Query 025486
Match_columns 252
No_of_seqs 80 out of 82
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 06:20:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025486.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025486hhsearch_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 7.8E-86 1.7E-90 600.6 18.9 222 1-237 1-222 (283)
2 PLN03060 inositol phosphatase- 100.0 7.8E-75 1.7E-79 509.9 16.3 170 70-243 2-171 (206)
3 PRK13266 Thf1-like protein; Re 100.0 2.2E-74 4.7E-79 512.6 16.8 176 68-244 2-182 (225)
4 TIGR03060 PS_II_psb29 photosys 100.0 3.2E-74 7E-79 508.4 15.8 173 68-244 2-180 (214)
5 PF11264 ThylakoidFormat: Thyl 100.0 1.4E-73 3.1E-78 504.7 15.9 173 72-244 1-177 (216)
6 PF11264 ThylakoidFormat: Thyl 94.7 0.041 8.9E-07 49.9 4.4 57 106-162 127-184 (216)
7 PRK13266 Thf1-like protein; Re 94.6 0.066 1.4E-06 48.9 5.5 63 99-161 125-188 (225)
8 TIGR03060 PS_II_psb29 photosys 94.3 0.055 1.2E-06 49.1 4.2 58 103-161 127-186 (214)
9 PLN03060 inositol phosphatase- 91.3 0.2 4.3E-06 45.3 3.3 49 107-161 130-178 (206)
10 PLN00047 photosystem II biogen 89.3 0.36 7.9E-06 45.6 3.3 48 108-161 184-231 (283)
11 TIGR00059 L17 ribosomal protei 60.8 16 0.00034 30.3 4.4 77 135-212 8-96 (112)
12 COG2206 c-di-GMP phosphodieste 59.2 89 0.0019 29.5 9.6 83 69-151 103-187 (344)
13 PRK10880 adenine DNA glycosyla 56.6 1.6E+02 0.0034 28.6 11.0 109 73-194 6-126 (350)
14 PF13170 DUF4003: Protein of u 55.5 61 0.0013 30.4 7.8 117 123-242 123-254 (297)
15 PF08542 Rep_fac_C: Replicatio 52.7 19 0.00042 26.6 3.4 42 132-178 1-42 (89)
16 PRK05591 rplQ 50S ribosomal pr 52.5 21 0.00045 29.6 3.8 77 135-212 10-98 (113)
17 PF01841 Transglut_core: Trans 47.6 10 0.00022 28.4 1.2 46 109-154 26-72 (113)
18 TIGR02147 Fsuc_second hypothet 46.1 88 0.0019 29.2 7.3 134 92-233 10-148 (271)
19 PRK13910 DNA glycosylase MutY; 46.1 2.6E+02 0.0057 26.4 10.5 71 124-194 13-89 (289)
20 TIGR01084 mutY A/G-specific ad 44.8 2.6E+02 0.0057 26.0 12.7 127 75-218 4-142 (275)
21 cd00192 PTKc Catalytic domain 40.6 36 0.00079 27.8 3.5 32 115-147 188-221 (262)
22 PF02861 Clp_N: Clp amino term 39.5 29 0.00063 23.0 2.3 27 138-164 25-51 (53)
23 COG4476 Uncharacterized protei 38.7 1.4E+02 0.003 24.2 6.3 82 83-166 2-83 (90)
24 COG3793 TerB Tellurite resista 36.5 1E+02 0.0022 26.9 5.7 36 137-172 65-100 (144)
25 PF13413 HTH_25: Helix-turn-he 36.3 49 0.0011 24.1 3.3 27 131-157 36-62 (62)
26 PF01196 Ribosomal_L17: Riboso 36.1 32 0.0007 27.6 2.5 58 154-212 22-82 (97)
27 COG0203 RplQ Ribosomal protein 33.8 51 0.0011 27.8 3.4 78 134-212 12-101 (116)
28 PF13446 RPT: A repeated domai 33.8 71 0.0015 22.7 3.7 47 134-180 14-60 (62)
29 cd05034 PTKc_Src_like Catalyti 31.8 47 0.001 27.7 2.9 20 115-135 185-204 (261)
30 PF01465 GRIP: GRIP domain; I 31.1 1.4E+02 0.0031 20.7 4.8 36 123-159 9-44 (46)
31 smart00219 TyrKc Tyrosine kina 30.4 68 0.0015 26.3 3.6 22 115-137 185-206 (258)
32 PF12069 DUF3549: Protein of u 30.0 57 0.0012 31.8 3.5 34 132-165 121-155 (340)
33 KOG1258 mRNA processing protei 30.0 1.5E+02 0.0031 31.1 6.5 124 71-210 62-190 (577)
34 PF05402 PqqD: Coenzyme PQQ sy 28.8 1.4E+02 0.003 21.0 4.5 42 124-169 21-62 (68)
35 cd05056 PTKc_FAK Catalytic dom 27.8 77 0.0017 26.7 3.6 20 115-135 189-208 (270)
36 cd05058 PTKc_Met_Ron Catalytic 26.3 1.7E+02 0.0036 24.4 5.3 21 115-136 183-203 (262)
37 PF09494 Slx4: Slx4 endonuclea 25.2 41 0.0009 24.5 1.3 28 142-169 1-35 (64)
38 PF06971 Put_DNA-bind_N: Putat 25.1 66 0.0014 23.0 2.3 16 145-160 33-48 (50)
39 PF08542 Rep_fac_C: Replicatio 24.8 1.8E+02 0.0038 21.4 4.6 44 121-165 23-66 (89)
40 PHA00666 putative protease 24.2 6E+02 0.013 23.9 10.8 32 131-162 93-124 (233)
41 PF07216 LcrG: LcrG protein; 24.1 59 0.0013 26.5 2.0 31 127-157 12-42 (93)
42 COG4867 Uncharacterized protei 24.0 1.3E+02 0.0029 31.1 4.9 44 162-210 192-244 (652)
43 PF01024 Colicin: Colicin pore 22.3 1.9E+02 0.0041 26.2 5.0 75 154-242 31-105 (187)
44 PF07268 EppA_BapA: Exported p 22.1 1.5E+02 0.0032 25.8 4.2 34 124-163 87-124 (139)
45 cd05043 PTK_Ryk Pseudokinase d 21.8 1.4E+02 0.0031 25.2 4.1 20 115-135 200-219 (280)
46 KOG4509 Uncharacterized conser 21.7 71 0.0015 29.5 2.3 50 175-225 75-124 (247)
47 TIGR00244 transcriptional regu 21.2 4.5E+02 0.0098 23.0 7.0 73 131-211 55-130 (147)
48 PF13443 HTH_26: Cro/C1-type H 20.2 1.3E+02 0.0028 20.6 3.0 33 124-157 25-57 (63)
49 PTZ00076 60S ribosomal protein 20.2 1E+02 0.0022 29.1 3.1 77 135-212 25-113 (253)
No 1
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=100.00 E-value=7.8e-86 Score=600.65 Aligned_cols=222 Identities=69% Similarity=1.075 Sum_probs=205.2
Q ss_pred CCccccccccccccccccccccccccccccccccccccccccceeeeeeeecCCCcceeeeeeccCCCCCCchhHhHHHH
Q 025486 1 MASLTSVAFTSIGQTSCQRKVNVSSTRSLVSNFEGFRFRTSLFCHCVRFRASSSSSRMIIQCMSTATDVPPTVAETKMNF 80 (252)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~TVSDTKr~F 80 (252)
|||++|++|++++|++ +++.+ .++|+++ ++|+|+ ||++++ +|+||+||+++++++||||||||+|
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 3447765 667776 666654 5999999999999999999999999
Q ss_pred HhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHH
Q 025486 81 LKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRID 160 (252)
Q Consensus 81 ~~~y~rPIpsIYRrvv~ELLVElHLLs~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~IF~Alc~Alg~DP~qyR~D 160 (252)
|++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||+|+|+||+|||+|
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 HHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhhhh
Q 025486 161 AQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKVRSTFFD 237 (252)
Q Consensus 161 A~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~a~~~dp~~L~kl~~~l~~ 237 (252)
|++|++||++++.+||++|+...|++++.|++||+++++|++||||||||||||+|||+++++||+.|+++|+.|+.
T Consensus 146 A~~l~~~A~~~s~~~l~~~l~~~~~l~~~l~~IA~~a~~~~~f~YSRlfAIGLf~LLe~a~~~d~~~l~~l~e~Lgl 222 (283)
T PLN00047 146 AAKLEEWARSQTGSSLVDFSSKEGEIEGILKDIAERAGSKGKFSYSRFFAIGLFRLLELANATEPTALEKLCAALNI 222 (283)
T ss_pred HHHHHHHHhcCCHHHHHHHHhcchHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCC
Confidence 99999999999999999999999999999999998887899999999999999999999999999877777665543
No 2
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=100.00 E-value=7.8e-75 Score=509.87 Aligned_cols=170 Identities=66% Similarity=1.116 Sum_probs=161.3
Q ss_pred CCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHh
Q 025486 70 PPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITA 149 (252)
Q Consensus 70 ~~TVSDTKr~F~~~y~rPIpsIYRrvv~ELLVElHLLs~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~IF~Alc~A 149 (252)
+||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||+|
T Consensus 2 ~~TVsDtKr~F~~~~p~pI~siYrrvv~ELLVE~HLl~~n~~f~yD~lfAlGlvt~fd~fm~GY~Pee~~~~IF~Alc~a 81 (206)
T PLN03060 2 VPTVADTKASFLKAYRKPIPSIYSNVIQELLVQQHLMRYNATYKYDPIFALGFVTVYDQLMDGYPNATDRDAIFKAYIEA 81 (206)
T ss_pred CCcHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHH
Q 025486 150 LKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLE 229 (252)
Q Consensus 150 lg~DP~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~a~~~dp~~L~ 229 (252)
+|+||+|||+||++|++||+|++.++|.+|++++|+.+..|+++++++++|++||||||||||||+|||.++++||+.++
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 99999999999999999999999999999999998888888888888889999999999999999999999999998776
Q ss_pred HHHHhhhhccCccc
Q 025486 230 KVRSTFFDNIGTSI 243 (252)
Q Consensus 230 kl~~~l~~~lgls~ 243 (252)
++|+ .|||++
T Consensus 162 ~l~~----~L~ls~ 171 (206)
T PLN03060 162 KLSK----ALNVSK 171 (206)
T ss_pred HHHH----HcCCCH
Confidence 6665 555554
No 3
>PRK13266 Thf1-like protein; Reviewed
Probab=100.00 E-value=2.2e-74 Score=512.57 Aligned_cols=176 Identities=39% Similarity=0.694 Sum_probs=165.0
Q ss_pred CCCCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHH
Q 025486 68 DVPPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYI 147 (252)
Q Consensus 68 ~~~~TVSDTKr~F~~~y~rPIpsIYRrvv~ELLVElHLLs~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~IF~Alc 147 (252)
+++||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||
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 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCc--chhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCC---
Q 025486 148 TALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKE--GEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA--- 222 (252)
Q Consensus 148 ~Alg~DP~qyR~DA~~l~~~A~~~s~~~l~~~~~~~--g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~a~~--- 222 (252)
+|+|+||+|||+||++|++||+|++.+||.+|++++ |+++.+++.++ .+++|++||||||||||||+|||.+++
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 45555555555 455799999999999999999999987
Q ss_pred CCHHHHHHHHHhhhhccCcccc
Q 025486 223 TEPTVLEKVRSTFFDNIGTSII 244 (252)
Q Consensus 223 ~dp~~L~kl~~~l~~~lgls~~ 244 (252)
+||+.+.++++.|.+.|||++-
T Consensus 161 ~d~~~~~~~l~~l~~~L~ls~~ 182 (225)
T PRK13266 161 KDEEKLNEALKDISEGLGLSKE 182 (225)
T ss_pred cCHHHHHHHHHHHHHHcCCCHH
Confidence 6999999999999999999874
No 4
>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=3.2e-74 Score=508.37 Aligned_cols=173 Identities=38% Similarity=0.650 Sum_probs=162.0
Q ss_pred CCCCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHH
Q 025486 68 DVPPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYI 147 (252)
Q Consensus 68 ~~~~TVSDTKr~F~~~y~rPIpsIYRrvv~ELLVElHLLs~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~IF~Alc 147 (252)
+++||||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||
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 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCHHHHHHHHHHHHHHHhcCCccccccccCCcch--hHH-HHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCC--
Q 025486 148 TALKEDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGE--VEG-LLKDIAERASGKGNFSYSRFFAVGLFRLLELANA-- 222 (252)
Q Consensus 148 ~Alg~DP~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~--~~~-~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~a~~-- 222 (252)
+|+|+||+|||+||++|++||+|++.++|.+|+++.|+ .+. +|++|| +|++||||||||||||+|||.+++
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 466665 599999999999999999999986
Q ss_pred -CCHHHHHHHHHhhhhccCcccc
Q 025486 223 -TEPTVLEKVRSTFFDNIGTSII 244 (252)
Q Consensus 223 -~dp~~L~kl~~~l~~~lgls~~ 244 (252)
+||+.+.++++.|.+.|||++-
T Consensus 158 ~~d~~~~~~~l~~l~~~L~ls~~ 180 (214)
T TIGR03060 158 DIDEEDLNEILKELSEALGLSYD 180 (214)
T ss_pred ccCHHHHHHHHHHHHHHcCCCHH
Confidence 4999999999999999999874
No 5
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=100.00 E-value=1.4e-73 Score=504.70 Aligned_cols=173 Identities=48% Similarity=0.827 Sum_probs=164.3
Q ss_pred chhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcC
Q 025486 72 TVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALK 151 (252)
Q Consensus 72 TVSDTKr~F~~~y~rPIpsIYRrvv~ELLVElHLLs~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~IF~Alc~Alg 151 (252)
|||||||+||++|||||||||||||||||||||||+||++|+|||||||||||+||+||+||||++|+++||+|||+|+|
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---CCHHH
Q 025486 152 EDPEQYRIDAQKLEEWARGQTASSLVEFPSK-EGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANA---TEPTV 227 (252)
Q Consensus 152 ~DP~qyR~DA~~l~~~A~~~s~~~l~~~~~~-~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~a~~---~dp~~ 227 (252)
+||+|||+||++|++||+|+|.+||.+|+++ .++.++.|++++.+|++|++||||||||||||+|||.+++ +|++.
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 9999999999999999999999999999987 4566677777777788899999999999999999999987 48899
Q ss_pred HHHHHHhhhhccCcccc
Q 025486 228 LEKVRSTFFDNIGTSII 244 (252)
Q Consensus 228 L~kl~~~l~~~lgls~~ 244 (252)
+.++++.|.+.||||+.
T Consensus 161 ~~~~l~~l~~~l~ls~~ 177 (216)
T PF11264_consen 161 RPEALEKLSEALGLSKE 177 (216)
T ss_pred HHHHHHHHHHHcCCCHH
Confidence 99999999999999864
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=94.72 E-value=0.041 Score=49.86 Aligned_cols=57 Identities=19% Similarity=0.294 Sum_probs=47.4
Q ss_pred hcccccccccccchhhHHHHHHHHhc-CCCCchhHHHHHHHHHHhcCCCHHHHHHHHH
Q 025486 106 MRYKRTYQYDPVFALGFVTVYDRLME-GYPSEEDREAIFQAYITALKEDPEQYRIDAQ 162 (252)
Q Consensus 106 Ls~n~~F~YDplFALG~VTvFd~fmq-GY~peed~~~IF~Alc~Alg~DP~qyR~DA~ 162 (252)
..-|..|.|.-+||+|+.+..+.--- .-..++.+..+.+.||+++|+.++++.+|-.
T Consensus 127 ia~~~~f~YSRl~AIGL~~LLe~a~~~~~~~~~~~~~~l~~l~~~l~ls~~kv~kDL~ 184 (216)
T PF11264_consen 127 IASNPKFKYSRLFAIGLFRLLELAGADLVKDEEKRPEALEKLSEALGLSKEKVEKDLD 184 (216)
T ss_pred HhcCCCCchHHHHHHHHHHHHHhcCcccccChhhHHHHHHHHHHHcCCCHHHHHhhHH
Confidence 34578999999999999999987654 2445677888999999999999999888764
No 7
>PRK13266 Thf1-like protein; Reviewed
Probab=94.62 E-value=0.066 Score=48.86 Aligned_cols=63 Identities=17% Similarity=0.292 Sum_probs=50.3
Q ss_pred HHHHHhhhcccccccccccchhhHHHHHHHHhcC-CCCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 025486 99 LIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEG-YPSEEDREAIFQAYITALKEDPEQYRIDA 161 (252)
Q Consensus 99 LLVElHLLs~n~~F~YDplFALG~VTvFd~fmqG-Y~peed~~~IF~Alc~Alg~DP~qyR~DA 161 (252)
|+-.++=..-|..|.|.-+||+|+.+..+.---. ...++++..+...+|+++|+..+.+.+|-
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 3333444457899999999999999999876542 45666889999999999999999877765
No 8
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=94.32 E-value=0.055 Score=49.08 Aligned_cols=58 Identities=19% Similarity=0.301 Sum_probs=47.5
Q ss_pred HhhhcccccccccccchhhHHHHHHHHhcCC--CCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 025486 103 QHLMRYKRTYQYDPVFALGFVTVYDRLMEGY--PSEEDREAIFQAYITALKEDPEQYRIDA 161 (252)
Q Consensus 103 lHLLs~n~~F~YDplFALG~VTvFd~fmqGY--~peed~~~IF~Alc~Alg~DP~qyR~DA 161 (252)
++=..-|..|.|.-+||+|+.+..+. .+|. ..++++..+...||+++|+..+.+.+|-
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 33344789999999999999999984 4443 4667788999999999999999877765
No 9
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=91.33 E-value=0.2 Score=45.33 Aligned_cols=49 Identities=20% Similarity=0.338 Sum_probs=40.3
Q ss_pred cccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 025486 107 RYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDA 161 (252)
Q Consensus 107 s~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~IF~Alc~Alg~DP~qyR~DA 161 (252)
.-|..|.|.-+||+|+.+..+.--.. |. .+.+.+|+++|+..+.+.+|-
T Consensus 130 ~~~~~f~YSRl~AIGL~~LLe~a~~~-----d~-~~l~~l~~~L~ls~~kv~kDL 178 (206)
T PLN03060 130 AGKTKFHYSRFFAIGLFRLLECAKAS-----DP-AVLEKLSKALNVSKRSVDRDL 178 (206)
T ss_pred hcCCCcchHHHHHHHHHHHHHHcCCC-----CH-HHHHHHHHHcCCCHHHHHhhH
Confidence 36799999999999999999876332 22 289999999999999877765
No 10
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=89.25 E-value=0.36 Score=45.59 Aligned_cols=48 Identities=17% Similarity=0.291 Sum_probs=39.0
Q ss_pred ccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHH
Q 025486 108 YKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDA 161 (252)
Q Consensus 108 ~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~IF~Alc~Alg~DP~qyR~DA 161 (252)
-|..|.|.-+||+|+.+..+.--- . |. .+.+.||+++|+.++.+.+|-
T Consensus 184 ~~~~f~YSRlfAIGLf~LLe~a~~-~----d~-~~l~~l~e~Lgls~~kv~KDL 231 (283)
T PLN00047 184 SKGKFSYSRFFAIGLFRLLELANA-T----EP-TALEKLCAALNINKRSVDRDL 231 (283)
T ss_pred cCCCcchHHHHHHHHHHHHHhcCC-C----CH-HHHHHHHHHcCCCHHHHHhhH
Confidence 579999999999999998876533 2 22 388889999999999977765
No 11
>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=60.78 E-value=16 Score=30.32 Aligned_cols=77 Identities=21% Similarity=0.308 Sum_probs=60.4
Q ss_pred CchhHHHHHHHHHHhcC---------CCHHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCC
Q 025486 135 SEEDREAIFQAYITALK---------EDPEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGN 202 (252)
Q Consensus 135 peed~~~IF~Alc~Alg---------~DP~qyR~DA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~n~~ 202 (252)
+.+||.+++..|+.+|= --++++|.-|++|..+|+..+.. .+..|+.....+..++..|+.+-+ +.+
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 34788999999999999976644 445666666678889999998876 455
Q ss_pred CcchhhHHHH
Q 025486 203 FSYSRFFAVG 212 (252)
Q Consensus 203 F~YSRlfAIG 212 (252)
--|+|+.=+|
T Consensus 87 GGYTRI~kl~ 96 (112)
T TIGR00059 87 GGYTRILKLG 96 (112)
T ss_pred CCeEEEEECC
Confidence 5899986655
No 12
>COG2206 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]
Probab=59.20 E-value=89 Score=29.47 Aligned_cols=83 Identities=10% Similarity=0.140 Sum_probs=67.8
Q ss_pred CCCchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhh--hcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHH
Q 025486 69 VPPTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHL--MRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAY 146 (252)
Q Consensus 69 ~~~TVSDTKr~F~~~y~rPIpsIYRrvv~ELLVElHL--Ls~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~IF~Al 146 (252)
......-.++........-+..+.+.++.+.++.+.+ +....+|.|---.-++..+.+=.-.-||+.++-++.-..|+
T Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kd~~t~~Hs~~va~~a~~ia~~lgl~~~~i~~l~~aal 182 (344)
T COG2206 103 IGEDILIAKLDATLAVRIELSKVAREIVKKALVALARGDIKAKDDYTYGHSVRVAELAEAIAKKLGLSEEKIEELALAGL 182 (344)
T ss_pred hhhhhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3445666666667777777788888899999999999 78888899999999999999988899998877777777888
Q ss_pred HHhcC
Q 025486 147 ITALK 151 (252)
Q Consensus 147 c~Alg 151 (252)
+.-+|
T Consensus 183 LHDIG 187 (344)
T COG2206 183 LHDIG 187 (344)
T ss_pred Hhhcc
Confidence 87766
No 13
>PRK10880 adenine DNA glycosylase; Provisional
Probab=56.58 E-value=1.6e+02 Score=28.57 Aligned_cols=109 Identities=17% Similarity=0.258 Sum_probs=66.3
Q ss_pred hhHhHHHHHhhCCC-c-----CCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHH----H
Q 025486 73 VAETKMNFLKLYKR-P-----IPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREA----I 142 (252)
Q Consensus 73 VSDTKr~F~~~y~r-P-----IpsIYRrvv~ELLVElHLLs~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~----I 142 (252)
.++.-.+.|..|.| . -..-|+-.|-|+|.|+==. . -+..+|++||+.||..++... =
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 56677788999886 3 3567999999999887411 1 255689999999986554221 1
Q ss_pred HHHHHHhcCC--CHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHH
Q 025486 143 FQAYITALKE--DPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIA 194 (252)
Q Consensus 143 F~Alc~Alg~--DP~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia 194 (252)
...+++.+|+ -...+++-|+.+.+.-.|.=.++..+.++-.|=...+...|.
T Consensus 73 l~~~~~glGyy~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl 126 (350)
T PRK10880 73 VLHLWTGLGYYARARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAIL 126 (350)
T ss_pred HHHHHHcCChHHHHHHHHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHH
Confidence 2245567887 455566666666554334333444444443453344555555
No 14
>PF13170 DUF4003: Protein of unknown function (DUF4003)
Probab=55.50 E-value=61 Score=30.40 Aligned_cols=117 Identities=17% Similarity=0.241 Sum_probs=77.0
Q ss_pred HHHHHHHhcCCCC-chhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhc--CCccccccccCC-----cc--hhH-----
Q 025486 123 VTVYDRLMEGYPS-EEDREAIFQAYITALKEDPEQYRIDAQKLEEWARG--QTASSLVEFPSK-----EG--EVE----- 187 (252)
Q Consensus 123 VTvFd~fmqGY~p-eed~~~IF~Alc~Alg~DP~qyR~DA~~l~~~A~~--~s~~~l~~~~~~-----~g--~~~----- 187 (252)
.++|+.+.+-+|= ....|-.|.+|+.....|++++-+..+.+-.+-+. .....=++|++. +| +.+
T Consensus 123 ~~iy~~mKk~H~fLTs~~D~~~a~lLA~~~~~~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~ 202 (297)
T PF13170_consen 123 KEIYKEMKKKHPFLTSPEDYPFAALLAMTSEDVEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVI 202 (297)
T ss_pred HHHHHHHHHhCccccCccchhHHHHHhcccccHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHH
Confidence 3457777776652 34567788999999999999999988888776553 333333334441 22 211
Q ss_pred HHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHHhhhhccCcc
Q 025486 188 GLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKVRSTFFDNIGTS 242 (252)
Q Consensus 188 ~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~a~~~dp~~L~kl~~~l~~~lgls 242 (252)
.+...+.+ .+-+.+|.=+-.|||..|++....+.-+.+.++...|.+..|+-
T Consensus 203 ~l~~~l~~---~~~kik~~~yp~lGlLall~~~~~~~~~~i~ev~~~L~~~k~~~ 254 (297)
T PF13170_consen 203 ELYNALKK---NGVKIKYMHYPTLGLLALLEDPEEKIVEEIKEVIDELKEQKGFG 254 (297)
T ss_pred HHHHHHHH---cCCccccccccHHHHHHhcCCchHHHHHHHHHHHHHHhhCcccC
Confidence 23344433 24455666688999999995443345588999999999888864
No 15
>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=52.65 E-value=19 Score=26.58 Aligned_cols=42 Identities=24% Similarity=0.327 Sum_probs=29.9
Q ss_pred CCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCcccccc
Q 025486 132 GYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVE 178 (252)
Q Consensus 132 GY~peed~~~IF~Alc~Alg~DP~qyR~DA~~l~~~A~~~s~~~l~~ 178 (252)
|.||+++-+.|++++.+. +-+..|+....+... |.+..+|+.
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 568889999999988876 778888888888775 777776664
No 16
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=52.52 E-value=21 Score=29.62 Aligned_cols=77 Identities=22% Similarity=0.304 Sum_probs=60.8
Q ss_pred CchhHHHHHHHHHHhcC---------CCHHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCC
Q 025486 135 SEEDREAIFQAYITALK---------EDPEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGN 202 (252)
Q Consensus 135 peed~~~IF~Alc~Alg---------~DP~qyR~DA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~n~~ 202 (252)
+.+||.+++.-++.+|= --+.++|.-|++|..+|+.-+.. .+..|+.....+..++..|+.+-+ +.+
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 56899999999999874 34678999999999999976654 344567666678888999998886 455
Q ss_pred CcchhhHHHH
Q 025486 203 FSYSRFFAVG 212 (252)
Q Consensus 203 F~YSRlfAIG 212 (252)
--|+|++-+|
T Consensus 89 GGYTRI~k~~ 98 (113)
T PRK05591 89 GGYTRILKLG 98 (113)
T ss_pred CCeEEEEECC
Confidence 5899988766
No 17
>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=47.56 E-value=10 Score=28.38 Aligned_cols=46 Identities=26% Similarity=0.375 Sum_probs=32.2
Q ss_pred ccccccc-ccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCH
Q 025486 109 KRTYQYD-PVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDP 154 (252)
Q Consensus 109 n~~F~YD-plFALG~VTvFd~fmqGY~peed~~~IF~Alc~Alg~DP 154 (252)
+.+++|| +-..-+-.++.+-|..|+=.-.+...+|.|||.++|.+.
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 18
>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=46.09 E-value=88 Score=29.19 Aligned_cols=134 Identities=14% Similarity=0.242 Sum_probs=77.1
Q ss_pred hhHHHHHHHHHHhhhccccccccccc-chhhHHH--HHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Q 025486 92 YNTVLQELIVQQHLMRYKRTYQYDPV-FALGFVT--VYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWA 168 (252)
Q Consensus 92 YRrvv~ELLVElHLLs~n~~F~YDpl-FALG~VT--vFd~fmqGY~peed~~~IF~Alc~Alg~DP~qyR~DA~~l~~~A 168 (252)
||..+++...+-.- .|..|.+=.+ -.+|+.+ -+-.+++|=++-. +.-..-+++++|+++..-. --+.|....
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 77777777776654 3445655555 2488776 5678889988766 5556778999999987732 233444444
Q ss_pred hcCCccccccccCCcchhHHHHHHHHHHhcCCCCC-cchhhHHHHHHHHHhhcCCC-CHHHHHHHHH
Q 025486 169 RGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNF-SYSRFFAVGLFRLLELANAT-EPTVLEKVRS 233 (252)
Q Consensus 169 ~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F-~YSRlfAIGLf~LLE~a~~~-dp~~L~kl~~ 233 (252)
+.++.++-..+..+ +..+...-..+.-+.+.| .|+.+..--|..|+.+.+.+ ||+.|.+.|.
T Consensus 85 ~ak~~~~k~~~~~~---~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~ 148 (271)
T TIGR02147 85 QAKTDTEKQQFFEE---MQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCF 148 (271)
T ss_pred ccCCHHHHHHHHHH---HHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhC
Confidence 44443322111110 000000000011112333 67788888888899877665 8876666653
No 19
>PRK13910 DNA glycosylase MutY; Provisional
Probab=46.08 E-value=2.6e+02 Score=26.36 Aligned_cols=71 Identities=13% Similarity=0.082 Sum_probs=40.9
Q ss_pred HHHHHHhcCCCCchhH----HHHHHHHHHhcCC--CHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHH
Q 025486 124 TVYDRLMEGYPSEEDR----EAIFQAYITALKE--DPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIA 194 (252)
Q Consensus 124 TvFd~fmqGY~peed~----~~IF~Alc~Alg~--DP~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia 194 (252)
-.|++||+-||..++. +.=...+++.+|+ -+..+++-|+.+.+--.|.-+.+..+.++-.|=-..+..+|.
T Consensus 13 ~yy~rf~~~fPt~e~La~a~~~el~~~~~glGyy~RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpGIG~kTA~aIl 89 (289)
T PRK13910 13 RFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAIL 89 (289)
T ss_pred HHHHHHHHHCCCHHHHHCCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCCCHHHHHHHH
Confidence 3789999999987764 2224457788998 455566666666554334333444443443443334444444
No 20
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=44.77 E-value=2.6e+02 Score=26.00 Aligned_cols=127 Identities=17% Similarity=0.200 Sum_probs=65.5
Q ss_pred HhHHHHHhhCCC------cCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHH----HH
Q 025486 75 ETKMNFLKLYKR------PIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAI----FQ 144 (252)
Q Consensus 75 DTKr~F~~~y~r------PIpsIYRrvv~ELLVElHLLs~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~I----F~ 144 (252)
+.-.+.|..+.| +-..-|.-.|-|+|.||= ++ --+..+|++|++.||..++.... ..
T Consensus 4 ~~l~~w~~~~~r~~lpWr~~~dpy~vlvseIL~QQT--~v-----------~~v~~~~~rl~~~fpt~~~La~a~~eeL~ 70 (275)
T TIGR01084 4 EDLLSWYDKYGRKTLPWRQNKTPYRVWLSEVMLQQT--QV-----------ATVIPYFERFLERFPTVQALANAPQDEVL 70 (275)
T ss_pred HHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHhhc--cH-----------HHHHHHHHHHHHhCCCHHHHHCcCHHHHH
Confidence 444567777765 234568999999998873 11 12457899999999866543221 22
Q ss_pred HHHHhcCCC--HHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHh
Q 025486 145 AYITALKED--PEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLE 218 (252)
Q Consensus 145 Alc~Alg~D--P~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE 218 (252)
.+++.+|+- ...+++-|+.+.+--.|.-.+++.+.++-.|=...+...|..-+-+.+.+ +.=..+.|++.
T Consensus 71 ~~~~~lG~y~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~----~vD~~v~RVl~ 142 (275)
T TIGR01084 71 KLWEGLGYYARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFALNKPYP----ILDGNVKRVLS 142 (275)
T ss_pred HHHHHCCcHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCC----cchHhHHHHHH
Confidence 334667872 33344444444443223333333333333442233444554333333322 12334555553
No 21
>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=40.62 E-value=36 Score=27.79 Aligned_cols=32 Identities=13% Similarity=0.329 Sum_probs=19.6
Q ss_pred cccchhhHHHHHHHHhcCCCCch--hHHHHHHHHH
Q 025486 115 DPVFALGFVTVYDRLMEGYPSEE--DREAIFQAYI 147 (252)
Q Consensus 115 DplFALG~VTvFd~fmqGY~pee--d~~~IF~Alc 147 (252)
..+|+||++ .|+.++.|++|-+ +...+++.+.
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 5666666777743 2333444443
No 22
>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=39.51 E-value=29 Score=22.97 Aligned_cols=27 Identities=30% Similarity=0.416 Sum_probs=22.2
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHH
Q 025486 138 DREAIFQAYITALKEDPEQYRIDAQKL 164 (252)
Q Consensus 138 d~~~IF~Alc~Alg~DP~qyR~DA~~l 164 (252)
+.+.++.-+++.+|.|++++++..++.
T Consensus 25 ~~~~~~~~il~~~~id~~~l~~~i~~~ 51 (53)
T PF02861_consen 25 DPDSIAARILKKLGIDPEQLKAAIEKA 51 (53)
T ss_dssp HTTSHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred hhhHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 345678888999999999999988765
No 23
>COG4476 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.69 E-value=1.4e+02 Score=24.25 Aligned_cols=82 Identities=21% Similarity=0.186 Sum_probs=69.8
Q ss_pred hCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHH
Q 025486 83 LYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQ 162 (252)
Q Consensus 83 ~y~rPIpsIYRrvv~ELLVElHLLs~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~IF~Alc~Alg~DP~qyR~DA~ 162 (252)
.|.+||+.=|.+ +|+.--+|++..=..+-=-.+=+.-|.-.|.+|-+=-|.-.+-..|+..+=++.|..+=|--++|+
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 899999999876655555567788888999999999999899999999999999999988888887
Q ss_pred HHHH
Q 025486 163 KLEE 166 (252)
Q Consensus 163 ~l~~ 166 (252)
...+
T Consensus 80 ~~~~ 83 (90)
T COG4476 80 ESEE 83 (90)
T ss_pred Hhhh
Confidence 6643
No 24
>COG3793 TerB Tellurite resistance protein [Inorganic ion transport and metabolism]
Probab=36.49 E-value=1e+02 Score=26.87 Aligned_cols=36 Identities=22% Similarity=0.219 Sum_probs=30.7
Q ss_pred hhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCC
Q 025486 137 EDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQT 172 (252)
Q Consensus 137 ed~~~IF~Alc~Alg~DP~qyR~DA~~l~~~A~~~s 172 (252)
+....||+.+|.+.+.|++.=+..+.++.+-.++.+
T Consensus 65 ~~i~~~~~~~~~~~~~d~~~gk~ea~~~I~~lk~d~ 100 (144)
T COG3793 65 NEINEIFETLVGSFDTDFEIGKREAMKEIEDLKHDT 100 (144)
T ss_pred HHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHhcCCh
Confidence 468899999999999999998888888888666554
No 25
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=36.29 E-value=49 Score=24.11 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=17.9
Q ss_pred cCCCCchhHHHHHHHHHHhcCCCHHHH
Q 025486 131 EGYPSEEDREAIFQAYITALKEDPEQY 157 (252)
Q Consensus 131 qGY~peed~~~IF~Alc~Alg~DP~qy 157 (252)
+++|++---......||+.||.||+++
T Consensus 36 ~~lp~~~y~rg~lr~Ya~~Lgld~~~l 62 (62)
T PF13413_consen 36 DSLPSPVYARGYLRKYARFLGLDPDEL 62 (62)
T ss_dssp CCSSSHHHHHHHHHHHHHHTT--HHHH
T ss_pred hhCCcHHHHHHHHHHHHHHhCcCcccC
Confidence 455555556677788899999998864
No 26
>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=36.10 E-value=32 Score=27.58 Aligned_cols=58 Identities=22% Similarity=0.334 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHH
Q 025486 154 PEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVG 212 (252)
Q Consensus 154 P~qyR~DA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIG 212 (252)
+.++|.-|++|..+|+..+.. .+..|+..+..+..+++.|+.+-+ +.+--|+|++=+|
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 567899999999999976543 566777766678888899998886 4566899876544
No 27
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=33.84 E-value=51 Score=27.79 Aligned_cols=78 Identities=22% Similarity=0.325 Sum_probs=58.3
Q ss_pred CCchhHHHHHHHHHHhcCC---------CHHHHHHHHHHHHHHHhcCCccc---cccccCCcchhHHHHHHHHHHhcCCC
Q 025486 134 PSEEDREAIFQAYITALKE---------DPEQYRIDAQKLEEWARGQTASS---LVEFPSKEGEVEGLLKDIAERASGKG 201 (252)
Q Consensus 134 ~peed~~~IF~Alc~Alg~---------DP~qyR~DA~~l~~~A~~~s~~~---l~~~~~~~g~~~~~l~~Ia~~~~~n~ 201 (252)
++..||.+++..|..+|=. .+..+|.-+++|.-+|+.-+... ...|+.++..++.++..|+.+-++.+
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 3568999999998888743 46779999999999999877763 44466667778889999987665433
Q ss_pred CCcchhhHHHH
Q 025486 202 NFSYSRFFAVG 212 (252)
Q Consensus 202 ~F~YSRlfAIG 212 (252)
=-|+|++=+|
T Consensus 92 -GGYtRIlK~g 101 (116)
T COG0203 92 -GGYTRILKLG 101 (116)
T ss_pred -CCeeEEEecC
Confidence 3688876444
No 28
>PF13446 RPT: A repeated domain in UCH-protein
Probab=33.83 E-value=71 Score=22.69 Aligned_cols=47 Identities=21% Similarity=0.336 Sum_probs=34.2
Q ss_pred CCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCcccccccc
Q 025486 134 PSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWARGQTASSLVEFP 180 (252)
Q Consensus 134 ~peed~~~IF~Alc~Alg~DP~qyR~DA~~l~~~A~~~s~~~l~~~~ 180 (252)
+|.-+-+.|-.++-..+..||.+.+.--++|...|.......|..|+
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 34444556666666666699999988888888888877777666654
No 29
>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=31.83 E-value=47 Score=27.65 Aligned_cols=20 Identities=15% Similarity=0.341 Sum_probs=14.2
Q ss_pred cccchhhHHHHHHHHhcCCCC
Q 025486 115 DPVFALGFVTVYDRLMEGYPS 135 (252)
Q Consensus 115 DplFALG~VTvFd~fmqGY~p 135 (252)
..+|++| ++.|+-+..|.+|
T Consensus 185 ~Di~slG-~il~~l~t~g~~p 204 (261)
T cd05034 185 SDVWSFG-ILLTEIVTYGRVP 204 (261)
T ss_pred hHHHHHH-HHHHHHHhCCCCC
Confidence 4699999 4556666667776
No 30
>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=31.13 E-value=1.4e+02 Score=20.68 Aligned_cols=36 Identities=25% Similarity=0.327 Sum_probs=25.1
Q ss_pred HHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHH
Q 025486 123 VTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRI 159 (252)
Q Consensus 123 VTvFd~fmqGY~peed~~~IF~Alc~Alg~DP~qyR~ 159 (252)
-.+.=+||.+=. ..+|+.+..++-.-++++|++.++
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 345667787755 356889999999999999999775
No 31
>smart00219 TyrKc Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
Probab=30.35 E-value=68 Score=26.32 Aligned_cols=22 Identities=14% Similarity=0.375 Sum_probs=15.3
Q ss_pred cccchhhHHHHHHHHhcCCCCch
Q 025486 115 DPVFALGFVTVYDRLMEGYPSEE 137 (252)
Q Consensus 115 DplFALG~VTvFd~fmqGY~pee 137 (252)
..+|+||++ .|+.+..|++|-+
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 4555666887743
No 32
>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=30.04 E-value=57 Score=31.82 Aligned_cols=34 Identities=24% Similarity=0.369 Sum_probs=29.6
Q ss_pred CCCCchhHHHHHHHHHH-hcCCCHHHHHHHHHHHH
Q 025486 132 GYPSEEDREAIFQAYIT-ALKEDPEQYRIDAQKLE 165 (252)
Q Consensus 132 GY~peed~~~IF~Alc~-Alg~DP~qyR~DA~~l~ 165 (252)
-|.|.++|-+.|+|+++ .++..|.+|.+.|+.-.
T Consensus 121 ~FkP~~~klA~fhA~v~~~L~~p~S~yye~a~~Yl 155 (340)
T PF12069_consen 121 TFKPSQEKLAMFHAQVRAQLGQPASQYYEHAQAYL 155 (340)
T ss_pred ccCCChHHHHHHHHHHHHHcCCCcchhHHHHHHHH
Confidence 37899999999999996 58999999999997643
No 33
>KOG1258 consensus mRNA processing protein [RNA processing and modification]
Probab=29.95 E-value=1.5e+02 Score=31.14 Aligned_cols=124 Identities=20% Similarity=0.213 Sum_probs=72.1
Q ss_pred CchhHhHHHHHhhCCCcCCcchhHHHHHHHHHHhhhcccccccccccchhhHHHHHHHHhcCCCCchhHHHHHHHHHHhc
Q 025486 71 PTVAETKMNFLKLYKRPIPSIYNTVLQELIVQQHLMRYKRTYQYDPVFALGFVTVYDRLMEGYPSEEDREAIFQAYITAL 150 (252)
Q Consensus 71 ~TVSDTKr~F~~~y~rPIpsIYRrvv~ELLVElHLLs~n~~F~YDplFALG~VTvFd~fmqGY~peed~~~IF~Alc~Al 150 (252)
-+....=..|...||.. -..|++..+ ++|.=-=+=-.+-||++=.+|.|=--++=.=+-+.|+.+
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 33444445666666653 235555544 333222222347788888899986666666678888999
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCcc-----ccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHH
Q 025486 151 KEDPEQYRIDAQKLEEWARGQTAS-----SLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFA 210 (252)
Q Consensus 151 g~DP~qyR~DA~~l~~~A~~~s~~-----~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfA 210 (252)
++||+++|..-+.-++.+...=.. -.++|-...+. ..-+..|-+++..+|..+|+|+|.
T Consensus 127 ~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~qks-~k~v~~iyeRileiP~~~~~~~f~ 190 (577)
T KOG1258|consen 127 NGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQKS-WKRVANIYERILEIPLHQLNRHFD 190 (577)
T ss_pred CCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhcccc-HHHHHHHHHHHHhhhhhHhHHHHH
Confidence 999999988777666654421100 01111111111 122333444666699999999987
No 34
>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=28.83 E-value=1.4e+02 Score=20.97 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=29.2
Q ss_pred HHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHh
Q 025486 124 TVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLEEWAR 169 (252)
Q Consensus 124 TvFd~fmqGY~peed~~~IF~Alc~Alg~DP~qyR~DA~~l~~~A~ 169 (252)
.+++.+ +| ....+.|-+++++..+.+|++.++|...+.+...
T Consensus 21 ~Iw~~~-~g---~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~ 62 (68)
T PF05402_consen 21 FIWELL-DG---PRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLR 62 (68)
T ss_dssp HHHHH---S---SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH
T ss_pred HHHHHc-cC---CCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 355555 44 2557889999999999999999999988877443
No 35
>cd05056 PTKc_FAK Catalytic domain of the Protein Tyrosine Kinase, Focal Adhesion Kinase. Protein Tyrosine Kinase (PTK) family; Focal Adhesion Kinase (FAK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FAK is a cytoplasmic (or nonreceptor) tyr kinase that contains an autophosphorylation site and a FERM domain at the N-terminus, a central tyr kinase domain, proline-rich regions, and a C-terminal FAT (focal adhesion targeting) domain. FAK activity is dependent on integrin-mediated cell adhesion, which facilitates N-terminal autophosphorylation. Full activation is achieved by the phosphorylation of its two adjacent A-loop tyrosines. FAK is important in mediating signaling initiated at sites of cell adhesions
Probab=27.84 E-value=77 Score=26.69 Aligned_cols=20 Identities=25% Similarity=0.527 Sum_probs=15.5
Q ss_pred cccchhhHHHHHHHHhcCCCC
Q 025486 115 DPVFALGFVTVYDRLMEGYPS 135 (252)
Q Consensus 115 DplFALG~VTvFd~fmqGY~p 135 (252)
..+|+||++ .|+.++.|++|
T Consensus 189 ~Di~slG~i-l~el~~~g~~p 208 (270)
T cd05056 189 SDVWMFGVC-MWEILMLGVKP 208 (270)
T ss_pred hhhHHHHHH-HHHHHHcCCCC
Confidence 579999954 56778888877
No 36
>cd05058 PTKc_Met_Ron Catalytic domain of the Protein Tyrosine Kinases, Met and Ron. Protein Tyrosine Kinase (PTK) family; Met and Ron; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Met and Ron are receptor tyr kinases (RTKs) composed of an alpha-beta heterodimer. The extracellular alpha chain is disulfide linked to the beta chain, which contains an extracellular ligand-binding region with a sema domain, a PSI domain and four IPT repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. Met binds to the ligand, hepatocyte growth factor/scatter factor (HGF/SF), and is also ca
Probab=26.29 E-value=1.7e+02 Score=24.40 Aligned_cols=21 Identities=19% Similarity=0.540 Sum_probs=15.4
Q ss_pred cccchhhHHHHHHHHhcCCCCc
Q 025486 115 DPVFALGFVTVYDRLMEGYPSE 136 (252)
Q Consensus 115 DplFALG~VTvFd~fmqGY~pe 136 (252)
..||++|+ +.|+-++.|.+|-
T Consensus 183 ~Di~slG~-~l~el~~~~~~~~ 203 (262)
T cd05058 183 SDVWSFGV-LLWELMTRGAPPY 203 (262)
T ss_pred HHHHHHHH-HHHHHHcCCCCCC
Confidence 56999997 5577777777764
No 37
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=25.20 E-value=41 Score=24.53 Aligned_cols=28 Identities=29% Similarity=0.742 Sum_probs=20.1
Q ss_pred HHHHHHHhcCCCHHHHHH-------HHHHHHHHHh
Q 025486 142 IFQAYITALKEDPEQYRI-------DAQKLEEWAR 169 (252)
Q Consensus 142 IF~Alc~Alg~DP~qyR~-------DA~~l~~~A~ 169 (252)
||+|+-+++.-||+-|.+ +-+.|.+|.+
T Consensus 1 l~~~lt~~I~~~p~l~ekIL~YePI~L~el~~~L~ 35 (64)
T PF09494_consen 1 LFEALTKLIRSDPELYEKILMYEPINLEELHAWLK 35 (64)
T ss_pred CHHHHHHHHHcCHHHHHHHHcCCCccHHHHHHHHH
Confidence 577888888888887766 3466666666
No 38
>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=25.06 E-value=66 Score=23.00 Aligned_cols=16 Identities=38% Similarity=0.380 Sum_probs=12.9
Q ss_pred HHHHhcCCCHHHHHHH
Q 025486 145 AYITALKEDPEQYRID 160 (252)
Q Consensus 145 Alc~Alg~DP~qyR~D 160 (252)
.|=+.+|.+|.|+|+|
T Consensus 33 ~La~~~gi~~~qVRKD 48 (50)
T PF06971_consen 33 ELAEALGITPAQVRKD 48 (50)
T ss_dssp HHHHHHTS-HHHHHHH
T ss_pred HHHHHHCCCHHHhccc
Confidence 4667899999999998
No 39
>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=24.77 E-value=1.8e+02 Score=21.39 Aligned_cols=44 Identities=16% Similarity=0.227 Sum_probs=31.4
Q ss_pred hHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 025486 121 GFVTVYDRLMEGYPSEEDREAIFQAYITALKEDPEQYRIDAQKLE 165 (252)
Q Consensus 121 G~VTvFd~fmqGY~peed~~~IF~Alc~Alg~DP~qyR~DA~~l~ 165 (252)
.-..+.+-+.+||++.+=-..|++.+... +.++.+-.+-.+.+.
T Consensus 23 ~~~~~~~l~~~G~s~~~Il~~l~~~l~~~-~~~~~~k~~i~~~la 66 (89)
T PF08542_consen 23 ARKKLYELLVEGYSASDILKQLHEVLVES-DIPDSQKAEILKILA 66 (89)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHHHHHTS-TSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHh-hccHHHHHHHHHHHH
Confidence 45567788889999999999999999999 767665444444443
No 40
>PHA00666 putative protease
Probab=24.23 E-value=6e+02 Score=23.87 Aligned_cols=32 Identities=19% Similarity=0.159 Sum_probs=28.6
Q ss_pred cCCCCchhHHHHHHHHHHhcCCCHHHHHHHHH
Q 025486 131 EGYPSEEDREAIFQAYITALKEDPEQYRIDAQ 162 (252)
Q Consensus 131 qGY~peed~~~IF~Alc~Alg~DP~qyR~DA~ 162 (252)
+|+..+.....-|..+|..+|++++|-++-..
T Consensus 93 EG~elD~~~l~~F~~~a~ElgLtqEQAQklvD 124 (233)
T PHA00666 93 EGVELDTGALGAFEPVARELNLTNEQAQKVVD 124 (233)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 99999999999999999999999999766443
No 41
>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=24.07 E-value=59 Score=26.54 Aligned_cols=31 Identities=13% Similarity=0.200 Sum_probs=24.4
Q ss_pred HHHhcCCCCchhHHHHHHHHHHhcCCCHHHH
Q 025486 127 DRLMEGYPSEEDREAIFQAYITALKEDPEQY 157 (252)
Q Consensus 127 d~fmqGY~peed~~~IF~Alc~Alg~DP~qy 157 (252)
++--..-+..+||..||+=||+.+|.+|+.-
T Consensus 12 ~~AE~AI~dsd~R~~llqEm~~gLg~~p~ag 42 (93)
T PF07216_consen 12 EQAELAIRDSDHRNDLLQEMLEGLGLGPVAG 42 (93)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHhcCCChhHH
Confidence 3333445677999999999999999999764
No 42
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=24.01 E-value=1.3e+02 Score=31.11 Aligned_cols=44 Identities=43% Similarity=0.627 Sum_probs=30.3
Q ss_pred HHHHHHHhcCCc-cccccccCCcch--------hHHHHHHHHHHhcCCCCCcchhhHH
Q 025486 162 QKLEEWARGQTA-SSLVEFPSKEGE--------VEGLLKDIAERASGKGNFSYSRFFA 210 (252)
Q Consensus 162 ~~l~~~A~~~s~-~~l~~~~~~~g~--------~~~~l~~Ia~~~~~n~~F~YSRlfA 210 (252)
.-|.+.++|... .|+.+|+.++|+ ++.++.+++.+++ .|||+++
T Consensus 192 dll~kh~~g~dt~~df~~fm~khge~fpe~pr~~~el~d~laAR~a-----aaSrf~n 244 (652)
T COG4867 192 DLLDKHARGEDTQRDFDEFMTKHGEFFPENPRNVEELLDSLAARAA-----AASRFRN 244 (652)
T ss_pred HHHHHhccCCCCcccHHHHHHhccccCCCCcccHHHHHHHHHHHHH-----HHHHHhh
Confidence 344456666543 477788876554 6788888887776 4999875
No 43
>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=22.30 E-value=1.9e+02 Score=26.19 Aligned_cols=75 Identities=21% Similarity=0.219 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCHHHHHHHHH
Q 025486 154 PEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEPTVLEKVRS 233 (252)
Q Consensus 154 P~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~a~~~dp~~L~kl~~ 233 (252)
.++|.+-|++|.+-++|+......+ .|+.+- +.+.|++-+.+.=-=--|...||..+ -+.+.+-..
T Consensus 31 G~Ky~~~A~elA~~~kGKkIRs~~d----------Al~s~e-K~~~n~~kK~~~kDr~AI~~Al~s~d---~~~~A~nl~ 96 (187)
T PF01024_consen 31 GEKYKKLAKELAEDAKGKKIRSVDD----------ALKSFE-KYKSNLNKKINAKDRDAIVNALESVD---AKDMAKNLA 96 (187)
T ss_dssp -HHHHHHHHHHHHHHHTGC---HHH----------HHHHHH-HHHTHTTCSS-HHHHHHHHHHHHT-----HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhcccccCCHHH----------HHHHHH-HHHhchhhhhhhccHHHHHHHHHHcC---HHHHHHHHH
Confidence 3689999999999999988775543 443332 33346666666655555666665443 344444444
Q ss_pred hhhhccCcc
Q 025486 234 TFFDNIGTS 242 (252)
Q Consensus 234 ~l~~~lgls 242 (252)
.++..+|+.
T Consensus 97 k~sK~fg~~ 105 (187)
T PF01024_consen 97 KFSKAFGIT 105 (187)
T ss_dssp HHHGGGTST
T ss_pred HHHHHhcch
Confidence 555555543
No 44
>PF07268 EppA_BapA: Exported protein precursor (EppA/BapA); InterPro: IPR009894 This family consists of a number of exported protein precursor (EppA and BapA) sequences which seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). bapA gene sequences are quite stable but the encoded proteins do not provoke a strong immune response in most individuals. Conversely, EppA proteins are much more antigenic but are more variable in sequence. It is thought that BapA and EppA play important roles during the B. burgdorferi infectious cycle [].
Probab=22.06 E-value=1.5e+02 Score=25.81 Aligned_cols=34 Identities=35% Similarity=0.689 Sum_probs=25.3
Q ss_pred HHHHHHhcCCCCchhHHHHHHHHHHhcCCC----HHHHHHHHHH
Q 025486 124 TVYDRLMEGYPSEEDREAIFQAYITALKED----PEQYRIDAQK 163 (252)
Q Consensus 124 TvFd~fmqGY~peed~~~IF~Alc~Alg~D----P~qyR~DA~~ 163 (252)
-.--.|++|||. +||+-|++ |+-| +|+|-+.|..
T Consensus 87 ~~I~~LI~gyp~-----~IFdyliq-LdsdkIDYaEKYGekA~~ 124 (139)
T PF07268_consen 87 EAINYLIDGYPD-----SIFDYLIQ-LDSDKIDYAEKYGEKARN 124 (139)
T ss_pred HHHHHHHcCCcH-----HHHHHHHH-hccccccHHHHHHHHHHH
Confidence 455689999973 49999988 7777 6677666654
No 45
>cd05043 PTK_Ryk Pseudokinase domain of Ryk (Receptor related to tyrosine kinase). Protein Tyrosine Kinase (PTK) family; Receptor related to tyrosine kinase (Ryk); pseudokinase domain. The PTKc (catalytic domain) family to which this subfamily belongs, 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. Ryk is a receptor tyr kinase (RTK) containing an extracellular region with two leucine-rich motifs, a transmembrane segment, and an intracellular inactive pseudokinase domain. The extracellular region of Ryk shows homology to the N-terminal domain of Wnt inhibitory factor-1 (WIF) and serves as the ligand (Wnt) binding domain of Ryk. Ryk is expressed in many different tissues both during development and in adults, suggesting a widespread function. It
Probab=21.80 E-value=1.4e+02 Score=25.22 Aligned_cols=20 Identities=15% Similarity=0.494 Sum_probs=13.4
Q ss_pred cccchhhHHHHHHHHhcCCCC
Q 025486 115 DPVFALGFVTVYDRLMEGYPS 135 (252)
Q Consensus 115 DplFALG~VTvFd~fmqGY~p 135 (252)
..||++|++ .|+-+..|-+|
T Consensus 200 ~Di~slG~~-l~el~~~g~~p 219 (280)
T cd05043 200 SDVWSFGVL-LWELMTLGQTP 219 (280)
T ss_pred hhHHHhHHH-HHHHhcCCCCC
Confidence 459999954 56666556665
No 46
>KOG4509 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.67 E-value=71 Score=29.48 Aligned_cols=50 Identities=20% Similarity=0.238 Sum_probs=25.3
Q ss_pred ccccccCCcchhHHHHHHHHHHhcCCCCCcchhhHHHHHHHHHhhcCCCCH
Q 025486 175 SLVEFPSKEGEVEGLLKDIAERASGKGNFSYSRFFAVGLFRLLELANATEP 225 (252)
Q Consensus 175 ~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSRlfAIGLf~LLE~a~~~dp 225 (252)
+|..+++++.+....-+.|. -+++...|.|-|+|.=-+=.-|-..-.+||
T Consensus 75 diekYLdqekEdgk~~eQ~K-I~~NaTG~SY~~iF~e~~dd~l~~V~ieD~ 124 (247)
T KOG4509|consen 75 DIEKYLDQEKEDGKTHEQIK-IAANATGFSYARIFGECCDDRLREVHIEDA 124 (247)
T ss_pred HHHHHhhhhccccchhhhhh-hhhccCcccHHHHHHHHHhhhhheeeecch
Confidence 44455554333222333332 122457899999998655444433333444
No 47
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=21.23 E-value=4.5e+02 Score=22.98 Aligned_cols=73 Identities=16% Similarity=0.267 Sum_probs=51.1
Q ss_pred cCCCCchhHHHHHHHHHHhcC---CCHHHHHHHHHHHHHHHhcCCccccccccCCcchhHHHHHHHHHHhcCCCCCcchh
Q 025486 131 EGYPSEEDREAIFQAYITALK---EDPEQYRIDAQKLEEWARGQTASSLVEFPSKEGEVEGLLKDIAERASGKGNFSYSR 207 (252)
Q Consensus 131 qGY~peed~~~IF~Alc~Alg---~DP~qyR~DA~~l~~~A~~~s~~~l~~~~~~~g~~~~~l~~Ia~~~~~n~~F~YSR 207 (252)
.|-+.+=|+++|.+.|..|+. .+++++.+-+..++.........++-+ ..=| +..++.|.+ =+.-.|=|
T Consensus 55 dG~re~Fdr~Kl~~gl~~Ac~KRpVs~e~ie~~v~~Ie~~l~~~~~~EI~S--~~IG--e~Vm~~L~~----lD~VAYVR 126 (147)
T TIGR00244 55 DGVREPFNREKLLRGMVRACEKRPVSFDDLEHAINHIEAQLRAQGEREVPS--ELIG--QMVMQYLKK----LDEVAYIR 126 (147)
T ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHcCCCcccH--HHHH--HHHHHHHhh----cCcchhhh
Confidence 355666789999999999997 688999999999999887766665542 1112 334455543 45557888
Q ss_pred hHHH
Q 025486 208 FFAV 211 (252)
Q Consensus 208 lfAI 211 (252)
|-.|
T Consensus 127 FASV 130 (147)
T TIGR00244 127 FASV 130 (147)
T ss_pred hhhh
Confidence 7654
No 48
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=20.23 E-value=1.3e+02 Score=20.60 Aligned_cols=33 Identities=18% Similarity=0.346 Sum_probs=18.3
Q ss_pred HHHHHHhcCCCCchhHHHHHHHHHHhcCCCHHHH
Q 025486 124 TVYDRLMEGYPSEEDREAIFQAYITALKEDPEQY 157 (252)
Q Consensus 124 TvFd~fmqGY~peed~~~IF~Alc~Alg~DP~qy 157 (252)
+.+.++..|- +..-.....+++|.++|.+|+++
T Consensus 25 ~tl~~~~~~~-~~~~~~~~l~~ia~~l~~~~~el 57 (63)
T PF13443_consen 25 STLSRILNGK-PSNPSLDTLEKIAKALNCSPEEL 57 (63)
T ss_dssp HHHHHHHTTT------HHHHHHHHHHHT--HHHC
T ss_pred HHHHHHHhcc-cccccHHHHHHHHHHcCCCHHHH
Confidence 3445555555 22335567889999999998874
No 49
>PTZ00076 60S ribosomal protein L17; Provisional
Probab=20.23 E-value=1e+02 Score=29.14 Aligned_cols=77 Identities=12% Similarity=0.081 Sum_probs=60.4
Q ss_pred CchhHHHHHHHHHHhcCC---------CHHHHHHHHHHHHHHHhcCCcc---ccccccCCcchhHHHHHHHHHHhcCCCC
Q 025486 135 SEEDREAIFQAYITALKE---------DPEQYRIDAQKLEEWARGQTAS---SLVEFPSKEGEVEGLLKDIAERASGKGN 202 (252)
Q Consensus 135 peed~~~IF~Alc~Alg~---------DP~qyR~DA~~l~~~A~~~s~~---~l~~~~~~~g~~~~~l~~Ia~~~~~n~~ 202 (252)
...||.+++.-++.+|=. -++.+|.-|++|.-+|+.-+.. .+.+|+.....+..++..||.+-+ +.+
T Consensus 25 ~ssHR~AlLRNLvtsLI~hERIeTTlaKAKELR~~AEKLITlAKk~tl~sRR~a~s~L~d~~av~KLF~eLAPRY~-dR~ 103 (253)
T PTZ00076 25 QPHHRWDSIKNQLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKVESMLRTPQGRRKLYEKYVPLYR-DRP 103 (253)
T ss_pred CHHHHHHHHHHHHHHHHHcCcEEecHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCHHHHHHHHHHhhhHhc-CCC
Confidence 468899999888888743 3677999999999999977755 344666667788899999998886 456
Q ss_pred CcchhhHHHH
Q 025486 203 FSYSRFFAVG 212 (252)
Q Consensus 203 F~YSRlfAIG 212 (252)
.-|+|++-+|
T Consensus 104 GGYTRIlK~~ 113 (253)
T PTZ00076 104 FFFTRVVNQW 113 (253)
T ss_pred CCeeEEEeCC
Confidence 6899998753
Done!