RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17021
(199 letters)
>3ei3_A DNA damage-binding protein 1; UV-damage, DDB, nucleotide excision
repair, xeroderma pigmentosum, cytoplasm, DNA repair;
HET: DNA PG4; 2.30A {Homo sapiens} PDB: 3ei1_A* 3ei2_A*
3ei4_A* 4a0l_A* 3e0c_A* 3i7k_A* 3i7h_A* 3i7l_A* 3i7n_A*
3i7o_A* 3i7p_A* 3i89_A* 3i8c_A* 3i8e_A* 2b5l_A 2b5m_A
2hye_A* 4a11_A* 4a0k_C* 4a0a_A* ...
Length = 1158
Score = 133 bits (336), Expect = 2e-36
Identities = 33/127 (25%), Positives = 57/127 (44%)
Query: 69 RLVGNAMEFVHKTSVDEVPYAMCPFQGALLVGVGRYLRLYDLGKKKLLRKCENKHLPNLI 128
+ ++ V + V Y+M F G LL + +RLY+ +K LR N + +
Sbjct: 870 QYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMA 929
Query: 129 VKIESMGHRIYVSDVQESVFLVRYKRYENQLLIFADDTQPRWITTSCVLDYNTVASADKF 188
+ +++ G I V D+ SV L+ YK E A D P W++ +LD + A+
Sbjct: 930 LYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENA 989
Query: 189 GNVCIVS 195
N+ +
Sbjct: 990 FNLFVCQ 996
Score = 60.4 bits (145), Expect = 4e-11
Identities = 21/94 (22%), Positives = 33/94 (35%), Gaps = 7/94 (7%)
Query: 1 MEFVHKTSVDEVPYAMCPFQGALLVGVGRYLRLYDLGKKKLLRKCENKVRIKGFRKAHQT 60
++ V + V Y+M F G LL + +RLY+ +K LR N
Sbjct: 876 LQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNH------YNNIMA 929
Query: 61 HTHSGRSDR-LVGNAMEFVHKTSVDEVPYAMCPF 93
+ D LVG+ M V + +
Sbjct: 930 LYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEI 963
>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 = 37.2 bits (85), Expect = 0.001
Identities = 6/25 (24%), Positives = 15/25 (60%), Gaps = 5/25 (20%)
Query: 144 QESVFLVRYKRYENQLLIFADDTQP 168
++++ K+ + L ++ADD+ P
Sbjct: 19 KQAL-----KKLQASLKLYADDSAP 38
Score = 28.4 bits (62), Expect = 0.95
Identities = 8/31 (25%), Positives = 14/31 (45%), Gaps = 11/31 (35%)
Query: 112 KKKLLRKCENKHL--------PNLIVK--IE 132
+K+ L+K + L P L +K +E
Sbjct: 18 EKQALKKLQAS-LKLYADDSAPALAIKATME 47
>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 = 37.1 bits (85), Expect = 0.003
Identities = 19/99 (19%), Positives = 36/99 (36%), Gaps = 30/99 (30%)
Query: 116 LRKCEN-----KHLPNLIVKIESMGH---------RIYVSDVQESV-FLVRYKRYENQLL 160
L+ C + + L L+ +I+ ++ + +Q + L++ K YEN LL
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL 248
Query: 161 IFADDTQPRWITTSCVLDYNTVASADKFGNVC-IVSTYR 198
+ + Q + F C I+ T R
Sbjct: 249 VL-LNVQNAKA-------------WNAFNLSCKILLTTR 273
Score = 34.8 bits (79), Expect = 0.018
Identities = 28/177 (15%), Positives = 55/177 (31%), Gaps = 40/177 (22%)
Query: 18 PFQGALLV--GV--GRYLRLYDLGKKKLL--RKCENKVRIKGFRKAHQT--HTHSGRSDR 69
P++ LLV V + ++L K LL R + + H + H +
Sbjct: 242 PYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD 301
Query: 70 LVGNAMEFVHK---TSVDEVPYAMC---PFQGALLVGVGRYLRLYDLGKKKLLRKCENKH 123
+ K ++P + P L + +R D +
Sbjct: 302 ---EVKSLLLKYLDCRPQDLPREVLTTNPR---RLSIIAESIR--D-------GLATWDN 346
Query: 124 LPNLIVKIESMGHRIYVS-DVQESVFLVRYKRYENQLLIFADDTQPRWITTS--CVL 177
+ V + + I S +V E Y++ ++L +F I T ++
Sbjct: 347 WKH--VNCDKLTTIIESSLNVLEPA---EYRKMFDRLSVFPPSA---HIPTILLSLI 395
Score = 27.9 bits (61), Expect = 2.5
Identities = 21/131 (16%), Positives = 43/131 (32%), Gaps = 38/131 (29%)
Query: 4 VHKTSVD--EVPYAMCPFQGALLVG-------VGRYLRLYDLGKK-KLLRKC-------E 46
+H++ VD +P +G +L+ + ++ L R E
Sbjct: 445 LHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLE 504
Query: 47 NKVRIKG-----------------FRKAHQTHTHSGRSDRLVGNAMEFVHK--TSVDEVP 87
K+R F K + + + +RLV ++F+ K ++
Sbjct: 505 QKIRHDSTAWNASGSILNTLQQLKFYKPYIC-DNDPKYERLVNAILDFLPKIEENLICSK 563
Query: 88 YAMCPFQGALL 98
Y + AL+
Sbjct: 564 Y-TDLLRIALM 573
>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 = 35.4 bits (81), Expect = 0.009
Identities = 15/92 (16%), Positives = 35/92 (38%), Gaps = 32/92 (34%)
Query: 53 GFRKAHQTHTHSGRSDRLVGNAMEFVHKTSVDE-VPYAMCPFQGALLVGVGRYLRLYDLG 111
G R ++ + ++ ++ +++E +E VP M L + +L
Sbjct: 307 GVR-CYEAYPNTSLPPSILEDSLE------NNEGVPSPM--------------LSISNLT 345
Query: 112 KKKLLRKCE--NKHLPNLIVKIESMGHRIYVS 141
++++ N HLP G ++ +S
Sbjct: 346 QEQVQDYVNKTNSHLPA--------GKQVEIS 369
Score = 33.1 bits (75), Expect = 0.066
Identities = 33/174 (18%), Positives = 58/174 (33%), Gaps = 47/174 (27%)
Query: 20 QGALLVGVGRYLRLYDLGK--KKLLRKCENKVRIK-GFR---------KAHQTHTHSGRS 67
QG+ G+G + LY K + + + +N + GF H +
Sbjct: 1624 QGSQEQGMG--MDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKG 1681
Query: 68 DRLVGNAMEFVHKTSVDEVPYAMCPFQGALLVGVGRYLRLYDL-GKKKLLRKCEN----- 121
R+ N + +T VD F+ + + Y +K LL +
Sbjct: 1682 KRIRENYSAMIFETIVDGKLKTEKIFK-----EINEHSTSYTFRSEKGLLSATQFTQPAL 1736
Query: 122 --------KHLPN--LIVKIESM-GHRI--Y-----VSDV---QESVFLVRYKR 154
+ L + LI + GH + Y ++DV + V +V Y R
Sbjct: 1737 TLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFY-R 1789
Score = 27.7 bits (61), Expect = 3.4
Identities = 19/121 (15%), Positives = 31/121 (25%), Gaps = 44/121 (36%)
Query: 94 QGALLVGVGRYLRLYDLGK--KKLLRKCENKHLPNL---IVKI-------------ESMG 135
QG+ G+G + LY K + + + +N I+ I G
Sbjct: 1624 QGSQEQGMG--MDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKG 1681
Query: 136 HRIYV-------------SDVQESVFLVRYKRYENQLLIFADD---------TQPRWITT 173
RI E +F + + F + TQP
Sbjct: 1682 KRIRENYSAMIFETIVDGKLKTEKIF--KEINEHSTSYTFRSEKGLLSATQFTQPALTLM 1739
Query: 174 S 174
Sbjct: 1740 E 1740
Score = 26.9 bits (59), Expect = 5.6
Identities = 18/140 (12%), Positives = 44/140 (31%), Gaps = 37/140 (26%)
Query: 53 GFRKAHQTH-THSGRSDRLVGNAM-EF---------VHKTSVDEVPYAMCPFQGALLVGV 101
G+ + + G+ D+++ + EF +H ++ LV
Sbjct: 66 GY-VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIH-ALAAKLL----QENDTTLVKT 119
Query: 102 GRYLRLYDLGKKKLLRKCENKHLPNLIVKIESMGHRI------------YVSDVQESVFL 149
++ Y + R + K L + ++ Y ++++
Sbjct: 120 KELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRD---- 175
Query: 150 VRYKRYE---NQLLIFADDT 166
Y+ Y L+ F+ +T
Sbjct: 176 -LYQTYHVLVGDLIKFSAET 194
>3bij_A Uncharacterized protein GSU0716; alpha-beta protein, structural
genomics, PSI-2, protein structure initiative; 2.50A
{Geobacter sulfurreducens pca}
Length = 285
Score = 27.5 bits (60), Expect = 2.7
Identities = 7/29 (24%), Positives = 10/29 (34%)
Query: 22 ALLVGVGRYLRLYDLGKKKLLRKCENKVR 50
AL +G+ + G L CE
Sbjct: 6 ALALGLNAVDPKHYGGWAGKLNACEADAE 34
Score = 27.5 bits (60), Expect = 3.1
Identities = 7/26 (26%), Positives = 10/26 (38%)
Query: 96 ALLVGVGRYLRLYDLGKKKLLRKCEN 121
AL +G+ + G L CE
Sbjct: 6 ALALGLNAVDPKHYGGWAGKLNACEA 31
>2d3o_1 Trigger factor, TF; ribosome, nascent chain, protein folding,
SRP; 3.35A {Deinococcus radiodurans} PDB: 2aar_7
Length = 112
Score = 26.4 bits (59), Expect = 3.2
Identities = 5/18 (27%), Positives = 8/18 (44%)
Query: 39 KKLLRKCENKVRIKGFRK 56
++ VR+ GFR
Sbjct: 28 DQVWAGLARDVRVPGFRP 45
>2nsc_A Trigger factor, TF; chaperone; 2.20A {Thermotoga maritima} PDB:
2nsb_A
Length = 109
Score = 25.9 bits (57), Expect = 4.6
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 39 KKLLRKCENKVRIKGFRK 56
K +R +V I GFRK
Sbjct: 29 DKAVRYLNQRVEIPGFRK 46
>1w26_A Trigger factor, TF; chaperone, protein folding, ribosome
associated protein, nascent chain, cell division,
isomerase; 2.7A {Escherichia coli} SCOP: a.223.1.1
d.241.2.1 d.26.1.1 PDB: 2vrh_A 1w2b_5
Length = 432
Score = 26.9 bits (60), Expect = 5.3
Identities = 10/18 (55%), Positives = 10/18 (55%)
Query: 39 KKLLRKCENKVRIKGFRK 56
K L KVRI GFRK
Sbjct: 29 KSELVNVAKKVRIDGFRK 46
>3gty_X Trigger factor, TF; chaperone-client complex, cell cycle, cell
division, chapero isomerase, rotamase,
ribonucleoprotein, binding; 3.40A {Thermotoga maritima}
PDB: 3gu0_A
Length = 433
Score = 26.9 bits (60), Expect = 5.4
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 39 KKLLRKCENKVRIKGFRK 56
K +R +V I GFRK
Sbjct: 29 DKAVRYLNQRVEIPGFRK 46
>1p9y_A Trigger factor, TF; alpha-beta protein, isomerase; 2.15A
{Escherichia coli} SCOP: d.241.2.1 PDB: 1oms_A*
Length = 121
Score = 25.7 bits (57), Expect = 6.5
Identities = 9/18 (50%), Positives = 9/18 (50%)
Query: 39 KKLLRKCENKVRIKGFRK 56
K L KVRI G RK
Sbjct: 32 KSELVNVAKKVRIDGLRK 49
>1t11_A Trigger factor, TF; helix-turn-helix, four-helix-bundle, ppiase,
chaperone; 2.50A {Vibrio cholerae} SCOP: a.223.1.1
d.241.2.1 d.26.1.1 PDB: 1l1p_A
Length = 392
Score = 26.5 bits (59), Expect = 7.8
Identities = 7/18 (38%), Positives = 7/18 (38%)
Query: 39 KKLLRKCENKVRIKGFRK 56
LR R GFRK
Sbjct: 32 AAELRNIAKNRRFDGFRK 49
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 0.140 0.423
Gapped
Lambda K H
0.267 0.0486 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,015,349
Number of extensions: 169529
Number of successful extensions: 368
Number of sequences better than 10.0: 1
Number of HSP's gapped: 366
Number of HSP's successfully gapped: 21
Length of query: 199
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 110
Effective length of database: 4,216,824
Effective search space: 463850640
Effective search space used: 463850640
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: 55 (25.5 bits)