Query 022333
Match_columns 299
No_of_seqs 82 out of 84
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 02:44:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022333.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022333hhsearch_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 5E-110 1E-114 776.1 25.1 283 1-298 1-283 (283)
2 PRK13266 Thf1-like protein; Re 100.0 1.7E-92 3.8E-97 642.8 22.1 214 68-282 2-224 (225)
3 PF11264 ThylakoidFormat: Thyl 100.0 2.8E-92 6.2E-97 638.3 20.8 208 72-279 1-216 (216)
4 PLN03060 inositol phosphatase- 100.0 9E-92 1.9E-96 631.1 20.6 205 70-274 2-206 (206)
5 TIGR03060 PS_II_psb29 photosys 100.0 4.7E-90 1E-94 622.9 19.5 203 68-274 2-214 (214)
6 PF11264 ThylakoidFormat: Thyl 94.2 0.064 1.4E-06 49.8 4.4 56 106-161 127-183 (216)
7 PRK13266 Thf1-like protein; Re 93.9 0.11 2.4E-06 48.5 5.6 63 99-161 125-188 (225)
8 TIGR03060 PS_II_psb29 photosys 93.5 0.094 2E-06 48.7 4.3 58 103-161 127-186 (214)
9 PLN03060 inositol phosphatase- 92.3 0.51 1.1E-05 43.8 7.2 47 200-246 41-93 (206)
10 PLN00047 photosystem II biogen 89.9 1 2.2E-05 43.6 7.0 47 200-246 94-146 (283)
11 PF11473 B2: RNA binding prote 66.4 5.7 0.00012 31.5 2.6 25 239-263 31-55 (73)
12 PF05099 TerB: Tellurite resis 58.2 38 0.00082 27.5 6.3 99 130-244 36-137 (140)
13 KOG0961 Predicted Zn2+-depende 58.0 62 0.0013 35.9 9.2 136 87-263 599-742 (1022)
14 COG1938 Archaeal enzymes of AT 57.5 89 0.0019 29.9 9.3 114 146-261 81-228 (244)
15 COG3793 TerB Tellurite resista 57.1 34 0.00073 30.4 6.1 73 137-241 65-141 (144)
16 PF03216 Rhabdo_ncap_2: Rhabdo 55.3 58 0.0013 32.5 7.8 164 90-265 76-262 (357)
17 TIGR02147 Fsuc_second hypothet 50.5 87 0.0019 30.0 8.2 145 92-247 10-161 (271)
18 PF10199 Adaptin_binding: Alph 46.8 22 0.00047 29.6 3.1 37 243-279 99-135 (137)
19 TIGR00059 L17 ribosomal protei 46.2 25 0.00054 29.9 3.4 77 135-212 8-96 (112)
20 PF08542 Rep_fac_C: Replicatio 45.7 27 0.00059 26.5 3.3 42 132-178 1-42 (89)
21 PRK05591 rplQ 50S ribosomal pr 44.4 31 0.00067 29.3 3.7 77 135-212 10-98 (113)
22 PF08220 HTH_DeoR: DeoR-like h 44.1 12 0.00027 27.2 1.1 23 225-247 14-36 (57)
23 PF06971 Put_DNA-bind_N: Putat 43.2 19 0.0004 26.5 1.9 23 225-247 28-50 (50)
24 PF01841 Transglut_core: Trans 41.6 14 0.0003 28.5 1.1 46 109-154 26-72 (113)
25 PF04772 Flu_B_M2: Influenza B 40.3 50 0.0011 27.5 4.2 35 236-270 43-77 (109)
26 COG2761 FrnE Predicted dithiol 36.7 3.8E+02 0.0082 25.4 10.3 112 128-246 47-161 (225)
27 PF08280 HTH_Mga: M protein tr 36.6 35 0.00076 24.9 2.5 27 227-253 21-47 (59)
28 cd00194 UBA Ubiquitin Associat 36.3 55 0.0012 21.3 3.2 31 225-256 2-32 (38)
29 KOG0212 Uncharacterized conser 35.7 2.1E+02 0.0046 31.1 8.9 99 138-243 122-225 (675)
30 PF08279 HTH_11: HTH domain; 35.5 40 0.00086 23.5 2.6 28 224-251 14-41 (55)
31 TIGR01128 holA DNA polymerase 34.4 3.5E+02 0.0077 24.5 10.3 41 142-182 135-177 (302)
32 COG4476 Uncharacterized protei 32.4 1.9E+02 0.004 24.1 6.3 82 83-166 2-83 (90)
33 PF13413 HTH_25: Helix-turn-he 32.4 59 0.0013 24.3 3.2 27 131-157 36-62 (62)
34 PRK10880 adenine DNA glycosyla 31.9 4.1E+02 0.0088 26.5 9.8 81 73-166 6-98 (350)
35 PF00382 TFIIB: Transcription 31.1 57 0.0012 24.2 3.0 26 228-253 1-26 (71)
36 PRK11861 bifunctional prephena 31.1 2.5E+02 0.0054 29.8 8.7 144 115-275 56-216 (673)
37 cd00192 PTKc Catalytic domain 30.4 65 0.0014 27.2 3.6 32 115-147 188-221 (262)
38 PF04391 DUF533: Protein of un 30.3 2.3E+02 0.005 25.9 7.3 21 224-244 162-182 (188)
39 TIGR02895 spore_sigI RNA polym 30.0 2E+02 0.0044 26.5 7.0 136 112-255 36-195 (218)
40 PRK10954 periplasmic protein d 30.0 1.6E+02 0.0035 26.0 6.2 27 222-248 120-146 (207)
41 PF02861 Clp_N: Clp amino term 29.9 52 0.0011 22.3 2.4 26 139-164 26-51 (53)
42 PRK09430 djlA Dna-J like membr 29.9 4.9E+02 0.011 24.7 12.3 120 116-250 52-176 (267)
43 PF08014 DUF1704: Domain of un 28.5 4.5E+02 0.0097 26.2 9.4 152 103-264 175-346 (349)
44 PF02082 Rrf2: Transcriptional 28.1 55 0.0012 25.0 2.5 43 204-246 2-46 (83)
45 PF01323 DSBA: DSBA-like thior 27.7 1.8E+02 0.0038 24.4 5.7 126 93-247 17-145 (193)
46 PF00627 UBA: UBA/TS-N domain; 27.3 60 0.0013 21.5 2.3 30 225-255 3-32 (37)
47 COG0203 RplQ Ribosomal protein 26.9 75 0.0016 27.4 3.3 78 134-212 12-101 (116)
48 PF05402 PqqD: Coenzyme PQQ sy 25.9 2.3E+02 0.0051 20.3 5.4 49 207-255 14-63 (68)
49 PF12200 DUF3597: Domain of un 25.4 2.8E+02 0.0061 24.4 6.5 70 183-257 48-120 (127)
50 PF01196 Ribosomal_L17: Riboso 25.3 62 0.0013 26.6 2.4 58 154-212 22-82 (97)
51 PF01024 Colicin: Colicin pore 24.9 1.5E+02 0.0033 27.4 5.1 77 154-241 31-108 (187)
52 smart00346 HTH_ICLR helix_turn 24.7 85 0.0018 23.5 3.0 37 211-249 8-44 (91)
53 smart00342 HTH_ARAC helix_turn 24.3 2E+02 0.0043 20.2 4.7 39 227-265 3-48 (84)
54 COG3867 Arabinogalactan endo-1 24.3 1.4E+02 0.003 30.3 5.0 114 115-249 25-157 (403)
55 PF01465 GRIP: GRIP domain; I 24.1 2.1E+02 0.0046 20.3 4.7 36 123-159 9-44 (46)
56 COG2207 AraC AraC-type DNA-bin 24.0 1.7E+02 0.0037 22.3 4.6 55 208-264 21-82 (127)
57 PF12597 DUF3767: Protein of u 23.6 1.1E+02 0.0023 26.1 3.6 89 163-271 18-113 (118)
58 KOG1258 mRNA processing protei 23.3 2.1E+02 0.0046 30.7 6.5 123 71-210 62-190 (577)
59 PRK08307 stage III sporulation 23.3 5.2E+02 0.011 22.8 8.7 71 185-255 66-139 (171)
60 cd05034 PTKc_Src_like Catalyti 23.2 82 0.0018 27.1 2.9 32 115-147 185-218 (261)
61 PF13446 RPT: A repeated domai 23.2 1.4E+02 0.0029 21.8 3.7 47 134-180 14-60 (62)
62 PRK08215 sporulation sigma fac 23.0 5.5E+02 0.012 23.4 8.4 30 226-258 226-255 (258)
63 PF09581 Spore_III_AF: Stage I 23.0 5E+02 0.011 22.5 8.9 29 189-218 5-34 (188)
64 COG3636 Predicted transcriptio 22.9 4.4E+02 0.0094 22.4 7.0 28 211-238 64-91 (100)
65 PF10798 YmgB: Biofilm develop 22.7 2.1E+02 0.0045 21.8 4.7 43 213-257 11-54 (61)
66 smart00219 TyrKc Tyrosine kina 21.8 1.2E+02 0.0025 25.7 3.6 22 115-137 185-206 (258)
67 TIGR02844 spore_III_D sporulat 21.7 61 0.0013 25.9 1.7 23 226-248 20-42 (80)
68 PF15614 WHIM3: WSTF, HB1, Itc 21.7 1.1E+02 0.0024 22.4 2.9 34 223-256 5-42 (46)
69 PF12824 MRP-L20: Mitochondria 21.3 1.8E+02 0.004 26.0 4.8 40 226-265 105-144 (164)
70 PF14075 UBN_AB: Ubinuclein co 20.7 6.9E+02 0.015 23.2 10.8 104 154-269 6-110 (214)
71 PF12069 DUF3549: Protein of u 20.7 1E+02 0.0023 30.8 3.4 32 133-164 122-154 (340)
72 cd08805 Death_ank1 Death domai 20.6 1.3E+02 0.0028 24.1 3.4 55 230-290 20-74 (84)
73 KOG3941 Intermediate in Toll s 20.5 53 0.0012 33.1 1.4 47 204-256 67-117 (406)
74 cd04758 Commd10 COMM_Domain co 20.4 6.1E+02 0.013 22.5 8.1 49 212-260 60-110 (186)
75 PRK15044 transcriptional regul 20.4 8.3E+02 0.018 24.1 10.8 131 74-246 97-229 (295)
76 PF07216 LcrG: LcrG protein; 20.3 75 0.0016 26.5 2.0 31 128-158 13-43 (93)
No 1
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=100.00 E-value=5e-110 Score=776.07 Aligned_cols=283 Identities=73% Similarity=1.114 Sum_probs=268.8
Q ss_pred CCccccccccccccccccccccccccccccccccccccccccceeeeeeeecCCCccceeeeeccCCCCCCchhHhHHHH
Q 022333 1 MASLTSVAFTSIGQTSCQRKVNVSSTRSLVSNFEGFRFRTSLFCHCVRFRASSSSSRMIIQCMSTATDVPPTVAETKMNF 80 (299)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~TVSDTKr~F 80 (299)
|||++|+||++++|++ .++.+ .++|+++ .+|+|+ ||++++ +|+||+||++++|++||||||||+|
T Consensus 1 ~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~---~~~~~~---------~~~~~~-~~~~~~~~~~~~~~~~TVSDTKr~F 65 (283)
T PLN00047 1 MAAVCSVSFPALGQSS-KARPA-PVSAARS---FASRFE---------VASRST-SRRVVHCMAAVTDVPPTVAETKAKF 65 (283)
T ss_pred CccccccChHhhcccc-cccCC-ccchhhh---hccccc---------cccccc-cceeeeehhhccCCCCcHHHHHHHH
Confidence 8999999999999997 54444 3447665 667776 677754 5999999999999999999999999
Q ss_pred HhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHhcCCCHHHHHHH
Q 022333 81 LKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRID 160 (299)
Q Consensus 81 ~~~y~rPIpsIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~D 160 (299)
|++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||+|+|+||+|||+|
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 022333 161 AQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNKR 240 (299)
Q Consensus 161 A~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~e 240 (299)
|++|++||+|++.++|.+|+...|++++.|++||+++++|++||||||||||||+|||.++++||+++++|+++|||+++
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 99999999999999999999999999999999998877899999999999999999999999999999999999999999
Q ss_pred hhhhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhHHhhcccccchHHHHhhhccccccC
Q 022333 241 SVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKREERTEPQKANEAIKKCLGEYLYSH 298 (299)
Q Consensus 241 kv~KDL~lYrsnLeKmaQA~elmeE~~~~EKKKreeR~~~~ka~~~~~~~~~~~~~~~ 298 (299)
+|+|||+|||||||||+||+|||||++++|||||++|+++||+++++++|+|++++.+
T Consensus 226 kv~KDLdlYrsnLeKm~QA~elmeE~~~~EkKKre~r~~~~~~~~~~~~~~~~~~~~~ 283 (283)
T PLN00047 226 SVDRDLDVYRGLLSKLVQAKELLKEYVEREKKKQEERAESQKANEAVTKCLGELEQAG 283 (283)
T ss_pred HHHhhHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHhcccchhccC
Confidence 9999999999999999999999999999999999999999999999999999998864
No 2
>PRK13266 Thf1-like protein; Reviewed
Probab=100.00 E-value=1.7e-92 Score=642.78 Aligned_cols=214 Identities=41% Similarity=0.722 Sum_probs=200.6
Q ss_pred CCCCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHH
Q 022333 68 DVPPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYI 147 (299)
Q Consensus 68 ~~~~TVSDTKr~F~~~y~rPIpsIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc 147 (299)
+++||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||
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 022333 148 TALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKE--GEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA--- 222 (299)
Q Consensus 148 ~Alg~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~~~~--g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~--- 222 (299)
+|+|+||+|||+||++|++||+|++.++|.+|++.. |+++.+++.|. .+++|++||||||||||||+|||.+++
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 44555555554 455699999999999999999999987
Q ss_pred CCH----HHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhHHhhccccc
Q 022333 223 TEP----TVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKREERTEPQK 282 (299)
Q Consensus 223 ~d~----~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE~~~~EKKKreeR~~~~k 282 (299)
+|| +++++||++||||.+||+|||+|||||||||+||+|||||++++||||||+|+++++
T Consensus 161 ~d~~~~~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeKm~Qa~el~ee~~~~erkKre~r~~~~~ 224 (225)
T PRK13266 161 KDEEKLNEALKDISEGLGLSKEKVEKDLDLYRSNLEKMEQALELIEETLEAERKKREQRQAEKA 224 (225)
T ss_pred cCHHHHHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 466 599999999999999999999999999999999999999999999999999987754
No 3
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=100.00 E-value=2.8e-92 Score=638.26 Aligned_cols=208 Identities=52% Similarity=0.898 Sum_probs=198.7
Q ss_pred chhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHhcC
Q 022333 72 TVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALK 151 (299)
Q Consensus 72 TVSDTKr~F~~~y~rPIpsIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc~Alg 151 (299)
|||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||+|+|
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 022333 152 EDPEQYRIDAQKLEEWARGQTASSLVEFPSK-EGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA-------T 223 (299)
Q Consensus 152 ~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~~~-~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~-------~ 223 (299)
+||+|||+||++|++||+|+|.++|.+|++. .++.++.|++++.+|++|++||||||||||||+|||.+++ .
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 4566667777777777899999999999999999999988 3
Q ss_pred CHHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhHHhhcc
Q 022333 224 EPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKREERTE 279 (299)
Q Consensus 224 d~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE~~~~EKKKreeR~~ 279 (299)
+++++++||++||||++||+|||+|||||||||+||+|||||++++||||||+|++
T Consensus 161 ~~~~l~~l~~~l~ls~~kv~kDL~lYrsnLeKm~qA~el~ee~~~~ErkKre~r~~ 216 (216)
T PF11264_consen 161 RPEALEKLSEALGLSKEKVEKDLDLYRSNLEKMAQAKELMEEILEAERKKREERAQ 216 (216)
T ss_pred HHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 46799999999999999999999999999999999999999999999999999963
No 4
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=100.00 E-value=9e-92 Score=631.14 Aligned_cols=205 Identities=70% Similarity=1.125 Sum_probs=200.6
Q ss_pred CCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHh
Q 022333 70 PPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITA 149 (299)
Q Consensus 70 ~~TVSDTKr~F~~~y~rPIpsIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc~A 149 (299)
+||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||+|
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 022333 150 LKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLE 229 (299)
Q Consensus 150 lg~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~ 229 (299)
+|+||+|||+||++|++||+|++.++|.+|++++|+....|++|++++++|++||||||||||||+|||.++++||++++
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 99999999999999999999999999999999988888888888888888999999999999999999999989999999
Q ss_pred HHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhH
Q 022333 230 KLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKR 274 (299)
Q Consensus 230 ~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE~~~~EKKKr 274 (299)
+||++|||+.+||+|||+|||||||||+||+|||||++++||||+
T Consensus 162 ~l~~~L~ls~~kv~kDL~lYrsnLeKm~qa~el~ee~~~~erkK~ 206 (206)
T PLN03060 162 KLSKALNVSKRSVDRDLDVYRNLLSKLAQAKELIKEYIDRSVCSV 206 (206)
T ss_pred HHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHHHhccC
Confidence 999999999999999999999999999999999999999999984
No 5
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=100.00 E-value=4.7e-90 Score=622.93 Aligned_cols=203 Identities=40% Similarity=0.693 Sum_probs=191.1
Q ss_pred CCCCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHH
Q 022333 68 DVPPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYI 147 (299)
Q Consensus 68 ~~~~TVSDTKr~F~~~y~rPIpsIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc 147 (299)
+++||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||
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 022333 148 TALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGE--VEG-LLKDIAERASGKGNFSYSRFFAVGLFRLLELANAT- 223 (299)
Q Consensus 148 ~Alg~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~--~~~-~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~- 223 (299)
+|+|+||+|||+||++|++||+|++.++|.+|++..|+ .+. +|++|| +|++||||||||||||+|||.+++.
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 567665 4999999999999999999998863
Q ss_pred --C----HHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhH
Q 022333 224 --E----PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKR 274 (299)
Q Consensus 224 --d----~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE~~~~EKKKr 274 (299)
| ++++++||++||||.+||+|||+|||||||||+||+|||||++++|||||
T Consensus 158 ~~d~~~~~~~l~~l~~~L~ls~~kv~KDL~lYrsnLeKm~Qa~el~ee~~~~erkKr 214 (214)
T TIGR03060 158 DIDEEDLNEILKELSEALGLSYDRVEKDLDLYKSNLEKMKQALELMEETLEAERRKR 214 (214)
T ss_pred ccCHHHHHHHHHHHHHHcCCCHHHHHhhHHHHHhHHHHHHHHHHHHHHHHHHHhccC
Confidence 4 45999999999999999999999999999999999999999999999986
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=94.17 E-value=0.064 Score=49.80 Aligned_cols=56 Identities=20% Similarity=0.294 Sum_probs=47.3
Q ss_pred hcccccccccccchhhHHHHHHHhhc-CCCCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 022333 106 MRYKRTYQYDPVFALGFVTVYDRLME-GYPSEEDREAIFQAYITALKEDPEQYRIDA 161 (299)
Q Consensus 106 Ls~n~~F~YDplFALGlVTvFd~fm~-GY~peed~~~IF~Alc~Alg~Dp~qyR~DA 161 (299)
..-|..|.|.-+||+|+.+..+.--- .-..++.+..+.+.||+++|+.++.+.+|-
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 244567788899999999999999999885
No 7
>PRK13266 Thf1-like protein; Reviewed
Probab=93.93 E-value=0.11 Score=48.55 Aligned_cols=63 Identities=17% Similarity=0.292 Sum_probs=50.9
Q ss_pred HHHHHhhhcccccccccccchhhHHHHHHHhhcC-CCCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 022333 99 LIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEG-YPSEEDREAIFQAYITALKEDPEQYRIDA 161 (299)
Q Consensus 99 LLVElHLLs~n~~F~YDplFALGlVTvFd~fm~G-Y~peed~~~IF~Alc~Alg~Dp~qyR~DA 161 (299)
|+-.++=..-|..|.|.-+||+|+.+..+.---. ...++++..+...||.++|+..+.+.+|-
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 45666889999999999999999988884
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=93.54 E-value=0.094 Score=48.73 Aligned_cols=58 Identities=19% Similarity=0.301 Sum_probs=48.0
Q ss_pred HhhhcccccccccccchhhHHHHHHHhhcCC--CCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 022333 103 QHLMRYKRTYQYDPVFALGFVTVYDRLMEGY--PSEEDREAIFQAYITALKEDPEQYRIDA 161 (299)
Q Consensus 103 lHLLs~n~~F~YDplFALGlVTvFd~fm~GY--~peed~~~IF~Alc~Alg~Dp~qyR~DA 161 (299)
++=..-|..|.|.-+||+|+.+..+. .+|. ..++++..+...||.++|+..+.+.+|-
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 4443 4567788999999999999999988884
No 9
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=92.28 E-value=0.51 Score=43.77 Aligned_cols=47 Identities=13% Similarity=0.387 Sum_probs=38.9
Q ss_pred CCCCcchhhHHHHHHHHHhh-cCCC----C-HHHHHHHHHhcCCChhhhhhhH
Q 022333 200 KGNFSYSRFFAVGLFRLLEL-ANAT----E-PTVLEKLCAVLNVNKRSVDRDL 246 (299)
Q Consensus 200 n~~F~YSRlfAIGLf~LLE~-~~~~----d-~~~l~~l~~~Lgls~ekv~KDL 246 (299)
|..|.|.-+||+||.+..+. .... | ....+.||+++|+.++.+.+|-
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=89.91 E-value=1 Score=43.63 Aligned_cols=47 Identities=15% Similarity=0.374 Sum_probs=38.9
Q ss_pred CCCCcchhhHHHHHHHHHhhc-CCC----C-HHHHHHHHHhcCCChhhhhhhH
Q 022333 200 KGNFSYSRFFAVGLFRLLELA-NAT----E-PTVLEKLCAVLNVNKRSVDRDL 246 (299)
Q Consensus 200 n~~F~YSRlfAIGLf~LLE~~-~~~----d-~~~l~~l~~~Lgls~ekv~KDL 246 (299)
|..|.|.-+||+||.+..+.- ... | ....+.||+++|+.++.+.+|-
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 899999999999999999433 332 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=66.43 E-value=5.7 Score=31.46 Aligned_cols=25 Identities=28% Similarity=0.292 Sum_probs=20.5
Q ss_pred hhhhhhhHHHHHhhHHHHHHHHHHH
Q 022333 239 KRSVDRDLDVYRNLLSKLLQAKELL 263 (299)
Q Consensus 239 ~ekv~KDL~lYrsnLeKmaQA~elm 263 (299)
+++|.||||-|+.-|.||++-.-=|
T Consensus 31 p~~V~kDLdn~kaCL~K~e~T~~r~ 55 (73)
T PF11473_consen 31 PNNVRKDLDNYKACLNKAEATVFRA 55 (73)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4699999999999999999865433
No 12
>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=58.20 E-value=38 Score=27.55 Aligned_cols=99 Identities=17% Similarity=0.194 Sum_probs=50.7
Q ss_pred hcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhH
Q 022333 130 MEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFF 209 (299)
Q Consensus 130 m~GY~peed~~~IF~Alc~Alg~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlf 209 (299)
-.|--.++++..|-+.+..-.++++.....-.+.+...... ..+.+..+..|.. .-....-..+
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 35666677788888888788888877766555444433222 2234445554421 1111111222
Q ss_pred HHHHHHHHhhcCC-C--CHHHHHHHHHhcCCChhhhhh
Q 022333 210 AVGLFRLLELANA-T--EPTVLEKLCAVLNVNKRSVDR 244 (299)
Q Consensus 210 AIGLf~LLE~~~~-~--d~~~l~~l~~~Lgls~ekv~K 244 (299)
--.++.+....|. . |.+.+.++++.||++.+.+++
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 345899999999999987754
No 13
>KOG0961 consensus Predicted Zn2+-dependent endopeptidase, insulinase superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=58.03 E-value=62 Score=35.92 Aligned_cols=136 Identities=25% Similarity=0.289 Sum_probs=91.8
Q ss_pred cCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhh--------cCCCCchhHHHHHHHHHHhcCCCHHHHH
Q 022333 87 PIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLM--------EGYPSEEDREAIFQAYITALKEDPEQYR 158 (299)
Q Consensus 87 PIpsIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm--------~GY~peed~~~IF~Alc~Alg~Dp~qyR 158 (299)
-||.=|-.+++| |+-|+.+-+.+-+.| .|+.-.+++|. .||+---.= -.-+..-+=+||+.++
T Consensus 599 tiptp~~~s~~~--v~~~~~s~~id~si~----~g~~G~~~~lvn~~Ikv~a~~Y~~~v~W---i~~~l~~~VfD~~Ri~ 669 (1022)
T KOG0961|consen 599 TIPTPVLTSADD--VAKHFTSDLIDHSIQ----VGVSGLYDRLVNLRIKVGADKYPLLVKW---IQIFLQGVVFDPSRIH 669 (1022)
T ss_pred CCCcchhhhHHH--HHHHHHhhhhhhhhc----ccccccchhheeEEEEEccCCcchhHHH---HHHHhhhhccCHHHHH
Confidence 456667777777 467887777765544 68888999986 689743322 2334567789999999
Q ss_pred HHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhcCCC
Q 022333 159 IDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVN 238 (299)
Q Consensus 159 ~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls 238 (299)
+-++++.. ++.+| +-++.|.-|-++++-||.-=.+--..|+-.++++-+.+
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 99998866 22232 12788888999999888643222234665555554443
Q ss_pred hhhhhhhHHHHHhhHHHHHHHHHHH
Q 022333 239 KRSVDRDLDVYRNLLSKLLQAKELL 263 (299)
Q Consensus 239 ~ekv~KDL~lYrsnLeKmaQA~elm 263 (299)
..+|++| =.+.|+|++|++.++
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 3556666 678899999988743
No 14
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=57.54 E-value=89 Score=29.95 Aligned_cols=114 Identities=17% Similarity=0.245 Sum_probs=63.5
Q ss_pred HHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccC--C---c--------chhHHHHHHHHHHhcCCCCCcchhhHHHH
Q 022333 146 YITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPS--K---E--------GEVEGLLKDIAERASGKGNFSYSRFFAVG 212 (299)
Q Consensus 146 lc~Alg~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~~--~---~--------g~~~~~l~~Ia~~~~~n~~F~YSRlfAIG 212 (299)
+.+-....|..+..-++++.+|++......++.+-. . + ++-+..+..+++ .+-..|.+-=+-+++
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 445567889999999999999999999888887652 1 0 011122333332 112334433222222
Q ss_pred HHHHHhhcCC---------------CCHHHH----HHHHHhcC--CChhhhhhhHHHHHhhHHHHHHHHH
Q 022333 213 LFRLLELANA---------------TEPTVL----EKLCAVLN--VNKRSVDRDLDVYRNLLSKLLQAKE 261 (299)
Q Consensus 213 Lf~LLE~~~~---------------~d~~~l----~~l~~~Lg--ls~ekv~KDL~lYrsnLeKmaQA~e 261 (299)
=.-|.+.... .||.+. +-|.+.+| ++.+++.|--..++.-|+||++..+
T Consensus 159 g~ll~e~~~r~i~a~~ll~et~~~~PDP~AAa~vve~lnk~~~l~V~td~L~keAe~i~~~lekl~eq~~ 228 (244)
T COG1938 159 GALLNECLKRGIPALVLLAETFGDRPDPRAAARVVEALNKMLGLNVDTDKLEKEAEEIEEQLEKLAEQLE 228 (244)
T ss_pred HHHHHHHHHcCCCeEEEeccccCCCCChHHHHHHHHHHHHHhcCccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1111122211 267644 43444444 6778888888888877777765443
No 15
>COG3793 TerB Tellurite resistance protein [Inorganic ion transport and metabolism]
Probab=57.08 E-value=34 Score=30.44 Aligned_cols=73 Identities=22% Similarity=0.266 Sum_probs=49.6
Q ss_pred hhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHH-HHHHHHhcCCCCCcchhhHHHHHHH
Q 022333 137 EDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLL-KDIAERASGKGNFSYSRFFAVGLFR 215 (299)
Q Consensus 137 ed~~~IF~Alc~Alg~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l-~~Ia~~~~~n~~F~YSRlfAIGLf~ 215 (299)
+....||+.+|.+.+.|++.=+..+.++.+-.++.+.. -+..| .+++=.
T Consensus 65 ~~i~~~~~~~~~~~~~d~~~gk~ea~~~I~~lk~d~e~-----------Ae~vL~vAv~VA------------------- 114 (144)
T COG3793 65 NEINEIFETLVGSFDTDFEIGKREAMKEIEDLKHDTEA-----------AEDVLRVAVAVA------------------- 114 (144)
T ss_pred HHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHhcCChHH-----------HHHHHHHHHHHh-------------------
Confidence 46889999999999999999898888888866554421 12222 222110
Q ss_pred HHhhcCCCC---HHHHHHHHHhcCCChhh
Q 022333 216 LLELANATE---PTVLEKLCAVLNVNKRS 241 (299)
Q Consensus 216 LLE~~~~~d---~~~l~~l~~~Lgls~ek 241 (299)
+..|.-| ...+++||.+|||++.+
T Consensus 115 --~aDG~~d~~E~avl~eI~~aLGL~p~~ 141 (144)
T COG3793 115 --EADGEFEAEERAVLREIAGALGLSPAE 141 (144)
T ss_pred --hcCCCCCHHHHHHHHHHHHHhCCCHHh
Confidence 1223333 45899999999998865
No 16
>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=55.28 E-value=58 Score=32.47 Aligned_cols=164 Identities=16% Similarity=0.165 Sum_probs=97.1
Q ss_pred cchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHh---cCCCHHHHHHH-HHHHH
Q 022333 90 SIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITA---LKEDPEQYRID-AQKLE 165 (299)
Q Consensus 90 sIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc~A---lg~Dp~qyR~D-A~~l~ 165 (299)
.-|-+.+ ++|++|-+.--+.+---+ + .-|+--=...+-+--.||.--+-+--.|..+ ...|-++.-+- -++|.
T Consensus 76 ~~~et~~-kiL~dmgFkv~~~p~a~~-~-~agi~~P~~~lA~tv~~en~~eiVkG~L~TCaLl~KY~VdKM~kY~~~KL~ 152 (357)
T PF03216_consen 76 DDTETKC-KILTDMGFKVTQVPRATP-I-EAGIMMPMRKLAETVNNENVMEIVKGLLMTCALLTKYSVDKMIKYIQNKLE 152 (357)
T ss_pred hhhhhHH-HHHHHhCceeEecccCCC-c-ccchhchHHHHHHHhChhhHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHH
Confidence 3344433 467777665554432221 1 1233333344444444444444444444333 23455554443 47899
Q ss_pred HHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHH------------------
Q 022333 166 EWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTV------------------ 227 (299)
Q Consensus 166 ~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~------------------ 227 (299)
++|.++...+|..|.... +.|+.|+.-+.+..+ -|--+.|+=|+ ++++++++.-
T Consensus 153 ~L~~sqGv~EL~~~~~~~----~~l~kl~~~vRpGQK-ltkaiyg~IL~---~l~dp~t~~~akal~a~rL~gTGMtmig 224 (357)
T PF03216_consen 153 RLATSQGVGELQHFSADR----AALAKLAACVRPGQK-LTKAIYGFILF---ELADPQTQRRAKALFAMRLNGTGMTMIG 224 (357)
T ss_pred HHhhccCcchhheecccH----HHHHHHHHhcCchhH-HHHHHHHHHHH---HhcCcccHHHHHHHHHhhhcCCCceehH
Confidence 999999999999988755 345555544432222 34444444333 5566766543
Q ss_pred -HHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHH
Q 022333 228 -LEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKE 265 (299)
Q Consensus 228 -l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE 265 (299)
..+-+..||.++..+--||- |+|+.+-.-|.+.||.-
T Consensus 225 lFtqAa~nlGa~pA~LLedLc-m~s~v~sarrivkLm~~ 262 (357)
T PF03216_consen 225 LFTQAAKNLGATPADLLEDLC-MGSLVESARRIVKLMRQ 262 (357)
T ss_pred HHHHHHHhcCCCcHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 33445789999999999995 89999999999999873
No 17
>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=50.48 E-value=87 Score=29.98 Aligned_cols=145 Identities=14% Similarity=0.265 Sum_probs=81.4
Q ss_pred hhHHHHHHHHHHhhhccccccccccc-chhhHHH--HHHHhhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Q 022333 92 YNTVLQELIVQQHLMRYKRTYQYDPV-FALGFVT--VYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWA 168 (299)
Q Consensus 92 Yrrvv~ELLVElHLLs~n~~F~YDpl-FALGlVT--vFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~DA~~l~~~A 168 (299)
||..+.+-..+-.- .|..|.+=.+ -.+||.+ -+..+++|=+|-. +.-..-+++++|+++..-. --..|....
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 3488876 5678899988766 5556788999999997632 233444444
Q ss_pred hcCCccccccccCCcchhHHHHHHHHHHhcCCCCC-cchhhHHHHHHHHHhhcCCC-CHHHHHHHHHhcC--CChhhhhh
Q 022333 169 RGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNF-SYSRFFAVGLFRLLELANAT-EPTVLEKLCAVLN--VNKRSVDR 244 (299)
Q Consensus 169 ~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F-~YSRlfAIGLf~LLE~~~~~-d~~~l~~l~~~Lg--ls~ekv~K 244 (299)
+..+.++-..+..+ +..+...-..+.-+.+.| .|+.+..-.|..|+...+.. ||+ .|++.++ +|.+.|+.
T Consensus 85 ~ak~~~~k~~~~~~---~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~---~ia~~l~p~is~~ev~~ 158 (271)
T TIGR02147 85 QAKTDTEKQQFFEE---MQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPE---ELAKRCFPKISAEQVKE 158 (271)
T ss_pred ccCCHHHHHHHHHH---HHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHH---HHHHHhCCCCCHHHHHH
Confidence 44443321111110 001100000011112333 67788888888888776654 655 3455555 56666655
Q ss_pred hHH
Q 022333 245 DLD 247 (299)
Q Consensus 245 DL~ 247 (299)
=|+
T Consensus 159 sL~ 161 (271)
T TIGR02147 159 SLD 161 (271)
T ss_pred HHH
Confidence 444
No 18
>PF10199 Adaptin_binding: Alpha and gamma adaptin binding protein p34; InterPro: IPR019341 p34 is a protein involved in membrane trafficking. It is known to interact with both alpha and gamma adaptin []. It has been speculated that p34 may play a chaperone role such as preventing the soluble adaptors from co-assembling with soluble clathrin, or helping to remove the adaptors from the coated vesicle. It may also aid in the recruitment of soluble adaptors onto the membrane [].
Probab=46.83 E-value=22 Score=29.62 Aligned_cols=37 Identities=16% Similarity=0.447 Sum_probs=32.0
Q ss_pred hhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhHHhhcc
Q 022333 243 DRDLDVYRNLLSKLLQAKELLKEYVDREKKKREERTE 279 (299)
Q Consensus 243 ~KDL~lYrsnLeKmaQA~elmeE~~~~EKKKreeR~~ 279 (299)
+.|++-+-.++.||.++++....+=..+||+++++..
T Consensus 99 ~~~~e~~e~lm~kl~~~R~~~~~lpd~qRr~~Aakva 135 (137)
T PF10199_consen 99 EDDVEDFEQLMSKLQAMRDMAASLPDEQRRRMAAKVA 135 (137)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 4466778889999999999999999999999998754
No 19
>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=46.19 E-value=25 Score=29.88 Aligned_cols=77 Identities=21% Similarity=0.308 Sum_probs=60.3
Q ss_pred CchhHHHHHHHHHHhcC---------CCHHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCC
Q 022333 135 SEEDREAIFQAYITALK---------EDPEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGN 202 (299)
Q Consensus 135 peed~~~IF~Alc~Alg---------~Dp~qyR~DA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~n~~ 202 (299)
+.+||.+++..|+.+|= --++++|.-|++|..+|+..+.. .+..|+.....+..++..|+.+-+ +.+
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 56899999999998873 35789999999999999976654 345666666678889999998876 455
Q ss_pred CcchhhHHHH
Q 022333 203 FSYSRFFAVG 212 (299)
Q Consensus 203 F~YSRlfAIG 212 (299)
.-|+|+.=+|
T Consensus 87 GGYTRI~kl~ 96 (112)
T TIGR00059 87 GGYTRILKLG 96 (112)
T ss_pred CCeEEEEECC
Confidence 5899987665
No 20
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=45.72 E-value=27 Score=26.50 Aligned_cols=42 Identities=24% Similarity=0.327 Sum_probs=28.0
Q ss_pred CCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCcccccc
Q 022333 132 GYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVE 178 (299)
Q Consensus 132 GY~peed~~~IF~Alc~Alg~Dp~qyR~DA~~l~~~A~~~s~~~l~~ 178 (299)
|.||+++-+.|++++.+. +-+..|.....+... |.+..+|+.
T Consensus 1 ~~p~~~~i~~i~~~~~~~---~~~~~~~~~~~l~~~--G~s~~~Il~ 42 (89)
T PF08542_consen 1 DWPPPEVIEEILESCLNG---DFKEARKKLYELLVE--GYSASDILK 42 (89)
T ss_dssp TS--HHHHHHHHHHHHHT---CHHHHHHHHHHHHHT--T--HHHHHH
T ss_pred CCCCHHHHHHHHHHHHhC---CHHHHHHHHHHHHHc--CCCHHHHHH
Confidence 568888888888888776 777777777777664 666666553
No 21
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=44.36 E-value=31 Score=29.29 Aligned_cols=77 Identities=22% Similarity=0.304 Sum_probs=60.7
Q ss_pred CchhHHHHHHHHHHhcC---------CCHHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCC
Q 022333 135 SEEDREAIFQAYITALK---------EDPEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGN 202 (299)
Q Consensus 135 peed~~~IF~Alc~Alg---------~Dp~qyR~DA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~n~~ 202 (299)
+.+||.+++.-++.+|= --+.++|.-|++|..+|+.-+.. .+..|+.....+..++..|+.+-+ +.+
T Consensus 10 ~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~aK~~~~~~rR~~~~~L~~~~~v~KLf~~lapry~-~R~ 88 (113)
T PRK05591 10 TSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHARRQAFARLRDKEAVHKLFDEIAPRYA-DRN 88 (113)
T ss_pred ChHHHHHHHHHHHHHHHHcCeEEecHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHhCCHHHHHHHHHHHHHHhC-cCC
Confidence 56899999999998874 34789999999999999976654 344566666678888899998886 455
Q ss_pred CcchhhHHHH
Q 022333 203 FSYSRFFAVG 212 (299)
Q Consensus 203 F~YSRlfAIG 212 (299)
.-|+|++-+|
T Consensus 89 GGYTRI~k~~ 98 (113)
T PRK05591 89 GGYTRILKLG 98 (113)
T ss_pred CCeEEEEECC
Confidence 5899988776
No 22
>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=44.14 E-value=12 Score=27.17 Aligned_cols=23 Identities=22% Similarity=0.455 Sum_probs=20.6
Q ss_pred HHHHHHHHHhcCCChhhhhhhHH
Q 022333 225 PTVLEKLCAVLNVNKRSVDRDLD 247 (299)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~ 247 (299)
.-.+++|++.+|.|...+.+||.
T Consensus 14 ~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHH
Confidence 44688999999999999999995
No 23
>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=43.17 E-value=19 Score=26.45 Aligned_cols=23 Identities=22% Similarity=0.371 Sum_probs=18.1
Q ss_pred HHHHHHHHHhcCCChhhhhhhHH
Q 022333 225 PTVLEKLCAVLNVNKRSVDRDLD 247 (299)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~ 247 (299)
--.-++|++.+|+++.-|.|||.
T Consensus 28 ~vSS~~La~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 28 RVSSQELAEALGITPAQVRKDLS 50 (50)
T ss_dssp EE-HHHHHHHHTS-HHHHHHHHH
T ss_pred eECHHHHHHHHCCCHHHhcccCC
Confidence 34677899999999999999984
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=41.64 E-value=14 Score=28.51 Aligned_cols=46 Identities=26% Similarity=0.375 Sum_probs=32.2
Q ss_pred ccccccc-ccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHhcCCCH
Q 022333 109 KRTYQYD-PVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDP 154 (299)
Q Consensus 109 n~~F~YD-plFALGlVTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp 154 (299)
+.++.|| +-..-+-.++.+-|..|+=.-.+...+|.|||.++|.+.
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 344444445666666777788999999999999999864
No 25
>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=40.27 E-value=50 Score=27.48 Aligned_cols=35 Identities=31% Similarity=0.533 Sum_probs=29.4
Q ss_pred CCChhhhhhhHHHHHhhHHHHHHHHHHHHHHHHHH
Q 022333 236 NVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDRE 270 (299)
Q Consensus 236 gls~ekv~KDL~lYrsnLeKmaQA~elmeE~~~~E 270 (299)
|=+++.++|...+.|-+-.|=-||+|-|++.+...
T Consensus 43 ~pnke~~nrevsilrh~yqkeiqaketmk~ils~n 77 (109)
T PF04772_consen 43 NPNKETINREVSILRHNYQKEIQAKETMKKILSNN 77 (109)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 45688899999999999999999999999988643
No 26
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=36.66 E-value=3.8e+02 Score=25.44 Aligned_cols=112 Identities=19% Similarity=0.203 Sum_probs=66.4
Q ss_pred HhhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCcc-ccccccCCcchhHHHHHHHHHHhcCCCCCcch
Q 022333 128 RLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTAS-SLVEFPSKEGEVEGLLKDIAERASGKGNFSYS 206 (299)
Q Consensus 128 ~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~DA~~l~~~A~~~s~~-~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YS 206 (299)
+++-..+|+ ....-+-|-+..|.++++ ++-.+.+++.+.....+ .+..+.-......+....- -++..++ .+-
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 455666665 334455566778888888 77778888877754443 1111100011122222111 1122333 455
Q ss_pred hhHHHHHHHHH--hhcCCCCHHHHHHHHHhcCCChhhhhhhH
Q 022333 207 RFFAVGLFRLL--ELANATEPTVLEKLCAVLNVNKRSVDRDL 246 (299)
Q Consensus 207 RlfAIGLf~LL--E~~~~~d~~~l~~l~~~Lgls~ekv~KDL 246 (299)
|+ .-.||..+ |-.+..|..+|-+|++..||..+.+.+||
T Consensus 121 ~~-~~~lf~AyF~eg~nI~D~dVL~diA~~~GLD~~~~~~~L 161 (225)
T COG2761 121 RF-LEALFEAYFEEGRNIGDEDVLADIAEEVGLDREEFKADL 161 (225)
T ss_pred HH-HHHHHHHHhccCCCCCcHHHHHHHHHHhCCCHHHHHHHH
Confidence 43 45777777 34455789999999999999999988887
No 27
>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=36.59 E-value=35 Score=24.88 Aligned_cols=27 Identities=22% Similarity=0.555 Sum_probs=21.9
Q ss_pred HHHHHHHhcCCChhhhhhhHHHHHhhH
Q 022333 227 VLEKLCAVLNVNKRSVDRDLDVYRNLL 253 (299)
Q Consensus 227 ~l~~l~~~Lgls~ekv~KDL~lYrsnL 253 (299)
.+++||+.||+|...+.+|++-.+..+
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 28
>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=36.28 E-value=55 Score=21.32 Aligned_cols=31 Identities=16% Similarity=0.276 Sum_probs=24.5
Q ss_pred HHHHHHHHHhcCCChhhhhhhHHHHHhhHHHH
Q 022333 225 PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKL 256 (299)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKm 256 (299)
++.+++|.+ ||++.+.+.+=|....+++++-
T Consensus 2 ~~~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A 32 (38)
T cd00194 2 EEKLEQLLE-MGFSREEARKALRATNNNVERA 32 (38)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHHHhCCCHHHH
Confidence 456677765 7999999999998888887663
No 29
>KOG0212 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.70 E-value=2.1e+02 Score=31.08 Aligned_cols=99 Identities=17% Similarity=0.173 Sum_probs=67.9
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHH
Q 022333 138 DREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLL 217 (299)
Q Consensus 138 d~~~IF~Alc~Alg~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LL 217 (299)
.-+.||+++|+-.....+..|.-|+-+-...+....++-. .=.++.....|.+++ ...-.|.|.|-|+-.++|
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 4578999999988876666766665554444322221111 113556667777777 445579999999999999
Q ss_pred hhcCCC-----CHHHHHHHHHhcCCChhhhh
Q 022333 218 ELANAT-----EPTVLEKLCAVLNVNKRSVD 243 (299)
Q Consensus 218 E~~~~~-----d~~~l~~l~~~Lgls~ekv~ 243 (299)
....+- -|+.+.-|.+.||=+.+.|.
T Consensus 195 ds~P~~~m~~yl~~~ldGLf~~LsD~s~eVr 225 (675)
T KOG0212|consen 195 DSVPDLEMISYLPSLLDGLFNMLSDSSDEVR 225 (675)
T ss_pred hcCCcHHHHhcchHHHHHHHHHhcCCcHHHH
Confidence 766552 37788888899988877775
No 30
>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=35.55 E-value=40 Score=23.47 Aligned_cols=28 Identities=32% Similarity=0.610 Sum_probs=22.3
Q ss_pred CHHHHHHHHHhcCCChhhhhhhHHHHHh
Q 022333 224 EPTVLEKLCAVLNVNKRSVDRDLDVYRN 251 (299)
Q Consensus 224 d~~~l~~l~~~Lgls~ekv~KDL~lYrs 251 (299)
++-..++|++.||+|...|.+||..-+.
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 31
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=34.39 E-value=3.5e+02 Score=24.46 Aligned_cols=41 Identities=17% Similarity=0.084 Sum_probs=30.7
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHhc--CCccccccccCC
Q 022333 142 IFQAYITALKEDPEQYRIDAQKLEEWARG--QTASSLVEFPSK 182 (299)
Q Consensus 142 IF~Alc~Alg~Dp~qyR~DA~~l~~~A~~--~s~~~l~~~~~~ 182 (299)
..+.|+..+|.|...++++-++|.-.+.+ .+.+++..+...
T Consensus 135 a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~ 177 (302)
T TIGR01128 135 AVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSD 177 (302)
T ss_pred HHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhh
Confidence 45677889999999999999999887654 444566665553
No 32
>COG4476 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.44 E-value=1.9e+02 Score=24.06 Aligned_cols=82 Identities=21% Similarity=0.186 Sum_probs=70.1
Q ss_pred hCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHH
Q 022333 83 LYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQ 162 (299)
Q Consensus 83 ~y~rPIpsIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~DA~ 162 (299)
.|.+||+.=|.+ +|+.--+|++..=..+==-.+=+.-|.-.|.+|-+=-|.-.+-..||..+=++.|..+=+-=++|+
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 899999999887666555567788889999999999999888999999999999999988888887
Q ss_pred HHHH
Q 022333 163 KLEE 166 (299)
Q Consensus 163 ~l~~ 166 (299)
...+
T Consensus 80 ~~~~ 83 (90)
T COG4476 80 ESEE 83 (90)
T ss_pred Hhhh
Confidence 6643
No 33
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=32.44 E-value=59 Score=24.30 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=17.5
Q ss_pred cCCCCchhHHHHHHHHHHhcCCCHHHH
Q 022333 131 EGYPSEEDREAIFQAYITALKEDPEQY 157 (299)
Q Consensus 131 ~GY~peed~~~IF~Alc~Alg~Dp~qy 157 (299)
+++|++---......||+.||.||+++
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 445555556667788889999998864
No 34
>PRK10880 adenine DNA glycosylase; Provisional
Probab=31.91 E-value=4.1e+02 Score=26.50 Aligned_cols=81 Identities=19% Similarity=0.308 Sum_probs=52.3
Q ss_pred hhHhHHHHHhhCCC-c-----CCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHH----H
Q 022333 73 VAETKMNFLKLYKR-P-----IPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREA----I 142 (299)
Q Consensus 73 VSDTKr~F~~~y~r-P-----IpsIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~----I 142 (299)
.++.-.+.|..|.| + -..-|+-.|-|+|.++==. . -+..+|++||+.||..++... =
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 56667788888886 3 4567999999999887411 1 255689999999986554221 1
Q ss_pred HHHHHHhcCC--CHHHHHHHHHHHHH
Q 022333 143 FQAYITALKE--DPEQYRIDAQKLEE 166 (299)
Q Consensus 143 F~Alc~Alg~--Dp~qyR~DA~~l~~ 166 (299)
...++..+|+ -+..+++-|+.+.+
T Consensus 73 l~~~~~glGyy~RAr~L~~~A~~i~~ 98 (350)
T PRK10880 73 VLHLWTGLGYYARARNLHKAAQQVAT 98 (350)
T ss_pred HHHHHHcCChHHHHHHHHHHHHHHHH
Confidence 2245567887 44444455555544
No 35
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=31.14 E-value=57 Score=24.15 Aligned_cols=26 Identities=15% Similarity=0.529 Sum_probs=18.6
Q ss_pred HHHHHHhcCCChhhhhhhHHHHHhhH
Q 022333 228 LEKLCAVLNVNKRSVDRDLDVYRNLL 253 (299)
Q Consensus 228 l~~l~~~Lgls~ekv~KDL~lYrsnL 253 (299)
++++|+.||||.+-.+.=.++|+...
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~ 26 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQ 26 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHH
Confidence 57899999999987777777776643
No 36
>PRK11861 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase; Provisional
Probab=31.11 E-value=2.5e+02 Score=29.81 Aligned_cols=144 Identities=21% Similarity=0.265 Sum_probs=82.3
Q ss_pred cccch---hhHHHHHHHhhcCC-----CCch---hHHHHHHHHHHhcCCCHHHHH-HHHHHHHHHHhcCCccccccccCC
Q 022333 115 DPVFA---LGFVTVYDRLMEGY-----PSEE---DREAIFQAYITALKEDPEQYR-IDAQKLEEWARGQTASSLVEFPSK 182 (299)
Q Consensus 115 DplFA---LGlVTvFd~fm~GY-----~pee---d~~~IF~Alc~Alg~Dp~qyR-~DA~~l~~~A~~~s~~~l~~~~~~ 182 (299)
=|+++ =|+-.+...|.+|. |.+. +.-..+..|...+|..+-.+- +++-++..+...++-
T Consensus 56 HPMaG~e~~G~~~a~~~Lf~~~~~il~p~~~~~~~~~~~~~~l~~~~Ga~~~~~~~~~HD~~~A~iShlpH--------- 126 (673)
T PRK11861 56 HPIAGRESSGVDAALADLYVGRNVVLCALPENAPDALARVEAMWRAARADVRAMSAEQHDRVFAAVSHLPH--------- 126 (673)
T ss_pred CCcCcCcchhhhhhChhHhCCCeEEEecCCCCCHHHHHHHHHHHHHcCCEEEECCHHHHHHHHHHHhhHHH---------
Confidence 47776 48888999999998 4332 233567777777774333222 234444443332221
Q ss_pred cchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHH--
Q 022333 183 EGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAK-- 260 (299)
Q Consensus 183 ~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~-- 260 (299)
-+..++++...++..-.+..-+|=|=|+-+-.....||+.-.+|+. -+++-|-+-|+-|...|+.+.++.
T Consensus 127 -----~~a~~l~~~~~~~~~~~~~~~~a~~gfrd~tRia~~~p~lw~di~~---~N~~~i~~~l~~~~~~l~~~~~~l~~ 198 (673)
T PRK11861 127 -----VLSFALVEQILGESDAELKFSYAAGGFRDFTRIAASSPEMWRDVCL---ANRAALLDELDAYTAVLARLRAAIDA 198 (673)
T ss_pred -----HHHHHHHHHHhhccChhHHHHhcccchhcccccccCCHHHHHHHHH---HCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1112222222111111222234555566554444568888777753 366778888999999999988887
Q ss_pred ---HHHHHHHHHHhhhHH
Q 022333 261 ---ELLKEYVDREKKKRE 275 (299)
Q Consensus 261 ---elmeE~~~~EKKKre 275 (299)
+-+++.+++-|+.|+
T Consensus 199 ~d~~~l~~~~~~~~~~r~ 216 (673)
T PRK11861 199 GDGAALEAVFARSRAARA 216 (673)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 467777766666665
No 37
>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=30.38 E-value=65 Score=27.16 Aligned_cols=32 Identities=13% Similarity=0.325 Sum_probs=19.6
Q ss_pred cccchhhHHHHHHHhhcCCCCchh--HHHHHHHHH
Q 022333 115 DPVFALGFVTVYDRLMEGYPSEED--REAIFQAYI 147 (299)
Q Consensus 115 DplFALGlVTvFd~fm~GY~peed--~~~IF~Alc 147 (299)
..+|+||++ .|+.++.|++|-.+ ...+++.+.
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 38
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=30.30 E-value=2.3e+02 Score=25.91 Aligned_cols=21 Identities=24% Similarity=0.390 Sum_probs=17.4
Q ss_pred CHHHHHHHHHhcCCChhhhhh
Q 022333 224 EPTVLEKLCAVLNVNKRSVDR 244 (299)
Q Consensus 224 d~~~l~~l~~~Lgls~ekv~K 244 (299)
|-..|+.|+..|||+++-|++
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 39
>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=30.02 E-value=2e+02 Score=26.52 Aligned_cols=136 Identities=11% Similarity=0.217 Sum_probs=76.5
Q ss_pred ccccccchhhHHHHHHHhhcCCCCchh-----------HHHHHHHHHHhc------CCC--HHHHHHH-HHHHHH----H
Q 022333 112 YQYDPVFALGFVTVYDRLMEGYPSEED-----------REAIFQAYITAL------KED--PEQYRID-AQKLEE----W 167 (299)
Q Consensus 112 F~YDplFALGlVTvFd~fm~GY~peed-----------~~~IF~Alc~Al------g~D--p~qyR~D-A~~l~~----~ 167 (299)
..+|.++..|++..++.+ +.|.|+.. +..|.+.+-.-. ..+ .++...+ ...+.+ +
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 568999999998888765 56776543 223333332211 111 1111111 111111 2
Q ss_pred HhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhcCCChhhhhhhHH
Q 022333 168 ARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLD 247 (299)
Q Consensus 168 A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~ekv~KDL~ 247 (299)
-+....++|..|...-.+-.-.|.++++ ..|+-.=||-.+|.+-..+ +.+++.++.|...=.||-..+.+-++
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 56677777777777777777777776
Q ss_pred HHHhhHHH
Q 022333 248 VYRNLLSK 255 (299)
Q Consensus 248 lYrsnLeK 255 (299)
+=|..||+
T Consensus 188 v~rktier 195 (218)
T TIGR02895 188 ISRKTIER 195 (218)
T ss_pred CCHHHHHH
Confidence 66666665
No 40
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=29.97 E-value=1.6e+02 Score=26.04 Aligned_cols=27 Identities=7% Similarity=0.076 Sum_probs=22.4
Q ss_pred CCCHHHHHHHHHhcCCChhhhhhhHHH
Q 022333 222 ATEPTVLEKLCAVLNVNKRSVDRDLDV 248 (299)
Q Consensus 222 ~~d~~~l~~l~~~Lgls~ekv~KDL~l 248 (299)
..+++.|.+++...|++.+++++.++-
T Consensus 120 ~~~~~~L~~~a~~~Gld~~~f~~~l~s 146 (207)
T PRK10954 120 IQSAADIRDVFIKAGVKGEDYDAAWNS 146 (207)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHhC
Confidence 356788999999999999999888754
No 41
>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=29.90 E-value=52 Score=22.35 Aligned_cols=26 Identities=27% Similarity=0.372 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHH
Q 022333 139 REAIFQAYITALKEDPEQYRIDAQKL 164 (299)
Q Consensus 139 ~~~IF~Alc~Alg~Dp~qyR~DA~~l 164 (299)
.+.++.-+++..|.|++++++..++.
T Consensus 26 ~~~~~~~il~~~~id~~~l~~~i~~~ 51 (53)
T PF02861_consen 26 PDSIAARILKKLGIDPEQLKAAIEKA 51 (53)
T ss_dssp TTSHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 45678888999999999999987765
No 42
>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional
Probab=29.86 E-value=4.9e+02 Score=24.68 Aligned_cols=120 Identities=18% Similarity=0.165 Sum_probs=72.5
Q ss_pred ccchhhHHHHHHHhh--cCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHH
Q 022333 116 PVFALGFVTVYDRLM--EGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDI 193 (299)
Q Consensus 116 plFALGlVTvFd~fm--~GY~peed~~~IF~Alc~Alg~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~I 193 (299)
..|...++.+.-.++ .|=-.+.+.+ ++..++..++.++++ |+.|..+-+.++... -++...+..|
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 345555666555555 4666666677 889999999999887 557778777665332 1245566666
Q ss_pred HHHhcCCCCCcchhhHHHHHHHHHhhcCCCC---HHHHHHHHHhcCCChhhhhhhHHHHH
Q 022333 194 AERASGKGNFSYSRFFAVGLFRLLELANATE---PTVLEKLCAVLNVNKRSVDRDLDVYR 250 (299)
Q Consensus 194 a~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d---~~~l~~l~~~Lgls~ekv~KDL~lYr 250 (299)
..... .+..-=+.|=-.|+.+--..|.-+ ...|.++|+.||++..-.++=+.+|.
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 111111112223344333334434 35899999999999877766666544
No 43
>PF08014 DUF1704: Domain of unknown function (DUF1704); InterPro: IPR012548 This family contains many hypothetical proteins.
Probab=28.53 E-value=4.5e+02 Score=26.17 Aligned_cols=152 Identities=20% Similarity=0.291 Sum_probs=107.9
Q ss_pred Hhhhc-ccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHH---HhcCCcccccc
Q 022333 103 QHLMR-YKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEW---ARGQTASSLVE 178 (299)
Q Consensus 103 lHLLs-~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~DA~~l~~~---A~~~s~~~l~~ 178 (299)
.|+++ +|..-|-=+++++| +.||-|.++.=++|.-++. -+.+|..++.-|-+..+. .+|.+-.++-.
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 56666655667777 4899999999999999985 689999999999988775 44556666666
Q ss_pred ccCCc-c-hhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCC-C-------------CHHHHHHHHHhcCCChhhh
Q 022333 179 FPSKE-G-EVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA-T-------------EPTVLEKLCAVLNVNKRSV 242 (299)
Q Consensus 179 ~~~~~-g-~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~-~-------------d~~~l~~l~~~Lgls~ekv 242 (299)
++... | +.+..+ .++.|+.-.+.|.=--+.-.|+..++.--.. . |-..|.+|.+.=.+.+++.
T Consensus 246 ~l~~~y~~~~~~af-~~~~Rv~RGg~FtKD~vYL~G~~~il~~~~~~~~~~~L~~GKvs~~d~~~l~el~~~g~l~~P~~ 324 (349)
T PF08014_consen 246 YLREFYGQDPEDAF-TITVRVFRGGGFTKDQVYLRGLLRILNYLRSGIDLPLLFVGKVSLEDVPRLRELVERGLLRPPKF 324 (349)
T ss_pred HHHHHhCCCHHHHH-HHHHHHHhcCCcchhHHHHHHHHHHHHHHHhccccchhhcccccHHHHHHHHHHHHCCCCCCCCc
Confidence 66554 4 333344 3444665556676556677788888733322 1 2347778888777888998
Q ss_pred hhhHHHHHhhHHHHHHHHHHHH
Q 022333 243 DRDLDVYRNLLSKLLQAKELLK 264 (299)
Q Consensus 243 ~KDL~lYrsnLeKmaQA~elme 264 (299)
--|.-.+-+.|+++-.-.+.|.
T Consensus 325 lp~~~~~~~~l~~~~~~~~~~~ 346 (349)
T PF08014_consen 325 LPPFFRDPEQLEKIMAFSEFLN 346 (349)
T ss_pred CCHHHhchhhHHHHHHHHHHhc
Confidence 8888888888988887766664
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=28.13 E-value=55 Score=25.02 Aligned_cols=43 Identities=21% Similarity=0.230 Sum_probs=31.3
Q ss_pred cchhhHHHHHHHHHhhcCCCC--HHHHHHHHHhcCCChhhhhhhH
Q 022333 204 SYSRFFAVGLFRLLELANATE--PTVLEKLCAVLNVNKRSVDRDL 246 (299)
Q Consensus 204 ~YSRlfAIGLf~LLE~~~~~d--~~~l~~l~~~Lgls~ekv~KDL 246 (299)
++|+-+-.+|--|+.++...+ +-..++|++.+|+|+.-+.|=+
T Consensus 2 ~~s~~~~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil 46 (83)
T PF02082_consen 2 KLSKRTDYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKIL 46 (83)
T ss_dssp ---HHHHHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHH
T ss_pred CCCcHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 478888888888887775543 4689999999999999887755
No 45
>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=27.72 E-value=1.8e+02 Score=24.39 Aligned_cols=126 Identities=24% Similarity=0.322 Sum_probs=65.5
Q ss_pred hHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCC
Q 022333 93 NTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQT 172 (299)
Q Consensus 93 rrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~DA~~l~~~A~~~s 172 (299)
.+.+++|+-+. .+.++.+=|+.=.+.... +.|.+|.+ +|.+++.-.+.+..||+...
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 45665555 78888888888888887654
Q ss_pred ccccccccCCc-chhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHH-h-hcCCCCHHHHHHHHHhcCCChhhhhhhHH
Q 022333 173 ASSLVEFPSKE-GEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLL-E-LANATEPTVLEKLCAVLNVNKRSVDRDLD 247 (299)
Q Consensus 173 ~~~l~~~~~~~-g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LL-E-~~~~~d~~~l~~l~~~Lgls~ekv~KDL~ 247 (299)
.. +. +.... +........+. .+...+ .+.+ +.-.||..+ + ..+..|++.|.++++..|++.+.+++.++
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 345667766 2 22346889999999999999988887764
No 46
>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=27.30 E-value=60 Score=21.47 Aligned_cols=30 Identities=7% Similarity=0.199 Sum_probs=22.9
Q ss_pred HHHHHHHHHhcCCChhhhhhhHHHHHhhHHH
Q 022333 225 PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSK 255 (299)
Q Consensus 225 ~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeK 255 (299)
++.+++|.+. ||+.+.+.+=|..-.+++++
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 99999999888777776654
No 47
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=26.91 E-value=75 Score=27.44 Aligned_cols=78 Identities=22% Similarity=0.325 Sum_probs=58.0
Q ss_pred CCchhHHHHHHHHHHhcCC---------CHHHHHHHHHHHHHHHhcCCccc---cccccCCcchhHHHHHHHHHHhcCCC
Q 022333 134 PSEEDREAIFQAYITALKE---------DPEQYRIDAQKLEEWARGQTASS---LVEFPSKEGEVEGLLKDIAERASGKG 201 (299)
Q Consensus 134 ~peed~~~IF~Alc~Alg~---------Dp~qyR~DA~~l~~~A~~~s~~~---l~~~~~~~g~~~~~l~~Ia~~~~~n~ 201 (299)
++..||.+++..|..+|=. -+..+|.-+++|.-+|+.-+... ...|+-+...++.++..|+.+-.+.+
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 3568999999998887643 46889999999999999887763 34466666678888899987665333
Q ss_pred CCcchhhHHHH
Q 022333 202 NFSYSRFFAVG 212 (299)
Q Consensus 202 ~F~YSRlfAIG 212 (299)
=-|+|++=+|
T Consensus 92 -GGYtRIlK~g 101 (116)
T COG0203 92 -GGYTRILKLG 101 (116)
T ss_pred -CCeeEEEecC
Confidence 3688876544
No 48
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=25.86 E-value=2.3e+02 Score=20.32 Aligned_cols=49 Identities=12% Similarity=0.241 Sum_probs=29.7
Q ss_pred hhHHHHHHHHHhhcCCCC-HHHHHHHHHhcCCChhhhhhhHHHHHhhHHH
Q 022333 207 RFFAVGLFRLLELANATE-PTVLEKLCAVLNVNKRSVDRDLDVYRNLLSK 255 (299)
Q Consensus 207 RlfAIGLf~LLE~~~~~d-~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeK 255 (299)
++-.+|-+-+--..+..+ .+.++.|++..+.+++.+++|+.-|-..|.+
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 455555443333345544 5689999999999999999999877665543
No 49
>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=25.45 E-value=2.8e+02 Score=24.35 Aligned_cols=70 Identities=23% Similarity=0.317 Sum_probs=43.1
Q ss_pred cchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCh---hhhhhhHHHHHhhHHHHH
Q 022333 183 EGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNK---RSVDRDLDVYRNLLSKLL 257 (299)
Q Consensus 183 ~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~---ekv~KDL~lYrsnLeKma 257 (299)
.-++..+|..++++.+.+-+|.-| -|=|+.||.+ ....+.=++|++.||++. +.....+-|.|-++.||+
T Consensus 48 ~VDV~avL~~~a~~~~~~LnWrtS---IVDLlKlLgl--DSSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm~kLA 120 (127)
T PF12200_consen 48 QVDVAAVLDALAAKNGQKLNWRTS---IVDLLKLLGL--DSSLAARKELAKELGYTGDYNDSASMNIWLHKQVMQKLA 120 (127)
T ss_dssp SEE-HHHHHHHHHHHSS---TTT----HHHHHHHT------SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHHHHHG
T ss_pred cccHHHHHHHHHHhcccccccHHH---HHHHHHHcCC--CCCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHH
Confidence 347889999998776555555443 3455555522 235678899999999977 567777888888888876
No 50
>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=25.26 E-value=62 Score=26.62 Aligned_cols=58 Identities=22% Similarity=0.334 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHH
Q 022333 154 PEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVG 212 (299)
Q Consensus 154 p~qyR~DA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIG 212 (299)
+.++|.-|++|..+|+..+.. .+..|+..+.-+..++..|+.+-+ +.+--|+|++-+|
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 578899999999999976544 566777755568888899998886 4556899886544
No 51
>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=24.88 E-value=1.5e+02 Score=27.36 Aligned_cols=77 Identities=21% Similarity=0.260 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCC-HHHHHHHH
Q 022333 154 PEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATE-PTVLEKLC 232 (299)
Q Consensus 154 p~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d-~~~l~~l~ 232 (299)
.++|.+-|+.|.+-++|+..-.. +..|+.+- +.+.|++-+.|.=-=-.|...||..+..| -+.|.+++
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 GEKYKKLAKELAEDAKGKKIRSV----------DDALKSFE-KYKSNLNKKINAKDRDAIVNALESVDAKDMAKNLAKFS 99 (187)
T ss_dssp -HHHHHHHHHHHHHHHTGC---H----------HHHHHHHH-HHHTHTTCSS-HHHHHHHHHHHHT--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhcccccCCH----------HHHHHHHH-HHHhchhhhhhhccHHHHHHHHHHcCHHHHHHHHHHHH
Confidence 46888999999999998886543 33555442 44557777777777777888888776655 45788999
Q ss_pred HhcCCChhh
Q 022333 233 AVLNVNKRS 241 (299)
Q Consensus 233 ~~Lgls~ek 241 (299)
..+|+-..-
T Consensus 100 K~fg~~~~~ 108 (187)
T PF01024_consen 100 KAFGITGKA 108 (187)
T ss_dssp GGGTSTTHH
T ss_pred HHhcchHHH
Confidence 999886543
No 52
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=24.74 E-value=85 Score=23.51 Aligned_cols=37 Identities=22% Similarity=0.307 Sum_probs=25.8
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHhcCCChhhhhhhHHHH
Q 022333 211 VGLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLDVY 249 (299)
Q Consensus 211 IGLf~LLE~~~~~d~~~l~~l~~~Lgls~ekv~KDL~lY 249 (299)
+.++.+|.. ...+-.+.+|++.+|++...|.++|...
T Consensus 8 ~~Il~~l~~--~~~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 8 LAVLRALAE--EPGGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred HHHHHHHHh--CCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 344555522 2245678899999999999999988543
No 53
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=24.33 E-value=2e+02 Score=20.20 Aligned_cols=39 Identities=26% Similarity=0.370 Sum_probs=22.6
Q ss_pred HHHHHHHhcCCChhhhhhhHHHHHh-------hHHHHHHHHHHHHH
Q 022333 227 VLEKLCAVLNVNKRSVDRDLDVYRN-------LLSKLLQAKELLKE 265 (299)
Q Consensus 227 ~l~~l~~~Lgls~ekv~KDL~lYrs-------nLeKmaQA~elmeE 265 (299)
.+++|++.+|++...+.+=+.-..+ +..+|.+|.+.|.+
T Consensus 3 ~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~~r~~~a~~~l~~ 48 (84)
T smart00342 3 TLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRD 48 (84)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHc
Confidence 4677778888887777665543321 23355555555543
No 54
>COG3867 Arabinogalactan endo-1,4-beta-galactosidase [Carbohydrate transport and metabolism]
Probab=24.27 E-value=1.4e+02 Score=30.26 Aligned_cols=114 Identities=22% Similarity=0.323 Sum_probs=63.0
Q ss_pred cccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHhcC---CCHHHHHHHHHHHHHHHhcCCccccccccC----------
Q 022333 115 DPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALK---EDPEQYRIDAQKLEEWARGQTASSLVEFPS---------- 181 (299)
Q Consensus 115 DplFALGlVTvFd~fm~GY~peed~~~IF~Alc~Alg---~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~~---------- 181 (299)
.|+|---+-++=+.|++|= |...|. +| .-.| +|..-.|+||-++++. .|.+---|.-|..
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-ENSGVKFFDTNGVRQDALQILKN-HGVNYVRLRVWNDPYDSNGNGYG 97 (403)
T ss_pred ccceeeeccCChHHhhccc----cHHHHH-HH-HHcCceEEccCChHHHHHHHHHH-cCcCeEEEEEecCCccCCCCccC
Confidence 3444444444556666664 233322 22 2223 6777889999888873 3444444555554
Q ss_pred -CcchhHHHHHHHHHHhcCCC-----CCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhcCCChhhhhhhHHHH
Q 022333 182 -KEGEVEGLLKDIAERASGKG-----NFSYSRFFAVGLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLDVY 249 (299)
Q Consensus 182 -~~g~~~~~l~~Ia~~~~~n~-----~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~ekv~KDL~lY 249 (299)
+.++++.. -.||+|++.++ .||||-++| ||.-..+=.++-+++.+-+++++--|
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 11133333 35788888776 699999986 22222222233456677777776444
No 55
>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=24.11 E-value=2.1e+02 Score=20.30 Aligned_cols=36 Identities=25% Similarity=0.327 Sum_probs=24.9
Q ss_pred HHHHHHhhcCCCCchhHHHHHHHHHHhcCCCHHHHHH
Q 022333 123 VTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRI 159 (299)
Q Consensus 123 VTvFd~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR~ 159 (299)
-.+.=+||.+=. ...++.+..++-.-++|+|++.+.
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 356889999999999999998875
No 56
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=23.98 E-value=1.7e+02 Score=22.26 Aligned_cols=55 Identities=29% Similarity=0.389 Sum_probs=34.5
Q ss_pred hHHHHHHHHHhhcCCCCHHHHHHHHHhcCCChhhhhhhHH-HHHhhHH------HHHHHHHHHH
Q 022333 208 FFAVGLFRLLELANATEPTVLEKLCAVLNVNKRSVDRDLD-VYRNLLS------KLLQAKELLK 264 (299)
Q Consensus 208 lfAIGLf~LLE~~~~~d~~~l~~l~~~Lgls~ekv~KDL~-lYrsnLe------KmaQA~elme 264 (299)
.+. -+..+|.. ...++..+++++..+|+|...+.+=.. .+--..- +|.+|+.++.
T Consensus 21 ~~~-~~~~~i~~-~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~~~~~~~Rl~~A~~lL~ 82 (127)
T COG2207 21 RLA-RALDYIEE-NLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPSQYLRQLRLEEARRLLR 82 (127)
T ss_pred HHH-HHHHHHHH-HhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 344 55556654 455567888889999999888887765 2222221 5566666554
No 57
>PF12597 DUF3767: Protein of unknown function (DUF3767); InterPro: IPR022533 This group of proteins includes mitochodrial cytochrome c oxidase proteins [], and some transmembrane domain-containing proteins of unknown function known as FAM36A. Proteins in this family are typically between 112 and 199 amino acids in length.
Probab=23.61 E-value=1.1e+02 Score=26.05 Aligned_cols=89 Identities=20% Similarity=0.143 Sum_probs=45.3
Q ss_pred HHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCC---CHH----HHHHHHHhc
Q 022333 163 KLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANAT---EPT----VLEKLCAVL 235 (299)
Q Consensus 163 ~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~---d~~----~l~~l~~~L 235 (299)
.+.+.+++.+.+|+..+..-.=-=++.|..|+. -++||+.+.|--.+.. +-. .+-.|+-+.
T Consensus 18 t~~~A~ksi~~~df~~~~~iPCfR~slL~Gi~~------------G~~vG~~~fl~~~~~~~A~nwavgsF~l~s~~~we 85 (118)
T PF12597_consen 18 TLSDAVKSIKLSDFRNVHKIPCFRDSLLYGIAG------------GFGVGGLRFLFTSNPRKAANWAVGSFFLGSLGSWE 85 (118)
T ss_pred cHHHHHHhcCHHHHhHHhcCCcHHHHHHHHHHH------------HHHHHhhhhcccCCCccchhhhhHHHHHHHHHHHH
Confidence 556666777777665443321123456666653 2578888887333321 211 222222211
Q ss_pred CCChhhhhhhHHHHHhhHHHHHHHHHHHHHHHHHHh
Q 022333 236 NVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREK 271 (299)
Q Consensus 236 gls~ekv~KDL~lYrsnLeKmaQA~elmeE~~~~EK 271 (299)
--.. .++....+|.+|+|+|++-...+.
T Consensus 86 ~Cr~--------~r~~~~~~~~~~~e~~~~k~~~~~ 113 (118)
T PF12597_consen 86 YCRY--------NRRKERQQMKRAVEAMQEKKRKKE 113 (118)
T ss_pred HHHH--------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1110 156666777777777776544444
No 58
>KOG1258 consensus mRNA processing protein [RNA processing and modification]
Probab=23.33 E-value=2.1e+02 Score=30.67 Aligned_cols=123 Identities=20% Similarity=0.214 Sum_probs=72.6
Q ss_pred CchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHhc
Q 022333 71 PTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITAL 150 (299)
Q Consensus 71 ~TVSDTKr~F~~~y~rPIpsIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc~Al 150 (299)
-+....=..|...||.. -+.|++..+ +.|.=-=+=-.+-||++=.+|.|=--++=.=+-+.|..+
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 34444455677777654 345666654 333221222347789999999986666666678888899
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCcc------ccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHH
Q 022333 151 KEDPEQYRIDAQKLEEWARGQTAS------SLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFA 210 (299)
Q Consensus 151 g~Dp~qyR~DA~~l~~~A~~~s~~------~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfA 210 (299)
++||+.+|.--+.-.+.+. ..-- -.++|.... ....-+..|-+++..+|.++|+|+|.
T Consensus 127 ~~d~~~lr~~fe~A~~~vG-~dF~S~~lWdkyie~en~q-ks~k~v~~iyeRileiP~~~~~~~f~ 190 (577)
T KOG1258|consen 127 NGDPETLRDLFERAKSYVG-LDFLSDPLWDKYIEFENGQ-KSWKRVANIYERILEIPLHQLNRHFD 190 (577)
T ss_pred CCCHHHHHHHHHHHHHhcc-cchhccHHHHHHHHHHhcc-ccHHHHHHHHHHHHhhhhhHhHHHHH
Confidence 9999998876655555433 1110 011111111 12223334445666699999999986
No 59
>PRK08307 stage III sporulation protein SpoAB; Provisional
Probab=23.32 E-value=5.2e+02 Score=22.83 Aligned_cols=71 Identities=10% Similarity=0.115 Sum_probs=37.6
Q ss_pred hhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCC--CCHHHHHHHHHhcCCCh-hhhhhhHHHHHhhHHH
Q 022333 185 EVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA--TEPTVLEKLCAVLNVNK-RSVDRDLDVYRNLLSK 255 (299)
Q Consensus 185 ~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~--~d~~~l~~l~~~Lgls~-ekv~KDL~lYrsnLeK 255 (299)
.....+..++++...++.-...-.|--.+=......+= .|-+.+.++...||.+. +-=.|=+++|..+|+.
T Consensus 66 ~~~~~f~~~a~~L~~~~g~s~~eaw~~~~~~~~~~~~L~~~d~eiL~~lg~~LG~~D~e~Q~k~i~L~~e~L~~ 139 (171)
T PRK08307 66 PISTLFQRFSERLESGEGETAYEAWEKALEENWKNTALKKEDIEILLQFGKTLGQSDREGQQKHIRLALEHLER 139 (171)
T ss_pred hHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhhccCCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHHHH
Confidence 34444455554443333334444444444333322211 24568888889999764 4445667777766654
No 60
>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=23.24 E-value=82 Score=27.06 Aligned_cols=32 Identities=9% Similarity=0.202 Sum_probs=18.8
Q ss_pred cccchhhHHHHHHHhhcCCCCc--hhHHHHHHHHH
Q 022333 115 DPVFALGFVTVYDRLMEGYPSE--EDREAIFQAYI 147 (299)
Q Consensus 115 DplFALGlVTvFd~fm~GY~pe--ed~~~IF~Alc 147 (299)
..+|++| ++.|.-+..|.+|- .+...+.+++.
T Consensus 185 ~Di~slG-~il~~l~t~g~~p~~~~~~~~~~~~~~ 218 (261)
T cd05034 185 SDVWSFG-ILLTEIVTYGRVPYPGMTNREVLEQVE 218 (261)
T ss_pred hHHHHHH-HHHHHHHhCCCCCCCCCCHHHHHHHHH
Confidence 4699999 45566666677763 22334444443
No 61
>PF13446 RPT: A repeated domain in UCH-protein
Probab=23.15 E-value=1.4e+02 Score=21.81 Aligned_cols=47 Identities=21% Similarity=0.336 Sum_probs=33.9
Q ss_pred CCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCcccccccc
Q 022333 134 PSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFP 180 (299)
Q Consensus 134 ~peed~~~IF~Alc~Alg~Dp~qyR~DA~~l~~~A~~~s~~~l~~~~ 180 (299)
+|.-+=+.|-.++-..+..||.+.+.--++|...|.......|..|+
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 44445556666666666699999988888888888877776666654
No 62
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=23.00 E-value=5.5e+02 Score=23.41 Aligned_cols=30 Identities=10% Similarity=0.183 Sum_probs=21.6
Q ss_pred HHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHH
Q 022333 226 TVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQ 258 (299)
Q Consensus 226 ~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQ 258 (299)
..+++|++.||++..+|.+= .+..|.||.+
T Consensus 226 ~t~~eIA~~lgis~~~V~~~---~~~al~kLr~ 255 (258)
T PRK08215 226 KTQMEVAEEIGISQAQVSRL---EKAALKHMRK 255 (258)
T ss_pred CCHHHHHHHHCcCHHHHHHH---HHHHHHHHHH
Confidence 37889999999999999653 3445555543
No 63
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=22.98 E-value=5e+02 Score=22.48 Aligned_cols=29 Identities=31% Similarity=0.559 Sum_probs=18.8
Q ss_pred HHHHHHHHhcCCCCC-cchhhHHHHHHHHHh
Q 022333 189 LLKDIAERASGKGNF-SYSRFFAVGLFRLLE 218 (299)
Q Consensus 189 ~l~~Ia~~~~~n~~F-~YSRlfAIGLf~LLE 218 (299)
+|..+.+..-+++++ +|=||+ +||+-++=
T Consensus 5 ll~~~ie~LlP~~~~kkYvr~v-~GLili~~ 34 (188)
T PF09581_consen 5 LLATFIEMLLPNSKYKKYVRFV-LGLILILA 34 (188)
T ss_pred HHHHHHHHhCCchhHHHHHHHH-HHHHHHHH
Confidence 344555555556666 788865 78888773
No 64
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=22.91 E-value=4.4e+02 Score=22.36 Aligned_cols=28 Identities=14% Similarity=0.241 Sum_probs=22.5
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHhcCCC
Q 022333 211 VGLFRLLELANATEPTVLEKLCAVLNVN 238 (299)
Q Consensus 211 IGLf~LLE~~~~~d~~~l~~l~~~Lgls 238 (299)
=|||+-|.-.|+.....+-+++.+||+.
T Consensus 64 e~LYkaLS~~GNPtf~Til~V~kAlG~r 91 (100)
T COG3636 64 EGLYKALSPGGNPTFDTILAVLKALGLR 91 (100)
T ss_pred HHHHHHhCCCCCCcHHHHHHHHHHcCce
Confidence 4899999666666777888999999974
No 65
>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=22.73 E-value=2.1e+02 Score=21.79 Aligned_cols=43 Identities=26% Similarity=0.364 Sum_probs=28.3
Q ss_pred HHHHHhhcCC-CCHHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHH
Q 022333 213 LFRLLELANA-TEPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLL 257 (299)
Q Consensus 213 Lf~LLE~~~~-~d~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKma 257 (299)
.-.||...+. +....+.+|...|..-.+-++.|. ||+.||-+.
T Consensus 11 v~ell~~g~~vsnKaII~~LI~~LE~e~Dv~~~dv--yR~~LEiVv 54 (61)
T PF10798_consen 11 VRELLASGGHVSNKAIILKLIHRLESESDVVQLDV--YRNALEIVV 54 (61)
T ss_dssp HHHHHHTT---SHHHHHHHHHHHHHT---HHHHHH--HHHHHHHHH
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHHhccccHHHHHH--HHHHHHHHH
Confidence 3445543333 456789999999999889888877 999998764
No 66
>smart00219 TyrKc Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
Probab=21.84 E-value=1.2e+02 Score=25.71 Aligned_cols=22 Identities=14% Similarity=0.375 Sum_probs=15.3
Q ss_pred cccchhhHHHHHHHhhcCCCCch
Q 022333 115 DPVFALGFVTVYDRLMEGYPSEE 137 (299)
Q Consensus 115 DplFALGlVTvFd~fm~GY~pee 137 (299)
..+|+||++ .|..+..|++|-+
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 4555666888743
No 67
>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=21.73 E-value=61 Score=25.85 Aligned_cols=23 Identities=22% Similarity=0.414 Sum_probs=20.6
Q ss_pred HHHHHHHHhcCCChhhhhhhHHH
Q 022333 226 TVLEKLCAVLNVNKRSVDRDLDV 248 (299)
Q Consensus 226 ~~l~~l~~~Lgls~ekv~KDL~l 248 (299)
-.+++|++.+|+|...|.+||.-
T Consensus 20 ~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 20 ATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCHHHHHHHhCCCHHHHHHHhcC
Confidence 36999999999999999999954
No 68
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=21.70 E-value=1.1e+02 Score=22.39 Aligned_cols=34 Identities=21% Similarity=0.351 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHhc----CCChhhhhhhHHHHHhhHHHH
Q 022333 223 TEPTVLEKLCAVL----NVNKRSVDRDLDVYRNLLSKL 256 (299)
Q Consensus 223 ~d~~~l~~l~~~L----gls~ekv~KDL~lYrsnLeKm 256 (299)
.+|+.+++|..+| |....++.++|+-++..+.++
T Consensus 5 ~~~e~ld~L~~aL~~prG~RE~~L~~~L~~~~k~~~~~ 42 (46)
T PF15614_consen 5 DDPEELDELLKALENPRGKRESKLKKELDKHRKGPLEI 42 (46)
T ss_pred cCHHHHHHHHHHHcCcccHhHHHHHHHHHHHhcchhhh
Confidence 3577888888888 788899999999888555443
No 69
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 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 [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=21.30 E-value=1.8e+02 Score=26.00 Aligned_cols=40 Identities=15% Similarity=0.027 Sum_probs=24.7
Q ss_pred HHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHH
Q 022333 226 TVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKE 265 (299)
Q Consensus 226 ~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE 265 (299)
....+|++.+|.|.-.|.-=...=+.-.++|++..|.+++
T Consensus 105 wTr~~LAkkF~~S~~fV~~v~~~~~e~~~~~~~~le~~k~ 144 (164)
T PF12824_consen 105 WTRKKLAKKFNCSPLFVSMVAPAPKEKKKEMEARLEAIKS 144 (164)
T ss_pred hhHHHHHHHhCCCHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence 4678888888888777654443333445555555555554
No 70
>PF14075 UBN_AB: Ubinuclein conserved middle domain
Probab=20.73 E-value=6.9e+02 Score=23.25 Aligned_cols=104 Identities=21% Similarity=0.246 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHH
Q 022333 154 PEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKLCA 233 (299)
Q Consensus 154 p~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l~~ 233 (299)
|..+.+....|.+.|+..+...=..|+ ..+++.+|=.|..... ..++=.=.++|.-|+..=+-...+|-+.+.
T Consensus 6 p~~l~~~I~~l~~~a~~~~~~gK~kff--~~~vn~lLL~ie~~~~-----~~~~~~R~~vy~hL~~~lPc~K~tL~kr~K 78 (214)
T PF14075_consen 6 PADLEERINDLKEAAKSSDGEGKKKFF--TSEVNPLLLDIELQCR-----ELNPSVRSAVYSHLESFLPCNKDTLLKRAK 78 (214)
T ss_pred CHHHHHHHHHHHHHHHhcCcCcccccC--CHHHHHHHHHHHHHHH-----HcCchhhHHHHHHHHHHCCCCHHHHHHHHH
Confidence 677888999999999866655444443 3468888877765442 344445578888886665545556666667
Q ss_pred hcCCChhhhhhhHHHHHhhHHHHHHHH-HHHHHHHHH
Q 022333 234 VLNVNKRSVDRDLDVYRNLLSKLLQAK-ELLKEYVDR 269 (299)
Q Consensus 234 ~Lgls~ekv~KDL~lYrsnLeKmaQA~-elmeE~~~~ 269 (299)
.|.+.. .+.+ -+.-|+||.+|. ++|.+.+++
T Consensus 79 kL~~~~--~~~~---l~e~L~KLk~aI~~~MP~q~~~ 110 (214)
T PF14075_consen 79 KLRLKE--QDDR---LKEPLQKLKEAIDRVMPEQIAK 110 (214)
T ss_pred HHHHHH--Hhhh---HHHHHHHHHHHHHHHHHHHHHH
Confidence 776544 3443 478899998886 355555544
No 71
>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=20.69 E-value=1e+02 Score=30.79 Aligned_cols=32 Identities=25% Similarity=0.432 Sum_probs=28.6
Q ss_pred CCCchhHHHHHHHHHH-hcCCCHHHHHHHHHHH
Q 022333 133 YPSEEDREAIFQAYIT-ALKEDPEQYRIDAQKL 164 (299)
Q Consensus 133 Y~peed~~~IF~Alc~-Alg~Dp~qyR~DA~~l 164 (299)
|.|.++|-+.|+|++. .++..|.+|.+.|+.-
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 5899999999998663
No 72
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=20.60 E-value=1.3e+02 Score=24.07 Aligned_cols=55 Identities=24% Similarity=0.207 Sum_probs=28.5
Q ss_pred HHHHhcCCChhhhhhhHHHHHhhHHHHHHHHHHHHHHHHHHhhhHHhhcccccchHHHHhh
Q 022333 230 KLCAVLNVNKRSVDRDLDVYRNLLSKLLQAKELLKEYVDREKKKREERTEPQKANEAIKKC 290 (299)
Q Consensus 230 ~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~elmeE~~~~EKKKreeR~~~~ka~~~~~~~ 290 (299)
+|+..||+|...+++=-.=|.++ --+|+.+++..-..++.+.- ..+.--.|+++|
T Consensus 20 ~Lar~L~vs~~dI~~I~~e~p~~--l~~Q~~~~L~~W~~r~g~~A----t~~~L~~AL~~i 74 (84)
T cd08805 20 ELARELQFSVEDINRIRVENPNS--LLEQSTALLNLWVDREGENA----KMSPLYPALYSI 74 (84)
T ss_pred HHHHHcCCCHHHHHHHHHhCCCC--HHHHHHHHHHHHHHhcCccc----hHHHHHHHHHHC
Confidence 34444455544333322222322 34789999998888776322 222344566665
No 73
>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]
Probab=20.50 E-value=53 Score=33.05 Aligned_cols=47 Identities=36% Similarity=0.441 Sum_probs=26.8
Q ss_pred cchhhHHHHHHHHHhhcCCC--CH--HHHHHHHHhcCCChhhhhhhHHHHHhhHHHH
Q 022333 204 SYSRFFAVGLFRLLELANAT--EP--TVLEKLCAVLNVNKRSVDRDLDVYRNLLSKL 256 (299)
Q Consensus 204 ~YSRlfAIGLf~LLE~~~~~--d~--~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKm 256 (299)
+=|=+-+|..|.==.--+-. |. .+|+.+.+- -|+|||++|+.+|.-|
T Consensus 67 K~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~ey------GVerDl~vYk~Llnvf 117 (406)
T KOG3941|consen 67 KDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEY------GVERDLDVYKGLLNVF 117 (406)
T ss_pred HHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHh------cchhhHHHHHHHHHhC
Confidence 45555666655422111222 21 245555432 4899999999999754
No 74
>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=20.39 E-value=6.1e+02 Score=22.49 Aligned_cols=49 Identities=12% Similarity=0.106 Sum_probs=37.0
Q ss_pred HHHHHHhhc-C-CCCHHHHHHHHHhcCCChhhhhhhHHHHHhhHHHHHHHH
Q 022333 212 GLFRLLELA-N-ATEPTVLEKLCAVLNVNKRSVDRDLDVYRNLLSKLLQAK 260 (299)
Q Consensus 212 GLf~LLE~~-~-~~d~~~l~~l~~~Lgls~ekv~KDL~lYrsnLeKmaQA~ 260 (299)
++..+|+.+ . ..+|+.+..--+.+|+++++++--...|..+.+.+..+.
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 445566543 2 346777666669999999999999999999988776665
No 75
>PRK15044 transcriptional regulator SirC; Provisional
Probab=20.37 E-value=8.3e+02 Score=24.06 Aligned_cols=131 Identities=12% Similarity=0.153 Sum_probs=67.7
Q ss_pred hHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHhhcCCCCchhHHHHHHHHHHhcCCC
Q 022333 74 AETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKED 153 (299)
Q Consensus 74 SDTKr~F~~~y~rPIpsIYrrvv~ELLVElHLLs~n~~F~YDplFALGlVTvFd~fm~GY~peed~~~IF~Alc~Alg~D 153 (299)
+|.-.+||+-|..-=+-+.+ .+-.-...+.|.+.|| .=+.-.||+++|.+-..++ +|+-+-.+
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 0011134555666666 4577889999999654433 55555555
Q ss_pred HHHHHHH--HHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHH
Q 022333 154 PEQYRID--AQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKL 231 (299)
Q Consensus 154 p~qyR~D--A~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~~~~~d~~~l~~l 231 (299)
.+.|.-- ---|.. ++.+. +....+..... ++.. -.+...++ .+..++..+++|
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 5544320 011111 11111 11222222111 1111 12344443 223567899999
Q ss_pred HHhcCCChhhhhhhH
Q 022333 232 CAVLNVNKRSVDRDL 246 (299)
Q Consensus 232 ~~~Lgls~ekv~KDL 246 (299)
|+.+|+|...+.|=+
T Consensus 215 A~~lgmS~~tL~R~F 229 (295)
T PRK15044 215 AGKLFMSVSSLKRKL 229 (295)
T ss_pred HHHhCCCHHHHHHHH
Confidence 999999999998744
No 76
>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=20.30 E-value=75 Score=26.49 Aligned_cols=31 Identities=13% Similarity=0.175 Sum_probs=24.3
Q ss_pred HhhcCCCCchhHHHHHHHHHHhcCCCHHHHH
Q 022333 128 RLMEGYPSEEDREAIFQAYITALKEDPEQYR 158 (299)
Q Consensus 128 ~fm~GY~peed~~~IF~Alc~Alg~Dp~qyR 158 (299)
+-=..-+..+||..||+=||..+|++|+.-.
T Consensus 13 ~AE~AI~dsd~R~~llqEm~~gLg~~p~ag~ 43 (93)
T PF07216_consen 13 QAELAIRDSDHRNDLLQEMLEGLGLGPVAGE 43 (93)
T ss_pred HHHHHHHhhHHHHHHHHHHHHhcCCChhHHH
Confidence 3334456679999999999999999997543
Done!