RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2224
(504 letters)
>gnl|CDD|240016 cd04658, Piwi_piwi-like_Euk, Piwi_piwi-like_Euk: PIWI domain,
Piwi-like subfamily found in eukaryotes. This domain is
found in Piwi and closely related proteins, where it is
believed to perform a crucial role in germline cells,
via RNA silencing. RNA silencing refers to a group of
related gene-silencing mechanisms mediated by short RNA
molecules, including siRNAs, miRNAs, and
heterochromatin-related guide RNAs. The mechanism in
Piwi is believed to be similar to that in Argonaute, the
central component of the RNA-induced silencing complex
(RISC). The PIWI domain is the C-terminal portion of
Argonaute and consists of two subdomains, one of which
provides the 5' anchoring of the guide RNA and the
other, the catalytic site for slicing.
Length = 448
Score = 160 bits (408), Expect = 4e-44
Identities = 81/293 (27%), Positives = 131/293 (44%), Gaps = 64/293 (21%)
Query: 273 RLMKPLGEITRVRPRERVAKFNVFRKRIE-NSEAKEVLKRWELALDTNLARVQGHILPPD 331
LMK L E T++ P+ER F +RI+ N +E+LK+W + LD+N ++QG +LPP+
Sbjct: 1 NLMKELAEHTKLNPKERYDTIRQFIQRIQKNPSVQELLKKWGIELDSNPLKIQGRVLPPE 60
Query: 332 SIIFSDPLKPFPVGPDANWTTPTRS-SVFRAPNLERWCVLTTGFMMADTENFLQLINKAA 390
II + +A+W R+ ++ A NL W ++ + E+FLQ + + A
Sbjct: 61 QIIMGN--VFVYANSNADWKREIRNQPLYDAVNLNNWVLIYPSRDQREAESFLQTLKQVA 118
Query: 391 QGMRFKVNRPNVIV---------------------------------------KK----- 406
M +++ P +I KK
Sbjct: 119 GPMGIQISPPKIIKVKDDRIETYIRALKDAFRSDPQLVVIILPGNKKDLYDAIKKFCCVE 178
Query: 407 -----------NLASKGAL-TIATKVAIQLCCKIGGAPWSVAVP---LKGLMVLGFDVTH 451
L K L +IA+K+A+Q+ K+GG PW+V +P LK M++G DV H
Sbjct: 179 CPVPSQVITSRTLKKKKNLRSIASKIALQINAKLGGIPWTVEIPPFILKNTMIVGIDVYH 238
Query: 452 DSDLKGSSYGALVASIDPQMSSWFSRVSPHRSGNEL-SNDIAVSVVHALHKYR 503
D+ K S VAS++ ++ WFS+ G E + + S+ AL Y+
Sbjct: 239 DTITKKKSVVGFVASLNKSITKWFSKYISQVRGQEEIIDSLGKSMKKALKAYK 291
>gnl|CDD|239211 cd02845, PAZ_piwi_like, PAZ domain, Piwi_like subfamily. In
multi-cellular organisms, the Piwi protein appears to be
essential for the maintenance of germline stem cells. In
the Drosophila male germline, Piwi was shown to be
involved in the silencing of retrotransposons in the
male gametes. The Piwi proteins share their domain
architecture with other members of the argonaute family.
The PAZ domain has been named after the proteins Piwi,
Argonaut, and Zwille. PAZ is found in two families of
proteins that are essential components of RNA-mediated
gene-silencing pathways, including RNA interference, the
Piwi and Dicer families. PAZ functions as a nucleic acid
binding domain, with a strong preference for
single-stranded nucleic acids (RNA or DNA) or RNA
duplexes with single-stranded 3' overhangs. It has been
suggested that the PAZ domain provides a unique mode for
the recognition of the two 3'-terminal nucleotides in
single-stranded nucleic acids and buries the 3' OH
group, and that it might recognize characteristic 3'
overhangs in siRNAs within RISC (RNA-induced silencing)
and other complexes.
Length = 117
Score = 150 bits (380), Expect = 8e-44
Identities = 55/128 (42%), Positives = 81/128 (63%), Gaps = 12/128 (9%)
Query: 139 IMLCVELSHKVLRKETVLDAWEQCRNDKYFYYRKFEAQMTNSIVLTKYNNKTYRVDDIQY 198
++ HK+ R+ET E+C ++ SIVLT+YNNKTYR+DDI +
Sbjct: 1 STTVLDRMHKLYRQETDERFREECEK-----------ELIGSIVLTRYNNKTYRIDDIDF 49
Query: 199 DVTPCSTFPMK-GENVSYIDYYQKKYNETIRNRNQPMIVHKSKLRELRAGQSEIIYLVPE 257
D TP STF G +++++YY+K+YN I + NQP++V + K R+ R G+ E IYL+PE
Sbjct: 50 DKTPLSTFKKSDGTEITFVEYYKKQYNIEITDLNQPLLVSRPKRRDPRGGEKEPIYLIPE 109
Query: 258 LCYLTGLS 265
LC+LTGL+
Sbjct: 110 LCFLTGLT 117
>gnl|CDD|198017 smart00949, PAZ, This domain is named PAZ after the proteins Piwi
Argonaut and Zwille. This domain is found in two
families of proteins that are involved in
post-transcriptional gene silencing. These are the Piwi
family and the Dicer family, that includes the Carpel
factory protein. The function of the domains is unknown
but has been suggested to mediate complex formation
between proteins of the Piwi and Dicer families by
hetero-dimerisation. The three-dimensional structure of
this domain has been solved. The PAZ domain is composed
of two subdomains. One subdomain is similar to the OB
fold, albeit with a different topology. The OB-fold is
well known as a single-stranded nucleic acid binding
fold. The second subdomain is composed of a beta-hairpin
followed by an alpha-helix. The PAZ domains shows
low-affinity nucleic acid binding and appears to
interact with the 3' ends of single-stranded regions of
RNA in the cleft between the two subdomains. PAZ can
bind the characteristic two-base 3' overhangs of siRNAs,
indicating that although PAZ may not be a primary
nucleic acid binding site in Dicer or RISC, it may
contribute to the specific and productive incorporation
of siRNAs and miRNAs into the RNAi pathway.
Length = 138
Score = 141 bits (357), Expect = 4e-40
Identities = 54/116 (46%), Positives = 81/116 (69%), Gaps = 1/116 (0%)
Query: 172 KFEAQMTNSIVLTKYNNKTYRVDDIQYDVTPCSTFPMK-GENVSYIDYYQKKYNETIRNR 230
+ + IVLT+YNNKTYR+DDI +++ P STF G +++++YY++KYN TIR+
Sbjct: 22 RCAKDLKGLIVLTRYNNKTYRIDDIDWNLAPKSTFEKSDGSEITFVEYYKQKYNITIRDP 81
Query: 231 NQPMIVHKSKLRELRAGQSEIIYLVPELCYLTGLSDDMRADFRLMKPLGEITRVRP 286
NQP++V + K R + G+ E + L PELC++TGL+D MR DF LMK + + TR+ P
Sbjct: 82 NQPLLVSRPKRRRNQNGKGEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
>gnl|CDD|216914 pfam02170, PAZ, PAZ domain. This domain is named PAZ after the
proteins Piwi Argonaut and Zwille. This domain is found
in two families of proteins that are involved in
post-transcriptional gene silencing. These are the Piwi
family and the Dicer family, that includes the Carpel
factory protein. The function of the domains is unknown
but has been suggested to mediate complex formation
between proteins of the Piwi and Dicer families by
hetero-dimerisation. The three-dimensional structure of
this domain has been solved. The PAZ domain is composed
of two subdomains. One subdomain is similar to the OB
fold, albeit with a different topology. The OB-fold is
well known as a single-stranded nucleic acid binding
fold. The second subdomain is composed of a beta-hairpin
followed by an alpha-helix. The PAZ domains shows
low-affinity nucleic acid binding and appears to
interact with the 3' ends of single-stranded regions of
RNA in the cleft between the two subdomains. PAZ can
bind the characteristic two-base 3' overhangs of siRNAs,
indicating that although PAZ may not be a primary
nucleic acid binding site in Dicer or RISC, it may
contribute to the specific and productive incorporation
of siRNAs and miRNAs into the RNAi pathway.
Length = 114
Score = 103 bits (258), Expect = 2e-26
Identities = 44/124 (35%), Positives = 64/124 (51%), Gaps = 11/124 (8%)
Query: 147 HKVLRKETVLDAWEQCRNDKYFYYRKFEAQMTNSIVLTKYNNKTYRVDDIQYDVTPCSTF 206
VL T + Q + KF + IV T YNN+TYR+D I +D TP STF
Sbjct: 1 QPVLDFLTDIL--TQRTPLGDDFREKFTKALKGLIVETTYNNRTYRIDGITWDPTPNSTF 58
Query: 207 PMKGEN-VSYIDYYQKKYNETIRNRNQPMIVHKSKLRELRAGQSEIIYLVPELCYLTGLS 265
P+K +S +Y+++KYN T++ N P++V K + YL PELC++TG
Sbjct: 59 PLKDGGEISVAEYFKEKYNITLKYPNLPLLVVGRKKKP--------NYLPPELCFITGGQ 110
Query: 266 DDMR 269
M+
Sbjct: 111 RYMK 114
>gnl|CDD|214930 smart00950, Piwi, This domain is found in the protein Piwi and its
relatives. The function of this domain is the dsRNA
guided hydrolysis of ssRNA. Determination of the crystal
structure of Argonaute reveals that PIWI is an RNase H
domain, and identifies Argonaute as Slicer, the enzyme
that cleaves mRNA in the RNAi RISC complex.. In
addition, Mg+2 dependence and production of 3'-OH and 5'
phosphate products are shared characteristics of RNaseH
and RISC. The PIWI domain core has a tertiary structure
belonging to the RNase H family of enzymes. RNase H fold
proteins all have a five-stranded mixed beta-sheet
surrounded by helices. By analogy to RNase H enzymes
which cleave single-stranded RNA guided by the DNA
strand in an RNA/DNA hybrid, the PIWI domain can be
inferred to cleave single-stranded RNA, for example
mRNA, guided by double stranded siRNA.
Length = 301
Score = 77.8 bits (192), Expect = 8e-16
Identities = 27/106 (25%), Positives = 45/106 (42%), Gaps = 5/106 (4%)
Query: 402 VIVKKNLASKGALTIATKVAIQLCCKIGGAPWSV---AVPLKGLMVLGFDVTHDSDLKGS 458
+ K + T VA+++ K+GG W + +PLK +++G DV+H S KG
Sbjct: 36 KTLDKVSKRRKLKQYLTNVALKINAKLGGINWVLDVPPIPLKPTLIIGIDVSHPSAGKGG 95
Query: 459 SYGALVASIDPQMSSWFSRV-SPHRSGNELSNDIAVSVVHALHKYR 503
S VA+ ++ S + S + + AL KY
Sbjct: 96 SVAPSVAAFVASG-NYLSGNFYQAFVREQGSRQLKEILREALKKYY 140
>gnl|CDD|216915 pfam02171, Piwi, Piwi domain. This domain is found in the protein
Piwi and its relatives. The function of this domain is
the dsRNA guided hydrolysis of ssRNA. Determination of
the crystal structure of Argonaute reveals that PIWI is
an RNase H domain, and identifies Argonaute as Slicer,
the enzyme that cleaves mRNA in the RNAi RISC complex.
In addition, Mg+2 dependence and production of 3'-OH and
5' phosphate products are shared characteristics of
RNaseH and RISC. The PIWI domain core has a tertiary
structure belonging to the RNase H family of enzymes.
RNase H fold proteins all have a five-stranded mixed
beta-sheet surrounded by helices. By analogy to RNase H
enzymes which cleave single-stranded RNA guided by the
DNA strand in an RNA/DNA hybrid, the PIWI domain can be
inferred to cleave single-stranded RNA, for example
mRNA, guided by double stranded siRNA.
Length = 296
Score = 66.6 bits (163), Expect = 4e-12
Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 3/91 (3%)
Query: 416 IATKVAIQLCCKIGGA-PWSVAVPLKGLMVLGFDVTHDS--DLKGSSYGALVASIDPQMS 472
T V +++ K+GG W V +P K +++GFD++H + S VAS+D
Sbjct: 45 TLTNVLLKINVKLGGLNYWIVEIPPKIDVIIGFDISHGTGGTDDNPSVVGFVASMDKHPQ 104
Query: 473 SWFSRVSPHRSGNELSNDIAVSVVHALHKYR 503
+ V SG EL + ++ +L +
Sbjct: 105 KYAGGVRYQASGQELIEPLKEIILESLRSFY 135
>gnl|CDD|239207 cd02825, PAZ, PAZ domain, named PAZ after the proteins Piwi
Argonaut and Zwille. PAZ is found in two families of
proteins that are essential components of RNA-mediated
gene-silencing pathways, including RNA interference, the
piwi and Dicer families. PAZ functions as a nucleic-acid
binding domain, with a strong preference for
single-stranded nucleic acids (RNA or DNA) or RNA
duplexes with single-stranded 3' overhangs. It has been
suggested that the PAZ domain provides a unique mode for
the recognition of the two 3'-terminal nucleotides in
single-stranded nucleic acids and buries the 3' OH
group, and that it might recognize characteristic 3'
overhangs in siRNAs within RISC (RNA-induced silencing)
and other complexes. This parent model also contains
structures of an archaeal PAZ domain.
Length = 115
Score = 55.9 bits (135), Expect = 9e-10
Identities = 26/94 (27%), Positives = 47/94 (50%), Gaps = 7/94 (7%)
Query: 171 RKFEAQMTNSIVLTKYN--NKTYRVDDIQYDVTPCSTFPMKGENVSYIDYYQKKYNETIR 228
+F ++ V +N N+ YR D P G+ +++ DY++++YN T+
Sbjct: 27 EEFTKELKGLKVEDTHNPLNRVYRPDGETRLKAPSQLKHSDGKEITFADYFKERYNLTLT 86
Query: 229 NRNQPMIVHKSKLRELRAGQSEIIYLVPELCYLT 262
+ NQP+++ K ++ S I L PELC +T
Sbjct: 87 DLNQPLLIVKFSSKK-----SYSILLPPELCVIT 115
>gnl|CDD|239210 cd02844, PAZ_CAF_like, PAZ domain, CAF_like subfamily. CAF (for
carpel factory) is a plant homolog of Dicer. CAF has
been implicated in flower morphogenesis and in early
Arabidopsis development and might function through
posttranscriptional regulation of specific mRNA
molecules. PAZ domains are named after the proteins
Piwi, Argonaut, and Zwille. PAZ is found in two families
of proteins that are essential components of
RNA-mediated gene-silencing pathways, including RNA
interference, the Piwi and Dicer families. PAZ functions
as a nucleic-acid binding domain, with a strong
preference for single-stranded nucleic acids (RNA or
DNA) or RNA duplexes with single-stranded 3' overhangs.
It has been suggested that the PAZ domain provides a
unique mode for the recognition of the two 3'-terminal
nucleotides in single-stranded nucleic acids and buries
the 3' OH group, and that it might recognize
characteristic 3' overhangs in siRNAs within RISC
(RNA-induced silencing) and other complexes.
Length = 135
Score = 53.2 bits (128), Expect = 1e-08
Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 18/98 (18%)
Query: 179 NSIVLTKYNNKTYRVDDIQYDVTPCSTFPMK--GENVSYIDYYQKKYNETIRNRNQPMIV 236
S+V +N + Y V D+ S+FP K +Y +Y+++KY + + NQP++
Sbjct: 33 GSVVTAPHNGRFY-VISGILDLNANSSFPGKEGLGYATYAEYFKEKYGIVLNHPNQPLLK 91
Query: 237 --HKSKLREL-------------RAGQSEIIYLVPELC 259
L L + + L PELC
Sbjct: 92 GKQIFNLHNLLHNRFEEKGESEEKEKDRYFVELPPELC 129
>gnl|CDD|239212 cd02846, PAZ_argonaute_like, PAZ domain, argonaute_like subfamily.
Argonaute is part of the RNA-induced silencing complex
(RISC), and is an endonuclease that plays a key role in
the RNA interference pathway. The PAZ domain has been
named after the proteins Piwi,Argonaut, and Zwille. PAZ
is found in two families of proteins that are essential
components of RNA-mediated gene-silencing pathways,
including RNA interference, the Piwi and Dicer families.
PAZ functions as a nucleic acid binding domain, with a
strong preference for single-stranded nucleic acids (RNA
or DNA) or RNA duplexes with single-stranded 3'
overhangs. It has been suggested that the PAZ domain
provides a unique mode for the recognition of the two
3'-terminal nucleotides in single-stranded nucleic acids
and buries the 3' OH group, and that it might recognize
characteristic 3' overhangs in siRNAs within RISC
(RNA-induced silencing) and other complexes.
Length = 114
Score = 46.5 bits (111), Expect = 2e-06
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 185 KYNNKTYRVDDIQYDVTPCSTFPMKGEN--VSYIDYYQKKYNETIRNRNQPMIVHKSKLR 242
N+ Y++ + + TF +K +S DY+++KYN ++ N P + K +
Sbjct: 43 GNTNRKYKIKGLSAEPASQQTFELKDGEKEISVADYFKEKYNIRLKYPNLPCLQVGRKGK 102
Query: 243 ELRAGQSEIIYLVPELC 259
YL ELC
Sbjct: 103 P--------NYLPMELC 111
>gnl|CDD|239209 cd02843, PAZ_dicer_like, PAZ domain, dicer_like subfamily. Dicer is
an RNAse involved in cleaving dsRNA in the RNA
interference pathway. It generates dsRNAs which are
approximately 20 bp long (siRNAs), which in turn target
hydrolysis of homologous RNAs. PAZ domains are named
after the proteins Piwi Argonaut and Zwille. PAZ is
found in two families of proteins that are essential
components of RNA-mediated gene-silencing pathways,
including RNA interference, the piwi and Dicer families.
PAZ functions as a nucleic-acid binding domain, with a
strong preference for single-stranded nucleic acids (RNA
or DNA) or RNA duplexes with single-stranded 3'
overhangs. It has been suggested that the PAZ domain
provides a unique mode for the recognition of the two
3'-terminal nucleotides in single-stranded nucleic acids
and buries the 3' OH group, and that it might recognize
characteristic 3' overhangs in siRNAs within RISC
(RNA-induced silencing) and other complexes.
Length = 122
Score = 43.2 bits (102), Expect = 3e-05
Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 6/69 (8%)
Query: 172 KFEA-QMTNSIVLTKYNN----KTYRVDDIQYDVTPCSTFPMKGENVSYIDYYQKKYNET 226
KF+A +++V+ Y N + + V +I D+ P S FP E ++ +YY+KKY
Sbjct: 35 KFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFP-GPEYETFEEYYKKKYKLD 93
Query: 227 IRNRNQPMI 235
I+N NQP++
Sbjct: 94 IQNLNQPLL 102
>gnl|CDD|240015 cd04657, Piwi_ago-like, Piwi_ago-like: PIWI domain, Argonaute-like
subfamily. Argonaute is the central component of the
RNA-induced silencing complex (RISC) and related
complexes. The PIWI domain is the C-terminal portion of
Argonaute and consists of two subdomains, one of which
provides the 5' anchoring of the guide RNA and the
other, the catalytic site for slicing.
Length = 426
Score = 41.8 bits (99), Expect = 5e-04
Identities = 53/247 (21%), Positives = 85/247 (34%), Gaps = 74/247 (29%)
Query: 307 EVLKRWELALDTNLARVQGHILPPDSIIFSDPLKPFPVGPDANWTTPTRSSVF-RAPNLE 365
LK + +++ + V G +LPP + + D K P + +W R F +
Sbjct: 1 PYLKEFGISVSKEMITVPGRVLPPPKLKYGDSSKTVPPR-NGSWNL--RGKKFLEGGPIR 57
Query: 366 RWCVLTTG------FMMADTENFLQLINKAAQG-----------------------MRFK 396
W VL AD NF+ + K G + K
Sbjct: 58 SWAVLNFAGPRRSREERADLRNFVDQLVKTVIGAGINITTAIASVEGRVEELFAKLKQAK 117
Query: 397 VNRPNVIV----KKNLASKGAL-TIA-TKVAIQLCC------------------------ 426
P +++ KK+ G + +A T++ I C
Sbjct: 118 GEGPQLVLVILPKKDSDIYGRIKRLADTELGIHTQCVLAKKVTKKGNPQYFANVALKINL 177
Query: 427 KIGGAPWSVAVPLKGL------MVLGFDVTH---DSDLKGSSYGALVASIDPQMSSWFSR 477
K+GG S+ ++ L MVLG DVTH S A+VAS+D ++ + +
Sbjct: 178 KLGGINHSLEPDIRPLLTKEPTMVLGADVTHPSPGDPAGAPSIAAVVASVDWHLAQYPAS 237
Query: 478 VS--PHR 482
V HR
Sbjct: 238 VRLQSHR 244
>gnl|CDD|239208 cd02826, Piwi-like, Piwi-like: PIWI domain. Domain found in
proteins involved in RNA silencing. RNA silencing refers
to a group of related gene-silencing mechanisms mediated
by short RNA molecules, including siRNAs, miRNAs, and
heterochromatin-related guide RNAs. The central
component of the RNA-induced silencing complex (RISC)
and related complexes is Argonaute. The PIWI domain is
the C-terminal portion of Argonaute and consists of two
subdomains, one of which provides the 5' anchoring of
the guide RNA and the other, the catalytic site for
slicing. This domain is also found in closely related
proteins, including the Piwi subfamily, where it is
believed to perform a crucial role in germline cells,
via a similar mechanism.
Length = 393
Score = 33.9 bits (78), Expect = 0.17
Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 419 KVAIQLCCKIGGAPWSVAVP---LKGLMVLGFDVTHDSDLKGSSYGALV 464
+ ++ K+GG + + P K + +GFDV+H + + V
Sbjct: 146 NLLRKVNSKLGGINYILDSPVKLFKSDIFIGFDVSHPDRRTVNGGPSAV 194
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1042
Score = 31.9 bits (72), Expect = 0.92
Identities = 42/245 (17%), Positives = 74/245 (30%), Gaps = 39/245 (15%)
Query: 53 KEMKLMSKKRDETPVELTIRH----VRVLEYGDAQYTQLFNILIRQTLRALDLKLLGRNY 108
K+ S+K T + + +R LE +Y + FN I +L L
Sbjct: 681 ALQKMQSEKEQLTYWKEMLAQCQTLLRELETHIEEYDREFN-EIENASSSLGSDL---AA 736
Query: 109 FDPAAKEDIPQYRLEVWPGWDTSMRQMENDIMLCVELSHKVLRKETVLDAWEQCRNDKYF 168
+ A + + + + T ++ + +V + F
Sbjct: 737 REDALNQSLKELMHQ----ARTVLKARTEAHF---NNNEEVTAALQTGAELSHLAAEIQF 789
Query: 169 YYRKFEAQMTNSIVLTKYNNKTYRVDDIQYDVTPCSTFPMKGENVSY-----------ID 217
+ R E T+ + + D C T + E I
Sbjct: 790 FNRLREED-THLLKTLEAEIGQEIPSDEDILNLQCETLVQEEEQFLSRLEEKSATLGEIT 848
Query: 218 YYQKKYNETIRNRNQPMIVHKSKLRELRAGQSEIIYLVPELCYLTGLSDDMRADFRLMKP 277
+ KY E +L +L Q++II L +L + + D L+K
Sbjct: 849 HQLLKYEEC-----------SKQLAQLTQEQAKIIQLSDKLNGINQIKIQFDGD-ALIKF 896
Query: 278 LGEIT 282
L EIT
Sbjct: 897 LHEIT 901
>gnl|CDD|221365 pfam11995, DUF3490, Domain of unknown function (DUF3490). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is about 160
amino acids in length. This domain is found associated
with pfam00225. This domain is found associated with
pfam00225. This domain has two conserved sequence
motifs: EVE and ESA.
Length = 162
Score = 29.3 bits (66), Expect = 3.1
Identities = 20/98 (20%), Positives = 45/98 (45%), Gaps = 10/98 (10%)
Query: 235 IVHKSKLREL-RAGQSEIIYLVPELCYLTGLSDDMRADFRLMKPLGEITRV-------RP 286
+VH++ L + ++ IY+ EL L+ L ++ ++ R
Sbjct: 20 LVHRTYFFLLFKGDPADQIYMEVELRRLSFLKQSFSQGGPALEGGRTLSLASSIKALTRE 79
Query: 287 RERVAKFNVFRKRIENSEAKEVLKRWELALDTNLARVQ 324
RE ++K + +KR+ E + + ++W + L++ R+Q
Sbjct: 80 REMLSK--LMQKRLTKEERERLYQKWGVPLNSKRRRLQ 115
>gnl|CDD|217383 pfam03136, Pup_ligase, Pup-ligase protein. Pupylation is a novel
protein modification system found in some bacteria. This
family of proteins are the enzyme that can conjugate
proteins of the Pup family to lysine residues in target
proteins marking them for degradation. The archetypal
protein in this family is PafA (proteasome accessory
factor) from Mycobacterium tuberculosis. It has been
suggested that these proteins are related to
gamma-glutamyl-cysteine synthetases.
Length = 445
Score = 29.6 bits (67), Expect = 4.3
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 287 RERVAKFNVFRKRIENSEAKEVLKRWELALDT 318
E KF R ++E ++VL WE LD
Sbjct: 305 LEAARKFVEDRGGTPDAETRDVLDLWERVLDA 336
>gnl|CDD|188441 TIGR03926, T7_EssB, type VII secretion protein EssB. Members of
this family are associated with type VII secretion of
WXG100 family targets in the Firmicutes, but not in the
Actinobacteria. This protein is designated YukC in
Bacillus subtilis and EssB is Staphylococcus aureus
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 377
Score = 29.6 bits (67), Expect = 4.4
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 16/66 (24%)
Query: 284 VRPRERVAKFNVFRKRIENSEAKEVLKRWELALDTNLARVQGH-------ILPPDSIIFS 336
+P F +K+ N + LAL NLA ++ H IL P++++F+
Sbjct: 60 YQPPPAAKSFESIKKKTRNE-------KLRLAL--NLADLEEHLNSRLTFILHPENLVFT 110
Query: 337 DPLKPF 342
L P
Sbjct: 111 KGLTPS 116
>gnl|CDD|181206 PRK08042, PRK08042, formate hydrogenlyase subunit 3; Reviewed.
Length = 593
Score = 29.0 bits (65), Expect = 6.1
Identities = 15/27 (55%), Positives = 17/27 (62%), Gaps = 7/27 (25%)
Query: 420 VAIQLCCKIGG--APW-----SVAVPL 439
VA+ +CC IGG APW S AVPL
Sbjct: 448 VALAICCVIGGVAAPWLLPMLSAAVPL 474
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 0.137 0.415
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,006,446
Number of extensions: 2543564
Number of successful extensions: 1886
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1872
Number of HSP's successfully gapped: 30
Length of query: 504
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 403
Effective length of database: 6,457,848
Effective search space: 2602512744
Effective search space used: 2602512744
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: 61 (27.3 bits)