
Query: 253 YPFYDNDPMIIESCP---DVYFTGNQSKFETKTIEIEKDKNVRLI 294
P+ D ++++ P VY ++ IE+ + +
Sbjct: 62 GPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFK 106
>2etv_A Iron(III) ABC transporter, periplasmic iron-bindi protein,
putative; periplasmic iron-binding protein, structural
genomics; HET: MLY; 1.70A {Thermotoga maritima} SCOP:
c.92.2.4
Length = 346
Score = 27.8 bits (61), Expect = 5.6
Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 4/78 (5%)
Query: 1 MIIESCPDVYFTGNQSKFETKTIEIEKGKSVSVLKLSDLNETDTEECV----IIGTLFKH 56
+I PDV F + I+ G V VL +L + E+ + G +
Sbjct: 91 SLITLQPDVVFITYVDRXTAXDIQEXTGIPVVVLSYGNLGTFEDEDLFRSIELAGXILGR 150
Query: 57 QQLKPNILKEISEELKLV 74
++ ++ I + +
Sbjct: 151 EERAHEVVDFIRXAQEDL 168
>2czc_A Glyceraldehyde-3-phosphate dehydrogenase; glycolysis, NAD,
oxidoreductase, structural genomics; HET: NAD; 2.00A
{Pyrococcus horikoshii} SCOP: c.2.1.3 d.81.1.1
Length = 334
Score = 27.4 bits (61), Expect = 5.9
Identities = 10/47 (21%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 80 THFVSDSDELILEDELQRIPLHGNIDIHNQVTGVVVAIKGTPVGNGK 126
+ S+E I E + + G ++ + + V + + TP G G
Sbjct: 49 IPVYAASEEFIPRFEKEGFEVAGTLN--DLLEKVDIIVDATPGGIGA 93
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
0.316 0.135 0.395
Gapped
Lambda K H
0.267 0.0796 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,923,647
Number of extensions: 291089
Number of successful extensions: 526
Number of sequences better than 10.0: 1
Number of HSP's gapped: 524
Number of HSP's successfully gapped: 25
Length of query: 327
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 233
Effective length of database: 4,077,219
Effective search space: 949992027
Effective search space used: 949992027
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 (21.6 bits)
S2: 57 (25.6 bits)