RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7864
(201 letters)
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 130 bits (330), Expect = 7e-36
Identities = 52/116 (44%), Positives = 77/116 (66%), Gaps = 4/116 (3%)
Query: 1 NLLPSERKKLLNKQKKAKRKELEKANAIAAAQEKREQHNKARQQTNNQDNDTDTPQQDEL 60
NL P+ERKKL KQ+KA++K EK A AA +K+ + + + + + +
Sbjct: 405 NLSPAERKKLRKKQRKAEKKA-EKEEAEKAAAKKKAEAAAKKAKGPDGETK---KVDPDP 460
Query: 61 IPDKLAKTEEPLEQAVKFLSPLQLLAKDRIETHLMAFEIYFRRQKPLLMLQSVKRA 116
+ +KLA+TE+PLE+A+KFL PL L+ D IETHL+AFE+Y R++K LL LQ++K A
Sbjct: 461 LGEKLARTEDPLEEAMKFLKPLLQLSPDNIETHLLAFEVYIRKKKYLLALQALKAA 516
>gnl|CDD|217329 pfam03033, Glyco_transf_28, Glycosyltransferase family 28
N-terminal domain. The glycosyltransferase family 28
includes monogalactosyldiacylglycerol synthase (EC
2.4.1.46) and UDP-N-acetylglucosamine transferase (EC
2.4.1.-). This N-terminal domain contains the acceptor
binding site and likely membrane association site. This
family also contains a large number of proteins that
probably have quite distinct activities.
Length = 136
Score = 30.4 bits (69), Expect = 0.26
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 142 GAEGDVHPAV---WEVLKSGLEPIMGSKPALE 170
G G V PAV W + + G E +G+ P LE
Sbjct: 7 GTRGHVFPAVALAWALRRRGHEVRLGTPPGLE 38
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 31.4 bits (71), Expect = 0.34
Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 12/91 (13%)
Query: 6 ERKKLLNKQKKAKRKELEKANAIAAAQEKREQHNKARQQTNNQDNDTDTPQQDELIPDKL 65
ERKK K++KAK KEL+K A ++ KA+ Q + T+ P++ K
Sbjct: 19 ERKK--KKEEKAKEKELKKLKA-------AQKEAKAKLQAQQASDGTNVPKKS---EKKS 66
Query: 66 AKTEEPLEQAVKFLSPLQLLAKDRIETHLMA 96
K + E F+ P + + + MA
Sbjct: 67 RKRDVEDENPEDFIDPDTPFGQKKRLSSQMA 97
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal.
This domain is found to the N-terminus of bacterial
signal peptidases of the S49 family (pfam01343).
Length = 154
Score = 29.8 bits (68), Expect = 0.53
Identities = 10/37 (27%), Positives = 15/37 (40%)
Query: 2 LLPSERKKLLNKQKKAKRKELEKANAIAAAQEKREQH 38
LL + K K +K K KA A +E+ +
Sbjct: 62 LLDKKELKAWEKAEKKAEKAKAKAEKKKAKKEEPKPR 98
>gnl|CDD|241396 cd13242, PH_puratrophin-1, Puratrophin-1 pleckstrin homology (PH)
domain. Puratrophin-1 (also called Purkinje cell
atrophy-associated protein 1 or PLEKHG4/Pleckstrin
homology domain-containing family G member 4) contains a
spectrin repeat, a RhoGEF (DH) domain, and a PH domain.
It is thought to function in intracellular signaling and
cytoskeleton dynamics at the Golgi. Puratrophin-1 is
expressed in kidney, Leydig cells in the testis,
epithelial cells in the prostate gland and Langerhans
islet in the pancreas. A single nucleotide substitution
in the puratrophin-1 gene were once thought to result in
autosomal dominant cerebellar ataxia (ADCA), but now it
has been demonstrated that this ataxia is a result of
defects in the BEAN gene. Puratrophin contains a domain
architecture similar to that of Dbl family members Dbs
and Trio. Dbs is a guanine nucleotide exchange factor
(GEF), which contains spectrin repeats, a RhoGEF (DH)
domain and a PH domain. The Dbs PH domain participates
in binding to both the Cdc42 and RhoA GTPases. Trio
plays an essential role in regulating the actin
cytoskeleton during axonal guidance and branching. Trio
is a multidomain signaling protein that contains two
RhoGEF(DH)-PH domains in tandem. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 136
Score = 29.2 bits (66), Expect = 0.68
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 6/27 (22%)
Query: 97 FEIYFRRQKP--LLMLQ----SVKRAW 117
FEI+FRR+K +LQ +K AW
Sbjct: 94 FEIWFRRRKSRDTYILQATSPEIKEAW 120
>gnl|CDD|148363 pfam06717, DUF1202, Protein of unknown function (DUF1202). This
family consists of several hypothetical bacterial
proteins of around 335 residues in length. Members of
this family are found exclusively in Escherichia coli
and Salmonella species and are often referred to as YggM
proteins. The function of this family is unknown.
Length = 308
Score = 29.2 bits (65), Expect = 1.3
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 2/75 (2%)
Query: 16 KAKRKELEKANAIAAAQEKREQHNKARQQTNNQDNDTDTPQQDELIPDKLAKTEEPLEQA 75
A RK+ E+ + Q++ N+ R+QT + + QD+ I L K + PL
Sbjct: 227 AACRKQSEECYEVPIQQKRDFDINEQRRQTFLKSQELSRKLQDDWI--TLEKGQYPLTMK 284
Query: 76 VKFLSPLQLLAKDRI 90
V L+ Q +I
Sbjct: 285 VSELNSQQSTILMKI 299
>gnl|CDD|227000 COG4653, COG4653, Predicted phage phi-C31 gp36 major capsid-like
protein [General function prediction only].
Length = 422
Score = 29.0 bits (65), Expect = 1.9
Identities = 16/84 (19%), Positives = 26/84 (30%), Gaps = 6/84 (7%)
Query: 2 LLPSERKKLLNKQKKAKRKELEKANAIAAAQEKREQHNKARQQTNNQDNDT-----DTPQ 56
L + +Q++ E E+ N A +R +K N D DT
Sbjct: 21 ALTRHATAIRAEQRRRGE-EAEEENRRLLADIERVGGDKLDAIPGNLDKDTAFLALIACV 79
Query: 57 QDELIPDKLAKTEEPLEQAVKFLS 80
L A+T +P +
Sbjct: 80 AARLKLGGAAETADPACREGPPAF 103
>gnl|CDD|224426 COG1509, KamA, Lysine 2,3-aminomutase [Amino acid transport and
metabolism].
Length = 369
Score = 28.4 bits (64), Expect = 2.5
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 148 HPAVWEVLKSGLEPIMGSKPALE 170
HP + EVL SG +P+ S LE
Sbjct: 156 HPEIREVLLSGGDPLSLSDKKLE 178
>gnl|CDD|215519 PLN02960, PLN02960, alpha-amylase.
Length = 897
Score = 28.6 bits (64), Expect = 2.8
Identities = 13/51 (25%), Positives = 23/51 (45%)
Query: 1 NLLPSERKKLLNKQKKAKRKELEKANAIAAAQEKREQHNKARQQTNNQDND 51
L+ +E ++L + RK K AA + ++ + K RQQ D +
Sbjct: 16 PLVHAEPRRLGASRVNLPRKIGFKITCFAAPRPRQPKQKKKRQQEPGSDAE 66
>gnl|CDD|237637 PRK14193, PRK14193, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 28.1 bits (63), Expect = 2.8
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 145 GDVHPAVWEV 154
GDVHP VWEV
Sbjct: 243 GDVHPDVWEV 252
>gnl|CDD|219621 pfam07890, Rrp15p, Rrp15p. Rrp15p is required for the formation
of 60S ribosomal subunits.
Length = 132
Score = 27.3 bits (61), Expect = 3.2
Identities = 16/38 (42%), Positives = 20/38 (52%)
Query: 5 SERKKLLNKQKKAKRKELEKANAIAAAQEKREQHNKAR 42
S KKLL +KK K ++LEK EKR+ K R
Sbjct: 25 SRSKKLLKAKKKLKSEKLEKKAKRQLRAEKRQALEKGR 62
>gnl|CDD|234504 TIGR04216, halo_surf_glyco, major cell surface glycoprotein.
Members of this family are the S-layer-forming
halobacterial major cell surface glycoprotein. The
highest scores below model cutoffs are fragmentary
paralogs to actual members of the family. Modifications
include at N-linked and O-linked glycosylation, a
C-terminal diphytanylglyceryl modification, and probable
cleavage of the PGF-CTERM tail.
Length = 782
Score = 28.3 bits (63), Expect = 3.2
Identities = 9/44 (20%), Positives = 16/44 (36%)
Query: 32 QEKREQHNKARQQTNNQDNDTDTPQQDELIPDKLAKTEEPLEQA 75
+ +R + T T P++ + TEEP E+
Sbjct: 710 ETERPDTTTSEDPTTTTTPTTTGPEETTETAEPTTTTEEPTEET 753
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 27.5 bits (62), Expect = 5.0
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 5 SERKKLLNKQKKAKRK 20
S ++KLL KQK+ K++
Sbjct: 565 SRKRKLLEKQKEGKKR 580
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 27.7 bits (62), Expect = 5.3
Identities = 34/141 (24%), Positives = 54/141 (38%), Gaps = 2/141 (1%)
Query: 4 PSERKKLLNKQKKAKRKELEKANAIAAAQEKREQHNKARQQTNN-QDNDTDTPQQDELIP 62
E L K + +E+E A A+A + Q KA N D D+P+ ++
Sbjct: 549 EEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPDSPEAWLMLG 608
Query: 63 DKLAKTEEPLEQAVKFLSPLQLLAKDRIETHLMAFEIYFRRQKPLLMLQSVKRAWALDPK 122
+ L +AV L L D L+ + Y + + S+KRA L P
Sbjct: 609 RAQLAAGD-LNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELKPD 667
Query: 123 NPTLHTCLIRLALFIEQMKGA 143
N L +L L ++ + A
Sbjct: 668 NTEAQIGLAQLLLAAKRTESA 688
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 27.3 bits (62), Expect = 5.6
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 5 SERKKLLNKQKKAKRK 20
S ++KLL KQK+ K++
Sbjct: 562 SRKRKLLEKQKEGKKR 577
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 27.6 bits (62), Expect = 6.0
Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 14/72 (19%)
Query: 13 KQKKAKRKELE---------KANAIAAAQEKREQHNKARQQTNNQDNDTDTPQQDELIPD 63
K KKA ++ K A+AAA R + KA QQ + + + + D
Sbjct: 558 KAKKAAQQAANAEAEEEVDPKKAAVAAAIA-RAKAKKAAQQAASAEPEEQVAEVD----P 612
Query: 64 KLAKTEEPLEQA 75
K A + +A
Sbjct: 613 KKAAVAAAIARA 624
>gnl|CDD|227509 COG5182, CUS1, Splicing factor 3b, subunit 2 [RNA processing and
modification].
Length = 429
Score = 27.3 bits (60), Expect = 6.5
Identities = 12/45 (26%), Positives = 17/45 (37%)
Query: 7 RKKLLNKQKKAKRKELEKANAIAAAQEKREQHNKARQQTNNQDND 51
RK+ N Q K KA A +R + K TN++
Sbjct: 7 RKRSGNNQNKNASVVNNKAEIAAMIDARRLEQKKKGGVTNSKGKT 51
>gnl|CDD|217898 pfam04107, GCS2, Glutamate-cysteine ligase family 2(GCS2). Also
known as gamma-glutamylcysteine synthetase and gamma-ECS
(EC:6.3.2.2). This enzyme catalyzes the first and rate
limiting step in de novo glutathione biosynthesis.
Members of this family are found in archaea, bacteria
and plants. May and Leaver discuss the possible
evolutionary origins of glutamate-cysteine ligase
enzymes in different organisms and suggest that it
evolved independently in different eukaryotes, from an
ancestral bacterial enzyme. They also state that
Arabidopsis thaliana gamma-glutamylcysteine synthetase
is structurally unrelated to mammalian, yeast and
Escherichia coli homologues. In plants, there are
separate cytosolic and chloroplast forms of the enzyme.
Length = 289
Score = 27.0 bits (60), Expect = 6.5
Identities = 10/79 (12%), Positives = 22/79 (27%), Gaps = 13/79 (16%)
Query: 96 AFEIYFRRQKPLLMLQSVKRAWALDPKNPTLH------------TCLIRLALFIEQMKGA 143
AFE Y R ++ +R W D + P L + + +
Sbjct: 195 AFERYARYALDTGIIFVRRRLW-WDGRPPGLPGETLELRIHDTTAFPPVRLRALLEARLL 253
Query: 144 EGDVHPAVWEVLKSGLEPI 162
+ + + + +
Sbjct: 254 DAQPDWRLDALPAAWTVAL 272
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 27.1 bits (60), Expect = 6.6
Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 7 RKKLLNKQKKAKRKEL--EKANAIAAAQEKREQHNKARQQTNNQDNDTDTPQQDELIPDK 64
RKK + ++++A +E+ E AAA + A + + +P +D ++
Sbjct: 346 RKKEIAQKRRAAEREINREARQERAAAMARARARRAAV-KAKKKGLIDASPNEDTPSENE 404
Query: 65 LAKTEEPLEQA 75
+K P +A
Sbjct: 405 ESKGSPPQVEA 415
>gnl|CDD|203441 pfam06421, LepA_C, GTP-binding protein LepA C-terminus. This
family consists of the C-terminal region of several
pro- and eukaryotic GTP-binding LepA proteins.
Length = 108
Score = 26.0 bits (58), Expect = 6.7
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 5 SERKKLLNKQKKAKRK 20
S +KKLL KQK+ K++
Sbjct: 73 SRKKKLLEKQKEGKKR 88
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 26.8 bits (60), Expect = 6.8
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 6 ERKKLLNKQKKAKRKELEKANA--IAAAQEKREQHNKARQQTN 46
E K L K+ K + ELEK ++ +E+ A++ N
Sbjct: 110 EELKQLEKELKKLKAELEKYEKNDPERIEKLKEETKVAKEAAN 152
>gnl|CDD|221012 pfam11169, DUF2956, Protein of unknown function (DUF2956). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 103
Score = 26.1 bits (58), Expect = 7.2
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 13 KQKKAKRKELEKANAIAAAQEKREQHNKARQQTNNQDNDTDTPQQ 57
KQ+KAK +E +KA K++ K RQ N+ + DT
Sbjct: 41 KQQKAKAREADKA-------RKQQLKAKQRQAANDDEEDTIESVT 78
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 26.7 bits (59), Expect = 8.6
Identities = 10/48 (20%), Positives = 19/48 (39%)
Query: 12 NKQKKAKRKELEKANAIAAAQEKREQHNKARQQTNNQDNDTDTPQQDE 59
+ + + A +EK +Q ++Q D D + Q+DE
Sbjct: 384 KLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKRQKDE 431
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
0.314 0.129 0.363
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,021,430
Number of extensions: 923746
Number of successful extensions: 1345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1251
Number of HSP's successfully gapped: 148
Length of query: 201
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 109
Effective length of database: 6,857,034
Effective search space: 747416706
Effective search space used: 747416706
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 (22.0 bits)
S2: 56 (25.4 bits)