Query 003359
Match_columns 827
No_of_seqs 230 out of 399
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 22:01:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003359.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003359hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1525 Sister chromatid cohes 100.0 5.9E-51 1.3E-55 487.6 20.9 247 12-261 3-257 (1266)
2 KOG1525 Sister chromatid cohes 99.8 4.2E-21 9.1E-26 232.1 6.3 246 13-261 409-671 (1266)
3 PF09465 LBR_tudor: Lamin-B re 99.1 2.6E-10 5.5E-15 95.1 6.4 43 712-754 7-49 (55)
4 smart00333 TUDOR Tudor domain. 97.5 0.00022 4.9E-09 57.9 6.0 44 712-757 4-48 (57)
5 smart00743 Agenet Tudor-like d 97.4 0.00042 9.2E-09 57.6 5.9 36 712-748 4-39 (61)
6 cd04508 TUDOR Tudor domains ar 97.3 0.00064 1.4E-08 53.5 5.8 43 714-757 1-44 (48)
7 PF09038 53-BP1_Tudor: Tumour 96.1 0.01 2.2E-07 57.4 5.6 45 709-754 1-45 (122)
8 PF06003 SMN: Survival motor n 95.2 0.042 9E-07 59.0 6.8 46 712-757 70-116 (264)
9 KOG4675 Uncharacterized conser 94.1 0.015 3.3E-07 62.6 0.3 63 707-769 155-225 (273)
10 KOG1992 Nuclear export recepto 91.0 2.5 5.4E-05 52.0 12.9 117 118-239 603-731 (960)
11 PF03378 CAS_CSE1: CAS/CSE pro 84.5 12 0.00027 43.2 12.8 139 80-228 45-194 (435)
12 PF05641 Agenet: Agenet domain 82.6 2.5 5.3E-05 36.6 4.9 35 713-748 3-40 (68)
13 PF01602 Adaptin_N: Adaptin N 80.0 24 0.00051 40.0 12.8 25 68-92 274-298 (526)
14 PF15057 DUF4537: Domain of un 77.8 5.6 0.00012 38.5 6.0 42 714-756 1-42 (124)
15 PF14500 MMS19_N: Dos2-interac 75.4 26 0.00056 37.9 10.9 172 68-266 6-184 (262)
16 KOG1060 Vesicle coat complex A 74.8 28 0.0006 43.4 11.8 175 29-231 213-426 (968)
17 PF11717 Tudor-knot: RNA bindi 73.5 9.3 0.0002 31.9 5.5 37 713-750 3-41 (55)
18 PF12348 CLASP_N: CLASP N term 73.2 1.1E+02 0.0023 31.1 14.2 181 24-224 17-204 (228)
19 PF01602 Adaptin_N: Adaptin N 70.9 7.2 0.00016 44.0 5.7 115 68-203 121-241 (526)
20 KOG0644 Uncharacterized conser 70.2 5.4 0.00012 49.4 4.7 44 713-756 981-1036(1113)
21 KOG1949 Uncharacterized conser 69.1 86 0.0019 39.1 13.9 149 22-207 205-374 (1005)
22 PTZ00429 beta-adaptin; Provisi 68.8 1.3E+02 0.0029 37.4 16.0 146 59-230 256-401 (746)
23 PF02985 HEAT: HEAT repeat; I 68.5 2.7 5.8E-05 30.9 1.1 25 68-92 7-31 (31)
24 KOG1248 Uncharacterized conser 67.5 1.4E+02 0.0031 38.8 16.0 158 72-238 708-873 (1176)
25 PF00567 TUDOR: Tudor domain; 67.3 12 0.00026 33.2 5.3 47 710-757 51-98 (121)
26 KOG0915 Uncharacterized conser 66.0 50 0.0011 43.8 11.9 165 28-202 989-1196(1702)
27 KOG1248 Uncharacterized conser 65.4 1.1E+02 0.0025 39.6 14.6 194 28-238 200-395 (1176)
28 PF05918 API5: Apoptosis inhib 65.3 74 0.0016 38.4 12.5 143 8-163 173-318 (556)
29 KOG1060 Vesicle coat complex A 58.5 1.7E+02 0.0038 36.9 14.0 171 55-254 318-502 (968)
30 PF05327 RRN3: RNA polymerase 54.7 1.1E+02 0.0023 36.6 11.6 100 23-138 45-155 (563)
31 PF03224 V-ATPase_H_N: V-ATPas 53.7 2.3E+02 0.005 30.9 13.1 123 28-166 27-157 (312)
32 PF12717 Cnd1: non-SMC mitotic 53.6 1.2E+02 0.0026 30.4 10.1 77 71-164 73-159 (178)
33 KOG1241 Karyopherin (importin) 53.5 94 0.002 38.9 10.8 47 67-116 557-607 (859)
34 PF12755 Vac14_Fab1_bd: Vacuol 52.4 42 0.00091 31.3 6.2 60 68-135 34-94 (97)
35 PF12348 CLASP_N: CLASP N term 52.2 1.4E+02 0.003 30.3 10.5 115 77-202 23-140 (228)
36 KOG1488 Translational represso 51.3 52 0.0011 39.2 8.1 97 144-250 273-376 (503)
37 smart00139 MyTH4 Domain in Myo 50.1 2.2E+02 0.0049 28.2 11.2 101 149-256 18-128 (144)
38 KOG2023 Nuclear transport rece 50.1 54 0.0012 40.4 8.1 115 129-243 580-712 (885)
39 PF08605 Rad9_Rad53_bind: Fung 49.2 35 0.00075 33.9 5.4 32 719-750 16-47 (131)
40 PF12719 Cnd3: Nuclear condens 48.0 2.3E+02 0.0049 30.8 11.8 174 63-245 67-289 (298)
41 KOG3026 Splicing factor SPF30 47.9 19 0.00041 39.1 3.6 35 713-747 93-127 (262)
42 PF02237 BPL_C: Biotin protein 47.8 56 0.0012 26.6 5.5 39 713-754 2-40 (48)
43 KOG4256 Kinetochore component 47.3 1.9E+02 0.0041 37.8 12.0 95 65-170 498-618 (2209)
44 PF03224 V-ATPase_H_N: V-ATPas 46.8 76 0.0017 34.5 8.1 112 55-185 146-269 (312)
45 KOG0213 Splicing factor 3b, su 46.6 3.5E+02 0.0077 34.4 13.9 133 25-162 506-688 (1172)
46 COG5215 KAP95 Karyopherin (imp 46.4 1.8E+02 0.004 35.7 11.4 116 149-265 531-698 (858)
47 PTZ00429 beta-adaptin; Provisi 46.0 3E+02 0.0064 34.6 13.6 27 68-95 147-173 (746)
48 cd00256 VATPase_H VATPase_H, r 43.6 5.7E+02 0.012 30.2 14.7 94 74-187 157-260 (429)
49 PF11935 DUF3453: Domain of un 43.5 3.8E+02 0.0081 28.6 12.4 50 51-102 35-84 (239)
50 PF14911 MMS22L_C: S-phase gen 42.3 5.9E+02 0.013 29.6 14.4 123 23-165 223-347 (373)
51 KOG2171 Karyopherin (importin) 42.2 2.4E+02 0.0052 36.7 12.2 84 67-162 86-169 (1075)
52 PLN00104 MYST -like histone ac 42.0 40 0.00087 39.6 5.3 38 711-748 54-97 (450)
53 PF12612 TFCD_C: Tubulin foldi 41.7 1.5E+02 0.0032 30.4 8.8 112 77-205 23-139 (193)
54 PF13513 HEAT_EZ: HEAT-like re 41.6 41 0.00089 27.0 3.9 47 40-88 9-55 (55)
55 PF11864 DUF3384: Domain of un 41.5 4.8E+02 0.01 30.4 13.8 111 121-237 147-260 (464)
56 PF08767 CRM1_C: CRM1 C termin 41.5 5.3E+02 0.012 28.7 13.6 101 27-137 88-198 (319)
57 PF14911 MMS22L_C: S-phase gen 36.9 4.3E+02 0.0094 30.6 12.3 158 101-261 139-335 (373)
58 PF02565 RecO_C: Recombination 35.2 93 0.002 27.9 5.6 59 77-139 5-64 (118)
59 PF12074 DUF3554: Domain of un 35.2 6.5E+02 0.014 27.7 15.8 95 27-132 36-136 (339)
60 cd07920 Pumilio Pumilio-family 34.8 3.7E+02 0.0079 28.8 10.8 14 243-256 233-247 (322)
61 cd00020 ARM Armadillo/beta-cat 34.3 1E+02 0.0022 27.1 5.5 64 69-138 15-79 (120)
62 KOG2022 Nuclear transport rece 34.2 5.7E+02 0.012 33.0 13.4 183 56-257 702-919 (982)
63 KOG1949 Uncharacterized conser 33.9 3.3E+02 0.0071 34.4 11.1 152 63-224 173-369 (1005)
64 PF05327 RRN3: RNA polymerase 33.1 4.6E+02 0.01 31.5 12.3 107 82-202 281-394 (563)
65 PF05997 Nop52: Nucleolar prot 32.8 2.5E+02 0.0055 29.7 9.1 140 33-181 19-162 (217)
66 PF13001 Ecm29: Proteasome sta 32.8 2.3E+02 0.0049 33.5 9.6 121 143-264 264-412 (501)
67 PF08568 Kinetochor_Ybp2: Unch 32.5 5.3E+02 0.012 31.3 12.8 124 26-185 36-176 (633)
68 PF13764 E3_UbLigase_R4: E3 ub 32.5 3.3E+02 0.0072 34.5 11.2 221 17-262 44-304 (802)
69 PF12717 Cnd1: non-SMC mitotic 32.3 5.3E+02 0.012 25.9 11.4 103 74-186 1-113 (178)
70 KOG1062 Vesicle coat complex A 32.3 3.9E+02 0.0085 33.9 11.5 165 58-243 384-568 (866)
71 KOG2051 Nonsense-mediated mRNA 32.1 2.8E+02 0.0062 36.0 10.5 75 151-226 703-790 (1128)
72 PRK05686 fliG flagellar motor 31.8 4.6E+02 0.01 29.4 11.4 44 67-117 31-74 (339)
73 cd00280 TRFH Telomeric Repeat 31.3 2.7E+02 0.0059 29.7 8.8 101 54-162 32-139 (200)
74 KOG2062 26S proteasome regulat 30.9 3.7E+02 0.0081 34.0 10.9 51 195-246 292-342 (929)
75 KOG0211 Protein phosphatase 2A 30.9 1E+03 0.022 30.3 14.8 138 70-227 527-668 (759)
76 cd04405 RhoGAP_BRCC3-like RhoG 30.8 2.2E+02 0.0048 31.1 8.3 108 102-209 104-227 (235)
77 KOG4338 Predicted lipoprotein 30.7 2.2E+02 0.0047 38.5 9.5 173 8-254 319-493 (1680)
78 KOG0301 Phospholipase A2-activ 30.6 4.9E+02 0.011 32.6 11.8 125 27-163 539-685 (745)
79 PF01423 LSM: LSM domain ; In 29.9 68 0.0015 27.0 3.6 29 710-739 4-32 (67)
80 PF04118 Dopey_N: Dopey, N-ter 29.8 2.8E+02 0.006 31.2 9.1 41 97-138 127-168 (307)
81 PF02576 DUF150: Uncharacteris 29.8 88 0.0019 30.6 4.8 42 707-750 80-124 (141)
82 KOG1824 TATA-binding protein-i 29.4 1.1E+03 0.025 31.0 14.8 124 67-203 699-827 (1233)
83 KOG4327 mRNA splicing protein 28.6 52 0.0011 35.1 3.1 44 713-756 70-114 (218)
84 cd00600 Sm_like The eukaryotic 28.4 82 0.0018 26.0 3.8 29 710-739 2-30 (63)
85 PF00514 Arm: Armadillo/beta-c 28.3 32 0.0007 26.3 1.2 23 68-90 19-41 (41)
86 PRK14637 hypothetical protein; 28.3 1.1E+02 0.0023 30.9 5.2 33 706-738 90-122 (151)
87 smart00288 VHS Domain present 28.0 1.6E+02 0.0035 28.6 6.2 68 165-233 10-77 (133)
88 COG5096 Vesicle coat complex, 28.0 2.8E+02 0.0062 34.9 9.5 24 68-91 134-157 (757)
89 PF07039 DUF1325: SGF29 tudor- 27.3 1.2E+02 0.0026 29.8 5.2 39 713-751 74-113 (130)
90 KOG2259 Uncharacterized conser 26.8 4.3E+02 0.0094 33.1 10.5 96 149-257 411-510 (823)
91 cd00197 VHS_ENTH_ANTH VHS, ENT 26.6 1.4E+02 0.0031 27.7 5.4 60 174-234 19-78 (115)
92 PF11707 Npa1: Ribosome 60S bi 25.9 3.6E+02 0.0077 30.0 9.2 164 25-238 147-315 (330)
93 KOG0686 COP9 signalosome, subu 25.7 44 0.00096 39.0 2.2 116 75-204 269-396 (466)
94 PF08385 DHC_N1: Dynein heavy 25.4 9E+02 0.019 28.2 12.7 33 32-64 99-131 (579)
95 COG5231 VMA13 Vacuolar H+-ATPa 25.1 2.6E+02 0.0055 32.4 7.8 110 68-194 156-276 (432)
96 cd07958 Anticodon_Ia_Leu_BEm A 25.0 1.8E+02 0.004 25.9 5.7 29 77-105 87-115 (117)
97 PF10508 Proteasom_PSMB: Prote 24.7 7.1E+02 0.015 29.4 11.7 115 68-189 84-213 (503)
98 PF07637 PSD5: Protein of unkn 24.0 1.7E+02 0.0038 25.2 5.0 59 10-72 3-61 (64)
99 cd07920 Pumilio Pumilio-family 23.8 9.1E+02 0.02 25.8 11.9 139 99-258 141-291 (322)
100 PF08558 TRF: Telomere repeat 23.7 1.9E+02 0.0042 31.1 6.4 123 81-207 11-157 (238)
101 PF14868 DUF4487: Domain of un 23.4 7.1E+02 0.015 30.4 11.5 123 102-241 377-509 (559)
102 KOG2759 Vacuolar H+-ATPase V1 23.2 2.7E+02 0.006 32.9 7.8 103 72-188 168-274 (442)
103 cd07961 Anticodon_Ia_Ile_ABEc 22.8 47 0.001 33.1 1.6 27 79-105 112-138 (183)
104 PF08863 YolD: YolD-like prote 22.4 2.4E+02 0.0051 25.0 5.8 42 716-757 46-87 (92)
105 KOG1058 Vesicle coat complex C 22.2 1.9E+02 0.004 36.6 6.5 29 69-97 142-173 (948)
106 PF04286 DUF445: Protein of un 22.2 1E+03 0.022 25.8 12.4 45 215-261 301-345 (367)
107 cd03568 VHS_STAM VHS domain fa 21.7 2.2E+02 0.0047 28.4 5.9 69 164-233 9-77 (144)
108 PRK09618 flgD flagellar basal 21.4 1.6E+02 0.0035 29.8 4.9 42 709-751 87-128 (142)
109 PRK00737 small nuclear ribonuc 21.3 1.3E+02 0.0028 26.5 3.8 30 710-740 10-39 (72)
110 cd01731 archaeal_Sm1 The archa 21.1 1.4E+02 0.0029 25.9 3.8 30 710-740 6-35 (68)
111 PF15611 EH_Signature: EH_Sign 21.0 1.1E+03 0.024 26.2 11.8 110 83-206 106-225 (389)
112 COG5215 KAP95 Karyopherin (imp 20.9 1.7E+03 0.037 28.0 13.7 222 33-261 472-735 (858)
113 KOG2025 Chromosome condensatio 20.9 5.4E+02 0.012 32.6 9.8 72 146-218 75-147 (892)
114 PF10363 DUF2435: Protein of u 20.5 7E+02 0.015 23.2 8.6 82 155-237 3-87 (92)
115 cd08050 TAF6 TATA Binding Prot 20.4 1.3E+03 0.027 26.2 13.5 125 101-239 174-317 (343)
116 cd01717 Sm_B The eukaryotic Sm 20.4 1.3E+02 0.0029 26.8 3.7 30 710-740 6-35 (79)
117 PF10165 Ric8: Guanine nucleot 20.2 6.5E+02 0.014 29.4 10.2 44 226-269 307-351 (446)
No 1
>KOG1525 consensus Sister chromatid cohesion complex Cohesin, subunit PDS5 [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=5.9e-51 Score=487.57 Aligned_cols=247 Identities=34% Similarity=0.552 Sum_probs=234.4
Q ss_pred HHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhh
Q 003359 12 EQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRI 91 (827)
Q Consensus 12 ~~l~~~G~kLi~~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRI 91 (827)
++.-.-||+++..+++++|||+||++|++||++++|++.+ .++|.|++.+|++++||+|+|+|||+||||||+|||||
T Consensus 3 ~~~~~~g~~~~~~~~s~~ell~rLk~l~~~l~~~~qd~~~--~~~~~pl~~~l~~~~~L~h~d~dvrllvacCvseilRi 80 (1266)
T KOG1525|consen 3 EQFYPPGCLTSLNPISKDELLKRLKKLANCLASLDQDNLD--LASLLPLADHLIKDFLLKHKDKDVRLLVACCVSEILRI 80 (1266)
T ss_pred ccccCCCCccccCcccHHHHHHHHHHHHHHHhhcccCchh--HHHHHHHHHHHhhHHHhcCCCcChhHHHHHHHHHHHHH
Confidence 3455679999999999999999999999999999999966 99999999999999999999999999999999999999
Q ss_pred cCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHHHhhcCCchh
Q 003359 92 TAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHF 171 (827)
Q Consensus 92 yAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr~~hp~k 171 (827)
|||||||++.||+|||+||++||.||.|+.+|||.|||||||+||+||.|++|.|.+|++|+.+||++||+++|.+||.+
T Consensus 81 ~aPeaPy~~~~lkdIf~~~~~q~~gL~d~~sp~f~r~~~lletl~~~k~~l~~~l~d~~e~~~~~f~~f~d~~~~~~~~~ 160 (1266)
T KOG1525|consen 81 YAPEAPYTDEQLKDIFQLILSQFSGLGDVESPYFKRYFYLLETLAKVKFCLLMLLEDCQELVHELFRTFFDLARKGHPKK 160 (1266)
T ss_pred hCCCCCCcHHHHHHHHHHHHHHHhhccCCCCcchhhHHHHHHHHHHhHHHheeeccchHHHHHHHHHHHHHHHhccccHH
Confidence 99999999999999999999999999999999999999999999999977777777899999999999999999999999
Q ss_pred HHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHHHHHHHHHHhc-------CCC-C
Q 003359 172 VFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSR-------GIA-L 243 (827)
Q Consensus 172 V~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLqp~I~q~l~S~-------Gi~-l 243 (827)
|+. |.+||+.+|.|.+.||.++|++||.+|+++.+++.+.|+.||..+|..|++.+.+.|++||++. +++ .
T Consensus 161 v~~-~~~i~~~li~e~d~v~~e~L~~ll~~lv~~~~~~~~~a~~la~~li~~~a~~~~~~i~~f~~~~~~~~~s~~~~~~ 239 (1266)
T KOG1525|consen 161 VFN-MLDIAIMLITEEDTVQSELLDVLLENLVKPGRDTIKEADKLASDLIERCADNLEDTIANFLNSCLTEYKSRQSSLK 239 (1266)
T ss_pred HHH-HHHHHHHHHHhhccchHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHhhhhhchhHHHHHHHHHhhccccccchh
Confidence 999 9999999999999999999999999999999999999999999999999999999999999974 222 3
Q ss_pred chhHHHHHHHhccCCCCC
Q 003359 244 DDYAEIVACICGSDDENP 261 (827)
Q Consensus 244 d~Y~eIV~sI~q~~s~~l 261 (827)
..||+||+.+-.+++..|
T Consensus 240 ~~~he~i~~L~~~~p~ll 257 (1266)
T KOG1525|consen 240 IKYHELILELWRIAPQLL 257 (1266)
T ss_pred hHHHHHHHHHHHhhHHHH
Confidence 789999999999887765
No 2
>KOG1525 consensus Sister chromatid cohesion complex Cohesin, subunit PDS5 [Cell cycle control, cell division, chromosome partitioning]
Probab=99.82 E-value=4.2e-21 Score=232.14 Aligned_cols=246 Identities=31% Similarity=0.370 Sum_probs=231.3
Q ss_pred HHHHhccccCCCCCC--HHHHHHHHHHH--------HHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhh
Q 003359 13 QLKDAGNLLLNPPSP--VDEVINLLDKV--------EHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVT 82 (827)
Q Consensus 13 ~l~~~G~kLi~~piS--~dELLKRLkkL--------~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVA 82 (827)
++..+|.+.+.++++ .++||..+-+. +-.|..+.|....++.+++.+++..|+.=.+..|++-++.+-..
T Consensus 409 ~~~~~~~k~~t~~~swIp~kLL~~~y~~~~~~r~~vE~il~~~L~P~~l~~q~Rmk~l~~~l~~~D~~a~kaf~~i~~~q 488 (1266)
T KOG1525|consen 409 CLRSAGGKEITPPFSWIPDKLLHLYYENDLDDRLLVERILAEYLVPYPLSTQERMKHLYQLLAGLDLNAHKAFNEILKRQ 488 (1266)
T ss_pred HhhccCcccccccccccchhHHhhHhhccccHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHhcccHhhhhHHHHHHHHH
Confidence 677899999999999 99999999877 78888889988888999999999999999999999999999999
Q ss_pred HHHHHHhh--hcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHH--HHHHHhhhhcceeeeccC---CchHHHHH
Q 003359 83 SCISEITR--ITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKAL--SILDTVAKVRSCLLMLDL---ECDKLVVE 155 (827)
Q Consensus 83 cCLADILR--IyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~--yLLEsLAeVKS~VLmlDL---e~ddLI~e 155 (827)
.||.+++| |.+|..||+++.|+.||..|+..+..|.|+.+..|.... .+|+.++.+++|+.|++. .|.++...
T Consensus 489 ~~ls~~vr~~I~~~k~~~~d~~~k~i~~~i~~i~~~lpD~~s~~~~~~~f~~~L~~~~~~~s~~~~L~~~~~~C~~l~~~ 568 (1266)
T KOG1525|consen 489 SRLSEEVRDYITLSKTPNTDDSMKKIFSKIVKISENLPDPSSRSYDSMKFADVLETLAKVRSCLVSLDSPSISCKELLIT 568 (1266)
T ss_pred HHHHHHHHHHhccccCCCccHhHHHHHHHHHHHHHhcCCchhhhhHHHHHHHHHHHHHHHHHHHHHHhccchhHHHHHHH
Confidence 99999999 999999999999999999999999999999887655544 599999999999999994 59999999
Q ss_pred HHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHHHHHHHH
Q 003359 156 MFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEA 235 (827)
Q Consensus 156 LFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLqp~I~q~ 235 (827)
||+.||..++..++.+++..|..+|++.|.+ |+.+++..|+..+...+......+..+++.|+..|+-++..|+.+.
T Consensus 569 v~~~l~e~~~~~~s~nlF~~~~~~li~~I~~---v~~di~~s~~~~ik~~~~~i~~~~~~l~e~v~~~~a~kl~~~lle~ 645 (1266)
T KOG1525|consen 569 VKEILFELGRKKQSKNLFSSMEKELIERIAE---VSLDILESISALIKLNNIVIAEVSLLLLEGVLSEKALKLKKYLLEA 645 (1266)
T ss_pred HHHHHHHHhhhccccchHHHHHHHHHHHhcc---hhhhhHHHHHHHHhhhhhhHHHHHhhcccccchhhHHhHHHHHHHH
Confidence 9999999999999999999999999999999 9999999999999888888899999999999999999999999999
Q ss_pred HHhcCCCCchhHHHHHHHhccCCCCC
Q 003359 236 VQSRGIALDDYAEIVACICGSDDENP 261 (827)
Q Consensus 236 l~S~Gi~ld~Y~eIV~sI~q~~s~~l 261 (827)
|.+.|..++-|++++.+||++.....
T Consensus 646 ls~~~~~~~~~s~~v~~i~~~~~~~~ 671 (1266)
T KOG1525|consen 646 LSSIHPDLFKYSESVLSILEKLFSEP 671 (1266)
T ss_pred hhhcCcchhhhhHHHHHHHHHhccch
Confidence 99999999999999999999998877
No 3
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=99.07 E-value=2.6e-10 Score=95.06 Aligned_cols=43 Identities=35% Similarity=0.676 Sum_probs=35.9
Q ss_pred cccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCCeeee
Q 003359 712 LVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDEEIL 754 (827)
Q Consensus 712 lVG~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YDDGD~E~L 754 (827)
..|.+|++|||++..||+|+|++||+.+..|+|.|+||++..|
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel~l 49 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTELEL 49 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EEEE
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEEEe
Confidence 3799999999999999999999999999999999999999544
No 4
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=97.51 E-value=0.00022 Score=57.87 Aligned_cols=44 Identities=23% Similarity=0.530 Sum_probs=39.8
Q ss_pred cccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccC-CCeeeeecC
Q 003359 712 LVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYAD-GDEEILNLK 757 (827)
Q Consensus 712 lVG~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YDD-GD~E~L~L~ 757 (827)
-+|..|.+.| .|..||.|+|+.+++. +...|.|.| |..+++.+.
T Consensus 4 ~~G~~~~a~~-~d~~wyra~I~~~~~~-~~~~V~f~D~G~~~~v~~~ 48 (57)
T smart00333 4 KVGDKVAARW-EDGEWYRARIIKVDGE-QLYEVFFIDYGNEEVVPPS 48 (57)
T ss_pred CCCCEEEEEe-CCCCEEEEEEEEECCC-CEEEEEEECCCccEEEeHH
Confidence 4799999999 9999999999999987 889999998 999988753
No 5
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=97.36 E-value=0.00042 Score=57.55 Aligned_cols=36 Identities=19% Similarity=0.337 Sum_probs=33.6
Q ss_pred cccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccC
Q 003359 712 LVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYAD 748 (827)
Q Consensus 712 lVG~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YDD 748 (827)
.+|.+|.+||+.+..||.|+|+.+++ .+++.|.|++
T Consensus 4 ~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V~~~~ 39 (61)
T smart00743 4 KKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLVRYLT 39 (61)
T ss_pred CCCCEEEEEECCCCEEEEEEEEEECC-CCEEEEEECC
Confidence 48999999999999999999999998 6789999998
No 6
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=97.28 E-value=0.00064 Score=53.50 Aligned_cols=43 Identities=19% Similarity=0.411 Sum_probs=38.4
Q ss_pred cCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccC-CCeeeeecC
Q 003359 714 GSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYAD-GDEEILNLK 757 (827)
Q Consensus 714 G~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YDD-GD~E~L~L~ 757 (827)
|..|.+.|++|..||.|+|..+++ .+.-.|.|.| |..+.+.+.
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~-~~~~~V~f~DyG~~~~v~~~ 44 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILS-DGKVEVFFVDYGNTEVVPLS 44 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECC-CCcEEEEEEcCCCcEEEeHH
Confidence 678999999999999999999998 7778899998 999988654
No 7
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=96.10 E-value=0.01 Score=57.35 Aligned_cols=45 Identities=24% Similarity=0.475 Sum_probs=34.8
Q ss_pred ccccccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCCeeee
Q 003359 709 NEQLVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDEEIL 754 (827)
Q Consensus 709 ge~lVG~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YDDGD~E~L 754 (827)
|.++||.||---|-.+.-||.|+|+.. ....+.+|.+|||.+..|
T Consensus 1 ~~~~iG~rV~AkWS~n~yyY~G~I~~~-~~~~kykv~FdDG~~~~v 45 (122)
T PF09038_consen 1 GSSFIGLRVFAKWSDNGYYYPGKITSD-KGKNKYKVLFDDGYECRV 45 (122)
T ss_dssp ---STT-EEEEESSTTSEEEEEEEEEE-ETTTEEEEEETTS-EEEE
T ss_pred CCcccccEEEEEEccCCcccCceEeec-CCCCeEEEEecCCcccee
Confidence 567999999999997777799999995 667899999999998644
No 8
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=95.23 E-value=0.042 Score=59.02 Aligned_cols=46 Identities=22% Similarity=0.434 Sum_probs=39.8
Q ss_pred cccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEcc-CCCeeeeecC
Q 003359 712 LVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYA-DGDEEILNLK 757 (827)
Q Consensus 712 lVG~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YD-DGD~E~L~L~ 757 (827)
-||-+|+..|-.|..||.++|++.+...+.-.|+|. -|..|.+.|.
T Consensus 70 kvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~ 116 (264)
T PF06003_consen 70 KVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLS 116 (264)
T ss_dssp -TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGG
T ss_pred CCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehh
Confidence 399999999999999999999999999999999998 5788888886
No 9
>KOG4675 consensus Uncharacterized conserved protein, contains ENT domain [General function prediction only]
Probab=94.14 E-value=0.015 Score=62.63 Aligned_cols=63 Identities=24% Similarity=0.425 Sum_probs=50.2
Q ss_pred ccccccccCeEEEeeCCCCceEEEEEEEecC-CCCeEEEEccCCC----eeeeecC---CccEEEecCCCC
Q 003359 707 ALNEQLVGSRIKVWWPMDETFYKGVVDNYDP-IKKKHRILYADGD----EEILNLK---KERWELIKGGSS 769 (827)
Q Consensus 707 ~~ge~lVG~RVkV~WP~D~~wY~G~V~sYd~-~tkkH~V~YDDGD----~E~L~L~---~Ek~e~l~~d~~ 769 (827)
..++.+||++|-.-||+++.||++.|+.|+. ....|.+.||-.+ .+|++|. .+.++|...+.+
T Consensus 155 ~pp~slvgr~v~~k~pdk~~~te~iit~~~~~~E~~~~l~~~~~~~~~p~~wvdl~~I~p~DIrw~g~~~~ 225 (273)
T KOG4675|consen 155 VPPESLVGRKVWIKWPDKRKFTEAIITQYDAEKEGHHLLVPDINDCNDPWEWVDLREISPEDIRWEGGDPG 225 (273)
T ss_pred CCchhhccccccccCcccccccccccccchhhhhhhhhcccccccccCCccccccccCCHHhccccCCCCC
Confidence 3456799999999999999999999999555 5567889998443 4677775 688888877655
No 10
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=91.04 E-value=2.5 Score=51.98 Aligned_cols=117 Identities=9% Similarity=0.123 Sum_probs=74.2
Q ss_pred CCCCCcchHHHHHHHHHhhhhcceeeeccCC---chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCC-CcHH
Q 003359 118 SHASGRYYMKALSILDTVAKVRSCLLMLDLE---CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESED-VSWD 193 (827)
Q Consensus 118 aD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe---~ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~-VP~e 193 (827)
.+|++|-| ++||+|+++-+= ...++-+ --.+...||=.|-.+.+.+. .+...+...||+.+++-+.. +|..
T Consensus 603 KNPs~P~f--nHYLFEsi~~li--~~t~~~~~~~vs~~e~aL~p~fq~Il~eDI-~EfiPYvfQlla~lve~~~~~ip~~ 677 (960)
T KOG1992|consen 603 KNPSNPQF--NHYLFESIGLLI--RKTCKANPSAVSSLEEALFPVFQTILSEDI-QEFIPYVFQLLAVLVEHSSGTIPDS 677 (960)
T ss_pred cCCCCchh--HHHHHHHHHHHH--HHHhccCchHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhcCCCCchh
Confidence 45667765 578999987651 1122333 12466777755555545443 34556777899999998876 7776
Q ss_pred HH---HHHHHHhhccCCCCChhhHHHHHHHHhhchHHHH-----HHHHHHHHhc
Q 003359 194 LL---RILLASVRKENQDVSPTSWKLGEKVFTKCAAKLK-----TNLKEAVQSR 239 (827)
Q Consensus 194 LL---DvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLq-----p~I~q~l~S~ 239 (827)
.. -+||+.-+..-..+.|+.-+|-..+|...+..+. .+|-.+|+.+
T Consensus 678 ~~~l~~~lLsp~lW~r~gNipalvrLl~aflk~g~~~~~~~~~l~~iLGifqkL 731 (960)
T KOG1992|consen 678 YSPLFPPLLSPNLWKRSGNIPALVRLLQAFLKTGSQIVEAADKLSGILGIFQKL 731 (960)
T ss_pred HHHHHHHhcCHHHHhhcCCcHHHHHHHHHHHhcCchhhcccccchhHHHHHHHH
Confidence 44 3344444445578889999998888887766554 3455666654
No 11
>PF03378 CAS_CSE1: CAS/CSE protein, C-terminus; InterPro: IPR005043 Mammalian cellular apoptosis susceptibility (CAS) proteins and the yeast chromosome-segregation protein, CSE1 are homologous []. CAS is involved in both cellular apoptosis and proliferation [, ]. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle [], as is the protein MEK, which is thought to regulate the intracellular localization (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway []. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins []. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins []. This entry represents the C-terminal portion of these proteins. Structural studies of the yeast CSE1 protein indicate that this domain binds to both the transport-orchestrating protein RanGTP and the cargo molecule that is being exported [].; GO: 0005515 protein binding; PDB: 1Z3H_B 1WA5_C.
Probab=84.51 E-value=12 Score=43.19 Aligned_cols=139 Identities=13% Similarity=0.237 Sum_probs=83.2
Q ss_pred hhhHHHHHHhhhcCCC-CCCCchHHHHHHHHHHHHhccc-CCCCCcchHHHHHHHHHhhhh-cceeeeccCCch---HHH
Q 003359 80 SVTSCISEITRITAPD-SPYDDELMKEFFQLAVSAFENL-SHASGRYYMKALSILDTVAKV-RSCLLMLDLECD---KLV 153 (827)
Q Consensus 80 yVAcCLADILRIyAPD-APYtDdqLKDIF~LfV~qf~~L-aD~ssp~F~q~~yLLEsLAeV-KS~VLmlDLe~d---dLI 153 (827)
|+.=||+=|+=++.-+ .||.+.-| +.++..|... .+|++|.|. +|+.|+|+.+ |. +++-+.+ .+-
T Consensus 45 ylMk~iMRvl~~~~e~~~p~~~~il----~~L~~il~~v~kNPsnP~Fn--HylFEsi~~lir~---~~~~~~~~v~~~E 115 (435)
T PF03378_consen 45 YLMKCIMRVLSVLQEDILPIAVEIL----QHLTAILKEVSKNPSNPRFN--HYLFESIGALIRF---VCEADPEAVSQFE 115 (435)
T ss_dssp HHHHHHHHHHHHSTTTTGGGHHHHH----HHHHHHHHHHHTS---HHHH--HHHHHHHHHHHHH---S-GGGHH---HHH
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHH----HHHHHHHHHHHhCCCCcchh--hhHHHHHHHHHHh---ccCCChhHHHHHH
Confidence 6677777776655555 56644222 2222222211 358889884 5788998876 42 2222222 456
Q ss_pred HHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccC--CCc---HHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHH
Q 003359 154 VEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESE--DVS---WDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKL 228 (827)
Q Consensus 154 ~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE--~VP---~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKL 228 (827)
..||-.|..+...+.. +...+.-.||+.+++-.. .+| ..++..||...+.+.+++.|+.-+|-...|..++..+
T Consensus 116 ~~L~P~f~~ILq~dV~-EF~PYvfQIla~Lle~~~~~~~p~~y~~L~~~Ll~p~lWe~~gniPalvrLL~a~i~k~~~~i 194 (435)
T PF03378_consen 116 EALFPPFQEILQQDVQ-EFIPYVFQILAQLLELRPSSPLPDAYKQLFPPLLSPALWERRGNIPALVRLLQAYIKKDPSFI 194 (435)
T ss_dssp HHHHHHHHHHHHTT-T-TTHHHHHHHHHHHHHHSS--S--TTTGGGHHHHTSGGGGGSTTTHHHHHHHHHHHHHHHGGG-
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHcCcchhccCCCcCcHHHHHHHHHHhCchhh
Confidence 6666666666665543 344555677888887655 455 4577888888888888889998889888888888765
No 12
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=82.64 E-value=2.5 Score=36.55 Aligned_cols=35 Identities=20% Similarity=0.225 Sum_probs=27.3
Q ss_pred ccCeEEEeeCCC---CceEEEEEEEecCCCCeEEEEccC
Q 003359 713 VGSRIKVWWPMD---ETFYKGVVDNYDPIKKKHRILYAD 748 (827)
Q Consensus 713 VG~RVkV~WP~D---~~wY~G~V~sYd~~tkkH~V~YDD 748 (827)
.|.+|+|+--.+ .+||.|+|....... +..|.|+|
T Consensus 3 ~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~-~~~V~Y~~ 40 (68)
T PF05641_consen 3 KGDEVEVSSDEDGFRGAWFPATVLKENGDD-KYLVEYDD 40 (68)
T ss_dssp TT-EEEEEE-SBTT--EEEEEEEEEEETT--EEEEEETT
T ss_pred CCCEEEEEEcCCCCCcEEEEEEEEEeCCCc-EEEEEECC
Confidence 589999988764 599999999999865 99999963
No 13
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=79.96 E-value=24 Score=39.98 Aligned_cols=25 Identities=28% Similarity=0.412 Sum_probs=22.0
Q ss_pred hhccCCCcCchhhhhHHHHHHhhhc
Q 003359 68 DLLRRSDMDVRLSVTSCISEITRIT 92 (827)
Q Consensus 68 ~LLkHkDkdVRayVAcCLADILRIy 92 (827)
.||.++|..||..+..||..|.+.+
T Consensus 274 ~lL~s~~~nvr~~~L~~L~~l~~~~ 298 (526)
T PF01602_consen 274 KLLSSSDPNVRYIALDSLSQLAQSN 298 (526)
T ss_dssp HHHTSSSHHHHHHHHHHHHHHCCHC
T ss_pred HHhhcccchhehhHHHHHHHhhccc
Confidence 5778999999999999999999885
No 14
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=77.79 E-value=5.6 Score=38.54 Aligned_cols=42 Identities=19% Similarity=0.374 Sum_probs=35.9
Q ss_pred cCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCCeeeeec
Q 003359 714 GSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDEEILNL 756 (827)
Q Consensus 714 G~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YDDGD~E~L~L 756 (827)
|.+|=..|+.|.-||.|+|..+- ..+...|.+++|+.+.+..
T Consensus 1 g~~VlAR~~~DG~YY~GtV~~~~-~~~~~lV~f~~~~~~~v~~ 42 (124)
T PF15057_consen 1 GQKVLARREEDGFYYPGTVKKCV-SSGQFLVEFDDGDTQEVPI 42 (124)
T ss_pred CCeEEEeeCCCCcEEeEEEEEcc-CCCEEEEEECCCCEEEeCh
Confidence 78899999999999999999998 5677888888888776543
No 15
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=75.39 E-value=26 Score=37.93 Aligned_cols=172 Identities=11% Similarity=0.179 Sum_probs=102.3
Q ss_pred hhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccC
Q 003359 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDL 147 (827)
Q Consensus 68 ~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDL 147 (827)
..|.+.|..+|+-.--||+++|-=+.|+. .+..|..-++.||.+-| .|.. .+...|.-+...+-|-.+
T Consensus 6 ~~Ltsed~~~R~ka~~~Ls~vL~~lp~~~-L~~~ev~~L~~F~~~rl---~D~~--------~~~~~l~gl~~L~~~~~~ 73 (262)
T PF14500_consen 6 EYLTSEDPIIRAKALELLSEVLERLPPDF-LSRQEVQVLLDFFCSRL---DDHA--------CVQPALKGLLALVKMKNF 73 (262)
T ss_pred hhhCCCCHHHHHHHHHHHHHHHHhCCHhh-ccHHHHHHHHHHHHHHh---ccHh--------hHHHHHHHHHHHHhCcCC
Confidence 46788999999999999999997655544 78899999999999866 3332 222223333333334444
Q ss_pred CchHHHHHHHHHHHHHhh-cCCchhHHHHHHHHHHHHhcc----cCCCcHHHHHHHHHHhhccCCCC--ChhhHHHHHHH
Q 003359 148 ECDKLVVEMFQHFLKVIR-SNHPHFVFAAMETIMTLVIDE----SEDVSWDLLRILLASVRKENQDV--SPTSWKLGEKV 220 (827)
Q Consensus 148 e~ddLI~eLFktFFdiVr-~~hp~kV~~~M~dILs~VIeE----sE~VP~eLLDvIL~~ll~~~ks~--~PaAy~LA~~V 220 (827)
.. +.+..|.+.||+-+. ..++...+...-.||..+++. ...+..+.+..++..+ .+.++. .-.
T Consensus 74 ~~-~~~~~i~~~l~~~~~~q~~~q~~R~~~~~ll~~l~~~~~~~l~~~~~~fv~~~i~~~-~gEkDPRnLl~-------- 143 (262)
T PF14500_consen 74 SP-ESAVKILRSLFQNVDVQSLPQSTRYAVYQLLDSLLENHREALQSMGDDFVYGFIQLI-DGEKDPRNLLL-------- 143 (262)
T ss_pred Ch-hhHHHHHHHHHHhCChhhhhHHHHHHHHHHHHHHHHHhHHHHHhchhHHHHHHHHHh-ccCCCHHHHHH--------
Confidence 32 225555555554332 346666666666666665554 3456777777776644 333332 222
Q ss_pred HhhchHHHHHHHHHHHHhcCCCCchhHHHHHHHhccCCCCCCCCCc
Q 003359 221 FTKCAAKLKTNLKEAVQSRGIALDDYAEIVACICGSDDENPQHGHL 266 (827)
Q Consensus 221 I~~CadKLqp~I~q~l~S~Gi~ld~Y~eIV~sI~q~~s~~l~~~~~ 266 (827)
.++|-+.|.+.|.- +-..+++.+|++.-|=++..-..+|..
T Consensus 144 ----~F~l~~~i~~~~~~-~~~~e~lFd~~~cYFPI~F~pp~~dp~ 184 (262)
T PF14500_consen 144 ----SFKLLKVILQEFDI-SEFAEDLFDVFSCYFPITFRPPPNDPY 184 (262)
T ss_pred ----HHHHHHHHHHhccc-chhHHHHHHHhhheeeeeeeCCCCCCC
Confidence 33444444444441 223456677777777777776666653
No 16
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=74.83 E-value=28 Score=43.41 Aligned_cols=175 Identities=18% Similarity=0.278 Sum_probs=108.4
Q ss_pred HHHHHHHHHHHHHHHhccc-CCchhhHHhhHH-HHHhhhhhhh--------------------cc---CCCcCchhhhhH
Q 003359 29 DEVINLLDKVEHLLANVEQ-APSRSMRDALLP-TMKGLITNDL--------------------LR---RSDMDVRLSVTS 83 (827)
Q Consensus 29 dELLKRLkkL~~eLs~lDQ-~~vdS~~~SL~p-l~k~LVs~~L--------------------Lk---HkDkdVRayVAc 83 (827)
+=|-+--++|+..|-+||. +++- +.+-|.. .+..|+.+.. .+ +-|.|+|+++-|
T Consensus 213 dLIHknyrklC~ll~dvdeWgQvv-lI~mL~RYAR~~l~~P~~~~~~~e~n~~~~~~~~~~~~~~~P~~~d~D~~lLL~s 291 (968)
T KOG1060|consen 213 DLIHKNYRKLCRLLPDVDEWGQVV-LINMLTRYARHQLPDPTVVDSSLEDNGRSCNLKDKYNEIRTPYVNDPDLKLLLQS 291 (968)
T ss_pred HHhhHHHHHHHhhccchhhhhHHH-HHHHHHHHHHhcCCCccccccccccCcccccccccccccCCCcccCccHHHHHHh
Confidence 4455666788888877754 3332 2333333 3456776633 12 238888877532
Q ss_pred --------------HHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCc
Q 003359 84 --------------CISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLEC 149 (827)
Q Consensus 84 --------------CLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ 149 (827)
..|.++-+.||-. |+.-|-+-+|+.|+. +... ++-+|.++|.+-.- -
T Consensus 292 tkpLl~S~n~sVVmA~aql~y~lAP~~-----~~~~i~kaLvrLLrs--~~~v-----qyvvL~nIa~~s~~-------~ 352 (968)
T KOG1060|consen 292 TKPLLQSRNPSVVMAVAQLFYHLAPKN-----QVTKIAKALVRLLRS--NREV-----QYVVLQNIATISIK-------R 352 (968)
T ss_pred ccHHHhcCCcHHHHHHHhHHHhhCCHH-----HHHHHHHHHHHHHhc--CCcc-----hhhhHHHHHHHHhc-------c
Confidence 2356777777754 788887777776652 2222 23567777765211 2
Q ss_pred hHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHH
Q 003359 150 DKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLK 229 (827)
Q Consensus 150 ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLq 229 (827)
..|+.-.|+.|| |+..-|..+-..-..||+.+++|+. -..+|..+..++...+.. . + ..|..-|.+|+..+-
T Consensus 353 ~~lF~P~lKsFf--v~ssDp~~vk~lKleiLs~La~esn--i~~ILrE~q~YI~s~d~~-f-a--a~aV~AiGrCA~~~~ 424 (968)
T KOG1060|consen 353 PTLFEPHLKSFF--VRSSDPTQVKILKLEILSNLANESN--ISEILRELQTYIKSSDRS-F-A--AAAVKAIGRCASRIG 424 (968)
T ss_pred hhhhhhhhhceE--eecCCHHHHHHHHHHHHHHHhhhcc--HHHHHHHHHHHHhcCchh-H-H--HHHHHHHHHHHHhhC
Confidence 356777777777 6777788888888999999999953 345666666666655552 2 2 245566888988754
Q ss_pred HH
Q 003359 230 TN 231 (827)
Q Consensus 230 p~ 231 (827)
..
T Consensus 425 sv 426 (968)
T KOG1060|consen 425 SV 426 (968)
T ss_pred ch
Confidence 33
No 17
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=73.53 E-value=9.3 Score=31.89 Aligned_cols=37 Identities=14% Similarity=0.273 Sum_probs=31.1
Q ss_pred ccCeEEEeeCCCCceEEEEEEEecCCCC--eEEEEccCCC
Q 003359 713 VGSRIKVWWPMDETFYKGVVDNYDPIKK--KHRILYADGD 750 (827)
Q Consensus 713 VG~RVkV~WP~D~~wY~G~V~sYd~~tk--kH~V~YDDGD 750 (827)
||.+|.++| .+..||.++|.......+ ...|.|..=+
T Consensus 3 vG~~v~~~~-~~~~~y~A~I~~~r~~~~~~~YyVHY~g~n 41 (55)
T PF11717_consen 3 VGEKVLCKY-KDGQWYEAKILDIREKNGEPEYYVHYQGWN 41 (55)
T ss_dssp TTEEEEEEE-TTTEEEEEEEEEEEECTTCEEEEEEETTST
T ss_pred cCCEEEEEE-CCCcEEEEEEEEEEecCCCEEEEEEcCCCC
Confidence 899999999 899999999999988653 6778887433
No 18
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=73.19 E-value=1.1e+02 Score=31.13 Aligned_cols=181 Identities=12% Similarity=0.163 Sum_probs=82.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHhc-ccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchH
Q 003359 24 PPSPVDEVINLLDKVEHLLANV-EQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL 102 (827)
Q Consensus 24 ~piS~dELLKRLkkL~~eLs~l-DQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdq 102 (827)
...+-++-+.-|+.|...+..- .+.........|..+...| ...+. ....-|-.-++-||.+|.+.+.. .
T Consensus 17 ~~~~W~~r~~al~~L~~l~~~~~~~~~~~~~~~~l~~~~~~i-~~~l~-d~Rs~v~~~A~~~l~~l~~~l~~-------~ 87 (228)
T PF12348_consen 17 SESDWEERVEALQKLRSLIKGNAPEDFPPDFVECLRQLLDAI-IKQLS-DLRSKVSKTACQLLSDLARQLGS-------H 87 (228)
T ss_dssp T-SSHHHHHHHHHHHHHHHHH-B-----HHHHHHHH---HHH-HH-S--HH---HHHHHHHHHHHHHHHHGG-------G
T ss_pred CccCHHHHHHHHHHHHHHHHcCCccccHHHHHHHHHHhHHHH-HHHHh-hhHHHHHHHHHHHHHHHHHHHhH-------h
Confidence 3445666666666666666654 2222222233333222222 22222 22233445566678888888543 3
Q ss_pred HHHHHHHHHHH-hcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHH
Q 003359 103 MKEFFQLAVSA-FENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMT 181 (827)
Q Consensus 103 LKDIF~LfV~q-f~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs 181 (827)
+...+..++.. |..+++............|..+...=++ ...++ +..+... ..+.+..|+......|.
T Consensus 88 ~~~~~~~~l~~Ll~~~~~~~~~i~~~a~~~L~~i~~~~~~-------~~~~~---~~~l~~~-~~~Kn~~vR~~~~~~l~ 156 (228)
T PF12348_consen 88 FEPYADILLPPLLKKLGDSKKFIREAANNALDAIIESCSY-------SPKIL---LEILSQG-LKSKNPQVREECAEWLA 156 (228)
T ss_dssp GHHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHHTTS-H---------HHH---HHHHHHH-TT-S-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHCCc-------HHHHH---HHHHHHH-HhCCCHHHHHHHHHHHH
Confidence 55556666665 5666766544445556666666543110 01221 3333333 23456677777777888
Q ss_pred HHhcccC----CCcHH-HHHHHHHHhhccCCCCChhhHHHHHHHHhhc
Q 003359 182 LVIDESE----DVSWD-LLRILLASVRKENQDVSPTSWKLGEKVFTKC 224 (827)
Q Consensus 182 ~VIeEsE----~VP~e-LLDvIL~~ll~~~ks~~PaAy~LA~~VI~~C 224 (827)
.+|.... .+... .++.|+..+...-.+..|..+..|+.++...
T Consensus 157 ~~l~~~~~~~~~l~~~~~~~~l~~~l~~~l~D~~~~VR~~Ar~~~~~l 204 (228)
T PF12348_consen 157 IILEKWGSDSSVLQKSAFLKQLVKALVKLLSDADPEVREAARECLWAL 204 (228)
T ss_dssp HHHTT-----GGG--HHHHHHHHHHHHHHHTSS-HHHHHHHHHHHHHH
T ss_pred HHHHHccchHhhhcccchHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence 8887765 12222 2344444444433455677777776665544
No 19
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=70.90 E-value=7.2 Score=44.03 Aligned_cols=115 Identities=16% Similarity=0.225 Sum_probs=60.5
Q ss_pred hhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHH-HHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeecc
Q 003359 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKE-FFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLD 146 (827)
Q Consensus 68 ~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKD-IF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlD 146 (827)
.+|.|++.-||--++.||..|+|. .|+ .+.+ ++..+...| .|++-..-...+++|..+ .
T Consensus 121 ~ll~~~~~~VRk~A~~~l~~i~~~-~p~------~~~~~~~~~l~~lL---~d~~~~V~~~a~~~l~~i----------~ 180 (526)
T PF01602_consen 121 KLLSDPSPYVRKKAALALLKIYRK-DPD------LVEDELIPKLKQLL---SDKDPSVVSAALSLLSEI----------K 180 (526)
T ss_dssp HHHHSSSHHHHHHHHHHHHHHHHH-CHC------CHHGGHHHHHHHHT---THSSHHHHHHHHHHHHHH----------H
T ss_pred HHhcCCchHHHHHHHHHHHHHhcc-CHH------HHHHHHHHHHhhhc---cCCcchhHHHHHHHHHHH----------c
Confidence 568899999999999999999999 232 2222 333333333 444422333344444444 1
Q ss_pred CCch---HHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCc--HHHHHHHHHHhh
Q 003359 147 LECD---KLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVS--WDLLRILLASVR 203 (827)
Q Consensus 147 Le~d---dLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP--~eLLDvIL~~ll 203 (827)
-+.+ .++..+|+.+...+. ...+-+...+..++..+.......+ ..++..|+..+.
T Consensus 181 ~~~~~~~~~~~~~~~~L~~~l~-~~~~~~q~~il~~l~~~~~~~~~~~~~~~~i~~l~~~l~ 241 (526)
T PF01602_consen 181 CNDDSYKSLIPKLIRILCQLLS-DPDPWLQIKILRLLRRYAPMEPEDADKNRIIEPLLNLLQ 241 (526)
T ss_dssp CTHHHHTTHHHHHHHHHHHHHT-CCSHHHHHHHHHHHTTSTSSSHHHHHHHHHHHHHHHHHH
T ss_pred cCcchhhhhHHHHHHHhhhccc-ccchHHHHHHHHHHHhcccCChhhhhHHHHHHHHHHHhh
Confidence 1111 455555555554442 3333344445555554444433444 445555555554
No 20
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=70.18 E-value=5.4 Score=49.36 Aligned_cols=44 Identities=16% Similarity=0.487 Sum_probs=35.3
Q ss_pred ccCeEEEeeCCC----CceEEEEEEEecCCC--------CeEEEEccCCCeeeeec
Q 003359 713 VGSRIKVWWPMD----ETFYKGVVDNYDPIK--------KKHRILYADGDEEILNL 756 (827)
Q Consensus 713 VG~RVkV~WP~D----~~wY~G~V~sYd~~t--------kkH~V~YDDGD~E~L~L 756 (827)
.+-++||||.+. .+|++|+|-+.-|.. .++.|+||.|+.+.+.-
T Consensus 981 ~~d~crvwwrda~~e~g~WWeG~ils~~pksp~fpdSpwery~v~~~~~e~~~~sp 1036 (1113)
T KOG0644|consen 981 CRDKCRVWWRDAGEEDGAWWEGRILSVKPKSPDFPDSPWERYIVRYDNTETELHSP 1036 (1113)
T ss_pred cccceeEEEccCCCcCCceeeeeeeeccCCCCCCCCCcceeEEEEecCCcccccCc
Confidence 588999999864 689999999977654 36899999997775543
No 21
>KOG1949 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.15 E-value=86 Score=39.09 Aligned_cols=149 Identities=22% Similarity=0.292 Sum_probs=80.1
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhcccCCchhh--------------------HHhhHHHHHhhhhhhhccCCCcCchhhh
Q 003359 22 LNPPSPVDEVINLLDKVEHLLANVEQAPSRSM--------------------RDALLPTMKGLITNDLLRRSDMDVRLSV 81 (827)
Q Consensus 22 i~~piS~dELLKRLkkL~~eLs~lDQ~~vdS~--------------------~~SL~pl~k~LVs~~LLkHkDkdVRayV 81 (827)
+.|.....+.=..|++-..+|..+=.++.-.. .+-+..++.- |-..+-...-.+||+.|
T Consensus 205 ~dpd~~~e~mD~i~~kQf~~l~~LL~d~~p~VRS~a~~gv~k~~s~fWe~iP~~i~~~ll~k-I~d~~a~dt~s~VR~sv 283 (1005)
T KOG1949|consen 205 RDPDLHAEEMDSIIQKQFEELYSLLEDPYPMVRSTAILGVCKITSKFWEMIPPTILIDLLKK-ITDELAFDTSSDVRCSV 283 (1005)
T ss_pred CCCCccHHHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHH-HHHHhhhccchheehhH
Confidence 34455556666667777777777655544211 1112222222 12233344556788888
Q ss_pred hHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcc-cCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHH
Q 003359 82 TSCISEITRITAPDSPYDDELMKEFFQLAVSAFEN-LSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHF 160 (827)
Q Consensus 82 AcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~-LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktF 160 (827)
--||-.|+- ..+---+|..++-.++. |.|.+-.----.+-||-.|-.|| |-.|
T Consensus 284 f~gl~~~l~---------np~sh~~le~~Lpal~~~l~D~se~VRvA~vd~ll~ik~vr-----------------a~~f 337 (1005)
T KOG1949|consen 284 FKGLPMILD---------NPLSHPLLEQLLPALRYSLHDNSEKVRVAFVDMLLKIKAVR-----------------AAKF 337 (1005)
T ss_pred hcCcHHHHc---------CccchhHHHHHHHhcchhhhccchhHHHHHHHHHHHHHhhh-----------------hhhh
Confidence 888877772 12333455555544442 12211111111112222222222 3346
Q ss_pred HHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCC
Q 003359 161 LKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQ 207 (827)
Q Consensus 161 FdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~k 207 (827)
|+++. |..||+.+=.++-.+.--++..|+..+++-++
T Consensus 338 ~~I~~----------~d~~l~~L~~d~~~v~rr~~~li~~s~lP~~k 374 (1005)
T KOG1949|consen 338 WKICP----------MDHILVRLETDSRPVSRRLVSLIFNSFLPVNK 374 (1005)
T ss_pred hcccc----------HHHHHHHHhccccHHHHHHHHHHHHhhcCCCC
Confidence 66655 77888887777778888899999999988776
No 22
>PTZ00429 beta-adaptin; Provisional
Probab=68.77 E-value=1.3e+02 Score=37.42 Aligned_cols=146 Identities=12% Similarity=0.105 Sum_probs=82.2
Q ss_pred HHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhh
Q 003359 59 PTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKV 138 (827)
Q Consensus 59 pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeV 138 (827)
.++..|. .+|+|.|..|-+-++.||..+.-.. ..+.++.++.-+...|-.|. ++ ...-+|-+|.+|..+
T Consensus 256 ~il~~l~--~~Lq~~N~AVVl~Aik~il~l~~~~------~~~~~~~~~~rl~~pLv~L~--ss-~~eiqyvaLr~I~~i 324 (746)
T PTZ00429 256 TLLTRVL--PRMSHQNPAVVMGAIKVVANLASRC------SQELIERCTVRVNTALLTLS--RR-DAETQYIVCKNIHAL 324 (746)
T ss_pred HHHHHHH--HHhcCCCHHHHHHHHHHHHHhcCcC------CHHHHHHHHHHHHHHHHHhh--CC-CccHHHHHHHHHHHH
Confidence 3444443 4588999999998888888775211 23556666655544433442 12 223445666665433
Q ss_pred cceeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHH
Q 003359 139 RSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGE 218 (827)
Q Consensus 139 KS~VLmlDLe~ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~ 218 (827)
-.. .-.++..-++.||-..+ -|..|...-.+||..+..+... ..||+-|..++. ...+.=.+.|-
T Consensus 325 ~~~-------~P~lf~~~~~~Ff~~~~--Dp~yIK~~KLeIL~~Lane~Nv--~~IL~EL~eYa~----d~D~ef~r~aI 389 (746)
T PTZ00429 325 LVI-------FPNLLRTNLDSFYVRYS--DPPFVKLEKLRLLLKLVTPSVA--PEILKELAEYAS----GVDMVFVVEVV 389 (746)
T ss_pred HHH-------CHHHHHHHHHhhhcccC--CcHHHHHHHHHHHHHHcCcccH--HHHHHHHHHHhh----cCCHHHHHHHH
Confidence 211 12566666777875433 4666877888999999887532 334555544443 22222223344
Q ss_pred HHHhhchHHHHH
Q 003359 219 KVFTKCAAKLKT 230 (827)
Q Consensus 219 ~VI~~CadKLqp 230 (827)
.-|..|+.++..
T Consensus 390 rAIg~lA~k~~~ 401 (746)
T PTZ00429 390 RAIASLAIKVDS 401 (746)
T ss_pred HHHHHHHHhChH
Confidence 446677776543
No 23
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=68.48 E-value=2.7 Score=30.92 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=21.4
Q ss_pred hhccCCCcCchhhhhHHHHHHhhhc
Q 003359 68 DLLRRSDMDVRLSVTSCISEITRIT 92 (827)
Q Consensus 68 ~LLkHkDkdVRayVAcCLADILRIy 92 (827)
++|.+++..||..++-||.+|.+.+
T Consensus 7 ~~l~D~~~~VR~~a~~~l~~i~~~~ 31 (31)
T PF02985_consen 7 QLLNDPSPEVRQAAAECLGAIAEHC 31 (31)
T ss_dssp HHHT-SSHHHHHHHHHHHHHHHHTS
T ss_pred HHcCCCCHHHHHHHHHHHHHHHhhC
Confidence 6788999999999999999998753
No 24
>KOG1248 consensus Uncharacterized conserved protein [Function unknown]
Probab=67.54 E-value=1.4e+02 Score=38.79 Aligned_cols=158 Identities=15% Similarity=0.132 Sum_probs=94.5
Q ss_pred CCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCC---
Q 003359 72 RSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE--- 148 (827)
Q Consensus 72 HkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe--- 148 (827)
..+.-+|+----||.-|++..- .+..--|+++|...+=.+.+.+...=+..|-+|-.|..+.++ +|..
T Consensus 708 s~~~~~~~~rl~~L~~L~~~~~------~e~~~~i~k~I~EvIL~~Ke~n~~aR~~Af~lL~~i~~i~~~---~d~g~e~ 778 (1176)
T KOG1248|consen 708 SSSSPAQASRLKCLKRLLKLLS------AEHCDLIPKLIPEVILSLKEVNVKARRNAFALLVFIGAIQSS---LDDGNEP 778 (1176)
T ss_pred ccchHHHHHHHHHHHHHHHhcc------HHHHHHHHHHHHHHHHhcccccHHHHhhHHHHHHHHHHHHhh---hcccccc
Confidence 3444567777789999998843 344444555555554455555555556678888888875444 4553
Q ss_pred chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHH-
Q 003359 149 CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAK- 227 (827)
Q Consensus 149 ~ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadK- 227 (827)
+.+.|.++|..++...-++-+..+-..+..|-..+-+....+..+.+.-+|..+--.=.++.|.-...|-..|..|..+
T Consensus 779 ~~~~lnefl~~Isagl~gd~~~~~as~Ivai~~il~e~~~~ld~~~l~~li~~V~~~L~s~sreI~kaAI~fikvlv~~~ 858 (1176)
T KOG1248|consen 779 ASAILNEFLSIISAGLVGDSTRVVASDIVAITHILQEFKNILDDETLEKLISMVCLYLASNSREIAKAAIGFIKVLVYKF 858 (1176)
T ss_pred hHHHHHHHHHHHHhhhcccHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHcC
Confidence 4567777777777653333334444446666566666777788888888887654333344444444554444444433
Q ss_pred ----HHHHHHHHHHh
Q 003359 228 ----LKTNLKEAVQS 238 (827)
Q Consensus 228 ----Lqp~I~q~l~S 238 (827)
|++++.++|-+
T Consensus 859 pe~~l~~~~~~LL~s 873 (1176)
T KOG1248|consen 859 PEECLSPHLEELLPS 873 (1176)
T ss_pred CHHHHhhhHHHHHHH
Confidence 45555444443
No 25
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=67.33 E-value=12 Score=33.17 Aligned_cols=47 Identities=17% Similarity=0.251 Sum_probs=35.4
Q ss_pred cccccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEc-cCCCeeeeecC
Q 003359 710 EQLVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILY-ADGDEEILNLK 757 (827)
Q Consensus 710 e~lVG~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~Y-DDGD~E~L~L~ 757 (827)
...+|..+-+.=+.|+.||.|+| ..+...+.-.|.| |-|..+.+...
T Consensus 51 ~~~~~~~~~~~~~~~~~w~Ra~I-~~~~~~~~~~V~~iD~G~~~~v~~~ 98 (121)
T PF00567_consen 51 ESNPGEGCLCVVSEDGRWYRAVI-TVDIDENQYKVFLIDYGNTEKVSAS 98 (121)
T ss_dssp T--TTEEEEEEETTTSEEEEEEE-EEEECTTEEEEEETTTTEEEEEEGG
T ss_pred ccccCCEEEEEEecCCceeeEEE-EEecccceeEEEEEecCceEEEcHH
Confidence 34467777788889999999999 5555667788887 67999886654
No 26
>KOG0915 consensus Uncharacterized conserved protein [Function unknown]
Probab=66.02 E-value=50 Score=43.77 Aligned_cols=165 Identities=15% Similarity=0.314 Sum_probs=94.9
Q ss_pred HHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhh--------------hhccC-CCcCchhhhhHH--HHHHhh
Q 003359 28 VDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITN--------------DLLRR-SDMDVRLSVTSC--ISEITR 90 (827)
Q Consensus 28 ~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~--------------~LLkH-kDkdVRayVAcC--LADILR 90 (827)
.++|-.-|++|-=-|++..=+|.-..++|+..+-+.||.. .||.+ .++.-|+--||| |+||+|
T Consensus 989 ~~kl~p~l~kLIPrLyRY~yDP~~~Vq~aM~sIW~~Li~D~k~~vd~y~neIl~eLL~~lt~kewRVReasclAL~dLl~ 1068 (1702)
T KOG0915|consen 989 GEKLEPYLKKLIPRLYRYQYDPDKKVQDAMTSIWNALITDSKKVVDEYLNEILDELLVNLTSKEWRVREASCLALADLLQ 1068 (1702)
T ss_pred HHhhhhHHHHhhHHHhhhccCCcHHHHHHHHHHHHHhccChHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHc
Confidence 3444455666666667766566655566666666666655 45555 889999999999 569998
Q ss_pred hcCCCCCCCc--hHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCC----chHHHHHHH-------
Q 003359 91 ITAPDSPYDD--ELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE----CDKLVVEMF------- 157 (827)
Q Consensus 91 IyAPDAPYtD--dqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe----~ddLI~eLF------- 157 (827)
= .|+++ +.|.+||..+|+....+.+. --.-..-....|+ |.||-|+|.. +.+.+--+.
T Consensus 1069 g----~~~~~~~e~lpelw~~~fRvmDDIKEs---VR~aa~~~~~~ls--Kl~vr~~d~~~~~~~~~~l~~iLPfLl~~g 1139 (1702)
T KOG0915|consen 1069 G----RPFDQVKEKLPELWEAAFRVMDDIKES---VREAADKAARALS--KLCVRICDVTNGAKGKEALDIILPFLLDEG 1139 (1702)
T ss_pred C----CChHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH--HHHhhhcccCCcccHHHHHHHHHHHHhccC
Confidence 6 67775 68888888777776554431 1111112222222 5678888874 222222221
Q ss_pred -------------HHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHh
Q 003359 158 -------------QHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASV 202 (827)
Q Consensus 158 -------------ktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~l 202 (827)
.++.+++. .-+..+-.+..+++-.+++-...+.+.||..+--++
T Consensus 1140 ims~v~evr~~si~tl~dl~K-ssg~~lkP~~~~LIp~ll~~~s~lE~~vLnYls~r~ 1196 (1702)
T KOG0915|consen 1140 IMSKVNEVRRFSIGTLMDLAK-SSGKELKPHFPKLIPLLLNAYSELEPQVLNYLSLRL 1196 (1702)
T ss_pred cccchHHHHHHHHHHHHHHHH-hchhhhcchhhHHHHHHHHHccccchHHHHHHHHhh
Confidence 22333322 122333344445555555666677777777665554
No 27
>KOG1248 consensus Uncharacterized conserved protein [Function unknown]
Probab=65.36 E-value=1.1e+02 Score=39.63 Aligned_cols=194 Identities=16% Similarity=0.160 Sum_probs=114.8
Q ss_pred HHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHH
Q 003359 28 VDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFF 107 (827)
Q Consensus 28 ~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF 107 (827)
+..+++-|.-|.+-|+.+--.. +.+++..|++. ..-.+.-|++.+--|+. ++|---+++.+..+.
T Consensus 200 ~t~v~~~L~Ll~~~~~~~p~~l-------i~sl~e~lL~i--~~~s~v~v~~~~~q~l~---~lf~~~~~~l~a~~~--- 264 (1176)
T KOG1248|consen 200 NTTVLRSLMLLRDVLSTFPRPL-------IKSLCEVLLNI--TTESPVLVLLEVLQCLH---SLFKKHPTALAAELN--- 264 (1176)
T ss_pred HHHHHHHHHHHHHhhccCCHHH-------HHHHHHHHHhh--cccchHHHHHHHHHHHH---HHHhcCCCcchHHHH---
Confidence 4445555555555555532221 22333333322 22233334444444444 444444446654433
Q ss_pred HHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCC-chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcc
Q 003359 108 QLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDE 186 (827)
Q Consensus 108 ~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe-~ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeE 186 (827)
-.++..+..|. ++..--..-++.|.-|.+-..|+-.+|.+ |-.=+..+|..||.+ -....+.+.....+++..|+.+
T Consensus 265 a~lL~al~~l~-ps~~D~~~t~~W~~v~~~~~~~la~~q~~~~~~~~~~~~~~~~t~-~~s~~~e~~q~a~q~l~~il~~ 342 (1176)
T KOG1248|consen 265 ARLLTALMTLS-PSENDDLLTVAWLKVLNEAHDILATLQEEKALQALPRLFSLFFTI-LESLIEELVQAASQSLKEILKE 342 (1176)
T ss_pred HHHHHHHHHhC-CCccchHHHHHHHHHHHHHHHHHHHhCHHHHHHhhhhhhhHHHHH-HhcccHHHHHHHHHHHHHHhcc
Confidence 23344444443 33333346677888888888888888887 667778888999984 4444566778889999999999
Q ss_pred cCCCcHHHHHHHHHHhhccC-CCCChhhHHHHHHHHhhchHHHHHHHHHHHHh
Q 003359 187 SEDVSWDLLRILLASVRKEN-QDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQS 238 (827)
Q Consensus 187 sE~VP~eLLDvIL~~ll~~~-ks~~PaAy~LA~~VI~~CadKLqp~I~q~l~S 238 (827)
+-.+-..+-..++..++... ....+..+++-..++..|...--|++...|+.
T Consensus 343 sv~~~~~~c~~~~~~~l~~kf~~~~~~ilqi~s~~fek~G~~s~~~l~~~L~~ 395 (1176)
T KOG1248|consen 343 SVTVIDALCSKQLHSLLDYKFHAVWRFILQILSALFEKCGELSGPELTKTLEG 395 (1176)
T ss_pred cCcccHHHHHHHHHHHHcchHHHHHHHHHHHHHHHHHHhhhhcCHHHHHHHHH
Confidence 88866666666666666432 22345555666667788887766777666664
No 28
>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=65.34 E-value=74 Score=38.41 Aligned_cols=143 Identities=17% Similarity=0.209 Sum_probs=75.8
Q ss_pred HHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhcc-cCCchhhHHhhHHHHHhhhh-hhhccCCCcCchhhhhHHH
Q 003359 8 IELEEQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVE-QAPSRSMRDALLPTMKGLIT-NDLLRRSDMDVRLSVTSCI 85 (827)
Q Consensus 8 ~ele~~l~~~G~kLi~~piS~dELLKRLkkL~~eLs~lD-Q~~vdS~~~SL~pl~k~LVs-~~LLkHkDkdVRayVAcCL 85 (827)
+|.|+.|.+.-++++.. .+.+|. ..|..+-.+|.-+. +.++.+ +..|..+..+.+. ..-+...|.+.=--+..|+
T Consensus 173 ~E~e~~i~~~ikkvL~D-VTaeEF-~l~m~lL~~lk~~~~~~t~~g-~qeLv~ii~eQa~Ld~~f~~sD~e~Idrli~C~ 249 (556)
T PF05918_consen 173 KEMEEFIVDEIKKVLQD-VTAEEF-ELFMSLLKSLKIYGGKQTIEG-RQELVDIIEEQADLDQPFDPSDPESIDRLISCL 249 (556)
T ss_dssp HHHHHHHHHHHHHHCTT---HHHH-HHHHHHHHTSGG---GSSHHH-HHHHHHHHHHHHTTTS---SSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh-ccHHHH-HHHHHHHHhCccccccCChHH-HHHHHHHHHHHhccCCCCCCcCHHHHHHHHHHH
Confidence 66777777777777642 444443 34445555555432 233433 3334444443321 2224555554333344555
Q ss_pred HHHhhhcCCCCCCCchHHHHHHHHHHHH-hcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHHH
Q 003359 86 SEITRITAPDSPYDDELMKEFFQLAVSA-FENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKV 163 (827)
Q Consensus 86 ADILRIyAPDAPYtDdqLKDIF~LfV~q-f~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFdi 163 (827)
-.-|=+|.+.+ .-..+|.++..+ |+.|.+... ...+.||..||++-++. .++++.+++..+|+.|...
T Consensus 250 ~~Alp~fs~~v-----~Sskfv~y~~~kvlP~l~~l~e---~~kl~lLk~lAE~s~~~--~~~d~~~~L~~i~~~L~~y 318 (556)
T PF05918_consen 250 RQALPFFSRGV-----SSSKFVNYMCEKVLPKLSDLPE---DRKLDLLKLLAELSPFC--GAQDARQLLPSIFQLLKKY 318 (556)
T ss_dssp HHHGGG-BTTB-------HHHHHHHHHHTCCCTT--------HHHHHHHHHHHHHTT------THHHHHHHHHHHHHTT
T ss_pred HHhhHHhcCCC-----ChHHHHHHHHHHhcCChhhCCh---HHHHHHHHHHHHHcCCC--CcccHHHHHHHHHHHHHHh
Confidence 54455554443 457888888888 888887632 56789999999998774 4555788888888888764
No 29
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=58.47 E-value=1.7e+02 Score=36.92 Aligned_cols=171 Identities=20% Similarity=0.200 Sum_probs=106.0
Q ss_pred HhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHH--HHHHH
Q 003359 55 DALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMK--ALSIL 132 (827)
Q Consensus 55 ~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q--~~yLL 132 (827)
+....++++|+. |--.+++||-.|-|||+-|-- .-+.+|.=.+..|--- +.+|+-.+ -..||
T Consensus 318 ~~~~~i~kaLvr---LLrs~~~vqyvvL~nIa~~s~-----------~~~~lF~P~lKsFfv~--ssDp~~vk~lKleiL 381 (968)
T KOG1060|consen 318 NQVTKIAKALVR---LLRSNREVQYVVLQNIATISI-----------KRPTLFEPHLKSFFVR--SSDPTQVKILKLEIL 381 (968)
T ss_pred HHHHHHHHHHHH---HHhcCCcchhhhHHHHHHHHh-----------cchhhhhhhhhceEee--cCCHHHHHHHHHHHH
Confidence 355677888888 445678899888888887652 2234555455553311 33444333 35677
Q ss_pred HHhhhhcceeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChh
Q 003359 133 DTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPT 212 (827)
Q Consensus 133 EsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~Pa 212 (827)
.+||.-..+ -++|+.|..-|+..+- .+...-..-+..+=.-.-.|+.-.|+-|+.-+..++....-.
T Consensus 382 s~La~esni------------~~ILrE~q~YI~s~d~-~faa~aV~AiGrCA~~~~sv~~tCL~gLv~Llsshde~Vv~e 448 (968)
T KOG1060|consen 382 SNLANESNI------------SEILRELQTYIKSSDR-SFAAAAVKAIGRCASRIGSVTDTCLNGLVQLLSSHDELVVAE 448 (968)
T ss_pred HHHhhhccH------------HHHHHHHHHHHhcCch-hHHHHHHHHHHHHHHhhCchhhHHHHHHHHHHhcccchhHHH
Confidence 777765533 3445555554554333 333322333344444556789999999999998888888777
Q ss_pred hHHHHHHHHhhchHHHHHHHHHHHHhcCC---C---------CchhHHHHHHHh
Q 003359 213 SWKLGEKVFTKCAAKLKTNLKEAVQSRGI---A---------LDDYAEIVACIC 254 (827)
Q Consensus 213 Ay~LA~~VI~~CadKLqp~I~q~l~S~Gi---~---------ld~Y~eIV~sI~ 254 (827)
|-...+.+|++-..+--.+|.+++..+.. + .-+|.++|..||
T Consensus 449 aV~vIk~Llq~~p~~h~~ii~~La~lldti~vp~ARA~IiWLige~~e~vpri~ 502 (968)
T KOG1060|consen 449 AVVVIKRLLQKDPAEHLEILFQLARLLDTILVPAARAGIIWLIGEYCEIVPRIA 502 (968)
T ss_pred HHHHHHHHHhhChHHHHHHHHHHHHHhhhhhhhhhhceeeeeehhhhhhcchhc
Confidence 77788888888887776677776664322 1 366777654444
No 30
>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=54.73 E-value=1.1e+02 Score=36.62 Aligned_cols=100 Identities=11% Similarity=0.205 Sum_probs=57.5
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchH
Q 003359 23 NPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL 102 (827)
Q Consensus 23 ~~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdq 102 (827)
..++++.+|...|+.|..+.+.++.. - ..+..+|++-..+...+.-|++|+.-++.=+. -...-
T Consensus 45 ~d~~~~~~l~~~L~~L~~~Vs~Ld~~-~-------~~LV~ail~~~W~~~~~~~v~~y~~Fl~~Lvs--------a~~~y 108 (563)
T PF05327_consen 45 KDAISVSQLIRWLKALSSCVSLLDSS-C-------KQLVEAILSLNWLGRDEDFVEAYIQFLINLVS--------AQPKY 108 (563)
T ss_dssp TTS--HHHHHHHHHHHHHGGGGG-SC-C-------HHHHHHHHT-TGGGS-HHHHHHHHHHHHHHHH--------H-GGG
T ss_pred cccccHHHHHHHHHHHHHHHHHhhhH-H-------HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHH--------hhHHH
Confidence 45678999999999999999999886 3 35666777777777777777777763321111 02356
Q ss_pred HHHHHHHHHHHhcccCC-----------CCCcchHHHHHHHHHhhhh
Q 003359 103 MKEFFQLAVSAFENLSH-----------ASGRYYMKALSILDTVAKV 138 (827)
Q Consensus 103 LKDIF~LfV~qf~~LaD-----------~ssp~F~q~~yLLEsLAeV 138 (827)
+..|+..+|..|..-.. ....-|.+.+.+|..|..+
T Consensus 109 l~~vl~~LV~~f~p~~~~~~~~~~~~~~~~~~~~~~vH~~L~~Il~l 155 (563)
T PF05327_consen 109 LSPVLSMLVKNFIPPPSSIAEWPGCPPEKRREIYERVHDALQKILRL 155 (563)
T ss_dssp HHHHHHHHHHGGGS-HHHHHH---------------HHHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCCccccccchhhhhhhhhhHHHHHHHHHHHHHH
Confidence 67777777777652211 1223566677777776543
No 31
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=53.70 E-value=2.3e+02 Score=30.89 Aligned_cols=123 Identities=20% Similarity=0.193 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHH--
Q 003359 28 VDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKE-- 105 (827)
Q Consensus 28 ~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKD-- 105 (827)
.++-+..+++++.....-.++-.+.....+..++-.|++.- ..+.++.-|+-..|.||++. -|+-.+-+..
T Consensus 27 s~~~~~~ik~~~~~~~~~~~~~~~~~~~~~~~~~l~lL~~~---~~~~d~v~yvL~li~dll~~----~~~~~~~~~~~~ 99 (312)
T PF03224_consen 27 SEEDLSLIKKLDKQSKEERRELLEEDGDQYASLFLNLLNKL---SSNDDTVQYVLTLIDDLLSD----DPSRVELFLELA 99 (312)
T ss_dssp -HHHHHHHHHHHHHHH-------------------HHHHHH------HHHHHHHHHHHHHHHH-----SSSSHHHHHHHH
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHhchhhHHHHHHHHHHHc---cCcHHHHHHHHHHHHHHHhc----CHHHHHHHHHhc
Confidence 34445666666666655533333333445555555555554 56888889999999999965 3444433333
Q ss_pred ------HHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHHHhhc
Q 003359 106 ------FFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRS 166 (827)
Q Consensus 106 ------IF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr~ 166 (827)
+|..|++ .|...+..-..+..++|..|+.-..- .......+++..||+.++.
T Consensus 100 ~~~~~~~~~~fl~---ll~~~D~~i~~~a~~iLt~Ll~~~~~------~~~~~~~~~l~~ll~~L~~ 157 (312)
T PF03224_consen 100 KQDDSDPYSPFLK---LLDRNDSFIQLKAAFILTSLLSQGPK------RSEKLVKEALPKLLQWLSS 157 (312)
T ss_dssp H-TTH--HHHHHH---H-S-SSHHHHHHHHHHHHHHHTSTTT--------HHHHHHHHHHHHHHHH-
T ss_pred ccccchhHHHHHH---HhcCCCHHHHHHHHHHHHHHHHcCCc------cccchHHHHHHHHHHHHHH
Confidence 5666665 33344444456677888877655321 1223234555666666554
No 32
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=53.61 E-value=1.2e+02 Score=30.45 Aligned_cols=77 Identities=19% Similarity=0.249 Sum_probs=44.9
Q ss_pred cCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCC-Cc-----ch----HHHHHHHHHhhhhcc
Q 003359 71 RRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHAS-GR-----YY----MKALSILDTVAKVRS 140 (827)
Q Consensus 71 kHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~s-sp-----~F----~q~~yLLEsLAeVKS 140 (827)
.-.|.+||.++..||.++++-.-|++ |++.|+..+..|.+.. .+ .. .-|-+||+.+.+
T Consensus 73 ~D~~~~Ir~~A~~~~~e~~~~~~~~~---------i~~~~~e~i~~l~~~~~~~~~~~~~~~~~~~I~~fll~~i~~--- 140 (178)
T PF12717_consen 73 VDENPEIRSLARSFFSELLKKRNPNI---------IYNNFPELISSLNNCYEHPVYGPLSREKRKKIYKFLLDFIDK--- 140 (178)
T ss_pred cCCCHHHHHHHHHHHHHHHHhccchH---------HHHHHHHHHHHHhCccccccccccCHHHHHHHHHHHHHHcCc---
Confidence 44567789999999999987765543 3666666666665532 22 12 223444444442
Q ss_pred eeeeccCCchHHHHHHHHHHHHHh
Q 003359 141 CLLMLDLECDKLVVEMFQHFLKVI 164 (827)
Q Consensus 141 ~VLmlDLe~ddLI~eLFktFFdiV 164 (827)
|-..+.|+..+++.|+..+
T Consensus 141 -----d~~~~~l~~kl~~~~~~~~ 159 (178)
T PF12717_consen 141 -----DKQKESLVEKLCQRFLNAV 159 (178)
T ss_pred -----HHHHHHHHHHHHHHHHHHc
Confidence 2224566777777666654
No 33
>KOG1241 consensus Karyopherin (importin) beta 1 [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=53.50 E-value=94 Score=38.88 Aligned_cols=47 Identities=17% Similarity=0.255 Sum_probs=34.7
Q ss_pred hhhccCCC----cCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcc
Q 003359 67 NDLLRRSD----MDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFEN 116 (827)
Q Consensus 67 ~~LLkHkD----kdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~ 116 (827)
...|.+.| .+++..++.||.-|+|+.+|++|-..++|-. +|++.|..
T Consensus 557 ~~~l~~~dr~q~~eLQs~Lc~~Lq~i~rk~~~~~~~~~d~iM~---lflri~~s 607 (859)
T KOG1241|consen 557 SQILSLADRAQLNELQSLLCNTLQSIIRKVGSDIREVSDQIMG---LFLRIFES 607 (859)
T ss_pred HHhccHhhHHHHHHHHHHHHHHHHHHHHHccccchhHHHHHHH---HHHHHHcC
Confidence 45666665 4689999999999999999998877666554 44444443
No 34
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=52.39 E-value=42 Score=31.30 Aligned_cols=60 Identities=15% Similarity=0.217 Sum_probs=37.2
Q ss_pred hhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhc-ccCCCCCcchHHHHHHHHHh
Q 003359 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFE-NLSHASGRYYMKALSILDTV 135 (827)
Q Consensus 68 ~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~-~LaD~ssp~F~q~~yLLEsL 135 (827)
..+...|.-||-|++-||-+|.+++- +++-.-|.-||..|. .++|++ +.=+..-.+|.+|
T Consensus 34 ~~~~D~d~rVRy~AcEaL~ni~k~~~-------~~~l~~f~~IF~~L~kl~~D~d-~~Vr~~a~~Ld~l 94 (97)
T PF12755_consen 34 KCFDDQDSRVRYYACEALYNISKVAR-------GEILPYFNEIFDALCKLSADPD-ENVRSAAELLDRL 94 (97)
T ss_pred HHcCCCcHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHcCCc-hhHHHHHHHHHHH
Confidence 45777888899999999999999952 333335555555533 334443 3334444555554
No 35
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=52.19 E-value=1.4e+02 Score=30.33 Aligned_cols=115 Identities=15% Similarity=0.246 Sum_probs=54.1
Q ss_pred chhhhhHHHHHHhhhcCCCCCCCc--hHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHH
Q 003359 77 VRLSVTSCISEITRITAPDSPYDD--ELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVV 154 (827)
Q Consensus 77 VRayVAcCLADILRIyAPDAPYtD--dqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~ 154 (827)
.|.-.--.|-.|++-.+|...+.+ ..|+++...|+.++. |..+.-....+.+|..|+..=.. .-+..+.
T Consensus 23 ~r~~al~~L~~l~~~~~~~~~~~~~~~~l~~~~~~i~~~l~---d~Rs~v~~~A~~~l~~l~~~l~~------~~~~~~~ 93 (228)
T PF12348_consen 23 ERVEALQKLRSLIKGNAPEDFPPDFVECLRQLLDAIIKQLS---DLRSKVSKTACQLLSDLARQLGS------HFEPYAD 93 (228)
T ss_dssp HHHHHHHHHHHHHHH-B-----HHHHHHHH---HHHHH-S----HH---HHHHHHHHHHHHHHHHGG------GGHHHHH
T ss_pred HHHHHHHHHHHHHHcCCccccHHHHHHHHHHhHHHHHHHHh---hhHHHHHHHHHHHHHHHHHHHhH------hHHHHHH
Confidence 333334445555555433322221 344555555555554 44467777888888888766111 1345666
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHH-HHHHHHHh
Q 003359 155 EMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDL-LRILLASV 202 (827)
Q Consensus 155 eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eL-LDvIL~~l 202 (827)
.++..+|..+.. ....|.......|..++.-+. .+..+ +..|...+
T Consensus 94 ~~l~~Ll~~~~~-~~~~i~~~a~~~L~~i~~~~~-~~~~~~~~~l~~~~ 140 (228)
T PF12348_consen 94 ILLPPLLKKLGD-SKKFIREAANNALDAIIESCS-YSPKILLEILSQGL 140 (228)
T ss_dssp HHHHHHHHGGG----HHHHHHHHHHHHHHHTTS--H--HHHHHHHHHHT
T ss_pred HHHHHHHHHHcc-ccHHHHHHHHHHHHHHHHHCC-cHHHHHHHHHHHHH
Confidence 777777775543 234566666777777777644 34566 34443333
No 36
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=51.34 E-value=52 Score=39.20 Aligned_cols=97 Identities=15% Similarity=0.309 Sum_probs=63.9
Q ss_pred eccCC-chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCC----CCChhhHHHHH
Q 003359 144 MLDLE-CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQ----DVSPTSWKLGE 218 (827)
Q Consensus 144 mlDLe-~ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~k----s~~PaAy~LA~ 218 (827)
.+|++ .-+||.+|+-++...+.+.+.--|+.-+. +.+|.+-|..|+..|...+. .+.|-..++..
T Consensus 273 ~id~~~~~~Li~ELd~~vl~~v~DQngnHViQK~i----------e~~p~~~~~Fiv~~f~~~~~~~~ls~~~YGCRVIQ 342 (503)
T KOG1488|consen 273 KVDVSLQIQLIDELDGHLLKCVKDQNGNHVIQKCI----------ETLPPDAWQFIVDFFSGDDNLLELSTHKYGCRVIQ 342 (503)
T ss_pred hcCHHHHHHHHHHHHhhHHHHHhhcccceehhhhh----------hccChHHHHHHHHHhcCCCceeEeeccCcccHHHH
Confidence 33444 56899999888888887655444433221 47999999999999987533 45777777888
Q ss_pred HHHhhchHH-HHHHHHHHHHhc-CCCCchhHHHH
Q 003359 219 KVFTKCAAK-LKTNLKEAVQSR-GIALDDYAEIV 250 (827)
Q Consensus 219 ~VI~~CadK-Lqp~I~q~l~S~-Gi~ld~Y~eIV 250 (827)
.++..|.+. .++.+......+ .+.-|.|.+-|
T Consensus 343 r~lE~c~~~~~~~i~~ei~~~~~~L~~dQygNYV 376 (503)
T KOG1488|consen 343 RILEHCSEDQKQPLMEEIIRNCDQLAQDQYGNYV 376 (503)
T ss_pred HHhhcCChHhhhHHHHHHHHHHHHHHhhhhhhHH
Confidence 888888765 344444444332 34457775543
No 37
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=50.12 E-value=2.2e+02 Score=28.23 Aligned_cols=101 Identities=17% Similarity=0.188 Sum_probs=60.7
Q ss_pred chHHHHHHHHHHHHHhhcCC---chhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhcc---CCC--CChhhHHHHHHH
Q 003359 149 CDKLVVEMFQHFLKVIRSNH---PHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKE---NQD--VSPTSWKLGEKV 220 (827)
Q Consensus 149 ~ddLI~eLFktFFdiVr~~h---p~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~---~ks--~~PaAy~LA~~V 220 (827)
....-++||+.++....+.. +......+..|+...++. .+|-|.|+-||++. |.+ ..--+|+|-.-+
T Consensus 18 ~~~~A~~iF~~Il~ymgd~~~~~~~~~~~l~~~i~~~~~~~-----~~LrDEiy~QLiKQtt~Np~~~s~~rgW~Ll~l~ 92 (144)
T smart00139 18 LQKEAVKIFKAILKFMGDLPLPKPDSHLDLVQFILQKGLAH-----PELRDEIYCQLIKQLTDNPSRQSEERGWELLYLC 92 (144)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHHHhcc-----HHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHH
Confidence 55777889998888665421 122344566777777753 56677777776642 222 223455544332
Q ss_pred --HhhchHHHHHHHHHHHHhcCCCCchhHHHHHHHhcc
Q 003359 221 --FTKCAAKLKTNLKEAVQSRGIALDDYAEIVACICGS 256 (827)
Q Consensus 221 --I~~CadKLqp~I~q~l~S~Gi~ld~Y~eIV~sI~q~ 256 (827)
+=-++..|.+||..||+..+...++ ..++..|+.
T Consensus 93 ~~~FpPS~~l~~yL~~~l~~~~~~~~~--~~~a~~c~~ 128 (144)
T smart00139 93 TSLFPPSERLLPYLLQFLSRRADQPSE--QGLAKYCLY 128 (144)
T ss_pred HhHcCChHHHHHHHHHHHHhcCCCccH--HHHHHHHHh
Confidence 2235678999999999986544332 445566664
No 38
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=50.10 E-value=54 Score=40.44 Aligned_cols=115 Identities=17% Similarity=0.225 Sum_probs=75.0
Q ss_pred HHHHHHhhhhcceeeeccCC-chHHHHHHHHHHHH----HhhcCCchhHH-------HHHHHHHHHHhcccC------CC
Q 003359 129 LSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLK----VIRSNHPHFVF-------AAMETIMTLVIDESE------DV 190 (827)
Q Consensus 129 ~yLLEsLAeVKS~VLmlDLe-~ddLI~eLFktFFd----iVr~~hp~kV~-------~~M~dILs~VIeEsE------~V 190 (827)
|-|||.|+.|-+.+-.--+| |..+...-|..+-. .....++..+. -.-.+.++.+++-.. .-
T Consensus 580 fPLLEClSsia~AL~~gF~P~~~~Vy~Rc~~il~~t~q~~~~~~~~~~~~~pdkdfiI~sLDL~SGLaegLg~~ie~Lva 659 (885)
T KOG2023|consen 580 FPLLECLSSIASALGVGFLPYAQPVYQRCFRILQKTLQLLAKVQQDPTVEAPDKDFIIVSLDLLSGLAEGLGSHIEPLVA 659 (885)
T ss_pred HHHHHHHHHHHHHHhccccccCHHHHHHHHHHHHHHHHHHHhccCCccccCCCcceEEEeHHHHhHHHHHhhhchHHHhh
Confidence 46888888887665555556 65554444432221 11222322211 122355555554322 23
Q ss_pred cHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHHHHHHHHHHhcCCCC
Q 003359 191 SWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIAL 243 (827)
Q Consensus 191 P~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLqp~I~q~l~S~Gi~l 243 (827)
+..++++||..+..+-....-.||.|--+++..|.+.+.|++..||--+|.-+
T Consensus 660 ~snl~~lll~C~~D~~peVRQS~FALLGDltk~c~~~v~p~~~~fl~~lg~Nl 712 (885)
T KOG2023|consen 660 QSNLLDLLLQCLQDEVPEVRQSAFALLGDLTKACFEHVIPNLADFLPILGANL 712 (885)
T ss_pred hccHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHhccchHHHHHHHHhhcC
Confidence 55689999999988888888889999999999999999999999998776543
No 39
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=49.24 E-value=35 Score=33.86 Aligned_cols=32 Identities=16% Similarity=0.370 Sum_probs=26.7
Q ss_pred EeeCCCCceEEEEEEEecCCCCeEEEEccCCC
Q 003359 719 VWWPMDETFYKGVVDNYDPIKKKHRILYADGD 750 (827)
Q Consensus 719 V~WP~D~~wY~G~V~sYd~~tkkH~V~YDDGD 750 (827)
||---+..||.|++.+.+....+..|.++||.
T Consensus 16 vW~~~~~~yYPa~~~~~~~~~~~~~V~Fedg~ 47 (131)
T PF08605_consen 16 VWAGYNLKYYPATCVGSGVDRDRSLVRFEDGT 47 (131)
T ss_pred eeecCCCeEeeEEEEeecCCCCeEEEEEecCc
Confidence 44333789999999999887778999999997
No 40
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=48.00 E-value=2.3e+02 Score=30.81 Aligned_cols=174 Identities=9% Similarity=0.142 Sum_probs=0.0
Q ss_pred hhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchH------HHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhh
Q 003359 63 GLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL------MKEFFQLAVSAFENLSHASGRYYMKALSILDTVA 136 (827)
Q Consensus 63 ~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdq------LKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLA 136 (827)
.|.-..+ ...+..||+-+.-||.||+-+|-++..-.... ...+.++|...|... +++ -+....|-++
T Consensus 67 ~l~~~~~-~~~~~~v~~~al~~l~Dll~~~g~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~-~~~-----~~~~a~EGl~ 139 (298)
T PF12719_consen 67 PLFLQAL-QKDDEEVKITALKALFDLLLTHGIDIFDSESDNDESVDSKSLLKILTKFLDSE-NPE-----LQAIAVEGLC 139 (298)
T ss_pred HHHHHHH-HhCCHHHHHHHHHHHHHHHHHcCchhccchhccCccchHhHHHHHHHHHHhcC-CHH-----HHHHHHHHHH
Q ss_pred hhcceeeeccCCchHHHHHHHHHHHHHhhc---------------------CCchhHHHHHHHHHHHHhcccCCC-----
Q 003359 137 KVRSCLLMLDLECDKLVVEMFQHFLKVIRS---------------------NHPHFVFAAMETIMTLVIDESEDV----- 190 (827)
Q Consensus 137 eVKS~VLmlDLe~ddLI~eLFktFFdiVr~---------------------~hp~kV~~~M~dILs~VIeEsE~V----- 190 (827)
+.=..-.+.| ...++..|+-.+|+-... .|+..+.......+..+..-.+..
T Consensus 140 KLlL~~~i~~--~~~vL~~Lll~yF~p~t~~~~~LrQ~L~~Ffp~y~~s~~~~Q~~l~~~f~~~l~~~~~~~~~~~~~~~ 217 (298)
T PF12719_consen 140 KLLLSGRISD--PPKVLSRLLLLYFNPSTEDNQRLRQCLSVFFPVYASSSPENQERLAEAFLPTLRTLSNAPDELDSPLA 217 (298)
T ss_pred HHHhcCCCCc--HHHHHHHHHHHHcCcccCCcHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhCcccccCchh
Q ss_pred ---cHHHHHHHHHHhhccCCCCChh------------hHHHHHHHHhhchHH--HHHHHHHHHHhcCCCCch
Q 003359 191 ---SWDLLRILLASVRKENQDVSPT------------SWKLGEKVFTKCAAK--LKTNLKEAVQSRGIALDD 245 (827)
Q Consensus 191 ---P~eLLDvIL~~ll~~~ks~~Pa------------Ay~LA~~VI~~CadK--Lqp~I~q~l~S~Gi~ld~ 245 (827)
+..+...++.-.-+........ |-.+...+...+..+ ....++++|..+-++.++
T Consensus 218 ~v~~~~v~~~lv~lt~~~~~~~~~~~~~~~~~~h~~La~~il~~i~~~~~~~~~~~k~~~~~L~~L~i~~~~ 289 (298)
T PF12719_consen 218 MVSPSQVASFLVDLTDPSKLVKESNQEIQNESVHVDLAIDILNEILSDPEKEKEERKALCKALSKLEISLDE 289 (298)
T ss_pred hCCHHHHHHHHHHHCChhhccCccccccccccHHHHHHHHHHHHHHhccccchHHHHHHHHHHhccccCcCC
No 41
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=47.95 E-value=19 Score=39.10 Aligned_cols=35 Identities=17% Similarity=0.487 Sum_probs=31.2
Q ss_pred ccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEcc
Q 003359 713 VGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYA 747 (827)
Q Consensus 713 VG~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YD 747 (827)
||.+|.+-|++|..||..+|....+-++.-.|.++
T Consensus 93 vg~K~~A~~~ddg~~y~AtIe~ita~~~~~ai~f~ 127 (262)
T KOG3026|consen 93 VGDKVQAVFSDDGQIYDATIEHITAMEGTVAIIFA 127 (262)
T ss_pred cCCEEEEeecCCCceEEeehhhccCCCCceeEEEe
Confidence 89999999999999999999999997776666665
No 42
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=47.75 E-value=56 Score=26.56 Aligned_cols=39 Identities=15% Similarity=0.262 Sum_probs=31.0
Q ss_pred ccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCCeeee
Q 003359 713 VGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDEEIL 754 (827)
Q Consensus 713 VG~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YDDGD~E~L 754 (827)
+|++|+|.+ .+..|.|++...|+ .+.=.|..+||..+.+
T Consensus 2 lG~~V~v~~--~~~~~~G~~~gId~-~G~L~v~~~~g~~~~i 40 (48)
T PF02237_consen 2 LGQEVRVET--GDGEIEGIAEGIDD-DGALLVRTEDGSIRTI 40 (48)
T ss_dssp TTSEEEEEE--TSCEEEEEEEEEET-TSEEEEEETTEEEEEE
T ss_pred CCCEEEEEE--CCeEEEEEEEEECC-CCEEEEEECCCCEEEE
Confidence 699999999 44567999999998 4777788888855544
No 43
>KOG4256 consensus Kinetochore component [Cell cycle control, cell division, chromosome partitioning]
Probab=47.29 E-value=1.9e+02 Score=37.78 Aligned_cols=95 Identities=18% Similarity=0.258 Sum_probs=50.0
Q ss_pred hhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCC------------------------CchHHHHHHHHHHHHhcccCCC
Q 003359 65 ITNDLLRRSDMDVRLSVTSCISEITRITAPDSPY------------------------DDELMKEFFQLAVSAFENLSHA 120 (827)
Q Consensus 65 Vs~~LLkHkDkdVRayVAcCLADILRIyAPDAPY------------------------tDdqLKDIF~LfV~qf~~LaD~ 120 (827)
..+.+++.-|. ..+.-|-|+-|++|-||--|-| +.+.++|||.-|++
T Consensus 498 AKkRlikdeDi-lalI~ad~lkevlgahaiiagf~eafePsrekfnesiW~eFlealhdaddlidIflefis-------- 568 (2209)
T KOG4256|consen 498 AKKRLIKDEDI-LALIEADCLKEVLGAHAIIAGFPEAFEPSREKFNESIWDEFLEALHDADDLIDIFLEFIS-------- 568 (2209)
T ss_pred HHHhhcchHHH-HHHHHHHHHHHHHhhhhhhccCccccCCchhhhcchhHHHHHHhhcccchHHHHHHHHhh--------
Confidence 34455555554 5667799999999988744332 12345555544442
Q ss_pred CCcchHHHHHHHHH-hhhhcceeeeccCC-chHHHHHHHHHHHHHhhcCCch
Q 003359 121 SGRYYMKALSILDT-VAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNHPH 170 (827)
Q Consensus 121 ssp~F~q~~yLLEs-LAeVKS~VLmlDLe-~ddLI~eLFktFFdiVr~~hp~ 170 (827)
...|.+.-||.-+ =|.+-+. .+.|.+ --.-+..||+.|.+.++.+.+.
T Consensus 569 -danftcAq~i~lRHganfedr-f~~deentisrLEsLfrmfidaiSadiSk 618 (2209)
T KOG4256|consen 569 -DANFTCAQVIFLRHGANFEDR-FCDDEENTISRLESLFRMFIDAISADISK 618 (2209)
T ss_pred -ccceeehhhHHHhhcCchhhh-hccchhhhHHHHHHHHHHHHHHhhhhHHH
Confidence 2333333333221 1222110 111111 1123899999999999886543
No 44
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=46.83 E-value=76 Score=34.52 Aligned_cols=112 Identities=15% Similarity=0.276 Sum_probs=52.8
Q ss_pred HhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHH------HHHHHHhcccC-CCCCcchHH
Q 003359 55 DALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFF------QLAVSAFENLS-HASGRYYMK 127 (827)
Q Consensus 55 ~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF------~LfV~qf~~La-D~ssp~F~q 127 (827)
..|..+..-|-+ .+.+.+.+++..+..||+.+||+ .+.+.+| ..++..|.... ...+..++-
T Consensus 146 ~~l~~ll~~L~~--~l~~~~~~~~~~av~~L~~LL~~---------~~~R~~f~~~~~v~~l~~iL~~~~~~~~~~~~Ql 214 (312)
T PF03224_consen 146 EALPKLLQWLSS--QLSSSDSELQYIAVQCLQNLLRS---------KEYRQVFWKSNGVSPLFDILRKQATNSNSSGIQL 214 (312)
T ss_dssp HHHHHHHHHHH---TT-HHHH---HHHHHHHHHHHTS---------HHHHHHHHTHHHHHHHHHHHH---------HHHH
T ss_pred HHHHHHHHHHHH--hhcCCCcchHHHHHHHHHHHhCc---------chhHHHHHhcCcHHHHHHHHHhhcccCCCCchhH
Confidence 456566665555 77888999999999999999987 3334333 34444432212 233444444
Q ss_pred HHHHHHHhhhhcceeeeccCCchHHHHH-----HHHHHHHHhhcCCchhHHHHHHHHHHHHhc
Q 003359 128 ALSILDTVAKVRSCLLMLDLECDKLVVE-----MFQHFLKVIRSNHPHFVFAAMETIMTLVID 185 (827)
Q Consensus 128 ~~yLLEsLAeVKS~VLmlDLe~ddLI~e-----LFktFFdiVr~~hp~kV~~~M~dILs~VIe 185 (827)
.||+| .|++++=++. +.+.+ +|..+.++++...-++|......|+.-+++
T Consensus 215 ~Y~~l-------l~lWlLSF~~-~~~~~~~~~~~i~~L~~i~~~~~KEKvvRv~la~l~Nl~~ 269 (312)
T PF03224_consen 215 QYQAL-------LCLWLLSFEP-EIAEELNKKYLIPLLADILKDSIKEKVVRVSLAILRNLLS 269 (312)
T ss_dssp HHHHH-------HHHHHHTTSH-HHHHHHHTTSHHHHHHHHHHH--SHHHHHHHHHHHHHTTS
T ss_pred HHHHH-------HHHHHHhcCH-HHHHHHhccchHHHHHHHHHhcccchHHHHHHHHHHHHHh
Confidence 44444 3566666652 12222 334444444444444444444444444443
No 45
>KOG0213 consensus Splicing factor 3b, subunit 1 [RNA processing and modification]
Probab=46.65 E-value=3.5e+02 Score=34.40 Aligned_cols=133 Identities=17% Similarity=0.151 Sum_probs=74.8
Q ss_pred CCCHHHHHHHHHHHHHHH----------HhcccCCc---hhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhh
Q 003359 25 PSPVDEVINLLDKVEHLL----------ANVEQAPS---RSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRI 91 (827)
Q Consensus 25 piS~dELLKRLkkL~~eL----------s~lDQ~~v---dS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRI 91 (827)
.+...+|+..|+.++.-= .-+.|-.. .+...-|.++.+- +. ..|.....-||..+|.||+-+.-.
T Consensus 506 algip~llpfLkavc~SkkSwqaRhTgIkivqqIail~Gcsvlphl~~lv~i-i~-~gl~De~qkVR~itAlalsalaea 583 (1172)
T KOG0213|consen 506 ALGIPALLPFLKAVCGSKKSWQARHTGIKIVQQIAILSGCSVLPHLKPLVKI-IE-HGLKDEQQKVRTITALALSALAEA 583 (1172)
T ss_pred HhCcHHHHHHHHHHhccccchhhhchhhHHHHHHHHHhcchhhhhhHHHHHH-HH-HhhcccchhhhhHHHHHHHHHHHh
Confidence 345667777777665422 11222100 1233444444433 23 345555667999999999998866
Q ss_pred cCCCCCCCchHHHHHHHHHHH---------------HhcccCCCCCcchHHHHH---HHHHhhhhc------------ce
Q 003359 92 TAPDSPYDDELMKEFFQLAVS---------------AFENLSHASGRYYMKALS---ILDTVAKVR------------SC 141 (827)
Q Consensus 92 yAPDAPYtDdqLKDIF~LfV~---------------qf~~LaD~ssp~F~q~~y---LLEsLAeVK------------S~ 141 (827)
- .||.-+++-.||..+-. .+.-|=.-..+-|.-||. ||-.+-+.. .+
T Consensus 584 a---~Pygie~fDsVlkpLwkgir~hrgk~laafLkAigyliplmd~eya~yyTrevmlil~rEf~sPDeemkkivLKVv 660 (1172)
T KOG0213|consen 584 A---TPYGIEQFDSVLKPLWKGIRQHRGKELAAFLKAIGYLIPLMDAEYASYYTREVMLILIREFGSPDEEMKKIVLKVV 660 (1172)
T ss_pred c---CCcchHHHHHHHHHHHHHHHHccChHHHHHHHHHhhccccccHHHHHHhHHHHHHHHHHhhCCChHHHHHHHHHHH
Confidence 3 57998888888876532 222222223445555555 554443321 11
Q ss_pred eeeccCC-------chHHHHHHHHHHHH
Q 003359 142 LLMLDLE-------CDKLVVEMFQHFLK 162 (827)
Q Consensus 142 VLmlDLe-------~ddLI~eLFktFFd 162 (827)
--||+-+ -.+++.++|+.|+.
T Consensus 661 ~qcc~t~Gv~~~y~r~dilp~ff~~fw~ 688 (1172)
T KOG0213|consen 661 KQCCATDGVEPAYIRFDILPEFFFSFWG 688 (1172)
T ss_pred HHHhcccCCCHHHHhhhhhHHHHhhhhh
Confidence 1234443 35889999999886
No 46
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=46.39 E-value=1.8e+02 Score=35.69 Aligned_cols=116 Identities=17% Similarity=0.281 Sum_probs=61.7
Q ss_pred chHHHHHHHHHHHHHhhcC------------------CchhHHHHHHHHHHHHhccc----CCCcHHHHHHHHHHhhccC
Q 003359 149 CDKLVVEMFQHFLKVIRSN------------------HPHFVFAAMETIMTLVIDES----EDVSWDLLRILLASVRKEN 206 (827)
Q Consensus 149 ~ddLI~eLFktFFdiVr~~------------------hp~kV~~~M~dILs~VIeEs----E~VP~eLLDvIL~~ll~~~ 206 (827)
|-+-+.+|.-.|++.+... .-+.+.+.+.++|..||--. +.+...++..+|.-+-+..
T Consensus 531 ~~d~V~~~~a~~~~~~~~kl~~~isv~~q~l~~eD~~~~~elqSN~~~vl~aiir~~~~~ie~v~D~lm~Lf~r~les~~ 610 (858)
T COG5215 531 CPDAVSDILAGFYDYTSKKLDECISVLGQILATEDQLLVEELQSNYIGVLEAIIRTRRRDIEDVEDQLMELFIRILESTK 610 (858)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHhccC
Confidence 3455566666677665531 12345555666667777643 4566666666655554443
Q ss_pred CCC---------ChhhHHHHHHHHhhchHHHHHHHHHHHH-------------------hcCCCCchhHHHHHH-HhccC
Q 003359 207 QDV---------SPTSWKLGEKVFTKCAAKLKTNLKEAVQ-------------------SRGIALDDYAEIVAC-ICGSD 257 (827)
Q Consensus 207 ks~---------~PaAy~LA~~VI~~CadKLqp~I~q~l~-------------------S~Gi~ld~Y~eIV~s-I~q~~ 257 (827)
+++ ...+-.|.+ =+...+.++-||+...|+ ++|..+..|.+++.+ +.|+-
T Consensus 611 ~t~~~~dV~~aIsal~~sl~e-~Fe~y~~~fiPyl~~aln~~d~~v~~~avglvgdlantl~~df~~y~d~~ms~LvQ~l 689 (858)
T COG5215 611 PTTAFGDVYTAISALSTSLEE-RFEQYASKFIPYLTRALNCTDRFVLNSAVGLVGDLANTLGTDFNIYADVLMSSLVQCL 689 (858)
T ss_pred CchhhhHHHHHHHHHHHHHHH-HHHHHHhhhhHHHHHHhcchhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHh
Confidence 322 111111111 244556667777766654 356667889887755 44554
Q ss_pred CCCC-CCCC
Q 003359 258 DENP-QHGH 265 (827)
Q Consensus 258 s~~l-~~~~ 265 (827)
++.. ++|.
T Consensus 690 ss~~~~R~l 698 (858)
T COG5215 690 SSEATHRDL 698 (858)
T ss_pred cChhhcccc
Confidence 4433 4444
No 47
>PTZ00429 beta-adaptin; Provisional
Probab=45.96 E-value=3e+02 Score=34.56 Aligned_cols=27 Identities=11% Similarity=0.053 Sum_probs=22.8
Q ss_pred hhccCCCcCchhhhhHHHHHHhhhcCCC
Q 003359 68 DLLRRSDMDVRLSVTSCISEITRITAPD 95 (827)
Q Consensus 68 ~LLkHkDkdVRayVAcCLADILRIyAPD 95 (827)
..|.|++.-||--+|.|+.-|+|+ .|+
T Consensus 147 k~L~D~~pYVRKtAalai~Kly~~-~pe 173 (746)
T PTZ00429 147 RAVADPDPYVRKTAAMGLGKLFHD-DMQ 173 (746)
T ss_pred HHhcCCCHHHHHHHHHHHHHHHhh-Ccc
Confidence 345799999999999999999997 444
No 48
>cd00256 VATPase_H VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example.
Probab=43.58 E-value=5.7e+02 Score=30.18 Aligned_cols=94 Identities=13% Similarity=0.293 Sum_probs=56.7
Q ss_pred CcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHH------HHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccC
Q 003359 74 DMDVRLSVTSCISEITRITAPDSPYDDELMKEFF------QLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDL 147 (827)
Q Consensus 74 DkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF------~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDL 147 (827)
+.+.+-.++.||+.+||+ +..+.+| .+++..|.. ....++-.|++| .|++++-+
T Consensus 157 ~~~~~~~~v~~L~~LL~~---------~~~R~~f~~~~~v~~L~~~L~~----~~~~~Ql~Y~~l-------l~lWlLSF 216 (429)
T cd00256 157 NNDYVQTAARCLQMLLRV---------DEYRFAFVLADGVPTLVKLLSN----ATLGFQLQYQSI-------FCIWLLTF 216 (429)
T ss_pred CcchHHHHHHHHHHHhCC---------chHHHHHHHccCHHHHHHHHhh----ccccHHHHHHHH-------HHHHHHhc
Confidence 466666777999999998 2233333 355554542 112333333333 35566655
Q ss_pred C--chHHH--HHHHHHHHHHhhcCCchhHHHHHHHHHHHHhccc
Q 003359 148 E--CDKLV--VEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDES 187 (827)
Q Consensus 148 e--~ddLI--~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEs 187 (827)
+ +.+.+ ..++..+.++++...-++|......|+.-+++-.
T Consensus 217 ~~~~~~~~~~~~~i~~l~~i~k~s~KEKvvRv~l~~l~Nll~~~ 260 (429)
T cd00256 217 NPHAAEVLKRLSLIQDLSDILKESTKEKVIRIVLAIFRNLISKR 260 (429)
T ss_pred cHHHHHhhccccHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhcc
Confidence 4 22333 3466777777777777888888888888888754
No 49
>PF11935 DUF3453: Domain of unknown function (DUF3453); InterPro: IPR021850 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 239 to 261 amino acids in length. ; PDB: 3ODS_A 3ODR_A 3O2Q_A 3O2T_A 3O2S_A 3GS3_A.
Probab=43.52 E-value=3.8e+02 Score=28.64 Aligned_cols=50 Identities=8% Similarity=0.183 Sum_probs=37.4
Q ss_pred hhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchH
Q 003359 51 RSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL 102 (827)
Q Consensus 51 dS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdq 102 (827)
..+++.+..+...+++. +.+.+.|||+.+.=.|--+.=++.|..++++..
T Consensus 35 ~~~W~~~~~lK~~Il~~--~~~~~~gvk~~~iKFle~vIl~qs~~~~~~~~~ 84 (239)
T PF11935_consen 35 EQLWESMNELKDRILSL--WDSENPGVKLAAIKFLERVILVQSPGSSDSPPR 84 (239)
T ss_dssp HHHHHHHHHHHHHHHHG--GGSSSHHHHHHHHHHHHHHHHHTS---TTS---
T ss_pred HHHHHHHHHHHHHHHHH--hcCCCchHHHHHHHHHHHHHHhcCCCCCCCccc
Confidence 46788888888888877 888899999998888888888888888776543
No 50
>PF14911 MMS22L_C: S-phase genomic integrity recombination mediator, C-terminal
Probab=42.29 E-value=5.9e+02 Score=29.60 Aligned_cols=123 Identities=15% Similarity=0.266 Sum_probs=79.1
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCC--c
Q 003359 23 NPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYD--D 100 (827)
Q Consensus 23 ~~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYt--D 100 (827)
.+|......|..|.+|-+.+. .|+ .+....-+..+.-.|...-++-|--.-||..+.--|-.|++-+. ..+.. .
T Consensus 223 ~p~p~l~~vL~fl~~Ll~~~~--~~~-~~~~~~~~~~~lp~lL~c~~~v~e~~~~k~~a~e~l~~mv~~~~-~~~~~~~~ 298 (373)
T PF14911_consen 223 APPPRLASVLAFLQQLLKRLQ--RQN-ENQILTLLRLVLPSLLECLMLVNEEPQVKKLATELLQYMVESCQ-VGSSGEPR 298 (373)
T ss_pred CCCCcHHHHHHHHHHHHHhcC--ccc-chhHHHHHHHhhHHHHHHHhhcCCCcchhHHHHHHHHHHHHccc-ccCcchHH
Confidence 356667788888888887765 121 11113334444455555556666667799888888888887765 22222 3
Q ss_pred hHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHHHhh
Q 003359 101 ELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIR 165 (827)
Q Consensus 101 dqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr 165 (827)
++|..+|.-|+.--- .-|-.+||.+|++||... .+||..||-++=..+.
T Consensus 299 ~~l~s~lrsfvqk~l------~~~t~~~f~~l~~vA~l~----------p~lV~~Lip~i~q~l~ 347 (373)
T PF14911_consen 299 EQLTSVLRSFVQKYL------AHYTYQYFQFLEKVAELD----------PQLVISLIPTIRQSLK 347 (373)
T ss_pred HHHHHHHHHHHHHHh------hhhhHHHHHHHHHHHHhC----------HHHHHHHHHHHHHHHH
Confidence 788888888887532 235567899999999986 4566666655544443
No 51
>KOG2171 consensus Karyopherin (importin) beta 3 [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=42.22 E-value=2.4e+02 Score=36.68 Aligned_cols=84 Identities=18% Similarity=0.235 Sum_probs=54.1
Q ss_pred hhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeecc
Q 003359 67 NDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLD 146 (827)
Q Consensus 67 ~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlD 146 (827)
..+++-.-.-||--+|=-||+|.|---|+ +--++.+|+|.+.. .++.+.-.-.++||-+|.++-.-.+.
T Consensus 86 ~~~~~E~~~~vr~k~~dviAeia~~~l~e------~WPell~~L~q~~~---S~~~~~rE~al~il~s~~~~~~~~~~-- 154 (1075)
T KOG2171|consen 86 EIIQSETEPSVRHKLADVIAEIARNDLPE------KWPELLQFLFQSTK---SPNPSLRESALLILSSLPETFGNTLQ-- 154 (1075)
T ss_pred HHHHhccchHHHHHHHHHHHHHHHhcccc------chHHHHHHHHHHhc---CCCcchhHHHHHHHHhhhhhhccccc--
Confidence 35666677789999999999999998887 56677777777754 34444444567888887766432221
Q ss_pred CCchHHHHHHHHHHHH
Q 003359 147 LECDKLVVEMFQHFLK 162 (827)
Q Consensus 147 Le~ddLI~eLFktFFd 162 (827)
+--+-|..||...+.
T Consensus 155 -~~~~~l~~lf~q~~~ 169 (1075)
T KOG2171|consen 155 -PHLDDLLRLFSQTMT 169 (1075)
T ss_pred -hhHHHHHHHHHHhcc
Confidence 112345555555543
No 52
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=42.02 E-value=40 Score=39.56 Aligned_cols=38 Identities=18% Similarity=0.242 Sum_probs=31.4
Q ss_pred ccccCeEEEeeCCCCceEEEEEEEecCCC------CeEEEEccC
Q 003359 711 QLVGSRIKVWWPMDETFYKGVVDNYDPIK------KKHRILYAD 748 (827)
Q Consensus 711 ~lVG~RVkV~WP~D~~wY~G~V~sYd~~t------kkH~V~YDD 748 (827)
--||.+|.++|..|..||.++|....... ...-|.|..
T Consensus 54 ~~VGekVla~~~~Dg~~~~A~VI~~R~~~~~~~~~~~YYVHY~g 97 (450)
T PLN00104 54 LEVGTRVMCRWRFDGKYHPVKVIERRRGGSGGPNDYEYYVHYTE 97 (450)
T ss_pred eccCCEEEEEECCCCCEEEEEEEEEeccCCCCCCCceEEEEEec
Confidence 34999999999999999999999988632 357788873
No 53
>PF12612 TFCD_C: Tubulin folding cofactor D C terminal; InterPro: IPR022577 This region is found in eukaryotes, and is typically between 182 and 199 amino acids in length. There is a single completely conserved residue R that may be functionally important. Tubulin folding cofactor D does not co-polymerise with microtubules either in vivo or in vitro, but instead modulates microtubule dynamics by sequestering beta-tubulin from GTP-bound alphabeta-heterodimers in microtubules [].
Probab=41.68 E-value=1.5e+02 Score=30.38 Aligned_cols=112 Identities=16% Similarity=0.240 Sum_probs=57.5
Q ss_pred chhhhhHHHHHHhhhcCCCCCCC--chHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHH
Q 003359 77 VRLSVTSCISEITRITAPDSPYD--DELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVV 154 (827)
Q Consensus 77 VRayVAcCLADILRIyAPDAPYt--DdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~ 154 (827)
||..++-||..|+.-..|..|+- .++|.+||..--.. ....-....+|.+.+-||. + +.+-.
T Consensus 23 vR~~A~~~l~~ll~~~~~~~~~ip~~~~L~~i~~~~~~~-~~~w~~~~~~F~~l~~LL~-------------~--~~y~~ 86 (193)
T PF12612_consen 23 VREVAGKCLQRLLHSQDPTIPHIPHREELQDIFPSESEA-SLNWSSSSEYFPRLVKLLD-------------L--PEYRY 86 (193)
T ss_pred HHHHHHHHHHHHhcCCCccccCCCcHHHHHHHccccccc-ccccCCHHHHHHHHHHHhc-------------c--HHHHH
Confidence 89999999999995554433333 36777777543322 0011123345655554432 1 13334
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHhc---ccCCCcHHHHHHHHHHhhcc
Q 003359 155 EMFQHFLKVIRSNHPHFVFAAMETIMTLVID---ESEDVSWDLLRILLASVRKE 205 (827)
Q Consensus 155 eLFktFFdiVr~~hp~kV~~~M~dILs~VIe---EsE~VP~eLLDvIL~~ll~~ 205 (827)
.++..++-.+- ...+.+......-|...|. +.......++..|+.-|..+
T Consensus 87 ~ll~Glv~S~G-~~tesl~~~s~~AL~~~~~~~~~~~~~~~~v~~~l~~il~~~ 139 (193)
T PF12612_consen 87 SLLSGLVVSAG-GLTESLVRASSAALLSYLRELSDSPEELEQVLSDLLSILKEN 139 (193)
T ss_pred HHHhHHHhcCC-CCchhHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHh
Confidence 44444443322 3455555555555555553 34445555566666555543
No 54
>PF13513 HEAT_EZ: HEAT-like repeat; PDB: 2Z5J_A 2OT8_B 2Z5O_A 2H4M_A 2QMR_A 1QBK_B 2Z5M_A 2Z5K_A 2Z5N_A 1GCJ_B ....
Probab=41.64 E-value=41 Score=27.00 Aligned_cols=47 Identities=19% Similarity=0.274 Sum_probs=31.7
Q ss_pred HHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHH
Q 003359 40 HLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEI 88 (827)
Q Consensus 40 ~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADI 88 (827)
..|..+-+...+.+...+..++..|+ .+|.+.+..||..++-||..|
T Consensus 9 ~aLg~l~~~~~~~~~~~~~~~~~~L~--~~L~d~~~~VR~~A~~aLg~l 55 (55)
T PF13513_consen 9 WALGRLAEGCPELLQPYLPELLPALI--PLLQDDDDSVRAAAAWALGNL 55 (55)
T ss_dssp HHHHCTTTTTHHHHHHHHHHHHHHHH--HHTTSSSHHHHHHHHHHHHCH
T ss_pred HHHhhHhcccHHHHHHHHHHHHHHHH--HHHcCCCHHHHHHHHHHHhcC
Confidence 34555555444444445556666666 677888889999999999765
No 55
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=41.47 E-value=4.8e+02 Score=30.44 Aligned_cols=111 Identities=13% Similarity=0.168 Sum_probs=70.9
Q ss_pred CCcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHH
Q 003359 121 SGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLA 200 (827)
Q Consensus 121 ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~ 200 (827)
+...+.+.+.+|.++-+..+..+ .++.+..|.+..+.+.+..........-..++..||- ...||.+-+..++.
T Consensus 147 ~~~~l~~ll~~l~nviKfn~~~l-----~e~~i~~lv~~i~~iC~~Ts~~~di~~~L~vldaii~-y~~iP~~sl~~~i~ 220 (464)
T PF11864_consen 147 EESNLSDLLQFLVNVIKFNFNYL-----DEDEISSLVDQICTICKSTSSEDDIEACLSVLDAIIT-YGDIPSESLSPCIE 220 (464)
T ss_pred hhhhHHHHHHHHHHHHhcCCCCC-----CHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHH-cCcCChHHHHHHHH
Confidence 45566777777777776665443 3456666666666664444444444444556666665 67899988887776
Q ss_pred Hhhc-cC-CCCChhhHHHHHHHH-hhchHHHHHHHHHHHH
Q 003359 201 SVRK-EN-QDVSPTSWKLGEKVF-TKCAAKLKTNLKEAVQ 237 (827)
Q Consensus 201 ~ll~-~~-ks~~PaAy~LA~~VI-~~CadKLqp~I~q~l~ 237 (827)
-|=. .+ .+-...+|+..+++| ..++..+=..++.+|.
T Consensus 221 vLCsi~~~~~l~~~~w~~m~nL~~S~~g~~~i~~L~~iL~ 260 (464)
T PF11864_consen 221 VLCSIVNSVSLCKPSWRTMRNLLKSHLGHSAIRTLCDILR 260 (464)
T ss_pred HHhhHhcccccchhHHHHHHHHHcCccHHHHHHHHHHHHc
Confidence 5421 11 244567899999988 4456677778888884
No 56
>PF08767 CRM1_C: CRM1 C terminal; InterPro: IPR014877 CRM1 (also known as Exportin1) mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 forms a complex with the NES containing protein and the small GTPase Ran. This region forms an alpha helical structure formed by six helical hairpin motifs that are structurally similar to the HEAT repeat, but share little sequence similarity to the HEAT repeat []. ; PDB: 3M1I_C 3GB8_A 1W9C_A 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D.
Probab=41.45 E-value=5.3e+02 Score=28.71 Aligned_cols=101 Identities=18% Similarity=0.258 Sum_probs=56.9
Q ss_pred CHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcC------chhhhhHHHHHHhhhcCCCCCCCc
Q 003359 27 PVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMD------VRLSVTSCISEITRITAPDSPYDD 100 (827)
Q Consensus 27 S~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkd------VRayVAcCLADILRIyAPDAPYtD 100 (827)
--.|.|..+..+-..|...-++.+.-+.+++-..-..+++..+..-++-- +|+.+..|..=++.+ +.
T Consensus 88 r~~evL~l~~~ii~kl~~~~~~~v~~I~~~vf~~Tl~MI~~d~~~yPe~r~~ff~LL~~i~~~~f~~l~~l-------p~ 160 (319)
T PF08767_consen 88 REPEVLSLMATIINKLGELIQPQVPQILEAVFECTLPMINKDFEEYPEHRVNFFKLLRAINEHCFPALLQL-------PP 160 (319)
T ss_dssp S-HHHHHHHHHHHHHHGGGCCCCHHHHHHHHHHHHHHHHSSTSSSSHHHHHHHHHHHHHHHHHHTHHHHHS--------H
T ss_pred cChhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHhhhhhChHHHHHHHHHHHHHHHHhHHHHHcC-------CH
Confidence 35678888888888888866666665666666666677777666544422 344455555555553 44
Q ss_pred hHHHHHHHHHHHHhcccCCCCCc----chHHHHHHHHHhhh
Q 003359 101 ELMKEFFQLAVSAFENLSHASGR----YYMKALSILDTVAK 137 (827)
Q Consensus 101 dqLKDIF~LfV~qf~~LaD~ssp----~F~q~~yLLEsLAe 137 (827)
++.+.++..++- ++.++... ...-...||+.++.
T Consensus 161 ~~f~~~idsi~w---g~kh~~~~I~~~~L~~l~~ll~~~~~ 198 (319)
T PF08767_consen 161 EQFKLVIDSIVW---GFKHTNREISETGLNILLELLNNVSK 198 (319)
T ss_dssp HHHHHHHHHHHH---HHTSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH---HhCCCcHHHHHHHHHHHHHHHHHHHh
Confidence 555555555544 44444433 33333444444444
No 57
>PF14911 MMS22L_C: S-phase genomic integrity recombination mediator, C-terminal
Probab=36.89 E-value=4.3e+02 Score=30.64 Aligned_cols=158 Identities=18% Similarity=0.233 Sum_probs=82.0
Q ss_pred hHHHHHHHHHHHHhcccCCCCCcchHHHHH-HHH----Hhhhhccee--------eeccCCchHHHHHHHHHHHHHhh--
Q 003359 101 ELMKEFFQLAVSAFENLSHASGRYYMKALS-ILD----TVAKVRSCL--------LMLDLECDKLVVEMFQHFLKVIR-- 165 (827)
Q Consensus 101 dqLKDIF~LfV~qf~~LaD~ssp~F~q~~y-LLE----sLAeVKS~V--------LmlDLe~ddLI~eLFktFFdiVr-- 165 (827)
.-++++|-+|+.-+..+.-..++|-.+..- |+. .+.--.+.. ++++-+ -..++.+.+++.++
T Consensus 139 ~ai~k~lpl~lqGl~~~~~~~dayL~~~l~~ii~~y~~~Fl~~~~~~~~~~l~~~~~~~~~---~~~~l~~~il~~i~~~ 215 (373)
T PF14911_consen 139 QAIRKSLPLFLQGLGRLSQRQDAYLNQQLRNIIQQYLPRFLPASPSKLVARLSTLLSAFTP---RNEELRKFILQVIRSN 215 (373)
T ss_pred HHHHHHHHHHHHHHHhcccccChHHHHHHHHHHHHHHhHhccCCCccccccccccccchhh---hhhHHHHHHHHHHHHH
Confidence 568899999998888888777877665421 111 111111111 122221 22233333333333
Q ss_pred -----cCCchhHHHHHHHHHHHHhcc----cCCCcHHHHHHHH----HHhhccC--CCCChhhHHHHHHHHhhch-----
Q 003359 166 -----SNHPHFVFAAMETIMTLVIDE----SEDVSWDLLRILL----ASVRKEN--QDVSPTSWKLGEKVFTKCA----- 225 (827)
Q Consensus 166 -----~~hp~kV~~~M~dILs~VIeE----sE~VP~eLLDvIL----~~ll~~~--ks~~PaAy~LA~~VI~~Ca----- 225 (827)
+.-|..-......++.+++.+ ....-..+++.++ ..++--+ ...-..|-.+-..++++|.
T Consensus 216 fl~~~~~~p~p~l~~vL~fl~~Ll~~~~~~~~~~~~~~~~~~lp~lL~c~~~v~e~~~~k~~a~e~l~~mv~~~~~~~~~ 295 (373)
T PF14911_consen 216 FLEFKGSAPPPRLASVLAFLQQLLKRLQRQNENQILTLLRLVLPSLLECLMLVNEEPQVKKLATELLQYMVESCQVGSSG 295 (373)
T ss_pred HhcCCCCCCCCcHHHHHHHHHHHHHhcCcccchhHHHHHHHhhHHHHHHHhhcCCCcchhHHHHHHHHHHHHcccccCcc
Confidence 233333334455556666666 2333333333333 3332222 2222333344455566676
Q ss_pred ---HHHHHHHHHHHHhcCCC-CchhHHHHHHHhccCCCCC
Q 003359 226 ---AKLKTNLKEAVQSRGIA-LDDYAEIVACICGSDDENP 261 (827)
Q Consensus 226 ---dKLqp~I~q~l~S~Gi~-ld~Y~eIV~sI~q~~s~~l 261 (827)
+.|...+++|.+..+.- --.|..++.+|+..+++.+
T Consensus 296 ~~~~~l~s~lrsfvqk~l~~~t~~~f~~l~~vA~l~p~lV 335 (373)
T PF14911_consen 296 EPREQLTSVLRSFVQKYLAHYTYQYFQFLEKVAELDPQLV 335 (373)
T ss_pred hHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCHHHH
Confidence 44777777777765333 4568999999999888765
No 58
>PF02565 RecO_C: Recombination protein O C terminal; InterPro: IPR003717 The damage avoidance-tolerance pathway(s) requires functional recA, recF, recO, and recR genes, suggesting the mechanism to be daughter strand gap repair. The ruvABC genes or the recG gene is also required. The RecG pathway appears to be more active than the RuvABC pathway []. RecO may contain a mononucleotide-binding fold [].; GO: 0006281 DNA repair, 0006310 DNA recombination; PDB: 3Q8D_B 1W3S_B 2V1C_C 1U5K_B.
Probab=35.18 E-value=93 Score=27.91 Aligned_cols=59 Identities=20% Similarity=0.306 Sum_probs=40.4
Q ss_pred chhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHH-HHHHHhhhhc
Q 003359 77 VRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKAL-SILDTVAKVR 139 (827)
Q Consensus 77 VRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~-yLLEsLAeVK 139 (827)
.|.++|+.++|++.-+.|+.- .-..+|.++...|..|....++...-.. ++|.-+...-
T Consensus 5 ~~~~~a~~~~El~~~~~~~~~----~~~~lf~ll~~~L~~L~~~~~~~~~~~~~f~l~ll~~~G 64 (118)
T PF02565_consen 5 ERLAYASYIAELLDRLLPEGE----PNPELFDLLLAALDALEEGEDPWLLLLIQFELKLLKLLG 64 (118)
T ss_dssp HHHHHHHHHHHHHHHHS-CTS------HHHHHHHHHHHHHHHCSSSHCHHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHHHHHcccCC----ChHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHcC
Confidence 578889999999988776531 1256999999999999877655444444 5666555544
No 59
>PF12074 DUF3554: Domain of unknown function (DUF3554); InterPro: IPR022716 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 287 to 356 amino acids in length. This domain is found associated with PF02985 from PFAM.
Probab=35.16 E-value=6.5e+02 Score=27.72 Aligned_cols=95 Identities=11% Similarity=0.120 Sum_probs=53.5
Q ss_pred CHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHH
Q 003359 27 PVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEF 106 (827)
Q Consensus 27 S~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDI 106 (827)
+-..|...|..+...|..++.+.++ .+.+.++. =|..+...||-....|+.++|+ .+.-.-....+..+
T Consensus 36 nE~aL~~~l~al~~~~~~~~~~~~~-------~~~~~~~k--Gl~~kk~~vR~~w~~~~~~~~~--~~~~~~~~~~~~~~ 104 (339)
T PF12074_consen 36 NEAALSALLSALFKHLFFLSSELPK-------KVVDAFKK--GLKDKKPPVRRAWLLCLGEALW--ESPNSDSLKFAEPF 104 (339)
T ss_pred CHHHHHHHHHHHHHHHHHhCcCCCH-------HHHHHHHH--HhcCCCCcHHHHHHHHHHHHHh--hccCchHHHHHHHH
Confidence 4455777777777777777433333 22222222 3455555699999999999999 11111112455566
Q ss_pred HHHHHHHhccc-CC-----CCCcchHHHHHHH
Q 003359 107 FQLAVSAFENL-SH-----ASGRYYMKALSIL 132 (827)
Q Consensus 107 F~LfV~qf~~L-aD-----~ssp~F~q~~yLL 132 (827)
.-.++..|..- .. ..+....-|++++
T Consensus 105 ~~~L~~~~~~~~~~p~~~~~~~~~~~a~~~l~ 136 (339)
T PF12074_consen 105 LPKLLQSLKEASANPLQSAQNGELVGAYVLLA 136 (339)
T ss_pred HHHHHHHHHHHHhCCCCccccccHHHHHHHHH
Confidence 55666655421 22 2344556666666
No 60
>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=34.78 E-value=3.7e+02 Score=28.80 Aligned_cols=14 Identities=7% Similarity=0.152 Sum_probs=6.2
Q ss_pred Cchh-HHHHHHHhcc
Q 003359 243 LDDY-AEIVACICGS 256 (827)
Q Consensus 243 ld~Y-~eIV~sI~q~ 256 (827)
.+.| +.||..++..
T Consensus 233 ~~k~Gs~Vve~~l~~ 247 (322)
T cd07920 233 CHKFASNVVEKCLKH 247 (322)
T ss_pred cCcchHHHHHHHHHH
Confidence 3444 4444444443
No 61
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=34.32 E-value=1e+02 Score=27.05 Aligned_cols=64 Identities=17% Similarity=0.124 Sum_probs=40.1
Q ss_pred hccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHH-HHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhh
Q 003359 69 LLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMK-EFFQLAVSAFENLSHASGRYYMKALSILDTVAKV 138 (827)
Q Consensus 69 LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLK-DIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeV 138 (827)
+|.+.+..+|..++.||..|..-. +++....+. +++..++..|. +.+..........|.+|+..
T Consensus 15 ~l~~~~~~~~~~a~~~l~~l~~~~---~~~~~~~~~~~~i~~l~~~l~---~~~~~v~~~a~~~L~~l~~~ 79 (120)
T cd00020 15 LLSSSDENVQREAAWALSNLSAGN---NDNIQAVVEAGGLPALVQLLK---SEDEEVVKAALWALRNLAAG 79 (120)
T ss_pred HHHcCCHHHHHHHHHHHHHHhcCC---HHHHHHHHHCCChHHHHHHHh---CCCHHHHHHHHHHHHHHccC
Confidence 667778899999999999887652 222223333 55666666553 34444555567777777654
No 62
>KOG2022 consensus Nuclear transport receptor LGL2 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=34.22 E-value=5.7e+02 Score=32.99 Aligned_cols=183 Identities=16% Similarity=0.270 Sum_probs=101.8
Q ss_pred hhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHh
Q 003359 56 ALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTV 135 (827)
Q Consensus 56 SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsL 135 (827)
.+-+++..+.+ .-++..| +.=|.|+..+--+.--..||..--|.+++.|+++ |- .++.+ -++
T Consensus 702 k~i~~~~kv~s-~~~~~s~----vve~~C~i~~~~v~~~~~sF~~p~l~~l~~Fi~r-~~-----~~~~a-------~tl 763 (982)
T KOG2022|consen 702 KAIPVFEKVLS-MWLGLSD----VVEASCIIMVKGVRSLLTSFPEPMLPSLCPFIVR-FL-----TSCLA-------VTL 763 (982)
T ss_pred HHHHHHHHHHH-HHhcchh----HHHHHHHHHHhccccccccchhhhHHHHHHHHHH-hc-----cchHH-------HHH
Confidence 34455555555 3343333 3567888888877666688989999999999999 53 12221 222
Q ss_pred hhhcceeeeccC--CchHHHHH----HHHHHHHHhh----cCCchhHHHHHHHHHHHHhcccCCCc----HHHHHHHHHH
Q 003359 136 AKVRSCLLMLDL--ECDKLVVE----MFQHFLKVIR----SNHPHFVFAAMETIMTLVIDESEDVS----WDLLRILLAS 201 (827)
Q Consensus 136 AeVKS~VLmlDL--e~ddLI~e----LFktFFdiVr----~~hp~kV~~~M~dILs~VIeEsE~VP----~eLLDvIL~~ 201 (827)
.-.+-|++|.-- .|-+|+.. +|+..|-+.. .++|..+...|. .++.+|.--..++ ...=..||.+
T Consensus 764 ~l~~~~l~~~~~~~~~~~lv~~~~~~~~q~sl~lf~~~~f~n~~Di~~~~~~-~v~~ilkk~P~~~~~~~~~~ts~i~~~ 842 (982)
T KOG2022|consen 764 SLIAACLLAKSTVEQCKPLVGQDMANAFQQSLLLFEQHPFSNQPDIYLQLIG-FVRQILKKIPKFLEPSMLAFTSLILIC 842 (982)
T ss_pred HHHHHHHHhhhccccccccHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH-HHHHHHHhCcCccccchHHHHHHHHHH
Confidence 223334443332 24444444 4444333333 245666666665 6666666544432 2233445533
Q ss_pred hh----ccCCCCChhhHHHHHHHHhhchHHHHHHHHHHHHhcCCC-----------------CchhHHHHHHHhccC
Q 003359 202 VR----KENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIA-----------------LDDYAEIVACICGSD 257 (827)
Q Consensus 202 ll----~~~ks~~PaAy~LA~~VI~~CadKLqp~I~q~l~S~Gi~-----------------ld~Y~eIV~sI~q~~ 257 (827)
+. .+.+.+..+|.++-..++..|....=-.+.+.++.-|-. +|-|++|+..++..-
T Consensus 843 a~~ll~~pE~~~i~aa~qF~t~~~~~~~s~~~~tv~~~V~~~G~~Li~~im~~vgg~~~RS~ld~~aDIL~al~~k~ 919 (982)
T KOG2022|consen 843 AFILLNSPEPTTIRAASQFLTALATYATSHDLVTVTSVVAEIGPILIYAIMRGVGGEASRSTLDALADILLALNAKF 919 (982)
T ss_pred HHHhcCCCccHHHHHHHHHHHHHHhhcccchhHHHHHHHHhcchHHHHHHHHHhcCcCccchhHHHHHHHHHHHHhh
Confidence 22 344445556666555577777765545555555543321 588899888876543
No 63
>KOG1949 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.89 E-value=3.3e+02 Score=34.41 Aligned_cols=152 Identities=18% Similarity=0.246 Sum_probs=84.7
Q ss_pred hhhhhhh---ccCCCcCchhhhhHHHHHHhhhcCCCCCCC--chHHHHHHHHHHHHhc------------ccCCCCCcc-
Q 003359 63 GLITNDL---LRRSDMDVRLSVTSCISEITRITAPDSPYD--DELMKEFFQLAVSAFE------------NLSHASGRY- 124 (827)
Q Consensus 63 ~LVs~~L---LkHkDkdVRayVAcCLADILRIyAPDAPYt--DdqLKDIF~LfV~qf~------------~LaD~ssp~- 124 (827)
-|.++.| |+-.|..||.-+|.-+.|.+=|--||+--. |..|..=|.++-+-|+ |+...-+-|
T Consensus 173 rL~~p~l~R~L~a~Ns~VrsnAa~lf~~~fP~~dpd~~~e~mD~i~~kQf~~l~~LL~d~~p~VRS~a~~gv~k~~s~fW 252 (1005)
T KOG1949|consen 173 RLYKPILWRGLKARNSEVRSNAALLFVEAFPIRDPDLHAEEMDSIIQKQFEELYSLLEDPYPMVRSTAILGVCKITSKFW 252 (1005)
T ss_pred HHHhHHHHHhhccCchhhhhhHHHHHHHhccCCCCCccHHHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHH
Confidence 3445555 566899999999999999999999998332 2333333333322221 000000000
Q ss_pred --------hHHHHHHHHH----------hhhhcceeeeccCC-chHHHHHHHHHHHHHhhc---CCchhHHHHHHHHHHH
Q 003359 125 --------YMKALSILDT----------VAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRS---NHPHFVFAAMETIMTL 182 (827)
Q Consensus 125 --------F~q~~yLLEs----------LAeVKS~VLmlDLe-~ddLI~eLFktFFdiVr~---~hp~kV~~~M~dILs~ 182 (827)
-.--.||... ++.++.+..|+|.+ |..++.. .+-.++. +.++.|+..|.+||..
T Consensus 253 e~iP~~i~~~ll~kI~d~~a~dt~s~VR~svf~gl~~~l~np~sh~~le~----~Lpal~~~l~D~se~VRvA~vd~ll~ 328 (1005)
T KOG1949|consen 253 EMIPPTILIDLLKKITDELAFDTSSDVRCSVFKGLPMILDNPLSHPLLEQ----LLPALRYSLHDNSEKVRVAFVDMLLK 328 (1005)
T ss_pred HHcCHHHHHHHHHHHHHHhhhccchheehhHhcCcHHHHcCccchhHHHH----HHHhcchhhhccchhHHHHHHHHHHH
Confidence 0111233332 34445556677776 6555444 4444443 5678899999999876
Q ss_pred Hhcc-----cCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhc
Q 003359 183 VIDE-----SEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKC 224 (827)
Q Consensus 183 VIeE-----sE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~C 224 (827)
|=+- -.-+|. |.||..|-. .+.|.++.++.-|+..|
T Consensus 329 ik~vra~~f~~I~~~---d~~l~~L~~---d~~~v~rr~~~li~~s~ 369 (1005)
T KOG1949|consen 329 IKAVRAAKFWKICPM---DHILVRLET---DSRPVSRRLVSLIFNSF 369 (1005)
T ss_pred HHhhhhhhhhccccH---HHHHHHHhc---cccHHHHHHHHHHHHhh
Confidence 5432 223554 455555533 44567777776666554
No 64
>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=33.12 E-value=4.6e+02 Score=31.49 Aligned_cols=107 Identities=15% Similarity=0.187 Sum_probs=63.8
Q ss_pred hHHHHHHhhhcCCCCCCCch-----HHHHHHHHHHHHhccc-CCCCCcchHHHHHHHHHhhhhcceeeeccCC-chHHHH
Q 003359 82 TSCISEITRITAPDSPYDDE-----LMKEFFQLAVSAFENL-SHASGRYYMKALSILDTVAKVRSCLLMLDLE-CDKLVV 154 (827)
Q Consensus 82 AcCLADILRIyAPDAPYtDd-----qLKDIF~LfV~qf~~L-aD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe-~ddLI~ 154 (827)
=+|+.-+|..+.+ .|+.. +...+|..++..|... =.+-...|.|++ +=-++.. +-+ ++.++.
T Consensus 281 D~im~~lf~~l~~--~~~~~~~~~~~~~~lf~~Ll~~F~~~ILpT~~sr~vQFl--~Fy~~s~-------~~~~~~~Fl~ 349 (563)
T PF05327_consen 281 DSIMDLLFEYLDS--CFTNGSLDEGNADSLFNTLLSIFESHILPTHKSRHVQFL--LFYFCSL-------DPELADAFLS 349 (563)
T ss_dssp HHHHHHHHHHHHH--HS-HHHHHSSTHHHHHHHHHHHHHHTCCCC-S-SSTTHH--HHHHHTT-------SHHHHHHHHH
T ss_pred HHHHHHHHHHHHH--hccCCccchhHHHHHHHHHHHHHHHHccCCCccchHHHH--HHHHHHc-------CchHHHHHHH
Confidence 3566666666555 45543 3666999999999843 334444566652 2222221 222 567777
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHh
Q 003359 155 EMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASV 202 (827)
Q Consensus 155 eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~l 202 (827)
.|++.+|+ ++.|..++..-..=|+..|.-+..||..++..+|..|
T Consensus 350 ~L~~~~~~---~~~~~~~R~~A~~YlaSflaRAk~v~~~~v~~~l~~L 394 (563)
T PF05327_consen 350 FLWKIAFD---PNQPPVTRQAAAAYLASFLARAKFVPLSTVRSVLSYL 394 (563)
T ss_dssp HHHHHHH----SSS-HHHHHHHHHHHHHHHHHBTT--HHHHHHHHHHH
T ss_pred HHHHHHhC---CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 77777773 5667778887788888888888888888776666544
No 65
>PF05997 Nop52: Nucleolar protein,Nop52; InterPro: IPR010301 Nop52 is believed to be involved in the generation of 28S rRNA [].; GO: 0006364 rRNA processing, 0030688 preribosome, small subunit precursor
Probab=32.82 E-value=2.5e+02 Score=29.66 Aligned_cols=140 Identities=14% Similarity=0.127 Sum_probs=71.1
Q ss_pred HHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHH
Q 003359 33 NLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVS 112 (827)
Q Consensus 33 KRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~ 112 (827)
+-|+.|..+|+.-.+... ...+..+-+.|-= ++-..--+-||--+|..|++|++.+.++. ..--=++-.|.-+.+
T Consensus 19 ~al~~l~~~l~~~~~~~~---~~~~~kLWKGLfy-~mWmsDkpl~Q~~la~~la~l~~~~~~~~-~~~~f~~~f~~tm~r 93 (217)
T PF05997_consen 19 RALKSLRKWLSKRSQLLT---ELDMLKLWKGLFY-CMWMSDKPLVQEELAEELASLIHSFPSEK-AALLFLKAFWETMRR 93 (217)
T ss_pred HHHHHHHHHHHhccccCC---HHHHHHHHHHHHH-HHHhcCCchhHHHHHHHHHHHHHhhcChH-HHHHHHHHHHHHHHH
Confidence 345677777777655421 2335555555542 22223335688899999999999987665 011223333444444
Q ss_pred HhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCC-chHHHHHHHHHHHHHh-hc-C-CchhHHHHHHHHHH
Q 003359 113 AFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVI-RS-N-HPHFVFAAMETIMT 181 (827)
Q Consensus 113 qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe-~ddLI~eLFktFFdiV-r~-~-hp~kV~~~M~dILs 181 (827)
.+.+|. .+=-.-||+|-+.---.++.++-.-. ..+++.++.+.+...+ .. + .|.-+..++.+|..
T Consensus 94 EW~~ID----~~R~DKf~~LvR~~~~~~~~~l~~~~w~~~~v~~~~~~l~~~~l~~~~~~p~Gl~~H~~Di~l 162 (217)
T PF05997_consen 94 EWDGID----RLRMDKFLMLVRRFLRQSFRFLKKNGWDKELVEEFNEILSETPLNPNDQVPNGLRYHFADIFL 162 (217)
T ss_pred HHcccH----HHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHccCCCcCCCchhHHHHHHHHHH
Confidence 455554 11112355555554444454444443 3344444444444432 11 1 34445555555543
No 66
>PF13001 Ecm29: Proteasome stabiliser; InterPro: IPR024372 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). Ecm29 tethers the proteasome core particle to the regulatory particle, stabilising the interaction between these two components [, , ].
Probab=32.81 E-value=2.3e+02 Score=33.50 Aligned_cols=121 Identities=14% Similarity=0.171 Sum_probs=0.0
Q ss_pred eeccCCchHHHHHHHHHHH------HHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhcc--CCCCChhhH
Q 003359 143 LMLDLECDKLVVEMFQHFL------KVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKE--NQDVSPTSW 214 (827)
Q Consensus 143 LmlDLe~ddLI~eLFktFF------diVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~--~ks~~PaAy 214 (827)
+..+++..++|..||..|+ +.-+.-.+..+..-+..+|.. =..+-...+.++.+++..|-.. +..-...+-
T Consensus 264 ~~~~~ed~~~V~~L~~Ly~G~~~~~~~~~~pa~~~lq~kIL~~L~k-S~~Aa~~~~~~~~i~~~~l~~~~~~~klk~~~l 342 (501)
T PF13001_consen 264 LSVSLEDPDLVDRLFDLYLGKGIPPENGRPPASPRLQEKILSLLSK-SVIAATSFPNILQIVFDGLYSDNTNSKLKSLAL 342 (501)
T ss_pred cCCCCCCHHHHHHHHHHHHhcCCchhcCCCCCCHHHHHHHHHHHHH-hHHHHhCCccHHHHHhccccCCccccccchhcc
Q ss_pred HHH---HHHHhhchHHHHHHHHHHHHhcCCCCch-----------------hHHHHHHHhccCCCCCCCC
Q 003359 215 KLG---EKVFTKCAAKLKTNLKEAVQSRGIALDD-----------------YAEIVACICGSDDENPQHG 264 (827)
Q Consensus 215 ~LA---~~VI~~CadKLqp~I~q~l~S~Gi~ld~-----------------Y~eIV~sI~q~~s~~l~~~ 264 (827)
++. ..++..|...+-..+..++.+-|.++-+ -|+.|..|+...+....+|
T Consensus 343 ~F~~~~~~~~~~~~~~~l~~l~~~i~~~g~p~~~~~~~~~~~~~~~~lR~~aYe~lG~L~~~~p~l~~~d 412 (501)
T PF13001_consen 343 QFIRGSSWIFKHISPQILKLLRPVILSQGWPLIQDSSSQSNSSEDIELRSLAYETLGLLAKRAPSLFSKD 412 (501)
T ss_pred hhhhcchHHhhhcCHHHHHHHHHHHHhcCccccccccccCCCcccHHHHHHHHHHHHHHHccCccccccc
No 67
>PF08568 Kinetochor_Ybp2: Uncharacterised protein family, YAP/Alf4/glomulin; InterPro: IPR013877 This is a family of proteins integrally involved in the central kinetochore. In baker's yeast the protein seems to be part of a macromolecular kinetochore complex and appears to contribute to the proper associations among the central kinetochore sub-complexes and the kinetochore-specific nucleosome. The family is localised in such a way as to bridge the COMA and Ndc80 complexes onto the centromeric nucleosome []. This family also includes aberrant root formation protein 4 and glomulin. Aberrant root formation protein 4 (Alf4) of Arabidopsis thaliana (Mouse-ear cress) is required for the initiation of lateral roots independent from auxin signalling. It may also function in maintaining the pericycle in the mitotically competent state needed for lateral root formation []. Glomulin (FAP68) is essential for normal development of the vasculature and may represent a naturally occurring ligand of the immunophilins FKBP59 and FKBP12 [, ].
Probab=32.53 E-value=5.3e+02 Score=31.26 Aligned_cols=124 Identities=19% Similarity=0.273 Sum_probs=69.7
Q ss_pred CCHHHHHHHHHHHHHHHHhcccCCchhh-HHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHH
Q 003359 26 SPVDEVINLLDKVEHLLANVEQAPSRSM-RDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMK 104 (827)
Q Consensus 26 iS~dELLKRLkkL~~eLs~lDQ~~vdS~-~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLK 104 (827)
.+.++--..|..|++.|.+ .|+-+..+ ++-...+...+....+ ..+.-.+--||-+|-|.+-| |
T Consensus 36 ~~~~~~~~~l~~L~~~L~~-n~~l~~~igWDL~~~l~~~~~~~~~-----~~~~~~~~~~l~~la~~gnP---------k 100 (633)
T PF08568_consen 36 YSNEEKEEFLPELLEILQD-NQELTYEIGWDLPKLLLPFLPSSEI-----SPCVDCCMKCLEELARLGNP---------K 100 (633)
T ss_pred cchhhHHHHHHHHHHHHhh-CHHHHHHccccCHHHHHHHhhhhhc-----chHHHHHHHHHHHHHHhCCH---------H
Confidence 4455556666777776643 23222211 2223334433333333 44556677778888888766 6
Q ss_pred HHHHHHHHHhcccCCCC---------------CcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHHHhhcCCc
Q 003359 105 EFFQLAVSAFENLSHAS---------------GRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHP 169 (827)
Q Consensus 105 DIF~LfV~qf~~LaD~s---------------sp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr~~hp 169 (827)
++|--+..++..|...+ ...|.-.|| ++.+|.++.+.-+...+|
T Consensus 101 E~~l~~~E~l~~l~~ed~~~~~~~~~~~~~~~~~~~~~kf~---------------------~Ll~~l~~~l~ri~t~~p 159 (633)
T PF08568_consen 101 ELLLKVCELLEELSPEDEDDEEDDESIERNQIEEPFDLKFY---------------------CLLELLQIVLKRIQTKYP 159 (633)
T ss_pred HHHHHHHHHHHhcccccccccccccccccccchhhhHHHHH---------------------HHHHHHHHHHHHhcccch
Confidence 77777777777766310 111111222 256777777777777788
Q ss_pred hh-HHHHHHHHHHHHhc
Q 003359 170 HF-VFAAMETIMTLVID 185 (827)
Q Consensus 170 ~k-V~~~M~dILs~VIe 185 (827)
.. |..++..|+..+=.
T Consensus 160 s~Fl~~~l~~i~~~~~~ 176 (633)
T PF08568_consen 160 SRFLAMALSAILNFLKN 176 (633)
T ss_pred hHHHHHHHHHHHHHHHh
Confidence 77 76666666665544
No 68
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=32.47 E-value=3.3e+02 Score=34.51 Aligned_cols=221 Identities=14% Similarity=0.229 Sum_probs=118.0
Q ss_pred hccccCCCCCCHHHHHHHHHHHHHHHHhcccCCchh--------hHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHH
Q 003359 17 AGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRS--------MRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEI 88 (827)
Q Consensus 17 ~G~kLi~~piS~dELLKRLkkL~~eLs~lDQ~~vdS--------~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADI 88 (827)
+++++|+..+++.+.-+++ ++.. .|.++-- .-++..+....|.+.. =.-.|.++....|.||++-
T Consensus 44 V~~~IisldL~v~~Vy~~v-----W~~~-~~~~pM~v~YR~~Gl~geAtE~~v~~l~~~~-~~~~d~e~~~~~~~v~~~~ 116 (802)
T PF13764_consen 44 VNNKIISLDLPVRDVYEKV-----WKPN-NQNPPMRVVYRMRGLDGEATEEFVESLEDDS-EEEEDPEQEFKIASVLAEC 116 (802)
T ss_pred ecCeeecCCCcHHHHHHHH-----hccc-CCCCCeEEEEeecCCCCccchhhHhhccCcc-ccccCHHHHHHHHHHhhcC
Confidence 5678889999999988888 4422 2322210 0134445555554432 1114555566666666531
Q ss_pred hhhcCCCCCCCchHHHHHHHHHHHHhcccCCC--CCcchHHHHHHHHHhhhhcce-eeeccCCchHHHHHHHHHHHHHhh
Q 003359 89 TRITAPDSPYDDELMKEFFQLAVSAFENLSHA--SGRYYMKALSILDTVAKVRSC-LLMLDLECDKLVVEMFQHFLKVIR 165 (827)
Q Consensus 89 LRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~--ssp~F~q~~yLLEsLAeVKS~-VLmlDLe~ddLI~eLFktFFdiVr 165 (827)
.-|.. +++.+..+.|. +-.....-+.||....+|+.+ -.++.+.+-..+...++.+|..-.
T Consensus 117 ------------gGL~~----ll~~l~~~~~~~~~~~ll~~llkLL~~c~Kv~~NR~~Ll~~~al~~LL~~L~~~l~~~~ 180 (802)
T PF13764_consen 117 ------------GGLEV----LLSRLDSIRDFSRGRELLQVLLKLLRYCCKVKVNRRALLELNALNRLLSVLNRALQANQ 180 (802)
T ss_pred ------------CCHHH----HHHHHHhhccccCcHHHHHHHHHHHHHHHhhHHHHHHHHHcCCHHHHHHHHHHHHhCcc
Confidence 11221 22223333332 223455667888888888766 344557777888888888887644
Q ss_pred cCCchhHHHHHHHHHHHHhcccCC--C---------------cHHHHHHHHHHhhccCCCCChh-hHHHHHHHHhhc---
Q 003359 166 SNHPHFVFAAMETIMTLVIDESED--V---------------SWDLLRILLASVRKENQDVSPT-SWKLGEKVFTKC--- 224 (827)
Q Consensus 166 ~~hp~kV~~~M~dILs~VIeEsE~--V---------------P~eLLDvIL~~ll~~~ks~~Pa-Ay~LA~~VI~~C--- 224 (827)
+.....+..-|..||..|+.|... + ..+-++.+|.++-......++. .-.|++ ||-.-
T Consensus 181 ~~~~~~i~E~LL~IiE~ll~ea~~~~~~~~~~~~~~~~~~~~~~~~v~~lL~~l~s~~~r~~~~i~~~l~R-iLP~Lt~G 259 (802)
T PF13764_consen 181 NSSQAEIAEQLLEIIESLLSEANSSSSSESKSSSSLSGSEEQDKEQVEMLLERLNSPFVRSNPQILQALAR-ILPFLTYG 259 (802)
T ss_pred ccccchHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccHHHHHHHHHHhcCccccCCHHHHHHHHH-HhhHHhcC
Confidence 344455666666666666666542 1 4566888888887554323332 223333 32211
Q ss_pred hHHHHHHHHHHHHhcCCCCchhH--------HHHHHHhccCCCCCC
Q 003359 225 AAKLKTNLKEAVQSRGIALDDYA--------EIVACICGSDDENPQ 262 (827)
Q Consensus 225 adKLqp~I~q~l~S~Gi~ld~Y~--------eIV~sI~q~~s~~l~ 262 (827)
....-.+|.++|.-. +.++.|. -.+...|+.......
T Consensus 260 ~~e~m~~Lv~~F~p~-l~f~~~D~~~~~~~~~~Le~F~~i~~~I~~ 304 (802)
T PF13764_consen 260 NEEKMDALVEHFKPY-LDFDKFDEEHSPDEQFKLECFCEIAEGIPN 304 (802)
T ss_pred CHHHHHHHHHHHHHh-cChhhcccccCchHHHHHHHHHHHHhcCCC
Confidence 112333455555542 4455552 335555555555543
No 69
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=32.26 E-value=5.3e+02 Score=25.87 Aligned_cols=103 Identities=14% Similarity=0.260 Sum_probs=58.6
Q ss_pred CcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhh-----hccee----ee
Q 003359 74 DMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAK-----VRSCL----LM 144 (827)
Q Consensus 74 DkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAe-----VKS~V----Lm 144 (827)
|..||.-+..||+|+.--| |. +-+.-+..+| ..|.|++-.-=.+.+.+|..|.. +|.-+ +.
T Consensus 1 ~~~vR~n~i~~l~DL~~r~-~~--~ve~~~~~l~-------~~L~D~~~~VR~~al~~Ls~Li~~d~ik~k~~l~~~~l~ 70 (178)
T PF12717_consen 1 DPSVRNNAIIALGDLCIRY-PN--LVEPYLPNLY-------KCLRDEDPLVRKTALLVLSHLILEDMIKVKGQLFSRILK 70 (178)
T ss_pred CHHHHHHHHHHHHHHHHhC-cH--HHHhHHHHHH-------HHHCCCCHHHHHHHHHHHHHHHHcCceeehhhhhHHHHH
Confidence 4678999999999999776 21 1122233333 34456543333344555555432 22211 11
Q ss_pred ccCCchHHHHHHHHHHHHHhhcC-CchhHHHHHHHHHHHHhcc
Q 003359 145 LDLECDKLVVEMFQHFLKVIRSN-HPHFVFAAMETIMTLVIDE 186 (827)
Q Consensus 145 lDLe~ddLI~eLFktFFdiVr~~-hp~kV~~~M~dILs~VIeE 186 (827)
+=.|.++-|..+=..||.-+... .|..+...+.+++..+-..
T Consensus 71 ~l~D~~~~Ir~~A~~~~~e~~~~~~~~~i~~~~~e~i~~l~~~ 113 (178)
T PF12717_consen 71 LLVDENPEIRSLARSFFSELLKKRNPNIIYNNFPELISSLNNC 113 (178)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHhCc
Confidence 11345667777777777755544 6777777777777765543
No 70
>KOG1062 consensus Vesicle coat complex AP-1, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.25 E-value=3.9e+02 Score=33.95 Aligned_cols=165 Identities=17% Similarity=0.197 Sum_probs=89.1
Q ss_pred HHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhh
Q 003359 58 LPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAK 137 (827)
Q Consensus 58 ~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAe 137 (827)
..+++.|+ .||...|.++|+-+|.=|+++.-=|||+-=|--++|-.||..-=+-. .+.--..+|.-||+
T Consensus 384 ~~mv~eLl--~fL~~~d~~~k~~~as~I~~laEkfaP~k~W~idtml~Vl~~aG~~V---------~~dv~~nll~LIa~ 452 (866)
T KOG1062|consen 384 RVMVKELL--EFLESSDEDFKADIASKIAELAEKFAPDKRWHIDTMLKVLKTAGDFV---------NDDVVNNLLRLIAN 452 (866)
T ss_pred HHHHHHHH--HHHHhccHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHhccccc---------chhhHHHHHHHHhc
Confidence 34455555 58999999999999999999999999998888777777776420000 00001111111111
Q ss_pred hcceeeeccCCchHHHHHHHHHHHHHhhcCCchh-HHHHHHHHHHHHhcccC-------------CC-cHHHHHHHHHHh
Q 003359 138 VRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHF-VFAAMETIMTLVIDESE-------------DV-SWDLLRILLASV 202 (827)
Q Consensus 138 VKS~VLmlDLe~ddLI~eLFktFFdiVr~~hp~k-V~~~M~dILs~VIeEsE-------------~V-P~eLLDvIL~~l 202 (827)
- . .++=..-|.-+|..+..+.... =...+..+++-+|.|.. .+ +.+++|.|..-+
T Consensus 453 ~------~----~e~~~y~~~rLy~a~~~~~~~~is~e~l~qVa~W~IGEYGdlll~~~~~~~p~~vtesdivd~l~~v~ 522 (866)
T KOG1062|consen 453 A------F----QELHEYAVLRLYLALSEDTLLDISQEPLLQVASWCIGEYGDLLLDGANEEEPIKVTESDIVDKLEKVL 522 (866)
T ss_pred C------C----cchhhHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHhhhhhHHhhcCccccCCCcCCHHHHHHHHHHHH
Confidence 1 0 0111111122222222211000 01123566667777766 22 256777776666
Q ss_pred hccCCCCChhhHHHHHHH-----HhhchHHHHHHHHHHHHhcCCCC
Q 003359 203 RKENQDVSPTSWKLGEKV-----FTKCAAKLKTNLKEAVQSRGIAL 243 (827)
Q Consensus 203 l~~~ks~~PaAy~LA~~V-----I~~CadKLqp~I~q~l~S~Gi~l 243 (827)
..+..+..--+|.|+.-. +..|..+++..|..|-.+..+.+
T Consensus 523 ~~~~s~~~tk~yal~Al~KLSsr~~s~~~ri~~lI~~~~~s~~~el 568 (866)
T KOG1062|consen 523 MSHSSDSTTKGYALTALLKLSSRFHSSSERIKQLISSYKSSLDTEL 568 (866)
T ss_pred HhccchHHHHHHHHHHHHHHHhhccccHHHHHHHHHHhcccccHHH
Confidence 655555444455554321 34567778888888777655554
No 71
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=32.07 E-value=2.8e+02 Score=36.04 Aligned_cols=75 Identities=12% Similarity=0.089 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHhhcCCc--hhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCC-------h----hhHHHH
Q 003359 151 KLVVEMFQHFLKVIRSNHP--HFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVS-------P----TSWKLG 217 (827)
Q Consensus 151 dLI~eLFktFFdiVr~~hp--~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~-------P----aAy~LA 217 (827)
.+|..+|..++-.+.-+++ ..=.-++.-.|+++.. .+.|...|+=-+|.+++.-...++ | --.+|+
T Consensus 703 ~VID~vlE~Ir~glEin~~~~nQrriA~aryL~ELyn-femvds~vIl~tLy~~i~~g~~~~~~~~~ldppddlFRirlV 781 (1128)
T KOG2051|consen 703 HVIDHVLEDIRPGLEINDYVSNQRRIALARYLGELYN-FEMVDSDVILNTLYHLISLGHFENLTPSALDPPDDLFRIRLV 781 (1128)
T ss_pred hhHHHHHHHHHhhhhcCcHHHHHHHHHHHHHHHHHhh-hhhhhHHHHHHHHHHHhcccccCCCCcccCCChHHHHHHHHH
Confidence 4566677766665543332 2223334444444332 345555555555555553222111 1 234688
Q ss_pred HHHHhhchH
Q 003359 218 EKVFTKCAA 226 (827)
Q Consensus 218 ~~VI~~Cad 226 (827)
..|+.+|..
T Consensus 782 ~~lL~tc~~ 790 (1128)
T KOG2051|consen 782 CMLLQTCGP 790 (1128)
T ss_pred HHHHHHccc
Confidence 889999988
No 72
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=31.83 E-value=4.6e+02 Score=29.38 Aligned_cols=44 Identities=9% Similarity=0.197 Sum_probs=32.6
Q ss_pred hhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhccc
Q 003359 67 NDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENL 117 (827)
Q Consensus 67 ~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~L 117 (827)
..+|.|=+.+.+.-++-+++-+=.| +.+++.+|..=|+..|.+-
T Consensus 31 a~VL~~L~~~e~~~l~~~ma~l~~v-------s~~~~~~vL~ef~~~~~~~ 74 (339)
T PRK05686 31 AKVLKHLTEEEVQKLSAAMANLRNV-------SPEQVEAVLEEFEDEFEAG 74 (339)
T ss_pred HHHHHcCCHHHHHHHHHHHHcCCCC-------CHHHHHHHHHHHHHHHHhc
Confidence 3678887877888888888877655 5568888877777777643
No 73
>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.
Probab=31.32 E-value=2.7e+02 Score=29.75 Aligned_cols=101 Identities=10% Similarity=0.068 Sum_probs=64.7
Q ss_pred HHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchH-------HHHHHHHHHHHhcccCCCCCcchH
Q 003359 54 RDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL-------MKEFFQLAVSAFENLSHASGRYYM 126 (827)
Q Consensus 54 ~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdq-------LKDIF~LfV~qf~~LaD~ssp~F~ 126 (827)
-.....++.+|+...+=.+....-.+++++||+=|--==.+|+-|+.+. --.||..|-+-+... .
T Consensus 32 Fr~~rdi~e~ll~~~~~~~a~~~k~l~i~QfLsRI~eG~~LD~~Fd~~~~~TPLESAl~v~~~I~~E~~~~----~---- 103 (200)
T cd00280 32 FRRTRDIAEALLVGPLKLTATQLKTLRIMQFLSRIAEGKNLDCQFENDEELTPLESALMVLESIEKEFSLP----E---- 103 (200)
T ss_pred HHHHHHHHHHHHhccccccccchhHhHHHHHHHHHHcCCCCCCccCCCCCcChHHHHHHHHHHHHHhcCCc----H----
Confidence 4566788888888777777778889999999987766667888888543 234555554444311 1
Q ss_pred HHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHH
Q 003359 127 KALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLK 162 (827)
Q Consensus 127 q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFd 162 (827)
.-+-..+.|-.+..+++|..-.-.+.-.++|+.+|.
T Consensus 104 ~lhe~i~~lik~~aV~VCm~~g~Fk~A~eiLkr~~~ 139 (200)
T cd00280 104 TLHEEIRKLIKEQAVAVCMENGEFKKAEEVLKRLFS 139 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHhc
Confidence 123344455555555565555555666667777776
No 74
>KOG2062 consensus 26S proteasome regulatory complex, subunit RPN2/PSMD1 [Posttranslational modification, protein turnover, chaperones]
Probab=30.89 E-value=3.7e+02 Score=34.04 Aligned_cols=51 Identities=16% Similarity=0.199 Sum_probs=27.9
Q ss_pred HHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHHHHHHHHHHhcCCCCchh
Q 003359 195 LRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIALDDY 246 (827)
Q Consensus 195 LDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLqp~I~q~l~S~Gi~ld~Y 246 (827)
++..++.|+.+|....-.=....+.| ++....-...|.+.|=..|+.-|.|
T Consensus 292 ik~~l~FL~~~N~tD~~iL~~iK~s~-r~sv~H~A~~iAN~fMh~GTT~D~F 342 (929)
T KOG2062|consen 292 IKLYLQFLLRHNNTDLLILEEIKESV-RNSVCHTATLIANAFMHAGTTSDTF 342 (929)
T ss_pred HHHHHHHHHHcCCchHHHHHHHHHHH-HHhhhhHHHHHHHHHHhcCCcchHH
Confidence 46666777777765543322333333 3333444445556565678886654
No 75
>KOG0211 consensus Protein phosphatase 2A regulatory subunit A and related proteins [Signal transduction mechanisms]
Probab=30.89 E-value=1e+03 Score=30.32 Aligned_cols=138 Identities=10% Similarity=0.113 Sum_probs=88.4
Q ss_pred ccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCc
Q 003359 70 LRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLEC 149 (827)
Q Consensus 70 LkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ 149 (827)
|.+..-.||-.+|-|+.-+.+.|-.+ | .....|++++...... .|..++.+|-+|+.+ ..+=.
T Consensus 527 l~d~v~~Ir~~aa~~l~~l~~~~G~~--w--~~~~~i~k~L~~~~q~-------~y~~R~t~l~si~~l------a~v~g 589 (759)
T KOG0211|consen 527 LPDHVYSIREAAARNLPALVETFGSE--W--ARLEEIPKLLAMDLQD-------NYLVRMTTLFSIHEL------AEVLG 589 (759)
T ss_pred hhhhHHHHHHHHHHHhHHHHHHhCcc--h--hHHHhhHHHHHHhcCc-------ccchhhHHHHHHHHH------HHHhc
Confidence 44556679999999999999998733 3 3566777777765543 788888888888822 22224
Q ss_pred hHHHHHHHHHHHHHhhcCCchhHH----HHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhch
Q 003359 150 DKLVVEMFQHFLKVIRSNHPHFVF----AAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCA 225 (827)
Q Consensus 150 ddLI~eLFktFFdiVr~~hp~kV~----~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~Ca 225 (827)
.++..+.|-.+|.-...+--.+|+ .++..|+..++. .+-.+.+-.++..|...+.-.-+-+..+|..+|..|.
T Consensus 590 ~ei~~~~Llp~~~~l~~D~vanVR~nvak~L~~i~~~L~~---~~~~~~v~pll~~L~~d~~~dvr~~a~~a~~~i~l~~ 666 (759)
T KOG0211|consen 590 QEITCEDLLPVFLDLVKDPVANVRINVAKHLPKILKLLDE---SVRDEEVLPLLETLSSDQELDVRYRAILAFGSIELSR 666 (759)
T ss_pred cHHHHHHHhHHHHHhccCCchhhhhhHHHHHHHHHhhcch---HHHHHHHHHHHHHhccCcccchhHHHHHHHHHHHHHH
Confidence 566666666666544545545554 445566555444 3445566677777777555556666777777666554
Q ss_pred HH
Q 003359 226 AK 227 (827)
Q Consensus 226 dK 227 (827)
-.
T Consensus 667 ~~ 668 (759)
T KOG0211|consen 667 LE 668 (759)
T ss_pred Hh
Confidence 33
No 76
>cd04405 RhoGAP_BRCC3-like RhoGAP_BRCC3-like: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of BRCC3-like proteins. This subgroup also contains two groups of closely related proteins, BRCC3 and DEPDC7, which both contain a C-terminal RhoGAP-like domain and an N-terminal DEP (Disheveled, Egl-10, and Pleckstrin) domain. The function(s) of BRCC3 and DEPDC7 are unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=30.78 E-value=2.2e+02 Score=31.09 Aligned_cols=108 Identities=14% Similarity=0.239 Sum_probs=73.2
Q ss_pred HHHHHHHHHHHHhcccCCC--CCcchHHHHHHHHHhh---------hhcceeeeccCCchHHHHHHHHHHHHHhhcCC--
Q 003359 102 LMKEFFQLAVSAFENLSHA--SGRYYMKALSILDTVA---------KVRSCLLMLDLECDKLVVEMFQHFLKVIRSNH-- 168 (827)
Q Consensus 102 qLKDIF~LfV~qf~~LaD~--ssp~F~q~~yLLEsLA---------eVKS~VLmlDLe~ddLI~eLFktFFdiVr~~h-- 168 (827)
-=+|||..+.+-|..|.+| .+.+|.-|..|++-+- .++.|++++.=+.-+++..|..-...++..+.
T Consensus 104 ~e~dv~~ti~qyf~~LpEPLLT~~l~~~~~~I~~ll~~~~~e~aleAlQl~~lLLP~enRe~Lq~LL~fl~~va~~~~~~ 183 (235)
T cd04405 104 FKRLLFKTIAKYYGQLKEPLLTFHLFDIFVGILELLGNGKEEVALEALQLCLLLLPPASRRELRRLLRFMARAAKNDMPR 183 (235)
T ss_pred hHHHHHHHHHHHHhcCCCccCcchHHHHHHHHHHHhcCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCccc
Confidence 3357888888888888775 5667777777777444 56677776666666777777776666655542
Q ss_pred -ch--hHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCC
Q 003359 169 -PH--FVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDV 209 (827)
Q Consensus 169 -p~--kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~ 209 (827)
.+ .-+..|..+.+..|--+..++....+.|+..++.+.+..
T Consensus 184 L~~~~~nR~~v~~~Fs~~ii~~~~l~~~~~~~LV~Fmmd~~~~i 227 (235)
T cd04405 184 LHKEIENRMLVKQTFSRAILCSKDLDEGLADLLVLFLMDHHQDI 227 (235)
T ss_pred cccccchHHHHHHHhhhHhcCccccCHHHHHHHHHHHHHcchhh
Confidence 12 223366677777776677888888888888887766543
No 77
>KOG4338 consensus Predicted lipoprotein [Lipid transport and metabolism]
Probab=30.74 E-value=2.2e+02 Score=38.48 Aligned_cols=173 Identities=13% Similarity=0.145 Sum_probs=0.0
Q ss_pred HHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHH
Q 003359 8 IELEEQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISE 87 (827)
Q Consensus 8 ~ele~~l~~~G~kLi~~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLAD 87 (827)
+.|++|+.+-|-.=..|+.....+-..|+.|..+-..+++.+.. ..+. .+.-|+.
T Consensus 319 e~Le~q~~~~~d~a~~pq~~e~~~~~kl~~l~s~a~~i~~~e~~----------------~~~e---------~~~tla~ 373 (1680)
T KOG4338|consen 319 EKLETQLLKPGDEAESPQLTESTSEQKLDLLESIAEQIEETENN----------------EPVE---------TRHTLAR 373 (1680)
T ss_pred HHHHHHHhcCCChhcCcccccchHHHHHHHHHHHHHHHhhhccc----------------cchh---------HHHHHHH
Q ss_pred HhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHHHhhcC
Q 003359 88 ITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSN 167 (827)
Q Consensus 88 ILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr~~ 167 (827)
+.|+ +|++ +.+||+.||++. |-+++.-...-+.++|.+++-.+-..
T Consensus 374 ~Vkl-~~e~--s~dqLk~i~r~~-------------------------------ve~~~~~~~~~ir~i~d~~l~~~gTk 419 (1680)
T KOG4338|consen 374 LVKL-LREP--SHDQLKKIYRLL-------------------------------VETCYVKAPEKIRELIDVALALAGTK 419 (1680)
T ss_pred HHHH-hccC--CHHHHHHHHHHH-------------------------------HhhhhccchHHHHHHHHHHHHHhhhh
Q ss_pred CchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchH--HHHHHHHHHHHhcCCCCch
Q 003359 168 HPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAA--KLKTNLKEAVQSRGIALDD 245 (827)
Q Consensus 168 hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~Cad--KLqp~I~q~l~S~Gi~ld~ 245 (827)
..-.+..+| ...+..+..+++.-+.--....-++..+|+.+|+.|.. -+.++-..+++ .....
T Consensus 420 ~ti~~~~~~------------v~~~k~itP~~as~ik~lv~~pfps~~ia~~liQ~~esf~~i~~d~~~lrQ---aa~l~ 484 (1680)
T KOG4338|consen 420 NTIQHITHH------------VLNQKSITPLEASRIKLLVEMPFPSLTIAEALIQLLESFHPISEDAEVLRQ---AAWLA 484 (1680)
T ss_pred HHHHHHHHH------------HhhhhhcchhHhhhhhhhhcCCCchHHHHHHHHHHHHhhcccCcccHHHHH---HHHHh
Q ss_pred hHHHHHHHh
Q 003359 246 YAEIVACIC 254 (827)
Q Consensus 246 Y~eIV~sI~ 254 (827)
|..+|.-+|
T Consensus 485 a~t~V~~v~ 493 (1680)
T KOG4338|consen 485 AGTAVRGVF 493 (1680)
T ss_pred hchHhhhhh
No 78
>KOG0301 consensus Phospholipase A2-activating protein (contains WD40 repeats) [Lipid transport and metabolism]
Probab=30.61 E-value=4.9e+02 Score=32.57 Aligned_cols=125 Identities=24% Similarity=0.230 Sum_probs=58.3
Q ss_pred CHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhh---hc--------------cC--CCcCchhhhhHHHHH
Q 003359 27 PVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITND---LL--------------RR--SDMDVRLSVTSCISE 87 (827)
Q Consensus 27 S~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~---LL--------------kH--kDkdVRayVAcCLAD 87 (827)
..++.+..| .+|..+.|-|.+-|--+|.-++-.+.++. ++ .. .+.--++++.=||+.
T Consensus 539 ~~~e~~~~l----~~l~~l~~wp~~~~fPalDilRl~v~h~~~~s~~~~~~~~~~~~~~li~~~~~~~an~ll~vR~L~N 614 (745)
T KOG0301|consen 539 YSSEVLQSL----LALAILLQWPVEMMFPALDILRLAVKHHSSNSLFCDREEGQNLVGTLIPILNADPANQLLVVRCLAN 614 (745)
T ss_pred ccchhHHHH----HHHHHHhcCCHHHhhhHHHHHHHHHhccchhhhhhhhhhhhHHHHhhhcccccchhHHHHHHHHHHH
Confidence 344444444 36667777777755555554443333221 11 11 123345666777777
Q ss_pred HhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccC---CchHHHHHHHHHHHHH
Q 003359 88 ITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDL---ECDKLVVEMFQHFLKV 163 (827)
Q Consensus 88 ILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDL---e~ddLI~eLFktFFdi 163 (827)
+| ++ |+.-.-+---+..+++.|....-.++..++..+ .++|--=|+.++.|- +.-+++...|.+.++-
T Consensus 615 ~f----~~-~~g~~~~~s~~~~i~~~~~~~~s~~~knl~ia~---atlaln~sv~l~~~~~~~~~~~~l~~ai~~~~e~ 685 (745)
T KOG0301|consen 615 LF----SN-PAGRELFMSRLESILDPVIEASSLSNKNLQIAL---ATLALNYSVLLIQDNEQLEGKEVLLSAISTLLEP 685 (745)
T ss_pred hc----cC-HHHHHHHHHHHHHHhhhhhhhhcccchhHHHHH---HHHHHHHHHHHHhcccccchHHHHHHHHHhhccc
Confidence 76 44 555443333355555555544433333433332 222222233333332 2334555555555543
No 79
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=29.86 E-value=68 Score=27.04 Aligned_cols=29 Identities=24% Similarity=0.530 Sum_probs=24.4
Q ss_pred cccccCeEEEeeCCCCceEEEEEEEecCCC
Q 003359 710 EQLVGSRIKVWWPMDETFYKGVVDNYDPIK 739 (827)
Q Consensus 710 e~lVG~RVkV~WP~D~~wY~G~V~sYd~~t 739 (827)
+.++|++|.|.--. ...|.|++.+||..-
T Consensus 4 ~~~~g~~V~V~l~~-g~~~~G~L~~~D~~~ 32 (67)
T PF01423_consen 4 QKLIGKRVRVELKN-GRTYRGTLVSFDQFM 32 (67)
T ss_dssp HHTTTSEEEEEETT-SEEEEEEEEEEETTE
T ss_pred HHhCCcEEEEEEeC-CEEEEEEEEEeechh
Confidence 46789999998884 578999999999743
No 80
>PF04118 Dopey_N: Dopey, N-terminal; InterPro: IPR007249 DopA is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures in the filamentous fungus Emericella nidulans (Aspergillus nidulans). DopA homologues are found in mammals. Saccharomyces cerevisiae DOP1 is essential for viability and, affects cellular morphogenesis [].
Probab=29.79 E-value=2.8e+02 Score=31.16 Aligned_cols=41 Identities=17% Similarity=0.457 Sum_probs=31.9
Q ss_pred CCCchHHHHHHH-HHHHHhcccCCCCCcchHHHHHHHHHhhhh
Q 003359 97 PYDDELMKEFFQ-LAVSAFENLSHASGRYYMKALSILDTVAKV 138 (827)
Q Consensus 97 PYtDdqLKDIF~-LfV~qf~~LaD~ssp~F~q~~yLLEsLAeV 138 (827)
|-.. .|+-++. ||+.-|+||.|.++.+|.+-+.||+.+...
T Consensus 127 pL~~-~L~p~l~~li~slLpGLede~sE~~~~~~~ll~~l~~~ 168 (307)
T PF04118_consen 127 PLGP-ALRPCLKGLILSLLPGLEDEGSEFFDRTLKLLDKLKEA 168 (307)
T ss_pred CccH-HHHHHHHHHHHHhccccccCCchHHHHHHHHHHHHHHh
Confidence 4444 5666666 445559999999999999999999999754
No 81
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=29.78 E-value=88 Score=30.56 Aligned_cols=42 Identities=14% Similarity=0.171 Sum_probs=29.4
Q ss_pred ccccccccCeEEEeeC---CCCceEEEEEEEecCCCCeEEEEccCCC
Q 003359 707 ALNEQLVGSRIKVWWP---MDETFYKGVVDNYDPIKKKHRILYADGD 750 (827)
Q Consensus 707 ~~ge~lVG~RVkV~WP---~D~~wY~G~V~sYd~~tkkH~V~YDDGD 750 (827)
..-...+|+.|+|++- ....+|.|.+.+++. ...++.++++.
T Consensus 80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~--~~i~l~~~~~~ 124 (141)
T PF02576_consen 80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE--DEITLEVEGKG 124 (141)
T ss_dssp HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET--TEEEEEEE-SS
T ss_pred HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC--CEEEEEECCcc
Confidence 3456779999999983 345799999999997 56777777663
No 82
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=29.35 E-value=1.1e+03 Score=30.95 Aligned_cols=124 Identities=9% Similarity=0.091 Sum_probs=65.4
Q ss_pred hhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHH-hcccCCCCCcchHHHHHHHHHhhhhcceeeec
Q 003359 67 NDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSA-FENLSHASGRYYMKALSILDTVAKVRSCLLML 145 (827)
Q Consensus 67 ~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~q-f~~LaD~ssp~F~q~~yLLEsLAeVKS~VLml 145 (827)
+.|+.-.|..|-.++.|||+=+++++ ..-+-.|-+.|+++ +..|..|-=+- .-|-.+-...-+++..
T Consensus 699 ~~Lisesdlhvt~~a~~~L~tl~~~~-------ps~l~~~~~~iL~~ii~ll~Spllqg-----~al~~~l~~f~alV~t 766 (1233)
T KOG1824|consen 699 PPLISESDLHVTQLAVAFLTTLAIIQ-------PSSLLKISNPILDEIIRLLRSPLLQG-----GALSALLLFFQALVIT 766 (1233)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHhcc-------cHHHHHHhhhhHHHHHHHhhCccccc-----hHHHHHHHHHHHHHhc
Confidence 36777788889999999999999883 23345566666666 44444221111 1111222222334445
Q ss_pred cCCchHHHHHHHHHH----HHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhh
Q 003359 146 DLECDKLVVEMFQHF----LKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVR 203 (827)
Q Consensus 146 DLe~ddLI~eLFktF----FdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll 203 (827)
+.++-+ +..+|... |+.+.+..++.....+..+...++.-+......+..-++..|.
T Consensus 767 ~~~~l~-y~~l~s~lt~PV~~~~~~~l~kqa~~siA~cvA~Lt~~~~~~s~s~a~kl~~~~~ 827 (1233)
T KOG1824|consen 767 KEPDLD-YISLLSLLTAPVYEQVTDGLHKQAYYSIAKCVAALTCACPQKSKSLATKLIQDLQ 827 (1233)
T ss_pred CCCCcc-HHHHHHHHcCCcccccccchhHHHHHHHHHHHHHHHHhccccchhHHHHHHHHHh
Confidence 555433 44444333 2223334555666666666666665555555555554444444
No 83
>KOG4327 consensus mRNA splicing protein SMN (survival motor neuron) [RNA processing and modification]
Probab=28.56 E-value=52 Score=35.06 Aligned_cols=44 Identities=25% Similarity=0.463 Sum_probs=35.2
Q ss_pred ccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEcc-CCCeeeeec
Q 003359 713 VGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYA-DGDEEILNL 756 (827)
Q Consensus 713 VG~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YD-DGD~E~L~L 756 (827)
||-.++--|-.+.++|.|+|++.+-......|+|= -|-.+.++|
T Consensus 70 Vgdkc~A~Y~e~g~~ypatidsi~~~~~tcvv~ylgygnr~Ev~l 114 (218)
T KOG4327|consen 70 VGDKCSAIYSEDGCIYPATIDSIDFKRETCVVVYLGYGNREEVNL 114 (218)
T ss_pred ecceeeeeeecCcccccceecccccccCceEEEEEeecchhhhhH
Confidence 89999999999999999999999987777777775 344443444
No 84
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=28.45 E-value=82 Score=26.02 Aligned_cols=29 Identities=28% Similarity=0.464 Sum_probs=24.0
Q ss_pred cccccCeEEEeeCCCCceEEEEEEEecCCC
Q 003359 710 EQLVGSRIKVWWPMDETFYKGVVDNYDPIK 739 (827)
Q Consensus 710 e~lVG~RVkV~WP~D~~wY~G~V~sYd~~t 739 (827)
+.++|++|.|--- |...|.|++.+||.--
T Consensus 2 ~~~~g~~V~V~l~-~g~~~~G~L~~~D~~~ 30 (63)
T cd00600 2 KDLVGKTVRVELK-DGRVLEGVLVAFDKYM 30 (63)
T ss_pred hHHCCCEEEEEEC-CCcEEEEEEEEECCCC
Confidence 4578999998777 5689999999999754
No 85
>PF00514 Arm: Armadillo/beta-catenin-like repeat; InterPro: IPR000225 The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others []. A subset of these proteins is conserved across eukaryotic kingdoms. In higher plants, some Arm-repeat proteins function in intracellular signalling like their mammalian counterparts, while others have novel functions []. The 3-dimensional fold of an armadillo repeat is known from the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit []. The cylindrical structure features a positively charged grove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.; GO: 0005515 protein binding; PDB: 2Z6G_A 1IQ1_C 3RZX_A 2C1M_A 3BTR_C 3OQS_A 3TPO_A 1IAL_A 1Q1S_C 1PJM_B ....
Probab=28.28 E-value=32 Score=26.34 Aligned_cols=23 Identities=17% Similarity=0.348 Sum_probs=20.5
Q ss_pred hhccCCCcCchhhhhHHHHHHhh
Q 003359 68 DLLRRSDMDVRLSVTSCISEITR 90 (827)
Q Consensus 68 ~LLkHkDkdVRayVAcCLADILR 90 (827)
.||+|.|.+|+-.++.||..|.|
T Consensus 19 ~ll~~~~~~v~~~a~~al~nl~~ 41 (41)
T PF00514_consen 19 QLLKSPDPEVQEEAAWALGNLAA 41 (41)
T ss_dssp HHTTSSSHHHHHHHHHHHHHHHT
T ss_pred HHHcCCCHHHHHHHHHHHHHHhC
Confidence 57789999999999999999865
No 86
>PRK14637 hypothetical protein; Provisional
Probab=28.27 E-value=1.1e+02 Score=30.94 Aligned_cols=33 Identities=24% Similarity=0.449 Sum_probs=27.0
Q ss_pred CccccccccCeEEEeeCCCCceEEEEEEEecCC
Q 003359 706 PALNEQLVGSRIKVWWPMDETFYKGVVDNYDPI 738 (827)
Q Consensus 706 ~~~ge~lVG~RVkV~WP~D~~wY~G~V~sYd~~ 738 (827)
...-...+|+.|+|.+.....|+.|++.+++..
T Consensus 90 ~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~ 122 (151)
T PRK14637 90 AAEFSIFVGETVKVWFECTGQWQVGTIAEADET 122 (151)
T ss_pred HHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC
Confidence 334567899999999866778889999999875
No 87
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=28.01 E-value=1.6e+02 Score=28.61 Aligned_cols=68 Identities=16% Similarity=0.225 Sum_probs=47.6
Q ss_pred hcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHHHHHH
Q 003359 165 RSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLK 233 (827)
Q Consensus 165 r~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLqp~I~ 233 (827)
++..+..=...+..|. .+|...+.-|.+.+..|...|...+....--|..|...++.+|+..+...|+
T Consensus 10 s~~l~~~dw~~~l~ic-D~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~ 77 (133)
T smart00288 10 SPSLLEEDWELILEIC-DLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVA 77 (133)
T ss_pred CcCCCCcCHHHHHHHH-HHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHH
Confidence 3344444344555554 3555667889999999999998777666666777888888899888765554
No 88
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=27.96 E-value=2.8e+02 Score=34.88 Aligned_cols=24 Identities=21% Similarity=0.358 Sum_probs=22.6
Q ss_pred hhccCCCcCchhhhhHHHHHHhhh
Q 003359 68 DLLRRSDMDVRLSVTSCISEITRI 91 (827)
Q Consensus 68 ~LLkHkDkdVRayVAcCLADILRI 91 (827)
.+|.|.+.-||-.+|.||..|+|+
T Consensus 134 ~~l~d~~ayVRk~Aalav~kly~l 157 (757)
T COG5096 134 KLLTDPHAYVRKTAALAVAKLYRL 157 (757)
T ss_pred HHccCCcHHHHHHHHHHHHHHHhc
Confidence 578999999999999999999998
No 89
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=27.29 E-value=1.2e+02 Score=29.84 Aligned_cols=39 Identities=15% Similarity=0.376 Sum_probs=29.0
Q ss_pred ccCeEEEeeCCCCceEEEEEEEecC-CCCeEEEEccCCCe
Q 003359 713 VGSRIKVWWPMDETFYKGVVDNYDP-IKKKHRILYADGDE 751 (827)
Q Consensus 713 VG~RVkV~WP~D~~wY~G~V~sYd~-~tkkH~V~YDDGD~ 751 (827)
.|.+|-=.||.=-+||.|+|.+--. ..+...+.++|.+.
T Consensus 74 ~g~~VLAlYP~TT~FY~A~V~~~p~~~~~~y~l~Fedd~~ 113 (130)
T PF07039_consen 74 KGTKVLALYPDTTCFYPATVVSPPKKKSGEYKLKFEDDED 113 (130)
T ss_dssp TT-EEEEE-TTSSEEEEEEEEEE-SSTTS-EEEEECTTTS
T ss_pred CCCEEEEECCCCceEEEEEEEeCCCCCCCcEEEEEeCCCC
Confidence 8999999999999999999999833 34678888875443
No 90
>KOG2259 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.83 E-value=4.3e+02 Score=33.15 Aligned_cols=96 Identities=18% Similarity=0.235 Sum_probs=65.4
Q ss_pred chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHH-
Q 003359 149 CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAK- 227 (827)
Q Consensus 149 ~ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadK- 227 (827)
|-+++.+||+.=+..||- +-...|..|... -.|..+.|+.||..|.. .++-.+.=+.+++..|-.-
T Consensus 411 aldfLvDMfNDE~~~VRL----~ai~aL~~Is~~-----l~i~eeql~~il~~L~D----~s~dvRe~l~elL~~~~~~d 477 (823)
T KOG2259|consen 411 ALDFLVDMFNDEIEVVRL----KAIFALTMISVH-----LAIREEQLRQILESLED----RSVDVREALRELLKNARVSD 477 (823)
T ss_pred HHHHHHHHhccHHHHHHH----HHHHHHHHHHHH-----heecHHHHHHHHHHHHh----cCHHHHHHHHHHHHhcCCCc
Confidence 558899999998888882 233334433332 36777889999998864 3455666666666666533
Q ss_pred ---HHHHHHHHHHhcCCCCchhHHHHHHHhccC
Q 003359 228 ---LKTNLKEAVQSRGIALDDYAEIVACICGSD 257 (827)
Q Consensus 228 ---Lqp~I~q~l~S~Gi~ld~Y~eIV~sI~q~~ 257 (827)
+.-.+..+|.++|.-..+-.+|+..++.+.
T Consensus 478 ~~~i~m~v~~lL~~L~kyPqDrd~i~~cm~~iG 510 (823)
T KOG2259|consen 478 LECIDMCVAHLLKNLGKYPQDRDEILRCMGRIG 510 (823)
T ss_pred HHHHHHHHHHHHHHhhhCCCCcHHHHHHHHHHh
Confidence 566777888888777766778887777654
No 91
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. 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 is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=26.56 E-value=1.4e+02 Score=27.66 Aligned_cols=60 Identities=13% Similarity=0.240 Sum_probs=41.3
Q ss_pred HHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHHHHHHH
Q 003359 174 AAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKE 234 (827)
Q Consensus 174 ~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLqp~I~q 234 (827)
..|..|...+ .+...-+.++++.|...+...+....--|-.|-..++.+|+..+..+|+.
T Consensus 19 ~~i~~i~d~~-~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~f~~~i~~ 78 (115)
T cd00197 19 PLIMEICDLI-NETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVAS 78 (115)
T ss_pred HHHHHHHHHH-HCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHHHHHHHHH
Confidence 4555555444 45566788899999999876554444456667788888888887766644
No 92
>PF11707 Npa1: Ribosome 60S biogenesis N-terminal; InterPro: IPR021714 Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits []. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre []. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length.
Probab=25.89 E-value=3.6e+02 Score=30.01 Aligned_cols=164 Identities=12% Similarity=0.167 Sum_probs=96.4
Q ss_pred CCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHH
Q 003359 25 PSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMK 104 (827)
Q Consensus 25 piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLK 104 (827)
+.-..+||..=..+...+..|.+|+.+-...-|..+...++....+...-+ ++++-.-||..|..+|.=+.|=....+.
T Consensus 147 ~~~~~~lL~~~~~~~~l~k~l~~D~~~~v~~iL~~l~~~Vl~~~~v~r~~K-~~~fn~~~L~~l~~Ly~~~~~~~~~~~~ 225 (330)
T PF11707_consen 147 PELKRDLLSQKKLMSALFKGLRKDPPETVILILETLKDKVLKDSSVSRSTK-CKLFNEWTLSQLASLYSRDGEDEKSSVA 225 (330)
T ss_pred HHHHHHHHHcCchHHHHHhcccCCCHHHHHHHHHHHHHHhccCCCCChhhh-hhhcCHHHHHHHHHHhcccCCcccchHH
Confidence 334555554444588888999998887566666777777777775555444 8888888999999898877771122333
Q ss_pred HHHHHHHHHhc-----ccCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHH
Q 003359 105 EFFQLAVSAFE-----NLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETI 179 (827)
Q Consensus 105 DIF~LfV~qf~-----~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr~~hp~kV~~~M~dI 179 (827)
+...-|+-.+- ||.=++...|..-. -..+
T Consensus 226 ~~vh~fL~~lcT~p~~Gv~f~d~~~~~~~~----------------------------------------------~~~~ 259 (330)
T PF11707_consen 226 DLVHEFLLALCTDPKHGVCFPDNGWYPRES----------------------------------------------DSGV 259 (330)
T ss_pred HHHHHHHHHHhcCCCcccccCCCCcCcCcc----------------------------------------------cccc
Confidence 32222222211 22112222221111 0000
Q ss_pred HHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHHHHHHHHHHh
Q 003359 180 MTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQS 238 (827)
Q Consensus 180 Ls~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLqp~I~q~l~S 238 (827)
....-...-.+.+.+|-.+|..|. ....+....|+-.|+..|.+=+.+|+..+-.+
T Consensus 260 ~~~~~~~~~~~~Nk~L~~ll~~lk---p~e~~~q~~Lvl~Il~~~PeLva~Y~~~~~~~ 315 (330)
T PF11707_consen 260 PVTINNKSFKINNKLLLNLLKKLK---PWEDDRQQELVLKILKACPELVAPYFNNLPYS 315 (330)
T ss_pred cccccCCCCCcccHHHHHHHHHCC---CCccHHHHHHHHHHHHHChHHHHHHHHhhhhh
Confidence 011112233566777777777553 33456778899999999999999999886444
No 93
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=25.69 E-value=44 Score=39.03 Aligned_cols=116 Identities=22% Similarity=0.291 Sum_probs=66.8
Q ss_pred cCchhhhhHHHHHHhhhcCCCCCCCchHHH------HHHHHHHHHhcccCCCCCcch-HHHHHHHHHhhhhcceeeeccC
Q 003359 75 MDVRLSVTSCISEITRITAPDSPYDDELMK------EFFQLAVSAFENLSHASGRYY-MKALSILDTVAKVRSCLLMLDL 147 (827)
Q Consensus 75 kdVRayVAcCLADILRIyAPDAPYtDdqLK------DIF~LfV~qf~~LaD~ssp~F-~q~~yLLEsLAeVKS~VLmlDL 147 (827)
.||-+|...|-. |+|+-.+|+ .-|++|+..-+.|.+.=..+| .+|-..|+.|.++|.=++ +|+
T Consensus 269 sdv~iYggLcAL---------Atfdr~~Lk~~vi~n~~Fk~flel~Pqlr~il~~fy~sky~~cl~~L~~~k~~ll-LD~ 338 (466)
T KOG0686|consen 269 SDVAIYGGLCAL---------ATFDRQDLKLNVIKNESFKLFLELEPQLREILFKFYSSKYASCLELLREIKPRLL-LDM 338 (466)
T ss_pred hhhHHHHhhHhh---------ccCCHHHHHHHHHcchhhhhHHhcChHHHHHHHHHhhhhHHHHHHHHHHhcccee-ech
Confidence 578888888843 788977776 568888887777766444443 456788899999985443 444
Q ss_pred CchHHHHHHHHHHHHHhhcC-----CchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhc
Q 003359 148 ECDKLVVEMFQHFLKVIRSN-----HPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRK 204 (827)
Q Consensus 148 e~ddLI~eLFktFFdiVr~~-----hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~ 204 (827)
=-.+=+ .++|+.||.. +.+-+-.-|..|-..+=.....+-.+|+.+|+..-+.
T Consensus 339 yLaphV----d~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~ 396 (466)
T KOG0686|consen 339 YLAPHV----DNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESELLELILEGKIS 396 (466)
T ss_pred hcchhH----HHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHHHHHHHHccchh
Confidence 211122 4445555532 1222222333333333223334666777788766543
No 94
>PF08385 DHC_N1: Dynein heavy chain, N-terminal region 1; InterPro: IPR013594 Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit []. The region featured in this family includes the sequences implicated in mediating these interactions []. It is thought to be flexible and not to adopt a rigid conformation [].
Probab=25.37 E-value=9e+02 Score=28.17 Aligned_cols=33 Identities=15% Similarity=0.282 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHhcccCCchhhHHhhHHHHHhh
Q 003359 32 INLLDKVEHLLANVEQAPSRSMRDALLPTMKGL 64 (827)
Q Consensus 32 LKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~L 64 (827)
++-|+.|...+..+.......+.+.+.+++.+|
T Consensus 99 ~~fL~~l~~~~~~l~~~~~~~i~~~i~~l~~~l 131 (579)
T PF08385_consen 99 NKFLKPLEPPFELLEASDLSEIQESIPPLFHHL 131 (579)
T ss_pred HHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHH
Confidence 344444444444555555556777777777776
No 95
>COG5231 VMA13 Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]
Probab=25.12 E-value=2.6e+02 Score=32.41 Aligned_cols=110 Identities=16% Similarity=0.169 Sum_probs=61.4
Q ss_pred hhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHH---HHHHHHHhc-ccCCCCCcchHHHHHHHHHhhhhcceee
Q 003359 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEF---FQLAVSAFE-NLSHASGRYYMKALSILDTVAKVRSCLL 143 (827)
Q Consensus 68 ~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDI---F~LfV~qf~-~LaD~ssp~F~q~~yLLEsLAeVKS~VL 143 (827)
+|+.+=|.-.|+++..||.++.-+ |+ |.+-..-+= |+ |+..+. .+++..= ||++|+ |++
T Consensus 156 kl~Q~i~~lTrlfav~cl~~l~~~--~e--~R~i~waentcs~r-~~e~l~n~vg~~ql----QY~SL~--------~iw 218 (432)
T COG5231 156 KLSQLIDFLTRLFAVSCLSNLEFD--VE--KRKIEWAENTCSRR-FMEILQNYVGVKQL----QYNSLI--------IIW 218 (432)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhh--HH--HHHHHHHHhhHHHH-HHHHHHhhhhhhhh----HHHHHH--------HHH
Confidence 456666666777888888887733 11 111111000 11 111111 2222222 333433 455
Q ss_pred eccCC--chHHHHHHHHHH---HHHhhcCCchhHHHHHHHHHHHHhccc--CCCcHHH
Q 003359 144 MLDLE--CDKLVVEMFQHF---LKVIRSNHPHFVFAAMETIMTLVIDES--EDVSWDL 194 (827)
Q Consensus 144 mlDLe--~ddLI~eLFktF---FdiVr~~hp~kV~~~M~dILs~VIeEs--E~VP~eL 194 (827)
++-++ |-++|..||..| ..+|+...-++|......|+..+|+-+ ..|.+.+
T Consensus 219 ~lTf~~~~aqdi~K~~dli~dli~iVk~~~keKV~Rlc~~Iv~n~~dK~pK~~I~~~l 276 (432)
T COG5231 219 ILTFSKECAQDIDKMDDLINDLIAIVKERAKEKVLRLCCGIVANVLDKSPKGYIFSPL 276 (432)
T ss_pred HHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhhhH
Confidence 55555 556666665544 557888888999999999999999965 3454443
No 96
>cd07958 Anticodon_Ia_Leu_BEm Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases. This domain is found in leucyl tRNA synthetases (LeuRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain. In contrast to other class Ia enzymes, the anticodon is not used as an identity element in LeuRS (with exceptions such as Saccharomyces cerevisiae and some other eukaryotes). No anticodon-binding site can be defined for this family, which includes bacterial and eukaryotic mitochondrial members, as well as LeuRS from the archaeal Halobacteria. LeuRS catalyzes the transfer of leucine to the 3'-end of its tRNA.
Probab=24.98 E-value=1.8e+02 Score=25.90 Aligned_cols=29 Identities=17% Similarity=0.164 Sum_probs=24.2
Q ss_pred chhhhhHHHHHHhhhcCCCCCCCchHHHH
Q 003359 77 VRLSVTSCISEITRITAPDSPYDDELMKE 105 (827)
Q Consensus 77 VRayVAcCLADILRIyAPDAPYtDdqLKD 105 (827)
+...+.-||..++++.+|=.|+..+++-+
T Consensus 87 ~~~~~~~~l~~~~~lL~P~~P~~aeei~~ 115 (117)
T cd07958 87 HAAVLREALETLVLLLAPFAPHIAEELWE 115 (117)
T ss_pred hHHHHHHHHHHHHHHHcccchHHHHHHHh
Confidence 66677788999999999999999887643
No 97
>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=24.68 E-value=7.1e+02 Score=29.41 Aligned_cols=115 Identities=16% Similarity=0.218 Sum_probs=64.3
Q ss_pred hhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhccee--e--
Q 003359 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCL--L-- 143 (827)
Q Consensus 68 ~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~V--L-- 143 (827)
..|.|.+..||.+++-.|..+.|- ++.-..--.=.+||.+++..+ .+++...-....-+|..|+...... +
T Consensus 84 ~gL~h~~~~Vr~l~l~~l~~~~~~--~~~~~~~~~~~~l~~~i~~~L---~~~d~~Va~~A~~~L~~l~~~~~~~~~l~~ 158 (503)
T PF10508_consen 84 RGLTHPSPKVRRLALKQLGRIARH--SEGAAQLLVDNELLPLIIQCL---RDPDLSVAKAAIKALKKLASHPEGLEQLFD 158 (503)
T ss_pred HHhcCCCHHHHHHHHHHHHHHhcC--CHHHHHHhcCccHHHHHHHHH---cCCcHHHHHHHHHHHHHHhCCchhHHHHhC
Confidence 356799999999887776655543 111000001124555555554 6787778888888888888765332 1
Q ss_pred ---eccCC------chHHHHHHHHHHHHHhhcCCchhHHHHHHH--HHHHHhcccCC
Q 003359 144 ---MLDLE------CDKLVVEMFQHFLKVIRSNHPHFVFAAMET--IMTLVIDESED 189 (827)
Q Consensus 144 ---mlDLe------~ddLI~eLFktFFdiVr~~hp~kV~~~M~d--ILs~VIeEsE~ 189 (827)
+..|. .+.+-.+++..+-.+. .++......+.+ ++..++.|.+.
T Consensus 159 ~~~~~~L~~l~~~~~~~vR~Rv~el~v~i~--~~S~~~~~~~~~sgll~~ll~eL~~ 213 (503)
T PF10508_consen 159 SNLLSKLKSLMSQSSDIVRCRVYELLVEIA--SHSPEAAEAVVNSGLLDLLLKELDS 213 (503)
T ss_pred cchHHHHHHHHhccCHHHHHHHHHHHHHHH--hcCHHHHHHHHhccHHHHHHHHhcC
Confidence 11111 1223334444443332 355666665554 77777777665
No 98
>PF07637 PSD5: Protein of unknown function (DUF1595); InterPro: IPR013043 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013042 from INTERPRO.
Probab=24.04 E-value=1.7e+02 Score=25.23 Aligned_cols=59 Identities=12% Similarity=0.073 Sum_probs=40.8
Q ss_pred HHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccC
Q 003359 10 LEEQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRR 72 (827)
Q Consensus 10 le~~l~~~G~kLi~~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkH 72 (827)
..+.|..+|.+.--.|.+.+| +.++-.+-.....-..+..+++. ..+..-|.++.||-.
T Consensus 3 a~~~l~~Fa~rAfRRp~~~~e-~~~~~~~~~~~~~~g~~~~~a~~---~~l~aiL~SP~FLY~ 61 (64)
T PF07637_consen 3 AREILRRFARRAFRRPLTDEE-VDRYLALYDSARAQGEDFEEALK---EALQAILCSPSFLYR 61 (64)
T ss_pred HHHHHHHHHHHHhCCCCCHHH-HHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHcCcchhcc
Confidence 456788899998889999999 77777776665554444444444 345556788888743
No 99
>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=23.81 E-value=9.1e+02 Score=25.81 Aligned_cols=139 Identities=12% Similarity=0.128 Sum_probs=66.5
Q ss_pred CchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCC-chHHHHHHHHHHHHHhhcCCchhHHHHHH
Q 003359 99 DDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNHPHFVFAAME 177 (827)
Q Consensus 99 tDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe-~ddLI~eLFktFFdiVr~~hp~kV~~~M~ 177 (827)
+.++...|+..|...+..|......+ ++++.+-+.- +-+ ...|+..+...+..++.+.+-.-|...+.
T Consensus 141 ~~~~~~~i~~~l~~~~~~l~~~~~G~-----~vvq~~l~~~------~~~~~~~l~~~l~~~~~~L~~d~~Gn~vvq~~l 209 (322)
T cd07920 141 PPEDLQFIIDAFKGNCVALSTHPYGC-----RVIQRCLEHC------SEEQREPLLEEILEHALELVQDQFGNYVVQHVL 209 (322)
T ss_pred CHHHHHHHHHHHHHHHHHHHcCcccc-----HHHHHHHHhC------CHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHH
Confidence 34566777777777666665322221 3333333221 111 34566777777777666655544544333
Q ss_pred HHHHHHhcccCCCcHHHHHHHHHHhhcc--CCCCChhhHHHHHHHHhhchHHHH-HHHHHHHHhc-------CCCCchh-
Q 003359 178 TIMTLVIDESEDVSWDLLRILLASVRKE--NQDVSPTSWKLGEKVFTKCAAKLK-TNLKEAVQSR-------GIALDDY- 246 (827)
Q Consensus 178 dILs~VIeEsE~VP~eLLDvIL~~ll~~--~ks~~PaAy~LA~~VI~~CadKLq-p~I~q~l~S~-------Gi~ld~Y- 246 (827)
+-. +....+.|+..|... .-..++-+..+++.++..+..+.. ..+..++... -+..|.|
T Consensus 210 -------~~~---~~~~~~~i~~~l~~~~~~l~~~k~Gs~Vve~~l~~~~~~~~~~ii~~l~~~~~~~~~l~~l~~d~~G 279 (322)
T cd07920 210 -------ELG---DPDDTSRIIEKLLGNIVQLSCHKFASNVVEKCLKHASKEERELIIDEILASGNETSALDTLMKDQYG 279 (322)
T ss_pred -------hcC---CHHHHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHCCHHHHHHHHHHHhcCCCchhHHHHHhCCCcc
Confidence 221 233344444444321 012334456677777777765543 3344443321 1224666
Q ss_pred HHHHHHHhccCC
Q 003359 247 AEIVACICGSDD 258 (827)
Q Consensus 247 ~eIV~sI~q~~s 258 (827)
+-||..+.....
T Consensus 280 n~Viq~~l~~~~ 291 (322)
T cd07920 280 NYVIQTALDVAK 291 (322)
T ss_pred cHHHHHHHHhCC
Confidence 445555554433
No 100
>PF08558 TRF: Telomere repeat binding factor (TRF); InterPro: IPR013867 Telomeres function to shield chromosome ends from degradation and end-to-end fusions, as well as preventing the activation of DNA damage checkpoints. Telomeric repeat binding factor (TRF) proteins TRF1 and TRF2 are major components of vertebrate telomeres required for regulation of telomere stability. TRF1 and TRF2 bind to telomeric DNA as homodimers. Dimerisation involves the TRF homology (TRFH) subdomain contained within the dimerisation domain. The TRFH subdomain is important not only for dimerisation, but for DNA binding, telomere localisation, and interactions with other telomeric proteins. The dimerisation domains of TRF1 and TRF2 show the same multi-helical structure, arranged in a solenoid conformation similar to TPR repeats, which can be divided into an alpha-alpha superhelix and a long alpha hairpin []. The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain IPR001005 from INTERPRO at the carboxy terminus []. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection []. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe (Fission yeast) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres []. This entry represents dimerisation domain.; GO: 0042162 telomeric DNA binding, 0042803 protein homodimerization activity; PDB: 3BQO_A 1H6O_A 3L82_A 3BUA_B 1H6P_B 3BU8_B.
Probab=23.72 E-value=1.9e+02 Score=31.08 Aligned_cols=123 Identities=15% Similarity=0.168 Sum_probs=61.5
Q ss_pred hhHHHHHHhhh--------cCCCCCCCc--hHHHHHHHHHHHHhcccCCCCCc--------chHHHHHHHHHhhhhccee
Q 003359 81 VTSCISEITRI--------TAPDSPYDD--ELMKEFFQLAVSAFENLSHASGR--------YYMKALSILDTVAKVRSCL 142 (827)
Q Consensus 81 VAcCLADILRI--------yAPDAPYtD--dqLKDIF~LfV~qf~~LaD~ssp--------~F~q~~yLLEsLAeVKS~V 142 (827)
+|.+|.-+||- .-||.+... ..|+++|+.+...+. ..+| .-....||.++|..+-..-
T Consensus 11 la~qlL~~~~~~p~~~~~~~~~~s~~~~~F~~l~~lFe~~~~~y~----~~~~~L~~~~l~~~~~e~~I~~~lrk~Nla~ 86 (238)
T PF08558_consen 11 LATQLLRAFSQSPDIISLVSDPDSERGESFRRLRDLFEATKRIYS----SDSPFLSVDELALQDKEQRICQTLRKANLAT 86 (238)
T ss_dssp HHHHHHHHHHC-------------T-HHHHHHHHHHHHHHCCT-S----CCTH--------HHHHHHHHHHHHHHHCTTT
T ss_pred HHHHHHHHHHHhhccchhhhccchHHHHHHHHHHHHHHHHHHHcC----CCCccchhhhhhhcchHHHHHHHHHHHHhhc
Confidence 44455555554 345555554 467777666655552 3344 4555677777776663321
Q ss_pred -eeccCCchH-HHHHHHHHHHHHhhcCCc---hhHHHHHHHHHHH-HhcccCCCcHHHHHHHHHHhhccCC
Q 003359 143 -LMLDLECDK-LVVEMFQHFLKVIRSNHP---HFVFAAMETIMTL-VIDESEDVSWDLLRILLASVRKENQ 207 (827)
Q Consensus 143 -LmlDLe~dd-LI~eLFktFFdiVr~~hp---~kV~~~M~dILs~-VIeEsE~VP~eLLDvIL~~ll~~~k 207 (827)
+..=+++++ =+.++=..||++.++++. +.....-..|-++ +|.-.+..+..-...||..+.+.+-
T Consensus 87 ~l~~~f~~~~i~~~el~~~Fl~if~pe~~~l~k~~~~L~l~LKtQa~i~~l~~~~~~~~~eiL~~lFp~~~ 157 (238)
T PF08558_consen 87 FLDSLFGTDEIGFLELAESFLDIFCPEDSKLLKSQEELYLDLKTQAVISALEKGPFRSAEEILDRLFPDDL 157 (238)
T ss_dssp -TTEE-SSSTS-HHHHHHHHHCCCCCCTC--HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHTSSSS
T ss_pred hHHHhcCCCCCCHHHHHHHHHHHHcccccchhhhHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHcCCCh
Confidence 222234444 345666889999888776 3333333333333 2222235666666677766665543
No 101
>PF14868 DUF4487: Domain of unknown function (DUF4487)
Probab=23.37 E-value=7.1e+02 Score=30.42 Aligned_cols=123 Identities=15% Similarity=0.174 Sum_probs=70.8
Q ss_pred HHHHHHHHHHHH---hcccCCCCCcchHHHHHHH-HHhhhhcceeeeccCCchHHHHHHHHHHHHHhhc-----C-Cchh
Q 003359 102 LMKEFFQLAVSA---FENLSHASGRYYMKALSIL-DTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRS-----N-HPHF 171 (827)
Q Consensus 102 qLKDIF~LfV~q---f~~LaD~ssp~F~q~~yLL-EsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr~-----~-hp~k 171 (827)
-..+|+...+.+ +.++.--+..-+.+-...| -.|+.+.+..-++|.....-|.+++..|...++. + +-..
T Consensus 377 ~~~~i~~~~~~~~~~~~~~~~~s~g~l~~~~~~LsalL~~c~~~~~~~d~~~~~~i~~ii~~lw~~~~~~~v~~~~~l~~ 456 (559)
T PF14868_consen 377 IVQEIFTLCFAFCQKWLSPSSCSLGELGQLNFALSALLQVCNSSGSTIDMKDQTFIVEIISQLWSFLSSKQVSSQPYLQQ 456 (559)
T ss_pred HHHHHHHHHHHHHHHhcccCCcCcchHhHHHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHhchhhhccchHHHH
Confidence 344555555554 4443333444555555555 5556667666666665666676777666665532 2 2245
Q ss_pred HHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHHHHHHHHHHhcCC
Q 003359 172 VFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGI 241 (827)
Q Consensus 172 V~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLqp~I~q~l~S~Gi 241 (827)
+...+..|+..+|... .++.+.-++.. +..-+...+.+.+++++.+|+.++|-
T Consensus 457 ~~~~lL~l~~~~~~~l---~~~~i~qv~~~--------------l~~l~~~~pp~~~kl~~~~FLs~lg~ 509 (559)
T PF14868_consen 457 TLSLLLSLLSFFIQLL---DPQLIEQVLTE--------------LTSLFKSEPPDHVKLALLDFLSSLGK 509 (559)
T ss_pred HHHHHHHHHHHHHHhc---ChHHHHHHHHH--------------HHHHHhhCCCccchHHHHHHHHHhcc
Confidence 6667777777776542 23333333221 22233466677799999999998764
No 102
>KOG2759 consensus Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]
Probab=23.23 E-value=2.7e+02 Score=32.86 Aligned_cols=103 Identities=13% Similarity=0.283 Sum_probs=67.3
Q ss_pred CCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCC---
Q 003359 72 RSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE--- 148 (827)
Q Consensus 72 HkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe--- 148 (827)
.-+.+....++-||-.+||+ |+-=|.- -.-+=.++++..+. .+...|+-+++++. |+.++.+.
T Consensus 168 ~~~~~~~~~~~rcLQ~ll~~--~eyR~~~-v~adg~~~l~~~l~----s~~~~~QlQYqsif-------ciWlLtFn~~~ 233 (442)
T KOG2759|consen 168 STNNDYIQFAARCLQTLLRV--DEYRYAF-VIADGVSLLIRILA----STKCGFQLQYQSIF-------CIWLLTFNPHA 233 (442)
T ss_pred cCCCchHHHHHHHHHHHhcC--cchhhee-eecCcchhhHHHHh----ccCcchhHHHHHHH-------HHHHhhcCHHH
Confidence 35666777888899999998 3322221 11111233344432 33445665555553 77888886
Q ss_pred chHH-HHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccC
Q 003359 149 CDKL-VVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESE 188 (827)
Q Consensus 149 ~ddL-I~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE 188 (827)
|+.+ -..+|+.+.++++...-++|...+..|+.-+|+-.+
T Consensus 234 ae~~~~~~li~~L~~Ivk~~~KEKV~Rivlai~~Nll~k~~ 274 (442)
T KOG2759|consen 234 AEKLKRFDLIQDLSDIVKESTKEKVTRIVLAIFRNLLDKGP 274 (442)
T ss_pred HHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCc
Confidence 4333 125788888899988899999999999999998874
No 103
>cd07961 Anticodon_Ia_Ile_ABEc Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases. This domain is found in isoleucyl tRNA synthetases (IleRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. This family includes bacterial, archaeal, and eukaryotic cytoplasmic members. IleRS catalyzes the transfer of isoleucine to the 3'-end of its tRNA.
Probab=22.84 E-value=47 Score=33.07 Aligned_cols=27 Identities=19% Similarity=0.384 Sum_probs=23.2
Q ss_pred hhhhHHHHHHhhhcCCCCCCCchHHHH
Q 003359 79 LSVTSCISEITRITAPDSPYDDELMKE 105 (827)
Q Consensus 79 ayVAcCLADILRIyAPDAPYtDdqLKD 105 (827)
..+..||..++++.||=+||..++|-.
T Consensus 112 ~~l~~~l~~ll~ll~P~~P~~aEElw~ 138 (183)
T cd07961 112 ATLYEVLLTLSRLMAPFTPFITEEIYQ 138 (183)
T ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 466789999999999999999987654
No 104
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=22.40 E-value=2.4e+02 Score=24.97 Aligned_cols=42 Identities=17% Similarity=0.237 Sum_probs=31.2
Q ss_pred eEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCCeeeeecC
Q 003359 716 RIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDEEILNLK 757 (827)
Q Consensus 716 RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YDDGD~E~L~L~ 757 (827)
+|.+|=.+.-.-|.|.|..+|+..+.=.+...+|+..++.|.
T Consensus 46 ~ity~~~g~~~~~~G~I~~id~~~~~l~~~~~~~~~~~I~~~ 87 (92)
T PF08863_consen 46 TITYYEDGYYQSVTGTIHKIDEINRTLKLKDEDGETEKIPFD 87 (92)
T ss_pred EEEEEECCeeEEEEEEEEEEcCCCCEEEEEeCCCCEEEEEhh
Confidence 344444444567889999999988877777767888888765
No 105
>KOG1058 consensus Vesicle coat complex COPI, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.24 E-value=1.9e+02 Score=36.57 Aligned_cols=29 Identities=28% Similarity=0.306 Sum_probs=25.3
Q ss_pred hccCCCcCchhhhhHHHHHHhhh---cCCCCC
Q 003359 69 LLRRSDMDVRLSVTSCISEITRI---TAPDSP 97 (827)
Q Consensus 69 LLkHkDkdVRayVAcCLADILRI---yAPDAP 97 (827)
=|+|...=||-++-|||..|++. .-||||
T Consensus 142 cleHrhsYVRrNAilaifsIyk~~~~L~pDap 173 (948)
T KOG1058|consen 142 CLEHRHSYVRRNAILAIFSIYKNFEHLIPDAP 173 (948)
T ss_pred HHhCcchhhhhhhheeehhHHhhhhhhcCChH
Confidence 37899999999999999999998 357776
No 106
>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=22.24 E-value=1e+03 Score=25.76 Aligned_cols=45 Identities=13% Similarity=0.218 Sum_probs=31.5
Q ss_pred HHHHHHHhhchHHHHHHHHHHHHhcCCCCchhHHHHHHHhccCCCCC
Q 003359 215 KLGEKVFTKCAAKLKTNLKEAVQSRGIALDDYAEIVACICGSDDENP 261 (827)
Q Consensus 215 ~LA~~VI~~CadKLqp~I~q~l~S~Gi~ld~Y~eIV~sI~q~~s~~l 261 (827)
..+..++..-...+...|.+-++ +.+.++-.++|..+...+-..+
T Consensus 301 ~~l~~~v~~~~~~i~~~V~~~l~--~~~~~~l~~~i~~~v~~dL~~I 345 (367)
T PF04286_consen 301 NLLERIVESNHIDIGEIVEEKLN--SLDDEELEELIESKVGKDLQWI 345 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHhHhh
Confidence 44455666666677777777777 5677888888888877665554
No 107
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=21.67 E-value=2.2e+02 Score=28.41 Aligned_cols=69 Identities=9% Similarity=0.209 Sum_probs=46.9
Q ss_pred hhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHHHHHH
Q 003359 164 IRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLK 233 (827)
Q Consensus 164 Vr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLqp~I~ 233 (827)
.++..+..=...+.+|.- +|...+.-|.+.+..|...|...+....--|..|.+.++.+|+..+...|+
T Consensus 9 Tse~l~~~dw~~il~icD-~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~eva 77 (144)
T cd03568 9 TDEKLTSENWGLILDVCD-KVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVA 77 (144)
T ss_pred cCccCCCcCHHHHHHHHH-HHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHh
Confidence 344444444445555544 444457788999999999987766666666777888888999988765554
No 108
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=21.45 E-value=1.6e+02 Score=29.79 Aligned_cols=42 Identities=14% Similarity=0.208 Sum_probs=33.5
Q ss_pred ccccccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCCe
Q 003359 709 NEQLVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDE 751 (827)
Q Consensus 709 ge~lVG~RVkV~WP~D~~wY~G~V~sYd~~tkkH~V~YDDGD~ 751 (827)
...+||+.|.+- -.|...+.|+|.+..-..+...+.|.||.+
T Consensus 87 a~slVGk~V~~~-~~~g~~~tG~V~~V~~~~g~~~~~~v~G~~ 128 (142)
T PRK09618 87 YSELIGKEVEWE-GEDGEIVSGTVTSVKQKDGDYPLVLDNGTW 128 (142)
T ss_pred HHHHhCCEEEEE-eCCCCEEEEEEEEEEEcCCcEEEEEECCEE
Confidence 568999999864 456679999999988777877788888844
No 109
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=21.33 E-value=1.3e+02 Score=26.52 Aligned_cols=30 Identities=17% Similarity=0.261 Sum_probs=24.3
Q ss_pred cccccCeEEEeeCCCCceEEEEEEEecCCCC
Q 003359 710 EQLVGSRIKVWWPMDETFYKGVVDNYDPIKK 740 (827)
Q Consensus 710 e~lVG~RVkV~WP~D~~wY~G~V~sYd~~tk 740 (827)
..++|++|.|.-- +..-|.|++.+||.--.
T Consensus 10 ~~~~~k~V~V~lk-~g~~~~G~L~~~D~~mN 39 (72)
T PRK00737 10 NNALNSPVLVRLK-GGREFRGELQGYDIHMN 39 (72)
T ss_pred HHhCCCEEEEEEC-CCCEEEEEEEEEcccce
Confidence 4568999999776 56789999999998544
No 110
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=21.09 E-value=1.4e+02 Score=25.86 Aligned_cols=30 Identities=13% Similarity=0.173 Sum_probs=24.3
Q ss_pred cccccCeEEEeeCCCCceEEEEEEEecCCCC
Q 003359 710 EQLVGSRIKVWWPMDETFYKGVVDNYDPIKK 740 (827)
Q Consensus 710 e~lVG~RVkV~WP~D~~wY~G~V~sYd~~tk 740 (827)
..++|++|.|--- +...|.|++.+||.--.
T Consensus 6 ~~~~~~~V~V~l~-~g~~~~G~L~~~D~~mN 35 (68)
T cd01731 6 KDSLNKPVLVKLK-GGKEVRGRLKSYDQHMN 35 (68)
T ss_pred HHhcCCEEEEEEC-CCCEEEEEEEEECCcce
Confidence 4568999998777 46789999999998554
No 111
>PF15611 EH_Signature: EH_Signature domain
Probab=20.95 E-value=1.1e+03 Score=26.15 Aligned_cols=110 Identities=17% Similarity=0.248 Sum_probs=65.4
Q ss_pred HHHHHHhhhcCCCCCCC--chHHH---HHHHHHHHHhcccCCCCC-cchH--HHHHHHHHhhhhcceeeeccCCchHHHH
Q 003359 83 SCISEITRITAPDSPYD--DELMK---EFFQLAVSAFENLSHASG-RYYM--KALSILDTVAKVRSCLLMLDLECDKLVV 154 (827)
Q Consensus 83 cCLADILRIyAPDAPYt--DdqLK---DIF~LfV~qf~~LaD~ss-p~F~--q~~yLLEsLAeVKS~VLmlDLe~ddLI~ 154 (827)
-++.++-.++.+++|.. ..-+. ++...|- --+|.+... .+|. ...++|+.+.... ..+++.
T Consensus 106 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~l~--~lgi~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~~ 174 (389)
T PF15611_consen 106 ELLRDIPELLSPNGPKWLAARLMQGDSSPLEELA--RLGIPPPHSSSWLWQALFSYYLEQIPELP---------DDEFLD 174 (389)
T ss_pred HHHHHhHhhhcccchHHHHHHHHhccccHHHHHH--HcCCCcccchhHHHHHHHHHHHHHHHhcC---------ChHHHH
Confidence 45666678889998833 33333 4444443 224444323 3332 2355666655544 456777
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHhc--ccCCCcHHHHHHHHHHhhccC
Q 003359 155 EMFQHFLKVIRSNHPHFVFAAMETIMTLVID--ESEDVSWDLLRILLASVRKEN 206 (827)
Q Consensus 155 eLFktFFdiVr~~hp~kV~~~M~dILs~VIe--EsE~VP~eLLDvIL~~ll~~~ 206 (827)
++++.+ .+ ...+......+..+|...++ ..+.+...+.+.||..+..+.
T Consensus 175 ~l~~~~--l~-~~~~~~~~~~~~~lL~~~~~~~~~~~~~~~l~~~~l~~~GdPr 225 (389)
T PF15611_consen 175 ELLKLL--LL-DGRPEQRKRALEALLERYIDRSPDEPVHEALRDLLLAIWGDPR 225 (389)
T ss_pred HHHHHH--hh-ccchhHHHHHHHHHHHHHHhcCccchhhHHHHHHHHHHhCCCC
Confidence 777774 23 33555555667777777776 234688888899998776554
No 112
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=20.89 E-value=1.7e+03 Score=27.96 Aligned_cols=222 Identities=13% Similarity=0.254 Sum_probs=114.3
Q ss_pred HHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhhHHHHHHhhhcCCCCCCCchHHHHHHHHHHH
Q 003359 33 NLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVS 112 (827)
Q Consensus 33 KRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHkDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF~LfV~ 112 (827)
.|..-|.+.+...+.....-+.+-|..+...|+.-.=+.--+...|+..-..|..+. .|+||+ -.+-+-.|+.++..
T Consensus 472 w~~~nlv~h~a~a~~~~~S~l~~fY~ai~~~Lv~~t~~~~Ne~n~R~s~fsaLgtli-~~~~d~--V~~~~a~~~~~~~~ 548 (858)
T COG5215 472 WRKENLVDHIAKAVREVESFLAKFYLAILNALVKGTELALNESNLRVSLFSALGTLI-LICPDA--VSDILAGFYDYTSK 548 (858)
T ss_pred HHHHhHHHhhhhhhccccchhHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHH-hhcchh--HHHHHHHHHHHHHH
Confidence 344455555665554333345667777888888766665555666766666777766 457775 23455566666654
Q ss_pred Hhc-------ccCCCCCc-----chHHHHHHHHHhhhhcceeeeccCC-chHHHHHHHHHHHHHhhcCC-chhHHHHHHH
Q 003359 113 AFE-------NLSHASGR-----YYMKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNH-PHFVFAAMET 178 (827)
Q Consensus 113 qf~-------~LaD~ssp-----~F~q~~yLLEsLAeVKS~VLmlDLe-~ddLI~eLFktFFdiVr~~h-p~kV~~~M~d 178 (827)
-|. ..-++++. .-..|..+|+.+-..+- -|++ .+|.+.+||=.++....+.+ -..|+..+..
T Consensus 549 kl~~~isv~~q~l~~eD~~~~~elqSN~~~vl~aiir~~~----~~ie~v~D~lm~Lf~r~les~~~t~~~~dV~~aIsa 624 (858)
T COG5215 549 KLDECISVLGQILATEDQLLVEELQSNYIGVLEAIIRTRR----RDIEDVEDQLMELFIRILESTKPTTAFGDVYTAISA 624 (858)
T ss_pred HHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC----CCcccHHHHHHHHHHHHHhccCCchhhhHHHHHHHH
Confidence 433 11122222 23446666666544321 3555 45655566555555443322 3567788888
Q ss_pred HHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHH------------------------HHHHHHH
Q 003359 179 IMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAK------------------------LKTNLKE 234 (827)
Q Consensus 179 ILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadK------------------------Lqp~I~q 234 (827)
+++.+=+-.+.--..++-.++..+..-+.-....|-.|.-++-+.-..+ |+|.|-.
T Consensus 625 l~~sl~e~Fe~y~~~fiPyl~~aln~~d~~v~~~avglvgdlantl~~df~~y~d~~ms~LvQ~lss~~~~R~lKPaiLS 704 (858)
T COG5215 625 LSTSLEERFEQYASKFIPYLTRALNCTDRFVLNSAVGLVGDLANTLGTDFNIYADVLMSSLVQCLSSEATHRDLKPAILS 704 (858)
T ss_pred HHHHHHHHHHHHHhhhhHHHHHHhcchhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcChhhccccchHHHH
Confidence 7776655544322222222222221111111112222222222222222 4555555
Q ss_pred HHHh----cCCCCchhHHHHHHHhccCCCCC
Q 003359 235 AVQS----RGIALDDYAEIVACICGSDDENP 261 (827)
Q Consensus 235 ~l~S----~Gi~ld~Y~eIV~sI~q~~s~~l 261 (827)
.|.. .|-.+-.|-+.|--+||..++.-
T Consensus 705 vFgDIAlaiga~F~~YL~~im~L~qqas~~~ 735 (858)
T COG5215 705 VFGDIALAIGANFESYLDMIMMLFQQASELD 735 (858)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHHHHHhccC
Confidence 4442 24446788888889999887765
No 113
>KOG2025 consensus Chromosome condensation complex Condensin, subunit G [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=20.85 E-value=5.4e+02 Score=32.64 Aligned_cols=72 Identities=21% Similarity=0.251 Sum_probs=56.1
Q ss_pred cCC-chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCChhhHHHHH
Q 003359 146 DLE-CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGE 218 (827)
Q Consensus 146 DLe-~ddLI~eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE~VP~eLLDvIL~~ll~~~ks~~PaAy~LA~ 218 (827)
+++ -+||+..+|.+++..+- .-..+|+.-...|+..+.+|.-.|+..|.+.|+..+...-.+..|+-+.-|.
T Consensus 75 q~d~e~DlV~~~f~hlLRg~E-skdk~VRfrvlqila~l~d~~~eidd~vfn~l~e~l~~Rl~Drep~VRiqAv 147 (892)
T KOG2025|consen 75 QLDKEEDLVAGTFYHLLRGTE-SKDKKVRFRVLQILALLSDENAEIDDDVFNKLNEKLLIRLKDREPNVRIQAV 147 (892)
T ss_pred ccCchhhHHHHHHHHHHhccc-CcchhHHHHHHHHHHHHhccccccCHHHHHHHHHHHHHHHhccCchHHHHHH
Confidence 444 46799999988887543 3457899999999999999999999999999998887665666666555553
No 114
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=20.48 E-value=7e+02 Score=23.20 Aligned_cols=82 Identities=16% Similarity=0.134 Sum_probs=51.3
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccC-C--CcHHHHHHHHHHhhccCCCCChhhHHHHHHHHhhchHHHHHH
Q 003359 155 EMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESE-D--VSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTN 231 (827)
Q Consensus 155 eLFktFFdiVr~~hp~kV~~~M~dILs~VIeEsE-~--VP~eLLDvIL~~ll~~~ks~~PaAy~LA~~VI~~CadKLqp~ 231 (827)
+.|+..+.-+.+..+. |+..=...|..+|.... . --+.++++++.++..++.=..-.|.+.-..++......+=+.
T Consensus 3 ~~~~~al~~L~dp~~P-vRa~gL~~L~~Li~~~~~~~~~~~~il~l~l~~L~d~DsyVYL~aI~~L~~La~~~p~~vl~~ 81 (92)
T PF10363_consen 3 ETLQEALSDLNDPLPP-VRAHGLVLLRKLIESKSEPVIDIPKILDLFLSQLKDEDSYVYLNAIKGLAALADRHPDEVLPI 81 (92)
T ss_pred HHHHHHHHHccCCCcc-hHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHHChHHHHHH
Confidence 4677777766665554 77777778888888776 2 224567777776665554445555555555666666655555
Q ss_pred HHHHHH
Q 003359 232 LKEAVQ 237 (827)
Q Consensus 232 I~q~l~ 237 (827)
+++.+.
T Consensus 82 L~~~y~ 87 (92)
T PF10363_consen 82 LLDEYA 87 (92)
T ss_pred HHHHHh
Confidence 555444
No 115
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=20.43 E-value=1.3e+03 Score=26.17 Aligned_cols=125 Identities=10% Similarity=0.155 Sum_probs=62.4
Q ss_pred hHHHHHHHHHHHHhcccCCCCCcchHHHHHHHHHhhhhcceeeeccCCchHHHHHHHHHHHHHhhcCCc--hhHHHHHHH
Q 003359 101 ELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHP--HFVFAAMET 178 (827)
Q Consensus 101 dqLKDIF~LfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLmlDLe~ddLI~eLFktFFdiVr~~hp--~kV~~~M~d 178 (827)
.++...|.-++..+.+ .....+..+|++|+.= -.-..|+--+.+-+.+.++.++. -.+...|..
T Consensus 174 ~Elq~yf~~It~a~~~------~~~~~r~~aL~sL~tD--------~gl~~LlPyf~~fI~~~v~~n~~~nl~~L~~lm~ 239 (343)
T cd08050 174 KELQLYFEEITEALVG------SNEEKRREALQSLRTD--------PGLQQLLPYFVRFIAEGVTVNLDQNLALLIYLMR 239 (343)
T ss_pred HHHHHHHHHHHHHHhC------CCHHHHHHHHHHhccC--------CCchhhhhHHHHHHHHHHHhhhcccHHHHHHHHH
Confidence 4556666666666553 2233444555555432 22345666666666667776654 334455556
Q ss_pred HHHHHhcccC-CC---cHHHHHHHHHHhhccCCCCCh------h----hHHHHHHHHhhchHH---HHHHHHHHHHhc
Q 003359 179 IMTLVIDESE-DV---SWDLLRILLASVRKENQDVSP------T----SWKLGEKVFTKCAAK---LKTNLKEAVQSR 239 (827)
Q Consensus 179 ILs~VIeEsE-~V---P~eLLDvIL~~ll~~~ks~~P------a----Ay~LA~~VI~~CadK---Lqp~I~q~l~S~ 239 (827)
++..+|.--. .| =++++-.+|..++...-...| + |..+...||..+... |++.|...|...
T Consensus 240 ~v~ALl~N~~l~le~Ylh~Lip~vltclv~~~l~~~~~~~~h~~LRd~AA~ll~~i~~~f~~~y~~l~~ri~~tl~k~ 317 (343)
T cd08050 240 MVRALLDNPNLHLEPYLHQLIPSVLTCLVAKQLCSRPPDDNHWALRDYAARLLAQICRKFSTSYNTLQPRITRTLLKA 317 (343)
T ss_pred HHHHHhcCCCCchHHhHHHHHHHHHHHhhhHhhcCCCCCchHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHH
Confidence 6666665421 11 122444444444433322222 2 223334566666654 777777555543
No 116
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=20.41 E-value=1.3e+02 Score=26.78 Aligned_cols=30 Identities=23% Similarity=0.296 Sum_probs=25.2
Q ss_pred cccccCeEEEeeCCCCceEEEEEEEecCCCC
Q 003359 710 EQLVGSRIKVWWPMDETFYKGVVDNYDPIKK 740 (827)
Q Consensus 710 e~lVG~RVkV~WP~D~~wY~G~V~sYd~~tk 740 (827)
..++|++|.|.-- |.+.|.|++.+||.-..
T Consensus 6 ~~~l~~~V~V~l~-dgR~~~G~L~~~D~~~N 35 (79)
T cd01717 6 LQLINYRLRVTLQ-DGRQFVGQFLAFDKHMN 35 (79)
T ss_pred HHHcCCEEEEEEC-CCcEEEEEEEEEcCccC
Confidence 4679999999887 66789999999997544
No 117
>PF10165 Ric8: Guanine nucleotide exchange factor synembryn; InterPro: IPR019318 Ric8 is involved in the EGL-30 neurotransmitter signalling pathway []. It is a guanine nucleotide exchange factor [] that regulates neurotransmitter secretion.
Probab=20.20 E-value=6.5e+02 Score=29.41 Aligned_cols=44 Identities=23% Similarity=0.274 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhcCCCCch-hHHHHHHHhccCCCCCCCCCcccc
Q 003359 226 AKLKTNLKEAVQSRGIALDD-YAEIVACICGSDDENPQHGHLIGS 269 (827)
Q Consensus 226 dKLqp~I~q~l~S~Gi~ld~-Y~eIV~sI~q~~s~~l~~~~~~~~ 269 (827)
+.|.-.+..++++....+.+ .++.++.||..+.+.+-+.+--|+
T Consensus 307 ~tL~~rLlrLmt~~~~~~k~~vaellf~Lc~~d~~~~v~~~GyG~ 351 (446)
T PF10165_consen 307 DTLRSRLLRLMTSPDPQLKDAVAELLFVLCKEDASRFVKYVGYGN 351 (446)
T ss_pred cchHHHHHHHhCCCCchHHHHHHHHHHHHHhhhHHHHHHHcCchh
Confidence 34666667767665544544 589999999988877755555444
Done!