Query 044799
Match_columns 304
No_of_seqs 182 out of 1540
Neff 8.7
Searched_HMMs 46136
Date Fri Mar 29 06:54:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044799.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044799hhsearch_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 1.4E-55 3.1E-60 408.5 16.6 266 30-298 170-493 (503)
2 cd07920 Pumilio Pumilio-family 100.0 5.6E-50 1.2E-54 365.5 23.7 262 30-297 37-319 (322)
3 KOG2049 Translational represso 100.0 7E-49 1.5E-53 367.0 21.5 271 33-303 211-535 (536)
4 COG5099 RNA-binding protein of 100.0 2.3E-41 4.9E-46 330.9 17.2 231 45-275 447-734 (777)
5 cd07920 Pumilio Pumilio-family 100.0 3.8E-38 8.2E-43 287.5 20.2 230 29-262 72-322 (322)
6 KOG1488 Translational represso 100.0 6.4E-37 1.4E-41 284.3 15.9 212 30-242 243-496 (503)
7 COG5099 RNA-binding protein of 100.0 4.2E-30 9.1E-35 251.9 20.0 187 81-271 447-649 (777)
8 KOG2050 Puf family RNA-binding 99.9 9.9E-27 2.1E-31 215.2 15.9 270 28-303 149-443 (652)
9 KOG2049 Translational represso 99.9 1.7E-26 3.6E-31 216.8 15.1 200 39-243 292-494 (536)
10 KOG2188 Predicted RNA-binding 99.9 6.9E-24 1.5E-28 198.2 19.7 232 30-262 90-605 (650)
11 KOG2050 Puf family RNA-binding 99.8 9.3E-20 2E-24 169.2 16.6 234 30-268 191-446 (652)
12 KOG2188 Predicted RNA-binding 99.7 8.5E-17 1.8E-21 151.0 16.8 199 41-242 338-606 (650)
13 KOG4574 RNA-binding protein (c 99.5 9.3E-15 2E-19 140.5 6.1 229 38-270 545-823 (1007)
14 KOG4574 RNA-binding protein (c 99.4 1.1E-12 2.5E-17 126.3 6.8 158 112-270 543-756 (1007)
15 PF00806 PUF: Pumilio-family R 98.5 3.5E-08 7.6E-13 59.3 1.4 30 187-216 4-33 (35)
16 PF00806 PUF: Pumilio-family R 98.5 6.5E-08 1.4E-12 58.2 1.8 27 115-141 4-30 (35)
17 smart00025 Pumilio Pumilio-lik 98.1 2.1E-06 4.6E-11 51.4 2.0 32 114-145 3-34 (36)
18 smart00025 Pumilio Pumilio-lik 97.9 6.4E-06 1.4E-10 49.3 2.3 34 37-70 2-35 (36)
19 PF08144 CPL: CPL (NUC119) dom 91.4 0.61 1.3E-05 37.6 6.0 66 145-210 58-134 (148)
20 PF08144 CPL: CPL (NUC119) dom 81.4 5.8 0.00013 31.9 6.3 75 180-267 57-134 (148)
21 PRK05686 fliG flagellar motor 79.2 52 0.0011 30.3 14.6 181 49-243 80-284 (339)
22 PF11510 FA_FANCE: Fanconi Ana 73.0 39 0.00085 29.9 9.6 166 55-230 41-213 (263)
23 PRK05686 fliG flagellar motor 70.1 90 0.0019 28.7 12.1 113 52-172 123-244 (339)
24 KOG1240 Protein kinase contain 52.0 82 0.0018 33.9 8.6 65 68-132 458-527 (1431)
25 PF08625 Utp13: Utp13 specific 37.7 76 0.0017 25.2 4.8 25 126-150 47-71 (141)
26 TIGR00207 fliG flagellar motor 34.9 3.6E+02 0.0079 24.7 12.0 55 103-157 174-231 (338)
27 PF03195 DUF260: Protein of un 30.9 92 0.002 23.3 4.0 52 155-206 31-83 (101)
28 PF07176 DUF1400: Alpha/beta h 29.8 2.6E+02 0.0056 21.7 6.6 96 39-139 19-121 (127)
29 PF04078 Rcd1: Cell differenti 27.9 4.3E+02 0.0093 23.4 8.8 11 162-172 202-212 (262)
30 KOG3821 Heparin sulfate cell s 26.9 6.3E+02 0.014 25.0 11.0 44 48-92 90-137 (563)
31 PF08625 Utp13: Utp13 specific 25.5 3.4E+02 0.0074 21.5 8.5 85 41-135 4-88 (141)
32 TIGR00207 fliG flagellar motor 24.9 5.5E+02 0.012 23.6 15.1 79 114-192 131-230 (338)
33 COG4399 Uncharacterized protei 24.9 5E+02 0.011 24.1 8.2 21 39-59 219-239 (376)
34 COG5145 RAD14 DNA excision rep 24.7 1.5E+02 0.0032 25.5 4.6 79 156-236 130-211 (292)
35 PF09770 PAT1: Topoisomerase I 24.1 97 0.0021 32.2 4.2 21 223-243 673-693 (808)
36 PF12231 Rif1_N: Rap1-interact 24.0 5.9E+02 0.013 23.6 12.3 25 75-102 77-101 (372)
37 cd07356 HN_L-whirlin_R1_like F 23.6 2.1E+02 0.0045 20.1 4.4 21 178-198 56-76 (78)
38 PF14005 YpjP: YpjP-like prote 21.2 1.6E+02 0.0035 23.2 3.9 34 141-174 4-37 (136)
39 PF05794 Tcp11: T-complex prot 20.1 5.1E+02 0.011 24.5 8.0 119 35-167 22-141 (441)
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=1.4e-55 Score=408.47 Aligned_cols=266 Identities=23% Similarity=0.320 Sum_probs=233.6
Q ss_pred cCcccccchhhHhhhccCcchhHHHHhhhcCCCH-HHHHHHHHHHHhcHHHhhcccccchHHHH----------------
Q 044799 30 KNALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDS-TITYKIFEAVYKYPFDLMTDGYGCHLARS---------------- 92 (304)
Q Consensus 30 ~~~~l~~~~g~i~~la~d~~gsr~lQ~~l~~~~~-e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~---------------- 92 (304)
.+.-+..+.|+++++++||+|||+||+-++.+++ +++..+|+++.+.+.+||+|.||||||||
T Consensus 170 ~~l~~~~~~~~~v~f~~Dq~GsrfiQqkl~~~~~~~ek~~if~ei~~~~~~L~~dvFGNyvIQkffE~gt~~q~~~l~~~ 249 (503)
T KOG1488|consen 170 KTLELVDIPGHLVEFAKDQHGSRFIQQKLETASDNEEKQAVFDEILPPALELMTDVFGNYVIQKFFEHGTEDQRNLLHSQ 249 (503)
T ss_pred ccccccccCCCceeecCCcccchHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhccCCHHHHHHHHHH
Confidence 3344455679999999999999999999999988 99999999999999999999999999999
Q ss_pred -----------------HHHHHHhcCChhHHHHHHHHHHHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHHHh--cH
Q 044799 93 -----------------MQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMN--HF 153 (304)
Q Consensus 93 -----------------vQkll~~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~--~~ 153 (304)
|||.|+....+...+++.+ |.++++.++.|++||||||+|+|+.|++...+|++.+.+ ++
T Consensus 250 ~~g~v~~Lsld~ygCRVIQkale~id~~~~~~Li~E-Ld~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv~~f~~~~~~ 328 (503)
T KOG1488|consen 250 IKGHVLELSLDMYGCRVIQKALEKVDVSLQIQLIDE-LDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVDFFSGDDNL 328 (503)
T ss_pred HHhhhhhhhcccccchhHHHHHHhcCHHHHHHHHHH-HHhhHHHHHhhcccceehhhhhhccChHHHHHHHHHhcCCCce
Confidence 9999999876666666655 899999999999999999999999999999999999999 99
Q ss_pred HHHhhccCccHHHHHHHhcCChhhHHHHHHHHHHhHHhhhcCCCcchhHHHHhccCCHhhHHHHHHHHHHhHHHhhccch
Q 044799 154 RELATHVRGCVSLNNFINEMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRC 233 (304)
Q Consensus 154 ~~la~~~~Gs~Vlq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~~GnyViQ~lL~~~~~~~~~~i~~~l~~~~~~Ls~~k~ 233 (304)
..+|+|+|||||||++++++++++...++++|..++.+|+.|+|||||||++|++++++.+..|+++|.+++++||.|||
T Consensus 329 ~~ls~~~YGCRVIQr~lE~c~~~~~~~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~I~~~l~~~ll~~Sq~Kf 408 (503)
T KOG1488|consen 329 LELSTHKYGCRVIQRILEHCSEDQKQPLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTIIIKCLLGNLLSMSQHKF 408 (503)
T ss_pred eEeeccCcccHHHHHHhhcCChHhhhHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhhHHHHHHhhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999998888999999999999999999
Q ss_pred hhHHHHHhhh-------hhhh---------------ccCCCCchhHHHHHHHhhCCccchHHHHHHHHhhcccccccccc
Q 044799 234 GSHLVEKYQR-------PSIF---------------TPCQHKYGNFVIQQALRVTKGFQMTERNIIQELGQSSFIQGIVP 291 (304)
Q Consensus 234 gs~Vvek~l~-------~~Ii---------------l~~~d~~GnyViq~~l~~~~~~~~~~~~~l~~l~~~~~~~~~~~ 291 (304)
+|+|||||+. .+|+ +++.|+|||||||++++.|++.++++ ++..+..+.-..+..+
T Consensus 409 ASnVVEk~~~~a~~~~r~~i~~Ei~~~~~~~~~~L~~mmkdQYgNYVVQkmi~~~~~~q~~~--i~~rI~~h~~~Lrk~s 486 (503)
T KOG1488|consen 409 ASNVVEKAFLFAPPLLRALIMNEIFPGYVEHPDALDIMMKDQYGNYVVQKMIDICGPEQREL--IKSRVKPHASRLRKFS 486 (503)
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHhcCCccCCccHHHHHHHHhhhhhHHHHHHHhcCHHHHHH--HHHHHHHHHHHHccCc
Confidence 9999999999 2333 12299999999999999998876532 1112222222235578
Q ss_pred ccceEee
Q 044799 292 FNFHVVS 298 (304)
Q Consensus 292 ~~~~i~~ 298 (304)
|||||+.
T Consensus 487 yGKhIia 493 (503)
T KOG1488|consen 487 YGKHIIA 493 (503)
T ss_pred cHHHHHH
Confidence 8888864
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=5.6e-50 Score=365.46 Aligned_cols=262 Identities=27% Similarity=0.386 Sum_probs=216.1
Q ss_pred cCcccccchhhHhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHHHHHHHHhcCChhHHHHH
Q 044799 30 KNALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLV 109 (304)
Q Consensus 30 ~~~~l~~~~g~i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~i 109 (304)
++.+++++.+++.+++.|++|++++|+++++++++++..|++++.+++.+|++|+||||++| ++++.+. +++...+
T Consensus 37 ~~~i~~~l~~~~~~l~~~~~g~~vvq~~l~~~~~~~~~~i~~~~~~~~~~l~~~~~g~~vlq---kll~~~~-~~~~~~i 112 (322)
T cd07920 37 KELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVVRLSLDMYGCRVIQ---KLLESIS-EEQISLL 112 (322)
T ss_pred HHHHHHHHHHhHHHHhcCccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcccchhHHHHH---HHHHhcC-HHHHHHH
Confidence 44555555555555555555555555555555555555555555555555555555555555 9999976 7777888
Q ss_pred HHHHHHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHhhccCccHHHHHHHhcCChhhHHHHHHHHHHhH
Q 044799 110 ISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRGPRRGGLLDLISSHA 189 (304)
Q Consensus 110 ~~~l~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la~~~~Gs~Vlq~~l~~~~~~~~~~l~~~l~~~~ 189 (304)
.+++.+++..|+.|++||||+|++++.+++++++.|++.+.+++.+++.|++||+|+|++++.++++++..+++++.+++
T Consensus 113 ~~~l~~~~~~L~~d~~gn~Vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~G~~vvq~~l~~~~~~~~~~l~~~l~~~~ 192 (322)
T cd07920 113 VKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHA 192 (322)
T ss_pred HHHHHHCHHHHhhcccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHcCccccHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence 88899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcCCCcchhHHHHhccCCHhhHHHHHHHHHHhHHHhhccchhhHHHHHhhh-------hhhh--c------------
Q 044799 190 EFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVEKYQR-------PSIF--T------------ 248 (304)
Q Consensus 190 ~~L~~d~~GnyViQ~lL~~~~~~~~~~i~~~l~~~~~~Ls~~k~gs~Vvek~l~-------~~Ii--l------------ 248 (304)
..|+.|+|||||||++|+.++++.++.+++.+.+++.+|+++||||+|+|+|++ +.|+ +
T Consensus 193 ~~L~~d~~Gn~vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~k~Gs~Vve~~l~~~~~~~~~~ii~~l~~~~~~~~~l~~ 272 (322)
T cd07920 193 LELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEKCLKHASKEERELIIDEILASGNETSALDT 272 (322)
T ss_pred HHHhcCCchhhHHHHHHhcCCHHHHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHCCHHHHHHHHHHHhcCCCchhHHHH
Confidence 999999999999999999999999999999999999999999999999999999 2333 1
Q ss_pred cCCCCchhHHHHHHHhhCCccchHHHHHHHHhhccccccccccccceEe
Q 044799 249 PCQHKYGNFVIQQALRVTKGFQMTERNIIQELGQSSFIQGIVPFNFHVV 297 (304)
Q Consensus 249 ~~~d~~GnyViq~~l~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~i~ 297 (304)
.++|+|||||||++|+.++++. ....+.++.++....+.++||++|+
T Consensus 273 l~~d~~Gn~Viq~~l~~~~~~~--~~~i~~~l~~~~~~L~~~~~G~~v~ 319 (322)
T cd07920 273 LMKDQYGNYVIQTALDVAKEEQ--RELLVEAIRPHLPSLRKSPYGKHIL 319 (322)
T ss_pred HhCCCcccHHHHHHHHhCCHHH--HHHHHHHHHHHHHHHcCCCcHHHHH
Confidence 1299999999999999999653 2334444555555568889999875
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=7e-49 Score=367.00 Aligned_cols=271 Identities=34% Similarity=0.460 Sum_probs=246.1
Q ss_pred ccccchhhHhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHH--------------------
Q 044799 33 LLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARS-------------------- 92 (304)
Q Consensus 33 ~l~~~~g~i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~-------------------- 92 (304)
.+.+..|.+..+|+|++||+++|+.+..++......|+.++.+++.+|+.|+||++++|+
T Consensus 211 ~~~~~~~~~~~~akd~~gc~~lq~~~~~~~~~~~~~if~~~~~~~~~Lm~d~fGny~vqkl~~~~~~eq~~~i~~~lts~ 290 (536)
T KOG2049|consen 211 SMVEIQGSINLIAKDQHGCRLLQKLLSEGTKVSILKIFLETIQDVPELMEDPFGNYLVQKLLEVCDEEQLTKIVSLLTSD 290 (536)
T ss_pred hhhccchhhhhhcccccCCcccccCcccCccccHHHHHHHHHHHHHHHHhccchhHHHHHHHHhhCHHHHHHHHHHHhcC
Confidence 346777999999999999999999999999999999999999999999999999999998
Q ss_pred ----------------HHHHHHhcCChhHHHHHHHHHHHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHH
Q 044799 93 ----------------MQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFREL 156 (304)
Q Consensus 93 ----------------vQkll~~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~l 156 (304)
+|++++...+.+++..+++++.+.++.|++|.||+||+|+|+..++++.++.+++.+..++.++
T Consensus 291 p~~fv~i~~N~~GTr~iQkl~~~~~~~dqI~~~~~ai~~~fl~L~~D~~g~~Viq~cl~~f~~~~~~~l~e~i~~~c~~i 370 (536)
T KOG2049|consen 291 PRLFVEICTNMYGTRAVQKLLGKSDSVDQISLFLDAIKPNFLHLIKDKNGNHVIQRCLRVFSKEKNEFLYEAILRYCLDL 370 (536)
T ss_pred ccceeEeeecCchhHHHHHHHhccccHHHHHHHHHHHHhhhHHhhhhcchhHHHHHHHHhcCchhhhHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCccHHHHHHHhcCChhhHHHHHHHHHHhHHhhhcCCCcchhHHHHhccCCHhhHHHHHHHHHHhHHHhhccchhhH
Q 044799 157 ATHVRGCVSLNNFINEMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSH 236 (304)
Q Consensus 157 a~~~~Gs~Vlq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~~GnyViQ~lL~~~~~~~~~~i~~~l~~~~~~Ls~~k~gs~ 236 (304)
|+|++||+|||+|++.....+|+.+++++..++..|+.|+|||||||++|+..++.....|+..|.+++++||.+||||+
T Consensus 371 A~~~hGCcvLq~cl~~~~~~~rd~Lv~~i~~naL~Ls~d~~GNyvVQyvl~L~~~~~t~~i~~~L~g~~veLS~qKfgS~ 450 (536)
T KOG2049|consen 371 ATDQHGCCVLQKCLDYSRGEQRDRLVEEISRNALLLSNDPYGNYVVQYVLELNDPSCTVNIAEKLRGHYVELSFQKFGSH 450 (536)
T ss_pred HHhccccchhHHHhcchhHHHHHHHHHHHHHHhHhhhcCccccchhhhhhhhcCcchHHHHHHhhhhHHHHHHHHhhccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhh------hhhh---ccC-------CCCchhHHHHHHHhhCCc-cchHHHHHHHHhhcc-ccccccccccceEee
Q 044799 237 LVEKYQR------PSIF---TPC-------QHKYGNFVIQQALRVTKG-FQMTERNIIQELGQS-SFIQGIVPFNFHVVS 298 (304)
Q Consensus 237 Vvek~l~------~~Ii---l~~-------~d~~GnyViq~~l~~~~~-~~~~~~~~l~~l~~~-~~~~~~~~~~~~i~~ 298 (304)
||||||+ ..|| |.+ +|+|||||||++|.+.+. .+..+...+..-..+ ....+..|+|+++..
T Consensus 451 vVEk~L~~~~~~~~~iV~ell~~~~~~~Ll~D~ygNyViq~AL~vtk~~~~~~~~~~lv~~~~~~~~~lr~~p~~~~~~~ 530 (536)
T KOG2049|consen 451 VVEKLLKVRESSRAQIVLELLSCDELDRLLRDPYGNYVIQTALRVTKVKLREDLFGLLVQKLMPRIRLLRNNPGGNIALI 530 (536)
T ss_pred HHHHHHhcCcchhhHHHHHHHccccHHHHhhCccchHHHHHHHHHhhhcccchhhHHHHHHHhhhhHHhhcCcccceeee
Confidence 9999999 2344 332 999999999999999985 333344333333232 344588999999988
Q ss_pred ecccC
Q 044799 299 YSSLT 303 (304)
Q Consensus 299 ~~~~~ 303 (304)
.-++.
T Consensus 531 ~~~~~ 535 (536)
T KOG2049|consen 531 KDSLR 535 (536)
T ss_pred hhccc
Confidence 76654
No 4
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-41 Score=330.91 Aligned_cols=231 Identities=29% Similarity=0.425 Sum_probs=211.9
Q ss_pred ccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHH--------------------------------
Q 044799 45 GKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARS-------------------------------- 92 (304)
Q Consensus 45 a~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~-------------------------------- 92 (304)
++||+|||.||+.|+.-+.++...++.++.+...+||.|.|||||+||
T Consensus 447 ~~Dq~g~r~LQk~Lds~s~~~~~~~~~e~~d~~~eLs~d~fGNyliQK~fe~~s~~q~~~ml~~~~~~~~~ls~~~~Gtr 526 (777)
T COG5099 447 CKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTR 526 (777)
T ss_pred cCCcHHHHHHHHHhcccchHHHHHHHHHHhhhhHHHHHhhhcchhhHHHHHhccHHHHHHHHHHhhhhHHHhhccccccH
Confidence 688888888888888888888888888888888888888888888888
Q ss_pred -HHHHHHhcCChhHHHHHHHHHHHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHhhccCccHHHHHHHh
Q 044799 93 -MQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFIN 171 (304)
Q Consensus 93 -vQkll~~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la~~~~Gs~Vlq~~l~ 171 (304)
+||+++...++++...+++++.+.+..|++|++||||+|+|++.++.+...+|++.+.+++.++++|+|||+|+|+|++
T Consensus 527 v~QK~id~~~t~~qi~~lv~~l~~~~~~li~dqngNHviqKci~~~~~~~~~fif~~~~~~~~~is~~r~Gs~vvq~~le 606 (777)
T COG5099 527 VLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLE 606 (777)
T ss_pred HHHHHHhccCchhhHHHHHHHhhhhhHHHHHhccCCHHHHHHHHhcCccccchHHHHHHhhhHhhhccccccHHHHHHHH
Confidence 8899999999999988889999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCChhhHHHHHHHHHHhHHhhhcCCCcchhHHHHhccCCHhhHHHHHHHHHH-hHHHhhccchhhHHHHHhhh-------
Q 044799 172 EMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKG-KFEELSLLRCGSHLVEKYQR------- 243 (304)
Q Consensus 172 ~~~~~~~~~l~~~l~~~~~~L~~d~~GnyViQ~lL~~~~~~~~~~i~~~l~~-~~~~Ls~~k~gs~Vvek~l~------- 243 (304)
.+..++...++++|..+...|++|+|||||||++|+.+.+..++.++..+.. ++++||+|||||+|||||++
T Consensus 607 ~~~~~~~~~~~~~Ii~~~~~L~~dq~GNyvvq~il~~g~~~~k~~i~~~~l~~~v~elS~~kfaSnvVeK~i~~~~~~~~ 686 (777)
T COG5099 607 NCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIKYASDSFK 686 (777)
T ss_pred hccHhHHHHHHHHHHHHHHhhccCCcchhhhhHHhhcCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchH
Confidence 9999999999999999999999999999999999999999999999998888 99999999999999999999
Q ss_pred -hhhh---c------------cCCCCchhHHHHHHHhhCCccchHHHH
Q 044799 244 -PSIF---T------------PCQHKYGNFVIQQALRVTKGFQMTERN 275 (304)
Q Consensus 244 -~~Ii---l------------~~~d~~GnyViq~~l~~~~~~~~~~~~ 275 (304)
++|+ + .+.|.|||||+|++++.....++.+..
T Consensus 687 ~~ril~~~~~~~~~~~~~l~~i~~d~y~Nyv~q~~~~~s~~~~~~l~~ 734 (777)
T COG5099 687 RSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLA 734 (777)
T ss_pred HHHHHHHHhcccccCChHHHHHHHhhhcchHHHHHHhhCchhhHHHHH
Confidence 2444 1 128999999999999999998765443
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=3.8e-38 Score=287.47 Aligned_cols=230 Identities=17% Similarity=0.182 Sum_probs=209.8
Q ss_pred ccCcccccchhhHhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHHHHHHHHhcCChhHHHH
Q 044799 29 GKNALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISL 108 (304)
Q Consensus 29 ~~~~~l~~~~g~i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~ 108 (304)
.+..+++++.|+++++|.|++||+++|++++.++++++..+++++.+++.+|++|+|||||+| ++++.+ +++..+.
T Consensus 72 ~~~~i~~~~~~~~~~l~~~~~g~~vlqkll~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Vvq---~~l~~~-~~~~~~~ 147 (322)
T cd07920 72 QRLQLLEKILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQ---KCIEKF-PPEDLQF 147 (322)
T ss_pred HHHHHHHHHHHHHHHHcccchhHHHHHHHHHhcCHHHHHHHHHHHHHCHHHHhhcccccHHHH---HHHHhC-CHHHHHH
Confidence 367788899999999999999999999999999999999999999999999999999999999 899986 4666777
Q ss_pred HHHHHHHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHhhccCccHHHHHHHhcCChhhHHHHHHHHHHh
Q 044799 109 VISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRGPRRGGLLDLISSH 188 (304)
Q Consensus 109 i~~~l~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la~~~~Gs~Vlq~~l~~~~~~~~~~l~~~l~~~ 188 (304)
+.+.+.+++.++++|++|++|+|++++.++++++..+++.+.+++..++.|+||++|+|++++..+++.+..+++.+.++
T Consensus 148 i~~~l~~~~~~l~~~~~G~~vvq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~~Gn~vvq~~l~~~~~~~~~~i~~~l~~~ 227 (322)
T cd07920 148 IIDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGN 227 (322)
T ss_pred HHHHHHHHHHHHHcCccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 88889999999999999999999999999999999999999999999999999999999999999888899999999999
Q ss_pred HHhhhcCCCcchhHHHHhccCCHhhHHHHHHHHH------HhHHHhhccchhhHHHHHhhh-------hhhh--c-----
Q 044799 189 AEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLK------GKFEELSLLRCGSHLVEKYQR-------PSIF--T----- 248 (304)
Q Consensus 189 ~~~L~~d~~GnyViQ~lL~~~~~~~~~~i~~~l~------~~~~~Ls~~k~gs~Vvek~l~-------~~Ii--l----- 248 (304)
+..|+.|+||++|++++++..++..++.+++.+. +++.+|+.|+||++|++++++ +.|+ +
T Consensus 228 ~~~l~~~k~Gs~Vve~~l~~~~~~~~~~ii~~l~~~~~~~~~l~~l~~d~~Gn~Viq~~l~~~~~~~~~~i~~~l~~~~~ 307 (322)
T cd07920 228 IVQLSCHKFASNVVEKCLKHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLP 307 (322)
T ss_pred HHHHHcCcchHHHHHHHHHHCCHHHHHHHHHHHhcCCCchhHHHHHhCCCcccHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999988999999985 589999999999999999999 2232 1
Q ss_pred -cCCCCchhHHHHHH
Q 044799 249 -PCQHKYGNFVIQQA 262 (304)
Q Consensus 249 -~~~d~~GnyViq~~ 262 (304)
-+.++||..|+.++
T Consensus 308 ~L~~~~~G~~v~~~~ 322 (322)
T cd07920 308 SLRKSPYGKHILAKL 322 (322)
T ss_pred HHcCCCcHHHHHHhC
Confidence 13889999998763
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=6.4e-37 Score=284.34 Aligned_cols=212 Identities=17% Similarity=0.223 Sum_probs=186.9
Q ss_pred cCcccccchhhHhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHH-----------------
Q 044799 30 KNALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARS----------------- 92 (304)
Q Consensus 30 ~~~~l~~~~g~i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~----------------- 92 (304)
++.+...+.|.+..||.|.+||||+|+.|+.-+.++...+++||-+++..+++|++||||+||
T Consensus 243 ~~~l~~~~~g~v~~Lsld~ygCRVIQkale~id~~~~~~Li~ELd~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv~~f 322 (503)
T KOG1488|consen 243 RNLLHSQIKGHVLELSLDMYGCRVIQKALEKVDVSLQIQLIDELDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVDFF 322 (503)
T ss_pred HHHHHHHHHhhhhhhhcccccchhHHHHHHhcCHHHHHHHHHHHHhhHHHHHhhcccceehhhhhhccChHHHHHHHHHh
Confidence 556666677777777888888888888887777777777777777777777788888888877
Q ss_pred ------------------HHHHHHhcCChhHHHHHHHHHHHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHH
Q 044799 93 ------------------MQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFR 154 (304)
Q Consensus 93 ------------------vQkll~~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~ 154 (304)
||+++|+|..++.. .++++|..++..|+.|+|||||||.++++..++.+..|++.+.+++.
T Consensus 323 ~~~~~~~~ls~~~YGCRVIQr~lE~c~~~~~~-~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~I~~~l~~~ll 401 (503)
T KOG1488|consen 323 SGDDNLLELSTHKYGCRVIQRILEHCSEDQKQ-PLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTIIIKCLLGNLL 401 (503)
T ss_pred cCCCceeEeeccCcccHHHHHHhhcCChHhhh-HHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhhHHHHHHhhHH
Confidence 88999998755544 47788999999999999999999999999999999999999999999
Q ss_pred HHhhccCccHHHHHHHhcCChhhHHHHHHHHHH-------hHHhhhcCCCcchhHHHHhccCCHhhHHHHHHHHHHhHHH
Q 044799 155 ELATHVRGCVSLNNFINEMRGPRRGGLLDLISS-------HAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEE 227 (304)
Q Consensus 155 ~la~~~~Gs~Vlq~~l~~~~~~~~~~l~~~l~~-------~~~~L~~d~~GnyViQ~lL~~~~~~~~~~i~~~l~~~~~~ 227 (304)
.+++|+|+|+||++|+.++++..|..+++++.+ .+..|+.|+|||||||++|+.+++++++.|...++.|+..
T Consensus 402 ~~Sq~KfASnVVEk~~~~a~~~~r~~i~~Ei~~~~~~~~~~L~~mmkdQYgNYVVQkmi~~~~~~q~~~i~~rI~~h~~~ 481 (503)
T KOG1488|consen 402 SMSQHKFASNVVEKAFLFAPPLLRALIMNEIFPGYVEHPDALDIMMKDQYGNYVVQKMIDICGPEQRELIKSRVKPHASR 481 (503)
T ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCccCCccHHHHHHHHhhhhhHHHHHHHhcCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999874 4678999999999999999999999999999999999999
Q ss_pred hhccchhhHHHHHhh
Q 044799 228 LSLLRCGSHLVEKYQ 242 (304)
Q Consensus 228 Ls~~k~gs~Vvek~l 242 (304)
|...+||-++++++=
T Consensus 482 Lrk~syGKhIia~le 496 (503)
T KOG1488|consen 482 LRKFSYGKHIIAKLE 496 (503)
T ss_pred HccCccHHHHHHHHH
Confidence 999999999998853
No 7
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=4.2e-30 Score=251.91 Aligned_cols=187 Identities=21% Similarity=0.270 Sum_probs=171.9
Q ss_pred hcccccchHHHHHHHHHHhcCChhHHHHHHHHHHHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHhhcc
Q 044799 81 MTDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHV 160 (304)
Q Consensus 81 ~~d~~gs~vvQ~vQkll~~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la~~~ 160 (304)
++|++|++.+| +.++. ...+..+.++.++.+...+|+.|.+||||+|+++|++...++..++..+.+++.+++.|+
T Consensus 447 ~~Dq~g~r~LQ---k~Lds-~s~~~~~~~~~e~~d~~~eLs~d~fGNyliQK~fe~~s~~q~~~ml~~~~~~~~~ls~~~ 522 (777)
T COG5099 447 CKDQHGSRFLQ---KLLDS-NSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHK 522 (777)
T ss_pred cCCcHHHHHHH---HHhcc-cchHHHHHHHHHHhhhhHHHHHhhhcchhhHHHHHhccHHHHHHHHHHhhhhHHHhhccc
Confidence 79999999999 88998 456667778888999999999999999999999999999999999999999999999999
Q ss_pred CccHHHHHHHhcCChhhH-HHHHHHHHHhHHhhhcCCCcchhHHHHhccCCHhhHHHHHHHHHHhHHHhhccchhhHHHH
Q 044799 161 RGCVSLNNFINEMRGPRR-GGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVE 239 (304)
Q Consensus 161 ~Gs~Vlq~~l~~~~~~~~-~~l~~~l~~~~~~L~~d~~GnyViQ~lL~~~~~~~~~~i~~~l~~~~~~Ls~~k~gs~Vve 239 (304)
|||||+|++++....+.. ..+++++.+++..|++|++||||+|++++....+....|++.+.+++.+++.|+|||+||+
T Consensus 523 ~Gtrv~QK~id~~~t~~qi~~lv~~l~~~~~~li~dqngNHviqKci~~~~~~~~~fif~~~~~~~~~is~~r~Gs~vvq 602 (777)
T COG5099 523 YGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQ 602 (777)
T ss_pred cccHHHHHHHhccCchhhHHHHHHHhhhhhHHHHHhccCCHHHHHHHHhcCccccchHHHHHHhhhHhhhccccccHHHH
Confidence 999999999999987764 4899999999999999999999999999999998899999999999999999999999999
Q ss_pred Hhhh-----------hhhh----ccCCCCchhHHHHHHHhhCCccch
Q 044799 240 KYQR-----------PSIF----TPCQHKYGNFVIQQALRVTKGFQM 271 (304)
Q Consensus 240 k~l~-----------~~Ii----l~~~d~~GnyViq~~l~~~~~~~~ 271 (304)
.|++ +.|+ .-++|+|||||||++|+.+..+..
T Consensus 603 ~~le~~~~~~~~~~~~~Ii~~~~~L~~dq~GNyvvq~il~~g~~~~k 649 (777)
T COG5099 603 RCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNK 649 (777)
T ss_pred HHHHhccHhHHHHHHHHHHHHHHhhccCCcchhhhhHHhhcCCCcch
Confidence 9999 2333 123999999999999999977643
No 8
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=9.9e-27 Score=215.21 Aligned_cols=270 Identities=16% Similarity=0.168 Sum_probs=200.6
Q ss_pred cccCccccc----chhhHhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHHHHHHHHhcCCh
Q 044799 28 YGKNALLAQ----PDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGS 103 (304)
Q Consensus 28 ~~~~~~l~~----~~g~i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~~~~~~ 103 (304)
..++.++.+ ++|++-+++.-|+.|||||.+++++++.+|..||++|.|.+++||+++||-|++| |++.+ .++
T Consensus 149 e~R~klv~el~~likg~i~~lv~aHDtSRViQt~Vky~s~~~r~~if~eL~p~~v~l~kskY~k~~v~---KmLky-Gsk 224 (652)
T KOG2050|consen 149 EERDKLVSELYKLIKGKISKLVFAHDTSRVIQTCVKYGSEAQREQIFEELLPFFVELAKSKYAKFFVQ---KMLKY-GSK 224 (652)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHhhhHHHHHHHHHhcCHHHHHHHHHHHhHHHHHHHHhHHHHHHHH---HHHhc-CCH
Confidence 335555554 4789999999999999999999999999999999999999999999999999999 99999 558
Q ss_pred hHHHHHHHHHHHhHHhhhccCCchHHHHHHHhh-CCcccHHHHHHHHHhcHHHHhhccCccHHHHHHHhcCChhhHHHHH
Q 044799 104 PCISLVISAAYRRFKDMMFSKEASSVIIKCLET-LDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRGPRRGGLL 182 (304)
Q Consensus 104 ~~~~~i~~~l~~~~~~L~~d~~gn~Viq~~l~~-~~~~~~~~ii~~l~~~~~~la~~~~Gs~Vlq~~l~~~~~~~~~~l~ 182 (304)
.+.+.|..++.+++..|+.|..|++|+...+.. .+.++|..++.+|.+..+.++.+ .--..|.+++... ++.+..|+
T Consensus 225 ~q~a~iI~sl~Ghv~kLlRH~eaa~Vve~ay~~~A~l~Qr~~li~EfYG~efqlfK~-sn~~Tl~kil~~~-pekk~~I~ 302 (652)
T KOG2050|consen 225 AQKAKIINSLRGHVVKLLRHREAAYVVEYAYNDFATLEQRQYLIQEFYGDEFQLFKD-SNDKTLDKILAEA-PEKKASIL 302 (652)
T ss_pred HHHHHHHHHHhhhHHHHHhhhHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHhc-cCcccHHHHHHhC-hHhHHHHH
Confidence 888888899999999999999999999998876 68899999999999999888888 4455566666553 34555555
Q ss_pred HHHHHhHHhhhcCC-Cc----chhHHHHhccCCHhhHHHHHHHHHHhHHHhhccchhhHHHHHhhh-------hhhh--c
Q 044799 183 DLISSHAEFLSKDP-SG----NYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVEKYQR-------PSIF--T 248 (304)
Q Consensus 183 ~~l~~~~~~L~~d~-~G----nyViQ~lL~~~~~~~~~~i~~~l~~~~~~Ls~~k~gs~Vvek~l~-------~~Ii--l 248 (304)
..+...+...+.-. -| ..++--++...+++.+..+++.+..-+.+|...+-||+|..+|++ +.|| |
T Consensus 303 ~~l~~~I~~v~eKg~v~~tivHk~mlEy~~~ade~e~~e~l~ll~elv~e~vHT~dGS~vAm~li~~a~aKeRK~IiK~~ 382 (652)
T KOG2050|consen 303 RHLKAIITPVAEKGSVDHTIVHKLMLEYLTIADEEEKSELLELLKELVPEMVHTRDGSRVAMKLIWHATAKERKLIIKNM 382 (652)
T ss_pred HHHHHHhHHHhhcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHhhCCHHHHHHHHHHH
Confidence 55554443332211 12 234444455566666666666666666666666666666666666 2344 1
Q ss_pred ------cCCCCchhHHHHHHHhhCCccchHHHHHHHHhhccccccccccccceEeeecccC
Q 044799 249 ------PCQHKYGNFVIQQALRVTKGFQMTERNIIQELGQSSFIQGIVPFNFHVVSYSSLT 303 (304)
Q Consensus 249 ------~~~d~~GnyViq~~l~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~i~~~~~~~ 303 (304)
.++|+|||.|+-++|++.||+.+.-.-+..++..+.-....++|||+|+.|-..+
T Consensus 383 K~h~~K~A~~~yGh~vlia~ldc~DDT~l~kk~i~~e~~~el~~li~Dk~Grrv~lyll~p 443 (652)
T KOG2050|consen 383 KEHVEKIANDEYGHLVLIALLDCTDDTKLLKKLIYDELKSELKSLISDKYGRRVILYLLAP 443 (652)
T ss_pred HHHHHHHHhhccCceehhhhhcccchHHHHHHHHHHHHHHHHHHHhccchhhhhhhhhccC
Confidence 1377888888888888888877655555556665555567778888887775443
No 9
>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=1.7e-26 Score=216.84 Aligned_cols=200 Identities=16% Similarity=0.171 Sum_probs=181.2
Q ss_pred hhHhhhccCcchhHHHHhhhcCC-CHHHHHHHHHHHHhcHHHhhcccccchHHHHHHHHHHhcCChhHHHHHHHHHHHhH
Q 044799 39 YDIVLLGKTEGGSLFLQKMLSGK-DSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRF 117 (304)
Q Consensus 39 g~i~~la~d~~gsr~lQ~~l~~~-~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~i~~~l~~~~ 117 (304)
+.++.++.|.+|+|.+|++++.. +.+|...+++.|.+.+..|++|.||+||+| +++..+. ++..+.+.+.+....
T Consensus 292 ~~fv~i~~N~~GTr~iQkl~~~~~~~dqI~~~~~ai~~~fl~L~~D~~g~~Viq---~cl~~f~-~~~~~~l~e~i~~~c 367 (536)
T KOG2049|consen 292 RLFVEICTNMYGTRAVQKLLGKSDSVDQISLFLDAIKPNFLHLIKDKNGNHVIQ---RCLRVFS-KEKNEFLYEAILRYC 367 (536)
T ss_pred cceeEeeecCchhHHHHHHHhccccHHHHHHHHHHHHhhhHHhhhhcchhHHHH---HHHHhcC-chhhhHHHHHHHHHH
Confidence 45777888888888888888776 445778889999999999999999999999 8999975 567788889999999
Q ss_pred HhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHhhccCccHHHHHHHhcCChhhHHHHHHHHHHhHHhhhcCCC
Q 044799 118 KDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRGPRRGGLLDLISSHAEFLSKDPS 197 (304)
Q Consensus 118 ~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la~~~~Gs~Vlq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~~ 197 (304)
.++|+|++|+.|+|+|+.....++++.+++++..+...++.|+||.+|||.+++.-.+.....|+..+.+++.+|+..+|
T Consensus 368 ~~iA~~~hGCcvLq~cl~~~~~~~rd~Lv~~i~~naL~Ls~d~~GNyvVQyvl~L~~~~~t~~i~~~L~g~~veLS~qKf 447 (536)
T KOG2049|consen 368 LDLATDQHGCCVLQKCLDYSRGEQRDRLVEEISRNALLLSNDPYGNYVVQYVLELNDPSCTVNIAEKLRGHYVELSFQKF 447 (536)
T ss_pred HHHHHhccccchhHHHhcchhHHHHHHHHHHHHHHhHhhhcCccccchhhhhhhhcCcchHHHHHHhhhhHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999997777789999999999999999999
Q ss_pred cchhHHHHhccCCHhhHHHHHHHHHH--hHHHhhccchhhHHHHHhhh
Q 044799 198 GNYVVQHVLGLGDLKYSEKICSLLKG--KFEELSLLRCGSHLVEKYQR 243 (304)
Q Consensus 198 GnyViQ~lL~~~~~~~~~~i~~~l~~--~~~~Ls~~k~gs~Vvek~l~ 243 (304)
|+|||+++|+..+.. ++.++..|.+ ++..|..++||.+|+++.++
T Consensus 448 gS~vVEk~L~~~~~~-~~~iV~ell~~~~~~~Ll~D~ygNyViq~AL~ 494 (536)
T KOG2049|consen 448 GSHVVEKLLKVRESS-RAQIVLELLSCDELDRLLRDPYGNYVIQTALR 494 (536)
T ss_pred ccHHHHHHHhcCcch-hhHHHHHHHccccHHHHhhCccchHHHHHHHH
Confidence 999999999997754 3677777777 99999999999999999998
No 10
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=6.9e-24 Score=198.18 Aligned_cols=232 Identities=21% Similarity=0.255 Sum_probs=194.1
Q ss_pred cCcccccchhhHhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHH-----------------
Q 044799 30 KNALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARS----------------- 92 (304)
Q Consensus 30 ~~~~l~~~~g~i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~----------------- 92 (304)
.|.+++|..|+.+.+|+|+-||+++|+++..++..+...++.++.+++..++.|+||+||+|+
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~~~~s 169 (650)
T KOG2188|consen 90 VNSIFEEVYGRELDLATNQIGSKVLEDLLGFSDSRQLCDFFSALNGVLRSIAQHRFGSHVLESALEKLAALVGQEAALLS 169 (650)
T ss_pred ehhHHHHhccceeehhccchhHHHHHHHhccCCchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhCccccccc
Confidence 445999999999999999999999999999999999999999999999999999999999999
Q ss_pred --------------------------------------------------------------------------------
Q 044799 93 -------------------------------------------------------------------------------- 92 (304)
Q Consensus 93 -------------------------------------------------------------------------------- 92 (304)
T Consensus 170 ~dea~~~ke~p~~t~e~~~~~m~nei~~~~~~~l~~~~~gshv~rt~~l~l~s~~~~~~~~~~~~~~~~~~~~~~~~~~~ 249 (650)
T KOG2188|consen 170 EDEAAVEKEGPFVTCENLLLLMLNEISPHVLKTLMELIFGSHVLRTILLLLFSMCPIAESEHKLALRKAAHRGMDDWDAV 249 (650)
T ss_pred hhhhcccccCcccccchHHHHHHHHhhHHHHHHHHHHHHhHHHHHHHHHHHccCcchhhhHHHHHHHHHhhccccchhhh
Confidence
Q ss_pred --------------------------------------------------------------------------------
Q 044799 93 -------------------------------------------------------------------------------- 92 (304)
Q Consensus 93 -------------------------------------------------------------------------------- 92 (304)
T Consensus 250 ~~~pqsFp~~l~~~i~~~l~~~~~~s~~~~~~~k~~~vDk~~s~v~q~~i~l~~~~~~~~~~~~~~~lv~~~~~~~e~d~ 329 (650)
T KOG2188|consen 250 TTPPQSFPQRLIVWICTGLSALQDVSESKKRDLKGYEVDKSSSNVLQKAIRLAFDENKNDQFMESPRLVTKFQLFNEKDG 329 (650)
T ss_pred hcChhhccHHHHHHHhhhccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhcchhhhhhhhHHHhhhhccccCc
Confidence
Q ss_pred ---------------------HHHHHHhcCChhHHHHHHHHHHHhHHhhhccCCchHHHHHHHhhCC-cccHHHHHHHHH
Q 044799 93 ---------------------MQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLD-EQKNEVLYLAAM 150 (304)
Q Consensus 93 ---------------------vQkll~~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Viq~~l~~~~-~~~~~~ii~~l~ 150 (304)
+..+++.++ +...+++...+.+++..|+.||.||+++|++|++.. .++...|++++.
T Consensus 330 ~~~kE~~~~k~~l~d~tgSrllE~Imeva~-~~~~~lf~~~f~~rl~~La~~p~aNF~lQrli~h~~~~e~v~~v~eeL~ 408 (650)
T KOG2188|consen 330 LWGKERSFLKELLSDQTGSRLLEVIMEVAS-ESLLSLFYIVFCGRLDELAVHPIANFPLQRLINHLTSLEDVGSVIEELA 408 (650)
T ss_pred ccccccHHHHHHHhcCcccHHHHHHHHhcC-HHHHHHHHHHHHHHHHHHHhCccccchHHHHHHhccCHHHHHHHHHHHh
Confidence 666777765 344477777788899999999999999999999887 677777777776
Q ss_pred hcHHHH-----------------------------------------------------------------hhccCccHH
Q 044799 151 NHFREL-----------------------------------------------------------------ATHVRGCVS 165 (304)
Q Consensus 151 ~~~~~l-----------------------------------------------------------------a~~~~Gs~V 165 (304)
+++.++ -.|+.||.+
T Consensus 409 P~~~~LL~~g~~gVv~sLia~~~rl~s~q~~~l~~Li~a~~~~~~~~k~il~~lL~~~~~~g~~~~~~~t~~~h~~ga~l 488 (650)
T KOG2188|consen 409 PKLSSLLEQGNSGVVASLIAASARLGSYQDKMLQQLIQAFHAASESKKNILPCLLFSLTLFGCVGEWFLTEKFHQKGAVL 488 (650)
T ss_pred HHHHHHHHcCCchHhHHHHHHHHhhchhHHHHHHHHHHHHhcCChhhcchHHHHHHHhhhcccccccccHHHHhhchhHH
Confidence 544333 123367888
Q ss_pred HHHHHhcCChh---hHHHHHHHHHHhHHhhhcCCCcchhHHHHhcc--CCHhhHHHHHHHHHHhHHHhhccchhhHHHHH
Q 044799 166 LNNFINEMRGP---RRGGLLDLISSHAEFLSKDPSGNYVVQHVLGL--GDLKYSEKICSLLKGKFEELSLLRCGSHLVEK 240 (304)
Q Consensus 166 lq~~l~~~~~~---~~~~l~~~l~~~~~~L~~d~~GnyViQ~lL~~--~~~~~~~~i~~~l~~~~~~Ls~~k~gs~Vvek 240 (304)
+|.++++..+. ....+.+...+++.+++++.+|+|||+++|.. .++..+++++..+.+++++|+++.|||+|+||
T Consensus 489 le~lv~f~k~~i~~litsll~L~~eqi~e~~~~~~~ShlIeavL~S~~l~~~~~~kLi~~l~g~~~~La~~~~GSrv~eK 568 (650)
T KOG2188|consen 489 LEELVNFSKTHIQTLITSLLSLSEEQILEMSCNGVGSHLIEAVLASKDLGEKIKEKLINILDGSFVTLALSTFGSRVFEK 568 (650)
T ss_pred HHHHHhhchhhhHHHHHHHHhhhHHHHHHHhcCCchHHHHHHHHHhccccHHHHHHHHHHhhccchheeecCcccHHHHH
Confidence 88888876542 25566666678899999999999999999998 55788999999999999999999999999999
Q ss_pred hhh-------hhhh--c------cCCCCchhHHHHHH
Q 044799 241 YQR-------PSIF--T------PCQHKYGNFVIQQA 262 (304)
Q Consensus 241 ~l~-------~~Ii--l------~~~d~~GnyViq~~ 262 (304)
|++ ..|. | -..++||.||..+.
T Consensus 569 ~wea~~~~~k~rIakeL~~~~~~vk~s~~gk~v~~~~ 605 (650)
T KOG2188|consen 569 CWEATDVLYKERIAKELVGIHNDVKSSKYGKFVMLNW 605 (650)
T ss_pred HHHHhhHHHHHHHHHHHHhhccccccCcchHHHHHhc
Confidence 999 2343 1 12899999997664
No 11
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=9.3e-20 Score=169.22 Aligned_cols=234 Identities=15% Similarity=0.143 Sum_probs=173.6
Q ss_pred cCcccccchhhHhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHHHHHHHHhcCChhHHHHH
Q 044799 30 KNALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLV 109 (304)
Q Consensus 30 ~~~~l~~~~g~i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~i 109 (304)
++.+++++.|.+++||++.+|-+++|++|.++++++++.|++++.||+..|+.|+.|++|+. -+.....+.+|++.+
T Consensus 191 r~~if~eL~p~~v~l~kskY~k~~v~KmLkyGsk~q~a~iI~sl~Ghv~kLlRH~eaa~Vve---~ay~~~A~l~Qr~~l 267 (652)
T KOG2050|consen 191 REQIFEELLPFFVELAKSKYAKFFVQKMLKYGSKAQKAKIINSLRGHVVKLLRHREAAYVVE---YAYNDFATLEQRQYL 267 (652)
T ss_pred HHHHHHHHhHHHHHHHHhHHHHHHHHHHHhcCCHHHHHHHHHHHhhhHHHHHhhhHHHHHHH---HHHHhhccHHHHHHH
Confidence 88999999999999999999999999999999999999999999999999999999999999 677766677888878
Q ss_pred HHHHHHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHhh-----ccCccHHHHHHHhcCChhhHHHHHHH
Q 044799 110 ISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELAT-----HVRGCVSLNNFINEMRGPRRGGLLDL 184 (304)
Q Consensus 110 ~~~l~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la~-----~~~Gs~Vlq~~l~~~~~~~~~~l~~~ 184 (304)
..++.+.-..+.++.+-- -+.++++.. |+.+..|.+.+.+.+..++. +..=..++-..++.|+++.+..+++.
T Consensus 268 i~EfYG~efqlfK~sn~~-Tl~kil~~~-pekk~~I~~~l~~~I~~v~eKg~v~~tivHk~mlEy~~~ade~e~~e~l~l 345 (652)
T KOG2050|consen 268 IQEFYGDEFQLFKDSNDK-TLDKILAEA-PEKKASILRHLKAIITPVAEKGSVDHTIVHKLMLEYLTIADEEEKSELLEL 345 (652)
T ss_pred HHHHhhHHHHHHhccCcc-cHHHHHHhC-hHhHHHHHHHHHHHhHHHhhcchhHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 788999988888883322 344455443 44566666666655433321 22334455555666666667777777
Q ss_pred HHHhHHhhhcCCCcchhHHHHhccCCHhhHHHHHHHHHHhHHHhhccchhhHHHHHhhh---hh------hh------cc
Q 044799 185 ISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVEKYQR---PS------IF------TP 249 (304)
Q Consensus 185 l~~~~~~L~~d~~GnyViQ~lL~~~~~~~~~~i~~~l~~~~~~Ls~~k~gs~Vvek~l~---~~------Ii------l~ 249 (304)
+.+.+.+++..+-|+.|..+++++++++.|+.|+..+++|+..++.+.||+.|+-.+|+ ++ |. |.
T Consensus 346 l~elv~e~vHT~dGS~vAm~li~~a~aKeRK~IiK~~K~h~~K~A~~~yGh~vlia~ldc~DDT~l~kk~i~~e~~~el~ 425 (652)
T KOG2050|consen 346 LKELVPEMVHTRDGSRVAMKLIWHATAKERKLIIKNMKEHVEKIANDEYGHLVLIALLDCTDDTKLLKKLIYDELKSELK 425 (652)
T ss_pred HHHHHHHHhcCCchHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHhhccCceehhhhhcccchHHHHHHHHHHHHHHHHH
Confidence 77777777777777777777777777777777777777777777777777777766666 22 21 11
Q ss_pred C--CCCchhHHHHHHHhhCCc
Q 044799 250 C--QHKYGNFVIQQALRVTKG 268 (304)
Q Consensus 250 ~--~d~~GnyViq~~l~~~~~ 268 (304)
+ .|+||+=|+++++.-.|.
T Consensus 426 ~li~Dk~Grrv~lyll~p~D~ 446 (652)
T KOG2050|consen 426 SLISDKYGRRVILYLLAPRDG 446 (652)
T ss_pred HHhccchhhhhhhhhccCCcc
Confidence 1 777777777777766444
No 12
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]
Probab=99.74 E-value=8.5e-17 Score=151.01 Aligned_cols=199 Identities=13% Similarity=0.189 Sum_probs=167.2
Q ss_pred HhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHHHHHHHHhcCChhHHHHHHHHHHHhHHhh
Q 044799 41 IVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRFKDM 120 (304)
Q Consensus 41 i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~i~~~l~~~~~~L 120 (304)
...+-.|+.|||+++.++..+++..+..+...+.+.+.+|+.|+.|||++| ++|++..+.+.+..|++++.|++..|
T Consensus 338 ~k~~l~d~tgSrllE~Imeva~~~~~~lf~~~f~~rl~~La~~p~aNF~lQ---rli~h~~~~e~v~~v~eeL~P~~~~L 414 (650)
T KOG2188|consen 338 LKELLSDQTGSRLLEVIMEVASESLLSLFYIVFCGRLDELAVHPIANFPLQ---RLINHLTSLEDVGSVIEELAPKLSSL 414 (650)
T ss_pred HHHHHhcCcccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhCccccchHH---HHHHhccCHHHHHHHHHHHhHHHHHH
Confidence 345566999999999999999999998888889999999999999999999 99999998999999999999999988
Q ss_pred hccCCc--------------h---HHHHHHHhhCCc--------------------------------------------
Q 044799 121 MFSKEA--------------S---SVIIKCLETLDE-------------------------------------------- 139 (304)
Q Consensus 121 ~~d~~g--------------n---~Viq~~l~~~~~-------------------------------------------- 139 (304)
....+- + -++|.+++.+-+
T Consensus 415 L~~g~~gVv~sLia~~~rl~s~q~~~l~~Li~a~~~~~~~~k~il~~lL~~~~~~g~~~~~~~t~~~h~~ga~lle~lv~ 494 (650)
T KOG2188|consen 415 LEQGNSGVVASLIAASARLGSYQDKMLQQLIQAFHAASESKKNILPCLLFSLTLFGCVGEWFLTEKFHQKGAVLLEELVN 494 (650)
T ss_pred HHcCCchHhHHHHHHHHhhchhHHHHHHHHHHHHhcCChhhcchHHHHHHHhhhcccccccccHHHHhhchhHHHHHHHh
Confidence 875442 2 245544443210
Q ss_pred ---ccHHHHHHHH----HhcHHHHhhccCccHHHHHHHhc--CChhhHHHHHHHHHHhHHhhhcCCCcchhHHHHhccCC
Q 044799 140 ---QKNEVLYLAA----MNHFRELATHVRGCVSLNNFINE--MRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGD 210 (304)
Q Consensus 140 ---~~~~~ii~~l----~~~~~~la~~~~Gs~Vlq~~l~~--~~~~~~~~l~~~l~~~~~~L~~d~~GnyViQ~lL~~~~ 210 (304)
.+...+++.+ .+++.++|++.+|||+|+.+++. ..+..+..++..+-.....|+.+.+|++|+.++.+..+
T Consensus 495 f~k~~i~~litsll~L~~eqi~e~~~~~~~ShlIeavL~S~~l~~~~~~kLi~~l~g~~~~La~~~~GSrv~eK~wea~~ 574 (650)
T KOG2188|consen 495 FSKTHIQTLITSLLSLSEEQILEMSCNGVGSHLIEAVLASKDLGEKIKEKLINILDGSFVTLALSTFGSRVFEKCWEATD 574 (650)
T ss_pred hchhhhHHHHHHHHhhhHHHHHHHhcCCchHHHHHHHHHhccccHHHHHHHHHHhhccchheeecCcccHHHHHHHHHhh
Confidence 0011112211 36789999999999999999988 66777999999999999999999999999999999999
Q ss_pred HhhHHHHHHHHHHhHHHhhccchhhHHHHHhh
Q 044799 211 LKYSEKICSLLKGKFEELSLLRCGSHLVEKYQ 242 (304)
Q Consensus 211 ~~~~~~i~~~l~~~~~~Ls~~k~gs~Vvek~l 242 (304)
+.+|+.|++.|.+--..+..++||-.|.-+|=
T Consensus 575 ~~~k~rIakeL~~~~~~vk~s~~gk~v~~~~~ 606 (650)
T KOG2188|consen 575 VLYKERIAKELVGIHNDVKSSKYGKFVMLNWD 606 (650)
T ss_pred HHHHHHHHHHHHhhccccccCcchHHHHHhcc
Confidence 99999999999999999999999999988764
No 13
>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]
Probab=99.53 E-value=9.3e-15 Score=140.47 Aligned_cols=229 Identities=16% Similarity=0.178 Sum_probs=189.5
Q ss_pred hhhHhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHHHHHHHHhcCChhHHHHHHHHHHHhH
Q 044799 38 DYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRF 117 (304)
Q Consensus 38 ~g~i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~i~~~l~~~~ 117 (304)
.++..++..|-.|.-++|+++++++...++........++..+..|.||.|..| |+++.+.++.+...+.....+..
T Consensus 545 LDe~~elsSdylGNtVvqkfFe~sS~~ik~aml~r~s~ylts~gvHknGtw~~q---k~ik~a~te~qik~iv~g~dpyc 621 (1007)
T KOG4574|consen 545 LDELPELSSDYLGNTVVQKFFELSSDIIKDAMLRRGSKYLTSMGVHKNGTWACQ---KIIKMAFTERQIKLIVRGVDPYC 621 (1007)
T ss_pred hccCCcchhhhhcchhhHHHHhhccHHHHHHHHhhhhhhhhhccccccchHHHH---HHHHHhhchhhhheeeeccCcch
Confidence 355667788888999999999999999999999999999999999999999999 99999888988888988899999
Q ss_pred HhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHhhccCccHHHHHHHhcCC--hhhHHHHHHH-HHHhHHhhhc
Q 044799 118 KDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMR--GPRRGGLLDL-ISSHAEFLSK 194 (304)
Q Consensus 118 ~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la~~~~Gs~Vlq~~l~~~~--~~~~~~l~~~-l~~~~~~L~~ 194 (304)
..+..|+|||||+|.+|...-+ -..++++.+..++.++.+.+||++.+.+|++... .++....++. +......++.
T Consensus 622 ~~l~~dqfgnyvaqd~LkF~fp-~nsFVfE~v~s~~~~ivQsrfGsravrAcle~lNa~~e~qsl~~~s~iIs~ss~lat 700 (1007)
T KOG4574|consen 622 TPLLNDQFGNYVAQDSLKFGFP-WNSFVFESVFSHFWDIVQSRFGSRAVRACLEALNANTEDQSLVRESCIISKSSYLAT 700 (1007)
T ss_pred hhHHHHhhcceeeeeehhccCc-cchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhccCchhhhhhhhhhhhhchhhhhh
Confidence 9999999999999999998644 4678899999999999999999999999998654 3333333333 3444788888
Q ss_pred CCCcchhHHHHhccCCHhhHH-HHHHHHHHhHHHhhccchhhHHHHHhhh--------hhhh-----------------c
Q 044799 195 DPSGNYVVQHVLGLGDLKYSE-KICSLLKGKFEELSLLRCGSHLVEKYQR--------PSIF-----------------T 248 (304)
Q Consensus 195 d~~GnyViQ~lL~~~~~~~~~-~i~~~l~~~~~~Ls~~k~gs~Vvek~l~--------~~Ii-----------------l 248 (304)
+..|-..|-++|+.+....+. .++..+.+++..+|+||-|+-+|.|++. +.|+ +
T Consensus 701 nsng~llvtw~lDns~~~nrh~~l~~~lt~el~~lC~h~Lgsttv~Kl~n~~qepvs~ekii~hlf~~~n~kd~~lt~Vl 780 (1007)
T KOG4574|consen 701 NSNGLLLVTWLLDNSSLPNRHTILAHGLTKELVMLCFHKLGSTTVLKLLNLRQEPVSREKIIEHLFHLRNFKDSALTEVL 780 (1007)
T ss_pred cCccceeeeeecccccccchhhHHhhhhhhccchhhhhhccchhhhhhhhcCCChHHHHHHHHHHhhccccccchhhhhh
Confidence 889999999999887644444 3455777889999999999999988888 1222 0
Q ss_pred ----------------cC-----CCCchhHHHHHHHhhCCccc
Q 044799 249 ----------------PC-----QHKYGNFVIQQALRVTKGFQ 270 (304)
Q Consensus 249 ----------------~~-----~d~~GnyViq~~l~~~~~~~ 270 (304)
+. .|+|++||.|.++.......
T Consensus 781 ~~~~~gpmfiikvi~~p~iel~f~dQf~kvvrq~il~~~a~~n 823 (1007)
T KOG4574|consen 781 TEANYGPMFIIKVITKPTIELAFRDQFIKVVRQVILNSPAVSN 823 (1007)
T ss_pred hhhccccceeeeeeccccchHHHHHHHHHHHHHHHHhcCCccH
Confidence 00 89999999999999887654
No 14
>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]
Probab=99.35 E-value=1.1e-12 Score=126.34 Aligned_cols=158 Identities=16% Similarity=0.181 Sum_probs=139.7
Q ss_pred HHHHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHhhccCccHHHHHHHhcCChh-hHHHHHHHHHHhHH
Q 044799 112 AAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRGP-RRGGLLDLISSHAE 190 (304)
Q Consensus 112 ~l~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la~~~~Gs~Vlq~~l~~~~~~-~~~~l~~~l~~~~~ 190 (304)
.+.+...++..|-.||-|+|+++++...-.++.+.+....++..+..|++|.++.|++++.+..+ +.+.++....+.+.
T Consensus 543 ~mLDe~~elsSdylGNtVvqkfFe~sS~~ik~aml~r~s~ylts~gvHknGtw~~qk~ik~a~te~qik~iv~g~dpyc~ 622 (1007)
T KOG4574|consen 543 LMLDELPELSSDYLGNTVVQKFFELSSDIIKDAMLRRGSKYLTSMGVHKNGTWACQKIIKMAFTERQIKLIVRGVDPYCT 622 (1007)
T ss_pred HHhccCCcchhhhhcchhhHHHHhhccHHHHHHHHhhhhhhhhhccccccchHHHHHHHHHhhchhhhheeeeccCcchh
Confidence 35677788888999999999999999999999999999999999999999999999999998655 57777788889999
Q ss_pred hhhcCCCcchhHHHHhccCCHhhHHHHHHHHHHhHHHhhccchhhHHHHHhhh--------------hhhh---------
Q 044799 191 FLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVEKYQR--------------PSIF--------- 247 (304)
Q Consensus 191 ~L~~d~~GnyViQ~lL~~~~~~~~~~i~~~l~~~~~~Ls~~k~gs~Vvek~l~--------------~~Ii--------- 247 (304)
.+..|+|||||+|..|..+-++. .++++.+..++..+...+||++.+-+|++ ..||
T Consensus 623 ~l~~dqfgnyvaqd~LkF~fp~n-sFVfE~v~s~~~~ivQsrfGsravrAcle~lNa~~e~qsl~~~s~iIs~ss~latn 701 (1007)
T KOG4574|consen 623 PLLNDQFGNYVAQDSLKFGFPWN-SFVFESVFSHFWDIVQSRFGSRAVRACLEALNANTEDQSLVRESCIISKSSYLATN 701 (1007)
T ss_pred hHHHHhhcceeeeeehhccCccc-hHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhccCchhhhhhhhhhhhhchhhhhhc
Confidence 99999999999999999988764 67789999999999999999999999999 0111
Q ss_pred --------------------------------ccCCCCchhHHHHHHHhhCCccc
Q 044799 248 --------------------------------TPCQHKYGNFVIQQALRVTKGFQ 270 (304)
Q Consensus 248 --------------------------------l~~~d~~GnyViq~~l~~~~~~~ 270 (304)
+.|.|.-|+-+|+|+++.+.+++
T Consensus 702 sng~llvtw~lDns~~~nrh~~l~~~lt~el~~lC~h~Lgsttv~Kl~n~~qepv 756 (1007)
T KOG4574|consen 702 SNGLLLVTWLLDNSSLPNRHTILAHGLTKELVMLCFHKLGSTTVLKLLNLRQEPV 756 (1007)
T ss_pred CccceeeeeecccccccchhhHHhhhhhhccchhhhhhccchhhhhhhhcCCChH
Confidence 12489999999999999998876
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=98.52 E-value=3.5e-08 Score=59.34 Aligned_cols=30 Identities=37% Similarity=0.377 Sum_probs=14.7
Q ss_pred HhHHhhhcCCCcchhHHHHhccCCHhhHHH
Q 044799 187 SHAEFLSKDPSGNYVVQHVLGLGDLKYSEK 216 (304)
Q Consensus 187 ~~~~~L~~d~~GnyViQ~lL~~~~~~~~~~ 216 (304)
+++..|++|+|||||||++|+..+++.++.
T Consensus 4 ~~~~~l~~d~~Gn~VvQk~le~~~~~~~~~ 33 (35)
T PF00806_consen 4 GNLVELSKDQYGNYVVQKCLEHASPEQRQL 33 (35)
T ss_dssp TTHHHHHTSTTHHHHHHHHHHHSSHHHHHH
T ss_pred HHHHHHHhccccCHHHHHHHHHCCHHHHHh
Confidence 344455555555555555555544444433
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=98.48 E-value=6.5e-08 Score=58.15 Aligned_cols=27 Identities=19% Similarity=0.345 Sum_probs=11.4
Q ss_pred HhHHhhhccCCchHHHHHHHhhCCccc
Q 044799 115 RRFKDMMFSKEASSVIIKCLETLDEQK 141 (304)
Q Consensus 115 ~~~~~L~~d~~gn~Viq~~l~~~~~~~ 141 (304)
+++..|+.|+|||||||++++..++++
T Consensus 4 ~~~~~l~~d~~Gn~VvQk~le~~~~~~ 30 (35)
T PF00806_consen 4 GNLVELSKDQYGNYVVQKCLEHASPEQ 30 (35)
T ss_dssp TTHHHHHTSTTHHHHHHHHHHHSSHHH
T ss_pred HHHHHHHhccccCHHHHHHHHHCCHHH
Confidence 334444444444444444444443333
No 17
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=98.07 E-value=2.1e-06 Score=51.44 Aligned_cols=32 Identities=19% Similarity=0.232 Sum_probs=17.2
Q ss_pred HHhHHhhhccCCchHHHHHHHhhCCcccHHHH
Q 044799 114 YRRFKDMMFSKEASSVIIKCLETLDEQKNEVL 145 (304)
Q Consensus 114 ~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~i 145 (304)
.+++.+|+.|+|||||+|++++..+++++..+
T Consensus 3 ~~~~~~l~~~~~g~~viqk~l~~~~~~~~~~i 34 (36)
T smart00025 3 KGHLLELSKDQYGNRVVQKLLEHASESQREQI 34 (36)
T ss_pred hHHHHHHHhcchhhHHHHHHHHHCCHHHHHHh
Confidence 34555555555555555555555555444443
No 18
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=97.94 E-value=6.4e-06 Score=49.30 Aligned_cols=34 Identities=21% Similarity=0.233 Sum_probs=23.3
Q ss_pred chhhHhhhccCcchhHHHHhhhcCCCHHHHHHHH
Q 044799 37 PDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIF 70 (304)
Q Consensus 37 ~~g~i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~ 70 (304)
+.+++.++|.|++||+++|++++.++++++..++
T Consensus 2 ~~~~~~~l~~~~~g~~viqk~l~~~~~~~~~~i~ 35 (36)
T smart00025 2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35 (36)
T ss_pred chHHHHHHHhcchhhHHHHHHHHHCCHHHHHHhh
Confidence 3566777777777777777777777776666554
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=91.43 E-value=0.61 Score=37.56 Aligned_cols=66 Identities=17% Similarity=0.267 Sum_probs=38.6
Q ss_pred HHHHHHhcHHHHhhccCccHHHHHHHhcCChhh---HHHHHHHHHHh--------HHhhhcCCCcchhHHHHhccCC
Q 044799 145 LYLAAMNHFRELATHVRGCVSLNNFINEMRGPR---RGGLLDLISSH--------AEFLSKDPSGNYVVQHVLGLGD 210 (304)
Q Consensus 145 ii~~l~~~~~~la~~~~Gs~Vlq~~l~~~~~~~---~~~l~~~l~~~--------~~~L~~d~~GnyViQ~lL~~~~ 210 (304)
+++.+..+..++..+..||.+|..++..+..+. ...|.+.+... -..++.+++|.+++.+++..+.
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 444445556666666777777777666654332 12222222222 2357788888888888887654
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=81.39 E-value=5.8 Score=31.89 Aligned_cols=75 Identities=20% Similarity=0.150 Sum_probs=45.9
Q ss_pred HHHHHHHHhHHhhhcCCCcchhHHHHhccCCHhh---HHHHHHHHHHhHHHhhccchhhHHHHHhhhhhhhccCCCCchh
Q 044799 180 GLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKY---SEKICSLLKGKFEELSLLRCGSHLVEKYQRPSIFTPCQHKYGN 256 (304)
Q Consensus 180 ~l~~~l~~~~~~L~~d~~GnyViQ~lL~~~~~~~---~~~i~~~l~~~~~~Ls~~k~gs~Vvek~l~~~Iil~~~d~~Gn 256 (304)
.|++.+.++...|+.+.+|..||..+|...+.+. .+.|++.+.+.+.. ..+-|- .+++ .+++|.
T Consensus 57 ~Ll~~i~~~~~~ll~~~~g~~~i~eiL~~~~gdk~~a~~Aia~~~~~~~~~--~~~~~e---~H~i--------~~p~~~ 123 (148)
T PF08144_consen 57 PLLEAIAENAEELLSSSFGCQFITEILLSATGDKSAALEAIASLAAEPLFP--GDIDEE---YHLI--------EHPFGH 123 (148)
T ss_pred HHHHHHHHhHHHHHhcCcccHHHHHHHhccCccHHHHHHHHHHHHhhccCC--CCCcCc---cchh--------cCchHH
Confidence 4555666788999999999999999999865332 22333333322110 000000 0111 789999
Q ss_pred HHHHHHHhhCC
Q 044799 257 FVIQQALRVTK 267 (304)
Q Consensus 257 yViq~~l~~~~ 267 (304)
+++.+++....
T Consensus 124 r~lK~Liq~~~ 134 (148)
T PF08144_consen 124 RMLKKLIQGDK 134 (148)
T ss_pred HHHHHHHHCCC
Confidence 99998887665
No 21
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=79.25 E-value=52 Score=30.26 Aligned_cols=181 Identities=12% Similarity=0.155 Sum_probs=98.5
Q ss_pred chhHHHHhhhcC-CCHHHHHHHHHHHHhcHHHhhcccccchHHHHHHHHHHhcCChhHHHHHHHHHHHhHHhhhccCCch
Q 044799 49 GGSLFLQKMLSG-KDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEAS 127 (304)
Q Consensus 49 ~gsr~lQ~~l~~-~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~i~~~l~~~~~~L~~d~~gn 127 (304)
.|-..+.++|.. .+++....+++++.+.-. .++++ . +.... ++....+.....|....++...-..
T Consensus 80 gg~~~~~~iL~~~l~~~~a~~il~~i~~~~~--------~~~fe---~-L~~ld-~~~l~~lL~~EhpqtiA~iLs~l~~ 146 (339)
T PRK05686 80 GGIDYARSLLEKALGEEKADSILERILESLG--------TSGFD---F-LRKMD-PQQLANFIRNEHPQTIALILSYLKP 146 (339)
T ss_pred ChHHHHHHHHHHHcCHHHHHHHHHHHhcccc--------CchHH---H-HhcCC-HHHHHHHHHhcCHHHHHHHHhCCCH
Confidence 445567777765 566666777777654311 24555 2 33333 3333344444566666666666666
Q ss_pred HHHHHHHhhCCcccHHHHHHHHH------------------hcHHHH----hhccCccHHHHHHHhcCChhhHHHHHHHH
Q 044799 128 SVIIKCLETLDEQKNEVLYLAAM------------------NHFREL----ATHVRGCVSLNNFINEMRGPRRGGLLDLI 185 (304)
Q Consensus 128 ~Viq~~l~~~~~~~~~~ii~~l~------------------~~~~~l----a~~~~Gs~Vlq~~l~~~~~~~~~~l~~~l 185 (304)
-+-.+++..+|+..+..++..+. ..+... ....-|...+-.+++..+......+++.|
T Consensus 147 ~~aa~vL~~l~~~~~~~v~~ria~l~~v~~~~~~~i~~~L~~~l~~~~~~~~~~~~g~~~~a~Iln~~~~~~~~~il~~L 226 (339)
T PRK05686 147 DQAAEILSLLPEELRADVMMRIATLEGVSPEALKEVEEVLEKKLSSMANADRTKMGGVKTVAEILNNLDRQTEKTILESL 226 (339)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHhhcccccccccCcHHHHHHHHhcCCchHHHHHHHHH
Confidence 66667777777666555554432 222221 13446788888999998877777777777
Q ss_pred HHhHHhhhcCCCc-chhHHHHhccCCHhhHHHHHHHHHHhHHHhhccchhhHHHHHhhh
Q 044799 186 SSHAEFLSKDPSG-NYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVEKYQR 243 (304)
Q Consensus 186 ~~~~~~L~~d~~G-nyViQ~lL~~~~~~~~~~i~~~l~~~~~~Ls~~k~gs~Vvek~l~ 243 (304)
...-..++..-=. -|+...++. -++.....+++.+-.....++..--..-+.++++.
T Consensus 227 ~~~d~~~a~~Ir~~mF~Fedl~~-l~~~~l~~ll~~v~~~~L~~ALkga~~~~~~~il~ 284 (339)
T PRK05686 227 EEEDPELAEKIKDLMFVFEDLVD-LDDRSIQRLLREVDNDVLALALKGASEELREKFLS 284 (339)
T ss_pred HhhCHHHHHHHHHHhcCHHHHhc-CCHHHHHHHHHhCCHHHHHHHHCCCCHHHHHHHHH
Confidence 6543333321100 122222222 33444555666555555555555444455555555
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=73.04 E-value=39 Score=29.92 Aligned_cols=166 Identities=15% Similarity=0.041 Sum_probs=71.3
Q ss_pred HhhhcCCCHHHHHHHHHHHH-hcHHHhhcccccchHHHHHHHHHHhcCChhHHHHHHHHHHHhHHhhhccCCchHHHHHH
Q 044799 55 QKMLSGKDSTITYKIFEAVY-KYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKC 133 (304)
Q Consensus 55 Q~~l~~~~~e~~~~i~~~l~-~~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Viq~~ 133 (304)
=+.+..+++.+.+.+.+.+. +.+.+=..-+.=++++. +-...+...-...+...+.|++..| +.-+++++...
T Consensus 41 lq~L~~csp~q~e~lc~~L~l~~lsd~~l~~lc~~ll~----Ls~dls~~~a~~l~~sl~LpkilsL--~~~ASR~L~sa 114 (263)
T PF11510_consen 41 LQFLNECSPSQVEMLCSQLQLPQLSDDGLLQLCSSLLA----LSPDLSHSNATVLLRSLFLPKILSL--EEPASRLLVSA 114 (263)
T ss_dssp HHGGGG--HHHHHHHHHHHTGGG--HHHHHHHHHHHHH-----SS---HHHHHHHHHHHHHHHHHH---SS---HHHHHH
T ss_pred HHHHHhCCHHHHHHHHHHhCcCCCCHHHHHHHHHHHHc----cCcccchhhHHHHHHHHHHHHHHhc--CCCccHHHHHH
Confidence 34556678889999988886 32222111111111111 0000111122334555567888877 44566666665
Q ss_pred HhhCCcccHHHHHHHHHhcHH-HHhhccCccHHHHHHH-h-cCChhhHHHHHHHHHHhHHhhhcCCCcchhHHHHhccCC
Q 044799 134 LETLDEQKNEVLYLAAMNHFR-ELATHVRGCVSLNNFI-N-EMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGD 210 (304)
Q Consensus 134 l~~~~~~~~~~ii~~l~~~~~-~la~~~~Gs~Vlq~~l-~-~~~~~~~~~l~~~l~~~~~~L~~d~~GnyViQ~lL~~~~ 210 (304)
+..+-...-..+++.+..-+. .-...+.=+-++.+++ + ...++.+..++..+. ++.-+..---|+|.+++...
T Consensus 115 l~~f~k~~p~~~~~all~PlL~~~~~g~~Q~eLl~rlvk~~~l~p~~~~l~l~~~L----~~~W~E~~~~Vlq~lL~~k~ 190 (263)
T PF11510_consen 115 LTSFCKKYPRPVCEALLVPLLQAPGLGPPQCELLCRLVKKECLEPDHRLLLLRQIL----ELVWNEETFLVLQSLLERKV 190 (263)
T ss_dssp HHHHHHHSHHHHHHHHHHHHHHSTT--HHHHHHHHHHHH-TTS-HHHHHHHHHHHH----HS---HHHHHHHHHHHTT--
T ss_pred HHHHHHhCcHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccCCHHHHHHHHHHHH----hCcCcHHHHHHHHHHHhcCC
Confidence 554434455555555543221 1122223455677777 3 334555665555544 33334444568999999875
Q ss_pred H---hhHHHHHHHHHHhHHHhhc
Q 044799 211 L---KYSEKICSLLKGKFEELSL 230 (304)
Q Consensus 211 ~---~~~~~i~~~l~~~~~~Ls~ 230 (304)
+ +....+++.+.+.-..++.
T Consensus 191 ~l~~~~~~~l~~~L~~~a~~~sk 213 (263)
T PF11510_consen 191 ELSQELFSLLVELLCEQAPQFSK 213 (263)
T ss_dssp ---HHHHHHHHHHHH--------
T ss_pred CCCHHHHHHHHHHHHHhhHhhhc
Confidence 3 3344566666655555543
No 23
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=70.13 E-value=90 Score=28.69 Aligned_cols=113 Identities=12% Similarity=0.083 Sum_probs=61.3
Q ss_pred HHHHhhhcCCCHHHHHHHHHHHHhcHHH----hhcccccchHHHHHHHHHHhcC-ChhHHHHHHHHHHHhHHhhh----c
Q 044799 52 LFLQKMLSGKDSTITYKIFEAVYKYPFD----LMTDGYGCHLARSMQKLIKLLV-GSPCISLVISAAYRRFKDMM----F 122 (304)
Q Consensus 52 r~lQ~~l~~~~~e~~~~i~~~l~~~~~~----L~~d~~gs~vvQ~vQkll~~~~-~~~~~~~i~~~l~~~~~~L~----~ 122 (304)
+.|+.+|...+|+....++..+.+.... ........-++. ++...-. +++....+-+.|...+.... .
T Consensus 123 ~~l~~lL~~EhpqtiA~iLs~l~~~~aa~vL~~l~~~~~~~v~~---ria~l~~v~~~~~~~i~~~L~~~l~~~~~~~~~ 199 (339)
T PRK05686 123 QQLANFIRNEHPQTIALILSYLKPDQAAEILSLLPEELRADVMM---RIATLEGVSPEALKEVEEVLEKKLSSMANADRT 199 (339)
T ss_pred HHHHHHHHhcCHHHHHHHHhCCCHHHHHHHHHhCCHHHHHHHHH---HHHccCCCCHHHHHHHHHHHHHHHhhccccccc
Confidence 4555555555555555555554433222 222222222222 2222111 24455556565566665432 2
Q ss_pred cCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHhhccCccHHHHHHHhc
Q 044799 123 SKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINE 172 (304)
Q Consensus 123 d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la~~~~Gs~Vlq~~l~~ 172 (304)
+.-|...+-.++..++.+..+.+++.+...=.+++ -.|-+++|.+
T Consensus 200 ~~~g~~~~a~Iln~~~~~~~~~il~~L~~~d~~~a-----~~Ir~~mF~F 244 (339)
T PRK05686 200 KMGGVKTVAEILNNLDRQTEKTILESLEEEDPELA-----EKIKDLMFVF 244 (339)
T ss_pred ccCcHHHHHHHHhcCCchHHHHHHHHHHhhCHHHH-----HHHHHHhcCH
Confidence 45577888999999999988899998886545554 2444444444
No 24
>KOG1240 consensus Protein kinase containing WD40 repeats [Signal transduction mechanisms]
Probab=52.01 E-value=82 Score=33.93 Aligned_cols=65 Identities=15% Similarity=0.193 Sum_probs=44.9
Q ss_pred HHHHHHHhcHHHhhcccccchHHHHHHHHHH---hcCC--hhHHHHHHHHHHHhHHhhhccCCchHHHHH
Q 044799 68 KIFEAVYKYPFDLMTDGYGCHLARSMQKLIK---LLVG--SPCISLVISAAYRRFKDMMFSKEASSVIIK 132 (304)
Q Consensus 68 ~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~---~~~~--~~~~~~i~~~l~~~~~~L~~d~~gn~Viq~ 132 (304)
..++.+.|++..|..|+++--=++++..+.+ ..+. +.....+.+.|-|++..|+.|...++|--.
T Consensus 458 ~~LDRVlPY~v~l~~Ds~a~Vra~Al~Tlt~~L~~Vr~~~~~daniF~eYlfP~L~~l~~d~~~~~vRia 527 (1431)
T KOG1240|consen 458 VKLDRVLPYFVHLLMDSEADVRATALETLTELLALVRDIPPSDANIFPEYLFPHLNHLLNDSSAQIVRIA 527 (1431)
T ss_pred HHHhhhHHHHHHHhcCchHHHHHHHHHHHHHHHhhccCCCcccchhhHhhhhhhhHhhhccCccceehhh
Confidence 4567888999999999998654444333333 2222 344567888899999999999776666443
No 25
>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=37.65 E-value=76 Score=25.22 Aligned_cols=25 Identities=20% Similarity=0.213 Sum_probs=11.5
Q ss_pred chHHHHHHHhhCCcccHHHHHHHHH
Q 044799 126 ASSVIIKCLETLDEQKNEVLYLAAM 150 (304)
Q Consensus 126 gn~Viq~~l~~~~~~~~~~ii~~l~ 150 (304)
|+--+..+++.+++++...+++.+.
T Consensus 47 g~~~l~~~i~~L~~~~l~~LL~~ir 71 (141)
T PF08625_consen 47 GSEELDEVIKKLDDEQLEKLLRFIR 71 (141)
T ss_pred hHHHHHHHHHhcCHHHHHHHHHHHH
Confidence 3444445555554444444444433
No 26
>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=34.86 E-value=3.6e+02 Score=24.75 Aligned_cols=55 Identities=9% Similarity=0.113 Sum_probs=31.3
Q ss_pred hhHHHHHHHHHHHhHHhhhc---cCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHh
Q 044799 103 SPCISLVISAAYRRFKDMMF---SKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELA 157 (304)
Q Consensus 103 ~~~~~~i~~~l~~~~~~L~~---d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la 157 (304)
++....+-+.|...+..... ..-|-..+..++..++....+.|++.+...-.+++
T Consensus 174 ~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN~~~~~~~~~il~~L~~~dp~la 231 (338)
T TIGR00207 174 PEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIINLMDRKTEKTIITSLEEFDPELA 231 (338)
T ss_pred HHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHHhCCchHHHHHHHHHHHhCHHHH
Confidence 33344444444444443332 22355677788888887777778777765444444
No 27
>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=30.92 E-value=92 Score=23.26 Aligned_cols=52 Identities=17% Similarity=0.252 Sum_probs=35.1
Q ss_pred HHhhccCccHHHHHHHhcCChhhHHHHHHHHHHhHHhhhcCC-CcchhHHHHh
Q 044799 155 ELATHVRGCVSLNNFINEMRGPRRGGLLDLISSHAEFLSKDP-SGNYVVQHVL 206 (304)
Q Consensus 155 ~la~~~~Gs~Vlq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~-~GnyViQ~lL 206 (304)
..+..-||..-|.++++..++++|...++.|.-....-..|| ||.+-+-..|
T Consensus 31 ~~vhkvFG~sni~k~L~~~~~~~R~~a~~Sl~yEA~~R~~dPv~Gc~G~i~~L 83 (101)
T PF03195_consen 31 ANVHKVFGVSNISKMLQELPPEQREDAMRSLVYEANARARDPVYGCVGIISQL 83 (101)
T ss_pred HHHHHHHchhHHHHHHHhCCccchhhHHHHHHHHHHhhccCCCcchHHHHHHH
Confidence 334455677778888888877778888877776666666666 6776443333
No 28
>PF07176 DUF1400: Alpha/beta hydrolase of unknown function (DUF1400); InterPro: IPR010802 This domain is specific to cyanobacterial proteins, its function and the function of the proteins it is associated with, are uncharacterised.
Probab=29.79 E-value=2.6e+02 Score=21.69 Aligned_cols=96 Identities=15% Similarity=0.072 Sum_probs=63.9
Q ss_pred hhHhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHh-------cHHHhhcccccchHHHHHHHHHHhcCChhHHHHHHH
Q 044799 39 YDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYK-------YPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLVIS 111 (304)
Q Consensus 39 g~i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~-------~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~i~~ 111 (304)
.++-.+|.+..-+.-|+..+...++++++.+-+.|.. .+..+...+.|-.+++.+-+++.. +.... =..
T Consensus 19 ~dLe~fa~tG~~~~~L~~~~~ll~~~~~~~lr~~L~~~~~~~~~~~~~lL~S~~G~~lL~~lg~vi~~---~~~~~-g~~ 94 (127)
T PF07176_consen 19 SDLETFAETGEISPELAFYLNLLSPQQRQQLRELLNTPIPIDPVFLSQLLNSPIGERLLDQLGKVIRT---PSGSN-GQQ 94 (127)
T ss_pred HHHHHHHHcCCCCHHHHHHHHhcCHhhHHHHHHHHcCCCCCCHHHHHHHhCChHHHHHHHHHHHHhcC---CCCcc-cHH
Confidence 4677788888888888888888888887777666652 455777889999999854444432 21111 123
Q ss_pred HHHHhHHhhhccCCchHHHHHHHhhCCc
Q 044799 112 AAYRRFKDMMFSKEASSVIIKCLETLDE 139 (304)
Q Consensus 112 ~l~~~~~~L~~d~~gn~Viq~~l~~~~~ 139 (304)
+++..+...+.++.|=- +-.+++.+|.
T Consensus 95 ALr~Ali~aa~~~~glt-~l~~L~~yP~ 121 (127)
T PF07176_consen 95 ALRSALILAASDPEGLT-LLNFLRAYPT 121 (127)
T ss_pred HHHHHHHHHhhCCCCcc-HHHHHHHCCC
Confidence 47777777777777444 4455566554
No 29
>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=27.91 E-value=4.3e+02 Score=23.43 Aligned_cols=11 Identities=18% Similarity=0.048 Sum_probs=5.8
Q ss_pred ccHHHHHHHhc
Q 044799 162 GCVSLNNFINE 172 (304)
Q Consensus 162 Gs~Vlq~~l~~ 172 (304)
..|++.+++.+
T Consensus 202 S~RLLKhIIrC 212 (262)
T PF04078_consen 202 SPRLLKHIIRC 212 (262)
T ss_dssp -HHHHHHHHHH
T ss_pred ChhHHHHHHHH
Confidence 55666665554
No 30
>KOG3821 consensus Heparin sulfate cell surface proteoglycan [Signal transduction mechanisms]
Probab=26.93 E-value=6.3e+02 Score=24.98 Aligned_cols=44 Identities=14% Similarity=0.227 Sum_probs=24.8
Q ss_pred cchhHHHHhhhcCCCHHHHHHHHHHHH----hcHHHhhcccccchHHHH
Q 044799 48 EGGSLFLQKMLSGKDSTITYKIFEAVY----KYPFDLMTDGYGCHLARS 92 (304)
Q Consensus 48 ~~gsr~lQ~~l~~~~~e~~~~i~~~l~----~~~~~L~~d~~gs~vvQ~ 92 (304)
++.|.+|+.+|.. +....+..|.++. ..+..|-...||+...|.
T Consensus 90 q~~s~~Lr~~l~s-~~r~F~E~f~ell~~ae~~l~~mF~~tYg~ly~qn 137 (563)
T KOG3821|consen 90 QDSSSVLRFVLAS-NARKFDEFFLELLRNAENSLNAMFSKTYGSLYPQN 137 (563)
T ss_pred HHhHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHH
Confidence 3445566655542 1122233333333 345567788999999997
No 31
>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=25.54 E-value=3.4e+02 Score=21.47 Aligned_cols=85 Identities=18% Similarity=0.108 Sum_probs=50.1
Q ss_pred HhhhccCcchhHHHHhhhcCCCHHHHHHHHHHHHhcHHHhhcccccchHHHHHHHHHHhcCChhHHHHHHHHHHHhHHhh
Q 044799 41 IVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRFKDM 120 (304)
Q Consensus 41 i~~la~d~~gsr~lQ~~l~~~~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~i~~~l~~~~~~L 120 (304)
+-++..+.+-..-+.-.|+-..|-..-.++..+.. .+--.+..|+-.+. ..+...+.++... +-..+.+.
T Consensus 4 L~N~l~~~~y~~Al~LAl~L~~P~~ll~i~~~~~~--~~~~~~~~g~~~l~---~~i~~L~~~~l~~-----LL~~ir~W 73 (141)
T PF08625_consen 4 LSNLLRQKDYKEALRLALKLDHPFRLLKILKDLLE--TEEDEDSIGSEELD---EVIKKLDDEQLEK-----LLRFIRDW 73 (141)
T ss_pred HHHHHHhhhHHHHHHHHHhcCCcHHHHHHHHHHHh--cccccccchHHHHH---HHHHhcCHHHHHH-----HHHHHHHh
Confidence 33445556666677777777777777777777764 11123333677777 7888876444332 33445555
Q ss_pred hccCCchHHHHHHHh
Q 044799 121 MFSKEASSVIIKCLE 135 (304)
Q Consensus 121 ~~d~~gn~Viq~~l~ 135 (304)
-++.--++|.|.++.
T Consensus 74 NTNsr~~~vAQ~vL~ 88 (141)
T PF08625_consen 74 NTNSRTSHVAQRVLN 88 (141)
T ss_pred hcccccHHHHHHHHH
Confidence 555555566655544
No 32
>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=24.91 E-value=5.5e+02 Score=23.60 Aligned_cols=79 Identities=13% Similarity=0.128 Sum_probs=44.1
Q ss_pred HHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHH------------------HhcHHHHh---hccCccHHHHHHHhc
Q 044799 114 YRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAA------------------MNHFRELA---THVRGCVSLNNFINE 172 (304)
Q Consensus 114 ~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l------------------~~~~~~la---~~~~Gs~Vlq~~l~~ 172 (304)
+|....+....-+.-.--.++..+|++.+..++..+ ...+..+. ...-|...+..+++.
T Consensus 131 hPQ~iAliLs~L~p~~AA~VL~~Lp~~~~~ei~~ria~l~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN~ 210 (338)
T TIGR00207 131 HPQTIALILSHLDPAQAADILSLFPEEVQAEVARRIATMGRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIINL 210 (338)
T ss_pred CHHHHHHHHHcCCHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHHh
Confidence 444444444444444455555566655555544322 22222222 223577889999999
Q ss_pred CChhhHHHHHHHHHHhHHhh
Q 044799 173 MRGPRRGGLLDLISSHAEFL 192 (304)
Q Consensus 173 ~~~~~~~~l~~~l~~~~~~L 192 (304)
.+....+.+++.|.+.-+.+
T Consensus 211 ~~~~~~~~il~~L~~~dp~l 230 (338)
T TIGR00207 211 MDRKTEKTIITSLEEFDPEL 230 (338)
T ss_pred CCchHHHHHHHHHHHhCHHH
Confidence 88777777777776533333
No 33
>COG4399 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.89 E-value=5e+02 Score=24.13 Aligned_cols=21 Identities=24% Similarity=0.333 Sum_probs=8.6
Q ss_pred hhHhhhccCcchhHHHHhhhc
Q 044799 39 YDIVLLGKTEGGSLFLQKMLS 59 (304)
Q Consensus 39 g~i~~la~d~~gsr~lQ~~l~ 59 (304)
..+.++-.+...-..+|+++.
T Consensus 219 ~ellkl~~~~~t~kilq~Ll~ 239 (376)
T COG4399 219 QELLKLLNREETKKILQQLLT 239 (376)
T ss_pred HHHHHHHccHHHHHHHHHHHH
Confidence 333444444444444444443
No 34
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=24.68 E-value=1.5e+02 Score=25.48 Aligned_cols=79 Identities=16% Similarity=0.188 Sum_probs=50.6
Q ss_pred HhhccCccHHHHHHHhcCChhhHHHHHHHHHHhHHhhhcCC--CcchhHHHHhccCCHhh-HHHHHHHHHHhHHHhhccc
Q 044799 156 LATHVRGCVSLNNFINEMRGPRRGGLLDLISSHAEFLSKDP--SGNYVVQHVLGLGDLKY-SEKICSLLKGKFEELSLLR 232 (304)
Q Consensus 156 la~~~~Gs~Vlq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~--~GnyViQ~lL~~~~~~~-~~~i~~~l~~~~~~Ls~~k 232 (304)
-..+-||+.|...|-...++.+ .++..-.-....|.+|+ .+.-..-.+....+... ...|.-.|+..+.+.|.+|
T Consensus 130 ~l~d~F~~~VC~~Cr~~~pdky--~llTKTeCk~dYlLTdpEL~dqelf~rL~kpNPH~gtws~M~Lylr~eVE~FA~kK 207 (292)
T COG5145 130 ELEDTFGISVCRSCRHSMPDKY--KLLTKTECKSDYLLTDPELKDQELFRRLQKPNPHKGTWSKMHLYLREEVEQFAIKK 207 (292)
T ss_pred HHHhhhcchhHHhhhhhcchhh--hhhhhhhhhhhhhcCChhhcchHHHHHhcCCCCCccchHHHHHHHHHHHHHHHHHh
Confidence 3456678888888877654332 33333223345666776 35455556666555332 5667778888999999999
Q ss_pred hhhH
Q 044799 233 CGSH 236 (304)
Q Consensus 233 ~gs~ 236 (304)
+||-
T Consensus 208 WGs~ 211 (292)
T COG5145 208 WGSL 211 (292)
T ss_pred cccH
Confidence 9984
No 35
>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=24.13 E-value=97 Score=32.19 Aligned_cols=21 Identities=10% Similarity=0.118 Sum_probs=18.0
Q ss_pred HhHHHhhccchhhHHHHHhhh
Q 044799 223 GKFEELSLLRCGSHLVEKYQR 243 (304)
Q Consensus 223 ~~~~~Ls~~k~gs~Vvek~l~ 243 (304)
.++.-++++|+|-.++-.+|.
T Consensus 673 ~~~~~i~~tk~Gls~lt~lls 693 (808)
T PF09770_consen 673 NNVSFIAQTKFGLSLLTMLLS 693 (808)
T ss_dssp HHHHHHHTSHHHHHHHHHHHH
T ss_pred CCceEEEEChHHHHHHHHHHH
Confidence 467778899999999998888
No 36
>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=24.01 E-value=5.9e+02 Score=23.64 Aligned_cols=25 Identities=12% Similarity=0.193 Sum_probs=14.2
Q ss_pred hcHHHhhcccccchHHHHHHHHHHhcCC
Q 044799 75 KYPFDLMTDGYGCHLARSMQKLIKLLVG 102 (304)
Q Consensus 75 ~~~~~L~~d~~gs~vvQ~vQkll~~~~~ 102 (304)
+.+.....+.++.+++. ..++.+..
T Consensus 77 ~~i~~~l~~d~~~~~i~---~~i~~l~~ 101 (372)
T PF12231_consen 77 PEIVSTLSDDFASFIID---HSIESLQN 101 (372)
T ss_pred HHHHhhCChHHHHHHHH---HHHHHHcC
Confidence 44555556666666666 55554433
No 37
>cd07356 HN_L-whirlin_R1_like First harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains. This subgroup contains the first of two harmonin_N_like domains of the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. This first harmonin_N_like domain precedes PDZ1, and is a putative protein-binding module based on its sequence similarity to the N-terminal domain of harmonin. This first harmonin_N_like domain has been assayed for interaction with the cytoplasmic domain of cadherin 23 (a component of the Usher network and an interacting partner of the harmonin N-domain), however no interaction could be detected. Th
Probab=23.60 E-value=2.1e+02 Score=20.13 Aligned_cols=21 Identities=24% Similarity=0.115 Sum_probs=14.7
Q ss_pred HHHHHHHHHHhHHhhhcCCCc
Q 044799 178 RGGLLDLISSHAEFLSKDPSG 198 (304)
Q Consensus 178 ~~~l~~~l~~~~~~L~~d~~G 198 (304)
.-.++..+.+...+++.|+|.
T Consensus 56 llplLr~vIP~sDq~lFDq~t 76 (78)
T cd07356 56 LLPLLRLVIPRSDQLLFDQYT 76 (78)
T ss_pred HHHHHHHHcccHHHHHHHHHh
Confidence 345566677888888888764
No 38
>PF14005 YpjP: YpjP-like protein
Probab=21.21 E-value=1.6e+02 Score=23.19 Aligned_cols=34 Identities=12% Similarity=0.031 Sum_probs=23.9
Q ss_pred cHHHHHHHHHhcHHHHhhccCccHHHHHHHhcCC
Q 044799 141 KNEVLYLAAMNHFRELATHVRGCVSLNNFINEMR 174 (304)
Q Consensus 141 ~~~~ii~~l~~~~~~la~~~~Gs~Vlq~~l~~~~ 174 (304)
....+++.+...+.+-|..++|.++...+=+...
T Consensus 4 ~~~~~~~~~~~~A~~qs~~KfG~kI~p~Iedef~ 37 (136)
T PF14005_consen 4 DHDDFIEQLMEEAEKQSYKKFGSKIGPVIEDEFR 37 (136)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 3455666677777777778889888877765543
No 39
>PF05794 Tcp11: T-complex protein 11; InterPro: IPR008862 This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the Saccharomyces cerevisiae Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants [].
Probab=20.09 E-value=5.1e+02 Score=24.49 Aligned_cols=119 Identities=11% Similarity=0.017 Sum_probs=66.6
Q ss_pred ccchhhHhhhccCcchhHHHHhhhcCC-CHHHHHHHHHHHHhcHHHhhcccccchHHHHHHHHHHhcCChhHHHHHHHHH
Q 044799 35 AQPDYDIVLLGKTEGGSLFLQKMLSGK-DSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLVISAA 113 (304)
Q Consensus 35 ~~~~g~i~~la~d~~gsr~lQ~~l~~~-~~e~~~~i~~~l~~~~~~L~~d~~gs~vvQ~vQkll~~~~~~~~~~~i~~~l 113 (304)
+...+++-+.+.+.+.-.+-+.+-... .....-.++++|++.+..|. ++..-+ .+-+.+.. +++...+
T Consensus 22 ~~~~~~vk~~~~~afWd~l~~el~~~~~~~~~~~~Ll~~ike~L~~ll----~~~~~~---~I~e~LD~----~li~Qq~ 90 (441)
T PF05794_consen 22 DSLEGRVKETMHKAFWDALREELEQDPPDYSRLPQLLEEIKEILLSLL----PSRLRQ---EIEEVLDL----ELIRQQL 90 (441)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHhhCCCChhHHHHHHHHHHHHHHHhc----CHHHHH---HHHHHCCh----HHHHHHH
Confidence 345677777777777777777766663 34455678888998888887 433333 33344332 2333334
Q ss_pred HHhHHhhhccCCchHHHHHHHhhCCcccHHHHHHHHHhcHHHHhhccCccHHHH
Q 044799 114 YRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLN 167 (304)
Q Consensus 114 ~~~~~~L~~d~~gn~Viq~~l~~~~~~~~~~ii~~l~~~~~~la~~~~Gs~Vlq 167 (304)
.....+ ...+..|++.-+-+++.| .|+.-++.+...+.+=+....+.-+|.
T Consensus 91 ~~g~~D--~~~l~~~i~~~l~~~CAP-~RD~~v~~l~~~~~~~~~~~~~~~~V~ 141 (441)
T PF05794_consen 91 EHGVLD--LVKLARFIISLLKKLCAP-MRDEEVKALVEKIEEGCTESSATDIVD 141 (441)
T ss_pred hcCCcC--HHHHHHHHHHHHHHhCCC-CCcHHHHHHHHHHHhccccCCHHHHHH
Confidence 333333 234456666666665544 355556666665543333333343333
Done!