Query 026790
Match_columns 233
No_of_seqs 229 out of 1654
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 12:44:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026790.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026790hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00095 clpC Clp protease ATP 99.8 4.5E-20 9.7E-25 185.4 18.3 141 81-224 1-141 (821)
2 TIGR03346 chaperone_ClpB ATP-d 99.8 2.8E-19 6E-24 180.3 18.5 139 85-225 1-139 (852)
3 TIGR02639 ClpA ATP-dependent C 99.8 9.6E-19 2.1E-23 173.9 17.8 135 85-222 1-137 (731)
4 PRK10865 protein disaggregatio 99.8 1.8E-17 3.9E-22 167.2 18.4 143 81-225 2-144 (857)
5 TIGR03345 VI_ClpV1 type VI sec 99.8 3.7E-17 7.9E-22 164.8 18.2 137 85-224 1-141 (852)
6 COG0542 clpA ATP-binding subun 99.7 7E-17 1.5E-21 159.4 17.8 139 84-228 1-139 (786)
7 PRK11034 clpA ATP-dependent Cl 99.6 7.1E-15 1.5E-19 146.4 17.6 135 85-222 2-139 (758)
8 KOG1051 Chaperone HSP104 and r 99.5 7E-14 1.5E-18 139.9 13.7 150 82-232 9-159 (898)
9 PF02861 Clp_N: Clp amino term 99.2 2.7E-11 5.8E-16 81.0 6.1 53 96-148 1-53 (53)
10 PF02861 Clp_N: Clp amino term 99.1 2.8E-10 6.1E-15 76.0 5.4 53 173-226 1-53 (53)
11 TIGR03346 chaperone_ClpB ATP-d 98.2 4E-06 8.7E-11 85.4 8.7 62 162-224 1-62 (852)
12 CHL00095 clpC Clp protease ATP 98.2 5.6E-06 1.2E-10 84.0 8.2 62 161-223 4-65 (821)
13 TIGR03345 VI_ClpV1 type VI sec 98.1 7.3E-06 1.6E-10 83.5 8.6 61 162-223 1-61 (852)
14 TIGR02639 ClpA ATP-dependent C 98.0 2E-05 4.3E-10 79.1 8.2 59 162-223 1-59 (731)
15 PRK10865 protein disaggregatio 97.9 4.1E-05 8.8E-10 78.2 8.4 63 161-224 5-67 (857)
16 PRK11034 clpA ATP-dependent Cl 97.6 0.00019 4.2E-09 72.3 8.0 59 162-223 2-60 (758)
17 COG0542 clpA ATP-binding subun 97.5 0.00036 7.7E-09 70.2 8.1 59 162-223 2-60 (786)
18 KOG1051 Chaperone HSP104 and r 96.6 0.0063 1.4E-07 62.2 7.8 59 160-219 10-69 (898)
19 cd00074 H2A Histone 2A; H2A is 81.7 1.7 3.7E-05 34.0 3.3 40 89-130 55-94 (115)
20 PLN00154 histone H2A; Provisio 81.0 1.5 3.2E-05 35.4 2.7 40 166-208 74-113 (136)
21 PTZ00017 histone H2A; Provisio 80.9 1.5 3.3E-05 35.2 2.7 39 90-130 63-101 (134)
22 KOG1756 Histone 2A [Chromatin 80.7 2.8 6.1E-05 33.3 4.1 40 89-130 62-101 (131)
23 PLN00154 histone H2A; Provisio 80.7 1.5 3.1E-05 35.4 2.6 39 90-130 75-113 (136)
24 cd00074 H2A Histone 2A; H2A is 79.1 2.3 5.1E-05 33.2 3.2 40 166-208 55-94 (115)
25 PTZ00017 histone H2A; Provisio 79.0 2 4.2E-05 34.6 2.8 40 166-208 62-101 (134)
26 PLN00153 histone H2A; Provisio 77.1 2.4 5.3E-05 33.8 2.8 39 90-130 60-98 (129)
27 PLN00157 histone H2A; Provisio 77.1 2.1 4.5E-05 34.3 2.5 41 89-131 61-101 (132)
28 smart00414 H2A Histone 2A. 75.8 2.7 5.8E-05 32.4 2.7 44 82-130 40-83 (106)
29 PLN00157 histone H2A; Provisio 75.5 2.6 5.7E-05 33.8 2.6 40 166-208 61-100 (132)
30 PLN00156 histone H2AX; Provisi 75.2 3 6.4E-05 33.7 2.9 39 90-130 65-103 (139)
31 smart00414 H2A Histone 2A. 73.1 3.6 7.9E-05 31.7 2.8 41 166-209 44-84 (106)
32 PLN00153 histone H2A; Provisio 72.9 3.8 8.2E-05 32.7 3.0 40 166-208 59-98 (129)
33 PLN00156 histone H2AX; Provisi 72.6 4 8.7E-05 33.0 3.0 40 166-208 64-103 (139)
34 KOG1756 Histone 2A [Chromatin 72.0 4.4 9.6E-05 32.2 3.1 41 166-209 62-102 (131)
35 PF08369 PCP_red: Proto-chloro 70.2 7.6 0.00016 25.2 3.4 27 90-116 18-44 (45)
36 PTZ00252 histone H2A; Provisio 66.8 5.4 0.00012 32.0 2.6 40 90-131 61-102 (134)
37 PF13551 HTH_29: Winged helix- 65.5 51 0.0011 24.1 9.7 83 115-198 5-93 (112)
38 PTZ00252 histone H2A; Provisio 58.4 11 0.00023 30.3 3.0 41 166-209 60-102 (134)
39 PF00125 Histone: Core histone 54.5 17 0.00038 25.3 3.3 29 166-195 44-72 (75)
40 PF13335 Mg_chelatase_2: Magne 54.2 29 0.00063 25.9 4.6 88 86-196 5-94 (96)
41 PF00125 Histone: Core histone 54.0 20 0.00043 24.9 3.5 30 88-117 43-72 (75)
42 COG5262 HTA1 Histone H2A [Chro 52.5 13 0.00027 29.3 2.4 40 89-130 61-100 (132)
43 smart00550 Zalpha Z-DNA-bindin 45.6 47 0.001 23.0 4.3 37 189-225 9-47 (68)
44 COG5262 HTA1 Histone H2A [Chro 45.2 20 0.00042 28.3 2.4 34 166-200 61-94 (132)
45 PF00808 CBFD_NFYB_HMF: Histon 40.7 50 0.0011 22.4 3.8 26 92-117 40-65 (65)
46 smart00803 TAF TATA box bindin 40.4 58 0.0012 22.6 4.0 34 84-117 31-64 (65)
47 smart00803 TAF TATA box bindin 39.9 54 0.0012 22.8 3.8 58 124-195 7-64 (65)
48 PRK10265 chaperone-modulator p 39.3 1.2E+02 0.0026 22.8 6.0 69 125-197 10-78 (101)
49 PF13412 HTH_24: Winged helix- 39.2 71 0.0015 20.0 4.1 38 189-226 6-43 (48)
50 PF08369 PCP_red: Proto-chloro 36.6 57 0.0012 21.0 3.3 27 167-194 18-44 (45)
51 PF00808 CBFD_NFYB_HMF: Histon 36.5 61 0.0013 22.0 3.7 26 169-195 40-65 (65)
52 PF13591 MerR_2: MerR HTH fami 35.0 1.6E+02 0.0034 21.3 5.8 61 125-189 3-63 (84)
53 PF12802 MarR_2: MarR family; 34.2 80 0.0017 20.5 3.9 37 189-225 8-46 (62)
54 PF12244 DUF3606: Protein of u 33.8 50 0.0011 22.3 2.8 27 202-228 22-48 (57)
55 PF13335 Mg_chelatase_2: Magne 31.8 93 0.002 23.2 4.3 33 85-117 60-93 (96)
56 cd07981 TAF12 TATA Binding Pro 31.7 1.1E+02 0.0023 21.6 4.3 34 86-119 33-66 (72)
57 cd07979 TAF9 TATA Binding Prot 31.5 92 0.002 24.2 4.3 61 124-200 6-68 (117)
58 PF01978 TrmB: Sugar-specific 31.5 52 0.0011 22.3 2.7 37 189-225 11-47 (68)
59 cd07981 TAF12 TATA Binding Pro 29.9 1.2E+02 0.0026 21.3 4.3 31 166-197 36-66 (72)
60 COG2317 Zn-dependent carboxype 28.8 4.9E+02 0.011 25.4 9.4 89 82-178 125-220 (497)
61 TIGR00122 birA_repr_reg BirA b 28.2 1E+02 0.0023 20.9 3.8 36 192-227 5-40 (69)
62 KOG0871 Class 2 transcription 27.6 1.2E+02 0.0026 24.9 4.4 37 84-120 31-79 (156)
63 PLN00035 histone H4; Provision 27.4 1.2E+02 0.0026 23.3 4.2 35 163-198 60-94 (103)
64 PF12554 MOZART1: Mitotic-spin 26.9 78 0.0017 20.9 2.7 19 207-225 30-48 (48)
65 PRK09416 lstR lineage-specific 26.7 1.6E+02 0.0035 23.6 5.0 47 158-209 18-64 (135)
66 PF05576 Peptidase_S37: PS-10 26.5 1E+02 0.0023 29.5 4.5 79 16-106 122-208 (448)
67 COG5247 BUR6 Class 2 transcrip 26.3 93 0.002 23.9 3.4 34 89-122 58-91 (113)
68 cd07979 TAF9 TATA Binding Prot 25.7 1.3E+02 0.0029 23.3 4.3 35 86-120 32-66 (117)
69 PTZ00306 NADH-dependent fumara 25.7 70 0.0015 34.4 3.6 139 46-197 5-160 (1167)
70 PRK11426 hypothetical protein; 25.5 1.4E+02 0.003 23.9 4.5 44 105-151 58-101 (132)
71 PF02269 TFIID-18kDa: Transcri 25.5 36 0.00079 25.3 1.1 38 85-122 32-69 (93)
72 PF02969 TAF: TATA box binding 25.2 1.8E+02 0.0038 20.4 4.4 33 85-117 33-65 (66)
73 KOG1659 Class 2 transcription 24.8 1.5E+02 0.0033 25.7 4.8 35 89-123 48-82 (224)
74 COG2036 HHT1 Histones H3 and H 24.5 1.4E+02 0.003 22.4 4.0 33 165-198 52-84 (91)
75 PF02269 TFIID-18kDa: Transcri 24.0 45 0.00097 24.8 1.3 37 163-200 33-69 (93)
76 cd00076 H4 Histone H4, one of 24.0 1.6E+02 0.0035 21.7 4.2 35 163-198 44-78 (85)
77 PF09415 CENP-X: CENP-S associ 23.8 1.2E+02 0.0026 21.6 3.4 29 87-115 34-63 (72)
78 PF01022 HTH_5: Bacterial regu 23.5 1.1E+02 0.0024 19.2 3.0 37 190-227 6-42 (47)
79 PTZ00015 histone H4; Provision 23.4 1.6E+02 0.0034 22.6 4.2 34 163-197 61-94 (102)
80 PF02662 FlpD: Methyl-viologen 22.7 87 0.0019 24.4 2.8 17 107-123 39-55 (124)
81 PF08279 HTH_11: HTH domain; 22.4 2.2E+02 0.0047 18.1 4.6 38 190-227 4-42 (55)
82 PF01978 TrmB: Sugar-specific 22.4 1.3E+02 0.0027 20.4 3.3 38 112-149 12-49 (68)
83 smart00418 HTH_ARSR helix_turn 22.0 2E+02 0.0043 18.0 4.1 29 198-226 8-36 (66)
84 KOG1757 Histone 2A [Chromatin 21.9 19 0.00041 28.1 -1.1 34 166-200 66-99 (131)
85 PF13404 HTH_AsnC-type: AsnC-t 21.7 2E+02 0.0042 18.0 3.8 35 190-224 6-41 (42)
86 smart00165 UBA Ubiquitin assoc 20.6 1.5E+02 0.0032 17.4 3.0 24 205-228 6-29 (37)
87 cd00194 UBA Ubiquitin Associat 20.5 1.5E+02 0.0032 17.5 3.0 24 205-228 6-29 (38)
88 smart00344 HTH_ASNC helix_turn 20.4 1.6E+02 0.0035 21.5 3.8 37 191-227 8-44 (108)
89 COG5251 TAF40 Transcription in 20.2 3.8E+02 0.0083 22.6 6.1 82 110-194 92-177 (199)
90 KOG1757 Histone 2A [Chromatin 20.2 18 0.00038 28.3 -1.6 32 90-121 67-98 (131)
91 PF12983 DUF3867: Protein of u 20.1 1.1E+02 0.0024 25.8 3.0 38 179-225 49-86 (186)
No 1
>CHL00095 clpC Clp protease ATP binding subunit
Probab=99.84 E-value=4.5e-20 Score=185.42 Aligned_cols=141 Identities=30% Similarity=0.495 Sum_probs=129.4
Q ss_pred CchhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCCC
Q 026790 81 KIPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERP 160 (233)
Q Consensus 81 ~~~rfT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~~~~~~~~ 160 (233)
||++||++++++|..|+.+|++++|.+|++||||+||+.++++.+.++|+++|++++.++.+++..+++.+.. .+..+
T Consensus 1 m~~rfT~~a~~vL~~A~~~A~~~~h~~V~~EHLLLaLL~~~~~~a~~iL~~~gid~~~l~~~l~~~l~~~~~~--~~~~~ 78 (821)
T CHL00095 1 MFERFTEKAIKVIMLSQEEARRLGHNFVGTEQILLGLIGEGTGIAARALKSMGVTLKDARIEVEKIIGRGTGF--VAVEI 78 (821)
T ss_pred ChhhHhHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHHHhcCCCC--Ccccc
Confidence 5889999999999999999999999999999999999999999999999999999999999999988764431 23468
Q ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHh
Q 026790 161 PLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSI 224 (233)
Q Consensus 161 ~~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~ 224 (233)
+||+.++++|+.|+.+|..+|+ ++|+++|||+||+.++++.+.++|+.+|++.+.+++.+...
T Consensus 79 ~~S~~~~~vL~~A~~~A~~~~~-~~I~~eHLLlALL~~~ds~a~~iL~~~gvd~~~L~~~l~~~ 141 (821)
T CHL00095 79 PFTPRAKRVLEMSLEEARDLGH-NYIGTEHLLLALLEEGEGVAARVLENLGVDLSKIRSLILNL 141 (821)
T ss_pred ccCHHHHHHHHHHHHHHHHhCC-CcccHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHH
Confidence 8999999999999999999999 99999999999999988888899999999999998887653
No 2
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=99.82 E-value=2.8e-19 Score=180.32 Aligned_cols=139 Identities=18% Similarity=0.200 Sum_probs=125.4
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCCCcCCH
Q 026790 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTE 164 (233)
Q Consensus 85 fT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~~~~~~~~~~S~ 164 (233)
||++++++|..|+.+|++++|.+|++||||+||+.++++.+.++|+++|+|++.+++++...+++.+...+.+..++||+
T Consensus 1 fT~~a~~vL~~A~~~A~~~~h~~V~~EHLLlaLl~~~~g~a~~iL~~~Gvd~~~l~~~l~~~l~~~~~~~~~~~~~~~S~ 80 (852)
T TIGR03346 1 FTEKFQEALQAAQSLALGRDHQQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQALEKELEKLPKVSGPGGQVYLSP 80 (852)
T ss_pred CCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHhcccccCCCCCCCCCcCH
Confidence 79999999999999999999999999999999999999999999999999999999999999987554222224678999
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhc
Q 026790 165 QAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSIN 225 (233)
Q Consensus 165 ~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~ 225 (233)
.++++|+.|+.+|..+|+ ++|+++|||+||+.++++ +.++|..+|++.+.+.+.+..++
T Consensus 81 ~~~~vLe~A~~~A~~~g~-~~I~teHLLlALl~e~~~-a~~iL~~~gi~~~~l~~~l~~~~ 139 (852)
T TIGR03346 81 ELNRLLNLAEKLAQKRGD-EFISSEHLLLALLDDKGT-LGKLLKEAGATADALEAAINAVR 139 (852)
T ss_pred HHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHcCCcc-HHHHHHHcCCCHHHHHHHHHhhc
Confidence 999999999999999999 999999999999998766 56899999999999988886654
No 3
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=99.81 E-value=9.6e-19 Score=173.91 Aligned_cols=135 Identities=21% Similarity=0.226 Sum_probs=120.6
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhC-CCCCCCC-CCCCCcC
Q 026790 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLG-KSDLFFF-SPERPPL 162 (233)
Q Consensus 85 fT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~-~~~~~~~-~~~~~~~ 162 (233)
||++++++|..|+.+|++++|.+|++||||+|||.+++ +.++|+++|++.+.+++++...+. ..+...+ .+..+++
T Consensus 1 ~~~~a~~~L~~A~~~A~~~~h~~V~~EHLLlaLL~~~~--~~~iL~~~gid~~~l~~~l~~~l~~~~p~~~~~~~~~~~~ 78 (731)
T TIGR02639 1 ISEELERILDAALEEAKKRRHEFVTLEHILLALLFDSD--AIEILEECGGDVEALRKDLEDYLENNLPSITEENEADPEQ 78 (731)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHcCch--HHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCCCCCCCCc
Confidence 68999999999999999999999999999999999876 579999999999999999999886 3332211 1245789
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHH
Q 026790 163 TEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAK 222 (233)
Q Consensus 163 S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~ 222 (233)
|+.++++|+.|+++|.++|+ ++|+++|||+||+.++++.+..+|+.+|++.+.+++.+.
T Consensus 79 S~~lk~vL~~A~~~A~~~g~-~~I~teHLLLALl~~~~~~a~~lL~~~gi~~~~l~~~l~ 137 (731)
T TIGR02639 79 TVGVQRVLQRALLHVKSAGK-KEIGIGDILVALFDEEDSHASYFLKSQGITRLDILEYIS 137 (731)
T ss_pred CHHHHHHHHHHHHHHHHcCC-CccCHHHHHHHHhcCcccHHHHHHHHcCCCHHHHHHHHH
Confidence 99999999999999999999 999999999999999888888899999999999988774
No 4
>PRK10865 protein disaggregation chaperone; Provisional
Probab=99.76 E-value=1.8e-17 Score=167.21 Aligned_cols=143 Identities=13% Similarity=0.125 Sum_probs=126.8
Q ss_pred CchhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCCC
Q 026790 81 KIPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERP 160 (233)
Q Consensus 81 ~~~rfT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~~~~~~~~ 160 (233)
++++||+.++++|..|+.+|++++|.+|+++|||++|+.++.+.+..+|..+|+|.+.++++++..+...+...+.+..+
T Consensus 2 ~~~~~~~~~~~~l~~a~~~a~~~~~~~~~~~hll~~l~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 81 (857)
T PRK10865 2 RLDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQLRTDINQALSRLPQVEGTGGDV 81 (857)
T ss_pred ChHHhCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHHhhCCCCCCCCCCC
Confidence 47899999999999999999999999999999999999999888999999999999999999999988765421122457
Q ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhc
Q 026790 161 PLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSIN 225 (233)
Q Consensus 161 ~~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~ 225 (233)
++|+.++++|+.|+.++..+|+ .+|+++|||+||+.++++. ..+|+.+|++.+.+.+.+..++
T Consensus 82 ~~~~~~~~~l~~a~~~~~~~~~-~~i~~~~ll~~~~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~ 144 (857)
T PRK10865 82 QPSQDLVRVLNLCDKLAQKRGD-NFISSELFVLAALESRGTL-ADILKAAGATTANITQAIEQMR 144 (857)
T ss_pred CcCHHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHcCcchH-HHHHHHcCCCHHHHHHHHHHhh
Confidence 8999999999999999999999 9999999999999886544 4589999999999988876654
No 5
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=99.75 E-value=3.7e-17 Score=164.79 Aligned_cols=137 Identities=22% Similarity=0.280 Sum_probs=120.8
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCCCcCCH
Q 026790 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTE 164 (233)
Q Consensus 85 fT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~~~~~~~~~~S~ 164 (233)
+|++++++|+.|+.+|++++|.+|+++|||+||+.++++.+.++|+.+|++++.++++++..+...+.. .+..+++|+
T Consensus 1 Lt~~a~~~L~~A~~~A~~~~h~~I~~eHLLlaLL~~~~~~~~~iL~~~Gvd~~~Lr~~le~~l~~~p~~--~~~~~~~S~ 78 (852)
T TIGR03345 1 LNPTSRRALEQAAALCVARGHPEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLARALDKLPRG--NTRTPVFSP 78 (852)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHHHhccCCCC--CCCCCCcCH
Confidence 589999999999999999999999999999999999888999999999999999999999999876542 223578999
Q ss_pred HHHHHHHHHHH-HHHHcCCCCCCCHHHHHHHHhhCCCc--hHHHHHHhC-CCCHHHHHHHHHHh
Q 026790 165 QAQRALDWAFN-EKLKSGESGEITTNHLLLGIWSEKES--AGHKILATL-GFNDEKAKEIAKSI 224 (233)
Q Consensus 165 ~~~kvLe~A~~-~A~~~g~~~~I~teHLLLALl~~~~~--~~~~iL~~l-Gvd~~~l~~~i~~~ 224 (233)
.++++|+.|+. .+..+|+ ++|+++|||+||++++++ .+..++..+ |++.+.+.+.+..+
T Consensus 79 ~l~~vL~~A~~~~a~~~g~-~~I~teHLLlALl~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 141 (852)
T TIGR03345 79 HLVELLQEAWLLASLELGD-GRIRSGHLLLALLTDPELRRLLGSISPELAKIDREALREALPAL 141 (852)
T ss_pred HHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHccccchhHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 99999999998 4567999 999999999999998765 455678887 99999998887654
No 6
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=99.74 E-value=7e-17 Score=159.36 Aligned_cols=139 Identities=26% Similarity=0.364 Sum_probs=129.4
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCCCcCC
Q 026790 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLT 163 (233)
Q Consensus 84 rfT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~~~~~~~~~~S 163 (233)
+||+++++++..|+.+|..++|++|+++|||++|+.++++. .++..+|++++.++.+++..+.+.+...+ . +.+|
T Consensus 1 ~~~~~~~~~l~~a~~~a~~~~h~~~~~eHll~~ll~~~~~~--~~l~~~~~~~~~l~~~~~~~~~~~~~~~~--~-~~~s 75 (786)
T COG0542 1 KLTERAQKALELAQELARMRRHEYVTPEHLLLALLDQPKGD--ELLNLCGIDLDKLRQELEEFIDKLPKVLG--S-PYLS 75 (786)
T ss_pred CcCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHcCCchH--HHHHHcCCCHHHHHHHHHHHHhccCCCCC--C-CCCC
Confidence 58999999999999999999999999999999999999876 99999999999999999999999887532 2 7789
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhcCcc
Q 026790 164 EQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSINEDT 228 (233)
Q Consensus 164 ~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~~~~ 228 (233)
+.++++++.|+.+|..+|+ +||+++|||+|++.++++.+.++|...|++...+++.+..+++..
T Consensus 76 ~~~~~~~~~a~~~a~~~~~-~~v~~~~llla~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 139 (786)
T COG0542 76 PRLKRVLERAWLLAQSLGD-EYVSTEHLLLALLNEPESVAAYILKKLGVTRKDVEELIEELRGGN 139 (786)
T ss_pred HHHHHHHHHHHHHHHhccC-ccccHHHHHHHHhcccchHHHHHHHhccCCHHHHHHHHHHHhccc
Confidence 9999999999999999999 999999999999999999999999999999999988998888653
No 7
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=99.64 E-value=7.1e-15 Score=146.44 Aligned_cols=135 Identities=21% Similarity=0.225 Sum_probs=117.5
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhCC-CCCCC--CCCCCCc
Q 026790 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGK-SDLFF--FSPERPP 161 (233)
Q Consensus 85 fT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~~-~~~~~--~~~~~~~ 161 (233)
+|+.+++++..|+.+|++++|.+|+++|||++|+.+++ +..+|+.+|++.+.+++.++..+.. .+... ..+..++
T Consensus 2 ~~~~~~~~l~~a~~~a~~~~~~~~~~~h~l~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (758)
T PRK11034 2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPS--AREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQ 79 (758)
T ss_pred cCHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHcChh--HHHHHHHcCCCHHHHHHHHHHHHhhcCCcCCCCCCcCCcC
Confidence 78999999999999999999999999999999998765 7999999999999999999998873 22110 1112467
Q ss_pred CCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHH
Q 026790 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAK 222 (233)
Q Consensus 162 ~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~ 222 (233)
++.+++++|+.|+.+|..+|+ .+|+++|||+||+.++++.+..+|+.+|++.+.+...+.
T Consensus 80 ~~~~~~~~l~~a~~~~~~~~~-~~i~~~~ll~a~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 139 (758)
T PRK11034 80 PTLSFQRVLQRAVFHVQSSGR-SEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFIS 139 (758)
T ss_pred CCHHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHhcCCcchHHHHHHHcCCCHHHHHHHHH
Confidence 899999999999999999999 999999999999999888888899999999888766543
No 8
>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.54 E-value=7e-14 Score=139.90 Aligned_cols=150 Identities=11% Similarity=-0.008 Sum_probs=135.3
Q ss_pred chhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHHcC-CCHHHHHHHHHHHhCCCCCCCCCCCCC
Q 026790 82 IPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANG-ITLFKVREETLNLLGKSDLFFFSPERP 160 (233)
Q Consensus 82 ~~rfT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~~G-vd~~~lr~~l~~~L~~~~~~~~~~~~~ 160 (233)
+..||++|.++|..|+.+|+++||.+++|+|++.+||.++++.+.+++.+.+ ++..++..-+...|.+.|..++++...
T Consensus 9 ~q~lT~~Aa~~L~~a~~~Arrrgh~qvtplH~~~~LLs~~t~~lr~ac~~~~~l~~ralelc~~v~l~rlpt~~~p~~sn 88 (898)
T KOG1051|consen 9 QQTLTEEAATVLKQAVTEARRRGHAQVTPLHVASTLLSSPTGILRRACIKSHPLQCRALELCFNVSLNRLPTSYGPPVSN 88 (898)
T ss_pred HhhhCHHHHHHHHHHHHHHHHcCCCCcchHHHHHHHHcCCchHHHHHHHhcCcccHHHHHHHHHHHHHhccCCCCCccch
Confidence 5679999999999999999999999999999999999999999999999999 999999999999999988875555667
Q ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhcCccccCC
Q 026790 161 PLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSINEDTILSF 232 (233)
Q Consensus 161 ~~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~~~~~~~~ 232 (233)
+++..+++++..+-+....+++ .||.+||+.|.++-.++..+.+++..+|++..+++..+...+|.+-+++
T Consensus 89 ~l~aalkr~qa~qrr~~~~~~~-~~vkvE~~~li~silDdp~vsrv~reag~~s~~vK~~ve~~~g~~~~~~ 159 (898)
T KOG1051|consen 89 ALMAALKRAQAHQRRGCEEQQQ-QAVKVELEQLILSILDDPSVSRVMREAGFSSSAVKSAVEQPVGQFRSPS 159 (898)
T ss_pred HhHHHHHHHHHHHHhcchhhcc-chhhHhHHhhheeeecCchHHHHHHHhcCChHHHHHHHHhhccccCCCC
Confidence 7888888888888888888999 9999999977777777888899999999999999999999888765543
No 9
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=99.22 E-value=2.7e-11 Score=81.01 Aligned_cols=53 Identities=25% Similarity=0.294 Sum_probs=49.8
Q ss_pred HHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhC
Q 026790 96 AELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLG 148 (233)
Q Consensus 96 A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~ 148 (233)
|+++|++++|.+|+++|||++|+.++++.+.++|+++|+|++.+++++++.++
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~~~~~~~il~~~~id~~~l~~~i~~~lg 53 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDPDSIAARILKKLGIDPEQLKAAIEKALG 53 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHTTSHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhhhHHHHHHHHHcCCCHHHHHHHHHHHhC
Confidence 78999999999999999999999999999999999999999999999998764
No 10
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=99.07 E-value=2.8e-10 Score=76.01 Aligned_cols=53 Identities=26% Similarity=0.369 Sum_probs=48.6
Q ss_pred HHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhcC
Q 026790 173 AFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSINE 226 (233)
Q Consensus 173 A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~~ 226 (233)
|..+|.++|| .||+++|||+||++++++.+.++|+++|+|++.+++.+.+++|
T Consensus 1 A~~~A~~~~~-~~i~~eHlL~all~~~~~~~~~il~~~~id~~~l~~~i~~~lg 53 (53)
T PF02861_consen 1 AQELARERGH-QYISPEHLLLALLEDPDSIAARILKKLGIDPEQLKAAIEKALG 53 (53)
T ss_dssp HHHHHHHTTB-SSE-HHHHHHHHHHHTTSHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred CHHHHHHcCC-CcccHHHHHHHHHhhhhHHHHHHHHHcCCCHHHHHHHHHHHhC
Confidence 5688999999 9999999999999999999999999999999999999988765
No 11
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=98.22 E-value=4e-06 Score=85.38 Aligned_cols=62 Identities=23% Similarity=0.282 Sum_probs=57.6
Q ss_pred CCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHh
Q 026790 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSI 224 (233)
Q Consensus 162 ~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~ 224 (233)
||+.++++|+.|..+|.++|| +||++||||+||+.++++.+.++|..+|+|.+.+++.+...
T Consensus 1 fT~~a~~vL~~A~~~A~~~~h-~~V~~EHLLlaLl~~~~g~a~~iL~~~Gvd~~~l~~~l~~~ 62 (852)
T TIGR03346 1 FTEKFQEALQAAQSLALGRDH-QQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQALEKE 62 (852)
T ss_pred CCHHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHH
Confidence 689999999999999999999 99999999999999988888899999999999998877653
No 12
>CHL00095 clpC Clp protease ATP binding subunit
Probab=98.16 E-value=5.6e-06 Score=84.02 Aligned_cols=62 Identities=21% Similarity=0.316 Sum_probs=57.9
Q ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHH
Q 026790 161 PLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKS 223 (233)
Q Consensus 161 ~~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~ 223 (233)
.||+.++++|+.|..+|.+++| +||++||||+||+.++++.+.++|..+|++.+.+.+.+..
T Consensus 4 rfT~~a~~vL~~A~~~A~~~~h-~~V~~EHLLLaLL~~~~~~a~~iL~~~gid~~~l~~~l~~ 65 (821)
T CHL00095 4 RFTEKAIKVIMLSQEEARRLGH-NFVGTEQILLGLIGEGTGIAARALKSMGVTLKDARIEVEK 65 (821)
T ss_pred hHhHHHHHHHHHHHHHHHHhCC-CcCcHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHH
Confidence 3799999999999999999999 9999999999999998888899999999999998887765
No 13
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=98.14 E-value=7.3e-06 Score=83.47 Aligned_cols=61 Identities=25% Similarity=0.294 Sum_probs=56.5
Q ss_pred CCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHH
Q 026790 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKS 223 (233)
Q Consensus 162 ~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~ 223 (233)
+|+.++++|+.|..+|.++|| +||+++|||+||+.++++.+.++|..+|++.+.+++.+..
T Consensus 1 Lt~~a~~~L~~A~~~A~~~~h-~~I~~eHLLlaLL~~~~~~~~~iL~~~Gvd~~~Lr~~le~ 61 (852)
T TIGR03345 1 LNPTSRRALEQAAALCVARGH-PEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLAR 61 (852)
T ss_pred CCHHHHHHHHHHHHHHHHhCC-CcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHH
Confidence 578999999999999999999 9999999999999988788889999999999998887765
No 14
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=97.98 E-value=2e-05 Score=79.09 Aligned_cols=59 Identities=25% Similarity=0.339 Sum_probs=53.6
Q ss_pred CCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHH
Q 026790 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKS 223 (233)
Q Consensus 162 ~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~ 223 (233)
+|+.++++|+.|..+|.++|| +||++||||+||+++++ +.++|..+|++.+.+.+.+..
T Consensus 1 ~~~~a~~~L~~A~~~A~~~~h-~~V~~EHLLlaLL~~~~--~~~iL~~~gid~~~l~~~l~~ 59 (731)
T TIGR02639 1 ISEELERILDAALEEAKKRRH-EFVTLEHILLALLFDSD--AIEILEECGGDVEALRKDLED 59 (731)
T ss_pred CCHHHHHHHHHHHHHHHHhCC-CcCcHHHHHHHHHcCch--HHHHHHHcCCCHHHHHHHHHH
Confidence 588999999999999999999 99999999999999765 457999999999999887765
No 15
>PRK10865 protein disaggregation chaperone; Provisional
Probab=97.88 E-value=4.1e-05 Score=78.17 Aligned_cols=63 Identities=21% Similarity=0.189 Sum_probs=58.0
Q ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHh
Q 026790 161 PLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSI 224 (233)
Q Consensus 161 ~~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~ 224 (233)
.||+.++++|+.|..+|.+++| .+|+++|||+||++++++.+.++|..+|+|.+.+++.+...
T Consensus 5 ~~~~~~~~~l~~a~~~a~~~~~-~~~~~~hll~~l~~~~~~~~~~~l~~~~~~~~~l~~~~~~~ 67 (857)
T PRK10865 5 RLTNKFQLALADAQSLALGHDN-QFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQLRTDINQA 67 (857)
T ss_pred HhCHHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3899999999999999999999 99999999999999888888899999999999988877653
No 16
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=97.59 E-value=0.00019 Score=72.32 Aligned_cols=59 Identities=19% Similarity=0.267 Sum_probs=53.8
Q ss_pred CCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHH
Q 026790 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKS 223 (233)
Q Consensus 162 ~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~ 223 (233)
+++.++++|+.|..+|.+++| ++|++||+|++|+.+++ +.++|+.+|++.+.+++.+..
T Consensus 2 ~~~~~~~~l~~a~~~a~~~~~-~~~~~~h~l~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~ 60 (758)
T PRK11034 2 LNQELELSLNMAFARAREHRH-EFMTVEHLLLALLSNPS--AREALEACSVDLVALRQELEA 60 (758)
T ss_pred cCHHHHHHHHHHHHHHHHcCC-CcchHHHHHHHHHcChh--HHHHHHHcCCCHHHHHHHHHH
Confidence 688999999999999999999 99999999999998754 678999999999998887765
No 17
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=97.48 E-value=0.00036 Score=70.17 Aligned_cols=59 Identities=27% Similarity=0.367 Sum_probs=54.5
Q ss_pred CCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHH
Q 026790 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKS 223 (233)
Q Consensus 162 ~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~ 223 (233)
|++.++++|+.|..+|...+| .||+++|||++|+.++++. .+|...|++.+.+++.+..
T Consensus 2 ~~~~~~~~l~~a~~~a~~~~h-~~~~~eHll~~ll~~~~~~--~~l~~~~~~~~~l~~~~~~ 60 (786)
T COG0542 2 LTERAQKALELAQELARMRRH-EYVTPEHLLLALLDQPKGD--ELLNLCGIDLDKLRQELEE 60 (786)
T ss_pred cCHHHHHHHHHHHHHHHHhCC-CcccHHHHHHHHHcCCchH--HHHHHcCCCHHHHHHHHHH
Confidence 789999999999999999999 9999999999999987765 7999999999999887655
No 18
>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]
Probab=96.62 E-value=0.0063 Score=62.18 Aligned_cols=59 Identities=19% Similarity=0.171 Sum_probs=53.9
Q ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCC-CCHHHHHH
Q 026790 160 PPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLG-FNDEKAKE 219 (233)
Q Consensus 160 ~~~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lG-vd~~~l~~ 219 (233)
-.||+++.++|..|+.+|++.|| +.+++.|++.|||..+.+...+++.+.+ ++-.+++.
T Consensus 10 q~lT~~Aa~~L~~a~~~Arrrgh-~qvtplH~~~~LLs~~t~~lr~ac~~~~~l~~ralel 69 (898)
T KOG1051|consen 10 QTLTEEAATVLKQAVTEARRRGH-AQVTPLHVASTLLSSPTGILRRACIKSHPLQCRALEL 69 (898)
T ss_pred hhhCHHHHHHHHHHHHHHHHcCC-CCcchHHHHHHHHcCCchHHHHHHHhcCcccHHHHHH
Confidence 45999999999999999999999 9999999999999999999999999988 77666664
No 19
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=81.74 E-value=1.7 Score=34.00 Aligned_cols=40 Identities=15% Similarity=0.173 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHH
Q 026790 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (233)
Q Consensus 89 a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~ 130 (233)
+.++++.|-+.|+..+...|+|+|+-+++-+|.+ ...+|.
T Consensus 55 ~aEIlelA~n~ak~~k~krItp~hi~lAi~nD~E--L~~L~~ 94 (115)
T cd00074 55 TAEVLELAGNAARDNKKKRITPRHLQLAVRNDEE--LNKLLK 94 (115)
T ss_pred HHHHHHHHHHHHHHcCCCeEcHHHHHHHHhccHH--HHHHHc
Confidence 3568999999999999999999999999987653 344554
No 20
>PLN00154 histone H2A; Provisional
Probab=80.97 E-value=1.5 Score=35.36 Aligned_cols=40 Identities=25% Similarity=0.288 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~ 208 (233)
+-++||.|.+.|...+. ..|++.||.+|+-.|++- .++|+
T Consensus 74 tAEVLELAGNaA~d~kk-~RItPrHi~lAIrnDeEL--~~Ll~ 113 (136)
T PLN00154 74 TAEVLELAGNASKDLKV-KRITPRHLQLAIRGDEEL--DTLIK 113 (136)
T ss_pred HHHHHHHHHHHHHhhCC-ceecHHHhhhhccCcHHH--HHHhc
Confidence 45799999999999999 999999999999987643 33554
No 21
>PTZ00017 histone H2A; Provisional
Probab=80.93 E-value=1.5 Score=35.23 Aligned_cols=39 Identities=15% Similarity=0.126 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHH
Q 026790 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (233)
Q Consensus 90 ~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~ 130 (233)
.++|+.|-+.|+..+...|+|+|+.+++-+|.+ ...+|.
T Consensus 63 aEILELAgNaa~d~kk~RItPrHi~lAI~nDeE--L~~Ll~ 101 (134)
T PTZ00017 63 AEVLELAGNAAKDNKKKRITPRHIQLAIRNDEE--LNKLLA 101 (134)
T ss_pred HHHHHHHHHHHHhcCCCeecHHHHHhhccCcHH--HHHHHc
Confidence 458999999999999999999999999987653 455654
No 22
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=80.70 E-value=2.8 Score=33.31 Aligned_cols=40 Identities=18% Similarity=0.149 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHH
Q 026790 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (233)
Q Consensus 89 a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~ 130 (233)
+.++++.|-+.|+..+-.-|+|.|+.+|+-+|.+ ..++|.
T Consensus 62 ~Aeile~agnaardnkk~ri~PrH~~lAI~NDeE--L~~lL~ 101 (131)
T KOG1756|consen 62 TAEILELAGNAARDNKKTRITPRHLQLAIRNDEE--LNKLLG 101 (131)
T ss_pred HHHHHHHhHHHhhhcCccccChHHHHHHHhCcHH--HHHHhc
Confidence 3578899999999999999999999999998753 567766
No 23
>PLN00154 histone H2A; Provisional
Probab=80.68 E-value=1.5 Score=35.36 Aligned_cols=39 Identities=10% Similarity=0.174 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHH
Q 026790 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (233)
Q Consensus 90 ~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~ 130 (233)
.++|+.|-+.|+..+...|+|.|+.+++-+|.+ ..++|.
T Consensus 75 AEVLELAGNaA~d~kk~RItPrHi~lAIrnDeE--L~~Ll~ 113 (136)
T PLN00154 75 AEVLELAGNASKDLKVKRITPRHLQLAIRGDEE--LDTLIK 113 (136)
T ss_pred HHHHHHHHHHHHhhCCceecHHHhhhhccCcHH--HHHHhc
Confidence 468999999999999999999999999987643 455553
No 24
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=79.11 E-value=2.3 Score=33.23 Aligned_cols=40 Identities=28% Similarity=0.372 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~ 208 (233)
+.++|+.|.+.|...+. ..|+++||-+|+-.|++- ..+++
T Consensus 55 ~aEIlelA~n~ak~~k~-krItp~hi~lAi~nD~EL--~~L~~ 94 (115)
T cd00074 55 TAEVLELAGNAARDNKK-KRITPRHLQLAVRNDEEL--NKLLK 94 (115)
T ss_pred HHHHHHHHHHHHHHcCC-CeEcHHHHHHHHhccHHH--HHHHc
Confidence 46799999999999999 999999999999987653 33554
No 25
>PTZ00017 histone H2A; Provisional
Probab=79.02 E-value=2 Score=34.59 Aligned_cols=40 Identities=30% Similarity=0.394 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~ 208 (233)
+.++||.|.+.|...+. ..|+++||.+|+-.|++- ..+|+
T Consensus 62 taEILELAgNaa~d~kk-~RItPrHi~lAI~nDeEL--~~Ll~ 101 (134)
T PTZ00017 62 TAEVLELAGNAAKDNKK-KRITPRHIQLAIRNDEEL--NKLLA 101 (134)
T ss_pred HHHHHHHHHHHHHhcCC-CeecHHHHHhhccCcHHH--HHHHc
Confidence 56799999999999999 999999999999987653 33554
No 26
>PLN00153 histone H2A; Provisional
Probab=77.13 E-value=2.4 Score=33.83 Aligned_cols=39 Identities=18% Similarity=0.125 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHH
Q 026790 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (233)
Q Consensus 90 ~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~ 130 (233)
.++++.|-+.|+..+...|+|+|+.+++-+|. ...++|.
T Consensus 60 aEVLELAgnaa~d~kk~RItPrHi~lAI~nDe--EL~~Ll~ 98 (129)
T PLN00153 60 AEVLELAGNAARDNKKNRIVPRHIQLAIRNDE--ELGKLLG 98 (129)
T ss_pred HHHHHHHHHHHHhcCCCccChHHHHhhccCcH--HHHHHHC
Confidence 46899999999999999999999999998765 3466665
No 27
>PLN00157 histone H2A; Provisional
Probab=77.12 E-value=2.1 Score=34.32 Aligned_cols=41 Identities=17% Similarity=0.151 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHH
Q 026790 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRA 131 (233)
Q Consensus 89 a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~ 131 (233)
+.++++.|-+.|+..+...|+|+|+.+++-+|.+ ...+|..
T Consensus 61 taEVLELAgnaa~d~kk~RItPrHi~lAI~nDeE--L~~Ll~~ 101 (132)
T PLN00157 61 AAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEE--LSKLLGG 101 (132)
T ss_pred HHHHHHHHHHHHHhcCCccccHHHHhhcccCcHH--HHHHHcC
Confidence 3458999999999999999999999999987653 4666653
No 28
>smart00414 H2A Histone 2A.
Probab=75.84 E-value=2.7 Score=32.43 Aligned_cols=44 Identities=16% Similarity=0.165 Sum_probs=34.3
Q ss_pred chhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHH
Q 026790 82 IPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (233)
Q Consensus 82 ~~rfT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~ 130 (233)
++.++ .++++.|-+.|+..+...|+|+|+-+++-+|.+ ...+|+
T Consensus 40 LEYLt---aEILeLagn~a~~~k~~rItp~hi~lAi~nD~E--L~~L~~ 83 (106)
T smart00414 40 LEYLT---AEVLELAGNAARDNKKRRITPRHLQLAIRNDEE--LNKLLK 83 (106)
T ss_pred HHHHH---HHHHHHHHHHHHhcCCCccchHHHhhhccCCHH--HHHHHc
Confidence 44444 458899999999999999999999999977543 445554
No 29
>PLN00157 histone H2A; Provisional
Probab=75.52 E-value=2.6 Score=33.77 Aligned_cols=40 Identities=25% Similarity=0.365 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~ 208 (233)
+.++||.|.+.|...+. ..|+++||.+|+-.|++- .++|+
T Consensus 61 taEVLELAgnaa~d~kk-~RItPrHi~lAI~nDeEL--~~Ll~ 100 (132)
T PLN00157 61 AAEVLELAGNAARDNKK-SRIVPRHIQLAVRNDEEL--SKLLG 100 (132)
T ss_pred HHHHHHHHHHHHHhcCC-ccccHHHHhhcccCcHHH--HHHHc
Confidence 56799999999999998 999999999999987653 33554
No 30
>PLN00156 histone H2AX; Provisional
Probab=75.24 E-value=3 Score=33.73 Aligned_cols=39 Identities=15% Similarity=0.123 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHH
Q 026790 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (233)
Q Consensus 90 ~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~ 130 (233)
.++++.|-+.|+..+...|+|+|+.+++-.|. ....+|.
T Consensus 65 aEVLELAgNaa~d~kk~RItPrHi~lAIrnDe--EL~~Ll~ 103 (139)
T PLN00156 65 AEVLELAGNAARDNKKNRIVPRHIQLAVRNDE--ELSKLLG 103 (139)
T ss_pred HHHHHHHHHHHHHcCCCcCcHHHHHhhccCcH--HHHHHHC
Confidence 45899999999999999999999999998765 3466665
No 31
>smart00414 H2A Histone 2A.
Probab=73.11 E-value=3.6 Score=31.68 Aligned_cols=41 Identities=29% Similarity=0.362 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHh
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILAT 209 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~ 209 (233)
+.++||.|.+.|...+. ..|+++||-+|+-.|++- ..+++.
T Consensus 44 taEILeLagn~a~~~k~-~rItp~hi~lAi~nD~EL--~~L~~~ 84 (106)
T smart00414 44 TAEVLELAGNAARDNKK-RRITPRHLQLAIRNDEEL--NKLLKG 84 (106)
T ss_pred HHHHHHHHHHHHHhcCC-CccchHHHhhhccCCHHH--HHHHcC
Confidence 46799999999999988 999999999999987653 335553
No 32
>PLN00153 histone H2A; Provisional
Probab=72.90 E-value=3.8 Score=32.72 Aligned_cols=40 Identities=25% Similarity=0.347 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~ 208 (233)
+.++||.|.+.|...+- ..|.++||.+|+-.|++- .++|+
T Consensus 59 taEVLELAgnaa~d~kk-~RItPrHi~lAI~nDeEL--~~Ll~ 98 (129)
T PLN00153 59 TAEVLELAGNAARDNKK-NRIVPRHIQLAIRNDEEL--GKLLG 98 (129)
T ss_pred HHHHHHHHHHHHHhcCC-CccChHHHHhhccCcHHH--HHHHC
Confidence 45799999999999888 999999999999987653 33555
No 33
>PLN00156 histone H2AX; Provisional
Probab=72.55 E-value=4 Score=32.99 Aligned_cols=40 Identities=25% Similarity=0.365 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~ 208 (233)
+-++||.|.+.|...+- ..|.++||.+|+-.|++- ..+|+
T Consensus 64 taEVLELAgNaa~d~kk-~RItPrHi~lAIrnDeEL--~~Ll~ 103 (139)
T PLN00156 64 AAEVLELAGNAARDNKK-NRIVPRHIQLAVRNDEEL--SKLLG 103 (139)
T ss_pred HHHHHHHHHHHHHHcCC-CcCcHHHHHhhccCcHHH--HHHHC
Confidence 45799999999999988 999999999999987653 33554
No 34
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=72.03 E-value=4.4 Score=32.23 Aligned_cols=41 Identities=29% Similarity=0.353 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHh
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILAT 209 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~ 209 (233)
.-++||.+-+.|+..+- ..|.+.||.+||-.|++ ..++|..
T Consensus 62 ~Aeile~agnaardnkk-~ri~PrH~~lAI~NDeE--L~~lL~~ 102 (131)
T KOG1756|consen 62 TAEILELAGNAARDNKK-TRITPRHLQLAIRNDEE--LNKLLGK 102 (131)
T ss_pred HHHHHHHhHHHhhhcCc-cccChHHHHHHHhCcHH--HHHHhcc
Confidence 45788999999999888 99999999999998764 3446653
No 35
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=70.20 E-value=7.6 Score=25.16 Aligned_cols=27 Identities=22% Similarity=0.081 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHH
Q 026790 90 IRSFAMAELEARKLKYPNTGTEAFLMG 116 (233)
Q Consensus 90 ~~vl~~A~~eA~~~~~~~I~~eHLLla 116 (233)
..+=..+...|++.|..+|+.+|+.-+
T Consensus 18 ~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 18 KKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 555567889999999999999998643
No 36
>PTZ00252 histone H2A; Provisional
Probab=66.80 E-value=5.4 Score=32.04 Aligned_cols=40 Identities=8% Similarity=0.091 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHH--cCCCCcCHHHHHHHHhhcCCChHHHHHHH
Q 026790 90 IRSFAMAELEARK--LKYPNTGTEAFLMGILVEGTSTTAKFLRA 131 (233)
Q Consensus 90 ~~vl~~A~~eA~~--~~~~~I~~eHLLlaLL~e~~~~a~~iL~~ 131 (233)
.++++.|-+.|++ .+...|+|+|+.+++-+|+ ...++|..
T Consensus 61 aEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDe--EL~~Ll~~ 102 (134)
T PTZ00252 61 AELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDD--DLGSLLKN 102 (134)
T ss_pred HHHHHHHHHHHHhccCCcccccHHHHHhhccChH--HHHHHHcC
Confidence 4589999999987 4558999999999998765 34666653
No 37
>PF13551 HTH_29: Winged helix-turn helix
Probab=65.46 E-value=51 Score=24.08 Aligned_cols=83 Identities=24% Similarity=0.127 Sum_probs=51.4
Q ss_pred HHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhCCCCCC----CCCCCCCc--CCHHHHHHHHHHHHHHHHcCCCCCCCH
Q 026790 115 MGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLF----FFSPERPP--LTEQAQRALDWAFNEKLKSGESGEITT 188 (233)
Q Consensus 115 laLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~----~~~~~~~~--~S~~~~kvLe~A~~~A~~~g~~~~I~t 188 (233)
+.++.++.+....+.+.+|++...+...+..+....... ...+..+. ++++....+......--..|. ...+.
T Consensus 5 l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~-~~~t~ 83 (112)
T PF13551_consen 5 LLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGR-SRWTL 83 (112)
T ss_pred HHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCC-CcccH
Confidence 344555543479999999999999999988866543110 01112222 788877777665554333355 56777
Q ss_pred HHHHHHHhhC
Q 026790 189 NHLLLGIWSE 198 (233)
Q Consensus 189 eHLLLALl~~ 198 (233)
+.|--.|+++
T Consensus 84 ~~l~~~l~~~ 93 (112)
T PF13551_consen 84 EELAEWLIEE 93 (112)
T ss_pred HHHHHHHHHh
Confidence 7777666443
No 38
>PTZ00252 histone H2A; Provisional
Probab=58.44 E-value=11 Score=30.33 Aligned_cols=41 Identities=10% Similarity=0.217 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHH--cCCCCCCCHHHHHHHHhhCCCchHHHHHHh
Q 026790 166 AQRALDWAFNEKLK--SGESGEITTNHLLLGIWSEKESAGHKILAT 209 (233)
Q Consensus 166 ~~kvLe~A~~~A~~--~g~~~~I~teHLLLALl~~~~~~~~~iL~~ 209 (233)
+.++||.|.+.|.+ ..- ..|.++||.+|+-.|++- .++|+.
T Consensus 60 taEVLELAgnaa~d~~~kk-~RItPrHi~lAIrNDeEL--~~Ll~~ 102 (134)
T PTZ00252 60 TAELLELSVKAAAQQAKKP-KRLTPRTVTLAVRHDDDL--GSLLKN 102 (134)
T ss_pred HHHHHHHHHHHHHhccCCc-ccccHHHHHhhccChHHH--HHHHcC
Confidence 45789999999865 444 689999999999987653 335653
No 39
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=54.54 E-value=17 Score=25.26 Aligned_cols=29 Identities=21% Similarity=0.126 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGI 195 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLAL 195 (233)
+.++|+.|...|...+. ..|+..||.+|+
T Consensus 44 ~~~il~~A~~~a~~~kR-~tI~~~DI~~A~ 72 (75)
T PF00125_consen 44 LVEILEEAGNLARHAKR-KTITPRDIQLAV 72 (75)
T ss_dssp HHHHHHHHHHHHHHTTB-SEEGHHHHHHHH
T ss_pred hhhhhhHHHHHHhhcCC-cEecHHHHHHHH
Confidence 56788889999999999 999999999986
No 40
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=54.16 E-value=29 Score=25.93 Aligned_cols=88 Identities=17% Similarity=0.056 Sum_probs=53.8
Q ss_pred cHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHHH-cCCCHHHHHHHHHHHhCCCCCCCCCCCCCcC-C
Q 026790 86 SARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRA-NGITLFKVREETLNLLGKSDLFFFSPERPPL-T 163 (233)
Q Consensus 86 T~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~~-~Gvd~~~lr~~l~~~L~~~~~~~~~~~~~~~-S 163 (233)
|..+++-|..|.....++..+... +.. +-...|.+ +.++. .....++..+.+.. + .
T Consensus 5 S~~ir~rV~~Ar~~Q~~R~~~~~~----------Na~-l~~~~l~~~~~l~~-~~~~~l~~~~~~~~----------lS~ 62 (96)
T PF13335_consen 5 SAEIRERVEAARERQRERYGGIKC----------NAQ-LPGEELRKYCPLSS-EAKKLLEQAAEKLN----------LSA 62 (96)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCc----------ccc-CCHHHHHhHcCCCH-HHHHHHHHHHHHcC----------cCH
Confidence 667777788887777765441111 111 11233333 33333 33333443333211 2 4
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHh
Q 026790 164 EQAQRALDWAFNEKLKSGESGEITTNHLLLGIW 196 (233)
Q Consensus 164 ~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl 196 (233)
....++|..|.-+|---|+ +.|+.+||.-||-
T Consensus 63 R~~~rilrvARTIADL~~~-~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 63 RGYHRILRVARTIADLEGS-ERITREHIAEALS 94 (96)
T ss_pred HHHHHHHHHHHHHHhHcCC-CCCCHHHHHHHHh
Confidence 5688999999999988899 9999999999873
No 41
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=53.96 E-value=20 Score=24.95 Aligned_cols=30 Identities=13% Similarity=0.071 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 026790 88 RAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (233)
Q Consensus 88 ~a~~vl~~A~~eA~~~~~~~I~~eHLLlaL 117 (233)
-..++++.|...|...+...|++.|+.+++
T Consensus 43 ~~~~il~~A~~~a~~~kR~tI~~~DI~~A~ 72 (75)
T PF00125_consen 43 LLVEILEEAGNLARHAKRKTITPRDIQLAV 72 (75)
T ss_dssp HHHHHHHHHHHHHHHTTBSEEGHHHHHHHH
T ss_pred hhhhhhhHHHHHHhhcCCcEecHHHHHHHH
Confidence 456778889999999999999999999886
No 42
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=52.47 E-value=13 Score=29.31 Aligned_cols=40 Identities=20% Similarity=0.130 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCChHHHHHH
Q 026790 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (233)
Q Consensus 89 a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~~a~~iL~ 130 (233)
+.++++.|-+.|+..+...|.|-||=+++-.|++ ...++.
T Consensus 61 ~aEilelAgNaA~d~kkkri~PrHlqlAIrnD~E--L~~l~~ 100 (132)
T COG5262 61 AAEILELAGNAARDNKKKRIIPRHLQLAIRNDEE--LNKLLG 100 (132)
T ss_pred HHHHHHHhhhhhhhcCcceechHHHHHHhcCcHH--HHHHhh
Confidence 4578899999999999999999999999988653 344444
No 43
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=45.60 E-value=47 Score=22.99 Aligned_cols=37 Identities=14% Similarity=0.251 Sum_probs=26.9
Q ss_pred HHHHHHHhhCCC--chHHHHHHhCCCCHHHHHHHHHHhc
Q 026790 189 NHLLLGIWSEKE--SAGHKILATLGFNDEKAKEIAKSIN 225 (233)
Q Consensus 189 eHLLLALl~~~~--~~~~~iL~~lGvd~~~l~~~i~~~~ 225 (233)
+.||-.|.+.++ ..+.++-+.+|++...+.+.+..+.
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~ 47 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE 47 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344444444444 5678888999999999999998765
No 44
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=45.17 E-value=20 Score=28.27 Aligned_cols=34 Identities=29% Similarity=0.340 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCC
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKE 200 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~ 200 (233)
+-++||.|-+.|+..+- ..|.+-||-+||-.|++
T Consensus 61 ~aEilelAgNaA~d~kk-kri~PrHlqlAIrnD~E 94 (132)
T COG5262 61 AAEILELAGNAARDNKK-KRIIPRHLQLAIRNDEE 94 (132)
T ss_pred HHHHHHHhhhhhhhcCc-ceechHHHHHHhcCcHH
Confidence 46889999999999999 99999999999998764
No 45
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=40.74 E-value=50 Score=22.40 Aligned_cols=26 Identities=15% Similarity=-0.052 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHcCCCCcCHHHHHHHH
Q 026790 92 SFAMAELEARKLKYPNTGTEAFLMGI 117 (233)
Q Consensus 92 vl~~A~~eA~~~~~~~I~~eHLLlaL 117 (233)
+...|...|...+...|+++|+..++
T Consensus 40 l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 40 LAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 34556677889999999999998875
No 46
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=40.42 E-value=58 Score=22.62 Aligned_cols=34 Identities=15% Similarity=-0.083 Sum_probs=30.2
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 026790 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (233)
Q Consensus 84 rfT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaL 117 (233)
-...++.+++..|...++..+-..++++++-++|
T Consensus 31 ~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Al 64 (65)
T smart00803 31 DVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSAL 64 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHh
Confidence 3467889999999999999999999999997775
No 47
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=39.87 E-value=54 Score=22.76 Aligned_cols=58 Identities=17% Similarity=0.174 Sum_probs=39.4
Q ss_pred hHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCCCcCCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Q 026790 124 TTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGI 195 (233)
Q Consensus 124 ~a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~~~~~~~~~~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLAL 195 (233)
...++.+..|+.. +.+++...|.. .....+.++++.|..++...+- +.++++++-.||
T Consensus 7 ~i~ria~~~Gi~r--is~~a~~~l~~-----------~~e~rl~~i~~~A~k~~~hakR-ktlt~~DI~~Al 64 (65)
T smart00803 7 TIKDVAESLGIGN--LSDEAAKLLAE-----------DVEYRIKEIVQEALKFMRHSKR-TTLTTSDIDSAL 64 (65)
T ss_pred HHHHHHHHCCCcc--ccHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHhCC-CeecHHHHHHHh
Confidence 4567777777762 22222222211 1245678899999999999999 999999998876
No 48
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=39.29 E-value=1.2e+02 Score=22.79 Aligned_cols=69 Identities=9% Similarity=-0.034 Sum_probs=49.7
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCCCcCCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhh
Q 026790 125 TAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWS 197 (233)
Q Consensus 125 a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~~~~~~~~~~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~ 197 (233)
...++..+|++.+-+.+-++.-+-..... .++...|+...-..++.+.+....++- |..+.. +.+-|++
T Consensus 10 ~~Elc~~~gi~~~~l~eLve~GlIep~~~--~~~~~~F~~~~l~r~~~a~rL~~dl~i-n~~gia-lvl~LLd 78 (101)
T PRK10265 10 ITEFCLHTGVSEEELNEIVGLGVIEPREI--QETTWVFDDHAAIVVQRAVRLRHELAL-DWPGIA-VALTLLD 78 (101)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCeecCCC--CcccceECHHHHHHHHHHHHHHHHcCC-CHHHHH-HHHHHHH
Confidence 46789999999999999887655443221 245567999999999999999998887 655443 3344443
No 49
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=39.16 E-value=71 Score=20.02 Aligned_cols=38 Identities=13% Similarity=0.235 Sum_probs=28.8
Q ss_pred HHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhcC
Q 026790 189 NHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSINE 226 (233)
Q Consensus 189 eHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~~ 226 (233)
..||..|.+++.....++-+.+|++...+.+.++++-.
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 35677777777777788889999999999999887653
No 50
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=36.59 E-value=57 Score=21.01 Aligned_cols=27 Identities=22% Similarity=0.089 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHcCCCCCCCHHHHHHH
Q 026790 167 QRALDWAFNEKLKSGESGEITTNHLLLG 194 (233)
Q Consensus 167 ~kvLe~A~~~A~~~g~~~~I~teHLLLA 194 (233)
+++=..+..+|+..|. ..|+.+|+.-|
T Consensus 18 ~~~r~~~E~~Ar~~G~-~~IT~e~v~~A 44 (45)
T PF08369_consen 18 KKLRDAAEKYARERGY-DEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHHHHHHHCT--SEE-HHHHHHH
T ss_pred HHHHHHHHHHHHHcCC-CeECHHHHHhh
Confidence 5666677889999999 99999998644
No 51
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=36.53 E-value=61 Score=21.97 Aligned_cols=26 Identities=12% Similarity=-0.015 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHcCCCCCCCHHHHHHHH
Q 026790 169 ALDWAFNEKLKSGESGEITTNHLLLGI 195 (233)
Q Consensus 169 vLe~A~~~A~~~g~~~~I~teHLLLAL 195 (233)
+...|+.++.+-+. ..|..+||..||
T Consensus 40 l~~~A~~~a~~~~r-kti~~~Dv~~Av 65 (65)
T PF00808_consen 40 LAKEANEIAQRDKR-KTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHHHTTS-SEE-HHHHHHHH
T ss_pred HHHHHHHHHHHcCC-CccCHHHHHHHC
Confidence 34456778888888 899999998875
No 52
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=34.98 E-value=1.6e+02 Score=21.26 Aligned_cols=61 Identities=18% Similarity=-0.007 Sum_probs=46.4
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCCCcCCHHHHHHHHHHHHHHHHcCCCCCCCHH
Q 026790 125 TAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFNEKLKSGESGEITTN 189 (233)
Q Consensus 125 a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~~~~~~~~~~S~~~~kvLe~A~~~A~~~g~~~~I~te 189 (233)
...++..+|++.+-+.+-++.-+-.... ......|+...-.-++.+.+....+|- |.-|.+
T Consensus 3 ~~e~~~~~~i~~~~l~~lve~Gli~p~~---~~~~~~f~~~~l~rl~~~~rL~~Dl~i-n~~gi~ 63 (84)
T PF13591_consen 3 LEEFCEACGIEPEFLRELVEEGLIEPEG---EEEEWYFSEEDLARLRRIRRLHRDLGI-NLEGIA 63 (84)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCeeecC---CCCeeeECHHHHHHHHHHHHHHHHcCC-CHHHHH
Confidence 3578899999999999888765544322 224567999999999999999999888 655543
No 53
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=34.21 E-value=80 Score=20.54 Aligned_cols=37 Identities=14% Similarity=0.265 Sum_probs=28.1
Q ss_pred HHHHHHHhhCCC--chHHHHHHhCCCCHHHHHHHHHHhc
Q 026790 189 NHLLLGIWSEKE--SAGHKILATLGFNDEKAKEIAKSIN 225 (233)
Q Consensus 189 eHLLLALl~~~~--~~~~~iL~~lGvd~~~l~~~i~~~~ 225 (233)
-++|..|...++ ....++-+.+|+++..+.+.++.+-
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~ 46 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLE 46 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356667777665 5778899999999999999887764
No 54
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=33.80 E-value=50 Score=22.34 Aligned_cols=27 Identities=11% Similarity=0.267 Sum_probs=22.5
Q ss_pred hHHHHHHhCCCCHHHHHHHHHHhcCcc
Q 026790 202 AGHKILATLGFNDEKAKEIAKSINEDT 228 (233)
Q Consensus 202 ~~~~iL~~lGvd~~~l~~~i~~~~~~~ 228 (233)
....+-+++|++.+++++++..++.++
T Consensus 22 ev~ywa~~~gvt~~~L~~AV~~vG~~~ 48 (57)
T PF12244_consen 22 EVRYWAKRFGVTEEQLREAVRAVGNSR 48 (57)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHHCcCH
Confidence 346678889999999999999988664
No 55
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=31.82 E-value=93 Score=23.17 Aligned_cols=33 Identities=21% Similarity=0.052 Sum_probs=27.1
Q ss_pred hcHH-HHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 026790 85 WSAR-AIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (233)
Q Consensus 85 fT~~-a~~vl~~A~~eA~~~~~~~I~~eHLLlaL 117 (233)
+|.+ ..+++..|.-.|--.+++.|+.+||.-||
T Consensus 60 lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl 93 (96)
T PF13335_consen 60 LSARGYHRILRVARTIADLEGSERITREHIAEAL 93 (96)
T ss_pred cCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHH
Confidence 3444 35677888899999999999999999886
No 56
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=31.69 E-value=1.1e+02 Score=21.56 Aligned_cols=34 Identities=9% Similarity=-0.146 Sum_probs=28.7
Q ss_pred cHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhh
Q 026790 86 SARAIRSFAMAELEARKLKYPNTGTEAFLMGILV 119 (233)
Q Consensus 86 T~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~ 119 (233)
..-+.+++..|...|+.+|...|..+-+.+++=.
T Consensus 33 e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 33 DDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 4556678888999999999999999999988744
No 57
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=31.50 E-value=92 Score=24.19 Aligned_cols=61 Identities=25% Similarity=0.245 Sum_probs=43.9
Q ss_pred hHHHHHHHcCCCH--HHHHHHHHHHhCCCCCCCCCCCCCcCCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCC
Q 026790 124 TTAKFLRANGITL--FKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKE 200 (233)
Q Consensus 124 ~a~~iL~~~Gvd~--~~lr~~l~~~L~~~~~~~~~~~~~~~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~ 200 (233)
....+|+++|+.. +.+...+.... -.-+..++.+|..+|.-.|- +.|+.+++-+|+-..-+
T Consensus 6 ~v~~iLk~~Gv~~~~~~v~~~Lle~~---------------~ry~~~il~dA~~~a~hA~r-~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 6 VIAAILKSMGITEYEPRVINQLLEFA---------------YRYTTDVLDDAKVYSEHAGK-ANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHCCCCccCHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHcCC-CCCCHHHHHHHHHHHhc
Confidence 4567888888762 23333332222 23467899999999999999 99999999999987543
No 58
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=31.49 E-value=52 Score=22.34 Aligned_cols=37 Identities=16% Similarity=0.295 Sum_probs=30.6
Q ss_pred HHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhc
Q 026790 189 NHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSIN 225 (233)
Q Consensus 189 eHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~ 225 (233)
..++.+|+..+...+.++-+.+|++...+.+.+..+-
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~ 47 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLE 47 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3567788877777788999999999999999888764
No 59
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=29.92 E-value=1.2e+02 Score=21.31 Aligned_cols=31 Identities=6% Similarity=0.016 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhh
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWS 197 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~ 197 (233)
+..+++.|..+|+-.|. +.|..+.+.+++=.
T Consensus 36 v~~v~~~a~~lAkHr~~-~tv~~~Di~l~l~r 66 (72)
T cd07981 36 VDDVVEDACRLAKHRKS-DTLEVKDVQLHLER 66 (72)
T ss_pred HHHHHHHHHHHHHHcCC-CCCCHHHHHHHHHH
Confidence 45677788999998999 89999999998754
No 60
>COG2317 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]
Probab=28.76 E-value=4.9e+02 Score=25.44 Aligned_cols=89 Identities=16% Similarity=0.123 Sum_probs=56.8
Q ss_pred chhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCC--hHHHHHHHcCCCHHHHHHHHHHHh----CCCCCC-C
Q 026790 82 IPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTS--TTAKFLRANGITLFKVREETLNLL----GKSDLF-F 154 (233)
Q Consensus 82 ~~rfT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~--~a~~iL~~~Gvd~~~lr~~l~~~L----~~~~~~-~ 154 (233)
|+.|.|.+.+++..+..+|..++... .|-.-|+-+.+.+.. .+.+++ +.|+.++...+ .+.... .
T Consensus 125 f~~F~p~Lekiv~l~re~A~~~~~~~-~pYdaLld~yEpG~t~~~i~~vF-------~~Lk~~L~~ll~kv~~~~~~~~~ 196 (497)
T COG2317 125 FSIFKPYLEKIVELKREFAEYRGYEE-HPYDALLDLYEPGLTVRDVDRVF-------AELKKELVPLLDKVLEKGKSPRS 196 (497)
T ss_pred HhhhhHHHHHHHHHHHHHHHhccccc-CcHHHHHHhhcCCCcHHHHHHHH-------HHHHHHHHHHHHHHHhccCCCcc
Confidence 99999999999999999999999998 555555555543321 122233 34444444444 333111 0
Q ss_pred CCCCCCcCCHHHHHHHHHHHHHHH
Q 026790 155 FSPERPPLTEQAQRALDWAFNEKL 178 (233)
Q Consensus 155 ~~~~~~~~S~~~~kvLe~A~~~A~ 178 (233)
......+|+.+-++.|-..+....
T Consensus 197 ~~~~~~~~~~e~q~~~~~~vl~~l 220 (497)
T COG2317 197 DLLEKEKYDKEKQEALGLRVLELL 220 (497)
T ss_pred cccccCCCCHHHHHHHHHHHHHHh
Confidence 122345789999998888877543
No 61
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=28.23 E-value=1e+02 Score=20.88 Aligned_cols=36 Identities=19% Similarity=0.354 Sum_probs=27.2
Q ss_pred HHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhcCc
Q 026790 192 LLGIWSEKESAGHKILATLGFNDEKAKEIAKSINED 227 (233)
Q Consensus 192 LLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~~~ 227 (233)
++.++.+....+.++-..+|++...+.+.+..+++.
T Consensus 5 il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~ 40 (69)
T TIGR00122 5 LLALLADNPFSGEKLGEALGMSRTAVNKHIQTLREW 40 (69)
T ss_pred HHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 344455555557788888999999999999888643
No 62
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=27.63 E-value=1.2e+02 Score=24.87 Aligned_cols=37 Identities=11% Similarity=-0.052 Sum_probs=28.5
Q ss_pred hhcHHHHHHHH------------HHHHHHHHcCCCCcCHHHHHHHHhhc
Q 026790 84 KWSARAIRSFA------------MAELEARKLKYPNTGTEAFLMGILVE 120 (233)
Q Consensus 84 rfT~~a~~vl~------------~A~~eA~~~~~~~I~~eHLLlaLL~e 120 (233)
+++.+++.+|. .|...|.+-...+|.+||++-||=.-
T Consensus 31 rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~L 79 (156)
T KOG0871|consen 31 RVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENL 79 (156)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHc
Confidence 67777777664 46667777888899999999988553
No 63
>PLN00035 histone H4; Provisional
Probab=27.41 E-value=1.2e+02 Score=23.29 Aligned_cols=35 Identities=6% Similarity=0.001 Sum_probs=28.9
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhC
Q 026790 163 TEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSE 198 (233)
Q Consensus 163 S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~ 198 (233)
..-+.+++.++..++.-.+- ..|.++++.+||=..
T Consensus 60 e~~l~~I~~dav~ya~HA~R-KTV~~~DV~~Alkr~ 94 (103)
T PLN00035 60 KIFLENVIRDAVTYTEHARR-KTVTAMDVVYALKRQ 94 (103)
T ss_pred HHHHHHHHHHHHHHHHhcCC-CcCcHHHHHHHHHHc
Confidence 34467788899999988898 999999999998654
No 64
>PF12554 MOZART1: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR022214 This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 105 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Probab=26.85 E-value=78 Score=20.90 Aligned_cols=19 Identities=26% Similarity=0.380 Sum_probs=15.6
Q ss_pred HHhCCCCHHHHHHHHHHhc
Q 026790 207 LATLGFNDEKAKEIAKSIN 225 (233)
Q Consensus 207 L~~lGvd~~~l~~~i~~~~ 225 (233)
|-..||+++++-..++++|
T Consensus 30 L~e~GVnPeaLA~vI~elr 48 (48)
T PF12554_consen 30 LCENGVNPEALAAVIKELR 48 (48)
T ss_pred HHHCCCCHHHHHHHHHHhC
Confidence 4457999999999998876
No 65
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=26.69 E-value=1.6e+02 Score=23.64 Aligned_cols=47 Identities=19% Similarity=0.228 Sum_probs=35.1
Q ss_pred CCCcCCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHh
Q 026790 158 ERPPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILAT 209 (233)
Q Consensus 158 ~~~~~S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~~~~~~iL~~ 209 (233)
.++.||+.-+++...-+.... . ..=.+.+++|++|.++ .+|..+.+.
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~~---~-~~~~~~l~IL~lL~~~-~yGYeI~k~ 64 (135)
T PRK09416 18 KHLSFSEQHQKAVREKIKQSS---E-KEEDILLAILQLLMNE-KTGYELLQL 64 (135)
T ss_pred hcCCcchhhHHHHHHHHHHHh---c-ccccHHHHHHHHHhCC-CCHHHHHHH
Confidence 457899998887766655443 3 5568999999999887 888777664
No 66
>PF05576 Peptidase_S37: PS-10 peptidase S37; InterPro: IPR008761 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. These group of serine peptidases belong to MEROPS peptidase family S37 (clan SC). The members of this group of secreted peptidases are restricted to bacteria. In Streptomyces lividans the peptidase removes tripeptides from the N terminus of extracellular proteins (tripeptidyl aminopeptidase,Tap) [, ].
Probab=26.48 E-value=1e+02 Score=29.52 Aligned_cols=79 Identities=18% Similarity=0.172 Sum_probs=55.7
Q ss_pred hhhHhhhcC--CCCCcCCcccccccccccCccccccccccccCCCcchhhhhccCCccC-CCCCCCCCCchhh-----cH
Q 026790 16 SQSFDAKRS--SAPSFLPSSSMFGNKLLIRPQLNSSRFVTKYHRSSATATVSFSLPTTV-KPETASPDKIPKW-----SA 87 (233)
Q Consensus 16 ~~~~~~~~~--~~s~~~~~~s~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~p~~~-~~~~~~~~~~~rf-----T~ 87 (233)
|+|++|.+. +..|-.-|.|=|+.- -.-.+||-|..=. +++.-.+|-.. +.+++ -+.+| |+
T Consensus 122 Hri~~A~K~iY~~kWISTG~SKGGmT-----a~y~rrFyP~DVD----~tVaYVAP~~~~~~eD~---~y~~Fl~~VGt~ 189 (448)
T PF05576_consen 122 HRIVQAFKPIYPGKWISTGGSKGGMT-----AVYYRRFYPDDVD----GTVAYVAPNDVVNREDS---RYDRFLEKVGTA 189 (448)
T ss_pred HHHHHHHHhhccCCceecCcCCCcee-----EEEEeeeCCCCCC----eeeeeecccccCcccch---hHHHHHHhcCCH
Confidence 677777664 347988888888888 7889999998532 44444455322 23332 25566 89
Q ss_pred HHHHHHHHHHHHHHHcCCC
Q 026790 88 RAIRSFAMAELEARKLKYP 106 (233)
Q Consensus 88 ~a~~vl~~A~~eA~~~~~~ 106 (233)
.+|+.|...|.++-.++.+
T Consensus 190 eCR~~l~~~Qre~L~RR~~ 208 (448)
T PF05576_consen 190 ECRDKLNDFQREALKRRDE 208 (448)
T ss_pred HHHHHHHHHHHHHHhhHHH
Confidence 9999999999999887654
No 67
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=26.33 E-value=93 Score=23.92 Aligned_cols=34 Identities=15% Similarity=0.037 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCC
Q 026790 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGT 122 (233)
Q Consensus 89 a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~ 122 (233)
+..++..+-.+|+..+...++.|||-.+...++.
T Consensus 58 l~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdek 91 (113)
T COG5247 58 LTEIVGLSLKEARKKSSKRMTSEFLKRATESDEK 91 (113)
T ss_pred HHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHH
Confidence 3456778889999999999999999999998765
No 68
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=25.72 E-value=1.3e+02 Score=23.26 Aligned_cols=35 Identities=9% Similarity=0.033 Sum_probs=30.1
Q ss_pred cHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhc
Q 026790 86 SARAIRSFAMAELEARKLKYPNTGTEAFLMGILVE 120 (233)
Q Consensus 86 T~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e 120 (233)
-..+.+++..|...|+..|...|+.+.+-+|+-.-
T Consensus 32 ~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r 66 (117)
T cd07979 32 YRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSR 66 (117)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 44567889999999999999999999999998654
No 69
>PTZ00306 NADH-dependent fumarate reductase; Provisional
Probab=25.67 E-value=70 Score=34.40 Aligned_cols=139 Identities=12% Similarity=0.024 Sum_probs=74.0
Q ss_pred ccccccccccCCCcchhhhhccCCccCCCCCCCCCCchhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHH------hh
Q 026790 46 LNSSRFVTKYHRSSATATVSFSLPTTVKPETASPDKIPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGI------LV 119 (233)
Q Consensus 46 ~~~~~f~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~rfT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaL------L~ 119 (233)
+.|+||-.-....++++|.+ ..||+.. -..-..-+|..|......+.......++..-+.++. ..
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~-----~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~mgt~~~~~~~~ 75 (1167)
T PTZ00306 5 ATQTQRRCAMADGRTSASVV-----VVDPEKA----AKERDRAARALLQDNFPELHVNQRAQLLYKGLEHTVPYTLKVVV 75 (1167)
T ss_pred chhhhhhhccccCcccceEE-----EECHHHH----hhHHHHHHHHHHHhccccCCCCcceeEEEecccccceEEEEEEe
Confidence 45777665544444447777 5788866 444566777888777555443333222222222222 11
Q ss_pred cC---CChHHHHHHHcCCCHHHHHHHHHHHhCCCCCCC--------CCCCCCcCCHHHHHHHHHHHHHHHHcCCCCCCCH
Q 026790 120 EG---TSTTAKFLRANGITLFKVREETLNLLGKSDLFF--------FSPERPPLTEQAQRALDWAFNEKLKSGESGEITT 188 (233)
Q Consensus 120 e~---~~~a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~~--------~~~~~~~~S~~~~kvLe~A~~~A~~~g~~~~I~t 188 (233)
.+ ...+...+++ -.++.-+.++..+....+.+ .....++.|+++.++|+.+.++++..+--=-++.
T Consensus 76 ~~~~~~~~~~~~~~~---~~~~~~~~i~~~~S~~~~~SelsrlN~~~~g~~~~vs~~l~~vl~~a~~~~~~t~G~FD~tv 152 (1167)
T PTZ00306 76 AGPVARQDADAVAKE---VLRSAFQMVDTHLNSFNPNSEVSRVNRMPVGEKHQMSAHLKRVMACCQRVYNSSGGCFDPAA 152 (1167)
T ss_pred CCCccchhhHHHHHH---HHHHHHHHHHHhcCCCCCcCHHHHHhCccCCCcEecCHHHHHHHHHHHHHHHhcCCCCCchh
Confidence 11 1111222332 13444445556665544322 0123477899999999999999987544033666
Q ss_pred HHHHHHHhh
Q 026790 189 NHLLLGIWS 197 (233)
Q Consensus 189 eHLLLALl~ 197 (233)
.- |+.+|.
T Consensus 153 g~-l~~lw~ 160 (1167)
T PTZ00306 153 GP-LVHELR 160 (1167)
T ss_pred HH-HHHHhc
Confidence 66 445553
No 70
>PRK11426 hypothetical protein; Provisional
Probab=25.54 E-value=1.4e+02 Score=23.93 Aligned_cols=44 Identities=9% Similarity=-0.018 Sum_probs=37.3
Q ss_pred CCCcCHHHHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhCCCC
Q 026790 105 YPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSD 151 (233)
Q Consensus 105 ~~~I~~eHLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~~~~ 151 (233)
|..|++++|--+|=. .....+-.+.|++.+++...+..+|+...
T Consensus 58 N~pIs~~ql~~~lG~---d~i~~lA~q~Gl~~~~~~~~LA~~LP~~V 101 (132)
T PRK11426 58 NQSVSGEQLESALGT---NAVSDLGQKLGVDTSTASSLLAEQLPKII 101 (132)
T ss_pred CCCCCHHHHHHHhCh---HHHHHHHHHHCcCHHHHHHHHHHHhHHHH
Confidence 789999999888733 35788999999999999999999998633
No 71
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=25.48 E-value=36 Score=25.32 Aligned_cols=38 Identities=13% Similarity=-0.032 Sum_probs=12.2
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCC
Q 026790 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGT 122 (233)
Q Consensus 85 fT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~ 122 (233)
..+....++..|...|...|...|.+++++..|=.++.
T Consensus 32 v~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~ 69 (93)
T PF02269_consen 32 VREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPK 69 (93)
T ss_dssp HHHHHHHHHHHHHC------------------------
T ss_pred HHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHH
Confidence 37888999999999999999999999999999988774
No 72
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=25.20 E-value=1.8e+02 Score=20.39 Aligned_cols=33 Identities=15% Similarity=-0.051 Sum_probs=27.3
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 026790 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (233)
Q Consensus 85 fT~~a~~vl~~A~~eA~~~~~~~I~~eHLLlaL 117 (233)
-+-+++++++.|...++..+...+++.++=.+|
T Consensus 33 veyrlreiiq~a~kfm~hskR~~Lt~~Di~~AL 65 (66)
T PF02969_consen 33 VEYRLREIIQEALKFMRHSKRTKLTTDDINSAL 65 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 467899999999999999999999999986665
No 73
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=24.75 E-value=1.5e+02 Score=25.74 Aligned_cols=35 Identities=3% Similarity=-0.143 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCC
Q 026790 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTS 123 (233)
Q Consensus 89 a~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~~~ 123 (233)
+..++..+..+++..+...|+++||-.+++.++..
T Consensus 48 l~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~F 82 (224)
T KOG1659|consen 48 LESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKF 82 (224)
T ss_pred HHHHHHHHHHHHHhcCccccCHHHHHHHHhccchh
Confidence 45677888999999999999999999999998763
No 74
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=24.54 E-value=1.4e+02 Score=22.38 Aligned_cols=33 Identities=6% Similarity=-0.012 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhC
Q 026790 165 QAQRALDWAFNEKLKSGESGEITTNHLLLGIWSE 198 (233)
Q Consensus 165 ~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~ 198 (233)
=+..+.+.|..+|...|- ..|..+++.+|+=..
T Consensus 52 ~~~~i~~~A~~~A~ha~R-KTV~~~DI~la~~~~ 84 (91)
T COG2036 52 YLEEIAEDAVELAEHAKR-KTVKAEDIKLALKRL 84 (91)
T ss_pred HHHHHHHHHHHHHHHcCC-CeecHHHHHHHHHHh
Confidence 356778889999999999 999999999998653
No 75
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=24.03 E-value=45 Score=24.84 Aligned_cols=37 Identities=16% Similarity=0.176 Sum_probs=8.8
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCC
Q 026790 163 TEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKE 200 (233)
Q Consensus 163 S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~ 200 (233)
...+..++..|...|...|. +.|.+|+|+.+|=.++.
T Consensus 33 ~~~i~~l~~~A~~~a~~rg~-~~i~~eDl~F~lR~D~~ 69 (93)
T PF02269_consen 33 REYIIELCQEAMEVAQRRGS-KKIKVEDLLFLLRKDPK 69 (93)
T ss_dssp HHHHHHHHHHHHC-------------------------
T ss_pred HHHHHHHHHHHHHHHhcccc-CcCcHHHHHHHHhcCHH
Confidence 34566677778888888898 99999999999988754
No 76
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=24.00 E-value=1.6e+02 Score=21.69 Aligned_cols=35 Identities=6% Similarity=0.030 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhC
Q 026790 163 TEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSE 198 (233)
Q Consensus 163 S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~ 198 (233)
..-+.+++.++..++.-.|- ..|+.+++.+||=..
T Consensus 44 ~~~l~~I~~dav~ya~Ha~R-KTVt~~DV~~alkr~ 78 (85)
T cd00076 44 KSYLEDVIRDAVTYTEHAKR-KTVTAMDVVYALKRQ 78 (85)
T ss_pred HHHHHHHHHHHHHHHHhcCC-CcCcHHHHHHHHHHC
Confidence 44567788889999988888 999999999988654
No 77
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=23.78 E-value=1.2e+02 Score=21.60 Aligned_cols=29 Identities=14% Similarity=-0.096 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHcCCCC-cCHHHHHH
Q 026790 87 ARAIRSFAMAELEARKLKYPN-TGTEAFLM 115 (233)
Q Consensus 87 ~~a~~vl~~A~~eA~~~~~~~-I~~eHLLl 115 (233)
--+++++..|..+|+.-|... |+.+||=-
T Consensus 34 iFV~EAv~Ra~~~a~~e~~~~~le~e~LEk 63 (72)
T PF09415_consen 34 IFVREAVARAAEQAEAEGDEGFLEVEHLEK 63 (72)
T ss_dssp HHHHHHHHHHHHHHHHTT-SSEE-HHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence 345667777888888888888 99999854
No 78
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=23.48 E-value=1.1e+02 Score=19.24 Aligned_cols=37 Identities=14% Similarity=0.167 Sum_probs=27.8
Q ss_pred HHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhcCc
Q 026790 190 HLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSINED 227 (233)
Q Consensus 190 HLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~~~ 227 (233)
.|+..|.+ ......++-+.+|++...+...+..+...
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 35666666 55677899999999999999988877643
No 79
>PTZ00015 histone H4; Provisional
Probab=23.45 E-value=1.6e+02 Score=22.59 Aligned_cols=34 Identities=3% Similarity=-0.069 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhh
Q 026790 163 TEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWS 197 (233)
Q Consensus 163 S~~~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~ 197 (233)
..-+.+++.+|..++.-.+- ..|.++++.+||=.
T Consensus 61 e~~l~~I~rdav~~aeHA~R-KTVt~~DV~~AlKr 94 (102)
T PTZ00015 61 KAFLENVVRDSTAYTEYARR-KTVTAMDVVYALKR 94 (102)
T ss_pred HHHHHHHHHHHHHHHHhcCC-CcccHHHHHHHHHh
Confidence 34466788889999988888 99999999998744
No 80
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=22.72 E-value=87 Score=24.44 Aligned_cols=17 Identities=12% Similarity=0.046 Sum_probs=12.0
Q ss_pred CcCHHHHHHHHhhcCCC
Q 026790 107 NTGTEAFLMGILVEGTS 123 (233)
Q Consensus 107 ~I~~eHLLlaLL~e~~~ 123 (233)
.|++.|+|.++.+--++
T Consensus 39 rv~~~~il~Af~~GADG 55 (124)
T PF02662_consen 39 RVDPEFILRAFEKGADG 55 (124)
T ss_pred ccCHHHHHHHHHcCCCE
Confidence 57888888888764443
No 81
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=22.43 E-value=2.2e+02 Score=18.11 Aligned_cols=38 Identities=18% Similarity=0.246 Sum_probs=27.3
Q ss_pred HHHHHHhhCCC-chHHHHHHhCCCCHHHHHHHHHHhcCc
Q 026790 190 HLLLGIWSEKE-SAGHKILATLGFNDEKAKEIAKSINED 227 (233)
Q Consensus 190 HLLLALl~~~~-~~~~~iL~~lGvd~~~l~~~i~~~~~~ 227 (233)
.||.-|++.++ ..+.++-+.+||+...+.+.++.++..
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~ 42 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREW 42 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 35555555544 566788889999999999999888643
No 82
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=22.43 E-value=1.3e+02 Score=20.35 Aligned_cols=38 Identities=21% Similarity=0.253 Sum_probs=32.4
Q ss_pred HHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhCC
Q 026790 112 AFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGK 149 (233)
Q Consensus 112 HLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~~ 149 (233)
.++..|+..+...+..+-+..|++...+...+.....+
T Consensus 12 ~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46677888888889999999999999999999887655
No 83
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=22.01 E-value=2e+02 Score=17.95 Aligned_cols=29 Identities=21% Similarity=0.278 Sum_probs=22.3
Q ss_pred CCCchHHHHHHhCCCCHHHHHHHHHHhcC
Q 026790 198 EKESAGHKILATLGFNDEKAKEIAKSINE 226 (233)
Q Consensus 198 ~~~~~~~~iL~~lGvd~~~l~~~i~~~~~ 226 (233)
.+.....++.+.+|++...+.+.+..+..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44556678888899999998888877653
No 84
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=21.86 E-value=19 Score=28.09 Aligned_cols=34 Identities=29% Similarity=0.303 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCC
Q 026790 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKE 200 (233)
Q Consensus 166 ~~kvLe~A~~~A~~~g~~~~I~teHLLLALl~~~~ 200 (233)
..+|||.|-+.++.+.- ..|++.||-||+=-+++
T Consensus 66 TaEVLeLAgNasKdLKv-KRitprHlqLAiRGDeE 99 (131)
T KOG1757|consen 66 TAEVLELAGNASKDLKV-KRITPRHLQLAIRGDEE 99 (131)
T ss_pred HHHHHHHccccccccee-eeccchhheeeecCcHH
Confidence 45788999988888888 99999999999987765
No 85
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=21.71 E-value=2e+02 Score=18.02 Aligned_cols=35 Identities=9% Similarity=0.280 Sum_probs=22.4
Q ss_pred HHHHHHhh-CCCchHHHHHHhCCCCHHHHHHHHHHh
Q 026790 190 HLLLGIWS-EKESAGHKILATLGFNDEKAKEIAKSI 224 (233)
Q Consensus 190 HLLLALl~-~~~~~~~~iL~~lGvd~~~l~~~i~~~ 224 (233)
.-++.+|. +...+..++=+.+|++...+.+-+..+
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 33455554 444445677778999999999888765
No 86
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=20.58 E-value=1.5e+02 Score=17.42 Aligned_cols=24 Identities=25% Similarity=0.429 Sum_probs=19.2
Q ss_pred HHHHhCCCCHHHHHHHHHHhcCcc
Q 026790 205 KILATLGFNDEKAKEIAKSINEDT 228 (233)
Q Consensus 205 ~iL~~lGvd~~~l~~~i~~~~~~~ 228 (233)
..|..+|++.+.+.+.+..-++++
T Consensus 6 ~~L~~mGf~~~~a~~aL~~~~~d~ 29 (37)
T smart00165 6 DQLLEMGFSREEALKALRAANGNV 29 (37)
T ss_pred HHHHHcCCCHHHHHHHHHHhCCCH
Confidence 367778999999988888877764
No 87
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=20.49 E-value=1.5e+02 Score=17.52 Aligned_cols=24 Identities=25% Similarity=0.531 Sum_probs=18.4
Q ss_pred HHHHhCCCCHHHHHHHHHHhcCcc
Q 026790 205 KILATLGFNDEKAKEIAKSINEDT 228 (233)
Q Consensus 205 ~iL~~lGvd~~~l~~~i~~~~~~~ 228 (233)
+.|..+|++.+.+.+.+..-++++
T Consensus 6 ~~L~~mGf~~~~~~~AL~~~~~d~ 29 (38)
T cd00194 6 EQLLEMGFSREEARKALRATNNNV 29 (38)
T ss_pred HHHHHcCCCHHHHHHHHHHhCCCH
Confidence 356678888888888888777764
No 88
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=20.44 E-value=1.6e+02 Score=21.51 Aligned_cols=37 Identities=11% Similarity=0.235 Sum_probs=28.0
Q ss_pred HHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhcCc
Q 026790 191 LLLGIWSEKESAGHKILATLGFNDEKAKEIAKSINED 227 (233)
Q Consensus 191 LLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~~~ 227 (233)
||.+|.+++.....++-+.+|++...+.+.+..+..+
T Consensus 8 il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 8 ILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4555555555566788889999999999999887654
No 89
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=20.24 E-value=3.8e+02 Score=22.56 Aligned_cols=82 Identities=15% Similarity=0.044 Sum_probs=59.1
Q ss_pred HHHHHHHHhhcCCChHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCCCcCCHH----HHHHHHHHHHHHHHcCCCCC
Q 026790 110 TEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQ----AQRALDWAFNEKLKSGESGE 185 (233)
Q Consensus 110 ~eHLLlaLL~e~~~~a~~iL~~~Gvd~~~lr~~l~~~L~~~~~~~~~~~~~~~S~~----~~kvLe~A~~~A~~~g~~~~ 185 (233)
--|+|++-|+++.---..+++..|.+...++.-+...++..... .-.+.++.= +-+++|.|.....++++...
T Consensus 92 r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~nQtVsp---Ni~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgp 168 (199)
T COG5251 92 RFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVANQTVSP---NIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGP 168 (199)
T ss_pred HHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHhccccCC---CeeeeeechhHHHHHHHHHHHHHHHHHhcccCC
Confidence 56899999988776678899999999999999988888875532 122322222 34677888887778888456
Q ss_pred CCHHHHHHH
Q 026790 186 ITTNHLLLG 194 (233)
Q Consensus 186 I~teHLLLA 194 (233)
..+.|+=-|
T Consensus 169 l~p~h~rea 177 (199)
T COG5251 169 LIPFHKREA 177 (199)
T ss_pred CChHHHHHH
Confidence 777776544
No 90
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=20.18 E-value=18 Score=28.29 Aligned_cols=32 Identities=13% Similarity=0.150 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcC
Q 026790 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVEG 121 (233)
Q Consensus 90 ~~vl~~A~~eA~~~~~~~I~~eHLLlaLL~e~ 121 (233)
.++++.|-|.++.++...|+|-||-|++-.|+
T Consensus 67 aEVLeLAgNasKdLKvKRitprHlqLAiRGDe 98 (131)
T KOG1757|consen 67 AEVLELAGNASKDLKVKRITPRHLQLAIRGDE 98 (131)
T ss_pred HHHHHHcccccccceeeeccchhheeeecCcH
Confidence 46889999999999999999999999987654
No 91
>PF12983 DUF3867: Protein of unknown function (DUF3867); InterPro: IPR024218 This entry represents a family of functionally uncharacterised proteins that are found in bacteria. Proteins in this family are approximately 190 amino acids in length.
Probab=20.13 E-value=1.1e+02 Score=25.77 Aligned_cols=38 Identities=21% Similarity=0.352 Sum_probs=30.3
Q ss_pred HcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhc
Q 026790 179 KSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSIN 225 (233)
Q Consensus 179 ~~g~~~~I~teHLLLALl~~~~~~~~~iL~~lGvd~~~l~~~i~~~~ 225 (233)
-+.. +-|+.|-++= .-.++|+++|+|++.++++++.++
T Consensus 49 Ymee-NNISqeKf~n--------iQkk~mERYGfd~~~iE~q~K~~G 86 (186)
T PF12983_consen 49 YMEE-NNISQEKFLN--------IQKKFMERYGFDPSEIEKQMKSMG 86 (186)
T ss_pred HHHH-cCCcHHHHHH--------HHHHHHHHhCCCHHHHHHHHHHcC
Confidence 3556 8888887652 235699999999999999999987
Done!