RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy198
(245 letters)
>gnl|CDD|216422 pfam01300, Sua5_yciO_yrdC, Telomere recombination. This domain has
been shown to bind preferentially to dsRNA. The domain
is found in SUA5 as well as HypF and YrdC. It has also
been shown to be required for telomere recombniation in
yeast.
Length = 178
Score = 177 bits (451), Expect = 3e-56
Identities = 72/181 (39%), Positives = 106/181 (58%), Gaps = 6/181 (3%)
Query: 42 QCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNKPLAICVSEITDIPKWADT 101
+ L++G +VA PTDT+YGL CDATN +A+ L EIK R +KPLA+ VS++ + K+AD
Sbjct: 1 EALRQGGIVAYPTDTVYGLGCDATNEEAVERLREIKGRPRDKPLAVMVSDLEQLKKYADE 60
Query: 102 HT-VSFELLAELLPGPVTIVFNRS-EHLNLELNPNVTKVAVRIPDHKFLRQLLKLMDSPL 159
+ +L PGP+T++ S L + P + V VR+PDH R LL+ + PL
Sbjct: 61 LEEAALKLAERFWPGPITLILPASKSSLPKLVTPGLGTVGVRLPDHPLARLLLEALGEPL 120
Query: 160 ALTSANESNEPSTLCINE-FQKLWSQLSVVIDGGIISNPERFGSTIVDLSEENVYSIVRK 218
TSAN S EPS E ++L + +++DGG I ST+VDL++ I+R+
Sbjct: 121 VATSANLSGEPSATDAEEVLEELGGIVDLILDGGRIPVGV--DSTVVDLTDGK-PRILRR 177
Query: 219 G 219
G
Sbjct: 178 G 178
>gnl|CDD|223088 COG0009, SUA5, Putative translation factor (SUA5) [Translation,
ribosomal structure and biogenesis].
Length = 211
Score = 162 bits (411), Expect = 7e-50
Identities = 75/191 (39%), Positives = 112/191 (58%), Gaps = 9/191 (4%)
Query: 33 DPKAALLAAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNKPLAICVSEI 92
P+A A + L+KG VVA PTDT+YGL DATN +A+ LYEIK+R +KPL + V+ +
Sbjct: 12 QPRAIEKAVEALRKGGVVAYPTDTVYGLGADATNEEAVERLYEIKQRPSDKPLILHVASL 71
Query: 93 TDIPKWADTHTVSFELLAELLPGPVTIVFNRSEHLNLEL-NPNVTKVAVRIPDHKFLRQL 151
+ ++AD V+ +LL PGP+T + ++ + L ++ +AVR+PDH L
Sbjct: 72 EQLKEYADVPDVARKLLKAFWPGPLTFILPATKEVPRRLVTAGLSTIAVRVPDHPIALAL 131
Query: 152 LKLMDSPLALTSANESNEPSTLCINE-FQKLWSQLSVVIDGGIISNPERFG--STIVDLS 208
++ + PLA TSAN S +PS E Q+ ++IDGG P R G STI+DL+
Sbjct: 132 IEALGEPLASTSANLSGQPSPTTAEEVRADFGGQVDLIIDGG----PCRGGLPSTIIDLT 187
Query: 209 EENVYSIVRKG 219
++ I+R G
Sbjct: 188 DDPPR-ILRPG 197
>gnl|CDD|232802 TIGR00057, TIGR00057, tRNA threonylcarbamoyl adenosine modification
protein, Sua5/YciO/YrdC/YwlC family. Has paralogs, but
YrdC called a tRNA modification protein. Ref 2 authors
say probably heteromultimeric complex. Paralogs may mean
its does the final binding to the tRNA [Protein
synthesis, tRNA and rRNA base modification].
Length = 201
Score = 140 bits (356), Expect = 8e-42
Identities = 64/193 (33%), Positives = 111/193 (57%), Gaps = 8/193 (4%)
Query: 40 AAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNKPLAICVSEITDIPKWA 99
A + L+KG +V PTDT+YG+ DA + A+ LY IK R NKPL + VS++++I K+A
Sbjct: 14 AVKILRKGGIVVYPTDTVYGIGADALDEDAVRRLYRIKGRPSNKPLTVLVSDLSEIEKYA 73
Query: 100 DTHTVSFELLAELLPGPVTIVFNRSEHLNLELNPNVTKVAVRIPDHKFLRQLLKLMDSPL 159
+ L+ + PGP+T+V ++ + ++ + +R+PD+ +LL+ + P+
Sbjct: 74 YVPDDAKRLMKKFWPGPLTLVLKKTPEIPRRVSGKRKTIGIRVPDNPIALELLEELGKPI 133
Query: 160 ALTSANESNEPSTLCINE-FQKLWSQLSVVIDGG--IISNPERFGSTIVDLSEENVYSIV 216
TSAN S +PS + E +L + ++ID G + P STI+DL+++ ++
Sbjct: 134 VATSANLSGKPSATDVEEAVDELGKLVDLIIDAGPCLGGEP----STIIDLTDDTP-KVL 188
Query: 217 RKGVCYDKILKIL 229
R+GV + I K+L
Sbjct: 189 REGVGSEPIEKVL 201
>gnl|CDD|182603 PRK10634, PRK10634, tRNA(ANN) t(6)A37 threonylcarbamoyladenosine
modification protein; Provisional.
Length = 190
Score = 67.8 bits (166), Expect = 6e-14
Identities = 40/134 (29%), Positives = 62/134 (46%), Gaps = 3/134 (2%)
Query: 40 AAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNKPLAICVSEITDIPKWA 99
A L + V+A PT+ ++G+ CD + A+ L E+K+R V+K L + + + +
Sbjct: 13 AVDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANYEQLKPYI 72
Query: 100 DTHTVSFELLAELL---PGPVTIVFNRSEHLNLELNPNVTKVAVRIPDHKFLRQLLKLMD 156
D ++ + PGPVT VF L +AVR+ DH + L +
Sbjct: 73 DDSMLTDAQRETIFSCWPGPVTFVFPAPATTPRWLTGRFDSLAVRVTDHPLVVALCQAYG 132
Query: 157 SPLALTSANESNEP 170
PL TSAN S P
Sbjct: 133 KPLVSTSANLSGLP 146
>gnl|CDD|183245 PRK11630, PRK11630, hypothetical protein; Provisional.
Length = 206
Score = 58.3 bits (141), Expect = 2e-10
Identities = 42/195 (21%), Positives = 92/195 (47%), Gaps = 13/195 (6%)
Query: 33 DPKAALL--AAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNKPLAICVS 90
+P+ L+ A + ++KG V+ PTD+ Y L C + A+ + I++ +
Sbjct: 11 NPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCR 70
Query: 91 EITDIPKWADTHTVSFELLAELLPGPVTIVFNRSEHLNLEL-NPNVTKVAVRIPDHKFLR 149
+++++ ++ V+F L+ PG T + ++ + L + +R+P +
Sbjct: 71 DLSELSTYSFVDNVAFRLMKNNTPGNYTFILKGTKEVPRRLLQEKRKTIGLRVPSNPIAL 130
Query: 150 QLLKLMDSPLALTS----ANESNEPSTLCINEFQKLWSQLSVVIDGGIISNPERFGSTIV 205
LL+ + P+ TS ++ E I + +L Q+ ++I GG + +T++
Sbjct: 131 ALLEALGEPMLSTSLMLPGSDFTESDPEEIKD--RLEKQVDLIIHGGYLGQQP---TTVI 185
Query: 206 DLSEENVYSIVRKGV 220
DL+ ++ +VR+GV
Sbjct: 186 DLT-DDTPVVVREGV 199
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 58.5 bits (142), Expect = 6e-10
Identities = 50/176 (28%), Positives = 83/176 (47%), Gaps = 15/176 (8%)
Query: 29 VKVTDPKAALLAAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNKPLAIC 88
+A AA+ LK G +VA+ + LACDA N +A+ L + K R KP A+
Sbjct: 192 AIAEANEAIRKAAKLLKVGKIVAIKGIGGFHLACDARNEEAVAKLRKRKNRP-LKPFAVM 250
Query: 89 VSEITDIPKWADTHTVSFELL-AELLPGPVTIVFNRSEHLNLELN--PNVTKVAVRIP-- 143
++ I ++A+ + ELL + P ++ + + LE N P + + V +P
Sbjct: 251 AKDLETIEEFAEVNDEEEELLTSPSRP---IVLLKKKKVFLLESNIAPGLHTIGVMLPYT 307
Query: 144 -DHKFLRQLLKLMDSPLALTSANESNEPSTLCINEFQKLWSQLSVVIDGGIISNPE 198
H L L + +D P +TSAN EP + I+ + L +L + D ++ N E
Sbjct: 308 PLHHLL--LQESLDIPYVMTSANLPGEP--MAIDNEEAL-EKLKGIADYFLLHNRE 358
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 57.5 bits (139), Expect = 1e-09
Identities = 48/163 (29%), Positives = 79/163 (48%), Gaps = 8/163 (4%)
Query: 36 AALLAAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNKPLAICVSEITDI 95
A L AA+ LKKG ++A+ + LACDA N + + L K R KP A+ ++
Sbjct: 164 ALLEAAKLLKKGKIIAIKGIGGFHLACDARNDEVVERLRLRKNRP-LKPFAVMSPDLESA 222
Query: 96 PKWADTHTVSFELLAELLPGPVTIVFNRSEHLNLELN--PNVTKVAVRIPDHKFLRQLLK 153
+ A+ + + ELL P ++ + + L N PN+ + V +P LL+
Sbjct: 223 EQHAELNNLECELL--TSPAAPIVLLRKKPDIKLAPNIAPNLPTIGVMLPYTPLHHLLLQ 280
Query: 154 LMDSPLALTSANESNEPSTLCINEFQKLWSQLSVVIDGGIISN 196
L+ PL +TSAN P + I+ + L +L + DG ++ N
Sbjct: 281 LLAFPLVMTSANLPGLP--MAIDNAEIL-DKLQGIADGFLVHN 320
>gnl|CDD|226810 COG4373, COG4373, Mu-like prophage FluMu protein gp28 [General
function prediction only].
Length = 509
Score = 31.1 bits (70), Expect = 0.61
Identities = 22/93 (23%), Positives = 27/93 (29%), Gaps = 6/93 (6%)
Query: 28 IVKVTDPKAALLAAQCLKKGCVVALPT--DTLYGLACDATNSKAINI---LYEIK-KRDV 81
I V P A T D C+ +S I L E +V
Sbjct: 212 ICNVDRPAWAPEVEAKWLAELRAIAGTDEDAQEEYMCNPKDSTGAYIPHALIEAAVAAEV 271
Query: 82 NKPLAICVSEITDIPKWADTHTVSFELLAELLP 114
+ SE DIP W V L +L P
Sbjct: 272 PDLIFELGSEFHDIPAWLRESEVLTWCLPDLRP 304
>gnl|CDD|131314 TIGR02261, benz_CoA_red_D, benzoyl-CoA reductase, bcr type, subunit
D. This model describes the D subunit of benzoyl-CoA
reductase, a 4-subunit enzyme. Many aromatic compounds
are metabolized by way of benzoyl-CoA. This family shows
sequence similarity to the A subunit (TIGR02259) and to
the 2-hydroxyglutaryl-CoA dehydratase alpha chain.
Length = 262
Score = 28.1 bits (62), Expect = 3.9
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 196 NPERFGSTIVDLSEENVYSIVRKGVCYDKILKILH 230
NPE+ L+E +V ++V +G+ ILK +H
Sbjct: 160 NPEKVSGICAVLAETDVINMVSRGISAPNILKGIH 194
>gnl|CDD|214846 smart00836, DALR_1, DALR anticodon binding domain. This all alpha
helical domain is the anticodon binding domain of
Arginyl tRNA synthetase. This domain is known as the
DALR domain after characteristic conserved amino acids.
Length = 122
Score = 26.8 bits (60), Expect = 5.8
Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 6/77 (7%)
Query: 120 VFNRSEHLNLELNPNVTKVAVRIPDHKFLRQLLKLMDSPLALTSANESNEPSTLC----- 174
+ ++ L + + + LLKL P L +A E EP L
Sbjct: 11 ILRKAGEAGETLPDIADADLSLLTEPEEWALLLKLARFPEVLEAAAEQLEPHRLANYLYD 70
Query: 175 -INEFQKLWSQLSVVID 190
F ++++ V+ +
Sbjct: 71 LAAAFHSFYNRVRVLGE 87
>gnl|CDD|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM1 of MRN1, also termed multicopy
suppressor of RSC-NHP6 synthetic lethality protein 1,
or post-transcriptional regulator of 69 kDa,which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 74
Score = 25.5 bits (56), Expect = 8.9
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 17 NAIALPSKMCSIVKVTDPKAALL--AAQCLKK 46
N LP K C+ + DP AA + LK+
Sbjct: 29 NVRILPEKNCAFISFLDPSAATAFHSDAILKR 60
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 0.406
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,382,784
Number of extensions: 1148198
Number of successful extensions: 979
Number of sequences better than 10.0: 1
Number of HSP's gapped: 969
Number of HSP's successfully gapped: 19
Length of query: 245
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 151
Effective length of database: 6,768,326
Effective search space: 1022017226
Effective search space used: 1022017226
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: 58 (26.0 bits)