Query 022130
Match_columns 302
No_of_seqs 164 out of 210
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 08:15:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022130.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022130hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3064 RNA-binding nuclear pr 100.0 1E-123 3E-128 860.7 23.2 289 1-298 1-297 (303)
2 COG5129 MAK16 Nuclear protein 100.0 1E-105 3E-110 733.6 18.9 285 2-300 1-297 (303)
3 PLN00040 Protein MAK16 homolog 100.0 1.3E-93 2.8E-98 651.5 20.8 195 1-195 1-195 (233)
4 PF01778 Ribosomal_L28e: Ribos 100.0 3E-34 6.5E-39 236.2 2.7 112 6-118 1-116 (117)
5 PF04874 Mak16: Mak16 protein 100.0 2.6E-30 5.7E-35 211.1 7.5 92 136-228 1-101 (101)
6 PTZ00197 60S ribosomal protein 98.1 1.7E-05 3.8E-10 69.4 8.9 124 2-129 3-127 (146)
7 KOG3064 RNA-binding nuclear pr 96.2 0.022 4.8E-07 54.8 8.4 30 137-166 142-171 (303)
8 KOG3412 60S ribosomal protein 94.9 0.11 2.4E-06 45.3 7.3 96 2-97 3-102 (133)
9 PF04931 DNA_pol_phi: DNA poly 90.4 0.18 3.9E-06 53.4 2.6 19 113-131 531-549 (784)
10 PF05764 YL1: YL1 nuclear prot 89.2 0.45 9.8E-06 44.1 3.9 8 208-215 42-49 (240)
11 KOG2038 CAATT-binding transcri 77.2 1.7 3.8E-05 47.5 2.6 20 157-176 831-850 (988)
12 KOG0526 Nucleosome-binding fac 75.9 2.2 4.7E-05 45.0 2.8 6 15-20 323-328 (615)
13 KOG2897 DNA-binding protein YL 69.1 6 0.00013 40.0 4.0 15 161-175 25-39 (390)
14 PF09073 BUD22: BUD22; InterP 67.1 36 0.00078 34.2 9.0 25 147-171 46-70 (432)
15 COG5406 Nucleosome binding fac 65.6 6.8 0.00015 42.6 3.8 6 208-213 939-944 (1001)
16 PF10650 zf-C3H1: Putative zin 64.7 3.6 7.7E-05 26.4 1.0 16 31-46 4-20 (23)
17 KOG1189 Global transcriptional 64.3 5.8 0.00013 43.6 3.1 8 185-192 848-855 (960)
18 PF04147 Nop14: Nop14-like fam 63.4 4.5 9.7E-05 43.9 2.1 12 160-171 286-297 (840)
19 KOG2141 Protein involved in hi 59.8 4.9 0.00011 43.8 1.5 18 136-153 139-156 (822)
20 KOG1991 Nuclear transport rece 54.4 10 0.00022 42.4 2.9 24 83-106 785-808 (1010)
21 COG2108 Uncharacterized conser 49.4 7.5 0.00016 38.9 0.9 16 34-49 34-51 (353)
22 PF07359 LEAP-2: Liver-express 43.2 8.8 0.00019 31.0 0.3 26 24-49 50-76 (77)
23 KOG2409 KRR1-interacting prote 41.6 66 0.0014 34.6 6.3 35 159-193 342-388 (647)
24 PF02724 CDC45: CDC45-like pro 40.9 21 0.00046 37.6 2.7 20 130-149 29-48 (622)
25 cd03479 Rieske_RO_Alpha_PhDO_l 40.6 28 0.00062 29.5 3.0 40 30-70 88-136 (144)
26 TIGR02150 IPP_isom_1 isopenten 39.4 38 0.00082 28.8 3.5 67 31-99 7-83 (158)
27 KOG0127 Nucleolar protein fibr 38.9 23 0.0005 37.9 2.5 10 12-21 48-57 (678)
28 cd03548 Rieske_RO_Alpha_OMO_CA 38.8 32 0.0007 28.8 3.0 44 30-74 81-133 (136)
29 KOG1903 Cell cycle-associated 38.7 56 0.0012 30.4 4.7 72 34-120 79-164 (217)
30 PF03637 Mob1_phocein: Mob1/ph 38.1 43 0.00093 29.9 3.8 25 34-65 47-71 (175)
31 cd03531 Rieske_RO_Alpha_KSH Th 38.0 33 0.00071 28.0 2.8 36 29-65 66-107 (115)
32 cd02681 MIT_calpain7_1 MIT: do 36.4 65 0.0014 25.4 4.2 44 85-128 21-70 (76)
33 cd02682 MIT_AAA_Arch MIT: doma 32.9 1.1E+02 0.0024 24.3 5.0 42 84-128 27-69 (75)
34 KOG1189 Global transcriptional 32.4 27 0.00058 38.8 1.8 13 154-166 848-860 (960)
35 KOG2712 Transcriptional coacti 31.5 25 0.00054 30.1 1.2 35 39-75 39-78 (108)
36 PF13132 DUF3950: Domain of un 30.6 57 0.0012 22.3 2.5 23 90-112 2-29 (30)
37 KOG2038 CAATT-binding transcri 29.9 31 0.00067 38.4 1.8 13 74-86 704-716 (988)
38 PF11705 RNA_pol_3_Rpc31: DNA- 29.5 33 0.00071 31.4 1.7 13 112-124 90-102 (233)
39 KOG0576 Mitogen-activated prot 29.3 14 0.00031 40.3 -0.7 17 163-179 17-33 (829)
40 PF03115 Astro_capsid: Astrovi 28.2 19 0.00042 39.4 0.0 37 52-88 579-617 (787)
41 COG1734 DksA DnaK suppressor p 28.0 3.5E+02 0.0076 23.2 7.5 12 164-175 70-81 (120)
42 cd07599 BAR_Rvs167p The Bin/Am 27.8 2.3E+02 0.0051 25.3 6.8 59 73-135 66-125 (216)
43 KOG4156 Claspin, protein media 27.6 1.1E+02 0.0025 33.9 5.4 19 163-181 937-956 (1329)
44 PF03153 TFIIA: Transcription 27.5 20 0.00042 34.7 -0.1 22 63-84 112-133 (375)
45 KOG1824 TATA-binding protein-i 26.3 69 0.0015 36.6 3.7 9 44-52 118-126 (1233)
46 cd02885 IPP_Isomerase Isopente 25.2 97 0.0021 26.3 3.7 66 30-97 9-86 (165)
47 PF11705 RNA_pol_3_Rpc31: DNA- 24.9 68 0.0015 29.4 2.9 12 161-172 120-131 (233)
48 cd03469 Rieske_RO_Alpha_N Ries 24.8 70 0.0015 25.3 2.6 34 31-65 69-112 (118)
49 cd03528 Rieske_RO_ferredoxin R 24.4 77 0.0017 24.3 2.7 32 30-62 65-97 (98)
50 cd02683 MIT_1 MIT: domain cont 23.2 1.9E+02 0.0042 22.5 4.7 40 85-127 28-68 (77)
51 smart00356 ZnF_C3H1 zinc finge 22.2 74 0.0016 19.0 1.8 20 27-48 6-26 (27)
52 KOG0943 Predicted ubiquitin-pr 21.8 42 0.00091 39.6 1.1 83 167-249 1705-1788(3015)
53 TIGR03031 cas_csx12 CRISPR-ass 21.8 51 0.0011 35.9 1.6 30 35-64 11-46 (802)
54 smart00745 MIT Microtubule Int 21.5 2.8E+02 0.006 20.6 5.2 41 85-128 30-71 (77)
55 PF04159 NB: NB glycoprotein; 21.5 46 0.00099 27.9 1.0 28 24-53 45-76 (100)
56 COG3657 Uncharacterized protei 21.2 1.1E+02 0.0025 25.9 3.2 21 166-186 32-52 (100)
57 COG4530 Uncharacterized protei 21.1 86 0.0019 27.4 2.6 9 179-187 35-43 (129)
58 KOG0739 AAA+-type ATPase [Post 21.0 1.2E+02 0.0025 31.1 3.8 45 83-127 23-73 (439)
59 smart00130 KR Kringle domain. 20.8 51 0.0011 25.9 1.1 11 23-33 47-57 (83)
60 PF11081 DUF2890: Protein of u 20.6 59 0.0013 30.1 1.6 7 221-227 36-42 (187)
61 PF06204 CBM_X: Putative carbo 20.4 89 0.0019 24.0 2.3 23 43-65 29-51 (66)
No 1
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=100.00 E-value=1.2e-123 Score=860.75 Aligned_cols=289 Identities=55% Similarity=0.896 Sum_probs=237.5
Q ss_pred CCCchhHHHhhcCCcceeeeecCCCCCcCCCCCcccccCCCCCCCCCCcceEEEeeCcEEEEEeechhhccCCchhhhhh
Q 022130 1 MQHDEVIWQVIRHNHCSFMAKIETGKFCRNPYNVTGICNRSSCPLANSRYATIRDHDGVFYLYMKTIERAHQPNQLWERV 80 (302)
Q Consensus 1 M~~D~vIW~iIn~~fCSfK~kt~~~~FCRNeyNvTGlCnR~SCPLANS~YATVre~~G~~yLymKt~ERah~P~klWEki 80 (302)
||||+|||+|||++|||||++|.+++||||+|||||||||+|||||||||||||+++|+||||||||||||||++|||+|
T Consensus 1 Mq~DeviW~vin~~~CS~k~kte~~~fCRNeyNvTGLCnR~SCPLANSrYATVre~~g~~yLymKt~ERaH~P~klwEri 80 (303)
T KOG3064|consen 1 MQSDEVIWQVINKSFCSYKIKTETQTFCRNEYNVTGLCNRSSCPLANSRYATVREENGVLYLYMKTIERAHMPRKLWERI 80 (303)
T ss_pred CcchHHHHHHhchhhcceeeeccccchhccccccceeeccccCcCccccceeEeecCCEEEEEEechhhhcCcHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCccHHHHHHHHHHhhcCCchHHHHHhhhHHHHHHHHHHHHHHHHhhc-CcceeeCchhhhHHHHHHHHHHHHHHhhhh
Q 022130 81 KLPRNYEKALEIIDKNLMYWPKFLVHKTKQRLTKMTQMRIRMRKLALKT-REKIMTTPRKEKKREARREEKAEKAAVLDK 159 (302)
Q Consensus 81 kLs~Ny~kALeqId~~L~yWpkflihKcKQRltkltQ~liRmRkl~l~~-~~klv~i~kK~erRe~~RE~KAl~aA~le~ 159 (302)
+||+||+|||+|||++|.|||+|++||||||||||||||||||+|+++. +.+|||+++|++|||++||+|||+||+|++
T Consensus 81 kLSkNyekALeQIde~Ll~Wp~~~~HKcKQRltklTQylir~rklalr~~q~~~vp~~~K~~rRE~rReeKALvAakldk 160 (303)
T KOG3064|consen 81 KLSKNYEKALEQIDEQLLYWPKYVIHKCKQRLTKLTQYLIRMRKLALRGRQKKLVPIKKKVERREKRREEKALVAAKLDK 160 (303)
T ss_pred hcchhHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHHhccCceEEeecchHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999995 457999999999999999999999999999
Q ss_pred hhHHHHHHHHhcCCCCCccccChHHHHHHHhhhhhccc---cchhhhhhhhhhhhcCCCCcc--hhhhhhhhcccccCCC
Q 022130 160 SIEKELLERLKKGVYGDIYNYPADKYNEILDKEQLAAD---DIEEDEEEAEIEFVEGYDDLE--EEEDIEDFGGLAVNKS 234 (302)
Q Consensus 160 ~IEkELleRLk~G~YGd~yn~~~~~~~k~l~~~~~~~e---~eeeee~~~~~E~v~d~e~~~--e~~d~ed~e~~~~~~~ 234 (302)
+||+|||.||++|+|||||||++++|+|+|++.+.++. ++++++++++.|||+|+++.+ +.+|++||.++...+.
T Consensus 161 aIekELm~RLk~G~Ygd~yn~~~~~fnK~l~~~e~d~~de~ee~~~~~~~e~E~v~~D~e~e~~e~~D~E~~~~~~~~~~ 240 (303)
T KOG3064|consen 161 AIEKELMERLKSGTYGDIYNFRQHAFNKALEAREEDDKDENEEEEEDEDAELEEVEGDGELEAEETDDSEDWDGDDDSDE 240 (303)
T ss_pred HHHHHHHHHHhcCCcCCcccchHHHHHHHHHhhhhcccccccccccchhhhhhhccCCcccccccccchhhhcccchhhh
Confidence 99999999999999999999999999999999855432 223556678999998765522 3455555555444332
Q ss_pred -C-CCCCCCCCCCCCCchhhHHHhhhhhhhhhHHhhhcCCCCCCCCCCcCCCceeEEeeccccccc
Q 022130 235 -S-LDDDDVGLDDNDDDETVAVEHKRVRRESSLALRKLGNDEGGTKPKKKARVLVEVEQEDTDGRQ 298 (302)
Q Consensus 235 -~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~~~~~~~~kkkr~~vEIEyE~E~e~q 298 (302)
+ +++++++++++|++++++ .|+.+.. +| .+.++++++|++|++||||||+|++..
T Consensus 241 ~~~s~~d~d~e~esd~de~Ee-----~K~~~k~--kk--~~~~~k~kkk~~r~~ve~E~E~e~e~~ 297 (303)
T KOG3064|consen 241 SDDSDEDSDSEDESDSDEIEE-----NKKESKK--KK--GKKAAKGKKKRPRVHVEIEYEEETEPR 297 (303)
T ss_pred hhhcccccccccCCchhhHHH-----hhhhhhh--cc--cCCCccccccCCcceEEeehhhccchh
Confidence 2 222222222222222222 1111111 11 123334555578889999999988743
No 2
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=100.00 E-value=1.3e-105 Score=733.60 Aligned_cols=285 Identities=42% Similarity=0.692 Sum_probs=238.5
Q ss_pred CCchhHHHhhcCCcceeeeecCCCCCcCCCCCcccccCCCCCCCCCCcceEEEeeCcEEEEEeechhhccCCchhhhhhc
Q 022130 2 QHDEVIWQVIRHNHCSFMAKIETGKFCRNPYNVTGICNRSSCPLANSRYATIRDHDGVFYLYMKTIERAHQPNQLWERVK 81 (302)
Q Consensus 2 ~~D~vIW~iIn~~fCSfK~kt~~~~FCRNeyNvTGlCnR~SCPLANS~YATVre~~G~~yLymKt~ERah~P~klWEkik 81 (302)
|+|++||||+|++||||+++|..||||||+|||||||+|+|||||||+|||||.++|.||||||||||||+|++||++|+
T Consensus 1 msDE~~Wqv~g~~fCS~rik~e~qnfCRNeyNVTGLC~RqSCPLANSrYATVr~dngkLyLymKtpERaH~P~klwerIk 80 (303)
T COG5129 1 MSDESLWQVSGENFCSFRIKTEEQNFCRNEYNVTGLCDRQSCPLANSRYATVRADNGKLYLYMKTPERAHVPRKLWERIK 80 (303)
T ss_pred CchhHHHHHccccccceeeecchhhhhhcccccceeeccccCcCccCcceEEEecCCEEEEEecChhhccCcHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccHHHHHHHHHHhhcCCchHHHHHhhhHHHHHHHHHHHHHHHHhhcCc-ceeeCchhhhHHHHHHHHHHHHHHhhhhh
Q 022130 82 LPRNYEKALEIIDKNLMYWPKFLVHKTKQRLTKMTQMRIRMRKLALKTRE-KIMTTPRKEKKREARREEKAEKAAVLDKS 160 (302)
Q Consensus 82 Ls~Ny~kALeqId~~L~yWpkflihKcKQRltkltQ~liRmRkl~l~~~~-klv~i~kK~erRe~~RE~KAl~aA~le~~ 160 (302)
||+||++||+|||++|.|||+|+|||||||||||||||+..|+|++..++ .+|++++|+.|||+.|++|||+||+||++
T Consensus 81 LSkNY~kAL~QIde~Ll~W~~~~iHkCKQrltkLTQyll~~RRLal~~e~~~y~~~kpK~~rRE~~RerKaL~aak~EKn 160 (303)
T COG5129 81 LSKNYEKALKQIDESLLFWDEKVIHKCKQRLTKLTQYLLKARRLALFKEHGEYMVRKPKMNRREKLRERKALNAAKFEKN 160 (303)
T ss_pred hhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccCchhhHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999887 69999999999999999999999999999
Q ss_pred hHHHHHHHHhcCCCCC-ccccChHHHHHHHhhhhhc-cc----cchhhhhhhhhhhhcCCCCcchhhhhhhhcccccCCC
Q 022130 161 IEKELLERLKKGVYGD-IYNYPADKYNEILDKEQLA-AD----DIEEDEEEAEIEFVEGYDDLEEEEDIEDFGGLAVNKS 234 (302)
Q Consensus 161 IEkELleRLk~G~YGd-~yn~~~~~~~k~l~~~~~~-~e----~eeeee~~~~~E~v~d~e~~~e~~d~ed~e~~~~~~~ 234 (302)
||+||+.||+||+||| ++|+.++.|+||+.+.+.- ++ ++|+++++++.|||.|+++ .+--+..|+++|.+++.
T Consensus 161 IekELm~RLkSGiYGd~pLnv~e~~wnK~~~~rE~~qde~e~~~eEeE~~d~elE~vtdD~e-~e~~~~~dlekWl~~~~ 239 (303)
T COG5129 161 IEKELMLRLKSGIYGDTPLNVREHLWNKAATEREKRQDEKERYVEEEEESDTELEAVTDDSE-KEKTKKKDLEKWLGSDQ 239 (303)
T ss_pred HHHHHHHHHhccccCCCccchHHHHHHHHHHHHhhccchhhhhhhhhhcccceeEeeccccc-cchhhHHHHHHHhcccc
Confidence 9999999999999998 9999999999999877543 21 2455667889999998765 33457778887777642
Q ss_pred ----C-CCCCCCCCCCCCCchhhHHHhhhhhhhhhHHhhhcCCCCCCCCCCcCCCceeEEeeccccccccc
Q 022130 235 ----S-LDDDDVGLDDNDDDETVAVEHKRVRRESSLALRKLGNDEGGTKPKKKARVLVEVEQEDTDGRQKA 300 (302)
Q Consensus 235 ----~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~~~~~~~~kkkr~~vEIEyE~E~e~q~~ 300 (302)
+ +.+++++++++|+|++++..-+.+++ | ..-.+|.++|+|+||||+|.+.|.+
T Consensus 240 ~~~ts~se~e~~sesesd~d~dednk~~~rkr-------k------~~~a~ksrkp~i~ieyeqe~e~e~~ 297 (303)
T COG5129 240 SMETSESEEEESSESESDEDEDEDNKGKIRKR-------K------TDDAKKSRKPHIHIEYEQERENEKI 297 (303)
T ss_pred chhccccccccccccccccccccccccchhhc-------c------cCchhhccCCceeeehHhhhhhccc
Confidence 2 22222222222222222211111111 1 1112456679999999999987654
No 3
>PLN00040 Protein MAK16 homolog; Provisional
Probab=100.00 E-value=1.3e-93 Score=651.52 Aligned_cols=195 Identities=79% Similarity=1.257 Sum_probs=192.2
Q ss_pred CCCchhHHHhhcCCcceeeeecCCCCCcCCCCCcccccCCCCCCCCCCcceEEEeeCcEEEEEeechhhccCCchhhhhh
Q 022130 1 MQHDEVIWQVIRHNHCSFMAKIETGKFCRNPYNVTGICNRSSCPLANSRYATIRDHDGVFYLYMKTIERAHQPNQLWERV 80 (302)
Q Consensus 1 M~~D~vIW~iIn~~fCSfK~kt~~~~FCRNeyNvTGlCnR~SCPLANS~YATVre~~G~~yLymKt~ERah~P~klWEki 80 (302)
|+||++||+||+++||||++|+.+++||||+|||||+|||+|||||||+||||+..+|.|||||||+||||+|+++|++|
T Consensus 1 m~SddLiW~IIr~~~csF~vK~~~~~Fcrnp~NltglcsrkycgLANsKyatV~~~~G~v~L~~Kt~erah~Pak~w~kv 80 (233)
T PLN00040 1 MQHDEVIWQVINHNHCSFKAKIDTGNFCRNKYNVTGLCNRSSCPLANSRYATIREEDGRFYLYMKTIERAHMPNKLWEKV 80 (233)
T ss_pred CCccchhhhhhcCcceeEEEccCCCcccCCCCcccccccccccccccceeeEEEEcCCEEEEEEecccccCCcccceEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCccHHHHHHHHHHhhcCCchHHHHHhhhHHHHHHHHHHHHHHHHhhcCcceeeCchhhhHHHHHHHHHHHHHHhhhhh
Q 022130 81 KLPRNYEKALEIIDKNLMYWPKFLVHKTKQRLTKMTQMRIRMRKLALKTREKIMTTPRKEKKREARREEKAEKAAVLDKS 160 (302)
Q Consensus 81 kLs~Ny~kALeqId~~L~yWpkflihKcKQRltkltQ~liRmRkl~l~~~~klv~i~kK~erRe~~RE~KAl~aA~le~~ 160 (302)
.||+||.+||+||+.+|.|||+|++||||||||||||||||||+|+++.++++|||++|++||+++||.||++||+||++
T Consensus 81 ~Lskn~rkalk~I~~~L~~w~~~~ihk~KqRltkl~q~lir~rkl~~~~~~~~~~~~~k~~rre~~re~Ka~~aa~le~~ 160 (233)
T PLN00040 81 KLSRNYEKALEQIDKHLAYWPKFLVHKNKQRLTKMTQYLIRMRKLALKTREKIVTTPRKLLKRERRRESKAQKAAQLEKS 160 (233)
T ss_pred ecCCCHHHHHHHHHHHHhhCcHHHHHHHHHHHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHhcCCCCCccccChHHHHHHHhhhhhc
Q 022130 161 IEKELLERLKKGVYGDIYNYPADKYNEILDKEQLA 195 (302)
Q Consensus 161 IEkELleRLk~G~YGd~yn~~~~~~~k~l~~~~~~ 195 (302)
||+|||+||++|+||||||||+.+|++||+..+.+
T Consensus 161 Ie~ELl~RL~~G~Yg~~yn~~~~~~~~~l~~~~~~ 195 (233)
T PLN00040 161 IEKELLERLKSGTYGDIYNFPSKSYNKVLEMEEVE 195 (233)
T ss_pred HHHHHHHHHhcCCCCccccCCHHHHHHHHhhhhhh
Confidence 99999999999999999999999999999977653
No 4
>PF01778 Ribosomal_L28e: Ribosomal L28e protein family; InterPro: IPR002672 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L28e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. In rat there are 9 or 10 copies of the L28 gene. The L28 protein contains a possible internal duplication of 9 residues [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1D_O 4A1B_O 4A18_O 4A19_O 3IZR_b.
Probab=100.00 E-value=3e-34 Score=236.18 Aligned_cols=112 Identities=32% Similarity=0.526 Sum_probs=94.7
Q ss_pred hHHHhhcCCcceeeeecC--CCCCcCCCCCcccccCCCCCCCCCCcceEEEee-CcEEEEEeechhhccCCchhhhhhcC
Q 022130 6 VIWQVIRHNHCSFMAKIE--TGKFCRNPYNVTGICNRSSCPLANSRYATIRDH-DGVFYLYMKTIERAHQPNQLWERVKL 82 (302)
Q Consensus 6 vIW~iIn~~fCSfK~kt~--~~~FCRNeyNvTGlCnR~SCPLANS~YATVre~-~G~~yLymKt~ERah~P~klWEkikL 82 (302)
+||+||+++|| |.+|+. +..||+++|||||+|++.+||||||+|+||+.. +|.+||++|+.+++|.|+++|.+|.|
T Consensus 1 L~W~iir~~~~-Fl~K~~~~~~~fs~ep~NL~~~~s~kysgLan~k~v~V~~~~~g~v~l~~K~~~~~~~P~k~~~~~~l 79 (117)
T PF01778_consen 1 LQWEIIRNNNC-FLVKRNGIGKTFSREPGNLTNLNSFKYSGLANSKAVGVRPAPNGGVVLVTKKPKRANKPAKSWEKVTL 79 (117)
T ss_dssp HHHHHHTTT-T-TEEEET--TEEEE--TT-SSSB-STTT-TTTSS--EECCCEGGGECCCEEE-----TTTT--EEEEEE
T ss_pred CEEEEecCcce-EEEEeCCCCCcccCCCCcccccccccccccccceeEEEEECCCCcEEEEEccccccCCCcceeEEEec
Confidence 69999999999 999999 899999999999999999999999999999999 99999999999999999999999999
Q ss_pred CccHHHHHHHHHHhhcC-CchHHHHHhhhHHHHHHHH
Q 022130 83 PRNYEKALEIIDKNLMY-WPKFLVHKTKQRLTKMTQM 118 (302)
Q Consensus 83 s~Ny~kALeqId~~L~y-WpkflihKcKQRltkltQ~ 118 (302)
++||.+||++|...+.+ |+..|++.|++|+++|.|+
T Consensus 80 ~k~~r~a~~~I~~~~~~~yr~dL~~~a~~R~s~i~~s 116 (117)
T PF01778_consen 80 SKNSRKALKSIKKQLAKKYRPDLRKAALRRASAILRS 116 (117)
T ss_dssp SSCHHHHHHHHHHHTSSTHHHHHCCHHHHHHHHHCCH
T ss_pred CccHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhc
Confidence 99999999999999999 9999999999999999875
No 5
>PF04874 Mak16: Mak16 protein C-terminal region; InterPro: IPR006958 The function of these proteins is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni (Blood fluke) Mak16 has been shown to target protein transport to the nucleolus [].
Probab=99.96 E-value=2.6e-30 Score=211.11 Aligned_cols=92 Identities=57% Similarity=0.896 Sum_probs=78.3
Q ss_pred CchhhhHHHHHHHHHHHHHHhhhhhhHHHHHHHHhcCCCCCc-cccChHHHHHHHhhhhhccc--------cchhhhhhh
Q 022130 136 TPRKEKKREARREEKAEKAAVLDKSIEKELLERLKKGVYGDI-YNYPADKYNEILDKEQLAAD--------DIEEDEEEA 206 (302)
Q Consensus 136 i~kK~erRe~~RE~KAl~aA~le~~IEkELleRLk~G~YGd~-yn~~~~~~~k~l~~~~~~~e--------~eeeee~~~ 206 (302)
|+||++||+++||.||++||+|+++||+|||+||++|||||+ ||||+.+|++||+..+.... +++++++++
T Consensus 1 I~kK~eRRE~~RE~KAl~AA~le~~IEkELLeRLk~G~Ygd~~yN~~~~~~~k~le~~~~~~~~e~e~ee~~eeeeee~~ 80 (101)
T PF04874_consen 1 IKKKVERREKRREEKALIAAKLEKSIEKELLERLKSGTYGDIPYNFPEEAFNKVLEEEEKEEEDEDEEEEEEEEEEEEEG 80 (101)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccCHHHHHHHHHHHhhcccchhhhhhhhHHHhhccC
Confidence 689999999999999999999999999999999999999998 99999999999998875421 123345678
Q ss_pred hhhhhcCCCCcchhhhhhhhcc
Q 022130 207 EIEFVEGYDDLEEEEDIEDFGG 228 (302)
Q Consensus 207 ~~E~v~d~e~~~e~~d~ed~e~ 228 (302)
++|||+|+++ .+++|++||+|
T Consensus 81 e~E~ved~~e-~ee~d~~D~Ed 101 (101)
T PF04874_consen 81 EVEYVEDDDE-EEEDDIEDIED 101 (101)
T ss_pred CeeeccCCcc-hhhhhhhhhhC
Confidence 9999998854 44567888764
No 6
>PTZ00197 60S ribosomal protein L28; Provisional
Probab=98.10 E-value=1.7e-05 Score=69.44 Aligned_cols=124 Identities=18% Similarity=0.381 Sum_probs=102.2
Q ss_pred CCchhHHHhhcCCcceeeeecCCCCCcCCCCCcccccCCCCCCCCCCcceEEEeeCcEEEEEeechhhccCCchhhhhhc
Q 022130 2 QHDEVIWQVIRHNHCSFMAKIETGKFCRNPYNVTGICNRSSCPLANSRYATIRDHDGVFYLYMKTIERAHQPNQLWERVK 81 (302)
Q Consensus 2 ~~D~vIW~iIn~~fCSfK~kt~~~~FCRNeyNvTGlCnR~SCPLANS~YATVre~~G~~yLymKt~ERah~P~klWEkik 81 (302)
.|++++|+||.++.| |-+|-.+..|-+-++|++|+=+...+-|||.+=.+|-.++|-+-|-+|..-..|.|++...++.
T Consensus 3 ~S~dL~W~iVRnnns-FLvKr~g~~FSrEP~NL~n~nS~KysGL~n~KaVgV~~~~kgVvv~tKk~k~~~kPak~~~~~t 81 (146)
T PTZ00197 3 HSTDLQWLLVRQNSK-FLQKRNGIRLSSDPFNNNANWTKRHCGFLNTKAAVVKTKGDRILVTTKDGSSNNKPKQMYKKTV 81 (146)
T ss_pred Cchheeeeeeeccce-eEEccCCCcccCCCCccccccccccccccccceEEEEecCCEEEEEEecCCCCCCCchheeEEe
Confidence 478999999977665 6666667779999999999999999999999999999667778888999999999999999999
Q ss_pred CCccHHHHHHHHHHhh-cCCchHHHHHhhhHHHHHHHHHHHHHHHHhhc
Q 022130 82 LPRNYEKALEIIDKNL-MYWPKFLVHKTKQRLTKMTQMRIRMRKLALKT 129 (302)
Q Consensus 82 Ls~Ny~kALeqId~~L-~yWpkflihKcKQRltkltQ~liRmRkl~l~~ 129 (302)
|+++.-++. |-..+ .|=|. |..-|-.|...|.--+.||.|.+.-.
T Consensus 82 lkkg~Rr~~--V~~~v~~YR~D-L~~aAlrRASAIlrs~~~~~~~~~~~ 127 (146)
T PTZ00197 82 MAAGVRASV--VSRAVAAVRPD-LASVAFRRARKMACTASRMKKVAAAR 127 (146)
T ss_pred eccCccHHH--HHHHHHhhCHH-HHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 999988873 43322 25555 77778888888888888888876543
No 7
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=96.21 E-value=0.022 Score=54.80 Aligned_cols=30 Identities=27% Similarity=0.399 Sum_probs=13.1
Q ss_pred chhhhHHHHHHHHHHHHHHhhhhhhHHHHH
Q 022130 137 PRKEKKREARREEKAEKAAVLDKSIEKELL 166 (302)
Q Consensus 137 ~kK~erRe~~RE~KAl~aA~le~~IEkELl 166 (302)
.++-.||+....-.|..--.||+.+=.=|-
T Consensus 142 ~rRE~rReeKALvAakldkaIekELm~RLk 171 (303)
T KOG3064|consen 142 ERREKRREEKALVAAKLDKAIEKELMERLK 171 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344444444444444444444444443333
No 8
>KOG3412 consensus 60S ribosomal protein L28 [Translation, ribosomal structure and biogenesis]
Probab=94.94 E-value=0.11 Score=45.30 Aligned_cols=96 Identities=19% Similarity=0.325 Sum_probs=65.0
Q ss_pred CCchhHHHhhcCCcceeeeec--CCCCCcCCCCCcccccCCCCCCCCCCcceEEE--eeCcEEEEEeechhhccCCchhh
Q 022130 2 QHDEVIWQVIRHNHCSFMAKI--ETGKFCRNPYNVTGICNRSSCPLANSRYATIR--DHDGVFYLYMKTIERAHQPNQLW 77 (302)
Q Consensus 2 ~~D~vIW~iIn~~fCSfK~kt--~~~~FCRNeyNvTGlCnR~SCPLANS~YATVr--e~~G~~yLymKt~ERah~P~klW 77 (302)
.|+.+||+||.++.|-.-.+. ..+.|-+-+.||.|.-+--.--|+|-+---|. .+++-+.+-+|-.-+|.-|++..
T Consensus 3 ~S~~L~W~VIRnNn~FL~k~r~~~k~~FstEpnNL~~vnS~rySGL~nkKtvgV~~aA~~kgvvv~~kk~K~aqkPAk~~ 82 (133)
T KOG3412|consen 3 TSGHLIWQVIRNNNAFLVKQRGNVKKQFSTEPNNLKNVNSYRYSGLANKKTVGVIPAADKKGVVVVTKKTKGAQKPAKSV 82 (133)
T ss_pred cccceeeeeeecCCceeeeeccccccccccCCcccccccccccccccccceeeeeecCCCceEEEEEeccccccCchhhh
Confidence 378999999977766553333 25667777777643332222223332222122 12445667788888999999999
Q ss_pred hhhcCCccHHHHHHHHHHhh
Q 022130 78 ERVKLPRNYEKALEIIDKNL 97 (302)
Q Consensus 78 EkikLs~Ny~kALeqId~~L 97 (302)
-+.-|..+.-.-|.-|-..+
T Consensus 83 ~k~~~~k~~r~s~k~la~~i 102 (133)
T KOG3412|consen 83 VKSTLKKEPRRSLKSLANQI 102 (133)
T ss_pred hHHHHhcccHHHHHHHHHHh
Confidence 99999999999999997766
No 9
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=90.40 E-value=0.18 Score=53.41 Aligned_cols=19 Identities=11% Similarity=0.134 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHhhcCc
Q 022130 113 TKMTQMRIRMRKLALKTRE 131 (302)
Q Consensus 113 tkltQ~liRmRkl~l~~~~ 131 (302)
....|.|.-+--|++-..+
T Consensus 531 ~~~f~~L~~~~~lq~~~~~ 549 (784)
T PF04931_consen 531 AQAFELLLSLVLLQLYNGP 549 (784)
T ss_pred HHHHHHHHHHHHHHHhcCC
Confidence 4556777777777665433
No 10
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=89.23 E-value=0.45 Score=44.07 Aligned_cols=8 Identities=25% Similarity=0.227 Sum_probs=4.3
Q ss_pred hhhhcCCC
Q 022130 208 IEFVEGYD 215 (302)
Q Consensus 208 ~E~v~d~e 215 (302)
.+|+++.+
T Consensus 42 ~ef~~~~~ 49 (240)
T PF05764_consen 42 EEFESEEE 49 (240)
T ss_pred ccccCCCc
Confidence 45665543
No 11
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=77.24 E-value=1.7 Score=47.53 Aligned_cols=20 Identities=25% Similarity=0.292 Sum_probs=12.7
Q ss_pred hhhhhHHHHHHHHhcCCCCC
Q 022130 157 LDKSIEKELLERLKKGVYGD 176 (302)
Q Consensus 157 le~~IEkELleRLk~G~YGd 176 (302)
++-.+-.|+|.|..-|--++
T Consensus 831 ~~~Ee~eeel~~~~~~~~~e 850 (988)
T KOG2038|consen 831 VDDEEFEEELWRFEDGSLPE 850 (988)
T ss_pred CchHHHHHHHHHhcCCcCcc
Confidence 55566667777777665444
No 12
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=75.92 E-value=2.2 Score=44.98 Aligned_cols=6 Identities=17% Similarity=0.257 Sum_probs=2.3
Q ss_pred cceeee
Q 022130 15 HCSFMA 20 (302)
Q Consensus 15 fCSfK~ 20 (302)
-|--|+
T Consensus 323 L~~rKi 328 (615)
T KOG0526|consen 323 LCGRKI 328 (615)
T ss_pred HhCcee
Confidence 333333
No 13
>KOG2897 consensus DNA-binding protein YL1 and related proteins [General function prediction only]
Probab=69.10 E-value=6 Score=40.01 Aligned_cols=15 Identities=20% Similarity=0.133 Sum_probs=5.7
Q ss_pred hHHHHHHHHhcCCCC
Q 022130 161 IEKELLERLKKGVYG 175 (302)
Q Consensus 161 IEkELleRLk~G~YG 175 (302)
++.|+..=--+-+||
T Consensus 25 Le~E~ed~~~~t~q~ 39 (390)
T KOG2897|consen 25 LESEEEDDEYSTTQG 39 (390)
T ss_pred hhhhhhhhHHhhhhc
Confidence 444443333333333
No 14
>PF09073 BUD22: BUD22; InterPro: IPR015158 BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal [].
Probab=67.08 E-value=36 Score=34.16 Aligned_cols=25 Identities=32% Similarity=0.308 Sum_probs=17.6
Q ss_pred HHHHHHHHHhhhhhhHHHHHHHHhc
Q 022130 147 REEKAEKAAVLDKSIEKELLERLKK 171 (302)
Q Consensus 147 RE~KAl~aA~le~~IEkELleRLk~ 171 (302)
+|..|+.+..|+..+..=|+..|-.
T Consensus 46 ~Ei~~lKslDl~~~a~~~l~~kLiK 70 (432)
T PF09073_consen 46 EEIEALKSLDLDQFAKRHLRSKLIK 70 (432)
T ss_pred HHHhhhccCCHHHHHHHHHHHHHHH
Confidence 3556666777788888777777766
No 15
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=65.57 E-value=6.8 Score=42.57 Aligned_cols=6 Identities=17% Similarity=0.302 Sum_probs=2.8
Q ss_pred hhhhcC
Q 022130 208 IEFVEG 213 (302)
Q Consensus 208 ~E~v~d 213 (302)
.||...
T Consensus 939 SEyeaS 944 (1001)
T COG5406 939 SEYEAS 944 (1001)
T ss_pred hhhhcc
Confidence 455543
No 16
>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Probab=64.70 E-value=3.6 Score=26.37 Aligned_cols=16 Identities=44% Similarity=1.227 Sum_probs=13.2
Q ss_pred CCCccc-ccCCCCCCCC
Q 022130 31 PYNVTG-ICNRSSCPLA 46 (302)
Q Consensus 31 eyNvTG-lCnR~SCPLA 46 (302)
.|-++| .||..+|+..
T Consensus 4 ~yEl~Gg~Cnd~~C~~Q 20 (23)
T PF10650_consen 4 PYELTGGVCNDPDCEFQ 20 (23)
T ss_pred ccccCCCeeCCCCCCcc
Confidence 366888 9999999864
No 17
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=64.33 E-value=5.8 Score=43.60 Aligned_cols=8 Identities=13% Similarity=0.439 Sum_probs=4.5
Q ss_pred HHHHHhhh
Q 022130 185 YNEILDKE 192 (302)
Q Consensus 185 ~~k~l~~~ 192 (302)
|.++|...
T Consensus 848 W~~ImKTI 855 (960)
T KOG1189|consen 848 WTKIMKTI 855 (960)
T ss_pred HHHHhhhh
Confidence 56666544
No 18
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=63.43 E-value=4.5 Score=43.94 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=8.7
Q ss_pred hhHHHHHHHHhc
Q 022130 160 SIEKELLERLKK 171 (302)
Q Consensus 160 ~IEkELleRLk~ 171 (302)
-+|.+=|.|++.
T Consensus 286 klE~~Rl~RM~g 297 (840)
T PF04147_consen 286 KLEEERLKRMRG 297 (840)
T ss_pred HHHHHHHhhhcc
Confidence 367888888764
No 19
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=59.76 E-value=4.9 Score=43.77 Aligned_cols=18 Identities=33% Similarity=0.300 Sum_probs=9.1
Q ss_pred CchhhhHHHHHHHHHHHH
Q 022130 136 TPRKEKKREARREEKAEK 153 (302)
Q Consensus 136 i~kK~erRe~~RE~KAl~ 153 (302)
|.-...+|+.++-+|-+.
T Consensus 139 ia~eed~~e~~~lEKkl~ 156 (822)
T KOG2141|consen 139 IATEEDDREINGLEKKLK 156 (822)
T ss_pred cccccchHHHhhHHHHHh
Confidence 344444555555555444
No 20
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=54.39 E-value=10 Score=42.43 Aligned_cols=24 Identities=25% Similarity=0.306 Sum_probs=12.9
Q ss_pred CccHHHHHHHHHHhhcCCchHHHH
Q 022130 83 PRNYEKALEIIDKNLMYWPKFLVH 106 (302)
Q Consensus 83 s~Ny~kALeqId~~L~yWpkflih 106 (302)
|.--.-||+.|=.+|.|=|.-.++
T Consensus 785 s~~~~~~leVvinalyynP~ltL~ 808 (1010)
T KOG1991|consen 785 SELRVMLLEVVINALYYNPKLTLG 808 (1010)
T ss_pred hHHHHHHHHHHHHHHHcCcHHHHH
Confidence 333344566666666666665443
No 21
>COG2108 Uncharacterized conserved protein related to pyruvate formate-lyase activating enzyme [General function prediction only]
Probab=49.38 E-value=7.5 Score=38.89 Aligned_cols=16 Identities=63% Similarity=1.346 Sum_probs=12.7
Q ss_pred cccccCCC--CCCCCCCc
Q 022130 34 VTGICNRS--SCPLANSR 49 (302)
Q Consensus 34 vTGlCnR~--SCPLANS~ 49 (302)
|||+||++ .|||+--+
T Consensus 34 vTG~C~~~CfYCPvs~~r 51 (353)
T COG2108 34 VTGLCNRSCFYCPVSDER 51 (353)
T ss_pred EecccCCCcccCcCCHHh
Confidence 89999985 68887554
No 22
>PF07359 LEAP-2: Liver-expressed antimicrobial peptide 2 precursor (LEAP-2); InterPro: IPR009955 This family consists of several mammalian liver-expressed antimicrobial peptide 2 (LEAP-2) sequences. LEAP-2 is a cysteine-rich, and cationic protein. LEAP-2 contains a core structure with two disulphide bonds formed by cysteine residues in relative 1-3 and 2-4 positions. LEAP-2 is synthesised as a 77-residue precursor, which is predominantly expressed in the liver and highly conserved among mammals. The largest native LEAP-2 form of 40 amino acid residues is generated from the precursor at a putative cleavage site for a furin-like endoprotease. In contrast to smaller LEAP-2 variants, this peptide exhibits dose-dependent antimicrobial activity against selected microbial model organisms []. The exact function of this family is unclear.; GO: 0042742 defense response to bacterium; PDB: 2L1Q_A.
Probab=43.23 E-value=8.8 Score=31.05 Aligned_cols=26 Identities=31% Similarity=0.764 Sum_probs=18.1
Q ss_pred CCCCcCCCC-CcccccCCCCCCCCCCc
Q 022130 24 TGKFCRNPY-NVTGICNRSSCPLANSR 49 (302)
Q Consensus 24 ~~~FCRNey-NvTGlCnR~SCPLANS~ 49 (302)
.+.+|||.| =+||+|.+.-|-|.-++
T Consensus 50 ~GAsCrd~~EC~T~lCR~~~CS~s~a~ 76 (77)
T PF07359_consen 50 IGASCRDNSECSTGLCRKGHCSLSVAQ 76 (77)
T ss_dssp TTSB-SSGGGBTTS-EETTEE-SS---
T ss_pred CcchhccchhhhHHHhcCCcccccccc
Confidence 678999999 89999999999987543
No 23
>KOG2409 consensus KRR1-interacting protein involved in 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=41.57 E-value=66 Score=34.57 Aligned_cols=35 Identities=20% Similarity=0.359 Sum_probs=23.2
Q ss_pred hhhHHHHHHHHhc--CCCCCc----------cccChHHHHHHHhhhh
Q 022130 159 KSIEKELLERLKK--GVYGDI----------YNYPADKYNEILDKEQ 193 (302)
Q Consensus 159 ~~IEkELleRLk~--G~YGd~----------yn~~~~~~~k~l~~~~ 193 (302)
+-=-+||.+.|.+ .+||+. =.|.+..|+++|...=
T Consensus 342 n~KrkEi~eKl~kl~kvaG~~~~~l~~~dL~~DFDPee~D~~Mqe~F 388 (647)
T KOG2409|consen 342 NLKRKEIEEKLEKLTKVAGNEEIPLTDTDLDDDFDPEEWDKKMQELF 388 (647)
T ss_pred HHHHHHHHHHHHHHHHHhccccCCCchhhhhcccCHHHHHHHHHHHh
Confidence 3334566666654 478862 2678899999988654
No 24
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=40.90 E-value=21 Score=37.62 Aligned_cols=20 Identities=10% Similarity=0.046 Sum_probs=12.6
Q ss_pred CcceeeCchhhhHHHHHHHH
Q 022130 130 REKIMTTPRKEKKREARREE 149 (302)
Q Consensus 130 ~~klv~i~kK~erRe~~RE~ 149 (302)
+-+||||.--.+=+....+.
T Consensus 29 ~~~l~PV~gy~el~~~~~~~ 48 (622)
T PF02724_consen 29 QYSLVPVSGYSELERAYEEL 48 (622)
T ss_pred CeeEEEeCCHHHHHHHHHHH
Confidence 45688887776655544444
No 25
>cd03479 Rieske_RO_Alpha_PhDO_like Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3,4-dioxygenase (CBDO), phenoxybenzoate dioxygenase (POB-dioxygenase) and 3-nitrobenzoate oxygenase (MnbA). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. PhDO and CBDO are two-component RO systems, containing oxygenase and reductase components. PhDO catalyzes the dihydroxylation of phthalate to form th
Probab=40.57 E-value=28 Score=29.49 Aligned_cols=40 Identities=25% Similarity=0.566 Sum_probs=27.6
Q ss_pred CCCCcccccCCCCCC---------CCCCcceEEEeeCcEEEEEeechhhc
Q 022130 30 NPYNVTGICNRSSCP---------LANSRYATIRDHDGVFYLYMKTIERA 70 (302)
Q Consensus 30 NeyNvTGlCnR~SCP---------LANS~YATVre~~G~~yLymKt~ERa 70 (302)
=.|++||-|-...|. +....|. |++.+|.+|+++-....+
T Consensus 88 w~F~~~G~~~~~P~~~~~~~~~~~~~l~~~~-v~~~~G~I~V~~~~~~~~ 136 (144)
T cd03479 88 WKFDVDGQCLEMPSEPPDSQLKQKVRQPAYP-VRERGGLVWAYMGPAEEA 136 (144)
T ss_pred cEECCCCCEEECCCCccccCCccccCcceEe-EEEECCEEEEECCCCCCC
Confidence 357788888765432 2456776 788899999999754333
No 26
>TIGR02150 IPP_isom_1 isopentenyl-diphosphate delta-isomerase, type 1. This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate.
Probab=39.40 E-value=38 Score=28.77 Aligned_cols=67 Identities=15% Similarity=0.262 Sum_probs=45.3
Q ss_pred CCCcccccCCCCCCCCC-----CcceEEEeeCcEEEEEeechhhccCCchhhh-----hhcCCccHHHHHHHHHHhhcC
Q 022130 31 PYNVTGICNRSSCPLAN-----SRYATIRDHDGVFYLYMKTIERAHQPNQLWE-----RVKLPRNYEKALEIIDKNLMY 99 (302)
Q Consensus 31 eyNvTGlCnR~SCPLAN-----S~YATVre~~G~~yLymKt~ERah~P~klWE-----kikLs~Ny~kALeqId~~L~y 99 (302)
..|.+|.+.|..+++.. +-++-|.+.+|.++|--....+.++|. +|. .+.... -+-|+..+.+.+-.
T Consensus 7 ~~~~~g~~~r~~~~~~~g~~h~~v~v~v~~~~g~vLl~kR~~~k~~~PG-~W~~~~gG~v~~GE-~eaa~REl~EE~Gl 83 (158)
T TIGR02150 7 NDNPIGTASKAEVHLQETPLHRAFSVFLFNEEGQLLLQRRALSKITWPG-VWTNSCCSHPLPGE-LEAAIRRLREELGI 83 (158)
T ss_pred CCCEeeeeeHHHhhhcCCCeEEEEEEEEEcCCCeEEEEeccCCCcCCCC-CccccccCCCCccc-HHHHHHHHHHHHCC
Confidence 45789999999999753 345667788899877543444445665 787 566555 46677777776643
No 27
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=38.88 E-value=23 Score=37.91 Aligned_cols=10 Identities=10% Similarity=0.252 Sum_probs=5.7
Q ss_pred cCCcceeeee
Q 022130 12 RHNHCSFMAK 21 (302)
Q Consensus 12 n~~fCSfK~k 21 (302)
|.+||+|-+-
T Consensus 48 GfgfVtFam~ 57 (678)
T KOG0127|consen 48 GFGFVTFAME 57 (678)
T ss_pred CccceeeehH
Confidence 3466666653
No 28
>cd03548 Rieske_RO_Alpha_OMO_CARDO Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole 1,9a-dioxygenase (CARDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OMO catalyzes the NADH-dependent oxidation of the N-heterocyclic aromatic compound 2-oxoquinoline to 8-hydroxy-2-oxoquinoline, the second step in the bacterial degradation of quinoline. OMO consists of a reductase component (OMR) and an oxygenase component (OMO) that together function to shuttle electrons from the
Probab=38.84 E-value=32 Score=28.80 Aligned_cols=44 Identities=16% Similarity=0.377 Sum_probs=29.8
Q ss_pred CCCCc-ccccCCC-CCC-------CCCCcceEEEeeCcEEEEEeechhhccCCc
Q 022130 30 NPYNV-TGICNRS-SCP-------LANSRYATIRDHDGVFYLYMKTIERAHQPN 74 (302)
Q Consensus 30 NeyNv-TGlCnR~-SCP-------LANS~YATVre~~G~~yLymKt~ERah~P~ 74 (302)
=.|++ ||.|... +.| ..-..|. |++.+|.+|+++=....|++|.
T Consensus 81 w~Fdl~tG~~~~~~~~p~~~~~~~~~L~~yp-v~~~~g~V~v~~~~~~~~~~~~ 133 (136)
T cd03548 81 WTYRLDDGKLVTILANPDDPLIGRTGLKTYP-VEEAKGMIFVFVGDGDYADPPP 133 (136)
T ss_pred cEEeCCCccEEEcccCCCccccccCCCceEe-EEEECCEEEEEeCCcccCCCCC
Confidence 35777 8988641 011 2234565 6678999999998888888874
No 29
>KOG1903 consensus Cell cycle-associated protein [Cell cycle control, cell division, chromosome partitioning]
Probab=38.73 E-value=56 Score=30.40 Aligned_cols=72 Identities=24% Similarity=0.470 Sum_probs=44.2
Q ss_pred cccccCCCCCCCC--CCcceEEEeeCcEEEEEeechhhccCCchhhhhhcCCccHHHHH-----HHHHHhhcC-------
Q 022130 34 VTGICNRSSCPLA--NSRYATIRDHDGVFYLYMKTIERAHQPNQLWERVKLPRNYEKAL-----EIIDKNLMY------- 99 (302)
Q Consensus 34 vTGlCnR~SCPLA--NS~YATVre~~G~~yLymKt~ERah~P~klWEkikLs~Ny~kAL-----eqId~~L~y------- 99 (302)
++..|++.|||.- .|+|--.-.+ |.. |-| +-+..-|. |..-| -||+..-.|
T Consensus 79 ise~Cte~sCP~MsGG~rYEY~WqD-~~~--ykk-Pt~L~Ap~-----------Ym~lLMDWIE~~INnE~vFPt~~~vp 143 (217)
T KOG1903|consen 79 ISEFCTETSCPVMSGGPRYEYRWQD-ERK--YKK-PTALSAPR-----------YMALLMDWIEVQINNEEVFPTSVGVP 143 (217)
T ss_pred HhhhccccCCCcccCCCcceeEecc-ccc--ccC-CccCCcHH-----------HHHHHHHHHHHhccccccccccCCCC
Confidence 4678999999975 5777654443 332 333 22222222 22222 255544333
Q ss_pred CchHHHHHhhhHHHHHHHHHH
Q 022130 100 WPKFLVHKTKQRLTKMTQMRI 120 (302)
Q Consensus 100 WpkflihKcKQRltkltQ~li 120 (302)
+||-++.-||.=||||..+..
T Consensus 144 FPKnF~qi~~KILtRLFRVFV 164 (217)
T KOG1903|consen 144 FPKNFLQICKKILTRLFRVFV 164 (217)
T ss_pred CcHhHHHHHHHHHHHHHHHHh
Confidence 899999999999999987654
No 30
>PF03637 Mob1_phocein: Mob1/phocein family; InterPro: IPR005301 Mob1 is an essential Saccharomyces cerevisiae (Baker's yeast) protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature []. This family also includes phocein Q9QYW3 from SWISSPROT, a rat protein that by yeast two hybrid interacts with striatin [].; PDB: 2HJN_A 1PI1_A 1R3B_A.
Probab=38.12 E-value=43 Score=29.94 Aligned_cols=25 Identities=24% Similarity=0.599 Sum_probs=15.6
Q ss_pred cccccCCCCCCCCCCcceEEEeeCcEEEEEee
Q 022130 34 VTGICNRSSCPLANSRYATIRDHDGVFYLYMK 65 (302)
Q Consensus 34 vTGlCnR~SCPLANS~YATVre~~G~~yLymK 65 (302)
|+..|+.++||--++- .+.-||+.-
T Consensus 47 v~e~Ct~~tCP~Msag-------~~~~Ylw~d 71 (175)
T PF03637_consen 47 VSEFCTPETCPTMSAG-------PNWEYLWAD 71 (175)
T ss_dssp HGGGS-TTTTSSEESS-------TTCEE-BSS
T ss_pred ccCcCCcccCcCccCC-------ccceeeeec
Confidence 4678999999986651 244566654
No 31
>cd03531 Rieske_RO_Alpha_KSH The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase component of 3-ketosteroid 9-alpha-hydroxylase (KSH). The terminal oxygenase component of KSH is a key enzyme in the microbial steroid degradation pathway, catalyzing the 9 alpha-hydroxylation of 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD). KSH is a two-component class IA monooxygenase, with terminal oxygenase (KshA) and oxygenase reductase (KshB) components. KSH activity has been found in many actino- and proteo- bacterial genera including Rhodococcus, Nocardia, Arthrobacter, Mycobacterium, and Burkholderia.
Probab=38.04 E-value=33 Score=27.98 Aligned_cols=36 Identities=14% Similarity=0.421 Sum_probs=23.1
Q ss_pred CCCCCcccccCCCCC----C-C-CCCcceEEEeeCcEEEEEee
Q 022130 29 RNPYNVTGICNRSSC----P-L-ANSRYATIRDHDGVFYLYMK 65 (302)
Q Consensus 29 RNeyNvTGlCnR~SC----P-L-ANS~YATVre~~G~~yLymK 65 (302)
.=.|++||-|....+ | . +-..| -|++.+|.+|+++=
T Consensus 66 g~~fd~~G~~~~~p~~~~~p~~~~l~~y-pv~~~~g~v~v~~~ 107 (115)
T cd03531 66 DWRWGGDGRCKAIPYARRVPPLARTRAW-PTLERNGQLFVWHD 107 (115)
T ss_pred CCEECCCCCEEECCcccCCCcccccceE-eEEEECCEEEEECC
Confidence 346788888776543 2 2 22345 45667899999874
No 32
>cd02681 MIT_calpain7_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=36.41 E-value=65 Score=25.39 Aligned_cols=44 Identities=11% Similarity=0.011 Sum_probs=24.9
Q ss_pred cHHHHHHHHHHhhcCCchH-HHH----HhhhH-HHHHHHHHHHHHHHHhh
Q 022130 85 NYEKALEIIDKNLMYWPKF-LVH----KTKQR-LTKMTQMRIRMRKLALK 128 (302)
Q Consensus 85 Ny~kALeqId~~L~yWpkf-lih----KcKQR-ltkltQ~liRmRkl~l~ 128 (302)
||++||.---+-+.+|-.+ +.+ +.|.. ..|+.+||-|...|+..
T Consensus 21 ~y~eA~~~Y~~aie~l~~~~~~~~~n~~~k~~ir~K~~eYl~RAE~Lk~~ 70 (76)
T cd02681 21 RYSEAVFYYKEAAQLLIYAEMAGTLNDSHLKTIQEKSNEYLDRAQALHQL 70 (76)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4454444444444444333 112 23333 68899999999888654
No 33
>cd02682 MIT_AAA_Arch MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in mostly archaebacterial AAA-ATPases. The molecular function of the MIT domain is unclear.
Probab=32.89 E-value=1.1e+02 Score=24.28 Aligned_cols=42 Identities=21% Similarity=0.373 Sum_probs=33.3
Q ss_pred ccHHHHHHHHHHhhcCCchHHHHHhhhH-HHHHHHHHHHHHHHHhh
Q 022130 84 RNYEKALEIIDKNLMYWPKFLVHKTKQR-LTKMTQMRIRMRKLALK 128 (302)
Q Consensus 84 ~Ny~kALeqId~~L~yWpkflihKcKQR-ltkltQ~liRmRkl~l~ 128 (302)
.+|.+|++++-+-|...|.-- .|.. ..||.+|+-|.-.|...
T Consensus 27 ~~Y~~aIe~L~q~~~~~pD~~---~k~~yr~ki~eY~~Rae~Lk~~ 69 (75)
T cd02682 27 TNYKKAIEVLSQIVKNYPDSP---TRLIYEQMINEYKRRIEVLEKQ 69 (75)
T ss_pred HHHHHHHHHHHHHHHhCCChH---HHHHHHHHHHHHHHHHHHHHHH
Confidence 479999999999998888743 3444 57899999998888655
No 34
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=32.44 E-value=27 Score=38.76 Aligned_cols=13 Identities=15% Similarity=0.192 Sum_probs=5.6
Q ss_pred HHhhhhhhHHHHH
Q 022130 154 AAVLDKSIEKELL 166 (302)
Q Consensus 154 aA~le~~IEkELl 166 (302)
=++|.++|-.-..
T Consensus 848 W~~ImKTI~dDP~ 860 (960)
T KOG1189|consen 848 WTKIMKTITDDPI 860 (960)
T ss_pred HHHHhhhhccCHH
Confidence 3444444444333
No 35
>KOG2712 consensus Transcriptional coactivator [Transcription]
Probab=31.49 E-value=25 Score=30.10 Aligned_cols=35 Identities=23% Similarity=0.419 Sum_probs=27.2
Q ss_pred CCCCCCCCCCcceEEEeeCcEEEE-----EeechhhccCCch
Q 022130 39 NRSSCPLANSRYATIRDHDGVFYL-----YMKTIERAHQPNQ 75 (302)
Q Consensus 39 nR~SCPLANS~YATVre~~G~~yL-----ymKt~ERah~P~k 75 (302)
.-..|-|.+-||+||++-+|+.|+ |+|+- --+|.+
T Consensus 39 ~~~i~~l~~~RrVtV~eFkGk~~VdIREyY~kdG--~mlPgk 78 (108)
T KOG2712|consen 39 DDNIFNLGKNRRVTVREFKGKILVDIREYYVKDG--KMLPGK 78 (108)
T ss_pred ccceeecCCceEEehhhcCCceEEehhHhhhccC--ccccCc
Confidence 345799999999999999999997 67733 345653
No 36
>PF13132 DUF3950: Domain of unknown function (DUF3950)
Probab=30.59 E-value=57 Score=22.29 Aligned_cols=23 Identities=22% Similarity=0.390 Sum_probs=18.9
Q ss_pred HHHHHHhh-----cCCchHHHHHhhhHH
Q 022130 90 LEIIDKNL-----MYWPKFLVHKTKQRL 112 (302)
Q Consensus 90 LeqId~~L-----~yWpkflihKcKQRl 112 (302)
|+||+..| .-+..|.+.-|+.||
T Consensus 2 leQI~~a~~~~~~~NFSaWV~dACr~kl 29 (30)
T PF13132_consen 2 LEQIEIALEQEGSGNFSAWVKDACRRKL 29 (30)
T ss_pred hHHHHHHHHhccCcChHHHHHHHHHHHh
Confidence 67888876 458889999999987
No 37
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=29.92 E-value=31 Score=38.38 Aligned_cols=13 Identities=31% Similarity=0.856 Sum_probs=10.6
Q ss_pred chhhhhhcCCccH
Q 022130 74 NQLWERVKLPRNY 86 (302)
Q Consensus 74 ~klWEkikLs~Ny 86 (302)
+.|||=-.||+.|
T Consensus 704 tslWEl~~ls~Hf 716 (988)
T KOG2038|consen 704 TSLWELLLLSKHF 716 (988)
T ss_pred chHHHHHHHhhhc
Confidence 4689999999875
No 38
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=29.50 E-value=33 Score=31.44 Aligned_cols=13 Identities=15% Similarity=0.325 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHHH
Q 022130 112 LTKMTQMRIRMRK 124 (302)
Q Consensus 112 ltkltQ~liRmRk 124 (302)
.+-|..|--|.++
T Consensus 90 ~~~ierYSdry~~ 102 (233)
T PF11705_consen 90 FDDIERYSDRYKK 102 (233)
T ss_pred cccHHHHHHHHhh
Confidence 5555555555444
No 39
>KOG0576 consensus Mitogen-activated protein kinase kinase kinase kinase (MAP4K), germinal center kinase family [Signal transduction mechanisms]
Probab=29.30 E-value=14 Score=40.34 Aligned_cols=17 Identities=53% Similarity=1.060 Sum_probs=15.3
Q ss_pred HHHHHHHhcCCCCCccc
Q 022130 163 KELLERLKKGVYGDIYN 179 (302)
Q Consensus 163 kELleRLk~G~YGd~yn 179 (302)
=|||.|+-+|+|||.|.
T Consensus 17 yellqrvgsgTygdvyK 33 (829)
T KOG0576|consen 17 YELLQRVGSGTYGDVYK 33 (829)
T ss_pred hhheeeecCCcccchhh
Confidence 38999999999999984
No 40
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=28.17 E-value=19 Score=39.40 Aligned_cols=37 Identities=24% Similarity=0.404 Sum_probs=12.5
Q ss_pred EEEeeCcEEEEEeechhh-ccCCc-hhhhhhcCCccHHH
Q 022130 52 TIRDHDGVFYLYMKTIER-AHQPN-QLWERVKLPRNYEK 88 (302)
Q Consensus 52 TVre~~G~~yLymKt~ER-ah~P~-klWEkikLs~Ny~k 88 (302)
+|.-..|.-||.+=+.-. .-.|. =+|..+.|+.|+.=
T Consensus 579 rv~l~~G~WYLl~st~i~~~~~~~gwvw~n~~l~~~~~~ 617 (787)
T PF03115_consen 579 RVRLNQGNWYLLQSTTIVNSPVPSGWVWNNNELGNNTTY 617 (787)
T ss_dssp EEEE-TT-EEEEEEEEEEESS---S---------TT--B
T ss_pred eEEecCCcEEEEEEEEEecCCCCceEEEEeeccCCCccc
Confidence 455668888887653323 33444 56998888887654
No 41
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=28.02 E-value=3.5e+02 Score=23.23 Aligned_cols=12 Identities=42% Similarity=1.016 Sum_probs=10.4
Q ss_pred HHHHHHhcCCCC
Q 022130 164 ELLERLKKGVYG 175 (302)
Q Consensus 164 ELleRLk~G~YG 175 (302)
-.|.|+..|+||
T Consensus 70 ~al~rIe~gtYG 81 (120)
T COG1734 70 SALDRIEEGTYG 81 (120)
T ss_pred HHHHHHHcCCcc
Confidence 457899999998
No 42
>cd07599 BAR_Rvs167p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 167 and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 167 (Rvs167p) and Schizosaccharomyces pombe Hob1 (homolog of Bin1). S. cerevisiae Rvs167p plays a role in regulation of the actin cytoskeleton, endocytosis, and sporulation. It forms a heterodimer with another BAR domain protein Rvs161p. Rvs161p and Rvs167p share common functions but are not interchangeable. Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. Rvs167p also interacts with the GTPase activating protein (GAP) Gyp5p, which is involved in ER to Golgi vesicle trafficking. BAR domains fo
Probab=27.84 E-value=2.3e+02 Score=25.29 Aligned_cols=59 Identities=24% Similarity=0.321 Sum_probs=45.5
Q ss_pred CchhhhhhcCCccHHHHHHHHHHhh-cCCchHHHHHhhhHHHHHHHHHHHHHHHHhhcCcceee
Q 022130 73 PNQLWERVKLPRNYEKALEIIDKNL-MYWPKFLVHKTKQRLTKMTQMRIRMRKLALKTREKIMT 135 (302)
Q Consensus 73 P~klWEkikLs~Ny~kALeqId~~L-~yWpkflihKcKQRltkltQ~liRmRkl~l~~~~klv~ 135 (302)
|...|+.+ .+|..+++.|+..+ ..|. .+....-..++.+..|+..++++-.++..|++-
T Consensus 66 ~~~~~~~~---~~y~~~~~~l~~~~~~~l~-~i~~~V~~P~~~~~~~~~~i~k~IkKR~~k~lD 125 (216)
T cd07599 66 PESTLARL---SRYVKALEELKKELLEELE-FFEERVILPAKELKKYIKKIRKTIKKRDHKKLD 125 (216)
T ss_pred cHHHHHHH---HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44556554 57999999998877 5575 778889999999999999998887777665444
No 43
>KOG4156 consensus Claspin, protein mediating phosphorylation and activation of Chk1 protein kinase in the DNA replication checkpoint response [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=27.57 E-value=1.1e+02 Score=33.91 Aligned_cols=19 Identities=26% Similarity=0.216 Sum_probs=12.0
Q ss_pred HHHHHHHhcCCCCC-ccccC
Q 022130 163 KELLERLKKGVYGD-IYNYP 181 (302)
Q Consensus 163 kELleRLk~G~YGd-~yn~~ 181 (302)
+|.|.-|++|-|-. +-.+|
T Consensus 937 ~E~~~nl~SGkFTsq~ast~ 956 (1329)
T KOG4156|consen 937 MEELLNLCSGKFTSQDASTP 956 (1329)
T ss_pred HHHHHhhccCcccccccccc
Confidence 46667788888754 43333
No 44
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=27.50 E-value=20 Score=34.65 Aligned_cols=22 Identities=18% Similarity=0.214 Sum_probs=0.0
Q ss_pred EeechhhccCCchhhhhhcCCc
Q 022130 63 YMKTIERAHQPNQLWERVKLPR 84 (302)
Q Consensus 63 ymKt~ERah~P~klWEkikLs~ 84 (302)
.+...-..++|.-+|-.+..+.
T Consensus 112 ~~~~~~~iq~~pG~~~~~~~P~ 133 (375)
T PF03153_consen 112 QVPAPPTIQQPPGQQYQVQVPS 133 (375)
T ss_dssp ----------------------
T ss_pred ccCCCCCccCCCccccCcccCC
Confidence 3444444555566665555543
No 45
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=26.35 E-value=69 Score=36.60 Aligned_cols=9 Identities=33% Similarity=0.353 Sum_probs=5.0
Q ss_pred CCCCCcceE
Q 022130 44 PLANSRYAT 52 (302)
Q Consensus 44 PLANS~YAT 52 (302)
|-+||.||+
T Consensus 118 P~~~~~la~ 126 (1233)
T KOG1824|consen 118 PSSSSFLAA 126 (1233)
T ss_pred Ccccccccc
Confidence 455555555
No 46
>cd02885 IPP_Isomerase Isopentenyl diphosphate (IPP) isomerase, a member of the Nudix hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mamm
Probab=25.18 E-value=97 Score=26.28 Aligned_cols=66 Identities=15% Similarity=0.203 Sum_probs=41.9
Q ss_pred CCCCcccccCCCCCCCCCCc-c----eEEEeeCcEEEEEeechh-hccCCchhhh-----hhcCCccHHHH-HHHHHHhh
Q 022130 30 NPYNVTGICNRSSCPLANSR-Y----ATIRDHDGVFYLYMKTIE-RAHQPNQLWE-----RVKLPRNYEKA-LEIIDKNL 97 (302)
Q Consensus 30 NeyNvTGlCnR~SCPLANS~-Y----ATVre~~G~~yLymKt~E-Rah~P~klWE-----kikLs~Ny~kA-LeqId~~L 97 (302)
...|+||.|-|+.=..-+.- . +-|++.+|.++| .|... ..++| .+|. .|.-..++..| +..+-+.+
T Consensus 9 ~~~~~~g~~~r~~~~~~~~~~~~~v~v~i~~~~~~iLl-~kR~~~~~~~P-g~w~~~~gG~ie~GEt~~eaa~REl~EEt 86 (165)
T cd02885 9 EDDNPIGTAEKLEAHLKGTLLHRAFSVFLFNSKGRLLL-QRRALSKYTFP-GLWTNTCCSHPLPGEGVKDAAQRRLREEL 86 (165)
T ss_pred CCCCCccccCHHHHhhcCCcceeEEEEEEEcCCCcEEE-EeccCCCccCC-CcccccccCCCCCCCCHHHHHHHHHHHHh
Confidence 35689999988887777766 3 335677888776 45332 23444 6676 56667777754 44555554
No 47
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=24.89 E-value=68 Score=29.40 Aligned_cols=12 Identities=42% Similarity=0.520 Sum_probs=6.2
Q ss_pred hHHHHHHHHhcC
Q 022130 161 IEKELLERLKKG 172 (302)
Q Consensus 161 IEkELleRLk~G 172 (302)
.-+||...+..+
T Consensus 120 fP~EL~~~~~~~ 131 (233)
T PF11705_consen 120 FPKELWPTLRKK 131 (233)
T ss_pred ChHHHHhhcccc
Confidence 345666555443
No 48
>cd03469 Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the i
Probab=24.82 E-value=70 Score=25.26 Aligned_cols=34 Identities=9% Similarity=0.251 Sum_probs=23.4
Q ss_pred CCCcccccCCCCCCC----------CCCcceEEEeeCcEEEEEee
Q 022130 31 PYNVTGICNRSSCPL----------ANSRYATIRDHDGVFYLYMK 65 (302)
Q Consensus 31 eyNvTGlCnR~SCPL----------ANS~YATVre~~G~~yLymK 65 (302)
.|+++|-|-...|.- .-..| .|+..+|.+|+++-
T Consensus 69 ~Fd~~G~~~~~P~~~~~~~~~~~~~~L~~~-~v~~~~g~v~v~~~ 112 (118)
T cd03469 69 TYDLDGKLVGVPREEGFPGFDKEKLGLRTV-PVEEWGGLIFVNLD 112 (118)
T ss_pred EECCCCcEEeCCcccccCCCCHHHCCCeEE-EEEEECCEEEEEcC
Confidence 677778777665532 24567 56668899999875
No 49
>cd03528 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the in
Probab=24.37 E-value=77 Score=24.26 Aligned_cols=32 Identities=19% Similarity=0.300 Sum_probs=16.5
Q ss_pred CCCCc-ccccCCCCCCCCCCcceEEEeeCcEEEE
Q 022130 30 NPYNV-TGICNRSSCPLANSRYATIRDHDGVFYL 62 (302)
Q Consensus 30 NeyNv-TGlCnR~SCPLANS~YATVre~~G~~yL 62 (302)
-.|++ ||-|...-|+..--.|.+.. .+|.+|+
T Consensus 65 ~~fd~~~G~~~~~p~~~~L~~~~v~~-~~g~v~v 97 (98)
T cd03528 65 GRFDLRTGKALSLPATEPLKTYPVKV-EDGDVYV 97 (98)
T ss_pred CEEECCCCcccCCCCCCCcceEeEEE-ECCEEEE
Confidence 34555 66665555554455554333 3555543
No 50
>cd02683 MIT_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with unknown function, co-occuring with an as yet undescribed domain. The molecular function of the MIT domain is unclear.
Probab=23.24 E-value=1.9e+02 Score=22.54 Aligned_cols=40 Identities=13% Similarity=0.151 Sum_probs=26.3
Q ss_pred cHHHHHHHHHHhhcCCchHHHHHhhhH-HHHHHHHHHHHHHHHh
Q 022130 85 NYEKALEIIDKNLMYWPKFLVHKTKQR-LTKMTQMRIRMRKLAL 127 (302)
Q Consensus 85 Ny~kALeqId~~L~yWpkflihKcKQR-ltkltQ~liRmRkl~l 127 (302)
+|.+||+.+-..|.|=|.- +.|+. .+|+.+|+-|.-.|..
T Consensus 28 ~Y~~aie~l~~~lk~e~d~---~~k~~~r~ki~eY~~RAE~Lk~ 68 (77)
T cd02683 28 CYQEGIDLLMQVLKGTKDE---AKKKNLRQKISEYMDRAEAIKK 68 (77)
T ss_pred HHHHHHHHHHHHHhhCCCH---HHHHHHHHHHHHHHHHHHHHHH
Confidence 5667777777777666643 33444 4678888888777643
No 51
>smart00356 ZnF_C3H1 zinc finger.
Probab=22.23 E-value=74 Score=19.00 Aligned_cols=20 Identities=25% Similarity=0.653 Sum_probs=14.7
Q ss_pred CcCCCCCcccccCCC-CCCCCCC
Q 022130 27 FCRNPYNVTGICNRS-SCPLANS 48 (302)
Q Consensus 27 FCRNeyNvTGlCnR~-SCPLANS 48 (302)
.|+.= .+|.|++. +|+.+.+
T Consensus 6 ~C~~~--~~g~C~~g~~C~~~H~ 26 (27)
T smart00356 6 LCKFF--KRGYCPYGDRCKFAHP 26 (27)
T ss_pred cCcCc--cCCCCCCCCCcCCCCc
Confidence 56654 88999986 7987654
No 52
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=21.79 E-value=42 Score=39.60 Aligned_cols=83 Identities=18% Similarity=0.211 Sum_probs=0.0
Q ss_pred HHHhcCCCCCccccChHHHHHHHhhhhhccccchhh-hhhhhhhhhcCCCCcchhhhhhhhcccccCCCCCCCCCCCCCC
Q 022130 167 ERLKKGVYGDIYNYPADKYNEILDKEQLAADDIEED-EEEAEIEFVEGYDDLEEEEDIEDFGGLAVNKSSLDDDDVGLDD 245 (302)
Q Consensus 167 eRLk~G~YGd~yn~~~~~~~k~l~~~~~~~e~eeee-e~~~~~E~v~d~e~~~e~~d~ed~e~~~~~~~~~~~~~~~~~~ 245 (302)
.||-+|.--|-.|-.-..-+-+-..-..++..-+++ ++.++..-.+.++++++++|.+|++--...-.+++++++++..
T Consensus 1705 rrllsgnttndtnaDnEEregq~~ef~GEed~~Dddnddddddd~EaEdddDddDdDdeD~d~~aea~aEdEe~eEgdeh 1784 (3015)
T KOG0943|consen 1705 RRLLSGNTTNDTNADNEEREGQEGEFAGEEDHHDDDNDDDDDDDAEAEDDDDDDDDDDEDMDLDAEAAAEDEEDEEGDEH 1784 (3015)
T ss_pred hhhccCCccCccccchhhhcCCcccccCcccccccccccccccchhhccccccccccccccccchhhhhccccccccccc
Q ss_pred CCCc
Q 022130 246 NDDD 249 (302)
Q Consensus 246 ~~~~ 249 (302)
+.|+
T Consensus 1785 eQDe 1788 (3015)
T KOG0943|consen 1785 EQDE 1788 (3015)
T ss_pred cccc
No 53
>TIGR03031 cas_csx12 CRISPR-associated protein, Csx12 family. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to PFAM model pfam01844, HNH endonuclease.
Probab=21.76 E-value=51 Score=35.92 Aligned_cols=30 Identities=30% Similarity=0.483 Sum_probs=24.7
Q ss_pred ccccCCC-----CCC-CCCCcceEEEeeCcEEEEEe
Q 022130 35 TGICNRS-----SCP-LANSRYATIRDHDGVFYLYM 64 (302)
Q Consensus 35 TGlCnR~-----SCP-LANS~YATVre~~G~~yLym 64 (302)
||.|.-+ +|| |+|++|.+|..+.|-+-|-|
T Consensus 11 TGvfs~~~~~~a~l~~ldn~~~~v~~~d~~sf~lsq 46 (802)
T TIGR03031 11 TGVFSSHLEAFAELPNLDNTKYSVILIDHNSFQLSQ 46 (802)
T ss_pred ceeehhhHhhccCCcccccccCceEEEeCCceeehh
Confidence 6777655 898 99999999999988877765
No 54
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=21.55 E-value=2.8e+02 Score=20.61 Aligned_cols=41 Identities=17% Similarity=0.199 Sum_probs=25.3
Q ss_pred cHHHHHHHHHHhhcCCchHHHHHhhhH-HHHHHHHHHHHHHHHhh
Q 022130 85 NYEKALEIIDKNLMYWPKFLVHKTKQR-LTKMTQMRIRMRKLALK 128 (302)
Q Consensus 85 Ny~kALeqId~~L~yWpkflihKcKQR-ltkltQ~liRmRkl~l~ 128 (302)
.|..|++.+...+.+=|. ...|+. ..|+.+|+-|+-.|...
T Consensus 30 ~Y~~a~e~l~~~~~~~~~---~~~~~~~~~k~~eyl~raE~lk~~ 71 (77)
T smart00745 30 LYKKAIEYLLEGIKVESD---SKRREAVKAKAAEYLDRAEEIKKS 71 (77)
T ss_pred HHHHHHHHHHHHhccCCC---HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466777777776655443 222333 35777888888777544
No 55
>PF04159 NB: NB glycoprotein; InterPro: IPR007288 The NB glycoprotein is found in Influenza type B virus. Its function is unknown.; GO: 0016021 integral to membrane
Probab=21.53 E-value=46 Score=27.86 Aligned_cols=28 Identities=36% Similarity=0.713 Sum_probs=21.1
Q ss_pred CCCCcCCCCCcccccCCCCCC----CCCCcceEE
Q 022130 24 TGKFCRNPYNVTGICNRSSCP----LANSRYATI 53 (302)
Q Consensus 24 ~~~FCRNeyNvTGlCnR~SCP----LANS~YATV 53 (302)
+.|-|.| ||-|||.|--|| .+|-|=++-
T Consensus 45 nrnncTn--N~Igl~krIkcsgcEpFcnkR~dis 76 (100)
T PF04159_consen 45 NRNNCTN--NVIGLCKRIKCSGCEPFCNKRGDIS 76 (100)
T ss_pred ccccccc--chhheeeccccCCCcccccccCCcC
Confidence 5677876 999999999994 666665443
No 56
>COG3657 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.22 E-value=1.1e+02 Score=25.90 Aligned_cols=21 Identities=29% Similarity=0.453 Sum_probs=17.6
Q ss_pred HHHHhcCCCCCccccChHHHH
Q 022130 166 LERLKKGVYGDIYNYPADKYN 186 (302)
Q Consensus 166 leRLk~G~YGd~yn~~~~~~~ 186 (302)
|.||..|-.||.-.+.+.+|+
T Consensus 32 l~rl~~GN~GD~kpvgeGV~E 52 (100)
T COG3657 32 LDRLALGNFGDVKPVGEGVSE 52 (100)
T ss_pred HHHHhcCCCcCccccccchhh
Confidence 479999999998888777773
No 57
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.11 E-value=86 Score=27.44 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=6.3
Q ss_pred ccChHHHHH
Q 022130 179 NYPADKYNE 187 (302)
Q Consensus 179 n~~~~~~~k 187 (302)
.||...|+.
T Consensus 35 s~P~s~fe~ 43 (129)
T COG4530 35 SYPRSYFEE 43 (129)
T ss_pred cchHHHHHh
Confidence 458888765
No 58
>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=21.01 E-value=1.2e+02 Score=31.11 Aligned_cols=45 Identities=31% Similarity=0.454 Sum_probs=34.7
Q ss_pred CccHHHHHHHHHHhhcCCchHHHHH-----hhhHH-HHHHHHHHHHHHHHh
Q 022130 83 PRNYEKALEIIDKNLMYWPKFLVHK-----TKQRL-TKMTQMRIRMRKLAL 127 (302)
Q Consensus 83 s~Ny~kALeqId~~L~yWpkflihK-----cKQRl-tkltQ~liRmRkl~l 127 (302)
-.||++||.--...|.|+=..|..- +|+-+ .|.||||-|.-+|+.
T Consensus 23 a~nY~eA~~lY~~aleYF~~~lKYE~~~~kaKd~IraK~~EYLdRAEkLK~ 73 (439)
T KOG0739|consen 23 AKNYEEALRLYQNALEYFLHALKYEANNKKAKDSIRAKFTEYLDRAEKLKA 73 (439)
T ss_pred hhchHHHHHHHHHHHHHHHHHHHhhhcChhHHHHHHHHHHHHHHHHHHHHH
Confidence 3699999998888898876655543 55555 488999999998864
No 59
>smart00130 KR Kringle domain. Named after a Danish pastry. Found in several serine proteases and in ROR-like receptors. Can occur in up to 38 copies (in apolipoprotein(a)). Plasminogen-like kringles possess affinity for free lysine and lysine- containing peptides.
Probab=20.80 E-value=51 Score=25.87 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=9.5
Q ss_pred CCCCCcCCCCC
Q 022130 23 ETGKFCRNPYN 33 (302)
Q Consensus 23 ~~~~FCRNeyN 33 (302)
-..|||||+-+
T Consensus 47 ~~hNyCRNPd~ 57 (83)
T smart00130 47 LEENYCRNPDG 57 (83)
T ss_pred ccccccCCCCC
Confidence 47899999987
No 60
>PF11081 DUF2890: Protein of unknown function (DUF2890); InterPro: IPR021304 This entry contains the 33kDa and 22kDa phosphoproteins from vertebrate adenoviruses.
Probab=20.65 E-value=59 Score=30.09 Aligned_cols=7 Identities=29% Similarity=0.852 Sum_probs=3.4
Q ss_pred hhhhhhc
Q 022130 221 EDIEDFG 227 (302)
Q Consensus 221 ~d~ed~e 227 (302)
++|++||
T Consensus 36 e~~e~wE 42 (187)
T PF11081_consen 36 EEMEEWE 42 (187)
T ss_pred hhhhhhh
Confidence 4555553
No 61
>PF06204 CBM_X: Putative carbohydrate binding domain ; InterPro: IPR009342 This domain is conserved in enzymes that have carbohydrates as substrate, and may be a carbohydrate-binding domain.; PDB: 3ACT_B 2CQT_A 3QFY_B 3QFZ_A 2CQS_A 3QG0_B 3AFJ_A 3ACS_A 1V7V_A 1V7X_A ....
Probab=20.35 E-value=89 Score=24.04 Aligned_cols=23 Identities=26% Similarity=0.417 Sum_probs=19.3
Q ss_pred CCCCCCcceEEEeeCcEEEEEee
Q 022130 43 CPLANSRYATIRDHDGVFYLYMK 65 (302)
Q Consensus 43 CPLANS~YATVre~~G~~yLymK 65 (302)
.=|||-.|.+++.+.|--|.+.+
T Consensus 29 n~LsNg~y~~mvt~~G~GySw~~ 51 (66)
T PF06204_consen 29 NVLSNGSYGVMVTNSGSGYSWAK 51 (66)
T ss_dssp EEE-SSSEEEEEETTSBEEEEES
T ss_pred EEeeCCcEEEEEcCCCceeeccc
Confidence 34899999999999999998765
Done!