Query 024283
Match_columns 269
No_of_seqs 82 out of 84
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 03:25:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024283.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024283hhsearch_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 2E-101 4E-106 709.3 22.6 254 1-269 1-254 (283)
2 PLN03060 inositol phosphatase- 100.0 7.6E-91 1.6E-95 617.1 19.9 200 70-269 2-201 (206)
3 PRK13266 Thf1-like protein; Re 100.0 1.7E-88 3.7E-93 608.7 20.2 201 68-269 2-211 (225)
4 PF11264 ThylakoidFormat: Thyl 100.0 1.3E-88 2.8E-93 606.5 19.0 198 72-269 1-206 (216)
5 TIGR03060 PS_II_psb29 photosys 100.0 1.6E-88 3.5E-93 605.1 18.7 198 68-269 2-209 (214)
6 PF11264 ThylakoidFormat: Thyl 94.5 0.051 1.1E-06 49.7 4.4 56 106-161 127-183 (216)
7 PRK13266 Thf1-like protein; Re 94.3 0.089 1.9E-06 48.5 5.5 63 99-161 125-188 (225)
8 TIGR03060 PS_II_psb29 photosys 94.0 0.071 1.5E-06 48.8 4.3 58 103-161 127-186 (214)
9 PLN03060 inositol phosphatase- 92.5 0.48 1E-05 43.3 7.2 47 200-246 41-93 (206)
10 PLN00047 photosystem II biogen 90.2 0.99 2.2E-05 43.1 7.0 47 200-246 94-146 (283)
11 PF11473 B2: RNA binding prote 71.4 4 8.7E-05 31.8 2.7 23 239-261 31-53 (73)
12 PF03216 Rhabdo_ncap_2: Rhabdo 67.7 40 0.00086 33.1 9.0 162 91-264 77-261 (357)
13 KOG0961 Predicted Zn2+-depende 67.5 36 0.00079 37.1 9.5 136 87-263 599-742 (1022)
14 COG3793 TerB Tellurite resista 65.2 21 0.00045 31.3 6.1 36 137-172 65-100 (144)
15 PF05099 TerB: Tellurite resis 64.5 25 0.00055 28.1 6.2 99 130-244 36-137 (140)
16 TIGR02147 Fsuc_second hypothet 55.2 78 0.0017 29.8 8.6 145 92-247 10-161 (271)
17 COG1938 Archaeal enzymes of AT 52.0 1.4E+02 0.0031 28.1 9.7 121 146-268 81-235 (244)
18 PF06971 Put_DNA-bind_N: Putat 51.9 12 0.00025 27.1 2.0 24 224-247 27-50 (50)
19 PF08220 HTH_DeoR: DeoR-like h 51.7 8.1 0.00018 27.7 1.2 23 225-247 14-36 (57)
20 PF04772 Flu_B_M2: Influenza B 50.5 28 0.0006 28.5 4.1 32 236-267 43-74 (109)
21 PF08542 Rep_fac_C: Replicatio 50.0 22 0.00048 26.6 3.4 41 132-177 1-41 (89)
22 TIGR00059 L17 ribosomal protei 49.5 21 0.00046 29.8 3.4 77 135-212 8-96 (112)
23 PRK05591 rplQ 50S ribosomal pr 47.0 28 0.0006 29.1 3.8 77 135-212 10-98 (113)
24 PF01841 Transglut_core: Trans 44.1 12 0.00027 28.3 1.2 46 109-154 26-72 (113)
25 cd00194 UBA Ubiquitin Associat 43.5 37 0.0008 21.8 3.2 31 225-256 2-32 (38)
26 PF08280 HTH_Mga: M protein tr 41.9 26 0.00057 25.1 2.5 27 227-253 21-47 (59)
27 COG2761 FrnE Predicted dithiol 40.6 3.1E+02 0.0067 25.6 10.3 113 128-247 47-162 (225)
28 PF08279 HTH_11: HTH domain; 40.3 31 0.00066 23.7 2.6 28 224-251 14-41 (55)
29 PF04391 DUF533: Protein of un 38.8 1.4E+02 0.0031 26.8 7.3 21 224-244 162-182 (188)
30 KOG0212 Uncharacterized conser 38.5 1.9E+02 0.004 31.0 8.9 102 138-246 122-230 (675)
31 PRK10954 periplasmic protein d 37.2 1.1E+02 0.0023 26.7 6.2 52 213-265 110-162 (207)
32 PRK10880 adenine DNA glycosyla 37.2 3.1E+02 0.0068 26.8 9.8 81 73-166 6-98 (350)
33 COG4476 Uncharacterized protei 36.7 1.5E+02 0.0033 24.2 6.3 82 83-166 2-83 (90)
34 PF02861 Clp_N: Clp amino term 36.0 37 0.00079 22.7 2.4 27 138-164 25-51 (53)
35 PF13413 HTH_25: Helix-turn-he 35.8 49 0.0011 24.3 3.2 27 131-157 36-62 (62)
36 PF00382 TFIIB: Transcription 35.5 44 0.00096 24.3 3.0 27 228-254 1-27 (71)
37 PRK09430 djlA Dna-J like membr 35.0 3.8E+02 0.0083 25.0 12.4 120 116-250 52-176 (267)
38 TIGR02895 spore_sigI RNA polym 34.4 1.6E+02 0.0035 26.8 7.0 136 112-255 36-195 (218)
39 cd00192 PTKc Catalytic domain 34.2 52 0.0011 27.3 3.5 32 115-147 188-221 (262)
40 PF00627 UBA: UBA/TS-N domain; 33.6 42 0.0009 21.9 2.3 30 225-255 3-32 (37)
41 COG3867 Arabinogalactan endo-1 32.7 87 0.0019 31.2 5.2 114 115-249 25-157 (403)
42 PF01024 Colicin: Colicin pore 32.1 3E+02 0.0064 25.1 8.2 78 154-242 31-109 (187)
43 PF01323 DSBA: DSBA-like thior 31.4 1.4E+02 0.0031 24.6 5.7 126 93-247 17-145 (193)
44 PF02082 Rrf2: Transcriptional 31.2 47 0.001 25.0 2.6 44 204-247 2-47 (83)
45 PF12200 DUF3597: Domain of un 30.9 2.1E+02 0.0045 24.7 6.6 71 183-258 48-121 (127)
46 PF08014 DUF1704: Domain of un 30.9 3.4E+02 0.0074 26.5 9.0 152 103-264 175-346 (349)
47 PRK08307 stage III sporulation 30.4 3.7E+02 0.0079 23.4 9.8 81 185-265 66-150 (171)
48 COG0203 RplQ Ribosomal protein 30.4 62 0.0013 27.5 3.3 78 134-212 12-101 (116)
49 smart00342 HTH_ARAC helix_turn 30.2 1.4E+02 0.0031 20.6 4.8 38 228-265 4-48 (84)
50 PF05402 PqqD: Coenzyme PQQ sy 29.1 2E+02 0.0043 20.4 5.4 49 207-255 14-63 (68)
51 PF01196 Ribosomal_L17: Riboso 29.1 50 0.0011 26.8 2.5 58 154-212 22-82 (97)
52 COG3636 Predicted transcriptio 29.1 3E+02 0.0064 23.0 6.9 28 211-238 64-91 (100)
53 cd04758 Commd10 COMM_Domain co 28.9 3.8E+02 0.0082 23.4 8.2 49 212-260 60-110 (186)
54 PF01465 GRIP: GRIP domain; I 28.9 1.6E+02 0.0035 20.6 4.7 36 123-159 9-44 (46)
55 COG2207 AraC AraC-type DNA-bin 28.7 1.3E+02 0.0029 22.5 4.7 53 212-265 24-83 (127)
56 KOG1258 mRNA processing protei 28.5 1.6E+02 0.0034 31.2 6.5 124 71-210 62-190 (577)
57 PF13446 RPT: A repeated domai 28.1 97 0.0021 22.2 3.7 47 134-180 14-60 (62)
58 smart00346 HTH_ICLR helix_turn 27.8 71 0.0015 23.6 3.0 26 224-249 19-44 (91)
59 PHA00666 putative protease 27.7 5.3E+02 0.012 24.4 9.8 32 131-162 93-124 (233)
60 PF14225 MOR2-PAG1_C: Cell mor 27.6 4.1E+02 0.0088 24.9 8.6 111 155-269 130-255 (262)
61 PRK15044 transcriptional regul 27.5 5.8E+02 0.013 24.8 10.9 149 74-265 97-254 (295)
62 cd05034 PTKc_Src_like Catalyti 27.3 62 0.0013 27.4 2.9 20 115-135 185-204 (261)
63 PF10798 YmgB: Biofilm develop 26.9 1.6E+02 0.0035 22.0 4.7 44 213-258 11-55 (61)
64 PF15614 WHIM3: WSTF, HB1, Itc 26.5 82 0.0018 22.7 2.9 34 223-256 5-42 (46)
65 PF12069 DUF3549: Protein of u 25.3 76 0.0016 31.3 3.5 32 133-164 122-154 (340)
66 smart00219 TyrKc Tyrosine kina 25.2 93 0.002 25.9 3.6 22 115-137 185-206 (258)
67 PF05402 PqqD: Coenzyme PQQ sy 23.9 1.8E+02 0.004 20.5 4.5 42 124-169 21-62 (68)
68 TIGR02844 spore_III_D sporulat 23.9 54 0.0012 25.8 1.8 23 226-248 20-42 (80)
69 cd03023 DsbA_Com1_like DsbA fa 23.7 2.6E+02 0.0057 21.7 5.7 25 223-247 83-107 (154)
70 PF06152 Phage_min_cap2: Phage 23.4 2.5E+02 0.0054 27.4 6.6 35 152-200 3-37 (361)
71 PRK13910 DNA glycosylase MutY; 23.4 3E+02 0.0065 26.3 7.0 43 124-166 13-61 (289)
72 cd05056 PTKc_FAK Catalytic dom 23.2 1E+02 0.0022 26.3 3.6 20 115-135 189-208 (270)
73 KOG0213 Splicing factor 3b, su 23.2 5.6E+02 0.012 28.8 9.5 106 104-239 764-876 (1172)
74 cd00092 HTH_CRP helix_turn_hel 22.9 1.7E+02 0.0038 20.1 4.1 26 225-250 25-50 (67)
75 PF13170 DUF4003: Protein of u 22.9 4.7E+02 0.01 24.8 8.1 119 123-247 123-260 (297)
76 KOG3941 Intermediate in Toll s 22.7 45 0.00099 33.0 1.4 49 202-256 65-117 (406)
77 PF07216 LcrG: LcrG protein; 22.5 65 0.0014 26.5 2.0 31 127-157 12-42 (93)
78 TIGR01084 mutY A/G-specific ad 22.5 6.6E+02 0.014 23.7 9.4 65 75-152 4-78 (275)
79 PF07638 Sigma70_ECF: ECF sigm 22.4 1.1E+02 0.0023 26.3 3.5 27 227-253 153-179 (185)
80 PRK10681 DNA-binding transcrip 22.2 61 0.0013 29.5 2.0 24 225-248 21-44 (252)
81 PRK07405 RNA polymerase sigma 22.2 1.4E+02 0.003 28.3 4.5 42 224-268 275-316 (317)
82 cd03019 DsbA_DsbA DsbA family, 22.2 3.2E+02 0.0068 22.2 6.1 36 212-247 84-121 (178)
83 PF08542 Rep_fac_C: Replicatio 22.0 2.1E+02 0.0045 21.2 4.6 45 121-166 23-67 (89)
84 PF00046 Homeobox: Homeobox do 21.9 1.2E+02 0.0027 20.7 3.1 26 218-243 20-45 (57)
85 cd03022 DsbA_HCCA_Iso DsbA fam 21.8 2.2E+02 0.0047 23.5 5.1 37 211-247 107-145 (192)
86 COG4867 Uncharacterized protei 21.7 1.4E+02 0.003 31.1 4.6 48 158-210 188-244 (652)
87 cd00086 homeodomain Homeodomai 21.3 1.8E+02 0.0039 19.5 3.8 22 223-244 25-46 (59)
88 PF07814 WAPL: Wings apart-lik 21.3 4.1E+02 0.0089 25.6 7.5 114 138-260 22-142 (361)
89 PF06012 DUF908: Domain of Unk 20.8 5.7E+02 0.012 24.3 8.3 49 113-161 186-235 (329)
90 PF07268 EppA_BapA: Exported p 20.5 1.7E+02 0.0036 25.7 4.2 34 124-163 87-124 (139)
91 smart00420 HTH_DEOR helix_turn 20.5 98 0.0021 20.0 2.3 23 226-248 15-37 (53)
92 PF05043 Mga: Mga helix-turn-h 20.3 96 0.0021 23.2 2.5 31 224-254 29-59 (87)
93 PRK08215 sporulation sigma fac 20.3 6.3E+02 0.014 22.6 9.4 30 226-258 226-255 (258)
94 cd07178 terB_like_YebE telluri 20.2 21 0.00045 28.3 -1.2 14 224-237 82-95 (95)
95 cd07766 DHQ_Fe-ADH Dehydroquin 20.1 7E+02 0.015 23.1 10.4 132 117-258 159-308 (332)
96 PRK04424 fatty acid biosynthes 20.0 55 0.0012 28.7 1.2 24 225-248 21-44 (185)
No 1
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=100.00 E-value=2e-101 Score=709.29 Aligned_cols=254 Identities=74% Similarity=1.138 Sum_probs=242.0
Q ss_pred CCccccccccccccccccccccccccccccccccccccccccceeeeeeeecCCCccceeeeeccCCCCCCchhHhHHHH
Q 024283 1 MASLTSVAFTSIGQTSCQRKVNVSSTRSLVSNFEGFRFRTSLFCHCVRFRASSSSSRMIIQCMSTATDVPPTVAETKMNF 80 (269)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~TVSDTKr~F 80 (269)
|||++|+||++++|++ ++++..++|+++ .+|+|+ +|++++ +|+||+||+++++++||||||||+|
T Consensus 1 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~---~~~~~~---------~~~~~~-~~~~~~~~~~~~~~~~TVSDTKr~F 65 (283)
T PLN00047 1 MAAVCSVSFPALGQSS--KARPAPVSAARS---FASRFE---------VASRST-SRRVVHCMAAVTDVPPTVAETKAKF 65 (283)
T ss_pred CccccccChHhhcccc--cccCCccchhhh---hccccc---------cccccc-cceeeeehhhccCCCCcHHHHHHHH
Confidence 8999999999999997 666666667775 667776 676654 5999999999999999999999999
Q ss_pred HhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHH
Q 024283 81 LKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRID 160 (269)
Q Consensus 81 ~~~y~rPI~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~d 160 (269)
|++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||+|+|+||+|||+|
T Consensus 66 ~~~yp~pIpsiYrrvvdELLVElHLLs~n~~F~yDplFALGlVtvfd~fm~GY~Pee~~~~IF~Alc~a~g~Dp~qyr~d 145 (283)
T PLN00047 66 LKSYKRPIPSIYSTVLQELLVQQHLMRYKKTYRYDPVFALGFVTVYDQLMEGYPSDEDRDAIFKAYIKALGEDPEQYRKD 145 (283)
T ss_pred HHhCCCCCcHHHHHHHHHHHHHHHHHHhccCceeCchhhhhhHHHHHHHHccCCChHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhcCCChh
Q 024283 161 AQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNKR 240 (269)
Q Consensus 161 A~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~e 240 (269)
|++|++||+|++.+|+++|+...|++++.|++||+++++|++||||||||||||+|||.++++||+++++||++|||+++
T Consensus 146 A~~l~~~A~~~s~~~l~~~l~~~~~l~~~l~~IA~~a~~~~~f~YSRlfAIGLf~LLe~a~~~d~~~l~~l~e~Lgls~~ 225 (283)
T PLN00047 146 AAKLEEWARSQTGSSLVDFSSKEGEIEGILKDIAERAGSKGKFSYSRFFAIGLFRLLELANATEPTALEKLCAALNINKR 225 (283)
T ss_pred HHHHHHHHhcCCHHHHHHHHhcchHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCHH
Confidence 99999999999999999999999999999999998887899999999999999999999999999999999999999999
Q ss_pred hhhhhHHHHHhhHHHHHHHHHHHHHHhcC
Q 024283 241 SVDRDLDVYRNLLSKLLQAKELLKEYVDR 269 (269)
Q Consensus 241 kv~KDL~lYrsnLeKmaQA~elmeE~ler 269 (269)
||+|||+|||||||||+||+|||||+++|
T Consensus 226 kv~KDLdlYrsnLeKm~QA~elmeE~~~~ 254 (283)
T PLN00047 226 SVDRDLDVYRGLLSKLVQAKELLKEYVER 254 (283)
T ss_pred HHHhhHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999975
No 2
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=100.00 E-value=7.6e-91 Score=617.11 Aligned_cols=200 Identities=72% Similarity=1.163 Sum_probs=195.6
Q ss_pred CCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHh
Q 024283 70 PPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITA 149 (269)
Q Consensus 70 ~~TVSDTKr~F~~~y~rPI~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc~A 149 (269)
+||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||+|
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 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHH
Q 024283 150 LKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLE 229 (269)
Q Consensus 150 lg~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~ 229 (269)
+|+||+|||+||+++++||+|++.++|.+|++++|+.+..|+++++++++|++||||||||||||+|||.++++||++++
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 99999999999999999999999999999999988888888888888889999999999999999999999989999999
Q ss_pred HHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHHHhcC
Q 024283 230 KLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDR 269 (269)
Q Consensus 230 ~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE~ler 269 (269)
+||++|||+++||+|||++||||||||+||+|||||++++
T Consensus 162 ~l~~~L~ls~~kv~kDL~lYrsnLeKm~qa~el~ee~~~~ 201 (206)
T PLN03060 162 KLSKALNVSKRSVDRDLDVYRNLLSKLAQAKELIKEYIDR 201 (206)
T ss_pred HHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999974
No 3
>PRK13266 Thf1-like protein; Reviewed
Probab=100.00 E-value=1.7e-88 Score=608.70 Aligned_cols=201 Identities=40% Similarity=0.722 Sum_probs=188.5
Q ss_pred CCCCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHH
Q 024283 68 DVPPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYI 147 (269)
Q Consensus 68 ~~~~TVSDTKr~F~~~y~rPI~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc 147 (269)
+++||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||
T Consensus 2 ~~~~TVSDtKr~F~~~~p~pI~siYrrvv~ELLVElHLl~~n~~F~yDplfAlGlvt~fd~fm~GY~Pee~~~~IF~Alc 81 (225)
T PRK13266 2 NNRRTVSDSKRAFYAAFPRPINSIYRRVVDELLVELHLLSVNSDFKYDPLFALGLVTVFDRFMQGYRPEEHKDSIFNALC 81 (225)
T ss_pred CCCCcHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCc--chhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCC---
Q 024283 148 TALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKE--GEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA--- 222 (269)
Q Consensus 148 ~Alg~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~~--g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~--- 222 (269)
+|+|+||+|||+||++|++||+|++.++|.+|++++ |+++.+++.++ .+++|++||||||||||||+|||.+++
T Consensus 82 ~a~~~dp~~~r~dA~~l~~~a~~~s~~~i~~~l~~~~~~~~~~l~~~l~-~ia~~~~f~YSRl~AIGL~~LLe~a~~~~~ 160 (225)
T PRK13266 82 QAVGFDPEQLRQDAERLLELAKGKSLKEILSWLTQKALGEPGGLLATLL-AIANNSKFKYSRLFAIGLYTLLEEAQPDLV 160 (225)
T ss_pred HHcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhccccccchhHHHHHH-HHhcCCCCchHHHHHHHHHHHHHhcCcccc
Confidence 999999999999999999999999999999999964 45555555554 455699999999999999999999987
Q ss_pred CCH----HHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHHHhcC
Q 024283 223 TEP----TVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDR 269 (269)
Q Consensus 223 ~d~----~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE~ler 269 (269)
+|| +++++||++||||++||+|||+|||||||||+||+|||||++++
T Consensus 161 ~d~~~~~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeKm~Qa~el~ee~~~~ 211 (225)
T PRK13266 161 KDEEKLNEALKDISEGLGLSKEKVEKDLDLYRSNLEKMEQALELIEETLEA 211 (225)
T ss_pred cCHHHHHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 466 59999999999999999999999999999999999999999974
No 4
>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=1.3e-88 Score=606.52 Aligned_cols=198 Identities=52% Similarity=0.890 Sum_probs=189.0
Q ss_pred chhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcC
Q 024283 72 TVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALK 151 (269)
Q Consensus 72 TVSDTKr~F~~~y~rPI~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc~Alg 151 (269)
|||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||+|+|
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 024283 152 EDPEQYRIDAQKLEEWARGQTASSLVEFPSK-EGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA-------T 223 (269)
Q Consensus 152 ~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~-~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~-------~ 223 (269)
+||+|||+||+++++||+|+|.++|.+|+++ .++.++.|++++.+|++|++||||||||||||+|||.+++ .
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 9999999999999999999999999999986 4566677777777778899999999999999999999988 3
Q ss_pred CHHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHHHhcC
Q 024283 224 EPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDR 269 (269)
Q Consensus 224 d~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE~ler 269 (269)
+++++++||++||||++||+|||++||||||||+||+|||||+++|
T Consensus 161 ~~~~l~~l~~~l~ls~~kv~kDL~lYrsnLeKm~qA~el~ee~~~~ 206 (216)
T PF11264_consen 161 RPEALEKLSEALGLSKEKVEKDLDLYRSNLEKMAQAKELMEEILEA 206 (216)
T ss_pred HHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 4679999999999999999999999999999999999999999874
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=1.6e-88 Score=605.12 Aligned_cols=198 Identities=39% Similarity=0.682 Sum_probs=185.7
Q ss_pred CCCCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHH
Q 024283 68 DVPPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYI 147 (269)
Q Consensus 68 ~~~~TVSDTKr~F~~~y~rPI~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc 147 (269)
+++||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||
T Consensus 2 ~~~~TVSDtKr~F~~~~p~pI~siYrrvv~ELLVElHLl~~n~~F~yDplfAlGlvt~fd~fm~GY~Pee~~~~IF~Alc 81 (214)
T TIGR03060 2 TERRTVSDSKRAFHAAFPRVIPPLYRRVVDELLVELHLLSHQSDFKYDPLFALGLVTVFDRFMEGYRPEEHLDALFDALC 81 (214)
T ss_pred CCCCcHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcch--hHH-HHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCC-
Q 024283 148 TALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGE--VEG-LLKDIAERASGKGNFSYSRFFAVGLFRLLELANAT- 223 (269)
Q Consensus 148 ~Alg~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~~g~--~~~-~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~- 223 (269)
+|+|+||+|||+||+++++||+|++.++|.+|+++.|+ .+. +|++|| +|++||||||||||||+|||.+++.
T Consensus 82 ~a~~~dp~~~r~dA~~l~~~a~~~s~~~i~~~l~~~~~~~~~~l~l~~ia----~n~~f~YSRl~AIGL~~LLe~a~~~~ 157 (214)
T TIGR03060 82 NSNGFDPEQLREDAKQLLEQAKGKGLDEILSWLTQANLSNGGGDTLQGIA----GRHKFKYSRLFAIGLYSLLEEAAPDK 157 (214)
T ss_pred HhcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhccccCCcchhHHHHHh----cCCCcchHHHHHHHHHHHHHhcCccc
Confidence 99999999999999999999999999999999987543 222 566665 5999999999999999999999863
Q ss_pred --C----HHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHHHhcC
Q 024283 224 --E----PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDR 269 (269)
Q Consensus 224 --d----~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE~ler 269 (269)
| ++++++||++||||.+||+|||+|||||||||+||+|||||++++
T Consensus 158 ~~d~~~~~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeKm~Qa~el~ee~~~~ 209 (214)
T TIGR03060 158 DIDEEDLNEILKELSEALGLSYDRVEKDLDLYKSNLEKMKQALELMEETLEA 209 (214)
T ss_pred ccCHHHHHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 4 459999999999999999999999999999999999999999974
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=94.47 E-value=0.051 Score=49.74 Aligned_cols=56 Identities=20% Similarity=0.294 Sum_probs=47.3
Q ss_pred hcccccccccccchhhHHHHHHHHhc-CCCCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 024283 106 MRYKRTYQYDPVFALGFVTVYDRLME-GYPSEEDREAIFQAYITALKEDPEQYRIDA 161 (269)
Q Consensus 106 Ls~n~~F~YDplFALG~VTvFd~fm~-GY~peed~~~IF~Alc~Alg~Dp~qyR~dA 161 (269)
..-|..|.|.-+||+|+.+..+.--- .-..++.+..+.+.||+++|+.++.+.+|-
T Consensus 127 ia~~~~f~YSRl~AIGL~~LLe~a~~~~~~~~~~~~~~l~~l~~~l~ls~~kv~kDL 183 (216)
T PF11264_consen 127 IASNPKFKYSRLFAIGLFRLLELAGADLVKDEEKRPEALEKLSEALGLSKEKVEKDL 183 (216)
T ss_pred HhcCCCCchHHHHHHHHHHHHHhcCcccccChhhHHHHHHHHHHHcCCCHHHHHhhH
Confidence 34578999999999999999987654 244567888899999999999999999885
No 7
>PRK13266 Thf1-like protein; Reviewed
Probab=94.26 E-value=0.089 Score=48.49 Aligned_cols=63 Identities=17% Similarity=0.292 Sum_probs=50.9
Q ss_pred HHHHHhhhcccccccccccchhhHHHHHHHHhcC-CCCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 024283 99 LIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEG-YPSEEDREAIFQAYITALKEDPEQYRIDA 161 (269)
Q Consensus 99 LLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~G-Y~peed~~~IF~Alc~Alg~Dp~qyR~dA 161 (269)
|+-.++=..-|..|.|.-+||+|+.+..+.---. ...++++..+...+|.++|+..+.+.+|-
T Consensus 125 l~~~l~~ia~~~~f~YSRl~AIGL~~LLe~a~~~~~~d~~~~~~~l~~l~~~L~ls~~kv~KDL 188 (225)
T PRK13266 125 LLATLLAIANNSKFKYSRLFAIGLYTLLEEAQPDLVKDEEKLNEALKDISEGLGLSKEKVEKDL 188 (225)
T ss_pred HHHHHHHHhcCCCCchHHHHHHHHHHHHHhcCcccccCHHHHHHHHHHHHHHcCCCHHHHHhhH
Confidence 3334444557899999999999999999876542 45666889999999999999999998884
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=93.97 E-value=0.071 Score=48.81 Aligned_cols=58 Identities=19% Similarity=0.301 Sum_probs=48.1
Q ss_pred HhhhcccccccccccchhhHHHHHHHHhcCC--CCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 024283 103 QHLMRYKRTYQYDPVFALGFVTVYDRLMEGY--PSEEDREAIFQAYITALKEDPEQYRIDA 161 (269)
Q Consensus 103 ~HLLs~n~~F~YDplFALG~VTvFd~fm~GY--~peed~~~IF~Alc~Alg~Dp~qyR~dA 161 (269)
++=..-|..|.|.-+||+|+.+..+. .+|. ..++++..+.+.+|+++|+..+.+.+|-
T Consensus 127 l~~ia~n~~f~YSRl~AIGL~~LLe~-a~~~~~~d~~~~~~~l~~l~~~L~ls~~kv~KDL 186 (214)
T TIGR03060 127 LQGIAGRHKFKYSRLFAIGLYSLLEE-AAPDKDIDEEDLNEILKELSEALGLSYDRVEKDL 186 (214)
T ss_pred HHHHhcCCCcchHHHHHHHHHHHHHh-cCcccccCHHHHHHHHHHHHHHcCCCHHHHHhhH
Confidence 34445789999999999999999984 4543 4567788999999999999999988884
No 9
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=92.50 E-value=0.48 Score=43.28 Aligned_cols=47 Identities=13% Similarity=0.387 Sum_probs=39.0
Q ss_pred CCCCcchhhHHHHHHHHHhh-cCCC----C-HHHHHHHHHhcCCChhhhhhhH
Q 024283 200 KGNFSYSRFFAVGLFRLLEL-ANAT----E-PTVLEKLCAVLNVNKRSVDRDL 246 (269)
Q Consensus 200 n~~F~YSRlfAIGLf~LLE~-~~~~----d-~~~l~~l~~~Lgls~ekv~KDL 246 (269)
|..|.|.-+||+||.+..+. .... + ....+.||+++|+.++.+.+|-
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 3479999999999999988886
No 10
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=90.16 E-value=0.99 Score=43.09 Aligned_cols=47 Identities=15% Similarity=0.377 Sum_probs=39.0
Q ss_pred CCCCcchhhHHHHHHHHHhh-cCCC----C-HHHHHHHHHhcCCChhhhhhhH
Q 024283 200 KGNFSYSRFFAVGLFRLLEL-ANAT----E-PTVLEKLCAVLNVNKRSVDRDL 246 (269)
Q Consensus 200 n~~F~YSRlfAIGLf~LLE~-~~~~----d-~~~l~~l~~~Lgls~ekv~KDL 246 (269)
|..|.|.-+||+||.+..+. .... | ....+.+|+++|+.++.+.+|-
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 3479999999999999988886
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=71.40 E-value=4 Score=31.84 Aligned_cols=23 Identities=30% Similarity=0.366 Sum_probs=19.6
Q ss_pred hhhhhhhHHHHHhhHHHHHHHHH
Q 024283 239 KRSVDRDLDVYRNLLSKLLQAKE 261 (269)
Q Consensus 239 ~ekv~KDL~lYrsnLeKmaQA~e 261 (269)
+++|.||||-|+.-|.||++-.-
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 46999999999999999998543
No 12
>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=67.69 E-value=40 Score=33.09 Aligned_cols=162 Identities=17% Similarity=0.162 Sum_probs=97.9
Q ss_pred chhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHh---cCCCHHHHHHH-HHHHHH
Q 024283 91 IYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITA---LKEDPEQYRID-AQKLEE 166 (269)
Q Consensus 91 IYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc~A---lg~Dp~qyR~d-A~~l~~ 166 (269)
-|-+.+ ++|++|-+.--+.+---+ + .-|+--=...+-+--.+|.--+-+--.|..+ ...|-++.-+- -++|.+
T Consensus 77 ~~et~~-kiL~dmgFkv~~~p~a~~-~-~agi~~P~~~lA~tv~~en~~eiVkG~L~TCaLl~KY~VdKM~kY~~~KL~~ 153 (357)
T PF03216_consen 77 DTETKC-KILTDMGFKVTQVPRATP-I-EAGIMMPMRKLAETVNNENVMEIVKGLLMTCALLTKYSVDKMIKYIQNKLER 153 (357)
T ss_pred hhhhHH-HHHHHhCceeEecccCCC-c-ccchhchHHHHHHHhChhhHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHH
Confidence 344333 467777665544432221 1 1233333444444444554444444444333 23455555443 478999
Q ss_pred HHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHH-------------------
Q 024283 167 WARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTV------------------- 227 (269)
Q Consensus 167 ~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~------------------- 227 (269)
+|.++...+|..|.... +.++.|+.-+.+..+ -|--+.|+=|+ ++++++++..
T Consensus 154 L~~sqGv~EL~~~~~~~----~~l~kl~~~vRpGQK-ltkaiyg~IL~---~l~dp~t~~~akal~a~rL~gTGMtmigl 225 (357)
T PF03216_consen 154 LATSQGVGELQHFSADR----AALAKLAACVRPGQK-LTKAIYGFILF---ELADPQTQRRAKALFAMRLNGTGMTMIGL 225 (357)
T ss_pred HhhccCcchhheecccH----HHHHHHHHhcCchhH-HHHHHHHHHHH---HhcCcccHHHHHHHHHhhhcCCCceehHH
Confidence 99999999999998865 455555544432222 34444444333 5566766543
Q ss_pred HHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHH
Q 024283 228 LEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLK 264 (269)
Q Consensus 228 l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elme 264 (269)
..+-+..||.++.++-.||- |+|+.+-.-|.+.||.
T Consensus 226 FtqAa~nlGa~pA~LLedLc-m~s~v~sarrivkLm~ 261 (357)
T PF03216_consen 226 FTQAAKNLGATPADLLEDLC-MGSLVESARRIVKLMR 261 (357)
T ss_pred HHHHHHhcCCCcHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence 33445789999999999995 8999999999999987
No 13
>KOG0961 consensus Predicted Zn2+-dependent endopeptidase, insulinase superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=67.53 E-value=36 Score=37.08 Aligned_cols=136 Identities=25% Similarity=0.280 Sum_probs=92.4
Q ss_pred cCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHh--------cCCCCchhHHHHHHHHHHhcCCCHHHHH
Q 024283 87 PIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLM--------EGYPSEEDREAIFQAYITALKEDPEQYR 158 (269)
Q Consensus 87 PI~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm--------~GY~peed~~~IF~Alc~Alg~Dp~qyR 158 (269)
-||.=|-++++| |+-|+.+-+.+-+.| .|+.-.+++|. .||+---.=- .-+.+-+=+||++++
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 TIPTPVLTSADD--VAKHFTSDLIDHSIQ----VGVSGLYDRLVNLRIKVGADKYPLLVKWI---QIFLQGVVFDPSRIH 669 (1022)
T ss_pred CCCcchhhhHHH--HHHHHHhhhhhhhhc----ccccccchhheeEEEEEccCCcchhHHHH---HHHhhhhccCHHHHH
Confidence 456667777777 466777777665544 68888999986 6897433322 334567779999999
Q ss_pred HHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhcCCC
Q 024283 159 IDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVN 238 (269)
Q Consensus 159 ~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls 238 (269)
+-++++.. ++.+| +-++.+.-|-++++-||.-=.+--..|+-.++++-+.+
T Consensus 670 ~~~~~~l~--------~i~~~------------------KRdg~~vlss~~~~~lY~~~slk~s~d~L~~Ek~l~ei--- 720 (1022)
T KOG0961|consen 670 QCAQKLLG--------EIRDR------------------KRDGCTVLSSAVASMLYGKNSLKISFDELVLEKLLEEI--- 720 (1022)
T ss_pred HHHHHHHh--------hhhhh------------------hcCccEehHHHHHHHHhcccchhhcccHHHHHHHHHHH---
Confidence 99988866 22222 12778888899999888643222234665566554443
Q ss_pred hhhhhhhHHHHHhhHHHHHHHHHHH
Q 024283 239 KRSVDRDLDVYRNLLSKLLQAKELL 263 (269)
Q Consensus 239 ~ekv~KDL~lYrsnLeKmaQA~elm 263 (269)
..+|++| =++.|+|++|++.++
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 3566777 678999999998854
No 14
>COG3793 TerB Tellurite resistance protein [Inorganic ion transport and metabolism]
Probab=65.24 E-value=21 Score=31.27 Aligned_cols=36 Identities=22% Similarity=0.219 Sum_probs=30.8
Q ss_pred hhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCC
Q 024283 137 EDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQT 172 (269)
Q Consensus 137 ed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~~s 172 (269)
+....||+.+|.+.+.|++.=+..+.++.+-.++.+
T Consensus 65 ~~i~~~~~~~~~~~~~d~~~gk~ea~~~I~~lk~d~ 100 (144)
T COG3793 65 NEINEIFETLVGSFDTDFEIGKREAMKEIEDLKHDT 100 (144)
T ss_pred HHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHhcCCh
Confidence 478899999999999999999999888888666554
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=64.55 E-value=25 Score=28.13 Aligned_cols=99 Identities=17% Similarity=0.194 Sum_probs=50.8
Q ss_pred hcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhH
Q 024283 130 MEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFF 209 (269)
Q Consensus 130 m~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlf 209 (269)
-.|--.++++..|-+.+.+-.+++++....-.+.+.+.... ..+.+..+..|.. .-....-..+
T Consensus 36 aDG~v~~~E~~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~------------~~~~~~~~~~l~~----~~~~~~r~~l 99 (140)
T PF05099_consen 36 ADGEVDPEEIEAIRQLLAERFGLSPEEAEELIELADELKQE------------PIDLEELLRELRD----SLSPEEREDL 99 (140)
T ss_dssp TTSS--CHHHHHHHHHHHHCGCGSCHHHHHHHHHHCHHHHH------------CCHHHHHHHHHCT----S--HHHHHHH
T ss_pred cCCCCCHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHhc------------cccHHHHHHHHHH----hhchHHHHHH
Confidence 35666678888888888788888877766555444433222 2234445554421 1111111222
Q ss_pred HHHHHHHHhhcCC-C--CHHHHHHHHHhcCCChhhhhh
Q 024283 210 AVGLFRLLELANA-T--EPTVLEKLCAVLNVNKRSVDR 244 (269)
Q Consensus 210 AIGLf~LLE~~~~-~--d~~~l~~l~~~Lgls~ekv~K 244 (269)
--.++.+....|. . |.+.+.++++.||++.+.+++
T Consensus 100 l~~l~~ia~ADG~~~~~E~~~l~~ia~~L~i~~~~~~~ 137 (140)
T PF05099_consen 100 LRMLIAIAYADGEISPEEQEFLRRIAEALGISEEDFQR 137 (140)
T ss_dssp HHHHHHHCTCTTC-SCCHHHHHHHHHHHCTS-SS----
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHHHHcCCCHHHHhc
Confidence 2233333333333 1 345899999999999987764
No 16
>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=55.20 E-value=78 Score=29.84 Aligned_cols=145 Identities=15% Similarity=0.271 Sum_probs=83.3
Q ss_pred hhHHHHHHHHHHhhhccccccccccc-chhhHHH--HHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Q 024283 92 YNTVLQELIVQQHLMRYKRTYQYDPV-FALGFVT--VYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWA 168 (269)
Q Consensus 92 Yrrvv~ELLVE~HLLs~n~~F~YDpl-FALG~VT--vFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A 168 (269)
||..+++-..+-.- .|..|.+=.+ -.+||.+ -+..+++|=+|-. +.-..-+++++|+++.+-. --..|....
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 77777777776554 3445666555 3488776 5678899988765 5556788999999997632 233444444
Q ss_pred hcCCccccccccCCcchhHHHHHHHHHHhcCCCCC-cchhhHHHHHHHHHhhcCCC-CHHHHHHHHHhcC--CChhhhhh
Q 024283 169 RGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNF-SYSRFFAVGLFRLLELANAT-EPTVLEKLCAVLN--VNKRSVDR 244 (269)
Q Consensus 169 ~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F-~YSRlfAIGLf~LLE~~~~~-d~~~l~~l~~~Lg--ls~ekv~K 244 (269)
+.++.++-..+.. +++.+...-..+.-+.+.| .|+.+..-.|..|+...+.. ||+ .|++.++ +|.+.|+.
T Consensus 85 ~ak~~~~k~~~~~---~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~---~ia~~l~p~is~~ev~~ 158 (271)
T TIGR02147 85 QAKTDTEKQQFFE---EMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPE---ELAKRCFPKISAEQVKE 158 (271)
T ss_pred ccCCHHHHHHHHH---HHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHH---HHHHHhCCCCCHHHHHH
Confidence 4444332111111 0011100000011112333 67778888888888776654 655 4666666 77777776
Q ss_pred hHH
Q 024283 245 DLD 247 (269)
Q Consensus 245 DL~ 247 (269)
=|+
T Consensus 159 sL~ 161 (271)
T TIGR02147 159 SLD 161 (271)
T ss_pred HHH
Confidence 665
No 17
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=52.03 E-value=1.4e+02 Score=28.11 Aligned_cols=121 Identities=17% Similarity=0.249 Sum_probs=72.1
Q ss_pred HHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccC--C---c--------chhHHHHHHHHHHhcCCCCCcchhhHHHH
Q 024283 146 YITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPS--K---E--------GEVEGLLKDIAERASGKGNFSYSRFFAVG 212 (269)
Q Consensus 146 lc~Alg~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~--~---~--------g~~~~~l~~Ia~~~~~n~~F~YSRlfAIG 212 (269)
+.+-....|+.+..-++++.+|++......++.+-. . + ++-+..+..+++ .+-..|.+-=+-+++
T Consensus 81 ~~~dv~I~p~~i~e~s~~v~~w~~~~~v~~ii~~~g~~~~~~~e~~~v~~va~~~~~~~~l~~--~~~~~~~~G~I~G~~ 158 (244)
T COG1938 81 LVSDVPIPPAVIYEISNAVVEWAEENGVEEVISLGGMPARLREEKPSVYGVATSEEKLEKLKD--LGAEPLEEGTIVGPS 158 (244)
T ss_pred EEecCCCCHHHHHHHHHHHHHHHHHcCCeEEEEecCCCcccccCCCceEEEecchhhhhHHhh--cCCCccccceeeccc
Confidence 445567889999999999999999998888876551 1 0 011122333332 112334443222222
Q ss_pred HHHHHhhcCC---------------CCHHHHHHHH----Hhc--CCChhhhhhhHHHHHhhHHHHHHHHHHHHHHhc
Q 024283 213 LFRLLELANA---------------TEPTVLEKLC----AVL--NVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVD 268 (269)
Q Consensus 213 Lf~LLE~~~~---------------~d~~~l~~l~----~~L--gls~ekv~KDL~lYrsnLeKmaQA~elmeE~le 268 (269)
=.-|.|.... .||.+...+. +.+ +++.+++.|--..++.-|+|+++..+-.++..+
T Consensus 159 g~ll~e~~~r~i~a~~ll~et~~~~PDP~AAa~vve~lnk~~~l~V~td~L~keAe~i~~~lekl~eq~~~~~~~~~ 235 (244)
T COG1938 159 GALLNECLKRGIPALVLLAETFGDRPDPRAAARVVEALNKMLGLNVDTDKLEKEAEEIEEQLEKLAEQLEKEEERVE 235 (244)
T ss_pred HHHHHHHHHcCCCeEEEeccccCCCCChHHHHHHHHHHHHHhcCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 1111122211 2676444444 333 478899999999999999999887776665443
No 18
>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=51.88 E-value=12 Score=27.07 Aligned_cols=24 Identities=25% Similarity=0.405 Sum_probs=18.5
Q ss_pred CHHHHHHHHHhcCCChhhhhhhHH
Q 024283 224 EPTVLEKLCAVLNVNKRSVDRDLD 247 (269)
Q Consensus 224 d~~~l~~l~~~Lgls~ekv~KDL~ 247 (269)
+--.-++|++.+|+++.-|.|||.
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 334678899999999999999984
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=51.72 E-value=8.1 Score=27.67 Aligned_cols=23 Identities=22% Similarity=0.455 Sum_probs=20.6
Q ss_pred HHHHHHHHHhcCCChhhhhhhHH
Q 024283 225 PTVLEKLCAVLNVNKRSVDRDLD 247 (269)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~ 247 (269)
.-.+++|++.+|.|...+.|||.
T Consensus 14 ~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHH
Confidence 44688999999999999999996
No 20
>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=50.53 E-value=28 Score=28.53 Aligned_cols=32 Identities=34% Similarity=0.565 Sum_probs=27.6
Q ss_pred CCChhhhhhhHHHHHhhHHHHHHHHHHHHHHh
Q 024283 236 NVNKRSVDRDLDVYRNLLSKLLQAKELLKEYV 267 (269)
Q Consensus 236 gls~ekv~KDL~lYrsnLeKmaQA~elmeE~l 267 (269)
|=+++.++|...+.|-+-.|=-||+|-||+++
T Consensus 43 ~pnke~~nrevsilrh~yqkeiqaketmk~il 74 (109)
T PF04772_consen 43 NPNKETINREVSILRHNYQKEIQAKETMKKIL 74 (109)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45688899999999999999999999999986
No 21
>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=49.95 E-value=22 Score=26.60 Aligned_cols=41 Identities=24% Similarity=0.325 Sum_probs=28.1
Q ss_pred CCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccc
Q 024283 132 GYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLV 177 (269)
Q Consensus 132 GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~~s~~~l~ 177 (269)
|.||+++-+.|++++.+. +-+..|.....+... |.+..+++
T Consensus 1 ~~p~~~~i~~i~~~~~~~---~~~~~~~~~~~l~~~--G~s~~~Il 41 (89)
T PF08542_consen 1 DWPPPEVIEEILESCLNG---DFKEARKKLYELLVE--GYSASDIL 41 (89)
T ss_dssp TS--HHHHHHHHHHHHHT---CHHHHHHHHHHHHHT--T--HHHHH
T ss_pred CCCCHHHHHHHHHHHHhC---CHHHHHHHHHHHHHc--CCCHHHHH
Confidence 568888888888888776 777777777777664 77766655
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=49.45 E-value=21 Score=29.81 Aligned_cols=77 Identities=21% Similarity=0.308 Sum_probs=59.9
Q ss_pred CchhHHHHHHHHHHhcC---------CCHHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCC
Q 024283 135 SEEDREAIFQAYITALK---------EDPEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGN 202 (269)
Q Consensus 135 peed~~~IF~Alc~Alg---------~Dp~qyR~dA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~n~~ 202 (269)
+.+||.+++..++.+|= --++++|.-|++|..+|+..+.. .+..|+.....+..++..|+.+-+ +.+
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 45799999999998873 35789999999999999976644 344566666678889999998876 455
Q ss_pred CcchhhHHHH
Q 024283 203 FSYSRFFAVG 212 (269)
Q Consensus 203 F~YSRlfAIG 212 (269)
.-|+|+.=+|
T Consensus 87 GGYTRI~kl~ 96 (112)
T TIGR00059 87 GGYTRILKLG 96 (112)
T ss_pred CCeEEEEECC
Confidence 5899987655
No 23
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=47.03 E-value=28 Score=29.14 Aligned_cols=77 Identities=22% Similarity=0.302 Sum_probs=60.3
Q ss_pred CchhHHHHHHHHHHhcC---------CCHHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCC
Q 024283 135 SEEDREAIFQAYITALK---------EDPEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGN 202 (269)
Q Consensus 135 peed~~~IF~Alc~Alg---------~Dp~qyR~dA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~n~~ 202 (269)
+.+||.+++.-++.+|= --+.++|.-|++|..+|+.-+.. .+..|+.....+..++..|+.+-++ .+
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 34788999999999999976654 3445666666788888999988864 55
Q ss_pred CcchhhHHHH
Q 024283 203 FSYSRFFAVG 212 (269)
Q Consensus 203 F~YSRlfAIG 212 (269)
.-|+|++-+|
T Consensus 89 GGYTRI~k~~ 98 (113)
T PRK05591 89 GGYTRILKLG 98 (113)
T ss_pred CCeEEEEECC
Confidence 5899988776
No 24
>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=44.12 E-value=12 Score=28.35 Aligned_cols=46 Identities=26% Similarity=0.375 Sum_probs=32.2
Q ss_pred ccccccc-ccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCH
Q 024283 109 KRTYQYD-PVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDP 154 (269)
Q Consensus 109 n~~F~YD-plFALG~VTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp 154 (269)
+.++.|| +-..-+-.++.+-|..|+=.-.+...+|.|||.++|.+.
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 3566666 344444445666666777778999999999999999864
No 25
>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=43.54 E-value=37 Score=21.78 Aligned_cols=31 Identities=16% Similarity=0.276 Sum_probs=24.9
Q ss_pred HHHHHHHHHhcCCChhhhhhhHHHHHhhHHHH
Q 024283 225 PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKL 256 (269)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKm 256 (269)
++.+++|.+ ||++.+.+.+=|....+++++-
T Consensus 2 ~~~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A 32 (38)
T cd00194 2 EEKLEQLLE-MGFSREEARKALRATNNNVERA 32 (38)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHHHhCCCHHHH
Confidence 456777766 7999999999999888887764
No 26
>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=41.91 E-value=26 Score=25.14 Aligned_cols=27 Identities=22% Similarity=0.555 Sum_probs=21.8
Q ss_pred HHHHHHHhcCCChhhhhhhHHHHHhhH
Q 024283 227 VLEKLCAVLNVNKRSVDRDLDVYRNLL 253 (269)
Q Consensus 227 ~l~~l~~~Lgls~ekv~KDL~lYrsnL 253 (269)
.+++||+.+|+|...+.+|++-.+..+
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 578999999999999999998766544
No 27
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=40.63 E-value=3.1e+02 Score=25.60 Aligned_cols=113 Identities=19% Similarity=0.200 Sum_probs=67.2
Q ss_pred HHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCcc-ccccccCCcchhHHHHHHHHHHhcCCCCCcch
Q 024283 128 RLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTAS-SLVEFPSKEGEVEGLLKDIAERASGKGNFSYS 206 (269)
Q Consensus 128 ~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~~s~~-~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YS 206 (269)
+++-..+|+ ....-+-|-+..|.++++ ++-.+.+++.+.....+ ....+.-......+....- -++..++ .+-
T Consensus 47 ~l~p~~~~~--g~~~~~~l~~k~g~~~~~-~~~~~~~~~~~~~~Gi~~~f~~~~~~~nt~~Ah~l~~--~A~~~G~-~~~ 120 (225)
T COG2761 47 ELDPDLPPE--GLDRKEYLAQKYGISEEQ-KAAHARLEELAEEEGIDFNFDAIVPAPNTLDAHRLIK--AAELQGK-AQD 120 (225)
T ss_pred ccCCCCCcc--cccHHHHHHHHhCccHHH-HHHHHHHHHhhHhcCcccchhhccCCCchHHHHHHHH--HHHHhCc-hHH
Confidence 455566664 344455666778888888 77778888877754443 1111100011122221111 1122333 455
Q ss_pred hhHHHHHHHHH--hhcCCCCHHHHHHHHHhcCCChhhhhhhHH
Q 024283 207 RFFAVGLFRLL--ELANATEPTVLEKLCAVLNVNKRSVDRDLD 247 (269)
Q Consensus 207 RlfAIGLf~LL--E~~~~~d~~~l~~l~~~Lgls~ekv~KDL~ 247 (269)
|+ .-.||..+ |-.+..|.++|-+|++..||..+.+.+||.
T Consensus 121 ~~-~~~lf~AyF~eg~nI~D~dVL~diA~~~GLD~~~~~~~L~ 162 (225)
T COG2761 121 RF-LEALFEAYFEEGRNIGDEDVLADIAEEVGLDREEFKADLA 162 (225)
T ss_pred HH-HHHHHHHHhccCCCCCcHHHHHHHHHHhCCCHHHHHHHHh
Confidence 53 45777777 344457899999999999999999999983
No 28
>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=40.31 E-value=31 Score=23.66 Aligned_cols=28 Identities=32% Similarity=0.610 Sum_probs=22.4
Q ss_pred CHHHHHHHHHhcCCChhhhhhhHHHHHh
Q 024283 224 EPTVLEKLCAVLNVNKRSVDRDLDVYRN 251 (269)
Q Consensus 224 d~~~l~~l~~~Lgls~ekv~KDL~lYrs 251 (269)
++-..++|++.||+|...|.+||..-+.
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 3467899999999999999999976544
No 29
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=38.82 E-value=1.4e+02 Score=26.80 Aligned_cols=21 Identities=24% Similarity=0.390 Sum_probs=17.5
Q ss_pred CHHHHHHHHHhcCCChhhhhh
Q 024283 224 EPTVLEKLCAVLNVNKRSVDR 244 (269)
Q Consensus 224 d~~~l~~l~~~Lgls~ekv~K 244 (269)
|-..|+.|+..|||+++-|++
T Consensus 162 Er~YL~~LA~aL~L~~~lv~~ 182 (188)
T PF04391_consen 162 ERAYLDELAQALGLDPDLVAQ 182 (188)
T ss_pred HHHHHHHHHHHhCcCHHHHHH
Confidence 456899999999999987653
No 30
>KOG0212 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.52 E-value=1.9e+02 Score=31.02 Aligned_cols=102 Identities=18% Similarity=0.178 Sum_probs=69.6
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHH
Q 024283 138 DREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLL 217 (269)
Q Consensus 138 d~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LL 217 (269)
.-+.||+++|+-.....+..|.-|+-+-...+....++=. .=.++.....+.+++ ...-.|.|.|-|+-.+.|
T Consensus 122 ~Fn~iFdvL~klsaDsd~~V~~~aeLLdRLikdIVte~~~-----tFsL~~~ipLL~eri--y~~n~~tR~flv~Wl~~L 194 (675)
T KOG0212|consen 122 YFNEIFDVLCKLSADSDQNVRGGAELLDRLIKDIVTESAS-----TFSLPEFIPLLRERI--YVINPMTRQFLVSWLYVL 194 (675)
T ss_pred chHHHHHHHHHHhcCCccccccHHHHHHHHHHHhcccccc-----ccCHHHHHHHHHHHH--hcCCchHHHHHHHHHHHH
Confidence 5678999999988776666676666554444422221111 113555666677777 444579999999999999
Q ss_pred hhcCCC-----CHHHHHHHHHhcCCChhhhh--hhH
Q 024283 218 ELANAT-----EPTVLEKLCAVLNVNKRSVD--RDL 246 (269)
Q Consensus 218 E~~~~~-----d~~~l~~l~~~Lgls~ekv~--KDL 246 (269)
....+- -|+.+.-|.+.||=+.+.|. +|.
T Consensus 195 ds~P~~~m~~yl~~~ldGLf~~LsD~s~eVr~~~~t 230 (675)
T KOG0212|consen 195 DSVPDLEMISYLPSLLDGLFNMLSDSSDEVRTLTDT 230 (675)
T ss_pred hcCCcHHHHhcchHHHHHHHHHhcCCcHHHHHHHHH
Confidence 766552 37788888899988887776 455
No 31
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=37.25 E-value=1.1e+02 Score=26.74 Aligned_cols=52 Identities=12% Similarity=0.097 Sum_probs=35.2
Q ss_pred HHHHH-hhcCCCCHHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHH
Q 024283 213 LFRLL-ELANATEPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKE 265 (269)
Q Consensus 213 Lf~LL-E~~~~~d~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE 265 (269)
+|..+ +..+..+++.|.++++..|++.+++++.++- ...-+++.+..++.++
T Consensus 110 lf~~i~~~~~~~~~~~L~~~a~~~Gld~~~f~~~l~s-~~~~~~v~~~~~~a~~ 162 (207)
T PRK10954 110 LFEGVQKTQTIQSAADIRDVFIKAGVKGEDYDAAWNS-FVVKSLVAQQEKAAAD 162 (207)
T ss_pred HHHHHHccCCCCCHHHHHHHHHHcCCCHHHHHHHHhC-hHHHHHHHHHHHHHHH
Confidence 44444 2223356788999999999999999998865 3345666666665544
No 32
>PRK10880 adenine DNA glycosylase; Provisional
Probab=37.19 E-value=3.1e+02 Score=26.85 Aligned_cols=81 Identities=19% Similarity=0.308 Sum_probs=52.5
Q ss_pred hhHhHHHHHhhCCC-c-----CCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHH----H
Q 024283 73 VAETKMNFLKLYKR-P-----IPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREA----I 142 (269)
Q Consensus 73 VSDTKr~F~~~y~r-P-----I~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~----I 142 (269)
.++.-.+.|..|.| + -..-|+-.|-|+|.|+==. . -+..+|++||+.||..++... =
T Consensus 6 ~~~~ll~W~~~~~r~~lpWr~~~dpy~ilVseILlQQT~v--~-----------~v~~~~~rl~~~fPt~~~La~a~~ee 72 (350)
T PRK10880 6 FSAQVLDWYDKYGRKTLPWQIDKTPYKVWLSEVMLQQTQV--A-----------TVIPYFERFMARFPTVTDLANAPLDE 72 (350)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhhccH--H-----------HHHHHHHHHHHHCcCHHHHHCcCHHH
Confidence 56667788999886 3 3566999999999887411 1 255689999999986554221 1
Q ss_pred HHHHHHhcCC--CHHHHHHHHHHHHH
Q 024283 143 FQAYITALKE--DPEQYRIDAQKLEE 166 (269)
Q Consensus 143 F~Alc~Alg~--Dp~qyR~dA~~l~~ 166 (269)
...+++.+|+ -...+++-|+.+.+
T Consensus 73 l~~~~~glGyy~RAr~L~~~A~~i~~ 98 (350)
T PRK10880 73 VLHLWTGLGYYARARNLHKAAQQVAT 98 (350)
T ss_pred HHHHHHcCChHHHHHHHHHHHHHHHH
Confidence 2245567787 44445555555544
No 33
>COG4476 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.74 E-value=1.5e+02 Score=24.18 Aligned_cols=82 Identities=21% Similarity=0.186 Sum_probs=70.3
Q ss_pred hCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHH
Q 024283 83 LYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQ 162 (269)
Q Consensus 83 ~y~rPI~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~ 162 (269)
.|.+||+.=|.+ +|+.--+|++..=..+==-.+=+.-|.-.|.+|-+=-|.-.+-..||..+=++.|..+=+-=++|+
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 589999999988 899999999887666555567788889999999999999999999999999999999988888887
Q ss_pred HHHH
Q 024283 163 KLEE 166 (269)
Q Consensus 163 ~l~~ 166 (269)
...+
T Consensus 80 ~~~~ 83 (90)
T COG4476 80 ESEE 83 (90)
T ss_pred Hhhh
Confidence 6643
No 34
>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=35.96 E-value=37 Score=22.73 Aligned_cols=27 Identities=30% Similarity=0.416 Sum_probs=22.3
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHH
Q 024283 138 DREAIFQAYITALKEDPEQYRIDAQKL 164 (269)
Q Consensus 138 d~~~IF~Alc~Alg~Dp~qyR~dA~~l 164 (269)
+.+.++.-+++..|.|++++++..++.
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 345678888999999999999988765
No 35
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=35.82 E-value=49 Score=24.31 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=17.9
Q ss_pred cCCCCchhHHHHHHHHHHhcCCCHHHH
Q 024283 131 EGYPSEEDREAIFQAYITALKEDPEQY 157 (269)
Q Consensus 131 ~GY~peed~~~IF~Alc~Alg~Dp~qy 157 (269)
+++|++---......||+.+|.||+++
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 455555556677788899999998864
No 36
>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=35.53 E-value=44 Score=24.33 Aligned_cols=27 Identities=15% Similarity=0.512 Sum_probs=21.0
Q ss_pred HHHHHHhcCCChhhhhhhHHHHHhhHH
Q 024283 228 LEKLCAVLNVNKRSVDRDLDVYRNLLS 254 (269)
Q Consensus 228 l~~l~~~Lgls~ekv~KDL~lYrsnLe 254 (269)
++++|+.||||.+-.+.=.++|+...+
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~ 27 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQE 27 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHH
Confidence 578999999999998888888887654
No 37
>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional
Probab=34.97 E-value=3.8e+02 Score=24.99 Aligned_cols=120 Identities=18% Similarity=0.165 Sum_probs=71.9
Q ss_pred ccchhhHHHHHHHHh--cCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHH
Q 024283 116 PVFALGFVTVYDRLM--EGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDI 193 (269)
Q Consensus 116 plFALG~VTvFd~fm--~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~I 193 (269)
..|...++.+.-.++ .|=-.+.+.+ ++..+++.++.++++ |+.|..+-+.++... -+++..+..|
T Consensus 52 ~~ff~a~~aLl~~vAkADG~Vse~Ei~-~~~~l~~~~~l~~~~-r~~a~~lf~~~k~~~-----------~~l~~~~~~~ 118 (267)
T PRK09430 52 ALFFNTTFAVMGHLAKAKGRVTEADIR-IASQLMDRMNLHGEA-RRAAQQAFREGKEPD-----------FPLREKLRQF 118 (267)
T ss_pred HHHHHHHHHHHHHHHhcCCCcCHHHHH-HHHHHHHHcCCCHHH-HHHHHHHHHHhcccC-----------CCHHHHHHHH
Confidence 345555555555555 4666667777 889999999999887 567788877665432 1245566666
Q ss_pred HHHhcCCCCCcchhhHHHHHHHHHhhcCCCC---HHHHHHHHHhcCCChhhhhhhHHHHH
Q 024283 194 AERASGKGNFSYSRFFAVGLFRLLELANATE---PTVLEKLCAVLNVNKRSVDRDLDVYR 250 (269)
Q Consensus 194 a~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d---~~~l~~l~~~Lgls~ekv~KDL~lYr 250 (269)
..... ++..-=+.|=-.|+.+--..|.-+ ...|.++|+.||++..-.++=+.+|.
T Consensus 119 ~~~~~--~r~~l~~~lL~~l~~vA~ADG~l~~~E~~~L~~Ia~~Lgis~~df~~~~~~~~ 176 (267)
T PRK09430 119 RSVCG--GRFDLLRMFLEIQIQAAFADGSLHPNERQVLYVIAEELGFSRFQFDQLLRMMQ 176 (267)
T ss_pred HHHhc--ccHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 54331 111111112223333333334434 35899999999999876666555544
No 38
>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=34.43 E-value=1.6e+02 Score=26.75 Aligned_cols=136 Identities=11% Similarity=0.212 Sum_probs=76.3
Q ss_pred ccccccchhhHHHHHHHHhcCCCCchh-----------HHHHHHHHHHhc------CCC--HHHHHHHH-HHHHH----H
Q 024283 112 YQYDPVFALGFVTVYDRLMEGYPSEED-----------REAIFQAYITAL------KED--PEQYRIDA-QKLEE----W 167 (269)
Q Consensus 112 F~YDplFALG~VTvFd~fm~GY~peed-----------~~~IF~Alc~Al------g~D--p~qyR~dA-~~l~~----~ 167 (269)
..+|.++..|+...++.. +.|.|+.. +..|.+.+-+-. ..+ .++...+. ....+ +
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 568999999999888765 56776543 223333332211 111 11111111 11111 2
Q ss_pred HhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhcCCChhhhhhhHH
Q 024283 168 ARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLD 247 (269)
Q Consensus 168 A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~ekv~KDL~ 247 (269)
-+....+||..|...-.+-.-.|.++++ ..|+-.=||-.||.+-..+ +.+|+.++.|-..=.||-..+.+-++
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 2233334555443322222234566664 3577666999999999988 56677777777666777777777766
Q ss_pred HHHhhHHH
Q 024283 248 VYRNLLSK 255 (269)
Q Consensus 248 lYrsnLeK 255 (269)
+=|..||+
T Consensus 188 v~rktier 195 (218)
T TIGR02895 188 ISRKTIER 195 (218)
T ss_pred CCHHHHHH
Confidence 66666665
No 39
>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=34.19 E-value=52 Score=27.33 Aligned_cols=32 Identities=13% Similarity=0.325 Sum_probs=19.6
Q ss_pred cccchhhHHHHHHHHhcCCCCchh--HHHHHHHHH
Q 024283 115 DPVFALGFVTVYDRLMEGYPSEED--REAIFQAYI 147 (269)
Q Consensus 115 DplFALG~VTvFd~fm~GY~peed--~~~IF~Alc 147 (269)
..+|+||++ .|+.++.|++|-.+ ...+++.+-
T Consensus 188 ~Di~slG~i-l~~l~~~g~~p~~~~~~~~~~~~~~ 221 (262)
T cd00192 188 SDVWSFGVL-LWEIFTLGATPYPGLSNEEVLEYLR 221 (262)
T ss_pred hccHHHHHH-HHHHHhcCCCCCCCCCHHHHHHHHH
Confidence 469999976 56666667877433 333444443
No 40
>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=33.56 E-value=42 Score=21.89 Aligned_cols=30 Identities=7% Similarity=0.199 Sum_probs=23.2
Q ss_pred HHHHHHHHHhcCCChhhhhhhHHHHHhhHHH
Q 024283 225 PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSK 255 (269)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeK 255 (269)
++.+++|.+. ||+.+.+.+=|..-.+++++
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 5678888888 99999999988777776654
No 41
>COG3867 Arabinogalactan endo-1,4-beta-galactosidase [Carbohydrate transport and metabolism]
Probab=32.69 E-value=87 Score=31.21 Aligned_cols=114 Identities=22% Similarity=0.319 Sum_probs=64.1
Q ss_pred cccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcC---CCHHHHHHHHHHHHHHHhcCCccccccccC----------
Q 024283 115 DPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALK---EDPEQYRIDAQKLEEWARGQTASSLVEFPS---------- 181 (269)
Q Consensus 115 DplFALG~VTvFd~fm~GY~peed~~~IF~Alc~Alg---~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~---------- 181 (269)
.|+|---+-++=+.|++|= |...|. +| +-.| +|..-.||||-++++.+ |.+---|.-|..
T Consensus 25 e~~~v~~v~~~~~dFikGa----Dis~l~-~l-E~~Gvkf~d~ng~~qD~~~iLK~~-GvNyvRlRvwndP~dsngn~yg 97 (403)
T COG3867 25 EDFFVFPVENSPNDFIKGA----DISSLI-EL-ENSGVKFFDTNGVRQDALQILKNH-GVNYVRLRVWNDPYDSNGNGYG 97 (403)
T ss_pred ccceeeeccCChHHhhccc----cHHHHH-HH-HHcCceEEccCChHHHHHHHHHHc-CcCeEEEEEecCCccCCCCccC
Confidence 3444444444556666664 333332 22 2223 56777899999888743 344334444543
Q ss_pred -CcchhHHHHHHHHHHhcCCC-----CCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhcCCChhhhhhhHHHH
Q 024283 182 -KEGEVEGLLKDIAERASGKG-----NFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLDVY 249 (269)
Q Consensus 182 -~~g~~~~~l~~Ia~~~~~n~-----~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~ekv~KDL~lY 249 (269)
+.++++.. -.||+|++.++ .||||-++| ||.-..+=.++-+++.|.+++++--|
T Consensus 98 gGnnD~~k~-ieiakRAk~~GmKVl~dFHYSDfwa-------------DPakQ~kPkaW~~l~fe~lk~avy~y 157 (403)
T COG3867 98 GGNNDLKKA-IEIAKRAKNLGMKVLLDFHYSDFWA-------------DPAKQKKPKAWENLNFEQLKKAVYSY 157 (403)
T ss_pred CCcchHHHH-HHHHHHHHhcCcEEEeeccchhhcc-------------ChhhcCCcHHhhhcCHHHHHHHHHHH
Confidence 11234443 35888888776 699999986 22222222334466778888887444
No 42
>PF01024 Colicin: Colicin pore forming domain; InterPro: IPR000293 Colicins are plasmid-encoded polypeptide toxins produced by and active against Escherichia coli and closely related bacteria. Colicins are released into the environment to reduce competition from other bacterial strains. Colicins bind to outer membrane receptors, using them to translocate to the cytoplasm or cytoplasmic membrane, where they exert their cytotoxic effect, including depolarisation of the cytoplasmic membrane, DNase activity, RNase activity, or inhibition of murein synthesis. Channel-forming colicins (colicins A, B, E1, Ia, Ib, and N) are transmembrane proteins that depolarize the cytoplasmic membrane, leading to dissipation of cellular energy []. These colicins contain at least three domains: an N-terminal translocation domain responsible for movement across the outer membrane and periplasmic space; a central domain responsible for receptor recognition; and a C-terminal cytotoxic domain responsible for channel formation in the cytoplasmic membrane []. This entry represents the C-terminal cytotoxic domain, which has a globin-like fold with additional helices at either end.; GO: 0019835 cytolysis, 0050829 defense response to Gram-negative bacterium, 0016021 integral to membrane; PDB: 2I88_A 1CII_A 1RH1_A 1COL_B 1A87_A 3FEW_X.
Probab=32.08 E-value=3e+02 Score=25.13 Aligned_cols=78 Identities=21% Similarity=0.246 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCC-HHHHHHHH
Q 024283 154 PEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATE-PTVLEKLC 232 (269)
Q Consensus 154 p~qyR~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d-~~~l~~l~ 232 (269)
.++|.+-|++|.+-++|+...... ..|+..- +.+.|++-+.+.=-=-.|...||..+.+| -+.|.+++
T Consensus 31 G~Ky~~~A~elA~~~kGKkIRs~~----------dAl~s~e-K~~~n~~kK~~~kDr~AI~~Al~s~d~~~~A~nl~k~s 99 (187)
T PF01024_consen 31 GEKYKKLAKELAEDAKGKKIRSVD----------DALKSFE-KYKSNLNKKINAKDRDAIVNALESVDAKDMAKNLAKFS 99 (187)
T ss_dssp -HHHHHHHHHHHHHHHTGC---HH----------HHHHHHH-HHHTHTTCSS-HHHHHHHHHHHHT--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhcccccCCHH----------HHHHHHH-HHHhchhhhhhhccHHHHHHHHHHcCHHHHHHHHHHHH
Confidence 468899999999999988876443 3444442 44457777777777777888888776665 45799999
Q ss_pred HhcCCChhhh
Q 024283 233 AVLNVNKRSV 242 (269)
Q Consensus 233 ~~Lgls~ekv 242 (269)
..+|+-..-+
T Consensus 100 K~fg~~~~~i 109 (187)
T PF01024_consen 100 KAFGITGKAI 109 (187)
T ss_dssp GGGTSTTHHH
T ss_pred HHhcchHHHh
Confidence 9999865443
No 43
>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=31.44 E-value=1.4e+02 Score=24.59 Aligned_cols=126 Identities=24% Similarity=0.322 Sum_probs=66.6
Q ss_pred hHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCC
Q 024283 93 NTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQT 172 (269)
Q Consensus 93 rrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~~s 172 (269)
.+.+++|+-+. .+.++.+=|+.=.+.... +.|.+|.+ +|.+++.-.+.+..||+...
T Consensus 17 ~~~l~~l~~~~----~~~~i~~~p~~l~~~~~~----~~~~~~~~---------------~~~~~~~~~~~~~~~a~~~g 73 (193)
T PF01323_consen 17 SPRLRKLRAEY----PDVEIEWRPFPLRPDMRR----SGGAPPAE---------------DPAKAEYMFQDLERWARRYG 73 (193)
T ss_dssp HHHHHHHHHHH----TTCEEEEEEESSSTHHHH----CT-SCGCG---------------SHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHh----cCCcEEEecccccccccc----CCCCCccc---------------ChhHHHHHHHHHHHHHHHhc
Confidence 44555544444 456666666654444222 45666554 78888888888888887654
Q ss_pred ccccccccCCc-chhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHH-h-hcCCCCHHHHHHHHHhcCCChhhhhhhHH
Q 024283 173 ASSLVEFPSKE-GEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLL-E-LANATEPTVLEKLCAVLNVNKRSVDRDLD 247 (269)
Q Consensus 173 ~~~l~~~~~~~-g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LL-E-~~~~~d~~~l~~l~~~Lgls~ekv~KDL~ 247 (269)
.. +. +.... +........+. .+...+ .+.+ +.-.||+.+ + ..+..|++.|.++++..|++.+.+++.++
T Consensus 74 i~-~~-~~~~~~~~s~~a~~~~~-~a~~~~--~~~~-~~~al~~a~~~~~~~i~~~~vl~~~~~~~Gld~~~~~~~~~ 145 (193)
T PF01323_consen 74 IP-FN-FPPPFPGNSRPAHRAAY-AAQEQG--KADA-FADALFRAYFVEGRDISDPDVLAEIAEEAGLDPDEFDAALD 145 (193)
T ss_dssp ---TB-TSSTHHHHHHHHHHHHH-HHHHHH--HHHH-HHHHHHHHHHTSST-TSSHHHHHHHHHHTT--HHHHHHHHT
T ss_pred Cc-cc-CCchhhhhhHHHHHHHH-HHHHhh--hhhH-HHHHHHHHHHhcccCCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 42 11 11110 11111111111 111111 2222 345667776 2 22336889999999999999999988775
No 44
>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=31.23 E-value=47 Score=24.98 Aligned_cols=44 Identities=20% Similarity=0.231 Sum_probs=31.7
Q ss_pred cchhhHHHHHHHHHhhcCCCC--HHHHHHHHHhcCCChhhhhhhHH
Q 024283 204 SYSRFFAVGLFRLLELANATE--PTVLEKLCAVLNVNKRSVDRDLD 247 (269)
Q Consensus 204 ~YSRlfAIGLf~LLE~~~~~d--~~~l~~l~~~Lgls~ekv~KDL~ 247 (269)
++|+-+-.+|--|+.++...+ +-..++|++.+|+|+.-+.|=+.
T Consensus 2 ~~s~~~~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 2 KLSKRTDYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp ---HHHHHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCcHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 478888888888887775543 46899999999999998887553
No 45
>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=30.87 E-value=2.1e+02 Score=24.74 Aligned_cols=71 Identities=23% Similarity=0.320 Sum_probs=43.6
Q ss_pred cchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCh---hhhhhhHHHHHhhHHHHHH
Q 024283 183 EGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNK---RSVDRDLDVYRNLLSKLLQ 258 (269)
Q Consensus 183 ~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~---ekv~KDL~lYrsnLeKmaQ 258 (269)
.-++..+|..++++.+.+-+|.-| -|=|+.||.+ ....+.=++|++.||++. +.....+-|.|-++.||+.
T Consensus 48 ~VDV~avL~~~a~~~~~~LnWrtS---IVDLlKlLgl--DSSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm~kLA~ 121 (127)
T PF12200_consen 48 QVDVAAVLDALAAKNGQKLNWRTS---IVDLLKLLGL--DSSLAARKELAKELGYTGDYNDSASMNIWLHKQVMQKLAE 121 (127)
T ss_dssp SEE-HHHHHHHHHHHSS---TTT----HHHHHHHT------SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHHHHHGG
T ss_pred cccHHHHHHHHHHhcccccccHHH---HHHHHHHcCC--CCCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHH
Confidence 347889999998776555555443 3455555522 235688899999999977 5677778888888888763
No 46
>PF08014 DUF1704: Domain of unknown function (DUF1704); InterPro: IPR012548 This family contains many hypothetical proteins.
Probab=30.86 E-value=3.4e+02 Score=26.53 Aligned_cols=152 Identities=20% Similarity=0.291 Sum_probs=108.0
Q ss_pred Hhhhc-ccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHH---HhcCCcccccc
Q 024283 103 QHLMR-YKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEW---ARGQTASSLVE 178 (269)
Q Consensus 103 ~HLLs-~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~---A~~~s~~~l~~ 178 (269)
.|+++ +|..-|-=+++++| ..||-|.++.=++|.-++. -+.+|..+|.-|-+..+. .+|.+-.++-.
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 46664 56666666667777 4899999999999999985 689999999999988775 34556556655
Q ss_pred ccCCc-c-hhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCC-C-------------CHHHHHHHHHhcCCChhhh
Q 024283 179 FPSKE-G-EVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA-T-------------EPTVLEKLCAVLNVNKRSV 242 (269)
Q Consensus 179 ~~~~~-g-~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~-~-------------d~~~l~~l~~~Lgls~ekv 242 (269)
++... | +.+..+ .++.|+.-.+.|.=--+.--|+..++.--.. . |-..|.++.+.=.+.+++.
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 55554 4 334444 3444666556666556677788888733322 1 2347788888778899998
Q ss_pred hhhHHHHHhhHHHHHHHHHHHH
Q 024283 243 DRDLDVYRNLLSKLLQAKELLK 264 (269)
Q Consensus 243 ~KDL~lYrsnLeKmaQA~elme 264 (269)
--|.-.+-+.|+++-.-.+.|.
T Consensus 325 lp~~~~~~~~l~~~~~~~~~~~ 346 (349)
T PF08014_consen 325 LPPFFRDPEQLEKIMAFSEFLN 346 (349)
T ss_pred CCHHHhchhhHHHHHHHHHHhc
Confidence 8888888899999887776664
No 47
>PRK08307 stage III sporulation protein SpoAB; Provisional
Probab=30.44 E-value=3.7e+02 Score=23.42 Aligned_cols=81 Identities=12% Similarity=0.124 Sum_probs=48.8
Q ss_pred hhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCC--CCHHHHHHHHHhcCCC-hhhhhhhHHHHHhhHHH-HHHHH
Q 024283 185 EVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA--TEPTVLEKLCAVLNVN-KRSVDRDLDVYRNLLSK-LLQAK 260 (269)
Q Consensus 185 ~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~--~d~~~l~~l~~~Lgls-~ekv~KDL~lYrsnLeK-maQA~ 260 (269)
.....+..+|++...++.-...-.|--.+=...+..+= .|-+.+.++.+.||.+ .+-=+|=+++|..+|+. +++|+
T Consensus 66 ~~~~~f~~~a~~L~~~~g~s~~eaw~~~~~~~~~~~~L~~~d~eiL~~lg~~LG~~D~e~Q~k~i~L~~e~L~~~~~~a~ 145 (171)
T PRK08307 66 PISTLFQRFSERLESGEGETAYEAWEKALEENWKNTALKKEDIEILLQFGKTLGQSDREGQQKHIRLALEHLEREEEEAE 145 (171)
T ss_pred hHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhhccCCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555544333334444444444443322211 2457899999999976 45557889999999987 46676
Q ss_pred HHHHH
Q 024283 261 ELLKE 265 (269)
Q Consensus 261 elmeE 265 (269)
+-++.
T Consensus 146 ~~~~k 150 (171)
T PRK08307 146 EEQKK 150 (171)
T ss_pred HHHHh
Confidence 66554
No 48
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=30.35 E-value=62 Score=27.51 Aligned_cols=78 Identities=22% Similarity=0.349 Sum_probs=57.9
Q ss_pred CCchhHHHHHHHHHHhcCC---------CHHHHHHHHHHHHHHHhcCCccc---cccccCCcchhHHHHHHHHHHhcCCC
Q 024283 134 PSEEDREAIFQAYITALKE---------DPEQYRIDAQKLEEWARGQTASS---LVEFPSKEGEVEGLLKDIAERASGKG 201 (269)
Q Consensus 134 ~peed~~~IF~Alc~Alg~---------Dp~qyR~dA~~l~~~A~~~s~~~---l~~~~~~~g~~~~~l~~Ia~~~~~n~ 201 (269)
++..||.+++..+..++=. .+..+|.-+++|.-+|+.-+... ...|+.+...++.++..|+.+-.+.+
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 3567999999998887743 46789999999999999877763 44466666678888899987665333
Q ss_pred CCcchhhHHHH
Q 024283 202 NFSYSRFFAVG 212 (269)
Q Consensus 202 ~F~YSRlfAIG 212 (269)
. -|+|++=+|
T Consensus 92 G-GYtRIlK~g 101 (116)
T COG0203 92 G-GYTRILKLG 101 (116)
T ss_pred C-CeeEEEecC
Confidence 3 688876444
No 49
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=30.17 E-value=1.4e+02 Score=20.59 Aligned_cols=38 Identities=26% Similarity=0.350 Sum_probs=20.9
Q ss_pred HHHHHHhcCCChhhhhhhHHHHH-------hhHHHHHHHHHHHHH
Q 024283 228 LEKLCAVLNVNKRSVDRDLDVYR-------NLLSKLLQAKELLKE 265 (269)
Q Consensus 228 l~~l~~~Lgls~ekv~KDL~lYr-------snLeKmaQA~elmeE 265 (269)
+++|++.+|++...+.+=+.-.. -+..+|.+|.+.|.+
T Consensus 4 ~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~~r~~~a~~~l~~ 48 (84)
T smart00342 4 LEDLAEALGMSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRD 48 (84)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHc
Confidence 55666666666666655443222 123466666666654
No 50
>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=29.12 E-value=2e+02 Score=20.38 Aligned_cols=49 Identities=12% Similarity=0.241 Sum_probs=29.7
Q ss_pred hhHHHHHHHHHhhcCCCC-HHHHHHHHHhcCCChhhhhhhHHHHHhhHHH
Q 024283 207 RFFAVGLFRLLELANATE-PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSK 255 (269)
Q Consensus 207 RlfAIGLf~LLE~~~~~d-~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeK 255 (269)
++-.+|-+-+--..+..+ .+..+.|++..+.+++.+++|+.-|-..|.+
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 444455443333345544 5689999999999999999999877666544
No 51
>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=29.10 E-value=50 Score=26.75 Aligned_cols=58 Identities=22% Similarity=0.334 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHH
Q 024283 154 PEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVG 212 (269)
Q Consensus 154 p~qyR~dA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIG 212 (269)
+.++|.-|++|..+|+..+.. .+..|+..+.-+..+++.|+.+-+ +.+--|+|++-+|
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 568899999999999976544 566677766568888899998886 4555899876544
No 52
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=29.06 E-value=3e+02 Score=22.97 Aligned_cols=28 Identities=14% Similarity=0.241 Sum_probs=22.5
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHhcCCC
Q 024283 211 VGLFRLLELANATEPTVLEKLCAVLNVN 238 (269)
Q Consensus 211 IGLf~LLE~~~~~d~~~l~~l~~~Lgls 238 (269)
=|||+-|.-.|+.....+-+++.+||+.
T Consensus 64 e~LYkaLS~~GNPtf~Til~V~kAlG~r 91 (100)
T COG3636 64 EGLYKALSPGGNPTFDTILAVLKALGLR 91 (100)
T ss_pred HHHHHHhCCCCCCcHHHHHHHHHHcCce
Confidence 4899999666666777888899999974
No 53
>cd04758 Commd10 COMM_Domain containing protein 10. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=28.87 E-value=3.8e+02 Score=23.42 Aligned_cols=49 Identities=12% Similarity=0.106 Sum_probs=37.4
Q ss_pred HHHHHHhhc-C-CCCHHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHH
Q 024283 212 GLFRLLELA-N-ATEPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAK 260 (269)
Q Consensus 212 GLf~LLE~~-~-~~d~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~ 260 (269)
++..+|+.+ . ..+|+.+.+--+.+|+++++++--...|..+.+.+..+.
T Consensus 60 ~l~~il~~A~k~nl~~~~L~~~L~~l~l~~e~~~~~~~~w~~~~~~l~~~l 110 (186)
T cd04758 60 TISFILEQAAYHNLKPSNLQQQLRNILLLEDKASAFVNAWEAEGEDVLEKL 110 (186)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566544 2 246777666669999999999999999999988877665
No 54
>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=28.87 E-value=1.6e+02 Score=20.59 Aligned_cols=36 Identities=25% Similarity=0.327 Sum_probs=24.9
Q ss_pred HHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHH
Q 024283 123 VTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRI 159 (269)
Q Consensus 123 VTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~ 159 (269)
-.+.=+||.+=. ..+|+.+..++-.-++++|++.+.
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 345667777755 468889999999999999999875
No 55
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=28.68 E-value=1.3e+02 Score=22.50 Aligned_cols=53 Identities=26% Similarity=0.370 Sum_probs=35.9
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHhcCCChhhhhhhHH-HHHhhH------HHHHHHHHHHHH
Q 024283 212 GLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLD-VYRNLL------SKLLQAKELLKE 265 (269)
Q Consensus 212 GLf~LLE~~~~~d~~~l~~l~~~Lgls~ekv~KDL~-lYrsnL------eKmaQA~elmeE 265 (269)
-+..+|.. ...++..+++++..+|+|...+.+=.. .+--.. -+|.+|+.++.+
T Consensus 24 ~~~~~i~~-~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~~~~~~~Rl~~A~~lL~~ 83 (127)
T COG2207 24 RALDYIEE-NLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPSQYLRQLRLEEARRLLRS 83 (127)
T ss_pred HHHHHHHH-HhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHc
Confidence 55555654 455557788888888888888887766 222222 278888888864
No 56
>KOG1258 consensus mRNA processing protein [RNA processing and modification]
Probab=28.51 E-value=1.6e+02 Score=31.17 Aligned_cols=124 Identities=20% Similarity=0.216 Sum_probs=72.7
Q ss_pred CchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhc
Q 024283 71 PTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITAL 150 (269)
Q Consensus 71 ~TVSDTKr~F~~~y~rPI~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc~Al 150 (269)
-+....=..|...||.. -..|++..+ +.|.=-=+=-.+-||++=.+|.|=--++=-=+-+.|..+
T Consensus 62 ~~~r~~y~~fL~kyPl~-~gyW~kfA~--------------~E~klg~~~~s~~Vfergv~aip~SvdlW~~Y~~f~~n~ 126 (577)
T KOG1258|consen 62 DALREVYDIFLSKYPLC-YGYWKKFAD--------------YEYKLGNAENSVKVFERGVQAIPLSVDLWLSYLAFLKNN 126 (577)
T ss_pred HHHHHHHHHHHhhCccH-HHHHHHHHH--------------HHHHhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcc
Confidence 34444455666666653 235565554 233221222347788998999986666666678888999
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCcc-----ccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHH
Q 024283 151 KEDPEQYRIDAQKLEEWARGQTAS-----SLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFA 210 (269)
Q Consensus 151 g~Dp~qyR~dA~~l~~~A~~~s~~-----~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfA 210 (269)
++||+++|.--+.-.+.+...=.. -.++|-... .-..-+..|-+++..+|..+|+|+|.
T Consensus 127 ~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~q-ks~k~v~~iyeRileiP~~~~~~~f~ 190 (577)
T KOG1258|consen 127 NGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQ-KSWKRVANIYERILEIPLHQLNRHFD 190 (577)
T ss_pred CCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhcc-ccHHHHHHHHHHHHhhhhhHhHHHHH
Confidence 999999988766665544421100 011111111 12223333445666699999999986
No 57
>PF13446 RPT: A repeated domain in UCH-protein
Probab=28.12 E-value=97 Score=22.21 Aligned_cols=47 Identities=21% Similarity=0.336 Sum_probs=34.1
Q ss_pred CCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCcccccccc
Q 024283 134 PSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFP 180 (269)
Q Consensus 134 ~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~ 180 (269)
+|.-+-+.|-.++-..+..||.+.+.--++|...|.......|..|+
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 44445556666666666699999988888888888877776666554
No 58
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=27.81 E-value=71 Score=23.56 Aligned_cols=26 Identities=23% Similarity=0.296 Sum_probs=20.7
Q ss_pred CHHHHHHHHHhcCCChhhhhhhHHHH
Q 024283 224 EPTVLEKLCAVLNVNKRSVDRDLDVY 249 (269)
Q Consensus 224 d~~~l~~l~~~Lgls~ekv~KDL~lY 249 (269)
++-.+.+|++.+|+++..|.++|..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 35678888888999999998888643
No 59
>PHA00666 putative protease
Probab=27.69 E-value=5.3e+02 Score=24.41 Aligned_cols=32 Identities=19% Similarity=0.159 Sum_probs=28.9
Q ss_pred cCCCCchhHHHHHHHHHHhcCCCHHHHHHHHH
Q 024283 131 EGYPSEEDREAIFQAYITALKEDPEQYRIDAQ 162 (269)
Q Consensus 131 ~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~ 162 (269)
+|+..+.....-|..+|..+|++++|-++-..
T Consensus 93 EG~elD~~~l~~F~~~a~ElgLtqEQAQklvD 124 (233)
T PHA00666 93 EGVELDTGALGAFEPVARELNLTNEQAQKVVD 124 (233)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 99999999999999999999999999776544
No 60
>PF14225 MOR2-PAG1_C: Cell morphogenesis C-terminal
Probab=27.56 E-value=4.1e+02 Score=24.90 Aligned_cols=111 Identities=22% Similarity=0.214 Sum_probs=67.4
Q ss_pred HHHHHHHHHHHHHHhcCCccccccccCC-----cchhHHHHHHHHHHhcCCCCC-cchhhHHHHHHHHHhhcCC-C-C--
Q 024283 155 EQYRIDAQKLEEWARGQTASSLVEFPSK-----EGEVEGLLKDIAERASGKGNF-SYSRFFAVGLFRLLELANA-T-E-- 224 (269)
Q Consensus 155 ~qyR~dA~~l~~~A~~~s~~~l~~~~~~-----~g~~~~~l~~Ia~~~~~n~~F-~YSRlfAIGLf~LLE~~~~-~-d-- 224 (269)
++.++-|+.|..+|+.....+|..-++. -.+.+..++.+.+.+. +..| +|+--.-+=|..+|+.... . .
T Consensus 130 ~~~~~~A~~La~~a~~~~~~~La~il~~ya~~~fr~~~dfl~~v~~~l~-~~f~P~~~~~~l~~Ll~lL~n~~~w~~~~~ 208 (262)
T PF14225_consen 130 QECIEIAEALAQVAEAQGLPNLARILSSYAKGRFRDKDDFLSQVVSYLR-EAFFPDHEFQILTFLLGLLENGPPWLRRKT 208 (262)
T ss_pred HHHHHHHHHHHHHHHhCCCccHHHHHHHHHhcCCCCHHHHHHHHHHHHH-HHhCchhHHHHHHHHHHHHhCCcHHHHHHH
Confidence 6778888888888887777666554431 1134455555544442 2333 5655555556666653211 1 1
Q ss_pred HHHHHHHHHhcCCChhhhhhhHHHHHhhHHHH-----HHHHHHHHHHhcC
Q 024283 225 PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKL-----LQAKELLKEYVDR 269 (269)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKm-----aQA~elmeE~ler 269 (269)
-.+|.-+.....+++. ...| +++-.+.=+ .||.+++++++.+
T Consensus 209 L~iL~~ll~~~d~~~~-~~~d--lispllrlL~t~~~~eAL~VLd~~v~~ 255 (262)
T PF14225_consen 209 LQILKVLLPHVDMRSP-HGAD--LISPLLRLLQTDLWMEALEVLDEIVTR 255 (262)
T ss_pred HHHHHHHhccccCCCC-cchH--HHHHHHHHhCCccHHHHHHHHHHHHhh
Confidence 2467777777888866 5555 466655433 5899999998764
No 61
>PRK15044 transcriptional regulator SirC; Provisional
Probab=27.47 E-value=5.8e+02 Score=24.75 Aligned_cols=149 Identities=14% Similarity=0.164 Sum_probs=79.1
Q ss_pred hHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCC
Q 024283 74 AETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKED 153 (269)
Q Consensus 74 SDTKr~F~~~y~rPI~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc~Alg~D 153 (269)
.|.-++||+-|..-=+-+.+ .+-.-...+.|.+.|+ .=+.-.||+++|.+-..++ +|+.+-.+
T Consensus 97 ~~~i~~f~~~~~~~~~~~~~--------~~~~~~~~k~~~~~~~-~p~~~~v~~~~~~~~~~~~--------~~~~~~~~ 159 (295)
T PRK15044 97 YDLMQKFYKVFYSTRNYNDR--------ELSLKTKPKYFFHADL-LPGMSDTFDSILHGVACPR--------VCSNVSID 159 (295)
T ss_pred HHHHHHHHHHhhhccccccc--------cccccCCCceecCCCC-CchHHHHHHHHhccccChh--------hhhhhccc
Confidence 47788999988422111110 0011134556666666 4577889999999654432 55555555
Q ss_pred HHHHHHH--HHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHH
Q 024283 154 PEQYRID--AQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKL 231 (269)
Q Consensus 154 p~qyR~d--A~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l 231 (269)
.+.|.-- ---|.. ++.+. +.+..+....+ ++.. -.+...++ .+..++..+++|
T Consensus 160 ~~~~~~~~l~~LLs~------------~l~~~-~~~~~L~~~~~---------is~~--~kV~~~I~-~nl~~~~SLeeL 214 (295)
T PRK15044 160 DHDYSYFSLMYLISA------------FVRKP-GGFDFLERAIK---------ITTK--EKVYNIII-SDLTRKWSQAEV 214 (295)
T ss_pred chHHHHHHHHHHHHH------------HHhcc-cchhhHHHHhh---------hhHH--HHHHHHHH-hCcccCCCHHHH
Confidence 5444320 001111 11211 11222222111 1111 11344443 223567899999
Q ss_pred HHhcCCChhhhhhhH-------HHHHhhHHHHHHHHHHHHH
Q 024283 232 CAVLNVNKRSVDRDL-------DVYRNLLSKLLQAKELLKE 265 (269)
Q Consensus 232 ~~~Lgls~ekv~KDL-------~lYrsnLeKmaQA~elmeE 265 (269)
|+.+|+|...+.|=+ .-|- +--||..|++++.+
T Consensus 215 A~~lgmS~~tL~R~Fk~eg~T~~~y~-~~~RL~~A~~LL~~ 254 (295)
T PRK15044 215 AGKLFMSVSSLKRKLAAEEVSFSKIY-LDARMNQAIKLLRM 254 (295)
T ss_pred HHHhCCCHHHHHHHHHHcCCCHHHHH-HHHHHHHHHHHHHc
Confidence 999999999998833 2222 23689999999864
No 62
>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=27.28 E-value=62 Score=27.37 Aligned_cols=20 Identities=15% Similarity=0.341 Sum_probs=14.3
Q ss_pred cccchhhHHHHHHHHhcCCCC
Q 024283 115 DPVFALGFVTVYDRLMEGYPS 135 (269)
Q Consensus 115 DplFALG~VTvFd~fm~GY~p 135 (269)
..+|++| ++.|+.+..|.+|
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 4566666667776
No 63
>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=26.94 E-value=1.6e+02 Score=22.00 Aligned_cols=44 Identities=25% Similarity=0.348 Sum_probs=28.7
Q ss_pred HHHHHhhcCC-CCHHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHH
Q 024283 213 LFRLLELANA-TEPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQ 258 (269)
Q Consensus 213 Lf~LLE~~~~-~d~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQ 258 (269)
.-.||...+. +....+.+|...|..-.+-++.|. ||+.||-+.+
T Consensus 11 v~ell~~g~~vsnKaII~~LI~~LE~e~Dv~~~dv--yR~~LEiVv~ 55 (61)
T PF10798_consen 11 VRELLASGGHVSNKAIILKLIHRLESESDVVQLDV--YRNALEIVVG 55 (61)
T ss_dssp HHHHHHTT---SHHHHHHHHHHHHHT---HHHHHH--HHHHHHHHHH
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHHhccccHHHHHH--HHHHHHHHHc
Confidence 3345543333 456789999999999899888877 9999987643
No 64
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=26.47 E-value=82 Score=22.70 Aligned_cols=34 Identities=21% Similarity=0.351 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHhc----CCChhhhhhhHHHHHhhHHHH
Q 024283 223 TEPTVLEKLCAVL----NVNKRSVDRDLDVYRNLLSKL 256 (269)
Q Consensus 223 ~d~~~l~~l~~~L----gls~ekv~KDL~lYrsnLeKm 256 (269)
.+|+.+++|.++| |....++.++|+-++..+.++
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 3578888888888 889999999999888655543
No 65
>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=25.33 E-value=76 Score=31.26 Aligned_cols=32 Identities=25% Similarity=0.432 Sum_probs=28.6
Q ss_pred CCCchhHHHHHHHHHH-hcCCCHHHHHHHHHHH
Q 024283 133 YPSEEDREAIFQAYIT-ALKEDPEQYRIDAQKL 164 (269)
Q Consensus 133 Y~peed~~~IF~Alc~-Alg~Dp~qyR~dA~~l 164 (269)
|.|.++|-+.|+|+++ .++..|.+|.+.|+.-
T Consensus 122 FkP~~~klA~fhA~v~~~L~~p~S~yye~a~~Y 154 (340)
T PF12069_consen 122 FKPSQEKLAMFHAQVRAQLGQPASQYYEHAQAY 154 (340)
T ss_pred cCCChHHHHHHHHHHHHHcCCCcchhHHHHHHH
Confidence 7899999999999996 5899999999998763
No 66
>smart00219 TyrKc Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
Probab=25.17 E-value=93 Score=25.92 Aligned_cols=22 Identities=14% Similarity=0.375 Sum_probs=15.4
Q ss_pred cccchhhHHHHHHHHhcCCCCch
Q 024283 115 DPVFALGFVTVYDRLMEGYPSEE 137 (269)
Q Consensus 115 DplFALG~VTvFd~fm~GY~pee 137 (269)
..+|++|.+ .|..+..|++|-+
T Consensus 185 ~Di~slG~i-~~~l~~~g~~p~~ 206 (258)
T smart00219 185 SDVWSFGVL-LWEIFTLGESPYP 206 (258)
T ss_pred hhHHHHHHH-HHHHHhCCCCCCC
Confidence 458999976 4555667888743
No 67
>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=23.92 E-value=1.8e+02 Score=20.53 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=29.1
Q ss_pred HHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHh
Q 024283 124 TVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWAR 169 (269)
Q Consensus 124 TvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~ 169 (269)
.+++.+ +| ....+.|-+++++..+.+|++.++|.....+...
T Consensus 21 ~Iw~~~-~g---~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~ 62 (68)
T PF05402_consen 21 FIWELL-DG---PRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLR 62 (68)
T ss_dssp HHHHH---S---SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH
T ss_pred HHHHHc-cC---CCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 345555 44 2578899999999999999999999988876443
No 68
>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=23.91 E-value=54 Score=25.76 Aligned_cols=23 Identities=22% Similarity=0.414 Sum_probs=20.5
Q ss_pred HHHHHHHHhcCCChhhhhhhHHH
Q 024283 226 TVLEKLCAVLNVNKRSVDRDLDV 248 (269)
Q Consensus 226 ~~l~~l~~~Lgls~ekv~KDL~l 248 (269)
-.++++++.+|+|...|.+||.-
T Consensus 20 ~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 20 ATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCHHHHHHHhCCCHHHHHHHhcC
Confidence 36999999999999999999953
No 69
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=23.70 E-value=2.6e+02 Score=21.70 Aligned_cols=25 Identities=12% Similarity=0.324 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHhcCCChhhhhhhHH
Q 024283 223 TEPTVLEKLCAVLNVNKRSVDRDLD 247 (269)
Q Consensus 223 ~d~~~l~~l~~~Lgls~ekv~KDL~ 247 (269)
.+++.+.++++.+|++.+++++.++
T Consensus 83 ~~~~~l~~~a~~~gl~~~~~~~~~~ 107 (154)
T cd03023 83 LNEESLLRIAKKAGLDEAKLKKDMD 107 (154)
T ss_pred CCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 4677888999999999999887764
No 70
>PF06152 Phage_min_cap2: Phage minor capsid protein 2; InterPro: IPR009319 This entry is represented by Bacteriophage A118, Gp4, the minor capsid protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=23.45 E-value=2.5e+02 Score=27.39 Aligned_cols=35 Identities=20% Similarity=0.266 Sum_probs=24.1
Q ss_pred CCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCC
Q 024283 152 EDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGK 200 (269)
Q Consensus 152 ~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n 200 (269)
++|+++.+.+..+.+.-..+- +.++..|+.+++..
T Consensus 3 Ltp~~l~~~~~~i~~ly~~lE--------------~~i~~~i~rri~~~ 37 (361)
T PF06152_consen 3 LTPEQLEKLADQIVDLYQELE--------------QEIIADIIRRIKKH 37 (361)
T ss_pred CCHHHHHHhHHHHHHHHHHHH--------------HHHHHHHHHHHHhc
Confidence 589999999998888655322 24667777666543
No 71
>PRK13910 DNA glycosylase MutY; Provisional
Probab=23.42 E-value=3e+02 Score=26.25 Aligned_cols=43 Identities=14% Similarity=0.193 Sum_probs=27.4
Q ss_pred HHHHHHhcCCCCchhH----HHHHHHHHHhcCC--CHHHHHHHHHHHHH
Q 024283 124 TVYDRLMEGYPSEEDR----EAIFQAYITALKE--DPEQYRIDAQKLEE 166 (269)
Q Consensus 124 TvFd~fm~GY~peed~----~~IF~Alc~Alg~--Dp~qyR~dA~~l~~ 166 (269)
-.|++||+-||..++. +.=...+++.+|+ -+..+++-|+.+.+
T Consensus 13 ~yy~rf~~~fPt~e~La~a~~~el~~~~~glGyy~RAr~L~~~A~~i~~ 61 (289)
T PRK13910 13 RFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICVK 61 (289)
T ss_pred HHHHHHHHHCCCHHHHHCCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 3789999999987664 2224457788998 44444444444443
No 72
>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=23.21 E-value=1e+02 Score=26.31 Aligned_cols=20 Identities=25% Similarity=0.527 Sum_probs=15.6
Q ss_pred cccchhhHHHHHHHHhcCCCC
Q 024283 115 DPVFALGFVTVYDRLMEGYPS 135 (269)
Q Consensus 115 DplFALG~VTvFd~fm~GY~p 135 (269)
..+|++|++ .|+.++.|++|
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 579999954 56778888887
No 73
>KOG0213 consensus Splicing factor 3b, subunit 1 [RNA processing and modification]
Probab=23.15 E-value=5.6e+02 Score=28.83 Aligned_cols=106 Identities=22% Similarity=0.266 Sum_probs=65.3
Q ss_pred hhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCc
Q 024283 104 HLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKE 183 (269)
Q Consensus 104 HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~~ 183 (269)
-|.-.|.+=+-|.+--+||-||-..|-.--+| +..-|-.-+..-|+-.|...|+.|..|..
T Consensus 764 il~Afqeqtt~d~vml~gfg~V~~~lg~r~kp--ylpqi~stiL~rLnnksa~vRqqaadlis----------------- 824 (1172)
T KOG0213|consen 764 ILYAFQEQTTEDSVMLLGFGTVVNALGGRVKP--YLPQICSTILWRLNNKSAKVRQQAADLIS----------------- 824 (1172)
T ss_pred HHHHHHhcccchhhhhhhHHHHHHHHhhcccc--chHHHHHHHHHHhcCCChhHHHHHHHHHH-----------------
Confidence 34555666667777777877776666543333 34457778888899999999999888765
Q ss_pred chhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHH-------HHHHHHHhcCCCh
Q 024283 184 GEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPT-------VLEKLCAVLNVNK 239 (269)
Q Consensus 184 g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~-------~l~~l~~~Lgls~ 239 (269)
.+...+. .-+.++-=...+|=||.-| |..+|| ++..|++.+|+.+
T Consensus 825 ----~la~Vlk----tc~ee~~m~~lGvvLyEyl---geeypEvLgsILgAikaI~nvigm~k 876 (1172)
T KOG0213|consen 825 ----SLAKVLK----TCGEEKLMGHLGVVLYEYL---GEEYPEVLGSILGAIKAIVNVIGMTK 876 (1172)
T ss_pred ----HHHHHHH----hccHHHHHHHhhHHHHHhc---CcccHHHHHHHHHHHHHHHHhccccc
Confidence 1112221 1344444455566666555 445554 5666777777553
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=22.90 E-value=1.7e+02 Score=20.07 Aligned_cols=26 Identities=19% Similarity=0.409 Sum_probs=21.6
Q ss_pred HHHHHHHHHhcCCChhhhhhhHHHHH
Q 024283 225 PTVLEKLCAVLNVNKRSVDRDLDVYR 250 (269)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~lYr 250 (269)
+-...+|++.+|++...|.+.|....
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~ 50 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELE 50 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45799999999999999998885443
No 75
>PF13170 DUF4003: Protein of unknown function (DUF4003)
Probab=22.89 E-value=4.7e+02 Score=24.84 Aligned_cols=119 Identities=18% Similarity=0.269 Sum_probs=73.0
Q ss_pred HHHHHHHhcCCCC-chhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhc--CCccccccccCC-----cc--hhH-----
Q 024283 123 VTVYDRLMEGYPS-EEDREAIFQAYITALKEDPEQYRIDAQKLEEWARG--QTASSLVEFPSK-----EG--EVE----- 187 (269)
Q Consensus 123 VTvFd~fm~GY~p-eed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~--~s~~~l~~~~~~-----~g--~~~----- 187 (269)
.++|+.+.+-+|= ....|-.|.+|+.....|++++-+..+.+-.+-+. .....=++|++. +| +..
T Consensus 123 ~~iy~~mKk~H~fLTs~~D~~~a~lLA~~~~~~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~ 202 (297)
T PF13170_consen 123 KEIYKEMKKKHPFLTSPEDYPFAALLAMTSEDVEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVI 202 (297)
T ss_pred HHHHHHHHHhCccccCccchhHHHHHhcccccHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHH
Confidence 3457777776652 34567789999999999999999998888776553 333333334431 22 211
Q ss_pred HHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCC----HHHHHHHHHhcCCChhhhhhhHH
Q 024283 188 GLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATE----PTVLEKLCAVLNVNKRSVDRDLD 247 (269)
Q Consensus 188 ~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d----~~~l~~l~~~Lgls~ekv~KDL~ 247 (269)
.+...+.+ .+-+.+|.=+-.|||..|++...... .+..+.|++.-|+. .+||..
T Consensus 203 ~l~~~l~~---~~~kik~~~yp~lGlLall~~~~~~~~~~i~ev~~~L~~~k~~~---~~k~~~ 260 (297)
T PF13170_consen 203 ELYNALKK---NGVKIKYMHYPTLGLLALLEDPEEKIVEEIKEVIDELKEQKGFG---WDKDFR 260 (297)
T ss_pred HHHHHHHH---cCCccccccccHHHHHHhcCCchHHHHHHHHHHHHHHhhCcccC---hhHHHH
Confidence 23344433 23455666688999999995333222 24566666665655 666653
No 76
>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]
Probab=22.66 E-value=45 Score=33.04 Aligned_cols=49 Identities=35% Similarity=0.394 Sum_probs=28.1
Q ss_pred CCcchhhHHHHHHHHHhhcCCC--CH--HHHHHHHHhcCCChhhhhhhHHHHHhhHHHH
Q 024283 202 NFSYSRFFAVGLFRLLELANAT--EP--TVLEKLCAVLNVNKRSVDRDLDVYRNLLSKL 256 (269)
Q Consensus 202 ~F~YSRlfAIGLf~LLE~~~~~--d~--~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKm 256 (269)
.=+=|=+-+|..|.==.--+-. |. .+|+.+.+- -|+|||++|+.+|.-|
T Consensus 65 RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~ey------GVerDl~vYk~Llnvf 117 (406)
T KOG3941|consen 65 RDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEY------GVERDLDVYKGLLNVF 117 (406)
T ss_pred ccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHh------cchhhHHHHHHHHHhC
Confidence 3345556666666432212222 21 355555432 4899999999999744
No 77
>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=22.52 E-value=65 Score=26.45 Aligned_cols=31 Identities=13% Similarity=0.200 Sum_probs=24.3
Q ss_pred HHHhcCCCCchhHHHHHHHHHHhcCCCHHHH
Q 024283 127 DRLMEGYPSEEDREAIFQAYITALKEDPEQY 157 (269)
Q Consensus 127 d~fm~GY~peed~~~IF~Alc~Alg~Dp~qy 157 (269)
++--..-+..+||..||+=+|..+|.+|+.-
T Consensus 12 ~~AE~AI~dsd~R~~llqEm~~gLg~~p~ag 42 (93)
T PF07216_consen 12 EQAELAIRDSDHRNDLLQEMLEGLGLGPVAG 42 (93)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHhcCCChhHH
Confidence 3333445667899999999999999999754
No 78
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=22.47 E-value=6.6e+02 Score=23.66 Aligned_cols=65 Identities=18% Similarity=0.339 Sum_probs=40.7
Q ss_pred HhHHHHHhhCCC------cCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHH----HH
Q 024283 75 ETKMNFLKLYKR------PIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAI----FQ 144 (269)
Q Consensus 75 DTKr~F~~~y~r------PI~sIYrrvv~ELLVE~HLLs~n~~F~YDplFALG~VTvFd~fm~GY~peed~~~I----F~ 144 (269)
+.-.++|..+.| +-..-|.-.|-|+|.|+= ++ =-+..+|++|++.||..++.... ..
T Consensus 4 ~~l~~w~~~~~r~~lpWr~~~dpy~vlvseIL~QQT--~v-----------~~v~~~~~rl~~~fpt~~~La~a~~eeL~ 70 (275)
T TIGR01084 4 EDLLSWYDKYGRKTLPWRQNKTPYRVWLSEVMLQQT--QV-----------ATVIPYFERFLERFPTVQALANAPQDEVL 70 (275)
T ss_pred HHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHhhc--cH-----------HHHHHHHHHHHHhCCCHHHHHCcCHHHHH
Confidence 344566777665 234568899999998873 11 12457899999999865443221 22
Q ss_pred HHHHhcCC
Q 024283 145 AYITALKE 152 (269)
Q Consensus 145 Alc~Alg~ 152 (269)
.++..+|+
T Consensus 71 ~~~~~lG~ 78 (275)
T TIGR01084 71 KLWEGLGY 78 (275)
T ss_pred HHHHHCCc
Confidence 23466777
No 79
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=22.36 E-value=1.1e+02 Score=26.32 Aligned_cols=27 Identities=30% Similarity=0.463 Sum_probs=23.0
Q ss_pred HHHHHHHhcCCChhhhhhhHHHHHhhH
Q 024283 227 VLEKLCAVLNVNKRSVDRDLDVYRNLL 253 (269)
Q Consensus 227 ~l~~l~~~Lgls~ekv~KDL~lYrsnL 253 (269)
..++|++.||+|+..|+|+|..=|.-|
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWL 179 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 578899999999999999998776544
No 80
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=22.24 E-value=61 Score=29.51 Aligned_cols=24 Identities=29% Similarity=0.466 Sum_probs=20.9
Q ss_pred HHHHHHHHHhcCCChhhhhhhHHH
Q 024283 225 PTVLEKLCAVLNVNKRSVDRDLDV 248 (269)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~l 248 (269)
.-.+++|++.||.|.+.+.|||..
T Consensus 21 ~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 21 KLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Confidence 446889999999999999999985
No 81
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=22.21 E-value=1.4e+02 Score=28.26 Aligned_cols=42 Identities=33% Similarity=0.537 Sum_probs=34.9
Q ss_pred CHHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHHHhc
Q 024283 224 EPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVD 268 (269)
Q Consensus 224 d~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE~le 268 (269)
++..+++|++.||+|.++|.. +.+.-|.||.+..+-+++++.
T Consensus 275 ~~~Tl~EIa~~lgiS~erVRq---i~~rAl~kLr~~~~~l~~~~~ 316 (317)
T PRK07405 275 QPLTLAKIGERLNISRERVRQ---IEREALSKLRKRKANIQEYLA 316 (317)
T ss_pred CCcCHHHHHHHHCcCHHHHHH---HHHHHHHHHHHHHHHHHHHHh
Confidence 355899999999999999986 457788888888888888764
No 82
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=22.18 E-value=3.2e+02 Score=22.17 Aligned_cols=36 Identities=19% Similarity=0.366 Sum_probs=25.3
Q ss_pred HHHHHHhhcCC--CCHHHHHHHHHhcCCChhhhhhhHH
Q 024283 212 GLFRLLELANA--TEPTVLEKLCAVLNVNKRSVDRDLD 247 (269)
Q Consensus 212 GLf~LLE~~~~--~d~~~l~~l~~~Lgls~ekv~KDL~ 247 (269)
-||......+. .+++.+.++++.+|++.+++++++.
T Consensus 84 ~lf~~~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~~~ 121 (178)
T cd03019 84 ALFEAIHEKRKRLLDPDDIRKIFLSQGVDKKKFDAAYN 121 (178)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 44555422222 4578899999999999998887763
No 83
>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=21.99 E-value=2.1e+02 Score=21.25 Aligned_cols=45 Identities=18% Similarity=0.248 Sum_probs=32.2
Q ss_pred hHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Q 024283 121 GFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEE 166 (269)
Q Consensus 121 G~VTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~dA~~l~~ 166 (269)
.-..+.+-+.+||++..=-..|++.+... +.++.+-.+-.+.+.+
T Consensus 23 ~~~~~~~l~~~G~s~~~Il~~l~~~l~~~-~~~~~~k~~i~~~la~ 67 (89)
T PF08542_consen 23 ARKKLYELLVEGYSASDILKQLHEVLVES-DIPDSQKAEILKILAE 67 (89)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHHHHHTS-TSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHh-hccHHHHHHHHHHHHH
Confidence 45567788889999999999999999999 7776655555554443
No 84
>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=21.90 E-value=1.2e+02 Score=20.66 Aligned_cols=26 Identities=19% Similarity=0.190 Sum_probs=20.3
Q ss_pred hhcCCCCHHHHHHHHHhcCCChhhhh
Q 024283 218 ELANATEPTVLEKLCAVLNVNKRSVD 243 (269)
Q Consensus 218 E~~~~~d~~~l~~l~~~Lgls~ekv~ 243 (269)
+...-.+.+..+.|+..+|++...|.
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 85
>cd03022 DsbA_HCCA_Iso DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is unique to bacteria that degrade polycyclic aromatic compounds. It is closely related to the eukaryotic protein, GSH transferase kappa (GSTK).
Probab=21.80 E-value=2.2e+02 Score=23.51 Aligned_cols=37 Identities=22% Similarity=0.357 Sum_probs=26.5
Q ss_pred HHHHHHH-hhc-CCCCHHHHHHHHHhcCCChhhhhhhHH
Q 024283 211 VGLFRLL-ELA-NATEPTVLEKLCAVLNVNKRSVDRDLD 247 (269)
Q Consensus 211 IGLf~LL-E~~-~~~d~~~l~~l~~~Lgls~ekv~KDL~ 247 (269)
--||+.. +.. +..+++.|.++++..|++.+.+.++++
T Consensus 107 ~~lf~a~~~~~~~i~~~~~l~~~a~~~Gld~~~~~~~~~ 145 (192)
T cd03022 107 RAVFRALWGEGLDIADPAVLAAVAAAAGLDADELLAAAD 145 (192)
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHHHcCCCHHHHHHHcC
Confidence 3456555 222 235788999999999999998877764
No 86
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=21.66 E-value=1.4e+02 Score=31.13 Aligned_cols=48 Identities=40% Similarity=0.517 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhcCCc-cccccccCCcch--------hHHHHHHHHHHhcCCCCCcchhhHH
Q 024283 158 RIDAQKLEEWARGQTA-SSLVEFPSKEGE--------VEGLLKDIAERASGKGNFSYSRFFA 210 (269)
Q Consensus 158 R~dA~~l~~~A~~~s~-~~l~~~~~~~g~--------~~~~l~~Ia~~~~~n~~F~YSRlfA 210 (269)
+.--.-|.+.++|... .|+.+|+.++|+ ++.++.+++.+++ .||||++
T Consensus 188 ~dlndll~kh~~g~dt~~df~~fm~khge~fpe~pr~~~el~d~laAR~a-----aaSrf~n 244 (652)
T COG4867 188 DDLNDLLDKHARGEDTQRDFDEFMTKHGEFFPENPRNVEELLDSLAARAA-----AASRFRN 244 (652)
T ss_pred HHHHHHHHHhccCCCCcccHHHHHHhccccCCCCcccHHHHHHHHHHHHH-----HHHHHhh
Confidence 3333444556666544 478888877654 6778888877776 4898875
No 87
>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=21.26 E-value=1.8e+02 Score=19.52 Aligned_cols=22 Identities=23% Similarity=0.252 Sum_probs=19.1
Q ss_pred CCHHHHHHHHHhcCCChhhhhh
Q 024283 223 TEPTVLEKLCAVLNVNKRSVDR 244 (269)
Q Consensus 223 ~d~~~l~~l~~~Lgls~ekv~K 244 (269)
.+.+.++.|++.+|++...|+.
T Consensus 25 P~~~~~~~la~~~~l~~~qV~~ 46 (59)
T cd00086 25 PSREEREELAKELGLTERQVKI 46 (59)
T ss_pred CCHHHHHHHHHHHCcCHHHHHH
Confidence 4678999999999999988864
No 88
>PF07814 WAPL: Wings apart-like protein regulation of heterochromatin; InterPro: IPR022771 This entry contains sequences expressed in eukaryotic organisms (metazoa, fungi, plants) bearing high similarity to the WAPL conserved region of D. melanogaster wings apart-like protein. This protein is involved in the regulation of heterochromatin structure []. hWAPL (Q7Z5K2 from SWISSPROT), the human homologue, is found to play a role in the development of cervical carcinogenesis, and is thought to have similar functions to Drosophila wapl protein []. Malfunction of the hWAPL pathway is thought to activate an apoptotic pathway that consequently leads to cell death []. This entry includes proteins from metazoa, fungi and plants.
Probab=21.26 E-value=4.1e+02 Score=25.63 Aligned_cols=114 Identities=18% Similarity=0.187 Sum_probs=64.1
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHH
Q 024283 138 DREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLL 217 (269)
Q Consensus 138 d~~~IF~Alc~Alg~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LL 217 (269)
|-+-||+.|= ...|...|.-+ +.+.|.-.-..+....+...|..+.+++.|.. .+.-.-+-+.+..++.+|
T Consensus 22 ev~ylld~l~---~~~~~s~Rr~s--ll~La~K~~~~~Fr~~~ra~g~~~~l~~~l~~----~~~d~~~~l~~a~i~~~l 92 (361)
T PF07814_consen 22 EVEYLLDGLE---SSSSSSVRRSS--LLELASKCADPQFRRQFRAHGLVKRLFKALSD----APDDDILALATAAILYVL 92 (361)
T ss_pred HHHHHHhhcc---cCCCccHHHHH--HHHHHHHhCCHHHHHHHHHcCcHHHHHHHhcc----ccchHHHHHHHHHHHHHH
Confidence 4444555442 12344444333 44555544444444444457777888888853 222227778888888888
Q ss_pred hhcCC-C----CHHHHHHHHHhcCCCh-hhhhhhH-HHHHhhHHHHHHHH
Q 024283 218 ELANA-T----EPTVLEKLCAVLNVNK-RSVDRDL-DVYRNLLSKLLQAK 260 (269)
Q Consensus 218 E~~~~-~----d~~~l~~l~~~Lgls~-ekv~KDL-~lYrsnLeKmaQA~ 260 (269)
-..+. . ++..++=+..-+++.. ..+.+|. ..++.+++|+.|..
T Consensus 93 ~~d~~~~~l~~~~~~~~ll~~Ll~~~~~~~~~~~~~~~~~~~lsk~~~~~ 142 (361)
T PF07814_consen 93 SRDGLNMHLLLDRDSLRLLLKLLKVDKSLDVPSDSDSSRKKNLSKVQQKS 142 (361)
T ss_pred ccCCcchhhhhchhHHHHHHHHhccccccccccchhhhhhhhhhHHHHHH
Confidence 54443 1 3334444455555322 2344555 48999999998864
No 89
>PF06012 DUF908: Domain of Unknown Function (DUF908); InterPro: IPR010309 This is a domain of unknown function found at the N terminus of a family of E3 ubiquitin protein ligases, including yeast TOM1, many of which appear to play a role in mRNA transcription and processing. This domain is found in association with and immediately N-terminal to another domain of unknown function: IPR010314 from INTERPRO.
Probab=20.80 E-value=5.7e+02 Score=24.29 Aligned_cols=49 Identities=22% Similarity=0.290 Sum_probs=39.3
Q ss_pred cccccchhhHHHHHHHHhcCCC-CchhHHHHHHHHHHhcCCCHHHHHHHH
Q 024283 113 QYDPVFALGFVTVYDRLMEGYP-SEEDREAIFQAYITALKEDPEQYRIDA 161 (269)
Q Consensus 113 ~YDplFALG~VTvFd~fm~GY~-peed~~~IF~Alc~Alg~Dp~qyR~dA 161 (269)
..+.+...-+-++|++.|+.|. |++++=.++.-+--|-++.-..+|+..
T Consensus 186 ~~~~~~~~s~~~i~~~~~~~~~iP~~~~f~ll~riR~A~af~~~~~R~~~ 235 (329)
T PF06012_consen 186 PSSDVRSESLQQILDKLMEDYNIPKESRFELLHRIRVAKAFSSSSYRRQL 235 (329)
T ss_pred cccccccCCHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 3455666778999999999965 778899999998888888888887754
No 90
>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=20.54 E-value=1.7e+02 Score=25.68 Aligned_cols=34 Identities=35% Similarity=0.689 Sum_probs=25.2
Q ss_pred HHHHHHhcCCCCchhHHHHHHHHHHhcCCC----HHHHHHHHHH
Q 024283 124 TVYDRLMEGYPSEEDREAIFQAYITALKED----PEQYRIDAQK 163 (269)
Q Consensus 124 TvFd~fm~GY~peed~~~IF~Alc~Alg~D----p~qyR~dA~~ 163 (269)
..--.|++|||. +||+-|++ |+-| +++|-+.|..
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 7777 6677666543
No 91
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=20.54 E-value=98 Score=20.02 Aligned_cols=23 Identities=30% Similarity=0.556 Sum_probs=19.9
Q ss_pred HHHHHHHHhcCCChhhhhhhHHH
Q 024283 226 TVLEKLCAVLNVNKRSVDRDLDV 248 (269)
Q Consensus 226 ~~l~~l~~~Lgls~ekv~KDL~l 248 (269)
-.+.+|++.+|++...+.++|+.
T Consensus 15 ~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 15 VSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHH
Confidence 46888999999999999999854
No 92
>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=20.35 E-value=96 Score=23.19 Aligned_cols=31 Identities=23% Similarity=0.371 Sum_probs=23.8
Q ss_pred CHHHHHHHHHhcCCChhhhhhhHHHHHhhHH
Q 024283 224 EPTVLEKLCAVLNVNKRSVDRDLDVYRNLLS 254 (269)
Q Consensus 224 d~~~l~~l~~~Lgls~ekv~KDL~lYrsnLe 254 (269)
++..++++|+.+++|...+.||+.--+..|.
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 3457999999999999999999976666554
No 93
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=20.29 E-value=6.3e+02 Score=22.64 Aligned_cols=30 Identities=10% Similarity=0.183 Sum_probs=22.3
Q ss_pred HHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHH
Q 024283 226 TVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQ 258 (269)
Q Consensus 226 ~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQ 258 (269)
..+++|++.||++..+|.+= .+..+.||.+
T Consensus 226 ~t~~eIA~~lgis~~~V~~~---~~~al~kLr~ 255 (258)
T PRK08215 226 KTQMEVAEEIGISQAQVSRL---EKAALKHMRK 255 (258)
T ss_pred CCHHHHHHHHCcCHHHHHHH---HHHHHHHHHH
Confidence 47889999999999999653 3555666554
No 94
>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=20.21 E-value=21 Score=28.30 Aligned_cols=14 Identities=36% Similarity=0.555 Sum_probs=12.0
Q ss_pred CHHHHHHHHHhcCC
Q 024283 224 EPTVLEKLCAVLNV 237 (269)
Q Consensus 224 d~~~l~~l~~~Lgl 237 (269)
|.+.|++|+.+||+
T Consensus 82 E~~~L~~la~aLgl 95 (95)
T cd07178 82 ERAYLDELAAALGL 95 (95)
T ss_pred HHHHHHHHHHHhCc
Confidence 45689999999996
No 95
>cd07766 DHQ_Fe-ADH Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH). Dehydroquinate synthase-like. This superfamily divides into two subgroups: the dehydroquinate synthase-like, and a large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. Dehydroquinate synthase-like group includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. The alcohol dehydrogenases in this superfamily contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alc
Probab=20.13 E-value=7e+02 Score=23.06 Aligned_cols=132 Identities=22% Similarity=0.200 Sum_probs=69.1
Q ss_pred cchhhHHHHHHHHhcCCCC-----------chhHHHHHHHHHHhc-CCCHHHHHHHHHHHHHHHhcCCccccccccCCcc
Q 024283 117 VFALGFVTVYDRLMEGYPS-----------EEDREAIFQAYITAL-KEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEG 184 (269)
Q Consensus 117 lFALG~VTvFd~fm~GY~p-----------eed~~~IF~Alc~Al-g~Dp~qyR~dA~~l~~~A~~~s~~~l~~~~~~~g 184 (269)
+++-|..-++...+++|-. .+-.+.|++.+-+++ +.|++...+-.........+.+.. .+.+
T Consensus 159 ~~~~g~~Dal~h~~E~~~~~~~~~~~~~~a~~~~~~l~~~l~~~~~~~~~~ar~~l~~as~~ag~~~~~~------~~~~ 232 (332)
T cd07766 159 QVASGGVDALSHALEAYSTKKSWPIADALAEKALETIEEDLPKAIEPGDYDALEKVVWAATLAGNGLFAA------KSGG 232 (332)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHcCC------Cccc
Confidence 4566777777777777732 344556666666666 444443332222221111111100 0011
Q ss_pred hhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCC------HHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHH
Q 024283 185 EVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATE------PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQ 258 (269)
Q Consensus 185 ~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d------~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQ 258 (269)
-..-..|+..+....+...---.||||-..++...... -+.+.++.+.+|+|..- +|+++-+..++++++
T Consensus 233 --~~~~H~i~h~l~~~~~i~HG~ava~~l~~~~~~~~~~~~~~~~~~~~i~~l~~~lglP~~l--~e~g~~~~~~~~~~~ 308 (332)
T cd07766 233 --LGAAHAIGHALTALEGIPHGEAVAVGLPAVLKVANDMNPEIEHAIEAVFKFLEDLGAPTDL--ADLGVSKEDIDKLAE 308 (332)
T ss_pred --chHhHHhhCHHhhCcCCChHHHHHHHHHHHHHHhhhcCHhHHHHHHHHHHHHHHCCCCCCH--HHcCCCHHHHHHHHH
Confidence 11223443333334456777788888888886554332 24688899999999642 234443444555544
No 96
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=20.03 E-value=55 Score=28.68 Aligned_cols=24 Identities=17% Similarity=0.072 Sum_probs=21.1
Q ss_pred HHHHHHHHHhcCCChhhhhhhHHH
Q 024283 225 PTVLEKLCAVLNVNKRSVDRDLDV 248 (269)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~l 248 (269)
.-.+++|++.+|.|...+.|||..
T Consensus 21 ~~~~~~La~~~~vS~~TiRRDl~~ 44 (185)
T PRK04424 21 FITDEELAEKFGVSIQTIRLDRME 44 (185)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHHH
Confidence 346889999999999999999973
Done!