RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021316
(314 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 = 165 bits (420), Expect = 1e-50
Identities = 62/195 (31%), Positives = 93/195 (47%), Gaps = 18/195 (9%)
Query: 95 ELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDIDTYTTG 154
E L++G + PTDT+Y + CD + A+ERLR IK KPL+++ L + Y
Sbjct: 1 EALRQGGIVAYPTDTVYGLGCDATNEEAVERLREIKGRPRDKPLAVMVSDLEQLKKYADE 60
Query: 155 FPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTTAKYSLRKHVGVRIPN 214
+ + PGP T IL ASK K V G VGVR+P+
Sbjct: 61 LE-------EAALKLAERFWPGPITLILPASKSSLPKLVTPG--------LGTVGVRLPD 105
Query: 215 DAICQAILQKMDAPLISTSVKWLKDNEWMVDPVVIADTYGPEGLDFVVDGGV-RVAEPST 273
+ + +L+ + PL++TS L D + + G +D ++DGG V ST
Sbjct: 106 HPLARLLLEALGEPLVATSAN-LSGEPSATDAEEVLEELG-GIVDLILDGGRIPVGVDST 163
Query: 274 VVDMTGTYPKIIRQG 288
VVD+T P+I+R+G
Sbjct: 164 VVDLTDGKPRILRRG 178
>gnl|CDD|223088 COG0009, SUA5, Putative translation factor (SUA5) [Translation,
ribosomal structure and biogenesis].
Length = 211
Score = 150 bits (382), Expect = 1e-44
Identities = 67/214 (31%), Positives = 100/214 (46%), Gaps = 19/214 (8%)
Query: 80 ADPSGADSWKLEPVVELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLS 139
P +E VE L++G V PTDT+Y + D + A+ERL IK KPL
Sbjct: 6 IHPENPQPRAIEKAVEALRKGGVVAYPTDTVYGLGADATNEEAVERLYEIKQRPSDKPLI 65
Query: 140 ILCRSLRDIDTYTTGFPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTT 199
+ SL + Y + +K PGP TFIL A+KEVP++ V G +T
Sbjct: 66 LHVASLEQLKEYADVPDV--------ARKLLKAFWPGPLTFILPATKEVPRRLVTAGLST 117
Query: 200 AKYSLRKHVGVRIPNDAICQAILQKMDAPLISTSVKWLKDNEWMVDPVVIADTYGPEGLD 259
+ VR+P+ I A+++ + PL STS L + +G + +D
Sbjct: 118 --------IAVRVPDHPIALALIEALGEPLASTSAN-LSGQPSPTTAEEVRADFGGQ-VD 167
Query: 260 FVVDGGV-RVAEPSTVVDMTGTYPKIIRQGKGPK 292
++DGG R PST++D+T P+I+R G
Sbjct: 168 LIIDGGPCRGGLPSTIIDLTDDPPRILRPGAISL 201
>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 = 129 bits (326), Expect = 2e-36
Identities = 63/204 (30%), Positives = 106/204 (51%), Gaps = 20/204 (9%)
Query: 90 LEPVVELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDID 149
+E V++L++G + V PTDT+Y I D A+ RL RIK +KPL++L L +I+
Sbjct: 11 IEQAVKILRKGGIVVYPTDTVYGIGADALDEDAVRRLYRIKGRPSNKPLTVLVSDLSEIE 70
Query: 150 TYTTGFPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTTAKYSLRKHVG 209
Y + D R +K PGP T +L + E+P++ RK +G
Sbjct: 71 KYA--YVPDDA------KRLMKKFWPGPLTLVLKKTPEIPRRVS---------GKRKTIG 113
Query: 210 VRIPNDAICQAILQKMDAPLISTSVKWLKDNEWMVDPVVIADTYGPEGLDFVVDGG-VRV 268
+R+P++ I +L+++ P+++TS L D D G + +D ++D G
Sbjct: 114 IRVPDNPIALELLEELGKPIVATSAN-LSGKPSATDVEEAVDELG-KLVDLIIDAGPCLG 171
Query: 269 AEPSTVVDMTGTYPKIIRQGKGPK 292
EPST++D+T PK++R+G G +
Sbjct: 172 GEPSTIIDLTDDTPKVLREGVGSE 195
>gnl|CDD|183245 PRK11630, PRK11630, hypothetical protein; Provisional.
Length = 206
Score = 128 bits (324), Expect = 4e-36
Identities = 64/198 (32%), Positives = 115/198 (58%), Gaps = 19/198 (9%)
Query: 94 VELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDIDTYTT 153
VE++++G V V PTD+ YA+ C ++ +A+ER+ RI+ + +++CR L ++ TY+
Sbjct: 21 VEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELSTYS- 79
Query: 154 GFPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTTAKYSLRKHVGVRIP 213
FR +K+ PG YTFIL +KEVP++ ++ RK +G+R+P
Sbjct: 80 -------FVDNVAFRLMKNNTPGNYTFILKGTKEVPRRLLQ--------EKRKTIGLRVP 124
Query: 214 NDAICQAILQKMDAPLISTSVKWLKDNEWM-VDPVVIADTYGPEGLDFVVDGGVRVAEPS 272
++ I A+L+ + P++STS+ L +++ DP I D + +D ++ GG +P+
Sbjct: 125 SNPIALALLEALGEPMLSTSLM-LPGSDFTESDPEEIKDRLEKQ-VDLIIHGGYLGQQPT 182
Query: 273 TVVDMTGTYPKIIRQGKG 290
TV+D+T P ++R+G G
Sbjct: 183 TVIDLTDDTPVVVREGVG 200
>gnl|CDD|182603 PRK10634, PRK10634, tRNA(ANN) t(6)A37 threonylcarbamoyladenosine
modification protein; Provisional.
Length = 190
Score = 48.2 bits (115), Expect = 1e-06
Identities = 38/144 (26%), Positives = 62/144 (43%), Gaps = 14/144 (9%)
Query: 90 LEPVVELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDID 149
+ V++L E V PT+ ++ + CD S +A+ RL +K K L ++ + +
Sbjct: 10 IAAAVDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANYEQLK 69
Query: 150 TYTTGFPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTTAKYSLRKHVG 209
Y D Q IF C PGP TF+ A P+ T ++ +
Sbjct: 70 PYIDDSMLTDAQRET-IFS----CWPGPVTFVFPAPATTPR------WLTGRFD---SLA 115
Query: 210 VRIPNDAICQAILQKMDAPLISTS 233
VR+ + + A+ Q PL+STS
Sbjct: 116 VRVTDHPLVVALCQAYGKPLVSTS 139
>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 = 37.4 bits (87), Expect = 0.009
Identities = 43/203 (21%), Positives = 76/203 (37%), Gaps = 30/203 (14%)
Query: 94 VELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDIDTYTT 153
+LLK+G + + + + CD ++ +ERLR KN P KP +++ L +
Sbjct: 169 AKLLKKGKIIAIKGIGGFHLACDARNDEVVERLRLRKN-RPLKPFAVMSPDLESAEQ--- 224
Query: 154 GFPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTTAKYSLRKHVGVRIP 213
HA + L P I+ K K ++ A +GV +P
Sbjct: 225 ---------HAELNNLECELLTSPAAPIVLLRK---KPDIKLAPNIAPNLPT--IGVMLP 270
Query: 214 NDAICQAILQKMDAPLISTSVKWLKDNEWMVDPVVIADTYGPEGLDFVVDGGV----RVA 269
+ +LQ + PL+ TS P+ I + + L + DG + R+
Sbjct: 271 YTPLHHLLLQLLAFPLVMTSANLPG------LPMAIDNAEILDKLQGIADGFLVHNRRIV 324
Query: 270 EP--STVVDMTGTYPKIIRQGKG 290
+VV +R+ +G
Sbjct: 325 NRVDDSVVQHVAGEILFLRRSRG 347
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 35.1 bits (81), Expect = 0.047
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 90 LEPVVELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDID 149
+ +LLK G + + + + CD ++ A+ +LR+ KN P KP +++ + L I+
Sbjct: 200 IRKAAKLLKVGKIVAIKGIGGFHLACDARNEEAVAKLRKRKN-RPLKPFAVMAKDLETIE 258
Query: 150 TY 151
+
Sbjct: 259 EF 260
>gnl|CDD|163651 cd07408, MPP_SA0022_N, Staphylococcus aureus SA0022 and related
proteins, N-terminal metallophosphatase domain. SA0022
is an uncharacterized Staphylococcus aureus UshA-like
protein with two putative domains, an N-terminal
metallophosphatase domain and a C-terminal nucleotidase
domain. SA0022 also contains a putative C-terminal cell
wall anchor domain. The N-terminal metallophosphatase
domain belongs to a large superfamily of distantly
related metallophosphatases (MPPs) that includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 257
Score = 31.9 bits (73), Expect = 0.38
Identities = 14/75 (18%), Positives = 25/75 (33%), Gaps = 23/75 (30%)
Query: 221 ILQKMDAPLISTSVKWLKDNEWMVDPVVIADTYGPEGLDFVVDGGVRVA----------- 269
+ ++ D P +S +V + + P I + + GV+V
Sbjct: 91 LSKEADFPFLSANVYDNDTGKRVFKPYKIKE----------LGNGVKVGVIGLTTPETAT 140
Query: 270 --EPSTVVDMTGTYP 282
P V D+T P
Sbjct: 141 KTHPKNVKDVTFEDP 155
>gnl|CDD|215053 PLN00094, PLN00094, aconitate hydratase 2; Provisional.
Length = 938
Score = 29.9 bits (67), Expect = 2.4
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 267 RVAEPSTVVDM-TGTYPKIIRQGKGPKLYWMEEEDANSTAIEDLIPS 312
RVAE STVV T +P R GKG +Y E A AI +P+
Sbjct: 841 RVAEKSTVVSTSTRNFPN--RLGKGANVYLASAELAAVAAILGRLPT 885
>gnl|CDD|239323 cd03025, DsbA_FrnE_like, DsbA family, FrnE-like subfamily; composed
of uncharacterized proteins containing a CXXC motif with
similarity to DsbA and FrnE. FrnE is presumed to be a
thiol oxidoreductase involved in polyketide
biosynthesis, specifically in the production of the
aromatic antibiotics frenolicin and nanaomycins.
Length = 193
Score = 28.1 bits (63), Expect = 4.9
Identities = 18/94 (19%), Positives = 26/94 (27%), Gaps = 13/94 (13%)
Query: 75 LMYVEADPSGADSWKLEPVVELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEP 134
L Y DP + EP++E LKE G + + L N
Sbjct: 3 LYYF-IDPLCGWCYGFEPLLEKLKEEYGGGIEVELHLGG------------LLPGNNARQ 49
Query: 135 SKPLSILCRSLRDIDTYTTGFPRGDGQGHANIFR 168
+ TG P G+ +F
Sbjct: 50 ITKQWRIYVHWHKARIALTGQPFGEDYLELLLFD 83
>gnl|CDD|219238 pfam06953, ArsD, Arsenical resistance operon trans-acting repressor
ArsD. This family consists of several bacterial
arsenical resistance operon trans-acting repressor ArsD
proteins. ArsD is a trans-acting repressor of the
arsRDABC operon that confers resistance to arsenicals
and antimonials in Escherichia coli. It possesses
two-pairs of vicinal cysteine residues, Cys(12)-Cys(13)
and Cys(112)-Cys(113), that potentially form separate
binding sites for the metalloids that trigger
dissociation of ArsD from the operon. However, as a
homodimer it has four vicinal cysteine pairs.
Length = 120
Score = 26.8 bits (60), Expect = 6.6
Identities = 17/65 (26%), Positives = 24/65 (36%), Gaps = 14/65 (21%)
Query: 230 ISTSVKWLKDNEWMVD-------PVVIADTYGPEGLDFVVDGGVRVAEPSTVVD----MT 278
+ + WLK N V+ P+ A+ F+ G P T+VD T
Sbjct: 29 FAADLDWLKQNGVEVERYNLAQQPMAFAEN--AVVKAFLETSGAEGL-PLTLVDGEIVKT 85
Query: 279 GTYPK 283
G YP
Sbjct: 86 GRYPT 90
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
0.318 0.135 0.409
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,352,142
Number of extensions: 1580613
Number of successful extensions: 1328
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1313
Number of HSP's successfully gapped: 19
Length of query: 314
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 217
Effective length of database: 6,635,264
Effective search space: 1439852288
Effective search space used: 1439852288
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)