Query 042018
Match_columns 346
No_of_seqs 240 out of 662
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 13:08:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042018.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042018hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00448 hypothetical protein; 100.0 3E-106 7E-111 786.0 29.7 333 3-343 1-372 (373)
2 KOG2917 Predicted exosome subu 100.0 1.8E-85 3.9E-90 601.9 22.2 236 3-238 1-250 (250)
3 TIGR00291 RNA_SBDS rRNA metabo 100.0 3.4E-75 7.4E-80 542.9 22.1 217 11-228 1-230 (231)
4 PRK13760 putative RNA-associat 100.0 1.5E-73 3.2E-78 531.6 21.7 213 12-225 2-227 (231)
5 COG1500 Predicted exosome subu 100.0 7.5E-71 1.6E-75 508.1 19.5 220 11-231 1-233 (234)
6 PF09377 SBDS_C: SBDS protein 100.0 1.1E-40 2.4E-45 285.4 12.4 123 97-219 1-125 (125)
7 PF01172 SBDS: Shwachman-Bodia 99.9 3E-28 6.5E-33 198.5 4.1 80 15-94 1-91 (91)
8 KOG2785 C2H2-type Zn-finger pr 99.7 4.8E-18 1.1E-22 167.3 3.7 54 283-337 2-55 (390)
9 KOG2505 Ankyrin repeat protein 99.5 8.5E-15 1.8E-19 148.5 4.1 52 283-335 65-116 (591)
10 smart00451 ZnF_U1 U1-like zinc 97.3 0.00015 3.2E-09 48.2 2.3 33 283-315 2-34 (35)
11 PF12171 zf-C2H2_jaz: Zinc-fin 96.9 0.00059 1.3E-08 43.4 1.8 27 284-310 1-27 (27)
12 PF12874 zf-met: Zinc-finger o 96.4 0.0015 3.3E-08 40.4 1.4 25 285-309 1-25 (25)
13 PF09186 DUF1949: Domain of un 93.7 0.27 5.7E-06 35.3 6.2 55 167-222 1-56 (56)
14 cd04097 mtEFG1_C mtEFG1_C: C-t 93.2 0.24 5.1E-06 38.6 5.5 62 163-224 4-66 (78)
15 PF00679 EFG_C: Elongation fac 93.2 0.28 6E-06 39.3 6.0 63 163-225 7-71 (89)
16 cd03710 BipA_TypA_C BipA_TypA_ 93.1 0.29 6.4E-06 38.3 5.9 63 163-225 4-68 (79)
17 KOG3408 U1-like Zn-finger-cont 92.9 0.06 1.3E-06 46.8 1.8 40 284-327 57-98 (129)
18 cd03711 Tet_C Tet_C: C-terminu 92.5 0.33 7.1E-06 37.8 5.4 63 163-225 4-67 (78)
19 cd03713 EFG_mtEFG_C EFG_mtEFG_ 92.2 0.3 6.6E-06 37.8 4.9 63 163-225 4-67 (78)
20 PF00096 zf-C2H2: Zinc finger, 92.2 0.073 1.6E-06 32.0 1.1 22 285-306 1-22 (23)
21 cd04096 eEF2_snRNP_like_C eEF2 91.9 0.32 6.9E-06 37.9 4.7 63 163-225 4-69 (80)
22 PF13894 zf-C2H2_4: C2H2-type 91.8 0.089 1.9E-06 31.1 1.1 22 285-306 1-22 (24)
23 cd01514 Elongation_Factor_C El 91.6 0.39 8.5E-06 37.2 5.0 63 163-225 4-68 (79)
24 cd03709 lepA_C lepA_C: This fa 91.6 0.51 1.1E-05 37.2 5.6 63 163-225 4-69 (80)
25 PF13912 zf-C2H2_6: C2H2-type 91.4 0.12 2.6E-06 32.3 1.4 24 285-308 2-25 (27)
26 cd04098 eEF2_C_snRNP eEF2_C_sn 91.4 0.46 1E-05 37.5 5.2 63 163-225 4-69 (80)
27 smart00838 EFG_C Elongation fa 90.8 0.54 1.2E-05 37.1 5.1 64 163-226 6-70 (85)
28 PF12756 zf-C2H2_2: C2H2 type 86.9 0.36 7.9E-06 37.8 1.6 29 284-312 50-78 (100)
29 PRK11568 hypothetical protein; 84.6 3.1 6.6E-05 39.0 6.7 66 161-227 135-201 (204)
30 PHA02768 hypothetical protein; 83.9 0.53 1.2E-05 35.6 1.1 26 283-308 4-29 (55)
31 TIGR00119 acolac_sm acetolacta 82.4 12 0.00026 33.7 9.4 105 116-225 10-145 (157)
32 TIGR00257 IMPACT_YIGZ uncharac 81.2 4.5 9.7E-05 37.9 6.4 66 161-227 135-201 (204)
33 PRK11895 ilvH acetolactate syn 80.7 11 0.00024 34.1 8.6 100 115-219 10-138 (161)
34 smart00355 ZnF_C2H2 zinc finge 79.8 1.2 2.7E-05 26.1 1.5 21 285-305 1-21 (26)
35 PHA00616 hypothetical protein 79.3 0.8 1.7E-05 33.1 0.6 22 285-306 2-23 (44)
36 COG5112 UFD2 U1-like Zn-finger 73.8 1.9 4.2E-05 36.9 1.6 44 284-332 55-100 (126)
37 KOG2462 C2H2-type Zn-finger pr 71.4 2.2 4.8E-05 41.9 1.5 27 283-309 214-240 (279)
38 KOG4727 U1-like Zn-finger prot 71.1 3.2 6.9E-05 38.3 2.4 56 258-315 50-106 (193)
39 PLN02748 tRNA dimethylallyltra 65.3 4.3 9.4E-05 42.5 2.3 34 283-316 417-451 (468)
40 PF12756 zf-C2H2_2: C2H2 type 58.4 3.2 7E-05 32.3 0.0 27 287-314 2-28 (100)
41 PRK05433 GTP-binding protein L 53.4 26 0.00057 37.7 5.8 61 163-223 407-469 (600)
42 PF10513 EPL1: Enhancer of pol 51.0 12 0.00025 32.9 2.3 26 308-334 130-155 (160)
43 CHL00100 ilvH acetohydroxyacid 50.4 59 0.0013 29.8 6.8 63 158-225 82-146 (174)
44 PF14257 DUF4349: Domain of un 50.0 28 0.00062 33.0 4.9 65 158-223 49-120 (262)
45 PHA00743 helix-turn-helix prot 48.9 30 0.00065 25.8 3.7 34 94-128 3-36 (51)
46 TIGR01393 lepA GTP-binding pro 48.7 41 0.00089 36.2 6.3 62 162-223 402-466 (595)
47 COG4049 Uncharacterized protei 47.3 7.5 0.00016 29.9 0.4 29 284-312 17-46 (65)
48 KOG2071 mRNA cleavage and poly 45.9 10 0.00022 40.9 1.2 27 284-310 418-446 (579)
49 KOG0465 Mitochondrial elongati 45.5 24 0.00052 38.6 4.0 63 163-225 636-699 (721)
50 PRK12740 elongation factor G; 45.0 36 0.00078 36.7 5.3 65 160-224 582-647 (668)
51 PRK12739 elongation factor G; 43.3 39 0.00085 36.8 5.3 65 160-224 600-665 (691)
52 TIGR01394 TypA_BipA GTP-bindin 43.0 54 0.0012 35.4 6.2 62 163-224 397-460 (594)
53 COG1739 Uncharacterized conser 41.0 94 0.002 29.1 6.7 109 116-226 79-200 (203)
54 PF08265 YL1_C: YL1 nuclear pr 40.7 14 0.00031 24.6 0.9 15 108-122 10-24 (30)
55 PF06220 zf-U1: U1 zinc finger 40.4 25 0.00055 24.4 2.2 32 284-315 3-36 (38)
56 PRK13351 elongation factor G; 39.4 54 0.0012 35.6 5.6 65 160-224 599-665 (687)
57 PF08790 zf-LYAR: LYAR-type C2 39.2 7.2 0.00016 25.8 -0.7 19 285-304 1-19 (28)
58 PRK00007 elongation factor G; 39.1 50 0.0011 36.0 5.3 64 161-224 604-668 (693)
59 PRK07560 elongation factor EF- 38.1 41 0.00089 36.9 4.5 65 160-224 625-690 (731)
60 PRK10218 GTP-binding protein; 37.6 72 0.0016 34.6 6.1 63 163-225 401-465 (607)
61 PF13878 zf-C2H2_3: zinc-finge 37.3 30 0.00065 24.3 2.2 22 284-305 13-36 (41)
62 PF08793 2C_adapt: 2-cysteine 35.5 25 0.00055 24.4 1.5 18 104-121 5-22 (37)
63 PF13913 zf-C2HC_2: zinc-finge 35.3 25 0.00055 22.1 1.4 20 285-305 3-22 (25)
64 PF04988 AKAP95: A-kinase anch 34.7 29 0.00063 31.8 2.2 40 285-325 1-41 (165)
65 PF09237 GAGA: GAGA factor; I 34.5 23 0.00049 26.8 1.2 24 283-306 23-46 (54)
66 PHA00732 hypothetical protein 34.4 27 0.00058 28.0 1.8 22 285-306 2-23 (79)
67 TIGR00484 EF-G translation elo 34.0 57 0.0012 35.5 4.7 64 161-224 601-665 (689)
68 PF13333 rve_2: Integrase core 32.2 22 0.00049 25.6 0.9 31 292-323 15-45 (52)
69 KOG0717 Molecular chaperone (D 32.1 25 0.00054 37.1 1.6 32 284-315 292-323 (508)
70 PLN00116 translation elongatio 31.9 48 0.001 37.2 3.8 66 160-225 727-795 (843)
71 KOG1074 Transcriptional repres 31.0 18 0.00039 40.6 0.4 26 283-310 632-657 (958)
72 PF10369 ALS_ss_C: Small subun 30.6 1.1E+02 0.0024 23.9 4.7 62 160-226 2-65 (75)
73 PF09080 K-cyclin_vir_C: K cyc 30.4 54 0.0012 27.4 2.9 60 93-157 20-82 (106)
74 COG3758 Uncharacterized protei 29.8 29 0.00063 32.5 1.4 94 1-112 1-100 (193)
75 PF07535 zf-DBF: DBF zinc fing 28.9 33 0.00071 25.3 1.3 25 283-310 4-28 (49)
76 cd04888 ACT_PheB-BS C-terminal 28.8 2.4E+02 0.0051 20.7 7.7 56 164-219 2-63 (76)
77 KOG1146 Homeobox protein [Gene 28.5 32 0.0007 40.5 1.8 38 283-320 517-554 (1406)
78 PF10739 DUF2550: Protein of u 28.4 77 0.0017 27.6 3.8 28 15-42 92-119 (129)
79 PF11931 DUF3449: Domain of un 28.4 19 0.00042 33.8 0.0 41 278-322 97-138 (196)
80 cd01247 PH_GPBP Goodpasture an 26.3 22 0.00048 28.6 0.0 37 7-43 39-75 (91)
81 TIGR00490 aEF-2 translation el 26.2 68 0.0015 35.2 3.7 65 160-224 623-688 (720)
82 PF13909 zf-H2C2_5: C2H2-type 25.2 42 0.0009 20.1 1.1 21 285-306 1-21 (24)
83 PF13465 zf-H2C2_2: Zinc-finge 24.8 33 0.0007 21.5 0.6 14 283-296 13-26 (26)
84 PF12907 zf-met2: Zinc-binding 24.3 37 0.00081 24.1 0.9 22 285-306 2-26 (40)
85 TIGR03321 alt_F1F0_F0_B altern 23.5 3.5E+02 0.0076 25.6 7.6 104 89-209 112-218 (246)
86 PTZ00416 elongation factor 2; 22.4 1.1E+02 0.0023 34.5 4.4 66 160-225 720-788 (836)
87 PRK04435 hypothetical protein; 21.8 5.3E+02 0.012 22.6 7.9 69 159-227 66-145 (147)
88 KOG1994 Predicted RNA binding 21.7 46 0.001 32.2 1.2 21 284-304 239-259 (268)
89 PF05605 zf-Di19: Drought indu 21.3 68 0.0015 23.3 1.8 28 284-313 2-29 (54)
90 PRK13883 conjugal transfer pro 21.1 2.6E+02 0.0056 25.3 5.7 50 141-190 33-82 (151)
91 KOG1074 Transcriptional repres 20.9 27 0.00059 39.3 -0.6 24 283-306 380-403 (958)
92 PF08133 Nuclease_act: Anticod 20.8 38 0.00081 21.8 0.3 10 307-316 11-20 (26)
93 COG0440 IlvH Acetolactate synt 20.2 4.9E+02 0.011 23.9 7.4 59 157-217 83-141 (163)
94 PF04988 AKAP95: A-kinase anch 20.0 52 0.0011 30.2 1.1 36 280-315 87-123 (165)
No 1
>PTZ00448 hypothetical protein; Provisional
Probab=100.00 E-value=3.4e-106 Score=785.96 Aligned_cols=333 Identities=37% Similarity=0.572 Sum_probs=305.5
Q ss_pred ccccCCCCceecceeEEEEEeeCCeEEEEEeecchhHHhhccCCCCchhhhhccccccccCCCccCChhhhhhh------
Q 042018 3 KTLVQPVGQKRLTNVAVVRLKKHGMRFEIACYKNKVLSWRSQVEKDLDEVLQSHTVYSNVSKGILAKSKDLIQH------ 76 (346)
Q Consensus 3 ~~i~~P~~q~~LtNvavVRlkk~GkrFEIacypnkv~~~R~G~e~dldeVLq~~~VF~NvsKG~~A~~~dL~ka------ 76 (346)
|+||||+||++||||+|||||++|+|||||||||+|++||+|+++|||||||+|+||+|||||++|+++||++|
T Consensus 1 m~i~qP~~qi~LtnvavVRlkk~GkrFEIacypnkv~~~R~G~e~dldeVLq~~~VF~NvsKG~~A~~edL~kaFGTtD~ 80 (373)
T PTZ00448 1 MSLFQPSNQIKLTNVAVVRYKSHGKRFEVACYKNKILNWRSGVEWDLDEVLQIRTIFANVSKGQLANSDDLNTVFGTNSI 80 (373)
T ss_pred CCccCCCCceEeeeeEEEEEeeCCEEEEEEECccHHHHHHcCCCCCHHHHhhhhheeecccccccCCHHHHHHHhCCCCH
Confidence 55999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -----hhcccccccccHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcHHHHHHHHhhcCcccCCCCCHHHHHHHHHHH
Q 042018 77 -----LILEKGELQVAGKERETQFSNQFRDIATIVMQKTVNSETQRPYTISMIERLMHEIHFAVDPNSSSKKQALEVIRE 151 (346)
Q Consensus 77 -----~IL~kGElQvs~~ER~~~le~~~r~I~~~Ia~~~VnP~T~rP~p~~~IE~Am~e~~~~Vdp~ksak~QalevIk~ 151 (346)
+||+|||+|||++||++++|+++|+||++||++||||+|++|||++|||+||+++||+|||+||+|+||+++||+
T Consensus 81 ~eI~k~IL~KGElQlt~~ER~~~~E~k~r~Ii~~Ia~~~InP~T~~P~P~~rIE~Am~e~~~~Vdp~Ksak~Qalevik~ 160 (373)
T PTZ00448 81 DNICKTILSKGEIQVSETERSYMLDKQFTDICHMLNRMTVNPKNNLPLSVKIIESELKDSGFSVSLNKTTKEQALKAFDI 160 (373)
T ss_pred HHHHHHHHhcCCcccCHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHhcCcccCCCCCHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCC--ccccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhcCceEEEEEee
Q 042018 152 LQKHFP--IKRSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNLQGRLEILAVS 229 (346)
Q Consensus 152 L~~~iP--I~ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~kG~~evl~~~ 229 (346)
|+++|| |+||+|+|+|.+|......++++|..|+...++.+.+++.|+++|+|+||.||.|+++ +|++|||+++
T Consensus 161 L~~iiPikiera~m~vki~~~~~~~~~~~~~l~~~~~~~~~~e~~~~~~~~~~~idP~~yR~~~~l----~g~l~v~~~~ 236 (373)
T PTZ00448 161 LKKRIPDQIERAKMMLKLSVDIVNKQNITKKLNEFNVFPISSEEKHNTYSITFLCEPRYYREIDQL----DCKLLLLDSN 236 (373)
T ss_pred HHHhCCcceeEEEEEEEEecccccHHHHHHHHhhcccccccccccCCceEEEEEECCccccchhcc----CceeEEEeee
Confidence 999999 7788888888888777889999999995444445556778999999999999999884 8999999999
Q ss_pred eee---------cCCccccccCCCCCCCCCCCCCCchhhhhhhHHHhhhhcc-CCCCCC------------CCc----cc
Q 042018 230 VHA---------EGDTSVDHYDDHEDVPSLPPKESADDVLKLSEKIEKQSLS-SGNGNT------------EGK----VK 283 (346)
Q Consensus 230 ~~~---------e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s-~~~~~~------------~~k----~~ 283 (346)
++. +|+.++|.+|++++.++++| .++...++++|+++++| ++++++ .++ ..
T Consensus 237 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 313 (373)
T PTZ00448 237 VKTIDKNSNQDNVEAIQLELSNKSDILFNSIT---NDPRHIIDKKLEKTEVSIKENANKFVKPIVSSLNIEESKREIKSN 313 (373)
T ss_pred ccccccccccccccccccccccccccchhccC---CChHHHHhHhhhhhccccccccccccccchhhhhhhhhccccccC
Confidence 999 99999999999999999999 34566899999999999 444442 011 02
Q ss_pred CccccccccccCChhHHHhhhcchhhhhhhhhhhcCCCCCChHHHHhhhhhhhhhhhhhh
Q 042018 284 QNKCSTCNAYVGDAKQYRDHFKSDWHKHNLKRKTRQLPPLTVEECLADMELDDSKADLKE 343 (346)
Q Consensus 284 ~~~C~tC~~~F~~~~~~r~H~kSdwHryNlKRk~~gl~plseee~F~~~~~~~~~~~~~~ 343 (346)
.++|++|++.|.+.++||.||||||||||||||++||||||+++ |++++.+-..+|++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~gLppvse~e-F~~~i~d~~~~~~~~ 372 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNARKMEPISEEE-FLELQQDIKLGFLAV 372 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHHhcCCCCCCHHH-HHHHHhhcccccccc
Confidence 57899999999999999999999999999999999999999999 999998877777653
No 2
>KOG2917 consensus Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-85 Score=601.94 Aligned_cols=236 Identities=55% Similarity=0.831 Sum_probs=231.7
Q ss_pred ccccCCCCceecceeEEEEEeeCCeEEEEEeecchhHHhhccCCCCchhhhhccccccccCCCccCChhhhhhh------
Q 042018 3 KTLVQPVGQKRLTNVAVVRLKKHGMRFEIACYKNKVLSWRSQVEKDLDEVLQSHTVYSNVSKGILAKSKDLIQH------ 76 (346)
Q Consensus 3 ~~i~~P~~q~~LtNvavVRlkk~GkrFEIacypnkv~~~R~G~e~dldeVLq~~~VF~NvsKG~~A~~~dL~ka------ 76 (346)
|.||||+||+||||||||||||+|+|||||||||||++||+|+|+|||||||+|+||.|||||++|+++||++|
T Consensus 1 ~~i~tP~nQirLTNVavVrlKK~GkRFEiAcYkNKV~~wRng~ekdlDEVLQthtVf~NVSKG~vAkk~dL~kaFg~~d~ 80 (250)
T KOG2917|consen 1 MSIFTPTNQIRLTNVAVVRLKKAGKRFEIACYKNKVVEWRNGVEKDLDEVLQTHTVFSNVSKGQVAKKEDLIKAFGTTDE 80 (250)
T ss_pred CCccCcCCceEEEEEEEEEEeccCceEEEEEecchhhhhhhcCcccHHHHHHHhHhhhhccccccccHHHHHHHhCCCcH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -----hhcccccccccHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcHHHHHHHHhhcCcccCCCCCHHHHHHHHHHH
Q 042018 77 -----LILEKGELQVAGKERETQFSNQFRDIATIVMQKTVNSETQRPYTISMIERLMHEIHFAVDPNSSSKKQALEVIRE 151 (346)
Q Consensus 77 -----~IL~kGElQvs~~ER~~~le~~~r~I~~~Ia~~~VnP~T~rP~p~~~IE~Am~e~~~~Vdp~ksak~QalevIk~ 151 (346)
+||.+||+|+|++||..+++..+|+|+++|+.+||||.|+||||+++||+||.++||+++||+|+|+||||+|++
T Consensus 81 ~~I~~eIl~kGe~QvsekeR~~~~~~~~r~I~~iv~~k~vnpetkRpyp~s~iekal~e~hfsv~~nk~sK~QaleaIkk 160 (250)
T KOG2917|consen 81 TEICKEILSKGELQVSEKERHSQLEKTFRDIVTIVAAKCVNPETKRPYPPSMIEKALQEIHFSVKTNKSSKQQALEAIKK 160 (250)
T ss_pred HHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCccCCcCCHHHHHHHHHhcceeecCCchHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCccccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc---CceEEEEEe
Q 042018 152 LQKHFPIKRSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL---QGRLEILAV 228 (346)
Q Consensus 152 L~~~iPI~ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~---kG~~evl~~ 228 (346)
|+++|||+||+|+|||.+|.+..+.+.++|.+|.+.++++++++++|+++|+|+||+||+|++++.++ +|++|||++
T Consensus 161 L~~~~pI~rarMrlRv~v~~~~~~~l~ekl~~l~~~ve~e~~~~~~~~~~~lI~pg~fr~~d~lvr~etk~kg~leiL~~ 240 (250)
T KOG2917|consen 161 LKEKMPIERARMRLRVSVPVKEGKELKEKLKELIDSVESEDWDPDQLECVCLIDPGCFREIDELVRKETKGKGRLEILDL 240 (250)
T ss_pred HHHhCchhhhceeEEEEEeccchHHHHHHHHHHhhccccccCCCCceEEEEEEcCCchHHHHHHHhhhccccceEEEEee
Confidence 99999999999999999999999999999999999999999999999999999999999999999988 999999999
Q ss_pred eeeecCCccc
Q 042018 229 SVHAEGDTSV 238 (346)
Q Consensus 229 ~~~~e~~~~~ 238 (346)
+++.+|++.+
T Consensus 241 ~e~~e~e~~~ 250 (250)
T KOG2917|consen 241 KEVEEGEECF 250 (250)
T ss_pred cccccccccC
Confidence 9999998753
No 3
>TIGR00291 RNA_SBDS rRNA metabolism protein, SBDS family. This protein family, possibly universal in both archaea and eukaryotes, appears to be involved in (ribosomal) RNA metabolism. Mutations in the human ortholog are associated with Shwachman-Bodian-Diamond syndrome.
Probab=100.00 E-value=3.4e-75 Score=542.90 Aligned_cols=217 Identities=28% Similarity=0.459 Sum_probs=210.4
Q ss_pred ceecceeEEEEEeeCCeEEEEEeecchhHHhhccCCCCchhhhhccccccccCCCccCChhhhhhh-----------hhc
Q 042018 11 QKRLTNVAVVRLKKHGMRFEIACYKNKVLSWRSQVEKDLDEVLQSHTVYSNVSKGILAKSKDLIQH-----------LIL 79 (346)
Q Consensus 11 q~~LtNvavVRlkk~GkrFEIacypnkv~~~R~G~e~dldeVLq~~~VF~NvsKG~~A~~~dL~ka-----------~IL 79 (346)
|++||||+|||||++|+|||||||||+|.+||+|.++||+||||+++||+|+|||++|+++||.++ +||
T Consensus 1 ~i~ltnv~ivR~k~~g~rFEI~~~p~~v~~~R~g~~~~l~eVL~~~~VF~n~skG~~As~~~L~k~FGT~d~~ei~~~IL 80 (231)
T TIGR00291 1 MVSLENAVIARLKKHGERFEVLVDPYLAADLREGIEVDFEDVLAIEEVFRDASKGEKASEEDLRKIFGTTDVDEVAEKII 80 (231)
T ss_pred CccccceEEEEEecCCceEEEEECHHHHHHHHcCCCCCHHHHhccceEEecCcccccCCHHHHHHHhCCCCHHHHHHHHH
Confidence 789999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcHHHHHHHHhhcCcccCCCCCHHHHHHHHHHHHHhhCCcc
Q 042018 80 EKGELQVAGKERETQFSNQFRDIATIVMQKTVNSETQRPYTISMIERLMHEIHFAVDPNSSSKKQALEVIRELQKHFPIK 159 (346)
Q Consensus 80 ~kGElQvs~~ER~~~le~~~r~I~~~Ia~~~VnP~T~rP~p~~~IE~Am~e~~~~Vdp~ksak~QalevIk~L~~~iPI~ 159 (346)
+|||+|+|++||++++|+++|+||++||++||||+|++|||++|||+||+++||+|||++|+|+||+++||+|+++|||+
T Consensus 81 ~kGeiQls~~eR~~~~e~k~~~Ii~~Ia~~~VnP~T~~P~p~~rIE~Am~e~~~~idp~k~ak~Qa~~vik~L~~iiPI~ 160 (231)
T TIGR00291 81 LKGEIQLTAEQRREMLEKKRNQIINIISRNTINPQTKKPHPPTRIEKALEEAKVHIDIFKSVEEQVLEIVKALKQIIPIK 160 (231)
T ss_pred hcCCccCCHHHHHHHHHHHHHHHHHHHHHhCcCCCCCCCCCHHHHHHHHHhcCcCcCCCCCHHHHHHHHHHHHhhhCCee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceEEEEEecCcchhHHHHHHHhhcccceeecC-CCCeEEEEEEecCCCchhHHHHhhhc-CceEEEEEe
Q 042018 160 RSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDN-SGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEILAV 228 (346)
Q Consensus 160 ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~-~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~evl~~ 228 (346)
|++|+++|++|+++++++++.|.+++. +.+++| +||+|.++++||||+|++|+++++++ +|++++.-+
T Consensus 161 ra~m~i~v~ip~~~~~~~~~~l~~~~~-i~~eew~~dgs~~~v~~I~pg~~~~~~~~l~~~tkG~~~~k~~ 230 (231)
T TIGR00291 161 FEKMKVAIKIPPERAGEAIEAISNFGA-VTPEEWQEDGSWICVGEIPSGNYRDLMTLLDKKTKGNVLTKVV 230 (231)
T ss_pred EeeEEEEEEeCHHHHHHHHHHHHHhcc-cchhhccCCCcEEEEEEECCccHHHHHHHHHhhcCCeeEEEEe
Confidence 999999999999999999999999996 677776 56799999999999999999999999 999988543
No 4
>PRK13760 putative RNA-associated protein; Provisional
Probab=100.00 E-value=1.5e-73 Score=531.61 Aligned_cols=213 Identities=25% Similarity=0.424 Sum_probs=206.1
Q ss_pred eecceeEEEEEeeCCeEEEEEeecchhHHhhccCCCCchhhhhccccccccCCCccCChhhhhhh-----------hhcc
Q 042018 12 KRLTNVAVVRLKKHGMRFEIACYKNKVLSWRSQVEKDLDEVLQSHTVYSNVSKGILAKSKDLIQH-----------LILE 80 (346)
Q Consensus 12 ~~LtNvavVRlkk~GkrFEIacypnkv~~~R~G~e~dldeVLq~~~VF~NvsKG~~A~~~dL~ka-----------~IL~ 80 (346)
+.|||++|||||+||+||||+||||+|.+||+|.++||+|||++++||+|+|||++|+++||.++ +||+
T Consensus 2 ~~l~n~~vvRlk~~g~~FEI~v~p~~v~~~R~g~~~~l~eVl~~~~VF~n~~kG~~As~~~L~~~FGT~d~~~i~~~IL~ 81 (231)
T PRK13760 2 VSLDDAVIARLESHGERFEILVDPDLALKFKEGKDVDIEDVLAVEEVFKDAKKGDKASEESLKKVFGTTDPLEIAEEIIK 81 (231)
T ss_pred CCccceEEEEEeeCCceEEEEECHHHHHHHHCCCCCCHHHHhccceEEecCccCCcCCHHHHHHHhCCCCHHHHHHHHHh
Confidence 57999999999999999999999999999999999999999999999999999999999999999 9999
Q ss_pred cccccccHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcHHHHHHHHhhcCcccCCCCCHHHHHHHHHHHHHhhCCccc
Q 042018 81 KGELQVAGKERETQFSNQFRDIATIVMQKTVNSETQRPYTISMIERLMHEIHFAVDPNSSSKKQALEVIRELQKHFPIKR 160 (346)
Q Consensus 81 kGElQvs~~ER~~~le~~~r~I~~~Ia~~~VnP~T~rP~p~~~IE~Am~e~~~~Vdp~ksak~QalevIk~L~~~iPI~r 160 (346)
|||+|+|++||++++|+++||||++||+|||||+|++|||++|||+||+++||+|||++|+|+||+++||+|+++|||+|
T Consensus 82 kGeiQlt~~eR~~~~e~k~r~Ii~~Ia~~~vnP~T~~P~p~~rIE~Am~e~~~~idp~k~ak~Qa~~vik~L~~~iPi~~ 161 (231)
T PRK13760 82 KGEIQLTAEQRREMLEEKRRQIINFIARNAINPQTGLPHPPQRIENAMEEARVHIDPFKSVEEQVKDIVKALRPIIPIKF 161 (231)
T ss_pred cCCccCCHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHhcCcccCCCCCHHHHHHHHHHHHHHhCCcce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEEecCcchhHHHHHHHhhcccceeecC-CCCeEEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 161 SPMRVGLTVPEQNISSLMEKLDAWNASIVSKDN-SGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 161 a~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~-~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
++|+++|++|+++++++++.|.+++ .+.+++| +||+|.++++||||+|++|+++|+++ +|++++
T Consensus 162 ~~~~~~v~iP~~~~~~~~~~l~~~~-~i~~eew~~dgs~~~v~~Ip~G~~~~~~~~~~~~tkG~~~~ 227 (231)
T PRK13760 162 EKARIAVKIPPEYAGKAYGELRKFG-EIKKEEWQSDGSWIAVLEIPAGLQNEFYDKLNKLTKGEAET 227 (231)
T ss_pred eeEEEEEEECHHHHHHHHHHHHhhc-ccchhhccCCCcEEEEEEECCccHHHHHHHHHHhcCCcEEE
Confidence 9999999999999999999999988 5677776 56799999999999999999999999 787665
No 5
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.5e-71 Score=508.13 Aligned_cols=220 Identities=29% Similarity=0.463 Sum_probs=214.1
Q ss_pred ceecceeEEEEEeeCCeEEEEEeecchhHHhhccCCCCchhhhhccccccccCCCccCChhhhhhh-----------hhc
Q 042018 11 QKRLTNVAVVRLKKHGMRFEIACYKNKVLSWRSQVEKDLDEVLQSHTVYSNVSKGILAKSKDLIQH-----------LIL 79 (346)
Q Consensus 11 q~~LtNvavVRlkk~GkrFEIacypnkv~~~R~G~e~dldeVLq~~~VF~NvsKG~~A~~~dL~ka-----------~IL 79 (346)
|++|+|++||||++||+|||||||||++++||+|.++||+||||+|+||.|||||++|+++||+++ +||
T Consensus 1 mv~l~~aviarlkk~GerFEvlvdP~~a~~~R~g~~vdleevLa~~~Vf~da~KG~~Ase~dL~k~FgTtd~~eI~~eIl 80 (234)
T COG1500 1 MVSLDDAVIARLKKHGERFEVLVDPNKALEYREGKEVDLEEVLATETVFKDASKGEKASEEDLKKAFGTTDPDEIAEEIL 80 (234)
T ss_pred CccchhheeeeeccCCeeEEEEECHhHHHHHHcCCCCCHHHHHhHHHHHHhccccccCCHHHHHHHhCCCCHHHHHHHHH
Confidence 689999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcHHHHHHHHhhcCcccCCCCCHHHHHHHHHHHHHhhCCcc
Q 042018 80 EKGELQVAGKERETQFSNQFRDIATIVMQKTVNSETQRPYTISMIERLMHEIHFAVDPNSSSKKQALEVIRELQKHFPIK 159 (346)
Q Consensus 80 ~kGElQvs~~ER~~~le~~~r~I~~~Ia~~~VnP~T~rP~p~~~IE~Am~e~~~~Vdp~ksak~QalevIk~L~~~iPI~ 159 (346)
++||+|||++||++|+|+++|+|+++|++|||||+|++||||+|||+||+|++|+|||+|||++||+++||+|++++||+
T Consensus 81 ~kGeiQlTaeqR~~m~e~k~rqIi~~IsRn~IdP~t~~P~Pp~rIe~Ameeakv~id~~K~ae~Qv~evlK~l~~i~pIr 160 (234)
T COG1500 81 KKGEIQLTAEQRREMLEEKKRQIINIISRNAIDPQTKAPHPPARIEKAMEEAKVHIDPFKSAEEQVQEVLKALRPIIPIR 160 (234)
T ss_pred hcCceeccHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHhcCcccCCCCCHHHHHHHHHHHHhhcCCce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceEEEEEecCcchhHHHHHHHhhcccceeecC-CCCeEEEEEEecCCCchhHHHHhhhc-CceEEEEEeeee
Q 042018 160 RSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDN-SGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEILAVSVH 231 (346)
Q Consensus 160 ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~-~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~evl~~~~~ 231 (346)
+++++++|.||+++++++++.|.++| .+..++| .||+|.++++||||+|++++++++++ +|++|+..+++.
T Consensus 161 fera~vaVkip~e~~~k~~~~l~k~g-~i~~eew~~dgsw~~~~~ipaG~q~e~~~~l~~~~kG~~q~k~l~~~ 233 (234)
T COG1500 161 FERAKVAVKIPVEYAGKAYGLLRKFG-EIKKEEWQEDGSWICVLEIPAGNQDEFYELLNELTKGEVQTKVLKVA 233 (234)
T ss_pred eeeeeEEEEecccccchHHHHHHHhh-hhhhhhcccCCceEEEEeeCcchHHHHHHHHHHhcCCcceeeeeeec
Confidence 99999999999999999999999999 5666666 78999999999999999999999998 999999988764
No 6
>PF09377 SBDS_C: SBDS protein C-terminal domain; InterPro: IPR018978 This entry represents the C-terminal domain of proteins that are highly conserved in species ranging from archaea to vertebrates and plants []. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS, OMIM 260400) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterised by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism [, ]. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. Together with the EF-2-like GTPase RIA1 (EfI1), it triggers the GTP-dependent release of TIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating TIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition []. A number of uncharacterised hydrophilic proteins of about 30 kDa share regions of similarity. These include, Mouse protein 22A3. Saccharomyces cerevisiae chromosome XII hypothetical protein YLR022c. Caenorhabditis elegans hypothetical protein W06E11.4. Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ0592. ; GO: 0042254 ribosome biogenesis; PDB: 2KDO_A 2L9N_A 2WBM_B 1P9Q_C 1T95_A.
Probab=100.00 E-value=1.1e-40 Score=285.45 Aligned_cols=123 Identities=40% Similarity=0.696 Sum_probs=113.3
Q ss_pred HHHHHHHHHHHHhcCCCCCCCCCcHHHHHHHHhhcCcccCCCCCHHHHHHHHHHHHHh--hCCccccceEEEEEecCcch
Q 042018 97 NQFRDIATIVMQKTVNSETQRPYTISMIERLMHEIHFAVDPNSSSKKQALEVIRELQK--HFPIKRSPMRVGLTVPEQNI 174 (346)
Q Consensus 97 ~~~r~I~~~Ia~~~VnP~T~rP~p~~~IE~Am~e~~~~Vdp~ksak~QalevIk~L~~--~iPI~ra~m~l~v~vp~~~~ 174 (346)
++|||||++||+|||||+||||||++|||+||+++||+|||++|+|+||+++||+|++ +|||+||+|+++|++|.+++
T Consensus 1 q~~keI~~~Ia~~~VnP~T~rP~p~~~IE~Am~e~~~~v~p~ksak~QalevIk~L~~~~~ipI~ra~m~l~v~ip~~~~ 80 (125)
T PF09377_consen 1 QKFKEIATIIAEKCVNPRTNRPYPPTRIEKAMKEAHFSVDPNKSAKQQALEVIKKLKEKQIIPIKRAKMRLRVTIPSKYA 80 (125)
T ss_dssp CHHHHHHHHHHHHEEBTTTTBTT-HHHHHHHHHHTTS-SSTTS-HHHHHHHHHHHHTT--TS--EEEEEEEEEEEBCCCH
T ss_pred ChHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHhCCcccCCCCCHHHHHHHHHHHHHHhCCCceeeeeEEEEEEeCHHHH
Confidence 4899999999999999999999999999999999999999999999999999999999 99999999999999999999
Q ss_pred hHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc
Q 042018 175 SSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL 219 (346)
Q Consensus 175 ~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~ 219 (346)
+++++.|.+++..++++++++|+|+++|+|+||+||+|+++|+++
T Consensus 81 ~~~~~~l~~~~~~i~~~~~~~~~~~~~~~i~pg~~r~l~~~v~~e 125 (125)
T PF09377_consen 81 KKVKDKLLKLGAKIEEEEQNDGSWEMVFLIDPGLYRELDELVNKE 125 (125)
T ss_dssp HHHHHHHHHHSEEEEEEEETTSCEEEEEEEEGGGHHHHHHHHHHH
T ss_pred HHHHHHHHHhhcEeeecccCCCeEEEEEEECCcchHHHHHHHccC
Confidence 999999999998776666789999999999999999999999874
No 7
>PF01172 SBDS: Shwachman-Bodian-Diamond syndrome (SBDS) protein ; InterPro: IPR019783 This entry represents the N-terminal domain of proteins that are highly conserved in species ranging from archaea to vertebrates and plants []. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS, OMIM 260400) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterised by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism [, ]. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. Together with the EF-2-like GTPase RIA1 (EfI1), it triggers the GTP-dependent release of TIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating TIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition []. A number of uncharacterised hydrophilic proteins of about 30 kDa share regions of similarity. These include, Mouse protein 22A3. Saccharomyces cerevisiae chromosome XII hypothetical protein YLR022c. Caenorhabditis elegans hypothetical protein W06E11.4. Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ0592. ; PDB: 1NYN_A 2WBM_B 1P9Q_C 1T95_A 2KDO_A 2L9N_A.
Probab=99.94 E-value=3e-28 Score=198.55 Aligned_cols=80 Identities=49% Similarity=0.679 Sum_probs=74.8
Q ss_pred ceeEEEEEeeCCeEEEEEeecchhHHhhccCCCCchhhhhccccccccCCCccCChhhhhhh-----------hhccccc
Q 042018 15 TNVAVVRLKKHGMRFEIACYKNKVLSWRSQVEKDLDEVLQSHTVYSNVSKGILAKSKDLIQH-----------LILEKGE 83 (346)
Q Consensus 15 tNvavVRlkk~GkrFEIacypnkv~~~R~G~e~dldeVLq~~~VF~NvsKG~~A~~~dL~ka-----------~IL~kGE 83 (346)
||+++||||++|++|||+||||+|.+||+|.++||++||+++.||+|++||..||+++|.++ .||++|+
T Consensus 1 tn~~~v~yk~~g~~fEi~v~p~~~~~~r~g~~~~l~~Vl~~~~IF~~~~kG~~As~~~L~~~FGT~d~~~ii~~IL~~Ge 80 (91)
T PF01172_consen 1 TNVVIVRYKKGGKRFEILVYPNKVEKYREGKSIPLDDVLQSFKIFTNVSKGERASKEDLENAFGTTDVDEIIKKILKKGE 80 (91)
T ss_dssp TTEEEEEEEETTEEEEEEEEHHHHHHHHCT-HCHHHHHBSSSSEEEETTTTEEE-HHHHHHHHSSS-HHHHHHHHHHHSE
T ss_pred CceEEEEEecCCceEEEEEecChHHHHhcCCCCCHHHHhheeeEEecCCcCCcCCHHHHHHHhCCCCHHHHHHHHHhcCC
Confidence 89999999999999999999999999999999999999999999999999999999999999 9999999
Q ss_pred ccccHHHHHHH
Q 042018 84 LQVAGKERETQ 94 (346)
Q Consensus 84 lQvs~~ER~~~ 94 (346)
+|+|++||++|
T Consensus 81 ~q~t~~~rr~m 91 (91)
T PF01172_consen 81 IQLTAEERREM 91 (91)
T ss_dssp EE--HHHHHHH
T ss_pred ccCChhhhhcC
Confidence 99999999986
No 8
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=99.70 E-value=4.8e-18 Score=167.34 Aligned_cols=54 Identities=48% Similarity=0.857 Sum_probs=50.9
Q ss_pred cCccccccccccCChhHHHhhhcchhhhhhhhhhhcCCCCCChHHHHhhhhhhhh
Q 042018 283 KQNKCSTCNAYVGDAKQYRDHFKSDWHKHNLKRKTRQLPPLTVEECLADMELDDS 337 (346)
Q Consensus 283 ~~~~C~tC~~~F~~~~~~r~H~kSdwHryNlKRk~~gl~plseee~F~~~~~~~~ 337 (346)
+.++|++|++.|++.++||.||||||||||||||+++|||||.|+ |++.+..+.
T Consensus 2 t~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~-F~~k~~s~~ 55 (390)
T KOG2785|consen 2 TGFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEE-FNEKVLSDD 55 (390)
T ss_pred CcceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHH-HhHHHhhhh
Confidence 479999999999999999999999999999999999999999999 999886654
No 9
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=99.50 E-value=8.5e-15 Score=148.53 Aligned_cols=52 Identities=38% Similarity=0.753 Sum_probs=49.9
Q ss_pred cCccccccccccCChhHHHhhhcchhhhhhhhhhhcCCCCCChHHHHhhhhhh
Q 042018 283 KQNKCSTCNAYVGDAKQYRDHFKSDWHKHNLKRKTRQLPPLTVEECLADMELD 335 (346)
Q Consensus 283 ~~~~C~tC~~~F~~~~~~r~H~kSdwHryNlKRk~~gl~plseee~F~~~~~~ 335 (346)
+...|+||++.|.++++||+||||||||+|+||+++|+|+||+++ |+.+...
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krkl~~~~ils~ed-Fe~i~s~ 116 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRKLRGKPILSEED-FEGIISS 116 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHH-HHHhhhc
Confidence 578899999999999999999999999999999999999999999 9999866
No 10
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=97.33 E-value=0.00015 Score=48.20 Aligned_cols=33 Identities=30% Similarity=0.478 Sum_probs=30.9
Q ss_pred cCccccccccccCChhHHHhhhcchhhhhhhhh
Q 042018 283 KQNKCSTCNAYVGDAKQYRDHFKSDWHKHNLKR 315 (346)
Q Consensus 283 ~~~~C~tC~~~F~~~~~~r~H~kSdwHryNlKR 315 (346)
..+.|..|+..|.+...++.|++|-.|+-|+++
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 468899999999999999999999999999986
No 11
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.88 E-value=0.00059 Score=43.44 Aligned_cols=27 Identities=37% Similarity=0.722 Sum_probs=24.9
Q ss_pred CccccccccccCChhHHHhhhcchhhh
Q 042018 284 QNKCSTCNAYVGDAKQYRDHFKSDWHK 310 (346)
Q Consensus 284 ~~~C~tC~~~F~~~~~~r~H~kSdwHr 310 (346)
++.|..|+..|.+...++.|++|-+|+
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence 478999999999999999999999995
No 12
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.45 E-value=0.0015 Score=40.35 Aligned_cols=25 Identities=28% Similarity=0.570 Sum_probs=23.3
Q ss_pred ccccccccccCChhHHHhhhcchhh
Q 042018 285 NKCSTCNAYVGDAKQYRDHFKSDWH 309 (346)
Q Consensus 285 ~~C~tC~~~F~~~~~~r~H~kSdwH 309 (346)
+.|..|++.|.+...++.|++|-.|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 5799999999999999999999876
No 13
>PF09186 DUF1949: Domain of unknown function (DUF1949); InterPro: IPR015269 Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement []. This entry contains the protein Impact, which is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea []. ; PDB: 2CVE_A 1VI7_A.
Probab=93.73 E-value=0.27 Score=35.32 Aligned_cols=55 Identities=16% Similarity=0.268 Sum_probs=46.8
Q ss_pred EEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-Cce
Q 042018 167 LTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGR 222 (346)
Q Consensus 167 v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~ 222 (346)
|++|-...+.+...|..++..+..+++++. ..+++.||+.....+...|.+. +|+
T Consensus 1 i~~~Y~~~~~v~~~l~~~~~~i~~~~y~~~-V~~~v~v~~~~~~~f~~~l~~~t~G~ 56 (56)
T PF09186_consen 1 ISCDYSQYGKVERLLEQNGIEIVDEDYTDD-VTLTVAVPEEEVEEFKAQLTDLTSGR 56 (56)
T ss_dssp EEE-CCCHHHHHHHHHHTTTEEEEEEECTT-EEEEEEEECCCHHHHHHHHHHHTTT-
T ss_pred CEechhhHHHHHHHHHHCCCEEEcceecce-EEEEEEECHHHHHHHHHHHHHHcCCC
Confidence 567888999999999999988888888555 9999999999999999999888 774
No 14
>cd04097 mtEFG1_C mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (desig
Probab=93.21 E-value=0.24 Score=38.61 Aligned_cols=62 Identities=26% Similarity=0.371 Sum_probs=51.1
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLE 224 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~e 224 (346)
+++.|.+|.++.+.++..|.+..+.+...+..++.+.+.+.+|....-.+.+-|+.. +|.+.
T Consensus 4 ~~~~I~~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~i~~~~P~~e~~g~~~~Lr~~T~G~~~ 66 (78)
T cd04097 4 MKVEVTAPTEFQGNVIGLLNKRKGTIVDTDTGEDEFTLEAEVPLNDMFGYSTELRSMTQGKGE 66 (78)
T ss_pred EEEEEEecHHHHHHHHHHHHHCCCEEeceEecCCeEEEEEEECHHHhhChHHHHHhhCCCcEE
Confidence 688999999999999999999888777666545678899999987777777777777 88764
No 15
>PF00679 EFG_C: Elongation factor G C-terminus; InterPro: IPR000640 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. This entry represents the C-terminal domain found in EF2 (or EF-G) of both prokaryotes and eukaryotes (also known as eEF2), as well as in some tetracycline-resistance proteins. This domain adopts a ferredoxin-like fold consisting of an alpha/beta sandwich with anti-parallel beta-sheets. It resembles the topology of domain III found in these elongation factors, with which it forms the C-terminal block, but these two domains cannot be superimposed []. This domain is often found associated with (IPR000795 from INTERPRO), which contains the signatures for the N terminus of the proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1WDT_A 2DY1_A 3CB4_F 3DEG_C 2EFG_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y ....
Probab=93.17 E-value=0.28 Score=39.25 Aligned_cols=63 Identities=25% Similarity=0.413 Sum_probs=52.2
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCC-CCeEEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNS-GSQLSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~-~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
|++.|.+|.++.+.++..|.+.++.+.+.+.. ++...+.+.+|--.-..+..-++.. +|++..
T Consensus 7 ~~~~I~~p~~~~g~v~~~l~~r~g~i~~~~~~~~~~~~i~~~iP~~~~~gf~~~Lr~~T~G~a~~ 71 (89)
T PF00679_consen 7 MSVEISVPEEYLGKVISDLSKRRGEILSMDPIGGDRVVIEAEIPVRELFGFRSELRSLTSGRASF 71 (89)
T ss_dssp EEEEEEEEGGGHHHHHHHHHHTT-EEEEEEEESTTEEEEEEEEEGGGHTTHHHHHHHHTTTS-EE
T ss_pred EEEEEEECHHHHHHHHHHhcccccEEEechhhhhhheeEEEEEChhhhhhHHHHhhccCCCEEEE
Confidence 78999999999999999999999888776654 6788899999988777888888888 887743
No 16
>cd03710 BipA_TypA_C BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secreti
Probab=93.08 E-value=0.29 Score=38.31 Aligned_cols=63 Identities=16% Similarity=0.219 Sum_probs=50.8
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCC-CeEEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSG-SQLSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~-~~~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
|++.|.+|.++.+.++..|.+..+.+...+..+ +.+.+.+.+|-...-.+..-|+.. +|.+..
T Consensus 4 ~~v~I~~P~~~~g~V~~~l~~rrg~i~~~~~~~~~~~~i~~~~P~~~~~~~~~~Lrs~T~G~a~~ 68 (79)
T cd03710 4 EELTIDVPEEYSGAVIEKLGKRKGEMVDMEPDGNGRTRLEFKIPSRGLIGFRSEFLTDTRGTGIM 68 (79)
T ss_pred EEEEEEeCchhhHHHHHHHHhCCCEEEccEECCCCEEEEEEEECHHHHcCcHHHHHhhCCCeEEE
Confidence 788999999999999999999888777655434 568899999977666777777777 888743
No 17
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=92.86 E-value=0.06 Score=46.75 Aligned_cols=40 Identities=43% Similarity=0.737 Sum_probs=34.9
Q ss_pred CccccccccccCChhHHHhhhcchhhhhhhhhhhcCCC--CCChHH
Q 042018 284 QNKCSTCNAYVGDAKQYRDHFKSDWHKHNLKRKTRQLP--PLTVEE 327 (346)
Q Consensus 284 ~~~C~tC~~~F~~~~~~r~H~kSdwHryNlKRk~~gl~--plseee 327 (346)
+|.|-.|.-.|.|...+..||||--| |||++.|. |-|++|
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~ktK~H----KrRvK~l~~~PySQee 98 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKTKVH----KRRVKELREVPYSQEE 98 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhccHH----HHHHHhcccCCccHHH
Confidence 78899999999999999999999999 56677765 667777
No 18
>cd03711 Tet_C Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=92.46 E-value=0.33 Score=37.82 Aligned_cols=63 Identities=19% Similarity=0.301 Sum_probs=50.0
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
|++.|.+|.++.+.++..|.+..+.+...+..++.+.+.+.+|-...-.+.+-++.. +|.+..
T Consensus 4 ~~~~i~~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~i~~~~P~~~~~g~~~~Lr~~T~G~~~~ 67 (78)
T cd03711 4 LRFELEVPQDALGRAMSDLAKMGATFEDPQIKGDEVTLEGTIPVATSQDYQSELPSYTHGEGVL 67 (78)
T ss_pred EEEEEEcCHHHHHHHHHHHHHcCCEeeCcEecCCEEEEEEEECHHHHhhHHHHhHhhcCCeEEE
Confidence 788999999999999999999887777655555778899999976665666666666 887753
No 19
>cd03713 EFG_mtEFG_C EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide
Probab=92.23 E-value=0.3 Score=37.78 Aligned_cols=63 Identities=27% Similarity=0.397 Sum_probs=51.1
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
|++.|.+|.++.+.++..|.+..+.+...+..++.+.+.+.+|.--.-.+.+.|+.. +|.+..
T Consensus 4 ~~~~I~~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~i~~~iP~~e~~~~~~~Lr~~T~G~a~~ 67 (78)
T cd03713 4 MKVEVTVPEEYMGDVIGDLSSRRGQILGTESRGGWKVIKAEVPLAEMFGYSTDLRSLTQGRGSF 67 (78)
T ss_pred EEEEEEcCHHHHHHHHHHHHHcCCceEceeccCCcEEEEEEcCHHHHhChHHHHHhhcCCeEEE
Confidence 788999999999999999999887777666556678889999977666777777777 887753
No 20
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=92.19 E-value=0.073 Score=32.02 Aligned_cols=22 Identities=18% Similarity=0.555 Sum_probs=20.1
Q ss_pred ccccccccccCChhHHHhhhcc
Q 042018 285 NKCSTCNAYVGDAKQYRDHFKS 306 (346)
Q Consensus 285 ~~C~tC~~~F~~~~~~r~H~kS 306 (346)
+.|..|+..|.+...++.|.+.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4699999999999999999876
No 21
>cd04096 eEF2_snRNP_like_C eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=91.92 E-value=0.32 Score=37.94 Aligned_cols=63 Identities=14% Similarity=0.144 Sum_probs=50.2
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCCC--eEEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGS--QLSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~--~~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
|++.|.+|.++.+.++..|.+..+.+...+..++ .+.+.+.+|-...-.+...|+.. +|++..
T Consensus 4 ~~~~I~~p~~~~g~V~~~l~~rrg~i~~~~~~~~~~~~~i~~~iP~~e~~~~~~~Lrs~T~G~~~~ 69 (80)
T cd04096 4 YLVEIQCPEDALGKVYSVLSKRRGHVLSEEPKEGTPLFEIKAYLPVIESFGFETDLRSATSGQAFP 69 (80)
T ss_pred EEEEEEEcHHHhhHHHHhhhhCeeEEeEEeecCCCccEEEEEEEeHHHHhCcHHHHHhhCCCCcEE
Confidence 7899999999999999999998887776554333 38889999977777777777777 887643
No 22
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=91.75 E-value=0.089 Score=31.07 Aligned_cols=22 Identities=18% Similarity=0.572 Sum_probs=18.0
Q ss_pred ccccccccccCChhHHHhhhcc
Q 042018 285 NKCSTCNAYVGDAKQYRDHFKS 306 (346)
Q Consensus 285 ~~C~tC~~~F~~~~~~r~H~kS 306 (346)
+.|..|+..|.+..+++.|.++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 4699999999999999999875
No 23
>cd01514 Elongation_Factor_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p. This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain. EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the
Probab=91.63 E-value=0.39 Score=37.18 Aligned_cols=63 Identities=27% Similarity=0.442 Sum_probs=52.6
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCC-CeEEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSG-SQLSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~-~~~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
+++.|.+|.++.+.++..|.+..+.+...+..+ +.+.+.+.+|-...-.+.+.++.. +|++..
T Consensus 4 ~~~~I~~p~~~~g~v~~~l~~rrg~v~~~~~~~~~~~~i~~~iP~~e~~g~~~~lr~~T~G~~~~ 68 (79)
T cd01514 4 MKVEITVPEEYLGAVIGDLSKRRGEILGMEPRGTGRVVIKAELPLAEMFGFATDLRSLTQGRASF 68 (79)
T ss_pred EEEEEEcCHHHHHHHHHHHHhcCCeeEeeEecCCCeEEEEEECCHHHHcCcHHHhhhhcCCeEEE
Confidence 688999999999999999999888777666545 678889999988877788888888 888754
No 24
>cd03709 lepA_C lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits significant homology to elongation factors (EFs) Tu and G. The function(s) of the proteins in this family are unknown. The N-terminal domain of LepA is homologous to a domain of similar size found in initiation factor 2 (IF2), and in EF-Tu and EF-G (factors required for translation in Escherichia coli). Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including S. cerevisiae GUF1) originated within the bacterial LepA family. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=91.57 E-value=0.51 Score=37.16 Aligned_cols=63 Identities=13% Similarity=0.218 Sum_probs=49.1
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCC-CeEEEEEEecCCCc-hhHHHHhhhc-CceEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSG-SQLSLICEMEPGLF-RDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~-~~~~~~~~I~pG~~-r~l~~~v~~~-kG~~ev 225 (346)
|++.|.+|.++.+.+++.|.+..+.+..-+..+ +...+.+.+|-... ..+..-+... +|+...
T Consensus 4 ~~v~i~vP~e~~G~V~~~l~~rrG~i~~~~~~~~~~~~i~~~~P~~~~~~g~~~~L~s~T~G~g~~ 69 (80)
T cd03709 4 VKATIITPSEYLGAIMELCQERRGVQKDMEYLDANRVMLTYELPLAEIVYDFFDKLKSISKGYASL 69 (80)
T ss_pred EEEEEEeCHHhhHHHHHHHHHhCCEEeccEecCCCeEEEEEECCHHHHhhhHHHHhHhhcCCEEEE
Confidence 788999999999999999999887776555433 47788889997665 5666666777 887654
No 25
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=91.37 E-value=0.12 Score=32.30 Aligned_cols=24 Identities=21% Similarity=0.469 Sum_probs=21.5
Q ss_pred ccccccccccCChhHHHhhhcchh
Q 042018 285 NKCSTCNAYVGDAKQYRDHFKSDW 308 (346)
Q Consensus 285 ~~C~tC~~~F~~~~~~r~H~kSdw 308 (346)
+.|..|+..|.+...++.|-++-+
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 679999999999999999987653
No 26
>cd04098 eEF2_C_snRNP eEF2_C_snRNP: This family includes a C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to the C-terminal domain of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=91.36 E-value=0.46 Score=37.46 Aligned_cols=63 Identities=17% Similarity=0.124 Sum_probs=50.9
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCCCe--EEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQ--LSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~--~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
|++.|++|.++.+.++..|.+..+.|...+..++. ..+.+.+|-..--.+..-|+.. +|++..
T Consensus 4 ~~~ei~~p~~~~g~v~~~L~~rrg~i~~~~~~~~~~~~~i~a~vP~~e~~~~~~~Lrs~T~G~~~~ 69 (80)
T cd04098 4 YEVEITCPADAVSAVYEVLSRRRGHVIYDTPIPGTPLYEVKAFIPVIESFGFETDLRVHTQGQAFC 69 (80)
T ss_pred EEEEEEECHHHHhHHHHHHhhCCcEEeeeeccCCCCcEEEEEECCHHHHhChHHHHHhhCCCceEE
Confidence 78999999999999999999998888766654455 7889999977766777777777 887654
No 27
>smart00838 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
Probab=90.80 E-value=0.54 Score=37.11 Aligned_cols=64 Identities=23% Similarity=0.332 Sum_probs=51.0
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEIL 226 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~evl 226 (346)
|++.|.+|.++.+.++..|.+..+.+...+..++.+.+.+.+|....-.+.+-++.. +|++...
T Consensus 6 ~~~~I~~p~~~~g~v~~~l~~rrG~i~~~~~~~~~~~i~~~iP~~~~~~~~~~Lrs~T~G~~~~~ 70 (85)
T smart00838 6 MKVEVTVPEEYMGDVIGDLNSRRGKIEGMEQRGGAQVIKAKVPLSEMFGYATDLRSATQGRATWS 70 (85)
T ss_pred EEEEEEeCHHHHHHHHHHHHHcCCEEECeeccCCcEEEEEECCHHHHhchHHHHHHhcCCeEEEE
Confidence 788999999999999999999887776655545678889999977766777777777 8887543
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=86.85 E-value=0.36 Score=37.79 Aligned_cols=29 Identities=24% Similarity=0.567 Sum_probs=25.1
Q ss_pred CccccccccccCChhHHHhhhcchhhhhh
Q 042018 284 QNKCSTCNAYVGDAKQYRDHFKSDWHKHN 312 (346)
Q Consensus 284 ~~~C~tC~~~F~~~~~~r~H~kSdwHryN 312 (346)
.+.|..|+..|.+...++.|.++..|...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~ 78 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKR 78 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCc
Confidence 58999999999999999999999999653
No 29
>PRK11568 hypothetical protein; Provisional
Probab=84.59 E-value=3.1 Score=39.04 Aligned_cols=66 Identities=15% Similarity=0.281 Sum_probs=55.8
Q ss_pred cceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEEEEE
Q 042018 161 SPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEILA 227 (346)
Q Consensus 161 a~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~evl~ 227 (346)
....+.|.+|-+..+.+...|..++..+..++++ +...+.+.+|+.....+.+.+.+. .|++++..
T Consensus 135 ~~~~~~i~~~y~~~~~v~~~l~~~~~~i~~~~y~-~~V~~~~~v~~~~~~~~~~~l~~~t~g~~~~~~ 201 (204)
T PRK11568 135 PLTEYTLQCEYAQLAGIEALLGQFDGKIVNSEYQ-AFVTLRVALPAAKVAEFSAKLADFSRGSLQLLA 201 (204)
T ss_pred EeEEEEEEECcchHHHHHHHHHHCCCEEEcceec-CCEEEEEEECHHHHHHHHHHHHHHhCCeEEEEe
Confidence 4466778889999999999999998777777774 458899999999999999999988 99887763
No 30
>PHA02768 hypothetical protein; Provisional
Probab=83.95 E-value=0.53 Score=35.59 Aligned_cols=26 Identities=15% Similarity=0.282 Sum_probs=23.7
Q ss_pred cCccccccccccCChhHHHhhhcchh
Q 042018 283 KQNKCSTCNAYVGDAKQYRDHFKSDW 308 (346)
Q Consensus 283 ~~~~C~tC~~~F~~~~~~r~H~kSdw 308 (346)
-++.|..||..|...+.+..|.++-|
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHhcC
Confidence 36789999999999999999999966
No 31
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=82.40 E-value=12 Score=33.66 Aligned_cols=105 Identities=19% Similarity=0.306 Sum_probs=72.1
Q ss_pred CCCCcHHHHHHHHhhcCcccC-----CCC------------CHHHHHHHHHHHHHhhCC------------ccccceEEE
Q 042018 116 QRPYTISMIERLMHEIHFAVD-----PNS------------SSKKQALEVIRELQKHFP------------IKRSPMRVG 166 (346)
Q Consensus 116 ~rP~p~~~IE~Am~e~~~~Vd-----p~k------------sak~QalevIk~L~~~iP------------I~ra~m~l~ 166 (346)
++|-...+|-.++.+.+|+|+ |.. +.+..+..+.|||.+.++ +.|.-|-++
T Consensus 10 n~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V~~d~~~i~qi~kQl~Kli~V~~V~~~~~~~~v~rEl~LiK 89 (157)
T TIGR00119 10 NEPGVLSRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIVVVGDDKVLEQITKQLNKLVDVIKVSDLTESAIVERELCLVK 89 (157)
T ss_pred CCCcHHHHHHHHHHhCCceEEEEEEeecCCCCEEEEEEEEECCHHHHHHHHHHHhcCccEEEEEecCCCcceeeEEEEEE
Confidence 567777777777777777663 221 236777788888876543 678899999
Q ss_pred EEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc--CceEEE
Q 042018 167 LTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL--QGRLEI 225 (346)
Q Consensus 167 v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~--kG~~ev 225 (346)
|..+.+....+......+.+.+.. .+.+++.+.+. |.-..++.++.-+ -|-+|+
T Consensus 90 v~~~~~~r~~i~~i~~~f~a~ivd--v~~~~~~ie~t---G~~~ki~~~~~~l~~~gi~e~ 145 (157)
T TIGR00119 90 VSAPGEGRDEIIRLTNIFRGRIVD--VSPDSYTVEVT---GDSDKIDAFLELLRPFGIKEV 145 (157)
T ss_pred EECCccCHHHHHHHHHHhCCEEEE--ecCCEEEEEEc---CCHHHHHHHHHHhhhcCCEEE
Confidence 999988888999999999987763 34556555554 4455555555554 354444
No 32
>TIGR00257 IMPACT_YIGZ uncharacterized protein, YigZ family. This uncharacterized protein family includes YigZ, which has been crystallized, from E. coli. YigZ is homologous to the protein product of the mouse IMPACT gene. Crystallography shows a two-domain stucture, and the C-terminal domain is suggested to bind nucleic acids. The function is unknown. Note that the ortholog from E. coli was shown fused to the pepQ gene in GenBank entry X54687. This caused occasional misidentification of this protein as pepQ; this family is found in a number of species that lack pepQ.
Probab=81.21 E-value=4.5 Score=37.94 Aligned_cols=66 Identities=14% Similarity=0.131 Sum_probs=55.1
Q ss_pred cceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEEEEE
Q 042018 161 SPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEILA 227 (346)
Q Consensus 161 a~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~evl~ 227 (346)
..-.+.|.+|-+..+.+...|..++..+.+.++++ ...+.+.+|+.....+.+.+.++ .|++++..
T Consensus 135 ~~~~~~~~~~y~~~~~v~~~l~~~~~~i~~~~y~~-~V~~~~~v~~~~~~~~~~~l~~~t~g~~~~~~ 201 (204)
T TIGR00257 135 ELEILSLHCDYKQLDALERELKKFQLEIIKSNFSN-NVVLVEISGTKENLAFSEQLTEISLGQLILKF 201 (204)
T ss_pred EEEEEEEEechhHHHHHHHHHHHCCCEEEeeEecC-CEEEEEEECHHHHHHHHHHHHHHhCCeEEEEe
Confidence 34566788888889999999999987777777754 58999999999999999999998 89887643
No 33
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=80.67 E-value=11 Score=34.06 Aligned_cols=100 Identities=17% Similarity=0.303 Sum_probs=71.6
Q ss_pred CCCCCcHHHHHHHHhhcCcccC-----CCC------------CHHHHHHHHHHHHHhhCC------------ccccceEE
Q 042018 115 TQRPYTISMIERLMHEIHFAVD-----PNS------------SSKKQALEVIRELQKHFP------------IKRSPMRV 165 (346)
Q Consensus 115 T~rP~p~~~IE~Am~e~~~~Vd-----p~k------------sak~QalevIk~L~~~iP------------I~ra~m~l 165 (346)
.++|-...+|-..+...+|+|. |.. ..+.....++|||.+.++ +.|.-+-+
T Consensus 10 eN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~~~~~~i~qi~kQl~KLidV~~V~~~~~~~~v~rEl~Li 89 (161)
T PRK11895 10 ENEPGVLSRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVTSGDEQVIEQITKQLNKLIDVLKVVDLTEEAHVERELALV 89 (161)
T ss_pred cCCCcHHHHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEEECCHHHHHHHHHHHhccccEEEEEecCCcchhheEEEEE
Confidence 3677778888888888877774 222 246778888899976544 66888999
Q ss_pred EEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc
Q 042018 166 GLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL 219 (346)
Q Consensus 166 ~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~ 219 (346)
+|..+......+......+.+.|.. .+.+++.+.+. |.-..++.+++-+
T Consensus 90 Kv~~~~~~r~~i~~i~~~f~a~ivd--v~~~~~~iE~t---G~~~ki~~~~~~l 138 (161)
T PRK11895 90 KVRASGENRAEILRLADIFRAKIVD--VTPESLTIEVT---GDSDKIDAFIDLL 138 (161)
T ss_pred EEECCcccHHHHHHHHHHhCCEEEE--ecCCEEEEEEe---CCHHHHHHHHHHh
Confidence 9999888888899999999987763 34556555555 4555555555555
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=79.78 E-value=1.2 Score=26.12 Aligned_cols=21 Identities=14% Similarity=0.607 Sum_probs=19.1
Q ss_pred ccccccccccCChhHHHhhhc
Q 042018 285 NKCSTCNAYVGDAKQYRDHFK 305 (346)
Q Consensus 285 ~~C~tC~~~F~~~~~~r~H~k 305 (346)
+.|..|+..|.+...+..|.+
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 369999999999999999987
No 35
>PHA00616 hypothetical protein
Probab=79.29 E-value=0.8 Score=33.15 Aligned_cols=22 Identities=23% Similarity=0.492 Sum_probs=20.1
Q ss_pred ccccccccccCChhHHHhhhcc
Q 042018 285 NKCSTCNAYVGDAKQYRDHFKS 306 (346)
Q Consensus 285 ~~C~tC~~~F~~~~~~r~H~kS 306 (346)
+.|..||..|.+.++++.|.++
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~ 23 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLS 23 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHH
Confidence 5799999999999999999865
No 36
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=73.78 E-value=1.9 Score=36.93 Aligned_cols=44 Identities=32% Similarity=0.539 Sum_probs=35.5
Q ss_pred CccccccccccCChhHHHhhhcchhhhhhhhhhhcCCC--CCChHHHHhhh
Q 042018 284 QNKCSTCNAYVGDAKQYRDHFKSDWHKHNLKRKTRQLP--PLTVEECLADM 332 (346)
Q Consensus 284 ~~~C~tC~~~F~~~~~~r~H~kSdwHryNlKRk~~gl~--plseee~F~~~ 332 (346)
++.|-.|...|.+...+..|-|+.-|+ |+++.|. |-|+++ -+..
T Consensus 55 qhYCieCaryf~t~~aL~~HkkgkvHk----RR~KelRevpytQe~-aeaA 100 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKKGKVHK----RRAKELREVPYTQED-AEAA 100 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhccchhH----HHHHHHhcCcchhHH-HHHH
Confidence 678999999999999999999999994 5666554 777777 4433
No 37
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=71.36 E-value=2.2 Score=41.85 Aligned_cols=27 Identities=22% Similarity=0.481 Sum_probs=24.2
Q ss_pred cCccccccccccCChhHHHhhhcchhh
Q 042018 283 KQNKCSTCNAYVGDAKQYRDHFKSDWH 309 (346)
Q Consensus 283 ~~~~C~tC~~~F~~~~~~r~H~kSdwH 309 (346)
+.|.|-.|+..|+|+..+|.|.++-=+
T Consensus 214 KPF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 214 KPFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred CCccCCcccchhcchHHHHHHHHhhcC
Confidence 589999999999999999999987544
No 38
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=71.05 E-value=3.2 Score=38.33 Aligned_cols=56 Identities=21% Similarity=0.381 Sum_probs=42.0
Q ss_pred hhhhhhHHHhhhhccCCC-CCCCCcccCccccccccccCChhHHHhhhcchhhhhhhhh
Q 042018 258 DVLKLSEKIEKQSLSSGN-GNTEGKVKQNKCSTCNAYVGDAKQYRDHFKSDWHKHNLKR 315 (346)
Q Consensus 258 ~~~~~~~~~~~~~~s~~~-~~~~~k~~~~~C~tC~~~F~~~~~~r~H~kSdwHryNlKR 315 (346)
--++|.++..+...+-+. ..++. .+|.|..|+..|.|.-.|-.|.----|.-||--
T Consensus 50 ykvdl~sKLgkt~vitk~tp~sq~--~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgm 106 (193)
T KOG4727|consen 50 YKVDLESKLGKTVVITKSTPRSQK--GGYYCDVCDCVVKDSINFLDHINGKKHQRNLGM 106 (193)
T ss_pred hhhHhHhhccceeEeccCCccccc--CceeeeecceeehhhHHHHHHhccHHHHHHHhh
Confidence 355677777666555222 23333 599999999999999999999998889888754
No 39
>PLN02748 tRNA dimethylallyltransferase
Probab=65.30 E-value=4.3 Score=42.55 Aligned_cols=34 Identities=21% Similarity=0.484 Sum_probs=30.6
Q ss_pred cCcccccccc-ccCChhHHHhhhcchhhhhhhhhh
Q 042018 283 KQNKCSTCNA-YVGDAKQYRDHFKSDWHKHNLKRK 316 (346)
Q Consensus 283 ~~~~C~tC~~-~F~~~~~~r~H~kSdwHryNlKRk 316 (346)
+.++|.+|+. .|-...+-..|.+|-=||.|+|+.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~ 451 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRL 451 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHH
Confidence 4788999997 798889999999999999999964
No 40
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=58.43 E-value=3.2 Score=32.31 Aligned_cols=27 Identities=19% Similarity=0.460 Sum_probs=0.0
Q ss_pred ccccccccCChhHHHhhhcchhhhhhhh
Q 042018 287 CSTCNAYVGDAKQYRDHFKSDWHKHNLK 314 (346)
Q Consensus 287 C~tC~~~F~~~~~~r~H~kSdwHryNlK 314 (346)
|..|+..|.+...++.|.+ ..|.+++-
T Consensus 2 C~~C~~~f~~~~~l~~H~~-~~H~~~~~ 28 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMK-KKHGFDIP 28 (100)
T ss_dssp ----------------------------
T ss_pred ccccccccccccccccccc-cccccccc
Confidence 9999999999999999995 67888765
No 41
>PRK05433 GTP-binding protein LepA; Provisional
Probab=53.38 E-value=26 Score=37.72 Aligned_cols=61 Identities=16% Similarity=0.252 Sum_probs=48.9
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCc-hhHHHHhhhc-CceE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLF-RDCDTLLRNL-QGRL 223 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~-r~l~~~v~~~-kG~~ 223 (346)
|++.|.+|.++.+.+++.+.+....+..-+..++...+.+.+|-.-. .++.+.++.. +|..
T Consensus 407 ~~~~i~~P~~~~G~vm~~~~~rRG~~~~~~~~~~~~~i~~~~Pl~e~~~~~~~~Lks~T~G~g 469 (600)
T PRK05433 407 VKATIIVPQEYVGAVMELCQEKRGVQKDMEYLGNRVELTYELPLAEIVFDFFDRLKSVSRGYA 469 (600)
T ss_pred EEEEEEecHHHHHHHHHHHHHcCCEEeCcEecCCeEEEEEEechHHhhhhHHHHhHhhcCCEE
Confidence 78999999999999999999887776665554566778889997666 6777777887 7765
No 42
>PF10513 EPL1: Enhancer of polycomb-like; InterPro: IPR019542 This domain is found at the N-terminal of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes []. It is also present at the N terminus of Jade family proteins.
Probab=51.05 E-value=12 Score=32.95 Aligned_cols=26 Identities=31% Similarity=0.314 Sum_probs=23.5
Q ss_pred hhhhhhhhhhcCCCCCChHHHHhhhhh
Q 042018 308 WHKHNLKRKTRQLPPLTVEECLADMEL 334 (346)
Q Consensus 308 wHryNlKRk~~gl~plseee~F~~~~~ 334 (346)
+..||-+|+..|+++||++. |+.+..
T Consensus 130 L~~~N~~r~~~~~~~ls~~~-FE~~md 155 (160)
T PF10513_consen 130 LELLNKKRKSDGLEPLSEED-FEIIMD 155 (160)
T ss_pred HHHHHHHhhhcCCCCCCHHH-HHHHHH
Confidence 57889999999999999999 998764
No 43
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=50.37 E-value=59 Score=29.79 Aligned_cols=63 Identities=24% Similarity=0.263 Sum_probs=44.0
Q ss_pred ccccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc--CceEEE
Q 042018 158 IKRSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL--QGRLEI 225 (346)
Q Consensus 158 I~ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~--kG~~ev 225 (346)
|.|.-|-++|..|.+....+......+++.|.. .+.+++.+.+. |.-..++.++.-+ -|-.|+
T Consensus 82 v~rEl~LiKv~~~~~~r~ei~~~~~~f~a~ivd--v~~~~~~ie~t---G~~~ki~a~~~~l~~~gi~e~ 146 (174)
T CHL00100 82 VERELMLIKINVNSQTRPEILEIAQIFRAKVVD--LSEESLILEVT---GDPGKIVAIEQLLEKFGIIEI 146 (174)
T ss_pred eeeEEEEEEEecCCcCHHHHHHHHHHhCCEEEE--ecCCEEEEEEc---CCHHHHHHHHHHhhhcCCEEE
Confidence 889999999999988888899999999887763 33455444443 5555666665555 344443
No 44
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=49.97 E-value=28 Score=32.99 Aligned_cols=65 Identities=18% Similarity=0.280 Sum_probs=44.3
Q ss_pred ccccceEEEEEecCcchhHHHHHHHhhcccceeecCC-------CCeEEEEEEecCCCchhHHHHhhhcCceE
Q 042018 158 IKRSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNS-------GSQLSLICEMEPGLFRDCDTLLRNLQGRL 223 (346)
Q Consensus 158 I~ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~-------~~~~~~~~~I~pG~~r~l~~~v~~~kG~~ 223 (346)
|+.+.|++.+.=+.+...++...+.++|..|.+.+.+ .....+++.|||..|..+.+.+.+. |.+
T Consensus 49 i~~~~l~lev~d~~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~-g~v 120 (262)
T PF14257_consen 49 IKTADLSLEVKDVEKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRVPADKFDSFLDELSEL-GKV 120 (262)
T ss_pred EEEEEEEEEECCHHHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEECHHHHHHHHHHHhcc-Cce
Confidence 6667777666444455666677777777777665542 3456889999999997777777655 444
No 45
>PHA00743 helix-turn-helix protein
Probab=48.87 E-value=30 Score=25.85 Aligned_cols=34 Identities=21% Similarity=0.432 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCCcHHHHHHHH
Q 042018 94 QFSNQFRDIATIVMQKTVNSETQRPYTISMIERLM 128 (346)
Q Consensus 94 ~le~~~r~I~~~Ia~~~VnP~T~rP~p~~~IE~Am 128 (346)
++++--|+..++||+.-||--|+. ||-..||+|+
T Consensus 3 eLD~~iReLLs~iheIKID~i~~~-~~k~kvekAl 36 (51)
T PHA00743 3 ELDEDVRELLSIIHEIKIDIITQS-YDKEKIEKAI 36 (51)
T ss_pred hhHHHHHHHHHHHHHHhhhhhccc-CCHHHHHHHH
Confidence 467778999999999999999999 9999999998
No 46
>TIGR01393 lepA GTP-binding protein LepA. LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown.
Probab=48.67 E-value=41 Score=36.23 Aligned_cols=62 Identities=15% Similarity=0.211 Sum_probs=49.6
Q ss_pred ceEEEEEecCcchhHHHHHHHhhcccceeecC-CCCeEEEEEEecCCCc-hhHHHHhhhc-CceE
Q 042018 162 PMRVGLTVPEQNISSLMEKLDAWNASIVSKDN-SGSQLSLICEMEPGLF-RDCDTLLRNL-QGRL 223 (346)
Q Consensus 162 ~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~-~~~~~~~~~~I~pG~~-r~l~~~v~~~-kG~~ 223 (346)
-|++.|.+|.++.+.+++.+......+..-+. .++...+.+.+|-.-. .++.+.++.+ +|..
T Consensus 402 ~~~~~i~~P~~~~G~vm~~~~~rRG~~~~~~~~~~~~~~i~~~~Plae~~~~~~~~Lks~T~G~g 466 (595)
T TIGR01393 402 YVKATIITPTEYLGPIMTLCQEKRGVQTNMEYLDPNRVELIYEMPLAEIVYDFFDKLKSISRGYA 466 (595)
T ss_pred eEEEEEEccHHHHHHHHHHHHHcCCEEeCcEEcCCCeEEEEEEeccchhhhchhHHhhhhcCCEE
Confidence 37899999999999999999988776665555 3346778889998774 7778888888 7765
No 47
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=47.31 E-value=7.5 Score=29.88 Aligned_cols=29 Identities=21% Similarity=0.352 Sum_probs=25.1
Q ss_pred CccccccccccCChhHHHhhh-cchhhhhh
Q 042018 284 QNKCSTCNAYVGDAKQYRDHF-KSDWHKHN 312 (346)
Q Consensus 284 ~~~C~tC~~~F~~~~~~r~H~-kSdwHryN 312 (346)
-+.|.-|+.-|-+...|..|. |+..|.+|
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH~~~~~ 46 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAHGWLFG 46 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHhhhhhc
Confidence 678999999999999998885 77778776
No 48
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=45.94 E-value=10 Score=40.86 Aligned_cols=27 Identities=30% Similarity=0.874 Sum_probs=23.8
Q ss_pred CccccccccccCChhHHHhhh--cchhhh
Q 042018 284 QNKCSTCNAYVGDAKQYRDHF--KSDWHK 310 (346)
Q Consensus 284 ~~~C~tC~~~F~~~~~~r~H~--kSdwHr 310 (346)
...|.+||..|++.++.+.|. +.|||+
T Consensus 418 pnqC~~CG~R~~~~ee~sk~md~H~dwh~ 446 (579)
T KOG2071|consen 418 PNQCKSCGLRFDDSEERSKHMDIHDDWHR 446 (579)
T ss_pred cchhcccccccccchhhhhHhhhhhhhhh
Confidence 468999999999999999886 689995
No 49
>KOG0465 consensus Mitochondrial elongation factor [Translation, ribosomal structure and biogenesis]
Probab=45.53 E-value=24 Score=38.60 Aligned_cols=63 Identities=27% Similarity=0.343 Sum_probs=47.6
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
|.|.|+.|.++.+.+.+-|.+..+.|.+.+.+++...+.+++|=..-=.-..-|+.+ +|+.|.
T Consensus 636 M~Vevt~P~EfqG~Vi~~L~kR~a~I~~~d~~~~~~ti~A~VPL~~mfgYss~LRslTqGkgef 699 (721)
T KOG0465|consen 636 MNVEVTTPEEFQGTVIGDLNKRKAQITGIDSSEDYKTIKAEVPLNEMFGYSSELRSLTQGKGEF 699 (721)
T ss_pred eeeEEecchhhhhhhhhhhhhcccEEecccCCCceEEEEecccHHHHhhhhhhhhhhhcCcceE
Confidence 999999999999999999999988887777677777888888843332233344555 776654
No 50
>PRK12740 elongation factor G; Reviewed
Probab=45.03 E-value=36 Score=36.67 Aligned_cols=65 Identities=25% Similarity=0.338 Sum_probs=51.4
Q ss_pred ccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEE
Q 042018 160 RSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLE 224 (346)
Q Consensus 160 ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~e 224 (346)
-.-|.+.|.+|.++.+.++..|.+..+.+.+.+..++.+.+.+.+|-.---.+.+-|+.. +|.+.
T Consensus 582 EPi~~~eI~~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~i~a~~P~~e~~g~~~~Lr~~T~G~a~ 647 (668)
T PRK12740 582 EPIMKVEVSVPEEFVGDVIGDLSSRRGRILGMESRGGGDVVRAEVPLAEMFGYATDLRSLTQGRGS 647 (668)
T ss_pred cceEEEEEEechhhhhhHHHHHHhCCCeEeccccCCCCEEEEEEcCHHHhhchHHHHHHhcCCeEE
Confidence 344889999999999999999999888887666544458889999976666666667777 88874
No 51
>PRK12739 elongation factor G; Reviewed
Probab=43.32 E-value=39 Score=36.81 Aligned_cols=65 Identities=20% Similarity=0.261 Sum_probs=51.8
Q ss_pred ccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEE
Q 042018 160 RSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLE 224 (346)
Q Consensus 160 ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~e 224 (346)
-.-|++.|.+|.++.+.+++.|.+..+.|.+.+..++...+.+.+|---.-.+..-|+.. +|.+-
T Consensus 600 EPi~~~eI~~p~~~~g~v~~~L~~RRg~i~~~~~~~~~~~i~a~vP~~e~~g~~~~Lr~~T~G~a~ 665 (691)
T PRK12739 600 EPIMKVEVVTPEEYMGDVIGDLNRRRGQIQGMEARGGAQIVKAFVPLSEMFGYATDLRSATQGRAT 665 (691)
T ss_pred cceEEEEEEEchHhhhhHHHHHHhcCCeEECccccCCcEEEEEEeCHHHhhccHHHHHhhccCceE
Confidence 344899999999999999999999888888766555667888999977666666666777 88764
No 52
>TIGR01394 TypA_BipA GTP-binding protein TypA/BipA. This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.
Probab=43.02 E-value=54 Score=35.35 Aligned_cols=62 Identities=16% Similarity=0.221 Sum_probs=45.9
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecC-CCCeEEEEEEecCCCchhHHHHhhhc-CceEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDN-SGSQLSLICEMEPGLFRDCDTLLRNL-QGRLE 224 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~-~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~e 224 (346)
|++.|.+|.++.+.+++.|....+.+..-+. .+|...+.+.+|.--.-.+..-+... +|+..
T Consensus 397 ~~~~i~vp~e~~G~v~~~l~~RrG~~~~~~~~~~~~~~i~~~vP~~~l~~y~~~l~s~T~G~g~ 460 (594)
T TIGR01394 397 EELTIDVPEEHVGAVIEKLGKRKGEMVDMEPSGNGRTRLEFKIPSRGLIGFRTEFLTDTRGTGI 460 (594)
T ss_pred EEEEEEechHHHHHHHHHHHHhCCEEeccEECCCCEEEEEEEeChHHhhhHHHHHHhhcCCeEE
Confidence 7899999999999999999998877765554 34456688999964444444445555 88764
No 53
>COG1739 Uncharacterized conserved protein [Function unknown]
Probab=41.04 E-value=94 Score=29.12 Aligned_cols=109 Identities=11% Similarity=0.077 Sum_probs=72.8
Q ss_pred CCCCcHHHHHHHHhhcCc-ccCCCC--------CHHHHH---HHHHHHHHhhCCccccceEEEEEecCcchhHHHHHHHh
Q 042018 116 QRPYTISMIERLMHEIHF-AVDPNS--------SSKKQA---LEVIRELQKHFPIKRSPMRVGLTVPEQNISSLMEKLDA 183 (346)
Q Consensus 116 ~rP~p~~~IE~Am~e~~~-~Vdp~k--------sak~Qa---levIk~L~~~iPI~ra~m~l~v~vp~~~~~~~~~~l~~ 183 (346)
|.|+.......-|.++.. .++.+. ....=+ .++++.... + -.+..-.+.+.++-...+.+...+..
T Consensus 79 G~P~l~~l~~~~l~n~~~vvtRyFGGikLG~GGLvrAY~~~v~~~l~~~~~-~-e~~~~~~~~~~~~y~~l~~l~~~l~~ 156 (203)
T COG1739 79 GKPMLAVLEKSDLVNVLVVVVRYFGGIKLGTGGLVRAYANAVKSALEAAEA-I-EKKEAKANHVGCAYRILGLLERLLKQ 156 (203)
T ss_pred CCcHHHHHhhcCccceEEEEEeccCCEEcCCcccHHHHHHHHHHHHHHhhc-c-hhhhhhheeeccchhhhHHHHHHHHh
Confidence 677776666666665422 222222 222222 223332221 1 22344556677777788888888888
Q ss_pred hcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEEEE
Q 042018 184 WNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEIL 226 (346)
Q Consensus 184 ~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~evl 226 (346)
+...++..++++++..+.+.++...+..+..++... .|.+++.
T Consensus 157 ~~~~i~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~g~~~~~ 200 (203)
T COG1739 157 NDDDVEEARYSGGSVLLTVRFRHIVIEAVSRLLKGNHIGPDRFK 200 (203)
T ss_pred ccceEEEeeecCCeEEEEEEechhhHHHHHHHHhhccCCceEEe
Confidence 876777788888889999999999999999999998 8887654
No 54
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=40.67 E-value=14 Score=24.61 Aligned_cols=15 Identities=27% Similarity=0.381 Sum_probs=12.1
Q ss_pred HhcCCCCCCCCCcHH
Q 042018 108 QKTVNSETQRPYTIS 122 (346)
Q Consensus 108 ~~~VnP~T~rP~p~~ 122 (346)
.++.||.||.||--.
T Consensus 10 A~Y~DP~T~l~Y~n~ 24 (30)
T PF08265_consen 10 ARYRDPKTGLPYANS 24 (30)
T ss_pred ccccCCCCCCcccCH
Confidence 478999999998543
No 55
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=40.40 E-value=25 Score=24.36 Aligned_cols=32 Identities=31% Similarity=0.559 Sum_probs=19.6
Q ss_pred Ccccccccccc-CCh-hHHHhhhcchhhhhhhhh
Q 042018 284 QNKCSTCNAYV-GDA-KQYRDHFKSDWHKHNLKR 315 (346)
Q Consensus 284 ~~~C~tC~~~F-~~~-~~~r~H~kSdwHryNlKR 315 (346)
.+-|--|++.| .|. ...+.|=.+-=|+-|+++
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 57899999999 444 567999999999999986
No 56
>PRK13351 elongation factor G; Reviewed
Probab=39.38 E-value=54 Score=35.58 Aligned_cols=65 Identities=20% Similarity=0.333 Sum_probs=49.9
Q ss_pred ccceEEEEEecCcchhHHHHHHHhhcccceeecCCC-CeEEEEEEecCCCchhHHHHhhhc-CceEE
Q 042018 160 RSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSG-SQLSLICEMEPGLFRDCDTLLRNL-QGRLE 224 (346)
Q Consensus 160 ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~-~~~~~~~~I~pG~~r~l~~~v~~~-kG~~e 224 (346)
-.-|++.|.+|.++.+.++..|.+..+.|.+.+..+ +.+.+.+.+|-----.+..-|+.. +|.+.
T Consensus 599 EPi~~~eI~~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~~i~a~vP~~e~~~~~~~Lrs~T~G~a~ 665 (687)
T PRK13351 599 EPIMELEITVPTEHVGDVLGDLSQRRGRIEGTEPRGDGEVLVKAEAPLAELFGYATRLRSMTKGRGS 665 (687)
T ss_pred cceEEEEEEechHhhhhHHHHHHhCCcEEeceecCCCcEEEEEEEECHHHhhChHHHHHhhcCCceE
Confidence 344899999999999999999999888887666433 333488899877666666667777 88764
No 57
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=39.22 E-value=7.2 Score=25.75 Aligned_cols=19 Identities=26% Similarity=0.644 Sum_probs=14.5
Q ss_pred ccccccccccCChhHHHhhh
Q 042018 285 NKCSTCNAYVGDAKQYRDHF 304 (346)
Q Consensus 285 ~~C~tC~~~F~~~~~~r~H~ 304 (346)
++|--|+..| +...++.|-
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 5799999999 578888874
No 58
>PRK00007 elongation factor G; Reviewed
Probab=39.06 E-value=50 Score=36.02 Aligned_cols=64 Identities=22% Similarity=0.348 Sum_probs=50.4
Q ss_pred cceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEE
Q 042018 161 SPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLE 224 (346)
Q Consensus 161 a~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~e 224 (346)
.-|++.|.+|.++.+.+++.|.+..+.|...+..++...+.+.+|---.-.+..-|+.. +|.+-
T Consensus 604 Pi~~~eI~~p~~~~g~v~~~L~~RRg~i~~~~~~~~~~~i~a~vP~~e~~g~~~~Lrs~T~G~a~ 668 (693)
T PRK00007 604 PIMKVEVVTPEEYMGDVIGDLNSRRGQIEGMEDRGGAKVIRAEVPLSEMFGYATDLRSMTQGRAT 668 (693)
T ss_pred CcEEEEEEechhhhhhHHHHHHhCCCeEecccccCCcEEEEEEcCHHHhhccHHHHHhhcCCceE
Confidence 44899999999999999999999887777655445567888899876666666667777 88764
No 59
>PRK07560 elongation factor EF-2; Reviewed
Probab=38.05 E-value=41 Score=36.93 Aligned_cols=65 Identities=14% Similarity=0.255 Sum_probs=49.9
Q ss_pred ccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEE
Q 042018 160 RSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLE 224 (346)
Q Consensus 160 ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~e 224 (346)
-.-|++.|.+|.++.+.++..|.+..+.|...+..++...+.+.+|---.-.+..-|+.. +|+..
T Consensus 625 EPi~~veI~~p~~~~g~v~~~L~~rrg~i~~~~~~~~~~~I~a~vP~~e~~gy~~~Lrs~T~G~~~ 690 (731)
T PRK07560 625 EPIQKVDINVPQDYMGAVTREIQGRRGKILDMEQEGDMAIIEAEAPVAEMFGFAGEIRSATEGRAL 690 (731)
T ss_pred ecEEEEEEEecHHHhhHHHHHHHhcCCeeeeeecCCCcEEEEEEEehHHhcCCchHHHhhCcCCce
Confidence 345899999999999999999999888887665544567788899876555556666776 77664
No 60
>PRK10218 GTP-binding protein; Provisional
Probab=37.63 E-value=72 Score=34.62 Aligned_cols=63 Identities=16% Similarity=0.161 Sum_probs=47.1
Q ss_pred eEEEEEecCcchhHHHHHHHhhcccceeecC-CCCeEEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 163 MRVGLTVPEQNISSLMEKLDAWNASIVSKDN-SGSQLSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 163 m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~-~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
+++.|.+|.++.+.+++.|......+..-+. .+|...+.+.||.--.-.+..-+... +|+.-.
T Consensus 401 ~~v~i~vP~e~~G~V~~~l~~RrG~~~~m~~~~~~~~~l~~~vP~~~l~~y~~~l~s~T~G~g~~ 465 (607)
T PRK10218 401 ENVTLDVEEQHQGSVMQALGERKGDLKNMNPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLL 465 (607)
T ss_pred EEEEEEechhhHHHHHHHHHhcCCEEeccEECCCCEEEEEEEcCHHHHhhHHHHhhhhCCCeEEE
Confidence 7889999999999999999998777765554 34556789999975554555555555 887643
No 61
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=37.35 E-value=30 Score=24.30 Aligned_cols=22 Identities=27% Similarity=0.551 Sum_probs=15.4
Q ss_pred Ccccccccccc--CChhHHHhhhc
Q 042018 284 QNKCSTCNAYV--GDAKQYRDHFK 305 (346)
Q Consensus 284 ~~~C~tC~~~F--~~~~~~r~H~k 305 (346)
..+|.+|+..+ .+.++-+.|-+
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~ 36 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKK 36 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHH
Confidence 56799999876 46666666643
No 62
>PF08793 2C_adapt: 2-cysteine adaptor domain; InterPro: IPR014901 The virus-specific 2-cysteine adaptor is found fused to OTU/A20-like peptidases and S/T protein kinases. The associations to these proteins indicate that they might function as viral adaptors connecting the kinases and OTU/A20 peptidases to specific targets [].
Probab=35.46 E-value=25 Score=24.41 Aligned_cols=18 Identities=28% Similarity=0.134 Sum_probs=14.7
Q ss_pred HHHHHhcCCCCCCCCCcH
Q 042018 104 TIVMQKTVNSETQRPYTI 121 (346)
Q Consensus 104 ~~Ia~~~VnP~T~rP~p~ 121 (346)
.|...-.+||.||||+-+
T Consensus 5 ~f~~np~~NP~Tgr~Ik~ 22 (37)
T PF08793_consen 5 EFHRNPTVNPITGRKIKP 22 (37)
T ss_pred HHHhCCCCCCCCCCcCCC
Confidence 467788899999999754
No 63
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=35.34 E-value=25 Score=22.07 Aligned_cols=20 Identities=20% Similarity=0.476 Sum_probs=16.1
Q ss_pred ccccccccccCChhHHHhhhc
Q 042018 285 NKCSTCNAYVGDAKQYRDHFK 305 (346)
Q Consensus 285 ~~C~tC~~~F~~~~~~r~H~k 305 (346)
..|..|+-.| ..+.+..|.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4699999999 5688888864
No 64
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=34.73 E-value=29 Score=31.78 Aligned_cols=40 Identities=33% Similarity=0.536 Sum_probs=32.8
Q ss_pred cccccccc-ccCChhHHHhhhcchhhhhhhhhhhcCCCCCCh
Q 042018 285 NKCSTCNA-YVGDAKQYRDHFKSDWHKHNLKRKTRQLPPLTV 325 (346)
Q Consensus 285 ~~C~tC~~-~F~~~~~~r~H~kSdwHryNlKRk~~gl~plse 325 (346)
|+|+.|.- +|. ..+.-.|+.|.+|+=-++.--..||-.+-
T Consensus 1 F~Cs~CKfrtf~-~~ei~~HleS~~H~E~~~~i~tkl~k~~~ 41 (165)
T PF04988_consen 1 FTCSFCKFRTFE-EKEIEKHLESKFHKETLKYIQTKLPKKTM 41 (165)
T ss_pred Cccceeeeeccc-HHHHHHHHccchHHHHHHHHHhcCChHHH
Confidence 68999975 565 68899999999999999987777876554
No 65
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=34.53 E-value=23 Score=26.78 Aligned_cols=24 Identities=21% Similarity=0.624 Sum_probs=16.6
Q ss_pred cCccccccccccCChhHHHhhhcc
Q 042018 283 KQNKCSTCNAYVGDAKQYRDHFKS 306 (346)
Q Consensus 283 ~~~~C~tC~~~F~~~~~~r~H~kS 306 (346)
...+|..|+..+.....+|.|...
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHH
T ss_pred CCCCCCcchhhccchhhHHHHHHH
Confidence 578899999999999999998753
No 66
>PHA00732 hypothetical protein
Probab=34.36 E-value=27 Score=27.96 Aligned_cols=22 Identities=18% Similarity=0.318 Sum_probs=18.1
Q ss_pred ccccccccccCChhHHHhhhcc
Q 042018 285 NKCSTCNAYVGDAKQYRDHFKS 306 (346)
Q Consensus 285 ~~C~tC~~~F~~~~~~r~H~kS 306 (346)
+.|..|+..|.+...++.|-+.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhc
Confidence 5688899889888888888763
No 67
>TIGR00484 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Probab=34.04 E-value=57 Score=35.55 Aligned_cols=64 Identities=25% Similarity=0.327 Sum_probs=49.8
Q ss_pred cceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEE
Q 042018 161 SPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLE 224 (346)
Q Consensus 161 a~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~e 224 (346)
.-|++.|.+|.++.+.+++.|.+..+.|...+..++...+.+.+|---.-.+..-|+.. +|..-
T Consensus 601 Pi~~~eI~~p~~~~g~v~~~L~~rrg~i~~~~~~~~~~~I~a~vP~~e~~g~~~~Lrs~T~G~~~ 665 (689)
T TIGR00484 601 PIMKVEVEVPEEYMGDVMGDLSSRRGIIEGMEARGNVQKIKAEVPLSEMFGYATDLRSFTQGRGT 665 (689)
T ss_pred CcEEEEEEecHHHhHhHHHHHHhcCCeEecccccCCcEEEEEEeCHHHHhChHHHHHHhcCCceE
Confidence 44889999999999999999999888777655445567888888876665666666777 88764
No 68
>PF13333 rve_2: Integrase core domain
Probab=32.19 E-value=22 Score=25.64 Aligned_cols=31 Identities=13% Similarity=0.173 Sum_probs=22.0
Q ss_pred cccCChhHHHhhhcchhhhhhhhhhhcCCCCC
Q 042018 292 AYVGDAKQYRDHFKSDWHKHNLKRKTRQLPPL 323 (346)
Q Consensus 292 ~~F~~~~~~r~H~kSdwHryNlKRk~~gl~pl 323 (346)
..|.+.++++..-..-.+-||-+| +.|++|+
T Consensus 15 ~~~~t~eel~~~I~~YI~~yN~~R-l~~lsP~ 45 (52)
T PF13333_consen 15 QKFKTREELKQAIDEYIDYYNNER-LKGLSPV 45 (52)
T ss_pred cccchHHHHHHHHHHHHHHhccCC-CCCcCHH
Confidence 355666777766666666689998 7788776
No 69
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=32.12 E-value=25 Score=37.12 Aligned_cols=32 Identities=31% Similarity=0.465 Sum_probs=30.2
Q ss_pred CccccccccccCChhHHHhhhcchhhhhhhhh
Q 042018 284 QNKCSTCNAYVGDAKQYRDHFKSDWHKHNLKR 315 (346)
Q Consensus 284 ~~~C~tC~~~F~~~~~~r~H~kSdwHryNlKR 315 (346)
.+.|-.|+.+|.+..++.-|=.|--|+=||-+
T Consensus 292 ~lyC~vCnKsFKseKq~kNHEnSKKHkenv~e 323 (508)
T KOG0717|consen 292 VLYCVVCNKSFKSEKQLKNHENSKKHKENVAE 323 (508)
T ss_pred ceEEeeccccccchHHHHhhHHHHHHHHHHHH
Confidence 48999999999999999999999999999874
No 70
>PLN00116 translation elongation factor EF-2 subunit; Provisional
Probab=31.86 E-value=48 Score=37.15 Aligned_cols=66 Identities=12% Similarity=0.084 Sum_probs=51.0
Q ss_pred ccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCe--EEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 160 RSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQ--LSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 160 ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~--~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
-.-|++.|++|.++.+.+++-|.+..+.|...+..++. +.+...+|-.---.+..-|+.. +|+...
T Consensus 727 EPi~~veI~~p~~~~G~V~~dL~~RRG~i~~~~~~~~t~~~~I~A~vPl~e~~gy~~~LRs~T~G~g~~ 795 (843)
T PLN00116 727 EPVYLVEIQAPEQALGGIYSVLNQKRGHVFEEMQRPGTPLYNIKAYLPVIESFGFSGTLRAATSGQAFP 795 (843)
T ss_pred eceeEEEEEccHHHHhHHHHHHHhcCCccceeeecCCCceEEEEEEeeHHHHcCCCHHHHhhCCCCCeE
Confidence 34489999999999999999999988888766653443 6788999976666666666777 887643
No 71
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=31.00 E-value=18 Score=40.61 Aligned_cols=26 Identities=23% Similarity=0.483 Sum_probs=22.9
Q ss_pred cCccccccccccCChhHHHhhhcchhhh
Q 042018 283 KQNKCSTCNAYVGDAKQYRDHFKSDWHK 310 (346)
Q Consensus 283 ~~~~C~tC~~~F~~~~~~r~H~kSdwHr 310 (346)
..|+|..||-.|.+...+|.||- -||
T Consensus 632 RPFkCKiCgRAFtTkGNLkaH~~--vHk 657 (958)
T KOG1074|consen 632 RPFKCKICGRAFTTKGNLKAHMS--VHK 657 (958)
T ss_pred Cccccccccchhccccchhhccc--ccc
Confidence 47999999999999999999995 454
No 72
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=30.63 E-value=1.1e+02 Score=23.90 Aligned_cols=62 Identities=23% Similarity=0.294 Sum_probs=40.3
Q ss_pred ccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc--CceEEEE
Q 042018 160 RSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL--QGRLEIL 226 (346)
Q Consensus 160 ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~--kG~~evl 226 (346)
|.-|-++|..+......+...+..|++.|.. .+.+++.+.+. |.-..++.+++.+ -|-+|+.
T Consensus 2 rEl~LiKV~~~~~~r~ei~~l~~~f~a~ivd--~~~~~~iie~t---G~~~kid~fi~~l~~~gi~Ei~ 65 (75)
T PF10369_consen 2 RELALIKVKATPENRSEILQLAEIFRARIVD--VSPDSIIIELT---GTPEKIDAFIKLLKPFGILEIA 65 (75)
T ss_dssp EEEEEEEEE-SCHHHHHHHHHHHHTT-EEEE--EETTEEEEEEE---E-HHHHHHHHHHSTGGGEEEEE
T ss_pred eEEEEEEEECCccCHHHHHHHHHHhCCEEEE--ECCCEEEEEEc---CCHHHHHHHHHHhhhcCCEEEE
Confidence 5667788888778888899999999987663 44566666665 4455566666655 4555543
No 73
>PF09080 K-cyclin_vir_C: K cyclin, C terminal; InterPro: IPR015164 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This domain adopts a secondary structure consisting of a five alpha-helix cyclin fold. Interaction with cyclin dependent kinases (CDKs) at a PSTAIRE sequence motif within the catalytic cleft of CDK results in the regulation of CDK activity []. ; PDB: 1G3N_C.
Probab=30.38 E-value=54 Score=27.43 Aligned_cols=60 Identities=15% Similarity=0.186 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCCCcHHHHHHH---HhhcCcccCCCCCHHHHHHHHHHHHHhhCC
Q 042018 93 TQFSNQFRDIATIVMQKTVNSETQRPYTISMIERL---MHEIHFAVDPNSSSKKQALEVIRELQKHFP 157 (346)
Q Consensus 93 ~~le~~~r~I~~~Ia~~~VnP~T~rP~p~~~IE~A---m~e~~~~Vdp~ksak~QalevIk~L~~~iP 157 (346)
+++.....++.+.|++-.|||.||- +|++.|-.| |=..+-.+ |.....-.++.+|.+.+.
T Consensus 20 e~L~~~H~~V~~~v~KAiV~P~TG~-Lp~SlvaAA~CAL~~~~~~~----P~~~~~~~~~~~LA~~~G 82 (106)
T PF09080_consen 20 EQLFAWHSEVVESVHKAIVNPKTGG-LPPSLVAAAGCALFSLGAAA----PPDTHSGGVVPQLAEALG 82 (106)
T ss_dssp TTHHHHHHHHHHHHHHHHCSTTGGG-S-HHHHHHHHHHHHS-GGGS------------HHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHhcCcccCC-CCHHHHHHhhhhhccccccC----CCccccccchHHHHHHhC
Confidence 4577788999999999999999996 788888876 32233333 222333455566655443
No 74
>COG3758 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.79 E-value=29 Score=32.54 Aligned_cols=94 Identities=16% Similarity=0.213 Sum_probs=54.5
Q ss_pred CC-ccccCCCCceecceeEEEEEeeCCeEEEEEeecch----hHHhhccCCCCchhhhhccccccccCCCccCChhhhhh
Q 042018 1 MS-KTLVQPVGQKRLTNVAVVRLKKHGMRFEIACYKNK----VLSWRSQVEKDLDEVLQSHTVYSNVSKGILAKSKDLIQ 75 (346)
Q Consensus 1 ms-~~i~~P~~q~~LtNvavVRlkk~GkrFEIacypnk----v~~~R~G~e~dldeVLq~~~VF~NvsKG~~A~~~dL~k 75 (346)
|| |+|-.|.+-.++. .=.-+|..=||+|||.- -++||--. -. =..+|.+..=..+..
T Consensus 1 mt~m~il~~~dy~~mP-----WkNgGG~T~EIav~P~~a~~~dF~WRiS~----At---------Va~~G~FS~fpGidR 62 (193)
T COG3758 1 MTMMRILRAEDYRRMP-----WKNGGGETNEIAVYPEGAAKRDFDWRISI----AT---------VAADGPFSLFPGIDR 62 (193)
T ss_pred CcceEeecccccccCC-----cccCCCceEEEEEcCCCccccccceEEEE----Ee---------eccCCCccccCCcce
Confidence 44 6666777766665 22237999999999985 45676431 11 112444443334444
Q ss_pred h-hhcccccccccHHHHHHHHHHHHHHHHHHHHHhcCC
Q 042018 76 H-LILEKGELQVAGKERETQFSNQFRDIATIVMQKTVN 112 (346)
Q Consensus 76 a-~IL~kGElQvs~~ER~~~le~~~r~I~~~Ia~~~Vn 112 (346)
. -+|+.|.+-|+...|.......=.|...+=+.-+|+
T Consensus 63 ~lsvLeG~gm~L~~~~~~~~~l~~~~qp~aF~gD~~v~ 100 (193)
T COG3758 63 ILSVLEGGGMTLSSAGRAPVVLLRPLQPFAFAGDVPVH 100 (193)
T ss_pred EEEEEecCceEEecCCCccceecCCCCcccccCCceEE
Confidence 4 788888888888877665544444444443333333
No 75
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=28.90 E-value=33 Score=25.33 Aligned_cols=25 Identities=28% Similarity=0.650 Sum_probs=20.9
Q ss_pred cCccccccccccCChhHHHhhhcchhhh
Q 042018 283 KQNKCSTCNAYVGDAKQYRDHFKSDWHK 310 (346)
Q Consensus 283 ~~~~C~tC~~~F~~~~~~r~H~kSdwHr 310 (346)
++-.|-.|.+.|++ +..|-+|+=|+
T Consensus 4 k~GYCE~C~~ky~~---l~~Hi~s~~Hr 28 (49)
T PF07535_consen 4 KPGYCENCRVKYDD---LEEHIQSEKHR 28 (49)
T ss_pred CCccCccccchhhh---HHHHhCCHHHH
Confidence 35679999999986 66889999995
No 76
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.79 E-value=2.4e+02 Score=20.69 Aligned_cols=56 Identities=13% Similarity=0.316 Sum_probs=38.9
Q ss_pred EEEEEecCcc--hhHHHHHHHhhcccceeecC---CCCeEEEEEEecCCCch-hHHHHhhhc
Q 042018 164 RVGLTVPEQN--ISSLMEKLDAWNASIVSKDN---SGSQLSLICEMEPGLFR-DCDTLLRNL 219 (346)
Q Consensus 164 ~l~v~vp~~~--~~~~~~~l~~~~~~v~~~e~---~~~~~~~~~~I~pG~~r-~l~~~v~~~ 219 (346)
++.+..+... ...+...|.+.+..+..-.. .++...+.+.++-.... .+..+++++
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~~~~~l~~l~~~L 63 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTSTMNGDIDELLEEL 63 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCchHHHHHHHHHHH
Confidence 5677777653 55677888888776654321 34667888888877776 888888877
No 77
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=28.52 E-value=32 Score=40.45 Aligned_cols=38 Identities=24% Similarity=0.438 Sum_probs=33.1
Q ss_pred cCccccccccccCChhHHHhhhcchhhhhhhhhhhcCC
Q 042018 283 KQNKCSTCNAYVGDAKQYRDHFKSDWHKHNLKRKTRQL 320 (346)
Q Consensus 283 ~~~~C~tC~~~F~~~~~~r~H~kSdwHryNlKRk~~gl 320 (346)
..+.|..|+++|.....+-.|.+|+.|+-|+.-...+.
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~ 554 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENA 554 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhcc
Confidence 47899999999999999999999999999987655443
No 78
>PF10739 DUF2550: Protein of unknown function (DUF2550); InterPro: IPR019675 The function of the proteins in this family is not known, though most members are annotated as either secreted or membrane proteins.
Probab=28.43 E-value=77 Score=27.59 Aligned_cols=28 Identities=18% Similarity=0.319 Sum_probs=24.1
Q ss_pred ceeEEEEEeeCCeEEEEEeecchhHHhh
Q 042018 15 TNVAVVRLKKHGMRFEIACYKNKVLSWR 42 (346)
Q Consensus 15 tNvavVRlkk~GkrFEIacypnkv~~~R 42 (346)
.++.||++..+|..||+|..|.....+.
T Consensus 92 ~~~~vv~~~~~~~~~ElAm~~~a~tgf~ 119 (129)
T PF10739_consen 92 PDAVVVECRSGGEEYELAMDPGALTGFV 119 (129)
T ss_pred CCeEEEEEEeCCcEEEEEeCcchHHHHH
Confidence 4789999999999999999998775544
No 79
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=28.40 E-value=19 Score=33.76 Aligned_cols=41 Identities=24% Similarity=0.442 Sum_probs=0.0
Q ss_pred CCCcccCccccccc-cccCChhHHHhhhcchhhhhhhhhhhcCCCC
Q 042018 278 TEGKVKQNKCSTCN-AYVGDAKQYRDHFKSDWHKHNLKRKTRQLPP 322 (346)
Q Consensus 278 ~~~k~~~~~C~tC~-~~F~~~~~~r~H~kSdwHryNlKRk~~gl~p 322 (346)
|.. ..|.|-.|| .++.-+..+..||.-.=|.|.||+ -|.|+
T Consensus 97 GL~--~ey~CEICGN~~Y~GrkaFekHF~E~rH~~Glrc--LGI~n 138 (196)
T PF11931_consen 97 GLG--VEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRC--LGIPN 138 (196)
T ss_dssp ----------------------------------------------
T ss_pred CCC--CeeeeEeCCCcceecHHHHHHhcChhHHHccChh--cCCCC
Confidence 455 389999996 567789999999999999999985 56653
No 80
>cd01247 PH_GPBP Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. The GPBP protein is a kinase that phosphorylates an N-terminal region of the alpha 3 chain of type IV collagen , which is commonly known as the goodpasture antigen. It has has an N-terminal PH domain and a C-terminal START domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cyt
Probab=26.28 E-value=22 Score=28.63 Aligned_cols=37 Identities=22% Similarity=0.208 Sum_probs=28.1
Q ss_pred CCCCceecceeEEEEEeeCCeEEEEEeecchhHHhhc
Q 042018 7 QPVGQKRLTNVAVVRLKKHGMRFEIACYKNKVLSWRS 43 (346)
Q Consensus 7 ~P~~q~~LtNvavVRlkk~GkrFEIacypnkv~~~R~ 43 (346)
.|.|.|.|++++|+.-.....+|||.+.++.++-.+.
T Consensus 39 ~~~G~I~L~~~~i~~~~~~~~~F~i~~~~~r~~~L~A 75 (91)
T cd01247 39 GCRGSIFLKKAIIAAHEFDENRFDISVNENVVWYLRA 75 (91)
T ss_pred CCcEEEECcccEEEcCCCCCCEEEEEeCCCeEEEEEe
Confidence 5889999999888866556689999987765544443
No 81
>TIGR00490 aEF-2 translation elongation factor aEF-2. This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.
Probab=26.19 E-value=68 Score=35.23 Aligned_cols=65 Identities=14% Similarity=0.240 Sum_probs=49.1
Q ss_pred ccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhhhc-CceEE
Q 042018 160 RSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLRNL-QGRLE 224 (346)
Q Consensus 160 ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~~~-kG~~e 224 (346)
-.-|++.|.+|.++.+.++.-|.+..+.|...+..++...+...+|-----.+..-|+.. +|+..
T Consensus 623 EPi~~~ei~~p~~~~g~v~~~L~~RRg~i~~~~~~~~~~~I~A~vP~~e~fgy~~~Lrs~T~G~a~ 688 (720)
T TIGR00490 623 EPYQKVFINVPQDMMGAATREIQNRRGQILEMKQEGDMVTIIAKAPVAEMFGFAGAIRGATSGRCL 688 (720)
T ss_pred cceEEEEEEccHHHHhHHHHHHhhCCceeeeeccCCCcEEEEEEEehHHhcCCcHHHHhhCCCCce
Confidence 344899999999999999999999888887655444556788888865555555566777 77764
No 82
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=25.24 E-value=42 Score=20.11 Aligned_cols=21 Identities=24% Similarity=0.570 Sum_probs=14.4
Q ss_pred ccccccccccCChhHHHhhhcc
Q 042018 285 NKCSTCNAYVGDAKQYRDHFKS 306 (346)
Q Consensus 285 ~~C~tC~~~F~~~~~~r~H~kS 306 (346)
+.|..|+-.-. ...++.|.+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 46999986555 7888888764
No 83
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=24.82 E-value=33 Score=21.47 Aligned_cols=14 Identities=29% Similarity=0.646 Sum_probs=11.8
Q ss_pred cCccccccccccCC
Q 042018 283 KQNKCSTCNAYVGD 296 (346)
Q Consensus 283 ~~~~C~tC~~~F~~ 296 (346)
..+.|..|+..|.+
T Consensus 13 k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 13 KPYKCPYCGKSFSN 26 (26)
T ss_dssp SSEEESSSSEEESS
T ss_pred CCCCCCCCcCeeCc
Confidence 48999999998863
No 84
>PF12907 zf-met2: Zinc-binding
Probab=24.29 E-value=37 Score=24.09 Aligned_cols=22 Identities=18% Similarity=0.460 Sum_probs=17.3
Q ss_pred cccccccccc---CChhHHHhhhcc
Q 042018 285 NKCSTCNAYV---GDAKQYRDHFKS 306 (346)
Q Consensus 285 ~~C~tC~~~F---~~~~~~r~H~kS 306 (346)
..|.+|..+| .+...+++||-+
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~en 26 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAEN 26 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHc
Confidence 4699998555 567889999876
No 85
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=23.50 E-value=3.5e+02 Score=25.59 Aligned_cols=104 Identities=16% Similarity=0.258 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHHHHHH---HHhcCCCCCCCCCcHHHHHHHHhhcCcccCCCCCHHHHHHHHHHHHHhhCCccccceEE
Q 042018 89 KERETQFSNQFRDIATIV---MQKTVNSETQRPYTISMIERLMHEIHFAVDPNSSSKKQALEVIRELQKHFPIKRSPMRV 165 (346)
Q Consensus 89 ~ER~~~le~~~r~I~~~I---a~~~VnP~T~rP~p~~~IE~Am~e~~~~Vdp~ksak~QalevIk~L~~~iPI~ra~m~l 165 (346)
.||...+++++++|++.. +++.+....+.-.--..|+..+++++ ...+.+.|++.-... ....| +.+.-
T Consensus 112 ~E~~~a~~~l~~ei~~la~~~A~kil~~~~d~~~~~~lid~~i~~l~----~l~~~~~~~l~~~~~-~~~~~---~~v~s 183 (246)
T TIGR03321 112 REQAALSDELRRRTGAEVFAIARKVLTDLADTDLEERMVDVFVQRLR----TLDPDEKAALAEALA-DSGNP---VLVRS 183 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhh----cCCHHHHHHHHHHHh-CCCCc---eEEEe
Confidence 457777777777776643 34433322211112266777776642 223445555522211 11122 22222
Q ss_pred EEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCc
Q 042018 166 GLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLF 209 (346)
Q Consensus 166 ~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~ 209 (346)
.+.++.+...++...|.+.. +..+.+.+.++|.+.
T Consensus 184 a~~l~~~~~~~i~~~l~~~~---------~~~v~~~~~vdp~li 218 (246)
T TIGR03321 184 AFELPEEQREQIRDTIRETL---------GPEIRLRFQTEPDLI 218 (246)
T ss_pred cCCCCHHHHHHHHHHHHHHH---------CCCeeEEeeeCchhc
Confidence 22233334445555554432 235667777777654
No 86
>PTZ00416 elongation factor 2; Provisional
Probab=22.35 E-value=1.1e+02 Score=34.46 Aligned_cols=66 Identities=12% Similarity=0.166 Sum_probs=49.1
Q ss_pred ccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCe--EEEEEEecCCCchhHHHHhhhc-CceEEE
Q 042018 160 RSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQ--LSLICEMEPGLFRDCDTLLRNL-QGRLEI 225 (346)
Q Consensus 160 ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~--~~~~~~I~pG~~r~l~~~v~~~-kG~~ev 225 (346)
-.-|++.|.+|.++.+.++..|.+..+.|...+..++. ..+...+|-----.+..-|+.. +|++-.
T Consensus 720 EPi~~veI~~p~~~lg~V~~dL~~RRG~i~~~~~~~~t~~~~I~a~vP~~e~~gy~~~LRs~T~G~g~~ 788 (836)
T PTZ00416 720 EPMFLVDITAPEDAMGGIYSVLNRRRGVVIGEEQRPGTPLSNIKAYLPVAESFGFTAALRAATSGQAFP 788 (836)
T ss_pred eeeEEEEEEEcHHHHhHHHHHHHhcCCCccCcccCCCCCcEEEEEEEehHHhcCCCHHHHhhCcCCceE
Confidence 34589999999999999999999988788766654444 6788888865555555555666 776543
No 87
>PRK04435 hypothetical protein; Provisional
Probab=21.79 E-value=5.3e+02 Score=22.57 Aligned_cols=69 Identities=16% Similarity=0.379 Sum_probs=42.9
Q ss_pred cccceEEEEEecCc--chhHHHHHHHhhcccceeecC---CCCeEEEEEEecCCCch-hHHHHhhhc---Cc--eEEEEE
Q 042018 159 KRSPMRVGLTVPEQ--NISSLMEKLDAWNASIVSKDN---SGSQLSLICEMEPGLFR-DCDTLLRNL---QG--RLEILA 227 (346)
Q Consensus 159 ~ra~m~l~v~vp~~--~~~~~~~~l~~~~~~v~~~e~---~~~~~~~~~~I~pG~~r-~l~~~v~~~---kG--~~evl~ 227 (346)
+...+.+.+.++.. ....+...|.+.+.+|..-.. .+|...+.+.|+-.... .+.+++.++ +| +++++.
T Consensus 66 ~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~i~~ 145 (147)
T PRK04435 66 KGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSMEGDIDELLEKLRNLDGVEKVELIG 145 (147)
T ss_pred CCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCChHHHHHHHHHHHHcCCCcEEEEEEe
Confidence 34556777777764 355677888888877754321 34556666666655554 777777766 66 455554
No 88
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=21.71 E-value=46 Score=32.24 Aligned_cols=21 Identities=19% Similarity=0.381 Sum_probs=20.1
Q ss_pred CccccccccccCChhHHHhhh
Q 042018 284 QNKCSTCNAYVGDAKQYRDHF 304 (346)
Q Consensus 284 ~~~C~tC~~~F~~~~~~r~H~ 304 (346)
-+.|-.||+.|.|.+.+-+|+
T Consensus 239 h~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 239 HYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ceEEEEeccccCCHHHHHHhC
Confidence 789999999999999999997
No 89
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=21.31 E-value=68 Score=23.28 Aligned_cols=28 Identities=14% Similarity=0.313 Sum_probs=21.9
Q ss_pred CccccccccccCChhHHHhhhcchhhhhhh
Q 042018 284 QNKCSTCNAYVGDAKQYRDHFKSDWHKHNL 313 (346)
Q Consensus 284 ~~~C~tC~~~F~~~~~~r~H~kSdwHryNl 313 (346)
.|+|..|+..| |...+..|+.. -|+..-
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~-~H~~~~ 29 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCED-EHRSES 29 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHh-HCcCCC
Confidence 68999999966 57899999976 466543
No 90
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=21.12 E-value=2.6e+02 Score=25.31 Aligned_cols=50 Identities=14% Similarity=0.287 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHhhCCccccceEEEEEecCcchhHHHHHHHhhccccee
Q 042018 141 SKKQALEVIRELQKHFPIKRSPMRVGLTVPEQNISSLMEKLDAWNASIVS 190 (346)
Q Consensus 141 ak~QalevIk~L~~~iPI~ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~ 190 (346)
+..=|-|++++|.+.+|=.+..+.|.-..|..++..+...|+.||=-|.+
T Consensus 33 a~~iA~D~v~qL~~~ypPA~Tt~~l~q~~~D~Fg~aL~~aLR~~GYaV~e 82 (151)
T PRK13883 33 QQKLATDAVQQLATLYPPAQTRFELQQPTPDAFGQALVKALRDKGYALLE 82 (151)
T ss_pred HHHHHHHHHHHHHHhCCCcceEEEEecCCCcHHHHHHHHHHHHcCeEEEe
Confidence 34568899999999998777666666666767888899999999955543
No 91
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=20.90 E-value=27 Score=39.28 Aligned_cols=24 Identities=17% Similarity=0.513 Sum_probs=21.8
Q ss_pred cCccccccccccCChhHHHhhhcc
Q 042018 283 KQNKCSTCNAYVGDAKQYRDHFKS 306 (346)
Q Consensus 283 ~~~~C~tC~~~F~~~~~~r~H~kS 306 (346)
..|.|+.|+-.|.+...++-||.-
T Consensus 380 RPfqCnvCG~~FSTkGNLKvH~~r 403 (958)
T KOG1074|consen 380 RPFQCNVCGNRFSTKGNLKVHFQR 403 (958)
T ss_pred CCeeecccccccccccceeeeeee
Confidence 478999999999999999999864
No 92
>PF08133 Nuclease_act: Anticodon nuclease activator family; InterPro: IPR012585 This family consists of the anticodon nuclease activator proteins. Pre-existing host tRNAs are reprocessed during Bacteriophage T4 infection of certain Escherichia coli strains. In this pathway, tRNA(Lys) is cleaved 5, by the anticodon nuclease to the wobble base and is later restored in polynucleotide kinase and RNA ligase reactions [].; GO: 0004518 nuclease activity, 0050792 regulation of viral reproduction
Probab=20.81 E-value=38 Score=21.82 Aligned_cols=10 Identities=50% Similarity=0.833 Sum_probs=7.9
Q ss_pred hhhhhhhhhh
Q 042018 307 DWHKHNLKRK 316 (346)
Q Consensus 307 dwHryNlKRk 316 (346)
.|||+|||-+
T Consensus 11 qfyr~nlk~~ 20 (26)
T PF08133_consen 11 QFYRHNLKTK 20 (26)
T ss_pred HHHHhhcccc
Confidence 4999999853
No 93
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=20.21 E-value=4.9e+02 Score=23.87 Aligned_cols=59 Identities=17% Similarity=0.197 Sum_probs=44.8
Q ss_pred CccccceEEEEEecCcchhHHHHHHHhhcccceeecCCCCeEEEEEEecCCCchhHHHHhh
Q 042018 157 PIKRSPMRVGLTVPEQNISSLMEKLDAWNASIVSKDNSGSQLSLICEMEPGLFRDCDTLLR 217 (346)
Q Consensus 157 PI~ra~m~l~v~vp~~~~~~~~~~l~~~~~~v~~~e~~~~~~~~~~~I~pG~~r~l~~~v~ 217 (346)
+++|.-|-+.+..++...+.+.....-+.+++. |-+..++.+.+.=+|+-...+.+++.
T Consensus 83 ~veRel~LiKv~~~~~~R~ei~~~~~ifr~~vv--Dvs~~~~~~eltG~~~ki~afi~~l~ 141 (163)
T COG0440 83 HVERELALIKVSAEGSERGEIARITEIFRASVV--DVSPESLTIELTGDEEKIEAFIRLLR 141 (163)
T ss_pred hhheeeEEEEEecCccchHHHHHHHHHhCceEE--ecCcceEEEEEeCChHHHHHHHHHhc
Confidence 488999999999998877778888877877655 34456777777777777766666665
No 94
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=20.01 E-value=52 Score=30.20 Aligned_cols=36 Identities=28% Similarity=0.584 Sum_probs=29.2
Q ss_pred CcccCccccccccccC-ChhHHHhhhcchhhhhhhhh
Q 042018 280 GKVKQNKCSTCNAYVG-DAKQYRDHFKSDWHKHNLKR 315 (346)
Q Consensus 280 ~k~~~~~C~tC~~~F~-~~~~~r~H~kSdwHryNlKR 315 (346)
.||....|..|++-.. .......|-+|--|.+|-|+
T Consensus 87 ~KVEa~hCsACd~~IP~~~~~vQ~Hl~S~~H~~Nrr~ 123 (165)
T PF04988_consen 87 KKVEAAHCSACDVFIPMQHSSVQKHLKSQDHNKNRRA 123 (165)
T ss_pred HHHHHhhhhHhhhhccCcHHHHHHHhccHHHHhhHHH
Confidence 4456789999998764 46778999999999999773
Done!