RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11709
(474 letters)
>gnl|CDD|216479 pfam01399, PCI, PCI domain. This domain has also been called the
PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
Length = 100
Score = 47.6 bits (114), Expect = 4e-07
Identities = 22/91 (24%), Positives = 48/91 (52%), Gaps = 5/91 (5%)
Query: 258 IHDLLNIFVAEKVNTYQDFYKQHKEYIVNKLGLDHQENL-RKMRLLTFMQLAETKTEMSF 316
DLL F + ++ +++ +++ +++ + E+L RK+R L +LA+ + +S
Sbjct: 1 YRDLLRAFYSGDLSDFEEILADNEDELLDDGLAELLEDLRRKIRELNLRRLAKPYSSISL 60
Query: 317 DMIQKELDLNPNQIEAF----IIDGKIAAKV 343
+ K L L+ +++E I DG+I K+
Sbjct: 61 SDLAKLLGLSVDEVEKILSKLIRDGRIRGKI 91
Score = 46.4 bits (111), Expect = 1e-06
Identities = 18/80 (22%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 396 IHDLLNIFVSEKVNTYQDFYKQHKEYIVNKLGLDHQENL-RKMRLLTFMQLAETKTEMSF 454
DLL F S ++ +++ +++ +++ + E+L RK+R L +LA+ + +S
Sbjct: 1 YRDLLRAFYSGDLSDFEEILADNEDELLDDGLAELLEDLRRKIRELNLRRLAKPYSSISL 60
Query: 455 DMIQKELDLNPNQIEAFIID 474
+ K L L+ +++E +
Sbjct: 61 SDLAKLLGLSVDEVEKILSK 80
>gnl|CDD|214803 smart00753, PAM, PCI/PINT associated module.
Length = 88
Score = 41.8 bits (99), Expect = 3e-05
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 4/52 (7%)
Query: 296 LRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAF----IIDGKIAAKV 343
RK+RL +QL+E + +S + K L L+ ++E I DG+I+AK+
Sbjct: 7 QRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58
Score = 38.8 bits (91), Expect = 4e-04
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 434 LRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAFIID 474
RK+RL +QL+E + +S + K L L+ ++E +
Sbjct: 7 QRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSK 47
>gnl|CDD|214509 smart00088, PINT, motif in proteasome subunits, Int-6, Nip-1 and
TRIP-15. Also called the PCI (Proteasome, COP9,
Initiation factor 3) domain. Unknown function.
Length = 88
Score = 41.8 bits (99), Expect = 3e-05
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 4/52 (7%)
Query: 296 LRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAF----IIDGKIAAKV 343
RK+RL +QL+E + +S + K L L+ ++E I DG+I+AK+
Sbjct: 7 QRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58
Score = 38.8 bits (91), Expect = 4e-04
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 434 LRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAFIID 474
RK+RL +QL+E + +S + K L L+ ++E +
Sbjct: 7 QRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSK 47
>gnl|CDD|221064 pfam11294, DUF3095, Protein of unknown function (DUF3095). Some
members in this bacterial family of proteins are
annotated as adenylyl cyclase however this cannot be
confirmed. Currently no function is known.
Length = 373
Score = 35.7 bits (83), Expect = 0.049
Identities = 29/127 (22%), Positives = 46/127 (36%), Gaps = 27/127 (21%)
Query: 66 IESVLNSIVSMLVLINPERAENLILAFS-EKLSKASDAKLG--PVTLRVLWLLFQSL--- 119
++ I +P E L + + L + A+ G + LR L +L Q+L
Sbjct: 209 YRDIIALIERDDRGGHPVPVEGPKLKWPPQGLDIEARARRGVGLLWLRRLKVLIQTLLGY 268
Query: 120 ---------EPTSPMRYHVYYHLVQIAQNADQIKSVFKDVDHLKQQFSQCPPSNEQMQKL 170
P RY L ++ +N+D K F D L+ C +Q +L
Sbjct: 269 LLFRTGLKLGGFDPRRY-----LQEVVENSDFRK--FDDG--LRMVID-CTS--DQRDRL 316
Query: 171 LRLLHQA 177
LL A
Sbjct: 317 EALLDAA 323
>gnl|CDD|147504 pfam05352, Phage_connector, Phage Connector (GP10). The head-tail
connector of bacteriophage 29 is composed of 12 36 kDa
subunits with 12 fold symmetry. It is the central
component of a rotary motor that packages the genomic
dsDNA into pre-formed proheads. This motor consists of
the head-tail connector, surrounded by a 29-encoded,
174-base, RNA and a viral ATPase protein.
Length = 281
Score = 34.5 bits (79), Expect = 0.11
Identities = 22/104 (21%), Positives = 46/104 (44%), Gaps = 6/104 (5%)
Query: 264 IFVAEKVNT-YQDFYKQHKEYIVNKLGLDHQENLRKM-RLLTFMQLAETKTEMSFDMIQK 321
IF +++++ Y + +K Y+V+KL + + L+TF+ + + ++
Sbjct: 181 IFAHKQLDSDYIEVFKTDAPYVVDKL---NAQKNAVWNELMTFLGIKNANLDKKERLVTS 237
Query: 322 ELDLNPNQIEAFIIDGKIAAKVMIELLSTYTAENAS-QAREDAQ 364
E+ N QIE+ + + EL++ N S + R D
Sbjct: 238 EVISNNEQIESSGNVYLKSRQEACELINELYGLNVSVKFRYDIV 281
Score = 33.7 bits (77), Expect = 0.18
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 402 IFVSEKVNT-YQDFYKQHKEYIVNKLGLDHQENLRKM-RLLTFMQLAETKTEMSFDMIQK 459
IF +++++ Y + +K Y+V+KL + + L+TF+ + + ++
Sbjct: 181 IFAHKQLDSDYIEVFKTDAPYVVDKL---NAQKNAVWNELMTFLGIKNANLDKKERLVTS 237
Query: 460 ELDLNPNQIEA 470
E+ N QIE+
Sbjct: 238 EVISNNEQIES 248
>gnl|CDD|225946 COG3412, COG3412, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 129
Score = 32.3 bits (74), Expect = 0.16
Identities = 12/48 (25%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 301 LLTFMQL--AETKTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVMIE 346
+L F L A+ EM+ +++ KE+ + +A +++G AA +++
Sbjct: 62 VLVFYDLGSAKLNAEMALELLDKEIAIKNILCDAPLVEGAYAAAALLQ 109
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 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 an 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. 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 mammalian,
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 the 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 = 27.5 bits (62), Expect = 3.7
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 25 VYLKNLGAEISDEK 38
VY+KNLG ++ DEK
Sbjct: 4 VYVKNLGEDMDDEK 17
>gnl|CDD|213341 cd05392, RasGAP_Neurofibromin_like, Ras-GTPase Activating Domain of
proteins similar to neurofibromin. Neurofibromin-like
proteins include the Saccharomyces cerevisiae RasGAP
proteins Ira1 and Ira2, the closest homolog of
neurofibromin, which is responsible for the human
autosomal dominant disease neurofibromatosis type I
(NF1). The RasGAP Ira1/2 proteins are negative
regulators of the Ras-cAMP signaling pathway and
conserved from yeast to human. In yeast Ras proteins are
activated by GEFs, and inhibited by two GAPs, Ira1 and
Ira2. Ras proteins activate the cAMP/protein kinase A
(PKA) pathway, which controls metabolism, stress
resistance, growth, and meiosis. Recent studies showed
that the kelch proteins Gpb1 and Gpb2 inhibit Ras
activity via association with Ira1 and Ira2. Gpb1/2 bind
to a conserved C-terminal domain of Ira1/2, and loss of
Gpb1/2 results in a destabilization of Ira1 and Ira2,
leading to elevated levels of Ras2-GTP and uninhibited
cAMP-PKA signaling. Since the Gpb1/2 binding domain on
Ira1/2 is conserved in the human neurofibromin protein,
the studies suggest that an analogous signaling
mechanism may contribute to the neoplastic development
of NF1.
Length = 317
Score = 29.2 bits (66), Expect = 5.2
Identities = 6/37 (16%), Positives = 12/37 (32%)
Query: 127 YHVYYHLVQIAQNADQIKSVFKDVDHLKQQFSQCPPS 163
+Y H ++I + + S L + F
Sbjct: 280 KFLYLHFLEIRKEVLKGSSSQGSDKELVETFKLIDEI 316
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 29.2 bits (66), Expect = 5.4
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 11/50 (22%)
Query: 108 TLRVLWLL----FQSLEPTSPMRYHVYYHLVQIAQNADQIKSVFKDVDHL 153
T RVL L F+ LEP SP Y ++ D + + DVD L
Sbjct: 86 TFRVLSALRVRLFEKLEPLSPALLLRY-------RSGDLLNRLVADVDAL 128
>gnl|CDD|119355 cd02876, GH18_SI-CLP, Stabilin-1 interacting chitinase-like protein
(SI-CLP) is a eukaryotic chitinase-like protein of
unknown function that interacts with the
endocytic/sorting transmembrane receptor stabilin-1 and
is secreted from the lysosome. SI-CLP has a glycosyl
hydrolase family 18 (GH18) domain but lacks a
chitin-binding domain. The catalytic amino acids of the
GH18 domain are not conserved in SI-CLP, similar to the
chitolectins YKL-39, YKL-40, and YM1/2. Human SI-CLP is
sorted to late endosomes and secretory lysosomes in
alternatively activated macrophages.
Length = 318
Score = 28.4 bits (64), Expect = 8.7
Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 12/78 (15%)
Query: 391 LEGELIHDLLNIFVSEK-----VNTYQDFYKQHK------EYIVNKLGLDHQENLRKMRL 439
EG DL ++ E+ + K++ E ++L + RK +
Sbjct: 75 FEGWSYQDLQSLLNDEQEREKLIKLLVTTAKKNHFDGIVLEVW-SQLAAYGVPDKRKELI 133
Query: 440 LTFMQLAETKTEMSFDMI 457
+ L ET + +I
Sbjct: 134 QLVIHLGETLHSANLKLI 151
>gnl|CDD|215368 PLN02683, PLN02683, pyruvate dehydrogenase E1 component subunit
beta.
Length = 356
Score = 28.2 bits (63), Expect = 9.3
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 11/37 (29%)
Query: 223 EDAQACILAALADPNTFLLHPLLTLKPVKFLEGELIH 259
EDA+ + AA+ DP+ PV FLE EL++
Sbjct: 175 EDARGLLKAAIRDPD-----------PVVFLENELLY 200
Score = 28.2 bits (63), Expect = 9.3
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 11/37 (29%)
Query: 361 EDAQACILAALADPNTFLLHPLLTLKPVKFLEGELIH 397
EDA+ + AA+ DP+ PV FLE EL++
Sbjct: 175 EDARGLLKAAIRDPD-----------PVVFLENELLY 200
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
0.320 0.134 0.373
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,836,317
Number of extensions: 2343989
Number of successful extensions: 2308
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2304
Number of HSP's successfully gapped: 53
Length of query: 474
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 374
Effective length of database: 6,502,202
Effective search space: 2431823548
Effective search space used: 2431823548
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: 61 (27.2 bits)