Query 048245
Match_columns 309
No_of_seqs 144 out of 1434
Neff 9.8
Searched_HMMs 46136
Date Fri Mar 29 07:44:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048245.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048245hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1488 Translational represso 100.0 6E-64 1.3E-68 446.6 21.8 300 1-309 188-497 (503)
2 cd07920 Pumilio Pumilio-family 100.0 2.5E-60 5.4E-65 421.2 31.5 298 1-307 19-322 (322)
3 KOG2049 Translational represso 100.0 3.3E-53 7.2E-58 381.2 22.9 306 1-307 226-532 (536)
4 COG5099 RNA-binding protein of 100.0 1.2E-49 2.7E-54 375.0 27.1 300 1-308 450-758 (777)
5 cd07920 Pumilio Pumilio-family 100.0 6.1E-45 1.3E-49 322.7 27.4 273 24-307 5-286 (322)
6 KOG1488 Translational represso 100.0 7.2E-43 1.6E-47 311.7 13.2 234 66-306 178-415 (503)
7 COG5099 RNA-binding protein of 100.0 8.2E-35 1.8E-39 274.9 15.8 227 73-307 447-677 (777)
8 KOG2049 Translational represso 100.0 2.2E-31 4.7E-36 240.4 18.0 270 25-306 214-491 (536)
9 KOG2050 Puf family RNA-binding 100.0 1E-28 2.3E-33 219.5 25.2 263 3-273 175-446 (652)
10 KOG2050 Puf family RNA-binding 100.0 5.1E-28 1.1E-32 215.2 24.4 293 4-307 134-440 (652)
11 KOG2188 Predicted RNA-binding 100.0 1.4E-27 3.1E-32 214.3 24.8 298 1-308 108-606 (650)
12 KOG2188 Predicted RNA-binding 99.9 7E-24 1.5E-28 190.7 18.0 284 19-307 90-569 (650)
13 KOG4574 RNA-binding protein (c 99.7 8.8E-18 1.9E-22 155.1 10.2 277 17-304 535-846 (1007)
14 KOG4574 RNA-binding protein (c 99.3 1.4E-12 3.1E-17 121.2 3.6 198 94-300 536-774 (1007)
15 PF00806 PUF: Pumilio-family R 98.6 4.9E-08 1.1E-12 56.2 3.0 35 25-59 1-35 (35)
16 PF00806 PUF: Pumilio-family R 98.5 1.1E-07 2.5E-12 54.6 3.1 31 250-284 5-35 (35)
17 smart00025 Pumilio Pumilio-lik 98.2 1.8E-06 3.9E-11 49.8 2.8 34 26-59 2-35 (36)
18 smart00025 Pumilio Pumilio-lik 98.1 3E-06 6.4E-11 48.9 2.6 32 249-284 4-35 (36)
19 PF08144 CPL: CPL (NUC119) dom 94.7 0.072 1.6E-06 41.4 5.0 66 207-272 58-134 (148)
20 PF08144 CPL: CPL (NUC119) dom 87.5 2.6 5.6E-05 32.7 6.5 31 135-165 58-88 (148)
21 PRK05686 fliG flagellar motor 86.4 24 0.00052 31.6 17.7 159 15-177 56-228 (339)
22 PF11510 FA_FANCE: Fanconi Ana 80.4 37 0.00079 29.1 11.6 108 67-185 98-214 (263)
23 PF08625 Utp13: Utp13 specific 74.5 37 0.0008 26.1 10.2 51 188-238 47-97 (141)
24 COG1747 Uncharacterized N-term 62.3 1.5E+02 0.0032 28.3 15.6 117 106-223 55-185 (711)
25 smart00288 VHS Domain present 62.1 67 0.0014 24.3 8.4 44 154-197 59-104 (133)
26 KOG1992 Nuclear export recepto 52.8 2.6E+02 0.0057 28.3 16.6 86 186-273 657-754 (960)
27 KOG1992 Nuclear export recepto 50.4 2.9E+02 0.0062 28.0 17.1 142 56-202 588-755 (960)
28 PF12231 Rif1_N: Rap1-interact 46.8 2.2E+02 0.0049 25.7 15.6 69 168-237 154-225 (372)
29 COG4399 Uncharacterized protei 46.7 2.2E+02 0.0047 25.6 9.3 16 163-178 334-349 (376)
30 PF14666 RICTOR_M: Rapamycin-i 44.5 1.4E+02 0.003 25.0 7.5 74 135-209 139-218 (226)
31 PRK05686 fliG flagellar motor 43.4 2.4E+02 0.0053 25.2 20.2 93 185-288 200-299 (339)
32 PF08625 Utp13: Utp13 specific 38.1 88 0.0019 24.0 5.0 52 116-167 47-98 (141)
33 PF09770 PAT1: Topoisomerase I 38.1 57 0.0012 33.0 5.1 52 18-72 553-616 (808)
34 KOG1078 Vesicle coat complex C 37.6 2.2E+02 0.0049 28.5 8.5 116 8-129 341-460 (865)
35 PF04286 DUF445: Protein of un 37.6 2.9E+02 0.0064 24.5 18.8 29 132-160 140-168 (367)
36 PF03195 DUF260: Protein of un 35.2 84 0.0018 22.6 4.2 42 151-192 37-79 (101)
37 PF04078 Rcd1: Cell differenti 33.4 82 0.0018 27.0 4.5 43 7-49 120-169 (262)
38 KOG2213 Apoptosis inhibitor 5/ 31.0 4.2E+02 0.0092 24.3 10.5 50 250-304 189-238 (460)
39 COG4399 Uncharacterized protei 30.3 4.1E+02 0.0089 23.9 13.0 6 251-256 323-328 (376)
40 cd03568 VHS_STAM VHS domain fa 30.1 2.6E+02 0.0055 21.5 11.2 56 154-221 59-115 (144)
41 TIGR00207 fliG flagellar motor 29.7 4.1E+02 0.0089 23.8 17.9 233 11-245 49-295 (338)
42 COG1536 FliG Flagellar motor s 29.2 4.2E+02 0.0092 23.8 17.6 84 92-175 133-226 (339)
43 COG1747 Uncharacterized N-term 28.8 5.3E+02 0.012 24.8 16.5 72 190-271 226-302 (711)
44 PF11640 TAN: Telomere-length 28.5 96 0.0021 24.1 4.0 66 189-258 86-152 (155)
45 PF12447 DUF3683: Protein of u 27.3 2.5E+02 0.0055 20.6 7.0 60 171-235 47-106 (115)
46 PF09770 PAT1: Topoisomerase I 26.9 81 0.0018 32.0 4.1 146 143-291 577-773 (808)
47 PF04858 TH1: TH1 protein; In 26.8 3.5E+02 0.0077 26.3 8.0 66 206-273 486-554 (584)
48 KOG3036 Protein involved in ce 26.3 4.2E+02 0.0091 22.7 8.1 30 6-35 148-178 (293)
49 COG5240 SEC21 Vesicle coat com 23.6 7E+02 0.015 24.4 11.8 172 38-213 356-533 (898)
50 PF04078 Rcd1: Cell differenti 23.4 1.3E+02 0.0028 25.8 4.0 40 10-49 3-50 (262)
51 PF10155 DUF2363: Uncharacteri 22.4 1.4E+02 0.003 22.5 3.7 40 4-44 83-122 (126)
52 PF04054 Not1: CCR4-Not comple 22.4 1.4E+02 0.003 27.2 4.3 81 188-270 263-352 (379)
53 PF12447 DUF3683: Protein of u 21.8 3.3E+02 0.0072 20.0 6.0 66 92-163 41-106 (115)
54 PF00790 VHS: VHS domain; Int 21.1 3.7E+02 0.0081 20.3 7.6 32 155-186 65-97 (140)
55 PF03448 MgtE_N: MgtE intracel 20.8 82 0.0018 22.1 2.1 17 123-139 9-25 (102)
56 PF04858 TH1: TH1 protein; In 20.7 3.6E+02 0.0078 26.3 6.8 69 169-237 485-554 (584)
57 PF02438 Adeno_100: Late 100kD 20.6 4.8E+02 0.01 25.1 7.3 59 112-174 286-344 (583)
58 PRK13883 conjugal transfer pro 20.5 70 0.0015 24.9 1.7 47 252-308 15-74 (151)
No 1
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6e-64 Score=446.62 Aligned_cols=300 Identities=25% Similarity=0.395 Sum_probs=287.8
Q ss_pred CchhHHHHHHhccCCH-HHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCC
Q 048245 1 EEGSQYLQEKLSSGDS-RILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGS 79 (309)
Q Consensus 1 ~~gsr~lq~~l~~~~~-e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs 79 (309)
|+|||++|..++..+. +++..+|+++.+.+.+||.|.+||||||+++++++++++..+...+. +++..||.|+|||
T Consensus 188 q~GsrfiQqkl~~~~~~~ek~~if~ei~~~~~~L~~dvFGNyvIQkffE~gt~~q~~~l~~~~~---g~v~~Lsld~ygC 264 (503)
T KOG1488|consen 188 QHGSRFIQQKLETASDNEEKQAVFDEILPPALELMTDVFGNYVIQKFFEHGTEDQRNLLHSQIK---GHVLELSLDMYGC 264 (503)
T ss_pred cccchHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhccCCHHHHHHHHHHHH---hhhhhhhcccccc
Confidence 7999999999999988 99999999999999999999999999999999999999999999999 9999999999999
Q ss_pred HHHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHH--hHHHHhcCccccHHHH
Q 048245 80 SSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALE--HCLYLACHEQGCINLN 157 (309)
Q Consensus 80 ~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~--~~~~l~~~~~gs~vvq 157 (309)
||+|+.|+.. ......+++.+ +.+++..+++|++||||||++++..+++.+.++++.+.+ ++..+|+|+|||+|||
T Consensus 265 RVIQkale~i-d~~~~~~Li~E-Ld~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv~~f~~~~~~~~ls~~~YGCRVIQ 342 (503)
T KOG1488|consen 265 RVIQKALEKV-DVSLQIQLIDE-LDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVDFFSGDDNLLELSTHKYGCRVIQ 342 (503)
T ss_pred hhHHHHHHhc-CHHHHHHHHHH-HHhhHHHHHhhcccceehhhhhhccChHHHHHHHHHhcCCCceeEeeccCcccHHHH
Confidence 9999999999 66666666666 799999999999999999999999999999999999999 9999999999999999
Q ss_pred HHHhccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCc
Q 048245 158 NFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNA 237 (309)
Q Consensus 158 ~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~ 237 (309)
++++++++++...++++|..++..|+.|+|||||||++|+++++..+..|++++.+++++++.|||+|+|||+||..++.
T Consensus 343 r~lE~c~~~~~~~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~I~~~l~~~ll~~Sq~KfASnVVEk~~~~a~~ 422 (503)
T KOG1488|consen 343 RILEHCSEDQKQPLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTIIIKCLLGNLLSMSQHKFASNVVEKAFLFAPP 422 (503)
T ss_pred HHhhcCChHhhhHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhhHHHHHHhhHHHHHHHHHHHHHHHHHHhhCCH
Confidence 99999999999999999999999999999999999999999999888899999999999999999999999999999998
Q ss_pred H--HHHHHHHhC-----chHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCccchhhhccC
Q 048245 238 V--HYIVEELLN-----SDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQKKK 309 (309)
Q Consensus 238 ~--~~i~~~l~~-----~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~~v~~k~~~ 309 (309)
. ..|++|++. ++.|..|+.|+|||||||++++.+++ .+++.|+..+++|..+|+..+||++|+++|-|
T Consensus 423 ~~r~~i~~Ei~~~~~~~~~~L~~mmkdQYgNYVVQkmi~~~~~----~q~~~i~~rI~~h~~~Lrk~syGKhIia~lek 497 (503)
T KOG1488|consen 423 LLRALIMNEIFPGYVEHPDALDIMMKDQYGNYVVQKMIDICGP----EQRELIKSRVKPHASRLRKFSYGKHIIAKLEK 497 (503)
T ss_pred HHHHHHHHHhcCCccCCccHHHHHHHHhhhhhHHHHHHHhcCH----HHHHHHHHHHHHHHHHHccCccHHHHHHHHHH
Confidence 8 889999998 26899999999999999999999988 99999999999999999999999999999854
No 2
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=100.00 E-value=2.5e-60 Score=421.19 Aligned_cols=298 Identities=31% Similarity=0.444 Sum_probs=289.0
Q ss_pred CchhHHHHHHhccCCHHHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCH
Q 048245 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSS 80 (309)
Q Consensus 1 ~~gsr~lq~~l~~~~~e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~ 80 (309)
|+|||++|++++.+++++++.+++++.|++.+||.|++||||+|+++++++++++..++..+. +++..++.|++||+
T Consensus 19 ~~gsr~lQ~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~g~~vvq~~l~~~~~~~~~~i~~~~~---~~~~~l~~~~~g~~ 95 (322)
T cd07920 19 QHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKIL---GHVVRLSLDMYGCR 95 (322)
T ss_pred chhhHHHHHHhccCCHHHHHHHHHHHHHhHHHHhcCccccHHHHHHHHhCCHHHHHHHHHHHH---HHHHHHcccchhHH
Confidence 589999999999999999999999999999999999999999999999999999999999999 99999999999999
Q ss_pred HHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHH
Q 048245 81 SVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFI 160 (309)
Q Consensus 81 vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l 160 (309)
++|++++.+ + +++...+.+++.+++..|+.|++||||+|++++.++++.+..+++.+.+++..+++|++||+|+|+++
T Consensus 96 vlqkll~~~-~-~~~~~~i~~~l~~~~~~L~~d~~gn~Vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~G~~vvq~~l 173 (322)
T cd07920 96 VIQKLLESI-S-EEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCL 173 (322)
T ss_pred HHHHHHHhc-C-HHHHHHHHHHHHHCHHHHhhcccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHcCccccHHHHHHH
Confidence 999999999 4 78888888989999999999999999999999999999999999999999999999999999999999
Q ss_pred hccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH--
Q 048245 161 DNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV-- 238 (309)
Q Consensus 161 ~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~-- 238 (309)
+.++++++..+++++.+++..++.|+|||||+|++++.++++.++.|++.+.+++++|++++|||+|+|+||+.+++.
T Consensus 174 ~~~~~~~~~~l~~~l~~~~~~L~~d~~Gn~vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~k~Gs~Vve~~l~~~~~~~~ 253 (322)
T cd07920 174 EHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEKCLKHASKEER 253 (322)
T ss_pred HhCCHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHhcCCHHHHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHCCHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred HHHHHHHhCc----hHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCccchhhhc
Q 048245 239 HYIVEELLNS----DQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQK 307 (309)
Q Consensus 239 ~~i~~~l~~~----~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~~v~~k~ 307 (309)
+.++++++.. +++.+|++|+|||||||++|+.+++ ..++.+++.|.+++.+|+.++|||+|++|+
T Consensus 254 ~~ii~~l~~~~~~~~~l~~l~~d~~Gn~Viq~~l~~~~~----~~~~~i~~~l~~~~~~L~~~~~G~~v~~~~ 322 (322)
T cd07920 254 ELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKE----EQRELLVEAIRPHLPSLRKSPYGKHILAKL 322 (322)
T ss_pred HHHHHHHhcCCCchhHHHHHhCCCcccHHHHHHHHhCCH----HHHHHHHHHHHHHHHHHcCCCcHHHHHHhC
Confidence 8899999873 4899999999999999999999997 899999999999999999999999999986
No 3
>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-53 Score=381.18 Aligned_cols=306 Identities=37% Similarity=0.535 Sum_probs=295.0
Q ss_pred CchhHHHHHHhccCCHHHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCH
Q 048245 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSS 80 (309)
Q Consensus 1 ~~gsr~lq~~l~~~~~e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~ 80 (309)
|+|||++|..+..++....+.+|.++..++.+|+.|++|++++|++++.|+++++..+...+..+++.++.++.+.+|++
T Consensus 226 ~~gc~~lq~~~~~~~~~~~~~if~~~~~~~~~Lm~d~fGny~vqkl~~~~~~eq~~~i~~~lts~p~~fv~i~~N~~GTr 305 (536)
T KOG2049|consen 226 QHGCRLLQKLLSEGTKVSILKIFLETIQDVPELMEDPFGNYLVQKLLEVCDEEQLTKIVSLLTSDPRLFVEICTNMYGTR 305 (536)
T ss_pred ccCCcccccCcccCccccHHHHHHHHHHHHHHHHhccchhHHHHHHHHhhCHHHHHHHHHHHhcCccceeEeeecCchhH
Confidence 68999999999999999999999999999999999999999999999999999999999999988999999999999999
Q ss_pred HHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHH
Q 048245 81 SVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFI 160 (309)
Q Consensus 81 vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l 160 (309)
.+|++++.. .+.+++..+.+++.+.+..|++|.||+||+|++++.+++++.+.+++.+...+.++|+|++||.|+|+|+
T Consensus 306 ~iQkl~~~~-~~~dqI~~~~~ai~~~fl~L~~D~~g~~Viq~cl~~f~~~~~~~l~e~i~~~c~~iA~~~hGCcvLq~cl 384 (536)
T KOG2049|consen 306 AVQKLLGKS-DSVDQISLFLDAIKPNFLHLIKDKNGNHVIQRCLRVFSKEKNEFLYEAILRYCLDLATDQHGCCVLQKCL 384 (536)
T ss_pred HHHHHHhcc-ccHHHHHHHHHHHHhhhHHhhhhcchhHHHHHHHHhcCchhhhHHHHHHHHHHHHHHHhccccchhHHHh
Confidence 999999999 8888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH-H
Q 048245 161 DNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV-H 239 (309)
Q Consensus 161 ~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~-~ 239 (309)
......+++.+++++..+...|+.|+|||||+|.+++.-++.....|++.|.+++++||.+||||+|||+||+..... .
T Consensus 385 ~~~~~~~rd~Lv~~i~~naL~Ls~d~~GNyvVQyvl~L~~~~~t~~i~~~L~g~~veLS~qKfgS~vVEk~L~~~~~~~~ 464 (536)
T KOG2049|consen 385 DYSRGEQRDRLVEEISRNALLLSNDPYGNYVVQYVLELNDPSCTVNIAEKLRGHYVELSFQKFGSHVVEKLLKVRESSRA 464 (536)
T ss_pred cchhHHHHHHHHHHHHHHhHhhhcCccccchhhhhhhhcCcchHHHHHHhhhhHHHHHHHHhhccHHHHHHHhcCcchhh
Confidence 999999999999999999999999999999999999999998999999999999999999999999999999999999 9
Q ss_pred HHHHHHhCchHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCccchhhhc
Q 048245 240 YIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQK 307 (309)
Q Consensus 240 ~i~~~l~~~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~~v~~k~ 307 (309)
.++.++++.+++.+|++|+|||||||++|..+........+..+++.+.+.+..|+++++|..+..++
T Consensus 465 ~iV~ell~~~~~~~Ll~D~ygNyViq~AL~vtk~~~~~~~~~~lv~~~~~~~~~lr~~p~~~~~~~~~ 532 (536)
T KOG2049|consen 465 QIVLELLSCDELDRLLRDPYGNYVIQTALRVTKVKLREDLFGLLVQKLMPRIRLLRNNPGGNIALIKD 532 (536)
T ss_pred HHHHHHHccccHHHHhhCccchHHHHHHHHHhhhcccchhhHHHHHHHhhhhHHhhcCcccceeeehh
Confidence 99999999789999999999999999999999853233789999999999999999999999988765
No 4
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-49 Score=375.00 Aligned_cols=300 Identities=27% Similarity=0.400 Sum_probs=287.5
Q ss_pred CchhHHHHHHhccCCHHHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCH
Q 048245 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSS 80 (309)
Q Consensus 1 ~~gsr~lq~~l~~~~~e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~ 80 (309)
|+|||+||+.|+.-+.++.+.++.++.+...+||.|.+||||+||+++++++.++..++..+. +++..++.|+||+|
T Consensus 450 q~g~r~LQk~Lds~s~~~~~~~~~e~~d~~~eLs~d~fGNyliQK~fe~~s~~q~~~ml~~~~---~~~~~ls~~~~Gtr 526 (777)
T COG5099 450 QHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSS---KHLVSLSVHKYGTR 526 (777)
T ss_pred cHHHHHHHHHhcccchHHHHHHHHHHhhhhHHHHHhhhcchhhHHHHHhccHHHHHHHHHHhh---hhHHHhhccccccH
Confidence 799999999999999999999999999999999999999999999999999999999999999 99999999999999
Q ss_pred HHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHH
Q 048245 81 SVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFI 160 (309)
Q Consensus 81 vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l 160 (309)
++|++++.. .++.+...+..++.+.+..+++|.+||||||++++.++.+....+++.+.+++.++++|+|||+|+|+|+
T Consensus 527 v~QK~id~~-~t~~qi~~lv~~l~~~~~~li~dqngNHviqKci~~~~~~~~~fif~~~~~~~~~is~~r~Gs~vvq~~l 605 (777)
T COG5099 527 VLQKAIDIV-STDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCL 605 (777)
T ss_pred HHHHHHhcc-CchhhHHHHHHHhhhhhHHHHHhccCCHHHHHHHHhcCccccchHHHHHHhhhHhhhccccccHHHHHHH
Confidence 999999999 8888888888889999999999999999999999999999999999999999999999999999999999
Q ss_pred hccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHH-hHHHhccCcchhHHHHHHHhcCCcH-
Q 048245 161 DNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRG-HYVDLSLTKCGSFVVQKFLKYQNAV- 238 (309)
Q Consensus 161 ~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~-~~~~l~~~~~gs~vve~~l~~~~~~- 238 (309)
+++..+....++++|..+...|++|+|||||||++|+.+.+..++.|+..+.. +++++++|||||.|||+|++.+.+.
T Consensus 606 e~~~~~~~~~~~~~Ii~~~~~L~~dq~GNyvvq~il~~g~~~~k~~i~~~~l~~~v~elS~~kfaSnvVeK~i~~~~~~~ 685 (777)
T COG5099 606 ENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIKYASDSF 685 (777)
T ss_pred HhccHhHHHHHHHHHHHHHHhhccCCcchhhhhHHhhcCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcch
Confidence 99999999999999999999999999999999999999999999999998887 9999999999999999999999988
Q ss_pred --HHHHHHHhC----chH-HHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCccchhhhcc
Q 048245 239 --HYIVEELLN----SDQ-ILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQKK 308 (309)
Q Consensus 239 --~~i~~~l~~----~~~-l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~~v~~k~~ 308 (309)
+.|+.++.. .+. +..|+.|+|||||+|+++..... ..+..+.+.+.++.+.|.+++||.++..++-
T Consensus 686 ~~~ril~~~~~~~~~~~~~l~~i~~d~y~Nyv~q~~~~~s~~----~~~~l~~~~i~~~~~~l~~s~~g~~i~~~le 758 (777)
T COG5099 686 KRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPE----IQRSLLARAIKKVIPSLKKSMYGQHILALLE 758 (777)
T ss_pred HHHHHHHHHhcccccCChHHHHHHHhhhcchHHHHHHhhCch----hhHHHHHHHHHHHHHHHhcCCccHHHHHHHH
Confidence 478888876 333 88999999999999999999999 9999999999999999999999999988763
No 5
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=100.00 E-value=6.1e-45 Score=322.70 Aligned_cols=273 Identities=20% Similarity=0.263 Sum_probs=260.7
Q ss_pred HHHH-hhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCHHHHHHHhhhcCChhHHHHHHHH
Q 048245 24 WVVS-GFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSA 102 (309)
Q Consensus 24 ~el~-~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~ 102 (309)
.+.. +++.+++.|++||+++|++++.++++++..+++.+. +++..++.|++|++|+|++++.+ ++++...+.+.
T Consensus 5 ~~~~~~~~~~l~~~~~gsr~lQ~~l~~~~~~~~~~i~~~l~---~~~~~l~~~~~g~~vvq~~l~~~--~~~~~~~i~~~ 79 (322)
T cd07920 5 QDIKAGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEIL---PHVVELMVDPFGNYVIQKLFEHG--TEEQRLQLLEK 79 (322)
T ss_pred HhccCcchhhccCCchhhHHHHHHhccCCHHHHHHHHHHHH---HhHHHHhcCccccHHHHHHHHhC--CHHHHHHHHHH
Confidence 4445 899999999999999999999999999999999999 99999999999999999999999 57788888888
Q ss_pred HHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHHhccChHHHHHHHHHHHHhHHhh
Q 048245 103 LKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASL 182 (309)
Q Consensus 103 l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l 182 (309)
+.+++..++.|++|++++|++++.++++++..+++++.+++..++.|++|++|+|++++.++++++..+++.+.+++..+
T Consensus 80 ~~~~~~~l~~~~~g~~vlqkll~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Vvq~~l~~~~~~~~~~i~~~l~~~~~~l 159 (322)
T cd07920 80 ILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVAL 159 (322)
T ss_pred HHHHHHHHcccchhHHHHHHHHHhcCHHHHHHHHHHHHHCHHHHhhcccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH--HHHHHHHhCchHHHHhhcCcCh
Q 048245 183 SRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV--HYIVEELLNSDQILQVASDKYG 260 (309)
Q Consensus 183 ~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~--~~i~~~l~~~~~l~~L~~d~~g 260 (309)
+.|++|++|+|++++..+++.++.+++.+.+++..|+.++||++|+|++++..++. +.+++.+.+ ++..|+.|+||
T Consensus 160 ~~~~~G~~vvq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~~Gn~vvq~~l~~~~~~~~~~i~~~l~~--~~~~l~~~k~G 237 (322)
T cd07920 160 STHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLG--NIVQLSCHKFA 237 (322)
T ss_pred HcCccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHhcCCHHHHHHHHHHHHH--HHHHHHcCcch
Confidence 99999999999999999999999999999999999999999999999999999877 888899887 99999999999
Q ss_pred hHHHHHHHhhccCCCcHHHHHHHHHHH------HHHHHhhhcCCCccchhhhc
Q 048245 261 NYVIQTALVETMRQDRLSVHQRLVTKL------QQHLAALRVMKYGSNKEIQK 307 (309)
Q Consensus 261 ~~Viq~~l~~~~~~~~~~~~~~l~~~l------~~~~~~L~~~~~g~~v~~k~ 307 (309)
++|++++++.++. ..++.+++++ .+++.+|+.++||++|+.++
T Consensus 238 s~Vve~~l~~~~~----~~~~~ii~~l~~~~~~~~~l~~l~~d~~Gn~Viq~~ 286 (322)
T cd07920 238 SNVVEKCLKHASK----EERELIIDEILASGNETSALDTLMKDQYGNYVIQTA 286 (322)
T ss_pred HHHHHHHHHHCCH----HHHHHHHHHHhcCCCchhHHHHHhCCCcccHHHHHH
Confidence 9999999999998 8899999999 46999999999999999875
No 6
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.2e-43 Score=311.73 Aligned_cols=234 Identities=21% Similarity=0.259 Sum_probs=225.8
Q ss_pred cchHHHhhccccCCHHHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHH
Q 048245 66 DQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLY 145 (309)
Q Consensus 66 ~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~ 145 (309)
.+.+...+.|++||+++|.-++.+ ...+....+++.+.+.+..||.|.+||||||++++.+..+++..+...+.+++..
T Consensus 178 ~~~~v~f~~Dq~GsrfiQqkl~~~-~~~~ek~~if~ei~~~~~~L~~dvFGNyvIQkffE~gt~~q~~~l~~~~~g~v~~ 256 (503)
T KOG1488|consen 178 PGHLVEFAKDQHGSRFIQQKLETA-SDNEEKQAVFDEILPPALELMTDVFGNYVIQKFFEHGTEDQRNLLHSQIKGHVLE 256 (503)
T ss_pred CCCceeecCCcccchHHHHhcccc-ccHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhccCCHHHHHHHHHHHHhhhhh
Confidence 388999999999999999999998 6558889999999999999999999999999999999999999999999999999
Q ss_pred HhcCccccHHHHHHHhccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHH--hHHHhccCcc
Q 048245 146 LACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRG--HYVDLSLTKC 223 (309)
Q Consensus 146 l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~--~~~~l~~~~~ 223 (309)
+|.++|||||+|+.++..+..+...++.+|.+++..++.|++||||||+++++.+++....|++.|.+ ++..++.|+|
T Consensus 257 Lsld~ygCRVIQkale~id~~~~~~Li~ELd~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv~~f~~~~~~~~ls~~~Y 336 (503)
T KOG1488|consen 257 LSLDMYGCRVIQKALEKVDVSLQIQLIDELDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVDFFSGDDNLLELSTHKY 336 (503)
T ss_pred hhcccccchhHHHHHHhcCHHHHHHHHHHHHhhHHHHHhhcccceehhhhhhccChHHHHHHHHHhcCCCceeEeeccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999 9999999999
Q ss_pred hhHHHHHHHhcCCcH--HHHHHHHhCchHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCcc
Q 048245 224 GSFVVQKFLKYQNAV--HYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGS 301 (309)
Q Consensus 224 gs~vve~~l~~~~~~--~~i~~~l~~~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~ 301 (309)
||||+|.+|+.+++. ..+++++.. ++..|++|+|||||||+++++.+. ..+..|.+.|.+++..++.+||+|
T Consensus 337 GCRVIQr~lE~c~~~~~~~i~~ei~~--~~~~L~~dQygNYVIQHVie~g~~----~~~~~I~~~l~~~ll~~Sq~KfAS 410 (503)
T KOG1488|consen 337 GCRVIQRILEHCSEDQKQPLMEEIIR--NCDQLAQDQYGNYVIQHVIEHGSP----YRDTIIIKCLLGNLLSMSQHKFAS 410 (503)
T ss_pred ccHHHHHHhhcCChHhhhHHHHHHHH--HHHHHHhhhhhhHHHHHHHhcCCh----hhhhhHHHHHHhhHHHHHHHHHHH
Confidence 999999999999998 569999998 999999999999999999999998 889999999999999999999999
Q ss_pred chhhh
Q 048245 302 NKEIQ 306 (309)
Q Consensus 302 ~v~~k 306 (309)
+|+||
T Consensus 411 nVVEk 415 (503)
T KOG1488|consen 411 NVVEK 415 (503)
T ss_pred HHHHH
Confidence 99998
No 7
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.2e-35 Score=274.86 Aligned_cols=227 Identities=23% Similarity=0.295 Sum_probs=215.3
Q ss_pred hccccCCHHHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccc
Q 048245 73 SVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQG 152 (309)
Q Consensus 73 ~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~g 152 (309)
+.|++|+|.||+.++.- ....++.++.++.+...+|+.|.+||||+|++++.+...++..++..+.+++..++.|+||
T Consensus 447 ~~Dq~g~r~LQk~Lds~--s~~~~~~~~~e~~d~~~eLs~d~fGNyliQK~fe~~s~~q~~~ml~~~~~~~~~ls~~~~G 524 (777)
T COG5099 447 CKDQHGSRFLQKLLDSN--SSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYG 524 (777)
T ss_pred cCCcHHHHHHHHHhccc--chHHHHHHHHHHhhhhHHHHHhhhcchhhHHHHHhccHHHHHHHHHHhhhhHHHhhccccc
Confidence 69999999999999996 5677888888899999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhccChHHHH-HHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHH
Q 048245 153 CINLNNFIDNMKGSRRK-QILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKF 231 (309)
Q Consensus 153 s~vvq~~l~~~~~~~~~-~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~ 231 (309)
|||+|++++....+... .++.++.+++..+++|++||||+|++++.........|++.+.+++.+++.++|||+|+|+|
T Consensus 525 trv~QK~id~~~t~~qi~~lv~~l~~~~~~li~dqngNHviqKci~~~~~~~~~fif~~~~~~~~~is~~r~Gs~vvq~~ 604 (777)
T COG5099 525 TRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRC 604 (777)
T ss_pred cHHHHHHHhccCchhhHHHHHHHhhhhhHHHHHhccCCHHHHHHHHhcCccccchHHHHHHhhhHhhhccccccHHHHHH
Confidence 99999999998766655 88999999999999999999999999999988899999999999999999999999999999
Q ss_pred HhcCCcH--HHHHHHHhCchHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHH-HHHhhhcCCCccchhhhc
Q 048245 232 LKYQNAV--HYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQ-HLAALRVMKYGSNKEIQK 307 (309)
Q Consensus 232 l~~~~~~--~~i~~~l~~~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~-~~~~L~~~~~g~~v~~k~ 307 (309)
++.+... +.++++++. +...|++|+|||||||++++.+.. ..+++++..+.. ++.+|+.++||+.|++|.
T Consensus 605 le~~~~~~~~~~~~~Ii~--~~~~L~~dq~GNyvvq~il~~g~~----~~k~~i~~~~l~~~v~elS~~kfaSnvVeK~ 677 (777)
T COG5099 605 LENCNSEDKENLVEEIIS--NSKYLSQDQYGNYVVQHILDNGAE----PNKERIIIKLLSKRVVELSTHKFASNVVEKC 677 (777)
T ss_pred HHhccHhHHHHHHHHHHH--HHHhhccCCcchhhhhHHhhcCCC----cchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999998 789999998 999999999999999999999998 789999998888 999999999999999996
No 8
>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=99.98 E-value=2.2e-31 Score=240.38 Aligned_cols=270 Identities=20% Similarity=0.226 Sum_probs=206.3
Q ss_pred HHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCHHHHHHHhhhcCChhHHHHHHHHHH
Q 048245 25 VVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALK 104 (309)
Q Consensus 25 el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~ 104 (309)
+..+.+..+++|+.|++++|+++..++......++..+. ..+..|..|++|+.++|++++.+ +++++..+...+.
T Consensus 214 ~~~~~~~~~akd~~gc~~lq~~~~~~~~~~~~~if~~~~---~~~~~Lm~d~fGny~vqkl~~~~--~~eq~~~i~~~lt 288 (536)
T KOG2049|consen 214 EIQGSINLIAKDQHGCRLLQKLLSEGTKVSILKIFLETI---QDVPELMEDPFGNYLVQKLLEVC--DEEQLTKIVSLLT 288 (536)
T ss_pred ccchhhhhhcccccCCcccccCcccCccccHHHHHHHHH---HHHHHHHhccchhHHHHHHHHhh--CHHHHHHHHHHHh
Confidence 344677778888888888888888888777777777777 78888888888888888888877 5566655555454
Q ss_pred H---HHhHhhcCCCchHHHHHHhccCCC-cchHHHHHHHHHhHHHHhcCccccHHHHHHHhccChHHHHHHHHHHHHhHH
Q 048245 105 R---LFKFLMMTKPGSSVILKCLEPSYN-HKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180 (309)
Q Consensus 105 ~---~~~~l~~~~~gs~vvq~~l~~~~~-~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~ 180 (309)
. .++.++.+.+|+..+|++++.... ++...+++++.+.+..+.++.+|.+|+|+|+...++...+.+.+.+..++.
T Consensus 289 s~p~~fv~i~~N~~GTr~iQkl~~~~~~~dqI~~~~~ai~~~fl~L~~D~~g~~Viq~cl~~f~~~~~~~l~e~i~~~c~ 368 (536)
T KOG2049|consen 289 SDPRLFVEICTNMYGTRAVQKLLGKSDSVDQISLFLDAIKPNFLHLIKDKNGNHVIQRCLRVFSKEKNEFLYEAILRYCL 368 (536)
T ss_pred cCccceeEeeecCchhHHHHHHHhccccHHHHHHHHHHHHhhhHHhhhhcchhHHHHHHHHhcCchhhhHHHHHHHHHHH
Confidence 4 477777888888888888876543 234566777778888888888888888888888877777777788888888
Q ss_pred hhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH--HHHHHHHhCchHHHHhhcCc
Q 048245 181 SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV--HYIVEELLNSDQILQVASDK 258 (309)
Q Consensus 181 ~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~--~~i~~~l~~~~~l~~L~~d~ 258 (309)
.++.|++|+.|+|++|......+|+.+++.+..+...|+.++||.+|||.+++.-... ..|+..|.+ +..+|+..+
T Consensus 369 ~iA~~~hGCcvLq~cl~~~~~~~rd~Lv~~i~~naL~Ls~d~~GNyvVQyvl~L~~~~~t~~i~~~L~g--~~veLS~qK 446 (536)
T KOG2049|consen 369 DLATDQHGCCVLQKCLDYSRGEQRDRLVEEISRNALLLSNDPYGNYVVQYVLELNDPSCTVNIAEKLRG--HYVELSFQK 446 (536)
T ss_pred HHHHhccccchhHHHhcchhHHHHHHHHHHHHHHhHhhhcCccccchhhhhhhhcCcchHHHHHHhhhh--HHHHHHHHh
Confidence 8888888888888888877777788888888888888888888888888888777666 777777777 788888888
Q ss_pred ChhHHHHHHHhhccCCCcHHHHHHHHHHHHH--HHHhhhcCCCccchhhh
Q 048245 259 YGNYVIQTALVETMRQDRLSVHQRLVTKLQQ--HLAALRVMKYGSNKEIQ 306 (309)
Q Consensus 259 ~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~--~~~~L~~~~~g~~v~~k 306 (309)
||||||+++|+..... +..++.+|.. .+..|..++||-.|+.+
T Consensus 447 fgS~vVEk~L~~~~~~-----~~~iV~ell~~~~~~~Ll~D~ygNyViq~ 491 (536)
T KOG2049|consen 447 FGSHVVEKLLKVRESS-----RAQIVLELLSCDELDRLLRDPYGNYVIQT 491 (536)
T ss_pred hccHHHHHHHhcCcch-----hhHHHHHHHccccHHHHhhCccchHHHHH
Confidence 8888888888877762 3666666666 77778888888877764
No 9
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1e-28 Score=219.53 Aligned_cols=263 Identities=16% Similarity=0.156 Sum_probs=232.4
Q ss_pred hhHHHHHHhccCCHHHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCHHH
Q 048245 3 GSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSV 82 (309)
Q Consensus 3 gsr~lq~~l~~~~~e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~vl 82 (309)
.||++|+++++|++++++.+|+|+.|.+.+||.++||.|++++++.++++.++..|+..+. |+++.|..|+.|+.|+
T Consensus 175 tSRViQt~Vky~s~~~r~~if~eL~p~~v~l~kskY~k~~v~KmLkyGsk~q~a~iI~sl~---Ghv~kLlRH~eaa~Vv 251 (652)
T KOG2050|consen 175 TSRVIQTCVKYGSEAQREQIFEELLPFFVELAKSKYAKFFVQKMLKYGSKAQKAKIINSLR---GHVVKLLRHREAAYVV 251 (652)
T ss_pred hHHHHHHHHHhcCHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHhcCCHHHHHHHHHHHh---hhHHHHHhhhHHHHHH
Confidence 6999999999999999999999999999999999999999999999999999999999999 9999999999999999
Q ss_pred HHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCc-ccc----HHHH
Q 048245 83 KKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHE-QGC----INLN 157 (309)
Q Consensus 83 q~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~-~gs----~vvq 157 (309)
+.++... .+.+++..+..++.+....++++.+--++ ..++... |+.+..|...+.+.+..++.-. .|. .++-
T Consensus 252 e~ay~~~-A~l~Qr~~li~EfYG~efqlfK~sn~~Tl-~kil~~~-pekk~~I~~~l~~~I~~v~eKg~v~~tivHk~ml 328 (652)
T KOG2050|consen 252 EYAYNDF-ATLEQRQYLIQEFYGDEFQLFKDSNDKTL-DKILAEA-PEKKASILRHLKAIITPVAEKGSVDHTIVHKLML 328 (652)
T ss_pred HHHHHhh-ccHHHHHHHHHHHhhHHHHHHhccCcccH-HHHHHhC-hHhHHHHHHHHHHHhHHHhhcchhHHHHHHHHHH
Confidence 9999987 67888888888899999999999544444 4444442 6677777777665544333221 122 3555
Q ss_pred HHHhccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCc
Q 048245 158 NFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNA 237 (309)
Q Consensus 158 ~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~ 237 (309)
.+++.|+++.+..++..+.+.++.++..+-|+.|.-.++.+++++.|+.|++.+.+++..+|.+.||+.|+-.+|++.++
T Consensus 329 Ey~~~ade~e~~e~l~ll~elv~e~vHT~dGS~vAm~li~~a~aKeRK~IiK~~K~h~~K~A~~~yGh~vlia~ldc~DD 408 (652)
T KOG2050|consen 329 EYLTIADEEEKSELLELLKELVPEMVHTRDGSRVAMKLIWHATAKERKLIIKNMKEHVEKIANDEYGHLVLIALLDCTDD 408 (652)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHhhccCceehhhhhcccch
Confidence 67788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred H----HHHHHHHhCchHHHHhhcCcChhHHHHHHHhhccC
Q 048245 238 V----HYIVEELLNSDQILQVASDKYGNYVIQTALVETMR 273 (309)
Q Consensus 238 ~----~~i~~~l~~~~~l~~L~~d~~g~~Viq~~l~~~~~ 273 (309)
+ +.|+.++.+ ++..+..|+||+.|+++++...+.
T Consensus 409 T~l~kk~i~~e~~~--el~~li~Dk~Grrv~lyll~p~D~ 446 (652)
T KOG2050|consen 409 TKLLKKLIYDELKS--ELKSLISDKYGRRVILYLLAPRDG 446 (652)
T ss_pred HHHHHHHHHHHHHH--HHHHHhccchhhhhhhhhccCCcc
Confidence 8 888899988 999999999999999999998544
No 10
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=5.1e-28 Score=215.19 Aligned_cols=293 Identities=17% Similarity=0.193 Sum_probs=251.6
Q ss_pred hHHHHHHhccCCH--HHHHHHHHHH----HhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhcccc
Q 048245 4 SQYLQEKLSSGDS--RILDKLFWVV----SGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKF 77 (309)
Q Consensus 4 sr~lq~~l~~~~~--e~~~~i~~el----~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~ 77 (309)
+.-|+..|...++ |.++++.+|+ ++++..|+.....++|||.++.++++++|..|++.+. |.++.||.++|
T Consensus 134 ~kslWEkLR~k~~~ke~R~klv~el~~likg~i~~lv~aHDtSRViQt~Vky~s~~~r~~if~eL~---p~~v~l~kskY 210 (652)
T KOG2050|consen 134 AKSLWEKLRRKTTPKEERDKLVSELYKLIKGKISKLVFAHDTSRVIQTCVKYGSEAQREQIFEELL---PFFVELAKSKY 210 (652)
T ss_pred HHHHHHHHhccCCcHHHHHHHHHHHHHHHhhhHHHHHHHhhhHHHHHHHHHhcCHHHHHHHHHHHh---HHHHHHHHhHH
Confidence 3456666765544 7788776665 5889999999999999999999999999999999999 99999999999
Q ss_pred CCHHHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhcc-CCCcchHHHHHHHHHhHHHHhcCccccHHH
Q 048245 78 GSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEP-SYNHKNDFIYQAALEHCLYLACHEQGCINL 156 (309)
Q Consensus 78 gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~-~~~~~~~~l~~~l~~~~~~l~~~~~gs~vv 156 (309)
|-+++|+++.++ ++.++..+.+.+++++..|+.|..|++|+...+.. ...++|..++.++.+.-..+..+ .--.-+
T Consensus 211 ~k~~v~KmLkyG--sk~q~a~iI~sl~Ghv~kLlRH~eaa~Vve~ay~~~A~l~Qr~~li~EfYG~efqlfK~-sn~~Tl 287 (652)
T KOG2050|consen 211 AKFFVQKMLKYG--SKAQKAKIINSLRGHVVKLLRHREAAYVVEYAYNDFATLEQRQYLIQEFYGDEFQLFKD-SNDKTL 287 (652)
T ss_pred HHHHHHHHHhcC--CHHHHHHHHHHHhhhHHHHHhhhHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHhc-cCcccH
Confidence 999999999998 78888888888999999999999999999999987 56789999999999987777776 344566
Q ss_pred HHHHhccChHHHHHHHHHHHHhHHhhccCC-Chh----HHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHH
Q 048245 157 NNFIDNMKGSRRKQILHLISVNAASLSRHR-SGN----YVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKF 231 (309)
Q Consensus 157 q~~l~~~~~~~~~~l~~~l~~~~~~l~~d~-~g~----~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~ 231 (309)
.+++... ++.+..|+..+...+...+.-. .|. .++--.+..++++.+..+++.+.+.+++|..++.||+|..+|
T Consensus 288 ~kil~~~-pekk~~I~~~l~~~I~~v~eKg~v~~tivHk~mlEy~~~ade~e~~e~l~ll~elv~e~vHT~dGS~vAm~l 366 (652)
T KOG2050|consen 288 DKILAEA-PEKKASILRHLKAIITPVAEKGSVDHTIVHKLMLEYLTIADEEEKSELLELLKELVPEMVHTRDGSRVAMKL 366 (652)
T ss_pred HHHHHhC-hHhHHHHHHHHHHHhHHHhhcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchHHHHHHH
Confidence 6777664 4677778888777766555432 232 333445667889999999999999999999999999999999
Q ss_pred HhcCCcH--HHHHHHHhCchHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCccchhhhc
Q 048245 232 LKYQNAV--HYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQK 307 (309)
Q Consensus 232 l~~~~~~--~~i~~~l~~~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~~v~~k~ 307 (309)
+..+++. +.|+..+-. ++..+|.|+||+.|+-.+|++.++|. ..++.|.+++.+++..+..++||++||.=+
T Consensus 367 i~~a~aKeRK~IiK~~K~--h~~K~A~~~yGh~vlia~ldc~DDT~--l~kk~i~~e~~~el~~li~Dk~Grrv~lyl 440 (652)
T KOG2050|consen 367 IWHATAKERKLIIKNMKE--HVEKIANDEYGHLVLIALLDCTDDTK--LLKKLIYDELKSELKSLISDKYGRRVILYL 440 (652)
T ss_pred HhhCCHHHHHHHHHHHHH--HHHHHHhhccCceehhhhhcccchHH--HHHHHHHHHHHHHHHHHhccchhhhhhhhh
Confidence 9999999 888899887 99999999999999999999999975 788999999999999999999999999754
No 11
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.4e-27 Score=214.33 Aligned_cols=298 Identities=18% Similarity=0.260 Sum_probs=235.8
Q ss_pred CchhHHHHHHhccCCHHHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhc--------------------------CHHH
Q 048245 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESC--------------------------NESQ 54 (309)
Q Consensus 1 ~~gsr~lq~~l~~~~~e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~--------------------------~~~~ 54 (309)
|-||++||+++.-++..+...+|..+.+++..++.|++|+||+|++++.. -++.
T Consensus 108 qi~Sk~le~l~~f~d~~ql~~ff~~~~g~lr~i~~~r~gshVle~~L~~~a~~vg~e~~~~s~dea~~~ke~p~~t~e~~ 187 (650)
T KOG2188|consen 108 QIGSKVLEDLLGFSDSRQLCDFFSALNGVLRSIAQHRFGSHVLESALEKLAALVGQEAALLSEDEAAVEKEGPFVTCENL 187 (650)
T ss_pred chhHHHHHHHhccCCchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhCccccccchhhhcccccCcccccchH
Confidence 56899999999999999999999999999999999999999999999872 1222
Q ss_pred HHHHHHHHhcccchHH-HhhccccCCHHHHHHHhhhcCCh----h------------------------------H----
Q 048245 55 LALIILKITFQDQLFL-LASVDKFGSSSVKKLIKVVAQSP----P------------------------------L---- 95 (309)
Q Consensus 55 ~~~l~~~l~~~~~~~~-~l~~~~~gs~vlq~ll~~~~~~~----~------------------------------~---- 95 (309)
...+...+. +++. .++.|.+|+||+.+++-.. ... + .
T Consensus 188 ~~~m~nei~---~~~~~~l~~~~~gshv~rt~~l~l-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pqsFp~~l~~~ 263 (650)
T KOG2188|consen 188 LLLMLNEIS---PHVLKTLMELIFGSHVLRTILLLL-FSMCPIAESEHKLALRKAAHRGMDDWDAVTTPPQSFPQRLIVW 263 (650)
T ss_pred HHHHHHHhh---HHHHHHHHHHHHhHHHHHHHHHHH-ccCcchhhhHHHHHHHHHhhccccchhhhhcChhhccHHHHHH
Confidence 344556666 7887 9999999999999998555 210 0 0
Q ss_pred ---------------H----------------HHHHH-HHH----H---------------------------HHhHhhc
Q 048245 96 ---------------L----------------YHVMS-ALK----R---------------------------LFKFLMM 112 (309)
Q Consensus 96 ---------------~----------------~~i~~-~l~----~---------------------------~~~~l~~ 112 (309)
. +.... ... + -...+..
T Consensus 264 i~~~l~~~~~~s~~~~~~~k~~~vDk~~s~v~q~~i~l~~~~~~~~~~~~~~~lv~~~~~~~e~d~~~~kE~~~~k~~l~ 343 (650)
T KOG2188|consen 264 ICTGLSALQDVSESKKRDLKGYEVDKSSSNVLQKAIRLAFDENKNDQFMESPRLVTKFQLFNEKDGLWGKERSFLKELLS 343 (650)
T ss_pred HhhhccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhcchhhhhhhhHHHhhhhccccCcccccccHHHHHHHh
Confidence 0 00000 000 0 0235566
Q ss_pred CCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHHhccC-hHHHHHHHHHHHHhHHhhcc-------
Q 048245 113 TKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMK-GSRRKQILHLISVNAASLSR------- 184 (309)
Q Consensus 113 ~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l~~~~-~~~~~~l~~~l~~~~~~l~~------- 184 (309)
|+.||++++.+++.++++....+...+.+++..++.|+.+..++|+++++.. .++...+++++.+++..+..
T Consensus 344 d~tgSrllE~Imeva~~~~~~lf~~~f~~rl~~La~~p~aNF~lQrli~h~~~~e~v~~v~eeL~P~~~~LL~~g~~gVv 423 (650)
T KOG2188|consen 344 DQTGSRLLEVIMEVASESLLSLFYIVFCGRLDELAVHPIANFPLQRLINHLTSLEDVGSVIEELAPKLSSLLEQGNSGVV 423 (650)
T ss_pred cCcccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhCccccchHHHHHHhccCHHHHHHHHHHHhHHHHHHHHcCCchHh
Confidence 8999999999999999888877777888999999999999999999999987 77788888888777665543
Q ss_pred ----------------------------------------------------------CCChhHHHHHHhhcCChh---h
Q 048245 185 ----------------------------------------------------------HRSGNYVVQHVLNLEDPF---L 203 (309)
Q Consensus 185 ----------------------------------------------------------d~~g~~viq~ll~~~~~~---~ 203 (309)
++.|+.++|.++.+..+- .
T Consensus 424 ~sLia~~~rl~s~q~~~l~~Li~a~~~~~~~~k~il~~lL~~~~~~g~~~~~~~t~~~h~~ga~lle~lv~f~k~~i~~l 503 (650)
T KOG2188|consen 424 ASLIAASARLGSYQDKMLQQLIQAFHAASESKKNILPCLLFSLTLFGCVGEWFLTEKFHQKGAVLLEELVNFSKTHIQTL 503 (650)
T ss_pred HHHHHHHHhhchhHHHHHHHHHHHHhcCChhhcchHHHHHHHhhhcccccccccHHHHhhchhHHHHHHHhhchhhhHHH
Confidence 224555666666654431 2
Q ss_pred HHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH----HHHHHHHhCchHHHHhhcCcChhHHHHHHHhhccCCCcHHH
Q 048245 204 IDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV----HYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSV 279 (309)
Q Consensus 204 ~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~----~~i~~~l~~~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~ 279 (309)
...+.....+++.+++++++||||||.+|...+.. +.++..+-+ .+++|+.+.||++|+.++|+.++. .+
T Consensus 504 itsll~L~~eqi~e~~~~~~~ShlIeavL~S~~l~~~~~~kLi~~l~g--~~~~La~~~~GSrv~eK~wea~~~----~~ 577 (650)
T KOG2188|consen 504 ITSLLSLSEEQILEMSCNGVGSHLIEAVLASKDLGEKIKEKLINILDG--SFVTLALSTFGSRVFEKCWEATDV----LY 577 (650)
T ss_pred HHHHHhhhHHHHHHHhcCCchHHHHHHHHHhccccHHHHHHHHHHhhc--cchheeecCcccHHHHHHHHHhhH----HH
Confidence 33444445578999999999999999999995544 778888776 899999999999999999999998 99
Q ss_pred HHHHHHHHHHHHHhhhcCCCccchhhhcc
Q 048245 280 HQRLVTKLQQHLAALRVMKYGSNKEIQKK 308 (309)
Q Consensus 280 ~~~l~~~l~~~~~~L~~~~~g~~v~~k~~ 308 (309)
|++|+.+|.+.-.+++.++||+.||.+.|
T Consensus 578 k~rIakeL~~~~~~vk~s~~gk~v~~~~~ 606 (650)
T KOG2188|consen 578 KERIAKELVGIHNDVKSSKYGKFVMLNWD 606 (650)
T ss_pred HHHHHHHHHhhccccccCcchHHHHHhcc
Confidence 99999999999999999999999998865
No 12
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=7e-24 Score=190.72 Aligned_cols=284 Identities=17% Similarity=0.207 Sum_probs=184.8
Q ss_pred HHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCHHHHHHHhhhcC-------
Q 048245 19 LDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQ------- 91 (309)
Q Consensus 19 ~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~------- 91 (309)
.+-+|+|+.+..+.+++++.||+++|.++..++..|...++..+. +.++.+++|++||||+|++++.+++
T Consensus 90 ~n~i~ee~~grel~l~tnqi~Sk~le~l~~f~d~~ql~~ff~~~~---g~lr~i~~~r~gshVle~~L~~~a~~vg~e~~ 166 (650)
T KOG2188|consen 90 VNSIFEEVYGRELDLATNQIGSKVLEDLLGFSDSRQLCDFFSALN---GVLRSIAQHRFGSHVLESALEKLAALVGQEAA 166 (650)
T ss_pred ehhHHHHhccceeehhccchhHHHHHHHhccCCchhHHHHHHHHh---hhHHHHHHHHHHHHHHHHHHHHHHHHhCcccc
Confidence 344999999999999999999999999999999999999999999 9999999999999999999976510
Q ss_pred -----------------ChhHHHHHHHHHHHHHh-HhhcCCCchHHHHHHhccCCCc----c------------------
Q 048245 92 -----------------SPPLLYHVMSALKRLFK-FLMMTKPGSSVILKCLEPSYNH----K------------------ 131 (309)
Q Consensus 92 -----------------~~~~~~~i~~~l~~~~~-~l~~~~~gs~vvq~~l~~~~~~----~------------------ 131 (309)
-++...++...+.+++. .+|.|.+|+||++.++...... .
T Consensus 167 ~~s~dea~~~ke~p~~t~e~~~~~m~nei~~~~~~~l~~~~~gshv~rt~~l~l~s~~~~~~~~~~~~~~~~~~~~~~~~ 246 (650)
T KOG2188|consen 167 LLSEDEAAVEKEGPFVTCENLLLLMLNEISPHVLKTLMELIFGSHVLRTILLLLFSMCPIAESEHKLALRKAAHRGMDDW 246 (650)
T ss_pred ccchhhhcccccCcccccchHHHHHHHHhhHHHHHHHHHHHHhHHHHHHHHHHHccCcchhhhHHHHHHHHHhhccccch
Confidence 02233455566888888 9999999999999988643321 0
Q ss_pred -------------hHHHHHHH-----------HHhHHHHhcC--------------------------------------
Q 048245 132 -------------NDFIYQAA-----------LEHCLYLACH-------------------------------------- 149 (309)
Q Consensus 132 -------------~~~l~~~l-----------~~~~~~l~~~-------------------------------------- 149 (309)
...++... ..++...+.+
T Consensus 247 ~~~~~~pqsFp~~l~~~i~~~l~~~~~~s~~~~~~~k~~~vDk~~s~v~q~~i~l~~~~~~~~~~~~~~~lv~~~~~~~e 326 (650)
T KOG2188|consen 247 DAVTTPPQSFPQRLIVWICTGLSALQDVSESKKRDLKGYEVDKSSSNVLQKAIRLAFDENKNDQFMESPRLVTKFQLFNE 326 (650)
T ss_pred hhhhcChhhccHHHHHHHhhhccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhcchhhhhhhhHHHhhhhccc
Confidence 00000000 0123333344
Q ss_pred ------------------ccccHHHHHHHhccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCC-hhhHHHHHHH
Q 048245 150 ------------------EQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLED-PFLIDAICFA 210 (309)
Q Consensus 150 ------------------~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~-~~~~~~i~~~ 210 (309)
+.|||+++.+++.++++....+...+.+.+..|+.++.+|+++|++|++.. ++....|++.
T Consensus 327 ~d~~~~kE~~~~k~~l~d~tgSrllE~Imeva~~~~~~lf~~~f~~rl~~La~~p~aNF~lQrli~h~~~~e~v~~v~ee 406 (650)
T KOG2188|consen 327 KDGLWGKERSFLKELLSDQTGSRLLEVIMEVASESLLSLFYIVFCGRLDELAVHPIANFPLQRLINHLTSLEDVGSVIEE 406 (650)
T ss_pred cCcccccccHHHHHHHhcCcccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhCccccchHHHHHHhccCHHHHHHHHHH
Confidence 445555555555555444433333344455555555555555555555443 4455555555
Q ss_pred HHHhHHHhcc--------------Ccchh---HHHHHHHhcC---CcH-------------------------------H
Q 048245 211 LRGHYVDLSL--------------TKCGS---FVVQKFLKYQ---NAV-------------------------------H 239 (309)
Q Consensus 211 l~~~~~~l~~--------------~~~gs---~vve~~l~~~---~~~-------------------------------~ 239 (309)
+.+++-.|-. .++|| .+++.++... ++. .
T Consensus 407 L~P~~~~LL~~g~~gVv~sLia~~~rl~s~q~~~l~~Li~a~~~~~~~~k~il~~lL~~~~~~g~~~~~~~t~~~h~~ga 486 (650)
T KOG2188|consen 407 LAPKLSSLLEQGNSGVVASLIAASARLGSYQDKMLQQLIQAFHAASESKKNILPCLLFSLTLFGCVGEWFLTEKFHQKGA 486 (650)
T ss_pred HhHHHHHHHHcCCchHhHHHHHHHHhhchhHHHHHHHHHHHHhcCChhhcchHHHHHHHhhhcccccccccHHHHhhchh
Confidence 5443222111 11111 1111111100 000 0
Q ss_pred HHHHHHhC-----------------chHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCccc
Q 048245 240 YIVEELLN-----------------SDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSN 302 (309)
Q Consensus 240 ~i~~~l~~-----------------~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~~ 302 (309)
.++++++. ..++.+++.+++|++||+.+++..+-. +..++++++.|.++..+|+.+.||||
T Consensus 487 ~lle~lv~f~k~~i~~litsll~L~~eqi~e~~~~~~~ShlIeavL~S~~l~--~~~~~kLi~~l~g~~~~La~~~~GSr 564 (650)
T KOG2188|consen 487 VLLEELVNFSKTHIQTLITSLLSLSEEQILEMSCNGVGSHLIEAVLASKDLG--EKIKEKLINILDGSFVTLALSTFGSR 564 (650)
T ss_pred HHHHHHHhhchhhhHHHHHHHHhhhHHHHHHHhcCCchHHHHHHHHHhcccc--HHHHHHHHHHhhccchheeecCcccH
Confidence 01111111 348999999999999999999995442 28999999999999999999999999
Q ss_pred hhhhc
Q 048245 303 KEIQK 307 (309)
Q Consensus 303 v~~k~ 307 (309)
|++|.
T Consensus 565 v~eK~ 569 (650)
T KOG2188|consen 565 VFEKC 569 (650)
T ss_pred HHHHH
Confidence 99985
No 13
>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]
Probab=99.74 E-value=8.8e-18 Score=155.12 Aligned_cols=277 Identities=18% Similarity=0.222 Sum_probs=226.8
Q ss_pred HHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCHHHHHHHhhhcCChhHH
Q 048245 17 RILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLL 96 (309)
Q Consensus 17 e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~ 96 (309)
.+.+.+.-+..++..++..|--||.|+|+++++++...++..+.... .++..+..|++|.+..|++++.+ -++.+.
T Consensus 535 pEied~ai~mLDe~~elsSdylGNtVvqkfFe~sS~~ik~aml~r~s---~ylts~gvHknGtw~~qk~ik~a-~te~qi 610 (1007)
T KOG4574|consen 535 PEIEDLAILMLDELPELSSDYLGNTVVQKFFELSSDIIKDAMLRRGS---KYLTSMGVHKNGTWACQKIIKMA-FTERQI 610 (1007)
T ss_pred hhHHHHHHHHhccCCcchhhhhcchhhHHHHhhccHHHHHHHHhhhh---hhhhhccccccchHHHHHHHHHh-hchhhh
Confidence 35555555666778889999999999999999999999999999999 99999999999999999999999 888889
Q ss_pred HHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHHhccC--hHHHHHHHHH
Q 048245 97 YHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMK--GSRRKQILHL 174 (309)
Q Consensus 97 ~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l~~~~--~~~~~~l~~~ 174 (309)
..+...+.+....++.|.|||||+|.+|...- ....++++....+++++....||++.+.+|++... .++....+..
T Consensus 611 k~iv~g~dpyc~~l~~dqfgnyvaqd~LkF~f-p~nsFVfE~v~s~~~~ivQsrfGsravrAcle~lNa~~e~qsl~~~s 689 (1007)
T KOG4574|consen 611 KLIVRGVDPYCTPLLNDQFGNYVAQDSLKFGF-PWNSFVFESVFSHFWDIVQSRFGSRAVRACLEALNANTEDQSLVRES 689 (1007)
T ss_pred heeeeccCcchhhHHHHhhcceeeeeehhccC-ccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhccCchhhhhhhhh
Confidence 99998899999999999999999999998743 36677889999999999999999999999998753 2333222233
Q ss_pred -HHHhHHhhccCCChhHHHHHHhhcCChhhHH-HHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH---HHHHHHHhC--
Q 048245 175 -ISVNAASLSRHRSGNYVVQHVLNLEDPFLID-AICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV---HYIVEELLN-- 247 (309)
Q Consensus 175 -l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~-~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~---~~i~~~l~~-- 247 (309)
+......+..+..|-..|.++++.+....+. .++..+.++++.+|+|+-|+-++.++++.+.+. +.|++.|+.
T Consensus 690 ~iIs~ss~latnsng~llvtw~lDns~~~nrh~~l~~~lt~el~~lC~h~Lgsttv~Kl~n~~qepvs~ekii~hlf~~~ 769 (1007)
T KOG4574|consen 690 CIISKSSYLATNSNGLLLVTWLLDNSSLPNRHTILAHGLTKELVMLCFHKLGSTTVLKLLNLRQEPVSREKIIEHLFHLR 769 (1007)
T ss_pred hhhhchhhhhhcCccceeeeeecccccccchhhHHhhhhhhccchhhhhhccchhhhhhhhcCCChHHHHHHHHHHhhcc
Confidence 4455778889999999999999987554444 445578899999999999999999999999887 788888874
Q ss_pred --------------------------chHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCcc
Q 048245 248 --------------------------SDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGS 301 (309)
Q Consensus 248 --------------------------~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~ 301 (309)
.+.+.....|+++++|.|.++...-.. -.++ +.|...+.-++.++||+
T Consensus 770 n~kd~~lt~Vl~~~~~gpmfiikvi~~p~iel~f~dQf~kvvrq~il~~~a~~-----narv-~~LleevgliSasksgs 843 (1007)
T KOG4574|consen 770 NFKDSALTEVLTEANYGPMFIIKVITKPTIELAFRDQFIKVVRQVILNSPAVS-----NARV-QRLLEEVGLISASKSGS 843 (1007)
T ss_pred ccccchhhhhhhhhccccceeeeeeccccchHHHHHHHHHHHHHHHHhcCCcc-----HHHH-HHHHHHHhhhccccchh
Confidence 235556668999999999999877652 2222 56666667777888887
Q ss_pred chh
Q 048245 302 NKE 304 (309)
Q Consensus 302 ~v~ 304 (309)
+-+
T Consensus 844 ~s~ 846 (1007)
T KOG4574|consen 844 QSI 846 (1007)
T ss_pred HHH
Confidence 644
No 14
>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]
Probab=99.29 E-value=1.4e-12 Score=121.21 Aligned_cols=198 Identities=21% Similarity=0.229 Sum_probs=158.0
Q ss_pred hHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHHhccC-hHHHHHHH
Q 048245 94 PLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMK-GSRRKQIL 172 (309)
Q Consensus 94 ~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l~~~~-~~~~~~l~ 172 (309)
+..+.... +.+...++-.|-.|+.|+|++++..+..-++.........+..+..|++|+++.|++++.+. +.+.+.++
T Consensus 536 Eied~ai~-mLDe~~elsSdylGNtVvqkfFe~sS~~ik~aml~r~s~ylts~gvHknGtw~~qk~ik~a~te~qik~iv 614 (1007)
T KOG4574|consen 536 EIEDLAIL-MLDELPELSSDYLGNTVVQKFFELSSDIIKDAMLRRGSKYLTSMGVHKNGTWACQKIIKMAFTERQIKLIV 614 (1007)
T ss_pred hHHHHHHH-HhccCCcchhhhhcchhhHHHHhhccHHHHHHHHhhhhhhhhhccccccchHHHHHHHHHhhchhhhheee
Confidence 33333333 67778888899999999999999988888888888888899999999999999999999975 44555566
Q ss_pred HHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH---HHHHHHH----
Q 048245 173 HLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV---HYIVEEL---- 245 (309)
Q Consensus 173 ~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~---~~i~~~l---- 245 (309)
.-..+.+..++.|+|||||+|..|+.+-|. ...|++....++.++...+||++-+.+|++..... +.++.+-
T Consensus 615 ~g~dpyc~~l~~dqfgnyvaqd~LkF~fp~-nsFVfE~v~s~~~~ivQsrfGsravrAcle~lNa~~e~qsl~~~s~iIs 693 (1007)
T KOG4574|consen 615 RGVDPYCTPLLNDQFGNYVAQDSLKFGFPW-NSFVFESVFSHFWDIVQSRFGSRAVRACLEALNANTEDQSLVRESCIIS 693 (1007)
T ss_pred eccCcchhhHHHHhhcceeeeeehhccCcc-chHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhccCchhhhhhhhhhhhh
Confidence 667789999999999999999999988764 46778999999999999999999999999887664 2221111
Q ss_pred ------------------hC---------------chHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHH
Q 048245 246 ------------------LN---------------SDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLA 292 (309)
Q Consensus 246 ------------------~~---------------~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~ 292 (309)
+. .+++..+|.|.-|+-+++++++.+.+ .. ..+.+.+|+.
T Consensus 694 ~ss~latnsng~llvtw~lDns~~~nrh~~l~~~lt~el~~lC~h~Lgsttv~Kl~n~~qe----pv---s~ekii~hlf 766 (1007)
T KOG4574|consen 694 KSSYLATNSNGLLLVTWLLDNSSLPNRHTILAHGLTKELVMLCFHKLGSTTVLKLLNLRQE----PV---SREKIIEHLF 766 (1007)
T ss_pred chhhhhhcCccceeeeeecccccccchhhHHhhhhhhccchhhhhhccchhhhhhhhcCCC----hH---HHHHHHHHHh
Confidence 00 34788889999999999999999888 44 5556667777
Q ss_pred hhhcCCCc
Q 048245 293 ALRVMKYG 300 (309)
Q Consensus 293 ~L~~~~~g 300 (309)
.+.+++-|
T Consensus 767 ~~~n~kd~ 774 (1007)
T KOG4574|consen 767 HLRNFKDS 774 (1007)
T ss_pred hccccccc
Confidence 77777666
No 15
>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains. The FBF-2 protein of Caenorhabditis elegans also has a Puf domain. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs [, ]. The same type of repetitive domain has been found in in a number of other proteins from all eukaryotic kingdoms. The Puf proteins characterised to date have been reported to bind to 3'-untranslated region (UTR) sequences encompassing a so-called UGUR tetranucleotide motif and thereby to repress gene expression by affecting mRNA translation or stability. In Saccharomyces cerevisiae (Baker's yeast), five proteins, termed Puf1p to Puf5p, bear six to eight Puf repeats []. Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. This suggests the existence of an extensive network of RNA-protein interactions that coordinate the post-transcriptional fate of large sets of cytotopically and functionally related RNAs through each stage of its lifecycle.; GO: 0003723 RNA binding; PDB: 3BX2_A 4DZS_B 3BX3_B 3BWT_A 3GVT_B 3GVO_A 1IB2_A 3Q0N_A 2YJY_A 1M8Z_A ....
Probab=98.58 E-value=4.9e-08 Score=56.21 Aligned_cols=35 Identities=34% Similarity=0.532 Sum_probs=31.2
Q ss_pred HHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHH
Q 048245 25 VVSGFTFELMSGQYGRFVFGKFIESCNESQLALII 59 (309)
Q Consensus 25 el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~ 59 (309)
++.|++.+|+.|+|||||+|++++.++++++..++
T Consensus 1 ~i~~~~~~l~~d~~Gn~VvQk~le~~~~~~~~~il 35 (35)
T PF00806_consen 1 EIKGNLVELSKDQYGNYVVQKCLEHASPEQRQLIL 35 (35)
T ss_dssp CHTTTHHHHHTSTTHHHHHHHHHHHSSHHHHHHHH
T ss_pred ChHHHHHHHHhccccCHHHHHHHHHCCHHHHHhhC
Confidence 36789999999999999999999999999887764
No 16
>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains. The FBF-2 protein of Caenorhabditis elegans also has a Puf domain. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs [, ]. The same type of repetitive domain has been found in in a number of other proteins from all eukaryotic kingdoms. The Puf proteins characterised to date have been reported to bind to 3'-untranslated region (UTR) sequences encompassing a so-called UGUR tetranucleotide motif and thereby to repress gene expression by affecting mRNA translation or stability. In Saccharomyces cerevisiae (Baker's yeast), five proteins, termed Puf1p to Puf5p, bear six to eight Puf repeats []. Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. This suggests the existence of an extensive network of RNA-protein interactions that coordinate the post-transcriptional fate of large sets of cytotopically and functionally related RNAs through each stage of its lifecycle.; GO: 0003723 RNA binding; PDB: 3BX2_A 4DZS_B 3BX3_B 3BWT_A 3GVT_B 3GVO_A 1IB2_A 3Q0N_A 2YJY_A 1M8Z_A ....
Probab=98.50 E-value=1.1e-07 Score=54.64 Aligned_cols=31 Identities=29% Similarity=0.616 Sum_probs=26.2
Q ss_pred HHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHH
Q 048245 250 QILQVASDKYGNYVIQTALVETMRQDRLSVHQRLV 284 (309)
Q Consensus 250 ~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~ 284 (309)
++.+|+.|+|||||||++|+.+++ ..++.|+
T Consensus 5 ~~~~l~~d~~Gn~VvQk~le~~~~----~~~~~il 35 (35)
T PF00806_consen 5 NLVELSKDQYGNYVVQKCLEHASP----EQRQLIL 35 (35)
T ss_dssp THHHHHTSTTHHHHHHHHHHHSSH----HHHHHHH
T ss_pred HHHHHHhccccCHHHHHHHHHCCH----HHHHhhC
Confidence 889999999999999999999776 6666653
No 17
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=98.16 E-value=1.8e-06 Score=49.79 Aligned_cols=34 Identities=41% Similarity=0.579 Sum_probs=30.3
Q ss_pred HHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHH
Q 048245 26 VSGFTFELMSGQYGRFVFGKFIESCNESQLALII 59 (309)
Q Consensus 26 l~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~ 59 (309)
+.+++.+|+.|++||+|+|++++.+++.++..++
T Consensus 2 ~~~~~~~l~~~~~g~~viqk~l~~~~~~~~~~i~ 35 (36)
T smart00025 2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35 (36)
T ss_pred chHHHHHHHhcchhhHHHHHHHHHCCHHHHHHhh
Confidence 4688999999999999999999999998887765
No 18
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=98.07 E-value=3e-06 Score=48.86 Aligned_cols=32 Identities=28% Similarity=0.584 Sum_probs=26.2
Q ss_pred hHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHH
Q 048245 249 DQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLV 284 (309)
Q Consensus 249 ~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~ 284 (309)
+++.+|+.|+|||||+|++++.++. ..++.++
T Consensus 4 ~~~~~l~~~~~g~~viqk~l~~~~~----~~~~~i~ 35 (36)
T smart00025 4 GHLLELSKDQYGNRVVQKLLEHASE----SQREQII 35 (36)
T ss_pred HHHHHHHhcchhhHHHHHHHHHCCH----HHHHHhh
Confidence 3788999999999999999999887 6666654
No 19
>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats [].; GO: 0003723 RNA binding
Probab=94.67 E-value=0.072 Score=41.37 Aligned_cols=66 Identities=11% Similarity=0.146 Sum_probs=45.9
Q ss_pred HHHHHHHhHHHhccCcchhHHHHHHHhcCCcH-----HHHHHHHhCc------hHHHHhhcCcChhHHHHHHHhhcc
Q 048245 207 ICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV-----HYIVEELLNS------DQILQVASDKYGNYVIQTALVETM 272 (309)
Q Consensus 207 i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~-----~~i~~~l~~~------~~l~~L~~d~~g~~Viq~~l~~~~ 272 (309)
+++.+..+..+|.+++.||.++-.+|..++.+ +.|++.+..+ +.=..+..+++|++++-++++...
T Consensus 58 Ll~~i~~~~~~ll~~~~g~~~i~eiL~~~~gdk~~a~~Aia~~~~~~~~~~~~~~e~H~i~~p~~~r~lK~Liq~~~ 134 (148)
T PF08144_consen 58 LLEAIAENAEELLSSSFGCQFITEILLSATGDKSAALEAIASLAAEPLFPGDIDEEYHLIEHPFGHRMLKKLIQGDK 134 (148)
T ss_pred HHHHHHHhHHHHHhcCcccHHHHHHHhccCccHHHHHHHHHHHHhhccCCCCCcCccchhcCchHHHHHHHHHHCCC
Confidence 34445566778999999999999999887544 3344333331 012357789999999999998765
No 20
>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats [].; GO: 0003723 RNA binding
Probab=87.50 E-value=2.6 Score=32.74 Aligned_cols=31 Identities=19% Similarity=0.313 Sum_probs=18.4
Q ss_pred HHHHHHHhHHHHhcCccccHHHHHHHhccCh
Q 048245 135 IYQAALEHCLYLACHEQGCINLNNFIDNMKG 165 (309)
Q Consensus 135 l~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~ 165 (309)
+++.+..+...+..+..||.++..++..+..
T Consensus 58 Ll~~i~~~~~~ll~~~~g~~~i~eiL~~~~g 88 (148)
T PF08144_consen 58 LLEAIAENAEELLSSSFGCQFITEILLSATG 88 (148)
T ss_pred HHHHHHHhHHHHHhcCcccHHHHHHHhccCc
Confidence 4444445566666666666666666666543
No 21
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=86.40 E-value=24 Score=31.57 Aligned_cols=159 Identities=13% Similarity=0.065 Sum_probs=74.5
Q ss_pred CHHHHHHHHHHHHhhHHHhc-cCcchhHHHHHHHhh-cCHHHHHHHHHHHhcccc--hHHHhhccccCCHHHHHHHhhhc
Q 048245 15 DSRILDKLFWVVSGFTFELM-SGQYGRFVFGKFIES-CNESQLALIILKITFQDQ--LFLLASVDKFGSSSVKKLIKVVA 90 (309)
Q Consensus 15 ~~e~~~~i~~el~~~~~~L~-~~~~g~~vlq~li~~-~~~~~~~~l~~~l~~~~~--~~~~l~~~~~gs~vlq~ll~~~~ 90 (309)
+++.++.++.+....+..-. ...-|.-.+..+++. .+++.-+.++..+....+ .+..+. ......++.++..-
T Consensus 56 s~~~~~~vL~ef~~~~~~~~~~~~gg~~~~~~iL~~~l~~~~a~~il~~i~~~~~~~~fe~L~--~ld~~~l~~lL~~E- 132 (339)
T PRK05686 56 SPEQVEAVLEEFEDEFEAGAYILMGGIDYARSLLEKALGEEKADSILERILESLGTSGFDFLR--KMDPQQLANFIRNE- 132 (339)
T ss_pred CHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHcCHHHHHHHHHHHhccccCchHHHHh--cCCHHHHHHHHHhc-
Confidence 45555555555555544322 233455557777774 666667778877763221 222221 22445555555554
Q ss_pred CChhHHHHHHHHHHHH----HhHhhcCCCchHHHHHHhccC--CCcchHHHHHHHHHhHHHHh----cCccccHHHHHHH
Q 048245 91 QSPPLLYHVMSALKRL----FKFLMMTKPGSSVILKCLEPS--YNHKNDFIYQAALEHCLYLA----CHEQGCINLNNFI 160 (309)
Q Consensus 91 ~~~~~~~~i~~~l~~~----~~~l~~~~~gs~vvq~~l~~~--~~~~~~~l~~~l~~~~~~l~----~~~~gs~vvq~~l 160 (309)
+++....+...+.+. +...+......-|+.++.... +++....+-+.+...+.... ...-|...+-.++
T Consensus 133 -hpqtiA~iLs~l~~~~aa~vL~~l~~~~~~~v~~ria~l~~v~~~~~~~i~~~L~~~l~~~~~~~~~~~~g~~~~a~Il 211 (339)
T PRK05686 133 -HPQTIALILSYLKPDQAAEILSLLPEELRADVMMRIATLEGVSPEALKEVEEVLEKKLSSMANADRTKMGGVKTVAEIL 211 (339)
T ss_pred -CHHHHHHHHhCCCHHHHHHHHHhCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHhhcccccccccCcHHHHHHHH
Confidence 444444444433332 222222233333344433321 12222222233333333211 2334556677777
Q ss_pred hccChHHHHHHHHHHHH
Q 048245 161 DNMKGSRRKQILHLISV 177 (309)
Q Consensus 161 ~~~~~~~~~~l~~~l~~ 177 (309)
...+......++..|..
T Consensus 212 n~~~~~~~~~il~~L~~ 228 (339)
T PRK05686 212 NNLDRQTEKTILESLEE 228 (339)
T ss_pred hcCCchHHHHHHHHHHh
Confidence 77776666666666553
No 22
>PF11510 FA_FANCE: Fanconi Anaemia group E protein FANCE; InterPro: IPR021025 Fanconi Anaemia (FA) is a cancer predisposition disorder characterised by chromosome fragility and hypersensitivity to genotoxic agents that suggest defects in the molecular mechanisms of DNA damage signalling and repair. In response to DNA damage, the FA core complex monoubiquitinates the FANCD2 protein. This ubiquitination targets FANCD2 to nuclear foci where it interacts with a variety of DNA repair proteins. The FA group E protein (FANCE) has an important role in DNA repair, functioning as the FANCD2-binding protein in the FA core complex []. This entry represents the C-terminal domain of FANCE, which consists predominantly of helices and does not contain any beta-strands. This domain folds in a continuous right-handed solenoidal pattern from its N terminus to its C terminus. ; PDB: 2ILR_A.
Probab=80.35 E-value=37 Score=29.14 Aligned_cols=108 Identities=12% Similarity=0.101 Sum_probs=43.6
Q ss_pred chHHHhhccccCCHHHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCC-CchH---HHHHHh--ccCCCcchHHHHHHHH
Q 048245 67 QLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTK-PGSS---VILKCL--EPSYNHKNDFIYQAAL 140 (309)
Q Consensus 67 ~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~-~gs~---vvq~~l--~~~~~~~~~~l~~~l~ 140 (309)
+.+..+ ..-+||++...+..+ ....-...+...+.| ++.++ .|+. ++-+++ +.++++.+..++..+.
T Consensus 98 pkilsL--~~~ASR~L~sal~~f-~k~~p~~~~~all~P----lL~~~~~g~~Q~eLl~rlvk~~~l~p~~~~l~l~~~L 170 (263)
T PF11510_consen 98 PKILSL--EEPASRLLVSALTSF-CKKYPRPVCEALLVP----LLQAPGLGPPQCELLCRLVKKECLEPDHRLLLLRQIL 170 (263)
T ss_dssp HHHHH---SS---HHHHHHHHHH-HHHSHHHHHHHHHHH----HHHSTT--HHHHHHHHHHHH-TTS-HHHHHHHHHHHH
T ss_pred HHHHhc--CCCccHHHHHHHHHH-HHhCcHHHHHHHHHH----HHcCCCCCHHHHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence 555555 456788776665544 222222222222333 23332 3333 566666 4455666665555544
Q ss_pred HhHHHHhcCccccHHHHHHHhccC---hHHHHHHHHHHHHhHHhhccC
Q 048245 141 EHCLYLACHEQGCINLNNFIDNMK---GSRRKQILHLISVNAASLSRH 185 (309)
Q Consensus 141 ~~~~~l~~~~~gs~vvq~~l~~~~---~~~~~~l~~~l~~~~~~l~~d 185 (309)
+- .-+..-..|+|.+++... ++....++..+..+...+++|
T Consensus 171 ~~----~W~E~~~~Vlq~lL~~k~~l~~~~~~~l~~~L~~~a~~~skS 214 (263)
T PF11510_consen 171 EL----VWNEETFLVLQSLLERKVELSQELFSLLVELLCEQAPQFSKS 214 (263)
T ss_dssp HS-------HHHHHHHHHHHTT-----HHHHHHHHHHHH--------S
T ss_pred hC----cCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhhHhhhcc
Confidence 32 222333458888887653 333344555565555555555
No 23
>PF08625 Utp13: Utp13 specific WD40 associated domain; InterPro: IPR013934 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp13 is a nucleolar protein and component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA []. Upt13 is also a component of the Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome []. Components of the Pwp2 complex are: Utp1 (Pwp2), Utp6, Utp12 (Dip2), Utp13, Utp18, and Utp21. The relationship between the Pwp2 complex and the t-Utps complex [] that also associates with the 5' end of nascent pre-18S rRNA is unclear. ; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=74.47 E-value=37 Score=26.09 Aligned_cols=51 Identities=14% Similarity=0.143 Sum_probs=26.9
Q ss_pred hhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH
Q 048245 188 GNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV 238 (309)
Q Consensus 188 g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~ 238 (309)
|+..+..++...++.....+++..+++-..--....|..|+-.+|...+++
T Consensus 47 g~~~l~~~i~~L~~~~l~~LL~~ir~WNTNsr~~~vAQ~vL~~il~~~~~~ 97 (141)
T PF08625_consen 47 GSEELDEVIKKLDDEQLEKLLRFIRDWNTNSRTSHVAQRVLNAILKSHPPE 97 (141)
T ss_pred hHHHHHHHHHhcCHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHhCCHH
Confidence 555666666655555555555555554433333334445555555555543
No 24
>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]
Probab=62.27 E-value=1.5e+02 Score=28.28 Aligned_cols=117 Identities=9% Similarity=-0.055 Sum_probs=75.7
Q ss_pred HHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHHhccChHHHHHHHH------------
Q 048245 106 LFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH------------ 173 (309)
Q Consensus 106 ~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~------------ 173 (309)
.+..+.+.+..-..+-.++..++...+.++++.++.++..++.++.+.+-+-+++....+++.-.+-.
T Consensus 55 g~~~~s~~~l~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~e~kmal~el~q~y~en~n~~l~~lWer~ve~dfnDvv~ 134 (711)
T COG1747 55 GIISLSKQLLDDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYGESKMALLELLQCYKENGNEQLYSLWERLVEYDFNDVVI 134 (711)
T ss_pred HHHHhhhccccchHHHHHHHHhccchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhcCchhhHHHHHHHHHhcchhHHH
Confidence 35556666666667778888888889999999999999999999988887777765544443222222
Q ss_pred --HHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcc
Q 048245 174 --LISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKC 223 (309)
Q Consensus 174 --~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~ 223 (309)
++...... +..+-......+++.+.-|.....-++.+++.++++..+..
T Consensus 135 ~ReLa~~yEk-ik~sk~a~~f~Ka~yrfI~~~q~~~i~evWeKL~~~i~dD~ 185 (711)
T COG1747 135 GRELADKYEK-IKKSKAAEFFGKALYRFIPRRQNAAIKEVWEKLPELIGDDK 185 (711)
T ss_pred HHHHHHHHHH-hchhhHHHHHHHHHHHhcchhhhhhHHHHHHHHHHhccccH
Confidence 22222223 44445555666666665565555666677777777554443
No 25
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=62.09 E-value=67 Score=24.28 Aligned_cols=44 Identities=11% Similarity=0.073 Sum_probs=28.8
Q ss_pred HHHHHHHhccChHHHHHHHHH-HHHhHHhhccCCChhH-HHHHHhh
Q 048245 154 INLNNFIDNMKGSRRKQILHL-ISVNAASLSRHRSGNY-VVQHVLN 197 (309)
Q Consensus 154 ~vvq~~l~~~~~~~~~~l~~~-l~~~~~~l~~d~~g~~-viq~ll~ 197 (309)
.+++.|+++|.......+.+. +...+..++.+++... |-+++++
T Consensus 59 ~lLe~~vkNcg~~f~~ev~s~~fl~~L~~l~~~~~~~~~Vk~kil~ 104 (133)
T smart00288 59 TLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKYPLPLVKKRILE 104 (133)
T ss_pred HHHHHHHHHCCHHHHHHHHhHHHHHHHHHHHcCCCCcHHHHHHHHH
Confidence 477788888877666666544 6677777777776654 4444443
No 26
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=52.78 E-value=2.6e+02 Score=28.26 Aligned_cols=86 Identities=14% Similarity=0.082 Sum_probs=48.1
Q ss_pred CChhHHHHHHhhcCCh---hhHHHHHHH-HHHhHHHhccC-cchhHHHHHHHhcCCcH-H--HHHHHHhCchHHHHh---
Q 048245 186 RSGNYVVQHVLNLEDP---FLIDAICFA-LRGHYVDLSLT-KCGSFVVQKFLKYQNAV-H--YIVEELLNSDQILQV--- 254 (309)
Q Consensus 186 ~~g~~viq~ll~~~~~---~~~~~i~~~-l~~~~~~l~~~-~~gs~vve~~l~~~~~~-~--~i~~~l~~~~~l~~L--- 254 (309)
||+-.++..+++...+ +.-..++.. +.+++.+..-+ +---++++.+++.++.. . .-+.-+++ .+..|
T Consensus 657 PYvfQlla~lve~~~~~ip~~~~~l~~~lLsp~lW~r~gNipalvrLl~aflk~g~~~~~~~~~l~~iLG--ifqkLiaS 734 (960)
T KOG1992|consen 657 PYVFQLLAVLVEHSSGTIPDSYSPLFPPLLSPNLWKRSGNIPALVRLLQAFLKTGSQIVEAADKLSGILG--IFQKLIAS 734 (960)
T ss_pred HHHHHHHHHHHHhcCCCCchhHHHHHHHhcCHHHHhhcCCcHHHHHHHHHHHhcCchhhcccccchhHHH--HHHHHhcC
Confidence 5666666667775543 223333332 23343332211 22246788888777654 1 22233333 33333
Q ss_pred -hcCcChhHHHHHHHhhccC
Q 048245 255 -ASDKYGNYVIQTALVETMR 273 (309)
Q Consensus 255 -~~d~~g~~Viq~~l~~~~~ 273 (309)
+.|.+|=|.+++++..-+.
T Consensus 735 ka~Dh~GF~LLn~i~~~~~~ 754 (960)
T KOG1992|consen 735 KANDHHGFYLLNTIIESIPP 754 (960)
T ss_pred cccchhHHHHHHHHHhcCCH
Confidence 4689999999999998876
No 27
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=50.41 E-value=2.9e+02 Score=28.01 Aligned_cols=142 Identities=12% Similarity=0.076 Sum_probs=74.0
Q ss_pred HHHHHHHhcccchHHHhhccccCCHHHHHHHhhh--------cCChhHHHHHHHHH--------HHHHhHhhcCCCchHH
Q 048245 56 ALIILKITFQDQLFLLASVDKFGSSSVKKLIKVV--------AQSPPLLYHVMSAL--------KRLFKFLMMTKPGSSV 119 (309)
Q Consensus 56 ~~l~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~--------~~~~~~~~~i~~~l--------~~~~~~l~~~~~gs~v 119 (309)
..++..+. .-+...++++-.++.=..+++.. ..++.....+...+ .+++.+++ ||+=.+
T Consensus 588 ~~~l~~Lt---eiv~~v~KNPs~P~fnHYLFEsi~~li~~t~~~~~~~vs~~e~aL~p~fq~Il~eDI~Efi--PYvfQl 662 (960)
T KOG1992|consen 588 PELLRQLT---EIVEEVSKNPSNPQFNHYLFESIGLLIRKTCKANPSAVSSLEEALFPVFQTILSEDIQEFI--PYVFQL 662 (960)
T ss_pred hHHHHHHH---HHHHHHhcCCCCchhHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHH
Confidence 45555565 66666666666655544444433 01222222222222 23333332 444444
Q ss_pred HHHHhccCCC---cchHHHHHHHH-HhHHHHhcCc-cccHHHHHHHhccChHHH-HHHHHHHHHhHHhh----ccCCChh
Q 048245 120 ILKCLEPSYN---HKNDFIYQAAL-EHCLYLACHE-QGCINLNNFIDNMKGSRR-KQILHLISVNAASL----SRHRSGN 189 (309)
Q Consensus 120 vq~~l~~~~~---~~~~~l~~~l~-~~~~~l~~~~-~gs~vvq~~l~~~~~~~~-~~l~~~l~~~~~~l----~~d~~g~ 189 (309)
+--+++...+ +....++..+. +++|+..-+- .-.++++.+++.++.... ..-+.-+.+.+..+ +.|.+|-
T Consensus 663 la~lve~~~~~ip~~~~~l~~~lLsp~lW~r~gNipalvrLl~aflk~g~~~~~~~~~l~~iLGifqkLiaSka~Dh~GF 742 (960)
T KOG1992|consen 663 LAVLVEHSSGTIPDSYSPLFPPLLSPNLWKRSGNIPALVRLLQAFLKTGSQIVEAADKLSGILGIFQKLIASKANDHHGF 742 (960)
T ss_pred HHHHHHhcCCCCchhHHHHHHHhcCHHHHhhcCCcHHHHHHHHHHHhcCchhhcccccchhHHHHHHHHhcCcccchhHH
Confidence 5555555443 34444544433 4555544432 344688888888753222 12233344555444 4688999
Q ss_pred HHHHHHhhcCChh
Q 048245 190 YVVQHVLNLEDPF 202 (309)
Q Consensus 190 ~viq~ll~~~~~~ 202 (309)
++++++++.-++.
T Consensus 743 ~LLn~i~~~~~~~ 755 (960)
T KOG1992|consen 743 YLLNTIIESIPPN 755 (960)
T ss_pred HHHHHHHhcCCHh
Confidence 9999999987665
No 28
>PF12231 Rif1_N: Rap1-interacting factor 1 N terminal; InterPro: IPR022031 This domain family is found in eukaryotes, and is typically between 135 and 146 amino acids in length. Rif1 is a protein which interacts with Rap1 to regulate telomere length. Interaction with telomeres limits their length. The N-terminal region contains many HEAT- and ARMADILLO- type repeats. These are helical folds which form extended curved proteins or RNA interface surfaces.
Probab=46.80 E-value=2.2e+02 Score=25.75 Aligned_cols=69 Identities=13% Similarity=-0.130 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhHHhhcc---CCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCc
Q 048245 168 RKQILHLISVNAASLSR---HRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNA 237 (309)
Q Consensus 168 ~~~l~~~l~~~~~~l~~---d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~ 237 (309)
+..++..+..+...... +.+..+++..++.... ..+...+....+--..+..++.-+..+..+++....
T Consensus 154 rL~i~~~ll~q~p~~M~~~~~~W~~~l~~~l~~~~k-~ir~~a~~l~~~~~~~l~~~~~~s~~~~~~~~~~~~ 225 (372)
T PF12231_consen 154 RLNIYKRLLSQFPQQMIKHADIWFPILFPDLLSSAK-DIRTKAISLLLEAKKCLGPNKELSKSVLEDLQRSLE 225 (372)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcch-HHHHHHHHHHHHHHHHhChhHHHHHHHHHHhccccc
Confidence 44444444444433222 1234466777776433 334444433333333444555556666666554443
No 29
>COG4399 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.74 E-value=2.2e+02 Score=25.56 Aligned_cols=16 Identities=19% Similarity=0.160 Sum_probs=6.8
Q ss_pred cChHHHHHHHHHHHHh
Q 048245 163 MKGSRRKQILHLISVN 178 (309)
Q Consensus 163 ~~~~~~~~l~~~l~~~ 178 (309)
.+.+..+.++-++..+
T Consensus 334 fs~~~lE~lV~~Is~k 349 (376)
T COG4399 334 FSLERLEKLVLEISRK 349 (376)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 3444444444444433
No 30
>PF14666 RICTOR_M: Rapamycin-insensitive companion of mTOR, middle domain
Probab=44.55 E-value=1.4e+02 Score=25.04 Aligned_cols=74 Identities=14% Similarity=0.063 Sum_probs=37.3
Q ss_pred HHHHHHHhHHHHhcCccccHHHHHH------HhccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHH
Q 048245 135 IYQAALEHCLYLACHEQGCINLNNF------IDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAIC 208 (309)
Q Consensus 135 l~~~l~~~~~~l~~~~~gs~vvq~~------l~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~ 208 (309)
+...+..-+..++.++.|-.++++. .+.+....+..++..+.+++ +...|...-.+++++|..++...|-.-.
T Consensus 139 l~~~Yf~~IG~lS~~~~Gl~lLe~~~if~~l~~i~~~~~~~~l~klil~~L-DY~~~~~~R~iLsKaLt~~s~~iRl~aT 217 (226)
T PF14666_consen 139 LSRGYFLFIGVLSSTPNGLKLLERWNIFTMLYHIFSLSSRDDLLKLILSSL-DYSVDGHPRIILSKALTSGSESIRLYAT 217 (226)
T ss_pred HHHHHHHHHHHHhCChhHHHHHHHCCHHHHHHHHHccCchHHHHHHHHhhC-CCCCccHHHHHHHHHHhcCCHHHHHHHH
Confidence 3344445577888888887666531 12222223344444444433 3334445556666666655554443333
Q ss_pred H
Q 048245 209 F 209 (309)
Q Consensus 209 ~ 209 (309)
+
T Consensus 218 ~ 218 (226)
T PF14666_consen 218 K 218 (226)
T ss_pred H
Confidence 3
No 31
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=43.39 E-value=2.4e+02 Score=25.17 Aligned_cols=93 Identities=16% Similarity=0.172 Sum_probs=52.6
Q ss_pred CCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCc------H-HHHHHHHhCchHHHHhhcC
Q 048245 185 HRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNA------V-HYIVEELLNSDQILQVASD 257 (309)
Q Consensus 185 d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~------~-~~i~~~l~~~~~l~~L~~d 257 (309)
+.-|...+-.+|+..+....+.+++.+...=.+++ -.|-+++|...+- . +.+++++-. ....+|-.
T Consensus 200 ~~~g~~~~a~Iln~~~~~~~~~il~~L~~~d~~~a-----~~Ir~~mF~Fedl~~l~~~~l~~ll~~v~~--~~L~~ALk 272 (339)
T PRK05686 200 KMGGVKTVAEILNNLDRQTEKTILESLEEEDPELA-----EKIKDLMFVFEDLVDLDDRSIQRLLREVDN--DVLALALK 272 (339)
T ss_pred ccCcHHHHHHHHhcCCchHHHHHHHHHHhhCHHHH-----HHHHHHhcCHHHHhcCCHHHHHHHHHhCCH--HHHHHHHC
Confidence 34577888899998888888888888775433332 2333333332222 1 445555432 44455555
Q ss_pred cChhHHHHHHHhhccCCCcHHHHHHHHHHHH
Q 048245 258 KYGNYVIQTALVETMRQDRLSVHQRLVTKLQ 288 (309)
Q Consensus 258 ~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~ 288 (309)
....-+-++++..-+. ..++.+-+++.
T Consensus 273 ga~~~~~~~il~nmS~----R~a~~l~eel~ 299 (339)
T PRK05686 273 GASEELREKFLSNMSK----RAAEMLREDLE 299 (339)
T ss_pred CCCHHHHHHHHHhcCH----HHHHHHHHHHH
Confidence 5555566777776665 44444444443
No 32
>PF08625 Utp13: Utp13 specific WD40 associated domain; InterPro: IPR013934 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp13 is a nucleolar protein and component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA []. Upt13 is also a component of the Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome []. Components of the Pwp2 complex are: Utp1 (Pwp2), Utp6, Utp12 (Dip2), Utp13, Utp18, and Utp21. The relationship between the Pwp2 complex and the t-Utps complex [] that also associates with the 5' end of nascent pre-18S rRNA is unclear. ; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=38.07 E-value=88 Score=24.03 Aligned_cols=52 Identities=8% Similarity=0.011 Sum_probs=27.9
Q ss_pred chHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHHhccChHH
Q 048245 116 GSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSR 167 (309)
Q Consensus 116 gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~ 167 (309)
|+.-+..++...+.++...+++.+...-..--+...+..|+..+++..++++
T Consensus 47 g~~~l~~~i~~L~~~~l~~LL~~ir~WNTNsr~~~vAQ~vL~~il~~~~~~~ 98 (141)
T PF08625_consen 47 GSEELDEVIKKLDDEQLEKLLRFIRDWNTNSRTSHVAQRVLNAILKSHPPEE 98 (141)
T ss_pred hHHHHHHHHHhcCHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHhCCHHH
Confidence 5566666676666666666666554433333333334445555555555443
No 33
>PF09770 PAT1: Topoisomerase II-associated protein PAT1; InterPro: IPR019167 Proteins in this entry are necessary for accurate chromosome transmission during cell division []. ; PDB: 2XER_C 2XES_B 2XEQ_D.
Probab=38.05 E-value=57 Score=33.04 Aligned_cols=52 Identities=13% Similarity=0.131 Sum_probs=39.6
Q ss_pred HHHHHHHHHHh------------hHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHh
Q 048245 18 ILDKLFWVVSG------------FTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLA 72 (309)
Q Consensus 18 ~~~~i~~el~~------------~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l 72 (309)
..+++++.++- .+..+++-+-|..+|-+++++.+.+++..|+..|. .++..|
T Consensus 553 ~~~~l~~~L~~~~~~~~~~~~~~~fi~~ls~~KGkkll~R~~~~l~~~q~~~il~~i~---~~l~~l 616 (808)
T PF09770_consen 553 LVEKLWESLKVMEPIGDSSSEPHPFISILSVRKGKKLLPRIFPFLSQEQRLTILTMIF---RHLDQL 616 (808)
T ss_dssp HHHHHHHHHHT--TTSSS---THHHHHHTTSHHHHHHHHHHGGGS-HHHHHHHHHHHH---HTH---
T ss_pred HHHHHHHhcCCCCCCCCCCCCCCcceEEEeeCChheeHHhhhhhCChhHHHHHHHHHH---HHhhhh
Confidence 34556666653 47788999999999999999999999999999888 777544
No 34
>KOG1078 consensus Vesicle coat complex COPI, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.61 E-value=2.2e+02 Score=28.46 Aligned_cols=116 Identities=12% Similarity=0.161 Sum_probs=74.5
Q ss_pred HHHhccCCHHHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccC----CHHHH
Q 048245 8 QEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFG----SSSVK 83 (309)
Q Consensus 8 q~~l~~~~~e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~g----s~vlq 83 (309)
-++|+.|+++.++.+...+..-..+++ |-+---+++++...|..-.++... +- +.+..+..+.-| ..++.
T Consensus 341 TtLLKTG~e~sv~rLm~qI~~fv~dis-DeFKivvvdai~sLc~~fp~k~~~--~m---~FL~~~Lr~eGg~e~K~aivd 414 (865)
T KOG1078|consen 341 TTLLKTGTESSVDRLMKQISSFVSDIS-DEFKIVVVDAIRSLCLKFPRKHTV--MM---NFLSNMLREEGGFEFKRAIVD 414 (865)
T ss_pred HHHHHhcchhHHHHHHHHHHHHHHhcc-ccceEEeHHHHHHHHhhccHHHHH--HH---HHHHHHHHhccCchHHHHHHH
Confidence 467888999999998888877777765 557777888887777654443221 11 222223333222 23455
Q ss_pred HHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCC
Q 048245 84 KLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYN 129 (309)
Q Consensus 84 ~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~ 129 (309)
.++.....+++.++.-...+...+.+...+..|-.++..+-..++.
T Consensus 415 ~Ii~iie~~pdsKe~~L~~LCefIEDce~~~i~~rILhlLG~EgP~ 460 (865)
T KOG1078|consen 415 AIIDIIEENPDSKERGLEHLCEFIEDCEFTQIAVRILHLLGKEGPK 460 (865)
T ss_pred HHHHHHHhCcchhhHHHHHHHHHHHhccchHHHHHHHHHHhccCCC
Confidence 5554442246666666666777788888888888888888877653
No 35
>PF04286 DUF445: Protein of unknown function (DUF445); InterPro: IPR007383 This entry contains proteins of unknown function. They are predicted to be transmembrane proteins with 2 or 3 TM domains.
Probab=37.59 E-value=2.9e+02 Score=24.45 Aligned_cols=29 Identities=14% Similarity=0.118 Sum_probs=13.0
Q ss_pred hHHHHHHHHHhHHHHhcCccccHHHHHHH
Q 048245 132 NDFIYQAALEHCLYLACHEQGCINLNNFI 160 (309)
Q Consensus 132 ~~~l~~~l~~~~~~l~~~~~gs~vvq~~l 160 (309)
.+.+.+.+...+.....++-+..-+..++
T Consensus 140 ~~~l~~~il~~i~~~l~~~e~~~~I~~~i 168 (367)
T PF04286_consen 140 HQKLLDRILEKIKEYLKSEETRERIRDLI 168 (367)
T ss_pred hHHHHHHHHHHHHHHHcCchHHHHHHHHH
Confidence 34444444444444444444443344333
No 36
>PF03195 DUF260: Protein of unknown function DUF260; InterPro: IPR004883 The lateral organ boundaries (LOB) gene is expressed at the adaxial base of initiating lateral organs and encodes a plant-specific protein of unknown function. The N-terminal one half of the LOB protein contains a conserved approximately 100-amino acid domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins and in proteins from a variety of other plant species. Genes encoding LOB domain (LBD) proteins are expressed in a variety of temporal- and tissue-specific patterns, suggesting that they may function in diverse processes [] The LOB domain contains conserved blocks of amino acids that identify the LBD gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is defining feature of the LOB domain, is present in all LBD proteins. It is possible that this motif forms a new zinc finger [].
Probab=35.25 E-value=84 Score=22.61 Aligned_cols=42 Identities=14% Similarity=0.286 Sum_probs=30.1
Q ss_pred cccHHHHHHHhccChHHHHHHHHHHHHhHHhhccCC-ChhHHH
Q 048245 151 QGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHR-SGNYVV 192 (309)
Q Consensus 151 ~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~-~g~~vi 192 (309)
+|..=+.++++..+++++...++.|.-.......|| ||++=+
T Consensus 37 FG~sni~k~L~~~~~~~R~~a~~Sl~yEA~~R~~dPv~Gc~G~ 79 (101)
T PF03195_consen 37 FGVSNISKMLQELPPEQREDAMRSLVYEANARARDPVYGCVGI 79 (101)
T ss_pred HchhHHHHHHHhCCccchhhHHHHHHHHHHhhccCCCcchHHH
Confidence 566677777877777888888888777777777776 565433
No 37
>PF04078 Rcd1: Cell differentiation family, Rcd1-like ; InterPro: IPR007216 Rcd1 (Required cell differentiation 1) -like proteins are found among a wide range of organisms []. Rcd1 was initially identified as an essential factor in nitrogen starvation-invoked differentiation in fission yeast. This results largely from a defect in nitrogen starvation-invoked induction of ste11+, a key transcriptional factor gene required for the onset of sexual development. It is one of the most conserved proteins in eukaryotes, and its mammalian homologue is expressed in a variety of differentiating tissues [, ]. The mammalian Rcd1 is a novel transcriptional cofactor and is critical for retinoic acid-induced differentiation of F9 mouse teratocarcinoma cells, at least in part, via forming complexes with retinoic acid receptor and activation transcription factor-2 (ATF-2) []. Two of the members in this family have been characterised as being involved in regulation of Ste11 regulated sex genes [, ].; PDB: 2FV2_B.
Probab=33.43 E-value=82 Score=26.97 Aligned_cols=43 Identities=12% Similarity=0.223 Sum_probs=17.3
Q ss_pred HHHHhccCCHHHHHHH-HHHHHhhHHHhccC------cchhHHHHHHHhh
Q 048245 7 LQEKLSSGDSRILDKL-FWVVSGFTFELMSG------QYGRFVFGKFIES 49 (309)
Q Consensus 7 lq~~l~~~~~e~~~~i-~~el~~~~~~L~~~------~~g~~vlq~li~~ 49 (309)
+-.+++..++|..+.+ -.|+.|-++..|.. -.+.|++||++..
T Consensus 120 IgaLvK~d~~evi~fLl~tEiiplcLr~me~GselSKtvAtfIlqKIL~d 169 (262)
T PF04078_consen 120 IGALVKTDDPEVISFLLQTEIIPLCLRIMEFGSELSKTVATFILQKILLD 169 (262)
T ss_dssp HHHHHTT--HHHHHHHHCTTHHHHHHHHHHHS-HHHHHHHHHHHHHHHHS
T ss_pred HHHHHcCCcHHHHHHHHhhchHHHHHHHHHhccHHHHHHHHHHHHHHHcc
Confidence 3345555555544432 23444444333321 1244555555543
No 38
>KOG2213 consensus Apoptosis inhibitor 5/fibroblast growth factor 2-interacting factor 2, and related proteins [Signal transduction mechanisms]
Probab=31.00 E-value=4.2e+02 Score=24.33 Aligned_cols=50 Identities=10% Similarity=0.047 Sum_probs=25.1
Q ss_pred HHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCccchh
Q 048245 250 QILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKE 304 (309)
Q Consensus 250 ~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~~v~ 304 (309)
.+.+|++-+-|--=+.. +..+++ +.-+++++.+....+--+....+++.+
T Consensus 189 ~lqeLa~~~e~~a~lda-f~~sD~----d~VdRfisCl~~AvPfFargapSskf~ 238 (460)
T KOG2213|consen 189 RLQELAEEQEGLADLDA-FNVSDA----DYVDRFISCLLMAVPFFARGAPSSKFV 238 (460)
T ss_pred HHHHHHHHHhhhhccCc-ccCCCh----HHHHHHHHHHHHhhhhhhcCCchhHHH
Confidence 44444443333322223 444554 666666666666655555554444443
No 39
>COG4399 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.26 E-value=4.1e+02 Score=23.91 Aligned_cols=6 Identities=0% Similarity=0.213 Sum_probs=2.2
Q ss_pred HHHhhc
Q 048245 251 ILQVAS 256 (309)
Q Consensus 251 l~~L~~ 256 (309)
+.++..
T Consensus 323 l~~~v~ 328 (376)
T COG4399 323 LEELVE 328 (376)
T ss_pred HHHHHH
Confidence 333333
No 40
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=30.14 E-value=2.6e+02 Score=21.52 Aligned_cols=56 Identities=9% Similarity=0.086 Sum_probs=35.2
Q ss_pred HHHHHHHhccChHHHHHHHHH-HHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccC
Q 048245 154 INLNNFIDNMKGSRRKQILHL-ISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLT 221 (309)
Q Consensus 154 ~vvq~~l~~~~~~~~~~l~~~-l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~ 221 (309)
.+++.|+++|+......+.+. +...+..++.++ .++.-++.+++.+..+-..+..+
T Consensus 59 ~LLe~~vkNCG~~fh~evask~Fl~eL~kl~~~~------------~~~~Vk~kil~li~~W~~~f~~~ 115 (144)
T cd03568 59 TLLDACAENCGKRFHQEVASRDFTQELKKLINDR------------VHPTVKEKLREVVKQWADEFKND 115 (144)
T ss_pred HHHHHHHHHCCHHHHHHHhhHHHHHHHHHHhccc------------CCHHHHHHHHHHHHHHHHHhCCC
Confidence 477888888887776666644 666677777665 23445566666665555444433
No 41
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=29.66 E-value=4.1e+02 Score=23.75 Aligned_cols=233 Identities=13% Similarity=0.050 Sum_probs=0.0
Q ss_pred hccCCHHHHHHHHHHHHhhHHHhc-cCcchhHHHHHHHhh-cCHHHHHHHHHHHhcccchH-HHhhccccCCHHHHHHHh
Q 048245 11 LSSGDSRILDKLFWVVSGFTFELM-SGQYGRFVFGKFIES-CNESQLALIILKITFQDQLF-LLASVDKFGSSSVKKLIK 87 (309)
Q Consensus 11 l~~~~~e~~~~i~~el~~~~~~L~-~~~~g~~vlq~li~~-~~~~~~~~l~~~l~~~~~~~-~~l~~~~~gs~vlq~ll~ 87 (309)
+..-++++.+.+++|....+..-. ...-|.-.++.+++. -+++.-..+++.+......- .-=.........|-.++.
T Consensus 49 l~~v~~~~~~~vl~eF~~~~~~~~~~~~g~~~~~~~~L~~alg~~~a~~il~~i~~~~~~~~~~~~L~~~~~~~la~~l~ 128 (338)
T TIGR00207 49 VTQIDNQQKDDVLEEFEQIAEAQAYINIGGLDYAREVLEKALGEEKAASILNDLTSSLQTAPGFEFLRKAEPQQIADFIQ 128 (338)
T ss_pred cCCCCHHHHHHHHHHHHHHHHhcCCccCChHHHHHHHHHHhcCHHHHHHHHHHHhcccccCchhHHHHCCCHHHHHHHHH
Q ss_pred hhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhcc------CCCcchHHHHHHHHHhHHHHh---cCccccHHHHH
Q 048245 88 VVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEP------SYNHKNDFIYQAALEHCLYLA---CHEQGCINLNN 158 (309)
Q Consensus 88 ~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~------~~~~~~~~l~~~l~~~~~~l~---~~~~gs~vvq~ 158 (309)
.- .++...++...+.+....-+-..+.-.....++.. .+++....+-+.+...+..+. ...-|...+..
T Consensus 129 ~E--hPQ~iAliLs~L~p~~AA~VL~~Lp~~~~~ei~~ria~l~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ 206 (338)
T TIGR00207 129 QE--HPQTIALILSHLDPAQAADILSLFPEEVQAEVARRIATMGRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAE 206 (338)
T ss_pred cc--CHHHHHHHHHcCCHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHH
Q ss_pred HHhccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH
Q 048245 159 FIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV 238 (309)
Q Consensus 159 ~l~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~ 238 (309)
+++..+......++..|...-..++..--...+.=.-|-.-++.....+++.+-....-+|-.--..-+-+++|..-+.-
T Consensus 207 ILN~~~~~~~~~il~~L~~~dp~la~~Ir~~mF~Fedl~~ld~~~l~~llrev~~~~L~~ALkga~~e~~~~il~nmS~R 286 (338)
T TIGR00207 207 IINLMDRKTEKTIITSLEEFDPELAEEIKKEMFVFEDIVDLDDRSIQRVLREVDSEDLLLALKGAEQPLREKFLNNMSQR 286 (338)
T ss_pred HHHhCCchHHHHHHHHHHHhCHHHHHHHHHHccCHHHHhcCCHHHHHHHHHhCCHHHHHHHHCcCCHHHHHHHHHHhhHH
Q ss_pred --HHHHHHH
Q 048245 239 --HYIVEEL 245 (309)
Q Consensus 239 --~~i~~~l 245 (309)
+.+-+++
T Consensus 287 ~a~~l~ee~ 295 (338)
T TIGR00207 287 AAEILKEDM 295 (338)
T ss_pred HHHHHHHHH
No 42
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=29.17 E-value=4.2e+02 Score=23.75 Aligned_cols=84 Identities=11% Similarity=0.036 Sum_probs=38.3
Q ss_pred ChhHHHHHHHHHHHH----HhHhhcCCCchHHHHHHhcc--CCCcchHHHHHHHHHhHHHHhc----CccccHHHHHHHh
Q 048245 92 SPPLLYHVMSALKRL----FKFLMMTKPGSSVILKCLEP--SYNHKNDFIYQAALEHCLYLAC----HEQGCINLNNFID 161 (309)
Q Consensus 92 ~~~~~~~i~~~l~~~----~~~l~~~~~gs~vvq~~l~~--~~~~~~~~l~~~l~~~~~~l~~----~~~gs~vvq~~l~ 161 (309)
.|....++...+.++ +...+.+..-.-|+.++..- .+++....+-..+.+++..... ..-|...+..++.
T Consensus 133 hPQtia~iLs~L~~~~aa~vL~~l~~e~r~~v~~Ria~l~~v~p~al~~i~~~l~~~l~~~~~~~~~~~gg~~~~aeIlN 212 (339)
T COG1536 133 HPQTIALILSYLPPDQAAEILSTLPEELRADVVKRIATLEGVSPEALAELENVLEKKLQSLVNEDYSKLGGIKAAAEILN 212 (339)
T ss_pred ccHHHHHHHHhcCHHHHHHHHHhCCHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHhhccccccccccHhHHHHHHH
Confidence 345555555544443 23333344444455554443 2233333444444444444422 2234455666666
Q ss_pred ccChHHHHHHHHHH
Q 048245 162 NMKGSRRKQILHLI 175 (309)
Q Consensus 162 ~~~~~~~~~l~~~l 175 (309)
+........+++.+
T Consensus 213 ~~d~~~e~~il~~l 226 (339)
T COG1536 213 LLDRGTEKTILESL 226 (339)
T ss_pred hcchhHHHHHHHHH
Confidence 66544444444443
No 43
>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]
Probab=28.77 E-value=5.3e+02 Score=24.77 Aligned_cols=72 Identities=24% Similarity=0.365 Sum_probs=46.7
Q ss_pred HHHHHHhhcC--ChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH---HHHHHHHhCchHHHHhhcCcChhHHH
Q 048245 190 YVVQHVLNLE--DPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV---HYIVEELLNSDQILQVASDKYGNYVI 264 (309)
Q Consensus 190 ~viq~ll~~~--~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~---~~i~~~l~~~~~l~~L~~d~~g~~Vi 264 (309)
.++-++|++. +...|+.|++.|++.+- |-.=+|..+..++.+ +.+...+ + .+..+..-.-||||.
T Consensus 226 ~Ilk~il~~d~k~~~ar~~~i~~lRd~y~-------~~~~~e~yl~~s~i~~~~rnf~~~l-~--dFek~m~f~eGnFVf 295 (711)
T COG1747 226 RILKHILEHDEKDVWARKEIIENLRDKYR-------GHSQLEEYLKISNISQSGRNFFEAL-N--DFEKLMHFDEGNFVF 295 (711)
T ss_pred HHHHHHhhhcchhhhHHHHHHHHHHHHhc-------cchhHHHHHHhcchhhccccHHHHH-H--HHHHHheeccCceEE
Confidence 4566666654 33468888888887653 223467777777766 4444443 3 577777778899987
Q ss_pred HHHHhhc
Q 048245 265 QTALVET 271 (309)
Q Consensus 265 q~~l~~~ 271 (309)
.+-|..+
T Consensus 296 HqtWgVG 302 (711)
T COG1747 296 HQTWGVG 302 (711)
T ss_pred ecccccc
Confidence 7667654
No 44
>PF11640 TAN: Telomere-length maintenance and DNA damage repair; InterPro: IPR021668 ATM is a large protein kinase, in humans, critical for responding to DNA double-strand breaks (DSBs). Tel1, the orthologue from budding yeast, also regulates responses to DSBs. Tel1 is important for maintaining viability and for phosphorylation of the DNA damage signal transducer kinase Rad53 (an orthologue of mammalian CHK2). In addition to functioning in the response to DSBs, numerous findings indicate that Tel1/ATM regulates telomeres. The overall domain structure of Tel1/ATM is shared by proteins of the phosphatidylinositol 3-kinase (PI3K)-related kinase (PIKK) family, but this family carries a unique and functionally important TAN sequence motif, near its N-terminal, LxxxKxxE/DRxxxL. which is conserved specifically in the Tel1/ATM subclass of the PIKKs. The TAN motif is essential for both telomere length maintenance and Tel1 action in response to DNA damage []. It is classified as an 2.7.11.1 from EC. ; GO: 0004674 protein serine/threonine kinase activity
Probab=28.53 E-value=96 Score=24.07 Aligned_cols=66 Identities=17% Similarity=0.196 Sum_probs=34.5
Q ss_pred hHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcHHHHHHHHhC-chHHHHhhcCc
Q 048245 189 NYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHYIVEELLN-SDQILQVASDK 258 (309)
Q Consensus 189 ~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~~~i~~~l~~-~~~l~~L~~d~ 258 (309)
++++..+++.+.+..+..-+..+..++.++..+++|+.+--...+. -.++..+++ +++...|..++
T Consensus 86 a~~lR~~ve~~~~~~k~kt~~~Ll~hI~~~l~~~~~~~~~p~~~Dy----~k~L~~iL~~~~~~ehL~~~~ 152 (155)
T PF11640_consen 86 ASALRLFVEKSNSRLKRKTVKALLDHITDLLPDPDDSLLEPLSLDY----SKILKAILSYPPHVEHLSPKQ 152 (155)
T ss_pred HHHHHHHHHHHHhhcccchHHHHHHHHHHHhhCCchhHHHHHHHHH----HHHHHHHHCCChHHHHCcHhh
Confidence 4555556665555566666677777777777666643222211111 233355554 34555555444
No 45
>PF12447 DUF3683: Protein of unknown function (DUF3683); InterPro: IPR022153 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF02754 from PFAM, PF01565 from PFAM, PF02913 from PFAM.
Probab=27.27 E-value=2.5e+02 Score=20.58 Aligned_cols=60 Identities=20% Similarity=0.228 Sum_probs=41.2
Q ss_pred HHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcC
Q 048245 171 ILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQ 235 (309)
Q Consensus 171 l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~ 235 (309)
++-++.+++.-.-.+| |+-+.+++ +|+.+..+++.+...+-++.....|..-|..++..+
T Consensus 47 mL~evlGDiwvv~RNP---yL~ddLld--~~~Rr~~L~~al~hrL~~I~~r~~~~~~V~~l~~aa 106 (115)
T PF12447_consen 47 MLFEVLGDIWVVRRNP---YLQDDLLD--NPKRRRALFEALRHRLDEIEKRANGNPRVLELLAAA 106 (115)
T ss_pred HHHHHhcceeeeecCc---hhHHHHcc--CHHHHHHHHHHHHHHHHHHHHhccCChHHHHHHHHH
Confidence 4444455544444444 56777887 688889999999988888887777776666666554
No 46
>PF09770 PAT1: Topoisomerase II-associated protein PAT1; InterPro: IPR019167 Proteins in this entry are necessary for accurate chromosome transmission during cell division []. ; PDB: 2XER_C 2XES_B 2XEQ_D.
Probab=26.87 E-value=81 Score=31.96 Aligned_cols=146 Identities=15% Similarity=0.140 Sum_probs=49.5
Q ss_pred HHHHhcCccccHHHHHHHhccChHHHHHHHHHHHHhHHhhcc---------------------CCChhHHHHHHhhcCCh
Q 048245 143 CLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSR---------------------HRSGNYVVQHVLNLEDP 201 (309)
Q Consensus 143 ~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~---------------------d~~g~~viq~ll~~~~~ 201 (309)
++.+....-|-.+|-++|.+.+.+++..|+..|..++..|.. |.+-..|+..+......
T Consensus 577 fi~~ls~~KGkkll~R~~~~l~~~q~~~il~~i~~~l~~l~vv~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~l~~~i~~ 656 (808)
T PF09770_consen 577 FISILSVRKGKKLLPRIFPFLSQEQRLTILTMIFRHLDQLDVVRRASYTDGEDQPLLIKRDDIELFLQAVMPPLMNVINE 656 (808)
T ss_dssp HHHHTTSHHHHHHHHHHGGGS-HHHHHHHHHHHHHTH-----------------HHHHHTTTTT--GGGGHHHS-HHHHH
T ss_pred ceEEEeeCChheeHHhhhhhCChhHHHHHHHHHHHHhhhhcccccccccccccCccccchHhHHHHHHHHHHHHHHHHHh
Confidence 555566666777888888888877777777777777632211 11222222222221111
Q ss_pred hhHHHHHH---HH--HHhHHHhccCcchhHHHHHHHhcC-------CcH-------HHHHHHHhCchHH-----HH----
Q 048245 202 FLIDAICF---AL--RGHYVDLSLTKCGSFVVQKFLKYQ-------NAV-------HYIVEELLNSDQI-----LQ---- 253 (309)
Q Consensus 202 ~~~~~i~~---~l--~~~~~~l~~~~~gs~vve~~l~~~-------~~~-------~~i~~~l~~~~~l-----~~---- 253 (309)
.....|+. .+ ..++.-++++|+|--++-.+|..+ +.. ..++..|+. .| ..
T Consensus 657 ~~~~~i~gll~~~~~~~~~~~i~~tk~Gls~lt~llsRae~l~~~~~~~~~~~~~W~~~~~~lf~--~l~~~~~~~~fp~ 734 (808)
T PF09770_consen 657 APFNEIIGLLGLLINNNNVSFIAQTKFGLSLLTMLLSRAELLKQSGSSSEEEWSQWTEFYDQLFD--SLEEPRLPSIFPP 734 (808)
T ss_dssp HHHHHHTTSTTT-S--HHHHHHHTSHHHHHHHHHHHHHHHHHHHT------HHHHHHHH---------------------
T ss_pred CCHHHHHHHHHHHHhCCCceEEEEChHHHHHHHHHHHHHHHhhccCCCCHHHHHHhhhhhhhccc--ccccccccccccc
Confidence 11111111 11 135667899999998887776443 111 455555555 33 11
Q ss_pred --hhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHH
Q 048245 254 --VASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHL 291 (309)
Q Consensus 254 --L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~ 291 (309)
-..+--.+||.|-+-..+-.. ..+.-+.|+.++++.+
T Consensus 735 ~~~~~~~~~~~vwq~la~~~~~~-~~~~q~~lv~~vrd~v 773 (808)
T PF09770_consen 735 DSSINSGDDSYVWQFLAALALGA-SPEQQQILVDEVRDRV 773 (808)
T ss_dssp ----------------------------------------
T ss_pred ccccccccccccccccccccccc-cccccccccccccccc
Confidence 123344578877766655332 1245555555555543
No 47
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=26.79 E-value=3.5e+02 Score=26.31 Aligned_cols=66 Identities=12% Similarity=0.058 Sum_probs=54.0
Q ss_pred HHHHHHHHhHHHhccCcchhHHHHHHHhcCCc-H--HHHHHHHhCchHHHHhhcCcChhHHHHHHHhhccC
Q 048245 206 AICFALRGHYVDLSLTKCGSFVVQKFLKYQNA-V--HYIVEELLNSDQILQVASDKYGNYVIQTALVETMR 273 (309)
Q Consensus 206 ~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~-~--~~i~~~l~~~~~l~~L~~d~~g~~Viq~~l~~~~~ 273 (309)
++-+.+.+.++.|..-.|--.|++.+-+.... . ..+++.|.. .+.+++.-||+.--++.++.....
T Consensus 486 e~kr~ilD~~V~L~s~G~VlPVl~~i~~~~~~~~iD~SLiRyFv~--eVLeii~PPYS~~Fv~~~l~ll~~ 554 (584)
T PF04858_consen 486 ELKRTILDRMVHLLSRGYVLPVLEYIRKCWARGDIDPSLIRYFVT--EVLEIIGPPYSPEFVQLFLPLLEN 554 (584)
T ss_pred HHHHHHHHHHHHHHhCCeeehHHHHHHHHHhccCCcHHHHHHHHH--HHHHHcCCCCCHHHHHHHHHHHhc
Confidence 44456677888888888888999888877554 2 788899988 899999999999999999887765
No 48
>KOG3036 consensus Protein involved in cell differentiation/sexual development [General function prediction only]
Probab=26.27 E-value=4.2e+02 Score=22.74 Aligned_cols=30 Identities=10% Similarity=0.206 Sum_probs=19.0
Q ss_pred HHHHHhccCCHHHHH-HHHHHHHhhHHHhcc
Q 048245 6 YLQEKLSSGDSRILD-KLFWVVSGFTFELMS 35 (309)
Q Consensus 6 ~lq~~l~~~~~e~~~-~i~~el~~~~~~L~~ 35 (309)
++-.+++.+++|-.. .+-.|+.|.++..|.
T Consensus 148 VIgaLvk~dd~eVi~fLl~TeIVPlCLrime 178 (293)
T KOG3036|consen 148 VIGALVKNDDQEVIRFLLTTEIVPLCLRIME 178 (293)
T ss_pred HHHHHHhcCcHHHHHHHHHhhhHHHHHHHHh
Confidence 456777888877433 345667777766554
No 49
>COG5240 SEC21 Vesicle coat complex COPI, gamma subunit [Intracellular trafficking and secretion]
Probab=23.55 E-value=7e+02 Score=24.39 Aligned_cols=172 Identities=10% Similarity=0.005 Sum_probs=0.0
Q ss_pred chhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCHHHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCch
Q 048245 38 YGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGS 117 (309)
Q Consensus 38 ~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs 117 (309)
.+.|-+-.++..++++..+.++..|. ..+.++ .|.|---++..+=..+..-+.....+.+.+.+-+.+-=-=.+.+
T Consensus 356 IstyAITtLLKTGt~e~idrLv~~I~---sfvhD~-SD~FKiI~ida~rsLsl~Fp~k~~s~l~FL~~~L~~eGg~eFK~ 431 (898)
T COG5240 356 ISTYAITTLLKTGTEETIDRLVNLIP---SFVHDM-SDGFKIIAIDALRSLSLLFPSKKLSYLDFLGSSLLQEGGLEFKK 431 (898)
T ss_pred chHHHHHHHHHcCchhhHHHHHHHHH---HHHHhh-ccCceEEeHHHHHHHHhhCcHHHHHHHHHHHHHHHhcccchHHH
Q ss_pred HHHHHHhc--cCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHHhccChHHHHHHHHHHHHhHHhhccCCChhHHHHHH
Q 048245 118 SVILKCLE--PSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHV 195 (309)
Q Consensus 118 ~vvq~~l~--~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~l 195 (309)
+.+..+.+ ...|+.++..++.++.-+.+--.|+..-+++--+=+.++...-....-.=.-|=.-|=++-.-+..+|.+
T Consensus 432 ~~Vdaisd~~~~~p~skEraLe~LC~fIEDcey~~I~vrIL~iLG~EgP~a~~P~~yvrhIyNR~iLEN~ivRsaAv~aL 511 (898)
T COG5240 432 YMVDAISDAMENDPDSKERALEVLCTFIEDCEYHQITVRILGILGREGPRAKTPGKYVRHIYNRLILENNIVRSAAVQAL 511 (898)
T ss_pred HHHHHHHHHHhhCchHHHHHHHHHHHHHhhcchhHHHHHHHHHhcccCCCCCCcchHHHHHHHHHHHhhhHHHHHHHHHH
Q ss_pred ----hhcCChhhHHHHHHHHHH
Q 048245 196 ----LNLEDPFLIDAICFALRG 213 (309)
Q Consensus 196 ----l~~~~~~~~~~i~~~l~~ 213 (309)
+...++-..+.+...+..
T Consensus 512 skf~ln~~d~~~~~sv~~~lkR 533 (898)
T COG5240 512 SKFALNISDVVSPQSVENALKR 533 (898)
T ss_pred HHhccCccccccHHHHHHHHHH
No 50
>PF04078 Rcd1: Cell differentiation family, Rcd1-like ; InterPro: IPR007216 Rcd1 (Required cell differentiation 1) -like proteins are found among a wide range of organisms []. Rcd1 was initially identified as an essential factor in nitrogen starvation-invoked differentiation in fission yeast. This results largely from a defect in nitrogen starvation-invoked induction of ste11+, a key transcriptional factor gene required for the onset of sexual development. It is one of the most conserved proteins in eukaryotes, and its mammalian homologue is expressed in a variety of differentiating tissues [, ]. The mammalian Rcd1 is a novel transcriptional cofactor and is critical for retinoic acid-induced differentiation of F9 mouse teratocarcinoma cells, at least in part, via forming complexes with retinoic acid receptor and activation transcription factor-2 (ATF-2) []. Two of the members in this family have been characterised as being involved in regulation of Ste11 regulated sex genes [, ].; PDB: 2FV2_B.
Probab=23.44 E-value=1.3e+02 Score=25.78 Aligned_cols=40 Identities=13% Similarity=0.110 Sum_probs=26.9
Q ss_pred HhccCCHHHHHHHHHHHH------hhHHHhccCcchh--HHHHHHHhh
Q 048245 10 KLSSGDSRILDKLFWVVS------GFTFELMSGQYGR--FVFGKFIES 49 (309)
Q Consensus 10 ~l~~~~~e~~~~i~~el~------~~~~~L~~~~~g~--~vlq~li~~ 49 (309)
+.+=.+++.++..+.|+. |++..+.=+.+|. -++|.++..
T Consensus 3 i~~L~~~~~Re~Al~eLsk~r~~~~~La~~LW~s~G~i~~LLqEIisi 50 (262)
T PF04078_consen 3 ILDLCNPETRENALLELSKKRESFPDLAPLLWHSFGTIAALLQEIISI 50 (262)
T ss_dssp HHHTSSHHHHHHHHHHHHHTCCC-TTHHHHHHTSTTHHHHHHHHHHGG
T ss_pred hHHhcCcchHHHHHHHHHHhhhcccchhHHHHcCCChHHHHHHHHHHH
Confidence 344467788888877774 5566666677774 467777764
No 51
>PF10155 DUF2363: Uncharacterized conserved protein (DUF2363); InterPro: IPR019312 This entry represents a region of 120 amino acids in proteins conserved from plants to humans. Their function is not known.
Probab=22.40 E-value=1.4e+02 Score=22.45 Aligned_cols=40 Identities=20% Similarity=0.295 Sum_probs=28.6
Q ss_pred hHHHHHHhccCCHHHHHHHHHHHHhhHHHhccCcchhHHHH
Q 048245 4 SQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFG 44 (309)
Q Consensus 4 sr~lq~~l~~~~~e~~~~i~~el~~~~~~L~~~~~g~~vlq 44 (309)
|.++|++++.+--.. ..++.|+.+-..+++.-+.++-+.+
T Consensus 83 cvfl~sLir~~i~~~-~~l~~evq~FClefs~i~Ea~~L~k 122 (126)
T PF10155_consen 83 CVFLQSLIRNKIIDV-EDLFIEVQAFCLEFSRIKEASALFK 122 (126)
T ss_pred HHHHHHHHHcCCCch-HHHHhhHHHHHHHHccHHHHHHHHH
Confidence 678899998876543 6688888888888877655554443
No 52
>PF04054 Not1: CCR4-Not complex component, Not1; InterPro: IPR007196 The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1p to Not5p), Caf1p, Caf40p, Caf130p and Ccr4p []. The Ccr4-Not complex regulates many different cellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress []. Caf1p and Ccr4p, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1p, a putative RNA helicase thought to be a component of the decapping complex []. Pop2, a component of the Ccr4-Not complex, functions as a deadenylase []. The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [].
Probab=22.40 E-value=1.4e+02 Score=27.24 Aligned_cols=81 Identities=15% Similarity=0.102 Sum_probs=55.5
Q ss_pred hhHHHHHHhhcCChhhHHHHHHHHHHhHHH-hccCcchhHHHHHHHhcC----CcH---HHHHHHHhCchHHHHhhcCcC
Q 048245 188 GNYVVQHVLNLEDPFLIDAICFALRGHYVD-LSLTKCGSFVVQKFLKYQ----NAV---HYIVEELLNSDQILQVASDKY 259 (309)
Q Consensus 188 g~~viq~ll~~~~~~~~~~i~~~l~~~~~~-l~~~~~gs~vve~~l~~~----~~~---~~i~~~l~~~~~l~~L~~d~~ 259 (309)
+--+++.++...+++.|-.++..+..++-- =+.+.|.|.++-.++... ... +.|.+-|++ ++..--=|||
T Consensus 263 ~~~ll~~Li~~ld~E~RY~ll~aiaNqLRYPN~HT~~Fs~~lL~lF~~~~~~~~~~~IqEqItRVLLE--Rliv~rPHPW 340 (379)
T PF04054_consen 263 HVTLLSKLIHELDPEGRYYLLSAIANQLRYPNSHTHFFSCVLLNLFSSDMNDPNDEDIQEQITRVLLE--RLIVNRPHPW 340 (379)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcCCCCccchhhhHHHHHHHHHH--HHhcCCCCCc
Confidence 446788899989999999999999887632 456778899999999822 222 556666655 4444445778
Q ss_pred hhHH-HHHHHhh
Q 048245 260 GNYV-IQTALVE 270 (309)
Q Consensus 260 g~~V-iq~~l~~ 270 (309)
|=-+ +-.+++.
T Consensus 341 GllitfiELikN 352 (379)
T PF04054_consen 341 GLLITFIELIKN 352 (379)
T ss_pred cHHHHHHHHHhC
Confidence 8665 3444443
No 53
>PF12447 DUF3683: Protein of unknown function (DUF3683); InterPro: IPR022153 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF02754 from PFAM, PF01565 from PFAM, PF02913 from PFAM.
Probab=21.83 E-value=3.3e+02 Score=20.00 Aligned_cols=66 Identities=5% Similarity=-0.027 Sum_probs=39.3
Q ss_pred ChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHHhcc
Q 048245 92 SPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNM 163 (309)
Q Consensus 92 ~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l~~~ 163 (309)
+.....|+.+ +.++++-.-.+| |+.+.+++. ++.+..+++++...+..+.....|..-+..++..+
T Consensus 41 TGRSARmL~e-vlGDiwvv~RNP---yL~ddLld~--~~Rr~~L~~al~hrL~~I~~r~~~~~~V~~l~~aa 106 (115)
T PF12447_consen 41 TGRSARMLFE-VLGDIWVVRRNP---YLQDDLLDN--PKRRRALFEALRHRLDEIEKRANGNPRVLELLAAA 106 (115)
T ss_pred ccHHHHHHHH-HhcceeeeecCc---hhHHHHccC--HHHHHHHHHHHHHHHHHHHHhccCChHHHHHHHHH
Confidence 3444555655 555454444444 355566655 56677777777777777777666665555555543
No 54
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=21.08 E-value=3.7e+02 Score=20.28 Aligned_cols=32 Identities=9% Similarity=0.132 Sum_probs=15.7
Q ss_pred HHHHHHhccChHHHHHHHH-HHHHhHHhhccCC
Q 048245 155 NLNNFIDNMKGSRRKQILH-LISVNAASLSRHR 186 (309)
Q Consensus 155 vvq~~l~~~~~~~~~~l~~-~l~~~~~~l~~d~ 186 (309)
++..|+++|++.....+.. .+...+..++.++
T Consensus 65 lld~lvkNcg~~f~~ev~~~~fl~~l~~l~~~~ 97 (140)
T PF00790_consen 65 LLDALVKNCGPRFHREVASKEFLDELVKLIKSK 97 (140)
T ss_dssp HHHHHHHHSHHHHHHHHTSHHHHHHHHHHHHHT
T ss_pred HHHHHHHcCCHHHHHHHhHHHHHHHHHHHHccC
Confidence 5566666665555444432 2444444444433
No 55
>PF03448 MgtE_N: MgtE intracellular N domain; InterPro: IPR006668 This domain is found at the N terminus of eubacterial magnesium transporters of the MgtE family IPR006667 from INTERPRO. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter [] shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains.; PDB: 2YVX_D 2ZY9_A 2YVZ_B 2YVY_A 2OUX_A 3KXR_A.
Probab=20.83 E-value=82 Score=22.08 Aligned_cols=17 Identities=12% Similarity=0.110 Sum_probs=8.2
Q ss_pred HhccCCCcchHHHHHHH
Q 048245 123 CLEPSYNHKNDFIYQAA 139 (309)
Q Consensus 123 ~l~~~~~~~~~~l~~~l 139 (309)
+++.++++.+..+++.+
T Consensus 9 ~l~~l~~~~~~~~~~~l 25 (102)
T PF03448_consen 9 LLEELPPEERAQLFRLL 25 (102)
T ss_dssp CCCTS-CCHHHHHHHHS
T ss_pred HHHhCCHHHHHHHHHhC
Confidence 34445555555555544
No 56
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.73 E-value=3.6e+02 Score=26.27 Aligned_cols=69 Identities=10% Similarity=-0.058 Sum_probs=52.1
Q ss_pred HHHHHHHHHhHHhhccCCChhHHHHHHhhcCCh-hhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCc
Q 048245 169 KQILHLISVNAASLSRHRSGNYVVQHVLNLEDP-FLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNA 237 (309)
Q Consensus 169 ~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~-~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~ 237 (309)
..+-+.+.+.+..|+.--|--+|+..+-++... ..-..++..|...+.+++.-||+...++.++.--..
T Consensus 485 le~kr~ilD~~V~L~s~G~VlPVl~~i~~~~~~~~iD~SLiRyFv~eVLeii~PPYS~~Fv~~~l~ll~~ 554 (584)
T PF04858_consen 485 LELKRTILDRMVHLLSRGYVLPVLEYIRKCWARGDIDPSLIRYFVTEVLEIIGPPYSPEFVQLFLPLLEN 554 (584)
T ss_pred HHHHHHHHHHHHHHHhCCeeehHHHHHHHHHhccCCcHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Confidence 344455667777777777777888888776543 455788999999999999999999888887765443
No 57
>PF02438 Adeno_100: Late 100kD protein; InterPro: IPR003381 The late 100 kDa protein is a non-structural viral protein involved in the transport of hexon from the cytoplasm to the nucleus.; GO: 0019060 intracellular transport of viral proteins in host cell
Probab=20.56 E-value=4.8e+02 Score=25.05 Aligned_cols=59 Identities=10% Similarity=0.156 Sum_probs=34.1
Q ss_pred cCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHHhccChHHHHHHHHH
Q 048245 112 MTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHL 174 (309)
Q Consensus 112 ~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~ 174 (309)
.++.|+.|+++.++. .+.++.+.+.+.--++--=....| |=|.+++..+-++...++..
T Consensus 286 eNRlnn~vlh~tL~g--e~rrDYv~DtIyLfLv~TWQTaMg--vWQQ~Lee~nl~~l~k~l~~ 344 (583)
T PF02438_consen 286 ENRLNNPVLHSTLEG--EDRRDYVRDTIYLFLVLTWQTAMG--VWQQCLEEENLKELEKLLQR 344 (583)
T ss_pred hccCcchHHHHHhcc--cchhhHHHhhHHHHHHHHHHHHHH--HHHHHhhHhHHHHHHHHHHH
Confidence 579999999999987 446677777654321110011112 55777776555444444443
No 58
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=20.55 E-value=70 Score=24.90 Aligned_cols=47 Identities=28% Similarity=0.348 Sum_probs=27.5
Q ss_pred HHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhh-------------hcCCCccchhhhcc
Q 048245 252 LQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAAL-------------RVMKYGSNKEIQKK 308 (309)
Q Consensus 252 ~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L-------------~~~~~g~~v~~k~~ 308 (309)
..+++.+||||+ + .+. ..-..|......++..+ ..++||...+.-||
T Consensus 15 aGCAt~~~gnf~-----~-~s~----~~a~~iA~D~v~qL~~~ypPA~Tt~~l~q~~~D~Fg~aL~~aLR 74 (151)
T PRK13883 15 GGCATSQYGNFV-----Q-ASA----ADQQKLATDAVQQLATLYPPAQTRFELQQPTPDAFGQALVKALR 74 (151)
T ss_pred hcccCCCCCccc-----c-cCH----HHHHHHHHHHHHHHHHhCCCcceEEEEecCCCcHHHHHHHHHHH
Confidence 456678899998 2 222 44555666666666555 22366666555554
Done!