RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4416
(290 letters)
>gnl|CDD|223099 COG0020, UppS, Undecaprenyl pyrophosphate synthase [Lipid
metabolism].
Length = 245
Score = 41.5 bits (98), Expect = 2e-04
Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 6/94 (6%)
Query: 199 DLLNSIVELGETNLSVSDTIMKERLQEKCPLPD-PEVAIVI---GRKLSSYGLLPWNIRL 254
D + I E + I +E + P+ ++I G + S L W
Sbjct: 152 DAVRKIAEDVAAGKLSPEDIDEELISSHLYTSGLPDPDLLIRTSGEQRLS-NFLLWQSAY 210
Query: 255 TEFFQFDNYY-DISASKFKNILRKYSKCEQRYGK 287
+E + D + D +R Y K E+R+G+
Sbjct: 211 SELYFTDVLWPDFRREDLLRAIRDYQKRERRFGR 244
>gnl|CDD|184846 PRK14838, PRK14838, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 242
Score = 33.3 bits (76), Expect = 0.10
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 213 SVSDTIMKERLQEKCPLPDPEVAIVIGRKLSSYGLLPWNIRLTEFFQFDNYY-DISASKF 271
+++ + E L +PDP++ I G ++ L W +E + D ++ D +
Sbjct: 162 EITEESISEHLTTNF-MPDPDLLIRTGGEIRLSNYLLWQCAYSELYFCDTFWPDFDEEEL 220
Query: 272 KNILRKYSKCEQRYGK 287
+ Y K E+R+GK
Sbjct: 221 CKAIYDYQKRERRFGK 236
>gnl|CDD|179281 PRK01326, prsA, foldase protein PrsA; Reviewed.
Length = 310
Score = 32.5 bits (74), Expect = 0.22
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 7/59 (11%)
Query: 162 KYYADDIVGILNIIEENLKWSNYKTELN--ILSRKQCESDLLNSIV--ELGETNLSVSD 216
KYY IV + E+ W +YK L IL++KQ +S+ N ++ L + N+ + D
Sbjct: 230 KYY---IVKVTKKTEKKSDWKDYKKRLKAIILAQKQNDSNFQNKVIAKALDKANVKIKD 285
>gnl|CDD|237830 PRK14835, PRK14835, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 275
Score = 32.5 bits (74), Expect = 0.23
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 229 LPDPEVAIVIGRKLSSYGLLPWNIRLTEFFQFDNYY-DISASKFKNILRKYSKCEQRYGK 287
+PDP+ I ++ G L W +E++ D Y+ F LR Y E+R+G+
Sbjct: 216 VPDPDFIIRTSGEIRLSGFLLWQSAYSEYYFCDVYWPGFRKVDFLRALRDYQGRERRFGR 275
>gnl|CDD|218840 pfam05985, EutC, Ethanolamine ammonia-lyase light chain (EutC).
This family consists of several bacterial ethanolamine
ammonia-lyase light chain (EutC) EC:4.3.1.7 sequences.
Ethanolamine ammonia-lyase is a bacterial enzyme that
catalyzes the adenosylcobalamin-dependent conversion of
certain vicinal amino alcohols to oxo compounds and
ammonia.
Length = 238
Score = 32.2 bits (74), Expect = 0.26
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 206 ELGETNLSVSDTIMKERLQEKCPLPDPEVAIVIGRKLSS 244
+LG L RL+ KC +P+V IVI LS+
Sbjct: 83 DLGRR-LDDESL---ARLKAKCV-KNPDVQIVIADGLSA 116
>gnl|CDD|237827 PRK14832, PRK14832, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 253
Score = 31.5 bits (71), Expect = 0.35
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 1/85 (1%)
Query: 204 IVELGETNLSVSDTIMKERLQEKCPLPDPEVAIVIGRKLSSYGLLPWNIRLTEFFQFDNY 263
+V+ G+ + + + E+ P P++ I ++ L W + TE + D
Sbjct: 162 LVQQGKLSADAVNEQLVEQHLYTADTPPPDLLIRTSGEMRLSNFLLWQMAYTEMYFTDIL 221
Query: 264 Y-DISASKFKNILRKYSKCEQRYGK 287
+ D + F L Y K ++R+G+
Sbjct: 222 WPDFDRAAFHQALLSYQKRDRRFGQ 246
>gnl|CDD|216392 pfam01255, Prenyltransf, Putative undecaprenyl diphosphate
synthase. Previously known as uncharacterized protein
family UPF0015, a single member of this family has been
identified as an undecaprenyl diphosphate synthase.
Length = 222
Score = 31.4 bits (72), Expect = 0.42
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 9/64 (14%)
Query: 229 LPDPEVAIVI---GRK-LSSYGLLPWNIRLTEFFQFDNYY-DISASKFKNILRKYSKCEQ 283
LPDP+ ++I G K LS++ L W E + D + D + +R Y E+
Sbjct: 163 LPDPD--LLIRTSGEKRLSNF--LLWQSAYAELYFTDTLWPDFTKEDLLRAIRDYQSRER 218
Query: 284 RYGK 287
R+GK
Sbjct: 219 RFGK 222
>gnl|CDD|237831 PRK14836, PRK14836, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 253
Score = 30.8 bits (70), Expect = 0.60
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 229 LPDPEVAIVIGRKLSSYGLLPWNIRLTEFFQFDNYY-DISASKFKNILRKYSKCEQRYGK 287
LP+P++ I +L L W + TE + D + D A + + L Y+ E+R+GK
Sbjct: 183 LPEPDLFIRTSGELRISNFLLWQLAYTELYFTDTLWPDFDAQELQQALEDYASRERRFGK 242
>gnl|CDD|179251 PRK01216, PRK01216, DNA polymerase IV; Validated.
Length = 351
Score = 30.5 bits (69), Expect = 1.0
Identities = 28/91 (30%), Positives = 35/91 (38%), Gaps = 23/91 (25%)
Query: 102 KNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEPNGIH 161
KN YNL IKN L +E +T+G S NK + + A+PNGI
Sbjct: 116 KNYQDAYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKPNGIK 164
Query: 162 KYYA------------DDIVGILNIIEENLK 180
DI GI +I E LK
Sbjct: 165 VIDDEEVKRFINELDIADIPGIGDITAEKLK 195
>gnl|CDD|235482 PRK05465, PRK05465, ethanolamine ammonia-lyase small subunit;
Provisional.
Length = 260
Score = 30.2 bits (69), Expect = 1.2
Identities = 9/24 (37%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 221 ERLQEKCPLPDPEVAIVIGRKLSS 244
E L+ +C +P+V IV+ LS+
Sbjct: 100 EALKAQCG-KNPDVQIVVADGLSA 122
>gnl|CDD|237825 PRK14828, PRK14828, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 256
Score = 30.1 bits (68), Expect = 1.2
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 229 LPDPEVAIVIG--RKLSSYGLLPWNIRLTEFFQFDNYY-DISASKFKNILRKYSKCEQRY 285
PDP++ I ++LS G + W +E++ + Y+ F LR YS+ E+R+
Sbjct: 197 QPDPDLVIRTSGEQRLS--GFMLWQSAHSEYYFCETYWPAFRKVDFLRALRDYSQRERRF 254
Query: 286 GK 287
GK
Sbjct: 255 GK 256
>gnl|CDD|173302 PRK14841, PRK14841, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 233
Score = 29.6 bits (66), Expect = 1.7
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 229 LPDPEVAIVIGRKLSSYGLLPWNIRLTEFFQFDNYY-DISASKFKNILRKYSKCEQRYG 286
+PDP++ I ++ L W +E + F + D + F + YSK E+R+G
Sbjct: 170 VPDPDLIIRTSGEMRLSNFLLWQSAYSELYFFKKLWPDFTKRDFLRAIESYSKRERRFG 228
>gnl|CDD|173301 PRK14840, PRK14840, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 250
Score = 29.0 bits (65), Expect = 2.3
Identities = 28/108 (25%), Positives = 49/108 (45%), Gaps = 9/108 (8%)
Query: 183 NY--KTELNILSRKQCESDLLNSIVELGETNLSVSDTIMKERLQEKCPLPDPEVAIVIGR 240
NY K EL + + K+ DL N + +S+ ++ L + LPDP++ I G
Sbjct: 149 NYGGKDEL-VRAFKKLHQDLANKKISSD----DISEELISSYL-DTSGLPDPDLLIRTGG 202
Query: 241 KLSSYGLLPWNIRLTEFFQFDNYY-DISASKFKNILRKYSKCEQRYGK 287
++ L W I TE + D + D + + ++ Y + +R GK
Sbjct: 203 EMRVSNFLLWQIAYTELYVTDVLWPDFTPNDLLEAIKTYQQRSRRGGK 250
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 29.1 bits (65), Expect = 3.3
Identities = 25/92 (27%), Positives = 38/92 (41%), Gaps = 12/92 (13%)
Query: 118 PLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEPNGIHKYYADDIVGILNIIEE 177
P+ EE +L L F F T++ L N SK E Y + ++ ILN IE
Sbjct: 322 PINEELKRLRLLFGF--------TRNELSSNIPFYSKYESEEAPSY--EILMEILNSIER 371
Query: 178 NLKWSNYKTELNILSRKQCESDLLNSIVELGE 209
K N ++ +L K + + L + G
Sbjct: 372 GSK--NLDKKIAVLEGKIRDHNYLKAFESDGL 401
>gnl|CDD|213036 cd11728, ADDz_Dnmt3b, ADDz domain of DNA (cytosine-5)
methyltransferases (C5-MTases) 3 b (Dnmt3b).
ADDz_Dnmt3b is an active catalytic domain of Dnmt3b.
Dnmt3b is a member of the Dnmt3 family and is a de novo
DNA methyltransferases that has an N-terminal variable
region followed by a conserved PWWP region and the
cysteine-rich ADDz domain. DNA methylation is an
important epigenetic mechanism involved in diverse
biological processes such as embryonic development, gene
expression, and genomic imprinting. The
methyltransferase activity of Dnmt3a is not only
responsible for the establishment of DNA methylation
pattern, but is also essential for the inheritance of
these patterns during mitosis. Dnmt3b is ubiquitously
expressed in most adult tissues. The ADDz_Dnmt3 domain
is a PHD-like zinc finger motif that contains two parts,
a C2-C2 and a PHD-like zinc finger. PHD zinc finger
domains have been identified in more than 40 proteins
that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif. A knockout of Dnmt3b has
been shown to be lethal in the mouse model.
Length = 150
Score = 27.4 bits (61), Expect = 6.4
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 242 LSSYGLLP----WNIRLTEFFQFDNYYDISASK 270
YG+L WN+RL EFF D + A K
Sbjct: 115 QRQYGVLQRRHDWNLRLQEFFTNDKGQEYEAPK 147
>gnl|CDD|216554 pfam01529, zf-DHHC, DHHC palmitoyltransferase. This family
includes the well known DHHC zinc binding domain as well
as three of the four conserved transmembrane regions
found in this family of palmitoyltransferase enzymes.
Length = 167
Score = 27.4 bits (61), Expect = 6.8
Identities = 12/56 (21%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 4 HRYFYKFLSLLAFCYYFLTSNIWTSLIYILNPLKLNKNLHNEIVNNKSTLFLTLIN 59
H+YF FL L +L + S Y++ ++ + I++ S++ L +++
Sbjct: 84 HKYFLLFLLYLTL---YLILLLVLSFYYLVYLIRNIELFFFLILSLFSSIILLVLS 136
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
0.321 0.138 0.412
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,696,097
Number of extensions: 1401055
Number of successful extensions: 1338
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1333
Number of HSP's successfully gapped: 45
Length of query: 290
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 194
Effective length of database: 6,679,618
Effective search space: 1295845892
Effective search space used: 1295845892
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.2 bits)