Query 008180
Match_columns 575
No_of_seqs 247 out of 1303
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 20:30:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008180.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008180hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07990 NABP: Nucleic acid bi 100.0 4.9E-53 1.1E-57 441.8 14.6 234 145-402 135-385 (385)
2 KOG1488 Translational represso 100.0 3.1E-40 6.8E-45 356.6 15.3 195 380-574 152-350 (503)
3 cd07920 Pumilio Pumilio-family 100.0 4.8E-33 1E-37 283.4 20.4 197 377-573 50-249 (322)
4 KOG1488 Translational represso 100.0 1.3E-33 2.8E-38 305.4 14.8 180 394-573 240-421 (503)
5 cd07920 Pumilio Pumilio-family 100.0 1.5E-32 3.2E-37 279.8 17.0 198 376-573 13-213 (322)
6 KOG2050 Puf family RNA-binding 100.0 4.1E-30 8.8E-35 278.0 16.3 198 365-575 136-409 (652)
7 COG5099 RNA-binding protein of 100.0 5.1E-29 1.1E-33 282.3 13.1 162 412-573 447-609 (777)
8 COG5099 RNA-binding protein of 99.9 1.6E-27 3.4E-32 270.3 15.5 178 397-574 504-683 (777)
9 KOG2049 Translational represso 99.9 2.7E-26 5.8E-31 250.6 12.3 198 376-573 256-460 (536)
10 KOG2049 Translational represso 99.9 1.9E-24 4.2E-29 236.1 12.5 173 401-573 212-388 (536)
11 KOG2050 Puf family RNA-binding 99.7 6.5E-16 1.4E-20 168.5 16.8 191 383-573 174-445 (652)
12 KOG2188 Predicted RNA-binding 99.6 5.3E-14 1.2E-18 154.9 15.7 168 407-574 337-575 (650)
13 KOG2188 Predicted RNA-binding 99.4 2.4E-12 5.2E-17 142.0 15.5 203 365-568 329-605 (650)
14 KOG4574 RNA-binding protein (c 99.0 1.5E-10 3.2E-15 130.8 3.1 168 406-574 582-754 (1007)
15 KOG4574 RNA-binding protein (c 98.9 6.3E-10 1.4E-14 125.7 4.3 143 430-573 534-677 (1007)
16 PF00806 PUF: Pumilio-family R 98.3 3E-07 6.5E-12 66.0 2.8 35 439-473 1-35 (35)
17 smart00025 Pumilio Pumilio-lik 98.0 3.7E-06 8.1E-11 58.9 2.2 34 440-473 2-35 (36)
18 PF00806 PUF: Pumilio-family R 98.0 5.8E-06 1.3E-10 59.4 3.1 33 476-508 2-34 (35)
19 smart00025 Pumilio Pumilio-lik 97.7 2.8E-05 6.1E-10 54.4 2.9 34 404-437 2-35 (36)
20 PF08144 CPL: CPL (NUC119) dom 84.0 4.3 9.3E-05 38.8 7.6 47 380-431 43-89 (148)
21 PRK05686 fliG flagellar motor 81.8 57 0.0012 35.0 15.8 129 414-551 78-229 (339)
22 PF09770 PAT1: Topoisomerase I 81.0 4.4 9.5E-05 48.1 7.8 148 407-554 576-775 (808)
23 PF08144 CPL: CPL (NUC119) dom 75.3 11 0.00024 36.0 7.3 62 510-571 60-132 (148)
24 TIGR00400 mgtE Mg2+ transporte 69.3 67 0.0014 35.7 12.7 81 420-512 22-102 (449)
25 KOG0166 Karyopherin (importin) 68.4 31 0.00067 39.4 9.9 131 416-547 256-406 (514)
26 PF09770 PAT1: Topoisomerase I 66.6 15 0.00032 43.8 7.3 93 443-535 576-694 (808)
27 PRK05686 fliG flagellar motor 66.3 1.2E+02 0.0027 32.5 13.5 86 429-514 121-228 (339)
28 PF04286 DUF445: Protein of un 64.8 1E+02 0.0022 32.1 12.5 19 539-557 290-308 (367)
29 KOG4368 Predicted RNA binding 62.8 1.4E+02 0.003 34.9 13.5 143 418-564 89-252 (757)
30 PF02854 MIF4G: MIF4G domain; 60.3 38 0.00082 31.7 7.6 13 544-556 171-183 (209)
31 PF10508 Proteasom_PSMB: Prote 54.1 3.7E+02 0.008 30.4 16.2 38 528-567 203-241 (503)
32 PF12231 Rif1_N: Rap1-interact 53.2 2.7E+02 0.0058 30.3 13.5 34 431-464 152-188 (372)
33 PF14666 RICTOR_M: Rapamycin-i 51.6 69 0.0015 32.8 8.2 130 415-549 82-221 (226)
34 PF05794 Tcp11: T-complex prot 50.7 59 0.0013 35.6 8.1 93 379-481 32-128 (441)
35 TIGR00207 fliG flagellar motor 48.0 3.9E+02 0.0084 28.9 14.6 27 488-514 199-225 (338)
36 PF10508 Proteasom_PSMB: Prote 44.7 5.1E+02 0.011 29.3 15.1 25 544-568 244-269 (503)
37 COG1747 Uncharacterized N-term 44.5 4.5E+02 0.0098 30.8 13.6 67 408-474 56-122 (711)
38 KOG1240 Protein kinase contain 44.4 1.6E+02 0.0035 37.2 10.9 73 385-457 444-525 (1431)
39 KOG1059 Vesicle coat complex A 43.9 85 0.0018 37.5 8.2 49 523-571 387-440 (877)
40 cd03561 VHS VHS domain family; 43.4 2.2E+02 0.0049 26.2 9.6 35 489-523 57-92 (133)
41 KOG3759 Uncharacterized RUN do 42.7 2.1E+02 0.0045 32.7 10.6 124 426-555 98-239 (621)
42 PF11510 FA_FANCE: Fanconi Ana 41.8 2.2E+02 0.0047 30.1 10.2 141 423-571 42-188 (263)
43 PF11573 Med23: Mediator compl 41.6 1.4E+02 0.003 38.1 10.1 107 463-571 56-179 (1341)
44 PF05794 Tcp11: T-complex prot 38.1 4.5E+02 0.0098 28.8 12.5 62 430-500 51-112 (441)
45 COG1536 FliG Flagellar motor s 38.0 5.7E+02 0.012 27.9 13.8 47 466-512 176-226 (339)
46 PF01603 B56: Protein phosphat 37.3 3.5E+02 0.0077 29.8 11.5 66 493-559 279-352 (409)
47 PF05918 API5: Apoptosis inhib 35.1 8E+02 0.017 28.7 14.4 32 538-569 239-270 (556)
48 PF04078 Rcd1: Cell differenti 34.3 3E+02 0.0064 29.2 9.7 46 489-535 159-212 (262)
49 PF08625 Utp13: Utp13 specific 33.9 4.2E+02 0.0091 25.2 10.6 24 453-476 47-70 (141)
50 PTZ00429 beta-adaptin; Provisi 33.6 5.8E+02 0.013 30.8 13.2 14 524-537 475-488 (746)
51 KOG0132 RNA polymerase II C-te 31.4 63 0.0014 38.7 4.7 13 457-469 47-59 (894)
52 KOG2759 Vacuolar H+-ATPase V1 31.3 1.7E+02 0.0038 32.9 7.8 31 541-571 312-343 (442)
53 PF10521 DUF2454: Protein of u 31.3 3.9E+02 0.0084 27.8 10.2 42 427-468 107-154 (282)
54 TIGR00400 mgtE Mg2+ transporte 31.3 2.3E+02 0.0049 31.5 8.9 53 495-548 73-126 (449)
55 COG4399 Uncharacterized protei 30.1 2.8E+02 0.006 30.7 8.9 29 399-427 212-240 (376)
56 cd03569 VHS_Hrs_Vps27p VHS dom 28.2 2.1E+02 0.0047 27.0 7.0 48 488-535 60-108 (142)
57 PF04054 Not1: CCR4-Not comple 27.9 5.2E+02 0.011 28.5 10.8 78 488-565 262-345 (379)
58 PF03448 MgtE_N: MgtE intracel 27.6 95 0.0021 26.5 4.2 48 465-512 26-73 (102)
59 PRK15039 transcriptional repre 27.5 3.1E+02 0.0067 24.4 7.4 74 383-476 7-81 (90)
60 TIGR00207 fliG flagellar motor 27.1 8.2E+02 0.018 26.4 16.7 30 522-551 197-226 (338)
61 COG2239 MgtE Mg/Co/Ni transpor 26.9 3.1E+02 0.0067 31.1 9.0 26 525-550 135-160 (451)
62 KOG2141 Protein involved in hi 26.8 1.7E+02 0.0037 35.0 7.1 25 476-500 383-407 (822)
63 PF04078 Rcd1: Cell differenti 26.5 74 0.0016 33.5 3.9 65 452-533 158-230 (262)
64 KOG2213 Apoptosis inhibitor 5/ 26.4 6.6E+02 0.014 28.4 11.1 39 461-499 206-244 (460)
65 PF12460 MMS19_C: RNAPII trans 25.1 6.7E+02 0.014 27.4 11.1 28 490-517 118-145 (415)
66 PF05327 RRN3: RNA polymerase 24.5 1E+03 0.023 27.4 12.9 70 430-501 50-121 (563)
67 PLN03083 E3 UFM1-protein ligas 24.0 3.5E+02 0.0077 32.9 9.1 17 74-90 81-97 (803)
68 PHA02741 hypothetical protein; 23.8 6E+02 0.013 23.7 10.4 127 413-543 17-150 (169)
69 KOG0132 RNA polymerase II C-te 23.7 78 0.0017 38.0 3.7 99 471-573 25-136 (894)
70 PF00790 VHS: VHS domain; Int 23.4 3.4E+02 0.0074 25.2 7.3 35 491-525 64-99 (140)
71 PRK07194 fliG flagellar motor 23.0 9.7E+02 0.021 25.8 17.1 28 522-550 195-222 (334)
72 PF10607 CLTH: CTLH/CRA C-term 22.0 6E+02 0.013 23.0 9.7 17 538-554 104-120 (145)
73 KOG2280 Vacuolar assembly/sort 21.9 9.6E+02 0.021 29.2 11.9 64 406-469 538-607 (829)
74 COG5240 SEC21 Vesicle coat com 21.9 1.4E+03 0.031 27.4 13.0 118 417-536 357-479 (898)
75 cd03561 VHS VHS domain family; 21.8 4.3E+02 0.0093 24.3 7.6 14 489-502 38-51 (133)
76 smart00288 VHS Domain present 21.8 5E+02 0.011 24.0 8.1 47 489-535 57-105 (133)
77 KOG2659 LisH motif-containing 21.7 7.8E+02 0.017 25.6 10.0 65 421-487 71-137 (228)
78 KOG1924 RhoA GTPase effector D 21.6 1.6E+03 0.034 27.8 17.2 49 401-449 715-763 (1102)
79 KOG1070 rRNA processing protei 21.5 1.7E+03 0.037 29.4 14.2 35 408-442 1448-1486(1710)
80 COG2733 Predicted membrane pro 21.4 1.2E+03 0.026 26.3 13.1 75 388-465 139-217 (415)
81 KOG2051 Nonsense-mediated mRNA 21.4 1.3E+03 0.027 29.3 13.0 35 537-571 661-711 (1128)
82 PRK14136 recX recombination re 21.0 7.4E+02 0.016 26.9 10.0 23 552-574 282-304 (309)
83 PF08625 Utp13: Utp13 specific 21.0 7.3E+02 0.016 23.6 11.0 105 460-570 20-138 (141)
84 KOG1070 rRNA processing protei 20.7 1.8E+03 0.04 29.1 14.3 44 528-571 1656-1700(1710)
85 PF00790 VHS: VHS domain; Int 20.6 2.9E+02 0.0064 25.6 6.3 13 418-430 44-56 (140)
No 1
>PF07990 NABP: Nucleic acid binding protein NABP; InterPro: IPR012940 This domain occurs in some putative nucleic acid binding proteins. One of these proteins has been partially characterised [] and contains two putative phosphorylation sites and a possible dimerisation / leucine zipper domain.
Probab=100.00 E-value=4.9e-53 Score=441.76 Aligned_cols=234 Identities=36% Similarity=0.571 Sum_probs=214.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCcccCCCCCCCCcccCCCCCCCCCCCCCC-CCCCC---CCCCccccCCCCCCCCC-----C
Q 008180 145 FYPSFQPSGAGVYPSQYNVGGYALNSALFPPFVAGYPSQGPVPMPFDA-TSGSS---FNIRTTSVSTGEGIPHI-----G 215 (575)
Q Consensus 145 ~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~---~~~~~~~~~~~~~~~~~-----~ 215 (575)
-||+++. +++-++||++|++. |+||++++++|++|++||+ +++++ ++++| |++|+++.++ +
T Consensus 135 ~~q~~~~-------~n~~~~gy~~n~~~-~s~~~~~~~~gn~p~~fd~~~~~s~~~~~~~~s--~~~g~~~~s~~~~~~~ 204 (385)
T PF07990_consen 135 PYQNSDN-------PNSSFGGYALNPAL-PSMMASQLNNGNIPPLFDNSAAASALASPGMDS--RSLGGGLDSGGNQGAS 204 (385)
T ss_pred cccCCCc-------ccccccccccCccc-hhhhhccccCCCCCccccccccchhhccCCCcc--cccCCccccccccccc
Confidence 4777777 34444999999998 9999999999999999999 55555 78888 9999999987 6
Q ss_pred Ccccc-hhcCCC-CCCCCCCCCCchhhhhccCCcccccccc-ccCCCCCCCCC-CCCCCCCCCchhhHhhhhhhhccccc
Q 008180 216 STQHQ-KFYGHQ-GLMLQSPFVDPLHMQYFQHPFGDAYNAS-VQHRLASSGVN-GALADPSSKKEPIVAAYMGDQNLQSS 291 (575)
Q Consensus 216 ~~~~~-~~~~~~-~~~~~~~~~d~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~q~~q~~ 291 (575)
|+||+ |+|||+ |.++|+||+||+|+||||++++++++.+ +.||+++|+++ ++++|+++.||+||++||++||+||+
T Consensus 205 d~~~l~r~gnq~~g~~lq~~~~DP~Y~Qylq~~~~aa~~~a~~~dP~~~R~~~G~s~~dl~~~qKayl~~lL~~QK~Qy~ 284 (385)
T PF07990_consen 205 DGQNLNRFGNQVAGSALQSPFVDPLYLQYLQAPEYAAQQAAAQNDPSVDRNYMGSSYMDLLGLQKAYLEALLAQQKSQYG 284 (385)
T ss_pred chhhhhhhcccccCcccCCCCCCchHHHHhccccchhhhhhccCCcccccCCcCccccchHHHHHHHHHHHHHHHHHhhC
Confidence 99999 999998 9999999999999999999999988888 99999999999 99999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCcccCCCCCCcCCCCCCCCCCCCCCCCCCCCCCccccccc---cCCCCCCCCCCCC-CCCCc
Q 008180 292 LNGGPSISNPRKVGMPVGGYYGGLPGMGVMGQFPTSPIASPVLPSSPVGSTSQLGLRH---EMRLPQGLNRNTG-IYSGW 367 (575)
Q Consensus 292 ~~~~~~~~~~~~~~~~~~~y~g~~p~~g~~~~y~~~~~~~p~~~~~~~~~~~~~~~~~---~~~~~s~~r~~~g-~~~~W 367 (575)
+ |+ .|+|..+++||| +|.||++|+|||+||++|++|++|+|+++ |+|+ ++||++++|+.+| .+++|
T Consensus 285 ~---P~----~~~~~~n~~y~g-np~~G~gm~Y~gsplaspvlPsspvG~gs--p~r~~er~~R~~s~mRn~~GG~~GsW 354 (385)
T PF07990_consen 285 V---PL----KKSGSMNHGYYG-NPSYGLGMPYPGSPLASPVLPSSPVGPGS--PLRHNERNMRFPSGMRNSSGGSMGSW 354 (385)
T ss_pred C---cc----ccCCCCCCCCCC-CCCccccCCCCCCCCcCCCCCCCCCCCCC--CCcCCccccccCcccccccccccccc
Confidence 8 76 899999999999 89999999999999999999999999997 6665 6999999999855 99999
Q ss_pred ccccccCCCcccCchHHHHHHHHHhcchhhHhHHH
Q 008180 368 QGQRTFEGQRTFEDSKKHSFLEELKSSNAQKFELS 402 (575)
Q Consensus 368 e~~r~~~~~k~~~d~~rskLLeeL~s~e~rk~iLs 402 (575)
+.++..+ +++.+.+.|||||+++|+|+|+|+
T Consensus 355 ~~d~g~~----~d~~~~sSlLEEFKsNKtr~FELS 385 (385)
T PF07990_consen 355 HSDAGGN----MDENFASSLLEEFKSNKTRSFELS 385 (385)
T ss_pred ccccccc----ccccchhHHHHHHhcCCccceecC
Confidence 9999877 899999999999999999999873
No 2
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.1e-40 Score=356.64 Aligned_cols=195 Identities=57% Similarity=0.927 Sum_probs=182.7
Q ss_pred CchHHHHHHHHHhcc-hhhHhHHHHHHHHHHHHhhCccccHHHHHHhhcCCH-HHHHHHHHHHhhhHHHhhcCccccHHH
Q 008180 380 EDSKKHSFLEELKSS-NAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSA-EEKVSVFKEVLPHASKLMTDVFGNYVI 457 (575)
Q Consensus 380 ~d~~rskLLeeL~s~-e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s~-Eer~~If~ELkp~iveLmtD~yGNyVV 457 (575)
+...++.+++++.+. ..+.+.+..+.+++++++.||+|||+||+.|+.++. +++..||+||.+.+.+||+|.||||||
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~v~f~~Dq~GsrfiQqkl~~~~~~~ek~~if~ei~~~~~~L~~dvFGNyvI 231 (503)
T KOG1488|consen 152 NSTGPSFLLDPFRSNSLSKTLELVDIPGHLVEFAKDQHGSRFIQQKLETASDNEEKQAVFDEILPPALELMTDVFGNYVI 231 (503)
T ss_pred CCCCCCccccccccccccccccccccCCCceeecCCcccchHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHhcCchh
Confidence 333445566666655 556677788999999999999999999999999988 999999999999999999999999999
Q ss_pred HHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHhCC
Q 008180 458 QKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVP 537 (575)
Q Consensus 458 QKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQK~Le~~~ 537 (575)
||+||+++.+|+..+...+++++..||+++||||||||+|+..+.+.+.+|++||.+++++|++|++||||||||+|+.+
T Consensus 232 QkffE~gt~~q~~~l~~~~~g~v~~Lsld~ygCRVIQkale~id~~~~~~Li~ELd~~vl~~v~DQngnHViQK~ie~~p 311 (503)
T KOG1488|consen 232 QKFFEHGTEDQRNLLHSQIKGHVLELSLDMYGCRVIQKALEKVDVSLQIQLIDELDGHLLKCVKDQNGNHVIQKCIETLP 311 (503)
T ss_pred hhhhccCCHHHHHHHHHHHHhhhhhhhcccccchhHHHHHHhcCHHHHHHHHHHHHhhHHHHHhhcccceehhhhhhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHH--HHHHHhcCcchHHHHHHHHhhcCC
Q 008180 538 AEKIEFIISAFRG--QVATLSTHPYGCRVIQPHNNASGF 574 (575)
Q Consensus 538 ~k~rk~IIk~L~~--~iveLSthkyGs~VVQK~Le~~dd 574 (575)
++.+.+|++.|.+ ++..||+|+|||||||++||+|..
T Consensus 312 ~~~~~Fiv~~f~~~~~~~~ls~~~YGCRVIQr~lE~c~~ 350 (503)
T KOG1488|consen 312 PDAWQFIVDFFSGDDNLLELSTHKYGCRVIQRILEHCSE 350 (503)
T ss_pred hHHHHHHHHHhcCCCceeEeeccCcccHHHHHHhhcCCh
Confidence 9999999999999 999999999999999999999863
No 3
>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=4.8e-33 Score=283.36 Aligned_cols=197 Identities=30% Similarity=0.430 Sum_probs=184.6
Q ss_pred cccCchHHHHHHHHHh---cchhhHhHHHHHHHHHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccc
Q 008180 377 RTFEDSKKHSFLEELK---SSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFG 453 (575)
Q Consensus 377 k~~~d~~rskLLeeL~---s~e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yG 453 (575)
.++.|++++.+++.+. +.+++..+++.+.|++++|+.|++|||+||++|+.++++++..|+++|.+++.+|++|+||
T Consensus 50 ~l~~~~~g~~vvq~~l~~~~~~~~~~i~~~~~~~~~~l~~~~~g~~vlqkll~~~~~~~~~~i~~~l~~~~~~L~~d~~g 129 (322)
T cd07920 50 ELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNG 129 (322)
T ss_pred HHhcCccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcccchhHHHHHHHHHhcCHHHHHHHHHHHHHCHHHHhhcccc
Confidence 3467777777777765 4567778899999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHHHHHHH
Q 008180 454 NYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCI 533 (575)
Q Consensus 454 NyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQK~L 533 (575)
|||||++|++++++++..|++.|.+++.+|+.|++||+|||++|+.++.+++..|+++|.+++..|+.|++||||||++|
T Consensus 130 n~Vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~G~~vvq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~~Gn~vvq~~l 209 (322)
T cd07920 130 NHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVL 209 (322)
T ss_pred cHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHcCccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhCChhhHHHHHHHHHHHHHHHhcCcchHHHHHHHHhhcC
Q 008180 534 ECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQPHNNASG 573 (575)
Q Consensus 534 e~~~~k~rk~IIk~L~~~iveLSthkyGs~VVQK~Le~~d 573 (575)
+..+++.++.|++.+.+++.+|++|+|||+||++||+.++
T Consensus 210 ~~~~~~~~~~i~~~l~~~~~~l~~~k~Gs~Vve~~l~~~~ 249 (322)
T cd07920 210 ELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEKCLKHAS 249 (322)
T ss_pred hcCCHHHHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHCC
Confidence 9999999999999999999999999999999999999875
No 4
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-33 Score=305.41 Aligned_cols=180 Identities=32% Similarity=0.434 Sum_probs=171.3
Q ss_pred chhhHhHHHHHHHHHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHH
Q 008180 394 SNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELA 473 (575)
Q Consensus 394 ~e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II 473 (575)
.++++.+...++|++.+||.|.+||||||+.|+.-+.++..+++.||-.++..+++|++|||||||+||..+++....|+
T Consensus 240 ~~q~~~l~~~~~g~v~~Lsld~ygCRVIQkale~id~~~~~~Li~ELd~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv 319 (503)
T KOG1488|consen 240 EDQRNLLHSQIKGHVLELSLDMYGCRVIQKALEKVDVSLQIQLIDELDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIV 319 (503)
T ss_pred HHHHHHHHHHHHhhhhhhhcccccchhHHHHHHhcCHHHHHHHHHHHHhhHHHHHhhcccceehhhhhhccChHHHHHHH
Confidence 34555666778899999999999999999999999999999999999899999999999999999999999999999999
Q ss_pred HHhhc--ChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHhCChhhHHHHHHHHHHH
Q 008180 474 EKLVG--QVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQ 551 (575)
Q Consensus 474 ~~L~g--~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQK~Le~~~~k~rk~IIk~L~~~ 551 (575)
+.|.+ ++..||.|+|||||||++||+++++++..|+++|..++..|+.|+|||||||++|+++.++++..|++.|.++
T Consensus 320 ~~f~~~~~~~~ls~~~YGCRVIQr~lE~c~~~~~~~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~I~~~l~~~ 399 (503)
T KOG1488|consen 320 DFFSGDDNLLELSTHKYGCRVIQRILEHCSEDQKQPLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTIIIKCLLGN 399 (503)
T ss_pred HHhcCCCceeEeeccCcccHHHHHHhhcCChHhhhHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhhHHHHHHhh
Confidence 99999 9999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCcchHHHHHHHHhhcC
Q 008180 552 VATLSTHPYGCRVIQPHNNASG 573 (575)
Q Consensus 552 iveLSthkyGs~VVQK~Le~~d 573 (575)
++++++|||+++||++||.++.
T Consensus 400 ll~~Sq~KfASnVVEk~~~~a~ 421 (503)
T KOG1488|consen 400 LLSMSQHKFASNVVEKAFLFAP 421 (503)
T ss_pred HHHHHHHHHHHHHHHHHHhhCC
Confidence 9999999999999999999764
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=1.5e-32 Score=279.81 Aligned_cols=198 Identities=25% Similarity=0.390 Sum_probs=179.4
Q ss_pred CcccCchHHHHHHHHHh---cchhhHhHHHHHHHHHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCcc
Q 008180 376 QRTFEDSKKHSFLEELK---SSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVF 452 (575)
Q Consensus 376 ~k~~~d~~rskLLeeL~---s~e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~y 452 (575)
..++.|+.++++++++. +++++..+++.+.+++.+++.|++|++|||++|++++++++..|++++.+++.+|++|+|
T Consensus 13 ~~l~~~~~gsr~lQ~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~g~~vvq~~l~~~~~~~~~~i~~~~~~~~~~l~~~~~ 92 (322)
T cd07920 13 VEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVVRLSLDMY 92 (322)
T ss_pred hhccCCchhhHHHHHHhccCCHHHHHHHHHHHHHhHHHHhcCccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcccch
Confidence 45678899999999877 457788889999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHHHHHH
Q 008180 453 GNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKC 532 (575)
Q Consensus 453 GNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQK~ 532 (575)
|++||||+|++++++++..|+++|.+++..|+.|.||++|||++++.++.+++..|+++|.+++..|+.|++|++|||+|
T Consensus 93 g~~vlqkll~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~G~~vvq~~ 172 (322)
T cd07920 93 GCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRC 172 (322)
T ss_pred hHHHHHHHHHhcCHHHHHHHHHHHHHCHHHHhhcccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHcCccccHHHHHH
Confidence 99999999999999999999999999999999999999999999999988999999999999999999999999999999
Q ss_pred HHhCChhhHHHHHHHHHHHHHHHhcCcchHHHHHHHHhhcC
Q 008180 533 IECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQPHNNASG 573 (575)
Q Consensus 533 Le~~~~k~rk~IIk~L~~~iveLSthkyGs~VVQK~Le~~d 573 (575)
|+..+++.++.|++.+.+++..|+.++||++|||++|+..+
T Consensus 173 l~~~~~~~~~~l~~~l~~~~~~L~~d~~Gn~vvq~~l~~~~ 213 (322)
T cd07920 173 LEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGD 213 (322)
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHhcCC
Confidence 99988889999999999999999999999999999998753
No 6
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=4.1e-30 Score=278.01 Aligned_cols=198 Identities=24% Similarity=0.364 Sum_probs=187.9
Q ss_pred CCcccccccCCCcccCchHHHHHHHHHhcchhhHhHHHHHHHHHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhH
Q 008180 365 SGWQGQRTFEGQRTFEDSKKHSFLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHA 444 (575)
Q Consensus 365 ~~We~~r~~~~~k~~~d~~rskLLeeL~s~e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~i 444 (575)
+-||.+|+++ +++++|.+++.++.. .++|+|.+|+..|+.|||||+|++++++++|+.||+||.|.+
T Consensus 136 slWEkLR~k~----~~ke~R~klv~el~~---------likg~i~~lv~aHDtSRViQt~Vky~s~~~r~~if~eL~p~~ 202 (652)
T KOG2050|consen 136 SLWEKLRRKT----TPKEERDKLVSELYK---------LIKGKISKLVFAHDTSRVIQTCVKYGSEAQREQIFEELLPFF 202 (652)
T ss_pred HHHHHHhccC----CcHHHHHHHHHHHHH---------HHhhhHHHHHHHhhhHHHHHHHHHhcCHHHHHHHHHHHhHHH
Confidence 4699999999 799999999999885 899999999999999999999999999999999999999999
Q ss_pred HHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHh-cCHHHHHHHHHHHHHH--------
Q 008180 445 SKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEV-IELHQKSQLVLELDGH-------- 515 (575)
Q Consensus 445 veLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~-~s~eqr~~II~EL~g~-------- 515 (575)
++||+++||.|+|||+|+||+++++..||+.|+||++.|.+|+.|+.||+.++.- ++.+||..|+.||++.
T Consensus 203 v~l~kskY~k~~v~KmLkyGsk~q~a~iI~sl~Ghv~kLlRH~eaa~Vve~ay~~~A~l~Qr~~li~EfYG~efqlfK~s 282 (652)
T KOG2050|consen 203 VELAKSKYAKFFVQKMLKYGSKAQKAKIINSLRGHVVKLLRHREAAYVVEYAYNDFATLEQRQYLIQEFYGDEFQLFKDS 282 (652)
T ss_pred HHHHHhHHHHHHHHHHHhcCCHHHHHHHHHHHhhhHHHHHhhhHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999999987754 7778888888887665
Q ss_pred -------------------------------------------------------------------HHHhhcCCchhHH
Q 008180 516 -------------------------------------------------------------------VMRCVRDQNGNHV 528 (575)
Q Consensus 516 -------------------------------------------------------------------l~~LvkDq~GNyV 528 (575)
+.+|++++.|+.|
T Consensus 283 n~~Tl~kil~~~pekk~~I~~~l~~~I~~v~eKg~v~~tivHk~mlEy~~~ade~e~~e~l~ll~elv~e~vHT~dGS~v 362 (652)
T KOG2050|consen 283 NDKTLDKILAEAPEKKASILRHLKAIITPVAEKGSVDHTIVHKLMLEYLTIADEEEKSELLELLKELVPEMVHTRDGSRV 362 (652)
T ss_pred CcccHHHHHHhChHhHHHHHHHHHHHhHHHhhcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchHHH
Confidence 6778899999999
Q ss_pred HHHHHHhCChhhHHHHHHHHHHHHHHHhcCcchHHHHHHHHhhcCCC
Q 008180 529 IQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQPHNNASGFQ 575 (575)
Q Consensus 529 IQK~Le~~~~k~rk~IIk~L~~~iveLSthkyGs~VVQK~Le~~ddT 575 (575)
..+||++++++.|+.|++.|++++.++|+|.||+.|+-.+|++.|||
T Consensus 363 Am~li~~a~aKeRK~IiK~~K~h~~K~A~~~yGh~vlia~ldc~DDT 409 (652)
T KOG2050|consen 363 AMKLIWHATAKERKLIIKNMKEHVEKIANDEYGHLVLIALLDCTDDT 409 (652)
T ss_pred HHHHHhhCCHHHHHHHHHHHHHHHHHHHhhccCceehhhhhcccchH
Confidence 99999999999999999999999999999999999999999999997
No 7
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=5.1e-29 Score=282.34 Aligned_cols=162 Identities=42% Similarity=0.642 Sum_probs=158.6
Q ss_pred hhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhH
Q 008180 412 SVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCR 491 (575)
Q Consensus 412 A~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSr 491 (575)
++|++|||+||++|+.-+.++.+.|+.|+.+.+.+||.|.||||||||+||+++.+|+..++..+.+++..|+.|+||||
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 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCHHHHH-HHHHHHHHHHHHhhcCCchhHHHHHHHHhCChhhHHHHHHHHHHHHHHHhcCcchHHHHHHHHh
Q 008180 492 VIQKALEVIELHQKS-QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQPHNN 570 (575)
Q Consensus 492 VVQKlLE~~s~eqr~-~II~EL~g~l~~LvkDq~GNyVIQK~Le~~~~k~rk~IIk~L~~~iveLSthkyGs~VVQK~Le 570 (575)
|+||+|+++.++++. .|+++|++.+..|++|++||||||||++....+...+|++.+.+++.++++|+|||+|||+|||
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 999999999988877 8899999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcC
Q 008180 571 ASG 573 (575)
Q Consensus 571 ~~d 573 (575)
+|.
T Consensus 607 ~~~ 609 (777)
T COG5099 607 NCN 609 (777)
T ss_pred hcc
Confidence 986
No 8
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=1.6e-27 Score=270.26 Aligned_cols=178 Identities=27% Similarity=0.358 Sum_probs=162.1
Q ss_pred hHhHHHHHHHHHHHHhhCccccHHHHHHhhcCCHHHH-HHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHH
Q 008180 397 QKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEK-VSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEK 475 (575)
Q Consensus 397 rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer-~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~ 475 (575)
+...+..+.+++++++.+.+|||++|++++..+.++. ..|++||.+.+..|.+|++|||||||+|+....+....|++.
T Consensus 504 ~~~ml~~~~~~~~~ls~~~~Gtrv~QK~id~~~t~~qi~~lv~~l~~~~~~li~dqngNHviqKci~~~~~~~~~fif~~ 583 (777)
T COG5099 504 KSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDS 583 (777)
T ss_pred HHHHHHHhhhhHHHhhccccccHHHHHHHhccCchhhHHHHHHHhhhhhHHHHHhccCCHHHHHHHHhcCccccchHHHH
Confidence 3345556678888888888888888888888855444 488999999999999999999999999999999999999999
Q ss_pred hhcChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHhCChhhHHHHHHHHHH-HHHH
Q 008180 476 LVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRG-QVAT 554 (575)
Q Consensus 476 L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQK~Le~~~~k~rk~IIk~L~~-~ive 554 (575)
+..++++++.|+|||+|||+|+|.+..+++..++++|..++..|+.|++||||||++|+.+.+..++.|+..+.. ++++
T Consensus 584 ~~~~~~~is~~r~Gs~vvq~~le~~~~~~~~~~~~~Ii~~~~~L~~dq~GNyvvq~il~~g~~~~k~~i~~~~l~~~v~e 663 (777)
T COG5099 584 INENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVE 663 (777)
T ss_pred HHhhhHhhhccccccHHHHHHHHhccHhHHHHHHHHHHHHHHhhccCCcchhhhhHHhhcCCCcchhHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999877 9999
Q ss_pred HhcCcchHHHHHHHHhhcCC
Q 008180 555 LSTHPYGCRVIQPHNNASGF 574 (575)
Q Consensus 555 LSthkyGs~VVQK~Le~~dd 574 (575)
||+||||+.||+|||+.+.+
T Consensus 664 lS~~kfaSnvVeK~i~~~~~ 683 (777)
T COG5099 664 LSTHKFASNVVEKCIKYASD 683 (777)
T ss_pred HHHHHHHHHHHHHHHhcCCc
Confidence 99999999999999998765
No 9
>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=2.7e-26 Score=250.61 Aligned_cols=198 Identities=24% Similarity=0.300 Sum_probs=182.5
Q ss_pred CcccCchHHHHHHHHHhc---chhhHhHHHHHHH---HHHHHhhCccccHHHHHHhhcC-CHHHHHHHHHHHhhhHHHhh
Q 008180 376 QRTFEDSKKHSFLEELKS---SNAQKFELSDIAG---RIVEFSVDQHGSRFIQQKLEHC-SAEEKVSVFKEVLPHASKLM 448 (575)
Q Consensus 376 ~k~~~d~~rskLLeeL~s---~e~rk~iLs~IkG---~VveLA~Dq~GSRVLQkLLe~~-s~Eer~~If~ELkp~iveLm 448 (575)
+++|.|+++..+++.+.+ .+++..+++.+.. .+++++.+.+|+|.||++++.. +.+|...++..|++.+..|+
T Consensus 256 ~~Lm~d~fGny~vqkl~~~~~~eq~~~i~~~lts~p~~fv~i~~N~~GTr~iQkl~~~~~~~dqI~~~~~ai~~~fl~L~ 335 (536)
T KOG2049|consen 256 PELMEDPFGNYLVQKLLEVCDEEQLTKIVSLLTSDPRLFVEICTNMYGTRAVQKLLGKSDSVDQISLFLDAIKPNFLHLI 335 (536)
T ss_pred HHHHhccchhHHHHHHHHhhCHHHHHHHHHHHhcCccceeEeeecCchhHHHHHHHhccccHHHHHHHHHHHHhhhHHhh
Confidence 566888999999987773 3445556666664 6999999999999999999887 56778889999999999999
Q ss_pred cCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHH
Q 008180 449 TDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHV 528 (575)
Q Consensus 449 tD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyV 528 (575)
+|.||+||||++|+..+++..+.|++.+..++.+||+|++||.|||+||.....++|..|++++..+.+.|+.|.+||||
T Consensus 336 ~D~~g~~Viq~cl~~f~~~~~~~l~e~i~~~c~~iA~~~hGCcvLq~cl~~~~~~~rd~Lv~~i~~naL~Ls~d~~GNyv 415 (536)
T KOG2049|consen 336 KDKNGNHVIQRCLRVFSKEKNEFLYEAILRYCLDLATDQHGCCVLQKCLDYSRGEQRDRLVEEISRNALLLSNDPYGNYV 415 (536)
T ss_pred hhcchhHHHHHHHHhcCchhhhHHHHHHHHHHHHHHHhccccchhHHHhcchhHHHHHHHHHHHHHHhHhhhcCccccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCChhhHHHHHHHHHHHHHHHhcCcchHHHHHHHHhhcC
Q 008180 529 IQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQPHNNASG 573 (575)
Q Consensus 529 IQK~Le~~~~k~rk~IIk~L~~~iveLSthkyGs~VVQK~Le~~d 573 (575)
||.+|+.-.......|+..|.+++++||++|||++||||||+...
T Consensus 416 VQyvl~L~~~~~t~~i~~~L~g~~veLS~qKfgS~vVEk~L~~~~ 460 (536)
T KOG2049|consen 416 VQYVLELNDPSCTVNIAEKLRGHYVELSFQKFGSHVVEKLLKVRE 460 (536)
T ss_pred hhhhhhhcCcchHHHHHHhhhhHHHHHHHHhhccHHHHHHHhcCc
Confidence 999999999999999999999999999999999999999999765
No 10
>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.9e-24 Score=236.10 Aligned_cols=173 Identities=30% Similarity=0.502 Sum_probs=162.6
Q ss_pred HHHHHHHHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhc--
Q 008180 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVG-- 478 (575)
Q Consensus 401 Ls~IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g-- 478 (575)
+..+.+.+..+|+|++|||++|++++.++.+....|+.|+..++.+||.|+||||+|||+++.++.+|+..|+..+..
T Consensus 212 ~~~~~~~~~~~akd~~gc~~lq~~~~~~~~~~~~~if~~~~~~~~~Lm~d~fGny~vqkl~~~~~~eq~~~i~~~lts~p 291 (536)
T KOG2049|consen 212 MVEIQGSINLIAKDQHGCRLLQKLLSEGTKVSILKIFLETIQDVPELMEDPFGNYLVQKLLEVCDEEQLTKIVSLLTSDP 291 (536)
T ss_pred hhccchhhhhhcccccCCcccccCcccCccccHHHHHHHHHHHHHHHHhccchhHHHHHHHHhhCHHHHHHHHHHHhcCc
Confidence 346678999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred -ChhhhccCcchhHHHHHHHHhcCHHHHH-HHHHHHHHHHHHhhcCCchhHHHHHHHHhCChhhHHHHHHHHHHHHHHHh
Q 008180 479 -QVLPLSLQMYGCRVIQKALEVIELHQKS-QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLS 556 (575)
Q Consensus 479 -~I~~Ls~hkyGSrVVQKlLE~~s~eqr~-~II~EL~g~l~~LvkDq~GNyVIQK~Le~~~~k~rk~IIk~L~~~iveLS 556 (575)
.|..+|.++||+++||++++.....++. .+++.|...+..|++|.||+||||+||...+++++++|++.+..++.+||
T Consensus 292 ~~fv~i~~N~~GTr~iQkl~~~~~~~dqI~~~~~ai~~~fl~L~~D~~g~~Viq~cl~~f~~~~~~~l~e~i~~~c~~iA 371 (536)
T KOG2049|consen 292 RLFVEICTNMYGTRAVQKLLGKSDSVDQISLFLDAIKPNFLHLIKDKNGNHVIQRCLRVFSKEKNEFLYEAILRYCLDLA 371 (536)
T ss_pred cceeEeeecCchhHHHHHHHhccccHHHHHHHHHHHHhhhHHhhhhcchhHHHHHHHHhcCchhhhHHHHHHHHHHHHHH
Confidence 6999999999999999999998775544 55678999999999999999999999999999999999999999999999
Q ss_pred cCcchHHHHHHHHhhcC
Q 008180 557 THPYGCRVIQPHNNASG 573 (575)
Q Consensus 557 thkyGs~VVQK~Le~~d 573 (575)
+|++||.|+|+||+...
T Consensus 372 ~~~hGCcvLq~cl~~~~ 388 (536)
T KOG2049|consen 372 TDQHGCCVLQKCLDYSR 388 (536)
T ss_pred HhccccchhHHHhcchh
Confidence 99999999999998764
No 11
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=99.68 E-value=6.5e-16 Score=168.55 Aligned_cols=191 Identities=18% Similarity=0.288 Sum_probs=168.3
Q ss_pred HHHHHHHHHh---cchhhHhHHHHHHHHHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccccHHHHH
Q 008180 383 KKHSFLEELK---SSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQK 459 (575)
Q Consensus 383 ~rskLLeeL~---s~e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGNyVVQK 459 (575)
..+++++.+. +...|..+++++.+.+++||...||-+++|++|+++++.++..|++++.+|++.|+.|+.|.|||.-
T Consensus 174 DtSRViQt~Vky~s~~~r~~if~eL~p~~v~l~kskY~k~~v~KmLkyGsk~q~a~iI~sl~Ghv~kLlRH~eaa~Vve~ 253 (652)
T KOG2050|consen 174 DTSRVIQTCVKYGSEAQREQIFEELLPFFVELAKSKYAKFFVQKMLKYGSKAQKAKIINSLRGHVVKLLRHREAAYVVEY 253 (652)
T ss_pred hhHHHHHHHHHhcCHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHhcCCHHHHHHHHHHHhhhHHHHHhhhHHHHHHHH
Confidence 4456666544 6778889999999999999999999999999999999999999999999999999999999999986
Q ss_pred Hhhc-CCHHHHHHHHHHhh-------------------------------------------------------------
Q 008180 460 FFEH-GSPDQRKELAEKLV------------------------------------------------------------- 477 (575)
Q Consensus 460 LfE~-gs~Eqr~~II~~L~------------------------------------------------------------- 477 (575)
++.- ++.+||..|+.+|.
T Consensus 254 ay~~~A~l~Qr~~li~EfYG~efqlfK~sn~~Tl~kil~~~pekk~~I~~~l~~~I~~v~eKg~v~~tivHk~mlEy~~~ 333 (652)
T KOG2050|consen 254 AYNDFATLEQRQYLIQEFYGDEFQLFKDSNDKTLDKILAEAPEKKASILRHLKAIITPVAEKGSVDHTIVHKLMLEYLTI 333 (652)
T ss_pred HHHhhccHHHHHHHHHHHhhHHHHHHhccCcccHHHHHHhChHhHHHHHHHHHHHhHHHhhcchhHHHHHHHHHHHHHHh
Confidence 6543 66677766555554
Q ss_pred --------------cChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHhCChhh--H
Q 008180 478 --------------GQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEK--I 541 (575)
Q Consensus 478 --------------g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQK~Le~~~~k~--r 541 (575)
..|.+|+..+-|++|.-+||.++++++|..||+.|++++..+++|+||+.|+-.+|+|.++.. .
T Consensus 334 ade~e~~e~l~ll~elv~e~vHT~dGS~vAm~li~~a~aKeRK~IiK~~K~h~~K~A~~~yGh~vlia~ldc~DDT~l~k 413 (652)
T KOG2050|consen 334 ADEEEKSELLELLKELVPEMVHTRDGSRVAMKLIWHATAKERKLIIKNMKEHVEKIANDEYGHLVLIALLDCTDDTKLLK 413 (652)
T ss_pred CCHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHhhccCceehhhhhcccchHHHHH
Confidence 344458888889999999999999999999999999999999999999999999999987654 6
Q ss_pred HHHHHHHHHHHHHHhcCcchHHHHHHHHhhcC
Q 008180 542 EFIISAFRGQVATLSTHPYGCRVIQPHNNASG 573 (575)
Q Consensus 542 k~IIk~L~~~iveLSthkyGs~VVQK~Le~~d 573 (575)
+.|++++.+.+..|..++||.+|++.++.-.|
T Consensus 414 k~i~~e~~~el~~li~Dk~Grrv~lyll~p~D 445 (652)
T KOG2050|consen 414 KLIYDELKSELKSLISDKYGRRVILYLLAPRD 445 (652)
T ss_pred HHHHHHHHHHHHHHhccchhhhhhhhhccCCc
Confidence 88999999999999999999999999987543
No 12
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]
Probab=99.55 E-value=5.3e-14 Score=154.85 Aligned_cols=168 Identities=19% Similarity=0.283 Sum_probs=129.7
Q ss_pred HHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCC-HHHHHHHHHHhhcChhhhcc
Q 008180 407 RIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGS-PDQRKELAEKLVGQVLPLSL 485 (575)
Q Consensus 407 ~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs-~Eqr~~II~~L~g~I~~Ls~ 485 (575)
-..++-.|+.|||+|+.+++.+++..+..+...++..+.+|+.++++||+||++|++.+ .++...|+++|.+++..|..
T Consensus 337 ~~k~~l~d~tgSrllE~Imeva~~~~~~lf~~~f~~rl~~La~~p~aNF~lQrli~h~~~~e~v~~v~eeL~P~~~~LL~ 416 (650)
T KOG2188|consen 337 FLKELLSDQTGSRLLEVIMEVASESLLSLFYIVFCGRLDELAVHPIANFPLQRLINHLTSLEDVGSVIEELAPKLSSLLE 416 (650)
T ss_pred HHHHHHhcCcccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhCccccchHHHHHHhccCHHHHHHHHHHHhHHHHHHHH
Confidence 34556668999999999999999888877777788899999999999999999999987 78888888888877666544
Q ss_pred Ccc--------------hhH---HHH------------------------------------------------HHHHhc
Q 008180 486 QMY--------------GCR---VIQ------------------------------------------------KALEVI 500 (575)
Q Consensus 486 hky--------------GSr---VVQ------------------------------------------------KlLE~~ 500 (575)
+-+ ||+ |+| .++.+.
T Consensus 417 ~g~~gVv~sLia~~~rl~s~q~~~l~~Li~a~~~~~~~~k~il~~lL~~~~~~g~~~~~~~t~~~h~~ga~lle~lv~f~ 496 (650)
T KOG2188|consen 417 QGNSGVVASLIAASARLGSYQDKMLQQLIQAFHAASESKKNILPCLLFSLTLFGCVGEWFLTEKFHQKGAVLLEELVNFS 496 (650)
T ss_pred cCCchHhHHHHHHHHhhchhHHHHHHHHHHHHhcCChhhcchHHHHHHHhhhcccccccccHHHHhhchhHHHHHHHhhc
Confidence 443 221 333 222222
Q ss_pred CHHHH---HHHHHHHHHHHHHhhcCCchhHHHHHHHHh--CChhhHHHHHHHHHHHHHHHhcCcchHHHHHHHHhhcCC
Q 008180 501 ELHQK---SQLVLELDGHVMRCVRDQNGNHVIQKCIEC--VPAEKIEFIISAFRGQVATLSTHPYGCRVIQPHNNASGF 574 (575)
Q Consensus 501 s~eqr---~~II~EL~g~l~~LvkDq~GNyVIQK~Le~--~~~k~rk~IIk~L~~~iveLSthkyGs~VVQK~Le~~dd 574 (575)
....+ ..|.+-....+.+++.+.+|+|||+.+|.. .+++.++.||..|.+.+++|+++.+||+|++|||+.++.
T Consensus 497 k~~i~~litsll~L~~eqi~e~~~~~~~ShlIeavL~S~~l~~~~~~kLi~~l~g~~~~La~~~~GSrv~eK~wea~~~ 575 (650)
T KOG2188|consen 497 KTHIQTLITSLLSLSEEQILEMSCNGVGSHLIEAVLASKDLGEKIKEKLINILDGSFVTLALSTFGSRVFEKCWEATDV 575 (650)
T ss_pred hhhhHHHHHHHHhhhHHHHHHHhcCCchHHHHHHHHHhccccHHHHHHHHHHhhccchheeecCcccHHHHHHHHHhhH
Confidence 22111 111111244588899999999999999998 788999999999999999999999999999999999873
No 13
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]
Probab=99.42 E-value=2.4e-12 Score=142.03 Aligned_cols=203 Identities=22% Similarity=0.292 Sum_probs=159.9
Q ss_pred CCcccccccCCCcccCchHHHHHHHHHhcc---hhhHhHHHHHHHHHHHHhhCccccHHHHHHhhcCC-HHHHHHHHHHH
Q 008180 365 SGWQGQRTFEGQRTFEDSKKHSFLEELKSS---NAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCS-AEEKVSVFKEV 440 (575)
Q Consensus 365 ~~We~~r~~~~~k~~~d~~rskLLeeL~s~---e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s-~Eer~~If~EL 440 (575)
+.|+..+..- --+..|+-.+.++|.++.. +........+.+++.+||.++.+..+||++|++.+ .++...||+||
T Consensus 329 ~~~~kE~~~~-k~~l~d~tgSrllE~Imeva~~~~~~lf~~~f~~rl~~La~~p~aNF~lQrli~h~~~~e~v~~v~eeL 407 (650)
T KOG2188|consen 329 GLWGKERSFL-KELLSDQTGSRLLEVIMEVASESLLSLFYIVFCGRLDELAVHPIANFPLQRLINHLTSLEDVGSVIEEL 407 (650)
T ss_pred cccccccHHH-HHHHhcCcccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhCccccchHHHHHHhccCHHHHHHHHHHH
Confidence 3488777432 1124677888999988743 33345667788999999999999999999999997 89999999999
Q ss_pred hhhHHHhhcCcccc-----------------HHHHHHhhcC--C-H-------------------------H--------
Q 008180 441 LPHASKLMTDVFGN-----------------YVIQKFFEHG--S-P-------------------------D-------- 467 (575)
Q Consensus 441 kp~iveLmtD~yGN-----------------yVVQKLfE~g--s-~-------------------------E-------- 467 (575)
.|++..|....+-- -++|.|++.. . + +
T Consensus 408 ~P~~~~LL~~g~~gVv~sLia~~~rl~s~q~~~l~~Li~a~~~~~~~~k~il~~lL~~~~~~g~~~~~~~t~~~h~~ga~ 487 (650)
T KOG2188|consen 408 APKLSSLLEQGNSGVVASLIAASARLGSYQDKMLQQLIQAFHAASESKKNILPCLLFSLTLFGCVGEWFLTEKFHQKGAV 487 (650)
T ss_pred hHHHHHHHHcCCchHhHHHHHHHHhhchhHHHHHHHHHHHHhcCChhhcchHHHHHHHhhhcccccccccHHHHhhchhH
Confidence 99998887644332 2333333210 0 0 0
Q ss_pred -----------HHHHHHHHh----hcChhhhccCcchhHHHHHHHHh--cCHHHHHHHHHHHHHHHHHhhcCCchhHHHH
Q 008180 468 -----------QRKELAEKL----VGQVLPLSLQMYGCRVIQKALEV--IELHQKSQLVLELDGHVMRCVRDQNGNHVIQ 530 (575)
Q Consensus 468 -----------qr~~II~~L----~g~I~~Ls~hkyGSrVVQKlLE~--~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQ 530 (575)
....+++.| ..+|.++|++.+|+||||.++.. +.+..+..||..|.+....|+.+.+|+||++
T Consensus 488 lle~lv~f~k~~i~~litsll~L~~eqi~e~~~~~~~ShlIeavL~S~~l~~~~~~kLi~~l~g~~~~La~~~~GSrv~e 567 (650)
T KOG2188|consen 488 LLEELVNFSKTHIQTLITSLLSLSEEQILEMSCNGVGSHLIEAVLASKDLGEKIKEKLINILDGSFVTLALSTFGSRVFE 567 (650)
T ss_pred HHHHHHhhchhhhHHHHHHHHhhhHHHHHHHhcCCchHHHHHHHHHhccccHHHHHHHHHHhhccchheeecCcccHHHH
Confidence 011122222 34788899999999999999998 7889999999999999999999999999999
Q ss_pred HHHHhCChhhHHHHHHHHHHHHHHHhcCcchHHHHHHH
Q 008180 531 KCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQPH 568 (575)
Q Consensus 531 K~Le~~~~k~rk~IIk~L~~~iveLSthkyGs~VVQK~ 568 (575)
||.+......|..|.++|.+--.+|..++||-+|..++
T Consensus 568 K~wea~~~~~k~rIakeL~~~~~~vk~s~~gk~v~~~~ 605 (650)
T KOG2188|consen 568 KCWEATDVLYKERIAKELVGIHNDVKSSKYGKFVMLNW 605 (650)
T ss_pred HHHHHhhHHHHHHHHHHHHhhccccccCcchHHHHHhc
Confidence 99999999999999999999999999999999998764
No 14
>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]
Probab=99.00 E-value=1.5e-10 Score=130.76 Aligned_cols=168 Identities=17% Similarity=0.233 Sum_probs=121.0
Q ss_pred HHHHHHhhCccccHHHHHHhhcC-CHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhc
Q 008180 406 GRIVEFSVDQHGSRFIQQKLEHC-SAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLS 484 (575)
Q Consensus 406 G~VveLA~Dq~GSRVLQkLLe~~-s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls 484 (575)
.++..+..|.+|.+..|++++.+ ++.+...|+.-+.+.+..|..|+|||||+|.+|+++-+. ..+|++.+..+++.+.
T Consensus 582 ~ylts~gvHknGtw~~qk~ik~a~te~qik~iv~g~dpyc~~l~~dqfgnyvaqd~LkF~fp~-nsFVfE~v~s~~~~iv 660 (1007)
T KOG4574|consen 582 KYLTSMGVHKNGTWACQKIIKMAFTERQIKLIVRGVDPYCTPLLNDQFGNYVAQDSLKFGFPW-NSFVFESVFSHFWDIV 660 (1007)
T ss_pred hhhhhccccccchHHHHHHHHHhhchhhhheeeeccCcchhhHHHHhhcceeeeeehhccCcc-chHHHHHHHHHHHHHH
Confidence 44555566667777777777766 445566666677777777777777777777777776653 4566788888888888
Q ss_pred cCcchhHHHHHHHHhcC--HHHHHHHHHHH-HHHHHHhhcCCchhHHHHHHHHhCChhhHHHH-HHHHHHHHHHHhcCcc
Q 008180 485 LQMYGCRVIQKALEVIE--LHQKSQLVLEL-DGHVMRCVRDQNGNHVIQKCIECVPAEKIEFI-ISAFRGQVATLSTHPY 560 (575)
Q Consensus 485 ~hkyGSrVVQKlLE~~s--~eqr~~II~EL-~g~l~~LvkDq~GNyVIQK~Le~~~~k~rk~I-Ik~L~~~iveLSthky 560 (575)
..+||++.|.+|||... .++....++.+ .-....+..+-+|-..|.++|+.+....+..| +..+.+++++||.|+-
T Consensus 661 QsrfGsravrAcle~lNa~~e~qsl~~~s~iIs~ss~latnsng~llvtw~lDns~~~nrh~~l~~~lt~el~~lC~h~L 740 (1007)
T KOG4574|consen 661 QSRFGSRAVRACLEALNANTEDQSLVRESCIISKSSYLATNSNGLLLVTWLLDNSSLPNRHTILAHGLTKELVMLCFHKL 740 (1007)
T ss_pred HHhhhhHHHHHHHHHhccCchhhhhhhhhhhhhchhhhhhcCccceeeeeecccccccchhhHHhhhhhhccchhhhhhc
Confidence 88888888888888743 33333222222 23356778888888888888888654455443 3457799999999999
Q ss_pred hHHHHHHHHhhcCC
Q 008180 561 GCRVIQPHNNASGF 574 (575)
Q Consensus 561 Gs~VVQK~Le~~dd 574 (575)
|+.+|+|+|+.+++
T Consensus 741 gsttv~Kl~n~~qe 754 (1007)
T KOG4574|consen 741 GSTTVLKLLNLRQE 754 (1007)
T ss_pred cchhhhhhhhcCCC
Confidence 99999999998875
No 15
>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]
Probab=98.92 E-value=6.3e-10 Score=125.73 Aligned_cols=143 Identities=20% Similarity=0.234 Sum_probs=127.2
Q ss_pred HHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhcCHHHH-HHH
Q 008180 430 AEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQK-SQL 508 (575)
Q Consensus 430 ~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr-~~I 508 (575)
..|.+.+.-+..++..+|..|--||-|+||+||++..-.++.+..+....+..+..|+||.|+.||+|+.+..+.. +.|
T Consensus 534 ~pEied~ai~mLDe~~elsSdylGNtVvqkfFe~sS~~ik~aml~r~s~ylts~gvHknGtw~~qk~ik~a~te~qik~i 613 (1007)
T KOG4574|consen 534 APEIEDLAILMLDELPELSSDYLGNTVVQKFFELSSDIIKDAMLRRGSKYLTSMGVHKNGTWACQKIIKMAFTERQIKLI 613 (1007)
T ss_pred chhHHHHHHHHhccCCcchhhhhcchhhHHHHhhccHHHHHHHHhhhhhhhhhccccccchHHHHHHHHHhhchhhhhee
Confidence 4556667778888999999999999999999999999999999999999999999999999999999999776544 455
Q ss_pred HHHHHHHHHHhhcCCchhHHHHHHHHhCChhhHHHHHHHHHHHHHHHhcCcchHHHHHHHHhhcC
Q 008180 509 VLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQPHNNASG 573 (575)
Q Consensus 509 I~EL~g~l~~LvkDq~GNyVIQK~Le~~~~k~rk~IIk~L~~~iveLSthkyGs~VVQK~Le~~d 573 (575)
++-.++....+..|++||||+|+||.+.-+ ...+|++.+..++.++.+.+||++-|-+||+..+
T Consensus 614 v~g~dpyc~~l~~dqfgnyvaqd~LkF~fp-~nsFVfE~v~s~~~~ivQsrfGsravrAcle~lN 677 (1007)
T KOG4574|consen 614 VRGVDPYCTPLLNDQFGNYVAQDSLKFGFP-WNSFVFESVFSHFWDIVQSRFGSRAVRACLEALN 677 (1007)
T ss_pred eeccCcchhhHHHHhhcceeeeeehhccCc-cchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhc
Confidence 666788899999999999999999998765 4578899999999999999999999999999776
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=98.35 E-value=3e-07 Score=66.04 Aligned_cols=35 Identities=43% Similarity=0.727 Sum_probs=26.6
Q ss_pred HHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHH
Q 008180 439 EVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELA 473 (575)
Q Consensus 439 ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II 473 (575)
|+.+++.+|++|+||||||||+|+++++++++.|+
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 46677788888888888888888887777776664
No 17
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=97.98 E-value=3.7e-06 Score=58.95 Aligned_cols=34 Identities=38% Similarity=0.627 Sum_probs=20.5
Q ss_pred HhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHH
Q 008180 440 VLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELA 473 (575)
Q Consensus 440 Lkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II 473 (575)
+++++.+|++|+||||||||+|++++++++..|+
T Consensus 2 ~~~~~~~l~~~~~g~~viqk~l~~~~~~~~~~i~ 35 (36)
T smart00025 2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35 (36)
T ss_pred chHHHHHHHhcchhhHHHHHHHHHCCHHHHHHhh
Confidence 3455666666666666666666666665555543
No 18
>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=97.98 E-value=5.8e-06 Score=59.36 Aligned_cols=33 Identities=33% Similarity=0.497 Sum_probs=17.5
Q ss_pred hhcChhhhccCcchhHHHHHHHHhcCHHHHHHH
Q 008180 476 LVGQVLPLSLQMYGCRVIQKALEVIELHQKSQL 508 (575)
Q Consensus 476 L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~I 508 (575)
|.+++.+|+.|+|||+|||++|+.++.+++..|
T Consensus 2 i~~~~~~l~~d~~Gn~VvQk~le~~~~~~~~~i 34 (35)
T PF00806_consen 2 IKGNLVELSKDQYGNYVVQKCLEHASPEQRQLI 34 (35)
T ss_dssp HTTTHHHHHTSTTHHHHHHHHHHHSSHHHHHHH
T ss_pred hHHHHHHHHhccccCHHHHHHHHHCCHHHHHhh
Confidence 345555555555555555555555555544443
No 19
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=97.71 E-value=2.8e-05 Score=54.45 Aligned_cols=34 Identities=38% Similarity=0.662 Sum_probs=31.6
Q ss_pred HHHHHHHHhhCccccHHHHHHhhcCCHHHHHHHH
Q 008180 404 IAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVF 437 (575)
Q Consensus 404 IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If 437 (575)
+++++.+|+.|++||||||++|+.++++++..|+
T Consensus 2 ~~~~~~~l~~~~~g~~viqk~l~~~~~~~~~~i~ 35 (36)
T smart00025 2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35 (36)
T ss_pred chHHHHHHHhcchhhHHHHHHHHHCCHHHHHHhh
Confidence 5689999999999999999999999999988876
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=84.04 E-value=4.3 Score=38.75 Aligned_cols=47 Identities=21% Similarity=0.341 Sum_probs=35.7
Q ss_pred CchHHHHHHHHHhcchhhHhHHHHHHHHHHHHhhCccccHHHHHHhhcCCHH
Q 008180 380 EDSKKHSFLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAE 431 (575)
Q Consensus 380 ~d~~rskLLeeL~s~e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s~E 431 (575)
.+..|..|++.+. -.+++.|..+..+|..+..||.||..+|..++.|
T Consensus 43 ~~~Rr~ELl~~~s-----p~Ll~~i~~~~~~ll~~~~g~~~i~eiL~~~~gd 89 (148)
T PF08144_consen 43 PEVRRKELLEAIS-----PPLLEAIAENAEELLSSSFGCQFITEILLSATGD 89 (148)
T ss_pred HHHHHHHHHHHhh-----HHHHHHHHHhHHHHHhcCcccHHHHHHHhccCcc
Confidence 4445556665444 3578888899999999999999999999887644
No 21
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=81.76 E-value=57 Score=34.96 Aligned_cols=129 Identities=11% Similarity=0.181 Sum_probs=79.6
Q ss_pred CccccHHHHHHhhc-CCHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHH
Q 008180 414 DQHGSRFIQQKLEH-CSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRV 492 (575)
Q Consensus 414 Dq~GSRVLQkLLe~-~s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrV 492 (575)
...|-..+..+|.. ..++.-..|++++...-. .+++..+ ...+++....++....+++..++...--..+
T Consensus 78 ~~gg~~~~~~iL~~~l~~~~a~~il~~i~~~~~--------~~~fe~L-~~ld~~~l~~lL~~EhpqtiA~iLs~l~~~~ 148 (339)
T PRK05686 78 LMGGIDYARSLLEKALGEEKADSILERILESLG--------TSGFDFL-RKMDPQQLANFIRNEHPQTIALILSYLKPDQ 148 (339)
T ss_pred cCChHHHHHHHHHHHcCHHHHHHHHHHHhcccc--------CchHHHH-hcCCHHHHHHHHHhcCHHHHHHHHhCCCHHH
Confidence 33556668888875 566777778777764311 2344433 3446666666666666666666666666666
Q ss_pred HHHHHHhcCHHHHHHHHHHH------------------HHHHHHhh----cCCchhHHHHHHHHhCChhhHHHHHHHHHH
Q 008180 493 IQKALEVIELHQKSQLVLEL------------------DGHVMRCV----RDQNGNHVIQKCIECVPAEKIEFIISAFRG 550 (575)
Q Consensus 493 VQKlLE~~s~eqr~~II~EL------------------~g~l~~Lv----kDq~GNyVIQK~Le~~~~k~rk~IIk~L~~ 550 (575)
-.++|...+.+.+..++..+ ...+.... ....|...+-.+|...+.+..+.|++.|..
T Consensus 149 aa~vL~~l~~~~~~~v~~ria~l~~v~~~~~~~i~~~L~~~l~~~~~~~~~~~~g~~~~a~Iln~~~~~~~~~il~~L~~ 228 (339)
T PRK05686 149 AAEILSLLPEELRADVMMRIATLEGVSPEALKEVEEVLEKKLSSMANADRTKMGGVKTVAEILNNLDRQTEKTILESLEE 228 (339)
T ss_pred HHHHHHhCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHhhcccccccccCcHHHHHHHHhcCCchHHHHHHHHHHh
Confidence 66666666665554444332 22222211 245688888889988888888888887754
Q ss_pred H
Q 008180 551 Q 551 (575)
Q Consensus 551 ~ 551 (575)
.
T Consensus 229 ~ 229 (339)
T PRK05686 229 E 229 (339)
T ss_pred h
Confidence 3
No 22
>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=81.00 E-value=4.4 Score=48.09 Aligned_cols=148 Identities=15% Similarity=0.233 Sum_probs=66.3
Q ss_pred HHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHH-----------------Hhh----cCccccHHHHHHhhcCC
Q 008180 407 RIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHAS-----------------KLM----TDVFGNYVIQKFFEHGS 465 (575)
Q Consensus 407 ~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iv-----------------eLm----tD~yGNyVVQKLfE~gs 465 (575)
.|+.|..-..|-++|-++|.+.+.+++..|+..|..|+. .+. .+-|-..|+..|+.+..
T Consensus 576 ~fi~~ls~~KGkkll~R~~~~l~~~q~~~il~~i~~~l~~l~vv~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~l~~~i~ 655 (808)
T PF09770_consen 576 PFISILSVRKGKKLLPRIFPFLSQEQRLTILTMIFRHLDQLDVVRRASYTDGEDQPLLIKRDDIELFLQAVMPPLMNVIN 655 (808)
T ss_dssp HHHHHTTSHHHHHHHHHHGGGS-HHHHHHHHHHHHHTH-----------------HHHHHTTTTT--GGGGHHHS-HHHH
T ss_pred cceEEEeeCChheeHHhhhhhCChhHHHHHHHHHHHHhhhhcccccccccccccCccccchHhHHHHHHHHHHHHHHHHH
Confidence 678888889999999999999999999999999999883 333 24455666666665554
Q ss_pred HHHHHHHHHHhh-----cChhhhccCcchhHHHHHHHHhcCH---------HHH-------HHHHHHH-HHHHHHh----
Q 008180 466 PDQRKELAEKLV-----GQVLPLSLQMYGCRVIQKALEVIEL---------HQK-------SQLVLEL-DGHVMRC---- 519 (575)
Q Consensus 466 ~Eqr~~II~~L~-----g~I~~Ls~hkyGSrVVQKlLE~~s~---------eqr-------~~II~EL-~g~l~~L---- 519 (575)
......|+..+. .++.-++++|+|.-+|-.+|..+.. ++. ..++..| .+++..|
T Consensus 656 ~~~~~~i~gll~~~~~~~~~~~i~~tk~Gls~lt~llsRae~l~~~~~~~~~~~~~W~~~~~~lf~~l~~~~~~~~fp~~ 735 (808)
T PF09770_consen 656 EAPFNEIIGLLGLLINNNNVSFIAQTKFGLSLLTMLLSRAELLKQSGSSSEEEWSQWTEFYDQLFDSLEEPRLPSIFPPD 735 (808)
T ss_dssp HHHHHHHTTSTTT-S--HHHHHHHTSHHHHHHHHHHHHHHHHHHHT------HHHHHHHH--------------------
T ss_pred hCCHHHHHHHHHHHHhCCCceEEEEChHHHHHHHHHHHHHHHhhccCCCCHHHHHHhhhhhhhccccccccccccccccc
Confidence 444444433221 2566799999999999998864321 111 1222223 2322222
Q ss_pred --hcCCchhHHHHHHHHh---CChhhHHHHHHHHHHHHHH
Q 008180 520 --VRDQNGNHVIQKCIEC---VPAEKIEFIISAFRGQVAT 554 (575)
Q Consensus 520 --vkDq~GNyVIQK~Le~---~~~k~rk~IIk~L~~~ive 554 (575)
..+-.-+||+|-+-.. ++.++-..|+.++++.|.+
T Consensus 736 ~~~~~~~~~~vwq~la~~~~~~~~~~q~~lv~~vrd~v~~ 775 (808)
T PF09770_consen 736 SSINSGDDSYVWQFLAALALGASPEQQQILVDEVRDRVME 775 (808)
T ss_dssp ----------------------------------------
T ss_pred cccccccccccccccccccccccccccccccccccccccc
Confidence 2446667888865554 3667778888888877754
No 23
>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=75.33 E-value=11 Score=35.99 Aligned_cols=62 Identities=18% Similarity=0.223 Sum_probs=37.6
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHhCChhhH---HHHHHHHHHH--------HHHHhcCcchHHHHHHHHhh
Q 008180 510 LELDGHVMRCVRDQNGNHVIQKCIECVPAEKI---EFIISAFRGQ--------VATLSTHPYGCRVIQPHNNA 571 (575)
Q Consensus 510 ~EL~g~l~~LvkDq~GNyVIQK~Le~~~~k~r---k~IIk~L~~~--------iveLSthkyGs~VVQK~Le~ 571 (575)
+.+..+...|+.+..|+.||..+|...+.+.. +.|++.+... -..+..+++|++++.+++..
T Consensus 60 ~~i~~~~~~ll~~~~g~~~i~eiL~~~~gdk~~a~~Aia~~~~~~~~~~~~~~e~H~i~~p~~~r~lK~Liq~ 132 (148)
T PF08144_consen 60 EAIAENAEELLSSSFGCQFITEILLSATGDKSAALEAIASLAAEPLFPGDIDEEYHLIEHPFGHRMLKKLIQG 132 (148)
T ss_pred HHHHHhHHHHHhcCcccHHHHHHHhccCccHHHHHHHHHHHHhhccCCCCCcCccchhcCchHHHHHHHHHHC
Confidence 33344556677777777777777776543322 2233333222 12477899999999998853
No 24
>TIGR00400 mgtE Mg2+ transporter (mgtE). This family of prokaryotic proteins models a class of Mg++ transporter first described in Bacillus firmus. May form a homodimer.
Probab=69.31 E-value=67 Score=35.69 Aligned_cols=81 Identities=12% Similarity=0.195 Sum_probs=37.6
Q ss_pred HHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHh
Q 008180 420 FIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEV 499 (575)
Q Consensus 420 VLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~ 499 (575)
.++.+|+...+.+...+++++.+.-..........-..-.+|++.+++.+..+++.+-. .-+..+++.
T Consensus 22 ~l~~~l~~~~~~dia~~l~~l~~~~~~~~~~~l~~~~~a~vl~~l~~~~~~~ll~~l~~------------~~~~~~~~~ 89 (449)
T TIGR00400 22 KIKEKFLKXQPXDIAEALKRLPGTELILLYRFLPKKIAVDTFSNLDQSTQNKLLNSFTN------------KEISEMINE 89 (449)
T ss_pred HHHHHHhcCCHHHHHHHHHhCCHHHHHHHHHhCChhhHHHHHHcCCHHHHHHHHHhCCH------------HHHHHHHHc
Confidence 34444444455555445444443322222222233334456666666666666665532 122334444
Q ss_pred cCHHHHHHHHHHH
Q 008180 500 IELHQKSQLVLEL 512 (575)
Q Consensus 500 ~s~eqr~~II~EL 512 (575)
.+.++...+++++
T Consensus 90 l~~dd~~~ll~~l 102 (449)
T TIGR00400 90 MNLDDVIDLLEEV 102 (449)
T ss_pred CChhHHHHHHHhC
Confidence 5555555555544
No 25
>KOG0166 consensus Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport]
Probab=68.41 E-value=31 Score=39.41 Aligned_cols=131 Identities=11% Similarity=0.126 Sum_probs=72.2
Q ss_pred cccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhh-----cCCHHHHHHHHH-HhhcChhhhccC---
Q 008180 416 HGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFE-----HGSPDQRKELAE-KLVGQVLPLSLQ--- 486 (575)
Q Consensus 416 ~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE-----~gs~Eqr~~II~-~L~g~I~~Ls~h--- 486 (575)
+.|+.|--+-+..++.....|-..+.+++++|..+.-++.++-++-- .|+++|...+++ .+...+..|...
T Consensus 256 Da~WAlsyLsdg~ne~iq~vi~~gvv~~LV~lL~~~~~~v~~PaLRaiGNIvtG~d~QTq~vi~~~~L~~l~~ll~~s~~ 335 (514)
T KOG0166|consen 256 DACWALSYLTDGSNEKIQMVIDAGVVPRLVDLLGHSSPKVVTPALRAIGNIVTGSDEQTQVVINSGALPVLSNLLSSSPK 335 (514)
T ss_pred HHHHHHHHHhcCChHHHHHHHHccchHHHHHHHcCCCcccccHHHhhccceeeccHHHHHHHHhcChHHHHHHHhccCcc
Confidence 45555655555544444444555677777777777777766444433 345666666665 233444444442
Q ss_pred ----cchhHHHHHHHHhcCHHHHHHHHHH-HHHHHHHhhcCC------chhHHHHHHHHhCChhhHHHHHHH
Q 008180 487 ----MYGCRVIQKALEVIELHQKSQLVLE-LDGHVMRCVRDQ------NGNHVIQKCIECVPAEKIEFIISA 547 (575)
Q Consensus 487 ----kyGSrVVQKlLE~~s~eqr~~II~E-L~g~l~~LvkDq------~GNyVIQK~Le~~~~k~rk~IIk~ 547 (575)
+.+||+|-.+-. .+.++...+++. |.+.++.++..- ...++|-.+...++++..+.+++.
T Consensus 336 ~~ikkEAcW~iSNItA-G~~~qiqaVida~l~p~Li~~l~~~ef~~rKEAawaIsN~ts~g~~~qi~yLv~~ 406 (514)
T KOG0166|consen 336 ESIKKEACWTISNITA-GNQEQIQAVIDANLIPVLINLLQTAEFDIRKEAAWAISNLTSSGTPEQIKYLVEQ 406 (514)
T ss_pred hhHHHHHHHHHHHhhc-CCHHHHHHHHHcccHHHHHHHHhccchHHHHHHHHHHHhhcccCCHHHHHHHHHc
Confidence 557777766654 555555555544 555555555432 234455555555555555555554
No 26
>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=66.60 E-value=15 Score=43.78 Aligned_cols=93 Identities=13% Similarity=0.146 Sum_probs=55.4
Q ss_pred hHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcch---------------------hHHHHHHHHhcC
Q 008180 443 HASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYG---------------------CRVIQKALEVIE 501 (575)
Q Consensus 443 ~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyG---------------------SrVVQKlLE~~s 501 (575)
.++.|+.-.-|+-+|-++|.+.+.+++..|+..|..++-.|..=+.| +.|+..++.++.
T Consensus 576 ~fi~~ls~~KGkkll~R~~~~l~~~q~~~il~~i~~~l~~l~vv~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~l~~~i~ 655 (808)
T PF09770_consen 576 PFISILSVRKGKKLLPRIFPFLSQEQRLTILTMIFRHLDQLDVVRRASYTDGEDQPLLIKRDDIELFLQAVMPPLMNVIN 655 (808)
T ss_dssp HHHHHTTSHHHHHHHHHHGGGS-HHHHHHHHHHHHHTH-----------------HHHHHTTTTT--GGGGHHHS-HHHH
T ss_pred cceEEEeeCChheeHHhhhhhCChhHHHHHHHHHHHHhhhhcccccccccccccCccccchHhHHHHHHHHHHHHHHHHH
Confidence 57889999999999999999999999999999999888544433222 222222222222
Q ss_pred HHHHHHHHH---HH--HHHHHHhhcCCchhHHHHHHHHh
Q 008180 502 LHQKSQLVL---EL--DGHVMRCVRDQNGNHVIQKCIEC 535 (575)
Q Consensus 502 ~eqr~~II~---EL--~g~l~~LvkDq~GNyVIQK~Le~ 535 (575)
......|+. .| ..++..+++++.|--+|..+|..
T Consensus 656 ~~~~~~i~gll~~~~~~~~~~~i~~tk~Gls~lt~llsR 694 (808)
T PF09770_consen 656 EAPFNEIIGLLGLLINNNNVSFIAQTKFGLSLLTMLLSR 694 (808)
T ss_dssp HHHHHHHTTSTTT-S--HHHHHHHTSHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHHHhCCCceEEEEChHHHHHHHHHHHH
Confidence 222222111 11 23566777888888888877764
No 27
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=66.28 E-value=1.2e+02 Score=32.47 Aligned_cols=86 Identities=8% Similarity=0.203 Sum_probs=43.7
Q ss_pred CHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHh------------------hcChhhh----ccC
Q 008180 429 SAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKL------------------VGQVLPL----SLQ 486 (575)
Q Consensus 429 s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L------------------~g~I~~L----s~h 486 (575)
.++....++....++...++...--.-+-.++|...+++.+..|+..+ ...+... ...
T Consensus 121 d~~~l~~lL~~EhpqtiA~iLs~l~~~~aa~vL~~l~~~~~~~v~~ria~l~~v~~~~~~~i~~~L~~~l~~~~~~~~~~ 200 (339)
T PRK05686 121 DPQQLANFIRNEHPQTIALILSYLKPDQAAEILSLLPEELRADVMMRIATLEGVSPEALKEVEEVLEKKLSSMANADRTK 200 (339)
T ss_pred CHHHHHHHHHhcCHHHHHHHHhCCCHHHHHHHHHhCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHhhcccccccc
Confidence 444444444444444444444444444444555555544444443332 2222221 123
Q ss_pred cchhHHHHHHHHhcCHHHHHHHHHHHHH
Q 008180 487 MYGCRVIQKALEVIELHQKSQLVLELDG 514 (575)
Q Consensus 487 kyGSrVVQKlLE~~s~eqr~~II~EL~g 514 (575)
.-|...+-.+|...+......|+..|..
T Consensus 201 ~~g~~~~a~Iln~~~~~~~~~il~~L~~ 228 (339)
T PRK05686 201 MGGVKTVAEILNNLDRQTEKTILESLEE 228 (339)
T ss_pred cCcHHHHHHHHhcCCchHHHHHHHHHHh
Confidence 4567777778887777766666666643
No 28
>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=64.76 E-value=1e+02 Score=32.06 Aligned_cols=19 Identities=16% Similarity=0.030 Sum_probs=8.6
Q ss_pred hhHHHHHHHHHHHHHHHhc
Q 008180 539 EKIEFIISAFRGQVATLST 557 (575)
Q Consensus 539 k~rk~IIk~L~~~iveLSt 557 (575)
+.++.|.+.+...+..+..
T Consensus 290 ~l~~~i~~~i~~~l~~~v~ 308 (367)
T PF04286_consen 290 ELREKINRFIENLLERIVE 308 (367)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444443
No 29
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=62.80 E-value=1.4e+02 Score=34.88 Aligned_cols=143 Identities=15% Similarity=0.158 Sum_probs=73.7
Q ss_pred cHHHHHHhhcC--CHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHH-HHHHHHHhhcChhhhccCcc----hh
Q 008180 418 SRFIQQKLEHC--SAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQ-RKELAEKLVGQVLPLSLQMY----GC 490 (575)
Q Consensus 418 SRVLQkLLe~~--s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eq-r~~II~~L~g~I~~Ls~hky----GS 490 (575)
.--||++|+.- +.++.+.+++.|...+.+=+.+.--| .+|++|+..+ ++.|+..|..+|..=+.|-| =-
T Consensus 89 ~~~~~k~l~~~~l~~~~~~~~l~~~~~~c~kd~is~~k~----w~f~~~~s~~~~e~~~~~l~n~~~~~~~~~~lrlh~~ 164 (757)
T KOG4368|consen 89 EQQMQKLLEETQLDMNEFDNLLQPIIDTCTKDAISAGKN----WMFSNAKSPPHCELMAGHLRNRITADGAHFELRLHLI 164 (757)
T ss_pred HHHHHHHHHhccCCHHHHHHHHHHHHHHHhHHHHHHhhh----hhhhcCCCchHHHHHHHHHHhhhcccccchhhhhhhH
Confidence 34578888764 56666666666555433333333233 3788887544 44455555555544333332 22
Q ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHHHH------hhcCCchhHHHHHHHHhCC--hhhHHHHHHHHH------HHHHHHh
Q 008180 491 RVIQKALEVIELHQKSQLVLELDGHVMR------CVRDQNGNHVIQKCIECVP--AEKIEFIISAFR------GQVATLS 556 (575)
Q Consensus 491 rVVQKlLE~~s~eqr~~II~EL~g~l~~------LvkDq~GNyVIQK~Le~~~--~k~rk~IIk~L~------~~iveLS 556 (575)
++|...+-+|..++...++..|...++. ++..+..+..+-++|.... .-.-+.|++.|. +...++-
T Consensus 165 ylind~~~hcqrk~~~~~~~~l~~~v~~~yc~~~~~~~e~~~~~~~~ll~~we~~~yf~ds~~~ql~~~~~~~~~~~~~~ 244 (757)
T KOG4368|consen 165 YLINDVLHHCQRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQSPALGLGQYQATL 244 (757)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhhhhhHhHHHHHHHHHHHHHhhcCchhHHHHHHhhhhhhhhhhHHHHH
Confidence 4455555566666666666666554433 2334455556666654421 111233444442 3334555
Q ss_pred cCcchHHH
Q 008180 557 THPYGCRV 564 (575)
Q Consensus 557 thkyGs~V 564 (575)
.+.||+-|
T Consensus 245 ~~~y~~~~ 252 (757)
T KOG4368|consen 245 INEYSSVV 252 (757)
T ss_pred HhhhhHHH
Confidence 66777643
No 30
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=60.34 E-value=38 Score=31.72 Aligned_cols=13 Identities=0% Similarity=0.100 Sum_probs=4.9
Q ss_pred HHHHHHHHHHHHh
Q 008180 544 IISAFRGQVATLS 556 (575)
Q Consensus 544 IIk~L~~~iveLS 556 (575)
.++.+...+..++
T Consensus 171 ~l~~~~~~~~~~~ 183 (209)
T PF02854_consen 171 ALDEIFERLQKYA 183 (209)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3333333333333
No 31
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=54.11 E-value=3.7e+02 Score=30.40 Aligned_cols=38 Identities=8% Similarity=0.235 Sum_probs=20.2
Q ss_pred HHHHHHHhCChhhHHHHHH-HHHHHHHHHhcCcchHHHHHH
Q 008180 528 VIQKCIECVPAEKIEFIIS-AFRGQVATLSTHPYGCRVIQP 567 (575)
Q Consensus 528 VIQK~Le~~~~k~rk~IIk-~L~~~iveLSthkyGs~VVQK 567 (575)
++.+++..... .+.+++ ...+-+.+|+..++|..-+.+
T Consensus 203 ll~~ll~eL~~--dDiLvqlnalell~~La~~~~g~~yL~~ 241 (503)
T PF10508_consen 203 LLDLLLKELDS--DDILVQLNALELLSELAETPHGLQYLEQ 241 (503)
T ss_pred HHHHHHHHhcC--ccHHHHHHHHHHHHHHHcChhHHHHHHh
Confidence 44444444433 233333 245666777777777665543
No 32
>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=53.22 E-value=2.7e+02 Score=30.25 Aligned_cols=34 Identities=12% Similarity=0.325 Sum_probs=15.5
Q ss_pred HHHHHHHHHHhhhHHHhhcCc---cccHHHHHHhhcC
Q 008180 431 EEKVSVFKEVLPHASKLMTDV---FGNYVIQKFFEHG 464 (575)
Q Consensus 431 Eer~~If~ELkp~iveLmtD~---yGNyVVQKLfE~g 464 (575)
.||-.++..+..++.+.|... +-.+++..++...
T Consensus 152 ~erL~i~~~ll~q~p~~M~~~~~~W~~~l~~~l~~~~ 188 (372)
T PF12231_consen 152 SERLNIYKRLLSQFPQQMIKHADIWFPILFPDLLSSA 188 (372)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 344445555555444444322 3345555555443
No 33
>PF14666 RICTOR_M: Rapamycin-insensitive companion of mTOR, middle domain
Probab=51.63 E-value=69 Score=32.76 Aligned_cols=130 Identities=15% Similarity=0.230 Sum_probs=68.3
Q ss_pred ccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCc--c-ccHHHHHHhhcCCHHH-HHHHHHHhhcChhhhccCcchh
Q 008180 415 QHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDV--F-GNYVIQKFFEHGSPDQ-RKELAEKLVGQVLPLSLQMYGC 490 (575)
Q Consensus 415 q~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~--y-GNyVVQKLfE~gs~Eq-r~~II~~L~g~I~~Ls~hkyGS 490 (575)
.-||.+++.+|+. .+..+....+++.+++.+..... + |...-..+| +++. ...+....-.-+-.|+.++.|-
T Consensus 82 ~vGc~L~~~Ll~~-~eG~~~l~~~~ll~qia~~L~~~d~~~g~~~~~~lf---s~~~l~~tl~~~Yf~~IG~lS~~~~Gl 157 (226)
T PF14666_consen 82 RVGCQLLETLLSS-PEGIKYLSESKLLPQIAECLAQVDPMSGITAHDPLF---SPQRLSTTLSRGYFLFIGVLSSTPNGL 157 (226)
T ss_pred HHHHHHHHHHHcC-cHHHHHHHHccHHHHHHHHHHHHhhhcCCccccccc---CHHHHHhhHHHHHHHHHHHHhCChhHH
Confidence 3588888988877 22233322344444444333222 1 221112222 1111 1222222222344688999999
Q ss_pred HHHHH------HHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHhCChhhHHHHHHHHH
Q 008180 491 RVIQK------ALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFR 549 (575)
Q Consensus 491 rVVQK------lLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQK~Le~~~~k~rk~IIk~L~ 549 (575)
.++++ +.+.++.+.+..++.-+...+ ....+...-.+++|+|..++.+.|..-.+.|.
T Consensus 158 ~lLe~~~if~~l~~i~~~~~~~~l~klil~~L-DY~~~~~~R~iLsKaLt~~s~~iRl~aT~~L~ 221 (226)
T PF14666_consen 158 KLLERWNIFTMLYHIFSLSSRDDLLKLILSSL-DYSVDGHPRIILSKALTSGSESIRLYATKHLR 221 (226)
T ss_pred HHHHHCCHHHHHHHHHccCchHHHHHHHHhhC-CCCCccHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 88875 333344444555555554443 44556677788889998887766655555443
No 34
>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=50.72 E-value=59 Score=35.60 Aligned_cols=93 Identities=17% Similarity=0.182 Sum_probs=55.8
Q ss_pred cCchHHHHHHHHHhcc--hhhH--hHHHHHHHHHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCcccc
Q 008180 379 FEDSKKHSFLEELKSS--NAQK--FELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGN 454 (575)
Q Consensus 379 ~~d~~rskLLeeL~s~--e~rk--~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGN 454 (575)
|.+.+...+.+++... .... ..+++|++.+..|. .++.-+.+-+....+ .|.+++...... ...+..
T Consensus 32 ~~~afWd~l~~el~~~~~~~~~~~~Ll~~ike~L~~ll----~~~~~~~I~e~LD~~---li~Qq~~~g~~D--~~~l~~ 102 (441)
T PF05794_consen 32 MHKAFWDALREELEQDPPDYSRLPQLLEEIKEILLSLL----PSRLRQEIEEVLDLE---LIRQQLEHGVLD--LVKLAR 102 (441)
T ss_pred HHHHHHHHHHHHHhhCCCChhHHHHHHHHHHHHHHHhc----CHHHHHHHHHHCChH---HHHHHHhcCCcC--HHHHHH
Confidence 7888888888888854 2222 36777888877777 444444444443332 233444443333 456778
Q ss_pred HHHHHHhhcCCHHHHHHHHHHhhcChh
Q 008180 455 YVIQKFFEHGSPDQRKELAEKLVGQVL 481 (575)
Q Consensus 455 yVVQKLfE~gs~Eqr~~II~~L~g~I~ 481 (575)
|++..+-++|.| .|++.++.+...+.
T Consensus 103 ~i~~~l~~~CAP-~RD~~v~~l~~~~~ 128 (441)
T PF05794_consen 103 FIISLLKKLCAP-MRDEEVKALVEKIE 128 (441)
T ss_pred HHHHHHHHhCCC-CCcHHHHHHHHHHH
Confidence 888888888875 34455555544443
No 35
>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=48.00 E-value=3.9e+02 Score=28.85 Aligned_cols=27 Identities=11% Similarity=0.394 Sum_probs=19.6
Q ss_pred chhHHHHHHHHhcCHHHHHHHHHHHHH
Q 008180 488 YGCRVIQKALEVIELHQKSQLVLELDG 514 (575)
Q Consensus 488 yGSrVVQKlLE~~s~eqr~~II~EL~g 514 (575)
-|...+-.+|...+......|++.|..
T Consensus 199 gG~~~~a~ILN~~~~~~~~~il~~L~~ 225 (338)
T TIGR00207 199 GGVRAVAEIINLMDRKTEKTIITSLEE 225 (338)
T ss_pred ChHHHHHHHHHhCCchHHHHHHHHHHH
Confidence 477788888888877777666666643
No 36
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=44.72 E-value=5.1e+02 Score=29.30 Aligned_cols=25 Identities=8% Similarity=0.202 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHhcCc-chHHHHHHH
Q 008180 544 IISAFRGQVATLSTHP-YGCRVIQPH 568 (575)
Q Consensus 544 IIk~L~~~iveLSthk-yGs~VVQK~ 568 (575)
|++.|...+.....++ .+...|--.
T Consensus 244 i~~~L~~~l~~~~~dp~~~~~~l~g~ 269 (503)
T PF10508_consen 244 IFDKLSNLLQDSEEDPRLSSLLLPGR 269 (503)
T ss_pred HHHHHHHHHhccccCCcccchhhhhH
Confidence 3334444444445555 444444333
No 37
>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]
Probab=44.46 E-value=4.5e+02 Score=30.77 Aligned_cols=67 Identities=10% Similarity=0.105 Sum_probs=38.5
Q ss_pred HHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHH
Q 008180 408 IVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAE 474 (575)
Q Consensus 408 VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~ 474 (575)
+..++...----.+-++|...+...+.+|++.|+..+.+...++.+-+-+-++......++.--|.+
T Consensus 56 ~~~~s~~~l~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~e~kmal~el~q~y~en~n~~l~~lWe 122 (711)
T COG1747 56 IISLSKQLLDDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYGESKMALLELLQCYKENGNEQLYSLWE 122 (711)
T ss_pred HHHhhhccccchHHHHHHHHhccchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhcCchhhHHHHH
Confidence 3344444333334445666667778888888888877777777766655444333333344443333
No 38
>KOG1240 consensus Protein kinase containing WD40 repeats [Signal transduction mechanisms]
Probab=44.39 E-value=1.6e+02 Score=37.16 Aligned_cols=73 Identities=15% Similarity=0.180 Sum_probs=41.4
Q ss_pred HHHHHHHhcchhhHhHHHHHHHHHHHHhhCccccHHHHHHh---------hcCCHHHHHHHHHHHhhhHHHhhcCccccH
Q 008180 385 HSFLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKL---------EHCSAEEKVSVFKEVLPHASKLMTDVFGNY 455 (575)
Q Consensus 385 skLLeeL~s~e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLL---------e~~s~Eer~~If~ELkp~iveLmtD~yGNy 455 (575)
..||.+|...-.-...|+.|...++.|..|+..--=++.+. +..++.+...+.+-|.|++..|..|.-.++
T Consensus 444 LeLl~~lS~~i~de~~LDRVlPY~v~l~~Ds~a~Vra~Al~Tlt~~L~~Vr~~~~~daniF~eYlfP~L~~l~~d~~~~~ 523 (1431)
T KOG1240|consen 444 LELLQELSTYIDDEVKLDRVLPYFVHLLMDSEADVRATALETLTELLALVRDIPPSDANIFPEYLFPHLNHLLNDSSAQI 523 (1431)
T ss_pred HHHHHHHhhhcchHHHHhhhHHHHHHHhcCchHHHHHHHHHHHHHHHhhccCCCcccchhhHhhhhhhhHhhhccCccce
Confidence 34444444333334556677777888887777643333222 223444555555667788888888865554
Q ss_pred HH
Q 008180 456 VI 457 (575)
Q Consensus 456 VV 457 (575)
|-
T Consensus 524 vR 525 (1431)
T KOG1240|consen 524 VR 525 (1431)
T ss_pred eh
Confidence 43
No 39
>KOG1059 consensus Vesicle coat complex AP-3, delta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.94 E-value=85 Score=37.51 Aligned_cols=49 Identities=10% Similarity=0.170 Sum_probs=29.1
Q ss_pred CchhHHHHHHHHhCChhhHHHHHHH-----HHHHHHHHhcCcchHHHHHHHHhh
Q 008180 523 QNGNHVIQKCIECVPAEKIEFIISA-----FRGQVATLSTHPYGCRVIQPHNNA 571 (575)
Q Consensus 523 q~GNyVIQK~Le~~~~k~rk~IIk~-----L~~~iveLSthkyGs~VVQK~Le~ 571 (575)
.|-+-.+-++|+.++......|.+. +...+..|....+|..+-+.++|.
T Consensus 387 ~yrdell~~II~iCS~snY~~ItdFEWYlsVlveLa~l~~~~~G~~I~eQi~Dv 440 (877)
T KOG1059|consen 387 NYRDELLTRIISICSQSNYQYITDFEWYLSVLVELARLEGTRHGSLIAEQIIDV 440 (877)
T ss_pred hHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHhccccchhhHHHHHHHHH
Confidence 4445556666666655544444332 234445566678888888888774
No 40
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=43.40 E-value=2.2e+02 Score=26.17 Aligned_cols=35 Identities=6% Similarity=0.020 Sum_probs=24.2
Q ss_pred hhHHHHHHHHhcCHHHHHHHHH-HHHHHHHHhhcCC
Q 008180 489 GCRVIQKALEVIELHQKSQLVL-ELDGHVMRCVRDQ 523 (575)
Q Consensus 489 GSrVVQKlLE~~s~eqr~~II~-EL~g~l~~LvkDq 523 (575)
+=.+++.|++.+...-..++.. ++...+..++.+.
T Consensus 57 AL~lLd~~vkNcg~~f~~~i~s~~fl~~l~~l~~~~ 92 (133)
T cd03561 57 ALTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNS 92 (133)
T ss_pred HHHHHHHHHHhCChHHHHHHhhHHHHHHHHHHhCCC
Confidence 3356777888887776667765 6666677777764
No 41
>KOG3759 consensus Uncharacterized RUN domain protein [Signal transduction mechanisms]
Probab=42.70 E-value=2.1e+02 Score=32.72 Aligned_cols=124 Identities=19% Similarity=0.256 Sum_probs=72.3
Q ss_pred hcCCHHHHHHHHHHHhhhHHHhhcCcc-----------ccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHH
Q 008180 426 EHCSAEEKVSVFKEVLPHASKLMTDVF-----------GNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQ 494 (575)
Q Consensus 426 e~~s~Eer~~If~ELkp~iveLmtD~y-----------GNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQ 494 (575)
-.+.+++|.+++.+|.+.+..=|.|-. ||-++.| ..+-.+++|..|+.++.+|-.-.|-.-- -
T Consensus 98 vea~p~er~~LLrdLedFAF~Gcpd~~~lq~~~s~~~~~~~~lek-----q~e~qkeLi~QLk~Ql~dLE~~AYe~Ge-g 171 (621)
T KOG3759|consen 98 VEADPSERLKLLRDLEDFAFKGCPDMNELQRLRSESESGNDVLEK-----QNERQKELIKQLKEQLEDLERTAYENGE-G 171 (621)
T ss_pred HcCCHHHHHHHHHHHHHHHhcCCCcccccccccccccccchhhhh-----hcchHHHHHHHHHHHHHHHHHHHHhcCC-C
Confidence 357889999999999998887777733 2222221 1133478889998888776554441100 0
Q ss_pred HHHHhcCHHHHHHHHHHHHHHH------HHhhcCCchhHHHHHHHHh-CChhhHHHHHHHHHHHHHHH
Q 008180 495 KALEVIELHQKSQLVLELDGHV------MRCVRDQNGNHVIQKCIEC-VPAEKIEFIISAFRGQVATL 555 (575)
Q Consensus 495 KlLE~~s~eqr~~II~EL~g~l------~~LvkDq~GNyVIQK~Le~-~~~k~rk~IIk~L~~~iveL 555 (575)
.+=...-.+.+..|++||+.++ ..|...+--..|=..+-+. .|.+.+..+++.|+.+|-+|
T Consensus 172 ~LPq~viLekQk~ilDeLr~Kl~lnl~i~~lsteelr~qVD~A~~q~VnP~k~KeQLV~QLkTQItDL 239 (621)
T KOG3759|consen 172 ELPQTVILEKQKAILDELREKLELNLDIDKLSTEELRRQVDDALKQLVNPFKEKEQLVDQLKTQITDL 239 (621)
T ss_pred cCchHHHHHHHHHHHHHHHHHhhccCCcccccHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHH
Confidence 0001111245567788887653 3344433333343333333 35677888888888777664
No 42
>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=41.84 E-value=2.2e+02 Score=30.09 Aligned_cols=141 Identities=13% Similarity=0.113 Sum_probs=0.0
Q ss_pred HHhhcCCHHHHHHHHHHHh-hhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhcC
Q 008180 423 QKLEHCSAEEKVSVFKEVL-PHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIE 501 (575)
Q Consensus 423 kLLe~~s~Eer~~If~ELk-p~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s 501 (575)
+.|..|++.+.+.|++++. +.+-+=..-++-.+++.-=-+..-..-...+-..|.+++..| ..-++|++..++..+-
T Consensus 42 q~L~~csp~q~e~lc~~L~l~~lsd~~l~~lc~~ll~Ls~dls~~~a~~l~~sl~LpkilsL--~~~ASR~L~sal~~f~ 119 (263)
T PF11510_consen 42 QFLNECSPSQVEMLCSQLQLPQLSDDGLLQLCSSLLALSPDLSHSNATVLLRSLFLPKILSL--EEPASRLLVSALTSFC 119 (263)
T ss_dssp HGGGG--HHHHHHHHHHHTGGG--HHHHHHHHHHHHH-SS---HHHHHHHHHHHHHHHHHH---SS---HHHHHHHHHHH
T ss_pred HHHHhCCHHHHHHHHHHhCcCCCCHHHHHHHHHHHHccCcccchhhHHHHHHHHHHHHHHhc--CCCccHHHHHHHHHHH
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCchhH---HHHHHH--HhCChhhHHHHHHHHHHHHHHHhcCcchHHHHHHHHhh
Q 008180 502 LHQKSQLVLELDGHVMRCVRDQNGNH---VIQKCI--ECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQPHNNA 571 (575)
Q Consensus 502 ~eqr~~II~EL~g~l~~LvkDq~GNy---VIQK~L--e~~~~k~rk~IIk~L~~~iveLSthkyGs~VVQK~Le~ 571 (575)
...-..+++.+...+ |-.-..|+. +|.+++ ++.+++++..++..+. ++.-++.=.-|+|.+++.
T Consensus 120 k~~p~~~~~all~Pl--L~~~~~g~~Q~eLl~rlvk~~~l~p~~~~l~l~~~L----~~~W~E~~~~Vlq~lL~~ 188 (263)
T PF11510_consen 120 KKYPRPVCEALLVPL--LQAPGLGPPQCELLCRLVKKECLEPDHRLLLLRQIL----ELVWNEETFLVLQSLLER 188 (263)
T ss_dssp HHSHHHHHHHHHHHH--HHSTT--HHHHHHHHHHHH-TTS-HHHHHHHHHHHH----HS---HHHHHHHHHHHTT
T ss_pred HhCcHHHHHHHHHHH--HcCCCCCHHHHHHHHHHHHhccCCHHHHHHHHHHHH----hCcCcHHHHHHHHHHHhc
No 43
>PF11573 Med23: Mediator complex subunit 23; InterPro: IPR021629 Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice.
Probab=41.62 E-value=1.4e+02 Score=38.13 Aligned_cols=107 Identities=10% Similarity=-0.046 Sum_probs=51.9
Q ss_pred cCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHHHHHHHHh--------hcCCchhHHHHHHHH
Q 008180 463 HGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRC--------VRDQNGNHVIQKCIE 534 (575)
Q Consensus 463 ~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL~g~l~~L--------vkDq~GNyVIQK~Le 534 (575)
..++|+++..++.+...+...+..+...++++.+...+.... ..-+.+.+.+..+ ..+...-.+|+|||.
T Consensus 56 ~~~~Ee~~~~ik~~l~~i~~~~~~~~~~~l~d~L~~~v~~~~--i~ar~vCe~lL~~~~l~~~~~~~W~~~F~lIrkiI~ 133 (1341)
T PF11573_consen 56 SMSEEEKESCIKQYLKYIHSQSHPRRYEFLFDLLETAVNNGI--IPARLVCEELLSSEKLFYLNSRFWQEKFKLIRKIIH 133 (1341)
T ss_pred cCCHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhCC--CChHHHHHHHhcccchhhhhhHHHHHHHHHHHHHhc
Confidence 345555555555555555544444444444444443332210 0001111111111 223334457777777
Q ss_pred hCChhhHHHHHHHHHHHHHH---------HhcCcchHHHHHHHHhh
Q 008180 535 CVPAEKIEFIISAFRGQVAT---------LSTHPYGCRVIQPHNNA 571 (575)
Q Consensus 535 ~~~~k~rk~IIk~L~~~ive---------LSthkyGs~VVQK~Le~ 571 (575)
..+=|-.+.|++.+.+.+.. +-.=...+.||+++||+
T Consensus 134 ~VDYKGvR~Ilk~~~eK~~~iP~~~~~~~~~~l~~~~~vi~~ilDR 179 (1341)
T PF11573_consen 134 GVDYKGVREILKICLEKMQQIPSSLSPEQLPQLLAVEEVIEHILDR 179 (1341)
T ss_pred ccCcHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHhCc
Confidence 77766666666666554432 12223456788888774
No 44
>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=38.13 E-value=4.5e+02 Score=28.78 Aligned_cols=62 Identities=15% Similarity=0.057 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhc
Q 008180 430 AEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVI 500 (575)
Q Consensus 430 ~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~ 500 (575)
....-.++++|++.+..|. .+..-+.+-+..+.+ .|.+.+...+.+ ..++..+|+..+-+.|
T Consensus 51 ~~~~~~Ll~~ike~L~~ll----~~~~~~~I~e~LD~~---li~Qq~~~g~~D--~~~l~~~i~~~l~~~C 112 (441)
T PF05794_consen 51 YSRLPQLLEEIKEILLSLL----PSRLRQEIEEVLDLE---LIRQQLEHGVLD--LVKLARFIISLLKKLC 112 (441)
T ss_pred hhHHHHHHHHHHHHHHHhc----CHHHHHHHHHHCChH---HHHHHHhcCCcC--HHHHHHHHHHHHHHhC
Confidence 3444567888888888888 444445555555543 223333333333 3445555555555554
No 45
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=37.98 E-value=5.7e+02 Score=27.92 Aligned_cols=47 Identities=17% Similarity=0.294 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhhcChhhhcc----CcchhHHHHHHHHhcCHHHHHHHHHHH
Q 008180 466 PDQRKELAEKLVGQVLPLSL----QMYGCRVIQKALEVIELHQKSQLVLEL 512 (575)
Q Consensus 466 ~Eqr~~II~~L~g~I~~Ls~----hkyGSrVVQKlLE~~s~eqr~~II~EL 512 (575)
++...+|-+.+..++..+.. ..-|.+++-.++...+......+++.|
T Consensus 176 p~al~~i~~~l~~~l~~~~~~~~~~~gg~~~~aeIlN~~d~~~e~~il~~l 226 (339)
T COG1536 176 PEALAELENVLEKKLQSLVNEDYSKLGGIKAAAEILNLLDRGTEKTILESL 226 (339)
T ss_pred HHHHHHHHHHHHHHHHhhccccccccccHhHHHHHHHhcchhHHHHHHHHH
Confidence 44444444444444444422 233666677777776654444444333
No 46
>PF01603 B56: Protein phosphatase 2A regulatory B subunit (B56 family); InterPro: IPR002554 Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family [].; GO: 0008601 protein phosphatase type 2A regulator activity, 0007165 signal transduction, 0000159 protein phosphatase type 2A complex; PDB: 2NYM_B 2NYL_B 2IAE_E 2NPP_B 3FGA_B 2JAK_A.
Probab=37.31 E-value=3.5e+02 Score=29.81 Aligned_cols=66 Identities=14% Similarity=0.220 Sum_probs=36.0
Q ss_pred HHHHHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHhCChhh--------HHHHHHHHHHHHHHHhcCc
Q 008180 493 IQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEK--------IEFIISAFRGQVATLSTHP 559 (575)
Q Consensus 493 VQKlLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQK~Le~~~~k~--------rk~IIk~L~~~iveLSthk 559 (575)
|+.+++...+++-..++..|-..+..|+...+ ..|.++++.....+. ++.|+..+.+.+.+.++.-
T Consensus 279 l~~il~~~~~~~f~~i~~~lf~~la~ci~S~h-~qVAErAl~~w~n~~~~~li~~~~~~i~p~i~~~L~~~~~~H 352 (409)
T PF01603_consen 279 LEEILEVLPPEEFQKIMVPLFKRLAKCISSPH-FQVAERALYFWNNEYFLSLISQNSRVILPIIFPALYRNSKNH 352 (409)
T ss_dssp HHHHHTT--HHHHHHHHHHHHHHHHHHHTSSS-HHHHHHHHGGGGSHHHHHHHHCTHHHHHHHHHHHHSSTTSS-
T ss_pred HHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCC-HHHHHHHHHHHCCHHHHHHHHhChHHHHHHHHHHHHHHHHHH
Confidence 44566666666666666666666666655544 346666666654332 4445555555555545433
No 47
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=35.07 E-value=8e+02 Score=28.73 Aligned_cols=32 Identities=19% Similarity=0.233 Sum_probs=14.3
Q ss_pred hhhHHHHHHHHHHHHHHHhcCcchHHHHHHHH
Q 008180 538 AEKIEFIISAFRGQVATLSTHPYGCRVIQPHN 569 (575)
Q Consensus 538 ~k~rk~IIk~L~~~iveLSthkyGs~VVQK~L 569 (575)
++..+.++..+...+.-.+....++..+.-++
T Consensus 239 ~e~Idrli~C~~~Alp~fs~~v~Sskfv~y~~ 270 (556)
T PF05918_consen 239 PESIDRLISCLRQALPFFSRGVSSSKFVNYMC 270 (556)
T ss_dssp HHHHHHHHHHHHHHGGG-BTTB--HHHHHHHH
T ss_pred HHHHHHHHHHHHHhhHHhcCCCChHHHHHHHH
Confidence 44455555555555444444444444444333
No 48
>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=34.29 E-value=3e+02 Score=29.16 Aligned_cols=46 Identities=17% Similarity=0.275 Sum_probs=22.5
Q ss_pred hhHHHHHHHH--------hcCHHHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHh
Q 008180 489 GCRVIQKALE--------VIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIEC 535 (575)
Q Consensus 489 GSrVVQKlLE--------~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQK~Le~ 535 (575)
+..++||++. +.+.+....+..-|..-+..|+.++ ..+++.+++.|
T Consensus 159 AtfIlqKIL~dd~GL~yiC~t~eRf~av~~vL~~mV~~l~~~p-S~RLLKhIIrC 212 (262)
T PF04078_consen 159 ATFILQKILLDDVGLNYICQTAERFFAVAMVLNKMVEQLVKQP-SPRLLKHIIRC 212 (262)
T ss_dssp HHHHHHHHHHSHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHS---HHHHHHHHHH
T ss_pred HHHHHHHHHcchhHHHHHhcCHHHHHHHHHHHHHHHHHHccCC-ChhHHHHHHHH
Confidence 5566777663 2334444445555555555555555 33455544444
No 49
>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=33.94 E-value=4.2e+02 Score=25.18 Aligned_cols=24 Identities=13% Similarity=0.202 Sum_probs=11.2
Q ss_pred ccHHHHHHhhcCCHHHHHHHHHHh
Q 008180 453 GNYVIQKFFEHGSPDQRKELAEKL 476 (575)
Q Consensus 453 GNyVVQKLfE~gs~Eqr~~II~~L 476 (575)
|+-.|..+++..+.++...+++.+
T Consensus 47 g~~~l~~~i~~L~~~~l~~LL~~i 70 (141)
T PF08625_consen 47 GSEELDEVIKKLDDEQLEKLLRFI 70 (141)
T ss_pred hHHHHHHHHHhcCHHHHHHHHHHH
Confidence 344444444444444444444443
No 50
>PTZ00429 beta-adaptin; Provisional
Probab=33.62 E-value=5.8e+02 Score=30.80 Aligned_cols=14 Identities=36% Similarity=0.719 Sum_probs=9.0
Q ss_pred chhHHHHHHHHhCC
Q 008180 524 NGNHVIQKCIECVP 537 (575)
Q Consensus 524 ~GNyVIQK~Le~~~ 537 (575)
++-++|+.+++...
T Consensus 475 ~a~~~L~~~i~~f~ 488 (746)
T PTZ00429 475 NGKDIIQRFIDTIM 488 (746)
T ss_pred hHHHHHHHHHhhhc
Confidence 35677877776543
No 51
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=31.43 E-value=63 Score=38.69 Aligned_cols=13 Identities=23% Similarity=0.698 Sum_probs=8.2
Q ss_pred HHHHhhcCCHHHH
Q 008180 457 IQKFFEHGSPDQR 469 (575)
Q Consensus 457 VQKLfE~gs~Eqr 469 (575)
|.|+|+.|.++++
T Consensus 47 VeKfi~kCkpe~K 59 (894)
T KOG0132|consen 47 VEKFIKKCKPEYK 59 (894)
T ss_pred HHHHHHhCCcccc
Confidence 4566666766655
No 52
>KOG2759 consensus Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]
Probab=31.35 E-value=1.7e+02 Score=32.87 Aligned_cols=31 Identities=23% Similarity=0.354 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHhc-CcchHHHHHHHHhh
Q 008180 541 IEFIISAFRGQVATLST-HPYGCRVIQPHNNA 571 (575)
Q Consensus 541 rk~IIk~L~~~iveLSt-hkyGs~VVQK~Le~ 571 (575)
.++|-+.|...+.+|+. ++|-+-|-...|+.
T Consensus 312 i~~L~e~L~~svq~LsSFDeY~sEl~sG~L~W 343 (442)
T KOG2759|consen 312 IEFLTEKLKNSVQDLSSFDEYKSELRSGRLEW 343 (442)
T ss_pred HHHHHHHHHHHHHhhccHHHHHHHHHhCCcCC
Confidence 56777778888888876 57777766655553
No 53
>PF10521 DUF2454: Protein of unknown function (DUF2454); InterPro: IPR018870 Putative protein of unknown function; subunit of the ASTRA complex which is part of the chromatin remodeling machinery; similar to Schizosaccharomyces pombe (Fission yeast) Tti2p; may interact with Rsm23p [].
Probab=31.28 E-value=3.9e+02 Score=27.81 Aligned_cols=42 Identities=12% Similarity=0.198 Sum_probs=23.7
Q ss_pred cCCHHHHHHHHHHHhhhHHHhhcCc------cccHHHHHHhhcCCHHH
Q 008180 427 HCSAEEKVSVFKEVLPHASKLMTDV------FGNYVIQKFFEHGSPDQ 468 (575)
Q Consensus 427 ~~s~Eer~~If~ELkp~iveLmtD~------yGNyVVQKLfE~gs~Eq 468 (575)
..+.......+.-+.|-+..|+-|. -|..++..+++......
T Consensus 107 ~~~~~~i~~~~~liiP~iL~llDD~~~~~K~~G~~lL~~ll~~~~~~~ 154 (282)
T PF10521_consen 107 QLDRPWISQHWPLIIPPILNLLDDYSPEIKIQGCQLLHHLLEKVPAAE 154 (282)
T ss_pred cCCcchHHHhhhHHHhhHHHHhcCCCHHHHHHHHHHHHHHHHhCChhh
Confidence 4444555556666666666666553 45556666666655443
No 54
>TIGR00400 mgtE Mg2+ transporter (mgtE). This family of prokaryotic proteins models a class of Mg++ transporter first described in Bacillus firmus. May form a homodimer.
Probab=31.26 E-value=2.3e+02 Score=31.54 Aligned_cols=53 Identities=17% Similarity=0.223 Sum_probs=28.8
Q ss_pred HHHHhcCHHHHHHHHHHHHH-HHHHhhcCCchhHHHHHHHHhCChhhHHHHHHHH
Q 008180 495 KALEVIELHQKSQLVLELDG-HVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAF 548 (575)
Q Consensus 495 KlLE~~s~eqr~~II~EL~g-~l~~LvkDq~GNyVIQK~Le~~~~k~rk~IIk~L 548 (575)
.+++..+.++...+++++.. .+..++ +.--....++++...+++.++.|-..+
T Consensus 73 ~ll~~l~~~~~~~~~~~l~~dd~~~ll-~~l~~~~~~~lL~~l~~~er~~i~~ll 126 (449)
T TIGR00400 73 KLLNSFTNKEISEMINEMNLDDVIDLL-EEVPANVVQQLLASSTEEERKAINLLL 126 (449)
T ss_pred HHHHhCCHHHHHHHHHcCChhHHHHHH-HhCCHHHHHHHHHcCCHHHHHHHHHHh
Confidence 35555555555555555532 333333 334444567777777777766554443
No 55
>COG4399 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.06 E-value=2.8e+02 Score=30.66 Aligned_cols=29 Identities=10% Similarity=0.170 Sum_probs=21.2
Q ss_pred hHHHHHHHHHHHHhhCccccHHHHHHhhc
Q 008180 399 FELSDIAGRIVEFSVDQHGSRFIQQKLEH 427 (575)
Q Consensus 399 ~iLs~IkG~VveLA~Dq~GSRVLQkLLe~ 427 (575)
...+.+...+..|-.+...-.+||+++..
T Consensus 212 ~~~drl~~ellkl~~~~~t~kilq~Ll~n 240 (376)
T COG4399 212 SLADRLQQELLKLLNREETKKILQQLLTN 240 (376)
T ss_pred HHHHHHHHHHHHHHccHHHHHHHHHHHHh
Confidence 34466777777788888888888888854
No 56
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=28.21 E-value=2.1e+02 Score=26.96 Aligned_cols=48 Identities=15% Similarity=0.250 Sum_probs=32.9
Q ss_pred chhHHHHHHHHhcCHHHHHHHH-HHHHHHHHHhhcCCchhHHHHHHHHh
Q 008180 488 YGCRVIQKALEVIELHQKSQLV-LELDGHVMRCVRDQNGNHVIQKCIEC 535 (575)
Q Consensus 488 yGSrVVQKlLE~~s~eqr~~II-~EL~g~l~~LvkDq~GNyVIQK~Le~ 535 (575)
++=.+++.|++.|...-..++. ++|...+..++.+..-..|-+++++.
T Consensus 60 ~AL~LLe~~vkNCG~~fh~evas~~fl~~l~~l~~~~~~~~Vk~kil~l 108 (142)
T cd03569 60 YALLLLESCVKNCGTHFHDEVASREFMDELKDLIKTTKNEEVRQKILEL 108 (142)
T ss_pred HHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHHcccCCHHHHHHHHHH
Confidence 3345788888888876666665 45777788888775555666666654
No 57
>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=27.89 E-value=5.2e+02 Score=28.53 Aligned_cols=78 Identities=10% Similarity=0.109 Sum_probs=43.2
Q ss_pred chhHHHHHHHHhcCHHHHHHHHHHHHHHHHH-hhcCCchhHHHHHHHH-----hCChhhHHHHHHHHHHHHHHHhcCcch
Q 008180 488 YGCRVIQKALEVIELHQKSQLVLELDGHVMR-CVRDQNGNHVIQKCIE-----CVPAEKIEFIISAFRGQVATLSTHPYG 561 (575)
Q Consensus 488 yGSrVVQKlLE~~s~eqr~~II~EL~g~l~~-LvkDq~GNyVIQK~Le-----~~~~k~rk~IIk~L~~~iveLSthkyG 561 (575)
-...++++++...+.+-|-.++..+..++.. =+++.+=+++|..++. ....+.++.|...|.+++.---=|++|
T Consensus 262 ~~~~ll~~Li~~ld~E~RY~ll~aiaNqLRYPN~HT~~Fs~~lL~lF~~~~~~~~~~~IqEqItRVLLERliv~rPHPWG 341 (379)
T PF04054_consen 262 PHVTLLSKLIHELDPEGRYYLLSAIANQLRYPNSHTHFFSCVLLNLFSSDMNDPNDEDIQEQITRVLLERLIVNRPHPWG 341 (379)
T ss_pred hHHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcCCCCccchhhhHHHHHHHHHHHHhcCCCCCcc
Confidence 3445666666666666666666555444322 2445555556666655 223344566666666666555556666
Q ss_pred HHHH
Q 008180 562 CRVI 565 (575)
Q Consensus 562 s~VV 565 (575)
-.|.
T Consensus 342 llit 345 (379)
T PF04054_consen 342 LLIT 345 (379)
T ss_pred HHHH
Confidence 5543
No 58
>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=27.61 E-value=95 Score=26.49 Aligned_cols=48 Identities=19% Similarity=0.235 Sum_probs=18.9
Q ss_pred CHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHH
Q 008180 465 SPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLEL 512 (575)
Q Consensus 465 s~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL 512 (575)
+++....|+..+......-.....+-.-+-.++.....++...|+.+|
T Consensus 26 ~~~~~a~vl~~l~~~~~~~il~~l~~~~~a~il~~m~~dd~~~ll~~L 73 (102)
T PF03448_consen 26 PPEKAAEVLEELDPDTQAEILEALSPEEAAEILAEMDSDDAADLLEEL 73 (102)
T ss_dssp -HHHHHHHHCTS-CCCCCHCCCCS-HHHHHHHHCCS-HHHHHHHHCCS
T ss_pred CHHHHHHHHHcCCHHHHHHHHHhCCHHHHHHHHHccChHHHHHHHHHC
Confidence 444444444444444333333333444444444444444444444444
No 59
>PRK15039 transcriptional repressor RcnR to maintain nickel and cobalt homeostasis; Provisional
Probab=27.49 E-value=3.1e+02 Score=24.39 Aligned_cols=74 Identities=15% Similarity=0.260 Sum_probs=38.9
Q ss_pred HHHHHHHHHhcchhhHhHHHHHHHHHHHHhhCccccHHHHHHhhcC-CHHHHHHHHHHHhhhHHHhhcCccccHHHHHHh
Q 008180 383 KKHSFLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHC-SAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFF 461 (575)
Q Consensus 383 ~rskLLeeL~s~e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~-s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLf 461 (575)
.+.+++.+|. .|.|++- =|+++++.. ...+...-+..++.-+..++.-....|+-.++.
T Consensus 7 ~k~~ll~RL~----------RIeGQv~----------gI~~Miee~~~C~dIl~Ql~Avr~Al~~~~~~vl~~hl~~cv~ 66 (90)
T PRK15039 7 DKQKLKARAS----------KIQGQVV----------ALKKMLDEPHECAAVLQQIAAIRGAVNGLMREVIKGHLTEHIV 66 (90)
T ss_pred hHHHHHHHHH----------HHHHHHH----------HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445666655 6778873 567777664 334444444555555555555555555555555
Q ss_pred hcCCHHHHHHHHHHh
Q 008180 462 EHGSPDQRKELAEKL 476 (575)
Q Consensus 462 E~gs~Eqr~~II~~L 476 (575)
+-.......+.+++|
T Consensus 67 ~~~~~~~~~~~i~el 81 (90)
T PRK15039 67 HQGDELKREEDLDVV 81 (90)
T ss_pred ccccccchHHHHHHH
Confidence 443322233444443
No 60
>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=27.06 E-value=8.2e+02 Score=26.39 Aligned_cols=30 Identities=13% Similarity=0.212 Sum_probs=23.9
Q ss_pred CCchhHHHHHHHHhCChhhHHHHHHHHHHH
Q 008180 522 DQNGNHVIQKCIECVPAEKIEFIISAFRGQ 551 (575)
Q Consensus 522 Dq~GNyVIQK~Le~~~~k~rk~IIk~L~~~ 551 (575)
...|...+..+|...+.+..+.|++.|...
T Consensus 197 ~~gG~~~~a~ILN~~~~~~~~~il~~L~~~ 226 (338)
T TIGR00207 197 KMGGVRAVAEIINLMDRKTEKTIITSLEEF 226 (338)
T ss_pred cCChHHHHHHHHHhCCchHHHHHHHHHHHh
Confidence 346888899999999888888888887543
No 61
>COG2239 MgtE Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]
Probab=26.87 E-value=3.1e+02 Score=31.08 Aligned_cols=26 Identities=8% Similarity=0.155 Sum_probs=10.8
Q ss_pred hhHHHHHHHHhCChhhHHHHHHHHHH
Q 008180 525 GNHVIQKCIECVPAEKIEFIISAFRG 550 (575)
Q Consensus 525 GNyVIQK~Le~~~~k~rk~IIk~L~~ 550 (575)
|..+-...+..-..-..+..++.++.
T Consensus 135 G~~Mt~e~v~l~~~~Tv~~al~~ir~ 160 (451)
T COG2239 135 GRIMTTEFVTLPEDVTVDEALDRIRE 160 (451)
T ss_pred hccceeeeEEeccCcCHHHHHHHHHH
Confidence 33333333333333334555555543
No 62
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=26.80 E-value=1.7e+02 Score=35.01 Aligned_cols=25 Identities=16% Similarity=0.183 Sum_probs=13.9
Q ss_pred hhcChhhhccCcchhHHHHHHHHhc
Q 008180 476 LVGQVLPLSLQMYGCRVIQKALEVI 500 (575)
Q Consensus 476 L~g~I~~Ls~hkyGSrVVQKlLE~~ 500 (575)
|...+..+.-+..|++.+|++++..
T Consensus 383 L~~~l~~~vg~eigahf~q~~ve~f 407 (822)
T KOG2141|consen 383 LAAMLHTMVGNEIGAHFLQTFVEDF 407 (822)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 3344445555566666666666543
No 63
>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=26.51 E-value=74 Score=33.49 Aligned_cols=65 Identities=15% Similarity=0.237 Sum_probs=34.4
Q ss_pred cccHHHHHHhhc--------CCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhcCC
Q 008180 452 FGNYVIQKFFEH--------GSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQ 523 (575)
Q Consensus 452 yGNyVVQKLfE~--------gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL~g~l~~LvkDq 523 (575)
-+.|++||++.. .+.|.+..+...|..-+..|+.++ .. .+++.+.....+|+.++
T Consensus 158 vAtfIlqKIL~dd~GL~yiC~t~eRf~av~~vL~~mV~~l~~~p-S~----------------RLLKhIIrCYlRLsdnp 220 (262)
T PF04078_consen 158 VATFILQKILLDDVGLNYICQTAERFFAVAMVLNKMVEQLVKQP-SP----------------RLLKHIIRCYLRLSDNP 220 (262)
T ss_dssp HHHHHHHHHHHSHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHS---H----------------HHHHHHHHHHHHHTTST
T ss_pred HHHHHHHHHHcchhHHHHHhcCHHHHHHHHHHHHHHHHHHccCC-Ch----------------hHHHHHHHHHHHHccCH
Confidence 467888888863 344444444444433333333222 33 44555555556666666
Q ss_pred chhHHHHHHH
Q 008180 524 NGNHVIQKCI 533 (575)
Q Consensus 524 ~GNyVIQK~L 533 (575)
.+.-.+.+|+
T Consensus 221 rar~aL~~~L 230 (262)
T PF04078_consen 221 RAREALRQCL 230 (262)
T ss_dssp THHHHHHHHS
T ss_pred HHHHHHHHhC
Confidence 6666666555
No 64
>KOG2213 consensus Apoptosis inhibitor 5/fibroblast growth factor 2-interacting factor 2, and related proteins [Signal transduction mechanisms]
Probab=26.45 E-value=6.6e+02 Score=28.42 Aligned_cols=39 Identities=10% Similarity=0.037 Sum_probs=28.4
Q ss_pred hhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHh
Q 008180 461 FEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEV 499 (575)
Q Consensus 461 fE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~ 499 (575)
|...+++..+.+|.++.-.+.-.++...+++-+..+-++
T Consensus 206 f~~sD~d~VdRfisCl~~AvPfFargapSskf~~y~n~~ 244 (460)
T KOG2213|consen 206 FNVSDADYVDRFISCLLMAVPFFARGAPSSKFVEYLNKH 244 (460)
T ss_pred ccCCChHHHHHHHHHHHHhhhhhhcCCchhHHHHHHHhh
Confidence 555667777788888877777788888888777765544
No 65
>PF12460 MMS19_C: RNAPII transcription regulator C-terminal; InterPro: IPR024687 This domain, approximately 60 amino acids in length, is found in the N-terminal region of MMS19 proteins. MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription [].
Probab=25.06 E-value=6.7e+02 Score=27.44 Aligned_cols=28 Identities=14% Similarity=0.268 Sum_probs=18.6
Q ss_pred hHHHHHHHHhcCHHHHHHHHHHHHHHHH
Q 008180 490 CRVIQKALEVIELHQKSQLVLELDGHVM 517 (575)
Q Consensus 490 SrVVQKlLE~~s~eqr~~II~EL~g~l~ 517 (575)
++|+..++...+.+++.++++++...+.
T Consensus 118 ~~l~~~iv~~l~~~~q~~~~~~~~~lf~ 145 (415)
T PF12460_consen 118 SRLINLIVRSLSPEKQQEILDELYSLFL 145 (415)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHc
Confidence 5666677777777777777766655443
No 66
>PF05327 RRN3: RNA polymerase I specific transcription initiation factor RRN3; InterPro: IPR007991 This family consists of several eukaryotic proteins which are homologous to the Saccharomyces cerevisiae RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in the S. cerevisiae [] RNA polymerase I complex within the nucleolus. In mammalian cells, the phosphorylation state of Rrn3 regulates rDNA transcription by determining the steady-state concentration of the Rrn3 [].; PDB: 3TJ1_B.
Probab=24.54 E-value=1e+03 Score=27.38 Aligned_cols=70 Identities=9% Similarity=0.106 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhh--hccCcchhHHHHHHHHhcC
Q 008180 430 AEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLP--LSLQMYGCRVIQKALEVIE 501 (575)
Q Consensus 430 ~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~--Ls~hkyGSrVVQKlLE~~s 501 (575)
..+...++.++..++..|-.+ -+-+|+.++..-.-..-..+++.+..-+.. -+...|-..|+.++++...
T Consensus 50 ~~~l~~~L~~L~~~Vs~Ld~~--~~~LV~ail~~~W~~~~~~~v~~y~~Fl~~Lvsa~~~yl~~vl~~LV~~f~ 121 (563)
T PF05327_consen 50 VSQLIRWLKALSSCVSLLDSS--CKQLVEAILSLNWLGRDEDFVEAYIQFLINLVSAQPKYLSPVLSMLVKNFI 121 (563)
T ss_dssp HHHHHHHHHHHHHGGGGG-SC--CHHHHHHHHT-TGGGS-HHHHHHHHHHHHHHHHH-GGGHHHHHHHHHHGGG
T ss_pred HHHHHHHHHHHHHHHHHhhhH--HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhcc
Confidence 456677777777777666665 777888888774311222333333322222 2456677778888887643
No 67
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=24.03 E-value=3.5e+02 Score=32.86 Aligned_cols=17 Identities=12% Similarity=0.200 Sum_probs=11.1
Q ss_pred hcccccchhHHHHHHHH
Q 008180 74 SAASQSDVSRAESRMRK 90 (575)
Q Consensus 74 ~~~~~~~~~~~~~~~~~ 90 (575)
+..-+.|..++|.+.++
T Consensus 81 a~~LnVD~~hiEr~~~~ 97 (803)
T PLN03083 81 ADTIGVDLYHVERQAQQ 97 (803)
T ss_pred hhhcCCCHHHHHHHHHH
Confidence 44455677788877665
No 68
>PHA02741 hypothetical protein; Provisional
Probab=23.83 E-value=6e+02 Score=23.73 Aligned_cols=127 Identities=13% Similarity=0.080 Sum_probs=70.1
Q ss_pred hCccccHHHHHHhhcCCHHHHHHHHHHHh--hh-HHHhhcCccccHHHHHHhhcCCHHHHHHHHHHhhcChhhhc-cC-c
Q 008180 413 VDQHGSRFIQQKLEHCSAEEKVSVFKEVL--PH-ASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLS-LQ-M 487 (575)
Q Consensus 413 ~Dq~GSRVLQkLLe~~s~Eer~~If~ELk--p~-iveLmtD~yGNyVVQKLfE~gs~Eqr~~II~~L~g~I~~Ls-~h-k 487 (575)
.+..|.-.|....+.+..+....++..+. .+ ..--.+|.+|...+.-....+..+...++++.|..+=..+- .+ .
T Consensus 17 ~~~~g~t~Lh~Aa~~g~~~~v~~l~~~~~~~~~ga~in~~d~~g~T~Lh~A~~~g~~~~~~~ii~~Ll~~gadin~~~~~ 96 (169)
T PHA02741 17 KNSEGENFFHEAARCGCFDIIARFTPFIRGDCHAAALNATDDAGQMCIHIAAEKHEAQLAAEIIDHLIELGADINAQEML 96 (169)
T ss_pred cccCCCCHHHHHHHcCCHHHHHHHHHHhccchhhhhhhccCCCCCcHHHHHHHcCChHHHHHHHHHHHHcCCCCCCCCcC
Confidence 45667777777777777766655544331 11 22236788899888887777765444555555543222221 12 3
Q ss_pred chhHHHHHHHHhcCHHHHHHHHHHHHH--HHHHhhcCCchhHHHHHHHHhCChhhHHH
Q 008180 488 YGCRVIQKALEVIELHQKSQLVLELDG--HVMRCVRDQNGNHVIQKCIECVPAEKIEF 543 (575)
Q Consensus 488 yGSrVVQKlLE~~s~eqr~~II~EL~g--~l~~LvkDq~GNyVIQK~Le~~~~k~rk~ 543 (575)
.|.-.+..+......+ +++.|.. .+.-=.+|.+|...+..++.....+..+.
T Consensus 97 ~g~TpLh~A~~~~~~~----iv~~Ll~~~g~~~~~~n~~g~tpL~~A~~~~~~~iv~~ 150 (169)
T PHA02741 97 EGDTALHLAAHRRDHD----LAEWLCCQPGIDLHFCNADNKSPFELAIDNEDVAMMQI 150 (169)
T ss_pred CCCCHHHHHHHcCCHH----HHHHHHhCCCCCCCcCCCCCCCHHHHHHHCCCHHHHHH
Confidence 5665555555444333 3333322 12222457778877777777665433333
No 69
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=23.73 E-value=78 Score=37.95 Aligned_cols=99 Identities=14% Similarity=0.138 Sum_probs=50.9
Q ss_pred HHHHHhhcChhhhccCcchhHHHHHHHHhcCHHHHH---HHHHHHHHH---HHHhhcCCchh-------HHHHHHHHhCC
Q 008180 471 ELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKS---QLVLELDGH---VMRCVRDQNGN-------HVIQKCIECVP 537 (575)
Q Consensus 471 ~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~---~II~EL~g~---l~~LvkDq~GN-------yVIQK~Le~~~ 537 (575)
.|++.-+..+..+...++=--.|+|+|..|..+.|. .+|+.|... -...-+|.+|+ +.++++++|.
T Consensus 25 Ki~~ITkaAikaIk~ykhVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~kd~F~prf~~n~~~tf~~L~~c~- 103 (894)
T KOG0132|consen 25 KILKITKAAIKAIKLYKHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKEKDVFGPRFSKNFTGTFQNLYECP- 103 (894)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhcccccccCCccchhHHHHHHHHHhcC-
Confidence 333333333444444444445677888888888773 223332111 11112333333 4566666654
Q ss_pred hhhHHHHHHHHHHHHHHHhcCcchHHHHHHHHhhcC
Q 008180 538 AEKIEFIISAFRGQVATLSTHPYGCRVIQPHNNASG 573 (575)
Q Consensus 538 ~k~rk~IIk~L~~~iveLSthkyGs~VVQK~Le~~d 573 (575)
.+++..||..+.-.- ..+=|-+-+||.+||-++
T Consensus 104 ~edks~iIrvlNlwq---kn~VfK~e~IqpLlDm~~ 136 (894)
T KOG0132|consen 104 QEDKSDIIRVLNLWQ---KNNVFKSEIIQPLLDMAD 136 (894)
T ss_pred HHHHHHHHHhhhhhh---cccchhHHHHHHHHHHHh
Confidence 456666666542110 011256778999998765
No 70
>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=23.40 E-value=3.4e+02 Score=25.16 Aligned_cols=35 Identities=3% Similarity=0.139 Sum_probs=19.5
Q ss_pred HHHHHHHHhcCHHHHHHHH-HHHHHHHHHhhcCCch
Q 008180 491 RVIQKALEVIELHQKSQLV-LELDGHVMRCVRDQNG 525 (575)
Q Consensus 491 rVVQKlLE~~s~eqr~~II-~EL~g~l~~LvkDq~G 525 (575)
.|++.|++.+......++. ++|...+..|+.+...
T Consensus 64 ~lld~lvkNcg~~f~~ev~~~~fl~~l~~l~~~~~~ 99 (140)
T PF00790_consen 64 TLLDALVKNCGPRFHREVASKEFLDELVKLIKSKKT 99 (140)
T ss_dssp HHHHHHHHHSHHHHHHHHTSHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHcCCHHHHHHHhHHHHHHHHHHHHccCCC
Confidence 4566666666666555554 3455555555554333
No 71
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=22.96 E-value=9.7e+02 Score=25.78 Aligned_cols=28 Identities=11% Similarity=0.266 Sum_probs=16.9
Q ss_pred CCchhHHHHHHHHhCChhhHHHHHHHHHH
Q 008180 522 DQNGNHVIQKCIECVPAEKIEFIISAFRG 550 (575)
Q Consensus 522 Dq~GNyVIQK~Le~~~~k~rk~IIk~L~~ 550 (575)
...|...+..+|+..+... +.+++.|..
T Consensus 195 ~~~G~~~aa~ILn~l~~~~-~~il~~L~~ 222 (334)
T PRK07194 195 KVIGVKQAADIINRFPGDR-QQLMEMLKE 222 (334)
T ss_pred cCCCHHHHHHHHHhCchhH-HHHHHHHHh
Confidence 3456667777777766333 556666543
No 72
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=22.05 E-value=6e+02 Score=23.05 Aligned_cols=17 Identities=18% Similarity=0.307 Sum_probs=10.0
Q ss_pred hhhHHHHHHHHHHHHHH
Q 008180 538 AEKIEFIISAFRGQVAT 554 (575)
Q Consensus 538 ~k~rk~IIk~L~~~ive 554 (575)
++.++.+++.|...+..
T Consensus 104 ~~~~~~la~~~~~~~l~ 120 (145)
T PF10607_consen 104 PERREELAEEFNSAILK 120 (145)
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 35566666666655444
No 73
>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.95 E-value=9.6e+02 Score=29.24 Aligned_cols=64 Identities=9% Similarity=0.108 Sum_probs=49.9
Q ss_pred HHHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhh------HHHhhcCccccHHHHHHhhcCCHHHH
Q 008180 406 GRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPH------ASKLMTDVFGNYVIQKFFEHGSPDQR 469 (575)
Q Consensus 406 G~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~------iveLmtD~yGNyVVQKLfE~gs~Eqr 469 (575)
.||.-|-.=.+-+.-|+++++.+..+....++-+|+.+ ...|..+++++-+-+++.++...+-.
T Consensus 538 ~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~~~~s~l~~~l~~~p~a~~lY~~~~r~~~~~~l 607 (829)
T KOG2280|consen 538 EQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNKLNRSSLFMTLRNQPLALSLYRQFMRHQDRATL 607 (829)
T ss_pred chhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHhchhhhHHHHHHHHhhchhhh
Confidence 46666777778889999999999999888888887763 35677899999999999886554433
No 74
>COG5240 SEC21 Vesicle coat complex COPI, gamma subunit [Intracellular trafficking and secretion]
Probab=21.92 E-value=1.4e+03 Score=27.36 Aligned_cols=118 Identities=16% Similarity=0.101 Sum_probs=60.2
Q ss_pred ccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccccHHHHHHhhcCC--HHHHHHHHHHhhcChhh---hccCcchhH
Q 008180 417 GSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGS--PDQRKELAEKLVGQVLP---LSLQMYGCR 491 (575)
Q Consensus 417 GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGNyVVQKLfE~gs--~Eqr~~II~~L~g~I~~---Ls~hkyGSr 491 (575)
..+-|-++|+.++.|..+.+++.|- .++.=+.|-|---+|..+=..+- +....-+++-|..-+.+ +-..+|.-.
T Consensus 357 styAITtLLKTGt~e~idrLv~~I~-sfvhD~SD~FKiI~ida~rsLsl~Fp~k~~s~l~FL~~~L~~eGg~eFK~~~Vd 435 (898)
T COG5240 357 STYAITTLLKTGTEETIDRLVNLIP-SFVHDMSDGFKIIAIDALRSLSLLFPSKKLSYLDFLGSSLLQEGGLEFKKYMVD 435 (898)
T ss_pred hHHHHHHHHHcCchhhHHHHHHHHH-HHHHhhccCceEEeHHHHHHHHhhCcHHHHHHHHHHHHHHHhcccchHHHHHHH
Confidence 3456777888888887777766553 33333445565555554322221 22222333322221111 222223333
Q ss_pred HHHHHHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHhC
Q 008180 492 VIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECV 536 (575)
Q Consensus 492 VVQKlLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQK~Le~~ 536 (575)
+|-.++++. ++.|...+++|...+..|-.++..-+++--+=+.+
T Consensus 436 aisd~~~~~-p~skEraLe~LC~fIEDcey~~I~vrIL~iLG~Eg 479 (898)
T COG5240 436 AISDAMEND-PDSKERALEVLCTFIEDCEYHQITVRILGILGREG 479 (898)
T ss_pred HHHHHHhhC-chHHHHHHHHHHHHHhhcchhHHHHHHHHHhcccC
Confidence 333444432 35566777888888777777766666554444443
No 75
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=21.80 E-value=4.3e+02 Score=24.32 Aligned_cols=14 Identities=21% Similarity=0.266 Sum_probs=5.9
Q ss_pred hhHHHHHHHHhcCH
Q 008180 489 GCRVIQKALEVIEL 502 (575)
Q Consensus 489 GSrVVQKlLE~~s~ 502 (575)
+.+.|.+=|.+.++
T Consensus 38 a~raL~krl~~~n~ 51 (133)
T cd03561 38 AARAIRKKIKYGNP 51 (133)
T ss_pred HHHHHHHHHcCCCH
Confidence 33444444444433
No 76
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=21.79 E-value=5e+02 Score=23.98 Aligned_cols=47 Identities=6% Similarity=0.109 Sum_probs=32.5
Q ss_pred hhHHHHHHHHhcCHHHHHHHH-HHHHHHHHHhhcCCchhH-HHHHHHHh
Q 008180 489 GCRVIQKALEVIELHQKSQLV-LELDGHVMRCVRDQNGNH-VIQKCIEC 535 (575)
Q Consensus 489 GSrVVQKlLE~~s~eqr~~II-~EL~g~l~~LvkDq~GNy-VIQK~Le~ 535 (575)
+=.+++.|++.|...-..++. ++|...+..++.+.+... |-+++++.
T Consensus 57 AL~lLe~~vkNcg~~f~~ev~s~~fl~~L~~l~~~~~~~~~Vk~kil~l 105 (133)
T smart00288 57 ALTLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKYPLPLVKKRILEL 105 (133)
T ss_pred HHHHHHHHHHHCCHHHHHHHHhHHHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence 345677788888777666665 347777778888777665 66666664
No 77
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=21.73 E-value=7.8e+02 Score=25.59 Aligned_cols=65 Identities=14% Similarity=0.145 Sum_probs=36.2
Q ss_pred HHHHhhcCCHHHHHHHHHHHhhhHHHhhcCccccHHH--HHHhhcCCHHHHHHHHHHhhcChhhhccCc
Q 008180 421 IQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVI--QKFFEHGSPDQRKELAEKLVGQVLPLSLQM 487 (575)
Q Consensus 421 LQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGNyVV--QKLfE~gs~Eqr~~II~~L~g~I~~Ls~hk 487 (575)
|+.+++.+.-++-..+++.|.|.+.+- |.+=.|-+ |++||........+.++.+..++...+...
T Consensus 71 Ir~~I~~G~Ie~Aie~in~l~PeiLd~--n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~~a~e~ 137 (228)
T KOG2659|consen 71 IRRAIEEGQIEEAIEKVNQLNPEILDT--NRELFFHLQQLHLIELIREGKTEEALEFAQTKLAPFAEEN 137 (228)
T ss_pred HHHHHHhccHHHHHHHHHHhChHHHcc--chhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHcccccccc
Confidence 566777777777666667776665443 33333333 456665554444555555555555544444
No 78
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=21.64 E-value=1.6e+03 Score=27.83 Aligned_cols=49 Identities=20% Similarity=0.306 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhc
Q 008180 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMT 449 (575)
Q Consensus 401 Ls~IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmt 449 (575)
+++|+--|.++-.+--..-+||.|+++..+.+...-+.||+....+|+.
T Consensus 715 yeeik~~ILevne~vLse~~iqnLik~lPe~E~l~~L~e~Kaeye~l~e 763 (1102)
T KOG1924|consen 715 YEEIKNVILEVNEDVLSESMIQNLIKHLPEQEQLNKLSELKAEYEDLPE 763 (1102)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCCC
Confidence 4455556666666666666677777666544444444666666655553
No 79
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=21.49 E-value=1.7e+03 Score=29.40 Aligned_cols=35 Identities=14% Similarity=0.047 Sum_probs=16.1
Q ss_pred HHHHhhCccccHHH----HHHhhcCCHHHHHHHHHHHhh
Q 008180 408 IVEFSVDQHGSRFI----QQKLEHCSAEEKVSVFKEVLP 442 (575)
Q Consensus 408 VveLA~Dq~GSRVL----QkLLe~~s~Eer~~If~ELkp 442 (575)
-..+-.+++.|.++ +-.|+....|.-.+|+++-++
T Consensus 1448 erlvrssPNSSi~WI~YMaf~LelsEiekAR~iaerAL~ 1486 (1710)
T KOG1070|consen 1448 ERLVRSSPNSSILWIRYMAFHLELSEIEKARKIAERALK 1486 (1710)
T ss_pred HHHHhcCCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhh
Confidence 33444556665544 333343444444455554443
No 80
>COG2733 Predicted membrane protein [Function unknown]
Probab=21.40 E-value=1.2e+03 Score=26.31 Aligned_cols=75 Identities=13% Similarity=0.198 Sum_probs=43.1
Q ss_pred HHHHhcchhhHhHHHHHHHHHHHHhhCccccHHHHHHhhcCCHHHHHHHHHHHhhhHHHhhcCcccc----HHHHHHhhc
Q 008180 388 LEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGN----YVIQKFFEH 463 (575)
Q Consensus 388 LeeL~s~e~rk~iLs~IkG~VveLA~Dq~GSRVLQkLLe~~s~Eer~~If~ELkp~iveLmtD~yGN----yVVQKLfE~ 463 (575)
++-+....-++++-+.+..++-+.--.+...++|.+++.... .+.|++++...+.....+..-. -+|+++++.
T Consensus 139 ~~lld~~~iq~~ik~~v~~~i~e~~~~~~~~~vL~~l~~d~r---~q~l~D~~~~~L~r~~~~~~v~~~i~~~i~r~~~e 215 (415)
T COG2733 139 LELLDDDDIQRVIKRAVIRAIAEVYLGPTAGRVLESLTADDR---HQALLDKLIDRLIRWLLNDKVREFIAAVIVRYLEE 215 (415)
T ss_pred HHHhCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHhccc---HHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHh
Confidence 333444445555556666777777777777777777664321 2567777777665555544433 344555544
Q ss_pred CC
Q 008180 464 GS 465 (575)
Q Consensus 464 gs 465 (575)
-.
T Consensus 216 e~ 217 (415)
T COG2733 216 EH 217 (415)
T ss_pred cC
Confidence 33
No 81
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=21.38 E-value=1.3e+03 Score=29.32 Aligned_cols=35 Identities=26% Similarity=0.310 Sum_probs=20.7
Q ss_pred ChhhHHHHHHHH--------------HHHHHHHh--cCcchHHHHHHHHhh
Q 008180 537 PAEKIEFIISAF--------------RGQVATLS--THPYGCRVIQPHNNA 571 (575)
Q Consensus 537 ~~k~rk~IIk~L--------------~~~iveLS--thkyGs~VVQK~Le~ 571 (575)
+++..+.+|+.| ...+.-|+ ...++-+||..+||.
T Consensus 661 D~e~~~yli~~~~k~w~iky~~i~~lA~llaGL~~y~~~fvi~VID~vlE~ 711 (1128)
T KOG2051|consen 661 DPEVKQYLISCFSKPWKIKYQNIHALASLLAGLSSYHPEFVIHVIDHVLED 711 (1128)
T ss_pred cHHHHHHHHHHhhhhhccccccHHHHHHHHHHHHhhchhhhhhhHHHHHHH
Confidence 455666666665 22333444 356777788887774
No 82
>PRK14136 recX recombination regulator RecX; Provisional
Probab=21.03 E-value=7.4e+02 Score=26.91 Aligned_cols=23 Identities=9% Similarity=0.015 Sum_probs=16.0
Q ss_pred HHHHhcCcchHHHHHHHHhhcCC
Q 008180 552 VATLSTHPYGCRVIQPHNNASGF 574 (575)
Q Consensus 552 iveLSthkyGs~VVQK~Le~~dd 574 (575)
+.-|..--|..-+|.++|+..++
T Consensus 282 iRfL~rRGFS~D~I~~vLk~~~d 304 (309)
T PRK14136 282 ARFLAARGFSSATIVKLLKVGDD 304 (309)
T ss_pred HHHHHHCCCCHHHHHHHHHhchh
Confidence 44466777888888888776553
No 83
>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=20.96 E-value=7.3e+02 Score=23.59 Aligned_cols=105 Identities=12% Similarity=0.152 Sum_probs=53.2
Q ss_pred HhhcCCHHHHHHHHHHhhcChhhhccCcchhHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhcCCchhHHHH----HHHHh
Q 008180 460 FFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQ----KCIEC 535 (575)
Q Consensus 460 LfE~gs~Eqr~~II~~L~g~I~~Ls~hkyGSrVVQKlLE~~s~eqr~~II~EL~g~l~~LvkDq~GNyVIQ----K~Le~ 535 (575)
.|+...|...-.|++.+.. ..--.+..|+..|+.++...+.++...+++-++ .--++.--++|.| .+|..
T Consensus 20 Al~L~~P~~ll~i~~~~~~--~~~~~~~~g~~~l~~~i~~L~~~~l~~LL~~ir----~WNTNsr~~~vAQ~vL~~il~~ 93 (141)
T PF08625_consen 20 ALKLDHPFRLLKILKDLLE--TEEDEDSIGSEELDEVIKKLDDEQLEKLLRFIR----DWNTNSRTSHVAQRVLNAILKS 93 (141)
T ss_pred HHhcCCcHHHHHHHHHHHh--cccccccchHHHHHHHHHhcCHHHHHHHHHHHH----HhhcccccHHHHHHHHHHHHHh
Confidence 4444445445555555442 111223337788999999888888776555443 2233333344444 44444
Q ss_pred CChhh------HHHHHHHHH----HHHHHHhcCcchHHHHHHHHh
Q 008180 536 VPAEK------IEFIISAFR----GQVATLSTHPYGCRVIQPHNN 570 (575)
Q Consensus 536 ~~~k~------rk~IIk~L~----~~iveLSthkyGs~VVQK~Le 570 (575)
.+++. .+.+++.|. .|+..|-.---.+++|.-++.
T Consensus 94 ~~~~~L~~~~~~~~~le~lipYteRH~~Rl~~L~q~syllDy~l~ 138 (141)
T PF08625_consen 94 HPPEELLKIPGLKEILEALIPYTERHFQRLDRLLQKSYLLDYTLQ 138 (141)
T ss_pred CCHHHHHccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55544 344555553 333344333344455544443
No 84
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=20.66 E-value=1.8e+03 Score=29.11 Aligned_cols=44 Identities=11% Similarity=0.133 Sum_probs=26.1
Q ss_pred HHHHHHHh-CChhhHHHHHHHHHHHHHHHhcCcchHHHHHHHHhh
Q 008180 528 VIQKCIEC-VPAEKIEFIISAFRGQVATLSTHPYGCRVIQPHNNA 571 (575)
Q Consensus 528 VIQK~Le~-~~~k~rk~IIk~L~~~iveLSthkyGs~VVQK~Le~ 571 (575)
+.+.+++. .+++..+++++...++-.+.-.++---+|=+|++|.
T Consensus 1656 lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde~~vE~VKarA~EY 1700 (1710)
T KOG1070|consen 1656 LFERVIELKLSIKKMKFFFKKWLEYEKSHGDEKNVEYVKARAKEY 1700 (1710)
T ss_pred HHHHHHhcCCChhHhHHHHHHHHHHHHhcCchhhHHHHHHHHHHH
Confidence 44444444 466777788877766655555555555666666554
No 85
>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=20.61 E-value=2.9e+02 Score=25.58 Aligned_cols=13 Identities=23% Similarity=0.575 Sum_probs=5.7
Q ss_pred cHHHHHHhhcCCH
Q 008180 418 SRFIQQKLEHCSA 430 (575)
Q Consensus 418 SRVLQkLLe~~s~ 430 (575)
.+.|++.|++.++
T Consensus 44 ~~~l~krl~~~~~ 56 (140)
T PF00790_consen 44 ARALRKRLKHGNP 56 (140)
T ss_dssp HHHHHHHHTTSSH
T ss_pred HHHHHHHHhCCCH
Confidence 3444444444443
Done!