Query 045690
Match_columns 220
No_of_seqs 103 out of 1382
Neff 9.8
Searched_HMMs 46136
Date Fri Mar 29 04:33:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045690.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045690hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14223 UBN2: gag-polypeptide 99.8 5.2E-20 1.1E-24 129.3 12.0 109 20-140 1-115 (119)
2 PF14227 UBN2_2: gag-polypepti 99.8 1E-18 2.2E-23 122.7 12.1 110 19-140 1-113 (119)
3 PF14244 UBN2_3: gag-polypepti 99.4 1.7E-13 3.6E-18 100.2 5.4 75 1-75 63-140 (152)
4 PF00098 zf-CCHC: Zinc knuckle 98.7 9.1E-09 2E-13 46.6 1.5 17 190-206 2-18 (18)
5 PF03732 Retrotrans_gag: Retro 98.5 2.7E-07 5.8E-12 61.6 5.9 71 19-106 26-96 (96)
6 COG5082 AIR1 Arginine methyltr 98.1 1.9E-06 4E-11 63.7 2.9 42 166-207 56-117 (190)
7 PF13696 zf-CCHC_2: Zinc knuck 97.9 3.9E-06 8.5E-11 43.4 1.0 21 188-208 8-28 (32)
8 PTZ00368 universal minicircle 97.7 2.6E-05 5.6E-10 56.7 2.1 37 171-207 78-122 (148)
9 KOG4400 E3 ubiquitin ligase in 97.4 0.00013 2.7E-09 58.2 2.7 42 171-212 144-188 (261)
10 PF03564 DUF1759: Protein of u 97.3 0.00069 1.5E-08 48.9 6.0 95 3-110 33-135 (145)
11 PTZ00368 universal minicircle 97.3 0.00023 5.1E-09 51.6 3.3 37 172-208 54-97 (148)
12 PF14787 zf-CCHC_5: GAG-polypr 97.0 0.00041 8.8E-09 36.6 1.6 21 190-210 4-24 (36)
13 KOG0119 Splicing factor 1/bran 97.0 0.0022 4.8E-08 54.0 6.3 47 161-207 252-304 (554)
14 smart00343 ZnF_C2HC zinc finge 96.9 0.00036 7.8E-09 34.7 0.8 18 190-207 1-18 (26)
15 PF13917 zf-CCHC_3: Zinc knuck 96.9 0.00064 1.4E-08 37.7 1.7 19 188-206 4-22 (42)
16 PF15288 zf-CCHC_6: Zinc knuck 96.6 0.002 4.3E-08 35.1 2.2 22 189-210 2-25 (40)
17 COG5082 AIR1 Arginine methyltr 96.3 0.0022 4.8E-08 47.6 1.9 38 171-208 98-140 (190)
18 PF14392 zf-CCHC_4: Zinc knuck 96.1 0.002 4.3E-08 37.4 0.5 18 189-206 32-49 (49)
19 COG5222 Uncharacterized conser 95.4 0.0095 2.1E-07 47.2 2.0 24 185-208 173-196 (427)
20 KOG0109 RNA-binding protein LA 95.3 0.0065 1.4E-07 48.0 0.8 19 190-208 162-180 (346)
21 PF00098 zf-CCHC: Zinc knuckle 95.2 0.016 3.4E-07 26.0 1.6 17 172-188 2-18 (18)
22 KOG4400 E3 ubiquitin ligase in 93.6 0.054 1.2E-06 43.1 2.5 43 169-211 71-115 (261)
23 PF14893 PNMA: PNMA 92.7 2 4.3E-05 35.4 10.3 54 18-73 228-282 (331)
24 PF02023 SCAN: SCAN domain; I 90.8 3.5 7.5E-05 27.4 10.1 79 44-134 5-84 (95)
25 KOG0341 DEAD-box protein abstr 85.7 0.36 7.8E-06 40.4 1.0 27 188-214 570-596 (610)
26 KOG0314 Predicted E3 ubiquitin 85.7 0.9 1.9E-05 38.8 3.3 38 172-209 135-179 (448)
27 TIGR03823 FliZ flagellar regul 82.6 6.4 0.00014 28.5 6.0 57 50-115 99-156 (168)
28 PRK11582 flagella biosynthesis 82.4 7.2 0.00016 28.2 6.2 56 51-115 100-156 (169)
29 PF12353 eIF3g: Eukaryotic tra 81.6 0.75 1.6E-05 32.4 1.1 22 186-208 104-125 (128)
30 KOG2044 5'-3' exonuclease HKE1 76.4 1.3 2.7E-05 40.3 1.1 21 189-209 261-281 (931)
31 PF03902 Gal4_dimer: Gal4-like 75.9 7.2 0.00016 23.1 3.8 46 59-104 2-47 (57)
32 PF07295 DUF1451: Protein of u 75.6 14 0.00031 26.6 6.1 26 172-197 114-139 (146)
33 PF05741 zf-nanos: Nanos RNA b 75.2 1.2 2.7E-05 26.2 0.5 18 190-207 35-55 (55)
34 KOG3116 Predicted C3H1-type Zn 70.2 1.2 2.5E-05 31.9 -0.4 21 189-209 28-48 (177)
35 TIGR03859 PQQ_PqqD coenzyme PQ 70.1 15 0.00032 23.5 4.8 31 5-35 29-59 (81)
36 KOG2673 Uncharacterized conser 66.2 3.2 7E-05 35.3 1.3 19 191-209 131-149 (485)
37 COG1198 PriA Primosomal protei 66.0 4.2 9.1E-05 37.3 2.1 22 189-210 463-484 (730)
38 PF07904 Eaf7: Chromatin modif 65.7 6.6 0.00014 25.8 2.5 27 8-34 27-58 (91)
39 COG2879 Uncharacterized small 65.2 23 0.00051 21.4 4.4 34 98-132 16-52 (65)
40 PF05402 PqqD: Coenzyme PQQ sy 65.0 14 0.00031 22.3 3.8 29 6-34 16-44 (68)
41 KOG2560 RNA splicing factor - 62.7 1.8 4E-05 36.7 -0.7 24 190-213 114-137 (529)
42 PF13376 OmdA: Bacteriocin-pro 62.3 29 0.00063 20.9 4.7 55 8-73 6-60 (63)
43 KOG0107 Alternative splicing f 61.9 4.2 9.1E-05 30.2 1.1 16 191-206 103-118 (195)
44 PRK11032 hypothetical protein; 60.0 60 0.0013 23.9 6.8 27 171-197 125-151 (160)
45 KOG3794 CBF1-interacting corep 55.2 5.2 0.00011 33.4 0.7 21 189-209 125-147 (453)
46 PF15616 TerY-C: TerY-C metal 54.5 8 0.00017 27.3 1.4 33 170-202 77-119 (131)
47 PF07754 DUF1610: Domain of un 53.6 9.7 0.00021 18.3 1.2 10 187-196 15-24 (24)
48 COG5179 TAF1 Transcription ini 52.4 28 0.00062 31.3 4.6 23 187-209 936-960 (968)
49 PF00607 Gag_p24: gag gene pro 50.9 66 0.0014 24.7 6.1 41 21-71 107-149 (206)
50 PF14684 Tricorn_C1: Tricorn p 47.5 32 0.0007 21.2 3.3 54 21-74 7-62 (70)
51 PF09297 zf-NADH-PPase: NADH p 47.0 9.3 0.0002 19.5 0.6 24 173-196 6-29 (32)
52 PF08203 RNA_polI_A14: Yeast R 46.7 45 0.00098 21.1 3.8 16 92-107 59-74 (76)
53 TIGR02642 phage_xxxx uncharact 46.7 12 0.00026 28.2 1.4 31 170-202 99-129 (186)
54 KOG4451 Uncharacterized conser 46.5 1E+02 0.0023 24.0 6.3 18 189-206 250-268 (286)
55 TIGR01385 TFSII transcription 46.3 1.6E+02 0.0036 24.0 10.4 18 57-74 181-198 (299)
56 PF06757 Ins_allergen_rp: Inse 45.3 1.2E+02 0.0027 22.4 6.7 98 22-136 46-145 (179)
57 KOG4602 Nanos and related prot 44.8 11 0.00023 29.7 0.9 19 190-208 270-291 (318)
58 PF07282 OrfB_Zn_ribbon: Putat 43.7 18 0.00039 22.1 1.7 29 171-199 29-57 (69)
59 KOG0403 Neoplastic transformat 42.6 75 0.0016 27.7 5.5 68 23-109 560-630 (645)
60 PRK00398 rpoP DNA-directed RNA 42.1 15 0.00033 20.5 1.1 25 173-197 6-30 (46)
61 KOG0109 RNA-binding protein LA 40.4 13 0.00028 30.0 0.8 18 172-189 162-179 (346)
62 PF07583 PSCyt2: Protein of un 39.8 89 0.0019 24.0 5.3 43 92-135 23-68 (208)
63 PRK04023 DNA polymerase II lar 39.1 23 0.0005 33.7 2.2 11 170-180 626-636 (1121)
64 COG3357 Predicted transcriptio 39.1 81 0.0017 20.7 4.1 34 163-196 51-84 (97)
65 smart00647 IBR In Between Ring 38.8 22 0.00048 21.0 1.5 20 185-204 45-64 (64)
66 PF08112 ATP-synt_E_2: ATP syn 38.7 72 0.0016 18.5 3.4 36 54-113 5-40 (56)
67 PHA00689 hypothetical protein 38.2 12 0.00027 21.3 0.3 11 188-198 17-27 (62)
68 cd07562 Peptidase_S41_TRI Tric 38.1 1.2E+02 0.0026 24.0 6.1 56 20-75 4-61 (266)
69 PF06424 PRP1_N: PRP1 splicing 38.0 1.2E+02 0.0026 21.5 5.2 52 20-74 63-115 (133)
70 PF07023 DUF1315: Protein of u 37.6 29 0.00063 22.9 2.0 21 98-118 2-23 (93)
71 TIGR00595 priA primosomal prot 37.6 24 0.00053 31.1 2.1 22 188-209 240-261 (505)
72 PF00790 VHS: VHS domain; Int 37.4 1.4E+02 0.003 21.1 5.7 44 19-62 37-81 (140)
73 COG5420 Uncharacterized conser 37.2 50 0.0011 20.0 2.7 40 56-113 6-45 (71)
74 COG5222 Uncharacterized conser 36.8 23 0.0005 28.7 1.6 18 172-189 178-195 (427)
75 COG3120 Uncharacterized protei 36.5 81 0.0017 22.1 4.0 33 55-88 91-123 (149)
76 PF01475 FUR: Ferric uptake re 35.6 69 0.0015 21.8 3.8 34 17-50 21-54 (120)
77 PRK14873 primosome assembly pr 35.3 29 0.00064 31.7 2.3 21 188-209 410-430 (665)
78 PF14567 SUKH_5: SMI1-KNR4 cel 35.1 1E+02 0.0022 21.9 4.5 47 58-116 1-50 (132)
79 COG2816 NPY1 NTP pyrophosphohy 34.5 28 0.0006 28.1 1.8 33 172-205 113-145 (279)
80 COG0484 DnaJ DnaJ-class molecu 33.7 45 0.00098 28.1 3.0 40 170-209 159-205 (371)
81 TIGR02606 antidote_CC2985 puta 33.5 1.2E+02 0.0026 18.7 4.6 33 103-135 5-37 (69)
82 PF09133 SANTA: SANTA (SANT As 33.2 47 0.001 21.9 2.5 20 94-113 71-90 (93)
83 PF00684 DnaJ_CXXCXGXG: DnaJ c 33.0 45 0.00098 20.2 2.3 39 169-207 14-62 (66)
84 KOG2203 GTP-binding protein [G 32.7 1.3E+02 0.0028 27.1 5.5 53 21-73 479-533 (772)
85 PF13797 Post_transc_reg: Post 32.6 75 0.0016 20.7 3.3 32 19-50 27-59 (87)
86 PF12169 DNA_pol3_gamma3: DNA 32.6 1.7E+02 0.0038 20.4 6.0 61 9-73 2-62 (143)
87 PRK02079 pyrroloquinoline quin 32.0 1.2E+02 0.0026 19.7 4.2 27 7-33 36-62 (88)
88 PF05310 Tenui_NS3: Tenuivirus 31.3 16 0.00035 27.1 0.0 18 187-204 97-114 (186)
89 PF14319 Zn_Tnp_IS91: Transpos 31.2 26 0.00057 23.9 1.1 25 172-196 44-68 (111)
90 KOG0122 Translation initiation 31.2 22 0.00047 28.0 0.7 19 189-208 120-138 (270)
91 PF03693 RHH_2: Uncharacterise 31.1 1.4E+02 0.0031 18.9 5.1 31 103-133 8-38 (80)
92 PF13248 zf-ribbon_3: zinc-rib 30.6 26 0.00057 16.9 0.7 8 189-196 17-24 (26)
93 PF12417 DUF3669: Zinc finger 30.4 46 0.001 20.7 2.0 20 17-36 38-57 (72)
94 PF13821 DUF4187: Domain of un 29.9 24 0.00051 20.8 0.6 18 190-207 29-50 (55)
95 PF02403 Seryl_tRNA_N: Seryl-t 29.7 1.7E+02 0.0038 19.4 6.2 36 40-75 51-86 (108)
96 PF09889 DUF2116: Uncharacteri 29.6 26 0.00057 21.0 0.7 17 188-204 3-20 (59)
97 PRK05580 primosome assembly pr 29.1 39 0.00085 31.0 2.1 21 189-209 409-429 (679)
98 cd07563 Peptidase_S41_IRBP Int 27.7 1.3E+02 0.0028 23.6 4.6 53 22-74 2-57 (250)
99 COG0542 clpA ATP-binding subun 27.7 3E+02 0.0065 26.0 7.3 65 24-93 306-370 (786)
100 PF15629 Perm-CXXC: Permuted s 27.7 31 0.00066 17.8 0.7 14 184-197 12-25 (32)
101 cd03564 ANTH_AP180_CALM ANTH d 27.3 2E+02 0.0044 19.5 5.8 47 15-61 27-75 (117)
102 PF11248 DUF3046: Protein of u 26.7 59 0.0013 19.8 1.9 23 12-34 36-58 (63)
103 PF14077 WD40_alt: Alternative 26.2 56 0.0012 18.4 1.6 30 37-66 16-45 (48)
104 PF00220 Hormone_4: Neurohypop 26.1 35 0.00075 12.2 0.5 6 201-206 3-8 (9)
105 KOG4204 Histone deacetylase co 25.7 2.1E+02 0.0045 22.5 5.2 53 18-71 126-178 (231)
106 COG4416 Com Mu-like prophage p 25.6 22 0.00048 20.8 -0.1 19 190-208 6-31 (60)
107 PF10013 DUF2256: Uncharacteri 25.6 44 0.00095 18.5 1.1 13 185-197 5-17 (42)
108 PF14965 BRI3BP: Negative regu 25.5 1.7E+02 0.0037 21.9 4.4 57 20-79 3-60 (177)
109 smart00583 SPK domain in SET a 25.1 2.3E+02 0.005 19.4 8.7 52 23-74 3-58 (114)
110 PF11855 DUF3375: Protein of u 24.9 1.7E+02 0.0036 25.7 5.1 94 21-117 101-203 (478)
111 PF08792 A2L_zn_ribbon: A2L zi 24.6 51 0.0011 17.1 1.2 25 172-196 5-29 (33)
112 PF11517 Nab2: Nuclear abundan 24.5 2.3E+02 0.0049 19.0 5.7 62 7-68 32-96 (107)
113 PF03705 CheR_N: CheR methyltr 24.0 1.5E+02 0.0033 16.9 5.4 45 23-67 6-53 (57)
114 PF03206 NifW: Nitrogen fixati 24.0 1.1E+02 0.0023 20.8 2.9 42 12-53 4-47 (105)
115 PF15508 NAAA-beta: beta subun 24.0 2.2E+02 0.0047 18.6 6.1 15 21-35 13-27 (95)
116 KOG2985 Uncharacterized conser 23.6 21 0.00046 28.1 -0.5 20 189-208 82-101 (306)
117 PRK07003 DNA polymerase III su 23.5 6.5E+02 0.014 24.0 9.7 99 8-115 232-330 (830)
118 PRK06036 translation initiatio 23.4 4.4E+02 0.0096 22.0 7.2 60 17-76 28-89 (339)
119 PF04439 Adenyl_transf: Strept 23.0 50 0.0011 26.7 1.5 16 22-37 220-235 (282)
120 cd07153 Fur_like Ferric uptake 23.0 1.9E+02 0.0042 19.2 4.3 35 17-51 14-48 (116)
121 cd01093 CRIB_PAK_like PAK (p21 22.8 57 0.0012 18.3 1.3 13 102-114 25-37 (46)
122 PF08844 DUF1815: Domain of un 22.8 33 0.00071 22.6 0.3 14 190-203 34-49 (105)
123 PF06689 zf-C4_ClpX: ClpX C4-t 22.6 35 0.00075 18.6 0.3 10 189-198 2-11 (41)
124 KOG3497 DNA-directed RNA polym 22.0 33 0.00072 20.5 0.2 8 190-197 6-13 (69)
125 PRK14291 chaperone protein Dna 22.0 97 0.0021 26.2 3.0 38 172-209 175-216 (382)
126 COG2995 PqiA Uncharacterized p 21.3 68 0.0015 27.2 1.9 36 164-202 214-249 (418)
127 PF03604 DNA_RNApol_7kD: DNA d 21.2 78 0.0017 16.3 1.5 10 187-196 16-25 (32)
128 COG1644 RPB10 DNA-directed RNA 21.2 39 0.00084 20.4 0.4 8 190-197 6-13 (63)
129 PF01485 IBR: IBR domain; Int 20.9 44 0.00094 19.6 0.6 19 186-204 46-64 (64)
130 PRK09263 anaerobic ribonucleos 20.8 62 0.0013 30.0 1.7 15 20-34 423-437 (711)
131 PF04439 Adenyl_transf: Strept 20.8 2.8E+02 0.0062 22.4 5.4 30 3-32 214-246 (282)
132 PF07851 TMPIT: TMPIT-like pro 20.7 2.6E+02 0.0056 23.3 5.1 64 24-88 4-70 (330)
133 PRK05772 translation initiatio 20.7 5.2E+02 0.011 21.9 11.4 62 16-77 40-103 (363)
134 PF05879 RHD3: Root hair defec 20.5 1.4E+02 0.003 27.9 3.9 90 6-112 436-526 (742)
135 KOG0119 Splicing factor 1/bran 20.5 51 0.0011 28.8 1.1 19 189-207 262-280 (554)
136 COG5415 Predicted integral mem 20.5 2.8E+02 0.006 21.5 4.8 27 172-198 194-224 (251)
137 PF09580 Spore_YhcN_YlaJ: Spor 20.4 3.5E+02 0.0076 19.7 5.9 52 22-73 119-176 (177)
138 cd03567 VHS_GGA VHS domain fam 20.3 3.3E+02 0.0071 19.4 8.7 45 19-63 33-78 (139)
139 PF13395 HNH_4: HNH endonuclea 20.3 44 0.00095 19.4 0.5 7 191-197 1-7 (54)
140 PRK14063 exodeoxyribonuclease 20.2 2.4E+02 0.0052 17.8 4.1 28 54-84 3-30 (76)
No 1
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=99.84 E-value=5.2e-20 Score=129.27 Aligned_cols=109 Identities=25% Similarity=0.407 Sum_probs=99.2
Q ss_pred ccHHHHHHHHHHHhccCCc---hhHhhHHHHHHHhh-cCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHH
Q 045690 20 KTAKDMWEYLKKVYNQDNT---AKCFHLEYEIARYS-QGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQS 95 (220)
Q Consensus 20 ~ta~~~W~~L~~~f~~~~~---~~~~~l~~~~~~~~-~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~ 95 (220)
+||+++|+.|+..|.+.+. +++..++.+|.+++ ++++||.+|+.+|..|+++|.++ |..+++ .+
T Consensus 1 ~tA~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~-g~~i~d-----------~~ 68 (119)
T PF14223_consen 1 KTAKEAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAI-GKPISD-----------ED 68 (119)
T ss_pred ChHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhc-CCcccc-----------hh
Confidence 5899999999999999988 99999999999998 58999999999999999999977 776655 66
Q ss_pred HHHHHHhhcchhHHHHHHhhhcCCCCC--CHHHHHHHHHHHHHHHHH
Q 045690 96 KRDQFLMKLRPEYKAARSNLMNRDLSP--SLDVCFKELLREEQRLAT 140 (220)
Q Consensus 96 ~~~~~l~gLp~~~~~~~~~~~~~~~~~--t~~e~~~~l~~~e~r~~~ 140 (220)
.+.++|+|||++|+.++..+....+.+ |++++++.|..+|.+...
T Consensus 69 ~v~~iL~~Lp~~y~~~~~~i~~~~~~~~~t~~el~~~L~~~E~~~~~ 115 (119)
T PF14223_consen 69 LVSKILRSLPPSYDTFVTAIRNSKDLPKMTLEELISRLLAEEMRLKS 115 (119)
T ss_pred HHHHHHhcCCchhHHHHHHHHhcCCCCcCCHHHHHHHHHHHHHHHHH
Confidence 677799999999999999999987777 999999999999988774
No 2
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=99.80 E-value=1e-18 Score=122.71 Aligned_cols=110 Identities=25% Similarity=0.317 Sum_probs=93.3
Q ss_pred CccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhc-CCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHH
Q 045690 19 YKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQ-GDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKR 97 (220)
Q Consensus 19 ~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~-~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~ 97 (220)
++||+++|+.|+..|...+.+....+.+.|...+. ++.+|.+|+.+|..++++|.++ |..+++ +.++
T Consensus 1 ~~ta~~~W~~L~~~y~~~~~~~~~~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~-g~~i~d-----------~~~~ 68 (119)
T PF14227_consen 1 CKTAKEMWDKLKKKYEKKSFANKIYLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSL-GVPIDD-----------EDKV 68 (119)
T ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhHhccchhHHHHHHHHHHHHHhhccc-cccchH-----------HHHH
Confidence 57999999999999997776666666666666655 6899999999999999999977 887766 4555
Q ss_pred HHHHhhcchhHHHHHHhhhcCC--CCCCHHHHHHHHHHHHHHHHH
Q 045690 98 DQFLMKLRPEYKAARSNLMNRD--LSPSLDVCFKELLREEQRLAT 140 (220)
Q Consensus 98 ~~~l~gLp~~~~~~~~~~~~~~--~~~t~~e~~~~l~~~e~r~~~ 140 (220)
..+|.+||++|++|+.++.... ..++++++...|..+|.++..
T Consensus 69 ~~lL~sLP~sy~~~~~~l~~~~~~~~~tl~~v~~~L~~ee~~~~~ 113 (119)
T PF14227_consen 69 IILLSSLPPSYDSFVTALLYSKPEDELTLEEVKSKLLQEEERRKK 113 (119)
T ss_pred HHHHHcCCHhHHHHHHHHHccCCCCCcCHHHHHHHHHHHHHHHHh
Confidence 5599999999999999988865 889999999999999987764
No 3
>PF14244 UBN2_3: gag-polypeptide of LTR copia-type
Probab=99.43 E-value=1.7e-13 Score=100.21 Aligned_cols=75 Identities=25% Similarity=0.660 Sum_probs=70.6
Q ss_pred CceecccccHHHHhccCCCccHHHHHHHHHHHhccCC-chhHhhHHHHHHHhhcCCCcHHHHHHHHHHHH--HHHhcc
Q 045690 1 MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDN-TAKCFHLEYEIARYSQGDLSIQNYLSGIQNLW--AKYVDM 75 (220)
Q Consensus 1 ~~~i~~sl~~~~~~~i~~~~ta~~~W~~L~~~f~~~~-~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~--~~L~~~ 75 (220)
++||+++|+++++..|..++||+++|+.|+++|...+ .++++.++.+|..++|++.+|.+|+.+|+.|+ .+|..+
T Consensus 63 ~swl~~sis~~i~~~i~~~~tak~~W~~L~~~f~~~~~~~r~~~L~~~l~~~kq~~~sv~ey~~~lk~l~~~~el~~~ 140 (152)
T PF14244_consen 63 LSWLLNSISPDILSTIIFCETAKEIWDALKERFSQKSNASRVFQLRNELHSLKQGDKSVTEYFNKLKSLWQEDELDEY 140 (152)
T ss_pred HHHHHHhhcHHHHhhhHhhhhHHHHHHHHHHHhhcccHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHhHHHHHhCc
Confidence 4799999999999999999999999999999999777 89999999999999999999999999999999 667654
No 4
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.69 E-value=9.1e-09 Score=46.61 Aligned_cols=17 Identities=47% Similarity=1.239 Sum_probs=16.0
Q ss_pred cccccccccccccCCCC
Q 045690 190 FCNYCKKPGHIIKECPT 206 (220)
Q Consensus 190 ~C~~C~k~GH~~~~C~~ 206 (220)
.||+|++.||++++||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999995
No 5
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=98.52 E-value=2.7e-07 Score=61.65 Aligned_cols=71 Identities=20% Similarity=0.372 Sum_probs=58.8
Q ss_pred CccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHH
Q 045690 19 YKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRD 98 (220)
Q Consensus 19 ~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~ 98 (220)
..|+.++-+.|...|.... ....++.+|.+++|+++||.+|+.+|..|+..+.. +. +|++++.
T Consensus 26 ~~~W~~~~~~~~~~f~~~~--~~~~~~~~l~~l~Q~~esv~~y~~rf~~l~~~~~~------~~---------~e~~~v~ 88 (96)
T PF03732_consen 26 FITWEEFKDAFRKRFFPPD--RKEQARQELNSLRQGNESVREYVNRFRELARRAPP------PM---------DEEMLVE 88 (96)
T ss_pred CCCHHHHHHHHHHHHhhhh--ccccchhhhhhhhccCCcHHHHHHHHHHHHHHCCC------Cc---------CHHHHHH
Confidence 4578888888888888643 46688899999999999999999999999998872 12 6688888
Q ss_pred HHHhhcch
Q 045690 99 QFLMKLRP 106 (220)
Q Consensus 99 ~~l~gLp~ 106 (220)
.|++||.|
T Consensus 89 ~f~~GL~~ 96 (96)
T PF03732_consen 89 RFIRGLRP 96 (96)
T ss_pred HHHHCCCC
Confidence 89999975
No 6
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=98.12 E-value=1.9e-06 Score=63.67 Aligned_cols=42 Identities=29% Similarity=0.824 Sum_probs=34.2
Q ss_pred CCCCCccccccCCCccccccccC-------------------ccccccccccccccCC-CCC
Q 045690 166 RDMRQVQCFSCKEYRHIIVNCAK-------------------KFCNYCKKPGHIIKEC-PTR 207 (220)
Q Consensus 166 ~~~~~~~~~~~~~~g~~~~~~~~-------------------~~C~~C~k~GH~~~~C-~~~ 207 (220)
.....+.|+.|+..||.+++|+. .+|+.||..||++++| |.+
T Consensus 56 ~~~~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~ 117 (190)
T COG5082 56 IREENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSK 117 (190)
T ss_pred ccccccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccCccc
Confidence 34455679999999999999981 1899999999999999 443
No 7
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=97.93 E-value=3.9e-06 Score=43.38 Aligned_cols=21 Identities=38% Similarity=0.942 Sum_probs=18.3
Q ss_pred CccccccccccccccCCCCCC
Q 045690 188 KKFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 188 ~~~C~~C~k~GH~~~~C~~~~ 208 (220)
.-.|+.|++.||++++||...
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~~ 28 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTNK 28 (32)
T ss_pred CCEeecCCCCCccHhHCCCCC
Confidence 347999999999999999843
No 8
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=97.66 E-value=2.6e-05 Score=56.66 Aligned_cols=37 Identities=32% Similarity=0.916 Sum_probs=25.6
Q ss_pred ccccccCCCccccccccCc--------cccccccccccccCCCCC
Q 045690 171 VQCFSCKEYRHIIVNCAKK--------FCNYCKKPGHIIKECPTR 207 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~~~--------~C~~C~k~GH~~~~C~~~ 207 (220)
..|+.|+..||.+..|+.. .||.|+..||++++||..
T Consensus 78 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~ 122 (148)
T PTZ00368 78 RSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNA 122 (148)
T ss_pred cccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCc
Confidence 3577777777777766552 477777777777777764
No 9
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=97.36 E-value=0.00013 Score=58.16 Aligned_cols=42 Identities=33% Similarity=0.790 Sum_probs=37.4
Q ss_pred ccccccCCCcccccccc---CccccccccccccccCCCCCCCCCc
Q 045690 171 VQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTRPQNCQ 212 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~---~~~C~~C~k~GH~~~~C~~~~~~~~ 212 (220)
..||+|+..||....|+ ...||.|++.||..++||.......
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~~~~~~~ 188 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPSKQKSKS 188 (261)
T ss_pred CccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCccccccc
Confidence 35999999999999999 7899999999999999998876543
No 10
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=97.33 E-value=0.00069 Score=48.90 Aligned_cols=95 Identities=15% Similarity=0.187 Sum_probs=67.5
Q ss_pred eecccccHHHHhccCC----CccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhc----CCCcHHHHHHHHHHHHHHHhc
Q 045690 3 WIMGSVDQSLVLNLKP----YKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQ----GDLSIQNYLSGIQNLWAKYVD 74 (220)
Q Consensus 3 ~i~~sl~~~~~~~i~~----~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~----~~~sv~ey~~~~~~l~~~L~~ 74 (220)
+|.+.|..+....|.+ ..+...+|+.|+.+|+... ..+..+..+|.+... +...+..++..+..++..|.+
T Consensus 33 ~L~~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~-~i~~~~~~~l~~l~~~~~~d~~~L~~~~~~v~~~i~~L~~ 111 (145)
T PF03564_consen 33 YLRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPR-RIIQALLEELRNLPPISNDDPEALRSLVDKVNNCIRALKA 111 (145)
T ss_pred HHHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCch-HHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555544 4678999999999999654 134566666666653 468899999999999999997
Q ss_pred ccccCCCcccHHHHHHHHHHHHHHHHHhhcchhHHH
Q 045690 75 MIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKA 110 (220)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~~~~ 110 (220)
+ |..+.+ ...+..|+..||++...
T Consensus 112 l-g~~~~~-----------~~l~~~i~~KLp~~~~~ 135 (145)
T PF03564_consen 112 L-GVNVDD-----------PLLISIILSKLPPEIRE 135 (145)
T ss_pred c-CCCCCC-----------HHHHHHHHHHCCHHHHH
Confidence 6 665433 44555699999988443
No 11
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=97.30 E-value=0.00023 Score=51.63 Aligned_cols=37 Identities=35% Similarity=0.977 Sum_probs=24.4
Q ss_pred cccccCCCccccccccCc-------cccccccccccccCCCCCC
Q 045690 172 QCFSCKEYRHIIVNCAKK-------FCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~-------~C~~C~k~GH~~~~C~~~~ 208 (220)
.|+.|+..||....|+.+ .|+.|++.||++++|+.+.
T Consensus 54 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~~ 97 (148)
T PTZ00368 54 SCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRA 97 (148)
T ss_pred ccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCcc
Confidence 466666667666666554 4777777777777776644
No 12
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=97.02 E-value=0.00041 Score=36.62 Aligned_cols=21 Identities=29% Similarity=0.608 Sum_probs=14.0
Q ss_pred cccccccccccccCCCCCCCC
Q 045690 190 FCNYCKKPGHIIKECPTRPQN 210 (220)
Q Consensus 190 ~C~~C~k~GH~~~~C~~~~~~ 210 (220)
-|+.|++-.||+++|+.+...
T Consensus 4 ~CprC~kg~Hwa~~C~sk~d~ 24 (36)
T PF14787_consen 4 LCPRCGKGFHWASECRSKTDV 24 (36)
T ss_dssp C-TTTSSSCS-TTT---TCCC
T ss_pred cCcccCCCcchhhhhhhhhcc
Confidence 599999999999999988754
No 13
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.98 E-value=0.0022 Score=54.04 Aligned_cols=47 Identities=26% Similarity=0.542 Sum_probs=39.4
Q ss_pred CCCCCCCCCCccccccCCCccccccccCc------cccccccccccccCCCCC
Q 045690 161 GKSKGRDMRQVQCFSCKEYRHIIVNCAKK------FCNYCKKPGHIIKECPTR 207 (220)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~------~C~~C~k~GH~~~~C~~~ 207 (220)
..+..+......|..|+..||++-.|+.. .|++|+-.||+..+|+..
T Consensus 252 lNgt~r~~d~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 252 LNGTLRDDDNRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred hCCCCCccccccccccCCCccccccCCcccccccccccccCCcccccccCCCc
Confidence 34444444556799999999999999877 899999999999999987
No 14
>smart00343 ZnF_C2HC zinc finger.
Probab=96.92 E-value=0.00036 Score=34.68 Aligned_cols=18 Identities=44% Similarity=1.084 Sum_probs=16.0
Q ss_pred cccccccccccccCCCCC
Q 045690 190 FCNYCKKPGHIIKECPTR 207 (220)
Q Consensus 190 ~C~~C~k~GH~~~~C~~~ 207 (220)
.|+.|++.||++++||..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 499999999999999844
No 15
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=96.88 E-value=0.00064 Score=37.73 Aligned_cols=19 Identities=37% Similarity=0.885 Sum_probs=17.0
Q ss_pred CccccccccccccccCCCC
Q 045690 188 KKFCNYCKKPGHIIKECPT 206 (220)
Q Consensus 188 ~~~C~~C~k~GH~~~~C~~ 206 (220)
...|.+|+..|||..+||.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3569999999999999995
No 16
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=96.59 E-value=0.002 Score=35.12 Aligned_cols=22 Identities=32% Similarity=0.609 Sum_probs=18.9
Q ss_pred ccccccccccccc--cCCCCCCCC
Q 045690 189 KFCNYCKKPGHII--KECPTRPQN 210 (220)
Q Consensus 189 ~~C~~C~k~GH~~--~~C~~~~~~ 210 (220)
.+|..||..||+. +.||.+.+.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~~ 25 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCWS 25 (40)
T ss_pred ccccccccccccccCccCCCCCCC
Confidence 4699999999999 789998754
No 17
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=96.33 E-value=0.0022 Score=47.64 Aligned_cols=38 Identities=29% Similarity=0.736 Sum_probs=31.9
Q ss_pred ccccccCCCcccccccc-Cc----cccccccccccccCCCCCC
Q 045690 171 VQCFSCKEYRHIIVNCA-KK----FCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~-~~----~C~~C~k~GH~~~~C~~~~ 208 (220)
..|+.|+..||.+..|. .+ .|+.|+..+|++++||...
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s~~Cp~~~ 140 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPSIW 140 (190)
T ss_pred cccccccccCccccccCcccccCcceeccCCCccccccCcccc
Confidence 57999999999999993 32 7999999999999998644
No 18
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=96.08 E-value=0.002 Score=37.36 Aligned_cols=18 Identities=50% Similarity=1.099 Sum_probs=16.5
Q ss_pred ccccccccccccccCCCC
Q 045690 189 KFCNYCKKPGHIIKECPT 206 (220)
Q Consensus 189 ~~C~~C~k~GH~~~~C~~ 206 (220)
..|++||..||..++||+
T Consensus 32 ~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECPK 49 (49)
T ss_pred hhhcCCCCcCcCHhHcCC
Confidence 379999999999999985
No 19
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.40 E-value=0.0095 Score=47.19 Aligned_cols=24 Identities=33% Similarity=0.718 Sum_probs=19.9
Q ss_pred cccCccccccccccccccCCCCCC
Q 045690 185 NCAKKFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 185 ~~~~~~C~~C~k~GH~~~~C~~~~ 208 (220)
.-+.-.||.||..|||..+||...
T Consensus 173 pPpgY~CyRCGqkgHwIqnCpTN~ 196 (427)
T COG5222 173 PPPGYVCYRCGQKGHWIQNCPTNQ 196 (427)
T ss_pred CCCceeEEecCCCCchhhcCCCCC
Confidence 334458999999999999999765
No 20
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=95.31 E-value=0.0065 Score=47.99 Aligned_cols=19 Identities=47% Similarity=0.875 Sum_probs=17.3
Q ss_pred cccccccccccccCCCCCC
Q 045690 190 FCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 190 ~C~~C~k~GH~~~~C~~~~ 208 (220)
.|+.||+.|||.++||...
T Consensus 162 ~cyrcGkeghwskEcP~~~ 180 (346)
T KOG0109|consen 162 GCYRCGKEGHWSKECPVDR 180 (346)
T ss_pred HheeccccccccccCCccC
Confidence 7999999999999999753
No 21
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=95.22 E-value=0.016 Score=25.98 Aligned_cols=17 Identities=47% Similarity=1.081 Sum_probs=15.2
Q ss_pred cccccCCCccccccccC
Q 045690 172 QCFSCKEYRHIIVNCAK 188 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~ 188 (220)
.|+.|+..||.++.|++
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 59999999999999874
No 22
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=93.62 E-value=0.054 Score=43.13 Aligned_cols=43 Identities=30% Similarity=0.738 Sum_probs=35.2
Q ss_pred CCccccccCCCcccccccc--CccccccccccccccCCCCCCCCC
Q 045690 169 RQVQCFSCKEYRHIIVNCA--KKFCNYCKKPGHIIKECPTRPQNC 211 (220)
Q Consensus 169 ~~~~~~~~~~~g~~~~~~~--~~~C~~C~k~GH~~~~C~~~~~~~ 211 (220)
....|+.|+..|+....|. ...|+.|+..||++++||......
T Consensus 71 ~~~~c~~~g~~~~~~~~~~~~~~~c~~C~~~gH~~~~c~~~~~~~ 115 (261)
T KOG4400|consen 71 PEVSCYICGEKGHLGRRCTRIAAACFNCGEGGHIERDCPEAGKEG 115 (261)
T ss_pred CCceeeecCCCCchhhcCcccchhhhhCCCCccchhhCCcccCcc
Confidence 3446889999998888777 459999999999999999876544
No 23
>PF14893 PNMA: PNMA
Probab=92.71 E-value=2 Score=35.45 Aligned_cols=54 Identities=24% Similarity=0.303 Sum_probs=44.8
Q ss_pred CCccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhc-CCCcHHHHHHHHHHHHHHHh
Q 045690 18 PYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQ-GDLSIQNYLSGIQNLWAKYV 73 (220)
Q Consensus 18 ~~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~-~~~sv~ey~~~~~~l~~~L~ 73 (220)
.-.|+.+..+.|+..|.... ....++..|.++.| .+|+|.+|+.++..+..+.-
T Consensus 228 P~~t~~~~l~aL~~~Fg~~e--s~~~~~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav 282 (331)
T PF14893_consen 228 PKQTAQDCLKALGQVFGSSE--SRETLEAKFLNTFQEPGEKLSAYVKRLESLLQKAV 282 (331)
T ss_pred CCCCHHHHHHHHHHhcCCcc--cHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHH
Confidence 45689999999999999543 25677888877766 69999999999999999964
No 24
>PF02023 SCAN: SCAN domain; InterPro: IPR003309 A number of C2H2-zinc finger proteins contain a highly conserved N-terminal motif termed the SCAN domain. The SCAN domain may play an important role in the assembly and function of this newly defined subclass of transcriptional regulators [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3LHR_B 4E6S_A 2FI2_A 1Y7Q_A.
Probab=90.75 E-value=3.5 Score=27.40 Aligned_cols=79 Identities=14% Similarity=0.114 Sum_probs=50.5
Q ss_pred HHHHHHHhhc-CCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHHHHHhhcchhHHHHHHhhhcCCCCC
Q 045690 44 LEYEIARYSQ-GDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDLSP 122 (220)
Q Consensus 44 l~~~~~~~~~-~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~~~~~~~~~~~~~~~~ 122 (220)
.++.|..... ++++..+++.++..|+.+=-. +...+. .++-|-..+++||..||++....+. ....-
T Consensus 5 ~r~~FR~~~~~~~~~p~e~~~rL~~l~~~WL~--pe~~tk------eqi~ellvlEQFL~~lP~e~~~wV~----e~~p~ 72 (95)
T PF02023_consen 5 YRQRFRSFQYQEGEGPREFLSRLRELCDRWLQ--PEVHTK------EQILELLVLEQFLNILPPEVQTWVR----ERKPE 72 (95)
T ss_dssp HHHHHHT--CCTTTSHHHHHHHHHHHHHHHH---TTTS-H------HHHHHHHHHHHHHHHS-HHHHHHHH----TCS-S
T ss_pred HHHHHhCCCCCCCCCHHHHHHHHHHHHHHhCc--cccCcH------HHHHHHHHHHHHHHHCCHHHHHHHH----hcCCC
Confidence 4667777765 599999999999999866531 211121 2236677788999999999777654 23344
Q ss_pred CHHHHHHHHHHH
Q 045690 123 SLDVCFKELLRE 134 (220)
Q Consensus 123 t~~e~~~~l~~~ 134 (220)
+.+++...+...
T Consensus 73 s~~ea~~Lae~~ 84 (95)
T PF02023_consen 73 SAEEAVALAEDY 84 (95)
T ss_dssp SHHHHHHHHHHH
T ss_pred CHHHHHHHHHHH
Confidence 677777665544
No 25
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=85.69 E-value=0.36 Score=40.35 Aligned_cols=27 Identities=33% Similarity=0.707 Sum_probs=22.0
Q ss_pred CccccccccccccccCCCCCCCCCccc
Q 045690 188 KKFCNYCKKPGHIIKECPTRPQNCQAS 214 (220)
Q Consensus 188 ~~~C~~C~k~GH~~~~C~~~~~~~~~~ 214 (220)
.+.|.|||..||-..+||+....++..
T Consensus 570 ~kGCayCgGLGHRItdCPKle~~~~k~ 596 (610)
T KOG0341|consen 570 EKGCAYCGGLGHRITDCPKLEAQQNKQ 596 (610)
T ss_pred ccccccccCCCcccccCchhhhhcchh
Confidence 347999999999999999987654443
No 26
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.67 E-value=0.9 Score=38.75 Aligned_cols=38 Identities=37% Similarity=0.830 Sum_probs=29.4
Q ss_pred cccccCCCccccccccCc-------cccccccccccccCCCCCCC
Q 045690 172 QCFSCKEYRHIIVNCAKK-------FCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~-------~C~~C~k~GH~~~~C~~~~~ 209 (220)
.|-.|...+|+...+... .|+.|+..|||.+.||.-..
T Consensus 135 ~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv~~ 179 (448)
T KOG0314|consen 135 VCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTVSG 179 (448)
T ss_pred eeeecccCccccccccccCCCCCCcceecCCCCCccceeccccCC
Confidence 466677777777655433 99999999999999987553
No 27
>TIGR03823 FliZ flagellar regulatory protein FliZ. FliZ is involved in the regulation of flagellar assembly and possibly also the down-regulation of the motile phenotype. FliZ interacts with the flagellar translational activator FlhCD complex.
Probab=82.55 E-value=6.4 Score=28.48 Aligned_cols=57 Identities=14% Similarity=0.176 Sum_probs=37.0
Q ss_pred HhhcCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHHHHHhhcchh-HHHHHHhh
Q 045690 50 RYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPE-YKAARSNL 115 (220)
Q Consensus 50 ~~~~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~-~~~~~~~~ 115 (220)
.......||.||+-+++.|=.-|. ...+|.+.+ .+...-..+...||.. +.+.+.++
T Consensus 99 QTeMshStvrEYVVRLRRLd~lL~---~~n~p~~~~------~~~~~~~~~~~~Lp~~~~nNyriAL 156 (168)
T TIGR03823 99 QTEMSHSTVREYVVRLRRLDELLV---AQNYPAEQF------QDGFLQERLADWLPSTATNNYRIAL 156 (168)
T ss_pred hhccccccHHHHHHHHHHHHHHHh---hccCCHHHh------ccchHHHHHHhhCchhhhhHHHHHH
Confidence 334456799999999999987776 345555333 4445556678888865 55554443
No 28
>PRK11582 flagella biosynthesis protein FliZ; Provisional
Probab=82.38 E-value=7.2 Score=28.25 Aligned_cols=56 Identities=13% Similarity=0.176 Sum_probs=36.6
Q ss_pred hhcCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHHHHHhhcchh-HHHHHHhh
Q 045690 51 YSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPE-YKAARSNL 115 (220)
Q Consensus 51 ~~~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~-~~~~~~~~ 115 (220)
......||.||+-+++.|=.-|. ...+|.+.+ .+...-..+...||.. +.+.+.++
T Consensus 100 TeMshSTvrEYVVRLRRLd~lL~---~~n~p~~~~------~~~~~~~~~~~~Lp~~~~nNyriAL 156 (169)
T PRK11582 100 TEMSHSTVREYVVRLRRLDEHLH---EQNIPLDLL------QDGFLDERLAPWLPDTSTNNYRIAL 156 (169)
T ss_pred cccccccHHHHHHHHHHHHHHHh---hccCCHHHh------cchhHHHHHHhhcchhhhhHHHHHH
Confidence 34456799999999999987776 345565333 4444555678888865 55554443
No 29
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=81.62 E-value=0.75 Score=32.41 Aligned_cols=22 Identities=32% Similarity=0.680 Sum_probs=17.8
Q ss_pred ccCccccccccccccccCCCCCC
Q 045690 186 CAKKFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 186 ~~~~~C~~C~k~GH~~~~C~~~~ 208 (220)
.....|..|+ -.||...||.+-
T Consensus 104 ~~~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 104 KSKVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred CceEEeCCCC-CCcccccCCccc
Confidence 3445899996 789999999863
No 30
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=76.38 E-value=1.3 Score=40.33 Aligned_cols=21 Identities=33% Similarity=0.898 Sum_probs=18.7
Q ss_pred ccccccccccccccCCCCCCC
Q 045690 189 KFCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 189 ~~C~~C~k~GH~~~~C~~~~~ 209 (220)
..|+.||..||.+++|.-.++
T Consensus 261 ~~C~~cgq~gh~~~dc~g~~~ 281 (931)
T KOG2044|consen 261 RRCFLCGQTGHEAKDCEGKPR 281 (931)
T ss_pred ccchhhcccCCcHhhcCCcCC
Confidence 479999999999999988755
No 31
>PF03902 Gal4_dimer: Gal4-like dimerisation domain; InterPro: IPR005600 The DNA binding domain (residues 1 to 147) of the yeast transcriptional activator GAL4 exists in solution in dimeric form, with the region responsible for dimerisation somewhere between residues 74 and 147. Experimental studies confirmed that the 'hydrophobic region' of the protein (residues 54-97, which contains a larger proportion of alpha-helix), is essential for dimerisation []. ; PDB: 1HBW_B 1D66_A 3COQ_A.
Probab=75.95 E-value=7.2 Score=23.07 Aligned_cols=46 Identities=22% Similarity=0.283 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHHHHHhhc
Q 045690 59 QNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKL 104 (220)
Q Consensus 59 ~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~gL 104 (220)
..|+++++.-...|+.++..-+|+.++..+.+..+...+..++.+|
T Consensus 2 RaHLTeVE~Rl~~lE~ll~~lfP~~did~lL~~~~~~~l~~il~~l 47 (57)
T PF03902_consen 2 RAHLTEVENRLEKLEQLLRELFPGEDIDDLLNDRDASDLKPILKKL 47 (57)
T ss_dssp HHHHHHHHHHHHHHHHHHCCCSSSSHHHHHHHHHSCHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHCCCcCHHHHHHcccHHHHHHHHHHh
Confidence 4677888888888887777777887776665544444555555444
No 32
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=75.55 E-value=14 Score=26.64 Aligned_cols=26 Identities=15% Similarity=0.287 Sum_probs=20.2
Q ss_pred cccccCCCccccccccCccccccccc
Q 045690 172 QCFSCKEYRHIIVNCAKKFCNYCKKP 197 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~C~k~ 197 (220)
.|-.|+..-+......-+.|..||..
T Consensus 114 ~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 114 VCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred ecccCCCEEEecCCCcCCCCCCCCCC
Confidence 58888888777666667789999874
No 33
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=75.21 E-value=1.2 Score=26.24 Aligned_cols=18 Identities=44% Similarity=1.082 Sum_probs=7.7
Q ss_pred ccccccccc---ccccCCCCC
Q 045690 190 FCNYCKKPG---HIIKECPTR 207 (220)
Q Consensus 190 ~C~~C~k~G---H~~~~C~~~ 207 (220)
.|..||..| |..+.||.+
T Consensus 35 ~Cp~CgAtGd~AHT~~yCP~k 55 (55)
T PF05741_consen 35 VCPICGATGDNAHTIKYCPKK 55 (55)
T ss_dssp --TTT---GGG---GGG-TT-
T ss_pred cCCCCcCcCccccccccCcCC
Confidence 799998765 999999964
No 34
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=70.22 E-value=1.2 Score=31.88 Aligned_cols=21 Identities=29% Similarity=0.700 Sum_probs=17.5
Q ss_pred ccccccccccccccCCCCCCC
Q 045690 189 KFCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 189 ~~C~~C~k~GH~~~~C~~~~~ 209 (220)
..|..|-..|||..+|..+.+
T Consensus 28 ~rCQKClq~GHWtYECk~kRk 48 (177)
T KOG3116|consen 28 ARCQKCLQAGHWTYECKNKRK 48 (177)
T ss_pred hhHHHHHhhccceeeecCcee
Confidence 359999999999999987653
No 35
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=70.10 E-value=15 Score=23.48 Aligned_cols=31 Identities=3% Similarity=0.086 Sum_probs=25.4
Q ss_pred cccccHHHHhccCCCccHHHHHHHHHHHhcc
Q 045690 5 MGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQ 35 (220)
Q Consensus 5 ~~sl~~~~~~~i~~~~ta~~~W~~L~~~f~~ 35 (220)
++.+-..|...+.+..|..+||+.|.+.|..
T Consensus 29 Ln~~g~~Iw~lldg~~tv~eI~~~L~~~Y~~ 59 (81)
T TIGR03859 29 LNDSAGEILELCDGKRSLAEIIQELAQRFPA 59 (81)
T ss_pred eChHHHHHHHHccCCCcHHHHHHHHHHHcCC
Confidence 3455667888888888999999999999986
No 36
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=66.21 E-value=3.2 Score=35.33 Aligned_cols=19 Identities=26% Similarity=0.742 Sum_probs=17.3
Q ss_pred ccccccccccccCCCCCCC
Q 045690 191 CNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 191 C~~C~k~GH~~~~C~~~~~ 209 (220)
||+|+..-|-.++||....
T Consensus 131 CFNC~g~~hsLrdC~rp~d 149 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPRPFD 149 (485)
T ss_pred ccccCCCCCccccCCCccc
Confidence 9999999999999998764
No 37
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=66.01 E-value=4.2 Score=37.30 Aligned_cols=22 Identities=27% Similarity=0.619 Sum_probs=19.2
Q ss_pred ccccccccccccccCCCCCCCC
Q 045690 189 KFCNYCKKPGHIIKECPTRPQN 210 (220)
Q Consensus 189 ~~C~~C~k~GH~~~~C~~~~~~ 210 (220)
-.|++||....+...||.....
T Consensus 463 L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 463 LRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred eEeCCCCCCCCCCCCCCCCCCC
Confidence 3899999999999999987643
No 38
>PF07904 Eaf7: Chromatin modification-related protein EAF7; InterPro: IPR012423 The Saccharomyces cerevisiae (Baker's yeast) member of this family P53911 from SWISSPROT is part of NuA4, the only essential histone acetyltransferase complex in S. cerevisiae involved in global histone acetylation []. ; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0043189 H4/H2A histone acetyltransferase complex
Probab=65.74 E-value=6.6 Score=25.85 Aligned_cols=27 Identities=26% Similarity=0.490 Sum_probs=21.1
Q ss_pred ccHHHHhc-----cCCCccHHHHHHHHHHHhc
Q 045690 8 VDQSLVLN-----LKPYKTAKDMWEYLKKVYN 34 (220)
Q Consensus 8 l~~~~~~~-----i~~~~ta~~~W~~L~~~f~ 34 (220)
|...+... +....|+.++|+.|.+.|.
T Consensus 27 I~~~l~~~~~~~~~~~~~t~~~IW~kL~~~Yd 58 (91)
T PF07904_consen 27 IVERLNNPGFDPKLNKHFTIDDIWKKLRTLYD 58 (91)
T ss_pred HHHHHhccccCCccCCcCCHHHHHHHHHHhcC
Confidence 34444455 6778899999999999997
No 39
>COG2879 Uncharacterized small protein [Function unknown]
Probab=65.17 E-value=23 Score=21.40 Aligned_cols=34 Identities=9% Similarity=0.245 Sum_probs=25.3
Q ss_pred HHHHhhcchhHHHHHHhhhc---CCCCCCHHHHHHHHH
Q 045690 98 DQFLMKLRPEYKAARSNLMN---RDLSPSLDVCFKELL 132 (220)
Q Consensus 98 ~~~l~gLp~~~~~~~~~~~~---~~~~~t~~e~~~~l~ 132 (220)
.+++-|+| +|++.+..+.. ..+.+|.+|+....+
T Consensus 16 ~~lmvGvp-dYdnYVehmr~~hPd~p~mT~~EFfrec~ 52 (65)
T COG2879 16 AKLMVGVP-DYDNYVEHMRKKHPDKPPMTYEEFFRECQ 52 (65)
T ss_pred HHHHcCCC-cHHHHHHHHHHhCcCCCcccHHHHHHHHH
Confidence 34788887 48999888887 456678888876554
No 40
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=64.96 E-value=14 Score=22.31 Aligned_cols=29 Identities=14% Similarity=0.163 Sum_probs=14.4
Q ss_pred ccccHHHHhccCCCccHHHHHHHHHHHhc
Q 045690 6 GSVDQSLVLNLKPYKTAKDMWEYLKKVYN 34 (220)
Q Consensus 6 ~sl~~~~~~~i~~~~ta~~~W~~L~~~f~ 34 (220)
+.....|...+.+..|..++.+.|.+.|.
T Consensus 16 n~~a~~Iw~~~~g~~t~~ei~~~l~~~y~ 44 (68)
T PF05402_consen 16 NETAAFIWELLDGPRTVEEIVDALAEEYD 44 (68)
T ss_dssp -THHHHHHHH--SSS-HHHHHHHHHHHTT
T ss_pred cHHHHHHHHHccCCCCHHHHHHHHHHHcC
Confidence 34444555555555666666666666664
No 41
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=62.66 E-value=1.8 Score=36.74 Aligned_cols=24 Identities=33% Similarity=0.737 Sum_probs=21.3
Q ss_pred cccccccccccccCCCCCCCCCcc
Q 045690 190 FCNYCKKPGHIIKECPTRPQNCQA 213 (220)
Q Consensus 190 ~C~~C~k~GH~~~~C~~~~~~~~~ 213 (220)
.|-+||--||-.++|--++.+.++
T Consensus 114 ACeNCGAmtHk~KDCmERPRK~gA 137 (529)
T KOG2560|consen 114 ACENCGAMTHKVKDCMERPRKVGA 137 (529)
T ss_pred hhhhhhhhhcchHHHhhcchhhcc
Confidence 799999999999999888876654
No 42
>PF13376 OmdA: Bacteriocin-protection, YdeI or OmpD-Associated
Probab=62.26 E-value=29 Score=20.86 Aligned_cols=55 Identities=22% Similarity=0.264 Sum_probs=37.2
Q ss_pred ccHHHHhccCCCccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHh
Q 045690 8 VDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYV 73 (220)
Q Consensus 8 l~~~~~~~i~~~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~ 73 (220)
|++++...+.....+.+.|+.|...|. +.+........+...-..++..++..|.
T Consensus 6 vP~dl~~aL~~~p~a~~~f~~l~~~~r-----------r~~i~wi~~AK~~etR~kRi~~~i~~l~ 60 (63)
T PF13376_consen 6 VPEDLEAALEANPEAKEFFESLTPSYR-----------REYIRWINSAKTEETRAKRIAKLIEMLA 60 (63)
T ss_pred CCHHHHHHHHCCHHHHHHHHHCCHHHH-----------HHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 688899999999999999998877443 3333333344456666666666665554
No 43
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=61.88 E-value=4.2 Score=30.19 Aligned_cols=16 Identities=38% Similarity=0.949 Sum_probs=14.5
Q ss_pred ccccccccccccCCCC
Q 045690 191 CNYCKKPGHIIKECPT 206 (220)
Q Consensus 191 C~~C~k~GH~~~~C~~ 206 (220)
|+.||..||+.+.|..
T Consensus 103 ~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 103 CYRCGERGHIGRNCKD 118 (195)
T ss_pred cccCCCcccccccccc
Confidence 9999999999999977
No 44
>PRK11032 hypothetical protein; Provisional
Probab=60.03 E-value=60 Score=23.86 Aligned_cols=27 Identities=15% Similarity=0.370 Sum_probs=21.6
Q ss_pred ccccccCCCccccccccCccccccccc
Q 045690 171 VQCFSCKEYRHIIVNCAKKFCNYCKKP 197 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~~~~C~~C~k~ 197 (220)
-.|-.|+..-+......-+.|..||..
T Consensus 125 LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 125 LVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred EEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 358888888888777777889999874
No 45
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=55.17 E-value=5.2 Score=33.43 Aligned_cols=21 Identities=43% Similarity=0.736 Sum_probs=17.1
Q ss_pred ccccccccccccc--cCCCCCCC
Q 045690 189 KFCNYCKKPGHII--KECPTRPQ 209 (220)
Q Consensus 189 ~~C~~C~k~GH~~--~~C~~~~~ 209 (220)
+.|..|++-||+. ++||..-.
T Consensus 125 VrC~kChkwGH~n~DreCplf~~ 147 (453)
T KOG3794|consen 125 VRCLKCHKWGHINTDRECPLFGK 147 (453)
T ss_pred eeEEeecccccccCCccCcchhh
Confidence 3899999999985 67997654
No 46
>PF15616 TerY-C: TerY-C metal binding domain
Probab=54.45 E-value=8 Score=27.31 Aligned_cols=33 Identities=24% Similarity=0.549 Sum_probs=22.6
Q ss_pred CccccccCCCccccc-cccCc---------ccccccccccccc
Q 045690 170 QVQCFSCKEYRHIIV-NCAKK---------FCNYCKKPGHIIK 202 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~-~~~~~---------~C~~C~k~GH~~~ 202 (220)
.+.|..|++.-..+- .|.+. +|.+|++.|.+..
T Consensus 77 ~PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~~~ 119 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEGSFGA 119 (131)
T ss_pred CCCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCeeeecc
Confidence 357888888744433 45443 8899999887754
No 47
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=53.64 E-value=9.7 Score=18.31 Aligned_cols=10 Identities=20% Similarity=0.291 Sum_probs=6.2
Q ss_pred cCcccccccc
Q 045690 187 AKKFCNYCKK 196 (220)
Q Consensus 187 ~~~~C~~C~k 196 (220)
....|..||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 3346777774
No 48
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=52.36 E-value=28 Score=31.26 Aligned_cols=23 Identities=26% Similarity=0.746 Sum_probs=17.9
Q ss_pred cCcccccccccccccc--CCCCCCC
Q 045690 187 AKKFCNYCKKPGHIIK--ECPTRPQ 209 (220)
Q Consensus 187 ~~~~C~~C~k~GH~~~--~C~~~~~ 209 (220)
..++|-.||..||+.. -||....
T Consensus 936 Ttr~C~nCGQvGHmkTNK~CP~f~s 960 (968)
T COG5179 936 TTRTCGNCGQVGHMKTNKACPKFSS 960 (968)
T ss_pred cceecccccccccccccccCccccC
Confidence 3468999999999975 5887543
No 49
>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid. This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....
Probab=50.94 E-value=66 Score=24.67 Aligned_cols=41 Identities=15% Similarity=0.303 Sum_probs=29.3
Q ss_pred cHHHHHHHHHHHhccC-CchhHhhHHHHHHHhhcC-CCcHHHHHHHHHHHHHH
Q 045690 21 TAKDMWEYLKKVYNQD-NTAKCFHLEYEIARYSQG-DLSIQNYLSGIQNLWAK 71 (220)
Q Consensus 21 ta~~~W~~L~~~f~~~-~~~~~~~l~~~~~~~~~~-~~sv~ey~~~~~~l~~~ 71 (220)
-+-..|..|...++.. + |....|| +|+..+|+++|..-+..
T Consensus 107 ~ai~Aw~~l~~~~~~~~~----------~~~I~QGp~Epf~dFv~rl~~a~~~ 149 (206)
T PF00607_consen 107 WAIKAWRKLPRKGSPGES----------FTKIKQGPKEPFADFVDRLQKAIRR 149 (206)
T ss_dssp HHHHHHHHHHHHHSSSST----------GGGH-S-TTSHHHHHHHHHHHHHHC
T ss_pred HHHHhhhccccccccccc----------HHHhhhccccchHHHHHHHHHHHhh
Confidence 4567888888888855 3 3356786 99999999999765543
No 50
>PF14684 Tricorn_C1: Tricorn protease C1 domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A.
Probab=47.47 E-value=32 Score=21.18 Aligned_cols=54 Identities=4% Similarity=0.102 Sum_probs=35.8
Q ss_pred cHHHHHHHHHHHhccC--CchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHhc
Q 045690 21 TAKDMWEYLKKVYNQD--NTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVD 74 (220)
Q Consensus 21 ta~~~W~~L~~~f~~~--~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~ 74 (220)
...++|..+++.|-.. ...-=..+...+......-.|-.++..-|..+..+|.+
T Consensus 7 ~F~~~W~~~~~~f~d~~~~gvDW~~~~~~Y~p~v~~~~~~~el~~vl~eMl~eL~~ 62 (70)
T PF14684_consen 7 MFDEAWRLVRENFYDPDMHGVDWDAVYDRYRPLVPAAKTRDELYDVLNEMLGELND 62 (70)
T ss_dssp HHHHHHHHHHHHSS-HHHHHHHHHHHHHHHHGGGGG--SHHHHHHHHHHHHHTT--
T ss_pred HHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHCC
Confidence 4568999999988743 22234466666776666777888888888888888873
No 51
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=47.00 E-value=9.3 Score=19.54 Aligned_cols=24 Identities=17% Similarity=0.310 Sum_probs=12.2
Q ss_pred ccccCCCccccccccCcccccccc
Q 045690 173 CFSCKEYRHIIVNCAKKFCNYCKK 196 (220)
Q Consensus 173 ~~~~~~~g~~~~~~~~~~C~~C~k 196 (220)
|..|+.+-..........|..|+.
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSSS-
T ss_pred cCcCCccccCCCCcCEeECCCCcC
Confidence 666777666666666667777764
No 52
>PF08203 RNA_polI_A14: Yeast RNA polymerase I subunit RPA14; InterPro: IPR013239 Saccharomyces cerevisiae RNA polymerase I (Pol I) is a complex consisting of 14 subunits. Subunit RPA14 forms part of a Pol I subcomplex consisting of RPA14 and and RPA43. The RPA14 and RPA43 heterodimer is proposed to play a role in the recruitment of Pol I to the promoter []. ; PDB: 2RF4_F.
Probab=46.70 E-value=45 Score=21.13 Aligned_cols=16 Identities=19% Similarity=0.154 Sum_probs=10.8
Q ss_pred HHHHHHHHHHhhcchh
Q 045690 92 HEQSKRDQFLMKLRPE 107 (220)
Q Consensus 92 ~d~~~~~~~l~gLp~~ 107 (220)
..-.+|.+-|+||||-
T Consensus 59 SQLKRiQRdlrGLPP~ 74 (76)
T PF08203_consen 59 SQLKRIQRDLRGLPPL 74 (76)
T ss_dssp HHHHHHHHHHHHS---
T ss_pred HHHHHHHHhhCCCCCC
Confidence 5567888899999984
No 53
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=46.69 E-value=12 Score=28.23 Aligned_cols=31 Identities=19% Similarity=0.449 Sum_probs=21.9
Q ss_pred CccccccCCCccccccccCcccccccccccccc
Q 045690 170 QVQCFSCKEYRHIIVNCAKKFCNYCKKPGHIIK 202 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~~~~~~~C~~C~k~GH~~~ 202 (220)
...|..|++.|...++. ..|..|+..|....
T Consensus 99 ~~~C~~C~G~G~~i~~~--~~C~~C~G~G~v~~ 129 (186)
T TIGR02642 99 SCKCPRCRGTGLIQRRQ--RECDTCAGTGRFRP 129 (186)
T ss_pred CCcCCCCCCeeEEecCC--CCCCCCCCccEEee
Confidence 44688888888664422 56889988887654
No 54
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=46.51 E-value=1e+02 Score=23.99 Aligned_cols=18 Identities=33% Similarity=0.661 Sum_probs=10.2
Q ss_pred ccccccccccc-cccCCCC
Q 045690 189 KFCNYCKKPGH-IIKECPT 206 (220)
Q Consensus 189 ~~C~~C~k~GH-~~~~C~~ 206 (220)
+.|-.|+..=| -+..||.
T Consensus 250 K~ClsChqqIHRNAPiCPl 268 (286)
T KOG4451|consen 250 KVCLSCHQQIHRNAPICPL 268 (286)
T ss_pred hHHHHHHHHHhcCCCCCcc
Confidence 46777766555 3455554
No 55
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=46.31 E-value=1.6e+02 Score=24.04 Aligned_cols=18 Identities=11% Similarity=0.322 Sum_probs=14.8
Q ss_pred cHHHHHHHHHHHHHHHhc
Q 045690 57 SIQNYLSGIQNLWAKYVD 74 (220)
Q Consensus 57 sv~ey~~~~~~l~~~L~~ 74 (220)
+..+|-.+++.|.-.|++
T Consensus 181 ~~~~Yk~k~Rsl~~NLKd 198 (299)
T TIGR01385 181 TEAAYKARYRSIYSNLRD 198 (299)
T ss_pred CcHHHHHHHHHHHHHccC
Confidence 456799999999988873
No 56
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=45.31 E-value=1.2e+02 Score=22.42 Aligned_cols=98 Identities=15% Similarity=0.150 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHhccCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHhcccccCCCcc-cHHHHHHHHHHHHHHHH
Q 045690 22 AKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIE-SLADVQGVHEQSKRDQF 100 (220)
Q Consensus 22 a~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~-~~~~~~~~~d~~~~~~~ 100 (220)
.+++|..|.+ .-..+..+..+...|-+|..|++.+..+. .+..+-+...... ....+ ...+..+
T Consensus 46 f~~l~~~l~~---------~pE~~~l~~yL~~~gldv~~~i~~i~~~l-~~~~~~p~~~~~~~~~~g~-----~g~~~di 110 (179)
T PF06757_consen 46 FKQLWQQLEA---------LPEVKALLDYLESAGLDVYYYINQINDLL-GLPPLNPTPSLSCSRGGGL-----NGFVDDI 110 (179)
T ss_pred HHHHHHHHHc---------CHHHHHHHHHHHHCCCCHHHHHHHHHHHH-cCCcCCCCcccccccCCCH-----HHHHHHH
Confidence 4566666555 33455555555667999999999999886 3332211100000 11111 3344556
Q ss_pred HhhcchhHHHHHHhhhc-CCCCCCHHHHHHHHHHHHH
Q 045690 101 LMKLRPEYKAARSNLMN-RDLSPSLDVCFKELLREEQ 136 (220)
Q Consensus 101 l~gLp~~~~~~~~~~~~-~~~~~t~~e~~~~l~~~e~ 136 (220)
+.-||-+ .++..+.. -.+.+.|.+++..+.+.|-
T Consensus 111 ~~~lP~~--~l~aL~~~K~~~s~~F~~f~~~l~S~ef 145 (179)
T PF06757_consen 111 LALLPRD--KLRALYEEKLATSPEFAEFVEALRSPEF 145 (179)
T ss_pred HHHCCHH--HHHHHHHHHHHCCHHHHHHHHHHcCHHH
Confidence 7777743 22222222 1223457777777777653
No 57
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=44.77 E-value=11 Score=29.72 Aligned_cols=19 Identities=42% Similarity=0.877 Sum_probs=16.9
Q ss_pred ccccccccc---ccccCCCCCC
Q 045690 190 FCNYCKKPG---HIIKECPTRP 208 (220)
Q Consensus 190 ~C~~C~k~G---H~~~~C~~~~ 208 (220)
.|..||-.| |..+.||...
T Consensus 270 VCPiCGATgDnAHTiKyCPl~~ 291 (318)
T KOG4602|consen 270 VCPICGATGDNAHTIKYCPLAF 291 (318)
T ss_pred cCccccccCCcccceecccccC
Confidence 899999888 9999999866
No 58
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=43.70 E-value=18 Score=22.08 Aligned_cols=29 Identities=14% Similarity=0.154 Sum_probs=19.4
Q ss_pred ccccccCCCccccccccCccccccccccc
Q 045690 171 VQCFSCKEYRHIIVNCAKKFCNYCKKPGH 199 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~~~~C~~C~k~GH 199 (220)
..|..|+.............|..||...|
T Consensus 29 q~C~~CG~~~~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHRNKKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCcccccccccccceEEcCCCCCEEC
Confidence 35788887766644455558888887644
No 59
>KOG0403 consensus Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms]
Probab=42.63 E-value=75 Score=27.70 Aligned_cols=68 Identities=15% Similarity=0.210 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhccCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHH---HHHHHHHH
Q 045690 23 KDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGV---HEQSKRDQ 99 (220)
Q Consensus 23 ~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~---~d~~~~~~ 99 (220)
.-||+.|++.|..+. -|+.+...-|.++.+.|.++ ...+|...-..-... .+.-.+.+
T Consensus 560 t~~ldLLk~cf~sgl------------------IT~nQMtkGf~RV~dsl~Dl-sLDvPna~ekf~~~Ve~~~~~G~i~~ 620 (645)
T KOG0403|consen 560 TMILDLLKECFKSGL------------------ITTNQMTKGFERVYDSLPDL-SLDVPNAYEKFERYVEECFQNGIISK 620 (645)
T ss_pred HHHHHHHHHHHhcCc------------------eeHHHhhhhhhhhhccCccc-ccCCCcHHHHHHHHHHHHHHcCchhH
Confidence 367777777776432 24444444455555555544 444444222111000 11123455
Q ss_pred HHhhcchhHH
Q 045690 100 FLMKLRPEYK 109 (220)
Q Consensus 100 ~l~gLp~~~~ 109 (220)
+|+-|||+|-
T Consensus 621 ~l~~~~~s~l 630 (645)
T KOG0403|consen 621 QLRDLCPSRL 630 (645)
T ss_pred Hhhhcchhhh
Confidence 7777887753
No 60
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.08 E-value=15 Score=20.50 Aligned_cols=25 Identities=20% Similarity=0.396 Sum_probs=13.7
Q ss_pred ccccCCCccccccccCccccccccc
Q 045690 173 CFSCKEYRHIIVNCAKKFCNYCKKP 197 (220)
Q Consensus 173 ~~~~~~~g~~~~~~~~~~C~~C~k~ 197 (220)
|.+|+..-.........+|.+||.+
T Consensus 6 C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 6 CARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred CCCCCCEEEECCCCCceECCCCCCe
Confidence 5555554333332235689999864
No 61
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=40.44 E-value=13 Score=29.97 Aligned_cols=18 Identities=22% Similarity=0.658 Sum_probs=16.5
Q ss_pred cccccCCCccccccccCc
Q 045690 172 QCFSCKEYRHIIVNCAKK 189 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~ 189 (220)
+|++|++.||+.+.|+..
T Consensus 162 ~cyrcGkeghwskEcP~~ 179 (346)
T KOG0109|consen 162 GCYRCGKEGHWSKECPVD 179 (346)
T ss_pred HheeccccccccccCCcc
Confidence 799999999999999864
No 62
>PF07583 PSCyt2: Protein of unknown function (DUF1549); InterPro: IPR011444 The function is not known. It is found associated with IPR022655 from INTERPRO. It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=39.76 E-value=89 Score=24.03 Aligned_cols=43 Identities=16% Similarity=0.135 Sum_probs=29.1
Q ss_pred HHHHHHHH---HHhhcchhHHHHHHhhhcCCCCCCHHHHHHHHHHHH
Q 045690 92 HEQSKRDQ---FLMKLRPEYKAARSNLMNRDLSPSLDVCFKELLREE 135 (220)
Q Consensus 92 ~d~~~~~~---~l~gLp~~~~~~~~~~~~~~~~~t~~e~~~~l~~~e 135 (220)
+|...+.+ =|.|+||..+.+...+... ..-..+.+++.|+..+
T Consensus 23 dd~~~lRRv~LDL~G~~PT~eEv~~Fl~d~-~~~kr~~lVd~LL~sp 68 (208)
T PF07583_consen 23 DDATFLRRVYLDLTGLPPTPEEVRAFLADP-SPDKREKLVDRLLASP 68 (208)
T ss_pred CHHHHHHHHHHHHhCCCcCHHHHHHHHhCC-ChhHHHHHHHHHHCCc
Confidence 34444444 3999999998887766543 3345888888887654
No 63
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.05 E-value=23 Score=33.73 Aligned_cols=11 Identities=27% Similarity=0.594 Sum_probs=7.2
Q ss_pred CccccccCCCc
Q 045690 170 QVQCFSCKEYR 180 (220)
Q Consensus 170 ~~~~~~~~~~g 180 (220)
...|..|+..+
T Consensus 626 ~RfCpsCG~~t 636 (1121)
T PRK04023 626 RRKCPSCGKET 636 (1121)
T ss_pred CccCCCCCCcC
Confidence 44677777765
No 64
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=39.05 E-value=81 Score=20.73 Aligned_cols=34 Identities=21% Similarity=0.177 Sum_probs=19.2
Q ss_pred CCCCCCCCccccccCCCccccccccCcccccccc
Q 045690 163 SKGRDMRQVQCFSCKEYRHIIVNCAKKFCNYCKK 196 (220)
Q Consensus 163 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~C~~C~k 196 (220)
+...-..+..|..||.--..-+-...-.|..|+.
T Consensus 51 g~~Llv~Pa~CkkCGfef~~~~ik~pSRCP~CKS 84 (97)
T COG3357 51 GKRLLVRPARCKKCGFEFRDDKIKKPSRCPKCKS 84 (97)
T ss_pred CceEEecChhhcccCccccccccCCcccCCcchh
Confidence 3334445667888887544422222336888865
No 65
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=38.75 E-value=22 Score=20.98 Aligned_cols=20 Identities=40% Similarity=0.856 Sum_probs=15.5
Q ss_pred cccCccccccccccccccCC
Q 045690 185 NCAKKFCNYCKKPGHIIKEC 204 (220)
Q Consensus 185 ~~~~~~C~~C~k~GH~~~~C 204 (220)
.|....|+.|+...|.-..|
T Consensus 45 ~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 45 KCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred CCCCeECCCCCCcCCCCCCC
Confidence 34556899999999977665
No 66
>PF08112 ATP-synt_E_2: ATP synthase epsilon subunit; InterPro: IPR012508 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. A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases []. A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore []. The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C []. A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species. The epsilon subunit is the smallest (7 kDa) of those found in the A1 complex. Unlike the A, B and C subunits, the epsilon subunit does not have a homologous counterpart in F- or V-ATPases []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain
Probab=38.67 E-value=72 Score=18.50 Aligned_cols=36 Identities=19% Similarity=0.250 Sum_probs=23.1
Q ss_pred CCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHHHHHhhcchhHHHHHH
Q 045690 54 GDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARS 113 (220)
Q Consensus 54 ~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~~~~~~~ 113 (220)
+..+|+.|++.+++-.++-. .+ ++..|+.+|+.+..
T Consensus 5 ~~~~~d~yI~~Lk~kLd~Kk-------~E-----------------il~~ln~EY~kiLk 40 (56)
T PF08112_consen 5 DKSTIDKYISILKSKLDEKK-------SE-----------------ILSNLNMEYEKILK 40 (56)
T ss_pred hhhhHHHHHHHHHHHHHHHH-------HH-----------------HHHHHHHHHHHHHH
Confidence 34578888887765544443 22 77778888877643
No 67
>PHA00689 hypothetical protein
Probab=38.16 E-value=12 Score=21.27 Aligned_cols=11 Identities=36% Similarity=0.803 Sum_probs=9.0
Q ss_pred Ccccccccccc
Q 045690 188 KKFCNYCKKPG 198 (220)
Q Consensus 188 ~~~C~~C~k~G 198 (220)
..+|..||+.|
T Consensus 17 avtckrcgktg 27 (62)
T PHA00689 17 AVTCKRCGKTG 27 (62)
T ss_pred eeehhhccccC
Confidence 35899999987
No 68
>cd07562 Peptidase_S41_TRI Tricorn protease; serine protease family S41. The tricorn protease (TRI), a member of the S41 peptidase family and named for its tricorn-like shape, exists only in some archaea and eubacteria. It has been shown to act as a carboxypeptidase, involved in the degradation of proteasomal products to preferentially yield di- and tripeptides, with subsequent and final degradations to free amino acid residues by tricorn interacting factors, F1, F2 and F3. Tricorn is a hexameric D3-symmetric protease of 720kD, and can self-associate further into a giant icosahedral capsid structure containing twenty copies of the complex. Each tricorn peptidase monomer consists of five structural domains: a six-bladed beta-propeller and a seven-bladed beta-propeller that limit access to the active site, the two domains (C1 and C2) that carry the active site residues, and a PDZ-like domain (proposed to be important for substrate recognition) between the C1 and C2 domains. The active sit
Probab=38.10 E-value=1.2e+02 Score=24.01 Aligned_cols=56 Identities=5% Similarity=0.112 Sum_probs=44.1
Q ss_pred ccHHHHHHHHHHHhccC--CchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHhcc
Q 045690 20 KTAKDMWEYLKKVYNQD--NTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDM 75 (220)
Q Consensus 20 ~ta~~~W~~L~~~f~~~--~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~~ 75 (220)
....++|..+++.|-.. ....-..++.++......-.+-.+|..-|..+..+|.+-
T Consensus 4 ~~fd~~w~~~~~~y~~~~~~g~dW~~~~~~y~~~~~~~~~~~e~~~~l~~ml~~L~d~ 61 (266)
T cd07562 4 QMFDEAWRLVRDNFYDPDMHGVDWDAVRAEYRPLLPRAATRAELADVLNEMLGELNDS 61 (266)
T ss_pred HHHHHHHHHHHhhccCCCCCCCCHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHcCC
Confidence 35678999999999733 333455777778777777889999999999999999854
No 69
>PF06424 PRP1_N: PRP1 splicing factor, N-terminal; InterPro: IPR010491 This domain is specific to the N-terminal part of the prp1 splicing factor, which is involved in mRNA splicing (and possibly also poly(A)+ RNA nuclear export and cell cycle progression). This domain is specific to the N terminus of the RNA splicing factor encoded by prp1 []. It is involved in mRNA splicing and possibly also poly(A)and RNA nuclear export and cell cycle progression.; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005634 nucleus
Probab=37.97 E-value=1.2e+02 Score=21.55 Aligned_cols=52 Identities=13% Similarity=0.287 Sum_probs=35.2
Q ss_pred ccHHHHHHHHHHHhc-cCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHhc
Q 045690 20 KTAKDMWEYLKKVYN-QDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVD 74 (220)
Q Consensus 20 ~ta~~~W~~L~~~f~-~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~ 74 (220)
.-|..||+.+..+-. .....+......+......+.-.|.+.|..|+ ..|..
T Consensus 63 ~EAD~Iy~~ID~rmd~Rrk~~re~~~~~e~e~~~~~~pkI~~QFaDLK---R~La~ 115 (133)
T PF06424_consen 63 EEADRIYESIDRRMDSRRKKRREAREKEEIEKYRKENPKIQQQFADLK---RSLAT 115 (133)
T ss_pred HHHHHHHHHHHHHHHhcccchhhhhhhhHHHhhhccCchHHHHHHHHH---HHHcc
Confidence 358899999999998 34434555666666666667777777666554 45553
No 70
>PF07023 DUF1315: Protein of unknown function (DUF1315); InterPro: IPR009749 This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Probab=37.59 E-value=29 Score=22.90 Aligned_cols=21 Identities=19% Similarity=0.425 Sum_probs=18.1
Q ss_pred HHHHhhcchh-HHHHHHhhhcC
Q 045690 98 DQFLMKLRPE-YKAARSNLMNR 118 (220)
Q Consensus 98 ~~~l~gLp~~-~~~~~~~~~~~ 118 (220)
..+|..|+|+ |+.++.++...
T Consensus 2 ~~li~~mtPevY~rL~~AVElG 23 (93)
T PF07023_consen 2 EQLIDSMTPEVYERLKQAVELG 23 (93)
T ss_pred hHHHHhCCHHHHHHHHHHHHhC
Confidence 3489999999 99999999983
No 71
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.57 E-value=24 Score=31.06 Aligned_cols=22 Identities=36% Similarity=0.676 Sum_probs=18.1
Q ss_pred CccccccccccccccCCCCCCC
Q 045690 188 KKFCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 188 ~~~C~~C~k~GH~~~~C~~~~~ 209 (220)
...|++||..--+-..||.-..
T Consensus 240 ~l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 240 KLRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred eEEcCCCcCcCCCCCCCCCCCC
Confidence 3489999998888889998754
No 72
>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=37.40 E-value=1.4e+02 Score=21.11 Aligned_cols=44 Identities=11% Similarity=0.013 Sum_probs=33.0
Q ss_pred CccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcC-CCcHHHHH
Q 045690 19 YKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQG-DLSIQNYL 62 (220)
Q Consensus 19 ~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~-~~sv~ey~ 62 (220)
...++++...|+.+....+..........+..+.+. |..+...+
T Consensus 37 ~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev 81 (140)
T PF00790_consen 37 PDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREV 81 (140)
T ss_dssp TTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHH
T ss_pred CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 668899999999999987766666667777777773 55665444
No 73
>COG5420 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]
Probab=37.18 E-value=50 Score=20.00 Aligned_cols=40 Identities=8% Similarity=0.073 Sum_probs=25.0
Q ss_pred CcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHHHHHhhcchhHHHHHH
Q 045690 56 LSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARS 113 (220)
Q Consensus 56 ~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~~~~~~~ 113 (220)
.++++--.+++.|..+...+ ...+-| +-.|||..|..+..
T Consensus 6 s~l~eiqkKvrkLqsrAg~a-km~LhD-----------------LAEgLP~~wtei~~ 45 (71)
T COG5420 6 SSLEEIQKKVRKLQSRAGQA-KMELHD-----------------LAEGLPVKWTEIMA 45 (71)
T ss_pred hhHHHHHHHHHHHHHHHHHH-HhhHHH-----------------HhccCCccHHHHHH
Confidence 35666666666666555432 333333 88999999887754
No 74
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=36.83 E-value=23 Score=28.67 Aligned_cols=18 Identities=33% Similarity=0.872 Sum_probs=15.8
Q ss_pred cccccCCCccccccccCc
Q 045690 172 QCFSCKEYRHIIVNCAKK 189 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~ 189 (220)
-||+|++.||+-..|+..
T Consensus 178 ~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 178 VCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred eEEecCCCCchhhcCCCC
Confidence 599999999999988654
No 75
>COG3120 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.52 E-value=81 Score=22.07 Aligned_cols=33 Identities=12% Similarity=-0.176 Sum_probs=20.3
Q ss_pred CCcHHHHHHHHHHHHHHHhcccccCCCcccHHHH
Q 045690 55 DLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADV 88 (220)
Q Consensus 55 ~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~ 88 (220)
..||+--+.-...|.---..+ |..+++++.-.+
T Consensus 91 KKSIDLey~VW~rLs~~a~~~-g~TLSetI~~li 123 (149)
T COG3120 91 KKSIDLEYAVWQRLSGLARRR-GKTLSETIVYLI 123 (149)
T ss_pred hccccHHHHHHHHHHHHHHHh-cCcHHHHHHHHH
Confidence 567776666666665544433 677776555555
No 76
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=35.56 E-value=69 Score=21.80 Aligned_cols=34 Identities=15% Similarity=0.129 Sum_probs=21.5
Q ss_pred CCCccHHHHHHHHHHHhccCCchhHhhHHHHHHH
Q 045690 17 KPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIAR 50 (220)
Q Consensus 17 ~~~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~ 50 (220)
...-|+.++|+.|+.....-+.+.+++.-..|..
T Consensus 21 ~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e 54 (120)
T PF01475_consen 21 PEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEE 54 (120)
T ss_dssp SSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHH
Confidence 4577999999999976655554555554444443
No 77
>PRK14873 primosome assembly protein PriA; Provisional
Probab=35.30 E-value=29 Score=31.73 Aligned_cols=21 Identities=19% Similarity=0.507 Sum_probs=16.4
Q ss_pred CccccccccccccccCCCCCCC
Q 045690 188 KKFCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 188 ~~~C~~C~k~GH~~~~C~~~~~ 209 (220)
...|++||..- .-..||.-..
T Consensus 410 ~l~Ch~CG~~~-~p~~Cp~Cgs 430 (665)
T PRK14873 410 TPRCRWCGRAA-PDWRCPRCGS 430 (665)
T ss_pred eeECCCCcCCC-cCccCCCCcC
Confidence 34899999865 6889998754
No 78
>PF14567 SUKH_5: SMI1-KNR4 cell-wall; PDB: 2PAG_A.
Probab=35.09 E-value=1e+02 Score=21.88 Aligned_cols=47 Identities=15% Similarity=0.232 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHH---HHHHhhcchhHHHHHHhhh
Q 045690 58 IQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKR---DQFLMKLRPEYKAARSNLM 116 (220)
Q Consensus 58 v~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~---~~~l~gLp~~~~~~~~~~~ 116 (220)
|.+++.+++.+..... + ...+|+ +++++ .+++-.||.+|..|.....
T Consensus 1 m~~~i~~L~~~~e~~~-~-~l~lpd----------~e~I~~~Ee~L~i~lP~eyk~fL~~~s 50 (132)
T PF14567_consen 1 MEDIIERLKELNEPVP-V-PLELPD----------DEQIVEAEEQLGISLPEEYKEFLLEAS 50 (132)
T ss_dssp -HHHHHHHHHH----S-S-----------------HHHHHHHHHHHT----HHHHHHHHHHT
T ss_pred ChHHHHHHHHhcCCcc-C-CCCCCC----------HHHHHHHHHHHCCCCCHHHHHHHHHCC
Confidence 4567777776665554 2 333343 22222 3488999999988865444
No 79
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=34.49 E-value=28 Score=28.05 Aligned_cols=33 Identities=18% Similarity=0.275 Sum_probs=26.6
Q ss_pred cccccCCCccccccccCccccccccccccccCCC
Q 045690 172 QCFSCKEYRHIIVNCAKKFCNYCKKPGHIIKECP 205 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~C~k~GH~~~~C~ 205 (220)
=|.+|+.+-..+.......|..|+. -|+-+.+|
T Consensus 113 FCg~CG~~~~~~~~g~~~~C~~cg~-~~fPR~dP 145 (279)
T COG2816 113 FCGRCGTKTYPREGGWARVCPKCGH-EHFPRIDP 145 (279)
T ss_pred CCCCCCCcCccccCceeeeCCCCCC-ccCCCCCC
Confidence 4888888888877888889999987 57777776
No 80
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=33.65 E-value=45 Score=28.11 Aligned_cols=40 Identities=20% Similarity=0.443 Sum_probs=27.8
Q ss_pred CccccccCCCccccccc------cCccccccccccccc-cCCCCCCC
Q 045690 170 QVQCFSCKEYRHIIVNC------AKKFCNYCKKPGHII-KECPTRPQ 209 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~~~------~~~~C~~C~k~GH~~-~~C~~~~~ 209 (220)
...|..|+..|...... ...+|..|+-.|++. .-|+.-..
T Consensus 159 ~~tC~tC~G~G~v~~~~~~g~~~~~~~C~~C~G~G~~i~~pC~~C~G 205 (371)
T COG0484 159 PKTCPTCNGSGQVRTVQRTGFFSFQQTCPTCNGTGKIIKDPCGKCKG 205 (371)
T ss_pred CCcCCCCCCcCeEEEEEeeeEEEEEEECCCCccceeECCCCCCCCCC
Confidence 44688888888654432 223899999999877 56776553
No 81
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=33.55 E-value=1.2e+02 Score=18.69 Aligned_cols=33 Identities=12% Similarity=0.008 Sum_probs=26.2
Q ss_pred hcchhHHHHHHhhhcCCCCCCHHHHHHHHHHHH
Q 045690 103 KLRPEYKAARSNLMNRDLSPSLDVCFKELLREE 135 (220)
Q Consensus 103 gLp~~~~~~~~~~~~~~~~~t~~e~~~~l~~~e 135 (220)
+||+++..|+.........-+..|++..++...
T Consensus 5 sL~~~~~~~i~~~V~sG~Y~s~SEVir~aLR~l 37 (69)
T TIGR02606 5 SLGEHLESFIRSQVQSGRYGSASEVVRAALRLL 37 (69)
T ss_pred ecCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Confidence 588999999988888877788888877765544
No 82
>PF09133 SANTA: SANTA (SANT Associated); InterPro: IPR015216 The SANTA domain (SANT associated) is approximately 90 amino acids in length and is conserved in eukaryotes. It is sometimes found in association with the SANT domain (IPR001005 from INTERPRO, also known as the Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling. Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha-helices. Many conserved hydrophobic residues are present which implies a possible role in protein-protein interactions.
Probab=33.16 E-value=47 Score=21.89 Aligned_cols=20 Identities=5% Similarity=0.134 Sum_probs=15.9
Q ss_pred HHHHHHHHhhcchhHHHHHH
Q 045690 94 QSKRDQFLMKLRPEYKAARS 113 (220)
Q Consensus 94 ~~~~~~~l~gLp~~~~~~~~ 113 (220)
...+.+|..|.|+.|+.+..
T Consensus 71 ~~v~~~F~~GFP~~W~~~~~ 90 (93)
T PF09133_consen 71 SEVIKKFMNGFPENWEEYIN 90 (93)
T ss_pred HHHHHHHhcCCCHHHHHHHH
Confidence 34556699999999998865
No 83
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=32.99 E-value=45 Score=20.21 Aligned_cols=39 Identities=21% Similarity=0.477 Sum_probs=23.9
Q ss_pred CCccccccCCCcccccccc--------Ccccccccccccc--ccCCCCC
Q 045690 169 RQVQCFSCKEYRHIIVNCA--------KKFCNYCKKPGHI--IKECPTR 207 (220)
Q Consensus 169 ~~~~~~~~~~~g~~~~~~~--------~~~C~~C~k~GH~--~~~C~~~ 207 (220)
....|..|...|.....-. ...|..|+-.|.+ ...|+.=
T Consensus 14 ~~~~C~~C~G~G~~~~~~~~~~~~~~~~~~C~~C~G~G~~i~~~~C~~C 62 (66)
T PF00684_consen 14 KPKTCPQCNGSGQVTRRQQTPGGVFQMQQTCPKCGGTGKIIEKDPCKTC 62 (66)
T ss_dssp T-EE-TTSSSSSEEEEEEESSSTTEEEEEE-TTTSSSSEE-TSSB-SSS
T ss_pred CCcCCcCCCCeeEEEEEEeCCCeEEEEEEECCCCcceeeEECCCCCCCC
Confidence 3446888888887654321 1289999999987 4667653
No 84
>KOG2203 consensus GTP-binding protein [General function prediction only]
Probab=32.68 E-value=1.3e+02 Score=27.14 Aligned_cols=53 Identities=9% Similarity=0.362 Sum_probs=42.0
Q ss_pred cHHHHHHHHHHHhccCCchhHhhHHHHHHHhh--cCCCcHHHHHHHHHHHHHHHh
Q 045690 21 TAKDMWEYLKKVYNQDNTAKCFHLEYEIARYS--QGDLSIQNYLSGIQNLWAKYV 73 (220)
Q Consensus 21 ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~--~~~~sv~ey~~~~~~l~~~L~ 73 (220)
-.++.|+.+++.|.......++.+.....-.. .+.++.++|+..|+.++...-
T Consensus 479 ~s~evW~ti~n~f~~e~n~av~~~~~~~~~f~~~~de~t~~~m~~nlk~~a~~~~ 533 (772)
T KOG2203|consen 479 ASKEVWDTIRNLFRRETNTAVYGLSNAVYGFEIGLDEETRDKMVKNLKNYAWGTV 533 (772)
T ss_pred cccccHHHHHHHHHhccchhHHHHhhcccccccccchhhHHHHHHHHHHHHHHHH
Confidence 45789999999999655566777777777666 567899999999998876654
No 85
>PF13797 Post_transc_reg: Post-transcriptional regulator
Probab=32.65 E-value=75 Score=20.69 Aligned_cols=32 Identities=22% Similarity=0.401 Sum_probs=20.3
Q ss_pred CccHHHHHHHHHHHhc-cCCchhHhhHHHHHHH
Q 045690 19 YKTAKDMWEYLKKVYN-QDNTAKCFHLEYEIAR 50 (220)
Q Consensus 19 ~~ta~~~W~~L~~~f~-~~~~~~~~~l~~~~~~ 50 (220)
.-|..++|++|.+.+- .....+++.+...+..
T Consensus 27 ~vt~~dlw~yl~~~~WK~~~~~~l~e~V~DIls 59 (87)
T PF13797_consen 27 SVTEEDLWSYLTEKKWKKKKPPRLHELVNDILS 59 (87)
T ss_pred cCCHHHHHHHHHHHHhccCCCcCHHHHHHHHHc
Confidence 3489999999998765 3333455544444443
No 86
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=32.60 E-value=1.7e+02 Score=20.36 Aligned_cols=61 Identities=8% Similarity=0.113 Sum_probs=41.9
Q ss_pred cHHHHhccCCCccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHh
Q 045690 9 DQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYV 73 (220)
Q Consensus 9 ~~~~~~~i~~~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~ 73 (220)
+.+....+-+..+-..+++.+.....++ .......+......|.++..++..+...+..+-
T Consensus 2 t~e~V~~~lG~v~~~~i~~l~~ai~~~d----~~~~l~~~~~l~~~G~d~~~~l~~L~~~~R~ll 62 (143)
T PF12169_consen 2 TAEDVREILGLVDEEQIFELLDAILEGD----AAEALELLNELLEQGKDPKQFLDDLIEYLRDLL 62 (143)
T ss_dssp -HHHHHHHHTHTSTHHHHHHHHHHHTT-----HHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCCHHHHHHHHHHHHcCC----HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3444555566666677777777777655 345666777778888999999999999888876
No 87
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=31.97 E-value=1.2e+02 Score=19.74 Aligned_cols=27 Identities=7% Similarity=0.102 Sum_probs=18.1
Q ss_pred cccHHHHhccCCCccHHHHHHHHHHHh
Q 045690 7 SVDQSLVLNLKPYKTAKDMWEYLKKVY 33 (220)
Q Consensus 7 sl~~~~~~~i~~~~ta~~~W~~L~~~f 33 (220)
..--.|+..+.+.+|..+|-+.|.+.|
T Consensus 36 etg~~Iw~~~DG~~tv~eIi~~L~~~y 62 (88)
T PRK02079 36 ESAGEILGLIDGKRTVAAIIAELQQQF 62 (88)
T ss_pred hHHHHHHHHccCCCCHHHHHHHHHHHc
Confidence 444556666677777777777777777
No 88
>PF05310 Tenui_NS3: Tenuivirus movement protein; InterPro: IPR007974 This family of ssRNA negative-strand crop plant tenuivirus proteins appears to combine PV2 [], NS2 [], NS3, and PV3 proteins. Plant viruses encode specific proteins known as movement proteins (MPs) to control their spread through plasmodesmata (PD) in walls between cells as well as from leaf to leaf via vascular-dependent transport. During this movement process, the virally encoded MPs interact with viral genomes for transport from the viral replication sites to the PDs in the walls of infected cells along the cytoskeleton and/or endoplasmic reticulum (ER) network. The virus is then thought to move through the PDs in the form of MP-associated ribonucleoprotein complexes or as virions []. The NS3 protein appears to function as an RNA silencing suppressor [].; PDB: 3AJF_A.
Probab=31.26 E-value=16 Score=27.15 Aligned_cols=18 Identities=28% Similarity=0.475 Sum_probs=0.0
Q ss_pred cCccccccccccccccCC
Q 045690 187 AKKFCNYCKKPGHIIKEC 204 (220)
Q Consensus 187 ~~~~C~~C~k~GH~~~~C 204 (220)
++.+||.|.|+.|++.+=
T Consensus 97 ~~tKCWlCdk~~~~~t~~ 114 (186)
T PF05310_consen 97 PKTKCWLCDKPSYQETDN 114 (186)
T ss_dssp ------------------
T ss_pred CccceEEecchhhhccCC
Confidence 445799999999988764
No 89
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=31.21 E-value=26 Score=23.92 Aligned_cols=25 Identities=20% Similarity=0.735 Sum_probs=19.9
Q ss_pred cccccCCCccccccccCcccccccc
Q 045690 172 QCFSCKEYRHIIVNCAKKFCNYCKK 196 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~C~k 196 (220)
.|..|+........|+.+.|..|+.
T Consensus 44 ~C~~Cg~~~~~~~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 44 RCEDCGHEKIVYNSCKNRHCPSCQA 68 (111)
T ss_pred ecCCCCceEEecCcccCcCCCCCCC
Confidence 5777888777777888888888875
No 90
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=31.20 E-value=22 Score=28.00 Aligned_cols=19 Identities=32% Similarity=0.774 Sum_probs=16.3
Q ss_pred ccccccccccccccCCCCCC
Q 045690 189 KFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 189 ~~C~~C~k~GH~~~~C~~~~ 208 (220)
..|..| +-.||..+||-+.
T Consensus 120 ~~CR~C-~gdHwt~~CPyK~ 138 (270)
T KOG0122|consen 120 VACRIC-KGDHWTTNCPYKD 138 (270)
T ss_pred eeeeec-CCCeeeecCCchh
Confidence 489999 7789999999765
No 91
>PF03693 RHH_2: Uncharacterised protein family (UPF0156); InterPro: IPR022789 This family of proteins are about 80 amino acids in length and their function is unknown. The proteins contain a conserved GRY motif. This family appears to be related to ribbon-helix-helix DNA-binding proteins. ; PDB: 3KXE_C.
Probab=31.06 E-value=1.4e+02 Score=18.95 Aligned_cols=31 Identities=26% Similarity=0.265 Sum_probs=22.9
Q ss_pred hcchhHHHHHHhhhcCCCCCCHHHHHHHHHH
Q 045690 103 KLRPEYKAARSNLMNRDLSPSLDVCFKELLR 133 (220)
Q Consensus 103 gLp~~~~~~~~~~~~~~~~~t~~e~~~~l~~ 133 (220)
+||++++.|+.+...+...-+..|++..++.
T Consensus 8 sL~~~~~~~i~~~V~sG~Y~s~SEvvR~aLR 38 (80)
T PF03693_consen 8 SLTPELEAFIEEQVASGRYSSASEVVREALR 38 (80)
T ss_dssp ---HHHHHHHHHHHCTTS-SSHHHHHHHHHH
T ss_pred ecCHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 5899999999999998888898888866544
No 92
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=30.61 E-value=26 Score=16.90 Aligned_cols=8 Identities=50% Similarity=1.223 Sum_probs=4.4
Q ss_pred cccccccc
Q 045690 189 KFCNYCKK 196 (220)
Q Consensus 189 ~~C~~C~k 196 (220)
..|.+||.
T Consensus 17 ~fC~~CG~ 24 (26)
T PF13248_consen 17 KFCPNCGA 24 (26)
T ss_pred ccChhhCC
Confidence 45666654
No 93
>PF12417 DUF3669: Zinc finger protein ; InterPro: IPR022137 This domain family is found in eukaryotes, and is typically between 64 and 80 amino acids in length.
Probab=30.44 E-value=46 Score=20.71 Aligned_cols=20 Identities=25% Similarity=0.526 Sum_probs=16.4
Q ss_pred CCCccHHHHHHHHHHHhccC
Q 045690 17 KPYKTAKDMWEYLKKVYNQD 36 (220)
Q Consensus 17 ~~~~ta~~~W~~L~~~f~~~ 36 (220)
...++..++|+.++..|...
T Consensus 38 ~~~~~~~~lW~~F~~~Yl~~ 57 (72)
T PF12417_consen 38 DCEKTDKELWNQFRSRYLET 57 (72)
T ss_pred ccchHHHHHHHHHHHHHHHH
Confidence 35678899999999999843
No 94
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=29.85 E-value=24 Score=20.81 Aligned_cols=18 Identities=22% Similarity=0.706 Sum_probs=10.9
Q ss_pred ccccccccccc----ccCCCCC
Q 045690 190 FCNYCKKPGHI----IKECPTR 207 (220)
Q Consensus 190 ~C~~C~k~GH~----~~~C~~~ 207 (220)
-|||||-.=-- .+.||-.
T Consensus 29 YC~~Cg~~Y~d~~dL~~~CPG~ 50 (55)
T PF13821_consen 29 YCFWCGTKYDDEEDLERNCPGP 50 (55)
T ss_pred eeeeeCCccCCHHHHHhCCCCC
Confidence 48888864332 3667754
No 95
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=29.65 E-value=1.7e+02 Score=19.42 Aligned_cols=36 Identities=11% Similarity=0.182 Sum_probs=25.3
Q ss_pred hHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHhcc
Q 045690 40 KCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDM 75 (220)
Q Consensus 40 ~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~~ 75 (220)
..-.+.+++...+..++.+.+...++..|-.++..+
T Consensus 51 ~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~l 86 (108)
T PF02403_consen 51 ERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKEL 86 (108)
T ss_dssp HHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHH
T ss_pred HHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHH
Confidence 344555566666666678888888888888888754
No 96
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=29.64 E-value=26 Score=21.00 Aligned_cols=17 Identities=35% Similarity=0.589 Sum_probs=10.6
Q ss_pred Ccccccccccc-ccccCC
Q 045690 188 KKFCNYCKKPG-HIIKEC 204 (220)
Q Consensus 188 ~~~C~~C~k~G-H~~~~C 204 (220)
-+.|.+||++= .-...|
T Consensus 3 HkHC~~CG~~Ip~~~~fC 20 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFC 20 (59)
T ss_pred CCcCCcCCCcCCcchhhh
Confidence 35799998763 334444
No 97
>PRK05580 primosome assembly protein PriA; Validated
Probab=29.05 E-value=39 Score=31.01 Aligned_cols=21 Identities=29% Similarity=0.499 Sum_probs=17.1
Q ss_pred ccccccccccccccCCCCCCC
Q 045690 189 KFCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 189 ~~C~~C~k~GH~~~~C~~~~~ 209 (220)
..|++||..-=....||.-..
T Consensus 409 l~Ch~Cg~~~~~~~~Cp~Cg~ 429 (679)
T PRK05580 409 LRCHHCGYQEPIPKACPECGS 429 (679)
T ss_pred EECCCCcCCCCCCCCCCCCcC
Confidence 479999988878888998754
No 98
>cd07563 Peptidase_S41_IRBP Interphotoreceptor retinoid-binding protein; serine protease family S41. Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium (RPE). IRBP is secreted by photoreceptors into the interphotoreceptor matrix (IPM) where it is rapidly turned over by a combination of RPE and photoreceptor endocytosis. It is the most abundant soluble protein component of the IPM, consisting of homologous modules, each repeat structure arising through the duplication (as in teleost IRBP) or quadruplication (in tetrapods) of an ancient gene, arisen in the early evolution of the vertebrate eye. IRBP has been shown to promote the release of all-trans retinol from photoreceptors
Probab=27.74 E-value=1.3e+02 Score=23.55 Aligned_cols=53 Identities=9% Similarity=-0.036 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHhccC--CchhHhhHHHHHHHhhc-CCCcHHHHHHHHHHHHHHHhc
Q 045690 22 AKDMWEYLKKVYNQD--NTAKCFHLEYEIARYSQ-GDLSIQNYLSGIQNLWAKYVD 74 (220)
Q Consensus 22 a~~~W~~L~~~f~~~--~~~~~~~l~~~~~~~~~-~~~sv~ey~~~~~~l~~~L~~ 74 (220)
...+|+.|++.|... ....-..++..+..... ...+-.++...|..+...|.+
T Consensus 2 ~~~~~~~~~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~l~D 57 (250)
T cd07563 2 FEALAKLLEENYAFPEAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQELGD 57 (250)
T ss_pred HHHHHHHHHHhCCChHHcccHHHHHHHHHhccccccCCCHHHHHHHHHHhhhccCC
Confidence 357899999999832 22345667777777777 788999999999988888753
No 99
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=27.70 E-value=3e+02 Score=25.96 Aligned_cols=65 Identities=15% Similarity=0.215 Sum_probs=49.6
Q ss_pred HHHHHHHHHhccCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHH
Q 045690 24 DMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHE 93 (220)
Q Consensus 24 ~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d 93 (220)
.-|+.-++.|+++. +|.+.|+...-+.-|+++-+.-++.|......+.+..++|+.+.....+++
T Consensus 306 TT~~EYRk~iEKD~-----AL~RRFQ~V~V~EPs~e~ti~ILrGlk~~yE~hH~V~i~D~Al~aAv~LS~ 370 (786)
T COG0542 306 TTLDEYRKYIEKDA-----ALERRFQKVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSD 370 (786)
T ss_pred ccHHHHHHHhhhch-----HHHhcCceeeCCCCCHHHHHHHHHHHHHHHHHccCceecHHHHHHHHHHHH
Confidence 34555555555543 577777777778899999999999999999999898888888777644333
No 100
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=27.68 E-value=31 Score=17.82 Aligned_cols=14 Identities=21% Similarity=0.548 Sum_probs=11.2
Q ss_pred ccccCccccccccc
Q 045690 184 VNCAKKFCNYCKKP 197 (220)
Q Consensus 184 ~~~~~~~C~~C~k~ 197 (220)
+-|...+||.|...
T Consensus 12 kLC~~~tCfsCNsi 25 (32)
T PF15629_consen 12 KLCDEETCFSCNSI 25 (32)
T ss_pred cccCCccccccccH
Confidence 46888899999864
No 101
>cd03564 ANTH_AP180_CALM ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. 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. AP180 and CALM play important roles in clathrin-mediated endocytosis. AP180 is a brain-specific clathrin-binding protein which stimulates clathrin assembly during the recycling of synaptic vesicles. The ANTH domain is structurally similar to the VHS domain and is composed of a superhelix of eight alpha helices. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that the ANTH domain is a universal component of the machine
Probab=27.26 E-value=2e+02 Score=19.47 Aligned_cols=47 Identities=9% Similarity=-0.055 Sum_probs=35.0
Q ss_pred ccCC-CccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcC-CCcHHHH
Q 045690 15 NLKP-YKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQG-DLSIQNY 61 (220)
Q Consensus 15 ~i~~-~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~-~~sv~ey 61 (220)
.... ..++.++|..|..+....+....+...-.++.+.++ .+++.+.
T Consensus 27 ~t~~~~~~~~~~~~~l~~Rl~~~~w~v~~K~LillH~llr~G~~~~~~~ 75 (117)
T cd03564 27 GTSSSPASIPSFASALSRRLLDRNWVVVLKALILLHRLLREGHPSFLQE 75 (117)
T ss_pred HHcCCCCCHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHhcCCHHHHHH
Confidence 3344 689999999999999887777777777778888885 4444443
No 102
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.69 E-value=59 Score=19.81 Aligned_cols=23 Identities=17% Similarity=0.384 Sum_probs=17.7
Q ss_pred HHhccCCCccHHHHHHHHHHHhc
Q 045690 12 LVLNLKPYKTAKDMWEYLKKVYN 34 (220)
Q Consensus 12 ~~~~i~~~~ta~~~W~~L~~~f~ 34 (220)
....|..=..++++|.+|+.-|+
T Consensus 36 ~~eAL~~G~dpr~VW~AlC~~~d 58 (63)
T PF11248_consen 36 AAEALEAGVDPRDVWRALCDAFD 58 (63)
T ss_pred HHHHHHcCCCHHHHHHHHHHHcC
Confidence 33445555689999999999997
No 103
>PF14077 WD40_alt: Alternative WD40 repeat motif
Probab=26.23 E-value=56 Score=18.40 Aligned_cols=30 Identities=13% Similarity=0.150 Sum_probs=23.5
Q ss_pred CchhHhhHHHHHHHhhcCCCcHHHHHHHHH
Q 045690 37 NTAKCFHLEYEIARYSQGDLSIQNYLSGIQ 66 (220)
Q Consensus 37 ~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~ 66 (220)
...|+..|..+...+++=+.++.+|-.+|.
T Consensus 16 l~vrv~eLEeEV~~LrKINrdLfdFSt~ii 45 (48)
T PF14077_consen 16 LRVRVSELEEEVRTLRKINRDLFDFSTRII 45 (48)
T ss_pred heeeHHHHHHHHHHHHHHhHHHHhhhhhhc
Confidence 456788888888888888888888877763
No 104
>PF00220 Hormone_4: Neurohypophysial hormones, N-terminal Domain; InterPro: IPR022423 Oxytocin (or ocytocin) and vasopressin [] are small (nine amino acid residues), structurally and functionally related neurohypophysial peptide hormones. Oxytocin causes contraction of the smooth muscle of the uterus and of the mammary gland while vasopressin has a direct antidiuretic action on the kidney and also causes vasoconstriction of the peripheral vessels. Like the majority of active peptides, both hormones are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Peptides belonging to this family are also found in birds, fish, reptiles and amphibians (mesotocin, isotocin, valitocin, glumitocin, aspargtocin, vasotocin, seritocin, asvatocin, phasvatocin), in worms (annetocin), octopi (cephalotocin), locust (locupressin or neuropeptide F1/F2) and in molluscs (conopressins G and S) []. The pattern developed to detect this category of peptides spans their entire sequence and includes four invariant amino acid residues. .; GO: 0005185 neurohypophyseal hormone activity, 0005576 extracellular region
Probab=26.11 E-value=35 Score=12.23 Aligned_cols=6 Identities=50% Similarity=1.448 Sum_probs=3.4
Q ss_pred ccCCCC
Q 045690 201 IKECPT 206 (220)
Q Consensus 201 ~~~C~~ 206 (220)
.++||.
T Consensus 3 i~nCP~ 8 (9)
T PF00220_consen 3 IRNCPI 8 (9)
T ss_pred cccCCC
Confidence 456663
No 105
>KOG4204 consensus Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics]
Probab=25.67 E-value=2.1e+02 Score=22.48 Aligned_cols=53 Identities=15% Similarity=0.228 Sum_probs=38.3
Q ss_pred CCccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHH
Q 045690 18 PYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAK 71 (220)
Q Consensus 18 ~~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~ 71 (220)
.+.-+..+.+.|+++|.... .-+......+...+.+..++.+...++..|+.+
T Consensus 126 ~~~~a~~fv~klk~rf~~~~-~v~~s~l~il~~y~~~~ks~~e~~~eV~~L~~~ 178 (231)
T KOG4204|consen 126 EFDRAISFVNKLKTRFQGDD-HVYKSFLEILRMYQEGNKSVSEVYQEVEALLQG 178 (231)
T ss_pred hHHHHHHHHHHHHHHhcCCH-HHHHHHHHHHHHHhhccchHHHHHHHHHHHHcc
Confidence 34567789999999999665 344455555666666789999988888776643
No 106
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=25.63 E-value=22 Score=20.75 Aligned_cols=19 Identities=32% Similarity=0.704 Sum_probs=11.4
Q ss_pred ccccccc-------ccccccCCCCCC
Q 045690 190 FCNYCKK-------PGHIIKECPTRP 208 (220)
Q Consensus 190 ~C~~C~k-------~GH~~~~C~~~~ 208 (220)
.|.+|+| .||+...||.-+
T Consensus 6 RC~~CnKlLa~a~~~~yle~KCPrCK 31 (60)
T COG4416 6 RCAKCNKLLAEAEGQAYLEKKCPRCK 31 (60)
T ss_pred ehHHHhHHHHhcccceeeeecCCccc
Confidence 4666654 467777777543
No 107
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=25.63 E-value=44 Score=18.50 Aligned_cols=13 Identities=38% Similarity=0.950 Sum_probs=8.9
Q ss_pred cccCccccccccc
Q 045690 185 NCAKKFCNYCKKP 197 (220)
Q Consensus 185 ~~~~~~C~~C~k~ 197 (220)
.=|.+.|..||.+
T Consensus 5 ~lp~K~C~~C~rp 17 (42)
T PF10013_consen 5 NLPSKICPVCGRP 17 (42)
T ss_pred cCCCCcCcccCCc
Confidence 3355678888875
No 108
>PF14965 BRI3BP: Negative regulator of p53/TP53
Probab=25.47 E-value=1.7e+02 Score=21.85 Aligned_cols=57 Identities=12% Similarity=0.317 Sum_probs=44.8
Q ss_pred ccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHhcccccC
Q 045690 20 KTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQG-DLSIQNYLSGIQNLWAKYVDMIYVQ 79 (220)
Q Consensus 20 ~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~-~~sv~ey~~~~~~l~~~L~~~~~~~ 79 (220)
..+..+|+.|...+..++ +..+.+.|.....- ..-|+-.+..+-.++.+|-+..|.+
T Consensus 3 ~~~~~~~~tl~s~~G~e~---v~~~~efls~~~~~~~~gis~~l~~l~~i~~dlL~~~Gid 60 (177)
T PF14965_consen 3 QAGRSVYQTLESWLGEEN---VRAVAEFLSRVTWRFSSGISSALNTLWRIWTDLLDVLGID 60 (177)
T ss_pred hHHHHHHHHHHHHhChHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence 357899999999999876 66666666666553 6678888999999999988777765
No 109
>smart00583 SPK domain in SET and PHD domain containing proteins and protein kinases.
Probab=25.07 E-value=2.3e+02 Score=19.38 Aligned_cols=52 Identities=12% Similarity=0.188 Sum_probs=37.6
Q ss_pred HHHHHHHHHHhccCCchh-H-hhHHHHHHHhhc-CCCcHHHHHHHHH-HHHHHHhc
Q 045690 23 KDMWEYLKKVYNQDNTAK-C-FHLEYEIARYSQ-GDLSIQNYLSGIQ-NLWAKYVD 74 (220)
Q Consensus 23 ~~~W~~L~~~f~~~~~~~-~-~~l~~~~~~~~~-~~~sv~ey~~~~~-~l~~~L~~ 74 (220)
..+|+.|.+.-.....+. . ..+..+|..... ...++..|..+|. .|+..+..
T Consensus 3 ~~~m~FL~ektk~~i~P~~~~~~~~~~F~~~~~~~~~s~~~~~~rf~~~Lap~i~~ 58 (114)
T smart00583 3 TRFMDFLVEKTKDAIEPLVVPLKVFEEFSKLEGNSLLSYETYYKRFHNKLAPNMIK 58 (114)
T ss_pred HHHHHHHHHHhhCCccCccchHHHHHHHHHhccCCcccHHHHHHHHHHHHHhhHhh
Confidence 468999999888543333 3 367777777776 5679999999987 66666663
No 110
>PF11855 DUF3375: Protein of unknown function (DUF3375); InterPro: IPR021804 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
Probab=24.89 E-value=1.7e+02 Score=25.71 Aligned_cols=94 Identities=14% Similarity=0.227 Sum_probs=52.1
Q ss_pred cHHHHHHHHHHH---hccCCchhHhhHHHHHHHhhcC-CCcHHHHHHHHHHHHH----HHhcc-cccCCCcccHHHHHHH
Q 045690 21 TAKDMWEYLKKV---YNQDNTAKCFHLEYEIARYSQG-DLSIQNYLSGIQNLWA----KYVDM-IYVQVPIESLADVQGV 91 (220)
Q Consensus 21 ta~~~W~~L~~~---f~~~~~~~~~~l~~~~~~~~~~-~~sv~ey~~~~~~l~~----~L~~~-~~~~~~~~~~~~~~~~ 91 (220)
.+..+...+... -...+.+++..+...+..+..+ +.+...=+..+..=.+ ++..+ .| .++. +...+..
T Consensus 101 ~a~~Al~~l~~L~~~~~~~TeSRl~tv~~~l~~la~~~~~Dp~~Ri~~Le~e~~~i~~EI~~l~aG-~~~~--ld~~~~~ 177 (478)
T PF11855_consen 101 AAEKALRFLERLEERRFVGTESRLNTVFDALRQLAEGTDPDPERRIAELEREIAEIDAEIDRLEAG-DVPV--LDDTQAR 177 (478)
T ss_pred HHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHCC-CCCC--CCHHHHH
Confidence 344444444443 3344667888888888888775 6666665555443332 23222 13 3322 1112222
Q ss_pred HHHHHHHHHHhhcchhHHHHHHhhhc
Q 045690 92 HEQSKRDQFLMKLRPEYKAARSNLMN 117 (220)
Q Consensus 92 ~d~~~~~~~l~gLp~~~~~~~~~~~~ 117 (220)
..-..|..+..+||.+|..+.+.+..
T Consensus 178 er~~~i~~la~~L~~DFr~V~~~~r~ 203 (478)
T PF11855_consen 178 ERARQILQLARELPADFRRVEDNFRE 203 (478)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555666789999999777655543
No 111
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=24.57 E-value=51 Score=17.09 Aligned_cols=25 Identities=16% Similarity=0.465 Sum_probs=14.4
Q ss_pred cccccCCCccccccccCcccccccc
Q 045690 172 QCFSCKEYRHIIVNCAKKFCNYCKK 196 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~C~k 196 (220)
.|..|+..+-.........|..|+.
T Consensus 5 ~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 5 KCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred EcCCCCCCeEEEecCCeEEcccCCc
Confidence 3555666665544444556777764
No 112
>PF11517 Nab2: Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); InterPro: IPR021083 Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N-terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1 []. The N-terminal domain of Nab2 shows a structure of a helical fold. The N-terminal domain of Nab2 is thought to mediate protein:protein interactions that facilitate the nuclear export of mRNA []. An essential hydrophobic Phe73 patch on the N-terminal domain is thought to be an important component of the interface between Nab2 and Mlp1 [].; PDB: 3LCN_B 2V75_A 2JPS_A.
Probab=24.47 E-value=2.3e+02 Score=19.03 Aligned_cols=62 Identities=15% Similarity=0.178 Sum_probs=37.2
Q ss_pred cccHHHHhccCCCccHHHHHHHHHHHhccCCchhHh-hHHHHHHHh--hcCCCcHHHHHHHHHHH
Q 045690 7 SVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCF-HLEYEIARY--SQGDLSIQNYLSGIQNL 68 (220)
Q Consensus 7 sl~~~~~~~i~~~~ta~~~W~~L~~~f~~~~~~~~~-~l~~~~~~~--~~~~~sv~ey~~~~~~l 68 (220)
.+.+-|.-+++.-.|..++.+.|-..|+.-+...+. -....|..+ -+.|++++.-+.+++..
T Consensus 32 YVAEyIvlLisNggs~esivqELssLFD~vs~~~l~~VVQtaF~ale~Lq~Ge~~e~iv~Ki~~~ 96 (107)
T PF11517_consen 32 YVAEYIVLLISNGGSVESIVQELSSLFDSVSTEALTDVVQTAFFALEALQQGETVENIVSKIRGM 96 (107)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHH-TTS-HHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHhheeeeCCCCHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHcc
Confidence 345667777788889999999999999855533332 244555555 33577887777777644
No 113
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=24.02 E-value=1.5e+02 Score=16.87 Aligned_cols=45 Identities=20% Similarity=0.177 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhc-cCCchhHhhHHHHHHHhhc--CCCcHHHHHHHHHH
Q 045690 23 KDMWEYLKKVYN-QDNTAKCFHLEYEIARYSQ--GDLSIQNYLSGIQN 67 (220)
Q Consensus 23 ~~~W~~L~~~f~-~~~~~~~~~l~~~~~~~~~--~~~sv~ey~~~~~~ 67 (220)
..+-+.|...++ .-.......+.+.+...+. +-.++.+|+..+..
T Consensus 6 ~~~~~~i~~~~Gi~l~~~K~~~l~rRl~~rm~~~~~~~~~~y~~~L~~ 53 (57)
T PF03705_consen 6 ERFRELIYRRTGIDLSEYKRSLLERRLARRMRALGLPSFAEYYELLRS 53 (57)
T ss_dssp HHHHHHHHHHH-----GGGHHHHHHHHHHHHHHHT---HHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCchhhHHHHHHHHHHHHHHcCCCCHHHHHHHHHh
Confidence 445566677776 4444566778888888876 56899999988754
No 114
>PF03206 NifW: Nitrogen fixation protein NifW; InterPro: IPR004893 Nitrogenase is a complex metalloenzyme composed of two proteins designated the Fe-protein and the MoFe-protein. Apart from these two proteins, a number of accessory proteins are essential for the maturation and assembly of nitrogenase. Even though experimental evidence suggests that these accessory proteins are required for nitrogenase activity, the exact roles played by many of these proteins in the functions of nitrogenase are unclear []. Using yeast two-hybrid screening it has been shown that NifW can interact with itself as well as NifZ. ; GO: 0009399 nitrogen fixation
Probab=24.00 E-value=1.1e+02 Score=20.83 Aligned_cols=42 Identities=17% Similarity=0.279 Sum_probs=31.4
Q ss_pred HHhccCCCccHHHHHHHHHHHhccC--CchhHhhHHHHHHHhhc
Q 045690 12 LVLNLKPYKTAKDMWEYLKKVYNQD--NTAKCFHLEYEIARYSQ 53 (220)
Q Consensus 12 ~~~~i~~~~ta~~~W~~L~~~f~~~--~~~~~~~l~~~~~~~~~ 53 (220)
++..+..+.+|.+..+.+.--|++. +..|+.-|++.-..+.+
T Consensus 4 ~l~~l~~L~sAEdFf~fF~V~YDp~vv~V~RLHILkrF~~yL~~ 47 (105)
T PF03206_consen 4 ILEELKKLSSAEDFFDFFGVPYDPKVVNVNRLHILKRFGQYLRA 47 (105)
T ss_pred HHHHHHhccCHHHHHHHhCCCcchhHHHHhhHHHHHHHHHHHHh
Confidence 5667788999999999999999944 55666666666555554
No 115
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=23.98 E-value=2.2e+02 Score=18.63 Aligned_cols=15 Identities=20% Similarity=0.565 Sum_probs=10.1
Q ss_pred cHHHHHHHHHHHhcc
Q 045690 21 TAKDMWEYLKKVYNQ 35 (220)
Q Consensus 21 ta~~~W~~L~~~f~~ 35 (220)
.+.+-|..+-..|..
T Consensus 13 pP~eRw~~i~~~~k~ 27 (95)
T PF15508_consen 13 PPEERWVQIAKDYKD 27 (95)
T ss_pred CHHHHHHHHHHHHHH
Confidence 567777777776653
No 116
>KOG2985 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.59 E-value=21 Score=28.11 Aligned_cols=20 Identities=25% Similarity=0.612 Sum_probs=17.2
Q ss_pred ccccccccccccccCCCCCC
Q 045690 189 KFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 189 ~~C~~C~k~GH~~~~C~~~~ 208 (220)
.-|..||..||..-+|+...
T Consensus 82 g~ckRcg~~ghl~fqcRn~~ 101 (306)
T KOG2985|consen 82 GSCKRCGRVGHLTFQCRNFL 101 (306)
T ss_pred cchhhccccchhhHHHhhhh
Confidence 45999999999999998754
No 117
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=23.50 E-value=6.5e+02 Score=23.98 Aligned_cols=99 Identities=16% Similarity=0.106 Sum_probs=43.0
Q ss_pred ccHHHHhccCCCccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHH
Q 045690 8 VDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLAD 87 (220)
Q Consensus 8 l~~~~~~~i~~~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~ 87 (220)
|+.+....+.+..+...+++.|...+.++ ...+...+..+...|-+...++..|..++.++. + ...+++.....
T Consensus 232 It~~~V~~~LG~~d~~~i~~ll~aL~~~d----~~~~l~~~~~l~~~g~~~~~~l~dLl~~l~~~~-~-~q~~~~~~~~~ 305 (830)
T PRK07003 232 VTETAVSGMLGALDQTYMVRLLDALAAGD----GPEILAVADEMALRSLSFSTALQDLASLLHRIA-W-AQFAPASVLDE 305 (830)
T ss_pred cCHHHHHHHhCCCCHHHHHHHHHHHHcCC----HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH-H-HHhCccccccc
Confidence 44444444445555555666666655543 223333344444434444444444444444433 1 11112211111
Q ss_pred HHHHHHHHHHHHHHhhcchhHHHHHHhh
Q 045690 88 VQGVHEQSKRDQFLMKLRPEYKAARSNL 115 (220)
Q Consensus 88 ~~~~~d~~~~~~~l~gLp~~~~~~~~~~ 115 (220)
..|...+..+-..|..++-....++
T Consensus 306 ---~~e~~~~~~~a~~~s~~~l~~~~qi 330 (830)
T PRK07003 306 ---WPEAADLRRFAELLSPEQVQLFYQI 330 (830)
T ss_pred ---cchHHHHHHHHHhCCHHHHHHHHHH
Confidence 1334455556666666544333333
No 118
>PRK06036 translation initiation factor IF-2B subunit alpha; Provisional
Probab=23.37 E-value=4.4e+02 Score=22.02 Aligned_cols=60 Identities=12% Similarity=0.043 Sum_probs=40.1
Q ss_pred CCCccHHHHHHHHHHHhccCCchh-Hhh-HHHHHHHhhcCCCcHHHHHHHHHHHHHHHhccc
Q 045690 17 KPYKTAKDMWEYLKKVYNQDNTAK-CFH-LEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMI 76 (220)
Q Consensus 17 ~~~~ta~~~W~~L~~~f~~~~~~~-~~~-l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~~~ 76 (220)
..++|..++|++++++--.+-++- +.. +--.+....-...++.+|...+....+.|.+..
T Consensus 28 ~~~~~~~~v~~aI~~m~vRGApaig~aaa~g~~l~~~~~~~~~~~~~~~~l~~~~~~L~~aR 89 (339)
T PRK06036 28 IECKTLESLCEAIKSLRVRGAPALGAAGGYGIALAARLSKAKDVDELLKDLKVAAETLKSTR 89 (339)
T ss_pred EEeCCHHHHHHHHHhCcccCchHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHhC
Confidence 458899999999999887554332 222 222222222234589999999999999998553
No 119
>PF04439 Adenyl_transf: Streptomycin adenylyltransferase; InterPro: IPR007530 Also known as aminoglycoside 6-adenylyltransferase (2.7.7 from EC), this protein confers resistance to aminoglycoside antibiotics.; PDB: 2PBE_A.
Probab=23.00 E-value=50 Score=26.70 Aligned_cols=16 Identities=25% Similarity=0.733 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHhccCC
Q 045690 22 AKDMWEYLKKVYNQDN 37 (220)
Q Consensus 22 a~~~W~~L~~~f~~~~ 37 (220)
+.++|+.|...|...+
T Consensus 220 ~~~~~~~l~~ty~~~~ 235 (282)
T PF04439_consen 220 PPEIWERLLSTYSDSD 235 (282)
T ss_dssp -HHHHHHHHTT---SS
T ss_pred CHHHHHHHHHHhCCCC
Confidence 4566777777776554
No 120
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=22.99 E-value=1.9e+02 Score=19.25 Aligned_cols=35 Identities=17% Similarity=0.104 Sum_probs=22.8
Q ss_pred CCCccHHHHHHHHHHHhccCCchhHhhHHHHHHHh
Q 045690 17 KPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARY 51 (220)
Q Consensus 17 ~~~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~ 51 (220)
...-|+.++|+.|++....-+.+.+|+....|...
T Consensus 14 ~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~ 48 (116)
T cd07153 14 DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEA 48 (116)
T ss_pred CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhC
Confidence 45678999999999876555545555544444433
No 121
>cd01093 CRIB_PAK_like PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. This subgroup of CRIB/PBD-domains is found N-terminal of Serine/Threonine kinase domains in PAK and PAK-like proteins.
Probab=22.85 E-value=57 Score=18.30 Aligned_cols=13 Identities=15% Similarity=0.184 Sum_probs=11.0
Q ss_pred hhcchhHHHHHHh
Q 045690 102 MKLRPEYKAARSN 114 (220)
Q Consensus 102 ~gLp~~~~~~~~~ 114 (220)
.|||++|+.+..+
T Consensus 25 ~glP~eW~~ll~~ 37 (46)
T cd01093 25 TGLPEEWQRLLKS 37 (46)
T ss_pred cCCCHHHHHHHHH
Confidence 8999999988664
No 122
>PF08844 DUF1815: Domain of unknown function (DUF1815); InterPro: IPR014943 This entry is about 100 amino acids in length and is functionally uncharacterised.
Probab=22.81 E-value=33 Score=22.62 Aligned_cols=14 Identities=14% Similarity=0.218 Sum_probs=8.7
Q ss_pred ccccc--ccccccccC
Q 045690 190 FCNYC--KKPGHIIKE 203 (220)
Q Consensus 190 ~C~~C--~k~GH~~~~ 203 (220)
.||.| |..+|-+..
T Consensus 34 sCYtC~dG~~~~~ASF 49 (105)
T PF08844_consen 34 SCYTCGDGRDMNSASF 49 (105)
T ss_pred EEEecCCCCCCCceeE
Confidence 48888 665565543
No 123
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=22.63 E-value=35 Score=18.65 Aligned_cols=10 Identities=40% Similarity=1.245 Sum_probs=4.7
Q ss_pred cccccccccc
Q 045690 189 KFCNYCKKPG 198 (220)
Q Consensus 189 ~~C~~C~k~G 198 (220)
..|.+||++.
T Consensus 2 ~~CSFCgr~~ 11 (41)
T PF06689_consen 2 KRCSFCGRPE 11 (41)
T ss_dssp -B-TTT--BT
T ss_pred CCccCCCCCH
Confidence 4699999875
No 124
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=21.98 E-value=33 Score=20.54 Aligned_cols=8 Identities=38% Similarity=0.630 Sum_probs=6.4
Q ss_pred cccccccc
Q 045690 190 FCNYCKKP 197 (220)
Q Consensus 190 ~C~~C~k~ 197 (220)
.||-|||.
T Consensus 6 RCFtCGKv 13 (69)
T KOG3497|consen 6 RCFTCGKV 13 (69)
T ss_pred Eeeecccc
Confidence 69999874
No 125
>PRK14291 chaperone protein DnaJ; Provisional
Probab=21.97 E-value=97 Score=26.25 Aligned_cols=38 Identities=18% Similarity=0.392 Sum_probs=22.9
Q ss_pred cccccCCCccccccc----cCccccccccccccccCCCCCCC
Q 045690 172 QCFSCKEYRHIIVNC----AKKFCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~----~~~~C~~C~k~GH~~~~C~~~~~ 209 (220)
.|..|...|...... ....|..|+..|-+...|+....
T Consensus 175 ~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~~~C~~C~G 216 (382)
T PRK14291 175 VCPTCGGSGEIYQRGGFFRISQTCPTCGGEGVLREPCSKCNG 216 (382)
T ss_pred cCCCCCCceEEEEecceEEEEecCCCCCCceEEccCCCCCCC
Confidence 455565555332211 12279999999977778877553
No 126
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=21.32 E-value=68 Score=27.22 Aligned_cols=36 Identities=17% Similarity=0.258 Sum_probs=25.8
Q ss_pred CCCCCCCccccccCCCccccccccCcccccccccccccc
Q 045690 164 KGRDMRQVQCFSCKEYRHIIVNCAKKFCNYCKKPGHIIK 202 (220)
Q Consensus 164 ~~~~~~~~~~~~~~~~g~~~~~~~~~~C~~C~k~GH~~~ 202 (220)
.+.+.+..-|..|...+... .+..|..||.++|..+
T Consensus 214 ~~~~~~~~~C~~C~~~~~~~---~~~~CpRC~~~Ly~rr 249 (418)
T COG2995 214 TGAREGLRSCLCCHYILPHD---AEPRCPRCGSKLYVRR 249 (418)
T ss_pred CCCcccceecccccccCCHh---hCCCCCCCCChhhccC
Confidence 34455556788888876553 4567999999998765
No 127
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=21.23 E-value=78 Score=16.32 Aligned_cols=10 Identities=20% Similarity=0.424 Sum_probs=6.3
Q ss_pred cCcccccccc
Q 045690 187 AKKFCNYCKK 196 (220)
Q Consensus 187 ~~~~C~~C~k 196 (220)
....|.+||.
T Consensus 16 ~~irC~~CG~ 25 (32)
T PF03604_consen 16 DPIRCPECGH 25 (32)
T ss_dssp STSSBSSSS-
T ss_pred CcEECCcCCC
Confidence 3457888875
No 128
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=21.17 E-value=39 Score=20.41 Aligned_cols=8 Identities=38% Similarity=0.629 Sum_probs=6.2
Q ss_pred cccccccc
Q 045690 190 FCNYCKKP 197 (220)
Q Consensus 190 ~C~~C~k~ 197 (220)
.||-||+.
T Consensus 6 RCFsCGkv 13 (63)
T COG1644 6 RCFSCGKV 13 (63)
T ss_pred EeecCCCC
Confidence 58888875
No 129
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=20.85 E-value=44 Score=19.59 Aligned_cols=19 Identities=37% Similarity=0.882 Sum_probs=13.8
Q ss_pred ccCccccccccccccccCC
Q 045690 186 CAKKFCNYCKKPGHIIKEC 204 (220)
Q Consensus 186 ~~~~~C~~C~k~GH~~~~C 204 (220)
|....|+.|+.+-|.--.|
T Consensus 46 C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 46 CGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp CCSEECSSSTSESCTTS-H
T ss_pred CCCcCccccCcccCCCCCC
Confidence 5566899999988875544
No 130
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.84 E-value=62 Score=29.98 Aligned_cols=15 Identities=20% Similarity=0.516 Sum_probs=11.3
Q ss_pred ccHHHHHHHHHHHhc
Q 045690 20 KTAKDMWEYLKKVYN 34 (220)
Q Consensus 20 ~ta~~~W~~L~~~f~ 34 (220)
.+-.++|+.|.++.+
T Consensus 423 ~d~~~F~~~Ld~~l~ 437 (711)
T PRK09263 423 GDEDKFWEILDERLE 437 (711)
T ss_pred CCHHHHHHHHHHHHH
Confidence 466788888888776
No 131
>PF04439 Adenyl_transf: Streptomycin adenylyltransferase; InterPro: IPR007530 Also known as aminoglycoside 6-adenylyltransferase (2.7.7 from EC), this protein confers resistance to aminoglycoside antibiotics.; PDB: 2PBE_A.
Probab=20.81 E-value=2.8e+02 Score=22.39 Aligned_cols=30 Identities=13% Similarity=0.254 Sum_probs=16.7
Q ss_pred eecccccHHHHhccCC---CccHHHHHHHHHHH
Q 045690 3 WIMGSVDQSLVLNLKP---YKTAKDMWEYLKKV 32 (220)
Q Consensus 3 ~i~~sl~~~~~~~i~~---~~ta~~~W~~L~~~ 32 (220)
+|...|++++...+.. ..+..++|++|..+
T Consensus 214 ~l~~~L~~~~~~~l~~ty~~~~~~~iw~aL~~~ 246 (282)
T PF04439_consen 214 YLKKYLPPEIWERLLSTYSDSDYEDIWQALFAM 246 (282)
T ss_dssp TGGGTS-HHHHHHHHTT---SSHHHHHHHHHHH
T ss_pred hHHHHCCHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 3455666666555543 34667777776663
No 132
>PF07851 TMPIT: TMPIT-like protein; InterPro: IPR012926 A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. ; GO: 0016021 integral to membrane
Probab=20.73 E-value=2.6e+02 Score=23.29 Aligned_cols=64 Identities=16% Similarity=0.250 Sum_probs=35.1
Q ss_pred HHHHHHHHHhcc-CCchhHh-hHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHhcccccCCCcccHHHH
Q 045690 24 DMWEYLKKVYNQ-DNTAKCF-HLEYEIARYSQG-DLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADV 88 (220)
Q Consensus 24 ~~W~~L~~~f~~-~~~~~~~-~l~~~~~~~~~~-~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~ 88 (220)
+=|+.|.+-|.. ....+.+ ....++...... ..+|.....+++.|...|... ....+.+....+
T Consensus 4 eEW~eL~~efq~Lqethr~Y~qKleel~~lQ~~C~ssI~~QkkrLk~L~~sLk~~-~~~~~~e~~~~i 70 (330)
T PF07851_consen 4 EEWEELQKEFQELQETHRSYKQKLEELSKLQDKCSSSISHQKKRLKELKKSLKRC-KKSLSAEERELI 70 (330)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCChhHHHHH
Confidence 347777777762 1112222 222333333333 678888888888888888855 333344333333
No 133
>PRK05772 translation initiation factor IF-2B subunit alpha; Provisional
Probab=20.70 E-value=5.2e+02 Score=21.86 Aligned_cols=62 Identities=5% Similarity=-0.101 Sum_probs=42.3
Q ss_pred cCCCccHHHHHHHHHHHhccCCchh-HhhHHHHHHHhhc-CCCcHHHHHHHHHHHHHHHhcccc
Q 045690 16 LKPYKTAKDMWEYLKKVYNQDNTAK-CFHLEYEIARYSQ-GDLSIQNYLSGIQNLWAKYVDMIY 77 (220)
Q Consensus 16 i~~~~ta~~~W~~L~~~f~~~~~~~-~~~l~~~~~~~~~-~~~sv~ey~~~~~~l~~~L~~~~~ 77 (220)
+..++|..++|++++++=-.+.++- +....-......+ .+.++.+|...+....+.|.+..+
T Consensus 40 ~~~~~~~~~v~~aI~~M~vRGApaigiaAa~glal~~~~~~~~~~~~~~~~l~~~~~~L~~aRP 103 (363)
T PRK05772 40 YVDLKTVEEVALAIRNMQVRGAPAIGITAGYGMVLALIENNVKTLDDAIRELTRAKTILDSARP 103 (363)
T ss_pred EEEeCCHHHHHHHHHhCcccCCcHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHhcCC
Confidence 3458899999999999888554333 2222222222333 355999999999999999976543
No 134
>PF05879 RHD3: Root hair defective 3 GTP-binding protein (RHD3); InterPro: IPR008803 This family consists of several eukaryotic root hair defective 3 like GTP-binding proteins. It has been speculated that the RHD3 protein is a member of a novel class of GTP-binding proteins that is widespread in eukaryotes and required for regulated cell enlargement []. The family also contains the homologous Saccharomyces cerevisiae synthetic construct enhancement of YOP1 (SEY1) protein which is involved in membrane trafficking [].; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=20.54 E-value=1.4e+02 Score=27.95 Aligned_cols=90 Identities=11% Similarity=0.288 Sum_probs=50.9
Q ss_pred ccccHHHHhccCCCccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHH-HHhcccccCCCccc
Q 045690 6 GSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWA-KYVDMIYVQVPIES 84 (220)
Q Consensus 6 ~sl~~~~~~~i~~~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~-~L~~~~~~~~~~~~ 84 (220)
..|.+.+...+.. -..++|+.+...|..........+......+--..+..++++.+|+.-.- .|. ..+
T Consensus 436 ~~l~e~v~~~l~~--~~~d~Wd~I~~~f~~~~~~~~~~~~~~~~~f~~s~~e~~~~~~~lr~~aw~~l~----~ki---- 505 (742)
T PF05879_consen 436 SELKEPVESLLEN--PSPDMWDRIRKLFESATESAVSKFSDRLKGFGLSEEENEKALKKLRRKAWSVLR----EKI---- 505 (742)
T ss_pred HHHhHHHHHHHhC--CChhhHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHH----HHH----
Confidence 3445555555544 34889999999998554344444444444443345677788777766542 222 111
Q ss_pred HHHHHHHHHHHHHHHHHhhcchhHHHHH
Q 045690 85 LADVQGVHEQSKRDQFLMKLRPEYKAAR 112 (220)
Q Consensus 85 ~~~~~~~~d~~~~~~~l~gLp~~~~~~~ 112 (220)
+|...-..++.-|...|+.+-
T Consensus 506 -------~e~~~~~~ll~~LkdRFe~~F 526 (742)
T PF05879_consen 506 -------REEASEDNLLIRLKDRFEDKF 526 (742)
T ss_pred -------HHHHhHhHHHHHHHHHHHHHh
Confidence 333333446677776666553
No 135
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=20.51 E-value=51 Score=28.76 Aligned_cols=19 Identities=37% Similarity=0.934 Sum_probs=17.9
Q ss_pred ccccccccccccccCCCCC
Q 045690 189 KFCNYCKKPGHIIKECPTR 207 (220)
Q Consensus 189 ~~C~~C~k~GH~~~~C~~~ 207 (220)
..|..|+..||-.-+||.+
T Consensus 262 ~~c~~cg~~~H~q~~cp~r 280 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGR 280 (554)
T ss_pred ccccccCCCccccccCCcc
Confidence 5899999999999999988
No 136
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=20.48 E-value=2.8e+02 Score=21.47 Aligned_cols=27 Identities=19% Similarity=0.431 Sum_probs=14.8
Q ss_pred cccccCCCccccccccC----cccccccccc
Q 045690 172 QCFSCKEYRHIIVNCAK----KFCNYCKKPG 198 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~----~~C~~C~k~G 198 (220)
-|..|............ ..|++|+...
T Consensus 194 IC~~C~hhngl~~~~ek~~~efiC~~Cn~~n 224 (251)
T COG5415 194 ICPQCHHHNGLYRLAEKPIIEFICPHCNHKN 224 (251)
T ss_pred ccccccccccccccccccchheecccchhhc
Confidence 46666554443333222 3788887654
No 137
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=20.41 E-value=3.5e+02 Score=19.74 Aligned_cols=52 Identities=10% Similarity=0.137 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHhcc------CCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHh
Q 045690 22 AKDMWEYLKKVYNQ------DNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYV 73 (220)
Q Consensus 22 a~~~W~~L~~~f~~------~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~ 73 (220)
.+++-+.++..+-. +.-..++.-.+.|....+.|+.+.+|..+|..+..+|.
T Consensus 119 ~~~V~~~v~~~~p~~~~V~Vs~D~~~~~ri~~~~~~~~~g~~~~~~~~~~~~i~~r~~ 176 (177)
T PF09580_consen 119 KKKVEKAVKSADPRIYNVYVSTDPDIFDRIRNLANRIRNGRPVSGFNDEIKEIVRRMF 176 (177)
T ss_pred HHHHHHHHHHhCCCccEEEEEcCHHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhhC
Confidence 34455555554432 22244556666666667788999999999999988774
No 138
>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=20.32 E-value=3.3e+02 Score=19.38 Aligned_cols=45 Identities=2% Similarity=-0.048 Sum_probs=33.0
Q ss_pred CccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcC-CCcHHHHHH
Q 045690 19 YKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQG-DLSIQNYLS 63 (220)
Q Consensus 19 ~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~-~~sv~ey~~ 63 (220)
...++++-.+|+.+....+.......-..+..+++. |..+...+.
T Consensus 33 ~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~eva 78 (139)
T cd03567 33 PEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVG 78 (139)
T ss_pred CccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHH
Confidence 457899999999999877666666667778888885 666644333
No 139
>PF13395 HNH_4: HNH endonuclease
Probab=20.25 E-value=44 Score=19.36 Aligned_cols=7 Identities=71% Similarity=1.882 Sum_probs=5.1
Q ss_pred ccccccc
Q 045690 191 CNYCKKP 197 (220)
Q Consensus 191 C~~C~k~ 197 (220)
|+|||+.
T Consensus 1 C~Y~g~~ 7 (54)
T PF13395_consen 1 CPYCGKP 7 (54)
T ss_pred CCCCCCC
Confidence 7788764
No 140
>PRK14063 exodeoxyribonuclease VII small subunit; Provisional
Probab=20.21 E-value=2.4e+02 Score=17.77 Aligned_cols=28 Identities=29% Similarity=0.424 Sum_probs=21.4
Q ss_pred CCCcHHHHHHHHHHHHHHHhcccccCCCccc
Q 045690 54 GDLSIQNYLSGIQNLWAKYVDMIYVQVPIES 84 (220)
Q Consensus 54 ~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~ 84 (220)
...|..+-+.++..|+.+|. ...+|.+.
T Consensus 3 ~~~sfEeal~~LE~Iv~~LE---~~~l~Lee 30 (76)
T PRK14063 3 NKLSFEEAISQLEHLVSKLE---QGDVPLEE 30 (76)
T ss_pred cccCHHHHHHHHHHHHHHHH---CCCCCHHH
Confidence 35789999999999999998 34455533
Done!