Query 039494
Match_columns 140
No_of_seqs 111 out of 1312
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 10:15:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039494.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039494hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00265 MADS_MEF2_like MEF2 (m 100.0 5.5E-31 1.2E-35 171.4 2.0 67 1-67 7-73 (77)
2 KOG0014 MADS box transcription 100.0 1.2E-29 2.7E-34 189.7 3.9 68 1-68 8-77 (195)
3 cd00266 MADS_SRF_like SRF-like 99.9 1.3E-28 2.9E-33 162.3 3.4 68 1-68 7-75 (83)
4 smart00432 MADS MADS domain. 99.9 1.3E-27 2.9E-32 147.7 2.6 53 1-53 7-59 (59)
5 PF00319 SRF-TF: SRF-type tran 99.9 1.3E-28 2.9E-33 147.8 -2.4 51 2-52 1-51 (51)
6 cd00120 MADS MADS: MCM1, Agamo 99.9 3.3E-27 7.1E-32 146.0 2.1 53 1-53 7-59 (59)
7 KOG0015 Regulator of arginine 99.7 1.3E-18 2.7E-23 136.3 2.1 60 1-60 69-128 (338)
8 COG5068 ARG80 Regulator of arg 99.3 1.5E-12 3.3E-17 106.1 2.1 60 1-60 88-147 (412)
9 PF01486 K-box: K-box region; 97.6 0.00017 3.6E-09 48.8 5.9 48 71-118 30-77 (100)
10 PF06698 DUF1192: Protein of u 77.8 9 0.00019 23.5 4.9 35 79-113 13-47 (59)
11 PF14071 YlbD_coat: Putative c 77.3 8 0.00017 27.2 5.2 50 83-139 73-122 (124)
12 PF09151 DUF1936: Domain of un 66.7 3.3 7.1E-05 22.1 0.9 27 28-54 3-31 (36)
13 PF10584 Proteasome_A_N: Prote 66.0 1 2.3E-05 22.4 -1.0 13 37-49 4-16 (23)
14 KOG3048 Molecular chaperone Pr 65.0 18 0.00039 26.2 4.7 34 82-115 8-41 (153)
15 COG1938 Archaeal enzymes of AT 64.8 33 0.00072 26.9 6.6 41 86-126 203-243 (244)
16 KOG4252 GTP-binding protein [S 60.3 36 0.00077 26.0 5.8 27 32-64 91-117 (246)
17 PF10491 Nrf1_DNA-bind: NLS-bi 59.4 10 0.00022 29.0 2.8 41 25-65 45-88 (214)
18 PRK01919 tatB sec-independent 56.0 6.1 0.00013 29.3 1.1 10 36-45 15-24 (169)
19 PRK04654 sec-independent trans 48.7 9.5 0.00021 29.3 1.2 9 36-44 15-23 (214)
20 PF02639 DUF188: Uncharacteriz 45.9 90 0.002 21.9 5.7 59 37-104 70-129 (130)
21 TIGR01916 F420_cofE F420-0:gam 41.0 25 0.00054 27.6 2.4 28 27-54 134-161 (243)
22 cd01365 KISc_KIF1A_KIF1B Kines 40.4 23 0.00049 28.8 2.3 26 29-54 83-111 (356)
23 COG3411 Ferredoxin [Energy pro 38.9 26 0.00057 21.8 1.9 28 37-64 18-46 (64)
24 COG4917 EutP Ethanolamine util 38.1 25 0.00054 25.3 1.9 24 28-51 59-82 (148)
25 PLN03230 acetyl-coenzyme A car 37.8 87 0.0019 26.7 5.3 22 89-110 104-125 (431)
26 PF09941 DUF2173: Uncharacteri 37.4 21 0.00046 24.5 1.4 41 24-65 2-45 (108)
27 smart00030 CLb CLUSTERIN Beta 37.0 1.1E+02 0.0023 23.5 5.2 57 53-117 112-172 (206)
28 COG0139 HisI Phosphoribosyl-AM 36.5 20 0.00044 24.7 1.2 38 10-47 50-96 (111)
29 PF08656 DASH_Dad3: DASH compl 35.9 1.1E+02 0.0024 19.7 4.5 63 53-115 3-66 (78)
30 PRK00124 hypothetical protein; 35.9 1.7E+02 0.0037 21.2 6.7 61 37-106 86-147 (151)
31 PF11944 DUF3461: Protein of u 35.7 55 0.0012 23.0 3.2 28 86-113 98-125 (125)
32 PF06937 EURL: EURL protein; 35.2 60 0.0013 26.0 3.7 35 82-116 214-248 (285)
33 KOG4316 Uncharacterized conser 34.8 14 0.00031 26.9 0.2 43 26-68 43-96 (172)
34 smart00782 PhnA_Zn_Ribbon PhnA 34.0 18 0.00039 21.0 0.5 22 21-42 2-23 (47)
35 PF06780 Erp_C: Erp protein C- 33.9 45 0.00098 24.1 2.6 38 74-112 53-90 (146)
36 PF10481 CENP-F_N: Cenp-F N-te 33.9 99 0.0022 24.9 4.8 34 104-137 179-220 (307)
37 TIGR03274 methan_mark_7 putati 33.6 2E+02 0.0043 23.2 6.4 25 18-44 140-164 (302)
38 PF13252 DUF4043: Protein of u 32.9 26 0.00056 28.8 1.5 23 25-47 271-293 (341)
39 KOG4637 Adaptor for phosphoino 32.6 40 0.00087 28.3 2.5 41 26-66 367-412 (464)
40 TIGR01478 STEVOR variant surfa 32.3 1.2E+02 0.0026 24.5 5.0 42 2-64 27-69 (295)
41 PF08188 Protamine_3: Spermato 32.1 74 0.0016 17.9 2.8 16 125-140 33-48 (48)
42 cd00106 KISc Kinesin motor dom 32.0 36 0.00079 27.0 2.2 25 30-54 74-101 (328)
43 PF14009 DUF4228: Domain of un 30.9 46 0.001 23.5 2.4 34 32-65 12-46 (181)
44 cd07022 S49_Sppa_36K_type Sign 30.7 1.8E+02 0.0039 21.7 5.7 84 22-112 85-172 (214)
45 TIGR02420 dksA RNA polymerase- 30.6 1.5E+02 0.0032 19.9 4.8 29 87-115 1-29 (110)
46 cd01371 KISc_KIF3 Kinesin moto 29.9 47 0.001 26.7 2.5 25 29-53 76-103 (333)
47 TIGR00161 conserved hypothetic 29.5 1.3E+02 0.0028 23.2 4.8 30 87-116 201-230 (238)
48 cd01368 KISc_KIF23_like Kinesi 29.0 43 0.00093 27.2 2.1 26 29-54 83-111 (345)
49 PRK09822 lipopolysaccharide co 28.9 24 0.00052 27.8 0.6 41 11-52 117-160 (269)
50 PRK00098 GTPase RsgA; Reviewed 28.7 59 0.0013 25.8 2.8 32 14-45 59-92 (298)
51 cd07023 S49_Sppa_N_C Signal pe 28.6 2.4E+02 0.0053 20.8 6.3 81 23-110 79-163 (208)
52 PF10083 DUF2321: Uncharacteri 28.3 44 0.00095 24.5 1.9 23 83-105 94-116 (158)
53 PRK13701 psiB plasmid SOS inhi 27.9 79 0.0017 22.7 3.0 51 83-139 9-65 (144)
54 COG4306 Uncharacterized protei 27.9 36 0.00078 24.2 1.3 20 119-138 63-82 (160)
55 PF08557 Lipid_DES: Sphingolip 27.3 24 0.00052 19.8 0.3 22 14-35 15-36 (39)
56 PF06361 RTBV_P12: Rice tungro 27.3 1.5E+02 0.0033 19.5 4.1 70 52-125 5-85 (110)
57 COG5068 ARG80 Regulator of arg 26.6 43 0.00094 28.2 1.8 46 1-52 18-63 (412)
58 cd01370 KISc_KIP3_like Kinesin 26.6 49 0.0011 26.7 2.1 26 29-54 82-110 (338)
59 cd01366 KISc_C_terminal Kinesi 26.5 50 0.0011 26.4 2.1 25 29-53 72-99 (329)
60 cd01374 KISc_CENP_E Kinesin mo 26.5 55 0.0012 26.1 2.3 25 30-54 69-96 (321)
61 PRK13293 F420-0--gamma-glutamy 26.2 61 0.0013 25.5 2.5 28 27-54 135-162 (245)
62 PHA02740 protein tyrosine phos 26.2 1.2E+02 0.0026 24.2 4.2 38 88-132 194-231 (298)
63 cd01363 Motor_domain Myosin an 26.0 43 0.00094 24.5 1.5 25 30-54 19-46 (186)
64 cd01376 KISc_KID_like Kinesin 25.6 61 0.0013 25.9 2.4 26 29-54 75-103 (319)
65 PRK13677 hypothetical protein; 25.3 1.1E+02 0.0023 21.5 3.2 30 84-113 96-125 (125)
66 cd01367 KISc_KIF2_like Kinesin 25.2 53 0.0011 26.3 2.0 25 29-53 79-106 (322)
67 COG4831 Roadblock/LC7 domain [ 25.1 68 0.0015 21.7 2.2 45 23-68 3-50 (109)
68 COG5179 TAF1 Transcription ini 24.8 70 0.0015 28.9 2.7 43 19-62 446-488 (968)
69 cd02980 TRX_Fd_family Thioredo 24.6 76 0.0017 19.2 2.3 29 32-61 47-76 (77)
70 PF00225 Kinesin: Kinesin moto 24.1 28 0.00061 27.8 0.2 24 29-52 69-95 (335)
71 cd01369 KISc_KHC_KIF5 Kinesin 24.1 55 0.0012 26.1 1.9 25 30-54 72-99 (325)
72 PF04873 EIN3: Ethylene insens 24.0 26 0.00056 29.0 0.0 39 18-56 53-92 (354)
73 PF00383 dCMP_cyt_deam_1: Cyti 23.7 68 0.0015 20.6 2.0 32 20-51 6-41 (102)
74 KOG3718 Carnitine O-acyltransf 23.5 2.8E+02 0.006 24.4 6.0 56 41-113 14-69 (609)
75 smart00129 KISc Kinesin motor, 23.3 70 0.0015 25.5 2.4 24 30-53 75-101 (335)
76 cd00468 HIT_like HIT family: H 23.2 1.5E+02 0.0033 18.0 3.6 25 83-107 31-55 (86)
77 KOG3802 Transcription factor O 23.1 9.6 0.00021 31.9 -2.6 41 12-66 213-253 (398)
78 KOG0183 20S proteasome, regula 23.1 44 0.00095 26.0 1.1 16 34-49 4-19 (249)
79 PF11232 Med25: Mediator compl 23.1 61 0.0013 23.6 1.8 20 30-49 109-128 (152)
80 PF11460 DUF3007: Protein of u 23.0 40 0.00086 23.0 0.8 21 80-100 83-103 (104)
81 cd03064 TRX_Fd_NuoE TRX-like [ 22.7 68 0.0015 19.9 1.8 28 32-62 52-80 (80)
82 PF06020 Roughex: Drosophila r 22.7 41 0.00089 27.2 0.9 16 29-44 183-198 (334)
83 PF09278 MerR-DNA-bind: MerR, 22.3 1.8E+02 0.0039 17.0 4.6 23 93-115 35-57 (65)
84 PF04120 Iron_permease: Low af 21.6 1.6E+02 0.0036 20.8 3.7 29 82-110 90-118 (132)
85 COG0099 RpsM Ribosomal protein 21.5 2.6E+02 0.0057 19.6 4.6 33 83-115 44-83 (121)
86 KOG0184 20S proteasome, regula 21.2 51 0.0011 25.7 1.1 21 29-49 3-23 (254)
87 COG4575 ElaB Uncharacterized c 21.2 2.1E+02 0.0046 19.5 4.0 29 85-113 32-60 (104)
88 PF06574 FAD_syn: FAD syntheta 20.7 78 0.0017 22.8 2.0 27 19-45 22-48 (157)
89 PF12068 DUF3548: Domain of un 20.6 52 0.0011 25.2 1.0 15 118-132 142-156 (213)
90 PF08432 Vfa1: AAA-ATPase Vps4 20.4 54 0.0012 24.3 1.1 13 32-44 11-23 (182)
91 COG5000 NtrY Signal transducti 20.2 58 0.0013 29.2 1.4 22 29-50 374-395 (712)
No 1
>cd00265 MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.96 E-value=5.5e-31 Score=171.40 Aligned_cols=67 Identities=39% Similarity=0.675 Sum_probs=64.5
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCCchhHHHHHHhhccch
Q 039494 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVANRFLGLNC 67 (140)
Q Consensus 1 ik~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~spsv~~vi~ry~~~~~ 67 (140)
|++|+|+.+|++||+||++||||||.|||+||||+||+|||||+|++|+|++|++++|++||...+.
T Consensus 7 i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~~~vl~ry~~~~~ 73 (77)
T cd00265 7 IKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERYQKTSG 73 (77)
T ss_pred eEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHHHhccc
Confidence 6899999999999999999999999999999999999999999999999999999999999987653
No 2
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=99.95 E-value=1.2e-29 Score=189.72 Aligned_cols=68 Identities=49% Similarity=0.799 Sum_probs=64.7
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCCch--hHHHHHHhhccchH
Q 039494 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPS--IEAVANRFLGLNCQ 68 (140)
Q Consensus 1 ik~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~sps--v~~vi~ry~~~~~~ 68 (140)
|++|+|+..|+|||+|||.||||||+||||||||+||+|||||+|++|+|++|+ |++|+++|......
T Consensus 8 i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~~~~~ 77 (195)
T KOG0014|consen 8 IKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLNLTEP 77 (195)
T ss_pred eeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHhhhhh
Confidence 789999999999999999999999999999999999999999999999999987 99999999886554
No 3
>cd00266 MADS_SRF_like SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.95 E-value=1.3e-28 Score=162.34 Aligned_cols=68 Identities=44% Similarity=0.663 Sum_probs=64.0
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCCch-hHHHHHHhhccchH
Q 039494 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPS-IEAVANRFLGLNCQ 68 (140)
Q Consensus 1 ik~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~sps-v~~vi~ry~~~~~~ 68 (140)
|++|+|+.+|++||+|||.||+|||+||||||||+||+|||||+|+.+.|++++ ++.++++|...+..
T Consensus 7 i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~~~~~ 75 (83)
T cd00266 7 IKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEVLSAL 75 (83)
T ss_pred eEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhhcCHh
Confidence 689999999999999999999999999999999999999999999999988766 99999999887754
No 4
>smart00432 MADS MADS domain.
Probab=99.94 E-value=1.3e-27 Score=147.72 Aligned_cols=53 Identities=43% Similarity=0.788 Sum_probs=51.5
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCCc
Q 039494 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNP 53 (140)
Q Consensus 1 ik~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~sp 53 (140)
|++|+|+..|++||+||+.||+|||+|||+||||+||+|||||+|++++|++|
T Consensus 7 i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~p 59 (59)
T smart00432 7 IKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFASP 59 (59)
T ss_pred eEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCCCCeeeccCC
Confidence 68999999999999999999999999999999999999999999999999886
No 5
>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....
Probab=99.93 E-value=1.3e-28 Score=147.78 Aligned_cols=51 Identities=47% Similarity=0.742 Sum_probs=46.7
Q ss_pred ccccCCCCcccccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCC
Q 039494 2 KKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGN 52 (140)
Q Consensus 2 k~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~s 52 (140)
|+|+|+..|++||+||+.||+|||.|||+||||+||+|||||+|++++|+|
T Consensus 1 K~I~n~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~~iv~~~~g~~~~f~s 51 (51)
T PF00319_consen 1 KRIENKSRRKVTFSKRKKGLFKKASELSTLCGVDVALIVFSPDGKLYTFPS 51 (51)
T ss_dssp S--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEEETTSEEEEEES
T ss_pred CCccchhHhHhHHHHHHhhhhhccceeeeecCCeEEEEEECCCCCEEEecC
Confidence 689999999999999999999999999999999999999999999999975
No 6
>cd00120 MADS MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.93 E-value=3.3e-27 Score=146.04 Aligned_cols=53 Identities=45% Similarity=0.735 Sum_probs=51.2
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCCc
Q 039494 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNP 53 (140)
Q Consensus 1 ik~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~sp 53 (140)
|++|+|+..|++||+||++||+|||+|||+||||+||+|||||+|+++.|++|
T Consensus 7 i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~~ 59 (59)
T cd00120 7 IKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWSS 59 (59)
T ss_pred eEEeeCcchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCCCCcccccCC
Confidence 68999999999999999999999999999999999999999999999999875
No 7
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.72 E-value=1.3e-18 Score=136.29 Aligned_cols=60 Identities=42% Similarity=0.634 Sum_probs=55.9
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCCchhHHHHH
Q 039494 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVAN 60 (140)
Q Consensus 1 ik~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~spsv~~vi~ 60 (140)
|++|+|+..|.+||+|||.||||||+|||||+|.+|-++|.|.+|.+|+|++|..+.||.
T Consensus 69 ~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpKLep~i~ 128 (338)
T KOG0015|consen 69 MEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPKLEPMIT 128 (338)
T ss_pred chhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEecccccccccc
Confidence 689999999999999999999999999999999999999999999999999988654443
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.27 E-value=1.5e-12 Score=106.10 Aligned_cols=60 Identities=38% Similarity=0.557 Sum_probs=56.3
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCCchhHHHHH
Q 039494 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVAN 60 (140)
Q Consensus 1 ik~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~spsv~~vi~ 60 (140)
|..|+|+.+|.|||+||+.||+|||.||++|.|.+|.++|.|..|.++.|+.|+.+.|+.
T Consensus 88 is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~~e~v~~ 147 (412)
T COG5068 88 ISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKLESVVK 147 (412)
T ss_pred cccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCccccccc
Confidence 678999999999999999999999999999999999999999999999999998666654
No 9
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=97.65 E-value=0.00017 Score=48.76 Aligned_cols=48 Identities=6% Similarity=0.099 Sum_probs=43.1
Q ss_pred HHHHhCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 039494 71 KRKETQPRWWETPVYEFNHQELLQMDATIDNLSRTFIAKLNEKTAAAS 118 (140)
Q Consensus 71 K~~~~~~~~~~~~l~~ls~~eL~~l~~~Le~~l~~v~~r~~~l~~~~~ 118 (140)
.++...+.+.|+++++|+++||..|+..|+..+..|++|+.++..++.
T Consensus 30 ~L~~~~R~~~GedL~~Ls~~eL~~LE~~Le~aL~~VR~rK~~~l~~~i 77 (100)
T PF01486_consen 30 SLQKELRHLMGEDLESLSLKELQQLEQQLESALKRVRSRKDQLLMEQI 77 (100)
T ss_pred HHHHHHhccccccccccchHHHHHHHHhhhhhHHHHHHHHHHHHHHHH
Confidence 366778889999999999999999999999999999999999877654
No 10
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=77.79 E-value=9 Score=23.47 Aligned_cols=35 Identities=14% Similarity=0.023 Sum_probs=29.1
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039494 79 WWETPVYEFNHQELLQMDATIDNLSRTFIAKLNEK 113 (140)
Q Consensus 79 ~~~~~l~~ls~~eL~~l~~~Le~~l~~v~~r~~~l 113 (140)
..+.+|+.||++||.+-...|+.-...++.-+...
T Consensus 13 ~ig~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~~K 47 (59)
T PF06698_consen 13 EIGEDLSLLSVEELEERIALLEAEIARLEAAIAKK 47 (59)
T ss_pred ccCCCchhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999998888877766543
No 11
>PF14071 YlbD_coat: Putative coat protein
Probab=77.34 E-value=8 Score=27.24 Aligned_cols=50 Identities=10% Similarity=0.153 Sum_probs=34.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCccccCCCCCCCcccC
Q 039494 83 PVYEFNHQELLQMDATIDNLSRTFIAKLNEKTAAASSSAAPPMYFHHGLGSFPMQFR 139 (140)
Q Consensus 83 ~l~~ls~~eL~~l~~~Le~~l~~v~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 (140)
-+..|+++++..-...+...+..|..=+.+- ++..+.++ .+....||.||
T Consensus 73 ~vKkmD~nq~q~hl~~~sqai~~vQ~~l~qF--q~~~~~~~-----~~~~~~PFsFr 122 (124)
T PF14071_consen 73 MVKKMDVNQMQKHLNNVSQAIGSVQQVLSQF--QGNGQKQS-----QRSPEHPFSFR 122 (124)
T ss_pred HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCCCCC-----CCCCCCCCccC
Confidence 4677899999988888888888887755442 22222222 56667999998
No 12
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=66.66 E-value=3.3 Score=22.14 Aligned_cols=27 Identities=26% Similarity=0.380 Sum_probs=18.0
Q ss_pred hhhcccccEEEEeecCCCCCccc--CCch
Q 039494 28 LVTLTVSAIARLVFSQSGKPFSF--GNPS 54 (140)
Q Consensus 28 Ls~LC~~~vavivfsp~gk~~~~--~sps 54 (140)
||--||+-|-+-||...|..-.| ++|.
T Consensus 3 lcpkcgvgvl~pvy~~kgeikvfrcsnpa 31 (36)
T PF09151_consen 3 LCPKCGVGVLEPVYNQKGEIKVFRCSNPA 31 (36)
T ss_dssp B-TTTSSSBEEEEE-TTS-EEEEEES-TT
T ss_pred cCCccCceEEEEeecCCCcEEEEEcCCCc
Confidence 67789999999999999954444 4453
No 13
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=66.02 E-value=1 Score=22.37 Aligned_cols=13 Identities=31% Similarity=0.542 Sum_probs=10.1
Q ss_pred EEEeecCCCCCcc
Q 039494 37 ARLVFSQSGKPFS 49 (140)
Q Consensus 37 avivfsp~gk~~~ 49 (140)
.+.+|||+|+++.
T Consensus 4 ~~t~FSp~Grl~Q 16 (23)
T PF10584_consen 4 SITTFSPDGRLFQ 16 (23)
T ss_dssp STTSBBTTSSBHH
T ss_pred CceeECCCCeEEe
Confidence 3458999999875
No 14
>KOG3048 consensus Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones]
Probab=65.03 E-value=18 Score=26.21 Aligned_cols=34 Identities=12% Similarity=0.123 Sum_probs=28.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039494 82 TPVYEFNHQELLQMDATIDNLSRTFIAKLNEKTA 115 (140)
Q Consensus 82 ~~l~~ls~~eL~~l~~~Le~~l~~v~~r~~~l~~ 115 (140)
-++..|++++|.++.+++|.-++.+.+-+++|.+
T Consensus 8 idltkLsleQL~~lk~q~dqEl~~lq~Sl~~L~~ 41 (153)
T KOG3048|consen 8 IDLTKLSLEQLGALKKQFDQELNFLQDSLNALKG 41 (153)
T ss_pred CChhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3688999999999999999988887776666544
No 15
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=64.82 E-value=33 Score=26.93 Aligned_cols=41 Identities=17% Similarity=0.380 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCcc
Q 039494 86 EFNHQELLQMDATIDNLSRTFIAKLNEKTAAASSSAAPPMY 126 (140)
Q Consensus 86 ~ls~~eL~~l~~~Le~~l~~v~~r~~~l~~~~~~~~~~~~~ 126 (140)
+.+.++|.+-.+.+++.++++.+++.+.........-+++|
T Consensus 203 ~V~td~L~keAe~i~~~lekl~eq~~~~~~~~~~~~e~~~y 243 (244)
T COG1938 203 NVDTDKLEKEAEEIEEQLEKLAEQLEKEEERVEREEEPPMY 243 (244)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccCC
Confidence 36788999999999999999888887765433333334444
No 16
>KOG4252 consensus GTP-binding protein [Signal transduction mechanisms]
Probab=60.29 E-value=36 Score=26.01 Aligned_cols=27 Identities=26% Similarity=0.271 Sum_probs=18.3
Q ss_pred ccccEEEEeecCCCCCcccCCchhHHHHHHhhc
Q 039494 32 TVSAIARLVFSQSGKPFSFGNPSIEAVANRFLG 64 (140)
Q Consensus 32 C~~~vavivfsp~gk~~~~~spsv~~vi~ry~~ 64 (140)
-||++||+|||-++.. + .+.+++=|..
T Consensus 91 rgaqa~vLVFSTTDr~-S-----Fea~~~w~~k 117 (246)
T KOG4252|consen 91 RGAQASVLVFSTTDRY-S-----FEATLEWYNK 117 (246)
T ss_pred ccccceEEEEecccHH-H-----HHHHHHHHHH
Confidence 5899999999987642 2 3555555544
No 17
>PF10491 Nrf1_DNA-bind: NLS-binding and DNA-binding and dimerisation domains of Nrf1; InterPro: IPR019525 Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila []. In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human []. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Q8C4C0 from SWISSPROT, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [].
Probab=59.43 E-value=10 Score=29.03 Aligned_cols=41 Identities=20% Similarity=0.178 Sum_probs=32.0
Q ss_pred hhhhhhcccccEEEEeecCCC---CCcccCCchhHHHHHHhhcc
Q 039494 25 VSELVTLTVSAIARLVFSQSG---KPFSFGNPSIEAVANRFLGL 65 (140)
Q Consensus 25 a~ELs~LC~~~vavivfsp~g---k~~~~~spsv~~vi~ry~~~ 65 (140)
..|++|=+|-+|+|+|.+|+- ..-.||..-.+.|+..|+..
T Consensus 45 ~de~~trvGqqavvl~~~p~kp~~~f~vfGa~pL~~vv~~~~~~ 88 (214)
T PF10491_consen 45 IDEYTTRVGQQAVVLCCTPSKPNPVFKVFGAAPLENVVRNLKPV 88 (214)
T ss_pred HHHHHHhhhceeEEEEecCCCCCCceeeecchhHHHHHHHHHHH
Confidence 468999999999999999974 22347876678888888653
No 18
>PRK01919 tatB sec-independent translocase; Provisional
Probab=55.96 E-value=6.1 Score=29.27 Aligned_cols=10 Identities=20% Similarity=0.298 Sum_probs=7.9
Q ss_pred EEEEeecCCC
Q 039494 36 IARLVFSQSG 45 (140)
Q Consensus 36 vavivfsp~g 45 (140)
||+|||+|..
T Consensus 15 VALiV~GPek 24 (169)
T PRK01919 15 VALVVIGPER 24 (169)
T ss_pred HHHheeCchH
Confidence 7889999943
No 19
>PRK04654 sec-independent translocase; Provisional
Probab=48.73 E-value=9.5 Score=29.29 Aligned_cols=9 Identities=22% Similarity=0.405 Sum_probs=6.7
Q ss_pred EEEEeecCC
Q 039494 36 IARLVFSQS 44 (140)
Q Consensus 36 vavivfsp~ 44 (140)
|++|||+|.
T Consensus 15 VALlV~GPe 23 (214)
T PRK04654 15 VALVVLGPE 23 (214)
T ss_pred HHHHhcCch
Confidence 577888883
No 20
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=45.93 E-value=90 Score=21.94 Aligned_cols=59 Identities=19% Similarity=0.341 Sum_probs=36.3
Q ss_pred EEEeecCCCCCcccCCchhHHHHH-HhhccchHHHHHHHhCcccccCCCCCCCHHHHHHHHHHHHHHHH
Q 039494 37 ARLVFSQSGKPFSFGNPSIEAVAN-RFLGLNCQMRKRKETQPRWWETPVYEFNHQELLQMDATIDNLSR 104 (140)
Q Consensus 37 avivfsp~gk~~~~~spsv~~vi~-ry~~~~~~l~K~~~~~~~~~~~~l~~ls~~eL~~l~~~Le~~l~ 104 (140)
.+.|.+|.|+.|+ .-+++..+. ||... |..+.-.. .......+.+|-+.|...|+..+.
T Consensus 70 ga~vl~~rG~~yt--~~nI~~~L~~R~~~~-----~lR~~G~~--~~gpk~~~~~d~~~F~~~L~~~l~ 129 (130)
T PF02639_consen 70 GAYVLNPRGKEYT--KENIDELLAMRHLMA-----KLRRAGKR--TKGPKKFTKKDRQRFANALDRLLQ 129 (130)
T ss_pred CCEEECCCCCCCC--HHHHHHHHHHHHHHH-----HHHHhCCC--CCCCCCCCHHHHHHHHHHHHHHHc
Confidence 3577889898876 223544443 44332 22222222 223477899999999999998764
No 21
>TIGR01916 F420_cofE F420-0:gamma-glutamyl ligase. This model represents an enzyme of coenzyme F(420) biosynthesis, as catalyzed by MJ0768 of Methanococcus jannaschii and by the N-terminal half of FbiB of Mycobacterium bovis strain BCG. Note that only two glutamates are ligated in M. jannaschii, but five to six in the Mycobacterium lineage. In M. jannaschii, CofE catalyzes the GTP-dependent addition of two L-glutamates.
Probab=40.96 E-value=25 Score=27.62 Aligned_cols=28 Identities=25% Similarity=0.423 Sum_probs=24.1
Q ss_pred hhhhcccccEEEEeecCCCCCcccCCch
Q 039494 27 ELVTLTVSAIARLVFSQSGKPFSFGNPS 54 (140)
Q Consensus 27 ELs~LC~~~vavivfsp~gk~~~~~sps 54 (140)
+|.-.+|++|+|||+...|.++--+.+.
T Consensus 134 ~l~~~~g~~v~VIItDt~gr~~R~G~~g 161 (243)
T TIGR01916 134 GLRELTGVDVGVIITDTNGRPFREGQVG 161 (243)
T ss_pred HHHHHHCCCEEEEEECCCCCccccCCCC
Confidence 5666799999999999999999888765
No 22
>cd01365 KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like proteins. KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively.
Probab=40.42 E-value=23 Score=28.84 Aligned_cols=26 Identities=15% Similarity=0.404 Sum_probs=20.9
Q ss_pred hhcccccEEEEeecCCC--CCcc-cCCch
Q 039494 29 VTLTVSAIARLVFSQSG--KPFS-FGNPS 54 (140)
Q Consensus 29 s~LC~~~vavivfsp~g--k~~~-~~sps 54 (140)
++|-|..+||++|++.| |-|+ ||.+.
T Consensus 83 ~~l~G~n~~i~ayGqtGSGKT~Tm~G~~~ 111 (356)
T cd01365 83 HAFEGYNVCLFAYGQTGSGKSYTMMGYKE 111 (356)
T ss_pred HHhCCCceEEEEecCCCCCCeEEecCCCC
Confidence 36889999999999986 7776 66654
No 23
>COG3411 Ferredoxin [Energy production and conversion]
Probab=38.94 E-value=26 Score=21.78 Aligned_cols=28 Identities=18% Similarity=0.193 Sum_probs=21.3
Q ss_pred EEEeecCCCCCcccCCch-hHHHHHHhhc
Q 039494 37 ARLVFSQSGKPFSFGNPS-IEAVANRFLG 64 (140)
Q Consensus 37 avivfsp~gk~~~~~sps-v~~vi~ry~~ 64 (140)
.++++.|+|-.|....|. +++|++....
T Consensus 18 Pvl~vYpegvWY~~V~p~~a~rIv~~hl~ 46 (64)
T COG3411 18 PVLVVYPEGVWYTRVDPEDARRIVQSHLL 46 (64)
T ss_pred CEEEEecCCeeEeccCHHHHHHHHHHHHh
Confidence 567888999998888764 7888876543
No 24
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=38.13 E-value=25 Score=25.28 Aligned_cols=24 Identities=17% Similarity=0.191 Sum_probs=19.6
Q ss_pred hhhcccccEEEEeecCCCCCcccC
Q 039494 28 LVTLTVSAIARLVFSQSGKPFSFG 51 (140)
Q Consensus 28 Ls~LC~~~vavivfsp~gk~~~~~ 51 (140)
+.++|+|+|-++|-+.+.+...|+
T Consensus 59 ~tt~~dadvi~~v~~and~~s~f~ 82 (148)
T COG4917 59 ITTLQDADVIIYVHAANDPESRFP 82 (148)
T ss_pred HHHhhccceeeeeecccCccccCC
Confidence 678999999999999887655544
No 25
>PLN03230 acetyl-coenzyme A carboxylase carboxyl transferase; Provisional
Probab=37.83 E-value=87 Score=26.67 Aligned_cols=22 Identities=14% Similarity=0.454 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 039494 89 HQELLQMDATIDNLSRTFIAKL 110 (140)
Q Consensus 89 ~~eL~~l~~~Le~~l~~v~~r~ 110 (140)
.+|+..|++.++.+.+.+-..+
T Consensus 104 ~~ei~~l~~~~~~~~~~i~~~L 125 (431)
T PLN03230 104 SAQIAELEERYDQVRRELYSRL 125 (431)
T ss_pred HHHHHHHHHHHHHHHHHHHhcC
Confidence 3678888888887777654443
No 26
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=37.38 E-value=21 Score=24.52 Aligned_cols=41 Identities=17% Similarity=0.260 Sum_probs=28.4
Q ss_pred hhhhhhhcccccEEEEeecCCCCCcccCC---chhHHHHHHhhcc
Q 039494 24 KVSELVTLTVSAIARLVFSQSGKPFSFGN---PSIEAVANRFLGL 65 (140)
Q Consensus 24 Ka~ELs~LC~~~vavivfsp~gk~~~~~s---psv~~vi~ry~~~ 65 (140)
+-.||..|-||-+ +..||++|++.+|-. +..-+++.++-..
T Consensus 2 ~l~~Lm~lpGv~A-Ag~Fs~~G~l~e~~G~l~~~~a~m~A~mc~A 45 (108)
T PF09941_consen 2 KLDKLMKLPGVVA-AGEFSDDGKLVEYKGELDEEMAEMLAKMCAA 45 (108)
T ss_pred cHHHhhcCCCeEE-EEEECCCCeEEeeecCCCHHHHHHHHHHHHH
Confidence 3468888899864 588999999998643 4445555555433
No 27
>smart00030 CLb CLUSTERIN Beta chain.
Probab=37.05 E-value=1.1e+02 Score=23.48 Aligned_cols=57 Identities=9% Similarity=0.098 Sum_probs=28.8
Q ss_pred chhHHHHHHhhccchHHHHHHHhCcccc--cCCCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHhhc
Q 039494 53 PSIEAVANRFLGLNCQMRKRKETQPRWW--ETPVYEFNHQELLQ--MDATIDNLSRTFIAKLNEKTAAA 117 (140)
Q Consensus 53 psv~~vi~ry~~~~~~l~K~~~~~~~~~--~~~l~~ls~~eL~~--l~~~Le~~l~~v~~r~~~l~~~~ 117 (140)
..|..-|++|.+...+ -..| |+.++.|...+-++ --+.|++.-..+..-++.|-..+
T Consensus 112 glVg~qlEefln~ssp--------f~~wingd~idsL~e~~~~q~~~~~~~Ed~fs~~~~~vd~lF~ds 172 (206)
T smart00030 112 GLVGRQLEEFLNQSSP--------FYFWMNGDRIDSLLENDRQQSHVLDVMEDSFSRASSIVDELFQDR 172 (206)
T ss_pred hhHHHHHHHHHhcCCC--------ceeecccchhhhHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466666666543322 1224 56677764443321 12355555556666666655544
No 28
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=36.54 E-value=20 Score=24.71 Aligned_cols=38 Identities=21% Similarity=0.248 Sum_probs=28.4
Q ss_pred cccccccccchhhhh---------hhhhhhcccccEEEEeecCCCCC
Q 039494 10 RLITFSKRTSGIYRK---------VSELVTLTVSAIARLVFSQSGKP 47 (140)
Q Consensus 10 R~~tf~KRr~gL~KK---------a~ELs~LC~~~vavivfsp~gk~ 47 (140)
+..-||+=|+-|.+| +-|+.+=||.|+-+++..|.|.+
T Consensus 50 ~~~y~SRSR~~lW~KGetSG~~q~v~~i~~DCD~Dall~~V~q~gg~ 96 (111)
T COG0139 50 EAHYYSRSRQELWTKGETSGHTQKVVEIRLDCDGDALLLLVEQIGGP 96 (111)
T ss_pred eEEEEEcchhhheccccccCceEEEEEEEcCCCCCEEEEEEEeCCCC
Confidence 344456666656554 67899999999999999996643
No 29
>PF08656 DASH_Dad3: DASH complex subunit Dad3; InterPro: IPR013965 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ].
Probab=35.92 E-value=1.1e+02 Score=19.69 Aligned_cols=63 Identities=14% Similarity=0.107 Sum_probs=37.1
Q ss_pred chhHHHHHHhhccchHHHHHHHhCcccc-cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039494 53 PSIEAVANRFLGLNCQMRKRKETQPRWW-ETPVYEFNHQELLQMDATIDNLSRTFIAKLNEKTA 115 (140)
Q Consensus 53 psv~~vi~ry~~~~~~l~K~~~~~~~~~-~~~l~~ls~~eL~~l~~~Le~~l~~v~~r~~~l~~ 115 (140)
|=-.+|+++|.++...|+++...+...- .+.-..--.++|++||..+.-...=.++-+..+..
T Consensus 3 pLEq~VL~eY~~La~~L~~L~~~l~~L~~~~~~~~~lL~~LR~LE~K~glV~TL~KaSVYslvl 66 (78)
T PF08656_consen 3 PLEQEVLDEYQRLADNLKTLSDTLKDLNSSNSPSEELLDGLRELERKIGLVYTLFKASVYSLVL 66 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4347899999998877766444444441 11122244677777777776655545555544443
No 30
>PRK00124 hypothetical protein; Validated
Probab=35.88 E-value=1.7e+02 Score=21.23 Aligned_cols=61 Identities=20% Similarity=0.323 Sum_probs=37.1
Q ss_pred EEEeecCCCCCcccCCchhHHHHH-HhhccchHHHHHHHhCcccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 039494 37 ARLVFSQSGKPFSFGNPSIEAVAN-RFLGLNCQMRKRKETQPRWWETPVYEFNHQELLQMDATIDNLSRTF 106 (140)
Q Consensus 37 avivfsp~gk~~~~~spsv~~vi~-ry~~~~~~l~K~~~~~~~~~~~~l~~ls~~eL~~l~~~Le~~l~~v 106 (140)
.+.+.+|.|+.|+ ..+++..+. ||. +.|..+.-. ....-.-.+.+|-+.|...|+..+...
T Consensus 86 ga~vl~prG~~yt--~~nI~~~L~~R~~-----~~~lR~~G~--~t~Gp~~~~~~Dr~~F~~~L~~~l~~~ 147 (151)
T PRK00124 86 GAIVLNPRGYIYT--NDNIDQLLAMRDL-----MATLRRSGI--RTGGPKPFTQEDRSRFEAELDKLIRRI 147 (151)
T ss_pred CCEEECCCCcCCC--HHHHHHHHHHHHH-----HHHHHHcCC--CCCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence 3478889998886 122333332 332 223332211 112456789999999999999998864
No 31
>PF11944 DUF3461: Protein of unknown function (DUF3461); InterPro: IPR020911 This entry describes proteins of unknown function.
Probab=35.68 E-value=55 Score=23.05 Aligned_cols=28 Identities=7% Similarity=0.112 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039494 86 EFNHQELLQMDATIDNLSRTFIAKLNEK 113 (140)
Q Consensus 86 ~ls~~eL~~l~~~Le~~l~~v~~r~~~l 113 (140)
.-=++||..|+..+...+..|.++++.|
T Consensus 98 ~kiL~dL~HLE~Vv~~KIaEIe~dlekL 125 (125)
T PF11944_consen 98 QKILDDLRHLEKVVNSKIAEIERDLEKL 125 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3346889999999999999999888753
No 32
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=35.25 E-value=60 Score=25.98 Aligned_cols=35 Identities=11% Similarity=0.210 Sum_probs=28.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039494 82 TPVYEFNHQELLQMDATIDNLSRTFIAKLNEKTAA 116 (140)
Q Consensus 82 ~~l~~ls~~eL~~l~~~Le~~l~~v~~r~~~l~~~ 116 (140)
+.+++|+.+||.+|...|......|-+.+.++..+
T Consensus 214 EeL~~Mt~~EL~qL~~~L~~qIq~vfeeLt~~vQE 248 (285)
T PF06937_consen 214 EELNSMTLDELKQLNEKLLQQIQDVFEELTQQVQE 248 (285)
T ss_pred HHhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56999999999999999998888887777554443
No 33
>KOG4316 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.80 E-value=14 Score=26.87 Aligned_cols=43 Identities=23% Similarity=0.176 Sum_probs=25.6
Q ss_pred hhhhhcccccEEEEeec----CCC--CCcccCC-----chhHHHHHHhhccchH
Q 039494 26 SELVTLTVSAIARLVFS----QSG--KPFSFGN-----PSIEAVANRFLGLNCQ 68 (140)
Q Consensus 26 ~ELs~LC~~~vavivfs----p~g--k~~~~~s-----psv~~vi~ry~~~~~~ 68 (140)
.++++||++...+.--. |+. ...-|+. -.+++||+||+++...
T Consensus 43 ~a~~~lcq~p~vla~r~a~~~Ps~~r~~t~Fs~~kGkrktvkaVldRFkRL~~G 96 (172)
T KOG4316|consen 43 SARNLLCQHPSVLANRMAPVLPSVVRSLTYFSARKGKRKTVKAVLDRFKRLHCG 96 (172)
T ss_pred hHHHhHhcCcHHHHhccCCCCcchhhhhhhhhhhhcccccHHHHHHHHHhcccC
Confidence 57889998875443211 221 1112332 1279999999987765
No 34
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=34.00 E-value=18 Score=21.03 Aligned_cols=22 Identities=14% Similarity=0.197 Sum_probs=17.7
Q ss_pred hhhhhhhhhhcccccEEEEeec
Q 039494 21 IYRKVSELVTLTVSAIARLVFS 42 (140)
Q Consensus 21 L~KKa~ELs~LC~~~vavivfs 42 (140)
|.+.+..-+-|||++..+.+|-
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~ 23 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYA 23 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEe
Confidence 5566777799999999888875
No 35
>PF06780 Erp_C: Erp protein C-terminus; InterPro: IPR009618 This entry represents the C terminus of bacterial Erp proteins that seem to be specific to Borrelia burgdorferi (a causative agent of Lyme disease). Borrelia Erp proteins are particularly heterogeneous, which might enable them to interact with a wide variety of host components [].
Probab=33.94 E-value=45 Score=24.06 Aligned_cols=38 Identities=16% Similarity=0.220 Sum_probs=29.6
Q ss_pred HhCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 039494 74 ETQPRWWETPVYEFNHQELLQMDATIDNLSRTFIAKLNE 112 (140)
Q Consensus 74 ~~~~~~~~~~l~~ls~~eL~~l~~~Le~~l~~v~~r~~~ 112 (140)
+.++..| +.++.-...+|..|...|+..+..+|.+++.
T Consensus 53 nSIy~~W-~~le~ee~~~L~~Ll~eL~~~R~~LR~Ki~e 90 (146)
T PF06780_consen 53 NSIYSTW-EDLEEEEESGLGKLLKELSDTRSSLRTKINE 90 (146)
T ss_pred chHHHHH-hccccchhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 4566678 5666556778888999999999999988866
No 36
>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []. Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].
Probab=33.87 E-value=99 Score=24.89 Aligned_cols=34 Identities=24% Similarity=0.282 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHhhcCCCC-CCCcccc-----CCCC--CCCcc
Q 039494 104 RTFIAKLNEKTAAASSSA-APPMYFH-----HGLG--SFPMQ 137 (140)
Q Consensus 104 ~~v~~r~~~l~~~~~~~~-~~~~~~~-----~~~~--~~~~~ 137 (140)
+.+...+..|.....+-. +...+.| |..+ -||||
T Consensus 179 krle~e~k~lq~k~~~q~~~qstmsHRdIArhQasSSVFsWQ 220 (307)
T PF10481_consen 179 KRLEAEVKALQAKKASQAAPQSTMSHRDIARHQASSSVFSWQ 220 (307)
T ss_pred hhHHHHHHHHhcccCCCcCccccccHHHHHHHhccCcccccc
Confidence 334444444444333332 3444555 4433 39998
No 37
>TIGR03274 methan_mark_7 putative methanogenesis marker protein 7. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=33.58 E-value=2e+02 Score=23.24 Aligned_cols=25 Identities=8% Similarity=-0.017 Sum_probs=17.8
Q ss_pred cchhhhhhhhhhhcccccEEEEeecCC
Q 039494 18 TSGIYRKVSELVTLTVSAIARLVFSQS 44 (140)
Q Consensus 18 r~gL~KKa~ELs~LC~~~vavivfsp~ 44 (140)
+.-+.+|+.-+-- |++++ ||+=+|+
T Consensus 140 k~hI~~K~rl~l~-i~iP~-VV~~~P~ 164 (302)
T TIGR03274 140 EDCIKKKMPLFRD-IDIPV-VVTGGPE 164 (302)
T ss_pred HHHHHHHHHHHhc-CCCCE-EEeCCCc
Confidence 3456778755534 89988 8888886
No 38
>PF13252 DUF4043: Protein of unknown function (DUF4043)
Probab=32.90 E-value=26 Score=28.81 Aligned_cols=23 Identities=17% Similarity=0.163 Sum_probs=18.0
Q ss_pred hhhhhhcccccEEEEeecCCCCC
Q 039494 25 VSELVTLTVSAIARLVFSQSGKP 47 (140)
Q Consensus 25 a~ELs~LC~~~vavivfsp~gk~ 47 (140)
+-.-++|||++++++.|+..+..
T Consensus 271 ~v~ralLlGaQA~~~A~G~~~~~ 293 (341)
T PF13252_consen 271 AVARALLLGAQALVIAFGKSGSG 293 (341)
T ss_pred ceeeeeeechhheeeeeeccCCC
Confidence 44567899999999999985433
No 39
>KOG4637 consensus Adaptor for phosphoinositide 3-kinase [Signal transduction mechanisms]
Probab=32.56 E-value=40 Score=28.34 Aligned_cols=41 Identities=12% Similarity=0.267 Sum_probs=29.1
Q ss_pred hhhhhcccccEEEEeecCCCCCcccCCch-----hHHHHHHhhccc
Q 039494 26 SELVTLTVSAIARLVFSQSGKPFSFGNPS-----IEAVANRFLGLN 66 (140)
Q Consensus 26 ~ELs~LC~~~vavivfsp~gk~~~~~sps-----v~~vi~ry~~~~ 66 (140)
.-|||+||-+|--.+.-.+...|-|..|. .++++..|...+
T Consensus 367 yalSV~~~~~V~HClIy~tatG~GFa~pyn~y~tlk~lV~hY~h~S 412 (464)
T KOG4637|consen 367 YALSVVHDGEVKHCLIYQTATGFGFAEPYNLYSTLKELVLHYQHTS 412 (464)
T ss_pred eEEEEEECCceeeeEEeeccccccccchhHHHHHHHHHHHHHhhhh
Confidence 35899999888555544555556666553 689999998876
No 40
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=32.33 E-value=1.2e+02 Score=24.50 Aligned_cols=42 Identities=17% Similarity=0.207 Sum_probs=27.2
Q ss_pred ccccCCCCcccccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCC-chhHHHHHHhhc
Q 039494 2 KKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGN-PSIEAVANRFLG 64 (140)
Q Consensus 2 k~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~s-psv~~vi~ry~~ 64 (140)
-.|+|.+.|..+=++ .||..|.+ +.| .|-+ |+|++|++.|..
T Consensus 27 ~li~n~tqr~t~~sR-------------~L~Ecel~---~~p-----~Y~nDpEmK~iid~~n~ 69 (295)
T TIGR01478 27 SYIQNNTQMTSTKSR-------------LLAEIQRP---KNP-----HYHNDPELKEIIDKLNE 69 (295)
T ss_pred ecccCccccccccce-------------ehhhhccc---cCC-----CCCCcHHHHHHHHHHhH
Confidence 357777777766332 36766653 333 3544 889999998865
No 41
>PF08188 Protamine_3: Spermatozal protamine family; InterPro: IPR012601 This entry consists of the spermatozal protamines. Spermatozal protamines play an important role in remodelling of the sperm chromatin during mammalian spermiogenesis. Nuclear elongation and chromatin condensation are concomitant with modifications in the basic protein complement associated with DNA. Somatic histones are initially replaced by testis-specific histone variants, then by transitional proteins, and ultimately by protamines [].; GO: 0003677 DNA binding, 0035092 sperm chromatin condensation, 0000228 nuclear chromosome
Probab=32.13 E-value=74 Score=17.93 Aligned_cols=16 Identities=31% Similarity=0.544 Sum_probs=12.6
Q ss_pred ccccCCCCCCCcccCC
Q 039494 125 MYFHHGLGSFPMQFRS 140 (140)
Q Consensus 125 ~~~~~~~~~~~~~~~~ 140 (140)
.|-.||+.--|-.||.
T Consensus 33 sfkahgflkqpprfrp 48 (48)
T PF08188_consen 33 SFKAHGFLKQPPRFRP 48 (48)
T ss_pred HHHhcccccCCCCCCC
Confidence 4778999988888874
No 42
>cd00106 KISc Kinesin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), in some its is found in the middle (M-type), or C-terminal (C-type). N-type and M-type kinesins are (+) end-directed motors, while C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coil
Probab=31.95 E-value=36 Score=27.03 Aligned_cols=25 Identities=28% Similarity=0.569 Sum_probs=19.7
Q ss_pred hcccccEEEEeecCCC--CCcc-cCCch
Q 039494 30 TLTVSAIARLVFSQSG--KPFS-FGNPS 54 (140)
Q Consensus 30 ~LC~~~vavivfsp~g--k~~~-~~sps 54 (140)
++.|..+|+++|++.| |-|+ +|++.
T Consensus 74 ~~~G~~~~i~~yG~tgSGKT~tl~G~~~ 101 (328)
T cd00106 74 VLEGYNGTIFAYGQTGSGKTYTMFGSPK 101 (328)
T ss_pred HhCCCceeEEEecCCCCCCeEEecCCCC
Confidence 4679999999999985 7776 66644
No 43
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=30.91 E-value=46 Score=23.50 Aligned_cols=34 Identities=26% Similarity=0.223 Sum_probs=24.5
Q ss_pred ccccEEEEeecCCCCCcccCCc-hhHHHHHHhhcc
Q 039494 32 TVSAIARLVFSQSGKPFSFGNP-SIEAVANRFLGL 65 (140)
Q Consensus 32 C~~~vavivfsp~gk~~~~~sp-sv~~vi~ry~~~ 65 (140)
|+...++-|..++|++..|..| .+.+|+..|=..
T Consensus 12 ~~~~~~vkvv~~~G~v~~~~~pv~a~evm~~~P~h 46 (181)
T PF14009_consen 12 SSSAATVKVVHPDGKVEEFKRPVTAAEVMLENPGH 46 (181)
T ss_pred cCCCceEEEEcCCCcEEEeCCCcCHHHHHHHCCCC
Confidence 3445555555589999999887 488999888544
No 44
>cd07022 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases.
Probab=30.72 E-value=1.8e+02 Score=21.72 Aligned_cols=84 Identities=11% Similarity=0.019 Sum_probs=47.2
Q ss_pred hhhhhhhhhcccccEEEEeecCCCCCccc----CCchhHHHHHHhhccchHHHHHHHhCcccccCCCCCCCHHHHHHHHH
Q 039494 22 YRKVSELVTLTVSAIARLVFSQSGKPFSF----GNPSIEAVANRFLGLNCQMRKRKETQPRWWETPVYEFNHQELLQMDA 97 (140)
Q Consensus 22 ~KKa~ELs~LC~~~vavivfsp~gk~~~~----~spsv~~vi~ry~~~~~~l~K~~~~~~~~~~~~l~~ls~~eL~~l~~ 97 (140)
..-+..|+..|| .|+-+|++..... ..+....+++++--.... ......+-.+++...++.++.+.++.
T Consensus 85 ~s~gy~lA~~aD----~i~a~~~a~~g~iG~~~~~~~~~~ll~k~Gi~~~~---~~~g~~K~~~~~~~~~s~~~re~~~~ 157 (214)
T cd07022 85 ASAAYWIASAAD----RIVVTPTAGVGSIGVVASHVDQSKALEKAGLKVTL---IFAGAHKVDGNPDEPLSDEARARLQA 157 (214)
T ss_pred hhHHHHHHhcCC----EEEEcCCCeEEeeeEEEecCCHHHHHHhCCCeEEE---EEcCCCccCCCCCCCCCHHHHHHHHH
Confidence 344566666666 3444565543222 234455555544211100 01112233456777999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q 039494 98 TIDNLSRTFIAKLNE 112 (140)
Q Consensus 98 ~Le~~l~~v~~r~~~ 112 (140)
.|+..-....+.+.+
T Consensus 158 ~l~~~~~~f~~~V~~ 172 (214)
T cd07022 158 EVDALYAMFVAAVAR 172 (214)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999887776665544
No 45
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=30.56 E-value=1.5e+02 Score=19.91 Aligned_cols=29 Identities=3% Similarity=0.163 Sum_probs=22.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039494 87 FNHQELLQMDATIDNLSRTFIAKLNEKTA 115 (140)
Q Consensus 87 ls~~eL~~l~~~Le~~l~~v~~r~~~l~~ 115 (140)
|+.+++..|...|...+..+.+++.+...
T Consensus 1 M~~~~l~~~k~~L~~~~~~L~~~i~~~~~ 29 (110)
T TIGR02420 1 MSEAQLEHFRKILLRWKQELLEEADKTLE 29 (110)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56788889999999888887777766543
No 46
>cd01371 KISc_KIF3 Kinesin motor domain, kinesins II or KIF3_like proteins. Subgroup of kinesins, which form heterotrimers composed of 2 kinesins and one non-motor accessory subunit. Kinesins II play important roles in ciliary transport, and have been implicated in neuronal transport, melanosome transport, the secretory pathway, and mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this group the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain
Probab=29.86 E-value=47 Score=26.73 Aligned_cols=25 Identities=24% Similarity=0.280 Sum_probs=20.2
Q ss_pred hhcccccEEEEeecCCC--CCcc-cCCc
Q 039494 29 VTLTVSAIARLVFSQSG--KPFS-FGNP 53 (140)
Q Consensus 29 s~LC~~~vavivfsp~g--k~~~-~~sp 53 (140)
+++-|..+|+++|++.| |-|+ +|.+
T Consensus 76 ~~~~G~n~~i~ayG~tgSGKTyTm~G~~ 103 (333)
T cd01371 76 SVLEGYNGTIFAYGQTGTGKTFTMEGVR 103 (333)
T ss_pred HHhCCCceeEEecCCCCCCCcEeecCCC
Confidence 57889999999999986 7776 5654
No 47
>TIGR00161 conserved hypothetical protein TIGR00161. This ortholog set includes MJ0106 from Methanococcus jannaschii and AF1251 from Archaeoglobus fulgidus, but not MJ1210 or AF0525.
Probab=29.46 E-value=1.3e+02 Score=23.19 Aligned_cols=30 Identities=10% Similarity=0.217 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039494 87 FNHQELLQMDATIDNLSRTFIAKLNEKTAA 116 (140)
Q Consensus 87 ls~~eL~~l~~~Le~~l~~v~~r~~~l~~~ 116 (140)
++.++|.+-.+.+++.++.+.++..+...+
T Consensus 201 id~~~L~e~Ae~ie~~~~el~e~~~~~~~~ 230 (238)
T TIGR00161 201 VDPEPLLKEAEAIESRLKKLAEQVQGMMSK 230 (238)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 578999999999999999888888775443
No 48
>cd01368 KISc_KIF23_like Kinesin motor domain, KIF23-like subgroup. Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, a
Probab=29.02 E-value=43 Score=27.19 Aligned_cols=26 Identities=15% Similarity=0.282 Sum_probs=20.9
Q ss_pred hhcccccEEEEeecCCC--CCcc-cCCch
Q 039494 29 VTLTVSAIARLVFSQSG--KPFS-FGNPS 54 (140)
Q Consensus 29 s~LC~~~vavivfsp~g--k~~~-~~sps 54 (140)
.++-|..+++++|+++| |-|+ +|.+.
T Consensus 83 ~~l~G~n~ti~aYGqtGSGKTyTm~G~~~ 111 (345)
T cd01368 83 DLLKGKNSLLFTYGVTNSGKTYTMQGSPG 111 (345)
T ss_pred HHhCCCceEEEEeCCCCCCCeEEecCCCC
Confidence 46789999999999986 7776 66654
No 49
>PRK09822 lipopolysaccharide core biosynthesis protein; Provisional
Probab=28.90 E-value=24 Score=27.77 Aligned_cols=41 Identities=15% Similarity=0.269 Sum_probs=29.9
Q ss_pred ccccccccchhhhhhhhhhhcccccE---EEEeecCCCCCcccCC
Q 039494 11 LITFSKRTSGIYRKVSELVTLTVSAI---ARLVFSQSGKPFSFGN 52 (140)
Q Consensus 11 ~~tf~KRr~gL~KKa~ELs~LC~~~v---avivfsp~gk~~~~~s 52 (140)
+.-|.+-|.|++||. .+..||+.+- +=|.||+.++..-|+.
T Consensus 117 ~~~~~~~~~~~~~~~-~~~~L~~~~~~l~~~v~fS~~~r~IGFSk 160 (269)
T PRK09822 117 RSFYRREKGGFLKKI-KFNILKRVHKALLISVPLSKRGRLAGFCK 160 (269)
T ss_pred hhhhhhccCchhhhh-HHHHHhhhhhhhEEEeeccccCCceeeee
Confidence 455677788999887 4788887654 4456898888777765
No 50
>PRK00098 GTPase RsgA; Reviewed
Probab=28.74 E-value=59 Score=25.78 Aligned_cols=32 Identities=19% Similarity=0.146 Sum_probs=24.6
Q ss_pred cccccchhhhhhh--hhhhcccccEEEEeecCCC
Q 039494 14 FSKRTSGIYRKVS--ELVTLTVSAIARLVFSQSG 45 (140)
Q Consensus 14 f~KRr~gL~KKa~--ELs~LC~~~vavivfsp~g 45 (140)
-..|+.-|..++. +..+.-+++++++|++..+
T Consensus 59 i~~R~~~l~R~~~~~~q~iaaniD~vllV~d~~~ 92 (298)
T PRK00098 59 IHERKNLLVRPPIFKSKLIAANVDQAVLVFAAKE 92 (298)
T ss_pred EeCCCceEECCCCccccceeecCCEEEEEEECCC
Confidence 5566666766664 6667899999999999864
No 51
>cd07023 S49_Sppa_N_C Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad
Probab=28.62 E-value=2.4e+02 Score=20.78 Aligned_cols=81 Identities=14% Similarity=0.126 Sum_probs=45.0
Q ss_pred hhhhhhhhcccccEEEEeecCCCCCcccC----CchhHHHHHHhhccchHHHHHHHhCcccccCCCCCCCHHHHHHHHHH
Q 039494 23 RKVSELVTLTVSAIARLVFSQSGKPFSFG----NPSIEAVANRFLGLNCQMRKRKETQPRWWETPVYEFNHQELLQMDAT 98 (140)
Q Consensus 23 KKa~ELs~LC~~~vavivfsp~gk~~~~~----spsv~~vi~ry~~~~~~l~K~~~~~~~~~~~~l~~ls~~eL~~l~~~ 98 (140)
.-+..|+..||. |+-+|++..-..+ ++....+++++--.... ......+-.+++.+.++.++.+.++..
T Consensus 79 s~g~~lA~aaD~----i~a~~~s~~g~iG~~~~~~~~~~~l~k~Gi~~~~---~~~g~~K~~~~~~~~~s~~~~e~~~~~ 151 (208)
T cd07023 79 SGGYYIAAAADK----IVANPTTITGSIGVIGQGPNLEELLDKLGIERDT---IKSGPGKDKGSPDRPLTEEERAILQAL 151 (208)
T ss_pred hHHHHHHhhCCE----EEECCCCeEEeCcEEEecCCHHHHHHhcCCceEE---EecCCCccCCCCCCCCCHHHHHHHHHH
Confidence 445566666663 5555655433322 24466666665322111 011112334456788999998888888
Q ss_pred HHHHHHHHHHHH
Q 039494 99 IDNLSRTFIAKL 110 (140)
Q Consensus 99 Le~~l~~v~~r~ 110 (140)
|+..-....+.+
T Consensus 152 l~~~~~~f~~~V 163 (208)
T cd07023 152 VDDIYDQFVDVV 163 (208)
T ss_pred HHHHHHHHHHHH
Confidence 887766654444
No 52
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.34 E-value=44 Score=24.50 Aligned_cols=23 Identities=17% Similarity=0.258 Sum_probs=18.0
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHH
Q 039494 83 PVYEFNHQELLQMDATIDNLSRT 105 (140)
Q Consensus 83 ~l~~ls~~eL~~l~~~Le~~l~~ 105 (140)
.+++|+.+|-+.|.+.+++++..
T Consensus 94 e~eeLs~deke~~~~sl~dL~~d 116 (158)
T PF10083_consen 94 EDEELSPDEKEQFKESLPDLTKD 116 (158)
T ss_pred HhhcCCHHHHHHHHhhhHHHhhc
Confidence 45788888888888888887763
No 53
>PRK13701 psiB plasmid SOS inhibition protein B; Provisional
Probab=27.93 E-value=79 Score=22.74 Aligned_cols=51 Identities=22% Similarity=0.246 Sum_probs=33.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCccccCCCC------CCCcccC
Q 039494 83 PVYEFNHQELLQMDATIDNLSRTFIAKLNEKTAAASSSAAPPMYFHHGLG------SFPMQFR 139 (140)
Q Consensus 83 ~l~~ls~~eL~~l~~~Le~~l~~v~~r~~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~ 139 (140)
-|..|+.+|+++..+.=++.+..+..-+...+ ..|.-..-||.| +||-|-|
T Consensus 9 ~l~tM~a~ElEd~R~~G~d~RR~Lt~aVm~~L------~~P~gW~~naEy~sEFgGffPVq~R 65 (144)
T PRK13701 9 VLQTMSAQEYEDIRAAGSDERRELTHAVMREL------DAPDGWTMNGEYGSEFGGFFPVQVR 65 (144)
T ss_pred HHhccCHHHHHHHHHHhHHHHHHhHHHHHhcc------CCCccceeehhhhccccCeeeEEEE
Confidence 47789999999998888887776655443321 235555555554 5888765
No 54
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.87 E-value=36 Score=24.24 Aligned_cols=20 Identities=25% Similarity=0.459 Sum_probs=16.8
Q ss_pred CCCCCCccccCCCCCCCccc
Q 039494 119 SSAAPPMYFHHGLGSFPMQF 138 (140)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~ 138 (140)
+-|.||.|-||-.+-|||-=
T Consensus 63 ~dye~psfchncgs~fpwte 82 (160)
T COG4306 63 GDYEPPSFCHNCGSRFPWTE 82 (160)
T ss_pred CCCCCcchhhcCCCCCCcHH
Confidence 44789999999999999953
No 55
>PF08557 Lipid_DES: Sphingolipid Delta4-desaturase (DES); InterPro: IPR013866 Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyses the formation of (E)-sphing-4-enine []. Some proteins in this entry have bifunctional delta 4-desaturase/C-4-hydroxylase activity. Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis []. This small protein associates with FA_desaturase IPR005804 from INTERPRO and appears to be specific to sphingolipid delta 4-desaturase. ; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0006633 fatty acid biosynthetic process, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=27.33 E-value=24 Score=19.78 Aligned_cols=22 Identities=23% Similarity=0.277 Sum_probs=19.3
Q ss_pred cccccchhhhhhhhhhhccccc
Q 039494 14 FSKRTSGIYRKVSELVTLTVSA 35 (140)
Q Consensus 14 f~KRr~gL~KKa~ELs~LC~~~ 35 (140)
-..||+-|+||=-|+--|+|.+
T Consensus 15 H~~RRk~IL~k~PeIk~L~G~d 36 (39)
T PF08557_consen 15 HASRRKEILKKHPEIKKLMGPD 36 (39)
T ss_pred cHHHHHHHHHhChHHHHHhCCC
Confidence 4579999999999999999876
No 56
>PF06361 RTBV_P12: Rice tungro bacilliform virus P12 protein; InterPro: IPR009417 This family consists of several Rice tungro bacilliform virus P12 proteins. The function of this family is unknown [].
Probab=27.30 E-value=1.5e+02 Score=19.53 Aligned_cols=70 Identities=16% Similarity=0.286 Sum_probs=36.7
Q ss_pred CchhHHHHHHhhccchHHHHHHHhCcccc-----------cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q 039494 52 NPSIEAVANRFLGLNCQMRKRKETQPRWW-----------ETPVYEFNHQELLQMDATIDNLSRTFIAKLNEKTAAASSS 120 (140)
Q Consensus 52 spsv~~vi~ry~~~~~~l~K~~~~~~~~~-----------~~~l~~ls~~eL~~l~~~Le~~l~~v~~r~~~l~~~~~~~ 120 (140)
.|..++-+++|+++... -.+..++-| +.++.+-.+-+|-.|. .++..++++.+++..+-..+.++
T Consensus 5 yptfke~lekf~~les~---ta~kdkf~wvftl~~ikttadvnlaskglvqlyalq-eidkkinnl~aqv~k~pttsgs~ 80 (110)
T PF06361_consen 5 YPTFKESLEKFQNLESD---TANKDKFNWVFTLQNIKTTADVNLASKGLVQLYALQ-EIDKKINNLSAQVSKIPTTSGSS 80 (110)
T ss_pred cchHHHHHHHHhccccc---cccccccceEEEecccceecccchhhhhHHHHHHHH-HHHhhhhhhHhhhhcCccCCCCC
Confidence 46788999999887543 111222223 2233333444544443 35666666666666655444444
Q ss_pred CCCCc
Q 039494 121 AAPPM 125 (140)
Q Consensus 121 ~~~~~ 125 (140)
++..+
T Consensus 81 sagai 85 (110)
T PF06361_consen 81 SAGAI 85 (110)
T ss_pred Cccee
Confidence 44333
No 57
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=26.63 E-value=43 Score=28.25 Aligned_cols=46 Identities=13% Similarity=0.174 Sum_probs=35.7
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCC
Q 039494 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGN 52 (140)
Q Consensus 1 ik~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~s 52 (140)
|+++.++..-..||.+|+.| ||+.+|+..+-+.++.-..-...|+.
T Consensus 18 i~~~~d~~~ps~~~~~~~~~------~~~~~~~g~~~~~~~~~~~~~~~~~~ 63 (412)
T COG5068 18 IQGDSDANIPSNTINRLSPG------ELSQQNDGKFDVMIFDSKHSVRVYSN 63 (412)
T ss_pred cccccccCCccccccccCcc------cchhhccCCcccccccccccccccCC
Confidence 56777888888999999999 99999999887777665444444544
No 58
>cd01370 KISc_KIP3_like Kinesin motor domain, KIP3-like subgroup. The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a sec
Probab=26.56 E-value=49 Score=26.75 Aligned_cols=26 Identities=19% Similarity=0.313 Sum_probs=20.4
Q ss_pred hhcccccEEEEeecCCC--CCcc-cCCch
Q 039494 29 VTLTVSAIARLVFSQSG--KPFS-FGNPS 54 (140)
Q Consensus 29 s~LC~~~vavivfsp~g--k~~~-~~sps 54 (140)
+++-|..+|+++|+++| |-|+ +|.++
T Consensus 82 ~~~~G~n~~i~ayGqtGSGKTyTm~G~~~ 110 (338)
T cd01370 82 GVLNGYNATVFAYGATGAGKTHTMLGTDS 110 (338)
T ss_pred HHHCCCCceEEeeCCCCCCCeEEEcCCCC
Confidence 45789999999999986 7776 56544
No 59
>cd01366 KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found at the C-terminus (C-type). C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for mi
Probab=26.51 E-value=50 Score=26.39 Aligned_cols=25 Identities=24% Similarity=0.494 Sum_probs=19.5
Q ss_pred hhcccccEEEEeecCCC--CCcc-cCCc
Q 039494 29 VTLTVSAIARLVFSQSG--KPFS-FGNP 53 (140)
Q Consensus 29 s~LC~~~vavivfsp~g--k~~~-~~sp 53 (140)
+++-|..+|++.|++.| |-|+ ++.+
T Consensus 72 ~~~~G~~~~i~ayG~tgSGKT~tl~G~~ 99 (329)
T cd01366 72 SALDGYNVCIFAYGQTGSGKTYTMEGPP 99 (329)
T ss_pred HHhCCCceEEEEeCCCCCCCcEEecCCC
Confidence 45679999999999985 7776 5653
No 60
>cd01374 KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to
Probab=26.47 E-value=55 Score=26.13 Aligned_cols=25 Identities=20% Similarity=0.300 Sum_probs=19.5
Q ss_pred hcccccEEEEeecCCC--CCcc-cCCch
Q 039494 30 TLTVSAIARLVFSQSG--KPFS-FGNPS 54 (140)
Q Consensus 30 ~LC~~~vavivfsp~g--k~~~-~~sps 54 (140)
++-|..+|+++|++.| |.|+ +|.+.
T Consensus 69 ~l~G~n~~i~ayG~tgSGKT~T~~G~~~ 96 (321)
T cd01374 69 ALEGYNGTIFAYGQTSSGKTFTMSGDEQ 96 (321)
T ss_pred HHCCCceeEEeecCCCCCCceeccCCCC
Confidence 5779999999999885 7777 55543
No 61
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=26.23 E-value=61 Score=25.46 Aligned_cols=28 Identities=25% Similarity=0.453 Sum_probs=23.1
Q ss_pred hhhhcccccEEEEeecCCCCCcccCCch
Q 039494 27 ELVTLTVSAIARLVFSQSGKPFSFGNPS 54 (140)
Q Consensus 27 ELs~LC~~~vavivfsp~gk~~~~~sps 54 (140)
+|.-.+|++|+|||....|.++-.+...
T Consensus 135 ~l~~~~g~~v~VIItDt~gr~~R~G~t~ 162 (245)
T PRK13293 135 GLEELTGKKVGVIITDTNGRPFRKGQRG 162 (245)
T ss_pred HHHHHHCCCEEEEEEcCCCcccccCCcc
Confidence 4666799999999999999888777644
No 62
>PHA02740 protein tyrosine phosphatase; Provisional
Probab=26.22 E-value=1.2e+02 Score=24.24 Aligned_cols=38 Identities=13% Similarity=0.235 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCccccCCCC
Q 039494 88 NHQELLQMDATIDNLSRTFIAKLNEKTAAASSSAAPPMYFHHGLG 132 (140)
Q Consensus 88 s~~eL~~l~~~Le~~l~~v~~r~~~l~~~~~~~~~~~~~~~~~~~ 132 (140)
+..++.+|...+......+. .....+..+|+..||+-|
T Consensus 194 ~~~~~l~fi~~V~~~~~~~~-------~~~~~~~~~PIVVHCSaG 231 (298)
T PHA02740 194 DPDAFIDFFCNIDDLCADLE-------KHKADGKIAPIIIDCIDG 231 (298)
T ss_pred CHHHHHHHHHHHHHHHHHHH-------HhhccCCCCCEEEECCCC
Confidence 56666666555554443322 222233367999999876
No 63
>cd01363 Motor_domain Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Probab=26.04 E-value=43 Score=24.45 Aligned_cols=25 Identities=20% Similarity=0.420 Sum_probs=18.9
Q ss_pred hcccccEEEEeecCCC--CCcc-cCCch
Q 039494 30 TLTVSAIARLVFSQSG--KPFS-FGNPS 54 (140)
Q Consensus 30 ~LC~~~vavivfsp~g--k~~~-~~sps 54 (140)
++.|-++|+++|++.| |-|+ ++.+.
T Consensus 19 ~~~G~n~~i~~yG~tGsGKT~Tm~G~~~ 46 (186)
T cd01363 19 ALDGYNVCIFAYGQTGSGKTYTMEGKRE 46 (186)
T ss_pred HhCCcceeEEEECCCCCcceEecCCCCC
Confidence 4679999999999995 6665 44443
No 64
>cd01376 KISc_KID_like Kinesin motor domain, KIF22/Kid-like subgroup. Members of this group might play a role in regulating chromosomal movement along microtubules in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through
Probab=25.55 E-value=61 Score=25.91 Aligned_cols=26 Identities=19% Similarity=0.469 Sum_probs=20.1
Q ss_pred hhcccccEEEEeecCCC--CCcc-cCCch
Q 039494 29 VTLTVSAIARLVFSQSG--KPFS-FGNPS 54 (140)
Q Consensus 29 s~LC~~~vavivfsp~g--k~~~-~~sps 54 (140)
+++-|..+|+++|+++| |-|+ +|.+.
T Consensus 75 ~~~~G~n~~i~ayG~tgSGKTyTm~G~~~ 103 (319)
T cd01376 75 HLLSGQNATVFAYGSTGAGKTHTMLGDPN 103 (319)
T ss_pred HHhCCCceEEEEECCCCCCCcEEEeCCcC
Confidence 46679999999999986 7776 55543
No 65
>PRK13677 hypothetical protein; Provisional
Probab=25.28 E-value=1.1e+02 Score=21.53 Aligned_cols=30 Identities=13% Similarity=0.145 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039494 84 VYEFNHQELLQMDATIDNLSRTFIAKLNEK 113 (140)
Q Consensus 84 l~~ls~~eL~~l~~~Le~~l~~v~~r~~~l 113 (140)
+..-=++||..|+..+....+.|.+.++.|
T Consensus 96 ~K~kiL~dLrHLE~Vv~~KIaEIe~dLekL 125 (125)
T PRK13677 96 LKRKILDDLRHLESVVANKISEIEADLEKL 125 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 333446889999999999999988877653
No 66
>cd01367 KISc_KIF2_like Kinesin motor domain, KIF2-like group. KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found in the middle (M-type) of the protein chain. M-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second (KIF2 may be slower). To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and lo
Probab=25.16 E-value=53 Score=26.33 Aligned_cols=25 Identities=16% Similarity=0.445 Sum_probs=19.8
Q ss_pred hhcccccEEEEeecCCC--CCcc-cCCc
Q 039494 29 VTLTVSAIARLVFSQSG--KPFS-FGNP 53 (140)
Q Consensus 29 s~LC~~~vavivfsp~g--k~~~-~~sp 53 (140)
+++-|..+|++.|+++| |-|+ +|.+
T Consensus 79 ~~~~G~n~~i~ayGqtGSGKTyTm~G~~ 106 (322)
T cd01367 79 HVFEGGVATCFAYGQTGSGKTYTMLGDE 106 (322)
T ss_pred HHhCCCceEEEeccCCCCCCceEecCcC
Confidence 46779999999999886 7776 5553
No 67
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=25.13 E-value=68 Score=21.73 Aligned_cols=45 Identities=24% Similarity=0.351 Sum_probs=29.8
Q ss_pred hhhhhhhhcccccEEEEeecCCCCCcccCC--ch-hHHHHHHhhccchH
Q 039494 23 RKVSELVTLTVSAIARLVFSQSGKPFSFGN--PS-IEAVANRFLGLNCQ 68 (140)
Q Consensus 23 KKa~ELs~LC~~~vavivfsp~gk~~~~~s--ps-v~~vi~ry~~~~~~ 68 (140)
.|-.||--+-||-+| =.|||+|++.+|-. |. +.++..++-.....
T Consensus 3 ekLdeLlqi~Gv~AA-Gefs~DGkLv~Ykgdm~k~~A~maAkmcaAnnm 50 (109)
T COG4831 3 EKLDELLQIKGVMAA-GEFSPDGKLVEYKGDMPKEMAEMAAKMCAANNM 50 (109)
T ss_pred hhHHHHhCccceeEe-ceeCCCCceEEeeCCCCHHHHHHHHHHHHHHHH
Confidence 466788888887654 67999999999865 33 34444555444333
No 68
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=24.82 E-value=70 Score=28.90 Aligned_cols=43 Identities=23% Similarity=0.470 Sum_probs=36.2
Q ss_pred chhhhhhhhhhhcccccEEEEeecCCCCCcccCCchhHHHHHHh
Q 039494 19 SGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVANRF 62 (140)
Q Consensus 19 ~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~spsv~~vi~ry 62 (140)
.+|+++|.||++=--+++.++=||. ..|+..+.|.|...|.-|
T Consensus 446 ~e~i~t~~elTvgDtsp~~L~EySE-e~P~~Lsn~GMas~l~nY 488 (968)
T COG5179 446 QEIIKTAGELTVGDTSPFSLFEYSE-EEPFFLSNPGMASLLNNY 488 (968)
T ss_pred hhhhccccceeccCCCceeeeeecc-cCceeecCchHHHHHHHH
Confidence 6799999999999999999999998 667777888887666655
No 69
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=24.60 E-value=76 Score=19.21 Aligned_cols=29 Identities=17% Similarity=0.243 Sum_probs=18.2
Q ss_pred ccccEEEEeecCCCCCcccCCch-hHHHHHH
Q 039494 32 TVSAIARLVFSQSGKPFSFGNPS-IEAVANR 61 (140)
Q Consensus 32 C~~~vavivfsp~gk~~~~~sps-v~~vi~r 61 (140)
|+..-.|+|. |.+..|...+|+ +.+|++.
T Consensus 47 C~~~P~v~i~-~~~~~y~~v~~~~~~~il~~ 76 (77)
T cd02980 47 CGLAPVVVVY-PDGVWYGRVTPEDVEEIVEE 76 (77)
T ss_pred ccCCCEEEEe-CCCeEEccCCHHHHHHHHHh
Confidence 5544444444 667777777764 6777765
No 70
>PF00225 Kinesin: Kinesin motor domain; InterPro: IPR001752 Kinesin [, , ] is a microtubule-associated force-producing protein that may play a role in organelle transport. The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds. The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyse ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerisation; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles. A number of proteins have been recently found that contain a domain similar to that of the kinesin 'motor' domain [, ]: Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end. Homo sapiens CENP-E []. CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation. H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end. Saccharomyces cerevisiae KAR3 protein, which is essential for nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis. S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles. Emericella nidulans (Aspergillus nidulans) bimC, which plays an important role in nuclear division. A. nidulans klpA. Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation. C. elegans osm-3. Xenopus laevis Eg5, which may be involved in mitosis. Arabidopsis thaliana KatA, KatB and katC. Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella. C. elegans hypothetical protein T09A5.2. The kinesin motor domain is located in the N-terminal part of most of the above proteins, with the exception of KAR3, klpA, and ncd where it is located in the C-terminal section. The kinesin motor domain contains about 330 amino acids. An ATP-binding motif of type A is found near position 80 to 90, the C-terminal half of the domain is involved in microtubule-binding.; GO: 0003777 microtubule motor activity, 0005524 ATP binding, 0007018 microtubule-based movement; PDB: 3NWN_A 2Y5W_A 2Y65_C 3BFN_A 2WBE_C 2ZFL_A 2ZFI_A 1I6I_A 2ZFM_A 1IA0_K ....
Probab=24.14 E-value=28 Score=27.78 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=18.1
Q ss_pred hhcccccEEEEeecCCC--CCcc-cCC
Q 039494 29 VTLTVSAIARLVFSQSG--KPFS-FGN 52 (140)
Q Consensus 29 s~LC~~~vavivfsp~g--k~~~-~~s 52 (140)
++|-|..+||++|++.| |-|+ +|.
T Consensus 69 ~~l~G~n~~i~ayG~tgSGKT~Tm~G~ 95 (335)
T PF00225_consen 69 SVLDGYNATIFAYGQTGSGKTYTMFGS 95 (335)
T ss_dssp HHHTT-EEEEEEEESTTSSHHHHHTBS
T ss_pred HhhcCCceEEEeecccccccccccccc
Confidence 46789999999999885 6665 565
No 71
>cd01369 KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup. Members of this group have been associated with organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-c
Probab=24.11 E-value=55 Score=26.11 Aligned_cols=25 Identities=24% Similarity=0.412 Sum_probs=19.6
Q ss_pred hcccccEEEEeecCCC--CCcc-cCCch
Q 039494 30 TLTVSAIARLVFSQSG--KPFS-FGNPS 54 (140)
Q Consensus 30 ~LC~~~vavivfsp~g--k~~~-~~sps 54 (140)
++-|..+++++|++.| |-|+ +|.+.
T Consensus 72 ~~~G~n~~i~ayG~tgSGKT~Tm~G~~~ 99 (325)
T cd01369 72 VLNGYNGTIFAYGQTGSGKTYTMEGPPG 99 (325)
T ss_pred HHcCccceEEEeCCCCCCceEEecCCCC
Confidence 5789999999999885 7776 55543
No 72
>PF04873 EIN3: Ethylene insensitive 3; InterPro: IPR006957 Ethylene insensitive 3 (EIN3) proteins are a family of plant DNA-binding proteins that regulate transcription in response to the gaseous plant hormone ethylene, and are essential for ethylene-mediated responses. In the presence of ethylene, dark-grown dicotyledonous seedlings undergo dramatic morphological changes collectively known as the 'triple response'. In Arabidopsis, these changes consist of a radial swelling of the hypocotyl, an exaggeration in the curvature of the apical hook, and the inhibition of cell elongation in the hypocotyl and root.; GO: 0005634 nucleus; PDB: 1WIJ_A.
Probab=23.96 E-value=26 Score=29.01 Aligned_cols=39 Identities=26% Similarity=0.284 Sum_probs=0.0
Q ss_pred cchhhhhhhhhhhcccccEEE-EeecCCCCCcccCCchhH
Q 039494 18 TSGIYRKVSELVTLTVSAIAR-LVFSQSGKPFSFGNPSIE 56 (140)
Q Consensus 18 r~gL~KKa~ELs~LC~~~vav-ivfsp~gk~~~~~spsv~ 56 (140)
-.||+|=+.=..-||+|..+| =+.+..|++.++++|+..
T Consensus 53 qd~ilkym~~~m~~~n~~gfvy~~~~~~~k~~~~~s~slr 92 (354)
T PF04873_consen 53 QDGILKYMFPEMELCNAPGFVYTIISSSGKPVEGVSPSLR 92 (354)
T ss_dssp ----------------------------------------
T ss_pred hhHHHHhhccccccccCceeeecCCCCCCCccCCcCCccc
Confidence 356666667778899999998 677778999999999965
No 73
>PF00383 dCMP_cyt_deam_1: Cytidine and deoxycytidylate deaminase zinc-binding region; InterPro: IPR002125 Cytidine deaminase (3.5.4.5 from EC) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (3.5.4.12 from EC) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [, ]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion. Such a region is also found in other proteins [, ]: Yeast cytosine deaminase (3.5.4.1 from EC) (gene FCY1) which transforms cytosine into uracil. Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA. Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate. Bacillus cereus blasticidin-S deaminase (3.5.4.23 from EC), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S. Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA. B. subtilis hypothetical protein yaaJ. Escherichia coli hypothetical protein yfhC. Yeast hypothetical protein YJL035c. ; GO: 0008270 zinc ion binding, 0016787 hydrolase activity; PDB: 3MPZ_C 3R2N_C 1WKQ_A 1TIY_B 2B3J_C 2O7P_B 2OBC_A 2G6V_B 2D30_B 2D5N_B ....
Probab=23.65 E-value=68 Score=20.62 Aligned_cols=32 Identities=19% Similarity=0.270 Sum_probs=23.2
Q ss_pred hhhhhhhhhhhcc----cccEEEEeecCCCCCcccC
Q 039494 20 GIYRKVSELVTLT----VSAIARLVFSQSGKPFSFG 51 (140)
Q Consensus 20 gL~KKa~ELs~LC----~~~vavivfsp~gk~~~~~ 51 (140)
-+++.|.+++... +..|+.+|++++|+....+
T Consensus 6 ~~m~~a~~~a~~s~~~~~~~vgaviv~~~~~~i~~g 41 (102)
T PF00383_consen 6 EFMRIAIELAKRSRPCGNFPVGAVIVDPDGKIIATG 41 (102)
T ss_dssp HHHHHHHHHHHTHBTTTSSSEEEEEEETTTEEEEEE
T ss_pred HHHHHHHHHHHhccccCCCCEEEEEEeccCccEEEE
Confidence 3567777777666 8899999999876644433
No 74
>KOG3718 consensus Carnitine O-acyltransferase CROT [Lipid transport and metabolism]
Probab=23.47 E-value=2.8e+02 Score=24.37 Aligned_cols=56 Identities=25% Similarity=0.249 Sum_probs=33.0
Q ss_pred ecCCCCCcccCCchhHHHHHHhhccchHHHHHHHhCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039494 41 FSQSGKPFSFGNPSIEAVANRFLGLNCQMRKRKETQPRWWETPVYEFNHQELLQMDATIDNLSRTFIAKLNEK 113 (140)
Q Consensus 41 fsp~gk~~~~~spsv~~vi~ry~~~~~~l~K~~~~~~~~~~~~l~~ls~~eL~~l~~~Le~~l~~v~~r~~~l 113 (140)
||-.+.+.+.|=|+.++.+++|..-..+ =.+.+|+.+.++..++....+.+++.+.
T Consensus 14 Fs~qdsLPSLPlPeLeETleKYl~s~~p-----------------f~tkeE~a~~ek~a~eFqsg~GaqLh~~ 69 (609)
T KOG3718|consen 14 FSFQDSLPSLPLPELEETLEKYLSSIQP-----------------FGTKEELAQAEKTADEFQSGVGAQLHEQ 69 (609)
T ss_pred ccccccCCCCCCchHHHHHHHHHHhccc-----------------CCCHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence 4555566666778999999999764332 1234555555555555555554444443
No 75
>smart00129 KISc Kinesin motor, catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.
Probab=23.32 E-value=70 Score=25.54 Aligned_cols=24 Identities=25% Similarity=0.501 Sum_probs=18.9
Q ss_pred hcccccEEEEeecCCC--CCcc-cCCc
Q 039494 30 TLTVSAIARLVFSQSG--KPFS-FGNP 53 (140)
Q Consensus 30 ~LC~~~vavivfsp~g--k~~~-~~sp 53 (140)
++-|..+|+++|++.| |-|+ +|++
T Consensus 75 ~~~G~~~~i~~yG~tgSGKT~tl~G~~ 101 (335)
T smart00129 75 VLEGYNATIFAYGQTGSGKTYTMSGTP 101 (335)
T ss_pred HhcCCceeEEEeCCCCCCCceEecCCC
Confidence 5789999999999986 6665 5553
No 76
>cd00468 HIT_like HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups.
Probab=23.24 E-value=1.5e+02 Score=18.01 Aligned_cols=25 Identities=8% Similarity=0.139 Sum_probs=18.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHH
Q 039494 83 PVYEFNHQELLQMDATIDNLSRTFI 107 (140)
Q Consensus 83 ~l~~ls~~eL~~l~~~Le~~l~~v~ 107 (140)
++.+|+.+++.++...+....+.+.
T Consensus 31 ~~~~l~~~~~~~l~~~~~~~~~~l~ 55 (86)
T cd00468 31 TLPDLDEALLADLVITAQRVAAELE 55 (86)
T ss_pred ChhHCCHHHHHHHHHHHHHHHHHHH
Confidence 5678888888888887776665554
No 77
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=23.14 E-value=9.6 Score=31.91 Aligned_cols=41 Identities=24% Similarity=0.319 Sum_probs=24.3
Q ss_pred cccccccchhhhhhhhhhhcccccEEEEeecCCCCCcccCCchhHHHHHHhhccc
Q 039494 12 ITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVANRFLGLN 66 (140)
Q Consensus 12 ~tf~KRr~gL~KKa~ELs~LC~~~vavivfsp~gk~~~~~spsv~~vi~ry~~~~ 66 (140)
-||+.||--| =.+.+||++-+--=.|+.|+ +..|-||..+.
T Consensus 213 K~FKqRRIkL--------GfTQaDVGlALG~lyGn~FS------QTTIcRFEALq 253 (398)
T KOG3802|consen 213 KTFKQRRIKL--------GFTQADVGLALGALYGNVFS------QTTICRFEALQ 253 (398)
T ss_pred HHHHhheecc--------ccchhHHHHHHHhhhCcccc------hhhhhHhHhhc
Confidence 3677776544 23677777766555566665 55566775544
No 78
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=23.07 E-value=44 Score=25.96 Aligned_cols=16 Identities=38% Similarity=0.403 Sum_probs=13.4
Q ss_pred ccEEEEeecCCCCCcc
Q 039494 34 SAIARLVFSQSGKPFS 49 (140)
Q Consensus 34 ~~vavivfsp~gk~~~ 49 (140)
-|-|+-||||+|.++.
T Consensus 4 ydraltvFSPDGhL~Q 19 (249)
T KOG0183|consen 4 YDRALTVFSPDGHLFQ 19 (249)
T ss_pred cccceEEECCCCCEEe
Confidence 4678899999998875
No 79
>PF11232 Med25: Mediator complex subunit 25 PTOV activation and synapsin 2; InterPro: IPR021394 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear []. ; PDB: 2KY6_A 2L23_A 2XNF_A 2L6U_A.
Probab=23.06 E-value=61 Score=23.63 Aligned_cols=20 Identities=20% Similarity=0.230 Sum_probs=16.2
Q ss_pred hcccccEEEEeecCCCCCcc
Q 039494 30 TLTVSAIARLVFSQSGKPFS 49 (140)
Q Consensus 30 ~LC~~~vavivfsp~gk~~~ 49 (140)
.-|++.|-+++|||+-+.|.
T Consensus 109 p~c~iKvL~LlYs~kk~~fl 128 (152)
T PF11232_consen 109 PPCEIKVLMLLYSPKKKAFL 128 (152)
T ss_dssp SSSS-SEEEEEEETTTTEEE
T ss_pred CCCceEEEEEEEcCCCceEE
Confidence 46999999999999888665
No 80
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=22.98 E-value=40 Score=23.02 Aligned_cols=21 Identities=24% Similarity=0.378 Sum_probs=17.8
Q ss_pred ccCCCCCCCHHHHHHHHHHHH
Q 039494 80 WETPVYEFNHQELLQMDATID 100 (140)
Q Consensus 80 ~~~~l~~ls~~eL~~l~~~Le 100 (140)
+.+.++.|+++|+..|...++
T Consensus 83 lqkRle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 83 LQKRLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHHHHhCCHHHHHHHHHHhc
Confidence 456789999999999998876
No 81
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] clu
Probab=22.71 E-value=68 Score=19.95 Aligned_cols=28 Identities=11% Similarity=0.203 Sum_probs=18.2
Q ss_pred ccccEEEEeecCCCCCcccCCch-hHHHHHHh
Q 039494 32 TVSAIARLVFSQSGKPFSFGNPS-IEAVANRF 62 (140)
Q Consensus 32 C~~~vavivfsp~gk~~~~~sps-v~~vi~ry 62 (140)
|+-..+|+| +|..|...+|+ +.+|++.+
T Consensus 52 C~~gP~v~v---~g~~y~~vt~~~i~~i~~~~ 80 (80)
T cd03064 52 CDLAPVMMI---NDDVYGRLTPEKVDAILEAL 80 (80)
T ss_pred CCCCCEEEE---CCEEECCCCHHHHHHHHHhC
Confidence 655555555 37777777764 77887754
No 82
>PF06020 Roughex: Drosophila roughex protein; InterPro: IPR009259 This family consists of several roughex (RUX) proteins specific to Drosophila species. Roughex can influence the intracellular distribution of cyclin A and is therefore defined as a distinct and specialised cell cycle inhibitor for cyclin A-dependent kinase activity []. Rux is though to regulate the metaphase to anaphase transition during development [].
Probab=22.69 E-value=41 Score=27.24 Aligned_cols=16 Identities=13% Similarity=0.119 Sum_probs=13.3
Q ss_pred hhcccccEEEEeecCC
Q 039494 29 VTLTVSAIARLVFSQS 44 (140)
Q Consensus 29 s~LC~~~vavivfsp~ 44 (140)
.-+||++||++||.-.
T Consensus 183 ~~~~~~EICLavYek~ 198 (334)
T PF06020_consen 183 GQVSGFEICLAVYEKG 198 (334)
T ss_pred CccccceEEeeehhhh
Confidence 3579999999999864
No 83
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=22.25 E-value=1.8e+02 Score=17.02 Aligned_cols=23 Identities=13% Similarity=0.111 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q 039494 93 LQMDATIDNLSRTFIAKLNEKTA 115 (140)
Q Consensus 93 ~~l~~~Le~~l~~v~~r~~~l~~ 115 (140)
.+....++..+..+.+++..+..
T Consensus 35 ~~~~~~l~~~~~~i~~~i~~L~~ 57 (65)
T PF09278_consen 35 ADRRALLEEKLEEIEEQIAELQA 57 (65)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34446677777788888777643
No 84
>PF04120 Iron_permease: Low affinity iron permease ; InterPro: IPR007251 Although originally identified as a low-affinity iron(II) permease [, ], Fet4 has since been shown to import several other transition metal ions, including copper [, ] and zinc []. Copper, cobalt, and cadmium inhibit Fet4 [, ]. Fet4 is an integral protein of the plasma membrane [, ]. FET4 is not essential, not even in fet3 fet4 double mutants []. Over expression of FET4 improves growth under alkaline conditions []. Transcription of FET4 is induced by Aft1 in response to low levels of iron [, , ] or by Zap1 in response to low zinc [, ], but not in response to low copper []. When the high-affinity iron permease component Fet3 is deleted, FET4 is induced by the addition of copper, zinc, cobalt, or manganese []. It is also induced under anaerobic conditions [, , ] and repressed by Rox1 in aerobic conditions [, ]. Rox1 attenuates the activation of FET4 by Aft1 or Zap1 []. ; GO: 0055085 transmembrane transport
Probab=21.60 E-value=1.6e+02 Score=20.81 Aligned_cols=29 Identities=10% Similarity=0.213 Sum_probs=23.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 039494 82 TPVYEFNHQELLQMDATIDNLSRTFIAKL 110 (140)
Q Consensus 82 ~~l~~ls~~eL~~l~~~Le~~l~~v~~r~ 110 (140)
-++++++.+||.++...++..-.....+.
T Consensus 90 i~iE~l~~~el~~~~~~~~~~~~~~~~~~ 118 (132)
T PF04120_consen 90 IDIEDLTEEELEEIRKRYERLAEQARERH 118 (132)
T ss_pred CCcccCCHHHHHHHHHHHHHHHHHhhhhc
Confidence 36999999999999999988776655544
No 85
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=21.46 E-value=2.6e+02 Score=19.58 Aligned_cols=33 Identities=18% Similarity=0.289 Sum_probs=25.1
Q ss_pred CCCCCCHHHHHHHHHHHH-------HHHHHHHHHHHHHHh
Q 039494 83 PVYEFNHQELLQMDATID-------NLSRTFIAKLNEKTA 115 (140)
Q Consensus 83 ~l~~ls~~eL~~l~~~Le-------~~l~~v~~r~~~l~~ 115 (140)
.+.+|+.+|+..+.+.++ ++...+..-++.|..
T Consensus 44 r~~eLteeei~~ir~~i~~~~~vegDLr~~v~~dIkRl~~ 83 (121)
T COG0099 44 RVGELTEEEIERLRDAIQNKYLVEGDLRREVRMDIKRLMK 83 (121)
T ss_pred hhccCCHHHHHHHHHHHHhcCeehhHHHHHHHHHHHHHHH
Confidence 578999999999999999 445566666666544
No 86
>KOG0184 consensus 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones]
Probab=21.17 E-value=51 Score=25.72 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=17.6
Q ss_pred hhcccccEEEEeecCCCCCcc
Q 039494 29 VTLTVSAIARLVFSQSGKPFS 49 (140)
Q Consensus 29 s~LC~~~vavivfsp~gk~~~ 49 (140)
||=+|-|.|.-+|||+|+.+.
T Consensus 3 sIGtGyDls~s~fSpdGrvfQ 23 (254)
T KOG0184|consen 3 SIGTGYDLSASTFSPDGRVFQ 23 (254)
T ss_pred cccccccccceeeCCCCceeh
Confidence 455688999999999999886
No 87
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=21.16 E-value=2.1e+02 Score=19.48 Aligned_cols=29 Identities=7% Similarity=0.110 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039494 85 YEFNHQELLQMDATIDNLSRTFIAKLNEK 113 (140)
Q Consensus 85 ~~ls~~eL~~l~~~Le~~l~~v~~r~~~l 113 (140)
.+.+.+|+.++...++..++.++.|+...
T Consensus 32 g~~a~~e~~~lR~r~~~~Lk~~r~rl~~~ 60 (104)
T COG4575 32 GSLAGDEAEELRSKAESALKEARDRLGDT 60 (104)
T ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHhh
Confidence 46788999999999999999999888664
No 88
>PF06574 FAD_syn: FAD synthetase; InterPro: IPR015864 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents prokaryotic-type FAD synthetase, which occurs primarily as part of a bifunctional enzyme.; GO: 0003919 FMN adenylyltransferase activity, 0009231 riboflavin biosynthetic process; PDB: 2X0K_B 3OP1_B 1T6Z_A 2I1L_A 1T6Y_B 1T6X_B 1S4M_A 1MRZ_A.
Probab=20.69 E-value=78 Score=22.76 Aligned_cols=27 Identities=15% Similarity=0.127 Sum_probs=22.2
Q ss_pred chhhhhhhhhhhcccccEEEEeecCCC
Q 039494 19 SGIYRKVSELVTLTVSAIARLVFSQSG 45 (140)
Q Consensus 19 ~gL~KKa~ELs~LC~~~vavivfsp~g 45 (140)
.-|+++|.|++---+...+|+.|+|.-
T Consensus 22 q~Li~~~~~~a~~~~~~~~v~tF~~~P 48 (157)
T PF06574_consen 22 QKLIKKAVEIAKEKGLKSVVLTFDPHP 48 (157)
T ss_dssp HHHHHHHHHHHHHCT-EEEEEEESS-C
T ss_pred HHHHHHHhhhhhhcccceEEEEcccCH
Confidence 358999999999999999999999863
No 89
>PF12068 DUF3548: Domain of unknown function (DUF3548); InterPro: IPR021935 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes and is typically between 184 to 216 amino acids in length. The domain is found associated with PF00566 from PFAM and at the N terminus of GYP7 proteins.
Probab=20.56 E-value=52 Score=25.25 Aligned_cols=15 Identities=33% Similarity=0.758 Sum_probs=12.0
Q ss_pred CCCCCCCccccCCCC
Q 039494 118 SSSAAPPMYFHHGLG 132 (140)
Q Consensus 118 ~~~~~~~~~~~~~~~ 132 (140)
..+.-||+|||||..
T Consensus 142 dG~~~p~L~Fh~gg~ 156 (213)
T PF12068_consen 142 DGTSLPPLHFHDGGS 156 (213)
T ss_pred CCCccCceEEecCCH
Confidence 445679999999986
No 90
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=20.40 E-value=54 Score=24.27 Aligned_cols=13 Identities=15% Similarity=0.176 Sum_probs=8.9
Q ss_pred ccccEEEEeecCC
Q 039494 32 TVSAIARLVFSQS 44 (140)
Q Consensus 32 C~~~vavivfsp~ 44 (140)
.++..|.|||-|+
T Consensus 11 ~~~k~C~IC~Kps 23 (182)
T PF08432_consen 11 TDAKACFICYKPS 23 (182)
T ss_pred CCCCceeEecCCC
Confidence 5677777777665
No 91
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=20.21 E-value=58 Score=29.23 Aligned_cols=22 Identities=14% Similarity=0.102 Sum_probs=19.7
Q ss_pred hhcccccEEEEeecCCCCCccc
Q 039494 29 VTLTVSAIARLVFSQSGKPFSF 50 (140)
Q Consensus 29 s~LC~~~vavivfsp~gk~~~~ 50 (140)
|+|.|+.++||+|.++|..+.+
T Consensus 374 ~VLsgvtaGVi~~d~~g~i~t~ 395 (712)
T COG5000 374 AVLSGLTAGVIGFDNRGCITTV 395 (712)
T ss_pred HHHhcCceeEEEEcCCCeeEee
Confidence 5999999999999999987763
Done!