Query psy8680
Match_columns 180
No_of_seqs 116 out of 169
Neff 2.4
Searched_HMMs 46136
Date Sat Aug 17 01:00:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8680.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8680hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3492|consensus 100.0 3.2E-78 6.9E-83 495.2 11.0 141 1-179 40-180 (180)
2 PF03657 UPF0113: Uncharacteri 100.0 2.7E-54 5.9E-59 345.5 3.7 124 1-174 38-162 (162)
3 COG1374 NIP7 Protein involved 100.0 7.7E-40 1.7E-44 268.7 6.7 131 2-176 45-176 (176)
4 smart00359 PUA Putative RNA-bi 98.7 2.3E-08 5E-13 67.1 5.6 72 95-166 2-74 (77)
5 KOG3492|consensus 98.1 1.4E-06 3E-11 72.9 1.5 28 66-93 105-132 (180)
6 TIGR00451 unchar_dom_2 unchara 98.0 1.4E-05 2.9E-10 58.9 5.6 61 101-162 38-99 (107)
7 PRK14560 putative RNA-binding 97.8 4.3E-05 9.4E-10 60.1 6.2 65 98-163 81-146 (160)
8 PF01472 PUA: PUA domain; Int 97.7 7.7E-05 1.7E-09 52.0 5.1 63 95-157 2-64 (74)
9 TIGR03684 arCOG00985 arCOG0415 97.7 0.00011 2.5E-09 57.1 6.0 68 96-164 72-140 (150)
10 PRK13794 hypothetical protein; 97.6 0.00039 8.5E-09 63.7 8.7 67 101-167 132-199 (479)
11 PF03657 UPF0113: Uncharacteri 97.3 6.7E-05 1.5E-09 60.9 0.9 87 23-138 62-156 (162)
12 PRK13534 7-cyano-7-deazaguanin 97.2 0.0013 2.9E-08 62.8 8.2 102 23-163 527-632 (639)
13 PRK13795 hypothetical protein; 96.9 0.0044 9.5E-08 58.6 8.8 61 101-161 134-194 (636)
14 COG5270 PUA domain (predicted 96.4 0.0073 1.6E-07 51.9 5.7 97 22-156 90-191 (202)
15 PF13636 Nol1_Nop2_Fmu_2: pre- 96.0 0.014 3.1E-07 43.2 4.8 80 19-146 10-90 (102)
16 COG1370 Prefoldin, molecular c 95.2 0.064 1.4E-06 44.6 6.3 86 36-159 58-146 (155)
17 TIGR00432 arcsn_tRNA_tgt tRNA- 95.0 0.069 1.5E-06 50.6 6.7 64 95-158 468-531 (540)
18 PRK04270 H/ACA RNA-protein com 94.7 0.048 1.1E-06 47.5 4.7 67 96-163 228-294 (300)
19 PRK05429 gamma-glutamyl kinase 93.9 0.078 1.7E-06 47.1 4.2 61 96-156 283-344 (372)
20 TIGR01027 proB glutamate 5-kin 92.5 0.17 3.6E-06 45.0 4.2 61 96-156 275-336 (363)
21 COG2016 Predicted RNA-binding 92.1 0.53 1.1E-05 39.2 6.3 63 95-157 78-141 (161)
22 PRK11933 yebU rRNA (cytosine-C 92.0 0.27 5.9E-06 45.6 5.1 98 2-149 357-455 (470)
23 TIGR00425 CBF5 rRNA pseudourid 91.4 0.33 7.1E-06 43.2 4.8 74 98-172 242-318 (322)
24 PRK13402 gamma-glutamyl kinase 80.7 2.3 5E-05 38.4 4.1 58 98-155 281-339 (368)
25 smart00359 PUA Putative RNA-bi 77.8 2.3 5E-05 28.2 2.5 30 56-85 1-30 (77)
26 COG3270 Uncharacterized conser 71.8 7.4 0.00016 31.7 4.4 36 18-55 31-66 (127)
27 PRK08557 hypothetical protein; 71.3 5.1 0.00011 37.0 3.8 105 22-172 43-152 (417)
28 PRK15128 23S rRNA m(5)C1962 me 58.8 13 0.00027 33.8 3.8 33 117-149 27-59 (396)
29 COG1549 Queuine tRNA-ribosyltr 50.3 30 0.00065 33.8 5.0 52 106-158 458-509 (519)
30 COG0263 ProB Glutamate 5-kinas 48.0 28 0.0006 32.7 4.2 55 101-156 287-342 (369)
31 COG2092 EFB1 Translation elong 43.6 10 0.00022 29.1 0.6 26 119-146 25-50 (88)
32 cd00182 TBOX T-box DNA binding 36.7 81 0.0018 26.4 5.0 88 34-135 24-123 (188)
33 PF09157 TruB-C_2: Pseudouridi 36.5 33 0.00072 22.5 2.2 40 101-146 8-47 (58)
34 PF13277 YmdB: YmdB-like prote 26.9 6.3 0.00014 34.8 -3.2 69 109-179 11-83 (253)
35 PF09707 Cas_Cas2CT1978: CRISP 25.1 47 0.001 24.9 1.6 33 118-151 43-75 (86)
36 PRK11558 putative ssRNA endonu 24.3 80 0.0017 24.4 2.7 46 118-164 45-92 (97)
37 PF08366 LLGL: LLGL2; InterPr 23.3 3.6E+02 0.0078 21.0 6.7 43 126-168 52-94 (105)
38 TIGR00282 metallophosphoestera 23.0 26 0.00056 30.6 -0.2 68 109-178 14-85 (266)
39 TIGR00489 aEF-1_beta translati 20.2 36 0.00078 25.6 0.1 26 119-146 25-50 (88)
No 1
>KOG3492|consensus
Probab=100.00 E-value=3.2e-78 Score=495.23 Aligned_cols=141 Identities=63% Similarity=1.114 Sum_probs=139.9
Q ss_pred CCCeEEEEcHHHHhhhcccCCCCeeeeeeeeeeeeecceEEEEeeehhhcccccceeEEeccccchhhhccccccccccc
Q psy8680 1 MRDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQFKVWVKPQADQQFLYGHNILKSGLA 80 (180)
Q Consensus 1 ~~~RVyYvse~il~~a~~~~~d~LlslGtc~GKFtKsgKFrl~ItaL~~LA~ya~~KVWvKp~~~~~~~~~~~~~~~~~a 80 (180)
|+||||||||.++++|++|+|+||+|+||||||||||||||||||||+||||||+||||+||
T Consensus 40 hkdRVyyvsEr~~k~a~~isr~~L~s~Gtc~GKFTKt~kfrlhitaL~~La~~Ak~KvWiKp------------------ 101 (180)
T KOG3492|consen 40 HKDRVYYVSERIMKLAACISRKNLVSLGTCFGKFTKTGKFRLHITALDYLAPYAKYKVWIKP------------------ 101 (180)
T ss_pred eCceEEeehHHHHHHHhhhcccceeEEeEEEeeeeccceEEEeeeehhhhhhhhheeEEecc------------------
Confidence 79999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccCCCCccceeeEeeecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCeE
Q psy8680 81 RITENTPKYQGVIFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAI 160 (180)
Q Consensus 81 ~i~e~~~~~~~~~~~~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~i 160 (180)
++||+|||||||||||++||||++|++||||||||||+||||||+||||++||++||++|
T Consensus 102 --------------------~~Em~flYGNhvlKs~vgRitd~~p~~~GVvVysm~DvPLGFGv~Akst~d~r~~dp~ai 161 (180)
T KOG3492|consen 102 --------------------NAEMQFLYGNHVLKSGVGRITDGIPQHQGVVVYSMNDVPLGFGVTAKSTQDCRKADPTAI 161 (180)
T ss_pred --------------------CcccceeecccchhcccceecCCCCCcceEEEEeccCCccccceeecCcccccccCCcEE
Confidence 999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecccceeeeecccccC
Q psy8680 161 VGFNQSDIGEYIRYMTNML 179 (180)
Q Consensus 161 VvfnqaDiGEYlR~e~~~~ 179 (180)
|+|||+|+|||||+|+++|
T Consensus 162 v~~hQaDiGEYlR~E~~l~ 180 (180)
T KOG3492|consen 162 VVLHQADIGEYLRNEDTLF 180 (180)
T ss_pred EEEEecchHHHhhcccccC
Confidence 9999999999999999986
No 2
>PF03657 UPF0113: Uncharacterised protein family (UPF0113); InterPro: IPR005155 This entry represents PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain containing proteins such as the ribosomal biogenesis factor NIP7 [, ]. PUA domains are predicted to bind RNA molecules with complex folded structures []. NIP7 is required for efficient 60S ribosome subunit biogenesis and has been shown to interact with another essential nucleolar protein, Nop8p, and the exosome subunit Rrp43p. These three proteins are required for 60S subunit synthesis and may be part of a dynamic complex involved in this process.; PDB: 1T5Y_A 1SQW_A 2P38_A.
Probab=100.00 E-value=2.7e-54 Score=345.46 Aligned_cols=124 Identities=65% Similarity=1.107 Sum_probs=111.4
Q ss_pred CCCeEEEEcHHHHhhhcccCCCCeeeeeeeeeeeeecc-eEEEEeeehhhcccccceeEEeccccchhhhcccccccccc
Q psy8680 1 MRDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSG-KFRLHITALSYLAPYAQFKVWVKPQADQQFLYGHNILKSGL 79 (180)
Q Consensus 1 ~~~RVyYvse~il~~a~~~~~d~LlslGtc~GKFtKsg-KFrl~ItaL~~LA~ya~~KVWvKp~~~~~~~~~~~~~~~~~ 79 (180)
|++||||||+++++.|++ +++++|+|||+|+|||++ ||||||||+++||+|+++||||||
T Consensus 38 ~~~~Vyyvs~~l~~~~~~--~~~~~s~G~~~G~f~k~~~kf~l~i~~l~~la~~~~~kvwvk~----------------- 98 (162)
T PF03657_consen 38 HKDRVYYVSEELMKLASN--RPNLYSLGTCLGKFTKKGKKFRLHITALDYLAPYAKNKVWVKP----------------- 98 (162)
T ss_dssp CTCEEEEEEHHHHCCCTT--CHHHHCCSEEEEEE-TTTSEEEEEGHHHHCCCCC-SSEEEE-H-----------------
T ss_pred ecceEEEECHHHHHHHhC--CCccceeceEEEEEecCCccceeeHHHHHHhhhccceeEEECC-----------------
Confidence 689999999999999998 899999999999999865 999999999999999999999999
Q ss_pred ceeccCCCCccceeeEeeecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCe
Q psy8680 80 ARITENTPKYQGVIFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLA 159 (180)
Q Consensus 80 a~i~e~~~~~~~~~~~~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~ 159 (180)
+|||+|||||||+||||+||||++|+| |||+||||+||||| |+..+|++
T Consensus 99 ---------------------~~e~~FLYGndV~ks~i~~i~e~~~~~--VvV~n~~d~~LGfG--------~~~~~~~~ 147 (162)
T PF03657_consen 99 ---------------------KAEMLFLYGNDVLKSSIGRITEDTPQN--VVVYNMNDVPLGFG--------CRKSDPDG 147 (162)
T ss_dssp ---------------------HHHHHHCTT--EEGGGEEEEETTS-TC--EEEEETTS-EEEEE--------ECSTCHCC
T ss_pred ---------------------CceEEeeecCCchHhhcEEecCCCCce--EEEEeCCCCeEEEE--------EeccCCCC
Confidence 999999999999999999999999999 99999999999999 77889999
Q ss_pred EEEEecccceeeeec
Q psy8680 160 IVGFNQSDIGEYIRY 174 (180)
Q Consensus 160 iVvfnqaDiGEYlR~ 174 (180)
++++||+|+|||||+
T Consensus 148 ~vv~~~~DiGeYLR~ 162 (162)
T PF03657_consen 148 KVVKNQADIGEYLRE 162 (162)
T ss_dssp CCCECCEEGGGT-S-
T ss_pred EEEEEcCcceeeecC
Confidence 999999999999995
No 3
>COG1374 NIP7 Protein involved in ribosomal biogenesis, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.7e-40 Score=268.74 Aligned_cols=131 Identities=44% Similarity=0.633 Sum_probs=127.2
Q ss_pred CCe-EEEEcHHHHhhhcccCCCCeeeeeeeeeeeeecceEEEEeeehhhcccccceeEEeccccchhhhccccccccccc
Q psy8680 2 RDR-VFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQFKVWVKPQADQQFLYGHNILKSGLA 80 (180)
Q Consensus 2 ~~R-VyYvse~il~~a~~~~~d~LlslGtc~GKFtKsgKFrl~ItaL~~LA~ya~~KVWvKp~~~~~~~~~~~~~~~~~a 80 (180)
++| ||+|++...++|+.+++.|++|+|||||+|+++|+||+|+++|.+||+++.+|+||+|
T Consensus 45 ~~r~v~~V~~~~~~l~~~i~r~np~~~G~~~g~~~~~~~fR~~~~~l~~la~~~~~k~~v~~------------------ 106 (176)
T COG1374 45 KDRDVYEVNEVVWKLAESIERKNPYSLGTFFGKRVKGGLFRKHVESLEELARIAIIKNYVKE------------------ 106 (176)
T ss_pred ccccEEEEeeehhhhhhcccccCcceeceeecccccCCeeeeehhhhHHHHHHhheeeeecc------------------
Confidence 578 9999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccCCCCccceeeEeeecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCeE
Q psy8680 81 RITENTPKYQGVIFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAI 160 (180)
Q Consensus 81 ~i~e~~~~~~~~~~~~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~i 160 (180)
++||+||||+| +|+|+.+|++.+|.+++|+||||||+|||||+.+.|+.|-+++-|++
T Consensus 107 --------------------~~e~~FLYg~~-lkd~~~e~~~~~~~~~~v~V~~~nd~~lgiGvg~~s~~ed~~~i~~~- 164 (176)
T COG1374 107 --------------------RGEMLFLYGND-LKDHVKEIIDEIPENGGVFVFNMNDVPLGIGVGALSPSEDGRLIKNA- 164 (176)
T ss_pred --------------------CceeEEEeccc-cchhhhhhccccCCcceEEEEEcCCCceEEEecccCchhhccccccc-
Confidence 99999999999 99999999999999999999999999999999999999988888877
Q ss_pred EEEecccceeeeeccc
Q psy8680 161 VGFNQSDIGEYIRYMT 176 (180)
Q Consensus 161 VvfnqaDiGEYlR~e~ 176 (180)
|+|+|||||.|+
T Consensus 165 ----l~D~GeYLRr~~ 176 (176)
T COG1374 165 ----LKDVGEYLRRGG 176 (176)
T ss_pred ----cchhhhhhhcCC
Confidence 999999999874
No 4
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=98.75 E-value=2.3e-08 Score=67.06 Aligned_cols=72 Identities=24% Similarity=0.327 Sum_probs=63.5
Q ss_pred EeeecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcC-CCeEEEEecc
Q psy8680 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD-PLAIVGFNQS 166 (180)
Q Consensus 95 ~~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~d-p~~iVvfnqa 166 (180)
++++++.+++.+++|++|+.+++.+++.+....+-|.|++.++.+||.|.+..++.++.+.. +.++++.++.
T Consensus 2 ~i~v~~~~~~~i~~g~~v~~~~v~~~~~~~~~g~~V~v~~~~g~~vg~G~~~~~s~~~~~~~~~~g~~v~~~~ 74 (77)
T smart00359 2 KVVVDDGAVKAILNGASLLAPGVVRVDGGIKEGDVVVIVDEKGEPLGIGLANMSSEEMARIKGEKGLAVKVRR 74 (77)
T ss_pred EEEEchhHHHHHHcCCCcccceeEEEeCCcCCCCEEEEEcCCCCEEEEEEEeCCHHHHHHHhccCceEEEEEE
Confidence 45666699999999999999999999999999999999999999999999999999999887 6666665543
No 5
>KOG3492|consensus
Probab=98.07 E-value=1.4e-06 Score=72.89 Aligned_cols=28 Identities=57% Similarity=1.038 Sum_probs=27.1
Q ss_pred hhhhccccccccccceeccCCCCcccee
Q psy8680 66 QQFLYGHNILKSGLARITENTPKYQGVI 93 (180)
Q Consensus 66 ~~~~~~~~~~~~~~a~i~e~~~~~~~~~ 93 (180)
||||||.|+||||+.||+|++|.+|||+
T Consensus 105 m~flYGNhvlKs~vgRitd~~p~~~GVv 132 (180)
T KOG3492|consen 105 MQFLYGNHVLKSGVGRITDGIPQHQGVV 132 (180)
T ss_pred cceeecccchhcccceecCCCCCcceEE
Confidence 7899999999999999999999999986
No 6
>TIGR00451 unchar_dom_2 uncharacterized domain 2. This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain.
Probab=98.01 E-value=1.4e-05 Score=58.87 Aligned_cols=61 Identities=26% Similarity=0.365 Sum_probs=53.1
Q ss_pred cccceeecccccccccceeecccCCCcceEEEEecC-CCceeeEeeecchhHhhhcCCCeEEE
Q psy8680 101 QAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMN-DVPLGFGVAAKSTAECKLADPLAIVG 162 (180)
Q Consensus 101 ~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmn-dvpLGFGvaakst~e~k~~dp~~iVv 162 (180)
.+...-+.|.+++..|+...++++.+.+-|.|++.+ +.|+|.|++..|+.|++..+ .++++
T Consensus 38 ~a~~~l~~Ga~L~~pGV~~~~~~~~~gd~V~I~~~~~~~~iavG~a~~~s~e~~~~~-~G~~v 99 (107)
T TIGR00451 38 GAVKFLKNGADVMRPGIVDADEDIKEGDDVVVVDENKDRPLAVGIALMSGEEMKEMD-KGKAV 99 (107)
T ss_pred hHHHHHHCCccccCCeeEeCCCCcCCCCEEEEEECCCCeEEEEEEEecCHHHHHhcC-CCeEE
Confidence 666655689999999999999999999999999987 89999999999999998874 35544
No 7
>PRK14560 putative RNA-binding protein; Provisional
Probab=97.84 E-value=4.3e-05 Score=60.15 Aligned_cols=65 Identities=18% Similarity=0.166 Sum_probs=55.0
Q ss_pred ecCcccceeecccccccccceeecccCCCcceEEEEecC-CCceeeEeeecchhHhhhcCCCeEEEE
Q psy8680 98 VKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMN-DVPLGFGVAAKSTAECKLADPLAIVGF 163 (180)
Q Consensus 98 ~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmn-dvpLGFGvaakst~e~k~~dp~~iVvf 163 (180)
|.+.+...-+.|.+++..|+..+++++.+.+-|+|++.+ +.|+|.|.+.-|+.|.+..+ .++++.
T Consensus 81 Vd~~a~~~i~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~~~~~~vavG~~~~s~~ei~~~~-kG~~v~ 146 (160)
T PRK14560 81 VDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEETHGKPLAVGRALMDGDEMVEEK-KGKAVK 146 (160)
T ss_pred EeccHHHHHHCCCceecCeeeeCCCCCCCCCEEEEEECCCCeEEEEEEEeeCHHHHhhcC-CceEEE
Confidence 333677767799999999999999999999999999987 99999999999999988543 455554
No 8
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=97.71 E-value=7.7e-05 Score=51.96 Aligned_cols=63 Identities=21% Similarity=0.287 Sum_probs=55.4
Q ss_pred EeeecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCC
Q psy8680 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADP 157 (180)
Q Consensus 95 ~~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp 157 (180)
+|+|+..+....+.|.+++-.|+.++.+++.+.+-|.|++.++.++|.|.+..|..|...+.-
T Consensus 2 ~vvVd~~a~~~i~~Ga~L~~~GV~~~~~~f~~gd~V~i~~~~g~~ia~G~a~~ss~ei~~~~~ 64 (74)
T PF01472_consen 2 RVVVDDGAVEAILNGASLFAPGVVEVDGDFRKGDEVAIVDEDGEVIAVGRANMSSEEIKKMKK 64 (74)
T ss_dssp EEEE-HHHHHHHHTTSEEEGGGEEEEETT--TTSEEEEEETTSSEEEEEEESSTHHHHHHHSS
T ss_pred EEEECccHHHHHHcCCCcchHHhEECCCCcCCCCEEEEEcCCCeEEEEEEEecCHHHHHHHcC
Confidence 356666888888999999999999999999999999999999999999999999999998873
No 9
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
Probab=97.67 E-value=0.00011 Score=57.11 Aligned_cols=68 Identities=21% Similarity=0.234 Sum_probs=56.8
Q ss_pred eeecCcccceeecccccccccceeecccCCCcceEEEEecC-CCceeeEeeecchhHhhhcCCCeEEEEe
Q psy8680 96 VWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMN-DVPLGFGVAAKSTAECKLADPLAIVGFN 164 (180)
Q Consensus 96 ~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmn-dvpLGFGvaakst~e~k~~dp~~iVvfn 164 (180)
|.|.+.+...-+-|.|++..|+..+++++.+.+-|+|++.+ +.|+|.|++.-|+++.+... .++++.+
T Consensus 72 v~Vd~~a~~~l~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~~~~~~vavG~a~~ss~ei~~~~-kG~av~~ 140 (150)
T TIGR03684 72 VVVDEGAVKFIINGADIMAPGIVSADPSIKEGDIVFVVDETHRKPLAVGIALMDAEEMEEEK-KGKAVKN 140 (150)
T ss_pred EEECccHHHHHhcCcccccCceecCCCCCCCCCEEEEEECCCCeEEEEEEEeeCHHHHhhcC-CCeEEEE
Confidence 34444777766799999999999999999999999999988 99999999999999998654 4555543
No 10
>PRK13794 hypothetical protein; Provisional
Probab=97.55 E-value=0.00039 Score=63.69 Aligned_cols=67 Identities=24% Similarity=0.309 Sum_probs=56.4
Q ss_pred cccceee-cccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCeEEEEeccc
Q psy8680 101 QAEQQFL-YGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSD 167 (180)
Q Consensus 101 ~aE~~FL-YG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~iVvfnqaD 167 (180)
.+...-+ .|.+|+..||..+++++...+-|+|++.+|.++|.|++..|++|.+..+...+|-.+.++
T Consensus 132 ga~~~v~~~G~~v~~~GV~~~~~~i~~gd~V~Iv~~~g~~iavG~a~~s~~ei~~~~~G~~Vkvr~~~ 199 (479)
T PRK13794 132 DVPKFIRNKGASVLRPGVAEASEDIEEGDDVIILDENGDVVGVGRARMSYEEIVNMEKGMVVKVRKSE 199 (479)
T ss_pred cHHHHHHhCCCeecCCceEEecCCcCCCCEEEEEcCCCcEEEEEEeecCHHHHHhccCceEEEEEecc
Confidence 4444444 899999999999999999999999999999999999999999999998775544444433
No 11
>PF03657 UPF0113: Uncharacterised protein family (UPF0113); InterPro: IPR005155 This entry represents PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain containing proteins such as the ribosomal biogenesis factor NIP7 [, ]. PUA domains are predicted to bind RNA molecules with complex folded structures []. NIP7 is required for efficient 60S ribosome subunit biogenesis and has been shown to interact with another essential nucleolar protein, Nop8p, and the exosome subunit Rrp43p. These three proteins are required for 60S subunit synthesis and may be part of a dynamic complex involved in this process.; PDB: 1T5Y_A 1SQW_A 2P38_A.
Probab=97.34 E-value=6.7e-05 Score=60.88 Aligned_cols=87 Identities=33% Similarity=0.429 Sum_probs=47.8
Q ss_pred Ceeeeeeeeeeee-e-----cceEEEEeeeh--hhcccccceeEEeccccchhhhccccccccccceeccCCCCccceee
Q psy8680 23 HLLALGTCFGKFT-K-----SGKFRLHITAL--SYLAPYAQFKVWVKPQADQQFLYGHNILKSGLARITENTPKYQGVIF 94 (180)
Q Consensus 23 ~LlslGtc~GKFt-K-----sgKFrl~ItaL--~~LA~ya~~KVWvKp~~~~~~~~~~~~~~~~~a~i~e~~~~~~~~~~ 94 (180)
..+++|+ |||++ | ++.+.|.=-|- =+|-|.|. |+||||.|++||+..+|+|++|++
T Consensus 62 ~G~~~G~-f~k~~~kf~l~i~~l~~la~~~~~kvwvk~~~e----------~~FLYGndV~ks~i~~i~e~~~~~----- 125 (162)
T PF03657_consen 62 LGTCLGK-FTKKGKKFRLHITALDYLAPYAKNKVWVKPKAE----------MLFLYGNDVLKSSIGRITEDTPQN----- 125 (162)
T ss_dssp CSEEEEE-E-TTTSEEEEEGHHHHCCCCC-SSEEEE-HHHH----------HHHCTT--EEGGGEEEEETTS-TC-----
T ss_pred eceEEEE-EecCCccceeeHHHHHHhhhccceeEEECCCce----------EEeeecCCchHhhcEEecCCCCce-----
Confidence 4567888 77543 1 33333222111 24566777 679999999999999999999988
Q ss_pred EeeecCcccceeecccccccccceeecccCCCcceEEEEecCCC
Q psy8680 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDV 138 (180)
Q Consensus 95 ~~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndv 138 (180)
|-|-+....+.=.| .. -+...+++|.|..|+
T Consensus 126 -VvV~n~~d~~LGfG---------~~---~~~~~~~vv~~~~Di 156 (162)
T PF03657_consen 126 -VVVYNMNDVPLGFG---------CR---KSDPDGKVVKNQADI 156 (162)
T ss_dssp -EEEEETTS-EEEEE---------EC---STCHCCCCCECCEEG
T ss_pred -EEEEeCCCCeEEEE---------Ee---ccCCCCEEEEEcCcc
Confidence 33333333333344 11 223457777776553
No 12
>PRK13534 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional
Probab=97.22 E-value=0.0013 Score=62.85 Aligned_cols=102 Identities=20% Similarity=0.269 Sum_probs=79.9
Q ss_pred Ceeeeeeeeeeee-ecceEEEEeeehhhcc---cccceeEEeccccchhhhccccccccccceeccCCCCccceeeEeee
Q psy8680 23 HLLALGTCFGKFT-KSGKFRLHITALSYLA---PYAQFKVWVKPQADQQFLYGHNILKSGLARITENTPKYQGVIFKVWV 98 (180)
Q Consensus 23 ~LlslGtc~GKFt-KsgKFrl~ItaL~~LA---~ya~~KVWvKp~~~~~~~~~~~~~~~~~a~i~e~~~~~~~~~~~~~~ 98 (180)
+++.=|..++-+. ..|.|.|++.+...|- ++.+++|.|..
T Consensus 527 ~I~vdg~~l~~l~~~dg~~~pt~~GA~~l~~~~~~~~~~V~Vd~------------------------------------ 570 (639)
T PRK13534 527 QVLDKGEILATMRANDGFLILSKEGAKRLHEKLPFPKYRVVVDK------------------------------------ 570 (639)
T ss_pred EEEECCEEEEEEEecCCEEEEcHHHHHHHHhccCCCCcEEEECC------------------------------------
Confidence 4454577787776 5778888888777763 23345566654
Q ss_pred cCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCeEEEE
Q psy8680 99 KPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGF 163 (180)
Q Consensus 99 ~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~iVvf 163 (180)
.++..-.=|.+|+.-|+...++++..++-|+|.+.+|.+||.|+|.-|..|.+..+- ++++.
T Consensus 571 --~a~~~v~~G~~v~apgVv~~d~~ir~gDeV~Vv~e~~~~lavG~A~~~~~em~~~~~-G~avk 632 (639)
T PRK13534 571 --ESEPFARKGKSVFAKFVIDCDEEIRPYDEVLVVNEDDELLAYGKALLNGRELMEFNY-GLAVK 632 (639)
T ss_pred --cchhhhhCCCcccCCcceecCCCCCCCCEEEEEecCCcEEEEEEEecCHHHHhhcCC-ceEEE
Confidence 666666689999999999999999999999999999999999999999999987654 44443
No 13
>PRK13795 hypothetical protein; Provisional
Probab=96.94 E-value=0.0044 Score=58.60 Aligned_cols=61 Identities=20% Similarity=0.177 Sum_probs=53.1
Q ss_pred cccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCeEE
Q psy8680 101 QAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIV 161 (180)
Q Consensus 101 ~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~iV 161 (180)
.+...-+-|.+|+..||..+++++.+.+-|+|.+.++.++|.|++..|++|.+..+....|
T Consensus 134 ga~~~v~~Ga~l~~~GI~~~~~~i~~gd~V~I~~e~g~~vavG~a~~s~~e~~~~~kG~~V 194 (636)
T PRK13795 134 GALEPIKNGKNVLAPGVVEADLDIKKGDEVVVVTEDGEVVGVGRAKMDGDDMIKRFRGRAV 194 (636)
T ss_pred cHHHHHHcCCcccCCceEEEeCCCCCCCEEEEEeCCCCEEEEEEeccCHHHHhhccCCeEE
Confidence 5555556899999999999999999999999999999999999999999999877664433
No 14
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=96.40 E-value=0.0073 Score=51.86 Aligned_cols=97 Identities=23% Similarity=0.303 Sum_probs=74.9
Q ss_pred CCeeeeeeeeeee--eecc---eEEEEeeehhhcccccceeEEeccccchhhhccccccccccceeccCCCCccceeeEe
Q psy8680 22 DHLLALGTCFGKF--TKSG---KFRLHITALSYLAPYAQFKVWVKPQADQQFLYGHNILKSGLARITENTPKYQGVIFKV 96 (180)
Q Consensus 22 d~LlslGtc~GKF--tKsg---KFrl~ItaL~~LA~ya~~KVWvKp~~~~~~~~~~~~~~~~~a~i~e~~~~~~~~~~~~ 96 (180)
|.++.-|-.||-. .-+. +|+|..++...|-.--+.-+|++-
T Consensus 90 dEIvvdG~i~g~i~fd~~k~rW~~~lk~eGAk~L~e~~~k~~~i~~---------------------------------- 135 (202)
T COG5270 90 DEIVVDGFIFGIIRFDLRKLRWRFGLKLEGAKLLLEKGKKGRKIDR---------------------------------- 135 (202)
T ss_pred ceEEecceEEEEEEecchhcccccccChHHHHHHHHhcCccEEEEc----------------------------------
Confidence 5677778888733 2111 666666666555444333445554
Q ss_pred eecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcC
Q psy8680 97 WVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD 156 (180)
Q Consensus 97 ~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~d 156 (180)
.++..-.-|.||+.-++...++++++++-|+|.+.|+-+.|+|.+.+|..+...-.
T Consensus 136 ----~~~E~~~Ng~nV~~~gV~e~~~~i~~~d~viVv~~ng~~vGVg~a~~~~~~~in~~ 191 (202)
T COG5270 136 ----GAVEPVKNGKNVLPPGVIEAEDSIERGDEVIVVSENGRVVGVGIAKKSYEELINPE 191 (202)
T ss_pred ----ccchhhhccCcccCCceeeccCCcccCCeEEEEecCCEEEEEEEEecCHHHhcCcc
Confidence 88888899999999999999999999999999999999999999999998876544
No 15
>PF13636 Nol1_Nop2_Fmu_2: pre-rRNA processing and ribosome biogenesis; PDB: 3M4X_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A.
Probab=96.00 E-value=0.014 Score=43.23 Aligned_cols=80 Identities=20% Similarity=0.331 Sum_probs=52.9
Q ss_pred cCCCCeeeeeeeeeeeeecceEEEEeeehhhccccccee-EEeccccchhhhccccccccccceeccCCCCccceeeEee
Q psy8680 19 FGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQFK-VWVKPQADQQFLYGHNILKSGLARITENTPKYQGVIFKVW 97 (180)
Q Consensus 19 ~~~d~LlslGtc~GKFtKsgKFrl~ItaL~~LA~ya~~K-VWvKp~~~~~~~~~~~~~~~~~a~i~e~~~~~~~~~~~~~ 97 (180)
+..-+++..|+-+|++.| +.|+.+-...-.+.+.+... |=+.
T Consensus 10 ~~~l~v~r~Gl~lg~~~k-~~f~Ps~~la~~~~~~~~~~~iel~------------------------------------ 52 (102)
T PF13636_consen 10 LPGLKVLRAGLYLGEIKK-NRFEPSHALAMALGPEATKNVIELD------------------------------------ 52 (102)
T ss_dssp -TTSEECECSEEEEEEET-TEEEEBHHHHHCB--GCCS-EEEET------------------------------------
T ss_pred cCCCeEEecCcEeeeEeC-CcEEECHHHHHhhCccccceEEECC------------------------------------
Confidence 444589999999999976 89999988877777766521 2222
Q ss_pred ecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeee
Q psy8680 98 VKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAA 146 (180)
Q Consensus 98 ~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaa 146 (180)
...=..||-|++|--+. ...|-++..-++.|||||...
T Consensus 53 --~e~a~~yl~Ge~i~~~~---------~~~G~vlv~~~g~~LG~gk~~ 90 (102)
T PF13636_consen 53 --DEQALRYLRGEDIELDP---------PDKGWVLVTYEGFPLGWGKYV 90 (102)
T ss_dssp --CHHHHHHHCT--EE-SS-----------EEEEEEEECCCEEEEEEEE
T ss_pred --HHHHHHHHcCCcccCCC---------CCCcEEEEEECCEeeEEEEee
Confidence 23445677787773222 377888888899999999985
No 16
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=95.19 E-value=0.064 Score=44.62 Aligned_cols=86 Identities=26% Similarity=0.314 Sum_probs=70.1
Q ss_pred ecceEEEEeeehhhcc---cccceeEEeccccchhhhccccccccccceeccCCCCccceeeEeeecCcccceeeccccc
Q psy8680 36 KSGKFRLHITALSYLA---PYAQFKVWVKPQADQQFLYGHNILKSGLARITENTPKYQGVIFKVWVKPQAEQQFLYGHNI 112 (180)
Q Consensus 36 KsgKFrl~ItaL~~LA---~ya~~KVWvKp~~~~~~~~~~~~~~~~~a~i~e~~~~~~~~~~~~~~~~~aE~~FLYG~~v 112 (180)
.+|-|.|++.+-..|- |+.+++|-|.. .+|---=-|.+|
T Consensus 58 ~DG~~tL~~~Ga~~L~~~l~~P~~RVvV~~--------------------------------------E~e~f~r~Gk~V 99 (155)
T COG1370 58 NDGLFTLTIEGARRLHRALPFPRMRVVVSD--------------------------------------EAEEFVRKGKSV 99 (155)
T ss_pred CCceEEechhhhHHHHhcCCCCceEEEecc--------------------------------------ccHHHHHhccch
Confidence 5677888888876664 35555555554 555555579999
Q ss_pred ccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCe
Q psy8680 113 LKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLA 159 (180)
Q Consensus 113 lKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~ 159 (180)
+--++....|++-.++=|+|.|++|..|+-|.+.-|..|.+..+--.
T Consensus 100 FaKfVi~~D~~iR~~dEvlVVne~d~LlAvGra~ls~~E~~~~~~G~ 146 (155)
T COG1370 100 FAKFVIDVDEEIRAGDEVLVVNEDDELLAVGRALLSGAEMREFERGM 146 (155)
T ss_pred hhhheeccCcccCCCCeEEEECCCCcEEEeeeEeecHHHHhhccccE
Confidence 99999999999999999999999999999999999999999877533
No 17
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one.
Probab=94.96 E-value=0.069 Score=50.64 Aligned_cols=64 Identities=19% Similarity=0.157 Sum_probs=57.3
Q ss_pred EeeecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCC
Q psy8680 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPL 158 (180)
Q Consensus 95 ~~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~ 158 (180)
.|.|...++.-|.=|++|+--|+....|++-.++=|+|.|.+|..||.|.|.-|..|....+--
T Consensus 468 rV~v~~~~~~f~~~g~~vfak~V~~ad~~IR~~dEV~vv~~~~~llavGra~lsg~em~~~~~G 531 (540)
T TIGR00432 468 RVAVNEESEPFARKGKSVFAKFIIDCDNNIRANDEVLIVNADDELLATGKALLCAEEMMDLNHG 531 (540)
T ss_pred EEEECCcchhhccCCCcccCCccccCCCCCCCCCeEEEEcCCCcEEEEEehhcCHHHHHhhcCc
Confidence 3445557888899999999999999999999999999999999999999999999998887653
No 18
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=94.74 E-value=0.048 Score=47.52 Aligned_cols=67 Identities=21% Similarity=0.220 Sum_probs=55.4
Q ss_pred eeecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCeEEEE
Q psy8680 96 VWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGF 163 (180)
Q Consensus 96 ~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~iVvf 163 (180)
+-+.+.+...+..|.++...++.++.++....+-|+|++.++.++|.|.+..|++|.+.. +.++++-
T Consensus 228 V~Lde~aa~~I~nG~~L~~~gi~~~~~~~~~gd~V~I~~~~G~~LAIG~~~~ss~el~~~-~kG~~vk 294 (300)
T PRK04270 228 IIIKDSAVDAIAHGAPLYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKA-EKGIVVD 294 (300)
T ss_pred eEECHHHHHHHHcCCccccCCceecccccCCCCEEEEEeCCCcEEEEEEEccCHHHHHhc-CCceEEE
Confidence 445556777788999999888888887776777799999999999999999999999987 6676664
No 19
>PRK05429 gamma-glutamyl kinase; Provisional
Probab=93.88 E-value=0.078 Score=47.09 Aligned_cols=61 Identities=15% Similarity=0.232 Sum_probs=53.4
Q ss_pred eeecCccccee-ecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcC
Q psy8680 96 VWVKPQAEQQF-LYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD 156 (180)
Q Consensus 96 ~~~~~~aE~~F-LYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~d 156 (180)
++|...|...- --|..++-+|+..++.++.+.+-|.|++.++.++|.|.+..|..|+++..
T Consensus 283 i~vd~gA~~al~~~g~sLl~~Gi~~v~g~f~~gd~V~i~~~~g~~va~G~~~~~s~e~~~~~ 344 (372)
T PRK05429 283 IVVDAGAVKALLERGKSLLPAGVTAVEGDFSRGDVVRIVDPDGREIARGLVNYSSDELRRIA 344 (372)
T ss_pred EEECccHHHHHHhcCCccCccchhheECcccCCCEEEEECCCCCEEEEEEecCCHHHHHHHc
Confidence 44444666655 58999999999999999999999999999999999999999999998764
No 20
>TIGR01027 proB glutamate 5-kinase. Bacterial ProB proteins hit the full length of this model, but the ProB-like domain of delta 1-pyrroline-5-carboxylate synthetase does not hit the C-terminal 100 residues of this model. The noise cutoff is set low enough to hit delta 1-pyrroline-5-carboxylate synthetase and other partial matches to this family.
Probab=92.52 E-value=0.17 Score=44.99 Aligned_cols=61 Identities=25% Similarity=0.348 Sum_probs=53.0
Q ss_pred eeecCcccceeec-ccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcC
Q psy8680 96 VWVKPQAEQQFLY-GHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD 156 (180)
Q Consensus 96 ~~~~~~aE~~FLY-G~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~d 156 (180)
++|...|+..-+- |..+|-+|+..+..++.+.+-|-|++.++.+||-|++..|..|+++.-
T Consensus 275 i~vD~gA~~al~~~g~sLl~~Gi~~v~g~F~~gd~v~i~~~~~~~ia~g~~~y~s~~~~~i~ 336 (363)
T TIGR01027 275 ITVDAGAEEALLERGKSLLPAGIVGVEGNFSRGEVVEILNPEGQDIGRGLVNYSSDELEKIK 336 (363)
T ss_pred EEEChhHHHHHHhcCCccCCccceeeECcccCCCEEEEECCCCCEEEEEEecCCHHHHHHHc
Confidence 3444466666665 899999999999999999999999999999999999999999998653
No 21
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=92.07 E-value=0.53 Score=39.19 Aligned_cols=63 Identities=22% Similarity=0.278 Sum_probs=56.6
Q ss_pred EeeecCcccceeecccccccccceeecccCCCcceEEEEecC-CCceeeEeeecchhHhhhcCC
Q psy8680 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMN-DVPLGFGVAAKSTAECKLADP 157 (180)
Q Consensus 95 ~~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmn-dvpLGFGvaakst~e~k~~dp 157 (180)
.|-|.-.|...-+-|-||+.-||-...+++++.+.|||.... +-||..|+|--|..|....+-
T Consensus 78 ~V~VD~GAvk~v~nGADvM~PGIv~~~~~ik~Gd~VvV~~e~~~~plAVG~alm~~~em~~~~k 141 (161)
T COG2016 78 VVVVDEGAVKFVLNGADVMAPGIVSADGEIKEGDIVVVVDEKKGRPLAVGIALMSGKEMEEKKK 141 (161)
T ss_pred EEEEcCccHhhhcCCCceeccceeecCCCccCCCEEEEEEcCCCCeeEEEeeccCHHHHhhhcC
Confidence 344455999999999999999999999999999999999998 999999999999999976554
No 22
>PRK11933 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
Probab=92.03 E-value=0.27 Score=45.60 Aligned_cols=98 Identities=16% Similarity=0.273 Sum_probs=61.7
Q ss_pred CCeEEEEcHHHHhhhcccCCCCeeeeeeeeeeeeecceEEEEeeehhhcccccc-eeEEeccccchhhhccccccccccc
Q psy8680 2 RDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQ-FKVWVKPQADQQFLYGHNILKSGLA 80 (180)
Q Consensus 2 ~~RVyYvse~il~~a~~~~~d~LlslGtc~GKFtKsgKFrl~ItaL~~LA~ya~-~KVWvKp~~~~~~~~~~~~~~~~~a 80 (180)
++++|++.+.+.. .+..-+++..|.++|++.| +.|..+-...-.|.+... ..+=+..
T Consensus 357 ~~~l~~~p~~~~~---~~~~l~v~r~Gl~lg~~kk-~rfePs~ala~~l~~~~~~~~~~l~~------------------ 414 (470)
T PRK11933 357 DKEVWLFPAGIEP---LIGKVRFSRIGIKLAETHK-KGYRWQHEAVIALASPDNANAFELTP------------------ 414 (470)
T ss_pred CCEEEEeccccch---hhcCCeEeeeceeEeeeec-CCeeEcHHHHHHhCcccccceEecCH------------------
Confidence 5788999885433 2444579999999999987 789888543323332222 1222222
Q ss_pred eeccCCCCccceeeEeeecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecch
Q psy8680 81 RITENTPKYQGVIFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKST 149 (180)
Q Consensus 81 ~i~e~~~~~~~~~~~~~~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst 149 (180)
..=..||-|+.|--+ +.+ ..|-+++.-++.|||||.....+
T Consensus 415 --------------------~~~~~Yl~ge~l~~~------~~~--~~G~~lv~~~g~~lG~gK~~~~~ 455 (470)
T PRK11933 415 --------------------QEAEEWYMGRDIYPQ------TAP--PAGEVIVTYQGQPIGLAKRVGNR 455 (470)
T ss_pred --------------------HHHHHHHCCCCccCC------CCC--CCCEEEEEECCEeeEEEEeeCCE
Confidence 333457777776321 222 25777777799999999987543
No 23
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=91.45 E-value=0.33 Score=43.19 Aligned_cols=74 Identities=26% Similarity=0.341 Sum_probs=56.5
Q ss_pred ecCcccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCeEEEEe---cccceeee
Q psy8680 98 VKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFN---QSDIGEYI 172 (180)
Q Consensus 98 ~~~~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~iVvfn---qaDiGEYl 172 (180)
+.+.....+..|.+|...++.+++++.+..+-|+|++.++.+||.|.+.-|+++.+..+ .+++|-. -.|.|-|=
T Consensus 242 Vd~~~a~~I~NG~~I~~pgv~~~d~~i~~gd~V~V~~~~G~~LAIGea~~s~~ei~~~~-kG~vV~~~~~~~~~~~~~ 318 (322)
T TIGR00425 242 VKDSAVDAICHGADLMVRGIARLEKGIEKGDTVAVITLKGEAVAVGIALMSTKDIANAD-KGVVADVKRVIMERGTYP 318 (322)
T ss_pred eCHHHHHHHHCCCccccccccccccccCCCCEEEEEECCCEEEEEEEEecCHHHHhhcC-CcEEEEEEEEeeCCCCCC
Confidence 44455666779999988888877766666667899998999999999999999998876 4555543 45666663
No 24
>PRK13402 gamma-glutamyl kinase; Provisional
Probab=80.72 E-value=2.3 Score=38.39 Aligned_cols=58 Identities=10% Similarity=0.114 Sum_probs=51.6
Q ss_pred ecCcccceeec-ccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhc
Q psy8680 98 VKPQAEQQFLY-GHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLA 155 (180)
Q Consensus 98 ~~~~aE~~FLY-G~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~ 155 (180)
|...|+.--+- |..+|-+|+.++.-++.+.+-|-|++.++..+|-|.+..|..|+++.
T Consensus 281 vd~ga~~al~~~~~sLl~~gi~~v~g~F~~gd~v~i~~~~g~~~~rg~~~y~s~~~~~i 339 (368)
T PRK13402 281 VENDFDRALDNHSEQLTSDDVVEIKGDFSVGDTILVRKGDGTKLAKGKSNYSSCLLNFI 339 (368)
T ss_pred ECccHHHHHHhcCCcccccceEEEeCEecCCCEEEEECCCCCEEEEEEccCCHHHHHHH
Confidence 33367776664 69999999999999999999999999999999999999999999865
No 25
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=77.84 E-value=2.3 Score=28.24 Aligned_cols=30 Identities=30% Similarity=0.388 Sum_probs=26.6
Q ss_pred eeEEeccccchhhhccccccccccceeccC
Q psy8680 56 FKVWVKPQADQQFLYGHNILKSGLARITEN 85 (180)
Q Consensus 56 ~KVWvKp~~~~~~~~~~~~~~~~~a~i~e~ 85 (180)
.+++|++.+.+.+++||+++.+|...+..+
T Consensus 1 ~~i~v~~~~~~~i~~g~~v~~~~v~~~~~~ 30 (77)
T smart00359 1 GKVVVDDGAVKAILNGASLLAPGVVRVDGG 30 (77)
T ss_pred CEEEEchhHHHHHHcCCCcccceeEEEeCC
Confidence 378999999999999999999999888753
No 26
>COG3270 Uncharacterized conserved protein [Function unknown]
Probab=71.76 E-value=7.4 Score=31.70 Aligned_cols=36 Identities=22% Similarity=0.195 Sum_probs=30.3
Q ss_pred ccCCCCeeeeeeeeeeeeecceEEEEeeehhhcccccc
Q psy8680 18 NFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQ 55 (180)
Q Consensus 18 ~~~~d~LlslGtc~GKFtKsgKFrl~ItaL~~LA~ya~ 55 (180)
+..+.+. -.|+-+|.|.| ..||+++++--.|+|-+.
T Consensus 31 ~l~k~~~-r~GI~lg~~~k-kg~r~s~e~~~al~p~~~ 66 (127)
T COG3270 31 CLFKEKI-HNGIKLGEIHK-KGYRWSHEGGFALAPPAV 66 (127)
T ss_pred chhhhhh-hcceEEEEEec-cCeeEEeeEEEEeCChhh
Confidence 4555666 88999999998 569999999999999887
No 27
>PRK08557 hypothetical protein; Provisional
Probab=71.33 E-value=5.1 Score=36.97 Aligned_cols=105 Identities=19% Similarity=0.193 Sum_probs=65.2
Q ss_pred CCeeeeeeeeeeee--e-cceEEEEeeehhhcccccceeEEeccccchhhhccccccccccceeccCCCCccceeeEeee
Q psy8680 22 DHLLALGTCFGKFT--K-SGKFRLHITALSYLAPYAQFKVWVKPQADQQFLYGHNILKSGLARITENTPKYQGVIFKVWV 98 (180)
Q Consensus 22 d~LlslGtc~GKFt--K-sgKFrl~ItaL~~LA~ya~~KVWvKp~~~~~~~~~~~~~~~~~a~i~e~~~~~~~~~~~~~~ 98 (180)
+.++.=|-+||-+. - ..+++++.++..++-. ..+|=|+|
T Consensus 43 ~ev~~~g~~~g~~~~~~~~~~w~~~p~~~~~~~~--~~~~~~~~------------------------------------ 84 (417)
T PRK08557 43 KRVYISEDQIGILEFDLLDLDWKFHPSPSYYLIE--EPKIKLKP------------------------------------ 84 (417)
T ss_pred hheeECCeEEEEEEEccccceeEEccchhhhhcc--Cceeeecc------------------------------------
Confidence 56778899999653 2 3477777776654422 22333332
Q ss_pred cCcccceeecccccccccceeecc--cCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCeEEEEecccceeee
Q psy8680 99 KPQAEQQFLYGHNILKSGLARITE--NTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDIGEYI 172 (180)
Q Consensus 99 ~~~aE~~FLYG~~vlKs~l~rite--ntp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~iVvfnqaDiGEYl 172 (180)
-..+|=|.+|....+.-+.| ++-.++-|+|-+ +..+|.|++..+..+.+.+.+-. ....+|+..++
T Consensus 85 ----~~~~~~g~~v~~~~~~~~~~~~~~~~~~~v~~~~--~~~~gvg~~~~~~~k~~~~~~~~--~~~~~~~~~~i 152 (417)
T PRK08557 85 ----TKRRLKGKYIKEELIENPEELNEILENDYVGVEI--GNFLGVGVKKEDRIKIKDLSLKK--ELDFEKIEDYL 152 (417)
T ss_pred ----cccccCCccccccccccccccccCCCCCEEEEec--CCEEEEEEeecceEEEEecccCC--CCCcccHHHHH
Confidence 34467777787777776666 555555333333 78999999988887777777643 23334554444
No 28
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=58.80 E-value=13 Score=33.78 Aligned_cols=33 Identities=12% Similarity=0.153 Sum_probs=24.4
Q ss_pred ceeecccCCCcceEEEEecCCCceeeEeeecch
Q psy8680 117 LARITENTPKYQGVIVLNMNDVPLGFGVAAKST 149 (180)
Q Consensus 117 l~ritentp~~~GVvV~nmndvpLGFGvaakst 149 (180)
|.++..+.+..+-|.|++.++.+||.|.....+
T Consensus 27 i~~~~~~~~~G~~v~v~~~~g~~lg~g~~n~~s 59 (396)
T PRK15128 27 VARMEGKASLGETIDIVDHQGKWLARGAYSPAS 59 (396)
T ss_pred hccccCCCCCCCEEEEEcCCCCEEEEEEECCCC
Confidence 345544455667789999999999999985443
No 29
>COG1549 Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis]
Probab=50.26 E-value=30 Score=33.77 Aligned_cols=52 Identities=21% Similarity=0.236 Sum_probs=45.0
Q ss_pred eecccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCC
Q psy8680 106 FLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPL 158 (180)
Q Consensus 106 FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~ 158 (180)
|.=-.+|++.|+.+.+|++-.++-|+|.- +|..+|.|+|+-|..|...+.-.
T Consensus 458 f~~~g~v~a~GV~da~edIrpnDeV~vv~-~~~v~gVGrA~msg~eM~~akkG 509 (519)
T COG1549 458 FIPRGSVFAPGVVDADEDIRPNDEVVVVH-GGEVRGVGRAVMSGREMVEAKKG 509 (519)
T ss_pred ccccccccccccccCCCCCCcCCEEEEEe-CCeEEEEeeeecChHHhcccCCc
Confidence 56667899999999999999999886654 78999999999999998887653
No 30
>COG0263 ProB Glutamate 5-kinase [Amino acid transport and metabolism]
Probab=48.03 E-value=28 Score=32.65 Aligned_cols=55 Identities=18% Similarity=0.230 Sum_probs=50.2
Q ss_pred cccceee-cccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcC
Q psy8680 101 QAEQQFL-YGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD 156 (180)
Q Consensus 101 ~aE~~FL-YG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~d 156 (180)
.|+.--+ .|+.+|-+|+..+.-++...+-|-|. .++..+|-|+...|.+|.++..
T Consensus 287 GA~~Al~~~gkSLLpaGV~~V~G~F~rGdvV~i~-~~g~~iarG~v~Y~s~el~~i~ 342 (369)
T COG0263 287 GAVEALLEQGKSLLPAGVTSVEGNFSRGDVVRIR-PQGGEIARGLVNYSSDELRKIA 342 (369)
T ss_pred cHHHHHHhcCCccccccceEeeeeecCCCEEEEe-cCCceeEeeeccCCHHHHHHHh
Confidence 8888888 99999999999999999999999999 7777999999999999987653
No 31
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=43.56 E-value=10 Score=29.13 Aligned_cols=26 Identities=31% Similarity=0.761 Sum_probs=18.9
Q ss_pred eecccCCCcceEEEEecCCCceeeEeee
Q psy8680 119 RITENTPKYQGVIVLNMNDVPLGFGVAA 146 (180)
Q Consensus 119 ritentp~~~GVvV~nmndvpLGFGvaa 146 (180)
+|.+..|+ |+.+..+...|+|||..|
T Consensus 25 ~ik~~l~~--g~~~~~~~~epIaFGLka 50 (88)
T COG2092 25 KIKEKLPE--GYELIKIEEEPIAFGLKA 50 (88)
T ss_pred HHHHhccc--cceeccceeEeeeeeeee
Confidence 45555544 555559999999999987
No 32
>cd00182 TBOX T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors.
Probab=36.66 E-value=81 Score=26.43 Aligned_cols=88 Identities=28% Similarity=0.544 Sum_probs=48.9
Q ss_pred eeecc-----eEEEEeeehhhcccccceeEEec--cccchhhhccc-cccccccceeccCCCCccceeeEeeecCcccce
Q psy8680 34 FTKSG-----KFRLHITALSYLAPYAQFKVWVK--PQADQQFLYGH-NILKSGLARITENTPKYQGVIFKVWVKPQAEQQ 105 (180)
Q Consensus 34 FtKsg-----KFrl~ItaL~~LA~ya~~KVWvK--p~~~~~~~~~~-~~~~~~~a~i~e~~~~~~~~~~~~~~~~~aE~~ 105 (180)
+||+| .+++.|++|+ |.+.|.|.++ |..+..|-|-. ....+|- .| |. .--++.+.|.+.
T Consensus 24 ITk~GRrmFP~l~~~vsGLd---p~~~Y~v~l~~~~~D~~Rykf~~~~W~~~g~---~e--~~---~~~~~~~HPdsp-- 90 (188)
T cd00182 24 ITKSGRRMFPTLKVKVSGLD---PNALYSVLMDLVPVDDHRYKFSGGKWVVAGK---AE--PH---LPPRVYVHPDSP-- 90 (188)
T ss_pred EecCCcccccceEEEEeCCC---cccceEEEEEEEEcCCcEEEecCCcEeEcCC---CC--CC---CCCceEECCCCC--
Confidence 67778 5678888865 6667777665 32233332211 0111111 12 11 122344444332
Q ss_pred eecccccccccc----eeecccCCCcceEEEEec
Q psy8680 106 FLYGHNILKSGL----ARITENTPKYQGVIVLNM 135 (180)
Q Consensus 106 FLYG~~vlKs~l----~ritentp~~~GVvV~nm 135 (180)
-.|.+.+|.++ .+||-+.....|.|++|.
T Consensus 91 -~tG~~wM~~~isF~kvKlTN~~~~~~~~i~L~S 123 (188)
T cd00182 91 -ATGAHWMKQPVSFDKLKLTNNTLDNNGHIILNS 123 (188)
T ss_pred -cCHHHHhhCccccchhhcccCCCCCCCEEEEec
Confidence 37888888887 588988877777776663
No 33
>PF09157 TruB-C_2: Pseudouridine synthase II TruB, C-terminal; InterPro: IPR015240 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1ZL3_A 1K8W_A 1R3F_A.
Probab=36.52 E-value=33 Score=22.49 Aligned_cols=40 Identities=23% Similarity=0.340 Sum_probs=26.4
Q ss_pred cccceeecccccccccceeecccCCCcceEEEEecCCCceeeEeee
Q psy8680 101 QAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAA 146 (180)
Q Consensus 101 ~aE~~FLYG~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaa 146 (180)
..-..|+-|+.|-- .+..+...-|=||+.++..||.|...
T Consensus 8 ~~~~~~~~Gq~v~~------~~~~~~~~~vrvy~~~~~FlGig~~~ 47 (58)
T PF09157_consen 8 EQAKRFLHGQRVRL------RDDAPPDGLVRVYDEDGRFLGIGEID 47 (58)
T ss_dssp HHHHHHTTT--B---------SS--SSSEEEEETTTTEEEEEEEE-
T ss_pred HHHHHHHCcCcccc------cCCCCCCceEEEECCCCEEEEEEEEc
Confidence 55667888888722 55666667888999999999999874
No 34
>PF13277 YmdB: YmdB-like protein; PDB: 2CV9_B 2Z06_C.
Probab=26.94 E-value=6.3 Score=34.85 Aligned_cols=69 Identities=22% Similarity=0.263 Sum_probs=48.5
Q ss_pred ccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCeEEEE----ecccceeeeecccccC
Q psy8680 109 GHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGF----NQSDIGEYIRYMTNML 179 (180)
Q Consensus 109 G~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~iVvf----nqaDiGEYlR~e~~~~ 179 (180)
|+..+|.+|.++.+.. .--.||.|-.+..=|||++.+...+...+--+.|..= .+.|+-+||..|..++
T Consensus 11 Gr~~v~~~Lp~L~~~~--~~DfVIaNgENaa~G~Git~~~~~~L~~~GvDviT~GNH~wdkkei~~~i~~~~~il 83 (253)
T PF13277_consen 11 GRRAVKEHLPELKEEY--GIDFVIANGENAAGGFGITPKIAEELFKAGVDVITMGNHIWDKKEIFDFIDKEPRIL 83 (253)
T ss_dssp HHHHHHHHHHHHGG----G-SEEEEE-TTTTTTSS--HHHHHHHHHHT-SEEE--TTTTSSTTHHHHHHH-SSEE
T ss_pred HHHHHHHHHHHHHhhc--CCCEEEECCcccCCCCCCCHHHHHHHHhcCCCEEecCcccccCcHHHHHHhcCCCcE
Confidence 6778888888887543 3347888888899999999999999999988888754 4678888888877654
No 35
>PF09707 Cas_Cas2CT1978: CRISPR-associated protein (Cas_Cas2CT1978); InterPro: IPR010152 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a minor branch of the Cas2 family of CRISPR-associated protein which are found in IPR003799 from INTERPRO. Cas2 is one of four protein families (Cas1 to Cas4) that are associated with CRISPR elements and always occur near a repeat cluster, usually in the order cas3-cas4-cas1-cas2. The function of Cas2 (and Cas1) is unknown. Cas3 proteins appear to be helicases while Cas4 proteins resemble RecB-type exonucleases, suggesting that these genes are involved in DNA metabolism or gene expression [].
Probab=25.05 E-value=47 Score=24.95 Aligned_cols=33 Identities=24% Similarity=0.290 Sum_probs=27.4
Q ss_pred eeecccCCCcceEEEEecCCCceeeEeeecchhH
Q psy8680 118 ARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAE 151 (180)
Q Consensus 118 ~ritentp~~~GVvV~nmndvpLGFGvaakst~e 151 (180)
.+++|..++...+.+++.++ +-||.+.......
T Consensus 43 ~~v~~~~~~G~a~m~~~~~n-eqG~~~~t~G~~~ 75 (86)
T PF09707_consen 43 ERVTEWIGDGSAVMVWSDNN-EQGFDFRTLGDPR 75 (86)
T ss_pred HHHHhhCCCccEEEEEccCC-CCCEEEEEeCCCC
Confidence 57888999999999999998 9999997654433
No 36
>PRK11558 putative ssRNA endonuclease; Provisional
Probab=24.29 E-value=80 Score=24.42 Aligned_cols=46 Identities=20% Similarity=0.179 Sum_probs=33.8
Q ss_pred eeecccCCCcceEEEEecCCCceeeEeeecchhH--hhhcCCCeEEEEe
Q psy8680 118 ARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAE--CKLADPLAIVGFN 164 (180)
Q Consensus 118 ~ritentp~~~GVvV~nmndvpLGFGvaakst~e--~k~~dp~~iVvfn 164 (180)
.+++|.++...+|.+++-|..+ ||.+....... .-..|....|-|.
T Consensus 45 ~~v~~~~~~G~avmv~~~~~eq-G~~~~t~G~~rr~~vD~DGl~Lv~~~ 92 (97)
T PRK11558 45 QQVTQLAEEGNVVMAWATNTES-GFEFQTFGENRRIPVDLDGLRLVSFL 92 (97)
T ss_pred HHHHHhCCCCcEEEEEcCCCCC-CcEEEecCCCCccEEecCCCEEEEec
Confidence 4678888999999999999888 99998776663 3444444445444
No 37
>PF08366 LLGL: LLGL2; InterPro: IPR013577 This domain is found in lethal giant larvae homologue 2 (LLGL2) proteins and syntaxin-binding proteins like tomosyn []. It has been identified in eukaryotes and tends to be found together with WD repeats (IPR001680 from INTERPRO).
Probab=23.32 E-value=3.6e+02 Score=20.97 Aligned_cols=43 Identities=19% Similarity=0.284 Sum_probs=37.9
Q ss_pred CcceEEEEecCCCceeeEeeecchhHhhhcCCCeEEEEecccc
Q psy8680 126 KYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDI 168 (180)
Q Consensus 126 ~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~iVvfnqaDi 168 (180)
+..-.++++|.--.+.|=+...+.-+|..-||.+++|.-+-|+
T Consensus 52 ~g~~~~~ldf~s~VIDF~~i~~~~~~~e~~~P~alvVL~e~eL 94 (105)
T PF08366_consen 52 QGKTHVVLDFTSRVIDFFTICESPWPNEFQDPYALVVLLEEEL 94 (105)
T ss_pred eCCEEEEEEcCCceEEEEEEcCCCCccccCCCcEEEEEEcCcE
Confidence 5677899999999999999998888888999999999877664
No 38
>TIGR00282 metallophosphoesterase, MG_246/BB_0505 family. A member of this family from Mycoplasma Pneumoniae has been crystallized and described as a novel phosphatase.
Probab=22.95 E-value=26 Score=30.59 Aligned_cols=68 Identities=16% Similarity=0.114 Sum_probs=47.1
Q ss_pred ccccccccceeecccCCCcceEEEEecCCCceeeEeeecchhHhhhcCCCeEEEEe-ccccee---eeeccccc
Q psy8680 109 GHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFN-QSDIGE---YIRYMTNM 178 (180)
Q Consensus 109 G~~vlKs~l~ritentp~~~GVvV~nmndvpLGFGvaakst~e~k~~dp~~iVvfn-qaDiGE---YlR~e~~~ 178 (180)
|+.++++.|.++-+.-+- -++|.|-....=|||.+.+..++.+.+.=+.+..=| -=|.|| +|..+..+
T Consensus 14 Gr~~l~~~L~~lk~~~~~--D~vIaNgEn~~gG~Gi~~~~~~~L~~~GvDviT~GNH~~Dkge~~~~i~~~~~~ 85 (266)
T TIGR00282 14 GRKIVKNNLPQLKSKYQA--DLVIANGENTTHGKGLTLKIYEFLKQSGVNYITMGNHTWFQKLILDVVINQKDL 85 (266)
T ss_pred HHHHHHHHHHHHHHhCCC--CEEEEcCcccCCCCCCCHHHHHHHHhcCCCEEEccchhccCcHHHHHHhccccc
Confidence 667778888887754443 266667655555799999999999988877776655 347777 56555443
No 39
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=20.20 E-value=36 Score=25.58 Aligned_cols=26 Identities=35% Similarity=0.804 Sum_probs=19.1
Q ss_pred eecccCCCcceEEEEecCCCceeeEeee
Q psy8680 119 RITENTPKYQGVIVLNMNDVPLGFGVAA 146 (180)
Q Consensus 119 ritentp~~~GVvV~nmndvpLGFGvaa 146 (180)
+|.+..| .|..+-.....|++||..|
T Consensus 25 ~ik~~~~--~g~~~~~~~~ePiaFGLka 50 (88)
T TIGR00489 25 KIKERIP--EGVEIRKIDEEPIAFGLVA 50 (88)
T ss_pred HHHHhCc--CCcEEeeeEEEeeecccee
Confidence 3444455 4666778899999999986
Done!