RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15562
(318 letters)
>gnl|CDD|220133 pfam09177, Syntaxin-6_N, Syntaxin 6, N-terminal. Members of this
family, which are found in the amino terminus of
various SNARE proteins, adopt a structure consisting of
an antiparallel three-helix bundle. Their exact
function has not been determined, though it is known
that they regulate the SNARE motif, as well as mediate
various protein-protein interactions involved in
membrane-transport.
Length = 96
Score = 65.0 bits (159), Expect = 2e-13
Identities = 31/64 (48%), Positives = 44/64 (68%), Gaps = 5/64 (7%)
Query: 1 EVSKAINKTRSLYKRWLELKEETYASNILRDELEWTTTELRNSLRSIEWDLEDLEDTINI 60
EV K+I+K RSLY+ WL ++ S+ EL+ T ELRN+L SIEWDLEDLE+ +++
Sbjct: 9 EVQKSIDKLRSLYRSWLRIR-----SDSNSPELDELTKELRNALESIEWDLEDLEEAVSV 63
Query: 61 LYNN 64
+ N
Sbjct: 64 VEAN 67
>gnl|CDD|203323 pfam05739, SNARE, SNARE domain. Most if not all vesicular membrane
fusion events in eukaryotic cells are believed to be
mediated by a conserved fusion machinery, the SNARE
[soluble N-ethylmaleimide-sensitive factor (NSF)
attachment protein (SNAP) receptors] machinery. The
SNARE domain is thought to act as a protein-protein
interaction module in the assembly of a SNARE protein
complex.
Length = 62
Score = 52.1 bits (126), Expect = 3e-09
Identities = 17/62 (27%), Positives = 36/62 (58%)
Query: 202 QDSQLDMLSETIGTLKTVSRNIGSELDEQALMLDEMGNEMECTESKLDATMKKVAKVLHI 261
+D L+ L +IG LK + ++G E++EQ +LD + + ++ T+S+++ K++ K
Sbjct: 1 RDEALEELESSIGELKQLFLDMGEEVEEQGELLDRIDDNVDNTQSRVERANKRLKKAARY 60
Query: 262 SN 263
Sbjct: 61 QK 62
>gnl|CDD|197699 smart00397, t_SNARE, Helical region found in SNAREs. All
alpha-helical motifs that form twisted and parallel
four-helix bundles in target soluble
N-ethylmaleimide-sensitive factor (NSF) attachment
protein (SNAP) receptor proteins. This motif found in
"Q-SNAREs".
Length = 66
Score = 44.1 bits (105), Expect = 2e-06
Identities = 18/65 (27%), Positives = 37/65 (56%)
Query: 194 QQSAMFDQQDSQLDMLSETIGTLKTVSRNIGSELDEQALMLDEMGNEMECTESKLDATMK 253
Q A +++D +L+ L ++I LK + ++G+EL+EQ LD + + ++ + L K
Sbjct: 2 QALAREEERDEELEQLEKSIQELKQIFLDMGTELEEQGEQLDRIEDNVDDADVNLKKANK 61
Query: 254 KVAKV 258
++ K
Sbjct: 62 RLKKA 66
>gnl|CDD|238115 cd00193, t_SNARE, Soluble NSF (N-ethylmaleimide-sensitive fusion
protein)-Attachment protein (SNAP) REceptor domain;
these alpha-helical motifs form twisted and parallel
heterotetrameric helix bundles; the core complex
contains one helix from a protein that is anchored in
the vesicle membrane (synaptobrevin), one helix from a
protein of the target membrane (syntaxin), and two
helices from another protein anchored in the target
membrane (SNAP-25); their interaction forms a core which
is composed of a polar zero layer, a flanking
leucine-zipper layer acts as a water tight shield to
isolate ionic interactions in the zero layer from the
surrounding solvent.
Length = 60
Score = 43.3 bits (103), Expect = 3e-06
Identities = 15/59 (25%), Positives = 35/59 (59%)
Query: 200 DQQDSQLDMLSETIGTLKTVSRNIGSELDEQALMLDEMGNEMECTESKLDATMKKVAKV 258
++D +L+ L +IG LK + ++G+E++EQ +LD + + ++ + + K++ K
Sbjct: 2 QERDEELEQLEASIGELKQIFLDLGTEVEEQGELLDRIEDNVDNADVNVKRANKRLKKA 60
>gnl|CDD|183872 PRK13149, PRK13149, H/ACA RNA-protein complex component Gar1;
Reviewed.
Length = 73
Score = 31.4 bits (72), Expect = 0.100
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 13/50 (26%)
Query: 252 MKKVAKVLHISNGEML-------DEMGNEMECTESKLDATMKKVAKVLHI 294
MK++ KVLH + L +G D +KK+ KV+ +
Sbjct: 1 MKRLGKVLHYAPKGKLIIRLDKQPPIG------SVVYDKKLKKIGKVVDV 44
>gnl|CDD|235558 PRK05683, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 676
Score = 32.4 bits (74), Expect = 0.33
Identities = 27/124 (21%), Positives = 48/124 (38%), Gaps = 19/124 (15%)
Query: 135 LSNSINQQSAMFDQQDSQLDMLSETIGTLTVQVRRQTK-YSKLNNQMDSPNRSWVSNSIN 193
LS N ++ Q + Q ++ + +T QV T + N Q+ + S S
Sbjct: 139 LSKRFN---SLSSQLNQQNSNINSQLSAMTDQVNNLTTSIASYNKQI-----AQASASGA 190
Query: 194 QQSAMFDQQDSQLDMLSETIGTLKTVSRN------IGSELDEQALMLDEMGNEMECTESK 247
+ + D +D + L+E +G V R+ IGS Q L++ N +
Sbjct: 191 TPNDLLDARDEAVRQLNELVGV-TVVERDGNYDVYIGS---GQPLVVGNTANTLSVVPGP 246
Query: 248 LDAT 251
D +
Sbjct: 247 SDPS 250
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 31.2 bits (71), Expect = 0.81
Identities = 35/244 (14%), Positives = 89/244 (36%), Gaps = 7/244 (2%)
Query: 18 ELKEETYASNILRDELEWTTTELRNSLRSIEWDLEDLEDTINILYNNFDFIEHLCMKDTM 77
EL+E+ EL EL L + +LE+L I+ L + +E +
Sbjct: 688 ELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEE 747
Query: 78 NYSREKDRGGDHMSSKPLLSDDFHSPSPVKISAPFGS-SRQTKYSKLNNQMDSPNR--SW 134
++ + + L + A + + +L ++ +
Sbjct: 748 RIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDE 807
Query: 135 LSNSINQQSAMFDQQDSQLDMLSETIGTLTVQVRRQTKYSKLNNQMDSPNRSWVSNSINQ 194
L + + +L+ L I ++ + + ++ + ++ I +
Sbjct: 808 LRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSE----DIESLAAEIEE 863
Query: 195 QSAMFDQQDSQLDMLSETIGTLKTVSRNIGSELDEQALMLDEMGNEMECTESKLDATMKK 254
+ ++ +S+L+ L +L+ + SEL+E + L E+ ++ +L+ +K
Sbjct: 864 LEELIEELESELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREK 923
Query: 255 VAKV 258
+A++
Sbjct: 924 LAQL 927
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 30.4 bits (69), Expect = 1.3
Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 3/73 (4%)
Query: 1 EVSKAINKTRSLYKRWLELKEETYASNILRDELEWTTTEL---RNSLRSIEWDLEDLEDT 57
E+ + + + Y +LELK+ EL+ EL L E LE+L
Sbjct: 589 ELEERLKELEPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEELRKE 648
Query: 58 INILYNNFDFIEH 70
+ L + E+
Sbjct: 649 LEELEKKYSEEEY 661
>gnl|CDD|150393 pfam09712, PHA_synth_III_E, Poly(R)-hydroxyalkanoic acid synthase
subunit (PHA_synth_III_E). This entry represents the
PhaE subunit of the heterodimeric class (class III) of
polymerase for poly(R)-hydroxyalkanoic acids (PHAs),
carbon and energy storage polymers of many bacteria. The
most common PHA is polyhydroxybutyrate but about 150
different constituent hydroxyalkanoic acids (HAs) have
been identified in various species.
Length = 293
Score = 29.8 bits (67), Expect = 1.9
Identities = 12/41 (29%), Positives = 18/41 (43%)
Query: 4 KAINKTRSLYKRWLELKEETYASNILRDELEWTTTELRNSL 44
+ R+LY W+E EE YA + +E L N+
Sbjct: 208 SQLTSARALYDLWVEAAEEAYAEVVASEEYAQIHGRLSNAQ 248
>gnl|CDD|235434 PRK05370, PRK05370, argininosuccinate synthase; Validated.
Length = 447
Score = 29.6 bits (67), Expect = 2.7
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 16/73 (21%)
Query: 150 DSQLDMLSETI---------GTLTVQVRRQTKYSKLNNQMDSPNRSWVSNSINQ---QSA 197
D Q ML E++ G +T+++RR YS LN SPN ++ ++ +SA
Sbjct: 338 DPQALMLRESLQRWVASAITGEVTLELRRGNDYSILNT--VSPNLTYKPERLSMEKVESA 395
Query: 198 MFDQQD--SQLDM 208
F D QL M
Sbjct: 396 AFSPDDRIGQLTM 408
>gnl|CDD|226173 COG3647, COG3647, Predicted membrane protein [Function unknown].
Length = 205
Score = 28.7 bits (64), Expect = 3.2
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 200 DQQDSQLDMLSETIGTLKTV 219
DQ D+Q DML +T+G L +
Sbjct: 173 DQWDAQKDMLCDTLGALTAL 192
Score = 28.3 bits (63), Expect = 3.7
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 147 DQQDSQLDMLSETIGTLT 164
DQ D+Q DML +T+G LT
Sbjct: 173 DQWDAQKDMLCDTLGALT 190
>gnl|CDD|225095 COG2184, Fic, Protein involved in cell division [Cell division and
chromosome partitioning].
Length = 201
Score = 28.5 bits (64), Expect = 3.8
Identities = 6/48 (12%), Positives = 15/48 (31%), Gaps = 1/48 (2%)
Query: 214 GTLKTVSRNIGSELDEQALMLDEMGNEMECTESKLDA-TMKKVAKVLH 260
G +TV + G ++ + E + +++ A
Sbjct: 77 GQFRTVGISKGDTRFANPSYIERALDYAEQWMPQETYDFVERAAHKYV 124
>gnl|CDD|146174 pfam03396, Pox_RNA_pol_35, Poxvirus DNA-directed RNA polymerase, 35
kD subunit.
Length = 292
Score = 28.5 bits (64), Expect = 5.2
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 64 NFDFIEHLCMKDTMNYSREKDRGGDHMSSKPLLSDDFHSPSPVKISAPFG 113
+ I L D ++RE + + KP+L ++F S P + AP G
Sbjct: 146 TEELINRLTFLDIEVFNRE------YANIKPILDENFRSIVPFIVIAPLG 189
>gnl|CDD|215591 PLN03124, PLN03124, poly [ADP-ribose] polymerase; Provisional.
Length = 643
Score = 28.3 bits (63), Expect = 7.0
Identities = 25/98 (25%), Positives = 33/98 (33%), Gaps = 7/98 (7%)
Query: 200 DQQDSQLDMLSETIGTLKTVSRNIGSELDEQALM--LDEMGNEMECTESKLDATMKKVAK 257
Q D + +S + V EL E A L G + + E A V
Sbjct: 60 RQDDGDDEPVSPKRIAIDEVKGMTVRELREAASERGLATTGRKKDLLERLCAALESDVKV 119
Query: 258 VLHISNGEMLDEM---GNEMECTESKLDATMKKVAKVL 292
+NG DE G+E E K+ KK VL
Sbjct: 120 G--SANGTGEDEKEKGGDEEREKEEKIVTATKKGRAVL 155
>gnl|CDD|236038 PRK07521, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 483
Score = 28.0 bits (63), Expect = 7.1
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 18/96 (18%)
Query: 135 LSNSINQ-----QSAMFDQQDSQLDMLSETIGTLTVQVRRQTKYSKLNNQMDSPNRSWVS 189
L+NS+N QSA D D+++ +T+ L Q NN + S +
Sbjct: 134 LANSLNDASDAVQSARADA-DAEIADSVDTLNDLLAQFE------DANNAVVS-----GT 181
Query: 190 NSINQQSAMFDQQDSQLDMLSETIGTLKTVSRNIGS 225
+ S DQ+D L +S+ +G + TV+R+
Sbjct: 182 ATGRDASDALDQRDKLLKQISQIVG-VTTVTRDNND 216
>gnl|CDD|204897 pfam12380, Peptidase_C62, Gill-associated viral 3C-like peptidase.
a positive-stranded RNA virus of prawns, that has been
called yellow head virus protease and gill-associated
virus 3C-like peptidase. The GAV cysteine protease is
predicted to be the key enzyme in the processing of the
GAV replicase polyprotein precursors, pp1a and pp1ab.
This protease employs a Cys(2968)-His(2879) catalytic
dyad.
Length = 284
Score = 27.7 bits (61), Expect = 7.9
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 87 GDHMSSKPLLSDDFHSPSPVKISAPFGSSRQTKYSKL 123
G+ LLSD++ + +KI +PF + + K++KL
Sbjct: 76 GEETHDIELLSDEYDATPFIKIDSPFAEATELKFAKL 112
>gnl|CDD|132501 TIGR03461, pabC_Proteo, aminodeoxychorismate lyase. Members of
this protein family are aminodeoxychorismate lyase (ADC
lyase), EC 4.1.3.38, the PabC protein of PABA
biosynthesis. PABA (para-aminobenzoate) is a precursor
of folate, needed for de novo purine biosynthesis. This
enzyme is a pyridoxal-phosphate-binding protein in the
class IV aminotransferase family (pfam01063)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Folic acid].
Length = 261
Score = 27.6 bits (62), Expect = 9.6
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 223 IGSELDEQ----ALMLDEMGNEMECTESKL 248
I +EL+ AL+LD GN +ECT + +
Sbjct: 148 IKAELENSEADEALVLDTDGNVVECTAANI 177
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 0.125 0.349
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,796,249
Number of extensions: 1327069
Number of successful extensions: 1049
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1043
Number of HSP's successfully gapped: 58
Length of query: 318
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 221
Effective length of database: 6,635,264
Effective search space: 1466393344
Effective search space used: 1466393344
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 (21.9 bits)
S2: 59 (26.4 bits)