RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 036919
(132 letters)
>gnl|CDD|180117 PRK05483, rplN, 50S ribosomal protein L14; Validated.
Length = 122
Score = 133 bits (337), Expect = 2e-41
Identities = 53/88 (60%), Positives = 64/88 (72%), Gaps = 2/88 (2%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAV 93
IQ T L VADNSG K VMCI+ L G ++ A +GD IVVSVKE +P KVKKG+VVKAV
Sbjct: 2 IQQETRLNVADNSGAKEVMCIKVLGGSKRRYASIGDVIVVSVKEAIPRGKVKKGDVVKAV 61
Query: 94 VVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
VVR R DGS+++FDDNA VL++N
Sbjct: 62 VVRTKKGVRRPDGSYIRFDDNAAVLLNN 89
>gnl|CDD|201105 pfam00238, Ribosomal_L14, Ribosomal protein L14p/L23e.
Length = 122
Score = 127 bits (323), Expect = 3e-39
Identities = 54/88 (61%), Positives = 67/88 (76%), Gaps = 2/88 (2%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAV 93
IQ+ T L VADNSG K V CI+ L G KK A++GD IVVSVK+ +P KVKKG+VVKAV
Sbjct: 2 IQVGTRLNVADNSGAKKVKCIKVLGGSRKKYAKVGDIIVVSVKKAIPKGKVKKGDVVKAV 61
Query: 94 VVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
+VR + R DGS+++FDDNAVVLI+N
Sbjct: 62 IVRTKKEVRRKDGSYIRFDDNAVVLINN 89
>gnl|CDD|223171 COG0093, RplN, Ribosomal protein L14 [Translation, ribosomal
structure and biogenesis].
Length = 122
Score = 116 bits (293), Expect = 7e-35
Identities = 51/88 (57%), Positives = 65/88 (73%), Gaps = 2/88 (2%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAV 93
IQ++T L VADNSG K VMCI+ L G ++ A +GD IVVSVK+ +P VKKG+VVKAV
Sbjct: 2 IQVQTRLNVADNSGAKEVMCIKVLGGSRRRYAGVGDIIVVSVKKAIPRGMVKKGDVVKAV 61
Query: 94 VVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
VVR + R DGS++KFDDNA V+I+
Sbjct: 62 VVRTKKEVRRPDGSYIKFDDNAAVIINP 89
>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 = 112 bits (281), Expect = 4e-33
Identities = 49/88 (55%), Positives = 63/88 (71%), Gaps = 2/88 (2%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAV 93
IQ ++ L VADNSG K V CI+ L G ++ A +GD IVV VK+ +PN KVKKG+VVKAV
Sbjct: 2 IQQQSRLNVADNSGAKKVQCIKVLGGSRRRYATVGDVIVVVVKDAIPNGKVKKGDVVKAV 61
Query: 94 VVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
+VR R DGS+++FDDNA VLI+
Sbjct: 62 IVRTKKGVRRKDGSYIRFDDNACVLINK 89
>gnl|CDD|176997 CHL00057, rpl14, ribosomal protein L14.
Length = 122
Score = 108 bits (272), Expect = 1e-31
Identities = 42/88 (47%), Positives = 59/88 (67%), Gaps = 2/88 (2%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAV 93
IQ +T L VADNSG + +MCI+ L +K A +GD I+ VKE +PN +K+ EVV+AV
Sbjct: 2 IQPQTYLNVADNSGARKLMCIRVLGASNRKYAHIGDVIIAVVKEAVPNMPLKRSEVVRAV 61
Query: 94 VVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
+VR + R +G ++FDDNA V+ID
Sbjct: 62 IVRTCKELKRDNGMIIRFDDNAAVVIDQ 89
>gnl|CDD|181478 PRK08571, rpl14p, 50S ribosomal protein L14P; Reviewed.
Length = 132
Score = 73.4 bits (181), Expect = 7e-18
Identities = 35/91 (38%), Positives = 51/91 (56%), Gaps = 9/91 (9%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKGKKVAR------LGDTIVVSVKEVMPNAKVKKGEV 89
+ + L ADN+G K V I K V R +GD +VVSVK+ P + +V
Sbjct: 12 LPVGARLVCADNTGAKEVEIISVKGYKGVKRRLPKAGVGDMVVVSVKKGTPEMR---KQV 68
Query: 90 VKAVVVRAAMDHGRCDGSFVKFDDNAVVLID 120
++AVVVR ++ R DG+ VKF+DNA V++
Sbjct: 69 LRAVVVRQRKEYRRPDGTRVKFEDNAAVIVT 99
>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 = 70.8 bits (174), Expect = 7e-17
Identities = 37/91 (40%), Positives = 52/91 (57%), Gaps = 9/91 (9%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKGKKVAR------LGDTIVVSVKEVMPNAKVKKGEV 89
+ + +L ADN+G K V I K V R +GD +VVSVK+ P + +V
Sbjct: 11 LPVGALLVCADNTGAKEVEVISVKGYKGVKRRLPCAGVGDMVVVSVKKGTPEMR---KQV 67
Query: 90 VKAVVVRAAMDHGRCDGSFVKFDDNAVVLID 120
KAVVVR ++ R DG+ VKF+DNAVV++
Sbjct: 68 FKAVVVRQRKEYRRPDGTRVKFEDNAVVIVT 98
>gnl|CDD|185418 PTZ00054, PTZ00054, 60S ribosomal protein L23; Provisional.
Length = 139
Score = 46.6 bits (111), Expect = 2e-07
Identities = 31/88 (35%), Positives = 47/88 (53%), Gaps = 11/88 (12%)
Query: 41 VLKVADNSGVKTVMCIQPLKGKK-------VARLGDTIVVSVKEVMPNAKVKKGEVVKAV 93
V+ ADNSG K + I +KG A LGD ++ +VK+ P + K V+ AV
Sbjct: 24 VVNCADNSGAKNLYIIA-VKGIHGRLNRLPSASLGDMVLATVKKGKPELRKK---VLNAV 79
Query: 94 VVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
++R R DG F+ F+DNA V+++
Sbjct: 80 IIRQRKAWRRKDGVFIYFEDNAGVIVNP 107
>gnl|CDD|219631 pfam07902, Gp58, gp58-like protein. Sequences found in this family
are derived from a number of bacteriophage and prophage
proteins. They are similar to gp58, a minor structural
protein of Lactococcus delbrueckii bacteriophage LL-H.
Length = 601
Score = 31.1 bits (70), Expect = 0.17
Identities = 13/55 (23%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 64 VARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHG-RCDGSFVKFDDNAVV 117
+++ GD+I++++K +P +K+ E++ A+ + +G + G + D N V
Sbjct: 336 ISQSGDSIMLAIKAKLPQSKMSASEIISAINLNR---YGVKISGKNIALDGNTTV 387
>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
exoribonucleases. This model is defined to identify a
pair of paralogous 3-prime exoribonucleases in E. coli,
plus the set of proteins apparently orthologous to one
or the other in other eubacteria. VacB was characterized
originally as required for the expression of virulence
genes, but is now recognized as the exoribonuclease
RNase R (Rnr). Its paralog in E. coli and H. influenzae
is designated exoribonuclease II (Rnb). Both are
involved in the degradation of mRNA, and consequently
have strong pleiotropic effects that may be difficult to
disentangle. Both these proteins share domain-level
similarity (RNB, S1) with a considerable number of other
proteins, and full-length similarity scoring below the
trusted cutoff to proteins associated with various
phenotypes but uncertain biochemistry; it may be that
these latter proteins are also 3-prime exoribonucleases
[Transcription, Degradation of RNA].
Length = 654
Score = 29.7 bits (67), Expect = 0.45
Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 2/59 (3%)
Query: 44 VADNSGVKTVMCIQPLKGKKVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHG 102
V D+ + + + K GD +VV + E + GE+ + ++ D
Sbjct: 99 VPDDPRIYLDIIVPKASVKNELAEGDKVVVELTEYPLRRNLFYGEITQ--ILGNNDDPL 155
>gnl|CDD|130789 TIGR01728, SsuA_fam, ABC transporter, substrate-binding protein,
aliphatic sulfonates family. Members of this family are
substrate-binding periplasmic proteins of ABC
transporters. This subfamily includes SsuA, a member of
a transporter operon needed to obtain sulfur from
aliphatic sulfonates. Related proteins outside the scope
of This model include taurine (NH2-CH2-CH2-S03H) binding
proteins, the probable sulfate ester binding protein
AtsR, and the probable aromatic sulfonate binding
protein AsfC. All these families make sulfur available
when Cys and sulfate levels are low. Please note that
phylogenetic analysis by neighbor-joining suggests that
a number of sequences belonging to this family have been
excluded because of scoring lower than taurine-binding
proteins [Transport and binding proteins, Other].
Length = 288
Score = 27.7 bits (62), Expect = 1.7
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 40 TVLKVADNSGVKTVMCIQPLKGKKVA 65
T + V S ++TV LKGK++A
Sbjct: 83 TAIVVIKGSPIRTV---ADLKGKRIA 105
>gnl|CDD|148056 pfam06223, Phage_tail_T, Minor tail protein T. Minor tail
protein T is located at the distal end and is involved
in the assembly of the initiator complex for tail
polymerisation.
Length = 103
Score = 26.8 bits (59), Expect = 1.9
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 5 FGGLGSLLSGLLTTSHEMASCNF 27
F L +L+ GL+T E A +F
Sbjct: 44 FATLKALVLGLVTGDPEDAPLDF 66
>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1. This model describes
ribosomal protein S1, RpsA. This protein is found in
most bacterial genomes in a single copy, but is not
present in the Mycoplasmas. It is heterogeneous with
respect to the number of repeats of the S1 RNA binding
domain described by PFAM model pfam00575: six repeats in
E. coli and most other bacteria, four in Bacillus
subtilis and some other species. rpsA is an essential
gene in E. coli but not in B. subtilis. It is associated
with the cytidylate kinase gene cmk in many species, and
fused to it in Treponema pallidum. RpsA is proposed
(Medline:97323001) to assist in mRNA degradation. This
model provides trusted hits to most long form (6 repeat)
examples of RpsA. Among homologs with only four repeats
are some to which other (perhaps secondary) functions
have been assigned [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 516
Score = 27.8 bits (62), Expect = 2.1
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 11/57 (19%)
Query: 71 IVVSVKEVMPN------AKVKKGEVVKAVVVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
I + VK++ N AK K G VVK V G+FV+ LI N
Sbjct: 425 ISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIK-----DFGAFVELPGGVEGLIRN 476
>gnl|CDD|179920 PRK05054, PRK05054, exoribonuclease II; Provisional.
Length = 644
Score = 27.1 bits (61), Expect = 2.9
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 59 LKGKKVARLGDTIVVSVKEV 78
+KG+ V +LGD I V++ EV
Sbjct: 613 IKGETVYKLGDVIDVTLAEV 632
>gnl|CDD|217905 pfam04114, Gaa1, Gaa1-like, GPI transamidase component. GPI
(glycosyl phosphatidyl inositol) transamidase is a
multi-protein complex. Gpi16, Gpi8 and Gaa1 for a
sub-complex of the GPI transamidase. GPI transamidase
that adds glycosylphosphatidylinositols (GPIs) to newly
synthesised proteins.
Length = 498
Score = 27.1 bits (60), Expect = 2.9
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 9 GSLLSGLLTTSHEMASCNFLSQLQRTFI 36
S+ + LL ++ ASC L L + F
Sbjct: 309 LSIPAYLLLSTISGASCFVLLILSQKFH 336
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 26.6 bits (58), Expect = 4.4
Identities = 14/38 (36%), Positives = 24/38 (63%)
Query: 47 NSGVKTVMCIQPLKGKKVARLGDTIVVSVKEVMPNAKV 84
+SGV+ V+ ++P K +VA+ V+SV E + A+V
Sbjct: 37 DSGVEVVVGVRPGKSFEVAKADGFEVMSVSEAVRTAQV 74
>gnl|CDD|215404 PLN02758, PLN02758, oxidoreductase, 2OG-Fe(II) oxygenase family
protein.
Length = 361
Score = 26.3 bits (58), Expect = 5.2
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 12/56 (21%)
Query: 40 TVLKVADNSGV-------KTVMCIQPLKGKKVARLGDTIVVSVKEVMPNAKVKKGE 88
TVL+ S V T + + P+ V +GDT+ EV+ N K K E
Sbjct: 240 TVLQQGKGSCVGLQILKDNTWVPVHPVPNALVINIGDTL-----EVLTNGKYKSVE 290
>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase/S1 RNA-binding domain protein; Reviewed.
Length = 647
Score = 26.1 bits (58), Expect = 7.4
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 15/64 (23%)
Query: 41 VLKVADNSGVKTVMCIQPLKGKKVARLGDTIVVSVKEVMPNA------KVKKGEVVKAVV 94
VLKV D V ++ I K + +S+K+++P+ K G +V V
Sbjct: 520 VLKVGDEIKVY-ILDIDKENKK--------LSLSLKKLLPDPWENVEEKYPVGSIVLGKV 570
Query: 95 VRAA 98
VR A
Sbjct: 571 VRIA 574
>gnl|CDD|241331 cd13177, RanBD2_RanBP2_mammal-like, Ran-binding protein 2, Ran
binding domain repeats 2. RanBP2 (also called E3
SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and
nuclear pore complex (NPC) protein Nup358) is a giant
nucleoporin that localizes to the cytosolic face of the
NPC. RanBP2 contains a leucine-rich region, 8
zinc-finger motifs, a cyclophilin A homologous domain,
and 4 RanBDs. Ran is a Ras-like nuclear small GTPase,
which regulates receptor-mediated transport between the
nucleus and the cytoplasm. RanGTP hydrolysis is
stimulated by RanGAP together with the Ran-binding
domain containing acessory proteins RanBP1 and RanBP2.
These accessory proteins stabilize the active GTP-bound
form of Ran. All eukaryotic cells contain RanBP1, but
in vertebrates however, the main RanBP seems to be
RanBP2. There is no RanBP2 ortholog in yeast. Transport
complex disassembly is accomplished by a small
ubiquitin-related modifier-1 (SUMO-1)-modified version
of RanGAP that is bound to RanBP2. RanBP1 acts as a
second line of defense against exported RanGTP-importin
complexes which have escaped from dissociation by
RanBP2. RanBP2 also interacts with the importin subunit
beta-1. RabBD shares structural similarity to the PH
domain, but lacks detectable sequence similarity. The
members here include human, chicken, frog, tunicates,
sea urchins, ticks, sea anemones, and sponges. RanBD
repeats 2 is present in this hierarchy.
Length = 117
Score = 25.4 bits (55), Expect = 7.9
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 33 RTFIQMRTVLKVADNSGVKTVMCIQPLKG 61
R ++ VLKV N + T M ++PL G
Sbjct: 46 RMLMRREQVLKVCANHWITTTMNLKPLSG 74
>gnl|CDD|188655 cd09823, peroxinectin_like, peroxinectin_like animal heme
peroxidases. Peroxinectin is an arthropod protein that
plays a role in invertebrate immunity mechanisms.
Specifically, peroxinectins are secreted as
cell-adhesive and opsonic peroxidases. The immunity
mechanism appears to involve an interaction between
peroxinectin and a transmembrane receptor of the
integrin family. Human myeloperoxidase, which is
included in this wider family, has also been reported to
interact with integrins.
Length = 378
Score = 25.6 bits (57), Expect = 9.0
Identities = 11/30 (36%), Positives = 13/30 (43%)
Query: 6 GGLGSLLSGLLTTSHEMASCNFLSQLQRTF 35
GGL LL GL T + F +L F
Sbjct: 212 GGLDPLLRGLATQPAQKVDRFFTDELTTHF 241
>gnl|CDD|206431 pfam14263, DUF4354, Domain of unknown function (DUF4354). Several
members of this family are annotated as being
ATP/GTP-binding site motif A (P-loop) proteins, but this
could not be confirmed. The one PDB:3NRF structure
solved for this family exhibits an immunoglobin-like
beta-sandwich fold. Crystal packing suggests that a
tetramer is a significant oligomerisation state, and a
disulfide bridge is formed between Cys 125 at the
C-terminal end of the monomer, and Cys 69.
Length = 124
Score = 25.0 bits (55), Expect = 9.7
Identities = 13/41 (31%), Positives = 18/41 (43%)
Query: 74 SVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSFVKFDDN 114
+V E + +K GE VK V A+ D VK D+
Sbjct: 84 TVDEKLTKGTLKPGESVKGFAVFASDDDSVYKARLVKLSDS 124
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
0.323 0.136 0.387
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,354,390
Number of extensions: 542300
Number of successful extensions: 651
Number of sequences better than 10.0: 1
Number of HSP's gapped: 640
Number of HSP's successfully gapped: 32
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)