RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5103
(109 letters)
>2h00_A Methyltransferase 10 domain containing protein; structural
genomics, structural genomics consortium, SGC; HET: SAH;
2.00A {Homo sapiens} SCOP: c.66.1.54
Length = 254
Score = 77.1 bits (189), Expect = 9e-19
Identities = 39/72 (54%), Positives = 54/72 (75%), Gaps = 2/72 (2%)
Query: 38 SGKLKFNFQNPDALRIFTTTLLRKDFGLNVEIPPMRLVPTLPLRLNYILWIEDLLEANQI 97
SG++ NF++P+A+R T TLLR+DFGL+++IP RL+PT+PLRLNYI W+EDL+
Sbjct: 2 SGRVSLNFKDPEAVRALTCTLLREDFGLSIDIPLERLIPTVPLRLNYIHWVEDLIGHQDS 61
Query: 98 --SSPITGIDIG 107
S+ GIDIG
Sbjct: 62 DKSTLRRGIDIG 73
>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 = 30.8 bits (70), Expect = 0.060
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLKFNFQ 46
+++ YPE+ + E+ L +N +
Sbjct: 177 GLREVLRLYPEYAQKFVSEIQHDLTYNLR 205
>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 = 0.061
Identities = 9/71 (12%), Positives = 20/71 (28%), Gaps = 27/71 (38%)
Query: 29 FRKHLHQELSGKLK--FNFQNPDALR-------IFTTTLLRKDFGLNVEIPPMRLVPTLP 79
++ +L+ ++ N P R +F IP + L
Sbjct: 347 WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF-----PPS----AHIPTILLS---- 393
Query: 80 LRLNYILWIED 90
++W +
Sbjct: 394 -----LIWFDV 399
Score = 25.6 bits (55), Expect = 5.2
Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 10/92 (10%)
Query: 17 PDFKQLAIEYPEFRKHLHQELSGKLKFNF-------QNPDALRIFTTTLLRKDFG-LNVE 68
D + + E H+ + + ++ F +LR ++ L
Sbjct: 39 QDMPKSILSKEEI-DHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSP 97
Query: 69 IPPMRLVPTLPLRLNYILWIEDLLEANQISSP 100
I + P++ R+ YI + L NQ+ +
Sbjct: 98 IKTEQRQPSMMTRM-YIEQRDRLYNDNQVFAK 128
>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 = 28.5 bits (63), Expect = 0.44
Identities = 25/129 (19%), Positives = 40/129 (31%), Gaps = 49/129 (37%)
Query: 12 KYRVPPDFKQLAIEYPEFRK--------------H----------LHQELSGKLKFNFQN 47
K + P Q I + E RK H ++++L +F
Sbjct: 395 KAKAPSGLDQSRIPFSE-RKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKN-NVSFNA 452
Query: 48 PDALRI-----FTTTLLRKDFGLNVEIPPMRLVP---TLPLRLNYILWIEDLLEANQISS 99
D ++I F + LR L+ I R+V LP++ W E
Sbjct: 453 KD-IQIPVYDTFDGSDLRV---LSGSISE-RIVDCIIRLPVK-----W-----ETTTQFK 497
Query: 100 PITGIDIGR 108
+D G
Sbjct: 498 ATHILDFGP 506
>2fgs_A Putative periplasmic protein; lipid binding protein, structural
genomics, protein structure initiative, PSI, nysgxrc;
2.90A {Campylobacter jejuni}
Length = 179
Score = 27.7 bits (62), Expect = 0.68
Identities = 3/19 (15%), Positives = 5/19 (26%)
Query: 54 FTTTLLRKDFGLNVEIPPM 72
+ R DF +
Sbjct: 134 LNGKIKRSDFKFATSTSTI 152
>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862,
csgid, structura genomics; 2.21A {Campylobacter jejuni
subsp}
Length = 248
Score = 27.5 bits (62), Expect = 0.69
Identities = 7/46 (15%), Positives = 17/46 (36%)
Query: 7 MHPRNKYRVPPDFKQLAIEYPEFRKHLHQELSGKLKFNFQNPDALR 52
MH + + D + + ++L L + F++ + L
Sbjct: 1 MHHHHHHSSGVDLGTENLYFQSNAMKNIEKLEQSLTYEFKDKNLLI 46
>2r76_A RARE lipoprotein B; alpha-beta protein, structural genomics,
PSI-2, protein STRU initiative, northeast structural
genomics consortium; 2.60A {Shewanella oneidensis}
Length = 152
Score = 27.1 bits (60), Expect = 0.79
Identities = 8/37 (21%), Positives = 18/37 (48%)
Query: 8 HPRNKYRVPPDFKQLAIEYPEFRKHLHQELSGKLKFN 44
+ Y++P QL++ + K L + + +L+ N
Sbjct: 4 KLQRSYQIPEQLNQLSLSSSDEYKELTRLVRERLRLN 40
>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 = 27.3 bits (61), Expect = 0.80
Identities = 5/30 (16%), Positives = 11/30 (36%), Gaps = 2/30 (6%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLKFNFQN 47
+++ Y F + L L +N +
Sbjct: 129 ALQKVLEFYTAFSHSFSRNL--ILTYNLRK 156
>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P;
2.25A {Thermus thermophilus} PDB: 3asy_A*
Length = 211
Score = 27.2 bits (61), Expect = 0.82
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 8/72 (11%)
Query: 29 FRKHLHQELSGKLKFNFQNPDALRI--FTTTLLRKDFGLNVEIP------PMRLVPTLPL 80
++ H L +L+ N+ +PDA + + GL VE+P R P+
Sbjct: 43 YKDLGHLPLEERLRVNYDHPDAFDLALYLEHAQALLRGLPVEMPVYDFRAYTRSPRRTPV 102
Query: 81 RLNYILWIEDLL 92
R ++ +E +L
Sbjct: 103 RPAPVVILEGIL 114
>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic
nucleotide-binding domain, structural genomics, joint
for structural genomics; 2.55A {Eubacterium rectale atcc
33656}
Length = 220
Score = 27.2 bits (61), Expect = 0.89
Identities = 1/25 (4%), Positives = 10/25 (40%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLK 42
+K + + + ++ ++ +
Sbjct: 110 IYKGIMKDSAPVANYTNELMATRFS 134
>1y0g_A Protein YCEI; lipid binding protein, lipocalin, cofactor, coenzyme,
dehydrogenase, hydrolase, predicted, structural
genomics; HET: 8PP; 2.20A {Escherichia coli} SCOP:
b.61.6.1
Length = 191
Score = 26.6 bits (59), Expect = 1.3
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 54 FTTTLLRKDFGLNVEIPPM 72
+ KDF + ++ P
Sbjct: 157 AEGKIKLKDFNIKTDLGPA 175
>3d2o_A UPF0343 protein NGO0387; bimodular tunnel fold, tunneling fold,
folate biosynthesis, GTP cyclohydrolase, metalloenzyme,
manganese; 2.04A {Neisseria gonorrhoeae} PDB: 3d1t_A
Length = 257
Score = 26.8 bits (59), Expect = 1.6
Identities = 11/59 (18%), Positives = 20/59 (33%), Gaps = 19/59 (32%)
Query: 62 DFGLNVEIPPMRLVP-----------------TLPLRLNYILWIEDLLEA--NQISSPI 101
+ V IP L P T+ L + + IE++++ Q S +
Sbjct: 134 GHSMKVMIPVTSLCPCSKEISQYGAHNQRSHVTVSLTSDAEVGIEEVIDYVETQASCQL 192
>2r5r_A UPF0343 protein NE1163; APC86493, DUF198, structural genomics,
PSI-2, protein structure initiative; 3.05A {Nitrosomonas
europaea atcc 19718}
Length = 271
Score = 26.4 bits (58), Expect = 1.7
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 19/61 (31%)
Query: 60 RKDFGLNVEIPPMRLVP-----------------TLPLRLNYILWIEDLLEA--NQISSP 100
+ F + V +P L P T+ +R N +WIED++ Q S
Sbjct: 142 QYSFTMKVIVPVTSLCPCSKKISDYGAHNQRSHVTISVRTNSFIWIEDIIRIAEEQASCE 201
Query: 101 I 101
+
Sbjct: 202 L 202
>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix,
transcription factor, CAMP-B proteins, CAMP receptor
protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP:
a.4.5.4 b.82.3.2
Length = 207
Score = 26.4 bits (59), Expect = 1.7
Identities = 5/25 (20%), Positives = 14/25 (56%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLK 42
F++L+ + E L +++ +L+
Sbjct: 99 KFRELSQQDSEILYTLGSQMADRLR 123
>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural
genomics, joint center for structural genomics, JCSG;
HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}
Length = 231
Score = 26.5 bits (59), Expect = 1.8
Identities = 4/26 (15%), Positives = 12/26 (46%)
Query: 17 PDFKQLAIEYPEFRKHLHQELSGKLK 42
F+ + +P +L + L+ ++
Sbjct: 110 EHFELILRRHPRVLWNLAEMLARRVT 135
>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration;
HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP:
a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A*
3e5q_A 2h6b_A* 2h6c_A
Length = 250
Score = 26.1 bits (58), Expect = 2.3
Identities = 1/25 (4%), Positives = 7/25 (28%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLK 42
+ + + + + K+
Sbjct: 111 SLRTVFRTDEDMIFEIFKNYLTKVA 135
>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 = 25.7 bits (57), Expect = 3.1
Identities = 6/25 (24%), Positives = 11/25 (44%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLK 42
+F ++ EYP R+ +L
Sbjct: 172 NFNEVLEEYPMMRRAFETVAIDRLD 196
>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA
transcription regulator, DNA binding protein; HET: HEM;
2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*
Length = 220
Score = 25.7 bits (57), Expect = 3.6
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLK 42
+F+ + +E+P F ++ + L LK
Sbjct: 101 NFQNIVVEFPAFSLNMVKVLGDLLK 125
>2cxa_A Leucyl/phenylalanyl-tRNA-protein transferase; aminoacyl-tRNA,
protein degradation, structural genomics, NPPSFA; HET:
MSE; 1.60A {Escherichia coli} SCOP: d.108.1.6 PDB:
2dps_A 2dpt_A* 2z3o_A* 2z3k_A* 2z3l_A* 2z3m_A* 2z3n_A*
2z3p_A*
Length = 256
Score = 25.4 bits (55), Expect = 4.1
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 23 AIEYP--EFRKHLHQELSGKLKFNFQNPDAL 51
A E P ++ +L+Q G+L NF P L
Sbjct: 216 ACEIPRRDYLNYLNQMRLGRLPNNFWVPRCL 246
>3hpe_A Conserved hypothetical secreted protein; HP1286, erucamide,
fatty-acid binding; HET: ERU; 2.10A {Helicobacter
pylori}
Length = 164
Score = 25.4 bits (56), Expect = 4.3
Identities = 5/19 (26%), Positives = 7/19 (36%)
Query: 54 FTTTLLRKDFGLNVEIPPM 72
+ RKDFG+
Sbjct: 130 AEGKINRKDFGIGKTFSDA 148
>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription,
transcription regulation; HET: BOG; 1.90A {Anabaena}
PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*
Length = 243
Score = 25.4 bits (56), Expect = 4.3
Identities = 6/25 (24%), Positives = 11/25 (44%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLK 42
+Q E PE + + LS ++
Sbjct: 127 QVEQALKENPELSMLMLRGLSSRIL 151
>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 = 25.4 bits (56), Expect = 4.5
Identities = 4/25 (16%), Positives = 11/25 (44%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLK 42
+ K+L + ++ Q L ++
Sbjct: 102 ELKELLSKNLTHFFYVFQTLQKQVS 126
>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 = 25.3 bits (56), Expect = 4.8
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 18 DFKQLAIEYPEFRKHLHQE 36
F Q+ E+P RK + +
Sbjct: 172 HFNQVLDEFPAMRKTMEEI 190
>1ft9_A Carbon monoxide oxidation system transcription regulator; heme
sensor, catabolite gene activator protein; HET: HEM;
2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1
Length = 222
Score = 24.9 bits (55), Expect = 5.4
Identities = 6/25 (24%), Positives = 7/25 (28%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLK 42
F+Q P L L L
Sbjct: 97 TFEQKLQTCPSMAWGLIAILGRALT 121
>1wub_A Conserved hypothetical protein TT1927B; beta-barrel, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; HET: OTP; 1.65A {Thermus thermophilus}
SCOP: b.61.6.1
Length = 178
Score = 25.0 bits (55), Expect = 5.6
Identities = 4/13 (30%), Positives = 7/13 (53%)
Query: 54 FTTTLLRKDFGLN 66
+ + RKD+ L
Sbjct: 133 ASGQINRKDWNLT 145
>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 = 24.6 bits (54), Expect = 7.1
Identities = 5/25 (20%), Positives = 9/25 (36%)
Query: 18 DFKQLAIEYPEFRKHLHQELSGKLK 42
DF+ L PE + + +
Sbjct: 109 DFQMLCSSSPEIAEIFRKTALERRG 133
>3fwm_A Penicillin-binding protein 1B; bacterial cell WALL synthesis,
antibiotics design, transferase, hydrolase; HET: M0E;
2.16A {Escherichia coli} PDB: 3fwl_A* 3vma_A*
Length = 751
Score = 25.0 bits (55), Expect = 7.3
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 20 KQLAIEYPEFRKHLHQELSGKLKFNFQNPDALRIFTT 56
+ P F + + QEL KL ++ ++IFTT
Sbjct: 352 GGVISPQPAFMQLVRQELQAKLGDKVKDLSGVKIFTT 388
>3q34_A YCEI-like family protein; structural genomics, PSI-2, protein
structure initiative, NE SGX research center for
structural genomics, nysgxrc; HET: UQ8; 1.70A
{Pseudomonas syringae}
Length = 184
Score = 24.5 bits (53), Expect = 7.9
Identities = 7/53 (13%), Positives = 17/53 (32%), Gaps = 6/53 (11%)
Query: 33 LH---QELSGKLKFNFQNPDALRIFT---TTLLRKDFGLNVEIPPMRLVPTLP 79
L + +L + ++ T + +DF + + +R L
Sbjct: 107 LRGKSHSYNAELLATRLDERRFQVVTLEPLVIHAQDFDMVSDFNALRNAAGLS 159
>2eef_A Protein phosphatase 1, regulatory (inhibitor) subunit 3B; CBM_21
domain, carbohydrate binding domain, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 156
Score = 24.1 bits (52), Expect = 9.9
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 17 PDFKQLAIEYPEFRKHLHQE 36
DF Q + +Y +FR L +
Sbjct: 15 LDFSQPSADYLDFRNRLQAD 34
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
0.325 0.144 0.438
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: 1,805,232
Number of extensions: 99689
Number of successful extensions: 322
Number of sequences better than 10.0: 1
Number of HSP's gapped: 322
Number of HSP's successfully gapped: 37
Length of query: 109
Length of database: 6,701,793
Length adjustment: 73
Effective length of query: 36
Effective length of database: 4,663,560
Effective search space: 167888160
Effective search space used: 167888160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.4 bits)