Query 013049
Match_columns 450
No_of_seqs 365 out of 1845
Neff 8.3
Searched_HMMs 46136
Date Thu Mar 28 23:53:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013049.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013049hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2712 Transcriptional coacti 100.0 2.4E-30 5.3E-35 203.0 5.2 72 89-160 36-107 (108)
2 PF14244 UBN2_3: gag-polypepti 99.8 1.1E-20 2.3E-25 167.1 13.6 130 185-327 6-136 (152)
3 PF02229 PC4: Transcriptional 99.8 6.2E-22 1.3E-26 142.7 3.9 55 94-148 1-56 (56)
4 PF14227 UBN2_2: gag-polypepti 99.8 2.8E-18 6.1E-23 145.2 12.6 111 272-382 1-114 (119)
5 PF14223 UBN2: gag-polypeptide 99.7 8.5E-17 1.8E-21 136.2 12.4 110 273-382 1-116 (119)
6 PF08766 DEK_C: DEK C terminal 99.5 2.6E-14 5.7E-19 102.6 6.7 54 5-60 1-54 (54)
7 KOG2266 Chromatin-associated p 98.6 4.2E-08 9.1E-13 97.0 5.3 63 4-68 520-582 (594)
8 PF13961 DUF4219: Domain of un 98.4 1.2E-07 2.6E-12 57.4 2.4 27 192-218 1-27 (27)
9 PF00098 zf-CCHC: Zinc knuckle 98.2 9.5E-07 2.1E-11 48.1 1.5 17 421-437 2-18 (18)
10 PF03564 DUF1759: Protein of u 98.0 7E-05 1.5E-09 65.4 10.8 102 249-352 27-135 (145)
11 PF13696 zf-CCHC_2: Zinc knuck 97.1 0.00022 4.7E-09 44.5 1.4 20 419-438 8-27 (32)
12 PF03732 Retrotrans_gag: Retro 96.9 0.0022 4.8E-08 51.0 5.7 69 274-348 28-96 (96)
13 PF13917 zf-CCHC_3: Zinc knuck 95.6 0.0088 1.9E-07 40.1 2.0 19 419-437 4-22 (42)
14 smart00343 ZnF_C2HC zinc finge 95.3 0.0071 1.5E-07 36.2 0.8 18 421-438 1-18 (26)
15 PF14787 zf-CCHC_5: GAG-polypr 94.7 0.015 3.2E-07 37.1 1.0 21 420-440 3-23 (36)
16 PF15288 zf-CCHC_6: Zinc knuck 93.9 0.038 8.2E-07 36.4 1.7 22 420-441 2-25 (40)
17 PF14392 zf-CCHC_4: Zinc knuck 93.7 0.028 6E-07 39.3 0.9 22 416-437 28-49 (49)
18 COG5082 AIR1 Arginine methyltr 91.7 0.081 1.8E-06 47.5 1.2 22 420-441 98-120 (190)
19 COG5222 Uncharacterized conser 89.9 0.35 7.7E-06 46.0 3.8 22 419-440 176-197 (427)
20 COG5082 AIR1 Arginine methyltr 89.8 0.14 2.9E-06 46.1 0.9 18 419-436 60-77 (190)
21 PTZ00368 universal minicircle 89.3 0.2 4.3E-06 43.8 1.6 18 420-437 130-147 (148)
22 KOG0109 RNA-binding protein LA 88.2 0.25 5.5E-06 47.0 1.6 23 419-441 160-182 (346)
23 COG4443 Uncharacterized protei 84.5 0.62 1.3E-05 34.0 1.6 39 108-149 31-70 (72)
24 PF14893 PNMA: PNMA 81.8 19 0.00041 35.8 11.4 71 272-344 229-302 (331)
25 KOG1946 RNA polymerase I trans 80.1 1.3 2.7E-05 41.8 2.4 51 10-62 8-58 (240)
26 PTZ00368 universal minicircle 75.8 1.6 3.5E-05 38.0 1.7 20 420-439 53-72 (148)
27 PF12353 eIF3g: Eukaryotic tra 73.5 1.8 3.9E-05 36.8 1.3 23 416-439 103-125 (128)
28 KOG4400 E3 ubiquitin ligase in 73.3 1.5 3.3E-05 42.0 1.0 19 420-438 144-162 (261)
29 PF02023 SCAN: SCAN domain; I 69.9 8 0.00017 31.0 4.3 74 297-373 5-82 (95)
30 KOG2044 5'-3' exonuclease HKE1 69.5 2.4 5.1E-05 46.0 1.4 25 416-440 257-281 (931)
31 KOG2560 RNA splicing factor - 69.1 1 2.2E-05 45.7 -1.3 26 416-441 109-134 (529)
32 KOG0341 DEAD-box protein abstr 59.9 4.1 8.9E-05 40.8 1.0 25 418-442 569-593 (610)
33 PF05741 zf-nanos: Nanos RNA b 59.0 4.1 9E-05 29.0 0.6 20 419-438 33-55 (55)
34 COG5179 TAF1 Transcription ini 58.1 53 0.0012 35.1 8.6 23 419-441 937-961 (968)
35 KOG0119 Splicing factor 1/bran 50.5 7.8 0.00017 39.9 1.2 19 420-438 286-304 (554)
36 PF10815 ComZ: ComZ; InterPro 50.2 24 0.00051 24.9 3.1 30 130-159 22-51 (56)
37 KOG4400 E3 ubiquitin ligase in 49.6 9.7 0.00021 36.5 1.7 24 418-441 163-186 (261)
38 KOG2673 Uncharacterized conser 45.6 8.6 0.00019 39.2 0.7 22 420-441 129-150 (485)
39 KOG3794 CBF1-interacting corep 40.1 12 0.00025 37.5 0.6 23 418-440 123-147 (453)
40 PF00550 PP-binding: Phosphopa 37.9 79 0.0017 22.6 4.8 37 8-44 2-51 (67)
41 PF04368 DUF507: Protein of un 37.0 96 0.0021 28.1 5.9 56 6-61 49-112 (183)
42 PF13551 HTH_29: Winged helix- 36.5 86 0.0019 25.0 5.3 37 8-44 61-101 (112)
43 PF09312 SurA_N: SurA N-termin 36.5 40 0.00086 28.0 3.2 46 4-55 67-112 (118)
44 TIGR02530 flg_new flagellar op 36.0 36 0.00079 27.2 2.7 22 131-152 27-48 (96)
45 KOG0107 Alternative splicing f 34.4 19 0.00041 32.1 1.0 18 420-437 101-118 (195)
46 PRK05828 acyl carrier protein; 34.0 76 0.0016 24.7 4.2 52 5-56 2-73 (84)
47 PF05696 DUF826: Protein of un 33.9 1.7E+02 0.0037 22.2 5.7 53 1-62 1-53 (78)
48 CHL00124 acpP acyl carrier pro 30.3 1.4E+02 0.0031 22.5 5.3 25 24-48 39-63 (82)
49 PF03705 CheR_N: CheR methyltr 30.2 96 0.0021 21.6 4.0 33 28-62 6-39 (57)
50 PF08880 QLQ: QLQ; InterPro: 29.2 50 0.0011 21.5 2.0 18 135-152 2-19 (37)
51 KOG0314 Predicted E3 ubiquitin 29.0 32 0.0007 35.5 1.7 25 418-442 157-181 (448)
52 PF12651 RHH_3: Ribbon-helix-h 28.6 87 0.0019 21.1 3.3 25 32-61 18-42 (44)
53 cd05500 Bromo_BDF1_2_I Bromodo 28.1 51 0.0011 26.6 2.4 75 136-210 1-77 (103)
54 PF09026 CENP-B_dimeris: Centr 27.3 21 0.00045 28.5 0.0 9 92-100 40-48 (101)
55 PF10410 DnaB_bind: DnaB-helic 26.8 1.6E+02 0.0035 20.5 4.7 40 3-43 18-57 (59)
56 COG4416 Com Mu-like prophage p 26.6 20 0.00044 25.2 -0.1 22 419-440 4-32 (60)
57 PF11248 DUF3046: Protein of u 26.6 1.1E+02 0.0024 22.5 3.7 40 249-289 20-60 (63)
58 PF01707 Peptidase_C9: Peptida 26.5 17 0.00038 32.7 -0.6 16 132-147 62-77 (202)
59 PRK12449 acyl carrier protein; 25.8 1.6E+02 0.0034 22.2 4.8 46 5-50 6-65 (80)
60 PF06526 DUF1107: Protein of u 25.6 1.2E+02 0.0025 22.5 3.7 44 108-158 19-63 (64)
61 PF01402 RHH_1: Ribbon-helix-h 25.4 1.8E+02 0.0038 18.4 4.3 25 31-60 14-38 (39)
62 PF02847 MA3: MA3 domain; Int 25.2 1.6E+02 0.0035 23.7 5.0 47 6-61 2-48 (113)
63 PRK05883 acyl carrier protein; 24.1 2.4E+02 0.0051 22.2 5.6 25 22-46 46-70 (91)
64 PF07571 DUF1546: Protein of u 24.0 3.2E+02 0.007 21.5 6.4 51 274-324 25-75 (92)
65 cd07936 SCAN SCAN oligomerizat 23.7 1E+02 0.0022 24.1 3.3 71 298-371 5-79 (85)
66 cd04754 Commd6 COMM_Domain con 23.7 1.8E+02 0.0038 22.8 4.5 43 111-155 42-85 (86)
67 PF13699 DUF4157: Domain of un 22.9 61 0.0013 24.9 1.9 17 29-45 5-21 (79)
68 smart00431 SCAN leucine rich r 22.9 1.1E+02 0.0024 25.4 3.4 73 297-372 4-80 (113)
69 PRK07117 acyl carrier protein; 22.5 3E+02 0.0064 21.1 5.7 52 5-56 6-73 (79)
70 KOG3926 F-box proteins [Amino 21.7 2.4E+02 0.0052 27.3 5.8 30 195-224 168-197 (332)
71 PF14568 SUKH_6: SMI1-KNR4 cel 21.7 70 0.0015 25.8 2.2 21 32-53 5-25 (120)
72 PF07827 KNTase_C: KNTase C-te 21.2 5.4E+02 0.012 22.2 7.5 34 343-376 88-121 (143)
73 KOG4602 Nanos and related prot 21.2 44 0.00095 31.6 0.9 23 418-440 267-292 (318)
74 KOG0377 Protein serine/threoni 21.1 3.5E+02 0.0076 28.0 7.2 73 248-322 544-616 (631)
75 PF13565 HTH_32: Homeodomain-l 21.1 1.6E+02 0.0035 21.7 4.0 34 7-42 33-66 (77)
76 PF01221 Dynein_light: Dynein 20.8 2E+02 0.0044 22.4 4.6 39 1-39 13-51 (89)
No 1
>KOG2712 consensus Transcriptional coactivator [Transcription]
Probab=99.96 E-value=2.4e-30 Score=202.96 Aligned_cols=72 Identities=43% Similarity=0.802 Sum_probs=69.2
Q ss_pred CCCCceEEEcCCceeeEEeeecCceeEeeEeEEecCCcccCCCcccccCHHHHHHHHhhhhHHHHHHHHhcc
Q 013049 89 DDGDSIICKLSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKMQS 160 (450)
Q Consensus 89 ~~~d~~~~~~~~~~~~~~~~~~g~~~~~ir~~~~~~~~~~p~~kgi~l~~~~~~~l~~~~~~i~~~~~~~~~ 160 (450)
+.++.++|.|+++|||||++|+|+.||||||||.+||+|+|||||||||.+||+.|++.+++|++||..+++
T Consensus 36 ~s~~~~i~~l~~~RrVtV~eFkGk~~VdIREyY~kdG~mlPgkKGISLs~~qW~~Lk~~~~eId~Al~~l~s 107 (108)
T KOG2712|consen 36 DSEDDNIFNLGKNRRVTVREFKGKILVDIREYYVKDGKMLPGKKGISLSLEQWSKLKEHIEEIDKALRKLSS 107 (108)
T ss_pred CcCccceeecCCceEEehhhcCCceEEehhHhhhccCccccCccccccCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 567789999999999999999999999999999999999999999999999999999999999999998875
No 2
>PF14244 UBN2_3: gag-polypeptide of LTR copia-type
Probab=99.85 E-value=1.1e-20 Score=167.05 Aligned_cols=130 Identities=22% Similarity=0.287 Sum_probs=117.4
Q ss_pred CCCcccccCCCChHHHHHHHHHHhhhcccceeccccccCCCCCCCCChhHHHhhHHHHHHHHhhhHHHHHHHHHhcchhH
Q 013049 185 FPTELHRFNGKNYRVWAQQIELLLKQLKVAYVLTDPCPIVTLCPQASSEEVTRVKAAERKWLNDNNICRHHILNFLSDHL 264 (450)
Q Consensus 185 ~~~~i~kLdG~Ny~~W~~~m~~~L~~~~l~~~l~~~~~~p~~~~~~~~~~~~~~~~~~~~W~~~d~~a~~~I~~sl~~~i 264 (450)
..+.+++|+|+||..|+..|+.+|.++|++++|+|..+.|+.+. ..+.+|.+.|.+++++|+++|++++
T Consensus 6 ~~i~~~kL~g~NY~~W~~~~~~~L~~~~l~~~i~g~~~~P~~~~-----------~~~~~W~~~d~~v~swl~~sis~~i 74 (152)
T PF14244_consen 6 QPITSIKLNGSNYLSWSQQMEMALRGKGLWGFIDGTIPKPPETD-----------PAYEKWERKDQLVLSWLLNSISPDI 74 (152)
T ss_pred CcccccCCCCccHHHHHHHHHHHHHhCCCcccccCccccccccc-----------hhhhhHHHhhhHHHHHHHHhhcHHH
Confidence 44666999999999999999999999999999999887775421 4689999999999999999999999
Q ss_pred HHHhhhccccHHHHHHHHHHHhcccc-hhhHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHH
Q 013049 265 YYQYSKRTSSAKELWEELKLVYLDEE-FGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIV 327 (450)
Q Consensus 265 ~~~i~~~~~ta~elW~~Lk~~y~~~~-~~~~~~l~~~l~~~k~~~~~sv~e~i~~~~~l~~~L~ 327 (450)
+..|.. +.||+++|+.|+++|...+ .++.+.+..++..++ +++.+|.+|+.+|+.++.++.
T Consensus 75 ~~~i~~-~~tak~~W~~L~~~f~~~~~~~r~~~L~~~l~~~k-q~~~sv~ey~~~lk~l~~~~e 136 (152)
T PF14244_consen 75 LSTIIF-CETAKEIWDALKERFSQKSNASRVFQLRNELHSLK-QGDKSVTEYFNKLKSLWQEDE 136 (152)
T ss_pred HhhhHh-hhhHHHHHHHHHHHhhcccHHHHHHHHHHHHHHHh-hCCCcHHHHHHHHHHHhHHHH
Confidence 999999 9999999999999999999 788889999999999 568999999999999994433
No 3
>PF02229 PC4: Transcriptional Coactivator p15 (PC4); InterPro: IPR003173 p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain []. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.; GO: 0003677 DNA binding, 0003713 transcription coactivator activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3PM7_B 2LTD_A 2LTT_B 3OBH_B 2L3A_B 2PHE_B 1PCF_B 2C62_B.
Probab=99.85 E-value=6.2e-22 Score=142.72 Aligned_cols=55 Identities=49% Similarity=0.951 Sum_probs=49.3
Q ss_pred eEEEcCCceeeEEeeecCceeEeeEeEEec-CCcccCCCcccccCHHHHHHHHhhh
Q 013049 94 IICKLSNKRTVAIQEFKGRAFVSIREYFRR-DGKLVPTAKGIALTSEQWRAFSKSL 148 (450)
Q Consensus 94 ~~~~~~~~~~~~~~~~~g~~~~~ir~~~~~-~~~~~p~~kgi~l~~~~~~~l~~~~ 148 (450)
++|.++.+|+|+|++|+|++||||||||++ ||+|+||||||||+++||.+|++++
T Consensus 1 ~~~~~~~~~rv~v~~fkG~~~vdIRe~y~~~~g~~~P~kKGIsL~~~q~~~l~~~l 56 (56)
T PF02229_consen 1 IIKNLGEKRRVSVSEFKGKPYVDIREWYEKKDGEWKPTKKGISLTPEQWKELKEAL 56 (56)
T ss_dssp -EETTEEEEEEEEEEETTSEEEEEEEEETTSSS-EEEEEEEEEE-HHHHHHHHHH-
T ss_pred CcccCCCeEEEEEEEeCCeEEEEEEeeEEcCCCcCcCcCCEEEcCHHHHHHHHhhC
Confidence 468999999999999999999999999997 9999999999999999999999864
No 4
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=99.77 E-value=2.8e-18 Score=145.21 Aligned_cols=111 Identities=27% Similarity=0.436 Sum_probs=105.7
Q ss_pred cccHHHHHHHHHHHhcccchhhHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHhhCCCCcH
Q 013049 272 TSSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLSWK 351 (450)
Q Consensus 272 ~~ta~elW~~Lk~~y~~~~~~~~~~l~~~l~~~k~~~~~sv~e~i~~~~~l~~~L~~~g~~i~d~~~~~~iL~sLp~~~~ 351 (450)
|+||+++|+.|+..|+..+.+.++.++++|+.++|.++.+|.+|+++|+.++++|..+|.+++|.+++..||.+||++|+
T Consensus 1 ~~ta~~~W~~L~~~y~~~~~~~~~~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~g~~i~d~~~~~~lL~sLP~sy~ 80 (119)
T PF14227_consen 1 CKTAKEMWDKLKKKYEKKSFANKIYLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSLGVPIDDEDKVIILLSSLPPSYD 80 (119)
T ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhHhccchhHHHHHHHHHHHHHhhccccccchHHHHHHHHHHcCCHhHH
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcC---CCCCHHHHHHHHHHHHHhhhhc
Q 013049 352 DFCIKLMRM---EYLTFTMLMDHIKAEEESRSHN 382 (450)
Q Consensus 352 ~~~~~l~~~---~~ltl~el~~~L~~eE~~~~~~ 382 (450)
+|++++.+. ..+|+++|+++|..+|.+++..
T Consensus 81 ~~~~~l~~~~~~~~~tl~~v~~~L~~ee~~~~~~ 114 (119)
T PF14227_consen 81 SFVTALLYSKPEDELTLEEVKSKLLQEEERRKKS 114 (119)
T ss_pred HHHHHHHccCCCCCcCHHHHHHHHHHHHHHHHhc
Confidence 999998753 6899999999999999888654
No 5
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=99.71 E-value=8.5e-17 Score=136.16 Aligned_cols=110 Identities=28% Similarity=0.336 Sum_probs=103.6
Q ss_pred ccHHHHHHHHHHHhcccch---hhHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHhhCCCC
Q 013049 273 SSAKELWEELKLVYLDEEF---GTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPLS 349 (450)
Q Consensus 273 ~ta~elW~~Lk~~y~~~~~---~~~~~l~~~l~~~k~~~~~sv~e~i~~~~~l~~~L~~~g~~i~d~~~~~~iL~sLp~~ 349 (450)
+||+++|+.|+..|.+.+. +....+..+|.+++|.++++|.+|+.+|..|+++|..+|.+++|..++..+|.|||++
T Consensus 1 ~tA~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~v~~iL~~Lp~~ 80 (119)
T PF14223_consen 1 KTAKEAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAIGKPISDEDLVSKILRSLPPS 80 (119)
T ss_pred ChHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhcCCcccchhHHHHHHhcCCch
Confidence 4899999999999999999 9999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhcC---CCCCHHHHHHHHHHHHHhhhhc
Q 013049 350 WKDFCIKLMRM---EYLTFTMLMDHIKAEEESRSHN 382 (450)
Q Consensus 350 ~~~~~~~l~~~---~~ltl~el~~~L~~eE~~~~~~ 382 (450)
|+.+++.+... ..+|+++|+.+|..+|.+.+..
T Consensus 81 y~~~~~~i~~~~~~~~~t~~el~~~L~~~E~~~~~~ 116 (119)
T PF14223_consen 81 YDTFVTAIRNSKDLPKMTLEELISRLLAEEMRLKSK 116 (119)
T ss_pred hHHHHHHHHhcCCCCcCCHHHHHHHHHHHHHHHHHc
Confidence 99999999864 3358999999999999888654
No 6
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=99.52 E-value=2.6e-14 Score=102.65 Aligned_cols=54 Identities=35% Similarity=0.735 Sum_probs=45.2
Q ss_pred hHHHHHHHHHHHhhcCCchhhhHHHHHHHHHHHhCCCCCCchhhHHHHHHHHHHHh
Q 013049 5 NEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLL 60 (450)
Q Consensus 5 ~~~~~~~~~~~~l~~~~~~~~t~~~~r~~~~~~~~~~l~~~~~k~~~~~~v~~~~~ 60 (450)
|...|++.|++||++|||+++|.++||++|++.||+||+ +||.||+++|+.||.
T Consensus 1 td~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~--~~K~~I~~~I~~~l~ 54 (54)
T PF08766_consen 1 TDEEIREAIREILREADLDTVTKKQVREQLEERFGVDLS--SRKKFIKELIDEFLS 54 (54)
T ss_dssp -HHHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--S--HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcH--HHHHHHHHHHHHHhC
Confidence 467899999999999999999999999999999999999 899999999999984
No 7
>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics]
Probab=98.61 E-value=4.2e-08 Score=96.96 Aligned_cols=63 Identities=17% Similarity=0.387 Sum_probs=57.7
Q ss_pred hhHHHHHHHHHHHhhcCCchhhhHHHHHHHHHHHhCCCCCCchhhHHHHHHHHHHHhhccccccC
Q 013049 4 VNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLSTTESTDN 68 (450)
Q Consensus 4 ~~~~~~~~~~~~~l~~~~~~~~t~~~~r~~~~~~~~~~l~~~~~k~~~~~~v~~~~~~~~~~~~~ 68 (450)
+|...|+..|.+||+.+||+|+|...|-++|...|++||+ +||.||..+|.+.|....+++++
T Consensus 520 PTdeelk~~V~kILk~vdfntaTm~dIlKkl~~~f~~dLt--~rK~~IK~~Ike~I~~~~de~e~ 582 (594)
T KOG2266|consen 520 PTDEELKEVVKKILKEVDFNTATMKDILKKLYAKFPIDLT--HRKDFIKDTIKELINKMADEEED 582 (594)
T ss_pred CcHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHhCCcccc--cchHHHHHHHHHHHHHhcchhhh
Confidence 6788999999999999999999999999999999999999 77999999999999887654333
No 8
>PF13961 DUF4219: Domain of unknown function (DUF4219)
Probab=98.45 E-value=1.2e-07 Score=57.44 Aligned_cols=27 Identities=22% Similarity=0.532 Sum_probs=25.5
Q ss_pred cCCCChHHHHHHHHHHhhhcccceecc
Q 013049 192 FNGKNYRVWAQQIELLLKQLKVAYVLT 218 (450)
Q Consensus 192 LdG~Ny~~W~~~m~~~L~~~~l~~~l~ 218 (450)
|||+||..|+.+|+.+|+..++|++|+
T Consensus 1 l~g~NY~~W~~~M~~~L~~~~lW~vVe 27 (27)
T PF13961_consen 1 LDGTNYSTWKIRMKAYLESQDLWDVVE 27 (27)
T ss_pred CCccCHHHHHHHHHHHHHHcchhhhhC
Confidence 799999999999999999999999873
No 9
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.16 E-value=9.5e-07 Score=48.06 Aligned_cols=17 Identities=41% Similarity=1.218 Sum_probs=16.0
Q ss_pred cccccCcccccccccCC
Q 013049 421 VCYNCRKKGHVAKHCHN 437 (450)
Q Consensus 421 ~C~~Cgk~GH~~~~C~~ 437 (450)
.||+||+.||++++||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999995
No 10
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=97.98 E-value=7e-05 Score=65.35 Aligned_cols=102 Identities=17% Similarity=0.175 Sum_probs=81.2
Q ss_pred hHHHHHHHHHhcchhHHHHhhhcc----ccHHHHHHHHHHHhcccchhhHHHHHHHHHHhh---ccccchHHHHHHHHHH
Q 013049 249 NNICRHHILNFLSDHLYYQYSKRT----SSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQ---MFDEKSVFEQALELNK 321 (450)
Q Consensus 249 d~~a~~~I~~sl~~~i~~~i~~~~----~ta~elW~~Lk~~y~~~~~~~~~~l~~~l~~~k---~~~~~sv~e~i~~~~~ 321 (450)
+..-+.+|.+.|.......|.+ + .+...+|+.|+.+|+.... ....++.++.++. ..+...+..++..+..
T Consensus 27 d~~K~~~L~~~L~G~A~~~i~~-~~~~~~~Y~~a~~~L~~~yg~~~~-i~~~~~~~l~~l~~~~~~d~~~L~~~~~~v~~ 104 (145)
T PF03564_consen 27 DIEKLNYLRSCLKGEAKELIRG-LPLSEENYEEAWELLEERYGNPRR-IIQALLEELRNLPPISNDDPEALRSLVDKVNN 104 (145)
T ss_pred HHHHHHHHHHHhcchHHHHHHc-ccccchhhHHHHHHHHHHhCCchH-HHHHHHHHHhccccccchhHHHHHHHHHHHHH
Confidence 4455677888888888888776 4 5668899999999965543 3345566666665 3455789999999999
Q ss_pred HHHHHHHcCCCcchHHHHHHHHhhCCCCcHH
Q 013049 322 IADSIVAAGMMIYENFHVSVILSKLPLSWKD 352 (450)
Q Consensus 322 l~~~L~~~g~~i~d~~~~~~iL~sLp~~~~~ 352 (450)
++..|..+|..+++..++.+|+.+||+....
T Consensus 105 ~i~~L~~lg~~~~~~~l~~~i~~KLp~~~~~ 135 (145)
T PF03564_consen 105 CIRALKALGVNVDDPLLISIILSKLPPEIRE 135 (145)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHCCHHHHH
Confidence 9999999999999999999999999987544
No 11
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=97.13 E-value=0.00022 Score=44.50 Aligned_cols=20 Identities=35% Similarity=0.813 Sum_probs=18.3
Q ss_pred cccccccCcccccccccCCc
Q 013049 419 TVVCYNCRKKGHVAKHCHNK 438 (450)
Q Consensus 419 ~~~C~~Cgk~GH~~~~C~~~ 438 (450)
...|+.|+++||+.++||..
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCEeecCCCCCccHhHCCCC
Confidence 47899999999999999993
No 12
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=96.89 E-value=0.0022 Score=51.05 Aligned_cols=69 Identities=13% Similarity=0.136 Sum_probs=55.3
Q ss_pred cHHHHHHHHHHHhcccchhhHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHhhCCC
Q 013049 274 SAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGMMIYENFHVSVILSKLPL 348 (450)
Q Consensus 274 ta~elW~~Lk~~y~~~~~~~~~~l~~~l~~~k~~~~~sv~e~i~~~~~l~~~L~~~g~~i~d~~~~~~iL~sLp~ 348 (450)
+-.++=..|..+|. .......+..++.++++ ++++|.+|+.+|+.++..+.. .+++..++..|+.||.+
T Consensus 28 ~W~~~~~~~~~~f~--~~~~~~~~~~~l~~l~Q-~~esv~~y~~rf~~l~~~~~~---~~~e~~~v~~f~~GL~~ 96 (96)
T PF03732_consen 28 TWEEFKDAFRKRFF--PPDRKEQARQELNSLRQ-GNESVREYVNRFRELARRAPP---PMDEEMLVERFIRGLRP 96 (96)
T ss_pred CHHHHHHHHHHHHh--hhhccccchhhhhhhhc-cCCcHHHHHHHHHHHHHHCCC---CcCHHHHHHHHHHCCCC
Confidence 44555556667773 33456677888999998 999999999999999999755 68999999999999964
No 13
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=95.56 E-value=0.0088 Score=40.09 Aligned_cols=19 Identities=42% Similarity=0.878 Sum_probs=17.5
Q ss_pred cccccccCcccccccccCC
Q 013049 419 TVVCYNCRKKGHVAKHCHN 437 (450)
Q Consensus 419 ~~~C~~Cgk~GH~~~~C~~ 437 (450)
...|..|++.||+..+|+.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4679999999999999996
No 14
>smart00343 ZnF_C2HC zinc finger.
Probab=95.31 E-value=0.0071 Score=36.16 Aligned_cols=18 Identities=50% Similarity=1.257 Sum_probs=16.0
Q ss_pred cccccCcccccccccCCc
Q 013049 421 VCYNCRKKGHVAKHCHNK 438 (450)
Q Consensus 421 ~C~~Cgk~GH~~~~C~~~ 438 (450)
.|++|++.||++++|+..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 499999999999999843
No 15
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=94.67 E-value=0.015 Score=37.15 Aligned_cols=21 Identities=33% Similarity=0.523 Sum_probs=13.4
Q ss_pred ccccccCcccccccccCCccc
Q 013049 420 VVCYNCRKKGHVAKHCHNKRL 440 (450)
Q Consensus 420 ~~C~~Cgk~GH~~~~C~~~~~ 440 (450)
..|+.|++..||+++|+.+..
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp -C-TTTSSSCS-TTT---TCC
T ss_pred ccCcccCCCcchhhhhhhhhc
Confidence 469999999999999998754
No 16
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=93.86 E-value=0.038 Score=36.40 Aligned_cols=22 Identities=36% Similarity=0.638 Sum_probs=19.2
Q ss_pred ccccccCcccccc--cccCCcccc
Q 013049 420 VVCYNCRKKGHVA--KHCHNKRLH 441 (450)
Q Consensus 420 ~~C~~Cgk~GH~~--~~C~~~~~~ 441 (450)
++|..||..||.. +.||.+...
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~~ 25 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCWS 25 (40)
T ss_pred ccccccccccccccCccCCCCCCC
Confidence 5799999999999 789998754
No 17
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=93.69 E-value=0.028 Score=39.27 Aligned_cols=22 Identities=27% Similarity=0.812 Sum_probs=18.6
Q ss_pred CCCcccccccCcccccccccCC
Q 013049 416 DSKTVVCYNCRKKGHVAKHCHN 437 (450)
Q Consensus 416 ~~~~~~C~~Cgk~GH~~~~C~~ 437 (450)
.+-+..|++||..||...+||.
T Consensus 28 E~lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 28 ERLPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred CCcChhhcCCCCcCcCHhHcCC
Confidence 3345789999999999999984
No 18
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=91.68 E-value=0.081 Score=47.51 Aligned_cols=22 Identities=36% Similarity=0.967 Sum_probs=17.1
Q ss_pred ccccccCccccccccc-CCcccc
Q 013049 420 VVCYNCRKKGHVAKHC-HNKRLH 441 (450)
Q Consensus 420 ~~C~~Cgk~GH~~~~C-~~~~~~ 441 (450)
.+|++||..||++++| |.+.++
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~~~~ 120 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSKDQQ 120 (190)
T ss_pred cccccccccCccccccCcccccC
Confidence 6899999999999999 454443
No 19
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.93 E-value=0.35 Score=46.03 Aligned_cols=22 Identities=36% Similarity=0.865 Sum_probs=19.1
Q ss_pred cccccccCcccccccccCCccc
Q 013049 419 TVVCYNCRKKGHVAKHCHNKRL 440 (450)
Q Consensus 419 ~~~C~~Cgk~GH~~~~C~~~~~ 440 (450)
...||.||..|||...||....
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred ceeEEecCCCCchhhcCCCCCC
Confidence 4789999999999999997543
No 20
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=89.78 E-value=0.14 Score=46.10 Aligned_cols=18 Identities=39% Similarity=1.158 Sum_probs=16.7
Q ss_pred cccccccCcccccccccC
Q 013049 419 TVVCYNCRKKGHVAKHCH 436 (450)
Q Consensus 419 ~~~C~~Cgk~GH~~~~C~ 436 (450)
...|++||+.||.+++||
T Consensus 60 ~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccchhcccCcccccCC
Confidence 467999999999999999
No 21
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=89.29 E-value=0.2 Score=43.79 Aligned_cols=18 Identities=39% Similarity=1.197 Sum_probs=9.4
Q ss_pred ccccccCcccccccccCC
Q 013049 420 VVCYNCRKKGHVAKHCHN 437 (450)
Q Consensus 420 ~~C~~Cgk~GH~~~~C~~ 437 (450)
..|++|+..||++++||.
T Consensus 130 ~~C~~Cg~~gH~~~dCp~ 147 (148)
T PTZ00368 130 KTCYNCGQTGHLSRDCPD 147 (148)
T ss_pred CccccCCCcCcccccCCC
Confidence 345555555555555554
No 22
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=88.23 E-value=0.25 Score=47.03 Aligned_cols=23 Identities=39% Similarity=0.806 Sum_probs=19.7
Q ss_pred cccccccCcccccccccCCcccc
Q 013049 419 TVVCYNCRKKGHVAKHCHNKRLH 441 (450)
Q Consensus 419 ~~~C~~Cgk~GH~~~~C~~~~~~ 441 (450)
.-.|+.||+.|||.++||.....
T Consensus 160 q~~cyrcGkeghwskEcP~~~~~ 182 (346)
T KOG0109|consen 160 QSGCYRCGKEGHWSKECPVDRTG 182 (346)
T ss_pred HHHheeccccccccccCCccCCC
Confidence 45799999999999999987553
No 23
>COG4443 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.50 E-value=0.62 Score=33.97 Aligned_cols=39 Identities=33% Similarity=0.566 Sum_probs=29.9
Q ss_pred eecCce-eEeeEeEEecCCcccCCCcccccCHHHHHHHHhhhh
Q 013049 108 EFKGRA-FVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLP 149 (450)
Q Consensus 108 ~~~g~~-~~~ir~~~~~~~~~~p~~kgi~l~~~~~~~l~~~~~ 149 (450)
.|.|+. -.|||.|-.+..+| | |||.||-+++.+|++.+.
T Consensus 31 SwNg~~~KyDiR~Wspdh~KM--G-KGiTLt~eE~~~l~d~l~ 70 (72)
T COG4443 31 SWNGRPPKYDIRAWSPDHSKM--G-KGITLTNEEFKALKDLLN 70 (72)
T ss_pred ccCCCCCcCcccccCcchhhh--c-CceeecHHHHHHHHHHHh
Confidence 466665 67999997654433 2 999999999999998764
No 24
>PF14893 PNMA: PNMA
Probab=81.83 E-value=19 Score=35.79 Aligned_cols=71 Identities=13% Similarity=0.171 Sum_probs=56.3
Q ss_pred cccHHHHHHHHHHHhcccchhhHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHcCC---CcchHHHHHHHHh
Q 013049 272 TSSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIADSIVAAGM---MIYENFHVSVILS 344 (450)
Q Consensus 272 ~~ta~elW~~Lk~~y~~~~~~~~~~l~~~l~~~k~~~~~sv~e~i~~~~~l~~~L~~~g~---~i~d~~~~~~iL~ 344 (450)
..++.+.-+.|...| .+..+...+..+|++..+..++++.+|+.++..+.......|. .-.|+.....++.
T Consensus 229 ~~t~~~~l~aL~~~F--g~~es~~~~~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav~k~a~~p~~adq~rl~q~l~ 302 (331)
T PF14893_consen 229 KQTAQDCLKALGQVF--GSSESRETLEAKFLNTFQEPGEKLSAYVKRLESLLQKAVEKGAIKPSEADQVRLRQVLS 302 (331)
T ss_pred CCCHHHHHHHHHHhc--CCcccHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHhcCCCccccCHHHHHHHHc
Confidence 478999999999999 5555678889999999999999999999999999999766552 2235555555554
No 25
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=80.15 E-value=1.3 Score=41.82 Aligned_cols=51 Identities=20% Similarity=0.158 Sum_probs=45.5
Q ss_pred HHHHHHHhhcCCchhhhHHHHHHHHHHHhCCCCCCchhhHHHHHHHHHHHhhc
Q 013049 10 RQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLST 62 (450)
Q Consensus 10 ~~~~~~~l~~~~~~~~t~~~~r~~~~~~~~~~l~~~~~k~~~~~~v~~~~~~~ 62 (450)
.-.+..||...|.+++|...||++++..+|++++ .+|..++..|..++...
T Consensus 8 ~~~~~~~l~~~~~~~lt~~~vr~~~~~~~~v~~~--~~k~~~~~~~~~~~~~~ 58 (240)
T KOG1946|consen 8 YLFKDYILSLKDQETLTPDDVRRAMAPRSGVDGT--AQKSLLAKAIDESSDED 58 (240)
T ss_pred hhhhHHHhcccccccCCHHHHHHHhccccCCCCc--chhhhhhhhhhcccccc
Confidence 3457889999999999999999999999999999 66999999999888653
No 26
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=75.77 E-value=1.6 Score=38.01 Aligned_cols=20 Identities=40% Similarity=1.041 Sum_probs=14.8
Q ss_pred ccccccCcccccccccCCcc
Q 013049 420 VVCYNCRKKGHVAKHCHNKR 439 (450)
Q Consensus 420 ~~C~~Cgk~GH~~~~C~~~~ 439 (450)
..|++|+..||++++||...
T Consensus 53 ~~C~~Cg~~GH~~~~Cp~~~ 72 (148)
T PTZ00368 53 RSCYNCGKTGHLSRECPEAP 72 (148)
T ss_pred cccCCCCCcCcCcccCCCcc
Confidence 46888888888888887754
No 27
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=73.48 E-value=1.8 Score=36.80 Aligned_cols=23 Identities=26% Similarity=0.563 Sum_probs=19.4
Q ss_pred CCCcccccccCcccccccccCCcc
Q 013049 416 DSKTVVCYNCRKKGHVAKHCHNKR 439 (450)
Q Consensus 416 ~~~~~~C~~Cgk~GH~~~~C~~~~ 439 (450)
....+.|.+|+ ..||-..||.+.
T Consensus 103 ~~~~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 103 GKSKVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred CCceEEeCCCC-CCcccccCCccc
Confidence 45678999997 789999999874
No 28
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=73.31 E-value=1.5 Score=42.05 Aligned_cols=19 Identities=32% Similarity=1.080 Sum_probs=17.6
Q ss_pred ccccccCcccccccccCCc
Q 013049 420 VVCYNCRKKGHVAKHCHNK 438 (450)
Q Consensus 420 ~~C~~Cgk~GH~~~~C~~~ 438 (450)
..||.||+.||+..+|+..
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred CccCCCCcCCcchhhCCCC
Confidence 7799999999999999965
No 29
>PF02023 SCAN: SCAN domain; InterPro: IPR003309 A number of C2H2-zinc finger proteins contain a highly conserved N-terminal motif termed the SCAN domain. The SCAN domain may play an important role in the assembly and function of this newly defined subclass of transcriptional regulators [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3LHR_B 4E6S_A 2FI2_A 1Y7Q_A.
Probab=69.92 E-value=8 Score=31.00 Aligned_cols=74 Identities=14% Similarity=0.113 Sum_probs=53.4
Q ss_pred HHHHHHHhhccccchHHHHHHHHHHHHHHHHHcC----CCcchHHHHHHHHhhCCCCcHHHHHHHhcCCCCCHHHHHHHH
Q 013049 297 QVKKYIEFQMFDEKSVFEQALELNKIADSIVAAG----MMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHI 372 (450)
Q Consensus 297 l~~~l~~~k~~~~~sv~e~i~~~~~l~~~L~~~g----~~i~d~~~~~~iL~sLp~~~~~~~~~l~~~~~ltl~el~~~L 372 (450)
.+++|.++.+..+.+..+++.++..++.+--..+ ..|-|-.+...||..||++...++. ...+-|..++...+
T Consensus 5 ~r~~FR~~~~~~~~~p~e~~~rL~~l~~~WL~pe~~tkeqi~ellvlEQFL~~lP~e~~~wV~---e~~p~s~~ea~~La 81 (95)
T PF02023_consen 5 YRQRFRSFQYQEGEGPREFLSRLRELCDRWLQPEVHTKEQILELLVLEQFLNILPPEVQTWVR---ERKPESAEEAVALA 81 (95)
T ss_dssp HHHHHHT--CCTTTSHHHHHHHHHHHHHHHH-TTTS-HHHHHHHHHHHHHHHHS-HHHHHHHH---TCS-SSHHHHHHHH
T ss_pred HHHHHhCCCCCCCCCHHHHHHHHHHHHHHhCccccCcHHHHHHHHHHHHHHHHCCHHHHHHHH---hcCCCCHHHHHHHH
Confidence 4678889999999999999999999999875433 3456788888999999988766665 34445777776655
Q ss_pred H
Q 013049 373 K 373 (450)
Q Consensus 373 ~ 373 (450)
.
T Consensus 82 e 82 (95)
T PF02023_consen 82 E 82 (95)
T ss_dssp H
T ss_pred H
Confidence 3
No 30
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=69.53 E-value=2.4 Score=46.02 Aligned_cols=25 Identities=36% Similarity=0.724 Sum_probs=21.2
Q ss_pred CCCcccccccCcccccccccCCccc
Q 013049 416 DSKTVVCYNCRKKGHVAKHCHNKRL 440 (450)
Q Consensus 416 ~~~~~~C~~Cgk~GH~~~~C~~~~~ 440 (450)
+.+...|+.||+.||.+++|..+.+
T Consensus 257 P~~~~~C~~cgq~gh~~~dc~g~~~ 281 (931)
T KOG2044|consen 257 PNKPRRCFLCGQTGHEAKDCEGKPR 281 (931)
T ss_pred CCCcccchhhcccCCcHhhcCCcCC
Confidence 3445679999999999999999866
No 31
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=69.06 E-value=1 Score=45.65 Aligned_cols=26 Identities=23% Similarity=0.484 Sum_probs=22.5
Q ss_pred CCCcccccccCcccccccccCCcccc
Q 013049 416 DSKTVVCYNCRKKGHVAKHCHNKRLH 441 (450)
Q Consensus 416 ~~~~~~C~~Cgk~GH~~~~C~~~~~~ 441 (450)
+...+.|.+||..||..++|..+.++
T Consensus 109 kyRKGACeNCGAmtHk~KDCmERPRK 134 (529)
T KOG2560|consen 109 KYRKGACENCGAMTHKVKDCMERPRK 134 (529)
T ss_pred HHhhhhhhhhhhhhcchHHHhhcchh
Confidence 44578899999999999999988764
No 32
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=59.92 E-value=4.1 Score=40.82 Aligned_cols=25 Identities=24% Similarity=0.421 Sum_probs=20.8
Q ss_pred CcccccccCcccccccccCCccccc
Q 013049 418 KTVVCYNCRKKGHVAKHCHNKRLHQ 442 (450)
Q Consensus 418 ~~~~C~~Cgk~GH~~~~C~~~~~~k 442 (450)
....|.|||..||-..+||+.-..+
T Consensus 569 ~~kGCayCgGLGHRItdCPKle~~~ 593 (610)
T KOG0341|consen 569 GEKGCAYCGGLGHRITDCPKLEAQQ 593 (610)
T ss_pred CccccccccCCCcccccCchhhhhc
Confidence 3567999999999999999976543
No 33
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=58.99 E-value=4.1 Score=29.04 Aligned_cols=20 Identities=40% Similarity=0.757 Sum_probs=8.3
Q ss_pred cccccccCccc---ccccccCCc
Q 013049 419 TVVCYNCRKKG---HVAKHCHNK 438 (450)
Q Consensus 419 ~~~C~~Cgk~G---H~~~~C~~~ 438 (450)
...|..||..| |..+.||.+
T Consensus 33 ~y~Cp~CgAtGd~AHT~~yCP~k 55 (55)
T PF05741_consen 33 KYVCPICGATGDNAHTIKYCPKK 55 (55)
T ss_dssp G---TTT---GGG---GGG-TT-
T ss_pred cCcCCCCcCcCccccccccCcCC
Confidence 46799999866 999999964
No 34
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=58.13 E-value=53 Score=35.08 Aligned_cols=23 Identities=35% Similarity=0.645 Sum_probs=18.7
Q ss_pred cccccccCcccccc--cccCCcccc
Q 013049 419 TVVCYNCRKKGHVA--KHCHNKRLH 441 (450)
Q Consensus 419 ~~~C~~Cgk~GH~~--~~C~~~~~~ 441 (450)
..+|-+||+.||++ +-||.....
T Consensus 937 tr~C~nCGQvGHmkTNK~CP~f~s~ 961 (968)
T COG5179 937 TRTCGNCGQVGHMKTNKACPKFSSK 961 (968)
T ss_pred ceecccccccccccccccCccccCC
Confidence 56899999999998 569987543
No 35
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=50.52 E-value=7.8 Score=39.93 Aligned_cols=19 Identities=32% Similarity=0.726 Sum_probs=17.8
Q ss_pred ccccccCcccccccccCCc
Q 013049 420 VVCYNCRKKGHVAKHCHNK 438 (450)
Q Consensus 420 ~~C~~Cgk~GH~~~~C~~~ 438 (450)
..|++|+-.||+..+|...
T Consensus 286 n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 286 NVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCcccccccCCCc
Confidence 3899999999999999988
No 36
>PF10815 ComZ: ComZ; InterPro: IPR024558 ComZ, which contains a leucine zipper motif, negatively regulates transcription of the ComG operon [].
Probab=50.21 E-value=24 Score=24.86 Aligned_cols=30 Identities=20% Similarity=0.312 Sum_probs=24.3
Q ss_pred CCcccccCHHHHHHHHhhhhHHHHHHHHhc
Q 013049 130 TAKGIALTSEQWRAFSKSLPAIDEAVVKMQ 159 (450)
Q Consensus 130 ~~kgi~l~~~~~~~l~~~~~~i~~~~~~~~ 159 (450)
-++||-|+.++...|++.+-.+-..--+++
T Consensus 22 ~k~GIeLsme~~qP~m~L~~~VM~eAYElG 51 (56)
T PF10815_consen 22 DKKGIELSMEMLQPLMQLLTKVMNEAYELG 51 (56)
T ss_pred HHcCccCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 479999999999999999988765544444
No 37
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=49.61 E-value=9.7 Score=36.52 Aligned_cols=24 Identities=33% Similarity=0.762 Sum_probs=21.3
Q ss_pred CcccccccCcccccccccCCcccc
Q 013049 418 KTVVCYNCRKKGHVAKHCHNKRLH 441 (450)
Q Consensus 418 ~~~~C~~Cgk~GH~~~~C~~~~~~ 441 (450)
....|+.|++.||..++||.....
T Consensus 163 ~~~~c~~c~~~~h~~~~C~~~~~~ 186 (261)
T KOG4400|consen 163 KGGTCFRCGKVGHGSRDCPSKQKS 186 (261)
T ss_pred CCCccccCCCcceecccCCccccc
Confidence 367899999999999999998765
No 38
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=45.56 E-value=8.6 Score=39.23 Aligned_cols=22 Identities=23% Similarity=0.505 Sum_probs=18.9
Q ss_pred ccccccCcccccccccCCcccc
Q 013049 420 VVCYNCRKKGHVAKHCHNKRLH 441 (450)
Q Consensus 420 ~~C~~Cgk~GH~~~~C~~~~~~ 441 (450)
..||+|+..-|-.++||.+...
T Consensus 129 ~~CFNC~g~~hsLrdC~rp~d~ 150 (485)
T KOG2673|consen 129 DPCFNCGGTPHSLRDCPRPFDF 150 (485)
T ss_pred ccccccCCCCCccccCCCcccc
Confidence 4499999999999999998763
No 39
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=40.06 E-value=12 Score=37.46 Aligned_cols=23 Identities=30% Similarity=0.699 Sum_probs=19.3
Q ss_pred CcccccccCcccccc--cccCCccc
Q 013049 418 KTVVCYNCRKKGHVA--KHCHNKRL 440 (450)
Q Consensus 418 ~~~~C~~Cgk~GH~~--~~C~~~~~ 440 (450)
..+.|+.|++-||.- ++||-+..
T Consensus 123 RNVrC~kChkwGH~n~DreCplf~~ 147 (453)
T KOG3794|consen 123 RNVRCLKCHKWGHINTDRECPLFGK 147 (453)
T ss_pred eeeeEEeecccccccCCccCcchhh
Confidence 468999999999986 78998755
No 40
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=37.92 E-value=79 Score=22.60 Aligned_cols=37 Identities=22% Similarity=0.490 Sum_probs=29.1
Q ss_pred HHHHHHHHHhh-------------cCCchhhhHHHHHHHHHHHhCCCCCC
Q 013049 8 RIRQTVMEVLK-------------NSDMEEMTEFKVRVEASERLGIDLSD 44 (450)
Q Consensus 8 ~~~~~~~~~l~-------------~~~~~~~t~~~~r~~~~~~~~~~l~~ 44 (450)
+|++.+.++|. +-.++++..-.+...+++.||+.++.
T Consensus 2 ~l~~~~~~~l~~~~~~i~~~~~~~~lG~DSl~~~~l~~~l~~~~g~~i~~ 51 (67)
T PF00550_consen 2 QLREIIAEVLGVDPEEIDPDTDFFDLGLDSLDAIELVSELEEEFGIKIPP 51 (67)
T ss_dssp HHHHHHHHHHTSSGGCTSTTSBTTTTTSSHHHHHHHHHHHHHHHTSSTTH
T ss_pred HHHHHHHHHHCcCHhhCCCCCCHHHhCCchHHHHHHHHHHHHHHcCCCCH
Confidence 46666666665 33477888999999999999999983
No 41
>PF04368 DUF507: Protein of unknown function (DUF507); InterPro: IPR007463 This entry represents a bacterial protein of unknown function.
Probab=36.98 E-value=96 Score=28.10 Aligned_cols=56 Identities=13% Similarity=0.194 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHhhc-------CCchhhhHH-HHHHHHHHHhCCCCCCchhhHHHHHHHHHHHhh
Q 013049 6 EGRIRQTVMEVLKN-------SDMEEMTEF-KVRVEASERLGIDLSDANHKRFIRGVVESFLLS 61 (450)
Q Consensus 6 ~~~~~~~~~~~l~~-------~~~~~~t~~-~~r~~~~~~~~~~l~~~~~k~~~~~~v~~~~~~ 61 (450)
.+.|.+.+++||.. .+++.-+.+ +|+++|..+.|+-|+..+|=.-|-++|-++|-+
T Consensus 49 E~~Lde~areiLe~~~~eie~~~id~r~mF~~iKkkLA~e~~~~l~~edr~~~lah~i~~~l~~ 112 (183)
T PF04368_consen 49 EEALDEEAREILEENEDEIEFMGIDYRQMFWMIKKKLAKERGFILNSEDRYNQLAHKILDELWE 112 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHhh
Confidence 44566666666653 334444555 899999999999999888888899999888864
No 42
>PF13551 HTH_29: Winged helix-turn helix
Probab=36.53 E-value=86 Score=24.99 Aligned_cols=37 Identities=24% Similarity=0.308 Sum_probs=26.4
Q ss_pred HHHHHHHHHhhcCC---chhhhHHHHHHHH-HHHhCCCCCC
Q 013049 8 RIRQTVMEVLKNSD---MEEMTEFKVRVEA-SERLGIDLSD 44 (450)
Q Consensus 8 ~~~~~~~~~l~~~~---~~~~t~~~~r~~~-~~~~~~~l~~ 44 (450)
..++.|.+++.+-. ....|...|+..| ++.+|+++|.
T Consensus 61 ~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~ 101 (112)
T PF13551_consen 61 EQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSP 101 (112)
T ss_pred HHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCH
Confidence 44455555555533 3467889999987 9999999993
No 43
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=36.46 E-value=40 Score=27.97 Aligned_cols=46 Identities=15% Similarity=0.359 Sum_probs=32.3
Q ss_pred hhHHHHHHHHHHHhhcCCchhhhHHHHHHHHHHHhCCCCCCchhhHHHHHHH
Q 013049 4 VNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVV 55 (450)
Q Consensus 4 ~~~~~~~~~~~~~l~~~~~~~~t~~~~r~~~~~~~~~~l~~~~~k~~~~~~v 55 (450)
++-..|.+.|..|.+...| |....+++|+. -|++.. .|+..||..+
T Consensus 67 vsd~evd~~i~~ia~~n~l---s~~ql~~~L~~-~G~s~~--~~r~~ir~~i 112 (118)
T PF09312_consen 67 VSDEEVDEAIANIAKQNNL---SVEQLRQQLEQ-QGISYE--EYREQIRKQI 112 (118)
T ss_dssp --HHHHHHHHHHHHHHTT-----HHHHHHHCHH-CT--HH--HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHcCC---CHHHHHHHHHH-cCCCHH--HHHHHHHHHH
Confidence 4567788889999888887 55677888876 488887 8888888765
No 44
>TIGR02530 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown.
Probab=36.01 E-value=36 Score=27.24 Aligned_cols=22 Identities=9% Similarity=0.567 Sum_probs=18.4
Q ss_pred CcccccCHHHHHHHHhhhhHHH
Q 013049 131 AKGIALTSEQWRAFSKSLPAID 152 (450)
Q Consensus 131 ~kgi~l~~~~~~~l~~~~~~i~ 152 (450)
..||.|+.+||..|.+.+....
T Consensus 27 ~R~I~l~~~~~~~i~~av~~A~ 48 (96)
T TIGR02530 27 ERNISINPDDWKKLLEAVEEAE 48 (96)
T ss_pred HcCCCCCHHHHHHHHHHHHHHH
Confidence 4799999999999988776655
No 45
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=34.37 E-value=19 Score=32.14 Aligned_cols=18 Identities=33% Similarity=1.206 Sum_probs=16.5
Q ss_pred ccccccCcccccccccCC
Q 013049 420 VVCYNCRKKGHVAKHCHN 437 (450)
Q Consensus 420 ~~C~~Cgk~GH~~~~C~~ 437 (450)
..|++||..||+.++|..
T Consensus 101 ~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 101 GFCYRCGERGHIGRNCKD 118 (195)
T ss_pred cccccCCCcccccccccc
Confidence 459999999999999988
No 46
>PRK05828 acyl carrier protein; Validated
Probab=34.00 E-value=76 Score=24.71 Aligned_cols=52 Identities=17% Similarity=0.344 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHHhhc----CC--------------chhhhHHHHHHHHHHHhCCCCCCchhhHH--HHHHHH
Q 013049 5 NEGRIRQTVMEVLKN----SD--------------MEEMTEFKVRVEASERLGIDLSDANHKRF--IRGVVE 56 (450)
Q Consensus 5 ~~~~~~~~~~~~l~~----~~--------------~~~~t~~~~r~~~~~~~~~~l~~~~~k~~--~~~~v~ 56 (450)
++..|-++|++||.. .+ ++++.--.+=..+|++||+.+++.+-..+ |.++|+
T Consensus 2 ~~~eI~~~i~~ii~e~~~~~~~d~i~~~~~~~dLg~DSLd~velv~~lE~~f~I~i~~e~~~~i~Tv~d~~~ 73 (84)
T PRK05828 2 QEMEILLKIKEIAKKKNFAVTLDESNINKPYRELKIDSLDMFSIIVSLESEFNIEFSDEKLMKLKNLADLIL 73 (84)
T ss_pred CHHHHHHHHHHHHHHhccCCCcccccCCCCHHhcCCCHHHHHHHHHHHHHHHCCCcCHHHHHhCCCHHHHHH
Confidence 366778888888875 22 33444556667788999998886543332 444443
No 47
>PF05696 DUF826: Protein of unknown function (DUF826); InterPro: IPR008544 This entry is represented by Bacteriophage 933W, Orf26. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=33.88 E-value=1.7e+02 Score=22.21 Aligned_cols=53 Identities=11% Similarity=0.216 Sum_probs=35.0
Q ss_pred CchhhHHHHHHHHHHHhhcCCchhhhHHHHHHHHHHHhCCCCCCchhhHHHHHHHHHHHhhc
Q 013049 1 METVNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLST 62 (450)
Q Consensus 1 ~~~~~~~~~~~~~~~~l~~~~~~~~t~~~~r~~~~~~~~~~l~~~~~k~~~~~~v~~~~~~~ 62 (450)
|+++.----.+.|+..|++-.....=..+||..|+.++ -+.|+.+.+..|-..
T Consensus 1 M~Eik~lVT~e~VK~aL~Se~V~~alK~qvr~~le~qi---------Da~VD~~L~~llg~~ 53 (78)
T PF05696_consen 1 MSEIKGLVTAEAVKQALRSEEVTSALKQQVRQNLEAQI---------DAEVDAALDELLGAP 53 (78)
T ss_pred CchhHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHhCCC
Confidence 44443333356788888887666666678888887765 356777777777544
No 48
>CHL00124 acpP acyl carrier protein; Validated
Probab=30.26 E-value=1.4e+02 Score=22.52 Aligned_cols=25 Identities=12% Similarity=0.385 Sum_probs=17.8
Q ss_pred hhhHHHHHHHHHHHhCCCCCCchhh
Q 013049 24 EMTEFKVRVEASERLGIDLSDANHK 48 (450)
Q Consensus 24 ~~t~~~~r~~~~~~~~~~l~~~~~k 48 (450)
++..-.+=..+|++|||.++..+..
T Consensus 39 Sl~~~eli~~le~~f~i~i~~~~~~ 63 (82)
T CHL00124 39 SLDVVELVMAIEEKFDIEIPDEDAE 63 (82)
T ss_pred HHHHHHHHHHHHHHHCCccCHHHHH
Confidence 3444566778999999999965443
No 49
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=30.23 E-value=96 Score=21.61 Aligned_cols=33 Identities=24% Similarity=0.246 Sum_probs=22.0
Q ss_pred HHHHHHHHHHhCCCCCCchhh-HHHHHHHHHHHhhc
Q 013049 28 FKVRVEASERLGIDLSDANHK-RFIRGVVESFLLST 62 (450)
Q Consensus 28 ~~~r~~~~~~~~~~l~~~~~k-~~~~~~v~~~~~~~ 62 (450)
..++..+....|+||+ +|| ..|..=|...+...
T Consensus 6 ~~~~~~i~~~~Gi~l~--~~K~~~l~rRl~~rm~~~ 39 (57)
T PF03705_consen 6 ERFRELIYRRTGIDLS--EYKRSLLERRLARRMRAL 39 (57)
T ss_dssp HHHHHHHHHHH-------GGGHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCc--hhhHHHHHHHHHHHHHHc
Confidence 3688899999999999 778 78888777777653
No 50
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=29.24 E-value=50 Score=21.50 Aligned_cols=18 Identities=17% Similarity=0.242 Sum_probs=15.4
Q ss_pred ccCHHHHHHHHhhhhHHH
Q 013049 135 ALTSEQWRAFSKSLPAID 152 (450)
Q Consensus 135 ~l~~~~~~~l~~~~~~i~ 152 (450)
++|.+||..|+..|-+..
T Consensus 2 ~FT~~Ql~~L~~Qi~ayK 19 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAYK 19 (37)
T ss_pred CCCHHHHHHHHHHHHHHH
Confidence 589999999999987665
No 51
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.01 E-value=32 Score=35.48 Aligned_cols=25 Identities=20% Similarity=0.356 Sum_probs=21.3
Q ss_pred CcccccccCcccccccccCCccccc
Q 013049 418 KTVVCYNCRKKGHVAKHCHNKRLHQ 442 (450)
Q Consensus 418 ~~~~C~~Cgk~GH~~~~C~~~~~~k 442 (450)
....|+.|+.+|||.+.||.....+
T Consensus 157 psy~c~rc~~~g~wikacptv~~~~ 181 (448)
T KOG0314|consen 157 PSYKCVKCPTPGPWIKACPTVSGSY 181 (448)
T ss_pred CCcceecCCCCCccceeccccCCcc
Confidence 3578999999999999999876643
No 52
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=28.63 E-value=87 Score=21.08 Aligned_cols=25 Identities=32% Similarity=0.498 Sum_probs=20.4
Q ss_pred HHHHHHhCCCCCCchhhHHHHHHHHHHHhh
Q 013049 32 VEASERLGIDLSDANHKRFIRGVVESFLLS 61 (450)
Q Consensus 32 ~~~~~~~~~~l~~~~~k~~~~~~v~~~~~~ 61 (450)
..++++.||.. =+.|++.|+.||.+
T Consensus 18 ~~ls~~t~i~~-----S~Ll~eAle~~l~k 42 (44)
T PF12651_consen 18 KELSEETGIPK-----SKLLREALEDYLEK 42 (44)
T ss_pred HHHHHHHCCCH-----HHHHHHHHHHHHHh
Confidence 46788889944 58899999999974
No 53
>cd05500 Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=28.09 E-value=51 Score=26.62 Aligned_cols=75 Identities=9% Similarity=0.112 Sum_probs=40.6
Q ss_pred cCHHHHHHHHhhhhHHHHHHHHhccccCCCCCCCCchhhhcccCCCCCCCCCcccccCC--CChHHHHHHHHHHhhh
Q 013049 136 LTSEQWRAFSKSLPAIDEAVVKMQSKLRSESSGEQNKDVANSMTSPLELFPTELHRFNG--KNYRVWAQQIELLLKQ 210 (450)
Q Consensus 136 l~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~sp~s~~~~~i~kLdG--~Ny~~W~~~m~~~L~~ 210 (450)
||.+||+.+.+++..|.+.=....-..|..+....-++....+..||....+.--.-+| .+...|...|..++..
T Consensus 1 ~t~~~~~~~~~ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~~kl~~~~Y~s~~~f~~D~~li~~N 77 (103)
T cd05500 1 MTKHQHKFLLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDN 77 (103)
T ss_pred CCHHHHHHHHHHHHHHHcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence 68899999999888876321000001111111112344455555666665555333334 3677777777777653
No 54
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=27.28 E-value=21 Score=28.48 Aligned_cols=9 Identities=0% Similarity=0.135 Sum_probs=1.5
Q ss_pred CceEEEcCC
Q 013049 92 DSIICKLSN 100 (450)
Q Consensus 92 d~~~~~~~~ 100 (450)
+..++.++.
T Consensus 40 e~p~p~fge 48 (101)
T PF09026_consen 40 EVPVPEFGE 48 (101)
T ss_dssp ------HHH
T ss_pred cccchhHHH
Confidence 444555553
No 55
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=26.75 E-value=1.6e+02 Score=20.49 Aligned_cols=40 Identities=15% Similarity=0.158 Sum_probs=29.7
Q ss_pred hhhHHHHHHHHHHHhhcCCchhhhHHHHHHHHHHHhCCCCC
Q 013049 3 TVNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLS 43 (450)
Q Consensus 3 ~~~~~~~~~~~~~~l~~~~~~~~t~~~~r~~~~~~~~~~l~ 43 (450)
++-|.+....+..+|.... +.+-..-..+++++.+|++..
T Consensus 18 ~egk~~~~~~~~~~i~~i~-~~i~r~~y~~~la~~~~i~~~ 57 (59)
T PF10410_consen 18 PEGKAEAVREAAPLIAQIP-DPIERELYIRELAERLGISED 57 (59)
T ss_dssp HHHHHHHHHHHHHHHTT---SHHHHHHHHHHHHHHCT-SST
T ss_pred HHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHhCcCcc
Confidence 4678888888888888876 666666778889999999865
No 56
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=26.65 E-value=20 Score=25.20 Aligned_cols=22 Identities=27% Similarity=0.635 Sum_probs=16.8
Q ss_pred cccccccCc-------ccccccccCCccc
Q 013049 419 TVVCYNCRK-------KGHVAKHCHNKRL 440 (450)
Q Consensus 419 ~~~C~~Cgk-------~GH~~~~C~~~~~ 440 (450)
...|.+|+| .||+...||.-+-
T Consensus 4 tiRC~~CnKlLa~a~~~~yle~KCPrCK~ 32 (60)
T COG4416 4 TIRCAKCNKLLAEAEGQAYLEKKCPRCKE 32 (60)
T ss_pred eeehHHHhHHHHhcccceeeeecCCccce
Confidence 467888887 5789999987543
No 57
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.60 E-value=1.1e+02 Score=22.51 Aligned_cols=40 Identities=15% Similarity=0.272 Sum_probs=30.6
Q ss_pred hHHHHHHHHHhcc-hhHHHHhhhccccHHHHHHHHHHHhccc
Q 013049 249 NNICRHHILNFLS-DHLYYQYSKRTSSAKELWEELKLVYLDE 289 (450)
Q Consensus 249 d~~a~~~I~~sl~-~~i~~~i~~~~~ta~elW~~Lk~~y~~~ 289 (450)
...|....+..|. ......+.. -..++++|.+|+..|.-.
T Consensus 20 ~~la~dhvL~~LGgrT~~eAL~~-G~dpr~VW~AlC~~~dVP 60 (63)
T PF11248_consen 20 RSLARDHVLSELGGRTAAEALEA-GVDPRDVWRALCDAFDVP 60 (63)
T ss_pred HHHHHhcchhhcCCcCHHHHHHc-CCCHHHHHHHHHHHcCCC
Confidence 4456667778888 566667777 799999999999998543
No 58
>PF01707 Peptidase_C9: Peptidase family C9; InterPro: IPR002620 The family of alphaviruses includes 26 known members. They infect a variety of hosts including mosquitoes, birds, rodents and other mammals with worldwide distribution. Alphaviruses also pose a potential threat to human health in many area. For example, Venezuelan Equine Encephalitis Virus (VEEV) causes encephalitis in humans as well as livestock in Central and South America, and some variants of Sinbis Virus (SIN) and Semliki Forest Virus (SFV) have been found to cause fever and arthritis in humans []. Alphaviruses possess a single-stranded RNA genome of approximately 12 kb. The genomic RNA of alphaviruses is translated into two polyproteins that, respectively, encode structural proteins and nonstructural proteins. The nonstructural proteins may be translated as one or two polyproteins, nsp123 or nsp1234, depending on the virus. These polyproteins are cleaved to generate nsp1, nsp2, nsp3 and nsp4 by a protease activity that resides within nsp2 []. The nsp2 protein of alphaviruses has multiple enzymatic acivities. Its N-terminal domain has been shown to possess ATPase and GTPase activity, RNA helicase activity and RNA 5'-triphosphatase activity []. The C-terminal nsp2pro domain of nsp2 is responsible for the regulation of 26S subgenome RNA synthesis, switching between negative- and positive-strand RNA synthesis, targeting nsp2 for nuclear transport and proteolytic processing of the nonstructural polyprotein [, ]. The nsp2pro domain is a member of peptidase family C9 of clan CA. The nsp2pro domain consists of two distinct subdomains. The nsp2pro N-terminal subdomain is largely alpha-helical and contains the catalytic dyad cysteine and histidine residues organised in a protein fold that differs significantly from any known cysteine protease or protein folds. The nsp2pro C-terminal subdomain displays structural similarity to S-adenosyl- L-methionine-dependent RNA methyltransferases and provides essential elements that contribute to substrate recognition and may also regulate the structure of the substrate binding cleft []. This entry represents the nsp2pro domain.; PDB: 3TRK_A 2HWK_A.
Probab=26.54 E-value=17 Score=32.68 Aligned_cols=16 Identities=44% Similarity=0.796 Sum_probs=9.9
Q ss_pred cccccCHHHHHHHHhh
Q 013049 132 KGIALTSEQWRAFSKS 147 (450)
Q Consensus 132 kgi~l~~~~~~~l~~~ 147 (450)
-||.||.+||+.|...
T Consensus 62 AGI~LT~~qW~~l~p~ 77 (202)
T PF01707_consen 62 AGIQLTAEQWSTLFPA 77 (202)
T ss_dssp TT----HHHHCCCHHH
T ss_pred cCcccCHHHHHHHhHH
Confidence 7999999999988743
No 59
>PRK12449 acyl carrier protein; Provisional
Probab=25.78 E-value=1.6e+02 Score=22.22 Aligned_cols=46 Identities=7% Similarity=0.135 Sum_probs=28.7
Q ss_pred hHHHHHHHHHHHhhc--------------CCchhhhHHHHHHHHHHHhCCCCCCchhhHH
Q 013049 5 NEGRIRQTVMEVLKN--------------SDMEEMTEFKVRVEASERLGIDLSDANHKRF 50 (450)
Q Consensus 5 ~~~~~~~~~~~~l~~--------------~~~~~~t~~~~r~~~~~~~~~~l~~~~~k~~ 50 (450)
...+|++.|.+++.- =.++++..-.+=..+|++|||.+++.+...+
T Consensus 6 i~~~l~~il~~~~~~~~~~i~~~~~l~~dlg~DSl~~~~li~~lE~~f~i~i~~~~~~~~ 65 (80)
T PRK12449 6 IFERLINLIQKQRSYLSLAITEQTHLKDDLAVDSIELVEFIINVEDEFHIAIPDEDVEDM 65 (80)
T ss_pred HHHHHHHHHHHHhCCCccccCCCCcHHHHcCCcHHHHHHHHHHHHHHhCCCCCHHHHHhC
Confidence 345556666665532 2234455556677899999999986655444
No 60
>PF06526 DUF1107: Protein of unknown function (DUF1107); InterPro: IPR009491 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2JRO_A.
Probab=25.64 E-value=1.2e+02 Score=22.45 Aligned_cols=44 Identities=18% Similarity=0.465 Sum_probs=26.0
Q ss_pred eecCceeEe-eEeEEecCCcccCCCcccccCHHHHHHHHhhhhHHHHHHHHh
Q 013049 108 EFKGRAFVS-IREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAIDEAVVKM 158 (450)
Q Consensus 108 ~~~g~~~~~-ir~~~~~~~~~~p~~kgi~l~~~~~~~l~~~~~~i~~~~~~~ 158 (450)
=|+|+.||+ |..|--+.|+.++-+++ . ..-...+.+|+..|..+
T Consensus 19 lF~Gr~~I~g~G~feFd~Gkillp~~~----~---~~~~~~~~EiN~~I~~L 63 (64)
T PF06526_consen 19 LFRGRIYIKGIGAFEFDNGKILLPKKA----D---KRHLSVMSEINQEIRRL 63 (64)
T ss_dssp H-SEEEEETTTEEEEEETTEE---SS---------HHHHHHHHHHHHHHHHH
T ss_pred HccceEEEEecccEEEcCCEEeCCccc----c---HHHHHHHHHHHHHHHhc
Confidence 389999984 77777789986654332 2 23455667777777654
No 61
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=25.42 E-value=1.8e+02 Score=18.45 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=19.8
Q ss_pred HHHHHHHhCCCCCCchhhHHHHHHHHHHHh
Q 013049 31 RVEASERLGIDLSDANHKRFIRGVVESFLL 60 (450)
Q Consensus 31 r~~~~~~~~~~l~~~~~k~~~~~~v~~~~~ 60 (450)
=.++.++.|. .+-.|||..|..||.
T Consensus 14 l~~~a~~~g~-----s~s~~ir~ai~~~l~ 38 (39)
T PF01402_consen 14 LDELAKELGR-----SRSELIREAIREYLE 38 (39)
T ss_dssp HHHHHHHHTS-----SHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCc-----CHHHHHHHHHHHHHh
Confidence 3566778887 556899999999985
No 62
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=25.17 E-value=1.6e+02 Score=23.65 Aligned_cols=47 Identities=23% Similarity=0.383 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHhhcCCchhhhHHHHHHHHHHHhCCCCCCchhhHHHHHHHHHHHhh
Q 013049 6 EGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDLSDANHKRFIRGVVESFLLS 61 (450)
Q Consensus 6 ~~~~~~~~~~~l~~~~~~~~t~~~~r~~~~~~~~~~l~~~~~k~~~~~~v~~~~~~ 61 (450)
|+++...|.+.+.+-|.++.-+.- .+|++. + .+..||+.+|...|++
T Consensus 2 rk~i~~~l~ey~~~~d~~ea~~~l------~el~~~-~--~~~~vv~~~l~~~le~ 48 (113)
T PF02847_consen 2 RKKIFSILMEYFSSGDVDEAVECL------KELKLP-S--QHHEVVKVILECALEE 48 (113)
T ss_dssp HHHHHHHHHHHHHHT-HHHHHHHH------HHTT-G-G--GHHHHHHHHHHHHHTS
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHH------HHhCCC-c--cHHHHHHHHHHHHhhc
Confidence 678888888888888887766543 346776 5 7889999999988865
No 63
>PRK05883 acyl carrier protein; Validated
Probab=24.12 E-value=2.4e+02 Score=22.22 Aligned_cols=25 Identities=28% Similarity=0.409 Sum_probs=17.4
Q ss_pred chhhhHHHHHHHHHHHhCCCCCCch
Q 013049 22 MEEMTEFKVRVEASERLGIDLSDAN 46 (450)
Q Consensus 22 ~~~~t~~~~r~~~~~~~~~~l~~~~ 46 (450)
++++.--.+-..+|+.|||.+...+
T Consensus 46 ~DSL~~v~lv~~lE~~fgI~i~~ee 70 (91)
T PRK05883 46 LDSVAFAVGMVAIEERLGVALSEED 70 (91)
T ss_pred CChHHHHHHHHHHHHHHCCCcCHHH
Confidence 3445545556689999999998553
No 64
>PF07571 DUF1546: Protein of unknown function (DUF1546); InterPro: IPR011442 These proteins are associated with IPR004823 from INTERPRO in transcription initiation factor TFIID subunit 6 (TAF6).; GO: 0051090 regulation of sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=24.05 E-value=3.2e+02 Score=21.48 Aligned_cols=51 Identities=6% Similarity=-0.041 Sum_probs=39.2
Q ss_pred cHHHHHHHHHHHhcccchhhHHHHHHHHHHhhccccchHHHHHHHHHHHHH
Q 013049 274 SAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKIAD 324 (450)
Q Consensus 274 ta~elW~~Lk~~y~~~~~~~~~~l~~~l~~~k~~~~~sv~e~i~~~~~l~~ 324 (450)
-|..+-..+...|+.....-+.++.+.|...-+++..++..+++.+..+..
T Consensus 25 ~AA~lL~~I~~~~~~~~~~L~~Ri~~tl~k~l~d~~~~~~t~YGAi~gL~~ 75 (92)
T PF07571_consen 25 FAASLLAQICRKFSSSYPTLQPRITRTLLKALLDPKKPLGTHYGAIVGLSA 75 (92)
T ss_pred HHHHHHHHHHHHhccccchHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 455666677778877777777788888888888888999999998777654
No 65
>cd07936 SCAN SCAN oligomerization domain. The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.
Probab=23.71 E-value=1e+02 Score=24.13 Aligned_cols=71 Identities=13% Similarity=0.075 Sum_probs=47.2
Q ss_pred HHHHHHhhccccchHHHHHHHHHHHHHHHHHcC----CCcchHHHHHHHHhhCCCCcHHHHHHHhcCCCCCHHHHHHH
Q 013049 298 VKKYIEFQMFDEKSVFEQALELNKIADSIVAAG----MMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDH 371 (450)
Q Consensus 298 ~~~l~~~k~~~~~sv~e~i~~~~~l~~~L~~~g----~~i~d~~~~~~iL~sLp~~~~~~~~~l~~~~~ltl~el~~~ 371 (450)
+++|..+.+.+..+..+++.+++.++.+--... ..|-+-.....||..||+.+...+. ...+-|-+++...
T Consensus 5 r~~FR~f~~~~~~~p~eal~~L~eLc~~WLrpe~~tkeqilelLVlEQfl~~lp~e~q~~v~---~~~p~s~eea~~l 79 (85)
T cd07936 5 RQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVR---ERKPESGEEAATL 79 (85)
T ss_pred HHHHhccccCCCCChHHHHHHHHHHHHHHcchhhcCHHHHHHHHHHHHHhhhCCHHHHHHHH---hcCCCCHHHHHHH
Confidence 567888889999999999999999988763322 2344556666777788886555433 3333455554433
No 66
>cd04754 Commd6 COMM_Domain containing protein 6. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=23.71 E-value=1.8e+02 Score=22.85 Aligned_cols=43 Identities=16% Similarity=0.411 Sum_probs=34.5
Q ss_pred CceeEeeEeEEec-CCcccCCCcccccCHHHHHHHHhhhhHHHHHH
Q 013049 111 GRAFVSIREYFRR-DGKLVPTAKGIALTSEQWRAFSKSLPAIDEAV 155 (450)
Q Consensus 111 g~~~~~ir~~~~~-~~~~~p~~kgi~l~~~~~~~l~~~~~~i~~~~ 155 (450)
|.+||.+-=-..+ +|...| +-+-||.+|+..|...+.++...|
T Consensus 42 ~~Pfl~l~L~V~~~~G~~~~--~~~EmTlpEFq~f~~~~~~~~a~l 85 (86)
T cd04754 42 NSPYVAVTLKVADPSGQVVT--KSFEMTIPEFQNFSRQFKEMAAVL 85 (86)
T ss_pred CCceEEEEEEEEccCCCccc--eEEEEcHHHHHHHHHHHHHHHHhc
Confidence 8888886655544 788866 599999999999999998887644
No 67
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=22.89 E-value=61 Score=24.92 Aligned_cols=17 Identities=35% Similarity=0.581 Sum_probs=15.1
Q ss_pred HHHHHHHHHhCCCCCCc
Q 013049 29 KVRVEASERLGIDLSDA 45 (450)
Q Consensus 29 ~~r~~~~~~~~~~l~~~ 45 (450)
.+|..+|..||+||+.-
T Consensus 5 ~~r~~~e~~~G~dl~~V 21 (79)
T PF13699_consen 5 SIRSRLERAFGADLSDV 21 (79)
T ss_pred HHHHHHHHHhCCCccce
Confidence 58999999999999954
No 68
>smart00431 SCAN leucine rich region.
Probab=22.87 E-value=1.1e+02 Score=25.41 Aligned_cols=73 Identities=11% Similarity=0.096 Sum_probs=51.3
Q ss_pred HHHHHHHhhccccchHHHHHHHHHHHHHHHHHcC----CCcchHHHHHHHHhhCCCCcHHHHHHHhcCCCCCHHHHHHHH
Q 013049 297 QVKKYIEFQMFDEKSVFEQALELNKIADSIVAAG----MMIYENFHVSVILSKLPLSWKDFCIKLMRMEYLTFTMLMDHI 372 (450)
Q Consensus 297 l~~~l~~~k~~~~~sv~e~i~~~~~l~~~L~~~g----~~i~d~~~~~~iL~sLp~~~~~~~~~l~~~~~ltl~el~~~L 372 (450)
.+++|.++.+.+.....+++.+++.|+..--... ..|-+-.....||..||..+...+. ...+-+-+++...+
T Consensus 4 ~r~~FR~f~y~e~~gp~eaL~~L~eLc~~WLrPe~~tKeqilElLVlEQFL~ilP~e~q~wv~---~~~p~sgeeav~l~ 80 (113)
T smart00431 4 FRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVR---EHHPESGEEAVTLL 80 (113)
T ss_pred HHHHhhccccCCCCChHHHHHHHHHHHHhhcChhhhhHHHHHHHHHHHHHhccCcHHHHHHHH---hcCCCCHHHHHHHH
Confidence 3567888889999999999999999988753322 2345566677778888888777643 33444666666554
No 69
>PRK07117 acyl carrier protein; Validated
Probab=22.50 E-value=3e+02 Score=21.06 Aligned_cols=52 Identities=13% Similarity=0.172 Sum_probs=29.0
Q ss_pred hHHHHHHHHHHHhhcCCchhhh--------------HHHHHHHHHHHhCCCCCCchhhHH--HHHHHH
Q 013049 5 NEGRIRQTVMEVLKNSDMEEMT--------------EFKVRVEASERLGIDLSDANHKRF--IRGVVE 56 (450)
Q Consensus 5 ~~~~~~~~~~~~l~~~~~~~~t--------------~~~~r~~~~~~~~~~l~~~~~k~~--~~~~v~ 56 (450)
.-.+|++.|.+++-+.|-+.+| .-.+=..++++||+.+++.+...+ |.++|+
T Consensus 6 i~~~v~~ii~e~~p~i~~~~I~~~~~l~DLg~DSlD~veiv~~led~f~i~I~~~~~~~i~Tv~d~v~ 73 (79)
T PRK07117 6 IFDILVRHIREVLPDLDQHQFQPEDSLVDLGANSMDRAEIVIMTLESLSLKIPLVEFAGAKNIGELAD 73 (79)
T ss_pred HHHHHHHHHHHHcCCCCHHHCCCCCChhhcCCChHHHHHHHHHHHHHHCCccCHHHHHhcCCHHHHHH
Confidence 3556667777776434444443 334445677777777776554433 444443
No 70
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=21.71 E-value=2.4e+02 Score=27.26 Aligned_cols=30 Identities=20% Similarity=0.343 Sum_probs=23.9
Q ss_pred CChHHHHHHHHHHhhhcccceeccccccCC
Q 013049 195 KNYRVWAQQIELLLKQLKVAYVLTDPCPIV 224 (450)
Q Consensus 195 ~Ny~~W~~~m~~~L~~~~l~~~l~~~~~~p 224 (450)
+|-..|+.+|+.+|.-..+...+.-..|.|
T Consensus 168 sn~~~w~~~m~til~~qqv~~~iqi~~~~~ 197 (332)
T KOG3926|consen 168 SNINLWKERMETILRWQQVLSQIQITEPDP 197 (332)
T ss_pred chHHHHHHHHHHHHHHHHHHHhhcccCCCc
Confidence 488999999999999888777666555554
No 71
>PF14568 SUKH_6: SMI1-KNR4 cell-wall; PDB: 2PRV_A.
Probab=21.66 E-value=70 Score=25.83 Aligned_cols=21 Identities=33% Similarity=0.669 Sum_probs=14.6
Q ss_pred HHHHHHhCCCCCCchhhHHHHH
Q 013049 32 VEASERLGIDLSDANHKRFIRG 53 (450)
Q Consensus 32 ~~~~~~~~~~l~~~~~k~~~~~ 53 (450)
.++|++||+.|. ++||.|+..
T Consensus 5 ~~~E~~Lg~~lP-~~Yk~fL~~ 25 (120)
T PF14568_consen 5 EEAEKKLGVKLP-EDYKEFLKE 25 (120)
T ss_dssp HHHHHHHTS----HHHHHHHHH
T ss_pred HHHHHHhCCCCC-HHHHHHHHH
Confidence 578999999998 568888774
No 72
>PF07827 KNTase_C: KNTase C-terminal domain; InterPro: IPR012481 Kanamycin nucleotidyltransferase (KNTase) is involved in conferring resistance to aminoglycoside antibiotics and catalyses the transfer of a nucleoside monophosphate group from a nucleotide to kanamycin. This enzyme is dimeric with each subunit being composed of two domains. The C-terminal domain contains five alpha helices, four of which are organised into an up-and-down alpha helical bundle. Residues found in this domain may contribute to this enzyme's active site []. ; GO: 0016779 nucleotidyltransferase activity, 0046677 response to antibiotic; PDB: 1KNY_A.
Probab=21.20 E-value=5.4e+02 Score=22.22 Aligned_cols=34 Identities=12% Similarity=0.120 Sum_probs=22.5
Q ss_pred HhhCCCCcHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 013049 343 LSKLPLSWKDFCIKLMRMEYLTFTMLMDHIKAEE 376 (450)
Q Consensus 343 L~sLp~~~~~~~~~l~~~~~ltl~el~~~L~~eE 376 (450)
|.++|+-|++++..+++..-.+.+.|...+...-
T Consensus 88 Lp~rP~Gyd~l~~lvm~G~L~d~~~i~~~cE~~W 121 (143)
T PF07827_consen 88 LPSRPSGYDELAQLVMSGQLTDPEKIYESCEALW 121 (143)
T ss_dssp SSS--TTHHHHHHHHHHTB---HHHHHHHHHHHH
T ss_pred CCCCCccHHHHHHHHhccccCCHHHHHHHHHHHH
Confidence 4567999999999999887677777777665443
No 73
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=21.17 E-value=44 Score=31.58 Aligned_cols=23 Identities=30% Similarity=0.501 Sum_probs=19.1
Q ss_pred CcccccccCccc---ccccccCCccc
Q 013049 418 KTVVCYNCRKKG---HVAKHCHNKRL 440 (450)
Q Consensus 418 ~~~~C~~Cgk~G---H~~~~C~~~~~ 440 (450)
....|..||..| |+.++||....
T Consensus 267 R~YVCPiCGATgDnAHTiKyCPl~~~ 292 (318)
T KOG4602|consen 267 RSYVCPICGATGDNAHTIKYCPLAFG 292 (318)
T ss_pred hhhcCccccccCCcccceecccccCC
Confidence 356789999988 99999998765
No 74
>KOG0377 consensus Protein serine/threonine phosphatase RDGC/PPEF, contains STphosphatase and EF-hand domains [Signal transduction mechanisms]
Probab=21.11 E-value=3.5e+02 Score=28.02 Aligned_cols=73 Identities=10% Similarity=0.061 Sum_probs=49.9
Q ss_pred hhHHHHHHHHHhcchhHHHHhhhccccHHHHHHHHHHHhcccchhhHHHHHHHHHHhhccccchHHHHHHHHHHH
Q 013049 248 DNNICRHHILNFLSDHLYYQYSKRTSSAKELWEELKLVYLDEEFGTKRSQVKKYIEFQMFDEKSVFEQALELNKI 322 (450)
Q Consensus 248 ~d~~a~~~I~~sl~~~i~~~i~~~~~ta~elW~~Lk~~y~~~~~~~~~~l~~~l~~~k~~~~~sv~e~i~~~~~l 322 (450)
++...+..|+..|+.+.-..|. .+-...+|+.|..++...-....+..+.+.+.+..++.-++.+|+..|+-.
T Consensus 544 r~ks~LetiF~~iD~D~SG~is--ldEF~~a~~l~~sh~~~~i~~~~i~~la~~mD~NkDG~IDlNEfLeAFrlv 616 (631)
T KOG0377|consen 544 RNKSSLETIFNIIDADNSGEIS--LDEFRTAWKLLSSHMNGAISDDEILELARSMDLNKDGKIDLNEFLEAFRLV 616 (631)
T ss_pred hchhhHHHHHHHhccCCCCcee--HHHHHHHHHHHHhhcCCCcCHHHHHHHHHhhccCCCCcccHHHHHHHHhhh
Confidence 3444455555555555444443 356778999999999766666667777777778777777888888877643
No 75
>PF13565 HTH_32: Homeodomain-like domain
Probab=21.05 E-value=1.6e+02 Score=21.73 Aligned_cols=34 Identities=15% Similarity=0.293 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhhcCCchhhhHHHHHHHHHHHhCCCC
Q 013049 7 GRIRQTVMEVLKNSDMEEMTEFKVRVEASERLGIDL 42 (450)
Q Consensus 7 ~~~~~~~~~~l~~~~~~~~t~~~~r~~~~~~~~~~l 42 (450)
..+++.|.+++.+-- ..|...|...|+++||+.+
T Consensus 33 ~e~~~~i~~~~~~~p--~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 33 PEQRERIIALIEEHP--RWTPREIAEYLEEEFGISV 66 (77)
T ss_pred HHHHHHHHHHHHhCC--CCCHHHHHHHHHHHhCCCC
Confidence 455566666666443 7789999999999999988
No 76
>PF01221 Dynein_light: Dynein light chain type 1 ; InterPro: IPR001372 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits (see IPR004273 from INTERPRO), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, ]. Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer alpha-beta core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].; GO: 0007017 microtubule-based process, 0005875 microtubule associated complex; PDB: 1F95_A 1F96_A 1F3C_A 3P8M_B 2XQQ_C 1RE6_A 1CMI_A 1PWK_A 1PWJ_A 4DS1_C ....
Probab=20.83 E-value=2e+02 Score=22.36 Aligned_cols=39 Identities=18% Similarity=0.149 Sum_probs=26.1
Q ss_pred CchhhHHHHHHHHHHHhhcCCchhhhHHHHHHHHHHHhC
Q 013049 1 METVNEGRIRQTVMEVLKNSDMEEMTEFKVRVEASERLG 39 (450)
Q Consensus 1 ~~~~~~~~~~~~~~~~l~~~~~~~~t~~~~r~~~~~~~~ 39 (450)
|+++-+..+.+.+.+.|+..+-+.-=...|.+.|.+++|
T Consensus 13 M~~~~~~~~~~~~~~a~~~~~~~~eiA~~iK~~lD~~yG 51 (89)
T PF01221_consen 13 MPEEMQEEAIELAKEALKKYQDEKEIAEFIKQELDKKYG 51 (89)
T ss_dssp S-HHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHS
T ss_pred CCHHHHHHHHHHHHHHHHHCCcHHHHHHHHHHHHhcccC
Confidence 677778888888888887755433344566677776665
Done!