Query 019893
Match_columns 334
No_of_seqs 230 out of 583
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:23:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019893.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019893hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08755 YccV-like: Hemimethyl 100.0 4.9E-35 1.1E-39 240.5 4.5 100 205-310 1-100 (100)
2 TIGR02097 yccV hemimethylated 100.0 7.2E-34 1.6E-38 235.1 7.6 100 206-310 2-101 (101)
3 PRK14129 heat shock protein Hs 99.9 4.3E-24 9.3E-29 176.8 7.5 90 206-300 4-93 (105)
4 COG3785 Uncharacterized conser 99.8 1.9E-21 4E-26 161.5 4.0 101 205-311 12-112 (116)
5 COG3880 Modulator of heat shoc 99.3 1.7E-12 3.6E-17 116.3 5.2 90 98-191 82-171 (176)
6 PF02151 UVR: UvrB/uvrC motif; 98.0 1E-05 2.2E-10 55.4 4.5 34 157-190 3-36 (36)
7 KOG4408 Putative Mg2+ and Co2+ 97.9 1.5E-05 3.3E-10 78.8 5.1 114 203-319 62-238 (386)
8 COG0556 UvrB Helicase subunit 95.2 0.046 1E-06 57.8 6.8 45 148-192 616-660 (663)
9 PRK00558 uvrC excinuclease ABC 94.3 0.055 1.2E-06 57.5 5.0 36 157-192 203-238 (598)
10 PRK05298 excinuclease ABC subu 93.4 0.11 2.4E-06 55.5 5.2 40 153-192 610-649 (652)
11 TIGR00631 uvrb excinuclease AB 93.0 0.1 2.3E-06 56.0 4.2 36 153-188 620-655 (655)
12 PRK12306 uvrC excinuclease ABC 92.7 0.15 3.2E-06 53.6 4.8 35 158-192 194-228 (519)
13 PRK14667 uvrC excinuclease ABC 92.5 0.14 3.1E-06 54.2 4.5 35 158-192 201-235 (567)
14 PRK14666 uvrC excinuclease ABC 92.5 0.16 3.4E-06 55.1 4.8 35 158-192 203-237 (694)
15 PRK07883 hypothetical protein; 92.2 0.15 3.2E-06 53.7 4.2 35 158-192 408-442 (557)
16 TIGR00194 uvrC excinuclease AB 92.0 0.22 4.8E-06 52.9 5.1 35 158-192 196-230 (574)
17 PRK14672 uvrC excinuclease ABC 91.8 0.22 4.7E-06 54.0 4.8 35 158-192 207-241 (691)
18 PRK14669 uvrC excinuclease ABC 91.8 0.24 5.2E-06 53.2 5.1 35 158-192 205-239 (624)
19 PRK14668 uvrC excinuclease ABC 90.0 0.33 7.2E-06 51.6 4.2 35 158-192 201-235 (577)
20 PRK14671 uvrC excinuclease ABC 89.9 0.34 7.4E-06 51.9 4.2 35 158-192 217-251 (621)
21 PRK14670 uvrC excinuclease ABC 89.5 0.38 8.3E-06 51.2 4.2 35 158-192 179-213 (574)
22 COG0322 UvrC Nuclease subunit 88.1 1.2 2.6E-05 47.6 6.6 34 158-191 204-237 (581)
23 PF04420 CHD5: CHD5-like prote 75.0 8.6 0.00019 34.3 6.1 46 150-195 41-86 (161)
24 PF09465 LBR_tudor: Lamin-B re 71.9 10 0.00022 28.8 4.9 28 204-231 2-33 (55)
25 KOG4825 Component of synaptic 66.2 16 0.00035 38.6 6.6 71 103-193 174-244 (666)
26 PF02151 UVR: UvrB/uvrC motif; 63.7 8.4 0.00018 26.2 2.8 32 102-133 4-35 (36)
27 PF02559 CarD_CdnL_TRCF: CarD- 62.1 9.5 0.00021 30.7 3.3 55 207-282 1-55 (98)
28 PRK00409 recombination and DNA 61.5 60 0.0013 36.0 10.3 23 207-229 636-658 (782)
29 KOG0412 Golgi transport comple 60.4 22 0.00047 39.3 6.5 46 146-191 115-163 (773)
30 PF00855 PWWP: PWWP domain; I 60.0 34 0.00075 26.2 6.1 56 208-282 1-59 (86)
31 TIGR01069 mutS2 MutS2 family p 57.4 69 0.0015 35.5 9.9 21 209-229 626-646 (771)
32 smart00293 PWWP domain with co 57.2 36 0.00077 25.5 5.5 59 208-281 1-62 (63)
33 PF00804 Syntaxin: Syntaxin; 55.2 96 0.0021 24.0 9.2 66 116-191 4-72 (103)
34 PRK11020 hypothetical protein; 52.3 41 0.0009 29.2 5.7 43 150-192 6-48 (118)
35 PF06667 PspB: Phage shock pro 50.9 37 0.0008 27.2 4.9 44 136-192 23-66 (75)
36 PF03961 DUF342: Protein of un 46.9 1.2E+02 0.0026 31.1 9.1 15 178-192 392-406 (451)
37 PF02211 NHase_beta: Nitrile h 45.4 45 0.00097 31.7 5.4 55 203-263 130-197 (222)
38 PF09340 NuA4: Histone acetylt 44.1 40 0.00086 27.0 4.1 14 220-233 38-51 (80)
39 cd05162 PWWP The PWWP domain, 43.8 64 0.0014 25.2 5.3 60 208-283 1-63 (87)
40 PRK09458 pspB phage shock prot 43.6 44 0.00096 26.9 4.3 44 137-193 24-67 (75)
41 PF11365 DUF3166: Protein of u 36.9 49 0.0011 27.8 3.7 44 160-213 5-48 (96)
42 TIGR02976 phageshock_pspB phag 36.6 80 0.0017 25.3 4.7 45 135-192 22-66 (75)
43 PF15591 Imm17: Immunity prote 35.3 31 0.00067 27.8 2.2 44 216-281 21-64 (74)
44 PF13805 Pil1: Eisosome compon 34.3 2E+02 0.0044 28.3 8.0 33 109-144 117-149 (271)
45 cd05835 Dnmt3b_related The PWW 33.2 86 0.0019 25.1 4.5 56 208-282 1-59 (87)
46 cd05837 MSH6_like The PWWP dom 31.5 1E+02 0.0022 25.8 4.9 66 207-284 2-70 (110)
47 cd05840 SPBC215_ISWI_like The 30.8 1.2E+02 0.0025 24.9 5.0 62 208-282 1-65 (93)
48 PRK11546 zraP zinc resistance 28.3 3.5E+02 0.0077 24.2 7.9 15 177-191 91-105 (143)
49 PF06442 DHFR_2: R67 dihydrofo 28.2 55 0.0012 26.0 2.5 27 203-229 19-46 (78)
50 PF12848 ABC_tran_2: ABC trans 28.2 2.7E+02 0.006 21.3 7.8 20 110-129 10-29 (85)
51 cd05834 HDGF_related The PWWP 27.3 1.6E+02 0.0034 23.5 5.1 55 207-283 2-59 (83)
52 PF09926 DUF2158: Uncharacteri 26.7 66 0.0014 24.1 2.6 21 208-228 1-21 (53)
53 PF10475 DUF2450: Protein of u 26.6 2.6E+02 0.0057 26.9 7.5 35 153-187 122-156 (291)
54 smart00333 TUDOR Tudor domain. 26.2 1.7E+02 0.0037 20.6 4.7 50 207-282 2-54 (57)
55 PF06133 DUF964: Protein of un 25.8 3.2E+02 0.007 21.9 6.8 73 118-192 3-75 (108)
56 KOG4253 Tryptophan-rich basic 24.6 2E+02 0.0042 26.6 5.7 44 153-196 48-91 (175)
57 TIGR00002 S16 ribosomal protei 24.5 53 0.0012 26.4 1.9 13 250-262 10-22 (78)
58 PF01486 K-box: K-box region; 24.4 3.7E+02 0.0081 21.7 6.9 38 154-191 47-84 (100)
59 PF08317 Spc7: Spc7 kinetochor 24.3 4.7E+02 0.01 25.7 8.8 39 124-167 182-220 (325)
60 CHL00005 rps16 ribosomal prote 23.4 53 0.0012 26.7 1.7 13 250-262 11-23 (82)
61 PF00886 Ribosomal_S16: Riboso 22.7 43 0.00093 25.6 1.0 13 250-262 4-16 (62)
62 PF07798 DUF1640: Protein of u 22.6 5.3E+02 0.012 23.1 8.2 18 152-169 83-100 (177)
63 KOG3419 Mitochondrial/chloropl 21.7 58 0.0013 28.1 1.6 13 250-262 12-24 (112)
64 PF13234 rRNA_proc-arch: rRNA- 21.6 5.9E+02 0.013 24.0 8.7 56 174-232 42-100 (268)
65 PF11855 DUF3375: Protein of u 21.4 4.1E+02 0.0089 27.7 8.2 68 113-188 138-205 (478)
66 PRK00040 rpsP 30S ribosomal pr 21.1 64 0.0014 25.8 1.7 13 250-262 11-23 (75)
67 PF04568 IATP: Mitochondrial A 21.0 2.1E+02 0.0047 24.1 4.9 28 156-191 72-99 (100)
68 PF05529 Bap31: B-cell recepto 20.8 4.2E+02 0.0092 23.7 7.2 32 152-188 157-188 (192)
69 TIGR00570 cdk7 CDK-activating 20.4 1.6E+02 0.0035 29.5 4.7 20 38-57 24-43 (309)
70 PRK14525 rpsP 30S ribosomal pr 20.4 66 0.0014 26.6 1.7 13 250-262 12-24 (88)
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=100.00 E-value=4.9e-35 Score=240.51 Aligned_cols=100 Identities=42% Similarity=0.744 Sum_probs=51.8
Q ss_pred ccccccccEEEEecCCeeEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccCCC
Q 019893 205 RFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASDQP 284 (334)
Q Consensus 205 ~VkFrVGQVVrHrrygYrGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~~p 284 (334)
.++|+|||||+||+|||+|||+|||+.|+++++|+.+++++.++. ++||||+||+++++. +..+||||+||++...+
T Consensus 1 ~~~f~vGqvv~Hr~~~y~GVIvgwD~~~~~~~~W~~~~~~~~~~~-~~qPfY~vLv~~~~~--~~~~YVaEenL~~~~~~ 77 (100)
T PF08755_consen 1 NVKFRVGQVVRHRRYGYRGVIVGWDPECQAPEEWIEQMGVDNLPR-RNQPFYHVLVDDRDS--PPVRYVAEENLEPDSTP 77 (100)
T ss_dssp --SS-TT-EEEETTT--EEEEEEEE-------------------------EEEEEEE-SS----EEEEEEGGGEEE---S
T ss_pred CcccccCCEEEEeeeCccEEEECcccccCCCchHHHhcccccccc-CCCCcEEEEEecCCc--cceEEecccccccCCCC
Confidence 379999999999999999999999999999999999999887766 999999999998754 45599999999887654
Q ss_pred CCCccCchhhhhhccccCCCCceeeC
Q 019893 285 DMARFDHPYISFLFYGTDTAGDFIPI 310 (334)
Q Consensus 285 ~~~pI~HP~ig~yF~rFD~~grYvPn 310 (334)
.++.||.|++||++||++ +|+||
T Consensus 78 --~~i~hp~i~~yF~~fd~~-~y~p~ 100 (100)
T PF08755_consen 78 --EPINHPEIGRYFKRFDGG-RYVPN 100 (100)
T ss_dssp ----TT-HHHHHHHHHHTT-------
T ss_pred --CCcCChHHHHHHHhhCCC-cCccC
Confidence 789999999999999876 89997
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=100.00 E-value=7.2e-34 Score=235.07 Aligned_cols=100 Identities=40% Similarity=0.656 Sum_probs=90.2
Q ss_pred cccccccEEEEecCCeeEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccCCCC
Q 019893 206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASDQPD 285 (334)
Q Consensus 206 VkFrVGQVVrHrrygYrGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~~p~ 285 (334)
++|+||||||||+|||+|||+||||.|+++++|+.+|+++..+. ++|||||||+++++.. +.++||||+||++..++
T Consensus 2 ~kf~IGqvvrHr~~~yrGVI~gwDp~~~~~eeW~~~~~~~~~p~-~~qPfYhvLv~~~~~~-~~~aYVaE~nL~~~~~~- 78 (101)
T TIGR02097 2 AKFRIGQVVRHKLFGYRGVVIDVDPEYSNTEEWLDAIPVEIRPL-RDQPFYHVLAEDDEGL-PYVAYVAEQNLLYDDSD- 78 (101)
T ss_pred ceecCCCEEEecccCCCEEEEeEChhccCChHHHHhhhcccCcc-cCCCceEEEEeCCCCc-ceeEEeehhhcccCCCC-
Confidence 68999999999999999999999999999999999999887665 9999999999986543 38899999999998765
Q ss_pred CCccCchhhhhhccccCCCCceeeC
Q 019893 286 MARFDHPYISFLFYGTDTAGDFIPI 310 (334)
Q Consensus 286 ~~pI~HP~ig~yF~rFD~~grYvPn 310 (334)
.+|.||.++.||+.|+++ +|+|+
T Consensus 79 -~~i~hP~~~~~F~~~~~~-~y~~~ 101 (101)
T TIGR02097 79 -EPIEHPQVDELFDGFDEG-LQKPR 101 (101)
T ss_pred -CCCCCCCHHHHHhhhccC-cccCC
Confidence 899999999999999765 79875
No 3
>PRK14129 heat shock protein HspQ; Provisional
Probab=99.90 E-value=4.3e-24 Score=176.76 Aligned_cols=90 Identities=23% Similarity=0.372 Sum_probs=78.4
Q ss_pred cccccccEEEEecCCeeEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccCCCC
Q 019893 206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASDQPD 285 (334)
Q Consensus 206 VkFrVGQVVrHrrygYrGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~~p~ 285 (334)
-||.|||+||||.|||||||++.||.|+.+++|...+..+ .+.++|||||||+++.+ +.+.++||||.||++.++
T Consensus 4 akF~IGQ~VrHrl~~yrGVV~DVDP~fs~~e~w~~~ia~~--~p~kdqPwYHvl~en~~-~~~v~tYVaE~nL~~d~s-- 78 (105)
T PRK14129 4 SKFGIGQQVRHSLLGYLGVVVDIDPEYSLEEPSPDELAVN--DELRAAPWYHVVMEDDD-GQPVHTYLAEAQLSSELQ-- 78 (105)
T ss_pred ccccCCcEEEEeecCCCeEEEeeCCCcCCCchhHHhhccC--CCccCCCceEEEEEcCC-CceEEEEeeecccCCCCC--
Confidence 4899999999999999999999999999999999998654 45689999999997643 334459999999999875
Q ss_pred CCccCchhhhhhccc
Q 019893 286 MARFDHPYISFLFYG 300 (334)
Q Consensus 286 ~~pI~HP~ig~yF~r 300 (334)
..++.||.++.+|..
T Consensus 79 ~epi~hP~l~elf~~ 93 (105)
T PRK14129 79 DEHPEQPSMDELAES 93 (105)
T ss_pred CCCCCCCCHHHHHHH
Confidence 489999999999974
No 4
>COG3785 Uncharacterized conserved protein [Function unknown]
Probab=99.83 E-value=1.9e-21 Score=161.52 Aligned_cols=101 Identities=31% Similarity=0.509 Sum_probs=88.2
Q ss_pred ccccccccEEEEecCCeeEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccCCC
Q 019893 205 RFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASDQP 284 (334)
Q Consensus 205 ~VkFrVGQVVrHrrygYrGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~~p 284 (334)
.-||.|||||||+.|+|+|||++.||++...++|...+..+ .++.++|||||||+++++ .+.++||+|.||....+
T Consensus 12 ~aKF~IGQvVRHrlfpfrGVV~DvDPeyanteew~~~ip~~-~rp~rdqPfYHllaEnde--~~yvaYvsEqnL~~d~s- 87 (116)
T COG3785 12 AAKFGIGQVVRHRLFPFRGVVFDVDPEYANTEEWPDEIPVN-IRPLRDQPFYHLLAENDE--TEYVAYVSEQNLVSDLS- 87 (116)
T ss_pred HhhcchhhhhhhhhcccceEEEecCcccccCccChhhcccc-ccccccCCceeeeeecCC--ccceeeehhhhcccccc-
Confidence 35899999999999999999999999999999999998654 357789999999998854 57899999999998865
Q ss_pred CCCccCchhhhhhccccCCCCceeeCh
Q 019893 285 DMARFDHPYISFLFYGTDTAGDFIPIK 311 (334)
Q Consensus 285 ~~~pI~HP~ig~yF~rFD~~grYvPn~ 311 (334)
..|+.||.++..|.+++. |.|.|..
T Consensus 88 -dep~~~Pqidelf~~~~~-g~~~pk~ 112 (116)
T COG3785 88 -DEPPRHPQIDELFDKIRK-GLQAPKL 112 (116)
T ss_pred -CCCCCCCCHHHHHHhhhc-ccccccc
Confidence 478999999999999865 4788763
No 5
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=99.31 E-value=1.7e-12 Score=116.25 Aligned_cols=90 Identities=24% Similarity=0.285 Sum_probs=80.5
Q ss_pred hhHhHhhhhhhhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHhhchhchhHH
Q 019893 98 FFFFQLDLATRVQCALNMEEYDIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALA 177 (334)
Q Consensus 98 ~f~~~~~~~~rlq~~~~~~~y~~a~~l~~~l~~i~~e~~~~~~~K~~~~~~~~a~d~a~qL~~Lk~~Lq~aI~~E~yE~A 177 (334)
+=|=+.-..+|+|||-+|..|.. +|.|-+.+|++. ...|.||.| .+.......+.+|..|+..||++|+.|+||+|
T Consensus 82 ~Tfk~f~~~g~fGCaeCY~tf~~--~i~pi~~rvq~g-~~~H~GK~P-~~~~~~i~~~~~I~~L~e~Lq~~i~~EefEeA 157 (176)
T COG3880 82 MTFKEFIQSGLFGCAECYKTFES--QISPIITRVQGG-YVEHVGKVP-KRIGRKINPKRKIIALKEALQDLIEREEFEEA 157 (176)
T ss_pred ccHHHHHHhcccchHHHHHHHHH--HhhHHHHHhhCC-ceeecCcCc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44556677899999999999999 999999999855 378999999 66777889999999999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q 019893 178 ADLRDQICKLEAES 191 (334)
Q Consensus 178 A~LRD~Ik~LE~~~ 191 (334)
|.+||+|+.|+++.
T Consensus 158 A~iRDqIr~Lk~k~ 171 (176)
T COG3880 158 AVIRDQIRALKAKN 171 (176)
T ss_pred HHHHHHHHHHHhhc
Confidence 99999999998764
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=98.00 E-value=1e-05 Score=55.41 Aligned_cols=34 Identities=35% Similarity=0.556 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHH
Q 019893 157 SIIRLRADLQKAIDSENYALAADLRDQICKLEAE 190 (334)
Q Consensus 157 qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~ 190 (334)
.|..|+.+|..|++.++||+||.|||+|..|+++
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 5778999999999999999999999999999764
No 7
>KOG4408 consensus Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism]
Probab=97.88 E-value=1.5e-05 Score=78.84 Aligned_cols=114 Identities=20% Similarity=0.312 Sum_probs=82.2
Q ss_pred ccccccccccEEEEecCCeeEEEE-cccccccCChhhHHHh--------------------hhh-------------hcC
Q 019893 203 NARFAFRLGQKVNHKIFGYRAVIC-GMDPVCCESSSWMEIA--------------------QVE-------------KLQ 248 (334)
Q Consensus 203 ~~~VkFrVGQVVrHrrygYrGVIv-GWD~~c~a~eeW~~~~--------------------~v~-------------~l~ 248 (334)
...-+|.-||.|+|+.|||+|||+ .|+..-. +|.... ... +.-
T Consensus 62 ~~~~~~etgqsF~h~~f~yvgvv~~~w~arlk---~wd~ln~~~~~aal~ega~e~dl~a~e~s~~~kLp~~~r~~yrev 138 (386)
T KOG4408|consen 62 EKTQKYETGQSFLHDTFGYVGVVLFPWAARLK---DWDDLNKYLEPAALKEGAREPDLDAVEASIGCKLPDDYRCSYREV 138 (386)
T ss_pred ccCCcccccceeeeeecccceEEEEechHhhh---hhhhcccccccchhhccCcccchhhhhhcccccCCCccccchhhc
Confidence 445689999999999999999997 7876221 111111 000 123
Q ss_pred CCCCCCeEEEEeecCCCCC--------------------------ceeeeecccCccccCCCCCCccCchhhhhhccc-c
Q 019893 249 QGPSQPFYQVLVDVHADPN--------------------------ILVAYVAEENLLASDQPDMARFDHPYISFLFYG-T 301 (334)
Q Consensus 249 ~g~~QPFY~VLvd~~d~~~--------------------------~~~~YVAEENLe~~~~p~~~pI~HP~ig~yF~r-F 301 (334)
.|..+.||+||.+.+|+++ +...||..+.|.+++..+..++.|..+..+|.- .
T Consensus 139 ~Gq~l~~yqvLi~~~d~sH~~~ev~~e~~t~~~nf~~r~~L~y~ipgld~v~hedilpyts~e~~~g~heLf~~~pdl~r 218 (386)
T KOG4408|consen 139 KGQTLTFYQVLIDMRDCSHIRSEVQTEAVTFLGNFDSRQGLKYAIPGLDYVSHEDILPYTSSEAVPGQHELFDQFPDLAR 218 (386)
T ss_pred CCeEEeehheeeecccCccccchhhhhhhhhhcCcccccchheecccceeEeeccccccccccccccchhhhhhhhhhhc
Confidence 6788999999999887653 457799999999999888899999777777541 1
Q ss_pred CC--CCceeeChhhHHhcCC
Q 019893 302 DT--AGDFIPIKQLREKYNR 319 (334)
Q Consensus 302 D~--~grYvPn~~Lre~YPd 319 (334)
|. ...|+-.+.|++.|-.
T Consensus 219 ~~~~~~~f~~q~tl~~W~e~ 238 (386)
T KOG4408|consen 219 DPAAIPPFVIQDTLTAWQES 238 (386)
T ss_pred CcccCCchhhhHHHHHHHhc
Confidence 32 2268888889988874
No 8
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=95.18 E-value=0.046 Score=57.77 Aligned_cols=45 Identities=29% Similarity=0.389 Sum_probs=39.6
Q ss_pred chhHHHHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 148 KSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 148 ~~~a~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+....+.+..|.+|+.+|++|-++-+||+||.|||+|++|+++..
T Consensus 616 ~~~~~e~~~~I~~Le~~M~~aA~~l~FE~Aa~lRD~i~~L~~~~~ 660 (663)
T COG0556 616 KMSKKELEKLIKKLEKEMKEAAKNLEFEEAARLRDEIKELKEELL 660 (663)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhc
Confidence 345667888899999999999999999999999999999987654
No 9
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=94.34 E-value=0.055 Score=57.48 Aligned_cols=36 Identities=25% Similarity=0.307 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 157 SIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 157 qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
-+.+|+.+|++|.++.+||+||.+||+|+.|++-.+
T Consensus 203 ~i~~L~~~M~~aa~~l~FE~Aa~~RD~i~aL~~~~~ 238 (598)
T PRK00558 203 VLKELEEKMEEASENLEFERAARYRDQIQALRRVQE 238 (598)
T ss_pred HHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHHh
Confidence 466799999999999999999999999999986654
No 10
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=93.41 E-value=0.11 Score=55.55 Aligned_cols=40 Identities=30% Similarity=0.378 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 153 DKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 153 d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
.....+..|+.+|++|.+.++||+||.+||+|+.|++...
T Consensus 610 ~~~~~~~~l~~~M~~aa~~l~fE~Aa~~Rd~i~~l~~~~~ 649 (652)
T PRK05298 610 ELEKLIKELEKQMKEAAKNLEFEEAARLRDEIKELKEELL 649 (652)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhc
Confidence 4445677899999999999999999999999999987654
No 11
>TIGR00631 uvrb excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
Probab=92.97 E-value=0.1 Score=55.97 Aligned_cols=36 Identities=28% Similarity=0.399 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHH
Q 019893 153 DKALSIIRLRADLQKAIDSENYALAADLRDQICKLE 188 (334)
Q Consensus 153 d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE 188 (334)
+....|..|+.+|++|.++.+||+||++||+|+.|+
T Consensus 620 ~~~~~i~~l~~~M~~aa~~l~FE~Aa~~RD~i~~L~ 655 (655)
T TIGR00631 620 ELKKLIKQLEKEMKQAARNLEFEEAARLRDEILELK 655 (655)
T ss_pred HHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence 445567789999999999999999999999999874
No 12
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=92.71 E-value=0.15 Score=53.58 Aligned_cols=35 Identities=20% Similarity=0.336 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+.+|+.+|++|-++.+||+||++||.|+.|+.-.+
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 55688999999999999999999999999975443
No 13
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=92.54 E-value=0.14 Score=54.22 Aligned_cols=35 Identities=26% Similarity=0.223 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+..|+++|+.|-++.+||+||++||.|+.|+.-.+
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 55789999999999999999999999999976544
No 14
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=92.50 E-value=0.16 Score=55.13 Aligned_cols=35 Identities=31% Similarity=0.387 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+..|+.+|++|.++.+||+||++||.|+.|+.-.+
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 55689999999999999999999999999976554
No 15
>PRK07883 hypothetical protein; Validated
Probab=92.23 E-value=0.15 Score=53.74 Aligned_cols=35 Identities=29% Similarity=0.413 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+.+|+.+|++|-++.+||+||++||+|+.|+.-.+
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 55789999999999999999999999999975443
No 16
>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=91.97 E-value=0.22 Score=52.86 Aligned_cols=35 Identities=29% Similarity=0.385 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+.+|+.+|++|-++.+||+||.+||.|+.|+.-.+
T Consensus 196 ~~~L~~~M~~aa~~l~FE~Aa~~Rd~i~~l~~~~~ 230 (574)
T TIGR00194 196 IKELEQKMEKASENLEFEEAARIRDQIAAVRELNE 230 (574)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHh
Confidence 55688999999999999999999999999975444
No 17
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=91.81 E-value=0.22 Score=54.04 Aligned_cols=35 Identities=26% Similarity=0.474 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+..|+.+|++|-++.+||+||++||.|+.|+.-.+
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 55689999999999999999999999999986554
No 18
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=91.81 E-value=0.24 Score=53.18 Aligned_cols=35 Identities=31% Similarity=0.323 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+..|+.+|+.|-++.+||+||++||.|+.|+.-.+
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 45689999999999999999999999999976544
No 19
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=90.05 E-value=0.33 Score=51.61 Aligned_cols=35 Identities=29% Similarity=0.374 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+..|+.+|++|-++.+||+||++||.|+.|+.-.+
T Consensus 201 ~~~l~~~m~~aa~~l~FE~Aa~~Rd~i~~l~~~~~ 235 (577)
T PRK14668 201 ADPLRREMEAAAQAQEFERAANLRDRLEAVEAFHG 235 (577)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Confidence 55789999999999999999999999999976544
No 20
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=89.89 E-value=0.34 Score=51.92 Aligned_cols=35 Identities=31% Similarity=0.390 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+..|+.+|++|-++.+||+||++||.|+.|+.-.+
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 55789999999999999999999999999975443
No 21
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=89.51 E-value=0.38 Score=51.15 Aligned_cols=35 Identities=20% Similarity=0.330 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+..|+.+|+.|-++.+||+||++||.|+.|+.-.+
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 55689999999999999999999999999976554
No 22
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=88.07 E-value=1.2 Score=47.64 Aligned_cols=34 Identities=32% Similarity=0.436 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHH
Q 019893 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAES 191 (334)
Q Consensus 158 L~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~ 191 (334)
+..|+++|++|-+..+||.||.+||.|+.|+.-.
T Consensus 204 ~~~L~~~M~~As~~l~FE~Aa~~RD~i~al~~l~ 237 (581)
T COG0322 204 LQELEEKMEEASENLDFERAARLRDQIKALEKLQ 237 (581)
T ss_pred HHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHH
Confidence 5578899999999999999999999999996544
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=74.98 E-value=8.6 Score=34.30 Aligned_cols=46 Identities=24% Similarity=0.307 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHHHHH
Q 019893 150 EAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLAAS 195 (334)
Q Consensus 150 ~a~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~aas 195 (334)
+-.....|+.++++++...=..++|.+.|+++-++.+|+++++...
T Consensus 41 ~~~~l~~Ei~~l~~E~~~iS~qDeFAkwaKl~Rk~~kl~~el~~~~ 86 (161)
T PF04420_consen 41 EQRQLRKEILQLKRELNAISAQDEFAKWAKLNRKLDKLEEELEKLN 86 (161)
T ss_dssp HHHHHHHHHHHHHHHHTTS-TTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456677888999999988888999999999999999998887433
No 24
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=71.94 E-value=10 Score=28.81 Aligned_cols=28 Identities=21% Similarity=0.328 Sum_probs=21.1
Q ss_pred cccccccccEEEEecCC----eeEEEEccccc
Q 019893 204 ARFAFRLGQKVNHKIFG----YRAVICGMDPV 231 (334)
Q Consensus 204 ~~VkFrVGQVVrHrryg----YrGVIvGWD~~ 231 (334)
|+.+|.+|.+|.-++-| |.|.|++.|+.
T Consensus 2 p~~k~~~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 2 PSRKFAIGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp SSSSS-SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred CcccccCCCEEEEECCCCCcEEEEEEEEeccc
Confidence 46899999999998877 69999998863
No 25
>KOG4825 consensus Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa) [Signal transduction mechanisms]
Probab=66.20 E-value=16 Score=38.60 Aligned_cols=71 Identities=27% Similarity=0.372 Sum_probs=49.7
Q ss_pred hhhhhhhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHhhchhchhHHHHHHH
Q 019893 103 LDLATRVQCALNMEEYDIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRD 182 (334)
Q Consensus 103 ~~~~~rlq~~~~~~~y~~a~~l~~~l~~i~~e~~~~~~~K~~~~~~~~a~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD 182 (334)
-.+..+.|-|.--|.|+-|+-+..-+.... ..| .+|.+|..+.-.||++|+|..|..+.|
T Consensus 174 gaidenKqeAVakEdfdlAKkaklAiaDLk------Ksg--------------eeleelEndKgcAVadEDfdlAkdkkd 233 (666)
T KOG4825|consen 174 GAIDENKQEAVAKEDFDLAKKAKLAIADLK------KSG--------------EELEELENDKGCAVADEDFDLAKDKKD 233 (666)
T ss_pred HHHHhhHHHHHhhhhhhHHHHHHHHHHHHH------HHH--------------HHHHHHhhcccccccchhhhHHHHHHH
Confidence 345566677777777776655544433321 111 246677778888999999999999999
Q ss_pred HHHHHHHHHHH
Q 019893 183 QICKLEAESLA 193 (334)
Q Consensus 183 ~Ik~LE~~~~a 193 (334)
+|..|..+..+
T Consensus 234 eiealRaeila 244 (666)
T KOG4825|consen 234 EIEALRAEILA 244 (666)
T ss_pred HHHHHHHHHHH
Confidence 99999877764
No 26
>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=63.69 E-value=8.4 Score=26.20 Aligned_cols=32 Identities=19% Similarity=0.456 Sum_probs=26.6
Q ss_pred HhhhhhhhhhccchHHHHHHHHHHHHHHHHHH
Q 019893 102 QLDLATRVQCALNMEEYDIAQQLRNKLTEVEE 133 (334)
Q Consensus 102 ~~~~~~rlq~~~~~~~y~~a~~l~~~l~~i~~ 133 (334)
.-+|...+.-|..-.+|+.|..||..|..|.+
T Consensus 4 i~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~~ 35 (36)
T PF02151_consen 4 IKELEEKMEEAVENEDFEKAARLRDQIKALKK 35 (36)
T ss_dssp HHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHc
Confidence 34677888889999999999999999999864
No 27
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=62.15 E-value=9.5 Score=30.70 Aligned_cols=55 Identities=24% Similarity=0.326 Sum_probs=36.0
Q ss_pred ccccccEEEEecCCeeEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccC
Q 019893 207 AFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASD 282 (334)
Q Consensus 207 kFrVGQVVrHrrygYrGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~ 282 (334)
.|++|+.|.|..+| .|+|.|.....- .+..+.||.+-.... ...|||-+++....
T Consensus 1 mf~~GD~VVh~~~G-v~~i~~i~~~~~---------------~~~~~~yy~L~~~~~-----~~i~vPv~~~~~i~ 55 (98)
T PF02559_consen 1 MFKIGDYVVHPNHG-VGRIEGIEEIEF---------------GGEKQEYYVLEYADD-----DTIYVPVDNADKIG 55 (98)
T ss_dssp T--TTSEEEETTTE-EEEEEEEEEEEC---------------TTEEEEEEEEEECCC-----EEEEEECCCGGGEE
T ss_pred CCCCCCEEEECCCc-eEEEEEEEEEee---------------CCeeEEEEEEEECCC-----CEEEEEcCChhhcc
Confidence 48999999999977 478888754321 233366666655442 27999999977663
No 28
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=61.49 E-value=60 Score=36.05 Aligned_cols=23 Identities=13% Similarity=0.368 Sum_probs=21.4
Q ss_pred ccccccEEEEecCCeeEEEEccc
Q 019893 207 AFRLGQKVNHKIFGYRAVICGMD 229 (334)
Q Consensus 207 kFrVGQVVrHrrygYrGVIvGWD 229 (334)
.++||+.|+.+.+|-.|.|+..+
T Consensus 636 ~~~~Gd~V~v~~~~~~g~v~~i~ 658 (782)
T PRK00409 636 ELKVGDEVKYLSLGQKGEVLSIP 658 (782)
T ss_pred CCCCCCEEEEccCCceEEEEEEc
Confidence 49999999999999999999885
No 29
>KOG0412 consensus Golgi transport complex COD1 protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.38 E-value=22 Score=39.27 Aligned_cols=46 Identities=20% Similarity=0.294 Sum_probs=36.8
Q ss_pred CCchhHHHHHHHHHHHHH---HHHHhhchhchhHHHHHHHHHHHHHHHH
Q 019893 146 SSKSEAQDKALSIIRLRA---DLQKAIDSENYALAADLRDQICKLEAES 191 (334)
Q Consensus 146 ~~~~~a~d~a~qL~~Lk~---~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~ 191 (334)
.+.++.+..+.++..|+. -.+.|++.|+||+||..-.++..|-++.
T Consensus 115 ~Rv~~clq~v~dvrdlk~C~~gv~~Al~seDyE~AA~~IhRflslD~~~ 163 (773)
T KOG0412|consen 115 NRVNECLQRVDDVRDLKNCIEGVDTALESEDYEKAATHIHRFLSLDQAL 163 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCHHH
Confidence 346677777777878777 7889999999999999999888884433
No 30
>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=60.01 E-value=34 Score=26.24 Aligned_cols=56 Identities=25% Similarity=0.218 Sum_probs=40.3
Q ss_pred cccccEEEEecCCe---eEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccC
Q 019893 208 FRLGQKVNHKIFGY---RAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASD 282 (334)
Q Consensus 208 FrVGQVVrHrrygY---rGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~ 282 (334)
|++|++|--|.-|| .|+|+.-+.... .......|.|..=+. ...+.|...+|.+..
T Consensus 1 f~~GdlVWaK~~g~pwWPa~V~~~~~~~~---------------~~~~~~~~~V~Ffg~----~~~~wv~~~~i~~f~ 59 (86)
T PF00855_consen 1 FRPGDLVWAKLKGYPWWPARVCDPDEKSK---------------KKRKDGHVLVRFFGD----NDYAWVKPSNIKPFS 59 (86)
T ss_dssp -STTEEEEEEETTSEEEEEEEEECCHCTS---------------CSSSSTEEEEEETTT----TEEEEEEGGGEEECC
T ss_pred CCCCCEEEEEeCCCCCCceEEeecccccc---------------cCCCCCEEEEEecCC----CCEEEECHHHhhChh
Confidence 78999999888887 599988762211 134467788887552 257899999998875
No 31
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=57.45 E-value=69 Score=35.53 Aligned_cols=21 Identities=29% Similarity=0.550 Sum_probs=19.9
Q ss_pred ccccEEEEecCCeeEEEEccc
Q 019893 209 RLGQKVNHKIFGYRAVICGMD 229 (334)
Q Consensus 209 rVGQVVrHrrygYrGVIvGWD 229 (334)
+||+.|+.+.+|-.|.|+.-+
T Consensus 626 ~~Gd~V~v~~~~~~g~v~~i~ 646 (771)
T TIGR01069 626 KIGDKVRIRYFGQKGKIVQIL 646 (771)
T ss_pred CCCCEEEEccCCceEEEEEEc
Confidence 999999999999999999885
No 32
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=57.16 E-value=36 Score=25.52 Aligned_cols=59 Identities=19% Similarity=0.252 Sum_probs=40.1
Q ss_pred cccccEEEEecCCe---eEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCcccc
Q 019893 208 FRLGQKVNHKIFGY---RAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLAS 281 (334)
Q Consensus 208 FrVGQVVrHrrygY---rGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~ 281 (334)
|++|++|-=|..|| .|.|+..+..- +. + ....+....|.|..-+. ...++|..++|.+.
T Consensus 1 f~~GdlVwaK~~G~p~WPa~V~~~~~~~---~~----~----~~~~~~~~~~~V~Ffg~----~~~awv~~~~l~p~ 62 (63)
T smart00293 1 FKPGDLVWAKMKGFPWWPALVVSPKETP---DN----I----RKRKRFENLYPVLFFGD----KDTAWISSSKLFPL 62 (63)
T ss_pred CCCCCEEEEECCCCCCCCeEEcCcccCC---hh----H----hhccCCCCEEEEEEeCC----CCEEEECccceeeC
Confidence 78999998888887 59998876421 11 0 11234456789887542 23589999999875
No 33
>PF00804 Syntaxin: Syntaxin; InterPro: IPR006011 Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of receptors for intracellular transport vesicles. Each target membrane may be identified by a specific member of the syntaxin family []. Members of the syntaxin family [, ] have a size ranging from 30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well conserved region, which seems to be in a coiled-coil conformation. ; GO: 0016020 membrane; PDB: 1S94_B 1EZ3_A 3C98_B 1BR0_A 1FIO_A 2XHE_B.
Probab=55.20 E-value=96 Score=23.96 Aligned_cols=66 Identities=12% Similarity=0.302 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHHHHHH---HHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHH
Q 019893 116 EEYDIAQQLRNKLTEVEEE---ISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAES 191 (334)
Q Consensus 116 ~~y~~a~~l~~~l~~i~~e---~~~~~~~K~~~~~~~~a~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~ 191 (334)
+.|+.+++|+..|..|... |..+|...-. +.. ...+...+|..|-.+.... +..++..|+.|++..
T Consensus 4 ~f~~~v~~i~~~i~~i~~~~~~l~~l~~~~l~-~~~-~d~~~~~el~~l~~~i~~~--------~~~~~~~lk~l~~~~ 72 (103)
T PF00804_consen 4 EFFDEVQEIREDIDKIKEKLNELRKLHKKILS-SPD-QDSELKRELDELTDEIKQL--------FQKIKKRLKQLSKDN 72 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SSS-HHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCC-cchhHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHh
Confidence 5688899999999999755 4444432222 222 2234455555555544444 478888888887663
No 34
>PRK11020 hypothetical protein; Provisional
Probab=52.32 E-value=41 Score=29.20 Aligned_cols=43 Identities=21% Similarity=0.127 Sum_probs=35.9
Q ss_pred hHHHHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 150 EAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 150 ~a~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
|-.....+|..++.+|..|+...+-+.-+.+.++|.+|+.++.
T Consensus 6 Eiq~L~drLD~~~~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~ 48 (118)
T PRK11020 6 EIKRLSDRLDAIRHKLAAASLRGDAEKYAQFEKEKATLEAEIA 48 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 3444556788889999999999999999999999999987765
No 35
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=50.92 E-value=37 Score=27.22 Aligned_cols=44 Identities=20% Similarity=0.179 Sum_probs=30.9
Q ss_pred HHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 136 SRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 136 ~~~~~~K~~~~~~~~a~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
..+...|+. ++.+-+.++..+|. +=++.|.+|+++|..||..+.
T Consensus 23 ~lHY~sk~~-~~~gLs~~d~~~L~------------~L~~~a~rm~eRI~tLE~ILd 66 (75)
T PF06667_consen 23 ILHYRSKWK-SSQGLSEEDEQRLQ------------ELYEQAERMEERIETLERILD 66 (75)
T ss_pred HHHHHHhcc-cCCCCCHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHc
Confidence 455555655 55555666665555 346789999999999998876
No 36
>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=46.87 E-value=1.2e+02 Score=31.13 Aligned_cols=15 Identities=20% Similarity=0.412 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHH
Q 019893 178 ADLRDQICKLEAESL 192 (334)
Q Consensus 178 A~LRD~Ik~LE~~~~ 192 (334)
..|..++..|+.+++
T Consensus 392 ~~l~~~~~~l~~~l~ 406 (451)
T PF03961_consen 392 KELKEELKELKEELE 406 (451)
T ss_pred HHHHHHHHHHHHHHH
Confidence 566666666665554
No 37
>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=45.40 E-value=45 Score=31.69 Aligned_cols=55 Identities=22% Similarity=0.281 Sum_probs=28.7
Q ss_pred ccccccccccEEEEec-------------CCeeEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecC
Q 019893 203 NARFAFRLGQKVNHKI-------------FGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVH 263 (334)
Q Consensus 203 ~~~VkFrVGQVVrHrr-------------ygYrGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~ 263 (334)
....+|+||+.|+-+. -|.+|+|+-....+-.++. . ..- .....||+|+|-++..
T Consensus 130 ~~~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~~g~~~~pd~----~-a~g-~~~~~~~lY~V~F~~~ 197 (222)
T PF02211_consen 130 DAPPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERVHGAFVFPDS----N-AHG-RGEAPQPLYTVRFDAR 197 (222)
T ss_dssp SSS-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEEEEEE--HHH----H-TTT-SSTT-EEEEEEEEEHH
T ss_pred CCCCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEEecCCCCcch----h-ccC-CCCCCcceEEEEecch
Confidence 3567999999999532 2458999954444443332 0 011 1223689999999754
No 38
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=44.05 E-value=40 Score=27.05 Aligned_cols=14 Identities=29% Similarity=0.361 Sum_probs=9.6
Q ss_pred CeeEEEEccccccc
Q 019893 220 GYRAVICGMDPVCC 233 (334)
Q Consensus 220 gYrGVIvGWD~~c~ 233 (334)
.|-.||-|||-...
T Consensus 38 ~~GNiikGfd~y~k 51 (80)
T PF09340_consen 38 PYGNIIKGFDGYLK 51 (80)
T ss_pred cCCCCeeChhhhhc
Confidence 35667889987543
No 39
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
Probab=43.81 E-value=64 Score=25.25 Aligned_cols=60 Identities=23% Similarity=0.211 Sum_probs=41.2
Q ss_pred cccccEEEEecCCe---eEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccCC
Q 019893 208 FRLGQKVNHKIFGY---RAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASDQ 283 (334)
Q Consensus 208 FrVGQVVrHrrygY---rGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~~ 283 (334)
|++|++|-=|.-|| .|+|+..+..-.. + ........|.|..-+. ...++|...+|.+.+.
T Consensus 1 f~~GdlVwaK~~g~pwWPa~V~~~~~~~~~---------~---~~~~~~~~~~V~Ffg~----~~~~wv~~~~l~pf~~ 63 (87)
T cd05162 1 FRPGDLVWAKMKGYPWWPALVVDPPKDSKK---------A---KKKAKEGKVLVLFFGD----KTFAWVGAERLKPFTE 63 (87)
T ss_pred CCCCCEEEEeCCCCCCCCEEEccccccchh---------h---hccCCCCEEEEEEeCC----CcEEEeCccceeeccc
Confidence 78999998777775 6999887643110 0 1223446799887542 3578999999988864
No 40
>PRK09458 pspB phage shock protein B; Provisional
Probab=43.57 E-value=44 Score=26.94 Aligned_cols=44 Identities=25% Similarity=0.230 Sum_probs=29.2
Q ss_pred HHHHhhcCCCCchhHHHHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHHH
Q 019893 137 RQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLA 193 (334)
Q Consensus 137 ~~~~~K~~~~~~~~a~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~a 193 (334)
.+-..|+. ++.+-+.++..+|. +-++.|.+++++|..||..+.+
T Consensus 24 LHY~sk~~-~~~~Ls~~d~~~L~------------~L~~~A~rm~~RI~tLE~ILDa 67 (75)
T PRK09458 24 LHYRSKRQ-GSQGLSQEEQQRLA------------QLTEKAERMRERIQALEAILDA 67 (75)
T ss_pred Hhhccccc-CCCCCCHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHcc
Confidence 34444554 44455555555554 3357899999999999988763
No 41
>PF11365 DUF3166: Protein of unknown function (DUF3166); InterPro: IPR021507 This eukaryotic family of proteins has no known function.
Probab=36.94 E-value=49 Score=27.77 Aligned_cols=44 Identities=30% Similarity=0.327 Sum_probs=31.1
Q ss_pred HHHHHHHHhhchhchhHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccccccE
Q 019893 160 RLRADLQKAIDSENYALAADLRDQICKLEAESLAASATALAFENARFAFRLGQK 213 (334)
Q Consensus 160 ~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~aas~~~l~~r~~~VkFrVGQV 213 (334)
.||.+||-+- |+|+.||-.|.+||.+.+ .+...-..++|.-|..
T Consensus 5 eLR~qLqFvE-----EEa~LlRRkl~ele~eN~-----~l~~EL~kyk~~~g~~ 48 (96)
T PF11365_consen 5 ELRRQLQFVE-----EEAELLRRKLSELEDENK-----QLTEELNKYKSKYGDL 48 (96)
T ss_pred HHHHHHHHHH-----HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHhcCCC
Confidence 6788888775 689999999999987765 2333444556655544
No 42
>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=36.60 E-value=80 Score=25.27 Aligned_cols=45 Identities=24% Similarity=0.214 Sum_probs=30.6
Q ss_pred HHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 135 ISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 135 ~~~~~~~K~~~~~~~~a~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
+.++-..|+. ++.+.+.++..+|.+ =++.|.+|+++|..||..+.
T Consensus 22 l~lHY~~k~~-~~~~ls~~d~~~L~~------------L~~~a~rm~eRI~tLE~ILd 66 (75)
T TIGR02976 22 LILHYRSKRK-TAASLSTDDQALLQE------------LYAKADRLEERIDTLERILD 66 (75)
T ss_pred HHHHHHhhhc-cCCCCCHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHc
Confidence 3455555655 445555566655553 36788999999999998775
No 43
>PF15591 Imm17: Immunity protein 17
Probab=35.30 E-value=31 Score=27.77 Aligned_cols=44 Identities=27% Similarity=0.310 Sum_probs=30.3
Q ss_pred EecCCeeEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCcccc
Q 019893 216 HKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLAS 281 (334)
Q Consensus 216 HrrygYrGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~ 281 (334)
|+.+|-+|||+|.-..=.. -==|.||+.+- ..+-|.+++.|++.
T Consensus 21 ~ei~Gk~GVVlG~SeeD~~------------------~~gY~Vli~d~----e~~~~~ee~~l~~T 64 (74)
T PF15591_consen 21 AEIWGKRGVVLGISEEDGG------------------NFGYSVLIFDM----ECCWYIEEDELEAT 64 (74)
T ss_pred hhhcCceeEEEEEecCCCc------------------EEEEEEEEeee----eeEEEechHHeeec
Confidence 4679999999997431110 11288998753 46789999998765
No 44
>PF13805 Pil1: Eisosome component PIL1; PDB: 3PLT_B.
Probab=34.33 E-value=2e+02 Score=28.34 Aligned_cols=33 Identities=24% Similarity=0.434 Sum_probs=20.8
Q ss_pred hhhccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 019893 109 VQCALNMEEYDIAQQLRNKLTEVEEEISRQLEAKRG 144 (334)
Q Consensus 109 lq~~~~~~~y~~a~~l~~~l~~i~~e~~~~~~~K~~ 144 (334)
.+++..|++|+. -|.. |-++|+.|.-.+..|..
T Consensus 117 ~~~a~~~d~yR~--~LK~-IR~~E~sl~p~R~~r~~ 149 (271)
T PF13805_consen 117 DQYADRLDQYRI--HLKS-IRNREESLQPSRDRRRK 149 (271)
T ss_dssp HHHHHHHHHHHH--HHHH-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH--HHHH-HHHHHHHHhHHHHHhHH
Confidence 357778888887 4444 55667666555555543
No 45
>cd05835 Dnmt3b_related The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=33.20 E-value=86 Score=25.09 Aligned_cols=56 Identities=18% Similarity=0.105 Sum_probs=39.7
Q ss_pred cccccEEEEecCCe---eEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccC
Q 019893 208 FRLGQKVNHKIFGY---RAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASD 282 (334)
Q Consensus 208 FrVGQVVrHrrygY---rGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~ 282 (334)
|.||++|-=|.-|| .|.|+.++..... ....+.|+|-.-+. ...++|..++|.+..
T Consensus 1 f~vGDlVWaK~kg~pwWP~~V~~~~~~~~~---------------~~~~~~~~V~fFGs----~~~a~v~~~~l~pf~ 59 (87)
T cd05835 1 FNVGDLVWGKIKGFPWWPGRVVSITVTSKR---------------PPVVGMRWVTWFGS----GTFSEVSVDKLSPFS 59 (87)
T ss_pred CCCCCEEEEecCCCCCCCeEEechhhcccc---------------cCCCCeEEEEEeCC----CCEeEECHHHCcChh
Confidence 78999998887776 6999987543211 22345688876542 357899999998875
No 46
>cd05837 MSH6_like The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. The role of the PWWP domain in MSH6 is not clear; MSH6 orthologs found in S. cerevisiae, Caenorhabditis elegans and Arabidopsis thaliana lack the PWWP domain. Histone methyltransferases (HMTases) induce the posttranslational methylation of lysine residues in histones and play a role in apoptosis. In the HMTase Whistle, the PWWP domain is necessary for HMTase activity. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain pro
Probab=31.53 E-value=1e+02 Score=25.76 Aligned_cols=66 Identities=21% Similarity=0.364 Sum_probs=41.5
Q ss_pred ccccccEEEEecCCe---eEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccCC
Q 019893 207 AFRLGQKVNHKIFGY---RAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASDQ 283 (334)
Q Consensus 207 kFrVGQVVrHrrygY---rGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~~ 283 (334)
+|.+|++|-=|.-|| .|+|+. |+.... ... .....+.-.-|+|.+=+. .+..++|++.+|.+.+.
T Consensus 2 ~~~~GdlVWaK~~g~PwWPa~V~~-~~~~~~---~~~-----~~~~~~~~~~~~V~FFG~---~~~~aWv~~~~l~pf~~ 69 (110)
T cd05837 2 KYQVGDLVWAKVSGYPWWPCMVCS-DPLLGT---YTK-----TKRNKRKPRQYHVQFFGD---NPERAWISEKSLKPFKG 69 (110)
T ss_pred CCCCCCEEEEeCCCCCCCCEEEec-ccccch---hhh-----hhhccCCCCeEEEEEcCC---CCCEEEecHHHccccCC
Confidence 699999997777776 699985 232110 100 111223345799976442 13578999999999975
Q ss_pred C
Q 019893 284 P 284 (334)
Q Consensus 284 p 284 (334)
.
T Consensus 70 ~ 70 (110)
T cd05837 70 S 70 (110)
T ss_pred c
Confidence 3
No 47
>cd05840 SPBC215_ISWI_like The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4. The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=30.77 E-value=1.2e+02 Score=24.89 Aligned_cols=62 Identities=19% Similarity=0.244 Sum_probs=41.8
Q ss_pred cccccEEEEecCCe---eEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccC
Q 019893 208 FRLGQKVNHKIFGY---RAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASD 282 (334)
Q Consensus 208 FrVGQVVrHrrygY---rGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~ 282 (334)
|++|++|-=|.-|| .|+|+..+.. +.. + -+....+...-|.|..=.. ...++|...+|.+.+
T Consensus 1 f~~GDlVwaK~~GyPwWPA~V~~~~~~---p~~----~--l~~~~~~~~~~~~V~FFg~----~~~~Wv~~~~l~pl~ 65 (93)
T cd05840 1 FQPGDRVLAKVKGFPAWPAIVVPEEML---PDS----V--LKGKKKKNKRTYPVMFFPD----GDYYWVPNKDLKPLT 65 (93)
T ss_pred CCCCCEEEEeCCCCCCCCEEECChHHC---CHH----H--HhcccCCCCCeEEEEEeCC----CcEEEEChhhcccCC
Confidence 78999999998887 5999876521 111 1 0001234456788887542 367999999998886
No 48
>PRK11546 zraP zinc resistance protein; Provisional
Probab=28.27 E-value=3.5e+02 Score=24.22 Aligned_cols=15 Identities=7% Similarity=0.104 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHH
Q 019893 177 AADLRDQICKLEAES 191 (334)
Q Consensus 177 AA~LRD~Ik~LE~~~ 191 (334)
...|..+|..|..++
T Consensus 91 I~aL~kEI~~Lr~kL 105 (143)
T PRK11546 91 INAVAKEMENLRQSL 105 (143)
T ss_pred HHHHHHHHHHHHHHH
Confidence 345555555555444
No 49
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself []. This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule []. Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug, 0055114 oxidation-reduction process; PDB: 1VIF_A 3SFM_A 2P4T_A 2GQV_A 2RK2_A 2RH2_A 2RK1_A 1VIE_A.
Probab=28.21 E-value=55 Score=26.04 Aligned_cols=27 Identities=19% Similarity=0.399 Sum_probs=16.6
Q ss_pred ccccccccccEEEEec-CCeeEEEEccc
Q 019893 203 NARFAFRLGQKVNHKI-FGYRAVICGMD 229 (334)
Q Consensus 203 ~~~VkFrVGQVVrHrr-ygYrGVIvGWD 229 (334)
+..-.|..|+.||-+. -.|.|-|+||=
T Consensus 19 ps~atf~~gdrvrkksgaawqg~vvgwy 46 (78)
T PF06442_consen 19 PSNATFGMGDRVRKKSGAAWQGQVVGWY 46 (78)
T ss_dssp --S-SS-TT-EEEESSSS--EEEEEEEE
T ss_pred ccccccccchhhhhcccccccceEeEEE
Confidence 3456799999999655 34899999994
No 50
>PF12848 ABC_tran_2: ABC transporter
Probab=28.17 E-value=2.7e+02 Score=21.25 Aligned_cols=20 Identities=15% Similarity=0.150 Sum_probs=13.3
Q ss_pred hhccchHHHHHHHHHHHHHH
Q 019893 110 QCALNMEEYDIAQQLRNKLT 129 (334)
Q Consensus 110 q~~~~~~~y~~a~~l~~~l~ 129 (334)
-++-||+.|....+.+....
T Consensus 10 ~Y~GnY~~y~~~k~~~~~~~ 29 (85)
T PF12848_consen 10 EYPGNYSDYLEQKEERRERQ 29 (85)
T ss_pred EeCCCHHHHHHHHHHHHHHH
Confidence 35679999999555554333
No 51
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=27.33 E-value=1.6e+02 Score=23.53 Aligned_cols=55 Identities=24% Similarity=0.283 Sum_probs=40.1
Q ss_pred ccccccEEEEecCCe---eEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccCC
Q 019893 207 AFRLGQKVNHKIFGY---RAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASDQ 283 (334)
Q Consensus 207 kFrVGQVVrHrrygY---rGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~~ 283 (334)
.|.+|++|-=|..|| .|.|+..+.. .....-|+|..-+. ...++|+..+|.+.+.
T Consensus 2 ~f~~GdlVwaK~kGyp~WPa~I~~~~~~------------------~~~~~~~~V~FfGt----~~~a~v~~~~l~pf~~ 59 (83)
T cd05834 2 QFKAGDLVFAKVKGYPAWPARVDEPEDW------------------KPPGKKYPVYFFGT----HETAFLKPEDLFPYTE 59 (83)
T ss_pred CCCCCCEEEEecCCCCCCCEEEeccccc------------------CCCCCEEEEEEeCC----CCEeEECHHHceeccc
Confidence 589999999888887 5888765431 12234599887542 3578999999998864
No 52
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=26.67 E-value=66 Score=24.05 Aligned_cols=21 Identities=29% Similarity=0.439 Sum_probs=18.2
Q ss_pred cccccEEEEecCCeeEEEEcc
Q 019893 208 FRLGQKVNHKIFGYRAVICGM 228 (334)
Q Consensus 208 FrVGQVVrHrrygYrGVIvGW 228 (334)
|++|+||+.|.-|-+-+|...
T Consensus 1 f~~GDvV~LKSGGp~MTV~~v 21 (53)
T PF09926_consen 1 FKIGDVVQLKSGGPRMTVTEV 21 (53)
T ss_pred CCCCCEEEEccCCCCeEEEEc
Confidence 789999999999988888744
No 53
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=26.64 E-value=2.6e+02 Score=26.88 Aligned_cols=35 Identities=20% Similarity=0.362 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHH
Q 019893 153 DKALSIIRLRADLQKAIDSENYALAADLRDQICKL 187 (334)
Q Consensus 153 d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~L 187 (334)
..-..+.+....++.+++..+|..|..|-.+.+.+
T Consensus 122 ~~i~~v~~~~~~l~~ll~~~dy~~Al~li~~~~~~ 156 (291)
T PF10475_consen 122 EQIKTVQQTQSRLQELLEEGDYPGALDLIEECQQL 156 (291)
T ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 33344455566899999999999998888777766
No 54
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=26.19 E-value=1.7e+02 Score=20.55 Aligned_cols=50 Identities=28% Similarity=0.321 Sum_probs=33.3
Q ss_pred ccccccEEEEec-CC--eeEEEEcccccccCChhhHHHhhhhhcCCCCCCCeEEEEeecCCCCCceeeeecccCccccC
Q 019893 207 AFRLGQKVNHKI-FG--YRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQVLVDVHADPNILVAYVAEENLLASD 282 (334)
Q Consensus 207 kFrVGQVVrHrr-yg--YrGVIvGWD~~c~a~eeW~~~~~v~~l~~g~~QPFY~VLvd~~d~~~~~~~YVAEENLe~~~ 282 (334)
.+++|+++.=+. -| |||.|++-++. ..|.|+..+. +....|+.+.|-+.+
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~----------------------~~~~V~f~D~----G~~~~v~~~~l~~l~ 54 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGE----------------------QLYEVFFIDY----GNEEVVPPSDLRPLP 54 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCC----------------------CEEEEEEECC----CccEEEeHHHeecCC
Confidence 578898886543 22 78999876431 4488887653 245788888876664
No 55
>PF06133 DUF964: Protein of unknown function (DUF964); InterPro: IPR010368 This entry consists of several relatively short bacterial and archaeal hypothetical sequences. It also includes YlbF and YmcA proteins which are involved in the formation of biofilms []. YlbF regulates sporulation prior to stage II, positively controlling the competence regulator ComK at a post-transcriptional level. It may also modulate the translation, stability or activity of ComS and may work together with YmcA to regulate community development [].; PDB: 2IAZ_C 2OEE_A 2OEQ_D 2PIH_A.
Probab=25.85 E-value=3.2e+02 Score=21.87 Aligned_cols=73 Identities=26% Similarity=0.311 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHH
Q 019893 118 YDIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESL 192 (334)
Q Consensus 118 y~~a~~l~~~l~~i~~e~~~~~~~K~~~~~~~~a~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~ 192 (334)
|+.|.+|...|.+-+ ++...+..+......+++...-.+...++..++.+=....+ .+.....++.+|+.++.
T Consensus 3 ~~~a~eL~~~I~~s~-ey~~~~~a~~~l~~d~e~~~l~~~f~~~q~~~~~~q~~g~~-~~~e~~~~l~~~~~~l~ 75 (108)
T PF06133_consen 3 YDKANELAEAIKESE-EYKRYKAAEEALEADPEAQKLIEEFQKLQQELQNAQMYGKE-PPKEEIEELQELQEELM 75 (108)
T ss_dssp HHHHHHHHHHHHTSH-HHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTTSC-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCH-HHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhccC-CcHHHHHHHHHHHHHHH
Confidence 555666666555432 23344444443334445554444445555555443222222 22455555555555443
No 56
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=24.56 E-value=2e+02 Score=26.59 Aligned_cols=44 Identities=27% Similarity=0.314 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHHHHHHH
Q 019893 153 DKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLAASA 196 (334)
Q Consensus 153 d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~~aas~ 196 (334)
....||.++|++|...=..++|.+-|+|--+|.+|.++.+..++
T Consensus 48 q~~~ei~dmKqelnavs~qD~fAkwaRlnRKi~kl~~ele~qs~ 91 (175)
T KOG4253|consen 48 QKVAEIQDMKQELNAVSMQDNFAKWARLNRKINKLDKELETQSK 91 (175)
T ss_pred HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34457888899998888888899999999999999777764443
No 57
>TIGR00002 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles.
Probab=24.48 E-value=53 Score=26.44 Aligned_cols=13 Identities=31% Similarity=0.743 Sum_probs=10.1
Q ss_pred CCCCCeEEEEeec
Q 019893 250 GPSQPFYQVLVDV 262 (334)
Q Consensus 250 g~~QPFY~VLvd~ 262 (334)
.+++|||+|.|.+
T Consensus 10 ~k~~PfYrIVv~d 22 (78)
T TIGR00002 10 RKKRPFYRIVVAD 22 (78)
T ss_pred CCCCCeEEEEEEe
Confidence 4679999998743
No 58
>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=24.41 E-value=3.7e+02 Score=21.69 Aligned_cols=38 Identities=18% Similarity=0.188 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHH
Q 019893 154 KALSIIRLRADLQKAIDSENYALAADLRDQICKLEAES 191 (334)
Q Consensus 154 ~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~ 191 (334)
.-.+|.+|..+|..++..-.-.+...+.++|..|+.+.
T Consensus 47 s~~eL~~LE~~Le~aL~~VR~rK~~~l~~~i~~l~~ke 84 (100)
T PF01486_consen 47 SLKELQQLEQQLESALKRVRSRKDQLLMEQIEELKKKE 84 (100)
T ss_pred chHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34467788889999998888778888888888885543
No 59
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=24.27 E-value=4.7e+02 Score=25.71 Aligned_cols=39 Identities=23% Similarity=0.281 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHH
Q 019893 124 LRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQK 167 (334)
Q Consensus 124 l~~~l~~i~~e~~~~~~~K~~~~~~~~a~d~a~qL~~Lk~~Lq~ 167 (334)
|+.+...+..|+..++..+.- ....++.+|..+|.+|..
T Consensus 182 l~~~~~~L~~e~~~Lk~~~~e-----~~~~D~~eL~~lr~eL~~ 220 (325)
T PF08317_consen 182 LRERKAELEEELENLKQLVEE-----IESCDQEELEALRQELAE 220 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHhh-----hhhcCHHHHHHHHHHHHH
Confidence 333333444454444444332 233344455555554433
No 60
>CHL00005 rps16 ribosomal protein S16
Probab=23.39 E-value=53 Score=26.74 Aligned_cols=13 Identities=15% Similarity=0.240 Sum_probs=10.2
Q ss_pred CCCCCeEEEEeec
Q 019893 250 GPSQPFYQVLVDV 262 (334)
Q Consensus 250 g~~QPFY~VLvd~ 262 (334)
.+++|||+|.|-+
T Consensus 11 ~kk~P~YrIVvad 23 (82)
T CHL00005 11 RKQQAVYRIVAID 23 (82)
T ss_pred CCCCCeEEEEEEe
Confidence 4679999998743
No 61
>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=22.69 E-value=43 Score=25.62 Aligned_cols=13 Identities=31% Similarity=0.743 Sum_probs=10.1
Q ss_pred CCCCCeEEEEeec
Q 019893 250 GPSQPFYQVLVDV 262 (334)
Q Consensus 250 g~~QPFY~VLvd~ 262 (334)
.+++|||+|.|-+
T Consensus 4 ~k~~P~YrIVv~d 16 (62)
T PF00886_consen 4 RKKRPFYRIVVAD 16 (62)
T ss_dssp STTEEEEEEEEEE
T ss_pred CCCCCeEEEEEEe
Confidence 4679999988743
No 62
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=22.59 E-value=5.3e+02 Score=23.06 Aligned_cols=18 Identities=28% Similarity=0.442 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHHHhh
Q 019893 152 QDKALSIIRLRADLQKAI 169 (334)
Q Consensus 152 ~d~a~qL~~Lk~~Lq~aI 169 (334)
.....++..|+.+|..-|
T Consensus 83 e~L~~eie~l~~~L~~ei 100 (177)
T PF07798_consen 83 EKLQREIEKLRQELREEI 100 (177)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344555555555555544
No 63
>KOG3419 consensus Mitochondrial/chloroplast ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=21.74 E-value=58 Score=28.06 Aligned_cols=13 Identities=31% Similarity=0.738 Sum_probs=10.4
Q ss_pred CCCCCeEEEEeec
Q 019893 250 GPSQPFYQVLVDV 262 (334)
Q Consensus 250 g~~QPFY~VLvd~ 262 (334)
.++.|||||+|-+
T Consensus 12 cknRPfY~Ivva~ 24 (112)
T KOG3419|consen 12 CKNRPFYRIVVAD 24 (112)
T ss_pred ccCCCeeEEEEee
Confidence 4679999999854
No 64
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=21.64 E-value=5.9e+02 Score=23.97 Aligned_cols=56 Identities=14% Similarity=0.004 Sum_probs=33.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccccccEEEEecCCe---eEEEEcccccc
Q 019893 174 YALAADLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGY---RAVICGMDPVC 232 (334)
Q Consensus 174 yE~AA~LRD~Ik~LE~~~~aas~~~l~~r~~~VkFrVGQVVrHrrygY---rGVIvGWD~~c 232 (334)
.+.=-.++.++..+++++.... ..+......+..|-||+-+.-++ -|||+..+...
T Consensus 42 v~~y~~l~~~l~~~~~~~~~~i---~~p~~~~~fL~~GRlV~v~~~~~~~~wgvvv~~~~~~ 100 (268)
T PF13234_consen 42 VEEYYDLRQELEELRKELRKII---TSPKYCLPFLQPGRLVVVRDGDRDFGWGVVVNFAKKS 100 (268)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHH---CTCCCHHHHS-TTEEEEEEETTCEEEEEEEEEEEE--
T ss_pred HHHHHHHHHHHHHHHHHHHHHH---hCcHHHHHhCCCCCEEEEecCCCccceeEEEeccccc
Confidence 4455677888888877665322 23333344789999998763222 48999887654
No 65
>PF11855 DUF3375: Protein of unknown function (DUF3375); InterPro: IPR021804 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
Probab=21.42 E-value=4.1e+02 Score=27.75 Aligned_cols=68 Identities=18% Similarity=0.354 Sum_probs=45.9
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHH
Q 019893 113 LNMEEYDIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLE 188 (334)
Q Consensus 113 ~~~~~y~~a~~l~~~l~~i~~e~~~~~~~K~~~~~~~~a~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE 188 (334)
.|-+-=..-..|+.++.+|+.||...+.|..+.-......|...+|..+=.+|=. || +.+++.++.|-
T Consensus 138 ~~~Dp~~Ri~~Le~e~~~i~~EI~~l~aG~~~~ld~~~~~er~~~i~~la~~L~~-----DF---r~V~~~~r~l~ 205 (478)
T PF11855_consen 138 TDPDPERRIAELEREIAEIDAEIDRLEAGDVPVLDDTQARERARQILQLARELPA-----DF---RRVEDNFRELD 205 (478)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHH-----HH---HHHHHHHHHHH
Confidence 3444444455899999999999999999977766777777777777765544433 22 55555555553
No 66
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=21.11 E-value=64 Score=25.77 Aligned_cols=13 Identities=31% Similarity=0.782 Sum_probs=10.2
Q ss_pred CCCCCeEEEEeec
Q 019893 250 GPSQPFYQVLVDV 262 (334)
Q Consensus 250 g~~QPFY~VLvd~ 262 (334)
.+++|||+|.|-+
T Consensus 11 ~k~~P~YrIVv~d 23 (75)
T PRK00040 11 AKKRPFYRIVVAD 23 (75)
T ss_pred CCCCCeEEEEEEe
Confidence 4679999998743
No 67
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=20.97 E-value=2.1e+02 Score=24.07 Aligned_cols=28 Identities=25% Similarity=0.381 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHhhchhchhHHHHHHHHHHHHHHHH
Q 019893 156 LSIIRLRADLQKAIDSENYALAADLRDQICKLEAES 191 (334)
Q Consensus 156 ~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE~~~ 191 (334)
.||..||.+|.+-| ..-+++|..||+.+
T Consensus 72 EqL~~Lk~kl~~e~--------~~~~k~i~~le~~I 99 (100)
T PF04568_consen 72 EQLKKLKEKLKEEI--------EHHRKEIDELEKHI 99 (100)
T ss_dssp HHHHHHHHHHHHHH--------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH--------HHHHHHHHHHHHhc
Confidence 35667777776655 45566777776654
No 68
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=20.77 E-value=4.2e+02 Score=23.75 Aligned_cols=32 Identities=22% Similarity=0.237 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHhhchhchhHHHHHHHHHHHHH
Q 019893 152 QDKALSIIRLRADLQKAIDSENYALAADLRDQICKLE 188 (334)
Q Consensus 152 ~d~a~qL~~Lk~~Lq~aI~~E~yE~AA~LRD~Ik~LE 188 (334)
.....++.+|+.+|.++- .+...|+++++.|+
T Consensus 157 ~~~~~ei~~lk~el~~~~-----~~~~~LkkQ~~~l~ 188 (192)
T PF05529_consen 157 KKLSEEIEKLKKELEKKE-----KEIEALKKQSEGLQ 188 (192)
T ss_pred hhhHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHH
Confidence 345566777777777743 22334555555544
No 69
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.42 E-value=1.6e+02 Score=29.53 Aligned_cols=20 Identities=20% Similarity=0.326 Sum_probs=16.4
Q ss_pred cCCchhhhhhhhhhhhhccc
Q 019893 38 GIDRPCFCHQFVQGLHLRVT 57 (334)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~ 57 (334)
..|+|-+|..|+..++..+.
T Consensus 24 ~~CGH~~C~sCv~~l~~~~~ 43 (309)
T TIGR00570 24 NVCGHTLCESCVDLLFVRGS 43 (309)
T ss_pred CCCCCcccHHHHHHHhcCCC
Confidence 47999999999999975543
No 70
>PRK14525 rpsP 30S ribosomal protein S16; Provisional
Probab=20.39 E-value=66 Score=26.55 Aligned_cols=13 Identities=31% Similarity=0.608 Sum_probs=10.0
Q ss_pred CCCCCeEEEEeec
Q 019893 250 GPSQPFYQVLVDV 262 (334)
Q Consensus 250 g~~QPFY~VLvd~ 262 (334)
.+++|||+|.|-+
T Consensus 12 ~k~~P~YrIVv~d 24 (88)
T PRK14525 12 THKAPFYHVVATD 24 (88)
T ss_pred CCCCCeEEEEEee
Confidence 4679999988743
Done!