RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780413|ref|YP_003064826.1| PAS/PAC sensor signal
transduction histidine kinase [Candidatus Liberibacter asiaticus str.
psy62]
(820 letters)
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase,
phosphoprotein, transferase, two-component regulatory
system; 3.80A {Thermotoga maritima}
Length = 349
Score = 194 bits (495), Expect = 6e-50
Identities = 78/355 (21%), Positives = 135/355 (38%), Gaps = 22/355 (6%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTE 515
SILE+ I ++++G I N+ +LFG E++L + + +
Sbjct: 12 SILESLETAIITLSKDGRITEWNKKAEQLFGLKKENVLGRRLKDLPD---FEEIGSVAES 68
Query: 516 ILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMHDISEWKQEKNKLSHAK 575
+ L G I + L I+ + +
Sbjct: 69 VFENKEPVFLNFYKFGER------YFNIRFSPFRNAKTQLLEGVIITIDDVTELYKYEEE 122
Query: 576 KIAEKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRSGN 635
+ + S + ARV+HEIR P+T I GF +K P +Y N I +
Sbjct: 123 RKRRERLSILGEMTARVAHEIRNPITIIGGFIMRMKKHLDDP---ETLKKYINIITNELS 179
Query: 636 LVLDIVNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIP 695
+ IV ++L+ SK + L F +L+E + E L + + I N
Sbjct: 180 RLETIVKEILEYSK---ERQVLEFTEFNLNELIREVYVLFEEKIRKMNIDFCFETDNEDL 236
Query: 696 RILADLRSVKQIALNILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEK 755
R+ AD +KQ+ +N++ NAI T G+I I++ +V + V ++G + EK
Sbjct: 237 RVEADRTRIKQVLINLVQNAIEATGENGKIKITSEDM-YTKVRVSVWNSGPPIPEELKEK 295
Query: 756 AMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810
PF + +GTGLGL + + +++ G G + P
Sbjct: 296 IFSPF------FTTKTQGTGLGLSICRKIIEDEHGGKIWTENRENGVVFIFEIPK 344
>2c2a_A Sensor histidine kinase; phosphotransfer, PHOQ, selenomethionyl
MAD, two-component systems, transferase; HET: ADP; 1.9A
{Thermotoga maritima} SCOP: a.30.2.1 d.122.1.3 PDB:
3dge_A*
Length = 258
Score = 190 bits (485), Expect = 8e-49
Identities = 62/256 (24%), Positives = 127/256 (49%), Gaps = 12/256 (4%)
Query: 558 MHDISEWKQEKNKLSHAKKIAEKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGP 617
M +++E +E +L ++ K++F+A +SHE+RTPLTAI ++E I G
Sbjct: 1 MENVTE-SKELERLKRIDRM-------KTEFIANISHELRTPLTAIKAYAETIY-NSLGE 51
Query: 618 LGNPRYIEYANYIDRSGNLVLDIVNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQL 677
L E+ I N + +++N+LLD S++E + ++ E V L + V A++ ++
Sbjct: 52 LDLSTLKEFLEVIIDQSNHLENLLNELLDFSRLERKSLQINREKVDLCDLVESAVNAIKE 111
Query: 678 YANEKRILIRTSF-ANNIPRILADLRSVKQIALNILSNAIHFTPSGGQIIISTTHTSNEE 736
+A+ + + D ++Q+ LN+L+N + ++ ++
Sbjct: 112 FASSHNVNVLFESNVPCPVEAYIDPTRIRQVLLNLLNNGVKYSKKDAPDKYVKVILDEKD 171
Query: 737 --VILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYI 794
V++ V D G+G+ ++ ++ + F ++ +S GTGLGL + K +V+ + G+ ++
Sbjct: 172 GGVLIIVEDNGIGIPDHAKDRIFEQFYRVDSSLTYEVPGTGLGLAITKEIVELHGGRIWV 231
Query: 795 FSTPAKGTLIEIIFPL 810
S KG+ + P
Sbjct: 232 ESEVGKGSRFFVWIPK 247
>3jz3_A Sensor protein QSEC; helix-turn-helix, kinase domain, ATP-binding,
cell inner MEM cell membrane, kinase, membrane,
nucleotide-binding; 2.50A {Escherichia coli}
Length = 222
Score = 182 bits (464), Expect = 2e-46
Identities = 41/223 (18%), Positives = 92/223 (41%), Gaps = 11/223 (4%)
Query: 587 DFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDLLD 646
F + +HE+R+PLTA+ +EV + P + + + +V+ LL
Sbjct: 4 RFTSDAAHELRSPLTALKVQTEVAQLSDDDP---QARKKALLQLHSGIDRATRLVDQLLT 60
Query: 647 ISKIESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSVKQ 706
+S+++S + L++ + ++ + A + +I +R + + + +
Sbjct: 61 LSRLDSLDNLQDVAEIPLEDLLQSSVMDIYHTAQQAKIDVRLTLNAHSIKRTGQPLLLSL 120
Query: 707 IALNILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQIPNS 766
+ N+L NA+ ++P G + ++ VRD G G+T L + + F + P
Sbjct: 121 LVRNLLDNAVRYSPQGSVVDVTL-----NADNFIVRDNGPGVTPEALARIGERFYRPPGQ 175
Query: 767 QQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFP 809
G+GLGL + + + + + G ++ +
Sbjct: 176 ---TATGSGLGLSIVQRIAKLHGMNVEFGNAEQGGFEAKVSWL 215
>3d36_A Sporulation kinase B; GHKL ATPase, four helix bundle, class I
two-component histidine kinase, phosphoprotein; HET:
ADP; 2.03A {Geobacillus stearothermophilus}
Length = 244
Score = 176 bits (449), Expect = 1e-44
Identities = 67/233 (28%), Positives = 113/233 (48%), Gaps = 16/233 (6%)
Query: 578 AEKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRSGNLV 637
AEK + + A +SHEIR PLTA GF ++I+ Q PL + +YA +
Sbjct: 8 AEKMEA-VTHLAASISHEIRNPLTAARGFIQLIEEQ---PLAADKRRQYARIAIEELDRA 63
Query: 638 LDIVNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRI 697
I+ D L +K E +++ + I +++ AN + I+ + A +
Sbjct: 64 EAIITDYLTFAKPAPETP----EKLNVKLEIERVIDILRPLANMSCVDIQATLAP--FSV 117
Query: 698 LADLRSVKQIALNILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAM 757
+ + +Q LN++ NAI P+GG + + + N V++R+ DTGVGMT +LE+
Sbjct: 118 IGEREKFRQCLLNVMKNAIEAMPNGGTLQVYVSI-DNGRVLIRIADTGVGMTKEQLERLG 176
Query: 758 KPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810
+P+ +GTGLG+ + ++++ G I S KGT + I PL
Sbjct: 177 EPYFTTKGV-----KGTGLGMMVVYRIIESMNGTIRIESEIHKGTTVSIYLPL 224
>1gkz_A [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase;
transferase, mitochondrial protein kinase, potassium;
HET: ADP; 2.2A {Rattus norvegicus} SCOP: a.29.5.1
d.122.1.4 PDB: 1gjv_A 1gkx_A*
Length = 388
Score = 173 bits (440), Expect = 1e-43
Identities = 40/388 (10%), Positives = 108/388 (27%), Gaps = 43/388 (11%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTE 515
S + +A + + N++ + L ++ ++
Sbjct: 3 SATDTHHVELARERSKTVTSFYNQSAIDVVAEKPSVRLTPTMMLYSGRSQDGSHLLKSGR 62
Query: 516 ILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMHDISEWKQEKNKLSHAK 575
L +L + G ++ I + Y ++++ K+
Sbjct: 63 YLQQELPVRIAHRIKGFRSLPFIIGCNPTILHV--HELYIRAFQKLTDFPPIKD------ 114
Query: 576 KIAEKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRSGN 635
+ + + + ++ + + +T + + + + S
Sbjct: 115 ---QADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKH---IEDEKLVRYFLDKTLTSRL 168
Query: 636 LVLDIVNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRILIR--TSFANN 693
+ + L + + + + + +S + + + + + K +
Sbjct: 169 GIRMLATHHLALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHV 228
Query: 694 IPRILADLRSVKQIALNILSNAIHFTPSGGQIIISTT-------HTSNEEVILRVRDTGV 746
R + I +L NA+ T ++ ++I+R+ D G
Sbjct: 229 AARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGG 288
Query: 747 GMTNYELEKAMKPF--------------------GQIPNSQQIRGEGTGLGLPLAKAMVD 786
G+ + +L++ M Q G G GLP ++A +
Sbjct: 289 GIAHKDLDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFGFGLPTSRAYAE 348
Query: 787 ANMGKFYIFSTPAKGTLIEIIFPLYDTS 814
G + S GT + + D
Sbjct: 349 YLGGSLQLQSLQGIGTDVYLRLRHIDGR 376
>1id0_A PHOQ histidine kinase; PHOQ/PHOP, signal transduction, transferase;
HET: ANP; 1.60A {Escherichia coli} SCOP: d.122.1.3 PDB:
3cgz_A 3cgy_A
Length = 152
Score = 111 bits (279), Expect = 8e-25
Identities = 27/151 (17%), Positives = 56/151 (37%), Gaps = 8/151 (5%)
Query: 660 EPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSVKQIALNILSNAIHFT 719
E + + S + K + I + I + + ++ N+L NA +
Sbjct: 2 ELHPVAPLLDNLTSALNKVYQRKGVNISLDISPEIS-FVGEQNDFVEVMGNVLDNACKYC 60
Query: 720 PSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGLP 779
+I + ++E + + V D G G+ + E ++ G G+GL
Sbjct: 61 LEFVEI---SARQTDEHLYIVVEDDGPGIPLSKREVIFDRGQRVDTL----RPGQGVGLA 113
Query: 780 LAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810
+A+ + + GK + G +E+IF
Sbjct: 114 VAREITEQYEGKIVAGESMLGGARMEVIFGR 144
>1bxd_A ENVZ(290-450), protein (osmolarity sensor protein (ENVZ));
histidine kinase, osmosensor, His-Asp phosphorelay
system, signal transduction; HET: ANP; NMR {Escherichia
coli} SCOP: d.122.1.3
Length = 161
Score = 110 bits (277), Expect = 1e-24
Identities = 35/154 (22%), Positives = 65/154 (42%), Gaps = 9/154 (5%)
Query: 657 LHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSVKQIALNILSNAI 716
+ E L+ + E I+ Y E I T+ + S+K+ N++ NA
Sbjct: 5 MPMEMADLNAVLGEVIAAESGYERE----IETALYPGSIEVKMHPLSIKRAVANMVVNAA 60
Query: 717 HFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGL 776
+ G I +S+ T +V D G G+ + + +PF + +++ GTGL
Sbjct: 61 RYG--NGWIKVSS-GTEPNRAWFQVEDDGPGIAPEQRKHLFQPFVRGDSAR--TISGTGL 115
Query: 777 GLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810
GL + + +VD + G + ++ G I P+
Sbjct: 116 GLAIVQRIVDNHNGMLELGTSERGGLSIRAWLPV 149
>1ysr_A Sensor-type histidine kinase PRRB; ATP-binding domain, structural
genomics, mycobacterium tuberculosis structural
proteomics project; 1.78A {Mycobacterium tuberculosis}
SCOP: d.122.1.3 PDB: 1ys3_A
Length = 150
Score = 107 bits (269), Expect = 1e-23
Identities = 25/152 (16%), Positives = 56/152 (36%), Gaps = 8/152 (5%)
Query: 659 FEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSVKQIALNILSNAIHF 718
PV + + + A + + + S I+ ++ N ++NA+
Sbjct: 5 HVPVDITDLLDRAAHDAARIYPDLDVSLVPS---PTCIIVGLPAGLRLAVDNAIANAVKH 61
Query: 719 TPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGL 778
+ ++ + +S V + + D G G+ E + + F + + G+GLGL
Sbjct: 62 GGAT--LVQLSAVSSRAGVEIAIDDNGSGVPEGERQVVFERFSRGSTA---SHSGSGLGL 116
Query: 779 PLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810
L + G + ++P G + + P
Sbjct: 117 ALVAQQAQLHGGTASLENSPLGGARLVLRLPG 148
>2q8g_A [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1; GHKL
ATPase/kinase family, pyruvate dehydrogenase complex,
mitochondrial kinase; HET: AZX; 1.90A {Homo sapiens}
PDB: 2q8f_A* 2q8h_A
Length = 407
Score = 106 bits (266), Expect = 2e-23
Identities = 52/368 (14%), Positives = 117/368 (31%), Gaps = 47/368 (12%)
Query: 491 DILRKPFTVFLEQNTPSVMNHYLT-EILSLDLRQ--------TLEKITLGSTKEEKLLSL 541
D P + E+ P ++ Y L ++Q EK + ++E + L
Sbjct: 2 DSGSSPAS---ERGVPGQVDFYARFSPSPLSMKQFLDFGSVNACEKTSFMFLRQELPVRL 58
Query: 542 RIIIK---KLPFSSCYSLTMHDISEW-KQEKNKLSHAKKIAEKESSHKSDFLARVSHEIR 597
I+K LP + + ++ + W Q +L K + +++ DF V
Sbjct: 59 ANIMKEISLLPDNLLRTPSVQLVQSWYIQSLQELLDFKDKSAEDAKAIYDFTDTVIRIRN 118
Query: 598 TPLTAII----GFSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDLLDISKIESG 653
I G E ++ P+ + + + S + ++N + +
Sbjct: 119 RHNDVIPTMAQGVIEYKESFGVDPVTSQNVQYFLDRFYMSRISIRMLLNQHSLLFGGKGK 178
Query: 654 KMNLH-------FEPVSLDEAVSEAISLVQLYANEKRI--------LIRTSFANNIPRIL 698
H ++ E + + + + I + +++
Sbjct: 179 GSPSHRKHIGSINPNCNVLEVIKDGYENARRLCDLYYINSPELELEELNAKSPGQPIQVV 238
Query: 699 ADLRSVKQIALNILSNAIHFTPSGGQI------IISTTHTSNEEVILRVRDTGVGMTNYE 752
+ + + NA+ T I NE++ +++ D G G+ +
Sbjct: 239 YVPSHLYHMVFELFKNAMRATMEHHANRGVYPPIQVHVTLGNEDLTVKMSDRGGGVPLRK 298
Query: 753 LEKAMKPF------GQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEI 806
+++ ++ S+ + G G GLP+++ G ++S GT I
Sbjct: 299 IDRLFNYMYSTAPRPRVETSRAVPLAGFGYGLPISRLYAQYFQGDLKLYSLEGYGTDAVI 358
Query: 807 IFPLYDTS 814
T
Sbjct: 359 YIKALSTD 366
>2e0a_A Pyruvate dehydrogenase kinase isozyme 4; PDK4, ATP-binding,
structural genomics, NPPSFA; HET: ANP; 1.86A {Homo
sapiens} PDB: 2zdx_A* 2zdy_A* 2zkj_A* 3d2r_A*
Length = 394
Score = 105 bits (262), Expect = 6e-23
Identities = 39/297 (13%), Positives = 85/297 (28%), Gaps = 35/297 (11%)
Query: 545 IKKLPFSSCYSLTMHDISE----WKQEKNKLSHAKKIAEKESSHKSDFLARVSHEIRTPL 600
I LP + + + Q L + + + SDF+ +
Sbjct: 55 IDILPTQL---VNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLIKVRNRHH 111
Query: 601 TAIIG----FSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDLLDISKIESGKMN 656
+ E P+ N + + + ++N + I
Sbjct: 112 NVVPTMAQGIIEYKDACTVDPVTNQNLQYFLDRFYMNRISTRMLMNQHILIFSDSQTGNP 171
Query: 657 LH----FEPVSLDEAVSEAISLVQLYANE--------KRILIRTSFANNIPRILADLRSV 704
H + V +A ++ ++ K + F + I+ +
Sbjct: 172 SHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHL 231
Query: 705 KQIALNILSNAIHFTPSGGQ------IIISTTHTSNEEVILRVRDTGVGMTNYELEKAMK 758
+ + NA+ T + I E++ +++ D G G+ +++
Sbjct: 232 HHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFS 291
Query: 759 PF------GQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFP 809
+ NS+ G G GLP+++ G ++S GT I
Sbjct: 292 YTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYFQGDLNLYSLSGYGTDAIIYLK 348
>3a0y_A Sensor protein; ATP-LID, kinase, phosphoprotein, transferase,
two-component regulatory system; 1.57A {Thermotoga
maritima} PDB: 3a0t_A* 3a0x_A 3a0w_A 3a0z_A
Length = 152
Score = 104 bits (261), Expect = 7e-23
Identities = 37/154 (24%), Positives = 64/154 (41%), Gaps = 7/154 (4%)
Query: 657 LHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSVKQIALNILSNAI 716
+ F +L+E + E L + + I N R+ AD +KQ+ +N++ NAI
Sbjct: 1 MEFTEFNLNELIREVYVLFEEKIRKMNIDFCFETDNEDLRVEADRTRIKQVLINLVQNAI 60
Query: 717 HFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGL 776
T G+I I T+ +V + V ++G + EK PF + +GTGL
Sbjct: 61 EATGENGKIKI-TSEDMYTKVRVSVWNSGPPIPEELKEKIFSPF------FTTKTQGTGL 113
Query: 777 GLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810
GL + + +++ G G + P
Sbjct: 114 GLSICRKIIEDEHGGKIWTENRENGVVFIFEIPK 147
>1y8o_A [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3; pyruvate
dehydrogenase kinase 3, lipoyl-bearing domain; HET: LPA
ADP; 2.48A {Homo sapiens} SCOP: a.29.5.1 d.122.1.4 PDB:
1y8n_A* 1y8p_A* 2pnr_A* 2q8i_A*
Length = 419
Score = 99.0 bits (246), Expect = 4e-21
Identities = 32/308 (10%), Positives = 96/308 (31%), Gaps = 32/308 (10%)
Query: 539 LSLRII-IKKLPFSSCYSLTMHDISEW-KQEKNKLSHAKKIAEKESSHKSDFLARVSHEI 596
L+ + + LP + ++ + W Q +L + + ++ +FL +
Sbjct: 70 LANTMREVNLLPDNLLNRPSVGLVQSWYMQSFLELLEYENKSPEDPQVLDNFLQVLIKVR 129
Query: 597 RTPLTAII----GFSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDLLDISKIES 652
+ G E + F P + + + + ++N + ++
Sbjct: 130 NRHNDVVPTMAQGVIEYKEKFGFDPFISTNIQYFLDRFYTNRISFRMLINQHTLLFGGDT 189
Query: 653 GKMNLHF-----EPVSLDEAVSEAISLVQLYANEK--------RILIRTSFANNIPRILA 699
++ ++ + V +A ++ + + +++
Sbjct: 190 NPVHPKHIGSIDPTCNVADVVKDAYETAKMLCEQYYLVAPELEVEEFNAKAPDKPIQVVY 249
Query: 700 DLRSVKQIALNILSNAIHFTP-------SGGQIIISTTHTSNEEVILRVRDTGVGMTNYE 752
+ + + N++ T G + + E++ +++ D G G+ +
Sbjct: 250 VPSHLFHMLFELFKNSMRATVELYEDRKEGYPAVKTLVTLGKEDLSIKISDLGGGVPLRK 309
Query: 753 LEKAMKPF------GQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEI 806
+++ + ++ G G GLP+++ G ++S GT I
Sbjct: 310 IDRLFNYMYSTAPRPSLEPTRAAPLAGFGYGLPISRLYARYFQGDLKLYSMEGVGTDAVI 369
Query: 807 IFPLYDTS 814
+
Sbjct: 370 YLKALSSE 377
>1r62_A Nitrogen regulation protein NR(II); PII, histidine kinase, two
component system, transferase; 1.60A {Escherichia coli
K12} SCOP: d.122.1.3
Length = 160
Score = 90.1 bits (223), Expect = 2e-18
Identities = 36/166 (21%), Positives = 65/166 (39%), Gaps = 18/166 (10%)
Query: 655 MNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSVKQIALNILSN 714
+ S+ + ++LV + + + + ++P + D ++Q+ LNI+ N
Sbjct: 1 LPGTRVTESIHKVAERVVTLVSMEL-PDNVRLIRDYDPSLPELAHDPDQIEQVLLNIVRN 59
Query: 715 AIHFTPSGGQIIISTTHTS----------NEEVILRVRDTGVGMTNYELEKAMKPFGQIP 764
A+ G II T T+ + V D G G+ + + P
Sbjct: 60 ALQALGPEGGEIILRTRTAFQLTLHGERYRLAARIDVEDNGPGIPPHLQDTLFYPM---- 115
Query: 765 NSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810
R GTGLGL +A+ ++D + GK S P T + P+
Sbjct: 116 --VSGREGGTGLGLSIARNLIDQHSGKIEFTSWP-GHTEFSVYLPI 158
>2btz_A Pyruvate dehydrogenase kinase isoenzyme 2; GHKL motif regulation,
transferase; 2.2A {Homo sapiens} PDB: 2bu2_A* 2bu5_A*
2bu6_A* 2bu7_A* 2bu8_A* 3crk_A* 1jm6_A* 3crl_A*
Length = 394
Score = 89.0 bits (220), Expect = 4e-18
Identities = 39/301 (12%), Positives = 90/301 (29%), Gaps = 30/301 (9%)
Query: 539 LSLRII-IKKLPFSSCYSLTMHDISEWKQEK-NKLSHAKKIAEKESSHKSDFLARVSHEI 596
L+ + I LP + ++ + W + + ++ S F +
Sbjct: 48 LANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIR 107
Query: 597 RTPLTAIIG----FSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDLLDISKIES 652
+ E P+ N + + S + ++N I +
Sbjct: 108 NRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGST 167
Query: 653 GKMNLH-----FEPVSLDEAVSEAISLVQ-------LYANEKRILIRTSFANNIP-RILA 699
+ ++ E V +A + + + + + I + + P ++
Sbjct: 168 NPAHPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVY 227
Query: 700 DLRSVKQIALNILSNAIHFTPSGGQI------IISTTHTSNEEVILRVRDTGVGMTNYEL 753
+ + + NA+ T + I E++ +++ D G G+ ++
Sbjct: 228 VPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKI 287
Query: 754 EKAMKPFGQIPNSQQIRG-----EGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIF 808
E+ + Q G G GLP+++ G +FS GT I
Sbjct: 288 ERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYL 347
Query: 809 P 809
Sbjct: 348 K 348
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 88.1 bits (218), Expect = 7e-18
Identities = 123/686 (17%), Positives = 203/686 (29%), Gaps = 277/686 (40%)
Query: 204 FSHLHEIKKGHSSVEKEKYDIFSQQSPP---PHLRMKNKVSSLTEYYAHK---------D 251
F ++++ + + E + F+ P L V Y + D
Sbjct: 27 FFIASQLQEQFNKILPEPTEGFAADDEPTTPAEL-----VGKFLGYVSSLVEPSKVGQFD 81
Query: 252 DVLKTEKYPLLTSEESSLPEQEDFHTI--NLNQYTK----------KQYFGTLQNNSKES 299
VL LT E+ E D H + L Q K Y T + +K
Sbjct: 82 QVLNL----CLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYI-TARIMAKRP 136
Query: 300 FEYLSHRNHPSLSAYFDEGENLTPETVDKCPIPFFVYS----HGNLFYANPSF--L--LL 351
F+ S SA F + + GN + F L L
Sbjct: 137 FD------KKSNSALFRAVGE------GNAQL----VAIFGGQGN---TDDYFEELRDLY 177
Query: 352 TKYKS-VDDI--EIAGGLSTLLDAPKLSDNNAIKPVMLYRSDRTCIAASARLHTIQW--N 406
Y V D+ A LS L+ +A K ++ + L+ ++W N
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTL----DAEK---VF---------TQGLNILEWLEN 221
Query: 407 RENSLAMTFIPFEKANQF----PENMPQNGIEPEDVDT-----RINKRKMEIEVMQLCSI 457
N P + P + P G+ + + + +L S
Sbjct: 222 PSN------TP---DKDYLLSIPISCPLIGV------IQLAHYVVTAKLLGFTPGELRSY 266
Query: 458 LEAT---SDGI---AII----NREGIILSTNRAVSKLF--------GYPVEDILRKPFTV 499
L+ S G+ I + E +S +A++ LF YP + P ++
Sbjct: 267 LKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSL---PPSI 323
Query: 500 F---LEQN--TPSVMNHYLTEILSL-DL-RQTLEKITLGST-----KEEKL-LSLR---- 542
LE N PS M LS+ +L ++ ++ + T +++ +SL
Sbjct: 324 LEDSLENNEGVPSPM-------LSISNLTQEQVQDY-VNKTNSHLPAGKQVEISLVNGAK 375
Query: 543 -IIIKKLPFSSCYSLTMHDISEWKQEKNKLSHAKKIAEKESSHKSDFLARVSHEIRTPLT 601
+++ P S Y L + L AK + + S R P
Sbjct: 376 NLVVSGPP-QSLYGLNLT-----------LRKAKAPSGLDQS-------------RIP-- 408
Query: 602 AIIGFSE---VIKNQRFGPLGNP---RYIEYANYIDRSGNLVLDIVNDLLDISKIESGKM 655
FSE N RF P+ +P + A+ D I DL+ + + K
Sbjct: 409 ----FSERKLKFSN-RFLPVASPFHSHLLVPAS--DL-------INKDLVKNNVSFNAKD 454
Query: 656 NLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSVKQI-------- 707
+ PV Y +R + RI V I
Sbjct: 455 -IQI-PV---------------YDTFDGSDLRVLSGSISERI------VDCIIRLPVKWE 491
Query: 708 -ALNILSNAIH---FTPSGGQIIISTTHTSNEEVILRVRDTGVG-MTNYELEKAMKPFGQ 762
A H F P GG S G+G +T+
Sbjct: 492 TTTQ--FKATHILDFGP-GG---AS----------------GLGVLTH------------ 517
Query: 763 IPNSQQIRGEGTGLGLPLAKAMVDAN 788
+ + +GTG+ + +A + D N
Sbjct: 518 -----RNK-DGTGVRVIVAGTL-DIN 536
Score = 82.3 bits (203), Expect = 4e-16
Identities = 111/569 (19%), Positives = 184/569 (32%), Gaps = 204/569 (35%)
Query: 334 FVYSHGNLFYANPSFLLLTKYKSVDDIEIAGGLSTLLDA-----PKLSDNNAIK-----P 383
SHG+L L+ T + S L + P+ ++ A P
Sbjct: 9 LTLSHGSL---EHVLLVPTASFFI--------ASQLQEQFNKILPEPTEGFAADDEPTTP 57
Query: 384 VMLYRSDRTCIAASARLHTIQWNRENSLAMTFIPFEKANQFPENMPQNGIE------PED 437
L +++ + L + FE N + + N I ++
Sbjct: 58 AELVGKFLGYVSSLVEPSK-VGQFDQVLNLCLTEFE--NCY---LEGNDIHALAAKLLQE 111
Query: 438 VDTRINKRKMEIEVMQLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPF 497
DT + K K +++ + R ++ S LF V + +
Sbjct: 112 NDTTLVKTK---------ELIKNYITARIMAKRP----FDKKSNSALFR-AVGEGNAQLV 157
Query: 498 TVFLEQ-NTPSVMNHYLTEILSLDLRQT----LEKITLGSTKEEKLLSLRIIIKKLP--F 550
+F Q NT + Y E L DL QT + L E L L +
Sbjct: 158 AIFGGQGNT----DDYFEE-LR-DLYQTYHVLVG--DLIKFSAETLSEL----IRTTLDA 205
Query: 551 SSCYSLTMHDISEWKQEKNKLSHAKKIAEKESSHKSDFL--ARVSHEIRTPLTAIIG--- 605
++ + +I EW L + ++ D+L +S PL IG
Sbjct: 206 EKVFTQGL-NILEW------LENP------SNTPDKDYLLSIPIS----CPL---IGVIQ 245
Query: 606 ---FSEVIKNQRFGPLG-NPRYIEYANYIDRSG------NLVLDIVNDLLDISKIESGKM 655
+ K LG P E +Y+ G LV + I++ +S
Sbjct: 246 LAHYVVTAKL-----LGFTPG--ELRSYL--KGATGHSQGLVTAVA-----IAETDS--- 288
Query: 656 NLHFEPVSLDEAVSEAISLV--------QLYANEKRILIRTSFANNIPRILAD------- 700
+E S +V +AI+++ + Y TS P IL D
Sbjct: 289 ---WE--SFFVSVRKAITVLFFIGVRCYEAYP-------NTSLP---PSILEDSLENNEG 333
Query: 701 -----LRSVKQIALNIL------SNAIHFTPSGGQIIISTTHTSNEEVILRVRDTG---- 745
L S+ + + +N+ H P+G Q+ IS + + V+ +G
Sbjct: 334 VPSPML-SISNLTQEQVQDYVNKTNS-HL-PAGKQVEISLVNGAKNLVV-----SGPPQS 385
Query: 746 -VGMTNYELEKAMKPFGQ----IPNSQ-----QIRGEGTGLGLP---------LAKA--M 784
G+ N L KA P G IP S+ R LP L A +
Sbjct: 386 LYGL-NLTLRKAKAPSGLDQSRIPFSERKLKFSNRF------LPVASPFHSHLLVPASDL 438
Query: 785 VDANMGKFYIFSTPAKGTLIEIIFPLYDT 813
++ ++ K + S AK +I P+YDT
Sbjct: 439 INKDLVKNNV-SFNAK----DIQIPVYDT 462
Score = 36.5 bits (84), Expect = 0.027
Identities = 40/180 (22%), Positives = 69/180 (38%), Gaps = 40/180 (22%)
Query: 643 DLLDISKIES---GKMNLHFEPVS----LDEAVSEAISLVQLYANEKRILIRTSFANNIP 695
DL SK + + HF+ LD ++ ++L + EK IR +++ I
Sbjct: 1634 DLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIF 1693
Query: 696 RILAD--LRSVKQIA-LNILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYE 752
+ D L++ K +N S + F G ++S T + + L
Sbjct: 1694 ETIVDGKLKTEKIFKEINEHSTSYTFRSEKG--LLSATQFTQPALTL------------- 1738
Query: 753 LEKA----MKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIF 808
+EKA +K G IP G G LA ++ D + S +L+E++F
Sbjct: 1739 MEKAAFEDLKSKGLIPADATFAGHSLGEYAALA-SLAD-------VMSIE---SLVEVVF 1787
Score = 35.3 bits (81), Expect = 0.050
Identities = 55/374 (14%), Positives = 97/374 (25%), Gaps = 167/374 (44%)
Query: 64 NTN-YLDSE-----NT---FVFDPI-------------PRTVR--FTWNIDAHGYLKEIS 99
NT+ Y + E T V D I FT ++ +L+
Sbjct: 165 NTDDYFE-ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLEN-P 222
Query: 100 EELPKTIGNY------AFKMIGM-RLCD--VS-DILHIDPNNHIGDLLKR--------Q- 140
P +Y + +IG+ +L V+ +L P G+L Q
Sbjct: 223 SNTPDK--DYLLSIPISCPLIGVIQLAHYVVTAKLLGFTP----GELRSYLKGATGHSQG 276
Query: 141 ----------NTW------------------------YGKTTLWPI---------EGTNL 157
++W Y T+L P EG
Sbjct: 277 LVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGV-- 334
Query: 158 YVPIDLAALPIYSRNREFSGFRGFGIVHVNRVDNDPR-ALGKRLDKKFSHLHEIKKGHSS 216
P P+ S + + ++K SHL K+ S
Sbjct: 335 --PS-----PMLS-------ISNL-----------TQEQVQDYVNKTNSHLPAGKQVEIS 369
Query: 217 VEKEKYDIFSQQS-----PPP-------HLRMKNKVSSLTEYYAHKDD--VLKTEKYPLL 262
+ + ++ PP LR K K S D + +E+
Sbjct: 370 L------VNGAKNLVVSGPPQSLYGLNLTLR-KAKAPS------GLDQSRIPFSERKLKF 416
Query: 263 TSEESSLPEQEDFHTINLNQYTKKQYFGTLQNNSKESFEYLSH---------RNHPSLSA 313
++ LP FH+ ++ K + + + + L
Sbjct: 417 SN--RFLPVASPFHS----HLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRV 470
Query: 314 YFDEGENLTPETVD 327
+++ VD
Sbjct: 471 L---SGSISERIVD 481
Score = 34.5 bits (79), Expect = 0.10
Identities = 39/223 (17%), Positives = 68/223 (30%), Gaps = 79/223 (35%)
Query: 5 SIISNPEDILTSNCKGNTQDLSKKKIDNGFETEKSKKENPCHDSFEQSN--FTDQNQESV 62
S+++ ++++ S G Q L G K + P +QS F+ + +
Sbjct: 369 SLVNGAKNLVVS---GPPQSLY------GLNLTLRKAKAP--SGLDQSRIPFS-ERKLKF 416
Query: 63 SNTNYLDSENTFVFDPIPRTVRFTWNIDAHG-YLKEISEELPKTIGNYAFKMIGMRLCDV 121
SN F P+ F H L S+ + K + +
Sbjct: 417 SNR----------FLPV--ASPF------HSHLLVPASDLINKDLVKNNVSF------NA 452
Query: 122 SDILHIDP--NNHIG-DLLKRQNTWYGK----------TTL---WPIEGTNLYVP----I 161
D + I P + G DL R L W T +
Sbjct: 453 KD-IQI-PVYDTFDGSDL--RV---LSGSISERIVDCIIRLPVKWE-TTTQF--KATHIL 502
Query: 162 D-----LAAL-PIYSRNREFSGFRGFGIVHVNRVDNDP-RALG 197
D + L + RN++ +G R ++ +D +P G
Sbjct: 503 DFGPGGASGLGVLTHRNKDGTGVR---VIVAGTLDINPDDDYG 542
>1b3q_A Protein (chemotaxis protein CHEA); histine kinase, signal
transduction, multi- domains protein; 2.60A {Thermotoga
maritima} SCOP: a.30.2.1 b.40.7.1 d.122.1.3 PDB: 2ch4_A*
Length = 379
Score = 70.5 bits (171), Expect = 2e-12
Identities = 40/267 (14%), Positives = 78/267 (29%), Gaps = 58/267 (21%)
Query: 585 KSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDL 644
K D L + E+ + I+ + + +D S + + I DL
Sbjct: 10 KLDNLMDLMGELVIARSRILETLKKYNIKE---------------LDESLSHLSRITLDL 54
Query: 645 LDISKIESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRS- 703
++ + V + + +V+ A + + +
Sbjct: 55 QNVV--------MKIRMVPISFVFNRFPRMVRDLAKKMNKEVNFIMRGEDTELDRTFVEE 106
Query: 704 VKQIALNILSNAIHFTPSGGQIIISTTHTS-----------NEEVILRVRDTGVGMTNY- 751
+ + L++L NAI + I+ V++ V D G G+
Sbjct: 107 IGEPLLHLLRNAIDHGIEPKEERIAKGKPPIGTLILSARHEGNNVVIEVEDDGRGIDKEK 166
Query: 752 ----------------------ELEKAMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANM 789
E+ + G + G G+G+ + K +V++
Sbjct: 167 IIRKAIEKGLIDESKAATLSDQEILNFLFVPGFSTKEKVSEVSGRGVGMDVVKNVVESLN 226
Query: 790 GKFYIFSTPAKGTLIEIIFPLYDTSHP 816
G I S KGT + I PL
Sbjct: 227 GSMGIESEKDKGTKVTIRLPLTLAIIC 253
>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2,
protein structure initiative, northeast structural
genomics consortium; 2.00A {Colwellia psychrerythraea}
Length = 124
Score = 65.0 bits (158), Expect = 7e-11
Identities = 19/124 (15%), Positives = 42/124 (33%), Gaps = 3/124 (2%)
Query: 447 MEIEVM-QLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNT 505
M ++++ Q + D I + + +G I+ N+ L+GY E + +P +
Sbjct: 1 MNVDILKQRAKAFDYVFDAIVVTDLQGFIIDWNKGSETLYGYSKEQAIGQPVNMLHVPGD 60
Query: 506 PSVMNHYLTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPF--SSCYSLTMHDISE 563
+ + + + T E L + + DI++
Sbjct: 61 TEHITSEVISAVENQGKWTGEIRMLHKDGHIGWIESMCVPIYGENYQMVGALGINRDITK 120
Query: 564 WKQE 567
K+E
Sbjct: 121 RKKE 124
>1i58_A Chemotaxis protein CHEA; beta-alpha sandwich, signaling protein,
transferase; HET: ACP ADP; 1.60A {Thermotoga maritima}
SCOP: d.122.1.3 PDB: 1i59_A* 1i5a_A* 1i5b_A* 1i5c_A*
1i5d_A*
Length = 189
Score = 62.7 bits (151), Expect = 3e-10
Identities = 31/184 (16%), Positives = 60/184 (32%), Gaps = 35/184 (19%)
Query: 662 VSLDEAVSEAISLVQLYANEKRILIRTSF-ANNIPRILADLRSVKQIALNILSNAIHFTP 720
V + + +V+ A + + + + + + L++L NAI
Sbjct: 5 VPISFVFNRFPRMVRDLAKKMNKEVNFIMRGEDTELDRTFVEEIGEPLLHLLRNAIDHGI 64
Query: 721 SGGQI-----------IISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQI 769
+ +I + V++ V D G G+ ++ + G I S+
Sbjct: 65 EPKEERIAKGKPPIGTLILSARHEGNNVVIEVEDDGRGIDKEKIIRKAIEKGLIDESKAA 124
Query: 770 R-----------------------GEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEI 806
G G+G+ + K +V++ G I S KGT + I
Sbjct: 125 TLSDQEILNFLFVPGFSTKEKVSEVSGRGVGMDVVKNVVESLNGSISIESEKDKGTKVTI 184
Query: 807 IFPL 810
PL
Sbjct: 185 RLPL 188
>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix
two-turns helix; 2.00A {Sulfolobus shibatae} SCOP:
a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A*
1z5a_A* 1z59_A* 1z5c_A* 2hkj_A*
Length = 471
Score = 58.4 bits (141), Expect = 6e-09
Identities = 22/112 (19%), Positives = 40/112 (35%), Gaps = 7/112 (6%)
Query: 700 DLRSVKQIALNILSNAIHFTPSGG-----QIIISTTHTSNEEVILRVRDTGVGMTNYELE 754
R++ Q ++ N++ T G +I I + + + V D G+G+ E+
Sbjct: 29 PARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVP 88
Query: 755 KAMKPFGQIPNSQQIRGEGT-GLGLPLAKAMVDANMGKF-YIFSTPAKGTLI 804
A + G GLG+ A + K I ++P I
Sbjct: 89 NAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRI 140
>1th8_A Anti-sigma F factor; SPOIIAB, SPOIIAA, anti-ANTI-sigma,
sporulation, serine kinase, transcription; HET: ADP;
2.40A {Geobacillus stearothermophilus} SCOP: d.122.1.3
PDB: 1thn_A* 1til_A* 1l0o_A* 1tid_A*
Length = 145
Score = 53.2 bits (127), Expect = 2e-07
Identities = 34/156 (21%), Positives = 63/156 (40%), Gaps = 28/156 (17%)
Query: 654 KMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSVKQIALNILS 713
+M+L F S +E+ + R+ + +F + + +L +K + ++
Sbjct: 4 EMHLQFSARSENESFA-------------RVTVA-AFVAQLDPTMDELTEIKTVVSEAVT 49
Query: 714 NAIHF---TPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIR 770
NAI G + IS + V L VRD GVG+ + E+A +P
Sbjct: 50 NAIIHGYNNDPNGIVSISVIIE-DGVVHLTVRDEGVGIPDI--EEARQPLFTTKPE---- 102
Query: 771 GEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEI 806
E +G+G + + M + + S KGT + +
Sbjct: 103 LERSGMGFTIMENF----MDEVIVESEVNKGTTVYL 134
>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein
structure initiati northeast structural genomics
consortium; 2.60A {Desulfitobacterium hafniense}
Length = 126
Score = 52.8 bits (126), Expect = 3e-07
Identities = 27/111 (24%), Positives = 43/111 (38%), Gaps = 1/111 (0%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTE 515
+ LE D I IINREG +L N AV K GY E+++ + L E
Sbjct: 3 NFLETIEDMILIINREGRLLYANTAVPKKLGYTHEELMSMHILTITSAGKMAEGEKILAE 62
Query: 516 ILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMHDISEWKQ 566
+ + +++L RI K C + D+S+ ++
Sbjct: 63 LFA-GKKESLPLSLEKKEGTSIPAKARIWQGKWHNEPCLFAIIKDLSKEER 112
>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism,
TYRR protein, nucleotide-binding, transcription
regulation, activator, repressor; HET: PG4; 2.3A
{Escherichia coli}
Length = 190
Score = 52.5 bits (125), Expect = 4e-07
Identities = 12/71 (16%), Positives = 27/71 (38%)
Query: 431 NGIEPEDVDTRINKRKMEIEVMQLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVE 490
I + E E + L ++LEA + + ++ + + N A +LFG ++
Sbjct: 59 RRIAGVTDVRTVPWMPSEREHLALSALLEALPEPVLSVDMKSKVDMANPASCQLFGQKLD 118
Query: 491 DILRKPFTVFL 501
+ +
Sbjct: 119 RLRNHTAAQLI 129
>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural
genomics, PSI-2, protein structure initiative; 2.40A
{Shewanella oneidensis}
Length = 129
Score = 50.7 bits (121), Expect = 1e-06
Identities = 18/115 (15%), Positives = 46/115 (40%), Gaps = 6/115 (5%)
Query: 453 QLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHY 512
+ ++ ++ + ++N G I S N+ ++L P + + + FL ++ + ++
Sbjct: 8 TIELFIQHLTEAMILVNANGFIRSCNQRSAELLDCPQVSLKGQDWRNFLTEHHQARYDNL 67
Query: 513 LTEILSLDLRQTL-----EKITLGSTKEEKLLSLRIIIKKLPFS-SCYSLTMHDI 561
L+ + L + T K + + I +P + + MHD+
Sbjct: 68 LSHDVQLGTNCGQPVQHPAQETTLICASGKAKDVELSISYIPGHEPMFVMVMHDL 122
>1joy_A Protein (ENVZ_ecoli); histidine kinase, sensory transduction,
osmolarity sensor protein, inner membrane,
phosphorylation, transferase; NMR {Escherichia coli}
SCOP: a.30.2.1
Length = 67
Score = 50.2 bits (120), Expect = 2e-06
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 10/76 (13%)
Query: 574 AKKIAEKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRS 633
A + + ++ +A VSH++RTPLT I +E++ Q A I++
Sbjct: 2 AAGVKQLADD-RTLLMAGVSHDLRTPLTRIRLATEMMSEQD---------GYLAESINKD 51
Query: 634 GNLVLDIVNDLLDISK 649
I+ +D +
Sbjct: 52 IEECNAIIEQFIDYLR 67
>1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A
{Escherichia coli K12} SCOP: d.110.3.2 PDB: 1v9z_A*
1vb6_A* 1s67_L* 1s66_L*
Length = 167
Score = 49.9 bits (118), Expect = 2e-06
Identities = 18/120 (15%), Positives = 36/120 (30%), Gaps = 4/120 (3%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTE 515
LE G +IN ++ N A KL+GY E+++ + + ++ Y+
Sbjct: 44 PALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRH 103
Query: 516 ILSLD----LRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMHDISEWKQEKNKL 571
+ E + + Y + D S +K +
Sbjct: 104 NREGGKARVEGMSRELQLEKKDGSKIWTRFALSKVSAEGKVYYLALVRDASVEMAQKEQT 163
>3fg8_A Uncharacterized protein RHA05790; PAS domain, structural genomics,
PSI-2, protein structure initiative, midwest center for
structural genomics; HET: 3PB; 1.80A {Rhodococcus SP}
Length = 118
Score = 48.2 bits (114), Expect = 7e-06
Identities = 12/108 (11%), Positives = 34/108 (31%), Gaps = 6/108 (5%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTE 515
++ G ++ + I+ N + +++L + T L + S + +
Sbjct: 16 NLYFQGGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRK 75
Query: 516 ILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMHDISE 563
+L+ Q +L + + S + D++
Sbjct: 76 VLATGREQQTRVDSL--YSPGMTIEVTAA----ADSGALVVHFRDVTA 117
>1ixm_A SPO0B, protein (sporulation response regulatory protein);
phosphotransferase, two component system; 2.60A
{Bacillus subtilis} SCOP: d.123.1.1 PDB: 2ftk_A* 1f51_A
Length = 192
Score = 47.4 bits (111), Expect = 1e-05
Identities = 22/224 (9%), Positives = 50/224 (22%), Gaps = 40/224 (17%)
Query: 558 MHDISEWKQEKNKLSHAKKIAEKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGP 617
M D+S+ ++E +S E L H+ L I G + K R
Sbjct: 1 MKDVSKNQEEN--ISDTALTNELI-----HLLGHSRHDWMNKLQLIKGNLSLQKYDRV-- 51
Query: 618 LGNPRYIEYANYIDRSGNLVLDIVNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQL 677
E L A +
Sbjct: 52 --FEMIEEMVIDAKHESKLSNLKT--------------------------PHLAFDFLTF 83
Query: 678 YANEKRILIRTSFANNIPRILADLRSVKQIALNILSNAIHFTPSGGQI---IISTTHTSN 734
+ + I + A + + ++ + + + T +
Sbjct: 84 NWKTHYMTLEYEVLGEIKDLSAYDQKLAKLMRKLFHLFDQAVSRESENHLTVSLQTDHPD 143
Query: 735 EEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGL 778
++IL + G + + + + + +
Sbjct: 144 RQLILYLDFHGAFADPSAFDDIRQNGYEDVDIMRFEITSHECLI 187
>3mxq_A Sensor protein; PSI2, MCSG, structural genomics, protein structure
initiativ midwest center for structural genomics; 2.78A
{Vibrio cholerae o1 biovar el tor}
Length = 152
Score = 47.0 bits (111), Expect = 2e-05
Identities = 15/127 (11%), Positives = 40/127 (31%), Gaps = 13/127 (10%)
Query: 453 QLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVF-------LEQNT 505
L +L+ S + I+ + +I+ N + E + K L++
Sbjct: 23 LLSELLDQLSFALCIVRNDYVIVKVNEYFESRVIFDGETMQGKNILELFPESADYLKRKI 82
Query: 506 PSVMNHYLTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSC------YSLTMH 559
+ + + S + + L + + ++ +P S L ++
Sbjct: 83 DTALVIESSSFSSWEQKPHLLPFKSSRPVSGEEEQMYQNLEVIPIHSEDGTIEHVCLCVY 142
Query: 560 DISEWKQ 566
D++
Sbjct: 143 DVTIQAS 149
>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET:
HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1
Length = 129
Score = 46.1 bits (109), Expect = 3e-05
Identities = 11/46 (23%), Positives = 21/46 (45%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFL 501
+ +A G ++ G+I NR S+L G E ++ + F +
Sbjct: 26 AEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEV 71
>2vv6_A FIXL, sensor protein FIXL; signaling protein, transferase,
phosphoprotein, nitrogen fixation, PER-ARNT-SIM,
metal-binding, PAS, iron; HET: HEM; 1.5A {Bradyrhizobium
japonicum} PDB: 1xj6_A* 1xj4_A* 2vv7_A* 2vv8_A* 1lsw_A*
1dp8_A* 1dp9_A* 1drm_A* 1lsv_A* 1dp6_A* 1lsx_A* 1lt0_A*
1y28_A* 2cmn_A* 1xj3_A* 1xj2_A* 2owh_A* 2owj_A*
Length = 119
Score = 45.0 bits (105), Expect = 7e-05
Identities = 17/114 (14%), Positives = 44/114 (38%), Gaps = 4/114 (3%)
Query: 462 SDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTEILSLDL 521
D + +I+ GII + A +LFG+ + + + + + + S + Y++ +
Sbjct: 3 PDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSD 62
Query: 522 RQTL----EKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMHDISEWKQEKNKL 571
+ + L I + ++ + D++E +Q + +L
Sbjct: 63 PHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTEHQQTQARL 116
>3ke6_A Protein RV1364C/MT1410; anti-sigma factor, anti-sigma factor
antagonist, phosphatase serine kinase, ATPase, unknown
function; 2.60A {Mycobacterium tuberculosis}
Length = 399
Score = 44.2 bits (104), Expect = 1e-04
Identities = 19/115 (16%), Positives = 34/115 (29%), Gaps = 25/115 (21%)
Query: 699 ADLRSVKQIALNILSNAIHFTPSG---GQIIISTTHTSNEEVILRVRDTGVGMTNYELEK 755
+D+ + + NA+ + I+++ + V V D G +
Sbjct: 293 SDIADIVHAISEFVENAVEHGYATDVSKGIVVAAALAGDGNVRASVIDRGQWKD--HRD- 349
Query: 756 AMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810
G G GL +A+A+V A GT + L
Sbjct: 350 --------------GARGRGRGLAMAEALVSE-AR----IMHGAGGTTATLTHRL 385
>3mr0_A Sensory box histidine kinase/response regulator; PAS fold,
structural genomics, PSI-2; HET: PG5; 1.49A
{Burkholderia thailandensis}
Length = 142
Score = 43.7 bits (103), Expect = 1e-04
Identities = 13/124 (10%), Positives = 41/124 (33%), Gaps = 4/124 (3%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKP--FTVFLEQNTPSVMNHYL 513
+ S G+ N + + + K+ GY ++ + + + + + L
Sbjct: 13 LAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAAL 72
Query: 514 TEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPF--SSCYSLTMHDISEWKQEKNKL 571
L +E + + + + R + D+++ K++++ L
Sbjct: 73 KAHLEHRDTYDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDAL 132
Query: 572 SHAK 575
++
Sbjct: 133 RVSR 136
>2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein,
decatenation, ATPase, drug design, DNA-binding,
magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus
shibatae}
Length = 530
Score = 43.3 bits (100), Expect = 2e-04
Identities = 20/108 (18%), Positives = 36/108 (33%), Gaps = 6/108 (5%)
Query: 700 DLRSVKQIALNILSNAIHFTPSGG-----QIIISTTHTSNEEVILRVRDTGVGMTNYELE 754
R++ Q ++ N++ T G +I I + + + V D G+G+ E+
Sbjct: 28 PARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVP 87
Query: 755 KAMKPFGQIPNSQQIRGEG-TGLGLPLAKAMVDANMGKFYIFSTPAKG 801
A + G GLG+ A + K T
Sbjct: 88 NAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVN 135
>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain,
mycobacteium tuberculos molecule binding domain; 2.30A
{Mycobacterium tuberculosis}
Length = 185
Score = 43.2 bits (101), Expect = 2e-04
Identities = 16/145 (11%), Positives = 40/145 (27%), Gaps = 10/145 (6%)
Query: 456 SILEATSDGIAII-NREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLT 514
I E + + + ++ N A D + +P + + L
Sbjct: 41 RIFEHIPAILVGLEGPDHRFVAVNAAYRGFSPL--LDTVGQPAREVYPELEGQQIYEMLD 98
Query: 515 EILSLDLRQTLEKITL-----GSTKEEKLLSLRI--IIKKLPFSSCYSLTMHDISEWKQE 567
+ Q+ + L GS EE+ + + L + D++ +
Sbjct: 99 RVYQTGEPQSGSEWRLQTDYDGSGVEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVRA 158
Query: 568 KNKLSHAKKIAEKESSHKSDFLARV 592
+ + + + D +
Sbjct: 159 RQAAEARVEELSERYRNVRDSATVM 183
>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase,
phosphoprotein, transferase, flavoprotein; HET: FAD;
2.34A {Methylococcus capsulatus}
Length = 227
Score = 43.0 bits (99), Expect = 3e-04
Identities = 7/48 (14%), Positives = 17/48 (35%)
Query: 465 IAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHY 512
++I + +G IL N + Y E+++ + +
Sbjct: 2 VSITDLQGRILYANDNFCAVSRYGREELVGQDHRIVNSGYHGKAYIRD 49
Score = 34.9 bits (78), Expect = 0.066
Identities = 20/175 (11%), Positives = 53/175 (30%), Gaps = 11/175 (6%)
Query: 338 HGNLFYANPSFLLLTKYKSVDDIEIAGGLSTLLDAPKLSDNNAIKPVMLYRSDRTCIAAS 397
G + YAN +F +++Y + E+ G ++++
Sbjct: 8 QGRILYANDNFCAVSRY-GRE--ELVGQDHRIVNSGYHGKAYIRDMWRTISRGNIWQGEF 64
Query: 398 ARLHTIQWNRENSLAMTFIPFEKANQFPENMPQNGIEPEDVDTRINKRKMEIEVMQLCSI 457
+ + + +++ E ++ +L
Sbjct: 65 CNRRKDGTRYWVDSTIVPLMDNAGKPRQYISIRR--------DITAQKEAEAQLARLKQA 116
Query: 458 LEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHY 512
++A S+ I + +R G I+ N A+ + G ++L + ++
Sbjct: 117 MDANSEMILLTDRAGRIIYANPALCRFSGMAEGELLGQSPSILDSPLADQETLAA 171
>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase,
cell adhesion, nucleotide-binding, protein engineering,
RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa}
PDB: 2wkr_A* 2wkp_A*
Length = 332
Score = 42.5 bits (99), Expect = 3e-04
Identities = 11/67 (16%), Positives = 23/67 (34%), Gaps = 3/67 (4%)
Query: 454 LCSILEATSDGIAIIN---REGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMN 510
L + LE I + + I+ + + +L Y E+IL + T
Sbjct: 13 LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATV 72
Query: 511 HYLTEIL 517
+ + +
Sbjct: 73 RKIRDAI 79
>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase
regulation, transferase; NMR {Homo sapiens} SCOP:
d.110.3.5
Length = 114
Score = 41.3 bits (96), Expect = 9e-04
Identities = 15/112 (13%), Positives = 43/112 (38%), Gaps = 5/112 (4%)
Query: 456 SILEATSDGIAIINRE-GIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLT 514
++ + I ++ + IL N L GY +D++ + T F ++ V+
Sbjct: 2 AMDPEFNKAIFTVDAKTTEILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDVVEALSE 61
Query: 515 EILSLDLRQTL--EKITLGSTKEEKLLSLRIIIKKLPFSS--CYSLTMHDIS 562
E + D + + ++ + + + + +K++ C + + +
Sbjct: 62 EHMEADGHAAVVFGTVVDIISRSGEKIPVSVWMKRMRQERRLCCVVVLEPVE 113
>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological
rhythms, cytoplasm, nucleus, phosphoprotein,
transcription; 2.40A {Mus musculus}
Length = 309
Score = 40.9 bits (94), Expect = 0.001
Identities = 9/54 (16%), Positives = 20/54 (37%), Gaps = 1/54 (1%)
Query: 448 EIEVMQLCSILEATSDGIAIINRE-GIILSTNRAVSKLFGYPVEDILRKPFTVF 500
++E + I++ ++ G IL + V+ +F + F F
Sbjct: 11 QVEGITSEYIVKNADMFAVAVSLVSGKILYISNQVASIFHCKKDAFSDAKFVEF 64
>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory
system, PAS, kinase, membrane, transferase, solid state
cell inner membrane; NMR {Escherichia coli}
Length = 118
Score = 40.2 bits (93), Expect = 0.002
Identities = 15/84 (17%), Positives = 35/84 (41%), Gaps = 9/84 (10%)
Query: 432 GIEPEDVDTRINKRKMEIEVMQLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVED 491
G+EP ++ T +R+ ++L++ +G+ ++ G + N A +L Y
Sbjct: 4 GLEPYEISTLFEQRQ---------AMLQSIKEGVVAVDDRGEVTLINDAAQELLNYRKSQ 54
Query: 492 ILRKPFTVFLEQNTPSVMNHYLTE 515
K T+ + ++ L +
Sbjct: 55 DDEKLSTLSHSWSQVVDVSEVLRD 78
>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG,
structural genomics, center for structural genomics;
1.65A {Burkholderia thailandensis} PDB: 3mqo_A
Length = 120
Score = 40.0 bits (93), Expect = 0.002
Identities = 12/117 (10%), Positives = 36/117 (30%), Gaps = 11/117 (9%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGY-PVEDILRKPFTVFLEQNTPSVMNHYLT 514
+ G+ + R+ +I N ++ +F + I R ++ + + ++
Sbjct: 7 TAFHLAPIGLVLS-RDRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERIS 65
Query: 515 EILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSS-----CYSLTMHDISEWKQ 566
++ ++I + E + T D+S ++
Sbjct: 66 PVMIAHGSYADDRIMKRAGGELFWCHVTGR----ALDRTAPLAAGVWTFEDLSATRR 118
>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM,
PAS, flavoprotein, signaling protein; HET: FMN; 1.45A
{Bacillus subtilis} PDB: 2pr6_A*
Length = 132
Score = 39.3 bits (90), Expect = 0.004
Identities = 20/122 (16%), Positives = 45/122 (36%), Gaps = 3/122 (2%)
Query: 456 SILEATSDGIAIIN---REGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHY 512
+L+ G+ I + + I+ N+ ++ GY E+IL K ++T
Sbjct: 3 HMLDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDN 62
Query: 513 LTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMHDISEWKQEKNKLS 572
+ L T++ L I ++ + + +DI++ K+ + L
Sbjct: 63 IRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPMEIEDKTYFVGIQNDITKQKEYEKLLE 122
Query: 573 HA 574
+
Sbjct: 123 DS 124
>2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding,
serine/threonine-protein kinase, light-induced signal
transduction, phototropin1; HET: FMN; 1.40A {Avena
sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A* 1g28_A*
Length = 146
Score = 38.5 bits (88), Expect = 0.007
Identities = 17/148 (11%), Positives = 47/148 (31%), Gaps = 10/148 (6%)
Query: 454 LCSILEATSDGIAIIN---REGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMN 510
L + LE I + + I+ + + +L Y E+IL + T
Sbjct: 4 LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATV 63
Query: 511 HYLTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFS--SCYSLTMHDISEWKQEK 568
+ + + T++ I + ++ + + + D +E ++
Sbjct: 64 RKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDA 123
Query: 569 NKLSHAKKIAEKESSHKSDFLARVSHEI 596
+ I + ++ + + E+
Sbjct: 124 AEREGVMLIKK-----TAENIDEAAKEL 146
>3olo_A Two-component sensor histidine kinase; structural genomics, PSI-2,
protein structure initiative, MI center for structural
genomics, MCSG, TRA; 2.09A {Nostoc SP}
Length = 118
Score = 38.1 bits (88), Expect = 0.007
Identities = 8/65 (12%), Positives = 16/65 (24%)
Query: 448 EIEVMQLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPS 507
E+E ++ + + L N A ++ Y E +L
Sbjct: 9 ELEFKFAHYLINNAVEASFCLGDNWQFLYVNDATCRMTEYSREQLLSMNLQDIDVDFALH 68
Query: 508 VMNHY 512
Sbjct: 69 DWEEI 73
>2q2e_B Type 2 DNA topoisomerase 6 subunit B; DNA-binding, SPO11, ATPase;
4.00A {Methanosarcina mazei}
Length = 621
Score = 37.9 bits (87), Expect = 0.009
Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 7/88 (7%)
Query: 702 RSVKQIALNILSNAIHFTPSGG---QIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMK 758
RS+ + NA+ G I++ T + V + + D G G+ ++ K
Sbjct: 36 RSLITTVKEAVDNALDACEEAGILPDILVQVERTGPDYVTVIIEDNGPGIVREQIPKVFA 95
Query: 759 PFGQ---IPNSQQIRGEGTGLGLPLAKA 783
+Q RG G+G+ A
Sbjct: 96 KLLYGSRFHALKQSRG-QQGIGISAAVL 122
>1nwz_A PYP, photoactive yellow protein; PAS, LOV, GAF, domains fold,
signaling protein; HET: HC4; 0.82A {Halorhodospira
halophila} SCOP: d.110.3.1 PDB: 1kou_A* 1ot9_A* 1otb_A*
1s4r_A* 1s4s_A* 1ts0_A* 1ts6_A* 1ts7_A* 1ts8_A* 1uwn_X*
1uwp_X* 2d01_A* 2phy_A* 2pyp_A* 2pyr_A* 2qj5_A* 2qj7_A*
2qws_A* 2zoh_A* 2zoi_A* ...
Length = 125
Score = 37.8 bits (87), Expect = 0.010
Identities = 18/108 (16%), Positives = 40/108 (37%), Gaps = 5/108 (4%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFT--VFLEQNTPSVMNHYL 513
L+ + G ++ +G IL N A + G + ++ K F V ++P +
Sbjct: 21 GQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK 80
Query: 514 TEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMHDI 561
+ S +L E + +++ +KK Y + + +
Sbjct: 81 EGVASGNLNTMFE---YTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV 125
>1wa9_A Period circadian protein; PAS domain, circadian rhythm, clock
protein, phosphorylation, polymorphism; 3.15A
{Drosophila melanogaster} PDB: 3gec_A
Length = 368
Score = 37.8 bits (86), Expect = 0.011
Identities = 39/300 (13%), Positives = 77/300 (25%), Gaps = 25/300 (8%)
Query: 339 GNLFYANPSFLLLTKY-------KSVDDI-------EIAGGLSTLLDAPKLSDNNAIKPV 384
G + Y PS + Y +S D A ++T + + +
Sbjct: 18 GIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATFASQITTGIPIAESRGSVPKDAK 77
Query: 385 MLYRSDRTCIAASARLHTIQWNRENSLAMTFIPFEKANQFPENMPQNGIEPEDVDTRINK 444
+ R S + E P N + + +
Sbjct: 78 STFCVMLRRYRGLKSGGFGVIGRPVSYEPFRLGLTFREAPEEARPDNYMVSNGTNMLLVI 137
Query: 445 RKMEI---EVMQLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVF- 500
I + + + + GII + A GY +D++ + F
Sbjct: 138 CATPIKSSYKVPDEILSQKSPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFY 197
Query: 501 ----LEQNTPSVMNHYLTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSC--Y 554
L + + + L LL P+S +
Sbjct: 198 HHEDLSVMKETYETVMKKGQTAGASFCSKPYRFLIQNGCYVLLETEWTSFVNPWSRKLEF 257
Query: 555 SLTMHDISEWKQEKNKLSHAKKIAEKESSHKSDFLARVSHEIRTPLTAII-GFSEVIKNQ 613
+ H + + ++ N A K S R+ +I L + S+ +K +
Sbjct: 258 VVGHHRVFQGPKQCNVFEAAPTCKLKISEEAQSRNTRIKEDIVKRLAETVSRPSDTVKQE 317
Score = 36.2 bits (82), Expect = 0.030
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 2/75 (2%)
Query: 461 TSDG--IAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTEILS 518
D I +GI+L T +++ + GYP + L + F F+ + +T +
Sbjct: 5 KEDSFCCVISMHDGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATFASQITTGIP 64
Query: 519 LDLRQTLEKITLGST 533
+ + ST
Sbjct: 65 IAESRGSVPKDAKST 79
>3cax_A Uncharacterized protein PF0695; structural genomics, unknown
function, PSI-2, protein structure initiative; 2.43A
{Pyrococcus furiosus dsm 3638}
Length = 369
Score = 36.8 bits (84), Expect = 0.021
Identities = 11/96 (11%), Positives = 30/96 (31%), Gaps = 1/96 (1%)
Query: 416 IPFEKANQFPENMPQNGIEPEDVDTRINKRKMEIEVMQLCSILEATSDGIAIINREGIIL 475
+P E + + I+ + + +L +I EA + I+++ +
Sbjct: 203 LPKEVQQALRGQPLEFDKTQLKREEDIDLGTGYLNIEELKAIFEALPVDVTFIDKDDRVR 262
Query: 476 STNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNH 511
+ ++F + R ++ V
Sbjct: 263 FFSP-GERIFTRTPSVLGRPVQLCHPPKSVYVVNKI 297
>2ayx_A Sensor kinase protein RCSC; two independent structural domains,
transferase; NMR {Escherichia coli} SCOP: c.23.1.1
c.23.1.6 PDB: 2ayz_A 2ayy_A
Length = 254
Score = 36.6 bits (84), Expect = 0.025
Identities = 9/60 (15%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 721 SGGQIIISTTHTSNEEVILR-VRDTGVGMTNYE-LEKAMKPFGQIPNSQQIRGEGTGLGL 778
SG + ++ + S + + ++ +G+ +T YE E + + +G +
Sbjct: 10 SGKRCWLAVRNASLCQFLETSLQRSGIVVTTYEGQEPTPEDVLITDEVVSKKWQGRAVVT 69
>3k3c_A Protein RV1364C/MT1410; sensor, PAS, signal transduction,
fatty-acid binding, sigma regulator, signaling protein;
HET: PLM; 1.62A {Mycobacterium tuberculosis} PDB: 3k3d_A
Length = 158
Score = 36.0 bits (82), Expect = 0.035
Identities = 12/132 (9%), Positives = 34/132 (25%), Gaps = 10/132 (7%)
Query: 456 SILEATSDGIAII-NREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLT 514
I E + + + ++ N A D + +P + + L
Sbjct: 21 RIFEHIPAILVGLEGPDHRFVAVNAAYRGFSPL--LDTVGQPAREVYPELEGQQIYEMLD 78
Query: 515 EILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFS-------SCYSLTMHDISEWKQE 567
+ Q+ + L + + + R + L + D++ +
Sbjct: 79 RVYQTGEPQSGSEWRLQTDYDGSGVEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVRA 138
Query: 568 KNKLSHAKKIAE 579
+ +
Sbjct: 139 RQAAEARVEELS 150
>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen
regulation protein, APC91440.4, PSI-2; HET: MSE; 1.83A
{Vibrio parahaemolyticus rimd 2210633}
Length = 115
Score = 35.6 bits (81), Expect = 0.042
Identities = 9/57 (15%), Positives = 20/57 (35%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHY 512
+IL I++ I N A LF + I+ + + ++ + +
Sbjct: 11 AILNNMVTATLILDDGLAIRYANPAAELLFSQSAKRIVEQSLSQLIQHASLDLALLT 67
>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural
genomics, midwest center for structural genomics; HET:
PGE; 2.49A {Geobacter sulfurreducens}
Length = 114
Score = 35.6 bits (81), Expect = 0.042
Identities = 11/64 (17%), Positives = 23/64 (35%)
Query: 453 QLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHY 512
+L E +A+ +RE L+ +R + +G DIL + + +
Sbjct: 4 RLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSHYDIFPEIGEEWKSVH 63
Query: 513 LTEI 516
+
Sbjct: 64 RRGL 67
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 35.7 bits (81), Expect = 0.043
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 24/81 (29%)
Query: 522 RQTLEKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMH---------DISEWKQ------ 566
R T E ++ +EE+ R K+L S M D+ EW Q
Sbjct: 79 RLTQEPESIRKWREEQ----R---KRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQV 131
Query: 567 EKNKLSHAKKIAEKESSHKSD 587
EKNK+++ +IA+K + D
Sbjct: 132 EKNKINN--RIADKAFYQQPD 150
Score = 34.5 bits (78), Expect = 0.11
Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 15/84 (17%)
Query: 183 IVHVNRVDNDPRALGKRLDKKFSHLHEIKKGHSSVEKE-----KYDI--FSQ-QSPPPHL 234
I +R+ +P ++ K +++ L E+ +E+E K D+ ++Q QS
Sbjct: 74 IAQADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVE- 132
Query: 235 RMKNKVSSL---TEYYAHKD-DVL 254
KNK+++ +Y D D++
Sbjct: 133 --KNKINNRIADKAFYQQPDADII 154
>2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing,
ATP-binding, chromophore, flavoprotein, FMN, kinase,
membrane, nucleotide-binding; HET: FMN; 2.00A
{Arabidopsis thaliana} PDB: 2z6c_A*
Length = 130
Score = 35.3 bits (80), Expect = 0.057
Identities = 10/119 (8%), Positives = 33/119 (27%), Gaps = 5/119 (4%)
Query: 453 QLCSILEATSDGIAIIN---REGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVM 509
+L + L + + I+ + + GY ++I+ + +T
Sbjct: 7 ELKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTDKNE 66
Query: 510 NHYLTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFS--SCYSLTMHDISEWKQ 566
+ + + + L + K + ++S++ +
Sbjct: 67 VAKIRDCVKNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDQGNTIKFIGMQVEVSKYTE 125
>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory
system, two-component signal transduction, transferase,
phosphorylation, SCOD; 1.7A {Bacillus subtilis}
Length = 111
Score = 33.6 bits (75), Expect = 0.17
Identities = 10/57 (17%), Positives = 22/57 (38%)
Query: 457 ILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYL 513
L+ +D A++ G I+ + GY +++ FL + ++ Y
Sbjct: 4 PLQTKTDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYF 60
>3ehh_A Sensor kinase (YOCF protein); four-helix bundle, GHL ATPase domain,
transferase; HET: MSE ADP; 2.10A {Bacillus subtilis}
PDB: 3ehj_A* 3gie_A* 3gif_A* 3gig_A* 3ehf_A*
Length = 218
Score = 33.2 bits (74), Expect = 0.24
Identities = 8/54 (14%), Positives = 17/54 (31%), Gaps = 2/54 (3%)
Query: 757 MKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810
+ + G GL + ++ G +I + GT + + P
Sbjct: 164 ITVSDDGTFKGEENSFSKGHGLLGMRERLEFANGSLHIDTEN--GTKLTMAIPN 215
>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain,
heterodimer, internal cavity, activator, angiogenesis,
congenital erythrocytosis; 1.17A {Homo sapiens} PDB:
3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 2b02_A*
2k7s_A 2a24_B
Length = 121
Score = 31.7 bits (71), Expect = 0.75
Identities = 16/107 (14%), Positives = 33/107 (30%), Gaps = 4/107 (3%)
Query: 465 IAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTP-SVMNHYLTEILSLDLRQ 523
I+ N EGI + GY +++L K F + + + +
Sbjct: 15 ISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVL 74
Query: 524 TLEKITLGSTKEEKLLSLRIIIKKLPFSS---CYSLTMHDISEWKQE 567
++ +E + + P+S T ++ QE
Sbjct: 75 SVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSSQE 121
>2vz8_A Fatty acid synthase; transferase, phosphopantetheine, multienzyme,
megasynthase, fatty acid synthesis; 3.2A {Sus scrofa}
PDB: 2vz9_A*
Length = 2512
Score = 31.7 bits (71), Expect = 0.78
Identities = 23/142 (16%), Positives = 44/142 (30%), Gaps = 14/142 (9%)
Query: 656 NLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSVKQIALNILSNA 715
N+ F + LD E + Q + + I+ + + V+ A ++
Sbjct: 1788 NVTFHGILLDSLFEEGGATWQEVSELLKAGIQEGVVQPLKCTVFPRTKVEA-AFRYMAQG 1846
Query: 716 IHFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQIPN-SQQIRGEGT 774
H G+++I + + + P+ S I G
Sbjct: 1847 KHI----GKVVIQVREEEQGPAPRGLPPIAL--------TGLSKTFCPPHKSYVITGGLG 1894
Query: 775 GLGLPLAKAMVDANMGKFYIFS 796
G GL LA+ + K + S
Sbjct: 1895 GFGLQLAQWLRLRGAQKLVLTS 1916
>1y4s_A Chaperone protein HTPG; HSP90, molecular chaperone, ATPase; HET:
ADP; 2.90A {Escherichia coli} PDB: 1y4u_A
Length = 559
Score = 31.6 bits (71), Expect = 0.82
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 735 EEVILRVRDTGVGMTNYELEKAMKPFGQIPNS 766
++ L + D GVGMT E+ G I S
Sbjct: 72 DKRTLTISDNGVGMTRDEVI---DHLGTIAKS 100
>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox
sensor, atomic resolution, transferase; HET: FAD; 1.04A
{Azotobacter vinelandii}
Length = 120
Score = 31.1 bits (69), Expect = 0.90
Identities = 15/57 (26%), Positives = 26/57 (45%)
Query: 456 SILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHY 512
+E I+I + + IL NRA + GY E++L K ++ TP ++
Sbjct: 9 QTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQA 65
>2vea_A Phytochrome-like protein CPH1; arginine finger, phosphorylation,
tandem GAF domain, knot, kinase, receptor, PAS domain,
chromophore; HET: CYC; 2.21A {Synechocystis SP} SCOP:
d.110.2.1 d.110.2.4 d.110.3.9
Length = 520
Score = 31.3 bits (70), Expect = 1.0
Identities = 5/37 (13%), Positives = 13/37 (35%)
Query: 465 IAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFL 501
+ + + I + + + G ED+L +
Sbjct: 33 VVLQEPDLTISQISANCTGILGRSPEDLLGRTLGEVF 69
>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV,
signaling protein; HET: FAD; 1.65A {Neurospora crassa}
PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A*
3hji_A*
Length = 149
Score = 30.4 bits (68), Expect = 1.6
Identities = 8/65 (12%), Positives = 21/65 (32%), Gaps = 5/65 (7%)
Query: 436 EDVDTRINKRKMEIEVMQLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRK 495
+ R N + V +++ ++ I+ + A + GY ++L +
Sbjct: 17 IQIMNRPNPQVELGPVDTSVALILCDLKQ-----KDTPIVYASEAFLYMTGYSNAEVLGR 71
Query: 496 PFTVF 500
Sbjct: 72 NCRFL 76
>2o1u_A Endoplasmin; GRP94, HSP82, HSP90, HTPG, chaperone, AMP-PNP, GP96;
HET: ANP; 2.40A {Canis lupus familiaris} PDB: 2o1v_A*
2o1w_A 2o1t_A
Length = 666
Score = 30.1 bits (67), Expect = 1.9
Identities = 16/32 (50%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 735 EEVILRVRDTGVGMTNYELEKAMKPFGQIPNS 766
E+ +L V DTGVGMT EL K G I S
Sbjct: 90 EKNLLHVTDTGVGMTREELVKN---LGTIAKS 118
>1d06_A Nitrogen fixation regulatory protein FIXL; oxygen sensor, histidine
kinase, PAS, high-resolution, two- component system;
HET: HEM; 1.40A {Rhizobium meliloti} SCOP: d.110.3.2
PDB: 1ew0_A*
Length = 130
Score = 30.0 bits (66), Expect = 2.2
Identities = 19/114 (16%), Positives = 49/114 (42%), Gaps = 4/114 (3%)
Query: 453 QLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHY 512
L SIL+ D + +G I+S N A + FGY E+++ + + + + + Y
Sbjct: 17 HLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGY 76
Query: 513 LTEILSLDLRQTLEKI--TLGSTKEEKLLSLRIIIKKLPFS--SCYSLTMHDIS 562
L ++ ++ + G K+ +++ + ++ ++ + D++
Sbjct: 77 LQRYMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRSGGERFFTGFIRDLT 130
>2ioq_A Chaperone protein HTPG; heat shock protein, HSP90; 3.50A
{Escherichia coli} PDB: 2iop_A
Length = 624
Score = 29.7 bits (66), Expect = 2.9
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 735 EEVILRVRDTGVGMTNYELEKAMKPFGQIPNS 766
++ L + D GVGMT E+ G I S
Sbjct: 72 DKRTLTISDNGVGMTRDEVIDH---LGTIAKS 100
>2cg9_A ATP-dependent molecular chaperone HSP82; chaperone complex, HSP90,
heat shock protein, ATP-binding, heat shock,
nucleotide-binding, acetylation; HET: ATP; 3.1A
{Saccharomyces cerevisiae}
Length = 677
Score = 29.3 bits (65), Expect = 3.8
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 735 EEVILRVRDTGVGMTNYELEKAMKPFGQIPNS 766
E+ +L +RD+G+GMT EL G I S
Sbjct: 71 EQKVLEIRDSGIGMTKAELINN---LGTIAKS 99
>2ool_A Sensor protein; bacteriophytochrome, photoconversion,
photoreceptor, biliverdin, signaling protein; HET: LBV;
2.20A {Rhodopseudomonas palustris CGA009} SCOP:
d.110.2.1 d.110.3.9
Length = 337
Score = 29.0 bits (64), Expect = 4.2
Identities = 8/37 (21%), Positives = 13/37 (35%)
Query: 465 IAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFL 501
+ + I S + V L P +L P +L
Sbjct: 46 FVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYL 82
>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog,
methyltransferase, structural genomics, NPPSFA; HET:
SFG; 2.55A {Pyrococcus horikoshii OT3}
Length = 450
Score = 28.9 bits (63), Expect = 4.6
Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 6/65 (9%)
Query: 700 DLRSVKQIALNILSNAIHFTPSGGQIIIST---THTSNEEVILRVRDTGVGMTNYELEKA 756
+ + Q+ +L +A GG+++ +T NE+ I + ++L
Sbjct: 360 KINEMSQLQRELLESAARLVKPGGRLLYTTCSIFKEENEKNIRWFLNVH---PEFKLVPL 416
Query: 757 MKPFG 761
P+
Sbjct: 417 KSPYD 421
>1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin,
electron transport; HET: FMN; 1.90A {Chlamydomonas
reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A*
Length = 109
Score = 28.1 bits (62), Expect = 7.6
Identities = 3/44 (6%), Positives = 13/44 (29%), Gaps = 3/44 (6%)
Query: 460 ATSDGIAIIN---REGIILSTNRAVSKLFGYPVEDILRKPFTVF 500
+ + + ++ + + GY +++L
Sbjct: 1 GLRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFL 44
>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain,
heterodimer, internal cavity, activator, angiogenesis,
congenital erythrocytosis; 1.17A {Homo sapiens} PDB:
3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A
Length = 117
Score = 27.8 bits (61), Expect = 9.6
Identities = 13/106 (12%), Positives = 35/106 (33%), Gaps = 3/106 (2%)
Query: 465 IAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTEILSLDLRQT 524
++ + + + +++L GY E++L + F M + + +
Sbjct: 12 LSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVS 71
Query: 525 LEKITLGSTKEEKLLSLRIIIKKLPFSS---CYSLTMHDISEWKQE 567
+ L L + + P + C + +SE ++
Sbjct: 72 GQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKN 117
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
1s1i_M
Length = 178
Score = 27.9 bits (62), Expect = 9.8
Identities = 18/138 (13%), Positives = 42/138 (30%), Gaps = 27/138 (19%)
Query: 463 DGIAIINREGIILSTNRAVSKL----FGYPVEDILRKPFTVFLEQNTPSVMNHYLTEILS 518
I ++ E + +S +KL F K F + + L ++S
Sbjct: 25 QKIVVVRAEELNISGEFFRNKLKYHDFLRKAT-AFNKTRGPFHFRAPSRIFYKALRGMVS 83
Query: 519 LDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMHDISEWKQEKNKLSHAKKIA 578
K G + +++L + K+++ + A ++
Sbjct: 84 -------HKTARG----------KAALERL---KVFEGIPPPYD--KKKRVVVPQALRVL 121
Query: 579 EKESSHKSDFLARVSHEI 596
+ K L ++S +
Sbjct: 122 RLKPGRKYTTLGKLSTSV 139
>2x11_B Ephrin-A5; receptor-signaling protein complex, developmental
protein, signaling platform, kinase, transferase,
neurogenesis, receptor, cataract; 4.83A {Homo sapiens}
Length = 177
Score = 28.0 bits (62), Expect = 9.8
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 392 TCIAASARLHTIQWNRENSL 411
C+AA A + + WN N
Sbjct: 25 GCVAAVADRYAVYWNSSNPR 44
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.316 0.134 0.387
Gapped
Lambda K H
0.267 0.0540 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 6,998,759
Number of extensions: 334567
Number of successful extensions: 953
Number of sequences better than 10.0: 1
Number of HSP's gapped: 890
Number of HSP's successfully gapped: 82
Length of query: 820
Length of database: 5,693,230
Length adjustment: 100
Effective length of query: 720
Effective length of database: 3,268,830
Effective search space: 2353557600
Effective search space used: 2353557600
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: 61 (27.7 bits)