RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6163
(137 letters)
>gnl|CDD|185418 PTZ00054, PTZ00054, 60S ribosomal protein L23; Provisional.
Length = 139
Score = 223 bits (569), Expect = 2e-76
Identities = 98/127 (77%), Positives = 113/127 (88%)
Query: 2 SKRGRGGSAGAKFRISLALPVGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMF 61
KRGRGG G KFR++L LPVGAV+NCADN+GAKNL++IAV+G+ GRLNRLP+A GDM
Sbjct: 1 MKRGRGGVGGNKFRVTLGLPVGAVVNCADNSGAKNLYIIAVKGIHGRLNRLPSASLGDMV 60
Query: 62 VATVKKGKPELRKKVMPAVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPV 121
+ATVKKGKPELRKKV+ AV+IRQRK +RR+DGVFIYFEDNAGVIVN KGEMKGSAITGPV
Sbjct: 61 LATVKKGKPELRKKVLNAVIIRQRKAWRRKDGVFIYFEDNAGVIVNPKGEMKGSAITGPV 120
Query: 122 AKENAQI 128
AKE A +
Sbjct: 121 AKECADL 127
>gnl|CDD|181478 PRK08571, rpl14p, 50S ribosomal protein L14P; Reviewed.
Length = 132
Score = 163 bits (416), Expect = 3e-53
Identities = 66/117 (56%), Positives = 86/117 (73%)
Query: 11 GAKFRISLALPVGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKP 70
G + +++ LPVGA + CADNTGAK + +I+V+G KG RLP AG GDM V +VKKG P
Sbjct: 3 GIRSKVTRGLPVGARLVCADNTGAKEVEIISVKGYKGVKRRLPKAGVGDMVVVSVKKGTP 62
Query: 71 ELRKKVMPAVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKENAQ 127
E+RK+V+ AVV+RQRK +RR DG + FEDNA VIV +G KG+ I GPVA+E A+
Sbjct: 63 EMRKQVLRAVVVRQRKEYRRPDGTRVKFEDNAAVIVTPEGTPKGTEIKGPVAREAAE 119
>gnl|CDD|132712 TIGR03673, rpl14p_arch, 50S ribosomal protein L14P. Part of the
50S ribosomal subunit. Forms a cluster with proteins L3
and L24e, part of which may contact the 16S rRNA in 2
intersubunit bridges.
Length = 131
Score = 156 bits (397), Expect = 2e-50
Identities = 70/117 (59%), Positives = 86/117 (73%)
Query: 11 GAKFRISLALPVGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKP 70
G + I+ ALPVGA++ CADNTGAK + VI+V+G KG RLP AG GDM V +VKKG P
Sbjct: 2 GIRAGITRALPVGALLVCADNTGAKEVEVISVKGYKGVKRRLPCAGVGDMVVVSVKKGTP 61
Query: 71 ELRKKVMPAVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKENAQ 127
E+RK+V AVV+RQRK +RR DG + FEDNA VIV GE KG+ I GPVA+E A+
Sbjct: 62 EMRKQVFKAVVVRQRKEYRRPDGTRVKFEDNAVVIVTPDGEPKGTEIKGPVAREAAE 118
>gnl|CDD|223171 COG0093, RplN, Ribosomal protein L14 [Translation, ribosomal
structure and biogenesis].
Length = 122
Score = 132 bits (335), Expect = 4e-41
Identities = 50/109 (45%), Positives = 66/109 (60%), Gaps = 7/109 (6%)
Query: 19 ALPVGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKP-ELRKK-- 75
+ V +N ADN+GAK + I V G R AG GD+ V +VKK P + KK
Sbjct: 1 MIQVQTRLNVADNSGAKEVMCIKVLGGSRRR----YAGVGDIIVVSVKKAIPRGMVKKGD 56
Query: 76 VMPAVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKE 124
V+ AVV+R +K RR DG +I F+DNA VI+N GE +G+ I GPVA+E
Sbjct: 57 VVKAVVVRTKKEVRRPDGSYIKFDDNAAVIINPDGEPRGTRIFGPVARE 105
>gnl|CDD|201105 pfam00238, Ribosomal_L14, Ribosomal protein L14p/L23e.
Length = 122
Score = 123 bits (311), Expect = 2e-37
Identities = 50/109 (45%), Positives = 70/109 (64%), Gaps = 7/109 (6%)
Query: 19 ALPVGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKG--KPELRK-K 75
+ VG +N ADN+GAK + I V G R A GD+ V +VKK K +++K
Sbjct: 1 MIQVGTRLNVADNSGAKKVKCIKVLGGS----RKKYAKVGDIIVVSVKKAIPKGKVKKGD 56
Query: 76 VMPAVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKE 124
V+ AV++R +K RR+DG +I F+DNA V++NNKGE KG+ I GPVA+E
Sbjct: 57 VVKAVIVRTKKEVRRKDGSYIRFDDNAVVLINNKGEPKGTRIFGPVARE 105
>gnl|CDD|180117 PRK05483, rplN, 50S ribosomal protein L14; Validated.
Length = 122
Score = 87.9 bits (219), Expect = 2e-23
Identities = 46/101 (45%), Positives = 62/101 (61%), Gaps = 7/101 (6%)
Query: 27 NCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKPELRKK---VMPAVVIR 83
N ADN+GAK + I V G R A GD+ V +VK+ P + K V+ AVV+R
Sbjct: 9 NVADNSGAKEVMCIKVLGGSKRRY----ASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVR 64
Query: 84 QRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKE 124
+K RR DG +I F+DNA V++NN GE +G+ I GPVA+E
Sbjct: 65 TKKGVRRPDGSYIRFDDNAAVLLNNDGEPRGTRIFGPVARE 105
>gnl|CDD|176997 CHL00057, rpl14, ribosomal protein L14.
Length = 122
Score = 82.6 bits (205), Expect = 2e-21
Identities = 39/101 (38%), Positives = 61/101 (60%), Gaps = 7/101 (6%)
Query: 27 NCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKPEL---RKKVMPAVVIR 83
N ADN+GA+ L I V G R A GD+ +A VK+ P + R +V+ AV++R
Sbjct: 9 NVADNSGARKLMCIRVLGASNR----KYAHIGDVIIAVVKEAVPNMPLKRSEVVRAVIVR 64
Query: 84 QRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKE 124
K +R +G+ I F+DNA V+++ +G KG+ + GP+A+E
Sbjct: 65 TCKELKRDNGMIIRFDDNAAVVIDQEGNPKGTRVFGPIARE 105
>gnl|CDD|130139 TIGR01067, rplN_bact, ribosomal protein L14, bacterial/organelle.
This model distinguishes bacterial and most organellar
examples of ribosomal protein L14 from all archaeal and
eukaryotic forms [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 122
Score = 77.4 bits (191), Expect = 2e-19
Identities = 43/105 (40%), Positives = 61/105 (58%), Gaps = 7/105 (6%)
Query: 23 GAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKPELRKK---VMPA 79
+ +N ADN+GAK + I V G R A GD+ V VK P + K V+ A
Sbjct: 5 QSRLNVADNSGAKKVQCIKVLGGSRR----RYATVGDVIVVVVKDAIPNGKVKKGDVVKA 60
Query: 80 VVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKE 124
V++R +K RR+DG +I F+DNA V++N E +G+ I GPVA+E
Sbjct: 61 VIVRTKKGVRRKDGSYIRFDDNACVLINKNKEPRGTRIFGPVARE 105
>gnl|CDD|241398 cd13244, PH_PLEKHG5_G6, Pleckstrin homology domain-containing
family G member 5 and 6 pleckstrin homology (PH) domain.
PLEKHG5 has a RhoGEF DH/double-homology domain in
tandem with a PH domain which is involved in
phospholipid binding. PLEKHG5 activates the nuclear
factor kappa B (NFKB1) signaling pathway. Mutations in
PLEKHG5 are associated with autosomal recessive distal
spinal muscular atrophy. PLEKHG6 (also called MyoGEF)
has no known function to date. 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 = 154
Score = 27.6 bits (62), Expect = 1.6
Identities = 10/45 (22%), Positives = 13/45 (28%), Gaps = 8/45 (17%)
Query: 59 DMFVATVKKGKPELRKKVMPAVVIRQRKPFRRRDGVFIYFEDNAG 103
DM + K E RK + R P V +D
Sbjct: 73 DMLLICKPVKKKEDRKVI--------RPPPLHDKIVVHELKDPGS 109
>gnl|CDD|216010 pfam00588, SpoU_methylase, SpoU rRNA Methylase family. This
family of proteins probably use S-AdoMet.
Length = 142
Score = 27.1 bits (61), Expect = 2.0
Identities = 9/46 (19%), Positives = 18/46 (39%)
Query: 22 VGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKK 67
+GA+ A GA L ++ + + A +G +F +
Sbjct: 15 LGAIARTAAAFGADGLILVEPRCADPYNPKAIRASAGALFHLPLVI 60
>gnl|CDD|197509 smart00086, PAC, Motif C-terminal to PAS motifs (likely to
contribute to PAS structural domain). PAC motif occurs
C-terminal to a subset of all known PAS motifs. It is
proposed to contribute to the PAS domain fold.
Length = 43
Score = 24.8 bits (55), Expect = 3.7
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 88 FRRRDGVFIYFEDNAGVIVNNKGEMKG 114
RR+DG +I+ +A I + GE++G
Sbjct: 6 LRRKDGSYIWVLVSASPIRDEDGEVEG 32
>gnl|CDD|225487 COG2936, COG2936, Predicted acyl esterases [General function
prediction only].
Length = 563
Score = 26.6 bits (59), Expect = 5.2
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 78 PAVVIRQRKPFRRRDGVF 95
P ++ R R P+R+R+G F
Sbjct: 46 PVLLSRTRLPYRKRNGTF 63
>gnl|CDD|213827 TIGR03554, F420_G6P_DH, glucose-6-phosphate dehydrogenase
(coenzyme-F420). This family consists of the
F420-dependent glucose-6-phosphate dehydrogenase of
Mycobacterium and Nocardia. It shows homology to several
other F420-dependent enzymes rather than to the NAD or
NADP-dependent glucose-6-phosphate dehydrogenases
[Energy metabolism, Pentose phosphate pathway].
Length = 331
Score = 26.1 bits (57), Expect = 6.9
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 54 AAGSGDMFVATVKKGKPELRKKVMPAVVIRQRKPFRRRDGV 94
A +GD F+ T KG+ +K+MPAV K R D +
Sbjct: 183 AGRAGDGFICTSGKGEELYTEKLMPAVAEGAAKADRDVDSI 223
>gnl|CDD|140341 PTZ00320, PTZ00320, ribosomal protein L14; Provisional.
Length = 188
Score = 25.8 bits (56), Expect = 8.0
Identities = 26/116 (22%), Positives = 53/116 (45%), Gaps = 9/116 (7%)
Query: 2 SKRGRGGSAGAKFRISLALPVGAVINCADNTGAKNLFVIAVQGVKGRLN--RLPAAGSGD 59
S R R G+ + + ++C DNT K++ +I+ + R R+ A +
Sbjct: 42 SYRSRWGTGAEGYGTGVPFSDQVKLHCVDNTNCKHVRLIS-KATAERFAHCRVFPAVAHR 100
Query: 60 MFVATVKKGKPEL-RKKVMPA-----VVIRQRKPFRRRDGVFIYFEDNAGVIVNNK 109
+ V K G+ E+ R +V P ++ +R+ R G+ F+ N +++N++
Sbjct: 101 VSVQRFKSGRGEVSRHRVKPGNIYWVCLLSRRQTNTRMSGLQTNFDRNTCILMNDQ 156
>gnl|CDD|200535 cd11274, Sema_plexin_A4, The Sema domain, a protein interacting
module, of Plexin A4. Plexin A4 forms a receptor
complex with neuropilins (NRPs) and transduces signals
for class 3 semaphorins in the nervous system. It
regulates facial nerve development by functioning as a
receptor for Sema3A/NRP1. Both plexins A3 and A4 are
essential for normal sympathetic development. They
function both cooperatively, to regulate the migration
of sympathetic neurons, and differentially, to guide
sympathetic axons. Plexin A4 is also expressed in
lymphoid tissues and functions in the immune system. It
negatively regulates T lymphocyte responses. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a ligand-recognition and -binding
module.
Length = 473
Score = 26.1 bits (57), Expect = 8.5
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 60 MFVATVKKGKPELRKKVMPAVVIRQRKPFRRRDGVFIY-FED 100
+F+AT GKPE P + R+ DG+F Y F D
Sbjct: 145 LFIATAVDGKPEY----FPTISSRKLTKNSEADGMFAYVFHD 182
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 0.139 0.407
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,112,686
Number of extensions: 661451
Number of successful extensions: 528
Number of sequences better than 10.0: 1
Number of HSP's gapped: 517
Number of HSP's successfully gapped: 23
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
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: 54 (24.5 bits)