RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8680
(180 letters)
>gnl|CDD|224293 COG1374, NIP7, Protein involved in ribosomal biogenesis, contains
PUA domain [Translation, ribosomal structure and
biogenesis].
Length = 176
Score = 102 bits (255), Expect = 7e-28
Identities = 58/169 (34%), Positives = 74/169 (43%), Gaps = 44/169 (26%)
Query: 5 VFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQFKVWVKPQA 64
V+ V+E + LAE+ + +LGT FGK K G FR H+ +L LA A
Sbjct: 49 VYEVNEVVWKLAESIERKNPYSLGTFFGKRVKGGLFRKHVESLEELARIA---------- 98
Query: 65 DQQFLYGHNILKSGLARITENTPKYQGVIFKVWVKPQAEQQFLYGHNILKSGLARITENT 124
I K +VK + E FLYG N LK + I +
Sbjct: 99 ----------------------------IIKNYVKERGEMLFLYG-NDLKDHVKEIIDEI 129
Query: 125 PKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDIGEYIR 173
P+ GV V NMNDVPLG GV A S +E D I D+GEY+R
Sbjct: 130 PENGGVFVFNMNDVPLGIGVGALSPSE----DGRLIKN-ALKDVGEYLR 173
>gnl|CDD|214635 smart00359, PUA, Putative RNA-binding Domain in PseudoUridine
synthase and Archaeosine transglycosylase.
Length = 76
Score = 66.9 bits (164), Expect = 2e-15
Identities = 18/75 (24%), Positives = 34/75 (45%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKL 154
KV V AE+ L G ++L G+ R+ + + V++++ PLG G+A S+ E
Sbjct: 2 KVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIAR 61
Query: 155 ADPLAIVGFNQSDIG 169
+ + +
Sbjct: 62 IKGKGLAVKVRRAVM 76
>gnl|CDD|217662 pfam03657, UPF0113, Uncharacterized protein family (UPF0113).
Length = 161
Score = 40.2 bits (94), Expect = 1e-04
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 13/78 (16%)
Query: 96 VWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLA 155
+ P+AE+ FLYG ++ K +A T G +++ N P G G+
Sbjct: 96 ARLNPKAEKLFLYGRDVFKDSIASHTS-----FGALIVVSNGQPDGLGIG-------NSR 143
Query: 156 DPLAIVGFNQSDIGEYIR 173
D L I+ N D+G Y+R
Sbjct: 144 DDLKIIK-NLKDLGWYLR 160
Score = 31.7 bits (72), Expect = 0.11
Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 5 VFYVSEKILTLAENFGPDHL---LALGTCFGKFTKSGKFRLHITALSYLAPYAQFK-VWV 60
V+YV + E + L +G+ G+ + +FRL + L + K +
Sbjct: 42 VYYVPWGLRRAVERL-LNPYSAGLNVGSIIGERGR--RFRLSLEGFFALLCNSPNKYARL 98
Query: 61 KPQADQQFLYGHNILKSGLARITE 84
P+A++ FLYG ++ K +A T
Sbjct: 99 NPKAEKLFLYGRDVFKDSIASHTS 122
>gnl|CDD|227595 COG5270, COG5270, PUA domain (predicted RNA-binding domain)
[Translation, ribosomal structure and biogenesis].
Length = 202
Score = 36.3 bits (84), Expect = 0.004
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 7/72 (9%)
Query: 87 PKYQGV-----IFK--VWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVP 139
K +G K + A + G N+L G+ ++ + VIV++ N
Sbjct: 115 LKLEGAKLLLEKGKKGRKIDRGAVEPVKNGKNVLPPGVIEAEDSIERGDEVIVVSENGRV 174
Query: 140 LGFGVAAKSTAE 151
+G G+A KS E
Sbjct: 175 VGVGIAKKSYEE 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 = 35.1 bits (81), Expect = 0.013
Identities = 22/92 (23%), Positives = 41/92 (44%)
Query: 65 DQQFLYGHNILKSGLARITENTPKYQGVIFKVWVKPQAEQQFLYGHNILKSGLARITENT 124
D + + +S L RI + + +V VK A +G +++ G+AR+ +
Sbjct: 209 DAYVFWKEDGDESYLRRIIKPMEYLLRHLKRVVVKDSAVDAICHGADLMVRGIARLEKGI 268
Query: 125 PKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD 156
K V+V+ + + G+A ST + AD
Sbjct: 269 EKGDTVVVITLKGEAVAVGIALMSTKDIANAD 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 = 30.1 bits (69), Expect = 0.14
Identities = 13/57 (22%), Positives = 26/57 (45%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAE 151
+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 = 28.6 bits (64), Expect = 0.81
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 109 GHNILKSGLARITENTPKYQGVIVLNMN-DVPLGFGVAAKSTAECKLAD 156
G ++++ G+ E+ + V+V++ N D PL G+A S E K D
Sbjct: 46 GADVMRPGIVDADEDIKEGDDVVVVDENKDRPLAVGIALMSGEEMKEMD 94
>gnl|CDD|237403 PRK13505, PRK13505, formate--tetrahydrofolate ligase; Provisional.
Length = 557
Score = 28.2 bits (64), Expect = 2.8
Identities = 19/58 (32%), Positives = 24/58 (41%), Gaps = 5/58 (8%)
Query: 107 LYGHNILKSGLARITENTPKYQG--VIVLNMNDVPLGFGVAAKSTAECKLADPLAIVG 162
YG K L +I K G ++V +N P G G KST L D L +G
Sbjct: 33 PYGKYKAKISLDKIKALKDKKDGKLILVTAINPTPAGEG---KSTVTVGLGDALNKIG 87
>gnl|CDD|236507 PRK09424, pntA, NAD(P) transhydrogenase subunit alpha; Provisional.
Length = 509
Score = 27.5 bits (62), Expect = 3.9
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 101 QAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDV 138
Q+ Q LYG N++ + P+ G IV++ +DV
Sbjct: 322 QSSQ--LYGTNLVN----LLKLLCPEKDGNIVVDFDDV 353
>gnl|CDD|240394 PTZ00386, PTZ00386, formyl tetrahydrofolate synthetase;
Provisional.
Length = 625
Score = 27.5 bits (61), Expect = 4.7
Identities = 17/37 (45%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 122 ENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPL 158
EN+P + V+V MN PLG G KST LA L
Sbjct: 63 ENSPNGKYVVVAGMNPTPLGEG---KSTTTIGLAQSL 96
>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 = 7.9
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 103 EQQFLYGHNILKSGLARITENTPKYQGVIVLNMND 137
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
0.323 0.139 0.419
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: 9,188,906
Number of extensions: 830569
Number of successful extensions: 618
Number of sequences better than 10.0: 1
Number of HSP's gapped: 616
Number of HSP's successfully gapped: 21
Length of query: 180
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 89
Effective length of database: 6,901,388
Effective search space: 614223532
Effective search space used: 614223532
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 (25.3 bits)