RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2632
(374 letters)
>gnl|CDD|234197 TIGR03399, RNA_3prim_cycl, RNA 3'-phosphate cyclase. Members of
this protein family are RNA 3'-phosphate cyclase
(6.5.1.4), an enzyme whose function is conserved from E.
coli to human. The modification this enzyme performs
enables certain RNA ligations to occur, although the
full biological roll for this enzyme is not fully
described. This model separates this enzyme from a
related protein, present only in eukaryotes, localized
to the nucleolus, and involved in ribosomal modification
[Transcription, RNA processing].
Length = 326
Score = 318 bits (817), Expect = e-107
Identities = 136/333 (40%), Positives = 196/333 (58%), Gaps = 11/333 (3%)
Query: 13 IDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQGRL 72
IDGS EGGGQILR A+ S L +P+ ++NIRA R KPGLA QHL + A +IC +
Sbjct: 3 IDGSYGEGGGQILRTALSLSALTGKPVRIYNIRANRPKPGLAPQHLTAVKAAAEICNAEV 62
Query: 73 ENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGGTNA 132
E A +GSTE+ F PG I G++ D TAGSVTL++Q LP LLF++G S++ V GGT+
Sbjct: 63 EGAELGSTELEFIPGKIRGGDYRFDIGTAGSVTLVLQTLLPALLFANGPSRVTVSGGTDV 122
Query: 133 DMAPPIDYYIHLWRPVFCHF-FNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQ 191
APP+DY +++ P+ +++ +RRGF+P+GGGEV + V PV+ ++P+EL +
Sbjct: 123 PWAPPVDYLRNVFLPLLERMGIRAELEL--LRRGFYPRGGGEVRLRVEPVKKLKPLELEE 180
Query: 192 RGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKAIGNG 251
RGEL V G A A + + A+ MA A + L K D + ++++ DK +G G
Sbjct: 181 RGELLRVSGIAHAA-NLPAHVAERMAKAAREELRKLGLDPEIEIEVL------DKGLGPG 233
Query: 252 SGVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQDQLIVMM 311
SG+ ++A T R G S + G AA++L + L DEH DQLI+ M
Sbjct: 234 SGIVLWAET-EHCRLGFSALGEKGKSAEKVGEEAAEQLLAELRSGAAVDEHLADQLILYM 292
Query: 312 ALAKGTSRVRVGQISLHTRTAIHIAELMTSAKF 344
ALA G SR ++++H RT I + E +F
Sbjct: 293 ALASGESRFTTSELTMHLRTNIWVIEQFLPVRF 325
>gnl|CDD|238446 cd00874, RNA_Cyclase_Class_II, RNA 3' phosphate cyclase domain
(class II). These proteins function as RNA cyclase to
catalyze the ATP-dependent conversion of 3'-phosphate to
a 2'.3'-cyclic phosphodiester at the end of RNA
molecule. A conserved catalytic histidine residue is
found in all members of this subfamily.
Length = 326
Score = 311 bits (799), Expect = e-105
Identities = 127/337 (37%), Positives = 185/337 (54%), Gaps = 12/337 (3%)
Query: 13 IDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQGRL 72
IDGS EGGGQILR A+ S + +P+ + NIRA R PGL+ QHL + A IC +
Sbjct: 1 IDGSYGEGGGQILRTALALSAVTGKPVRIVNIRANRSNPGLSRQHLTAVRAAARICNAEV 60
Query: 73 ENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGGTNA 132
E A +GSTE+ F PG I G++ D TAGS+TL++Q LP LLF+ G S + + GGT+
Sbjct: 61 EGAELGSTELEFEPGKIKGGDYEFDIGTAGSITLVLQTLLPALLFADGPSTVTISGGTDV 120
Query: 133 DMAPPIDYYIHLWRPVFCHF-FNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQ 191
APPIDY ++ P+ +++ +RRGF+P+GGGEV + V P + + P+ L +
Sbjct: 121 PWAPPIDYLRNVTLPLLERMGIEAELEV--LRRGFYPRGGGEVVLTVEPSKLLPPLLLEE 178
Query: 192 RGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKAIGNG 251
RGE+ + G + A + + A+ A+ A L K+ + +++ A+G G
Sbjct: 179 RGEIEKIRGISHAA-NLPPHVAERQAEAAAALLRKA-LGLQIEIEPEDQS-----ALGPG 231
Query: 252 SGVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQDQLIVMM 311
SG+ ++A +R G + G AA+EL + L DEH DQLI M
Sbjct: 232 SGIVLWAEYEH-SRLGFSALGKKGVPAEKVGEEAAEELLAYLSSGAAVDEHLADQLIPFM 290
Query: 312 ALAKGTSRVRVGQISLHTRTAIHIAELMTSAKFNIIE 348
ALA G S R G+++LH +T I + E KF I E
Sbjct: 291 ALAGG-SEFRTGELTLHLQTNIWVIEKFLGVKFRIEE 326
>gnl|CDD|216322 pfam01137, RTC, RNA 3'-terminal phosphate cyclase. RNA cyclases
are a family of RNA-modifying enzymes that are conserved
in all cellular organisms. They catalyze the
ATP-dependent conversion of the 3'-phosphate to the
2',3'-cyclic phosphodiester at the end of RNA, in a
reaction involving formation of the covalent AMP-cyclase
intermediate. The structure of RTC demonstrates that
RTCs are comprised two domain. The larger domain
contains an insert domain of approximately 100 amino
acids.
Length = 330
Score = 292 bits (750), Expect = 2e-97
Identities = 137/336 (40%), Positives = 184/336 (54%), Gaps = 6/336 (1%)
Query: 13 IDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQGRL 72
IDGS EGGGQILR A+ S L +P+ + NIRA R PGL QHL+ + I +
Sbjct: 1 IDGSYGEGGGQILRTALALSALTGKPVRIVNIRANRPNPGLRRQHLSAVRALAKITNAEV 60
Query: 73 ENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGGTNA 132
E A +GSTE+ F PG I G++ D TAGS+TL++Q LPLLLF+ G S++ +KGGT+
Sbjct: 61 EGAEVGSTELEFRPGTIRGGDYRVDIGTAGSITLVLQTLLPLLLFAKGPSRITLKGGTDV 120
Query: 133 DMAPPIDYYIHLWRPVFCHFFNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQR 192
APP+DY ++ P+ F ++ +RRGF+P+GGGEV + V PV+ +RPI L +R
Sbjct: 121 PWAPPVDYIRNVTLPLLEKFG-IEGELKVLRRGFYPRGGGEVLLTVPPVKPLRPIHLVER 179
Query: 193 GELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKAIGNGS 252
G++ + G A+ V + A+ AD A L K PD +T + G G
Sbjct: 180 GKVKKIRGIAYST-RVPPHVAEREADAAKARLNKLLPD---VYIVTDVRRGDTGGSGGGG 235
Query: 253 GVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQDQLIVMMA 312
+ I AAT G G + G AAKEL L DEH DQLI+ MA
Sbjct: 236 SITILAATLEGCTLGADALGKKGKPAEKVGEEAAKELLEELESGAAVDEHLADQLILYMA 295
Query: 313 LAKGTSRVRVGQISLHTRTAIHIAELMTSAKFNIIE 348
LA G S RVG+++LH T I + E KF I E
Sbjct: 296 LAGG-SEFRVGELTLHLVTNIRVIEQFLGVKFEIEE 330
>gnl|CDD|235255 PRK04204, PRK04204, RNA 3'-terminal-phosphate cyclase; Provisional.
Length = 343
Score = 287 bits (737), Expect = 2e-95
Identities = 127/350 (36%), Positives = 184/350 (52%), Gaps = 22/350 (6%)
Query: 9 DVLNIDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDIC 68
++ IDGS EGGGQILR A+ S + +P + NIRA R PGL QHL + A +IC
Sbjct: 1 RMIEIDGSYGEGGGQILRTALALSAITGKPFRITNIRANRPNPGLLRQHLTAVKAAAEIC 60
Query: 69 QGRLENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKG 128
+E A +GS E++F PG I G++ D TAGS+TL++Q LP LLF+ G S++ + G
Sbjct: 61 NAEVEGAELGSQELVFIPGPIRGGDYRFDIGTAGSITLVLQTVLPALLFADGPSRVTITG 120
Query: 129 GTNADMAPPIDYYIHLWRPVFCHFFNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIE 188
GT+ APPIDY + P +I +RRGF+P GGGEV ++V P + +RP+E
Sbjct: 121 GTDVPWAPPIDYIRRVTLP-LLRRMGIEAEIELLRRGFYPAGGGEVALEVEPSK-LRPLE 178
Query: 189 LTQRGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKAI 248
L +RGEL + G + VA + + A+ A A + L S + ++ + + +
Sbjct: 179 LLERGELLRIRGISHVA-NLPEHVAERQAKAAAELLALSLGLIEIEINVEEL----SRGL 233
Query: 249 GNGSGVYIFAATSTGARYSGGCNGSPRTSPGECGL-------NAAKELWSSLCENICFDE 301
G GSG+ ++A G + GE G AA+EL L DE
Sbjct: 234 GPGSGIVLWAE------SEHITEGF--DALGERGKPAEVVGEEAAEELLRYLASGAAVDE 285
Query: 302 HTQDQLIVMMALAKGTSRVRVGQISLHTRTAIHIAELMTSAKFNIIEHED 351
H DQLI+ MALA G V +++ H T I + E KF + E++
Sbjct: 286 HLADQLILPMALAGGEGSFTVAELTSHLLTNIWVVEKFLPVKFEVEEYDG 335
>gnl|CDD|223507 COG0430, RCL1, RNA 3'-terminal phosphate cyclase [RNA processing
and modification].
Length = 341
Score = 262 bits (671), Expect = 2e-85
Identities = 131/349 (37%), Positives = 184/349 (52%), Gaps = 10/349 (2%)
Query: 9 DVLNIDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDIC 68
++ IDGS EGGGQILR A+ S L +P+ + NIRAGR PGL QHL + A +IC
Sbjct: 1 RMIEIDGSYGEGGGQILRTALALSALTGKPVRIENIRAGRANPGLKRQHLTAVRAAAEIC 60
Query: 69 QGRLENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKG 128
+E A +GSTE++F PG I G++ D TAGS+TL++Q LPLLLF+ G S++ V G
Sbjct: 61 NAEVEGAELGSTELVFRPGKIRGGDYRVDIGTAGSITLVLQTLLPLLLFADGPSRITVTG 120
Query: 129 GTNADMAPPIDYYIHLWRPVFCHFFNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIE 188
GT+ APP+DY + PV ++ ++RGF+P+GGGEV + V P + P+
Sbjct: 121 GTDVPWAPPVDYIRRVTLPVLRKMGIE-CELEVLKRGFYPRGGGEVLLTVEPPKEKLPLH 179
Query: 189 LTQRGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKAI 248
LT+RGE+ V G A + + A+ A+ A + L K + + Y +
Sbjct: 180 LTERGEIEKVRGIAHST-NLPPHVAERQAEAAKELLGKLGLE------VEIYTEVRRGGL 232
Query: 249 GNGSGVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQDQLI 308
GSG+ ++A S G+R G S G AAKEL L DEH DQLI
Sbjct: 233 SPGSGIVLWAE-SEGSRIGADALGEKGKSAEVVGEEAAKELLRELESGAAVDEHLADQLI 291
Query: 309 VMMALAKGTSRVRVGQISLHTRTAIHIAELMTSAKFNIIEHEDKSCIIE 357
MALA G V +++ H T I + E +F + E +E
Sbjct: 292 PYMALA-GIGEFTVAEVTSHLLTNIWVIERFLGVEFEVEGEEGGPGKVE 339
>gnl|CDD|238183 cd00295, RNA_Cyclase, RNA 3' phosphate cyclase domain - RNA
phosphate cyclases are enzymes that catalyze the
ATP-dependent conversion of 3'-phosphate at the end of
RNA into 2', 3'-cyclic phosphodiester bond. The enzymes
are conserved in eucaryotes, bacteria and archaea. The
exact biological role of this enzyme is unknown, but it
has been proposed that it is likely to function in
cellular RNA metabolism and processing. RNA phosphate
cyclase has been characterized in human (with at least
three isozymes), and E. coli, and it seems to be
taxonomically widespread. The crystal structure of RNA
phospate cyclase shows that it consists of two domains.
The larger domain contains three repeats of a fold
originally identified in the bacterial translation
initiation factor IF3.
Length = 338
Score = 151 bits (382), Expect = 1e-42
Identities = 93/341 (27%), Positives = 145/341 (42%), Gaps = 8/341 (2%)
Query: 13 IDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQGRL 72
+DG+ EGG +ILR A+ + + +P + IRA PGL QHL+ L A++IC +
Sbjct: 1 LDGAKGEGGCEILRHALSLAMISGQPFRIEGIRADEADPGLKDQHLSALKAAEEICGASV 60
Query: 73 ENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGGTNA 132
E A +G IF PGNI G+ +AG L ++ L LF+ G S+L + GGT+
Sbjct: 61 EEAELGGQRFIFRPGNIIGGDVRFACGSAGGCGLFLEPILIACLFADGPSRLELSGGTDN 120
Query: 133 DMAPPIDYYIHLWRPVFCHFFNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQR 192
+ A D+ P+ F D ++R GF GG + + + L +R
Sbjct: 121 NEAIGADFIRRSLEPLLAKIFIHG-DELELRHGFRGAAGGGGAEENFLCASFKELLLGER 179
Query: 193 G-ELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKI-TTYQLSSDKAIGN 250
G E + +A G ++ A A+ S+ F+ + I Q + G
Sbjct: 180 GSEFGRQFRGEGIAAGTRVPPA--FAEREIASAAGSFNLFEPDIFILPDDQRGDECGNGP 237
Query: 251 GSGVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQDQLIVM 310
G+ + + A + G + G S + AKEL + DE+ DQL++
Sbjct: 238 GNSISLEAESEKGCSEAAEHCGEAGESAEDVAAFCAKELKEVIASGAAVDEYLADQLLLG 297
Query: 311 MALAKGTSRVRVGQISLHTRTAIHIA---ELMTSAKFNIIE 348
MALA V H + A E + +F IE
Sbjct: 298 MALAGEAGEFIVAGPLCHLLQLTNFARDVEAFFNCEFRFIE 338
>gnl|CDD|234198 TIGR03400, 18S_RNA_Rcl1p, 18S rRNA biogenesis protein RCL1.
Members of this strictly eukaryotic protein family are
not RNA 3'-phosphate cyclase (6.5.1.4), but rather a
homolog with a distinct function, found in the nucleolus
and required for ribosomal RNA processing. Homo sapiens
has both a member of this RCL (RNA terminal phosphate
cyclase like) family and EC 6.5.1.4, while Saccharomyces
has a member of this family only.
Length = 360
Score = 141 bits (359), Expect = 6e-39
Identities = 93/364 (25%), Positives = 167/364 (45%), Gaps = 21/364 (5%)
Query: 21 GGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQG-RLENAHIGS 79
G + R +V S L +P+ + IR+ PGL ++ L + + + G ++E ++ G
Sbjct: 5 GSRNFRQRLVLSTLSGKPVRITKIRSDDENPGLRDYEVSFLRLLEKVTNGSKIEISYTG- 63
Query: 80 TEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGGTNADMAPPID 139
T +I+ PG IT G+ + T+ + ++ L L FS + +KG TN+ P +D
Sbjct: 64 TTVIYKPGLITGGSVTHECPTSRGIGYYLEPLLLLAPFSKKPLSITLKGITNSTGDPSVD 123
Query: 140 YYIHLWRPVFCHFFNF--NIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQRGELTA 197
P+ F +++ ++RG P GGGEV + ++ ++ I LT+RG +
Sbjct: 124 TIRTATLPLLKKFGIPDEGLELKILKRGAPPLGGGEVELRCPVIKQLKTIHLTERGRVKR 183
Query: 198 VWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKAIGN-GSGVYI 256
+ G A+ + V + A M D A L PD + ITT + + G G+ +
Sbjct: 184 IRGVAY-STRVSPSLANRMIDAARGVLNNLLPD----VYITTDVWKGKNSGKSPGYGLSL 238
Query: 257 FAATSTGARYSGGCNGSPR--TSPGECGLNAAKELWSSLCENICFDEHTQDQLIVMMALA 314
A T+ G S SP + P + G AA L + + C D Q +++MAL
Sbjct: 239 VAETTNGCIISAEAVSSPGEPSLPEDLGKRAAYLLLEEIYKGGCVDSTHQPLALLLMALG 298
Query: 315 KG-TSRVRVGQISLHTRTAI-HIAELMTSAKFNI----IEHEDKSCIIECQGMGFVNKNW 368
+ S++R+G++S +T + I E F + ++ ++ C G+G+ N +
Sbjct: 299 QEDVSKLRLGKLSEYTVEFLRDIKEF-FGVTFKLKDDKSDNGSGKVLLTCVGIGYTNVS- 356
Query: 369 GRKT 372
+K
Sbjct: 357 -KKI 359
>gnl|CDD|238794 cd01553, EPT_RTPC-like, This domain family includes the
Enolpyruvate transferase (EPT) family and the RNA 3'
phosphate cyclase family (RTPC). These 2 families differ
in that EPT is formed by 3 repeats of an alpha-beta
structural domain while RTPC has 3 similar repeats with
a 4th slightly different domain inserted between the 2nd
and 3rd repeat. They evidently share the same active
site location, although the catalytic residues differ.
Length = 211
Score = 94.3 bits (234), Expect = 1e-22
Identities = 69/183 (37%), Positives = 97/183 (53%), Gaps = 9/183 (4%)
Query: 13 IDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQGRL 72
+DG+ +GGGQILR +V + + PI V IR R KPGL QHL L + IC +
Sbjct: 1 LDGAGGKGGGQILRSFLVLAAISGGPITVTGIRPDRAKPGLLRQHLTFLKALEKICGATV 60
Query: 73 ENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGGTNA 132
E +GS I F PG + G+ +AGS T ++Q LPLLLF+ G ++L V GGT+
Sbjct: 61 EGGELGSDRISFRPGTVRGGDVRFAIGSAGSCTDVLQTILPLLLFAKGPTRLTVTGGTDN 120
Query: 133 DMAPPIDY----YIHLWRPVFCHFFNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIE 188
APP D+ + H + +R GF+P GGG V +V+PV+ + +
Sbjct: 121 PSAPPADFIRFVLEPELAKIGAH-----QEETLLRHGFYPAGGGVVATEVSPVEKLNTAQ 175
Query: 189 LTQ 191
L Q
Sbjct: 176 LRQ 178
>gnl|CDD|238447 cd00875, RNA_Cyclase_Class_I, RNA 3' phosphate cyclase domain
(class I) This subfamily of cyclase-like proteins are
encoded in eukaryotic genomes. They lack a conserved
catalytic histidine residue required for cyclase
activity, so probably do not function as cyclases. They
are believed to play a role in ribosomal RNA processing
and assembly.
Length = 341
Score = 95.1 bits (237), Expect = 5e-22
Identities = 80/325 (24%), Positives = 132/325 (40%), Gaps = 14/325 (4%)
Query: 20 GGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQG-RLENAHIG 78
G R +V + L +PI + IR+ PGL ++ L + + + G +E ++ G
Sbjct: 8 KGSNFFRQRLVLATLSGKPIIIKKIRSDDTNPGLRDHEVSFLRLLEKVTNGSVIEISYTG 67
Query: 79 STEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGGTNADMAPPI 138
T +I+ PG IT G D + + ++ L L F + +KG TN+ P +
Sbjct: 68 -TTLIYKPGLITGGVLNHDCPVSRGIGYFLEPLLLLAPFGKKPLSITLKGITNSTGDPSV 126
Query: 139 DYYIHLWRPVFCHFFNFN--IDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQRGELT 196
D P+ F + +++ ++RG P GGGEV + + P G +
Sbjct: 127 DSIRTATLPLLKKFGIPDEELELKILKRGVAPGGGGEVGFRCPVRKPLTPHLNDSPGRIK 186
Query: 197 AVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKA-IGNGSGVY 255
+ G A+ V + A M D A L PD + I T D + G G+
Sbjct: 187 RIRGVAYST-RVSPSIANRMIDAARGVLNPFIPD----VYIYTDVRKGDNSGKSPGFGIS 241
Query: 256 IFAATSTGARYSGGCNGSPR---TSPGECGLNAAKELWSSLCENICFDEHTQDQLIVMMA 312
+ A T+TG YS P + G A +L + C D + Q +++MA
Sbjct: 242 LVAETTTGVLYSAENVSPAGGESEVPEDLGRECAYQLLEEISRGGCVDSYQQPLALLLMA 301
Query: 313 LAKG-TSRVRVGQISLHTRTAIHIA 336
L R+R+G + IH+
Sbjct: 302 LGSEDVGRLRLGGPLIDEEFKIHLL 326
>gnl|CDD|203195 pfam05189, RTC_insert, RNA 3'-terminal phosphate cyclase (RTC),
insert domain. RNA cyclases are a family of
RNA-modifying enzymes that are conserved in all cellular
organisms. They catalyze the ATP-dependent conversion of
the 3'-phosphate to the 2',3'-cyclic phosphodiester at
the end of RNA, in a reaction involving formation of the
covalent AMP-cyclase intermediate. The structure of RTC
demonstrates that RTCs are comprised two domain. The
larger domain contains an insert domain of approximately
100 amino acids.
Length = 101
Score = 59.5 bits (145), Expect = 3e-11
Identities = 30/100 (30%), Positives = 43/100 (43%), Gaps = 6/100 (6%)
Query: 190 TQRGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKAIG 249
+RG + + G A+VA V + A+ MAD A L K PD + I T + D
Sbjct: 1 VERGRIKRIRGVAYVAR-VPPHVAERMADAARGVLNKPLPD----VYIETDKRGRDSGKS 55
Query: 250 NGSGVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKEL 289
GSG+ + A T T G + G AA++L
Sbjct: 56 PGSGITLVAETETC-TLGADALGERGVPAEDVGEEAAEQL 94
>gnl|CDD|241485 cd13331, PH_Avo1, Avo1 Pleckstrin homology (PH) domain. Target of
rapamycin (TOR) is a highly conserved serine/threonine
protein kinase and a central controller of the growth,
metabolism and ageing of eukaryotic cells. TOR assembles
into two protein complexes termed TOR complex 1 (TORC1)
and TOR complex 2 (TORC2) which function as central
nodes in a complex network of signal transduction
pathways that are involved in normal physiological as
well as pathogenic events. TORC1 mediates the
rapamycin-sensitive signalling branch, which positively
regulates anabolic processes and negatively regulates
catabolic processes. TORC2 signalling is rapamycinin
insensitive and is involved in the spatial aspects of
cell growth by controlling the actin cytoskeleton and
cell polarity. In Saccharomyces cerevisiae, TORC2 is
involved in the regulation of ceramide metabolism. In S.
cerevisiae, TORC1 consists of the proteins Kog1, Lst8,
Tco89 and either Tor1 or Tor2, while TORC2 is consists
of the proteins Avo1, Avo2, Avo3, Bit61, Lst8 and Tor2.
The C-terminal domain of the Saccharomyces cerevisiae
TORC2 component Avo1 is required for plasma-membrane
localization of TORC2 and is essential for yeast
viability. The C-termini of Avo1 and Sin1, its Human
ortholog, both have the pleckstrin homology (PH) domain
fold. Comparison with known PH-domain structures
suggests a putative binding site for phosphoinositides.
PH domains have diverse functions, but in generally are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 108
Score = 29.3 bits (65), Expect = 1.3
Identities = 12/38 (31%), Positives = 15/38 (39%)
Query: 147 PVFCHFFNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYI 184
P HF + HD + +F VN V V YI
Sbjct: 66 PSHAHFKITYLSNHDYKHLYFESDAATVNEIVLKVNYI 103
>gnl|CDD|129806 TIGR00723, ttdB_fumA_fumB, hydro-lyases, Fe-S type,
tartrate/fumarate subfamily, beta region. A number of
Fe-S cluster-containing hydro-lyases share a conserved
motif, including argininosuccinate lyase,
adenylosuccinate lyase, aspartase, class I fumarate
hydratase (fumarase), and tartrate dehydratase (see
PROSITE:PDOC00147). This model represents a subset of
closely related proteins or modules, including the E.
coli tartrate dehydratase beta chain and the C-terminal
region of the class I fumarase (where the N-terminal
region is homologous to the tartrate dehydratase alpha
chain). The activity of archaeal proteins in this
subfamily has not been established.
Length = 168
Score = 29.7 bits (67), Expect = 1.6
Identities = 22/83 (26%), Positives = 32/83 (38%), Gaps = 10/83 (12%)
Query: 57 HLNG-LIVAKDICQGRLENAHIGSTE--------IIFYPGNITSGNFYADSKTAGSVTLI 107
+L G + A+D RL E +I++ G I + N + + G T
Sbjct: 13 YLTGTIFTARDEAHARLLELIDEGKELPFDLNGSVIYHAGPIVTKNGEWEVVSVGPTTSA 72
Query: 108 -MQVALPLLLFSSGQSQLIVKGG 129
M P LL G +I KGG
Sbjct: 73 RMNPFEPELLEKLGVMAIIGKGG 95
>gnl|CDD|132355 TIGR03312, Se_sel_red_FAD, probable selenate reductase, FAD-binding
subunit. This protein is suggested by Bebien, et al.,
to be the FAD-binding subunit of a
molydbopterin-containing selenate reductase. Our
comparative genomics suggests it to be a subunit of a
selenium-dependent molybdenum hydroxylase for an unknown
substrate.
Length = 257
Score = 29.5 bits (66), Expect = 2.5
Identities = 13/39 (33%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 182 QYIRPIELTQRGELTAVWGH--AFVAGGVKMNTAQTMAD 218
Q+ RP Q EL + AGG K+N T D
Sbjct: 3 QFFRPESTIQALELKKRHTGVAVWFAGGSKLNATPTRTD 41
>gnl|CDD|236486 PRK09369, PRK09369, UDP-N-acetylglucosamine
1-carboxyvinyltransferase; Validated.
Length = 417
Score = 28.5 bits (65), Expect = 5.8
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 17/47 (36%)
Query: 304 QDQLIVMMALAKGTSRV----------------RVG-QISLHTRTAI 333
Q Q + ++ A+GTS + R+G I + TA+
Sbjct: 308 QAQFMALLTQAEGTSVITETIFENRFMHVPELIRMGADIEVDGHTAV 354
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of this
protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 28.8 bits (65), Expect = 6.1
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 4/32 (12%)
Query: 160 HDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQ 191
+R FF GGGE V T ++PI L
Sbjct: 1028 ARIRDAFFRSGGGEPAVSFT----LKPISLDP 1055
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
0.322 0.138 0.421
Gapped
Lambda K H
0.267 0.0872 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,876,400
Number of extensions: 1802071
Number of successful extensions: 1253
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1221
Number of HSP's successfully gapped: 23
Length of query: 374
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 276
Effective length of database: 6,590,910
Effective search space: 1819091160
Effective search space used: 1819091160
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: 60 (26.6 bits)