Query 002421
Match_columns 925
No_of_seqs 228 out of 399
Neff 3.6
Searched_HMMs 46136
Date Thu Mar 28 23:37:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002421.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002421hhsearch_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 1E-50 2.3E-55 488.8 19.0 247 12-261 3-257 (1266)
2 KOG1525 Sister chromatid cohes 99.7 3.8E-17 8.2E-22 199.8 14.2 247 13-262 409-672 (1266)
3 PF09465 LBR_tudor: Lamin-B re 99.0 8.7E-10 1.9E-14 93.0 6.3 44 712-755 7-50 (55)
4 smart00333 TUDOR Tudor domain. 97.4 0.00031 6.6E-09 57.7 5.8 44 712-757 4-48 (57)
5 smart00743 Agenet Tudor-like d 97.2 0.00057 1.2E-08 57.4 5.5 36 712-748 4-39 (61)
6 cd04508 TUDOR Tudor domains ar 97.2 0.00085 1.9E-08 53.4 5.7 43 714-757 1-44 (48)
7 PF09038 53-BP1_Tudor: Tumour 95.7 0.017 3.6E-07 56.6 5.3 45 709-754 1-45 (122)
8 PF06003 SMN: Survival motor n 94.4 0.091 2E-06 57.0 6.8 47 712-758 70-117 (264)
9 KOG4675 Uncharacterized conser 92.2 0.043 9.2E-07 59.9 0.2 60 707-766 155-222 (273)
10 KOG1992 Nuclear export recepto 90.2 1.9 4.2E-05 53.4 11.1 117 118-239 603-731 (960)
11 PF03378 CAS_CSE1: CAS/CSE pro 84.5 5.3 0.00011 46.6 9.9 139 80-228 45-194 (435)
12 PF05641 Agenet: Agenet domain 81.2 2.9 6.3E-05 36.6 4.8 35 713-748 3-40 (68)
13 PF01602 Adaptin_N: Adaptin N 80.0 17 0.00038 41.4 11.8 24 69-92 275-298 (526)
14 PF15057 DUF4537: Domain of un 78.0 4.9 0.00011 39.3 5.8 42 714-756 1-42 (124)
15 KOG1949 Uncharacterized conser 77.6 39 0.00085 42.2 14.0 149 22-207 205-374 (1005)
16 KOG1248 Uncharacterized conser 74.3 35 0.00076 44.4 13.0 195 28-239 200-396 (1176)
17 KOG0644 Uncharacterized conser 74.0 3.9 8.4E-05 51.0 4.7 44 713-756 981-1036(1113)
18 PF12348 CLASP_N: CLASP N term 71.9 92 0.002 32.0 13.4 181 24-224 17-204 (228)
19 PTZ00429 beta-adaptin; Provisi 71.6 75 0.0016 39.9 14.8 146 59-230 256-401 (746)
20 PF14500 MMS19_N: Dos2-interac 71.3 24 0.00052 38.6 9.5 171 68-265 6-183 (262)
21 PF11717 Tudor-knot: RNA bindi 70.4 11 0.00025 31.8 5.4 37 713-750 3-41 (55)
22 PF05918 API5: Apoptosis inhib 69.1 39 0.00085 41.0 11.4 144 7-163 172-318 (556)
23 PF01602 Adaptin_N: Adaptin N 68.1 5.4 0.00012 45.4 4.0 115 68-203 121-241 (526)
24 KOG0915 Uncharacterized conser 64.7 66 0.0014 43.2 12.6 165 28-202 989-1196(1702)
25 KOG1060 Vesicle coat complex A 64.4 1E+02 0.0022 39.3 13.5 155 55-238 318-474 (968)
26 KOG0213 Splicing factor 3b, su 63.1 1.1E+02 0.0023 39.0 13.3 133 25-162 506-688 (1172)
27 PF00567 TUDOR: Tudor domain; 62.9 16 0.00035 32.8 5.2 47 710-757 51-98 (121)
28 PF12719 Cnd3: Nuclear condens 62.1 2.1E+02 0.0045 31.4 14.5 66 35-115 4-74 (298)
29 PF02985 HEAT: HEAT repeat; I 60.4 2.9 6.3E-05 31.2 0.0 25 68-92 7-31 (31)
30 KOG1248 Uncharacterized conser 60.4 1.3E+02 0.0029 39.5 14.0 161 72-241 708-876 (1176)
31 PF12717 Cnd1: non-SMC mitotic 60.0 68 0.0015 32.5 9.7 77 71-164 73-159 (178)
32 PF03224 V-ATPase_H_N: V-ATPas 55.6 91 0.002 34.3 10.4 123 28-166 27-157 (312)
33 PF12348 CLASP_N: CLASP N term 54.6 88 0.0019 32.1 9.6 90 102-202 50-140 (228)
34 PF12074 DUF3554: Domain of un 53.3 3.6E+02 0.0078 30.0 14.8 96 26-132 35-136 (339)
35 PTZ00429 beta-adaptin; Provisi 50.7 1.5E+02 0.0032 37.5 12.2 26 69-95 148-173 (746)
36 smart00139 MyTH4 Domain in Myo 49.2 2E+02 0.0044 28.9 10.9 101 149-256 18-128 (144)
37 KOG3026 Splicing factor SPF30 49.0 18 0.00038 39.8 3.6 35 713-747 93-127 (262)
38 KOG1241 Karyopherin (importin) 46.2 1.7E+02 0.0038 37.1 11.5 47 67-116 557-607 (859)
39 PF02237 BPL_C: Biotin protein 46.0 58 0.0013 26.9 5.4 39 713-754 2-40 (48)
40 PF12612 TFCD_C: Tubulin foldi 45.0 1.3E+02 0.0027 31.2 9.0 112 77-205 23-139 (193)
41 KOG2023 Nuclear transport rece 44.9 74 0.0016 39.8 8.2 111 129-243 580-712 (885)
42 PF12755 Vac14_Fab1_bd: Vacuol 44.0 46 0.001 31.4 5.1 60 68-135 34-94 (97)
43 KOG2051 Nonsense-mediated mRNA 43.8 1.2E+02 0.0025 39.7 9.8 88 151-239 703-811 (1128)
44 cd00256 VATPase_H VATPase_H, r 43.6 3.2E+02 0.007 32.5 12.9 94 74-187 157-260 (429)
45 PF12719 Cnd3: Nuclear condens 42.2 2.2E+02 0.0048 31.2 10.8 166 71-242 74-286 (298)
46 PLN00104 MYST -like histone ac 42.2 40 0.00087 40.0 5.4 37 712-748 55-97 (450)
47 KOG4338 Predicted lipoprotein 42.0 1.2E+02 0.0027 41.0 10.0 173 8-254 319-493 (1680)
48 PF08605 Rad9_Rad53_bind: Fung 41.9 51 0.0011 33.1 5.4 35 715-751 14-48 (131)
49 PF11935 DUF3453: Domain of un 41.0 2.8E+02 0.0061 29.9 11.1 174 51-255 35-210 (239)
50 PF03224 V-ATPase_H_N: V-ATPas 41.0 68 0.0015 35.3 6.7 35 55-91 146-180 (312)
51 PF11864 DUF3384: Domain of un 39.1 5.1E+02 0.011 30.6 13.6 111 121-237 147-260 (464)
52 PF14911 MMS22L_C: S-phase gen 39.0 4.6E+02 0.0099 30.8 13.0 123 23-165 223-347 (373)
53 KOG1949 Uncharacterized conser 38.5 2.2E+02 0.0048 36.2 10.7 152 63-224 173-369 (1005)
54 PF05997 Nop52: Nucleolar prot 38.5 4.2E+02 0.0091 28.4 11.8 163 33-204 19-195 (217)
55 KOG1488 Translational represso 36.7 88 0.0019 37.8 7.1 94 145-248 274-374 (503)
56 PF08767 CRM1_C: CRM1 C termin 35.3 5.3E+02 0.012 29.0 12.5 101 27-137 88-198 (319)
57 smart00288 VHS Domain present 34.0 1E+02 0.0022 30.3 6.0 68 164-232 9-76 (133)
58 COG5215 KAP95 Karyopherin (imp 32.9 5.8E+02 0.012 32.1 12.7 221 34-261 473-735 (858)
59 PF13513 HEAT_EZ: HEAT-like re 32.9 45 0.00098 27.1 2.9 46 41-88 10-55 (55)
60 PF05327 RRN3: RNA polymerase 32.5 3.1E+02 0.0067 33.3 10.8 100 23-138 45-155 (563)
61 KOG4256 Kinetochore component 32.4 3.5E+02 0.0076 36.0 11.2 104 65-170 498-618 (2209)
62 PF02565 RecO_C: Recombination 32.4 82 0.0018 28.6 4.8 59 77-139 5-64 (118)
63 PF14911 MMS22L_C: S-phase gen 32.3 4.9E+02 0.011 30.6 11.9 156 101-261 139-335 (373)
64 PF10508 Proteasom_PSMB: Prote 32.2 4.9E+02 0.011 31.1 12.2 114 69-189 85-213 (503)
65 PF04118 Dopey_N: Dopey, N-ter 32.0 2.6E+02 0.0056 31.8 9.4 41 97-138 127-168 (307)
66 KOG0211 Protein phosphatase 2A 31.7 7.6E+02 0.017 31.7 14.1 137 70-226 527-667 (759)
67 KOG2022 Nuclear transport rece 31.3 5.8E+02 0.013 33.3 12.9 185 55-258 701-920 (982)
68 cd04405 RhoGAP_BRCC3-like RhoG 31.2 2E+02 0.0043 31.8 8.1 107 102-208 104-226 (235)
69 PF08568 Kinetochor_Ybp2: Unch 30.5 4.7E+02 0.01 32.1 11.9 34 153-186 143-177 (633)
70 cd00197 VHS_ENTH_ANTH VHS, ENT 29.9 1.1E+02 0.0024 28.7 5.4 61 173-234 18-78 (115)
71 cd00020 ARM Armadillo/beta-cat 29.8 85 0.0019 27.8 4.4 64 69-138 15-79 (120)
72 COG5215 KAP95 Karyopherin (imp 29.7 5.1E+02 0.011 32.6 11.6 118 149-266 531-699 (858)
73 COG5096 Vesicle coat complex, 29.3 1.8E+02 0.0038 37.0 8.2 24 68-91 134-157 (757)
74 PF05327 RRN3: RNA polymerase 29.1 1.6E+02 0.0035 35.6 7.7 21 139-159 61-81 (563)
75 cd00280 TRFH Telomeric Repeat 28.8 2.3E+02 0.005 30.7 7.8 101 54-162 32-139 (200)
76 PF00790 VHS: VHS domain; Int 28.0 1.4E+02 0.0031 29.3 5.9 69 163-232 13-81 (140)
77 KOG0212 Uncharacterized conser 27.8 7.1E+02 0.015 31.2 12.4 71 24-96 161-243 (675)
78 PF01423 LSM: LSM domain ; In 27.5 78 0.0017 27.0 3.6 29 710-739 4-32 (67)
79 PF12460 MMS19_C: RNAPII trans 27.4 7.5E+02 0.016 28.6 12.4 201 33-238 17-237 (415)
80 KOG0301 Phospholipase A2-activ 27.3 4.7E+02 0.01 33.1 11.0 90 27-125 539-647 (745)
81 KOG1060 Vesicle coat complex A 26.8 2.5E+02 0.0055 36.0 8.8 126 85-237 307-432 (968)
82 PF04147 Nop14: Nop14-like fam 26.8 1.5E+02 0.0034 37.6 7.3 42 189-230 486-527 (840)
83 cd03568 VHS_STAM VHS domain fa 26.3 1.4E+02 0.0031 30.0 5.7 68 164-232 9-76 (144)
84 KOG2759 Vacuolar H+-ATPase V1 26.1 3.5E+02 0.0077 32.4 9.4 102 72-188 168-274 (442)
85 KOG1991 Nuclear transport rece 26.1 1.4E+03 0.03 30.3 15.0 196 32-242 616-816 (1010)
86 cd00600 Sm_like The eukaryotic 25.6 98 0.0021 25.9 3.8 29 710-739 2-30 (63)
87 cd07920 Pumilio Pumilio-family 25.3 3.7E+02 0.008 29.1 9.0 19 100-118 70-88 (322)
88 PF07637 PSD5: Protein of unkn 25.1 1.5E+02 0.0033 25.9 5.0 59 10-72 3-61 (64)
89 PF08558 TRF: Telomere repeat 25.1 2.3E+02 0.005 30.9 7.3 113 92-208 30-158 (238)
90 KOG2062 26S proteasome regulat 24.5 3.7E+02 0.008 34.5 9.5 51 195-246 292-342 (929)
91 PF10350 DUF2428: Putative dea 24.0 9.6E+02 0.021 26.1 14.2 103 95-204 86-196 (255)
92 PF02854 MIF4G: MIF4G domain; 24.0 6.9E+02 0.015 24.5 10.6 50 188-237 117-173 (209)
93 PF02576 DUF150: Uncharacteris 23.8 1.2E+02 0.0027 29.9 4.6 40 709-750 82-124 (141)
94 KOG1058 Vesicle coat complex C 23.7 1.6E+02 0.0036 37.4 6.4 29 69-97 142-173 (948)
95 KOG0686 COP9 signalosome, subu 23.7 42 0.00092 39.6 1.6 116 75-204 269-396 (466)
96 PF10363 DUF2435: Protein of u 23.6 5.6E+02 0.012 24.2 8.6 82 155-237 3-87 (92)
97 PF07039 DUF1325: SGF29 tudor- 23.5 1.6E+02 0.0035 29.4 5.3 39 713-751 74-113 (130)
98 PF10165 Ric8: Guanine nucleot 23.2 9.2E+02 0.02 28.5 12.2 43 226-268 307-350 (446)
99 KOG4327 mRNA splicing protein 23.1 75 0.0016 34.4 3.1 35 713-747 70-104 (218)
100 PF02854 MIF4G: MIF4G domain; 23.0 5.6E+02 0.012 25.1 9.0 166 13-203 3-180 (209)
101 PRK14718 ribonuclease III; Pro 23.0 3.3E+02 0.0072 32.9 8.5 32 80-113 44-75 (467)
102 PRK14086 dnaA chromosomal repl 22.8 4.3E+02 0.0093 33.0 9.7 75 128-203 399-479 (617)
103 PF14868 DUF4487: Domain of un 22.6 7.5E+02 0.016 30.6 11.6 123 102-241 377-509 (559)
104 KOG1824 TATA-binding protein-i 22.4 1.2E+03 0.026 31.2 13.3 125 67-204 699-828 (1233)
105 PRK14637 hypothetical protein; 22.4 1.3E+02 0.0028 30.8 4.6 30 709-738 93-122 (151)
106 cd07961 Anticodon_Ia_Ile_ABEc 21.2 50 0.0011 33.3 1.4 27 79-105 112-138 (183)
107 PF13001 Ecm29: Proteasome sta 21.2 2.7E+02 0.0059 33.2 7.6 100 143-243 264-374 (501)
108 COG5218 YCG1 Chromosome conden 20.9 1.8E+03 0.039 28.2 16.4 86 127-217 66-152 (885)
109 COG5231 VMA13 Vacuolar H+-ATPa 20.6 2.4E+02 0.0052 33.0 6.6 55 141-195 216-277 (432)
110 KOG4407 Predicted Rho GTPase-a 20.5 3.5E+02 0.0075 36.7 8.5 230 81-364 1180-1462(1973)
111 KOG2022 Nuclear transport rece 20.3 9.7E+02 0.021 31.5 12.0 90 146-237 499-591 (982)
112 PF00514 Arm: Armadillo/beta-c 20.2 37 0.00079 26.4 0.2 22 69-90 20-41 (41)
113 PF04084 ORC2: Origin recognit 20.1 1.6E+02 0.0035 33.4 5.2 106 98-203 114-240 (326)
114 PF10151 DUF2359: Uncharacteri 20.1 1.4E+03 0.03 27.8 12.9 58 55-112 72-135 (469)
No 1
>KOG1525 consensus Sister chromatid cohesion complex Cohesin, subunit PDS5 [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1e-50 Score=488.79 Aligned_cols=247 Identities=34% Similarity=0.549 Sum_probs=233.5
Q ss_pred HHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhh
Q 002421 12 EQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRI 91 (925)
Q Consensus 12 ~~L~~~G~KLis~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRI 91 (925)
++.-.-||+++..+++++|||+||++|+.||++++|++.+ .++|.|++.+|+++.||+|+|+|||+||||||+|||||
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 3455779999999999999999999999999999999966 99999999999999999999999999999999999999
Q ss_pred cCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHhhcCCchh
Q 002421 92 TAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHF 171 (925)
Q Consensus 92 yAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~dhp~k 171 (925)
|||||||++.||+|||+||++||.||.|+.+|||.|||||||+||.||.|++|.|.+|++|+.+||++||+++|.+||.+
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 HHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHHHHHHHhcCC-------C-C
Q 002421 172 VFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGI-------A-L 243 (925)
Q Consensus 172 V~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~l~s~Gi-------~-L 243 (925)
|+. |.+||+.+|.|.+.||.++|++||.+|+++.+++.+.|++||..+|..|++.+.+.|++||++.-+ + .
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 999999999999999999999999999999999999999999999999999999999999996422 2 3
Q ss_pred cchHHHHHHHhccCCCCC
Q 002421 244 DDYAEIVACICGSDDENP 261 (925)
Q Consensus 244 d~Y~eIV~sIcq~~s~~l 261 (925)
..||++|+.+-.+++..|
T Consensus 240 ~~~he~i~~L~~~~p~ll 257 (1266)
T KOG1525|consen 240 IKYHELILELWRIAPQLL 257 (1266)
T ss_pred hHHHHHHHHHHHhhHHHH
Confidence 679999999888876655
No 2
>KOG1525 consensus Sister chromatid cohesion complex Cohesin, subunit PDS5 [Cell cycle control, cell division, chromosome partitioning]
Probab=99.71 E-value=3.8e-17 Score=199.76 Aligned_cols=247 Identities=31% Similarity=0.370 Sum_probs=232.2
Q ss_pred HHHHhccccCCCCCC--HHHHHHHHHHH--------HHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehh
Q 002421 13 QLKDAGNLLLNPPSP--VDEVINLLDKV--------EHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVT 82 (925)
Q Consensus 13 ~L~~~G~KLis~piS--~dELLKRLkkL--------~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVA 82 (925)
+++.+|.+.+.++++ .++||..+-+. +-.|..+.|....++.+++.+++..|+.=.+..|++-++.+-..
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 78888899988889999999999999999999999999999999
Q ss_pred hHHhhhhh--hcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHH--HHHHHhhhhceeeeeccC---CchHHHHH
Q 002421 83 SCISEITR--ITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKAL--SILDTVAKVRSCLLMLDL---ECDKLVVE 155 (925)
Q Consensus 83 cCLADILR--IyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~--yLLEsLAeVKS~VLMlDL---e~ddLI~e 155 (925)
.||.+++| |.+|..||+++.|+.||..|+..+..|.|+.+..|.... .+|+.++.+++|+.|++. .|.++...
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 HHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHHHHH
Q 002421 156 MFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEA 235 (925)
Q Consensus 156 LFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~ 235 (925)
||+.||..++..++.+++..|..+|++.|.+ |+.+++..|+..+...+......+..|++.|+..|+-++..|+.+.
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 9999999999999988888899999999999999999999999999
Q ss_pred HHhcCCCCcchHHHHHHHhccCCCCCC
Q 002421 236 VQSRGIALDDYAEIVACICGSDDENPQ 262 (925)
Q Consensus 236 l~s~Gi~Ld~Y~eIV~sIcq~~s~~l~ 262 (925)
|...+-.+.-|++++.+||+......+
T Consensus 646 ls~~~~~~~~~s~~v~~i~~~~~~~~~ 672 (1266)
T KOG1525|consen 646 LSSIHPDLFKYSESVLSILEKLFSEPD 672 (1266)
T ss_pred hhhcCcchhhhhHHHHHHHHHhccchh
Confidence 999999999999999999999988773
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=98.98 E-value=8.7e-10 Score=93.03 Aligned_cols=44 Identities=34% Similarity=0.667 Sum_probs=36.3
Q ss_pred cccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCcceeee
Q 002421 712 LVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDEEILN 755 (925)
Q Consensus 712 lVG~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YDDGD~E~L~ 755 (925)
-.|.+|.+|||++..||+|.|++||..+..|+|.|+||++..|.
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel~lk 50 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTELELK 50 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EEEEE
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEEEec
Confidence 37999999999999999999999999999999999999995443
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=97.43 E-value=0.00031 Score=57.69 Aligned_cols=44 Identities=23% Similarity=0.530 Sum_probs=39.8
Q ss_pred cccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccC-CcceeeecC
Q 002421 712 LVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYAD-GDEEILNLK 757 (925)
Q Consensus 712 lVG~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YDD-GD~E~L~L~ 757 (925)
-+|..|.+.| .|..||.|+|+.+++. +...|.|.| |..+++.+.
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 3799999999 9999999999999987 889999998 999988654
No 5
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=97.25 E-value=0.00057 Score=57.40 Aligned_cols=36 Identities=19% Similarity=0.337 Sum_probs=33.6
Q ss_pred cccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccC
Q 002421 712 LVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYAD 748 (925)
Q Consensus 712 lVG~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YDD 748 (925)
.+|.+|.+||+.+..||.|+|+.++. .+++.|.|++
T Consensus 4 ~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V~~~~ 39 (61)
T smart00743 4 KKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLVRYLT 39 (61)
T ss_pred CCCCEEEEEECCCCEEEEEEEEEECC-CCEEEEEECC
Confidence 37999999999999999999999998 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=97.18 E-value=0.00085 Score=53.37 Aligned_cols=43 Identities=19% Similarity=0.411 Sum_probs=38.3
Q ss_pred cCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccC-CcceeeecC
Q 002421 714 GSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYAD-GDEEILNLK 757 (925)
Q Consensus 714 G~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YDD-GD~E~L~L~ 757 (925)
|..|-+.|++|..||.|+|..+++ ...-.|.|.| |..+.+.+.
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 6778899998 999987654
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=95.73 E-value=0.017 Score=56.59 Aligned_cols=45 Identities=24% Similarity=0.475 Sum_probs=34.9
Q ss_pred ccccccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCcceee
Q 002421 709 NEQLVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDEEIL 754 (925)
Q Consensus 709 ge~lVG~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YDDGD~E~L 754 (925)
|.++||.||---|-.+.-||.|+|+.. ....+.+|.+|||.+..|
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 568999999999997777799999995 667889999999998644
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=94.37 E-value=0.091 Score=57.03 Aligned_cols=47 Identities=21% Similarity=0.429 Sum_probs=40.1
Q ss_pred cccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEcc-CCcceeeecCc
Q 002421 712 LVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYA-DGDEEILNLKK 758 (925)
Q Consensus 712 lVG~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YD-DGD~E~L~L~~ 758 (925)
-||-+|...|-.|..||.++|++.+...+.-.|+|. -|..|++.|..
T Consensus 70 kvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~d 117 (264)
T PF06003_consen 70 KVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLSD 117 (264)
T ss_dssp -TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGGG
T ss_pred CCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehhh
Confidence 399999999999999999999999999999999998 57778888774
No 9
>KOG4675 consensus Uncharacterized conserved protein, contains ENT domain [General function prediction only]
Probab=92.24 E-value=0.043 Score=59.90 Aligned_cols=60 Identities=25% Similarity=0.448 Sum_probs=43.6
Q ss_pred ccccccccCeEEEeeCCCCceEEEEEEEecC-CCCeEEEEccCCcc----eeeecC---cceEEEeeC
Q 002421 707 ALNEQLVGSRIKVWWPMDETFYKGVVDNYDP-IKKKHRILYADGDE----EILNLK---KERWELIKG 766 (925)
Q Consensus 707 ~~ge~lVG~RVkV~WP~D~~wY~G~V~syd~-~tkkH~V~YDDGD~----E~L~L~---~Ek~e~l~~ 766 (925)
..++.+||++|..-||+++.||++.|+.|+. ...+|.+.||--+. +|++|. .+.++|...
T Consensus 155 ~pp~slvgr~v~~k~pdk~~~te~iit~~~~~~E~~~~l~~~~~~~~~p~~wvdl~~I~p~DIrw~g~ 222 (273)
T KOG4675|consen 155 VPPESLVGRKVWIKWPDKRKFTEAIITQYDAEKEGHHLLVPDINDCNDPWEWVDLREISPEDIRWEGG 222 (273)
T ss_pred CCchhhccccccccCcccccccccccccchhhhhhhhhcccccccccCCccccccccCCHHhccccCC
Confidence 3456799999999999999999999999655 45678888884442 444443 355555444
No 10
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=90.19 E-value=1.9 Score=53.42 Aligned_cols=117 Identities=9% Similarity=0.123 Sum_probs=75.9
Q ss_pred CCCCCcchhHHHHHHHHhhhhceeeeeccCC---chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCC-CcHH
Q 002421 118 SHASGRYYMKALSILDTVAKVRSCLLMLDLE---CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESED-VSWD 193 (925)
Q Consensus 118 aD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe---~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~-VP~e 193 (925)
.+|++|.| ++||+|+++-+= ...++-+ --.+...||=.|-.+.+.+. .+...+...||+.+++-+.. +|..
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 578999997651 1122333 13577777766655555444 34456778899999999877 7776
Q ss_pred HH---HHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHH-----HHHHHHHHhc
Q 002421 194 LL---RILLASVRKENQDVSPTSWKLGEKVFTKCAAKLK-----TNLKEAVQSR 239 (925)
Q Consensus 194 VL---DvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLq-----p~I~q~l~s~ 239 (925)
+. -+||+.-+..-..+.|+.-+|-..+|...+..+. .+|..+|+.+
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 43 3444444445578899999998888887665543 4566677755
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=84.52 E-value=5.3 Score=46.58 Aligned_cols=139 Identities=12% Similarity=0.244 Sum_probs=82.5
Q ss_pred ehhhHHhhhhhhcCCC-CCCChhHHHHHHHHHHHHhccc-CCCCCcchhHHHHHHHHhhhh-ceeeeeccCCch---HHH
Q 002421 80 SVTSCISEITRITAPD-SPYDDELMKEFFQLAVSAFENL-SHASGRYYMKALSILDTVAKV-RSCLLMLDLECD---KLV 153 (925)
Q Consensus 80 yVAcCLADILRIyAPD-APYtDdqLKDIFqLfV~qf~~L-aD~ssp~F~q~~yLLEsLAeV-KS~VLMlDLe~d---dLI 153 (925)
|+.=||+=|+=++.-+ .||.+.-|. .++..|... .+|++|.|. +|+.|+|+.+ |. +++-+.+ .+-
T Consensus 45 ylMk~iMRvl~~~~e~~~p~~~~il~----~L~~il~~v~kNPsnP~Fn--HylFEsi~~lir~---~~~~~~~~v~~~E 115 (435)
T PF03378_consen 45 YLMKCIMRVLSVLQEDILPIAVEILQ----HLTAILKEVSKNPSNPRFN--HYLFESIGALIRF---VCEADPEAVSQFE 115 (435)
T ss_dssp HHHHHHHHHHHHSTTTTGGGHHHHHH----HHHHHHHHHHTS---HHHH--HHHHHHHHHHHHH---S-GGGHH---HHH
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHH----HHHHHHHHHHhCCCCcchh--hhHHHHHHHHHHh---ccCCChhHHHHHH
Confidence 5566666666554444 566442222 222222211 358888874 5788999876 42 2222222 566
Q ss_pred HHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccC--CCc---HHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhH
Q 002421 154 VEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESE--DVS---WDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKL 228 (925)
Q Consensus 154 ~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE--~VP---~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKL 228 (925)
..||-.|..+...+..+ ...+.-.||+.+++-.. .+| ..++..||...+.+.+.+.|+.-+|-...|..++..+
T Consensus 116 ~~L~P~f~~ILq~dV~E-F~PYvfQIla~Lle~~~~~~~p~~y~~L~~~Ll~p~lWe~~gniPalvrLL~a~i~k~~~~i 194 (435)
T PF03378_consen 116 EALFPPFQEILQQDVQE-FIPYVFQILAQLLELRPSSPLPDAYKQLFPPLLSPALWERRGNIPALVRLLQAYIKKDPSFI 194 (435)
T ss_dssp HHHHHHHHHHHHTT-TT-THHHHHHHHHHHHHHSS--S--TTTGGGHHHHTSGGGGGSTTTHHHHHHHHHHHHHHHGGG-
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHcCcchhccCCCcCcHHHHHHHHHHhCchhh
Confidence 66677777766655443 33555567777777765 455 4577888888888888899998889888888887755
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=81.23 E-value=2.9 Score=36.56 Aligned_cols=35 Identities=20% Similarity=0.225 Sum_probs=27.1
Q ss_pred ccCeEEEeeCCC---CceEEEEEEEecCCCCeEEEEccC
Q 002421 713 VGSRIKVWWPMD---ETFYKGVVDNYDPIKKKHRILYAD 748 (925)
Q Consensus 713 VG~RVkV~WP~D---~~wY~G~V~syd~~tkkH~V~YDD 748 (925)
.|.+|.|+--.+ .+||.|+|....... +..|.|+|
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 588999988664 599999999999865 89999963
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=79.99 E-value=17 Score=41.41 Aligned_cols=24 Identities=29% Similarity=0.422 Sum_probs=21.6
Q ss_pred cccCCCcCceeehhhHHhhhhhhc
Q 002421 69 LLRRSDMDVRLSVTSCISEITRIT 92 (925)
Q Consensus 69 LLkHKDkdVRayVAcCLADILRIy 92 (925)
||.++|..||.++..||..|.+.+
T Consensus 275 lL~s~~~nvr~~~L~~L~~l~~~~ 298 (526)
T PF01602_consen 275 LLSSSDPNVRYIALDSLSQLAQSN 298 (526)
T ss_dssp HHTSSSHHHHHHHHHHHHHHCCHC
T ss_pred HhhcccchhehhHHHHHHHhhccc
Confidence 778999999999999999999886
No 14
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=78.05 E-value=4.9 Score=39.34 Aligned_cols=42 Identities=19% Similarity=0.374 Sum_probs=36.0
Q ss_pred cCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCcceeeec
Q 002421 714 GSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDEEILNL 756 (925)
Q Consensus 714 G~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YDDGD~E~L~L 756 (925)
|.+|=..|+.|.-||.|+|..+- ..+...|.+++|+.+.+..
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 5677888998888876543
No 15
>KOG1949 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.57 E-value=39 Score=42.23 Aligned_cols=149 Identities=23% Similarity=0.320 Sum_probs=84.5
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhccCCCchhhH--------------------HhhHHHHHhhhhhhcccCCCcCceeeh
Q 002421 22 LNPPSPVDEVINLLDKVEHLLANVEQAPSRSMR--------------------DALLPTMKGLITNDLLRRSDMDVRLSV 81 (925)
Q Consensus 22 is~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~--------------------~SL~pl~k~LVs~~LLkHKDkdVRayV 81 (925)
+.|.....+.=..|++-+.+|..+=.++.-..+ +-+..++.- |-..+-...-.+||+.|
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 355555677777788888888877555543111 112222222 22334445666888888
Q ss_pred hhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcc-cCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHH
Q 002421 82 TSCISEITRITAPDSPYDDELMKEFFQLAVSAFEN-LSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHF 160 (925)
Q Consensus 82 AcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~-LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktF 160 (925)
--||-.|+- .| +---+|..++-.+.. |.|.+-.----.+-||-.|-.|| |-.|
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-----NP----LSHPLLEQLLPALRYSLHDNSEKVRVAFVDMLLKIKAVR-----------------AAKF 337 (1005)
T ss_pred hcCcHHHHc-----Cc----cchhHHHHHHHhcchhhhccchhHHHHHHHHHHHHHhhh-----------------hhhh
Confidence 888888872 22 223345544444442 22221111111122222222222 3356
Q ss_pred HHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCC
Q 002421 161 LKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQ 207 (925)
Q Consensus 161 FdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~k 207 (925)
|+++. |..||+.+=.++-.+.--++..|+..+++-++
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 78888888778778888899999999998776
No 16
>KOG1248 consensus Uncharacterized conserved protein [Function unknown]
Probab=74.31 E-value=35 Score=44.39 Aligned_cols=195 Identities=16% Similarity=0.149 Sum_probs=118.1
Q ss_pred HHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHH
Q 002421 28 VDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFF 107 (925)
Q Consensus 28 ~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIF 107 (925)
+..+++-|.-|.+-|+.+--.. +.+++..|++. ..-.+.-|++.+--||. ++|-=-++|.+..+.-
T Consensus 200 ~t~v~~~L~Ll~~~~~~~p~~l-------i~sl~e~lL~i--~~~s~v~v~~~~~q~l~---~lf~~~~~~l~a~~~a-- 265 (1176)
T KOG1248|consen 200 NTTVLRSLMLLRDVLSTFPRPL-------IKSLCEVLLNI--TTESPVLVLLEVLQCLH---SLFKKHPTALAAELNA-- 265 (1176)
T ss_pred HHHHHHHHHHHHHhhccCCHHH-------HHHHHHHHHhh--cccchHHHHHHHHHHHH---HHHhcCCCcchHHHHH--
Confidence 4445555555555555532221 23344443332 22233434444444444 4444444466554432
Q ss_pred HHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCC-chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcc
Q 002421 108 QLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDE 186 (925)
Q Consensus 108 qLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe-~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeE 186 (925)
.++..+..|. ++..--..-++.|.-|.+-..|+-..|.+ |-.=+..+|..||.+ -....+.+.....+++..|+.+
T Consensus 266 -~lL~al~~l~-ps~~D~~~t~~W~~v~~~~~~~la~~q~~~~~~~~~~~~~~~~t~-~~s~~~e~~q~a~q~l~~il~~ 342 (1176)
T KOG1248|consen 266 -RLLTALMTLS-PSENDDLLTVAWLKVLNEAHDILATLQEEKALQALPRLFSLFFTI-LESLIEELVQAASQSLKEILKE 342 (1176)
T ss_pred -HHHHHHHHhC-CCccchHHHHHHHHHHHHHHHHHHHhCHHHHHHhhhhhhhHHHHH-HhcccHHHHHHHHHHHHHHhcc
Confidence 3333333333 33333346678888888888888888888 767778889999984 4444567778899999999999
Q ss_pred cCCCcHHHHHHHHHHhhccCC-CCCchHHHHHHHHHHhhhHhHHHHHHHHHHhc
Q 002421 187 SEDVSWDLLRILLASVRKENQ-DVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSR 239 (925)
Q Consensus 187 SE~VP~eVLDvIL~~fl~~~k-s~~PaAykLA~~VI~~CadKLqp~I~q~l~s~ 239 (925)
+-.|-..+...+|..++...- ...+..+++-..++..|+..--|++...|+.+
T Consensus 343 sv~~~~~~c~~~~~~~l~~kf~~~~~~ilqi~s~~fek~G~~s~~~l~~~L~~l 396 (1176)
T KOG1248|consen 343 SVTVIDALCSKQLHSLLDYKFHAVWRFILQILSALFEKCGELSGPELTKTLEGL 396 (1176)
T ss_pred cCcccHHHHHHHHHHHHcchHHHHHHHHHHHHHHHHHHhhhhcCHHHHHHHHHH
Confidence 988767766666766665432 23455556666678888887778887777743
No 17
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=74.02 E-value=3.9 Score=51.02 Aligned_cols=44 Identities=16% Similarity=0.474 Sum_probs=35.9
Q ss_pred ccCeEEEeeCCC----CceEEEEEEEecCCCC--------eEEEEccCCcceeeec
Q 002421 713 VGSRIKVWWPMD----ETFYKGVVDNYDPIKK--------KHRILYADGDEEILNL 756 (925)
Q Consensus 713 VG~RVkV~WP~D----~~wY~G~V~syd~~tk--------kH~V~YDDGD~E~L~L 756 (925)
.+-++||||.+. .+|++|+|-+.-|..- ++.|+||.++.+.+.-
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 688999999864 6899999999877553 6899999997776544
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=71.88 E-value=92 Score=31.97 Aligned_cols=181 Identities=12% Similarity=0.168 Sum_probs=81.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHhc-cCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhH
Q 002421 24 PPSPVDEVINLLDKVEHLLANV-EQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL 102 (925)
Q Consensus 24 ~piS~dELLKRLkkL~~eLs~l-DQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdq 102 (925)
...+-++-+.-|+.|...+..- .+.........|..+...| ...+. ....-|-.-++-||.+|.+.+...
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-DLRSKVSKTACQLLSDLARQLGSH------- 87 (228)
T ss_dssp T-SSHHHHHHHHHHHHHHHHH-B-----HHHHHHHH---HHH-HH-S--HH---HHHHHHHHHHHHHHHHGGG-------
T ss_pred CccCHHHHHHHHHHHHHHHHcCCccccHHHHHHHHHHhHHHH-HHHHh-hhHHHHHHHHHHHHHHHHHHHhHh-------
Confidence 3445666666666666666654 2222222223333222222 22222 222224445566788888875443
Q ss_pred HHHHHHHHHHH-hcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHH
Q 002421 103 MKEFFQLAVSA-FENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMT 181 (925)
Q Consensus 103 LKDIFqLfV~q-f~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs 181 (925)
+...+..|+.. |..+++............|..|...=++ ...++ |..+... ..+.+..|+......|.
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 55555555555 5666766544555556666666553110 11222 3333333 23556777777777888
Q ss_pred HHhcccC----CCcHH-HHHHHHHHhhccCCCCCchHHHHHHHHHHhh
Q 002421 182 LVIDESE----DVSWD-LLRILLASVRKENQDVSPTSWKLGEKVFTKC 224 (925)
Q Consensus 182 ~VIeESE----~VP~e-VLDvIL~~fl~~~ks~~PaAykLA~~VI~~C 224 (925)
.+|.... .+... .++.|+..+...-.+..|..+..|+.++..-
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 8887776 12222 2344444444433455666666666655443
No 19
>PTZ00429 beta-adaptin; Provisional
Probab=71.60 E-value=75 Score=39.94 Aligned_cols=146 Identities=12% Similarity=0.105 Sum_probs=82.5
Q ss_pred HHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhh
Q 002421 59 PTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKV 138 (925)
Q Consensus 59 pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeV 138 (925)
.++..|. .+|+|.+..|-+-++.||..+.-.. ..+.++.++.-+...|-.|. ++ ...-+|-+|.+|..+
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 3588999999988888888775211 23556666655544433442 12 223445566665333
Q ss_pred ceeeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHH
Q 002421 139 RSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGE 218 (925)
Q Consensus 139 KS~VLMlDLe~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~ 218 (925)
-.. .-.++..-++.||-..+ -|..|...-.+||..+..+... .+||+.|..++. ...+.=.+.+-
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 110 13566666788875433 4666877888999999887542 345555554443 22222223344
Q ss_pred HHHHhhhHhHHH
Q 002421 219 KVFTKCAAKLKT 230 (925)
Q Consensus 219 ~VI~~CadKLqp 230 (925)
.-|..|+.++..
T Consensus 390 rAIg~lA~k~~~ 401 (746)
T PTZ00429 390 RAIASLAIKVDS 401 (746)
T ss_pred HHHHHHHHhChH
Confidence 456677777654
No 20
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=71.25 E-value=24 Score=38.60 Aligned_cols=171 Identities=12% Similarity=0.184 Sum_probs=96.1
Q ss_pred hcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccC
Q 002421 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDL 147 (925)
Q Consensus 68 ~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDL 147 (925)
..|.+.|..+|+-.--||+++|-=+.|+. .+..|+.-++.||.+-| .|... +...|.-+...+-|-.+
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---DDHAC--------VQPALKGLLALVKMKNF 73 (262)
T ss_pred hhhCCCCHHHHHHHHHHHHHHHHhCCHhh-ccHHHHHHHHHHHHHHh---ccHhh--------HHHHHHHHHHHHhCcCC
Confidence 36788999999999999999997655544 78899999999999866 33322 22222222333333344
Q ss_pred CchHHHHHHHHHHHHHhh-cCCchhHHHHHHHHHHHHhcc----cCCCcHHHHHHHHHHhhccCCC--CCchHHHHHHHH
Q 002421 148 ECDKLVVEMFQHFLKVIR-SNHPHFVFAAMETIMTLVIDE----SEDVSWDLLRILLASVRKENQD--VSPTSWKLGEKV 220 (925)
Q Consensus 148 e~ddLI~eLFktFFdiVr-~dhp~kV~~~M~dILs~VIeE----SE~VP~eVLDvIL~~fl~~~ks--~~PaAykLA~~V 220 (925)
.. +.+..|.+.||+-+. ..++...+...-.||..+++. ...+..+.+..++..+ .+.++ ..-.++.|.
T Consensus 74 ~~-~~~~~i~~~l~~~~~~q~~~q~~R~~~~~ll~~l~~~~~~~l~~~~~~fv~~~i~~~-~gEkDPRnLl~~F~l~--- 148 (262)
T PF14500_consen 74 SP-ESAVKILRSLFQNVDVQSLPQSTRYAVYQLLDSLLENHREALQSMGDDFVYGFIQLI-DGEKDPRNLLLSFKLL--- 148 (262)
T ss_pred Ch-hhHHHHHHHHHHhCChhhhhHHHHHHHHHHHHHHHHHhHHHHHhchhHHHHHHHHHh-ccCCCHHHHHHHHHHH---
Confidence 32 235555555554332 345666666665666555554 3446677777766644 33333 233333333
Q ss_pred HHhhhHhHHHHHHHHHHhcCCCCcchHHHHHHHhccCCCCCCCCC
Q 002421 221 FTKCAAKLKTNLKEAVQSRGIALDDYAEIVACICGSDDENPQHGH 265 (925)
Q Consensus 221 I~~CadKLqp~I~q~l~s~Gi~Ld~Y~eIV~sIcq~~s~~l~~~~ 265 (925)
+.|.+.|.- +-...++.++++.-|=++.....||.
T Consensus 149 ---------~~i~~~~~~-~~~~e~lFd~~~cYFPI~F~pp~~dp 183 (262)
T PF14500_consen 149 ---------KVILQEFDI-SEFAEDLFDVFSCYFPITFRPPPNDP 183 (262)
T ss_pred ---------HHHHHhccc-chhHHHHHHHhhheeeeeeeCCCCCC
Confidence 333333331 12233445555555556555555544
No 21
>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=70.39 E-value=11 Score=31.78 Aligned_cols=37 Identities=14% Similarity=0.273 Sum_probs=31.1
Q ss_pred ccCeEEEeeCCCCceEEEEEEEecCCCC--eEEEEccCCc
Q 002421 713 VGSRIKVWWPMDETFYKGVVDNYDPIKK--KHRILYADGD 750 (925)
Q Consensus 713 VG~RVkV~WP~D~~wY~G~V~syd~~tk--kH~V~YDDGD 750 (925)
||.+|-++| .+..||.++|.......+ ...|.|..=+
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 899999999999988553 5778887444
No 22
>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=69.12 E-value=39 Score=41.05 Aligned_cols=144 Identities=17% Similarity=0.211 Sum_probs=76.3
Q ss_pred HHHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhcc-CCCchhhHHhhHHHHHhhhh-hhcccCCCcCceeehhhH
Q 002421 7 EIELEEQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVE-QAPSRSMRDALLPTMKGLIT-NDLLRRSDMDVRLSVTSC 84 (925)
Q Consensus 7 ~~ele~~L~~~G~KLis~piS~dELLKRLkkL~~eLs~lD-Q~~vdS~~~SL~pl~k~LVs-~~LLkHKDkdVRayVAcC 84 (925)
++|.|+.|.+.-++++.. .+.+|. ..|..+-.+|.-+- +.++.+ +..|-.+..+.+. ..-+...|.+.=--+..|
T Consensus 172 ~~E~e~~i~~~ikkvL~D-VTaeEF-~l~m~lL~~lk~~~~~~t~~g-~qeLv~ii~eQa~Ld~~f~~sD~e~Idrli~C 248 (556)
T PF05918_consen 172 QKEMEEFIVDEIKKVLQD-VTAEEF-ELFMSLLKSLKIYGGKQTIEG-RQELVDIIEEQADLDQPFDPSDPESIDRLISC 248 (556)
T ss_dssp -HHHHHHHHHHHHHHCTT---HHHH-HHHHHHHHTSGG---GSSHHH-HHHHHHHHHHHHTTTS---SSSHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHh-ccHHHH-HHHHHHHHhCccccccCChHH-HHHHHHHHHHHhccCCCCCCcCHHHHHHHHHH
Confidence 367777777777777753 444443 34445555555432 233433 3335444443321 222455554433234445
Q ss_pred HhhhhhhcCCCCCCChhHHHHHHHHHHHH-hcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHH
Q 002421 85 ISEITRITAPDSPYDDELMKEFFQLAVSA-FENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKV 163 (925)
Q Consensus 85 LADILRIyAPDAPYtDdqLKDIFqLfV~q-f~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdi 163 (925)
+-.-|=+|.+.+ .-..+|.+|..+ |+.|.+... ...+.||..||++-++. .++++.+++..+|+.|...
T Consensus 249 ~~~Alp~fs~~v-----~Sskfv~y~~~kvlP~l~~l~e---~~kl~lLk~lAE~s~~~--~~~d~~~~L~~i~~~L~~y 318 (556)
T PF05918_consen 249 LRQALPFFSRGV-----SSSKFVNYMCEKVLPKLSDLPE---DRKLDLLKLLAELSPFC--GAQDARQLLPSIFQLLKKY 318 (556)
T ss_dssp HHHHGGG-BTTB-------HHHHHHHHHHTCCCTT--------HHHHHHHHHHHHHTT------THHHHHHHHHHHHHTT
T ss_pred HHHhhHHhcCCC-----ChHHHHHHHHHHhcCChhhCCh---HHHHHHHHHHHHHcCCC--CcccHHHHHHHHHHHHHHh
Confidence 444454544433 457788888887 888887622 56789999999997774 4555778888888888764
No 23
>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=68.14 E-value=5.4 Score=45.40 Aligned_cols=115 Identities=16% Similarity=0.225 Sum_probs=59.9
Q ss_pred hcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHH-HHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeecc
Q 002421 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKE-FFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLD 146 (925)
Q Consensus 68 ~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKD-IFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlD 146 (925)
.+|.|.+.-||--++.||..|+|. .|+ .+.. ++..+...| .|++-..-...+++|..+ .
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 468899999999999999999999 232 2222 233333333 444422333344444444 1
Q ss_pred CCch---HHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCc--HHHHHHHHHHhh
Q 002421 147 LECD---KLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVS--WDLLRILLASVR 203 (925)
Q Consensus 147 Le~d---dLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~VP--~eVLDvIL~~fl 203 (925)
-+.+ .++..+|+.+...+. ...+-+...+..++..+.......+ ..++..|+..+.
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 455555555555442 3333344444455554444433344 445555555544
No 24
>KOG0915 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.72 E-value=66 Score=43.17 Aligned_cols=165 Identities=15% Similarity=0.314 Sum_probs=95.7
Q ss_pred HHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhh--------------hcccC-CCcCceeehhhH--Hhhhhh
Q 002421 28 VDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITN--------------DLLRR-SDMDVRLSVTSC--ISEITR 90 (925)
Q Consensus 28 ~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~--------------~LLkH-KDkdVRayVAcC--LADILR 90 (925)
.++|-.-|++|-=-|.+..=+|.-..++|+..+-+.||.. .||.+ .++.-|+--||| |+||||
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 3444455666666666666666555666666666666655 45554 889999999999 569998
Q ss_pred hcCCCCCCCh--hHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCC----chHHHHHHH-------
Q 002421 91 ITAPDSPYDD--ELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE----CDKLVVEMF------- 157 (925)
Q Consensus 91 IyAPDAPYtD--dqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe----~ddLI~eLF------- 157 (925)
= .|+++ +.|.+||..+|+....+.+. --.-..-....|+ |.||-|+|.. +.+.+--+.
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 7 67775 68888887777776554431 1111112222222 5688888884 222222221
Q ss_pred -------------HHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHh
Q 002421 158 -------------QHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASV 202 (925)
Q Consensus 158 -------------ktFFdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~f 202 (925)
.++.+++. .-+..+-.++.+++-.+++-...+.+.||..+--++
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 23333322 122333444555555566666677777777765554
No 25
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=64.38 E-value=1e+02 Score=39.30 Aligned_cols=155 Identities=19% Similarity=0.167 Sum_probs=94.6
Q ss_pred HhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhH--HHHHH
Q 002421 55 DALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMK--ALSIL 132 (925)
Q Consensus 55 ~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q--~~yLL 132 (925)
+....++++|+. |--.+++||-.|-|||+-|--. -+.+|.=.+..|--- +.+|+-.+ -..||
T Consensus 318 ~~~~~i~kaLvr---LLrs~~~vqyvvL~nIa~~s~~-----------~~~lF~P~lKsFfv~--ssDp~~vk~lKleiL 381 (968)
T KOG1060|consen 318 NQVTKIAKALVR---LLRSNREVQYVVLQNIATISIK-----------RPTLFEPHLKSFFVR--SSDPTQVKILKLEIL 381 (968)
T ss_pred HHHHHHHHHHHH---HHhcCCcchhhhHHHHHHHHhc-----------chhhhhhhhhceEee--cCCHHHHHHHHHHHH
Confidence 355667788887 4446678998888888766421 233444444443211 23343333 25677
Q ss_pred HHhhhhceeeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCch
Q 002421 133 DTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPT 212 (925)
Q Consensus 133 EsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~Pa 212 (925)
.+||.-..+ -++|+.|..-|+..+- .+...-..-+..+=.-.-.|+..+|+-|+.-+..++....-.
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 777765433 3444444444454333 333333333444555556789999999999998888877777
Q ss_pred HHHHHHHHHHhhhHhHHHHHHHHHHh
Q 002421 213 SWKLGEKVFTKCAAKLKTNLKEAVQS 238 (925)
Q Consensus 213 AykLA~~VI~~CadKLqp~I~q~l~s 238 (925)
|-...+.+|.+-..+--.+|.+++..
T Consensus 449 aV~vIk~Llq~~p~~h~~ii~~La~l 474 (968)
T KOG1060|consen 449 AVVVIKRLLQKDPAEHLEILFQLARL 474 (968)
T ss_pred HHHHHHHHHhhChHHHHHHHHHHHHH
Confidence 77777888887777666666666653
No 26
>KOG0213 consensus Splicing factor 3b, subunit 1 [RNA processing and modification]
Probab=63.13 E-value=1.1e+02 Score=38.97 Aligned_cols=133 Identities=17% Similarity=0.162 Sum_probs=75.8
Q ss_pred CCCHHHHHHHHHHHHHHHH----------hccCCCc---hhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhh
Q 002421 25 PSPVDEVINLLDKVEHLLA----------NVEQAPS---RSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRI 91 (925)
Q Consensus 25 piS~dELLKRLkkL~~eLs----------~lDQ~~v---dS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRI 91 (925)
.+...+|+..|+.++.-=. -+.|-.. .+...-|.++.+- + ..+|.....-||..+|.||+-+.-.
T Consensus 506 algip~llpfLkavc~SkkSwqaRhTgIkivqqIail~Gcsvlphl~~lv~i-i-~~gl~De~qkVR~itAlalsalaea 583 (1172)
T KOG0213|consen 506 ALGIPALLPFLKAVCGSKKSWQARHTGIKIVQQIAILSGCSVLPHLKPLVKI-I-EHGLKDEQQKVRTITALALSALAEA 583 (1172)
T ss_pred HhCcHHHHHHHHHHhccccchhhhchhhHHHHHHHHHhcchhhhhhHHHHHH-H-HHhhcccchhhhhHHHHHHHHHHHh
Confidence 4556778888877764321 1122110 1233444554443 2 2355666677999999999998866
Q ss_pred cCCCCCCChhHHHHHHHHHH---------------HHhcccCCCCCcchhHHHH---HHHHhhhh------------cee
Q 002421 92 TAPDSPYDDELMKEFFQLAV---------------SAFENLSHASGRYYMKALS---ILDTVAKV------------RSC 141 (925)
Q Consensus 92 yAPDAPYtDdqLKDIFqLfV---------------~qf~~LaD~ssp~F~q~~y---LLEsLAeV------------KS~ 141 (925)
- .||.-+++-.||..+- ..+.-|=.-..+.|.-||. ||-.+-+. |.+
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 5799888888887652 2222222223445555555 44443322 112
Q ss_pred eeeccCC-------chHHHHHHHHHHHH
Q 002421 142 LLMLDLE-------CDKLVVEMFQHFLK 162 (925)
Q Consensus 142 VLMlDLe-------~ddLI~eLFktFFd 162 (925)
--||+-+ -.+++.++|+.|+.
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 2234443 25889999999886
No 27
>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=62.91 E-value=16 Score=32.78 Aligned_cols=47 Identities=17% Similarity=0.251 Sum_probs=35.1
Q ss_pred cccccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEc-cCCcceeeecC
Q 002421 710 EQLVGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILY-ADGDEEILNLK 757 (925)
Q Consensus 710 e~lVG~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~Y-DDGD~E~L~L~ 757 (925)
...+|..+-+.=+.|+.||.|.| ..+.....-.|.| |-|..+.+...
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 5555567777877 68988886554
No 28
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=62.05 E-value=2.1e+02 Score=31.42 Aligned_cols=66 Identities=29% Similarity=0.331 Sum_probs=37.4
Q ss_pred HHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCcee-----ehhhHHhhhhhhcCCCCCCChhHHHHHHHH
Q 002421 35 LDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRL-----SVTSCISEITRITAPDSPYDDELMKEFFQL 109 (925)
Q Consensus 35 LkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRa-----yVAcCLADILRIyAPDAPYtDdqLKDIFqL 109 (925)
|.-+..-|..+...-.+ ..+|..+...||.+.+-++ |..||. +--|||.|- +.-.+-|.+
T Consensus 4 L~i~~~lL~~~~~~~~~--~~~l~~ll~~lI~P~v~~~-~~~vR~~al~cLGl~~Lld~------------~~a~~~l~l 68 (298)
T PF12719_consen 4 LSITQSLLENVSSSLSP--NISLESLLDSLILPAVQSS-DPAVRELALKCLGLCCLLDK------------ELAKEHLPL 68 (298)
T ss_pred HHHHHHHHHhccccCCC--cchHHHHHHHHHHHHhcCC-CHHHHHHHHHHHHHHHHhCh------------HHHHHHHHH
Confidence 33444445555421111 3456689999999987655 435554 445555443 445566667
Q ss_pred HHHHhc
Q 002421 110 AVSAFE 115 (925)
Q Consensus 110 fV~qf~ 115 (925)
|+.+|.
T Consensus 69 ~~~~~~ 74 (298)
T PF12719_consen 69 FLQALQ 74 (298)
T ss_pred HHHHHH
Confidence 777663
No 29
>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=60.38 E-value=2.9 Score=31.16 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=21.3
Q ss_pred hcccCCCcCceeehhhHHhhhhhhc
Q 002421 68 DLLRRSDMDVRLSVTSCISEITRIT 92 (925)
Q Consensus 68 ~LLkHKDkdVRayVAcCLADILRIy 92 (925)
++|.+.+..||..++-||.+|.+.+
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 4788999999999999999998753
No 30
>KOG1248 consensus Uncharacterized conserved protein [Function unknown]
Probab=60.36 E-value=1.3e+02 Score=39.48 Aligned_cols=161 Identities=15% Similarity=0.115 Sum_probs=98.2
Q ss_pred CCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCC---
Q 002421 72 RSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE--- 148 (925)
Q Consensus 72 HKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe--- 148 (925)
..+.-+|+--.-||.-|++..- .+..--|+++|...+=.+.+.+...=+..|-+|-.|..+.++ +|..
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 3444567777789999998853 344445556665555455555555556678888888875444 4553
Q ss_pred chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHh-
Q 002421 149 CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAK- 227 (925)
Q Consensus 149 ~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadK- 227 (925)
..+.|.++|..++...-++-+..+-..+..|-..+-+....+..+.|.-+|..+--.=.+..+.-...|-..|..|-.+
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 4567777777777653333333443446666666777777899998888887754333344455455555555554443
Q ss_pred ----HHHHHHHHHHhcCC
Q 002421 228 ----LKTNLKEAVQSRGI 241 (925)
Q Consensus 228 ----Lqp~I~q~l~s~Gi 241 (925)
|++++.++|-+++.
T Consensus 859 pe~~l~~~~~~LL~sll~ 876 (1176)
T KOG1248|consen 859 PEECLSPHLEELLPSLLA 876 (1176)
T ss_pred CHHHHhhhHHHHHHHHHH
Confidence 46666555555433
No 31
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=60.01 E-value=68 Score=32.53 Aligned_cols=77 Identities=21% Similarity=0.270 Sum_probs=44.8
Q ss_pred cCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCC-Cc-----chhH----HHHHHHHhhhhce
Q 002421 71 RRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHAS-GR-----YYMK----ALSILDTVAKVRS 140 (925)
Q Consensus 71 kHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~s-sp-----~F~q----~~yLLEsLAeVKS 140 (925)
.-.|.+||.++..||.++++-.-|++ |++.|+..+..|.+.. .+ ...+ |-+||+.+.+
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 44566788888888888887765554 4666666666666532 22 1222 3344444432
Q ss_pred eeeeccCCchHHHHHHHHHHHHHh
Q 002421 141 CLLMLDLECDKLVVEMFQHFLKVI 164 (925)
Q Consensus 141 ~VLMlDLe~ddLI~eLFktFFdiV 164 (925)
|-..+.|+..+++.|+..+
T Consensus 141 -----d~~~~~l~~kl~~~~~~~~ 159 (178)
T PF12717_consen 141 -----DKQKESLVEKLCQRFLNAV 159 (178)
T ss_pred -----HHHHHHHHHHHHHHHHHHc
Confidence 2224566666666666654
No 32
>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=55.63 E-value=91 Score=34.34 Aligned_cols=123 Identities=20% Similarity=0.195 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHH--
Q 002421 28 VDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKE-- 105 (925)
Q Consensus 28 ~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKD-- 105 (925)
.++-+..+++++.....-.+.-.+.....+..++-.|++.- ..+.++.-|+-..|.|||+. -|+-.+-+..
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 34445666666666655533333323345555555555554 56888899999999999975 4444443333
Q ss_pred ------HHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHhhc
Q 002421 106 ------FFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRS 166 (925)
Q Consensus 106 ------IFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~ 166 (925)
+|..|++ .|...+..-..+..++|..|+.-.. ........+++..||+.++.
T Consensus 100 ~~~~~~~~~~fl~---ll~~~D~~i~~~a~~iLt~Ll~~~~------~~~~~~~~~~l~~ll~~L~~ 157 (312)
T PF03224_consen 100 KQDDSDPYSPFLK---LLDRNDSFIQLKAAFILTSLLSQGP------KRSEKLVKEALPKLLQWLSS 157 (312)
T ss_dssp H-TTH--HHHHHH---H-S-SSHHHHHHHHHHHHHHHTSTT------T--HHHHHHHHHHHHHHHH-
T ss_pred ccccchhHHHHHH---HhcCCCHHHHHHHHHHHHHHHHcCC------ccccchHHHHHHHHHHHHHH
Confidence 5666665 3344444456667888888765531 11233335566666666664
No 33
>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=54.63 E-value=88 Score=32.09 Aligned_cols=90 Identities=13% Similarity=0.237 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHH
Q 002421 102 LMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMT 181 (925)
Q Consensus 102 qLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs 181 (925)
.|+++...|+.++. |..+.-....+.+|..|+..=. -.-+..+..++..+|..+.. ....|.......|.
T Consensus 50 ~l~~~~~~i~~~l~---d~Rs~v~~~A~~~l~~l~~~l~------~~~~~~~~~~l~~Ll~~~~~-~~~~i~~~a~~~L~ 119 (228)
T PF12348_consen 50 CLRQLLDAIIKQLS---DLRSKVSKTACQLLSDLARQLG------SHFEPYADILLPPLLKKLGD-SKKFIREAANNALD 119 (228)
T ss_dssp HHH---HHHHH-S----HH---HHHHHHHHHHHHHHHHG------GGGHHHHHHHHHHHHHGGG----HHHHHHHHHHHH
T ss_pred HHHHhHHHHHHHHh---hhHHHHHHHHHHHHHHHHHHHh------HhHHHHHHHHHHHHHHHHcc-ccHHHHHHHHHHHH
Confidence 44455555555554 4446677788888888876611 11345667777777776553 23456667777777
Q ss_pred HHhcccCCCcHHH-HHHHHHHh
Q 002421 182 LVIDESEDVSWDL-LRILLASV 202 (925)
Q Consensus 182 ~VIeESE~VP~eV-LDvIL~~f 202 (925)
.++.-+. .+..+ +..|...+
T Consensus 120 ~i~~~~~-~~~~~~~~~l~~~~ 140 (228)
T PF12348_consen 120 AIIESCS-YSPKILLEILSQGL 140 (228)
T ss_dssp HHHTTS--H--HHHHHHHHHHT
T ss_pred HHHHHCC-cHHHHHHHHHHHHH
Confidence 7777654 44666 34443333
No 34
>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=53.31 E-value=3.6e+02 Score=30.01 Aligned_cols=96 Identities=11% Similarity=0.126 Sum_probs=53.4
Q ss_pred CCHHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHH
Q 002421 26 SPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKE 105 (925)
Q Consensus 26 iS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKD 105 (925)
.+-..|.-.|..|...|..+..+.++ .+...++. =|..+...||-....|+.++|+ .+.-.-....+..
T Consensus 35 ~nE~aL~~~l~al~~~~~~~~~~~~~-------~~~~~~~k--Gl~~kk~~vR~~w~~~~~~~~~--~~~~~~~~~~~~~ 103 (339)
T PF12074_consen 35 SNEAALSALLSALFKHLFFLSSELPK-------KVVDAFKK--GLKDKKPPVRRAWLLCLGEALW--ESPNSDSLKFAEP 103 (339)
T ss_pred cCHHHHHHHHHHHHHHHHHhCcCCCH-------HHHHHHHH--HhcCCCCcHHHHHHHHHHHHHh--hccCchHHHHHHH
Confidence 34455777777777777777333333 22222222 3455555699999999999999 1111111345555
Q ss_pred HHHHHHHHhccc-CC-----CCCcchhHHHHHH
Q 002421 106 FFQLAVSAFENL-SH-----ASGRYYMKALSIL 132 (925)
Q Consensus 106 IFqLfV~qf~~L-aD-----~ssp~F~q~~yLL 132 (925)
|...++..|..- .. ..+....-|++++
T Consensus 104 ~~~~L~~~~~~~~~~p~~~~~~~~~~~a~~~l~ 136 (339)
T PF12074_consen 104 FLPKLLQSLKEASANPLQSAQNGELVGAYVLLA 136 (339)
T ss_pred HHHHHHHHHHHHHhCCCCccccccHHHHHHHHH
Confidence 655566555421 11 2344556666666
No 35
>PTZ00429 beta-adaptin; Provisional
Probab=50.72 E-value=1.5e+02 Score=37.50 Aligned_cols=26 Identities=12% Similarity=0.059 Sum_probs=22.4
Q ss_pred cccCCCcCceeehhhHHhhhhhhcCCC
Q 002421 69 LLRRSDMDVRLSVTSCISEITRITAPD 95 (925)
Q Consensus 69 LLkHKDkdVRayVAcCLADILRIyAPD 95 (925)
.|.|++.-||--+|.|+.-|+|+ .|+
T Consensus 148 ~L~D~~pYVRKtAalai~Kly~~-~pe 173 (746)
T PTZ00429 148 AVADPDPYVRKTAAMGLGKLFHD-DMQ 173 (746)
T ss_pred HhcCCCHHHHHHHHHHHHHHHhh-Ccc
Confidence 45799999999999999999997 444
No 36
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=49.24 E-value=2e+02 Score=28.88 Aligned_cols=101 Identities=17% Similarity=0.187 Sum_probs=61.1
Q ss_pred chHHHHHHHHHHHHHhhcCC---chhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhcc---CC--CCCchHHHHHHHH
Q 002421 149 CDKLVVEMFQHFLKVIRSNH---PHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKE---NQ--DVSPTSWKLGEKV 220 (925)
Q Consensus 149 ~ddLI~eLFktFFdiVr~dh---p~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~---~k--s~~PaAykLA~~V 220 (925)
....-++||+.++....+.. +......+..|+...|+. .+|-|.|+-||++. |. ...--+|+|-.-+
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 55777889998888765421 122344566677777653 56777777776642 22 2233456664433
Q ss_pred HH--hhhHhHHHHHHHHHHhcCCCCcchHHHHHHHhcc
Q 002421 221 FT--KCAAKLKTNLKEAVQSRGIALDDYAEIVACICGS 256 (925)
Q Consensus 221 I~--~CadKLqp~I~q~l~s~Gi~Ld~Y~eIV~sIcq~ 256 (925)
+. -++..|.+||..||+......+. ..++..|+.
T Consensus 93 ~~~FpPS~~l~~yL~~~l~~~~~~~~~--~~~a~~c~~ 128 (144)
T smart00139 93 TSLFPPSERLLPYLLQFLSRRADQPSE--QGLAKYCLY 128 (144)
T ss_pred HhHcCChHHHHHHHHHHHHhcCCCccH--HHHHHHHHh
Confidence 32 45678999999999976543322 344566664
No 37
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=49.02 E-value=18 Score=39.77 Aligned_cols=35 Identities=17% Similarity=0.487 Sum_probs=30.8
Q ss_pred ccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEcc
Q 002421 713 VGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYA 747 (925)
Q Consensus 713 VG~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YD 747 (925)
||.+|.+-|++|..||..+|....+-.+.--|.++
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 89999999999999999999999997666666654
No 38
>KOG1241 consensus Karyopherin (importin) beta 1 [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=46.23 E-value=1.7e+02 Score=37.11 Aligned_cols=47 Identities=17% Similarity=0.255 Sum_probs=34.5
Q ss_pred hhcccCCC----cCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcc
Q 002421 67 NDLLRRSD----MDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFEN 116 (925)
Q Consensus 67 ~~LLkHKD----kdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~ 116 (925)
...|.+.| .+++..++.||.-|+|+.+|++|-..++|-. +|++.|..
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 45666666 4688999999999999999998877666544 44444443
No 39
>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=46.04 E-value=58 Score=26.86 Aligned_cols=39 Identities=15% Similarity=0.262 Sum_probs=31.3
Q ss_pred ccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCcceee
Q 002421 713 VGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDEEIL 754 (925)
Q Consensus 713 VG~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YDDGD~E~L 754 (925)
+|++|+|.+ ....|.|.+...|+ .+.=.|..+||..+.+
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 45677999999998 4777888888855544
No 40
>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=45.04 E-value=1.3e+02 Score=31.22 Aligned_cols=112 Identities=16% Similarity=0.240 Sum_probs=56.3
Q ss_pred ceeehhhHHhhhhhhcCCCCCCC--hhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHH
Q 002421 77 VRLSVTSCISEITRITAPDSPYD--DELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVV 154 (925)
Q Consensus 77 VRayVAcCLADILRIyAPDAPYt--DdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~ 154 (925)
||..++-||..|+.-..|..|+- .++|.+||..--.. ....-....+|.+.+-||. ++ .+-.
T Consensus 23 vR~~A~~~l~~ll~~~~~~~~~ip~~~~L~~i~~~~~~~-~~~w~~~~~~F~~l~~LL~-------------~~--~y~~ 86 (193)
T PF12612_consen 23 VREVAGKCLQRLLHSQDPTIPHIPHREELQDIFPSESEA-SLNWSSSSEYFPRLVKLLD-------------LP--EYRY 86 (193)
T ss_pred HHHHHHHHHHHHhcCCCccccCCCcHHHHHHHccccccc-ccccCCHHHHHHHHHHHhc-------------cH--HHHH
Confidence 88888888888885444432333 36777777543322 0011122335555544432 11 3334
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHhc---ccCCCcHHHHHHHHHHhhcc
Q 002421 155 EMFQHFLKVIRSNHPHFVFAAMETIMTLVID---ESEDVSWDLLRILLASVRKE 205 (925)
Q Consensus 155 eLFktFFdiVr~dhp~kV~~~M~dILs~VIe---ESE~VP~eVLDvIL~~fl~~ 205 (925)
.++..++-.+- ...+.+......-|...|. +.......++..|+.-|..+
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 34445555666666555543
No 41
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=44.88 E-value=74 Score=39.77 Aligned_cols=111 Identities=16% Similarity=0.282 Sum_probs=74.8
Q ss_pred HHHHHHhhhhceeeeeccCC-chHHHHHHHHHHHHHhh--------cCCchhH-------HHHHHHHHHHHhcccC----
Q 002421 129 LSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIR--------SNHPHFV-------FAAMETIMTLVIDESE---- 188 (925)
Q Consensus 129 ~yLLEsLAeVKS~VLMlDLe-~ddLI~eLFktFFdiVr--------~dhp~kV-------~~~M~dILs~VIeESE---- 188 (925)
|-|||-|+.|-+.+-.--+| |..+ |+-+|+++. ..++..+ .-.-.++++.+++-..
T Consensus 580 fPLLEClSsia~AL~~gF~P~~~~V----y~Rc~~il~~t~q~~~~~~~~~~~~~pdkdfiI~sLDL~SGLaegLg~~ie 655 (885)
T KOG2023|consen 580 FPLLECLSSIASALGVGFLPYAQPV----YQRCFRILQKTLQLLAKVQQDPTVEAPDKDFIIVSLDLLSGLAEGLGSHIE 655 (885)
T ss_pred HHHHHHHHHHHHHHhccccccCHHH----HHHHHHHHHHHHHHHHhccCCccccCCCcceEEEeHHHHhHHHHHhhhchH
Confidence 46888888887665555556 5544 444444444 2332222 1122355555444332
Q ss_pred C--CcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHHHHHHHhcCCCC
Q 002421 189 D--VSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIAL 243 (925)
Q Consensus 189 ~--VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~l~s~Gi~L 243 (925)
. -+..++++||..+..+-..+.-.||.|--+++..|.+.+.|++..||--+|.-+
T Consensus 656 ~Lva~snl~~lll~C~~D~~peVRQS~FALLGDltk~c~~~v~p~~~~fl~~lg~Nl 712 (885)
T KOG2023|consen 656 PLVAQSNLLDLLLQCLQDEVPEVRQSAFALLGDLTKACFEHVIPNLADFLPILGANL 712 (885)
T ss_pred HHhhhccHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHhccchHHHHHHHHhhcC
Confidence 1 345588999999998888888889999999999999999999999998766543
No 42
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=44.01 E-value=46 Score=31.43 Aligned_cols=60 Identities=15% Similarity=0.217 Sum_probs=37.1
Q ss_pred hcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhc-ccCCCCCcchhHHHHHHHHh
Q 002421 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFE-NLSHASGRYYMKALSILDTV 135 (925)
Q Consensus 68 ~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~-~LaD~ssp~F~q~~yLLEsL 135 (925)
..|...|.-||-|++-||-+|.+++- +++-.-|.-||..|. .++|++ +.=+..-.+|.+|
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 46778888899999999999999952 233334555555433 334443 3334444555554
No 43
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=43.79 E-value=1.2e+02 Score=39.69 Aligned_cols=88 Identities=14% Similarity=0.075 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHhhcCCc--hhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCC-------c----hHHHHH
Q 002421 151 KLVVEMFQHFLKVIRSNHP--HFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVS-------P----TSWKLG 217 (925)
Q Consensus 151 dLI~eLFktFFdiVr~dhp--~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~-------P----aAykLA 217 (925)
.+|..+|..++-.+.-+++ ..=+.++.-.|+++. -.+.|...|+=-+|.+++.-...++ | --.+|+
T Consensus 703 ~VID~vlE~Ir~glEin~~~~nQrriA~aryL~ELy-nfemvds~vIl~tLy~~i~~g~~~~~~~~~ldppddlFRirlV 781 (1128)
T KOG2051|consen 703 HVIDHVLEDIRPGLEINDYVSNQRRIALARYLGELY-NFEMVDSDVILNTLYHLISLGHFENLTPSALDPPDDLFRIRLV 781 (1128)
T ss_pred hhHHHHHHHHHhhhhcCcHHHHHHHHHHHHHHHHHh-hhhhhhHHHHHHHHHHHhcccccCCCCcccCCChHHHHHHHHH
Confidence 4667777777765543332 223334444444433 2355666666666666654322222 2 245788
Q ss_pred HHHHHhhhH--------hHHHHHHHHHHhc
Q 002421 218 EKVFTKCAA--------KLKTNLKEAVQSR 239 (925)
Q Consensus 218 ~~VI~~Cad--------KLqp~I~q~l~s~ 239 (925)
..|+.+|+. +--.++.-||+..
T Consensus 782 ~~lL~tc~~yf~rgs~kkkl~~fL~~fq~Y 811 (1128)
T KOG2051|consen 782 CMLLQTCGPYFTRGSTKKKLDQFLVAFQRY 811 (1128)
T ss_pred HHHHHHcccccccchhHHHHHHHHHHHHHH
Confidence 889999998 4444555555543
No 44
>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=43.56 E-value=3.2e+02 Score=32.50 Aligned_cols=94 Identities=12% Similarity=0.260 Sum_probs=55.8
Q ss_pred CcCceeehhhHHhhhhhhcCCCCCCChhHHHHH------HHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccC
Q 002421 74 DMDVRLSVTSCISEITRITAPDSPYDDELMKEF------FQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDL 147 (925)
Q Consensus 74 DkdVRayVAcCLADILRIyAPDAPYtDdqLKDI------FqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDL 147 (925)
+.+.+-.++.||+.+||+ +..+.+ +.+++..|..- ...++-.|++| .|++++-+
T Consensus 157 ~~~~~~~~v~~L~~LL~~---------~~~R~~f~~~~~v~~L~~~L~~~----~~~~Ql~Y~~l-------l~lWlLSF 216 (429)
T cd00256 157 NNDYVQTAARCLQMLLRV---------DEYRFAFVLADGVPTLVKLLSNA----TLGFQLQYQSI-------FCIWLLTF 216 (429)
T ss_pred CcchHHHHHHHHHHHhCC---------chHHHHHHHccCHHHHHHHHhhc----cccHHHHHHHH-------HHHHHHhc
Confidence 456666677999999998 222333 33555555421 12333333333 25555555
Q ss_pred C--chHHH--HHHHHHHHHHhhcCCchhHHHHHHHHHHHHhccc
Q 002421 148 E--CDKLV--VEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDES 187 (925)
Q Consensus 148 e--~ddLI--~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeES 187 (925)
+ +.+.+ ..++..+.++++...-++|......|+.-+++-.
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 45
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=42.19 E-value=2.2e+02 Score=31.23 Aligned_cols=166 Identities=10% Similarity=0.129 Sum_probs=87.8
Q ss_pred cCCCcCceeehhhHHhhhhhhcCCCCCCChh------HHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeee
Q 002421 71 RRSDMDVRLSVTSCISEITRITAPDSPYDDE------LMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLM 144 (925)
Q Consensus 71 kHKDkdVRayVAcCLADILRIyAPDAPYtDd------qLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLM 144 (925)
...+..||+-+.-||.||+-+|-++..-... ....|.++|...|... +++ -+....|-|++.=..-.+
T Consensus 74 ~~~~~~v~~~al~~l~Dll~~~g~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~-~~~-----~~~~a~EGl~KLlL~~~i 147 (298)
T PF12719_consen 74 QKDDEEVKITALKALFDLLLTHGIDIFDSESDNDESVDSKSLLKILTKFLDSE-NPE-----LQAIAVEGLCKLLLSGRI 147 (298)
T ss_pred HhCCHHHHHHHHHHHHHHHHHcCchhccchhccCccchHhHHHHHHHHHHhcC-CHH-----HHHHHHHHHHHHHhcCCC
Confidence 4468899999999999999999877433322 3566666666666544 111 233444444442111111
Q ss_pred cc--------------CC--chHHHHHHHHHHHHHhhcCC---chhHHHHHHHHHHHHhcccCC-------C-cHHHHHH
Q 002421 145 LD--------------LE--CDKLVVEMFQHFLKVIRSNH---PHFVFAAMETIMTLVIDESED-------V-SWDLLRI 197 (925)
Q Consensus 145 lD--------------Le--~ddLI~eLFktFFdiVr~dh---p~kV~~~M~dILs~VIeESE~-------V-P~eVLDv 197 (925)
.| =. .+.-+.+....||......+ +..+.......+..+..-.+. | +..|...
T Consensus 148 ~~~~~vL~~Lll~yF~p~t~~~~~LrQ~L~~Ffp~y~~s~~~~Q~~l~~~f~~~l~~~~~~~~~~~~~~~~v~~~~v~~~ 227 (298)
T PF12719_consen 148 SDPPKVLSRLLLLYFNPSTEDNQRLRQCLSVFFPVYASSSPENQERLAEAFLPTLRTLSNAPDELDSPLAMVSPSQVASF 227 (298)
T ss_pred CcHHHHHHHHHHHHcCcccCCcHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhCcccccCchhhCCHHHHHHH
Confidence 11 11 23566666677777544433 444555555556655555443 1 3334444
Q ss_pred HHHHhhccC-----C---CCCchHHHHHHHHHHhh----hHh--HHHHHHHHHHhcCCC
Q 002421 198 LLASVRKEN-----Q---DVSPTSWKLGEKVFTKC----AAK--LKTNLKEAVQSRGIA 242 (925)
Q Consensus 198 IL~~fl~~~-----k---s~~PaAykLA~~VI~~C----adK--Lqp~I~q~l~s~Gi~ 242 (925)
++.-.-+.. . ...+....||.+++..- ..+ ....++++|..+-++
T Consensus 228 lv~lt~~~~~~~~~~~~~~~~~~h~~La~~il~~i~~~~~~~~~~~k~~~~~L~~L~i~ 286 (298)
T PF12719_consen 228 LVDLTDPSKLVKESNQEIQNESVHVDLAIDILNEILSDPEKEKEERKALCKALSKLEIS 286 (298)
T ss_pred HHHHCChhhccCccccccccccHHHHHHHHHHHHHHhccccchHHHHHHHHHHhccccC
Confidence 433221111 1 12344455666655533 333 667777777765444
No 46
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=42.18 E-value=40 Score=40.02 Aligned_cols=37 Identities=19% Similarity=0.263 Sum_probs=30.7
Q ss_pred cccCeEEEeeCCCCceEEEEEEEecCCC------CeEEEEccC
Q 002421 712 LVGSRIKVWWPMDETFYKGVVDNYDPIK------KKHRILYAD 748 (925)
Q Consensus 712 lVG~RVkV~WP~D~~wY~G~V~syd~~t------kkH~V~YDD 748 (925)
-||.+|.++|..|..||.++|....... ...-|.|..
T Consensus 55 ~VGekVla~~~~Dg~~~~A~VI~~R~~~~~~~~~~~YYVHY~g 97 (450)
T PLN00104 55 EVGTRVMCRWRFDGKYHPVKVIERRRGGSGGPNDYEYYVHYTE 97 (450)
T ss_pred ccCCEEEEEECCCCCEEEEEEEEEeccCCCCCCCceEEEEEec
Confidence 4999999999999999999999988633 356777763
No 47
>KOG4338 consensus Predicted lipoprotein [Lipid transport and metabolism]
Probab=42.01 E-value=1.2e+02 Score=40.97 Aligned_cols=173 Identities=13% Similarity=0.137 Sum_probs=0.0
Q ss_pred HHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhh
Q 002421 8 IELEEQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISE 87 (925)
Q Consensus 8 ~ele~~L~~~G~KLis~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLAD 87 (925)
+.||.++++-|-.=..|+.....+-..|+.|..+-..+++.+-.-... .+.-|+.
T Consensus 319 e~Le~q~~~~~d~a~~pq~~e~~~~~kl~~l~s~a~~i~~~e~~~~~e-------------------------~~~tla~ 373 (1680)
T KOG4338|consen 319 EKLETQLLKPGDEAESPQLTESTSEQKLDLLESIAEQIEETENNEPVE-------------------------TRHTLAR 373 (1680)
T ss_pred HHHHHHHhcCCChhcCcccccchHHHHHHHHHHHHHHHhhhccccchh-------------------------HHHHHHH
Q ss_pred hhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHhhcC
Q 002421 88 ITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSN 167 (925)
Q Consensus 88 ILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~d 167 (925)
+.|+ +|++ +.+||+.||++. |-+++.-...-|.++|.+++..+-..
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 CchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhH--hHHHHHHHHHHhcCCCCcc
Q 002421 168 HPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAA--KLKTNLKEAVQSRGIALDD 245 (925)
Q Consensus 168 hp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~Cad--KLqp~I~q~l~s~Gi~Ld~ 245 (925)
..-.+...| ...++.+..+++.-+.--....-++..+|+.+|+.|.. .+.++-..+++ .....
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 002421 246 YAEIVACIC 254 (925)
Q Consensus 246 Y~eIV~sIc 254 (925)
|..+|.-+|
T Consensus 485 a~t~V~~v~ 493 (1680)
T KOG4338|consen 485 AGTAVRGVF 493 (1680)
T ss_pred hchHhhhhh
No 48
>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=41.87 E-value=51 Score=33.12 Aligned_cols=35 Identities=9% Similarity=0.198 Sum_probs=28.6
Q ss_pred CeEEEeeCCCCceEEEEEEEecCCCCeEEEEccCCcc
Q 002421 715 SRIKVWWPMDETFYKGVVDNYDPIKKKHRILYADGDE 751 (925)
Q Consensus 715 ~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YDDGD~ 751 (925)
..|...| ...||.|++.+.+....+..|.|+||..
T Consensus 14 ~avW~~~--~~~yYPa~~~~~~~~~~~~~V~Fedg~~ 48 (131)
T PF08605_consen 14 NAVWAGY--NLKYYPATCVGSGVDRDRSLVRFEDGTY 48 (131)
T ss_pred cceeecC--CCeEeeEEEEeecCCCCeEEEEEecCce
Confidence 3444545 7899999999998877789999999983
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=40.98 E-value=2.8e+02 Score=29.93 Aligned_cols=174 Identities=13% Similarity=0.105 Sum_probs=85.9
Q ss_pred hhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHH
Q 002421 51 RSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALS 130 (925)
Q Consensus 51 dS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~y 130 (925)
..+++.+..+...+++. +.+.+.|||+.+.=.|--+.=++.|..++++..... ..--.|+.
T Consensus 35 ~~~W~~~~~lK~~Il~~--~~~~~~gvk~~~iKFle~vIl~qs~~~~~~~~~~~~------~~d~SL~~----------- 95 (239)
T PF11935_consen 35 EQLWESMNELKDRILSL--WDSENPGVKLAAIKFLERVILVQSPGSSDSPPRRGS------PNDFSLSS----------- 95 (239)
T ss_dssp HHHHHHHHHHHHHHHHG--GGSSSHHHHHHHHHHHHHHHHHTS---TTS---GGG------TTS--GGG-----------
T ss_pred HHHHHHHHHHHHHHHHH--hcCCCchHHHHHHHHHHHHHHhcCCCCCCCcccccc------ccCCCHHH-----------
Confidence 36788888888888887 888899999988888888888888887766543000 00001211
Q ss_pred HHHHhhhhceeeeeccCC--chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCC
Q 002421 131 ILDTVAKVRSCLLMLDLE--CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQD 208 (925)
Q Consensus 131 LLEsLAeVKS~VLMlDLe--~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks 208 (925)
|..-..++-.-.|+ +..|+..|+..|+... ++..++..+.+-|..|+--=...-.-||.+|+..-......
T Consensus 96 ----vp~~Hp~l~~~~Le~Ea~~lL~~Ll~~l~~~~---i~~~~~~a~insL~~Iak~RP~~~~~Il~~ll~~~~~~~~~ 168 (239)
T PF11935_consen 96 ----VPPNHPLLNPQQLEAEANGLLDRLLDVLQSPH---ISSPLLTAIINSLSNIAKQRPQFMSRILPALLSFNPNLSPM 168 (239)
T ss_dssp ----S-TT-SSS-HHHHHHHHHHHHHHHHHHHC-TT-----HHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHS----
T ss_pred ----cCCCCCcCCHHHHHHHHHHHHHHHHHHHhhcc---cchHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhcCcccccc
Confidence 11112222222333 5666666666666432 35555555566666666555555555666665543222011
Q ss_pred CCchHHHHHHHHHHhhhHhHHHHHHHHHHhcCCCCcchHHHHHHHhc
Q 002421 209 VSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIALDDYAEIVACICG 255 (925)
Q Consensus 209 ~~PaAykLA~~VI~~CadKLqp~I~q~l~s~Gi~Ld~Y~eIV~sIcq 255 (925)
..+.-+.++..-+ ...|+-.|..+|..-.. ..|..-+...+.
T Consensus 169 ~~~~~~~~~v~sv---~k~lk~~l~~llk~~~~--~~~~~~i~~~L~ 210 (239)
T PF11935_consen 169 QPPTLSKLQVKSV---EKTLKIFLLHLLKHPAS--SPFQGRITQALT 210 (239)
T ss_dssp --TTCSHHHHHHH---HHHHHHHHHHHHTSGGG--GGGHHHHHHHHH
T ss_pred CCccchHHHHHHH---HHHHHHHHHHHHCCCCc--hhhHHHHHHHHH
Confidence 1222233332222 22345555555553222 266654444444
No 50
>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=40.96 E-value=68 Score=35.27 Aligned_cols=35 Identities=23% Similarity=0.389 Sum_probs=23.9
Q ss_pred HhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhh
Q 002421 55 DALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRI 91 (925)
Q Consensus 55 ~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRI 91 (925)
..|..+..-|-+ ++.+.+.+++..+..||+.+||+
T Consensus 146 ~~l~~ll~~L~~--~l~~~~~~~~~~av~~L~~LL~~ 180 (312)
T PF03224_consen 146 EALPKLLQWLSS--QLSSSDSELQYIAVQCLQNLLRS 180 (312)
T ss_dssp HHHHHHHHHHH---TT-HHHH---HHHHHHHHHHHTS
T ss_pred HHHHHHHHHHHH--hhcCCCcchHHHHHHHHHHHhCc
Confidence 456566655555 77888999999999999999987
No 51
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=39.08 E-value=5.1e+02 Score=30.57 Aligned_cols=111 Identities=13% Similarity=0.163 Sum_probs=69.2
Q ss_pred CCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHH
Q 002421 121 SGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLA 200 (925)
Q Consensus 121 ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~ 200 (925)
+...+.+.+.+|.++-+..+..+ .++.|..|-+..+.+.+..........-..++-.||- ...||.+-+..++.
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 44566777777777777665543 3455566666666654444444444444566666665 67899888877776
Q ss_pred Hhhc-cC-CCCCchHHHHHHHHHH-hhhHhHHHHHHHHHH
Q 002421 201 SVRK-EN-QDVSPTSWKLGEKVFT-KCAAKLKTNLKEAVQ 237 (925)
Q Consensus 201 ~fl~-~~-ks~~PaAykLA~~VI~-~CadKLqp~I~q~l~ 237 (925)
-|=. .+ ..-...+|++.+.+|. .++...=..++.+|.
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 1345578888888884 456666677777773
No 52
>PF14911 MMS22L_C: S-phase genomic integrity recombination mediator, C-terminal
Probab=39.00 E-value=4.6e+02 Score=30.84 Aligned_cols=123 Identities=15% Similarity=0.260 Sum_probs=79.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCC--h
Q 002421 23 NPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYD--D 100 (925)
Q Consensus 23 s~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYt--D 100 (925)
.+|....-.|..|.+|-+.+..-.++ ....-+..+.-.|...-++-|--.-||..+.--|-.|++-+. ..+.. .
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 APPPRLASVLAFLQQLLKRLQRQNEN---QILTLLRLVLPSLLECLMLVNEEPQVKKLATELLQYMVESCQ-VGSSGEPR 298 (373)
T ss_pred CCCCcHHHHHHHHHHHHHhcCcccch---hHHHHHHHhhHHHHHHHhhcCCCcchhHHHHHHHHHHHHccc-ccCcchHH
Confidence 35666777888888887776521221 122333444445555556666677799888888888887665 22222 4
Q ss_pred hHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHhh
Q 002421 101 ELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIR 165 (925)
Q Consensus 101 dqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr 165 (925)
++|..+|.-||.--- .-|-.+||.+|++||... .+||..||-++=..++
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 4666666655544443
No 53
>KOG1949 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.47 E-value=2.2e+02 Score=36.19 Aligned_cols=152 Identities=18% Similarity=0.227 Sum_probs=85.4
Q ss_pred hhhhhhc---ccCCCcCceeehhhHHhhhhhhcCCCCCCC--hhHHHHHHHHHHHHhc------------ccCC------
Q 002421 63 GLITNDL---LRRSDMDVRLSVTSCISEITRITAPDSPYD--DELMKEFFQLAVSAFE------------NLSH------ 119 (925)
Q Consensus 63 ~LVs~~L---LkHKDkdVRayVAcCLADILRIyAPDAPYt--DdqLKDIFqLfV~qf~------------~LaD------ 119 (925)
-|.++.| |+-.|..||.-+|.-+.|.+=|--||+--. |..|..=|.++-+.|+ |+..
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 3444545 566899999999999999999999998333 2333333333332222 0000
Q ss_pred ---CCCcchhHHHHHHHH----------hhhhceeeeeccCC-chHHHHHHHHHHHHHhhc---CCchhHHHHHHHHHHH
Q 002421 120 ---ASGRYYMKALSILDT----------VAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRS---NHPHFVFAAMETIMTL 182 (925)
Q Consensus 120 ---~ssp~F~q~~yLLEs----------LAeVKS~VLMlDLe-~ddLI~eLFktFFdiVr~---dhp~kV~~~M~dILs~ 182 (925)
|..-.-.--.||... ++.++.+..|+|.+ |..++ +..+-.++. +.++.|+..|.+||..
T Consensus 253 e~iP~~i~~~ll~kI~d~~a~dt~s~VR~svf~gl~~~l~np~sh~~l----e~~Lpal~~~l~D~se~VRvA~vd~ll~ 328 (1005)
T KOG1949|consen 253 EMIPPTILIDLLKKITDELAFDTSSDVRCSVFKGLPMILDNPLSHPLL----EQLLPALRYSLHDNSEKVRVAFVDMLLK 328 (1005)
T ss_pred HHcCHHHHHHHHHHHHHHhhhccchheehhHhcCcHHHHcCccchhHH----HHHHHhcchhhhccchhHHHHHHHHHHH
Confidence 000011112233333 34455566677777 55444 444444443 6678899999999876
Q ss_pred Hhcc-----cCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhh
Q 002421 183 VIDE-----SEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKC 224 (925)
Q Consensus 183 VIeE-----SE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~C 224 (925)
|=+- -.-+|. |.||..|-. .+.|.+++++.-|+..|
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 5332 234554 455555543 34566777776655544
No 54
>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=38.47 E-value=4.2e+02 Score=28.41 Aligned_cols=163 Identities=14% Similarity=0.142 Sum_probs=86.9
Q ss_pred HHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHH
Q 002421 33 NLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVS 112 (925)
Q Consensus 33 KRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~ 112 (925)
+-|+.|..+|+.-.+... ...+..+-+.|-=- +-..--+-||--+|..|++|++.+.++. ..--=++-.|.-+.+
T Consensus 19 ~al~~l~~~l~~~~~~~~---~~~~~kLWKGLfy~-mWmsDkpl~Q~~la~~la~l~~~~~~~~-~~~~f~~~f~~tm~r 93 (217)
T PF05997_consen 19 RALKSLRKWLSKRSQLLT---ELDMLKLWKGLFYC-MWMSDKPLVQEELAEELASLIHSFPSEK-AALLFLKAFWETMRR 93 (217)
T ss_pred HHHHHHHHHHHhccccCC---HHHHHHHHHHHHHH-HHhcCCchhHHHHHHHHHHHHHhhcChH-HHHHHHHHHHHHHHH
Confidence 345677777776655421 23345555554322 2223335688889999999999987765 011223333334444
Q ss_pred HhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCC-chHHHHHHHHHHHHHh-hc-C-CchhHHHHHHHHHHHHhcccC
Q 002421 113 AFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVI-RS-N-HPHFVFAAMETIMTLVIDESE 188 (925)
Q Consensus 113 qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe-~ddLI~eLFktFFdiV-r~-d-hp~kV~~~M~dILs~VIeESE 188 (925)
.+.+|. .+=-.-||+|-+.---.++.+|-.-. ..+++.++.+.|...+ .. + .|.-+..++.+|...-++...
T Consensus 94 EW~~ID----~~R~DKf~~LvR~~~~~~~~~l~~~~w~~~~v~~~~~~l~~~~l~~~~~~p~Gl~~H~~Di~ldEL~k~~ 169 (217)
T PF05997_consen 94 EWDGID----RLRMDKFLMLVRRFLRQSFRFLKKNGWDKELVEEFNEILSETPLNPNDQVPNGLRYHFADIFLDELEKVG 169 (217)
T ss_pred HHcccH----HHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHccCCCcCCCchhHHHHHHHHHHHHHHHHh
Confidence 455554 12122356666655555565555554 4455555555555532 11 1 455566666666554333322
Q ss_pred ----------CCcHHHHHHHHHHhhc
Q 002421 189 ----------DVSWDLLRILLASVRK 204 (925)
Q Consensus 189 ----------~VP~eVLDvIL~~fl~ 204 (925)
.++.+.+..||..|..
T Consensus 170 ~~~~~~~e~~~~~~~~~~~ll~PF~~ 195 (217)
T PF05997_consen 170 GSESEDEEEENLPAEPLLLLLEPFVK 195 (217)
T ss_pred cccccchhcccCCHHHHHHHHHHHHH
Confidence 2666666666666553
No 55
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=36.71 E-value=88 Score=37.80 Aligned_cols=94 Identities=16% Similarity=0.322 Sum_probs=61.0
Q ss_pred ccCC-chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCC----CCCchHHHHHHH
Q 002421 145 LDLE-CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQ----DVSPTSWKLGEK 219 (925)
Q Consensus 145 lDLe-~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~k----s~~PaAykLA~~ 219 (925)
+|++ .-+||.+|+-++...+.+.+.--|+.-+. +.+|.+-|..|+..|...+. .+.|-..++.-+
T Consensus 274 id~~~~~~Li~ELd~~vl~~v~DQngnHViQK~i----------e~~p~~~~~Fiv~~f~~~~~~~~ls~~~YGCRVIQr 343 (503)
T KOG1488|consen 274 VDVSLQIQLIDELDGHLLKCVKDQNGNHVIQKCI----------ETLPPDAWQFIVDFFSGDDNLLELSTHKYGCRVIQR 343 (503)
T ss_pred cCHHHHHHHHHHHHhhHHHHHhhcccceehhhhh----------hccChHHHHHHHHHhcCCCceeEeeccCcccHHHHH
Confidence 3444 56899999888888888755544533322 47999999999999987543 457777777777
Q ss_pred HHHhhhHhHHH-HHHHHHHhc-CCCCcchHH
Q 002421 220 VFTKCAAKLKT-NLKEAVQSR-GIALDDYAE 248 (925)
Q Consensus 220 VI~~CadKLqp-~I~q~l~s~-Gi~Ld~Y~e 248 (925)
+++.|...=+. .+..+...+ .+.-|.|.+
T Consensus 344 ~lE~c~~~~~~~i~~ei~~~~~~L~~dQygN 374 (503)
T KOG1488|consen 344 ILEHCSEDQKQPLMEEIIRNCDQLAQDQYGN 374 (503)
T ss_pred HhhcCChHhhhHHHHHHHHHHHHHHhhhhhh
Confidence 78888765333 333322221 133466766
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=35.28 E-value=5.3e+02 Score=29.04 Aligned_cols=101 Identities=18% Similarity=0.269 Sum_probs=58.2
Q ss_pred CHHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcC------ceeehhhHHhhhhhhcCCCCCCCh
Q 002421 27 PVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMD------VRLSVTSCISEITRITAPDSPYDD 100 (925)
Q Consensus 27 S~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkd------VRayVAcCLADILRIyAPDAPYtD 100 (925)
--.|.|..+..+...|...-++.+.-+.+++-..-..+++..+..-++-- +|+++..|..=++.+ +.
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 36688888888888888876666666667776666777777766554422 344455555555553 44
Q ss_pred hHHHHHHHHHHHHhcccCCCCCcc----hhHHHHHHHHhhh
Q 002421 101 ELMKEFFQLAVSAFENLSHASGRY----YMKALSILDTVAK 137 (925)
Q Consensus 101 dqLKDIFqLfV~qf~~LaD~ssp~----F~q~~yLLEsLAe 137 (925)
++++.++..++- ++.++...- ..-...||+.++.
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 444444333 3333444444444
No 57
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=34.00 E-value=1e+02 Score=30.28 Aligned_cols=68 Identities=16% Similarity=0.243 Sum_probs=49.1
Q ss_pred hhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHH
Q 002421 164 IRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNL 232 (925)
Q Consensus 164 Vr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I 232 (925)
.++..+..=...+..|.- +|...+.-|.+.+..|...|...++.+.--|..|...++.+|+..+...|
T Consensus 9 Ts~~l~~~dw~~~l~icD-~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev 76 (133)
T smart00288 9 TSPSLLEEDWELILEICD-LINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEV 76 (133)
T ss_pred cCcCCCCcCHHHHHHHHH-HHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHH
Confidence 344444444455555544 45555789999999999999987777777778888888899998876555
No 58
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=32.90 E-value=5.8e+02 Score=32.14 Aligned_cols=221 Identities=13% Similarity=0.263 Sum_probs=113.0
Q ss_pred HHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHH
Q 002421 34 LLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSA 113 (925)
Q Consensus 34 RLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~q 113 (925)
|..-|.+.|.......+--+.+-|..+...|+.-.=+.--+...|+..-..|..+. +|+||+= .+-+-.|+.++..-
T Consensus 473 ~~~nlv~h~a~a~~~~~S~l~~fY~ai~~~Lv~~t~~~~Ne~n~R~s~fsaLgtli-~~~~d~V--~~~~a~~~~~~~~k 549 (858)
T COG5215 473 RKENLVDHIAKAVREVESFLAKFYLAILNALVKGTELALNESNLRVSLFSALGTLI-LICPDAV--SDILAGFYDYTSKK 549 (858)
T ss_pred HHHhHHHhhhhhhccccchhHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHH-hhcchhH--HHHHHHHHHHHHHH
Confidence 33445555555553333335667777888888766665556666766667777766 4577752 34555566665443
Q ss_pred hc-------ccCCCCCc-----chhHHHHHHHHhhhhceeeeeccCC-chHHHHHHHHHHHHHhhcCC-chhHHHHHHHH
Q 002421 114 FE-------NLSHASGR-----YYMKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNH-PHFVFAAMETI 179 (925)
Q Consensus 114 f~-------~LaD~ssp-----~F~q~~yLLEsLAeVKS~VLMlDLe-~ddLI~eLFktFFdiVr~dh-p~kV~~~M~dI 179 (925)
|. .+-+.++. .-..|..+|+.+-..+- -|++ ..|.+.+||=.++....+.+ -..|+..+..+
T Consensus 550 l~~~isv~~q~l~~eD~~~~~elqSN~~~vl~aiir~~~----~~ie~v~D~lm~Lf~r~les~~~t~~~~dV~~aIsal 625 (858)
T COG5215 550 LDECISVLGQILATEDQLLVEELQSNYIGVLEAIIRTRR----RDIEDVEDQLMELFIRILESTKPTTAFGDVYTAISAL 625 (858)
T ss_pred HHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC----CCcccHHHHHHHHHHHHHhccCCchhhhHHHHHHHHH
Confidence 32 22222222 23446666766544321 3565 45655555555555443332 35677888887
Q ss_pred HHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHh------------------------HHHHHHHH
Q 002421 180 MTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAK------------------------LKTNLKEA 235 (925)
Q Consensus 180 Ls~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadK------------------------Lqp~I~q~ 235 (925)
++.+=+-.+.--..++-.++..+...+.-....|-.|.-++-+.-..+ |+|.|...
T Consensus 626 ~~sl~e~Fe~y~~~fiPyl~~aln~~d~~v~~~avglvgdlantl~~df~~y~d~~ms~LvQ~lss~~~~R~lKPaiLSv 705 (858)
T COG5215 626 STSLEERFEQYASKFIPYLTRALNCTDRFVLNSAVGLVGDLANTLGTDFNIYADVLMSSLVQCLSSEATHRDLKPAILSV 705 (858)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHhcchhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcChhhccccchHHHHH
Confidence 776555544322222223333222111112222333333333333333 34444444
Q ss_pred HH----hcCCCCcchHHHHHHHhccCCCCC
Q 002421 236 VQ----SRGIALDDYAEIVACICGSDDENP 261 (925)
Q Consensus 236 l~----s~Gi~Ld~Y~eIV~sIcq~~s~~l 261 (925)
|. ..|--+-.|-++|--+||..++.-
T Consensus 706 FgDIAlaiga~F~~YL~~im~L~qqas~~~ 735 (858)
T COG5215 706 FGDIALAIGANFESYLDMIMMLFQQASELD 735 (858)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHHHHHhccC
Confidence 43 122235678888888888877655
No 59
>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=32.90 E-value=45 Score=27.11 Aligned_cols=46 Identities=20% Similarity=0.286 Sum_probs=30.9
Q ss_pred HHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhh
Q 002421 41 LLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEI 88 (925)
Q Consensus 41 eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADI 88 (925)
.|..+-+...+.+...+..++..|+ .+|.+.+..||..++-||..|
T Consensus 10 aLg~l~~~~~~~~~~~~~~~~~~L~--~~L~d~~~~VR~~A~~aLg~l 55 (55)
T PF13513_consen 10 ALGRLAEGCPELLQPYLPELLPALI--PLLQDDDDSVRAAAAWALGNL 55 (55)
T ss_dssp HHHCTTTTTHHHHHHHHHHHHHHHH--HHTTSSSHHHHHHHHHHHHCH
T ss_pred HHhhHhcccHHHHHHHHHHHHHHHH--HHHcCCCHHHHHHHHHHHhcC
Confidence 4555544444444445555666666 577888889999999998765
No 60
>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=32.47 E-value=3.1e+02 Score=33.30 Aligned_cols=100 Identities=11% Similarity=0.205 Sum_probs=55.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhH
Q 002421 23 NPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL 102 (925)
Q Consensus 23 s~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdq 102 (925)
..++++.+|...|+.|..+.+.|+.. - ..+..+|++-..+...+.-|++|+.-++.=+. -...-
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 35666777777777777667777653221110 01345
Q ss_pred HHHHHHHHHHHhcccCC-----------CCCcchhHHHHHHHHhhhh
Q 002421 103 MKEFFQLAVSAFENLSH-----------ASGRYYMKALSILDTVAKV 138 (925)
Q Consensus 103 LKDIFqLfV~qf~~LaD-----------~ssp~F~q~~yLLEsLAeV 138 (925)
+..|+..+|..|.--.. ....-|.+.+.+|..|..+
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 56666666666542211 1233566677777776543
No 61
>KOG4256 consensus Kinetochore component [Cell cycle control, cell division, chromosome partitioning]
Probab=32.41 E-value=3.5e+02 Score=35.96 Aligned_cols=104 Identities=15% Similarity=0.231 Sum_probs=50.1
Q ss_pred hhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCC----h---hHHHHHHHHHHHHhcccCC--------CCCcchhHHH
Q 002421 65 ITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYD----D---ELMKEFFQLAVSAFENLSH--------ASGRYYMKAL 129 (925)
Q Consensus 65 Vs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYt----D---dqLKDIFqLfV~qf~~LaD--------~ssp~F~q~~ 129 (925)
..+.+|+.-|. ..+.-|-|+-+++|-||--|-|. . .----||.+|+..|-+-.| .+...|.+.-
T Consensus 498 AKkRlikdeDi-lalI~ad~lkevlgahaiiagf~eafePsrekfnesiW~eFlealhdaddlidIflefisdanftcAq 576 (2209)
T KOG4256|consen 498 AKKRLIKDEDI-LALIEADCLKEVLGAHAIIAGFPEAFEPSREKFNESIWDEFLEALHDADDLIDIFLEFISDANFTCAQ 576 (2209)
T ss_pred HHHhhcchHHH-HHHHHHHHHHHHHhhhhhhccCccccCCchhhhcchhHHHHHHhhcccchHHHHHHHHhhccceeehh
Confidence 33445544444 55677999999999887444322 1 1112233344333221111 1223333333
Q ss_pred HHHHH-hhhhceeeeeccCC-chHHHHHHHHHHHHHhhcCCch
Q 002421 130 SILDT-VAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNHPH 170 (925)
Q Consensus 130 yLLEs-LAeVKS~VLMlDLe-~ddLI~eLFktFFdiVr~dhp~ 170 (925)
||.-+ =|.+-+. .+.|.+ --.-+..||+.|.+.++.+.+.
T Consensus 577 ~i~lRHganfedr-f~~deentisrLEsLfrmfidaiSadiSk 618 (2209)
T KOG4256|consen 577 VIFLRHGANFEDR-FCDDEENTISRLESLFRMFIDAISADISK 618 (2209)
T ss_pred hHHHhhcCchhhh-hccchhhhHHHHHHHHHHHHHHhhhhHHH
Confidence 33222 1222111 111111 1223899999999999987543
No 62
>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=32.40 E-value=82 Score=28.60 Aligned_cols=59 Identities=20% Similarity=0.301 Sum_probs=40.0
Q ss_pred ceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHH-HHHHHhhhhc
Q 002421 77 VRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKAL-SILDTVAKVR 139 (925)
Q Consensus 77 VRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~-yLLEsLAeVK 139 (925)
.+.++|+.++|++.-+.|+.-- -..+|.++...|..|....++...-.. ++|.-|...-
T Consensus 5 ~~~~~a~~~~El~~~~~~~~~~----~~~lf~ll~~~L~~L~~~~~~~~~~~~~f~l~ll~~~G 64 (118)
T PF02565_consen 5 ERLAYASYIAELLDRLLPEGEP----NPELFDLLLAALDALEEGEDPWLLLLIQFELKLLKLLG 64 (118)
T ss_dssp HHHHHHHHHHHHHHHHS-CTS------HHHHHHHHHHHHHHHCSSSHCHHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHHHHHcccCCC----hHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHcC
Confidence 5678899999999887755321 245999999999999877655444444 5666555544
No 63
>PF14911 MMS22L_C: S-phase genomic integrity recombination mediator, C-terminal
Probab=32.32 E-value=4.9e+02 Score=30.60 Aligned_cols=156 Identities=19% Similarity=0.256 Sum_probs=79.8
Q ss_pred hHHHHHHHHHHHHhcccCCCCCcchhHHHH-HHH----Hhhhhceee--------eeccCCchHHHHHHHHHHHHHhh--
Q 002421 101 ELMKEFFQLAVSAFENLSHASGRYYMKALS-ILD----TVAKVRSCL--------LMLDLECDKLVVEMFQHFLKVIR-- 165 (925)
Q Consensus 101 dqLKDIFqLfV~qf~~LaD~ssp~F~q~~y-LLE----sLAeVKS~V--------LMlDLe~ddLI~eLFktFFdiVr-- 165 (925)
.-++++|-+|+.-+..+.-..++|-.+..- |+. .+.--.+.+ ++++-+ -..++.+.+++.++
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 568999999999888888888887666421 111 111111111 122222 22233333333333
Q ss_pred -----cCCchhHHHHHHHHHHHHhcc----cCCCcHHHHHHHH----HHhhccCCCCCchHHHHH----HHHHHhhh---
Q 002421 166 -----SNHPHFVFAAMETIMTLVIDE----SEDVSWDLLRILL----ASVRKENQDVSPTSWKLG----EKVFTKCA--- 225 (925)
Q Consensus 166 -----~dhp~kV~~~M~dILs~VIeE----SE~VP~eVLDvIL----~~fl~~~ks~~PaAykLA----~~VI~~Ca--- 225 (925)
..-|+.-......++.+++.+ ....-..+++++| .+++--+ ..|...++| ..+++.|.
T Consensus 216 fl~~~~~~p~p~l~~vL~fl~~Ll~~~~~~~~~~~~~~~~~~lp~lL~c~~~v~--e~~~~k~~a~e~l~~mv~~~~~~~ 293 (373)
T PF14911_consen 216 FLEFKGSAPPPRLASVLAFLQQLLKRLQRQNENQILTLLRLVLPSLLECLMLVN--EEPQVKKLATELLQYMVESCQVGS 293 (373)
T ss_pred HhcCCCCCCCCcHHHHHHHHHHHHHhcCcccchhHHHHHHHhhHHHHHHHhhcC--CCcchhHHHHHHHHHHHHcccccC
Confidence 233333334555566666666 2333333344433 3333222 234444444 44556676
Q ss_pred -----HhHHHHHHHHHHhcCCCC-cchHHHHHHHhccCCCCC
Q 002421 226 -----AKLKTNLKEAVQSRGIAL-DDYAEIVACICGSDDENP 261 (925)
Q Consensus 226 -----dKLqp~I~q~l~s~Gi~L-d~Y~eIV~sIcq~~s~~l 261 (925)
+.|...+.+|.+.....- -.|..++.+|+..+.+..
T Consensus 294 ~~~~~~~l~s~lrsfvqk~l~~~t~~~f~~l~~vA~l~p~lV 335 (373)
T PF14911_consen 294 SGEPREQLTSVLRSFVQKYLAHYTYQYFQFLEKVAELDPQLV 335 (373)
T ss_pred cchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCHHHH
Confidence 456677777777553332 346788888887776554
No 64
>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=32.18 E-value=4.9e+02 Score=31.07 Aligned_cols=114 Identities=16% Similarity=0.221 Sum_probs=64.0
Q ss_pred cccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceee--e---
Q 002421 69 LLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCL--L--- 143 (925)
Q Consensus 69 LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~V--L--- 143 (925)
.|.|.+..||.+++-.|..+.|- ++.-..--.=.+||.+++..+ .+++...-....-+|..|+...... |
T Consensus 85 gL~h~~~~Vr~l~l~~l~~~~~~--~~~~~~~~~~~~l~~~i~~~L---~~~d~~Va~~A~~~L~~l~~~~~~~~~l~~~ 159 (503)
T PF10508_consen 85 GLTHPSPKVRRLALKQLGRIARH--SEGAAQLLVDNELLPLIIQCL---RDPDLSVAKAAIKALKKLASHPEGLEQLFDS 159 (503)
T ss_pred HhcCCCHHHHHHHHHHHHHHhcC--CHHHHHHhcCccHHHHHHHHH---cCCcHHHHHHHHHHHHHHhCCchhHHHHhCc
Confidence 56799999999887776555543 111000001123555555544 6777777888888888888765333 1
Q ss_pred --eccCC------chHHHHHHHHHHHHHhhcCCchhHHHHHHH--HHHHHhcccCC
Q 002421 144 --MLDLE------CDKLVVEMFQHFLKVIRSNHPHFVFAAMET--IMTLVIDESED 189 (925)
Q Consensus 144 --MlDLe------~ddLI~eLFktFFdiVr~dhp~kV~~~M~d--ILs~VIeESE~ 189 (925)
+..|. .+.+-..++..+-.+. .++......+.+ ++..++.|.+.
T Consensus 160 ~~~~~L~~l~~~~~~~vR~Rv~el~v~i~--~~S~~~~~~~~~sgll~~ll~eL~~ 213 (503)
T PF10508_consen 160 NLLSKLKSLMSQSSDIVRCRVYELLVEIA--SHSPEAAEAVVNSGLLDLLLKELDS 213 (503)
T ss_pred chHHHHHHHHhccCHHHHHHHHHHHHHHH--hcCHHHHHHHHhccHHHHHHHHhcC
Confidence 11111 1223334444444432 355666665554 77777777665
No 65
>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=31.96 E-value=2.6e+02 Score=31.77 Aligned_cols=41 Identities=17% Similarity=0.457 Sum_probs=31.8
Q ss_pred CCChhHHHHHHH-HHHHHhcccCCCCCcchhHHHHHHHHhhhh
Q 002421 97 PYDDELMKEFFQ-LAVSAFENLSHASGRYYMKALSILDTVAKV 138 (925)
Q Consensus 97 PYtDdqLKDIFq-LfV~qf~~LaD~ssp~F~q~~yLLEsLAeV 138 (925)
|-.. .|+-++. ||+.-|+||.|.++.+|.+-+.||+.|...
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 4445 5555555 455569999999999999999999999754
No 66
>KOG0211 consensus Protein phosphatase 2A regulatory subunit A and related proteins [Signal transduction mechanisms]
Probab=31.72 E-value=7.6e+02 Score=31.66 Aligned_cols=137 Identities=10% Similarity=0.111 Sum_probs=88.6
Q ss_pred ccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCc
Q 002421 70 LRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLEC 149 (925)
Q Consensus 70 LkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ 149 (925)
|.+..-.||-.+|-|+.-+.+.|-.+ | .....|++++...... .|-.++.+|-+|+.+ ..+=.
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 55556679999999999999998732 2 3556777777765543 788888888888822 22225
Q ss_pred hHHHHHHHHHHHHHhhcCCchhHH----HHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhh
Q 002421 150 DKLVVEMFQHFLKVIRSNHPHFVF----AAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCA 225 (925)
Q Consensus 150 ddLI~eLFktFFdiVr~dhp~kV~----~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~Ca 225 (925)
.++..+.|-.+|.-...+--.+|+ .++..|+..++. .+-.+.|-.++..|...+.-.-+.+..+|..+|..|.
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 666666666666655555555554 445566655544 3445556677777777555556667777777666554
Q ss_pred H
Q 002421 226 A 226 (925)
Q Consensus 226 d 226 (925)
-
T Consensus 667 ~ 667 (759)
T KOG0211|consen 667 L 667 (759)
T ss_pred H
Confidence 3
No 67
>KOG2022 consensus Nuclear transport receptor LGL2 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=31.33 E-value=5.8e+02 Score=33.29 Aligned_cols=185 Identities=16% Similarity=0.242 Sum_probs=104.6
Q ss_pred HhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHH
Q 002421 55 DALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDT 134 (925)
Q Consensus 55 ~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEs 134 (925)
..+-++...+.+ .-|+..| +.=|.|+..+--+.--..||..--|.+++.|+++ |-. ++. +-+
T Consensus 701 ~k~i~~~~kv~s-~~~~~s~----vve~~C~i~~~~v~~~~~sF~~p~l~~l~~Fi~r-~~~-----~~~-------a~t 762 (982)
T KOG2022|consen 701 QKAIPVFEKVLS-MWLGLSD----VVEASCIIMVKGVRSLLTSFPEPMLPSLCPFIVR-FLT-----SCL-------AVT 762 (982)
T ss_pred HHHHHHHHHHHH-HHhcchh----HHHHHHHHHHhccccccccchhhhHHHHHHHHHH-hcc-----chH-------HHH
Confidence 334455555555 3344333 3668888888887666688999999999999999 531 222 222
Q ss_pred hhhhceeeeeccC--CchHHHHHHH----HHHHHHhh----cCCchhHHHHHHHHHHHHhcccCCCcH----HHHHHHHH
Q 002421 135 VAKVRSCLLMLDL--ECDKLVVEMF----QHFLKVIR----SNHPHFVFAAMETIMTLVIDESEDVSW----DLLRILLA 200 (925)
Q Consensus 135 LAeVKS~VLMlDL--e~ddLI~eLF----ktFFdiVr----~dhp~kV~~~M~dILs~VIeESE~VP~----eVLDvIL~ 200 (925)
+.-++-|++|.-- .|-+|+...| +..|-+.. .++|..+...|. .++.+|.--..++. ..-..||.
T Consensus 763 l~l~~~~l~~~~~~~~~~~lv~~~~~~~~q~sl~lf~~~~f~n~~Di~~~~~~-~v~~ilkk~P~~~~~~~~~~ts~i~~ 841 (982)
T KOG2022|consen 763 LSLIAACLLAKSTVEQCKPLVGQDMANAFQQSLLLFEQHPFSNQPDIYLQLIG-FVRQILKKIPKFLEPSMLAFTSLILI 841 (982)
T ss_pred HHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH-HHHHHHHhCcCccccchHHHHHHHHH
Confidence 2333334444333 2544544444 44333333 256666666665 66667665544332 23345553
Q ss_pred Hhh----ccCCCCCchHHHHHHHHHHhhhHhHHHHHHHHHHhcCC-----------------CCcchHHHHHHHhccCC
Q 002421 201 SVR----KENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGI-----------------ALDDYAEIVACICGSDD 258 (925)
Q Consensus 201 ~fl----~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~l~s~Gi-----------------~Ld~Y~eIV~sIcq~~s 258 (925)
++. .+.+.+..+|.+.-..++..|....=-.+.+.++..|- .+|-|++|+..+.....
T Consensus 842 ~a~~ll~~pE~~~i~aa~qF~t~~~~~~~s~~~~tv~~~V~~~G~~Li~~im~~vgg~~~RS~ld~~aDIL~al~~k~~ 920 (982)
T KOG2022|consen 842 CAFILLNSPEPTTIRAASQFLTALATYATSHDLVTVTSVVAEIGPILIYAIMRGVGGEASRSTLDALADILLALNAKFF 920 (982)
T ss_pred HHHHhcCCCccHHHHHHHHHHHHHHhhcccchhHHHHHHHHhcchHHHHHHHHHhcCcCccchhHHHHHHHHHHHHhhh
Confidence 322 34444555566665557777766554455555554332 25888888887765543
No 68
>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=31.18 E-value=2e+02 Score=31.83 Aligned_cols=107 Identities=14% Similarity=0.231 Sum_probs=74.1
Q ss_pred HHHHHHHHHHHHhcccCCC--CCcchhHHHHHHHHhh---------hhceeeeeccCCchHHHHHHHHHHHHHhhcCC--
Q 002421 102 LMKEFFQLAVSAFENLSHA--SGRYYMKALSILDTVA---------KVRSCLLMLDLECDKLVVEMFQHFLKVIRSNH-- 168 (925)
Q Consensus 102 qLKDIFqLfV~qf~~LaD~--ssp~F~q~~yLLEsLA---------eVKS~VLMlDLe~ddLI~eLFktFFdiVr~dh-- 168 (925)
-=++||..+.+-|..|.+| .+.+|.-|..|++-+- .++.|++++.=+.-+++..|..-+..++..+.
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 3457888888888888775 5667777777777544 56777777666666777777776766666542
Q ss_pred -ch--hHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCC
Q 002421 169 -PH--FVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQD 208 (925)
Q Consensus 169 -p~--kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks 208 (925)
.. .-+..|..+.+..|--+..++....+.|+..++.+.+.
T Consensus 184 L~~~~~nR~~v~~~Fs~~ii~~~~l~~~~~~~LV~Fmmd~~~~ 226 (235)
T cd04405 184 LHKEIENRMLVKQTFSRAILCSKDLDEGLADLLVLFLMDHHQD 226 (235)
T ss_pred cccccchHHHHHHHhhhHhcCccccCHHHHHHHHHHHHHcchh
Confidence 12 22346777777777777788887788888877776654
No 69
>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=30.50 E-value=4.7e+02 Score=32.09 Aligned_cols=34 Identities=24% Similarity=0.437 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhhcCCchh-HHHHHHHHHHHHhcc
Q 002421 153 VVEMFQHFLKVIRSNHPHF-VFAAMETIMTLVIDE 186 (925)
Q Consensus 153 I~eLFktFFdiVr~dhp~k-V~~~M~dILs~VIeE 186 (925)
+.+|.++.+.-+...+|.. |..++..|+..+=.-
T Consensus 143 Ll~~l~~~l~ri~t~~ps~Fl~~~l~~i~~~~~~~ 177 (633)
T PF08568_consen 143 LLELLQIVLKRIQTKYPSRFLAMALSAILNFLKNN 177 (633)
T ss_pred HHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHhc
Confidence 6777778888777888887 766666666655443
No 70
>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=29.93 E-value=1.1e+02 Score=28.68 Aligned_cols=61 Identities=13% Similarity=0.256 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHHHH
Q 002421 173 FAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKE 234 (925)
Q Consensus 173 ~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I~q 234 (925)
...|..|...+ .+....+.++++.|...+...+....--|-.|.+.++.+|+..+..+|..
T Consensus 18 ~~~i~~i~d~~-~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~f~~~i~~ 78 (115)
T cd00197 18 WPLIMEICDLI-NETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVAS 78 (115)
T ss_pred HHHHHHHHHHH-HCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHHHHHHHHH
Confidence 35555655544 45566788899999999876655555556677788888888887766543
No 71
>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=29.85 E-value=85 Score=27.79 Aligned_cols=64 Identities=17% Similarity=0.124 Sum_probs=40.0
Q ss_pred cccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHH-HHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhh
Q 002421 69 LLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMK-EFFQLAVSAFENLSHASGRYYMKALSILDTVAKV 138 (925)
Q Consensus 69 LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLK-DIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeV 138 (925)
+|.+.+..+|..++.||..|..-. +++....+. +++..++..|. +.+........++|.+|+..
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 667778889999999998887652 222233333 55666666543 34444555567777777654
No 72
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=29.68 E-value=5.1e+02 Score=32.59 Aligned_cols=118 Identities=14% Similarity=0.245 Sum_probs=59.8
Q ss_pred chHHHHHHHHHHHHHhhcC------------------CchhHHHHHHHHHHHHhccc----CCCcHHHHHHHHHHhhccC
Q 002421 149 CDKLVVEMFQHFLKVIRSN------------------HPHFVFAAMETIMTLVIDES----EDVSWDLLRILLASVRKEN 206 (925)
Q Consensus 149 ~ddLI~eLFktFFdiVr~d------------------hp~kV~~~M~dILs~VIeES----E~VP~eVLDvIL~~fl~~~ 206 (925)
|-+-+.+|.-.||+.+... .-+.|.+.+.++|..||--. +.+...++.++|.-+-...
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 4455666666777765531 12344555566666676544 4455556655555444433
Q ss_pred CCCCc-----hHHHHHH---HHHHhhhHhHHHHHHHHHH-------------------hcCCCCcchHHHHH-HHhccCC
Q 002421 207 QDVSP-----TSWKLGE---KVFTKCAAKLKTNLKEAVQ-------------------SRGIALDDYAEIVA-CICGSDD 258 (925)
Q Consensus 207 ks~~P-----aAykLA~---~VI~~CadKLqp~I~q~l~-------------------s~Gi~Ld~Y~eIV~-sIcq~~s 258 (925)
+.+.- +--.|+. +=+..-+.++-||+...|+ ++|..+..|.+++. ++.|+-+
T Consensus 611 ~t~~~~dV~~aIsal~~sl~e~Fe~y~~~fiPyl~~aln~~d~~v~~~avglvgdlantl~~df~~y~d~~ms~LvQ~ls 690 (858)
T COG5215 611 PTTAFGDVYTAISALSTSLEERFEQYASKFIPYLTRALNCTDRFVLNSAVGLVGDLANTLGTDFNIYADVLMSSLVQCLS 690 (858)
T ss_pred CchhhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHhcchhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhc
Confidence 32200 0001111 1234455567777766665 34445678888554 4555444
Q ss_pred CCC-CCCCC
Q 002421 259 ENP-QHGHL 266 (925)
Q Consensus 259 ~~l-~~~~~ 266 (925)
+.. +++..
T Consensus 691 s~~~~R~lK 699 (858)
T COG5215 691 SEATHRDLK 699 (858)
T ss_pred Chhhccccc
Confidence 433 55554
No 73
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=29.32 E-value=1.8e+02 Score=36.99 Aligned_cols=24 Identities=21% Similarity=0.358 Sum_probs=22.5
Q ss_pred hcccCCCcCceeehhhHHhhhhhh
Q 002421 68 DLLRRSDMDVRLSVTSCISEITRI 91 (925)
Q Consensus 68 ~LLkHKDkdVRayVAcCLADILRI 91 (925)
.+|+|.+.-||-.+|.||..|+|+
T Consensus 134 ~~l~d~~ayVRk~Aalav~kly~l 157 (757)
T COG5096 134 KLLTDPHAYVRKTAALAVAKLYRL 157 (757)
T ss_pred HHccCCcHHHHHHHHHHHHHHHhc
Confidence 478999999999999999999998
No 74
>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=29.09 E-value=1.6e+02 Score=35.62 Aligned_cols=21 Identities=33% Similarity=0.708 Sum_probs=8.8
Q ss_pred ceeeeeccCCchHHHHHHHHH
Q 002421 139 RSCLLMLDLECDKLVVEMFQH 159 (925)
Q Consensus 139 KS~VLMlDLe~ddLI~eLFkt 159 (925)
..||-++|=.|..||..+++.
T Consensus 61 ~~~Vs~Ld~~~~~LV~ail~~ 81 (563)
T PF05327_consen 61 SSCVSLLDSSCKQLVEAILSL 81 (563)
T ss_dssp HHGGGGG-SCCHHHHHHHHT-
T ss_pred HHHHHHhhhHHHHHHHHHHcC
Confidence 334444444455555544444
No 75
>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=28.80 E-value=2.3e+02 Score=30.68 Aligned_cols=101 Identities=10% Similarity=0.064 Sum_probs=64.6
Q ss_pred HHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhH-------HHHHHHHHHHHhcccCCCCCcchh
Q 002421 54 RDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL-------MKEFFQLAVSAFENLSHASGRYYM 126 (925)
Q Consensus 54 ~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdq-------LKDIFqLfV~qf~~LaD~ssp~F~ 126 (925)
-.....++.+|+..-+=.+....-.+++++||+=|--==.+|+-|+.+. --.||..|=+-+... .
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 4556778888888777777778888999999987776667888888543 234455444443311 1
Q ss_pred HHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHH
Q 002421 127 KALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLK 162 (925)
Q Consensus 127 q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFd 162 (925)
.-+-.++.|-.+..+++|..-.-.++-.++|+.+|.
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 123444555555656666655555666677777775
No 76
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=27.99 E-value=1.4e+02 Score=29.35 Aligned_cols=69 Identities=16% Similarity=0.251 Sum_probs=47.2
Q ss_pred HhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHH
Q 002421 163 VIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNL 232 (925)
Q Consensus 163 iVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I 232 (925)
++++..+..=...+..| ..+|.....-+.+++..|-..|...+....-.|-.|...++.+|+..|...|
T Consensus 13 ATs~~~~~~Dw~~~l~i-cD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev 81 (140)
T PF00790_consen 13 ATSESLPSPDWSLILEI-CDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREV 81 (140)
T ss_dssp HT-TTSSS--HHHHHHH-HHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHH
T ss_pred HhCcCCCCCCHHHHHHH-HHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 44444444434444443 3466666788899999999999887766667777788888889988876654
No 77
>KOG0212 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.82 E-value=7.1e+02 Score=31.18 Aligned_cols=71 Identities=23% Similarity=0.259 Sum_probs=51.9
Q ss_pred CCCCHHHHHHHHH------------HHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhh
Q 002421 24 PPSPVDEVINLLD------------KVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRI 91 (925)
Q Consensus 24 ~piS~dELLKRLk------------kL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRI 91 (925)
...+.++++.+|. -|-++|.-++--|.-.|.+-|..+..-|.+ +|.-...+||-.+-.||.++|+=
T Consensus 161 ~tFsL~~~ipLL~eriy~~n~~tR~flv~Wl~~Lds~P~~~m~~yl~~~ldGLf~--~LsD~s~eVr~~~~t~l~~fL~e 238 (675)
T KOG0212|consen 161 STFSLPEFIPLLRERIYVINPMTRQFLVSWLYVLDSVPDLEMISYLPSLLDGLFN--MLSDSSDEVRTLTDTLLSEFLAE 238 (675)
T ss_pred cccCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhcCCcHHHHhcchHHHHHHHH--HhcCCcHHHHHHHHHHHHHHHHH
Confidence 3667777777776 367788888877776666555555555543 67778899999999999999987
Q ss_pred cCCCC
Q 002421 92 TAPDS 96 (925)
Q Consensus 92 yAPDA 96 (925)
.+-++
T Consensus 239 I~s~P 243 (675)
T KOG0212|consen 239 IRSSP 243 (675)
T ss_pred HhcCc
Confidence 66443
No 78
>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=27.52 E-value=78 Score=27.04 Aligned_cols=29 Identities=24% Similarity=0.580 Sum_probs=24.6
Q ss_pred cccccCeEEEeeCCCCceEEEEEEEecCCC
Q 002421 710 EQLVGSRIKVWWPMDETFYKGVVDNYDPIK 739 (925)
Q Consensus 710 e~lVG~RVkV~WP~D~~wY~G~V~syd~~t 739 (925)
+.++|++|.|.-- +...|.|++.+||..-
T Consensus 4 ~~~~g~~V~V~l~-~g~~~~G~L~~~D~~~ 32 (67)
T PF01423_consen 4 QKLIGKRVRVELK-NGRTYRGTLVSFDQFM 32 (67)
T ss_dssp HHTTTSEEEEEET-TSEEEEEEEEEEETTE
T ss_pred HHhCCcEEEEEEe-CCEEEEEEEEEeechh
Confidence 4678999999888 4588999999999743
No 79
>PF12460 MMS19_C: RNAPII transcription regulator C-terminal; InterPro: IPR024687 This domain, approximately 60 amino acids in length, is found in the N-terminal region of MMS19 proteins. MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription [].
Probab=27.40 E-value=7.5e+02 Score=28.57 Aligned_cols=201 Identities=14% Similarity=0.134 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhcCCCCCCCh-hHHHH--HHHH
Q 002421 33 NLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDD-ELMKE--FFQL 109 (925)
Q Consensus 33 KRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtD-dqLKD--IFqL 109 (925)
.+.+..-+.|..+--.+.- ...+.+-....+..-+=...+.+.-..+.-||..++.-..-+.++.+ ....+ |...
T Consensus 17 ~~~~~~L~~l~~ls~~~~i--~~~~~~~ll~kl~~~~~~~~~~~~~~~il~tl~~~~~~~~~~~~~~~~~~y~~~~lv~~ 94 (415)
T PF12460_consen 17 SNYERILEALAALSTSPQI--LETLSIRLLNKLSIVCQSESSSDYCHAILSTLQSLLEKKQEDKQFEDNSWYFHRILVPR 94 (415)
T ss_pred hHHHHHHHHHHHHHCChhH--HHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhcccccccchHHHHHHhHHHHH
Q ss_pred HHHHhcccCCCCCcchhHHHHHHHHhhhh-ceeeeeccCC-chHHHHHHHHHHH----------HHhhcC-CchhHHHHH
Q 002421 110 AVSAFENLSHASGRYYMKALSILDTVAKV-RSCLLMLDLE-CDKLVVEMFQHFL----------KVIRSN-HPHFVFAAM 176 (925)
Q Consensus 110 fV~qf~~LaD~ssp~F~q~~yLLEsLAeV-KS~VLMlDLe-~ddLI~eLFktFF----------diVr~d-hp~kV~~~M 176 (925)
|++.+-...+.+.. ....+|+.++.+ +.++..++.+ .+.++.++|..|+ ...... .+......+
T Consensus 95 l~~~~~~~~~~~~~---~~~~~L~~~~~l~~~iv~~l~~~~q~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~l~ 171 (415)
T PF12460_consen 95 LFELALQASDQSSD---LDDRVLELLSRLINLIVRSLSPEKQQEILDELYSLFLSPKSFSPFQPSSSTISEQQSRLVILF 171 (415)
T ss_pred HHHHHHhhcccccc---cchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHccccccCCCCccccccccccccHHHHH
Q ss_pred HHHHHHHhcccC-CCcHHHHHHHHHHhhccC-CCCCchHHHHHHHHHHh--hhHhHHHHHHHHHHh
Q 002421 177 ETIMTLVIDESE-DVSWDLLRILLASVRKEN-QDVSPTSWKLGEKVFTK--CAAKLKTNLKEAVQS 238 (925)
Q Consensus 177 ~dILs~VIeESE-~VP~eVLDvIL~~fl~~~-ks~~PaAykLA~~VI~~--CadKLqp~I~q~l~s 238 (925)
..|+..+=-++. .-..++++-++.-..... ......+.++..-+++. ..+.+..++..+++.
T Consensus 172 ~~il~~l~~~~~~~~~~~ll~~l~~~~~~~~~~~~~~~~~~~la~LvNK~~~~~~l~~~l~~~~~~ 237 (415)
T PF12460_consen 172 SAILCSLRKDVSLPDLEELLQSLLNLALSSEDEFSRLAALQLLASLVNKWPDDDDLDEFLDSLLQS 237 (415)
T ss_pred HHHHHcCCcccCccCHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHcCCCChhhHHHHHHHHHhh
No 80
>KOG0301 consensus Phospholipase A2-activating protein (contains WD40 repeats) [Lipid transport and metabolism]
Probab=27.32 E-value=4.7e+02 Score=33.13 Aligned_cols=90 Identities=21% Similarity=0.182 Sum_probs=43.0
Q ss_pred CHHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhc---c--------------cC--CCcCceeehhhHHhh
Q 002421 27 PVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDL---L--------------RR--SDMDVRLSVTSCISE 87 (925)
Q Consensus 27 S~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~L---L--------------kH--KDkdVRayVAcCLAD 87 (925)
..++.+..| .+|..+.|-|++-|--+|.-++-.+.++.+ + .. .+.--++++.=||+.
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 366677777777555555555443332211 1 11 122334556666666
Q ss_pred hhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcch
Q 002421 88 ITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYY 125 (925)
Q Consensus 88 ILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F 125 (925)
+| ++ |+...-+---+..+++.|....-.++..+
T Consensus 615 ~f----~~-~~g~~~~~s~~~~i~~~~~~~~s~~~knl 647 (745)
T KOG0301|consen 615 LF----SN-PAGRELFMSRLESILDPVIEASSLSNKNL 647 (745)
T ss_pred hc----cC-HHHHHHHHHHHHHHhhhhhhhhcccchhH
Confidence 66 34 55444333334555555544443333333
No 81
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.79 E-value=2.5e+02 Score=35.99 Aligned_cols=126 Identities=16% Similarity=0.263 Sum_probs=81.6
Q ss_pred HhhhhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHh
Q 002421 85 ISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVI 164 (925)
Q Consensus 85 LADILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiV 164 (925)
.|.++-+.||-. |+.-|-+-+|+.|+. +... ++-+|.++|.+-.- -..|+...|+.|| |
T Consensus 307 ~aql~y~lAP~~-----~~~~i~kaLvrLLrs--~~~v-----qyvvL~nIa~~s~~-------~~~lF~P~lKsFf--v 365 (968)
T KOG1060|consen 307 VAQLFYHLAPKN-----QVTKIAKALVRLLRS--NREV-----QYVVLQNIATISIK-------RPTLFEPHLKSFF--V 365 (968)
T ss_pred HHhHHHhhCCHH-----HHHHHHHHHHHHHhc--CCcc-----hhhhHHHHHHHHhc-------chhhhhhhhhceE--e
Confidence 356777777754 788787777776542 2222 23567777665211 2367777777777 6
Q ss_pred hcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHHHHHHH
Q 002421 165 RSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQ 237 (925)
Q Consensus 165 r~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~l~ 237 (925)
+..-|..+-..=..||+.++.|+. -..+|..+..++...+.. .+ ..|.+-|..|+..+-..-...|+
T Consensus 366 ~ssDp~~vk~lKleiLs~La~esn--i~~ILrE~q~YI~s~d~~--fa--a~aV~AiGrCA~~~~sv~~tCL~ 432 (968)
T KOG1060|consen 366 RSSDPTQVKILKLEILSNLANESN--ISEILRELQTYIKSSDRS--FA--AAAVKAIGRCASRIGSVTDTCLN 432 (968)
T ss_pred ecCCHHHHHHHHHHHHHHHhhhcc--HHHHHHHHHHHHhcCchh--HH--HHHHHHHHHHHHhhCchhhHHHH
Confidence 777788888888999999999963 345666666666665552 22 24556688999887554444444
No 82
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=26.78 E-value=1.5e+02 Score=37.64 Aligned_cols=42 Identities=10% Similarity=0.164 Sum_probs=24.7
Q ss_pred CCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHH
Q 002421 189 DVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKT 230 (925)
Q Consensus 189 ~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp 230 (925)
.++..+|+.|+..|..=.+...-.+....+.+|..+...+.+
T Consensus 486 ~~~~~~ld~L~~~L~~Laq~~p~~~a~~~r~~L~~~~~~~~~ 527 (840)
T PF04147_consen 486 PPPFEVLDSLIPHLYDLAQKYPEEAAECFREVLKEMQKRFRK 527 (840)
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 567777777777765444444444445555556665555544
No 83
>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=26.32 E-value=1.4e+02 Score=30.01 Aligned_cols=68 Identities=10% Similarity=0.213 Sum_probs=47.9
Q ss_pred hhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHH
Q 002421 164 IRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNL 232 (925)
Q Consensus 164 Vr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I 232 (925)
.++..+..=...+.+|.-.| ...+.-|.+.+..|...|...+....--|..|.+.++.+|+..+...|
T Consensus 9 Tse~l~~~dw~~il~icD~I-~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~ev 76 (144)
T cd03568 9 TDEKLTSENWGLILDVCDKV-KSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEV 76 (144)
T ss_pred cCccCCCcCHHHHHHHHHHH-hcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHH
Confidence 44444444445555555444 444788999999999999877766666778888888999998876555
No 84
>KOG2759 consensus Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]
Probab=26.11 E-value=3.5e+02 Score=32.39 Aligned_cols=102 Identities=13% Similarity=0.290 Sum_probs=67.3
Q ss_pred CCCcCceeehhhHHhhhhhhcCCCCCCChh-HHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCC--
Q 002421 72 RSDMDVRLSVTSCISEITRITAPDSPYDDE-LMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE-- 148 (925)
Q Consensus 72 HKDkdVRayVAcCLADILRIyAPDAPYtDd-qLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe-- 148 (925)
.-+.+....++-||-.+||+ | +|... ..-+=.++++..+. .....|+-+++++. |+.++.+.
T Consensus 168 ~~~~~~~~~~~rcLQ~ll~~--~--eyR~~~v~adg~~~l~~~l~----s~~~~~QlQYqsif-------ciWlLtFn~~ 232 (442)
T KOG2759|consen 168 STNNDYIQFAARCLQTLLRV--D--EYRYAFVIADGVSLLIRILA----STKCGFQLQYQSIF-------CIWLLTFNPH 232 (442)
T ss_pred cCCCchHHHHHHHHHHHhcC--c--chhheeeecCcchhhHHHHh----ccCcchhHHHHHHH-------HHHHhhcCHH
Confidence 35666777888899999998 3 33321 11111233344332 33345665555553 77888886
Q ss_pred -chHH-HHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccC
Q 002421 149 -CDKL-VVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESE 188 (925)
Q Consensus 149 -~ddL-I~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE 188 (925)
|+.+ -..+|+.+.++++...-++|...+..|+.-+|+-.+
T Consensus 233 ~ae~~~~~~li~~L~~Ivk~~~KEKV~Rivlai~~Nll~k~~ 274 (442)
T KOG2759|consen 233 AAEKLKRFDLIQDLSDIVKESTKEKVTRIVLAIFRNLLDKGP 274 (442)
T ss_pred HHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCc
Confidence 4332 125788888899998999999999999999998874
No 85
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=26.11 E-value=1.4e+03 Score=30.35 Aligned_cols=196 Identities=12% Similarity=0.149 Sum_probs=105.3
Q ss_pred HHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhH-HhhhhhhcCCCCCCChhHHHHHHHHH
Q 002421 32 INLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSC-ISEITRITAPDSPYDDELMKEFFQLA 110 (925)
Q Consensus 32 LKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcC-LADILRIyAPDAPYtDdqLKDIFqLf 110 (925)
+-.|..++.-|..+++-+. ....|.++....+..-|-+|.-. .|-=|| |++=+=.+.|+. .-+|-.+|.++
T Consensus 616 ~GiL~Ti~Til~s~e~~p~--vl~~le~~~l~vi~~iL~~~i~d---fyeE~~ei~~~~t~~~~~I---sp~mW~ll~li 687 (1010)
T KOG1991|consen 616 SGILRTISTILLSLENHPE--VLKQLEPIVLPVIGFILKNDITD---FYEELLEIVSSLTFLSKEI---SPIMWGLLELI 687 (1010)
T ss_pred HHHHHHHHHHHHHHhccHH--HHHHHHHHHHHHHHHHHHHhhHH---HHHHHHHHHhhhhhhhccc---CHHHHHHHHHH
Confidence 4567888888888888763 25566666666666555444321 233333 555444445542 24788888888
Q ss_pred HHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCC
Q 002421 111 VSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDV 190 (925)
Q Consensus 111 V~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~V 190 (925)
...|. +...-||..+.-+|.++-.+-.--++..-.--.++.+|.+..+.. .+....=......||..+|-.+...
T Consensus 688 ~e~~~---~~~~dyf~d~~~~l~N~vt~g~~~~~s~~~y~~il~~i~~~~l~~--e~~~D~d~~~a~kLle~iiL~~kg~ 762 (1010)
T KOG1991|consen 688 LEVFQ---DDGIDYFTDMMPALHNYVTYGTPSLLSNPDYLQILLEIIKKVLTS--ENGEDSDCESACKLLEVIILNCKGL 762 (1010)
T ss_pred HHHHh---hhhHHHHHHHHHHHhhheeeCchhhhccchHHHHHHHHHHHHHcC--CCCchHHHHHHHHHHHHHHHHhcCc
Confidence 88876 344668888888888876664333322222234555555555432 1222222223445555555555554
Q ss_pred cHHH----HHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHHHHHHHhcCCC
Q 002421 191 SWDL----LRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIA 242 (925)
Q Consensus 191 P~eV----LDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~l~s~Gi~ 242 (925)
..+. +.+.+..+... ......+.++-+|+-+|-.-=-.-..++|...|..
T Consensus 763 ~dq~iplf~~~a~~~l~~~--~e~s~~~~~~leVvinalyynP~ltL~iLe~~~~~ 816 (1010)
T KOG1991|consen 763 LDQYIPLFLELALSRLTRE--VETSELRVMLLEVVINALYYNPKLTLGILENQGFL 816 (1010)
T ss_pred HhhHhHHHHHHHHHHHhcc--ccchHHHHHHHHHHHHHHHcCcHHHHHHHHHcCCc
Confidence 3333 34444444432 23445666777776666543222234445544443
No 86
>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=25.57 E-value=98 Score=25.92 Aligned_cols=29 Identities=28% Similarity=0.464 Sum_probs=24.2
Q ss_pred cccccCeEEEeeCCCCceEEEEEEEecCCC
Q 002421 710 EQLVGSRIKVWWPMDETFYKGVVDNYDPIK 739 (925)
Q Consensus 710 e~lVG~RVkV~WP~D~~wY~G~V~syd~~t 739 (925)
+.++|++|.|--- |..-|.|++.+||.--
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 6699999999999754
No 87
>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=25.33 E-value=3.7e+02 Score=29.08 Aligned_cols=19 Identities=16% Similarity=0.204 Sum_probs=9.2
Q ss_pred hhHHHHHHHHHHHHhcccC
Q 002421 100 DELMKEFFQLAVSAFENLS 118 (925)
Q Consensus 100 DdqLKDIFqLfV~qf~~La 118 (925)
+++...||..|...+..|.
T Consensus 70 ~~~~~~i~~~~~~~~~~l~ 88 (322)
T cd07920 70 EEQRLQLLEKILGHVVRLS 88 (322)
T ss_pred HHHHHHHHHHHHHHHHHHc
Confidence 4455555555554444443
No 88
>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=25.13 E-value=1.5e+02 Score=25.91 Aligned_cols=59 Identities=12% Similarity=0.104 Sum_probs=41.2
Q ss_pred HHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccC
Q 002421 10 LEEQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRR 72 (925)
Q Consensus 10 le~~L~~~G~KLis~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkH 72 (925)
..+.|..+|.+.--.|++.+| +.+|-.+-.....-..+..+++.. .+.--|.++.||-.
T Consensus 3 a~~~l~~Fa~rAfRRp~~~~e-~~~~~~~~~~~~~~g~~~~~a~~~---~l~aiL~SP~FLY~ 61 (64)
T PF07637_consen 3 AREILRRFARRAFRRPLTDEE-VDRYLALYDSARAQGEDFEEALKE---ALQAILCSPSFLYR 61 (64)
T ss_pred HHHHHHHHHHHHhCCCCCHHH-HHHHHHHHHHHHHcCCCHHHHHHH---HHHHHHcCcchhcc
Confidence 456788999999999999999 777777766665545544444443 44556888888743
No 89
>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=25.09 E-value=2.3e+02 Score=30.90 Aligned_cols=113 Identities=15% Similarity=0.192 Sum_probs=56.0
Q ss_pred cCCCCCCCh--hHHHHHHHHHHHHhcccCCCCCc--------chhHHHHHHHHhhhhceeee-eccCCchH-HHHHHHHH
Q 002421 92 TAPDSPYDD--ELMKEFFQLAVSAFENLSHASGR--------YYMKALSILDTVAKVRSCLL-MLDLECDK-LVVEMFQH 159 (925)
Q Consensus 92 yAPDAPYtD--dqLKDIFqLfV~qf~~LaD~ssp--------~F~q~~yLLEsLAeVKS~VL-MlDLe~dd-LI~eLFkt 159 (925)
.-||.+... ..|+++|+.+...+. ..+| .-....||.++|..+.-.-. .+=+++++ =..++=..
T Consensus 30 ~~~~s~~~~~F~~l~~lFe~~~~~y~----~~~~~L~~~~l~~~~~e~~I~~~lrk~Nla~~l~~~f~~~~i~~~el~~~ 105 (238)
T PF08558_consen 30 SDPDSERGESFRRLRDLFEATKRIYS----SDSPFLSVDELALQDKEQRICQTLRKANLATFLDSLFGTDEIGFLELAES 105 (238)
T ss_dssp -----T-HHHHHHHHHHHHHHCCT-S----CCTH--------HHHHHHHHHHHHHHHCTTT-TTEE-SSSTS-HHHHHHH
T ss_pred hccchHHHHHHHHHHHHHHHHHHHcC----CCCccchhhhhhhcchHHHHHHHHHHHHhhchHHHhcCCCCCCHHHHHHH
Confidence 345555554 467777766665552 3344 44556777777766532211 12224444 34566688
Q ss_pred HHHHhhcCCc---hhHHHHHHHHHHH-HhcccCCCcHHHHHHHHHHhhccCCC
Q 002421 160 FLKVIRSNHP---HFVFAAMETIMTL-VIDESEDVSWDLLRILLASVRKENQD 208 (925)
Q Consensus 160 FFdiVr~dhp---~kV~~~M~dILs~-VIeESE~VP~eVLDvIL~~fl~~~ks 208 (925)
||++..+++. +.....-..|-++ +|.-.+..+..-...||..+.+.+-.
T Consensus 106 Fl~if~pe~~~l~k~~~~L~l~LKtQa~i~~l~~~~~~~~~eiL~~lFp~~~~ 158 (238)
T PF08558_consen 106 FLDIFCPEDSKLLKSQEELYLDLKTQAVISALEKGPFRSAEEILDRLFPDDLE 158 (238)
T ss_dssp HHCCCCCCTC--HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHTSSSST
T ss_pred HHHHHcccccchhhhHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHcCCChh
Confidence 9998888776 3333333333333 22222356666667777776665543
No 90
>KOG2062 consensus 26S proteasome regulatory complex, subunit RPN2/PSMD1 [Posttranslational modification, protein turnover, chaperones]
Probab=24.49 E-value=3.7e+02 Score=34.47 Aligned_cols=51 Identities=16% Similarity=0.199 Sum_probs=25.5
Q ss_pred HHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHHHHHHHhcCCCCcch
Q 002421 195 LRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIALDDY 246 (925)
Q Consensus 195 LDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~l~s~Gi~Ld~Y 246 (925)
++..++.|+.+|....-.=....+.| ++....-...|...|-..|+..|.|
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 45666777777765443222222222 3333333334455555567776654
No 91
>PF10350 DUF2428: Putative death-receptor fusion protein (DUF2428); InterPro: IPR019442 This domain is found in a family of proteins of unknown function that are conserved from plants to humans. Several of these proteins have been annotated as being HEAT repeat-containing proteins while others are designated as death-receptor interacting proteins, but neither of these has yet been confirmed. Aberrations in the genes encoding these proteins have been observed in benign thyroid adenomas [].
Probab=24.01 E-value=9.6e+02 Score=26.12 Aligned_cols=103 Identities=15% Similarity=0.167 Sum_probs=56.9
Q ss_pred CCCCChhHHHHHHHHHHHHhcccCCCC--CcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHhhcCCchh-
Q 002421 95 DSPYDDELMKEFFQLAVSAFENLSHAS--GRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHF- 171 (925)
Q Consensus 95 DAPYtDdqLKDIFqLfV~qf~~LaD~s--sp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~dhp~k- 171 (925)
....+.++++.|..+|+.+|-.+.+.. ...|.-...+-+.|-..+ +-+-.+|..+..+.+++.+.......
T Consensus 86 ~~~ls~~~i~~ig~~l~~~L~~~rHrGAfe~~~~~f~~lc~~l~~~~------~~~l~~LP~~WL~~~l~~i~~~~~~~~ 159 (255)
T PF10350_consen 86 NSLLSPDQIEKIGELLIEQLLEIRHRGAFESVYPGFTALCRRLWSSN------NPELSELPEEWLDELLEAIESKGQQKL 159 (255)
T ss_pred ccCCCHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHhcCC------CchHHHhHHHHHHHHHHHHhccccccc
Confidence 455667999999999999999887743 112222223333332211 11123567777777777666552221
Q ss_pred --HHH---HHHHHHHHHhcccCCCcHHHHHHHHHHhhc
Q 002421 172 --VFA---AMETIMTLVIDESEDVSWDLLRILLASVRK 204 (925)
Q Consensus 172 --V~~---~M~dILs~VIeESE~VP~eVLDvIL~~fl~ 204 (925)
.+. +=--|+..+..|...-+ .++...+..|+.
T Consensus 160 ~iTRRSAGLP~~i~aiL~ae~~~~~-~ll~~~~~~Ll~ 196 (255)
T PF10350_consen 160 SITRRSAGLPFLILAILSAEPSNSR-PLLHRTMKSLLE 196 (255)
T ss_pred ccccccCcHHHHHHHHHhcCCCcch-hHHHHHHHHHHH
Confidence 111 11234444445555444 777777777664
No 92
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=23.98 E-value=6.9e+02 Score=24.46 Aligned_cols=50 Identities=16% Similarity=0.193 Sum_probs=32.3
Q ss_pred CCCcHHHHHHHHHHhhccCCC-----CCchHHHHHHHHHHhhhHhHH--HHHHHHHH
Q 002421 188 EDVSWDLLRILLASVRKENQD-----VSPTSWKLGEKVFTKCAAKLK--TNLKEAVQ 237 (925)
Q Consensus 188 E~VP~eVLDvIL~~fl~~~ks-----~~PaAykLA~~VI~~CadKLq--p~I~q~l~ 237 (925)
..|+..++-.+|..|+..... .......++..++..|+..|. ....+.+.
T Consensus 117 ~vv~~~~i~~~l~~ll~~~~~~~~~~~~~~~ie~~~~lL~~~G~~l~~~~~~~~~l~ 173 (209)
T PF02854_consen 117 GVVSEKIIFDILRELLSDGTDECQPPPDEENIECLCTLLKTCGKKLENSEESPKALD 173 (209)
T ss_dssp TSSCHHHHHHHHHHHHHHTSHHCCHHTCHHHHHHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred ccccchhHHHHHHHHHhcccccccCCCcHhHHHHHHHHHHHHHHHHhcCCCchhHHH
Confidence 346666666666666544322 345677788899999999998 55444443
No 93
>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=23.76 E-value=1.2e+02 Score=29.92 Aligned_cols=40 Identities=15% Similarity=0.218 Sum_probs=28.4
Q ss_pred ccccccCeEEEeeC---CCCceEEEEEEEecCCCCeEEEEccCCc
Q 002421 709 NEQLVGSRIKVWWP---MDETFYKGVVDNYDPIKKKHRILYADGD 750 (925)
Q Consensus 709 ge~lVG~RVkV~WP---~D~~wY~G~V~syd~~tkkH~V~YDDGD 750 (925)
=...+|+.|+|++- ....+|.|.+..++. ...++.+.++.
T Consensus 82 ~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~--~~i~l~~~~~~ 124 (141)
T PF02576_consen 82 FERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE--DEITLEVEGKG 124 (141)
T ss_dssp HHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET--TEEEEEEE-SS
T ss_pred HHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC--CEEEEEECCcc
Confidence 35679999999983 345899999999997 56677777663
No 94
>KOG1058 consensus Vesicle coat complex COPI, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.72 E-value=1.6e+02 Score=37.40 Aligned_cols=29 Identities=28% Similarity=0.306 Sum_probs=25.5
Q ss_pred cccCCCcCceeehhhHHhhhhhh---cCCCCC
Q 002421 69 LLRRSDMDVRLSVTSCISEITRI---TAPDSP 97 (925)
Q Consensus 69 LLkHKDkdVRayVAcCLADILRI---yAPDAP 97 (925)
=|+|...=||-.+-|||..|++. .-||||
T Consensus 142 cleHrhsYVRrNAilaifsIyk~~~~L~pDap 173 (948)
T KOG1058|consen 142 CLEHRHSYVRRNAILAIFSIYKNFEHLIPDAP 173 (948)
T ss_pred HHhCcchhhhhhhheeehhHHhhhhhhcCChH
Confidence 47999999999999999999998 457776
No 95
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=23.71 E-value=42 Score=39.62 Aligned_cols=116 Identities=22% Similarity=0.291 Sum_probs=66.3
Q ss_pred cCceeehhhHHhhhhhhcCCCCCCChhHHH------HHHHHHHHHhcccCCCCCcch-hHHHHHHHHhhhhceeeeeccC
Q 002421 75 MDVRLSVTSCISEITRITAPDSPYDDELMK------EFFQLAVSAFENLSHASGRYY-MKALSILDTVAKVRSCLLMLDL 147 (925)
Q Consensus 75 kdVRayVAcCLADILRIyAPDAPYtDdqLK------DIFqLfV~qf~~LaD~ssp~F-~q~~yLLEsLAeVKS~VLMlDL 147 (925)
.||-+|...|-. |+|+-.+|+ .-|++|+..-+.|.+.=..|| .+|-..|+.|.+++.=++ +|+
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 456666666632 788877776 568888887776666444444 456778899999986443 444
Q ss_pred CchHHHHHHHHHHHHHhhcC-----CchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhc
Q 002421 148 ECDKLVVEMFQHFLKVIRSN-----HPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRK 204 (925)
Q Consensus 148 e~ddLI~eLFktFFdiVr~d-----hp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~ 204 (925)
=--+=+ .++|+.||.. +.+-+-.-|..|-..+=.....+-.+|+.+|+..-+.
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 211112 4555555542 1222222333333333333334667788888876553
No 96
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=23.59 E-value=5.6e+02 Score=24.16 Aligned_cols=82 Identities=16% Similarity=0.134 Sum_probs=51.2
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccC-C--CcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHH
Q 002421 155 EMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESE-D--VSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTN 231 (925)
Q Consensus 155 eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE-~--VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~ 231 (925)
+.|+..+.-+.+..++ |+..=...|..+|.... . --+.++++++.++..++.=..-.|.+.-..++......+=+.
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 5677777766666555 77777778888888877 2 223566777776665554445555555555666666555445
Q ss_pred HHHHHH
Q 002421 232 LKEAVQ 237 (925)
Q Consensus 232 I~q~l~ 237 (925)
+++.+.
T Consensus 82 L~~~y~ 87 (92)
T PF10363_consen 82 LLDEYA 87 (92)
T ss_pred HHHHHh
Confidence 444443
No 97
>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=23.48 E-value=1.6e+02 Score=29.40 Aligned_cols=39 Identities=15% Similarity=0.376 Sum_probs=29.0
Q ss_pred ccCeEEEeeCCCCceEEEEEEEecC-CCCeEEEEccCCcc
Q 002421 713 VGSRIKVWWPMDETFYKGVVDNYDP-IKKKHRILYADGDE 751 (925)
Q Consensus 713 VG~RVkV~WP~D~~wY~G~V~syd~-~tkkH~V~YDDGD~ 751 (925)
.|.+|-=.||.=-+||.|+|.+--. ..+...+.++|.+.
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 34668888875544
No 98
>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=23.15 E-value=9.2e+02 Score=28.55 Aligned_cols=43 Identities=23% Similarity=0.274 Sum_probs=26.3
Q ss_pred HhHHHHHHHHHHhcCCCCcc-hHHHHHHHhccCCCCCCCCCCCC
Q 002421 226 AKLKTNLKEAVQSRGIALDD-YAEIVACICGSDDENPQHGHLIG 268 (925)
Q Consensus 226 dKLqp~I~q~l~s~Gi~Ld~-Y~eIV~sIcq~~s~~l~~~~~~~ 268 (925)
+-|.-.+..++.+....+.+ .++.++.||..+.+.+-+.+.-|
T Consensus 307 ~tL~~rLlrLmt~~~~~~k~~vaellf~Lc~~d~~~~v~~~GyG 350 (446)
T PF10165_consen 307 DTLRSRLLRLMTSPDPQLKDAVAELLFVLCKEDASRFVKYVGYG 350 (446)
T ss_pred cchHHHHHHHhCCCCchHHHHHHHHHHHHHhhhHHHHHHHcCch
Confidence 34555556666554434444 57888999988877765444433
No 99
>KOG4327 consensus mRNA splicing protein SMN (survival motor neuron) [RNA processing and modification]
Probab=23.09 E-value=75 Score=34.36 Aligned_cols=35 Identities=20% Similarity=0.421 Sum_probs=30.7
Q ss_pred ccCeEEEeeCCCCceEEEEEEEecCCCCeEEEEcc
Q 002421 713 VGSRIKVWWPMDETFYKGVVDNYDPIKKKHRILYA 747 (925)
Q Consensus 713 VG~RVkV~WP~D~~wY~G~V~syd~~tkkH~V~YD 747 (925)
||-.+.--|-.+.++|.|+|++.+-......|+|=
T Consensus 70 Vgdkc~A~Y~e~g~~ypatidsi~~~~~tcvv~yl 104 (218)
T KOG4327|consen 70 VGDKCSAIYSEDGCIYPATIDSIDFKRETCVVVYL 104 (218)
T ss_pred ecceeeeeeecCcccccceecccccccCceEEEEE
Confidence 89999999999999999999999977776666664
No 100
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=23.00 E-value=5.6e+02 Score=25.10 Aligned_cols=166 Identities=14% Similarity=0.155 Sum_probs=80.9
Q ss_pred HHHHhccccCCCCCCHHHHHHHHHHHHHHHHhccCCCchhhHHhhHHHHHhhhhhhcccCCCcCceeehhhHHhhhhhhc
Q 002421 13 QLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRIT 92 (925)
Q Consensus 13 ~L~~~G~KLis~piS~dELLKRLkkL~~eLs~lDQ~~vdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLADILRIy 92 (925)
.+..+-++|- +...+.++.-|..+.... + ...+..++..++......+ .-+.+|+.+|-.=..++
T Consensus 3 ~v~~~lnklt--~~n~~~~~~~l~~~~~~~--------~--~~~~~~i~~~i~~~a~~~~--~~~~~~a~l~~~l~~~~- 67 (209)
T PF02854_consen 3 KVRGILNKLT--PSNFESIIDELIKLNWSD--------D--PETLKEIVKLIFEKAVEEP--NFSPLYARLCAALNSRF- 67 (209)
T ss_dssp HHHHHHHHCS--STTHHHHHHHHHHHHHHS--------C--HHHHHHHHHHHHHHHHHSG--GGHHHHHHHHHHHHHHC-
T ss_pred hHHHHHHHCC--HHHHHHHHHHHHHHHhhc--------c--HHHHHHHHHHHhhhhhcCc--hHHHHHHHHHHHHhccc-
Confidence 4455555654 555666666555443322 1 3455667777777777666 55667777774422222
Q ss_pred CCCCCCChhHHHHHHHHHHHHhcc------cCCCCCcchhHHHHHHHHhhhhceeeeeccCCchHHHHHHHHHHHHHhhc
Q 002421 93 APDSPYDDELMKEFFQLAVSAFEN------LSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRS 166 (925)
Q Consensus 93 APDAPYtDdqLKDIFqLfV~qf~~------LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~ 166 (925)
| .+-...+...+...|.. +.........+...++.=|++.=.+- +=...+|.+++..++.....
T Consensus 68 -~-----~~f~~~ll~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~----vv~~~~i~~~l~~ll~~~~~ 137 (209)
T PF02854_consen 68 -P-----SEFRSLLLNRCQEEFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFG----VVSEKIIFDILRELLSDGTD 137 (209)
T ss_dssp -H-----HHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHHHHHHHHTSH
T ss_pred -h-----hhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhc----cccchhHHHHHHHHHhcccc
Confidence 1 12222233333333443 22233334444555555555441111 11345666666666664332
Q ss_pred ----CCchhHHHHHHHHHHHHhcccC--CCcHHHHHHHHHHhh
Q 002421 167 ----NHPHFVFAAMETIMTLVIDESE--DVSWDLLRILLASVR 203 (925)
Q Consensus 167 ----dhp~kV~~~M~dILs~VIeESE--~VP~eVLDvIL~~fl 203 (925)
.-...-..++..+|..+=...+ ......++.||..+.
T Consensus 138 ~~~~~~~~~~ie~~~~lL~~~G~~l~~~~~~~~~l~~~~~~~~ 180 (209)
T PF02854_consen 138 ECQPPPDEENIECLCTLLKTCGKKLENSEESPKALDEIFERLQ 180 (209)
T ss_dssp HCCHHTCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred cccCCCcHhHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHH
Confidence 1112334455555555544444 455556666666554
No 101
>PRK14718 ribonuclease III; Provisional
Probab=23.00 E-value=3.3e+02 Score=32.86 Aligned_cols=32 Identities=6% Similarity=0.009 Sum_probs=22.1
Q ss_pred ehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHH
Q 002421 80 SVTSCISEITRITAPDSPYDDELMKEFFQLAVSA 113 (925)
Q Consensus 80 yVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~q 113 (925)
++-+||++.|.-.-|+ ++..+|..+...+|+.
T Consensus 44 VL~liVse~Lf~~fPd--l~EGeLT~LRS~LVSn 75 (467)
T PRK14718 44 VLNCAVAALLFQRFGK--LDEGDLSRVRANLVKQ 75 (467)
T ss_pred HHHHHHHHHHHHHCCC--CCHHHHHHHHHHHhhh
Confidence 4566777777766666 3467888887777765
No 102
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=22.76 E-value=4.3e+02 Score=32.97 Aligned_cols=75 Identities=12% Similarity=0.118 Sum_probs=36.7
Q ss_pred HHHHHHHhhhh-ceeeeeccCCchH---HHHHHHHHHHHHhhcC-CchhHHHHHHHHHHHHhc-ccCCCcHHHHHHHHHH
Q 002421 128 ALSILDTVAKV-RSCLLMLDLECDK---LVVEMFQHFLKVIRSN-HPHFVFAAMETIMTLVID-ESEDVSWDLLRILLAS 201 (925)
Q Consensus 128 ~~yLLEsLAeV-KS~VLMlDLe~dd---LI~eLFktFFdiVr~d-hp~kV~~~M~dILs~VIe-ESE~VP~eVLDvIL~~ 201 (925)
.|+|+..+.+- +.+|+..|....+ |...|..-|-..+.-. .+...+. +..||..... ..=.|+.+|++.|+.+
T Consensus 399 LF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~Et-R~aIL~kka~~r~l~l~~eVi~yLa~r 477 (617)
T PRK14086 399 FFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELET-RIAILRKKAVQEQLNAPPEVLEFIASR 477 (617)
T ss_pred HHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHH-HHHHHHHHHHhcCCCCCHHHHHHHHHh
Confidence 45666666553 6677777775322 2233444443322211 2333333 3333333333 3334777777777766
Q ss_pred hh
Q 002421 202 VR 203 (925)
Q Consensus 202 fl 203 (925)
+-
T Consensus 478 ~~ 479 (617)
T PRK14086 478 IS 479 (617)
T ss_pred cc
Confidence 43
No 103
>PF14868 DUF4487: Domain of unknown function (DUF4487)
Probab=22.62 E-value=7.5e+02 Score=30.61 Aligned_cols=123 Identities=15% Similarity=0.174 Sum_probs=70.9
Q ss_pred HHHHHHHHHHHHhc---ccCCCCCcchhHHHHHH-HHhhhhceeeeeccCCchHHHHHHHHHHHHHhhc-----C-Cchh
Q 002421 102 LMKEFFQLAVSAFE---NLSHASGRYYMKALSIL-DTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRS-----N-HPHF 171 (925)
Q Consensus 102 qLKDIFqLfV~qf~---~LaD~ssp~F~q~~yLL-EsLAeVKS~VLMlDLe~ddLI~eLFktFFdiVr~-----d-hp~k 171 (925)
-..+|+..++.+.. ++.--+..-+.+-...| -.|+.+.+..-++|.....-|.+++..|...++. + .-..
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 34556666555544 43333444555555555 5556667766666665666677777666665532 2 2245
Q ss_pred HHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHHhhhHhHHHHHHHHHHhcCC
Q 002421 172 VFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGI 241 (925)
Q Consensus 172 V~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~l~s~Gi 241 (925)
+...+..|+..+|... .++.+.-++.. +..-+...+.+.+++++.+|+.++|-
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 6677777777776553 23333333221 22223356667799999999998774
No 104
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=22.42 E-value=1.2e+03 Score=31.17 Aligned_cols=125 Identities=9% Similarity=0.090 Sum_probs=66.0
Q ss_pred hhcccCCCcCceeehhhHHhhhhhhcCCCCCCChhHHHHHHHHHHHH-hcccCCCCCcchhHHHHHHHHhhhhceeeeec
Q 002421 67 NDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSA-FENLSHASGRYYMKALSILDTVAKVRSCLLML 145 (925)
Q Consensus 67 ~~LLkHKDkdVRayVAcCLADILRIyAPDAPYtDdqLKDIFqLfV~q-f~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMl 145 (925)
+.|+.-.|..|-.++.|||+=+++++ ..-|-.|-+.|+++ +..|..|-=+- .-|-.+-...-+++..
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 35777788889899999999999883 22334555666665 44444221111 1111222222333445
Q ss_pred cCCchHHHHHHHHHH----HHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhc
Q 002421 146 DLECDKLVVEMFQHF----LKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRK 204 (925)
Q Consensus 146 DLe~ddLI~eLFktF----FdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~ 204 (925)
+.++-+ +..+|... |+-+.+..++.....+..+...++.-+......+..-++..|..
T Consensus 767 ~~~~l~-y~~l~s~lt~PV~~~~~~~l~kqa~~siA~cvA~Lt~~~~~~s~s~a~kl~~~~~s 828 (1233)
T KOG1824|consen 767 KEPDLD-YISLLSLLTAPVYEQVTDGLHKQAYYSIAKCVAALTCACPQKSKSLATKLIQDLQS 828 (1233)
T ss_pred CCCCcc-HHHHHHHHcCCcccccccchhHHHHHHHHHHHHHHHHhccccchhHHHHHHHHHhC
Confidence 555433 44444333 22233345566666666666666666655555555555554443
No 105
>PRK14637 hypothetical protein; Provisional
Probab=22.36 E-value=1.3e+02 Score=30.76 Aligned_cols=30 Identities=23% Similarity=0.494 Sum_probs=25.6
Q ss_pred ccccccCeEEEeeCCCCceEEEEEEEecCC
Q 002421 709 NEQLVGSRIKVWWPMDETFYKGVVDNYDPI 738 (925)
Q Consensus 709 ge~lVG~RVkV~WP~D~~wY~G~V~syd~~ 738 (925)
=...+|+.|+|.+...+.|+.|++..++..
T Consensus 93 f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~ 122 (151)
T PRK14637 93 FSIFVGETVKVWFECTGQWQVGTIAEADET 122 (151)
T ss_pred HHHhCCCEEEEEECCCCcEEEEEEEEEeCC
Confidence 367799999999866778889999999874
No 106
>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=21.23 E-value=50 Score=33.26 Aligned_cols=27 Identities=19% Similarity=0.384 Sum_probs=23.2
Q ss_pred eehhhHHhhhhhhcCCCCCCChhHHHH
Q 002421 79 LSVTSCISEITRITAPDSPYDDELMKE 105 (925)
Q Consensus 79 ayVAcCLADILRIyAPDAPYtDdqLKD 105 (925)
..+..||..++++.||=+||..++|-.
T Consensus 112 ~~l~~~l~~ll~ll~P~~P~~aEElw~ 138 (183)
T cd07961 112 ATLYEVLLTLSRLMAPFTPFITEEIYQ 138 (183)
T ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 366789999999999999999987654
No 107
>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=21.16 E-value=2.7e+02 Score=33.18 Aligned_cols=100 Identities=16% Similarity=0.234 Sum_probs=0.0
Q ss_pred eeccCCchHHHHHHHHHHH------HHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhcc--CCCCCchHH
Q 002421 143 LMLDLECDKLVVEMFQHFL------KVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKE--NQDVSPTSW 214 (925)
Q Consensus 143 LMlDLe~ddLI~eLFktFF------diVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~--~ks~~PaAy 214 (925)
+..+++..++|..||..|+ +.-+.-.+..+..-+..+|.. =..+-...+.++.+++..|-.. +..-...+-
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---HHHHHhhhHhHHHHHHHHHHhcCCCC
Q 002421 215 KLG---EKVFTKCAAKLKTNLKEAVQSRGIAL 243 (925)
Q Consensus 215 kLA---~~VI~~CadKLqp~I~q~l~s~Gi~L 243 (925)
+.. ..++..|...+-..+..++.+.|.++
T Consensus 343 ~F~~~~~~~~~~~~~~~l~~l~~~i~~~g~p~ 374 (501)
T PF13001_consen 343 QFIRGSSWIFKHISPQILKLLRPVILSQGWPL 374 (501)
T ss_pred hhhhcchHHhhhcCHHHHHHHHHHHHhcCccc
No 108
>COG5218 YCG1 Chromosome condensation complex Condensin, subunit G [Chromatin structure and dynamics / Cell division and chromosome partitioning]
Probab=20.88 E-value=1.8e+03 Score=28.21 Aligned_cols=86 Identities=21% Similarity=0.180 Sum_probs=58.9
Q ss_pred HHHHHHHHhhhhceeeeeccCC-chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCcHHHHHHHHHHhhcc
Q 002421 127 KALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKE 205 (925)
Q Consensus 127 q~~yLLEsLAeVKS~VLMlDLe-~ddLI~eLFktFFdiVr~dhp~kV~~~M~dILs~VIeESE~VP~eVLDvIL~~fl~~ 205 (925)
+.+.+|.++-+ -.|.|.| ..+|+..+|.+++..+- .--++|+.-...||..|.+-...|...|...|+..+...
T Consensus 66 Ril~fl~~f~~----Y~~~~dpeg~~~V~~~~~h~lRg~e-skdk~VR~r~lqila~~~d~v~eIDe~l~N~L~ekl~~R 140 (885)
T COG5218 66 RILSFLKRFFE----YDMPDDPEGEELVAGTFYHLLRGTE-SKDKKVRKRSLQILALLSDVVREIDEVLANGLLEKLSER 140 (885)
T ss_pred HHHHHHHHHHH----hcCCCChhhhHHHHHHHHHHHhccc-CcchhHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHH
Confidence 34555555544 2466776 68999999998887644 234779988899999888888888888888887777654
Q ss_pred CCCCCchHHHHH
Q 002421 206 NQDVSPTSWKLG 217 (925)
Q Consensus 206 ~ks~~PaAykLA 217 (925)
--...|+-+.-|
T Consensus 141 ~~DRE~~VR~eA 152 (885)
T COG5218 141 LFDREKAVRREA 152 (885)
T ss_pred HhcchHHHHHHH
Confidence 444445444333
No 109
>COG5231 VMA13 Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]
Probab=20.64 E-value=2.4e+02 Score=32.99 Aligned_cols=55 Identities=18% Similarity=0.274 Sum_probs=38.2
Q ss_pred eeeeccCC--chHHHHHHHHH---HHHHhhcCCchhHHHHHHHHHHHHhccc--CCCcHHHH
Q 002421 141 CLLMLDLE--CDKLVVEMFQH---FLKVIRSNHPHFVFAAMETIMTLVIDES--EDVSWDLL 195 (925)
Q Consensus 141 ~VLMlDLe--~ddLI~eLFkt---FFdiVr~dhp~kV~~~M~dILs~VIeES--E~VP~eVL 195 (925)
|++++-++ |-++|..||.. +..+|+...-++|......|+..+|+-+ ..|.+.+|
T Consensus 216 ~iw~lTf~~~~aqdi~K~~dli~dli~iVk~~~keKV~Rlc~~Iv~n~~dK~pK~~I~~~ll 277 (432)
T COG5231 216 IIWILTFSKECAQDIDKMDDLINDLIAIVKERAKEKVLRLCCGIVANVLDKSPKGYIFSPLL 277 (432)
T ss_pred HHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhhhHh
Confidence 44555554 55666655544 4557888888999999999999999965 44544443
No 110
>KOG4407 consensus Predicted Rho GTPase-activating protein [General function prediction only]
Probab=20.47 E-value=3.5e+02 Score=36.70 Aligned_cols=230 Identities=16% Similarity=0.178 Sum_probs=0.0
Q ss_pred hhhHHhh--------hhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhHHHHHHHHhhhhceeeeeccCC----
Q 002421 81 VTSCISE--------ITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE---- 148 (925)
Q Consensus 81 VAcCLAD--------ILRIyAPDAPYtDdqLKDIFqLfV~qf~~LaD~ssp~F~q~~yLLEsLAeVKS~VLMlDLe---- 148 (925)
+||||+| |.|| |-..-.+.-|.-+-..+-| |.|++
T Consensus 1180 ~C~~vVEt~Gl~~vGIYRI-------------------------------PGN~AAIs~l~E~ln~~~f--~~~v~~~Dd 1226 (1973)
T KOG4407|consen 1180 ACVCVVETYGLDTVGIYRI-------------------------------PGNTAAISALKESLNNRGF--LSKVESLDD 1226 (1973)
T ss_pred HHHHHHhhcCccceeEEec-------------------------------CCcHHHHHHHHHHHhcccc--chhhhcccc
Q ss_pred ---chHHHHHHHHHHHH-HhhcCCchhHHHHHH------------HHHHHHhcccCCCcHHHHHHHHHHhhccCCCC---
Q 002421 149 ---CDKLVVEMFQHFLK-VIRSNHPHFVFAAME------------TIMTLVIDESEDVSWDLLRILLASVRKENQDV--- 209 (925)
Q Consensus 149 ---~ddLI~eLFktFFd-iVr~dhp~kV~~~M~------------dILs~VIeESE~VP~eVLDvIL~~fl~~~ks~--- 209 (925)
.-.+|-.|.+.||. +--+=++.+....+. -.|..||.....-+.+-|..|+.+|..-..+.
T Consensus 1227 rWrDvNVVSSLLK~F~RkLPepL~t~~~Y~~FIeAnrk~~~l~Rl~~Lr~l~~~LPrhhYeTlkfLi~HL~~Vt~nsdvN 1306 (1973)
T KOG4407|consen 1227 RWRDVNVVSSLLKMFLRKLPEPLLTDKLYPFFIEANRKSTHLNRLHKLRNLLRKLPRHHYETLKFLIVHLSEVTKNSDVN 1306 (1973)
T ss_pred chhhhHHHHHHHHHHHHhCCcccccccchhhhhhhcccccHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHhcccccc
Q ss_pred ----CchHHHHHHHHHHhhhHhHHHHHHHHHHhcCCCCcchHHHHHHHhccC------------------CCCCCCCCCC
Q 002421 210 ----SPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIALDDYAEIVACICGSD------------------DENPQHGHLI 267 (925)
Q Consensus 210 ----~PaAykLA~~VI~~CadKLqp~I~q~l~s~Gi~Ld~Y~eIV~sIcq~~------------------s~~l~~~~~~ 267 (925)
...|..++=.||+..-|.|...|...-..+ .||+.+.+-. ....|++...
T Consensus 1307 kMEprNLAi~FGPsiVRts~Dnm~tmVthM~dQc--------kIVEtLI~~~dwfF~esg~te~~~~~Q~~~~~q~~~~p 1378 (1973)
T KOG4407|consen 1307 KMEPRNLAIMFGPSIVRTSDDNMATMVTHMSDQC--------KIVETLIHYNDWFFDESGTTEDAVPEQHPADGQNPLEP 1378 (1973)
T ss_pred cccccceeEEeccceeccCCccHHHHhhcchhhh--------hHHHHHHhhhhheeccCCCccccccccCccccCCCCCc
Q ss_pred CcccccccCCCCCCCCCCcccCCCCCcccccccCccccccCCccccccccccccccccccccccccccCCCCCCCCcccc
Q 002421 268 GSENQLATKEPDPPCLGEVVHDVDGISKSVTSNGTAASRNEDSVVKDKLSNVLERCSQVERSQSIDAKCSAGPDTSDSLR 347 (925)
Q Consensus 268 ~~~~~~~~~e~~~~~~~~v~~~~d~~~ks~~~ng~a~~~~d~~~~~~~~~kk~~~~~~~~~s~~~~~~~n~e~~~~~~~k 347 (925)
+--..+.-.+++.....+ ...--...+--.||--..+.++...--.-+...-..+.+..++..-+....-+++++...
T Consensus 1379 ~~~h~l~~igvT~~s~~d--~s~~~~ql~rK~~g~~~a~~~~~~~g~~V~s~~~~nsr~~k~~~~~~~~Sts~~~~~tt~ 1456 (1973)
T KOG4407|consen 1379 GGYHVLVPIGVTAASFND--MSNFMPQLIRKANGDQAAAMMNEGKGQKVKSMLRRNSRRDKSKSKLKIESTSPAAVNTTT 1456 (1973)
T ss_pred cccccccccccccccccc--hhhhhhhhhhhcccchhhhccccccchhHhhhhhhccccccCccccccccCChhhcccee
Q ss_pred cccCCCCCCcCCccCCC
Q 002421 348 NVKSETEPESAPRKRGR 364 (925)
Q Consensus 348 ~~~~~~~~~~~~~Kr~~ 364 (925)
+ .||+|
T Consensus 1457 ~-----------~k~~~ 1462 (1973)
T KOG4407|consen 1457 I-----------AKRGW 1462 (1973)
T ss_pred e-----------ccccc
No 111
>KOG2022 consensus Nuclear transport receptor LGL2 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.35 E-value=9.7e+02 Score=31.47 Aligned_cols=90 Identities=11% Similarity=0.169 Sum_probs=55.1
Q ss_pred cCCchHHHHHHHHHHHHH-hhcCCchhHHHHHHHH--HHHHhcccCCCcHHHHHHHHHHhhccCCCCCchHHHHHHHHHH
Q 002421 146 DLECDKLVVEMFQHFLKV-IRSNHPHFVFAAMETI--MTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFT 222 (925)
Q Consensus 146 DLe~ddLI~eLFktFFdi-Vr~dhp~kV~~~M~dI--Ls~VIeESE~VP~eVLDvIL~~fl~~~ks~~PaAykLA~~VI~ 222 (925)
+..-.+-|..+|++.+.+ ++.-.|+-+.++|..| +..-+.|-..-=+..|..||..+- +...+--|---...+|+
T Consensus 499 ~~t~~~~i~rl~~~~asik~S~~n~ql~~Tss~~igs~s~~l~e~P~~ln~sl~~L~~~Lh--~sk~s~q~i~tl~tlC~ 576 (982)
T KOG2022|consen 499 GETESTWIPRLFETSASIKLSAPNPQLLSTSSDLIGSLSNWLGEHPMYLNPSLPLLFQGLH--NSKESEQAISTLKTLCE 576 (982)
T ss_pred CcchhHHHHHHHHhccccccccCChhHHHHHHHHHHHHHHHHhcCCcccCchHHHHHHHhc--CchHHHHHHHHHHHHHH
Confidence 334678899999999985 3322344455555433 223333333322334777777764 22223333334678999
Q ss_pred hhhHhHHHHHHHHHH
Q 002421 223 KCAAKLKTNLKEAVQ 237 (925)
Q Consensus 223 ~CadKLqp~I~q~l~ 237 (925)
.|...|.||+.+|++
T Consensus 577 ~C~~~L~py~d~~~a 591 (982)
T KOG2022|consen 577 TCPESLDPYADQFSA 591 (982)
T ss_pred hhhhhCchHHHHHHH
Confidence 999999999988876
No 112
>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=20.21 E-value=37 Score=26.42 Aligned_cols=22 Identities=18% Similarity=0.350 Sum_probs=19.9
Q ss_pred cccCCCcCceeehhhHHhhhhh
Q 002421 69 LLRRSDMDVRLSVTSCISEITR 90 (925)
Q Consensus 69 LLkHKDkdVRayVAcCLADILR 90 (925)
||+|.|.+|+-.++.||..|.|
T Consensus 20 ll~~~~~~v~~~a~~al~nl~~ 41 (41)
T PF00514_consen 20 LLKSPDPEVQEEAAWALGNLAA 41 (41)
T ss_dssp HTTSSSHHHHHHHHHHHHHHHT
T ss_pred HHcCCCHHHHHHHHHHHHHHhC
Confidence 7789999999999999998865
No 113
>PF04084 ORC2: Origin recognition complex subunit 2 ; InterPro: IPR007220 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 2, which binds the origin of replication. It plays a role in chromosome replication and mating type transcriptional silencing.; GO: 0006260 DNA replication, 0000808 origin recognition complex, 0005634 nucleus
Probab=20.09 E-value=1.6e+02 Score=33.43 Aligned_cols=106 Identities=16% Similarity=0.180 Sum_probs=62.8
Q ss_pred CChhHHHHHHHHHHHHhccc----------CCCCCcchh--HHHHHHHHhhhhceeeeeccCC--c-----hHHHHHHHH
Q 002421 98 YDDELMKEFFQLAVSAFENL----------SHASGRYYM--KALSILDTVAKVRSCLLMLDLE--C-----DKLVVEMFQ 158 (925)
Q Consensus 98 YtDdqLKDIFqLfV~qf~~L----------aD~ssp~F~--q~~yLLEsLAeVKS~VLMlDLe--~-----ddLI~eLFk 158 (925)
+...+..+...++++.|... .+.++|.+. +...+|..||.+..|-|++=+| - |.....-|+
T Consensus 114 ~~~~~~~~~~~~i~~~l~~~~~~~~l~lvIHnIDg~~LR~~~~Q~~La~LA~~p~I~lIASiDhinapLLWd~~~~~~fn 193 (326)
T PF04084_consen 114 KKPKSPSEQLDFIISYLESRPSPPPLYLVIHNIDGPSLRNEKAQSLLAQLASIPNIHLIASIDHINAPLLWDSSKLSRFN 193 (326)
T ss_pred cccCCHHHHHHHHHHHHhccCCCCceEEEEECCCChhhcChHHHHHHHHHHcCCCeEEEEeccCCCcccccChhhHhhCC
Confidence 33445555556666665554 346778754 6788999999999999988887 2 233344555
Q ss_pred HHHHHhhcCCchhHHHHHHHHHHHHhcccCC--CcHHHHHHHHHHhh
Q 002421 159 HFLKVIRSNHPHFVFAAMETIMTLVIDESED--VSWDLLRILLASVR 203 (925)
Q Consensus 159 tFFdiVr~dhp~kV~~~M~dILs~VIeESE~--VP~eVLDvIL~~fl 203 (925)
=+|.-+..-.|=.++....+.+..++.-+.. +..+=+..+|..|-
T Consensus 194 f~~hd~tT~~pY~~E~~~~~~l~~~~g~s~~~~~~~~~~~~VL~SLt 240 (326)
T PF04084_consen 194 FLWHDVTTFAPYTEETSFEDSLHSLLGKSGSRVGGLSGAKHVLKSLT 240 (326)
T ss_pred EEEEeCCCCCCHHHHhccccchhhhhcccccccccHHHHHHHHHHCC
Confidence 5555445445555655555544444433322 55555666665543
No 114
>PF10151 DUF2359: Uncharacterised conserved protein (DUF2359); InterPro: IPR019308 This is a 450 amino acid region of a family of proteins conserved from insects to humans. The function is not known.
Probab=20.08 E-value=1.4e+03 Score=27.80 Aligned_cols=58 Identities=14% Similarity=0.154 Sum_probs=37.1
Q ss_pred HhhHHHHHhhhhhhcccCC--CcCceeehhhHHhhhhhhcCC-CCCCCh---hHHHHHHHHHHH
Q 002421 55 DALLPTMKGLITNDLLRRS--DMDVRLSVTSCISEITRITAP-DSPYDD---ELMKEFFQLAVS 112 (925)
Q Consensus 55 ~SL~pl~k~LVs~~LLkHK--DkdVRayVAcCLADILRIyAP-DAPYtD---dqLKDIFqLfV~ 112 (925)
.++.++.-.++.+=|+.|. -++.|+.-.-=+-.|||++=| ...... ++|..||-.+-.
T Consensus 72 K~~s~~vi~yleriL~~~~~~~~g~~li~p~~F~~ll~~~f~~~~~~~k~l~e~l~~~yp~LK~ 135 (469)
T PF10151_consen 72 KSYSPYVIQYLERILSLHGNVTKGERLIPPQEFFPLLRLTFPPSNSLSKALQERLEAIYPRLKE 135 (469)
T ss_pred CCcchHHHHHHHHHHhcCcccccCcCCCCHHHHHHHHHHhcCCcccCCHHHHHHHHHHHHHHHH
Confidence 5567777788888888887 457777777788888887443 333322 345555544433
Done!