Query 033046
Match_columns 128
No_of_seqs 108 out of 412
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 09:09:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033046.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033046hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3502 Uncharacterized protei 100.0 2.6E-42 5.5E-47 248.3 8.5 110 9-125 2-112 (115)
2 PF06108 DUF952: Protein of un 100.0 8.8E-39 1.9E-43 224.3 1.8 92 16-114 1-93 (93)
3 PF01885 PTS_2-RNA: RNA 2'-pho 95.1 0.027 5.9E-07 43.8 3.8 74 5-88 100-175 (186)
4 COG1859 KptA RNA:NAD 2'-phosph 94.6 0.11 2.3E-06 41.8 6.0 75 5-88 115-191 (211)
5 PRK00819 RNA 2'-phosphotransfe 94.1 0.049 1.1E-06 42.4 3.0 72 7-88 91-164 (179)
6 PTZ00315 2'-phosphotransferase 78.5 2.9 6.2E-05 38.2 4.0 70 10-88 476-549 (582)
7 PF13983 YsaB: YsaB-like lipop 55.8 5 0.00011 27.4 0.6 12 34-46 63-75 (77)
8 KOG2871 Uncharacterized conser 42.0 10 0.00022 33.4 0.5 50 40-92 323-374 (449)
9 cd05703 S1_Rrp5_repeat_hs12_sc 40.1 18 0.00039 23.4 1.3 36 39-75 24-64 (73)
10 COG3232 HpaF 5-carboxymethyl-2 32.4 44 0.00094 25.0 2.5 42 39-80 58-114 (127)
11 COG1093 SUI2 Translation initi 32.3 53 0.0011 27.5 3.2 41 34-75 32-75 (269)
12 KOG1618 Predicted phosphatase 32.1 11 0.00024 32.7 -0.8 33 88-126 217-252 (389)
13 cd05696 S1_Rrp5_repeat_hs4 S1_ 31.8 20 0.00044 22.9 0.6 35 39-74 26-63 (71)
14 PTZ00248 eukaryotic translatio 30.3 25 0.00054 29.9 1.0 38 38-75 42-81 (319)
15 cd05707 S1_Rrp5_repeat_sc11 S1 29.1 39 0.00084 20.9 1.5 35 39-74 24-61 (68)
16 KOG0190 Protein disulfide isom 26.9 75 0.0016 28.7 3.4 57 42-101 396-462 (493)
17 PF09456 RcsC: RcsC Alpha-Beta 24.9 83 0.0018 22.1 2.7 32 28-59 59-92 (92)
18 PF02155 GCR: Glucocorticoid r 23.3 35 0.00076 29.7 0.7 14 39-52 248-261 (370)
19 PRK04980 hypothetical protein; 22.1 1.1E+02 0.0023 22.0 2.9 30 38-72 71-100 (102)
20 cd05698 S1_Rrp5_repeat_hs6_sc5 20.4 53 0.0012 20.2 0.9 36 39-74 24-61 (70)
21 PF05582 Peptidase_U57: YabG p 20.0 1.4E+02 0.0031 25.2 3.6 59 8-70 103-161 (287)
No 1
>COG3502 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=2.6e-42 Score=248.27 Aligned_cols=110 Identities=40% Similarity=0.648 Sum_probs=106.2
Q ss_pred CCceEEEecChhhHHHHHhCCCCCCCCCCCCCCeEeccchhcHHHHHHhhcCCCCCcEEEEEEcCCCCCCceEEeecCCC
Q 033046 9 RGEFVYRISTASEWEELQKNGSTFGGELDKSSGCFHLSKLDQVQPTLQNFFLNSKEDLYLLQIGAKKLGDGLIYELVDGL 88 (128)
Q Consensus 9 ~~~~iyhI~~~~~W~~a~~~G~~~~~~ld~~dGFIH~St~~Qv~~va~~ff~~~~~~lvlL~ID~~~L~~~l~wE~~~gg 88 (128)
.+.+||||++++.|++|++.|+|.++++|.+|||||+||++||..||+|+|++ |.+|+||.||+++|+++||||+++||
T Consensus 2 ~~~~iykI~~~~~W~~A~~~G~f~~~svd~~dGfIH~St~~Qv~~tAar~f~G-Q~dLlLl~iD~aaLg~~lryE~srgg 80 (115)
T COG3502 2 SPATIYKITPRALWAAARAAGSFEGASVDDADGFIHLSTAAQVRETAARHFRG-QADLLLLAIDPAALGDELRYEPSRGG 80 (115)
T ss_pred CcceeeeeCCHHHHHHHHHcCCcCCCCcccccceEEechHHHHHHHHHHHhcC-CcceEEEEecHHHcCCcceeecCCCC
Confidence 46899999999999999999999999998899999999999999999999999 99999999999999999999999999
Q ss_pred CCCceeeCCCCCCCCCCccceEEEEEeec-CCCeeeec
Q 033046 89 NSFPHFYGPSRSFTPLPLDVVTKADKLSL-SDGRFSCS 125 (128)
Q Consensus 89 ~~FPHiYG~~~~~~~Lp~~aV~~v~~l~~-~dG~f~~~ 125 (128)
.+||||||| ||++||++|.+++. .||.|.++
T Consensus 81 ~lFPHLYgp------L~l~AV~~~~pl~l~~DG~~~~p 112 (115)
T COG3502 81 ALFPHLYGP------LPLDAVTWVAPLPLGADGLFQFP 112 (115)
T ss_pred ccccccccc------cchhHheecccCCCCCCCCCCCC
Confidence 999999998 99999999999995 69999876
No 2
>PF06108 DUF952: Protein of unknown function (DUF952); InterPro: IPR009297 This family consists of several hypothetical bacterial and plant proteins of unknown function.; PDB: 2O0Q_A 2O0P_A 2JQN_A.
Probab=100.00 E-value=8.8e-39 Score=224.33 Aligned_cols=92 Identities=48% Similarity=0.766 Sum_probs=79.4
Q ss_pred ecChhhHHHHHhCCCCCCCCCCCCCCeEeccchhcHHHHHHhhcCCCCCcEEEEEEcCCCCCCceEEeecC-CCCCCcee
Q 033046 16 ISTASEWEELQKNGSTFGGELDKSSGCFHLSKLDQVQPTLQNFFLNSKEDLYLLQIGAKKLGDGLIYELVD-GLNSFPHF 94 (128)
Q Consensus 16 I~~~~~W~~a~~~G~~~~~~ld~~dGFIH~St~~Qv~~va~~ff~~~~~~lvlL~ID~~~L~~~l~wE~~~-gg~~FPHi 94 (128)
|+++++|++++..|.|.++++|++|||||||+++||..|+++||++ +++|+||+||+++|++.||||+++ +|++||||
T Consensus 1 I~~~~~W~~a~~~g~y~~~~ld~~dGFIH~St~~Qv~~ta~~ff~~-~~~l~lL~id~~~l~~~l~wE~~~~~g~~FPHl 79 (93)
T PF06108_consen 1 ILTAEEWEAAQASGEYPGSSLDTSDGFIHLSTAEQVPGTANRFFAG-QEDLVLLKIDPDKLGAELRWEPSEGGGELFPHL 79 (93)
T ss_dssp EEEHHHHHHHHHHSEE---HHHHHHTSEE-EEHHHHHHHHHHHSTT---SEEEEEEESGGGTTTEEEEEGG-GGSEEEEE
T ss_pred CCCHHHHHHhHHcCCCCCCccccCCCEEEcCCHHHHHHHHHHHcCC-CCCEEEEEEeHHHcCCcceeccCCCCCCcCCcC
Confidence 7899999999999999999999679999999999999999999999 999999999999999999999987 67999999
Q ss_pred eCCCCCCCCCCccceEEEEE
Q 033046 95 YGPSRSFTPLPLDVVTKADK 114 (128)
Q Consensus 95 YG~~~~~~~Lp~~aV~~v~~ 114 (128)
||+ ||++||++|.+
T Consensus 80 Yg~------l~~~aVv~v~~ 93 (93)
T PF06108_consen 80 YGP------LPLDAVVEVKE 93 (93)
T ss_dssp SS-------EEGGGEEE---
T ss_pred CCC------CChHHHhhccC
Confidence 998 99999999863
No 3
>PF01885 PTS_2-RNA: RNA 2'-phosphotransferase, Tpt1 / KptA family; InterPro: IPR002745 The final step of tRNA splicing in Saccharomyces cerevisiae (Baker's yeast) requires 2'-phosphotransferase (Tpt1) to transfer the 2'-phosphate from ligated tRNA to NAD, producing mature tRNA and ADP ribose-1' '-2' '-cyclic phosphate. Yeast and Mus musculus (Mouse) Tpt1 protein and bacterial KptA protein can catalyze the conversion of the generated intermediate to both product and the original substrate, these enzymes likely use the same reaction mechanism. Step 1 of this reaction is strikingly similar to the ADP-ribosylation of proteins catalyzed by a number of bacterial toxins. KptA, a functional Tpt1 protein homologue from Escherichia coli is strikingly similar to yeast Tpt1 in its kinetic parameters, although E. coli is not known to have a 2'-phosphorylated RNA substrate [,].; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 1WFX_A.
Probab=95.11 E-value=0.027 Score=43.83 Aligned_cols=74 Identities=22% Similarity=0.234 Sum_probs=42.6
Q ss_pred cccCCCceEEEecChhhHHHHHhCCCCCCCCCCCCCCeEeccchhcHH-HHHHhhcCCCCCcEEEEEEcCCC-CCCceEE
Q 033046 5 AEEERGEFVYRISTASEWEELQKNGSTFGGELDKSSGCFHLSKLDQVQ-PTLQNFFLNSKEDLYLLQIGAKK-LGDGLIY 82 (128)
Q Consensus 5 ~~~~~~~~iyhI~~~~~W~~a~~~G~~~~~~ld~~dGFIH~St~~Qv~-~va~~ff~~~~~~lvlL~ID~~~-L~~~l~w 82 (128)
.++..|..+||-+..+.|+..++.| +.+. .-.+||||+...-. .+..| ....++|.||..+ +.+.++|
T Consensus 100 ~~~~~p~~lyHGT~~~~~~~I~~~G-L~~m----~R~hVHls~~~~~a~~sG~R-----~~~~V~i~Id~~~a~~~Gi~f 169 (186)
T PF01885_consen 100 PEEEPPPILYHGTYRKAWPSILEEG-LKPM----GRNHVHLSTGPETAVISGMR-----RSCPVLIYIDAAKALEDGIKF 169 (186)
T ss_dssp -SS---SEEEE--BGGGHHHHHHH--B-------SSSSEEEES-HHHHHHHHTT-----SSSBEEEEEEHHHHHHTT---
T ss_pred cccCCCCEEEEccchhhHHHHHHhC-CCCC----CCCEEEEeeccCCceeecCC-----CCCeEEEEEcHHHHHHCCCeE
Confidence 4556789999999999999999999 5554 24589999773333 33333 2358999999965 4667888
Q ss_pred eecCCC
Q 033046 83 ELVDGL 88 (128)
Q Consensus 83 E~~~gg 88 (128)
-.+.+|
T Consensus 170 ~~s~n~ 175 (186)
T PF01885_consen 170 YRSSNG 175 (186)
T ss_dssp EE-SSS
T ss_pred EEeCCc
Confidence 776544
No 4
>COG1859 KptA RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]
Probab=94.62 E-value=0.11 Score=41.82 Aligned_cols=75 Identities=17% Similarity=0.128 Sum_probs=53.5
Q ss_pred cccCCCceEEEecChhhHHHHHhCCCCCCCCCCCCCCeEeccchh-cHHHHHHhhcCCCCCcEEEEEEcCCCCC-CceEE
Q 033046 5 AEEERGEFVYRISTASEWEELQKNGSTFGGELDKSSGCFHLSKLD-QVQPTLQNFFLNSKEDLYLLQIGAKKLG-DGLIY 82 (128)
Q Consensus 5 ~~~~~~~~iyhI~~~~~W~~a~~~G~~~~~~ld~~dGFIH~St~~-Qv~~va~~ff~~~~~~lvlL~ID~~~L~-~~l~w 82 (128)
.+...|..+||=+.++.|....+.|-++ . + --+||||+.. .-..|+.+ .. +..|+|.||..++- +.++.
T Consensus 115 ~~~~~p~~LyhGTs~~~l~~I~~~Gi~P-m--~--R~~VHLS~~~~~A~~vg~r-h~---~~pVvL~IDa~~l~~~G~~~ 185 (211)
T COG1859 115 PEAEPPAVLYHGTSPEFLPSILEEGLKP-M--K--RRHVHLSADYETAKQVGLR-HS---GSPVVLEIDAESLREDGYKF 185 (211)
T ss_pred CCCCCCcEEEecCChhhhHHHHHhcCcc-c--c--CceEEecCCHHHHHHHhhc-cC---CCcEEEEEehHHHHhCCceE
Confidence 3456778999999999999999999543 3 2 3479999644 44445553 22 36899999998874 46776
Q ss_pred eecCCC
Q 033046 83 ELVDGL 88 (128)
Q Consensus 83 E~~~gg 88 (128)
-.+.++
T Consensus 186 ~rs~n~ 191 (211)
T COG1859 186 YRSENG 191 (211)
T ss_pred EEcCCc
Confidence 666544
No 5
>PRK00819 RNA 2'-phosphotransferase; Reviewed
Probab=94.10 E-value=0.049 Score=42.41 Aligned_cols=72 Identities=13% Similarity=0.151 Sum_probs=52.2
Q ss_pred cCCCceEEEecChhhHHHHHhCCCCCCCCCCCCCCeEeccchh-cHHHHHHhhcCCCCCcEEEEEEcCCCC-CCceEEee
Q 033046 7 EERGEFVYRISTASEWEELQKNGSTFGGELDKSSGCFHLSKLD-QVQPTLQNFFLNSKEDLYLLQIGAKKL-GDGLIYEL 84 (128)
Q Consensus 7 ~~~~~~iyhI~~~~~W~~a~~~G~~~~~~ld~~dGFIH~St~~-Qv~~va~~ff~~~~~~lvlL~ID~~~L-~~~l~wE~ 84 (128)
...|..+||=+....|+...+.| +.+. .--+||||+.. +-..+..|. +..++|.||..+. ++.+++-.
T Consensus 91 ~~~P~~lyHGT~~~~~~~I~~~G-L~pm----~R~hVHLs~~~~~a~~~G~R~-----~~~vil~Id~~~~~~~Gi~f~~ 160 (179)
T PRK00819 91 DTPPAVLYHGTSSEELDSILEEG-LKPM----KRHYVHLSTDIETAREVGARH-----GSPVILEVDAECMRKRGIKFYK 160 (179)
T ss_pred CCCCceeEeCCCHHHHHHHHHhC-CCcc----CCCeEEecCCcccCeEEcccC-----CCeEEEEEeHHHHHhCCCEEEE
Confidence 34678999999999999999988 4444 24589999743 222334443 3689999999765 66788877
Q ss_pred cCCC
Q 033046 85 VDGL 88 (128)
Q Consensus 85 ~~gg 88 (128)
+.+|
T Consensus 161 s~n~ 164 (179)
T PRK00819 161 AENG 164 (179)
T ss_pred eCCC
Confidence 7665
No 6
>PTZ00315 2'-phosphotransferase; Provisional
Probab=78.54 E-value=2.9 Score=38.21 Aligned_cols=70 Identities=13% Similarity=0.013 Sum_probs=49.2
Q ss_pred CceEEEecChhhHHHHHhCCCCCCCCCCCCCCeEeccchhcH---HHHHHhhcCCCCCcEEEEEEcCCCC-CCceEEeec
Q 033046 10 GEFVYRISTASEWEELQKNGSTFGGELDKSSGCFHLSKLDQV---QPTLQNFFLNSKEDLYLLQIGAKKL-GDGLIYELV 85 (128)
Q Consensus 10 ~~~iyhI~~~~~W~~a~~~G~~~~~~ld~~dGFIH~St~~Qv---~~va~~ff~~~~~~lvlL~ID~~~L-~~~l~wE~~ 85 (128)
+..+||=+....|+..++.|.+.+.. --+||||+...- ..+..|. +..|+|.||..+. .+.+++-.+
T Consensus 476 ~~~lyHGT~~~~~~sI~~~G~L~~M~----R~HVHLs~~~~~~~~v~sG~R~-----~~~Vli~IDa~k~~~dGi~fy~S 546 (582)
T PTZ00315 476 VPVAVHGTYWSAWKAIQRCGYLSTMT----RQHIHFAKGLINDEQVISGMRN-----NVQLFLYLDVAAVLADGVALYES 546 (582)
T ss_pred CCeEEeCCcHHHHHHHHHcCCccccC----CCeEEecCCCCCcCceEeeccC-----CceEEEEEEHHHHHhCCCeEEEe
Confidence 45899999999999999999554442 347999974321 1233333 3578999999755 567888777
Q ss_pred CCC
Q 033046 86 DGL 88 (128)
Q Consensus 86 ~gg 88 (128)
.+|
T Consensus 547 ~Ng 549 (582)
T PTZ00315 547 SNG 549 (582)
T ss_pred CCc
Confidence 655
No 7
>PF13983 YsaB: YsaB-like lipoprotein
Probab=55.78 E-value=5 Score=27.35 Aligned_cols=12 Identities=42% Similarity=0.736 Sum_probs=6.0
Q ss_pred CCCCCCCC-eEecc
Q 033046 34 GELDKSSG-CFHLS 46 (128)
Q Consensus 34 ~~ld~~dG-FIH~S 46 (128)
.++| .|| |.|||
T Consensus 63 CSFD-~dGqFLHLS 75 (77)
T PF13983_consen 63 CSFD-ADGQFLHLS 75 (77)
T ss_pred EeEC-CCCcEEEee
Confidence 3455 344 55665
No 8
>KOG2871 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.02 E-value=10 Score=33.39 Aligned_cols=50 Identities=20% Similarity=0.216 Sum_probs=35.8
Q ss_pred CCeEeccchhcHHHHHHhhcCCCCCcEEEEE--EcCCCCCCceEEeecCCCCCCc
Q 033046 40 SGCFHLSKLDQVQPTLQNFFLNSKEDLYLLQ--IGAKKLGDGLIYELVDGLNSFP 92 (128)
Q Consensus 40 dGFIH~St~~Qv~~va~~ff~~~~~~lvlL~--ID~~~L~~~l~wE~~~gg~~FP 92 (128)
.|||-||--+||....|+-++. +..+.|-+ ||++.++ +.-+.+-.|+.||
T Consensus 323 ~nfis~s~~~~vm~~~N~~vse-~a~v~l~~~~l~pE~~~--iil~~d~lg~~~p 374 (449)
T KOG2871|consen 323 NNFISCSGLQIVMTALNRLVSE-PAYVMLMRQPLDPESLG--IILLEDFLGEFFP 374 (449)
T ss_pred CCeeecHHHHHHHHHhcccccC-HHHHHHhcCccChhhcc--eEEeccccccccC
Confidence 5799999999999999999997 66555443 7888775 3333333345555
No 9
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=40.11 E-value=18 Score=23.42 Aligned_cols=36 Identities=11% Similarity=0.216 Sum_probs=23.8
Q ss_pred CCCeEeccchh----cHHHHHHhhcCCCCC-cEEEEEEcCCC
Q 033046 39 SSGCFHLSKLD----QVQPTLQNFFLNSKE-DLYLLQIGAKK 75 (128)
Q Consensus 39 ~dGFIH~St~~----Qv~~va~~ff~~~~~-~lvlL~ID~~~ 75 (128)
=+||||.|... .+....++|-.| +. +..++.||.++
T Consensus 24 i~G~i~~~~ls~~~~~~~~~~~~~~vG-~~v~~kV~~id~~~ 64 (73)
T cd05703 24 VKGRIPLLDLSDDVSVLEHPEKKFPIG-QALKAKVVGVDKEH 64 (73)
T ss_pred cEEEEEHHHcCCccccccCHHHhCCCC-CEEEEEEEEEeCCC
Confidence 48999998543 245555656666 33 57778888864
No 10
>COG3232 HpaF 5-carboxymethyl-2-hydroxymuconate isomerase [Amino acid transport and metabolism]
Probab=32.44 E-value=44 Score=25.02 Aligned_cols=42 Identities=19% Similarity=0.241 Sum_probs=23.6
Q ss_pred CCCeEecc-------chhcHH-------HHHHhhcCCCCC-cEEEEEEcCCCCCCce
Q 033046 39 SSGCFHLS-------KLDQVQ-------PTLQNFFLNSKE-DLYLLQIGAKKLGDGL 80 (128)
Q Consensus 39 ~dGFIH~S-------t~~Qv~-------~va~~ff~~~~~-~lvlL~ID~~~L~~~l 80 (128)
+++|||+| +.+|-. .++.-+|+...+ ..+-|.+....++..+
T Consensus 58 ~~aFvH~tl~IgaGRs~e~rq~vge~Lf~~l~~~~A~l~a~r~lals~Ei~E~d~~~ 114 (127)
T COG3232 58 DDAFVHMTLKIGAGRSEEQRQEVGEALFAVLTAHFAPLFAQRYLALSFEIRELDPTL 114 (127)
T ss_pred CcceEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHhhhhhccceeEEEEHHHhCchh
Confidence 69999998 344444 455556655333 3555554444444433
No 11
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=32.26 E-value=53 Score=27.46 Aligned_cols=41 Identities=17% Similarity=0.235 Sum_probs=23.6
Q ss_pred CCCCCCCCeEeccch--hcHHHHHHhhcCCCCCc-EEEEEEcCCC
Q 033046 34 GELDKSSGCFHLSKL--DQVQPTLQNFFLNSKED-LYLLQIGAKK 75 (128)
Q Consensus 34 ~~ld~~dGFIH~St~--~Qv~~va~~ff~~~~~~-lvlL~ID~~~ 75 (128)
..++-.+||||.|.- --|..+-+..-.| +.. ..+|++|+.+
T Consensus 32 ~EY~g~Eg~ihiSEvas~wVknIrd~vkeg-qkvV~kVlrVd~~r 75 (269)
T COG1093 32 DEYPGKEGFIHISEVASGWVKNIRDYVKEG-QKVVAKVLRVDPKR 75 (269)
T ss_pred eccCCeeeeEEHHHHHHHHHHHHHHHhhcC-CeEEEEEEEEcCCC
Confidence 344446899999953 3444444433344 332 4567777764
No 12
>KOG1618 consensus Predicted phosphatase [General function prediction only]
Probab=32.12 E-value=11 Score=32.68 Aligned_cols=33 Identities=24% Similarity=0.427 Sum_probs=21.0
Q ss_pred CCCCc--eeeCCCCCCCCCCccceEEEEEeec-CCCeeeecc
Q 033046 88 LNSFP--HFYGPSRSFTPLPLDVVTKADKLSL-SDGRFSCSL 126 (128)
Q Consensus 88 g~~FP--HiYG~~~~~~~Lp~~aV~~v~~l~~-~dG~f~~~~ 126 (128)
+...| |||-. ..++..-.++ +++| +-|+|.+||
T Consensus 217 ~~~~Phipiy~s-----N~DLlW~~e~-~lpR~G~GaF~l~l 252 (389)
T KOG1618|consen 217 TGPYPHIPIYAS-----NMDLLWMAEY-KLPRFGHGAFRLCL 252 (389)
T ss_pred CCCCCCCceEEe-----cccccccccC-CCccccchHHHHHH
Confidence 46789 88853 2444333332 3665 799999986
No 13
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=31.83 E-value=20 Score=22.89 Aligned_cols=35 Identities=20% Similarity=0.263 Sum_probs=19.7
Q ss_pred CCCeEeccch--hcHHHHHHhhcCCCCC-cEEEEEEcCC
Q 033046 39 SSGCFHLSKL--DQVQPTLQNFFLNSKE-DLYLLQIGAK 74 (128)
Q Consensus 39 ~dGFIH~St~--~Qv~~va~~ff~~~~~-~lvlL~ID~~ 74 (128)
-+||||.|.. +.+...-++|-.| +. ...++.+|+.
T Consensus 26 v~G~i~~s~l~~~~~~~~~~~~~vG-~~v~~kV~~id~~ 63 (71)
T cd05696 26 LLGFVHISHLSDDKVPSDTGPFKAG-TTHKARIIGYSPM 63 (71)
T ss_pred CEEEEEHHHCCcchhcCcccccCCC-CEEEEEEEEEeCC
Confidence 5799999843 3344444445555 22 3555566653
No 14
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=30.34 E-value=25 Score=29.90 Aligned_cols=38 Identities=16% Similarity=0.283 Sum_probs=22.2
Q ss_pred CCCCeEeccchh--cHHHHHHhhcCCCCCcEEEEEEcCCC
Q 033046 38 KSSGCFHLSKLD--QVQPTLQNFFLNSKEDLYLLQIGAKK 75 (128)
Q Consensus 38 ~~dGFIH~St~~--Qv~~va~~ff~~~~~~lvlL~ID~~~ 75 (128)
.-+||||.|.-. .+..+-+.+=-|-.-.+.+|+||..+
T Consensus 42 gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ek 81 (319)
T PTZ00248 42 DIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEK 81 (319)
T ss_pred CcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCC
Confidence 369999999533 33333333333412357788888764
No 15
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.05 E-value=39 Score=20.95 Aligned_cols=35 Identities=11% Similarity=0.132 Sum_probs=19.6
Q ss_pred CCCeEeccch--hcHHHHHHhhcCCCCC-cEEEEEEcCC
Q 033046 39 SSGCFHLSKL--DQVQPTLQNFFLNSKE-DLYLLQIGAK 74 (128)
Q Consensus 39 ~dGFIH~St~--~Qv~~va~~ff~~~~~-~lvlL~ID~~ 74 (128)
-+||||.|.. +.+...-+.|--+ +. .+.++.+|.+
T Consensus 24 ~~G~v~~s~l~~~~~~~~~~~~~~G-d~v~~~v~~~d~~ 61 (68)
T cd05707 24 VDARVRVSELSDSYLKDWKKRFKVG-QLVKGKIVSIDPD 61 (68)
T ss_pred CEEEEEHHHCCchhhcCHhhccCCC-CEEEEEEEEEeCC
Confidence 5899999954 3344444444444 21 3444556653
No 16
>KOG0190 consensus Protein disulfide isomerase (prolyl 4-hydroxylase beta subunit) [Posttranslational modification, protein turnover, chaperones]
Probab=26.88 E-value=75 Score=28.65 Aligned_cols=57 Identities=16% Similarity=0.273 Sum_probs=36.8
Q ss_pred eEeccc-hhcHHHHHHhhcCCCCCcEEEEEEcCCCCCC---------ceEEeecCCCCCCceeeCCCCCC
Q 033046 42 CFHLSK-LDQVQPTLQNFFLNSKEDLYLLQIGAKKLGD---------GLIYELVDGLNSFPHFYGPSRSF 101 (128)
Q Consensus 42 FIH~St-~~Qv~~va~~ff~~~~~~lvlL~ID~~~L~~---------~l~wE~~~gg~~FPHiYG~~~~~ 101 (128)
+.||=. +.++...|+ .|++ .+++++.+||...=+- .|.|=+ .|+...|-+|++.|+-
T Consensus 396 CgHCk~laP~~eeLAe-~~~~-~~~vviAKmDaTaNd~~~~~~~~fPTI~~~p-ag~k~~pv~y~g~R~l 462 (493)
T KOG0190|consen 396 CGHCKALAPIYEELAE-KYKD-DENVVIAKMDATANDVPSLKVDGFPTILFFP-AGHKSNPVIYNGDRTL 462 (493)
T ss_pred cchhhhhhhHHHHHHH-HhcC-CCCcEEEEeccccccCccccccccceEEEec-CCCCCCCcccCCCcch
Confidence 679854 446666666 5677 8899999999975442 123322 2456778888665554
No 17
>PF09456 RcsC: RcsC Alpha-Beta-Loop (ABL); InterPro: IPR019017 This domain is found in the C terminus of the signal transduction response regulator (phospho-relay) kinase RcsC, between the ATP-binding region (IPR003594 from INTERPRO) and the receiver region (IPR001789 from INTERPRO). This domain forms a discrete alpha/beta/loop structure []. The Rcs signalling pathway controls a variety of physiological functions like capsule synthesis, cell division or motility in prokaryotes. The Rcs regulation cascade, involving a multi-step phosphorelay between the two membrane-bound hybrid sensor kinases RcsC and RcsD and the global regulator RcsB, is, up to now, one of the most complicated regulatory systems in bacteria []. ; GO: 0004673 protein histidine kinase activity, 0004871 signal transducer activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent, 0018106 peptidyl-histidine phosphorylation, 0005886 plasma membrane, 0016021 integral to membrane; PDB: 2AYY_A 2AYX_A.
Probab=24.91 E-value=83 Score=22.09 Aligned_cols=32 Identities=13% Similarity=0.352 Sum_probs=21.9
Q ss_pred CCCCCCCCCCCCCC-eEecc-chhcHHHHHHhhc
Q 033046 28 NGSTFGGELDKSSG-CFHLS-KLDQVQPTLQNFF 59 (128)
Q Consensus 28 ~G~~~~~~ld~~dG-FIH~S-t~~Qv~~va~~ff 59 (128)
++.+-|.+..++.| ++|-. ++..+...++|.|
T Consensus 59 s~~hiG~p~E~~pg~Wl~sTat~~eL~~LL~rIy 92 (92)
T PF09456_consen 59 SRRHIGPPQERRPGYWLHSTATPHELPALLDRIY 92 (92)
T ss_dssp ESS-SSS--TTSTTEEEEESS-TTHHHHHHHHHC
T ss_pred chHhCCCccccCCCcEEeccCCHHHHHHHHHHhC
Confidence 34678889999999 56653 6889999999876
No 18
>PF02155 GCR: Glucocorticoid receptor; InterPro: IPR001409 Steroid or nuclear hormone receptors (NRs) constitute an important super- family of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [, ]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity. NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed "orphan" receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members. The glucocorticoid receptor consists of 3 functional and structural domains: an N-terminal (modulatory) domain; a DNA binding domain that mediates specific binding to target DNA sequences (ligand-responsive elements); and a hormone binding domain. The N-terminal domain is unique to the glucocorticoid receptors; it spans the first 440 residues, and is primarily responsible for transcriptional activation. The smaller (around 65 residues), highly-conserved central portion of the protein is the DNA binding domain, which plays a role in DNA binding specificity, homo- dimerisation and in interactions with other proteins. The hormone binding domain comprises approximately 250 residues at the C terminus of the receptor. This domain mediates receptor activity via interaction with heat shock proteins and cyclophilins, or with hormone.; GO: 0003677 DNA binding, 0004883 glucocorticoid receptor activity, 0005496 steroid binding, 0006355 regulation of transcription, DNA-dependent, 0042921 glucocorticoid receptor signaling pathway, 0043402 glucocorticoid mediated signaling pathway, 0005634 nucleus
Probab=23.34 E-value=35 Score=29.73 Aligned_cols=14 Identities=7% Similarity=0.173 Sum_probs=11.3
Q ss_pred CCCeEeccchhcHH
Q 033046 39 SSGCFHLSKLDQVQ 52 (128)
Q Consensus 39 ~dGFIH~St~~Qv~ 52 (128)
+|.|||++|+.-|.
T Consensus 248 KDdFIqLcTPGVIK 261 (370)
T PF02155_consen 248 KDDFIQLCTPGVIK 261 (370)
T ss_pred cccceEeecCceee
Confidence 67999999987553
No 19
>PRK04980 hypothetical protein; Provisional
Probab=22.11 E-value=1.1e+02 Score=21.96 Aligned_cols=30 Identities=13% Similarity=0.444 Sum_probs=25.1
Q ss_pred CCCCeEeccchhcHHHHHHhhcCCCCCcEEEEEEc
Q 033046 38 KSSGCFHLSKLDQVQPTLQNFFLNSKEDLYLLQIG 72 (128)
Q Consensus 38 ~~dGFIH~St~~Qv~~va~~ff~~~~~~lvlL~ID 72 (128)
++||| +.+++..+.+..|.+ .++|.+++..
T Consensus 71 ~qEg~----sL~elk~~i~~iYp~-~~~lyvI~f~ 100 (102)
T PRK04980 71 EQENM----TLPELKQVIAEIYPN-LDQLYVIEFK 100 (102)
T ss_pred HHhCC----CHHHHHHHHHHHCCC-CceEEEEEEE
Confidence 36788 588999999999999 8889988753
No 20
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.40 E-value=53 Score=20.23 Aligned_cols=36 Identities=14% Similarity=0.209 Sum_probs=19.8
Q ss_pred CCCeEeccchh--cHHHHHHhhcCCCCCcEEEEEEcCC
Q 033046 39 SSGCFHLSKLD--QVQPTLQNFFLNSKEDLYLLQIGAK 74 (128)
Q Consensus 39 ~dGFIH~St~~--Qv~~va~~ff~~~~~~lvlL~ID~~ 74 (128)
-+||||.|... .+...-..|..+-.=.+.++.+|..
T Consensus 24 ~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~ 61 (70)
T cd05698 24 VKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPE 61 (70)
T ss_pred CEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCC
Confidence 58999998542 3333333444441124566667664
No 21
>PF05582 Peptidase_U57: YabG peptidase U57; InterPro: IPR008764 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of B. subtilis [].
Probab=20.03 E-value=1.4e+02 Score=25.17 Aligned_cols=59 Identities=14% Similarity=0.128 Sum_probs=45.4
Q ss_pred CCCceEEEecChhhHHHHHhCCCCCCCCCCCCCCeEeccchhcHHHHHHhhcCCCCCcEEEEE
Q 033046 8 ERGEFVYRISTASEWEELQKNGSTFGGELDKSSGCFHLSKLDQVQPTLQNFFLNSKEDLYLLQ 70 (128)
Q Consensus 8 ~~~~~iyhI~~~~~W~~a~~~G~~~~~~ld~~dGFIH~St~~Qv~~va~~ff~~~~~~lvlL~ 70 (128)
.+|..|.||---+++-.-+- ..|.--.++ ..| +|++..+|=..+.+..-.- ++|++||.
T Consensus 103 ~~PGkVLHlDGD~~YL~~Cl-~~Ykql~i~-a~G-~~~~E~eqp~~i~~Ll~~~-~PDIlViT 161 (287)
T PF05582_consen 103 ERPGKVLHLDGDEEYLNKCL-KVYKQLGIP-AVG-IHVPEKEQPEKIYRLLEEY-RPDILVIT 161 (287)
T ss_pred CCCCeEEEecCCHHHHHHHH-HHHHHcCCc-eEE-EEechHHhhHHHHHHHHHc-CCCEEEEe
Confidence 57889999988777765443 267777777 688 8999888877777766666 77899987
Done!