RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18092
(183 letters)
>gnl|CDD|216697 pfam01784, NIF3, NIF3 (NGG1p interacting factor 3). This family
contains several NIF3 (NGG1p interacting factor 3)
protein homologues. NIF3 interacts with the yeast
transcriptional coactivator NGG1p which is part of the
ADA complex, the exact function of this interaction is
unknown.
Length = 237
Score = 83.1 bits (206), Expect = 7e-20
Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 4/67 (5%)
Query: 116 SDLDEIMINSIAVCAGSGGELL---RGKKADLYITGEMSHHDVLDATHRGTTVLLLEHSD 172
DLD+ I +A+C GSGG L+ + K ADL ITGE+ HHD LDA +G ++ H
Sbjct: 163 GDLDK-PIKKVAICGGSGGSLIEEAKAKGADLLITGELKHHDALDAKEKGIALIDAGHYA 221
Query: 173 SERPFLQ 179
+ER L+
Sbjct: 222 TERFGLK 228
>gnl|CDD|223404 COG0327, COG0327, Uncharacterized conserved protein [Function
unknown].
Length = 250
Score = 69.6 bits (171), Expect = 7e-15
Identities = 28/83 (33%), Positives = 39/83 (46%), Gaps = 6/83 (7%)
Query: 100 SIHTVANTSTHVLIKDSDLDEIMINSIAVCAGSGGELL---RGKKADLYITGEMSHHDVL 156
I ++KD I +AVC+GSG L + D YITG++SHH
Sbjct: 148 RIKAKLGRPPLRVVKDGSE---EIKRVAVCSGSGQGFLSEAAAEGVDAYITGDLSHHTAH 204
Query: 157 DATHRGTTVLLLEHSDSERPFLQ 179
DA G +V+ H +ERP L+
Sbjct: 205 DARELGLSVIDAGHYATERPGLK 227
>gnl|CDD|213534 TIGR00486, YbgI_SA1388, dinuclear metal center protein, YbgI/SA1388
family. The characterization of this family of
uncharacterized proteins as orthologous is tentative.
Members are found in all three domains of life. Several
members (from Bacillus subtilis, Listeria monocytogenes,
and Mycobacterium tuberculosis - all classified as
Firmicutes within the Eubacteria) share a long insert
relative to other members [Unknown function, General].
Length = 249
Score = 58.6 bits (142), Expect = 7e-11
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 122 MINSIAVCAGSGGELL---RGKKADLYITGEMSHHDVLDATHRGTTVLLLEHSDSERPFL 178
+ +AV +GSG + + D YITG++SHH A G V+ H +ER L
Sbjct: 166 YVKKVAVVSGSGLSFIMKALREGVDAYITGDLSHHTAHLARELGLNVIDAGHYATERGGL 225
Query: 179 Q 179
+
Sbjct: 226 R 226
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 31.1 bits (71), Expect = 0.32
Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 25/80 (31%)
Query: 112 LIKDSDLDEIMINSIAVCAGSGGELLR-------GKKADLYITGEMSHHDVLD------- 157
++K +L++++ V SGGEL R ++ADLY+ E S + LD
Sbjct: 439 IVKPLNLEDLLERP--VDELSGGELQRVAIAAALSREADLYLLDEPSAY--LDVEQRIIV 494
Query: 158 -------ATHRGTTVLLLEH 170
+ T L+++H
Sbjct: 495 AKVIRRFIENNEKTALVVDH 514
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 30.2 bits (69), Expect = 0.55
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 10/52 (19%)
Query: 112 LIKDSDLDEIMINSIAVCAGSGGELLR-------GKKADLYITGE-MSHHDV 155
+IK L+ ++ + V SGGEL R + ADLY+ E +H DV
Sbjct: 437 IIKPLQLERLLDKN--VKDLSGGELQRVAIAACLSRDADLYLLDEPSAHLDV 486
>gnl|CDD|140232 PTZ00205, PTZ00205, DNA polymerase kappa; Provisional.
Length = 571
Score = 30.0 bits (67), Expect = 0.64
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 46 LSSFSLRFRDDKTARDTVSRVVTRLFAMEKIPGS---NPTINKKKLDSYF---DGKHFGV 99
+S++ RF KTA D S + R+F K+ S PT K+ S +G+H +
Sbjct: 236 VSAYIERFEGTKTAEDVASELRVRVFGETKLTASAGIGPTAALAKIASNINKPNGQH-DL 294
Query: 100 SIHTVANTSTHV 111
++HT + T+V
Sbjct: 295 NLHTRGDVMTYV 306
>gnl|CDD|184910 PRK14946, PRK14946, DNA polymerase III subunit beta; Provisional.
Length = 366
Score = 29.4 bits (66), Expect = 1.1
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 14/57 (24%)
Query: 43 SPILSSFSLRFRDDK---TARDTVSRVVTRLFAMEKIPGSNP-----TINKKKLDSY 91
PILS+ +L+ D+ +A DT+ FA EKI SNP +I+ K L +
Sbjct: 152 QPILSAINLKSEDNFLHFSATDTIR------FASEKIEISNPSRIDISISAKNLKDF 202
>gnl|CDD|234196 TIGR03397, acid_phos_Burk, acid phosphatase, Burkholderia-type. A
member of this family, AcpA from Burkholderia mallei,
has been charactized as a surface-bound glycoprotein
with acid phosphatase activity, as can be shown with the
colorigenic substrate 5-bromo-4-chloro-3-indolyl
phosphate. This family shares regions of sequence
similarity with phosphocholine-preferring phospholipase
C enzymes (TIGR03396) from many of the same species.
Length = 483
Score = 29.0 bits (65), Expect = 1.6
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 45 ILSSFSLRFRDDKTARDTVS--RVVTRLFAMEKIPG 78
++S F+ + D T DT S R +TR F + +PG
Sbjct: 422 VVSPFAKKGYVDHTPYDTTSILRFITRRFGLPPLPG 457
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 28.5 bits (64), Expect = 2.0
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 132 SGGELLR-------GKKADLYITGEMSHHDVLDATHR 161
SGGEL R K AD+Y+ E S + LD R
Sbjct: 117 SGGELQRVAIAACLSKDADIYLLDEPSAY--LDVEQR 151
>gnl|CDD|184794 PRK14697, PRK14697, bifunctional
5'-methylthioadenosine/S-adenosylhomocysteine
nucleosidase/phosphatase; Provisional.
Length = 233
Score = 28.4 bits (63), Expect = 2.1
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 105 ANTSTHVLIKDSDLDEIMINSIAVCAGSGGELLRGKKADLYITGEMSHHDV 155
A T LI D+D I+ +A GG K D+ I+ ++HHDV
Sbjct: 56 AAACTQTLIHKFDVDAIINTGVA-----GGLHPDVKVGDIVISTNVTHHDV 101
>gnl|CDD|237212 PRK12808, PRK12808, flagellin; Provisional.
Length = 476
Score = 28.4 bits (63), Expect = 2.1
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 12/66 (18%)
Query: 79 SNPTINKKKLDSYFDGKHFGVSIHTVANTSTHVLIKDSDLDEIMINSIAVCAGSGGELLR 138
SN +IN + LDS K G+ +K + L+ + IN +++ A + E +
Sbjct: 138 SNSSINIQTLDSSDGDKQIGID------------LKSATLEALGINDLSIGANTDIEAVS 185
Query: 139 GKKADL 144
K A L
Sbjct: 186 TKIAAL 191
>gnl|CDD|234806 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional.
Length = 1809
Score = 28.3 bits (63), Expect = 2.7
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 21/61 (34%)
Query: 132 SGGELLR----------GKKADLYI-----TGEMSH------HDVLDATHRGTTVLLLEH 170
SGGE+ R KK LY+ TG +H + + TH+G TV+++EH
Sbjct: 811 SGGEIQRLKLAYELLAPSKKPTLYVLDEPTTGLHTHDIKALIYVLQSLTHQGHTVVIIEH 870
Query: 171 S 171
+
Sbjct: 871 N 871
>gnl|CDD|234541 TIGR04320, Surf_Exclu_PgrA, SEC10/PgrA surface exclusion domain.
This model describes a conserved domain found in surface
proteins of a number of Firmutes. Many members have
LPXTG C-terminal anchoring motifs and a substantial
number have the KxYKxGKxW putative sorting signal at the
N-terminus. The tetracycline resistance plasmid pCF10 in
Enterococcus faecalis promotes conjugal plasmid transfer
in response to sex pheromones, but PgrA/Sec10 encoded by
that plasmid, a member of this family, specifically
inhibits the ability of cells to receive homologous
plasmids. The phenomenon is called surface exclusion.
Length = 356
Score = 28.2 bits (63), Expect = 2.7
Identities = 6/32 (18%), Positives = 10/32 (31%)
Query: 88 LDSYFDGKHFGVSIHTVANTSTHVLIKDSDLD 119
G + GVSI + H + +
Sbjct: 207 DGKGNPGAYLGVSISNDGGVNIHFVNFNDSYI 238
>gnl|CDD|222616 pfam14239, RRXRR, RRXRR protein. This domain is found in bacteria,
eukaryotes and viruses, and is approximately 180 amino
acids in length. It contains a conserved RRXRR motif. It
is often found in association with pfam01844.
Length = 174
Score = 27.1 bits (61), Expect = 3.8
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 10/38 (26%)
Query: 33 DNVRSRNGWLSPILSSFSLRFRDDKTARDTVSRVVTRL 70
N + GWL+P SL+ R DT R V RL
Sbjct: 113 LNRKRPKGWLAP-----SLQHR-----VDTTLRWVKRL 140
>gnl|CDD|178888 PRK00132, rpsI, 30S ribosomal protein S9; Reviewed.
Length = 130
Score = 26.6 bits (60), Expect = 4.4
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 11/37 (29%)
Query: 57 KTARDTVSRVVTRLFAMEKIPGS-NPTINKKKLDSYF 92
KTA V+RV RL PGS T+N + L+ YF
Sbjct: 13 KTA---VARV--RL-----KPGSGKITVNGRDLEEYF 39
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammals, such
as ovary and testis. It may play an important role in
germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 26.0 bits (58), Expect = 4.5
Identities = 12/24 (50%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 1 MLYREVSTIGSPAFIRVCL-LSTR 23
MLY S G IRVC L TR
Sbjct: 15 MLYEIFSPAGPVLSIRVCRDLITR 38
>gnl|CDD|152611 pfam12176, MtaB, Methanol-cobalamin methyltransferase B subunit.
This family of proteins is found in bacteria and
archaea. Proteins in this family are approximately 460
amino acids in length. MtaB folds as a TIM barrel and
contains a novel zinc-binding motif. Zinc(II) lies at
the bottom of a funnel formed at the C-terminal
beta-barrel end and ligates to two cysteinyl sulfurs
(Cys-220 and Cys-269) and one carboxylate oxygen
(Glu-164). The function of this protein is to catalyze
the cleavage of the C O bond in methanol by an SN2
mechanism. It complexes with MtaA and MtaC to perform
this function.
Length = 460
Score = 27.4 bits (61), Expect = 5.4
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 83 INKKKLDSYFDGKHFGVSI---HTVANT---STHVLIKDSDLDEIMINSIAVCAGSGGEL 136
K ++ Y D +G+ HT+A+ + ++ D +M+ + CA +G ++
Sbjct: 103 AQKTIMEEYHD--KYGIKCALRHTIADIREEREFLGLRRGDKYSVMLEAFEACAENGADI 160
Query: 137 L 137
L
Sbjct: 161 L 161
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
0.322 0.137 0.404
Gapped
Lambda K H
0.267 0.0799 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,329,649
Number of extensions: 850627
Number of successful extensions: 674
Number of sequences better than 10.0: 1
Number of HSP's gapped: 670
Number of HSP's successfully gapped: 24
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
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 (21.9 bits)
S2: 56 (25.2 bits)