Query 004863
Match_columns 726
No_of_seqs 140 out of 221
Neff 3.7
Searched_HMMs 46136
Date Thu Mar 28 14:10:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004863.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004863hhsearch_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 6.8E-52 1.5E-56 488.5 22.4 246 13-261 4-257 (1266)
2 KOG1525 Sister chromatid cohes 99.7 1.5E-17 3.2E-22 198.9 16.1 247 13-262 409-672 (1266)
3 KOG1992 Nuclear export recepto 92.1 2.2 4.7E-05 51.8 13.7 117 118-239 603-731 (960)
4 PF01602 Adaptin_N: Adaptin N 84.1 10 0.00023 41.9 11.7 25 68-92 274-298 (526)
5 PF09465 LBR_tudor: Lamin-B re 81.5 0.83 1.8E-05 38.6 1.5 13 713-725 8-20 (55)
6 PF03378 CAS_CSE1: CAS/CSE pro 79.7 31 0.00066 39.4 13.4 137 80-228 45-194 (435)
7 PF12348 CLASP_N: CLASP N term 76.8 82 0.0018 31.3 14.1 181 24-224 17-204 (228)
8 KOG0915 Uncharacterized conser 75.8 52 0.0011 43.0 14.8 165 28-202 989-1196(1702)
9 PF14500 MMS19_N: Dos2-interac 74.8 36 0.00079 36.2 11.6 174 68-266 6-184 (262)
10 KOG1248 Uncharacterized conser 74.6 72 0.0016 40.7 15.4 193 28-237 200-394 (1176)
11 PF01602 Adaptin_N: Adaptin N 73.2 6.6 0.00014 43.4 6.0 118 67-203 120-241 (526)
12 PF05918 API5: Apoptosis inhib 72.6 46 0.00099 39.4 12.7 144 7-163 172-318 (556)
13 PF02985 HEAT: HEAT repeat; I 72.6 2 4.4E-05 31.0 1.2 25 68-92 7-31 (31)
14 PTZ00429 beta-adaptin; Provisi 69.8 2.2E+02 0.0049 35.0 17.9 147 59-231 256-402 (746)
15 KOG1248 Uncharacterized conser 69.5 1.6E+02 0.0034 37.9 16.7 157 72-237 708-872 (1176)
16 KOG0213 Splicing factor 3b, su 68.2 1.3E+02 0.0028 37.4 15.0 133 25-162 506-688 (1172)
17 KOG1949 Uncharacterized conser 66.8 1.1E+02 0.0023 37.8 14.0 145 23-207 206-374 (1005)
18 KOG1060 Vesicle coat complex A 66.7 53 0.0012 40.5 11.7 171 29-228 213-423 (968)
19 KOG1060 Vesicle coat complex A 61.5 1.3E+02 0.0029 37.3 13.6 173 55-256 318-504 (968)
20 PF12755 Vac14_Fab1_bd: Vacuol 60.6 27 0.00059 31.9 6.3 60 68-135 34-94 (97)
21 PF03224 V-ATPase_H_N: V-ATPas 58.4 1.1E+02 0.0024 32.7 11.4 123 28-166 27-157 (312)
22 PF05327 RRN3: RNA polymerase 57.8 61 0.0013 38.0 10.0 107 82-202 281-394 (563)
23 PTZ00429 beta-adaptin; Provisi 57.7 3E+02 0.0065 33.9 15.9 27 68-95 147-173 (746)
24 PF14911 MMS22L_C: S-phase gen 56.2 2.9E+02 0.0062 31.5 14.4 122 24-165 224-347 (373)
25 PF05327 RRN3: RNA polymerase 55.3 1.1E+02 0.0023 36.0 11.5 100 23-138 45-155 (563)
26 PF12717 Cnd1: non-SMC mitotic 54.6 1.2E+02 0.0026 29.8 10.2 78 70-164 72-159 (178)
27 PF12348 CLASP_N: CLASP N term 52.4 2E+02 0.0043 28.7 11.4 116 76-202 22-140 (228)
28 smart00139 MyTH4 Domain in Myo 51.6 2.1E+02 0.0046 27.9 11.1 101 149-256 18-128 (144)
29 PF12719 Cnd3: Nuclear condens 51.2 2E+02 0.0044 30.6 11.9 166 71-242 74-286 (298)
30 KOG2171 Karyopherin (importin) 51.1 1.7E+02 0.0037 37.4 12.6 158 67-237 86-288 (1075)
31 KOG4256 Kinetochore component 49.6 2.1E+02 0.0045 37.0 12.7 94 66-170 499-618 (2209)
32 PF12612 TFCD_C: Tubulin foldi 48.6 1.3E+02 0.0029 30.1 9.5 35 76-110 22-58 (193)
33 KOG2023 Nuclear transport rece 47.8 93 0.002 38.0 9.4 112 128-243 579-712 (885)
34 KOG1241 Karyopherin (importin) 47.6 2.9E+02 0.0063 34.4 13.4 46 67-112 557-606 (859)
35 COG5215 KAP95 Karyopherin (imp 46.8 2.5E+02 0.0055 34.2 12.4 116 149-265 531-698 (858)
36 PF02854 MIF4G: MIF4G domain; 46.5 2.2E+02 0.0047 27.1 10.3 50 188-237 117-173 (209)
37 PF13513 HEAT_EZ: HEAT-like re 46.3 33 0.00073 27.0 4.0 47 40-88 9-55 (55)
38 PF14911 MMS22L_C: S-phase gen 46.2 2.4E+02 0.0052 32.1 11.9 161 101-261 139-335 (373)
39 PF03224 V-ATPase_H_N: V-ATPas 46.0 91 0.002 33.3 8.4 35 55-91 146-180 (312)
40 PF12717 Cnd1: non-SMC mitotic 44.3 3.2E+02 0.007 26.9 12.4 138 74-226 1-157 (178)
41 PF12460 MMS19_C: RNAPII trans 43.8 5.1E+02 0.011 29.0 14.4 162 74-239 56-238 (415)
42 KOG1993 Nuclear transport rece 43.1 87 0.0019 38.9 8.3 121 134-266 544-673 (978)
43 PF11935 DUF3453: Domain of un 42.5 3.9E+02 0.0085 28.0 12.2 125 51-201 35-161 (239)
44 cd00020 ARM Armadillo/beta-cat 41.0 74 0.0016 27.3 5.6 66 68-139 14-80 (120)
45 PF08767 CRM1_C: CRM1 C termin 40.9 5.2E+02 0.011 28.3 13.4 82 27-115 88-175 (319)
46 KOG2051 Nonsense-mediated mRNA 39.8 2E+02 0.0043 36.8 10.7 75 151-226 703-790 (1128)
47 KOG1949 Uncharacterized conser 39.5 2.4E+02 0.0052 35.1 11.0 152 63-224 173-369 (1005)
48 PF02565 RecO_C: Recombination 39.3 79 0.0017 27.8 5.7 59 77-139 5-64 (118)
49 PF05997 Nop52: Nucleolar prot 39.0 2.2E+02 0.0047 29.6 9.6 163 33-204 19-195 (217)
50 PF04118 Dopey_N: Dopey, N-ter 38.9 1.8E+02 0.0039 32.0 9.4 41 97-138 127-168 (307)
51 PF12074 DUF3554: Domain of un 38.5 5.4E+02 0.012 27.8 15.9 96 26-132 35-136 (339)
52 PF10165 Ric8: Guanine nucleot 38.4 1.4E+02 0.003 34.1 8.8 41 226-266 307-348 (446)
53 PF08568 Kinetochor_Ybp2: Unch 38.2 4.2E+02 0.0091 31.5 12.9 124 26-185 36-176 (633)
54 cd04405 RhoGAP_BRCC3-like RhoG 37.7 1.8E+02 0.0039 31.3 8.8 107 102-208 104-226 (235)
55 cd00280 TRFH Telomeric Repeat 36.2 1.3E+02 0.0028 31.6 7.3 101 54-162 32-139 (200)
56 PF08558 TRF: Telomere repeat 35.5 1.1E+02 0.0024 32.3 6.9 123 81-207 11-157 (238)
57 PF08385 DHC_N1: Dynein heavy 35.4 6.9E+02 0.015 28.5 13.7 33 32-64 99-131 (579)
58 KOG0211 Protein phosphatase 2A 35.3 9.4E+02 0.02 30.0 15.3 143 62-225 520-666 (759)
59 KOG1410 Nuclear transport rece 35.0 4.6E+02 0.0099 32.7 12.3 155 87-263 844-1027(1082)
60 smart00288 VHS Domain present 34.8 99 0.0021 29.5 5.9 68 165-233 10-77 (133)
61 KOG1488 Translational represso 33.9 1.5E+02 0.0032 35.0 8.2 81 149-239 279-364 (503)
62 COG5215 KAP95 Karyopherin (imp 33.6 6.5E+02 0.014 30.9 13.1 221 34-261 473-735 (858)
63 KOG2022 Nuclear transport rece 32.9 6.4E+02 0.014 32.1 13.3 182 55-255 701-917 (982)
64 PF14868 DUF4487: Domain of un 32.6 3.9E+02 0.0085 32.0 11.4 125 102-243 377-511 (559)
65 KOG0686 COP9 signalosome, subu 32.5 29 0.00062 39.9 2.2 116 75-204 269-396 (466)
66 KOG0301 Phospholipase A2-activ 32.0 5.3E+02 0.011 31.9 12.2 116 40-163 548-685 (745)
67 COG5231 VMA13 Vacuolar H+-ATPa 32.0 2E+02 0.0042 32.8 8.3 99 68-187 156-267 (432)
68 cd00197 VHS_ENTH_ANTH VHS, ENT 31.8 1E+02 0.0022 28.1 5.2 60 174-234 19-78 (115)
69 COG5218 YCG1 Chromosome conden 31.7 1.1E+03 0.023 29.3 16.4 88 126-218 65-153 (885)
70 KOG1824 TATA-binding protein-i 31.5 1.1E+03 0.024 30.6 15.0 124 67-203 699-827 (1233)
71 PRK05686 fliG flagellar motor 31.4 6.9E+02 0.015 27.5 12.4 60 67-133 31-90 (339)
72 PF00514 Arm: Armadillo/beta-c 31.4 28 0.0006 26.2 1.3 23 68-90 19-41 (41)
73 PF11864 DUF3384: Domain of un 30.8 6.2E+02 0.013 29.0 12.3 110 121-236 147-259 (464)
74 KOG2344 Exocyst component prot 29.8 1.1E+02 0.0023 36.9 6.3 34 221-258 382-415 (623)
75 cd07958 Anticodon_Ia_Leu_BEm A 29.6 1.5E+02 0.0033 25.8 5.9 29 77-105 87-115 (117)
76 COG5096 Vesicle coat complex, 29.6 2.8E+02 0.0061 34.3 9.8 24 68-91 134-157 (757)
77 PF08405 Calici_PP_N: Viral po 28.8 1.3E+02 0.0027 33.8 6.2 88 100-202 133-232 (358)
78 PF07637 PSD5: Protein of unkn 28.8 1.3E+02 0.0028 25.5 5.0 59 10-72 3-61 (64)
79 TIGR00207 fliG flagellar motor 28.7 8E+02 0.017 27.2 12.4 45 68-119 29-73 (338)
80 cd07961 Anticodon_Ia_Ile_ABEc 27.8 34 0.00074 33.4 1.6 27 79-105 112-138 (183)
81 KOG2759 Vacuolar H+-ATPase V1 27.2 2.5E+02 0.0053 32.7 8.2 111 63-188 159-274 (442)
82 PF04147 Nop14: Nop14-like fam 27.1 1.5E+02 0.0033 36.7 7.2 46 185-230 482-527 (840)
83 PF14631 FancD2: Fanconi anaem 26.4 6.3E+02 0.014 33.6 12.6 197 26-255 960-1160(1426)
84 cd03568 VHS_STAM VHS domain fa 26.4 1.5E+02 0.0033 28.9 5.8 69 164-233 9-77 (144)
85 KOG1062 Vesicle coat complex A 26.1 8.2E+02 0.018 30.9 12.6 165 58-243 384-568 (866)
86 PRK14086 dnaA chromosomal repl 25.9 7.1E+02 0.015 30.3 12.0 16 189-204 502-517 (617)
87 smart00543 MIF4G Middle domain 25.8 5.9E+02 0.013 24.3 13.2 132 82-229 17-155 (200)
88 KOG4338 Predicted lipoprotein 25.7 3.9E+02 0.0084 35.9 10.3 173 8-254 319-493 (1680)
89 PF15611 EH_Signature: EH_Sign 25.5 9E+02 0.019 26.3 12.3 111 83-207 106-226 (389)
90 PF10363 DUF2435: Protein of u 25.3 5.3E+02 0.011 23.6 8.6 82 155-237 3-87 (92)
91 PLN02959 aminoacyl-tRNA ligase 25.2 84 0.0018 39.9 4.6 30 77-106 847-876 (1084)
92 PF08767 CRM1_C: CRM1 C termin 25.1 5.7E+02 0.012 28.0 10.4 77 150-226 112-198 (319)
93 PF10508 Proteasom_PSMB: Prote 25.1 8E+02 0.017 28.5 12.0 115 68-189 84-213 (503)
94 PF11707 Npa1: Ribosome 60S bi 24.9 4.4E+02 0.0096 28.7 9.5 165 25-239 147-316 (330)
95 KOG1991 Nuclear transport rece 24.8 1.6E+03 0.035 29.0 16.1 198 32-244 616-818 (1010)
96 cd07920 Pumilio Pumilio-family 24.7 5.7E+02 0.012 26.8 10.0 17 101-117 71-87 (322)
97 PLN03076 ARF guanine nucleotid 24.6 6.6E+02 0.014 34.3 12.3 130 30-165 373-516 (1780)
98 KOG1991 Nuclear transport rece 24.1 3.1E+02 0.0066 35.0 8.8 55 73-137 435-491 (1010)
99 PF00790 VHS: VHS domain; Int 23.9 2.1E+02 0.0045 27.3 6.1 69 163-232 13-81 (140)
100 cd00020 ARM Armadillo/beta-cat 23.8 73 0.0016 27.3 2.8 61 69-136 57-119 (120)
101 cd05394 RasGAP_RASA2 RASA2 (or 23.5 5.6E+02 0.012 28.7 9.9 38 61-100 38-75 (313)
102 PF02854 MIF4G: MIF4G domain; 23.4 6.4E+02 0.014 23.9 11.0 166 13-203 3-180 (209)
103 smart00188 IL10 Interleukin-10 22.7 53 0.0012 32.5 1.9 50 34-92 4-54 (137)
104 KOG0929 Guanine nucleotide exc 22.5 3.5E+02 0.0075 36.0 9.1 80 72-165 1185-1264(1514)
105 PF02106 Fanconi_C: Fanconi an 22.2 4.3E+02 0.0094 31.6 9.1 85 139-224 186-302 (559)
106 PF04928 PAP_central: Poly(A) 22.2 6.5E+02 0.014 27.1 9.9 45 63-115 72-117 (254)
107 cd03569 VHS_Hrs_Vps27p VHS dom 22.1 2.9E+02 0.0063 26.9 6.7 59 174-233 23-81 (142)
108 PF10151 DUF2359: Uncharacteri 22.0 1.2E+03 0.025 27.6 12.5 143 55-205 72-226 (469)
109 PF05004 IFRD: Interferon-rela 21.9 1.7E+02 0.0036 31.9 5.6 43 59-103 228-274 (309)
110 PLN02381 valyl-tRNA synthetase 21.7 71 0.0015 40.5 3.1 31 77-107 840-870 (1066)
111 PF12719 Cnd3: Nuclear condens 21.5 1E+03 0.022 25.4 17.4 52 56-115 23-74 (298)
112 PLN03076 ARF guanine nucleotid 21.5 1.4E+03 0.03 31.4 14.4 38 58-97 1346-1383(1780)
113 KOG1241 Karyopherin (importin) 21.2 1.1E+03 0.024 29.8 12.3 68 69-137 454-527 (859)
114 PF06213 CobT: Cobalamin biosy 21.2 7.1E+02 0.015 26.7 10.0 94 47-146 6-109 (282)
115 PF14666 RICTOR_M: Rapamycin-i 21.1 6.1E+02 0.013 26.8 9.3 43 192-237 179-221 (226)
116 cd03567 VHS_GGA VHS domain fam 21.1 2.8E+02 0.0061 27.1 6.4 69 164-233 10-78 (139)
117 PF10395 Utp8: Utp8 family; I 20.2 6E+02 0.013 31.2 10.0 58 100-157 459-532 (670)
118 KOG3674 FtsJ-like RNA methyltr 20.2 1.1E+02 0.0024 36.3 3.9 50 93-142 12-76 (696)
No 1
>KOG1525 consensus Sister chromatid cohesion complex Cohesin, subunit PDS5 [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=6.8e-52 Score=488.48 Aligned_cols=246 Identities=35% Similarity=0.558 Sum_probs=233.3
Q ss_pred HHHHhccccCCCCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhc
Q 004863 13 QLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRIT 92 (726)
Q Consensus 13 ~l~~~G~kLis~piStdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIy 92 (726)
+.-.-||+++..+++++|||+||++|..||++++|++.+ .++|.|++.+|+++.||+|+|+|||+|||||++||||||
T Consensus 4 ~~~~~g~~~~~~~~s~~ell~rLk~l~~~l~~~~qd~~~--~~~~~pl~~~l~~~~~L~h~d~dvrllvacCvseilRi~ 81 (1266)
T KOG1525|consen 4 QFYPPGCLTSLNPISKDELLKRLKKLANCLASLDQDNLD--LASLLPLADHLIKDFLLKHKDKDVRLLVACCVSEILRIY 81 (1266)
T ss_pred cccCCCCccccCcccHHHHHHHHHHHHHHHhhcccCchh--HHHHHHHHHHHhhHHHhcCCCcChhHHHHHHHHHHHHHh
Confidence 445679999999999999999999999999999999966 899999999999999999999999999999999999999
Q ss_pred CCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHHhhcCCchhH
Q 004863 93 APDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFV 172 (726)
Q Consensus 93 APDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~dhp~~V 172 (726)
||||||++.||+|||+||++||.||.|+.+|||.|||||||+||.||.|++|.|.+|++|+.+||.+||+++|.+||.+|
T Consensus 82 aPeaPy~~~~lkdIf~~~~~q~~gL~d~~sp~f~r~~~lletl~~~k~~l~~~l~d~~e~~~~~f~~f~d~~~~~~~~~v 161 (1266)
T KOG1525|consen 82 APEAPYTDEQLKDIFQLILSQFSGLGDVESPYFKRYFYLLETLAKVKFCLLMLLEDCQELVHELFRTFFDLARKGHPKKV 161 (1266)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHhhccCCCCcchhhHHHHHHHHHHhHHHheeeccchHHHHHHHHHHHHHHHhccccHHH
Confidence 99999999999999999999999999999999999999999999999888887778999999999999999999999999
Q ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHHHHHHhc-------CCCc-h
Q 004863 173 FAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSR-------GIAL-D 244 (726)
Q Consensus 173 ~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~~ns~-------G~~L-~ 244 (726)
+. |.+||+.+|.|.+.||.++|++||.+|+++.+++.+.|+.||..+|..|++.+.+.|++||++. +.++ .
T Consensus 162 ~~-~~~i~~~li~e~d~v~~e~L~~ll~~lv~~~~~~~~~a~~la~~li~~~a~~~~~~i~~f~~~~~~~~~s~~~~~~~ 240 (1266)
T KOG1525|consen 162 FN-MLDIAIMLITEEDTVQSELLDVLLENLVKPGRDTIKEADKLASDLIERCADNLEDTIANFLNSCLTEYKSRQSSLKI 240 (1266)
T ss_pred HH-HHHHHHHHHHhhccchHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHhhhhhchhHHHHHHHHHhhccccccchhh
Confidence 99 9999999999999999999999999999999999999999999999999999999999999754 2223 4
Q ss_pred hHHHHHHHHhcCCCCCC
Q 004863 245 DYAEIVACICGSDDENP 261 (726)
Q Consensus 245 ~YseIv~sIcq~~s~~~ 261 (726)
.||+||+.+-.+++.++
T Consensus 241 ~~he~i~~L~~~~p~ll 257 (1266)
T KOG1525|consen 241 KYHELILELWRIAPQLL 257 (1266)
T ss_pred HHHHHHHHHHHhhHHHH
Confidence 89999999999887665
No 2
>KOG1525 consensus Sister chromatid cohesion complex Cohesin, subunit PDS5 [Cell cycle control, cell division, chromosome partitioning]
Probab=99.74 E-value=1.5e-17 Score=198.87 Aligned_cols=247 Identities=31% Similarity=0.376 Sum_probs=231.7
Q ss_pred HHHHhccccCCCCCC--HHHHHHHHHHH--------HHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhH
Q 004863 13 QLKDAGNLLLNPPSP--VDEVINLLDKV--------EHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVT 82 (726)
Q Consensus 13 ~l~~~G~kLis~piS--tdELLKRLkkL--------~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVA 82 (726)
++..+|.+.+.++.+ .++||..+-+. +-.|..+.|....++++++.+++..|+.=.+..|++-++.+-..
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 78888999988888999999999999999999999999999999
Q ss_pred HHHHHHhh--hcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHH--HHHHHhhhhhhheeecc---CCchHHHHH
Q 004863 83 SCISEITR--ITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKAL--SILDTVAKVRSCLLMLD---LECDKLVVE 155 (726)
Q Consensus 83 cCLaDILR--IyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~--yLLEsLAeVKS~VLmlD---LE~ddLI~e 155 (726)
.||.+++| |.+|..||+++.|+.||..|+..+..|.|+.+..|.... .+|+.++.+++|+.|++ +.|.++...
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 999999999999999999999999999999887555443 59999999999999999 569999999
Q ss_pred HHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHHHH
Q 004863 156 MFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEA 235 (726)
Q Consensus 156 LFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~ 235 (726)
||+.||..++..++.+++..|..+|++.|.+ |+.+++..|+..+...+......+..+++.|+..|+-++.+||.+.
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 HHhcCCCchhHHHHHHHHhcCCCCCCC
Q 004863 236 VQSRGIALDDYAEIVACICGSDDENPQ 262 (726)
Q Consensus 236 ~ns~G~~L~~YseIv~sIcq~~s~~~~ 262 (726)
|...+..+..|++++.+||+...+..+
T Consensus 646 ls~~~~~~~~~s~~v~~i~~~~~~~~~ 672 (1266)
T KOG1525|consen 646 LSSIHPDLFKYSESVLSILEKLFSEPD 672 (1266)
T ss_pred hhhcCcchhhhhHHHHHHHHHhccchh
Confidence 999999999999999999999988773
No 3
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=92.11 E-value=2.2 Score=51.77 Aligned_cols=117 Identities=9% Similarity=0.140 Sum_probs=73.9
Q ss_pred CCCCCcchhhHHHHHHHhhhhhhheeeccCC---chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCC-CCHH
Q 004863 118 SHASGRYYMKALSILDTVAKVRSCLLMLDLE---CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESED-VSWD 193 (726)
Q Consensus 118 sD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE---~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~-VP~e 193 (726)
.+|++|-| ++||+|+++-+=- ..++-+ --.+...||=.|-.+.+.+. .+...+...||+.+++-+.. +|..
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--NHYLFESIGLLIR--KTCKANPSAVSSLEEALFPVFQTILSEDI-QEFIPYVFQLLAVLVEHSSGTIPDS 677 (960)
T ss_pred cCCCCchh--HHHHHHHHHHHHH--HHhccCchHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhcCCCCchh
Confidence 44566633 5789999976511 123333 13466777755555545443 34556677899999998876 7766
Q ss_pred H---HHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHH-----HHHHHHHHhc
Q 004863 194 L---LRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLK-----TNLKEAVQSR 239 (726)
Q Consensus 194 V---LDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLq-----p~I~q~~ns~ 239 (726)
. +-.||+.-+..-....|+.-+|-...|...+..+. .+|-.+|+.|
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 4 34444444555678889988888888877665544 4455666655
No 4
>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=84.08 E-value=10 Score=41.88 Aligned_cols=25 Identities=28% Similarity=0.412 Sum_probs=22.1
Q ss_pred hhccCCCcCchhhhHHHHHHHhhhc
Q 004863 68 DLLRRSDMDVRLSVTSCISEITRIT 92 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILRIy 92 (726)
.||.++|..||..+..||..|.+.+
T Consensus 274 ~lL~s~~~nvr~~~L~~L~~l~~~~ 298 (526)
T PF01602_consen 274 KLLSSSDPNVRYIALDSLSQLAQSN 298 (526)
T ss_dssp HHHTSSSHHHHHHHHHHHHHHCCHC
T ss_pred HHhhcccchhehhHHHHHHHhhccc
Confidence 5778999999999999999999885
No 5
>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=81.50 E-value=0.83 Score=38.57 Aligned_cols=13 Identities=31% Similarity=0.780 Sum_probs=9.6
Q ss_pred ccCeeEEecCCCC
Q 004863 713 VGSRIKVWWPMDE 725 (726)
Q Consensus 713 VGsriKVWWP~D~ 725 (726)
.|.+|.||||++.
T Consensus 8 ~Ge~V~~rWP~s~ 20 (55)
T PF09465_consen 8 IGEVVMVRWPGSS 20 (55)
T ss_dssp SS-EEEEE-TTTS
T ss_pred CCCEEEEECCCCC
Confidence 5899999999985
No 6
>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=79.72 E-value=31 Score=39.37 Aligned_cols=137 Identities=12% Similarity=0.217 Sum_probs=82.7
Q ss_pred hhHHHHHHHhhhcCCC-CCCChh---HHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhh-hhheeeccCCch---H
Q 004863 80 SVTSCISEITRITAPD-SPYDDE---LMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKV-RSCLLMLDLECD---K 151 (726)
Q Consensus 80 yVAcCLaDILRIyAPD-APYtDd---qLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeV-KS~VLmlDLE~d---d 151 (726)
|+.=||+=|+=++.-+ .||.+. +|-.|+..+. .+|++|.|. +|+.|+|+.+ |. +++-+.+ .
T Consensus 45 ylMk~iMRvl~~~~e~~~p~~~~il~~L~~il~~v~------kNPsnP~Fn--HylFEsi~~lir~---~~~~~~~~v~~ 113 (435)
T PF03378_consen 45 YLMKCIMRVLSVLQEDILPIAVEILQHLTAILKEVS------KNPSNPRFN--HYLFESIGALIRF---VCEADPEAVSQ 113 (435)
T ss_dssp HHHHHHHHHHHHSTTTTGGGHHHHHHHHHHHHHHHH------TS---HHHH--HHHHHHHHHHHHH---S-GGGHH---H
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH------hCCCCcchh--hhHHHHHHHHHHh---ccCCChhHHHH
Confidence 6667777666555544 566442 2222322222 347788665 5678888776 42 2222222 5
Q ss_pred HHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccC--CCC---HHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHH
Q 004863 152 LVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESE--DVS---WDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAA 226 (726)
Q Consensus 152 LI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE--~VP---~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~Cad 226 (726)
+-..||-.|..+...+.. +...+.-.||+.+++-.. .+| ..++..||...+.+.+...|+.-+|-...|..++.
T Consensus 114 ~E~~L~P~f~~ILq~dV~-EF~PYvfQIla~Lle~~~~~~~p~~y~~L~~~Ll~p~lWe~~gniPalvrLL~a~i~k~~~ 192 (435)
T PF03378_consen 114 FEEALFPPFQEILQQDVQ-EFIPYVFQILAQLLELRPSSPLPDAYKQLFPPLLSPALWERRGNIPALVRLLQAYIKKDPS 192 (435)
T ss_dssp HHHHHHHHHHHHHHTT-T-TTHHHHHHHHHHHHHHSS--S--TTTGGGHHHHTSGGGGGSTTTHHHHHHHHHHHHHHHGG
T ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHcCcchhccCCCcCcHHHHHHHHHHhCch
Confidence 566666666666665543 334455667888887665 454 56788888888888888889988888888888877
Q ss_pred HH
Q 004863 227 KL 228 (726)
Q Consensus 227 KL 228 (726)
.+
T Consensus 193 ~i 194 (435)
T PF03378_consen 193 FI 194 (435)
T ss_dssp G-
T ss_pred hh
Confidence 54
No 7
>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=76.78 E-value=82 Score=31.34 Aligned_cols=181 Identities=12% Similarity=0.168 Sum_probs=81.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHhc-ccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhH
Q 004863 24 PPSPVDEVINLLDKVEHLLANV-EQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL 102 (726)
Q Consensus 24 ~piStdELLKRLkkL~~eLs~l-DQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdq 102 (726)
...+-++-+.-|+.|...+..- .+.....+...|..+...| ...+. ....-|-.-++-||.+|.+.+...
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 3345566666666666666654 2222232223333222121 12222 122224445566788888885443
Q ss_pred HHHHHHHHHHH-hcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHH
Q 004863 103 MKEFFQLAVSA-FENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMT 181 (726)
Q Consensus 103 LKDIFqLfV~q-f~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs 181 (726)
+...+..++.. |..+++............|..+...=++ ...++ |..+... ..+.+..|+......|.
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 44455555554 5666665444445556666665543110 01221 3333333 33556777777777888
Q ss_pred HHhcccC----CCCHH-HHHHHHHHhhccCCCCCchHHHHHHHHHhhh
Q 004863 182 LVIDESE----DVSWD-LLRILLASVRKENQDVSPTSWKLGEKVFTKC 224 (726)
Q Consensus 182 ~VIeESE----~VP~e-VLDvIL~~ll~~~ks~~PaAykLA~~VI~~C 224 (726)
.+|.... .+... .++.|+..+...-.+..|..+..|+.++...
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 8887766 12222 2344444444443455666677776655444
No 8
>KOG0915 consensus Uncharacterized conserved protein [Function unknown]
Probab=75.77 E-value=52 Score=43.02 Aligned_cols=165 Identities=15% Similarity=0.314 Sum_probs=95.1
Q ss_pred HHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhh--------------hhccC-CCcCchhhhHHH--HHHHhh
Q 004863 28 VDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITN--------------DLLRR-SDMDVRLSVTSC--ISEITR 90 (726)
Q Consensus 28 tdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~--------------~LLkH-KDkdVRayVAcC--LaDILR 90 (726)
.++|-.-|++|-=-|.+..=+|.-..++|...+-..||.. .||.+ .++.-|+--||| |+||+|
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 4455555666666677776666555566666666666655 45555 889999999999 569998
Q ss_pred hcCCCCCCCh--hHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCC----chHHHHHHH-------
Q 004863 91 ITAPDSPYDD--ELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE----CDKLVVEMF------- 157 (726)
Q Consensus 91 IyAPDAPYtD--dqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE----~ddLI~eLF------- 157 (726)
= .|+++ +.|.+||..+|+....+.+. --.-..-....|+ |.||-|+|.. +.+.+--+.
T Consensus 1069 g----~~~~~~~e~lpelw~~~fRvmDDIKEs---VR~aa~~~~~~ls--Kl~vr~~d~~~~~~~~~~l~~iLPfLl~~g 1139 (1702)
T KOG0915|consen 1069 G----RPFDQVKEKLPELWEAAFRVMDDIKES---VREAADKAARALS--KLCVRICDVTNGAKGKEALDIILPFLLDEG 1139 (1702)
T ss_pred C----CChHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH--HHHhhhcccCCcccHHHHHHHHHHHHhccC
Confidence 6 67776 68888887777776554431 1111111222222 6688888884 222222221
Q ss_pred -------------HHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHh
Q 004863 158 -------------QHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASV 202 (726)
Q Consensus 158 -------------ktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~l 202 (726)
.++.+++. .-+..+-.++.+++-.+++-...+.+.||..+--++
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 22233222 112333444445555566666677777777766554
No 9
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=74.79 E-value=36 Score=36.20 Aligned_cols=174 Identities=11% Similarity=0.182 Sum_probs=104.0
Q ss_pred hhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccC
Q 004863 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDL 147 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDL 147 (726)
..|.+.|..+|+-.--||+++|-=+.|+. .+..|..-++.||.+-| .|... +...|.-....+-|-.+
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 45778899999999999999997655554 78899999999999866 34322 22223333333334444
Q ss_pred CchHHHHHHHHHHHHHhh-cCCchhHHHHHHHHHHHHhcc----cCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHh
Q 004863 148 ECDKLVVEMFQHFLKVIR-SNHPHFVFAAMETIMTLVIDE----SEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFT 222 (726)
Q Consensus 148 E~ddLI~eLFktFFdiVr-~dhp~~V~~~M~dIMs~VIeE----SE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~ 222 (726)
. .+.+..|.+.||+-+. ..++...+...-.||..+++. ...+..+.+..++.. +.+.++. - .++
T Consensus 74 ~-~~~~~~i~~~l~~~~~~q~~~q~~R~~~~~ll~~l~~~~~~~l~~~~~~fv~~~i~~-~~gEkDP--R------nLl- 142 (262)
T PF14500_consen 74 S-PESAVKILRSLFQNVDVQSLPQSTRYAVYQLLDSLLENHREALQSMGDDFVYGFIQL-IDGEKDP--R------NLL- 142 (262)
T ss_pred C-hhhHHHHHHHHHHhCChhhhhHHHHHHHHHHHHHHHHHhHHHHHhchhHHHHHHHHH-hccCCCH--H------HHH-
Confidence 3 2235555555554333 345666666666666655554 345667777766664 3444442 1 111
Q ss_pred hhHHHHHHHHHHHHHhcCCCchhHHHHHHHHhcCCCCCCCCCCc
Q 004863 223 KCAAKLKTNLKEAVQSRGIALDDYAEIVACICGSDDENPQHGHL 266 (726)
Q Consensus 223 ~CadKLqp~I~q~~ns~G~~L~~YseIv~sIcq~~s~~~~~~~~ 266 (726)
-.++|-+.|.+.|. ++-...++-+|++.-|-++.....||..
T Consensus 143 -~~F~l~~~i~~~~~-~~~~~e~lFd~~~cYFPI~F~pp~~dp~ 184 (262)
T PF14500_consen 143 -LSFKLLKVILQEFD-ISEFAEDLFDVFSCYFPITFRPPPNDPY 184 (262)
T ss_pred -HHHHHHHHHHHhcc-cchhHHHHHHHhhheeeeeeeCCCCCCC
Confidence 13455555555554 2333456777777777787777766653
No 10
>KOG1248 consensus Uncharacterized conserved protein [Function unknown]
Probab=74.64 E-value=72 Score=40.72 Aligned_cols=193 Identities=16% Similarity=0.155 Sum_probs=110.6
Q ss_pred HHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHH
Q 004863 28 VDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFF 107 (726)
Q Consensus 28 tdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIF 107 (726)
+..+++-|.=|.+-|+.+--..+ .+++..|++. ..-.+.-|++.+--|+. ++|-=-++|.+..+..
T Consensus 200 ~t~v~~~L~Ll~~~~~~~p~~li-------~sl~e~lL~i--~~~s~v~v~~~~~q~l~---~lf~~~~~~l~a~~~a-- 265 (1176)
T KOG1248|consen 200 NTTVLRSLMLLRDVLSTFPRPLI-------KSLCEVLLNI--TTESPVLVLLEVLQCLH---SLFKKHPTALAAELNA-- 265 (1176)
T ss_pred HHHHHHHHHHHHHhhccCCHHHH-------HHHHHHHHhh--cccchHHHHHHHHHHHH---HHHhcCCCcchHHHHH--
Confidence 44455555555555555322212 2333333322 22333444444444444 4444444466644432
Q ss_pred HHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCC-chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcc
Q 004863 108 QLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDE 186 (726)
Q Consensus 108 qLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE-~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeE 186 (726)
.++..+..|. ++..--..-++.|.-|.+-..|+-.+|.+ |=.=+..+|..||.+-- ...+.+.....+++..|+.+
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-PSENDDLLTVAWLKVLNEAHDILATLQEEKALQALPRLFSLFFTILE-SLIEELVQAASQSLKEILKE 342 (1176)
T ss_pred -HHHHHHHHhC-CCccchHHHHHHHHHHHHHHHHHHHhCHHHHHHhhhhhhhHHHHHHh-cccHHHHHHHHHHHHHHhcc
Confidence 2333333333 22222366788888888888888888887 66677788888888444 44466777888999999999
Q ss_pred cCCCCHHHHHHHHHHhhccCC-CCCchHHHHHHHHHhhhHHHHHHHHHHHHH
Q 004863 187 SEDVSWDLLRILLASVRKENQ-DVSPTSWKLGEKVFTKCAAKLKTNLKEAVQ 237 (726)
Q Consensus 187 SE~VP~eVLDvIL~~ll~~~k-s~~PaAykLA~~VI~~CadKLqp~I~q~~n 237 (726)
+-.|-..+-..+|..++...- ...+..+++-..++..|+..--|++...+.
T Consensus 343 sv~~~~~~c~~~~~~~l~~kf~~~~~~ilqi~s~~fek~G~~s~~~l~~~L~ 394 (1176)
T KOG1248|consen 343 SVTVIDALCSKQLHSLLDYKFHAVWRFILQILSALFEKCGELSGPELTKTLE 394 (1176)
T ss_pred cCcccHHHHHHHHHHHHcchHHHHHHHHHHHHHHHHHHhhhhcCHHHHHHHH
Confidence 888666666666666664332 234445555566677777665555555554
No 11
>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=73.20 E-value=6.6 Score=43.40 Aligned_cols=118 Identities=15% Similarity=0.209 Sum_probs=59.8
Q ss_pred hhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHH-HHHHHHHHhcccCCCCCcchhhHHHHHHHh-hhhhhheee
Q 004863 67 NDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKE-FFQLAVSAFENLSHASGRYYMKALSILDTV-AKVRSCLLM 144 (726)
Q Consensus 67 ~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKD-IFqLfV~qf~~LsD~ssp~Y~q~~yLLEsL-AeVKS~VLm 144 (726)
..+|.|.+.-||--++.||..|+|. .|+ .+.+ ++..+...| .|.+-..-...+++|..+ ..-+.+
T Consensus 120 ~~ll~~~~~~VRk~A~~~l~~i~~~-~p~------~~~~~~~~~l~~lL---~d~~~~V~~~a~~~l~~i~~~~~~~--- 186 (526)
T PF01602_consen 120 IKLLSDPSPYVRKKAALALLKIYRK-DPD------LVEDELIPKLKQLL---SDKDPSVVSAALSLLSEIKCNDDSY--- 186 (526)
T ss_dssp HHHHHSSSHHHHHHHHHHHHHHHHH-CHC------CHHGGHHHHHHHHT---THSSHHHHHHHHHHHHHHHCTHHHH---
T ss_pred HHHhcCCchHHHHHHHHHHHHHhcc-CHH------HHHHHHHHHHhhhc---cCCcchhHHHHHHHHHHHccCcchh---
Confidence 3568899999999999999999999 233 2222 333333333 444422233344444444 100110
Q ss_pred ccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCC--HHHHHHHHHHhh
Q 004863 145 LDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVS--WDLLRILLASVR 203 (726)
Q Consensus 145 lDLE~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP--~eVLDvIL~~ll 203 (726)
-.++..+|+.+...+. ...+-+...+..++..+.......+ ..++..|+..+.
T Consensus 187 -----~~~~~~~~~~L~~~l~-~~~~~~q~~il~~l~~~~~~~~~~~~~~~~i~~l~~~l~ 241 (526)
T PF01602_consen 187 -----KSLIPKLIRILCQLLS-DPDPWLQIKILRLLRRYAPMEPEDADKNRIIEPLLNLLQ 241 (526)
T ss_dssp -----TTHHHHHHHHHHHHHT-CCSHHHHHHHHHHHTTSTSSSHHHHHHHHHHHHHHHHHH
T ss_pred -----hhhHHHHHHHhhhccc-ccchHHHHHHHHHHHhcccCChhhhhHHHHHHHHHHHhh
Confidence 0345555555554442 3333344444455554444433344 445555555544
No 12
>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=72.64 E-value=46 Score=39.43 Aligned_cols=144 Identities=16% Similarity=0.196 Sum_probs=76.4
Q ss_pred HHHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhcc-cCCchhhHHhhHHHHHhhhh-hhhccCCCcCchhhhHHH
Q 004863 7 EIELEEQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVE-QAPSRSMRDALLPTMKGLIT-NDLLRRSDMDVRLSVTSC 84 (726)
Q Consensus 7 ~~ele~~l~~~G~kLis~piStdELLKRLkkL~~eLs~lD-Q~pvdS~~~SL~pl~k~LVs-~~LLkHKDkdVRayVAcC 84 (726)
++|.|+.+.+.-.+++.. .+.+|. ..|..+..+|.-+. +.++.++ ..|..+..+.+. ..-+...|.+.=--+..|
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-ELFMSLLKSLKIYGGKQTIEGR-QELVDIIEEQADLDQPFDPSDPESIDRLISC 248 (556)
T ss_dssp -HHHHHHHHHHHHHHCTT---HHHH-HHHHHHHHTSGG---GSSHHHH-HHHHHHHHHHHTTTS---SSSHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHh-ccHHHH-HHHHHHHHhCccccccCChHHH-HHHHHHHHHHhccCCCCCCcCHHHHHHHHHH
Confidence 366677777666666642 344433 34445555555432 2334333 335444443221 222455555433334455
Q ss_pred HHHHhhhcCCCCCCChhHHHHHHHHHHHH-hcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHH
Q 004863 85 ISEITRITAPDSPYDDELMKEFFQLAVSA-FENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKV 163 (726)
Q Consensus 85 LaDILRIyAPDAPYtDdqLKDIFqLfV~q-f~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdi 163 (726)
+-.-+=+|.+.+ .-..+|.++..+ |+.|.+... ...+.||..||++-++. .++++.+++..+|+.|...
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 555455554433 457888998888 888888733 67889999999998774 4666888888888888764
No 13
>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=72.58 E-value=2 Score=31.00 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=21.4
Q ss_pred hhccCCCcCchhhhHHHHHHHhhhc
Q 004863 68 DLLRRSDMDVRLSVTSCISEITRIT 92 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILRIy 92 (726)
++|.+.+..||..++-||.+|.+.+
T Consensus 7 ~~l~D~~~~VR~~a~~~l~~i~~~~ 31 (31)
T PF02985_consen 7 QLLNDPSPEVRQAAAECLGAIAEHC 31 (31)
T ss_dssp HHHT-SSHHHHHHHHHHHHHHHHTS
T ss_pred HHcCCCCHHHHHHHHHHHHHHHhhC
Confidence 6788999999999999999998753
No 14
>PTZ00429 beta-adaptin; Provisional
Probab=69.78 E-value=2.2e+02 Score=34.96 Aligned_cols=147 Identities=12% Similarity=0.117 Sum_probs=83.4
Q ss_pred HHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhh
Q 004863 59 PTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKV 138 (726)
Q Consensus 59 pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeV 138 (726)
.++..|. .+|+|.+..|-+-++.||..+.-.. +.+.++.++.-+...+-.|.. ....-+|-+|.+|..+
T Consensus 256 ~il~~l~--~~Lq~~N~AVVl~Aik~il~l~~~~------~~~~~~~~~~rl~~pLv~L~s---s~~eiqyvaLr~I~~i 324 (746)
T PTZ00429 256 TLLTRVL--PRMSHQNPAVVMGAIKVVANLASRC------SQELIERCTVRVNTALLTLSR---RDAETQYIVCKNIHAL 324 (746)
T ss_pred HHHHHHH--HHhcCCCHHHHHHHHHHHHHhcCcC------CHHHHHHHHHHHHHHHHHhhC---CCccHHHHHHHHHHHH
Confidence 3444443 4588999999998888888774211 235566666555444334421 2224556666665433
Q ss_pred hhheeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHH
Q 004863 139 RSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGE 218 (726)
Q Consensus 139 KS~VLmlDLE~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~ 218 (726)
-.. .-.++..-++.||-.. +-|..|...-.+||..+..+... ..||+.|..++. ...+.=.+.|.
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-------FPNLLRTNLDSFYVRY--SDPPFVKLEKLRLLLKLVTPSVA--PEILKELAEYAS----GVDMVFVVEVV 389 (746)
T ss_pred HHH-------CHHHHHHHHHhhhccc--CCcHHHHHHHHHHHHHHcCcccH--HHHHHHHHHHhh----cCCHHHHHHHH
Confidence 211 1356666677787543 34666877778999988887532 345555554443 22222223344
Q ss_pred HHHhhhHHHHHHH
Q 004863 219 KVFTKCAAKLKTN 231 (726)
Q Consensus 219 ~VI~~CadKLqp~ 231 (726)
.-|..|+.++...
T Consensus 390 rAIg~lA~k~~~~ 402 (746)
T PTZ00429 390 RAIASLAIKVDSV 402 (746)
T ss_pred HHHHHHHHhChHH
Confidence 4466777776543
No 15
>KOG1248 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.50 E-value=1.6e+02 Score=37.91 Aligned_cols=157 Identities=15% Similarity=0.129 Sum_probs=93.8
Q ss_pred CCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCC---
Q 004863 72 RSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE--- 148 (726)
Q Consensus 72 HKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE--- 148 (726)
..+.-+|+----||.-|++..- .+..--|+++|...+=.+.+.+...=+..|-+|-.|..+.++ +|..
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 3445577777889999999843 344445566666655455555555556678888888875444 5553
Q ss_pred chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHH-
Q 004863 149 CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAK- 227 (726)
Q Consensus 149 ~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadK- 227 (726)
..+.|.++|..++...-++-...+-..+..|-..+-+....+..+.+.-+|..+---=.+..|.-...|...|..|-.+
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 3567777777777653333334444446666556666777799988888887654322333344444444444444433
Q ss_pred ----HHHHHHHHHH
Q 004863 228 ----LKTNLKEAVQ 237 (726)
Q Consensus 228 ----Lqp~I~q~~n 237 (726)
|++++.+++.
T Consensus 859 pe~~l~~~~~~LL~ 872 (1176)
T KOG1248|consen 859 PEECLSPHLEELLP 872 (1176)
T ss_pred CHHHHhhhHHHHHH
Confidence 4555544443
No 16
>KOG0213 consensus Splicing factor 3b, subunit 1 [RNA processing and modification]
Probab=68.22 E-value=1.3e+02 Score=37.40 Aligned_cols=133 Identities=17% Similarity=0.160 Sum_probs=76.0
Q ss_pred CCCHHHHHHHHHHHHHHH----------HhcccCCc---hhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhh
Q 004863 25 PSPVDEVINLLDKVEHLL----------ANVEQAPS---RSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRI 91 (726)
Q Consensus 25 piStdELLKRLkkL~~eL----------s~lDQ~pv---dS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRI 91 (726)
.+...+|+..|+.++.-= .-+.|-.. .+...-|.++.+- +. ..|.....-||..+|.||+-+.-.
T Consensus 506 algip~llpfLkavc~SkkSwqaRhTgIkivqqIail~Gcsvlphl~~lv~i-i~-~gl~De~qkVR~itAlalsalaea 583 (1172)
T KOG0213|consen 506 ALGIPALLPFLKAVCGSKKSWQARHTGIKIVQQIAILSGCSVLPHLKPLVKI-IE-HGLKDEQQKVRTITALALSALAEA 583 (1172)
T ss_pred HhCcHHHHHHHHHHhccccchhhhchhhHHHHHHHHHhcchhhhhhHHHHHH-HH-HhhcccchhhhhHHHHHHHHHHHh
Confidence 345677888888776432 22222111 1233444444433 22 345556667999999999998866
Q ss_pred cCCCCCCChhHHHHHHHHHHH---------------HhcccCCCCCcchhhHHH---HHHHhhhh------------hhh
Q 004863 92 TAPDSPYDDELMKEFFQLAVS---------------AFENLSHASGRYYMKALS---ILDTVAKV------------RSC 141 (726)
Q Consensus 92 yAPDAPYtDdqLKDIFqLfV~---------------qf~~LsD~ssp~Y~q~~y---LLEsLAeV------------KS~ 141 (726)
- .||.-+++-.||..+-. .+.-|=.-..+.|.-||. ||-.+-+. |.+
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 4 57999999988887532 222222223445555555 54443221 112
Q ss_pred eeeccCC-------chHHHHHHHHHHHH
Q 004863 142 LLMLDLE-------CDKLVVEMFQHFLK 162 (726)
Q Consensus 142 VLmlDLE-------~ddLI~eLFktFFd 162 (726)
--||+-+ -.+++-++|+.|..
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 25888999999886
No 17
>KOG1949 consensus Uncharacterized conserved protein [Function unknown]
Probab=66.81 E-value=1.1e+02 Score=37.81 Aligned_cols=145 Identities=23% Similarity=0.342 Sum_probs=78.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcccCCchhh-H-------------------HhhHHHHHhhhhhhhccCCCcCchhhhH
Q 004863 23 NPPSPVDEVINLLDKVEHLLANVEQAPSRSM-R-------------------DALLPTMKGLITNDLLRRSDMDVRLSVT 82 (726)
Q Consensus 23 s~piStdELLKRLkkL~~eLs~lDQ~pvdS~-~-------------------~SL~pl~k~LVs~~LLkHKDkdVRayVA 82 (726)
.|.....+.=..|++-..+|..+=.++.-+. - +-+..++.- |-..+-...-.+||+.|-
T Consensus 206 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~svf 284 (1005)
T KOG1949|consen 206 DPDLHAEEMDSIIQKQFEELYSLLEDPYPMVRSTAILGVCKITSKFWEMIPPTILIDLLKK-ITDELAFDTSSDVRCSVF 284 (1005)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHH-HHHHhhhccchheehhHh
Confidence 4445556666677777777777655544211 0 111222222 122344445567787777
Q ss_pred HHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHH----HH
Q 004863 83 SCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEM----FQ 158 (726)
Q Consensus 83 cCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eL----Fk 158 (726)
-||-.|+- .| +---+|..++-.+.. .|+++...||... -+|+..+ |-
T Consensus 285 ~gl~~~l~-----np----~sh~~le~~Lpal~~-------------~l~D~se~VRvA~-------vd~ll~ik~vra~ 335 (1005)
T KOG1949|consen 285 KGLPMILD-----NP----LSHPLLEQLLPALRY-------------SLHDNSEKVRVAF-------VDMLLKIKAVRAA 335 (1005)
T ss_pred cCcHHHHc-----Cc----cchhHHHHHHHhcch-------------hhhccchhHHHHH-------HHHHHHHHhhhhh
Confidence 77777762 22 223344444444432 2233333333211 0111111 33
Q ss_pred HHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCC
Q 004863 159 HFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQ 207 (726)
Q Consensus 159 tFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~k 207 (726)
.||+++. |..||+.+=.++-.+.--++..|+..+++-++
T Consensus 336 ~f~~I~~----------~d~~l~~L~~d~~~v~rr~~~li~~s~lP~~k 374 (1005)
T KOG1949|consen 336 KFWKICP----------MDHILVRLETDSRPVSRRLVSLIFNSFLPVNK 374 (1005)
T ss_pred hhhcccc----------HHHHHHHHhccccHHHHHHHHHHHHhhcCCCC
Confidence 4666655 77788877777777888899999999998776
No 18
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.74 E-value=53 Score=40.53 Aligned_cols=171 Identities=19% Similarity=0.275 Sum_probs=105.5
Q ss_pred HHHHHHHHHHHHHHHhcccC-Cc--hhhHHhhHHHHHhhhhhhh--------------------cc---CCCcCchhhhH
Q 004863 29 DEVINLLDKVEHLLANVEQA-PS--RSMRDALLPTMKGLITNDL--------------------LR---RSDMDVRLSVT 82 (726)
Q Consensus 29 dELLKRLkkL~~eLs~lDQ~-pv--dS~~~SL~pl~k~LVs~~L--------------------Lk---HKDkdVRayVA 82 (726)
+-|-+--++|+..|-+||.= ++ -.|...| .+..|+.+.. .+ +-|.|+|+++-
T Consensus 213 dLIHknyrklC~ll~dvdeWgQvvlI~mL~RY--AR~~l~~P~~~~~~~e~n~~~~~~~~~~~~~~~P~~~d~D~~lLL~ 290 (968)
T KOG1060|consen 213 DLIHKNYRKLCRLLPDVDEWGQVVLINMLTRY--ARHQLPDPTVVDSSLEDNGRSCNLKDKYNEIRTPYVNDPDLKLLLQ 290 (968)
T ss_pred HHhhHHHHHHHhhccchhhhhHHHHHHHHHHH--HHhcCCCccccccccccCcccccccccccccCCCcccCccHHHHHH
Confidence 34445566777777766432 11 1343333 3456666633 12 23788887643
Q ss_pred H--------------HHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCC
Q 004863 83 S--------------CISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE 148 (726)
Q Consensus 83 c--------------CLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE 148 (726)
| ..|.++-+.||-. |+.-|-+-+|+.|+. +. .-++-+|.++|.+-.-
T Consensus 291 stkpLl~S~n~sVVmA~aql~y~lAP~~-----~~~~i~kaLvrLLrs--~~-----~vqyvvL~nIa~~s~~------- 351 (968)
T KOG1060|consen 291 STKPLLQSRNPSVVMAVAQLFYHLAPKN-----QVTKIAKALVRLLRS--NR-----EVQYVVLQNIATISIK------- 351 (968)
T ss_pred hccHHHhcCCcHHHHHHHhHHHhhCCHH-----HHHHHHHHHHHHHhc--CC-----cchhhhHHHHHHHHhc-------
Confidence 2 2356677777754 778777777776552 11 2244567777665321
Q ss_pred chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHH
Q 004863 149 CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKL 228 (726)
Q Consensus 149 ~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKL 228 (726)
-..|+...|+.|| |+..-|..+-..=..||+.++.|+. -..+|..+..++...+.. .. ..|..-|.+|+..+
T Consensus 352 ~~~lF~P~lKsFf--v~ssDp~~vk~lKleiLs~La~esn--i~~ILrE~q~YI~s~d~~-fa---a~aV~AiGrCA~~~ 423 (968)
T KOG1060|consen 352 RPTLFEPHLKSFF--VRSSDPTQVKILKLEILSNLANESN--ISEILRELQTYIKSSDRS-FA---AAAVKAIGRCASRI 423 (968)
T ss_pred chhhhhhhhhceE--eecCCHHHHHHHHHHHHHHHhhhcc--HHHHHHHHHHHHhcCchh-HH---HHHHHHHHHHHHhh
Confidence 2467777777887 6777788888788999999999953 355677777777666552 22 24556688888875
No 19
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.45 E-value=1.3e+02 Score=37.34 Aligned_cols=173 Identities=20% Similarity=0.194 Sum_probs=106.2
Q ss_pred HhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhh--HHHHH
Q 004863 55 DALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMK--ALSIL 132 (726)
Q Consensus 55 ~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q--~~yLL 132 (726)
+....++++|+. |--.+++||-.|-|||+-|-- .-+.+|.=.+..|--- +.+|+-.+ -..||
T Consensus 318 ~~~~~i~kaLvr---LLrs~~~vqyvvL~nIa~~s~-----------~~~~lF~P~lKsFfv~--ssDp~~vk~lKleiL 381 (968)
T KOG1060|consen 318 NQVTKIAKALVR---LLRSNREVQYVVLQNIATISI-----------KRPTLFEPHLKSFFVR--SSDPTQVKILKLEIL 381 (968)
T ss_pred HHHHHHHHHHHH---HHhcCCcchhhhHHHHHHHHh-----------cchhhhhhhhhceEee--cCCHHHHHHHHHHHH
Confidence 345677888888 445678899888888887652 2234555555554321 23444333 35677
Q ss_pred HHhhhhhhheeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCch
Q 004863 133 DTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPT 212 (726)
Q Consensus 133 EsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~Pa 212 (726)
.+||.-..+ -++|+.|...|+..+- .+...-..-+..+=.-.-.|+.-+|+-|+.-+..++....-.
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 777765543 3445555555554443 333333333444555556789999999999888887777667
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHHHhc---CCC---------chhHHHHHHHHhcC
Q 004863 213 SWKLGEKVFTKCAAKLKTNLKEAVQSR---GIA---------LDDYAEIVACICGS 256 (726)
Q Consensus 213 AykLA~~VI~~CadKLqp~I~q~~ns~---G~~---------L~~YseIv~sIcq~ 256 (726)
|-..-+.+|++-..+--.+|.+++..+ -++ +.+|.+++--||-+
T Consensus 449 aV~vIk~Llq~~p~~h~~ii~~La~lldti~vp~ARA~IiWLige~~e~vpri~PD 504 (968)
T KOG1060|consen 449 AVVVIKRLLQKDPAEHLEILFQLARLLDTILVPAARAGIIWLIGEYCEIVPRIAPD 504 (968)
T ss_pred HHHHHHHHHhhChHHHHHHHHHHHHHhhhhhhhhhhceeeeeehhhhhhcchhchH
Confidence 767777778777776666777666433 111 35777776655543
No 20
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=60.61 E-value=27 Score=31.94 Aligned_cols=60 Identities=15% Similarity=0.217 Sum_probs=36.9
Q ss_pred hhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhc-ccCCCCCcchhhHHHHHHHh
Q 004863 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFE-NLSHASGRYYMKALSILDTV 135 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~-~LsD~ssp~Y~q~~yLLEsL 135 (726)
..+...|..||-|++-||.+|.+++- +++-.-|.-||..|. .++|++ +.=+..-.+|.+|
T Consensus 34 ~~~~D~d~rVRy~AcEaL~ni~k~~~-------~~~l~~f~~IF~~L~kl~~D~d-~~Vr~~a~~Ld~l 94 (97)
T PF12755_consen 34 KCFDDQDSRVRYYACEALYNISKVAR-------GEILPYFNEIFDALCKLSADPD-ENVRSAAELLDRL 94 (97)
T ss_pred HHcCCCcHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHcCCc-hhHHHHHHHHHHH
Confidence 45777888899999999999999952 333334555555433 334443 3344444555544
No 21
>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=58.44 E-value=1.1e+02 Score=32.69 Aligned_cols=123 Identities=20% Similarity=0.186 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHH--
Q 004863 28 VDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKE-- 105 (726)
Q Consensus 28 tdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKD-- 105 (726)
.++-+..+++++.....-.+.-.+.....+..++-.|++.- ..+.++.-|+-..|.||++. -|+-.+-+..
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 34445666666666555433322322334555555555554 56888888999999999965 3444433333
Q ss_pred ------HHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHHhhc
Q 004863 106 ------FFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRS 166 (726)
Q Consensus 106 ------IFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~ 166 (726)
+|.-|++ .|...+..-..+..++|-.|+.-..-- ......+++..||+.++.
T Consensus 100 ~~~~~~~~~~fl~---ll~~~D~~i~~~a~~iLt~Ll~~~~~~------~~~~~~~~l~~ll~~L~~ 157 (312)
T PF03224_consen 100 KQDDSDPYSPFLK---LLDRNDSFIQLKAAFILTSLLSQGPKR------SEKLVKEALPKLLQWLSS 157 (312)
T ss_dssp H-TTH--HHHHHH---H-S-SSHHHHHHHHHHHHHHHTSTTT--------HHHHHHHHHHHHHHHH-
T ss_pred ccccchhHHHHHH---HhcCCCHHHHHHHHHHHHHHHHcCCcc------ccchHHHHHHHHHHHHHH
Confidence 5666665 333444444566778887776543211 223334566666666664
No 22
>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=57.77 E-value=61 Score=37.98 Aligned_cols=107 Identities=15% Similarity=0.185 Sum_probs=63.3
Q ss_pred HHHHHHHhhhcCCCCCCChh-----HHHHHHHHHHHHhcccC-CCCCcchhhHHHHHHHhhhhhhheeeccCC-chHHHH
Q 004863 82 TSCISEITRITAPDSPYDDE-----LMKEFFQLAVSAFENLS-HASGRYYMKALSILDTVAKVRSCLLMLDLE-CDKLVV 154 (726)
Q Consensus 82 AcCLaDILRIyAPDAPYtDd-----qLKDIFqLfV~qf~~Ls-D~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE-~ddLI~ 154 (726)
=+|+.-+|..+.+ .|+.. +...+|..++..|...= .+-...|-|++ +=-++.. +-+ ++.++.
T Consensus 281 D~im~~lf~~l~~--~~~~~~~~~~~~~~lf~~Ll~~F~~~ILpT~~sr~vQFl--~Fy~~s~-------~~~~~~~Fl~ 349 (563)
T PF05327_consen 281 DSIMDLLFEYLDS--CFTNGSLDEGNADSLFNTLLSIFESHILPTHKSRHVQFL--LFYFCSL-------DPELADAFLS 349 (563)
T ss_dssp HHHHHHHHHHHHH--HS-HHHHHSSTHHHHHHHHHHHHHHTCCCC-S-SSTTHH--HHHHHTT-------SHHHHHHHHH
T ss_pred HHHHHHHHHHHHH--hccCCccchhHHHHHHHHHHHHHHHHccCCCccchHHHH--HHHHHHc-------CchHHHHHHH
Confidence 3566666666555 45543 36669999999998443 23344566652 2222221 222 567777
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHh
Q 004863 155 EMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASV 202 (726)
Q Consensus 155 eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~l 202 (726)
.|++.+| +++.|..++..-..-|+..|.-+..||.+++..+|..|
T Consensus 350 ~L~~~~~---~~~~~~~~R~~A~~YlaSflaRAk~v~~~~v~~~l~~L 394 (563)
T PF05327_consen 350 FLWKIAF---DPNQPPVTRQAAAAYLASFLARAKFVPLSTVRSVLSYL 394 (563)
T ss_dssp HHHHHHH----SSS-HHHHHHHHHHHHHHHHHBTT--HHHHHHHHHHH
T ss_pred HHHHHHh---CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 7777777 35667777777778888888888888887766665543
No 23
>PTZ00429 beta-adaptin; Provisional
Probab=57.66 E-value=3e+02 Score=33.93 Aligned_cols=27 Identities=11% Similarity=0.053 Sum_probs=22.3
Q ss_pred hhccCCCcCchhhhHHHHHHHhhhcCCC
Q 004863 68 DLLRRSDMDVRLSVTSCISEITRITAPD 95 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILRIyAPD 95 (726)
..|.|.+.-||--+|.|+.-|+|+ .|+
T Consensus 147 k~L~D~~pYVRKtAalai~Kly~~-~pe 173 (746)
T PTZ00429 147 RAVADPDPYVRKTAAMGLGKLFHD-DMQ 173 (746)
T ss_pred HHhcCCCHHHHHHHHHHHHHHHhh-Ccc
Confidence 345789999999999999999997 444
No 24
>PF14911 MMS22L_C: S-phase genomic integrity recombination mediator, C-terminal
Probab=56.20 E-value=2.9e+02 Score=31.50 Aligned_cols=122 Identities=15% Similarity=0.262 Sum_probs=78.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCC--hh
Q 004863 24 PPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYD--DE 101 (726)
Q Consensus 24 ~piStdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYt--Dd 101 (726)
+|....-.|..|.+|-..+..-.+ +....-+..+.-.|...-++-|--.-||..+.--|-.|++-+. ..+.. .+
T Consensus 224 p~p~l~~vL~fl~~Ll~~~~~~~~---~~~~~~~~~~lp~lL~c~~~v~e~~~~k~~a~e~l~~mv~~~~-~~~~~~~~~ 299 (373)
T PF14911_consen 224 PPPRLASVLAFLQQLLKRLQRQNE---NQILTLLRLVLPSLLECLMLVNEEPQVKKLATELLQYMVESCQ-VGSSGEPRE 299 (373)
T ss_pred CCCcHHHHHHHHHHHHHhcCcccc---hhHHHHHHHhhHHHHHHHhhcCCCcchhHHHHHHHHHHHHccc-ccCcchHHH
Confidence 566677788888888777652111 1112233444455555556666677799888888888887765 22222 37
Q ss_pred HHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHHhh
Q 004863 102 LMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIR 165 (726)
Q Consensus 102 qLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr 165 (726)
+|..+|.-|+.---. -|-.+||.+|++||... .+||..||-++=..++
T Consensus 300 ~l~s~lrsfvqk~l~------~~t~~~f~~l~~vA~l~----------p~lV~~Lip~i~q~l~ 347 (373)
T PF14911_consen 300 QLTSVLRSFVQKYLA------HYTYQYFQFLEKVAELD----------PQLVISLIPTIRQSLK 347 (373)
T ss_pred HHHHHHHHHHHHHhh------hhhHHHHHHHHHHHHhC----------HHHHHHHHHHHHHHHH
Confidence 888888888876332 34578999999999986 4566666655544433
No 25
>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=55.27 E-value=1.1e+02 Score=36.00 Aligned_cols=100 Identities=11% Similarity=0.205 Sum_probs=57.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhH
Q 004863 23 NPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL 102 (726)
Q Consensus 23 s~piStdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdq 102 (726)
..++++.+|...|+.|..+.+.++.. - ..+..+|++-..+...+.-|++|+.-++.=+. -...-
T Consensus 45 ~d~~~~~~l~~~L~~L~~~Vs~Ld~~-~-------~~LV~ail~~~W~~~~~~~v~~y~~Fl~~Lvs--------a~~~y 108 (563)
T PF05327_consen 45 KDAISVSQLIRWLKALSSCVSLLDSS-C-------KQLVEAILSLNWLGRDEDFVEAYIQFLINLVS--------AQPKY 108 (563)
T ss_dssp TTS--HHHHHHHHHHHHHGGGGG-SC-C-------HHHHHHHHT-TGGGS-HHHHHHHHHHHHHHHH--------H-GGG
T ss_pred cccccHHHHHHHHHHHHHHHHHhhhH-H-------HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHH--------hhHHH
Confidence 45678999999999999999999886 3 35666777777777777777777763321111 02356
Q ss_pred HHHHHHHHHHHhcccCC-----------CCCcchhhHHHHHHHhhhh
Q 004863 103 MKEFFQLAVSAFENLSH-----------ASGRYYMKALSILDTVAKV 138 (726)
Q Consensus 103 LKDIFqLfV~qf~~LsD-----------~ssp~Y~q~~yLLEsLAeV 138 (726)
+..|+..+|..|.--.. ....-|.+.+.+|..|..+
T Consensus 109 l~~vl~~LV~~f~p~~~~~~~~~~~~~~~~~~~~~~vH~~L~~Il~l 155 (563)
T PF05327_consen 109 LSPVLSMLVKNFIPPPSSIAEWPGCPPEKRREIYERVHDALQKILRL 155 (563)
T ss_dssp HHHHHHHHHHGGGS-HHHHHH---------------HHHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCCccccccchhhhhhhhhhHHHHHHHHHHHHHH
Confidence 67777777777652211 1123566777777777654
No 26
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=54.63 E-value=1.2e+02 Score=29.81 Aligned_cols=78 Identities=22% Similarity=0.283 Sum_probs=45.7
Q ss_pred ccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCC-Cc-----chhh----HHHHHHHhhhhh
Q 004863 70 LRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHAS-GR-----YYMK----ALSILDTVAKVR 139 (726)
Q Consensus 70 LkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~s-sp-----~Y~q----~~yLLEsLAeVK 139 (726)
|.-.|.+||.++..||.++++-.-|++ |++.|+..+..|.+.. .+ ...+ |-+||+.+.+
T Consensus 72 l~D~~~~Ir~~A~~~~~e~~~~~~~~~---------i~~~~~e~i~~l~~~~~~~~~~~~~~~~~~~I~~fll~~i~~-- 140 (178)
T PF12717_consen 72 LVDENPEIRSLARSFFSELLKKRNPNI---------IYNNFPELISSLNNCYEHPVYGPLSREKRKKIYKFLLDFIDK-- 140 (178)
T ss_pred HcCCCHHHHHHHHHHHHHHHHhccchH---------HHHHHHHHHHHHhCccccccccccCHHHHHHHHHHHHHHcCc--
Confidence 345567799999999999988765543 3566666666665532 22 2222 3344444432
Q ss_pred hheeeccCCchHHHHHHHHHHHHHh
Q 004863 140 SCLLMLDLECDKLVVEMFQHFLKVI 164 (726)
Q Consensus 140 S~VLmlDLE~ddLI~eLFktFFdiV 164 (726)
|-..+.|+..+++.|+..+
T Consensus 141 ------d~~~~~l~~kl~~~~~~~~ 159 (178)
T PF12717_consen 141 ------DKQKESLVEKLCQRFLNAV 159 (178)
T ss_pred ------HHHHHHHHHHHHHHHHHHc
Confidence 2224566777777776654
No 27
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=52.37 E-value=2e+02 Score=28.67 Aligned_cols=116 Identities=15% Similarity=0.252 Sum_probs=54.9
Q ss_pred CchhhhHHHHHHHhhhcCCCCCCCh--hHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHH
Q 004863 76 DVRLSVTSCISEITRITAPDSPYDD--ELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLV 153 (726)
Q Consensus 76 dVRayVAcCLaDILRIyAPDAPYtD--dqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI 153 (726)
..|.-.--.|-.|++-.+|...+.+ ..|+++...|+.++. |..+.-....+.+|..|+..=.. .-+..+
T Consensus 22 ~~r~~al~~L~~l~~~~~~~~~~~~~~~~l~~~~~~i~~~l~---d~Rs~v~~~A~~~l~~l~~~l~~------~~~~~~ 92 (228)
T PF12348_consen 22 EERVEALQKLRSLIKGNAPEDFPPDFVECLRQLLDAIIKQLS---DLRSKVSKTACQLLSDLARQLGS------HFEPYA 92 (228)
T ss_dssp HHHHHHHHHHHHHHHH-B-----HHHHHHHH---HHHHH-S----HH---HHHHHHHHHHHHHHHHGG------GGHHHH
T ss_pred HHHHHHHHHHHHHHHcCCccccHHHHHHHHHHhHHHHHHHHh---hhHHHHHHHHHHHHHHHHHHHhH------hHHHHH
Confidence 3344444455555555533322222 345555555655554 44466777788888888765111 134566
Q ss_pred HHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHH-HHHHHHHh
Q 004863 154 VEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDL-LRILLASV 202 (726)
Q Consensus 154 ~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eV-LDvIL~~l 202 (726)
..++..+|..+.. ....|.......|..++.-+. .+..+ +..|...+
T Consensus 93 ~~~l~~Ll~~~~~-~~~~i~~~a~~~L~~i~~~~~-~~~~~~~~~l~~~~ 140 (228)
T PF12348_consen 93 DILLPPLLKKLGD-SKKFIREAANNALDAIIESCS-YSPKILLEILSQGL 140 (228)
T ss_dssp HHHHHHHHHGGG----HHHHHHHHHHHHHHHTTS--H--HHHHHHHHHHT
T ss_pred HHHHHHHHHHHcc-ccHHHHHHHHHHHHHHHHHCC-cHHHHHHHHHHHHH
Confidence 7777777775543 234566666777777777544 34566 34443333
No 28
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=51.57 E-value=2.1e+02 Score=27.92 Aligned_cols=101 Identities=17% Similarity=0.172 Sum_probs=60.6
Q ss_pred chHHHHHHHHHHHHHhhcCC---chhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhcc---CCC--CCchHHHHHHHH
Q 004863 149 CDKLVVEMFQHFLKVIRSNH---PHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKE---NQD--VSPTSWKLGEKV 220 (726)
Q Consensus 149 ~ddLI~eLFktFFdiVr~dh---p~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~---~ks--~~PaAykLA~~V 220 (726)
....-++||+.++....+.. +......+..|+...++ ..+|-|.|+-||++. |.+ ..--+|+|-.-+
T Consensus 18 ~~~~A~~iF~~Il~ymgd~~~~~~~~~~~l~~~i~~~~~~-----~~~LrDEiy~QLiKQtt~Np~~~s~~rgW~Ll~l~ 92 (144)
T smart00139 18 LQKEAVKIFKAILKFMGDLPLPKPDSHLDLVQFILQKGLA-----HPELRDEIYCQLIKQLTDNPSRQSEERGWELLYLC 92 (144)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHHHhc-----cHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHH
Confidence 55777889999888765421 12234455667777765 367788888887742 222 222455554433
Q ss_pred H--hhhHHHHHHHHHHHHHhcCCCchhHHHHHHHHhcC
Q 004863 221 F--TKCAAKLKTNLKEAVQSRGIALDDYAEIVACICGS 256 (726)
Q Consensus 221 I--~~CadKLqp~I~q~~ns~G~~L~~YseIv~sIcq~ 256 (726)
+ =-++..|.+||..|+++.+..... ..++..|..
T Consensus 93 ~~~FpPS~~l~~yL~~~l~~~~~~~~~--~~~a~~c~~ 128 (144)
T smart00139 93 TSLFPPSERLLPYLLQFLSRRADQPSE--QGLAKYCLY 128 (144)
T ss_pred HhHcCChHHHHHHHHHHHHhcCCCccH--HHHHHHHHh
Confidence 2 235678999999999865544322 444555654
No 29
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=51.22 E-value=2e+02 Score=30.56 Aligned_cols=166 Identities=10% Similarity=0.124 Sum_probs=87.3
Q ss_pred cCCCcCchhhhHHHHHHHhhhcCCCCCCChh------HHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheee
Q 004863 71 RRSDMDVRLSVTSCISEITRITAPDSPYDDE------LMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLM 144 (726)
Q Consensus 71 kHKDkdVRayVAcCLaDILRIyAPDAPYtDd------qLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLm 144 (726)
...+..||+-+.-||.||+-.|-++..-... ....|.++|...|... + + .-+....|-+++.=..-.+
T Consensus 74 ~~~~~~v~~~al~~l~Dll~~~g~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~-~---~--~~~~~a~EGl~KLlL~~~i 147 (298)
T PF12719_consen 74 QKDDEEVKITALKALFDLLLTHGIDIFDSESDNDESVDSKSLLKILTKFLDSE-N---P--ELQAIAVEGLCKLLLSGRI 147 (298)
T ss_pred HhCCHHHHHHHHHHHHHHHHHcCchhccchhccCccchHhHHHHHHHHHHhcC-C---H--HHHHHHHHHHHHHHhcCCC
Confidence 4468889999999999999999877433322 3566666666666543 1 1 1233334444332111111
Q ss_pred cc--------------CC--chHHHHHHHHHHHHHhhcCC---chhHHHHHHHHHHHHhcccCC-------C-CHHHHHH
Q 004863 145 LD--------------LE--CDKLVVEMFQHFLKVIRSNH---PHFVFAAMETIMTLVIDESED-------V-SWDLLRI 197 (726)
Q Consensus 145 lD--------------LE--~ddLI~eLFktFFdiVr~dh---p~~V~~~M~dIMs~VIeESE~-------V-P~eVLDv 197 (726)
.| =. .+.-+.+....||......+ +..+.......+..+..-.+. | +..+...
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 33566777777777555443 455666666666666554443 2 2233333
Q ss_pred HHHHhhccC-----C-C--CCchHHHHHHHHHhhhH----HH--HHHHHHHHHHhcCCC
Q 004863 198 LLASVRKEN-----Q-D--VSPTSWKLGEKVFTKCA----AK--LKTNLKEAVQSRGIA 242 (726)
Q Consensus 198 IL~~ll~~~-----k-s--~~PaAykLA~~VI~~Ca----dK--Lqp~I~q~~ns~G~~ 242 (726)
++.-.-+.. . . ..+....||.+++..-. .+ ....++++|+.+-++
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 332211111 1 1 13444556655554442 33 667777777766544
No 30
>KOG2171 consensus Karyopherin (importin) beta 3 [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=51.09 E-value=1.7e+02 Score=37.43 Aligned_cols=158 Identities=16% Similarity=0.200 Sum_probs=90.2
Q ss_pred hhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeecc
Q 004863 67 NDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLD 146 (726)
Q Consensus 67 ~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlD 146 (726)
..+++-.-.-||--+|=-|++|.|---|+ +--++.+|+|.+.. .++.+.-.-.++||-+|.++-.-.+.
T Consensus 86 ~~~~~E~~~~vr~k~~dviAeia~~~l~e------~WPell~~L~q~~~---S~~~~~rE~al~il~s~~~~~~~~~~-- 154 (1075)
T KOG2171|consen 86 EIIQSETEPSVRHKLADVIAEIARNDLPE------KWPELLQFLFQSTK---SPNPSLRESALLILSSLPETFGNTLQ-- 154 (1075)
T ss_pred HHHHhccchHHHHHHHHHHHHHHHhcccc------chHHHHHHHHHHhc---CCCcchhHHHHHHHHhhhhhhccccc--
Confidence 45666677789999999999999998887 55667777777654 23334444467888777765432211
Q ss_pred CCchHHHHHHHHHHHHHhhc---------------CC---------chhHHHHHHHHHHHHhcccCC-------------
Q 004863 147 LECDKLVVEMFQHFLKVIRS---------------NH---------PHFVFAAMETIMTLVIDESED------------- 189 (726)
Q Consensus 147 LE~ddLI~eLFktFFdiVr~---------------dh---------p~~V~~~M~dIMs~VIeESE~------------- 189 (726)
+--+-+..||...+.-.+. .+ =..+...|..+|..+|+.-+.
T Consensus 155 -~~~~~l~~lf~q~~~d~s~~vr~~a~rA~~a~~~~~~~~~~~~~~~~~llP~~l~vl~~~i~~~d~~~a~~~l~~l~El 233 (1075)
T KOG2171|consen 155 -PHLDDLLRLFSQTMTDPSSPVRVAAVRALGAFAEYLENNKSEVDKFRDLLPSLLNVLQEVIQDGDDDAAKSALEALIEL 233 (1075)
T ss_pred -hhHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHhccchHHHHHHHHHhHHHHHHhHhhhhccchHHHHHHHHHHHHH
Confidence 1123455555444431110 01 112334455666666665544
Q ss_pred --CCHHHHHHHHHHhh------ccCCCCCchHHHHHHHHHhhhHHHHHHHHHHHHH
Q 004863 190 --VSWDLLRILLASVR------KENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQ 237 (726)
Q Consensus 190 --VP~eVLDvIL~~ll------~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~~n 237 (726)
..+.++...|.+++ -.++.-....+.+|-.+|..++.. .|..+....
T Consensus 234 ~e~~pk~l~~~l~~ii~~~l~Ia~n~~l~~~~R~~ALe~ivs~~e~-Ap~~~k~~~ 288 (1075)
T KOG2171|consen 234 LESEPKLLRPHLSQIIQFSLEIAKNKELENSIRHLALEFLVSLSEY-APAMCKKLA 288 (1075)
T ss_pred HhhchHHHHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHh-hHHHhhhch
Confidence 12222333333322 245666777888888888777766 555554443
No 31
>KOG4256 consensus Kinetochore component [Cell cycle control, cell division, chromosome partitioning]
Probab=49.59 E-value=2.1e+02 Score=36.96 Aligned_cols=94 Identities=17% Similarity=0.245 Sum_probs=49.9
Q ss_pred hhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCC------------------------hhHHHHHHHHHHHHhcccCCCC
Q 004863 66 TNDLLRRSDMDVRLSVTSCISEITRITAPDSPYD------------------------DELMKEFFQLAVSAFENLSHAS 121 (726)
Q Consensus 66 s~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYt------------------------DdqLKDIFqLfV~qf~~LsD~s 121 (726)
...+++.-|. ..+.-|-|+-|++|-||--|-|. .+.++|||.-|+ +
T Consensus 499 KkRlikdeDi-lalI~ad~lkevlgahaiiagf~eafePsrekfnesiW~eFlealhdaddlidIflefi---------s 568 (2209)
T KOG4256|consen 499 KKRLIKDEDI-LALIEADCLKEVLGAHAIIAGFPEAFEPSREKFNESIWDEFLEALHDADDLIDIFLEFI---------S 568 (2209)
T ss_pred HHhhcchHHH-HHHHHHHHHHHHHhhhhhhccCccccCCchhhhcchhHHHHHHhhcccchHHHHHHHHh---------h
Confidence 3445554454 56677999999999887444322 234445544443 1
Q ss_pred CcchhhHHHHHHH-hhhhhhheeeccCC-chHHHHHHHHHHHHHhhcCCch
Q 004863 122 GRYYMKALSILDT-VAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNHPH 170 (726)
Q Consensus 122 sp~Y~q~~yLLEs-LAeVKS~VLmlDLE-~ddLI~eLFktFFdiVr~dhp~ 170 (726)
...|.+.-||.-+ =|.+-+. .+.|.+ --.-+..||+.|.+.++.+.+.
T Consensus 569 danftcAq~i~lRHganfedr-f~~deentisrLEsLfrmfidaiSadiSk 618 (2209)
T KOG4256|consen 569 DANFTCAQVIFLRHGANFEDR-FCDDEENTISRLESLFRMFIDAISADISK 618 (2209)
T ss_pred ccceeehhhHHHhhcCchhhh-hccchhhhHHHHHHHHHHHHHHhhhhHHH
Confidence 2333333333222 1222111 011111 1223889999999999987553
No 32
>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=48.63 E-value=1.3e+02 Score=30.14 Aligned_cols=35 Identities=20% Similarity=0.369 Sum_probs=24.0
Q ss_pred CchhhhHHHHHHHhhhcCCCCCCC--hhHHHHHHHHH
Q 004863 76 DVRLSVTSCISEITRITAPDSPYD--DELMKEFFQLA 110 (726)
Q Consensus 76 dVRayVAcCLaDILRIyAPDAPYt--DdqLKDIFqLf 110 (726)
.||..++-||..|+.-..|.-|+- .++|.+||..-
T Consensus 22 rvR~~A~~~l~~ll~~~~~~~~~ip~~~~L~~i~~~~ 58 (193)
T PF12612_consen 22 RVREVAGKCLQRLLHSQDPTIPHIPHREELQDIFPSE 58 (193)
T ss_pred HHHHHHHHHHHHHhcCCCccccCCCcHHHHHHHcccc
Confidence 399999999999995544432333 36788777643
No 33
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=47.84 E-value=93 Score=38.04 Aligned_cols=112 Identities=17% Similarity=0.298 Sum_probs=74.4
Q ss_pred HHHHHHHhhhhhhheeeccCC-chHHHHHHHHHHHHHhh--------cCC------chh-HHHHHHHHHHHHhccc----
Q 004863 128 ALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIR--------SNH------PHF-VFAAMETIMTLVIDES---- 187 (726)
Q Consensus 128 ~~yLLEsLAeVKS~VLmlDLE-~ddLI~eLFktFFdiVr--------~dh------p~~-V~~~M~dIMs~VIeES---- 187 (726)
-|-|||-|+.|-+.+=.--++ |+ .+|+-+|+++. ..+ |.+ ....-.++++.+++-.
T Consensus 579 LfPLLEClSsia~AL~~gF~P~~~----~Vy~Rc~~il~~t~q~~~~~~~~~~~~~pdkdfiI~sLDL~SGLaegLg~~i 654 (885)
T KOG2023|consen 579 LFPLLECLSSIASALGVGFLPYAQ----PVYQRCFRILQKTLQLLAKVQQDPTVEAPDKDFIIVSLDLLSGLAEGLGSHI 654 (885)
T ss_pred HHHHHHHHHHHHHHHhccccccCH----HHHHHHHHHHHHHHHHHHhccCCccccCCCcceEEEeHHHHhHHHHHhhhch
Confidence 456788888776654433344 44 44555555544 222 222 1112235555554432
Q ss_pred C--CCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHHHHHHhcCCCc
Q 004863 188 E--DVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIAL 243 (726)
Q Consensus 188 E--~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~~ns~G~~L 243 (726)
+ .-+..++++||..+..+-....-.||-|--+++..|.+.+.|++..|+--||..|
T Consensus 655 e~Lva~snl~~lll~C~~D~~peVRQS~FALLGDltk~c~~~v~p~~~~fl~~lg~Nl 712 (885)
T KOG2023|consen 655 EPLVAQSNLLDLLLQCLQDEVPEVRQSAFALLGDLTKACFEHVIPNLADFLPILGANL 712 (885)
T ss_pred HHHhhhccHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHhccchHHHHHHHHhhcC
Confidence 2 2355699999999998888888889999999999999999999999998777654
No 34
>KOG1241 consensus Karyopherin (importin) beta 1 [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=47.63 E-value=2.9e+02 Score=34.40 Aligned_cols=46 Identities=13% Similarity=0.193 Sum_probs=34.1
Q ss_pred hhhccCCC----cCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHH
Q 004863 67 NDLLRRSD----MDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVS 112 (726)
Q Consensus 67 ~~LLkHKD----kdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~ 112 (726)
...|.+.| .+++..++.||.-|+|+.+||+|-..++|-..|--++.
T Consensus 557 ~~~l~~~dr~q~~eLQs~Lc~~Lq~i~rk~~~~~~~~~d~iM~lflri~~ 606 (859)
T KOG1241|consen 557 SQILSLADRAQLNELQSLLCNTLQSIIRKVGSDIREVSDQIMGLFLRIFE 606 (859)
T ss_pred HHhccHhhHHHHHHHHHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHc
Confidence 45666666 46899999999999999999988776665544443333
No 35
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=46.85 E-value=2.5e+02 Score=34.16 Aligned_cols=116 Identities=17% Similarity=0.281 Sum_probs=59.8
Q ss_pred chHHHHHHHHHHHHHhhcC------------------CchhHHHHHHHHHHHHhccc----CCCCHHHHHHHHHHhhccC
Q 004863 149 CDKLVVEMFQHFLKVIRSN------------------HPHFVFAAMETIMTLVIDES----EDVSWDLLRILLASVRKEN 206 (726)
Q Consensus 149 ~ddLI~eLFktFFdiVr~d------------------hp~~V~~~M~dIMs~VIeES----E~VP~eVLDvIL~~ll~~~ 206 (726)
|-+-+.+|.-.||+.+... .-+.+.+.+.++|..||--. +.+...++.++|.-+-+..
T Consensus 531 ~~d~V~~~~a~~~~~~~~kl~~~isv~~q~l~~eD~~~~~elqSN~~~vl~aiir~~~~~ie~v~D~lm~Lf~r~les~~ 610 (858)
T COG5215 531 CPDAVSDILAGFYDYTSKKLDECISVLGQILATEDQLLVEELQSNYIGVLEAIIRTRRRDIEDVEDQLMELFIRILESTK 610 (858)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHhccC
Confidence 3455566666677665531 12345556667777777643 4455555555554444332
Q ss_pred CCC---------CchHHHHHHHHHhhhHHHHHHHHHHHHH-------------------hcCCCchhHHHHHHH-HhcCC
Q 004863 207 QDV---------SPTSWKLGEKVFTKCAAKLKTNLKEAVQ-------------------SRGIALDDYAEIVAC-ICGSD 257 (726)
Q Consensus 207 ks~---------~PaAykLA~~VI~~CadKLqp~I~q~~n-------------------s~G~~L~~YseIv~s-Icq~~ 257 (726)
+.+ ...+-.|.+ =+..-+.++.||+...++ +||..+..|++++.+ +.|+-
T Consensus 611 ~t~~~~dV~~aIsal~~sl~e-~Fe~y~~~fiPyl~~aln~~d~~v~~~avglvgdlantl~~df~~y~d~~ms~LvQ~l 689 (858)
T COG5215 611 PTTAFGDVYTAISALSTSLEE-RFEQYASKFIPYLTRALNCTDRFVLNSAVGLVGDLANTLGTDFNIYADVLMSSLVQCL 689 (858)
T ss_pred CchhhhHHHHHHHHHHHHHHH-HHHHHHhhhhHHHHHHhcchhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHh
Confidence 321 111111221 245556667777665543 345556778777655 44544
Q ss_pred CCCC-CCCC
Q 004863 258 DENP-QHGH 265 (726)
Q Consensus 258 s~~~-~~~~ 265 (726)
++.. .++.
T Consensus 690 ss~~~~R~l 698 (858)
T COG5215 690 SSEATHRDL 698 (858)
T ss_pred cChhhcccc
Confidence 4433 5444
No 36
>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=46.55 E-value=2.2e+02 Score=27.06 Aligned_cols=50 Identities=16% Similarity=0.193 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHHHHhhccCCC-----CCchHHHHHHHHHhhhHHHHH--HHHHHHHH
Q 004863 188 EDVSWDLLRILLASVRKENQD-----VSPTSWKLGEKVFTKCAAKLK--TNLKEAVQ 237 (726)
Q Consensus 188 E~VP~eVLDvIL~~ll~~~ks-----~~PaAykLA~~VI~~CadKLq--p~I~q~~n 237 (726)
..|+..++-.+|..|+..... .......++..++..|+..|. ....+.+.
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 344677888999999999998 55555554
No 37
>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=46.31 E-value=33 Score=26.99 Aligned_cols=47 Identities=19% Similarity=0.274 Sum_probs=31.6
Q ss_pred HHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHH
Q 004863 40 HLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEI 88 (726)
Q Consensus 40 ~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDI 88 (726)
..|..+-+...+.+...+..++..|+ .+|.+.+..||..++-||..|
T Consensus 9 ~aLg~l~~~~~~~~~~~~~~~~~~L~--~~L~d~~~~VR~~A~~aLg~l 55 (55)
T PF13513_consen 9 WALGRLAEGCPELLQPYLPELLPALI--PLLQDDDDSVRAAAAWALGNL 55 (55)
T ss_dssp HHHHCTTTTTHHHHHHHHHHHHHHHH--HHTTSSSHHHHHHHHHHHHCH
T ss_pred HHHhhHhcccHHHHHHHHHHHHHHHH--HHHcCCCHHHHHHHHHHHhcC
Confidence 34555555444444445555666666 677888889999999999765
No 38
>PF14911 MMS22L_C: S-phase genomic integrity recombination mediator, C-terminal
Probab=46.21 E-value=2.4e+02 Score=32.09 Aligned_cols=161 Identities=18% Similarity=0.248 Sum_probs=82.2
Q ss_pred hHHHHHHHHHHHHhcccCCCCCcchhhHHH-HHH----Hhhhhhhheeecc-----CCchHHHHHHHHHHHHHhh-----
Q 004863 101 ELMKEFFQLAVSAFENLSHASGRYYMKALS-ILD----TVAKVRSCLLMLD-----LECDKLVVEMFQHFLKVIR----- 165 (726)
Q Consensus 101 dqLKDIFqLfV~qf~~LsD~ssp~Y~q~~y-LLE----sLAeVKS~VLmlD-----LE~ddLI~eLFktFFdiVr----- 165 (726)
.-++++|-+|+.-+..+.-..++|-.+..- |.. .+.--.+....+- .-...-..++.+.+++.++
T Consensus 139 ~ai~k~lpl~lqGl~~~~~~~dayL~~~l~~ii~~y~~~Fl~~~~~~~~~~l~~~~~~~~~~~~~l~~~il~~i~~~fl~ 218 (373)
T PF14911_consen 139 QAIRKSLPLFLQGLGRLSQRQDAYLNQQLRNIIQQYLPRFLPASPSKLVARLSTLLSAFTPRNEELRKFILQVIRSNFLE 218 (373)
T ss_pred HHHHHHHHHHHHHHHhcccccChHHHHHHHHHHHHHHhHhccCCCccccccccccccchhhhhhHHHHHHHHHHHHHHhc
Confidence 568888989888888777777777665421 111 1111111111111 1011122233333333333
Q ss_pred --cCCchhHHHHHHHHHHHHhcc----cCCCCHHHHHHHH----HHhhccC--CCCCchHHHHHHHHHhhhH--------
Q 004863 166 --SNHPHFVFAAMETIMTLVIDE----SEDVSWDLLRILL----ASVRKEN--QDVSPTSWKLGEKVFTKCA-------- 225 (726)
Q Consensus 166 --~dhp~~V~~~M~dIMs~VIeE----SE~VP~eVLDvIL----~~ll~~~--ks~~PaAykLA~~VI~~Ca-------- 225 (726)
+.-|..-......++.+++.+ ....-..+++.+| ..++--+ ...-..|-.+-..++++|.
T Consensus 219 ~~~~~p~p~l~~vL~fl~~Ll~~~~~~~~~~~~~~~~~~lp~lL~c~~~v~e~~~~k~~a~e~l~~mv~~~~~~~~~~~~ 298 (373)
T PF14911_consen 219 FKGSAPPPRLASVLAFLQQLLKRLQRQNENQILTLLRLVLPSLLECLMLVNEEPQVKKLATELLQYMVESCQVGSSGEPR 298 (373)
T ss_pred CCCCCCCCcHHHHHHHHHHHHHhcCcccchhHHHHHHHhhHHHHHHHhhcCCCcchhHHHHHHHHHHHHcccccCcchHH
Confidence 233333334455555666666 2333333333333 3322222 2222334444455566776
Q ss_pred HHHHHHHHHHHHhcCCCch-hHHHHHHHHhcCCCCCC
Q 004863 226 AKLKTNLKEAVQSRGIALD-DYAEIVACICGSDDENP 261 (726)
Q Consensus 226 dKLqp~I~q~~ns~G~~L~-~YseIv~sIcq~~s~~~ 261 (726)
+.|+..+++|...-+..-+ .|..++.+|...+.+..
T Consensus 299 ~~l~s~lrsfvqk~l~~~t~~~f~~l~~vA~l~p~lV 335 (373)
T PF14911_consen 299 EQLTSVLRSFVQKYLAHYTYQYFQFLEKVAELDPQLV 335 (373)
T ss_pred HHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCHHHH
Confidence 5578888888865555555 68899999988877654
No 39
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=46.04 E-value=91 Score=33.32 Aligned_cols=35 Identities=23% Similarity=0.389 Sum_probs=23.4
Q ss_pred HhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhh
Q 004863 55 DALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRI 91 (726)
Q Consensus 55 ~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRI 91 (726)
..|..+..-|-+ .+.+.+.+++..+..||+.+||+
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 455555555554 77888999999999999999987
No 40
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=44.32 E-value=3.2e+02 Score=26.88 Aligned_cols=138 Identities=15% Similarity=0.268 Sum_probs=74.8
Q ss_pred CcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhh-----hhhhhe---eec
Q 004863 74 DMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVA-----KVRSCL---LML 145 (726)
Q Consensus 74 DkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLA-----eVKS~V---Lml 145 (726)
|+.||.-+..||+|+.--| |. +-+.-+..+| ..|.|++-.-=.+.+.+|..|. .+|.-+ ++.
T Consensus 1 ~~~vR~n~i~~l~DL~~r~-~~--~ve~~~~~l~-------~~L~D~~~~VR~~al~~Ls~Li~~d~ik~k~~l~~~~l~ 70 (178)
T PF12717_consen 1 DPSVRNNAIIALGDLCIRY-PN--LVEPYLPNLY-------KCLRDEDPLVRKTALLVLSHLILEDMIKVKGQLFSRILK 70 (178)
T ss_pred CHHHHHHHHHHHHHHHHhC-cH--HHHhHHHHHH-------HHHCCCCHHHHHHHHHHHHHHHHcCceeehhhhhHHHHH
Confidence 4679999999999999776 21 1122233333 3455654333344555555552 222211 111
Q ss_pred c-CCchHHHHHHHHHHHHHhhcC-CchhHHHHHHHHHHHHhcccC-----CCCHH----HHHHHHHHhhccCCCCCchHH
Q 004863 146 D-LECDKLVVEMFQHFLKVIRSN-HPHFVFAAMETIMTLVIDESE-----DVSWD----LLRILLASVRKENQDVSPTSW 214 (726)
Q Consensus 146 D-LE~ddLI~eLFktFFdiVr~d-hp~~V~~~M~dIMs~VIeESE-----~VP~e----VLDvIL~~ll~~~ks~~PaAy 214 (726)
- .|.+.-|..+=..||.-+... .|..+...+.+++..+-...+ .+..+ +++.||..+-+ .....
T Consensus 71 ~l~D~~~~Ir~~A~~~~~e~~~~~~~~~i~~~~~e~i~~l~~~~~~~~~~~~~~~~~~~I~~fll~~i~~-----d~~~~ 145 (178)
T PF12717_consen 71 LLVDENPEIRSLARSFFSELLKKRNPNIIYNNFPELISSLNNCYEHPVYGPLSREKRKKIYKFLLDFIDK-----DKQKE 145 (178)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHhCccccccccccCHHHHHHHHHHHHHHcCc-----HHHHH
Confidence 1 256677777778888755544 677777788887776555322 24443 44444444432 12344
Q ss_pred HHHHHHHhhhHH
Q 004863 215 KLGEKVFTKCAA 226 (726)
Q Consensus 215 kLA~~VI~~Cad 226 (726)
.|.+++|.....
T Consensus 146 ~l~~kl~~~~~~ 157 (178)
T PF12717_consen 146 SLVEKLCQRFLN 157 (178)
T ss_pred HHHHHHHHHHHH
Confidence 555555554443
No 41
>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=43.81 E-value=5.1e+02 Score=29.01 Aligned_cols=162 Identities=14% Similarity=0.154 Sum_probs=81.9
Q ss_pred CcCchhhhHHHHHHHhhhcCCCCCCChh-HHHH--HHHHHHHHhcccCCCCCcchhhHHHHHHHhhhh-hhheeeccCC-
Q 004863 74 DMDVRLSVTSCISEITRITAPDSPYDDE-LMKE--FFQLAVSAFENLSHASGRYYMKALSILDTVAKV-RSCLLMLDLE- 148 (726)
Q Consensus 74 DkdVRayVAcCLaDILRIyAPDAPYtDd-qLKD--IFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeV-KS~VLmlDLE- 148 (726)
+.+.-..+.-||..++.-..-+.++.+. ...+ |...|++.+-...+.+.. ....+|+.++.+ +.++-.++.+
T Consensus 56 ~~~~~~~il~tl~~~~~~~~~~~~~~~~~~y~~~~lv~~l~~~~~~~~~~~~~---~~~~~L~~~~~l~~~iv~~l~~~~ 132 (415)
T PF12460_consen 56 SSDYCHAILSTLQSLLEKKQEDKQFEDNSWYFHRILVPRLFELALQASDQSSD---LDDRVLELLSRLINLIVRSLSPEK 132 (415)
T ss_pred ChHHHHHHHHHHHHHHHhcccccccchHHHHHHhHHHHHHHHHHHhhcccccc---cchHHHHHHHHHHHHHHHhCCHHH
Confidence 3334444455566666555555534432 2222 444444443222222222 566778888887 7788788886
Q ss_pred chHHHHHHHHHHH----------HHhhc-CCchhHHHHHHHHHHHHhcccCCCC--HHHHHHHHHHhhccC-CCCCchHH
Q 004863 149 CDKLVVEMFQHFL----------KVIRS-NHPHFVFAAMETIMTLVIDESEDVS--WDLLRILLASVRKEN-QDVSPTSW 214 (726)
Q Consensus 149 ~ddLI~eLFktFF----------diVr~-dhp~~V~~~M~dIMs~VIeESE~VP--~eVLDvIL~~ll~~~-ks~~PaAy 214 (726)
.+.++.++|..|+ ..... ..+......+..|+..+=-+. .+| .++++-++.-..... ......+.
T Consensus 133 q~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~l~~~il~~l~~~~-~~~~~~~ll~~l~~~~~~~~~~~~~~~~~ 211 (415)
T PF12460_consen 133 QQEILDELYSLFLSPKSFSPFQPSSSTISEQQSRLVILFSAILCSLRKDV-SLPDLEELLQSLLNLALSSEDEFSRLAAL 211 (415)
T ss_pred HHHHHHHHHHHHccccccCCCCccccccccccccHHHHHHHHHHcCCccc-CccCHHHHHHHHHHHHHcCCChHHHHHHH
Confidence 7788999999998 11100 133334333344443322222 233 234444444433322 22334455
Q ss_pred HHHHHHHhhh--HHHHHHHHHHHHHhc
Q 004863 215 KLGEKVFTKC--AAKLKTNLKEAVQSR 239 (726)
Q Consensus 215 kLA~~VI~~C--adKLqp~I~q~~ns~ 239 (726)
++..-+++++ .+.+..++..+++..
T Consensus 212 ~~la~LvNK~~~~~~l~~~l~~~~~~~ 238 (415)
T PF12460_consen 212 QLLASLVNKWPDDDDLDEFLDSLLQSI 238 (415)
T ss_pred HHHHHHHcCCCChhhHHHHHHHHHhhh
Confidence 5666677774 344666666665443
No 42
>KOG1993 consensus Nuclear transport receptor KAP120 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=43.11 E-value=87 Score=38.88 Aligned_cols=121 Identities=12% Similarity=0.195 Sum_probs=74.7
Q ss_pred HhhhhhhheeeccC-C-----chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhccc-CCCCHHHHHHHHHHh--hc
Q 004863 134 TVAKVRSCLLMLDL-E-----CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDES-EDVSWDLLRILLASV--RK 204 (726)
Q Consensus 134 sLAeVKS~VLmlDL-E-----~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeES-E~VP~eVLDvIL~~l--l~ 204 (726)
.|+.++++-+|+|= + -.+++..||-.+|.+...--.-.-...+...|+.+|+-. +.|. +.+-.|++.| +.
T Consensus 544 ~Ltt~~tlkl~vDD~nF~~dsFlp~lenlf~~lfkll~~~~e~Dtk~~VL~~ls~lI~r~~e~I~-P~~~~ivq~lp~LW 622 (978)
T KOG1993|consen 544 RLTTARTLKLVVDDWNFSEDSFLPYLENLFVLLFKLLKAVEECDTKTSVLNLLSTLIERVSEHIA-PYASTIVQYLPLLW 622 (978)
T ss_pred ehHHHHHHHHhhhhccCChhhhhhhHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHhhh-HHHHHHHHHHHHHH
Confidence 35666666655553 3 135667788888776654333333445677777777754 4464 5555555543 33
Q ss_pred cCCCCCchHHHHHHHHHhhhHHHHHHHHHHHHHhcCCCchhHHHHHHHHhcCCCCCCCCCCc
Q 004863 205 ENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIALDDYAEIVACICGSDDENPQHGHL 266 (726)
Q Consensus 205 ~~ks~~PaAykLA~~VI~~CadKLqp~I~q~~ns~G~~L~~YseIv~sIcq~~s~~~~~~~~ 266 (726)
+.....|. |+..| =..+.+|++++|-.-..++.++|.|.+-..|--+-.|+
T Consensus 623 e~s~~e~l---Lr~al--------L~~L~~lV~alg~qS~~~~~fL~pVIel~~D~~sP~hv 673 (978)
T KOG1993|consen 623 EESEEEPL---LRCAL--------LATLRNLVNALGAQSFEFYPFLYPVIELSTDPSSPEHV 673 (978)
T ss_pred hhhccCcH---HHHHH--------HHHHHHHHHHhccCCccchHHHHHHHHHhcCCCCCcee
Confidence 44444442 33333 34578999999998888999999999866665555555
No 43
>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=42.51 E-value=3.9e+02 Score=27.96 Aligned_cols=125 Identities=12% Similarity=0.125 Sum_probs=67.3
Q ss_pred hhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHH
Q 004863 51 RSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALS 130 (726)
Q Consensus 51 dS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~y 130 (726)
..+++.+..+...+++. +.+.+.|||+.+.=.|--+.=++.|..++++..... ..--.|+.
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 36788888888888877 888899999998888888888888888776543000 00001211
Q ss_pred HHHHhhhhhhheeeccC--CchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHH
Q 004863 131 ILDTVAKVRSCLLMLDL--ECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLAS 201 (726)
Q Consensus 131 LLEsLAeVKS~VLmlDL--E~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ 201 (726)
|..-..++-.-.| |+..|+..|+..|+... .+..+...+.+-|..|+--=...-.-||.+|+..
T Consensus 96 ----vp~~Hp~l~~~~Le~Ea~~lL~~Ll~~l~~~~---i~~~~~~a~insL~~Iak~RP~~~~~Il~~ll~~ 161 (239)
T PF11935_consen 96 ----VPPNHPLLNPQQLEAEANGLLDRLLDVLQSPH---ISSPLLTAIINSLSNIAKQRPQFMSRILPALLSF 161 (239)
T ss_dssp ----S-TT-SSS-HHHHHHHHHHHHHHHHHHHC-TT-----HHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHH
T ss_pred ----cCCCCCcCCHHHHHHHHHHHHHHHHHHHhhcc---cchHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhc
Confidence 1111222222233 35666666666665422 3555555555555555555444545555555544
No 44
>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=40.96 E-value=74 Score=27.30 Aligned_cols=66 Identities=17% Similarity=0.119 Sum_probs=41.3
Q ss_pred hhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHH-HHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhh
Q 004863 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMK-EFFQLAVSAFENLSHASGRYYMKALSILDTVAKVR 139 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLK-DIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVK 139 (726)
.+|.+.+..+|..++.||..|..-. +++...-+. +++..++..|. +.+........+.|.+|+...
T Consensus 14 ~~l~~~~~~~~~~a~~~l~~l~~~~---~~~~~~~~~~~~i~~l~~~l~---~~~~~v~~~a~~~L~~l~~~~ 80 (120)
T cd00020 14 SLLSSSDENVQREAAWALSNLSAGN---NDNIQAVVEAGGLPALVQLLK---SEDEEVVKAALWALRNLAAGP 80 (120)
T ss_pred HHHHcCCHHHHHHHHHHHHHHhcCC---HHHHHHHHHCCChHHHHHHHh---CCCHHHHHHHHHHHHHHccCc
Confidence 3667778899999999999887652 222223333 56666666553 344445556677777776543
No 45
>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=40.92 E-value=5.2e+02 Score=28.27 Aligned_cols=82 Identities=17% Similarity=0.266 Sum_probs=48.3
Q ss_pred CHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcC------chhhhHHHHHHHhhhcCCCCCCCh
Q 004863 27 PVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMD------VRLSVTSCISEITRITAPDSPYDD 100 (726)
Q Consensus 27 StdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkd------VRayVAcCLaDILRIyAPDAPYtD 100 (726)
-..|.|..+..+...|...-++...-+.+++-..-..+++..+..-++-- +|+++..|..=++.+ +.
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 35678888888888888766665655566666666677777666544422 344555565555554 44
Q ss_pred hHHHHHHHHHHHHhc
Q 004863 101 ELMKEFFQLAVSAFE 115 (726)
Q Consensus 101 dqLKDIFqLfV~qf~ 115 (726)
++.+.++..++-.+.
T Consensus 161 ~~f~~~idsi~wg~k 175 (319)
T PF08767_consen 161 EQFKLVIDSIVWGFK 175 (319)
T ss_dssp HHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHhC
Confidence 555555555544443
No 46
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=39.78 E-value=2e+02 Score=36.82 Aligned_cols=75 Identities=12% Similarity=0.089 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHhhcCCc--hhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCC-------c----hHHHHH
Q 004863 151 KLVVEMFQHFLKVIRSNHP--HFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVS-------P----TSWKLG 217 (726)
Q Consensus 151 dLI~eLFktFFdiVr~dhp--~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~-------P----aAykLA 217 (726)
.+|..+|..++-.+--+++ ..=+.++.-.|+++.. .+.|...|+=-+|.+++.-...++ | --.+|+
T Consensus 703 ~VID~vlE~Ir~glEin~~~~nQrriA~aryL~ELyn-femvds~vIl~tLy~~i~~g~~~~~~~~~ldppddlFRirlV 781 (1128)
T KOG2051|consen 703 HVIDHVLEDIRPGLEINDYVSNQRRIALARYLGELYN-FEMVDSDVILNTLYHLISLGHFENLTPSALDPPDDLFRIRLV 781 (1128)
T ss_pred hhHHHHHHHHHhhhhcCcHHHHHHHHHHHHHHHHHhh-hhhhhHHHHHHHHHHHhcccccCCCCcccCCChHHHHHHHHH
Confidence 4566666666665543332 2233344444444332 345666666666666664322221 1 235788
Q ss_pred HHHHhhhHH
Q 004863 218 EKVFTKCAA 226 (726)
Q Consensus 218 ~~VI~~Cad 226 (726)
..|+.+|+.
T Consensus 782 ~~lL~tc~~ 790 (1128)
T KOG2051|consen 782 CMLLQTCGP 790 (1128)
T ss_pred HHHHHHccc
Confidence 889999987
No 47
>KOG1949 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.50 E-value=2.4e+02 Score=35.05 Aligned_cols=152 Identities=18% Similarity=0.246 Sum_probs=83.1
Q ss_pred hhhhhhh---ccCCCcCchhhhHHHHHHHhhhcCCCCCCC--hhHHHHHHHHHHHHhc------------ccCCCCCcc-
Q 004863 63 GLITNDL---LRRSDMDVRLSVTSCISEITRITAPDSPYD--DELMKEFFQLAVSAFE------------NLSHASGRY- 124 (726)
Q Consensus 63 ~LVs~~L---LkHKDkdVRayVAcCLaDILRIyAPDAPYt--DdqLKDIFqLfV~qf~------------~LsD~ssp~- 124 (726)
-|.++.| |+-.|..||.-+|.-+.|.+=|--||+--. |..|..=|.++-+.|+ |+...-+-|
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 3444555 466899999999999999999999998322 2233333333322221 000000000
Q ss_pred --------hhhHHHHHHH----------hhhhhhheeeccCC-chHHHHHHHHHHHHHhhc---CCchhHHHHHHHHHHH
Q 004863 125 --------YMKALSILDT----------VAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRS---NHPHFVFAAMETIMTL 182 (726)
Q Consensus 125 --------Y~q~~yLLEs----------LAeVKS~VLmlDLE-~ddLI~eLFktFFdiVr~---dhp~~V~~~M~dIMs~ 182 (726)
-.--.||... ++.++.+..|+|-+ |.. +|+..+-.++. +.++.|+..|.+||..
T Consensus 253 e~iP~~i~~~ll~kI~d~~a~dt~s~VR~svf~gl~~~l~np~sh~----~le~~Lpal~~~l~D~se~VRvA~vd~ll~ 328 (1005)
T KOG1949|consen 253 EMIPPTILIDLLKKITDELAFDTSSDVRCSVFKGLPMILDNPLSHP----LLEQLLPALRYSLHDNSEKVRVAFVDMLLK 328 (1005)
T ss_pred HHcCHHHHHHHHHHHHHHhhhccchheehhHhcCcHHHHcCccchh----HHHHHHHhcchhhhccchhHHHHHHHHHHH
Confidence 0111233332 23344455566665 544 44444554443 6678899999999876
Q ss_pred Hhc-----ccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhh
Q 004863 183 VID-----ESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKC 224 (726)
Q Consensus 183 VIe-----ESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~C 224 (726)
|=+ =-.-+|. |.||..|-. ...|.++.++.-|+..|
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 533 2234554 455555543 34466777776665544
No 48
>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=39.33 E-value=79 Score=27.79 Aligned_cols=59 Identities=20% Similarity=0.306 Sum_probs=39.7
Q ss_pred chhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHH-HHHHHhhhhh
Q 004863 77 VRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKAL-SILDTVAKVR 139 (726)
Q Consensus 77 VRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~-yLLEsLAeVK 139 (726)
.|.++|+.++|++.-+.|+.- .-..+|.++...|..|....++...-.. ++|.-+...-
T Consensus 5 ~~~~~a~~~~El~~~~~~~~~----~~~~lf~ll~~~L~~L~~~~~~~~~~~~~f~l~ll~~~G 64 (118)
T PF02565_consen 5 ERLAYASYIAELLDRLLPEGE----PNPELFDLLLAALDALEEGEDPWLLLLIQFELKLLKLLG 64 (118)
T ss_dssp HHHHHHHHHHHHHHHHS-CTS------HHHHHHHHHHHHHHHCSSSHCHHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHHHHHcccCC----ChHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHcC
Confidence 578889999999988776531 1246999999999999876655444444 5555555443
No 49
>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=38.98 E-value=2.2e+02 Score=29.60 Aligned_cols=163 Identities=14% Similarity=0.140 Sum_probs=86.6
Q ss_pred HHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHH
Q 004863 33 NLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVS 112 (726)
Q Consensus 33 KRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~ 112 (726)
+-|+.|..+|+.-.+... ...+..+-+.|-= ++-..--+-||--+|..|++|++.+.++. ..--=++-.|.-+.+
T Consensus 19 ~al~~l~~~l~~~~~~~~---~~~~~kLWKGLfy-~mWmsDkpl~Q~~la~~la~l~~~~~~~~-~~~~f~~~f~~tm~r 93 (217)
T PF05997_consen 19 RALKSLRKWLSKRSQLLT---ELDMLKLWKGLFY-CMWMSDKPLVQEELAEELASLIHSFPSEK-AALLFLKAFWETMRR 93 (217)
T ss_pred HHHHHHHHHHHhccccCC---HHHHHHHHHHHHH-HHHhcCCchhHHHHHHHHHHHHHhhcChH-HHHHHHHHHHHHHHH
Confidence 345677777776655421 1234455555432 22223335688899999999999987664 011233444444444
Q ss_pred HhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCC-chHHHHHHHHHHHHHh-hc-C-CchhHHHHHHHHHHHHhccc-
Q 004863 113 AFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVI-RS-N-HPHFVFAAMETIMTLVIDES- 187 (726)
Q Consensus 113 qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE-~ddLI~eLFktFFdiV-r~-d-hp~~V~~~M~dIMs~VIeES- 187 (726)
.+.+|.. +=-.-||+|-+.---.++.++-.-. ..+++.++.+.|...+ .. + .|.-+..++.+|...=++..
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 EWDGIDR----LRMDKFLMLVRRFLRQSFRFLKKNGWDKELVEEFNEILSETPLNPNDQVPNGLRYHFADIFLDELEKVG 169 (217)
T ss_pred HHcccHH----HHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHccCCCcCCCchhHHHHHHHHHHHHHHHHh
Confidence 5555542 1122366666655555666555554 4455555555555532 11 1 45556666666644333221
Q ss_pred ---------CCCCHHHHHHHHHHhhc
Q 004863 188 ---------EDVSWDLLRILLASVRK 204 (726)
Q Consensus 188 ---------E~VP~eVLDvIL~~ll~ 204 (726)
+.++.+.+..+|..|..
T Consensus 170 ~~~~~~~e~~~~~~~~~~~ll~PF~~ 195 (217)
T PF05997_consen 170 GSESEDEEEENLPAEPLLLLLEPFVK 195 (217)
T ss_pred cccccchhcccCCHHHHHHHHHHHHH
Confidence 12566666666666553
No 50
>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=38.93 E-value=1.8e+02 Score=32.04 Aligned_cols=41 Identities=17% Similarity=0.457 Sum_probs=32.0
Q ss_pred CCChhHHHHHHH-HHHHHhcccCCCCCcchhhHHHHHHHhhhh
Q 004863 97 PYDDELMKEFFQ-LAVSAFENLSHASGRYYMKALSILDTVAKV 138 (726)
Q Consensus 97 PYtDdqLKDIFq-LfV~qf~~LsD~ssp~Y~q~~yLLEsLAeV 138 (726)
|-.. .|+-++. ||+.-|+||.|.++.+|.+-+.||+.+...
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 4455 6666666 445559999999999999999999999754
No 51
>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=38.52 E-value=5.4e+02 Score=27.79 Aligned_cols=96 Identities=11% Similarity=0.126 Sum_probs=53.4
Q ss_pred CCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHH
Q 004863 26 SPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKE 105 (726)
Q Consensus 26 iStdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKD 105 (726)
.+-..|...|..+...|..++.+.++ .+.+.++. =|..+...||-....|+.++|+ .+...-.-..+..
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 1111111245555
Q ss_pred HHHHHHHHhccc-CC-----CCCcchhhHHHHH
Q 004863 106 FFQLAVSAFENL-SH-----ASGRYYMKALSIL 132 (726)
Q Consensus 106 IFqLfV~qf~~L-sD-----~ssp~Y~q~~yLL 132 (726)
|.-.++..|..- .. ..+....-|++++
T Consensus 104 ~~~~L~~~~~~~~~~p~~~~~~~~~~~a~~~l~ 136 (339)
T PF12074_consen 104 FLPKLLQSLKEASANPLQSAQNGELVGAYVLLA 136 (339)
T ss_pred HHHHHHHHHHHHHhCCCCccccccHHHHHHHHH
Confidence 655556555421 22 2234555666666
No 52
>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=38.42 E-value=1.4e+02 Score=34.12 Aligned_cols=41 Identities=20% Similarity=0.199 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhcCCCch-hHHHHHHHHhcCCCCCCCCCCc
Q 004863 226 AKLKTNLKEAVQSRGIALD-DYAEIVACICGSDDENPQHGHL 266 (726)
Q Consensus 226 dKLqp~I~q~~ns~G~~L~-~YseIv~sIcq~~s~~~~~~~~ 266 (726)
+.|.-.|..+.++....+. -.++.++.+|..+.+..-..+.
T Consensus 307 ~tL~~rLlrLmt~~~~~~k~~vaellf~Lc~~d~~~~v~~~G 348 (446)
T PF10165_consen 307 DTLRSRLLRLMTSPDPQLKDAVAELLFVLCKEDASRFVKYVG 348 (446)
T ss_pred cchHHHHHHHhCCCCchHHHHHHHHHHHHHhhhHHHHHHHcC
Confidence 3455556666654444454 5699999999988776644443
No 53
>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=38.17 E-value=4.2e+02 Score=31.52 Aligned_cols=124 Identities=19% Similarity=0.273 Sum_probs=69.5
Q ss_pred CCHHHHHHHHHHHHHHHHhcccCCchhh-HHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHH
Q 004863 26 SPVDEVINLLDKVEHLLANVEQAPSRSM-RDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMK 104 (726)
Q Consensus 26 iStdELLKRLkkL~~eLs~lDQ~pvdS~-~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLK 104 (726)
.+.++--..|..|++.|.+ .|+-+..+ ++-..++...+....+ ..+.-.+--||-+|-|.+-| |
T Consensus 36 ~~~~~~~~~l~~L~~~L~~-n~~l~~~igWDL~~~l~~~~~~~~~-----~~~~~~~~~~l~~la~~gnP---------k 100 (633)
T PF08568_consen 36 YSNEEKEEFLPELLEILQD-NQELTYEIGWDLPKLLLPFLPSSEI-----SPCVDCCMKCLEELARLGNP---------K 100 (633)
T ss_pred cchhhHHHHHHHHHHHHhh-CHHHHHHccccCHHHHHHHhhhhhc-----chHHHHHHHHHHHHHHhCCH---------H
Confidence 4445556666677776643 23322211 2323344433333333 44566677788888888766 6
Q ss_pred HHHHHHHHHhcccCCCC---------------CcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHHhhcCCc
Q 004863 105 EFFQLAVSAFENLSHAS---------------GRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHP 169 (726)
Q Consensus 105 DIFqLfV~qf~~LsD~s---------------sp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~dhp 169 (726)
++|--+..++..|...+ ...|.-.|| ++.+|.++.+.-+...+|
T Consensus 101 E~~l~~~E~l~~l~~ed~~~~~~~~~~~~~~~~~~~~~kf~---------------------~Ll~~l~~~l~ri~t~~p 159 (633)
T PF08568_consen 101 ELLLKVCELLEELSPEDEDDEEDDESIERNQIEEPFDLKFY---------------------CLLELLQIVLKRIQTKYP 159 (633)
T ss_pred HHHHHHHHHHHhcccccccccccccccccccchhhhHHHHH---------------------HHHHHHHHHHHHhcccch
Confidence 77777777777766311 001111111 256777777777777888
Q ss_pred hh-HHHHHHHHHHHHhc
Q 004863 170 HF-VFAAMETIMTLVID 185 (726)
Q Consensus 170 ~~-V~~~M~dIMs~VIe 185 (726)
.. +..++..|+..+=.
T Consensus 160 s~Fl~~~l~~i~~~~~~ 176 (633)
T PF08568_consen 160 SRFLAMALSAILNFLKN 176 (633)
T ss_pred hHHHHHHHHHHHHHHHh
Confidence 77 66666666665543
No 54
>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=37.75 E-value=1.8e+02 Score=31.29 Aligned_cols=107 Identities=14% Similarity=0.231 Sum_probs=73.5
Q ss_pred HHHHHHHHHHHHhcccCCC--CCcchhhHHHHHHHhh---------hhhhheeeccCCchHHHHHHHHHHHHHhhcCC--
Q 004863 102 LMKEFFQLAVSAFENLSHA--SGRYYMKALSILDTVA---------KVRSCLLMLDLECDKLVVEMFQHFLKVIRSNH-- 168 (726)
Q Consensus 102 qLKDIFqLfV~qf~~LsD~--ssp~Y~q~~yLLEsLA---------eVKS~VLmlDLE~ddLI~eLFktFFdiVr~dh-- 168 (726)
-=++||..+.+-|..|..| .+.+|.-|..|++-+- .++.|++++.=+.-+++..|..-+..++..+.
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 3347888888888888775 4567777777777444 56777777766666777777776666666542
Q ss_pred -ch--hHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCC
Q 004863 169 -PH--FVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQD 208 (726)
Q Consensus 169 -p~--~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks 208 (726)
.. .-+..|..+.+..|--+..++....+.|+..++.+.+.
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 22336677777777777788888888888888776654
No 55
>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=36.18 E-value=1.3e+02 Score=31.58 Aligned_cols=101 Identities=10% Similarity=0.064 Sum_probs=67.6
Q ss_pred HHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhH-------HHHHHHHHHHHhcccCCCCCcchh
Q 004863 54 RDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDEL-------MKEFFQLAVSAFENLSHASGRYYM 126 (726)
Q Consensus 54 ~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdq-------LKDIFqLfV~qf~~LsD~ssp~Y~ 126 (726)
-.....++.+|+...+=.+....-.+++++||+=|--==.+|+-|+.+. --.||..|-+-+... .
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 4456788899988777777778889999999987766667888898643 234555555444311 2
Q ss_pred hHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHH
Q 004863 127 KALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLK 162 (726)
Q Consensus 127 q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFd 162 (726)
.-+-..+.|-.+..+++|..-.-.+.-.++|+.+|.
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 233445555566666666666556667777777776
No 56
>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=35.51 E-value=1.1e+02 Score=32.33 Aligned_cols=123 Identities=14% Similarity=0.173 Sum_probs=62.3
Q ss_pred hHHHHHHHhhh--------cCCCCCCCh--hHHHHHHHHHHHHhcccCCCCCc--------chhhHHHHHHHhhhhhhhe
Q 004863 81 VTSCISEITRI--------TAPDSPYDD--ELMKEFFQLAVSAFENLSHASGR--------YYMKALSILDTVAKVRSCL 142 (726)
Q Consensus 81 VAcCLaDILRI--------yAPDAPYtD--dqLKDIFqLfV~qf~~LsD~ssp--------~Y~q~~yLLEsLAeVKS~V 142 (726)
+|.+|.-+||- .-||.+... ..|+++|+.+...+. ..+| .-....||.++|..+-..-
T Consensus 11 la~qlL~~~~~~p~~~~~~~~~~s~~~~~F~~l~~lFe~~~~~y~----~~~~~L~~~~l~~~~~e~~I~~~lrk~Nla~ 86 (238)
T PF08558_consen 11 LATQLLRAFSQSPDIISLVSDPDSERGESFRRLRDLFEATKRIYS----SDSPFLSVDELALQDKEQRICQTLRKANLAT 86 (238)
T ss_dssp HHHHHHHHHHC-------------T-HHHHHHHHHHHHHHCCT-S----CCTH--------HHHHHHHHHHHHHHHCTTT
T ss_pred HHHHHHHHHHHhhccchhhhccchHHHHHHHHHHHHHHHHHHHcC----CCCccchhhhhhhcchHHHHHHHHHHHHhhc
Confidence 44445545544 345665554 477777776665552 2344 4455677777776663322
Q ss_pred eec-cCCchH-HHHHHHHHHHHHhhcCCc---hhHHHHHHHHHHH-HhcccCCCCHHHHHHHHHHhhccCC
Q 004863 143 LML-DLECDK-LVVEMFQHFLKVIRSNHP---HFVFAAMETIMTL-VIDESEDVSWDLLRILLASVRKENQ 207 (726)
Q Consensus 143 Lml-DLE~dd-LI~eLFktFFdiVr~dhp---~~V~~~M~dIMs~-VIeESE~VP~eVLDvIL~~ll~~~k 207 (726)
.+. =+++++ =..++=..||++..+++. +.....-..|-++ +|.-.+..+..-...||..+.+.+-
T Consensus 87 ~l~~~f~~~~i~~~el~~~Fl~if~pe~~~l~k~~~~L~l~LKtQa~i~~l~~~~~~~~~eiL~~lFp~~~ 157 (238)
T PF08558_consen 87 FLDSLFGTDEIGFLELAESFLDIFCPEDSKLLKSQEELYLDLKTQAVISALEKGPFRSAEEILDRLFPDDL 157 (238)
T ss_dssp -TTEE-SSSTS-HHHHHHHHHCCCCCCTC--HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHTSSSS
T ss_pred hHHHhcCCCCCCHHHHHHHHHHHHcccccchhhhHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHcCCCh
Confidence 221 125444 245666889998888776 3333333344333 2222235666777777777666553
No 57
>PF08385 DHC_N1: Dynein heavy chain, N-terminal region 1; InterPro: IPR013594 Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit []. The region featured in this family includes the sequences implicated in mediating these interactions []. It is thought to be flexible and not to adopt a rigid conformation [].
Probab=35.39 E-value=6.9e+02 Score=28.51 Aligned_cols=33 Identities=15% Similarity=0.282 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHhcccCCchhhHHhhHHHHHhh
Q 004863 32 INLLDKVEHLLANVEQAPSRSMRDALLPTMKGL 64 (726)
Q Consensus 32 LKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~L 64 (726)
.+-|+.|...+..+.......+.+.+.+++.+|
T Consensus 99 ~~fL~~l~~~~~~l~~~~~~~i~~~i~~l~~~l 131 (579)
T PF08385_consen 99 NKFLKPLEPPFELLEASDLSEIQESIPPLFHHL 131 (579)
T ss_pred HHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHH
Confidence 344444444445555555556777777777776
No 58
>KOG0211 consensus Protein phosphatase 2A regulatory subunit A and related proteins [Signal transduction mechanisms]
Probab=35.27 E-value=9.4e+02 Score=30.04 Aligned_cols=143 Identities=11% Similarity=0.106 Sum_probs=89.6
Q ss_pred HhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhh
Q 004863 62 KGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSC 141 (726)
Q Consensus 62 k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~ 141 (726)
..|.... |.+..-.||-.+|-|+..+.+.|- +.| .....|++++...... .|..++.+|-+|+.+
T Consensus 520 ~~l~~~~-l~d~v~~Ir~~aa~~l~~l~~~~G--~~w--~~~~~i~k~L~~~~q~-------~y~~R~t~l~si~~l--- 584 (759)
T KOG0211|consen 520 AELLRTW-LPDHVYSIREAAARNLPALVETFG--SEW--ARLEEIPKLLAMDLQD-------NYLVRMTTLFSIHEL--- 584 (759)
T ss_pred HHHHHhh-hhhhHHHHHHHHHHHhHHHHHHhC--cch--hHHHhhHHHHHHhcCc-------ccchhhHHHHHHHHH---
Confidence 3334333 444556699999999999999988 333 3456777777765543 788899999888832
Q ss_pred eeeccCCchHHHHHHHHHHHHHhhcCCchhHHH----HHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHH
Q 004863 142 LLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFA----AMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLG 217 (726)
Q Consensus 142 VLmlDLE~ddLI~eLFktFFdiVr~dhp~~V~~----~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA 217 (726)
..+=..++..+.|-.+|.-...+--.+|+. ++..|+..++. .+-.+.+-.++..|...+.-.-+.++.+|
T Consensus 585 ---a~v~g~ei~~~~Llp~~~~l~~D~vanVR~nvak~L~~i~~~L~~---~~~~~~v~pll~~L~~d~~~dvr~~a~~a 658 (759)
T KOG0211|consen 585 ---AEVLGQEITCEDLLPVFLDLVKDPVANVRINVAKHLPKILKLLDE---SVRDEEVLPLLETLSSDQELDVRYRAILA 658 (759)
T ss_pred ---HHHhccHHHHHHHhHHHHHhccCCchhhhhhHHHHHHHHHhhcch---HHHHHHHHHHHHHhccCcccchhHHHHHH
Confidence 222245666666666666555555556554 44555554444 34445566667777765555556666777
Q ss_pred HHHHhhhH
Q 004863 218 EKVFTKCA 225 (726)
Q Consensus 218 ~~VI~~Ca 225 (726)
..+|..|.
T Consensus 659 ~~~i~l~~ 666 (759)
T KOG0211|consen 659 FGSIELSR 666 (759)
T ss_pred HHHHHHHH
Confidence 76665554
No 59
>KOG1410 consensus Nuclear transport receptor RanBP16 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=34.98 E-value=4.6e+02 Score=32.71 Aligned_cols=155 Identities=17% Similarity=0.261 Sum_probs=94.8
Q ss_pred HHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchh----hHHHHHHHhhhh-hhheeeccCCchHHHHHHHHHHH
Q 004863 87 EITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYM----KALSILDTVAKV-RSCLLMLDLECDKLVVEMFQHFL 161 (726)
Q Consensus 87 DILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~----q~~yLLEsLAeV-KS~VLmlDLE~ddLI~eLFktFF 161 (726)
-+||+ |.|.-|-|..+.||.-|-.+.+.+=-.|. -||.+||-|-.= =+|+ +.|+ ...|=+++
T Consensus 844 GVFrL------YGD~~l~daL~~fvKm~lsIp~sD~l~Y~Klsqsyy~llE~l~qdhm~Fi--~nL~-----~~vfm~ll 910 (1082)
T KOG1410|consen 844 GVFRL------YGDSALDDALQTFVKMLLSIPHSDLLSYRKLSQSYYNLLEVLTQDHMPFI--TNLE-----PDVFMYLL 910 (1082)
T ss_pred ceeee------eCchHHHHHHHHHHHHHhcCCHHHHHhHHHHHHHHhhHHHHHHhccchhh--hcCc-----HHHHHHHH
Confidence 45666 57888999999999988766655443443 378888887544 2333 3343 23555566
Q ss_pred HHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCC-----CCchHHHHHHHHHhhhHHHHHHHHHHHH
Q 004863 162 KVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQD-----VSPTSWKLGEKVFTKCAAKLKTNLKEAV 236 (726)
Q Consensus 162 diVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks-----~~PaAykLA~~VI~~CadKLqp~I~q~~ 236 (726)
..|..+... +- +| |+..+-.-=.-++.-++.++....+. ..|++.+++- .|..|.+-|+..++-.+
T Consensus 911 ~Si~sGLt~-lD----t~---v~ssccsslD~i~tYlfk~itr~~~p~~~~~~tpa~~r~l~-~i~q~Pdil~qml~tl~ 981 (1082)
T KOG1410|consen 911 RSISSGLTS-LD----TI---VSSSCCSSLDTIVTYLFKRITRSTKPTRKVGMTPAGDRFLH-AIQQHPDILQQMLSTLI 981 (1082)
T ss_pred HHHHhccch-hh----HH---HHhHHHHHHHHHHHHHHHHHhccCCCcCcCCCChhHHHHHH-HHHhChHHHHHHHHHHH
Confidence 655544321 11 11 11111111112445555566554443 6888888885 68999999988888777
Q ss_pred H-----------hcCCCc--------hhHHHHHHHHhcCCCCCCCC
Q 004863 237 Q-----------SRGIAL--------DDYAEIVACICGSDDENPQH 263 (726)
Q Consensus 237 n-----------s~G~~L--------~~YseIv~sIcq~~s~~~~~ 263 (726)
+ +++++| ++|++.=++|....+...|.
T Consensus 982 ~ii~Fedc~nQWSlSRPlLgLILi~E~~fSdlk~~l~ssQp~dkqq 1027 (1082)
T KOG1410|consen 982 NIIMFEDCRNQWSLSRPLLGLILINEKYFSDLKASLTSSQPYDKQQ 1027 (1082)
T ss_pred HHHhHHhhcccccccchhhHHHhhhHHHHHHHHHHHhcCCCcchhH
Confidence 6 345553 48999999998777655544
No 60
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=34.84 E-value=99 Score=29.50 Aligned_cols=68 Identities=16% Similarity=0.225 Sum_probs=48.9
Q ss_pred hcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHH
Q 004863 165 RSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLK 233 (726)
Q Consensus 165 r~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~ 233 (726)
++..+..=...+..|. .+|...+.-|.+.+..|...|...++...--|..|...++.+|+..+...|+
T Consensus 10 s~~l~~~dw~~~l~ic-D~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~ 77 (133)
T smart00288 10 SPSLLEEDWELILEIC-DLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVA 77 (133)
T ss_pred CcCCCCcCHHHHHHHH-HHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHH
Confidence 3344444344455553 3556667889999999999999877777677788888889999988866654
No 61
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=33.86 E-value=1.5e+02 Score=34.97 Aligned_cols=81 Identities=12% Similarity=0.258 Sum_probs=54.2
Q ss_pred chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCC----CCCchHHHHHHHHHhhh
Q 004863 149 CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQ----DVSPTSWKLGEKVFTKC 224 (726)
Q Consensus 149 ~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~k----s~~PaAykLA~~VI~~C 224 (726)
.-+||.+|+-+++..+.+.+.--|+.-+. +.+|.+-|.-|+..|...+. .+.|-..++.-.++..|
T Consensus 279 ~~~Li~ELd~~vl~~v~DQngnHViQK~i----------e~~p~~~~~Fiv~~f~~~~~~~~ls~~~YGCRVIQr~lE~c 348 (503)
T KOG1488|consen 279 QIQLIDELDGHLLKCVKDQNGNHVIQKCI----------ETLPPDAWQFIVDFFSGDDNLLELSTHKYGCRVIQRILEHC 348 (503)
T ss_pred HHHHHHHHHhhHHHHHhhcccceehhhhh----------hccChHHHHHHHHHhcCCCceeEeeccCcccHHHHHHhhcC
Confidence 56899999888888888755544533221 47999999999999987533 35666667777777777
Q ss_pred HHH-HHHHHHHHHHhc
Q 004863 225 AAK-LKTNLKEAVQSR 239 (726)
Q Consensus 225 adK-Lqp~I~q~~ns~ 239 (726)
.+. .++.+......+
T Consensus 349 ~~~~~~~i~~ei~~~~ 364 (503)
T KOG1488|consen 349 SEDQKQPLMEEIIRNC 364 (503)
T ss_pred ChHhhhHHHHHHHHHH
Confidence 654 344444444333
No 62
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=33.59 E-value=6.5e+02 Score=30.94 Aligned_cols=221 Identities=13% Similarity=0.260 Sum_probs=112.9
Q ss_pred HHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHH
Q 004863 34 LLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSA 113 (726)
Q Consensus 34 RLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~q 113 (726)
|..-|.+.+...+.....-+..-|..+...|+.-.=+.--+...|+..-..|..+. .|+||+= .+-+-.|+.++..-
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 33455556666654433345667777888888766666566667777777777766 4577752 24455566665443
Q ss_pred hc-------ccCCCCCc-----chhhHHHHHHHhhhhhhheeeccCC-chHHHHHHHHHHHHHhhcC-CchhHHHHHHHH
Q 004863 114 FE-------NLSHASGR-----YYMKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSN-HPHFVFAAMETI 179 (726)
Q Consensus 114 f~-------~LsD~ssp-----~Y~q~~yLLEsLAeVKS~VLmlDLE-~ddLI~eLFktFFdiVr~d-hp~~V~~~M~dI 179 (726)
|. +.-++++. ....|..+|+.+-..+ --|++ ..|.+.+||=.++....+. .-..|+..+..+
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 LDECISVLGQILATEDQLLVEELQSNYIGVLEAIIRTR----RRDIEDVEDQLMELFIRILESTKPTTAFGDVYTAISAL 625 (858)
T ss_pred HHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhc----CCCcccHHHHHHHHHHHHHhccCCchhhhHHHHHHHHH
Confidence 33 22222222 2344566666654332 23564 4555555554444433332 235577777777
Q ss_pred HHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHH------------------------HHHHHHHHH
Q 004863 180 MTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAA------------------------KLKTNLKEA 235 (726)
Q Consensus 180 Ms~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~Cad------------------------KLqp~I~q~ 235 (726)
++.+=+-.+.--..++-.++..+...+.-....|-.|.-++-+.-.. .|+|.|-..
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 77655544432222222222222111111111122222222222222 255666555
Q ss_pred HH----hcCCCchhHHHHHHHHhcCCCCCC
Q 004863 236 VQ----SRGIALDDYAEIVACICGSDDENP 261 (726)
Q Consensus 236 ~n----s~G~~L~~YseIv~sIcq~~s~~~ 261 (726)
|. .+|..+.-|-+.+--+||..++.-
T Consensus 706 FgDIAlaiga~F~~YL~~im~L~qqas~~~ 735 (858)
T COG5215 706 FGDIALAIGANFESYLDMIMMLFQQASELD 735 (858)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHHHHHhccC
Confidence 53 335556678777778999887766
No 63
>KOG2022 consensus Nuclear transport receptor LGL2 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=32.94 E-value=6.4e+02 Score=32.11 Aligned_cols=182 Identities=16% Similarity=0.288 Sum_probs=100.7
Q ss_pred HhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHH
Q 004863 55 DALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDT 134 (726)
Q Consensus 55 ~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEs 134 (726)
..+-++...+.+ .-++..| +.=|.|+..+--+.--..||..--|.+++.|+++ |- .++ .+-+
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-FL-----TSC-------LAVT 762 (982)
T ss_pred HHHHHHHHHHHH-HHhcchh----HHHHHHHHHHhccccccccchhhhHHHHHHHHHH-hc-----cch-------HHHH
Confidence 344555555555 3333333 3567888888877666678988999999999999 53 122 1122
Q ss_pred hhhhhhheeeccC--CchHHHHH----HHHHHHHHhh----cCCchhHHHHHHHHHHHHhcccCCCC----HHHHHHHHH
Q 004863 135 VAKVRSCLLMLDL--ECDKLVVE----MFQHFLKVIR----SNHPHFVFAAMETIMTLVIDESEDVS----WDLLRILLA 200 (726)
Q Consensus 135 LAeVKS~VLmlDL--E~ddLI~e----LFktFFdiVr----~dhp~~V~~~M~dIMs~VIeESE~VP----~eVLDvIL~ 200 (726)
+.-++-|++|.-- .|-+|+.. +|+..|-+.. .++|..+...|. .++.+|.--..++ ...-..||.
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 2333444444333 25444444 4444443333 255666666665 6666776554433 234445553
Q ss_pred Hhh----ccCCCCCchHHHHHHHHHhhhHHHHHHHHHHHHHhcCCC-----------------chhHHHHHHHHhc
Q 004863 201 SVR----KENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIA-----------------LDDYAEIVACICG 255 (726)
Q Consensus 201 ~ll----~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~~ns~G~~-----------------L~~YseIv~sIcq 255 (726)
++. .+.+.+..+|.+.-..++..|....=-.+.++++..|.. ++-|++||..+..
T Consensus 842 ~a~~ll~~pE~~~i~aa~qF~t~~~~~~~s~~~~tv~~~V~~~G~~Li~~im~~vgg~~~RS~ld~~aDIL~al~~ 917 (982)
T KOG2022|consen 842 CAFILLNSPEPTTIRAASQFLTALATYATSHDLVTVTSVVAEIGPILIYAIMRGVGGEASRSTLDALADILLALNA 917 (982)
T ss_pred HHHHhcCCCccHHHHHHHHHHHHHHhhcccchhHHHHHHHHhcchHHHHHHHHHhcCcCccchhHHHHHHHHHHHH
Confidence 322 333444445555555577777665544555555544432 4678888776654
No 64
>PF14868 DUF4487: Domain of unknown function (DUF4487)
Probab=32.64 E-value=3.9e+02 Score=31.97 Aligned_cols=125 Identities=14% Similarity=0.166 Sum_probs=71.8
Q ss_pred HHHHHHHHHHHHhcccCC---CCCcchhhHHHHH-HHhhhhhhheeeccCCchHHHHHHHHHHHHHhhc-----C-Cchh
Q 004863 102 LMKEFFQLAVSAFENLSH---ASGRYYMKALSIL-DTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRS-----N-HPHF 171 (726)
Q Consensus 102 qLKDIFqLfV~qf~~LsD---~ssp~Y~q~~yLL-EsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~-----d-hp~~ 171 (726)
-..+|+...+.+...-.+ -+..-+.+-...| -.|+.+.+..-++|.....-|.+++..|...++. + .-..
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 345566655555443333 3344455555544 5556666666666665566666776666665532 2 2245
Q ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHHHHHHhcCCCc
Q 004863 172 VFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIAL 243 (726)
Q Consensus 172 V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~~ns~G~~L 243 (726)
+...+..|+..+|... .++.+.-++.. +..-+...+.+.+++++.+|+.++|.-.
T Consensus 457 ~~~~lL~l~~~~~~~l---~~~~i~qv~~~--------------l~~l~~~~pp~~~kl~~~~FLs~lg~~~ 511 (559)
T PF14868_consen 457 TLSLLLSLLSFFIQLL---DPQLIEQVLTE--------------LTSLFKSEPPDHVKLALLDFLSSLGKLF 511 (559)
T ss_pred HHHHHHHHHHHHHHhc---ChHHHHHHHHH--------------HHHHHhhCCCccchHHHHHHHHHhcccc
Confidence 6666777777776542 23333333321 2223346667779999999999998653
No 65
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=32.50 E-value=29 Score=39.93 Aligned_cols=116 Identities=22% Similarity=0.291 Sum_probs=67.7
Q ss_pred cCchhhhHHHHHHHhhhcCCCCCCChhHHH------HHHHHHHHHhcccCCCCCcch-hhHHHHHHHhhhhhhheeeccC
Q 004863 75 MDVRLSVTSCISEITRITAPDSPYDDELMK------EFFQLAVSAFENLSHASGRYY-MKALSILDTVAKVRSCLLMLDL 147 (726)
Q Consensus 75 kdVRayVAcCLaDILRIyAPDAPYtDdqLK------DIFqLfV~qf~~LsD~ssp~Y-~q~~yLLEsLAeVKS~VLmlDL 147 (726)
.||-+|...|-. |+|+-.+|+ .-|++|+..-+.|.+.=..+| .+|-..|+.|.++|.=++ +|+
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 577888888843 789987777 568888887777766444443 456778888888886543 454
Q ss_pred CchHHHHHHHHHHHHHhhcC-----CchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhc
Q 004863 148 ECDKLVVEMFQHFLKVIRSN-----HPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRK 204 (726)
Q Consensus 148 E~ddLI~eLFktFFdiVr~d-----hp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~ 204 (726)
=--+=+ .++|+.||.. +..-+-.-|..|-..+=.....+-.+|+.+|++.-+.
T Consensus 339 yLaphV----d~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~ 396 (466)
T KOG0686|consen 339 YLAPHV----DNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESELLELILEGKIS 396 (466)
T ss_pred hcchhH----HHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHHHHHHHHccchh
Confidence 211122 4455555532 1222222333333333223334667788888876553
No 66
>KOG0301 consensus Phospholipase A2-activating protein (contains WD40 repeats) [Lipid transport and metabolism]
Probab=32.04 E-value=5.3e+02 Score=31.85 Aligned_cols=116 Identities=22% Similarity=0.210 Sum_probs=53.9
Q ss_pred HHHHhcccCCchhhHHhhHHHHHhhhhhhh-------------ccC------CCcCchhhhHHHHHHHhhhcCCCCCCCh
Q 004863 40 HLLANVEQAPSRSMRDALLPTMKGLITNDL-------------LRR------SDMDVRLSVTSCISEITRITAPDSPYDD 100 (726)
Q Consensus 40 ~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~L-------------LkH------KDkdVRayVAcCLaDILRIyAPDAPYtD 100 (726)
.+|..+.|-|.+-|.-+|.-++-.+.++.. +.+ .+.--++++.=||+.+| ++ |+.-
T Consensus 548 ~~l~~l~~wp~~~~fPalDilRl~v~h~~~~s~~~~~~~~~~~~~~li~~~~~~~an~ll~vR~L~N~f----~~-~~g~ 622 (745)
T KOG0301|consen 548 LALAILLQWPVEMMFPALDILRLAVKHHSSNSLFCDREEGQNLVGTLIPILNADPANQLLVVRCLANLF----SN-PAGR 622 (745)
T ss_pred HHHHHHhcCCHHHhhhHHHHHHHHHhccchhhhhhhhhhhhHHHHhhhcccccchhHHHHHHHHHHHhc----cC-HHHH
Confidence 366677777777555555544433332211 111 12334566666777776 44 5554
Q ss_pred hHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccC---CchHHHHHHHHHHHHH
Q 004863 101 ELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDL---ECDKLVVEMFQHFLKV 163 (726)
Q Consensus 101 dqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDL---E~ddLI~eLFktFFdi 163 (726)
.-+---+..+.+.|....--++..++..+ .++|--=|+.++.|- +.-+++...|.+.++-
T Consensus 623 ~~~~s~~~~i~~~~~~~~s~~~knl~ia~---atlaln~sv~l~~~~~~~~~~~~l~~ai~~~~e~ 685 (745)
T KOG0301|consen 623 ELFMSRLESILDPVIEASSLSNKNLQIAL---ATLALNYSVLLIQDNEQLEGKEVLLSAISTLLEP 685 (745)
T ss_pred HHHHHHHHHHhhhhhhhhcccchhHHHHH---HHHHHHHHHHHHhcccccchHHHHHHHHHhhccc
Confidence 44444455555555544433333333332 222222233333332 2334555555555543
No 67
>COG5231 VMA13 Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]
Probab=31.97 E-value=2e+02 Score=32.83 Aligned_cols=99 Identities=16% Similarity=0.227 Sum_probs=58.9
Q ss_pred hhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHH-------HHHHhc-ccCCCCCcchhhHHHHHHHhhhhh
Q 004863 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQL-------AVSAFE-NLSHASGRYYMKALSILDTVAKVR 139 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqL-------fV~qf~-~LsD~ssp~Y~q~~yLLEsLAeVK 139 (726)
+|++.=|.-.|+++..|+.++.-+ .+-++|--+ |+..+. .+++. --||++|+
T Consensus 156 kl~Q~i~~lTrlfav~cl~~l~~~---------~e~R~i~waentcs~r~~e~l~n~vg~~----qlQY~SL~------- 215 (432)
T COG5231 156 KLSQLIDFLTRLFAVSCLSNLEFD---------VEKRKIEWAENTCSRRFMEILQNYVGVK----QLQYNSLI------- 215 (432)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhh---------HHHHHHHHHHhhHHHHHHHHHHhhhhhh----hhHHHHHH-------
Confidence 566777777788888888888733 222222111 111111 11221 13444443
Q ss_pred hheeeccCC--chHHHHHHHH---HHHHHhhcCCchhHHHHHHHHHHHHhccc
Q 004863 140 SCLLMLDLE--CDKLVVEMFQ---HFLKVIRSNHPHFVFAAMETIMTLVIDES 187 (726)
Q Consensus 140 S~VLmlDLE--~ddLI~eLFk---tFFdiVr~dhp~~V~~~M~dIMs~VIeES 187 (726)
|++++-++ |-++|..||. .+..+|+...-++|......|+..+|+-+
T Consensus 216 -~iw~lTf~~~~aqdi~K~~dli~dli~iVk~~~keKV~Rlc~~Iv~n~~dK~ 267 (432)
T COG5231 216 -IIWILTFSKECAQDIDKMDDLINDLIAIVKERAKEKVLRLCCGIVANVLDKS 267 (432)
T ss_pred -HHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 55555564 5556655554 45557888888999999999999999955
No 68
>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=31.84 E-value=1e+02 Score=28.14 Aligned_cols=60 Identities=13% Similarity=0.240 Sum_probs=42.2
Q ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHHH
Q 004863 174 AAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKE 234 (726)
Q Consensus 174 ~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~q 234 (726)
..|..|...+ .+...-+.++++.|...+...+....--|-.|-+.++.+|+..+..+|+.
T Consensus 19 ~~i~~i~d~~-~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~f~~~i~~ 78 (115)
T cd00197 19 PLIMEICDLI-NETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVAS 78 (115)
T ss_pred HHHHHHHHHH-HCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHHHHHHHHH
Confidence 4455554444 55566788899999999876655445556677788889998888777654
No 69
>COG5218 YCG1 Chromosome condensation complex Condensin, subunit G [Chromatin structure and dynamics / Cell division and chromosome partitioning]
Probab=31.75 E-value=1.1e+03 Score=29.28 Aligned_cols=88 Identities=20% Similarity=0.153 Sum_probs=60.5
Q ss_pred hhHHHHHHHhhhhhhheeeccCC-chHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhc
Q 004863 126 MKALSILDTVAKVRSCLLMLDLE-CDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRK 204 (726)
Q Consensus 126 ~q~~yLLEsLAeVKS~VLmlDLE-~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~ 204 (726)
.+.+.+|.++-++ .|.|.+ ..+|+..+|.|++..+- .--++|+.-...||..|.+-...|...|...|+..+..
T Consensus 65 dRil~fl~~f~~Y----~~~~dpeg~~~V~~~~~h~lRg~e-skdk~VR~r~lqila~~~d~v~eIDe~l~N~L~ekl~~ 139 (885)
T COG5218 65 DRILSFLKRFFEY----DMPDDPEGEELVAGTFYHLLRGTE-SKDKKVRKRSLQILALLSDVVREIDEVLANGLLEKLSE 139 (885)
T ss_pred HHHHHHHHHHHHh----cCCCChhhhHHHHHHHHHHHhccc-CcchhHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHH
Confidence 4455566555442 466665 68999999988887543 23477998889999988888777888888888777765
Q ss_pred cCCCCCchHHHHHH
Q 004863 205 ENQDVSPTSWKLGE 218 (726)
Q Consensus 205 ~~ks~~PaAykLA~ 218 (726)
.--...|+-+.-|.
T Consensus 140 R~~DRE~~VR~eAv 153 (885)
T COG5218 140 RLFDREKAVRREAV 153 (885)
T ss_pred HHhcchHHHHHHHH
Confidence 54444555444443
No 70
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=31.50 E-value=1.1e+03 Score=30.57 Aligned_cols=124 Identities=9% Similarity=0.088 Sum_probs=63.4
Q ss_pred hhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHH-hcccCCCCCcchhhHHHHHHHhhhhhhheeec
Q 004863 67 NDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSA-FENLSHASGRYYMKALSILDTVAKVRSCLLML 145 (726)
Q Consensus 67 ~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~q-f~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLml 145 (726)
+.|+.-.|..|-.++.|||+=+++++ ..-+-.|-+.|+++ +..|..|-=+ .. -|-.+-...-+++..
T Consensus 699 ~~Lisesdlhvt~~a~~~L~tl~~~~-------ps~l~~~~~~iL~~ii~ll~Spllq--g~---al~~~l~~f~alV~t 766 (1233)
T KOG1824|consen 699 PPLISESDLHVTQLAVAFLTTLAIIQ-------PSSLLKISNPILDEIIRLLRSPLLQ--GG---ALSALLLFFQALVIT 766 (1233)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHhcc-------cHHHHHHhhhhHHHHHHHhhCcccc--ch---HHHHHHHHHHHHHhc
Confidence 36777788889999999999999883 23335556666665 4444322111 11 111111222233344
Q ss_pred cCCchHHHHHHHHHH----HHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhh
Q 004863 146 DLECDKLVVEMFQHF----LKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVR 203 (726)
Q Consensus 146 DLE~ddLI~eLFktF----FdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll 203 (726)
+.++-+ +..+|... |+-+.+..++.....+..+...++.-+......+..-++..|.
T Consensus 767 ~~~~l~-y~~l~s~lt~PV~~~~~~~l~kqa~~siA~cvA~Lt~~~~~~s~s~a~kl~~~~~ 827 (1233)
T KOG1824|consen 767 KEPDLD-YISLLSLLTAPVYEQVTDGLHKQAYYSIAKCVAALTCACPQKSKSLATKLIQDLQ 827 (1233)
T ss_pred CCCCcc-HHHHHHHHcCCcccccccchhHHHHHHHHHHHHHHHHhccccchhHHHHHHHHHh
Confidence 444333 34444332 2222334555555566666655555555555555555554444
No 71
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=31.44 E-value=6.9e+02 Score=27.54 Aligned_cols=60 Identities=12% Similarity=0.109 Sum_probs=38.8
Q ss_pred hhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHH
Q 004863 67 NDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILD 133 (726)
Q Consensus 67 ~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLE 133 (726)
..+|.|=+.+.+.-++-+++-+=.| +.+++.+|..=|+..|.+-.......+..-..||.
T Consensus 31 a~VL~~L~~~e~~~l~~~ma~l~~v-------s~~~~~~vL~ef~~~~~~~~~~~~gg~~~~~~iL~ 90 (339)
T PRK05686 31 AKVLKHLTEEEVQKLSAAMANLRNV-------SPEQVEAVLEEFEDEFEAGAYILMGGIDYARSLLE 90 (339)
T ss_pred HHHHHcCCHHHHHHHHHHHHcCCCC-------CHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHH
Confidence 3678888877888888888877655 55688888877887776433222233333344444
No 72
>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=31.43 E-value=28 Score=26.23 Aligned_cols=23 Identities=17% Similarity=0.348 Sum_probs=20.5
Q ss_pred hhccCCCcCchhhhHHHHHHHhh
Q 004863 68 DLLRRSDMDVRLSVTSCISEITR 90 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILR 90 (726)
.||+|.|.+|+-.++.||..|.|
T Consensus 19 ~ll~~~~~~v~~~a~~al~nl~~ 41 (41)
T PF00514_consen 19 QLLKSPDPEVQEEAAWALGNLAA 41 (41)
T ss_dssp HHTTSSSHHHHHHHHHHHHHHHT
T ss_pred HHHcCCCHHHHHHHHHHHHHHhC
Confidence 57789999999999999998865
No 73
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=30.83 E-value=6.2e+02 Score=28.97 Aligned_cols=110 Identities=13% Similarity=0.165 Sum_probs=63.8
Q ss_pred CCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHH
Q 004863 121 SGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLA 200 (726)
Q Consensus 121 ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~ 200 (726)
+...+.+.|.+|.++-+..+..+ .++.+..|-+..+.+.+..........-..++-.||- ...||.+-+..++.
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 34456667777776666655442 3445555555555554433333333444555555555 66788888877775
Q ss_pred Hhhc-cC-CCCCchHHHHHHHHH-hhhHHHHHHHHHHHH
Q 004863 201 SVRK-EN-QDVSPTSWKLGEKVF-TKCAAKLKTNLKEAV 236 (726)
Q Consensus 201 ~ll~-~~-ks~~PaAykLA~~VI-~~CadKLqp~I~q~~ 236 (726)
-|=. .+ .+-...+|+..+++| ..++..+=..+|.++
T Consensus 221 vLCsi~~~~~l~~~~w~~m~nL~~S~~g~~~i~~L~~iL 259 (464)
T PF11864_consen 221 VLCSIVNSVSLCKPSWRTMRNLLKSHLGHSAIRTLCDIL 259 (464)
T ss_pred HHhhHhcccccchhHHHHHHHHHcCccHHHHHHHHHHHH
Confidence 5421 11 133456888888887 444566666777777
No 74
>KOG2344 consensus Exocyst component protein and related proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.77 E-value=1.1e+02 Score=36.87 Aligned_cols=34 Identities=12% Similarity=0.060 Sum_probs=28.5
Q ss_pred HhhhHHHHHHHHHHHHHhcCCCchhHHHHHHHHhcCCC
Q 004863 221 FTKCAAKLKTNLKEAVQSRGIALDDYAEIVACICGSDD 258 (726)
Q Consensus 221 I~~CadKLqp~I~q~~ns~G~~L~~YseIv~sIcq~~s 258 (726)
..-....|.+|+++|++.+. +|...|..|++...
T Consensus 382 ~gG~VHpLTryvmnyl~~L~----dy~~tL~~il~~~~ 415 (623)
T KOG2344|consen 382 PGGGVHPLTRYVMNYLNFLA----DYKDTLEQLLMEDP 415 (623)
T ss_pred CCCCcChhHHHHHHHHHHHH----HHHHHHHHHHhccc
Confidence 45556789999999999653 99999999999875
No 75
>cd07958 Anticodon_Ia_Leu_BEm Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases. This domain is found in leucyl tRNA synthetases (LeuRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain. In contrast to other class Ia enzymes, the anticodon is not used as an identity element in LeuRS (with exceptions such as Saccharomyces cerevisiae and some other eukaryotes). No anticodon-binding site can be defined for this family, which includes bacterial and eukaryotic mitochondrial members, as well as LeuRS from the archaeal Halobacteria. LeuRS catalyzes the transfer of leucine to the 3'-end of its tRNA.
Probab=29.59 E-value=1.5e+02 Score=25.84 Aligned_cols=29 Identities=17% Similarity=0.164 Sum_probs=24.4
Q ss_pred chhhhHHHHHHHhhhcCCCCCCChhHHHH
Q 004863 77 VRLSVTSCISEITRITAPDSPYDDELMKE 105 (726)
Q Consensus 77 VRayVAcCLaDILRIyAPDAPYtDdqLKD 105 (726)
+...+.-||..++++.+|=.|+..+++-.
T Consensus 87 ~~~~~~~~l~~~~~lL~P~~P~~aeei~~ 115 (117)
T cd07958 87 HAAVLREALETLVLLLAPFAPHIAEELWE 115 (117)
T ss_pred hHHHHHHHHHHHHHHHcccchHHHHHHHh
Confidence 66677788999999999999999887643
No 76
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=29.55 E-value=2.8e+02 Score=34.34 Aligned_cols=24 Identities=21% Similarity=0.358 Sum_probs=22.6
Q ss_pred hhccCCCcCchhhhHHHHHHHhhh
Q 004863 68 DLLRRSDMDVRLSVTSCISEITRI 91 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILRI 91 (726)
.+|.|.+.-||-.+|.||..|+|+
T Consensus 134 ~~l~d~~ayVRk~Aalav~kly~l 157 (757)
T COG5096 134 KLLTDPHAYVRKTAALAVAKLYRL 157 (757)
T ss_pred HHccCCcHHHHHHHHHHHHHHHhc
Confidence 578999999999999999999998
No 77
>PF08405 Calici_PP_N: Viral polyprotein N-terminal; InterPro: IPR013614 This domain is found at the N terminus of non-structural viral polyproteins of the Caliciviridae subfamily. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity, 0044419 interspecies interaction between organisms
Probab=28.82 E-value=1.3e+02 Score=33.80 Aligned_cols=88 Identities=24% Similarity=0.410 Sum_probs=59.7
Q ss_pred hhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccC-Cch----------HHHHHHHHHHHHHhhcCC
Q 004863 100 DELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDL-ECD----------KLVVEMFQHFLKVIRSNH 168 (726)
Q Consensus 100 DdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDL-E~d----------dLI~eLFktFFdiVr~dh 168 (726)
|..|+.+-..++-.+..| |.+-+ .+-|+.+|..+|+.-| .|| -|+.+||-.|..
T Consensus 133 dsKl~~v~d~iL~al~~L-------~srpi--k~ll~k~KPLNllnil~scdwTF~GVVe~lillaELfgIfWt------ 197 (358)
T PF08405_consen 133 DSKLEKVRDAILCALNSL-------FSRPI--KDLLGKLKPLNLLNILASCDWTFGGVVEALILLAELFGIFWT------ 197 (358)
T ss_pred chhhhhhhhHHHHHHHHH-------hhhHH--HHHHhhcccHHHHHHHHhCCCcHHHHHHHHHHHHHHhcccCC------
Confidence 466777777776666543 23322 5566777776665555 244 577888888884
Q ss_pred chhHHHHHHHHHHHHhccc-CCCCHHHHHHHHHHh
Q 004863 169 PHFVFAAMETIMTLVIDES-EDVSWDLLRILLASV 202 (726)
Q Consensus 169 p~~V~~~M~dIMs~VIeES-E~VP~eVLDvIL~~l 202 (726)
|.+|-++|..++....-+. +++..+|+-+||.-+
T Consensus 198 PPDVssfiasl~~d~~~qGPedla~d~vP~~lGGi 232 (358)
T PF08405_consen 198 PPDVSSFIASLLGDFQLQGPEDLAKDLVPVLLGGI 232 (358)
T ss_pred CccHHHHHHHHcccccccCcchHHHHHHHHHhhhh
Confidence 8889888888877766555 457778888888654
No 78
>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=28.79 E-value=1.3e+02 Score=25.53 Aligned_cols=59 Identities=12% Similarity=0.073 Sum_probs=41.0
Q ss_pred HHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccC
Q 004863 10 LEEQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRR 72 (726)
Q Consensus 10 le~~l~~~G~kLis~piStdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkH 72 (726)
..+.|..+|.+.--.|.+.+| +.++-.+-.....-..+..+++. .++.--|.++.||-.
T Consensus 3 a~~~l~~Fa~rAfRRp~~~~e-~~~~~~~~~~~~~~g~~~~~a~~---~~l~aiL~SP~FLY~ 61 (64)
T PF07637_consen 3 AREILRRFARRAFRRPLTDEE-VDRYLALYDSARAQGEDFEEALK---EALQAILCSPSFLYR 61 (64)
T ss_pred HHHHHHHHHHHHhCCCCCHHH-HHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHcCcchhcc
Confidence 456788899998889999999 77777776666554554444444 345556788888743
No 79
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=28.74 E-value=8e+02 Score=27.21 Aligned_cols=45 Identities=11% Similarity=0.195 Sum_probs=28.7
Q ss_pred hhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCC
Q 004863 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSH 119 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD 119 (726)
.+|+|=+.+----++-+++.|=.| +.+++..|..=|...|..-+.
T Consensus 29 ~vlk~L~~~ei~~l~~~m~~l~~v-------~~~~~~~vl~eF~~~~~~~~~ 73 (338)
T TIGR00207 29 EVFKHLSQEEIETLSAEIANVTQI-------DNQQKDDVLEEFEQIAEAQAY 73 (338)
T ss_pred HHHHcCCHHHHHHHHHHHHhcCCC-------CHHHHHHHHHHHHHHHHhcCC
Confidence 566775533333555666666555 668888888777777765443
No 80
>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=27.78 E-value=34 Score=33.36 Aligned_cols=27 Identities=19% Similarity=0.384 Sum_probs=23.3
Q ss_pred hhhHHHHHHHhhhcCCCCCCChhHHHH
Q 004863 79 LSVTSCISEITRITAPDSPYDDELMKE 105 (726)
Q Consensus 79 ayVAcCLaDILRIyAPDAPYtDdqLKD 105 (726)
..+..||..++++.||=+||..++|-.
T Consensus 112 ~~l~~~l~~ll~ll~P~~P~~aEElw~ 138 (183)
T cd07961 112 ATLYEVLLTLSRLMAPFTPFITEEIYQ 138 (183)
T ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 466789999999999999999987654
No 81
>KOG2759 consensus Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]
Probab=27.24 E-value=2.5e+02 Score=32.73 Aligned_cols=111 Identities=14% Similarity=0.313 Sum_probs=70.0
Q ss_pred hhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChh-HHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhh
Q 004863 63 GLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDE-LMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSC 141 (726)
Q Consensus 63 ~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDd-qLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~ 141 (726)
..+...+=+.-+.+....++-||-.+||+ | +|... ..-+=.++++..+. .+...|+-+|+++. |
T Consensus 159 ~~l~~~l~~~~~~~~~~~~~rcLQ~ll~~--~--eyR~~~v~adg~~~l~~~l~----s~~~~~QlQYqsif-------c 223 (442)
T KOG2759|consen 159 GFLKEQLQSSTNNDYIQFAARCLQTLLRV--D--EYRYAFVIADGVSLLIRILA----STKCGFQLQYQSIF-------C 223 (442)
T ss_pred HHHHHHHhccCCCchHHHHHHHHHHHhcC--c--chhheeeecCcchhhHHHHh----ccCcchhHHHHHHH-------H
Confidence 33333333335666777888899999998 3 33321 11111233344332 23344555555543 7
Q ss_pred eeeccCC---chHH-HHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccC
Q 004863 142 LLMLDLE---CDKL-VVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESE 188 (726)
Q Consensus 142 VLmlDLE---~ddL-I~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE 188 (726)
+.++++. |+.+ -..+|+.+.++++...-++|...+..|+.-+|+-.+
T Consensus 224 iWlLtFn~~~ae~~~~~~li~~L~~Ivk~~~KEKV~Rivlai~~Nll~k~~ 274 (442)
T KOG2759|consen 224 IWLLTFNPHAAEKLKRFDLIQDLSDIVKESTKEKVTRIVLAIFRNLLDKGP 274 (442)
T ss_pred HHHhhcCHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCc
Confidence 8888885 4332 226788888899988899999999999999998874
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=27.14 E-value=1.5e+02 Score=36.67 Aligned_cols=46 Identities=9% Similarity=0.171 Sum_probs=25.8
Q ss_pred cccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHH
Q 004863 185 DESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKT 230 (726)
Q Consensus 185 eESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp 230 (726)
.....++..+|+.|+..|..=.+...-.+....+.+|..+...+.+
T Consensus 482 ~~~~~~~~~~ld~L~~~L~~Laq~~p~~~a~~~r~~L~~~~~~~~~ 527 (840)
T PF04147_consen 482 SQDSPPPFEVLDSLIPHLYDLAQKYPEEAAECFREVLKEMQKRFRK 527 (840)
T ss_pred cccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3333678888888887765433333334444445555555555544
No 83
>PF14631 FancD2: Fanconi anaemia protein FancD2 nuclease; PDB: 3S4W_B.
Probab=26.44 E-value=6.3e+02 Score=33.62 Aligned_cols=197 Identities=13% Similarity=0.151 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHH
Q 004863 26 SPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKE 105 (726)
Q Consensus 26 iStdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKD 105 (726)
+...||+=+|+.|...|..+--.+.......|..-...-+.-..|.+.+.. -|+.|+..+|- .|..
T Consensus 960 Lgp~eLlFLLeDL~~KLe~~l~~~~~kr~pflk~~~~~~~gf~~l~q~~~~---ev~~~v~~llp-----------~l~~ 1025 (1426)
T PF14631_consen 960 LGPPELLFLLEDLVQKLEHVLTPSKAKRAPFLKAKGSKNIGFSHLCQRSPQ---EVASCVVQLLP-----------HLCN 1025 (1426)
T ss_dssp --HHHHHHHHHHHHHHHHHHH----------------------TTTTS-HH---HHHHHHHHHHH-----------HHHH
T ss_pred cCHHHHHHHHHHHHHHHHHhcCCcccccCchhhhcccccccchhHhhcCHH---HHHHHHHHHHH-----------HHHH
Q ss_pred HHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHH---HhhcCCchhHHHHHHHHHHH
Q 004863 106 FFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLK---VIRSNHPHFVFAAMETIMTL 182 (726)
Q Consensus 106 IFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFd---iVr~dhp~~V~~~M~dIMs~ 182 (726)
.+.-+...|..|....+..+..--.-.+..-.+++|. .++.++|..+|. .-...+..-+...+..|...
T Consensus 1026 hLE~~~~~fq~l~~e~~~v~d~~~~~~~e~~~~~sc~--------~~~l~~~~~ifsw~~f~~~~~~~lL~~~L~~la~r 1097 (1426)
T PF14631_consen 1026 HLENIHNYFQCLISENDGVVDGPDLFVQEFQYMSSCY--------QLLLQIFHTIFSWSGFSSPENRDLLKSALRSLASR 1097 (1426)
T ss_dssp HHHHHHHHHHH---------------HHHHHHHHHHH--------HHHHHHHHHHHT-TTTTSSTTHHHHHHHHHTT-TT
T ss_pred HHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHHH--------HHHHHHHHHHhccccccchhhHHHHHHHHHHHHhh
Q ss_pred HhcccCCCC-HHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHHHHHHhcCCCchhHHHHHHHHhc
Q 004863 183 VIDESEDVS-WDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIALDDYAEIVACICG 255 (726)
Q Consensus 183 VIeESE~VP-~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~~ns~G~~L~~YseIv~sIcq 255 (726)
+.......+ .+++.-+|.+|....... +....|..+++-+ +.+...+..-..+.+.++++|.
T Consensus 1098 ~~~~~~~~~~~~l~~~~f~Yl~~~~~s~--~~~~~A~~L~~ll---------~~l~~~~~~~~~~~~~ia~la~ 1160 (1426)
T PF14631_consen 1098 LKSKEKDQSLEELVSQSFKYLENFAKSV--PSLSCAVCLLQLL---------QSLSEKSSNPAQNKEKIAKLAR 1160 (1426)
T ss_dssp S--S-SS--HHHHHHHHHHHHHGGGGG----SHHHHHHHHHHH---------HHHHTT------HHHHHHHHHH
T ss_pred cccccccCCHHHHHHHHHHHHHHHHHhc--CcHHHHHHHHHHH---------HHHHhccchhHHHHHHHHHHHH
No 84
>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=26.43 E-value=1.5e+02 Score=28.92 Aligned_cols=69 Identities=9% Similarity=0.209 Sum_probs=47.9
Q ss_pred hhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHH
Q 004863 164 IRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLK 233 (726)
Q Consensus 164 Vr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~ 233 (726)
.++..+..=...+.+|.- +|...+.-|.+.+..|...|...+....--|..|.+.++.||+..+...|+
T Consensus 9 Tse~l~~~dw~~il~icD-~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~eva 77 (144)
T cd03568 9 TDEKLTSENWGLILDVCD-KVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVA 77 (144)
T ss_pred cCccCCCcCHHHHHHHHH-HHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHh
Confidence 344444443445555544 444457788999999999998777666667778888889999988766554
No 85
>KOG1062 consensus Vesicle coat complex AP-1, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.14 E-value=8.2e+02 Score=30.90 Aligned_cols=165 Identities=17% Similarity=0.200 Sum_probs=91.2
Q ss_pred HHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhh
Q 004863 58 LPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAK 137 (726)
Q Consensus 58 ~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAe 137 (726)
..+++.|+ .||...|.++|+-+|.-|+++.-=|||+-=|--++|-.||..-=+-. .+.--..+|.-||+
T Consensus 384 ~~mv~eLl--~fL~~~d~~~k~~~as~I~~laEkfaP~k~W~idtml~Vl~~aG~~V---------~~dv~~nll~LIa~ 452 (866)
T KOG1062|consen 384 RVMVKELL--EFLESSDEDFKADIASKIAELAEKFAPDKRWHIDTMLKVLKTAGDFV---------NDDVVNNLLRLIAN 452 (866)
T ss_pred HHHHHHHH--HHHHhccHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHhccccc---------chhhHHHHHHHHhc
Confidence 44555665 58999999999999999999999999998888788877776420000 01111112221111
Q ss_pred hhhheeeccCCchHHHHHHHHHHHHHhhcCCchh-HHHHHHHHHHHHhcccC-------------CCC-HHHHHHHHHHh
Q 004863 138 VRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHF-VFAAMETIMTLVIDESE-------------DVS-WDLLRILLASV 202 (726)
Q Consensus 138 VKS~VLmlDLE~ddLI~eLFktFFdiVr~dhp~~-V~~~M~dIMs~VIeESE-------------~VP-~eVLDvIL~~l 202 (726)
- . .++=..-|.-+|..+..+.... =...+..+++-+|.|.. .+. .+++|.|..-+
T Consensus 453 ~------~----~e~~~y~~~rLy~a~~~~~~~~is~e~l~qVa~W~IGEYGdlll~~~~~~~p~~vtesdivd~l~~v~ 522 (866)
T KOG1062|consen 453 A------F----QELHEYAVLRLYLALSEDTLLDISQEPLLQVASWCIGEYGDLLLDGANEEEPIKVTESDIVDKLEKVL 522 (866)
T ss_pred C------C----cchhhHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHhhhhhHHhhcCccccCCCcCCHHHHHHHHHHHH
Confidence 1 0 1111122222233222221100 01123666777777776 222 56777777666
Q ss_pred hccCCCCCchHHHHHHHH-----HhhhHHHHHHHHHHHHHhcCCCc
Q 004863 203 RKENQDVSPTSWKLGEKV-----FTKCAAKLKTNLKEAVQSRGIAL 243 (726)
Q Consensus 203 l~~~ks~~PaAykLA~~V-----I~~CadKLqp~I~q~~ns~G~~L 243 (726)
..+..+..--+|-|+.-. +..|..+++..|..|-.++.+.|
T Consensus 523 ~~~~s~~~tk~yal~Al~KLSsr~~s~~~ri~~lI~~~~~s~~~el 568 (866)
T KOG1062|consen 523 MSHSSDSTTKGYALTALLKLSSRFHSSSERIKQLISSYKSSLDTEL 568 (866)
T ss_pred HhccchHHHHHHHHHHHHHHHhhccccHHHHHHHHHHhcccccHHH
Confidence 655554433455544321 34457778888888776665554
No 86
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=25.95 E-value=7.1e+02 Score=30.30 Aligned_cols=16 Identities=25% Similarity=0.297 Sum_probs=8.9
Q ss_pred CCCHHHHHHHHHHhhc
Q 004863 189 DVSWDLLRILLASVRK 204 (726)
Q Consensus 189 ~VP~eVLDvIL~~ll~ 204 (726)
.|..+++..+|..++.
T Consensus 502 ~itl~la~~vL~~~~~ 517 (617)
T PRK14086 502 PVDLGLTEIVLRDLIP 517 (617)
T ss_pred CCCHHHHHHHHHHhhc
Confidence 3555566666655543
No 87
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=25.83 E-value=5.9e+02 Score=24.30 Aligned_cols=132 Identities=15% Similarity=0.177 Sum_probs=63.2
Q ss_pred HHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHH
Q 004863 82 TSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFL 161 (726)
Q Consensus 82 AcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFF 161 (726)
.-.+.+|.+++..+ ++..+.|..+|+..-.... .-.++|..-.+.|...-. ++ ...||..+.+.|.
T Consensus 17 ~~~~~~l~~~~~~~----~~~~~~l~~~i~~~~~~~~-~~~~~ya~L~~~l~~~~~--------~f-~~~ll~~~~~~f~ 82 (200)
T smart00543 17 ESIIKELLKLNNSD----KNLRKYILELIFEKAVEEP-NFIPAYARLCALLNAKNP--------DF-GSLLLERLQEEFE 82 (200)
T ss_pred HHHHHHHHHHHccC----HHHHHHHHHHHHHHHHcCc-chHHHHHHHHHHHHHHHH--------HH-HHHHHHHHHHHHH
Confidence 34445555555432 4566666666666543222 224555555555544321 11 2455666666655
Q ss_pred HHhhc---CCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCC----CCchHHHHHHHHHhhhHHHHH
Q 004863 162 KVIRS---NHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQD----VSPTSWKLGEKVFTKCAAKLK 229 (726)
Q Consensus 162 diVr~---dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks----~~PaAykLA~~VI~~CadKLq 229 (726)
..... .+-..+.. ....|..+. -...|+..++-.++..++..... ...-...++..++..|+..|.
T Consensus 83 ~~~e~~~~~~~~~~~~-~i~fl~eL~-~~~~i~~~~i~~~l~~ll~~~~~~~~~~~~~~ve~l~~lL~~~G~~l~ 155 (200)
T smart00543 83 KGLESEEESDKQRRLG-LVRFLGELY-NFQVLTSKIILELLKELLNDLTKLDPPRSDFSVECLLSLLPTCGKDLE 155 (200)
T ss_pred HHHHHHHHHhhhhHHh-HHHHHHHHH-HcccCcHHHHHHHHHHHHhccCCCCCCCcHHHHHHHHHHHHHhhHHHc
Confidence 42111 11111111 111122111 22346655555566665543322 223566777788888888887
No 88
>KOG4338 consensus Predicted lipoprotein [Lipid transport and metabolism]
Probab=25.68 E-value=3.9e+02 Score=35.85 Aligned_cols=173 Identities=14% Similarity=0.145 Sum_probs=0.0
Q ss_pred HHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHH
Q 004863 8 IELEEQLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISE 87 (726)
Q Consensus 8 ~ele~~l~~~G~kLis~piStdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaD 87 (726)
+.|++|+++-|-.=..|+.....+-..|+.|..+-..+++.+.. .++- .+.-|+.
T Consensus 319 e~Le~q~~~~~d~a~~pq~~e~~~~~kl~~l~s~a~~i~~~e~~------~~~e-------------------~~~tla~ 373 (1680)
T KOG4338|consen 319 EKLETQLLKPGDEAESPQLTESTSEQKLDLLESIAEQIEETENN------EPVE-------------------TRHTLAR 373 (1680)
T ss_pred HHHHHHHhcCCChhcCcccccchHHHHHHHHHHHHHHHhhhccc------cchh-------------------HHHHHHH
Q ss_pred HhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHHhhcC
Q 004863 88 ITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSN 167 (726)
Q Consensus 88 ILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~d 167 (726)
+.|+ +|++ +.+||+.||.+. |-+++.-...-+.++|.+++..+-..
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--HHHHHHHHHHHhcCCCchh
Q 004863 168 HPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAA--KLKTNLKEAVQSRGIALDD 245 (726)
Q Consensus 168 hp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~Cad--KLqp~I~q~~ns~G~~L~~ 245 (726)
..-.+..+| ...+..+..+++.-+.--....-++..+|+.+|+.|.. -+.++-....+ ..+..
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 004863 246 YAEIVACIC 254 (726)
Q Consensus 246 YseIv~sIc 254 (726)
|+-+|+-+|
T Consensus 485 a~t~V~~v~ 493 (1680)
T KOG4338|consen 485 AGTAVRGVF 493 (1680)
T ss_pred hchHhhhhh
No 89
>PF15611 EH_Signature: EH_Signature domain
Probab=25.55 E-value=9e+02 Score=26.33 Aligned_cols=111 Identities=17% Similarity=0.241 Sum_probs=65.6
Q ss_pred HHHHHHhhhcCCCCCCC--hhHHH---HHHHHHHHHhcccCCCCCc-chh--hHHHHHHHhhhhhhheeeccCCchHHHH
Q 004863 83 SCISEITRITAPDSPYD--DELMK---EFFQLAVSAFENLSHASGR-YYM--KALSILDTVAKVRSCLLMLDLECDKLVV 154 (726)
Q Consensus 83 cCLaDILRIyAPDAPYt--DdqLK---DIFqLfV~qf~~LsD~ssp-~Y~--q~~yLLEsLAeVKS~VLmlDLE~ddLI~ 154 (726)
-++.++-.++.+++|.. ..-|. ++...|- --+|.+.... +|. ...|+|+.+.... ..+++.
T Consensus 106 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~l~--~lgi~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~~ 174 (389)
T PF15611_consen 106 ELLRDIPELLSPNGPKWLAARLMQGDSSPLEELA--RLGIPPPHSSSWLWQALFSYYLEQIPELP---------DDEFLD 174 (389)
T ss_pred HHHHHhHhhhcccchHHHHHHHHhccccHHHHHH--HcCCCcccchhHHHHHHHHHHHHHHHhcC---------ChHHHH
Confidence 45666778889998833 33333 4444443 2244443333 322 2345555555544 456777
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHhc--ccCCCCHHHHHHHHHHhhccCC
Q 004863 155 EMFQHFLKVIRSNHPHFVFAAMETIMTLVID--ESEDVSWDLLRILLASVRKENQ 207 (726)
Q Consensus 155 eLFktFFdiVr~dhp~~V~~~M~dIMs~VIe--ESE~VP~eVLDvIL~~ll~~~k 207 (726)
++++.+ .+ ...+......+..+|...++ ..+.+...+.+.||..+..+.-
T Consensus 175 ~l~~~~--l~-~~~~~~~~~~~~~lL~~~~~~~~~~~~~~~l~~~~l~~~GdPr~ 226 (389)
T PF15611_consen 175 ELLKLL--LL-DGRPEQRKRALEALLERYIDRSPDEPVHEALRDLLLAIWGDPRL 226 (389)
T ss_pred HHHHHH--hh-ccchhHHHHHHHHHHHHHHhcCccchhhHHHHHHHHHHhCCCCC
Confidence 777774 23 33555555667777777776 2446888889999987776553
No 90
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=25.32 E-value=5.3e+02 Score=23.56 Aligned_cols=82 Identities=16% Similarity=0.134 Sum_probs=50.6
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccC-C--CCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHH
Q 004863 155 EMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESE-D--VSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTN 231 (726)
Q Consensus 155 eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE-~--VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~ 231 (726)
+.|+..+.-+.+..+. |+..=...|..+|.... . --+.++++++.++..++.=..-.|.+.-..++......+=+.
T Consensus 3 ~~~~~al~~L~dp~~P-vRa~gL~~L~~Li~~~~~~~~~~~~il~l~l~~L~d~DsyVYL~aI~~L~~La~~~p~~vl~~ 81 (92)
T PF10363_consen 3 ETLQEALSDLNDPLPP-VRAHGLVLLRKLIESKSEPVIDIPKILDLFLSQLKDEDSYVYLNAIKGLAALADRHPDEVLPI 81 (92)
T ss_pred HHHHHHHHHccCCCcc-hHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHHChHHHHHH
Confidence 4677777766665554 67777778888888776 2 223566666666655544344455555555566666655556
Q ss_pred HHHHHH
Q 004863 232 LKEAVQ 237 (726)
Q Consensus 232 I~q~~n 237 (726)
+++.|.
T Consensus 82 L~~~y~ 87 (92)
T PF10363_consen 82 LLDEYA 87 (92)
T ss_pred HHHHHh
Confidence 665554
No 91
>PLN02959 aminoacyl-tRNA ligase
Probab=25.18 E-value=84 Score=39.90 Aligned_cols=30 Identities=23% Similarity=0.080 Sum_probs=25.2
Q ss_pred chhhhHHHHHHHhhhcCCCCCCChhHHHHH
Q 004863 77 VRLSVTSCISEITRITAPDSPYDDELMKEF 106 (726)
Q Consensus 77 VRayVAcCLaDILRIyAPDAPYtDdqLKDI 106 (726)
.+..+.-||..++||.||=+||..++|-.-
T Consensus 847 ~~~~L~~vl~~~l~LLaP~~PfiaEEiW~~ 876 (1084)
T PLN02959 847 NRDLVWRFMDVQTRLITPICPHYAEHVWRE 876 (1084)
T ss_pred HHHHHHHHHHHHHHHHhhhhhHHHHHHHHh
Confidence 455778899999999999999999876643
No 92
>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=25.14 E-value=5.7e+02 Score=27.96 Aligned_cols=77 Identities=8% Similarity=0.143 Sum_probs=36.8
Q ss_pred hHHHHHHHHHHHHHhhcCCc------hhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCch----HHHHHHH
Q 004863 150 DKLVVEMFQHFLKVIRSNHP------HFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPT----SWKLGEK 219 (726)
Q Consensus 150 ddLI~eLFktFFdiVr~dhp------~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~Pa----AykLA~~ 219 (726)
..++..+|..-+..++.++- ...+..|..|......-.-.+|++....++..+..+-+.+.+. +......
T Consensus 112 ~~I~~~vf~~Tl~MI~~d~~~yPe~r~~ff~LL~~i~~~~f~~l~~lp~~~f~~~idsi~wg~kh~~~~I~~~~L~~l~~ 191 (319)
T PF08767_consen 112 PQILEAVFECTLPMINKDFEEYPEHRVNFFKLLRAINEHCFPALLQLPPEQFKLVIDSIVWGFKHTNREISETGLNILLE 191 (319)
T ss_dssp HHHHHHHHHHHHHHHSSTSSSSHHHHHHHHHHHHHHHHHHTHHHHHS-HHHHHHHHHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhhhhhChHHHHHHHHHHHHHHHHhHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence 45555666666666654322 2233333333333333333477777777777766554444333 3333344
Q ss_pred HHhhhHH
Q 004863 220 VFTKCAA 226 (726)
Q Consensus 220 VI~~Cad 226 (726)
+++++..
T Consensus 192 ll~~~~~ 198 (319)
T PF08767_consen 192 LLNNVSK 198 (319)
T ss_dssp HHHHHHH
T ss_pred HHHHHHh
Confidence 4444444
No 93
>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=25.10 E-value=8e+02 Score=28.47 Aligned_cols=115 Identities=16% Similarity=0.218 Sum_probs=64.5
Q ss_pred hhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhhe--e--
Q 004863 68 DLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCL--L-- 143 (726)
Q Consensus 68 ~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~V--L-- 143 (726)
..|.|.+..||.+++-.|..+.|- ++.-..--.=.+||.+++..+ .+++...-.....+|..|+...... |
T Consensus 84 ~gL~h~~~~Vr~l~l~~l~~~~~~--~~~~~~~~~~~~l~~~i~~~L---~~~d~~Va~~A~~~L~~l~~~~~~~~~l~~ 158 (503)
T PF10508_consen 84 RGLTHPSPKVRRLALKQLGRIARH--SEGAAQLLVDNELLPLIIQCL---RDPDLSVAKAAIKALKKLASHPEGLEQLFD 158 (503)
T ss_pred HHhcCCCHHHHHHHHHHHHHHhcC--CHHHHHHhcCccHHHHHHHHH---cCCcHHHHHHHHHHHHHHhCCchhHHHHhC
Confidence 356799999999887776555543 111000001124555555554 6777777788888888888764333 1
Q ss_pred ---eccCC------chHHHHHHHHHHHHHhhcCCchhHHHHHHH--HHHHHhcccCC
Q 004863 144 ---MLDLE------CDKLVVEMFQHFLKVIRSNHPHFVFAAMET--IMTLVIDESED 189 (726)
Q Consensus 144 ---mlDLE------~ddLI~eLFktFFdiVr~dhp~~V~~~M~d--IMs~VIeESE~ 189 (726)
+.+|. .+.+-..++..+-.+. .++......+.+ ++..++.|.+.
T Consensus 159 ~~~~~~L~~l~~~~~~~vR~Rv~el~v~i~--~~S~~~~~~~~~sgll~~ll~eL~~ 213 (503)
T PF10508_consen 159 SNLLSKLKSLMSQSSDIVRCRVYELLVEIA--SHSPEAAEAVVNSGLLDLLLKELDS 213 (503)
T ss_pred cchHHHHHHHHhccCHHHHHHHHHHHHHHH--hcCHHHHHHHHhccHHHHHHHHhcC
Confidence 11111 1223334444444432 355666666654 77777777766
No 94
>PF11707 Npa1: Ribosome 60S biogenesis N-terminal; InterPro: IPR021714 Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits []. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre []. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length.
Probab=24.87 E-value=4.4e+02 Score=28.75 Aligned_cols=165 Identities=12% Similarity=0.161 Sum_probs=96.3
Q ss_pred CCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHH
Q 004863 25 PSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMK 104 (726)
Q Consensus 25 piStdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLK 104 (726)
+.-..+||..=..+...+..|.+|+.+-...-|..+...++....+...-+ ++++-.-||..|..+|.=+.|=....+.
T Consensus 147 ~~~~~~lL~~~~~~~~l~k~l~~D~~~~v~~iL~~l~~~Vl~~~~v~r~~K-~~~fn~~~L~~l~~Ly~~~~~~~~~~~~ 225 (330)
T PF11707_consen 147 PELKRDLLSQKKLMSALFKGLRKDPPETVILILETLKDKVLKDSSVSRSTK-CKLFNEWTLSQLASLYSRDGEDEKSSVA 225 (330)
T ss_pred HHHHHHHHHcCchHHHHHhcccCCCHHHHHHHHHHHHHHhccCCCCChhhh-hhhcCHHHHHHHHHHhcccCCcccchHH
Confidence 333555554444588888899998887666666777777777776655444 7888888999999888877771112222
Q ss_pred HHHHHHHHHhc-----ccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHH
Q 004863 105 EFFQLAVSAFE-----NLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETI 179 (726)
Q Consensus 105 DIFqLfV~qf~-----~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~dhp~~V~~~M~dI 179 (726)
+...-|+-.+- ||.=++...|..-. -..+
T Consensus 226 ~~vh~fL~~lcT~p~~Gv~f~d~~~~~~~~----------------------------------------------~~~~ 259 (330)
T PF11707_consen 226 DLVHEFLLALCTDPKHGVCFPDNGWYPRES----------------------------------------------DSGV 259 (330)
T ss_pred HHHHHHHHHHhcCCCcccccCCCCcCcCcc----------------------------------------------cccc
Confidence 22222222211 12112221111111 0000
Q ss_pred HHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHHHHHHhc
Q 004863 180 MTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSR 239 (726)
Q Consensus 180 Ms~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~~ns~ 239 (726)
....-...-.+...+|-.+|..|. ....+....|+-.|+..|.+=+.+|+..+-..+
T Consensus 260 ~~~~~~~~~~~~Nk~L~~ll~~lk---p~e~~~q~~Lvl~Il~~~PeLva~Y~~~~~~~~ 316 (330)
T PF11707_consen 260 PVTINNKSFKINNKLLLNLLKKLK---PWEDDRQQELVLKILKACPELVAPYFNNLPYSL 316 (330)
T ss_pred cccccCCCCCcccHHHHHHHHHCC---CCccHHHHHHHHHHHHHChHHHHHHHHhhhhhC
Confidence 011112233566677777776443 234557889999999999999999998875443
No 95
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=24.75 E-value=1.6e+03 Score=29.03 Aligned_cols=198 Identities=12% Similarity=0.143 Sum_probs=108.7
Q ss_pred HHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHH-HHHHhhhcCCCCCCChhHHHHHHHHH
Q 004863 32 INLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSC-ISEITRITAPDSPYDDELMKEFFQLA 110 (726)
Q Consensus 32 LKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcC-LaDILRIyAPDAPYtDdqLKDIFqLf 110 (726)
+-.|+.++.-|..+++-|.= ...|.|+....+..-|-+|.- -.|-=|| |++=+=.+.|+. .-+|-.+|.++
T Consensus 616 ~GiL~Ti~Til~s~e~~p~v--l~~le~~~l~vi~~iL~~~i~---dfyeE~~ei~~~~t~~~~~I---sp~mW~ll~li 687 (1010)
T KOG1991|consen 616 SGILRTISTILLSLENHPEV--LKQLEPIVLPVIGFILKNDIT---DFYEELLEIVSSLTFLSKEI---SPIMWGLLELI 687 (1010)
T ss_pred HHHHHHHHHHHHHHhccHHH--HHHHHHHHHHHHHHHHHHhhH---HHHHHHHHHHhhhhhhhccc---CHHHHHHHHHH
Confidence 45677888888888886532 445555555555544444432 2333333 555554555542 24788999999
Q ss_pred HHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHhcccCCC
Q 004863 111 VSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRSNHPHFVFAAMETIMTLVIDESEDV 190 (726)
Q Consensus 111 V~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~dhp~~V~~~M~dIMs~VIeESE~V 190 (726)
...|. +...-||..+.-.|.++-.+-.--++-.-.--.++.+|.+..+..- +....=......||..||-.+...
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---DDGIDYFTDMMPALHNYVTYGTPSLLSNPDYLQILLEIIKKVLTSE--NGEDSDCESACKLLEVIILNCKGL 762 (1010)
T ss_pred HHHHh---hhhHHHHHHHHHHHhhheeeCchhhhccchHHHHHHHHHHHHHcCC--CCchHHHHHHHHHHHHHHHHhcCc
Confidence 88886 3345688888889998766643322222222345555555555321 222222222344555555555553
Q ss_pred CHH----HHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHHHHHHhcCCCch
Q 004863 191 SWD----LLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQSRGIALD 244 (726)
Q Consensus 191 P~e----VLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~~ns~G~~L~ 244 (726)
... .+.+.+..+... ......+.++-+|+-+|-.-=-.-.-+.+...|...+
T Consensus 763 ~dq~iplf~~~a~~~l~~~--~e~s~~~~~~leVvinalyynP~ltL~iLe~~~~~~~ 818 (1010)
T KOG1991|consen 763 LDQYIPLFLELALSRLTRE--VETSELRVMLLEVVINALYYNPKLTLGILENQGFLNN 818 (1010)
T ss_pred HhhHhHHHHHHHHHHHhcc--ccchHHHHHHHHHHHHHHHcCcHHHHHHHHHcCCccc
Confidence 333 344444555443 2344677788888877765433334455666666543
No 96
>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=24.68 E-value=5.7e+02 Score=26.80 Aligned_cols=17 Identities=12% Similarity=0.132 Sum_probs=7.4
Q ss_pred hHHHHHHHHHHHHhccc
Q 004863 101 ELMKEFFQLAVSAFENL 117 (726)
Q Consensus 101 dqLKDIFqLfV~qf~~L 117 (726)
++...||..|...+..|
T Consensus 71 ~~~~~i~~~~~~~~~~l 87 (322)
T cd07920 71 EQRLQLLEKILGHVVRL 87 (322)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 44444444444444333
No 97
>PLN03076 ARF guanine nucleotide exchange factor (ARF-GEF); Provisional
Probab=24.64 E-value=6.6e+02 Score=34.29 Aligned_cols=130 Identities=15% Similarity=0.223 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHHHHhcccCCch-hhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCCh--hHHHHH
Q 004863 30 EVINLLDKVEHLLANVEQAPSR-SMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDD--ELMKEF 106 (726)
Q Consensus 30 ELLKRLkkL~~eLs~lDQ~pvd-S~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtD--dqLKDI 106 (726)
++-..|-.|+=-+.-++....- .....|..+.+.=+-..||++.-..+-.....|+.=++.|+ .. ..||.=
T Consensus 373 ~~rsKllsL~Li~~ile~~g~~f~~~~~fi~~ik~~Lc~sL~~n~~S~~~~vf~lsl~If~~L~------~~~R~~LK~e 446 (1780)
T PLN03076 373 LMRGKILALELLKILLENAGAVFRTSDRFLGAIKQYLCLSLLKNSASSLMIIFQLSCSIFISLV------SRFRAGLKAE 446 (1780)
T ss_pred HHHHHHHHHHHHHHHHhcccHhhhcCHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH------HHHHHHHHHH
Confidence 3444444555444444443221 11223333444444455555544444333333333333331 11 455544
Q ss_pred HHHHHHH--hcccCCCCCcchhhHHHHHHHhhhh-hhheeeccC----Cc----hHHHHHHHHHHHHHhh
Q 004863 107 FQLAVSA--FENLSHASGRYYMKALSILDTVAKV-RSCLLMLDL----EC----DKLVVEMFQHFLKVIR 165 (726)
Q Consensus 107 FqLfV~q--f~~LsD~ssp~Y~q~~yLLEsLAeV-KS~VLmlDL----E~----ddLI~eLFktFFdiVr 165 (726)
+.+|+.. |+-|....++.|.|..++|+.|..+ +-=-+|+|| || ..|+.+|-+.+..++-
T Consensus 447 ievF~~~I~l~ile~~~~~s~~qK~~~L~~L~~lc~dp~~lveiyvNYDCD~~~~NifE~lv~~Lsk~a~ 516 (1780)
T PLN03076 447 IGVFFPMIVLRVLENVAQPNFQQKMIVLRFLDKLCVDSQILVDIFINYDCDVNSSNIFERMVNGLLKTAQ 516 (1780)
T ss_pred HHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCccHHHHHHhccCCCCCCchHHHHHHHHHHHHhc
Confidence 4455544 3334445578899999999999887 333444554 44 4666666666665544
No 98
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=24.13 E-value=3.1e+02 Score=34.96 Aligned_cols=55 Identities=20% Similarity=0.269 Sum_probs=34.2
Q ss_pred CCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHH--hcccCCCCCcchhhHHHHHHHhhh
Q 004863 73 SDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSA--FENLSHASGRYYMKALSILDTVAK 137 (726)
Q Consensus 73 KDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~q--f~~LsD~ssp~Y~q~~yLLEsLAe 137 (726)
+|.-.|++.+.| +||+= .+|| ++++..|+-+ |+.+.++-+-.-.|..++|-.++.
T Consensus 435 kdGAL~~vgsl~--~~L~K---~s~~-----~~~mE~flv~hVfP~f~s~~g~Lrarac~vl~~~~~ 491 (1010)
T KOG1991|consen 435 KDGALRMVGSLA--SILLK---KSPY-----KSQMEYFLVNHVFPEFQSPYGYLRARACWVLSQFSS 491 (1010)
T ss_pred hhhHHHHHHHHH--HHHcc---CCch-----HHHHHHHHHHHhhHhhcCchhHHHHHHHHHHHHHHh
Confidence 455556666655 77754 3444 6677777766 777776665555666666666653
No 99
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=23.86 E-value=2.1e+02 Score=27.33 Aligned_cols=69 Identities=16% Similarity=0.251 Sum_probs=47.1
Q ss_pred HhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHH
Q 004863 163 VIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNL 232 (726)
Q Consensus 163 iVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I 232 (726)
+.++..+..=...+..| ..+|.....-+.+++..|-..|...+....-.|-.|...++.+|+..+...|
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 44444444333444443 3466666788899999999999887766666777888888999988887665
No 100
>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=23.85 E-value=73 Score=27.33 Aligned_cols=61 Identities=15% Similarity=0.136 Sum_probs=35.2
Q ss_pred hccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHH-HHHH-hcccCCCCCcchhhHHHHHHHhh
Q 004863 69 LLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQL-AVSA-FENLSHASGRYYMKALSILDTVA 136 (726)
Q Consensus 69 LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqL-fV~q-f~~LsD~ssp~Y~q~~yLLEsLA 136 (726)
+|.+.|..|+..++-||..|.+-.. .....+... ++.. +..|.+.+........++|.+|+
T Consensus 57 ~l~~~~~~v~~~a~~~L~~l~~~~~-------~~~~~~~~~g~l~~l~~~l~~~~~~~~~~a~~~l~~l~ 119 (120)
T cd00020 57 LLKSEDEEVVKAALWALRNLAAGPE-------DNKLIVLEAGGVPKLVNLLDSSNEDIQKNATGALSNLA 119 (120)
T ss_pred HHhCCCHHHHHHHHHHHHHHccCcH-------HHHHHHHHCCChHHHHHHHhcCCHHHHHHHHHHHHHhh
Confidence 5667899999999999999975421 112222221 2333 22334444445566667776664
No 101
>cd05394 RasGAP_RASA2 RASA2 (or GAP1(m)) is a member of the GAP1 family of Ras GTPase-activating proteins that includes GAP1_IP4BP (or RASA3), CAPRI, and RASAL. In vitro, RASA2 has been shown to bind inositol 1,3,4,5-tetrakisphosphate (IP4), the water soluble inositol head group of the lipid second messenger phosphatidylinositol 3,4,5-trisphosphate (PIP3). In vivo studies also demonstrated that RASA2 binds PIP3, and it is recruited to the plasma membrane following agonist stimulation of PI 3-kinase. Furthermore, the membrane translocation is a consequence of the ability of its pleckstrin homology (PH) domain to bind PIP3.
Probab=23.49 E-value=5.6e+02 Score=28.65 Aligned_cols=38 Identities=11% Similarity=0.146 Sum_probs=25.6
Q ss_pred HHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCCh
Q 004863 61 MKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDD 100 (726)
Q Consensus 61 ~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtD 100 (726)
+..||. ||.|.+.-+-.+-+.|-.||.|..-|..=|-.
T Consensus 38 a~~Lvr--lf~~~~~~~~fl~~li~~Ev~~t~~~~tLFRg 75 (313)
T cd05394 38 VLPLVR--LLLHHQKLVPFVAAVAELDLKDTQEANTIFRG 75 (313)
T ss_pred HHHHHH--HHHhcCcHHHHHHHHHHHHHHhcCCHhhHhhc
Confidence 334665 77777777777778888888877655555543
No 102
>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=23.39 E-value=6.4e+02 Score=23.88 Aligned_cols=166 Identities=14% Similarity=0.159 Sum_probs=79.7
Q ss_pred HHHHhccccCCCCCCHHHHHHHHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhc
Q 004863 13 QLKDAGNLLLNPPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRIT 92 (726)
Q Consensus 13 ~l~~~G~kLis~piStdELLKRLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIy 92 (726)
.+..+-++|- +...+.++.-|..+.... + ...+..++..+++.....+ .-+.+|+..|-.=..++
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 4445555554 455666665555443322 1 2345666667777666666 55777777774422222
Q ss_pred CCCCCCChhHHHHHHHHHHHHhcc------cCCCCCcchhhHHHHHHHhhhhhhheeeccCCchHHHHHHHHHHHHHhhc
Q 004863 93 APDSPYDDELMKEFFQLAVSAFEN------LSHASGRYYMKALSILDTVAKVRSCLLMLDLECDKLVVEMFQHFLKVIRS 166 (726)
Q Consensus 93 APDAPYtDdqLKDIFqLfV~qf~~------LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~ddLI~eLFktFFdiVr~ 166 (726)
| .+-...+...+...|.. +.........+...++.=|++.=.+-+ =...+|.+++..++.....
T Consensus 68 -~-----~~f~~~ll~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~v----v~~~~i~~~l~~ll~~~~~ 137 (209)
T PF02854_consen 68 -P-----SEFRSLLLNRCQEEFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFGV----VSEKIIFDILRELLSDGTD 137 (209)
T ss_dssp -H-----HHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS----SCHHHHHHHHHHHHHHTSH
T ss_pred -h-----hhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhcc----ccchhHHHHHHHHHhcccc
Confidence 1 22222333333344443 222233344445555555554421111 1345666666666664332
Q ss_pred C----CchhHHHHHHHHHHHHhcccC--CCCHHHHHHHHHHhh
Q 004863 167 N----HPHFVFAAMETIMTLVIDESE--DVSWDLLRILLASVR 203 (726)
Q Consensus 167 d----hp~~V~~~M~dIMs~VIeESE--~VP~eVLDvIL~~ll 203 (726)
. -...-..++..+|..+=...+ ......++.+|..+.
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 1 112333445555555444444 455556666666554
No 103
>smart00188 IL10 Interleukin-10 family. Interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells.
Probab=22.73 E-value=53 Score=32.47 Aligned_cols=50 Identities=22% Similarity=0.290 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhcccCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHH-HHHHhhhc
Q 004863 34 LLDKVEHLLANVEQAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSC-ISEITRIT 92 (726)
Q Consensus 34 RLkkL~~eLs~lDQ~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcC-LaDILRIy 92 (726)
+|++|....+++...-. +.+. +-.-|+...+|+ +++.+.+|| +.+|||.|
T Consensus 4 ~L~eLR~~f~~Ik~~~q--~kD~---~~~vll~~~ll~----~~k~~~gC~~l~ell~FY 54 (137)
T smart00188 4 MLRELRAAFSRVKTFFQ--MKDQ---LDNILLTESLLE----DFKGYLGCQALSEMIQFY 54 (137)
T ss_pred HHHHHHHHHHHHHHHHH--ccch---HhhHhhhHHHHH----HhCCCcchHHHHHHHHHH
Confidence 45666666665533200 0122 222366667775 588899999 78899985
No 104
>KOG0929 consensus Guanine nucleotide exchange factor [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.49 E-value=3.5e+02 Score=36.05 Aligned_cols=80 Identities=18% Similarity=0.342 Sum_probs=57.3
Q ss_pred CCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCCCCcchhhHHHHHHHhhhhhhheeeccCCchH
Q 004863 72 RSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHASGRYYMKALSILDTVAKVRSCLLMLDLECDK 151 (726)
Q Consensus 72 HKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~ssp~Y~q~~yLLEsLAeVKS~VLmlDLE~dd 151 (726)
-.+.+||.+.---+-+||+=|.-+ |+.+--.+||.++|.-|..+....... .+.-.+.+++.. +-.
T Consensus 1185 ~~~~~vr~~al~vlF~il~~~g~~--F~~~~We~v~~~~fpIF~~~~~~~~~~-~~~eW~~tT~~~-----------Al~ 1250 (1514)
T KOG0929|consen 1185 DYRLEVRKRALEVLFDILKEHGDD--FSKEFWEDVFRILFPIFDNVKLDEDES-EKDEWLSTTCNH-----------ALQ 1250 (1514)
T ss_pred ccHHHHHHHHHHHHHHHHHhhhhh--ccHHHHHHHHHheeecccccCcccchh-hhhHHHHHHHHH-----------HHH
Confidence 366778877777788888876655 677889999998899999887766554 222244444322 456
Q ss_pred HHHHHHHHHHHHhh
Q 004863 152 LVVEMFQHFLKVIR 165 (726)
Q Consensus 152 LI~eLFktFFdiVr 165 (726)
++++||..||+.++
T Consensus 1251 ~~v~lf~~~~~~l~ 1264 (1514)
T KOG0929|consen 1251 ALVDLFTQFFKQLN 1264 (1514)
T ss_pred HHHHHHHHHHHHHH
Confidence 78889999998776
No 105
>PF02106 Fanconi_C: Fanconi anaemia group C protein; InterPro: IPR000686 Fanconi anaemia (FA) [, , ] is a recessive inherited disease characterised by defective DNA repair. FA cells are sensitive to DNA cross-linking agents that cause chromosomal instability and cell death. The disease is manifested clinically by progressive pancytopenia, variable physical anomalies, and predisposition to malignancy. Four complementation groups have been identified, designated A to D. The gene for group C (FACC) has been cloned. Expression of the FACC cDNA corrects the phenotypic defect of FA(C) cells, resulting in normalized cell growth in the presence of DNA cross-linking agents such as mitomycin C (MMC). Gene transfer of the FACC gene should provide a survival advantage to transduced hematopoietic cells, suggesting that FA might be an ideal candidate for gene therapy []. The function of the FACC gene is not known. Immunofluorescence and sub-cellular fractionation studies of human cell lines, and COS-7 cells transiently expressing human FACC, showed the protein to be located primarily in the cytoplasm. Yet, placement of a nuclear localisation signal at the N terminus of FACC directed the hybrid protein to the nuclei of transfected COS-7 cells. Such findings suggest an indirect role for FACC in regulating DNA repair in this group of Fanconi anaemia [].; GO: 0006281 DNA repair
Probab=22.17 E-value=4.3e+02 Score=31.65 Aligned_cols=85 Identities=15% Similarity=0.348 Sum_probs=62.5
Q ss_pred hhheeeccC-CchHHHHHHH------------HHHHHHhhc-------------------CCchhHHHHHHHHHHHHhcc
Q 004863 139 RSCLLMLDL-ECDKLVVEMF------------QHFLKVIRS-------------------NHPHFVFAAMETIMTLVIDE 186 (726)
Q Consensus 139 KS~VLmlDL-E~ddLI~eLF------------ktFFdiVr~-------------------dhp~~V~~~M~dIMs~VIeE 186 (726)
..||.++-+ +...||..|- ..||+.|++ .|-..++..|..++..+|.-
T Consensus 186 ~~CiPLvTlpd~~PLveaLL~~hg~~~~e~L~~eFleaVneAfl~kki~L~esAvvsLWlrhLPSLE~A~L~Lle~lis~ 265 (559)
T PF02106_consen 186 RVCIPLVTLPDFEPLVEALLTYHGHEPQEVLSPEFLEAVNEAFLSKKISLSESAVVSLWLRHLPSLEKAVLHLLEKLISS 265 (559)
T ss_pred HHHHHHhcCcccchHHHHHHHhCCCChHHHhcHHHHHHHHHHHHhcccCCcHHHHHHHHHhhcchHHHHHHHHHHHHHhc
Confidence 456666666 3556666655 478998886 46677889999999999998
Q ss_pred cCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhh
Q 004863 187 SEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKC 224 (726)
Q Consensus 187 SE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~C 224 (726)
....+.++--.|=..+++. ...+|+-|+..-+++++.
T Consensus 266 ~~~sl~~~e~~i~dSlLPq-aA~HpaIFriVdeifr~a 302 (559)
T PF02106_consen 266 ERNSLQRMECFIKDSLLPQ-AACHPAIFRIVDEIFRNA 302 (559)
T ss_pred CCccHHHHHHHHHhhhchh-hhcchHHHHHHHHHHHHH
Confidence 7777877777666777766 667888888887777543
No 106
>PF04928 PAP_central: Poly(A) polymerase central domain; InterPro: IPR007012 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolutio has been determined []. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta-sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.; GO: 0004652 polynucleotide adenylyltransferase activity, 0006351 transcription, DNA-dependent; PDB: 1Q79_A 1Q78_A 1F5A_A 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A.
Probab=22.16 E-value=6.5e+02 Score=27.05 Aligned_cols=45 Identities=22% Similarity=0.324 Sum_probs=33.5
Q ss_pred hhhhhhhccC-CCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhc
Q 004863 63 GLITNDLLRR-SDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFE 115 (726)
Q Consensus 63 ~LVs~~LLkH-KDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~ 115 (726)
++....+|.+ .+..+|.+-+|+.+|.++=..|+. +.|+..++.++
T Consensus 72 ~~~~~~~l~~ld~~s~~sLnG~Rv~~~il~~Vp~~--------~~Fr~~lR~IK 117 (254)
T PF04928_consen 72 DLLDDDPLRNLDEASVRSLNGVRVTDYILRLVPNQ--------ETFRTALRFIK 117 (254)
T ss_dssp -TT-GGGGTT--HHHHHHHHHHHHHHHHHCTSS-H--------HHHHHHHHHHH
T ss_pred ccCCchhhhCCCHhhccCcccccHHHHHHHHCCCH--------HHHHHHHHHHH
Confidence 6677788877 557899999999888887778887 88888888765
No 107
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=22.07 E-value=2.9e+02 Score=26.89 Aligned_cols=59 Identities=17% Similarity=0.215 Sum_probs=43.7
Q ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHH
Q 004863 174 AAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLK 233 (726)
Q Consensus 174 ~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~ 233 (726)
..+..|.- +|...+.-|-+.+..|-..|...+....--|..|.+.++.+|+.++...|+
T Consensus 23 ~~ileicD-~In~~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~eva 81 (142)
T cd03569 23 ASILEICD-MIRSKDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVA 81 (142)
T ss_pred HHHHHHHH-HHhCCCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHh
Confidence 33444433 445556678999999999998887777777888889999999988765544
No 108
>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=21.97 E-value=1.2e+03 Score=27.59 Aligned_cols=143 Identities=17% Similarity=0.151 Sum_probs=72.7
Q ss_pred HhhHHHHHhhhhhhhccCC--CcCchhhhHHHHHHHhhhcCC-CCCCCh---hHHHHHHHHHHHH-hcccCCCCCcchhh
Q 004863 55 DALLPTMKGLITNDLLRRS--DMDVRLSVTSCISEITRITAP-DSPYDD---ELMKEFFQLAVSA-FENLSHASGRYYMK 127 (726)
Q Consensus 55 ~SL~pl~k~LVs~~LLkHK--DkdVRayVAcCLaDILRIyAP-DAPYtD---dqLKDIFqLfV~q-f~~LsD~ssp~Y~q 127 (726)
.++.++.-.++.+=|+.|. -++.|+.-.-=+-.|||++=| ...... ++|..||-.+-.. |.+ .+.+ ...+
T Consensus 72 K~~s~~vi~yleriL~~~~~~~~g~~li~p~~F~~ll~~~f~~~~~~~k~l~e~l~~~yp~LK~la~~~--~p~s-~~~~ 148 (469)
T PF10151_consen 72 KSYSPYVIQYLERILSLHGNVTKGERLIPPQEFFPLLRLTFPPSNSLSKALQERLEAIYPRLKELAFAG--KPGS-TLHT 148 (469)
T ss_pred CCcchHHHHHHHHHHhcCcccccCcCCCCHHHHHHHHHHhcCCcccCCHHHHHHHHHHHHHHHHHHhcC--Cchh-HHHH
Confidence 4567777788888888887 457777777788888998443 333222 4555555544433 332 2222 2233
Q ss_pred HHHHHHHhhhhhhheeeccC--C-chHHHHHHHHH--HHHHhhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHh
Q 004863 128 ALSILDTVAKVRSCLLMLDL--E-CDKLVVEMFQH--FLKVIRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASV 202 (726)
Q Consensus 128 ~~yLLEsLAeVKS~VLmlDL--E-~ddLI~eLFkt--FFdiVr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~l 202 (726)
+|-.+-.++ ...|- .++ | ++-||.-|.+. +|..=|..+++++... ..+|..|+++-..++..+-. -|..+
T Consensus 149 ~f~~~l~~~-~~~~~--~~~~~E~~~~li~CLt~d~~c~~~Wr~lY~knl~~S-~llL~~l~~~W~~~s~KL~k-~l~~T 223 (469)
T PF10151_consen 149 YFPSFLSKA-TPECP--PELKKELISILIWCLTQDPDCFKVWRQLYKKNLKQS-VLLLKHLDDEWKESSKKLSK-SLKET 223 (469)
T ss_pred HHHHHHHHh-cccCC--HHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhHHHH-HHHHHHHHHhHHhhhHHHHH-HHHHH
Confidence 333322222 11110 011 0 11222222222 4444444455555443 34677777777777777665 44554
Q ss_pred hcc
Q 004863 203 RKE 205 (726)
Q Consensus 203 l~~ 205 (726)
+..
T Consensus 224 l~s 226 (469)
T PF10151_consen 224 LKS 226 (469)
T ss_pred HHH
Confidence 443
No 109
>PF05004 IFRD: Interferon-related developmental regulator (IFRD); InterPro: IPR007701 Interferon-related developmental regulator (IFRD1) is the human homologue of the Rattus norvegicus early response protein PC4 and its murine homologue TIS7 []. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary for muscle differentiation and that it might have a role in signal transduction. This entry also contains IFRD2 and its murine equivalent SKMc15, which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis [].
Probab=21.94 E-value=1.7e+02 Score=31.95 Aligned_cols=43 Identities=33% Similarity=0.536 Sum_probs=31.8
Q ss_pred HHHHhhhhhhhccCCCcCchhhhHHHHH---HHhhhcCCCCCCCh-hHH
Q 004863 59 PTMKGLITNDLLRRSDMDVRLSVTSCIS---EITRITAPDSPYDD-ELM 103 (726)
Q Consensus 59 pl~k~LVs~~LLkHKDkdVRayVAcCLa---DILRIyAPDAPYtD-dqL 103 (726)
..+..|+ .||.+.|.+||+.++-||+ |+.|-...+.+|.+ ++|
T Consensus 228 ~~~~~l~--~lL~s~d~~VRiAAGEaiAll~E~~~~~~~~~~~~~~~~l 274 (309)
T PF05004_consen 228 EALPALS--ELLDSDDVDVRIAAGEAIALLYELARDHEEDFLYEDMEEL 274 (309)
T ss_pred HHHHHHH--HHhcCCCHHHHHHHHHHHHHHHHHhhcccccccccCHHHH
Confidence 3344444 3999999999999999977 88887777776765 344
No 110
>PLN02381 valyl-tRNA synthetase
Probab=21.72 E-value=71 Score=40.48 Aligned_cols=31 Identities=16% Similarity=0.238 Sum_probs=24.8
Q ss_pred chhhhHHHHHHHhhhcCCCCCCChhHHHHHH
Q 004863 77 VRLSVTSCISEITRITAPDSPYDDELMKEFF 107 (726)
Q Consensus 77 VRayVAcCLaDILRIyAPDAPYtDdqLKDIF 107 (726)
.+..+..||-.++|+.||=+||..++|-..|
T Consensus 840 a~~~L~~vL~~llrLL~PfmPfitEELw~~L 870 (1066)
T PLN02381 840 AQDTLWICLDTGLRLLHPFMPFVTEELWQRL 870 (1066)
T ss_pred HHHHHHHHHHHHHHHHHhHhHHHHHHHHHHh
Confidence 3445667899999999999999999875544
No 111
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=21.53 E-value=1e+03 Score=25.43 Aligned_cols=52 Identities=27% Similarity=0.373 Sum_probs=30.3
Q ss_pred hhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCChhHHHHHHHHHHHHhc
Q 004863 56 ALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDDELMKEFFQLAVSAFE 115 (726)
Q Consensus 56 SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtDdqLKDIFqLfV~qf~ 115 (726)
+|..+...||.+.+-++ |..||...--||.=.- + ++.+.-.+-|.+|+.+|.
T Consensus 23 ~l~~ll~~lI~P~v~~~-~~~vR~~al~cLGl~~-L------ld~~~a~~~l~l~~~~~~ 74 (298)
T PF12719_consen 23 SLESLLDSLILPAVQSS-DPAVRELALKCLGLCC-L------LDKELAKEHLPLFLQALQ 74 (298)
T ss_pred hHHHHHHHHHHHHhcCC-CHHHHHHHHHHHHHHH-H------hChHHHHHHHHHHHHHHH
Confidence 55688999999887655 4456554444433111 1 122455666777777773
No 112
>PLN03076 ARF guanine nucleotide exchange factor (ARF-GEF); Provisional
Probab=21.50 E-value=1.4e+03 Score=31.42 Aligned_cols=38 Identities=18% Similarity=0.182 Sum_probs=30.1
Q ss_pred HHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCC
Q 004863 58 LPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSP 97 (726)
Q Consensus 58 ~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAP 97 (726)
-|+...|.. +....+.+||-.+--.|-+||.-|-...|
T Consensus 1346 ~pLL~~Ls~--l~~D~RlEVR~~ALqtLF~iL~~yG~~Fs 1383 (1780)
T PLN03076 1346 FPLLAGLSE--LSFDPRPEIRKSALQVLFDTLRNHGHLFS 1383 (1780)
T ss_pred HHHHHHHHH--HhcCCcHHHHHHHHHHHHHHHHHhhccCC
Confidence 567777766 34478999999999999999988877755
No 113
>KOG1241 consensus Karyopherin (importin) beta 1 [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.23 E-value=1.1e+03 Score=29.79 Aligned_cols=68 Identities=13% Similarity=0.249 Sum_probs=38.3
Q ss_pred hccCCCcCchhhhHHH-----HHHHhhhcCCCCCCChhHHHHHHHHHHHHhcccCCC-CCcchhhHHHHHHHhhh
Q 004863 69 LLRRSDMDVRLSVTSC-----ISEITRITAPDSPYDDELMKEFFQLAVSAFENLSHA-SGRYYMKALSILDTVAK 137 (726)
Q Consensus 69 LLkHKDkdVRayVAcC-----LaDILRIyAPDAPYtDdqLKDIFqLfV~qf~~LsD~-ssp~Y~q~~yLLEsLAe 137 (726)
|+.--...-|+...|| |+|-.-=.+|..|-++. +.-.|..||.+|-+..|- +..-+.-|...-+.|-+
T Consensus 454 l~~gL~DePrva~N~CWAf~~Laea~~eA~~s~~qt~~-~t~~y~~ii~~Ll~~tdr~dgnqsNLR~AAYeALmE 527 (859)
T KOG1241|consen 454 LLEGLNDEPRVASNVCWAFISLAEAAYEAAVSNGQTDP-ATPFYEAIIGSLLKVTDRADGNQSNLRSAAYEALME 527 (859)
T ss_pred HHHHhhhCchHHHHHHHHHHHHHHHHHHhccCCCCCCc-cchhHHHHHHHHHhhccccccchhhHHHHHHHHHHH
Confidence 3334444567888888 45555555666622221 117889999987766663 32334445555455444
No 114
>PF06213 CobT: Cobalamin biosynthesis protein CobT; InterPro: IPR006538 These proteins are CobT subunits of the aerobic cobalt chelatase (aerobic cobalamin biosynthesis pathway). Pseudomonas denitrificans CobT has been experimentally characterised [, ]. Aerobic cobalt chelatase consists of three subunits, CobT, CobN (IPR003672 from INTERPRO) and CobS (IPR006537 from INTERPRO). Cobalamin (vitamin B12) can be complexed with metal via the ATP-dependent reactions (aerobic pathway) (e.g., in P. denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in Salmonella typhimurium) [, ]. The corresponding cobalt chelatases are not homologous. However, aerobic cobalt chelatase subunits CobN and CobS are homologous to Mg-chelatase subunits BchH and BchI, respectively []. CobT, too, has been found to be remotely related to the third subunit of Mg-chelatase, BchD (involved in bacteriochlorophyll synthesis, e.g., in Rhodobacter capsulatus) []. Nomenclature note: CobT of the aerobic pathway P. denitrificans is not a homologue of CobT of the anaerobic pathway (Salmonella typhimurium, Escherichia coli). Therefore, annotation of any members of this family as nicotinate-mononucleotide--5,6-dimethylbenzimidazole phosphoribosyltransferases is erroneous.
Probab=21.21 E-value=7.1e+02 Score=26.73 Aligned_cols=94 Identities=17% Similarity=0.129 Sum_probs=46.4
Q ss_pred cCCchhhHHhhHHHHHhhhhhhhccCCCcCchhhhHHHHHHHhhhcCCCCCCCh--hHHHHHHHHHHHHhc-ccCCCCCc
Q 004863 47 QAPSRSMRDALLPTMKGLITNDLLRRSDMDVRLSVTSCISEITRITAPDSPYDD--ELMKEFFQLAVSAFE-NLSHASGR 123 (726)
Q Consensus 47 Q~pvdS~~~SL~pl~k~LVs~~LLkHKDkdVRayVAcCLaDILRIyAPDAPYtD--dqLKDIFqLfV~qf~-~LsD~ssp 123 (726)
+.+.+...++|..++.+|....=|.=.-.+-++|+ +=-+|+.|.+|-+. ..|- +++=+.+.+. +|...+-.
T Consensus 6 ~~~~e~fk~Al~~~~rAia~~~~l~V~~~~~~a~~-----~g~~i~lP~lp~~~~~~~~~-~~RG~aD~~Al~lr~~D~~ 79 (282)
T PF06213_consen 6 ESPAEPFKRALAAVARAIAGDFELEVRFGGDRAYT-----DGNRIRLPALPRDLSEEDIA-ALRGYADHEALHLRHHDFK 79 (282)
T ss_pred CCcHHHHHHHHHHHHHHHcCCCCceEEeCCCCcCc-----CCCeeECCCCCCcCCHHHHH-HHHhHHHHHHHHHHhcCHH
Confidence 44556677888888888877432221112222221 23357889988543 3443 3333333322 33333322
Q ss_pred ch-------hhHHHHHHHhhhhhhheeecc
Q 004863 124 YY-------MKALSILDTVAKVRSCLLMLD 146 (726)
Q Consensus 124 ~Y-------~q~~yLLEsLAeVKS~VLmlD 146 (726)
.| ...-+|.+-|..+|.=.+|..
T Consensus 80 lh~~~~p~~~~ar~lfn~lEq~RvE~~g~~ 109 (282)
T PF06213_consen 80 LHRRLRPQGPVARALFNALEQARVEALGAR 109 (282)
T ss_pred HHHhhCCCChHHHHHHHHHHHHHHHHHhhh
Confidence 22 233456666666664444333
No 115
>PF14666 RICTOR_M: Rapamycin-insensitive companion of mTOR, middle domain
Probab=21.12 E-value=6.1e+02 Score=26.80 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHHHHHH
Q 004863 192 WDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLKEAVQ 237 (726)
Q Consensus 192 ~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~q~~n 237 (726)
.+++..||..| +-+....++.+-.+++..+...++.|..+++.
T Consensus 179 ~~l~klil~~L---DY~~~~~~R~iLsKaLt~~s~~iRl~aT~~L~ 221 (226)
T PF14666_consen 179 DDLLKLILSSL---DYSVDGHPRIILSKALTSGSESIRLYATKHLR 221 (226)
T ss_pred HHHHHHHHhhC---CCCCccHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 34444444444 22333345666666777777777777777764
No 116
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=21.09 E-value=2.8e+02 Score=27.14 Aligned_cols=69 Identities=7% Similarity=0.203 Sum_probs=47.2
Q ss_pred hhcCCchhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccCCCCCchHHHHHHHHHhhhHHHHHHHHH
Q 004863 164 IRSNHPHFVFAAMETIMTLVIDESEDVSWDLLRILLASVRKENQDVSPTSWKLGEKVFTKCAAKLKTNLK 233 (726)
Q Consensus 164 Vr~dhp~~V~~~M~dIMs~VIeESE~VP~eVLDvIL~~ll~~~ks~~PaAykLA~~VI~~CadKLqp~I~ 233 (726)
.++.....=...+.+|.-.| .....-|.+.+..|...|...++...--|-.|.+.++.||+..+...|+
T Consensus 10 T~~~l~~~dw~~ileicD~I-n~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~eva 78 (139)
T cd03567 10 TNPSNREEDWEAIQAFCEQI-NKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVG 78 (139)
T ss_pred cCccCCCCCHHHHHHHHHHH-HcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHH
Confidence 33334333344455554444 4445678899999999988777666667778888889999998876665
No 117
>PF10395 Utp8: Utp8 family; InterPro: IPR018843 Utp8 is an essential component of the nuclear tRNA export machinery in Saccharomyces cerevisiae (Baker's yeast). It is a tRNA binding protein that acts at a step between tRNA maturation /aminoacylation, and translocation of the tRNA across the nuclear pore complex [].
Probab=20.22 E-value=6e+02 Score=31.24 Aligned_cols=58 Identities=14% Similarity=0.321 Sum_probs=40.9
Q ss_pred hhHHHHHHHHHHHHhcccCC-C--------CCcchhhH--HHHHHHhhhh-----hhheeeccCCchHHHHHHH
Q 004863 100 DELMKEFFQLAVSAFENLSH-A--------SGRYYMKA--LSILDTVAKV-----RSCLLMLDLECDKLVVEMF 157 (726)
Q Consensus 100 DdqLKDIFqLfV~qf~~LsD-~--------ssp~Y~q~--~yLLEsLAeV-----KS~VLmlDLE~ddLI~eLF 157 (726)
..=|..|+.|||.+|..=.= | .+|.|+-. --||+.|..= +.+|-|-.|+|++|+.+||
T Consensus 459 ~~Fi~~vl~LIF~~f~d~efvPe~tLtYLLThPLFP~~~T~gLL~~l~~~prL~kQAIvTCPNlPl~eLl~qL~ 532 (670)
T PF10395_consen 459 PEFIEKVLDLIFDNFKDPEFVPEKTLTYLLTHPLFPIEYTKGLLELLRNNPRLFKQAIVTCPNLPLDELLQQLF 532 (670)
T ss_pred HHHHHHHHHHHhhhccccccCchhhhhhhhcCCCCchhhhhhHHHHhhcChhHHHHHhccCCCCcHHHHHHHHH
Confidence 35678888888887761100 2 46666543 4577777643 5678899999999999999
No 118
>KOG3674 consensus FtsJ-like RNA methyltransferase [RNA processing and modification]
Probab=20.21 E-value=1.1e+02 Score=36.30 Aligned_cols=50 Identities=16% Similarity=0.426 Sum_probs=38.6
Q ss_pred CCCCCCChhHHHHHHHHHHHHhc---------ccCCCCCcc------hhhHHHHHHHhhhhhhhe
Q 004863 93 APDSPYDDELMKEFFQLAVSAFE---------NLSHASGRY------YMKALSILDTVAKVRSCL 142 (726)
Q Consensus 93 APDAPYtDdqLKDIFqLfV~qf~---------~LsD~ssp~------Y~q~~yLLEsLAeVKS~V 142 (726)
+|-+-|....++|||+||+..|. .|.+|+-.. |....-+++.|+.|+.-+
T Consensus 12 ~p~~~fs~~~~~d~~~lF~k~F~y~kpl~nswqlp~Pdq~l~~e~yeF~a~~~l~~qln~vk~kl 76 (696)
T KOG3674|consen 12 NPVNLFSEKEIKDYYNLFIKDFNYCKPLPNSWQLPNPDQALFSEFYEFSAQTNLLTQLNMVKRKL 76 (696)
T ss_pred CCccccCcchHHHHHHHHHHhcccCCcCCCcccCCCchhhhhhhhhhHHHHhhHHHHHHHHHHHh
Confidence 56667888999999999999885 466666443 455677999999998754
Done!