RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12115
(154 letters)
>4f8a_A Potassium voltage-gated channel subfamily H membe; probable
regulatory domain of potassium channel, membrane PR
transport protein; 2.20A {Mus musculus}
Length = 160
Score = 83.9 bits (208), Expect = 1e-21
Identities = 47/67 (70%), Positives = 56/67 (83%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFARNLLL 60
+ KGDVFGD FWK+ + QS ANVRALTYCDLH IKRD L +VL+FY AF++SF+RNL+L
Sbjct: 91 LGKGDVFGDVFWKEATLAQSCANVRALTYCDLHVIKRDALQKVLEFYTAFSHSFSRNLIL 150
Query: 61 TYNLRHR 67
TYNLR R
Sbjct: 151 TYNLRKR 157
Score = 60.0 bits (146), Expect = 3e-12
Identities = 31/43 (72%), Positives = 38/43 (88%)
Query: 85 LTYCDLHTIKRDRLLEVLDFYQAFANSFARNLLLTYNLRHRLV 127
LTYCDLH IKRD L +VL+FY AF++SF+RNL+LTYNLR R+V
Sbjct: 117 LTYCDLHVIKRDALQKVLEFYTAFSHSFSRNLILTYNLRKRIV 159
>3ukn_A Novel protein similar to vertebrate potassium VOL channel,
subfamily H (EAG-related)...; KCNH, ELK, ERG, CNBD,
CNBHD, C-linker, ION channel; 2.20A {Danio rerio} PDB:
3ukt_B 3ukv_B
Length = 212
Score = 73.2 bits (180), Expect = 6e-17
Identities = 29/70 (41%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFARNL-- 58
+ KGD+ G V ++ ANV+ALTYCDL I L EVL Y +A F +
Sbjct: 139 LGKGDLIGSDSLTKEQVIKTNANVKALTYCDLQYISLKGLREVLRLYPEYAQKFVSEIQH 198
Query: 59 LLTYNLRHRK 68
LTYNLR
Sbjct: 199 DLTYNLREGS 208
Score = 48.1 bits (115), Expect = 1e-07
Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 85 LTYCDLHTIKRDRLLEVLDFYQAFANSFARNL--LLTYNLRHRLVSNM 130
LTYCDL I L EVL Y +A F + LTYNLR +++
Sbjct: 165 LTYCDLQYISLKGLREVLRLYPEYAQKFVSEIQHDLTYNLREGSGADL 212
>3bpz_A Potassium/sodium hyperpolarization-activated cyclic
nucleotide-gated channel 2; CNBD, C-linker, pacemaker,
HCN, HCN2, CAP, PKA, CAMP, ION channel; HET: CMP; 1.65A
{Mus musculus} PDB: 3ffq_A 1q3e_A* 1q43_A* 1q5o_A*
3u10_A* 2q0a_A* 3etq_A* 3u11_A* 3otf_A* 3u0z_A*
Length = 202
Score = 54.6 bits (132), Expect = 4e-10
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFAR 56
+S G FG+ G+ A+VRA TYC L+++ D EVL+ Y +F
Sbjct: 136 LSDGSYFGEICLLTR--GRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFET 189
Score = 35.8 bits (83), Expect = 0.003
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 85 LTYCDLHTIKRDRLLEVLDFYQAFANSFAR 114
TYC L+++ D EVL+ Y +F
Sbjct: 160 DTYCRLYSLSVDNFNEVLEEYPMMRRAFET 189
>2ptm_A Hyperpolarization-activated (IH) channel; ION channel, cyclic
nucleotide binding domain, C-linker, CAM SPHCN1, HCN;
HET: CMP; 1.93A {Strongylocentrotus purpuratus}
Length = 198
Score = 53.8 bits (130), Expect = 9e-10
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFAR 56
+S G FG+ + A+V+ TYC L ++ +VLD + A +
Sbjct: 136 LSDGSYFGEICLLTR--ERRVASVKCETYCTLFSLSVQHFNQVLDEFPAMRKTMEE 189
Score = 34.5 bits (80), Expect = 0.005
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 85 LTYCDLHTIKRDRLLEVLDFYQAFANSFAR 114
TYC L ++ +VLD + A +
Sbjct: 160 ETYCTLFSLSVQHFNQVLDEFPAMRKTMEE 189
>1wgp_A Probable cyclic nucleotide-gated ION channel 6; cyclic nucleotide
monophosphate, CNMP, CNMP-binding, structural genomics;
NMR {Arabidopsis thaliana} SCOP: b.82.3.2
Length = 137
Score = 45.2 bits (107), Expect = 6e-07
Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 7/60 (11%)
Query: 1 MSKGDVFGD-------SFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANS 53
+ +GD GD + + S V+ALT + + D L V ++ S
Sbjct: 76 LKEGDFCGDELLTWALDPKSGSNLPSSTRTVKALTEVEAFALIADELKFVASQFRRSGPS 135
Score = 31.7 bits (72), Expect = 0.041
Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 3/54 (5%)
Query: 58 LLLTYNLRHRKRDSINLFVSSIISRIPLTYCDLHTIKRDRLLEVLDFYQAFANS 111
LLT+ L + ++ ++ + LT + + D L V ++ S
Sbjct: 85 ELLTWALDPKSGSNLPSSTRTVKA---LTEVEAFALIADELKFVASQFRRSGPS 135
>1vp6_A CNBD, cyclic-nucleotide binding domain of mesorhizobium LOTI CNG
potassium channel; dimer helical bundle beta barrel core
with cyclic AMP bound; HET: CMP; 1.70A {Mesorhizobium
loti} SCOP: b.82.3.2 PDB: 3cl1_A* 2k0g_A* 2kxl_A 3clp_A*
1u12_A 3co2_A
Length = 138
Score = 33.8 bits (78), Expect = 0.007
Identities = 7/38 (18%), Positives = 12/38 (31%)
Query: 21 AANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFARNL 58
+A V A T L ++ + A F +
Sbjct: 91 SATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTA 128
>3mdp_A Cyclic nucleotide-binding domain (CNMP-BD) protei; structural
genomics, joint center for structural genomics; HET:
MSE; 1.90A {Geobacter metallireducens}
Length = 142
Score = 33.8 bits (78), Expect = 0.007
Identities = 14/67 (20%), Positives = 23/67 (34%), Gaps = 4/67 (5%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFARNLLL 60
+ G +FG S ++ RA + I RL E+ + QA N+
Sbjct: 78 VVPGAIFGVSSLIKP--YHYTSSARATKPVRVVDINGARLREMSENNQALGQVLMNNVAA 135
Query: 61 TYNLRHR 67
+ R
Sbjct: 136 A--VLAR 140
>3gyd_A CNMP-BD protein, cyclic nucleotide-binding domain; nucleotide
binding protein, structural genomics; HET: MSE CMP;
1.79A {Methylobacillus flagellatus KT}
Length = 187
Score = 33.6 bits (77), Expect = 0.014
Identities = 16/69 (23%), Positives = 24/69 (34%), Gaps = 6/69 (8%)
Query: 1 MSKGDVFGD-SFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFARNLL 59
+ G + G+ S +A+ A D + RD L ++L N LL
Sbjct: 108 VGAGAIIGEMSMIDG---MPRSASCVASLPTDFAVLSRDALYQLLANMPKLGNKVLIRLL 164
Query: 60 --LTYNLRH 66
LT R
Sbjct: 165 QLLTARFRE 173
>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat
transcription; HET: PR3; 2.3A {Listeria monocytogenes}
SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A
Length = 238
Score = 31.2 bits (71), Expect = 0.092
Identities = 9/83 (10%), Positives = 19/83 (22%), Gaps = 2/83 (2%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFARNLLL 60
V F + IK + L E+L + L
Sbjct: 64 YKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQ--TL 121
Query: 61 TYNLRHRKRDSINLFVSSIISRI 83
+ + + ++ + I
Sbjct: 122 QKQVSYSLAKFNDFSINGKLGSI 144
>3tnp_B CAMP-dependent protein kinase type II-beta regula subunit; PKA RIIB
tetrameric holoenzyme, transferase; HET: SEP TPO; 2.30A
{Mus musculus} PDB: 3tnq_A* 1cx4_A* 2qvs_B*
Length = 416
Score = 31.3 bits (70), Expect = 0.10
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 2/44 (4%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVL 44
+G FG+ N AA+ A+ + +L
Sbjct: 342 CFRGQYFGELALVTNKP--RAASAHAIGTVKCLAMDVQAFERLL 383
>3shr_A CGMP-dependent protein kinase 1; cyclic nucleotide binding domains,
cyclic nucleotide protein transferase, PKG; HET: CMP;
2.50A {Bos taurus}
Length = 299
Score = 30.3 bits (68), Expect = 0.25
Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 6/75 (8%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFARNLLL 60
+ KGD FG+ + V ANV A I RD ++ +N +
Sbjct: 227 LGKGDWFGEKALQGEDV--RTANVIAAEAVTCLVIDRDSFKHLIGGLDDVSNKAYED--- 281
Query: 61 TYNLRHRKRDSINLF 75
+ + F
Sbjct: 282 -AEAKAKYEAEAAFF 295
>2pqq_A Putative transcriptional regulator; APC7345, streptomyces
coelicolor structural genomics, PSI-2, protein structure
initiative; 2.00A {Streptomyces coelicolor A3}
Length = 149
Score = 29.5 bits (67), Expect = 0.25
Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 4/59 (6%)
Query: 1 MSKGDVFGD-SFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFARNL 58
+ ++ G+ S + G A ALT L + L L+ A + R +
Sbjct: 74 VGPSELIGELSLFDP---GPRTATGTALTEVKLLALGHGDLQPWLNVRPEVATALLRAV 129
>2z69_A DNR protein; beta barrel, dimerization helix, transcription
regulator; 2.10A {Pseudomonas aeruginosa}
Length = 154
Score = 29.2 bits (66), Expect = 0.29
Identities = 9/59 (15%), Positives = 17/59 (28%), Gaps = 3/59 (5%)
Query: 1 MSKGDVFGD-SFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFARNL 58
++ + F + + D A +A+ L L L A + L
Sbjct: 81 TNERNTFAEAMMFMDT--PNYVATAQAVVPSQLFRFSNKAYLRQLQDNTPLALALLAKL 137
>4din_B CAMP-dependent protein kinase type I-beta regulat subunit,
CAMP-dependent protein kinase catalytic subunit A;
isoform diversity; HET: TPO SEP ATP; 3.70A {Homo
sapiens}
Length = 381
Score = 29.7 bits (66), Expect = 0.36
Identities = 12/44 (27%), Positives = 15/44 (34%), Gaps = 2/44 (4%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVL 44
+ D FG+ N AA V A + R R VL
Sbjct: 318 LGPSDYFGEIALLLNRP--RAATVVARGPLKCVKLDRPRFERVL 359
>3of1_A CAMP-dependent protein kinase regulatory subunit; cyclic nucleotide
binding domain, evolution, PKA signaling, transfer; HET:
CMP; 2.21A {Saccharomyces cerevisiae}
Length = 246
Score = 29.4 bits (66), Expect = 0.45
Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 2/44 (4%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVL 44
+ D FG+ ++ A V A + T+ + +L
Sbjct: 190 LKDHDYFGEVALLNDLP--RQATVTATKRTKVATLGKSGFQRLL 231
>2qcs_B CAMP-dependent protein kinase type I-alpha regula subunit,
CAMP-dependent protein kinase, alpha-catalytic SU;
cyclic adenosine monophosphate; HET: SEP TPO ANP TAM;
2.20A {Bos taurus} PDB: 1rl3_A* 1rgs_A* 1ne6_A* 1ne4_A*
Length = 291
Score = 29.2 bits (65), Expect = 0.57
Identities = 12/44 (27%), Positives = 15/44 (34%), Gaps = 2/44 (4%)
Query: 1 MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVL 44
+ D FG+ N AA V A + R R VL
Sbjct: 227 LGPSDYFGEIALLMNRP--KAATVVARGPLKCVKLDRPRFERVL 268
>1vq8_E 50S ribosomal protein L6P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: d.141.1.1 d.141.1.1 PDB:
1vq4_E* 1vq5_E* 1vq6_E* 1vq7_E* 1s72_E* 1vq9_E* 1vqk_E*
1vql_E* 1vqm_E* 1vqn_E* 1vqo_E* 1vqp_E* 1yhq_E* 1yi2_E*
1yij_E* 1yit_E* 1yj9_E* 1yjn_E* 1yjw_E* 2otj_E* ...
Length = 178
Score = 27.1 bits (61), Expect = 1.9
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 16 AVGQSAANVRALT 28
AVGQ+AA++ LT
Sbjct: 141 AVGQTAADIEQLT 153
>3iz5_F 60S ribosomal protein L9 (L6P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_F
Length = 190
Score = 26.2 bits (58), Expect = 4.0
Identities = 4/13 (30%), Positives = 6/13 (46%)
Query: 16 AVGQSAANVRALT 28
V +SAA +
Sbjct: 152 LVSRSAALINQKC 164
>3u5e_H L8, RP24, YL11, 60S ribosomal protein L9-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_F
1s1i_H 3izs_F* 3j16_F 3o5h_I 3o58_I 3u5i_H 3jyw_H
Length = 191
Score = 26.1 bits (58), Expect = 4.3
Identities = 4/13 (30%), Positives = 9/13 (69%)
Query: 16 AVGQSAANVRALT 28
V Q+AA+++ +
Sbjct: 153 DVSQNAADLQQIC 165
>4a17_E RPL9, 60S ribosomal protein L9; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_E 4a1c_E 4a1e_E
Length = 188
Score = 26.2 bits (58), Expect = 4.9
Identities = 3/13 (23%), Positives = 5/13 (38%)
Query: 16 AVGQSAANVRALT 28
V Q+ A +
Sbjct: 151 NVSQTCALIHQSC 163
>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix-H
helix, HHH motif, three helix bundle, methanopyrus
kandleri isomerase; 2.30A {Methanopyrus kandleri} SCOP:
a.60.2.4 a.60.2.4 a.60.2.4 a.60.2.4 a.267.1.1 PDB:
2csd_A
Length = 519
Score = 26.2 bits (57), Expect = 5.3
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 33 HTIKRDRLLEVL-DFYQAFANSFARNLLLTYNLRHRKRDSINLFVSSIISRIPLTYCDLH 91
H +RDRLLE L + + + + R+ L + KRD + ++ I L D +
Sbjct: 246 HVKRRDRLLEELYEHLEELSERYLRHPLTRRWIVEHKRDIMRRYLEQRIVECALKLQDRY 305
Query: 92 TIKRD 96
I+ D
Sbjct: 306 GIRED 310
>3m6z_A Topoisomerase V; helix-hairpin-helix, conformational changes I
protein; HET: PO4; 1.40A {Methanopyrus kandleri} PDB:
3m6k_A* 3m7d_A 3m7g_A
Length = 380
Score = 26.2 bits (57), Expect = 5.6
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 33 HTIKRDRLLEVL-DFYQAFANSFARNLLLTYNLRHRKRDSINLFVSSIISRIPLTYCDLH 91
H +RDRLLE L + + + + R+ L + KRD + ++ I L D +
Sbjct: 246 HVKRRDRLLEELYEHLEELSERYLRHPLTRRWIVEHKRDIMRRYLEQRIVECALKLQDRY 305
Query: 92 TIKRD 96
I+ D
Sbjct: 306 GIRED 310
>3ocp_A PRKG1 protein; serine/threonine kinase, TF2I and IRAG, transferase;
HET: CMP; 2.49A {Homo sapiens} PDB: 3od0_A* 3ogj_A*
Length = 139
Score = 25.4 bits (56), Expect = 5.9
Identities = 6/25 (24%), Positives = 9/25 (36%)
Query: 21 AANVRALTYCDLHTIKRDRLLEVLD 45
A V+ L L I R ++
Sbjct: 105 TATVKTLVNVKLWAIDRQCFQTIMM 129
>2zkr_e 60S ribosomal protein L9; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 192
Score = 25.4 bits (56), Expect = 7.1
Identities = 5/13 (38%), Positives = 7/13 (53%)
Query: 16 AVGQSAANVRALT 28
V SAA ++ T
Sbjct: 153 LVSNSAALIQQAT 165
>1rl6_A Protein (ribosomal protein L6); RNA-binding protein, gentamicin
resistance, alpha/beta protein; 2.00A {Geobacillus
stearothermophilus} SCOP: d.141.1.1 d.141.1.1 PDB:
1giy_H 1ml5_h* 1c04_B 1yl3_H 2b66_H 2b9n_H 2b9p_H 1eg0_J
487d_J
Length = 177
Score = 25.1 bits (56), Expect = 7.8
Identities = 7/11 (63%), Positives = 10/11 (90%)
Query: 17 VGQSAANVRAL 27
VG+ AAN+RA+
Sbjct: 140 VGELAANIRAV 150
>3r8s_G 50S ribosomal protein L6; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_E
1p86_E 2awb_G 2aw4_G 2i2v_G 2j28_G 2i2t_G* 2qao_G*
2qba_G* 2qbc_G* 2qbe_G 2qbg_G 2qbi_G* 2qbk_G* 2qov_G
2qox_G 2qoz_G* 2qp1_G* 2rdo_G 2vhm_G ...
Length = 176
Score = 25.1 bits (56), Expect = 8.1
Identities = 6/11 (54%), Positives = 9/11 (81%)
Query: 17 VGQSAANVRAL 27
+GQ AA++RA
Sbjct: 140 IGQVAADLRAY 150
>3pna_A CAMP-dependent protein kinase type I-alpha regula subunit;
beta-barrel, CAMP-binding, catalytic subunit,
transferase; HET: CMP; 1.50A {Bos taurus} PDB: 3fhi_B*
3iia_A 3plq_A* 1u7e_B* 3pvb_B*
Length = 154
Score = 25.0 bits (55), Expect = 9.6
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 21 AANVRALTYCDLHTIKRDRLLEVL 44
AA V+A T L I RD +L
Sbjct: 120 AATVKAKTNVKLWGIDRDSYRRIL 143
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
0.328 0.139 0.408
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,287,967
Number of extensions: 124360
Number of successful extensions: 268
Number of sequences better than 10.0: 1
Number of HSP's gapped: 265
Number of HSP's successfully gapped: 41
Length of query: 154
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 69
Effective length of database: 4,328,508
Effective search space: 298667052
Effective search space used: 298667052
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)