RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12449
(102 letters)
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A
{Human herpesvirus 1} PDB: 1dml_B*
Length = 1193
Score = 73.7 bits (180), Expect = 4e-17
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 7 KELKEAM-TLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQG 61
K+++ + + +LD +Q A+K+ NSVYGFTG Q G LPC T G
Sbjct: 744 KQIRSRIPQSSPEEAVLLDKQQAAIKVVCNSVYGFTGVQHGLLPCLHVAATVTTIG 799
>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 = 71.9 bits (176), Expect = 2e-16
Identities = 34/57 (59%), Positives = 39/57 (68%), Gaps = 2/57 (3%)
Query: 7 KELKEAM--TLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQG 61
K K+ + D FK+ VL+GRQLALKISANSVYGFTGA VGKLPC + T G
Sbjct: 609 KRAKKDLRDEKDPFKRDVLNGRQLALKISANSVYGFTGATVGKLPCLAISSSVTAYG 665
Score = 24.9 bits (54), Expect = 5.8
Identities = 15/23 (65%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 1 MVKFGTKELKEAMTL-DEFKKKV 22
MVKFGT +LKEAM L E K V
Sbjct: 701 MVKFGTTDLKEAMDLGTEAAKYV 723
>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 = 69.4 bits (170), Expect = 2e-15
Identities = 20/46 (43%), Positives = 29/46 (63%), Gaps = 2/46 (4%)
Query: 7 KELKEAM--TLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPC 50
+++K M T+D +KK+LD RQ A+KI ANS YG+ G + C
Sbjct: 461 QKIKRKMKATVDPLEKKLLDYRQRAIKILANSFYGYYGYAKARWYC 506
>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 = 68.7 bits (168), Expect = 3e-15
Identities = 13/44 (29%), Positives = 21/44 (47%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPC 50
K+ + E +K + D Q A+K+ N+ YG GA+ L
Sbjct: 544 KKKAKNPNNSEEQKLLYDVVQRAMKVFINATYGVFGAETFPLYA 587
>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 = 60.1 bits (146), Expect = 3e-12
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 16 DEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPC 50
DE K++ ALKI N+ YG G +
Sbjct: 481 DEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFD 515
>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT;
1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A*
3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A*
3spz_A* 3ne6_A* 3nhg_A* 3si6_A* 3scx_A* 3sjj_A* 3snn_A*
3ngi_A* 3lzi_A* 3lzj_A* 3ndk_A* ...
Length = 903
Score = 32.6 bits (73), Expect = 0.013
Identities = 9/46 (19%), Positives = 15/46 (32%)
Query: 3 KFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKL 48
K K L E + + + Q+ K N + G G +
Sbjct: 532 KLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGALGNVWFRY 577
>1xao_A YDJ1, mitochondrial protein import protein MAS5; beta sheets,
chaperone; 2.07A {Saccharomyces cerevisiae}
Length = 121
Score = 26.8 bits (60), Expect = 0.88
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 9 LKEAMTLDEFKKKVLDGRQLALKISANSV 37
L A+ EF + + G L + I V
Sbjct: 17 LLTAIAGGEFALEHVSGDWLKVGIVPGEV 45
>3aup_A SBG7S, BG, basic 7S globulin; pepsin-like fold, plant protein;
1.91A {Glycine max}
Length = 403
Score = 27.4 bits (60), Expect = 0.88
Identities = 7/27 (25%), Positives = 10/27 (37%), Gaps = 1/27 (3%)
Query: 52 LWTQCQTCQGSL-HEQVICTSRDCPIF 77
LW C+ S ++ C S C
Sbjct: 47 LWVNCEQQYSSKTYQAPFCHSTQCSRA 73
>2imh_A Hypothetical protein UNP Q5LQD5_silpo; structural genomics, unknown
function, PSI-2, protein struct initiative; HET: MSE;
1.57A {Silicibacter pomeroyi} SCOP: d.153.1.7
Length = 231
Score = 26.5 bits (58), Expect = 1.4
Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 2/47 (4%)
Query: 24 DGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSL--HEQVI 68
RQLA + FTG++ + + G++ V+
Sbjct: 82 AYRQLAAMDLLGNAAAFTGSENQDIKGSVTFASGIASGNMLGDNSVL 128
>3r6b_A Thrombospondin-1; cell adhesion, disulfide bond, EGF-like domain,
TSP-1 type 1; 2.40A {Homo sapiens}
Length = 153
Score = 25.5 bits (56), Expect = 3.3
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 57 QTCQGSLHEQVICTSRDCPI 76
+ C G + E IC +DCP+
Sbjct: 105 KDCVGDVTENQICNKQDCPL 124
Score = 24.3 bits (53), Expect = 8.2
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 59 CQGSLHEQVICTSRDCPI 76
C+G E C CPI
Sbjct: 50 CEGEARETKACKKDACPI 67
>1vex_A F-spondin; TSR, cell adhesion; NMR {Rattus norvegicus}
Length = 56
Score = 24.3 bits (53), Expect = 3.7
Identities = 5/17 (29%), Positives = 7/17 (41%)
Query: 59 CQGSLHEQVICTSRDCP 75
C L + C +CP
Sbjct: 40 CNEDLEQAEKCMLPECP 56
>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 = 25.2 bits (54), Expect = 4.6
Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 11/74 (14%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSLHEQ 66
K ++ + F+ LD R L KI +S + QL ++
Sbjct: 482 KNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL---------KFYKP 532
Query: 67 VICTSRDCPIFYMR 80
IC + P +
Sbjct: 533 YIC--DNDPKYERL 544
>2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA
complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP:
c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A*
2pyj_A* 2pyl_A* 2pzs_A*
Length = 575
Score = 24.9 bits (53), Expect = 6.1
Identities = 6/42 (14%), Positives = 12/42 (28%)
Query: 14 TLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQ 55
K + K+ NS+YG + + +
Sbjct: 366 KWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLK 407
>1pci_A Procaricain; zymogen, hydrolase, thiol protease; 3.20A {Carica
papaya} SCOP: d.3.1.1
Length = 322
Score = 24.9 bits (55), Expect = 6.5
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 13 MTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQL-WTQ 55
++ DEF +K + G + I + F + LP + W +
Sbjct: 73 LSNDEFNEKYV-GSLIDATIEQSYDEEFINEDIVNLPENVDWRK 115
>1y2m_A Phenylalanine ammonia-lyase; alpha helices; HET: MSE; 1.60A
{Rhodosporidium toruloides} PDB: 1t6j_A* 1t6p_A*
Length = 716
Score = 24.7 bits (54), Expect = 7.0
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 16 DEFKKKVLDGRQLALKISANSVYGFT 41
DE + K+ + + SVYG T
Sbjct: 88 DEIRSKIDKSVEFLRSQLSMSVYGVT 113
>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 = 24.6 bits (53), Expect = 8.2
Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 2/35 (5%)
Query: 5 GTKELKEAMT--LDEFKKKVLDGRQLALKISANSV 37
G + +T L+ K + +D +L +S V
Sbjct: 1857 GDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEV 1891
>3cia_A Cold-active aminopeptidase; psychrohilic, hydrolase; 2.70A
{Colwellia psychrerythraea}
Length = 605
Score = 24.4 bits (53), Expect = 8.8
Identities = 8/63 (12%), Positives = 23/63 (36%), Gaps = 5/63 (7%)
Query: 2 VKFGTKELKEAMTLDEFKKKVLDGRQLALKISANS----VYGFTGAQV-GKLPCQLWTQC 56
V + + + + L+ +++ + ++ + + Q GK L++Q
Sbjct: 86 VNYDLAKRDDVLGSKLTINTPLNAKKVRVYYNSTEKATGLQWLSAEQTAGKEKPFLFSQN 145
Query: 57 QTC 59
Q
Sbjct: 146 QAI 148
>3ojy_A Complement component C8 alpha chain; macpf, lipocalin, immune
system; HET: TPO BMA; 2.51A {Homo sapiens}
Length = 554
Score = 24.6 bits (52), Expect = 9.6
Identities = 7/23 (30%), Positives = 9/23 (39%), Gaps = 3/23 (13%)
Query: 53 WTQCQTCQGSLHEQVICTSRDCP 75
WT C CQ ++ S P
Sbjct: 17 WTDCFPCQD---KKYRHRSLLQP 36
>1by8_A Protein (procathepsin K); hydrolase(sulfhydryl proteinase), papain;
2.60A {Homo sapiens} SCOP: d.3.1.1 PDB: 7pck_A
Length = 314
Score = 24.1 bits (53), Expect = 9.9
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 13 MTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLP 49
MT +E +K+ G ++ L S ++ + G+ P
Sbjct: 66 MTSEEVVQKMT-GLKVPLSHSRSNDTLYIPEWEGRAP 101
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
0.324 0.136 0.420
Gapped
Lambda K H
0.267 0.0479 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,518,649
Number of extensions: 73298
Number of successful extensions: 258
Number of sequences better than 10.0: 1
Number of HSP's gapped: 258
Number of HSP's successfully gapped: 37
Length of query: 102
Length of database: 6,701,793
Length adjustment: 67
Effective length of query: 35
Effective length of database: 4,831,086
Effective search space: 169088010
Effective search space used: 169088010
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: 51 (24.0 bits)