Query 024144
Match_columns 272
No_of_seqs 61 out of 63
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 02:24:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024144.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024144hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10483 Elong_Iki1: Elongator 99.9 5.5E-26 1.2E-30 209.4 14.3 194 17-263 10-216 (280)
2 PF09807 DUF2348: Uncharacteri 99.2 2.5E-09 5.4E-14 97.9 18.6 183 18-213 18-211 (249)
3 PF06745 KaiC: KaiC; InterPro 98.3 1.4E-05 3E-10 70.0 12.3 137 50-212 42-185 (226)
4 TIGR03877 thermo_KaiC_1 KaiC d 97.9 0.00031 6.8E-09 62.8 13.9 144 50-211 44-193 (237)
5 PRK04328 hypothetical protein; 97.7 0.00042 9.1E-09 62.8 11.8 144 50-211 46-195 (249)
6 PRK06067 flagellar accessory p 97.7 0.0012 2.7E-08 58.3 14.3 136 51-212 49-187 (234)
7 COG2874 FlaH Predicted ATPases 97.3 0.0093 2E-07 55.1 14.3 137 50-212 51-190 (235)
8 PRK09302 circadian clock prote 97.3 0.0045 9.9E-08 61.3 13.1 131 50-211 296-433 (509)
9 PRK09302 circadian clock prote 96.7 0.036 7.8E-07 55.0 14.1 137 50-211 54-200 (509)
10 TIGR02655 circ_KaiC circadian 96.7 0.13 2.8E-06 51.2 17.4 94 50-174 286-381 (484)
11 TIGR03881 KaiC_arch_4 KaiC dom 96.2 0.25 5.4E-06 43.3 14.3 138 51-212 44-189 (229)
12 COG0467 RAD55 RecA-superfamily 96.0 0.064 1.4E-06 48.4 10.2 142 50-212 46-193 (260)
13 cd01124 KaiC KaiC is a circadi 95.9 0.16 3.4E-06 42.5 11.5 135 51-212 23-164 (187)
14 TIGR02655 circ_KaiC circadian 95.7 0.17 3.7E-06 50.3 12.4 137 50-211 44-190 (484)
15 TIGR03878 thermo_KaiC_2 KaiC d 95.5 0.17 3.6E-06 46.3 10.8 133 51-211 60-203 (259)
16 TIGR03880 KaiC_arch_3 KaiC dom 94.8 0.45 9.8E-06 41.7 11.1 130 51-211 40-177 (224)
17 KOG4723 Uncharacterized conser 94.8 0.17 3.7E-06 46.7 8.5 73 16-96 16-90 (248)
18 PF05625 PAXNEB: PAXNEB protei 94.6 0.32 6.9E-06 47.1 10.5 69 148-216 202-280 (363)
19 PRK08533 flagellar accessory p 94.4 0.45 9.8E-06 42.8 10.3 127 53-211 50-184 (230)
20 PRK05973 replicative DNA helic 93.5 1.6 3.6E-05 40.2 12.2 62 15-83 59-120 (237)
21 cd00984 DnaB_C DnaB helicase C 93.0 0.5 1.1E-05 41.4 8.0 93 148-253 125-236 (242)
22 TIGR02237 recomb_radB DNA repa 92.6 1.2 2.7E-05 38.3 9.6 39 53-94 38-77 (209)
23 PRK09361 radB DNA repair and r 92.4 7 0.00015 34.1 14.4 65 148-212 109-190 (225)
24 PRK04301 radA DNA repair and r 91.1 3.7 8E-05 38.5 11.7 39 56-94 137-177 (317)
25 PRK11823 DNA repair protein Ra 91.0 15 0.00032 36.7 16.3 115 53-211 106-230 (446)
26 cd01121 Sms Sms (bacterial rad 90.1 20 0.00043 35.1 16.2 115 54-212 109-233 (372)
27 TIGR02236 recomb_radA DNA repa 89.1 17 0.00037 33.6 14.3 38 57-94 131-170 (310)
28 cd01393 recA_like RecA is a b 88.1 9.9 0.00021 32.9 11.3 39 56-94 54-94 (226)
29 PTZ00035 Rad51 protein; Provis 87.6 27 0.00059 33.5 15.6 40 55-94 152-193 (337)
30 cd01123 Rad51_DMC1_radA Rad51_ 87.4 6 0.00013 34.5 9.6 40 55-94 53-94 (235)
31 PF03192 DUF257: Pyrococcus pr 86.2 22 0.00049 32.2 12.9 153 21-213 13-187 (210)
32 TIGR02238 recomb_DMC1 meiotic 84.7 23 0.0005 33.8 12.8 41 54-94 129-171 (313)
33 cd01394 radB RadB. The archaea 81.9 28 0.0006 30.1 11.3 64 148-211 105-185 (218)
34 PLN03187 meiotic recombination 80.5 14 0.00031 35.8 9.8 39 56-94 161-201 (344)
35 TIGR00416 sms DNA repair prote 79.1 66 0.0014 32.3 14.2 114 54-212 121-245 (454)
36 PRK09354 recA recombinase A; P 77.9 39 0.00085 33.1 11.9 41 32-81 72-112 (349)
37 PF05763 DUF835: Protein of un 77.2 4.8 0.0001 34.2 4.8 50 123-177 57-106 (136)
38 cd01125 repA Hexameric Replica 75.3 59 0.0013 28.9 12.0 142 53-217 39-195 (239)
39 cd00983 recA RecA is a bacter 72.2 47 0.001 32.2 10.8 26 53-80 81-106 (325)
40 TIGR02012 tigrfam_recA protein 71.2 35 0.00075 33.0 9.6 47 32-91 67-113 (321)
41 PF08423 Rad51: Rad51; InterP 60.4 25 0.00055 32.2 6.2 41 55-95 72-114 (256)
42 TIGR02239 recomb_RAD51 DNA rep 60.1 1.6E+02 0.0035 28.0 17.1 39 56-94 131-171 (316)
43 PLN03186 DNA repair protein RA 59.4 1.8E+02 0.0038 28.3 17.6 38 57-94 159-198 (342)
44 PF14417 MEDS: MEDS: MEthanoge 54.0 46 0.00099 28.9 6.4 137 38-200 30-174 (191)
45 cd01120 RecA-like_NTPases RecA 53.0 1.1E+02 0.0023 23.9 13.3 64 148-211 87-164 (165)
46 TIGR00665 DnaB replicative DNA 48.9 73 0.0016 31.0 7.6 22 53-74 222-243 (434)
47 PF00004 AAA: ATPase family as 43.9 51 0.0011 25.2 4.7 57 19-75 58-120 (132)
48 TIGR03439 methyl_EasF probable 43.5 2.1E+02 0.0045 27.6 9.6 47 54-102 101-149 (319)
49 cd01122 GP4d_helicase GP4d_hel 42.9 2.4E+02 0.0053 25.1 18.1 21 55-75 59-79 (271)
50 PF13481 AAA_25: AAA domain; P 41.9 26 0.00056 29.4 2.9 26 53-78 68-93 (193)
51 PHA02542 41 41 helicase; Provi 39.3 4.3E+02 0.0093 26.8 16.8 175 15-212 185-386 (473)
52 PRK09519 recA DNA recombinatio 34.9 2.8E+02 0.0061 30.4 9.9 30 51-82 84-113 (790)
53 PF13911 AhpC-TSA_2: AhpC/TSA 34.7 37 0.00081 26.6 2.6 44 44-98 2-45 (115)
54 PF13466 STAS_2: STAS domain 33.4 92 0.002 22.6 4.4 34 44-80 47-80 (80)
55 PF06866 DUF1256: Protein of u 32.4 2.1E+02 0.0045 25.5 7.1 34 37-71 9-42 (163)
56 PRK06321 replicative DNA helic 29.6 6.1E+02 0.013 25.7 13.5 52 16-73 222-273 (472)
57 PF04655 APH_6_hur: Aminoglyco 28.9 21 0.00046 33.1 0.4 24 186-212 162-185 (253)
58 KOG1406 Peroxisomal 3-ketoacyl 28.1 39 0.00085 33.0 2.0 39 57-96 265-303 (408)
59 KOG3124 Pyrroline-5-carboxylat 27.8 32 0.0007 32.8 1.4 42 14-56 214-262 (267)
60 PF07411 DUF1508: Domain of un 25.4 70 0.0015 22.5 2.4 18 235-252 2-19 (49)
61 PF11382 DUF3186: Protein of u 25.3 1.3E+02 0.0028 28.7 5.0 62 37-101 65-130 (308)
62 PF09087 Cyc-maltodext_N: Cycl 23.9 1.6E+02 0.0034 23.6 4.4 58 201-258 23-84 (88)
63 PF09967 DUF2201: VWA-like dom 23.7 1.9E+02 0.004 23.8 5.1 40 22-65 2-41 (126)
64 TIGR03438 probable methyltrans 23.5 1.2E+02 0.0026 28.3 4.3 38 54-100 257-295 (301)
65 smart00455 RBD Raf-like Ras-bi 23.1 53 0.0011 24.7 1.5 35 67-104 23-57 (70)
66 COG0257 RpmJ Ribosomal protein 22.7 67 0.0014 22.3 1.8 13 242-254 15-27 (38)
67 COG4544 Uncharacterized conser 21.7 1.3E+02 0.0029 28.6 4.2 56 33-95 63-118 (260)
No 1
>PF10483 Elong_Iki1: Elongator subunit Iki1; InterPro: IPR019519 Histone acetylation protein (Hap) 2 (also known as Elongator complex protein 5) is one of three histone acetyltransferases proteins that, in yeasts, are found associated with elongating forms of RNA polymerase II (Elongator). The Haps can be isolated in two forms, as a six-subunit complex with Elongator, and as a complex of the three proteins on their own. The role of the Hap complex in transcription is still speculative, being possibly to keep the histone acetylation activity of free Elongator in check, allowing histone acetylation only in the presence of a transcribing polymerase, or the interaction with Haps might render Elongator susceptible to modifications thereby altering its activity []. This protein family also contains Dermal papilla-derived protein 6, which also belong to the ELP5 family. ; PDB: 4A8J_B 4EJS_B.
Probab=99.94 E-value=5.5e-26 Score=209.35 Aligned_cols=194 Identities=21% Similarity=0.231 Sum_probs=118.6
Q ss_pred CCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCC
Q 024144 17 EHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTD 96 (272)
Q Consensus 17 e~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysD 96 (272)
|..|+++|.||++.|+ ..++++ +|+..+.++..||+|+||.+++ .+ |+|... +.+
T Consensus 10 d~spl~Li~DSl~q~a-~~Ll~e-------~i~~a~~~~~~V~~lsfEt~~~--~~-----~~d~~~-~~~--------- 64 (280)
T PF10483_consen 10 DASPLTLILDSLEQSA-RPLLKE-------FIRRAKSRNEKVHFLSFETLNK--PE-----YADSFI-NAR--------- 64 (280)
T ss_dssp S--SEEEEEEBTTB-S-HHHHHH-------HHHHHTS----EEEEESS--S----T-----T-SEEE-ETT---------
T ss_pred CCCCeEEEEEcccccC-HHHHHH-------HHHHHHcCCCeEEEEEeEeCCC--cc-----cCCeec-ccc---------
Confidence 3789999999999985 665555 4456688999999999999888 44 666444 222
Q ss_pred CCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc
Q 024144 97 PLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS 176 (272)
Q Consensus 97 PLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~ 176 (272)
+|+- .+++..+.........+++.+++|+||||+||++|+++ .++++|++|.+
T Consensus 65 --~~~~------------------------~~i~~~i~s~~~~~~~~~~~~~lVvIDSLn~ll~~~~~-~l~~fLssl~~ 117 (280)
T PF10483_consen 65 --GKSL------------------------QDIVKEIKSHLPSSSSSPTKKFLVVIDSLNYLLNHHPC-QLSQFLSSLLS 117 (280)
T ss_dssp --SS-H------------------------HHHHHHHHHTS--SS-SS---EEEEES-GGGS-GG----GHHHHHHHH--
T ss_pred --CCCH------------------------HHHHHHHHhhcccccccCCCCeEEEEEcchHHHHHHHH-HHHHHHHhccc
Confidence 2221 11112333321111223344699999999999999999 99999999998
Q ss_pred CCceeEEEeeecccc-------cchhhHhHHhhhheeEEEeecCCccccccccccchhhhhh------ccccceEEEEEE
Q 024144 177 HDQVSSIFWLLHSDL-------HEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLE------QNFRKGKFHVRF 243 (272)
Q Consensus 177 ~~~vssVl~LLHsDL-------He~~~v~ALe~LSstvvtv~P~~~~~~~~~~~~~~~~~l~------~n~~k~~~~vr~ 243 (272)
+++ ++|+|++|+|+ |+|+++++|+|||||+++|+|........+..-+++.-++ .|..+.+++++.
T Consensus 118 ~p~-~svv~~~H~Dl~~~~~~~~~P~~l~lL~~LATtii~v~~~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~~l~~ 196 (280)
T PF10483_consen 118 SPQ-SSVVGLYHTDLLPPSQNPYYPSPLSLLSYLATTIITVEPLSHISADKEALDRSLSKPEFGLGEGLNGVGFVLELEN 196 (280)
T ss_dssp -TT-EEEEEEEETTS---TTB-TS--HHHHHHHH-SEEEEEEE---SS--HHHHHHHHHTT---SS---S-SEEEEEEEE
T ss_pred CCC-cEEEEEEccCcCcccccccCcCHHHHHHHhceEEEEEcccCccchhHHHHHhhhhhcccChhhhccCceEEEEEEE
Confidence 787 78999999999 9999999999999999999999988766666555555443 556689999999
Q ss_pred eccCCcEEEEEEEEEecccc
Q 024144 244 KRRNGRVRVMKYLLSWQASN 263 (272)
Q Consensus 244 KrRnGRV~~~~~~~~~~~~~ 263 (272)
|||+||+..+.|++.+....
T Consensus 197 RrksGR~~~e~~~~~~~~~~ 216 (280)
T PF10483_consen 197 RRKSGRVVSEWFVIDINSHI 216 (280)
T ss_dssp E-TTS-EEEEEEEEETTTTE
T ss_pred EcCCCCcEeEEEEEecCCCc
Confidence 99999999999999876543
No 2
>PF09807 DUF2348: Uncharacterized conserved protein (DUF2348); InterPro: IPR018627 Members of this family of putative uncharacterised proteins have no known function.
Probab=99.18 E-value=2.5e-09 Score=97.87 Aligned_cols=183 Identities=19% Similarity=0.245 Sum_probs=127.9
Q ss_pred CCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccC
Q 024144 18 HAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYT 95 (272)
Q Consensus 18 ~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ys 95 (272)
..-.++|+|+ .+++ .=+..|++. .+++ .+..|.+|+|..+.+.|...++|-|++-... +.+++++|+.+
T Consensus 18 ~g~~ili~d~-~~dg-sFLlh~~L~---~~Lk----~~~~V~fv~~~q~~~HY~~v~~KLG~NL~~~~~~gql~fiD~l~ 88 (249)
T PF09807_consen 18 PGKLILIEDC-ETDG-SFLLHHFLS---QYLK----AGCKVCFVAFSQSFSHYNNVAQKLGVNLSAAKEKGQLVFIDGLK 88 (249)
T ss_pred CCeEEEEEcC-CCCc-hhHHHHHHH---HHhc----CCCcEEEEEccCCHHHHHHHHHhhEecchHhccCCcEEEeehhh
Confidence 3447999999 8875 556667553 3333 5668999999999999999999999997752 34799999999
Q ss_pred CCCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHH-hcChHHHHHHHHhh
Q 024144 96 DPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR-HASISSVAGILSNL 174 (272)
Q Consensus 96 DPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~-h~s~~~vc~lL~~L 174 (272)
++++|--....++... +..+.--.+...|.+++..|.+..+...+ .++ ++|+||-||.|+- ..+..+|..+++.+
T Consensus 89 ~~~~~l~~~~~~~~~~--~~~~l~~~~~~~L~~L~~~I~~~l~~~~~-~~~-~~liIDdls~Ll~lG~s~~~vldF~~yc 164 (249)
T PF09807_consen 89 SSLDLLFDEDSSDEPN--PLKFLREDNASSLRSLYEFIQEALSPADS-NGS-VVLIIDDLSVLLSLGVSSNDVLDFIHYC 164 (249)
T ss_pred hhhhhhhccccccCCc--cccccccCCcchHHHHHHHHHHHHhhccC-CCC-eEEEEeCHHHHHHcCCCHHHHHHHHHHH
Confidence 8887742111000100 11111111234578888887776663233 233 8999999999997 34455788889888
Q ss_pred hc---CCceeEEEeeeccccc---c-h-hhHhHHhhhheeEEEeecC
Q 024144 175 RS---HDQVSSIFWLLHSDLH---E-I-KFTSVLEYLSSMVASVEPF 213 (272)
Q Consensus 175 r~---~~~vssVl~LLHsDLH---e-~-~~v~ALe~LSstvvtv~P~ 213 (272)
+. ...-.+++.|+|.|-- + . .....|+|+|..+|+++|+
T Consensus 165 ra~l~~~~~~~lVvl~h~d~~~~~e~~~~l~~~L~h~a~l~i~v~~L 211 (249)
T PF09807_consen 165 RATLCSESNGSLVVLVHCDIDDEDEENDLLLNSLAHMADLVITVEPL 211 (249)
T ss_pred HHHhccccCCCEEEEEecCCCCccchHHHHHHHHHHHhcEEEEecCC
Confidence 84 2234588899998865 2 2 2789999999999999995
No 3
>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....
Probab=98.28 E-value=1.4e-05 Score=70.02 Aligned_cols=137 Identities=20% Similarity=0.243 Sum_probs=89.9
Q ss_pred hhccc-cceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 024144 50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (272)
Q Consensus 50 a~~~q-~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (272)
++..+ ++.+..+.+|-+|+++.+-++..|+|.+.. +.++.++|+++...+|.. . ++..+
T Consensus 42 ~~~~~~ge~vlyvs~ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~~~~~~-~-----------------~~~~l 103 (226)
T PF06745_consen 42 NGLKNFGEKVLYVSFEEPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERIGWSP-N-----------------DLEEL 103 (226)
T ss_dssp HHHHHHT--EEEEESSS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGST-TS-C-----------------CHHHH
T ss_pred HhhhhcCCcEEEEEecCCHHHHHHHHHHcCCcHHHHhhcCCEEEEecccccccccc-c-----------------CHHHH
Confidence 46677 999999999999999999999999876542 335999999999988872 1 22233
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEeeecccccchhhHhHHhh-
Q 024144 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLHSDLHEIKFTSVLEY- 202 (272)
Q Consensus 127 ~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LLHsDLHe~~~v~ALe~- 202 (272)
...+...++.. ++ -.|+||||+.+....+...+-..|+.|.+. ..+..++-.-..+-+++.....+++
T Consensus 104 ~~~i~~~i~~~-------~~-~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~llt~~~~~~~~~~~~~~i~~~ 175 (226)
T PF06745_consen 104 LSKIREAIEEL-------KP-DRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTLLTSEMPSGSEDDGTFGIEHY 175 (226)
T ss_dssp HHHHHHHHHHH-------TS-SEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEEEEEEESSSSSSSSSTSHHHH
T ss_pred HHHHHHHHHhc-------CC-CEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEEEEEccccCcccccccchhhh
Confidence 22223333322 23 589999999996666766665566665542 3455554444344555666666765
Q ss_pred hheeEEEeec
Q 024144 203 LSSMVASVEP 212 (272)
Q Consensus 203 LSstvvtv~P 212 (272)
++.++|.+.=
T Consensus 176 l~D~vI~L~~ 185 (226)
T PF06745_consen 176 LADGVIELRY 185 (226)
T ss_dssp HSSEEEEEEE
T ss_pred cccEEEEEEE
Confidence 9999999964
No 4
>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family. Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.
Probab=97.92 E-value=0.00031 Score=62.77 Aligned_cols=144 Identities=17% Similarity=0.177 Sum_probs=84.1
Q ss_pred hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (272)
Q Consensus 50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (272)
.+..+++.+..|.+|-+|+++.+-++..|+|... -..++.++|||++-.++...... -+..+..++.
T Consensus 44 ~~~~~ge~~lyvs~ee~~~~i~~~~~~~g~~~~~~~~~g~l~~~d~~~~~~~~~~~~~~-----------~~~~~~~~~~ 112 (237)
T TIGR03877 44 NGLQMGEPGIYVALEEHPVQVRRNMAQFGWDVRKYEEEGKFAIVDAFTGGIGEAAEREK-----------YVVKDPTDVR 112 (237)
T ss_pred HHHHcCCcEEEEEeeCCHHHHHHHHHHhCCCHHHHhhcCCEEEEecccccccccccccc-----------ccccCcccHH
Confidence 3456799999999999999999999999988542 13479999999985554431110 0111222344
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh---HHHHHHHHhhhcCCceeEEEeeecccccchhh-HhHHhhh
Q 024144 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKF-TSVLEYL 203 (272)
Q Consensus 128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~---~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~~-v~ALe~L 203 (272)
.++..+.+..+ +.++ -.|+||||+.++...+. ..+-++.+.+++. .+..++ .-|.+..+... ...++|+
T Consensus 113 ~~~~~i~~~i~----~~~~-~~vVIDSls~l~~~~~~~~r~~l~~l~~~lk~~-~~t~ll-t~~~~~~~~~~~~~~~~~~ 185 (237)
T TIGR03877 113 ELIDVLRQAIR----DINA-KRVVIDSVTTLYITKPAMARSIVMQLKRVLSGL-GCTSIF-VSQVSVGERGFGGPGVEHA 185 (237)
T ss_pred HHHHHHHHHHH----HhCC-CEEEEcChhHhhcCChHHHHHHHHHHHHHHHhC-CCEEEE-EECcccccccccccceEEE
Confidence 44444444322 1223 37999999998764332 1233344445543 333333 33332222111 1246899
Q ss_pred heeEEEee
Q 024144 204 SSMVASVE 211 (272)
Q Consensus 204 Sstvvtv~ 211 (272)
+-++|.+.
T Consensus 186 ~D~vI~L~ 193 (237)
T TIGR03877 186 VDGIIRLD 193 (237)
T ss_pred EeEEEEEE
Confidence 99998885
No 5
>PRK04328 hypothetical protein; Provisional
Probab=97.75 E-value=0.00042 Score=62.81 Aligned_cols=144 Identities=19% Similarity=0.177 Sum_probs=83.9
Q ss_pred hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (272)
Q Consensus 50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (272)
.+..+++.+..+.+|-+|+.+++-+++.|+|... -+.++.++|+|+.-.+....... + +..+..++.
T Consensus 46 ~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~~~l~iid~~~~~~~~~~~~~~----------~-~~~~~~~~~ 114 (249)
T PRK04328 46 NGLQMGEPGVYVALEEHPVQVRRNMRQFGWDVRKYEEEGKFAIVDAFTGGIGSAAKREK----------Y-VVKDPDDVR 114 (249)
T ss_pred HHHhcCCcEEEEEeeCCHHHHHHHHHHcCCCHHHHhhcCCEEEEecccccccccccccc----------c-cccCcccHH
Confidence 4567799999999999999999999999987543 13479999999987765431110 1 111223344
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh---HHHHHHHHhhhcCCceeEEEeeecccccchhh-HhHHhhh
Q 024144 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKF-TSVLEYL 203 (272)
Q Consensus 128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~---~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~~-v~ALe~L 203 (272)
.++..+.+..+ +.++ -.|+||||+.|.+..+- ..+.++.+.|++.+ +..++- .|.+..+... -..++|+
T Consensus 115 ~~~~~i~~~i~----~~~~-~~vVIDSlt~l~~~~~~~~r~~~~~l~~~lk~~g-~t~llt-~e~~~~~~~~~~~~~~~~ 187 (249)
T PRK04328 115 ELIDVLRQAIK----DIGA-KRVVIDSVSTLYLTKPAMARSIVMQLKRVLSGLG-CTAIFV-SQVSVGERGFGGPGVEHA 187 (249)
T ss_pred HHHHHHHHHHH----hhCC-CEEEEeChhHhhcCChHHHHHHHHHHHHHHHhCC-CEEEEE-ECccccccccCCCCcEEE
Confidence 44344333222 1233 37999999998764321 12344445555433 333322 2333222111 1236888
Q ss_pred heeEEEee
Q 024144 204 SSMVASVE 211 (272)
Q Consensus 204 Sstvvtv~ 211 (272)
+-++|.+.
T Consensus 188 ~D~vI~L~ 195 (249)
T PRK04328 188 VDGIIRLD 195 (249)
T ss_pred EEEEEEEE
Confidence 88888875
No 6
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=97.73 E-value=0.0012 Score=58.34 Aligned_cols=136 Identities=17% Similarity=0.247 Sum_probs=93.4
Q ss_pred hccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhH
Q 024144 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (272)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (272)
+..+++.+..+.+|.+|+++.+-+++.|+|.... ...+.++|.+..+..|... +.+++-.
T Consensus 49 ~~~~g~~~~y~~~e~~~~~~~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~------------------~~~~ll~ 110 (234)
T PRK06067 49 ALKQGKKVYVITTENTSKSYLKQMESVKIDISDFFLWGYLRIFPLNTEGFEWNST------------------LANKLLE 110 (234)
T ss_pred HHhCCCEEEEEEcCCCHHHHHHHHHHCCCChhHHHhCCCceEEeccccccccCcc------------------hHHHHHH
Confidence 4457999999999999999999999999886541 3357778877666655431 1222222
Q ss_pred HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC-CceeEEEeeecccccchhhHhHHhhhheeE
Q 024144 129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH-DQVSSIFWLLHSDLHEIKFTSVLEYLSSMV 207 (272)
Q Consensus 129 l~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~-~~vssVl~LLHsDLHe~~~v~ALe~LSstv 207 (272)
.+...++. .++ -.|+|||++.++...+...+..++..|+.. ..=..++...|.+.+.+.....+++++-.+
T Consensus 111 ~l~~~i~~-------~~~-~~iviDs~t~~~~~~~~~~~~~~l~~l~~l~~~g~tvllt~~~~~~~~~~~~~~~~l~Dgv 182 (234)
T PRK06067 111 LIIEFIKS-------KRE-DVIIIDSLTIFATYAEEDDILNFLTEAKNLVDLGKTILITLHPYAFSEELLSRIRSICDVY 182 (234)
T ss_pred HHHHHHHh-------cCC-CEEEEecHHHHHhcCCHHHHHHHHHHHHHHHhCCCEEEEEecCCcCCHHHHHHHHhheEEE
Confidence 22222221 233 379999999998878887777775555331 112456777787777677778899999999
Q ss_pred EEeec
Q 024144 208 ASVEP 212 (272)
Q Consensus 208 vtv~P 212 (272)
+.+.-
T Consensus 183 I~L~~ 187 (234)
T PRK06067 183 LKLRA 187 (234)
T ss_pred EEEEe
Confidence 98875
No 7
>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=97.29 E-value=0.0093 Score=55.12 Aligned_cols=137 Identities=17% Similarity=0.196 Sum_probs=108.4
Q ss_pred hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (272)
Q Consensus 50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (272)
..-.++..|..|.-|.+--+|..-|..-|.|..- ++.++.|.-...+|..|+.... +
T Consensus 51 G~L~~g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G~l~~~~~~~~~~~~~~~~~---------------------~ 109 (235)
T COG2874 51 GFLMNGYRVTYVSTELTVREFIKQMESLSYDVSDFLLSGRLLFFPVNLEPVNWGRRSA---------------------R 109 (235)
T ss_pred HHHhCCceEEEEEechhHHHHHHHHHhcCCCchHHHhcceeEEEEecccccccChHHH---------------------H
Confidence 3556788999999999999999999988877554 5667777777779999998433 2
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc-CCceeEEEeeecccccchhhHhHHhhhhee
Q 024144 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS-HDQVSSIFWLLHSDLHEIKFTSVLEYLSSM 206 (272)
Q Consensus 128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~-~~~vssVl~LLHsDLHe~~~v~ALe~LSst 206 (272)
+++..+++..| ..-+. +|.|||||..+.+.+..+|-+++..+|+ ++.=.-|+--+|.+.-.+.++.-++..+++
T Consensus 110 ~~L~~l~~~~k---~~~~d--ViIIDSls~~~~~~~~~~vl~fm~~~r~l~d~gKvIilTvhp~~l~e~~~~rirs~~d~ 184 (235)
T COG2874 110 KLLDLLLEFIK---RWEKD--VIIIDSLSAFATYDSEDAVLNFMTFLRKLSDLGKVIILTVHPSALDEDVLTRIRSACDV 184 (235)
T ss_pred HHHHHHHhhHH---hhcCC--EEEEecccHHhhcccHHHHHHHHHHHHHHHhCCCEEEEEeChhhcCHHHHHHHHHhhhe
Confidence 22233333322 11244 8999999999999999999999999998 456677888999999999999999999999
Q ss_pred EEEeec
Q 024144 207 VASVEP 212 (272)
Q Consensus 207 vvtv~P 212 (272)
-+.++-
T Consensus 185 ~l~L~~ 190 (235)
T COG2874 185 YLRLRL 190 (235)
T ss_pred eEEEEh
Confidence 888854
No 8
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=97.27 E-value=0.0045 Score=61.33 Aligned_cols=131 Identities=18% Similarity=0.243 Sum_probs=83.9
Q ss_pred hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (272)
Q Consensus 50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (272)
.+..+++.+..+.||-+|+.+.+-++..|+|.+. -+..+.+++.+.++.+++. .+.
T Consensus 296 ~~~~~g~~~~yis~e~~~~~i~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~----------------------~~~ 353 (509)
T PRK09302 296 AACRRGERCLLFAFEESRAQLIRNARSWGIDLEKMEEKGLLKIICARPESYGLED----------------------HLI 353 (509)
T ss_pred HHHhCCCcEEEEEecCCHHHHHHHHHHcCCChHHHhhcCCceeecCCcccCCHHH----------------------HHH
Confidence 3456799999999999999999999988887544 1235778887776665543 111
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEeee-cccc-cchhhHhHHhh
Q 024144 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLL-HSDL-HEIKFTSVLEY 202 (272)
Q Consensus 128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LL-HsDL-He~~~v~ALe~ 202 (272)
.+ ...++. .++ -.|+||||+.+....+...+-+.|..|.+. -.+..++-.. +.+. +.+.....++|
T Consensus 354 ~i-~~~i~~-------~~~-~~vVIDslt~l~~~~~~~~~~~~l~~l~~~~k~~~~t~l~t~~~~~~~g~~~~~~~~~~~ 424 (509)
T PRK09302 354 II-KREIEE-------FKP-SRVAIDPLSALARGGSLNEFRQFVIRLTDYLKSEEITGLFTNLTPDFMGSHSITESHISS 424 (509)
T ss_pred HH-HHHHHH-------cCC-CEEEEcCHHHHHHhCCHHHHHHHHHHHHHHHHhCCCeEEEEeccccccCCCCCCcCceEE
Confidence 11 222221 234 379999999999877766555555544331 3455555432 2221 23333345899
Q ss_pred hheeEEEee
Q 024144 203 LSSMVASVE 211 (272)
Q Consensus 203 LSstvvtv~ 211 (272)
++.++|.+.
T Consensus 425 l~D~vI~L~ 433 (509)
T PRK09302 425 LTDTWILLQ 433 (509)
T ss_pred eeeEEEEEE
Confidence 999999986
No 9
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=96.75 E-value=0.036 Score=55.02 Aligned_cols=137 Identities=18% Similarity=0.191 Sum_probs=85.6
Q ss_pred hhccc-cceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 024144 50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (272)
Q Consensus 50 a~~~q-~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (272)
.+..+ ++.+..+.+|-+|+++.+-++..|+|.+.. +.++.+.|.|.+|..|.. ... . ++
T Consensus 54 ~~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~g~l~~~~~~~~~~~~~~-~~~----------~-------~~ 115 (509)
T PRK09302 54 NGIKRFDEPGVFVTFEESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSEQEE-AGE----------Y-------DL 115 (509)
T ss_pred HHHHhcCCCEEEEEccCCHHHHHHHHHHcCCCHHHHhhCCeEEEEecCcccccccc-ccc----------c-------cH
Confidence 35555 899999999999999999999999986552 346999999999988864 110 1 23
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH-----HHHHHHHhhhcCCceeEEEeeeccccc-c-hhhHhH
Q 024144 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS-----SVAGILSNLRSHDQVSSIFWLLHSDLH-E-IKFTSV 199 (272)
Q Consensus 127 ~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~-----~vc~lL~~Lr~~~~vssVl~LLHsDLH-e-~~~v~A 199 (272)
..++..+.+..+ +.++ -.|+|||++.+....... .+.+++..|++. .+..++. -|..-. + ....+.
T Consensus 116 ~~l~~~l~~~i~----~~~~-~~vVIDSls~l~~~~d~~~~~r~~l~~L~~~Lk~~-g~TvLlt-~~~~~~~~~~~~~~~ 188 (509)
T PRK09302 116 EALFIRIEYAID----KIGA-KRVVLDSIEALFSGFSNEAVVRRELRRLFAWLKQK-GVTAVIT-GERGDEYGPLTRYGV 188 (509)
T ss_pred HHHHHHHHHHHH----hhCC-CEEEECCHHHHHhhccCHHHHHHHHHHHHHHHHhC-CCEEEEE-ECCccCcCCccccCc
Confidence 333334333222 1233 469999999987654332 344455555543 3333333 343321 1 111224
Q ss_pred HhhhheeEEEee
Q 024144 200 LEYLSSMVASVE 211 (272)
Q Consensus 200 Le~LSstvvtv~ 211 (272)
.+|++..++.|.
T Consensus 189 ~~~laDgVI~L~ 200 (509)
T PRK09302 189 EEFVSDCVIILR 200 (509)
T ss_pred eEEEeeEEEEEe
Confidence 588999999887
No 10
>TIGR02655 circ_KaiC circadian clock protein KaiC. Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.
Probab=96.68 E-value=0.13 Score=51.24 Aligned_cols=94 Identities=22% Similarity=0.306 Sum_probs=60.4
Q ss_pred hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (272)
Q Consensus 50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (272)
+++.+++.+..+.||=|++++..=+++-|+|.+. ...++.+++.+....+..+ .+.
T Consensus 286 ~~~~~ge~~~y~s~eEs~~~i~~~~~~lg~~~~~~~~~g~l~~~~~~p~~~~~~~----------------------~~~ 343 (484)
T TIGR02655 286 NACANKERAILFAYEESRAQLLRNAYSWGIDFEEMEQQGLLKIICAYPESAGLED----------------------HLQ 343 (484)
T ss_pred HHHHCCCeEEEEEeeCCHHHHHHHHHHcCCChHHHhhCCcEEEEEcccccCChHH----------------------HHH
Confidence 4556889999999999999999999999988543 1235888887643332111 122
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhh
Q 024144 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNL 174 (272)
Q Consensus 128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~L 174 (272)
.+...+.+ .++ -.|+||||+.+....+..++-..++.|
T Consensus 344 ~i~~~i~~--------~~~-~~vvIDsi~~~~~~~~~~~~r~~~~~l 381 (484)
T TIGR02655 344 IIKSEIAD--------FKP-ARIAIDSLSALARGVSNNAFRQFVIGV 381 (484)
T ss_pred HHHHHHHH--------cCC-CEEEEcCHHHHHHhcCHHHHHHHHHHH
Confidence 22222322 233 379999999998766655544333333
No 11
>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family. Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.
Probab=96.17 E-value=0.25 Score=43.26 Aligned_cols=138 Identities=12% Similarity=0.089 Sum_probs=75.2
Q ss_pred hccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCC--CCcccccCCccccccccccccccchhhh
Q 024144 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPL--GWKNWLIDKDISQEASSLSSFCQDVRNL 126 (272)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPL--GW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (272)
+..+++.+..+.+|.+++.+.+-+++.|++.... +.++.+.|.++... .|.- . .. ++.++
T Consensus 44 ~~~~g~~~~~is~e~~~~~i~~~~~~~g~~~~~~~~~~~l~i~d~~~~~~~~~~~~-~-----------~~----~~~~~ 107 (229)
T TIGR03881 44 GLRDGDPVIYVTTEESRESIIRQAAQFGMDFEKAIEEGKLVIIDALMKEKEDEWSL-R-----------EL----SIEEL 107 (229)
T ss_pred HHhcCCeEEEEEccCCHHHHHHHHHHhCCCHHHHhhcCCEEEEEcccccccccccc-c-----------cC----CHHHH
Confidence 3346889999999999999998888899886642 34688888775431 1221 0 01 23333
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc---CCceeEEEeeecccc-cchhhHhHHhh
Q 024144 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS---HDQVSSIFWLLHSDL-HEIKFTSVLEY 202 (272)
Q Consensus 127 ~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~---~~~vssVl~LLHsDL-He~~~v~ALe~ 202 (272)
..-+....+.. + .++ -.|+|||++.++...+.. .-..+..|.+ ...+..++ .-|-.. -++.....++|
T Consensus 108 ~~~i~~~~~~~----~-~~~-~~vvIDsl~~l~~~~~~~-~r~~~~~l~~~l~~~~~tvil-~~~~~~~~~~~~~~~~~~ 179 (229)
T TIGR03881 108 LNKVIEAKKYL----G-YGH-ARLVIDSMSAFWLDKPAM-ARKYSYYLKRVLNRWNFTILL-TSQYAITTSQAFGFGIEH 179 (229)
T ss_pred HHHHHHHHHhh----c-cCc-eEEEecCchhhhccChHH-HHHHHHHHHHHHHhCCCEEEE-EecccccCCCCcccceEE
Confidence 32222222211 0 122 478999999998755432 1222222222 12333333 334222 12222235788
Q ss_pred hheeEEEeec
Q 024144 203 LSSMVASVEP 212 (272)
Q Consensus 203 LSstvvtv~P 212 (272)
++-.+|.+.-
T Consensus 180 l~D~vI~L~~ 189 (229)
T TIGR03881 180 VADGIIRFRK 189 (229)
T ss_pred EEeEEEEEEE
Confidence 8888888763
No 12
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=96.03 E-value=0.064 Score=48.37 Aligned_cols=142 Identities=20% Similarity=0.254 Sum_probs=87.1
Q ss_pred hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (272)
Q Consensus 50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (272)
.++..++.+..+.+|-+|++.++-+++.|.|.+. -+..+.++|.|+.+.+=.. . .-.+..++.
T Consensus 46 ~~~~~ge~vlyvs~~e~~~~l~~~~~~~g~d~~~~~~~g~l~i~d~~~~~~~~~~-~--------------~~~~~~~~~ 110 (260)
T COG0467 46 EGAREGEPVLYVSTEESPEELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLVS-I--------------VVGDPLDLE 110 (260)
T ss_pred HHHhcCCcEEEEEecCCHHHHHHHHHHcCCCHHHHhhcCCEEEEEcccccccccc-c--------------cccCCccHH
Confidence 4666699999999999999999999999998753 2345889998888774221 0 000112333
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHH-HHHHhhhcC-CceeEEEeeecccccchhhH--hHHhhh
Q 024144 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVA-GILSNLRSH-DQVSSIFWLLHSDLHEIKFT--SVLEYL 203 (272)
Q Consensus 128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc-~lL~~Lr~~-~~vssVl~LLHsDLHe~~~v--~ALe~L 203 (272)
++...+.+..+ .-++ ..++|||++.+......+... ..+..+.+. ..-. +.+++.+|....... +-.+|+
T Consensus 111 ~l~~~I~~~~~----~~~~-~~~ViDsi~~~~~~~~~~~~~r~~~~~l~~~~~~~~-~t~~~~~~~~~~~~~~~~~~~~~ 184 (260)
T COG0467 111 ELLDRIREIVE----KEGA-DRVVIDSITELTLYLNDPALVRRILLLLKRFLKKLG-VTSLLTTEAPVEERGESGVEEYI 184 (260)
T ss_pred HHHHHHHHHHH----HhCC-CEEEEeCCchHhhhcCchHHHHHHHHHHHHHHHhCC-CEEEEEecccccCCCccceEEEE
Confidence 33334444322 1222 689999999776666666554 444444442 1222 444555554332111 456668
Q ss_pred heeEEEeec
Q 024144 204 SSMVASVEP 212 (272)
Q Consensus 204 Sstvvtv~P 212 (272)
+..++.+..
T Consensus 185 vdgvI~l~~ 193 (260)
T COG0467 185 VDGVIRLDL 193 (260)
T ss_pred EEEEEEEee
Confidence 888888876
No 13
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=95.94 E-value=0.16 Score=42.46 Aligned_cols=135 Identities=20% Similarity=0.151 Sum_probs=79.6
Q ss_pred hccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhH
Q 024144 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (272)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (272)
+..+++.+.++.+|-+++.+.+-+++.|++.+.+ ...+.+.|.+...+...+ . +...++..
T Consensus 23 ~~~~g~~v~~~s~e~~~~~~~~~~~~~g~~~~~l~~~g~l~~~d~~~~~~s~~~--------------~---~~~~~~~~ 85 (187)
T cd01124 23 GLARGEPGLYVTLEESPEELIENAESLGWDLERLEDEGLLAIVDADPDEIGPAE--------------S---SLRLELIQ 85 (187)
T ss_pred HHHCCCcEEEEECCCCHHHHHHHHHHcCCChHHHHhcCCeEEEecCccccchhh--------------h---hhhHHHHH
Confidence 4467899999999999999999999889885531 234677775554442111 0 00001111
Q ss_pred HHHHHHHhccCccCCCCCcEEEEEechhHHHH---hcChHHHHHHHHhhhcCCceeEEEeeeccccc-c-hhhHhHHhhh
Q 024144 129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR---HASISSVAGILSNLRSHDQVSSIFWLLHSDLH-E-IKFTSVLEYL 203 (272)
Q Consensus 129 l~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~---h~s~~~vc~lL~~Lr~~~~vssVl~LLHsDLH-e-~~~v~ALe~L 203 (272)
.+...+.. .++ -.|+||+++.++. ......+-+++..|++. .+. ++..-|..-. + ......++|+
T Consensus 86 ~i~~~~~~-------~~~-~~lviD~~~~~~~~~~~~~~~~i~~l~~~l~~~-g~t-vi~v~~~~~~~~~~~~~~~~~~~ 155 (187)
T cd01124 86 RLKDAIEE-------FKA-KRVVIDSVSGLLLMEQSTARLEIRRLLFALKRF-GVT-TLLTSEQSGLEGTGFGGGDVEYL 155 (187)
T ss_pred HHHHHHHH-------hCC-CEEEEeCcHHHhhcChHHHHHHHHHHHHHHHHC-CCE-EEEEeccccCCCcccCcCceeEe
Confidence 11222111 233 5899999999987 44445556677777754 333 3333343221 1 2333567888
Q ss_pred heeEEEeec
Q 024144 204 SSMVASVEP 212 (272)
Q Consensus 204 Sstvvtv~P 212 (272)
+..++.++-
T Consensus 156 aD~ii~l~~ 164 (187)
T cd01124 156 VDGVIRLRL 164 (187)
T ss_pred eeEEEEEEE
Confidence 888887764
No 14
>TIGR02655 circ_KaiC circadian clock protein KaiC. Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.
Probab=95.66 E-value=0.17 Score=50.35 Aligned_cols=137 Identities=19% Similarity=0.192 Sum_probs=82.5
Q ss_pred hhccc-cceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 024144 50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (272)
Q Consensus 50 a~~~q-~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (272)
+++.+ ++.+..|.||=+|+++.+-+++.|+|-+.. ..++.++|.+..+ |..... ..+ ++
T Consensus 44 ~g~~~~ge~~lyvs~eE~~~~l~~~~~~~G~~~~~~~~~g~l~~~~~~~~~--~~~~~~---------~~~-------~l 105 (484)
T TIGR02655 44 NGIIHFDEPGVFVTFEESPQDIIKNARSFGWDLQKLVDEGKLFILDASPDP--EGQDVV---------GGF-------DL 105 (484)
T ss_pred HHHHhCCCCEEEEEEecCHHHHHHHHHHcCCCHHHHhhcCceEEEecCchh--cccccc---------ccC-------CH
Confidence 46666 899999999999999999999999986531 3468888875433 222110 001 22
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH-----HHHHHHHhhhcCCceeEEEeeec-ccccch-hhHhH
Q 024144 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS-----SVAGILSNLRSHDQVSSIFWLLH-SDLHEI-KFTSV 199 (272)
Q Consensus 127 ~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~-----~vc~lL~~Lr~~~~vssVl~LLH-sDLHe~-~~v~A 199 (272)
..++..+.+... .+++ --|+|||++.+....+.. .+.++++.|++. .+..++- -| .+...+ ...+.
T Consensus 106 ~~~l~~i~~~ls----~g~~-qRVvIDSl~aL~~~~~~~~~~r~~l~~Li~~L~~~-g~TvLLt-sh~~~~~~~~~~~~~ 178 (484)
T TIGR02655 106 SALIERINYAIR----KYKA-KRVSIDSVTAVFQQYDAVSVVRREIFRLVARLKQI-GVTTVMT-TERIEEYGPIARYGV 178 (484)
T ss_pred HHHHHHHHHHHH----HhCC-cEEEEeehhHhhhhcCchHHHHHHHHHHHHHHHHC-CCEEEEE-ecCcccccccccCCc
Confidence 333333333211 1233 479999999987655542 345566666642 3444443 34 232221 12223
Q ss_pred HhhhheeEEEee
Q 024144 200 LEYLSSMVASVE 211 (272)
Q Consensus 200 Le~LSstvvtv~ 211 (272)
.+|++-.+|.+.
T Consensus 179 ~e~laDgVI~L~ 190 (484)
T TIGR02655 179 EEFVSDNVVILR 190 (484)
T ss_pred eeEeeeeEEEEE
Confidence 599999999886
No 15
>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family. This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.
Probab=95.50 E-value=0.17 Score=46.32 Aligned_cols=133 Identities=14% Similarity=0.126 Sum_probs=70.3
Q ss_pred hccccceeEEEEeecChHH----HHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 024144 51 GKSQSRGLVVVAYSRSPSF----YVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (272)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~----y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (272)
++.+++.+..+.+|-++++ +..-.++.|+|.+...++++++|..+.+- .. .++
T Consensus 60 ~a~~Ge~vlyis~Ee~~~~~~~~l~~~a~~~g~d~~~~~~~l~~id~~~~~~-----~~------------------~~~ 116 (259)
T TIGR03878 60 QASRGNPVLFVTVESPANFVYTSLKERAKAMGVDFDKIEENIILIDAASSTE-----LR------------------ENV 116 (259)
T ss_pred HHhCCCcEEEEEecCCchHHHHHHHHHHHHcCCCHHHHhCCEEEEECCCchh-----hh------------------hhH
Confidence 5567999999999976653 33334566777655456788888765321 00 012
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH---HHHHHHHhhhcCCceeEEEeeecccc---cc-hhhHhH
Q 024144 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS---SVAGILSNLRSHDQVSSIFWLLHSDL---HE-IKFTSV 199 (272)
Q Consensus 127 ~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~---~vc~lL~~Lr~~~~vssVl~LLHsDL---He-~~~v~A 199 (272)
..++..+.+..+ +.++ =.|+||||+.+.+..... .+-+++..|++.+.-.-++.-.+.+. .. +..-..
T Consensus 117 ~~l~~~l~~~i~----~~~~-~~vVIDSls~l~~~~~~~~r~~~~~L~~~lk~~~~t~ll~~e~~~~~~~~~~~~~~~~~ 191 (259)
T TIGR03878 117 PNLLATLAYAIK----EYKV-KNTVIDSITGLYEAKEMMAREIVRQLFNFMKKWYQTALFVSQKRSGHEELSAEAAGGYA 191 (259)
T ss_pred HHHHHHHHHHHH----hhCC-CEEEEcCchHhcccchHHHHHHHHHHHHHHHHcCCeEEEEeccccCcccccccccCCcc
Confidence 222233322211 1233 379999999876543211 12334444454333222333233322 11 111125
Q ss_pred HhhhheeEEEee
Q 024144 200 LEYLSSMVASVE 211 (272)
Q Consensus 200 Le~LSstvvtv~ 211 (272)
++|++-.+|.+.
T Consensus 192 ~~~l~D~vI~L~ 203 (259)
T TIGR03878 192 VSHIVDGTIVLA 203 (259)
T ss_pred eeEeeccEEEEe
Confidence 799999988886
No 16
>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family. This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.
Probab=94.81 E-value=0.45 Score=41.70 Aligned_cols=130 Identities=14% Similarity=0.194 Sum_probs=75.9
Q ss_pred hccccceeEEEEeecChHHHHHHHhhcCcCccC-CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHH
Q 024144 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS-SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKL 129 (272)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s-~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl 129 (272)
+..+++.+..+.+|-+++.+.+-++..|++... .++++.++|....-. ...++.+...
T Consensus 40 ~~~~g~~~~y~s~e~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---------------------~~~~~~l~~~ 98 (224)
T TIGR03880 40 GLKNGEKAMYISLEEREERILGYAKSKGWDLEDYIDKSLYIVRLDPSDF---------------------KTSLNRIKNE 98 (224)
T ss_pred HHhCCCeEEEEECCCCHHHHHHHHHHcCCChHHHHhCCeEEEecCHHHH---------------------HhhHHHHHHH
Confidence 445789999999999999999999988887543 122466776321100 0012222221
Q ss_pred HHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh-----HHHHHHHHhhhcCCceeEEEeeecccccch--hhHhHHhh
Q 024144 130 YSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-----SSVAGILSNLRSHDQVSSIFWLLHSDLHEI--KFTSVLEY 202 (272)
Q Consensus 130 ~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~-----~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~--~~v~ALe~ 202 (272)
+...++. .++ -.|+|||++.+-.-.+. ..+..++..|++. .+ .++-.-|.+-..+ ...+.+++
T Consensus 99 ~~~~i~~-------~~~-~~vVIDsls~l~~~~~~~~~~r~~l~~l~~~lk~~-~~-tvll~s~~~~~~~~~~~~~~~~~ 168 (224)
T TIGR03880 99 LPILIKE-------LGA-SRVVIDPISLLETLFDDDAERRTELFRFYSSLRET-GV-TTILTSEADKTNVFASKYGLIEY 168 (224)
T ss_pred HHHHHHH-------hCC-CEEEEcChHHHhhhcCCHHHHHHHHHHHHHHHHhC-CC-EEEEEEcccCCCCCccCCCceEE
Confidence 1122221 223 36789999987222222 3556777777754 33 3444456543332 22456899
Q ss_pred hheeEEEee
Q 024144 203 LSSMVASVE 211 (272)
Q Consensus 203 LSstvvtv~ 211 (272)
++..++.+.
T Consensus 169 l~D~vI~L~ 177 (224)
T TIGR03880 169 LADGVIILK 177 (224)
T ss_pred EEeEEEEEe
Confidence 999999984
No 17
>KOG4723 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.77 E-value=0.17 Score=46.73 Aligned_cols=73 Identities=21% Similarity=0.378 Sum_probs=56.9
Q ss_pred CCCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEec
Q 024144 16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDC 93 (272)
Q Consensus 16 ge~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ 93 (272)
.|+--+++++|+..+| |.-+|-|++. -..+++ +.+.+++|.++.+.|--.+++-|.|-.. .+.+++++|.
T Consensus 16 ~EqgkltLl~d~~eT~-gsFl~H~~l~---~~Lkan----~~~cFlaf~k~fshy~i~~rKlG~~l~t~k~rgqlvF~dg 87 (248)
T KOG4723|consen 16 PEQGKLTLLLDTRETP-GSFLFHYYLY---HALKAN----ESTCFLAFSKTFSHYAISMRKLGMDLKTKKNRGQLVFIDG 87 (248)
T ss_pred CCCccEEEEeecccCC-ceeeHHHHHH---HHHhcC----CcEEEEEeecchhHHHHHHHHhCCceeecccCCcEEEEhh
Confidence 4666789999999998 5777777542 222222 8999999999999999999999999877 2335999998
Q ss_pred cCC
Q 024144 94 YTD 96 (272)
Q Consensus 94 ysD 96 (272)
++=
T Consensus 88 l~~ 90 (248)
T KOG4723|consen 88 LSM 90 (248)
T ss_pred hhh
Confidence 873
No 18
>PF05625 PAXNEB: PAXNEB protein; InterPro: IPR008728 The RNA polymerase II elongator complex is a major histone acetyltransferase component of the RNA polymerase II (RNAPII) holoenzyme and is involved in transcriptional elongation [, ]. It may also play some role in wobble uridine tRNA modification []. This entry represents the ELP4 subunit. ELP4 is not required for the association of the complex with nascent RNA transcript, but is required for complex integrity and histone acetyltransferase activity. It is also required for an early step in synthesis of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups present on uridines at the wobble position in tRNA in yeast species.; GO: 0006357 regulation of transcription from RNA polymerase II promoter, 0033588 Elongator holoenzyme complex; PDB: 4EJS_A 4A8J_A.
Probab=94.62 E-value=0.32 Score=47.15 Aligned_cols=69 Identities=23% Similarity=0.232 Sum_probs=49.7
Q ss_pred EEEEEechhHHHHhcCh----HHHHHHHHhhhc----CCceeEEEeeeccccc--chhhHhHHhhhheeEEEeecCCcc
Q 024144 148 FSIAIDSVSEMVRHASI----SSVAGILSNLRS----HDQVSSIFWLLHSDLH--EIKFTSVLEYLSSMVASVEPFNQA 216 (272)
Q Consensus 148 ~tVaIDSLS~LL~h~s~----~~vc~lL~~Lr~----~~~vssVl~LLHsDLH--e~~~v~ALe~LSstvvtv~P~~~~ 216 (272)
.=|+|-||..-+-..+- ..+.++|+.||. +..-..++--+=.+|- .+..+..||+++-++|.|+|....
T Consensus 202 ~RI~I~sl~SP~w~~~~~~~~~~ll~FL~~LR~LlR~~~s~~v~~iTlP~~L~~~~~~~~~~l~~l~D~vi~Le~F~~~ 280 (363)
T PF05625_consen 202 LRIVIPSLGSPLWYPPSASQPSELLRFLHSLRALLRKYSSNAVAMITLPSHLYPRSPSLVRRLEHLADGVIELESFAGS 280 (363)
T ss_dssp EEEEETTTT-TTTS-GGGGBHHHHHHHHHHHHHHHHHTTTTEEEEEEEEGTTS---HHHHHHHHHHSSEEEEEEE--HH
T ss_pred EEEEEcCCCCcccCCcccccHHHHHHHHHHHHHHHhccCCCEEEEEEECHHHhccChHHHHHHHHhCCEEEEeecCCCc
Confidence 67899887765543322 248999999987 3555555556677877 799999999999999999999876
No 19
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=94.40 E-value=0.45 Score=42.81 Aligned_cols=127 Identities=14% Similarity=0.201 Sum_probs=71.1
Q ss_pred cccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHH
Q 024144 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY 130 (272)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~ 130 (272)
.+++.+..+.+|.+++++.+.+++.|+|.+. ....+.++++|..-.+. .+.+..+
T Consensus 50 ~~g~~~~yi~~e~~~~~~~~~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~-----------------------~~~~~~l 106 (230)
T PRK08533 50 QNGYSVSYVSTQLTTTEFIKQMMSLGYDINKKLISGKLLYIPVYPLLSGN-----------------------SEKRKFL 106 (230)
T ss_pred hCCCcEEEEeCCCCHHHHHHHHHHhCCchHHHhhcCcEEEEEecccccCh-----------------------HHHHHHH
Confidence 4678889999999999999999998987653 23467777776321111 0111122
Q ss_pred HHHHHhccCccCCCCCcEEEEEechhHHHHhcCh----HHHHHHHHhhhcCCceeEEEeeecccccc--hhhHhHHhhhh
Q 024144 131 SLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI----SSVAGILSNLRSHDQVSSIFWLLHSDLHE--IKFTSVLEYLS 204 (272)
Q Consensus 131 ~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~----~~vc~lL~~Lr~~~~vssVl~LLHsDLHe--~~~v~ALe~LS 204 (272)
..+.+..+ ..++ -.++||+++.++....- ..+.++|..|++... .++- .| |... .....-++|++
T Consensus 107 ~~il~~~~----~~~~-~~lVIDe~t~~l~~~~d~~~~~~l~~~l~~l~~~g~--tvi~-t~-~~~~~~~~~~~~~~~~~ 177 (230)
T PRK08533 107 KKLMNTRR----FYEK-DVIIIDSLSSLISNDASEVAVNDLMAFFKRISSLNK--VIIL-TA-NPKELDESVLTILRTAA 177 (230)
T ss_pred HHHHHHHH----hcCC-CEEEEECccHHhcCCcchHHHHHHHHHHHHHHhCCC--EEEE-Ee-cccccccccceeEEEee
Confidence 22232211 1123 37999999999854322 345666666654322 2222 22 2221 11223467777
Q ss_pred eeEEEee
Q 024144 205 SMVASVE 211 (272)
Q Consensus 205 stvvtv~ 211 (272)
-++|.+.
T Consensus 178 DgvI~L~ 184 (230)
T PRK08533 178 TMLIRLE 184 (230)
T ss_pred eEEEEEE
Confidence 7777665
No 20
>PRK05973 replicative DNA helicase; Provisional
Probab=93.45 E-value=1.6 Score=40.16 Aligned_cols=62 Identities=13% Similarity=-0.025 Sum_probs=40.4
Q ss_pred cCCCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccC
Q 024144 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS 83 (272)
Q Consensus 15 ~ge~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s 83 (272)
.|=.++.+++---=...+=+.+..+|+. .+..+++.|.++.||-+|++..+=++..|+|.+.
T Consensus 59 GGl~~Gsl~LIaG~PG~GKT~lalqfa~-------~~a~~Ge~vlyfSlEes~~~i~~R~~s~g~d~~~ 120 (237)
T PRK05973 59 SQLKPGDLVLLGARPGHGKTLLGLELAV-------EAMKSGRTGVFFTLEYTEQDVRDRLRALGADRAQ 120 (237)
T ss_pred CCCCCCCEEEEEeCCCCCHHHHHHHHHH-------HHHhcCCeEEEEEEeCCHHHHHHHHHHcCCChHH
Confidence 4555554444322233333444444332 3445789999999999999999999999988666
No 21
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=93.05 E-value=0.5 Score=41.43 Aligned_cols=93 Identities=19% Similarity=0.134 Sum_probs=51.4
Q ss_pred EEEEEechhHHHHhc----ChHHHHHHHHhhhcC-CceeEEEeeecc------c-------ccchhhHhHHhhhheeEEE
Q 024144 148 FSIAIDSVSEMVRHA----SISSVAGILSNLRSH-DQVSSIFWLLHS------D-------LHEIKFTSVLEYLSSMVAS 209 (272)
Q Consensus 148 ~tVaIDSLS~LL~h~----s~~~vc~lL~~Lr~~-~~vssVl~LLHs------D-------LHe~~~v~ALe~LSstvvt 209 (272)
-.|+||+|+.+-... ....+...+..|+.- .+.-..+.+++. + ++.-+-.+++++.|.+++.
T Consensus 125 ~~vvID~l~~l~~~~~~~~~~~~~~~~~~~L~~la~~~~~~ii~~~q~~r~~~~~~~~~~~~~~~~gS~~i~~~aD~vi~ 204 (242)
T cd00984 125 GLIVIDYLQLMSGSKKKGNRQQEVAEISRSLKLLAKELNVPVIALSQLSRGVESRADKRPMLSDLRESGSIEQDADVVMF 204 (242)
T ss_pred CEEEEcCchhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEecccChhhhccCCCCCCHHHHhhhcccccCCCEEEE
Confidence 489999999664322 113344555555531 223333444441 1 2333445788999999999
Q ss_pred eecCCccccccccccchhhhhhccccceEEEEE-EeccCCcEEEE
Q 024144 210 VEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVR-FKRRNGRVRVM 253 (272)
Q Consensus 210 v~P~~~~~~~~~~~~~~~~~l~~n~~k~~~~vr-~KrRnGRV~~~ 253 (272)
+.+...... .+..++.+.|+ .|.|+|..-..
T Consensus 205 l~~~~~~~~-------------~~~~~~~~~l~v~KnR~G~~g~~ 236 (242)
T cd00984 205 LYRDEYYNK-------------ESESKGIAEIIVAKNRNGPTGTV 236 (242)
T ss_pred Eeccccccc-------------ccCCCCceEEEEECCCCCCCeeE
Confidence 987532110 11223334443 58899987764
No 22
>TIGR02237 recomb_radB DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).
Probab=92.55 E-value=1.2 Score=38.25 Aligned_cols=39 Identities=13% Similarity=0.298 Sum_probs=27.3
Q ss_pred cccceeEEEEeec-ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144 53 SQSRGLVVVAYSR-SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (272)
Q Consensus 53 ~q~~~Vhvl~fe~-Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (272)
.+++.+..+.+|. +|+.+.+.++.. ++ ....++++++++
T Consensus 38 ~~g~~v~yi~~e~~~~~rl~~~~~~~-~~--~~~~~i~~~~~~ 77 (209)
T TIGR02237 38 RQGKKVVYIDTEGLSPERFKQIAEDR-PE--RALSNFIVFEVF 77 (209)
T ss_pred hCCCeEEEEECCCCCHHHHHHHHHhC-hH--HHhcCEEEEECC
Confidence 4578999999996 899888866643 12 113568888763
No 23
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=92.41 E-value=7 Score=34.14 Aligned_cols=65 Identities=23% Similarity=0.176 Sum_probs=37.9
Q ss_pred EEEEEechhHHHHhc-----C----hHHHHHHHHhhhc----CCceeEEEeeecccccc----hhhHhHHhhhheeEEEe
Q 024144 148 FSIAIDSVSEMVRHA-----S----ISSVAGILSNLRS----HDQVSSIFWLLHSDLHE----IKFTSVLEYLSSMVASV 210 (272)
Q Consensus 148 ~tVaIDSLS~LL~h~-----s----~~~vc~lL~~Lr~----~~~vssVl~LLHsDLHe----~~~v~ALe~LSstvvtv 210 (272)
=.|+|||++.+.+.. . ...+.+.++.|++ +....=+..-++.+.+. +---..++|++++++.+
T Consensus 109 ~lvVIDsi~al~~~~~~~~~~~~~~~~~l~~~l~~L~~~a~~~~v~vi~tnq~~~~~~~~~~~~~gg~~~~~~~d~ii~l 188 (225)
T PRK09361 109 GLIVLDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHDLAVVITNQVYSDIDSDGLRPLGGHTLEHWSKTILRL 188 (225)
T ss_pred cEEEEeCcHHHhHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhCCEEEEEccceecCCCCcccCCCcchhhhhccEEEEE
Confidence 379999999987642 1 1234554444433 33333333444455542 21123789999999998
Q ss_pred ec
Q 024144 211 EP 212 (272)
Q Consensus 211 ~P 212 (272)
..
T Consensus 189 ~~ 190 (225)
T PRK09361 189 EK 190 (225)
T ss_pred EE
Confidence 66
No 24
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=91.10 E-value=3.7 Score=38.45 Aligned_cols=39 Identities=21% Similarity=0.269 Sum_probs=31.1
Q ss_pred ceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (272)
Q Consensus 56 ~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (272)
..+..+.+|. +|+.+.+.+++.|+|.+..-+++++++++
T Consensus 137 ~~~~yi~te~~f~~~rl~~~~~~~g~~~~~~l~~i~~~~~~ 177 (317)
T PRK04301 137 GKAVYIDTEGTFRPERIEQMAEALGLDPDEVLDNIHVARAY 177 (317)
T ss_pred ceEEEEeCCCCcCHHHHHHHHHHcCCChHhhhccEEEEeCC
Confidence 5788999998 69999999998888876545567777764
No 25
>PRK11823 DNA repair protein RadA; Provisional
Probab=90.97 E-value=15 Score=36.68 Aligned_cols=115 Identities=22% Similarity=0.177 Sum_probs=62.9
Q ss_pred cccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHH
Q 024144 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (272)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~ 132 (272)
.+++.|..+.+|-+++.+..-.++.|++. +++.+.+ + .++..+...
T Consensus 106 ~~g~~vlYvs~Ees~~qi~~ra~rlg~~~----~~l~~~~----e--------------------------~~l~~i~~~ 151 (446)
T PRK11823 106 AAGGKVLYVSGEESASQIKLRAERLGLPS----DNLYLLA----E--------------------------TNLEAILAT 151 (446)
T ss_pred hcCCeEEEEEccccHHHHHHHHHHcCCCh----hcEEEeC----C--------------------------CCHHHHHHH
Confidence 35788899999999998877677777762 2333221 0 012222222
Q ss_pred HHHhccCccCCCCCcEEEEEechhHHHHh------cChHHHHHHHHhhhc---CCceeEE-EeeecccccchhhHhHHhh
Q 024144 133 IIEQGKGLIGQGKDRFSIAIDSVSEMVRH------ASISSVAGILSNLRS---HDQVSSI-FWLLHSDLHEIKFTSVLEY 202 (272)
Q Consensus 133 i~e~~~~~~~~~k~~~tVaIDSLS~LL~h------~s~~~vc~lL~~Lr~---~~~vssV-l~LLHsDLHe~~~v~ALe~ 202 (272)
+.+ .++ -.|+|||++.+..- .+..++-..+..|.+ ...+.-+ ++-+..|-.-.+. ..++|
T Consensus 152 i~~--------~~~-~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~~ak~~~itvilv~hvtk~~~~ag~-~~leh 221 (446)
T PRK11823 152 IEE--------EKP-DLVVIDSIQTMYSPELESAPGSVSQVRECAAELMRLAKQRGIAVFLVGHVTKEGAIAGP-RVLEH 221 (446)
T ss_pred HHh--------hCC-CEEEEechhhhccccccCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEeeccCCCCcCCc-chhhh
Confidence 222 234 47999999998652 123334333333333 1223222 2223233222222 56999
Q ss_pred hheeEEEee
Q 024144 203 LSSMVASVE 211 (272)
Q Consensus 203 LSstvvtv~ 211 (272)
++.+++.++
T Consensus 222 lvD~Vi~le 230 (446)
T PRK11823 222 MVDTVLYFE 230 (446)
T ss_pred hCeEEEEEE
Confidence 999999775
No 26
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=90.05 E-value=20 Score=35.06 Aligned_cols=115 Identities=21% Similarity=0.178 Sum_probs=62.6
Q ss_pred ccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHHH
Q 024144 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (272)
Q Consensus 54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i 133 (272)
+++.|..+.+|-+++....-.++.|++ ..++.+.+. .++..++..+
T Consensus 109 ~g~~VlYvs~EEs~~qi~~Ra~rlg~~----~~~l~l~~e------------------------------~~le~I~~~i 154 (372)
T cd01121 109 RGGKVLYVSGEESPEQIKLRADRLGIS----TENLYLLAE------------------------------TNLEDILASI 154 (372)
T ss_pred cCCeEEEEECCcCHHHHHHHHHHcCCC----cccEEEEcc------------------------------CcHHHHHHHH
Confidence 457888889999998887766666666 233433220 0122222222
Q ss_pred HHhccCccCCCCCcEEEEEechhHHHHhc------ChHHHHHHHHhhhc---CCceeEE-EeeecccccchhhHhHHhhh
Q 024144 134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA------SISSVAGILSNLRS---HDQVSSI-FWLLHSDLHEIKFTSVLEYL 203 (272)
Q Consensus 134 ~e~~~~~~~~~k~~~tVaIDSLS~LL~h~------s~~~vc~lL~~Lr~---~~~vssV-l~LLHsDLHe~~~v~ALe~L 203 (272)
.+ .++ -.|+|||++.+.... +..++-..+..|.+ ...+.-+ ++-+..|-+-.+ .+.|+|+
T Consensus 155 ~~--------~~~-~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~lak~~~itvilvghvtk~g~~aG-~~~leh~ 224 (372)
T cd01121 155 EE--------LKP-DLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMRFAKERNIPIFIVGHVTKEGSIAG-PKVLEHM 224 (372)
T ss_pred Hh--------cCC-cEEEEcchHHhhccccccCCCCHHHHHHHHHHHHHHHHHcCCeEEEEeeccCCCcccC-cccchhh
Confidence 22 234 479999999996532 13444333333333 2223222 222333332222 2579999
Q ss_pred heeEEEeec
Q 024144 204 SSMVASVEP 212 (272)
Q Consensus 204 Sstvvtv~P 212 (272)
+.+++.++-
T Consensus 225 vD~Vi~le~ 233 (372)
T cd01121 225 VDTVLYFEG 233 (372)
T ss_pred ceEEEEEEc
Confidence 999998764
No 27
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=89.08 E-value=17 Score=33.63 Aligned_cols=38 Identities=18% Similarity=0.279 Sum_probs=29.7
Q ss_pred eeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144 57 GLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (272)
Q Consensus 57 ~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (272)
.+..+.+|- +|+.+.+.++..|++.+...+++.+..++
T Consensus 131 ~~~yi~te~~f~~~rl~~~~~~~gl~~~~~~~~i~i~~~~ 170 (310)
T TIGR02236 131 KAVYIDTENTFRPERIMQMAEARGLDPDEVLKNIYVARAY 170 (310)
T ss_pred eEEEEECCCCCCHHHHHHHHHHcCCCHHHHhhceEEEecC
Confidence 788888888 79999999998888865545667777654
No 28
>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.
Probab=88.05 E-value=9.9 Score=32.92 Aligned_cols=39 Identities=26% Similarity=0.281 Sum_probs=27.6
Q ss_pred ceeEEEEeecC--hHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144 56 RGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCY 94 (272)
Q Consensus 56 ~~Vhvl~fe~S--pe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (272)
..|..+..|.+ ++.+.+.....+.+.....+++++.+++
T Consensus 54 ~~v~yi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~ 94 (226)
T cd01393 54 GKVVYIDTEGAFRPERLVQLAVRFGLDPEEVLDNIYVARPY 94 (226)
T ss_pred ceEEEEecCCCCCHHHHHHHHHHhccchhhhhccEEEEeCC
Confidence 77888888876 6677777777776655445677777763
No 29
>PTZ00035 Rad51 protein; Provisional
Probab=87.63 E-value=27 Score=33.54 Aligned_cols=40 Identities=20% Similarity=0.272 Sum_probs=29.4
Q ss_pred cceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (272)
Q Consensus 55 ~~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (272)
+..+..+..|. +|+...+..++.|++.+..-.++.+.++|
T Consensus 152 ~g~vvyIdtE~~f~~eri~~ia~~~g~~~~~~l~nI~~~~~~ 193 (337)
T PTZ00035 152 EGKVLYIDTEGTFRPERIVQIAERFGLDPEDVLDNIAYARAY 193 (337)
T ss_pred CceEEEEEccCCCCHHHHHHHHHHhCCChHhHhhceEEEccC
Confidence 45677888887 48888888888888876655667666654
No 30
>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
Probab=87.40 E-value=6 Score=34.48 Aligned_cols=40 Identities=23% Similarity=0.284 Sum_probs=31.3
Q ss_pred cceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (272)
Q Consensus 55 ~~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (272)
.+++..+.+|. +++.+.+.+++.|.+.....+++++.++|
T Consensus 53 ~~~viyi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~ 94 (235)
T cd01123 53 EGKAVYIDTEGTFRPERLVQIAERFGLDPEEVLDNIYVARAY 94 (235)
T ss_pred CccEEEEeCCCCcCHHHHHHHHHHhccChHhHhcCEEEEecC
Confidence 46788888888 57888888888888776656778887764
No 31
>PF03192 DUF257: Pyrococcus protein of unknown function, DUF257; InterPro: IPR005489 This family of proteins is of unknown function.; PDB: 2EKD_C.
Probab=86.16 E-value=22 Score=32.22 Aligned_cols=153 Identities=17% Similarity=0.278 Sum_probs=90.8
Q ss_pred ceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEe--------
Q 024144 21 ALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILD-------- 92 (272)
Q Consensus 21 ~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D-------- 92 (272)
+++|+-+-.++ +.++ ++..++.++.++-.|.|..+==+-..|..-|+..|+|.+. -+++-++-
T Consensus 13 ~VLVEy~S~~~--~el~------~~~li~~~~~~~~~vlI~DilDtl~i~~~~l~~~Gi~~~~-l~~~~VIKiGG~~~~G 83 (210)
T PF03192_consen 13 TVLVEYSSSSP--PELL------FYELIKWAREKGYPVLIDDILDTLHIYKKHLELMGIDTDI-LDNIKVIKIGGRIEVG 83 (210)
T ss_dssp EEEEEE-TTS---THHH------HHHHHH---T-SS-BEEEEETTHHHHHHHHHHHTT---HH-HHCSEEEEES-S---S
T ss_pred EEEEEeCCCCc--HHHH------HHHHHHHhhhcCCCEEEEEcCCCHHHHHHHHHHcCCCccc-ccCceEEEecCeeeee
Confidence 56777665333 3333 4556667888888999998888888999999999999775 12233332
Q ss_pred -------ccCCCCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHH--HhcC
Q 024144 93 -------CYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMV--RHAS 163 (272)
Q Consensus 93 -------~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL--~h~s 163 (272)
..+||--|. +.+..+.+. ... +.++...+=-+.-++ ...+
T Consensus 84 nVv~ri~~~~d~~~~~--------------------------k~Y~~~~~~---~~~--~~~~i~ivlGiekl~~~~~~~ 132 (210)
T PF03192_consen 84 NVVGRIPITSDPSVYL--------------------------KEYEEILEK---VLE--KEKVINIVLGIEKLFYFFENS 132 (210)
T ss_dssp EEEEEE-----BBTTB--------------------------HHHHHHHTT--------S-SEEEEEE-HHHHH-HH-S-
T ss_pred eEEEEEecccChHHHH--------------------------HHHHHHHHH---Hhc--cCCeEEEEecHHHHHHHHhcc
Confidence 222222222 222333332 111 222555555677777 4468
Q ss_pred hHHHHHHHHhhhcC--CceeEEEeeecccccch---hhHhHHhhhheeEEEeecC
Q 024144 164 ISSVAGILSNLRSH--DQVSSIFWLLHSDLHEI---KFTSVLEYLSSMVASVEPF 213 (272)
Q Consensus 164 ~~~vc~lL~~Lr~~--~~vssVl~LLHsDLHe~---~~v~ALe~LSstvvtv~P~ 213 (272)
...+..++..+.+. ..=..-|..+..|+-+. .++..||-+||+|+.+...
T Consensus 133 ~~e~~~~~~~i~~~lg~~~r~a~yfiN~dvl~~~~~~~l~~LEeiattVi~i~~~ 187 (210)
T PF03192_consen 133 PRELILFFNSISRFLGNERRIAFYFINRDVLEKISPEVLPLLEEIATTVIEIEKE 187 (210)
T ss_dssp HHHHHHHHHHHHCCTT-TTEEEEEEEEHHHHHHHHHHHHHHHHHHSSEEEEEETT
T ss_pred HHHHHHHHHHHHHhcCCCceEEEEEEchHHhcccCchHHHHHHHHhhheEEEecC
Confidence 99999999999875 33445788999999986 8888999999999999874
No 32
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=84.69 E-value=23 Score=33.75 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=32.5
Q ss_pred ccceeEEEEeecC--hHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144 54 QSRGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCY 94 (272)
Q Consensus 54 q~~~Vhvl~fe~S--pe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (272)
.+..+..+.+|-+ |+.+.+.+++.|+|++..-+++.+.++|
T Consensus 129 ~~~~vvYIdtE~~f~~eRi~~~a~~~g~d~~~~l~~i~~~~~~ 171 (313)
T TIGR02238 129 GNGKVAYIDTEGTFRPDRIRAIAERFGVDPDAVLDNILYARAY 171 (313)
T ss_pred CCCeEEEEEcCCCCCHHHHHHHHHHcCCChHHhcCcEEEecCC
Confidence 3568889999994 9999999999999977655677766655
No 33
>cd01394 radB RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
Probab=81.91 E-value=28 Score=30.14 Aligned_cols=64 Identities=23% Similarity=0.127 Sum_probs=35.1
Q ss_pred EEEEEechhHHHHhcCh---------HHHHHHHHhhhc----CCceeEEEeeeccccc----chhhHhHHhhhheeEEEe
Q 024144 148 FSIAIDSVSEMVRHASI---------SSVAGILSNLRS----HDQVSSIFWLLHSDLH----EIKFTSVLEYLSSMVASV 210 (272)
Q Consensus 148 ~tVaIDSLS~LL~h~s~---------~~vc~lL~~Lr~----~~~vssVl~LLHsDLH----e~~~v~ALe~LSstvvtv 210 (272)
-.|+|||++.+.+.... ..+.+.++.|+. +....=+.+-+..+.. .|.--..++|++.+++.+
T Consensus 105 ~lvvIDsi~~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~~~vi~t~q~~~~~~~~~~~p~~g~~~~~~~d~~i~l 184 (218)
T cd01394 105 DLVVVDSATALYRLELGDDDTTIKNYRELAKQLTFLLWLARKHDVAVVITNQVYSDVGSGSVRPLGGHTLEHWSKVILRL 184 (218)
T ss_pred cEEEEechHHhhhHHhcCccchHHHHHHHHHHHHHHHHHHHHhCCEEEEecCCEEcCCCCcccccCCcchhcceeEEEEE
Confidence 48999999999753221 134555444443 2322222333333332 122122689999999988
Q ss_pred e
Q 024144 211 E 211 (272)
Q Consensus 211 ~ 211 (272)
.
T Consensus 185 ~ 185 (218)
T cd01394 185 E 185 (218)
T ss_pred E
Confidence 6
No 34
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=80.48 E-value=14 Score=35.81 Aligned_cols=39 Identities=21% Similarity=0.256 Sum_probs=31.9
Q ss_pred ceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (272)
Q Consensus 56 ~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (272)
..+..+.+|. +|+-+.+..++.|+|++..-++|.+.++|
T Consensus 161 ~~vvyIdTE~tF~peRl~~ia~~~g~d~~~~l~~I~~~~~~ 201 (344)
T PLN03187 161 GKVAYIDTEGTFRPDRIVPIAERFGMDADAVLDNIIYARAY 201 (344)
T ss_pred ceEEEEEcCCCCCHHHHHHHHHHcCCChhhhcCeEEEecCC
Confidence 5788999998 79999999999999977655677766654
No 35
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=79.07 E-value=66 Score=32.28 Aligned_cols=114 Identities=19% Similarity=0.128 Sum_probs=60.9
Q ss_pred ccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHHH
Q 024144 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (272)
Q Consensus 54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i 133 (272)
+++.|..+.+|-+++.+..-.++.|++ .+++.+++.. ++..+...+
T Consensus 121 ~g~kvlYvs~EEs~~qi~~ra~rlg~~----~~~l~~~~e~------------------------------~~~~I~~~i 166 (454)
T TIGR00416 121 NQMKVLYVSGEESLQQIKMRAIRLGLP----EPNLYVLSET------------------------------NWEQICANI 166 (454)
T ss_pred cCCcEEEEECcCCHHHHHHHHHHcCCC----hHHeEEcCCC------------------------------CHHHHHHHH
Confidence 456788889998988877655666665 2345544310 111121222
Q ss_pred HHhccCccCCCCCcEEEEEechhHHHHhc------ChHHHHHH---HHhhhcCCceeEEEeeecccccc--hhhHhHHhh
Q 024144 134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA------SISSVAGI---LSNLRSHDQVSSIFWLLHSDLHE--IKFTSVLEY 202 (272)
Q Consensus 134 ~e~~~~~~~~~k~~~tVaIDSLS~LL~h~------s~~~vc~l---L~~Lr~~~~vssVl~LLHsDLHe--~~~v~ALe~ 202 (272)
.+ .++ -.|+|||++.+.... +..++-.. |..+-+...+..++- -|-.-.+ .++ ..++|
T Consensus 167 ~~--------~~~-~~vVIDSIq~l~~~~~~~~~g~~~q~r~~~~~L~~~ak~~giTvllt-~hvtkeg~~aG~-~~le~ 235 (454)
T TIGR00416 167 EE--------ENP-QACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIV-GHVTKEGSIAGP-KVLEH 235 (454)
T ss_pred Hh--------cCC-cEEEEecchhhcccccccCCCCHHHHHHHHHHHHHHHHHhCCEEEEE-eccccCCccCCc-ccEee
Confidence 22 234 369999999986431 12334333 333322233333322 2422211 122 46899
Q ss_pred hheeEEEeec
Q 024144 203 LSSMVASVEP 212 (272)
Q Consensus 203 LSstvvtv~P 212 (272)
++.+++.++-
T Consensus 236 lvD~VI~Le~ 245 (454)
T TIGR00416 236 MVDTVLYFEG 245 (454)
T ss_pred eceEEEEEec
Confidence 9999998864
No 36
>PRK09354 recA recombinase A; Provisional
Probab=77.88 E-value=39 Score=33.09 Aligned_cols=41 Identities=10% Similarity=0.030 Sum_probs=28.0
Q ss_pred chhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCc
Q 024144 32 FGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDI 81 (272)
Q Consensus 32 ~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~ 81 (272)
+=+.+..|++. .+..+++.+..+.+|-+++. +.+++.|+|.
T Consensus 72 GKTtLal~~~~-------~~~~~G~~~~yId~E~s~~~--~~a~~lGvdl 112 (349)
T PRK09354 72 GKTTLALHAIA-------EAQKAGGTAAFIDAEHALDP--VYAKKLGVDI 112 (349)
T ss_pred CHHHHHHHHHH-------HHHHcCCcEEEECCccchHH--HHHHHcCCCH
Confidence 34555666443 23356888999999998885 5567778883
No 37
>PF05763 DUF835: Protein of unknown function (DUF835); InterPro: IPR008553 The members of this archaebacterial protein entry are around 250-300 amino acid residues in length. The function of these proteins is not known.
Probab=77.16 E-value=4.8 Score=34.18 Aligned_cols=50 Identities=24% Similarity=0.300 Sum_probs=36.8
Q ss_pred hhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC
Q 024144 123 VRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH 177 (272)
Q Consensus 123 v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~ 177 (272)
+.+|..+...+.+--+ +.+. -+|+||++=-|+.++|+.++..+|+.|+-+
T Consensus 57 Pt~L~~l~~~i~~fl~----~~~~-~vViiD~lEYL~l~NgF~~v~KFL~~LkD~ 106 (136)
T PF05763_consen 57 PTNLHKLLDTIVRFLK----ENGN-GVVIIDGLEYLILENGFESVLKFLASLKDY 106 (136)
T ss_pred chhhHHHHHHHHHHHH----hCCC-cEEEEecHHHHHHHcCHHHHHHHHHHhHHH
Confidence 4455555455555322 2122 399999999999999999999999999964
No 38
>cd01125 repA Hexameric Replicative Helicase RepA. RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.
Probab=75.32 E-value=59 Score=28.85 Aligned_cols=142 Identities=14% Similarity=0.068 Sum_probs=73.0
Q ss_pred cccceeEEEEeecChHHHHHHHhhcCcCc--cCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHH
Q 024144 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDI--ASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY 130 (272)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~--~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~ 130 (272)
.+...|.+++.|-++++..+=++..+..- +....++.+.+....|+.+..... . .....+.
T Consensus 39 ~~~~~Vlyi~~Ed~~~~i~~Rl~~i~~~~~~~~~~~rl~~~~g~~~~l~~~~~~~-----------~---~~~~~~~--- 101 (239)
T cd01125 39 TEPGRVVYLSAEDPREEIHRRLEAILQHLEPDDAGDRLFIDSGRIQPISIAREGR-----------I---IVVPEFE--- 101 (239)
T ss_pred CCCceEEEEECCCCHHHHHHHHHHHHhhcCCcCcccceEEeccCCCceecccCCc-----------c---cccHHHH---
Confidence 35678999999999998776555543321 111345555433222332211000 0 0122233
Q ss_pred HHHHHhccCccCCCCCcEEEEEechhHHHH--hcChHHHHHHHHhhhcC-CceeEEEeeecccccch----------hhH
Q 024144 131 SLIIEQGKGLIGQGKDRFSIAIDSVSEMVR--HASISSVAGILSNLRSH-DQVSSIFWLLHSDLHEI----------KFT 197 (272)
Q Consensus 131 ~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~--h~s~~~vc~lL~~Lr~~-~~vssVl~LLHsDLHe~----------~~v 197 (272)
.+++..+ ..++ -.|+||+++.+-. .......-+++..|++. .+-.+.+.++|.+-... +=.
T Consensus 102 -~l~~~~~----~~~~-~lvviDpl~~~~~~~~~d~~~~~~~~~~L~~~a~~~g~avl~v~H~~K~~~~~~~~~~~~rGs 175 (239)
T cd01125 102 -RIIEQLL----IRRI-DLVVIDPLVSFHGVSENDNGAMDAVIKALRRIAAQTGAAILLVHHVRKGSAKDGDTQEAARGA 175 (239)
T ss_pred -HHHHHHH----hcCC-CEEEECChHHhCCCCcCCHHHHHHHHHHHHHHHHHhCCEEEEEeccCcccccCcccccccCcH
Confidence 3333221 1233 5899999988711 12233444445554431 22334555667666432 225
Q ss_pred hHHhhhheeEEEeecCCccc
Q 024144 198 SVLEYLSSMVASVEPFNQAA 217 (272)
Q Consensus 198 ~ALe~LSstvvtv~P~~~~~ 217 (272)
.||..-+.++..+.|.....
T Consensus 176 sal~~~~r~~~~l~~~~~~~ 195 (239)
T cd01125 176 SALVDGARWVRALTRMTSEE 195 (239)
T ss_pred HHHhcccceEEEEeeCCHHH
Confidence 67777778888888876544
No 39
>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange.
Probab=72.19 E-value=47 Score=32.16 Aligned_cols=26 Identities=12% Similarity=0.127 Sum_probs=19.4
Q ss_pred cccceeEEEEeecChHHHHHHHhhcCcC
Q 024144 53 SQSRGLVVVAYSRSPSFYVDLLKRRGID 80 (272)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d 80 (272)
.++..+.++.+|-+++. +.+++.|+|
T Consensus 81 ~~g~~~vyId~E~~~~~--~~a~~lGvd 106 (325)
T cd00983 81 KLGGTVAFIDAEHALDP--VYAKKLGVD 106 (325)
T ss_pred HcCCCEEEECccccHHH--HHHHHcCCC
Confidence 46778889999888774 456677777
No 40
>TIGR02012 tigrfam_recA protein RecA. This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.
Probab=71.18 E-value=35 Score=32.98 Aligned_cols=47 Identities=9% Similarity=0.056 Sum_probs=29.4
Q ss_pred chhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEE
Q 024144 32 FGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHIL 91 (272)
Q Consensus 32 ~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~ 91 (272)
+=+.+..|++.. ...++..+.++.+|-+++. ..+++.|+|. +++++.
T Consensus 67 GKTtLaL~~~~~-------~~~~g~~v~yId~E~~~~~--~~a~~lGvd~----~~l~v~ 113 (321)
T TIGR02012 67 GKTTLALHAIAE-------AQKAGGTAAFIDAEHALDP--VYARKLGVDI----DNLLVS 113 (321)
T ss_pred CHHHHHHHHHHH-------HHHcCCcEEEEcccchhHH--HHHHHcCCCH----HHeEEe
Confidence 334555665432 3346788889999988775 3466778873 456643
No 41
>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51. It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....
Probab=60.43 E-value=25 Score=32.25 Aligned_cols=41 Identities=20% Similarity=0.300 Sum_probs=29.5
Q ss_pred cceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEeccC
Q 024144 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYT 95 (272)
Q Consensus 55 ~~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~ys 95 (272)
+..|+.+..|. +++-+.+.+++++++.+..-++|++..+|+
T Consensus 72 ~~~vvyidTe~~f~~~Rl~~i~~~~~~~~~~~l~~I~v~~~~~ 114 (256)
T PF08423_consen 72 GGKVVYIDTEGTFSPERLQQIAERFGLDPEEILDNIFVIRVFD 114 (256)
T ss_dssp SSEEEEEESSSSS-HHHHHHHHHHTTS-HHHHHHTEEEEE-SS
T ss_pred CCceEEEeCCCCCCHHHHHHHhhccccccchhhhceeeeecCC
Confidence 45688888887 788899999999888766556788877663
No 42
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=60.14 E-value=1.6e+02 Score=28.04 Aligned_cols=39 Identities=13% Similarity=0.217 Sum_probs=28.2
Q ss_pred ceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (272)
Q Consensus 56 ~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (272)
..+..+.+|. +|+-+.+..++.|++++..-+++++.++|
T Consensus 131 ~~vvyIdtE~~f~~~Rl~~ia~~~~~~~~~~l~~i~~~~~~ 171 (316)
T TIGR02239 131 GKALYIDTEGTFRPERLLAIAERYGLNPEDVLDNVAYARAY 171 (316)
T ss_pred ceEEEEECCCCCCHHHHHHHHHHcCCChHHhhccEEEEecC
Confidence 4677788888 68888888888888876545567666654
No 43
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=59.38 E-value=1.8e+02 Score=28.31 Aligned_cols=38 Identities=13% Similarity=0.226 Sum_probs=30.3
Q ss_pred eeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144 57 GLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (272)
Q Consensus 57 ~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (272)
.+..+.+|. +|+-..+..++.|+|.+..-+++++.++|
T Consensus 159 ~vlyIdtE~~f~~eRl~qia~~~~~~~~~~l~~i~~~~~~ 198 (342)
T PLN03186 159 KAMYIDTEGTFRPQRLIQIAERFGLNGADVLENVAYARAY 198 (342)
T ss_pred eEEEEECCCCccHHHHHHHHHHcCCChhhhccceEEEecC
Confidence 688999999 79999999999998876545667776654
No 44
>PF14417 MEDS: MEDS: MEthanogen/methylotroph, DcmR Sensory domain
Probab=54.05 E-value=46 Score=28.90 Aligned_cols=137 Identities=14% Similarity=0.120 Sum_probs=80.7
Q ss_pred HHHHHHHHHHHHhhccccceeEEEEe-ecChHHHHHHHhhcCcCccC--CCCeEEEEeccC--CCCCCcccccCCccccc
Q 024144 38 NYVLTQLSNYILAGKSQSRGLVVVAY-SRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYT--DPLGWKNWLIDKDISQE 112 (272)
Q Consensus 38 ~h~~~~l~s~i~a~~~q~~~Vhvl~f-e~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ys--DPLGW~~~~~~~~~~~~ 112 (272)
..++..+.++|++|-.+++.+.++.= ....+...+.|++.|+|.+. -...+.++|... -+-|+-+...
T Consensus 30 ~e~~~~~~~Fi~~GL~~ge~~l~v~~~~~~~~~l~~~L~~~~~d~~~~~~~gqL~~~~~~~~Y~~~g~f~~~~------- 102 (191)
T PF14417_consen 30 EELLEVLVPFIREGLARGERCLYVAPDPRRVEELRDELRKAGPDVEQYLDSGQLELLDAEEWYLPDGRFDPAR------- 102 (191)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEECCCCCHHHHHHHHHhcCCchhhcccCCCEEEecchhhhccCCCcCHHH-------
Confidence 55677799999999999999999998 78899999999999887655 234688887521 1122211000
Q ss_pred cccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHH---HHhhhcCCceeEEEeeecc
Q 024144 113 ASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGI---LSNLRSHDQVSSIFWLLHS 189 (272)
Q Consensus 113 ~s~~~~~~~~v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~l---L~~Lr~~~~vssVl~LLHs 189 (272)
-+..+.+.+..... +|-+.+-++-| .+|.++. +...+.+. +..+-. ..-...++.-..
T Consensus 103 ---------~i~~~~~~~~~a~~-------~G~~~lRv~ge-~~w~~~~-~~~~l~~yE~~ln~~~~-~~~~~~lC~Yd~ 163 (191)
T PF14417_consen 103 ---------MIAFWRAALEQALA-------EGYRGLRVIGE-MTWALRS-GWEELLRYEALLNRLFA-EHPFTALCAYDR 163 (191)
T ss_pred ---------HHHHHHHHHHHHHh-------CCCCcEEEEEe-chhhccc-cHHHHHHHHHHHHHHhc-CCCEEEEeccch
Confidence 02222222122221 23334778888 7888877 55544322 222222 234445566666
Q ss_pred cccchhhHhHH
Q 024144 190 DLHEIKFTSVL 200 (272)
Q Consensus 190 DLHe~~~v~AL 200 (272)
+.-.+.++..+
T Consensus 164 ~~~~~~~~~~~ 174 (191)
T PF14417_consen 164 RRFSPEVLADA 174 (191)
T ss_pred HhCCHHHHHHH
Confidence 66666655444
No 45
>cd01120 RecA-like_NTPases RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Probab=53.02 E-value=1.1e+02 Score=23.90 Aligned_cols=64 Identities=16% Similarity=0.176 Sum_probs=38.8
Q ss_pred EEEEEechhHHHHhcC------hHHHHHHHHhhhcC--CceeEEEeeecccccc------hhhHhHHhhhheeEEEee
Q 024144 148 FSIAIDSVSEMVRHAS------ISSVAGILSNLRSH--DQVSSIFWLLHSDLHE------IKFTSVLEYLSSMVASVE 211 (272)
Q Consensus 148 ~tVaIDSLS~LL~h~s------~~~vc~lL~~Lr~~--~~vssVl~LLHsDLHe------~~~v~ALe~LSstvvtv~ 211 (272)
-.++||+++.++.... ...+.+.|.+|... ..=..++...|.+-=+ .+...+++|++.+++.+.
T Consensus 87 ~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~l~ 164 (165)
T cd01120 87 DLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSGDKGDPRLTRGAQNLEDIADTVIVLS 164 (165)
T ss_pred EEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEEEecCCccccCcccccCccceeeecceEEEEe
Confidence 6899999999886532 23445556655542 1234455566644211 113467899988888763
No 46
>TIGR00665 DnaB replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.
Probab=48.88 E-value=73 Score=30.97 Aligned_cols=22 Identities=5% Similarity=0.045 Sum_probs=18.0
Q ss_pred cccceeEEEEeecChHHHHHHH
Q 024144 53 SQSRGLVVVAYSRSPSFYVDLL 74 (272)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~l 74 (272)
.++..|.++.+|-++++...=+
T Consensus 222 ~~g~~vl~~SlEm~~~~i~~R~ 243 (434)
T TIGR00665 222 KEGKPVAFFSLEMSAEQLAMRM 243 (434)
T ss_pred hCCCeEEEEeCcCCHHHHHHHH
Confidence 3578899999999999987633
No 47
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=43.87 E-value=51 Score=25.24 Aligned_cols=57 Identities=21% Similarity=0.203 Sum_probs=44.8
Q ss_pred CCceeecccCCCCchhh------HHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHh
Q 024144 19 APALTIKDSKASPFGFD------VFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLK 75 (272)
Q Consensus 19 ap~l~i~Dsl~~~~g~~------v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk 75 (272)
.|.+++-|.++.-++.. ....++..|...+.....+...+.|++....++.....+.
T Consensus 58 ~~~vl~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~ 120 (132)
T PF00004_consen 58 KPCVLFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALL 120 (132)
T ss_dssp TSEEEEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHH
T ss_pred cceeeeeccchhcccccccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHH
Confidence 58999999997765443 5677788888888887777777888888888887777665
No 48
>TIGR03439 methyl_EasF probable methyltransferase domain, EasF family. This model represents an uncharacterized domain of about 300 amino acids with homology to S-adenosylmethionine-dependent methyltransferases. Proteins with this domain are exclusively fungal. A few, such as EasF from Neotyphodium lolii, are associated with the biosynthesis of ergot alkaloids, a class of fungal secondary metabolites. EasF may, in fact, be the AdoMet:dimethylallyltryptophan N-methyltransferase, the enzyme that follows tryptophan dimethylallyltransferase (DMATS) in ergot alkaloid biosynthesis. Several other members of this family, including mug158 (meiotically up-regulated gene 158 protein) from Schizosaccharomyces pombe, contain an additional uncharacterized domain DUF323 (pfam03781).
Probab=43.51 E-value=2.1e+02 Score=27.64 Aligned_cols=47 Identities=26% Similarity=0.215 Sum_probs=33.3
Q ss_pred ccceeEEEEeecChHHHHHHHhhcCcC-ccCCCCeEE-EEeccCCCCCCcc
Q 024144 54 QSRGLVVVAYSRSPSFYVDLLKRRGID-IASSHDWIH-ILDCYTDPLGWKN 102 (272)
Q Consensus 54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d-~~s~~~ri~-i~D~ysDPLGW~~ 102 (272)
+++.++.+++|+|.+...+..++- . .+.++-.+. +.--|+||+.|-.
T Consensus 101 ~~~~~~Y~plDIS~~~L~~a~~~L--~~~~~p~l~v~~l~gdy~~~l~~l~ 149 (319)
T TIGR03439 101 QKKSVDYYALDVSRSELQRTLAEL--PLGNFSHVRCAGLLGTYDDGLAWLK 149 (319)
T ss_pred cCCCceEEEEECCHHHHHHHHHhh--hhccCCCeEEEEEEecHHHHHhhcc
Confidence 456799999999999999887754 3 222222332 5667999999875
No 49
>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
Probab=42.87 E-value=2.4e+02 Score=25.07 Aligned_cols=21 Identities=5% Similarity=-0.113 Sum_probs=17.9
Q ss_pred cceeEEEEeecChHHHHHHHh
Q 024144 55 SRGLVVVAYSRSPSFYVDLLK 75 (272)
Q Consensus 55 ~~~Vhvl~fe~Spe~y~~~lk 75 (272)
+..|.++.+|-++++...-+.
T Consensus 59 g~~vl~iS~E~~~~~~~~r~~ 79 (271)
T cd01122 59 GVRVGTISLEEPVVRTARRLL 79 (271)
T ss_pred CceEEEEEcccCHHHHHHHHH
Confidence 889999999999998877553
No 50
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=41.94 E-value=26 Score=29.39 Aligned_cols=26 Identities=12% Similarity=0.061 Sum_probs=17.0
Q ss_pred cccceeEEEEeecChHHHHHHHhhcC
Q 024144 53 SQSRGLVVVAYSRSPSFYVDLLKRRG 78 (272)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G 78 (272)
.+...|..+.+|.+++++..-+++.+
T Consensus 68 ~~~~~Vl~i~~E~~~~~~~~rl~~~~ 93 (193)
T PF13481_consen 68 PRPGRVLYISLEDSESQIARRLRALL 93 (193)
T ss_dssp -----EEEEESSS-HHHHHHHHHHHH
T ss_pred ccCceEEEEeccCCHHHHHHHHHHHh
Confidence 36789999999999988888777653
No 51
>PHA02542 41 41 helicase; Provisional
Probab=39.32 E-value=4.3e+02 Score=26.85 Aligned_cols=175 Identities=10% Similarity=0.013 Sum_probs=84.0
Q ss_pred cCCCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHH--hhcCcCccCCCCeEEEEe
Q 024144 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLL--KRRGIDIASSHDWIHILD 92 (272)
Q Consensus 15 ~ge~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~l--k~~G~d~~s~~~ri~i~D 92 (272)
.|-+++.+.|--.-+.-+=+.+..++. ..+ +.+++.|.++.+|-++++...=+ ...|++... +. .
T Consensus 185 gGl~~G~LiiIaarPgmGKTtfalniA----~~~---a~~g~~Vl~fSLEM~~~ql~~Rl~a~~~~i~~~~----l~--~ 251 (473)
T PHA02542 185 GGAERKTLNVLLAGVNVGKSLGLCSLA----ADY---LQQGYNVLYISMEMAEEVIAKRIDANLLDVSLDD----ID--D 251 (473)
T ss_pred CCCCCCcEEEEEcCCCccHHHHHHHHH----HHH---HhcCCcEEEEeccCCHHHHHHHHHHHHcCCCHHH----Hh--h
Confidence 355555555544444433344444433 222 24688999999999999887743 334455322 21 1
Q ss_pred ccCCCCCCcccccCCccccccccccccc------cchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHH------
Q 024144 93 CYTDPLGWKNWLIDKDISQEASSLSSFC------QDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR------ 160 (272)
Q Consensus 93 ~ysDPLGW~~~~~~~~~~~~~s~~~~~~------~~v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~------ 160 (272)
+ ++-.|.+.......-. ..++.+. -++.++++...+... .+ ..+. -.|+||.|..|--
T Consensus 252 -l-~~~~~~~~~~~~~~~~--~~~l~I~~~d~~~lt~~~ir~~~rrlk~-~~----g~~~-dlVvIDYLqL~~~~~~~~~ 321 (473)
T PHA02542 252 -L-SKAEYKAKMEKLRSKT--QGKLIIKQYPTGGAHAGHFRALLNELKL-KK----NFKP-DVIIVDYLGICASSRLRVS 321 (473)
T ss_pred -c-CHHHHHHHHHHHHHHh--CCCceeecCCCCCCCHHHHHHHHHHHHH-hc----CCCC-CEEEEechhhccCCcccCC
Confidence 1 1233442111000000 0001000 135566655222221 11 0123 4899999977631
Q ss_pred ----hcChHHHHHHHHhhhcC-CceeEEEeeeccc--------ccchhhHhHHhhhheeEEEeec
Q 024144 161 ----HASISSVAGILSNLRSH-DQVSSIFWLLHSD--------LHEIKFTSVLEYLSSMVASVEP 212 (272)
Q Consensus 161 ----h~s~~~vc~lL~~Lr~~-~~vssVl~LLHsD--------LHe~~~v~ALe~LSstvvtv~P 212 (272)
..-...+++-|.+|-+- ....=++.-+.-+ +..-+-.+++|+.|..++.+.-
T Consensus 322 ~~nr~~ei~~Isr~LK~lAkel~vpVi~lsQLnR~~e~r~dP~lsDLreSG~IEqdAD~vl~l~r 386 (473)
T PHA02542 322 SENSYTYVKAIAEELRGLAVEHDVVVWTAAQTTRSGWDSSDVDMSDTAESAGLPATADFMLAVIE 386 (473)
T ss_pred CCChHHHHHHHHHHHHHHHHHhCCeEEEEEeeCccccccCCCcchhcccccchHhhcCEEEEEec
Confidence 11134566777776652 2222222223222 2233556899999999988843
No 52
>PRK09519 recA DNA recombination protein RecA; Reviewed
Probab=34.86 E-value=2.8e+02 Score=30.35 Aligned_cols=30 Identities=13% Similarity=0.198 Sum_probs=21.3
Q ss_pred hccccceeEEEEeecChHHHHHHHhhcCcCcc
Q 024144 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIA 82 (272)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~ 82 (272)
+..+++.+..+.+|-+++ .+-+++.|+|.+
T Consensus 84 a~~~G~~v~yId~E~t~~--~~~A~~lGvDl~ 113 (790)
T PRK09519 84 AQAAGGVAAFIDAEHALD--PDYAKKLGVDTD 113 (790)
T ss_pred HHHcCCcEEEECCccchh--HHHHHHcCCChh
Confidence 345778888888888777 345667788843
No 53
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=34.66 E-value=37 Score=26.61 Aligned_cols=44 Identities=20% Similarity=0.236 Sum_probs=27.6
Q ss_pred HHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCC
Q 024144 44 LSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPL 98 (272)
Q Consensus 44 l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPL 98 (272)
|++...+-.+.+-.+++|+++-.+. -.++++.++++ .+.|.||-
T Consensus 2 L~~~~~~l~~~gv~lv~I~~g~~~~-~~~f~~~~~~p----------~~ly~D~~ 45 (115)
T PF13911_consen 2 LSRRKPELEAAGVKLVVIGCGSPEG-IEKFCELTGFP----------FPLYVDPE 45 (115)
T ss_pred hhHhHHHHHHcCCeEEEEEcCCHHH-HHHHHhccCCC----------CcEEEeCc
Confidence 3444444555677788999887755 55555556665 24678883
No 54
>PF13466 STAS_2: STAS domain
Probab=33.40 E-value=92 Score=22.58 Aligned_cols=34 Identities=21% Similarity=0.252 Sum_probs=24.5
Q ss_pred HHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcC
Q 024144 44 LSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGID 80 (272)
Q Consensus 44 l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d 80 (272)
|.+..+..+.++..+.+.+ .++..+.+++..|+|
T Consensus 47 L~~~~~~~~~~g~~~~l~~---~~~~~~~ll~~~gld 80 (80)
T PF13466_consen 47 LLAAARRARARGRQLRLTG---PSPALRRLLELLGLD 80 (80)
T ss_pred HHHHHHHHHHCCCeEEEEc---CCHHHHHHHHHhCcC
Confidence 4555556777888888876 445588888888876
No 55
>PF06866 DUF1256: Protein of unknown function (DUF1256); InterPro: IPR009665 This family consists of several uncharacterised bacterial proteins, which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown.
Probab=32.41 E-value=2.1e+02 Score=25.49 Aligned_cols=34 Identities=12% Similarity=0.023 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHhhccccceeEEEEeecChHHHH
Q 024144 37 FNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYV 71 (272)
Q Consensus 37 ~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~ 71 (272)
...+...|++.+.+. .+.--+..+|-|||.-+-+
T Consensus 9 ~~~l~~~L~~~~~~~-~~~iv~lCIGTDRstGDsL 42 (163)
T PF06866_consen 9 PEKLANFLYSLIPKH-NREIVFLCIGTDRSTGDSL 42 (163)
T ss_pred HHHHHHHHHHHHhhc-CCCEEEEEECCCCCccccc
Confidence 344555566766655 4444555566677765433
No 56
>PRK06321 replicative DNA helicase; Provisional
Probab=29.64 E-value=6.1e+02 Score=25.72 Aligned_cols=52 Identities=6% Similarity=-0.041 Sum_probs=29.7
Q ss_pred CCCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHH
Q 024144 16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDL 73 (272)
Q Consensus 16 ge~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~ 73 (272)
|=+++-+.|----.+-+=+....+ ++.++ +..++..|.++.+|-++++..+=
T Consensus 222 Gl~~G~LiiiaarPgmGKTafal~----ia~~~--a~~~g~~v~~fSLEMs~~ql~~R 273 (472)
T PRK06321 222 GFSPSNLMILAARPAMGKTALALN----IAENF--CFQNRLPVGIFSLEMTVDQLIHR 273 (472)
T ss_pred CCCCCcEEEEEeCCCCChHHHHHH----HHHHH--HHhcCCeEEEEeccCCHHHHHHH
Confidence 455555555433333333333333 22222 12357889999999999988773
No 57
>PF04655 APH_6_hur: Aminoglycoside/hydroxyurea antibiotic resistance kinase; InterPro: IPR006748 The aminoglycosides are a large group of biologically active bacterial secondary metabolites, best known for their antibiotic properties []. Aminoglycoside phosphotransferases achieve inactivation of these enzymes by phosphorylation, utilising ATP. Likewise, hydroxyurea is inactivated by phosphorylation of the hydroxy group in the hydroxylamine moiety.; GO: 0016773 phosphotransferase activity, alcohol group as acceptor, 0006468 protein phosphorylation, 0019748 secondary metabolic process
Probab=28.94 E-value=21 Score=33.08 Aligned_cols=24 Identities=29% Similarity=0.414 Sum_probs=18.4
Q ss_pred eecccccchhhHhHHhhhheeEEEeec
Q 024144 186 LLHSDLHEIKFTSVLEYLSSMVASVEP 212 (272)
Q Consensus 186 LLHsDLHe~~~v~ALe~LSstvvtv~P 212 (272)
+||+|||...++.+=. ..++-+-|
T Consensus 162 lLHGDLH~~NIL~~~~---~~WlaIDP 185 (253)
T PF04655_consen 162 LLHGDLHHGNILAAGR---RGWLAIDP 185 (253)
T ss_pred eeccccchHhhhccCC---CCceEeCC
Confidence 8999999999987654 45666655
No 58
>KOG1406 consensus Peroxisomal 3-ketoacyl-CoA-thiolase P-44/SCP2 [Lipid transport and metabolism]
Probab=28.06 E-value=39 Score=33.01 Aligned_cols=39 Identities=13% Similarity=0.292 Sum_probs=31.1
Q ss_pred eeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCC
Q 024144 57 GLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTD 96 (272)
Q Consensus 57 ~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysD 96 (272)
.+-+++||-+.+.-+.+..+.|+.++. -+-|..||||+-
T Consensus 265 ~ikm~gfdm~~~aa~~l~aksgltpnd-vqvielhdcfs~ 303 (408)
T KOG1406|consen 265 LIKMAGFDMTRLAAKRLFAKSGLTPND-VQVIELHDCFSA 303 (408)
T ss_pred hhhhhcchHHHHHHHHHHHHcCCCccc-ceEEEeecccch
Confidence 455677888777777788888998888 677899999984
No 59
>KOG3124 consensus Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]
Probab=27.79 E-value=32 Score=32.80 Aligned_cols=42 Identities=31% Similarity=0.364 Sum_probs=27.5
Q ss_pred ccCCCCCceeecccCCCCchhhH-HHHHHHH------HHHHHHhhccccc
Q 024144 14 LEGEHAPALTIKDSKASPFGFDV-FNYVLTQ------LSNYILAGKSQSR 56 (272)
Q Consensus 14 l~ge~ap~l~i~Dsl~~~~g~~v-~~h~~~~------l~s~i~a~~~q~~ 56 (272)
++.++-|+ .++|+++||+|+.+ +.|++.+ +...+.++..|.+
T Consensus 214 l~s~qHP~-~Lkd~V~SPgG~TI~glh~LE~ggfRs~linaVeaa~~r~~ 262 (267)
T KOG3124|consen 214 LASGQHPA-QLKDDVCSPGGTTIYGLHALEKGGFRSGLINAVEAATKRAR 262 (267)
T ss_pred HhccCCcH-HHhCCCCCCCcchHHHHHHHHhCCchhHHHHHHHHHHHHHH
Confidence 34444454 46999999999887 6677765 4555555555444
No 60
>PF07411 DUF1508: Domain of unknown function (DUF1508); InterPro: IPR010879 This domain is found in a family of proteins, which have no known function. Members of this family are often found as tandem repeats and in some cases represent the whole protein.; PDB: 3BID_H 2K49_A 2K8E_A 2K7I_A.
Probab=25.39 E-value=70 Score=22.52 Aligned_cols=18 Identities=39% Similarity=0.672 Sum_probs=14.0
Q ss_pred cceEEEEEEeccCCcEEE
Q 024144 235 RKGKFHVRFKRRNGRVRV 252 (272)
Q Consensus 235 ~k~~~~vr~KrRnGRV~~ 252 (272)
..|+++.|+|-.||+|.-
T Consensus 2 ~~g~~~f~L~a~ng~via 19 (49)
T PF07411_consen 2 SDGQFRFRLKAGNGEVIA 19 (49)
T ss_dssp TTSEEEEEEE-TTS-EEE
T ss_pred CCCCEEEEEEcCCCCEEE
Confidence 357899999999999987
No 61
>PF11382 DUF3186: Protein of unknown function (DUF3186); InterPro: IPR021522 This bacterial family of proteins has no known function.
Probab=25.26 E-value=1.3e+02 Score=28.67 Aligned_cols=62 Identities=19% Similarity=0.334 Sum_probs=48.3
Q ss_pred HHHHHHHHHHHHHhhccccceeEEEEeecCh----HHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCc
Q 024144 37 FNYVLTQLSNYILAGKSQSRGLVVVAYSRSP----SFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWK 101 (272)
Q Consensus 37 ~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Sp----e~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~ 101 (272)
.+.|+.++...+.+++..++.|.||...... +.-.+.+++.|-.. ..++.+-|-|.||-.=+
T Consensus 65 ~d~f~~~~~~~lv~g~L~g~~V~vV~~p~a~~~~~~~v~~~L~~AGA~v---~g~i~lt~~~~d~~~~~ 130 (308)
T PF11382_consen 65 ADQFIAAVAPRLVAGRLTGRSVAVVTLPGADDEDVDAVRELLEQAGATV---TGRITLTDKFLDPEQAD 130 (308)
T ss_pred HHHHHHHHHHHHhcCccCCCEEEEEEcCCCChHHHHHHHHHHHHCCCeE---EEEEEEchhhcChhhHH
Confidence 5677888888888999999999999965443 35567777777764 34799999999998533
No 62
>PF09087 Cyc-maltodext_N: Cyclomaltodextrinase, N-terminal; InterPro: IPR015171 This domain is found at the N terminus of cyclomaltodextrinase. The domain assumes a beta-sandwich structure composed of the eight antiparallel beta-strands. A ten residue linker is also present at the C-terminal end, which connects the N-terminal domain to a distal domain in the protein. This domain participates in oligomerisation of the protein, wherein the N-terminal domain of one subunit contacts the active centre of the other subunit, and is also required for binding of cyclodextrin to substrate []. ; PDB: 3EDK_B 3EDD_A 3EDJ_B 3EDE_A 1H3G_B 3EDF_B.
Probab=23.89 E-value=1.6e+02 Score=23.62 Aligned_cols=58 Identities=19% Similarity=0.289 Sum_probs=34.6
Q ss_pred hhhheeEEEee-cCCccccccccccchhhhh---hccccceEEEEEEeccCCcEEEEEEEEE
Q 024144 201 EYLSSMVASVE-PFNQAAFGQRVDLENLSML---EQNFRKGKFHVRFKRRNGRVRVMKYLLS 258 (272)
Q Consensus 201 e~LSstvvtv~-P~~~~~~~~~~~~~~~~~l---~~n~~k~~~~vr~KrRnGRV~~~~~~~~ 258 (272)
+-++++.+++. |+.....-.+.+=.|--|+ ..+..-|+|.+.|++.+|+....-|.|-
T Consensus 23 ~nI~~~~v~i~~~gV~i~~v~~~~npNYLFv~L~i~~akpg~~~i~~~~~~~~~~~~~Y~Lk 84 (88)
T PF09087_consen 23 KNIASAEVSISYPGVTIKKVVKTDNPNYLFVYLDISDAKPGTFTINFKKGDKKKTTFDYELK 84 (88)
T ss_dssp TTGGGSEEEE-BTTEEEEEEEE-SSTTEEEEEEEE-T--SEEEEEEEEET-TEEEEEEEEEE
T ss_pred CCcccCEEEEeCCCeEEEEEEecCCCCEEEEEEecCCCCCcEEEEEEEcCCCceEEEEeEec
Confidence 35777888887 4443333333333343333 2366779999999999999999888764
No 63
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=23.73 E-value=1.9e+02 Score=23.82 Aligned_cols=40 Identities=10% Similarity=0.120 Sum_probs=29.2
Q ss_pred eeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeec
Q 024144 22 LTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSR 65 (272)
Q Consensus 22 l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~ 65 (272)
...-|+-.|.. -..+..|++++++..+.. ...|+|+.||-
T Consensus 2 ~vaiDtSGSis-~~~l~~fl~ev~~i~~~~---~~~v~vi~~D~ 41 (126)
T PF09967_consen 2 VVAIDTSGSIS-DEELRRFLSEVAGILRRF---PAEVHVIQFDA 41 (126)
T ss_pred EEEEECCCCCC-HHHHHHHHHHHHHHHHhC---CCCEEEEEECC
Confidence 34567777775 567888888888766555 45599999984
No 64
>TIGR03438 probable methyltransferase. This model represents a distinct set of uncharacterized proteins found in the bacteria. Analysis by PSI-BLAST shows remote sequence homology to methyltransferases
Probab=23.47 E-value=1.2e+02 Score=28.29 Aligned_cols=38 Identities=21% Similarity=0.370 Sum_probs=26.7
Q ss_pred ccceeEEE-EeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCC
Q 024144 54 QSRGLVVV-AYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGW 100 (272)
Q Consensus 54 q~~~Vhvl-~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW 100 (272)
+++.+|+- ..--+++++..+++..||. +.+.|+||.+|
T Consensus 257 ~ge~ih~e~S~ky~~~~~~~~l~~aGf~---------~~~~~~d~~~~ 295 (301)
T TIGR03438 257 AGETIHTENSYKFSLERFAALAAAAGLR---------PEQVWTDPNDW 295 (301)
T ss_pred CCCEEeEEEecCCCHHHHHHHHHHCCCc---------eeEEEECCCCC
Confidence 34444442 2346788999999977655 67889999887
No 65
>smart00455 RBD Raf-like Ras-binding domain.
Probab=23.08 E-value=53 Score=24.74 Aligned_cols=35 Identities=20% Similarity=0.268 Sum_probs=23.9
Q ss_pred hHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccc
Q 024144 67 PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWL 104 (272)
Q Consensus 67 pe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~ 104 (272)
-|.....|+++|++++. ..+++-.=..|+.|++..
T Consensus 23 ~e~L~~~~~kr~l~~~~---~~v~~~g~~k~ldl~~~~ 57 (70)
T smart00455 23 RDALAKALKKRGLNPEC---CVVRLRGEKKPLDLNQPI 57 (70)
T ss_pred HHHHHHHHHHcCCCHHH---EEEEEcCCCcceecCCcc
Confidence 45677889999999766 233332334899999843
No 66
>COG0257 RpmJ Ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=22.66 E-value=67 Score=22.29 Aligned_cols=13 Identities=46% Similarity=0.723 Sum_probs=10.1
Q ss_pred EEeccCCcEEEEE
Q 024144 242 RFKRRNGRVRVMK 254 (272)
Q Consensus 242 r~KrRnGRV~~~~ 254 (272)
.+=||.|||.+.|
T Consensus 15 kivrRkGrv~VIc 27 (38)
T COG0257 15 KIVRRKGRVYVIC 27 (38)
T ss_pred eEEEecCEEEEEe
Confidence 3568999998876
No 67
>COG4544 Uncharacterized conserved protein [Function unknown]
Probab=21.69 E-value=1.3e+02 Score=28.56 Aligned_cols=56 Identities=13% Similarity=0.177 Sum_probs=40.4
Q ss_pred hhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccC
Q 024144 33 GFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYT 95 (272)
Q Consensus 33 g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ys 95 (272)
|.....=|+..|.+..++.+..+.-|||+- =++-|.--|+..||| ..|++|..|++
T Consensus 63 g~ga~~GaAaAl~~~g~~~r~~gpVvWi~t---r~dlf~paL~~~Gl~----~~RlifVea~~ 118 (260)
T COG4544 63 GAGAADGAAAALAVLGLAARRGGPVVWILT---REDLFPPALAAFGLD----PERLIFVEARK 118 (260)
T ss_pred CccchhhHHHHHHHHhhhcccCCCEEEEEe---cccccchhHhhcCCC----hhhEEEEeCCc
Confidence 344445566778888777888888888877 445444448889999 67799998764
Done!