RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15420
(187 letters)
>gnl|CDD|219925 pfam08598, Sds3, Sds3-like. Repression of gene transcription is
mediated by histone deacetylases containing
repressor-co-repressor complexes, which are recruited to
promoters of target genes via interactions with
sequence-specific transcription factors. The
co-repressor complex contains a core of at least seven
proteins. This family represents the conserved region
found in Sds3, Dep1 and BRMS1-homologue p40 proteins.
Length = 184
Score = 112 bits (282), Expect = 1e-31
Identities = 70/172 (40%), Positives = 101/172 (58%), Gaps = 12/172 (6%)
Query: 11 LREQLYRERIVEVESKLNEVELGQAKEYLLPLQKLQDNMRIRTEVAAILRQYKLNNVQNQ 70
LR+QLYRER+ +++++L + G EYL PL+ L++ R +VA + R+YKL ++ +
Sbjct: 17 LRDQLYRERLAQLQTELELLLQGTHPEYLEPLKDLEERRDDRLKVAELRREYKLECIERE 76
Query: 71 YNAEEQATRQNLENEKSLLYDHMKEELEEKIRRLEEDRNSVDINADLWFFEHNKRGSNQN 130
Y AE QA +Q E EK LL + + EELEEKI RLEE+R S+DI + GS+ N
Sbjct: 77 YEAERQAAKQEFEKEKRLLRERLLEELEEKIYRLEEERRSLDITDSDYGLL----GSHPN 132
Query: 131 PLSSK--RGPKGFNRMKSRRKAVTVSG------PYIVYMLRDEEIIEDWTII 174
+ K R + R+K S PYI+YML++EEI+ED T I
Sbjct: 133 RRTRKLRRRVNSPELVAKRKKKNNESSDLSGLAPYILYMLKEEEILEDLTAI 184
>gnl|CDD|234575 PRK00016, PRK00016, metal-binding heat shock protein; Provisional.
Length = 159
Score = 31.0 bits (71), Expect = 0.21
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 12/47 (25%)
Query: 73 AEEQATRQN--LENEKSLL----------YDHMKEELEEKIRRLEED 107
AEEQA Q LE E + L YDH+++E E++ LEE+
Sbjct: 98 AEEQAEEQGHSLERELAHLTVHGILHLLGYDHIEDEEAEEMFGLEEE 144
>gnl|CDD|223396 COG0319, COG0319, Predicted metal-dependent hydrolase [General
function prediction only].
Length = 153
Score = 30.7 bits (70), Expect = 0.22
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 12/47 (25%)
Query: 73 AEEQATRQN--LENEKSLL----------YDHMKEELEEKIRRLEED 107
AEEQA Q LE E + L YDH ++E EE++ LEE+
Sbjct: 93 AEEQAKEQGHSLERELAHLTIHGILHLLGYDHEEDEEEEEMEELEEE 139
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 30.3 bits (69), Expect = 0.64
Identities = 25/117 (21%), Positives = 49/117 (41%), Gaps = 26/117 (22%)
Query: 11 LREQLYRERIVEVESKLNEVE-----LGQAKEYLLPLQKLQDNMRI-RTEVAAILRQYKL 64
L+E+L ER+ ++ S L ++ L L PL++ + + + E + +L
Sbjct: 36 LKEELSNERLRKLRSLLTKLSEALDKLRSYLPKLNPLREEKKKVSVKSLEELIKDVEEEL 95
Query: 65 NNVQNQYNAEEQATRQNLENEKSLLYDHMKEELEEKIRRLEEDRNSV----DINADL 117
++ + LE E S ELE +I+ LE++ + + + DL
Sbjct: 96 EKIEKEIKE--------LEEEIS--------ELENEIKELEQEIERLEPWGNFDLDL 136
>gnl|CDD|225937 COG3402, COG3402, Uncharacterized conserved protein [Function
unknown].
Length = 161
Score = 29.3 bits (66), Expect = 0.80
Identities = 27/107 (25%), Positives = 49/107 (45%), Gaps = 11/107 (10%)
Query: 5 SFVPVGLREQLYRERIVEVESKLNEVELGQAK----EYLLPLQKLQDNMRIRTEVAAILR 60
+ V + + QL R R+ E + +E+++ ++P ++Q + TE +LR
Sbjct: 61 AVVTLFIIPQLVRYRVWRYEVEEDELDIQHGILVRTRTVIPYVRVQ---HVDTEQGPLLR 117
Query: 61 QYKLNNVQNQYNAEEQATRQNLENEKSLLYDHMKEELEEKIRRLEED 107
+Y L V A T + L+ E++ D ++E L R EED
Sbjct: 118 RYGLATVT-ITTASSDHTIEALDREEA---DRLRERLANLARVREED 160
>gnl|CDD|233050 TIGR00609, recB, exodeoxyribonuclease V, beta subunit. The RecBCD
holoenzyme is a multifunctional nuclease with potent
ATP-dependent exodeoxyribonuclease activity. Ejection of
RecD, as occurs at chi recombinational hotspots,
cripples exonuclease activity in favor of recombinagenic
helicase activity. All proteins in this family for which
functions are known are DNA-DNA helicases that are used
as part of an exonuclease-helicase complex (made up of
RecBCD homologs) that function to generate substrates
for the initiation of recombination and recombinational
repair. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1087
Score = 30.1 bits (68), Expect = 0.84
Identities = 16/43 (37%), Positives = 18/43 (41%), Gaps = 5/43 (11%)
Query: 76 QATRQNLENEKSLLYDHMK-----EELEEKIRRLEEDRNSVDI 113
Q N+ SLL EE EE+I RLE D V I
Sbjct: 613 QEAAHQERNKLSLLRWLEDQISNEEEEEEEIIRLESDAELVKI 655
>gnl|CDD|146097 pfam03290, Peptidase_C57, Vaccinia virus I7 processing peptidase.
Length = 423
Score = 28.1 bits (63), Expect = 2.7
Identities = 10/55 (18%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 5 SFVPVGLREQLYRERIVEVESKLNEVELGQAKEYLLPLQ----KLQDNMRIRTEV 55
S +P+ + +L ++ + +N EL + + L+ +QD + T +
Sbjct: 61 SCIPISILLELVNRGVLSAPNDINNDELAIKRALVNELKDKYINIQDIFTLPTSI 115
>gnl|CDD|221371 pfam12004, DUF3498, Domain of unknown function (DUF3498). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 433 to 538 amino acids in length. This domain is
found associated with pfam00616, pfam00168. This domain
has two conserved sequence motifs: DLQ and PLSFQNP.
Length = 489
Score = 28.1 bits (62), Expect = 2.8
Identities = 22/90 (24%), Positives = 44/90 (48%), Gaps = 15/90 (16%)
Query: 22 EVESKLNEVELGQAKEYLLPLQKLQDNMRIRTEVAAILRQYKLNNVQNQYNAEEQATRQN 81
E E++ N E QA++Y + +L++ +R+ +V+ E + Q
Sbjct: 352 EYETEENREEGTQAEKYEQEIARLKERLRV--------------SVRRLEEYERRLLGQE 397
Query: 82 LENEKSLL-YDHMKEELEEKIRRLEEDRNS 110
+ +K L Y E+ EE++RR +E+++S
Sbjct: 398 QQMQKLLQEYQARLEDSEERLRRQQEEKDS 427
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 28.1 bits (63), Expect = 2.9
Identities = 24/95 (25%), Positives = 48/95 (50%), Gaps = 3/95 (3%)
Query: 17 RERIVEVESKLNEVELGQAKEYLLPLQKLQDNMRIRTEVAAILRQYKLNNVQNQYNAEEQ 76
+E+ E+ SKL E EL E + Q + E + ++Y+ ++ + + +
Sbjct: 195 KEKREELLSKLEE-ELLARLESKEAALEKQLRLEFEREKEELRKKYE-EKLRQELERQAE 252
Query: 77 ATRQNLENEKSLLYDHMKEELEEKIR-RLEEDRNS 110
A Q L+NE +L ++ E ++I+ ++EE+RN
Sbjct: 253 AHEQKLKNELALQAIELQREFNKEIKEKVEEERNG 287
Score = 28.1 bits (63), Expect = 3.6
Identities = 18/89 (20%), Positives = 40/89 (44%), Gaps = 6/89 (6%)
Query: 18 ERIVEVESKLNEVELGQAKEYLLPLQKLQDNMRIRTEVAAILRQYKLNNVQNQYNAEEQA 77
E + ++ KL E++ + +E L++ ++ + + +L + + A E+
Sbjct: 170 EELDQLSKKLAELKAEEEEELERALKEKREEL-LSKLEEELLARLESKEA-----ALEKQ 223
Query: 78 TRQNLENEKSLLYDHMKEELEEKIRRLEE 106
R E EK L +E+L +++ R E
Sbjct: 224 LRLEFEREKEELRKKYEEKLRQELERQAE 252
>gnl|CDD|182106 PRK09841, PRK09841, cryptic autophosphorylating protein tyrosine
kinase Etk; Provisional.
Length = 726
Score = 28.0 bits (62), Expect = 3.7
Identities = 31/81 (38%), Positives = 43/81 (53%), Gaps = 10/81 (12%)
Query: 31 ELGQAKEYLLPLQKLQDNMRIRTEVAAILRQYKLNNVQNQYNAEEQATRQNLENEKSLLY 90
EL QA+E L ++ +D++ + E A+L Q + NV NQ N E R E E S LY
Sbjct: 282 ELDQAEEKLNVYRQQRDSVDLNLEAKAVLEQ--IVNVDNQLN--ELTFR---EAEISQLY 334
Query: 91 --DH-MKEELEEKIRRLEEDR 108
DH L EK + LE++R
Sbjct: 335 KKDHPTYRALLEKRQTLEQER 355
>gnl|CDD|179953 PRK05174, PRK05174, 3-hydroxydecanoyl-(acyl carrier protein)
dehydratase; Validated.
Length = 172
Score = 27.1 bits (61), Expect = 3.8
Identities = 8/10 (80%), Positives = 8/10 (80%)
Query: 112 DINADLWFFE 121
DIN DLWFF
Sbjct: 60 DINPDLWFFG 69
>gnl|CDD|216059 pfam00685, Sulfotransfer_1, Sulfotransferase domain.
Length = 254
Score = 27.3 bits (61), Expect = 4.3
Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 7/61 (11%)
Query: 90 YDHMKEELEEKIRRLEE------DRNSVDINADLWFFEHNK-RGSNQNPLSSKRGPKGFN 142
Y+ +K++ +I+++ E +D FE+ K K F
Sbjct: 163 YEDLKKDPRGEIKKIAEFLGIPLTEEELDKIVKHLSFENMKGNPCLNYSKLPKHEVSPFF 222
Query: 143 R 143
R
Sbjct: 223 R 223
>gnl|CDD|216162 pfam00866, Ring_hydroxyl_B, Ring hydroxylating beta subunit. This
subunit has a similar structure to NTF-2 and scytalone
dehydratase.
Length = 145
Score = 26.8 bits (60), Expect = 4.4
Identities = 8/36 (22%), Positives = 18/36 (50%)
Query: 74 EEQATRQNLENEKSLLYDHMKEELEEKIRRLEEDRN 109
++ ++E S ++D + LE+++ RL R
Sbjct: 31 TRTRRDRDPQSEASAIFDDDRRGLEDRVFRLRTGRA 66
>gnl|CDD|172675 PRK14187, PRK14187, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 294
Score = 27.5 bits (61), Expect = 4.7
Identities = 19/73 (26%), Positives = 29/73 (39%), Gaps = 1/73 (1%)
Query: 72 NAEEQATRQNLENEKSLLYDHMKE-ELEEKIRRLEEDRNSVDINADLWFFEHNKRGSNQN 130
N + +A L +E LL + E L EKI L D + I L H + N
Sbjct: 52 NKQRKAEMLGLRSETILLPSTISESSLIEKINELNNDDSVHGILVQLPVPNHIDKNLIIN 111
Query: 131 PLSSKRGPKGFNR 143
+ ++ GF+
Sbjct: 112 TIDPEKDVDGFHN 124
>gnl|CDD|234644 PRK00115, hemE, uroporphyrinogen decarboxylase; Validated.
Length = 346
Score = 27.0 bits (61), Expect = 5.7
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 10/44 (22%)
Query: 30 VELGQAKEYLLPLQKLQDNM----------RIRTEVAAILRQYK 63
V+L +A+ + + LQ N+ I EV AIL
Sbjct: 270 VDLAEARRRVGDKKALQGNLDPAVLLAPPEAIEEEVRAILDGGG 313
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 27.4 bits (61), Expect = 5.9
Identities = 23/116 (19%), Positives = 39/116 (33%), Gaps = 24/116 (20%)
Query: 16 YRERIVEVESKLNEVE-------------------LGQAKEYLLPLQKLQDNMRIRTEVA 56
Y+ER E E KL E L + E Q+L+ +R
Sbjct: 170 YKERKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELAL 229
Query: 57 AILRQYKLNNVQNQYNAEEQATRQNLENEKSLLYDHMKEELEEKIRRLEEDRNSVD 112
+ + +L + E + LE + L EE E++I L+ + +
Sbjct: 230 LLAKLKELRKELEELEEELSRLEEELEELQEEL-----EEAEKEIEELKSELEELR 280
Score = 27.0 bits (60), Expect = 6.7
Identities = 19/98 (19%), Positives = 38/98 (38%), Gaps = 4/98 (4%)
Query: 12 REQLYRERIVEVESKLNEVELGQAKEYLLPLQKLQDNMRIRTEVAAILRQYKLNNVQNQY 71
+ E++ E+E +L E+E + E L + + + E + + ++ +
Sbjct: 836 EIEELEEKLDELEEELEELE--KELEELKEELEELEAEKEELEDELKELEEEKEELEEEL 893
Query: 72 NAEEQATRQNLENEKSLLYDHMKEELEEKIRRLEEDRN 109
E + E+ EELE K+ RLE +
Sbjct: 894 --RELESELAELKEEIEKLRERLEELEAKLERLEVELP 929
>gnl|CDD|232796 TIGR00043, TIGR00043, probable rRNA maturation factor YbeY. This
metalloprotein family is represented by a single member
sequence only in nearly every bacterium. Crystallography
demonstrated metal-binding activity, possibly to nickel.
It is a predicted to be a metallohydrolase, and more
recently it was shown that mutants have a ribosomal RNA
processing defect [Protein synthesis, Other].
Length = 110
Score = 26.1 bits (58), Expect = 6.7
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 12/46 (26%)
Query: 73 AEEQATRQNLENEKSLL------------YDHMKEELEEKIRRLEE 106
A+EQA E+ L YDH E+ E+++ LEE
Sbjct: 58 AKEQAKEYGHSLERELAHLTVHGLLHLLGYDHETEDEEKEMFALEE 103
>gnl|CDD|181081 PRK07681, PRK07681, aspartate aminotransferase; Provisional.
Length = 399
Score = 27.1 bits (60), Expect = 7.0
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 128 NQNPLSSKRGPKGFN---RMKSRRKAVTVSGPYIVYMLRDEEIIEDWTIIK 175
P+S P + S K+ +++G I YM+ +EEI+ T K
Sbjct: 215 GNKPISFLSVPGAKEVGVEINSLSKSYSLAGSRIGYMIGNEEIVRALTQFK 265
>gnl|CDD|220415 pfam09809, MRP-L27, Mitochondrial ribosomal protein L27. Members
of this family of proteins are components of the
mitochondrial ribosome large subunit. They are also
involved in apoptosis and cell cycle regulation.
Length = 113
Score = 25.8 bits (57), Expect = 7.2
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 124 KRGSNQNPLSSKRGPKGFNRMKSRRKAVTVSGPYIVYMLRDEEIIEDWTII 174
K G+ + PL+SKRG K F K R SG I + W +
Sbjct: 1 KGGNRRFPLTSKRGNKTFY--KGRG----ASG--IGRHTSSGRYVIIWEKV 43
>gnl|CDD|221819 pfam12869, tRNA_anti-like, tRNA_anti-like. This is a family of
bacterial, archeael and viral proteins that is related
to the tRNA_anti family pfam01336. The major
characteristic of families like tRNA_anti is their
OB-fold, and many of them bind DNA.
Length = 143
Score = 26.3 bits (58), Expect = 7.3
Identities = 9/40 (22%), Positives = 20/40 (50%)
Query: 13 EQLYRERIVEVESKLNEVELGQAKEYLLPLQKLQDNMRIR 52
+Q Y +I+EV + E+ G+ Y++ L+ + +
Sbjct: 60 DQKYLGKIIEVSGTITEITKGEGDNYIVLLRTESNFAGVL 99
>gnl|CDD|234775 PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
Length = 588
Score = 27.0 bits (61), Expect = 8.2
Identities = 5/19 (26%), Positives = 15/19 (78%)
Query: 44 KLQDNMRIRTEVAAILRQY 62
++Q N+++R++V + +R +
Sbjct: 136 EMQKNLKLRSKVTSAIRNF 154
>gnl|CDD|220844 pfam10675, DUF2489, Protein of unknown function (DUF2489). This is
a bacterial family of uncharacterized proteins.
Length = 131
Score = 26.0 bits (58), Expect = 8.7
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 163 RDEEIIEDWTIIKKAMSQRKCDLT 186
R I+E II +AM Q +C+L+
Sbjct: 33 RRARILESIRIIARAMLQEQCELS 56
>gnl|CDD|216891 pfam02130, UPF0054, Uncharacterized protein family UPF0054.
Length = 142
Score = 26.1 bits (58), Expect = 9.2
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 12/46 (26%)
Query: 73 AEEQATRQN--LENEKSLL----------YDHMKEELEEKIRRLEE 106
A +A E E + L YDH ++E E++ LEE
Sbjct: 90 AAREAKEYGHSFERELAHLLVHGLLHLLGYDHEEDEEAEEMEALEE 135
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
0.316 0.133 0.372
Gapped
Lambda K H
0.267 0.0749 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,556,525
Number of extensions: 889387
Number of successful extensions: 1616
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1575
Number of HSP's successfully gapped: 174
Length of query: 187
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 96
Effective length of database: 6,901,388
Effective search space: 662533248
Effective search space used: 662533248
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: 56 (25.3 bits)