RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5648
(327 letters)
>gnl|CDD|219280 pfam07052, Hep_59, Hepatocellular carcinoma-associated antigen 59.
This family represents a conserved region approximately
100 residues long within mammalian hepatocellular
carcinoma-associated antigen 59 and similar proteins.
Family members are found in a variety of eukaryotes,
mainly as hypothetical proteins.
Length = 102
Score = 133 bits (337), Expect = 3e-39
Identities = 56/106 (52%), Positives = 73/106 (68%), Gaps = 4/106 (3%)
Query: 121 TQFSAETNKRDEDEEMMKYIEEQLSKRKKGEETKEGGQGEEGGVNYCSPEEAALQAVPDH 180
+F+ ET +RDED MMKYIEE+L+KRK G+ + + N E L A+P+H
Sbjct: 1 DRFTKETGQRDEDAHMMKYIEEELAKRK-GQAADADAEDSDKAANNLKRAEDELYALPEH 59
Query: 181 LRQSSTHQSEEMLSNQMLSGIPEVDLGIEAKIRNIEATEEAKLKLL 226
L+ ++EEMLSNQML GIPEVDLGIEAK++NIE TE+AK +LL
Sbjct: 60 LK---VKKNEEMLSNQMLGGIPEVDLGIEAKLKNIERTEKAKRRLL 102
>gnl|CDD|177199 MTH00141, COX3, cytochrome c oxidase subunit III; Provisional.
Length = 259
Score = 33.7 bits (78), Expect = 0.097
Identities = 15/40 (37%), Positives = 16/40 (40%), Gaps = 12/40 (30%)
Query: 270 VYFLLLQYSEAILVMRKYCNWSKF-FADGTY---FFASVG 305
VYF LQ E Y + F ADG Y FF G
Sbjct: 169 VYFTFLQAGE-------YY-EASFSIADGVYGSTFFVLTG 200
>gnl|CDD|150575 pfam09919, DUF2149, Uncharacterized conserved protein (DUF2149).
This domain, found in various hypothetical prokaryotic
proteins, has no known function.
Length = 91
Score = 30.7 bits (70), Expect = 0.26
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 123 FSAE--TNKRDEDEEMMKYIEEQLSKRKKGEETKE--GGQGEEGGVNY 166
S E T ++ + M+ IE++ + K+ +ET + GG+GE G Y
Sbjct: 32 LSDEDVTIVKNPGKPDMEIIEKKGKEIKRYKETGQDGGGEGERLGTAY 79
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 31.5 bits (72), Expect = 0.71
Identities = 27/100 (27%), Positives = 37/100 (37%), Gaps = 24/100 (24%)
Query: 36 SEEEDSEEEMEALKKLEEMKSLQKLRQRPNGVSIISLTVGEKVAEEDELLVKDPFKIKSG 95
+EEE ++EE E LKKLE ++LR R G + EED D
Sbjct: 259 TEEELAKEEAERLKKLEA----ERLR-RMRGE------EEDDEEEEDSKESAD------- 300
Query: 96 GLVNMSALKSGQVKKVDDAYDTGIGTQFSAETNKRDEDEE 135
L DD + G G + E +DE+
Sbjct: 301 ------DLDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDED 334
>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572). Family of
eukaryotic proteins with undetermined function.
Length = 321
Score = 30.5 bits (69), Expect = 1.1
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 37 EEEDSEEEMEALKKLEEMKSLQKLRQ 62
DS+ EME L++LEE+K LQ R
Sbjct: 140 RTADSKREMEVLERLEELKELQSRRA 165
>gnl|CDD|223068 PHA03384, PHA03384, early DNA-binding protein E2A; Provisional.
Length = 445
Score = 30.4 bits (69), Expect = 1.2
Identities = 20/89 (22%), Positives = 30/89 (33%), Gaps = 2/89 (2%)
Query: 1 MSEEGSSQHI--KSEDSSPQPIKFKSRKKNLRTRKDSSEEEDSEEEMEALKKLEEMKSLQ 58
M GSS S+DS KK R R EEE+ EEE E + ++
Sbjct: 1 MRGRGSSSDSPYSSDDSPSLEPPELPPKKKGRRRVSPVEEEEEEEEAEVVAVGFSYPPVR 60
Query: 59 KLRQRPNGVSIISLTVGEKVAEEDELLVK 87
R + + L + ++
Sbjct: 61 ISRGKDGKRPVRPLKEEKDSEKKASTEAA 89
>gnl|CDD|224400 COG1483, COG1483, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 774
Score = 30.5 bits (69), Expect = 1.5
Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 1/62 (1%)
Query: 22 FKSRKKNLRTRKDSSEEEDSEEEMEALKKL-EEMKSLQKLRQRPNGVSIISLTVGEKVAE 80
+ + ++ ++ E E +E ++ + EE SL K R +P ++ G+
Sbjct: 499 SERVESSVEELIETREGEVIDELVKKKDEFVEEGLSLAKRRGKPPEDHVLFFKAGDVNVA 558
Query: 81 ED 82
E
Sbjct: 559 EI 560
>gnl|CDD|215961 pfam00510, COX3, Cytochrome c oxidase subunit III.
Length = 258
Score = 29.5 bits (67), Expect = 1.8
Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 10/39 (25%)
Query: 270 VYFLLLQYSEAILVMRKYCNWSKFFADGTY---FFASVG 305
VYF LQ E Y +DG Y FF + G
Sbjct: 168 VYFTGLQAYE-------YYEAPFTISDGVYGSTFFMATG 199
>gnl|CDD|238834 cd01665, Cyt_c_Oxidase_III, Cytochrome c oxidase subunit III.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is a
multi-chain transmembrane protein located in the inner
membrane of mitochondria and the cell membrane of
prokaryotes. CcO catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in bacteria
and up to 13 in mammalian mitochondria. Only subunits I
and II are essential for function, but subunit III,
which is also conserved, is believed to play a role in
assembly of the multimer complex. Rhodobacter CcO
subunit III stabilizes the integrity of the binuclear
center in subunit I. Subunits I, II, and III of
mammalian CcO are encoded within the mitochondrial
genome and the remaining 10 subunits are encoded within
the nuclear genome. Subunit III contains bound
phospholipids in several crystal structures and is
proposed to contain a "lipid pool." These phospholipids
are believed to intrinsic constituents similar to
cofactors of the enzyme.
Length = 243
Score = 29.0 bits (66), Expect = 2.8
Identities = 15/50 (30%), Positives = 17/50 (34%), Gaps = 18/50 (36%)
Query: 270 VYFLLLQYSEAILVMRKYCNWSKF-FADGTY---FFASVGNSGENHFAGF 315
VYF LQ E Y + F +D Y FF G F G
Sbjct: 155 VYFTGLQAYE-------Y-YEASFTISDSVYGSTFFMLTG------FHGL 190
>gnl|CDD|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed.
Length = 925
Score = 29.6 bits (67), Expect = 3.0
Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 83 ELLVKDPFKIKSGGLVNMSALKSGQVKKVDDAYDTGIGTQFSAETNKRDEDEEMMKYIEE 142
E ++K+ F I +N L V+ ++D +FS + + EE+ +Y+ E
Sbjct: 631 EQILKNSFIILKNNTINYKEL----VEFLNDNLLRITHFKFSEKDFENYHKEELAQYLIE 686
Query: 143 QLSK 146
L++
Sbjct: 687 ALNE 690
>gnl|CDD|177238 MTH00189, COX3, cytochrome c oxidase subunit III; Provisional.
Length = 260
Score = 28.8 bits (65), Expect = 3.2
Identities = 16/49 (32%), Positives = 17/49 (34%), Gaps = 16/49 (32%)
Query: 270 VYFLLLQYSEAILVMRKYCNWSKFFADGTY---FFASVGNSGENHFAGF 315
VYF LLQ E Y AD Y FF + G F G
Sbjct: 170 VYFTLLQAME-------YYEAPFTIADSVYGSTFFVATG------FHGL 205
>gnl|CDD|217072 pfam02503, PP_kinase, Polyphosphate kinase middle domain.
Polyphosphate kinase (Ppk) catalyzes the formation of
polyphosphate from ATP, with chain lengths of up to a
thousand or more orthophosphate molecules.
Length = 204
Score = 28.2 bits (64), Expect = 4.3
Identities = 9/21 (42%), Positives = 18/21 (85%)
Query: 131 DEDEEMMKYIEEQLSKRKKGE 151
+E E++++ IE++L KR++GE
Sbjct: 118 EEAEDLLEAIEKELKKRRRGE 138
>gnl|CDD|218143 pfam04551, GcpE, GcpE protein. In a variety of organisms,
including plants and several eubacteria, isoprenoids are
synthesised by the mevalonate-independent
2-C-methyl-D-erythritol 4-phosphate (MEP) pathway.
Although different enzymes of this pathway have been
described, the terminal biosynthetic steps of the MEP
pathway have not been fully elucidated. GcpE gene of
Escherichia coli is involved in this pathway.
Length = 345
Score = 28.2 bits (64), Expect = 5.9
Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 15/64 (23%)
Query: 39 EDSEEEMEALKKLEEMKSLQKLRQRPNGVSIISL-TVG------EKVAEEDELLV---KD 88
ED EE++ ++ LQ L R GV IIS T G KVA+E E + K
Sbjct: 231 EDPVEEVKVAFEI-----LQSLGLRKRGVEIISCPTCGRTLFDLIKVAKEVEERLSHLKK 285
Query: 89 PFKI 92
P K+
Sbjct: 286 PLKV 289
>gnl|CDD|183573 PRK12524, PRK12524, RNA polymerase sigma factor; Provisional.
Length = 196
Score = 27.5 bits (61), Expect = 7.8
Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 2/40 (5%)
Query: 171 EAALQAVPDHLRQSSTHQSEEMLSNQMLSGIPEVDLGIEA 210
+AAL A+P+ RQ+ + E LSN ++ + E+ G+EA
Sbjct: 131 DAALAALPERQRQAVVLRHIEGLSNPEIAEVMEI--GVEA 168
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.311 0.129 0.361
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,511,226
Number of extensions: 1606093
Number of successful extensions: 1899
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1870
Number of HSP's successfully gapped: 83
Length of query: 327
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 230
Effective length of database: 6,635,264
Effective search space: 1526110720
Effective search space used: 1526110720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 59 (26.6 bits)