Query 029953
Match_columns 185
No_of_seqs 157 out of 1092
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 06:14:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029953.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029953hhsearch_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 99.5 5.9E-13 1.3E-17 128.7 13.1 103 81-185 1-103 (821)
2 TIGR03346 chaperone_ClpB ATP-d 99.4 1.5E-12 3.1E-17 126.4 13.3 101 85-185 1-101 (852)
3 TIGR02639 ClpA ATP-dependent C 99.3 1.3E-11 2.7E-16 118.1 12.8 99 85-185 1-101 (731)
4 PRK10865 protein disaggregatio 99.3 2.4E-11 5.1E-16 118.2 13.3 104 82-185 3-106 (857)
5 PF02861 Clp_N: Clp amino term 99.3 8.1E-12 1.7E-16 80.6 6.2 53 96-148 1-53 (53)
6 TIGR03345 VI_ClpV1 type VI sec 99.3 4.1E-11 8.8E-16 116.5 13.2 99 85-185 1-100 (852)
7 COG0542 clpA ATP-binding subun 99.2 3.3E-10 7.2E-15 108.4 12.2 97 84-185 1-97 (786)
8 PRK11034 clpA ATP-dependent Cl 99.0 4.4E-09 9.5E-14 101.2 12.6 99 85-185 2-103 (758)
9 KOG1051 Chaperone HSP104 and r 98.8 2.1E-08 4.5E-13 97.4 9.7 104 82-185 9-113 (898)
10 CHL00095 clpC Clp protease ATP 98.1 1.1E-05 2.3E-10 78.7 8.9 67 84-150 79-145 (821)
11 TIGR02639 ClpA ATP-dependent C 98.0 2.1E-05 4.5E-10 75.7 7.9 62 84-145 77-138 (731)
12 TIGR03346 chaperone_ClpB ATP-d 97.7 9.6E-05 2.1E-09 72.4 8.2 63 84-147 77-139 (852)
13 COG0542 clpA ATP-binding subun 97.4 0.00098 2.1E-08 64.6 9.5 80 62-149 59-138 (786)
14 TIGR03345 VI_ClpV1 type VI sec 97.1 0.0017 3.6E-08 63.9 8.2 63 84-146 75-141 (852)
15 PRK11034 clpA ATP-dependent Cl 97.1 0.0016 3.5E-08 63.2 8.1 61 84-144 79-139 (758)
16 PRK10865 protein disaggregatio 96.9 0.0034 7.4E-08 61.7 8.2 63 84-147 82-144 (857)
17 KOG1051 Chaperone HSP104 and r 94.9 0.07 1.5E-06 52.8 6.7 123 20-149 26-154 (898)
18 cd00074 H2A Histone 2A; H2A is 88.8 0.71 1.5E-05 34.9 4.1 41 89-131 55-95 (115)
19 PTZ00017 histone H2A; Provisio 87.5 0.75 1.6E-05 35.7 3.5 45 83-132 59-103 (134)
20 PLN00154 histone H2A; Provisio 86.7 0.93 2E-05 35.3 3.7 39 90-130 75-113 (136)
21 KOG1756 Histone 2A [Chromatin 86.2 1.1 2.3E-05 34.5 3.7 42 89-132 62-103 (131)
22 PLN00157 histone H2A; Provisio 85.9 0.88 1.9E-05 35.2 3.1 42 89-132 61-102 (132)
23 PLN00153 histone H2A; Provisio 85.7 1.1 2.4E-05 34.6 3.6 40 90-131 60-99 (129)
24 smart00414 H2A Histone 2A. 85.0 1.2 2.7E-05 33.1 3.5 40 90-131 45-84 (106)
25 PLN00156 histone H2AX; Provisi 84.0 1.5 3.3E-05 34.2 3.7 41 90-132 65-105 (139)
26 PTZ00252 histone H2A; Provisio 80.1 2.4 5.2E-05 32.9 3.5 41 90-132 61-103 (134)
27 PF08369 PCP_red: Proto-chloro 76.5 4.7 0.0001 25.3 3.5 27 90-116 18-44 (45)
28 COG5262 HTA1 Histone H2A [Chro 64.0 11 0.00024 28.8 3.6 40 89-130 61-100 (132)
29 PF00125 Histone: Core histone 59.5 14 0.0003 24.8 3.3 32 86-117 41-72 (75)
30 TIGR02337 HpaR homoprotocatech 51.7 89 0.0019 22.6 9.4 72 108-179 28-105 (118)
31 PF01978 TrmB: Sugar-specific 46.8 39 0.00085 22.1 3.9 39 112-150 12-50 (68)
32 PF00808 CBFD_NFYB_HMF: Histon 46.1 38 0.00082 22.2 3.7 27 91-117 39-65 (65)
33 smart00803 TAF TATA box bindin 42.6 54 0.0012 22.0 4.0 34 84-117 31-64 (65)
34 PF09415 CENP-X: CENP-S associ 42.0 40 0.00086 23.2 3.4 32 84-115 31-63 (72)
35 cd07979 TAF9 TATA Binding Prot 40.6 57 0.0012 24.5 4.3 38 83-120 29-66 (117)
36 PF13412 HTH_24: Winged helix- 40.2 84 0.0018 18.9 4.6 38 112-149 7-44 (48)
37 PF09862 DUF2089: Protein of u 39.4 1.3E+02 0.0028 22.6 6.1 56 114-172 42-97 (113)
38 COG5247 BUR6 Class 2 transcrip 38.7 55 0.0012 24.4 3.8 76 40-121 8-90 (113)
39 KOG1659 Class 2 transcription 37.2 87 0.0019 26.3 5.2 35 87-121 46-80 (224)
40 PF13335 Mg_chelatase_2: Magne 36.9 84 0.0018 22.6 4.6 30 88-117 64-93 (96)
41 cd07981 TAF12 TATA Binding Pro 36.2 85 0.0019 21.3 4.3 35 85-119 32-66 (72)
42 smart00550 Zalpha Z-DNA-bindin 35.4 1.2E+02 0.0027 20.1 5.0 41 111-151 9-51 (68)
43 PF12802 MarR_2: MarR family; 34.0 1.1E+02 0.0024 19.1 4.4 40 111-150 8-49 (62)
44 KOG1757 Histone 2A [Chromatin 33.4 10 0.00023 28.6 -0.7 31 90-120 67-97 (131)
45 KOG0869 CCAAT-binding factor, 31.9 1.9E+02 0.0041 23.2 6.1 38 84-121 51-100 (168)
46 PF02269 TFIID-18kDa: Transcri 31.3 27 0.00058 25.1 1.2 39 83-121 30-68 (93)
47 KOG0871 Class 2 transcription 30.4 59 0.0013 25.8 3.0 36 84-119 31-78 (156)
48 TIGR02928 orc1/cdc6 family rep 29.4 1.9E+02 0.0041 24.9 6.4 61 87-147 241-301 (365)
49 PRK00411 cdc6 cell division co 28.9 1.9E+02 0.0041 25.2 6.4 60 88-147 250-309 (394)
50 PF02969 TAF: TATA box binding 27.1 1.6E+02 0.0035 19.9 4.4 34 84-117 32-65 (66)
51 PRK11426 hypothetical protein; 26.6 1.6E+02 0.0034 22.8 4.8 44 105-151 58-101 (132)
52 PF04221 RelB: RelB antitoxin; 25.3 2E+02 0.0044 19.8 4.8 24 124-147 15-38 (83)
53 COG2761 FrnE Predicted dithiol 24.3 4.3E+02 0.0094 22.2 7.6 34 111-144 124-162 (225)
54 PF04405 ScdA_N: Domain of Unk 24.0 1.3E+02 0.0028 19.6 3.4 19 126-144 35-53 (56)
55 PF05402 PqqD: Coenzyme PQQ sy 23.8 2.1E+02 0.0045 18.4 5.3 40 109-148 17-59 (68)
56 PF14290 DUF4370: Domain of un 23.8 4.4E+02 0.0096 22.1 8.6 100 65-175 75-177 (239)
57 PLN00035 histone H4; Provision 22.1 2E+02 0.0043 21.3 4.4 36 84-119 58-93 (103)
58 PF02291 TFIID-31kDa: Transcri 22.0 1.7E+02 0.0038 22.4 4.2 37 83-119 40-76 (129)
59 COG5150 Class 2 transcription 21.7 1.5E+02 0.0033 23.0 3.8 36 84-119 30-77 (148)
60 PF01323 DSBA: DSBA-like thior 21.6 2.8E+02 0.0061 21.1 5.5 40 125-182 126-165 (193)
61 COG1474 CDC6 Cdc6-related prot 21.4 3.7E+02 0.008 24.0 6.8 60 86-145 231-290 (366)
62 PF08784 RPA_C: Replication pr 21.2 1.4E+02 0.003 21.1 3.4 27 125-151 68-94 (102)
63 smart00344 HTH_ASNC helix_turn 20.8 2.3E+02 0.005 19.8 4.5 38 113-150 8-45 (108)
64 PLN02749 Uncharacterized prote 20.4 4.5E+02 0.0098 21.0 8.8 100 65-175 9-111 (173)
No 1
>CHL00095 clpC Clp protease ATP binding subunit
Probab=99.46 E-value=5.9e-13 Score=128.71 Aligned_cols=103 Identities=30% Similarity=0.485 Sum_probs=93.7
Q ss_pred CchhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCCCC
Q 029953 81 KIPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERP 160 (185)
Q Consensus 81 m~~~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~~~~~~~~~~i 160 (185)
|+.+||++++++|..|+++|++++|.+|++||||+||+.++++.+.++|+.+|++.+.++..++..++..+.. .+..+
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 5779999999999999999999999999999999999999888999999999999999999999988765432 12468
Q ss_pred CCCHHHHHHHHHHHHHHHHcCCCCC
Q 029953 161 PLTEQAQRALDWAFNEKLKSGSLCI 185 (185)
Q Consensus 161 ~~s~~a~~~Le~A~~~A~~lGd~yI 185 (185)
++++.++++|+.|..+|..+|+++|
T Consensus 79 ~~S~~~~~vL~~A~~~A~~~~~~~I 103 (821)
T CHL00095 79 PFTPRAKRVLEMSLEEARDLGHNYI 103 (821)
T ss_pred ccCHHHHHHHHHHHHHHHHhCCCcc
Confidence 9999999999999999999999886
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=99.43 E-value=1.5e-12 Score=126.45 Aligned_cols=101 Identities=17% Similarity=0.124 Sum_probs=91.3
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCCCCCCCH
Q 029953 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTE 164 (185)
Q Consensus 85 fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~~~~~~~~~~i~~s~ 164 (185)
||+.++++|..|+.+|++++|.+|++||||+||+.++++.+.++|+++|+|.+.+++.++..++..+...+.+..+++|+
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 68999999999999999999999999999999999988889999999999999999999999887554322124688999
Q ss_pred HHHHHHHHHHHHHHHcCCCCC
Q 029953 165 QAQRALDWAFNEKLKSGSLCI 185 (185)
Q Consensus 165 ~a~~~Le~A~~~A~~lGd~yI 185 (185)
.++++|+.|+.+|..+|++||
T Consensus 81 ~~~~vLe~A~~~A~~~g~~~I 101 (852)
T TIGR03346 81 ELNRLLNLAEKLAQKRGDEFI 101 (852)
T ss_pred HHHHHHHHHHHHHHHcCCCcc
Confidence 999999999999999999986
No 3
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=99.33 E-value=1.3e-11 Score=118.15 Aligned_cols=99 Identities=21% Similarity=0.172 Sum_probs=86.4
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhc-CCCCCCC-CCCCCCC
Q 029953 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLG-KSDLFFF-SPERPPL 162 (185)
Q Consensus 85 fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~-~~~~~~~-~~~~i~~ 162 (185)
+|++++++|..|+++|++++|.+|++||||+||+++++ +.++|+.+|++.+.+++.++..++ ..+...+ .+..+++
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 58999999999999999999999999999999999864 568999999999999999999886 3332211 1245889
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCC
Q 029953 163 TEQAQRALDWAFNEKLKSGSLCI 185 (185)
Q Consensus 163 s~~a~~~Le~A~~~A~~lGd~yI 185 (185)
|+.++++|+.|+.+|..+|++||
T Consensus 79 S~~lk~vL~~A~~~A~~~g~~~I 101 (731)
T TIGR02639 79 TVGVQRVLQRALLHVKSAGKKEI 101 (731)
T ss_pred CHHHHHHHHHHHHHHHHcCCCcc
Confidence 99999999999999999999987
No 4
>PRK10865 protein disaggregation chaperone; Provisional
Probab=99.31 E-value=2.4e-11 Score=118.16 Aligned_cols=104 Identities=13% Similarity=0.068 Sum_probs=93.1
Q ss_pred chhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCCCCC
Q 029953 82 IPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPP 161 (185)
Q Consensus 82 ~~~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~~~~~~~~~~i~ 161 (185)
+.+||+.++++|..|..+|.+++|.+|++||||++|+.++++.+..+|+.+|+|.+.+++.++..++..+...+....++
T Consensus 3 ~~~~~~~~~~~l~~a~~~a~~~~~~~~~~~hll~~l~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 82 (857)
T PRK10865 3 LDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQLRTDINQALSRLPQVEGTGGDVQ 82 (857)
T ss_pred hHHhCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHHhhCCCCCCCCCCCC
Confidence 56899999999999999999999999999999999999887888999999999999999999998877664221124578
Q ss_pred CCHHHHHHHHHHHHHHHHcCCCCC
Q 029953 162 LTEQAQRALDWAFNEKLKSGSLCI 185 (185)
Q Consensus 162 ~s~~a~~~Le~A~~~A~~lGd~yI 185 (185)
+|+.++++|+.|+.+|..+|+.||
T Consensus 83 ~~~~~~~~l~~a~~~~~~~~~~~i 106 (857)
T PRK10865 83 PSQDLVRVLNLCDKLAQKRGDNFI 106 (857)
T ss_pred cCHHHHHHHHHHHHHHHHcCCCcc
Confidence 999999999999999999999876
No 5
>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=99.29 E-value=8.1e-12 Score=80.62 Aligned_cols=53 Identities=25% Similarity=0.294 Sum_probs=49.7
Q ss_pred HHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhc
Q 029953 96 AELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLG 148 (185)
Q Consensus 96 A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~ 148 (185)
|+++|++++|.+|++||||+||++++++.+.++|+++|+|.+++++++++.++
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 78999999999999999999999999999999999999999999999998875
No 6
>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=99.28 E-value=4.1e-11 Score=116.46 Aligned_cols=99 Identities=20% Similarity=0.193 Sum_probs=88.2
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCCCCCCCH
Q 029953 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTE 164 (185)
Q Consensus 85 fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~~~~~~~~~~i~~s~ 164 (185)
+|++++++|..|+++|++++|.+|++||||+||+.++++.+..+|+.+|++.+.+++.++..+...+... +..+++|+
T Consensus 1 Lt~~a~~~L~~A~~~A~~~~h~~I~~eHLLlaLL~~~~~~~~~iL~~~Gvd~~~Lr~~le~~l~~~p~~~--~~~~~~S~ 78 (852)
T TIGR03345 1 LNPTSRRALEQAAALCVARGHPEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLARALDKLPRGN--TRTPVFSP 78 (852)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHHHhccCCCCC--CCCCCcCH
Confidence 5899999999999999999999999999999999988788899999999999999999999887665421 23578999
Q ss_pred HHHHHHHHHHH-HHHHcCCCCC
Q 029953 165 QAQRALDWAFN-EKLKSGSLCI 185 (185)
Q Consensus 165 ~a~~~Le~A~~-~A~~lGd~yI 185 (185)
.++++|+.|+. .+..+|++||
T Consensus 79 ~l~~vL~~A~~~~a~~~g~~~I 100 (852)
T TIGR03345 79 HLVELLQEAWLLASLELGDGRI 100 (852)
T ss_pred HHHHHHHHHHHHHHHHcCCCcc
Confidence 99999999997 4667999886
No 7
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=99.15 E-value=3.3e-10 Score=108.39 Aligned_cols=97 Identities=24% Similarity=0.294 Sum_probs=90.0
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q 029953 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLT 163 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~~~~~~~~~~i~~s 163 (185)
+||++++++|..|+.+|...+|.++++||||++|+.++++. .++..+|++.+.++..++..+.+.+...+ . +.++
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 48999999999999999999999999999999999988665 89999999999999999999999887643 2 7889
Q ss_pred HHHHHHHHHHHHHHHHcCCCCC
Q 029953 164 EQAQRALDWAFNEKLKSGSLCI 185 (185)
Q Consensus 164 ~~a~~~Le~A~~~A~~lGd~yI 185 (185)
+.+.++++.|+.+|..+|++||
T Consensus 76 ~~~~~~~~~a~~~a~~~~~~~v 97 (786)
T COG0542 76 PRLKRVLERAWLLAQSLGDEYV 97 (786)
T ss_pred HHHHHHHHHHHHHHHhccCccc
Confidence 9999999999999999999986
No 8
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=99.00 E-value=4.4e-09 Score=101.24 Aligned_cols=99 Identities=20% Similarity=0.177 Sum_probs=84.9
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcC-CCCCCC--CCCCCC
Q 029953 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGK-SDLFFF--SPERPP 161 (185)
Q Consensus 85 fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~-~~~~~~--~~~~i~ 161 (185)
+|+.++++|..|.++|.+++|.+|++||||++|+.+++ +..+|+.+|++.+.+++.++..++. .+...+ .+..++
T Consensus 2 ~~~~~~~~l~~a~~~a~~~~~~~~~~~h~l~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (758)
T PRK11034 2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPS--AREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQ 79 (758)
T ss_pred cCHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHcChh--HHHHHHHcCCCHHHHHHHHHHHHhhcCCcCCCCCCcCCcC
Confidence 78999999999999999999999999999999998753 8999999999999999999998863 221111 113467
Q ss_pred CCHHHHHHHHHHHHHHHHcCCCCC
Q 029953 162 LTEQAQRALDWAFNEKLKSGSLCI 185 (185)
Q Consensus 162 ~s~~a~~~Le~A~~~A~~lGd~yI 185 (185)
++..++++|+.|+.+|..+|+++|
T Consensus 80 ~~~~~~~~l~~a~~~~~~~~~~~i 103 (758)
T PRK11034 80 PTLSFQRVLQRAVFHVQSSGRSEV 103 (758)
T ss_pred CCHHHHHHHHHHHHHHHHcCCCcc
Confidence 899999999999999999999876
No 9
>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]
Probab=98.80 E-value=2.1e-08 Score=97.36 Aligned_cols=104 Identities=12% Similarity=-0.025 Sum_probs=91.2
Q ss_pred chhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcC-CCHHHHHHHHHHHhcCCCCCCCCCCCC
Q 029953 82 IPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANG-ITLFKVREETLNLLGKSDLFFFSPERP 160 (185)
Q Consensus 82 ~~~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~G-Id~~~l~~~I~~~l~~~~~~~~~~~~i 160 (185)
...||++|..+|..|+.+|+++||.+++|+|++.+|+.++++.+.+++.+.+ ++..+++..+.-.+.+.|..++.+...
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 3579999999999999999999999999999999999999999999999999 999999999998898888776545566
Q ss_pred CCCHHHHHHHHHHHHHHHHcCCCCC
Q 029953 161 PLTEQAQRALDWAFNEKLKSGSLCI 185 (185)
Q Consensus 161 ~~s~~a~~~Le~A~~~A~~lGd~yI 185 (185)
+++.++++++..+.+....+++.||
T Consensus 89 ~l~aalkr~qa~qrr~~~~~~~~~v 113 (898)
T KOG1051|consen 89 ALMAALKRAQAHQRRGCEEQQQQAV 113 (898)
T ss_pred HhHHHHHHHHHHHHhcchhhccchh
Confidence 7778888888888777777777664
No 10
>CHL00095 clpC Clp protease ATP binding subunit
Probab=98.11 E-value=1.1e-05 Score=78.67 Aligned_cols=67 Identities=37% Similarity=0.534 Sum_probs=62.3
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCC
Q 029953 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKS 150 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~ 150 (185)
.||+.++++|..|..+|..+++.+|+++|||+||+.++++.+..+|+.+|++.+.++..+...++..
T Consensus 79 ~~S~~~~~vL~~A~~~A~~~~~~~I~~eHLLlALL~~~ds~a~~iL~~~gvd~~~L~~~l~~~l~~~ 145 (821)
T CHL00095 79 PFTPRAKRVLEMSLEEARDLGHNYIGTEHLLLALLEEGEGVAARVLENLGVDLSKIRSLILNLIGEI 145 (821)
T ss_pred ccCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHHhccc
Confidence 6999999999999999999999999999999999999888889999999999999999998876543
No 11
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=97.98 E-value=2.1e-05 Score=75.70 Aligned_cols=62 Identities=21% Similarity=0.274 Sum_probs=57.8
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHH
Q 029953 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLN 145 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~ 145 (185)
.+|+.++++|..|..+|..+++.+|+++|||+||+.++++.+..+|+.+|++.+.+.+.+..
T Consensus 77 ~~S~~lk~vL~~A~~~A~~~g~~~I~teHLLLALl~~~~~~a~~lL~~~gi~~~~l~~~l~~ 138 (731)
T TIGR02639 77 EQTVGVQRVLQRALLHVKSAGKKEIGIGDILVALFDEEDSHASYFLKSQGITRLDILEYISH 138 (731)
T ss_pred CcCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHhcCcccHHHHHHHHcCCCHHHHHHHHHh
Confidence 68999999999999999999999999999999999988888888999999999999888763
No 12
>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=97.75 E-value=9.6e-05 Score=72.37 Aligned_cols=63 Identities=21% Similarity=0.171 Sum_probs=57.4
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHh
Q 029953 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLL 147 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l 147 (185)
.||+.++++|..|..+|..+++.+|+++|||+||+.++++ +..+|..+|++.+.+++.+....
T Consensus 77 ~~S~~~~~vLe~A~~~A~~~g~~~I~teHLLlALl~e~~~-a~~iL~~~gi~~~~l~~~l~~~~ 139 (852)
T TIGR03346 77 YLSPELNRLLNLAEKLAQKRGDEFISSEHLLLALLDDKGT-LGKLLKEAGATADALEAAINAVR 139 (852)
T ss_pred CcCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHcCCcc-HHHHHHHcCCCHHHHHHHHHhhc
Confidence 6899999999999999999999999999999999998765 67899999999999988887544
No 13
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=97.38 E-value=0.00098 Score=64.64 Aligned_cols=80 Identities=30% Similarity=0.278 Sum_probs=68.0
Q ss_pred hHhhhcCCCcCCCCCCCCCCchhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHH
Q 029953 62 ATVSFSLPTTVKPETASPDKIPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVRE 141 (185)
Q Consensus 62 ~~~l~~~P~~~~p~~~~~~m~~~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~ 141 (185)
+..+.+.|++.+. ..+|+.+.+++..|..+|...++.+|+++|||++++.++++.+..+|+.+|++...+.+
T Consensus 59 ~~~~~~~~~~~~~--------~~~s~~~~~~~~~a~~~a~~~~~~~v~~~~llla~~~~~~~~~~~~l~~~~~~~~~~~~ 130 (786)
T COG0542 59 EEFIDKLPKVLGS--------PYLSPRLKRVLERAWLLAQSLGDEYVSTEHLLLALLNEPESVAAYILKKLGVTRKDVEE 130 (786)
T ss_pred HHHHhccCCCCCC--------CCCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhcccchHHHHHHHhccCCHHHHHH
Confidence 4446667763332 26799999999999999999999999999999999999988999999999999999977
Q ss_pred HHHHHhcC
Q 029953 142 ETLNLLGK 149 (185)
Q Consensus 142 ~I~~~l~~ 149 (185)
.+..+.+.
T Consensus 131 ~~~~~~~~ 138 (786)
T COG0542 131 LIEELRGG 138 (786)
T ss_pred HHHHHhcc
Confidence 77776654
No 14
>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=97.13 E-value=0.0017 Score=63.90 Aligned_cols=63 Identities=16% Similarity=0.102 Sum_probs=54.3
Q ss_pred hhcHHHHHHHHHHHH-HHHHcCCCCcCHHHHHHHHhhcCCc--hHHHHHHHc-CCCHHHHHHHHHHH
Q 029953 84 KWSARAIRSFAMAEL-EARKLKYPNTGTEAFLMGILVEGTS--TTAKFLRAN-GITLFKVREETLNL 146 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~-~A~~~~~~~I~~eHLLlALl~e~~~--~a~~iL~~~-GId~~~l~~~I~~~ 146 (185)
.+|+.+.++|..|.. .+..+++.+|+++|||+||+.++++ .+..++..+ |++.+.+.+.+...
T Consensus 75 ~~S~~l~~vL~~A~~~~a~~~g~~~I~teHLLlALl~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 141 (852)
T TIGR03345 75 VFSPHLVELLQEAWLLASLELGDGRIRSGHLLLALLTDPELRRLLGSISPELAKIDREALREALPAL 141 (852)
T ss_pred CcCHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHccccchhHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 689999999999997 5667999999999999999998654 556688887 99999998888764
No 15
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=97.13 E-value=0.0016 Score=63.20 Aligned_cols=61 Identities=16% Similarity=0.126 Sum_probs=55.1
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHH
Q 029953 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETL 144 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~ 144 (185)
.++..++++|..|..+|...++.+|+++|||+||+.++++.+..+|+.+|++...+...+.
T Consensus 79 ~~~~~~~~~l~~a~~~~~~~~~~~i~~~~ll~a~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 139 (758)
T PRK11034 79 QPTLSFQRVLQRAVFHVQSSGRSEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFIS 139 (758)
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcchHHHHHHHcCCCHHHHHHHHH
Confidence 4688899999999999999999999999999999998888888999999999888766644
No 16
>PRK10865 protein disaggregation chaperone; Provisional
Probab=96.91 E-value=0.0034 Score=61.74 Aligned_cols=63 Identities=21% Similarity=0.217 Sum_probs=55.9
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHh
Q 029953 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLL 147 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l 147 (185)
.+|+.+.++|..|..+|...++.+|+++|||++|+.+++ ....+|+.+|++.+.+++.+....
T Consensus 82 ~~~~~~~~~l~~a~~~~~~~~~~~i~~~~ll~~~~~~~~-~~~~~l~~~~~~~~~~~~~~~~~~ 144 (857)
T PRK10865 82 QPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRG-TLADILKAAGATTANITQAIEQMR 144 (857)
T ss_pred CcCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHcCcc-hHHHHHHHcCCCHHHHHHHHHHhh
Confidence 689999999999999999999999999999999999864 445689999999999988876544
No 17
>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]
Probab=94.88 E-value=0.07 Score=52.78 Aligned_cols=123 Identities=15% Similarity=0.140 Sum_probs=90.0
Q ss_pred cccCCCCCCcCCC---ccccccccccccccccccccc-cccCcc--hhhHhhhcCCCcCCCCCCCCCCchhhcHHHHHHH
Q 029953 20 DAKRSSAPSFLPS---SSMFGNKLLIRPQLNSSRFVT-KYHRSS--ATATVSFSLPTTVKPETASPDKIPKWSARAIRSF 93 (185)
Q Consensus 20 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~fv~-~~~~~~--~~~~~l~~~P~~~~p~~~~~~m~~~fT~~a~~vL 93 (185)
.++|.|-+.+-|+ +.++..+=|+-+++-+++ .| ++ |.- .....+.++|++.+|.. -+.++..+.++.
T Consensus 26 ~Arrrgh~qvtplH~~~~LLs~~t~~lr~ac~~~-~~l~~-ralelc~~v~l~rlpt~~~p~~-----sn~l~aalkr~q 98 (898)
T KOG1051|consen 26 EARRRGHAQVTPLHVASTLLSSPTGILRRACIKS-HPLQC-RALELCFNVSLNRLPTSYGPPV-----SNALMAALKRAQ 98 (898)
T ss_pred HHHHcCCCCcchHHHHHHHHcCCchHHHHHHHhc-CcccH-HHHHHHHHHHHHhccCCCCCcc-----chHhHHHHHHHH
Confidence 4567777777776 577777777655554441 11 01 110 01334889999666442 247899999999
Q ss_pred HHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcC
Q 029953 94 AMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGK 149 (185)
Q Consensus 94 ~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~ 149 (185)
..+.......++++|.+||+.+.++-.++..+.++++++|.+..+++..|+..++.
T Consensus 99 a~qrr~~~~~~~~~vkvE~~~li~silDdp~vsrv~reag~~s~~vK~~ve~~~g~ 154 (898)
T KOG1051|consen 99 AHQRRGCEEQQQQAVKVELEQLILSILDDPSVSRVMREAGFSSSAVKSAVEQPVGQ 154 (898)
T ss_pred HHHHhcchhhccchhhHhHHhhheeeecCchHHHHHHHhcCChHHHHHHHHhhccc
Confidence 99999999999999999999666655556789999999999999999999988763
No 18
>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=88.80 E-value=0.71 Score=34.91 Aligned_cols=41 Identities=15% Similarity=0.181 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHH
Q 029953 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRA 131 (185)
Q Consensus 89 a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~ 131 (185)
+.+++..|-+.|+..+...|.++||-+|+-.| .....+|+.
T Consensus 55 ~aEIlelA~n~ak~~k~krItp~hi~lAi~nD--~EL~~L~~~ 95 (115)
T cd00074 55 TAEVLELAGNAARDNKKKRITPRHLQLAVRND--EELNKLLKG 95 (115)
T ss_pred HHHHHHHHHHHHHHcCCCeEcHHHHHHHHhcc--HHHHHHHcC
Confidence 45689999999999999999999999999765 355666663
No 19
>PTZ00017 histone H2A; Provisional
Probab=87.47 E-value=0.75 Score=35.72 Aligned_cols=45 Identities=16% Similarity=0.115 Sum_probs=36.1
Q ss_pred hhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHc
Q 029953 83 PKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRAN 132 (185)
Q Consensus 83 ~~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~ 132 (185)
++++. ++|+.|-+.|++.+...|.++||.+|+-.| .....+|+..
T Consensus 59 EYLta---EILELAgNaa~d~kk~RItPrHi~lAI~nD--eEL~~Ll~~v 103 (134)
T PTZ00017 59 EYLTA---EVLELAGNAAKDNKKKRITPRHIQLAIRND--EELNKLLAGV 103 (134)
T ss_pred HHHHH---HHHHHHHHHHHhcCCCeecHHHHHhhccCc--HHHHHHHcCC
Confidence 45554 588899999999999999999999999765 3567777643
No 20
>PLN00154 histone H2A; Provisional
Probab=86.74 E-value=0.93 Score=35.28 Aligned_cols=39 Identities=10% Similarity=0.182 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHH
Q 029953 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (185)
Q Consensus 90 ~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~ 130 (185)
.++|+.|-+.|++.+...|.|.||.+|+-.| ....++|+
T Consensus 75 AEVLELAGNaA~d~kk~RItPrHi~lAIrnD--eEL~~Ll~ 113 (136)
T PLN00154 75 AEVLELAGNASKDLKVKRITPRHLQLAIRGD--EELDTLIK 113 (136)
T ss_pred HHHHHHHHHHHHhhCCceecHHHhhhhccCc--HHHHHHhc
Confidence 4689999999999999999999999999764 35566664
No 21
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=86.20 E-value=1.1 Score=34.52 Aligned_cols=42 Identities=17% Similarity=0.129 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHc
Q 029953 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRAN 132 (185)
Q Consensus 89 a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~ 132 (185)
+.++++.|-+.|++.+-..|.|.|+.+||-.| ....++|...
T Consensus 62 ~Aeile~agnaardnkk~ri~PrH~~lAI~ND--eEL~~lL~~v 103 (131)
T KOG1756|consen 62 TAEILELAGNAARDNKKTRITPRHLQLAIRND--EELNKLLGKV 103 (131)
T ss_pred HHHHHHHhHHHhhhcCccccChHHHHHHHhCc--HHHHHHhccc
Confidence 45788899999999999999999999999875 3667887644
No 22
>PLN00157 histone H2A; Provisional
Probab=85.86 E-value=0.88 Score=35.25 Aligned_cols=42 Identities=17% Similarity=0.138 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHc
Q 029953 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRAN 132 (185)
Q Consensus 89 a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~ 132 (185)
+.++|+.|-+.|+..+...|.++||.+|+-.| .....+|+..
T Consensus 61 taEVLELAgnaa~d~kk~RItPrHi~lAI~nD--eEL~~Ll~~v 102 (132)
T PLN00157 61 AAEVLELAGNAARDNKKSRIVPRHIQLAVRND--EELSKLLGGV 102 (132)
T ss_pred HHHHHHHHHHHHHhcCCccccHHHHhhcccCc--HHHHHHHcCc
Confidence 34589999999999999999999999999764 3667777643
No 23
>PLN00153 histone H2A; Provisional
Probab=85.70 E-value=1.1 Score=34.58 Aligned_cols=40 Identities=18% Similarity=0.130 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHH
Q 029953 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRA 131 (185)
Q Consensus 90 ~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~ 131 (185)
.++|+.|-+.|++.+...|.|+||.+++-.| ....++|+.
T Consensus 60 aEVLELAgnaa~d~kk~RItPrHi~lAI~nD--eEL~~Ll~~ 99 (129)
T PLN00153 60 AEVLELAGNAARDNKKNRIVPRHIQLAIRND--EELGKLLGE 99 (129)
T ss_pred HHHHHHHHHHHHhcCCCccChHHHHhhccCc--HHHHHHHCC
Confidence 4589999999999999999999999999764 366777764
No 24
>smart00414 H2A Histone 2A.
Probab=84.96 E-value=1.2 Score=33.12 Aligned_cols=40 Identities=18% Similarity=0.185 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHH
Q 029953 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRA 131 (185)
Q Consensus 90 ~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~ 131 (185)
.++|+.|-+.|++.+...|+++|+.+|+-.| .....+|+.
T Consensus 45 aEILeLagn~a~~~k~~rItp~hi~lAi~nD--~EL~~L~~~ 84 (106)
T smart00414 45 AEVLELAGNAARDNKKRRITPRHLQLAIRND--EELNKLLKG 84 (106)
T ss_pred HHHHHHHHHHHHhcCCCccchHHHhhhccCC--HHHHHHHcC
Confidence 4588899999999999999999999999764 356667764
No 25
>PLN00156 histone H2AX; Provisional
Probab=83.96 E-value=1.5 Score=34.24 Aligned_cols=41 Identities=15% Similarity=0.116 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHc
Q 029953 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRAN 132 (185)
Q Consensus 90 ~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~ 132 (185)
.++|+.|-+.|+..+-..|.|+||.+++-.| .....+|+..
T Consensus 65 aEVLELAgNaa~d~kk~RItPrHi~lAIrnD--eEL~~Ll~~v 105 (139)
T PLN00156 65 AEVLELAGNAARDNKKNRIVPRHIQLAVRND--EELSKLLGSV 105 (139)
T ss_pred HHHHHHHHHHHHHcCCCcCcHHHHHhhccCc--HHHHHHHCCC
Confidence 4589999999999999999999999999764 4667778743
No 26
>PTZ00252 histone H2A; Provisional
Probab=80.10 E-value=2.4 Score=32.93 Aligned_cols=41 Identities=7% Similarity=0.074 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHH--cCCCCcCHHHHHHHHhhcCCchHHHHHHHc
Q 029953 90 IRSFAMAELEARK--LKYPNTGTEAFLMGILVEGTSTTAKFLRAN 132 (185)
Q Consensus 90 ~~vL~~A~~~A~~--~~~~~I~~eHLLlALl~e~~~~a~~iL~~~ 132 (185)
.++|+.|-+.|++ .+-..|.|+||.+++-.| ....++|+..
T Consensus 61 aEVLELAgnaa~d~~~kk~RItPrHi~lAIrND--eEL~~Ll~~v 103 (134)
T PTZ00252 61 AELLELSVKAAAQQAKKPKRLTPRTVTLAVRHD--DDLGSLLKNV 103 (134)
T ss_pred HHHHHHHHHHHHhccCCcccccHHHHHhhccCh--HHHHHHHcCC
Confidence 4588999999977 455799999999999764 3667788754
No 27
>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=76.54 E-value=4.7 Score=25.30 Aligned_cols=27 Identities=22% Similarity=0.081 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHH
Q 029953 90 IRSFAMAELEARKLKYPNTGTEAFLMG 116 (185)
Q Consensus 90 ~~vL~~A~~~A~~~~~~~I~~eHLLlA 116 (185)
.++=..++.+|++.|...|+.+|+.-+
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 566678999999999999999998654
No 28
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=64.01 E-value=11 Score=28.77 Aligned_cols=40 Identities=20% Similarity=0.130 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHH
Q 029953 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (185)
Q Consensus 89 a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~ 130 (185)
+.++++.|-|.|+..+-..|.|-||-+||-.|+ ....++.
T Consensus 61 ~aEilelAgNaA~d~kkkri~PrHlqlAIrnD~--EL~~l~~ 100 (132)
T COG5262 61 AAEILELAGNAARDNKKKRIIPRHLQLAIRNDE--ELNKLLG 100 (132)
T ss_pred HHHHHHHhhhhhhhcCcceechHHHHHHhcCcH--HHHHHhh
Confidence 467889999999999999999999999998753 4455544
No 29
>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=59.54 E-value=14 Score=24.83 Aligned_cols=32 Identities=13% Similarity=0.046 Sum_probs=27.6
Q ss_pred cHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 029953 86 SARAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (185)
Q Consensus 86 T~~a~~vL~~A~~~A~~~~~~~I~~eHLLlAL 117 (185)
-.-+.+++..|.+.|...+...|++.|+.+|+
T Consensus 41 E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~ 72 (75)
T PF00125_consen 41 EYLLVEILEEAGNLARHAKRKTITPRDIQLAV 72 (75)
T ss_dssp HHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHH
T ss_pred hhhhhhhhhHHHHHHhhcCCcEecHHHHHHHH
Confidence 44556788889999999999999999999986
No 30
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=51.75 E-value=89 Score=22.57 Aligned_cols=72 Identities=10% Similarity=-0.113 Sum_probs=49.8
Q ss_pred cCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCCCCC---CC---CCCCCCCCHHHHHHHHHHHHHHHH
Q 029953 108 TGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLF---FF---SPERPPLTEQAQRALDWAFNEKLK 179 (185)
Q Consensus 108 I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~~~~---~~---~~~~i~~s~~a~~~Le~A~~~A~~ 179 (185)
..-.++|..|..++.-....+-+.+|++...+-..+..+..++=.. .+ -...+.+|+..+++++........
T Consensus 28 ~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~~~~~~ 105 (118)
T TIGR02337 28 EQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLSPQIEE 105 (118)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhhHHHHH
Confidence 3334566666665544578999999999999988888876543211 01 113578999999999988776654
No 31
>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=46.82 E-value=39 Score=22.10 Aligned_cols=39 Identities=21% Similarity=0.250 Sum_probs=32.5
Q ss_pred HHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCC
Q 029953 112 AFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKS 150 (185)
Q Consensus 112 HLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~ 150 (185)
.++..|+.++...+..|-+..|++...+...+..+..++
T Consensus 12 ~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~G 50 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKG 50 (68)
T ss_dssp HHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 466777777777889999999999999999999887654
No 32
>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=46.05 E-value=38 Score=22.17 Aligned_cols=27 Identities=15% Similarity=-0.073 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 029953 91 RSFAMAELEARKLKYPNTGTEAFLMGI 117 (185)
Q Consensus 91 ~vL~~A~~~A~~~~~~~I~~eHLLlAL 117 (185)
.+...|...|...+-..|..+||..++
T Consensus 39 ~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 39 YLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 344556677888888899999998775
No 33
>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=42.56 E-value=54 Score=21.99 Aligned_cols=34 Identities=15% Similarity=-0.083 Sum_probs=30.6
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 029953 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlAL 117 (185)
.+..++.+++..|..+++..+-..++++++-+||
T Consensus 31 ~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Al 64 (65)
T smart00803 31 DVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSAL 64 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHh
Confidence 4678899999999999999999999999998775
No 34
>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=41.96 E-value=40 Score=23.24 Aligned_cols=32 Identities=13% Similarity=-0.118 Sum_probs=23.9
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCC-cCHHHHHH
Q 029953 84 KWSARAIRSFAMAELEARKLKYPN-TGTEAFLM 115 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~~A~~~~~~~-I~~eHLLl 115 (185)
++.-=+++++.+|...|+.-|... |+.+||--
T Consensus 31 yl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEk 63 (72)
T PF09415_consen 31 YLRIFVREAVARAAEQAEAEGDEGFLEVEHLEK 63 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence 445556777888999999999888 99999864
No 35
>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=40.58 E-value=57 Score=24.45 Aligned_cols=38 Identities=8% Similarity=-0.034 Sum_probs=32.7
Q ss_pred hhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhc
Q 029953 83 PKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVE 120 (185)
Q Consensus 83 ~~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e 120 (185)
+..-..+.+++..|..+|+..|-..|+.+.+-+|+-..
T Consensus 29 e~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r 66 (117)
T cd07979 29 EFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSR 66 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 34566778999999999999999999999999998543
No 36
>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=40.17 E-value=84 Score=18.93 Aligned_cols=38 Identities=18% Similarity=0.047 Sum_probs=28.7
Q ss_pred HHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcC
Q 029953 112 AFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGK 149 (185)
Q Consensus 112 HLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~ 149 (185)
.+|..|.+++.-...++-+.+|++...+...+..+...
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 46667777776667889999999999999998887654
No 37
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=39.42 E-value=1.3e+02 Score=22.62 Aligned_cols=56 Identities=14% Similarity=0.119 Sum_probs=37.0
Q ss_pred HHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCCCCCCCHHHHHHHHH
Q 029953 114 LMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDW 172 (185)
Q Consensus 114 LlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~~~~~~~~~~i~~s~~a~~~Le~ 172 (185)
+...+.. .+....+=+.+||++..+|..+++++.+..-.. .....-...-.+||+.
T Consensus 42 i~~Fi~~-rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~--~~~~~~~~~~~~IL~~ 97 (113)
T PF09862_consen 42 IKLFIKN-RGNLKEMEKELGISYPTVRNRLDKIIEKLGYEE--DEEEEEEDERKEILDK 97 (113)
T ss_pred HHHHHHh-cCCHHHHHHHHCCCcHHHHHHHHHHHHHhCCCC--CcccccchhHHHHHHH
Confidence 3444444 467799999999999999999999886544311 1223444555666653
No 38
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=38.69 E-value=55 Score=24.38 Aligned_cols=76 Identities=11% Similarity=0.017 Sum_probs=46.7
Q ss_pred cc-cccccccccccccccCcchhhHhhhcCCCcCCCCCCCCC------CchhhcHHHHHHHHHHHHHHHHcCCCCcCHHH
Q 029953 40 LL-IRPQLNSSRFVTKYHRSSATATVSFSLPTTVKPETASPD------KIPKWSARAIRSFAMAELEARKLKYPNTGTEA 112 (185)
Q Consensus 40 ~~-~~~~~~~~~fv~~~~~~~~~~~~l~~~P~~~~p~~~~~~------m~~~fT~~a~~vL~~A~~~A~~~~~~~I~~eH 112 (185)
|| -++|-+|++.-.+.+ .+.-.-+++ .+.+.++.. +..-+---+..++....++|+..+...|+.||
T Consensus 8 ~~t~~k~n~~~~~ktrFP--~ar~KkIMQ----~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~ 81 (113)
T COG5247 8 MGTMPKQNSQKKKKTRFP--IARLKKIMQ----LDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEF 81 (113)
T ss_pred CCCCCCCchhhhhhhcCC--HHHHHHHHH----hhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHH
Confidence 55 578888987766654 111122332 222211100 00112223566778889999999999999999
Q ss_pred HHHHHhhcC
Q 029953 113 FLMGILVEG 121 (185)
Q Consensus 113 LLlALl~e~ 121 (185)
|-.++..++
T Consensus 82 lk~a~~sde 90 (113)
T COG5247 82 LKRATESDE 90 (113)
T ss_pred HHHHHhhhH
Confidence 999998764
No 39
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=37.19 E-value=87 Score=26.31 Aligned_cols=35 Identities=3% Similarity=-0.159 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcC
Q 029953 87 ARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEG 121 (185)
Q Consensus 87 ~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~ 121 (185)
-=+..++..+.++++..+...|+++||-.++..++
T Consensus 46 lFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~ 80 (224)
T KOG1659|consen 46 LFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDP 80 (224)
T ss_pred HHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccc
Confidence 34677888999999999999999999999998875
No 40
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=36.89 E-value=84 Score=22.55 Aligned_cols=30 Identities=13% Similarity=-0.049 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 029953 88 RAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (185)
Q Consensus 88 ~a~~vL~~A~~~A~~~~~~~I~~eHLLlAL 117 (185)
...++|..|-.+|--.+...|+.+||.-||
T Consensus 64 ~~~rilrvARTIADL~~~~~I~~~hi~EAl 93 (96)
T PF13335_consen 64 GYHRILRVARTIADLEGSERITREHIAEAL 93 (96)
T ss_pred HHHHHHHHHHHHHhHcCCCCCCHHHHHHHH
Confidence 345677778888999999999999999887
No 41
>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=36.18 E-value=85 Score=21.25 Aligned_cols=35 Identities=9% Similarity=-0.176 Sum_probs=29.0
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhh
Q 029953 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILV 119 (185)
Q Consensus 85 fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~ 119 (185)
...-+.+++..|..+|+..|...|..+-+.+++=.
T Consensus 32 ~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 32 ADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 34556678888999999999999999999998744
No 42
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=35.39 E-value=1.2e+02 Score=20.07 Aligned_cols=41 Identities=22% Similarity=0.186 Sum_probs=29.7
Q ss_pred HHHHHHHhhcCC--chHHHHHHHcCCCHHHHHHHHHHHhcCCC
Q 029953 111 EAFLMGILVEGT--STTAKFLRANGITLFKVREETLNLLGKSD 151 (185)
Q Consensus 111 eHLLlALl~e~~--~~a~~iL~~~GId~~~l~~~I~~~l~~~~ 151 (185)
+.+|..|...++ -.+..|-+.+|++...+.+.+..+...+-
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~ 51 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGK 51 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 344444545444 46789999999999999999988765544
No 43
>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=34.03 E-value=1.1e+02 Score=19.09 Aligned_cols=40 Identities=20% Similarity=0.103 Sum_probs=30.2
Q ss_pred HHHHHHHhhcCC--chHHHHHHHcCCCHHHHHHHHHHHhcCC
Q 029953 111 EAFLMGILVEGT--STTAKFLRANGITLFKVREETLNLLGKS 150 (185)
Q Consensus 111 eHLLlALl~e~~--~~a~~iL~~~GId~~~l~~~I~~~l~~~ 150 (185)
.++|..|...++ -....|-+.+|++...+...+..+..++
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G 49 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG 49 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 456667776665 4789999999999999999988876543
No 44
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=33.37 E-value=10 Score=28.62 Aligned_cols=31 Identities=13% Similarity=0.163 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhhc
Q 029953 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVE 120 (185)
Q Consensus 90 ~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e 120 (185)
.++|+.|-|.++.++...|+|-||-||+=.|
T Consensus 67 aEVLeLAgNasKdLKvKRitprHlqLAiRGD 97 (131)
T KOG1757|consen 67 AEVLELAGNASKDLKVKRITPRHLQLAIRGD 97 (131)
T ss_pred HHHHHHcccccccceeeeccchhheeeecCc
Confidence 4688899999999999999999999999654
No 45
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=31.86 E-value=1.9e+02 Score=23.21 Aligned_cols=38 Identities=18% Similarity=0.160 Sum_probs=27.8
Q ss_pred hhcHHHHHHHHH------------HHHHHHHcCCCCcCHHHHHHHHhhcC
Q 029953 84 KWSARAIRSFAM------------AELEARKLKYPNTGTEAFLMGILVEG 121 (185)
Q Consensus 84 ~fT~~a~~vL~~------------A~~~A~~~~~~~I~~eHLLlALl~e~ 121 (185)
+++.+|++.+.+ |.+.+.+-+-..|.-|.||+||-.-+
T Consensus 51 KIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 51 KISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred ccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 567777766654 44556667778899999999996543
No 46
>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=31.28 E-value=27 Score=25.14 Aligned_cols=39 Identities=13% Similarity=-0.055 Sum_probs=13.6
Q ss_pred hhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcC
Q 029953 83 PKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEG 121 (185)
Q Consensus 83 ~~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~ 121 (185)
+-....+..++..|.+.|...|...|++|+|+..|=.++
T Consensus 30 ~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~ 68 (93)
T PF02269_consen 30 DIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDP 68 (93)
T ss_dssp HHHHHHHHHHHHHHHC-----------------------
T ss_pred HHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCH
Confidence 346888999999999999999999999999999997765
No 47
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=30.41 E-value=59 Score=25.77 Aligned_cols=36 Identities=11% Similarity=-0.028 Sum_probs=27.6
Q ss_pred hhcHHHHHHHH------------HHHHHHHHcCCCCcCHHHHHHHHhh
Q 029953 84 KWSARAIRSFA------------MAELEARKLKYPNTGTEAFLMGILV 119 (185)
Q Consensus 84 ~fT~~a~~vL~------------~A~~~A~~~~~~~I~~eHLLlALl~ 119 (185)
+++.+++++|. .|.+.+.+-.-..|.+||++.||=.
T Consensus 31 rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~ 78 (156)
T KOG0871|consen 31 RVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALEN 78 (156)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHH
Confidence 56666666654 4667777888889999999999844
No 48
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=29.39 E-value=1.9e+02 Score=24.87 Aligned_cols=61 Identities=13% Similarity=-0.047 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHh
Q 029953 87 ARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLL 147 (185)
Q Consensus 87 ~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l 147 (185)
..+.+++..|...|...+...|+.+|+-.|+-.-..+...+.++.+......+..++....
T Consensus 241 R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~~~i~~l~~~~~~~l~ai~~~~ 301 (365)
T TIGR02928 241 RKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLLELIRGLPTHSKLVLLAIANLA 301 (365)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 4566677788888888888999999998876433223345556655555555566665544
No 49
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=28.89 E-value=1.9e+02 Score=25.22 Aligned_cols=60 Identities=17% Similarity=0.031 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHh
Q 029953 88 RAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLL 147 (185)
Q Consensus 88 ~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l 147 (185)
.+.+++..|...|...+...|+.+|+-.|+-.-..+.....++.+......+..++....
T Consensus 250 ~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~~~~~~~L~~~~k~~L~ai~~~~ 309 (394)
T PRK00411 250 VAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHLSEVLRTLPLHEKLLLRAIVRLL 309 (394)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 344667777788888888999999998887543334456667666665556666655443
No 50
>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=27.07 E-value=1.6e+02 Score=19.88 Aligned_cols=34 Identities=15% Similarity=-0.044 Sum_probs=28.1
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 029953 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlAL 117 (185)
-.+-+++++++.|.+.++..+-..++++++=.||
T Consensus 32 dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~AL 65 (66)
T PF02969_consen 32 DVEYRLREIIQEALKFMRHSKRTKLTTDDINSAL 65 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 4578899999999999999999999999987665
No 51
>PRK11426 hypothetical protein; Provisional
Probab=26.58 E-value=1.6e+02 Score=22.83 Aligned_cols=44 Identities=9% Similarity=-0.018 Sum_probs=36.6
Q ss_pred CCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCCC
Q 029953 105 YPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSD 151 (185)
Q Consensus 105 ~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~~ 151 (185)
+.-|++++|--++=. ..+..+-.+.|++.+++...+-+.++..-
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 678999999988743 36788999999999999999988887543
No 52
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=25.29 E-value=2e+02 Score=19.82 Aligned_cols=24 Identities=21% Similarity=0.231 Sum_probs=16.2
Q ss_pred hHHHHHHHcCCCHHHHHHHHHHHh
Q 029953 124 TTAKFLRANGITLFKVREETLNLL 147 (185)
Q Consensus 124 ~a~~iL~~~GId~~~l~~~I~~~l 147 (185)
.+..+|+++|++.......+...+
T Consensus 15 ~a~~il~~~Glt~s~ai~~fl~qi 38 (83)
T PF04221_consen 15 EAEAILEELGLTLSDAINMFLKQI 38 (83)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHH
Confidence 468899999999877766655443
No 53
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=24.35 E-value=4.3e+02 Score=22.24 Aligned_cols=34 Identities=18% Similarity=0.256 Sum_probs=19.8
Q ss_pred HHHHHHHhhcCCc-----hHHHHHHHcCCCHHHHHHHHH
Q 029953 111 EAFLMGILVEGTS-----TTAKFLRANGITLFKVREETL 144 (185)
Q Consensus 111 eHLLlALl~e~~~-----~a~~iL~~~GId~~~l~~~I~ 144 (185)
+-|+-+.+.++.+ .+..|-.+.|+|.+++++.+.
T Consensus 124 ~~lf~AyF~eg~nI~D~dVL~diA~~~GLD~~~~~~~L~ 162 (225)
T COG2761 124 EALFEAYFEEGRNIGDEDVLADIAEEVGLDREEFKADLA 162 (225)
T ss_pred HHHHHHHhccCCCCCcHHHHHHHHHHhCCCHHHHHHHHh
Confidence 3444555554422 346666777888777776544
No 54
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=23.99 E-value=1.3e+02 Score=19.57 Aligned_cols=19 Identities=21% Similarity=0.127 Sum_probs=9.5
Q ss_pred HHHHHHcCCCHHHHHHHHH
Q 029953 126 AKFLRANGITLFKVREETL 144 (185)
Q Consensus 126 ~~iL~~~GId~~~l~~~I~ 144 (185)
...+++.|+|.+++.++++
T Consensus 35 ~eA~~~~~ld~~~vl~~L~ 53 (56)
T PF04405_consen 35 EEACEEKGLDPEEVLEELN 53 (56)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 4444555555555555444
No 55
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=23.79 E-value=2.1e+02 Score=18.35 Aligned_cols=40 Identities=15% Similarity=0.183 Sum_probs=22.9
Q ss_pred CHHHHHHHHhhcCCc---hHHHHHHHcCCCHHHHHHHHHHHhc
Q 029953 109 GTEAFLMGILVEGTS---TTAKFLRANGITLFKVREETLNLLG 148 (185)
Q Consensus 109 ~~eHLLlALl~e~~~---~a~~iL~~~GId~~~l~~~I~~~l~ 148 (185)
++...++-+++.+.+ .+..+.++++++.+.+++.+...+.
T Consensus 17 ~~a~~Iw~~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~ 59 (68)
T PF05402_consen 17 ETAAFIWELLDGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLE 59 (68)
T ss_dssp THHHHHHHH--SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 344556666654322 3466777889999888888777654
No 56
>PF14290 DUF4370: Domain of unknown function (DUF4370)
Probab=23.78 E-value=4.4e+02 Score=22.14 Aligned_cols=100 Identities=23% Similarity=0.194 Sum_probs=66.5
Q ss_pred hhcCCCcCCCCCCCCC---CchhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHH
Q 029953 65 SFSLPTTVKPETASPD---KIPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVRE 141 (185)
Q Consensus 65 l~~~P~~~~p~~~~~~---m~~~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~ 141 (185)
..-+|...+|+..+.- |--.|++--..++..+.....+..+...+.|-|--. -.+++.++++|.....++-
T Consensus 75 ~~hlP~i~Dp~i~~afKdLmAasW~elp~svv~~akkalSk~tdD~AGqeaL~nv------fRAAeAvEeFgG~L~tLrm 148 (239)
T PF14290_consen 75 VSHLPAISDPEIEKAFKDLMAASWDELPDSVVNEAKKALSKNTDDKAGQEALKNV------FRAAEAVEEFGGILVTLRM 148 (239)
T ss_pred cccCCCCCCHHHHHHHHHHHhcchhhCCHHHHHHHHHHHhccCccchhHHHHHHH------HHHHHHHHHhhhhHHHHHH
Confidence 4457776666621110 112355555566677777777778888888766533 2467889999999999999
Q ss_pred HHHHHhcCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q 029953 142 ETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFN 175 (185)
Q Consensus 142 ~I~~~l~~~~~~~~~~~~i~~s~~a~~~Le~A~~ 175 (185)
+|++..+-.... .-|+.....++|+-+..
T Consensus 149 ~idDl~GlsGEn-----v~PLP~~~~~Al~t~y~ 177 (239)
T PF14290_consen 149 EIDDLCGLSGEN-----VKPLPDYIENALRTAYK 177 (239)
T ss_pred HHHHhcCCCCCC-----CCCCcHHHHHHHHHHHH
Confidence 999998865543 34666677777776654
No 57
>PLN00035 histone H4; Provisional
Probab=22.14 E-value=2e+02 Score=21.31 Aligned_cols=36 Identities=3% Similarity=-0.161 Sum_probs=30.4
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhh
Q 029953 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILV 119 (185)
Q Consensus 84 ~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~ 119 (185)
-+...+.+++..|..+|...+-..|..+.+.++|=.
T Consensus 58 vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr 93 (103)
T PLN00035 58 VLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 456777788889999999999999999999988744
No 58
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=22.01 E-value=1.7e+02 Score=22.39 Aligned_cols=37 Identities=8% Similarity=-0.064 Sum_probs=29.9
Q ss_pred hhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhh
Q 029953 83 PKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILV 119 (185)
Q Consensus 83 ~~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~ 119 (185)
+..-.-+.++|..|..+|...|...|+.+.+-+|+-.
T Consensus 40 EfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~ 76 (129)
T PF02291_consen 40 EFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQS 76 (129)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHH
Confidence 3345667889999999999999999999999999853
No 59
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=21.72 E-value=1.5e+02 Score=22.97 Aligned_cols=36 Identities=11% Similarity=0.038 Sum_probs=25.5
Q ss_pred hhcHHHHHHHHH------------HHHHHHHcCCCCcCHHHHHHHHhh
Q 029953 84 KWSARAIRSFAM------------AELEARKLKYPNTGTEAFLMGILV 119 (185)
Q Consensus 84 ~fT~~a~~vL~~------------A~~~A~~~~~~~I~~eHLLlALl~ 119 (185)
.||.++++++.. |.+.+.+-.-..|..||++.||-.
T Consensus 30 ~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALen 77 (148)
T COG5150 30 VFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALEN 77 (148)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHh
Confidence 577777777643 344555556678999999999843
No 60
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=21.56 E-value=2.8e+02 Score=21.14 Aligned_cols=40 Identities=15% Similarity=0.104 Sum_probs=25.1
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCC
Q 029953 125 TAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFNEKLKSGS 182 (185)
Q Consensus 125 a~~iL~~~GId~~~l~~~I~~~l~~~~~~~~~~~~i~~s~~a~~~Le~A~~~A~~lGd 182 (185)
+..++++.|+|.+++.+.+. ++..++.++.....|..+|-
T Consensus 126 l~~~~~~~Gld~~~~~~~~~------------------~~~~~~~~~~~~~~a~~~gv 165 (193)
T PF01323_consen 126 LAEIAEEAGLDPDEFDAALD------------------SPEVKAALEEDTAEARQLGV 165 (193)
T ss_dssp HHHHHHHTT--HHHHHHHHT------------------SHHHHHHHHHHHHHHHHTTC
T ss_pred HHHHHHHcCCcHHHHHHHhc------------------chHHHHHHHHHHHHHHHcCC
Confidence 57788889999888776644 24456666666666666553
No 61
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=21.40 E-value=3.7e+02 Score=24.03 Aligned_cols=60 Identities=10% Similarity=-0.051 Sum_probs=41.1
Q ss_pred cHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHH
Q 029953 86 SARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLN 145 (185)
Q Consensus 86 T~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~ 145 (185)
...+..++..|-+.|.+.+...++.+|+-.+.-........+.++.+-....-+...+..
T Consensus 231 AR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~~~~L~~~~ki~L~~i~~ 290 (366)
T COG1474 231 ARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEVLKTLPLHQKIVLLAIVE 290 (366)
T ss_pred HHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHHHHcCCHhHHHHHHHHHH
Confidence 456778889999999999999999999999943333334455566554443333333333
No 62
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=21.23 E-value=1.4e+02 Score=21.11 Aligned_cols=27 Identities=15% Similarity=0.127 Sum_probs=22.0
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHhcCCC
Q 029953 125 TAKFLRANGITLFKVREETLNLLGKSD 151 (185)
Q Consensus 125 a~~iL~~~GId~~~l~~~I~~~l~~~~ 151 (185)
...|.++++++.++|+++|+.+...+-
T Consensus 68 v~~I~~~l~~~~~~v~~al~~L~~eG~ 94 (102)
T PF08784_consen 68 VDEIAQQLGMSENEVRKALDFLSNEGH 94 (102)
T ss_dssp HHHHHHHSTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHhCCe
Confidence 567788889999999999999887654
No 63
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=20.83 E-value=2.3e+02 Score=19.84 Aligned_cols=38 Identities=13% Similarity=0.169 Sum_probs=28.4
Q ss_pred HHHHHhhcCCchHHHHHHHcCCCHHHHHHHHHHHhcCC
Q 029953 113 FLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKS 150 (185)
Q Consensus 113 LLlALl~e~~~~a~~iL~~~GId~~~l~~~I~~~l~~~ 150 (185)
+|..|..++......+-+.+|++...+.+.+..+...+
T Consensus 8 il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 8 ILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 44455555544568888999999999999999887543
No 64
>PLN02749 Uncharacterized protein At1g47420
Probab=20.42 E-value=4.5e+02 Score=21.02 Aligned_cols=100 Identities=24% Similarity=0.231 Sum_probs=61.5
Q ss_pred hhcCCCcCCCCCCCCC---CchhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhhcCCchHHHHHHHcCCCHHHHHH
Q 029953 65 SFSLPTTVKPETASPD---KIPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVRE 141 (185)
Q Consensus 65 l~~~P~~~~p~~~~~~---m~~~fT~~a~~vL~~A~~~A~~~~~~~I~~eHLLlALl~e~~~~a~~iL~~~GId~~~l~~ 141 (185)
+..+|...+|..-..- |--.|+.---.++..+.+...+..+...+.|-|--.. .+++...++|.....++-
T Consensus 9 ~~~lP~i~Dp~i~~afkdLma~sW~elp~sv~~~~kkalsk~tddkagqeaL~nvf------rAAeAveeFgG~L~sLrm 82 (173)
T PLN02749 9 VSHLPEISDPEILKAFKDLMAASWDELPDSVVNDAKKALSKNTDDKAGQEALKNVF------RAAEAVEEFGGTLVSLRM 82 (173)
T ss_pred cccCCCCCCHHHHHHHHHHHhcchhhCChHHHHHHHHHHhcCCcchhhHHHHHHHH------HHHHHHHHHhhHHHHHHH
Confidence 3446766666521000 0012333333445555555555556677777654332 457889999999999999
Q ss_pred HHHHHhcCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q 029953 142 ETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFN 175 (185)
Q Consensus 142 ~I~~~l~~~~~~~~~~~~i~~s~~a~~~Le~A~~ 175 (185)
+|++..+-.... .-|+.....++|+-|..
T Consensus 83 eidDl~GlsGEn-----v~PLPd~~~~Al~tay~ 111 (173)
T PLN02749 83 EIDDLIGLSGEN-----VKPLPDYIENALETAYQ 111 (173)
T ss_pred HHHHhcCCCCCC-----CCCCcHHHHHHHHHHHH
Confidence 999998865543 34667777777777654
Done!