Query 035248
Match_columns 69
No_of_seqs 31 out of 33
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 10:23:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035248.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035248hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02238 COX7a: Cytochrome c o 99.8 5.6E-22 1.2E-26 120.6 3.0 54 11-64 1-56 (56)
2 cd00928 Cyt_c_Oxidase_VIIa Cyt 97.4 0.00019 4.2E-09 43.8 3.0 50 12-62 3-54 (55)
3 PF00382 TFIIB: Transcription 86.8 2.1 4.5E-05 24.7 4.4 38 11-56 12-49 (71)
4 PF13150 DUF3989: Protein of u 85.5 0.99 2.1E-05 28.9 2.7 27 39-65 31-57 (85)
5 PRK10927 essential cell divisi 74.0 2.3 5E-05 33.5 1.9 22 44-65 37-58 (319)
6 PRK12757 cell division protein 72.1 2.7 5.8E-05 31.9 1.8 22 44-65 2-23 (256)
7 PF05889 SLA_LP_auto_ag: Solub 66.1 2.9 6.4E-05 33.4 1.0 16 53-68 23-38 (389)
8 PF15012 DUF4519: Domain of un 65.6 2.8 6.1E-05 25.9 0.7 19 34-53 27-45 (56)
9 TIGR03531 selenium_SpcS O-phos 63.4 3.4 7.4E-05 32.5 0.9 17 52-68 71-87 (444)
10 PRK00423 tfb transcription ini 62.6 17 0.00036 26.9 4.3 40 9-56 138-177 (310)
11 PF04588 HIG_1_N: Hypoxia indu 60.5 8 0.00017 22.3 1.9 24 40-64 5-28 (54)
12 PF01661 Macro: Macro domain; 60.4 1.6 3.4E-05 25.9 -1.1 33 18-63 79-111 (118)
13 cd00095 IFab Interferon alpha, 59.2 5.9 0.00013 27.2 1.4 26 5-33 106-131 (152)
14 cd06579 TM_PBP1_transp_AraH_li 51.6 8.7 0.00019 26.9 1.3 24 41-64 1-25 (263)
15 PF00798 Arena_glycoprot: Aren 51.1 4.9 0.00011 33.4 -0.0 25 37-61 14-38 (487)
16 smart00076 IFabd Interferon al 50.7 11 0.00023 25.1 1.5 20 12-33 80-99 (117)
17 cd06574 TM_PBP1_branched-chain 48.8 7.6 0.00017 27.3 0.6 22 43-64 3-26 (266)
18 smart00506 A1pp Appr-1"-p proc 47.8 3.5 7.6E-05 25.1 -1.1 20 35-63 107-126 (133)
19 cd02907 Macro_Af1521_BAL_like 46.9 4.1 8.9E-05 27.2 -0.9 19 35-62 111-129 (175)
20 PF09988 DUF2227: Uncharacteri 46.4 11 0.00024 26.6 1.2 18 32-49 3-21 (169)
21 cd06580 TM_PBP1_transp_TpRbsC_ 45.3 13 0.00029 25.8 1.4 23 42-64 2-25 (234)
22 PLN03155 cytochrome c oxidase 44.0 17 0.00038 23.1 1.6 32 26-63 7-38 (63)
23 cd02903 Macro_BAL_like Macro d 43.5 4.4 9.6E-05 26.2 -1.1 20 35-63 104-123 (137)
24 PF05887 Trypan_PARP: Procycli 43.0 8 0.00017 27.8 0.0 15 37-51 125-139 (143)
25 PF04971 Lysis_S: Lysis protei 42.8 17 0.00036 23.2 1.4 29 34-62 1-29 (68)
26 cd02908 Macro_Appr_pase_like M 41.0 5.5 0.00012 26.4 -1.0 11 34-44 103-113 (165)
27 COG0063 Predicted sugar kinase 39.0 19 0.00041 27.1 1.5 29 11-39 176-204 (284)
28 cd02906 Macro_1 Macro domain, 38.5 6.8 0.00015 26.0 -0.9 18 36-62 117-134 (147)
29 PRK00431 RNase III inhibitor; 38.0 7.3 0.00016 25.9 -0.8 11 34-44 110-120 (177)
30 PRK09478 mglC beta-methylgalac 36.6 23 0.00051 26.1 1.6 28 37-64 45-73 (336)
31 PF01456 Mucin: Mucin-like gly 36.5 25 0.00054 22.5 1.5 15 39-53 125-139 (143)
32 PF02224 Cytidylate_kin: Cytid 36.4 22 0.00048 25.0 1.4 32 11-45 49-80 (157)
33 PHA02241 hypothetical protein 36.3 19 0.00041 26.7 1.1 19 4-22 57-75 (182)
34 cd00211 PTS_IIA_fru PTS_IIA, P 35.9 30 0.00065 20.8 1.7 29 17-46 33-61 (136)
35 PF13171 DUF4004: Protein of u 35.4 32 0.00069 25.6 2.1 20 7-26 45-64 (199)
36 KOG0871 Class 2 transcription 35.3 15 0.00032 26.8 0.4 34 9-47 114-148 (156)
37 PF14610 DUF4448: Protein of u 35.2 20 0.00044 24.4 1.0 24 37-60 159-182 (189)
38 PF00143 Interferon: Interfero 34.8 19 0.00041 24.8 0.8 27 5-33 106-132 (162)
39 PF10043 DUF2279: Predicted pe 34.4 29 0.00063 22.3 1.6 25 28-52 9-33 (85)
40 COG5505 Predicted integral mem 34.4 40 0.00087 27.6 2.7 55 10-66 184-242 (384)
41 COG4298 Uncharacterized protei 34.0 49 0.0011 22.5 2.7 29 34-62 11-39 (95)
42 cd02905 Macro_GDAP2_like Macro 33.4 8.7 0.00019 25.6 -1.0 9 36-44 107-115 (140)
43 KOG0488 Transcription factor B 32.7 21 0.00045 27.2 0.8 12 12-23 188-199 (309)
44 PF11798 IMS_HHH: IMS family H 32.5 11 0.00024 19.8 -0.5 6 63-68 17-22 (32)
45 PF12841 YvrJ: YvrJ protein fa 32.0 30 0.00065 19.5 1.2 17 37-56 3-19 (38)
46 PF11127 DUF2892: Protein of u 31.5 28 0.0006 19.9 1.0 23 32-54 6-28 (66)
47 PRK11618 inner membrane ABC tr 31.5 32 0.0007 24.9 1.6 26 39-64 40-66 (317)
48 PF14674 FANCI_S1-cap: FANCI s 31.1 89 0.0019 19.3 3.3 36 16-59 16-51 (53)
49 PF00716 Peptidase_S21: Assemb 30.7 37 0.00081 26.4 1.9 25 9-33 184-208 (325)
50 cd03330 Macro_2 Macro domain, 30.7 9.4 0.0002 24.1 -1.1 9 36-44 103-111 (133)
51 cd06582 TM_PBP1_LivH_like Tran 30.1 36 0.00077 23.9 1.6 25 40-64 4-30 (272)
52 PHA00101 internal virion prote 29.9 38 0.00083 25.4 1.8 15 39-53 4-18 (194)
53 COG2003 RadC DNA repair protei 29.4 37 0.00081 25.5 1.7 11 7-17 9-19 (224)
54 COG3162 Predicted membrane pro 28.8 47 0.001 22.7 1.9 25 37-61 59-83 (102)
55 TIGR03011 sulf_tusB_dsrH sulfu 28.4 12 0.00027 22.4 -0.8 36 27-62 1-37 (94)
56 KOG4288 Predicted oxidoreducta 28.1 42 0.00091 26.5 1.8 52 5-58 167-229 (283)
57 TIGR03010 sulf_tusC_dsrF sulfu 28.0 19 0.00042 22.7 -0.0 22 42-63 20-47 (116)
58 PF15284 PAGK: Phage-encoded v 27.5 54 0.0012 20.6 1.9 22 34-55 1-22 (61)
59 TIGR03409 urea_trans_UrtB urea 27.4 39 0.00084 24.1 1.4 25 40-64 10-36 (291)
60 PF00873 ACR_tran: AcrB/AcrD/A 27.3 52 0.0011 27.6 2.3 25 33-57 356-380 (1021)
61 TIGR01297 CDF cation diffusion 26.4 41 0.00089 22.9 1.3 39 26-64 49-87 (268)
62 PF00342 PGI: Phosphoglucose i 26.3 63 0.0014 25.9 2.5 35 27-61 214-250 (486)
63 COG1405 SUA7 Transcription ini 26.2 44 0.00095 25.3 1.6 14 43-56 233-246 (285)
64 COG1969 HyaC Ni,Fe-hydrogenase 26.1 1E+02 0.0022 23.7 3.5 53 6-59 96-151 (227)
65 PF05510 Sarcoglycan_2: Sarcog 24.9 49 0.0011 26.6 1.7 21 35-55 284-304 (386)
66 TIGR00914 2A0601 heavy metal e 24.9 57 0.0012 27.8 2.1 29 35-63 368-398 (1051)
67 cd06581 TM_PBP1_LivM_like Tran 24.8 41 0.00089 23.6 1.1 20 45-64 5-26 (268)
68 smart00385 CYCLIN domain prese 24.7 67 0.0015 16.8 1.7 16 41-56 36-51 (83)
69 TIGR00993 3a0901s04IAP86 chlor 24.6 64 0.0014 28.4 2.4 16 11-26 439-454 (763)
70 cd02901 Macro_Poa1p_like Macro 24.3 15 0.00032 23.2 -1.1 27 14-44 90-116 (140)
71 COG0283 Cmk Cytidylate kinase 24.3 54 0.0012 24.7 1.7 32 11-44 106-137 (222)
72 PF10525 Engrail_1_C_sig: Engr 24.3 25 0.00055 19.8 0.0 14 50-63 9-22 (32)
73 PF06724 DUF1206: Domain of Un 24.2 93 0.002 18.1 2.4 30 31-60 42-71 (73)
74 PF04906 Tweety: Tweety; Inte 24.1 1.2E+02 0.0026 23.6 3.6 19 2-25 2-20 (406)
75 COG1114 BrnQ Branched-chain am 23.7 44 0.00094 27.5 1.2 32 36-68 46-77 (431)
76 PF00344 SecY: SecY translocas 23.6 2.4E+02 0.0051 21.0 5.0 57 10-66 35-109 (346)
77 PRK09204 secY preprotein trans 23.2 1.9E+02 0.0042 22.6 4.6 58 9-66 106-180 (426)
78 cd00043 CYCLIN Cyclin box fold 22.9 75 0.0016 16.8 1.7 16 41-56 42-57 (88)
79 KOG4238 Bifunctional ATP sulfu 22.3 30 0.00066 29.4 0.1 40 10-49 275-316 (627)
80 PRK13240 pbsY photosystem II p 22.1 89 0.0019 18.1 2.0 20 37-56 5-25 (40)
81 PRK05443 polyphosphate kinase; 21.8 1.4E+02 0.003 25.4 3.8 60 5-66 505-574 (691)
82 TIGR03622 urea_t_UrtB_arc urea 21.8 60 0.0013 23.1 1.5 24 41-64 11-36 (283)
83 PF11589 DUF3244: Domain of un 21.8 22 0.00049 22.1 -0.6 22 21-42 4-25 (106)
84 CHL00196 psbY photosystem II p 21.5 95 0.0021 17.7 2.0 20 37-56 5-25 (36)
85 PF04781 DUF627: Protein of un 21.5 27 0.00059 23.6 -0.3 32 26-57 56-87 (111)
86 COG0841 AcrB Cation/multidrug 21.3 50 0.0011 29.0 1.2 23 35-57 356-378 (1009)
87 TIGR00190 thiC thiamine biosyn 21.2 1.6E+02 0.0035 24.4 4.0 42 8-50 266-317 (423)
88 cd02749 Macro Macro domain, a 21.1 18 0.00039 22.5 -1.1 10 35-44 110-119 (147)
89 PRK09588 hypothetical protein; 21.1 9.2 0.0002 29.9 -3.0 29 40-68 267-299 (376)
90 smart00359 PUA Putative RNA-bi 21.1 20 0.00043 20.0 -0.8 12 52-63 45-56 (77)
91 cd02900 Macro_Appr_pase Macro 20.2 25 0.00055 24.8 -0.7 19 35-62 152-170 (186)
92 PF13170 DUF4003: Protein of u 20.2 1.1E+02 0.0024 22.9 2.6 34 8-41 113-147 (297)
93 PF10565 NMDAR2_C: N-methyl D- 20.1 34 0.00075 29.7 0.0 15 51-65 22-36 (681)
94 PF00689 Cation_ATPase_C: Cati 20.1 58 0.0012 20.8 1.0 45 3-61 34-78 (182)
No 1
>PF02238 COX7a: Cytochrome c oxidase subunit VIIa; InterPro: IPR003177 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. This family is composed of the heart and liver isoforms of cytochrome c oxidase subunit VIIa. ; GO: 0004129 cytochrome-c oxidase activity, 0009055 electron carrier activity, 0005746 mitochondrial respiratory chain; PDB: 2DYS_J 3AG3_W 3AG1_J 1OCC_J 3ABL_J 3AG4_J 3ABM_J 2EIL_W 3AG2_W 2EIM_W ....
Probab=99.84 E-value=5.6e-22 Score=120.60 Aligned_cols=54 Identities=43% Similarity=0.580 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHhhhhhcccccCCC--CchhhhhhhHHHHHHHHHHhhhhhhhcccc
Q 035248 11 REKLLEKQKHFQSIHKHTYLKGPM--DKITSVAIPIALAASSLYLIGRGIYNMSHG 64 (69)
Q Consensus 11 Rekl~e~Q~yfQ~i~khtyLKG~~--DkItSvaIPlalaassl~ligRGiyNMShG 64 (69)
|||+.|+|++||+..+|+||||+. |.++|+++||++++++.+|+++|+||||||
T Consensus 1 ~nkv~e~Qk~FQ~~~g~vhLKGg~~D~~Ly~~Tm~L~~~gt~~~l~~l~~a~~p~k 56 (56)
T PF02238_consen 1 RNKVPEKQKLFQEDNGHVHLKGGYMDDILYRVTMPLTVAGTSYCLYGLGIANMPKK 56 (56)
T ss_dssp ---HHHHHHHHHSSSS-TTTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTS---
T ss_pred CcchHHHHHHHcCCCCcEEecCCcccchHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 799999999999999999999998 999999999999999999999999999996
No 2
>cd00928 Cyt_c_Oxidase_VIIa Cytochrome c oxidase subunit VIIa. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIIa has two tissue-specific isoforms that are expressed in a developmental manner. VIIa-H is expressed in heart and skeletal muscle but not smooth muscle. VIIa-L is expressed in liver and non-muscle tissues.
Probab=97.38 E-value=0.00019 Score=43.81 Aligned_cols=50 Identities=30% Similarity=0.278 Sum_probs=41.4
Q ss_pred HHHHHHHHHHhhhh-hcccccCC-CCchhhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248 12 EKLLEKQKHFQSIH-KHTYLKGP-MDKITSVAIPIALAASSLYLIGRGIYNMS 62 (69)
Q Consensus 12 ekl~e~Q~yfQ~i~-khtyLKG~-~DkItSvaIPlalaassl~ligRGiyNMS 62 (69)
+|+-|+|+-||.-- ..+||||. .|+|.-. +=.+|++.++..+..-+|.||
T Consensus 3 nkv~~~Qk~FQ~~ng~PV~LKGG~~D~~LYr-~Tm~L~~vG~~~~~~~l~~~~ 54 (55)
T cd00928 3 NKVKELQKKFQADDGLPVHLKGGVVDRILYR-LTMALTVVGTGYSLYLLYMLS 54 (55)
T ss_pred chhHHHHHHhcCCCCceEEecCCchhHHHHH-HHHHHHHHhHHHHHHHHHHHh
Confidence 68999999999986 79999988 7998765 346778888888888888776
No 3
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=86.82 E-value=2.1 Score=24.70 Aligned_cols=38 Identities=24% Similarity=0.418 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhhhhhcccccCCCCchhhhhhhHHHHHHHHHHhhh
Q 035248 11 REKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGR 56 (69)
Q Consensus 11 Rekl~e~Q~yfQ~i~khtyLKG~~DkItSvaIPlalaassl~ligR 56 (69)
.+=.=...+.|+...+...++|+. |.++||+++|+..|
T Consensus 12 ~~v~~~A~~i~~~~~~~~~~~Gr~--------~~~iaAA~iY~acr 49 (71)
T PF00382_consen 12 EDVRERAKEIYKKAQERGLLKGRS--------PESIAAACIYLACR 49 (71)
T ss_dssp HHHHHHHHHHHHHHHHTTTSTTS---------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCcccCC--------HHHHHHHHHHHHHH
Confidence 333445678888888888899986 89999999999887
No 4
>PF13150 DUF3989: Protein of unknown function (DUF3989)
Probab=85.55 E-value=0.99 Score=28.94 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=21.2
Q ss_pred hhhhhHHHHHHHHHHhhhhhhhccccC
Q 035248 39 SVAIPIALAASSLYLIGRGIYNMSHGI 65 (69)
Q Consensus 39 SvaIPlalaassl~ligRGiyNMShGi 65 (69)
=++.=+.+|+.|+|+++++|||+-.+-
T Consensus 31 vl~ml~~fa~l~ly~~~~ai~~~Gk~~ 57 (85)
T PF13150_consen 31 VLVMLVLFAALCLYMTVSAIYDIGKED 57 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCc
Confidence 345556788999999999999995443
No 5
>PRK10927 essential cell division protein FtsN; Provisional
Probab=74.04 E-value=2.3 Score=33.51 Aligned_cols=22 Identities=32% Similarity=0.469 Sum_probs=16.9
Q ss_pred HHHHHHHHHHhhhhhhhccccC
Q 035248 44 IALAASSLYLIGRGIYNMSHGI 65 (69)
Q Consensus 44 lalaassl~ligRGiyNMShGi 65 (69)
+|||++.|.+..=|+|-++|+.
T Consensus 37 ~alAvavlv~fiGGLyFith~k 58 (319)
T PRK10927 37 VAIAAAVLVTFIGGLYFITHHK 58 (319)
T ss_pred HHHHHHHHHHHhhheEEEecCC
Confidence 5666666777778999999943
No 6
>PRK12757 cell division protein FtsN; Provisional
Probab=72.07 E-value=2.7 Score=31.86 Aligned_cols=22 Identities=32% Similarity=0.480 Sum_probs=18.0
Q ss_pred HHHHHHHHHHhhhhhhhccccC
Q 035248 44 IALAASSLYLIGRGIYNMSHGI 65 (69)
Q Consensus 44 lalaassl~ligRGiyNMShGi 65 (69)
+|||++-+.+..=|+|-++|+.
T Consensus 2 ~alava~lv~f~gGLyfi~h~k 23 (256)
T PRK12757 2 VALAVAVLVTFIGGLYFITHNK 23 (256)
T ss_pred HHHHHHHHHHHhhheEEEecCC
Confidence 5777777888888999999943
No 7
>PF05889 SLA_LP_auto_ag: Soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen); InterPro: IPR008829 This family consists of several eukaryotic and archaeal proteins which are related to the Homo sapiens soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis []. The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway []. The archaeal sequences Q8TXK0 from SWISSPROT and Q8TYR3 from SWISSPROT are annotated as being pyridoxal phosphate-dependent enzymes.; GO: 0016740 transferase activity; PDB: 2E7J_B 2E7I_B 2Z67_C 3HL2_D 3BC8_A 3BCA_A 3BCB_A.
Probab=66.10 E-value=2.9 Score=33.35 Aligned_cols=16 Identities=44% Similarity=0.958 Sum_probs=14.1
Q ss_pred HhhhhhhhccccCCCC
Q 035248 53 LIGRGIYNMSHGIGKK 68 (69)
Q Consensus 53 ligRGiyNMShGigkK 68 (69)
|..|-.|++.|||||.
T Consensus 23 lv~~r~~~~~Hgigrs 38 (389)
T PF05889_consen 23 LVARRHYGFAHGIGRS 38 (389)
T ss_dssp HHHHHTTTHCSTBSBT
T ss_pred HhhccccccccCcCCC
Confidence 5788999999999984
No 8
>PF15012 DUF4519: Domain of unknown function (DUF4519)
Probab=65.64 E-value=2.8 Score=25.93 Aligned_cols=19 Identities=37% Similarity=0.627 Sum_probs=13.3
Q ss_pred CCchhhhhhhHHHHHHHHHH
Q 035248 34 MDKITSVAIPIALAASSLYL 53 (69)
Q Consensus 34 ~DkItSvaIPlalaassl~l 53 (69)
.++|++|++|. |++..+++
T Consensus 27 ~~kv~tVVlP~-l~~~~~~I 45 (56)
T PF15012_consen 27 QQKVFTVVLPT-LAAVFLFI 45 (56)
T ss_pred HHhheeEehhH-HHHHHHHH
Confidence 36899999996 45544444
No 9
>TIGR03531 selenium_SpcS O-phosphoseryl-tRNA(Sec) selenium transferase. In the archaea and eukaryotes, the conversion of the mischarged serine to selenocysteine (Sec) on its tRNA is accomplished in two steps. This enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase, acts second, after a phosphophorylation step catalyzed by a homolog of the bacterial SelA protein.
Probab=63.44 E-value=3.4 Score=32.54 Aligned_cols=17 Identities=41% Similarity=0.839 Sum_probs=14.7
Q ss_pred HHhhhhhhhccccCCCC
Q 035248 52 YLIGRGIYNMSHGIGKK 68 (69)
Q Consensus 52 ~ligRGiyNMShGigkK 68 (69)
-|+-|--||+.|||||.
T Consensus 71 ~~~~~~~~~~~hgigr~ 87 (444)
T TIGR03531 71 KLVARRHYRFCHGIGRS 87 (444)
T ss_pred hhhhhcccceecCCCCc
Confidence 46788999999999985
No 10
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=62.61 E-value=17 Score=26.88 Aligned_cols=40 Identities=20% Similarity=0.263 Sum_probs=32.1
Q ss_pred CcHHHHHHHHHHHhhhhhcccccCCCCchhhhhhhHHHHHHHHHHhhh
Q 035248 9 RPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGR 56 (69)
Q Consensus 9 ~PRekl~e~Q~yfQ~i~khtyLKG~~DkItSvaIPlalaassl~ligR 56 (69)
.|..-.=+++.+|+.+..+-.+||+. .-+++|+++|+..|
T Consensus 138 Lp~~v~e~A~~iyk~~~~~~~~rgrs--------~~~i~AAclYiACR 177 (310)
T PRK00423 138 LPRSVREEAAVIYRKAVEKGLIRGRS--------IEGVVAAALYAACR 177 (310)
T ss_pred CCHHHHHHHHHHHHHHHhcCcccCCC--------HHHHHHHHHHHHHH
Confidence 35555667889999999889999983 25889999999887
No 11
>PF04588 HIG_1_N: Hypoxia induced protein conserved region; InterPro: IPR007667 The hypoxia induced gene 1 (HIG1) or hypoglycemia/hypoxia inducible mitochondrial protein (HIMP1) is up-regulated by stresses of the microenvironment such as low oxygen or low glucose conditions. HIG1 is a mitochondrial inner membrane protein, which is ubiquitously expressed. It is predicted to be an integral membrane protein consisting of two hydrophobic helices, 21-23 residues in length that might tend to form a hairpin-like loop across the bilayer. HIG1 could be implied in apoptotic or cytoprotective signals. HIG1 is a member of a well conserved eukaryote protein family. The predicted transmembrane helice (TMH) and loop regions represent the most highly conserved regions in these proteins [, ]. The profile we developed covers the predicted TMH and loop regions. This domain is found in proteins thought to be involved in the response to hypoxia []. It is also found in altered inheritance of mitochondria proteins.; PDB: 2LOM_A 2LON_A.
Probab=60.49 E-value=8 Score=22.33 Aligned_cols=24 Identities=29% Similarity=0.587 Sum_probs=17.2
Q ss_pred hhhhHHHHHHHHHHhhhhhhhcccc
Q 035248 40 VAIPIALAASSLYLIGRGIYNMSHG 64 (69)
Q Consensus 40 vaIPlalaassl~ligRGiyNMShG 64 (69)
.-+|+++++++. .++.|+|||..|
T Consensus 5 plv~ig~~~~~~-~l~~g~~~~~~g 28 (54)
T PF04588_consen 5 PLVPIGMLATVG-ALAYGLYNFRRG 28 (54)
T ss_dssp -CHHHHHHHHHH-HHHHHHHHHTSS
T ss_pred cHHHHHHHHHHH-HHHHHHHHhcCC
Confidence 446888777654 467899999866
No 12
>PF01661 Macro: Macro domain; InterPro: IPR002589 The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose, an NAD metabolite or related ligands. Binding to ADP-ribose could be either covalent or non-covalent []: in certain cases it is believed to bind non-covalently []; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein []. The domain was described originally in association with ADP-ribose 1''-phosphate (Appr-1''-P) processing activity (A1pp) of the yeast YBR022W protein []. The domain is also called Macro domain as it is the C-terminal domain of mammalian core histone macro-H2A [, ]. Macro domain proteins can be found in eukaryotes, in (mostly pathogenic) bacteria, in archaea and in ssRNA viruses, such as coronaviruses, Rubella and Hepatitis E viruses. In vertebrates the domain occurs e.g. in histone macroH2A, in predicted poly-ADP-ribose polymerases (PARPs) and in B aggressive lymphoma (BAL) protein. The macro domain can be associated with catalytic domains, such as PARP, or sirtuin. The Macro domain can recognise ADP-ribose or in some cases poly-ADP-ribose, which can be involved in ADP-ribosylation reactions that occur in important processes, such as chromatin biology, DNA repair and transcription regulation []. The human macroH2A1.1 Macro domain binds an NAD metabolite O-acetyl-ADP-ribose []. The Macro domain has been suggested to play a regulatory role in ADP-ribosylation, which is involved in inter- and intracellular signaling, transcriptional regulation, DNA repair pathways and maintenance of genomic stability, telomere dynamics, cell differentiation and proliferation, and necrosis and apoptosis. The 3D structure of the Macro domain has a mixed alpha/beta fold of a mixed beta sheet sandwiched between four helices. Several Macro domain only domains are shorter than the structure of AF1521 and lack either the first strand or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [, , , ]. ; PDB: 2DX6_A 2XD7_D 3Q71_A 2FAV_B 1SPV_A 3EKE_A 3EJF_A 1YD9_B 3GPG_B 3GPQ_A ....
Probab=60.45 E-value=1.6 Score=25.92 Aligned_cols=33 Identities=24% Similarity=0.458 Sum_probs=21.2
Q ss_pred HHHHhhhhhcccccCCCCchhhhhhhHHHHHHHHHHhhhhhhhccc
Q 035248 18 QKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63 (69)
Q Consensus 18 Q~yfQ~i~khtyLKG~~DkItSvaIPlalaassl~ligRGiyNMSh 63 (69)
.+.|+++-+. -..+.+.||++|+ ||-|+++.++
T Consensus 79 ~~~~~~~l~~----a~~~~~~sIa~P~---------ig~G~~g~~~ 111 (118)
T PF01661_consen 79 ESAYRNALQK----AEENGIKSIAFPA---------IGTGIGGFPW 111 (118)
T ss_dssp HHHHHHHHHH----HHHTTTSEEEEES---------TTSSTTSBTH
T ss_pred HHHHHHHHHH----HHHcCCcccccCc---------ccCCCCCCCH
Confidence 4455555443 2446788999997 6677776654
No 13
>cd00095 IFab Interferon alpha, beta. Includes also interferon omega and tau. Different from interferon gamma family. Type I interferons(alpha, beta) belong to the larger helical cytokine superfamily, which includes growth hormones, interleukins, several colony-stimulating factors and several other regulatory molecules. All function as regulators of cellular activty by interacting with cell-surface receptors and activating various signalling pathways. Interferons produce antiviral and antiproliferative responses in cells. Receptor specificity determines function of the various members of the family.
Probab=59.24 E-value=5.9 Score=27.17 Aligned_cols=26 Identities=46% Similarity=0.685 Sum_probs=19.7
Q ss_pred CCCCCcHHHHHHHHHHHhhhhhcccccCC
Q 035248 5 EVPFRPREKLLEKQKHFQSIHKHTYLKGP 33 (69)
Q Consensus 5 e~PF~PRekl~e~Q~yfQ~i~khtyLKG~ 33 (69)
+.| ..++..++-.+|||.| +.|||..
T Consensus 106 ~~~-~~~~~~l~lk~YF~rI--~~yLk~K 131 (152)
T cd00095 106 ETP-GPRNTHLHLRKYFQRI--QLYLKEK 131 (152)
T ss_pred cCC-ccccchhHHHHHHHHH--HHHHHhC
Confidence 344 4445678889999999 7799886
No 14
>cd06579 TM_PBP1_transp_AraH_like Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group also contains E. coli RbsC, AlsC, and MglC, which are TMs of other monosaccharide transporters, the ribose transporter, the D-allose transporter and the galactose transporter, respectively. The D-allose transporter may also be involved in low affinity ribose transport. These transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. Proteins in this subgroup have a single TM which homodimerizes to ge
Probab=51.64 E-value=8.7 Score=26.94 Aligned_cols=24 Identities=25% Similarity=0.306 Sum_probs=17.0
Q ss_pred hhhHHHHHHHHHHhh-hhhhhcccc
Q 035248 41 AIPIALAASSLYLIG-RGIYNMSHG 64 (69)
Q Consensus 41 aIPlalaassl~lig-RGiyNMShG 64 (69)
+.|+++++.++.++. -|+.|++||
T Consensus 1 ~~~~~l~a~g~~l~~~~g~~n~a~g 25 (263)
T cd06579 1 AAVLGILALGMTLVIITGGIDLSVG 25 (263)
T ss_pred ChHHHHHHHHHHHHHHHcCccccHH
Confidence 467888877765543 288898886
No 15
>PF00798 Arena_glycoprot: Arenavirus glycoprotein; InterPro: IPR001535 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. Tacaribe virus (TACV) is an arenavirus that is genetically and antigenically closely related to Junin arenavirus (JUNV), the aetiological agent of Argentine haemorrhagic fever (AHF). It is well established that TACV protects experimental animals fully against an otherwise lethal challenge with JUNV. It has been established that it is the heterologous glycoprotein that protects against JUNV challenge. A recombinant vaccinia virus that expresses JUNV glycoprotein precursor (VV-GJun) protected seventy-two percent of the animals inoculated with two doses of VV-GJun against the lethal JUNV challenge [].; GO: 0019031 viral envelope; PDB: 3KAS_B 1S7U_F 3QUK_F 3QUL_L 1S7W_C 1S7V_F 1S7X_I 1S7R_F 2L0Z_A 1N5A_L ....
Probab=51.14 E-value=4.9 Score=33.37 Aligned_cols=25 Identities=40% Similarity=0.502 Sum_probs=1.0
Q ss_pred hhhhhhhHHHHHHHHHHhhhhhhhc
Q 035248 37 ITSVAIPIALAASSLYLIGRGIYNM 61 (69)
Q Consensus 37 ItSvaIPlalaassl~ligRGiyNM 61 (69)
|..=|+=+||+|.|+.-|.+||||.
T Consensus 14 Ii~EAlNIALIaVSiIaIlKGvvNl 38 (487)
T PF00798_consen 14 IIQEALNIALIAVSIIAILKGVVNL 38 (487)
T ss_dssp ---------------------S---
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555888999999999999999996
No 16
>smart00076 IFabd Interferon alpha, beta and delta. Interferons produce antiviral and antiproliferative responses in cells. They are classified into five groups, all of them related but gamma-interferon.
Probab=50.67 E-value=11 Score=25.09 Aligned_cols=20 Identities=40% Similarity=0.509 Sum_probs=17.1
Q ss_pred HHHHHHHHHHhhhhhcccccCC
Q 035248 12 EKLLEKQKHFQSIHKHTYLKGP 33 (69)
Q Consensus 12 ekl~e~Q~yfQ~i~khtyLKG~ 33 (69)
+..++-.+|||.| +.|||+.
T Consensus 80 ~~~l~lk~YF~rI--~~yLk~K 99 (117)
T smart00076 80 NTHLALRKYFQRI--QLYLKEK 99 (117)
T ss_pred cchHHHHHHHHHH--HHHHHhC
Confidence 5678889999999 7799876
No 17
>cd06574 TM_PBP1_branched-chain-AA_like Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of monosaccharides including ribose, galactose, and arabinose. These transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. This group includes Escherichia coli LivM and LivH, two TMs which heterodimerize to form the translocation pathway of the E. coli branched-chain AA LIV-1/LS transporter. This transporter is comprised of two TMs (LivM and LivH), two ABCs (LivG and LivF), and one of two alternative PBP
Probab=48.75 E-value=7.6 Score=27.34 Aligned_cols=22 Identities=23% Similarity=0.387 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHhhh--hhhhcccc
Q 035248 43 PIALAASSLYLIGR--GIYNMSHG 64 (69)
Q Consensus 43 Plalaassl~ligR--GiyNMShG 64 (69)
++++.|.++.++-+ |+.|++||
T Consensus 3 ~~~l~alg~~l~~~~~g~~n~a~~ 26 (266)
T cd06574 3 IYAILALGVYIVFRILGFPDLTVD 26 (266)
T ss_pred eehHHHHHHHHHHHHcCCcchhHH
Confidence 67888888888876 99999997
No 18
>smart00506 A1pp Appr-1"-p processing enzyme. Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson & Fuji).
Probab=47.76 E-value=3.5 Score=25.07 Aligned_cols=20 Identities=60% Similarity=0.926 Sum_probs=14.0
Q ss_pred CchhhhhhhHHHHHHHHHHhhhhhhhccc
Q 035248 35 DKITSVAIPIALAASSLYLIGRGIYNMSH 63 (69)
Q Consensus 35 DkItSvaIPlalaassl~ligRGiyNMSh 63 (69)
.+++|||||+ ||-|+++.++
T Consensus 107 ~~~~sIa~P~---------igtG~~g~~~ 126 (133)
T smart00506 107 LGITSVAIPL---------IGTGIYGVPK 126 (133)
T ss_pred cCCCEEEECC---------ccCCCCCCCH
Confidence 4689999996 5556665544
No 19
>cd02907 Macro_Af1521_BAL_like Macro domain, Af1521- and BAL-like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. The macro domains in this family show similarity to Af1521, a protein from Archaeoglobus fulgidus containing a stand-alone macro domain. Af1521 binds ADP-ribose and exhibits phosphatase activity toward Appr-1"-p. Also included in this family are the N-terminal (or first) macro domains
Probab=46.86 E-value=4.1 Score=27.15 Aligned_cols=19 Identities=37% Similarity=0.672 Sum_probs=13.8
Q ss_pred CchhhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248 35 DKITSVAIPIALAASSLYLIGRGIYNMS 62 (69)
Q Consensus 35 DkItSvaIPlalaassl~ligRGiyNMS 62 (69)
+.++|||+|+ ||-|+++++
T Consensus 111 ~~~~SIA~P~---------lgtG~~g~p 129 (175)
T cd02907 111 LGLRSIAIPA---------ISSGIFGFP 129 (175)
T ss_pred cCCCEEEECC---------cccCCCCCC
Confidence 4799999998 466665554
No 20
>PF09988 DUF2227: Uncharacterized metal-binding protein (DUF2227); InterPro: IPR019250 This entry represents hypothetical bacterial proteins that possess metal binding properties; however, their exact function has not yet been determined.
Probab=46.39 E-value=11 Score=26.64 Aligned_cols=18 Identities=39% Similarity=0.613 Sum_probs=15.1
Q ss_pred CC-CCchhhhhhhHHHHHH
Q 035248 32 GP-MDKITSVAIPIALAAS 49 (69)
Q Consensus 32 G~-~DkItSvaIPlalaas 49 (69)
|+ ||+||=.++|++++++
T Consensus 3 GrtHD~Itl~~lp~~~~~~ 21 (169)
T PF09988_consen 3 GRTHDRITLWSLPLVAAAT 21 (169)
T ss_pred CChhHHHHHHHHHHHHHHH
Confidence 66 9999999999887754
No 21
>cd06580 TM_PBP1_transp_TpRbsC_like Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters, which are mainly involved in the uptake of branched-chain amino acids (AAs) or in the uptake of monosaccharides including ribose, galactose, and arabinose, and which generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction.
Probab=45.30 E-value=13 Score=25.80 Aligned_cols=23 Identities=26% Similarity=0.492 Sum_probs=17.1
Q ss_pred hhHHHHHHHHHHh-hhhhhhcccc
Q 035248 42 IPIALAASSLYLI-GRGIYNMSHG 64 (69)
Q Consensus 42 IPlalaassl~li-gRGiyNMShG 64 (69)
+|++|.|.++.++ .-|+.|++||
T Consensus 2 ~~~~l~alG~~l~~~~g~~n~a~~ 25 (234)
T cd06580 2 TPLILAALGVAISFRAGVFNIGLE 25 (234)
T ss_pred hHHHHHHHHHHHHHHcCceeehhh
Confidence 6788887776554 3588999987
No 22
>PLN03155 cytochrome c oxidase subunit 5C; Provisional
Probab=43.97 E-value=17 Score=23.08 Aligned_cols=32 Identities=34% Similarity=0.638 Sum_probs=21.2
Q ss_pred hcccccCCCCchhhhhhhHHHHHHHHHHhhhhhhhccc
Q 035248 26 KHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63 (69)
Q Consensus 26 khtyLKG~~DkItSvaIPlalaassl~ligRGiyNMSh 63 (69)
.|.-||||+ .|.-|+|-++ |.|+.=|+|-|-|
T Consensus 7 ah~~~~gPs-vvKEI~iG~~-----LGL~AG~~WKmhH 38 (63)
T PLN03155 7 AHATLKGPS-VVKELCIGLT-----LGLAAGGLWKMHH 38 (63)
T ss_pred eeeeccCCc-hhhhHHHHhH-----HHHhhhhHHHHhh
Confidence 477889996 5677777664 4455556666654
No 23
>cd02903 Macro_BAL_like Macro domain, BAL_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. Members of this family show similarity to BAL (B-aggressive lymphoma) proteins, which contain one to three macro domains. Most BAL family macro domains belong to this family except for the most N-terminal domain in multiple-domain containing proteins. Most BAL proteins also contain a C-termin
Probab=43.51 E-value=4.4 Score=26.23 Aligned_cols=20 Identities=30% Similarity=0.489 Sum_probs=14.6
Q ss_pred CchhhhhhhHHHHHHHHHHhhhhhhhccc
Q 035248 35 DKITSVAIPIALAASSLYLIGRGIYNMSH 63 (69)
Q Consensus 35 DkItSvaIPlalaassl~ligRGiyNMSh 63 (69)
..++|||||. ||-|++..+.
T Consensus 104 ~~~~SIAfP~---------igtG~~g~p~ 123 (137)
T cd02903 104 LSYTSISFPA---------IGTGNLGFPK 123 (137)
T ss_pred CCCcEEEECC---------CcCcCCCCCH
Confidence 4699999997 5666666553
No 24
>PF05887 Trypan_PARP: Procyclic acidic repetitive protein (PARP); InterPro: IPR008882 This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of T. brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated [].; GO: 0016020 membrane; PDB: 2X34_B 2X32_B.
Probab=42.98 E-value=8 Score=27.80 Aligned_cols=15 Identities=47% Similarity=0.702 Sum_probs=0.0
Q ss_pred hhhhhhhHHHHHHHH
Q 035248 37 ITSVAIPIALAASSL 51 (69)
Q Consensus 37 ItSvaIPlalaassl 51 (69)
..||++|+|++|++|
T Consensus 125 ~~sv~~p~a~~a~~~ 139 (143)
T PF05887_consen 125 FKSVAMPFAFAAVGM 139 (143)
T ss_dssp ---------------
T ss_pred ccccccccccccccc
Confidence 469999999999876
No 25
>PF04971 Lysis_S: Lysis protein S ; InterPro: IPR007054 The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane [].
Probab=42.84 E-value=17 Score=23.20 Aligned_cols=29 Identities=34% Similarity=0.212 Sum_probs=20.6
Q ss_pred CCchhhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248 34 MDKITSVAIPIALAASSLYLIGRGIYNMS 62 (69)
Q Consensus 34 ~DkItSvaIPlalaassl~ligRGiyNMS 62 (69)
||||+.-+-.-+.+++..|-+.+=+..+|
T Consensus 1 mdki~tg~aYgtSag~~~~wl~~lld~~s 29 (68)
T PF04971_consen 1 MDKITTGAAYGTSAGSAGYWLLQLLDQFS 29 (68)
T ss_pred CchhhhhhccccchhhHHHHHHHHHhccC
Confidence 68888888777777777776665555444
No 26
>cd02908 Macro_Appr_pase_like Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. This family is composed of uncharacterized proteins that show similarity to Appr-1"-pase, containing conserved putative active site residues. Appr-1"-pase is a phosphatase specific for ADP-ribose-1"-monophosphate.
Probab=41.00 E-value=5.5 Score=26.37 Aligned_cols=11 Identities=27% Similarity=0.522 Sum_probs=9.2
Q ss_pred CCchhhhhhhH
Q 035248 34 MDKITSVAIPI 44 (69)
Q Consensus 34 ~DkItSvaIPl 44 (69)
...++|||+|+
T Consensus 103 ~~~~~sIa~P~ 113 (165)
T cd02908 103 ENGLRSIAFPA 113 (165)
T ss_pred HcCCCEEEECc
Confidence 35799999997
No 27
>COG0063 Predicted sugar kinase [Carbohydrate transport and metabolism]
Probab=39.05 E-value=19 Score=27.06 Aligned_cols=29 Identities=17% Similarity=0.187 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhhhhhcccccCCCCchhh
Q 035248 11 REKLLEKQKHFQSIHKHTYLKGPMDKITS 39 (69)
Q Consensus 11 Rekl~e~Q~yfQ~i~khtyLKG~~DkItS 39 (69)
++++-..|++=|....-+-|||..|.|.+
T Consensus 176 ~~r~~~a~~~a~~~~~vvVLKG~~tvI~~ 204 (284)
T COG0063 176 VDRLEAARELAAKYGAVVVLKGAVTVIAD 204 (284)
T ss_pred cchHHHHHHHHHHcCCEEEEeCCCCEEEc
Confidence 56788889998999999999999999987
No 28
>cd02906 Macro_1 Macro domain, Unknown family 1. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. This family is composed of uncharacterized proteins containing a macro domain, either as a stand-alone domain or in addition to a C-terminal SIR2 (silent information regulator 2) domain.
Probab=38.50 E-value=6.8 Score=26.03 Aligned_cols=18 Identities=22% Similarity=0.508 Sum_probs=14.0
Q ss_pred chhhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248 36 KITSVAIPIALAASSLYLIGRGIYNMS 62 (69)
Q Consensus 36 kItSvaIPlalaassl~ligRGiyNMS 62 (69)
.++|||+|+ |+-|+|.+.
T Consensus 117 ~~~sIA~P~---------i~tG~~g~p 134 (147)
T cd02906 117 GLKSIAFCC---------ISTGLFGFP 134 (147)
T ss_pred CCCEEEECc---------ccccCCCCC
Confidence 589999997 667777654
No 29
>PRK00431 RNase III inhibitor; Provisional
Probab=38.03 E-value=7.3 Score=25.92 Aligned_cols=11 Identities=27% Similarity=0.335 Sum_probs=9.2
Q ss_pred CCchhhhhhhH
Q 035248 34 MDKITSVAIPI 44 (69)
Q Consensus 34 ~DkItSvaIPl 44 (69)
.+.++|||+|+
T Consensus 110 ~~~~~sIa~P~ 120 (177)
T PRK00431 110 ELGLRSIAFPA 120 (177)
T ss_pred HcCCceEEECc
Confidence 45799999997
No 30
>PRK09478 mglC beta-methylgalactoside transporter inner membrane component; Provisional
Probab=36.63 E-value=23 Score=26.12 Aligned_cols=28 Identities=21% Similarity=0.093 Sum_probs=20.2
Q ss_pred hhhhhhhHHHHHHHH-HHhhhhhhhcccc
Q 035248 37 ITSVAIPIALAASSL-YLIGRGIYNMSHG 64 (69)
Q Consensus 37 ItSvaIPlalaassl-~ligRGiyNMShG 64 (69)
+.+.+.|+++.|.++ +.+.-|..|+|||
T Consensus 45 ~l~~~~~l~l~alG~~~v~~~g~idls~g 73 (336)
T PRK09478 45 ILTQSSVRIIIALGVAGLIVTQGTDLSAG 73 (336)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCchHHHH
Confidence 345577888888776 3345677899997
No 31
>PF01456 Mucin: Mucin-like glycoprotein; InterPro: IPR000458 This family of trypanosomal proteins resemble vertebrate mucins. The protein consists of three regions. The N and C terminii are conserved between all members of the family, whereas the central region is not well conserved and contains a large number of threonine residues which can be glycosylated []. Indirect evidence suggested that these genes might encode the core protein of parasite mucins, glycoproteins that were proposed to be involved in the interaction with, and invasion of, mammalian host cells.
Probab=36.45 E-value=25 Score=22.52 Aligned_cols=15 Identities=40% Similarity=0.459 Sum_probs=12.3
Q ss_pred hhhhhHHHHHHHHHH
Q 035248 39 SVAIPIALAASSLYL 53 (69)
Q Consensus 39 SvaIPlalaassl~l 53 (69)
-|--||.||+|+|--
T Consensus 125 wv~apl~la~salay 139 (143)
T PF01456_consen 125 WVCAPLLLAVSALAY 139 (143)
T ss_pred HHHHHHHHHHHHHHH
Confidence 378899999999853
No 32
>PF02224 Cytidylate_kin: Cytidylate kinase; InterPro: IPR011994 Cytidylate kinase (2.7.4.14 from EC) catalyses the phosphorylation of cytidine 5'-monophosphate (dCMP) to cytidine 5'-diphosphate (dCDP) in the presence of ATP or GTP. ; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase-containing compound metabolic process; PDB: 3R20_A 4DIE_A 3R8C_B 2H92_B 1KDT_A 1KDP_B 2FEO_A 1KDO_B 2CMK_A 1KDR_A ....
Probab=36.36 E-value=22 Score=24.95 Aligned_cols=32 Identities=31% Similarity=0.425 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhhhhhcccccCCCCchhhhhhhHH
Q 035248 11 REKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIA 45 (69)
Q Consensus 11 Rekl~e~Q~yfQ~i~khtyLKG~~DkItSvaIPla 45 (69)
|+.|++.|+-|.+ .+-.-+-||- |++|.+|=|
T Consensus 49 R~~l~~~Qr~~a~-~~~vV~eGRD--igTvVfPdA 80 (157)
T PF02224_consen 49 REALVEIQREIAK-KGGVVMEGRD--IGTVVFPDA 80 (157)
T ss_dssp HHHHHHHHHHHHT-TSCEEEEESS--CCCCCCTT-
T ss_pred HHHHHHHHHHHHH-cCCeEEecCC--CceEEcCCC
Confidence 8999999999988 5666677773 888988865
No 33
>PHA02241 hypothetical protein
Probab=36.33 E-value=19 Score=26.70 Aligned_cols=19 Identities=42% Similarity=0.810 Sum_probs=16.1
Q ss_pred CCCCCCcHHHHHHHHHHHh
Q 035248 4 TEVPFRPREKLLEKQKHFQ 22 (69)
Q Consensus 4 ~e~PF~PRekl~e~Q~yfQ 22 (69)
.|-|.--.|++++.|+||.
T Consensus 57 ~e~~~itke~~i~eqry~~ 75 (182)
T PHA02241 57 NEYPYITKEKLIEEQRYFR 75 (182)
T ss_pred hhcchhhHHHHHhHhhhee
Confidence 3567778999999999995
No 34
>cd00211 PTS_IIA_fru PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=35.87 E-value=30 Score=20.76 Aligned_cols=29 Identities=17% Similarity=0.225 Sum_probs=21.9
Q ss_pred HHHHHhhhhhcccccCCCCchhhhhhhHHH
Q 035248 17 KQKHFQSIHKHTYLKGPMDKITSVAIPIAL 46 (69)
Q Consensus 17 ~Q~yfQ~i~khtyLKG~~DkItSvaIPlal 46 (69)
.+.|.|++.+..-+ |++--.+.||||=+.
T Consensus 33 ~~~~~~~l~~Re~~-~~t~i~~~iAlPH~~ 61 (136)
T cd00211 33 EEEYIEALLEREKE-GSTGIGNGIAIPHAK 61 (136)
T ss_pred HHHHHHHHHHHHHh-CCCcccCceecCCCC
Confidence 57799999887555 777666889999544
No 35
>PF13171 DUF4004: Protein of unknown function (DUF4004)
Probab=35.42 E-value=32 Score=25.57 Aligned_cols=20 Identities=40% Similarity=0.723 Sum_probs=17.0
Q ss_pred CCCcHHHHHHHHHHHhhhhh
Q 035248 7 PFRPREKLLEKQKHFQSIHK 26 (69)
Q Consensus 7 PF~PRekl~e~Q~yfQ~i~k 26 (69)
-|.||||+++.=.-.|+++.
T Consensus 45 TFFPrekIL~RIekI~~mKd 64 (199)
T PF13171_consen 45 TFFPREKILERIEKIQKMKD 64 (199)
T ss_pred ccCcHHHHHHHHHHHHHhcc
Confidence 58999999999888888764
No 36
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=35.33 E-value=15 Score=26.77 Aligned_cols=34 Identities=35% Similarity=0.515 Sum_probs=24.6
Q ss_pred CcHHHHHHHH-HHHhhhhhcccccCCCCchhhhhhhHHHH
Q 035248 9 RPREKLLEKQ-KHFQSIHKHTYLKGPMDKITSVAIPIALA 47 (69)
Q Consensus 9 ~PRekl~e~Q-~yfQ~i~khtyLKG~~DkItSvaIPlala 47 (69)
.|+|+|++.| .-||+.+.-. ++-=+||+.|-+..
T Consensus 114 i~eEEL~~qQqeLf~~ARar~-----~~~~~sv~~p~~~~ 148 (156)
T KOG0871|consen 114 IPEEELLRQQQELFAKARARL-----MQQAASVAQPVAAE 148 (156)
T ss_pred CCHHHHHHHHHHHHHHHHHHH-----HhccccccCCcccc
Confidence 4788888765 5799888322 67778888887543
No 37
>PF14610 DUF4448: Protein of unknown function (DUF4448)
Probab=35.16 E-value=20 Score=24.39 Aligned_cols=24 Identities=21% Similarity=0.440 Sum_probs=18.4
Q ss_pred hhhhhhhHHHHHHHHHHhhhhhhh
Q 035248 37 ITSVAIPIALAASSLYLIGRGIYN 60 (69)
Q Consensus 37 ItSvaIPlalaassl~ligRGiyN 60 (69)
..-|++|+++++..+.|++.=.+|
T Consensus 159 ~laI~lPvvv~~~~~~~~~~~~~~ 182 (189)
T PF14610_consen 159 ALAIALPVVVVVLALIMYGFFFWN 182 (189)
T ss_pred eEEEEccHHHHHHHHHHHhhheee
Confidence 566899999999888887754443
No 38
>PF00143 Interferon: Interferon alpha/beta domain; InterPro: IPR000471 Interferons [] are proteins which produce antiviral and antiproliferative responses in cells. On the basis of their sequence interferons are classified into five groups: alpha, alpha-II (or omega), beta, delta (or trophoblast). The sequence differences may possibly cause different responses to various inducers, or result in the recognition of different target cell types []. The main conserved structural feature of interferons is a disulphide bond that, except in mouse beta interferon, occurs in all alpha, beta and omega sequences.; GO: 0005126 cytokine receptor binding, 0006952 defense response, 0005576 extracellular region; PDB: 3UX9_C 3PIW_A 1AU1_B 1WU3_I 3PIV_B 1B5L_A 3SE4_B 3OQ3_A 2KZ1_A 1ITF_A ....
Probab=34.84 E-value=19 Score=24.82 Aligned_cols=27 Identities=37% Similarity=0.520 Sum_probs=19.3
Q ss_pred CCCCCcHHHHHHHHHHHhhhhhcccccCC
Q 035248 5 EVPFRPREKLLEKQKHFQSIHKHTYLKGP 33 (69)
Q Consensus 5 e~PF~PRekl~e~Q~yfQ~i~khtyLKG~ 33 (69)
|.|.....-.++-.+||+.|+ .|||..
T Consensus 106 ~~~~~~~~~~l~lkkYF~rI~--~yLk~K 132 (162)
T PF00143_consen 106 ESPLMREDSSLALKKYFQRIS--KYLKEK 132 (162)
T ss_dssp SSHHHHHHHHHHHHHHHHHHH--HHHHHT
T ss_pred cccccccchhHHHHHHHHHHH--HHHHhc
Confidence 445544445678899999997 478875
No 39
>PF10043 DUF2279: Predicted periplasmic lipoprotein (DUF2279); InterPro: IPR018736 This domain has no known function.
Probab=34.43 E-value=29 Score=22.32 Aligned_cols=25 Identities=32% Similarity=0.258 Sum_probs=20.5
Q ss_pred ccccCCCCchhhhhhhHHHHHHHHH
Q 035248 28 TYLKGPMDKITSVAIPIALAASSLY 52 (69)
Q Consensus 28 tyLKG~~DkItSvaIPlalaassl~ 52 (69)
+-|.|+.||...+.+..+|++.+-.
T Consensus 9 ~tl~~r~DK~~Hf~~Sa~laa~~~~ 33 (85)
T PF10043_consen 9 DTLAGRADKAQHFIASAALAAAGNA 33 (85)
T ss_pred ccccccccHHHHHHHHHHHHHhhcc
Confidence 4688999999999888888876654
No 40
>COG5505 Predicted integral membrane protein [Function unknown]
Probab=34.42 E-value=40 Score=27.56 Aligned_cols=55 Identities=25% Similarity=0.379 Sum_probs=40.0
Q ss_pred cHHHHHHHHHHHhhhhhcccccC-C---CCchhhhhhhHHHHHHHHHHhhhhhhhccccCC
Q 035248 10 PREKLLEKQKHFQSIHKHTYLKG-P---MDKITSVAIPIALAASSLYLIGRGIYNMSHGIG 66 (69)
Q Consensus 10 PRekl~e~Q~yfQ~i~khtyLKG-~---~DkItSvaIPlalaassl~ligRGiyNMShGig 66 (69)
|.|..++.|.= ....+-+|=|= | +|-|--..|-++++|.|. +|++-.-|||||.+
T Consensus 184 pdesKL~A~~~-e~a~~e~ywKrkp~Sl~D~afl~Gislav~AVa~-~Is~~l~~~s~gl~ 242 (384)
T COG5505 184 PDESKLKADGN-EGASAESYWKRKPISLKDIAFLAGISLAVVAVAM-KISGYLKSISHGLL 242 (384)
T ss_pred ccHHHHhhhhh-hhhhhhhhhhcCCccHHHHHHHhhHHHHHHHHHH-HHHhhccccccccc
Confidence 56666666643 44455666655 3 688888888888888874 78899999999975
No 41
>COG4298 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.96 E-value=49 Score=22.49 Aligned_cols=29 Identities=21% Similarity=0.354 Sum_probs=21.6
Q ss_pred CCchhhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248 34 MDKITSVAIPIALAASSLYLIGRGIYNMS 62 (69)
Q Consensus 34 ~DkItSvaIPlalaassl~ligRGiyNMS 62 (69)
-|-=+-|..--|-.+.|+||.+=||||..
T Consensus 11 ~dspawi~f~waafg~s~~m~~~gi~~lP 39 (95)
T COG4298 11 NDSPAWIMFNWAAFGASYFMLGLGIWLLP 39 (95)
T ss_pred CCCchhHhHHHHHHHHHHHHHHHHhheec
Confidence 45555555566777889999999999863
No 42
>cd02905 Macro_GDAP2_like Macro domain, GDAP2_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. This family contains proteins similar to human GDAP2, the ganglioside induced differentiation associated protein 2, whose gene is expressed at a higher level in differentiated Neuro2a cells compared with non-differentiated cells. GDAP2 contains an N-terminal macro domain and a C-terminal
Probab=33.39 E-value=8.7 Score=25.55 Aligned_cols=9 Identities=22% Similarity=0.449 Sum_probs=7.9
Q ss_pred chhhhhhhH
Q 035248 36 KITSVAIPI 44 (69)
Q Consensus 36 kItSvaIPl 44 (69)
.++|||+|+
T Consensus 107 ~~~SIAfPa 115 (140)
T cd02905 107 GLESIALCV 115 (140)
T ss_pred CCCEEEECC
Confidence 588999997
No 43
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=32.71 E-value=21 Score=27.19 Aligned_cols=12 Identities=50% Similarity=0.509 Sum_probs=10.0
Q ss_pred HHHHHHHHHHhh
Q 035248 12 EKLLEKQKHFQS 23 (69)
Q Consensus 12 ekl~e~Q~yfQ~ 23 (69)
||-||+|||+-.
T Consensus 188 EkrF~~QKYLS~ 199 (309)
T KOG0488|consen 188 EKRFEKQKYLSV 199 (309)
T ss_pred HHHHHHhhcccH
Confidence 899999999743
No 44
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=32.46 E-value=11 Score=19.83 Aligned_cols=6 Identities=83% Similarity=1.265 Sum_probs=3.5
Q ss_pred ccCCCC
Q 035248 63 HGIGKK 68 (69)
Q Consensus 63 hGigkK 68 (69)
||||+|
T Consensus 17 ~GIG~k 22 (32)
T PF11798_consen 17 WGIGKK 22 (32)
T ss_dssp TTS-HH
T ss_pred CCccHH
Confidence 677764
No 45
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=31.97 E-value=30 Score=19.49 Aligned_cols=17 Identities=53% Similarity=0.946 Sum_probs=12.2
Q ss_pred hhhhhhhHHHHHHHHHHhhh
Q 035248 37 ITSVAIPIALAASSLYLIGR 56 (69)
Q Consensus 37 ItSvaIPlalaassl~ligR 56 (69)
|-+|+.|.+.| +||+.|
T Consensus 3 I~n~GFPi~va---~yLL~R 19 (38)
T PF12841_consen 3 ISNVGFPIAVA---IYLLVR 19 (38)
T ss_pred hhhcCcHHHHH---HHHHHH
Confidence 56788898654 677666
No 46
>PF11127 DUF2892: Protein of unknown function (DUF2892); InterPro: IPR021309 This family is conserved in bacteria. The function is not known.
Probab=31.46 E-value=28 Score=19.95 Aligned_cols=23 Identities=35% Similarity=0.465 Sum_probs=16.6
Q ss_pred CCCCchhhhhhhHHHHHHHHHHh
Q 035248 32 GPMDKITSVAIPIALAASSLYLI 54 (69)
Q Consensus 32 G~~DkItSvaIPlalaassl~li 54 (69)
|+.|++.++.+-+++.+.+++-.
T Consensus 6 g~~dR~~R~~~G~~l~~~~~~~~ 28 (66)
T PF11127_consen 6 GTTDRIVRIIIGIVLLALGLLGL 28 (66)
T ss_pred chHHHHHHHHHHHHHHHHHHHhc
Confidence 56788888888777776666544
No 47
>PRK11618 inner membrane ABC transporter permease protein YjfF; Provisional
Probab=31.45 E-value=32 Score=24.91 Aligned_cols=26 Identities=15% Similarity=0.209 Sum_probs=17.8
Q ss_pred hhhhhHHHHHHHHHHhh-hhhhhcccc
Q 035248 39 SVAIPIALAASSLYLIG-RGIYNMSHG 64 (69)
Q Consensus 39 SvaIPlalaassl~lig-RGiyNMShG 64 (69)
+.+.++++.|.++-++. -|.-|+|||
T Consensus 40 ~~~~~~~llAlG~~lv~~~G~inls~g 66 (317)
T PRK11618 40 TDNAFLGIVAVGMTFVILSGGIDLSVG 66 (317)
T ss_pred HHHHHHHHHHHHHHHHHHhCCchHHHH
Confidence 44567788776655544 477899997
No 48
>PF14674 FANCI_S1-cap: FANCI solenoid 1 cap; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=31.07 E-value=89 Score=19.25 Aligned_cols=36 Identities=31% Similarity=0.459 Sum_probs=25.5
Q ss_pred HHHHHHhhhhhcccccCCCCchhhhhhhHHHHHHHHHHhhhhhh
Q 035248 16 EKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIY 59 (69)
Q Consensus 16 e~Q~yfQ~i~khtyLKG~~DkItSvaIPlalaassl~ligRGiy 59 (69)
+-|+|.|++.. |..|++----|+=+=...-+.|||+
T Consensus 16 ~LQ~~Lq~L~e--------deLt~~lt~~AlKGk~~Gallr~If 51 (53)
T PF14674_consen 16 ELQKFLQTLKE--------DELTDLLTNQALKGKDVGALLRGIF 51 (53)
T ss_dssp HHHHHHHHH-S---------SHHHHHHHHHH-HHHHHTHHHHHH
T ss_pred HHHHHHHHcch--------hHHHHHHHHHhhcchHHHHHHHHHh
Confidence 57999999863 6677777677777777777888886
No 49
>PF00716 Peptidase_S21: Assemblin (Peptidase family S21) This is family S21 in the peptidase classification. ; InterPro: IPR001847 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S21 (assemblin family, clan 21). A number of viral proteases have been discovered and their sequence similarity is very low. Studies with protease inhibitors suggest that the Herpesviridae protease is a serine protease belonging to either the trypsin-like or subtilisin-like families; it is not inhibited by inhibitors of Cys, Asp or metallo proteases.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1VZV_A 3NJQ_A 1O6E_A 1AT3_A 1NJT_B 1WPO_A 1CMV_A 1IED_B 1NKK_A 1NJU_B ....
Probab=30.73 E-value=37 Score=26.42 Aligned_cols=25 Identities=40% Similarity=0.591 Sum_probs=19.6
Q ss_pred CcHHHHHHHHHHHhhhhhcccccCC
Q 035248 9 RPREKLLEKQKHFQSIHKHTYLKGP 33 (69)
Q Consensus 9 ~PRekl~e~Q~yfQ~i~khtyLKG~ 33 (69)
|=|=.+++.+|--..|.+|||||-.
T Consensus 184 rdR~~~l~~dr~~a~i~~~tYlkAS 208 (325)
T PF00716_consen 184 RDRWELLKYDRRVAGISGHTYLKAS 208 (325)
T ss_dssp TTHHHHHHHHHHHTTBTSSSSS---
T ss_pred HHHHHHHHHHHHhcCCCCCceeecc
Confidence 4577789999999999999999965
No 50
>cd03330 Macro_2 Macro domain, Unknown family 2. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. This family is composed of uncharacterized proteins containing a stand-alone macro domain.
Probab=30.68 E-value=9.4 Score=24.10 Aligned_cols=9 Identities=56% Similarity=0.689 Sum_probs=7.7
Q ss_pred chhhhhhhH
Q 035248 36 KITSVAIPI 44 (69)
Q Consensus 36 kItSvaIPl 44 (69)
.+.|||||+
T Consensus 103 ~~~sIA~P~ 111 (133)
T cd03330 103 GIESVAFPA 111 (133)
T ss_pred CCCEEEECc
Confidence 588999996
No 51
>cd06582 TM_PBP1_LivH_like Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of branched-chain amino acids (AAs). These types of transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. E. coli LivH forms a heterodimer with another TM, LivM, to generate the transmembrane pore. LivM is not included in this subgroup. The LIV-1/LS transporter is comprised of two TMs (LivM and LivH), two ABCs (LivG and LivF), and one of two alternative PBPs, LivJ (LIV-BP) or LivK (LS-BP). In addition to transpo
Probab=30.14 E-value=36 Score=23.93 Aligned_cols=25 Identities=40% Similarity=0.487 Sum_probs=19.3
Q ss_pred hhhhHHHHHHHHHHhhh--hhhhcccc
Q 035248 40 VAIPIALAASSLYLIGR--GIYNMSHG 64 (69)
Q Consensus 40 vaIPlalaassl~ligR--GiyNMShG 64 (69)
.+..+++.|.++-++.+ |+.|+||+
T Consensus 4 ~~~i~~l~alg~~l~~~~~G~~~l~~~ 30 (272)
T cd06582 4 LGAIYALIALGLTLIFGVTGVINFAHG 30 (272)
T ss_pred HHHHHHHHHHHHHHHHHHhCceehHhH
Confidence 45567888888877764 99999986
No 52
>PHA00101 internal virion protein B
Probab=29.86 E-value=38 Score=25.41 Aligned_cols=15 Identities=33% Similarity=0.532 Sum_probs=12.2
Q ss_pred hhhhhHHHHHHHHHH
Q 035248 39 SVAIPIALAASSLYL 53 (69)
Q Consensus 39 SvaIPlalaassl~l 53 (69)
.||||+|+++++.-|
T Consensus 4 ~aaIpiA~~ga~aim 18 (194)
T PHA00101 4 MAAIPIAMMGAQAIM 18 (194)
T ss_pred hhhhHHHHHHHHHHH
Confidence 589999999998433
No 53
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=29.45 E-value=37 Score=25.46 Aligned_cols=11 Identities=55% Similarity=0.776 Sum_probs=8.9
Q ss_pred CCCcHHHHHHH
Q 035248 7 PFRPREKLLEK 17 (69)
Q Consensus 7 PF~PRekl~e~ 17 (69)
.=||||||++.
T Consensus 9 ~~rPRErll~~ 19 (224)
T COG2003 9 NERPRERLLKL 19 (224)
T ss_pred ccchHHHHHHh
Confidence 35899999875
No 54
>COG3162 Predicted membrane protein [Function unknown]
Probab=28.85 E-value=47 Score=22.71 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=22.2
Q ss_pred hhhhhhhHHHHHHHHHHhhhhhhhc
Q 035248 37 ITSVAIPIALAASSLYLIGRGIYNM 61 (69)
Q Consensus 37 ItSvaIPlalaassl~ligRGiyNM 61 (69)
.++.+||+|...-.+-.+.-|||-+
T Consensus 59 ~Vt~Gip~gvg~fv~tfVlt~IYv~ 83 (102)
T COG3162 59 SVTRGIPFGVGVFVMTFVLTGIYVR 83 (102)
T ss_pred ceehhHhHHHHHHHHHHHHHHHHhh
Confidence 6788999999999999999999965
No 55
>TIGR03011 sulf_tusB_dsrH sulfur relay protein TusB/DsrH. The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide in tRNAs for Glu, Lys, and Gln. The sulfur relay complex TusBCD is also found, under the designation DsrEFH, in phototrophic and chemotrophic sulfur bacteria, such as Chromatium vinosum. In these organisms, it seems the primary purpose is related to sulfur flux, such as oxidation from sulfide to molecular sulfur to sulfate.
Probab=28.41 E-value=12 Score=22.44 Aligned_cols=36 Identities=19% Similarity=0.408 Sum_probs=21.5
Q ss_pred cccccCCCCch-hhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248 27 HTYLKGPMDKI-TSVAIPIALAASSLYLIGRGIYNMS 62 (69)
Q Consensus 27 htyLKG~~DkI-tSvaIPlalaassl~ligRGiyNMS 62 (69)
||.-|.||..- .+-+..+++..-+++|++-|+|...
T Consensus 1 hi~~~sP~~~~~~~~~l~~~~~~d~vll~~DgV~~l~ 37 (94)
T TIGR03011 1 HTVKKSPFEDNDLELCLRLLGPGDAILLLQDGVYAAL 37 (94)
T ss_pred CcccCCCCccchHHHHHHhcCCCCeEEEehhhHHHHh
Confidence 34445554333 4445555555667888888888765
No 56
>KOG4288 consensus Predicted oxidoreductase [General function prediction only]
Probab=28.11 E-value=42 Score=26.48 Aligned_cols=52 Identities=21% Similarity=0.420 Sum_probs=38.2
Q ss_pred CCCCCcH----------HHHHHHHHHHhhh-hhcccccCCCCchhhhhhhHHHHHHHHHHhhhhh
Q 035248 5 EVPFRPR----------EKLLEKQKHFQSI-HKHTYLKGPMDKITSVAIPIALAASSLYLIGRGI 58 (69)
Q Consensus 5 e~PF~PR----------ekl~e~Q~yfQ~i-~khtyLKG~~DkItSvaIPlalaassl~ligRGi 58 (69)
-|||-|| -.|+.+|. |..| -+.-+.-|- -.+++.-+||-++++.|.|+..+.
T Consensus 167 ~~~~i~rGY~~gKR~AE~Ell~~~~-~rgiilRPGFiyg~-R~v~g~~~pL~~vg~pl~~~~~~a 229 (283)
T KOG4288|consen 167 LPPLIPRGYIEGKREAEAELLKKFR-FRGIILRPGFIYGT-RNVGGIKSPLHTVGEPLEMVLKFA 229 (283)
T ss_pred CCCccchhhhccchHHHHHHHHhcC-CCceeeccceeecc-cccCcccccHHhhhhhHHHHHHhh
Confidence 3788888 23555555 4443 355566565 788999999999999999998775
No 57
>TIGR03010 sulf_tusC_dsrF sulfur relay protein TusC/DsrF. The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide in tRNAs for Glu, Lys, and Gln. The sulfur relay complex TusBCD is also found, under the designation DsrEFH, in phototrophic and chemotrophic sulfur bacteria, such as Chromatium vinosum. In these organisms, it seems the primary purpose is related to sulfur flux, such as oxidation from sulfide to molecular sulfur to sulfate.
Probab=28.02 E-value=19 Score=22.68 Aligned_cols=22 Identities=27% Similarity=0.545 Sum_probs=16.0
Q ss_pred hhHHHHHH------HHHHhhhhhhhccc
Q 035248 42 IPIALAAS------SLYLIGRGIYNMSH 63 (69)
Q Consensus 42 IPlalaas------sl~ligRGiyNMSh 63 (69)
+=+||+++ ++|+++.|+|+.-.
T Consensus 20 l~~al~~aa~~~eV~vff~~DGV~~l~~ 47 (116)
T TIGR03010 20 LDALLAASAFDEDIGVFFIDDGVLQLLK 47 (116)
T ss_pred HHHHHHHHhccCCeEEEEechHHHHHhc
Confidence 33466654 49999999999654
No 58
>PF15284 PAGK: Phage-encoded virulence factor
Probab=27.47 E-value=54 Score=20.62 Aligned_cols=22 Identities=18% Similarity=0.258 Sum_probs=17.2
Q ss_pred CCchhhhhhhHHHHHHHHHHhh
Q 035248 34 MDKITSVAIPIALAASSLYLIG 55 (69)
Q Consensus 34 ~DkItSvaIPlalaassl~lig 55 (69)
|.++-||..++.|+.+|.....
T Consensus 1 Mkk~ksifL~l~~~LsA~~FSa 22 (61)
T PF15284_consen 1 MKKFKSIFLALVFILSAAGFSA 22 (61)
T ss_pred ChHHHHHHHHHHHHHHHhhhhH
Confidence 3578899999999888876544
No 59
>TIGR03409 urea_trans_UrtB urea ABC transporter, permease protein UrtB. Members of this protein family are ABC transporter permease proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.
Probab=27.37 E-value=39 Score=24.13 Aligned_cols=25 Identities=36% Similarity=0.470 Sum_probs=19.4
Q ss_pred hhhhHHHHHHHHHHhhh--hhhhcccc
Q 035248 40 VAIPIALAASSLYLIGR--GIYNMSHG 64 (69)
Q Consensus 40 vaIPlalaassl~ligR--GiyNMShG 64 (69)
.+.++++.|.++-++.. |+-|++||
T Consensus 10 ~~~i~~i~Alg~~l~~g~~G~~n~a~~ 36 (291)
T TIGR03409 10 LGSILLLAALGLAITFGQMGVINMAHG 36 (291)
T ss_pred HHHHHHHHHHHHHHHHHHhCceeHHHH
Confidence 45677888888888743 89999997
No 60
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=27.30 E-value=52 Score=27.60 Aligned_cols=25 Identities=20% Similarity=0.398 Sum_probs=18.4
Q ss_pred CCCchhhhhhhHHHHHHHHHHhhhh
Q 035248 33 PMDKITSVAIPIALAASSLYLIGRG 57 (69)
Q Consensus 33 ~~DkItSvaIPlalaassl~ligRG 57 (69)
|.=-|++++||+.++++-++|-.-|
T Consensus 356 r~~liv~~~IPisi~~t~~~m~~~g 380 (1021)
T PF00873_consen 356 RSALIVALSIPISILGTFIFMYLFG 380 (1021)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 4456889999999988876664444
No 61
>TIGR01297 CDF cation diffusion facilitator family transporter. This model describes a broadly distributed family of transporters, a number of which have been shown to transport divalent cations of cobalt, cadmium and/or zinc. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.
Probab=26.40 E-value=41 Score=22.94 Aligned_cols=39 Identities=13% Similarity=0.301 Sum_probs=30.5
Q ss_pred hcccccCCCCchhhhhhhHHHHHHHHHHhhhhhhhcccc
Q 035248 26 KHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSHG 64 (69)
Q Consensus 26 khtyLKG~~DkItSvaIPlalaassl~ligRGiyNMShG 64 (69)
+|+|=.|+.+.+.+...-+.+..++++++..++.++-++
T Consensus 49 ~~pyG~~r~E~l~~l~~~~~l~~~~~~~~~~si~~l~~~ 87 (268)
T TIGR01297 49 RHPFGHGRAEILAALLNGLFLVVVALFILYEAIERLINP 87 (268)
T ss_pred CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 577777888888888888888888888888888776554
No 62
>PF00342 PGI: Phosphoglucose isomerase The structure is C alpha atoms only with no sequence assignment.; InterPro: IPR001672 Phosphoglucose isomerase (5.3.1.9 from EC) (PGI) [, ] is a dimeric enzyme that catalyses the reversible isomerization of glucose-6-phosphate and fructose-6-phosphate. PGI is involved in different pathways: in most higher organisms it is involved in glycolysis; in mammals it is involved in gluconeogenesis; in plants in carbohydrate biosynthesis; in some bacteria it provides a gateway for fructose into the Entner-Doudouroff pathway. The multifunctional protein, PGI, is also known as neuroleukin (a neurotrophic factor that mediates the differentiation of neurons), autocrine motility factor (a tumour-secreted cytokine that regulates cell motility), differentiation and maturation mediator and myofibril-bound serine proteinase inhibitor, and has different roles inside and outside the cell. In the cytoplasm, it catalyses the second step in glycolysis, while outside the cell it serves as a nerve growth factor and cytokine []. PGI from Bacillus stearothermophilus has an open twisted alpha/beta structural motif consisting of two globular domains and two protruding parts. It has been suggested that the top part of the large domain together with one of the protruding loops might participate in inducing the neurotrophic activity []. The structure of rabbit muscle phosphoglucose isomerase complexed with various inhibitors shows that the enzyme is a dimer with two alpha/beta-sandwich domains in each subunit. The location of the bound D-gluconate 6-phosphate inhibitor leads to the identification of residues involved in substrate specificity. In addition, the positions of amino acid residues that are substituted in the genetic disease nonspherocytic hemolytic anemia suggest how these substitutions can result in altered catalysis or protein stability [, ].; GO: 0004347 glucose-6-phosphate isomerase activity, 0006094 gluconeogenesis, 0006096 glycolysis; PDB: 1ZZG_B 1JIQ_A 1IRI_B 1IAT_A 1JLH_C 1NUH_A 1KOJ_A 1HOX_A 1G98_B 1DQR_A ....
Probab=26.34 E-value=63 Score=25.89 Aligned_cols=35 Identities=23% Similarity=0.407 Sum_probs=24.9
Q ss_pred cccccCCCCchhhhhhhHHHHH--HHHHHhhhhhhhc
Q 035248 27 HTYLKGPMDKITSVAIPIALAA--SSLYLIGRGIYNM 61 (69)
Q Consensus 27 htyLKG~~DkItSvaIPlalaa--ssl~ligRGiyNM 61 (69)
.-++=|||-.-+.|.+|+|+|. .-+-=+.+|-..|
T Consensus 214 ~d~VGGRfSv~SaVGlp~ala~G~~~~~~lL~GA~~m 250 (486)
T PF00342_consen 214 PDWVGGRFSVLSAVGLPLALAGGFIDFEELLAGARAM 250 (486)
T ss_dssp -TTS-GGGTTTSGGGHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccccccccCCCCCchHHHHHcChhhHHHHHHHHHHH
Confidence 4578899999999999999998 3344555665544
No 63
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=26.16 E-value=44 Score=25.28 Aligned_cols=14 Identities=43% Similarity=0.721 Sum_probs=12.5
Q ss_pred hHHHHHHHHHHhhh
Q 035248 43 PIALAASSLYLIGR 56 (69)
Q Consensus 43 Plalaassl~ligR 56 (69)
|.+|||+++||.++
T Consensus 233 P~glAaaaiy~as~ 246 (285)
T COG1405 233 PAGLAAAAIYLASL 246 (285)
T ss_pred chhHHHHHHHHHHH
Confidence 99999999999765
No 64
>COG1969 HyaC Ni,Fe-hydrogenase I cytochrome b subunit [Energy production and conversion]
Probab=26.10 E-value=1e+02 Score=23.66 Aligned_cols=53 Identities=23% Similarity=0.269 Sum_probs=38.2
Q ss_pred CCCCcHHH---HHHHHHHHhhhhhcccccCCCCchhhhhhhHHHHHHHHHHhhhhhh
Q 035248 6 VPFRPREK---LLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIY 59 (69)
Q Consensus 6 ~PF~PRek---l~e~Q~yfQ~i~khtyLKG~~DkItSvaIPlalaassl~ligRGiy 59 (69)
+||-+|+- +.+.-|.+==+.|+.|+||-++.|.-||- ..+-..++|||..|+-
T Consensus 96 ~~fw~k~w~eg~~~~ik~Ylfl~kkPh~~~~~NPia~~Ay-Ff~~lmiv~MiltGf~ 151 (227)
T COG1969 96 VPFWRKAWWEGVWYQIKWYLFLGKKPHTKGGHNPIAQVAY-FFYFLMIVFMILTGFA 151 (227)
T ss_pred hhhhHHHHHHHHHHHhhhheeecCCCccccccCHHHHHHH-HHHHHHHHHHHHHhHH
Confidence 57777653 33455666667799999999998777775 3455577889888864
No 65
>PF05510 Sarcoglycan_2: Sarcoglycan alpha/epsilon; InterPro: IPR008908 Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localisation of these proteins along the nonjunctional sarcolemma is not clear []. This family contains alpha and epsilon members.; GO: 0016012 sarcoglycan complex
Probab=24.88 E-value=49 Score=26.56 Aligned_cols=21 Identities=33% Similarity=0.548 Sum_probs=16.6
Q ss_pred CchhhhhhhHHHHHHHHHHhh
Q 035248 35 DKITSVAIPIALAASSLYLIG 55 (69)
Q Consensus 35 DkItSvaIPlalaassl~lig 55 (69)
|-+..++||+++++.-+++++
T Consensus 284 d~~vtl~iPl~i~llL~llLs 304 (386)
T PF05510_consen 284 DFLVTLAIPLIIALLLLLLLS 304 (386)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 558899999999887766654
No 66
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=24.85 E-value=57 Score=27.83 Aligned_cols=29 Identities=24% Similarity=0.307 Sum_probs=19.7
Q ss_pred CchhhhhhhHHHHHHHHHHhhhh--hhhccc
Q 035248 35 DKITSVAIPIALAASSLYLIGRG--IYNMSH 63 (69)
Q Consensus 35 DkItSvaIPlalaassl~ligRG--iyNMSh 63 (69)
=-|..++||+++.++-++|-.-| +..||-
T Consensus 368 ~liv~~~iP~s~~~~~~~m~~~g~sln~~sl 398 (1051)
T TIGR00914 368 ALIAATVIPLSLLITFIGMVFQGISANLMSL 398 (1051)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCcHHHHHH
Confidence 34788999999988876665444 344443
No 67
>cd06581 TM_PBP1_LivM_like Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of branched-chain amino acids (AAs). These types of transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. E. coli LivM forms a heterodimer with another TM, LivH, to generate the transmembrane pore. LivH is not included in this subgroup. The LIV-1/LS transporter is comprised of two TMs (LivM and LivH), two ABCs (LivG and LivF), and one of two alternative PBPs, LivJ (LIV-BP) or LivK (LS-BP). In addition to transpo
Probab=24.82 E-value=41 Score=23.64 Aligned_cols=20 Identities=30% Similarity=0.401 Sum_probs=13.1
Q ss_pred HHHHHHHHHhhh--hhhhcccc
Q 035248 45 ALAASSLYLIGR--GIYNMSHG 64 (69)
Q Consensus 45 alaassl~ligR--GiyNMShG 64 (69)
++.|.++-++.+ |+-|+|||
T Consensus 5 ~l~a~G~~lv~~~~g~in~s~g 26 (268)
T cd06581 5 AILALGLNLLLGYAGQLSLGHA 26 (268)
T ss_pred HHHHHHHHHHhhhhhhcChHHH
Confidence 455555555553 78899987
No 68
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=24.66 E-value=67 Score=16.83 Aligned_cols=16 Identities=38% Similarity=0.596 Sum_probs=11.0
Q ss_pred hhhHHHHHHHHHHhhh
Q 035248 41 AIPIALAASSLYLIGR 56 (69)
Q Consensus 41 aIPlalaassl~ligR 56 (69)
.=|-.+|++++|+-.|
T Consensus 36 ~~~~~ia~a~l~lA~k 51 (83)
T smart00385 36 YSPSLIAAAALYLAAK 51 (83)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 3466777788887665
No 69
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.
Probab=24.56 E-value=64 Score=28.40 Aligned_cols=16 Identities=31% Similarity=0.540 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHhhhhh
Q 035248 11 REKLLEKQKHFQSIHK 26 (69)
Q Consensus 11 Rekl~e~Q~yfQ~i~k 26 (69)
||||+.|-|+=..+++
T Consensus 439 r~kl~~kkq~ke~~~r 454 (763)
T TIGR00993 439 RVKLLQKKQWREELKR 454 (763)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 7888888888666653
No 70
>cd02901 Macro_Poa1p_like Macro domain, Poa1p_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. Members of this family show similarity to the yeast protein Poa1p, reported to be a phosphatase specific for Appr-1"-p, a tRNA splicing metabolite. Poa1p may play a role in tRNA splicing regulation.
Probab=24.31 E-value=15 Score=23.18 Aligned_cols=27 Identities=26% Similarity=0.362 Sum_probs=16.0
Q ss_pred HHHHHHHHhhhhhcccccCCCCchhhhhhhH
Q 035248 14 LLEKQKHFQSIHKHTYLKGPMDKITSVAIPI 44 (69)
Q Consensus 14 l~e~Q~yfQ~i~khtyLKG~~DkItSvaIPl 44 (69)
+-.-++.+.++..+.- -.++.|||+|.
T Consensus 90 ~~~l~~~l~~~~~~a~----~~~~~sva~P~ 116 (140)
T cd02901 90 YEAIEKSLRELRAHAR----DNGIKSVAMPR 116 (140)
T ss_pred HHHHHHHHHHHHHHHH----HcCCCEEeeCC
Confidence 3344555666655531 14688999995
No 71
>COG0283 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=24.28 E-value=54 Score=24.69 Aligned_cols=32 Identities=28% Similarity=0.325 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhhhhhcccccCCCCchhhhhhhH
Q 035248 11 REKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPI 44 (69)
Q Consensus 11 Rekl~e~Q~yfQ~i~khtyLKG~~DkItSvaIPl 44 (69)
||.|++.||-|-.-.+-.-+-||. |.+|..|=
T Consensus 106 R~~l~~~Qr~~a~~~~~~V~dGRD--iGTvV~Pd 137 (222)
T COG0283 106 REALVKLQRAFAKNGPGIVADGRD--IGTVVFPD 137 (222)
T ss_pred HHHHHHHHHHHHhcCCCEEEecCC--CcceECCC
Confidence 899999999998887667777773 67777774
No 72
>PF10525 Engrail_1_C_sig: Engrailed homeobox C-terminal signature domain; InterPro: IPR019549 Homeodomain proteins are transcription factors that share a related DNA-binding homeodomain []. The homeodomain was initially identified in Drosophila melanogaster (Fruit fly) homeotic and segmentation proteins, but is well conserved throughout metazoans [, ]. The homeodomain binds DNA through a helix-turn-helix (HTH) structure, consisting of approximately 20 residues []. The HTH motif is comprised of two alpha-helices that make intimate contacts with the DNA; the second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions. These interactions occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA. The first helix helps to stabilise the structure and is joined to the second through a short turn. Most proteins which contain a homeobox domain can be classified [, ], on the basis of their sequence characteristics, into three subfamilies, engrailed, antennapedia and paired. A number of different proteins contain homeodomains, including Drosophila engrailed, yeast mating type proteins, hepatocyte nuclear factor 1a and Hox proteins. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The homeodomain motif is very similar in sequence identity and structure to domains in other DNA-binding proteins, including recombinases, GARP response regulators, human telomeric protein, AraC type transcriptional activator and tetracycline repressor [, , ]. This entry represents a conserved region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain and forms a kind of a signature pattern for this subfamily of proteins []. ; PDB: 2HOS_A 2HOT_A.
Probab=24.26 E-value=25 Score=19.81 Aligned_cols=14 Identities=43% Similarity=0.797 Sum_probs=0.0
Q ss_pred HHHHhhhhhhhccc
Q 035248 50 SLYLIGRGIYNMSH 63 (69)
Q Consensus 50 sl~ligRGiyNMSh 63 (69)
++-|+..|+||-|-
T Consensus 9 Al~LmaqGLyNHsT 22 (32)
T PF10525_consen 9 ALQLMAQGLYNHST 22 (32)
T ss_dssp --------------
T ss_pred HHHHHHHHhhcccc
Confidence 36788999999774
No 73
>PF06724 DUF1206: Domain of Unknown Function (DUF1206); InterPro: IPR009597 This region consists of two a pair of transmembrane helices and occurs three times in each of the family member proteins.
Probab=24.16 E-value=93 Score=18.11 Aligned_cols=30 Identities=13% Similarity=0.340 Sum_probs=21.1
Q ss_pred cCCCCchhhhhhhHHHHHHHHHHhhhhhhh
Q 035248 31 KGPMDKITSVAIPIALAASSLYLIGRGIYN 60 (69)
Q Consensus 31 KG~~DkItSvaIPlalaassl~ligRGiyN 60 (69)
.-|.-++.=+++-++|++.++|.+.+++|.
T Consensus 42 ~~p~G~~ll~~vg~gli~~gi~~~~~a~~~ 71 (73)
T PF06724_consen 42 EQPFGRWLLGAVGLGLIGYGIWQFVKAVYR 71 (73)
T ss_pred hCCCcHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345666666777778888888887777763
No 74
>PF04906 Tweety: Tweety; InterPro: IPR006990 None of the members of the tweety (tty) family have been functionally characterised. However, they are considered to be transmembrane proteins with five potential membrane-spanning regions. A number of potential functions have been suggested on the basis of homology to the yeast FTR1 and FTH1 iron transporter proteins and the mammalian neurotensin receptors 1 and 2 in that they have a similar hydrophobicity profiles although there is no detectable sequence homology to the tweety-related proteins. It has been proposed that the tweety-related proteins could be involved in transport of iron or other divalent cations or alternatively that they may be membrane-bound receptors [].
Probab=24.07 E-value=1.2e+02 Score=23.60 Aligned_cols=19 Identities=21% Similarity=0.387 Sum_probs=14.7
Q ss_pred CCCCCCCCcHHHHHHHHHHHhhhh
Q 035248 2 SETEVPFRPREKLLEKQKHFQSIH 25 (69)
Q Consensus 2 ~~~e~PF~PRekl~e~Q~yfQ~i~ 25 (69)
+.+..+|+|+| +.|+|++.
T Consensus 2 ~~~~~~F~p~~-----~~Y~qsL~ 20 (406)
T PF04906_consen 2 QPVSSTFNPQD-----EEYQQSLL 20 (406)
T ss_pred CCCCCCCCCCC-----HHHHHHHH
Confidence 45678999986 47888874
No 75
>COG1114 BrnQ Branched-chain amino acid permeases [Amino acid transport and metabolism]
Probab=23.70 E-value=44 Score=27.48 Aligned_cols=32 Identities=28% Similarity=0.513 Sum_probs=26.5
Q ss_pred chhhhhhhHHHHHHHHHHhhhhhhhccccCCCC
Q 035248 36 KITSVAIPIALAASSLYLIGRGIYNMSHGIGKK 68 (69)
Q Consensus 36 kItSvaIPlalaassl~ligRGiyNMShGigkK 68 (69)
.+|.|.+|+ |...++-..|+|+.+++.-|||.
T Consensus 46 llTgVglPl-LgiIa~a~~g~~~~~l~~~i~~~ 77 (431)
T COG1114 46 LLTGVGLPL-LGIIAVALYGGGVESLATRIGPW 77 (431)
T ss_pred HHHHhhHHH-HHHHHhhccCCCHHHHhhhccch
Confidence 368899998 66677778889999999999874
No 76
>PF00344 SecY: SecY translocase; InterPro: IPR002208 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The eubacterial secY protein [] interacts with the signal sequences of secretory proteins as well as with two other components of the protein translocation system: secA and secE. SecY is an integral plasma membrane protein of 419 to 492 amino acid residues that apparently contains 10 transmembrane (TM), 6 cytoplasmic and 5 periplasmic regions. Cytoplasmic regions 2 and 3, and TM domains 1, 2, 4, 5, 7 and 10 are well conserved: the conserved cytoplasmic regions are believed to interact with cytoplasmic secretion factors, while the TM domains may participate in protein export []. Homologs of secY are found in archaebacteria []. SecY is also encoded in the chloroplast genome of some algae [] where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0015031 protein transport, 0016020 membrane; PDB: 3J01_A 2ZJS_Y 2ZQP_Y 2WWA_A 2WW9_A 2YXR_A 1RHZ_A 3KCR_A 3DKN_A 2YXQ_A ....
Probab=23.57 E-value=2.4e+02 Score=21.03 Aligned_cols=57 Identities=28% Similarity=0.177 Sum_probs=39.7
Q ss_pred cHHHHHHHHHHH-------hhhhhcccccCC-----------CCchhhhhhhHHHHHHHHHHhhhhhhhccccCC
Q 035248 10 PREKLLEKQKHF-------QSIHKHTYLKGP-----------MDKITSVAIPIALAASSLYLIGRGIYNMSHGIG 66 (69)
Q Consensus 10 PRekl~e~Q~yf-------Q~i~khtyLKG~-----------~DkItSvaIPlalaassl~ligRGiyNMShGig 66 (69)
-|+|+-..|+|+ |++---.+++.. .+-+..+.+-+.|.+.|++++-=+==|-.+|+|
T Consensus 35 ~~~~~~~~tr~ltl~~a~iqa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~L~~G~~i~~wL~e~it~~GiG 109 (346)
T PF00344_consen 35 GRKKLNRYTRYLTLILAVIQAIGIVLSLGYYGSVSPLILSSGSGFINYLLIVLQLVAGSMILIWLSELITKYGIG 109 (346)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSSSTTC-TTSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSS
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 477888888874 444322122211 245667889999999999998877777778888
No 77
>PRK09204 secY preprotein translocase subunit SecY; Reviewed
Probab=23.20 E-value=1.9e+02 Score=22.61 Aligned_cols=58 Identities=26% Similarity=0.293 Sum_probs=37.1
Q ss_pred CcHHHHHHHHHHH-------hhhhhcccccCCCC---ch-------hhhhhhHHHHHHHHHHhhhhhhhccccCC
Q 035248 9 RPREKLLEKQKHF-------QSIHKHTYLKGPMD---KI-------TSVAIPIALAASSLYLIGRGIYNMSHGIG 66 (69)
Q Consensus 9 ~PRekl~e~Q~yf-------Q~i~khtyLKG~~D---kI-------tSvaIPlalaassl~ligRGiyNMShGig 66 (69)
.-|+|+-+.|||+ |++---.++.+.++ .+ .-+.+-+.|.+.|++++-=|=-+..+|||
T Consensus 106 ~gr~k~~~~tr~ltl~~a~iQs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~L~~Gs~i~~wL~e~It~~GiG 180 (426)
T PRK09204 106 AGRRKINQYTRYLTVVLAFVQSIGIAAGLNSMSGGGGLVPIPPGFFFYLTIVITLTAGTMFLMWLGEQITERGIG 180 (426)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCccccccCCccHHHHHHHHHHHHHHHHHHHHHHHHHhccCcc
Confidence 4578888888874 44432222343221 11 34566778999999998877777778887
No 78
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=22.91 E-value=75 Score=16.76 Aligned_cols=16 Identities=38% Similarity=0.609 Sum_probs=12.2
Q ss_pred hhhHHHHHHHHHHhhh
Q 035248 41 AIPIALAASSLYLIGR 56 (69)
Q Consensus 41 aIPlalaassl~ligR 56 (69)
--|-.+|++++|+-.+
T Consensus 42 ~~~~~ia~a~l~lA~k 57 (88)
T cd00043 42 RSPSLVAAAALYLAAK 57 (88)
T ss_pred CChHHHHHHHHHHHHH
Confidence 3477888888888766
No 79
>KOG4238 consensus Bifunctional ATP sulfurylase/adenosine 5'-phosphosulfate kinase [Nucleotide transport and metabolism]
Probab=22.28 E-value=30 Score=29.45 Aligned_cols=40 Identities=30% Similarity=0.570 Sum_probs=30.8
Q ss_pred cHHHHHHHHHHHhhhhhcccccCC--CCchhhhhhhHHHHHH
Q 035248 10 PREKLLEKQKHFQSIHKHTYLKGP--MDKITSVAIPIALAAS 49 (69)
Q Consensus 10 PRekl~e~Q~yfQ~i~khtyLKG~--~DkItSvaIPlalaas 49 (69)
|-.-..+..+|.|++|=-+-|.|. .|-+++.+||+.|.+|
T Consensus 275 pl~gfmrereylq~mhf~~lld~khaf~g~in~sipivl~~s 316 (627)
T KOG4238|consen 275 PLKGFMREREYLQVMHFDTLLDGKHAFDGVINMSIPIVLPVS 316 (627)
T ss_pred cchhHHHHHHHHHHhhhhhhhcccccccccccccccEEEecc
Confidence 344456677899999987777775 7888999999877655
No 80
>PRK13240 pbsY photosystem II protein Y; Reviewed
Probab=22.11 E-value=89 Score=18.06 Aligned_cols=20 Identities=35% Similarity=0.564 Sum_probs=13.6
Q ss_pred hhhhhhhHHHHHH-HHHHhhh
Q 035248 37 ITSVAIPIALAAS-SLYLIGR 56 (69)
Q Consensus 37 ItSvaIPlalaas-sl~ligR 56 (69)
+-=|..|+.+|++ ++|-|||
T Consensus 5 lliVl~Pil~A~~Wa~fNIg~ 25 (40)
T PRK13240 5 LLIVLAPILAAAGWAVFNIGK 25 (40)
T ss_pred HHHHHHHHHHHHHHHHHHhhH
Confidence 3447788888776 5677765
No 81
>PRK05443 polyphosphate kinase; Provisional
Probab=21.81 E-value=1.4e+02 Score=25.36 Aligned_cols=60 Identities=30% Similarity=0.346 Sum_probs=41.2
Q ss_pred CCCCCcHHHHHHHH-HHHhhhhh----cccccCCCCchhhhhhhHHH-----HHHHHHHhhhhhhhccccCC
Q 035248 5 EVPFRPREKLLEKQ-KHFQSIHK----HTYLKGPMDKITSVAIPIAL-----AASSLYLIGRGIYNMSHGIG 66 (69)
Q Consensus 5 e~PF~PRekl~e~Q-~yfQ~i~k----htyLKG~~DkItSvaIPlal-----aassl~ligRGiyNMShGig 66 (69)
-+||.+|+++++.= +-.++.++ ++++|=++ ++.=.|=-|| +++-+=||.|||--+.-||-
T Consensus 505 ~sP~~~~~~l~~~i~~ei~~Ak~G~~a~I~ik~n~--l~d~~ii~aL~~As~~GV~V~liVRGiC~l~pgip 574 (691)
T PRK05443 505 VSPFTLRERLLELIDREIANARAGKPARIIAKMNS--LVDPQIIDALYEASQAGVKIDLIVRGICCLRPGVP 574 (691)
T ss_pred ecCccHHHHHHHHHHHHHHHHhcCCCCEEEEEcCC--CCCHHHHHHHHHHHHCCCeEEEEEecccccCCCCC
Confidence 36999999998743 23444444 79999887 5555554444 34445689999988888853
No 82
>TIGR03622 urea_t_UrtB_arc urea ABC transporter, permease protein UrtB. Members of this protein family are ABC transporter permease subunits restricted to the Archaea. Several lines of evidence suggest this protein is functionally analogous, as well as homologous, to the UrtB subunit of the Corynebacterium glutamicum urea transporter. All members of the operon show sequence similarity to urea transport subunits, the gene is located near the urease structural subunits in two of three species, and partial phylogenetic profiling identifies this permease subunit as closely matching the profile of urea utilization.
Probab=21.79 E-value=60 Score=23.15 Aligned_cols=24 Identities=42% Similarity=0.492 Sum_probs=19.3
Q ss_pred hhhHHHHHHHHHHhh--hhhhhcccc
Q 035248 41 AIPIALAASSLYLIG--RGIYNMSHG 64 (69)
Q Consensus 41 aIPlalaassl~lig--RGiyNMShG 64 (69)
...+++.|.++-++. -|+-|+|||
T Consensus 11 ~~~~~llAlg~~lv~g~~G~inla~g 36 (283)
T TIGR03622 11 FAFIVLAAVGLAVIFGMMGVINLAHG 36 (283)
T ss_pred HHHHHHHHHHHHHHHHHhCCeeHHHH
Confidence 457888888888875 389999997
No 83
>PF11589 DUF3244: Domain of unknown function (DUF3244); InterPro: IPR021638 This family of proteins with unknown function appear to be restricted to Bacteroidetes. The protein may have an immunoglobulin-like beta-sandwich fold however this cannot be confirmed. ; PDB: 3D33_B 3SD2_A.
Probab=21.78 E-value=22 Score=22.11 Aligned_cols=22 Identities=36% Similarity=0.428 Sum_probs=5.7
Q ss_pred HhhhhhcccccCCCCchhhhhh
Q 035248 21 FQSIHKHTYLKGPMDKITSVAI 42 (69)
Q Consensus 21 fQ~i~khtyLKG~~DkItSvaI 42 (69)
||..+|++.|||..|.-...+|
T Consensus 4 ~~~~~r~I~l~g~~~~~~~RSi 25 (106)
T PF11589_consen 4 MQSMRRPIPLKGKWDDKTHRSI 25 (106)
T ss_dssp -----EEE--EEE---------
T ss_pred cceeceeEEecceeccCCCccc
Confidence 6788889999999833344444
No 84
>CHL00196 psbY photosystem II protein Y; Provisional
Probab=21.55 E-value=95 Score=17.73 Aligned_cols=20 Identities=45% Similarity=0.717 Sum_probs=13.7
Q ss_pred hhhhhhhHHHHHH-HHHHhhh
Q 035248 37 ITSVAIPIALAAS-SLYLIGR 56 (69)
Q Consensus 37 ItSvaIPlalaas-sl~ligR 56 (69)
+.=|..|+.+|++ ++|=|||
T Consensus 5 lliVl~Pil~A~~Wa~fNIg~ 25 (36)
T CHL00196 5 LLVIAAPVLAAASWALFNIGR 25 (36)
T ss_pred HHHHHHHHHHHHHHHHHHhHH
Confidence 3457789888776 5676665
No 85
>PF04781 DUF627: Protein of unknown function (DUF627); InterPro: IPR006866 This domain represents the N-terminal region of several plant proteins of unknown function.
Probab=21.45 E-value=27 Score=23.59 Aligned_cols=32 Identities=22% Similarity=0.283 Sum_probs=22.6
Q ss_pred hcccccCCCCchhhhhhhHHHHHHHHHHhhhh
Q 035248 26 KHTYLKGPMDKITSVAIPIALAASSLYLIGRG 57 (69)
Q Consensus 26 khtyLKG~~DkItSvaIPlalaassl~ligRG 57 (69)
|.+||+|.-|--..-..--..+|.|||.+++-
T Consensus 56 k~~yLl~sve~~s~a~~Lsp~~A~~L~~la~~ 87 (111)
T PF04781_consen 56 KFRYLLGSVECFSRAVELSPDSAHSLFELASQ 87 (111)
T ss_pred HHHHHHHhHHHHHHHhccChhHHHHHHHHHHH
Confidence 68899998766544444445668999988864
No 86
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=21.34 E-value=50 Score=29.00 Aligned_cols=23 Identities=22% Similarity=0.405 Sum_probs=18.4
Q ss_pred CchhhhhhhHHHHHHHHHHhhhh
Q 035248 35 DKITSVAIPIALAASSLYLIGRG 57 (69)
Q Consensus 35 DkItSvaIPlalaassl~ligRG 57 (69)
--|..+|||++|.++-.+|-.-|
T Consensus 356 tlI~~iaiPlsLlgtf~~m~~~G 378 (1009)
T COG0841 356 TLIPALAVPVSLLGTFAVMYAFG 378 (1009)
T ss_pred eEEeeeechHHHHHHHHHHHHhC
Confidence 46889999999999877665554
No 87
>TIGR00190 thiC thiamine biosynthesis protein ThiC. The thiC ortholog is designated thiA in Bacillus subtilis.
Probab=21.24 E-value=1.6e+02 Score=24.36 Aligned_cols=42 Identities=29% Similarity=0.397 Sum_probs=29.8
Q ss_pred CCcHHHHHHHHHHHhhhh--hcccccCC--------CCchhhhhhhHHHHHHH
Q 035248 8 FRPREKLLEKQKHFQSIH--KHTYLKGP--------MDKITSVAIPIALAASS 50 (69)
Q Consensus 8 F~PRekl~e~Q~yfQ~i~--khtyLKG~--------~DkItSvaIPlalaass 50 (69)
-.|=+++-..-+.-+.+- ..-|+-|| ||-||| ||-.|+||++
T Consensus 266 HvPl~~I~~nv~lqK~lc~~APfYvLGPLvTDiApGYDHIts-AIGgAiAa~~ 317 (423)
T TIGR00190 266 HVPLDQIEANVRLQKELCDEAPFYVLGPLVTDIAPGYDHITS-AIGAAIAGWA 317 (423)
T ss_pred CCcHHHHHHHHHHHHHhhCCCCeeecCCcccccCCCchHHHH-HHHHHHHHHc
Confidence 456666655555555554 47898886 899998 8999988864
No 88
>cd02749 Macro Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes.
Probab=21.10 E-value=18 Score=22.46 Aligned_cols=10 Identities=40% Similarity=0.753 Sum_probs=8.6
Q ss_pred CchhhhhhhH
Q 035248 35 DKITSVAIPI 44 (69)
Q Consensus 35 DkItSvaIPl 44 (69)
+.+.|||||+
T Consensus 110 ~~~~sIa~P~ 119 (147)
T cd02749 110 KGIKSIAFPL 119 (147)
T ss_pred cCCCEEEECC
Confidence 4799999996
No 89
>PRK09588 hypothetical protein; Reviewed
Probab=21.10 E-value=9.2 Score=29.87 Aligned_cols=29 Identities=28% Similarity=0.502 Sum_probs=25.4
Q ss_pred hhhhHHHHHHHHHHhhhh----hhhccccCCCC
Q 035248 40 VAIPIALAASSLYLIGRG----IYNMSHGIGKK 68 (69)
Q Consensus 40 vaIPlalaassl~ligRG----iyNMShGigkK 68 (69)
|-||......|.-+.|+| .|.-|||=||+
T Consensus 267 viIPGSMg~~Syi~~G~g~~~s~~S~~HGAGR~ 299 (376)
T PRK09588 267 VVIPGSRGDYSYLVKPVASEESLFSLAHGAGRK 299 (376)
T ss_pred eEeccCCCCceEEEEccCChhhhcCCCCcccch
Confidence 789999999998888888 78899999985
No 90
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=21.08 E-value=20 Score=19.99 Aligned_cols=12 Identities=42% Similarity=0.537 Sum_probs=8.8
Q ss_pred HHhhhhhhhccc
Q 035248 52 YLIGRGIYNMSH 63 (69)
Q Consensus 52 ~ligRGiyNMSh 63 (69)
-.+|+|++|++-
T Consensus 45 ~~vg~G~~~~~s 56 (77)
T smart00359 45 EPLGIGLANMSS 56 (77)
T ss_pred CEEEEEEEeCCH
Confidence 456888888864
No 91
>cd02900 Macro_Appr_pase Macro domain, Appr-1"-pase family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. The yeast protein Ymx7 and related proteins in this family contain a stand-alone macro domain and may be specific phosphatases catalyzing the conversion of ADP-ribose-1"-monophosphate (Appr-1"-p) to ADP-ribose. Appr-1"-p is an intermediate in a metabolic pathway involved in pre-tRNA splicing.
Probab=20.17 E-value=25 Score=24.82 Aligned_cols=19 Identities=21% Similarity=0.517 Sum_probs=14.2
Q ss_pred CchhhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248 35 DKITSVAIPIALAASSLYLIGRGIYNMS 62 (69)
Q Consensus 35 DkItSvaIPlalaassl~ligRGiyNMS 62 (69)
..|.|||+|. ||-|+|.+.
T Consensus 152 ~~i~sIa~P~---------igTGvgg~p 170 (186)
T cd02900 152 QEINTLVLPG---------LGTGYGGVP 170 (186)
T ss_pred CCCCEEEECc---------hhcCCCCCC
Confidence 6799999997 566666553
No 92
>PF13170 DUF4003: Protein of unknown function (DUF4003)
Probab=20.17 E-value=1.1e+02 Score=22.86 Aligned_cols=34 Identities=18% Similarity=0.274 Sum_probs=27.7
Q ss_pred CCcHHHHHHHHHHHhhhh-hcccccCCCCchhhhh
Q 035248 8 FRPREKLLEKQKHFQSIH-KHTYLKGPMDKITSVA 41 (69)
Q Consensus 8 F~PRekl~e~Q~yfQ~i~-khtyLKG~~DkItSva 41 (69)
=.+++.+-+...-|+.++ +|-+|-|+.|....|-
T Consensus 113 ~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~l 147 (297)
T PF13170_consen 113 EDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAAL 147 (297)
T ss_pred ccHHHHHHHHHHHHHHHHHhCccccCccchhHHHH
Confidence 346788888899999999 5999999999766553
No 93
>PF10565 NMDAR2_C: N-methyl D-aspartate receptor 2B3 C-terminus; InterPro: IPR018884 This domain is found at the C terminus of many NMDA-receptor proteins, many of which are also associated with IPR001320 from INTERPRO and IPR001828 from INTERPRO. This region is predicted to be a large extra-cellular domain of the NMDA receptor proteins, being highly hydrophilic, and is thought to be integrally involved in the function of the receptor. The region also carries a number of potential N-glycosylation sites []. ; PDB: 3NFL_H.
Probab=20.14 E-value=34 Score=29.69 Aligned_cols=15 Identities=53% Similarity=1.074 Sum_probs=0.0
Q ss_pred HHHhhhhhhhccccC
Q 035248 51 LYLIGRGIYNMSHGI 65 (69)
Q Consensus 51 l~ligRGiyNMShGi 65 (69)
+|-|.||||...||+
T Consensus 22 lf~iSRGIySCihGV 36 (681)
T PF10565_consen 22 LFSISRGIYSCIHGV 36 (681)
T ss_dssp ---------------
T ss_pred EEEeecccccccccc
Confidence 678999999999997
No 94
>PF00689 Cation_ATPase_C: Cation transporting ATPase, C-terminus; InterPro: IPR006068 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved C-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3A3Y_A 2ZXE_A 2XZB_A 3B9B_A 3N5K_A 3FPS_A 3B9R_A 1WPG_C 2AGV_A 2O9J_A ....
Probab=20.11 E-value=58 Score=20.82 Aligned_cols=45 Identities=22% Similarity=0.276 Sum_probs=24.0
Q ss_pred CCCCCCCcHHHHHHHHHHHhhhhhcccccCCCCchhhhhhhHHHHHHHHHHhhhhhhhc
Q 035248 3 ETEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNM 61 (69)
Q Consensus 3 ~~e~PF~PRekl~e~Q~yfQ~i~khtyLKG~~DkItSvaIPlalaassl~ligRGiyNM 61 (69)
|.+||=.|+|.|+.+.-..+ |.-.++..++++...|..+...++.
T Consensus 34 m~r~Pr~~~~~l~~~~~~~~--------------i~~~g~~~~~~~~~~f~~~~~~~~~ 78 (182)
T PF00689_consen 34 MKRPPRDPNEPLINKRLLRR--------------ILIQGLIMAAACFFAFFLGLYIFGW 78 (182)
T ss_dssp GGS---TTTS-SSSHHHHHH--------------HCCHHHHHHHHHHHHHHHHHHSTCS
T ss_pred hhccccccchhhccHHhHhH--------------HHHHHHHHHHHHHHHHHHHhhcccc
Confidence 56677778887776654332 2334566666666666666654433
Done!