RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8679
(221 letters)
>gnl|CDD|224293 COG1374, NIP7, Protein involved in ribosomal biogenesis, contains
PUA domain [Translation, ribosomal structure and
biogenesis].
Length = 176
Score = 119 bits (299), Expect = 7e-34
Identities = 61/163 (37%), Positives = 86/163 (52%), Gaps = 11/163 (6%)
Query: 61 IGSNVKLLIDRP-DGTYCFR---EMRDR-VFYVSEKILTLAENFGPDHLLALGTCFGKFT 115
G ++ + + + + F +++DR V+ V+E + LAE+ + +LGT FGK
Sbjct: 20 EGDLIRKELSKYGELDHLFFHLLKVKDRDVYEVNEVVWKLAESIERKNPYSLGTFFGKRV 79
Query: 116 KSGKFRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVL 175
K G FR H+ +L LA A K +VK + E FLYG N LK + I + P+ GV V
Sbjct: 80 KGGLFRKHVESLEELARIAIIKNYVKERGEMLFLYG-NDLKDHVKEIIDEIPENGGVFVF 138
Query: 176 NMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDIGEYIRCED 218
NMNDVPLG GV A S +E D I D+GEY+R
Sbjct: 139 NMNDVPLGIGVGALSPSE----DGRLIKN-ALKDVGEYLRRGG 176
>gnl|CDD|214635 smart00359, PUA, Putative RNA-binding Domain in PseudoUridine
synthase and Archaeosine transglycosylase.
Length = 76
Score = 66.9 bits (164), Expect = 5e-15
Identities = 18/75 (24%), Positives = 34/75 (45%)
Query: 137 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKL 196
KV V AE+ L G ++L G+ R+ + + V++++ PLG G+A S+ E
Sbjct: 2 KVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIAR 61
Query: 197 ADPLAIVGFNQSDIG 211
+ + +
Sbjct: 62 IKGKGLAVKVRRAVM 76
>gnl|CDD|217662 pfam03657, UPF0113, Uncharacterized protein family (UPF0113).
Length = 161
Score = 44.0 bits (104), Expect = 9e-06
Identities = 35/135 (25%), Positives = 58/135 (42%), Gaps = 20/135 (14%)
Query: 85 VFYVSEKILTLAENFGPDHL---LALGTCFGKFTKSGKFRLHITALSYLAPYAQFK-VWV 140
V+YV + E + L +G+ G+ + +FRL + L + K +
Sbjct: 42 VYYVPWGLRRAVERL-LNPYSAGLNVGSIIGERGR--RFRLSLEGFFALLCNSPNKYARL 98
Query: 141 KPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPL 200
P+AE+ FLYG ++ K +A T G +++ N P G G+ D L
Sbjct: 99 NPKAEKLFLYGRDVFKDSIASHTS-----FGALIVVSNGQPDGLGIG-------NSRDDL 146
Query: 201 AIVGFNQSDIGEYIR 215
I+ N D+G Y+R
Sbjct: 147 KIIK-NLKDLGWYLR 160
>gnl|CDD|227595 COG5270, COG5270, PUA domain (predicted RNA-binding domain)
[Translation, ribosomal structure and biogenesis].
Length = 202
Score = 34.0 bits (78), Expect = 0.038
Identities = 15/56 (26%), Positives = 26/56 (46%)
Query: 138 VWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAE 193
+ A + G N+L G+ ++ + VIV++ N +G G+A KS E
Sbjct: 131 RKIDRGAVEPVKNGKNVLPPGVIEAEDSIERGDEVIVVSENGRVVGVGIAKKSYEE 186
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This
family, found in archaea and eukaryotes, includes the
only archaeal proteins markedly similar to bacterial
TruB, the tRNA pseudouridine 55 synthase. However, among
two related yeast proteins, the archaeal set matches
yeast YLR175w far better than YNL292w. The first, termed
centromere/microtubule binding protein 5 (CBF5), is an
apparent rRNA pseudouridine synthase, while the second
is the exclusive tRNA pseudouridine 55 synthase for both
cytosolic and mitochondrial compartments. It is unclear
whether archaeal proteins found by this model modify
tRNA, rRNA, or both [Protein synthesis, tRNA and rRNA
base modification].
Length = 322
Score = 32.8 bits (75), Expect = 0.096
Identities = 17/62 (27%), Positives = 31/62 (50%)
Query: 137 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKL 196
+V VK A +G +++ G+AR+ + K V+V+ + + G+A ST +
Sbjct: 239 RVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIAN 298
Query: 197 AD 198
AD
Sbjct: 299 AD 300
>gnl|CDD|201816 pfam01472, PUA, PUA domain. The PUA domain named after
Pseudouridine synthase and Archaeosine transglycosylase,
was detected in archaeal and eukaryotic pseudouridine
synthases, archaeal archaeosine synthases, a family of
predicted ATPases that may be involved in RNA
modification, a family of predicted archaeal and
bacterial rRNA methylases. Additionally, the PUA domain
was detected in a family of eukaryotic proteins that
also contain a domain homologous to the translation
initiation factor eIF1/SUI1; these proteins may comprise
a novel type of translation factors. Unexpectedly, the
PUA domain was detected also in bacterial and yeast
glutamate kinases; this is compatible with the
demonstrated role of these enzymes in the regulation of
the expression of other genes. It is predicted that the
PUA domain is an RNA binding domain.
Length = 74
Score = 29.8 bits (68), Expect = 0.25
Identities = 13/57 (22%), Positives = 26/57 (45%)
Query: 137 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAE 193
+V V A + L G ++L G+ + + + V+V+ + G+A S+ E
Sbjct: 2 RVVVDDGAVEAILNGASLLAPGVVEVDGDFRRGDEVVVVTEKGELVAVGLANYSSEE 58
>gnl|CDD|129543 TIGR00451, unchar_dom_2, uncharacterized domain 2. This
uncharacterized domain is found a number of enzymes and
uncharacterized proteins, often at the C-terminus. It is
found in some but not all members of a family of related
tRNA-guanine transglycosylases (tgt), which exchange a
guanine base for some modified base without breaking the
phosphodiester backbone of the tRNA. It is also found in
rRNA pseudouridine synthase, another enzyme of RNA base
modification not otherwise homologous to tgt. It is
found, again at the C-terminus, in two putative
glutamate 5-kinases. It is also found in a family of
small, uncharacterized archaeal proteins consisting
mostly of this domain.
Length = 107
Score = 28.2 bits (63), Expect = 1.3
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 151 GHNILKSGLARITENTPKYQGVIVLNMN-DVPLGFGVAAKSTAECKLAD 198
G ++++ G+ E+ + V+V++ N D PL G+A S E K D
Sbjct: 46 GADVMRPGIVDADEDIKEGDDVVVVDENKDRPLAVGIALMSGEEMKEMD 94
>gnl|CDD|236507 PRK09424, pntA, NAD(P) transhydrogenase subunit alpha; Provisional.
Length = 509
Score = 28.3 bits (64), Expect = 3.3
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 143 QAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDV 180
Q+ Q LYG N++ + P+ G IV++ +DV
Sbjct: 322 QSSQ--LYGTNLVN----LLKLLCPEKDGNIVVDFDDV 353
>gnl|CDD|222791 PHA00431, PHA00431, internal virion protein C.
Length = 746
Score = 28.6 bits (64), Expect = 3.5
Identities = 14/53 (26%), Positives = 22/53 (41%)
Query: 2 NQVIHNIGSNVKLLIDRPDGTYCFREMRDRVFYVSEKILTLAENFGPDHLLAL 54
Q I +K +I RP G +++ DR ++ T E G + AL
Sbjct: 240 AQAEQVISQTLKDVIQRPGGANFLQQLEDRKVTLNGAETTYKELMGEEQWNAL 292
>gnl|CDD|237403 PRK13505, PRK13505, formate--tetrahydrofolate ligase; Provisional.
Length = 557
Score = 28.2 bits (64), Expect = 3.8
Identities = 19/58 (32%), Positives = 24/58 (41%), Gaps = 5/58 (8%)
Query: 149 LYGHNILKSGLARITENTPKYQG--VIVLNMNDVPLGFGVAAKSTAECKLADPLAIVG 204
YG K L +I K G ++V +N P G G KST L D L +G
Sbjct: 33 PYGKYKAKISLDKIKALKDKKDGKLILVTAINPTPAGEG---KSTVTVGLGDALNKIG 87
>gnl|CDD|217760 pfam03849, Tfb2, Transcription factor Tfb2.
Length = 365
Score = 27.6 bits (62), Expect = 5.1
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 132 PYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMND 179
P A WVKP++++Q LKS I TP + +N
Sbjct: 47 PAADLDKWVKPESKKQHEEAIKRLKS--LHIITETPSGGKKQSIRLNP 92
>gnl|CDD|237455 PRK13637, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 287
Score = 27.3 bits (61), Expect = 5.8
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 19 PDGTYCFREMRDRVFYVSEKILTLAE 44
P TY R++R + F + + I T+ E
Sbjct: 247 PQVTYLVRKLRKKGFNIPDDIFTIEE 272
Score = 27.3 bits (61), Expect = 5.8
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 72 PDGTYCFREMRDRVFYVSEKILTLAE 97
P TY R++R + F + + I T+ E
Sbjct: 247 PQVTYLVRKLRKKGFNIPDDIFTIEE 272
>gnl|CDD|233200 TIGR00940, 2a6301s01, Tmonovalent cation:proton antiporter. This
family of proteins constists of bacterial multicomponent
K+:H+ and Na+:H+ antiporters. The best characterized
systems are the PhaABCDEFG system of Rhizobium meliloti
which functions in pH adaptation and as a K+ efflux
system and the MnhABCDEFG system of Staphylococcus
aureus which functions as a Na+:H+ antiporter [Transport
and binding proteins, Cations and iron carrying
compounds].
Length = 793
Score = 27.5 bits (61), Expect = 6.8
Identities = 30/117 (25%), Positives = 47/117 (40%), Gaps = 18/117 (15%)
Query: 56 TCFGNIGSNVKL-LIDRPDGTYCFREMRDRVFYVSEKILTLAENFGPDHLLALGTCFGKF 114
T FG + L L+ + G++ + + L FG +L L G F
Sbjct: 166 TVFGGLAMLGGLILLGKITGSFSIDAVIASADAIRNSPL-----FGTAMVLVL---LGAF 217
Query: 115 TKSGKFRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQG 171
TKS +F HI +L P A P +L+ ++K+GL + TP + G
Sbjct: 218 TKSAQFPFHI----WL-PDAM----EAPTPVSAYLHSATMVKAGLYLLARFTPVFAG 265
>gnl|CDD|240394 PTZ00386, PTZ00386, formyl tetrahydrofolate synthetase;
Provisional.
Length = 625
Score = 27.5 bits (61), Expect = 7.3
Identities = 17/37 (45%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 164 ENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPL 200
EN+P + V+V MN PLG G KST LA L
Sbjct: 63 ENSPNGKYVVVAGMNPTPLGEG---KSTTTIGLAQSL 96
>gnl|CDD|198178 cd09923, SH2_SOCS_family, Src homology 2 (SH2) domain found in
suppressor of cytokine signaling (SOCS) family. SH2
domain found in SOCS proteins. SOCS was first
recognized as a group of cytokine-inducible SH2 (CIS)
domain proteins comprising eight family members in
human (CIS and SOCS1-SOCS7). In addition to the SH2
domain, SOCS proteins have a variable N-terminal domain
and a conserved SOCS box in the C-terminal domain. SOCS
proteins bind to a substrate via their SH2 domain. The
prototypical members, CIS and SOCS1-SOCS3, have been
shown to regulate growth hormone signaling in vitro and
in a classic negative feedback response compete for
binding at phosphotyrosine sites in JAK kinase and
receptor pathways to displace effector proteins and
target bound receptors for proteasomal degradation.
Loss of SOCS activity results in excessive cytokine
signaling associated with a variety of hematopoietic,
autoimmune, and inflammatory diseases and certain
cancers. Members (SOCS4-SOCS7) were identified by their
conserved SOCS box, an adapter motif of 3 helices that
associates substrate binding domains, such as the SOCS
SH2 domain, ankryin, and WD40 with ubiquitin ligase
components. These show limited cytokine induction. In
general SH2 domains are involved in signal
transduction. They typically bind pTyr-containing
ligands via two surface pockets, a pTyr and hydrophobic
binding pocket, allowing proteins with SH2 domains to
localize to tyrosine phosphorylated sites.
Length = 81
Score = 25.6 bits (57), Expect = 7.8
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 13 KLLIDRPDGTYCFREMRDRVFYVS 36
+LL +P+GT+ R+ D + S
Sbjct: 14 ELLAGKPEGTFLVRDSSDSRYLFS 37
Score = 25.6 bits (57), Expect = 7.8
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 66 KLLIDRPDGTYCFREMRDRVFYVS 89
+LL +P+GT+ R+ D + S
Sbjct: 14 ELLAGKPEGTFLVRDSSDSRYLFS 37
>gnl|CDD|111089 pfam02157, Man-6-P_recep, Mannose-6-phosphate receptor. This
family includes both Cation-dependent and cation
independent mannose-6-phosphate receptors.
Length = 278
Score = 26.9 bits (59), Expect = 7.8
Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 9 GSNVKLLIDRPDGTY---CFREMRDRVFYVSEKILTLAENFGP 48
GSN +LI + Y C +E R V +S TLA NF P
Sbjct: 115 GSNWIMLIYKGGDEYDNHCGKEQRRAVVMISCNRHTLAANFNP 157
Score = 26.9 bits (59), Expect = 7.8
Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 62 GSNVKLLIDRPDGTY---CFREMRDRVFYVSEKILTLAENFGP 101
GSN +LI + Y C +E R V +S TLA NF P
Sbjct: 115 GSNWIMLIYKGGDEYDNHCGKEQRRAVVMISCNRHTLAANFNP 157
>gnl|CDD|238810 cd01578, AcnA_Mitochon_Swivel, Mitochondrial aconitase A swivel
domain. Aconitase (also known as aconitate hydratase and
citrate hydro-lyase) catalyzes the reversible
isomerization of citrate and isocitrate as part of the
TCA cycle. This is the aconitase swivel domain, which
undergoes swivelling conformational change in the enzyme
mechanism. In eukaryotes two isozymes of aconitase are
known to exist: one found in the mitochondrial matrix
and the other found in the cytoplasm. This is the
mitochondrial form. The mitochondrial product is coded
by a nuclear gene. Most members of this subfamily are
mitochondrial but there are some bacterial members.
Length = 149
Score = 26.3 bits (58), Expect = 9.3
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 145 EQQFLYGHNILKSGLARITENTPKYQGVIVLNMND 179
E + L G I+ ARI E K QG++ L D
Sbjct: 91 EPRHLGGRAIITKSFARIHETNLKKQGLLPLTFAD 125
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
0.324 0.142 0.435
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: 11,432,395
Number of extensions: 1082716
Number of successful extensions: 848
Number of sequences better than 10.0: 1
Number of HSP's gapped: 846
Number of HSP's successfully gapped: 28
Length of query: 221
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 128
Effective length of database: 6,812,680
Effective search space: 872023040
Effective search space used: 872023040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.7 bits)