Query 024416
Match_columns 268
No_of_seqs 89 out of 91
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 04:26:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024416.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024416hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4173 Alpha-SNAP protein [In 98.3 7.8E-08 1.7E-12 87.4 -1.0 69 75-143 79-154 (253)
2 PF13894 zf-C2H2_4: C2H2-type 96.8 0.0005 1.1E-08 39.7 0.9 24 102-125 1-24 (24)
3 PF00096 zf-C2H2: Zinc finger, 96.8 0.00048 1E-08 40.6 0.6 23 102-125 1-23 (23)
4 PF04959 ARS2: Arsenite-resist 95.4 0.0043 9.2E-08 56.5 -0.1 34 98-131 74-107 (214)
5 PF12171 zf-C2H2_jaz: Zinc-fin 94.7 0.016 3.4E-07 35.8 1.1 23 101-123 1-23 (27)
6 smart00355 ZnF_C2H2 zinc finge 94.5 0.021 4.5E-07 32.8 1.4 24 102-126 1-24 (26)
7 PF13912 zf-C2H2_6: C2H2-type 94.2 0.022 4.9E-07 34.6 1.1 24 102-125 2-25 (27)
8 PF12874 zf-met: Zinc-finger o 93.0 0.046 1E-06 32.6 0.9 22 102-123 1-22 (25)
9 PHA00616 hypothetical protein 92.3 0.049 1.1E-06 38.6 0.5 26 102-127 2-27 (44)
10 PHA00733 hypothetical protein 92.1 0.17 3.6E-06 42.4 3.5 51 75-127 73-125 (128)
11 PF12756 zf-C2H2_2: C2H2 type 90.7 0.12 2.7E-06 38.5 1.2 28 101-128 50-78 (100)
12 PHA02768 hypothetical protein; 89.2 0.21 4.6E-06 36.9 1.4 24 102-125 6-29 (55)
13 PHA00732 hypothetical protein 82.5 0.82 1.8E-05 35.6 1.7 23 103-125 3-25 (79)
14 PF05605 zf-Di19: Drought indu 81.7 0.98 2.1E-05 32.0 1.7 27 101-128 2-28 (54)
15 smart00451 ZnF_U1 U1-like zinc 80.8 0.97 2.1E-05 28.6 1.3 24 101-124 3-26 (35)
16 PF15018 InaF-motif: TRP-inter 78.5 2.2 4.7E-05 29.6 2.5 22 221-242 11-32 (38)
17 KOG2482 Predicted C2H2-type Zn 78.4 1.3 2.9E-05 43.7 2.1 35 98-132 192-226 (423)
18 PF12273 RCR: Chitin synthesis 78.2 1.2 2.6E-05 36.8 1.4 16 237-252 16-31 (130)
19 PHA00732 hypothetical protein 76.7 2.7 5.8E-05 32.7 2.9 40 85-128 9-50 (79)
20 PF13465 zf-H2C2_2: Zinc-finge 76.6 1.2 2.6E-05 27.4 0.8 20 94-113 7-26 (26)
21 PF10537 WAC_Acf1_DNA_bd: ATP- 73.4 2.2 4.8E-05 34.8 1.8 29 82-110 8-39 (102)
22 PF12756 zf-C2H2_2: C2H2 type 73.2 1.1 2.4E-05 33.3 0.0 28 103-130 1-28 (100)
23 KOG2462 C2H2-type Zn-finger pr 72.5 1.9 4E-05 41.2 1.3 49 73-123 213-265 (279)
24 PF09237 GAGA: GAGA factor; I 72.0 1.7 3.7E-05 32.2 0.7 31 98-128 21-51 (54)
25 PF09777 OSTMP1: Osteopetrosis 71.0 6.8 0.00015 36.1 4.6 28 222-249 191-218 (237)
26 KOG1074 Transcriptional repres 69.7 1.5 3.3E-05 47.3 0.1 53 74-128 352-408 (958)
27 PF13913 zf-C2HC_2: zinc-finge 69.6 2.6 5.6E-05 26.0 1.1 20 102-122 3-22 (25)
28 PF07874 DUF1660: Prophage pro 64.5 1.8 4E-05 33.0 -0.4 39 77-122 4-64 (64)
29 KOG2462 C2H2-type Zn-finger pr 63.8 4.8 0.0001 38.5 2.1 57 85-147 169-227 (279)
30 COG5236 Uncharacterized conser 61.7 3.1 6.7E-05 41.4 0.5 49 102-150 221-292 (493)
31 PHA00733 hypothetical protein 59.0 6.3 0.00014 33.0 1.8 25 99-123 71-95 (128)
32 PF15145 DUF4577: Domain of un 57.4 16 0.00034 31.2 3.9 46 217-263 58-104 (128)
33 PF13908 Shisa: Wnt and FGF in 56.6 16 0.00036 31.4 4.0 11 200-210 48-58 (179)
34 PF02699 YajC: Preprotein tran 56.1 5.8 0.00013 30.8 1.1 36 227-262 5-40 (82)
35 TIGR00739 yajC preprotein tran 53.1 5.5 0.00012 31.3 0.5 35 228-262 7-41 (84)
36 PF05545 FixQ: Cbb3-type cytoc 53.0 14 0.00031 25.8 2.5 28 227-254 12-40 (49)
37 KOG3623 Homeobox transcription 51.9 7 0.00015 42.2 1.2 46 77-124 242-304 (1007)
38 PF13909 zf-H2C2_5: C2H2-type 51.8 6.2 0.00013 23.2 0.5 24 102-126 1-24 (24)
39 PRK00464 nrdR transcriptional 51.1 6.8 0.00015 34.2 0.8 43 76-119 1-46 (154)
40 PF00672 HAMP: HAMP domain; I 51.0 11 0.00023 26.6 1.7 36 225-260 4-39 (70)
41 PRK05585 yajC preprotein trans 50.1 7.3 0.00016 31.9 0.8 35 229-263 23-57 (106)
42 PF11027 DUF2615: Protein of u 48.7 55 0.0012 27.1 5.7 53 186-239 17-72 (103)
43 COG1327 Predicted transcriptio 48.4 9.3 0.0002 33.8 1.2 40 76-115 1-42 (156)
44 PF02892 zf-BED: BED zinc fing 47.5 11 0.00025 25.1 1.3 28 98-125 13-44 (45)
45 KOG3576 Ovo and related transc 47.1 7.9 0.00017 36.2 0.6 48 74-123 116-167 (267)
46 KOG4628 Predicted E3 ubiquitin 46.9 11 0.00024 37.1 1.5 51 217-267 164-216 (348)
47 COG4736 CcoQ Cbb3-type cytochr 46.8 19 0.00041 27.2 2.5 27 225-252 10-37 (60)
48 PF04780 DUF629: Protein of un 44.5 11 0.00024 38.4 1.2 33 99-131 55-87 (466)
49 KOG3408 U1-like Zn-finger-cont 42.7 11 0.00024 32.3 0.8 27 98-124 54-80 (129)
50 TIGR01478 STEVOR variant surfa 42.1 20 0.00044 34.6 2.5 86 90-178 82-179 (295)
51 PHA02768 hypothetical protein; 41.8 12 0.00027 27.7 0.8 36 77-114 7-44 (55)
52 PTZ00370 STEVOR; Provisional 41.6 21 0.00045 34.5 2.5 33 146-178 147-179 (296)
53 PRK05886 yajC preprotein trans 41.4 12 0.00027 31.0 0.9 19 229-247 9-27 (109)
54 PF03597 CcoS: Cytochrome oxid 41.2 36 0.00077 24.1 3.0 27 221-247 2-28 (45)
55 COG1862 YajC Preprotein transl 40.6 12 0.00026 30.5 0.7 30 226-255 11-40 (97)
56 PLN03086 PRLI-interacting fact 40.5 19 0.0004 37.6 2.2 43 77-126 435-477 (567)
57 PF06024 DUF912: Nucleopolyhed 40.2 28 0.00061 28.0 2.8 19 229-247 70-89 (101)
58 smart00614 ZnF_BED BED zinc fi 40.0 14 0.0003 25.7 0.8 28 100-127 17-49 (50)
59 PF12273 RCR: Chitin synthesis 40.0 16 0.00034 30.2 1.3 24 230-253 6-29 (130)
60 PF12669 P12: Virus attachment 39.3 14 0.00031 27.2 0.9 18 229-246 5-23 (58)
61 KOG3993 Transcription factor ( 38.6 10 0.00022 38.6 -0.1 29 100-128 355-383 (500)
62 cd03737 SOCS_SOCS3 SOCS (suppr 38.0 41 0.00089 23.5 2.9 32 164-195 3-36 (42)
63 smart00734 ZnF_Rad18 Rad18-lik 37.6 21 0.00045 22.3 1.2 21 103-124 3-23 (26)
64 PHA02819 hypothetical protein; 37.0 66 0.0014 25.2 4.1 23 221-243 45-67 (71)
65 PF05443 ROS_MUCR: ROS/MUCR tr 36.6 15 0.00033 31.3 0.7 28 96-126 67-94 (132)
66 PHA02650 hypothetical protein; 36.5 81 0.0017 25.3 4.7 22 221-242 48-69 (81)
67 PF12575 DUF3753: Protein of u 36.3 77 0.0017 24.8 4.5 15 229-243 55-69 (72)
68 PF02009 Rifin_STEVOR: Rifin/s 36.3 26 0.00056 33.7 2.3 8 135-142 95-102 (299)
69 PHA03054 IMV membrane protein; 36.0 84 0.0018 24.7 4.6 23 221-243 47-69 (72)
70 KOG1074 Transcriptional repres 35.7 23 0.0005 38.8 2.0 48 86-133 888-939 (958)
71 TIGR02736 cbb3_Q_epsi cytochro 35.4 27 0.00059 26.2 1.8 32 229-261 7-39 (56)
72 PF04024 PspC: PspC domain; I 34.7 43 0.00094 24.8 2.8 28 219-247 31-58 (61)
73 TIGR00244 transcriptional regu 34.6 20 0.00043 31.4 1.1 43 76-118 1-45 (147)
74 TIGR00847 ccoS cytochrome oxid 34.3 58 0.0013 23.8 3.3 27 221-247 3-29 (51)
75 KOG3608 Zn finger proteins [Ge 33.5 12 0.00025 37.6 -0.5 41 84-124 220-260 (467)
76 PF12907 zf-met2: Zinc-binding 32.7 22 0.00048 24.7 0.9 26 102-127 2-30 (40)
77 PHA02844 putative transmembran 32.6 82 0.0018 24.9 4.1 20 224-243 50-69 (75)
78 PRK06531 yajC preprotein trans 32.4 18 0.00038 30.3 0.4 32 230-262 9-40 (113)
79 PF04995 CcmD: Heme exporter p 31.6 21 0.00045 24.8 0.6 39 224-263 6-44 (46)
80 PF06796 NapE: Periplasmic nit 31.4 55 0.0012 24.4 2.8 19 228-246 31-49 (56)
81 PHA02291 hypothetical protein 30.1 55 0.0012 27.9 3.0 30 218-247 4-33 (132)
82 PHA02975 hypothetical protein; 29.7 1E+02 0.0022 24.0 4.1 20 224-243 46-65 (69)
83 PHA03099 epidermal growth fact 27.9 77 0.0017 27.6 3.5 39 217-255 94-136 (139)
84 KOG3576 Ovo and related transc 27.8 24 0.00051 33.2 0.5 42 100-147 116-157 (267)
85 KOG2754 Oligosaccharyltransfer 27.3 35 0.00076 34.4 1.6 29 222-250 406-434 (443)
86 CHL00066 psbH photosystem II p 26.9 87 0.0019 24.6 3.4 35 208-242 23-58 (73)
87 PLN00055 photosystem II reacti 26.8 91 0.002 24.5 3.4 36 207-242 22-58 (73)
88 PF15102 TMEM154: TMEM154 prot 26.5 30 0.00065 30.3 0.8 27 221-247 58-84 (146)
89 PF09538 FYDLN_acid: Protein o 26.3 25 0.00055 29.0 0.3 14 100-113 8-21 (108)
90 PRK09678 DNA-binding transcrip 26.0 29 0.00063 26.9 0.6 40 76-115 2-43 (72)
91 PRK02624 psbH photosystem II r 25.9 87 0.0019 24.1 3.1 36 207-242 10-46 (64)
92 PRK12387 formate hydrogenlyase 25.8 40 0.00088 29.1 1.6 24 98-121 111-134 (180)
93 TIGR02972 TMAO_torE trimethyla 25.8 82 0.0018 22.8 2.8 19 228-246 23-41 (47)
94 TIGR02978 phageshock_pspC phag 25.7 65 0.0014 27.1 2.7 27 221-247 33-60 (121)
95 PHA02662 ORF131 putative membr 25.7 1.6E+02 0.0036 27.6 5.5 29 210-238 178-206 (226)
96 TIGR02973 nitrate_rd_NapE peri 25.3 87 0.0019 22.2 2.8 18 228-245 18-35 (42)
97 PF04246 RseC_MucC: Positive r 25.1 65 0.0014 26.5 2.6 22 228-249 101-122 (135)
98 PF14004 DUF4227: Protein of u 24.9 78 0.0017 24.5 2.8 20 224-243 8-27 (71)
99 PF00957 Synaptobrevin: Synapt 24.7 86 0.0019 23.9 3.0 13 230-242 73-85 (89)
100 COG3087 FtsN Cell division pro 24.4 1.6E+02 0.0034 28.3 5.2 57 210-268 5-61 (264)
101 PF01102 Glycophorin_A: Glycop 24.3 75 0.0016 26.9 2.8 18 223-240 71-88 (122)
102 PF05337 CSF-1: Macrophage col 24.2 26 0.00055 33.8 0.0 31 219-249 225-255 (285)
103 COG5189 SFP1 Putative transcri 23.8 35 0.00077 33.9 0.9 52 74-125 348-422 (423)
104 PHA02849 putative transmembran 23.4 90 0.002 25.0 2.9 18 226-243 20-37 (82)
105 cd03745 SOCS_WSB2_SWIP2 SOCS ( 23.1 81 0.0018 21.7 2.3 31 165-195 4-37 (39)
106 TIGR00915 2A0602 The (Largely 22.7 98 0.0021 34.1 4.0 20 223-242 1009-1028(1044)
107 smart00834 CxxC_CXXC_SSSS Puta 21.4 33 0.00071 22.2 0.1 16 99-114 3-18 (41)
108 PF00558 Vpu: Vpu protein; In 21.4 83 0.0018 25.1 2.4 28 223-250 8-35 (81)
109 PHA03164 hypothetical protein; 21.2 1.2E+02 0.0025 24.5 3.1 30 218-247 56-86 (88)
110 PF00737 PsbH: Photosystem II 21.2 1.4E+02 0.0029 22.2 3.3 34 208-241 8-42 (52)
111 KOG2231 Predicted E3 ubiquitin 21.2 51 0.0011 35.2 1.5 71 55-128 52-141 (669)
112 PHA02657 hypothetical protein; 21.1 1E+02 0.0022 25.2 2.9 19 225-243 29-47 (95)
113 cd03738 SOCS_SOCS4 SOCS (suppr 20.8 1.3E+02 0.0029 22.4 3.2 32 166-197 5-39 (56)
114 PF05702 Herpes_UL49_5: Herpes 20.7 1.1E+02 0.0025 25.2 3.1 69 174-249 23-94 (98)
115 PF06422 PDR_CDR: CDR ABC tran 20.5 1.6E+02 0.0034 23.6 3.9 30 216-247 47-76 (103)
116 PF11395 DUF2873: Protein of u 20.3 1.6E+02 0.0034 20.7 3.3 15 222-236 9-23 (43)
117 cd03746 SOCS_WSB1_SWIP1 SOCS ( 20.1 59 0.0013 22.3 1.2 32 164-195 3-37 (40)
No 1
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.32 E-value=7.8e-08 Score=87.40 Aligned_cols=69 Identities=23% Similarity=0.575 Sum_probs=60.9
Q ss_pred CCCCCCCCCCccccchhhhhhhh-cCcccccccccccCCchhhHhhhhhccccccccCC--cc----Cchhhhccc
Q 024416 75 SSKCRLHPDNDMFRDQEQHKIHV-DINEWRCGYCKKSFRAEKFLDQHFDNRHNNLLNVS--HG----KCLADLCGA 143 (268)
Q Consensus 75 ~~~C~L~P~~D~F~~~E~~k~h~-~~h~wrC~~CgK~F~sE~~LDlHidnrH~~ll~~~--~~----~CLaD~Cd~ 143 (268)
...|+.--.-.+|-.-+.|+.|| ..|.+-|.+|+|.|||.+.||.||-|-|+++.+.. |+ .||+|+|..
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~ 154 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTE 154 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhh
Confidence 34588777778999999999999 88999999999999999999999999999987764 43 899999974
No 2
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.79 E-value=0.0005 Score=39.70 Aligned_cols=24 Identities=42% Similarity=0.848 Sum_probs=20.7
Q ss_pred cccccccccCCchhhHhhhhhccc
Q 024416 102 WRCGYCKKSFRAEKFLDQHFDNRH 125 (268)
Q Consensus 102 wrC~~CgK~F~sE~~LDlHidnrH 125 (268)
|+|.+|++.|++..-|..|+.+.|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 689999999999999999999876
No 3
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.76 E-value=0.00048 Score=40.58 Aligned_cols=23 Identities=35% Similarity=0.833 Sum_probs=21.3
Q ss_pred cccccccccCCchhhHhhhhhccc
Q 024416 102 WRCGYCKKSFRAEKFLDQHFDNRH 125 (268)
Q Consensus 102 wrC~~CgK~F~sE~~LDlHidnrH 125 (268)
++|..|+|.|++...|..||.. |
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~-H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR-H 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH-H
T ss_pred CCCCCCCCccCCHHHHHHHHhH-C
Confidence 5899999999999999999987 5
No 4
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=95.35 E-value=0.0043 Score=56.49 Aligned_cols=34 Identities=32% Similarity=0.787 Sum_probs=27.8
Q ss_pred cCcccccccccccCCchhhHhhhhhccccccccC
Q 024416 98 DINEWRCGYCKKSFRAEKFLDQHFDNRHNNLLNV 131 (268)
Q Consensus 98 ~~h~wrC~~CgK~F~sE~~LDlHidnrH~~ll~~ 131 (268)
+.+.|+|..|+|-|..++|+-+||.|+|.+.|..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ve~ 107 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEKVEE 107 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHHHHH
Confidence 3467999999999999999999999999998763
No 5
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.66 E-value=0.016 Score=35.82 Aligned_cols=23 Identities=35% Similarity=0.755 Sum_probs=20.5
Q ss_pred ccccccccccCCchhhHhhhhhc
Q 024416 101 EWRCGYCKKSFRAEKFLDQHFDN 123 (268)
Q Consensus 101 ~wrC~~CgK~F~sE~~LDlHidn 123 (268)
++.|..|+|.|.+|..++.|+..
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCCcccCCCCcCCHHHHHHHHcc
Confidence 47899999999999999999964
No 6
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.55 E-value=0.021 Score=32.85 Aligned_cols=24 Identities=33% Similarity=0.797 Sum_probs=21.2
Q ss_pred cccccccccCCchhhHhhhhhcccc
Q 024416 102 WRCGYCKKSFRAEKFLDQHFDNRHN 126 (268)
Q Consensus 102 wrC~~CgK~F~sE~~LDlHidnrH~ 126 (268)
++|..|+|.|.+...|..|+. .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhc
Confidence 479999999999999999998 554
No 7
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=94.21 E-value=0.022 Score=34.57 Aligned_cols=24 Identities=25% Similarity=0.541 Sum_probs=21.5
Q ss_pred cccccccccCCchhhHhhhhhccc
Q 024416 102 WRCGYCKKSFRAEKFLDQHFDNRH 125 (268)
Q Consensus 102 wrC~~CgK~F~sE~~LDlHidnrH 125 (268)
.+|..|++.|.++..|-.|+...|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 589999999999999999996554
No 8
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=92.99 E-value=0.046 Score=32.59 Aligned_cols=22 Identities=41% Similarity=0.831 Sum_probs=20.3
Q ss_pred cccccccccCCchhhHhhhhhc
Q 024416 102 WRCGYCKKSFRAEKFLDQHFDN 123 (268)
Q Consensus 102 wrC~~CgK~F~sE~~LDlHidn 123 (268)
|.|..|++.|.++..|..|+.-
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 7899999999999999999863
No 9
>PHA00616 hypothetical protein
Probab=92.28 E-value=0.049 Score=38.58 Aligned_cols=26 Identities=27% Similarity=0.517 Sum_probs=23.5
Q ss_pred cccccccccCCchhhHhhhhhccccc
Q 024416 102 WRCGYCKKSFRAEKFLDQHFDNRHNN 127 (268)
Q Consensus 102 wrC~~CgK~F~sE~~LDlHidnrH~~ 127 (268)
.+|+.|||.|.....|..|+-..|..
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 58999999999999999999777764
No 10
>PHA00733 hypothetical protein
Probab=92.15 E-value=0.17 Score=42.39 Aligned_cols=51 Identities=25% Similarity=0.325 Sum_probs=41.2
Q ss_pred CCCCCCCCCCccccchhhhhhhhc--CcccccccccccCCchhhHhhhhhccccc
Q 024416 75 SSKCRLHPDNDMFRDQEQHKIHVD--INEWRCGYCKKSFRAEKFLDQHFDNRHNN 127 (268)
Q Consensus 75 ~~~C~L~P~~D~F~~~E~~k~h~~--~h~wrC~~CgK~F~sE~~LDlHidnrH~~ 127 (268)
|-.|+.. .-.|......+.|.. .+.+.|..|+|.|.....|..|+...|+-
T Consensus 73 Py~C~~C--gk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 73 PYVCPLC--LMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred CccCCCC--CCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHHHhcCc
Confidence 4456543 246888888888885 56789999999999999999999999974
No 11
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.66 E-value=0.12 Score=38.54 Aligned_cols=28 Identities=36% Similarity=0.930 Sum_probs=23.2
Q ss_pred ccccccccccCCchhhHhhhhhcc-cccc
Q 024416 101 EWRCGYCKKSFRAEKFLDQHFDNR-HNNL 128 (268)
Q Consensus 101 ~wrC~~CgK~F~sE~~LDlHidnr-H~~l 128 (268)
.|+|.+|++.|.+..-|..||... |...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~ 78 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKR 78 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCc
Confidence 599999999999999999999975 5544
No 12
>PHA02768 hypothetical protein; Provisional
Probab=89.23 E-value=0.21 Score=36.90 Aligned_cols=24 Identities=17% Similarity=0.499 Sum_probs=21.8
Q ss_pred cccccccccCCchhhHhhhhhccc
Q 024416 102 WRCGYCKKSFRAEKFLDQHFDNRH 125 (268)
Q Consensus 102 wrC~~CgK~F~sE~~LDlHidnrH 125 (268)
++|.+|||.|.....|-.|+...+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC
Confidence 589999999999999999999855
No 13
>PHA00732 hypothetical protein
Probab=82.48 E-value=0.82 Score=35.55 Aligned_cols=23 Identities=26% Similarity=0.374 Sum_probs=11.7
Q ss_pred ccccccccCCchhhHhhhhhccc
Q 024416 103 RCGYCKKSFRAEKFLDQHFDNRH 125 (268)
Q Consensus 103 rC~~CgK~F~sE~~LDlHidnrH 125 (268)
+|..|||.|.+...|..|+...|
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~r~~H 25 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHARRNH 25 (79)
T ss_pred cCCCCCCccCCHHHHHHHhhccc
Confidence 35555555555555555554333
No 14
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=81.72 E-value=0.98 Score=32.03 Aligned_cols=27 Identities=30% Similarity=0.571 Sum_probs=23.0
Q ss_pred ccccccccccCCchhhHhhhhhcccccc
Q 024416 101 EWRCGYCKKSFRAEKFLDQHFDNRHNNL 128 (268)
Q Consensus 101 ~wrC~~CgK~F~sE~~LDlHidnrH~~l 128 (268)
.++|.|||| -.++.-|-.|+++.|..-
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSE 28 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCC
Confidence 578999999 566788999999999863
No 15
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=80.75 E-value=0.97 Score=28.58 Aligned_cols=24 Identities=21% Similarity=0.620 Sum_probs=21.2
Q ss_pred ccccccccccCCchhhHhhhhhcc
Q 024416 101 EWRCGYCKKSFRAEKFLDQHFDNR 124 (268)
Q Consensus 101 ~wrC~~CgK~F~sE~~LDlHidnr 124 (268)
.+.|..|++.|.++..+..|+..+
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 578999999999999999998654
No 16
>PF15018 InaF-motif: TRP-interacting helix
Probab=78.54 E-value=2.2 Score=29.55 Aligned_cols=22 Identities=32% Similarity=0.644 Sum_probs=17.9
Q ss_pred hHHHHHHHHHHHHHHHHHHhhh
Q 024416 221 VFYLSISILTLMLLPIFYLIVY 242 (268)
Q Consensus 221 ~~y~~~~~~~l~~l~lfY~~v~ 242 (268)
+.|+...-+..++|.+||+++|
T Consensus 11 ~~Yl~~VSl~Ai~LsiYY~f~W 32 (38)
T PF15018_consen 11 VAYLFSVSLAAIVLSIYYIFFW 32 (38)
T ss_pred HHHHHHHHHHHHHHHHHHheee
Confidence 4577777777788999999988
No 17
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=78.44 E-value=1.3 Score=43.67 Aligned_cols=35 Identities=29% Similarity=0.673 Sum_probs=29.1
Q ss_pred cCcccccccccccCCchhhHhhhhhccccccccCC
Q 024416 98 DINEWRCGYCKKSFRAEKFLDQHFDNRHNNLLNVS 132 (268)
Q Consensus 98 ~~h~wrC~~CgK~F~sE~~LDlHidnrH~~ll~~~ 132 (268)
.-+.++|+||.|.|+....|--||.++-.--||++
T Consensus 192 kL~r~~CLyCekifrdkntLkeHMrkK~HrrinPk 226 (423)
T KOG2482|consen 192 KLERLRCLYCEKIFRDKNTLKEHMRKKRHRRINPK 226 (423)
T ss_pred HHhhheeeeeccccCCcHHHHHHHHhccCcccCCC
Confidence 55899999999999999999999987654444554
No 18
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=78.22 E-value=1.2 Score=36.84 Aligned_cols=16 Identities=25% Similarity=0.441 Sum_probs=6.6
Q ss_pred HHHhhhheeccccccc
Q 024416 237 FYLIVYLYQREMRGGT 252 (268)
Q Consensus 237 fY~~v~~~~r~~~~~~ 252 (268)
|.++.+.-+|.+|+|.
T Consensus 16 ~~~~~~~~rRR~r~G~ 31 (130)
T PF12273_consen 16 LFLFYCHNRRRRRRGL 31 (130)
T ss_pred HHHHHHHHHHHhhcCC
Confidence 3333344444444433
No 19
>PHA00732 hypothetical protein
Probab=76.67 E-value=2.7 Score=32.70 Aligned_cols=40 Identities=28% Similarity=0.360 Sum_probs=30.6
Q ss_pred ccccchhhhhhhhc--CcccccccccccCCchhhHhhhhhcccccc
Q 024416 85 DMFRDQEQHKIHVD--INEWRCGYCKKSFRAEKFLDQHFDNRHNNL 128 (268)
Q Consensus 85 D~F~~~E~~k~h~~--~h~wrC~~CgK~F~sE~~LDlHidnrH~~l 128 (268)
..|......+.|.. ....+|..|||.|. .|..|+ ..++++
T Consensus 9 k~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~-~~~~~~ 50 (79)
T PHA00732 9 FTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHF-YSQYDI 50 (79)
T ss_pred CccCCHHHHHHHhhcccCCCccCCCCCEeC---Chhhhh-cccCCc
Confidence 46888999999984 33469999999998 489999 444443
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=76.57 E-value=1.2 Score=27.43 Aligned_cols=20 Identities=35% Similarity=0.876 Sum_probs=16.2
Q ss_pred hhhhcCcccccccccccCCc
Q 024416 94 KIHVDINEWRCGYCKKSFRA 113 (268)
Q Consensus 94 k~h~~~h~wrC~~CgK~F~s 113 (268)
+.|.+.-.+.|.+|+|.|.+
T Consensus 7 ~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 7 RTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHSSSSSEEESSSSEEESS
T ss_pred hhcCCCCCCCCCCCcCeeCc
Confidence 45666777999999999974
No 21
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=73.43 E-value=2.2 Score=34.77 Aligned_cols=29 Identities=28% Similarity=0.508 Sum_probs=25.3
Q ss_pred CCCccccchhhhhhhh---cCccccccccccc
Q 024416 82 PDNDMFRDQEQHKIHV---DINEWRCGYCKKS 110 (268)
Q Consensus 82 P~~D~F~~~E~~k~h~---~~h~wrC~~CgK~ 110 (268)
..+++|++||+|-..+ +...|.|...||+
T Consensus 8 ~T~EiF~dYe~Y~~R~~~y~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 8 FTGEIFRDYEEYLKRMILYNQRVWTCEITGKS 39 (102)
T ss_pred CCCcccCCHHHHHHHHHHHhCCeeEEecCCCC
Confidence 4578999999998876 8899999999984
No 22
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=73.23 E-value=1.1 Score=33.35 Aligned_cols=28 Identities=29% Similarity=0.555 Sum_probs=0.0
Q ss_pred ccccccccCCchhhHhhhhhcccccccc
Q 024416 103 RCGYCKKSFRAEKFLDQHFDNRHNNLLN 130 (268)
Q Consensus 103 rC~~CgK~F~sE~~LDlHidnrH~~ll~ 130 (268)
+|.+|+..|.+..-|-.||.+.|.-.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~ 28 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP 28 (100)
T ss_dssp ----------------------------
T ss_pred Cccccccccccccccccccccccccccc
Confidence 6999999999999999999999985544
No 23
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=72.49 E-value=1.9 Score=41.19 Aligned_cols=49 Identities=24% Similarity=0.546 Sum_probs=39.3
Q ss_pred ccCCCCCCCCCCccccchhhhhhhhcCc----ccccccccccCCchhhHhhhhhc
Q 024416 73 EISSKCRLHPDNDMFRDQEQHKIHVDIN----EWRCGYCKKSFRAEKFLDQHFDN 123 (268)
Q Consensus 73 ~l~~~C~L~P~~D~F~~~E~~k~h~~~h----~wrC~~CgK~F~sE~~LDlHidn 123 (268)
+=|-.|+ -++..|+|-..+..|.++| .++|.-|+|.|--..||++|.|-
T Consensus 213 EKPF~C~--hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 213 EKPFSCP--HCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred CCCccCC--cccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 3566777 2356899999988888654 68999999999999999999764
No 24
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=72.00 E-value=1.7 Score=32.16 Aligned_cols=31 Identities=23% Similarity=0.400 Sum_probs=23.5
Q ss_pred cCcccccccccccCCchhhHhhhhhcccccc
Q 024416 98 DINEWRCGYCKKSFRAEKFLDQHFDNRHNNL 128 (268)
Q Consensus 98 ~~h~wrC~~CgK~F~sE~~LDlHidnrH~~l 128 (268)
..+--+|..|+-+++.++-|.+|++-+|...
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 6678899999999999999999999999753
No 25
>PF09777 OSTMP1: Osteopetrosis-associated transmembrane protein 1 precursor; InterPro: IPR019172 Osteopetrosis-associated transmembrane protein 1 (OSTM1) is required for osteoclast and melanocyte maturation and function. Mutations in OSTM1 give rise to autosomal recessive osteopetrosis, also called autosomal recessive Albers-Schonberg disease [, ].
Probab=70.96 E-value=6.8 Score=36.11 Aligned_cols=28 Identities=29% Similarity=0.561 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhheecccc
Q 024416 222 FYLSISILTLMLLPIFYLIVYLYQREMR 249 (268)
Q Consensus 222 ~y~~~~~~~l~~l~lfY~~v~~~~r~~~ 249 (268)
+.++++.+++++.++||+.+|++.+...
T Consensus 191 ~~i~v~~~vl~lpv~FY~~s~~~~~~~~ 218 (237)
T PF09777_consen 191 AVIAVSVFVLFLPVLFYLSSYLHSERKK 218 (237)
T ss_pred HHHHHHHHHHHHHHHHHHhheeeecccc
Confidence 3455666666777899999999988755
No 26
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=69.75 E-value=1.5 Score=47.32 Aligned_cols=53 Identities=23% Similarity=0.579 Sum_probs=45.2
Q ss_pred cCCCCCCCCCCccccchhhhhhhhcCcc----cccccccccCCchhhHhhhhhcccccc
Q 024416 74 ISSKCRLHPDNDMFRDQEQHKIHVDINE----WRCGYCKKSFRAEKFLDQHFDNRHNNL 128 (268)
Q Consensus 74 l~~~C~L~P~~D~F~~~E~~k~h~~~h~----wrC~~CgK~F~sE~~LDlHidnrH~~l 128 (268)
..-+|+|. ..+|..+...++|++.|+ ++|..||-.|-|.--|..|+...|...
T Consensus 352 ~khkCr~C--akvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~ 408 (958)
T KOG1074|consen 352 FKHKCRFC--AKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREKY 408 (958)
T ss_pred ccchhhhh--HhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeeccccC
Confidence 34477775 379999999999997776 789999999999999999999887755
No 27
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=69.59 E-value=2.6 Score=26.04 Aligned_cols=20 Identities=25% Similarity=0.554 Sum_probs=16.7
Q ss_pred cccccccccCCchhhHhhhhh
Q 024416 102 WRCGYCKKSFRAEKFLDQHFD 122 (268)
Q Consensus 102 wrC~~CgK~F~sE~~LDlHid 122 (268)
-.|..||+.| ....|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4699999999 7778888875
No 28
>PF07874 DUF1660: Prophage protein (DUF1660); InterPro: IPR012455 This entry is represented by Bacteriophage bIL285, Orf33. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=64.46 E-value=1.8 Score=33.03 Aligned_cols=39 Identities=36% Similarity=0.783 Sum_probs=25.3
Q ss_pred CCCCCCCCccccchhhhhhhhcCcccccccc----------------------cccCCchhhHhhhhh
Q 024416 77 KCRLHPDNDMFRDQEQHKIHVDINEWRCGYC----------------------KKSFRAEKFLDQHFD 122 (268)
Q Consensus 77 ~C~L~P~~D~F~~~E~~k~h~~~h~wrC~~C----------------------gK~F~sE~~LDlHid 122 (268)
-|.|.-|.-.|..++. +-+|.|.-| ++.|| |+-||+|||
T Consensus 4 ~CKLFGHKw~~~~~~~------~~~~~C~RC~~~k~~~~~~~~~~NrsDlDesenv~~-ekwldkhmd 64 (64)
T PF07874_consen 4 MCKLFGHKWTFNPYGM------YMEWKCERCKIVKATANRFAADFNRSDLDESENVFP-EKWLDKHMD 64 (64)
T ss_pred hhhhcCCCCCCCCccc------chhHHHHHHHHHHhhHhhhhhhhccccccccccccH-HHHhhhhcC
Confidence 4666655544444433 445667666 45688 999999997
No 29
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=63.82 E-value=4.8 Score=38.49 Aligned_cols=57 Identities=23% Similarity=0.517 Sum_probs=41.6
Q ss_pred ccccchhhhhhhhcCcc--cccccccccCCchhhHhhhhhccccccccCCccCchhhhccccccc
Q 024416 85 DMFRDQEQHKIHVDINE--WRCGYCKKSFRAEKFLDQHFDNRHNNLLNVSHGKCLADLCGALHCD 147 (268)
Q Consensus 85 D~F~~~E~~k~h~~~h~--wrC~~CgK~F~sE~~LDlHidnrH~~ll~~~~~~CLaD~Cd~L~Cd 147 (268)
-.|...-.++-|+++|. ..|+.|||.|---++|.-||...=.. +..+|- .|+.-+-|
T Consensus 169 K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGE----KPF~C~--hC~kAFAD 227 (279)
T KOG2462|consen 169 KVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGE----KPFSCP--HCGKAFAD 227 (279)
T ss_pred ceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCC----CCccCC--cccchhcc
Confidence 37888899999998876 78899999999999999998654321 223554 45554444
No 30
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=61.72 E-value=3.1 Score=41.44 Aligned_cols=49 Identities=22% Similarity=0.387 Sum_probs=36.7
Q ss_pred cccccccccCCchhhHhhhhhcccc-----ccccCCcc------------------Cchhhhcccccccccc
Q 024416 102 WRCGYCKKSFRAEKFLDQHFDNRHN-----NLLNVSHG------------------KCLADLCGALHCDFVM 150 (268)
Q Consensus 102 wrC~~CgK~F~sE~~LDlHidnrH~-----~ll~~~~~------------------~CLaD~Cd~L~Cd~~~ 150 (268)
..|.+|.+.||+..-|-.|+.++|. +.++...- .|-...|-.-.|-++.
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~vf~ 292 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVFP 292 (493)
T ss_pred chhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEEec
Confidence 5799999999999999999999997 33332211 6777777766676653
No 31
>PHA00733 hypothetical protein
Probab=59.00 E-value=6.3 Score=32.96 Aligned_cols=25 Identities=24% Similarity=0.534 Sum_probs=22.5
Q ss_pred CcccccccccccCCchhhHhhhhhc
Q 024416 99 INEWRCGYCKKSFRAEKFLDQHFDN 123 (268)
Q Consensus 99 ~h~wrC~~CgK~F~sE~~LDlHidn 123 (268)
...+.|..|||.|.+...|.+|+..
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~ 95 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRY 95 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhc
Confidence 4578999999999999999999974
No 32
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=57.35 E-value=16 Score=31.16 Aligned_cols=46 Identities=15% Similarity=0.410 Sum_probs=27.6
Q ss_pred CCCchHHHHHHHHHHHHHHHHHHhhh-heecccccccccccccccccc
Q 024416 217 KQPSVFYLSISILTLMLLPIFYLIVY-LYQREMRGGTQELKRIPRVGR 263 (268)
Q Consensus 217 ~~~~~~y~~~~~~~l~~l~lfY~~v~-~~~r~~~~~~~~l~r~~~~~~ 263 (268)
..+++|++.+++.++|-|++.-+++| ..|.+ .+--+-=||+.-+|+
T Consensus 58 g~~~lffvglii~LivSLaLVsFvIFLiiQTg-nkMddvSrRL~aEgK 104 (128)
T PF15145_consen 58 GSRSLFFVGLIIVLIVSLALVSFVIFLIIQTG-NKMDDVSRRLTAEGK 104 (128)
T ss_pred CceeehHHHHHHHHHHHHHHHHHHHHheeecc-chHHHHHHHHHhccC
Confidence 35667777777777777776555555 45555 435555566655553
No 33
>PF13908 Shisa: Wnt and FGF inhibitory regulator
Probab=56.60 E-value=16 Score=31.42 Aligned_cols=11 Identities=27% Similarity=0.616 Sum_probs=5.8
Q ss_pred cCCCCCCCCcc
Q 024416 200 DAHKCPRKSQP 210 (268)
Q Consensus 200 d~~TC~~~~k~ 210 (268)
|..+|+.+..+
T Consensus 48 ~q~~C~~~~~~ 58 (179)
T PF13908_consen 48 DQGSCDNYDTP 58 (179)
T ss_pred ccccccccccc
Confidence 34466665544
No 34
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 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 (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=56.09 E-value=5.8 Score=30.77 Aligned_cols=36 Identities=22% Similarity=0.367 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHhhhheeccccccccccccccccc
Q 024416 227 SILTLMLLPIFYLIVYLYQREMRGGTQELKRIPRVG 262 (268)
Q Consensus 227 ~~~~l~~l~lfY~~v~~~~r~~~~~~~~l~r~~~~~ 262 (268)
.+++++++++||++.+.-++.-++..+++..-=+.|
T Consensus 5 li~lv~~~~i~yf~~~rpqkk~~k~~~~m~~~Lk~G 40 (82)
T PF02699_consen 5 LIPLVIIFVIFYFLMIRPQKKQQKEHQEMLASLKPG 40 (82)
T ss_dssp HHHHHHHHHHHHHHTHHHHHHHHHHHTTGGG-----
T ss_pred HHHHHHHHHHHhhheecHHHHHHHHHHHHHHcCCCC
Confidence 344557777889888877776555555555544444
No 35
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=53.09 E-value=5.5 Score=31.25 Aligned_cols=35 Identities=23% Similarity=0.441 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHhhhheeccccccccccccccccc
Q 024416 228 ILTLMLLPIFYLIVYLYQREMRGGTQELKRIPRVG 262 (268)
Q Consensus 228 ~~~l~~l~lfY~~v~~~~r~~~~~~~~l~r~~~~~ 262 (268)
+++++++++||++.+.=||.-++..+++...-+.|
T Consensus 7 ~~~vv~~~i~yf~~~rpqkK~~k~~~~m~~~L~~G 41 (84)
T TIGR00739 7 LPLVLIFLIFYFLIIRPQRKRRKAHKKLIESLKKG 41 (84)
T ss_pred HHHHHHHHHHHHheechHHHHHHHHHHHHHhCCCC
Confidence 34455677888887765555444445554444444
No 36
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=52.97 E-value=14 Score=25.78 Aligned_cols=28 Identities=21% Similarity=0.399 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHH-hhhheeccccccccc
Q 024416 227 SILTLMLLPIFYL-IVYLYQREMRGGTQE 254 (268)
Q Consensus 227 ~~~~l~~l~lfY~-~v~~~~r~~~~~~~~ 254 (268)
++.++++.++|+. ++|.|.++-|+.-++
T Consensus 12 ~~~~v~~~~~F~gi~~w~~~~~~k~~~e~ 40 (49)
T PF05545_consen 12 SIGTVLFFVFFIGIVIWAYRPRNKKRFEE 40 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHcccchhhHHH
Confidence 3444555555655 455665553433333
No 37
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=51.95 E-value=7 Score=42.23 Aligned_cols=46 Identities=24% Similarity=0.555 Sum_probs=37.4
Q ss_pred CCCCCCCCccccchhhhhhhhcC-----------------cccccccccccCCchhhHhhhhhcc
Q 024416 77 KCRLHPDNDMFRDQEQHKIHVDI-----------------NEWRCGYCKKSFRAEKFLDQHFDNR 124 (268)
Q Consensus 77 ~C~L~P~~D~F~~~E~~k~h~~~-----------------h~wrC~~CgK~F~sE~~LDlHidnr 124 (268)
.|+|.- -.|+..++.+.|... -.+.|.+|||.|.-.|+|.-|+.-.
T Consensus 242 sC~lCs--ytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIH 304 (1007)
T KOG3623|consen 242 SCMLCS--YTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIH 304 (1007)
T ss_pred cchhhh--hhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheee
Confidence 477653 579999999988855 3588999999999999999998644
No 38
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=51.84 E-value=6.2 Score=23.21 Aligned_cols=24 Identities=25% Similarity=0.591 Sum_probs=18.4
Q ss_pred cccccccccCCchhhHhhhhhcccc
Q 024416 102 WRCGYCKKSFRAEKFLDQHFDNRHN 126 (268)
Q Consensus 102 wrC~~CgK~F~sE~~LDlHidnrH~ 126 (268)
.+|..|.=+-. +.-|..|+...|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 47899998887 8899999998874
No 39
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=51.08 E-value=6.8 Score=34.15 Aligned_cols=43 Identities=16% Similarity=0.268 Sum_probs=27.3
Q ss_pred CCCCCCCCCc-cccchhhhhh--hhcCcccccccccccCCchhhHhh
Q 024416 76 SKCRLHPDND-MFRDQEQHKI--HVDINEWRCGYCKKSFRAEKFLDQ 119 (268)
Q Consensus 76 ~~C~L~P~~D-~F~~~E~~k~--h~~~h~wrC~~CgK~F~sE~~LDl 119 (268)
|.||+.-+.| --.+-..+.. ++..+ .+|..||+.|.+=.-+..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~-~~c~~c~~~f~~~e~~~~ 46 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRR-RECLACGKRFTTFERVEL 46 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeee-eeccccCCcceEeEeccC
Confidence 6799887666 3333333333 45444 899999999976544443
No 40
>PF00672 HAMP: HAMP domain; InterPro: IPR003660 The HAMP linker domain (present in Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases) is an approximately 50-amino acid alpha-helical region. It is found in bacterial sensor and chemotaxis proteins and in eukaryotic histidine kinases. The bacterial proteins are usually integral membrane proteins and part of a two-component signal transduction pathway. One or several copies of the HAMP domain can be found in association with other domains, such as the histidine kinase domain, the bacterial chemotaxis sensory transducer domain, the PAS repeat, the EAL domain, the GGDEF domain, the protein phosphatase 2C-like domain, the guanylate cyclase domain, or the response regulatory domain. It has been suggested that the HAMP domain possesses a role of regulating the phosphorylation or methylation of homodimeric receptors by transmitting the conformational changes in periplasmic ligand-binding domains to cytoplasmic signalling kinase and methyl-acceptor domains.; GO: 0004871 signal transducer activity, 0007165 signal transduction, 0016021 integral to membrane; PDB: 3PJX_A 3PJW_A 3ZX6_B 2Y20_B 2Y0Q_D 2Y21_H 3ZRW_C 2L7H_B 2LFS_B 2L7I_B ....
Probab=51.05 E-value=11 Score=26.60 Aligned_cols=36 Identities=22% Similarity=0.362 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHhhhheeccccccccccccccc
Q 024416 225 SISILTLMLLPIFYLIVYLYQREMRGGTQELKRIPR 260 (268)
Q Consensus 225 ~~~~~~l~~l~lfY~~v~~~~r~~~~~~~~l~r~~~ 260 (268)
++.+++++++++.|++.....+..++.++.++++++
T Consensus 4 ~~~~~~~~~~~~~~~~~~~i~~pl~~l~~~~~~i~~ 39 (70)
T PF00672_consen 4 LFLIILLLSLLLAWLLARRITRPLRRLSDAMQRIAQ 39 (70)
T ss_dssp HHHHHHHHHHHHHHH--HTTCCCHHHHHHHCCCCHT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 344455556666677777777777777777777763
No 41
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=50.08 E-value=7.3 Score=31.89 Aligned_cols=35 Identities=14% Similarity=0.296 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhhhheecccccccccccccccccc
Q 024416 229 LTLMLLPIFYLIVYLYQREMRGGTQELKRIPRVGR 263 (268)
Q Consensus 229 ~~l~~l~lfY~~v~~~~r~~~~~~~~l~r~~~~~~ 263 (268)
.+++++++||++++.=||..++..+++..--+.|-
T Consensus 23 ~lvii~~i~yf~~~RpqkK~~k~~~~~~~~Lk~Gd 57 (106)
T PRK05585 23 PLVVFFAIFYFLIIRPQQKRQKEHKKMLSSLAKGD 57 (106)
T ss_pred HHHHHHHHHHHHhccHHHHHHHHHHHHHHhcCCCC
Confidence 34456668888888766665556666665555553
No 42
>PF11027 DUF2615: Protein of unknown function (DUF2615); InterPro: IPR020309 This entry represents a group of uncharacterised protein from the Metazoa, including CD034 (or C4orf34) and YQF4 (or C34C12.4).
Probab=48.71 E-value=55 Score=27.11 Aligned_cols=53 Identities=13% Similarity=0.486 Sum_probs=25.9
Q ss_pred chHHHHHHHHH--hhccCCCC-CCCCccCCCCCCCCCchHHHHHHHHHHHHHHHHHH
Q 024416 186 SASRLHELFLR--QFCDAHKC-PRKSQPFPKGGRKQPSVFYLSISILTLMLLPIFYL 239 (268)
Q Consensus 186 Sa~rL~~~f~~--~~Cd~~TC-~~~~k~f~~~~~~~~~~~y~~~~~~~l~~l~lfY~ 239 (268)
+=.||-.++.. ++|.-..| .+..+ .+++.......++.++.+++++++++|++
T Consensus 17 AMrRLl~~LRqsQ~~CTDteC~~d~~g-~p~~~~~~~~~~~~~~~~w~~~A~~ly~~ 72 (103)
T PF11027_consen 17 AMRRLLNLLRQSQNYCTDTECLQDLPG-LPQSSGDGGNSMFMMMMLWMVLAMALYLL 72 (103)
T ss_pred HHHHHHHHHHHhhCccCcchhhccCCC-CCCcCCCCCccHHHHHHHHHHHHHHHHHc
Confidence 44577774432 37888888 44443 22221122233444445555555555543
No 43
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=48.44 E-value=9.3 Score=33.78 Aligned_cols=40 Identities=15% Similarity=0.279 Sum_probs=24.3
Q ss_pred CCCCCCCCCc--cccchhhhhhhhcCcccccccccccCCchh
Q 024416 76 SKCRLHPDND--MFRDQEQHKIHVDINEWRCGYCKKSFRAEK 115 (268)
Q Consensus 76 ~~C~L~P~~D--~F~~~E~~k~h~~~h~wrC~~CgK~F~sE~ 115 (268)
|.|||..|.| +--+-..-.-.--.-.-.|..||+.|.|=.
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE 42 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFE 42 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccccchhh
Confidence 7899998877 322222111111123467999999998844
No 44
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=47.54 E-value=11 Score=25.12 Aligned_cols=28 Identities=29% Similarity=0.681 Sum_probs=19.3
Q ss_pred cCcccccccccccCCch----hhHhhhhhccc
Q 024416 98 DINEWRCGYCKKSFRAE----KFLDQHFDNRH 125 (268)
Q Consensus 98 ~~h~wrC~~CgK~F~sE----~~LDlHidnrH 125 (268)
.....+|.+|+|.+... .-|-.|+.+.|
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 46778999999999875 67888887776
No 45
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=47.11 E-value=7.9 Score=36.21 Aligned_cols=48 Identities=27% Similarity=0.438 Sum_probs=28.3
Q ss_pred cCCCCCCCCCCccccchhhhhhhh----cCcccccccccccCCchhhHhhhhhc
Q 024416 74 ISSKCRLHPDNDMFRDQEQHKIHV----DINEWRCGYCKKSFRAEKFLDQHFDN 123 (268)
Q Consensus 74 l~~~C~L~P~~D~F~~~E~~k~h~----~~h~wrC~~CgK~F~sE~~LDlHidn 123 (268)
....|.+.- ..|.-|--...|. +.-.+-|.+|||.|....-|..|+..
T Consensus 116 d~ftCrvCg--K~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rt 167 (267)
T KOG3576|consen 116 DSFTCRVCG--KKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRT 167 (267)
T ss_pred Ceeeeehhh--hhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcc
Confidence 344555442 3566666555555 33445677777777777777766644
No 46
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.85 E-value=11 Score=37.09 Aligned_cols=51 Identities=22% Similarity=0.299 Sum_probs=37.1
Q ss_pred CCCchHHH-HHHHHHHHHHHHHHHhhhheeccccccc-ccccccccccccCCC
Q 024416 217 KQPSVFYL-SISILTLMLLPIFYLIVYLYQREMRGGT-QELKRIPRVGRKAKP 267 (268)
Q Consensus 217 ~~~~~~y~-~~~~~~l~~l~lfY~~v~~~~r~~~~~~-~~l~r~~~~~~~~~~ 267 (268)
..|+.+++ .+++++++.+.+-|.++|.+.++.+.+. +.++|..|+-.|+-|
T Consensus 164 ~~ws~~~~~~i~~l~v~~il~~~f~i~~~~~~~~~r~~~~~~r~~k~~l~~~p 216 (348)
T KOG4628|consen 164 SPWSILAISLISLLTVVAILVTCFFIYRIRRLIRARNRLRRNRLIKRLLKKLP 216 (348)
T ss_pred CcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhHHHHHhhCC
Confidence 34555654 7777888888888999998888875444 477788877776655
No 47
>COG4736 CcoQ Cbb3-type cytochrome oxidase, subunit 3 [Posttranslational modification, protein turnover, chaperones]
Probab=46.76 E-value=19 Score=27.17 Aligned_cols=27 Identities=19% Similarity=0.408 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHhhhh-eeccccccc
Q 024416 225 SISILTLMLLPIFYLIVYL-YQREMRGGT 252 (268)
Q Consensus 225 ~~~~~~l~~l~lfY~~v~~-~~r~~~~~~ 252 (268)
+-++.|+++.++||.++|. |.++ ||+.
T Consensus 10 a~a~~t~~~~l~fiavi~~ayr~~-~K~~ 37 (60)
T COG4736 10 ADAWGTIAFTLFFIAVIYFAYRPG-KKGE 37 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccc-chhh
Confidence 4456677777778877774 4444 4443
No 48
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=44.51 E-value=11 Score=38.37 Aligned_cols=33 Identities=24% Similarity=0.443 Sum_probs=28.8
Q ss_pred CcccccccccccCCchhhHhhhhhccccccccC
Q 024416 99 INEWRCGYCKKSFRAEKFLDQHFDNRHNNLLNV 131 (268)
Q Consensus 99 ~h~wrC~~CgK~F~sE~~LDlHidnrH~~ll~~ 131 (268)
---|.|..|.|.|++..-+-.||++.|..-+.+
T Consensus 55 WrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P 87 (466)
T PF04780_consen 55 WRFWICPRCSKKFSDAESCLSHMEQEHPAGLKP 87 (466)
T ss_pred eeEeeCCcccceeCCHHHHHHHHHHhhhhhcCh
Confidence 346999999999999999999999999976544
No 49
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=42.68 E-value=11 Score=32.31 Aligned_cols=27 Identities=26% Similarity=0.520 Sum_probs=24.2
Q ss_pred cCcccccccccccCCchhhHhhhhhcc
Q 024416 98 DINEWRCGYCKKSFRAEKFLDQHFDNR 124 (268)
Q Consensus 98 ~~h~wrC~~CgK~F~sE~~LDlHidnr 124 (268)
...++.|.+|-+.|-++.-|+.|+...
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhcc
Confidence 558999999999999999999999743
No 50
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=42.09 E-value=20 Score=34.55 Aligned_cols=86 Identities=19% Similarity=0.192 Sum_probs=39.8
Q ss_pred hhhhhhhhcCccccc-ccccccCCc-------hhhHhhhhhccc---cccccCCc-cCchhhhcccccccccccCCCCCC
Q 024416 90 QEQHKIHVDINEWRC-GYCKKSFRA-------EKFLDQHFDNRH---NNLLNVSH-GKCLADLCGALHCDFVMNSKSSRS 157 (268)
Q Consensus 90 ~E~~k~h~~~h~wrC-~~CgK~F~s-------E~~LDlHidnrH---~~ll~~~~-~~CLaD~Cd~L~Cd~~~~~~~~~~ 157 (268)
+|+|++.+..+.-+| +.|+|.-.+ |.|-..-=|++| .+=..+.. ++=-...|+ |.-.++.+..+.
T Consensus 82 f~e~~e~~~k~~~K~k~~~d~e~~~klEKel~e~~~~~fg~e~~imlksgm~~n~d~~s~ss~ce---ctd~n~~~l~~~ 158 (295)
T TIGR01478 82 YEQLQELVEKNRTKSTGGNGAEPMSTIEKELLEKYEEMFGDESHIMLKSGMYTNDDDKLKDKSCE---CTNQKIELLSST 158 (295)
T ss_pred HHHHHHHHHhcCCcccccCCcchhhHHHHHHHHHHHHHhCCccchhhhcCCCCCccccccCCcee---eeccccchhhhc
Confidence 566777774444444 457776653 222222233444 11111111 100134454 544444444455
Q ss_pred CCCHHHHHHHHHHHHHHhccc
Q 024416 158 KCNPAAVAKNRHLCESLANRC 178 (268)
Q Consensus 158 ~C~~aa~~~~r~~Ce~l~~sC 178 (268)
+=...=...++|.|-.=+-+|
T Consensus 159 Kg~DkYLkhLK~rC~~gi~~C 179 (295)
T TIGR01478 159 KVHDNYLKNLKKGCTAGVGTC 179 (295)
T ss_pred ccchHHHHhhhccCCCeeEee
Confidence 555555566666665555555
No 51
>PHA02768 hypothetical protein; Provisional
Probab=41.75 E-value=12 Score=27.65 Aligned_cols=36 Identities=11% Similarity=0.352 Sum_probs=28.5
Q ss_pred CCCCCCCCccccchhhhhhhhcCcc--cccccccccCCch
Q 024416 77 KCRLHPDNDMFRDQEQHKIHVDINE--WRCGYCKKSFRAE 114 (268)
Q Consensus 77 ~C~L~P~~D~F~~~E~~k~h~~~h~--wrC~~CgK~F~sE 114 (268)
+|+-- ...|..-+.+..|.+.|+ .+|..|+|.|..-
T Consensus 7 ~C~~C--GK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 7 ECPIC--GEIYIKRKSMITHLRKHNTNLKLSNCKRISLRT 44 (55)
T ss_pred Ccchh--CCeeccHHHHHHHHHhcCCcccCCcccceeccc
Confidence 56533 468999999999996666 8999999999843
No 52
>PTZ00370 STEVOR; Provisional
Probab=41.65 E-value=21 Score=34.55 Aligned_cols=33 Identities=21% Similarity=0.374 Sum_probs=17.6
Q ss_pred ccccccCCCCCCCCCHHHHHHHHHHHHHHhccc
Q 024416 146 CDFVMNSKSSRSKCNPAAVAKNRHLCESLANRC 178 (268)
Q Consensus 146 Cd~~~~~~~~~~~C~~aa~~~~r~~Ce~l~~sC 178 (268)
|.-.++.+..+++=...=...++|.|-.=+-+|
T Consensus 147 ctd~n~~~l~~~kg~DkYLkhLK~rC~~gi~~C 179 (296)
T PTZ00370 147 CTDINNVKLAKTKGRDKYLKHLKHRCTGGICSC 179 (296)
T ss_pred eeecccchhhhcccchHHHhhhhccCCCeeEee
Confidence 444444444445555555566666665555454
No 53
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=41.45 E-value=12 Score=31.03 Aligned_cols=19 Identities=21% Similarity=0.219 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHhhhheecc
Q 024416 229 LTLMLLPIFYLIVYLYQRE 247 (268)
Q Consensus 229 ~~l~~l~lfY~~v~~~~r~ 247 (268)
.+++++++||+++..=|+.
T Consensus 9 ~lv~i~~i~yF~~iRPQkK 27 (109)
T PRK05886 9 PFLLIMGGFMYFASRRQRK 27 (109)
T ss_pred HHHHHHHHHHHHHccHHHH
Confidence 3344566778776655544
No 54
>PF03597 CcoS: Cytochrome oxidase maturation protein cbb3-type; InterPro: IPR004714 Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation []. Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase.
Probab=41.21 E-value=36 Score=24.13 Aligned_cols=27 Identities=11% Similarity=0.288 Sum_probs=19.7
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhheecc
Q 024416 221 VFYLSISILTLMLLPIFYLIVYLYQRE 247 (268)
Q Consensus 221 ~~y~~~~~~~l~~l~lfY~~v~~~~r~ 247 (268)
++|+++.+-++++++..+.++|-.++|
T Consensus 2 ~l~~lip~sl~l~~~~l~~f~Wavk~G 28 (45)
T PF03597_consen 2 ILYILIPVSLILGLIALAAFLWAVKSG 28 (45)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHccC
Confidence 566666666667777778888887776
No 55
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=40.56 E-value=12 Score=30.49 Aligned_cols=30 Identities=27% Similarity=0.485 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHhhhheecccccccccc
Q 024416 226 ISILTLMLLPIFYLIVYLYQREMRGGTQEL 255 (268)
Q Consensus 226 ~~~~~l~~l~lfY~~v~~~~r~~~~~~~~l 255 (268)
.++.+++++++||+++|.=||.-.+..|++
T Consensus 11 ~ll~~vl~~~ifyFli~RPQrKr~K~~~~m 40 (97)
T COG1862 11 LLLPLVLIFAIFYFLIIRPQRKRMKEHQEL 40 (97)
T ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Confidence 444556777899999998777644444444
No 56
>PLN03086 PRLI-interacting factor K; Provisional
Probab=40.48 E-value=19 Score=37.60 Aligned_cols=43 Identities=23% Similarity=0.447 Sum_probs=28.7
Q ss_pred CCCCCCCCccccchhhhhhhhcCcccccccccccCCchhhHhhhhhcccc
Q 024416 77 KCRLHPDNDMFRDQEQHKIHVDINEWRCGYCKKSFRAEKFLDQHFDNRHN 126 (268)
Q Consensus 77 ~C~L~P~~D~F~~~E~~k~h~~~h~wrC~~CgK~F~sE~~LDlHidnrH~ 126 (268)
.||-+.+..+|...+- +.| |.|.+||+.|+ ...|..|+...|.
T Consensus 435 ~Cp~~~Cg~v~~r~el-~~H-----~~C~~Cgk~f~-~s~LekH~~~~Hk 477 (567)
T PLN03086 435 VCPHDGCGIVLRVEEA-KNH-----VHCEKCGQAFQ-QGEMEKHMKVFHE 477 (567)
T ss_pred eCCcccccceeecccc-ccC-----ccCCCCCCccc-hHHHHHHHHhcCC
Confidence 3443345556643222 333 69999999997 5678999999873
No 57
>PF06024 DUF912: Nucleopolyhedrovirus protein of unknown function (DUF912); InterPro: IPR009261 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf78; it is a family of uncharacterised viral proteins.
Probab=40.24 E-value=28 Score=27.96 Aligned_cols=19 Identities=37% Similarity=0.570 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHhhhhe-ecc
Q 024416 229 LTLMLLPIFYLIVYLY-QRE 247 (268)
Q Consensus 229 ~~l~~l~lfY~~v~~~-~r~ 247 (268)
.++.+++++|+|.|++ -||
T Consensus 70 s~v~IlVily~IyYFVILRe 89 (101)
T PF06024_consen 70 SFVCILVILYAIYYFVILRE 89 (101)
T ss_pred HHHHHHHHHhhheEEEEEec
Confidence 3345555667777744 455
No 58
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=40.02 E-value=14 Score=25.73 Aligned_cols=28 Identities=25% Similarity=0.610 Sum_probs=22.9
Q ss_pred cccccccccccCCch-----hhHhhhhhccccc
Q 024416 100 NEWRCGYCKKSFRAE-----KFLDQHFDNRHNN 127 (268)
Q Consensus 100 h~wrC~~CgK~F~sE-----~~LDlHidnrH~~ 127 (268)
..-.|.+|+|.+... ..|-.|+.++|..
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~~ 49 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHPA 49 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCcC
Confidence 356899999999776 4899999988753
No 59
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=39.97 E-value=16 Score=30.19 Aligned_cols=24 Identities=13% Similarity=0.458 Sum_probs=11.9
Q ss_pred HHHHHHHHHHhhhheecccccccc
Q 024416 230 TLMLLPIFYLIVYLYQREMRGGTQ 253 (268)
Q Consensus 230 ~l~~l~lfY~~v~~~~r~~~~~~~ 253 (268)
+++++++|-+|+.++++-.||..+
T Consensus 6 ~iii~~i~l~~~~~~~~~rRR~r~ 29 (130)
T PF12273_consen 6 AIIIVAILLFLFLFYCHNRRRRRR 29 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhc
Confidence 334444555555555555443333
No 60
>PF12669 P12: Virus attachment protein p12 family
Probab=39.29 E-value=14 Score=27.15 Aligned_cols=18 Identities=11% Similarity=0.213 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHh-hhheec
Q 024416 229 LTLMLLPIFYLI-VYLYQR 246 (268)
Q Consensus 229 ~~l~~l~lfY~~-v~~~~r 246 (268)
.++++++++|++ .+++++
T Consensus 5 ~~Ii~~~~~~v~~r~~~k~ 23 (58)
T PF12669_consen 5 GIIILAAVAYVAIRKFIKD 23 (58)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 344555566654 555544
No 61
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=38.61 E-value=10 Score=38.62 Aligned_cols=29 Identities=24% Similarity=0.519 Sum_probs=25.5
Q ss_pred cccccccccccCCchhhHhhhhhcccccc
Q 024416 100 NEWRCGYCKKSFRAEKFLDQHFDNRHNNL 128 (268)
Q Consensus 100 h~wrC~~CgK~F~sE~~LDlHidnrH~~l 128 (268)
.-+-|.+|||.|+...||-+|.-..|...
T Consensus 355 gi~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 355 GIFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred ceeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 46889999999999999999988887754
No 62
>cd03737 SOCS_SOCS3 SOCS (suppressors of cytokine signaling) box of SOCS3-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS3, like CIS1 and SOCS1, is involved in the down-regulation of the JAK/STAT pathway. SOCS3 inhibits JAK activity indirectly through recruitment to the cytokine receptors. SOCS3 has been shown to play an essential role in placental development and a non-essential role in embryo development. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=37.96 E-value=41 Score=23.54 Aligned_cols=32 Identities=19% Similarity=0.298 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhcccCCCCCCcch--HHHHHHHH
Q 024416 164 VAKNRHLCESLANRCFPINQGPSA--SRLHELFL 195 (268)
Q Consensus 164 ~~~~r~~Ce~l~~sCFP~~~g~Sa--~rL~~~f~ 195 (268)
+..++|+|+..++.+.+..++-.. .+|.+|+.
T Consensus 3 v~SLQHLCR~~In~~~~~~~~~~~LP~~Lk~yL~ 36 (42)
T cd03737 3 VSTLQHLCRKTVNGHLDSYEKRTQLPLPIKEFLD 36 (42)
T ss_pred cccHHHHHHHHHHHhcCcccchhhccHHHHHHHH
Confidence 346899999999999875433111 36888754
No 63
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=37.58 E-value=21 Score=22.33 Aligned_cols=21 Identities=24% Similarity=0.711 Sum_probs=18.3
Q ss_pred ccccccccCCchhhHhhhhhcc
Q 024416 103 RCGYCKKSFRAEKFLDQHFDNR 124 (268)
Q Consensus 103 rC~~CgK~F~sE~~LDlHidnr 124 (268)
.|.-|++.+ ++..++.|+|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD~C 23 (26)
T smart00734 3 QCPVCFREV-PENLINSHLDSC 23 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHHHh
Confidence 588999999 889999999954
No 64
>PHA02819 hypothetical protein; Provisional
Probab=36.96 E-value=66 Score=25.19 Aligned_cols=23 Identities=30% Similarity=0.551 Sum_probs=12.1
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhh
Q 024416 221 VFYLSISILTLMLLPIFYLIVYL 243 (268)
Q Consensus 221 ~~y~~~~~~~l~~l~lfY~~v~~ 243 (268)
.-+++++++++++++++.++.|+
T Consensus 45 ~~~~~ii~l~~~~~~~~~~flYL 67 (71)
T PHA02819 45 LRYYLIIGLVTIVFVIIFIIFYL 67 (71)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444555555666666654
No 65
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=36.56 E-value=15 Score=31.35 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=17.1
Q ss_pred hhcCcccccccccccCCchhhHhhhhhcccc
Q 024416 96 HVDINEWRCGYCKKSFRAEKFLDQHFDNRHN 126 (268)
Q Consensus 96 h~~~h~wrC~~CgK~F~sE~~LDlHidnrH~ 126 (268)
-+....-.|.+|||.|.+ |..|+..+|+
T Consensus 67 SI~~d~i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 67 SITPDYIICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp TB-SS-EE-TBT--EESB---HHHHHHHTT-
T ss_pred ccccCeeEEccCCcccch---HHHHHHHccC
Confidence 345566799999999976 4788888876
No 66
>PHA02650 hypothetical protein; Provisional
Probab=36.55 E-value=81 Score=25.26 Aligned_cols=22 Identities=5% Similarity=-0.022 Sum_probs=11.0
Q ss_pred hHHHHHHHHHHHHHHHHHHhhh
Q 024416 221 VFYLSISILTLMLLPIFYLIVY 242 (268)
Q Consensus 221 ~~y~~~~~~~l~~l~lfY~~v~ 242 (268)
.-+++++++++++++++.++.|
T Consensus 48 ~~~~~ii~i~~v~i~~l~~flY 69 (81)
T PHA02650 48 NGQNFIFLIFSLIIVALFSFFV 69 (81)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444455555555555555
No 67
>PF12575 DUF3753: Protein of unknown function (DUF3753); InterPro: IPR009175 This group represents an uncharacterised conserved protein belonging to poxvirus family I2.
Probab=36.31 E-value=77 Score=24.82 Aligned_cols=15 Identities=20% Similarity=0.631 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHhhhh
Q 024416 229 LTLMLLPIFYLIVYL 243 (268)
Q Consensus 229 ~~l~~l~lfY~~v~~ 243 (268)
+++++++++..++|+
T Consensus 55 ii~v~ii~~l~flYL 69 (72)
T PF12575_consen 55 IIFVLIIVLLTFLYL 69 (72)
T ss_pred HHHHHHHHHHHHHHh
Confidence 333444444455554
No 68
>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].
Probab=36.26 E-value=26 Score=33.68 Aligned_cols=8 Identities=50% Similarity=1.020 Sum_probs=4.5
Q ss_pred Cchhhhcc
Q 024416 135 KCLADLCG 142 (268)
Q Consensus 135 ~CLaD~Cd 142 (268)
.||--+|.
T Consensus 95 ~CL~Cg~~ 102 (299)
T PF02009_consen 95 GCLKCGCG 102 (299)
T ss_pred hhhhhcCc
Confidence 56655554
No 69
>PHA03054 IMV membrane protein; Provisional
Probab=36.05 E-value=84 Score=24.67 Aligned_cols=23 Identities=26% Similarity=0.590 Sum_probs=12.2
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhh
Q 024416 221 VFYLSISILTLMLLPIFYLIVYL 243 (268)
Q Consensus 221 ~~y~~~~~~~l~~l~lfY~~v~~ 243 (268)
.-+++++++++++++++.++.|+
T Consensus 47 ~~~~~ii~l~~v~~~~l~~flYL 69 (72)
T PHA03054 47 GWYWLIIIFFIVLILLLLIYLYL 69 (72)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444555556666666664
No 70
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=35.70 E-value=23 Score=38.76 Aligned_cols=48 Identities=17% Similarity=0.355 Sum_probs=38.8
Q ss_pred cccchhhhhhhhcCcc----cccccccccCCchhhHhhhhhccccccccCCc
Q 024416 86 MFRDQEQHKIHVDINE----WRCGYCKKSFRAEKFLDQHFDNRHNNLLNVSH 133 (268)
Q Consensus 86 ~F~~~E~~k~h~~~h~----wrC~~CgK~F~sE~~LDlHidnrH~~ll~~~~ 133 (268)
-|...-+.++|.++|. +.|.+|++.|-+.--|..||...|-.--..+|
T Consensus 888 ~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 888 QFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred cccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 6999999999997654 89999999999999999999965554433333
No 71
>TIGR02736 cbb3_Q_epsi cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial. Members of this protein family are restricted to the epsilon branch of the Proteobacteria. All members are found in operons containing the other three structural subunits of the cbb3 type of cytochrome c oxidase. These small proteins show remote sequence similarity to the CcoQ subunit in other cytochrome c oxidase systems, so this family is assumed to represent the epsilonproteobacterial variant of CcoQ.
Probab=35.37 E-value=27 Score=26.16 Aligned_cols=32 Identities=25% Similarity=0.698 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHhhh-heecccccccccccccccc
Q 024416 229 LTLMLLPIFYLIVY-LYQREMRGGTQELKRIPRV 261 (268)
Q Consensus 229 ~~l~~l~lfY~~v~-~~~r~~~~~~~~l~r~~~~ 261 (268)
+|+++++++|-.+| +|+++ |+|..|-.+-++.
T Consensus 7 ~ti~lvv~LYgY~yhLYrse-k~G~rdYEKY~~L 39 (56)
T TIGR02736 7 FTLLLVIFLYAYIYHLYRSQ-KKGERDYEKYANL 39 (56)
T ss_pred HHHHHHHHHHHHHHHhhhhh-cccccCHHHHhhh
Confidence 34444445555444 67777 6687776665543
No 72
>PF04024 PspC: PspC domain; InterPro: IPR007168 This domain is found in Phage shock protein C (PspC) that is thought to be a transcriptional regulator. The presumed domain is 60 amino acid residues in length.
Probab=34.69 E-value=43 Score=24.79 Aligned_cols=28 Identities=18% Similarity=0.368 Sum_probs=18.6
Q ss_pred CchHHHHHHHHHHHHHHHHHHhhhheecc
Q 024416 219 PSVFYLSISILTLMLLPIFYLIVYLYQRE 247 (268)
Q Consensus 219 ~~~~y~~~~~~~l~~l~lfY~~v~~~~r~ 247 (268)
..+.++++++++.. .++.|+++|+.-.+
T Consensus 31 vRl~~v~l~~~~~~-~~l~Y~~~w~~lP~ 58 (61)
T PF04024_consen 31 VRLIFVVLTFFTGG-GILLYLILWLLLPK 58 (61)
T ss_pred HHHHHHHHHHHHhH-HHHHHHHHHHHcCC
Confidence 34556665555544 77999999986543
No 73
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=34.60 E-value=20 Score=31.45 Aligned_cols=43 Identities=9% Similarity=0.200 Sum_probs=24.5
Q ss_pred CCCCCCCCCc--cccchhhhhhhhcCcccccccccccCCchhhHh
Q 024416 76 SKCRLHPDND--MFRDQEQHKIHVDINEWRCGYCKKSFRAEKFLD 118 (268)
Q Consensus 76 ~~C~L~P~~D--~F~~~E~~k~h~~~h~wrC~~CgK~F~sE~~LD 118 (268)
|.||+.-+.| +--+-..-+-..---.-.|..||+.|.|-.-+.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve 45 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAE 45 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecc
Confidence 7899887755 222211111111123467999999999865443
No 74
>TIGR00847 ccoS cytochrome oxidase maturation protein, cbb3-type. CcoS from Rhodobacter capsulatus has been shown essential for incorporation of redox-active prosthetic groups (heme, Cu) into cytochrome cbb(3) oxidase. FixS of Bradyrhizobium japonicum appears to have the same function. Members of this family are found so far in organisms with a cbb3-type cytochrome oxidase, including Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Caulobacter crescentus, Bradyrhizobium japonicum, and Rhodobacter capsulatus.
Probab=34.28 E-value=58 Score=23.76 Aligned_cols=27 Identities=11% Similarity=0.071 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhheecc
Q 024416 221 VFYLSISILTLMLLPIFYLIVYLYQRE 247 (268)
Q Consensus 221 ~~y~~~~~~~l~~l~lfY~~v~~~~r~ 247 (268)
++|+++.+-++++++..+.++|-.++|
T Consensus 3 il~~LIpiSl~l~~~~l~~f~Wavk~G 29 (51)
T TIGR00847 3 ILTILIPISLLLGGVGLVAFLWSLKSG 29 (51)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence 567777777777777778888877766
No 75
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=33.47 E-value=12 Score=37.58 Aligned_cols=41 Identities=24% Similarity=0.515 Sum_probs=0.0
Q ss_pred CccccchhhhhhhhcCcccccccccccCCchhhHhhhhhcc
Q 024416 84 NDMFRDQEQHKIHVDINEWRCGYCKKSFRAEKFLDQHFDNR 124 (268)
Q Consensus 84 ~D~F~~~E~~k~h~~~h~wrC~~CgK~F~sE~~LDlHidnr 124 (268)
++-|.++=.-..-..++-++|..|.|.|-||+.|-.|+-+.
T Consensus 220 ~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rH 260 (467)
T KOG3608|consen 220 KTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRH 260 (467)
T ss_pred ccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHh
No 76
>PF12907 zf-met2: Zinc-binding
Probab=32.69 E-value=22 Score=24.74 Aligned_cols=26 Identities=31% Similarity=0.700 Sum_probs=20.9
Q ss_pred cccccccccC---CchhhHhhhhhccccc
Q 024416 102 WRCGYCKKSF---RAEKFLDQHFDNRHNN 127 (268)
Q Consensus 102 wrC~~CgK~F---~sE~~LDlHidnrH~~ 127 (268)
-+|..|.-.| .++.-|..|.||+|.-
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 3688888555 6778899999999985
No 77
>PHA02844 putative transmembrane protein; Provisional
Probab=32.64 E-value=82 Score=24.90 Aligned_cols=20 Identities=20% Similarity=0.507 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q 024416 224 LSISILTLMLLPIFYLIVYL 243 (268)
Q Consensus 224 ~~~~~~~l~~l~lfY~~v~~ 243 (268)
++++++++++++++.++.|+
T Consensus 50 ~~ii~i~~v~~~~~~~flYL 69 (75)
T PHA02844 50 IWILTIIFVVFATFLTFLYL 69 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33344444555555555554
No 78
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=32.43 E-value=18 Score=30.27 Aligned_cols=32 Identities=13% Similarity=0.205 Sum_probs=13.5
Q ss_pred HHHHHHHHHHhhhheeccccccccccccccccc
Q 024416 230 TLMLLPIFYLIVYLYQREMRGGTQELKRIPRVG 262 (268)
Q Consensus 230 ~l~~l~lfY~~v~~~~r~~~~~~~~l~r~~~~~ 262 (268)
+++++++||+ ++.=|+.-.+-.+++..--+.|
T Consensus 9 ~vv~~~i~yf-~iRPQkKr~Ke~~em~~sLk~G 40 (113)
T PRK06531 9 FVVMLGLIFF-MQRQQKKQAQERQNQLNAIQKG 40 (113)
T ss_pred HHHHHHHHHh-eechHHHHHHHHHHHHHhcCCC
Confidence 3445556664 3433333222334444333333
No 79
>PF04995 CcmD: Heme exporter protein D (CcmD); InterPro: IPR007078 The CcmD protein is part of a C-type cytochrome biogenesis operon []. The exact function of this protein is uncertain. It has been proposed that CcmC, CcmD and CcmE interact directly with each other, establishing a cytoplasm to periplasm haem delivery pathway for cytochrome c maturation []. This protein is found fused to CcmE in P52224 from SWISSPROT. These proteins contain a predicted transmembrane helix.; GO: 0006810 transport, 0016021 integral to membrane
Probab=31.65 E-value=21 Score=24.85 Aligned_cols=39 Identities=28% Similarity=0.273 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHhhhheecccccccccccccccccc
Q 024416 224 LSISILTLMLLPIFYLIVYLYQREMRGGTQELKRIPRVGR 263 (268)
Q Consensus 224 ~~~~~~~l~~l~lfY~~v~~~~r~~~~~~~~l~r~~~~~~ 263 (268)
|+.+...+.++++..++++.+.+. |+..++|+|....++
T Consensus 6 yVW~sYg~t~~~l~~l~~~~~~~~-r~~~~~l~~~~~r~~ 44 (46)
T PF04995_consen 6 YVWSSYGVTALVLAGLIVWSLRRR-RRLRKELKRLEAREQ 44 (46)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHhHc
Confidence 344445556666667777777666 557788887665544
No 80
>PF06796 NapE: Periplasmic nitrate reductase protein NapE; InterPro: IPR010649 This family consists of several bacterial periplasmic nitrate reductase NapE proteins. Seven genes, napKEFDABC, encoding the periplasmic nitrate reductase system were cloned from the denitrifying phototrophic bacterium Rhodobacter sphaeroides. NapE is thought to be a transmembrane protein [].
Probab=31.44 E-value=55 Score=24.45 Aligned_cols=19 Identities=32% Similarity=0.578 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHhhhheec
Q 024416 228 ILTLMLLPIFYLIVYLYQR 246 (268)
Q Consensus 228 ~~~l~~l~lfY~~v~~~~r 246 (268)
+++++++..|-++||++|-
T Consensus 31 iL~v~~Vg~YGF~VWm~Q~ 49 (56)
T PF06796_consen 31 ILAVAFVGGYGFIVWMYQI 49 (56)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3455667789999999874
No 81
>PHA02291 hypothetical protein
Probab=30.06 E-value=55 Score=27.86 Aligned_cols=30 Identities=20% Similarity=0.662 Sum_probs=22.7
Q ss_pred CCchHHHHHHHHHHHHHHHHHHhhhheecc
Q 024416 218 QPSVFYLSISILTLMLLPIFYLIVYLYQRE 247 (268)
Q Consensus 218 ~~~~~y~~~~~~~l~~l~lfY~~v~~~~r~ 247 (268)
+.++||+++.++++..+..||.--++|-..
T Consensus 4 K~~iFYiL~~~VL~~si~sY~~sS~~Y~~~ 33 (132)
T PHA02291 4 KASIFYILVVIVLAFSISSYYISSFMYHDK 33 (132)
T ss_pred chhhHHHHHHHHHHHHHHHHhhheeeeecc
Confidence 345899998888888888888777666543
No 82
>PHA02975 hypothetical protein; Provisional
Probab=29.70 E-value=1e+02 Score=24.04 Aligned_cols=20 Identities=15% Similarity=0.383 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q 024416 224 LSISILTLMLLPIFYLIVYL 243 (268)
Q Consensus 224 ~~~~~~~l~~l~lfY~~v~~ 243 (268)
++++++++++++++..+.|+
T Consensus 46 ~~ii~i~~v~~~~~~~flYL 65 (69)
T PHA02975 46 ILIIFIIFITCIAVFTFLYL 65 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33333444555555555554
No 83
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=27.87 E-value=77 Score=27.60 Aligned_cols=39 Identities=18% Similarity=0.380 Sum_probs=24.3
Q ss_pred CCCchHHHH----HHHHHHHHHHHHHHhhhheecccccccccc
Q 024416 217 KQPSVFYLS----ISILTLMLLPIFYLIVYLYQREMRGGTQEL 255 (268)
Q Consensus 217 ~~~~~~y~~----~~~~~l~~l~lfY~~v~~~~r~~~~~~~~l 255 (268)
..+..-|++ +++++++++..+-+++|-|-|..+.--||.
T Consensus 94 ~n~~t~Yia~~~il~il~~i~is~~~~~~yr~~r~~~~~~~~~ 136 (139)
T PHA03099 94 PNTTTSYIPSPGIVLVLVGIIITCCLLSVYRFTRRTKLPLQDM 136 (139)
T ss_pred ccchhhhhhhhHHHHHHHHHHHHHHHHhhheeeecccCchhhc
Confidence 344445666 555555666666677777777766666664
No 84
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=27.76 E-value=24 Score=33.17 Aligned_cols=42 Identities=26% Similarity=0.725 Sum_probs=30.4
Q ss_pred cccccccccccCCchhhHhhhhhccccccccCCccCchhhhccccccc
Q 024416 100 NEWRCGYCKKSFRAEKFLDQHFDNRHNNLLNVSHGKCLADLCGALHCD 147 (268)
Q Consensus 100 h~wrC~~CgK~F~sE~~LDlHidnrH~~ll~~~~~~CLaD~Cd~L~Cd 147 (268)
..+.|..|||.|.-.+.|+.||. .|+++ ++-.| -.|+.-.=|
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~k-ch~~v---kr~lc--t~cgkgfnd 157 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLK-CHSDV---KRHLC--TFCGKGFND 157 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhh-hccHH---HHHHH--hhccCcccc
Confidence 67899999999999999999996 45554 34333 355554444
No 85
>KOG2754 consensus Oligosaccharyltransferase, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=27.35 E-value=35 Score=34.44 Aligned_cols=29 Identities=17% Similarity=0.379 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhheeccccc
Q 024416 222 FYLSISILTLMLLPIFYLIVYLYQREMRG 250 (268)
Q Consensus 222 ~y~~~~~~~l~~l~lfY~~v~~~~r~~~~ 250 (268)
.=|.+++|.+|+-.+++.+||++.++...
T Consensus 406 ypYyas~fs~m~g~~~Fs~vfL~~k~~~~ 434 (443)
T KOG2754|consen 406 YPYYASCFSMMAGFFLFSFVFLYHKDVPV 434 (443)
T ss_pred chHHHHHHHHHHHHheeeEEEEEecCCcc
Confidence 33556788888888999999999998763
No 86
>CHL00066 psbH photosystem II protein H
Probab=26.93 E-value=87 Score=24.64 Aligned_cols=35 Identities=17% Similarity=0.335 Sum_probs=18.7
Q ss_pred CccCCCC-CCCCCchHHHHHHHHHHHHHHHHHHhhh
Q 024416 208 SQPFPKG-GRKQPSVFYLSISILTLMLLPIFYLIVY 242 (268)
Q Consensus 208 ~k~f~~~-~~~~~~~~y~~~~~~~l~~l~lfY~~v~ 242 (268)
.||+..+ |+..++..-..+-+++++++++|++|+-
T Consensus 23 LKPLNSeyGkvapgWGTtp~Mgv~m~lf~vfl~iiL 58 (73)
T CHL00066 23 LKPLNSEYGKVAPGWGTTPLMGVAMALFAVFLSIIL 58 (73)
T ss_pred ccccccccCcccCCccchHHHHHHHHHHHHHHHHHH
Confidence 4566443 5444444444444555566666666654
No 87
>PLN00055 photosystem II reaction center protein H; Provisional
Probab=26.75 E-value=91 Score=24.54 Aligned_cols=36 Identities=17% Similarity=0.306 Sum_probs=18.6
Q ss_pred CCccCCCC-CCCCCchHHHHHHHHHHHHHHHHHHhhh
Q 024416 207 KSQPFPKG-GRKQPSVFYLSISILTLMLLPIFYLIVY 242 (268)
Q Consensus 207 ~~k~f~~~-~~~~~~~~y~~~~~~~l~~l~lfY~~v~ 242 (268)
..||+..+ |+..++..-..+-+++++++++|++|+-
T Consensus 22 lLKPLNSeyGkvapgWGTtp~Mg~~m~lf~vfl~iil 58 (73)
T PLN00055 22 LLKPLNSEYGKVAPGWGTTPLMGVAMALFAVFLSIIL 58 (73)
T ss_pred cccccccccCcccCCccchhHHHHHHHHHHHHHHHHH
Confidence 34566443 5444444444444555555666666554
No 88
>PF15102 TMEM154: TMEM154 protein family
Probab=26.51 E-value=30 Score=30.32 Aligned_cols=27 Identities=19% Similarity=0.456 Sum_probs=14.3
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhheecc
Q 024416 221 VFYLSISILTLMLLPIFYLIVYLYQRE 247 (268)
Q Consensus 221 ~~y~~~~~~~l~~l~lfY~~v~~~~r~ 247 (268)
++++++-+++|++|+++-.++..+.|.
T Consensus 58 iLmIlIP~VLLvlLLl~vV~lv~~~kR 84 (146)
T PF15102_consen 58 ILMILIPLVLLVLLLLSVVCLVIYYKR 84 (146)
T ss_pred EEEEeHHHHHHHHHHHHHHHheeEEee
Confidence 555555545555555555555555544
No 89
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=26.29 E-value=25 Score=28.98 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=11.5
Q ss_pred cccccccccccCCc
Q 024416 100 NEWRCGYCKKSFRA 113 (268)
Q Consensus 100 h~wrC~~CgK~F~s 113 (268)
..++|..||+.||.
T Consensus 8 tKR~Cp~CG~kFYD 21 (108)
T PF09538_consen 8 TKRTCPSCGAKFYD 21 (108)
T ss_pred CcccCCCCcchhcc
Confidence 45789999999984
No 90
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=25.98 E-value=29 Score=26.86 Aligned_cols=40 Identities=15% Similarity=0.219 Sum_probs=27.8
Q ss_pred CCCCCCCCCccccchhhhhhhhcCcccccc--cccccCCchh
Q 024416 76 SKCRLHPDNDMFRDQEQHKIHVDINEWRCG--YCKKSFRAEK 115 (268)
Q Consensus 76 ~~C~L~P~~D~F~~~E~~k~h~~~h~wrC~--~CgK~F~sE~ 115 (268)
|.||+--+.+.-++-......+..-.++|. +||..|.+-.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEE
Confidence 678888777644444444444666778998 9999998743
No 91
>PRK02624 psbH photosystem II reaction center protein H; Provisional
Probab=25.92 E-value=87 Score=24.06 Aligned_cols=36 Identities=19% Similarity=0.359 Sum_probs=19.1
Q ss_pred CCccCCCC-CCCCCchHHHHHHHHHHHHHHHHHHhhh
Q 024416 207 KSQPFPKG-GRKQPSVFYLSISILTLMLLPIFYLIVY 242 (268)
Q Consensus 207 ~~k~f~~~-~~~~~~~~y~~~~~~~l~~l~lfY~~v~ 242 (268)
..||+..+ |+..++..-..+-++++++.++|.+|+-
T Consensus 10 lLkpLNSEyGKVaPGWGTTplMgv~m~Lf~vFl~iiL 46 (64)
T PRK02624 10 LLKPLNSEYGKVVPGWGTTPVMAVFMVLFLVFLLIIL 46 (64)
T ss_pred hccccccccCcccCCccchHHHHHHHHHHHHHHHHHH
Confidence 34666554 5544444444444555556666666554
No 92
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=25.83 E-value=40 Score=29.14 Aligned_cols=24 Identities=21% Similarity=0.505 Sum_probs=19.5
Q ss_pred cCcccccccccccCCchhhHhhhh
Q 024416 98 DINEWRCGYCKKSFRAEKFLDQHF 121 (268)
Q Consensus 98 ~~h~wrC~~CgK~F~sE~~LDlHi 121 (268)
.....+|..|||-|.+.+.++.=+
T Consensus 111 ~~~~~~C~~CG~~f~~~~~i~~~~ 134 (180)
T PRK12387 111 EFALCNCRVCGRPFAVQKEIDYAI 134 (180)
T ss_pred eeCcccchhhCCccccHHHHHHHH
Confidence 457789999999999998777443
No 93
>TIGR02972 TMAO_torE trimethylamine N-oxide reductase system, TorE protein. Members of this small, apparent transmembrane protein are designated TorE and occur in operons for the trimethylamine N-oxide (TMAO) reductase system. Members are closely related to the NapE protein of the related periplasmic nitrate reductase system. It may be that TorE is an integral membrane subunit of a complex with the reductase TorA.
Probab=25.77 E-value=82 Score=22.83 Aligned_cols=19 Identities=21% Similarity=0.376 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHhhhheec
Q 024416 228 ILTLMLLPIFYLIVYLYQR 246 (268)
Q Consensus 228 ~~~l~~l~lfY~~v~~~~r 246 (268)
+++++++..|-++||++|-
T Consensus 23 iLsV~~Vg~YGF~vWm~Q~ 41 (47)
T TIGR02972 23 ILSVAGIGGYGFIIWMIQA 41 (47)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4455667789999999883
No 94
>TIGR02978 phageshock_pspC phage shock protein C. All members of this protein family are the phage shock protein PspC. These proteins contain a PspC domain, as do other members of the larger family of proteins described by Pfam model pfam04024. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor, PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin overexpression, ethanol, heat shock, and protein export defects.
Probab=25.74 E-value=65 Score=27.09 Aligned_cols=27 Identities=11% Similarity=0.275 Sum_probs=15.9
Q ss_pred hHHHHHHHHHHH-HHHHHHHhhhheecc
Q 024416 221 VFYLSISILTLM-LLPIFYLIVYLYQRE 247 (268)
Q Consensus 221 ~~y~~~~~~~l~-~l~lfY~~v~~~~r~ 247 (268)
++++++++++.. +.++.|+++|++--.
T Consensus 33 l~~vl~~~~~~~~~~ll~Y~i~w~~lp~ 60 (121)
T TIGR02978 33 ILVVSALLFGGGFFVLVAYIALWLLLDK 60 (121)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHHhc
Confidence 445554444432 234569999987654
No 95
>PHA02662 ORF131 putative membrane protein; Provisional
Probab=25.71 E-value=1.6e+02 Score=27.56 Aligned_cols=29 Identities=10% Similarity=0.220 Sum_probs=16.7
Q ss_pred cCCCCCCCCCchHHHHHHHHHHHHHHHHH
Q 024416 210 PFPKGGRKQPSVFYLSISILTLMLLPIFY 238 (268)
Q Consensus 210 ~f~~~~~~~~~~~y~~~~~~~l~~l~lfY 238 (268)
+|..+|-..|.+++.++.++++.++++-|
T Consensus 178 ~~~~~~~~~W~i~~~v~~i~~i~vv~i~~ 206 (226)
T PHA02662 178 GLAEGGTPPWTLLLAVAAVTVLGVVAVSL 206 (226)
T ss_pred ccccCCCCcchhHHHHHHHHHHHHHHHHH
Confidence 56665555666777666555545544433
No 96
>TIGR02973 nitrate_rd_NapE periplasmic nitrate reductase, NapE protein. NapE, homologous to TorE (TIGR02972), is a membrane protein of unknown function that is part of the periplasmic nitrate reductase system; it may be part of the enzyme complex. The periplasmic nitrate reductase allows for nitrate respiration in anaerobic conditions.
Probab=25.25 E-value=87 Score=22.20 Aligned_cols=18 Identities=22% Similarity=0.563 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHhhhhee
Q 024416 228 ILTLMLLPIFYLIVYLYQ 245 (268)
Q Consensus 228 ~~~l~~l~lfY~~v~~~~ 245 (268)
+++++++..|-++||++|
T Consensus 18 iLsV~~V~~YGF~vWm~Q 35 (42)
T TIGR02973 18 VLSVITVGGYGFAVWMYQ 35 (42)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 455666778999999998
No 97
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=25.13 E-value=65 Score=26.47 Aligned_cols=22 Identities=27% Similarity=0.535 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHhhhheecccc
Q 024416 228 ILTLMLLPIFYLIVYLYQREMR 249 (268)
Q Consensus 228 ~~~l~~l~lfY~~v~~~~r~~~ 249 (268)
++.++++++.|++++.+.|..+
T Consensus 101 l~~l~~l~~~~~~~~~~~~~~~ 122 (135)
T PF04246_consen 101 LGGLLGLALGFLILRLFDRRLK 122 (135)
T ss_pred HHHHHHHHHHHHHHHHHHhhhc
Confidence 3445666778888888877755
No 98
>PF14004 DUF4227: Protein of unknown function (DUF4227)
Probab=24.90 E-value=78 Score=24.54 Aligned_cols=20 Identities=20% Similarity=0.348 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q 024416 224 LSISILTLMLLPIFYLIVYL 243 (268)
Q Consensus 224 ~~~~~~~l~~l~lfY~~v~~ 243 (268)
.++++|+...++.||.++|+
T Consensus 8 k~~~LF~~~T~lfYy~~~w~ 27 (71)
T PF14004_consen 8 KFFLLFTGCTLLFYYAILWV 27 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34556777777788999886
No 99
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=24.66 E-value=86 Score=23.85 Aligned_cols=13 Identities=15% Similarity=0.536 Sum_probs=5.3
Q ss_pred HHHHHHHHHHhhh
Q 024416 230 TLMLLPIFYLIVY 242 (268)
Q Consensus 230 ~l~~l~lfY~~v~ 242 (268)
++++++++|++++
T Consensus 73 ~~iv~~~~~~i~~ 85 (89)
T PF00957_consen 73 IIIVIIIILIIII 85 (89)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HhhhhhhhhHHHH
Confidence 3334444444444
No 100
>COG3087 FtsN Cell division protein [Cell division and chromosome partitioning]
Probab=24.42 E-value=1.6e+02 Score=28.25 Aligned_cols=57 Identities=9% Similarity=-0.024 Sum_probs=27.4
Q ss_pred cCCCCCCCCCchHHHHHHHHHHHHHHHHHHhhhheecccccccccccccccccccCCCC
Q 024416 210 PFPKGGRKQPSVFYLSISILTLMLLPIFYLIVYLYQREMRGGTQELKRIPRVGRKAKPS 268 (268)
Q Consensus 210 ~f~~~~~~~~~~~y~~~~~~~l~~l~lfY~~v~~~~r~~~~~~~~l~r~~~~~~~~~~~ 268 (268)
.+++.++...+.++..+.+-++++++++|++.-.+...-.--.+.=+ .+.+.+-||+
T Consensus 5 ~~s~r~~~~~~~~~~~i~~~viv~~~~~~~~~t~~~~~~~p~~~~~~--t~~~lp~~Pe 61 (264)
T COG3087 5 STSRRARPQVGPTFVAIAAAVIVTFIGGLYFITHHKKAPIPFLSNQG--TGSLLPNKPE 61 (264)
T ss_pred ccCccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccccccccccCC--ccCCCCCCCc
Confidence 44554444455555555555556666666555555544332222211 4455554553
No 101
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=24.30 E-value=75 Score=26.88 Aligned_cols=18 Identities=22% Similarity=0.263 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 024416 223 YLSISILTLMLLPIFYLI 240 (268)
Q Consensus 223 y~~~~~~~l~~l~lfY~~ 240 (268)
+-+++++++++|+|+|++
T Consensus 71 ~gv~aGvIg~Illi~y~i 88 (122)
T PF01102_consen 71 FGVMAGVIGIILLISYCI 88 (122)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 333344444444444444
No 102
>PF05337 CSF-1: Macrophage colony stimulating factor-1 (CSF-1); InterPro: IPR008001 Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic lineage. This lineage includes mononuclear phagocytic precursors, blood monocytes, tissue macrophages, osteoclasts, and microglia of the brain, all of which possess cell surface receptors for CSF-1. The protein has also been linked with male fertility [] and mutations in the Csf-1 gene have been found to cause osteopetrosis and failure of tooth eruption [].; GO: 0005125 cytokine activity, 0008083 growth factor activity, 0016021 integral to membrane; PDB: 3EJJ_A.
Probab=24.15 E-value=26 Score=33.77 Aligned_cols=31 Identities=32% Similarity=0.473 Sum_probs=0.0
Q ss_pred CchHHHHHHHHHHHHHHHHHHhhhheecccc
Q 024416 219 PSVFYLSISILTLMLLPIFYLIVYLYQREMR 249 (268)
Q Consensus 219 ~~~~y~~~~~~~l~~l~lfY~~v~~~~r~~~ 249 (268)
..+||+++--+++|+|++=-|..|.|+|..+
T Consensus 225 ~~vf~lLVPSiILVLLaVGGLLfYr~rrRs~ 255 (285)
T PF05337_consen 225 GFVFYLLVPSIILVLLAVGGLLFYRRRRRSH 255 (285)
T ss_dssp -------------------------------
T ss_pred cccccccccchhhhhhhccceeeeccccccc
Confidence 4588999999999999999999888888544
No 103
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=23.79 E-value=35 Score=33.86 Aligned_cols=52 Identities=25% Similarity=0.480 Sum_probs=42.5
Q ss_pred cCCCCCCCCCCccccchhhhhhhh-cCc----------------------ccccccccccCCchhhHhhhhhccc
Q 024416 74 ISSKCRLHPDNDMFRDQEQHKIHV-DIN----------------------EWRCGYCKKSFRAEKFLDQHFDNRH 125 (268)
Q Consensus 74 l~~~C~L~P~~D~F~~~E~~k~h~-~~h----------------------~wrC~~CgK~F~sE~~LDlHidnrH 125 (268)
-|-.||.+-+...|..|...|-|- ..| -+||..|+|.+.+-.-|.-|..-.|
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~Hsh 422 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKHSH 422 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccccC
Confidence 467899999888999999888776 333 4699999999999888888876655
No 104
>PHA02849 putative transmembrane protein; Provisional
Probab=23.40 E-value=90 Score=25.00 Aligned_cols=18 Identities=22% Similarity=0.635 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHHHhhhh
Q 024416 226 ISILTLMLLPIFYLIVYL 243 (268)
Q Consensus 226 ~~~~~l~~l~lfY~~v~~ 243 (268)
+.++++++..+-|+++|+
T Consensus 20 i~v~v~vI~i~~flLlyL 37 (82)
T PHA02849 20 ILVFVLVISFLAFMLLYL 37 (82)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344444444444444443
No 105
>cd03745 SOCS_WSB2_SWIP2 SOCS (suppressors of cytokine signaling) box of WSB2/SWiP2-like proteins. This family consists of WSB-2 (SOCS-box-containing WD-40 protein) and SWiP-2 (SOCS box and WD-repeats in Protein). No functional information is available for WSB2 or SWiP-2, but limited information is available for the isoforms WSB-1 and SWiP-1. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=23.14 E-value=81 Score=21.73 Aligned_cols=31 Identities=19% Similarity=0.355 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhcccCCCCCCcc---hHHHHHHHH
Q 024416 165 AKNRHLCESLANRCFPINQGPS---ASRLHELFL 195 (268)
Q Consensus 165 ~~~r~~Ce~l~~sCFP~~~g~S---a~rL~~~f~ 195 (268)
..++|+|+..++.+.+.....+ -.+|.+|+.
T Consensus 4 ~SLQHLCR~~I~~~~~~~~~~~LPLP~~Lk~yL~ 37 (39)
T cd03745 4 PSLRHLCRKALRHFLTTYQVLALPIPKKMKEFLT 37 (39)
T ss_pred ccHHHHHHHHHHHhccccccccCCCcHHHHHHHc
Confidence 4589999999999986544322 137888753
No 106
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=22.69 E-value=98 Score=34.08 Aligned_cols=20 Identities=25% Similarity=0.856 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHhhh
Q 024416 223 YLSISILTLMLLPIFYLIVY 242 (268)
Q Consensus 223 y~~~~~~~l~~l~lfY~~v~ 242 (268)
.+++.+++|+++|.+|.+++
T Consensus 1009 L~~st~ltL~vvP~ly~~~~ 1028 (1044)
T TIGR00915 1009 MVTATVLAIFFVPLFYVVVR 1028 (1044)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44566788888888888644
No 107
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.43 E-value=33 Score=22.25 Aligned_cols=16 Identities=38% Similarity=0.835 Sum_probs=12.1
Q ss_pred CcccccccccccCCch
Q 024416 99 INEWRCGYCKKSFRAE 114 (268)
Q Consensus 99 ~h~wrC~~CgK~F~sE 114 (268)
..+.+|..||+.|.-.
T Consensus 3 ~Y~y~C~~Cg~~fe~~ 18 (41)
T smart00834 3 IYEYRCEDCGHTFEVL 18 (41)
T ss_pred CEEEEcCCCCCEEEEE
Confidence 3467999999988643
No 108
>PF00558 Vpu: Vpu protein; InterPro: IPR008187 The Human immunodeficiency virus 1 (HIV-1) Vpu protein acts in the degradation of CD4 in the endoplasmic reticulum and in the enhancement of virion release from the plasma membrane of infected cells [].; GO: 0019076 release of virus from host; PDB: 2JPX_A 1PI8_A 2GOH_A 2GOF_A 1PI7_A 1PJE_A 1VPU_A 2K7Y_A.
Probab=21.38 E-value=83 Score=25.08 Aligned_cols=28 Identities=21% Similarity=0.447 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHhhhheeccccc
Q 024416 223 YLSISILTLMLLPIFYLIVYLYQREMRG 250 (268)
Q Consensus 223 y~~~~~~~l~~l~lfY~~v~~~~r~~~~ 250 (268)
-++++++++++.++.+.+||...|..++
T Consensus 8 ~iialiv~~iiaIvvW~iv~ieYrk~~r 35 (81)
T PF00558_consen 8 AIIALIVALIIAIVVWTIVYIEYRKIKR 35 (81)
T ss_dssp HHHHHHHHHHHHHHHHHHH---------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555556777777755555443
No 109
>PHA03164 hypothetical protein; Provisional
Probab=21.23 E-value=1.2e+02 Score=24.46 Aligned_cols=30 Identities=23% Similarity=0.361 Sum_probs=12.8
Q ss_pred CCchHHHH-HHHHHHHHHHHHHHhhhheecc
Q 024416 218 QPSVFYLS-ISILTLMLLPIFYLIVYLYQRE 247 (268)
Q Consensus 218 ~~~~~y~~-~~~~~l~~l~lfY~~v~~~~r~ 247 (268)
+++.|.++ ..++.+++.++|-+.||-..|+
T Consensus 56 ktftFlvLtgLaIamILfiifvlyvFnVnr~ 86 (88)
T PHA03164 56 KTFTFLVLTGLAIAMILFIIFVLYVFNVNRG 86 (88)
T ss_pred heeehHHHHHHHHHHHHHHHHHHHheeeccC
Confidence 33344333 3333334444555555544444
No 110
>PF00737 PsbH: Photosystem II 10 kDa phosphoprotein; InterPro: IPR001056 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight phosphoprotein PsbH found in PSII. The phosphorylation site of PsbH is located in the N terminus, where reversible phosphorylation is light-dependent and redox-controlled. PsbH is necessary for the photoprotection of PSII, being required for: (1) the rapid degradation of photodamaged D1 core protein to prevent further oxidative damage to the PSII core, and (2) the insertion of newly synthesised D1 protein into the thylakoid membrane []. PsbH may also regulate the transfer of electrons from D2 (Qa) to D1 (Qb) in the reaction core.; GO: 0042301 phosphate ion binding, 0015979 photosynthesis, 0050821 protein stabilization, 0009523 photosystem II, 0016020 membrane; PDB: 3PRR_H 2AXT_h 3BZ2_H 3BZ1_H 4FBY_W 3PRQ_H 3KZI_H 1S5L_h 3A0H_H 3ARC_H ....
Probab=21.22 E-value=1.4e+02 Score=22.19 Aligned_cols=34 Identities=21% Similarity=0.377 Sum_probs=13.3
Q ss_pred CccCCCC-CCCCCchHHHHHHHHHHHHHHHHHHhh
Q 024416 208 SQPFPKG-GRKQPSVFYLSISILTLMLLPIFYLIV 241 (268)
Q Consensus 208 ~k~f~~~-~~~~~~~~y~~~~~~~l~~l~lfY~~v 241 (268)
.||+..+ |+..++..-..+-+++++++++|.+|+
T Consensus 8 LKpLNSeyGkVaPGWGTtplM~~~m~lf~vfl~ii 42 (52)
T PF00737_consen 8 LKPLNSEYGKVAPGWGTTPLMGVFMALFAVFLLII 42 (52)
T ss_dssp CCCCCCSTT--BSTTTTHHHHHHHHHHHHHHHHHH
T ss_pred cccccccCCCcCCCccchHHHHHHHHHHHHHHHHH
Confidence 3566544 443333222223333444444454444
No 111
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.19 E-value=51 Score=35.20 Aligned_cols=71 Identities=17% Similarity=0.233 Sum_probs=46.0
Q ss_pred HHHHHHhhccccccccccccCCCCCCCCCCc---cc-cchhhhhhhhcCcccccccccccCC---------------chh
Q 024416 55 AWGVIEEYLMPFVEQVQYEISSKCRLHPDND---MF-RDQEQHKIHVDINEWRCGYCKKSFR---------------AEK 115 (268)
Q Consensus 55 arkIi~e~L~P~~e~~~~~l~~~C~L~P~~D---~F-~~~E~~k~h~~~h~wrC~~CgK~F~---------------sE~ 115 (268)
..+....+..|+...- ....|.+.+|.| +| .+-..|-.-..-+...|..|++.|. +-.
T Consensus 52 ~~~s~~~~~~~~~t~~---~~~~~~~~~~e~~~~if~~d~~~y~~~~~~~~~~C~~C~~~~~~~~~~~~~~~c~~~~s~~ 128 (669)
T KOG2231|consen 52 ETKSNGDSSDAVGTFP---EGRKCDFDEHEDTCVIFFADKLTYTKLEACLHHSCHICDRRFRALYNKKECLHCTEFKSVE 128 (669)
T ss_pred eeeccccccccccccc---cccccccccccceeeeeeccccHHHHHHHHHhhhcCccccchhhhcccCCCccccchhHHH
Confidence 3344444444444321 336799999877 55 3333333333566799999999994 778
Q ss_pred hHhhhhhcccccc
Q 024416 116 FLDQHFDNRHNNL 128 (268)
Q Consensus 116 ~LDlHidnrH~~l 128 (268)
.|+.||--.|+-.
T Consensus 129 ~Lk~H~~~~H~~~ 141 (669)
T KOG2231|consen 129 NLKNHMRDQHKLH 141 (669)
T ss_pred HHHHHHHHhhhhh
Confidence 9999998888743
No 112
>PHA02657 hypothetical protein; Provisional
Probab=21.12 E-value=1e+02 Score=25.16 Aligned_cols=19 Identities=26% Similarity=0.728 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHhhhh
Q 024416 225 SISILTLMLLPIFYLIVYL 243 (268)
Q Consensus 225 ~~~~~~l~~l~lfY~~v~~ 243 (268)
++.+|++++..+-|+++|+
T Consensus 29 Vitvfv~vI~il~flLLYL 47 (95)
T PHA02657 29 VFTIFIFVVCILIYLLIYL 47 (95)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4445555555555555554
No 113
>cd03738 SOCS_SOCS4 SOCS (suppressors of cytokine signaling) box of SOCS4-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=20.78 E-value=1.3e+02 Score=22.43 Aligned_cols=32 Identities=16% Similarity=0.393 Sum_probs=23.1
Q ss_pred HHHHHHHHHhcccCCCCC-C--cchHHHHHHHHHh
Q 024416 166 KNRHLCESLANRCFPINQ-G--PSASRLHELFLRQ 197 (268)
Q Consensus 166 ~~r~~Ce~l~~sCFP~~~-g--~Sa~rL~~~f~~~ 197 (268)
.++|+|+..++++.+.++ + |=-.+|.+|+.+.
T Consensus 5 SLQHLCR~~I~~~t~~~~I~~LPLP~~LK~YLkeY 39 (56)
T cd03738 5 SLQHICRTVICNCTTYDGIDALPIPSSMKLYLKEY 39 (56)
T ss_pred CHHHHHHHHHHhcCCccccccCCCCHHHHHHHHhC
Confidence 379999999999998653 1 2224888986653
No 114
>PF05702 Herpes_UL49_5: Herpesvirus UL49.5 envelope/tegument protein; InterPro: IPR008647 UL49.5 protein consists of 98 amino acids with a calculated molecular mass of 10,155 Da. It contains putative signal peptide and transmembrane domains but lacks a consensus sequence for N glycosylation. UL49.5 protein is an O-glycosylated structural component of the viral envelope [].
Probab=20.68 E-value=1.1e+02 Score=25.16 Aligned_cols=69 Identities=16% Similarity=0.171 Sum_probs=35.3
Q ss_pred HhcccCCCCCCcchHH-HHHHHHHhhccCCCCCCCCccCCCCCCCCCchHHHHHHHHHHHHHHH--HHHhhhheecccc
Q 024416 174 LANRCFPINQGPSASR-LHELFLRQFCDAHKCPRKSQPFPKGGRKQPSVFYLSISILTLMLLPI--FYLIVYLYQREMR 249 (268)
Q Consensus 174 l~~sCFP~~~g~Sa~r-L~~~f~~~~Cd~~TC~~~~k~f~~~~~~~~~~~y~~~~~~~l~~l~l--fY~~v~~~~r~~~ 249 (268)
+...++|++.-+.+.+ =.+-|++- +|.... +|-..+....+++|+..+.++++++. |-.+.=++.+++-
T Consensus 23 l~~~~~~~~~~~~~~~e~~~~FW~a-----~CSArG--v~i~~~s~asV~FY~sL~aV~vall~~aY~aCfRlft~s~~ 94 (98)
T PF05702_consen 23 LSRAASPDGALDIAREESRRDFWSA-----ACSARG--VPIDFPSAASVLFYVSLLAVCVALLAYAYRACFRLFTASMF 94 (98)
T ss_pred HHHhcCCCCccchhHhHHHhccccc-----ccccCc--eecCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 3445667654444321 11236554 455544 34444456777777766666666553 2333335555543
No 115
>PF06422 PDR_CDR: CDR ABC transporter; InterPro: IPR010929 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). In yeast, the PDR and CDR ABC transporters display extensive sequence homology, and confer resistance to several anti-fungal compounds by actively transporting their substrates out of the cell. These transporters have two homologous halves, each with an N-terminal intracellular hydrophilic region that contains an ATP-binding site, followed by a C-terminal membrane-associated region containing six transmembrane segments []. This entry represents a domain of the PDR/CDR ABC transporter comprising extracellular loop 3, transmembrane segment 6 and a linker region.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane
Probab=20.54 E-value=1.6e+02 Score=23.59 Aligned_cols=30 Identities=10% Similarity=-0.003 Sum_probs=15.0
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHHhhhheecc
Q 024416 216 RKQPSVFYLSISILTLMLLPIFYLIVYLYQRE 247 (268)
Q Consensus 216 ~~~~~~~y~~~~~~~l~~l~lfY~~v~~~~r~ 247 (268)
+.|++++.+++.+++ -++++++.+.+...+
T Consensus 47 h~WRN~GIli~f~i~--f~~~~~~~~e~~~~~ 76 (103)
T PF06422_consen 47 HRWRNFGILIAFWIF--FIVLTLLATEFIKFE 76 (103)
T ss_pred chhhhHHHHHHHHHH--HHHHHHHHHHHhccc
Confidence 367777655544443 333444444444444
No 116
>PF11395 DUF2873: Protein of unknown function (DUF2873); InterPro: IPR021532 This entry is represented by the human SARS coronavirus, Orf7b; it is a family of uncharacterised viral proteins.
Probab=20.25 E-value=1.6e+02 Score=20.75 Aligned_cols=15 Identities=40% Similarity=0.656 Sum_probs=6.6
Q ss_pred HHHHHHHHHHHHHHH
Q 024416 222 FYLSISILTLMLLPI 236 (268)
Q Consensus 222 ~y~~~~~~~l~~l~l 236 (268)
+|+.+..+.+.++++
T Consensus 9 fylc~l~~llflv~i 23 (43)
T PF11395_consen 9 FYLCFLSFLLFLVII 23 (43)
T ss_pred HHHHHHHHHHHHHHH
Confidence 455444444433333
No 117
>cd03746 SOCS_WSB1_SWIP1 SOCS (suppressors of cytokine signaling) box of WSB1/SWiP1-like proteins. This subfamily contains WSB-1 (SOCS-box-containing WD-40 protein), part of an E3 ubiquitin ligase for the thyroid-hormone-activating type 2 iodothyronine deiodinase (D2) and SWiP-1 (SOCS box and WD-repeats in Protein), a WD40-containing protein that is expressed in embryonic structures of chickens and regulated by Sonic Hedgehog (Shh). The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=20.13 E-value=59 Score=22.35 Aligned_cols=32 Identities=34% Similarity=0.520 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHhcccCCCCCCcc---hHHHHHHHH
Q 024416 164 VAKNRHLCESLANRCFPINQGPS---ASRLHELFL 195 (268)
Q Consensus 164 ~~~~r~~Ce~l~~sCFP~~~g~S---a~rL~~~f~ 195 (268)
+..++|+|+..++.+++...-.. -.+|.+|+.
T Consensus 3 v~sLQhLCR~~Ir~~~~~~~i~~LpLP~~Lk~YL~ 37 (40)
T cd03746 3 VASLQHLCRMAIRRVMPTQQVKELPIPSKLLEFLT 37 (40)
T ss_pred CcCHHHHHHHHHHHHccccccccCCCCHHHHHHHh
Confidence 45689999999999998653211 236777765
Done!