Query 020759
Match_columns 321
No_of_seqs 218 out of 521
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 04:55:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020759.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020759hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08755 YccV-like: Hemimethyl 99.9 2.2E-28 4.7E-33 199.4 0.4 83 206-289 2-98 (100)
2 TIGR02097 yccV hemimethylated 99.9 4.6E-26 1E-30 187.8 4.7 83 206-289 2-99 (101)
3 PRK14129 heat shock protein Hs 99.7 3.1E-18 6.7E-23 142.1 5.9 65 206-272 4-75 (105)
4 COG3880 Modulator of heat shoc 99.7 5E-18 1.1E-22 151.2 5.0 93 94-191 73-171 (176)
5 COG3785 Uncharacterized conser 99.6 2.9E-16 6.3E-21 131.1 2.8 66 206-272 13-84 (116)
6 PF02151 UVR: UvrB/uvrC motif; 98.0 8.6E-06 1.9E-10 55.7 3.9 34 157-190 3-36 (36)
7 PRK00558 uvrC excinuclease ABC 94.7 0.051 1.1E-06 57.2 5.6 35 158-192 204-238 (598)
8 COG0556 UvrB Helicase subunit 94.2 0.093 2E-06 55.5 6.2 40 153-192 621-660 (663)
9 KOG4408 Putative Mg2+ and Co2+ 93.7 0.05 1.1E-06 54.4 2.9 26 204-229 63-89 (386)
10 PRK12306 uvrC excinuclease ABC 93.1 0.16 3.6E-06 52.8 5.7 35 158-192 194-228 (519)
11 PRK14671 uvrC excinuclease ABC 93.0 0.15 3.3E-06 54.1 5.4 35 158-192 217-251 (621)
12 TIGR00194 uvrC excinuclease AB 92.8 0.19 4.2E-06 52.9 5.9 72 158-230 196-271 (574)
13 PRK14667 uvrC excinuclease ABC 92.8 0.16 3.5E-06 53.4 5.2 35 158-192 201-235 (567)
14 PRK14666 uvrC excinuclease ABC 92.5 0.2 4.3E-06 54.1 5.5 35 158-192 203-237 (694)
15 PRK05298 excinuclease ABC subu 92.5 0.18 3.9E-06 53.4 5.1 36 157-192 614-649 (652)
16 TIGR00631 uvrb excinuclease AB 92.1 0.14 3.1E-06 54.4 3.8 32 157-188 624-655 (655)
17 PRK07883 hypothetical protein; 92.0 0.15 3.3E-06 53.1 3.8 35 158-192 408-442 (557)
18 PRK14672 uvrC excinuclease ABC 91.5 0.3 6.6E-06 52.6 5.5 35 158-192 207-241 (691)
19 PRK14669 uvrC excinuclease ABC 91.4 0.34 7.3E-06 51.6 5.7 35 158-192 205-239 (624)
20 PRK14670 uvrC excinuclease ABC 90.4 0.46 9.9E-06 50.2 5.5 35 158-192 179-213 (574)
21 PRK14668 uvrC excinuclease ABC 89.8 0.34 7.4E-06 51.1 4.0 34 158-191 201-234 (577)
22 COG0322 UvrC Nuclease subunit 89.6 0.49 1.1E-05 50.1 5.0 75 158-232 204-281 (581)
23 PF04420 CHD5: CHD5-like prote 60.2 9.4 0.0002 33.8 3.2 42 153-194 44-85 (161)
24 KOG0412 Golgi transport comple 53.8 42 0.00091 37.1 7.2 35 154-188 123-160 (773)
25 PF10186 Atg14: UV radiation r 53.2 83 0.0018 28.9 8.3 19 98-117 2-20 (302)
26 PRK00420 hypothetical protein; 52.2 20 0.00044 30.7 3.8 25 96-120 24-52 (112)
27 PF05605 zf-Di19: Drought indu 51.1 10 0.00023 27.5 1.7 9 109-117 32-40 (54)
28 PRK00409 recombination and DNA 49.5 1.5E+02 0.0033 32.7 10.8 23 207-229 636-658 (782)
29 PF02211 NHase_beta: Nitrile h 49.2 17 0.00038 34.3 3.2 57 202-264 129-198 (222)
30 KOG3419 Mitochondrial/chloropl 46.0 15 0.00032 31.7 2.0 18 250-267 12-30 (112)
31 PF00653 BIR: Inhibitor of Apo 39.4 12 0.00026 28.3 0.5 25 68-107 24-48 (70)
32 KOG4825 Component of synaptic 39.1 60 0.0013 34.6 5.5 37 157-193 208-244 (666)
33 TIGR00002 S16 ribosomal protei 38.5 23 0.0005 28.5 2.0 15 250-264 10-25 (78)
34 PF09926 DUF2158: Uncharacteri 37.0 29 0.00062 26.0 2.2 24 208-231 1-24 (53)
35 CHL00005 rps16 ribosomal prote 36.7 26 0.00056 28.6 2.0 15 250-264 11-26 (82)
36 PF11365 DUF3166: Protein of u 36.0 37 0.0008 28.5 2.9 29 160-193 5-33 (96)
37 PRK14520 rpsP 30S ribosomal pr 36.0 25 0.00054 31.9 2.0 15 250-264 12-27 (155)
38 PRK09458 pspB phage shock prot 35.3 64 0.0014 26.1 4.0 19 174-192 48-66 (75)
39 PF13717 zinc_ribbon_4: zinc-r 34.7 14 0.0003 25.4 0.1 23 96-118 3-35 (36)
40 PRK14525 rpsP 30S ribosomal pr 34.1 30 0.00064 28.6 2.0 15 250-264 12-27 (88)
41 cd00022 BIR Baculoviral inhibi 32.4 22 0.00049 26.4 1.0 25 68-107 22-46 (69)
42 PRK14521 rpsP 30S ribosomal pr 31.5 32 0.0007 32.0 2.0 15 250-264 12-27 (186)
43 PF00886 Ribosomal_S16: Riboso 31.0 26 0.00056 26.8 1.1 15 250-264 4-19 (62)
44 PRK00040 rpsP 30S ribosomal pr 30.6 37 0.00081 27.1 2.0 15 250-264 11-26 (75)
45 COG0228 RpsP Ribosomal protein 30.5 35 0.00077 28.3 1.9 15 250-264 11-26 (87)
46 PF10845 DUF2576: Protein of u 28.8 20 0.00044 26.6 0.2 9 298-306 31-39 (48)
47 PF13719 zinc_ribbon_5: zinc-r 28.5 20 0.00044 24.5 0.1 24 96-119 3-36 (37)
48 PRK14524 rpsP 30S ribosomal pr 26.9 47 0.001 27.7 2.0 15 250-264 11-26 (94)
49 PF13462 Thioredoxin_4: Thiore 26.8 43 0.00093 27.6 1.8 22 107-131 20-41 (162)
50 PF01486 K-box: K-box region; 25.2 2.7E+02 0.0058 22.4 6.2 36 157-192 50-85 (100)
51 KOG0739 AAA+-type ATPase [Post 24.8 62 0.0013 33.2 2.8 107 109-226 56-171 (439)
52 PRK14523 rpsP 30S ribosomal pr 24.7 52 0.0011 29.4 2.0 15 250-264 11-26 (137)
53 PRK14522 rpsP 30S ribosomal pr 24.0 55 0.0012 28.5 2.0 15 250-264 12-27 (116)
54 PF09862 DUF2089: Protein of u 23.9 29 0.00063 29.9 0.3 22 98-119 1-23 (113)
55 PRK11020 hypothetical protein; 23.2 2.1E+02 0.0046 25.1 5.3 38 155-192 11-48 (118)
56 PF03961 DUF342: Protein of un 22.7 5.7E+02 0.012 26.0 9.2 39 178-216 392-434 (451)
57 cd03023 DsbA_Com1_like DsbA fa 22.2 62 0.0013 26.1 1.9 20 108-130 14-33 (154)
58 TIGR02976 phageshock_pspB phag 21.9 1.5E+02 0.0032 23.8 3.9 19 174-192 48-66 (75)
59 PF12510 Smoothelin: Smootheli 21.6 2.1E+02 0.0046 21.8 4.5 38 150-190 16-53 (54)
60 PF00855 PWWP: PWWP domain; I 20.4 1.1E+02 0.0023 23.2 2.8 22 208-229 1-25 (86)
61 smart00238 BIR Baculoviral inh 20.0 53 0.0011 24.5 1.0 25 68-107 24-48 (71)
62 PF09237 GAGA: GAGA factor; I 20.0 46 0.00099 25.5 0.6 21 110-130 26-46 (54)
No 1
>PF08755 YccV-like: Hemimethylated DNA-binding protein YccV like; InterPro: IPR011722 This entry describes the small protein from Escherichia coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein []. The model entry describes a domain in longer eukaryotic proteins.; PDB: 1VBV_A.
Probab=99.94 E-value=2.2e-28 Score=199.39 Aligned_cols=83 Identities=33% Similarity=0.633 Sum_probs=41.4
Q ss_pred cccccCcEEEeeecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCC------ccCccccccC-----C
Q 020759 206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRIC------WLLTNQTWQG-----L 274 (321)
Q Consensus 206 vkFrVGQVvrHR~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r------~v~~~ql~~~-----~ 274 (321)
++|+|||+|+||+|||+|||+|||+.|.++++|+.+++++.++. ++||||+||||++ |++++++.+. +
T Consensus 2 ~~f~vGqvv~Hr~~~y~GVIvgwD~~~~~~~~W~~~~~~~~~~~-~~qPfY~vLv~~~~~~~~~YVaEenL~~~~~~~~i 80 (100)
T PF08755_consen 2 VKFRVGQVVRHRRYGYRGVIVGWDPECQAPEEWIEQMGVDNLPR-RNQPFYHVLVDDRDSPPVRYVAEENLEPDSTPEPI 80 (100)
T ss_dssp -SS-TT-EEEETTT--EEEEEEEE-------------------------EEEEEEE-SS--EEEEEEGGGEEE---S--T
T ss_pred cccccCCEEEEeeeCccEEEECcccccCCCchHHHhcccccccc-CCCCcEEEEEecCCccceEEecccccccCCCCCCc
Confidence 68999999999999999999999999999999999999887766 9999999999974 4666655331 1
Q ss_pred ---CccceeeeecceEEE
Q 020759 275 ---IIPIFLSCFTGRIQL 289 (321)
Q Consensus 275 ---~i~~~f~~FdGr~y~ 289 (321)
.|+.||+.|||.+|+
T Consensus 81 ~hp~i~~yF~~fd~~~y~ 98 (100)
T PF08755_consen 81 NHPEIGRYFKRFDGGRYV 98 (100)
T ss_dssp T-HHHHHHHHHHTT----
T ss_pred CChHHHHHHHhhCCCcCc
Confidence 667999999999997
No 2
>TIGR02097 yccV hemimethylated DNA binding domain. This model describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein. The model also describes a domain in longer eukaryotic proteins.
Probab=99.92 E-value=4.6e-26 Score=187.81 Aligned_cols=83 Identities=29% Similarity=0.525 Sum_probs=70.9
Q ss_pred cccccCcEEEeeecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCCc-------cCccccccC-----
Q 020759 206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICW-------LLTNQTWQG----- 273 (321)
Q Consensus 206 vkFrVGQVvrHR~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r~-------v~~~ql~~~----- 273 (321)
++|+|||+|+||+|||+|||+||||.|.++++|+.+|+++.++. ++||||||||++++ |++++|-..
T Consensus 2 ~kf~IGqvvrHr~~~yrGVI~gwDp~~~~~eeW~~~~~~~~~p~-~~qPfYhvLv~~~~~~~~~aYVaE~nL~~~~~~~~ 80 (101)
T TIGR02097 2 AKFRIGQVVRHKLFGYRGVVIDVDPEYSNTEEWLDAIPVEIRPL-RDQPFYHVLAEDDEGLPYVAYVAEQNLLYDDSDEP 80 (101)
T ss_pred ceecCCCEEEecccCCCEEEEeEChhccCChHHHHhhhcccCcc-cCCCceEEEEeCCCCcceeEEeehhhcccCCCCCC
Confidence 68999999999999999999999999999999999999887655 99999999998643 556555441
Q ss_pred C---CccceeeeecceEEE
Q 020759 274 L---IIPIFLSCFTGRIQL 289 (321)
Q Consensus 274 ~---~i~~~f~~FdGr~y~ 289 (321)
+ .|..+|+.|||.+|.
T Consensus 81 i~hP~~~~~F~~~~~~~y~ 99 (101)
T TIGR02097 81 IEHPQVDELFDGFDEGLQK 99 (101)
T ss_pred CCCCCHHHHHhhhccCccc
Confidence 2 344899999999885
No 3
>PRK14129 heat shock protein HspQ; Provisional
Probab=99.73 E-value=3.1e-18 Score=142.06 Aligned_cols=65 Identities=23% Similarity=0.393 Sum_probs=55.6
Q ss_pred cccccCcEEEeeecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCC-------ccCcccccc
Q 020759 206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRIC-------WLLTNQTWQ 272 (321)
Q Consensus 206 vkFrVGQVvrHR~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r-------~v~~~ql~~ 272 (321)
.+|.|||+||||+|||||||+|.||+|..+++|+..+..+ .+.++||||||||++. |+++.+|.+
T Consensus 4 akF~IGQ~VrHrl~~yrGVV~DVDP~fs~~e~w~~~ia~~--~p~kdqPwYHvl~en~~~~~v~tYVaE~nL~~ 75 (105)
T PRK14129 4 SKFGIGQQVRHSLLGYLGVVVDIDPEYSLEEPSPDELAVN--DELRAAPWYHVVMEDDDGQPVHTYLAEAQLSS 75 (105)
T ss_pred ccccCCcEEEEeecCCCeEEEeeCCCcCCCchhHHhhccC--CCccCCCceEEEEEcCCCceEEEEeeecccCC
Confidence 4899999999999999999999999999999999999654 6789999999999653 345555554
No 4
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=99.71 E-value=5e-18 Score=151.18 Aligned_cols=93 Identities=24% Similarity=0.258 Sum_probs=81.1
Q ss_pred Cceeeecccccccc-----cccccccHHhhHHHHHHHHHHHHHHHHHhhhhhcccCC-CcchhHHHHHHHHHHHHHHHHH
Q 020759 94 EDILFFFFQLDLAT-----RVQCALNMEEYDIAQQLRNKLTEVEEEISRQLEAKRGL-SSKSEAQDKALSIIRLRADLQK 167 (321)
Q Consensus 94 ~~i~cf~cqldl~~-----RLgCp~cYe~F~~a~~Lr~~L~~ih~~~~~~h~GK~p~-~~~~~~~d~a~qLlqLr~~L~~ 167 (321)
+.+.|+.||+++.. |+||+.||.+|.. .|.|.+++||++.. .|+||+|. .++.+. -..+|+.|+..|++
T Consensus 73 e~l~C~~C~~Tfk~f~~~g~fGCaeCY~tf~~--~i~pi~~rvq~g~~-~H~GK~P~~~~~~i~--~~~~I~~L~e~Lq~ 147 (176)
T COG3880 73 ELLGCHNCGMTFKEFIQSGLFGCAECYKTFES--QISPIITRVQGGYV-EHVGKVPKRIGRKIN--PKRKIIALKEALQD 147 (176)
T ss_pred HHhcCccccccHHHHHHhcccchHHHHHHHHH--HhhHHHHHhhCCce-eecCcCccccccccc--HHHHHHHHHHHHHH
Confidence 36899999998865 9999999999997 99999999999954 38999995 333444 44569999999999
Q ss_pred hhchhhHHHhhHHHHHHhhHHHhh
Q 020759 168 AIDSENYALAADLRDQICKLEAES 191 (321)
Q Consensus 168 AI~~E~YE~AA~LRD~Ir~Leeq~ 191 (321)
+|+.||||+||.+||+|+.|+++.
T Consensus 148 ~i~~EefEeAA~iRDqIr~Lk~k~ 171 (176)
T COG3880 148 LIEREEFEEAAVIRDQIRALKAKN 171 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhc
Confidence 999999999999999999999773
No 5
>COG3785 Uncharacterized conserved protein [Function unknown]
Probab=99.60 E-value=2.9e-16 Score=131.07 Aligned_cols=66 Identities=27% Similarity=0.509 Sum_probs=57.1
Q ss_pred cccccCcEEEeeecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCCc------cCcccccc
Q 020759 206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICW------LLTNQTWQ 272 (321)
Q Consensus 206 vkFrVGQVvrHR~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r~------v~~~ql~~ 272 (321)
.||.|||+|||++|+|+|||++.||++..+++|...+.++ .++-++|||||+|+++.+ +.+.+|.+
T Consensus 13 aKF~IGQvVRHrlfpfrGVV~DvDPeyanteew~~~ip~~-~rp~rdqPfYHllaEnde~~yvaYvsEqnL~~ 84 (116)
T COG3785 13 AKFGIGQVVRHRLFPFRGVVFDVDPEYANTEEWPDEIPVN-IRPLRDQPFYHLLAENDETEYVAYVSEQNLVS 84 (116)
T ss_pred hhcchhhhhhhhhcccceEEEecCcccccCccChhhcccc-ccccccCCceeeeeecCCccceeeehhhhccc
Confidence 5899999999999999999999999999999999999654 478999999999997653 44445555
No 6
>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.
Probab=97.98 E-value=8.6e-06 Score=55.73 Aligned_cols=34 Identities=35% Similarity=0.556 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHh
Q 020759 157 SIIRLRADLQKAIDSENYALAADLRDQICKLEAE 190 (321)
Q Consensus 157 qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq 190 (321)
.|..|+.+|..|++.++||+||.|||.|..|++|
T Consensus 3 ~i~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~~q 36 (36)
T PF02151_consen 3 LIKELEEKMEEAVENEDFEKAARLRDQIKALKKQ 36 (36)
T ss_dssp HHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHcC
Confidence 3778899999999999999999999999999875
No 7
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=94.70 E-value=0.051 Score=57.22 Aligned_cols=35 Identities=26% Similarity=0.325 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+.+|+.+|++|.++.+||+||.+||.|..|+.-.+
T Consensus 204 i~~L~~~M~~aa~~l~FE~Aa~~RD~i~aL~~~~~ 238 (598)
T PRK00558 204 LKELEEKMEEASENLEFERAARYRDQIQALRRVQE 238 (598)
T ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHHh
Confidence 66888999999999999999999999999997655
No 8
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=94.24 E-value=0.093 Score=55.48 Aligned_cols=40 Identities=30% Similarity=0.412 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 153 DKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 153 d~a~qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+.+..|..|+.+|++|-++-+||+||.|||.|.+|+++..
T Consensus 621 e~~~~I~~Le~~M~~aA~~l~FE~Aa~lRD~i~~L~~~~~ 660 (663)
T COG0556 621 ELEKLIKKLEKEMKEAAKNLEFEEAARLRDEIKELKEELL 660 (663)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhc
Confidence 4455688999999999999999999999999999998754
No 9
>KOG4408 consensus Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism]
Probab=93.66 E-value=0.05 Score=54.41 Aligned_cols=26 Identities=27% Similarity=0.450 Sum_probs=21.9
Q ss_pred cccccccCcEEEeeecCceEEEE-ccc
Q 020759 204 ARFAFRLGQKVNHKIFGYRAVIC-GMD 229 (321)
Q Consensus 204 ~~vkFrVGQVvrHR~ygYrGVIv-GWD 229 (321)
..-+|.-||.|+|+.|||+|||+ -|+
T Consensus 63 ~~~~~etgqsF~h~~f~yvgvv~~~w~ 89 (386)
T KOG4408|consen 63 KTQKYETGQSFLHDTFGYVGVVLFPWA 89 (386)
T ss_pred cCCcccccceeeeeecccceEEEEech
Confidence 34589999999999999999988 344
No 10
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=93.07 E-value=0.16 Score=52.82 Aligned_cols=35 Identities=20% Similarity=0.336 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+.+|+.+|++|-+..+||+||.+||.|+.|+.-..
T Consensus 194 ~~~L~~~M~~aa~~l~FE~Aa~~RD~l~~l~~~~~ 228 (519)
T PRK12306 194 IEKLEEEMAEKAKNQQFERALVIRDEINAIENLQE 228 (519)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHh
Confidence 56788899999999999999999999999986433
No 11
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=93.03 E-value=0.15 Score=54.07 Aligned_cols=35 Identities=31% Similarity=0.390 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+.+|+.+|++|-+..+||+||++||.|+.|+.-..
T Consensus 217 ~~~L~~~M~~as~~l~FE~Aa~~RD~i~~l~~~~~ 251 (621)
T PRK14671 217 IRSLTEEMQRAAAELKFEEAAELKDQIESLKRYAE 251 (621)
T ss_pred HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHh
Confidence 56788899999999999999999999999986443
No 12
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=92.84 E-value=0.19 Score=52.86 Aligned_cols=72 Identities=22% Similarity=0.278 Sum_probs=45.2
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhhhhhhhhhhcccccc---ccccCcEEEeeecCce-EEEEcccc
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESLAASATALAFENARF---AFRLGQKVNHKIFGYR-AVICGMDP 230 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~aasa~a~~~~n~~v---kFrVGQVvrHR~ygYr-GVIvGWDp 230 (321)
+.+|+.+|++|-++.+||+||.+||.|+.|+.-............+..+ ....|..+.+ +|-+| |.|+|.+.
T Consensus 196 ~~~L~~~M~~aa~~l~FE~Aa~~Rd~i~~l~~~~~~Q~v~~~~~~d~Dvi~~~~~~~~~~v~-v~~vR~G~l~~~~~ 271 (574)
T TIGR00194 196 IKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVSLTDLIDLDIIAVAFDGNVAAIQ-VFFIRQGKLIGRDQ 271 (574)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhcCeeecCCCCCceEEEEEEcCCcEEEE-EEEEECCEEeccee
Confidence 5578889999999999999999999999998654421111111122222 2333444333 33344 78887763
No 13
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=92.78 E-value=0.16 Score=53.45 Aligned_cols=35 Identities=26% Similarity=0.223 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+..|+.+|++|-++.+||+||++||.|+.|+.-..
T Consensus 201 ~~~L~~~M~~aa~~l~FE~Aa~~RD~i~~l~~~~~ 235 (567)
T PRK14667 201 LPELYDKIEEYSQKLMFEKAAVIRDQILALENLIK 235 (567)
T ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHh
Confidence 56788899999999999999999999999987544
No 14
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=92.54 E-value=0.2 Score=54.06 Aligned_cols=35 Identities=31% Similarity=0.387 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+..|+.+|++|-++.+||+||++||.|+.|+.-..
T Consensus 203 ~~~L~~~M~~AAe~l~FE~AA~lRD~i~aL~~~~~ 237 (694)
T PRK14666 203 VDALRTEMEAASEALEFERAAVLRDQIRAVERTVE 237 (694)
T ss_pred HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHh
Confidence 56788899999999999999999999999987544
No 15
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=92.45 E-value=0.18 Score=53.37 Aligned_cols=36 Identities=33% Similarity=0.434 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 157 SIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 157 qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
.+..|+.+|++|.++.+||+||.+||+|+.|+....
T Consensus 614 ~~~~l~~~M~~aa~~l~fE~Aa~~Rd~i~~l~~~~~ 649 (652)
T PRK05298 614 LIKELEKQMKEAAKNLEFEEAARLRDEIKELKEELL 649 (652)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhc
Confidence 477888999999999999999999999999997643
No 16
>TIGR00631 uvrb excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
Probab=92.07 E-value=0.14 Score=54.42 Aligned_cols=32 Identities=31% Similarity=0.469 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhhchhhHHHhhHHHHHHhhHH
Q 020759 157 SIIRLRADLQKAIDSENYALAADLRDQICKLE 188 (321)
Q Consensus 157 qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Le 188 (321)
.|..|+.+|++|.++.+||+||.+||+|+.|+
T Consensus 624 ~i~~l~~~M~~aa~~l~FE~Aa~~RD~i~~L~ 655 (655)
T TIGR00631 624 LIKQLEKEMKQAARNLEFEEAARLRDEILELK 655 (655)
T ss_pred HHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence 47788999999999999999999999999874
No 17
>PRK07883 hypothetical protein; Validated
Probab=91.98 E-value=0.15 Score=53.14 Aligned_cols=35 Identities=29% Similarity=0.413 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+.+|+.+|++|-++.+||+||++||+|+.|+.-..
T Consensus 408 ~~~l~~~M~~aa~~l~FE~Aa~~Rd~i~~l~~~~~ 442 (557)
T PRK07883 408 LAALRARIDRLAAAERFEEAARLRDRLAALLRALA 442 (557)
T ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence 56788899999999999999999999999986443
No 18
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=91.54 E-value=0.3 Score=52.62 Aligned_cols=35 Identities=26% Similarity=0.474 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+.+|+.+|++|-++.+||+||++||.|+.|+.-..
T Consensus 207 l~~L~~~M~~AA~~l~FE~AA~lRD~i~aL~~~~~ 241 (691)
T PRK14672 207 VARLEKRMKRAVRQEAFEAAARIRDDIQAIRCITH 241 (691)
T ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHh
Confidence 56788899999999999999999999999985433
No 19
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=91.42 E-value=0.34 Score=51.64 Aligned_cols=35 Identities=31% Similarity=0.323 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+..|+.+|+.|-++.+||+||++||.|+.|+.-..
T Consensus 205 ~~~L~~~M~~aa~~l~FE~Aa~~RD~i~~l~~~~~ 239 (624)
T PRK14669 205 ARSLRARMEAAALEMQFELAAKYRDLITTVEELEE 239 (624)
T ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHh
Confidence 55788899999999999999999999999986544
No 20
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=90.36 E-value=0.46 Score=50.19 Aligned_cols=35 Identities=20% Similarity=0.330 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+.+|+.+|..|-++.+||+||++||.|+.|+.-..
T Consensus 179 ~~~L~~~M~~aa~~l~FE~Aa~~RD~i~al~~~~~ 213 (574)
T PRK14670 179 LSQIEIKMKEAIQKEDFEAAIKLKETKRSLIEISQ 213 (574)
T ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHh
Confidence 56788899999999999999999999999987544
No 21
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=89.84 E-value=0.34 Score=51.08 Aligned_cols=34 Identities=29% Similarity=0.428 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhh
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAES 191 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~ 191 (321)
+..|+.+|++|-++.+||+||.+||.|+.|+.-.
T Consensus 201 ~~~l~~~m~~aa~~l~FE~Aa~~Rd~i~~l~~~~ 234 (577)
T PRK14668 201 ADPLRREMEAAAQAQEFERAANLRDRLEAVEAFH 234 (577)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence 5678899999999999999999999999998644
No 22
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=89.63 E-value=0.49 Score=50.15 Aligned_cols=75 Identities=21% Similarity=0.188 Sum_probs=50.4
Q ss_pred HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhhhh--h-hhhhhccccccccccCcEEEeeecCceEEEEcccccc
Q 020759 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESLAA--S-ATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVC 232 (321)
Q Consensus 158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~aa--s-a~a~~~~n~~vkFrVGQVvrHR~ygYrGVIvGWDp~c 232 (321)
+..|+.+|++|-+..+||+||.+||.|..|+.-.... . .+....+.-...+.-|....+..+-..|-++|-+..+
T Consensus 204 ~~~L~~~M~~As~~l~FE~Aa~~RD~i~al~~l~~~q~v~~~~~~~~Dv~a~~~~~~~~~v~vf~~R~Gkllg~~~~f 281 (581)
T COG0322 204 LQELEEKMEEASENLDFERAARLRDQIKALEKLQEKQAVSLFKLQDLDVIAGAVDGGEACVQVFFVRGGKLLGRRAYF 281 (581)
T ss_pred HHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHHhccccccCCccchhhheeeecCCeEEEEEEEeecchhcCCccee
Confidence 5678889999999999999999999999998655421 1 1112222333355556666665555557777766433
No 23
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=60.24 E-value=9.4 Score=33.84 Aligned_cols=42 Identities=24% Similarity=0.290 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhhhh
Q 020759 153 DKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLAA 194 (321)
Q Consensus 153 d~a~qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~aa 194 (321)
+...++.+++.++..-=..++|.+.|+++-++.+|+++.+..
T Consensus 44 ~l~~Ei~~l~~E~~~iS~qDeFAkwaKl~Rk~~kl~~el~~~ 85 (161)
T PF04420_consen 44 QLRKEILQLKRELNAISAQDEFAKWAKLNRKLDKLEEELEKL 85 (161)
T ss_dssp HHHHHHHHHHHHHTTS-TTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344468888888888777889999999999999999988743
No 24
>KOG0412 consensus Golgi transport complex COD1 protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=53.81 E-value=42 Score=37.08 Aligned_cols=35 Identities=23% Similarity=0.376 Sum_probs=26.4
Q ss_pred HHHHHHHHHH---HHHHhhchhhHHHhhHHHHHHhhHH
Q 020759 154 KALSIIRLRA---DLQKAIDSENYALAADLRDQICKLE 188 (321)
Q Consensus 154 ~a~qLlqLr~---~L~~AI~~E~YE~AA~LRD~Ir~Le 188 (321)
...++..|+. .+..|++.||||.||..-.++..|.
T Consensus 123 ~v~dvrdlk~C~~gv~~Al~seDyE~AA~~IhRflslD 160 (773)
T KOG0412|consen 123 RVDDVRDLKNCIEGVDTALESEDYEKAATHIHRFLSLD 160 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcC
Confidence 3334555554 7889999999999998888877763
No 25
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=53.20 E-value=83 Score=28.91 Aligned_cols=19 Identities=16% Similarity=0.207 Sum_probs=16.4
Q ss_pred eecccccccccccccccHHh
Q 020759 98 FFFFQLDLATRVQCALNMEE 117 (321)
Q Consensus 98 cf~cqldl~~RLgCp~cYe~ 117 (321)
|++|+ .-.+++-|+.|-..
T Consensus 2 C~iC~-~~~~~~~C~~C~~~ 20 (302)
T PF10186_consen 2 CPICH-NSRRRFYCANCVNN 20 (302)
T ss_pred CCCCC-CCCCCeECHHHHHH
Confidence 99999 57789999999765
No 26
>PRK00420 hypothetical protein; Validated
Probab=52.17 E-value=20 Score=30.72 Aligned_cols=25 Identities=20% Similarity=0.183 Sum_probs=20.3
Q ss_pred eeeeccccccc----ccccccccHHhhHH
Q 020759 96 ILFFFFQLDLA----TRVQCALNMEEYDI 120 (321)
Q Consensus 96 i~cf~cqldl~----~RLgCp~cYe~F~~ 120 (321)
..||.||+.|. |...||.|=+.+..
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeeee
Confidence 34999998766 49999999987764
No 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=51.12 E-value=10 Score=27.48 Aligned_cols=9 Identities=22% Similarity=0.516 Sum_probs=4.1
Q ss_pred ccccccHHh
Q 020759 109 VQCALNMEE 117 (321)
Q Consensus 109 LgCp~cYe~ 117 (321)
+-||.|-..
T Consensus 32 v~CPiC~~~ 40 (54)
T PF05605_consen 32 VVCPICSSR 40 (54)
T ss_pred ccCCCchhh
Confidence 445555443
No 28
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=49.53 E-value=1.5e+02 Score=32.71 Aligned_cols=23 Identities=13% Similarity=0.368 Sum_probs=21.6
Q ss_pred ccccCcEEEeeecCceEEEEccc
Q 020759 207 AFRLGQKVNHKIFGYRAVICGMD 229 (321)
Q Consensus 207 kFrVGQVvrHR~ygYrGVIvGWD 229 (321)
.|++||.|+.+.+|-.|.|+..+
T Consensus 636 ~~~~Gd~V~v~~~~~~g~v~~i~ 658 (782)
T PRK00409 636 ELKVGDEVKYLSLGQKGEVLSIP 658 (782)
T ss_pred CCCCCCEEEEccCCceEEEEEEc
Confidence 49999999999999999999986
No 29
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=49.20 E-value=17 Score=34.25 Aligned_cols=57 Identities=19% Similarity=0.156 Sum_probs=32.2
Q ss_pred cccccccccCcEEEe-------------eecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCCc
Q 020759 202 ENARFAFRLGQKVNH-------------KIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICW 264 (321)
Q Consensus 202 ~n~~vkFrVGQVvrH-------------R~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r~ 264 (321)
.....+|+|||.|+- -.-|..|+|.-.-..+-.++.- . .- .....||+|.|-++.++
T Consensus 129 ~~~~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~~g~~~~pd~~---a--~g-~~~~~~~lY~V~F~~~e 198 (222)
T PF02211_consen 129 VDAPPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERVHGAFVFPDSN---A--HG-RGEAPQPLYTVRFDARE 198 (222)
T ss_dssp TSSS-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEEEEEE--HHHH---T--TT-SSTT-EEEEEEEEEHHH
T ss_pred CCCCCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEEecCCCCcchh---c--cC-CCCCCcceEEEEecchh
Confidence 345579999999984 2357789999666655554421 1 11 12338899999998653
No 30
>KOG3419 consensus Mitochondrial/chloroplast ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=46.05 E-value=15 Score=31.70 Aligned_cols=18 Identities=17% Similarity=0.263 Sum_probs=13.0
Q ss_pred CCCCCceEEEE-eCCccCc
Q 020759 250 GPSQPFYQLLR-RICWLLT 267 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~v~~ 267 (321)
-++.|||||+| |.|.+.+
T Consensus 12 cknRPfY~Ivva~~r~~rd 30 (112)
T KOG3419|consen 12 CKNRPFYRIVVADSRKRRD 30 (112)
T ss_pred ccCCCeeEEEEeecccccc
Confidence 46889999996 5665444
No 31
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=39.39 E-value=12 Score=28.28 Aligned_cols=25 Identities=28% Similarity=0.668 Sum_probs=20.1
Q ss_pred eecccccccCCCCCCCccccccccccCceeeecccccccc
Q 020759 68 ANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLAT 107 (321)
Q Consensus 68 ~~~~~~~~~~~~~~~~~~~e~s~s~n~~i~cf~cqldl~~ 107 (321)
+.|||.+.|. +..+.|++||+.+.+
T Consensus 24 A~aGFyy~~~---------------~d~v~C~~C~~~l~~ 48 (70)
T PF00653_consen 24 ARAGFYYTGT---------------GDRVRCFYCGLELDN 48 (70)
T ss_dssp HHTTEEEESS---------------TTEEEETTTTEEEES
T ss_pred HHCCCEEcCC---------------CCEEEEeccCCEEeC
Confidence 6789999763 678899999997753
No 32
>KOG4825 consensus Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa) [Signal transduction mechanisms]
Probab=39.08 E-value=60 Score=34.60 Aligned_cols=37 Identities=38% Similarity=0.480 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhhh
Q 020759 157 SIIRLRADLQKAIDSENYALAADLRDQICKLEAESLA 193 (321)
Q Consensus 157 qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~a 193 (321)
+|.+|..+--.||+.|||..|..+.|+|..|..+..+
T Consensus 208 eleelEndKgcAVadEDfdlAkdkkdeiealRaeila 244 (666)
T KOG4825|consen 208 ELEELENDKGCAVADEDFDLAKDKKDEIEALRAEILA 244 (666)
T ss_pred HHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHH
Confidence 4666666667899999999999999999999887663
No 33
>TIGR00002 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles.
Probab=38.52 E-value=23 Score=28.48 Aligned_cols=15 Identities=20% Similarity=0.421 Sum_probs=11.8
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
-+++|||+|.| |.|.
T Consensus 10 ~k~~PfYrIVv~d~r~ 25 (78)
T TIGR00002 10 RKKRPFYRIVVADSRS 25 (78)
T ss_pred CCCCCeEEEEEEecCC
Confidence 57899999996 6554
No 34
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=37.03 E-value=29 Score=26.02 Aligned_cols=24 Identities=29% Similarity=0.461 Sum_probs=20.6
Q ss_pred cccCcEEEeeecCceEEEEccccc
Q 020759 208 FRLGQKVNHKIFGYRAVICGMDPV 231 (321)
Q Consensus 208 FrVGQVvrHR~ygYrGVIvGWDp~ 231 (321)
|++||+|+.|.-|-+.+|....+.
T Consensus 1 f~~GDvV~LKSGGp~MTV~~v~~~ 24 (53)
T PF09926_consen 1 FKIGDVVQLKSGGPRMTVTEVGPN 24 (53)
T ss_pred CCCCCEEEEccCCCCeEEEEcccc
Confidence 889999999999999999855443
No 35
>CHL00005 rps16 ribosomal protein S16
Probab=36.69 E-value=26 Score=28.56 Aligned_cols=15 Identities=13% Similarity=0.275 Sum_probs=11.8
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
-+++|||+|.| |.|.
T Consensus 11 ~kk~P~YrIVvadsr~ 26 (82)
T CHL00005 11 RKQQAVYRIVAIDVRS 26 (82)
T ss_pred CCCCCeEEEEEEeCCC
Confidence 57899999996 6554
No 36
>PF11365 DUF3166: Protein of unknown function (DUF3166); InterPro: IPR021507 This eukaryotic family of proteins has no known function.
Probab=35.98 E-value=37 Score=28.52 Aligned_cols=29 Identities=34% Similarity=0.338 Sum_probs=24.3
Q ss_pred HHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhhh
Q 020759 160 RLRADLQKAIDSENYALAADLRDQICKLEAESLA 193 (321)
Q Consensus 160 qLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~a 193 (321)
.||.+|+-+- |+|+.||-.|.+|+.+...
T Consensus 5 eLR~qLqFvE-----EEa~LlRRkl~ele~eN~~ 33 (96)
T PF11365_consen 5 ELRRQLQFVE-----EEAELLRRKLSELEDENKQ 33 (96)
T ss_pred HHHHHHHHHH-----HHHHHHHHHHHHHHHHHHH
Confidence 5677787775 6899999999999998883
No 37
>PRK14520 rpsP 30S ribosomal protein S16; Provisional
Probab=35.98 E-value=25 Score=31.90 Aligned_cols=15 Identities=13% Similarity=0.133 Sum_probs=11.7
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
.+++|||+|.| |.|.
T Consensus 12 ~kk~PfYrIVVaDsR~ 27 (155)
T PRK14520 12 KIRNPQYRIVVADSRT 27 (155)
T ss_pred CCCCCeEEEEEeecCC
Confidence 57899999996 6553
No 38
>PRK09458 pspB phage shock protein B; Provisional
Probab=35.29 E-value=64 Score=26.12 Aligned_cols=19 Identities=32% Similarity=0.216 Sum_probs=16.4
Q ss_pred HHHhhHHHHHHhhHHHhhh
Q 020759 174 YALAADLRDQICKLEAESL 192 (321)
Q Consensus 174 YE~AA~LRD~Ir~Leeq~~ 192 (321)
+++|-+|+++|..||.-.+
T Consensus 48 ~~~A~rm~~RI~tLE~ILD 66 (75)
T PRK09458 48 TEKAERMRERIQALEAILD 66 (75)
T ss_pred HHHHHHHHHHHHHHHHHHc
Confidence 5789999999999997655
No 39
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=34.67 E-value=14 Score=25.35 Aligned_cols=23 Identities=17% Similarity=0.176 Sum_probs=15.5
Q ss_pred eeeecccccccc----------cccccccHHhh
Q 020759 96 ILFFFFQLDLAT----------RVQCALNMEEY 118 (321)
Q Consensus 96 i~cf~cqldl~~----------RLgCp~cYe~F 118 (321)
|.|+.|+..+.- .++|+.|-+.|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 567777765543 67888887665
No 40
>PRK14525 rpsP 30S ribosomal protein S16; Provisional
Probab=34.05 E-value=30 Score=28.61 Aligned_cols=15 Identities=20% Similarity=0.366 Sum_probs=11.8
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
-+++|||+|.| |.|.
T Consensus 12 ~k~~P~YrIVv~dsr~ 27 (88)
T PRK14525 12 THKAPFYHVVATDSRN 27 (88)
T ss_pred CCCCCeEEEEEeecCC
Confidence 57899999996 6554
No 41
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=32.38 E-value=22 Score=26.35 Aligned_cols=25 Identities=32% Similarity=0.743 Sum_probs=18.9
Q ss_pred eecccccccCCCCCCCccccccccccCceeeecccccccc
Q 020759 68 ANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLAT 107 (321)
Q Consensus 68 ~~~~~~~~~~~~~~~~~~~e~s~s~n~~i~cf~cqldl~~ 107 (321)
+.|||.+.|. +..+.|++|++.+..
T Consensus 22 a~~Gfyy~~~---------------~d~v~C~~C~~~~~~ 46 (69)
T cd00022 22 AEAGFYYTGR---------------GDEVKCFFCGLELKN 46 (69)
T ss_pred HHcCCeEcCC---------------CCEEEeCCCCCCccC
Confidence 4678888654 346889999998765
No 42
>PRK14521 rpsP 30S ribosomal protein S16; Provisional
Probab=31.50 E-value=32 Score=32.03 Aligned_cols=15 Identities=13% Similarity=0.197 Sum_probs=11.7
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
-+++|||+|.| |.|.
T Consensus 12 ~KkrPfYrIVVaDsR~ 27 (186)
T PRK14521 12 RKGKAFYWIVAADSRA 27 (186)
T ss_pred CCCCCeEEEEEEeCCC
Confidence 57899999996 6554
No 43
>PF00886 Ribosomal_S16: Ribosomal protein S16; InterPro: IPR000307 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 S16 is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups: Eubacterial S16. Algal and plant chloroplast S16. Cyanelle S16. Neurospora crassa mitochondrial S24 (cyt-21). S16 proteins have about 100 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2Y14_P 3UZ6_S 2J02_P 1HNZ_P 3V26_P 3KNL_P 1N34_P 2J00_P 1HNW_P 3OHC_P ....
Probab=31.01 E-value=26 Score=26.82 Aligned_cols=15 Identities=20% Similarity=0.421 Sum_probs=11.3
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
-+++|||+|.| |.+.
T Consensus 4 ~k~~P~YrIVv~d~r~ 19 (62)
T PF00886_consen 4 RKKRPFYRIVVADSRS 19 (62)
T ss_dssp STTEEEEEEEEEETTS
T ss_pred CCCCCeEEEEEEeCCc
Confidence 46899999996 5543
No 44
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=30.58 E-value=37 Score=27.12 Aligned_cols=15 Identities=20% Similarity=0.454 Sum_probs=11.7
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
-+++|||++.| |.|.
T Consensus 11 ~k~~P~YrIVv~d~r~ 26 (75)
T PRK00040 11 AKKRPFYRIVVADSRS 26 (75)
T ss_pred CCCCCeEEEEEEecCC
Confidence 57899999996 5553
No 45
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=30.48 E-value=35 Score=28.28 Aligned_cols=15 Identities=20% Similarity=0.452 Sum_probs=11.5
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
.++.|||++.| |.|.
T Consensus 11 ~kk~P~YrIVVaDsrs 26 (87)
T COG0228 11 SKKRPFYRIVVADSRS 26 (87)
T ss_pred CccCCeEEEEEeccCC
Confidence 57899999996 5543
No 46
>PF10845 DUF2576: Protein of unknown function (DUF2576); InterPro: IPR022556 The function of this viral family of proteins is unknown. The entry contains Orf5 from Autographa californica nuclear polyhedrosis virus (AcMNPV).
Probab=28.79 E-value=20 Score=26.59 Aligned_cols=9 Identities=78% Similarity=1.354 Sum_probs=5.5
Q ss_pred ccccccCcc
Q 020759 298 CERSTTGLD 306 (321)
Q Consensus 298 ~~~~~~~~~ 306 (321)
|+||+||+|
T Consensus 31 ctRs~t~fD 39 (48)
T PF10845_consen 31 CTRSTTGFD 39 (48)
T ss_pred HHhcCCCcc
Confidence 666666665
No 47
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=28.48 E-value=20 Score=24.52 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=15.6
Q ss_pred eeeecccccccc----------cccccccHHhhH
Q 020759 96 ILFFFFQLDLAT----------RVQCALNMEEYD 119 (321)
Q Consensus 96 i~cf~cqldl~~----------RLgCp~cYe~F~ 119 (321)
|.||.|+..+.- ++.||.|-..|.
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 557777654432 777888876664
No 48
>PRK14524 rpsP 30S ribosomal protein S16; Provisional
Probab=26.87 E-value=47 Score=27.75 Aligned_cols=15 Identities=27% Similarity=0.435 Sum_probs=11.7
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
.++.|||+|.| |.|.
T Consensus 11 ~KkrPfYrIVvadsr~ 26 (94)
T PRK14524 11 KRKQPFYRIVVVDSRK 26 (94)
T ss_pred CCCCCeEEEEEEecCC
Confidence 57899999996 6554
No 49
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=26.75 E-value=43 Score=27.55 Aligned_cols=22 Identities=18% Similarity=0.221 Sum_probs=16.7
Q ss_pred ccccccccHHhhHHHHHHHHHHHHH
Q 020759 107 TRVQCALNMEEYDIAQQLRNKLTEV 131 (321)
Q Consensus 107 ~RLgCp~cYe~F~~a~~Lr~~L~~i 131 (321)
.-++||+|...+. .|.+++++.
T Consensus 20 ~d~~Cp~C~~~~~---~~~~~~~~~ 41 (162)
T PF13462_consen 20 FDFQCPHCAKFHE---ELEKLLKKY 41 (162)
T ss_dssp E-TTSHHHHHHHH---HHHHHHHHH
T ss_pred ECCCCHhHHHHHH---HHhhhhhhc
Confidence 3569999999887 577877773
No 50
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=25.23 E-value=2.7e+02 Score=22.43 Aligned_cols=36 Identities=19% Similarity=0.207 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 157 SIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 157 qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
+|.+|...|..++....--+.-.+.++|..|+.+..
T Consensus 50 eL~~LE~~Le~aL~~VR~rK~~~l~~~i~~l~~ke~ 85 (100)
T PF01486_consen 50 ELQQLEQQLESALKRVRSRKDQLLMEQIEELKKKER 85 (100)
T ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578888899999988887788888888888887655
No 51
>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=24.83 E-value=62 Score=33.16 Aligned_cols=107 Identities=22% Similarity=0.208 Sum_probs=62.1
Q ss_pred ccccccHHhhHHHHHHHHHHHHHHHHHhhhhhccc-----CC----CcchhHHHHHHHHHHHHHHHHHhhchhhHHHhhH
Q 020759 109 VQCALNMEEYDIAQQLRNKLTEVEEEISRQLEAKR-----GL----SSKSEAQDKALSIIRLRADLQKAIDSENYALAAD 179 (321)
Q Consensus 109 LgCp~cYe~F~~a~~Lr~~L~~ih~~~~~~h~GK~-----p~----~~~~~~~d~a~qLlqLr~~L~~AI~~E~YE~AA~ 179 (321)
.-.+.|+|..+.|..|+.-|++.+....+ .|+. |. -+..+..|..-+-..||..|..||-.|.- -.
T Consensus 56 ~IraK~~EYLdRAEkLK~yL~~~~~~~~k--~~~~a~a~~~~~k~~ds~~eg~d~~pe~kKLr~~L~sAIv~EKP---NV 130 (439)
T KOG0739|consen 56 SIRAKFTEYLDRAEKLKAYLKEKEKGAGK--KGDEAVATVPKGKKKDSDGEGEDDEPEKKKLRSALNSAIVREKP---NV 130 (439)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCCC--CCccccCCCCCCCCCCccccccCCChhHHHHHHHhhhhhhccCC---CC
Confidence 34688999999999999999987754432 2222 11 11112222322345778888888855432 22
Q ss_pred HHHHHhhHHHhhhhhhhhhhhccccccccccCcEEEeeecCceEEEE
Q 020759 180 LRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVIC 226 (321)
Q Consensus 180 LRD~Ir~Leeq~~aasa~a~~~~n~~vkFrVGQVvrHR~ygYrGVIv 226 (321)
=.+-+.-||..+++...++.- .++| =|+|.|++-.++|+..
T Consensus 131 kWsDVAGLE~AKeALKEAVIL----PIKF--PqlFtGkR~PwrgiLL 171 (439)
T KOG0739|consen 131 KWSDVAGLEGAKEALKEAVIL----PIKF--PQLFTGKRKPWRGILL 171 (439)
T ss_pred chhhhccchhHHHHHHhheee----cccc--hhhhcCCCCcceeEEE
Confidence 233344555544433222111 1344 4889999988999877
No 52
>PRK14523 rpsP 30S ribosomal protein S16; Provisional
Probab=24.66 E-value=52 Score=29.40 Aligned_cols=15 Identities=20% Similarity=0.410 Sum_probs=11.7
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
-+++|||+|.| |.|.
T Consensus 11 rKkrPfYRIVVaDsRs 26 (137)
T PRK14523 11 SKKNPFYHIVVADRRK 26 (137)
T ss_pred CCCCCeEEEEEEecCC
Confidence 57899999996 6543
No 53
>PRK14522 rpsP 30S ribosomal protein S16; Provisional
Probab=23.99 E-value=55 Score=28.49 Aligned_cols=15 Identities=13% Similarity=0.177 Sum_probs=11.8
Q ss_pred CCCCCceEEEE-eCCc
Q 020759 250 GPSQPFYQLLR-RICW 264 (321)
Q Consensus 250 gr~QPFYhVLV-D~r~ 264 (321)
-+++|||+|.| |.|.
T Consensus 12 ~KkrPfYrIVVaDsR~ 27 (116)
T PRK14522 12 RRNHVVYRLVLADVES 27 (116)
T ss_pred CCCCCeEEEEEeecCC
Confidence 57899999996 6554
No 54
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=23.86 E-value=29 Score=29.85 Aligned_cols=22 Identities=23% Similarity=0.252 Sum_probs=15.7
Q ss_pred eeccccccc-ccccccccHHhhH
Q 020759 98 FFFFQLDLA-TRVQCALNMEEYD 119 (321)
Q Consensus 98 cf~cqldl~-~RLgCp~cYe~F~ 119 (321)
||.||=.|. ++|.||.|-...+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i~ 23 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEIE 23 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEEE
Confidence 778887665 3888888876543
No 55
>PRK11020 hypothetical protein; Provisional
Probab=23.18 E-value=2.1e+02 Score=25.06 Aligned_cols=38 Identities=21% Similarity=0.127 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759 155 ALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (321)
Q Consensus 155 a~qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~ 192 (321)
..+|..++.+|..|+...|-|.-+++.++|.+|+.+..
T Consensus 11 ~drLD~~~~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~ 48 (118)
T PRK11020 11 SDRLDAIRHKLAAASLRGDAEKYAQFEKEKATLEAEIA 48 (118)
T ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 34577788888889888888888888888888877655
No 56
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=22.66 E-value=5.7e+02 Score=25.97 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=19.6
Q ss_pred hHHHHHHhhHHHhhhhh----hhhhhhccccccccccCcEEEe
Q 020759 178 ADLRDQICKLEAESLAA----SATALAFENARFAFRLGQKVNH 216 (321)
Q Consensus 178 A~LRD~Ir~Leeq~~aa----sa~a~~~~n~~vkFrVGQVvrH 216 (321)
..|.+++..|+++.... ...+...-.+.+.+.+|....-
T Consensus 392 ~~l~~~~~~l~~~l~~~~~~~~I~v~~~vypgv~i~i~~~~~~ 434 (451)
T PF03961_consen 392 KELKEELKELKEELERSYKEARIKVRKRVYPGVEIHIGNKSYK 434 (451)
T ss_pred HHHHHHHHHHHHHHHhhccceEEEECCEEECCEEEEECCEEEE
Confidence 55666666666554422 1122233345566666665543
No 57
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=22.24 E-value=62 Score=26.06 Aligned_cols=20 Identities=20% Similarity=0.270 Sum_probs=14.7
Q ss_pred cccccccHHhhHHHHHHHHHHHH
Q 020759 108 RVQCALNMEEYDIAQQLRNKLTE 130 (321)
Q Consensus 108 RLgCp~cYe~F~~a~~Lr~~L~~ 130 (321)
-..||+|+..+. .|.+++.+
T Consensus 14 D~~Cp~C~~~~~---~l~~~~~~ 33 (154)
T cd03023 14 DYNCGYCKKLAP---ELEKLLKE 33 (154)
T ss_pred CCCChhHHHhhH---HHHHHHHH
Confidence 468999999876 67665543
No 58
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=21.90 E-value=1.5e+02 Score=23.78 Aligned_cols=19 Identities=37% Similarity=0.310 Sum_probs=16.0
Q ss_pred HHHhhHHHHHHhhHHHhhh
Q 020759 174 YALAADLRDQICKLEAESL 192 (321)
Q Consensus 174 YE~AA~LRD~Ir~Leeq~~ 192 (321)
+++|-+|+++|..||.-..
T Consensus 48 ~~~a~rm~eRI~tLE~ILd 66 (75)
T TIGR02976 48 YAKADRLEERIDTLERILD 66 (75)
T ss_pred HHHHHHHHHHHHHHHHHHc
Confidence 5788999999999997655
No 59
>PF12510 Smoothelin: Smoothelin cytoskeleton protein; InterPro: IPR022189 This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00307 from PFAM. Smoothelin is a cytoskeletal protein specifically expressed in differentiated smooth muscle cells and has been shown to co-localize with smooth muscle alpha actin.
Probab=21.63 E-value=2.1e+02 Score=21.83 Aligned_cols=38 Identities=18% Similarity=0.195 Sum_probs=27.2
Q ss_pred hHHHHHHHHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHh
Q 020759 150 EAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAE 190 (321)
Q Consensus 150 ~~~d~a~qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq 190 (321)
..++.-..+..|..-|..+ .+||+-..||-.|+.|.++
T Consensus 16 ~~l~~I~De~~L~kmLe~~---~dyeeRr~IRaaiR~lr~~ 53 (54)
T PF12510_consen 16 EELESIEDEEVLEKMLEAT---TDYEERRRIRAAIRELRKK 53 (54)
T ss_pred HHHHHhhhHHHHHHHHHHh---ccHHHHHHHHHHHHHHHhc
Confidence 3344444455566566666 5999999999999999865
No 60
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=20.40 E-value=1.1e+02 Score=23.24 Aligned_cols=22 Identities=45% Similarity=0.718 Sum_probs=19.6
Q ss_pred cccCcEEEeeecCce---EEEEccc
Q 020759 208 FRLGQKVNHKIFGYR---AVICGMD 229 (321)
Q Consensus 208 FrVGQVvrHR~ygYr---GVIvGWD 229 (321)
|.+|++|=-|.-||. |+|++-+
T Consensus 1 f~~GdlVWaK~~g~pwWPa~V~~~~ 25 (86)
T PF00855_consen 1 FRPGDLVWAKLKGYPWWPARVCDPD 25 (86)
T ss_dssp -STTEEEEEEETTSEEEEEEEEECC
T ss_pred CCCCCEEEEEeCCCCCCceEEeecc
Confidence 789999999999998 9999887
No 61
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=20.02 E-value=53 Score=24.47 Aligned_cols=25 Identities=28% Similarity=0.602 Sum_probs=18.1
Q ss_pred eecccccccCCCCCCCccccccccccCceeeecccccccc
Q 020759 68 ANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLAT 107 (321)
Q Consensus 68 ~~~~~~~~~~~~~~~~~~~e~s~s~n~~i~cf~cqldl~~ 107 (321)
+.||+.|.|- +..+.|++|++.+..
T Consensus 24 A~~Gfyy~~~---------------~d~v~C~~C~~~l~~ 48 (71)
T smart00238 24 AEAGFYYTGV---------------GDEVKCFFCGGELDN 48 (71)
T ss_pred HHcCCeECCC---------------CCEEEeCCCCCCcCC
Confidence 4677777652 336889999998766
No 62
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=20.01 E-value=46 Score=25.45 Aligned_cols=21 Identities=19% Similarity=0.297 Sum_probs=12.5
Q ss_pred cccccHHhhHHHHHHHHHHHH
Q 020759 110 QCALNMEEYDIAQQLRNKLTE 130 (321)
Q Consensus 110 gCp~cYe~F~~a~~Lr~~L~~ 130 (321)
-||.|+.+++.+..|+.-|+-
T Consensus 26 tCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 26 TCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp E-TTT--EESSHHHHHHHHHH
T ss_pred CCCcchhhccchhhHHHHHHH
Confidence 478888888877777765543
Done!