RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1109
(79 letters)
>1v54_G Cytochrome C oxidase polypeptide VIA-heart; oxidoreductase; HET:
FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos
taurus} SCOP: f.23.2.1 PDB: 1v55_G* 2dyr_G* 2dys_G*
2eij_G* 2eik_G* 2eil_G* 2eim_G* 2ein_G* 2zxw_G* 3abk_G*
3abl_G* 3abm_G* 3ag1_G* 3ag2_G* 3ag3_G* 3ag4_G* 3asn_G*
3aso_G* 2occ_G* 1oco_G* ...
Length = 85
Score = 63.3 bits (154), Expect = 2e-15
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 18 AMKSSAGNPDAVKLWRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
+ + WR LT+ ALP AL + +L H RP F+ +L IR
Sbjct: 2 SAAKGDHGGTGARTWRFLTFGLALPSVALCTLNSWLHS----GHRERPAFIPYHHLRIRT 57
Query: 78 RN 79
+
Sbjct: 58 KP 59
>2y69_G Cytochrome C oxidase polypeptide 6A2; electron transport, complex
IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK
PGV DMU; 1.95A {Bos taurus}
Length = 97
Score = 63.4 bits (154), Expect = 3e-15
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 7/69 (10%)
Query: 14 STSPAMKSSAGN---PDAVKLWRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKR 70
S S + S+A + WR LT+ ALP AL + +L H RP F+
Sbjct: 7 SLSRGLASAAKGDHGGTGARTWRFLTFGLALPSVALCTLNSWLHS----GHRERPAFIPY 62
Query: 71 EYLYIRNRN 79
+L IR +
Sbjct: 63 HHLRIRTKP 71
>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA
binding, DNA repair, mismatch recognition; HET: DNA ADP;
2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12
c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A*
1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*
Length = 800
Score = 25.1 bits (56), Expect = 3.0
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 49 VYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
V V L +A ++ P F+ + + I
Sbjct: 554 VLVNLAERAYTLNYTCPTFIDKPGIRITE 582
>1vlo_A Aminomethyltransferase; NP417381, tetrahydrofolat dependent) of
glycine cleavage system, structural genomics, protein
structure initiative; HET: MSE; 1.70A {Escherichia coli
K12} SCOP: b.44.2.1 d.250.1.1 PDB: 3a8j_A* 3a8i_A*
3a8k_A*
Length = 381
Score = 24.8 bits (55), Expect = 3.1
Identities = 8/19 (42%), Positives = 8/19 (42%)
Query: 25 NPDAVKLWRNLTYFGALPC 43
N A WR L G PC
Sbjct: 213 NEKAADFWRALVEAGVKPC 231
>3ukm_A Potassium channel subfamily K member 1; membrane protein,
eukaryotic, two-pore DO potassium channel, K2P channel,
membrane; HET: UND; 3.40A {Homo sapiens}
Length = 280
Score = 24.0 bits (51), Expect = 5.8
Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 8/56 (14%)
Query: 30 KLWRNLTYFGALPCC----ALVG--VYVYLEHQAEEEHHVRPEFVKREYLYIRNRN 79
+ + T FG L + G V+ +E E+ +R E K + ++
Sbjct: 5 EASNSATMFGFLVLGYLLYLVFGAVVFSSVELPYEDL--LRQELRKLKRRFLEEHE 58
>3um7_A Potassium channel subfamily K member 4; potassium ION channel,
metal transport; 3.31A {Homo sapiens}
Length = 309
Score = 24.0 bits (51), Expect = 7.0
Identities = 13/71 (18%), Positives = 22/71 (30%), Gaps = 5/71 (7%)
Query: 14 STSPAMKSSAGNPDAVKLWRNLTYFGALPCC---ALVG--VYVYLEHQAEEEHHVRPEFV 68
P S P + R+ T L + G V+ LE E++ V
Sbjct: 9 PARPLQAGSGAGPAPGRAMRSTTLLALLALVLLYLVSGALVFRALEQPHEQQAQRELGEV 68
Query: 69 KREYLYIRNRN 79
+ ++L
Sbjct: 69 REKFLRAHPCV 79
>2vat_A Acetyl-COA--deacetylcephalosporin C acetyltransferase; A/B-
hydrolase fold, acyltransferase, acetyl coenzyme A,
antibiotic biosynthesis; HET: COA; 2.2A {Acremonium
chrysogenum} SCOP: c.69.1.40 PDB: 2vav_A* 2vax_A*
Length = 444
Score = 23.5 bits (51), Expect = 9.0
Identities = 10/74 (13%), Positives = 21/74 (28%), Gaps = 14/74 (18%)
Query: 9 MMRKFSTSPAMKSSAGNPDAVKLWRNLTYFGALPCCALVGVYV---YLEHQAEEEHHVRP 65
M +F +P +++ A + YL +QA+
Sbjct: 290 MDERFHMAPGVQAGRNISSQDAKKEINGTDSGNSHRAGQPIEAVSSYLRYQAQ------- 342
Query: 66 EFVKR----EYLYI 75
+F Y+ +
Sbjct: 343 KFAASFDANCYIAM 356
>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch
recognition, mismatched unpaired DNA binding protein-DNA
complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B*
3thy_B* 3thz_B*
Length = 918
Score = 23.7 bits (52), Expect = 9.3
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 57 AEEEHHVRPEFVKREYLYIRN 77
A++ + RP + + I+N
Sbjct: 625 AKQGDYCRPTVQEERKIVIKN 645
>2z3y_A Lysine-specific histone demethylase 1; chromatin, nucleosome,
transcription, LSD1, alternative splicing, chromatin
regulator, coiled coil; HET: F2N; 2.25A {Homo sapiens}
SCOP: a.4.1.18 c.3.1.2 d.16.1.5 PDB: 2ejr_A* 2z5u_A*
3abt_A* 3abu_A* 2y48_A* 2v1d_A* 2h94_A* 2iw5_A* 2uxn_A*
2uxx_A* 2hko_A* 2dw4_A* 2x0l_A* 2l3d_A
Length = 662
Score = 23.7 bits (50), Expect = 9.4
Identities = 7/27 (25%), Positives = 12/27 (44%), Gaps = 6/27 (22%)
Query: 58 EEEHHVRPEFVKRE------YLYIRNR 78
+E P+ + +L+IRNR
Sbjct: 19 SQEAACFPDIISGPQQTQKVFLFIRNR 45
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
0.323 0.134 0.416
Gapped
Lambda K H
0.267 0.0481 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,278,922
Number of extensions: 61186
Number of successful extensions: 133
Number of sequences better than 10.0: 1
Number of HSP's gapped: 131
Number of HSP's successfully gapped: 11
Length of query: 79
Length of database: 6,701,793
Length adjustment: 48
Effective length of query: 31
Effective length of database: 5,361,585
Effective search space: 166209135
Effective search space used: 166209135
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.0 bits)