RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1931
(145 letters)
>gnl|CDD|203903 pfam08312, cwf21, cwf21 domain. The cwf21 family is involved in
mRNA splicing. It has been isolated as a subcomplex of
the splicosome in Schizosaccharomyces pombe. The
function of the cwf21 domain is to bind directly to the
spliceosomal protein Prp8. Mutations in the cwf21 domain
prevent Prp8 from binding. The structure of this domain
has recently been solved which shows this domain to be
composed of two alpha helices.
Length = 46
Score = 51.0 bits (123), Expect = 7e-10
Identities = 23/46 (50%), Positives = 35/46 (76%)
Query: 57 LDHEKKRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNVE 102
L+HE+KR+IE++CLEL++ LEEQG +E E++ KV R L + +E
Sbjct: 1 LEHERKREIEVKCLELRDKLEEQGLSEEEIEEKVDELRKKLLEELE 46
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 28.5 bits (63), Expect = 1.3
Identities = 27/91 (29%), Positives = 40/91 (43%), Gaps = 3/91 (3%)
Query: 7 LTTARGSGTNG-YVQRNWSLVRKTKEKTNLKTEKDLERMDAMNNKQPNREILDHEKKRKI 65
+ T R SG G +V S VR T TN ER N + + + ++K+
Sbjct: 201 IDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLKAKLYQKKL 260
Query: 66 ELQCLELQELLEEQGFNEIEVDAKVMAYRLH 96
E Q EL E+ EQ EI +++ +Y H
Sbjct: 261 EEQQAELDEIRGEQ--KEIGWGSQIRSYVFH 289
>gnl|CDD|223681 COG0608, RecJ, Single-stranded DNA-specific exonuclease [DNA
replication, recombination, and repair].
Length = 491
Score = 27.8 bits (62), Expect = 2.4
Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 45 DAMNNKQPNREILDHEKKRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNVEKI 104
D NR +++ KR + ++ LL+ G + + A + + +
Sbjct: 181 DVQPLTGENRILVNQGLKRLRKSGRPGIKALLKLAGRDTRQPTASDIGFII--------- 231
Query: 105 NEPPLDELGRVMDDTSLKFPLL 126
P ++ GR + D LL
Sbjct: 232 -GPRINAAGR-LGDAKAGVELL 251
>gnl|CDD|224927 COG2016, COG2016, Predicted RNA-binding protein (contains PUA
domain) [Translation, ribosomal structure and
biogenesis].
Length = 161
Score = 27.3 bits (61), Expect = 2.7
Identities = 7/43 (16%), Positives = 17/43 (39%)
Query: 62 KRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNVEKI 104
K++ L E+++L+E+ E + + +I
Sbjct: 4 KQRHFLSKKEVKKLVEKLEEYSGEELPGKAEVEVAKCDDKFEI 46
>gnl|CDD|223801 COG0729, COG0729, Outer membrane protein [Cell envelope biogenesis,
outer membrane].
Length = 594
Score = 27.3 bits (61), Expect = 3.6
Identities = 8/43 (18%), Positives = 18/43 (41%)
Query: 4 GIGLTTARGSGTNGYVQRNWSLVRKTKEKTNLKTEKDLERMDA 46
G+G +T G+G ++ R + + L+ ++A
Sbjct: 283 GVGYSTDVGAGLEAGWEKRNLFGRGHSLRIESEISAPLQTLEA 325
>gnl|CDD|233161 TIGR00870, trp, transient-receptor-potential calcium channel
protein. The Transient Receptor Potential Ca2+ Channel
(TRP-CC) Family (TC. 1.A.4)The TRP-CC family has also
been called the store-operated calcium channel (SOC)
family. The prototypical members include the Drosophila
retinal proteinsTRP and TRPL (Montell and Rubin, 1989;
Hardie and Minke, 1993). SOC members of the family
mediate the entry of extracellular Ca2+ into cells in
responseto depletion of intracellular Ca2+ stores
(Clapham, 1996) and agonist stimulated production of
inositol-1,4,5 trisphosphate (IP3). One member of the
TRP-CCfamily, mammalian Htrp3, has been shown to form a
tight complex with the IP3 receptor (TC #1.A.3.2.1).
This interaction is apparently required for IP3
tostimulate Ca2+ release via Htrp3. The vanilloid
receptor subtype 1 (VR1), which is the receptor for
capsaicin (the ?hot? ingredient in chili peppers) and
servesas a heat-activated ion channel in the pain
pathway (Caterina et al., 1997), is also a member of
this family. The stretch-inhibitable non-selective
cation channel(SIC) is identical to the vanilloid
receptor throughout all of its first 700 residues, but
it exhibits a different sequence in its last 100
residues. VR1 and SICtransport monovalent cations as
well as Ca2+. VR1 is about 10x more permeable to Ca2+
than to monovalent ions. Ca2+ overload probably causes
cell deathafter chronic exposure to capsaicin.
(McCleskey and Gold, 1999) [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 743
Score = 27.4 bits (61), Expect = 3.7
Identities = 22/73 (30%), Positives = 27/73 (36%), Gaps = 2/73 (2%)
Query: 39 KDLERMDAMNNKQPNREILDHEKKRKIELQCLELQELLEEQGFNEIEV-DAKVMAYRLHL 97
+DLE +N P+R IE + LEL ELL V D + A L
Sbjct: 35 RDLEEPKKLNINCPDRLGRSALFVAAIENENLELTELLLNLS-CRGAVGDTLLHAISLEY 93
Query: 98 NKNVEKINEPPLD 110
VE I L
Sbjct: 94 VDAVEAILLHLLA 106
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 27.1 bits (60), Expect = 4.2
Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 14/95 (14%)
Query: 42 ERMDAM-----NNKQPNREILDHEKKRKIE----LQCLELQELLEEQGFNEIEVDAKVMA 92
E+M+A+ ++ + + LD + K K+E LEL +L+ G I V K
Sbjct: 578 EKMEALKAEVASSGASSGDELDDDLKEKVEKMKKEIELELAGVLKSMGLEVIGVTKKNKD 637
Query: 93 YRLH-----LNKNVEKINEPPLDELGRVMDDTSLK 122
L + +E +NE ++ RV+ + LK
Sbjct: 638 TAEQTPPPNLQEKIESLNEEINKKIERVIRSSDLK 672
>gnl|CDD|240647 cd12170, 2-Hacid_dh_9, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 294
Score = 26.5 bits (59), Expect = 5.3
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 20/78 (25%)
Query: 58 DHEKKRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNVEKINEPPLDELG--RV 115
D E K ++ L L ELL+ ++ L KNV + E + LG ++
Sbjct: 174 DAEAK---GIRYLPLNELLKT---VDV--------ICTCLPKNVILLGEEEFELLGDGKI 219
Query: 116 MDDTSL----KFPLLQKW 129
+ +TSL + L+KW
Sbjct: 220 LFNTSLGPSFEVEALKKW 237
>gnl|CDD|234737 PRK00366, ispG, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate
synthase; Reviewed.
Length = 360
Score = 26.6 bits (60), Expect = 5.9
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 16/40 (40%)
Query: 74 ELLEEQGFNEIEVDAK-------VMAYR---------LHL 97
++LEE GF++I++ K + AYR LHL
Sbjct: 167 KILEELGFDDIKISVKASDVQDLIAAYRLLAKRCDYPLHL 206
>gnl|CDD|215160 PLN02286, PLN02286, arginine-tRNA ligase.
Length = 576
Score = 26.1 bits (58), Expect = 8.3
Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 36 KTEKDLERMDAMNNKQPNREILDHEKKRKIELQCLELQELLEE 78
K+ KD++ + K+ + +LDH +R + L L+ E++EE
Sbjct: 474 KSGKDIDEL-----KKTGKIVLDHPDERALGLHLLQFPEVVEE 511
>gnl|CDD|226111 COG3583, COG3583, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 309
Score = 25.9 bits (57), Expect = 9.1
Identities = 14/105 (13%), Positives = 36/105 (34%), Gaps = 11/105 (10%)
Query: 28 KTKEKTNLKTEKDLERMDAMNNKQPNR-EILDHEKKRKIELQCLELQELLEEQGFN---- 82
++K + + +N + + E+ D K R + + +LL+ +
Sbjct: 127 GPQDKIAPALDTVPKNGLKLNIESAKQVELNDGGKVRTVWTTATTVADLLKAEKIPLGKS 186
Query: 83 ---EIEVDAKV---MAYRLHLNKNVEKINEPPLDELGRVMDDTSL 121
+DA + M ++ + +D ++D S+
Sbjct: 187 DRVNPALDAPIKENMDIQVTRVNSKTDKENEQVDFETVYVEDPSM 231
>gnl|CDD|236033 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed.
Length = 289
Score = 25.8 bits (57), Expect = 9.4
Identities = 7/10 (70%), Positives = 9/10 (90%)
Query: 18 YVQRNWSLVR 27
Y+ RNWS+VR
Sbjct: 108 YILRNWSIVR 117
>gnl|CDD|217501 pfam03339, Pox_L3_FP4, Poxvirus L3/FP4 protein.
Length = 319
Score = 25.9 bits (57), Expect = 10.0
Identities = 24/125 (19%), Positives = 47/125 (37%), Gaps = 35/125 (28%)
Query: 16 NGYVQRNWSLVRKTKEKTNLKTEKDLERMDAMNNKQPNREILDHEKKRKIELQCLE---- 71
N + +N L T +KTE D ++ ++ + +EK+R I C
Sbjct: 5 NASIDKNLPLNNTLLPNTFVKTENDKCILEDFIEQR----LCTYEKERSIYSDCYAGFYY 60
Query: 72 --LQELLEEQGFNEIEVDAKVMAYRLHLNKNVEKINEPPLDELGRVMDDTSLKFPLLQKW 129
L+++ +E+ +E+ A V + + +L FPL+
Sbjct: 61 KLLKQVDDEEANCWLELSALVRSKK-------------------------ALGFPLVYGA 95
Query: 130 QRLSH 134
+R S+
Sbjct: 96 KRHSY 100
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
0.315 0.134 0.387
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,341,888
Number of extensions: 665457
Number of successful extensions: 603
Number of sequences better than 10.0: 1
Number of HSP's gapped: 602
Number of HSP's successfully gapped: 51
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
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: 42 (22.0 bits)
S2: 54 (24.7 bits)