RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7904
(181 letters)
>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin
remodeling, contains bromodomain [Chromatin structure
and dynamics / Transcription].
Length = 371
Score = 51.7 bits (124), Expect = 3e-08
Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 3/86 (3%)
Query: 25 GFTEIVFCAVNCSVQVLGYGTYMMNHLKEYHKKH---EIYHFLTFAAKDAIGYFTRQGFT 81
F EIVF A+ G G+ +M HLK KK +I L +A AI F +Q F
Sbjct: 100 RFDEIVFLAIESVTPESGLGSLLMAHLKTSVKKRKTPKIEDELLYADNKAIAKFKKQLFL 159
Query: 82 KDIKLPKHLYEGYIKDYEDAMLMHCE 107
+D + ++ G E
Sbjct: 160 RDGRFLSSIFLGLPSKREYPDYYEII 185
>gnl|CDD|216007 pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family. This
family contains proteins with N-acetyltransferase
functions such as Elp3-related proteins.
Length = 80
Score = 41.5 bits (98), Expect = 1e-05
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 3/68 (4%)
Query: 17 CFRMFPTQGFTEIVFCAVNCSVQVLGYGTYMMNHLKEYHKK---HEIYHFLTFAAKDAIG 73
+ EI AV+ + G GT ++ L+EY ++ I + + AI
Sbjct: 13 LSIIDEEGNVAEIEGLAVDPEYRGKGIGTALLEALEEYARELGLKRIELEVLEDNEAAIA 72
Query: 74 YFTRQGFT 81
+ + GF
Sbjct: 73 LYEKLGFK 80
>gnl|CDD|222185 pfam13508, Acetyltransf_7, Acetyltransferase (GNAT) domain. This
domain catalyzes N-acetyltransferase reactions.
Length = 79
Score = 39.5 bits (93), Expect = 6e-05
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 17 CFRMFPTQGFTEIVFCAVNCSVQVLGYGTYMMNHLKEYHKKHEIYHFLTFAAKDAIGYFT 76
R+ P I AV+ + GYG+ ++ HL E + ++ FA A ++
Sbjct: 17 FLRLRPIGEGAYIGGVAVDPEYRGQGYGSKLLRHLLEELGEKPLF---LFAHPQAKKFYE 73
Query: 77 RQGFTK 82
+ GF
Sbjct: 74 KLGFEP 79
>gnl|CDD|235535 PRK05621, PRK05621, F0F1 ATP synthase subunit gamma; Validated.
Length = 284
Score = 33.5 bits (78), Expect = 0.042
Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 19/89 (21%)
Query: 47 MMNHLKEYHKKHEIYHFLTFAAKDAIGYFTRQGFTKDIKLPKHLYEGYIK--DYEDA--- 101
++ +KE + + + K + +F R+G Y G +E+A
Sbjct: 98 VLELIKELEAQGKEVKLIVIGRK-GVDFFKRRGIN-----VVAEYTGLGDQPTFEEAIGI 151
Query: 102 ------MLMHCEIDK-RIVYTHFVS-VTQ 122
+ E D+ IVY FV+ ++Q
Sbjct: 152 AKKLLDAYDNGEFDELYIVYNKFVNTLSQ 180
>gnl|CDD|223532 COG0456, RimI, Acetyltransferases [General function prediction
only].
Length = 177
Score = 32.3 bits (73), Expect = 0.077
Identities = 18/104 (17%), Positives = 37/104 (35%), Gaps = 10/104 (9%)
Query: 5 KLWCLGILWISICFRMFPTQGFTEIVFCAVNCSVQVLGYGTYMMNHLKEYHKKHEIYHFL 64
K+ ++ + +G I AV+ + G G +++ E ++ + +
Sbjct: 72 KVVGFLLVRVVDGRPSADHEG--HIYNLAVDPEYRGRGIGRALLDEALERLRERGLADKI 129
Query: 65 T-FAAKD---AIGYFTRQGFTKDIKLPKHLYEGYIKDYEDAMLM 104
+ AIG + + GF + Y DA+LM
Sbjct: 130 VLEVRESNEAAIGLYRKLGFEVVKIRKNY----YADGNGDALLM 169
>gnl|CDD|233292 TIGR01146, ATPsyn_F1gamma, ATP synthase, F1 gamma subunit. This
model describes the ATP synthase gamma subunit in
bacteria and its equivalents in organelles, namely,
mitochondria and chloroplast. F1/F0-ATP synthase is a
multisubunit, membrane associated enzyme found in
bacteria and organelles of higher eukaryotes, namely,
mitochondria and chloroplast. This enzyme is principally
involed in the synthesis of ATP from ADP and inorganic
phosphate by coupling the energy derived from the proton
electrochemical gradient across the biological membrane.
A brief description of this multisubunit enzyme complex:
F1 and F0 represent two major clusters of subunits. The
gamma subunit is the part of F1 cluster. Surrounding the
gamma subunit in a cylinder-like structure are three
alpha and three subunits in an alternating fashion. This
is the central catalytic unit whose different
conformations permit the binding of ADP and inorganic
phosphate and release of ATP [Energy metabolism,
ATP-proton motive force interconversion].
Length = 286
Score = 31.9 bits (73), Expect = 0.14
Identities = 20/97 (20%), Positives = 31/97 (31%), Gaps = 14/97 (14%)
Query: 47 MMNHLKEYHKKHEIYHFLTFAAKDAIGYFTRQG--FTKDIK-LPKHLYEGYIKDYEDAML 103
+ KE + + K +F R+G + L D +L
Sbjct: 98 VRARAKELKAAGKEVKLVVIGRK-GRSFFKRRGDNIVASVTGLSDQPTFEEASGIADKLL 156
Query: 104 ---MHCEIDK-RIVYTHFVSVTQSQKHIINYITEQKL 136
E D+ IVY FVSV + T ++L
Sbjct: 157 DAFDSGEFDEVYIVYNKFVSVISQE------PTVKQL 187
>gnl|CDD|224361 COG1444, COG1444, Predicted P-loop ATPase fused to an
acetyltransferase [General function prediction only].
Length = 758
Score = 32.0 bits (73), Expect = 0.18
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 10/73 (13%)
Query: 21 FPTQGFTEIVFCAVNCSVQVLGYGTYMMNHLKEYHKKHEIYHFL--TFAAKDAIGYF-TR 77
F IV AV+ +Q +G G+ ++ L E +K +L +F + + F R
Sbjct: 526 FAKLVGWRIVRIAVHPELQRMGIGSRLLALLIEEARKG--LDWLGVSFGYTEELLRFWLR 583
Query: 78 QGFTKDIKLPKHL 90
GF +P HL
Sbjct: 584 NGF-----VPVHL 591
>gnl|CDD|215808 pfam00231, ATP-synt, ATP synthase.
Length = 288
Score = 31.0 bits (71), Expect = 0.30
Identities = 19/107 (17%), Positives = 37/107 (34%), Gaps = 32/107 (29%)
Query: 46 YMMNHLKEYHKKHEIYHFLTFAAKDAIGYFTRQG---------------FTKDIKLPKHL 90
+ +KE + + + K +F R+G F + ++ L
Sbjct: 98 AALELIKELKAEGKEVDLIVIGKK-GRDFFKRRGKNIIAEFTGLGDKPTFEEAAEIADEL 156
Query: 91 YEGYIKDYEDAMLMHCEIDK-RIVYTHFVSVTQSQKHIINYITEQKL 136
E ++ E D+ +VY FV+ SQ+ T ++L
Sbjct: 157 IELFLNG---------EYDEVYLVYNKFVNA-LSQE-----PTVEQL 188
>gnl|CDD|233477 TIGR01575, rimI, ribosomal-protein-alanine acetyltransferase.
Members of this model belong to the GCN5-related
N-acetyltransferase (GNAT) superfamily. This model
covers prokarotes and the archaea. The seed contains a
characterized accession for Gram negative E. coli. An
untraceable characterized accession (PIR|S66013) for
Gram positive B. subtilis scores well (205.0) in the
full alignment. Characterized members are lacking in the
archaea. Noise cutoff (72.4) was set to exclude M. loti
paralog of rimI. Trusted cutoff (80.0) was set at next
highest scoring member in the mini-database [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 131
Score = 30.0 bits (68), Expect = 0.32
Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 7/80 (8%)
Query: 28 EIVFCAVNCSVQVLGYGTYMMNHLKEYHKKHEI-YHFLTFAAKD--AIGYFTRQGFTKDI 84
I+ AV Q G G ++ L + K + FL + A + + GF +I
Sbjct: 56 HILNIAVKPEYQGQGIGRALLRELIDEAKGRGVNEIFLEVRVSNIAAQALYKKLGF-NEI 114
Query: 85 KLPKHLYEGYIKDYEDAMLM 104
+ ++ Y EDA++M
Sbjct: 115 AIRRNYYP---DPGEDAIVM 131
>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional.
Length = 242
Score = 30.4 bits (68), Expect = 0.45
Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 4/82 (4%)
Query: 94 YIKDYEDAMLMHCEIDKRIVYTHFVSVTQSQKHIINYITEQKLERVQGVQPGLKCFSEDC 153
YI + D L C I T+++++T+ H+ N K +R+ G + + S D
Sbjct: 21 YIDEPNDIRLTVCIIQNINNITYYINITKINPHLANQFRAWK-KRIAG-RDYMTNLSRDT 78
Query: 154 AICSCNLTVKRTVKYCRKYQNI 175
I LT T++ C+K +NI
Sbjct: 79 GIQQSKLT--ETIRNCQKNRNI 98
>gnl|CDD|236637 PRK09970, PRK09970, xanthine dehydrogenase subunit XdhA;
Provisional.
Length = 759
Score = 30.1 bits (68), Expect = 0.63
Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 10/64 (15%)
Query: 80 FTKDIKLPKHLYEGYIKDYEDAMLMHCEIDKRIVYT------HFVSVTQSQ-KHIINYIT 132
+ IK + +G YE ++ HC ++ Y V+ +Q HI+ +
Sbjct: 167 VQQTIKAADYQVQG---HYETPIVQHCHMENVTSYAYMEDDGRITIVSSTQIPHIVRRVV 223
Query: 133 EQKL 136
Q L
Sbjct: 224 GQAL 227
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 30.2 bits (69), Expect = 0.63
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 91 YEGYIKDYEDAMLMHCEIDKRIVYT--HF 117
+ GY +YEDA+++ +R ++T H
Sbjct: 684 WNGY--NYEDAIIISERSVERDLFTSIHI 710
>gnl|CDD|223302 COG0224, AtpG, F0F1-type ATP synthase, gamma subunit [Energy
production and conversion].
Length = 287
Score = 29.5 bits (67), Expect = 0.80
Identities = 21/101 (20%), Positives = 39/101 (38%), Gaps = 20/101 (19%)
Query: 46 YMMNHLKEYHKKHEIYHFLTFAAKDAIGYFTRQGFTKDIKLPKHLYEGYIKDYEDA---- 101
+ N +KE K + L K I +F ++G+ ++ L + +E+A
Sbjct: 95 KVENLIKELKNKGKEV-KLILIGKKGIDFFKKRGY-NILESFTGLGD--NPSFEEAIQIA 150
Query: 102 -----MLMHCEIDK-RIVYTHFVSVTQSQKHIINYITEQKL 136
+ EID+ +VY F + + T Q+L
Sbjct: 151 DKILDAFLEGEIDELYLVYNKFKNA------LSQEPTVQQL 185
>gnl|CDD|173926 cd04301, NAT_SF, N-Acyltransferase superfamily: Various enzymes
that characteristically catalyze the transfer of an
acyl group to a substrate. NAT (N-Acyltransferase) is
a large superfamily of enzymes that mostly catalyze the
transfer of an acyl group to a substrate and are
implicated in a variety of functions, ranging from
bacterial antibiotic resistance to circadian rhythms in
mammals. Members include GCN5-related
N-Acetyltransferases (GNAT) such as Aminoglycoside
N-acetyltransferases, Histone N-acetyltransferase (HAT)
enzymes, and Serotonin N-acetyltransferase, which
catalyze the transfer of an acetyl group to a
substrate. The kinetic mechanism of most GNATs involves
the ordered formation of a ternary complex: the
reaction begins with Acetyl Coenzyme A (AcCoA) binding,
followed by binding of substrate, then direct transfer
of the acetyl group from AcCoA to the substrate,
followed by product and subsequent CoA release. Other
family members include Arginine/ornithine
N-succinyltransferase, Myristoyl-CoA: protein
N-myristoyltransferase, and Acyl-homoserinelactone
synthase which have a similar catalytic mechanism but
differ in types of acyl groups transferred.
Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB
nonribosomal peptidyltransferases which catalyze
similar peptidyltransferase reactions are also
included.
Length = 65
Score = 27.2 bits (61), Expect = 1.4
Identities = 6/48 (12%), Positives = 13/48 (27%)
Query: 16 ICFRMFPTQGFTEIVFCAVNCSVQVLGYGTYMMNHLKEYHKKHEIYHF 63
I AV + G G+ ++ +E ++
Sbjct: 15 SLSPDGSGGDTAYIGDLAVLPEYRGKGIGSALLEAAEEEARERGAKRL 62
>gnl|CDD|224167 COG1246, ArgA, N-acetylglutamate synthase and related
acetyltransferases [Amino acid transport and
metabolism].
Length = 153
Score = 27.7 bits (62), Expect = 2.8
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 9/75 (12%)
Query: 42 GYGTYMMNHLKEYHKKHEIYHFLTFA-AKDAIGYFTRQGFTK-DI-KLPKHLYEGYIKDY 98
G G ++ L ++ I F + +F +GFT+ D +LP+ ++ Y
Sbjct: 81 GRGERLLERLLADARELGIKEL--FVLTTRSPEFFAERGFTRVDKDELPEEVWSSYNFCE 138
Query: 99 ----EDAMLMHCEID 109
A + E+
Sbjct: 139 RRSKCLAFDLLRELG 153
>gnl|CDD|236012 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated.
Length = 373
Score = 28.2 bits (63), Expect = 2.9
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 12/39 (30%)
Query: 61 YHFLTFAAKDAIGYFTRQGFTK-------DIKLPKHLYE 92
Y F T+A ++ RQ T+ I+LP HLYE
Sbjct: 187 YKFSTYAT-----WWIRQAITRAIADQSRTIRLPVHLYE 220
>gnl|CDD|222340 pfam13718, GNAT_acetyltr_2, GNAT acetyltransferase 2. This domain
has N-acetyltransferase activity. It has a GCN5-related
N-acetyltransferase (GNAT) fold.
Length = 169
Score = 27.4 bits (62), Expect = 3.4
Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 21 FPTQGFTEIVFCAVNCSVQVLGYGTYMMNHLKEYHKKHEIYHFL 64
F + IV AV+ Q +GYG+ ++ L++Y+ +L
Sbjct: 83 FASLSGARIVRIAVHPDYQRMGYGSRLLELLEQYYIPEG-VDYL 125
>gnl|CDD|225700 COG3158, Kup, K+ transporter [Inorganic ion transport and
metabolism].
Length = 627
Score = 28.0 bits (63), Expect = 3.6
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 45 TYMMNHLKEYHKKHEIYHFLTF 66
++++LK HE FLT
Sbjct: 494 RALLHNLKHNKVLHERNVFLTV 515
>gnl|CDD|222309 pfam13673, Acetyltransf_10, Acetyltransferase (GNAT) domain. This
family contains proteins with N-acetyltransferase
functions such as Elp3-related proteins.
Length = 118
Score = 26.5 bits (59), Expect = 4.4
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 42 GYGTYMMNHLK-EYHKKHEIYHFLTFAAKDAIGYFTRQGF 80
G G +++ ++ E K + T A+ A ++ R GF
Sbjct: 81 GIGRALLDAIEAEARKGIKRLT--TEASLLARPFYLRLGF 118
>gnl|CDD|233048 TIGR00605, rad4, DNA repair protein rad4. All proteins in this
family for which functions are known are involved in
targeting nucleotide excision repair to specific regions
of the genome.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 = 713
Score = 26.8 bits (59), Expect = 8.2
Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 16/83 (19%)
Query: 92 EGYIKDYEDAMLMHCEIDKRIVYTHFVSVTQSQKHIINYITEQKLERVQGVQPGLKCFSE 151
+ I D ED + + I S+ + H + Y+ E+ L++ Q ++PG K
Sbjct: 462 KRTIDDIEDQEFLRRHESEGIP----KSIQDLKNHPL-YVLERHLKKTQALKPGKKA--- 513
Query: 152 DCAICSCNLTVKRTVK--YCRKY 172
C L Y RK
Sbjct: 514 ------CTLGFVNGKAGVYSRKD 530
>gnl|CDD|236445 PRK09277, PRK09277, aconitate hydratase; Validated.
Length = 888
Score = 26.6 bits (60), Expect = 8.3
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 37 SVQVLGYGT---YMMNHLKEYHKKHEIYHFL 64
SVQV +GT + N E+ + E Y FL
Sbjct: 131 SVQVDYFGTPDAFEKNVELEFERNEERYQFL 161
>gnl|CDD|213394 cd12151, F1-ATPase_gamma, mitochondrial ATP synthase gamma subunit.
The F-ATPase is found in bacterial plasma membranes,
mitochondrial inner membranes and in chloroplast
thylakoid membranes. It has also been found in the
archaea Methanosarcina barkeri. It uses a proton
gradient to drive ATP synthesis and hydrolyzes ATP to
build the proton gradient. The extrinisic membrane
domain of F-ATPases is composed of alpha, beta, gamma,
delta, and epsilon (not present in bacteria) subunits
with a stoichiometry of 3:3:1:1:1. Alpha and beta
subunit form the globular catalytic moiety, a hexameric
ring of alternating subunits. Gamma, delta and epsilon
subunits form a stalk, connecting F1 to F0, the integral
membrane proton translocating domain.
Length = 282
Score = 26.4 bits (59), Expect = 9.4
Identities = 19/88 (21%), Positives = 29/88 (32%), Gaps = 14/88 (15%)
Query: 46 YMMNHLKEYHKKHEIYHFLTFAAKDAIGYFTRQG------FTKDIKLPKHLYEGYIKDYE 99
+KE K + K Y R+G F+ P Y E
Sbjct: 97 AAEELIKEADGKE--VKLIVVGKK-GRDYLKRRGYNIALPFSDIGDDP--TYFEAASIIE 151
Query: 100 DAMLM--HCEIDK-RIVYTHFVSVTQSQ 124
+ +L + EID+ I+Y F S +
Sbjct: 152 ELILDFLNGEIDEVYIIYNKFKSAISQE 179
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
0.328 0.142 0.462
Gapped
Lambda K H
0.267 0.0852 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,180,970
Number of extensions: 821658
Number of successful extensions: 869
Number of sequences better than 10.0: 1
Number of HSP's gapped: 865
Number of HSP's successfully gapped: 40
Length of query: 181
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 90
Effective length of database: 6,901,388
Effective search space: 621124920
Effective search space used: 621124920
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: 56 (25.1 bits)