Query psy12448
Match_columns 168
No_of_seqs 135 out of 583
Neff 7.4
Searched_HMMs 46136
Date Fri Aug 16 19:33:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12448.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12448hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00166 DNA polymerase delta 100.0 1.9E-36 4.1E-41 284.3 11.2 153 1-160 892-1045(1054)
2 KOG0969|consensus 100.0 2.7E-36 5.8E-41 268.0 5.3 156 1-159 900-1055(1066)
3 KOG0968|consensus 100.0 7.1E-31 1.5E-35 239.9 6.0 154 1-162 1318-1482(1488)
4 PF14260 zf-C4pol: C4-type zin 99.9 4.2E-22 9E-27 133.3 7.1 73 75-149 1-73 (73)
5 KOG0970|consensus 99.1 1.1E-10 2.5E-15 108.6 5.7 127 1-129 1167-1332(1429)
6 PF00136 DNA_pol_B: DNA polyme 98.2 8.6E-07 1.9E-11 77.8 2.3 40 1-40 411-450 (466)
7 COG0417 PolB DNA polymerase el 98.1 9.6E-07 2.1E-11 82.3 2.3 45 1-46 736-780 (792)
8 PF08996 zf-DNA_Pol: DNA Polym 95.4 0.015 3.3E-07 45.4 3.3 59 72-130 18-90 (188)
9 PF13240 zinc_ribbon_2: zinc-r 90.0 0.18 3.8E-06 26.0 1.1 22 74-98 1-22 (23)
10 PF13248 zf-ribbon_3: zinc-rib 88.5 0.28 6.1E-06 25.8 1.2 24 72-98 2-25 (26)
11 PF10571 UPF0547: Uncharacteri 85.7 0.49 1.1E-05 25.1 1.2 24 73-99 1-24 (26)
12 PF09889 DUF2116: Uncharacteri 85.1 1.6 3.5E-05 27.8 3.6 24 72-98 3-27 (59)
13 COG4068 Uncharacterized protei 76.6 7.8 0.00017 24.7 4.4 22 72-96 8-30 (64)
14 TIGR03826 YvyF flagellar opero 74.0 3.4 7.3E-05 30.8 2.8 26 71-100 80-105 (137)
15 PRK00420 hypothetical protein; 72.6 2.4 5.2E-05 30.5 1.6 27 71-97 22-48 (112)
16 PRK14714 DNA polymerase II lar 72.0 1.4 3E-05 43.4 0.4 23 72-99 667-689 (1337)
17 PF07282 OrfB_Zn_ribbon: Putat 71.1 2.3 5.1E-05 27.2 1.2 32 66-98 23-55 (69)
18 PF09538 FYDLN_acid: Protein o 68.8 3.3 7.2E-05 29.5 1.6 29 72-100 9-37 (108)
19 PF14446 Prok-RING_1: Prokaryo 68.1 2.5 5.4E-05 26.5 0.8 28 72-100 5-32 (54)
20 PF03604 DNA_RNApol_7kD: DNA d 66.0 6 0.00013 21.9 2.0 25 74-98 2-26 (32)
21 PF12773 DZR: Double zinc ribb 64.5 3.1 6.7E-05 24.9 0.7 21 75-98 1-21 (50)
22 PF01286 XPA_N: XPA protein N- 63.5 5.3 0.00012 22.6 1.5 27 72-98 3-33 (34)
23 smart00659 RPOLCX RNA polymera 62.8 5 0.00011 23.9 1.3 26 73-98 3-28 (44)
24 PF09986 DUF2225: Uncharacteri 61.9 3.1 6.8E-05 33.0 0.5 16 69-84 2-17 (214)
25 COG1645 Uncharacterized Zn-fin 57.2 4.6 9.9E-05 29.9 0.6 26 71-97 27-52 (131)
26 TIGR02300 FYDLN_acid conserved 54.4 9.4 0.0002 28.1 1.8 29 72-100 9-37 (129)
27 PRK00398 rpoP DNA-directed RNA 54.1 8 0.00017 22.8 1.2 27 72-98 3-30 (46)
28 PF14471 DUF4428: Domain of un 52.0 5.4 0.00012 24.5 0.2 25 74-98 1-29 (51)
29 PF03833 PolC_DP2: DNA polymer 51.9 4.8 0.0001 38.3 0.0 23 72-99 655-677 (900)
30 PHA03082 DNA-dependent RNA pol 51.2 27 0.00059 22.1 3.3 35 90-124 5-39 (63)
31 PF06677 Auto_anti-p27: Sjogre 50.2 9.6 0.00021 22.4 1.1 26 71-96 16-41 (41)
32 PF05864 Chordopox_RPO7: Chord 47.9 30 0.00066 21.9 3.1 35 90-124 5-39 (63)
33 TIGR03826 YvyF flagellar opero 47.5 6.9 0.00015 29.1 0.2 30 72-103 3-32 (137)
34 PRK04023 DNA polymerase II lar 47.1 6.1 0.00013 38.4 -0.1 22 72-98 626-647 (1121)
35 COG2093 DNA-directed RNA polym 46.9 12 0.00025 24.2 1.2 24 72-98 4-27 (64)
36 PRK06266 transcription initiat 46.5 29 0.00063 26.8 3.6 46 73-118 118-170 (178)
37 PF08274 PhnA_Zn_Ribbon: PhnA 46.2 6.8 0.00015 21.4 0.0 26 73-98 3-28 (30)
38 TIGR00201 comF comF family pro 46.0 11 0.00024 29.0 1.2 21 75-98 1-21 (190)
39 PF14803 Nudix_N_2: Nudix N-te 43.5 6.6 0.00014 22.1 -0.3 23 74-96 2-29 (34)
40 PF07754 DUF1610: Domain of un 43.1 18 0.00038 18.8 1.3 22 75-96 1-23 (24)
41 PF09862 DUF2089: Protein of u 42.7 8.6 0.00019 27.7 0.1 20 75-97 1-20 (113)
42 COG4888 Uncharacterized Zn rib 40.8 15 0.00032 26.0 1.1 29 72-100 22-57 (104)
43 COG1996 RPC10 DNA-directed RNA 40.6 14 0.00031 22.6 0.8 27 72-98 6-33 (49)
44 PF09297 zf-NADH-PPase: NADH p 39.8 11 0.00025 20.4 0.3 26 72-97 3-29 (32)
45 COG1439 Predicted nucleic acid 39.7 19 0.00041 28.0 1.6 24 72-98 139-162 (177)
46 cd00350 rubredoxin_like Rubred 38.3 35 0.00077 18.6 2.2 26 74-100 3-28 (33)
47 PRK12496 hypothetical protein; 37.5 24 0.00051 26.9 1.8 26 72-98 127-152 (164)
48 cd00729 rubredoxin_SM Rubredox 36.7 36 0.00079 18.9 2.1 27 73-100 3-29 (34)
49 PF05191 ADK_lid: Adenylate ki 36.6 24 0.00052 20.0 1.3 25 73-97 2-29 (36)
50 TIGR00269 conserved hypothetic 36.2 17 0.00036 25.4 0.7 20 72-96 80-99 (104)
51 PF01783 Ribosomal_L32p: Ribos 35.7 26 0.00057 21.7 1.5 21 72-96 26-46 (56)
52 PF08746 zf-RING-like: RING-li 35.6 18 0.00039 21.2 0.7 22 124-145 1-22 (43)
53 TIGR00354 polC DNA polymerase, 33.8 13 0.00028 36.0 -0.1 22 72-98 625-646 (1095)
54 PHA02942 putative transposase; 33.5 25 0.00054 30.5 1.6 33 65-98 319-351 (383)
55 PF04423 Rad50_zn_hook: Rad50 32.6 40 0.00088 20.4 2.0 31 74-116 22-52 (54)
56 PRK09401 reverse gyrase; Revie 31.4 37 0.00081 33.8 2.5 26 72-97 7-33 (1176)
57 TIGR00373 conserved hypothetic 31.4 40 0.00087 25.4 2.2 38 74-111 111-155 (158)
58 smart00834 CxxC_CXXC_SSSS Puta 30.7 35 0.00075 19.0 1.4 26 73-98 6-35 (41)
59 PF12172 DUF35_N: Rubredoxin-l 30.4 18 0.0004 20.2 0.2 24 72-98 11-34 (37)
60 COG4530 Uncharacterized protei 30.1 64 0.0014 23.3 2.9 46 72-117 9-54 (129)
61 PRK12286 rpmF 50S ribosomal pr 29.4 29 0.00063 21.8 1.0 22 72-97 27-48 (57)
62 PF10170 C6_DPF: Cysteine-rich 27.9 28 0.00062 24.4 0.8 15 135-149 58-72 (97)
63 PRK14559 putative protein seri 27.6 36 0.00078 31.7 1.6 33 73-108 28-60 (645)
64 PF10764 Gin: Inhibitor of sig 27.6 14 0.00031 22.2 -0.7 25 74-98 1-27 (46)
65 smart00661 RPOL9 RNA polymeras 27.5 41 0.00088 19.9 1.4 23 75-97 3-28 (52)
66 PRK01343 zinc-binding protein; 27.1 39 0.00084 21.3 1.2 23 72-96 9-32 (57)
67 PRK13130 H/ACA RNA-protein com 26.8 41 0.00089 21.1 1.3 20 73-97 6-25 (56)
68 PF04981 NMD3: NMD3 family ; 26.7 30 0.00065 27.7 0.8 24 75-100 1-24 (236)
69 PF02318 FYVE_2: FYVE-type zin 26.6 37 0.00081 24.2 1.2 26 72-97 54-79 (118)
70 PRK08351 DNA-directed RNA poly 26.5 41 0.00088 21.5 1.3 21 73-98 4-24 (61)
71 PRK14715 DNA polymerase II lar 26.4 21 0.00045 36.0 -0.2 22 72-98 674-695 (1627)
72 PRK11827 hypothetical protein; 26.2 37 0.0008 21.6 1.0 27 72-98 8-35 (60)
73 PF00130 C1_1: Phorbol esters/ 25.9 36 0.00079 20.2 1.0 27 71-97 10-36 (53)
74 PRK11595 DNA utilization prote 25.9 27 0.00058 27.7 0.4 24 73-98 6-29 (227)
75 PF14149 YhfH: YhfH-like prote 25.9 11 0.00024 21.7 -1.3 13 72-84 13-25 (37)
76 PF08792 A2L_zn_ribbon: A2L zi 25.9 36 0.00078 18.9 0.8 26 73-98 4-30 (33)
77 PF14353 CpXC: CpXC protein 25.7 33 0.00072 24.5 0.9 14 72-85 38-51 (128)
78 PF08271 TF_Zn_Ribbon: TFIIB z 24.8 28 0.00062 20.1 0.3 8 90-97 20-27 (43)
79 PRK10220 hypothetical protein; 24.5 37 0.00081 24.3 0.9 29 72-100 3-31 (111)
80 PF06827 zf-FPG_IleRS: Zinc fi 24.3 23 0.00049 18.8 -0.2 25 73-97 2-29 (30)
81 TIGR00686 phnA alkylphosphonat 24.2 35 0.00077 24.4 0.7 28 73-100 3-30 (109)
82 COG0675 Transposase and inacti 24.0 36 0.00079 27.6 0.9 26 68-98 306-331 (364)
83 TIGR02098 MJ0042_CXXC MJ0042 f 23.7 45 0.00097 18.5 1.0 26 73-98 3-34 (38)
84 PF09723 Zn-ribbon_8: Zinc rib 23.5 55 0.0012 18.9 1.4 25 73-97 6-34 (42)
85 TIGR01206 lysW lysine biosynth 22.9 50 0.0011 20.5 1.1 26 73-98 3-31 (54)
86 PF10186 Atg14: UV radiation r 22.9 94 0.002 25.0 3.1 21 74-99 1-21 (302)
87 PF09779 Ima1_N: Ima1 N-termin 22.6 81 0.0017 23.0 2.4 41 88-128 72-128 (131)
88 PRK14811 formamidopyrimidine-D 22.4 43 0.00094 27.5 1.0 29 72-100 235-266 (269)
89 TIGR01031 rpmF_bact ribosomal 22.2 46 0.00099 20.7 0.9 22 72-97 26-47 (55)
90 PF05605 zf-Di19: Drought indu 21.6 1.1E+02 0.0023 18.4 2.5 27 72-98 2-40 (54)
91 PF10886 DUF2685: Protein of u 21.6 56 0.0012 20.4 1.2 25 73-97 2-31 (54)
92 PHA02610 uvsY.-2 hypothetical 21.1 57 0.0012 20.2 1.1 25 73-97 2-31 (53)
93 PRK00564 hypA hydrogenase nick 20.8 63 0.0014 23.1 1.5 28 71-98 70-97 (117)
94 PRK06393 rpoE DNA-directed RNA 20.7 58 0.0013 21.1 1.1 21 73-98 6-26 (64)
95 PRK12495 hypothetical protein; 20.6 56 0.0012 26.3 1.3 27 71-98 41-67 (226)
96 PF01258 zf-dskA_traR: Prokary 20.5 26 0.00055 19.5 -0.5 24 74-97 5-32 (36)
97 PRK10445 endonuclease VIII; Pr 20.4 55 0.0012 26.7 1.2 27 71-97 234-263 (263)
98 PRK03681 hypA hydrogenase nick 20.3 68 0.0015 22.8 1.6 28 71-98 69-96 (114)
99 PF10146 zf-C4H2: Zinc finger- 20.2 29 0.00063 28.0 -0.4 24 72-98 194-217 (230)
No 1
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=100.00 E-value=1.9e-36 Score=284.29 Aligned_cols=153 Identities=51% Similarity=0.974 Sum_probs=143.3
Q ss_pred CCCCChHHHhhcCCCCChhHHhhcccchHHHHHhcccccchhHHHhhhcCCcceeeeecCccccccccccccccccccCc
Q psy12448 1 MKAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGDKAESILLRGDHTRTKIVSTSRVGALSMFVQKKQTCIGCKV 80 (168)
Q Consensus 1 ~~a~~P~~~l~~~l~lD~~YYI~kqiipPL~Rif~~i~~d~~~~w~~~~~~~r~~~~~~~~~~~i~~f~~~s~~C~~C~~ 80 (168)
|||++|+++++++++||++|||+ ||+|||+|||++||+| +.+||. |+|+|...+.++++++|++|++++.+|++|+.
T Consensus 892 ~ra~~p~~~~~~~~~iD~~YYi~-ql~~pl~Ri~~~i~~~-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~ 968 (1054)
T PTZ00166 892 ERAEDPLYVLENNIPIDTQYYLD-QIKNPLLRIFEGVMDN-PDSLFS-GEHTRHITISSSSKGGLSKFVKKQLQCLGCKS 968 (1054)
T ss_pred hhccCHHHHHhcCCCCCHHHHHH-HHHHHHHHHHHHhhcC-HHHHhc-cCccceeeecCCCcccHHHHHhcCcccCCCCC
Confidence 68999999999999999999999 9999999999999999 699986 89999988877888999999988999999999
Q ss_pred ccccCCCCCcCCccc-cCChHHHHHHHHHHHHHHHHHHHHHHHHcccccCCCCCcccCcCCCCCccceecccccccchhH
Q psy12448 81 VLHDTSLSNALCNFC-LAKEKQYYEAENDKYQQLEKKFCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQSCGHNVK 159 (168)
Q Consensus 81 ~~~~~~~~~~lC~~C-~~~~~~~~~~l~~~~~~~e~~~~~~~~~C~~C~~~~~~~~~C~s~dCpv~Y~R~k~~~~l~~~~ 159 (168)
++.. +++|.+| ..++++++..+..+++.+|.++..+|++||+|+|+++.++.|.|.||||||+|.|++++|++++
T Consensus 969 ~~~~----~~~c~~c~~~~~~~~~~~~~~~~~~~e~~~~~~~~~c~~c~g~~~~~~~c~~~dc~i~y~r~k~~~~~~~~~ 1044 (1054)
T PTZ00166 969 VIKE----GALCDNCNQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQ 1044 (1054)
T ss_pred CCCC----CCcCccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCcccCCCCchhheehhHHHHHHHHH
Confidence 9864 5899999 7888899999999999999999999999999999999999999999999999999999998876
Q ss_pred H
Q psy12448 160 R 160 (168)
Q Consensus 160 ~ 160 (168)
.
T Consensus 1045 ~ 1045 (1054)
T PTZ00166 1045 E 1045 (1054)
T ss_pred H
Confidence 4
No 2
>KOG0969|consensus
Probab=100.00 E-value=2.7e-36 Score=267.98 Aligned_cols=156 Identities=59% Similarity=1.074 Sum_probs=147.5
Q ss_pred CCCCChHHHhhcCCCCChhHHhhcccchHHHHHhcccccchhHHHhhhcCCcceeeeecCccccccccccccccccccCc
Q psy12448 1 MKAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGDKAESILLRGDHTRTKIVSTSRVGALSMFVQKKQTCIGCKV 80 (168)
Q Consensus 1 ~~a~~P~~~l~~~l~lD~~YYI~kqiipPL~Rif~~i~~d~~~~w~~~~~~~r~~~~~~~~~~~i~~f~~~s~~C~~C~~ 80 (168)
+|+|||.+|++||++||+.|||++||..||.|||+||.+| +++-+..|+|+|...+.++++|+|+.|.+++.+|++|+.
T Consensus 900 ~rsEDP~fVLenNipiD~~yYL~nQlsKPllrIfePILg~-~~~~l~~g~htR~~~v~~~~~gGl~~F~kk~~tC~gCk~ 978 (1066)
T KOG0969|consen 900 ERSEDPLYVLENNIPIDTRYYLENQLSKPLLRIFEPILGD-AEKELLRGDHTRTITVTTSKVGGLMAFAKKVETCLGCKA 978 (1066)
T ss_pred cCCCCCeEEecCCCCcchHHHHhhhhhhhHHHHhhhhhCc-hhhccccccceeEEEeecccccchhhhhhhccccccccc
Confidence 5899999999999999999999999999999999999998 576677899999999988899999999999999999999
Q ss_pred ccccCCCCCcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHHcccccCCCCCcccCcCCCCCccceecccccccchhH
Q psy12448 81 VLHDTSLSNALCNFCLAKEKQYYEAENDKYQQLEKKFCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQSCGHNVK 159 (168)
Q Consensus 81 ~~~~~~~~~~lC~~C~~~~~~~~~~l~~~~~~~e~~~~~~~~~C~~C~~~~~~~~~C~s~dCpv~Y~R~k~~~~l~~~~ 159 (168)
++..+ ..++|.+|..+.++++.+.....+.+|.+|..+|+.||+|+|+.|+.+.|+|.||||||+|.|+.++|++..
T Consensus 979 ~~~~~--~~~~C~~C~~r~~~lyqk~v~~~~~lee~fsrlWt~Cqrcqgs~h~~vic~~rdCpifymr~kv~keL~~~~ 1055 (1066)
T KOG0969|consen 979 PLRKG--EQALCENCLPRSSELYQKQVSHVNDLEEKFSRLWTECQRCQGSLHEEVICSNRDCPIFYMRQKVRKELQEQV 1055 (1066)
T ss_pred ccccc--cchhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhheeccCCCCchhhHHHHHHHHHHHH
Confidence 99875 456999999999999999999999999999999999999999999999999999999999999999998764
No 3
>KOG0968|consensus
Probab=99.96 E-value=7.1e-31 Score=239.92 Aligned_cols=154 Identities=30% Similarity=0.492 Sum_probs=130.1
Q ss_pred CCCCChHHHhhc-CCCCChhHHhhcccchHHHHHhcccccchhHHHhhhcCCcceeeeec------Cccccccccccccc
Q psy12448 1 MKAEDPIYVLEN-NVPIDSNYYLENQLSKPLIRIFSPILGDKAESILLRGDHTRTKIVST------SRVGALSMFVQKKQ 73 (168)
Q Consensus 1 ~~a~~P~~~l~~-~l~lD~~YYI~kqiipPL~Rif~~i~~d~~~~w~~~~~~~r~~~~~~------~~~~~i~~f~~~s~ 73 (168)
+++++|+++|++ .++||+.|||+|||||||.|+|++||+| +.+|| .++||.++.+. ...++|+.|+. +.
T Consensus 1318 ~~vvsP~efL~~~~~rLn~~YYINk~iiPpL~Rvf~LiG~~-v~~W~--~Empk~krtS~~~te~e~~~~tid~f~t-s~ 1393 (1488)
T KOG0968|consen 1318 SRVVSPEEFLRNPTYRLNTFYYINKQIIPPLDRVFNLIGAD-VDSWY--HEMPKSKRTSLKLTETEKGGITIDTFVT-SK 1393 (1488)
T ss_pred HHhcCHHHHhcCCceeccceeeehhhccchHHHHhhhcccc-hhhHH--HhccccccccccccccccCCceeeEEEe-ec
Confidence 468899999997 4999999999999999999999999999 69999 46666433321 23347899996 89
Q ss_pred cccccCcccccCCCCCcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHHcccccCCC---CCcccCcCCCCCccceecc
Q psy12448 74 TCIGCKVVLHDTSLSNALCNFCLAKEKQYYEAENDKYQQLEKKFCQLWTQCQTCQGSL---HEQVICTSRDCPIFYMRKK 150 (168)
Q Consensus 74 ~C~~C~~~~~~~~~~~~lC~~C~~~~~~~~~~l~~~~~~~e~~~~~~~~~C~~C~~~~---~~~~~C~s~dCpv~Y~R~k 150 (168)
+|..|-..+. +..+|.+|+++|+.+++.+..+.+++|+++.++.++|++|+|.. +..+.|.|++|||||.|.|
T Consensus 1394 hC~~c~~~~~----~~~lC~~Clqnp~~~a~~~v~~~~~l~re~~~L~~iCr~Cs~~~~~~~~~v~C~S~~C~V~y~r~k 1469 (1488)
T KOG0968|consen 1394 HCSSCCSRIG----STQLCSDCLQNPSATALALVQKGRELERERSQLITICRSCSGSSQRDGQVVKCNSLTCPVFYTRSK 1469 (1488)
T ss_pred cccchhcccc----cchhHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccccccccccccCchhhhHHH
Confidence 9999844443 36899999999999999999999999999999999999999954 3478999999999999999
Q ss_pred cccccc-hhHHHh
Q psy12448 151 VQSCGH-NVKRAR 162 (168)
Q Consensus 151 ~~~~l~-~~~~~~ 162 (168)
+++++. ++..++
T Consensus 1470 ~er~l~~qae~~~ 1482 (1488)
T KOG0968|consen 1470 VERYLRAQAETAH 1482 (1488)
T ss_pred HHHHHHhhHHHHH
Confidence 999998 444443
No 4
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=99.87 E-value=4.2e-22 Score=133.26 Aligned_cols=73 Identities=38% Similarity=0.869 Sum_probs=69.0
Q ss_pred ccccCcccccCCCCCcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHHcccccCCCCCcccCcCCCCCccceec
Q psy12448 75 CIGCKVVLHDTSLSNALCNFCLAKEKQYYEAENDKYQQLEKKFCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRK 149 (168)
Q Consensus 75 C~~C~~~~~~~~~~~~lC~~C~~~~~~~~~~l~~~~~~~e~~~~~~~~~C~~C~~~~~~~~~C~s~dCpv~Y~R~ 149 (168)
|++||++++.+ +++||++|+.+++.+++.++.+++..|+++.++|.+|++|+|+.+.++.|+|+||||||+|+
T Consensus 1 C~~C~~~~~~~--~~~lC~~C~~~~~~~~~~l~~~~~~~E~~~~~l~~iC~~C~~~~~~~~~C~s~DCpV~Y~R~ 73 (73)
T PF14260_consen 1 CLVCGAKTQEG--ESPLCSNCRSDPQQTIYNLLSRLRELERRFNELWTICQSCSGSLHEEIECDSLDCPVFYERV 73 (73)
T ss_pred CCCCCCcCCCC--CCCcCcccCcChHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCCCCCcccCCCCCcceeeC
Confidence 89999999874 35999999999999999999999999999999999999999998899999999999999995
No 5
>KOG0970|consensus
Probab=99.09 E-value=1.1e-10 Score=108.58 Aligned_cols=127 Identities=23% Similarity=0.365 Sum_probs=90.9
Q ss_pred CCCCChHHHhhc--CCCCChhHHhhcccchHHHHHhcccccchh---HHHhhhcCCcceeeeecCc----------cccc
Q psy12448 1 MKAEDPIYVLEN--NVPIDSNYYLENQLSKPLIRIFSPILGDKA---ESILLRGDHTRTKIVSTSR----------VGAL 65 (168)
Q Consensus 1 ~~a~~P~~~l~~--~l~lD~~YYI~kqiipPL~Rif~~i~~d~~---~~w~~~~~~~r~~~~~~~~----------~~~i 65 (168)
+||++|.++..+ +|.||+.|||.+||.||++|+.++|.|.++ .+|| |..++..+....+ -.++
T Consensus 1167 ~RAyh~~e~~~~~~~l~iD~~YYLa~QIhPvV~Rlve~Iegt~a~riae~L--GlDstkyr~~~~~q~~~~a~s~~~s~~ 1244 (1429)
T KOG0970|consen 1167 ERAYHPDEVMPDEDNLAIDYNYYLAQQIHPVVERLVEPIEGTDAVRIAECL--GLDSTKYRRHEGNQKENSALSPDESTL 1244 (1429)
T ss_pred hcccChHhhCccCcceeechhhHhhhhcchhHHHHhhhhcccCHHHHHHHh--CCCchhhhhhhcchhhhhhhCCCcchh
Confidence 589999999974 499999999999999999999999998422 3676 7666554321100 0111
Q ss_pred ---cccc---cccccccccCcccccC------C------CCCcCCccccCCh----HHHHHHHHHHHHHHHHHHHHHHHH
Q psy12448 66 ---SMFV---QKKQTCIGCKVVLHDT------S------LSNALCNFCLAKE----KQYYEAENDKYQQLEKKFCQLWTQ 123 (168)
Q Consensus 66 ---~~f~---~~s~~C~~C~~~~~~~------~------~~~~lC~~C~~~~----~~~~~~l~~~~~~~e~~~~~~~~~ 123 (168)
.+|+ .....|+.|+.+.... + ....-|..|...+ ..+..++..+++..-.+|+..|.+
T Consensus 1245 td~~~~~~ce~~~l~CptC~~~~~~~~~~~~~s~~~~~~~l~~~Ca~Cq~~~~~~~~~i~nq~~~qir~fV~~yy~g~lv 1324 (1429)
T KOG0970|consen 1245 TDVERFKDCEPLTLRCPTCSTENSRAFAVDKVSEMSRKEVLSLYCARCQQEPIESPASITNQVERQIRCFVSLYYLGWLV 1324 (1429)
T ss_pred cchhhhccccceEEECCCCCCcccccccccCcccchhhhHhhhcChhhhcCCccchHHHHHHHHHHHHHHHHHHhhhhee
Confidence 2442 1368999998765532 0 0133488998766 355666778889999999999999
Q ss_pred cc--cccC
Q psy12448 124 CQ--TCQG 129 (168)
Q Consensus 124 C~--~C~~ 129 (168)
|. +|..
T Consensus 1325 Cdd~tC~~ 1332 (1429)
T KOG0970|consen 1325 CDDPTCGF 1332 (1429)
T ss_pred ecCccccc
Confidence 98 7776
No 6
>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006134 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [].; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 1NOY_A 1NOZ_B 2CW7_A 2CW8_A 1WNS_A 2XHB_A 2VWK_A 2VWJ_A 1TGO_A ....
Probab=98.17 E-value=8.6e-07 Score=77.84 Aligned_cols=40 Identities=55% Similarity=0.870 Sum_probs=36.3
Q ss_pred CCCCChHHHhhcCCCCChhHHhhcccchHHHHHhcccccc
Q psy12448 1 MKAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGD 40 (168)
Q Consensus 1 ~~a~~P~~~l~~~l~lD~~YYI~kqiipPL~Rif~~i~~d 40 (168)
+++++|+++.+++++||++|||++||+|||+|+|++++.+
T Consensus 411 ~~~~~~~~~~~~~~~iD~~yYi~~ql~~pl~ril~~~~~~ 450 (466)
T PF00136_consen 411 ERAEDPEYVKENNLPIDYEYYIEKQLLPPLERILEPLGWN 450 (466)
T ss_dssp CSEETTTHHHHTTS-BSHHHHHHTTHHHHHHHHHHTCTTT
T ss_pred hhccChhhhhccCCCcchHHHHhhccHHHHHHHHHHhcCC
Confidence 5788999999989999999999999999999999999886
No 7
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=98.15 E-value=9.6e-07 Score=82.34 Aligned_cols=45 Identities=42% Similarity=0.616 Sum_probs=40.3
Q ss_pred CCCCChHHHhhcCCCCChhHHhhcccchHHHHHhcccccchhHHHh
Q psy12448 1 MKAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGDKAESIL 46 (168)
Q Consensus 1 ~~a~~P~~~l~~~l~lD~~YYI~kqiipPL~Rif~~i~~d~~~~w~ 46 (168)
+||+.|..+.+++++||++||++|||+||++||+++||++ ..+|.
T Consensus 736 ~ra~~~~~~~~~~~~iD~~YY~~~Ql~~~~~ril~~i~~~-~~~~~ 780 (792)
T COG0417 736 ERAEPPELVDEENSPIDYEYYITKQLLPALERILEPIGGN-FAELK 780 (792)
T ss_pred ccccCceecccccccCCHHHHHhccchHHHHHHHHHhccc-Hhhhc
Confidence 5788888888888999999999999999999999999998 46655
No 8
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=95.45 E-value=0.015 Score=45.39 Aligned_cols=59 Identities=19% Similarity=0.373 Sum_probs=40.7
Q ss_pred cccccccCcccccC----------CCCCcCCccccCCh--HHHHHHHHHHHHHHHHHHHHHHHHccc--ccCC
Q psy12448 72 KQTCIGCKVVLHDT----------SLSNALCNFCLAKE--KQYYEAENDKYQQLEKKFCQLWTQCQT--CQGS 130 (168)
Q Consensus 72 s~~C~~C~~~~~~~----------~~~~~lC~~C~~~~--~~~~~~l~~~~~~~e~~~~~~~~~C~~--C~~~ 130 (168)
..+|+.|++..... ...+..|++|.... ..+..+|...+|...++|++.|.+|.. |...
T Consensus 18 ~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~~~~~l~Nql~l~iR~~i~~YY~gwl~Cdd~~C~~~ 90 (188)
T PF08996_consen 18 KLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPLSPASLVNQLELQIREHISRYYEGWLVCDDPTCGNR 90 (188)
T ss_dssp EEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B--HHHHHHHHHHHHHHHHHHHHH--CCCCTCCCHHC
T ss_pred EeECCCCCCCccccccccCCccccccCcCcCCCCCCcCCHHHHHHHHHHHHHHHHHHHHHhCceeCcccccCc
Confidence 67999999887642 12478899998753 367778889999999999999999996 9863
No 9
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.96 E-value=0.18 Score=25.99 Aligned_cols=22 Identities=23% Similarity=0.611 Sum_probs=17.9
Q ss_pred cccccCcccccCCCCCcCCccccCC
Q psy12448 74 TCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 74 ~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
.|..||.++.. +...|++|..+
T Consensus 1 ~Cp~CG~~~~~---~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIED---DAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCC---cCcchhhhCCc
Confidence 38899999987 57899999764
No 10
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=88.45 E-value=0.28 Score=25.84 Aligned_cols=24 Identities=25% Similarity=0.562 Sum_probs=19.1
Q ss_pred cccccccCcccccCCCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
...|+.||..+.. +...|++|...
T Consensus 2 ~~~Cp~Cg~~~~~---~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDP---DAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCCc---ccccChhhCCC
Confidence 3589999998776 57899999764
No 11
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=85.74 E-value=0.49 Score=25.11 Aligned_cols=24 Identities=25% Similarity=0.551 Sum_probs=19.2
Q ss_pred ccccccCcccccCCCCCcCCccccCCh
Q psy12448 73 QTCIGCKVVLHDTSLSNALCNFCLAKE 99 (168)
Q Consensus 73 ~~C~~C~~~~~~~~~~~~lC~~C~~~~ 99 (168)
.+|+.|++.+.. +...|+.|..+.
T Consensus 1 K~CP~C~~~V~~---~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPE---SAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchh---hcCcCCCCCCCC
Confidence 379999999886 568899998654
No 12
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=85.11 E-value=1.6 Score=27.77 Aligned_cols=24 Identities=17% Similarity=0.548 Sum_probs=19.5
Q ss_pred cccccccCcccccCCCCCcCCc-cccCC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCN-FCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~-~C~~~ 98 (168)
-.+|++||++++. +...|+ .|+.+
T Consensus 3 HkHC~~CG~~Ip~---~~~fCS~~C~~~ 27 (59)
T PF09889_consen 3 HKHCPVCGKPIPP---DESFCSPKCREE 27 (59)
T ss_pred CCcCCcCCCcCCc---chhhhCHHHHHH
Confidence 4699999999987 578995 68754
No 13
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=76.57 E-value=7.8 Score=24.67 Aligned_cols=22 Identities=18% Similarity=0.629 Sum_probs=17.2
Q ss_pred cccccccCcccccCCCCCcCCcc-cc
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNF-CL 96 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~-C~ 96 (168)
-.+|++||+.++. +..+|++ |+
T Consensus 8 H~HC~VCg~aIp~---de~~CSe~C~ 30 (64)
T COG4068 8 HRHCVVCGKAIPP---DEQVCSEECG 30 (64)
T ss_pred CccccccCCcCCC---ccchHHHHHH
Confidence 5799999999987 5678853 54
No 14
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=74.04 E-value=3.4 Score=30.78 Aligned_cols=26 Identities=23% Similarity=0.585 Sum_probs=21.8
Q ss_pred ccccccccCcccccCCCCCcCCccccCChH
Q psy12448 71 KKQTCIGCKVVLHDTSLSNALCNFCLAKEK 100 (168)
Q Consensus 71 ~s~~C~~C~~~~~~~~~~~~lC~~C~~~~~ 100 (168)
....|-.||.++.. |-+|++|..+-.
T Consensus 80 l~~~CE~CG~~I~~----Gr~C~~C~~~l~ 105 (137)
T TIGR03826 80 LGYPCERCGTSIRE----GRLCDSCAGELK 105 (137)
T ss_pred CcCcccccCCcCCC----CCccHHHHHHHH
Confidence 57899999999986 689999987643
No 15
>PRK00420 hypothetical protein; Validated
Probab=72.57 E-value=2.4 Score=30.51 Aligned_cols=27 Identities=15% Similarity=0.303 Sum_probs=20.3
Q ss_pred ccccccccCcccccCCCCCcCCccccC
Q psy12448 71 KKQTCIGCKVVLHDTSLSNALCNFCLA 97 (168)
Q Consensus 71 ~s~~C~~C~~~~~~~~~~~~lC~~C~~ 97 (168)
.+.+|+.||.++..-.....+|+.|..
T Consensus 22 l~~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred ccCCCCCCCCcceecCCCceECCCCCC
Confidence 478999999988751123588999976
No 16
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=72.02 E-value=1.4 Score=43.44 Aligned_cols=23 Identities=17% Similarity=0.476 Sum_probs=18.5
Q ss_pred cccccccCcccccCCCCCcCCccccCCh
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAKE 99 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~~ 99 (168)
...|+.||+.+.. ..|++|.+..
T Consensus 667 ~rkCPkCG~~t~~-----~fCP~CGs~t 689 (1337)
T PRK14714 667 RRRCPSCGTETYE-----NRCPDCGTHT 689 (1337)
T ss_pred EEECCCCCCcccc-----ccCcccCCcC
Confidence 4789999998754 5999998773
No 17
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=71.15 E-value=2.3 Score=27.20 Aligned_cols=32 Identities=22% Similarity=0.188 Sum_probs=23.5
Q ss_pred cccccccccccccCccccc-CCCCCcCCccccCC
Q psy12448 66 SMFVQKKQTCIGCKVVLHD-TSLSNALCNFCLAK 98 (168)
Q Consensus 66 ~~f~~~s~~C~~C~~~~~~-~~~~~~lC~~C~~~ 98 (168)
+.++. |.+|+.||..... .......|++|...
T Consensus 23 ~~~~T-Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 23 DEAYT-SQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CCCCC-ccCccCcccccccccccceEEcCCCCCE
Confidence 44554 8999999998776 22357899999864
No 18
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=68.78 E-value=3.3 Score=29.54 Aligned_cols=29 Identities=24% Similarity=0.456 Sum_probs=21.7
Q ss_pred cccccccCcccccCCCCCcCCccccCChH
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAKEK 100 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~~~ 100 (168)
+.+|+.||+++-.=+.+.++|+.|+...+
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGTEFP 37 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCCccC
Confidence 68999999987641125688999987644
No 19
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=68.07 E-value=2.5 Score=26.46 Aligned_cols=28 Identities=21% Similarity=0.293 Sum_probs=22.0
Q ss_pred cccccccCcccccCCCCCcCCccccCChH
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAKEK 100 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~~~ 100 (168)
...|..||+++..+ .+..+|+.|...-.
T Consensus 5 ~~~C~~Cg~~~~~~-dDiVvCp~CgapyH 32 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG-DDIVVCPECGAPYH 32 (54)
T ss_pred CccChhhCCcccCC-CCEEECCCCCCccc
Confidence 57899999999643 26899999987543
No 20
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=66.05 E-value=6 Score=21.95 Aligned_cols=25 Identities=16% Similarity=0.279 Sum_probs=16.7
Q ss_pred cccccCcccccCCCCCcCCccccCC
Q psy12448 74 TCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 74 ~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
.|..||.....+..+..-|+.|..+
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCe
Confidence 4778888777654567888888754
No 21
>PF12773 DZR: Double zinc ribbon
Probab=64.52 E-value=3.1 Score=24.87 Aligned_cols=21 Identities=24% Similarity=0.573 Sum_probs=10.2
Q ss_pred ccccCcccccCCCCCcCCccccCC
Q psy12448 75 CIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 75 C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
|..|++++.. +...|+.|...
T Consensus 1 Cp~Cg~~~~~---~~~fC~~CG~~ 21 (50)
T PF12773_consen 1 CPHCGTPNPD---DAKFCPHCGTP 21 (50)
T ss_pred CCCcCCcCCc---cccCChhhcCC
Confidence 4455555443 34455555544
No 22
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=63.47 E-value=5.3 Score=22.56 Aligned_cols=27 Identities=22% Similarity=0.539 Sum_probs=12.7
Q ss_pred cccccccCcccccC----CCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDT----SLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~----~~~~~lC~~C~~~ 98 (168)
...|..|+++.... ..+-.||..|+..
T Consensus 3 ~~~C~eC~~~f~dSyL~~~F~~~VCD~CRD~ 33 (34)
T PF01286_consen 3 YPKCDECGKPFMDSYLLNNFDLPVCDKCRDK 33 (34)
T ss_dssp -EE-TTT--EES-SSCCCCTS-S--TTT-ST
T ss_pred CchHhHhCCHHHHHHHHHhCCccccccccCC
Confidence 35788998887653 3467899999753
No 23
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=62.80 E-value=5 Score=23.90 Aligned_cols=26 Identities=19% Similarity=0.206 Sum_probs=18.9
Q ss_pred ccccccCcccccCCCCCcCCccccCC
Q psy12448 73 QTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 73 ~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
-.|..||........+..-|++|..+
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCce
Confidence 46888988776543467889988764
No 24
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=61.86 E-value=3.1 Score=33.04 Aligned_cols=16 Identities=31% Similarity=0.455 Sum_probs=12.3
Q ss_pred ccccccccccCccccc
Q psy12448 69 VQKKQTCIGCKVVLHD 84 (168)
Q Consensus 69 ~~~s~~C~~C~~~~~~ 84 (168)
|.++.+|++|++..+.
T Consensus 2 y~k~~~CPvC~~~F~~ 17 (214)
T PF09986_consen 2 YDKKITCPVCGKEFKT 17 (214)
T ss_pred CCCceECCCCCCeeee
Confidence 3467899999888774
No 25
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=57.25 E-value=4.6 Score=29.87 Aligned_cols=26 Identities=19% Similarity=0.492 Sum_probs=20.6
Q ss_pred ccccccccCcccccCCCCCcCCccccC
Q psy12448 71 KKQTCIGCKVVLHDTSLSNALCNFCLA 97 (168)
Q Consensus 71 ~s~~C~~C~~~~~~~~~~~~lC~~C~~ 97 (168)
...+|+.||.++-.++ ...+|+.|..
T Consensus 27 L~~hCp~Cg~PLF~Kd-G~v~CPvC~~ 52 (131)
T COG1645 27 LAKHCPKCGTPLFRKD-GEVFCPVCGY 52 (131)
T ss_pred HHhhCcccCCcceeeC-CeEECCCCCc
Confidence 4789999999997642 2488999983
No 26
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=54.37 E-value=9.4 Score=28.09 Aligned_cols=29 Identities=14% Similarity=0.123 Sum_probs=22.1
Q ss_pred cccccccCcccccCCCCCcCCccccCChH
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAKEK 100 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~~~ 100 (168)
+..|+.||+++-.=+.+.++|+.|....+
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQFP 37 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCccC
Confidence 68999999987642236799999987644
No 27
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=54.15 E-value=8 Score=22.84 Aligned_cols=27 Identities=15% Similarity=0.461 Sum_probs=17.1
Q ss_pred cccccccCcccccCCC-CCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDTSL-SNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~-~~~lC~~C~~~ 98 (168)
...|..||..+..... ....|+.|...
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 3578888887754311 25678888753
No 28
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=52.04 E-value=5.4 Score=24.49 Aligned_cols=25 Identities=24% Similarity=0.430 Sum_probs=18.1
Q ss_pred cccccCcccccC----CCCCcCCccccCC
Q psy12448 74 TCIGCKVVLHDT----SLSNALCNFCLAK 98 (168)
Q Consensus 74 ~C~~C~~~~~~~----~~~~~lC~~C~~~ 98 (168)
.|..||+++..- -.++.||++|...
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~K 29 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKK 29 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHH
Confidence 488898876531 2367999999865
No 29
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=51.92 E-value=4.8 Score=38.32 Aligned_cols=23 Identities=17% Similarity=0.397 Sum_probs=0.0
Q ss_pred cccccccCcccccCCCCCcCCccccCCh
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAKE 99 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~~ 99 (168)
...|..||..+.. ..|+.|....
T Consensus 655 ~r~Cp~Cg~~t~~-----~~Cp~CG~~T 677 (900)
T PF03833_consen 655 RRRCPKCGKETFY-----NRCPECGSHT 677 (900)
T ss_dssp ----------------------------
T ss_pred cccCcccCCcchh-----hcCcccCCcc
Confidence 5688889888764 6788887653
No 30
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=51.16 E-value=27 Score=22.13 Aligned_cols=35 Identities=17% Similarity=0.185 Sum_probs=26.7
Q ss_pred cCCccccCChHHHHHHHHHHHHHHHHHHHHHHHHc
Q psy12448 90 ALCNFCLAKEKQYYEAENDKYQQLEKKFCQLWTQC 124 (168)
Q Consensus 90 ~lC~~C~~~~~~~~~~l~~~~~~~e~~~~~~~~~C 124 (168)
.+|..|+.|-++.-..|+.+...++.-+......|
T Consensus 5 lVCsTCGrDlSeeRy~Lli~~~~L~~Vl~~v~~~C 39 (63)
T PHA03082 5 LVCSTCGRDLSEERYRLLIKKKSLKKVLRTVKNSC 39 (63)
T ss_pred eeecccCcchhHHHHHHHHHHhhHHHHHHHhhccc
Confidence 68999999998888888877776666666555554
No 31
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=50.16 E-value=9.6 Score=22.36 Aligned_cols=26 Identities=19% Similarity=0.384 Sum_probs=18.4
Q ss_pred ccccccccCcccccCCCCCcCCcccc
Q psy12448 71 KKQTCIGCKVVLHDTSLSNALCNFCL 96 (168)
Q Consensus 71 ~s~~C~~C~~~~~~~~~~~~lC~~C~ 96 (168)
...+|+.|+.++-.......+|..|.
T Consensus 16 L~~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred hcCccCCCCCeeEEecCCCEECCCCC
Confidence 57899999988875212357888873
No 32
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=47.85 E-value=30 Score=21.91 Aligned_cols=35 Identities=17% Similarity=0.155 Sum_probs=25.9
Q ss_pred cCCccccCChHHHHHHHHHHHHHHHHHHHHHHHHc
Q psy12448 90 ALCNFCLAKEKQYYEAENDKYQQLEKKFCQLWTQC 124 (168)
Q Consensus 90 ~lC~~C~~~~~~~~~~l~~~~~~~e~~~~~~~~~C 124 (168)
.+|+.|+.|-++.-..|+.+...+..-+......|
T Consensus 5 lvCSTCGrDlSeeRy~Lli~~~~Lk~Vl~~v~n~C 39 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYRLLIKEMSLKKVLRTVKNSC 39 (63)
T ss_pred eeecccCCcchHHHHHHHHHHhhHHHHHHHhhccc
Confidence 68999999988877777777666666665555444
No 33
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=47.47 E-value=6.9 Score=29.12 Aligned_cols=30 Identities=20% Similarity=0.563 Sum_probs=21.9
Q ss_pred cccccccCcccccCCCCCcCCccccCChHHHH
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAKEKQYY 103 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~~~~~~ 103 (168)
...|..||+....+ ...+|++|.......+
T Consensus 3 l~nC~~CgklF~~~--~~~iCp~C~~~~e~~f 32 (137)
T TIGR03826 3 LANCPKCGRLFVKT--GRDVCPSCYEEEEREF 32 (137)
T ss_pred Cccccccchhhhhc--CCccCHHHhHHHHHHH
Confidence 35899999988863 3579999987544333
No 34
>PRK04023 DNA polymerase II large subunit; Validated
Probab=47.06 E-value=6.1 Score=38.39 Aligned_cols=22 Identities=23% Similarity=0.596 Sum_probs=17.3
Q ss_pred cccccccCcccccCCCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
...|..||..+.. ..|++|...
T Consensus 626 ~RfCpsCG~~t~~-----frCP~CG~~ 647 (1121)
T PRK04023 626 RRKCPSCGKETFY-----RRCPFCGTH 647 (1121)
T ss_pred CccCCCCCCcCCc-----ccCCCCCCC
Confidence 5689999988643 689999876
No 35
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=46.92 E-value=12 Score=24.18 Aligned_cols=24 Identities=21% Similarity=0.704 Sum_probs=18.8
Q ss_pred cccccccCcccccCCCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
-..|..|+..++. +.-+|+.|.+.
T Consensus 4 ~kAC~~Ck~l~~~---d~e~CP~Cgs~ 27 (64)
T COG2093 4 EKACKNCKRLTPE---DTEICPVCGST 27 (64)
T ss_pred hHHHhhccccCCC---CCccCCCCCCc
Confidence 3578899988876 56789999875
No 36
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=46.53 E-value=29 Score=26.79 Aligned_cols=46 Identities=13% Similarity=0.273 Sum_probs=31.0
Q ss_pred ccccccCcccccC--CCCCcCCccccC-----ChHHHHHHHHHHHHHHHHHHH
Q psy12448 73 QTCIGCKVVLHDT--SLSNALCNFCLA-----KEKQYYEAENDKYQQLEKKFC 118 (168)
Q Consensus 73 ~~C~~C~~~~~~~--~~~~~lC~~C~~-----~~~~~~~~l~~~~~~~e~~~~ 118 (168)
-.|+.|+...+.- ...+-.|+.|.. +....+..|..++..++..+.
T Consensus 118 Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~~l~~~~~ 170 (178)
T PRK06266 118 FFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEYDNSELIKELKEQIKELEEELK 170 (178)
T ss_pred EECCCCCcEEeHHHHhhcCCcCCCCCCCCeecccHHHHHHHHHHHHHHHHHhc
Confidence 3799999887642 113688999987 455666666677776666543
No 37
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=46.19 E-value=6.8 Score=21.44 Aligned_cols=26 Identities=15% Similarity=0.217 Sum_probs=12.2
Q ss_pred ccccccCcccccCCCCCcCCccccCC
Q psy12448 73 QTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 73 ~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
..|+.|+...+-.++...+|+.|...
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCPECGHE 28 (30)
T ss_dssp ---TTT-----EE-SSSEEETTTTEE
T ss_pred CCCCCCCCcceeccCCEEeCCccccc
Confidence 36888877665433457889999753
No 38
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=45.96 E-value=11 Score=29.01 Aligned_cols=21 Identities=29% Similarity=0.542 Sum_probs=14.0
Q ss_pred ccccCcccccCCCCCcCCccccCC
Q psy12448 75 CIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 75 C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
|..|++.+.. ...+|.+|...
T Consensus 1 C~~C~~~~~~---~~~~C~~C~~~ 21 (190)
T TIGR00201 1 CSLCGRPYQS---VHALCRQCGSW 21 (190)
T ss_pred CCcccccccc---ccCCchhhCCc
Confidence 7778877654 24678888653
No 39
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=43.51 E-value=6.6 Score=22.09 Aligned_cols=23 Identities=22% Similarity=0.431 Sum_probs=11.5
Q ss_pred cccccCcccccC-----CCCCcCCcccc
Q psy12448 74 TCIGCKVVLHDT-----SLSNALCNFCL 96 (168)
Q Consensus 74 ~C~~C~~~~~~~-----~~~~~lC~~C~ 96 (168)
-|+.||.++... +....+|+.|.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTT
T ss_pred ccccccChhhhhcCCCCCccceECCCCC
Confidence 478888887642 12357888885
No 40
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=43.10 E-value=18 Score=18.79 Aligned_cols=22 Identities=18% Similarity=0.397 Sum_probs=10.5
Q ss_pred ccccCcccccCC-CCCcCCcccc
Q psy12448 75 CIGCKVVLHDTS-LSNALCNFCL 96 (168)
Q Consensus 75 C~~C~~~~~~~~-~~~~lC~~C~ 96 (168)
|..|+..+.... ...-.|++|.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 455655554321 1235566664
No 41
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=42.66 E-value=8.6 Score=27.69 Aligned_cols=20 Identities=25% Similarity=0.399 Sum_probs=9.4
Q ss_pred ccccCcccccCCCCCcCCccccC
Q psy12448 75 CIGCKVVLHDTSLSNALCNFCLA 97 (168)
Q Consensus 75 C~~C~~~~~~~~~~~~lC~~C~~ 97 (168)
|++||..+.- ...-|++|..
T Consensus 1 CPvCg~~l~v---t~l~C~~C~t 20 (113)
T PF09862_consen 1 CPVCGGELVV---TRLKCPSCGT 20 (113)
T ss_pred CCCCCCceEE---EEEEcCCCCC
Confidence 5555555443 2344555543
No 42
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=40.79 E-value=15 Score=25.95 Aligned_cols=29 Identities=21% Similarity=0.383 Sum_probs=19.0
Q ss_pred cccccccCcccccC-------CCCCcCCccccCChH
Q psy12448 72 KQTCIGCKVVLHDT-------SLSNALCNFCLAKEK 100 (168)
Q Consensus 72 s~~C~~C~~~~~~~-------~~~~~lC~~C~~~~~ 100 (168)
.-+|+.|+...... +.-.++|.+|....+
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 34899998765431 113588999987544
No 43
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.61 E-value=14 Score=22.59 Aligned_cols=27 Identities=15% Similarity=0.454 Sum_probs=19.2
Q ss_pred cccccccCccccc-CCCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHD-TSLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~-~~~~~~lC~~C~~~ 98 (168)
.-.|..||..+.. ....+.-|+.|..+
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 5679999988762 12357889999764
No 44
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=39.75 E-value=11 Score=20.42 Aligned_cols=26 Identities=15% Similarity=0.226 Sum_probs=13.5
Q ss_pred cccccccCcccccC-CCCCcCCccccC
Q psy12448 72 KQTCIGCKVVLHDT-SLSNALCNFCLA 97 (168)
Q Consensus 72 s~~C~~C~~~~~~~-~~~~~lC~~C~~ 97 (168)
..-|..||.++... .+-..+|++|..
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 35688898887753 224578888864
No 45
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=39.73 E-value=19 Score=28.02 Aligned_cols=24 Identities=25% Similarity=0.809 Sum_probs=20.7
Q ss_pred cccccccCcccccCCCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
..+|.+|+..++. ...+|+.|+.+
T Consensus 139 ~~rC~GC~~~f~~---~~~~Cp~CG~~ 162 (177)
T COG1439 139 RLRCHGCKRIFPE---PKDFCPICGSP 162 (177)
T ss_pred eEEEecCceecCC---CCCcCCCCCCc
Confidence 6899999999984 57899999876
No 46
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=38.26 E-value=35 Score=18.63 Aligned_cols=26 Identities=19% Similarity=0.454 Sum_probs=18.3
Q ss_pred cccccCcccccCCCCCcCCccccCChH
Q psy12448 74 TCIGCKVVLHDTSLSNALCNFCLAKEK 100 (168)
Q Consensus 74 ~C~~C~~~~~~~~~~~~lC~~C~~~~~ 100 (168)
.|.+||-..... .....|+.|.....
T Consensus 3 ~C~~CGy~y~~~-~~~~~CP~Cg~~~~ 28 (33)
T cd00350 3 VCPVCGYIYDGE-EAPWVCPVCGAPKD 28 (33)
T ss_pred ECCCCCCEECCC-cCCCcCcCCCCcHH
Confidence 689999876642 13578999987543
No 47
>PRK12496 hypothetical protein; Provisional
Probab=37.52 E-value=24 Score=26.91 Aligned_cols=26 Identities=23% Similarity=0.746 Sum_probs=19.5
Q ss_pred cccccccCcccccCCCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
...|.+|++..+.+ .....|+.|++.
T Consensus 127 ~~~C~gC~~~~~~~-~~~~~C~~CG~~ 152 (164)
T PRK12496 127 RKVCKGCKKKYPED-YPDDVCEICGSP 152 (164)
T ss_pred eEECCCCCccccCC-CCCCcCCCCCCh
Confidence 46799999998642 134689999875
No 48
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=36.73 E-value=36 Score=18.85 Aligned_cols=27 Identities=19% Similarity=0.396 Sum_probs=18.5
Q ss_pred ccccccCcccccCCCCCcCCccccCChH
Q psy12448 73 QTCIGCKVVLHDTSLSNALCNFCLAKEK 100 (168)
Q Consensus 73 ~~C~~C~~~~~~~~~~~~lC~~C~~~~~ 100 (168)
-.|.+||....+. .....|+.|.....
T Consensus 3 ~~C~~CG~i~~g~-~~p~~CP~Cg~~~~ 29 (34)
T cd00729 3 WVCPVCGYIHEGE-EAPEKCPICGAPKE 29 (34)
T ss_pred EECCCCCCEeECC-cCCCcCcCCCCchH
Confidence 4799999876542 12468999987643
No 49
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=36.57 E-value=24 Score=19.98 Aligned_cols=25 Identities=20% Similarity=0.547 Sum_probs=17.0
Q ss_pred ccccccCcccccC---CCCCcCCccccC
Q psy12448 73 QTCIGCKVVLHDT---SLSNALCNFCLA 97 (168)
Q Consensus 73 ~~C~~C~~~~~~~---~~~~~lC~~C~~ 97 (168)
..|..||...+.. +....+|+.|..
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCC
Confidence 3688888877642 124578998876
No 50
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=36.19 E-value=17 Score=25.43 Aligned_cols=20 Identities=20% Similarity=0.566 Sum_probs=16.5
Q ss_pred cccccccCcccccCCCCCcCCcccc
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCL 96 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~ 96 (168)
...|-.||.++.+ .+|..|.
T Consensus 80 ~~~C~~CG~pss~-----~iC~~C~ 99 (104)
T TIGR00269 80 LRRCERCGEPTSG-----RICKACK 99 (104)
T ss_pred CCcCCcCcCcCCc-----cccHhhh
Confidence 4689999999764 7999995
No 51
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=35.72 E-value=26 Score=21.72 Aligned_cols=21 Identities=19% Similarity=0.400 Sum_probs=17.0
Q ss_pred cccccccCcccccCCCCCcCCcccc
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCL 96 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~ 96 (168)
...|..||+.... .-+|.+|+
T Consensus 26 l~~c~~cg~~~~~----H~vc~~cG 46 (56)
T PF01783_consen 26 LVKCPNCGEPKLP----HRVCPSCG 46 (56)
T ss_dssp EEESSSSSSEEST----TSBCTTTB
T ss_pred eeeeccCCCEecc----cEeeCCCC
Confidence 5789999987664 58999995
No 52
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=35.64 E-value=18 Score=21.23 Aligned_cols=22 Identities=27% Similarity=0.853 Sum_probs=10.6
Q ss_pred cccccCCCCCcccCcCCCCCcc
Q psy12448 124 CQTCQGSLHEQVICTSRDCPIF 145 (168)
Q Consensus 124 C~~C~~~~~~~~~C~s~dCpv~ 145 (168)
|..|..-....+.|.+.||++-
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r 22 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVR 22 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--E
T ss_pred CcccchhHeeeccCCCCccCch
Confidence 5667775566789999999984
No 53
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=33.77 E-value=13 Score=36.04 Aligned_cols=22 Identities=18% Similarity=0.292 Sum_probs=18.4
Q ss_pred cccccccCcccccCCCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
...|+.||+.+.. ..|+.|...
T Consensus 625 ~RKCPkCG~yTlk-----~rCP~CG~~ 646 (1095)
T TIGR00354 625 IRKCPQCGKESFW-----LKCPVCGEL 646 (1095)
T ss_pred EEECCCCCccccc-----ccCCCCCCc
Confidence 5689999999765 789999876
No 54
>PHA02942 putative transposase; Provisional
Probab=33.45 E-value=25 Score=30.45 Aligned_cols=33 Identities=12% Similarity=0.218 Sum_probs=22.3
Q ss_pred ccccccccccccccCcccccCCCCCcCCccccCC
Q psy12448 65 LSMFVQKKQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 65 i~~f~~~s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
++.+|. |.+|+.||......+.....|++|+..
T Consensus 319 V~p~yT-Sq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 319 VNPSYS-SVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred ECCCCC-CccCCCCCCccCcCCCCEEECCCCCCE
Confidence 345664 899999998654311135789999863
No 55
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=32.55 E-value=40 Score=20.42 Aligned_cols=31 Identities=16% Similarity=0.350 Sum_probs=14.0
Q ss_pred cccccCcccccCCCCCcCCccccCChHHHHHHHHHHHHHHHHH
Q psy12448 74 TCIGCKVVLHDTSLSNALCNFCLAKEKQYYEAENDKYQQLEKK 116 (168)
Q Consensus 74 ~C~~C~~~~~~~~~~~~lC~~C~~~~~~~~~~l~~~~~~~e~~ 116 (168)
.|++|+.++.. .....++-.+..+++....+
T Consensus 22 ~CPlC~r~l~~------------e~~~~li~~~~~~i~~~~~~ 52 (54)
T PF04423_consen 22 CCPLCGRPLDE------------EHRQELIKKYKSEIEELPEK 52 (54)
T ss_dssp E-TTT--EE-H------------HHHHHHHHHHHHHHHHHHH-
T ss_pred cCCCCCCCCCH------------HHHHHHHHHHHHHHHhhhhc
Confidence 77777777654 12245555555555554443
No 56
>PRK09401 reverse gyrase; Reviewed
Probab=31.42 E-value=37 Score=33.84 Aligned_cols=26 Identities=27% Similarity=0.553 Sum_probs=20.2
Q ss_pred cccccccCcccccC-CCCCcCCccccC
Q psy12448 72 KQTCIGCKVVLHDT-SLSNALCNFCLA 97 (168)
Q Consensus 72 s~~C~~C~~~~~~~-~~~~~lC~~C~~ 97 (168)
...|++||..+... -..|..|..|+.
T Consensus 7 ~~~cpnc~g~i~~~rl~~g~~c~~cl~ 33 (1176)
T PRK09401 7 KNSCPNCGGDISDERLEKGLPCEKCLP 33 (1176)
T ss_pred cccCCCCCCcCcHhHHhcCCcChhhCC
Confidence 47899999988752 114789999997
No 57
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=31.42 E-value=40 Score=25.41 Aligned_cols=38 Identities=18% Similarity=0.190 Sum_probs=22.6
Q ss_pred cccccCcccccC--CCCCcCCccccC-----ChHHHHHHHHHHHH
Q psy12448 74 TCIGCKVVLHDT--SLSNALCNFCLA-----KEKQYYEAENDKYQ 111 (168)
Q Consensus 74 ~C~~C~~~~~~~--~~~~~lC~~C~~-----~~~~~~~~l~~~~~ 111 (168)
.|+.|+...+.- ...+-.|+.|.. +.+..+..|..++.
T Consensus 111 ~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~~dn~~~i~~l~~~i~ 155 (158)
T TIGR00373 111 ICPNMCVRFTFNEAMELNFTCPRCGAMLDYLDNSEAIEKLEEQIK 155 (158)
T ss_pred ECCCCCcEeeHHHHHHcCCcCCCCCCEeeeccCHHHHHHHHHHHH
Confidence 689998877642 013578999976 34444444444433
No 58
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=30.65 E-value=35 Score=19.05 Aligned_cols=26 Identities=19% Similarity=0.301 Sum_probs=16.5
Q ss_pred ccccccCcccccC----CCCCcCCccccCC
Q psy12448 73 QTCIGCKVVLHDT----SLSNALCNFCLAK 98 (168)
Q Consensus 73 ~~C~~C~~~~~~~----~~~~~lC~~C~~~ 98 (168)
-.|..||...... ......|+.|...
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 4788888855421 1235678888863
No 59
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=30.40 E-value=18 Score=20.16 Aligned_cols=24 Identities=25% Similarity=0.584 Sum_probs=13.1
Q ss_pred cccccccCcccccCCCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
..+|..||...-. ...+|+.|.+.
T Consensus 11 ~~rC~~Cg~~~~p---Pr~~Cp~C~s~ 34 (37)
T PF12172_consen 11 GQRCRDCGRVQFP---PRPVCPHCGSD 34 (37)
T ss_dssp EEE-TTT--EEES-----SEETTTT--
T ss_pred EEEcCCCCCEecC---CCcCCCCcCcc
Confidence 5689999887554 35789999754
No 60
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.12 E-value=64 Score=23.27 Aligned_cols=46 Identities=11% Similarity=-0.030 Sum_probs=32.6
Q ss_pred cccccccCcccccCCCCCcCCccccCChHHHHHHHHHHHHHHHHHH
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAKEKQYYEAENDKYQQLEKKF 117 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~~~~~~~~l~~~~~~~e~~~ 117 (168)
+..|+.|++++-.-+...++|+.|....+..++.-....+.+|..-
T Consensus 9 KridPetg~KFYDLNrdPiVsPytG~s~P~s~fe~~t~~~~~e~e~ 54 (129)
T COG4530 9 KRIDPETGKKFYDLNRDPIVSPYTGKSYPRSYFEETTPDAAAEEEE 54 (129)
T ss_pred cccCccccchhhccCCCccccCcccccchHHHHHhhchhhhhhHHH
Confidence 5678888887654223679999999988888887765555555443
No 61
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=29.43 E-value=29 Score=21.76 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=17.5
Q ss_pred cccccccCcccccCCCCCcCCccccC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLA 97 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~ 97 (168)
...|..||+.... .-+|.+|..
T Consensus 27 l~~C~~CG~~~~~----H~vC~~CG~ 48 (57)
T PRK12286 27 LVECPNCGEPKLP----HRVCPSCGY 48 (57)
T ss_pred ceECCCCCCccCC----eEECCCCCc
Confidence 4679999998764 579999975
No 62
>PF10170 C6_DPF: Cysteine-rich domain; InterPro: IPR018785 This entry represents the N-terminal approximately 100 amino acids of a family of proteins found in a range of organisms, including human, chicken and Drosophila [, , ]. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Probab=27.91 E-value=28 Score=24.36 Aligned_cols=15 Identities=33% Similarity=1.192 Sum_probs=12.2
Q ss_pred ccCcCCCCCccceec
Q psy12448 135 VICTSRDCPIFYMRK 149 (168)
Q Consensus 135 ~~C~s~dCpv~Y~R~ 149 (168)
.-|.+.+|.+||.+.
T Consensus 58 ~VC~~~~CSlFYtkr 72 (97)
T PF10170_consen 58 PVCVGQDCSLFYTKR 72 (97)
T ss_pred ceEcCCCccEEeeCc
Confidence 358889999999873
No 63
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.63 E-value=36 Score=31.69 Aligned_cols=33 Identities=21% Similarity=0.309 Sum_probs=24.8
Q ss_pred ccccccCcccccCCCCCcCCccccCChHHHHHHHHH
Q psy12448 73 QTCIGCKVVLHDTSLSNALCNFCLAKEKQYYEAEND 108 (168)
Q Consensus 73 ~~C~~C~~~~~~~~~~~~lC~~C~~~~~~~~~~l~~ 108 (168)
..|+.||..+.. +...|++|.....+..-.++.
T Consensus 28 ~~Cp~CG~~~~~---~~~fC~~CG~~~~~~~~~~~~ 60 (645)
T PRK14559 28 KPCPQCGTEVPV---DEAHCPNCGAETGTIWWAIIA 60 (645)
T ss_pred CcCCCCCCCCCc---ccccccccCCcccchhhhhcc
Confidence 579999998876 478999999887765544443
No 64
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=27.58 E-value=14 Score=22.15 Aligned_cols=25 Identities=20% Similarity=0.469 Sum_probs=16.3
Q ss_pred cccccCcccccC--CCCCcCCccccCC
Q psy12448 74 TCIGCKVVLHDT--SLSNALCNFCLAK 98 (168)
Q Consensus 74 ~C~~C~~~~~~~--~~~~~lC~~C~~~ 98 (168)
.|+.|+++-..| -....+|.+|...
T Consensus 1 ~CiiC~~~~~~GI~I~~~fIC~~CE~~ 27 (46)
T PF10764_consen 1 KCIICGKEKEEGIHIYGKFICSDCEKE 27 (46)
T ss_pred CeEeCCCcCCCCEEEECeEehHHHHHH
Confidence 478888876653 1135788888653
No 65
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=27.50 E-value=41 Score=19.86 Aligned_cols=23 Identities=22% Similarity=0.401 Sum_probs=11.7
Q ss_pred ccccCcccccCCC---CCcCCccccC
Q psy12448 75 CIGCKVVLHDTSL---SNALCNFCLA 97 (168)
Q Consensus 75 C~~C~~~~~~~~~---~~~lC~~C~~ 97 (168)
|+.||..+..... ...+|+.|..
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCC
Confidence 6667666543211 1355666653
No 66
>PRK01343 zinc-binding protein; Provisional
Probab=27.14 E-value=39 Score=21.34 Aligned_cols=23 Identities=17% Similarity=0.489 Sum_probs=16.2
Q ss_pred cccccccCcccccCCCCCcCCcc-cc
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNF-CL 96 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~-C~ 96 (168)
...|+.|+++.... ..+.|+. |+
T Consensus 9 ~~~CP~C~k~~~~~--~rPFCS~RC~ 32 (57)
T PRK01343 9 TRPCPECGKPSTRE--AYPFCSERCR 32 (57)
T ss_pred CCcCCCCCCcCcCC--CCcccCHHHh
Confidence 67999999987642 3567754 54
No 67
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.76 E-value=41 Score=21.11 Aligned_cols=20 Identities=25% Similarity=0.675 Sum_probs=11.5
Q ss_pred ccccccCcccccCCCCCcCCccccC
Q psy12448 73 QTCIGCKVVLHDTSLSNALCNFCLA 97 (168)
Q Consensus 73 ~~C~~C~~~~~~~~~~~~lC~~C~~ 97 (168)
..|..||..+-. .+|+.|..
T Consensus 6 r~C~~CgvYTLk-----~~CP~CG~ 25 (56)
T PRK13130 6 RKCPKCGVYTLK-----EICPVCGG 25 (56)
T ss_pred eECCCCCCEEcc-----ccCcCCCC
Confidence 456666665543 45666654
No 68
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=26.68 E-value=30 Score=27.72 Aligned_cols=24 Identities=25% Similarity=0.517 Sum_probs=15.7
Q ss_pred ccccCcccccCCCCCcCCccccCChH
Q psy12448 75 CIGCKVVLHDTSLSNALCNFCLAKEK 100 (168)
Q Consensus 75 C~~C~~~~~~~~~~~~lC~~C~~~~~ 100 (168)
|+.||.++... ...+|.+|....-
T Consensus 1 C~~CG~~~~~~--~~~lC~~C~~~~~ 24 (236)
T PF04981_consen 1 CPRCGREIEPL--IDGLCPDCYLKRF 24 (236)
T ss_pred CCCCCCCCCCc--ccccChHHhcccC
Confidence 78888876642 2358888875543
No 69
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=26.59 E-value=37 Score=24.17 Aligned_cols=26 Identities=15% Similarity=0.294 Sum_probs=15.8
Q ss_pred cccccccCcccccCCCCCcCCccccC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLA 97 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~ 97 (168)
..+|+.|+.++..-.+.+.+|.+|..
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~ 79 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKH 79 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTE
T ss_pred CcchhhhCCcccccCCCCCcCCcCCc
Confidence 67899998876532224677877764
No 70
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=26.51 E-value=41 Score=21.52 Aligned_cols=21 Identities=19% Similarity=0.700 Sum_probs=15.3
Q ss_pred ccccccCcccccCCCCCcCCccccCC
Q psy12448 73 QTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 73 ~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
..|..|+..+.. ..|++|.+.
T Consensus 4 kAC~~C~~i~~~-----~~CP~Cgs~ 24 (61)
T PRK08351 4 KACRHCHYITTE-----DRCPVCGSR 24 (61)
T ss_pred hhhhhCCcccCC-----CcCCCCcCC
Confidence 478888887754 468888764
No 71
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=26.39 E-value=21 Score=36.03 Aligned_cols=22 Identities=27% Similarity=0.516 Sum_probs=18.2
Q ss_pred cccccccCcccccCCCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
...|+.||+.+.. ..|+.|...
T Consensus 674 ~~~Cp~Cg~~~~~-----~~Cp~CG~~ 695 (1627)
T PRK14715 674 FFKCPKCGKVGLY-----HVCPFCGTR 695 (1627)
T ss_pred eeeCCCCCCcccc-----ccCcccCCc
Confidence 5689999998765 789999864
No 72
>PRK11827 hypothetical protein; Provisional
Probab=26.17 E-value=37 Score=21.63 Aligned_cols=27 Identities=15% Similarity=0.220 Sum_probs=19.1
Q ss_pred cccccccCcccccC-CCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDT-SLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~-~~~~~lC~~C~~~ 98 (168)
-..|+.|+..+... ..+..+|..|.-.
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~la 35 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLA 35 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCee
Confidence 46899998887642 2246889998754
No 73
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=25.92 E-value=36 Score=20.17 Aligned_cols=27 Identities=19% Similarity=0.385 Sum_probs=16.8
Q ss_pred ccccccccCcccccCCCCCcCCccccC
Q psy12448 71 KKQTCIGCKVVLHDTSLSNALCNFCLA 97 (168)
Q Consensus 71 ~s~~C~~C~~~~~~~~~~~~lC~~C~~ 97 (168)
....|.+|++.+.+...++..|..|..
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGL 36 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCC
Confidence 467888898888332235777877753
No 74
>PRK11595 DNA utilization protein GntX; Provisional
Probab=25.89 E-value=27 Score=27.73 Aligned_cols=24 Identities=21% Similarity=0.530 Sum_probs=16.5
Q ss_pred ccccccCcccccCCCCCcCCccccCC
Q psy12448 73 QTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 73 ~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
..|+.|++.+..+ ...+|+.|...
T Consensus 6 ~~C~~C~~~~~~~--~~~lC~~C~~~ 29 (227)
T PRK11595 6 GLCWLCRMPLALS--HWGICSVCSRA 29 (227)
T ss_pred CcCccCCCccCCC--CCcccHHHHhh
Confidence 5799999876542 23588888654
No 75
>PF14149 YhfH: YhfH-like protein
Probab=25.88 E-value=11 Score=21.72 Aligned_cols=13 Identities=15% Similarity=0.611 Sum_probs=9.1
Q ss_pred cccccccCccccc
Q psy12448 72 KQTCIGCKVVLHD 84 (168)
Q Consensus 72 s~~C~~C~~~~~~ 84 (168)
...|..||+.+..
T Consensus 13 ~K~C~~CG~~i~E 25 (37)
T PF14149_consen 13 PKKCTECGKEIEE 25 (37)
T ss_pred CcccHHHHHHHHH
Confidence 5677777777664
No 76
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=25.86 E-value=36 Score=18.87 Aligned_cols=26 Identities=19% Similarity=0.345 Sum_probs=16.4
Q ss_pred ccccccCccccc-CCCCCcCCccccCC
Q psy12448 73 QTCIGCKVVLHD-TSLSNALCNFCLAK 98 (168)
Q Consensus 73 ~~C~~C~~~~~~-~~~~~~lC~~C~~~ 98 (168)
..|..|+...-. +..+..+|..|...
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 578888765443 22246788888753
No 77
>PF14353 CpXC: CpXC protein
Probab=25.71 E-value=33 Score=24.54 Aligned_cols=14 Identities=21% Similarity=0.347 Sum_probs=10.6
Q ss_pred cccccccCcccccC
Q psy12448 72 KQTCIGCKVVLHDT 85 (168)
Q Consensus 72 s~~C~~C~~~~~~~ 85 (168)
..+|+.||....-.
T Consensus 38 ~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 38 SFTCPSCGHKFRLE 51 (128)
T ss_pred EEECCCCCCceecC
Confidence 67888888877653
No 78
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=24.76 E-value=28 Score=20.10 Aligned_cols=8 Identities=25% Similarity=0.584 Sum_probs=4.0
Q ss_pred cCCccccC
Q psy12448 90 ALCNFCLA 97 (168)
Q Consensus 90 ~lC~~C~~ 97 (168)
.+|.+|..
T Consensus 20 ~vC~~CG~ 27 (43)
T PF08271_consen 20 LVCPNCGL 27 (43)
T ss_dssp EEETTT-B
T ss_pred EECCCCCC
Confidence 46666643
No 79
>PRK10220 hypothetical protein; Provisional
Probab=24.46 E-value=37 Score=24.30 Aligned_cols=29 Identities=14% Similarity=0.250 Sum_probs=21.8
Q ss_pred cccccccCcccccCCCCCcCCccccCChH
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAKEK 100 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~~~ 100 (168)
...|+.|....+-...+..+|+.|.....
T Consensus 3 lP~CP~C~seytY~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 3 LPHCPKCNSEYTYEDNGMYICPECAHEWN 31 (111)
T ss_pred CCcCCCCCCcceEcCCCeEECCcccCcCC
Confidence 35799998887754446789999987654
No 80
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=24.27 E-value=23 Score=18.82 Aligned_cols=25 Identities=28% Similarity=0.551 Sum_probs=12.6
Q ss_pred ccccccCcccccC---CCCCcCCccccC
Q psy12448 73 QTCIGCKVVLHDT---SLSNALCNFCLA 97 (168)
Q Consensus 73 ~~C~~C~~~~~~~---~~~~~lC~~C~~ 97 (168)
..|..|+..+... .....+|+.|..
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCcC
Confidence 3688888877642 123578888864
No 81
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=24.20 E-value=35 Score=24.36 Aligned_cols=28 Identities=18% Similarity=0.387 Sum_probs=21.3
Q ss_pred ccccccCcccccCCCCCcCCccccCChH
Q psy12448 73 QTCIGCKVVLHDTSLSNALCNFCLAKEK 100 (168)
Q Consensus 73 ~~C~~C~~~~~~~~~~~~lC~~C~~~~~ 100 (168)
..|+.|+....-......+|+.|.....
T Consensus 3 p~CP~C~seytY~dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQLICPSCLYEWN 30 (109)
T ss_pred CcCCcCCCcceEecCCeeECcccccccc
Confidence 4799998887754446789999987654
No 82
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.04 E-value=36 Score=27.60 Aligned_cols=26 Identities=23% Similarity=0.390 Sum_probs=19.5
Q ss_pred cccccccccccCcccccCCCCCcCCccccCC
Q psy12448 68 FVQKKQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 68 f~~~s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
++ .|.+|..||. +.. ....|+.|...
T Consensus 306 ~~-tS~~C~~cg~-~~~---r~~~C~~cg~~ 331 (364)
T COG0675 306 YY-TSKTCPCCGH-LSG---RLFKCPRCGFV 331 (364)
T ss_pred CC-CcccccccCC-ccc---eeEECCCCCCe
Confidence 44 3899999999 432 35789999864
No 83
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=23.72 E-value=45 Score=18.49 Aligned_cols=26 Identities=19% Similarity=0.381 Sum_probs=14.0
Q ss_pred ccccccCcccccC------CCCCcCCccccCC
Q psy12448 73 QTCIGCKVVLHDT------SLSNALCNFCLAK 98 (168)
Q Consensus 73 ~~C~~C~~~~~~~------~~~~~lC~~C~~~ 98 (168)
..|+.|++...-. ......|++|...
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 4677777744321 0112577777653
No 84
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=23.45 E-value=55 Score=18.89 Aligned_cols=25 Identities=16% Similarity=0.259 Sum_probs=15.8
Q ss_pred ccccccCcccccC----CCCCcCCccccC
Q psy12448 73 QTCIGCKVVLHDT----SLSNALCNFCLA 97 (168)
Q Consensus 73 ~~C~~C~~~~~~~----~~~~~lC~~C~~ 97 (168)
-+|..||.....- ......|+.|..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 4688888554421 124678888877
No 85
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=22.95 E-value=50 Score=20.53 Aligned_cols=26 Identities=19% Similarity=0.400 Sum_probs=17.3
Q ss_pred ccccccCcccccCC---CCCcCCccccCC
Q psy12448 73 QTCIGCKVVLHDTS---LSNALCNFCLAK 98 (168)
Q Consensus 73 ~~C~~C~~~~~~~~---~~~~lC~~C~~~ 98 (168)
..|+.||..+.-.. +.-..|+.|...
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGae 31 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAE 31 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCE
Confidence 47999998877531 134678888753
No 86
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=22.85 E-value=94 Score=24.99 Aligned_cols=21 Identities=19% Similarity=0.496 Sum_probs=15.4
Q ss_pred cccccCcccccCCCCCcCCccccCCh
Q psy12448 74 TCIGCKVVLHDTSLSNALCNFCLAKE 99 (168)
Q Consensus 74 ~C~~C~~~~~~~~~~~~lC~~C~~~~ 99 (168)
.|.+|+..- ....|.+|....
T Consensus 1 ~C~iC~~~~-----~~~~C~~C~~~~ 21 (302)
T PF10186_consen 1 QCPICHNSR-----RRFYCANCVNNR 21 (302)
T ss_pred CCCCCCCCC-----CCeECHHHHHHH
Confidence 599998332 358999998764
No 87
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=22.56 E-value=81 Score=23.01 Aligned_cols=41 Identities=17% Similarity=0.489 Sum_probs=26.6
Q ss_pred CCcCCccccCChHHHHHHH---------------HHHHHHHHHHHHHHH-HHccccc
Q psy12448 88 SNALCNFCLAKEKQYYEAE---------------NDKYQQLEKKFCQLW-TQCQTCQ 128 (168)
Q Consensus 88 ~~~lC~~C~~~~~~~~~~l---------------~~~~~~~e~~~~~~~-~~C~~C~ 128 (168)
++++|..|..+..-.+..| ..++....+++.+-. .+|.+|.
T Consensus 72 ~~~fC~~C~~NQ~L~~~~LA~f~P~~e~p~y~~~~~e~~~Yr~~LE~rYP~lC~~C~ 128 (131)
T PF09779_consen 72 SNIFCSTCNKNQHLKINQLASFLPDPEDPEYANYEEELPEYRRSLEQRYPQLCSSCE 128 (131)
T ss_pred CChhHHHHHHHHHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHhhHhhhhhh
Confidence 5789999987654333333 235555666666666 7888885
No 88
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.40 E-value=43 Score=27.47 Aligned_cols=29 Identities=17% Similarity=0.432 Sum_probs=21.8
Q ss_pred cccccccCcccccC---CCCCcCCccccCChH
Q psy12448 72 KQTCIGCKVVLHDT---SLSNALCNFCLAKEK 100 (168)
Q Consensus 72 s~~C~~C~~~~~~~---~~~~~lC~~C~~~~~ 100 (168)
-..|+.||..+... +.....|+.|+..++
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~~~ 266 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQPLRP 266 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCcCCCC
Confidence 46899999988742 235689999987654
No 89
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=22.18 E-value=46 Score=20.66 Aligned_cols=22 Identities=18% Similarity=0.375 Sum_probs=17.0
Q ss_pred cccccccCcccccCCCCCcCCccccC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLA 97 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~ 97 (168)
...|..||+.... .-+|.+|..
T Consensus 26 l~~C~~cG~~~~~----H~vc~~cG~ 47 (55)
T TIGR01031 26 LVVCPNCGEFKLP----HRVCPSCGY 47 (55)
T ss_pred ceECCCCCCcccC----eeECCccCe
Confidence 4579999997654 578999974
No 90
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=21.60 E-value=1.1e+02 Score=18.45 Aligned_cols=27 Identities=22% Similarity=0.556 Sum_probs=17.3
Q ss_pred cccccccCcccccC------------CCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDT------------SLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~------------~~~~~lC~~C~~~ 98 (168)
+.+|+.|++.+... .....+|+-|...
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 34788888854422 1235889999763
No 91
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=21.55 E-value=56 Score=20.38 Aligned_cols=25 Identities=24% Similarity=0.513 Sum_probs=17.5
Q ss_pred ccccccCcccccC----CCCCcCCcc-ccC
Q psy12448 73 QTCIGCKVVLHDT----SLSNALCNF-CLA 97 (168)
Q Consensus 73 ~~C~~C~~~~~~~----~~~~~lC~~-C~~ 97 (168)
..|++|+.++... +..|++|+. |.+
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~g~C~~ 31 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHPGVCAQ 31 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCcHHHHH
Confidence 3699999998863 335777764 643
No 92
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=21.15 E-value=57 Score=20.19 Aligned_cols=25 Identities=16% Similarity=0.441 Sum_probs=17.2
Q ss_pred ccccccCcccccC----CCCCcCCcc-ccC
Q psy12448 73 QTCIGCKVVLHDT----SLSNALCNF-CLA 97 (168)
Q Consensus 73 ~~C~~C~~~~~~~----~~~~~lC~~-C~~ 97 (168)
..|++|+.++..- +..|++|+. |..
T Consensus 2 ~iCvvCK~Pi~~al~v~T~~Gpvh~g~C~~ 31 (53)
T PHA02610 2 KICVVCKQPIEKALVVETEKGPVHPGPCYN 31 (53)
T ss_pred ceeeeeCCchhhceEEecCCCCCCChhHHH
Confidence 4799999998642 346788764 643
No 93
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.78 E-value=63 Score=23.08 Aligned_cols=28 Identities=25% Similarity=0.622 Sum_probs=17.1
Q ss_pred ccccccccCcccccCCCCCcCCccccCC
Q psy12448 71 KKQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 71 ~s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
....|..||............|+.|.+.
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCCC
Confidence 4678888887665421112248888764
No 94
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=20.69 E-value=58 Score=21.05 Aligned_cols=21 Identities=19% Similarity=0.468 Sum_probs=14.7
Q ss_pred ccccccCcccccCCCCCcCCccccCC
Q psy12448 73 QTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 73 ~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
..|..|+..+.. ..|+.|.+.
T Consensus 6 ~AC~~C~~i~~~-----~~Cp~Cgs~ 26 (64)
T PRK06393 6 RACKKCKRLTPE-----KTCPVHGDE 26 (64)
T ss_pred hhHhhCCcccCC-----CcCCCCCCC
Confidence 468888877643 478888764
No 95
>PRK12495 hypothetical protein; Provisional
Probab=20.64 E-value=56 Score=26.32 Aligned_cols=27 Identities=15% Similarity=0.392 Sum_probs=19.7
Q ss_pred ccccccccCcccccCCCCCcCCccccCC
Q psy12448 71 KKQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 71 ~s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
...+|..||.+|..- ....+|..|...
T Consensus 41 sa~hC~~CG~PIpa~-pG~~~Cp~CQ~~ 67 (226)
T PRK12495 41 TNAHCDECGDPIFRH-DGQEFCPTCQQP 67 (226)
T ss_pred chhhcccccCcccCC-CCeeECCCCCCc
Confidence 467999999999852 124679999753
No 96
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=20.49 E-value=26 Score=19.50 Aligned_cols=24 Identities=21% Similarity=0.501 Sum_probs=14.5
Q ss_pred cccccCcccccC----CCCCcCCccccC
Q psy12448 74 TCIGCKVVLHDT----SLSNALCNFCLA 97 (168)
Q Consensus 74 ~C~~C~~~~~~~----~~~~~lC~~C~~ 97 (168)
.|..||+.+... .....+|..|..
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~ 32 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQE 32 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhC
Confidence 499999988753 123577887753
No 97
>PRK10445 endonuclease VIII; Provisional
Probab=20.36 E-value=55 Score=26.72 Aligned_cols=27 Identities=22% Similarity=0.436 Sum_probs=20.1
Q ss_pred ccccccccCcccccC---CCCCcCCccccC
Q psy12448 71 KKQTCIGCKVVLHDT---SLSNALCNFCLA 97 (168)
Q Consensus 71 ~s~~C~~C~~~~~~~---~~~~~lC~~C~~ 97 (168)
....|+.||.++... +.....|+.|+.
T Consensus 234 ~g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ~ 263 (263)
T PRK10445 234 DGEACERCGGIIEKTTLSSRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCCCEeEEEEECCCCcEECCCCcC
Confidence 358899999988742 235688999963
No 98
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.28 E-value=68 Score=22.79 Aligned_cols=28 Identities=14% Similarity=0.270 Sum_probs=18.2
Q ss_pred ccccccccCcccccCCCCCcCCccccCC
Q psy12448 71 KKQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 71 ~s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
....|..|+............|+.|.+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 4678999988765421112459999864
No 99
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=20.16 E-value=29 Score=28.02 Aligned_cols=24 Identities=33% Similarity=0.854 Sum_probs=20.4
Q ss_pred cccccccCcccccCCCCCcCCccccCC
Q psy12448 72 KQTCIGCKVVLHDTSLSNALCNFCLAK 98 (168)
Q Consensus 72 s~~C~~C~~~~~~~~~~~~lC~~C~~~ 98 (168)
=.+|..|+..++. +.++|+=|...
T Consensus 194 MK~C~sC~qqIHR---NAPiCPlCK~K 217 (230)
T PF10146_consen 194 MKTCQSCHQQIHR---NAPICPLCKAK 217 (230)
T ss_pred cchhHhHHHHHhc---CCCCCcccccc
Confidence 4699999999998 58999999754
Done!