Query 026654
Match_columns 235
No_of_seqs 80 out of 82
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 10:51:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026654.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026654hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00047 photosystem II biogen 100.0 4E-100 8E-105 688.5 24.0 232 3-234 52-283 (283)
2 PRK13266 Thf1-like protein; Re 100.0 1.6E-95 4E-100 642.8 22.6 215 3-218 1-224 (225)
3 PF11264 ThylakoidFormat: Thyl 100.0 1.5E-94 3.3E-99 633.7 21.3 208 8-215 1-216 (216)
4 PLN03060 inositol phosphatase- 100.0 4.8E-94 1E-98 626.5 21.3 205 6-210 2-206 (206)
5 TIGR03060 PS_II_psb29 photosys 100.0 4.3E-93 9.4E-98 623.5 20.1 204 3-210 1-214 (214)
6 PF11264 ThylakoidFormat: Thyl 95.2 0.03 6.6E-07 50.2 4.7 55 44-98 129-184 (216)
7 PRK13266 Thf1-like protein; Re 94.9 0.06 1.3E-06 48.6 5.9 56 42-97 132-188 (225)
8 TIGR03060 PS_II_psb29 photosys 94.7 0.046 1E-06 49.0 4.6 55 42-97 130-186 (214)
9 PLN03060 inositol phosphatase- 93.5 0.3 6.4E-06 43.7 7.1 47 136-182 41-93 (206)
10 PLN00047 photosystem II biogen 91.1 0.74 1.6E-05 43.0 7.0 47 136-182 94-146 (283)
11 PF11473 B2: RNA binding prote 70.5 4.5 9.7E-05 30.7 2.7 23 175-197 31-53 (73)
12 TIGR02147 Fsuc_second hypothet 59.2 74 0.0016 29.4 8.9 145 28-183 10-161 (271)
13 PF03216 Rhabdo_ncap_2: Rhabdo 58.6 74 0.0016 30.6 8.9 105 88-201 138-262 (357)
14 COG3793 TerB Tellurite resista 58.0 36 0.00078 29.1 6.2 36 73-108 65-100 (144)
15 PF05099 TerB: Tellurite resis 56.5 45 0.00097 26.2 6.3 97 66-180 36-137 (140)
16 KOG0961 Predicted Zn2+-depende 54.9 85 0.0019 33.7 9.4 136 23-199 599-742 (1022)
17 PF06971 Put_DNA-bind_N: Putat 54.2 11 0.00023 26.6 2.0 24 160-183 27-50 (50)
18 PF01841 Transglut_core: Trans 50.7 5.6 0.00012 29.7 0.2 46 45-90 26-72 (113)
19 PF08220 HTH_DeoR: DeoR-like h 50.4 15 0.00032 25.7 2.3 23 161-183 14-36 (57)
20 PF08542 Rep_fac_C: Replicatio 50.2 24 0.00051 25.9 3.5 42 68-114 1-42 (89)
21 KOG0212 Uncharacterized conser 46.6 1.2E+02 0.0027 31.5 8.9 99 74-179 122-225 (675)
22 TIGR00059 L17 ribosomal protei 45.7 26 0.00055 28.6 3.3 77 71-148 8-96 (112)
23 PF08280 HTH_Mga: M protein tr 44.0 28 0.00061 24.4 2.9 27 163-189 21-47 (59)
24 PF10199 Adaptin_binding: Alph 43.8 26 0.00057 28.1 3.1 37 179-215 99-135 (137)
25 PRK05591 rplQ 50S ribosomal pr 43.7 32 0.0007 28.0 3.6 77 71-148 10-98 (113)
26 PF13413 HTH_25: Helix-turn-he 42.8 33 0.00073 24.6 3.2 27 67-93 36-62 (62)
27 PF08279 HTH_11: HTH domain; 42.3 28 0.00061 23.3 2.7 28 160-187 14-41 (55)
28 PRK10880 adenine DNA glycosyla 39.8 3E+02 0.0066 26.3 10.0 82 8-102 5-98 (350)
29 cd00194 UBA Ubiquitin Associat 39.8 48 0.001 20.7 3.3 31 161-192 2-32 (38)
30 PF04772 Flu_B_M2: Influenza B 37.8 63 0.0014 25.8 4.3 35 172-206 43-77 (109)
31 TIGR02895 spore_sigI RNA polym 37.2 2.3E+02 0.005 25.2 8.3 136 48-191 36-195 (218)
32 COG4476 Uncharacterized protei 36.8 1.5E+02 0.0034 23.5 6.2 81 19-101 2-82 (90)
33 PHA00666 putative protease 36.6 3.5E+02 0.0075 25.0 9.6 33 66-98 92-124 (233)
34 KOG1258 mRNA processing protei 35.1 1.1E+02 0.0025 31.4 6.7 87 59-146 99-190 (577)
35 PF00382 TFIIB: Transcription 35.0 48 0.001 23.6 3.0 26 164-189 1-26 (71)
36 COG1938 Archaeal enzymes of AT 34.9 78 0.0017 29.2 5.0 35 82-116 81-115 (244)
37 PF02861 Clp_N: Clp amino term 34.8 39 0.00085 22.1 2.4 27 74-100 25-51 (53)
38 cd00192 PTKc Catalytic domain 33.9 57 0.0012 26.6 3.7 22 51-73 188-209 (262)
39 PF02082 Rrf2: Transcriptional 33.0 46 0.00099 24.5 2.7 43 140-182 2-46 (83)
40 PF01465 GRIP: GRIP domain; I 32.6 1.3E+02 0.0029 20.5 4.7 36 59-95 9-44 (46)
41 PF00627 UBA: UBA/TS-N domain; 31.8 48 0.001 21.0 2.3 30 161-191 3-32 (37)
42 PF07216 LcrG: LcrG protein; 29.8 43 0.00092 26.8 2.1 31 64-94 13-43 (93)
43 smart00346 HTH_ICLR helix_turn 28.4 71 0.0015 23.1 3.1 37 147-185 8-44 (91)
44 cd05034 PTKc_Src_like Catalyti 28.4 65 0.0014 26.8 3.2 20 51-71 185-204 (261)
45 COG2761 FrnE Predicted dithiol 27.4 4.8E+02 0.01 23.8 8.9 111 64-182 47-161 (225)
46 PF13446 RPT: A repeated domai 26.7 1.2E+02 0.0025 21.3 3.8 47 70-116 14-60 (62)
47 PRK10954 periplasmic protein d 26.4 2.2E+02 0.0047 24.3 6.2 36 149-184 110-146 (207)
48 PF12200 DUF3597: Domain of un 26.1 3E+02 0.0065 23.2 6.6 70 119-193 48-120 (127)
49 PF04391 DUF533: Protein of un 25.7 3.5E+02 0.0076 23.8 7.4 21 160-180 162-182 (188)
50 smart00219 TyrKc Tyrosine kina 25.7 1E+02 0.0022 25.3 3.8 22 51-73 185-206 (258)
51 PF05402 PqqD: Coenzyme PQQ sy 25.5 2.3E+02 0.005 19.5 5.5 49 143-191 14-63 (68)
52 PRK08215 sporulation sigma fac 25.5 4.1E+02 0.0089 23.4 7.9 29 163-194 227-255 (258)
53 TIGR02844 spore_III_D sporulat 25.1 52 0.0011 25.2 1.8 22 163-184 21-42 (80)
54 PF13443 HTH_26: Cro/C1-type H 24.7 93 0.002 21.1 2.9 33 60-93 25-57 (63)
55 PF08855 DUF1825: Domain of un 24.3 2.4E+02 0.0053 23.0 5.7 74 88-176 5-87 (108)
56 PRK13910 DNA glycosylase MutY; 24.0 3.1E+02 0.0067 25.6 7.1 42 60-101 13-60 (289)
57 COG0203 RplQ Ribosomal protein 24.0 94 0.002 25.8 3.2 78 70-148 12-101 (116)
58 PF00046 Homeobox: Homeobox do 23.9 1.1E+02 0.0024 20.4 3.2 26 154-179 20-45 (57)
59 PRK11861 bifunctional prephena 23.8 6.3E+02 0.014 25.9 9.8 144 51-211 56-216 (673)
60 PF08014 DUF1704: Domain of un 23.7 6.5E+02 0.014 24.1 9.5 152 39-200 175-346 (349)
61 PF10798 YmgB: Biofilm develop 23.5 2.2E+02 0.0048 20.7 4.8 43 149-193 11-54 (61)
62 PF12069 DUF3549: Protein of u 23.4 88 0.0019 30.1 3.4 33 69-101 122-155 (340)
63 smart00420 HTH_DEOR helix_turn 23.3 82 0.0018 19.9 2.3 23 162-184 15-37 (53)
64 TIGR02573 LcrG_PcrG type III s 22.9 77 0.0017 25.2 2.4 27 68-94 14-40 (90)
65 PF01323 DSBA: DSBA-like thior 22.9 2.6E+02 0.0056 22.6 5.7 128 27-183 15-145 (193)
66 TIGR01128 holA DNA polymerase 22.6 5.2E+02 0.011 22.6 10.6 41 78-118 135-177 (302)
67 PF07638 Sigma70_ECF: ECF sigm 22.2 1.1E+02 0.0024 25.7 3.5 26 164-189 154-179 (185)
68 PRK10681 DNA-binding transcrip 21.8 65 0.0014 28.7 2.1 24 161-184 21-44 (252)
69 smart00342 HTH_ARAC helix_turn 21.8 2.6E+02 0.0056 18.9 4.8 21 163-183 3-23 (84)
70 PF15614 WHIM3: WSTF, HB1, Itc 21.8 1.2E+02 0.0026 21.2 3.0 34 159-192 5-42 (46)
71 cd05056 PTKc_FAK Catalytic dom 21.8 1.3E+02 0.0027 25.3 3.8 20 51-71 189-208 (270)
72 PF07268 EppA_BapA: Exported p 21.6 1.7E+02 0.0037 24.9 4.4 34 60-99 87-124 (139)
73 PF01196 Ribosomal_L17: Riboso 21.4 82 0.0018 24.9 2.4 58 90-148 22-82 (97)
74 cd00092 HTH_CRP helix_turn_hel 21.3 2.1E+02 0.0045 19.2 4.2 26 161-186 25-50 (67)
75 cd05122 PKc_STE Catalytic doma 21.2 1.5E+02 0.0032 23.9 3.9 20 51-72 178-197 (253)
76 cd05058 PTKc_Met_Ron Catalytic 21.1 1.3E+02 0.0028 25.0 3.7 21 51-72 183-203 (262)
77 cd00086 homeodomain Homeodomai 20.9 1.9E+02 0.0042 18.9 3.9 22 159-180 25-46 (59)
78 PF05043 Mga: Mga helix-turn-h 20.7 97 0.0021 22.7 2.5 31 160-190 29-59 (87)
79 KOG3941 Intermediate in Toll s 20.7 53 0.0012 31.8 1.4 50 137-192 64-117 (406)
80 cd07178 terB_like_YebE telluri 20.6 22 0.00047 27.6 -1.0 14 160-173 82-95 (95)
81 PRK04424 fatty acid biosynthes 20.4 55 0.0012 28.1 1.3 23 161-183 21-43 (185)
No 1
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=100.00 E-value=3.8e-100 Score=688.46 Aligned_cols=232 Identities=82% Similarity=1.242 Sum_probs=227.8
Q ss_pred CCCCCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccCccccccchhhhHHHHHHHHhcCCCCchhHHHHHHHH
Q 026654 3 SDVPPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAY 82 (235)
Q Consensus 3 ~~~~~TVSDTKr~F~~~~~~pI~siYrrvv~ELLVe~HLl~~n~~F~yD~lfAlG~vt~fd~fm~GY~pe~~~~~IF~Al 82 (235)
++++||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+||
T Consensus 52 ~~~~~TVSDTKr~F~~~yp~pIpsiYrrvvdELLVElHLLs~n~~F~yDplFALGlVtvfd~fm~GY~Pee~~~~IF~Al 131 (283)
T PLN00047 52 TDVPPTVAETKAKFLKSYKRPIPSIYSTVLQELLVQQHLMRYKKTYRYDPVFALGFVTVYDQLMEGYPSDEDRDAIFKAY 131 (283)
T ss_pred cCCCCcHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHHhccCceeCchhhhhhHHHHHHHHccCCChHHHHHHHHHH
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCCCCHH
Q 026654 83 ITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPT 162 (235)
Q Consensus 83 c~a~~~Dp~q~r~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~~d~~ 162 (235)
|+|+|+||++||+||++|++||+|+|.+++.+|+...|+++++|++||+++++|++||||||||||||+|||.++++||+
T Consensus 132 c~a~g~Dp~qyr~dA~~l~~~A~~~s~~~l~~~l~~~~~l~~~l~~IA~~a~~~~~f~YSRlfAIGLf~LLe~a~~~d~~ 211 (283)
T PLN00047 132 IKALGEDPEQYRKDAAKLEEWARSQTGSSLVDFSSKEGEIEGILKDIAERAGSKGKFSYSRFFAIGLFRLLELANATEPT 211 (283)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhcchHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHhcCCCCHH
Confidence 99999999999999999999999999999999999999999999999988778999999999999999999999999999
Q ss_pred HHHHHHHhcCCChhhhHhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhHHhhccchhhhHHHHHhhhhccccC
Q 026654 163 VLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKREERTEPQKANEAIKKCLGEYLYSH 234 (235)
Q Consensus 163 ~l~~l~~~Lgls~~kv~kDL~lYrs~LeKm~QA~el~eE~~~~ekKKre~r~~~~~~~~~~~~~~~~~~~~~ 234 (235)
.+++||++|||++++|+|||+|||||||||+||+|||||++++|||||++|+++||+|+++|+|+|++++.+
T Consensus 212 ~l~~l~e~Lgls~~kv~KDLdlYrsnLeKm~QA~elmeE~~~~EkKKre~r~~~~~~~~~~~~~~~~~~~~~ 283 (283)
T PLN00047 212 ALEKLCAALNINKRSVDRDLDVYRGLLSKLVQAKELLKEYVEREKKKQEERAESQKANEAVTKCLGELEQAG 283 (283)
T ss_pred HHHHHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHhcccchhccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999998764
No 2
>PRK13266 Thf1-like protein; Reviewed
Probab=100.00 E-value=1.6e-95 Score=642.85 Aligned_cols=215 Identities=40% Similarity=0.717 Sum_probs=201.8
Q ss_pred CCCCCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccCccccccchhhhHHHHHHHHhcCCCCchhHHHHHHHH
Q 026654 3 SDVPPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAY 82 (235)
Q Consensus 3 ~~~~~TVSDTKr~F~~~~~~pI~siYrrvv~ELLVe~HLl~~n~~F~yD~lfAlG~vt~fd~fm~GY~pe~~~~~IF~Al 82 (235)
|+++||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+||
T Consensus 1 m~~~~TVSDtKr~F~~~~p~pI~siYrrvv~ELLVElHLl~~n~~F~yDplfAlGlvt~fd~fm~GY~Pee~~~~IF~Al 80 (225)
T PRK13266 1 MNNRRTVSDSKRAFYAAFPRPINSIYRRVVDELLVELHLLSVNSDFKYDPLFALGLVTVFDRFMQGYRPEEHKDSIFNAL 80 (225)
T ss_pred CCCCCcHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCc--chhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCC--
Q 026654 83 ITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKE--GEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA-- 158 (235)
Q Consensus 83 c~a~~~Dp~q~r~dA~~l~~~A~~~s~~~l~~~~~~~--g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~-- 158 (235)
|+|+|+||++||+||++|++||+|+|.++|.+|+... |+++.+++.+. .+++|++||||||||||||+|||.+++
T Consensus 81 c~a~~~dp~~~r~dA~~l~~~a~~~s~~~i~~~l~~~~~~~~~~l~~~l~-~ia~~~~f~YSRl~AIGL~~LLe~a~~~~ 159 (225)
T PRK13266 81 CQAVGFDPEQLRQDAERLLELAKGKSLKEILSWLTQKALGEPGGLLATLL-AIANNSKFKYSRLFAIGLYTLLEEAQPDL 159 (225)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhccccccchhHHHHHH-HHhcCCCCchHHHHHHHHHHHHHhcCccc
Confidence 9999999999999999999999999999999999764 45555555555 455699999999999999999999987
Q ss_pred -CCH----HHHHHHHHhcCCChhhhHhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhHHhhccchh
Q 026654 159 -TEP----TVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKREERTEPQK 218 (235)
Q Consensus 159 -~d~----~~l~~l~~~Lgls~~kv~kDL~lYrs~LeKm~QA~el~eE~~~~ekKKre~r~~~~~ 218 (235)
+|| +.+++||++||||.+||+|||+|||||||||+||+|||+|++++|||||++|+++++
T Consensus 160 ~~d~~~~~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeKm~Qa~el~ee~~~~erkKre~r~~~~~ 224 (225)
T PRK13266 160 VKDEEKLNEALKDISEGLGLSKEKVEKDLDLYRSNLEKMEQALELIEETLEAERKKREQRQAEKA 224 (225)
T ss_pred ccCHHHHHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 466 579999999999999999999999999999999999999999999999999988764
No 3
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=100.00 E-value=1.5e-94 Score=633.69 Aligned_cols=208 Identities=52% Similarity=0.898 Sum_probs=198.2
Q ss_pred chhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccCccccccchhhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcC
Q 026654 8 TVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALK 87 (235)
Q Consensus 8 TVSDTKr~F~~~~~~pI~siYrrvv~ELLVe~HLl~~n~~F~yD~lfAlG~vt~fd~fm~GY~pe~~~~~IF~Alc~a~~ 87 (235)
|||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||+|+|
T Consensus 1 TVsDtKr~F~~~~~~pI~siYrrvv~ELLVe~HLl~~n~~F~yD~lfalG~vt~fd~fm~GY~p~~~~~~If~Alc~a~~ 80 (216)
T PF11264_consen 1 TVSDTKRAFYKAFPRPIPSIYRRVVDELLVELHLLSVNKDFQYDPLFALGLVTVFDRFMQGYPPEEDKDSIFNALCQALG 80 (216)
T ss_pred ChhHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHhcCCCChhHHHHHHHHHHHHcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHhcCCccccccccCC-cchhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCC-------C
Q 026654 88 EDPEQYRIDAQKLEEWARGQTASSLVEFPSK-EGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA-------T 159 (235)
Q Consensus 88 ~Dp~q~r~dA~~l~~~A~~~s~~~l~~~~~~-~g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~-------~ 159 (235)
+||++||+||+++++||+|+|..+|.+|++. .++.++.|++++.+|++|++||||||||||||+|||.+++ .
T Consensus 81 ~dp~~~r~dA~~l~~~a~~~s~~~l~~~l~~~~~~~~~~l~~~~~~ia~~~~f~YSRl~AIGL~~LLe~a~~~~~~~~~~ 160 (216)
T PF11264_consen 81 FDPEQYRQDAEKLEEWAKGKSIEDLLSWLSQKGGEGDNPLAAILQAIASNPKFKYSRLFAIGLFRLLELAGADLVKDEEK 160 (216)
T ss_pred CCHHHHHHHHHHHHHHHHcCCHHHHHHHHhccccccchHHHHHHHHHhcCCCCchHHHHHHHHHHHHHhcCcccccChhh
Confidence 9999999999999999999999999999976 4456666767777777899999999999999999999988 3
Q ss_pred CHHHHHHHHHhcCCChhhhHhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhHHhhcc
Q 026654 160 EPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKREERTE 215 (235)
Q Consensus 160 d~~~l~~l~~~Lgls~~kv~kDL~lYrs~LeKm~QA~el~eE~~~~ekKKre~r~~ 215 (235)
+++.+++||++||||.+||+|||++||||||||+||++||+|++++||||||+|++
T Consensus 161 ~~~~l~~l~~~l~ls~~kv~kDL~lYrsnLeKm~qA~el~ee~~~~ErkKre~r~~ 216 (216)
T PF11264_consen 161 RPEALEKLSEALGLSKEKVEKDLDLYRSNLEKMAQAKELMEEILEAERKKREERAQ 216 (216)
T ss_pred HHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 46889999999999999999999999999999999999999999999999999964
No 4
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=100.00 E-value=4.8e-94 Score=626.50 Aligned_cols=205 Identities=70% Similarity=1.125 Sum_probs=200.1
Q ss_pred CCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccCccccccchhhhHHHHHHHHhcCCCCchhHHHHHHHHHHh
Q 026654 6 PPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITA 85 (235)
Q Consensus 6 ~~TVSDTKr~F~~~~~~pI~siYrrvv~ELLVe~HLl~~n~~F~yD~lfAlG~vt~fd~fm~GY~pe~~~~~IF~Alc~a 85 (235)
+||||||||+||++||||||||||||||||||||||||||++|+|||||||||||+||+||+||||++|+++||+|||+|
T Consensus 2 ~~TVsDtKr~F~~~~p~pI~siYrrvv~ELLVE~HLl~~n~~f~yD~lfAlGlvt~fd~fm~GY~Pee~~~~IF~Alc~a 81 (206)
T PLN03060 2 VPTVADTKASFLKAYRKPIPSIYSNVIQELLVQQHLMRYNATYKYDPIFALGFVTVYDQLMDGYPNATDRDAIFKAYIEA 81 (206)
T ss_pred CCcHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCCCCHHHHH
Q 026654 86 LKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLE 165 (235)
Q Consensus 86 ~~~Dp~q~r~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~~d~~~l~ 165 (235)
+|+||+|||+||++|++||+|+|.++|.+|++++|+....|++++.++++|++||||||||||||+|||.++++||+.++
T Consensus 82 ~~~dp~~~r~dA~~l~~~a~~~s~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~f~YSRl~AIGL~~LLe~a~~~d~~~l~ 161 (206)
T PLN03060 82 LGEDPDQYRKDAKKLEEWASSQSASGIADFNSGDGEVEAVLKDIAERAAGKTKFHYSRFFAIGLFRLLECAKASDPAVLE 161 (206)
T ss_pred cCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhcccccchHHHHHHHHhhcCCCcchHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 99999999999999999999999999999999988878888888888888999999999999999999999989999999
Q ss_pred HHHHhcCCChhhhHhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhH
Q 026654 166 KLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKR 210 (235)
Q Consensus 166 ~l~~~Lgls~~kv~kDL~lYrs~LeKm~QA~el~eE~~~~ekKKr 210 (235)
+||++||||.+||+|||++||||||||+||+|||+|++++||||+
T Consensus 162 ~l~~~L~ls~~kv~kDL~lYrsnLeKm~qa~el~ee~~~~erkK~ 206 (206)
T PLN03060 162 KLSKALNVSKRSVDRDLDVYRNLLSKLAQAKELIKEYIDRSVCSV 206 (206)
T ss_pred HHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHHHhccC
Confidence 999999999999999999999999999999999999999999984
No 5
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=100.00 E-value=4.3e-93 Score=623.46 Aligned_cols=204 Identities=40% Similarity=0.687 Sum_probs=192.2
Q ss_pred CCCCCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccCccccccchhhhHHHHHHHHhcCCCCchhHHHHHHHH
Q 026654 3 SDVPPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAY 82 (235)
Q Consensus 3 ~~~~~TVSDTKr~F~~~~~~pI~siYrrvv~ELLVe~HLl~~n~~F~yD~lfAlG~vt~fd~fm~GY~pe~~~~~IF~Al 82 (235)
|+++||||||||+||++||||||||||||||||||||||||||++|+|||||||||||+||+||+||||++|+++||+||
T Consensus 1 M~~~~TVSDtKr~F~~~~p~pI~siYrrvv~ELLVElHLl~~n~~F~yDplfAlGlvt~fd~fm~GY~Pee~~~~IF~Al 80 (214)
T TIGR03060 1 MTERRTVSDSKRAFHAAFPRVIPPLYRRVVDELLVELHLLSHQSDFKYDPLFALGLVTVFDRFMEGYRPEEHLDALFDAL 80 (214)
T ss_pred CCCCCcHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcch--hHH-HHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCCC
Q 026654 83 ITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGE--VEG-LLKDIAERASGKGNFSYSRFFAVGLFRLLELANAT 159 (235)
Q Consensus 83 c~a~~~Dp~q~r~dA~~l~~~A~~~s~~~l~~~~~~~g~--~~~-~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~~ 159 (235)
|+|+|+||+|||+||+++++||+|+|.++|.+|+...|. .+. +|++|| +|++||||||||||||+|||.+++.
T Consensus 81 c~a~~~dp~~~r~dA~~l~~~a~~~s~~~i~~~l~~~~~~~~~~l~l~~ia----~n~~f~YSRl~AIGL~~LLe~a~~~ 156 (214)
T TIGR03060 81 CNSNGFDPEQLREDAKQLLEQAKGKGLDEILSWLTQANLSNGGGDTLQGIA----GRHKFKYSRLFAIGLYSLLEEAAPD 156 (214)
T ss_pred HHhcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhccccCCcchhHHHHHh----cCCCcchHHHHHHHHHHHHHhcCcc
Confidence 999999999999999999999999999999999977542 222 566666 4999999999999999999998863
Q ss_pred ---C----HHHHHHHHHhcCCChhhhHhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhH
Q 026654 160 ---E----PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKR 210 (235)
Q Consensus 160 ---d----~~~l~~l~~~Lgls~~kv~kDL~lYrs~LeKm~QA~el~eE~~~~ekKKr 210 (235)
| ++.+++||++||||.+||+|||+|||||||||+||+|||+|++++|||||
T Consensus 157 ~~~d~~~~~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeKm~Qa~el~ee~~~~erkKr 214 (214)
T TIGR03060 157 KDIDEEDLNEILKELSEALGLSYDRVEKDLDLYKSNLEKMKQALELMEETLEAERRKR 214 (214)
T ss_pred cccCHHHHHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHHHhccC
Confidence 4 45799999999999999999999999999999999999999999999986
No 6
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=95.16 E-value=0.03 Score=50.16 Aligned_cols=55 Identities=20% Similarity=0.294 Sum_probs=46.6
Q ss_pred ccCccccccchhhhHHHHHHHHhc-CCCCchhHHHHHHHHHHhcCCCHHHHHHHHH
Q 026654 44 YKRTYQYDPVFALGFVTVYDRLME-GYPSEEDREAIFQAYITALKEDPEQYRIDAQ 98 (235)
Q Consensus 44 ~n~~F~yD~lfAlG~vt~fd~fm~-GY~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~ 98 (235)
-|..|.|.-+||+|+.+..+.--- .-..++.+..+...||+++|+.++.+.+|-.
T Consensus 129 ~~~~f~YSRl~AIGL~~LLe~a~~~~~~~~~~~~~~l~~l~~~l~ls~~kv~kDL~ 184 (216)
T PF11264_consen 129 SNPKFKYSRLFAIGLFRLLELAGADLVKDEEKRPEALEKLSEALGLSKEKVEKDLD 184 (216)
T ss_pred cCCCCchHHHHHHHHHHHHHhcCcccccChhhHHHHHHHHHHHcCCCHHHHHhhHH
Confidence 478999999999999999987654 2445678888999999999999999998853
No 7
>PRK13266 Thf1-like protein; Reviewed
Probab=94.90 E-value=0.06 Score=48.60 Aligned_cols=56 Identities=18% Similarity=0.316 Sum_probs=47.5
Q ss_pred hcccCccccccchhhhHHHHHHHHhcC-CCCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 026654 42 MRYKRTYQYDPVFALGFVTVYDRLMEG-YPSEEDREAIFQAYITALKEDPEQYRIDA 97 (235)
Q Consensus 42 l~~n~~F~yD~lfAlG~vt~fd~fm~G-Y~pe~~~~~IF~Alc~a~~~Dp~q~r~dA 97 (235)
..-|..|.|+-+||+|+.+..+.---. ...++++..+...+|.++|+..+.+.+|-
T Consensus 132 ia~~~~f~YSRl~AIGL~~LLe~a~~~~~~d~~~~~~~l~~l~~~L~ls~~kv~KDL 188 (225)
T PRK13266 132 IANNSKFKYSRLFAIGLYTLLEEAQPDLVKDEEKLNEALKDISEGLGLSKEKVEKDL 188 (225)
T ss_pred HhcCCCCchHHHHHHHHHHHHHhcCcccccCHHHHHHHHHHHHHHcCCCHHHHHhhH
Confidence 346899999999999999999876542 45566889999999999999999988884
No 8
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=94.70 E-value=0.046 Score=49.00 Aligned_cols=55 Identities=20% Similarity=0.347 Sum_probs=46.5
Q ss_pred hcccCccccccchhhhHHHHHHHHhcCC--CCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 026654 42 MRYKRTYQYDPVFALGFVTVYDRLMEGY--PSEEDREAIFQAYITALKEDPEQYRIDA 97 (235)
Q Consensus 42 l~~n~~F~yD~lfAlG~vt~fd~fm~GY--~pe~~~~~IF~Alc~a~~~Dp~q~r~dA 97 (235)
..-|..|.|+-+||+|+.+..+. .+|. ..++++..+...+|.++|+..+.+.+|-
T Consensus 130 ia~n~~f~YSRl~AIGL~~LLe~-a~~~~~~d~~~~~~~l~~l~~~L~ls~~kv~KDL 186 (214)
T TIGR03060 130 IAGRHKFKYSRLFAIGLYSLLEE-AAPDKDIDEEDLNEILKELSEALGLSYDRVEKDL 186 (214)
T ss_pred HhcCCCcchHHHHHHHHHHHHHh-cCcccccCHHHHHHHHHHHHHHcCCCHHHHHhhH
Confidence 34689999999999999999984 4443 4567788999999999999999988884
No 9
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=93.46 E-value=0.3 Score=43.68 Aligned_cols=47 Identities=13% Similarity=0.387 Sum_probs=38.7
Q ss_pred CCCCcchHHHHHHHHHHHhh-cCCC----C-HHHHHHHHHhcCCChhhhHhhH
Q 026654 136 KGNFSYSRFFAVGLFRLLEL-ANAT----E-PTVLEKLCAVLNVNKRSVDRDL 182 (235)
Q Consensus 136 ~~~f~YSRlfAIGLf~LLE~-~~~~----d-~~~l~~l~~~Lgls~~kv~kDL 182 (235)
|..|.|+-+||+||.+..+. .... + ....+.+|+++|+.++.+.+|-
T Consensus 41 n~~f~yD~lfAlGlvt~fd~fm~GY~Pee~~~~IF~Alc~a~~~dp~~~r~dA 93 (206)
T PLN03060 41 NATYKYDPIFALGFVTVYDQLMDGYPNATDRDAIFKAYIEALGEDPDQYRKDA 93 (206)
T ss_pred ccCceeCchHHhhHHHHHHHHHcCCCChHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 89999999999999999943 3332 2 2458999999999999988886
No 10
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=91.12 E-value=0.74 Score=43.00 Aligned_cols=47 Identities=15% Similarity=0.377 Sum_probs=38.7
Q ss_pred CCCCcchHHHHHHHHHHHhh-cCCC----C-HHHHHHHHHhcCCChhhhHhhH
Q 026654 136 KGNFSYSRFFAVGLFRLLEL-ANAT----E-PTVLEKLCAVLNVNKRSVDRDL 182 (235)
Q Consensus 136 ~~~f~YSRlfAIGLf~LLE~-~~~~----d-~~~l~~l~~~Lgls~~kv~kDL 182 (235)
|..|.|+-+||+||.+..+. .... | ....+.+|+++|+.++.+.+|-
T Consensus 94 n~~F~yDplFALGlVtvfd~fm~GY~Pee~~~~IF~Alc~a~g~Dp~qyr~dA 146 (283)
T PLN00047 94 KKTYRYDPVFALGFVTVYDQLMEGYPSDEDRDAIFKAYIKALGEDPEQYRKDA 146 (283)
T ss_pred ccCceeCchhhhhhHHHHHHHHccCCChHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 89999999999999999943 3332 2 2458999999999999988886
No 11
>PF11473 B2: RNA binding protein B2; InterPro: IPR024377 Protein B2 binds double-strand RNA (dsRNA) with high affinity and suppresses the host RNA silencing-based antiviral response. B2 is expressed by the insect Flock House virus (FHV) as a counter-defense mechanism against antiviral RNA silencing during infection. In vitro, B2 binds to dsRNA as a dimer and inhibits the cleavage of it by Dicer. B2 blocks cleavage of the FHV genome by Dicer and also the incorporation of FHV small interfering RNAs into the RNA-induced silencing complex [].; PDB: 2AZ2_A 2B9Z_A 2AZ0_A.
Probab=70.47 E-value=4.5 Score=30.72 Aligned_cols=23 Identities=30% Similarity=0.366 Sum_probs=19.6
Q ss_pred hhhhHhhHHHHHhhHHHHHHHHH
Q 026654 175 KRSVDRDLDVYRNLLSKLLQAKE 197 (235)
Q Consensus 175 ~~kv~kDL~lYrs~LeKm~QA~e 197 (235)
+++|.||||-|+.-|.||++-.-
T Consensus 31 p~~V~kDLdn~kaCL~K~e~T~~ 53 (73)
T PF11473_consen 31 PNNVRKDLDNYKACLNKAEATVF 53 (73)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHH
Confidence 46999999999999999988543
No 12
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=59.20 E-value=74 Score=29.37 Aligned_cols=145 Identities=14% Similarity=0.265 Sum_probs=82.9
Q ss_pred hhHHHHHHHHHHhhhcccCccccccc-hhhhHHH--HHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Q 026654 28 YNTVLQELIVQQHLMRYKRTYQYDPV-FALGFVT--VYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWA 104 (235)
Q Consensus 28 Yrrvv~ELLVe~HLl~~n~~F~yD~l-fAlG~vt--~fd~fm~GY~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~~l~~~A 104 (235)
||..+.+-..+-.- .|..|++=.+ -.+||.+ -+..+++|=+|-. +.-..-+++++|+++..-. --..|....
T Consensus 10 YR~fl~d~ye~rk~--~~p~fS~R~fa~~~G~ss~s~L~~v~~Gkr~Ls--~~~~~k~a~~l~L~~~E~~-yF~~lV~f~ 84 (271)
T TIGR02147 10 YRKYLRDYYEERKK--TDPAFSWRFFAEKAGFSSTSYLNDIIKGKKNLT--KRMIPKFAEALGLDEKEAA-YFEAMVNFG 84 (271)
T ss_pred HHHHHHHHHHHHhc--cCcCcCHHHHHHHhCCCCHHHHHHHHcCCCCCC--HHHHHHHHHHcCCCHHHHH-HHHHHHHHh
Confidence 77788887777543 3445666666 3488876 5678899998765 5566788999999997632 233444444
Q ss_pred hcCCccccccccCCcchhHHHHHHHHHHhcCCCCC-cchHHHHHHHHHHHhhcCCC-CHHHHHHHHHhcC--CChhhhHh
Q 026654 105 RGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNF-SYSRFFAVGLFRLLELANAT-EPTVLEKLCAVLN--VNKRSVDR 180 (235)
Q Consensus 105 ~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~~~~f-~YSRlfAIGLf~LLE~~~~~-d~~~l~~l~~~Lg--ls~~kv~k 180 (235)
+..+.++-..+..+ +..+...-..+.-+.+.| .|+.+..-.|..|+...+.. ||+ .|+..++ +|.+.|+.
T Consensus 85 ~ak~~~~k~~~~~~---~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~---~ia~~l~p~is~~ev~~ 158 (271)
T TIGR02147 85 QAKTDTEKQQFFEE---MQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPE---ELAKRCFPKISAEQVKE 158 (271)
T ss_pred ccCCHHHHHHHHHH---HHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHH---HHHHHhCCCCCHHHHHH
Confidence 44444322221110 000000000011112333 67788888888888776554 655 3555555 66666665
Q ss_pred hHH
Q 026654 181 DLD 183 (235)
Q Consensus 181 DL~ 183 (235)
=|+
T Consensus 159 sL~ 161 (271)
T TIGR02147 159 SLD 161 (271)
T ss_pred HHH
Confidence 554
No 13
>PF03216 Rhabdo_ncap_2: Rhabdovirus nucleoprotein; InterPro: IPR004902 This is a family of Rhabdovirus nucleocapsid proteins. These proteins undergo phosphorylation.; GO: 0019013 viral nucleocapsid
Probab=58.59 E-value=74 Score=30.56 Aligned_cols=105 Identities=18% Similarity=0.208 Sum_probs=72.1
Q ss_pred CCHHHHHHH-HHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCCCCHHH---
Q 026654 88 EDPEQYRID-AQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTV--- 163 (235)
Q Consensus 88 ~Dp~q~r~d-A~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~~d~~~--- 163 (235)
.|-++.-+- -++|.++|.++...++..|....+ .++.|+.-+.+..+ -|--+.|+=|+ ++++++++..
T Consensus 138 Y~VdKM~kY~~~KL~~L~~sqGv~EL~~~~~~~~----~l~kl~~~vRpGQK-ltkaiyg~IL~---~l~dp~t~~~aka 209 (357)
T PF03216_consen 138 YSVDKMIKYIQNKLERLATSQGVGELQHFSADRA----ALAKLAACVRPGQK-LTKAIYGFILF---ELADPQTQRRAKA 209 (357)
T ss_pred hcHHHHHHHHHHHHHHHhhccCcchhheecccHH----HHHHHHHhcCchhH-HHHHHHHHHHH---HhcCcccHHHHHH
Confidence 344444333 478999999999999999987655 45666654432222 34444444333 5566766533
Q ss_pred ----------------HHHHHHhcCCChhhhHhhHHHHHhhHHHHHHHHHHHHH
Q 026654 164 ----------------LEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKE 201 (235)
Q Consensus 164 ----------------l~~l~~~Lgls~~kv~kDL~lYrs~LeKm~QA~el~eE 201 (235)
..+-+..||.++..+--||- |+|+.+-.-|.+.||.-
T Consensus 210 l~a~rL~gTGMtmiglFtqAa~nlGa~pA~LLedLc-m~s~v~sarrivkLm~~ 262 (357)
T PF03216_consen 210 LFAMRLNGTGMTMIGLFTQAAKNLGATPADLLEDLC-MGSLVESARRIVKLMRQ 262 (357)
T ss_pred HHHhhhcCCCceehHHHHHHHHhcCCCcHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 34445789999999999995 89999999999999873
No 14
>COG3793 TerB Tellurite resistance protein [Inorganic ion transport and metabolism]
Probab=58.01 E-value=36 Score=29.09 Aligned_cols=36 Identities=22% Similarity=0.219 Sum_probs=30.1
Q ss_pred hhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCC
Q 026654 73 EDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQT 108 (235)
Q Consensus 73 ~~~~~IF~Alc~a~~~Dp~q~r~dA~~l~~~A~~~s 108 (235)
+....||+.+|.+.+.|++.=+..+.++.+-.++.+
T Consensus 65 ~~i~~~~~~~~~~~~~d~~~gk~ea~~~I~~lk~d~ 100 (144)
T COG3793 65 NEINEIFETLVGSFDTDFEIGKREAMKEIEDLKHDT 100 (144)
T ss_pred HHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHhcCCh
Confidence 478899999999999999988888888876666544
No 15
>PF05099 TerB: Tellurite resistance protein TerB; InterPro: IPR007791 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Direct interaction between DnaK and djlA is needed for the induction of the wcaABCDE operon which is involved in the synthesis of a colanic acid polysaccharide capsule. The colanic acid capsule may help the bacterium survive conditions outside the host [, ]; PDB: 2H5N_D 2JXU_A.
Probab=56.54 E-value=45 Score=26.19 Aligned_cols=97 Identities=20% Similarity=0.240 Sum_probs=49.7
Q ss_pred hcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcc-hHH
Q 026654 66 MEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSY-SRF 144 (235)
Q Consensus 66 m~GY~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~~~~f~Y-SRl 144 (235)
-.|--.++++..|-+.+..-.++++.....-.+.+...... ..+.+..+..|. +.+.. -|.
T Consensus 36 aDG~v~~~E~~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~------------~~~~~~~~~~l~------~~~~~~~r~ 97 (140)
T PF05099_consen 36 ADGEVDPEEIEAIRQLLAERFGLSPEEAEELIELADELKQE------------PIDLEELLRELR------DSLSPEERE 97 (140)
T ss_dssp TTSS--CHHHHHHHHHHHHCGCGSCHHHHHHHHHHCHHHHH------------CCHHHHHHHHHC------TS--HHHHH
T ss_pred cCCCCCHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHhc------------cccHHHHHHHHH------HhhchHHHH
Confidence 45666778888888888888888877766554444333222 223333444442 22111 222
Q ss_pred -HHHHHHHHHhhcCCC---CHHHHHHHHHhcCCChhhhHh
Q 026654 145 -FAVGLFRLLELANAT---EPTVLEKLCAVLNVNKRSVDR 180 (235)
Q Consensus 145 -fAIGLf~LLE~~~~~---d~~~l~~l~~~Lgls~~kv~k 180 (235)
+--.++.+....|.- +.+.+.++++.||++.+.+++
T Consensus 98 ~ll~~l~~ia~ADG~~~~~E~~~l~~ia~~L~i~~~~~~~ 137 (140)
T PF05099_consen 98 DLLRMLIAIAYADGEISPEEQEFLRRIAEALGISEEDFQR 137 (140)
T ss_dssp HHHHHHHHHCTCTTC-SCCHHHHHHHHHHHCTS-SS----
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHHHHcCCCHHHHhc
Confidence 222333333333331 345699999999999987753
No 16
>KOG0961 consensus Predicted Zn2+-dependent endopeptidase, insulinase superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=54.86 E-value=85 Score=33.66 Aligned_cols=136 Identities=24% Similarity=0.275 Sum_probs=91.1
Q ss_pred cCCcchhHHHHHHHHHHhhhcccCccccccchhhhHHHHHHHHh--------cCCCCchhHHHHHHHHHHhcCCCHHHHH
Q 026654 23 PIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLM--------EGYPSEEDREAIFQAYITALKEDPEQYR 94 (235)
Q Consensus 23 pI~siYrrvv~ELLVe~HLl~~n~~F~yD~lfAlG~vt~fd~fm--------~GY~pe~~~~~IF~Alc~a~~~Dp~q~r 94 (235)
.||.=|-++++++ +-|+.+-+.+-+.| .|+.-.+++|. .||+---.=- .-+..-+=+||++++
T Consensus 599 tiptp~~~s~~~v--~~~~~s~~id~si~----~g~~G~~~~lvn~~Ikv~a~~Y~~~v~Wi---~~~l~~~VfD~~Ri~ 669 (1022)
T KOG0961|consen 599 TIPTPVLTSADDV--AKHFTSDLIDHSIQ----VGVSGLYDRLVNLRIKVGADKYPLLVKWI---QIFLQGVVFDPSRIH 669 (1022)
T ss_pred CCCcchhhhHHHH--HHHHHhhhhhhhhc----ccccccchhheeEEEEEccCCcchhHHHH---HHHhhhhccCHHHHH
Confidence 3566677777774 66787777665544 68888999986 6897433322 334567779999999
Q ss_pred HHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCC
Q 026654 95 IDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVN 174 (235)
Q Consensus 95 ~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls 174 (235)
+-++++.. ++.+| - -++.|.-|-++++-||.-=.+--..|+-.++++-+.+
T Consensus 670 ~~~~~~l~--------~i~~~-----------------K-Rdg~~vlss~~~~~lY~~~slk~s~d~L~~Ek~l~ei--- 720 (1022)
T KOG0961|consen 670 QCAQKLLG--------EIRDR-----------------K-RDGCTVLSSAVASMLYGKNSLKISFDELVLEKLLEEI--- 720 (1022)
T ss_pred HHHHHHHh--------hhhhh-----------------h-cCccEehHHHHHHHHhcccchhhcccHHHHHHHHHHH---
Confidence 99998863 33333 1 2788888999999888643222234665555554443
Q ss_pred hhhhHhhHHHHHhhHHHHHHHHHHH
Q 026654 175 KRSVDRDLDVYRNLLSKLLQAKELL 199 (235)
Q Consensus 175 ~~kv~kDL~lYrs~LeKm~QA~el~ 199 (235)
..+|++| =.+.|+|++|++.++
T Consensus 721 ~~~v~n~---~~~Il~~~e~mR~y~ 742 (1022)
T KOG0961|consen 721 SKDVMNN---PEAILEKLEQMRSYA 742 (1022)
T ss_pred HHHHhcC---HHHHHHHHHHHHHHH
Confidence 3456666 578899999988743
No 17
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=54.25 E-value=11 Score=26.61 Aligned_cols=24 Identities=25% Similarity=0.405 Sum_probs=18.5
Q ss_pred CHHHHHHHHHhcCCChhhhHhhHH
Q 026654 160 EPTVLEKLCAVLNVNKRSVDRDLD 183 (235)
Q Consensus 160 d~~~l~~l~~~Lgls~~kv~kDL~ 183 (235)
+.-.-.+|++.+|+++.-|.|||.
T Consensus 27 ~~vSS~~La~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 27 ERVSSQELAEALGITPAQVRKDLS 50 (50)
T ss_dssp SEE-HHHHHHHHTS-HHHHHHHHH
T ss_pred eeECHHHHHHHHCCCHHHhcccCC
Confidence 334567899999999999999984
No 18
>PF01841 Transglut_core: Transglutaminase-like superfamily; InterPro: IPR002931 This domain is found in many proteins known to have transglutaminase activity, i.e. which cross-link proteins through an acyl-transfer reaction between the gamma-carboxamide group of peptide-bound glutamine and the epsilon-amino group of peptide-bound lysine, resulting in a epsilon-(gamma-glutamyl)lysine isopeptide bond. Tranglutaminases have been found in a diverse range of species, from bacteria through to mammals. The enzymes require calcium binding and their activity leads to post-translational modification of proteins through acyl-transfer reactions, involving peptidyl glutamine residues as acyl donors and a variety of primary amines as acyl acceptors, with the generation of proteinase resistant isopeptide bonds []. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' []. On the basis of the experimentally demonstrated activity of the Methanobacterium phage psiM2 pseudomurein endoisopeptidase [], it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease []. A subunit of plasma Factor XIII revealed that each Factor XIIIA subunit is composed of four domains (termed N-terminal beta-sandwich, core domain (containing the catalytic and the regulatory sites), and C-terminal beta-barrels 1 and 2) and that two monomers assemble into the native dimer through the surfaces in domains 1 and 2, in opposite orientation. This organisation in four domains is highly conserved during evolution among transglutaminase isoforms [].; PDB: 2F4M_A 2F4O_A 1GGY_B 1FIE_B 1GGU_B 1GGT_B 1F13_A 1QRK_B 1EVU_A 1EX0_B ....
Probab=50.68 E-value=5.6 Score=29.73 Aligned_cols=46 Identities=26% Similarity=0.375 Sum_probs=31.3
Q ss_pred cCccccc-cchhhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCH
Q 026654 45 KRTYQYD-PVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDP 90 (235)
Q Consensus 45 n~~F~yD-~lfAlG~vt~fd~fm~GY~pe~~~~~IF~Alc~a~~~Dp 90 (235)
+.++.|+ +-..-+-.++.+-|..|+=.-.+...+|.|||.++|.+.
T Consensus 26 ~~~~~y~~~~~~~~~~~~~~~l~~~~G~C~~~a~l~~allr~~Gipa 72 (113)
T PF01841_consen 26 RSNIRYDDPNYSPGPRDASEVLRSGRGDCEDYASLFVALLRALGIPA 72 (113)
T ss_dssp CCCCCEC-TCCCCCCTTHHHHHHCEEESHHHHHHHHHHHHHHHT--E
T ss_pred HhCcEEeCCCCCCCCCCHHHHHHcCCCccHHHHHHHHHHHhhCCCce
Confidence 3556666 333444444666666777778899999999999999864
No 19
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=50.42 E-value=15 Score=25.68 Aligned_cols=23 Identities=22% Similarity=0.455 Sum_probs=20.3
Q ss_pred HHHHHHHHHhcCCChhhhHhhHH
Q 026654 161 PTVLEKLCAVLNVNKRSVDRDLD 183 (235)
Q Consensus 161 ~~~l~~l~~~Lgls~~kv~kDL~ 183 (235)
.-.+++|++.+|.|...+.+||.
T Consensus 14 ~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHH
Confidence 34588999999999999999995
No 20
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=50.19 E-value=24 Score=25.91 Aligned_cols=42 Identities=24% Similarity=0.327 Sum_probs=28.2
Q ss_pred CCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCcccccc
Q 026654 68 GYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVE 114 (235)
Q Consensus 68 GY~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~~l~~~A~~~s~~~l~~ 114 (235)
|.||+++-+.|++++.+. +-...|.....+... |.|..+|..
T Consensus 1 ~~p~~~~i~~i~~~~~~~---~~~~~~~~~~~l~~~--G~s~~~Il~ 42 (89)
T PF08542_consen 1 DWPPPEVIEEILESCLNG---DFKEARKKLYELLVE--GYSASDILK 42 (89)
T ss_dssp TS--HHHHHHHHHHHHHT---CHHHHHHHHHHHHHT--T--HHHHHH
T ss_pred CCCCHHHHHHHHHHHHhC---CHHHHHHHHHHHHHc--CCCHHHHHH
Confidence 568888888888888776 777777777777654 777766653
No 21
>KOG0212 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.62 E-value=1.2e+02 Score=31.55 Aligned_cols=99 Identities=18% Similarity=0.214 Sum_probs=67.8
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHH
Q 026654 74 DREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLL 153 (235)
Q Consensus 74 ~~~~IF~Alc~a~~~Dp~q~r~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LL 153 (235)
.-+.||+++|+-........|.-|+-+-...+....++=.+| .++.....+.+++ ...-.++|.|-|+-.++|
T Consensus 122 ~Fn~iFdvL~klsaDsd~~V~~~aeLLdRLikdIVte~~~tF-----sL~~~ipLL~eri--y~~n~~tR~flv~Wl~~L 194 (675)
T KOG0212|consen 122 YFNEIFDVLCKLSADSDQNVRGGAELLDRLIKDIVTESASTF-----SLPEFIPLLRERI--YVINPMTRQFLVSWLYVL 194 (675)
T ss_pred chHHHHHHHHHHhcCCccccccHHHHHHHHHHHhcccccccc-----CHHHHHHHHHHHH--hcCCchHHHHHHHHHHHH
Confidence 457899999998887777777666655444442222111111 3455566677777 444579999999999999
Q ss_pred hhcCCC-----CHHHHHHHHHhcCCChhhhH
Q 026654 154 ELANAT-----EPTVLEKLCAVLNVNKRSVD 179 (235)
Q Consensus 154 E~~~~~-----d~~~l~~l~~~Lgls~~kv~ 179 (235)
....+- -|+.+.-|.+.||=+.+.|.
T Consensus 195 ds~P~~~m~~yl~~~ldGLf~~LsD~s~eVr 225 (675)
T KOG0212|consen 195 DSVPDLEMISYLPSLLDGLFNMLSDSSDEVR 225 (675)
T ss_pred hcCCcHHHHhcchHHHHHHHHHhcCCcHHHH
Confidence 766552 26778888889988887776
No 22
>TIGR00059 L17 ribosomal protein L17. Eubacterial and mitochondrial. The mitochondrial form, from yeast, contains an additional 110 amino acids C-terminal to the region found by this model.
Probab=45.73 E-value=26 Score=28.64 Aligned_cols=77 Identities=21% Similarity=0.308 Sum_probs=60.1
Q ss_pred CchhHHHHHHHHHHhcC---------CCHHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCC
Q 026654 71 SEEDREAIFQAYITALK---------EDPEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGN 138 (235)
Q Consensus 71 pe~~~~~IF~Alc~a~~---------~Dp~q~r~dA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~~~~ 138 (235)
+.+||.+++..++.+|= --+.++|.-|++|..+|+..+.. .+..|+.....+..++..|+.+-. +.+
T Consensus 8 ~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rR~~~~~l~~~~~v~KLf~~lapry~-~R~ 86 (112)
T TIGR00059 8 TSAHRKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRREAKAYIRNKEIVHKLFSEIAPRYA-QRP 86 (112)
T ss_pred CHHHHHHHHHHHHHHHHHCCeEEECHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHhCCHHHHHHHHHHHHHHhC-CCC
Confidence 46799999999999873 35789999999999999976643 445666666678888999998875 455
Q ss_pred CcchHHHHHH
Q 026654 139 FSYSRFFAVG 148 (235)
Q Consensus 139 f~YSRlfAIG 148 (235)
.-|+|+.=+|
T Consensus 87 GGYTRI~kl~ 96 (112)
T TIGR00059 87 GGYTRILKLG 96 (112)
T ss_pred CCeEEEEECC
Confidence 5899987655
No 23
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=43.97 E-value=28 Score=24.38 Aligned_cols=27 Identities=22% Similarity=0.555 Sum_probs=21.6
Q ss_pred HHHHHHHhcCCChhhhHhhHHHHHhhH
Q 026654 163 VLEKLCAVLNVNKRSVDRDLDVYRNLL 189 (235)
Q Consensus 163 ~l~~l~~~Lgls~~kv~kDL~lYrs~L 189 (235)
.+++||+.+|+|...+.+|++-.+..+
T Consensus 21 ~~~ela~~l~~S~rti~~~i~~L~~~f 47 (59)
T PF08280_consen 21 TLKELAKKLNISERTIKNDINELNEFF 47 (59)
T ss_dssp BHHHHHHHCTS-HHHHHHHHHHHHTT-
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 478999999999999999998766543
No 24
>PF10199 Adaptin_binding: Alpha and gamma adaptin binding protein p34; InterPro: IPR019341 p34 is a protein involved in membrane trafficking. It is known to interact with both alpha and gamma adaptin []. It has been speculated that p34 may play a chaperone role such as preventing the soluble adaptors from co-assembling with soluble clathrin, or helping to remove the adaptors from the coated vesicle. It may also aid in the recruitment of soluble adaptors onto the membrane [].
Probab=43.75 E-value=26 Score=28.07 Aligned_cols=37 Identities=16% Similarity=0.447 Sum_probs=31.8
Q ss_pred HhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhHHhhcc
Q 026654 179 DRDLDVYRNLLSKLLQAKELLKEYVDREKKKREERTE 215 (235)
Q Consensus 179 ~kDL~lYrs~LeKm~QA~el~eE~~~~ekKKre~r~~ 215 (235)
+.|++-+-.+++||.++++....+=..+||+++.+.+
T Consensus 99 ~~~~e~~e~lm~kl~~~R~~~~~lpd~qRr~~Aakva 135 (137)
T PF10199_consen 99 EDDVEDFEQLMSKLQAMRDMAASLPDEQRRRMAAKVA 135 (137)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 4466678889999999999999999999999998754
No 25
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=43.70 E-value=32 Score=28.05 Aligned_cols=77 Identities=22% Similarity=0.302 Sum_probs=60.5
Q ss_pred CchhHHHHHHHHHHhcC---------CCHHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCC
Q 026654 71 SEEDREAIFQAYITALK---------EDPEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGN 138 (235)
Q Consensus 71 pe~~~~~IF~Alc~a~~---------~Dp~q~r~dA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~~~~ 138 (235)
+.+||.+++..++.+|= --+.++|.-|++|..+|+.-+.. .+..|+.....+..++..|+.+-.+ .+
T Consensus 10 ~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~aK~~~~~~rR~~~~~L~~~~~v~KLf~~lapry~~-R~ 88 (113)
T PRK05591 10 TSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHARRQAFARLRDKEAVHKLFDEIAPRYAD-RN 88 (113)
T ss_pred ChHHHHHHHHHHHHHHHHcCeEEecHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHhCCHHHHHHHHHHHHHHhCc-CC
Confidence 56799999999999874 34789999999999999976653 3445666666788888999988764 55
Q ss_pred CcchHHHHHH
Q 026654 139 FSYSRFFAVG 148 (235)
Q Consensus 139 f~YSRlfAIG 148 (235)
.-|+|++-+|
T Consensus 89 GGYTRI~k~~ 98 (113)
T PRK05591 89 GGYTRILKLG 98 (113)
T ss_pred CCeEEEEECC
Confidence 5899988776
No 26
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=42.75 E-value=33 Score=24.60 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=17.2
Q ss_pred cCCCCchhHHHHHHHHHHhcCCCHHHH
Q 026654 67 EGYPSEEDREAIFQAYITALKEDPEQY 93 (235)
Q Consensus 67 ~GY~pe~~~~~IF~Alc~a~~~Dp~q~ 93 (235)
+++|++---......+|+.+|.||+.+
T Consensus 36 ~~lp~~~y~rg~lr~Ya~~Lgld~~~l 62 (62)
T PF13413_consen 36 DSLPSPVYARGYLRKYARFLGLDPDEL 62 (62)
T ss_dssp CCSSSHHHHHHHHHHHHHHTT--HHHH
T ss_pred hhCCcHHHHHHHHHHHHHHhCcCcccC
Confidence 345555556667778888999998764
No 27
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=42.31 E-value=28 Score=23.31 Aligned_cols=28 Identities=32% Similarity=0.610 Sum_probs=22.0
Q ss_pred CHHHHHHHHHhcCCChhhhHhhHHHHHh
Q 026654 160 EPTVLEKLCAVLNVNKRSVDRDLDVYRN 187 (235)
Q Consensus 160 d~~~l~~l~~~Lgls~~kv~kDL~lYrs 187 (235)
++-..++|++.||+|...|.+||..-+.
T Consensus 14 ~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 14 EPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp TSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3456889999999999999999976544
No 28
>PRK10880 adenine DNA glycosylase; Provisional
Probab=39.80 E-value=3e+02 Score=26.35 Aligned_cols=82 Identities=18% Similarity=0.301 Sum_probs=52.4
Q ss_pred chhHhHHHHHhhCCC-c-----CCcchhHHHHHHHHHHhhhcccCccccccchhhhHHHHHHHHhcCCCCchhHHH----
Q 026654 8 TVAETKMNFLKLYKR-P-----IPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREA---- 77 (235)
Q Consensus 8 TVSDTKr~F~~~~~~-p-----I~siYrrvv~ELLVe~HLl~~n~~F~yD~lfAlG~vt~fd~fm~GY~pe~~~~~---- 77 (235)
..++.-.+.|..|.| + -..-|+-.|-|+|.++= + -=-+..+|++||+.||..++...
T Consensus 5 ~~~~~ll~W~~~~~r~~lpWr~~~dpy~ilVseILlQQT------~-------v~~v~~~~~rl~~~fPt~~~La~a~~e 71 (350)
T PRK10880 5 QFSAQVLDWYDKYGRKTLPWQIDKTPYKVWLSEVMLQQT------Q-------VATVIPYFERFMARFPTVTDLANAPLD 71 (350)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhhc------c-------HHHHHHHHHHHHHHCcCHHHHHCcCHH
Confidence 356677788999886 3 45679999999998852 1 11255789999999986544221
Q ss_pred HHHHHHHhcCC--CHHHHHHHHHHHHH
Q 026654 78 IFQAYITALKE--DPEQYRIDAQKLEE 102 (235)
Q Consensus 78 IF~Alc~a~~~--Dp~q~r~dA~~l~~ 102 (235)
=...++..+|+ -+..+++-|+.+.+
T Consensus 72 el~~~~~glGyy~RAr~L~~~A~~i~~ 98 (350)
T PRK10880 72 EVLHLWTGLGYYARARNLHKAAQQVAT 98 (350)
T ss_pred HHHHHHHcCChHHHHHHHHHHHHHHHH
Confidence 12245567887 44444455555543
No 29
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=39.76 E-value=48 Score=20.71 Aligned_cols=31 Identities=16% Similarity=0.276 Sum_probs=24.3
Q ss_pred HHHHHHHHHhcCCChhhhHhhHHHHHhhHHHH
Q 026654 161 PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKL 192 (235)
Q Consensus 161 ~~~l~~l~~~Lgls~~kv~kDL~lYrs~LeKm 192 (235)
++.+++|.+ +|++.+.+.+=|....+++++-
T Consensus 2 ~~~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A 32 (38)
T cd00194 2 EEKLEQLLE-MGFSREEARKALRATNNNVERA 32 (38)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHHHhCCCHHHH
Confidence 456667666 8999999999998888887653
No 30
>PF04772 Flu_B_M2: Influenza B matrix protein 2 (BM2); InterPro: IPR006859 BM2 is synthesised in the late phase of infection and incorporated into the virion. It may be phosphorylated in vivo. The function of BM2 is unknown [].; PDB: 2LJB_D 2LJC_A 2KIX_B 2KJ1_C.
Probab=37.83 E-value=63 Score=25.77 Aligned_cols=35 Identities=31% Similarity=0.533 Sum_probs=29.2
Q ss_pred CCChhhhHhhHHHHHhhHHHHHHHHHHHHHHHHHH
Q 026654 172 NVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDRE 206 (235)
Q Consensus 172 gls~~kv~kDL~lYrs~LeKm~QA~el~eE~~~~e 206 (235)
|=+++.++|...+.|-+-.|=-||+|-|++.+...
T Consensus 43 ~pnke~~nrevsilrh~yqkeiqaketmk~ils~n 77 (109)
T PF04772_consen 43 NPNKETINREVSILRHNYQKEIQAKETMKKILSNN 77 (109)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 44678899999999999999999999999988643
No 31
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=37.20 E-value=2.3e+02 Score=25.20 Aligned_cols=136 Identities=11% Similarity=0.217 Sum_probs=70.3
Q ss_pred cccccchhhhHHHHHHHHhcCCCCchh-----------HHHHHHHHHHhc------CCC--HHHHHHH-HHHHHH----H
Q 026654 48 YQYDPVFALGFVTVYDRLMEGYPSEED-----------REAIFQAYITAL------KED--PEQYRID-AQKLEE----W 103 (235)
Q Consensus 48 F~yD~lfAlG~vt~fd~fm~GY~pe~~-----------~~~IF~Alc~a~------~~D--p~q~r~d-A~~l~~----~ 103 (235)
..+|.++..|++..++.+ +.|.|+.. +..|.+.+-... ..+ .++...+ .....+ +
T Consensus 36 ~e~dDlvQ~glial~eAi-~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~ 114 (218)
T TIGR02895 36 TKSDDELSIGLIAFNEAI-ESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQKYQNLLYLDEDYDENPLEFNKSMEEYRNEI 114 (218)
T ss_pred CChhHHHHHHHHHHHHHH-HHCCCCCCCCHHHHHHHHHHHHHHHHHHhcccccCeeeCCchHHHHHHHHHHHHHHHHHHH
Confidence 578999999999888765 56776443 223333333211 111 1111111 111111 2
Q ss_pred HhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCChhhhHhhHH
Q 026654 104 ARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLD 183 (235)
Q Consensus 104 A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~~kv~kDL~ 183 (235)
-+....++|..|...-.+-.-.|.++++ ..|+-.=||-.||.+-..+ +.+++.++.|...=.||-..+.+-++
T Consensus 115 ~~~~~~eEI~~~~~~L~~~gi~~~dLv~---~sPkh~d~r~~~i~ia~~~----~~~~~l~~~l~~kk~LP~k~l~~~~~ 187 (218)
T TIGR02895 115 ENENRRLEILEYKKLLKQFGIEFVELVK---VSPKHRDTRKKAIKIAKVI----VENEELLEYLIRKKKLPIKEIEERVR 187 (218)
T ss_pred ccccHHHHHHHHHHHHHHcCCcHHHHhh---cCCCCHHHHHHHHHHHHHH----hcCHHHHHHHHHhCCCCHHHHHHHcC
Confidence 2233335565554332222334667775 3567566999999999988 45555544444444444444444444
Q ss_pred HHHhhHHH
Q 026654 184 VYRNLLSK 191 (235)
Q Consensus 184 lYrs~LeK 191 (235)
+=|..|++
T Consensus 188 v~rktier 195 (218)
T TIGR02895 188 ISRKTIER 195 (218)
T ss_pred CCHHHHHH
Confidence 44444443
No 32
>COG4476 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.80 E-value=1.5e+02 Score=23.47 Aligned_cols=81 Identities=20% Similarity=0.174 Sum_probs=69.1
Q ss_pred hCCCcCCcchhHHHHHHHHHHhhhcccCccccccchhhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHH
Q 026654 19 LYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQ 98 (235)
Q Consensus 19 ~~~~pI~siYrrvv~ELLVe~HLl~~n~~F~yD~lfAlG~vt~fd~fm~GY~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~ 98 (235)
.|.+||+.=|.+ +|+.--+|++..=..+==-.+=+.-|.-.|.+|-+=-|+-.+-..||..+=++.|.++=+-=++|+
T Consensus 2 ~y~yPldldWsT--EE~~~Vl~Ffn~VE~aYE~gv~~~~ll~~Yr~FK~IVPsK~eEKql~r~FE~~SgyS~Y~~vk~ak 79 (90)
T COG4476 2 EYSYPLDLDWST--EEMISVLHFFNAVELAYEKGVDAEDLLGSYRRFKEIVPSKAEEKQLGRDFEKSSGYSLYQAVKKAK 79 (90)
T ss_pred CcCCCCCCCccH--HHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhcCchHHHHHHhHHHHHhcCccHHHHHHHHH
Confidence 589999999987 788888999877666555567788889999999999999999999999999999999988888877
Q ss_pred HHH
Q 026654 99 KLE 101 (235)
Q Consensus 99 ~l~ 101 (235)
...
T Consensus 80 ~~~ 82 (90)
T COG4476 80 ESE 82 (90)
T ss_pred Hhh
Confidence 654
No 33
>PHA00666 putative protease
Probab=36.56 E-value=3.5e+02 Score=24.99 Aligned_cols=33 Identities=18% Similarity=0.148 Sum_probs=29.0
Q ss_pred hcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHH
Q 026654 66 MEGYPSEEDREAIFQAYITALKEDPEQYRIDAQ 98 (235)
Q Consensus 66 m~GY~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~ 98 (235)
=+|+..+.....-|..+|..+|++++|-++-..
T Consensus 92 PEG~elD~~~l~~F~~~a~ElgLtqEQAQklvD 124 (233)
T PHA00666 92 AEGVELDTGALGAFEPVARELNLTNEQAQKVVD 124 (233)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 389999999999999999999999999776543
No 34
>KOG1258 consensus mRNA processing protein [RNA processing and modification]
Probab=35.08 E-value=1.1e+02 Score=31.45 Aligned_cols=87 Identities=20% Similarity=0.237 Sum_probs=50.1
Q ss_pred HHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCc-----cccccccCCcchhHHHHHHHHHHh
Q 026654 59 VTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTA-----SSLVEFPSKEGEVEGLLKDIAERA 133 (235)
Q Consensus 59 vt~fd~fm~GY~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~~l~~~A~~~s~-----~~l~~~~~~~g~~~~~l~~Ia~~~ 133 (235)
+-||++=.+|.|=.-++=.=+-+.|..+++||+.+|.--++-.+.+...=. +-.++|-+..+. ..-+..|-+++
T Consensus 99 ~~Vfergv~aip~SvdlW~~Y~~f~~n~~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~qks-~k~v~~iyeRi 177 (577)
T KOG1258|consen 99 VKVFERGVQAIPLSVDLWLSYLAFLKNNNGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQKS-WKRVANIYERI 177 (577)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhcccc-HHHHHHHHHHH
Confidence 455666666665444444456688888999999999776666554441100 111222222221 12223334455
Q ss_pred cCCCCCcchHHHH
Q 026654 134 SGKGNFSYSRFFA 146 (235)
Q Consensus 134 ~~~~~f~YSRlfA 146 (235)
..+|.++|+|+|.
T Consensus 178 leiP~~~~~~~f~ 190 (577)
T KOG1258|consen 178 LEIPLHQLNRHFD 190 (577)
T ss_pred HhhhhhHhHHHHH
Confidence 5699999999987
No 35
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=34.97 E-value=48 Score=23.63 Aligned_cols=26 Identities=15% Similarity=0.529 Sum_probs=18.6
Q ss_pred HHHHHHhcCCChhhhHhhHHHHHhhH
Q 026654 164 LEKLCAVLNVNKRSVDRDLDVYRNLL 189 (235)
Q Consensus 164 l~~l~~~Lgls~~kv~kDL~lYrs~L 189 (235)
++++|+.||||.+-++.=.++|+...
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~ 26 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQ 26 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHH
Confidence 57899999999987777777776643
No 36
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=34.93 E-value=78 Score=29.17 Aligned_cols=35 Identities=11% Similarity=0.248 Sum_probs=29.8
Q ss_pred HHHhcCCCHHHHHHHHHHHHHHHhcCCcccccccc
Q 026654 82 YITALKEDPEQYRIDAQKLEEWARGQTASSLVEFP 116 (235)
Q Consensus 82 lc~a~~~Dp~q~r~dA~~l~~~A~~~s~~~l~~~~ 116 (235)
+.+-....|..+..-|.++.+|++......++.+-
T Consensus 81 ~~~dv~I~p~~i~e~s~~v~~w~~~~~v~~ii~~~ 115 (244)
T COG1938 81 LVSDVPIPPAVIYEISNAVVEWAEENGVEEVISLG 115 (244)
T ss_pred EEecCCCCHHHHHHHHHHHHHHHHHcCCeEEEEec
Confidence 45566788999999999999999999888888765
No 37
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=34.83 E-value=39 Score=22.09 Aligned_cols=27 Identities=30% Similarity=0.416 Sum_probs=22.3
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHH
Q 026654 74 DREAIFQAYITALKEDPEQYRIDAQKL 100 (235)
Q Consensus 74 ~~~~IF~Alc~a~~~Dp~q~r~dA~~l 100 (235)
+.+.++.-+++.+|.|++++++..++.
T Consensus 25 ~~~~~~~~il~~~~id~~~l~~~i~~~ 51 (53)
T PF02861_consen 25 DPDSIAARILKKLGIDPEQLKAAIEKA 51 (53)
T ss_dssp HTTSHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred hhhHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 345678889999999999999987765
No 38
>cd00192 PTKc Catalytic domain of Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family, catalytic domain. This PTKc family is part of a larger superfamily that includes the catalytic domains of protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. They can be classified into receptor and non-receptor tyr kinases. PTKs play important roles in many cellular processes including, lymphocyte activation, epithelium growth and maintenance, metabolism control, organogenesis regulation, survival, proliferation, differentiation, migration, adhesion, motility, and morphogenesis. Receptor tyr kinases (RTKs) are integral membrane proteins which contain an extracellular ligand-binding region, a transmembrane segment, and an intracellular tyr kinase domain. RTKs are usually activated through ligan
Probab=33.90 E-value=57 Score=26.64 Aligned_cols=22 Identities=14% Similarity=0.378 Sum_probs=15.5
Q ss_pred ccchhhhHHHHHHHHhcCCCCch
Q 026654 51 DPVFALGFVTVYDRLMEGYPSEE 73 (235)
Q Consensus 51 D~lfAlG~vt~fd~fm~GY~pe~ 73 (235)
..+|+||++ .|..++.|++|-.
T Consensus 188 ~Di~slG~i-l~~l~~~g~~p~~ 209 (262)
T cd00192 188 SDVWSFGVL-LWEIFTLGATPYP 209 (262)
T ss_pred hccHHHHHH-HHHHHhcCCCCCC
Confidence 469999976 5566666787743
No 39
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=33.02 E-value=46 Score=24.52 Aligned_cols=43 Identities=21% Similarity=0.230 Sum_probs=31.4
Q ss_pred cchHHHHHHHHHHHhhcCCCC--HHHHHHHHHhcCCChhhhHhhH
Q 026654 140 SYSRFFAVGLFRLLELANATE--PTVLEKLCAVLNVNKRSVDRDL 182 (235)
Q Consensus 140 ~YSRlfAIGLf~LLE~~~~~d--~~~l~~l~~~Lgls~~kv~kDL 182 (235)
++|+-+-.+|-.|+.++...+ +-..++|++.+|+|+.-+.|=+
T Consensus 2 ~~s~~~~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil 46 (83)
T PF02082_consen 2 KLSKRTDYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKIL 46 (83)
T ss_dssp ---HHHHHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHH
T ss_pred CCCcHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 478888889988888775543 4579999999999999887755
No 40
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=32.57 E-value=1.3e+02 Score=20.45 Aligned_cols=36 Identities=25% Similarity=0.327 Sum_probs=24.9
Q ss_pred HHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHH
Q 026654 59 VTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRI 95 (235)
Q Consensus 59 vt~fd~fm~GY~pe~~~~~IF~Alc~a~~~Dp~q~r~ 95 (235)
-.+.=+||.+=. ...++.+..++..-++|+|++.+.
T Consensus 9 KNvl~~fl~~~~-~~~~~~llpvi~tlL~fs~~e~~~ 44 (46)
T PF01465_consen 9 KNVLLQFLESRE-PSEREQLLPVIATLLKFSPEEKQK 44 (46)
T ss_dssp HHHHHHHHTTSS----HHHHHHHHHHHTT--HHHHHH
T ss_pred HHHHHHHhcCCc-hhhHHHHHHHHHHHHCCCHHHHHh
Confidence 345667777754 468889999999999999998774
No 41
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=31.77 E-value=48 Score=21.03 Aligned_cols=30 Identities=7% Similarity=0.199 Sum_probs=22.6
Q ss_pred HHHHHHHHHhcCCChhhhHhhHHHHHhhHHH
Q 026654 161 PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSK 191 (235)
Q Consensus 161 ~~~l~~l~~~Lgls~~kv~kDL~lYrs~LeK 191 (235)
++.+++|.+. ||+.+.+.+=|..-.+++++
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~ 32 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVER 32 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHH
Confidence 5678888887 99999998888766666553
No 42
>PF07216 LcrG: LcrG protein; InterPro: IPR009863 This family consists of several bacterial LcrG proteins. Yersiniae are equipped with the Yop virulon, an apparatus that allows extracellular bacteria to deliver toxic Yop proteins inside the host cell cytosol in order to sabotage the communication networks of the host cell or even to cause cell death. LcrG is a component of the Yop virulon involved in the regulation of secretion of the Yops []. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the prot ein is believed to make a 1:1 complex with PcrV (LcrV) []. Mutations in LcrG cause premature secretion of effector proteins into the medium [].
Probab=29.79 E-value=43 Score=26.76 Aligned_cols=31 Identities=13% Similarity=0.175 Sum_probs=24.2
Q ss_pred HHhcCCCCchhHHHHHHHHHHhcCCCHHHHH
Q 026654 64 RLMEGYPSEEDREAIFQAYITALKEDPEQYR 94 (235)
Q Consensus 64 ~fm~GY~pe~~~~~IF~Alc~a~~~Dp~q~r 94 (235)
+-=..-+..+||..||+=+|.++|++|+.-.
T Consensus 13 ~AE~AI~dsd~R~~llqEm~~gLg~~p~ag~ 43 (93)
T PF07216_consen 13 QAELAIRDSDHRNDLLQEMLEGLGLGPVAGE 43 (93)
T ss_pred HHHHHHHhhHHHHHHHHHHHHhcCCChhHHH
Confidence 3334445678999999999999999997543
No 43
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=28.41 E-value=71 Score=23.07 Aligned_cols=37 Identities=22% Similarity=0.307 Sum_probs=25.7
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHhcCCChhhhHhhHHHH
Q 026654 147 VGLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLDVY 185 (235)
Q Consensus 147 IGLf~LLE~~~~~d~~~l~~l~~~Lgls~~kv~kDL~lY 185 (235)
+.++.+|... ..+-.+.+|++.+|+|...|.++|...
T Consensus 8 ~~Il~~l~~~--~~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 8 LAVLRALAEE--PGGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred HHHHHHHHhC--CCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3445555222 235668899999999999999988543
No 44
>cd05034 PTKc_Src_like Catalytic domain of Src kinase-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Src kinase subfamily; catalytic (c) domain. Src subfamily members include Src, Lck, Hck, Blk, Lyn, Fgr, Fyn, Yrk, and Yes. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Src (or c-Src) proteins are cytoplasmic (or non-receptor) tyr kinases which are anchored to the plasma membrane. They contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-t
Probab=28.36 E-value=65 Score=26.81 Aligned_cols=20 Identities=15% Similarity=0.341 Sum_probs=14.2
Q ss_pred ccchhhhHHHHHHHHhcCCCC
Q 026654 51 DPVFALGFVTVYDRLMEGYPS 71 (235)
Q Consensus 51 D~lfAlG~vt~fd~fm~GY~p 71 (235)
..+|++| ++.|.-+..|.+|
T Consensus 185 ~Di~slG-~il~~l~t~g~~p 204 (261)
T cd05034 185 SDVWSFG-ILLTEIVTYGRVP 204 (261)
T ss_pred hHHHHHH-HHHHHHHhCCCCC
Confidence 4699999 4556666667776
No 45
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.43 E-value=4.8e+02 Score=23.79 Aligned_cols=111 Identities=20% Similarity=0.188 Sum_probs=64.7
Q ss_pred HHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCc-chhHHHH-HHHHHHhcCCCCCcc
Q 026654 64 RLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKE-GEVEGLL-KDIAERASGKGNFSY 141 (235)
Q Consensus 64 ~fm~GY~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~~l~~~A~~~s~~~l~~~~~~~-g~~~~~l-~~Ia~~~~~~~~f~Y 141 (235)
+++-..+|+ ....-+-|-+..|.++++ ++-.+.++..+.....+ -++... +.+.... ..+..-+...++ .+
T Consensus 47 ~l~p~~~~~--g~~~~~~l~~k~g~~~~~-~~~~~~~~~~~~~~Gi~---~~f~~~~~~~nt~~Ah~l~~~A~~~G~-~~ 119 (225)
T COG2761 47 ELDPDLPPE--GLDRKEYLAQKYGISEEQ-KAAHARLEELAEEEGID---FNFDAIVPAPNTLDAHRLIKAAELQGK-AQ 119 (225)
T ss_pred ccCCCCCcc--cccHHHHHHHHhCccHHH-HHHHHHHHHhhHhcCcc---cchhhccCCCchHHHHHHHHHHHHhCc-hH
Confidence 345556664 334455566777888888 77777777777754432 111111 1111111 011111112333 44
Q ss_pred hHHHHHHHHHHH--hhcCCCCHHHHHHHHHhcCCChhhhHhhH
Q 026654 142 SRFFAVGLFRLL--ELANATEPTVLEKLCAVLNVNKRSVDRDL 182 (235)
Q Consensus 142 SRlfAIGLf~LL--E~~~~~d~~~l~~l~~~Lgls~~kv~kDL 182 (235)
-|+ .-.||..+ |-.+..|...|-+|++..||..+.+.+||
T Consensus 120 ~~~-~~~lf~AyF~eg~nI~D~dVL~diA~~~GLD~~~~~~~L 161 (225)
T COG2761 120 DRF-LEALFEAYFEEGRNIGDEDVLADIAEEVGLDREEFKADL 161 (225)
T ss_pred HHH-HHHHHHHHhccCCCCCcHHHHHHHHHHhCCCHHHHHHHH
Confidence 443 45777777 33445789999999999999999988887
No 46
>PF13446 RPT: A repeated domain in UCH-protein
Probab=26.71 E-value=1.2e+02 Score=21.26 Aligned_cols=47 Identities=21% Similarity=0.336 Sum_probs=34.3
Q ss_pred CCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCcccccccc
Q 026654 70 PSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFP 116 (235)
Q Consensus 70 ~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~~l~~~A~~~s~~~l~~~~ 116 (235)
+|.-+=+.|-.++-..+..+|.+.+.--++|...|.......|..|+
T Consensus 14 ~~~~~Dd~Ii~~f~~~~~~~P~~~~~~r~AL~~Ia~~R~S~~L~~fl 60 (62)
T PF13446_consen 14 DEDTDDDFIISAFQSKVNDDPSQKDTLREALRVIAESRNSDRLRSFL 60 (62)
T ss_pred CCCCCHHHHHHHHHHHHHcChHhHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 44445556666666666699999988888888888877777776664
No 47
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=26.40 E-value=2.2e+02 Score=24.32 Aligned_cols=36 Identities=11% Similarity=0.141 Sum_probs=26.3
Q ss_pred HHHHH-hhcCCCCHHHHHHHHHhcCCChhhhHhhHHH
Q 026654 149 LFRLL-ELANATEPTVLEKLCAVLNVNKRSVDRDLDV 184 (235)
Q Consensus 149 Lf~LL-E~~~~~d~~~l~~l~~~Lgls~~kv~kDL~l 184 (235)
+|..+ +..+..+++.|.+++...|++.+++++.++-
T Consensus 110 lf~~i~~~~~~~~~~~L~~~a~~~Gld~~~f~~~l~s 146 (207)
T PRK10954 110 LFEGVQKTQTIQSAADIRDVFIKAGVKGEDYDAAWNS 146 (207)
T ss_pred HHHHHHccCCCCCHHHHHHHHHHcCCCHHHHHHHHhC
Confidence 55555 2223357788999999999999999888754
No 48
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=26.07 E-value=3e+02 Score=23.17 Aligned_cols=70 Identities=23% Similarity=0.317 Sum_probs=43.5
Q ss_pred cchhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCh---hhhHhhHHHHHhhHHHHH
Q 026654 119 EGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNK---RSVDRDLDVYRNLLSKLL 193 (235)
Q Consensus 119 ~g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~---~kv~kDL~lYrs~LeKm~ 193 (235)
.-++..+|..+++..+.+-+|.-| -|-|+.||.+ ....+.=++|+..||++. +.....+-|.|-++.|++
T Consensus 48 ~VDV~avL~~~a~~~~~~LnWrtS---IVDLlKlLgl--DSSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm~kLA 120 (127)
T PF12200_consen 48 QVDVAAVLDALAAKNGQKLNWRTS---IVDLLKLLGL--DSSLAARKELAKELGYTGDYNDSASMNIWLHKQVMQKLA 120 (127)
T ss_dssp SEE-HHHHHHHHHHHSS---TTT----HHHHHHHT------SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHHHHHG
T ss_pred cccHHHHHHHHHHhcccccccHHH---HHHHHHHcCC--CCCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHH
Confidence 347889999988776555555443 3455555522 245788899999999976 667777888888888876
No 49
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=25.68 E-value=3.5e+02 Score=23.77 Aligned_cols=21 Identities=24% Similarity=0.390 Sum_probs=17.0
Q ss_pred CHHHHHHHHHhcCCChhhhHh
Q 026654 160 EPTVLEKLCAVLNVNKRSVDR 180 (235)
Q Consensus 160 d~~~l~~l~~~Lgls~~kv~k 180 (235)
|-..|+.|+..|||+..-|+.
T Consensus 162 Er~YL~~LA~aL~L~~~lv~~ 182 (188)
T PF04391_consen 162 ERAYLDELAQALGLDPDLVAQ 182 (188)
T ss_pred HHHHHHHHHHHhCcCHHHHHH
Confidence 345699999999999987653
No 50
>smart00219 TyrKc Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
Probab=25.68 E-value=1e+02 Score=25.28 Aligned_cols=22 Identities=14% Similarity=0.375 Sum_probs=15.4
Q ss_pred ccchhhhHHHHHHHHhcCCCCch
Q 026654 51 DPVFALGFVTVYDRLMEGYPSEE 73 (235)
Q Consensus 51 D~lfAlG~vt~fd~fm~GY~pe~ 73 (235)
..+|++|++ .|..+..|++|-.
T Consensus 185 ~Di~slG~i-~~~l~~~g~~p~~ 206 (258)
T smart00219 185 SDVWSFGVL-LWEIFTLGESPYP 206 (258)
T ss_pred hhHHHHHHH-HHHHHhCCCCCCC
Confidence 559999976 4555666887743
No 51
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=25.49 E-value=2.3e+02 Score=19.53 Aligned_cols=49 Identities=12% Similarity=0.241 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhhcCCCC-HHHHHHHHHhcCCChhhhHhhHHHHHhhHHH
Q 026654 143 RFFAVGLFRLLELANATE-PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSK 191 (235)
Q Consensus 143 RlfAIGLf~LLE~~~~~d-~~~l~~l~~~Lgls~~kv~kDL~lYrs~LeK 191 (235)
++-.+|-+-+--..+..+ .+.++.+++..+.+++.+++|+.-|-..|.+
T Consensus 14 ~Ln~~a~~Iw~~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~ 63 (68)
T PF05402_consen 14 TLNETAAFIWELLDGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLRE 63 (68)
T ss_dssp ---THHHHHHHH--SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH
T ss_pred cccHHHHHHHHHccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 455555443333355544 5679999999999999999999877666543
No 52
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=25.47 E-value=4.1e+02 Score=23.36 Aligned_cols=29 Identities=10% Similarity=0.188 Sum_probs=21.1
Q ss_pred HHHHHHHhcCCChhhhHhhHHHHHhhHHHHHH
Q 026654 163 VLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQ 194 (235)
Q Consensus 163 ~l~~l~~~Lgls~~kv~kDL~lYrs~LeKm~Q 194 (235)
.+.+|++.||+|..+|.+= .+..+.||.+
T Consensus 227 t~~eIA~~lgis~~~V~~~---~~~al~kLr~ 255 (258)
T PRK08215 227 TQMEVAEEIGISQAQVSRL---EKAALKHMRK 255 (258)
T ss_pred CHHHHHHHHCcCHHHHHHH---HHHHHHHHHH
Confidence 4889999999999999653 3445555543
No 53
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=25.07 E-value=52 Score=25.21 Aligned_cols=22 Identities=23% Similarity=0.424 Sum_probs=20.0
Q ss_pred HHHHHHHhcCCChhhhHhhHHH
Q 026654 163 VLEKLCAVLNVNKRSVDRDLDV 184 (235)
Q Consensus 163 ~l~~l~~~Lgls~~kv~kDL~l 184 (235)
.++++++.+|+|...|.+||.-
T Consensus 21 ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 21 TVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CHHHHHHHhCCCHHHHHHHhcC
Confidence 5899999999999999999954
No 54
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=24.72 E-value=93 Score=21.15 Aligned_cols=33 Identities=21% Similarity=0.418 Sum_probs=18.8
Q ss_pred HHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHH
Q 026654 60 TVYDRLMEGYPSEEDREAIFQAYITALKEDPEQY 93 (235)
Q Consensus 60 t~fd~fm~GY~pe~~~~~IF~Alc~a~~~Dp~q~ 93 (235)
+.+.++..|-+ ..=.....+++|.++|.+|+++
T Consensus 25 ~tl~~~~~~~~-~~~~~~~l~~ia~~l~~~~~el 57 (63)
T PF13443_consen 25 STLSRILNGKP-SNPSLDTLEKIAKALNCSPEEL 57 (63)
T ss_dssp HHHHHHHTTT------HHHHHHHHHHHT--HHHC
T ss_pred HHHHHHHhccc-ccccHHHHHHHHHHcCCCHHHH
Confidence 44555666652 3344567889999999998864
No 55
>PF08855 DUF1825: Domain of unknown function (DUF1825); InterPro: IPR014954 These roteins are uncharacterised and are principally found in cyanobacteria.
Probab=24.32 E-value=2.4e+02 Score=23.02 Aligned_cols=74 Identities=19% Similarity=0.212 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHHHHHHHhcCCcc-ccccccCCcchhHHH--HHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCCCCHH--
Q 026654 88 EDPEQYRIDAQKLEEWARGQTAS-SLVEFPSKEGEVEGL--LKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPT-- 162 (235)
Q Consensus 88 ~Dp~q~r~dA~~l~~~A~~~s~~-~l~~~~~~~g~~~~~--l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~~d~~-- 162 (235)
||.++++++++.+-+.......- .-..-.+++|...-+ ...+.+ .-+--|.| |+++ .||+
T Consensus 5 F~SeiVq~e~~~if~~yq~l~~~~~~~~~fd~egK~~~Id~m~~Lid----kqkiF~~R---------l~LS--dD~~Ak 69 (108)
T PF08855_consen 5 FDSEIVQDELQDIFEDYQELMQMGSKYGKFDREGKKIHIDKMEELID----KQKIFYKR---------LELS--DDPEAK 69 (108)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHH----HHHHHHHH---------HHhc--cCHHHH
Confidence 57788888888877654433220 001112334432111 122222 11113444 3555 5554
Q ss_pred ----HHHHHHHhcCCChh
Q 026654 163 ----VLEKLCAVLNVNKR 176 (235)
Q Consensus 163 ----~l~~l~~~Lgls~~ 176 (235)
.+...+..+|+++.
T Consensus 70 ~m~~qi~~~~~~fG~~~~ 87 (108)
T PF08855_consen 70 DMKEQINAQLNQFGYTPQ 87 (108)
T ss_pred HHHHHHHHHHHHcCCCcc
Confidence 38888999999983
No 56
>PRK13910 DNA glycosylase MutY; Provisional
Probab=24.05 E-value=3.1e+02 Score=25.62 Aligned_cols=42 Identities=14% Similarity=0.210 Sum_probs=26.6
Q ss_pred HHHHHHhcCCCCchhHH----HHHHHHHHhcCC--CHHHHHHHHHHHH
Q 026654 60 TVYDRLMEGYPSEEDRE----AIFQAYITALKE--DPEQYRIDAQKLE 101 (235)
Q Consensus 60 t~fd~fm~GY~pe~~~~----~IF~Alc~a~~~--Dp~q~r~dA~~l~ 101 (235)
-.|++||+-||..++.. .=...+++.+|+ -+..+++-|+.+.
T Consensus 13 ~yy~rf~~~fPt~e~La~a~~~el~~~~~glGyy~RAr~L~~~A~~i~ 60 (289)
T PRK13910 13 RFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICV 60 (289)
T ss_pred HHHHHHHHHCCCHHHHHCCCHHHHHHHHHcCCcHHHHHHHHHHHHHHH
Confidence 37999999999776642 224457788998 3334444444443
No 57
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=23.95 E-value=94 Score=25.77 Aligned_cols=78 Identities=22% Similarity=0.325 Sum_probs=57.4
Q ss_pred CCchhHHHHHHHHHHhcCC---------CHHHHHHHHHHHHHHHhcCCccc---cccccCCcchhHHHHHHHHHHhcCCC
Q 026654 70 PSEEDREAIFQAYITALKE---------DPEQYRIDAQKLEEWARGQTASS---LVEFPSKEGEVEGLLKDIAERASGKG 137 (235)
Q Consensus 70 ~pe~~~~~IF~Alc~a~~~---------Dp~q~r~dA~~l~~~A~~~s~~~---l~~~~~~~g~~~~~l~~Ia~~~~~~~ 137 (235)
++..||.+++..+..|+=. -+..+|.-+++|.-+|+.-+... ...|+-....++.++..|+.+-.+.+
T Consensus 12 rtsshR~amlrnla~sLi~he~I~TT~~KAKelr~~vEkLITlaK~~~l~~RR~a~~~l~d~~~v~kLF~~iapry~~R~ 91 (116)
T COG0203 12 RTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLANRRLAFARLRDKDAVKKLFDEIAPRYAERN 91 (116)
T ss_pred CCHHHHHHHHHHHHHHHHHcCceeecHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHcccHHHHHHHHHHhChhhcCCC
Confidence 3567999999999888743 46789999999999999877643 34456656678888888887664333
Q ss_pred CCcchHHHHHH
Q 026654 138 NFSYSRFFAVG 148 (235)
Q Consensus 138 ~f~YSRlfAIG 148 (235)
=-|+|++=+|
T Consensus 92 -GGYtRIlK~g 101 (116)
T COG0203 92 -GGYTRILKLG 101 (116)
T ss_pred -CCeeEEEecC
Confidence 3688876544
No 58
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=23.94 E-value=1.1e+02 Score=20.42 Aligned_cols=26 Identities=19% Similarity=0.190 Sum_probs=20.3
Q ss_pred hhcCCCCHHHHHHHHHhcCCChhhhH
Q 026654 154 ELANATEPTVLEKLCAVLNVNKRSVD 179 (235)
Q Consensus 154 E~~~~~d~~~l~~l~~~Lgls~~kv~ 179 (235)
+...-.+.+..+.|+..+|++...|.
T Consensus 20 ~~~~~p~~~~~~~la~~l~l~~~~V~ 45 (57)
T PF00046_consen 20 QENPYPSKEEREELAKELGLTERQVK 45 (57)
T ss_dssp HHSSSCHHHHHHHHHHHHTSSHHHHH
T ss_pred HHhccccccccccccccccccccccc
Confidence 33333567889999999999999885
No 59
>PRK11861 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase; Provisional
Probab=23.78 E-value=6.3e+02 Score=25.89 Aligned_cols=144 Identities=19% Similarity=0.262 Sum_probs=82.1
Q ss_pred ccchh---hhHHHHHHHHhcCC-----CCc---hhHHHHHHHHHHhcCCCHHHHH-HHHHHHHHHHhcCCccccccccCC
Q 026654 51 DPVFA---LGFVTVYDRLMEGY-----PSE---EDREAIFQAYITALKEDPEQYR-IDAQKLEEWARGQTASSLVEFPSK 118 (235)
Q Consensus 51 D~lfA---lG~vt~fd~fm~GY-----~pe---~~~~~IF~Alc~a~~~Dp~q~r-~dA~~l~~~A~~~s~~~l~~~~~~ 118 (235)
=|+++ =|+-.++..|.+|. |.+ .+.-..+..|..++|..+-.+- +++-++.++...++- ++
T Consensus 56 HPMaG~e~~G~~~a~~~Lf~~~~~il~p~~~~~~~~~~~~~~l~~~~Ga~~~~~~~~~HD~~~A~iShlpH--~~----- 128 (673)
T PRK11861 56 HPIAGRESSGVDAALADLYVGRNVVLCALPENAPDALARVEAMWRAARADVRAMSAEQHDRVFAAVSHLPH--VL----- 128 (673)
T ss_pred CCcCcCcchhhhhhChhHhCCCeEEEecCCCCCHHHHHHHHHHHHHcCCEEEECCHHHHHHHHHHHhhHHH--HH-----
Confidence 47776 48888999999998 433 2233567777777774333222 234444433332221 11
Q ss_pred cchhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCChhhhHhhHHHHHhhHHHHHHHH--
Q 026654 119 EGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAK-- 196 (235)
Q Consensus 119 ~g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~~kv~kDL~lYrs~LeKm~QA~-- 196 (235)
..++++...+...-.+..-+|=|=|+-+-.....||+.-.+|+. -+++-|-+-|+-|...|+.+.++.
T Consensus 129 -------a~~l~~~~~~~~~~~~~~~~a~~gfrd~tRia~~~p~lw~di~~---~N~~~i~~~l~~~~~~l~~~~~~l~~ 198 (673)
T PRK11861 129 -------SFALVEQILGESDAELKFSYAAGGFRDFTRIAASSPEMWRDVCL---ANRAALLDELDAYTAVLARLRAAIDA 198 (673)
T ss_pred -------HHHHHHHHhhccChhHHHHhcccchhcccccccCCHHHHHHHHH---HCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 12222222111111222245555566664444567887666654 366777888899999999888887
Q ss_pred ---HHHHHHHHHHhhhHH
Q 026654 197 ---ELLKEYVDREKKKRE 211 (235)
Q Consensus 197 ---el~eE~~~~ekKKre 211 (235)
+-+++.+++-|+.|+
T Consensus 199 ~d~~~l~~~~~~~~~~r~ 216 (673)
T PRK11861 199 GDGAALEAVFARSRAARA 216 (673)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 466677766665554
No 60
>PF08014 DUF1704: Domain of unknown function (DUF1704); InterPro: IPR012548 This family contains many hypothetical proteins.
Probab=23.74 E-value=6.5e+02 Score=24.08 Aligned_cols=152 Identities=20% Similarity=0.291 Sum_probs=107.0
Q ss_pred Hhhhc-ccCccccccchhhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHH---HhcCCcccccc
Q 026654 39 QHLMR-YKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEW---ARGQTASSLVE 114 (235)
Q Consensus 39 ~HLl~-~n~~F~yD~lfAlG~vt~fd~fm~GY~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~~l~~~---A~~~s~~~l~~ 114 (235)
.|+++ +|..-|-=+++++| ..||-|.++.=++|.-++. -+..|..++.-|-++.+. .+|.|-.++-.
T Consensus 175 vH~lt~~Ng~~QPl~~l~~G--------lp~~~~TQEGLAvl~E~l~-g~~~~~Rl~~La~RV~Av~~m~~ga~F~e~F~ 245 (349)
T PF08014_consen 175 VHLLTTLNGRAQPLKILSLG--------LPGYTPTQEGLAVLSEYLS-GSLTPWRLRLLAYRVIAVDSMEKGASFSETFR 245 (349)
T ss_pred hhhccccccccCCcHHhCCC--------CCCCCCCchHHHHHHHHHh-CCCCHHHHHHHHHHHHHHHHHhcCCCHHHHHH
Confidence 46654 56666665666666 4899999999999999985 689999999999988775 44556666666
Q ss_pred ccCCc-c-hhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHhhcCC-C-------------CHHHHHHHHHhcCCChhhh
Q 026654 115 FPSKE-G-EVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA-T-------------EPTVLEKLCAVLNVNKRSV 178 (235)
Q Consensus 115 ~~~~~-g-~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LLE~~~~-~-------------d~~~l~~l~~~Lgls~~kv 178 (235)
++... | +.+..+ .++.|+.-.+.|.=--+.-.|+..++.--.. . |-..+.++.+.=.+.+++.
T Consensus 246 ~l~~~y~~~~~~af-~~~~Rv~RGg~FtKD~vYL~G~~~il~~~~~~~~~~~L~~GKvs~~d~~~l~el~~~g~l~~P~~ 324 (349)
T PF08014_consen 246 YLREFYGQDPEDAF-TITVRVFRGGGFTKDQVYLRGLLRILNYLRSGIDLPLLFVGKVSLEDVPRLRELVERGLLRPPKF 324 (349)
T ss_pred HHHHHhCCCHHHHH-HHHHHHHhcCCcchhHHHHHHHHHHHHHHHhccccchhhcccccHHHHHHHHHHHHCCCCCCCCc
Confidence 66554 4 455555 4444665556676556677788888733322 1 2345777777777888888
Q ss_pred HhhHHHHHhhHHHHHHHHHHHH
Q 026654 179 DRDLDVYRNLLSKLLQAKELLK 200 (235)
Q Consensus 179 ~kDL~lYrs~LeKm~QA~el~e 200 (235)
--|.--+-+.|+++-.-.+.|.
T Consensus 325 lp~~~~~~~~l~~~~~~~~~~~ 346 (349)
T PF08014_consen 325 LPPFFRDPEQLEKIMAFSEFLN 346 (349)
T ss_pred CCHHHhchhhHHHHHHHHHHhc
Confidence 8888888888888877666553
No 61
>PF10798 YmgB: Biofilm development protein YmgB/AriR; InterPro: IPR024753 YmgB is part of the three gene cluster ymgABC which has a role in biofilm development and stability. YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility and also protects the cell from acid, which indicates that YmgB has an important function in acid-resistance []. YmgB binds as a dimer to genes which are important for biofilm formation via a ligand. Due to its important function in acid resistance it is also known as AriR (regulator of acid resistance influenced by indole) [].; GO: 0042710 biofilm formation, 0071229 cellular response to acid; PDB: 2OXL_B.
Probab=23.47 E-value=2.2e+02 Score=20.72 Aligned_cols=43 Identities=26% Similarity=0.364 Sum_probs=27.8
Q ss_pred HHHHHhhcCC-CCHHHHHHHHHhcCCChhhhHhhHHHHHhhHHHHH
Q 026654 149 LFRLLELANA-TEPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLL 193 (235)
Q Consensus 149 Lf~LLE~~~~-~d~~~l~~l~~~Lgls~~kv~kDL~lYrs~LeKm~ 193 (235)
.-.|+...+. +....+.+|...|..-.+-++.|. ||+.||-+-
T Consensus 11 v~ell~~g~~vsnKaII~~LI~~LE~e~Dv~~~dv--yR~~LEiVv 54 (61)
T PF10798_consen 11 VRELLASGGHVSNKAIILKLIHRLESESDVVQLDV--YRNALEIVV 54 (61)
T ss_dssp HHHHHHTT---SHHHHHHHHHHHHHT---HHHHHH--HHHHHHHHH
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHHhccccHHHHHH--HHHHHHHHH
Confidence 3445543333 346678899999988889888877 999998654
No 62
>PF12069 DUF3549: Protein of unknown function (DUF3549); InterPro: IPR021936 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 340 amino acids in length. This protein has a conserved LDE sequence motif.
Probab=23.41 E-value=88 Score=30.15 Aligned_cols=33 Identities=24% Similarity=0.391 Sum_probs=29.1
Q ss_pred CCCchhHHHHHHHHHH-hcCCCHHHHHHHHHHHH
Q 026654 69 YPSEEDREAIFQAYIT-ALKEDPEQYRIDAQKLE 101 (235)
Q Consensus 69 Y~pe~~~~~IF~Alc~-a~~~Dp~q~r~dA~~l~ 101 (235)
|.|.++|-+.|+|++. .++..|.+|.+.|+.-.
T Consensus 122 FkP~~~klA~fhA~v~~~L~~p~S~yye~a~~Yl 155 (340)
T PF12069_consen 122 FKPSQEKLAMFHAQVRAQLGQPASQYYEHAQAYL 155 (340)
T ss_pred cCCChHHHHHHHHHHHHHcCCCcchhHHHHHHHH
Confidence 7899999999999996 58999999999987643
No 63
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=23.29 E-value=82 Score=19.95 Aligned_cols=23 Identities=30% Similarity=0.556 Sum_probs=19.7
Q ss_pred HHHHHHHHhcCCChhhhHhhHHH
Q 026654 162 TVLEKLCAVLNVNKRSVDRDLDV 184 (235)
Q Consensus 162 ~~l~~l~~~Lgls~~kv~kDL~l 184 (235)
-.+.+|++.+|++...|.++|..
T Consensus 15 ~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 15 VSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHH
Confidence 45788999999999999998854
No 64
>TIGR02573 LcrG_PcrG type III secretion protein LcrG. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the protein is believed to make a 1:1 complex with PcrV (LcrV). Mutants of LcrG cause premature secretion of effector proteins into the medium.
Probab=22.86 E-value=77 Score=25.18 Aligned_cols=27 Identities=15% Similarity=0.229 Sum_probs=22.5
Q ss_pred CCCCchhHHHHHHHHHHhcCCCHHHHH
Q 026654 68 GYPSEEDREAIFQAYITALKEDPEQYR 94 (235)
Q Consensus 68 GY~pe~~~~~IF~Alc~a~~~Dp~q~r 94 (235)
+-...+||..||+=+|.++|..|+.-.
T Consensus 14 AI~dsd~R~~llqEm~~gLgl~p~ag~ 40 (90)
T TIGR02573 14 AIRDSDERNDLLQEMWQGLGLGPVAGE 40 (90)
T ss_pred HHhchHHHHHHHHHHHHHcCCChHHHH
Confidence 345678999999999999999997654
No 65
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=22.86 E-value=2.6e+02 Score=22.58 Aligned_cols=128 Identities=23% Similarity=0.318 Sum_probs=65.5
Q ss_pred chhHHHHHHHHHHhhhcccCccccccchhhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhc
Q 026654 27 IYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARG 106 (235)
Q Consensus 27 iYrrvv~ELLVe~HLl~~n~~F~yD~lfAlG~vt~fd~fm~GY~pe~~~~~IF~Alc~a~~~Dp~q~r~dA~~l~~~A~~ 106 (235)
+-.+.+++++-+. .+.++.+=|+.=.+.... +.|.+|.+ +|.+++.-.+.+..||+.
T Consensus 15 ~~~~~l~~l~~~~----~~~~i~~~p~~l~~~~~~----~~~~~~~~---------------~~~~~~~~~~~~~~~a~~ 71 (193)
T PF01323_consen 15 LASPRLRKLRAEY----PDVEIEWRPFPLRPDMRR----SGGAPPAE---------------DPAKAEYMFQDLERWARR 71 (193)
T ss_dssp HHHHHHHHHHHHH----TTCEEEEEEESSSTHHHH----CT-SCGCG---------------SHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh----cCCcEEEecccccccccc----CCCCCccc---------------ChhHHHHHHHHHHHHHHH
Confidence 3344555554443 456666666654444222 45555554 788888888888888876
Q ss_pred CCccccccccCCc-chhHHHHHHHHHHhcCCCCCcchHHHHHHHHHHH-h-hcCCCCHHHHHHHHHhcCCChhhhHhhHH
Q 026654 107 QTASSLVEFPSKE-GEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLL-E-LANATEPTVLEKLCAVLNVNKRSVDRDLD 183 (235)
Q Consensus 107 ~s~~~l~~~~~~~-g~~~~~l~~Ia~~~~~~~~f~YSRlfAIGLf~LL-E-~~~~~d~~~l~~l~~~Lgls~~kv~kDL~ 183 (235)
.... ..+.... +........+. .+...+ ... -+.-.||..+ + ..+..|++.|.++++..|++.+.+.+.++
T Consensus 72 ~gi~--~~~~~~~~~~s~~a~~~~~-~a~~~~--~~~-~~~~al~~a~~~~~~~i~~~~vl~~~~~~~Gld~~~~~~~~~ 145 (193)
T PF01323_consen 72 YGIP--FNFPPPFPGNSRPAHRAAY-AAQEQG--KAD-AFADALFRAYFVEGRDISDPDVLAEIAEEAGLDPDEFDAALD 145 (193)
T ss_dssp HT----TBTSSTHHHHHHHHHHHHH-HHHHHH--HHH-HHHHHHHHHHHTSST-TSSHHHHHHHHHHTT--HHHHHHHHT
T ss_pred hcCc--ccCCchhhhhhHHHHHHHH-HHHHhh--hhh-HHHHHHHHHHHhcccCCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 5442 1111111 11111111111 111111 222 2345667766 2 22336888999999999999988887764
No 66
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=22.60 E-value=5.2e+02 Score=22.55 Aligned_cols=41 Identities=17% Similarity=0.084 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHhc--CCccccccccCC
Q 026654 78 IFQAYITALKEDPEQYRIDAQKLEEWARG--QTASSLVEFPSK 118 (235)
Q Consensus 78 IF~Alc~a~~~Dp~q~r~dA~~l~~~A~~--~s~~~l~~~~~~ 118 (235)
..+.|+..+|.|...++++-++|.-.+.+ .|.+++..+...
T Consensus 135 a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~ 177 (302)
T TIGR01128 135 AVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSD 177 (302)
T ss_pred HHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhh
Confidence 45677888899999999999999887654 444666666643
No 67
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=22.25 E-value=1.1e+02 Score=25.68 Aligned_cols=26 Identities=31% Similarity=0.493 Sum_probs=22.3
Q ss_pred HHHHHHhcCCChhhhHhhHHHHHhhH
Q 026654 164 LEKLCAVLNVNKRSVDRDLDVYRNLL 189 (235)
Q Consensus 164 l~~l~~~Lgls~~kv~kDL~lYrs~L 189 (235)
.++|++.||+|...|.|+|..=|.-|
T Consensus 154 ~~EIA~~lgiS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 154 VEEIAERLGISERTVRRRLRRARAWL 179 (185)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 78899999999999999997766444
No 68
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=21.84 E-value=65 Score=28.73 Aligned_cols=24 Identities=29% Similarity=0.466 Sum_probs=21.2
Q ss_pred HHHHHHHHHhcCCChhhhHhhHHH
Q 026654 161 PTVLEKLCAVLNVNKRSVDRDLDV 184 (235)
Q Consensus 161 ~~~l~~l~~~Lgls~~kv~kDL~l 184 (235)
.-.+.+|++.||.|...+.|||..
T Consensus 21 ~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 21 KLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Confidence 345889999999999999999984
No 69
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=21.77 E-value=2.6e+02 Score=18.87 Aligned_cols=21 Identities=29% Similarity=0.468 Sum_probs=14.3
Q ss_pred HHHHHHHhcCCChhhhHhhHH
Q 026654 163 VLEKLCAVLNVNKRSVDRDLD 183 (235)
Q Consensus 163 ~l~~l~~~Lgls~~kv~kDL~ 183 (235)
.+++|++.+|++...+.+=+.
T Consensus 3 ~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 3 TLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 356777777877777766554
No 70
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=21.77 E-value=1.2e+02 Score=21.24 Aligned_cols=34 Identities=21% Similarity=0.351 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHhc----CCChhhhHhhHHHHHhhHHHH
Q 026654 159 TEPTVLEKLCAVL----NVNKRSVDRDLDVYRNLLSKL 192 (235)
Q Consensus 159 ~d~~~l~~l~~~L----gls~~kv~kDL~lYrs~LeKm 192 (235)
.+|+.+.+|..+| |....++.++|+-++..+.++
T Consensus 5 ~~~e~ld~L~~aL~~prG~RE~~L~~~L~~~~k~~~~~ 42 (46)
T PF15614_consen 5 DDPEELDELLKALENPRGKRESKLKKELDKHRKGPLEI 42 (46)
T ss_pred cCHHHHHHHHHHHcCcccHhHHHHHHHHHHHhcchhhh
Confidence 3577888888888 788899999998888555443
No 71
>cd05056 PTKc_FAK Catalytic domain of the Protein Tyrosine Kinase, Focal Adhesion Kinase. Protein Tyrosine Kinase (PTK) family; Focal Adhesion Kinase (FAK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FAK is a cytoplasmic (or nonreceptor) tyr kinase that contains an autophosphorylation site and a FERM domain at the N-terminus, a central tyr kinase domain, proline-rich regions, and a C-terminal FAT (focal adhesion targeting) domain. FAK activity is dependent on integrin-mediated cell adhesion, which facilitates N-terminal autophosphorylation. Full activation is achieved by the phosphorylation of its two adjacent A-loop tyrosines. FAK is important in mediating signaling initiated at sites of cell adhesions
Probab=21.77 E-value=1.3e+02 Score=25.35 Aligned_cols=20 Identities=25% Similarity=0.527 Sum_probs=15.6
Q ss_pred ccchhhhHHHHHHHHhcCCCC
Q 026654 51 DPVFALGFVTVYDRLMEGYPS 71 (235)
Q Consensus 51 D~lfAlG~vt~fd~fm~GY~p 71 (235)
..+|++|++ .|..++-|.+|
T Consensus 189 ~Di~slG~i-l~el~~~g~~p 208 (270)
T cd05056 189 SDVWMFGVC-MWEILMLGVKP 208 (270)
T ss_pred hhhHHHHHH-HHHHHHcCCCC
Confidence 579999964 56678788887
No 72
>PF07268 EppA_BapA: Exported protein precursor (EppA/BapA); InterPro: IPR009894 This family consists of a number of exported protein precursor (EppA and BapA) sequences which seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). bapA gene sequences are quite stable but the encoded proteins do not provoke a strong immune response in most individuals. Conversely, EppA proteins are much more antigenic but are more variable in sequence. It is thought that BapA and EppA play important roles during the B. burgdorferi infectious cycle [].
Probab=21.58 E-value=1.7e+02 Score=24.91 Aligned_cols=34 Identities=35% Similarity=0.689 Sum_probs=25.0
Q ss_pred HHHHHHhcCCCCchhHHHHHHHHHHhcCCC----HHHHHHHHHH
Q 026654 60 TVYDRLMEGYPSEEDREAIFQAYITALKED----PEQYRIDAQK 99 (235)
Q Consensus 60 t~fd~fm~GY~pe~~~~~IF~Alc~a~~~D----p~q~r~dA~~ 99 (235)
...-.|+.|||. +||+-|++ |+-| +++|-..|..
T Consensus 87 ~~I~~LI~gyp~-----~IFdyliq-LdsdkIDYaEKYGekA~~ 124 (139)
T PF07268_consen 87 EAINYLIDGYPD-----SIFDYLIQ-LDSDKIDYAEKYGEKARN 124 (139)
T ss_pred HHHHHHHcCCcH-----HHHHHHHH-hccccccHHHHHHHHHHH
Confidence 455689999973 49999988 7776 5666666543
No 73
>PF01196 Ribosomal_L17: Ribosomal protein L17; InterPro: IPR000456 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3F1F_R 1VSP_L 3PYV_N 3PYR_N 3PYO_N 1VSA_L 3MS1_N 3F1H_R 3D5B_R 3MRZ_N ....
Probab=21.44 E-value=82 Score=24.89 Aligned_cols=58 Identities=22% Similarity=0.334 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHHhcCCc---cccccccCCcchhHHHHHHHHHHhcCCCCCcchHHHHHH
Q 026654 90 PEQYRIDAQKLEEWARGQTA---SSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVG 148 (235)
Q Consensus 90 p~q~r~dA~~l~~~A~~~s~---~~l~~~~~~~g~~~~~l~~Ia~~~~~~~~f~YSRlfAIG 148 (235)
+.++|.-|++|..+|+..+. ..+.+|+....-+..++..|+.+-. +.+--|+|++-+|
T Consensus 22 Ake~r~~aErlIt~ak~~~~~~~r~~~~~l~~~~~v~KLf~~l~pRy~-~r~GgYTRi~kl~ 82 (97)
T PF01196_consen 22 AKELRPYAERLITLAKKGDLHARRQALSWLRDKELVKKLFKELAPRYA-DRNGGYTRIIKLG 82 (97)
T ss_dssp HHHHHHHHHHHHHHHTSSTHHHHHHHHHCSSSHHHHHHHHTTHHHHTT-TSSS-SEEEEEEE
T ss_pred HHHHHHHHHHHHHHhccCcHHHHHHHHHHhcchHHHHHHHHHHHHHHc-cCCCCeEEEEeCC
Confidence 56789999999999997654 4566777756677888899998885 4555799876544
No 74
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=21.28 E-value=2.1e+02 Score=19.24 Aligned_cols=26 Identities=19% Similarity=0.409 Sum_probs=21.2
Q ss_pred HHHHHHHHHhcCCChhhhHhhHHHHH
Q 026654 161 PTVLEKLCAVLNVNKRSVDRDLDVYR 186 (235)
Q Consensus 161 ~~~l~~l~~~Lgls~~kv~kDL~lYr 186 (235)
+-...+|++.+|++...|.+-|.-..
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~ 50 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELE 50 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45689999999999999988875443
No 75
>cd05122 PKc_STE Catalytic domain of STE family Protein Kinases. Protein Kinases (PKs), STE family, catalytic (c) domain. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. The STE family is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases (STKs), protein tyrosine kinases (PTKs), RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). This family is composed of STKs, and some dual-specificity PKs that phosphorylate both threonine and tyrosine residues of target proteins. Most members are kinases involved in mitogen-activated protein kinase (MAPK) signaling cascades, acting as MAPK kinases (MAPKKs), MAPK kinase kinases (MAPKKKs), or MAPK kinase kinase kinases (MAP4Ks). The MAPK signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core
Probab=21.23 E-value=1.5e+02 Score=23.88 Aligned_cols=20 Identities=25% Similarity=0.509 Sum_probs=13.5
Q ss_pred ccchhhhHHHHHHHHhcCCCCc
Q 026654 51 DPVFALGFVTVYDRLMEGYPSE 72 (235)
Q Consensus 51 D~lfAlG~vt~fd~fm~GY~pe 72 (235)
..+|++|++ .|.-+ -|.+|-
T Consensus 178 ~Dv~slG~i-l~~l~-~g~~p~ 197 (253)
T cd05122 178 ADIWSLGIT-AIELA-EGKPPY 197 (253)
T ss_pred ccHHHHHHH-HHHHH-hCCCCC
Confidence 679999987 44444 465554
No 76
>cd05058 PTKc_Met_Ron Catalytic domain of the Protein Tyrosine Kinases, Met and Ron. Protein Tyrosine Kinase (PTK) family; Met and Ron; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Met and Ron are receptor tyr kinases (RTKs) composed of an alpha-beta heterodimer. The extracellular alpha chain is disulfide linked to the beta chain, which contains an extracellular ligand-binding region with a sema domain, a PSI domain and four IPT repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. Met binds to the ligand, hepatocyte growth factor/scatter factor (HGF/SF), and is also ca
Probab=21.12 E-value=1.3e+02 Score=24.97 Aligned_cols=21 Identities=19% Similarity=0.540 Sum_probs=15.6
Q ss_pred ccchhhhHHHHHHHHhcCCCCc
Q 026654 51 DPVFALGFVTVYDRLMEGYPSE 72 (235)
Q Consensus 51 D~lfAlG~vt~fd~fm~GY~pe 72 (235)
..||++|+ +.|+-++.|.||-
T Consensus 183 ~Di~slG~-~l~el~~~~~~~~ 203 (262)
T cd05058 183 SDVWSFGV-LLWELMTRGAPPY 203 (262)
T ss_pred HHHHHHHH-HHHHHHcCCCCCC
Confidence 57999997 5577777777764
No 77
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=20.86 E-value=1.9e+02 Score=18.92 Aligned_cols=22 Identities=23% Similarity=0.252 Sum_probs=19.0
Q ss_pred CCHHHHHHHHHhcCCChhhhHh
Q 026654 159 TEPTVLEKLCAVLNVNKRSVDR 180 (235)
Q Consensus 159 ~d~~~l~~l~~~Lgls~~kv~k 180 (235)
.+.+.++.|+..+|++...|+.
T Consensus 25 P~~~~~~~la~~~~l~~~qV~~ 46 (59)
T cd00086 25 PSREEREELAKELGLTERQVKI 46 (59)
T ss_pred CCHHHHHHHHHHHCcCHHHHHH
Confidence 4678899999999999988864
No 78
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=20.72 E-value=97 Score=22.67 Aligned_cols=31 Identities=23% Similarity=0.371 Sum_probs=23.4
Q ss_pred CHHHHHHHHHhcCCChhhhHhhHHHHHhhHH
Q 026654 160 EPTVLEKLCAVLNVNKRSVDRDLDVYRNLLS 190 (235)
Q Consensus 160 d~~~l~~l~~~Lgls~~kv~kDL~lYrs~Le 190 (235)
++..++++|+.+++|...+.+|+.--+..|.
T Consensus 29 ~~~s~~~la~~~~iS~sti~~~i~~l~~~l~ 59 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRSTIYRDIKKLNKYLK 59 (87)
T ss_dssp SEEEHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3456999999999999999999976666554
No 79
>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]
Probab=20.69 E-value=53 Score=31.82 Aligned_cols=50 Identities=34% Similarity=0.384 Sum_probs=29.2
Q ss_pred CCCcchHHHHHHHHHHHhhcCCC--C--HHHHHHHHHhcCCChhhhHhhHHHHHhhHHHH
Q 026654 137 GNFSYSRFFAVGLFRLLELANAT--E--PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKL 192 (235)
Q Consensus 137 ~~f~YSRlfAIGLf~LLE~~~~~--d--~~~l~~l~~~Lgls~~kv~kDL~lYrs~LeKm 192 (235)
..=+=|=+-+|..|.==+--+-. | -.+|+.+.+- -|+|||++|+.+|.=|
T Consensus 64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~ey------GVerDl~vYk~Llnvf 117 (406)
T KOG3941|consen 64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEY------GVERDLDVYKGLLNVF 117 (406)
T ss_pred cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHh------cchhhHHHHHHHHHhC
Confidence 33355666677666533222222 2 1345554442 4899999999999754
No 80
>cd07178 terB_like_YebE tellurium resistance terB-like protein, subgroup 3. This family includes several uncharacterized bacterial proteins including an Escherichia coli protein called YebE. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=20.57 E-value=22 Score=27.57 Aligned_cols=14 Identities=36% Similarity=0.555 Sum_probs=11.6
Q ss_pred CHHHHHHHHHhcCC
Q 026654 160 EPTVLEKLCAVLNV 173 (235)
Q Consensus 160 d~~~l~~l~~~Lgl 173 (235)
+...|++||.+||+
T Consensus 82 E~~~L~~la~aLgl 95 (95)
T cd07178 82 ERAYLDELAAALGL 95 (95)
T ss_pred HHHHHHHHHHHhCc
Confidence 34669999999996
No 81
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=20.44 E-value=55 Score=28.07 Aligned_cols=23 Identities=17% Similarity=0.102 Sum_probs=20.3
Q ss_pred HHHHHHHHHhcCCChhhhHhhHH
Q 026654 161 PTVLEKLCAVLNVNKRSVDRDLD 183 (235)
Q Consensus 161 ~~~l~~l~~~Lgls~~kv~kDL~ 183 (235)
.-.+++|++.+|.|...+.|||.
T Consensus 21 ~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 21 FITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHH
Confidence 34588999999999999999995
Done!