RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14372
(210 letters)
>1mc0_A 3',5'-cyclic nucleotide phosphodiesterase 2A; GAF domain, 3',5'
guanosine monophosphate, hydrolase; HET: PCG; 2.86A {Mus
musculus} SCOP: d.110.2.1 d.110.2.1
Length = 368
Score = 73.5 bits (180), Expect = 1e-15
Identities = 33/127 (25%), Positives = 49/127 (38%), Gaps = 28/127 (22%)
Query: 43 STPEIRIPWGCGIVGYVAESGEPVNIPDAYLVS--TPQIRIPWGCGIVCYLAESGEPVNI 100
+ EIRIP GI G+VA +G+ +NIPDAY + G L I
Sbjct: 240 ESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILC-----FPI 294
Query: 101 PDA-------YLLINKFDDLAFSKNDENFVEA--------------YEKAVIAMAKQSVT 139
+ L+NK + FSK DE+ A Y+K A + +
Sbjct: 295 KNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLA 354
Query: 140 LDVLSYH 146
+++ Y
Sbjct: 355 NEMMMYL 361
Score = 63.1 bits (153), Expect = 4e-12
Identities = 18/91 (19%), Positives = 33/91 (36%), Gaps = 9/91 (9%)
Query: 42 VSTPEIRIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIRIPWGCGIVCYLA------ESG 95
V E+ P G +G V E + + + D Q++ GC + L +
Sbjct: 69 VLGEEVSFPLTMGRLGQVVEDKQCIQLKDLTSDDVQQLQNMLGCELQAMLCVPVISRATD 128
Query: 96 EPVNIPDAYLLINKFDDLAFSKNDENFVEAY 126
+ V + NK F+ DE+ ++
Sbjct: 129 QVVALA---CAFNKLGGDFFTDEDEHVIQHC 156
>3dba_A CONE CGMP-specific 3',5'-cyclic phosphodiesterase alpha'; 3', GAF
domain, cyclic nucleotide phosphodiesterase hydrolase,
lipoprotein, membrane; HET: 35G; 2.57A {Gallus gallus}
Length = 180
Score = 62.5 bits (152), Expect = 1e-12
Identities = 27/128 (21%), Positives = 42/128 (32%), Gaps = 16/128 (12%)
Query: 9 RAS-YLLYSIPWGCGIVCYLAESGEPVNIPDAYLVSTPEIRIPWGCGIVGYVAESGEPVN 67
R S ++ S + L D + E P GI G+VA + + N
Sbjct: 42 RCSMFICRSRNGIPEVATRLLNVTPTSKFEDNLVNPDKETVFPLDIGIAGWVAHTKKFFN 101
Query: 68 IPDAYLVSTPQIRIPWGCG-----IVCYLAESGEPVNIPDAYL----LINKFDDLAFSKN 118
IPD + + G ++ P+ L +NK + FSK
Sbjct: 102 IPDVKKNNHFSDYLDKKTGYTTVNMMAI------PITQGKEVLAVVMALNKLNASEFSKE 155
Query: 119 DENFVEAY 126
DE + Y
Sbjct: 156 DEEVFKKY 163
>3ibj_A CGMP-dependent 3',5'-cyclic phosphodiesterase; PDE2A, GAF-domains,
allosteric regulation hydrolase, membrane; 3.02A {Homo
sapiens}
Length = 691
Score = 61.6 bits (149), Expect = 2e-11
Identities = 17/87 (19%), Positives = 33/87 (37%), Gaps = 10/87 (11%)
Query: 46 EIRIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIRIPWGCGIVCYLA------ESGEPVN 99
E+ P G +G V E + + + D Q++ GC + L + + V
Sbjct: 74 EVSFPLT-GCLGQVVEDKKSIQLKDLTSEDVQQLQSMLGCELQAMLCVPVISRATDQVVA 132
Query: 100 IPDAYLLINKFDDLAFSKNDENFVEAY 126
+ NK + F+ DE+ ++
Sbjct: 133 LA---CAFNKLEGDLFTDEDEHVIQHC 156
Score = 54.7 bits (131), Expect = 5e-09
Identities = 31/95 (32%), Positives = 45/95 (47%), Gaps = 18/95 (18%)
Query: 43 STPEIRIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIRIPWG---------CGIVCY--L 91
+ EIRIP GI G+VA +G+ +NIPDAY G I+C+
Sbjct: 240 ESYEIRIPADQGIAGHVATTGQILNIPDAY----AHPLFYRGVDDSTGFRTRNILCFPIK 295
Query: 92 AESGEPVNIPDAYLLINKFDDLAFSKNDENFVEAY 126
E+ E + + L+NK + FSK DE+ A+
Sbjct: 296 NENQEVIGV---AELVNKINGPWFSKFDEDLATAF 327
>3bjc_A CGMP-specific 3',5'-cyclic phosphodiesterase; PDE5, erectIle
dysfunction, inhibitor design, allosteric enzyme,
alternative splicing, CGMP binding; HET: WAN; 2.00A
{Homo sapiens} SCOP: a.211.1.2 PDB: 3mf0_A 3lfv_A 2xss_A
2k31_A*
Length = 878
Score = 61.0 bits (147), Expect = 3e-11
Identities = 33/127 (25%), Positives = 45/127 (35%), Gaps = 13/127 (10%)
Query: 9 RASYLLYSIPWGCGIVCYLAESGEPVNIPDAYLVSTPEIRIPWGCGIVGYVAESGEPVNI 68
R S L ++ + VS IR+ W GIVG+VA GEP+NI
Sbjct: 187 RYSLFLVCED-SSNDKFLISRLFDVAEGSTLEEVSNNCIRLEWNKGIVGHVAALGEPLNI 245
Query: 69 PDAYLVS--TPQIRIPWGCGIVCYLAESGEPVNIPDAYL-----LINKFDDL--AFSKND 119
DAY ++ G L P+ + INK F++ D
Sbjct: 246 KDAYEDPRFNAEVDQITGYKTQSILC---MPIKNHREEVVGVAQAINKKSGNGGTFTEKD 302
Query: 120 ENFVEAY 126
E AY
Sbjct: 303 EKDFAAY 309
Score = 54.8 bits (131), Expect = 4e-09
Identities = 42/160 (26%), Positives = 66/160 (41%), Gaps = 27/160 (16%)
Query: 29 ESGEPVNIPDAYLVSTPEIRIPWGCGIVGYVAESGEPVNIPDAY--------LVSTPQIR 80
+ ++ YV + EP+NIPD +T +
Sbjct: 388 HMECEELEKSSDTLTREHDANKINYMYAQYVKNTMEPLNIPDVSKDKRFPWTTENTGNVN 447
Query: 81 IPWGCGIVCYLAESGEPVNIPDAYLLINKFDDL-----AFSKNDENFVEA---------- 125
++C ++G+ + L+NK ++ F++NDE F+EA
Sbjct: 448 QQCIRSLLCTPIKNGKKNKVIGVCQLVNKMEENTGKVKPFNRNDEQFLEAFVIFCGLGIQ 507
Query: 126 ----YEKAVIAMAKQSVTLDVLSYHASASLEDAQRLRSNN 161
YE AMAKQ VTL+VLSYHASA+ E+ + L+S
Sbjct: 508 NTQMYEAVERAMAKQMVTLEVLSYHASAAEEETRELQSLA 547
Score = 41.0 bits (95), Expect = 2e-04
Identities = 8/46 (17%), Positives = 14/46 (30%)
Query: 59 VAESGEPVNIPDAYLVSTPQIRIPWGCGIVCYLAESGEPVNIPDAY 104
V + ++ Y+ + EP+NIPD
Sbjct: 386 VFHMECEELEKSSDTLTREHDANKINYMYAQYVKNTMEPLNIPDVS 431
Score = 34.4 bits (78), Expect = 0.024
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 16 SIPWGCGIVCYLAESGEPVNIPDAY 40
+ Y+ + EP+NIPD
Sbjct: 407 ANKINYMYAQYVKNTMEPLNIPDVS 431
>2e4s_A CAMP and CAMP-inhibited CGMP 3',5'-cyclic phosphodiesterase 10A;
GAF domain, structural genomics, NPPSFA; HET: MSE CMP;
2.10A {Homo sapiens} PDB: 2zmf_A*
Length = 189
Score = 57.4 bits (139), Expect = 1e-10
Identities = 29/105 (27%), Positives = 40/105 (38%), Gaps = 9/105 (8%)
Query: 28 AESGEPVNIPDAYLVSTPEIRIPWGCGIVGYVAESGEPVNIPDAYLVS--TPQIRIPWGC 85
T EIR GI G VA +GE +NIPDAY ++ + G
Sbjct: 65 LFDIGEEKEGKPVFKKTKEIRFSIEKGIAGQVARTGEVLNIPDAYADPRFNREVDLYTGY 124
Query: 86 GIVCYLA----ESGEPVNIPDAYLLINKFDDLAFSKNDENFVEAY 126
L G + + ++NK AFSK DEN + +
Sbjct: 125 TTRNILCMPIVSRGSVIGV--VQ-MVNKISGSAFSKTDENNFKMF 166
Score = 38.5 bits (90), Expect = 5e-04
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 16 SIPWGCGIVCYLAESGEPVNIPDAY 40
GI +A +GE +NIPDAY
Sbjct: 85 RFSIEKGIAGQVARTGEVLNIPDAY 109
>2w3g_A DOSS, two component sensor histidine kinase DEVS (GAF family
protein); redox sensor, heme, hypoxia, GAF domain,
transferase; HET: HEM; 1.40A {Mycobacterium
tuberculosis} PDB: 2w3d_A* 2w3f_A* 2w3e_A* 2w3h_A*
2y79_A* 2y8h_A* 2vzw_A*
Length = 153
Score = 47.6 bits (114), Expect = 2e-07
Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 7/82 (8%)
Query: 48 RIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIRIPWGCGIVCYLAESGEPVNIPDAYL-- 105
+P G G++G + E +P+ + D P+ + +L G PV + D
Sbjct: 56 HLPKGLGVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFL---GVPVRVRDESFGT 112
Query: 106 --LINKFDDLAFSKNDENFVEA 125
L +K + FS +DE V+A
Sbjct: 113 LYLTDKTNGQPFSDDDEVLVQA 134
Score = 31.1 bits (71), Expect = 0.12
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 17 IPWGCGIVCYLAESGEPVNIPDAY 40
+P G G++ L E +P+ + D
Sbjct: 57 LPKGLGVIGLLIEDPKPLRLDDVS 80
>1ykd_A Adenylate cyclase; GAF domain, bound cyclic AMP ligand, lyase; HET:
CMP; 1.90A {Anabaena SP}
Length = 398
Score = 49.1 bits (116), Expect = 3e-07
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 36 IPDAYLVSTPEIRIPWGCGIVGYVAESGEPVNIP-DAY 72
+ + EIRIP GI G VA + VNIP D Y
Sbjct: 63 VAAGEGDRSLEIRIPADKGIAGEVATFKQVVNIPFDFY 100
Score = 42.2 bits (98), Expect = 5e-05
Identities = 15/30 (50%), Positives = 19/30 (63%)
Query: 43 STPEIRIPWGCGIVGYVAESGEPVNIPDAY 72
ST E+R+P G G G VA SG+ +NIP
Sbjct: 257 STKELRVPIGKGFAGIVAASGQKLNIPFDL 286
Score = 40.6 bits (94), Expect = 2e-04
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 68 IPDAYLVSTPQIRIPWGCGIVCYLAESGEPVNIP-DAY 104
+ + +IRIP GI +A + VNIP D Y
Sbjct: 63 VAAGEGDRSLEIRIPADKGIAGEVATFKQVVNIPFDFY 100
Score = 36.8 bits (84), Expect = 0.003
Identities = 23/144 (15%), Positives = 50/144 (34%), Gaps = 13/144 (9%)
Query: 75 STPQIRIPWGCGIVCYLAESGEPVNIPDAYLLINKFDDLAFSKNDENFVEAYEKAVIAM- 133
ST ++R+P G G +A SG+ +NIP D A +K + +++ M
Sbjct: 257 STKELRVPIGKGFAGIVAASGQKLNIPFDL---YDHPDSATAKQIDQQNGYRTCSLLCMP 313
Query: 134 --AKQSVTLDVLSY-----HASASLEDAQRLRSNNSSLIVPMAKQSVT-LDVLSYHASAS 185
+ V + + + ++ + A +
Sbjct: 314 VFNGDQELIGVTQLVNKKKTGEFPPYNPETWPIAPECFQASFDRNDEEFMEAFNIQAGVA 373
Query: 186 LEDAQRLRRTNKTKEEQNREENSY 209
L++AQ + +E+ +R + +
Sbjct: 374 LQNAQLFATVKQ-QEQGSRSHHHH 396
Score = 35.6 bits (81), Expect = 0.008
Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 15 YSIPWGCGIVCYLAESGEPVNIP-DAY 40
IP GI +A + VNIP D Y
Sbjct: 74 IRIPADKGIAGEVATFKQVVNIPFDFY 100
Score = 35.6 bits (81), Expect = 0.009
Identities = 28/117 (23%), Positives = 42/117 (35%), Gaps = 16/117 (13%)
Query: 15 YSIPWGCGIVCYLAESGEPVNIPDAYLVSTPEIRIPWGCGI---VGYVAES--GEPVNIP 69
+P G G +A SG+ +NIP I GY S PV
Sbjct: 261 LRVPIGKGFAGIVAASGQKLNIPF---DLYDHPDSATAKQIDQQNGYRTCSLLCMPVFNG 317
Query: 70 DAYLVSTPQIRIPWGCGIVCYLAESGEPVNIPDAYLLINKFDDLAFSKNDENFVEAY 126
D L+ Q +V P P+ + + + +F +NDE F+EA+
Sbjct: 318 DQELIGVTQ--------LVNKKKTGEFPPYNPETWPIAPECFQASFDRNDEEFMEAF 366
>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 = 48.5 bits (115), Expect = 6e-07
Identities = 50/258 (19%), Positives = 84/258 (32%), Gaps = 85/258 (32%)
Query: 4 AEFLSRASYLLYSI-----------PWGCGIVCYLAESGEPVNIPD-AYLVSTPEIRIPW 51
+ + ++ L + G I+ +L P N PD YL+S P I P
Sbjct: 185 GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLEN---PSNTPDKDYLLSIP-ISCP- 239
Query: 52 GCGIVGYVAESGEPVNIPDAYLVS------TPQIRIPWGCGIVCYLAESGEPVNIPDAYL 105
++G + + Y+V+ TP + G +G + A +
Sbjct: 240 ---LIGVIQLA--------HYVVTAKLLGFTPGELRSYLKGA------TGHSQGLVTA-V 281
Query: 106 LINKFDDLAFSKNDENFVEAYEKAV-----IAMAKQ------SVTLDVLSY-----HASA 149
I A + + E+F + KA+ I + S+ +L
Sbjct: 282 AI------AETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVP 335
Query: 150 S-------LEDAQ---RLRSNNSSLIVPMAKQ-SVTLD------VLSYHASASLED-AQR 191
S L Q + NS L P KQ ++L V+S SL
Sbjct: 336 SPMLSISNLTQEQVQDYVNKTNSHL--PAGKQVEISLVNGAKNLVVSGPP-QSLYGLNLT 392
Query: 192 LRR-TNKTKEEQNREENS 208
LR+ + +Q+R S
Sbjct: 393 LRKAKAPSGLDQSRIPFS 410
Score = 34.6 bits (79), Expect = 0.021
Identities = 25/144 (17%), Positives = 37/144 (25%), Gaps = 58/144 (40%)
Query: 66 VNIPDAYLVSTP---------------------QIRIPWG----CGIVCYLAESGEPVNI 100
VN +VS P Q RIP+ +L PV
Sbjct: 371 VNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFL-----PVAS 425
Query: 101 P--DAYLLINKFDDLAFSKNDENFVEAYEKAVIAMAKQSVTLDVLS-----YHASASLED 153
P L V A + + K +V+ + Y D
Sbjct: 426 PFHSHLL-----------------VPASDLINKDLVKNNVSFNAKDIQIPVYDT----FD 464
Query: 154 AQRLRSNNSSLIVPMAKQSVTLDV 177
LR + S+ + + L V
Sbjct: 465 GSDLRVLSGSISERIVDCIIRLPV 488
>3oov_A Methyl-accepting chemotaxis protein, putative; structural genomics,
PSI-2, protein structure initiative; 2.20A {Geobacter
sulfurreducens}
Length = 169
Score = 44.2 bits (105), Expect = 5e-06
Identities = 9/95 (9%), Positives = 28/95 (29%), Gaps = 6/95 (6%)
Query: 37 PDAYLVSTPEIRIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIRIPWGCGIVCYLAES-- 94
+ + + + G++ + I D T I ++S
Sbjct: 57 TADFNPAGVVLPLDQRGGVITKCFTDRQVYMIDDVSAYPTDFRLQSPYDAIRALRSKSFV 116
Query: 95 GEPVNIPD----AYLLINKFDDLAFSKNDENFVEA 125
P+ + + + N+ + + D + ++
Sbjct: 117 ICPIVVKGEAIGVFAVDNRSSRRSLNDTDVDTIKL 151
Score = 33.1 bits (76), Expect = 0.029
Identities = 5/65 (7%), Positives = 15/65 (23%), Gaps = 3/65 (4%)
Query: 69 PDAYLVSTPQIRIPWGCGIVCYLAESGEPVNIPDAYLLINKFDDLAFSKNDENFVEAYEK 128
+ + + + G++ + I D D + K
Sbjct: 57 TADFNPAGVVLPLDQRGGVITKCFTDRQVYMIDDVS---AYPTDFRLQSPYDAIRALRSK 113
Query: 129 AVIAM 133
+ +
Sbjct: 114 SFVIC 118
Score = 30.0 bits (68), Expect = 0.36
Identities = 3/26 (11%), Positives = 7/26 (26%)
Query: 15 YSIPWGCGIVCYLAESGEPVNIPDAY 40
+ G++ + I D
Sbjct: 67 LPLDQRGGVITKCFTDRQVYMIDDVS 92
>3trc_A Phosphoenolpyruvate-protein phosphotransferase; signal
transduction; HET: MSE; 1.65A {Coxiella burnetii}
Length = 171
Score = 43.8 bits (104), Expect = 5e-06
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 5/83 (6%)
Query: 46 EIRIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIRIPWGCGIVCYLAESGEPVNIPDAY- 104
++R+ +G G++G V E EP+N+ DA P + G Y G P+
Sbjct: 70 KLRLKFGEGLIGLVGEREEPINLADAP--LHPAYKHRPELGEEDYHGFLGIPIIEQGELL 127
Query: 105 --LLINKFDDLAFSKNDENFVEA 125
L+I + + F++ +E F
Sbjct: 128 GILVIQQLESHHFAEEEEAFCVT 150
Score = 31.9 bits (73), Expect = 0.072
Identities = 9/40 (22%), Positives = 19/40 (47%)
Query: 1 MRTAEFLSRASYLLYSIPWGCGIVCYLAESGEPVNIPDAY 40
+ + L+ + +G G++ + E EP+N+ DA
Sbjct: 57 LMATQGLNSKQVGKLRLKFGEGLIGLVGEREEPINLADAP 96
>3ci6_A Phosphoenolpyruvate-protein phosphotransferase;
PEP-phosphotransferase, GAF domain, structura genomics,
PSI-2, protein structure initiative; HET: MSE P4G; 1.55A
{Acinetobacter SP}
Length = 171
Score = 43.5 bits (103), Expect = 8e-06
Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 7/84 (8%)
Query: 46 EIRIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIRIPWGCGIVCYLAESGEPVNIPDAYL 105
+ + G+VG V + E VN+ +A + G Y + G PV +
Sbjct: 72 HVSLQLSEGLVGLVGQREEIVNLENAS--KHERFAYLPETGEEIYNSFLGVPVMYRRKVM 129
Query: 106 ----LINKFDDLAFSKNDENFVEA 125
+ NK FS+ E+F+
Sbjct: 130 GVLVVQNKQPQ-DFSEAAESFLVT 152
Score = 31.1 bits (71), Expect = 0.15
Identities = 9/40 (22%), Positives = 19/40 (47%)
Query: 1 MRTAEFLSRASYLLYSIPWGCGIVCYLAESGEPVNIPDAY 40
+ ++ L+ S S+ G+V + + E VN+ +A
Sbjct: 59 LMASKGLNPESVGHVSLQLSEGLVGLVGQREEIVNLENAS 98
>3e0y_A Conserved domain protein; APC87688.2, geobacter sulfurreducens PCA,
structural genomics, PSI-2, midwest center for
structural G MCSG; 3.10A {Geobacter sulfurreducens}
Length = 181
Score = 42.7 bits (101), Expect = 2e-05
Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 14/96 (14%)
Query: 46 EIRIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIRIPWGC---GIVCYLA----ESGEPV 98
+IRI G GI G VA G+ +++ A P+ R L+ + E
Sbjct: 75 KIRIKIGDGITGSVARDGQYISLSRAS--QDPRYRYFPELQEEKYNSMLSFPIGDKKEVY 132
Query: 99 NIPDAYLLINKFDDLAFSKNDENFVEAYEKAVIAMA 134
+ + +N +F +++ FV +I A
Sbjct: 133 GV----INLNTTSIRSFHEDEIYFVSIIA-NLILTA 163
Score = 29.2 bits (66), Expect = 0.76
Identities = 8/40 (20%), Positives = 14/40 (35%)
Query: 1 MRTAEFLSRASYLLYSIPWGCGIVCYLAESGEPVNIPDAY 40
+ A I G GI +A G+ +++ A
Sbjct: 62 LAATHGFDPAFIGKIRIKIGDGITGSVARDGQYISLSRAS 101
>3mmh_A FRMSR, methionine-R-sulfoxide reductase; oxidoreductase; HET: SME
MRD; 1.25A {Neisseria meningitidis}
Length = 167
Score = 36.3 bits (84), Expect = 0.003
Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 4/68 (5%)
Query: 5 EFLSRASYLLY-SIPWG-CGIVCYLAESGEPVNIPDAYLVSTPEIRIPWGCGIVGYVAES 62
L+ + +L + W G YL ++ + + RIP+G G+ G
Sbjct: 34 ANLANTAAVLKEAFGWFWVGF--YLVDTRSDELVLAPFQGPLACTRIPFGRGVCGQAWAK 91
Query: 63 GEPVNIPD 70
G V + D
Sbjct: 92 GGTVVVGD 99
>3p01_A Two-component response regulator; PSI-2, midwest center for
structural genomics, protein struc initiative, MCSG,
signali protein; 2.65A {Nostoc SP}
Length = 184
Score = 33.0 bits (76), Expect = 0.031
Identities = 5/52 (9%), Positives = 11/52 (21%), Gaps = 2/52 (3%)
Query: 21 CGIVCYLAESGEPVNIPDAYLVSTPEIRIPWGCGIVGYVAESGEPVNIPDAY 72
C + + E I Y + +G+ +
Sbjct: 65 CIL--QMLEGQTLSTIQGFYSQQGTVNNWLNQDPLTNEAIATGQIQVAANIA 114
>2qyb_A Membrane protein, putative; GAF domain, domain of putative
membrane protein, PSI-2, MCSG structural genomics;
2.40A {Geobacter sulfurreducens pca}
Length = 181
Score = 31.6 bits (72), Expect = 0.094
Identities = 6/35 (17%), Positives = 11/35 (31%)
Query: 46 EIRIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIR 80
+ P +G S + D ++ P R
Sbjct: 65 KDWEPEIETYIGEAFLSNRLQFVNDTQYMTKPLTR 99
>3o5y_A Sensor protein; GAF domain, histidine, kinase, PSI, MCSG,
structural genomics, midwest center for structural
genomics, protein S initiative; 2.45A {Bacillus
halodurans}
Length = 165
Score = 31.5 bits (72), Expect = 0.11
Identities = 2/24 (8%), Positives = 6/24 (25%)
Query: 48 RIPWGCGIVGYVAESGEPVNIPDA 71
IP + + + +
Sbjct: 54 TIPKEQSLYWSALDQRQTIFRSLT 77
Score = 25.8 bits (57), Expect = 9.9
Identities = 3/36 (8%), Positives = 7/36 (19%)
Query: 68 IPDAYLVSTPQIRIPWGCGIVCYLAESGEPVNIPDA 103
P IP + + + +
Sbjct: 42 YPKGSHSLDIGSTIPKEQSLYWSALDQRQTIFRSLT 77
>1vhm_A Protein YEBR; structural genomics, unknown function; HET: MES;
2.10A {Escherichia coli} SCOP: d.110.2.1
Length = 195
Score = 31.4 bits (71), Expect = 0.12
Identities = 29/128 (22%), Positives = 42/128 (32%), Gaps = 22/128 (17%)
Query: 7 LSRASYLLYS----IPWGCGIVCYLAESGEPVNIPDAYLVSTPEIRIPWGCGIVGYVAES 62
L+ S LLY I W G YL E V P + +RIP G G+ G
Sbjct: 48 LANTSALLYERLTDINW-AGF--YLLEDDTLVLGP--FQGKIACVRIPVGRGVCGTAVAR 102
Query: 63 GEPVNIPDA-----YLVSTPQIRIPWGCGIVCYLAESGEPVNIPDAYLLINKFDDLAFSK 117
+ I D ++ IV L + + + D I+ F+
Sbjct: 103 NQVQRIEDVHVFDGHIACDAASN----SEIVLPLVVKNQIIGVLD----IDSTVFGRFTD 154
Query: 118 NDENFVEA 125
DE +
Sbjct: 155 EDEQGLRQ 162
>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 = 31.0 bits (69), Expect = 0.35
Identities = 25/216 (11%), Positives = 50/216 (23%), Gaps = 76/216 (35%)
Query: 32 EPVNIPDAYLVSTPEIRIPWGCGIVGYVAESGEPVNI-------------PDAYLVSTPQ 78
+IP L + W + + + P +S P
Sbjct: 383 PSAHIPTILLS------LIWFDV------IKSDVMVVVNKLHKYSLVEKQPKESTISIPS 430
Query: 79 IRIPWGCGIVCYLAESGEPVNIP-------DAYLLINKFDDLAFSKN-DENFVEAYEKAV 130
I YL + N D Y + FD + + ++
Sbjct: 431 I----------YLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH---- 476
Query: 131 IAMAKQSVTLDVLSYHASASLED----------------AQRLRSNNSSLIVPMAKQSVT 174
+ +H Q++R ++++ + +
Sbjct: 477 ------------IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTL 524
Query: 175 LDVLSYHASASLEDAQRLRRTNKTKE-EQNREENSY 209
+ Y D + R N + EEN
Sbjct: 525 QQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLI 560
>1f5m_A GAF; CGMP binding, signaling protein; 1.90A {Saccharomyces
cerevisiae} SCOP: d.110.2.1 PDB: 3ko6_A*
Length = 180
Score = 29.9 bits (67), Expect = 0.45
Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 17/88 (19%)
Query: 7 LSRASYLLY--------SIPWGCGIVCYLAESGEP-VNIPDAYLVSTPEIRIPWGCGIVG 57
LS AS L++ I W G Y+ ++ E I + I +G G+ G
Sbjct: 46 LSNASSLIWHAYKSLAVDINW-AG--FYVTQASEENTLILGPFQGKVACQMIQFGKGVCG 102
Query: 58 YVAESGEPVNIPDA-----YLVSTPQIR 80
A + E +PD ++ + +
Sbjct: 103 TAASTKETQIVPDVNKYPGHIACDGETK 130
>3eea_A GAF domain/HD domain protein; structural genomics, PSI, MCSG,
protein structure initiative, midwest center for
structural genomics; HET: PG6; 1.80A {Geobacter
sulfurreducens}
Length = 162
Score = 28.9 bits (65), Expect = 0.74
Identities = 5/37 (13%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 36 IPDAYLVSTPEIRI-PWGCGIVGYVAESGEPVNIPDA 71
+P ++L E+ + P ++ + + + + D
Sbjct: 54 LPASFLPVFREMPLAPDKIPLLKSMLRKRQHLMLTDP 90
>3ksh_A Putative uncharacterized protein; FRMSR, free-Met-R-SO,
oxidoreductase; 1.50A {Staphylococcus aureus} PDB:
3ksf_A 3ksi_A 3ksg_A*
Length = 160
Score = 28.7 bits (64), Expect = 0.92
Identities = 19/68 (27%), Positives = 23/68 (33%), Gaps = 9/68 (13%)
Query: 7 LSRASYLLYS----IPWGCGIVCYLAESGEPVNIPDAYLVSTPEIRIPWGCGIVGYVAES 62
LS S LL I W G YL E E I + + IP G G+ G
Sbjct: 36 LSNMSALLNDNLDQINW-VGF--YLLEQNE--LILGPFQGHPACVHIPIGKGVCGTAVSE 90
Query: 63 GEPVNIPD 70
+ D
Sbjct: 91 RRTQVVAD 98
>3rfb_A Putative uncharacterized protein; FRMSR, GAF, oxidoreductase,
SME; HET: SME; 2.30A {Streptococcus pneumoniae}
Length = 171
Score = 28.3 bits (63), Expect = 1.1
Identities = 22/68 (32%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 7 LSRASYLLYS----IPWGCGIVCYLAESGEPVNIPDAYLVSTPEIRIPWGCGIVGYVAES 62
LS AS L+ S + G YL + E V P + IRI G G+ G A
Sbjct: 37 LSNASALIKSRFPNTVF-AGF--YLFDGKELVLGP--FQGGVSCIRIALGKGVCGEAAHF 91
Query: 63 GEPVNIPD 70
E V + D
Sbjct: 92 QETVIVGD 99
>1x4r_A PARP14 protein; WWE domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus}
Length = 99
Score = 26.2 bits (57), Expect = 3.4
Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 151 LEDAQRLRSNNSSLIVPMAKQSVTLDVLSYHASASLEDAQRLRRTNKTKEEQ 202
LE A ++ +V + Q T+D+ + A+A ++R K
Sbjct: 48 LEVA--WKAKKKDTVVQIHNQDFTVDLSTNTATAPQGQTFTVQRLVKASGPS 97
>3shp_A Putative acetyltransferase STHE_0691; PSI-biology, midwest center
for structural genomics, MCSG; HET: SRT; 2.21A
{Sphaerobacter thermophilus}
Length = 176
Score = 26.6 bits (58), Expect = 4.6
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 131 IAMAKQSVTLDVLSYHASASLEDAQRLRSNNSSLIVPMAKQSVTLDVLSYHASASLEDAQ 190
I KQ+ +L +H + L+DA LR+ L+VP + L V++ +A D Q
Sbjct: 78 IEFGKQTASL---RFHMAPWLDDADVLRAEALELVVPWLRDEHELLVITVEIAA---DEQ 131
Query: 191 R 191
R
Sbjct: 132 R 132
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.7 bits (58), Expect = 4.8
Identities = 10/67 (14%), Positives = 22/67 (32%), Gaps = 18/67 (26%)
Query: 152 EDAQRLRSNNSSLIVPMAKQSVTLDVLSYHASASLED--------AQRLRRTNKTKEE-- 201
E +RL+ + A V A LE+ ++ + N+ ++
Sbjct: 93 EQRKRLQELD-------AASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAF 145
Query: 202 -QNREEN 207
Q + +
Sbjct: 146 YQQPDAD 152
>2vjw_A GAF-B, GAF family protein; histidine kinase, hypoxia sensing,
hydrolase; HET: MSE; 2.0A {Mycobacterium smegmatis}
PDB: 2vks_A
Length = 149
Score = 26.3 bits (58), Expect = 4.8
Identities = 4/24 (16%), Positives = 6/24 (25%)
Query: 48 RIPWGCGIVGYVAESGEPVNIPDA 71
IP +G P +
Sbjct: 55 AIPVQDNAIGQAFRDRAPRRLDVL 78
>1dgn_A Iceberg (protease inhibitor); antiparallel six-helix bundle,
greek-KEY, hydrolase inhibitor; NMR {Homo sapiens} SCOP:
a.77.1.3
Length = 89
Score = 25.6 bits (56), Expect = 5.2
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 2/54 (3%)
Query: 154 AQRLRSNNSSLIVPMAKQSVT--LDVLSYHASASLEDAQRLRRTNKTKEEQNRE 205
Q LR I + ++ LD L S ED ++R N T ++ R
Sbjct: 2 DQLLRKKRRIFIHSVGAGTINALLDCLLEDEVISQEDMNKVRDENDTVMDKARV 55
>3llu_A RAS-related GTP-binding protein C; structural genomics consortium,
SGC, cytoplasm, nucleotide-binding, nucleus,
phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB:
2q3f_A*
Length = 196
Score = 26.5 bits (58), Expect = 5.4
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 101 PDAYL--LINKFDDLAFSKNDENFVEAYEKAVIAMAKQSVTLDVLSYHASASLED 153
PD I+K D L+ E + +++A +A + LS++ + S+ D
Sbjct: 128 PDMNFEVFIHKVDGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLT-SIYD 181
>1xff_A D-fructose-6-, glucosamine--fructose-6-phosphate aminotransferase
[isomerizing]; complex (transferase/inhibitor),
glutamine amidotransferase; HET: GLU; 1.80A
{Escherichia coli} SCOP: d.153.1.1 PDB: 1xfg_A*
Length = 240
Score = 25.9 bits (58), Expect = 8.2
Identities = 6/9 (66%), Positives = 8/9 (88%)
Query: 53 CGIVGYVAE 61
CGIVG +A+
Sbjct: 1 CGIVGAIAQ 9
>1o66_A 3-methyl-2-oxobutanoate hydroxymethyltransferase; structural
genomics; HET: MSE; 1.75A {Neisseria meningitidis
serogroup B} SCOP: c.1.12.8 PDB: 1o68_A*
Length = 275
Score = 26.0 bits (58), Expect = 8.5
Identities = 12/61 (19%), Positives = 19/61 (31%), Gaps = 14/61 (22%)
Query: 137 SVTLDVLSYHASASLEDAQRLRSNNSSLIVPMAKQSVTLDVLSYHASA--SLEDAQRLRR 194
V+L + YH R +++IV L +Y S + A L
Sbjct: 59 PVSLRDMCYHTECV------ARGAKNAMIV------SDLPFGAYQQSKEQAFAAAAELMA 106
Query: 195 T 195
Sbjct: 107 A 107
>2bpl_A Glucosamine--fructose-6-phosphate aminotransferase [isomerizing];
amidotransferase, ammonia channeling, glucosamine 6-
phosphate synthase; HET: F6R; 2.05A {Escherichia coli}
SCOP: c.80.1.1 d.153.1.1 PDB: 1jxa_A* 2j6h_A* 2vf4_X
2vf5_X* 3ooj_A*
Length = 608
Score = 26.3 bits (59), Expect = 8.9
Identities = 6/9 (66%), Positives = 8/9 (88%)
Query: 53 CGIVGYVAE 61
CGIVG +A+
Sbjct: 1 CGIVGAIAQ 9
>3hcy_A Putative two-component sensor histidine kinase PR; two-component
sensor histidine kinase protein, structural GE PSI,
MCSG; 2.80A {Sinorhizobium meliloti}
Length = 151
Score = 25.7 bits (57), Expect = 8.9
Identities = 4/20 (20%), Positives = 7/20 (35%)
Query: 52 GCGIVGYVAESGEPVNIPDA 71
G A EP+ + +
Sbjct: 53 GHSPWITGANEPEPIFVENV 72
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.316 0.132 0.391
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,150,016
Number of extensions: 184949
Number of successful extensions: 532
Number of sequences better than 10.0: 1
Number of HSP's gapped: 506
Number of HSP's successfully gapped: 61
Length of query: 210
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 121
Effective length of database: 4,216,824
Effective search space: 510235704
Effective search space used: 510235704
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: 55 (25.0 bits)