RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2882
(1428 letters)
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil
dynamics, inhibitor design, complex
(polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP:
a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A*
1taq_A*
Length = 832
Score = 347 bits (893), Expect = e-103
Identities = 90/268 (33%), Positives = 140/268 (52%), Gaps = 9/268 (3%)
Query: 779 IDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRN 838
+DG YR F+AL + PV A+YG K L K K + +FDAK +FR+
Sbjct: 17 VDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALK-EDGDAVIVVFDAKAPSFRH 75
Query: 839 ILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNL 898
Y YKA R P + Q+ LI ++V +G L + G EADDV+ +LAK+A K
Sbjct: 76 EAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKA-EKEGY 134
Query: 899 KVIISTNDKDMAQLVSNKIALIN-NNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLP 957
+V I T DKD+ QL+S++I +++ + + ++G+ P++ DY +L GD SDNLP
Sbjct: 135 EVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTGDESDNLP 194
Query: 958 GVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDL 1017
GVK IG KTA KLL ++ SLE ++ N + +K I + + ++ L + ++TD L
Sbjct: 195 GVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLKLSWDLAKVRTDLPL 254
Query: 1018 TKNIVSIPESLILQPKDEKLLMQLFNKY 1045
+ + D + L +
Sbjct: 255 E------VDFAKRREPDRERLRAFLERL 276
>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily,
SH3-like domain, produc structure, DNA damage, DNA
repair, exonuclease; HET: TMP; 1.50A {Escherichia coli}
SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A*
3hp9_A*
Length = 482
Score = 293 bits (750), Expect = 1e-87
Identities = 170/473 (35%), Positives = 259/473 (54%), Gaps = 12/473 (2%)
Query: 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLIT 369
STFL++DYETFG + DRP QFAAIRTD N I P + YCKPA D+LP P A LIT
Sbjct: 8 QSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLIT 67
Query: 370 KITPQFCLNNGIPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYERE 429
ITPQ G E FA+ I +F P T +GYN + FDDE+TR +F+RN +PY
Sbjct: 68 GITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWS 127
Query: 430 WKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDV 489
W+++ SRWDL++V++A Y L P GI WP ++G PSF+LEHL+ N + H AHDA++DV
Sbjct: 128 WQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHSNAHDAMADV 187
Query: 490 RATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMW 549
AT+ +A+L++ PRLF+++ + R K ++A I P +P +++ MF + S +
Sbjct: 188 YATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVA 247
Query: 550 PICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFK--EDIPISMIHLNRSP 607
P+ HP N+N +I +L D L D + +R+ L K +P+ ++H+N+ P
Sbjct: 248 PLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCP 307
Query: 608 IVISNLKVLSSNLMFRYKFDLNCAFKNIKCASSILNNTYIWKKIFLDYKINNSDLELNID 667
++ L R + N+K IF + + N+D
Sbjct: 308 VLA-QANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTP--SDNVD 364
Query: 668 EELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYRARNFIETLSYKEL 727
+LYN F S D + I+ P+ L ++ F +K++E+L+F YRARNF TL Y E
Sbjct: 365 AQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQ 424
Query: 728 KRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKA--NEHDTKILNALLMYGK 778
+RW ++R F + + + E++ L+++ ++ +L AL Y
Sbjct: 425 QRWLEHRRQVFTPE-----FLQGYADELQMLVQQYADDKEKVALLKALWQYAD 472
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage
T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A
Length = 290
Score = 280 bits (718), Expect = 1e-85
Identities = 47/274 (17%), Positives = 101/274 (36%), Gaps = 23/274 (8%)
Query: 779 IDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRN 838
+DG++ +R + + ++ L K+Y A + D FR
Sbjct: 24 VDGTNLGFRFKHNNS--------KKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRL 75
Query: 839 ILYPSYKATRKKMPYNLILQINLIHQM----------VKAIGWPILIIKGVEADDVIGTL 888
P YK R + + + + + +P I+GVEADD+ +
Sbjct: 76 EHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYI 135
Query: 889 AKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NNKIHDRTTIISRFGVSP-EKIVDY 945
K V + + D D L+++K++ + + + + V E+ +
Sbjct: 136 VKLI-GHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISL 194
Query: 946 FSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGV-IGKNLRFALNWLPK 1004
+++GD+ DN+ GV+ IG K ++ ++ ++ +II+ +NL + L +
Sbjct: 195 KAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFR 254
Query: 1005 LKKILTIKTDCDLTKNIVSIPESLILQPKDEKLL 1038
++ + T C V ++
Sbjct: 255 NLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIA 288
>2do8_A UPF0301 protein HD_1794; NESG, GFT structral genomics, HDR14,
structural genomics, PSI, protein structure initiative;
NMR {Haemophilus ducreyi} SCOP: d.310.1.1
Length = 188
Score = 207 bits (529), Expect = 1e-61
Identities = 66/187 (35%), Positives = 109/187 (58%), Gaps = 10/187 (5%)
Query: 1073 NLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTDMTINILLDNDSNLKLKL 1132
NL F+IA P +FD V+Y+CEHN NG G+IIN PTD+++ LL ++
Sbjct: 4 NLQGKFIIATPEMDDEYFDRTVIYICEHNDNGTIGVIINTPTDLSVLELLT-------RM 56
Query: 1133 VPNTKEFILEKTTKTIMFGGPIQIDRGFVLHNITNEKSPIFNSTLNIASDISLTTSRDIL 1192
+ + + ++ GGP+ DRGF++H+ T+ + F + + DI+LTTS D+L
Sbjct: 57 DFQMAKPRIYTQDQMVLNGGPVNQDRGFIVHSKTDHE---FTHSYKVTDDITLTTSGDVL 113
Query: 1193 ESFSRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIVDANSEVIFNVPCEQRFFAAVKL 1252
+SF P + ++ LGCS W QLE+EI N+WL+ +AN++ +F R+ A ++
Sbjct: 114 DSFGTQTAPEKFIVCLGCSTWKPHQLEQEIAQNYWLLSEANNQTLFETSYLDRWVEANEM 173
Query: 1253 LGVNPLI 1259
LG++ ++
Sbjct: 174 LGISGIL 180
>2haf_A Putative translation repressor; alpha/beta, X-RAY crystallography,
structural genomics, PSI, protein structure initiative;
2.88A {Vibrio cholerae} SCOP: d.310.1.1 PDB: 2aj2_A
Length = 211
Score = 200 bits (509), Expect = 1e-58
Identities = 77/212 (36%), Positives = 125/212 (58%), Gaps = 12/212 (5%)
Query: 1055 NISDENYDIDCSDAKSLFNLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPT 1114
++S+ + DI+ + NLTNHFL+AMP P+F +V+Y+CEHN +GA G++IN P
Sbjct: 2 SLSNHSSDIEVGHS---MNLTNHFLVAMPSMKDPYFKRSVIYICEHNQDGAMGLMINAPI 58
Query: 1115 DMTINILLDNDSNLKLKLVPNTKEFILEKTTKTIMFGGPIQIDRGFVLHNITNEKSPIFN 1174
D+T+ +L ++ + P + E K + GGP+ DRGF+LH +
Sbjct: 59 DITVGGMLK-----QVDIEPAYPQSHQENLKKPVFNGGPVSEDRGFILHR----PRDHYE 109
Query: 1175 STLNIASDISLTTSRDILESFSRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIVDANS 1234
S++ + DI++TTS+DIL P +++LG SGW AGQLE E+ N WL ++A+
Sbjct: 110 SSMKMTDDIAVTTSKDILTVLGTEAEPEGYIVALGYSGWSAGQLEVELTENSWLTIEADP 169
Query: 1235 EVIFNVPCEQRFFAAVKLLGVNPLIIGIAFGN 1266
E+IFN P +++ A++ LG++P + G+
Sbjct: 170 ELIFNTPVHEKWQKAIQKLGISPAQLSSDAGH 201
>2ew0_A Hypothetical protein aciad0353; Q5FF54, ASR1, NESG, structural
genomics, PSI, protein struct initiative; 1.40A
{Acinetobacter SP} SCOP: d.310.1.1
Length = 192
Score = 196 bits (501), Expect = 1e-57
Identities = 69/199 (34%), Positives = 110/199 (55%), Gaps = 15/199 (7%)
Query: 1073 NLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTDMTINILLDNDSNLKLKL 1132
LT+ LIA P + FF V+YL H+ GA GIIIN+P + I LL++ L +
Sbjct: 5 YLTHRCLIAPPEMADDFFANTVIYLARHDEEGAQGIIINRPAGIQIKELLND---LDIDA 61
Query: 1133 VPNTKEFILEKTTKTIMFGGPIQIDRGFVLHNITNEKSPIFNSTLNIASDISLTTSRDIL 1192
++ GGP++ + GFVLH P ++S++ + ++ +TTS+DIL
Sbjct: 62 DNVNPH--------EVLQGGPLRPEAGFVLHT----GQPTWHSSIAVGENVCITTSKDIL 109
Query: 1193 ESFSRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIVDANSEVIFNVPCEQRFFAAVKL 1252
++ + +G + I+LG + WG QLE+EI WLI DA+ ++IFN+P + R+ AA K
Sbjct: 110 DAIAHNEGVGRYQIALGYASWGKNQLEDEIARGDWLICDADMDLIFNLPYDDRWDAAYKK 169
Query: 1253 LGVNPLIIGIAFGNTLIKH 1271
+GV+ + G+ L H
Sbjct: 170 IGVDRTWLASEIGHALEHH 188
>2gzo_A UPF0301 protein SO3346; GFT-protein structure, nesgc, alpha-beta,
structural genomics, PSI, protein structure initiative;
NMR {Shewanella oneidensis} SCOP: d.310.1.1
Length = 195
Score = 195 bits (498), Expect = 2e-57
Identities = 68/194 (35%), Positives = 108/194 (55%), Gaps = 10/194 (5%)
Query: 1073 NLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTDMTINILLDNDSNLKLKL 1132
+L NHFLIAMP FF+ V+YLCEH+ GA G++INKP + +N LL+ + L
Sbjct: 3 SLQNHFLIAMPSLDDTFFERTVIYLCEHDEKGAMGLVINKPLGIEVNSLLEQ---MDLPT 59
Query: 1133 VPNTKEFILEKTTKTIMFGGPIQIDRGFVLHNITNEKSPIFNSTLNIASDISLTTSRDIL 1192
+ + + ++ GGP+ DRGFVLH P + ++ + S + LTTSRD+L
Sbjct: 60 EQVSADLAMGSQ---VLMGGPVSQDRGFVLHT----SQPYWANSTELGSGLMLTTSRDVL 112
Query: 1193 ESFSRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIVDANSEVIFNVPCEQRFFAAVKL 1252
+ P + L++LG +GW QLE+E+ +N WL + A+ ++F++ E R+ A +
Sbjct: 113 TAIGSKRSPDKFLVALGYAGWSKNQLEQELADNSWLTIPADHALLFDINHEDRWQQASRS 172
Query: 1253 LGVNPLIIGIAFGN 1266
LG + G+
Sbjct: 173 LGFEAWQLSTQAGH 186
>3r8s_H 50S ribosomal protein L9; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_F
1p86_F 1vs8_H 1vs6_H 2aw4_H 2awb_H 2gya_F 2gyc_F 1vt2_H
2i2v_H 2j28_H 2i2t_H* 2qao_H* 2qba_H* 2qbc_H* 2qbe_H
2qbg_H 2qbi_H* 2qbk_H* 2qov_H ...
Length = 149
Score = 176 bits (448), Expect = 3e-51
Identities = 54/135 (40%), Positives = 81/135 (60%), Gaps = 1/135 (0%)
Query: 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFT 233
MQVILL + NLG LG+ + VK GYARNFL+P+ KA ATK I+ FE +R +LE
Sbjct: 1 MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE 60
Query: 234 IFLNAKKIGEEIKKLN-INIIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNN 292
+ A E+I L + I K+G +GKLFGS+ DI + G+++ K++++LPN
Sbjct: 61 VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG 120
Query: 293 SIKKIGNYYIDILLH 307
++ G + + +H
Sbjct: 121 VLRTTGEHEVSFQVH 135
>2gs5_A Conserved hypothetical protein; corvnebacterium diphtheria,
structural genomics, PSI; 1.50A {Corynebacterium
diphtheriae nctc 13129ORGANISM_TAXID} SCOP: d.310.1.1
PDB: 2hrx_A
Length = 198
Score = 176 bits (448), Expect = 2e-50
Identities = 26/193 (13%), Positives = 61/193 (31%), Gaps = 24/193 (12%)
Query: 1073 NLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTDMTINILLDNDSNLKLKL 1132
L+A P + F +V+ + EH+ FG+ + +D+ + ++ K
Sbjct: 15 PAPGMVLVAAPSMESEDFARSVILIIEHSEYATFGVNLASRSDVAVFNVIPEWVPCVTK- 73
Query: 1133 VPNTKEFILEKTTKTIMFGGPIQIDRGFVLHNITNEKSPIFNSTLNIASDISLTTSRDIL 1192
+ + GGP+ + +++ +R ++
Sbjct: 74 ------------PQALYIGGPLNQQSVVGVG------VTAQGVDAARVDNLTRLANRLVM 115
Query: 1193 ESFSRGDGP-----SQLLISLGCSGWGAGQLEEEIMNNHWLIVDANSEVIFNVPCEQRFF 1247
+ S + + G + W GQL +EI N W + A + +
Sbjct: 116 VNLGADPEEIKPLVSGMRLFAGHAEWAPGQLAQEIENGDWFVAPALPSDVTAPGSVDVWG 175
Query: 1248 AAVKLLGVNPLII 1260
++ + +
Sbjct: 176 DVMRRQPMPLPLY 188
>1div_A Ribosomal protein L9; rRNA-binding; 2.60A {Geobacillus
stearothermophilus} SCOP: d.99.1.1 d.100.1.1 PDB: 1giy_K
1yl3_K 2b66_I 2b9n_I 2b9p_I 487d_K
Length = 149
Score = 171 bits (436), Expect = 2e-49
Identities = 54/135 (40%), Positives = 83/135 (61%), Gaps = 2/135 (1%)
Query: 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFT 233
M+VI LKD+ GK GEI V +GYA NFL + A AT +K E ++ K ++ A
Sbjct: 1 MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQKEQRQAAE 60
Query: 234 IFLNAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKK-GLKIEKNKIKLPNN 292
NAKK+ E+++KL + I K+G G+LFGS+T+ I + L+ + GLK++K KI+L +
Sbjct: 61 ELANAKKLKEQLEKLTVTIPAKAGEGGRLFGSITSKQIAESLQAQHGLKLDKRKIELADA 120
Query: 293 SIKKIGNYYIDILLH 307
I+ +G + + LH
Sbjct: 121 -IRALGYTNVPVKLH 134
>3v2d_I 50S ribosomal protein L9; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2j03_I 2jl6_I 2jl8_I 2v47_I 2v49_I 2wdi_I 2wdj_I 2wdl_I
2wdn_I 2wh2_I 2x9s_I 2x9u_I 2xg0_I 2xg2_I 3hux_I 3huz_I
3i8f_K 3i8i_K 3i9c_K 3i9e_K ...
Length = 148
Score = 167 bits (425), Expect = 5e-48
Identities = 45/135 (33%), Positives = 79/135 (58%), Gaps = 3/135 (2%)
Query: 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFT 233
M+VILL+ + NLG +G+++ VK GYARN+L+P+ A AT+ +K E + K
Sbjct: 1 MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE 60
Query: 234 IFLNAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKK-GLKIEKNKIKLPNN 292
A+++ E ++ L + I ++G + K++GSVT DI + L ++ G+ I+ ++ L
Sbjct: 61 RKAEAERLKEILENLTLTIPVRAG-ETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKP 119
Query: 293 SIKKIGNYYIDILLH 307
IK++G Y + H
Sbjct: 120 -IKELGEYVLTYKPH 133
>3bbo_J Ribosomal protein L9; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 197
Score = 168 bits (428), Expect = 7e-48
Identities = 42/139 (30%), Positives = 78/139 (56%), Gaps = 4/139 (2%)
Query: 171 RKNMQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKT 230
+K +VIL +D+ +LGK G+++ VK G+ RNFL+P KA+ T ++KE + + ++E
Sbjct: 47 KKLRKVILKEDVTDLGKQGQLLDVKAGFFRNFLLPTGKAQLMTPLLLKELKMEDERIEAE 106
Query: 231 AFTIFLNAKKIGEEIKKLN-INIIKKSGVDGKLFGSVTNSDIVKELEKK-GLKIEKNKIK 288
+ A+++ + + + +K G +FGSVT D+V ++ + I+K +
Sbjct: 107 KQRVKEEAQQLAMVFQTVGAFKVKRKGGKGKLIFGSVTAQDLVDIIKSQLQKDIDKRLVS 166
Query: 289 LPNNSIKKIGNYYIDILLH 307
LP I++ G Y ++ LH
Sbjct: 167 LPE--IRETGEYIAELKLH 183
>1nkw_F 50S ribosomal protein L9; ribosome, large subunit, X- RAY
structure, peptidyl-transferase, peptide bond formation;
3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB:
1nwx_F* 1nwy_F* 1sm1_F* 1xbp_F* 1pnu_F 1pny_F 1vor_I
1vou_I 1vow_I 1voy_I 1vp0_I
Length = 146
Score = 166 bits (423), Expect = 8e-48
Identities = 46/134 (34%), Positives = 79/134 (58%), Gaps = 3/134 (2%)
Query: 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFT 233
MQVILL+ LGK GE++ VK+GYARN+LIP+ A AT+ +K E + +EK
Sbjct: 1 MQVILLEPS-RLGKTGEVVSVKDGYARNWLIPQGLAVSATRTNMKTLEAQLRSIEKRQAQ 59
Query: 234 IFLNAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNS 293
A+ + + + + + ++G +GK++G+VT+ D+ L++ G +++ KI +P
Sbjct: 60 EKAVAEDLASRLNGVAVELSVRAG-EGKIYGAVTHQDVANSLDQLGFDVDRRKIDMPKT- 117
Query: 294 IKKIGNYYIDILLH 307
+K++G Y I H
Sbjct: 118 VKEVGEYDIAYRAH 131
>3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F
1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F
2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F*
2vho_F ...
Length = 135
Score = 120 bits (304), Expect = 4e-32
Identities = 44/91 (48%), Positives = 63/91 (69%)
Query: 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRF 60
MIERY I +GKIHRLEDWGRR LAY I K+ KAHY+ N+E ++ + E+ET+FRF
Sbjct: 21 MIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRF 80
Query: 61 NDAILRYLTIKTKKVETEESSFLRFIQKKEK 91
NDA++R + ++TK TE S ++ ++ +
Sbjct: 81 NDAVIRSMVMRTKHAVTEASPMVKAKDERRE 111
>3r8n_F 30S ribosomal protein S6; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_F 3fih_F* 3iy8_F 2wwl_F 3oar_F 3oaq_F
3ofb_F 3ofa_F 3ofp_F 3ofx_F 3ofy_F 3ofo_F 3r8o_F 4a2i_F
2gy9_F 2gyb_F
Length = 100
Score = 116 bits (292), Expect = 7e-31
Identities = 44/80 (55%), Positives = 58/80 (72%)
Query: 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRF 60
MIERY I +GKIHRLEDWGRR LAY I K+ KAHY+ N+E ++ + E+ET+FRF
Sbjct: 21 MIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRF 80
Query: 61 NDAILRYLTIKTKKVETEES 80
NDA++R + ++TK TE S
Sbjct: 81 NDAVIRSMVMRTKHAVTEAS 100
>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG,
structure initiative, PSI, joint center for structural
GENO translation; 1.70A {Thermotoga maritima} SCOP:
d.58.14.1
Length = 140
Score = 108 bits (272), Expect = 1e-27
Identities = 30/92 (32%), Positives = 45/92 (48%), Gaps = 1/92 (1%)
Query: 1 MIERYKKIIIS-GKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFR 59
++ER KKII KGKI ++E G R AY+IKK + Y + + L E+E +R
Sbjct: 39 LVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGDYTVIYFRCDGQNLQELENFYR 98
Query: 60 FNDAILRYLTIKTKKVETEESSFLRFIQKKEK 91
I+R+ T + +E +E R E
Sbjct: 99 VTPEIIRWQTFRRFDLEKKERKAQREKAAAEA 130
>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RIBO protein S6,
RNA-binding, rRNA-binding, protein folding; 2.3A
{Aquifex aeolicus} SCOP: d.58.14.1
Length = 110
Score = 106 bits (268), Expect = 2e-27
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEI-NKKTLLEIETSFR 59
E+ K+ I G+I EDWG R LAY I+K A Y + N + E++ +
Sbjct: 28 KFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYFLVQFKTENPQLPNELDFQLK 87
Query: 60 FNDAILRYLTIKTKKVETEESS 81
++ ++R+L I+ K+ E ++++
Sbjct: 88 IDEDVIRWLNIQIKESEVKKNA 109
>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease, hydrolase,
endonuclease; 1.50A {Enterobacteria phage T4} PDB: 2ihn_A
3h8w_A 3h8j_A 1tfr_A 3h8s_A
Length = 305
Score = 112 bits (282), Expect = 3e-27
Identities = 47/295 (15%), Positives = 87/295 (29%), Gaps = 23/295 (7%)
Query: 779 IDGSSCIYRAFYALPDIRNIDNFPVGALY----GTIKMLRKLYKNYRATYIACIFDAKGK 834
ID S + + + + + +IK K K T I D
Sbjct: 18 IDFSQIALSTALV--NFPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKS 75
Query: 835 N-FRNILYPSYKATRKKMPYNL--------ILQINLIHQMVKAIGWPILIIKGVEADDVI 885
+R YK R K +I ++ + + ++ I EA+D I
Sbjct: 76 GYWRRDFAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEANDHI 135
Query: 886 GTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDY 945
L K+ + K++I ++D D QL + + S E
Sbjct: 136 AVLVKKF-SLEGHKILIISSDGDFTQLHKYPNVKQWSPM---HKKWVKIKSGSAEIDCMT 191
Query: 946 FSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKL 1005
L GD DN+ VK ++ + + + +
Sbjct: 192 KILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIANDREQAKVLLTESEYNRY 251
Query: 1006 KKILTIKTDCDLTKNIVS--IPESLILQPKDEKLLMQLFNKYNIPLKNHDDNISD 1058
K+ L + + NI S + + + F K L ++I++
Sbjct: 252 KENLVLIDFDYIPDNIASNIVNYYNSYKLPPRGKIYSYFVKAG--LSKLTNSINE 304
>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A
{Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A
1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F*
1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F*
1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ...
Length = 101
Score = 105 bits (264), Expect = 4e-27
Identities = 13/80 (16%), Positives = 39/80 (48%)
Query: 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRF 60
E ++ + + ++ ++ G R LAY I K + +++ + +E+ + + ++ R
Sbjct: 22 EKEIIQRALENYGARVEKVAILGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRI 81
Query: 61 NDAILRYLTIKTKKVETEES 80
D + R + +K+++ +
Sbjct: 82 RDNVRRVMVVKSQEPFLANA 101
>2gm2_A Conserved hypothetical protein; MTH938-like fold, structural
genomics, PSI, protein structure initiative; NMR
{Xanthomonas campestris PV}
Length = 132
Score = 105 bits (264), Expect = 1e-26
Identities = 35/123 (28%), Positives = 54/123 (43%), Gaps = 1/123 (0%)
Query: 1305 MELKKIINTKHQTIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDFIH 1364
M L + + A K N +SF++ P+ W + L
Sbjct: 1 MPLNQEHPDYTYALRAADGRHAKV-NEQILQQSFILMPDELVEHWPVPSLGQLQPAHMDA 59
Query: 1365 ISKFNPSVVILGTGNIQHFIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAMLA 1424
+ NP+V++LGTG Q F + + IG+E M N AA RTYN+L S+ + LA
Sbjct: 60 VLALNPAVILLGTGERQQFPSTDVLAACLTRGIGLEAMTNAAAARTYNVLASEGRRVALA 119
Query: 1425 LIL 1427
+I+
Sbjct: 120 MIV 122
>3r3t_A 30S ribosomal protein S6; structural genomics, center for
structural genomics of infec diseases, csgid,
beta-barrel, cytosol; 2.30A {Bacillus anthracis}
Length = 99
Score = 104 bits (261), Expect = 1e-26
Identities = 19/74 (25%), Positives = 44/74 (59%)
Query: 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRF 60
++ER+ ++ + +I ++WG+R LAY+I + + Y+ N+ N + + E + +
Sbjct: 25 LVERFAGVLTNNGAEIINTKEWGKRRLAYEINDLREGFYMILNVNANAEAINEFDRLAKI 84
Query: 61 NDAILRYLTIKTKK 74
N+ ILR++ +K ++
Sbjct: 85 NEDILRHIVVKEEE 98
>2fi9_A Outer membrane protein; bartonella hense protein structure
initiative, midwest center for structural genomics, MCSG;
1.80A {Bartonella henselae} SCOP: c.103.1.1
Length = 128
Score = 96.8 bits (241), Expect = 1e-23
Identities = 28/124 (22%), Positives = 55/124 (44%), Gaps = 5/124 (4%)
Query: 1305 MELKKIINTKHQTIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDF-- 1362
+++++ I AY N G +F + + S + P I+ T++D
Sbjct: 5 IQIREAHFPGRAPIDAYGNGGFRF-ADMSHRGSIICIPSG--IYGIDMTGPVPTQEDISR 61
Query: 1363 IHISKFNPSVVILGTGNIQHFIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAM 1422
+ V+++GTG + +L +L +K I + M+ AA RT+N+L+++D
Sbjct: 62 VLEESDQIEVLLIGTGVELLRLPEELRVLLWEKRISSDTMSTGAAVRTFNVLLAEDRAVA 121
Query: 1423 LALI 1426
L
Sbjct: 122 ALLF 125
>2vqe_R 30S ribosomal protein S18; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: a.4.8.1 PDB: 1fka_R
1fjg_R 1gix_U* 1hnw_R* 1hnx_R* 1hnz_R* 1hr0_R 1ibk_R*
1ibl_R* 1ibm_R 1j5e_R 1jgo_U* 1jgp_U* 1jgq_U* 1ml5_U*
1n32_R* 1n33_R* 1n34_R 1n36_R 1xmo_R* ...
Length = 88
Score = 94.3 bits (235), Expect = 3e-23
Identities = 18/66 (27%), Positives = 31/66 (46%)
Query: 103 KNRFKQKRQQQNPLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSH 162
+ + +++ RK + T+ DY+++E LK F+ E GKI+ R TG
Sbjct: 2 STKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGK 61
Query: 163 YQRQIT 168
QR +
Sbjct: 62 EQRILA 67
>3i1m_R 30S ribosomal protein S18; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_R* 1vs5_R 3i1o_R 3i1q_R 3i1s_R
3i1z_R 3i21_R 3izv_V* 3izw_V* 3kc4_R 3or9_R 3ora_R
3sfs_R* 3uoq_R* 2qal_R* 1p6g_R 1p87_R 2aw7_R 2avy_R
2i2u_R ...
Length = 75
Score = 91.5 bits (228), Expect = 2e-22
Identities = 30/52 (57%), Positives = 43/52 (82%)
Query: 117 FKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQIT 168
F+R+KFCRFT +++IDYKDI TLK++I E+GKI+ +R+TGT + YQRQ+
Sbjct: 5 FRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLA 56
>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 168
Score = 91.5 bits (227), Expect = 3e-21
Identities = 17/83 (20%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKA---------HYICFNIEINKKTL 51
+ ++Y++++++G + + G LAY IK+ KA Y+ F +++
Sbjct: 83 LTQKYEELLVAGGAMYVEVFNRGVIPLAYSIKRKNKAGETNNYLDGIYLLFTYFTKPESI 142
Query: 52 LEIETSFRFNDAILRYLTIKTKK 74
+E + +D ++R + K +K
Sbjct: 143 SPLEAALVTDDDVIRSSSFKIRK 165
>3cpk_A Uncharacterized protein Q7W7N7_borpa; BPP2477, BER31, NESG,
structural genomics, PSI-2, protein structure initiative;
2.50A {Bordetella parapertussis 12822} PDB: 2k2e_A
Length = 150
Score = 89.4 bits (221), Expect = 7e-21
Identities = 35/148 (23%), Positives = 64/148 (43%), Gaps = 25/148 (16%)
Query: 1305 MELKKIINTKHQTIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDFIH 1364
M+L T T+ AY + ++ N + ++ + +PE W + + +T
Sbjct: 1 MKLHTDPATALNTVTAYGDGYIEV-NQVRFSHAIAFAPEGPVASWPVQRPADITASLLQQ 59
Query: 1365 ISKF------------------------NPSVVILGTGNIQHFIHPKLTYILTQKNIGIE 1400
+ P V+++GTG QH + P+ L +G+E
Sbjct: 60 AAGLAEVVRDPLAFLDEPEAGAGARPANAPEVLLVGTGRRQHLLGPEQVRPLLAMGVGVE 119
Query: 1401 CMNNQAACRTYNILVSDDIKAMLALILD 1428
M+ QAA RTYNIL+++ + ++AL+ D
Sbjct: 120 AMDTQAAARTYNILMAEGRRVVVALLPD 147
>2fvt_A Conserved hypothetical protein; MTH938-like fold, structural
genomics, PSI, protein structure initiative; NMR
{Rhodopseudomonas palustris} SCOP: c.103.1.1
Length = 135
Score = 88.5 bits (219), Expect = 1e-20
Identities = 28/113 (24%), Positives = 46/113 (40%), Gaps = 4/113 (3%)
Query: 1316 QTIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDF--IHISKFNPSVV 1373
I AY G F G+ + S L P+ W + K + + + + +
Sbjct: 14 AAIDAYGKGGFYF-AGMSHQGSLLFLPD-AVWGWDVTKPEQIDRYSLQRVFDNANAIDTL 71
Query: 1374 ILGTGNIQHFIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAMLALI 1426
I+GTG +L L N+ ++ M A RTYNI++ + + ALI
Sbjct: 72 IVGTGADVWIAPRQLREALRGVNVVLDTMQTGPAIRTYNIMIGERRRVAAALI 124
>2hba_A BL17, 50S ribosomal protein L9; NTL9, K12M, RNA binding protein;
1.25A {Geobacillus stearothermophilus} SCOP: d.100.1.1
PDB: 1cqu_A 2hbb_A 2hvf_A
Length = 52
Score = 85.0 bits (211), Expect = 2e-20
Identities = 23/51 (45%), Positives = 31/51 (60%)
Query: 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKR 224
M+VI LKD+ +GK GEI V +GYA NFL + A AT +K E ++
Sbjct: 1 MKVIFLKDVKGMGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQK 51
>3bbn_R Ribosomal protein S18; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 103
Score = 77.1 bits (190), Expect = 5e-17
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 111 QQQNPLFKRKKFCRFTVMNIK---QIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQI 167
+ + P K K+ R + I+ +IDY+++ + FI E GKI++ R+ QR I
Sbjct: 3 KSKRPFIKSKRSFRRRLPPIQSGDRIDYRNMSLISRFISEQGKILSRRVNRLTLKQQRLI 62
Query: 168 T 168
T
Sbjct: 63 T 63
>3r8n_R 30S ribosomal protein S18; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_R 3fih_R* 3iy8_R 2wwl_R
3oar_R 3oaq_R 3ofb_R 3ofa_R 3ofp_R 3ofx_R 3ofy_R 3ofo_R
3r8o_R 4a2i_R
Length = 55
Score = 69.1 bits (170), Expect = 8e-15
Identities = 22/37 (59%), Positives = 31/37 (83%)
Query: 132 QIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQIT 168
+IDYKDI TLK++I E+GKI+ +R+TGT + YQRQ+
Sbjct: 1 EIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLA 37
>2ab1_A Hypothetical protein; HS.95870, DUF498, structural genomics, protein
structure INI PSI, center for eukaryotic structural
genomics, CESG; 2.59A {Homo sapiens} SCOP: c.103.1.1 PDB:
2q4q_A
Length = 122
Score = 71.5 bits (175), Expect = 8e-15
Identities = 16/117 (13%), Positives = 37/117 (31%), Gaps = 7/117 (5%)
Query: 1317 TIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNF-----LTKKDFIHISKFNPS 1371
I + + +K + K V P W + + D + +
Sbjct: 5 EIASLSWGQMKVKGSNTTYKDCKVWPG-GSRTWDWRETGTEHSPGVQPADVKEVVEKGVQ 63
Query: 1372 VVILGTGNIQHF-IHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAMLALIL 1427
+++G G + + L + I + + + A + YN LV+ ++
Sbjct: 64 TLVIGRGMSEALKVPSSTVEYLKKHGIDVRVLQTEQAVKEYNALVAQGVRVGGVFHS 120
>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 = 78.0 bits (191), Expect = 2e-14
Identities = 97/632 (15%), Positives = 206/632 (32%), Gaps = 165/632 (26%)
Query: 646 YIWKKIFLDYKIN-NSDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNF-CFEN 703
Y +K I ++ + + +++ + +SK++ + I+ S + F +
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEE-ID-HIIMSKDAVSGTLRLFWTLLS 73
Query: 704 KKLEELIFLYRARNFIETL---SYKELK-RWK-----KYRISRFYN-KKNNLYNIN-MF- 751
K+ EE++ + F+E + +YK L K ++R Y +++ LYN N +F
Sbjct: 74 KQ-EEMV-----QKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA 127
Query: 752 ---------YLEIESLLKKANEHDTKILNALLMYGKIDGSSCIYRAFYALPDIRNIDNFP 802
YL++ L + +++ +L GK + + A +
Sbjct: 128 KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK----TWV--ALDVCLSYKVQCKMD 181
Query: 803 VGALY----------GTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMP 852
+ ++ML+KL I + ++ + NI + +
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQ-----IDPNWTSRSDHSSNIKLRIHSIQAELR- 235
Query: 853 YNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNL--KVIISTNDKDMA 910
L+ L++ +V +A NL K++++T K +
Sbjct: 236 -RLLKS----KPYENC-----LLV----LLNV---QNAKAWNAFNLSCKILLTTRFKQVT 278
Query: 911 QLVSN----KIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMS-DNLPG-VKKIGP 964
+S I+L +++ ++P+++ D +LP V P
Sbjct: 279 DFLSAATTTHISLDHHSM-----------TLTPDEVKSLLLKYLDCRPQDLPREVLTTNP 327
Query: 965 KTAVKLL----------------NQYNSLENIINNA-NNIKGVIGKNLRFALNWLPK--- 1004
+ ++ + L II ++ N ++ + + L+ P
Sbjct: 328 -RRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH 386
Query: 1005 -------------------------LKKILTIKTDCDLTKNIVSIPESLILQPKDEKLL- 1038
K L K + T +I SI L ++ ++E L
Sbjct: 387 IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALH 446
Query: 1039 MQLFNKYNIPLKNHDDNISDENYDIDCSDAKSLFNLTNHFLIAMPG-----FSTPFFD-- 1091
+ + YNIP D++ D ++ +H F F D
Sbjct: 447 RSIVDHYNIPKTFDSDDLIP-----PYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFR 501
Query: 1092 ---GAVVYLCEHNSNGAFGIIINKPTDMTI--NILLDNDSNLKLKLVPNTKEFILEKTTK 1146
+ + + A G I+N + + DND + +LV +F+ +
Sbjct: 502 FLEQKIRHDS--TAWNASGSILNTLQQLKFYKPYICDNDPKYE-RLVNAILDFLPKIEEN 558
Query: 1147 TIM--FGGPIQIDRGFVLHNITNEKSPIFNST 1176
I + ++I + E IF
Sbjct: 559 LICSKYTDLLRI-------ALMAEDEAIFEEA 583
Score = 64.5 bits (156), Expect = 2e-10
Identities = 104/698 (14%), Positives = 211/698 (30%), Gaps = 211/698 (30%)
Query: 38 HYICFNIEINK-----KTLLEIETSFRFNDAILRYLTIKTKKVETEESSFLRFIQKKEKV 92
H+ + E + K +L + F DA + K + ++ + I KE++
Sbjct: 3 HHHHMDFETGEHQYQYKDILSV-----FEDAFVDNFDCK----DVQD--MPKSILSKEEI 51
Query: 93 LKMIFGKKNNKNR----FKQKRQQQNPLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQEN 148
I K+ + F +Q + ++ F V + +I+Y F+
Sbjct: 52 -DHIIMSKDAVSGTLRLFWTLLSKQEEMVQK-----F-VEEVLRINY-------KFLMSP 97
Query: 149 GKIMAARLTGTCSHYQRQITFIRKNMQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNK 208
K + + Y Q + + QV ++ L ++ R L+ +
Sbjct: 98 IKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL--------RQALL---E 146
Query: 209 ARHATKFVIKEFEEKRIKLE------KTAFTI-FLNAKKIGEEIKKLNINI--IKKSGVD 259
R K + ++ KT + + K+ K++ I +
Sbjct: 147 LRP----------AKNVLIDGVLGSGKTWVALDVCLSYKV---QCKMDFKIFWLN----- 188
Query: 260 GKLFGSV-TNSDIVKELEKKGLKIEKN---------KIKLPNNSIKKIGNYYID------ 303
+ + +++ L+K +I+ N IKL +SI+ +
Sbjct: 189 ---LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN 245
Query: 304 --ILLHNGNSTFLWYDYETFGLNVR-----RDRP---FQFAAIRTDIMLN------TIDN 347
++L N + W F L+ + R + F AA T I L+ T D
Sbjct: 246 CLLVLLNVQNAKAW---NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE 302
Query: 348 PIMLYCK----PAPDFLPDPRACLITKITPQFC------LNNGI--PEY-------KFAS 388
L K D LP P+ + +G+ + K +
Sbjct: 303 VKSLLLKYLDCRPQD-LP-REVL---TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTT 357
Query: 389 IIEKIF--LKPGTISVGYN--TILFDD----EITRFMFWRNLINPYEREWKNNCSRWDLI 440
IIE L+P ++ ++ I + W ++I N ++ L+
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417
Query: 441 NVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIR 500
+S I K + + L H S V++ + K D
Sbjct: 418 EKQPKESTISIPSIYLELKVKLENEYAL-HRSIVDHYNIPKTFD---------------- 460
Query: 501 NNN---PRLFNFILSLRKKKYVLAEIGWPIARPFFYIT-HMFSSKHS---------YISL 547
+++ P L + + +I H+ + +H ++
Sbjct: 461 SDDLIPPYLDQYF--------------------YSHIGHHLKNIEHPERMTLFRMVFLDF 500
Query: 548 MWPICIHPMNKNILITWNLLHDPKKFL--LNDINKIRDYLCFKKNSFKE---DI----PI 598
+ + + I + L L + + Y+C ++ I P
Sbjct: 501 RF------LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPK 554
Query: 599 SMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIK 636
+L S +L LM + A K ++
Sbjct: 555 IEENLICSK----YTDLLRIALMAEDEAIFEEAHKQVQ 588
Score = 52.5 bits (125), Expect = 1e-06
Identities = 75/595 (12%), Positives = 162/595 (27%), Gaps = 177/595 (29%)
Query: 940 EKIVDYFSLIGDMSDNLPGVKKIGPKTAVK-LLNQYNSLENII--------NNANNIKGV 990
+ VD F D+ D + K + ++ +++ + ++
Sbjct: 27 DAFVDNFD-CKDVQDMPKSILS---KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKF 82
Query: 991 IGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLL--MQLFNKYNIP 1048
+ + LR +L IKT+ S+ + ++ +D +L Q+F KYN+
Sbjct: 83 VEEVLRINYKFLMS-----PIKTEQ----RQPSMMTRMYIEQRD-RLYNDNQVFAKYNVS 132
Query: 1049 LKNHDDNISDENYDIDCSDAKSLFNLTNHFLIA---MPGFSTPFFDG-----AVVY---- 1096
+ ++L L + + G G V
Sbjct: 133 RLQPYLKLR-----------QALLELRPAKNVLIDGVLGS------GKTWVALDVCLSYK 175
Query: 1097 LCEHNSNGAFGIIINKPTDMTINILLDNDSNLKLKLVPNTKEFILEKTTKTIMFGGPIQI 1156
+ F + + + +L+ L ++ PN + I ++I
Sbjct: 176 VQCKMDFKIFWLNLKN--CNSPETVLEMLQKLLYQIDPNWTS--RSDHSSNI----KLRI 227
Query: 1157 DRGFVLHNITNEKSPIFNS-----TLNIASDISLTTSRDILESFSRGDGPSQLLI----- 1206
H+I E + S L + ++ + +F + ++L+
Sbjct: 228 ------HSIQAELRRLLKSKPYENCLLVLLNVQ---NAKAWNAF---NLSCKILLTTRFK 275
Query: 1207 SLGCSGWGAGQLEEEIMNNHWLIVDANSEVIF----NVPCEQRFFAAVKL----LGVNPL 1258
+ A + ++ + + + + + L L NP
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ-------DLPREVLTTNPR 328
Query: 1259 IIGIAFGNTLIKHA------------KPLKIIHSITNKAKFNEISKLVEK---------- 1296
+ I ++ K II S N + E K+ ++
Sbjct: 329 RLSI-IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI 387
Query: 1297 --------WKPNT-------VKKMELKKIINTKHQTIVAYTNYGVKFRNGIFYTKSFLVS 1341
W V K+ ++ K + + V
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSLVE-KQPKESTISIPSIYLE--------LKVK 438
Query: 1342 PEIDP-----IFWSINKYNFLTKKD---------------FI--HISKFNPSVVILGTGN 1379
E + I ++ YN D I H+ +
Sbjct: 439 LENEYALHRSI---VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM 495
Query: 1380 IQ---HFIHPKLTYILTQKNIGIECMNNQAACRTYN--ILVSDDI-KAMLALILD 1428
+ F+ K+ + T N +N + Y I +D + ++ ILD
Sbjct: 496 VFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILD 550
>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase;
2.30A {Xanthomonas campestris PV}
Length = 194
Score = 63.0 bits (152), Expect = 3e-11
Identities = 31/195 (15%), Positives = 54/195 (27%), Gaps = 24/195 (12%)
Query: 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLIT 369
N +W D E GL+ RD + A I TD LN + L + + L
Sbjct: 8 NDRLIWIDLEMTGLDTDRDSIIEIATIVTDAQLNVLAEGPELAIAHSLETLEAMDEWNRN 67
Query: 370 KITPQFCLNNGIPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYERE 429
+ + + E + + R ++
Sbjct: 68 QHRRSGLWQRVLDSQVTHAQAEAQTVAFLGEWIRAGASPMCGN--SICQDRRFLHRQMSR 125
Query: 430 WKNNCS--RWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALS 487
+ D+ + + +P + K++ AH ALS
Sbjct: 126 LERYFHYRNLDVSTIKELARRWAPAVASGFAKSS--------------------AHTALS 165
Query: 488 DVRATLGLARLIRNN 502
DVR ++ R R
Sbjct: 166 DVRDSIDELRHYRQF 180
>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 = 64.7 bits (157), Expect = 2e-10
Identities = 85/568 (14%), Positives = 167/568 (29%), Gaps = 209/568 (36%)
Query: 139 ETLKD-FIQENGKIMAARLTGTCSHYQ---------RQITFIRKNMQVILLKDIPNLGKL 188
L++ F KI+ G + + + + ++ L + +G+
Sbjct: 31 SQLQEQFN----KILPEPTEGFAADDEPTTPAELVGKFLGYVSS------LVEPSKVGQF 80
Query: 189 GEIIKVK-NGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFTI--FLNAKKI-GEE 244
+++ + + +L + HA K +E L KT I ++ A+ +
Sbjct: 81 DQVLNLCLTEFENCYL--EGNDIHA--LAAKLLQENDTTLVKTKELIKNYITARIMAKRP 136
Query: 245 IKKLNINIIKKSGVDGK-----LFGSVTNSDI-VKELEKKGLKIEKNKIKLPNNSIKKIG 298
K + + + ++ +G +FG N+D +EL + +
Sbjct: 137 FDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRD----------------LYQTY 180
Query: 299 NYYIDILLHNGNSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPD 358
+ + L+ T + +I+ ++NP P D
Sbjct: 181 HVLVGDLIKFSAETL-----SELIRTTLDAEKVFTQGL--NIL-EWLENPSN---TPDKD 229
Query: 359 FLPD-PRAC-LITKITPQF------CLNNGIPEYKFASIIEKIFLKPGTISVGYNTIL-- 408
+L P +C LI + Q G + S ++ G +
Sbjct: 230 YLLSIPISCPLIG-VI-QLAHYVVTAKLLGFTPGELRSYLK------GATGHSQGLVTAV 281
Query: 409 ----------FDD---EITRFMFW---RNLINPYEREWKNNCSRWDLINVIKAF--YVLS 450
F + +F+ R C A+ L
Sbjct: 282 AIAETDSWESFFVSVRKAITVLFFIGVR-------------CYE--------AYPNTSLP 320
Query: 451 PYGITWPYKNN-GKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIR---NNNPR- 505
P + +NN G PS L ++NL+ ++ D ++ + L + + N +
Sbjct: 321 PSILEDSLENNEGVPSPMLS----ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN 376
Query: 506 ---------LFNFILSLRKKKYVLAEIGW-------------------PIARPFFYITHM 537
L+ L+LRK K A G P+A PF
Sbjct: 377 LVVSGPPQSLYGLNLTLRKAK---APSGLDQSRIPFSERKLKFSNRFLPVASPF------ 427
Query: 538 FSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKEDIP 597
HS +LL + D+ +++ + F + IP
Sbjct: 428 ----HS---------------------HLLVPASDLINKDL--VKNNVSFNAKDIQ--IP 458
Query: 598 ISMIHLNRSPIVI-----SNLKVLSSNL 620
V S+L+VLS ++
Sbjct: 459 -----------VYDTFDGSDLRVLSGSI 475
Score = 59.3 bits (143), Expect = 1e-08
Identities = 81/538 (15%), Positives = 152/538 (28%), Gaps = 191/538 (35%)
Query: 702 ENKKLEELI--FL-YRARNFIETLSYKELKRWKKYRISRFYNK--KNNLYNINMFYLEIE 756
E EL+ FL Y + +E + + ++ F N + N +I+
Sbjct: 53 EPTTPAELVGKFLGYVSSL-VEPSKVGQFDQVLNLCLTEFENCYLEGN--DIHAL---AA 106
Query: 757 SLLKKANEHDTKILNALLMYGKIDGSSCIYRAFYALPDIRNIDNFPVGALY-----GTIK 811
LL++ + K + Y A R D AL+ G +
Sbjct: 107 KLLQENDTTLVKTKELIKNY---------ITARIMAK--RPFDKKSNSALFRAVGEGNAQ 155
Query: 812 M----------------LRKLYKNYRATYIACIFDAKGKNFRNI---------LYP---- 842
+ LR LY+ Y + + + + ++
Sbjct: 156 LVAIFGGQGNTDDYFEELRDLYQTYH-VLVGDLIKFSAETLSELIRTTLDAEKVFTQGLN 214
Query: 843 -----SYKATRKKMPY--------NLILQINLIHQMV--KAIGW-PILIIKGVEADDVIG 886
+ Y LI I L H +V K +G+ P G
Sbjct: 215 ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTP-------------G 261
Query: 887 TLAK--QAVTKHNLKVI----ISTND--KDMAQLVSNKIAL----------------INN 922
L + T H+ ++ I+ D + V I + +
Sbjct: 262 ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP 321
Query: 923 NKIHDR--------TTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974
+ + D + ++S ++ E++ + + +LP K++ + L+N
Sbjct: 322 SILEDSLENNEGVPSPMLSISNLTQEQV---QDYVNKTNSHLPAGKQV----EISLVNGA 374
Query: 975 N---------SLENIINNANNIKGVIGKN----------LRFALNWLPKLKKILTIKTDC 1015
SL + K G + L+F+ +LP
Sbjct: 375 KNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLP------------ 422
Query: 1016 DLTKNIVSIPE-SLILQPKDEKLLMQLFNKY--------NIP---------LKNHDDNIS 1057
V+ P S +L P + + L IP L+ +IS
Sbjct: 423 ------VASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS 476
Query: 1058 DENYDIDCSDA----KSLFNLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGI-II 1110
+ D + H L PG ++ + L N +G G+ +I
Sbjct: 477 ERIVDCIIRLPVKWETTTQFKATHILDFGPGGAS-----GLGVLTHRNKDGT-GVRVI 528
Score = 51.6 bits (123), Expect = 2e-06
Identities = 47/297 (15%), Positives = 93/297 (31%), Gaps = 107/297 (36%)
Query: 1068 AKSLFNLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTDMTI--------- 1118
A+ ++N ++ GFS I+IN P ++TI
Sbjct: 1642 AQDVWNRADNHFKDTYGFSIL------------------DIVINNPVNLTIHFGGEKGKR 1683
Query: 1119 ------NILLDNDSNLKLKLVPNTKEFILEKTTKTIMFGGPIQIDRGFVLHNITNEKSPI 1172
++ + + KLK KE I E +T F +G +L
Sbjct: 1684 IRENYSAMIFETIVDGKLKTEKIFKE-INEHSTS-YTFRSE----KG-LL---------- 1726
Query: 1173 FNSTLN--IASDISLTTSRDILESF-SRGDGPSQLLI---SLG-----CSGWGAGQLEEE 1221
++T A + E S+G P+ SLG S A + E
Sbjct: 1727 -SATQFTQPA---LTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALAS--LADVMSIE 1780
Query: 1222 IMNNHWLIVDANSEVIFN--------VPCEQRFFAAVKLLGVNPLIIGIAFGNTLIKHAK 1273
EV+F VP ++ + ++ +NP + +F ++
Sbjct: 1781 ---------SL-VEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQ--- 1827
Query: 1274 PLKIIHSITNK-------AKFNE------IS---KLVEKWKPNTVKKMELKKIINTK 1314
++ + + +N + + ++ N + ++L+KI +
Sbjct: 1828 --YVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVT-NVLNFIKLQKIDIIE 1881
Score = 49.7 bits (118), Expect = 9e-06
Identities = 89/593 (15%), Positives = 164/593 (27%), Gaps = 242/593 (40%)
Query: 37 AHYICF------------NIEINKKTLLEIETSF-RFND--------------------A 63
++ + ++ L E E + ND
Sbjct: 62 GKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKE 121
Query: 64 ILR-YL----TIKTKKVETEESSFLRFIQKKEKVLKMIF-GKKNNKNRFKQKRQQQNPLF 117
+++ Y+ K + S+ R + + L IF G+ N + F++ R L+
Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRD----LY 177
Query: 118 KRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQITFIRKNMQVI 177
+ Y + + D I+ A L+ + + ++
Sbjct: 178 Q---------------TYHVL--VGDLIKF----SAETLSELIRTTLDAEKVFTQGLNIL 216
Query: 178 -LLKD---IPNLGKLGEI------IKV-----------KNGYARNFLIPKNKARHAT--- 213
L++ P+ L I I V G+ L K AT
Sbjct: 217 EWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKG--ATGHS 274
Query: 214 KFVI-----------KEFEEKRIKLEKTAFTIFLNAKKIGEEIKK------LNINIIKKS 256
+ ++ + F K F IG + L +I++ S
Sbjct: 275 QGLVTAVAIAETDSWESFFVSVRKAITVLF-------FIGVRCYEAYPNTSLPPSILEDS 327
Query: 257 GVDGKLFG------SVTNSDIVKELEKKGLKIEK-NKIKLPNNSIKKIGNYYIDILLHNG 309
+ + G S++N ++++ + K N LP ++I L NG
Sbjct: 328 LENNE--GVPSPMLSISNLTQ-EQVQD---YVNKTNS-HLPAGK-------QVEISLVNG 373
Query: 310 NSTF--------LWYDYETFGLNVRRDR----------PF-QFAAIRTDIMLNTIDNPIM 350
L+ L +R+ + PF + R
Sbjct: 374 AKNLVVSGPPQSLY----GLNLTLRKAKAPSGLDQSRIPFSE----R------------- 412
Query: 351 LYCKPAPD--FLPDPRACLITKITPQF---CLNNGIPEYKFASIIEKIFLKPG--TISVG 403
K FLP + +P F L + + I V
Sbjct: 413 ---KLKFSNRFLP------VA--SP-FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV- 459
Query: 404 YNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGK 463
Y+T FD +L R + S +++ I + P + W K
Sbjct: 460 YDT--FD--------GSDL-----RVLSGSISE-RIVDCI----IRLP--VKWETTTQFK 497
Query: 464 PSFKLEH-LSF-------VNNLSHKKAHDALSDVRATLGLARLI----RNNNP 504
+ H L F + L+H+ + T G R+I + NP
Sbjct: 498 AT----HILDFGPGGASGLGVLTHR-------NKDGT-G-VRVIVAGTLDINP 537
Score = 48.9 bits (116), Expect = 1e-05
Identities = 58/330 (17%), Positives = 117/330 (35%), Gaps = 103/330 (31%)
Query: 749 NM---FYLEIES---LLKKANEHDTKILNALLMYGKIDGSSCIYRAFYALPDIRNIDNFP 802
M Y ++ + +A+ H YG +++ DI + N P
Sbjct: 1630 GMGMDLYKTSKAAQDVWNRADNHFKDT------YG------------FSILDI--VINNP 1669
Query: 803 VG-ALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKM---PYNLILQ 858
V ++ + +++ +NY A I D K K I + + L+
Sbjct: 1670 VNLTIHFGGEKGKRIRENYSAMIFETIVDGKLK-TEKIFKEINEHSTSYTFRSEKGLLSA 1728
Query: 859 -------INLIHQMVKAIGWPILIIKGVEADDVI--GTLAKQAVTKHNL----------K 899
+ L+ KA + L KG+ D G H+L
Sbjct: 1729 TQFTQPALTLME---KAA-FEDLKSKGLIPADATFAG---------HSLGEYAALASLAD 1775
Query: 900 VIISTNDKDMAQLV-----SNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSD 954
V+ S + + ++V + ++A+ + +I ++P ++ FS +
Sbjct: 1776 VM-SI--ESLVEVVFYRGMTMQVAVPRDELGRSNYGMI---AINPGRVAASFSQ--EALQ 1827
Query: 955 NLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG---VIGKNLRFALNWLPKLKKIL-T 1010
+ V+++G +T +E I+N N++ V +LR AL+ + +L
Sbjct: 1828 YV--VERVGKRTG-------WLVE-IVNY--NVENQQYVAAGDLR-ALD---TVTNVLNF 1871
Query: 1011 IKTDCDLTKNI--VSIPESLILQPKDEKLL 1038
IK + I + + +SL L+ + L
Sbjct: 1872 IKL-----QKIDIIELQKSLSLEEVEGHLF 1896
Score = 48.5 bits (115), Expect = 2e-05
Identities = 69/432 (15%), Positives = 138/432 (31%), Gaps = 133/432 (30%)
Query: 1022 VSIPESL---ILQPKDEKLLMQLFNKYNIPLKNHDDNISDENYDIDCSDAKSLFNLTNHF 1078
+ +P + Q +++ FNK L + + ++ + + L F
Sbjct: 20 LLVPTASFFIASQLQEQ------FNKI---LPEPTEGFAADD------EPTTPAELVGKF 64
Query: 1079 LIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKP-TDMTINILLDND------------ 1125
L G+ V L E + G F ++N T+ L ND
Sbjct: 65 L----GY--------VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEN 112
Query: 1126 --SNLKLKLV-------------PNTKE-----F--ILEKTTKTI-MFGGPIQ--IDRGF 1160
+ +K K + P K+ F + E + + +FGG Q D F
Sbjct: 113 DTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG--QGNTDDYF 170
Query: 1161 VLHNITNEKSPIFNSTLNIASDISLTTSRDILESFSRGDGPSQLLISLGCS--GWGAGQL 1218
E ++ + + D+ + S + L R ++ + + G + W L
Sbjct: 171 ------EELRDLYQTYHVLVGDL-IKFSAETLSELIRTTLDAEKVFTQGLNILEW----L 219
Query: 1219 EEEIM--NNHWLIVDANSEV----IFNVPCEQRFFAAVKLLGVNPLIIGIAFGNT--LIK 1270
E + +L + + I + + KLLG P G
Sbjct: 220 ENPSNTPDKDYL---LSIPISCPLIGVIQLAH-YVVTAKLLGFTP---GELRSYLKGATG 272
Query: 1271 HAKPLKIIHSITNKAKFNEISKLVEKWKPNTVKKMELKKIINTK-HQT---------IVA 1320
H++ L +T A + E + + K + + I + ++ I+
Sbjct: 273 HSQGL-----VT--AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILE 325
Query: 1321 YTNYGVKFRNGIFYTKSFLVS---PEIDPIFWSINKYN-FLTKKDFIHISKFN-PSVVIL 1375
+ ++ G S ++S + + +NK N L + IS N +++
Sbjct: 326 DS---LENNEG---VPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVV 379
Query: 1376 GTGNIQHFIHPK 1387
+G P+
Sbjct: 380 -SG------PPQ 384
Score = 45.0 bits (106), Expect = 2e-04
Identities = 101/608 (16%), Positives = 156/608 (25%), Gaps = 239/608 (39%)
Query: 856 ILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSN 915
L+ N IH + + ++ + + + K+ + I + S
Sbjct: 95 YLEGNDIHALAAKL----------LQENDTTLVKTKELIKNYITARIMAKRPFDKKSNS- 143
Query: 916 KIALINNNKIHDRTTIISRFG--VSPEKIVDYF-----------SLIGDMSDNLPGVKKI 962
AL +++ FG + + DYF L+GD+ +K
Sbjct: 144 --ALFRAVGE-GNAQLVAIFGGQGNTD---DYFEELRDLYQTYHVLVGDL------IKFS 191
Query: 963 GPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWL------PKLKKILTIKTDCD 1016
L +I + + V + L L WL P D D
Sbjct: 192 AET-----------LSELIRTTLDAEKVFTQGLNI-LEWLENPSNTP----------DKD 229
Query: 1017 -LTKNIVSIPESLILQPKDEKLLMQLFNKYNIPLKNHDDNISDENYDIDCSDAKSLFNLT 1075
L +S P LI ++QL + Y + K + L T
Sbjct: 230 YLLSIPISCP--LIG-------VIQLAH-YVVTAKLLGFTPGEL--------RSYLKGAT 271
Query: 1076 NH-------FLIAMPGFSTPFFDGAVVYL-------CEHNSNGAFGIIINKPTDMTINIL 1121
H IA FF + A+ T + +IL
Sbjct: 272 GHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVR--CYEAYP-----NTSLPPSIL 324
Query: 1122 LDNDSNLKLKLVPNTKEFILEKTTKTIMFG--GPIQIDRGFVLHNI--TNEKSPIFNSTL 1177
D+ N + + M + + V + TN P +
Sbjct: 325 EDSLEN--------------NEGVPSPMLSISN---LTQEQVQDYVNKTNSHLP-AGKQV 366
Query: 1178 NIASDISLTTSRDILESF--SRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIVDANSE 1235
I SL + S GP Q L L L + A S
Sbjct: 367 EI----SLVNGAK---NLVVS---GPPQSLYGL------NLTLRK---------AKAPSG 401
Query: 1236 V-IFNVPCEQR---F---FAAV------KLL-GVNPLIIGIAFGNTLIKHAKPLKIIHSI 1281
+ +P +R F F V LL + LI N + +AK ++I
Sbjct: 402 LDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQI---- 457
Query: 1282 TNKAKFNEISKLVEKWKPNTVKKMELKKIINTKHQTIVAYTNYGVKFRNGIFYTKSFLVS 1341
P V T G R S +S
Sbjct: 458 -----------------P-------------------VYDTFDGSDLR-----VLSGSIS 476
Query: 1342 PEI------DPIFWSINKYNFLTKKDFIHISKFNPSVVILGTGNIQHFIHPKLTYILTQK 1395
I P+ W T+ HI F P G G LT +
Sbjct: 477 ERIVDCIIRLPVKWET-----TTQFKATHILDFGPGGA-SGLGV------------LTHR 518
Query: 1396 NI---GIE 1400
N G+
Sbjct: 519 NKDGTGVR 526
Score = 41.2 bits (96), Expect = 0.003
Identities = 23/124 (18%), Positives = 40/124 (32%), Gaps = 28/124 (22%)
Query: 131 KQIDYKDIETL----KDFIQENGKIMAARLTGTCSHYQRQITFIRKNMQVILLKDIPNLG 186
+ D +T D + N + G IR+N ++ + I +
Sbjct: 1647 NRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKR------IRENYSAMIFETIVD-- 1698
Query: 187 KLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFT---IFLNAKKIGE 243
G + I K H+T + F ++ L T FT + L K E
Sbjct: 1699 ----------GKLKTEKIFKEINEHSTSYT---FRSEKGLLSATQFTQPALTLMEKAAFE 1745
Query: 244 EIKK 247
++K
Sbjct: 1746 DLKS 1749
>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase,
mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB:
1yta_A 1j9a_A
Length = 180
Score = 57.6 bits (138), Expect = 2e-09
Identities = 29/197 (14%), Positives = 62/197 (31%), Gaps = 28/197 (14%)
Query: 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLIT 369
+ +W D E GL+ RDR + A + TD LN + + + + L +
Sbjct: 4 ENNLIWIDLEMTGLDPERDRIIEIATLVTDANLNILAEGPTIAVHQSDEQLALMDDWNVR 63
Query: 370 KITPQFCLNNGIPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYERE 429
T ++E++ + E+ F + + +
Sbjct: 64 THTAS-------------GLVERVK--------ASTMGDREAELATLEFLKQWVPAGKSP 102
Query: 430 WKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSF----KLEHLSFVNNLSHKKAHDA 485
N D + K L Y + Y+ + + ++ + + H A
Sbjct: 103 ICGNSIGQDRRFLFKYMPELEAY---FHYRYLDVSTLKELARRWKPEILDGFTKQGTHQA 159
Query: 486 LSDVRATLGLARLIRNN 502
+ D+R ++ R +
Sbjct: 160 MDDIRESVAELAYYREH 176
>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella
burnetii}
Length = 186
Score = 56.4 bits (135), Expect = 5e-09
Identities = 31/197 (15%), Positives = 63/197 (31%), Gaps = 28/197 (14%)
Query: 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLIT 369
+ +W D E GL+ RDR + A I T+ L+ + L
Sbjct: 8 DDNLIWLDLEMTGLDPERDRIIEIATIVTNSHLDILAEGPAFAIHQPDKLLTAMD----N 63
Query: 370 KITPQFCLNNGIPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYERE 429
T + + K +S+ E + E F ++ +
Sbjct: 64 WNTSHHTASGLLERVKNSSVDEV-----------------EAETLTLAFLEKYVSAGKSP 106
Query: 430 WKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSH----KKAHDA 485
N D + + L+ + + Y++ + K+ + ++ + H A
Sbjct: 107 LCGNSVCQDRRFLSRYMPRLNQF---FHYRHLDVTTLKILAQRWAPQIAAAHIKESQHLA 163
Query: 486 LSDVRATLGLARLIRNN 502
L D+R ++ R R +
Sbjct: 164 LQDIRDSIEELRYYRAH 180
>1ihn_A Hypothetical protein MTH938; methanobacterium thermoautotrophicum,
unknown function; 2.20A
{Methanothermobacterthermautotrophicus} SCOP: c.103.1.1
Length = 113
Score = 53.8 bits (129), Expect = 8e-09
Identities = 14/103 (13%), Positives = 28/103 (27%), Gaps = 15/103 (14%)
Query: 1330 NGIFYTKSFLVSP----EIDPIFWSINKYN---FLTKKDFIHISKFNPSVVILGTGNIQH 1382
G Y +V S KY + +++ + + P +I+G+G
Sbjct: 15 RGREYRSDIVVHVDGSVTPRRKEISRRKYGTSHVMAEEELEELLEEKPESIIIGSGVHGA 74
Query: 1383 FIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAMLAL 1425
+ A + YN S + +
Sbjct: 75 LETGF--------RSDATVLPTCEAIKRYNEERSAGRRVAAII 109
>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease,
homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus
musculus} PDB: 3u6f_B*
Length = 314
Score = 54.4 bits (130), Expect = 1e-07
Identities = 34/211 (16%), Positives = 62/211 (29%), Gaps = 33/211 (15%)
Query: 305 LLHNGNSTFLWYDYETFGLNVRRDRPFQFAAIR--TDIMLNTIDNPIMLYCKPAPDFLPD 362
L H T ++ D E GL R + + + NT + P P + D
Sbjct: 6 LPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVD 65
Query: 363 -------------PRACLITKITPQFCLNNGIPEYKFASIIEKIF------LKPGTISVG 403
P A IT ++ G +F + + V
Sbjct: 66 KLSLCIAPGKACSPGASEITGLSKAELEVQGRQ--RFDDNLAILLRAFLQRQPQPCCLVA 123
Query: 404 YNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGK 463
+N +D F + + + + ++ I A L + P N +
Sbjct: 124 HNGDRYD-----FPLLQTELARLSTPSPLDGTF--CVDSIAALKALEQ--ASSPSGNGSR 174
Query: 464 PSFKLEHL-SFVNNLSHKKAHDALSDVRATL 493
S+ L + + + + +H A V L
Sbjct: 175 KSYSLGSIYTRLYWQAPTDSHTAEGHVLTLL 205
>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline
type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus
musculus} PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A*
3b6p_A* 2o4i_A 2oa8_A
Length = 242
Score = 52.3 bits (125), Expect = 3e-07
Identities = 32/205 (15%), Positives = 60/205 (29%), Gaps = 33/205 (16%)
Query: 311 STFLWYDYETFGLNVRRDRPFQFAAIR--TDIMLNTIDNPIMLYCKPAPDFLPD------ 362
T ++ D E GL R + + + NT + P P + D
Sbjct: 12 QTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCI 71
Query: 363 -------PRACLITKITPQFCLNNGIPEYKFASIIEKIF------LKPGTISVGYNTILF 409
P A IT ++ G +F + + V +N +
Sbjct: 72 APGKACSPGASEITGLSKAELEVQGRQ--RFDDNLAILLRAFLQRQPQPCCLVAHNGDRY 129
Query: 410 DDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLE 469
D F + + + + ++ I A L + P N + S+ L
Sbjct: 130 D-----FPLLQTELARLSTPSPLDGTF--CVDSIAALKALEQ--ASSPSGNGSRKSYSLG 180
Query: 470 HL-SFVNNLSHKKAHDALSDVRATL 493
+ + + + +H A D L
Sbjct: 181 SIYTRLYWQAPTDSHTAEGDDLTLL 205
>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap
binding site, hydrolase-DNA complex, DNA repair,
replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A*
3q8m_A*
Length = 341
Score = 50.6 bits (121), Expect = 2e-06
Identities = 25/104 (24%), Positives = 47/104 (45%), Gaps = 10/104 (9%)
Query: 902 ISTNDKDM----AQLVSNKIALINNNKIH----DRTTIISRFGVSPEKIVDYFSLIGDMS 953
+T D D + ++ + K+ + I+ G++ E+ VD L+G S
Sbjct: 174 AATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLG--S 231
Query: 954 DNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRF 997
D ++ IGPK AV L+ ++ S+E I+ + K + +N
Sbjct: 232 DYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLH 275
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap
DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A
{Homo sapiens} SCOP: a.60.7.1 c.120.1.2
Length = 379
Score = 51.1 bits (122), Expect = 2e-06
Identities = 45/256 (17%), Positives = 89/256 (34%), Gaps = 49/256 (19%)
Query: 779 IDGSSCIYRAFYALPD----IRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIF----- 829
ID S IY+ A+ ++N + L G ++ +N I ++
Sbjct: 32 IDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENG----IKPVYVFDGK 87
Query: 830 ---------------DAKGKNFRNILYPSYKATRKKMPYNLILQINLIH-----QMVKAI 869
A+ + + + ++++ H ++ +
Sbjct: 88 PPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLM 147
Query: 870 GWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDM----AQLVSNKIALINNNKI 925
G P L EA+ L K +T D D + ++ + K+
Sbjct: 148 GIPYLDAPS-EAEASCAALVKAGKVY-----AAATEDMDCLTFGSPVLMRHLTASEAKKL 201
Query: 926 H----DRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII 981
+ I+ G++ E+ VD L+G SD ++ IGPK AV L+ ++ S+E I+
Sbjct: 202 PIQEFHLSRILQELGLNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSIEEIV 259
Query: 982 NNANNIKGVIGKNLRF 997
+ K + +N
Sbjct: 260 RRLDPNKYPVPENWLH 275
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3
turn-helix, hydrophobic wedge, 3' FLA site,
hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus}
SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A
Length = 336
Score = 49.8 bits (119), Expect = 3e-06
Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 931 IISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINN 983
+ R G++ E+++D L+G +D GVK +G K A+ + Y + +
Sbjct: 214 NLKRLGLTREQLIDIAILVG--TDYNEGVKGVGVKKALNYIKTYGDIFRALKA 264
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo
sapiens} SCOP: c.55.3.5
Length = 238
Score = 46.8 bits (111), Expect = 2e-05
Identities = 27/202 (13%), Positives = 47/202 (23%), Gaps = 30/202 (14%)
Query: 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFL--------PD 362
TF++ D E GL + + P L P+
Sbjct: 10 ETFVFLDLEATGLPSVEPEIAELSLFAVHRSSLENPEHDESGALVLPRVLDKLTLCMCPE 69
Query: 363 ----PRACLITKITPQFCLNNGIPEYKFASIIEKI------FLKPGTISVGYNTILFDDE 412
+A IT ++ + F + + V +N +D
Sbjct: 70 RPFTAKASEITGLSSEGLARCRKA--GFDGAVVRTLQAFLSRQAGPICLVAHNGFDYD-- 125
Query: 413 ITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHL- 471
F + + ++ + A L + + L L
Sbjct: 126 ---FPLLCAELRRLGARLPRD---TVCLDTLPALRGLDRAHSHGTRARGRQ-GYSLGSLF 178
Query: 472 SFVNNLSHKKAHDALSDVRATL 493
AH A DV L
Sbjct: 179 HRYFRAEPSAAHSAEGDVHTLL 200
>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure,
backbone dynamics, folding, ribonucleoprotein,
RNA-binding, rRNA-binding; NMR {Thermus thermophilus}
Length = 96
Score = 43.8 bits (103), Expect = 2e-05
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 2 IERYKKIIISGKGKIHRLEDWGRRSLAYQIKK 33
E ++ + + ++ ++E+ G R LAY I K
Sbjct: 65 KEIIQRALENYGARVEKVEELGLRRLAYPIAK 96
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair,
DNA-binding, endonuclease, metal-BIND excision repair,
DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus
solfataricus}
Length = 346
Score = 45.3 bits (107), Expect = 1e-04
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 931 IISRFGVSPEKIVDYFSLIGDMSD-NLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG 989
++ + G++ E+++D LIG +D N G++ IGP+ A+K++ +Y +E + K
Sbjct: 212 LLKKLGITREQLIDIGILIG--TDYNPDGIRGIGPERALKIIKKYGKIEKAMEYGEISKK 269
Query: 990 VIGKNLRFA 998
I N+
Sbjct: 270 DINFNIDEI 278
>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2 function
project, S2F, unknown function; 1.60A {Escherichia coli}
SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A
Length = 138
Score = 42.9 bits (102), Expect = 1e-04
Identities = 13/43 (30%), Positives = 25/43 (58%)
Query: 1260 IGIAFGNTLIKHAKPLKIIHSITNKAKFNEISKLVEKWKPNTV 1302
IG+A G + A+PL I + +N I +L+++W+P+ +
Sbjct: 15 IGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEI 57
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA
replication, RTH, RAD27, DNA repair; 2.00A
{Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2
PDB: 1a77_A
Length = 326
Score = 44.1 bits (104), Expect = 2e-04
Identities = 17/95 (17%), Positives = 38/95 (40%), Gaps = 8/95 (8%)
Query: 902 ISTNDKDM-----AQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSD-N 955
+ + D D ++V N ++ + ++ +S + ++D +G +D N
Sbjct: 169 VVSQDYDALLYGAPRVVRNLTTTKEMPELIELNEVLEDLRISLDDLIDIAIFMG--TDYN 226
Query: 956 LPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGV 990
GVK IG K A +L+ + + + +
Sbjct: 227 PGGVKGIGFKRAYELVRSGVAKDVLKKEVEYYDEI 261
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus
amylolyticus}
Length = 363
Score = 44.1 bits (104), Expect = 2e-04
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 931 IISRFGVSPEKIVDYFSLIGDMSDNLP-GVKKIGPKTAVKLLNQYNSLENIINN 983
++ + G++ E ++D L+G +D P G + IGPK A++L+ Y +E I
Sbjct: 229 LLVQLGITLENLIDIGILLG--TDYNPDGFEGIGPKKALQLVKAYGGIEKIPKP 280
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication,
transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1
c.120.1.2 PDB: 1mc8_A
Length = 340
Score = 40.3 bits (94), Expect = 0.003
Identities = 12/59 (20%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 931 IISRFGVSPEKIVDYFSLIGDMSDNLP-GVKKIGPKTAVKLLNQYNSLENIINNANNIK 988
++ ++ EK+++ L+G +D P G+K IG K A++++ +++
Sbjct: 215 VLKELKLTREKLIELAILVG--TDYNPGGIKGIGLKKALEIVRHSKDPLAKFQKQSDVD 271
>2cyj_A Hypothetical protein PH1505; conserved hypothetical protein,
structural genomics, NPPSFA; HET: OCS; 1.50A {Pyrococcus
horikoshii} SCOP: c.103.1.1
Length = 118
Score = 38.0 bits (88), Expect = 0.003
Identities = 12/96 (12%), Positives = 28/96 (29%), Gaps = 8/96 (8%)
Query: 1330 NGIFYTKSFLVSPEIDPIFW----SINKYNF---LTKKDFIHISKFNPSVVILGTGNIQH 1382
+G + ++ P S K+ L ++ + V+++GTG
Sbjct: 14 DGKEFDHDIVIYPSGRIERRMKEISKKKHGTSHKLDPEELEKYLVEDFDVLLVGTGIYGM 73
Query: 1383 FIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDD 1418
+ L + + + A + L
Sbjct: 74 LSLLPESKKLVED-KEVIEKPTKEALKLLEELWGKK 108
>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA
complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A
3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A*
3v9s_A* 3v9x_A* 3va0_A* 2is3_A
Length = 235
Score = 38.3 bits (89), Expect = 0.010
Identities = 32/186 (17%), Positives = 50/186 (26%), Gaps = 28/186 (15%)
Query: 317 DYETFGLNVRRDRPFQFAAIRTDIMLN---TIDNPIMLYCKPAPDFLPDPRACLITKITP 373
D ET G N + D + AAI + D + + +P P A I P
Sbjct: 43 DVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDP 102
Query: 374 QFCLNNGIPE-------YKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPY 426
+ +K K I V +N FD R +
Sbjct: 103 NDPDRGAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNAN-FDHSFMMAAAERASL--- 158
Query: 427 EREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDAL 486
+ + + F + G+ K + + +AH AL
Sbjct: 159 ---------KRNPFHPFATFDTAALAGLALGQTVLSK---ACQTAGM--DFDSTQAHSAL 204
Query: 487 SDVRAT 492
D T
Sbjct: 205 YDTERT 210
>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken
structural genomics/proteomics initiative, RSGI, unknown
function; NMR {Thermus thermophilus} SCOP: c.55.3.8
Length = 98
Score = 34.8 bits (81), Expect = 0.024
Identities = 7/43 (16%), Positives = 14/43 (32%)
Query: 1260 IGIAFGNTLIKHAKPLKIIHSITNKAKFNEISKLVEKWKPNTV 1302
IG+A G + A + T + + V + +
Sbjct: 13 IGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKL 55
>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5'
exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB:
3cm5_A 3cm6_A
Length = 308
Score = 37.7 bits (87), Expect = 0.025
Identities = 37/210 (17%), Positives = 69/210 (32%), Gaps = 19/210 (9%)
Query: 312 TFLWYDYETFGLNVRRDRPF---QFAAIRTDIMLNTIDNPI--MLYCKPAPDFLPDPRAC 366
T L D+ET +D P QFA + D+ + I I Y KP +
Sbjct: 20 TLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKPVLNRTLTKNCV 79
Query: 367 LITKITPQFCLNNGIPEYKFASIIEKI--FLKPGTISVGYNTILFDDEITRFMFWRNLIN 424
T I + ++ F + E+ +L + G + D + + +
Sbjct: 80 DFTGIPQRS-IDTADT---FDVVYEQFQQWLITLGLEEGKFAFVCDSRQDLWRIAQYQMK 135
Query: 425 PYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHK-KAH 483
+ ++ IN+ K F + + ++ +L +AH
Sbjct: 136 LSNIQMPAFFRQY--INLYKIFTNEMDRM----GPKELSATTNIGKMNEYYDLPTIGRAH 189
Query: 484 DALSDVRATLGLA-RLIRNNNPRLFNFILS 512
DA+ D + R+I N +L+
Sbjct: 190 DAMDDCLNIATILQRMINMGAKVTVNELLT 219
>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase;
1.96A {Bacillus subtilis} SCOP: c.55.3.8
Length = 150
Score = 35.7 bits (83), Expect = 0.035
Identities = 6/45 (13%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 1260 IGIAFGNTLIKHAKPLKIIH--SITNKAKFNEISKLVEKWKPNTV 1302
+G+A + + A+ ++ I + +S+L++ + + +
Sbjct: 15 LGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKI 59
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A
{Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Length = 352
Score = 36.9 bits (85), Expect = 0.042
Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 3/73 (4%)
Query: 935 FGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKN 994
+ EK L G D L ++ IG A K+L N+ + I+ I + N
Sbjct: 208 DVFTEEKFRYMCILSG--CDYLSSLRGIGLAKACKVLRLANNPD-IVKVIKKIGHYLKMN 264
Query: 995 LRFALNWLPKLKK 1007
+ +++ +
Sbjct: 265 ITVPEDYINGFIR 277
>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS
protein structure initiative, midwest center for
structural genomics; 2.09A {Pseudomonas aeruginosa}
SCOP: c.55.3.5
Length = 224
Score = 34.7 bits (80), Expect = 0.13
Identities = 37/188 (19%), Positives = 51/188 (27%), Gaps = 32/188 (17%)
Query: 317 DYETFGLNVRRDRPFQFAA--IRTDIMLNTIDNPIML-YCKPAPDFLPDPRACLITKITP 373
D ET G N D + AA + D +P +P A T I
Sbjct: 35 DVETGGFNSATDALLEIAATTVGMDEKGFLFPEHTYFFRIEPFEGANIEPAALEFTGIKL 94
Query: 374 QFCLNNGIPEY-KFASIIEKI--FLK----PGTISVGYNTILFDDEITRFMFWRNLINPY 426
L + E I I LK I VG+N FD F+
Sbjct: 95 DHPLRMAVQEEAALTEIFRGIRKALKANGCKRAILVGHN-SSFD---LGFLNAAVARTGI 150
Query: 427 EREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLS--FVNNLSHKKAHD 484
+R + S +D + Y L +++AH
Sbjct: 151 KRNPFHPFSSFDTATLAGLAY----------------GQTVLAKACQAAGMEFDNREAHS 194
Query: 485 ALSDVRAT 492
A D T
Sbjct: 195 ARYDTEKT 202
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase;
HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5
Length = 89
Score = 32.1 bits (73), Expect = 0.23
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 952 MSDNLPGVKKIGPKTAVKLLNQYNSLENIIN 982
+++ L VK + + LL + SLE +I
Sbjct: 17 VTECLTTVKSVNKTDSQTLLTTFGSLEQLIA 47
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA
repair, endonuclease, helix-hairpin-helix, DNA binding
protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5
Length = 91
Score = 31.3 bits (71), Expect = 0.37
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 952 MSDNLPGVKKIGPKTAVKLLNQYNSLENIIN 982
+++ L VK + + LL + SLE +I
Sbjct: 30 VTECLTTVKSVNKTDSQTLLTTFGSLEQLIA 60
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding
domain, homodimer, hydrolase; 1.45A {Pyrococcus
furiosus} SCOP: a.60.2.5
Length = 75
Score = 30.7 bits (70), Expect = 0.54
Identities = 8/29 (27%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 954 DNLPGVKKIGPKTAVKLLNQYNSLENIIN 982
+ LP V A +LL + S+E +
Sbjct: 17 EGLPHV---SATLARRLLKHFGSVERVFT 42
>1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition,
structures of 3'- exonuclease and ITS RNA complex,
hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens}
Length = 299
Score = 33.0 bits (75), Expect = 0.58
Identities = 36/229 (15%), Positives = 70/229 (30%), Gaps = 32/229 (13%)
Query: 272 VKELEKKGLKIEKNKIKLPNNSIKKIGNYYIDILLHNGNSTFLWYDYET----FGLNVRR 327
VK++ KK LK K KL +YY D+E
Sbjct: 48 VKDVLKKRLKNYYKKQKLMLKESNFADSYY---------DYICIIDFEATCEEGNPPEFV 98
Query: 328 DRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFA 387
+F + + I++ Y +P + +T IT Q ++ F
Sbjct: 99 HEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGIT-QDQVDRADT---FP 154
Query: 388 SIIEKI--FLKPGTISVGYNTILF-DDEITRFMFWRNLINPYEREWKNNCSRWDLINVIK 444
+++K+ +K + Y L D F ++ +W IN+ K
Sbjct: 155 QVLKKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKW--INIRK 212
Query: 445 AFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHK-KAHDALSDVRAT 492
++ + + KL + + + + + L D +
Sbjct: 213 SY---------GNFYKVPRSQTKLTIMLEKLGMDYDGRPNCGLDDSKNI 252
>1l4a_C S-SNAP25 fusion protein; snare, snare complex, membrane fusion,
neurotransmission, endocytosis/exocytosis complex; 2.95A
{Loligo pealei} SCOP: h.1.15.1
Length = 83
Score = 30.3 bits (68), Expect = 0.84
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 960 KKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKK 1007
K+ G +T V L Q L+ I + I ++++ A L ++K
Sbjct: 40 KEAGIRTLVMLDEQGEQLDRIEEGLDQIN----QDMKDAEKNLEGMEK 83
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A
{Homo sapiens}
Length = 349
Score = 32.7 bits (74), Expect = 0.96
Identities = 39/258 (15%), Positives = 84/258 (32%), Gaps = 41/258 (15%)
Query: 245 IKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNSIKKIGNYYIDI 304
I +++ ++ + KL + VK++ KK LK K KL +YY
Sbjct: 76 INRMSKEELRAKLSEFKL-----ETRGVKDVLKKRLKNYYKKQKLMLKESNFADSYY--- 127
Query: 305 LLHNGNSTFLWYDYET----FGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFL 360
D+E +F + + I++ Y +P +
Sbjct: 128 ------DYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQ 181
Query: 361 PDPRACLITKITPQFCLNNGIPEYKFASIIEKI--FLKPGTISVGYNTIL---FDDEITR 415
+T IT Q ++ F +++K+ +K + Y L ++++
Sbjct: 182 LSDFCISLTGIT-QDQVDRADT---FPQVLKKVIDLMKLKELGTKYKYSLLTDGSWDMSK 237
Query: 416 FMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVN 475
F+ ++ +W IN+ K++ + + KL +
Sbjct: 238 FL--NIQCQLSRLKYPPFAKKW--INIRKSYGN---------FYKVPRSQTKLTIMLEKL 284
Query: 476 NLSHK-KAHDALSDVRAT 492
+ + + H L D +
Sbjct: 285 GMDYDGRPHCGLDDSKNI 302
>1pvm_A Conserved hypothetical protein TA0289; structural genomics, CBS
domain, PSI, protein structure initiative; 1.50A
{Thermoplasma acidophilum dsm 1728} SCOP: d.37.1.1
g.41.13.1 PDB: 2qh1_A
Length = 184
Score = 30.8 bits (70), Expect = 2.3
Identities = 6/30 (20%), Positives = 14/30 (46%)
Query: 259 DGKLFGSVTNSDIVKELEKKGLKIEKNKIK 288
+G G ++ I+K + K ++ I+
Sbjct: 49 NGNDVGLLSERSIIKRFIPRNKKPDEVPIR 78
>2o16_A Acetoin utilization protein ACUB, putative; structural genomics,
unknown function, PSI-2, protein struct initiative;
1.90A {Vibrio cholerae} SCOP: d.37.1.1
Length = 160
Score = 30.4 bits (69), Expect = 2.7
Identities = 6/39 (15%), Positives = 15/39 (38%)
Query: 259 DGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNSIKKI 297
+ KL G V+ D++ E + + + ++
Sbjct: 45 NKKLLGIVSQRDLLAAQESSLQRSAQGDSLAFETPLFEV 83
>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics,
exonuclease, PSI-2, protein structure initiative; HET:
DNA; 2.50A {Thermotoga maritima MSB8}
Length = 186
Score = 30.2 bits (69), Expect = 2.9
Identities = 38/202 (18%), Positives = 70/202 (34%), Gaps = 66/202 (32%)
Query: 310 NSTFLWYDYETFGLNVRRDRPFQFAAIR------TDIMLNTIDNPIMLYCKPAPDFLPDP 363
++TF+ D+ET GL+ + D + A++ D +T+ P +
Sbjct: 11 DATFVVLDFETTGLDPQVDEIIEIGAVKIQGGQIVDEY-HTLIKP----SREISRK---- 61
Query: 364 RACLITKITPQFCLNNGI--------PEYKFASIIEKI--FLKPGTISVGYNTILFDDEI 413
++IT GI ++ + FL+ +I V +N FD
Sbjct: 62 ----SSEIT-------GITQEMLENKR--SIEEVLPEFLGFLE-DSIIVAHN-ANFD--- 103
Query: 414 TRFM---FWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470
RF+ + + +ER + D + + K+ S+ L+
Sbjct: 104 YRFLRLWIKKVMGLDWERPY------IDTLALAKSLL---------KL-----RSYSLDS 143
Query: 471 LSFVNNLSHKKAHDALSDVRAT 492
+ L + H AL D R T
Sbjct: 144 VVEKLGLGPFRHHRALDDARVT 165
>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC,
coiled coil, GTP- binding, nucleotide-binding, immune
system; HET: GDP; 2.15A {Homo sapiens}
Length = 239
Score = 30.7 bits (69), Expect = 3.2
Identities = 11/94 (11%), Positives = 38/94 (40%), Gaps = 12/94 (12%)
Query: 38 HYICFNIEINKKTLLEIETSFR----FNDAILRYLTI-KTKKVETEESSFLRFIQKKEKV 92
H + + + + T E + + + F + ++ + T+K + +++ ++++ +
Sbjct: 114 HALLLVVPLGRYTEEEHKATEKILKMFGERARSFMILIFTRKDDLGDTNLHDYLREAPED 173
Query: 93 LKMIFGKK-------NNKNRFKQKRQQQNPLFKR 119
++ + NNK ++ Q+ L
Sbjct: 174 IQDLMDIFGDRYCALNNKATGAEQEAQRAQLLGL 207
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin
helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB:
2nrv_A 2nrw_A 2nrx_A 2nrz_A
Length = 220
Score = 30.2 bits (69), Expect = 4.3
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 954 DNLPGVKKIGPKTAVKLLNQYNSLENI 980
DN+PG IGP KL+ + SLENI
Sbjct: 171 DNVPG---IGPIRKKKLIEHFGSLENI 194
>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto;
diacyl lipopeptide, innate immunity, Leu repeat, cell
membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG;
2.90A {Mus musculus}
Length = 562
Score = 30.6 bits (69), Expect = 4.8
Identities = 24/212 (11%), Positives = 58/212 (27%), Gaps = 14/212 (6%)
Query: 544 YISLMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKEDIPISMIHL 603
+I + N +L + +N +L ++ ++
Sbjct: 182 HIKGGETESLQIPNTTVLHLVFHPNSLFSVQVNMSVNALGHLQLSNIKLNDENCQRLMTF 241
Query: 604 NRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCAS----SILNNTYIWKKIFLDYKINN 659
L ++ + F+ +I N T + ++ +
Sbjct: 242 LSELTRGPTLLNVTLQHIETTWKCSVKLFQFFWPRPVEYLNIYNLTITERIDREEFTYSE 301
Query: 660 SDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVN------FCFENKKLEELIFLY 713
+ L+ + E + N ++ M+ K LS + C FL
Sbjct: 302 TALKSLMIEHVKNQVFLFSKEALYSVFAEMNIKMLSISDTPFIHMVCP--PSPSSFTFLN 359
Query: 714 RARNFIETLSYKELKRWKKYRISRFYNKKNNL 745
+N ++ K+ + ++N L
Sbjct: 360 FTQNVFTDSVFQGCSTLKR--LQTLILQRNGL 389
>3kpb_A Uncharacterized protein MJ0100; CBS domain, S-adenosylmethionine,
conformational change, unknown function; HET: SAM; 1.60A
{Methanocaldococcus jannaschii} PDB: 3kpd_A* 3kpc_A*
Length = 122
Score = 29.0 bits (66), Expect = 4.9
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 259 DGKLFGSVTNSDIVKELEKKGLKIE 283
GKL G +T+ DI K L + IE
Sbjct: 41 HGKLVGIITSWDIAKALAQNKKTIE 65
>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 = 29.5 bits (65), Expect = 5.0
Identities = 8/27 (29%), Positives = 15/27 (55%), Gaps = 8/27 (29%)
Query: 276 EKKGLK-IEKNKIKL--PNN----SIK 295
EK+ LK ++ +KL ++ +IK
Sbjct: 18 EKQALKKLQ-ASLKLYADDSAPALAIK 43
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision
repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA
excision; 1.90A {Bacillus stearothermophilus}
Length = 226
Score = 29.8 bits (68), Expect = 6.1
Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 954 DNLPGVKKIGPKTAVKLLNQYNSLENI 980
D++PG +G K LLN + S++ +
Sbjct: 176 DDIPG---VGEKRKKALLNYFGSVKKM 199
>2r7r_A RNA-dependent RNA polymerase; viral protein, RNA-dependent RNA
polymerase, single subunit polymerase fold, fingers,
PALM, thumb; 2.60A {Simian rotavirus} PDB: 2r7q_A 2r7s_A
2r7t_A 2r7u_A 2r7v_A 2r7w_A* 2r7x_A* 2r7o_A
Length = 1095
Score = 30.2 bits (67), Expect = 6.4
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 1278 IHSITNKAKFNEISKLVEKWKPNTVKKMELKKIINTKHQTIVAY-TNYGVKFRNGIFYTK 1336
+ I + + IS+L+ K+ EL K+I+ I Y + G+ + Y
Sbjct: 918 TYQIEDDGSKSAISRLISKYSVYKPSIEELYKVISLHENEIQLYLISLGIPKIDADTYVG 977
Query: 1337 S 1337
S
Sbjct: 978 S 978
>2vyo_A ECU11_0510, chitooligosaccharide deacetylase; CE4 esterase, native
protein, microsporidian, chitin deacetylase, hydrolase,
inactive; 1.50A {Encephalitozoon cuniculi}
Length = 254
Score = 29.3 bits (66), Expect = 7.8
Identities = 13/94 (13%), Positives = 30/94 (31%), Gaps = 18/94 (19%)
Query: 236 LNAKKIGEEIKKLNINIIKKSGVDGKLF-----GSVTNSDIVKELEKKGLKI-------- 282
L+ + + + I SG + + NS++ L ++G+
Sbjct: 98 LSQDALENNVDREIDTIDGLSGTEIRYAAVPICNGQVNSEMYNILTERGVLPVGYTFCPY 157
Query: 283 ----EKNKIKLPNNSIKKIGNYYIDILLHNGNST 312
+ + + +I IL+H+G
Sbjct: 158 DYDDPVGEFESMIEGSDPKHHSFI-ILMHDGQEA 190
>3fg1_A Allene oxide synthase-lipoxygenase protein; arichidonic metabolism,
dioxygenase, fatty ACI biosynthesis, heme, iron, lipid
synthesis, lyase; HET: GOL; 1.85A {Plexaura homomalla}
PDB: 3fg4_A* 3fg3_A* 2fnq_A
Length = 696
Score = 29.9 bits (66), Expect = 8.9
Identities = 14/87 (16%), Positives = 31/87 (35%)
Query: 1174 NSTLNIASDISLTTSRDILESFSRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIVDAN 1233
+ ++ D+ T + SR L I + + ++ + +
Sbjct: 162 KTHDDLPRDVQFTDEKSRSYQESRKAALVNLGIGSLFTMFENWDSYDDYHILYRNWILGG 221
Query: 1234 SEVIFNVPCEQRFFAAVKLLGVNPLII 1260
+ + + E R+F L G NP+I+
Sbjct: 222 TPNMADRWHEDRWFGYQFLNGANPVIL 248
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
0.322 0.139 0.414
Gapped
Lambda K H
0.267 0.0492 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 21,979,501
Number of extensions: 1391899
Number of successful extensions: 3314
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3217
Number of HSP's successfully gapped: 127
Length of query: 1428
Length of database: 6,701,793
Length adjustment: 106
Effective length of query: 1322
Effective length of database: 3,742,167
Effective search space: 4947144774
Effective search space used: 4947144774
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 64 (29.0 bits)