RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9699
(123 letters)
>gnl|CDD|219145 pfam06703, SPC25, Microsomal signal peptidase 25 kDa subunit
(SPC25). This family consists of several microsomal
signal peptidase 25 kDa subunit proteins. Translocation
of polypeptide chains across the endoplasmic reticulum
(ER) membrane is triggered by signal sequences.
Subsequently, signal recognition particle interacts with
its membrane receptor and the ribosome-bound nascent
chain is targeted to the ER where it is transferred into
a protein-conducting channel. At some point, a second
signal sequence recognition event takes place in the
membrane and translocation of the nascent chain through
the membrane occurs. The signal sequence of most
secretory and membrane proteins is cleaved off at this
stage. Cleavage occurs by the signal peptidase complex
(SPC) as soon as the lumenal domain of the translocating
polypeptide is large enough to expose its cleavage site
to the enzyme. The signal peptidase complex is possibly
also involved in proteolytic events in the ER membrane
other than the processing of the signal sequence, for
example the further digestion of the cleaved signal
peptide or the degradation of membrane proteins.
Mammalian signal peptidase is as a complex of five
different polypeptide chains. This family represents the
25 kDa subunit (SPC25).
Length = 161
Score = 105 bits (265), Expect = 3e-30
Identities = 45/105 (42%), Positives = 60/105 (57%), Gaps = 4/105 (3%)
Query: 16 PVLIMCVTTYFLMMGILTLYTTYKEKGIFAVA-KKDHI---VWEASSYLKKYDDMYNLVL 71
PVLI CV YF++ GILTL++ + EKGI V +KD SS LKKYD +Y L +
Sbjct: 57 PVLIACVALYFVLSGILTLWSKFVEKGIVYVGKRKDGFSGEKLTISSSLKKYDPLYTLTI 116
Query: 72 QYKDTKTGVTRSEQFNKSVANYFDETGLLLPDLVENDVSRLHNSI 116
KD + R + KS A +FDE G + DL E +S L N++
Sbjct: 117 TVKDKSSSSQREVELTKSFAEFFDEDGYFVEDLFEKWLSELLNAL 161
>gnl|CDD|181224 PRK08084, PRK08084, DNA replication initiation factor; Provisional.
Length = 235
Score = 27.7 bits (62), Expect = 1.5
Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 17/63 (26%)
Query: 51 HIVWEASSYLKKYDDMYNLVLQYKDTKTGVTRSEQFNKSVANYFDETGLLLPDLVENDVS 110
+WE + + D+YN +L+ T+ +T + L LPDL S
Sbjct: 112 DELWEMAIF-----DLYNRILESGRTRLLITGDRPPR--------QLNLGLPDL----AS 154
Query: 111 RLH 113
RL
Sbjct: 155 RLD 157
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 27.4 bits (61), Expect = 1.8
Identities = 31/112 (27%), Positives = 45/112 (40%), Gaps = 24/112 (21%)
Query: 3 YLPRNFTPVKRFEPVLIMCVTTYFLMMGILTLYTTYKEKGIFAVAKKDHIVWEASSYLKK 62
Y+P TP + + +M + F + G T+ T E+GI V ++ IV
Sbjct: 199 YIP---TPERETDKPFLMPIEDVFSITGRGTVVTGRVERGIVKVGEEVEIV--------- 246
Query: 63 YDDMYNLVLQYKDT-KTGVTRSEQFNKSV--ANYFDETGLLLPDLVENDVSR 111
KDT KT VT E F K + D GLLL + ++ R
Sbjct: 247 ---------GLKDTRKTTVTGVEMFRKELDEGRAGDNVGLLLRGIKREEIER 289
>gnl|CDD|220548 pfam10067, DUF2306, Predicted membrane protein (DUF2306).
Members of this family of hypothetical bacterial
proteins have no known function.
Length = 102
Score = 26.1 bits (58), Expect = 2.9
Identities = 9/41 (21%), Positives = 16/41 (39%), Gaps = 5/41 (12%)
Query: 23 TTYFLMMGILTLYTTYKEKGIFAVAKKD---HIVWEASSYL 60
+ ++ +LTL T + A + + H W SY
Sbjct: 41 FSPIHLLSLLTLITLV--LAVRAARRGNIAAHRAWMIRSYA 79
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 26.7 bits (59), Expect = 3.7
Identities = 30/111 (27%), Positives = 42/111 (37%), Gaps = 20/111 (18%)
Query: 3 YLPRNFTPVKRFEPVLIMCVTTYFLMMGILTLYTTYKEKGIFAVAKKDHIVWEASSYLKK 62
Y+P PV+ + +M + F + G T+ T E+G V ++ IV
Sbjct: 250 YIP---EPVRVLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEIVG-------- 298
Query: 63 YDDMYNLVLQYKDTKTGVTRSEQFNKSVAN--YFDETGLLLPDLVENDVSR 111
+ KT VT E F K + D GLLL L DV R
Sbjct: 299 -------LRPGGPLKTTVTGVEMFKKILDQGQAGDNVGLLLRGLKREDVQR 342
>gnl|CDD|233815 TIGR02294, nickel_nikA, nickel ABC transporter, nickel/metallophore
periplasmic binding protein. Members of this family are
periplasmic nickel-binding proteins of nickel ABC
transporters. Most appear to be lipoproteins. This
protein was previously (circa 2003) thought to mediate
binding to nickel through water molecules, but is now
thought to involve a chelating organic molecule, perhaps
butane-1,2,4-tricarboxylate, acting as a metallophore
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 500
Score = 25.9 bits (57), Expect = 6.3
Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 1/60 (1%)
Query: 43 IFAVAKKDHIVWEASSYLKKYDDMYNLVLQYKDTKTGVTRSEQFNKSVANYFDETGLLLP 102
I A+ K H A S L D++ + + R E + K++ + + +P
Sbjct: 410 ISAMRAKGHGDESAQSGLANKDEIDKSIGDALASTDETERQELY-KNILTTLHDEAVYIP 468
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 26.0 bits (57), Expect = 7.4
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 35 YTTYKEKGIF--AVAKKDHIVWEASSYLKKYDDMYNLVLQYKDTKT 78
Y + + G+ AV K H V K + D++NL+LQ D T
Sbjct: 540 YVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGT 585
>gnl|CDD|149916 pfam09002, DUF1887, Domain of unknown function (DUF1887). This
domain is found in a set of hypothetical bacterial
proteins.
Length = 379
Score = 25.5 bits (56), Expect = 7.9
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 89 SVANYFDETGLLLPDLVENDVSRLHNSILAEKKKE 123
Y +E LLL DL E ++ IL +E
Sbjct: 209 KQQGYLNELNLLLEDLAETGLATYEGGILTFLDEE 243
>gnl|CDD|182070 PRK09776, PRK09776, putative diguanylate cyclase; Provisional.
Length = 1092
Score = 25.4 bits (56), Expect = 9.7
Identities = 10/44 (22%), Positives = 15/44 (34%), Gaps = 11/44 (25%)
Query: 1 MWYLPRNFTPV-----------KRFEPVLIMCVTTYFLMMGILT 33
+ YLP FT + R E LI T + + +
Sbjct: 190 LLYLPWPFTFIIVLLMWSAVRLPRMEAFLIFLTTVMMVSLMMAA 233
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 0.136 0.403
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,205,957
Number of extensions: 524379
Number of successful extensions: 462
Number of sequences better than 10.0: 1
Number of HSP's gapped: 461
Number of HSP's successfully gapped: 25
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
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 (21.8 bits)
S2: 53 (24.1 bits)