RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026381
(239 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 (421), Expect = 8e-52
Identities = 62/195 (31%), Positives = 93/195 (47%), Gaps = 18/195 (9%)
Query: 20 ELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDIDTYTTG 79
E L++G + PTDT+Y + CD + A+ERLR IK KPL+++ L + Y
Sbjct: 1 EALRQGGIVAYPTDTVYGLGCDATNEEAVERLREIKGRPRDKPLAVMVSDLEQLKKYADE 60
Query: 80 FPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTTAKYSLRKHVGVRIPN 139
+ + PGP T IL ASK K V G VGVR+P+
Sbjct: 61 LE-------EAALKLAERFWPGPITLILPASKSSLPKLVTPG--------LGTVGVRLPD 105
Query: 140 DAICQAILQKMDAPLISTSVKWLKDNEWMVDPVVIADTYGPEGLDFVVDGGV-RVAEPST 198
+ + +L+ + PL++TS L D + + G +D ++DGG V ST
Sbjct: 106 HPLARLLLEALGEPLVATSAN-LSGEPSATDAEEVLEELG-GIVDLILDGGRIPVGVDST 163
Query: 199 VVDMTGTYPKIIRQG 213
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 (381), Expect = 2e-45
Identities = 67/214 (31%), Positives = 100/214 (46%), Gaps = 19/214 (8%)
Query: 5 ADPSGADSWKLEPVVELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLS 64
P +E VE L++G V PTDT+Y + D + A+ERL IK KPL
Sbjct: 6 IHPENPQPRAIEKAVEALRKGGVVAYPTDTVYGLGADATNEEAVERLYEIKQRPSDKPLI 65
Query: 65 ILCRSLRDIDTYTTGFPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTT 124
+ SL + Y + +K PGP TFIL A+KEVP++ V G +T
Sbjct: 66 LHVASLEQLKEYADVPDV--------ARKLLKAFWPGPLTFILPATKEVPRRLVTAGLST 117
Query: 125 AKYSLRKHVGVRIPNDAICQAILQKMDAPLISTSVKWLKDNEWMVDPVVIADTYGPEGLD 184
+ VR+P+ I A+++ + PL STS L + +G + +D
Sbjct: 118 --------IAVRVPDHPIALALIEALGEPLASTSAN-LSGQPSPTTAEEVRADFGGQ-VD 167
Query: 185 FVVDGGV-RVAEPSTVVDMTGTYPKIIRQGKGPK 217
++DGG R PST++D+T P+I+R G
Sbjct: 168 LIIDGGPCRGGLPSTIIDLTDDPPRILRPGAISL 201
>gnl|CDD|183245 PRK11630, PRK11630, hypothetical protein; Provisional.
Length = 206
Score = 129 bits (325), Expect = 3e-37
Identities = 64/198 (32%), Positives = 115/198 (58%), Gaps = 19/198 (9%)
Query: 19 VELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDIDTYTT 78
VE++++G V V PTD+ YA+ C ++ +A+ER+ RI+ + +++CR L ++ TY+
Sbjct: 21 VEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELSTYS- 79
Query: 79 GFPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTTAKYSLRKHVGVRIP 138
FR +K+ PG YTFIL +KEVP++ ++ RK +G+R+P
Sbjct: 80 -------FVDNVAFRLMKNNTPGNYTFILKGTKEVPRRLLQ--------EKRKTIGLRVP 124
Query: 139 NDAICQAILQKMDAPLISTSVKWLKDNEWM-VDPVVIADTYGPEGLDFVVDGGVRVAEPS 197
++ I A+L+ + P++STS+ L +++ DP I D + +D ++ GG +P+
Sbjct: 125 SNPIALALLEALGEPMLSTSLM-LPGSDFTESDPEEIKDRLEKQ-VDLIIHGGYLGQQPT 182
Query: 198 TVVDMTGTYPKIIRQGKG 215
TV+D+T P ++R+G G
Sbjct: 183 TVIDLTDDTPVVVREGVG 200
>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 = 128 bits (324), Expect = 5e-37
Identities = 63/204 (30%), Positives = 106/204 (51%), Gaps = 20/204 (9%)
Query: 15 LEPVVELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDID 74
+E V++L++G + V PTDT+Y I D A+ RL RIK +KPL++L L +I+
Sbjct: 11 IEQAVKILRKGGIVVYPTDTVYGIGADALDEDAVRRLYRIKGRPSNKPLTVLVSDLSEIE 70
Query: 75 TYTTGFPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTTAKYSLRKHVG 134
Y + D R +K PGP T +L + E+P++ RK +G
Sbjct: 71 KYA--YVPDDA------KRLMKKFWPGPLTLVLKKTPEIPRRVS---------GKRKTIG 113
Query: 135 VRIPNDAICQAILQKMDAPLISTSVKWLKDNEWMVDPVVIADTYGPEGLDFVVDGG-VRV 193
+R+P++ I +L+++ P+++TS L D D G + +D ++D G
Sbjct: 114 IRVPDNPIALELLEELGKPIVATSAN-LSGKPSATDVEEAVDELG-KLVDLIIDAGPCLG 171
Query: 194 AEPSTVVDMTGTYPKIIRQGKGPK 217
EPST++D+T PK++R+G G +
Sbjct: 172 GEPSTIIDLTDDTPKVLREGVGSE 195
>gnl|CDD|182603 PRK10634, PRK10634, tRNA(ANN) t(6)A37 threonylcarbamoyladenosine
modification protein; Provisional.
Length = 190
Score = 48.2 bits (115), Expect = 5e-07
Identities = 38/144 (26%), Positives = 62/144 (43%), Gaps = 14/144 (9%)
Query: 15 LEPVVELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDID 74
+ V++L E V PT+ ++ + CD S +A+ RL +K K L ++ + +
Sbjct: 10 IAAAVDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANYEQLK 69
Query: 75 TYTTGFPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTTAKYSLRKHVG 134
Y D Q IF C PGP TF+ A P+ T ++ +
Sbjct: 70 PYIDDSMLTDAQRET-IFS----CWPGPVTFVFPAPATTPR------WLTGRFD---SLA 115
Query: 135 VRIPNDAICQAILQKMDAPLISTS 158
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 = 37.8 bits (88), Expect = 0.004
Identities = 43/203 (21%), Positives = 76/203 (37%), Gaps = 30/203 (14%)
Query: 19 VELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDIDTYTT 78
+LLK+G + + + + CD ++ +ERLR KN P KP +++ L +
Sbjct: 169 AKLLKKGKIIAIKGIGGFHLACDARNDEVVERLRLRKN-RPLKPFAVMSPDLESAEQ--- 224
Query: 79 GFPRGDGQGHANIFRAVKHCLPGPYTFILTASKEVPKKCVRYGTTTAKYSLRKHVGVRIP 138
HA + L P I+ K K ++ A +GV +P
Sbjct: 225 ---------HAELNNLECELLTSPAAPIVLLRK---KPDIKLAPNIAPNLPT--IGVMLP 270
Query: 139 NDAICQAILQKMDAPLISTSVKWLKDNEWMVDPVVIADTYGPEGLDFVVDGGV----RVA 194
+ +LQ + PL+ TS P+ I + + L + DG + R+
Sbjct: 271 YTPLHHLLLQLLAFPLVMTSANLPG------LPMAIDNAEILDKLQGIADGFLVHNRRIV 324
Query: 195 EP--STVVDMTGTYPKIIRQGKG 215
+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 = 0.029
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 15 LEPVVELLKEGAVGVVPTDTLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDID 74
+ +LLK G + + + + CD ++ A+ +LR+ KN P KP +++ + L I+
Sbjct: 200 IRKAAKLLKVGKIVAIKGIGGFHLACDARNEEAVAKLRKRKN-RPLKPFAVMAKDLETIE 258
Query: 75 TY 76
+
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 = 30.7 bits (70), Expect = 0.57
Identities = 14/75 (18%), Positives = 25/75 (33%), Gaps = 23/75 (30%)
Query: 146 ILQKMDAPLISTSVKWLKDNEWMVDPVVIADTYGPEGLDFVVDGGVRVA----------- 194
+ ++ D P +S +V + + P I + + GV+V
Sbjct: 91 LSKEADFPFLSANVYDNDTGKRVFKPYKIKE----------LGNGVKVGVIGLTTPETAT 140
Query: 195 --EPSTVVDMTGTYP 207
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 = 1.4
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 192 RVAEPSTVVDM-TGTYPKIIRQGKGPKLYWMEEEDANSTAIEDLIPS 237
RVAE STVV T +P R GKG +Y E A AI +P+
Sbjct: 841 RVAEKSTVVSTSTRNFPN--RLGKGANVYLASAELAAVAAILGRLPT 885
>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 = 26.4 bits (59), Expect = 6.8
Identities = 17/65 (26%), Positives = 24/65 (36%), Gaps = 14/65 (21%)
Query: 155 ISTSVKWLKDNEWMVD-------PVVIADTYGPEGLDFVVDGGVRVAEPSTVVD----MT 203
+ + WLK N V+ P+ A+ F+ G P T+VD T
Sbjct: 29 FAADLDWLKQNGVEVERYNLAQQPMAFAEN--AVVKAFLETSGAEGL-PLTLVDGEIVKT 85
Query: 204 GTYPK 208
G YP
Sbjct: 86 GRYPT 90
>gnl|CDD|216025 pfam00617, RasGEF, RasGEF domain. Guanine nucleotide exchange
factor for Ras-like small GTPases.
Length = 185
Score = 27.1 bits (61), Expect = 7.1
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 34 TLYAIVCDLKSHSAIERLRRIKNVEPSKPLSILCRSLRDI 73
+L AI+ L + S I RL++ + K +L L ++
Sbjct: 93 SLMAIISGL-NSSPISRLKKTWELVSKKYKKLL-EELEEL 130
>gnl|CDD|224593 COG1679, COG1679, Predicted aconitase [General function prediction
only].
Length = 403
Score = 27.3 bits (61), Expect = 8.0
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 173 VIADTYGPEGLDFV---VDGGVRVAEPSTV 199
V T G GL+F+ + G RV+ P+T+
Sbjct: 52 VSYKTIGDAGLEFLEDLAEMGARVSVPTTL 81
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 0.136 0.413
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: 12,508,840
Number of extensions: 1180686
Number of successful extensions: 968
Number of sequences better than 10.0: 1
Number of HSP's gapped: 953
Number of HSP's successfully gapped: 24
Length of query: 239
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 145
Effective length of database: 6,768,326
Effective search space: 981407270
Effective search space used: 981407270
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: 57 (25.6 bits)