RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8183
(223 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 30.4 bits (69), Expect = 0.047
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 38 NLQSHSRCHQTDKPYKCNSCYKCFV 62
NL+ H R H +KPYKC C K F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 25.8 bits (57), Expect = 2.5
Identities = 14/23 (60%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 13 RRTHTGDKPYKCRHPGCVKAFSQ 35
RTHTG+KPYKC C K+FS
Sbjct: 6 MRTHTGEKPYKCPV--CGKSFSS 26
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 29.2 bits (66), Expect = 0.14
Identities = 8/22 (36%), Positives = 16/22 (72%)
Query: 84 ICQYCGKSYTQETYLSKHMQKH 105
C CGKS+++++ L +H++ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 29.0 bits (65), Expect = 0.17
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 83 HICQYCGKSYTQETYLSKHMQKH 105
+ C CGK + ++ L +HM+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|176462 cd01357, Aspartase, Aspartase. This subgroup contains Escherichia
coli aspartase (L-aspartate ammonia-lyase), Bacillus
aspartase and related proteins. It is a member of the
Lyase class I family, which includes both aspartase
(L-aspartate ammonia-lyase) and fumarase class II
enzymes. Members of this family for the most part
catalyze similar beta-elimination reactions in which a
C-N or C-O bond is cleaved with the release of fumarate
as one of the products. These proteins are active as
tetramers. The four active sites of the homotetrameric
enzyme are each formed by residues from three different
subunits. Aspartase catalyzes the reversible deamination
of aspartic acid.
Length = 450
Score = 30.6 bits (70), Expect = 0.58
Identities = 14/40 (35%), Positives = 17/40 (42%), Gaps = 15/40 (37%)
Query: 173 SSGPNTPVSVAVSNSFPNQLISLHQIRNYAHQPGSTLMPG 212
SSGP L +I A QPGS++MPG
Sbjct: 294 SSGPRA---------------GLGEINLPAVQPGSSIMPG 318
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 30.4 bits (68), Expect = 0.66
Identities = 23/137 (16%), Positives = 42/137 (30%), Gaps = 14/137 (10%)
Query: 24 CRHPGCVKAFSQLSNLQSHSRCHQT-DKPYKCNSCYKCFVDETALLEHIP-KHKDSKHLK 81
R + S +S S + P K C F + L H+ + + LK
Sbjct: 261 PRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVNHSGESLK 320
Query: 82 THIC--QYCGKSYTQETYLSKHMQKHA----------ERSDKRPPIIGIPRAALENPHYW 129
C CGK +++ L +H+ H S K P++ +
Sbjct: 321 PFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKD 380
Query: 130 PKVSPDTANNLSMGLPH 146
K + + + +
Sbjct: 381 LKNDKKSETLSNSCIRN 397
Score = 28.5 bits (63), Expect = 3.0
Identities = 30/180 (16%), Positives = 60/180 (33%), Gaps = 12/180 (6%)
Query: 14 RTHTGDKPYKCRHPGCVKAFSQLSNLQSHSRCHQTDKPYKCN-SCYKCFVDETALLEHIP 72
R+HTG+KP +C + GC K+FS+ L H R H + + S ++
Sbjct: 54 RSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLPLSNSKASSSSLSSS 113
Query: 73 KHKDSKHLKTHICQYCGKSYTQET---YLSKHMQKHAER--------SDKRPPIIGIPRA 121
+ + S + +++ + + + + A
Sbjct: 114 SSNSNDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTPQSNSLHPPLPA 173
Query: 122 ALENPHYWPKVSPDTANNLSMGLPHHQHHLNHHQAYLPYNTISFPGKVMQQSSGPNTPVS 181
+ +S ++N+S +P + +Y ++ S SS P T S
Sbjct: 174 NSLSKDPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNS 233
Score = 27.4 bits (60), Expect = 7.9
Identities = 16/51 (31%), Positives = 24/51 (47%)
Query: 13 RRTHTGDKPYKCRHPGCVKAFSQLSNLQSHSRCHQTDKPYKCNSCYKCFVD 63
TH +PY C++P C K+F++ NL H + H P C+ D
Sbjct: 408 IITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFRRD 458
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 26.8 bits (59), Expect = 0.84
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 83 HICQYCGKSYTQETYLSKHMQKH 105
C CGKS++ + L +H++KH
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 30.1 bits (67), Expect = 1.1
Identities = 21/73 (28%), Positives = 27/73 (36%), Gaps = 19/73 (26%)
Query: 18 GDKPYKCRHPGCVKAFSQLSNLQSHSR-CHQT------------------DKPYKCNSCY 58
KPYKC GC K + + L+ H HQ DKPY+C C
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCD 405
Query: 59 KCFVDETALLEHI 71
K + + L H
Sbjct: 406 KRYKNLNGLKYHR 418
>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid).
Members of this family are bacterial proteins with a
conserved motif [KR]FYDLN, sometimes flanked by a pair
of CXXC motifs, followed by a long region of low
complexity sequence in which roughly half the residues
are Asp and Glu, including multiple runs of five or more
acidic residues. The function of members of this family
is unknown.
Length = 104
Score = 28.0 bits (63), Expect = 1.8
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 84 ICQYCGKSYTQETYLSKHMQKHAERSDKRP 113
+C CG+ E S+ AE + K+
Sbjct: 28 VCPKCGEEVPPEVAKSRAPAADAEDAAKKD 57
>gnl|CDD|183992 PRK13353, PRK13353, aspartate ammonia-lyase; Provisional.
Length = 473
Score = 29.2 bits (66), Expect = 1.9
Identities = 15/41 (36%), Positives = 18/41 (43%), Gaps = 15/41 (36%)
Query: 172 QSSGPNTPVSVAVSNSFPNQLISLHQIRNYAHQPGSTLMPG 212
SSGP T L +I A QPGS++MPG
Sbjct: 298 LSSGPRT---------------GLGEINLPAVQPGSSIMPG 323
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 27.9 bits (62), Expect = 2.3
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 51 PYKCNSCYKCFVDETALLEHIPKHKDSKHLKTHICQYCGKSYTQETYLSKHM-QKH 105
PY C C F +L +HI + ++H K C CGK + H+ +KH
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHI---RYTEHSKV--CPVCGKEFRNTDSTLDHVCKKH 123
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 29.0 bits (65), Expect = 2.4
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 154 HQAYLPYNT---ISFPGKVMQQSSGPNTPVSVAVSNS-FPNQLISLHQIRN 200
A+ Y+T I G S+GPN + V V N +P L L+QI N
Sbjct: 68 QPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFN 118
>gnl|CDD|223958 COG1027, AspA, Aspartate ammonia-lyase [Amino acid transport and
metabolism].
Length = 471
Score = 28.4 bits (64), Expect = 2.8
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 15/40 (37%)
Query: 173 SSGPNTPVSVAVSNSFPNQLISLHQIRNYAHQPGSTLMPG 212
SSGP L++I A Q GS++MPG
Sbjct: 300 SSGPRA---------------GLNEINLPAVQAGSSIMPG 324
>gnl|CDD|237031 PRK12273, aspA, aspartate ammonia-lyase; Provisional.
Length = 472
Score = 28.6 bits (65), Expect = 3.0
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 15/40 (37%)
Query: 173 SSGPNTPVSVAVSNSFPNQLISLHQIRNYAHQPGSTLMPG 212
SSGP L++I A Q GS++MPG
Sbjct: 301 SSGPRA---------------GLNEINLPAVQAGSSIMPG 325
>gnl|CDD|217952 pfam04189, Gcd10p, Gcd10p family. eIF-3 is a multi-subunit complex
that stimulates translation initiation in vitro at
several different steps. This family corresponds to the
gamma subunit if eIF3. The Yeast protein Gcd10p has also
been shown to be part of a complex with the
methyltransferase Gcd14p that is involved in modifying
tRNA.
Length = 299
Score = 28.4 bits (64), Expect = 3.0
Identities = 24/132 (18%), Positives = 43/132 (32%), Gaps = 32/132 (24%)
Query: 71 IPKHKDSKHLKTHICQYCGKSYTQETYLSKHMQKHAERSDKRPPIIGIPRAALENPHYWP 130
+ + + H KT +++QE YL + +K+ +R P E +Y
Sbjct: 131 VENSE-TFHTKT--------AFSQEKYLKRKKKKYLKRFTVLRP---SISLLAE--YYIE 176
Query: 131 K-------VSPDTANNLSMGLPHHQHHLN--HHQAYLPYNTIS--FPGKVMQQSSGPNTP 179
K + DT L + L N YL + ++++ G
Sbjct: 177 KDPQKILDLRFDT---LGLIL----TLANVRPGGRYLVVDETGGLLVAAMLERMGGEGKI 229
Query: 180 VSVAVSNSFPNQ 191
V + PN
Sbjct: 230 VQIHEGEHPPNL 241
>gnl|CDD|192691 pfam11000, DUF2840, Protein of unknown function (DUF2840). This
bacterial family of proteins have no known function.
Length = 149
Score = 27.6 bits (62), Expect = 3.5
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 116 IGIPRAALENPHYWPKVSPDTANNLSMGLPHHQHHLNHHQAYL 158
+GI A P +W V N L+ GLP + H A+L
Sbjct: 107 LGI-DPADVAPDHWRHV----HNRLAAGLPPRPYTAERHAAWL 144
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 28.3 bits (63), Expect = 3.7
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 1/61 (1%)
Query: 101 HMQKHAERSDKRPPIIGIPRAALENPHYWPKVSPDTANNLSMGLPHHQHHLNHHQAYLPY 160
H RS K P +G L +PH+ K S +N P + + H +P
Sbjct: 170 HAGAPNARSRKEIPSLGSQSMQLPSPHFRQKFSSSDTSNGFSY-PSIRKNSRHSSNSMPS 228
Query: 161 N 161
Sbjct: 229 F 229
>gnl|CDD|215187 PLN02328, PLN02328, lysine-specific histone demethylase 1 homolog.
Length = 808
Score = 28.4 bits (63), Expect = 3.8
Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 133 SPDTANNLSMGLPHHQHHLNHHQAYLPYNTISFPGKVMQQSSGPNTPVSVAVSNSFPNQL 192
SP+T +LS Q+ N Q T S ++ PNT + VS+S ++
Sbjct: 24 SPETDLSLSPS-QSEQNIENDGQNSP--ETQSPLTELQPSPLPPNTTLDAPVSDSQGDES 80
Query: 193 ISLHQIRNYAHQPGST 208
S Q +N P ST
Sbjct: 81 SSEQQPQN----PNST 92
>gnl|CDD|187556 cd05245, SDR_a2, atypical (a) SDRs, subgroup 2. This subgroup
contains atypical SDRs, one member is identified as
Escherichia coli protein ybjT, function unknown.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine-rich NAD(P)-binding
motif consensus that generally matches the extended
SDRs, TGXXGXXG, but lacks the characteristic active site
residues of the SDRs. This subgroup has basic residues
(HXXXR) in place of the active site motif YXXXK, these
may have a catalytic role. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 28.1 bits (63), Expect = 3.9
Identities = 18/76 (23%), Positives = 23/76 (30%), Gaps = 11/76 (14%)
Query: 102 MQKHAERSDKRPPIIGIPRAALENPHYW----PKVSPDTANNLSMGLPH----HQHHLNH 153
M++ AE R I+ +P W V A L GL H
Sbjct: 216 MERFAEVRGLRRWILPVPVLTPRLSSLWVGLVTPVPNSIARPLIEGLKHDVVVDDDRA-- 273
Query: 154 HQAYLPYNTISFPGKV 169
+ P I FP V
Sbjct: 274 -RDLFPVRLIPFPDAV 288
>gnl|CDD|224416 COG1499, NMD3, NMD protein affecting ribosome stability and mRNA
decay [Translation, ribosomal structure and
biogenesis].
Length = 355
Score = 28.1 bits (63), Expect = 4.2
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 57 CYKCFVDETALLEHIPKHKDSKHLKTHICQYCGKSYTQ 94
C C+V+ T L+E IP + +C++CG +
Sbjct: 24 CGDCYVETTPLIE-IP-----DEVNVEVCRHCGAYRIR 55
>gnl|CDD|173163 PRK14700, PRK14700, recombination factor protein RarA; Provisional.
Length = 300
Score = 27.7 bits (61), Expect = 4.6
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 12/61 (19%)
Query: 53 KCNSCYKCFVDETALL---------EHIPKHKDSKHLKTHICQYCGKSYTQETYLSKHMQ 103
K N+CYK L+ +H+ +KDS +L H Y SY + YL ++
Sbjct: 216 KSNACYKALAQAQQLVKSLGNIDVPQHLKNYKDSNYLYPH--NY-PNSYVIQQYLPDNII 272
Query: 104 K 104
+
Sbjct: 273 Q 273
>gnl|CDD|233754 TIGR02163, napH_, ferredoxin-type protein, NapH/MauN family. Most
members of this family are the NapH protein, found next
to NapG,in operons that encode the periplasmic nitrate
reductase. Some species with this reductase lack NapC
but accomplish electron transfer to NapAB in some other
manner, likely to involve NapH, NapG, and/or some other
protein. A few members of this protein are designated
MauN and are found in methylamine utilization operons in
species that appear to lack a periplasmic nitrate
reductase.
Length = 255
Score = 27.7 bits (62), Expect = 4.9
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 53 KCNSCYKCF--VDETALLEHIPKHKDSKHL-KTHICQYCGK 90
KC +C CF E +L +P K L + C CG+
Sbjct: 202 KCTNCMDCFNVCPEPQVLR-MPLKKGGSTLVLSGDCTLCGR 241
>gnl|CDD|130302 TIGR01235, pyruv_carbox, pyruvate carboxylase. This enzyme plays a
role in gluconeogensis but not glycolysis [Energy
metabolism, Glycolysis/gluconeogenesis].
Length = 1143
Score = 27.9 bits (62), Expect = 5.8
Identities = 22/84 (26%), Positives = 30/84 (35%), Gaps = 8/84 (9%)
Query: 131 KVSPDTANNLSMGLPHHQHHLNHHQAYLPYNTISFPGKVMQQSSGP-NTPVSVAVSNSFP 189
KV+P + M L + L P +SFP V++ G P FP
Sbjct: 871 KVTPSSKVVGDMALFMVSNDLTVDDVVEPAEELSFPDSVVEFLKGDIGQPHG-----GFP 925
Query: 190 NQLIS--LHQIRNYAHQPGSTLMP 211
L L + +PGS L P
Sbjct: 926 EPLQKKVLKGEKPITVRPGSLLEP 949
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
0.317 0.131 0.417
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,765,352
Number of extensions: 915893
Number of successful extensions: 871
Number of sequences better than 10.0: 1
Number of HSP's gapped: 863
Number of HSP's successfully gapped: 45
Length of query: 223
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 130
Effective length of database: 6,812,680
Effective search space: 885648400
Effective search space used: 885648400
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 (21.7 bits)
S2: 57 (25.9 bits)