Query 031792
Match_columns 153
No_of_seqs 169 out of 307
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 05:24:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031792.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031792hhsearch_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 7.6E-32 1.7E-36 201.1 5.4 79 73-151 30-108 (108)
2 PF02229 PC4: Transcriptional 99.9 3.4E-24 7.4E-29 143.1 3.7 55 84-138 1-56 (56)
3 PF08766 DEK_C: DEK C terminal 99.4 2.9E-13 6.3E-18 89.2 5.3 51 5-57 1-51 (54)
4 KOG2266 Chromatin-associated p 98.8 9E-09 2E-13 93.9 5.2 53 3-57 519-571 (594)
5 COG4443 Uncharacterized protei 89.9 0.22 4.8E-06 35.0 1.9 39 98-139 31-70 (72)
6 KOG1946 RNA polymerase I trans 78.3 1.8 4E-05 36.7 2.6 44 10-55 8-51 (240)
7 PRK05828 acyl carrier protein; 56.7 23 0.00049 25.1 4.1 42 5-46 2-61 (84)
8 TIGR02530 flg_new flagellar op 56.3 13 0.00028 27.7 2.9 21 121-141 27-47 (96)
9 PF10815 ComZ: ComZ; InterPro 55.9 19 0.00041 24.4 3.3 30 120-149 22-51 (56)
10 PF13551 HTH_29: Winged helix- 53.4 37 0.00081 23.4 4.8 43 9-51 62-108 (112)
11 PF00550 PP-binding: Phosphopa 49.1 50 0.0011 20.8 4.6 37 8-44 2-51 (67)
12 PF10410 DnaB_bind: DnaB-helic 48.3 67 0.0014 20.1 5.0 40 3-43 18-57 (59)
13 PF01707 Peptidase_C9: Peptida 38.6 6.8 0.00015 32.7 -1.1 14 122-135 62-75 (202)
14 PRK12449 acyl carrier protein; 36.3 1.2E+02 0.0027 20.2 5.1 27 22-48 37-63 (80)
15 PF13565 HTH_32: Homeodomain-l 35.7 78 0.0017 20.7 4.0 34 7-42 33-66 (77)
16 CHL00124 acpP acyl carrier pro 35.5 86 0.0019 21.1 4.3 24 23-46 38-61 (82)
17 PF08848 DUF1818: Domain of un 35.2 46 0.001 25.6 3.1 30 124-153 29-58 (117)
18 cd07999 GH7_CBH_EG Glycosyl hy 32.4 56 0.0012 29.8 3.6 40 91-130 257-307 (386)
19 PF13101 DUF3945: Protein of u 31.8 30 0.00066 22.9 1.4 20 118-137 26-46 (59)
20 PF08988 DUF1895: Protein of u 31.6 76 0.0017 22.0 3.5 24 126-149 38-61 (68)
21 PF08880 QLQ: QLQ; InterPro: 31.6 49 0.0011 20.3 2.2 16 125-140 2-17 (37)
22 cd04754 Commd6 COMM_Domain con 31.1 1.3E+02 0.0029 21.9 4.8 43 101-145 42-85 (86)
23 COG2921 Uncharacterized conser 30.5 37 0.0008 25.1 1.8 26 116-141 49-83 (90)
24 PF13699 DUF4157: Domain of un 30.2 38 0.00083 23.7 1.8 16 29-44 5-20 (79)
25 PF07544 Med9: RNA polymerase 29.8 89 0.0019 21.9 3.6 31 123-153 49-83 (83)
26 PF06831 H2TH: Formamidopyrimi 29.1 97 0.0021 22.0 3.8 46 105-150 37-87 (92)
27 PF11325 DUF3127: Domain of un 28.9 92 0.002 22.5 3.6 18 93-110 64-81 (84)
28 TIGR02501 type_III_yscE type I 28.5 91 0.002 21.5 3.4 24 126-149 37-60 (67)
29 PRK05350 acyl carrier protein; 28.4 1.2E+02 0.0026 20.6 4.0 24 23-46 39-62 (82)
30 PF09312 SurA_N: SurA N-termin 28.3 66 0.0014 23.5 2.9 45 5-55 68-112 (118)
31 COG5129 MAK16 Nuclear protein 27.8 1.3E+02 0.0027 26.2 4.8 43 82-135 38-80 (303)
32 COG4746 Uncharacterized protei 27.0 54 0.0012 23.7 2.1 37 5-43 4-40 (80)
33 PF01221 Dynein_light: Dynein 25.8 1.7E+02 0.0037 20.3 4.5 39 1-39 13-51 (89)
34 PF14164 YqzH: YqzH-like prote 25.0 84 0.0018 21.8 2.7 18 124-141 24-41 (64)
35 PRK05883 acyl carrier protein; 24.8 1.2E+02 0.0026 21.5 3.6 23 22-44 46-68 (91)
36 PF01436 NHL: NHL repeat; Int 23.9 80 0.0017 17.5 2.1 19 77-96 9-27 (28)
37 PF12949 HeH: HeH/LEM domain; 23.9 73 0.0016 19.4 2.0 31 23-54 2-32 (35)
38 KOG1748 Acyl carrier protein/N 23.4 68 0.0015 25.1 2.2 41 4-44 49-89 (131)
39 PF06526 DUF1107: Protein of u 23.0 1.4E+02 0.003 20.7 3.4 43 99-149 20-64 (64)
40 COG3415 Transposase and inacti 22.1 1.1E+02 0.0024 23.9 3.2 41 11-54 70-110 (138)
41 PF04358 DsrC: DsrC like prote 22.0 56 0.0012 24.4 1.5 20 117-136 30-49 (109)
42 PF00840 Glyco_hydro_7: Glycos 21.9 94 0.002 28.8 3.2 47 90-136 280-339 (433)
43 PF00466 Ribosomal_L10: Riboso 21.4 2.4E+02 0.0051 19.6 4.6 42 1-43 1-51 (100)
44 PF12651 RHH_3: Ribbon-helix-h 20.8 1.8E+02 0.0038 18.1 3.4 26 122-147 5-38 (44)
45 PF14568 SUKH_6: SMI1-KNR4 cel 20.6 67 0.0015 22.2 1.6 22 32-54 5-26 (120)
No 1
>KOG2712 consensus Transcriptional coactivator [Transcription]
Probab=99.97 E-value=7.6e-32 Score=201.07 Aligned_cols=79 Identities=51% Similarity=0.826 Sum_probs=72.2
Q ss_pred CCcccCCCCCeEEEEeCCceeEEEeeeCCceeEeeeeEEecCCcccCCCcccccCHHHHHHHHHhHHHHHHHHHHhhcc
Q 031792 73 DNAEYDDEGNLIICQLNKKRRVTIQDFKGKTLVSIREYYTKGGKELPSAKGISLTEEQWSALRKNVSAIDTAVKKMQSR 151 (153)
Q Consensus 73 ~~~~~d~~gd~~~~~Ls~~rrvtV~~fkG~~~VdIRE~Y~kdG~~~P~kKGIsLt~eqw~~l~~~~~~I~~ai~~l~~~ 151 (153)
.++.-++.++..+|+|+++|||||++|+|+.||||||||.++|+++||+||||||.+||..|++++++|++||..|++.
T Consensus 30 ~k~~d~~s~~~~i~~l~~~RrVtV~eFkGk~~VdIREyY~kdG~mlPgkKGISLs~~qW~~Lk~~~~eId~Al~~l~s~ 108 (108)
T KOG2712|consen 30 EKPKDDDSEDDNIFNLGKNRRVTVREFKGKILVDIREYYVKDGKMLPGKKGISLSLEQWSKLKEHIEEIDKALRKLSSG 108 (108)
T ss_pred cCcccCCcCccceeecCCceEEehhhcCCceEEehhHhhhccCccccCccccccCHHHHHHHHHHHHHHHHHHHHhccC
Confidence 3344446667777999999999999999999999999999999999999999999999999999999999999999873
No 2
>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=99.89 E-value=3.4e-24 Score=143.15 Aligned_cols=55 Identities=53% Similarity=0.900 Sum_probs=49.3
Q ss_pred EEEEeCCceeEEEeeeCCceeEeeeeEEec-CCcccCCCcccccCHHHHHHHHHhH
Q 031792 84 IICQLNKKRRVTIQDFKGKTLVSIREYYTK-GGKELPSAKGISLTEEQWSALRKNV 138 (153)
Q Consensus 84 ~~~~Ls~~rrvtV~~fkG~~~VdIRE~Y~k-dG~~~P~kKGIsLt~eqw~~l~~~~ 138 (153)
++|.++.++||+|++|+|++|||||+||.+ +|+|+||+|||||+++||..|++++
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 8999999999999999999999864
No 3
>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=99.42 E-value=2.9e-13 Score=89.20 Aligned_cols=51 Identities=37% Similarity=0.596 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHhhhcCCcchhhHHHHHHHHhHHcCCCCCChhHHHHHhhhhhh
Q 031792 5 TKAKIEGTVREILVKSDMTETTEFQIRKQASEKMGLDLSQPEYKAFVRHKSKE 57 (153)
Q Consensus 5 sk~~i~~~V~eILk~aDl~t~Te~~vR~~l~~~lgvdLs~~~~K~~Vr~~i~~ 57 (153)
|.++|+..|++||++|||+++|.++||++|+++||+||++ ||.||+++|..
T Consensus 1 td~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~~--~K~~I~~~I~~ 51 (54)
T PF08766_consen 1 TDEEIREAIREILREADLDTVTKKQVREQLEERFGVDLSS--RKKFIKELIDE 51 (54)
T ss_dssp -HHHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--SH--HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcHH--HHHHHHHHHHH
Confidence 5679999999999999999999999999999999999997 99999998753
No 4
>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics]
Probab=98.76 E-value=9e-09 Score=93.90 Aligned_cols=53 Identities=28% Similarity=0.418 Sum_probs=51.1
Q ss_pred hHHHHHHHHHHHHhhhcCCcchhhHHHHHHHHhHHcCCCCCChhHHHHHhhhhhh
Q 031792 3 AETKAKIEGTVREILVKSDMTETTEFQIRKQASEKMGLDLSQPEYKAFVRHKSKE 57 (153)
Q Consensus 3 ~~sk~~i~~~V~eILk~aDl~t~Te~~vR~~l~~~lgvdLs~~~~K~~Vr~~i~~ 57 (153)
.||..+|+.+|.+||+.+||+++|...|.++|..+|++||++ ||.||..+|++
T Consensus 519 ePTdeelk~~V~kILk~vdfntaTm~dIlKkl~~~f~~dLt~--rK~~IK~~Ike 571 (594)
T KOG2266|consen 519 EPTDEELKEVVKKILKEVDFNTATMKDILKKLYAKFPIDLTH--RKDFIKDTIKE 571 (594)
T ss_pred CCcHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHhCCccccc--chHHHHHHHHH
Confidence 589999999999999999999999999999999999999999 99999999865
No 5
>COG4443 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.85 E-value=0.22 Score=35.04 Aligned_cols=39 Identities=31% Similarity=0.555 Sum_probs=30.7
Q ss_pred eeCCce-eEeeeeEEecCCcccCCCcccccCHHHHHHHHHhHH
Q 031792 98 DFKGKT-LVSIREYYTKGGKELPSAKGISLTEEQWSALRKNVS 139 (153)
Q Consensus 98 ~fkG~~-~VdIRE~Y~kdG~~~P~kKGIsLt~eqw~~l~~~~~ 139 (153)
.|+|.+ -.|||.|-.+..++ -|||+||.+++..|++.+.
T Consensus 31 SwNg~~~KyDiR~Wspdh~KM---GKGiTLt~eE~~~l~d~l~ 70 (72)
T COG4443 31 SWNGRPPKYDIRAWSPDHSKM---GKGITLTNEEFKALKDLLN 70 (72)
T ss_pred ccCCCCCcCcccccCcchhhh---cCceeecHHHHHHHHHHHh
Confidence 588876 78999997654333 3899999999999998764
No 6
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=78.34 E-value=1.8 Score=36.73 Aligned_cols=44 Identities=18% Similarity=0.133 Sum_probs=39.0
Q ss_pred HHHHHHhhhcCCcchhhHHHHHHHHhHHcCCCCCChhHHHHHhhhh
Q 031792 10 EGTVREILVKSDMTETTEFQIRKQASEKMGLDLSQPEYKAFVRHKS 55 (153)
Q Consensus 10 ~~~V~eILk~aDl~t~Te~~vR~~l~~~lgvdLs~~~~K~~Vr~~i 55 (153)
.-.+..||...|++++|...||++++..+|+++.. .|..++..+
T Consensus 8 ~~~~~~~l~~~~~~~lt~~~vr~~~~~~~~v~~~~--~k~~~~~~~ 51 (240)
T KOG1946|consen 8 YLFKDYILSLKDQETLTPDDVRRAMAPRSGVDGTA--QKSLLAKAI 51 (240)
T ss_pred hhhhHHHhcccccccCCHHHHHHHhccccCCCCcc--hhhhhhhhh
Confidence 34577899999999999999999999999999988 888887665
No 7
>PRK05828 acyl carrier protein; Validated
Probab=56.68 E-value=23 Score=25.12 Aligned_cols=42 Identities=17% Similarity=0.266 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhhhcC------------------CcchhhHHHHHHHHhHHcCCCCCChh
Q 031792 5 TKAKIEGTVREILVKS------------------DMTETTEFQIRKQASEKMGLDLSQPE 46 (153)
Q Consensus 5 sk~~i~~~V~eILk~a------------------Dl~t~Te~~vR~~l~~~lgvdLs~~~ 46 (153)
++.+|-++|++||.+. +++++..-.+--.++++||+.++..+
T Consensus 2 ~~~eI~~~i~~ii~e~~~~~~~d~i~~~~~~~dLg~DSLd~velv~~lE~~f~I~i~~e~ 61 (84)
T PRK05828 2 QEMEILLKIKEIAKKKNFAVTLDESNINKPYRELKIDSLDMFSIIVSLESEFNIEFSDEK 61 (84)
T ss_pred CHHHHHHHHHHHHHHhccCCCcccccCCCCHHhcCCCHHHHHHHHHHHHHHHCCCcCHHH
Confidence 4678888888888862 23455566777888999999988733
No 8
>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=56.31 E-value=13 Score=27.70 Aligned_cols=21 Identities=24% Similarity=0.558 Sum_probs=17.4
Q ss_pred CcccccCHHHHHHHHHhHHHH
Q 031792 121 AKGISLTEEQWSALRKNVSAI 141 (153)
Q Consensus 121 kKGIsLt~eqw~~l~~~~~~I 141 (153)
..||+|+.++|..|-+++...
T Consensus 27 ~R~I~l~~~~~~~i~~av~~A 47 (96)
T TIGR02530 27 ERNISINPDDWKKLLEAVEEA 47 (96)
T ss_pred HcCCCCCHHHHHHHHHHHHHH
Confidence 479999999999998866544
No 9
>PF10815 ComZ: ComZ; InterPro: IPR024558 ComZ, which contains a leucine zipper motif, negatively regulates transcription of the ComG operon [].
Probab=55.89 E-value=19 Score=24.39 Aligned_cols=30 Identities=20% Similarity=0.283 Sum_probs=23.7
Q ss_pred CCcccccCHHHHHHHHHhHHHHHHHHHHhh
Q 031792 120 SAKGISLTEEQWSALRKNVSAIDTAVKKMQ 149 (153)
Q Consensus 120 ~kKGIsLt~eqw~~l~~~~~~I~~ai~~l~ 149 (153)
-++||-|++++...|...+-.+=+.--.||
T Consensus 22 ~k~GIeLsme~~qP~m~L~~~VM~eAYElG 51 (56)
T PF10815_consen 22 DKKGIELSMEMLQPLMQLLTKVMNEAYELG 51 (56)
T ss_pred HHcCccCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 479999999999999998877755544444
No 10
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.41 E-value=37 Score=23.38 Aligned_cols=43 Identities=16% Similarity=0.248 Sum_probs=28.1
Q ss_pred HHHHHHHhhhcC---CcchhhHHHHHHHH-hHHcCCCCCChhHHHHH
Q 031792 9 IEGTVREILVKS---DMTETTEFQIRKQA-SEKMGLDLSQPEYKAFV 51 (153)
Q Consensus 9 i~~~V~eILk~a---Dl~t~Te~~vR~~l-~~~lgvdLs~~~~K~~V 51 (153)
..+.|.+++.+- +....|...|+..+ ++.+|+++|.+.=..++
T Consensus 62 ~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 62 QRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred HHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 344555555533 33568889999987 99999999974333333
No 11
>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=49.15 E-value=50 Score=20.79 Aligned_cols=37 Identities=11% Similarity=0.335 Sum_probs=28.6
Q ss_pred HHHHHHHHhhh-------------cCCcchhhHHHHHHHHhHHcCCCCCC
Q 031792 8 KIEGTVREILV-------------KSDMTETTEFQIRKQASEKMGLDLSQ 44 (153)
Q Consensus 8 ~i~~~V~eILk-------------~aDl~t~Te~~vR~~l~~~lgvdLs~ 44 (153)
+|.+.+.++|. +-.++++..-.+...+++.||+.++.
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 45556666664 33477889999999999999999986
No 12
>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=48.30 E-value=67 Score=20.10 Aligned_cols=40 Identities=13% Similarity=0.178 Sum_probs=30.3
Q ss_pred hHHHHHHHHHHHHhhhcCCcchhhHHHHHHHHhHHcCCCCC
Q 031792 3 AETKAKIEGTVREILVKSDMTETTEFQIRKQASEKMGLDLS 43 (153)
Q Consensus 3 ~~sk~~i~~~V~eILk~aDl~t~Te~~vR~~l~~~lgvdLs 43 (153)
++-|.+....+..+|.... +.+--....+++++.+|++..
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 5678888889999998877 666667788889999999875
No 13
>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=38.56 E-value=6.8 Score=32.68 Aligned_cols=14 Identities=64% Similarity=0.975 Sum_probs=8.8
Q ss_pred cccccCHHHHHHHH
Q 031792 122 KGISLTEEQWSALR 135 (153)
Q Consensus 122 KGIsLt~eqw~~l~ 135 (153)
-||.||.+||+.|.
T Consensus 62 AGI~LT~~qW~~l~ 75 (202)
T PF01707_consen 62 AGIQLTAEQWSTLF 75 (202)
T ss_dssp TT----HHHHCCCH
T ss_pred cCcccCHHHHHHHh
Confidence 69999999999876
No 14
>PRK12449 acyl carrier protein; Provisional
Probab=36.28 E-value=1.2e+02 Score=20.18 Aligned_cols=27 Identities=0% Similarity=0.133 Sum_probs=19.9
Q ss_pred cchhhHHHHHHHHhHHcCCCCCChhHH
Q 031792 22 MTETTEFQIRKQASEKMGLDLSQPEYK 48 (153)
Q Consensus 22 l~t~Te~~vR~~l~~~lgvdLs~~~~K 48 (153)
++++..-.+-..+++.||+.++..+..
T Consensus 37 ~DSl~~~~li~~lE~~f~i~i~~~~~~ 63 (80)
T PRK12449 37 VDSIELVEFIINVEDEFHIAIPDEDVE 63 (80)
T ss_pred CcHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence 445666677888999999999874433
No 15
>PF13565 HTH_32: Homeodomain-like domain
Probab=35.68 E-value=78 Score=20.72 Aligned_cols=34 Identities=12% Similarity=0.209 Sum_probs=26.3
Q ss_pred HHHHHHHHHhhhcCCcchhhHHHHHHHHhHHcCCCC
Q 031792 7 AKIEGTVREILVKSDMTETTEFQIRKQASEKMGLDL 42 (153)
Q Consensus 7 ~~i~~~V~eILk~aDl~t~Te~~vR~~l~~~lgvdL 42 (153)
.++++.|.+++.+-- ..|...|...|+.+||+.+
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 456566666666443 7789999999999999987
No 16
>CHL00124 acpP acyl carrier protein; Validated
Probab=35.46 E-value=86 Score=21.06 Aligned_cols=24 Identities=8% Similarity=0.248 Sum_probs=18.0
Q ss_pred chhhHHHHHHHHhHHcCCCCCChh
Q 031792 23 TETTEFQIRKQASEKMGLDLSQPE 46 (153)
Q Consensus 23 ~t~Te~~vR~~l~~~lgvdLs~~~ 46 (153)
+++..-.+-..++++||+.++...
T Consensus 38 DSl~~~eli~~le~~f~i~i~~~~ 61 (82)
T CHL00124 38 DSLDVVELVMAIEEKFDIEIPDED 61 (82)
T ss_pred cHHHHHHHHHHHHHHHCCccCHHH
Confidence 345556677889999999999733
No 17
>PF08848 DUF1818: Domain of unknown function (DUF1818); InterPro: IPR014947 This entry represents a small family of uncharacterised cyanobacterial proteins. ; PDB: 2IT9_A 2NVN_A.
Probab=35.24 E-value=46 Score=25.61 Aligned_cols=30 Identities=17% Similarity=0.409 Sum_probs=26.6
Q ss_pred cccCHHHHHHHHHhHHHHHHHHHHhhcccC
Q 031792 124 ISLTEEQWSALRKNVSAIDTAVKKMQSRIM 153 (153)
Q Consensus 124 IsLt~eqw~~l~~~~~~I~~ai~~l~~~~~ 153 (153)
|-||..+|..|+..+..+.+.+..|.+.+|
T Consensus 29 iELT~~E~~~f~~Ll~~L~~q~~~i~~eLM 58 (117)
T PF08848_consen 29 IELTEAEFNDFCRLLQQLAEQMQAIADELM 58 (117)
T ss_dssp EEE-HHHHHHHHHHHHHHHHHHHCCHTTSS
T ss_pred eeecHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 899999999999999999999998887665
No 18
>cd07999 GH7_CBH_EG Glycosyl hydrolase family 7. Glycosyl hydrolase family 7 contains eukaryotic endoglucanases (EGs) and cellobiohydrolases (CBHs) that hydrolyze glycosidic bonds using a double-displacement mechanism. This leads to a net retention of the conformation at the anomeric carbon. Both enzymes work synergistically in the degradation of cellulose,which is the main component of plant cell wall, and is composed of beta-1,4 linked glycosyl units. EG cleaves the beta-1,4 linkages of cellulose and CBH cleaves off cellobiose disaccharide units from the reducing end of the chain. In general, the O-glycosyl hydrolases are a widespread group of enzymes that hydrolyze the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycoside hydrolase family 7.
Probab=32.35 E-value=56 Score=29.85 Aligned_cols=40 Identities=35% Similarity=0.571 Sum_probs=28.0
Q ss_pred ceeEEEeeeC---CceeEeeeeEEecCCcccCCCc----cc----ccCHHH
Q 031792 91 KRRVTIQDFK---GKTLVSIREYYTKGGKELPSAK----GI----SLTEEQ 130 (153)
Q Consensus 91 ~rrvtV~~fk---G~~~VdIRE~Y~kdG~~~P~kK----GI----sLt~eq 130 (153)
++.-.|..|- |-.|..||-+|..+|+..|..+ |+ |||.+-
T Consensus 257 k~fTVVTQFit~~~G~LteIrR~YVQ~GkvI~n~~~~~~g~~~~~sitd~f 307 (386)
T cd07999 257 KPFTVVTQFVTNDGGKLTEIKRLYIQNGKVIESAVVNIEGIPPGNSITDDF 307 (386)
T ss_pred CCeEEEEEeEeCCCCCcceeeEEEEECCEEEeCCCccccCCCCCCccCHHH
Confidence 3344466796 4589999999999998765442 43 787754
No 19
>PF13101 DUF3945: Protein of unknown function (DUF3945)
Probab=31.76 E-value=30 Score=22.90 Aligned_cols=20 Identities=40% Similarity=0.687 Sum_probs=15.8
Q ss_pred cCC-CcccccCHHHHHHHHHh
Q 031792 118 LPS-AKGISLTEEQWSALRKN 137 (153)
Q Consensus 118 ~P~-kKGIsLt~eqw~~l~~~ 137 (153)
.|. -+|+.||++|...|++.
T Consensus 26 ip~~i~g~~Ls~~q~~~L~~G 46 (59)
T PF13101_consen 26 IPDKIKGVELSPEQKEDLREG 46 (59)
T ss_pred ccceecCccCCHHHHHHHHCC
Confidence 354 36999999999999864
No 20
>PF08988 DUF1895: Protein of unknown function (DUF1895); InterPro: IPR015081 The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop. The function of this protein is, as yet, unknown. ; PDB: 1ZW0_B 2P58_A 2UWJ_E 2Q1K_D 3PH0_B.
Probab=31.64 E-value=76 Score=21.97 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=20.9
Q ss_pred cCHHHHHHHHHhHHHHHHHHHHhh
Q 031792 126 LTEEQWSALRKNVSAIDTAVKKMQ 149 (153)
Q Consensus 126 Lt~eqw~~l~~~~~~I~~ai~~l~ 149 (153)
++|+||..+.....+|..|+.-++
T Consensus 38 ~~P~eyQq~q~~~~AieAA~~Vie 61 (68)
T PF08988_consen 38 GTPQEYQQLQQQYDAIEAAIAVIE 61 (68)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 689999999999999999987654
No 21
>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=31.64 E-value=49 Score=20.33 Aligned_cols=16 Identities=31% Similarity=0.397 Sum_probs=13.3
Q ss_pred ccCHHHHHHHHHhHHH
Q 031792 125 SLTEEQWSALRKNVSA 140 (153)
Q Consensus 125 sLt~eqw~~l~~~~~~ 140 (153)
++|+.||..|+..+-.
T Consensus 2 ~FT~~Ql~~L~~Qi~a 17 (37)
T PF08880_consen 2 PFTPAQLQELRAQILA 17 (37)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 5899999999987643
No 22
>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=31.06 E-value=1.3e+02 Score=21.95 Aligned_cols=43 Identities=9% Similarity=0.264 Sum_probs=33.5
Q ss_pred CceeEeeeeEEec-CCcccCCCcccccCHHHHHHHHHhHHHHHHHH
Q 031792 101 GKTLVSIREYYTK-GGKELPSAKGISLTEEQWSALRKNVSAIDTAV 145 (153)
Q Consensus 101 G~~~VdIRE~Y~k-dG~~~P~kKGIsLt~eqw~~l~~~~~~I~~ai 145 (153)
|.+||.+-==..+ +|...| +=+-||.+|+..|...+..+.+-|
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 8899886554444 788866 489999999999999888776543
No 23
>COG2921 Uncharacterized conserved protein [Function unknown]
Probab=30.55 E-value=37 Score=25.09 Aligned_cols=26 Identities=31% Similarity=0.267 Sum_probs=16.5
Q ss_pred cccCCCcc---------cccCHHHHHHHHHhHHHH
Q 031792 116 KELPSAKG---------ISLTEEQWSALRKNVSAI 141 (153)
Q Consensus 116 ~~~P~kKG---------IsLt~eqw~~l~~~~~~I 141 (153)
.|+|+.|| +..+.||...|-..+.++
T Consensus 49 ~~k~SSkGnY~svsI~i~A~~~EQ~e~ly~eL~~~ 83 (90)
T COG2921 49 SWKPSSKGNYLSVSITIRATNIEQVEALYRELRKH 83 (90)
T ss_pred eeccCCCCceEEEEEEEEECCHHHHHHHHHHHhhC
Confidence 45666666 345678877777665544
No 24
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=30.20 E-value=38 Score=23.66 Aligned_cols=16 Identities=38% Similarity=0.590 Sum_probs=14.9
Q ss_pred HHHHHHhHHcCCCCCC
Q 031792 29 QIRKQASEKMGLDLSQ 44 (153)
Q Consensus 29 ~vR~~l~~~lgvdLs~ 44 (153)
.+|..++..||+||+.
T Consensus 5 ~~r~~~e~~~G~dl~~ 20 (79)
T PF13699_consen 5 SIRSRLERAFGADLSD 20 (79)
T ss_pred HHHHHHHHHhCCCccc
Confidence 5899999999999998
No 25
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=29.80 E-value=89 Score=21.94 Aligned_cols=31 Identities=19% Similarity=0.324 Sum_probs=20.4
Q ss_pred ccccCHHHHHHHH----HhHHHHHHHHHHhhcccC
Q 031792 123 GISLTEEQWSALR----KNVSAIDTAVKKMQSRIM 153 (153)
Q Consensus 123 GIsLt~eqw~~l~----~~~~~I~~ai~~l~~~~~ 153 (153)
||+-|+++|..-. +.+..-.+-|.+++++.|
T Consensus 49 gi~~s~eeq~~~i~~Le~~i~~k~~~L~~~~~~~~ 83 (83)
T PF07544_consen 49 GIDRSVEEQEEEIEELEEQIRKKREVLQKFKERVM 83 (83)
T ss_pred CccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 5999999996544 444455566666666554
No 26
>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....
Probab=29.12 E-value=97 Score=22.03 Aligned_cols=46 Identities=20% Similarity=0.289 Sum_probs=30.2
Q ss_pred EeeeeEEec----CCcccCCCcccccCHHHHHHHHHhHHHH-HHHHHHhhc
Q 031792 105 VSIREYYTK----GGKELPSAKGISLTEEQWSALRKNVSAI-DTAVKKMQS 150 (153)
Q Consensus 105 VdIRE~Y~k----dG~~~P~kKGIsLt~eqw~~l~~~~~~I-~~ai~~l~~ 150 (153)
-.|-.||.+ .-...|..+.-+|+.+||..|..++..| ..||+.-++
T Consensus 37 aGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~~vl~~ai~~gg~ 87 (92)
T PF06831_consen 37 AGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIKRVLREAIEVGGT 87 (92)
T ss_dssp TT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHHHHHHHHHHTT-B
T ss_pred ccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 334455554 2568899999999999999988887665 555554333
No 27
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=28.89 E-value=92 Score=22.47 Aligned_cols=18 Identities=22% Similarity=0.519 Sum_probs=15.0
Q ss_pred eEEEeeeCCceeEeeeeE
Q 031792 93 RVTIQDFKGKTLVSIREY 110 (153)
Q Consensus 93 rvtV~~fkG~~~VdIRE~ 110 (153)
.+.-|+|.|+-|.|||-|
T Consensus 64 ~i~~RE~~gr~fn~i~aW 81 (84)
T PF11325_consen 64 NIEGREWNGRWFNSIRAW 81 (84)
T ss_pred EeeccEecceEeeEeEEE
Confidence 455678999999999986
No 28
>TIGR02501 type_III_yscE type III secretion system protein, YseE family. Members of this family are found exclusively in type III secretion appparatus gene clusters in bacteria. Those bacteria with a protein from this family tend to target animal cells, as does Yersinia pestis. This protein is small (about 70 amino acids) and not well characterized.
Probab=28.49 E-value=91 Score=21.47 Aligned_cols=24 Identities=21% Similarity=0.288 Sum_probs=19.5
Q ss_pred cCHHHHHHHHHhHHHHHHHHHHhh
Q 031792 126 LTEEQWSALRKNVSAIDTAVKKMQ 149 (153)
Q Consensus 126 Lt~eqw~~l~~~~~~I~~ai~~l~ 149 (153)
-||+||..+...+.+++.|++-++
T Consensus 37 ~tp~qYq~l~~~~~A~~aA~~II~ 60 (67)
T TIGR02501 37 GDPQQYQEWQLLADAIEAAIKIIE 60 (67)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 489999888888888888887543
No 29
>PRK05350 acyl carrier protein; Provisional
Probab=28.38 E-value=1.2e+02 Score=20.64 Aligned_cols=24 Identities=8% Similarity=0.130 Sum_probs=17.9
Q ss_pred chhhHHHHHHHHhHHcCCCCCChh
Q 031792 23 TETTEFQIRKQASEKMGLDLSQPE 46 (153)
Q Consensus 23 ~t~Te~~vR~~l~~~lgvdLs~~~ 46 (153)
+++.--.+--.++++||+.++...
T Consensus 39 DSld~veli~~lE~~fgI~i~~~~ 62 (82)
T PRK05350 39 DSIDAVDLVVHLQKLTGKKIKPEE 62 (82)
T ss_pred CHHHHHHHHHHHHHHHCCccCHHH
Confidence 445556677889999999998733
No 30
>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=28.33 E-value=66 Score=23.52 Aligned_cols=45 Identities=16% Similarity=0.451 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHhhhcCCcchhhHHHHHHHHhHHcCCCCCChhHHHHHhhhh
Q 031792 5 TKAKIEGTVREILVKSDMTETTEFQIRKQASEKMGLDLSQPEYKAFVRHKS 55 (153)
Q Consensus 5 sk~~i~~~V~eILk~aDl~t~Te~~vR~~l~~~lgvdLs~~~~K~~Vr~~i 55 (153)
+-.+|...+..|.+..+| |....+++|+.. |++... |+..+|..+
T Consensus 68 sd~evd~~i~~ia~~n~l---s~~ql~~~L~~~-G~s~~~--~r~~ir~~i 112 (118)
T PF09312_consen 68 SDEEVDEAIANIAKQNNL---SVEQLRQQLEQQ-GISYEE--YREQIRKQI 112 (118)
T ss_dssp -HHHHHHHHHHHHHHTT-----HHHHHHHCHHC-T--HHH--HHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHcCC---CHHHHHHHHHHc-CCCHHH--HHHHHHHHH
Confidence 334566666666666555 344556666553 665544 666666554
No 31
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=27.85 E-value=1.3e+02 Score=26.23 Aligned_cols=43 Identities=23% Similarity=0.512 Sum_probs=31.5
Q ss_pred CeEEEEeCCceeEEEeeeCCceeEeeeeEEecCCcccCCCcccccCHHHHHHHH
Q 031792 82 NLIICQLNKKRRVTIQDFKGKTLVSIREYYTKGGKELPSAKGISLTEEQWSALR 135 (153)
Q Consensus 82 d~~~~~Ls~~rrvtV~~fkG~~~VdIRE~Y~kdG~~~P~kKGIsLt~eqw~~l~ 135 (153)
+.+.|.|.+.|+.||+.-+|+-|+ |.+. | --...+..-|..++
T Consensus 38 ~RqSCPLANSrYATVr~dngkLyL-----ymKt----p--ERaH~P~klwerIk 80 (303)
T COG5129 38 DRQSCPLANSRYATVRADNGKLYL-----YMKT----P--ERAHVPRKLWERIK 80 (303)
T ss_pred ccccCcCccCcceEEEecCCEEEE-----EecC----h--hhccCcHHHHHHHH
Confidence 467799999999999999999986 5553 2 23445566676554
No 32
>COG4746 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.03 E-value=54 Score=23.68 Aligned_cols=37 Identities=16% Similarity=0.199 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhhhcCCcchhhHHHHHHHHhHHcCCCCC
Q 031792 5 TKAKIEGTVREILVKSDMTETTEFQIRKQASEKMGLDLS 43 (153)
Q Consensus 5 sk~~i~~~V~eILk~aDl~t~Te~~vR~~l~~~lgvdLs 43 (153)
-+++|+.++.++|+.||+---+.-.+-..| .-|.|++
T Consensus 4 v~~e~~~qiv~~~k~a~fPInn~~eL~~AL--P~G~dtt 40 (80)
T COG4746 4 VREEIREQIVEALKGADFPINNPEELVAAL--PSGPDTT 40 (80)
T ss_pred HHHHHHHHHHHHHccCCCCCCCHHHHHHhc--cCCCCCC
Confidence 468999999999999999765544443333 2355554
No 33
>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=25.79 E-value=1.7e+02 Score=20.35 Aligned_cols=39 Identities=21% Similarity=0.214 Sum_probs=21.8
Q ss_pred CChHHHHHHHHHHHHhhhcCCcchhhHHHHHHHHhHHcC
Q 031792 1 MKAETKAKIEGTVREILVKSDMTETTEFQIRKQASEKMG 39 (153)
Q Consensus 1 M~~~sk~~i~~~V~eILk~aDl~t~Te~~vR~~l~~~lg 39 (153)
|+++-+.++...+.+.|+..+-+.--+..|.+.|.+++|
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 666777777777777777554332233445555555544
No 34
>PF14164 YqzH: YqzH-like protein
Probab=24.97 E-value=84 Score=21.79 Aligned_cols=18 Identities=28% Similarity=0.702 Sum_probs=14.5
Q ss_pred cccCHHHHHHHHHhHHHH
Q 031792 124 ISLTEEQWSALRKNVSAI 141 (153)
Q Consensus 124 IsLt~eqw~~l~~~~~~I 141 (153)
+.||+++|+.|.+.+...
T Consensus 24 ~pls~~E~~~L~~~i~~~ 41 (64)
T PF14164_consen 24 MPLSDEEWEELCKHIQER 41 (64)
T ss_pred CCCCHHHHHHHHHHHHHH
Confidence 339999999999977554
No 35
>PRK05883 acyl carrier protein; Validated
Probab=24.77 E-value=1.2e+02 Score=21.54 Aligned_cols=23 Identities=17% Similarity=0.180 Sum_probs=17.6
Q ss_pred cchhhHHHHHHHHhHHcCCCCCC
Q 031792 22 MTETTEFQIRKQASEKMGLDLSQ 44 (153)
Q Consensus 22 l~t~Te~~vR~~l~~~lgvdLs~ 44 (153)
++++.--.+--.++++||+.+..
T Consensus 46 ~DSL~~v~lv~~lE~~fgI~i~~ 68 (91)
T PRK05883 46 LDSVAFAVGMVAIEERLGVALSE 68 (91)
T ss_pred CChHHHHHHHHHHHHHHCCCcCH
Confidence 44566566677899999999987
No 36
>PF01436 NHL: NHL repeat; InterPro: IPR001258 The NHL repeat, named after NCL-1, HT2A and Lin-41, is found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C terminus alpha-amidation of biological peptides []. In many it occurs in tandem arrays, for example in the ringfinger beta-box, coiled-coil (RBCC) eukaryotic growth regulators []. The 'Brain Tumor' protein (Brat) is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller [, ]. The NHL repeats are also found in serine/threonine protein kinase (STPK) in diverse range of pathogenic bacteria. These STPK are transmembrane receptors with a intracellular N-terminal kinase domain and extracellular C-terminal sensor domain. In the STPK, PknD, from Mycobacterium tuberculosis, the sensor domain forms a rigid, six-bladed b-propeller composed of NHL repeats with a flexible tether to the transmembrane domain.; GO: 0005515 protein binding; PDB: 3FVZ_A 3FW0_A 1RWL_A 1RWI_A 1Q7F_A.
Probab=23.91 E-value=80 Score=17.49 Aligned_cols=19 Identities=26% Similarity=0.635 Sum_probs=13.0
Q ss_pred cCCCCCeEEEEeCCceeEEE
Q 031792 77 YDDEGNLIICQLNKKRRVTI 96 (153)
Q Consensus 77 ~d~~gd~~~~~Ls~~rrvtV 96 (153)
.+++|+.++++ +++.||.+
T Consensus 9 v~~~g~i~VaD-~~n~rV~v 27 (28)
T PF01436_consen 9 VDSDGNIYVAD-SGNHRVQV 27 (28)
T ss_dssp EETTSEEEEEE-CCCTEEEE
T ss_pred EeCCCCEEEEE-CCCCEEEE
Confidence 46788888876 55556543
No 37
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=23.87 E-value=73 Score=19.40 Aligned_cols=31 Identities=19% Similarity=0.218 Sum_probs=18.9
Q ss_pred chhhHHHHHHHHhHHcCCCCCChhHHHHHhhh
Q 031792 23 TETTEFQIRKQASEKMGLDLSQPEYKAFVRHK 54 (153)
Q Consensus 23 ~t~Te~~vR~~l~~~lgvdLs~~~~K~~Vr~~ 54 (153)
.++|-..+|..|.++ ||+..+..+|+..=.+
T Consensus 2 ~sltV~~Lk~iL~~~-~I~~ps~AkKaeLv~L 32 (35)
T PF12949_consen 2 KSLTVAQLKRILDEH-GIEFPSNAKKAELVAL 32 (35)
T ss_dssp TT--SHHHHHHHHHH-T---SSS--SHHHHHH
T ss_pred CcCcHHHHHHHHHHc-CCCCCCCCCHHHHHHH
Confidence 467778899999988 9999998888876443
No 38
>KOG1748 consensus Acyl carrier protein/NADH-ubiquinone oxidoreductase, NDUFAB1/SDAP subunit [Energy production and conversion; Lipid transport and metabolism; Secondary metabolites biosynthesis, transport and catabolism]
Probab=23.38 E-value=68 Score=25.14 Aligned_cols=41 Identities=17% Similarity=0.263 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhhhcCCcchhhHHHHHHHHhHHcCCCCCC
Q 031792 4 ETKAKIEGTVREILVKSDMTETTEFQIRKQASEKMGLDLSQ 44 (153)
Q Consensus 4 ~sk~~i~~~V~eILk~aDl~t~Te~~vR~~l~~~lgvdLs~ 44 (153)
-++.++..+|..|+|.-|=-+.+--.........||+|=-+
T Consensus 49 l~k~~v~~RVl~VVk~~dki~~~k~~~~s~f~~DLGlDSLD 89 (131)
T KOG1748|consen 49 LAKKEVVDRVLDVVKKFDKIDPSKLTTDSDFFKDLGLDSLD 89 (131)
T ss_pred hhHHHHHHHHHHHHHHhhcCCccccchhhHHHHhcCCcccc
Confidence 37889999999999988776666667777777788877655
No 39
>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=23.00 E-value=1.4e+02 Score=20.70 Aligned_cols=43 Identities=21% Similarity=0.484 Sum_probs=25.3
Q ss_pred eCCceeEe-eeeEEecCCccc-CCCcccccCHHHHHHHHHhHHHHHHHHHHhh
Q 031792 99 FKGKTLVS-IREYYTKGGKEL-PSAKGISLTEEQWSALRKNVSAIDTAVKKMQ 149 (153)
Q Consensus 99 fkG~~~Vd-IRE~Y~kdG~~~-P~kKGIsLt~eqw~~l~~~~~~I~~ai~~l~ 149 (153)
|+|..||+ +-.|--+.|+.+ |.++ .. .-...+.+|+..|..|+
T Consensus 20 F~Gr~~I~g~G~feFd~Gkillp~~~-----~~---~~~~~~~EiN~~I~~L~ 64 (64)
T PF06526_consen 20 FRGRIYIKGIGAFEFDNGKILLPKKA-----DK---RHLSVMSEINQEIRRLS 64 (64)
T ss_dssp -SEEEEETTTEEEEEETTEE---SS-------H---HHHHHHHHHHHHHHHH-
T ss_pred ccceEEEEecccEEEcCCEEeCCccc-----cH---HHHHHHHHHHHHHHhcC
Confidence 89999885 455544789876 4433 22 34456668888887763
No 40
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.13 E-value=1.1e+02 Score=23.87 Aligned_cols=41 Identities=12% Similarity=0.098 Sum_probs=33.7
Q ss_pred HHHHHhhhcCCcchhhHHHHHHHHhHHcCCCCCChhHHHHHhhh
Q 031792 11 GTVREILVKSDMTETTEFQIRKQASEKMGLDLSQPEYKAFVRHK 54 (153)
Q Consensus 11 ~~V~eILk~aDl~t~Te~~vR~~l~~~lgvdLs~~~~K~~Vr~~ 54 (153)
+.+.++|++=| .|...++..++.+||+..+...--.|++++
T Consensus 70 ~~l~e~~~~k~---wTl~~~~~~l~~e~gv~y~~~~v~~~l~~~ 110 (138)
T COG3415 70 EILLERLREKD---WTLKELVEELGLEFGVWYHASAVRRLLHEL 110 (138)
T ss_pred HHHHHHHhccc---chHHHHHHHHhhhcCeEEeHHHHHHHHHHc
Confidence 56778888777 899999999999999999975556666665
No 41
>PF04358 DsrC: DsrC like protein; InterPro: IPR007453 DsrC (P45573 from SWISSPROT) has been observed to co-purify with Desulphovibrio vulgaris dissimilatory sulphite reductase []. However, DsrC appears to be only loosely associated to the sulphite reductase, which suggests that it may not be an integral part of the dissimilatory sulphite reductase. Many proteins in this entry are found in organisms such as Escherichia coli and Haemophilus influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins []. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds []. Also included in this entry is TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Many proteins in this entry are annotated as the third (gamma) subunit of dissimilatory sulphite reductase ; PDB: 2V4J_F 2A5W_C 1SAU_A 1JI8_A 1YX3_A.
Probab=21.99 E-value=56 Score=24.44 Aligned_cols=20 Identities=40% Similarity=0.818 Sum_probs=12.1
Q ss_pred ccCCCcccccCHHHHHHHHH
Q 031792 117 ELPSAKGISLTEEQWSALRK 136 (153)
Q Consensus 117 ~~P~kKGIsLt~eqw~~l~~ 136 (153)
.+--.-||.||.++|..+.-
T Consensus 30 ~lA~~egI~Ltd~HW~vI~f 49 (109)
T PF04358_consen 30 ALAKEEGIELTDEHWEVIRF 49 (109)
T ss_dssp HHHHCTT-S--HHHHHHHHH
T ss_pred HHHHHcCCCCCHHHHHHHHH
Confidence 34445799999999987653
No 42
>PF00840 Glyco_hydro_7: Glycosyl hydrolase family 7; InterPro: IPR001722 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 7 GH7 from CAZY comprises enzymes with several known activities; endoglucanase (3.2.1.4 from EC); cellobiohydrolase (3.2.1.91 from EC). These enzymes were formerly known as cellulase family C. Exoglucanases and cellobiohydrolases [] play a role in the conversion of cellulose to glucose by cutting the dissaccharide cellobiose from the nonreducing end of the cellulose polymer chain. Structurally, cellulases and xylanases generally consist of a catalytic domain joined to a cellulose-binding domain (CBD) via a linker region that is rich in proline and/or hydroxy-amino acids. In type I exoglucanases, the CBD domain is found at the C-terminal extremity of these enzyme (this short domain forms a hairpin loop structure stabilised by 2 disulphide bridges).; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 2Y9N_A 2Y9L_A 2RFW_D 2RFZ_A 2RFY_D 2RG0_C 1EG1_C 1OVW_D 2OVW_A 4OVW_A ....
Probab=21.92 E-value=94 Score=28.83 Aligned_cols=47 Identities=32% Similarity=0.521 Sum_probs=29.5
Q ss_pred CceeEEEeeeCCc-----eeEeeeeEEecCCcccCCCc----cc----ccCHHHHHHHHH
Q 031792 90 KKRRVTIQDFKGK-----TLVSIREYYTKGGKELPSAK----GI----SLTEEQWSALRK 136 (153)
Q Consensus 90 ~~rrvtV~~fkG~-----~~VdIRE~Y~kdG~~~P~kK----GI----sLt~eqw~~l~~ 136 (153)
.++.-.|..|-.. .|+.||-||..+|+..|..+ |+ |||.+-=.+-+.
T Consensus 280 tkkfTVVTQFit~~~t~G~L~EIrR~YVQnGkvI~n~~~~~~g~~~~nsItd~fC~~~~~ 339 (433)
T PF00840_consen 280 TKKFTVVTQFITDDGTTGDLSEIRRLYVQNGKVIQNPKVNIPGLPGFNSITDEFCSAQKS 339 (433)
T ss_dssp TSEEEEEEEEEETTSSTS-EEEEEEEEEETTEEEESSSEESTTSESSSSBSHHHHHHHHH
T ss_pred CCccEEEEEeecCCCCccccceeeEEEEECCEEEeCCCcccCCCCCCCccCHHHHhhhcc
Confidence 3444456668654 49999999999998764432 32 577754444443
No 43
>PF00466 Ribosomal_L10: Ribosomal protein L10; InterPro: IPR001790 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. On the basis of sequence similarities the following prokaryotic and eukaryotic ribosomal proteins can be grouped: Bacterial 50S ribosomal protein L10; Archaebacterial acidic ribosomal protein P0 homologue (L10E); Eukaryotic 60S ribosomal protein P0 (L10E). This entry represents the ribosomal protein L10P family, with includes the above mentioned ribosomal proteins.; GO: 0042254 ribosome biogenesis, 0005622 intracellular; PDB: 3A1Y_G 3D5D_J 3PYT_I 3PYV_I 3D5B_J 3PYO_I 3PYR_I 3MS1_I 3MRZ_I 1VQ9_G ....
Probab=21.38 E-value=2.4e+02 Score=19.57 Aligned_cols=42 Identities=29% Similarity=0.424 Sum_probs=32.4
Q ss_pred CChHHHHHHHHHHHHhhhcC---------CcchhhHHHHHHHHhHHcCCCCC
Q 031792 1 MKAETKAKIEGTVREILVKS---------DMTETTEFQIRKQASEKMGLDLS 43 (153)
Q Consensus 1 M~~~sk~~i~~~V~eILk~a---------Dl~t~Te~~vR~~l~~~lgvdLs 43 (153)
|..+.|..+.+.|.++|.++ .|....-..+|+++... |+.+.
T Consensus 1 m~~~~K~~~v~~~~~~l~~~~~v~v~~~~~l~~~~~~~lR~~l~~~-~~~~~ 51 (100)
T PF00466_consen 1 MTKEKKEEIVEELKELLKKSKYVIVVDYNGLSANQLQELRKELRKK-GGKFK 51 (100)
T ss_dssp -SCHHHHHHHHHHHHHHHCSSEEEEEECTTSCHHHHHHHHHHHHHH-TEEEE
T ss_pred CcHHHHHHHHHHHHHHHHhCCEEEEEEeCCCCHHHHHHHHHHHHhc-CcEEE
Confidence 77888999999999999988 45566667899999877 44443
No 44
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=20.78 E-value=1.8e+02 Score=18.10 Aligned_cols=26 Identities=19% Similarity=0.272 Sum_probs=19.2
Q ss_pred cccccCHHHHHHHHHhHH--------HHHHHHHH
Q 031792 122 KGISLTEEQWSALRKNVS--------AIDTAVKK 147 (153)
Q Consensus 122 KGIsLt~eqw~~l~~~~~--------~I~~ai~~ 147 (153)
=+++|+.+.+..|..... -|++||..
T Consensus 5 ~t~~l~~el~~~L~~ls~~t~i~~S~Ll~eAle~ 38 (44)
T PF12651_consen 5 FTFSLDKELYEKLKELSEETGIPKSKLLREALED 38 (44)
T ss_pred EEEecCHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 378999999999988763 34666654
No 45
>PF14568 SUKH_6: SMI1-KNR4 cell-wall; PDB: 2PRV_A.
Probab=20.65 E-value=67 Score=22.22 Aligned_cols=22 Identities=32% Similarity=0.776 Sum_probs=16.6
Q ss_pred HHHhHHcCCCCCChhHHHHHhhh
Q 031792 32 KQASEKMGLDLSQPEYKAFVRHK 54 (153)
Q Consensus 32 ~~l~~~lgvdLs~~~~K~~Vr~~ 54 (153)
.+++++||+.|.. +||.|++..
T Consensus 5 ~~~E~~Lg~~lP~-~Yk~fL~~~ 26 (120)
T PF14568_consen 5 EEAEKKLGVKLPE-DYKEFLKEY 26 (120)
T ss_dssp HHHHHHHTS---H-HHHHHHHHC
T ss_pred HHHHHHhCCCCCH-HHHHHHHHc
Confidence 5789999999985 899999976
Done!