Query 023377
Match_columns 283
No_of_seqs 61 out of 63
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 03:35:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023377.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023377hhsearch_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 5.3E-25 1.1E-29 203.8 11.7 184 17-253 10-206 (280)
2 PF09807 DUF2348: Uncharacteri 99.2 6.7E-10 1.4E-14 102.1 16.8 203 18-247 18-231 (249)
3 PF06745 KaiC: KaiC; InterPro 98.3 4.9E-06 1.1E-10 73.2 8.9 137 50-212 42-185 (226)
4 TIGR03877 thermo_KaiC_1 KaiC d 97.9 0.00013 2.8E-09 65.5 11.9 143 51-211 45-193 (237)
5 PRK06067 flagellar accessory p 97.8 0.00069 1.5E-08 60.2 14.4 137 51-213 49-188 (234)
6 PRK04328 hypothetical protein; 97.8 0.00032 7E-09 63.8 12.1 144 50-211 46-195 (249)
7 COG2874 FlaH Predicted ATPases 97.4 0.0066 1.4E-07 56.4 15.1 168 13-213 20-191 (235)
8 PRK09302 circadian clock prote 97.1 0.0031 6.8E-08 62.8 10.1 132 50-212 296-434 (509)
9 PRK09302 circadian clock prote 96.9 0.012 2.7E-07 58.6 11.9 137 50-211 54-200 (509)
10 TIGR03881 KaiC_arch_4 KaiC dom 96.2 0.17 3.7E-06 44.5 13.7 137 52-212 45-189 (229)
11 cd01124 KaiC KaiC is a circadi 96.0 0.14 3.1E-06 42.9 11.6 136 51-213 23-165 (187)
12 TIGR02655 circ_KaiC circadian 95.9 0.14 2.9E-06 51.4 12.8 130 50-211 286-423 (484)
13 COG0467 RAD55 RecA-superfamily 95.9 0.11 2.5E-06 47.0 11.1 147 50-217 46-198 (260)
14 TIGR02655 circ_KaiC circadian 95.7 0.14 3E-06 51.3 11.8 137 50-211 44-190 (484)
15 TIGR03878 thermo_KaiC_2 KaiC d 95.5 0.15 3.3E-06 46.8 10.5 134 51-212 60-204 (259)
16 PF05625 PAXNEB: PAXNEB protei 95.3 0.16 3.5E-06 49.5 10.4 90 126-216 179-280 (363)
17 KOG4723 Uncharacterized conser 95.1 0.11 2.5E-06 48.2 8.4 73 16-96 16-90 (248)
18 TIGR03880 KaiC_arch_3 KaiC dom 94.8 0.47 1E-05 41.8 11.2 130 51-211 40-177 (224)
19 PRK08533 flagellar accessory p 94.3 0.67 1.4E-05 42.0 11.3 130 53-212 50-185 (230)
20 TIGR02237 recomb_radB DNA repa 93.5 1.2 2.5E-05 38.6 10.8 125 53-212 38-178 (209)
21 PRK05973 replicative DNA helic 93.2 1.9 4.1E-05 40.0 12.3 62 15-83 59-120 (237)
22 PRK04301 radA DNA repair and r 91.9 2.8 6E-05 39.5 11.8 39 56-94 137-177 (317)
23 TIGR02236 recomb_radA DNA repa 91.7 1.9 4.1E-05 40.2 10.5 38 57-94 131-170 (310)
24 PRK09361 radB DNA repair and r 91.5 9.1 0.0002 33.6 14.0 124 53-212 49-190 (225)
25 cd00984 DnaB_C DnaB helicase C 91.4 0.67 1.5E-05 40.8 6.8 67 148-214 125-209 (242)
26 PRK11823 DNA repair protein Ra 89.7 19 0.00042 36.1 16.0 115 53-211 106-230 (446)
27 cd01121 Sms Sms (bacterial rad 89.6 22 0.00049 34.9 16.2 115 54-212 109-233 (372)
28 cd01393 recA_like RecA is a b 89.5 7.1 0.00015 34.0 11.5 74 56-161 54-129 (226)
29 cd01123 Rad51_DMC1_radA Rad51_ 89.1 3.5 7.5E-05 36.1 9.3 75 55-160 53-129 (235)
30 cd01125 repA Hexameric Replica 86.4 16 0.00035 32.6 12.0 142 53-217 39-195 (239)
31 PTZ00035 Rad51 protein; Provis 86.2 16 0.00036 35.2 12.7 40 55-94 152-193 (337)
32 TIGR02238 recomb_DMC1 meiotic 86.0 16 0.00034 35.0 12.4 41 54-94 129-171 (313)
33 cd01394 radB RadB. The archaea 83.3 24 0.00053 30.7 11.5 64 148-211 105-185 (218)
34 TIGR02239 recomb_RAD51 DNA rep 83.2 34 0.00074 32.7 13.3 39 56-94 131-171 (316)
35 PLN03187 meiotic recombination 81.9 13 0.00027 36.4 10.0 39 56-94 161-201 (344)
36 PRK09354 recA recombinase A; P 80.0 32 0.0007 33.9 12.1 41 32-81 72-112 (349)
37 PF03192 DUF257: Pyrococcus pr 78.4 51 0.0011 30.1 12.1 153 21-213 13-187 (210)
38 PF05763 DUF835: Protein of un 77.8 5.3 0.00012 34.1 5.3 51 122-177 56-106 (136)
39 TIGR02012 tigrfam_recA protein 76.4 23 0.00049 34.5 9.8 48 30-90 65-112 (321)
40 cd01122 GP4d_helicase GP4d_hel 75.1 63 0.0014 29.0 17.0 21 55-75 59-79 (271)
41 PLN03186 DNA repair protein RA 73.2 96 0.0021 30.3 15.6 38 57-94 159-198 (342)
42 cd00983 recA RecA is a bacter 72.9 46 0.001 32.4 10.9 120 53-213 81-224 (325)
43 PF08423 Rad51: Rad51; InterP 68.8 21 0.00046 33.0 7.4 76 55-162 72-149 (256)
44 TIGR00416 sms DNA repair prote 54.6 1.7E+02 0.0036 29.7 11.3 114 54-212 121-245 (454)
45 PF13481 AAA_25: AAA domain; P 54.3 13 0.00028 31.4 3.0 26 53-78 68-93 (193)
46 PF14417 MEDS: MEDS: MEthanoge 53.7 46 0.001 29.1 6.4 137 38-200 30-174 (191)
47 PF02150 RNA_POL_M_15KD: RNA p 50.8 3.9 8.4E-05 27.4 -0.6 14 260-273 2-15 (35)
48 TIGR03600 phage_DnaB phage rep 50.4 51 0.0011 32.2 6.8 67 148-214 307-390 (421)
49 TIGR03439 methyl_EasF probable 48.7 1.4E+02 0.0031 28.9 9.5 91 54-155 101-200 (319)
50 cd01120 RecA-like_NTPases RecA 45.7 1.5E+02 0.0032 23.3 13.1 64 148-211 87-164 (165)
51 PF00004 AAA: ATPase family as 40.6 62 0.0013 24.9 4.7 57 19-75 58-120 (132)
52 PRK09519 recA DNA recombinatio 38.3 1.7E+02 0.0036 32.2 8.9 122 51-213 84-229 (790)
53 PRK10954 periplasmic protein d 35.6 12 0.00026 33.0 -0.1 22 244-267 33-54 (207)
54 PF13466 STAS_2: STAS domain 31.3 97 0.0021 22.6 4.3 34 44-80 47-80 (80)
55 PF13911 AhpC-TSA_2: AhpC/TSA 30.7 48 0.001 26.2 2.7 44 44-98 2-45 (115)
56 PF06866 DUF1256: Protein of u 30.3 2.3E+02 0.0051 25.3 7.1 33 37-70 9-41 (163)
57 TIGR00665 DnaB replicative DNA 29.9 1.8E+02 0.004 28.4 7.1 22 53-74 222-243 (434)
58 PF04655 APH_6_hur: Aminoglyco 29.5 21 0.00045 33.4 0.4 25 186-213 162-186 (253)
59 KOG1406 Peroxisomal 3-ketoacyl 25.6 46 0.00099 32.8 2.0 39 57-96 265-303 (408)
60 smart00455 RBD Raf-like Ras-bi 25.6 46 0.001 25.2 1.6 36 67-105 23-58 (70)
61 KOG3124 Pyrroline-5-carboxylat 24.9 39 0.00085 32.5 1.4 42 14-56 214-262 (267)
62 PF11382 DUF3186: Protein of u 24.5 1.4E+02 0.0029 28.7 5.0 61 37-100 65-129 (308)
63 PRK08114 cystathionine beta-ly 24.5 37 0.0008 33.7 1.2 60 27-103 80-143 (395)
64 smart00661 RPOL9 RNA polymeras 23.0 27 0.0006 24.0 -0.0 13 261-273 2-14 (52)
65 PRK04296 thymidine kinase; Pro 22.7 3.6E+02 0.0078 23.4 6.9 98 148-266 80-185 (190)
66 TIGR03438 probable methyltrans 22.7 1.3E+02 0.0028 28.3 4.3 38 54-100 257-295 (301)
67 TIGR03438 probable methyltrans 21.8 4.4E+02 0.0096 24.6 7.8 92 57-156 88-181 (301)
68 PF00006 ATP-synt_ab: ATP synt 21.2 5.3E+02 0.012 23.5 7.9 78 54-160 40-119 (215)
69 PF09967 DUF2201: VWA-like dom 20.6 2.4E+02 0.0051 23.4 5.1 39 23-65 3-41 (126)
70 PF07411 DUF1508: Domain of un 20.2 95 0.0021 22.0 2.3 18 236-253 3-20 (49)
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=99.92 E-value=5.3e-25 Score=203.83 Aligned_cols=184 Identities=23% Similarity=0.240 Sum_probs=111.9
Q ss_pred CCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCC
Q 023377 17 EHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTD 96 (283)
Q Consensus 17 e~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySD 96 (283)
|..|+++|.||++.|+ ..+++++ |+..+.++..||+|+||.+++ .+ |+|... +.+
T Consensus 10 d~spl~Li~DSl~q~a-~~Ll~e~-------i~~a~~~~~~V~~lsfEt~~~--~~-----~~d~~~-~~~--------- 64 (280)
T PF10483_consen 10 DASPLTLILDSLEQSA-RPLLKEF-------IRRAKSRNEKVHFLSFETLNK--PE-----YADSFI-NAR--------- 64 (280)
T ss_dssp S--SEEEEEEBTTB-S-HHHHHHH-------HHHHTS----EEEEESS--S----T-----T-SEEE-ETT---------
T ss_pred CCCCeEEEEEcccccC-HHHHHHH-------HHHHHcCCCeEEEEEeEeCCC--cc-----cCCeec-ccc---------
Confidence 3789999999999984 6666665 445688999999999999888 44 667444 222
Q ss_pred CCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc
Q 023377 97 PLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS 176 (283)
Q Consensus 97 PLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~ 176 (283)
+|+ +.+++..|.........+++.+++|+||||+||++|+++ .++++|++|.+
T Consensus 65 --~~~------------------------~~~i~~~i~s~~~~~~~~~~~~~lVvIDSLn~ll~~~~~-~l~~fLssl~~ 117 (280)
T PF10483_consen 65 --GKS------------------------LQDIVKEIKSHLPSSSSSPTKKFLVVIDSLNYLLNHHPC-QLSQFLSSLLS 117 (280)
T ss_dssp --SS-------------------------HHHHHHHHHHTS--SS-SS---EEEEES-GGGS-GG----GHHHHHHHH--
T ss_pred --CCC------------------------HHHHHHHHHhhcccccccCCCCeEEEEEcchHHHHHHHH-HHHHHHHhccc
Confidence 222 122223333331112222344699999999999999999 99999999998
Q ss_pred CCceeEEEeeecccc-------cchhhHhHHhhhheeEEEeecCCcccccccccchhhhhhh------ccccceeEEEEE
Q 023377 177 HDQVSSIFWLLHSDL-------HEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLE------QNFRKGKFHVRF 243 (283)
Q Consensus 177 ~~~vssVl~LLHsDL-------He~~~v~ALe~LSstvvtv~P~~~~~~~~~~~~~~~~~l~------~n~~k~~~~vr~ 243 (283)
+++ ++|+|++|+|+ |+|+++++|+|||||+++|+|.......+++.-+++..++ .|..+.++++++
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 9999999999999999999999998877776666665554 556689999999
Q ss_pred eccCCceehh
Q 023377 244 KRRNGRVRVM 253 (283)
Q Consensus 244 KrRnGRV~~~ 253 (283)
|||+||+...
T Consensus 197 RrksGR~~~e 206 (280)
T PF10483_consen 197 RRKSGRVVSE 206 (280)
T ss_dssp E-TTS-EEEE
T ss_pred EcCCCCcEeE
Confidence 9999997653
No 2
>PF09807 DUF2348: Uncharacterized conserved protein (DUF2348); InterPro: IPR018627 Members of this family of putative uncharacterised proteins have no known function.
Probab=99.21 E-value=6.7e-10 Score=102.13 Aligned_cols=203 Identities=19% Similarity=0.264 Sum_probs=141.0
Q ss_pred CCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccC
Q 023377 18 HAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYT 95 (283)
Q Consensus 18 ~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~yS 95 (283)
..-.++|+|+ .++ |.=+..|++ +..++ .+..|.+|+|..+.+.|...++|-|.+-... +.+++++|..+
T Consensus 18 ~g~~ili~d~-~~d-gsFLlh~~L---~~~Lk----~~~~V~fv~~~q~~~HY~~v~~KLG~NL~~~~~~gql~fiD~l~ 88 (249)
T PF09807_consen 18 PGKLILIEDC-ETD-GSFLLHHFL---SQYLK----AGCKVCFVAFSQSFSHYNNVAQKLGVNLSAAKEKGQLVFIDGLK 88 (249)
T ss_pred CCeEEEEEcC-CCC-chhHHHHHH---HHHhc----CCCcEEEEEccCCHHHHHHHHHhhEecchHhccCCcEEEeehhh
Confidence 3446999999 887 566777884 44444 5568999999999999999999999997752 34799999999
Q ss_pred CCCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHH-hcChHHHHHHHHhh
Q 023377 96 DPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR-HASISSVAGILSNL 174 (283)
Q Consensus 96 DPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~-h~s~~~vc~lL~~L 174 (283)
++++|--....++... +..+.--.+...|.+++..|.+..+...+ .++ ++|+||-||.|+- ..+..+|-.+++.+
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 8887742211000100 11111111234588898988888883333 333 8999999999997 34455788899888
Q ss_pred hc---CCceeEEEeeeccccc---c-h-hhHhHHhhhheeEEEeecCCcccccccccchhhhhhhccccceeEEEEEecc
Q 023377 175 RS---HDQVSSIFWLLHSDLH---E-I-KFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRR 246 (283)
Q Consensus 175 r~---~~~vssVl~LLHsDLH---e-~-~~v~ALe~LSstvvtv~P~~~~~~~~~~~~~~~~~l~~n~~k~~~~vr~KrR 246 (283)
+. ...-.+++.|+|.|-- + . .....|+|+|..+|+++|+.-+- ++. =-|+++|.-|+.
T Consensus 165 ra~l~~~~~~~lVvl~h~d~~~~~e~~~~l~~~L~h~a~l~i~v~~L~TG~--s~D------------VhGqL~v~~r~~ 230 (249)
T PF09807_consen 165 RATLCSESNGSLVVLVHCDIDDEDEENDLLLNSLAHMADLVITVEPLPTGY--SKD------------VHGQLTVLWRGN 230 (249)
T ss_pred HHHhccccCCCEEEEEecCCCCccchHHHHHHHHHHHhcEEEEecCCCCcc--ccc------------ceEEEEEEEccC
Confidence 84 2234588899998865 2 2 27899999999999999965533 111 137888866654
Q ss_pred C
Q 023377 247 N 247 (283)
Q Consensus 247 n 247 (283)
.
T Consensus 231 ~ 231 (249)
T PF09807_consen 231 S 231 (249)
T ss_pred C
Confidence 3
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=98.25 E-value=4.9e-06 Score=73.22 Aligned_cols=137 Identities=20% Similarity=0.241 Sum_probs=90.0
Q ss_pred hhccc-cceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 023377 50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (283)
Q Consensus 50 a~~~q-~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (283)
++..+ ++.+..+.+|-+|+++.+-++..|+|.+.. +.+++++|+++...+|... ++..+
T Consensus 42 ~~~~~~ge~vlyvs~ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~~~~~~~------------------~~~~l 103 (226)
T PF06745_consen 42 NGLKNFGEKVLYVSFEEPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERIGWSPN------------------DLEEL 103 (226)
T ss_dssp HHHHHHT--EEEEESSS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGST-TSC------------------CHHHH
T ss_pred HhhhhcCCcEEEEEecCCHHHHHHHHHHcCCcHHHHhhcCCEEEEeccccccccccc------------------CHHHH
Confidence 46677 999999999999999999999999876542 3359999999999988821 22233
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEeeecccccchhhHhHHhh-
Q 023377 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLHSDLHEIKFTSVLEY- 202 (283)
Q Consensus 127 ~sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LLHsDLHe~~~v~ALe~- 202 (283)
...+...++..+ + -.|+||||+.+....+....-..+++|.+. ..+..++-.-..+-+++.....+++
T Consensus 104 ~~~i~~~i~~~~-------~-~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~llt~~~~~~~~~~~~~~i~~~ 175 (226)
T PF06745_consen 104 LSKIREAIEELK-------P-DRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTLLTSEMPSGSEDDGTFGIEHY 175 (226)
T ss_dssp HHHHHHHHHHHT-------S-SEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEEEEEEESSSSSSSSSTSHHHH
T ss_pred HHHHHHHHHhcC-------C-CEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEEEEEccccCcccccccchhhh
Confidence 322233333222 2 489999999996667766666666666542 3455554444344555666666766
Q ss_pred hheeEEEeec
Q 023377 203 LSSMVASVEP 212 (283)
Q Consensus 203 LSstvvtv~P 212 (283)
++.++|.+.=
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=97.94 E-value=0.00013 Score=65.54 Aligned_cols=143 Identities=17% Similarity=0.181 Sum_probs=85.8
Q ss_pred hccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhH
Q 023377 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (283)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (283)
+..+++.+..+.+|-+|+++.+-++..|+|... -..++.++|+|++-.++...... -+..+..++..
T Consensus 45 ~~~~ge~~lyvs~ee~~~~i~~~~~~~g~~~~~~~~~g~l~~~d~~~~~~~~~~~~~~-----------~~~~~~~~~~~ 113 (237)
T TIGR03877 45 GLQMGEPGIYVALEEHPVQVRRNMAQFGWDVRKYEEEGKFAIVDAFTGGIGEAAEREK-----------YVVKDPTDVRE 113 (237)
T ss_pred HHHcCCcEEEEEeeCCHHHHHHHHHHhCCCHHHHhhcCCEEEEecccccccccccccc-----------ccccCcccHHH
Confidence 446799999999999999999999999988542 13479999999985554432110 11112234455
Q ss_pred HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh---HHHHHHHHhhhcCCceeEEEeeecccccchhh-HhHHhhhh
Q 023377 129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKF-TSVLEYLS 204 (283)
Q Consensus 129 l~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~---~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~~-v~ALe~LS 204 (283)
++..+.+..+ +.++ -.|+||||+.++...+. ..+-++.+.+++.+ +..++ .-|.+..+... ...++|++
T Consensus 114 ~~~~i~~~i~----~~~~-~~vVIDSls~l~~~~~~~~r~~l~~l~~~lk~~~-~t~ll-t~~~~~~~~~~~~~~~~~~~ 186 (237)
T TIGR03877 114 LIDVLRQAIR----DINA-KRVVIDSVTTLYITKPAMARSIVMQLKRVLSGLG-CTSIF-VSQVSVGERGFGGPGVEHAV 186 (237)
T ss_pred HHHHHHHHHH----HhCC-CEEEEcChhHhhcCChHHHHHHHHHHHHHHHhCC-CEEEE-EECcccccccccccceEEEE
Confidence 5555555444 1122 27999999998764432 12333444455433 33333 23332222111 12478999
Q ss_pred eeEEEee
Q 023377 205 SMVASVE 211 (283)
Q Consensus 205 stvvtv~ 211 (283)
-++|.+.
T Consensus 187 D~vI~L~ 193 (237)
T TIGR03877 187 DGIIRLD 193 (237)
T ss_pred eEEEEEE
Confidence 9999886
No 5
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=97.83 E-value=0.00069 Score=60.22 Aligned_cols=137 Identities=20% Similarity=0.270 Sum_probs=94.8
Q ss_pred hccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhH
Q 023377 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (283)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (283)
+..+++.+..+.+|.+|+++.+-+++.|+|.... ...+.++|.+..+..|... +. ..
T Consensus 49 ~~~~g~~~~y~~~e~~~~~~~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~------------------~~---~~ 107 (234)
T PRK06067 49 ALKQGKKVYVITTENTSKSYLKQMESVKIDISDFFLWGYLRIFPLNTEGFEWNST------------------LA---NK 107 (234)
T ss_pred HHhCCCEEEEEEcCCCHHHHHHHHHHCCCChhHHHhCCCceEEeccccccccCcc------------------hH---HH
Confidence 4457999999999999999999999999886541 3357777777666655432 11 22
Q ss_pred HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC-CceeEEEeeecccccchhhHhHHhhhheeE
Q 023377 129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH-DQVSSIFWLLHSDLHEIKFTSVLEYLSSMV 207 (283)
Q Consensus 129 l~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~-~~vssVl~LLHsDLHe~~~v~ALe~LSstv 207 (283)
++..+.+..+ +.++ -.|+|||++.++...+...+.+++..|+.. ..=..++...|.+.+.+.....+++++-.+
T Consensus 108 ll~~l~~~i~----~~~~-~~iviDs~t~~~~~~~~~~~~~~l~~l~~l~~~g~tvllt~~~~~~~~~~~~~~~~l~Dgv 182 (234)
T PRK06067 108 LLELIIEFIK----SKRE-DVIIIDSLTIFATYAEEDDILNFLTEAKNLVDLGKTILITLHPYAFSEELLSRIRSICDVY 182 (234)
T ss_pred HHHHHHHHHH----hcCC-CEEEEecHHHHHhcCCHHHHHHHHHHHHHHHhCCCEEEEEecCCcCCHHHHHHHHhheEEE
Confidence 3333333333 1122 379999999998878887777775555331 122456777787777777778899999999
Q ss_pred EEeecC
Q 023377 208 ASVEPF 213 (283)
Q Consensus 208 vtv~P~ 213 (283)
+.+.-.
T Consensus 183 I~L~~~ 188 (234)
T PRK06067 183 LKLRAE 188 (234)
T ss_pred EEEEee
Confidence 999753
No 6
>PRK04328 hypothetical protein; Provisional
Probab=97.80 E-value=0.00032 Score=63.85 Aligned_cols=144 Identities=19% Similarity=0.177 Sum_probs=86.7
Q ss_pred hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 023377 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (283)
Q Consensus 50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (283)
.+..+++.+..+.+|-+|+.+++-+++.|+|... -+.++.++|+|+.-.|....... -+..+..++.
T Consensus 46 ~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~~~l~iid~~~~~~~~~~~~~~-----------~~~~~~~~~~ 114 (249)
T PRK04328 46 NGLQMGEPGVYVALEEHPVQVRRNMRQFGWDVRKYEEEGKFAIVDAFTGGIGSAAKREK-----------YVVKDPDDVR 114 (249)
T ss_pred HHHhcCCcEEEEEeeCCHHHHHHHHHHcCCCHHHHhhcCCEEEEecccccccccccccc-----------ccccCcccHH
Confidence 3567799999999999999999999999987543 13479999999987765431110 1112233455
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh---HHHHHHHHhhhcCCceeEEEeeecccccchhh-HhHHhhh
Q 023377 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKF-TSVLEYL 203 (283)
Q Consensus 128 sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~---~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~~-v~ALe~L 203 (283)
.++..+.+..+ +.++ -.|+||||+.|.+..+- ..+.++.+.|++.+ +..++- .|.+..+... -..++|+
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 55555555444 1122 37999999998764321 12344445555533 333322 2333222111 1246889
Q ss_pred heeEEEee
Q 023377 204 SSMVASVE 211 (283)
Q Consensus 204 Sstvvtv~ 211 (283)
+-++|.+.
T Consensus 188 ~D~vI~L~ 195 (249)
T PRK04328 188 VDGIIRLD 195 (249)
T ss_pred EEEEEEEE
Confidence 99999885
No 7
>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=97.44 E-value=0.0066 Score=56.44 Aligned_cols=168 Identities=15% Similarity=0.146 Sum_probs=123.9
Q ss_pred cc-cCCCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEE
Q 023377 13 GL-EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIH 89 (283)
Q Consensus 13 ~l-~ge~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~ 89 (283)
+| .|=+.|.|++-.-=.+++=..+.+-++ -..-.++..+..+.-|.+--+|..-|..-|.|..- ++.++.
T Consensus 20 rLGGGiP~GsL~lIEGd~~tGKSvLsqr~~-------YG~L~~g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G~l~ 92 (235)
T COG2874 20 RLGGGIPVGSLILIEGDNGTGKSVLSQRFA-------YGFLMNGYRVTYVSTELTVREFIKQMESLSYDVSDFLLSGRLL 92 (235)
T ss_pred hccCCCccCeEEEEECCCCccHHHHHHHHH-------HHHHhCCceEEEEEechhHHHHHHHHHhcCCCchHHHhcceeE
Confidence 45 346666665433333333233222221 13556788999999999999999999988877554 566777
Q ss_pred EEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHH
Q 023377 90 ILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAG 169 (283)
Q Consensus 90 i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~ 169 (283)
|.-...+|..|+.... +++++.++|..| .-. +. +|.|||||..+.+.+..++-+
T Consensus 93 ~~~~~~~~~~~~~~~~---------------------~~~L~~l~~~~k-~~~--~d--ViIIDSls~~~~~~~~~~vl~ 146 (235)
T COG2874 93 FFPVNLEPVNWGRRSA---------------------RKLLDLLLEFIK-RWE--KD--VIIIDSLSAFATYDSEDAVLN 146 (235)
T ss_pred EEEecccccccChHHH---------------------HHHHHHHHhhHH-hhc--CC--EEEEecccHHhhcccHHHHHH
Confidence 8777779999998633 334455566555 222 44 899999999999999999999
Q ss_pred HHHhhhc-CCceeEEEeeecccccchhhHhHHhhhheeEEEeecC
Q 023377 170 ILSNLRS-HDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPF 213 (283)
Q Consensus 170 lL~~Lr~-~~~vssVl~LLHsDLHe~~~v~ALe~LSstvvtv~P~ 213 (283)
++..+|+ +++=.-|+--+|.+.-.+.++.-++..+++-+.++-.
T Consensus 147 fm~~~r~l~d~gKvIilTvhp~~l~e~~~~rirs~~d~~l~L~~~ 191 (235)
T COG2874 147 FMTFLRKLSDLGKVIILTVHPSALDEDVLTRIRSACDVYLRLRLE 191 (235)
T ss_pred HHHHHHHHHhCCCEEEEEeChhhcCHHHHHHHHHhhheeEEEEhh
Confidence 9999998 4566778889999999999999999999999888653
No 8
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=97.11 E-value=0.0031 Score=62.79 Aligned_cols=132 Identities=16% Similarity=0.223 Sum_probs=83.7
Q ss_pred hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 023377 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (283)
Q Consensus 50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (283)
.+..+++.+..+.||-+|+.+.+-++..|+|.+. -+..+.+++.+.++.+|+..
T Consensus 296 ~~~~~g~~~~yis~e~~~~~i~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~------------------------ 351 (509)
T PRK09302 296 AACRRGERCLLFAFEESRAQLIRNARSWGIDLEKMEEKGLLKIICARPESYGLEDH------------------------ 351 (509)
T ss_pred HHHhCCCcEEEEEecCCHHHHHHHHHHcCCChHHHhhcCCceeecCCcccCCHHHH------------------------
Confidence 3456799999999999999999999988887544 12356778877666544321
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEeee-cccc-cchhhHhHHhh
Q 023377 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLL-HSDL-HEIKFTSVLEY 202 (283)
Q Consensus 128 sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LL-HsDL-He~~~v~ALe~ 202 (283)
+..+.+..+ +.++ -.|+||||+.+....+...+-+.|..|.+. -.+..++-.. +.+. +.+.....++|
T Consensus 352 --~~~i~~~i~----~~~~-~~vVIDslt~l~~~~~~~~~~~~l~~l~~~~k~~~~t~l~t~~~~~~~g~~~~~~~~~~~ 424 (509)
T PRK09302 352 --LIIIKREIE----EFKP-SRVAIDPLSALARGGSLNEFRQFVIRLTDYLKSEEITGLFTNLTPDFMGSHSITESHISS 424 (509)
T ss_pred --HHHHHHHHH----HcCC-CEEEEcCHHHHHHhCCHHHHHHHHHHHHHHHHhCCCeEEEEeccccccCCCCCCcCceEE
Confidence 112222222 1233 379999999999877766555555544331 3455555433 2222 23333345899
Q ss_pred hheeEEEeec
Q 023377 203 LSSMVASVEP 212 (283)
Q Consensus 203 LSstvvtv~P 212 (283)
++.++|.+.=
T Consensus 425 l~D~vI~L~~ 434 (509)
T PRK09302 425 LTDTWILLQY 434 (509)
T ss_pred eeeEEEEEEE
Confidence 9999999963
No 9
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=96.87 E-value=0.012 Score=58.56 Aligned_cols=137 Identities=18% Similarity=0.175 Sum_probs=87.3
Q ss_pred hhccc-cceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 023377 50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (283)
Q Consensus 50 a~~~q-~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (283)
.+..+ ++.+..+.+|-+|+++.+-++.-|+|.+.. +.++.+.|.+.+|..|... . ..++
T Consensus 54 ~~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~g~l~~~~~~~~~~~~~~~-~-----------------~~~~ 115 (509)
T PRK09302 54 NGIKRFDEPGVFVTFEESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSEQEEA-G-----------------EYDL 115 (509)
T ss_pred HHHHhcCCCEEEEEccCCHHHHHHHHHHcCCCHHHHhhCCeEEEEecCccccccccc-c-----------------cccH
Confidence 34555 899999999999999999999999986552 3469999999999888642 1 0133
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH-----HHHHHHHhhhcCCceeEEEeeeccccc-c-hhhHhH
Q 023377 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS-----SVAGILSNLRSHDQVSSIFWLLHSDLH-E-IKFTSV 199 (283)
Q Consensus 127 ~sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~-----~vc~lL~~Lr~~~~vssVl~LLHsDLH-e-~~~v~A 199 (283)
.+++..+.+..+ +.++ -.|+|||++.+....... .+.+++..|++. .+..++. -|..-. + ....+.
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 444455555444 1222 369999999987654332 344455555543 3333333 353321 1 111234
Q ss_pred HhhhheeEEEee
Q 023377 200 LEYLSSMVASVE 211 (283)
Q Consensus 200 Le~LSstvvtv~ 211 (283)
.++++..++.+.
T Consensus 189 ~~~laDgVI~L~ 200 (509)
T PRK09302 189 EEFVSDCVIILR 200 (509)
T ss_pred eEEEeeEEEEEe
Confidence 588999999886
No 10
>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=96.24 E-value=0.17 Score=44.54 Aligned_cols=137 Identities=14% Similarity=0.146 Sum_probs=76.9
Q ss_pred ccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCC--CCcccccCCccccccccccccccchhhhh
Q 023377 52 KSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPL--GWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (283)
Q Consensus 52 ~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ySDPL--GW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (283)
..+++.+..+.+|.+++.+.+-+++.|++.... +.++.+.|.++... .|.-. .. ++.++.
T Consensus 45 ~~~g~~~~~is~e~~~~~i~~~~~~~g~~~~~~~~~~~l~i~d~~~~~~~~~~~~~------------~~----~~~~~~ 108 (229)
T TIGR03881 45 LRDGDPVIYVTTEESRESIIRQAAQFGMDFEKAIEEGKLVIIDALMKEKEDEWSLR------------EL----SIEELL 108 (229)
T ss_pred HhcCCeEEEEEccCCHHHHHHHHHHhCCCHHHHhhcCCEEEEEccccccccccccc------------cC----CHHHHH
Confidence 346889999999999999998888899886642 34688888765431 12210 01 222332
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc---CCceeEEEeeecccc-cchhhHhHHhhh
Q 023377 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS---HDQVSSIFWLLHSDL-HEIKFTSVLEYL 203 (283)
Q Consensus 128 sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~---~~~vssVl~LLHsDL-He~~~v~ALe~L 203 (283)
..+.+..+ ..+ .++ -.|+|||++.++...+.. .-+.+..|.+ ...+..++ .-|-.. -++.....++|+
T Consensus 109 ---~~i~~~~~-~~~-~~~-~~vvIDsl~~l~~~~~~~-~r~~~~~l~~~l~~~~~tvil-~~~~~~~~~~~~~~~~~~l 180 (229)
T TIGR03881 109 ---NKVIEAKK-YLG-YGH-ARLVIDSMSAFWLDKPAM-ARKYSYYLKRVLNRWNFTILL-TSQYAITTSQAFGFGIEHV 180 (229)
T ss_pred ---HHHHHHHH-hhc-cCc-eEEEecCchhhhccChHH-HHHHHHHHHHHHHhCCCEEEE-EecccccCCCCcccceEEE
Confidence 33333332 111 122 478999999998755432 2222222322 12333333 344222 222222357899
Q ss_pred heeEEEeec
Q 023377 204 SSMVASVEP 212 (283)
Q Consensus 204 Sstvvtv~P 212 (283)
+-.+|.+.-
T Consensus 181 ~D~vI~L~~ 189 (229)
T TIGR03881 181 ADGIIRFRK 189 (229)
T ss_pred EeEEEEEEE
Confidence 999998874
No 11
>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=96.01 E-value=0.14 Score=42.88 Aligned_cols=136 Identities=18% Similarity=0.119 Sum_probs=82.0
Q ss_pred hccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhH
Q 023377 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (283)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (283)
+..+++.+.++.+|-+++.+.+-+++.|++.+.+ +..+.+.|.+...+...+. . ... .
T Consensus 23 ~~~~g~~v~~~s~e~~~~~~~~~~~~~g~~~~~l~~~g~l~~~d~~~~~~s~~~~-~----------------~~~---~ 82 (187)
T cd01124 23 GLARGEPGLYVTLEESPEELIENAESLGWDLERLEDEGLLAIVDADPDEIGPAES-S----------------LRL---E 82 (187)
T ss_pred HHHCCCcEEEEECCCCHHHHHHHHHHcCCChHHHHhcCCeEEEecCccccchhhh-h----------------hhH---H
Confidence 4467899999999999999999999889885531 2346777755444421110 0 000 1
Q ss_pred HHHHHHHhccCccCCCCCcEEEEEechhHHHH---hcChHHHHHHHHhhhcCCceeEEEeeeccccc-c-hhhHhHHhhh
Q 023377 129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR---HASISSVAGILSNLRSHDQVSSIFWLLHSDLH-E-IKFTSVLEYL 203 (283)
Q Consensus 129 l~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~---h~s~~~vc~lL~~Lr~~~~vssVl~LLHsDLH-e-~~~v~ALe~L 203 (283)
++..+.+..+ +.++ -.|+||+++.++. ......+-+++..|++. .+. ++..-|..-. + ......++++
T Consensus 83 ~~~~i~~~~~----~~~~-~~lviD~~~~~~~~~~~~~~~~i~~l~~~l~~~-g~t-vi~v~~~~~~~~~~~~~~~~~~~ 155 (187)
T cd01124 83 LIQRLKDAIE----EFKA-KRVVIDSVSGLLLMEQSTARLEIRRLLFALKRF-GVT-TLLTSEQSGLEGTGFGGGDVEYL 155 (187)
T ss_pred HHHHHHHHHH----HhCC-CEEEEeCcHHHhhcChHHHHHHHHHHHHHHHHC-CCE-EEEEeccccCCCcccCcCceeEe
Confidence 2222332222 1122 4899999999987 44445566777777764 333 3333443222 1 2334678999
Q ss_pred heeEEEeecC
Q 023377 204 SSMVASVEPF 213 (283)
Q Consensus 204 Sstvvtv~P~ 213 (283)
+..++.++-.
T Consensus 156 aD~ii~l~~~ 165 (187)
T cd01124 156 VDGVIRLRLD 165 (187)
T ss_pred eeEEEEEEEE
Confidence 9999988653
No 12
>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=95.90 E-value=0.14 Score=51.36 Aligned_cols=130 Identities=16% Similarity=0.235 Sum_probs=76.8
Q ss_pred hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 023377 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (283)
Q Consensus 50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (283)
+++.+++.+..+.||=|++++..=+++-|+|.+. ...++.+++.+....+. .
T Consensus 286 ~~~~~ge~~~y~s~eEs~~~i~~~~~~lg~~~~~~~~~g~l~~~~~~p~~~~~--------------------------~ 339 (484)
T TIGR02655 286 NACANKERAILFAYEESRAQLLRNAYSWGIDFEEMEQQGLLKIICAYPESAGL--------------------------E 339 (484)
T ss_pred HHHHCCCeEEEEEeeCCHHHHHHHHHHcCCChHHHhhCCcEEEEEcccccCCh--------------------------H
Confidence 3556889999999999999999999999987543 12358888865432211 1
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHH----hhhcCCceeEEEeeecccc--cchhhHhHHh
Q 023377 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILS----NLRSHDQVSSIFWLLHSDL--HEIKFTSVLE 201 (283)
Q Consensus 128 sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~----~Lr~~~~vssVl~LLHsDL--He~~~v~ALe 201 (283)
..+..+.+..+ +.++ -.|+||||+.+....+..++-..++ .|++ ..+..++...=.++ +.+-.-.-++
T Consensus 340 ~~~~~i~~~i~----~~~~-~~vvIDsi~~~~~~~~~~~~r~~~~~l~~~lk~-~~it~~~t~~~~~~~~~~~~~~~~~s 413 (484)
T TIGR02655 340 DHLQIIKSEIA----DFKP-ARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQ-EEITGFFTNTSDQFMGSHSITDSHIS 413 (484)
T ss_pred HHHHHHHHHHH----HcCC-CEEEEcCHHHHHHhcCHHHHHHHHHHHHHHHhh-CCCeEEEeecccccccCCccCCCCee
Confidence 12223333232 1122 3799999999987666665544333 3443 44554444322221 1111113468
Q ss_pred hhheeEEEee
Q 023377 202 YLSSMVASVE 211 (283)
Q Consensus 202 ~LSstvvtv~ 211 (283)
||+-.+|.+.
T Consensus 414 ~l~D~ii~l~ 423 (484)
T TIGR02655 414 TITDTILMLQ 423 (484)
T ss_pred EeeeEEEEEE
Confidence 8888888774
No 13
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=95.85 E-value=0.11 Score=47.00 Aligned_cols=147 Identities=19% Similarity=0.214 Sum_probs=92.5
Q ss_pred hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 023377 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (283)
Q Consensus 50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (283)
.++..++.+..+.+|-+|++.++-+++.|.|.+. -+..+.++|.++.+.+=... .-.+..++.
T Consensus 46 ~~~~~ge~vlyvs~~e~~~~l~~~~~~~g~d~~~~~~~g~l~i~d~~~~~~~~~~~---------------~~~~~~~~~ 110 (260)
T COG0467 46 EGAREGEPVLYVSTEESPEELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLVSI---------------VVGDPLDLE 110 (260)
T ss_pred HHHhcCCcEEEEEecCCHHHHHHHHHHcCCCHHHHhhcCCEEEEEccccccccccc---------------cccCCccHH
Confidence 4566699999999999999999999999998753 23458899988877632210 001122444
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHH-HHHHhhhcC-CceeEEEeeecccccchhhH--hHHhhh
Q 023377 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVA-GILSNLRSH-DQVSSIFWLLHSDLHEIKFT--SVLEYL 203 (283)
Q Consensus 128 sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc-~lL~~Lr~~-~~vssVl~LLHsDLHe~~~v--~ALe~L 203 (283)
++...|.+..+ .. + ...++|||++.+......+... ..+..+.+. ..-. +.+++.+|....... +-.+++
T Consensus 111 ~l~~~I~~~~~-~~---~-~~~~ViDsi~~~~~~~~~~~~~r~~~~~l~~~~~~~~-~t~~~~~~~~~~~~~~~~~~~~~ 184 (260)
T COG0467 111 ELLDRIREIVE-KE---G-ADRVVIDSITELTLYLNDPALVRRILLLLKRFLKKLG-VTSLLTTEAPVEERGESGVEEYI 184 (260)
T ss_pred HHHHHHHHHHH-Hh---C-CCEEEEeCCchHhhhcCchHHHHHHHHHHHHHHHhCC-CEEEEEecccccCCCccceEEEE
Confidence 45555555555 11 1 2689999999766666666554 444444442 2222 445555554332222 466678
Q ss_pred heeEEEeecCCccc
Q 023377 204 SSMVASVEPFNQAA 217 (283)
Q Consensus 204 Sstvvtv~P~~~~~ 217 (283)
+..++.+.......
T Consensus 185 vdgvI~l~~~~~~~ 198 (260)
T COG0467 185 VDGVIRLDLKEIEG 198 (260)
T ss_pred EEEEEEEeeecccC
Confidence 88999887754433
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=95.68 E-value=0.14 Score=51.35 Aligned_cols=137 Identities=19% Similarity=0.187 Sum_probs=83.9
Q ss_pred hhccc-cceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 023377 50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (283)
Q Consensus 50 a~~~q-~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (283)
+++.+ ++.+..+.||=+|+++.+-+++.|+|-+.. ..++.++|.+..+ |..... +--++
T Consensus 44 ~g~~~~ge~~lyvs~eE~~~~l~~~~~~~G~~~~~~~~~g~l~~~~~~~~~--~~~~~~----------------~~~~l 105 (484)
T TIGR02655 44 NGIIHFDEPGVFVTFEESPQDIIKNARSFGWDLQKLVDEGKLFILDASPDP--EGQDVV----------------GGFDL 105 (484)
T ss_pred HHHHhCCCCEEEEEEecCHHHHHHHHHHcCCCHHHHhhcCceEEEecCchh--cccccc----------------ccCCH
Confidence 45566 899999999999999999999999986531 3468888875332 222110 00123
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH-----HHHHHHHhhhcCCceeEEEeeec-ccccch-hhHhH
Q 023377 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS-----SVAGILSNLRSHDQVSSIFWLLH-SDLHEI-KFTSV 199 (283)
Q Consensus 127 ~sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~-----~vc~lL~~Lr~~~~vssVl~LLH-sDLHe~-~~v~A 199 (283)
..++..+.+... + +++ --|+|||++.+....+.. .+.++++.|++. .+..++- -| .+...+ ...+.
T Consensus 106 ~~~l~~i~~~ls---~-g~~-qRVvIDSl~aL~~~~~~~~~~r~~l~~Li~~L~~~-g~TvLLt-sh~~~~~~~~~~~~~ 178 (484)
T TIGR02655 106 SALIERINYAIR---K-YKA-KRVSIDSVTAVFQQYDAVSVVRREIFRLVARLKQI-GVTTVMT-TERIEEYGPIARYGV 178 (484)
T ss_pred HHHHHHHHHHHH---H-hCC-cEEEEeehhHhhhhcCchHHHHHHHHHHHHHHHHC-CCEEEEE-ecCcccccccccCCc
Confidence 344444444333 1 233 479999999987655542 345566667642 3444443 34 232221 12223
Q ss_pred HhhhheeEEEee
Q 023377 200 LEYLSSMVASVE 211 (283)
Q Consensus 200 Le~LSstvvtv~ 211 (283)
.+|++-.+|.+.
T Consensus 179 ~e~laDgVI~L~ 190 (484)
T TIGR02655 179 EEFVSDNVVILR 190 (484)
T ss_pred eeEeeeeEEEEE
Confidence 599999999986
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=95.47 E-value=0.15 Score=46.84 Aligned_cols=134 Identities=13% Similarity=0.103 Sum_probs=72.8
Q ss_pred hccccceeEEEEeecChHH----HHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 023377 51 GKSQSRGLVVVAYSRSPSF----YVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (283)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~----y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (283)
++.+++.+..+.+|-++++ ++.-.++.|+|.+...++++++|..+.+-- . .++
T Consensus 60 ~a~~Ge~vlyis~Ee~~~~~~~~l~~~a~~~g~d~~~~~~~l~~id~~~~~~~-----~------------------~~~ 116 (259)
T TIGR03878 60 QASRGNPVLFVTVESPANFVYTSLKERAKAMGVDFDKIEENIILIDAASSTEL-----R------------------ENV 116 (259)
T ss_pred HHhCCCcEEEEEecCCchHHHHHHHHHHHHcCCCHHHHhCCEEEEECCCchhh-----h------------------hhH
Confidence 4567999999999976653 333345667776554567888886653210 0 123
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH---HHHHHHHhhhcCCceeEEEeeecccc---cc-hhhHhH
Q 023377 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS---SVAGILSNLRSHDQVSSIFWLLHSDL---HE-IKFTSV 199 (283)
Q Consensus 127 ~sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~---~vc~lL~~Lr~~~~vssVl~LLHsDL---He-~~~v~A 199 (283)
..++..+.+..+ +.++ =.|+|||++.+.+..... .+-++++.|++.+.-.-++.-.+.+. .. +..-..
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 334444444333 1122 379999999876543321 12334444454333222333333322 11 111125
Q ss_pred HhhhheeEEEeec
Q 023377 200 LEYLSSMVASVEP 212 (283)
Q Consensus 200 Le~LSstvvtv~P 212 (283)
++|++-.+|.+.=
T Consensus 192 ~~~l~D~vI~L~~ 204 (259)
T TIGR03878 192 VSHIVDGTIVLAK 204 (259)
T ss_pred eeEeeccEEEEee
Confidence 8999999998873
No 16
>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=95.26 E-value=0.16 Score=49.46 Aligned_cols=90 Identities=20% Similarity=0.142 Sum_probs=58.3
Q ss_pred hhHHHHHHHHhccCc--cCCCCCcEEEEEechhHHHHhcCh----HHHHHHHHhhhc----CCceeEEEeeeccccc--c
Q 023377 126 LDKLYSLIIEQGKGL--IGQGKDRFSIAIDSVSEMVRHASI----SSVAGILSNLRS----HDQVSSIFWLLHSDLH--E 193 (283)
Q Consensus 126 L~sl~~si~e~~r~~--~~~~k~~~tVaIDSLS~LL~h~s~----~~vc~lL~~Lr~----~~~vssVl~LLHsDLH--e 193 (283)
.+.+++.|.+..+.. .. ++.-.=|+|-||..-+-..+- ..+.++|+.||. +..-..++--+=.+|- .
T Consensus 179 ~~~ll~~i~~~i~~~~~~~-~~~v~RI~I~sl~SP~w~~~~~~~~~~ll~FL~~LR~LlR~~~s~~v~~iTlP~~L~~~~ 257 (363)
T PF05625_consen 179 YRSLLQQIQQIISKSGFSP-PSKVLRIVIPSLGSPLWYPPSASQPSELLRFLHSLRALLRKYSSNAVAMITLPSHLYPRS 257 (363)
T ss_dssp HHHHHHHHHHHHHH----T-TTSEEEEEETTTT-TTTS-GGGGBHHHHHHHHHHHHHHHHHTTTTEEEEEEEEGTTS---
T ss_pred HHHHHHHHHHHHHhhccCC-CCceEEEEEcCCCCcccCCcccccHHHHHHHHHHHHHHHhccCCCEEEEEEECHHHhccC
Confidence 455555555554421 12 232267899887665543322 248999999987 3555555556677777 7
Q ss_pred hhhHhHHhhhheeEEEeecCCcc
Q 023377 194 IKFTSVLEYLSSMVASVEPFNQA 216 (283)
Q Consensus 194 ~~~v~ALe~LSstvvtv~P~~~~ 216 (283)
+..+..||+++-++|.|+|....
T Consensus 258 ~~~~~~l~~l~D~vi~Le~F~~~ 280 (363)
T PF05625_consen 258 PSLVRRLEHLADGVIELESFAGS 280 (363)
T ss_dssp HHHHHHHHHHSSEEEEEEE--HH
T ss_pred hHHHHHHHHhCCEEEEeecCCCc
Confidence 99999999999999999999876
No 17
>KOG4723 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.13 E-value=0.11 Score=48.21 Aligned_cols=73 Identities=21% Similarity=0.378 Sum_probs=57.9
Q ss_pred CCCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEec
Q 023377 16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDC 93 (283)
Q Consensus 16 ge~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ 93 (283)
.|+--..+++|+..+| |.-+|-|++ +-..+++ +.+.+++|.++.+.|--.+++-|.|-.. .+.+++++|.
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-GSFLFHYYL---YHALKAN----ESTCFLAFSKTFSHYAISMRKLGMDLKTKKNRGQLVFIDG 87 (248)
T ss_pred CCCccEEEEeecccCC-ceeeHHHHH---HHHHhcC----CcEEEEEeecchhHHHHHHHHhCCceeecccCCcEEEEhh
Confidence 4666789999999998 577777774 3333333 8999999999999999999999999877 2335999998
Q ss_pred cCC
Q 023377 94 YTD 96 (283)
Q Consensus 94 ySD 96 (283)
++=
T Consensus 88 l~~ 90 (248)
T KOG4723|consen 88 LSM 90 (248)
T ss_pred hhh
Confidence 873
No 18
>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=94.82 E-value=0.47 Score=41.82 Aligned_cols=130 Identities=14% Similarity=0.152 Sum_probs=75.7
Q ss_pred hccccceeEEEEeecChHHHHHHHhhcCcCccC-CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHH
Q 023377 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS-SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKL 129 (283)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s-~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl 129 (283)
+..+++.+..+.+|-+++.+.+-++..|++... .++++.++|....-. ...++.+.
T Consensus 40 ~~~~g~~~~y~s~e~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---------------------~~~~~~l~-- 96 (224)
T TIGR03880 40 GLKNGEKAMYISLEEREERILGYAKSKGWDLEDYIDKSLYIVRLDPSDF---------------------KTSLNRIK-- 96 (224)
T ss_pred HHhCCCeEEEEECCCCHHHHHHHHHHcCCChHHHHhCCeEEEecCHHHH---------------------HhhHHHHH--
Confidence 445689999999999999999999888877543 122466666321100 00111222
Q ss_pred HHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh-----HHHHHHHHhhhcCCceeEEEeeecccccch--hhHhHHhh
Q 023377 130 YSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-----SSVAGILSNLRSHDQVSSIFWLLHSDLHEI--KFTSVLEY 202 (283)
Q Consensus 130 ~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~-----~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~--~~v~ALe~ 202 (283)
..+.+..+ +.++ -.|+|||++.+-.-.+. ..+..++..|++. .+ .++-.-|.+-+.+ ...+.+++
T Consensus 97 -~~~~~~i~----~~~~-~~vVIDsls~l~~~~~~~~~~r~~l~~l~~~lk~~-~~-tvll~s~~~~~~~~~~~~~~~~~ 168 (224)
T TIGR03880 97 -NELPILIK----ELGA-SRVVIDPISLLETLFDDDAERRTELFRFYSSLRET-GV-TTILTSEADKTNVFASKYGLIEY 168 (224)
T ss_pred -HHHHHHHH----HhCC-CEEEEcChHHHhhhcCCHHHHHHHHHHHHHHHHhC-CC-EEEEEEcccCCCCCccCCCceEE
Confidence 22222221 1122 36789999987222222 3556777777754 33 3444456543332 22456899
Q ss_pred hheeEEEee
Q 023377 203 LSSMVASVE 211 (283)
Q Consensus 203 LSstvvtv~ 211 (283)
++..++.+.
T Consensus 169 l~D~vI~L~ 177 (224)
T TIGR03880 169 LADGVIILK 177 (224)
T ss_pred EEeEEEEEe
Confidence 999999994
No 19
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=94.35 E-value=0.67 Score=41.96 Aligned_cols=130 Identities=13% Similarity=0.193 Sum_probs=74.8
Q ss_pred cccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHH
Q 023377 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY 130 (283)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~ 130 (283)
.+++.+..+.+|.+++++.+.+++.|+|.+. ....+.+++++..-.++ .+.+..+
T Consensus 50 ~~g~~~~yi~~e~~~~~~~~~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~-----------------------~~~~~~l 106 (230)
T PRK08533 50 QNGYSVSYVSTQLTTTEFIKQMMSLGYDINKKLISGKLLYIPVYPLLSGN-----------------------SEKRKFL 106 (230)
T ss_pred hCCCcEEEEeCCCCHHHHHHHHHHhCCchHHHhhcCcEEEEEecccccCh-----------------------HHHHHHH
Confidence 4678889999999999999999988887653 23456777766321111 1112222
Q ss_pred HHHHHhccCccCCCCCcEEEEEechhHHHHhcCh----HHHHHHHHhhhcCCceeEEEeeecccccchhhHhHHhhhhee
Q 023377 131 SLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI----SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSM 206 (283)
Q Consensus 131 ~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~----~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~~v~ALe~LSst 206 (283)
..+.+..+ . .++ -.++||+++.++....- ..+.++|..|++... .++-..|.+.=......-++|++-+
T Consensus 107 ~~il~~~~-~---~~~-~~lVIDe~t~~l~~~~d~~~~~~l~~~l~~l~~~g~--tvi~t~~~~~~~~~~~~~~~~~~Dg 179 (230)
T PRK08533 107 KKLMNTRR-F---YEK-DVIIIDSLSSLISNDASEVAVNDLMAFFKRISSLNK--VIILTANPKELDESVLTILRTAATM 179 (230)
T ss_pred HHHHHHHH-h---cCC-CEEEEECccHHhcCCcchHHHHHHHHHHHHHHhCCC--EEEEEecccccccccceeEEEeeeE
Confidence 33333322 1 123 37999999999854322 345666666655322 2222222111112222357899999
Q ss_pred EEEeec
Q 023377 207 VASVEP 212 (283)
Q Consensus 207 vvtv~P 212 (283)
+|.+.=
T Consensus 180 vI~L~~ 185 (230)
T PRK08533 180 LIRLEV 185 (230)
T ss_pred EEEEEE
Confidence 888863
No 20
>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=93.50 E-value=1.2 Score=38.63 Aligned_cols=125 Identities=14% Similarity=0.143 Sum_probs=65.7
Q ss_pred cccceeEEEEeec-ChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHH
Q 023377 53 SQSRGLVVVAYSR-SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYS 131 (283)
Q Consensus 53 ~q~~~Vhvl~fe~-Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~ 131 (283)
.+++.+..+.+|. +|+.+.+.++.. ++ ....++++++++ |+. ++...+.
T Consensus 38 ~~g~~v~yi~~e~~~~~rl~~~~~~~-~~--~~~~~i~~~~~~-~~~--------------------------~~~~~~~ 87 (209)
T TIGR02237 38 RQGKKVVYIDTEGLSPERFKQIAEDR-PE--RALSNFIVFEVF-DFD--------------------------EQGVAIQ 87 (209)
T ss_pred hCCCeEEEEECCCCCHHHHHHHHHhC-hH--HHhcCEEEEECC-CHH--------------------------HHHHHHH
Confidence 3578999999996 899888866643 12 113567877763 111 1111223
Q ss_pred HHHHhccCccCCCCCcEEEEEechhHHHHhcCh-------HHHHHHHHhhhc---CCceeEEE-eeecccccc----hhh
Q 023377 132 LIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-------SSVAGILSNLRS---HDQVSSIF-WLLHSDLHE----IKF 196 (283)
Q Consensus 132 si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~-------~~vc~lL~~Lr~---~~~vssVl-~LLHsDLHe----~~~ 196 (283)
.+.+... . .++ =.|+||||+.+.+.... ..+.+.+..|++ ...+.-++ .-+-.+.++ |--
T Consensus 88 ~l~~~~~---~-~~~-~lvVIDSis~l~~~~~~~~~~~~~~~l~~~~~~L~~~~~~~~v~vl~t~~~~~~~~~~~~~~~g 162 (209)
T TIGR02237 88 KTSKFID---R-DSA-SLVVVDSFTALYRLELSDDRISRNRELARQLTLLLSLARKKNLAVVITNQVYTDVNNGTLRPLG 162 (209)
T ss_pred HHHHHHh---h-cCc-cEEEEeCcHHHhHHHhCCccHHHHHHHHHHHHHHHHHHHHcCCEEEEEcccEEecCCCCCcCCC
Confidence 3333222 1 122 37999999998763311 123333333432 22222222 222233332 221
Q ss_pred HhHHhhhheeEEEeec
Q 023377 197 TSVLEYLSSMVASVEP 212 (283)
Q Consensus 197 v~ALe~LSstvvtv~P 212 (283)
-..++|++.+++.++-
T Consensus 163 g~~~~~~~d~vi~l~~ 178 (209)
T TIGR02237 163 GHLLEHWSKVILRLEK 178 (209)
T ss_pred cchhheeeeEEEEEEe
Confidence 2368999999998864
No 21
>PRK05973 replicative DNA helicase; Provisional
Probab=93.22 E-value=1.9 Score=40.00 Aligned_cols=62 Identities=13% Similarity=-0.025 Sum_probs=40.7
Q ss_pred cCCCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccC
Q 023377 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS 83 (283)
Q Consensus 15 ~ge~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s 83 (283)
.|=..+.+++---=...+=+.+..+++. .+..+++.|.++.+|-+|++..+=++..|+|.+.
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 4555554444332233333444444432 3445689999999999999999999999988665
No 22
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=91.86 E-value=2.8 Score=39.51 Aligned_cols=39 Identities=21% Similarity=0.269 Sum_probs=30.6
Q ss_pred ceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 023377 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (283)
Q Consensus 56 ~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (283)
..+..+.+|. +|+.+.+.+++.|+|.+..-+++++++++
T Consensus 137 ~~~~yi~te~~f~~~rl~~~~~~~g~~~~~~l~~i~~~~~~ 177 (317)
T PRK04301 137 GKAVYIDTEGTFRPERIEQMAEALGLDPDEVLDNIHVARAY 177 (317)
T ss_pred ceEEEEeCCCCcCHHHHHHHHHHcCCChHhhhccEEEEeCC
Confidence 5788999998 69999999988888876544567777654
No 23
>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=91.75 E-value=1.9 Score=40.16 Aligned_cols=38 Identities=18% Similarity=0.279 Sum_probs=29.2
Q ss_pred eeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 023377 57 GLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (283)
Q Consensus 57 ~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (283)
.+..+.+|- +|+.+.+.++..|++.+...+++.+..++
T Consensus 131 ~~~yi~te~~f~~~rl~~~~~~~gl~~~~~~~~i~i~~~~ 170 (310)
T TIGR02236 131 KAVYIDTENTFRPERIMQMAEARGLDPDEVLKNIYVARAY 170 (310)
T ss_pred eEEEEECCCCCCHHHHHHHHHHcCCCHHHHhhceEEEecC
Confidence 788888888 79999999998888865545567776653
No 24
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=91.49 E-value=9.1 Score=33.62 Aligned_cols=124 Identities=17% Similarity=0.148 Sum_probs=65.3
Q ss_pred cccceeEEEEee-cChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHH
Q 023377 53 SQSRGLVVVAYS-RSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYS 131 (283)
Q Consensus 53 ~q~~~Vhvl~fe-~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~ 131 (283)
.+++.+..+.+| .+++-+.+..+. +.+...+++++.+. ..+. ++...+.
T Consensus 49 ~~~~~v~yi~~e~~~~~r~~~~~~~---~~~~~~~~~~~~~~----~~~~-----------------------~~~~~i~ 98 (225)
T PRK09361 49 KNGKKVIYIDTEGLSPERFKQIAGE---DFEELLSNIIIFEP----SSFE-----------------------EQSEAIR 98 (225)
T ss_pred HCCCeEEEEECCCCCHHHHHHHHhh---ChHhHhhCeEEEeC----CCHH-----------------------HHHHHHH
Confidence 357899999999 566666664442 21221234555552 2111 2222222
Q ss_pred HHHHhccCccCCCCCcEEEEEechhHHHHhc-----C----hHHHHHHHHhhhc----CCceeEEEeeecccccc----h
Q 023377 132 LIIEQGKGLIGQGKDRFSIAIDSVSEMVRHA-----S----ISSVAGILSNLRS----HDQVSSIFWLLHSDLHE----I 194 (283)
Q Consensus 132 si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~-----s----~~~vc~lL~~Lr~----~~~vssVl~LLHsDLHe----~ 194 (283)
.+.+..+ .++ =.|+|||++.+.+.. . ...+.+.++.|++ +....=+..-++.+.+. +
T Consensus 99 ~~~~~~~-----~~~-~lvVIDsi~al~~~~~~~~~~~~~~~~~l~~~l~~L~~~a~~~~v~vi~tnq~~~~~~~~~~~~ 172 (225)
T PRK09361 99 KAEKLAK-----ENV-GLIVLDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHDLAVVITNQVYSDIDSDGLRP 172 (225)
T ss_pred HHHHHHH-----hcc-cEEEEeCcHHHhHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhCCEEEEEccceecCCCCcccC
Confidence 3332222 122 389999999987642 1 1234554444433 33333333444555542 2
Q ss_pred hhHhHHhhhheeEEEeec
Q 023377 195 KFTSVLEYLSSMVASVEP 212 (283)
Q Consensus 195 ~~v~ALe~LSstvvtv~P 212 (283)
---..++|++++++.+..
T Consensus 173 ~gg~~~~~~~d~ii~l~~ 190 (225)
T PRK09361 173 LGGHTLEHWSKTILRLEK 190 (225)
T ss_pred CCcchhhhhccEEEEEEE
Confidence 112378999999999876
No 25
>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=91.45 E-value=0.67 Score=40.83 Aligned_cols=67 Identities=18% Similarity=0.119 Sum_probs=38.8
Q ss_pred EEEEEechhHHHHhc----ChHHHHHHHHhhhcC-CceeEEEeeecc------c-------ccchhhHhHHhhhheeEEE
Q 023377 148 FSIAIDSVSEMVRHA----SISSVAGILSNLRSH-DQVSSIFWLLHS------D-------LHEIKFTSVLEYLSSMVAS 209 (283)
Q Consensus 148 ~tVaIDSLS~LL~h~----s~~~vc~lL~~Lr~~-~~vssVl~LLHs------D-------LHe~~~v~ALe~LSstvvt 209 (283)
-.|+||+++.+-... .-..+...+..|+.- .+.-..++++|. + ++.-+-.+++++.|.+++.
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 489999999664332 113344555555531 223333444441 1 2333445788999999999
Q ss_pred eecCC
Q 023377 210 VEPFN 214 (283)
Q Consensus 210 v~P~~ 214 (283)
+.+..
T Consensus 205 l~~~~ 209 (242)
T cd00984 205 LYRDE 209 (242)
T ss_pred Eeccc
Confidence 98754
No 26
>PRK11823 DNA repair protein RadA; Provisional
Probab=89.70 E-value=19 Score=36.06 Aligned_cols=115 Identities=21% Similarity=0.195 Sum_probs=62.7
Q ss_pred cccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHH
Q 023377 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (283)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~s 132 (283)
.+++.|..+.+|-+++....-.++.|++ .+++.+.+ + . ++..+...
T Consensus 106 ~~g~~vlYvs~Ees~~qi~~ra~rlg~~----~~~l~~~~---e--------~-------------------~l~~i~~~ 151 (446)
T PRK11823 106 AAGGKVLYVSGEESASQIKLRAERLGLP----SDNLYLLA---E--------T-------------------NLEAILAT 151 (446)
T ss_pred hcCCeEEEEEccccHHHHHHHHHHcCCC----hhcEEEeC---C--------C-------------------CHHHHHHH
Confidence 3578889999999999887767777776 22333221 0 0 12222222
Q ss_pred HHHhccCccCCCCCcEEEEEechhHHHHh------cChHHHHHHHHhhhc---CCceeEE-EeeecccccchhhHhHHhh
Q 023377 133 IIEQGKGLIGQGKDRFSIAIDSVSEMVRH------ASISSVAGILSNLRS---HDQVSSI-FWLLHSDLHEIKFTSVLEY 202 (283)
Q Consensus 133 i~e~~r~~~~~~k~~~tVaIDSLS~LL~h------~s~~~vc~lL~~Lr~---~~~vssV-l~LLHsDLHe~~~v~ALe~ 202 (283)
+ + +.++ -.|+|||++.+... .+..++-..+..|.+ ...+.-+ ++-+..|-+-.+. ..++|
T Consensus 152 i----~----~~~~-~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~~ak~~~itvilv~hvtk~~~~ag~-~~leh 221 (446)
T PRK11823 152 I----E----EEKP-DLVVIDSIQTMYSPELESAPGSVSQVRECAAELMRLAKQRGIAVFLVGHVTKEGAIAGP-RVLEH 221 (446)
T ss_pred H----H----hhCC-CEEEEechhhhccccccCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEeeccCCCCcCCc-chhhh
Confidence 2 2 1233 47999999998752 123344333333333 1223222 2223233222222 56999
Q ss_pred hheeEEEee
Q 023377 203 LSSMVASVE 211 (283)
Q Consensus 203 LSstvvtv~ 211 (283)
++.+++.++
T Consensus 222 lvD~Vi~le 230 (446)
T PRK11823 222 MVDTVLYFE 230 (446)
T ss_pred hCeEEEEEE
Confidence 999999886
No 27
>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=89.56 E-value=22 Score=34.92 Aligned_cols=115 Identities=20% Similarity=0.184 Sum_probs=62.2
Q ss_pred ccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHHH
Q 023377 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (283)
Q Consensus 54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~si 133 (283)
+++.|..+.+|-+++....-.++-|++ ..++.+.+. .++..++..+
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 457788889999998877766666665 233433210 0122222222
Q ss_pred HHhccCccCCCCCcEEEEEechhHHHHhc------ChHHHHHHHHhhhc---CCceeEE-EeeecccccchhhHhHHhhh
Q 023377 134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA------SISSVAGILSNLRS---HDQVSSI-FWLLHSDLHEIKFTSVLEYL 203 (283)
Q Consensus 134 ~e~~r~~~~~~k~~~tVaIDSLS~LL~h~------s~~~vc~lL~~Lr~---~~~vssV-l~LLHsDLHe~~~v~ALe~L 203 (283)
+ +.++ -.|+|||++.+.... +..++-..+..|.+ ...+.-+ ++-+..|-+-.+ .+.|+|+
T Consensus 155 ----~----~~~~-~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~lak~~~itvilvghvtk~g~~aG-~~~leh~ 224 (372)
T cd01121 155 ----E----ELKP-DLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMRFAKERNIPIFIVGHVTKEGSIAG-PKVLEHM 224 (372)
T ss_pred ----H----hcCC-cEEEEcchHHhhccccccCCCCHHHHHHHHHHHHHHHHHcCCeEEEEeeccCCCcccC-cccchhh
Confidence 1 1233 479999999996532 13444333333333 2223222 222333332222 2589999
Q ss_pred heeEEEeec
Q 023377 204 SSMVASVEP 212 (283)
Q Consensus 204 Sstvvtv~P 212 (283)
+.+++.++-
T Consensus 225 vD~Vi~le~ 233 (372)
T cd01121 225 VDTVLYFEG 233 (372)
T ss_pred ceEEEEEEc
Confidence 999998764
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=89.49 E-value=7.1 Score=33.98 Aligned_cols=74 Identities=20% Similarity=0.213 Sum_probs=45.1
Q ss_pred ceeEEEEeecC--hHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHHH
Q 023377 56 RGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (283)
Q Consensus 56 ~~Vhvl~fe~S--pe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~si 133 (283)
..|..+..|.+ ++.+.+.....+.+.....+++++.++++ ..++...+..+
T Consensus 54 ~~v~yi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~~---------------------------~~~~~~~l~~~ 106 (226)
T cd01393 54 GKVVYIDTEGAFRPERLVQLAVRFGLDPEEVLDNIYVARPYN---------------------------GEQQLEIVEEL 106 (226)
T ss_pred ceEEEEecCCCCCHHHHHHHHHHhccchhhhhccEEEEeCCC---------------------------HHHHHHHHHHH
Confidence 77888888876 66777777777666554455677776531 12233333333
Q ss_pred HHhccCccCCCCCcEEEEEechhHHHHh
Q 023377 134 IEQGKGLIGQGKDRFSIAIDSVSEMVRH 161 (283)
Q Consensus 134 ~e~~r~~~~~~k~~~tVaIDSLS~LL~h 161 (283)
.+..+ +.+. -.|+||||+.+.+.
T Consensus 107 ~~~~~----~~~~-~lvVIDsis~l~~~ 129 (226)
T cd01393 107 ERIMS----SGRV-DLVVVDSVAALFRK 129 (226)
T ss_pred HHHhh----cCCe-eEEEEcCcchhhhh
Confidence 33211 1233 48999999998764
No 29
>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=89.06 E-value=3.5 Score=36.15 Aligned_cols=75 Identities=19% Similarity=0.186 Sum_probs=48.9
Q ss_pred cceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHH
Q 023377 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (283)
Q Consensus 55 ~~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~s 132 (283)
.+++..+..|. +++.+.+.+++.|.+.....+++++.++|+ ..++..++..
T Consensus 53 ~~~viyi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~~---------------------------~~~l~~~l~~ 105 (235)
T cd01123 53 EGKAVYIDTEGTFRPERLVQIAERFGLDPEEVLDNIYVARAYN---------------------------SDHQLQLLEE 105 (235)
T ss_pred CccEEEEeCCCCcCHHHHHHHHHHhccChHhHhcCEEEEecCC---------------------------HHHHHHHHHH
Confidence 46788888888 578888888888887666566777777542 1123333344
Q ss_pred HHHhccCccCCCCCcEEEEEechhHHHH
Q 023377 133 IIEQGKGLIGQGKDRFSIAIDSVSEMVR 160 (283)
Q Consensus 133 i~e~~r~~~~~~k~~~tVaIDSLS~LL~ 160 (283)
+.+..+ ..+++ =.|+|||++.+.+
T Consensus 106 l~~~l~---~~~~~-~liVIDSis~~~~ 129 (235)
T cd01123 106 LEAILI---ESSRI-KLVIVDSVTALFR 129 (235)
T ss_pred HHHHHh---hcCCe-eEEEEeCcHHHHH
Confidence 433333 11133 5899999999875
No 30
>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=86.36 E-value=16 Score=32.62 Aligned_cols=142 Identities=13% Similarity=0.077 Sum_probs=74.9
Q ss_pred cccceeEEEEeecChHHHHHHHhhcCcCc--cCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHH
Q 023377 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDI--ASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY 130 (283)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~--~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~ 130 (283)
.+...|.+++.|-++++..+=++..+..- +....++.+.+....|+.+... +.......+
T Consensus 39 ~~~~~Vlyi~~Ed~~~~i~~Rl~~i~~~~~~~~~~~rl~~~~g~~~~l~~~~~------------------~~~~~~~~~ 100 (239)
T cd01125 39 TEPGRVVYLSAEDPREEIHRRLEAILQHLEPDDAGDRLFIDSGRIQPISIARE------------------GRIIVVPEF 100 (239)
T ss_pred CCCceEEEEECCCCHHHHHHHHHHHHhhcCCcCcccceEEeccCCCceecccC------------------CcccccHHH
Confidence 35678999999999998776555543321 1113455544322222222110 000112233
Q ss_pred HHHHHhccCccCCCCCcEEEEEechhHHHH--hcChHHHHHHHHhhhcC-CceeEEEeeecccccch----------hhH
Q 023377 131 SLIIEQGKGLIGQGKDRFSIAIDSVSEMVR--HASISSVAGILSNLRSH-DQVSSIFWLLHSDLHEI----------KFT 197 (283)
Q Consensus 131 ~si~e~~r~~~~~~k~~~tVaIDSLS~LL~--h~s~~~vc~lL~~Lr~~-~~vssVl~LLHsDLHe~----------~~v 197 (283)
..+++..+ . .++ -.|+||+++.+-. .......-+++..|++. .+-...+.++|.+-... +=.
T Consensus 101 ~~l~~~~~-~---~~~-~lvviDpl~~~~~~~~~d~~~~~~~~~~L~~~a~~~g~avl~v~H~~K~~~~~~~~~~~~rGs 175 (239)
T cd01125 101 ERIIEQLL-I---RRI-DLVVIDPLVSFHGVSENDNGAMDAVIKALRRIAAQTGAAILLVHHVRKGSAKDGDTQEAARGA 175 (239)
T ss_pred HHHHHHHH-h---cCC-CEEEECChHHhCCCCcCCHHHHHHHHHHHHHHHHHhCCEEEEEeccCcccccCcccccccCcH
Confidence 44454443 1 133 5899999988711 12233444445554431 22334555667666432 225
Q ss_pred hHHhhhheeEEEeecCCccc
Q 023377 198 SVLEYLSSMVASVEPFNQAA 217 (283)
Q Consensus 198 ~ALe~LSstvvtv~P~~~~~ 217 (283)
.||..-+.++..+.|.....
T Consensus 176 sal~~~~r~~~~l~~~~~~~ 195 (239)
T cd01125 176 SALVDGARWVRALTRMTSEE 195 (239)
T ss_pred HHHhcccceEEEEeeCCHHH
Confidence 67777788888888877655
No 31
>PTZ00035 Rad51 protein; Provisional
Probab=86.22 E-value=16 Score=35.24 Aligned_cols=40 Identities=20% Similarity=0.272 Sum_probs=28.8
Q ss_pred cceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 023377 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (283)
Q Consensus 55 ~~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (283)
+..+..+..|. +|+...+..++.|++.+..-.++.+.++|
T Consensus 152 ~g~vvyIdtE~~f~~eri~~ia~~~g~~~~~~l~nI~~~~~~ 193 (337)
T PTZ00035 152 EGKVLYIDTEGTFRPERIVQIAERFGLDPEDVLDNIAYARAY 193 (337)
T ss_pred CceEEEEEccCCCCHHHHHHHHHHhCCChHhHhhceEEEccC
Confidence 45677788887 48888888888888876655667666544
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=85.99 E-value=16 Score=35.04 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=32.1
Q ss_pred ccceeEEEEeecC--hHHHHHHHhhcCcCccCCCCeEEEEecc
Q 023377 54 QSRGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCY 94 (283)
Q Consensus 54 q~~~Vhvl~fe~S--pe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (283)
.+..+..+..|-+ |+...+.+++.|+|++..-+++.+.++|
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 9999999999999877655667766554
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=83.32 E-value=24 Score=30.69 Aligned_cols=64 Identities=23% Similarity=0.127 Sum_probs=35.3
Q ss_pred EEEEEechhHHHHhcCh---------HHHHHHHHhhhc----CCceeEEEeeeccccc----chhhHhHHhhhheeEEEe
Q 023377 148 FSIAIDSVSEMVRHASI---------SSVAGILSNLRS----HDQVSSIFWLLHSDLH----EIKFTSVLEYLSSMVASV 210 (283)
Q Consensus 148 ~tVaIDSLS~LL~h~s~---------~~vc~lL~~Lr~----~~~vssVl~LLHsDLH----e~~~v~ALe~LSstvvtv 210 (283)
-.|+|||++.+.+.... ..+.+.++.|+. +....=+.+-+..+.. .|.--..++|++.+++.+
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 3333223333333332 122122689999999998
Q ss_pred e
Q 023377 211 E 211 (283)
Q Consensus 211 ~ 211 (283)
.
T Consensus 185 ~ 185 (218)
T cd01394 185 E 185 (218)
T ss_pred E
Confidence 6
No 34
>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=83.16 E-value=34 Score=32.73 Aligned_cols=39 Identities=13% Similarity=0.217 Sum_probs=27.6
Q ss_pred ceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 023377 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (283)
Q Consensus 56 ~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (283)
..+..+..|. +|+-+.+..++.|++++..-+++++.++|
T Consensus 131 ~~vvyIdtE~~f~~~Rl~~ia~~~~~~~~~~l~~i~~~~~~ 171 (316)
T TIGR02239 131 GKALYIDTEGTFRPERLLAIAERYGLNPEDVLDNVAYARAY 171 (316)
T ss_pred ceEEEEECCCCCCHHHHHHHHHHcCCChHHhhccEEEEecC
Confidence 4677788888 68888888888888866545566666543
No 35
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=81.86 E-value=13 Score=36.45 Aligned_cols=39 Identities=21% Similarity=0.256 Sum_probs=31.6
Q ss_pred ceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 023377 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (283)
Q Consensus 56 ~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (283)
..+..+.+|. +|+-+.+..++.|+|++..-++|++.++|
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 79999999999999877655677766654
No 36
>PRK09354 recA recombinase A; Provisional
Probab=79.99 E-value=32 Score=33.89 Aligned_cols=41 Identities=10% Similarity=0.030 Sum_probs=28.1
Q ss_pred chhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCc
Q 023377 32 FGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDI 81 (283)
Q Consensus 32 ~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~ 81 (283)
+=+.+..|++. .+..+++.+..+.+|-+++. +.+++.|+|.
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 44555666643 23356888999999998885 5567778883
No 37
>PF03192 DUF257: Pyrococcus protein of unknown function, DUF257; InterPro: IPR005489 This family of proteins is of unknown function.; PDB: 2EKD_C.
Probab=78.38 E-value=51 Score=30.14 Aligned_cols=153 Identities=17% Similarity=0.257 Sum_probs=90.0
Q ss_pred ceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEe--------
Q 023377 21 ALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILD-------- 92 (283)
Q Consensus 21 ~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D-------- 92 (283)
+++|+-+-.++ +.++ ++..++.++.++-.|.|..+==+-..|..-|+..|+|.+. -+++-++-
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 56777665332 3332 3445667788888999998888888999999999999776 12333332
Q ss_pred -------ccCCCCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHH--HhcC
Q 023377 93 -------CYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMV--RHAS 163 (283)
Q Consensus 93 -------~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL--~h~s 163 (283)
..+||--|. +.+..+++... . +.++...+=-+.-++ ...+
T Consensus 84 nVv~ri~~~~d~~~~~--------------------------k~Y~~~~~~~~---~--~~~~i~ivlGiekl~~~~~~~ 132 (210)
T PF03192_consen 84 NVVGRIPITSDPSVYL--------------------------KEYEEILEKVL---E--KEKVINIVLGIEKLFYFFENS 132 (210)
T ss_dssp EEEEEE-----BBTTB--------------------------HHHHHHHTT--------S-SEEEEEE-HHHHH-HH-S-
T ss_pred eEEEEEecccChHHHH--------------------------HHHHHHHHHHh---c--cCCeEEEEecHHHHHHHHhcc
Confidence 222222222 22333333222 1 212555555677777 4468
Q ss_pred hHHHHHHHHhhhcC--CceeEEEeeecccccch---hhHhHHhhhheeEEEeecC
Q 023377 164 ISSVAGILSNLRSH--DQVSSIFWLLHSDLHEI---KFTSVLEYLSSMVASVEPF 213 (283)
Q Consensus 164 ~~~vc~lL~~Lr~~--~~vssVl~LLHsDLHe~---~~v~ALe~LSstvvtv~P~ 213 (283)
...+..++..+.+. ..=..-|..+..|+-+. .++..||-+||+|+.+...
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 38
>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=77.84 E-value=5.3 Score=34.08 Aligned_cols=51 Identities=25% Similarity=0.301 Sum_probs=40.4
Q ss_pred chhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC
Q 023377 122 DVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH 177 (283)
Q Consensus 122 ~v~~L~sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~ 177 (283)
++.+|..+...+.+-.+. . ++ -+|+||++=-|+.++|+.++..+|+.|+-+
T Consensus 56 ~Pt~L~~l~~~i~~fl~~-~--~~--~vViiD~lEYL~l~NgF~~v~KFL~~LkD~ 106 (136)
T PF05763_consen 56 SPTNLHKLLDTIVRFLKE-N--GN--GVVIIDGLEYLILENGFESVLKFLASLKDY 106 (136)
T ss_pred CchhhHHHHHHHHHHHHh-C--CC--cEEEEecHHHHHHHcCHHHHHHHHHHhHHH
Confidence 355677776777776662 1 12 399999999999999999999999999964
No 39
>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=76.36 E-value=23 Score=34.45 Aligned_cols=48 Identities=10% Similarity=0.088 Sum_probs=29.7
Q ss_pred CCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEE
Q 023377 30 SPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHI 90 (283)
Q Consensus 30 ~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i 90 (283)
..+=+.+..|++.+ ...++..+.++.+|-+++. ..+++.|+|. +++++
T Consensus 65 GsGKTtLaL~~~~~-------~~~~g~~v~yId~E~~~~~--~~a~~lGvd~----~~l~v 112 (321)
T TIGR02012 65 SSGKTTLALHAIAE-------AQKAGGTAAFIDAEHALDP--VYARKLGVDI----DNLLV 112 (321)
T ss_pred CCCHHHHHHHHHHH-------HHHcCCcEEEEcccchhHH--HHHHHcCCCH----HHeEE
Confidence 33335555666432 3345788889999988775 3466778873 44664
No 40
>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=75.10 E-value=63 Score=29.03 Aligned_cols=21 Identities=5% Similarity=-0.113 Sum_probs=17.9
Q ss_pred cceeEEEEeecChHHHHHHHh
Q 023377 55 SRGLVVVAYSRSPSFYVDLLK 75 (283)
Q Consensus 55 ~~~Vhvl~fe~Spe~y~~~lk 75 (283)
+..|.++.+|-++++...-+.
T Consensus 59 g~~vl~iS~E~~~~~~~~r~~ 79 (271)
T cd01122 59 GVRVGTISLEEPVVRTARRLL 79 (271)
T ss_pred CceEEEEEcccCHHHHHHHHH
Confidence 889999999999998877553
No 41
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=73.18 E-value=96 Score=30.30 Aligned_cols=38 Identities=13% Similarity=0.226 Sum_probs=29.8
Q ss_pred eeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 023377 57 GLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (283)
Q Consensus 57 ~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y 94 (283)
.+..+.+|. +|+-..+..++.|+|.+..-+++++.++|
T Consensus 159 ~vlyIdtE~~f~~eRl~qia~~~~~~~~~~l~~i~~~~~~ 198 (342)
T PLN03186 159 KAMYIDTEGTFRPQRLIQIAERFGLNGADVLENVAYARAY 198 (342)
T ss_pred eEEEEECCCCccHHHHHHHHHHcCCChhhhccceEEEecC
Confidence 688999999 79999999998888876544567666654
No 42
>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=72.87 E-value=46 Score=32.43 Aligned_cols=120 Identities=17% Similarity=0.166 Sum_probs=63.4
Q ss_pred cccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHH
Q 023377 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (283)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~s 132 (283)
.++..+.++.+|-+++. +.+++.|+| -+++++.+ |.. ..++.....
T Consensus 81 ~~g~~~vyId~E~~~~~--~~a~~lGvd----~~~l~v~~----p~~-----------------------~eq~l~i~~- 126 (325)
T cd00983 81 KLGGTVAFIDAEHALDP--VYAKKLGVD----LDNLLISQ----PDT-----------------------GEQALEIAD- 126 (325)
T ss_pred HcCCCEEEECccccHHH--HHHHHcCCC----HHHheecC----CCC-----------------------HHHHHHHHH-
Confidence 45778889999888774 456667777 33455332 321 112211111
Q ss_pred HHHhccCccCCCCCcEEEEEechhHHHHhcCh-------------HHHHHHHHhhhc----CCceeEEEeeecccc----
Q 023377 133 IIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-------------SSVAGILSNLRS----HDQVSSIFWLLHSDL---- 191 (283)
Q Consensus 133 i~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~-------------~~vc~lL~~Lr~----~~~vssVl~LLHsDL---- 191 (283)
++.+ +++. -.|+|||++.+..+... -.+.+.|+.|.. +....=+..-++.+.
T Consensus 127 --~li~----s~~~-~lIVIDSvaal~~~~E~~~~~~~~~~~~qaR~l~~~Lr~L~~~~~k~~~~vI~tNQvr~~ig~~~ 199 (325)
T cd00983 127 --SLVR----SGAV-DLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSINKSNTTVIFINQLREKIGVMF 199 (325)
T ss_pred --HHHh----ccCC-CEEEEcchHhhcccccccccccccchHHHHHHHHHHHHHHHHHHHhCCCEEEEEEcccccccccc
Confidence 1222 1233 58999999999865321 113455555543 322222222233332
Q ss_pred ---cchhhHhHHhhhheeEEEeecC
Q 023377 192 ---HEIKFTSVLEYLSSMVASVEPF 213 (283)
Q Consensus 192 ---He~~~v~ALe~LSstvvtv~P~ 213 (283)
+.+-==.+|+|.|++.+.+.-.
T Consensus 200 g~~e~~~GG~~L~~~ss~rl~lrk~ 224 (325)
T cd00983 200 GNPETTTGGNALKFYSSVRLDIRRI 224 (325)
T ss_pred CCCccCCCchHHhhhcceEEEEEee
Confidence 1111124799999999998654
No 43
>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=68.79 E-value=21 Score=32.96 Aligned_cols=76 Identities=21% Similarity=0.262 Sum_probs=46.9
Q ss_pred cceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHH
Q 023377 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (283)
Q Consensus 55 ~~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~s 132 (283)
+..|+.+..|. +++-+.+.+++++++.+..-++|++..+|+ ..++..++..
T Consensus 72 ~~~vvyidTe~~f~~~Rl~~i~~~~~~~~~~~l~~I~v~~~~~---------------------------~~~l~~~L~~ 124 (256)
T PF08423_consen 72 GGKVVYIDTEGTFSPERLQQIAERFGLDPEEILDNIFVIRVFD---------------------------LEELLELLEQ 124 (256)
T ss_dssp SSEEEEEESSSSS-HHHHHHHHHHTTS-HHHHHHTEEEEE-SS---------------------------HHHHHHHHHH
T ss_pred CCceEEEeCCCCCCHHHHHHHhhccccccchhhhceeeeecCC---------------------------HHHHHHHHHH
Confidence 45688888887 788899999998887665556777777653 1122223232
Q ss_pred HHHhccCccCCCCCcEEEEEechhHHHHhc
Q 023377 133 IIEQGKGLIGQGKDRFSIAIDSVSEMVRHA 162 (283)
Q Consensus 133 i~e~~r~~~~~~k~~~tVaIDSLS~LL~h~ 162 (283)
+.+... . .+. =.|+|||++.+.|..
T Consensus 125 l~~~l~---~-~~i-kLIVIDSIaalfr~e 149 (256)
T PF08423_consen 125 LPKLLS---E-SKI-KLIVIDSIAALFRSE 149 (256)
T ss_dssp HHHHHH---H-SCE-EEEEEETSSHHHHHH
T ss_pred HHhhcc---c-cce-EEEEecchHHHHHHH
Confidence 222222 1 233 489999999999853
No 44
>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=54.59 E-value=1.7e+02 Score=29.66 Aligned_cols=114 Identities=18% Similarity=0.115 Sum_probs=60.3
Q ss_pred ccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHHH
Q 023377 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (283)
Q Consensus 54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~si 133 (283)
+++.|..+.+|-+++....-.++.|++ .+++.+++.. ++..+
T Consensus 121 ~g~kvlYvs~EEs~~qi~~ra~rlg~~----~~~l~~~~e~------------------------------~~~~I---- 162 (454)
T TIGR00416 121 NQMKVLYVSGEESLQQIKMRAIRLGLP----EPNLYVLSET------------------------------NWEQI---- 162 (454)
T ss_pred cCCcEEEEECcCCHHHHHHHHHHcCCC----hHHeEEcCCC------------------------------CHHHH----
Confidence 456788889998988877655666665 2345443310 11111
Q ss_pred HHhccCccCCCCCcEEEEEechhHHHHhc------ChHHHHHH---HHhhhcCCceeEEEeeecccccc--hhhHhHHhh
Q 023377 134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA------SISSVAGI---LSNLRSHDQVSSIFWLLHSDLHE--IKFTSVLEY 202 (283)
Q Consensus 134 ~e~~r~~~~~~k~~~tVaIDSLS~LL~h~------s~~~vc~l---L~~Lr~~~~vssVl~LLHsDLHe--~~~v~ALe~ 202 (283)
.+..+ +.++ -.|+|||++.+.... +..++-.. |.++-+...+..++- -|-.-.+ .++ ..++|
T Consensus 163 ~~~i~----~~~~-~~vVIDSIq~l~~~~~~~~~g~~~q~r~~~~~L~~~ak~~giTvllt-~hvtkeg~~aG~-~~le~ 235 (454)
T TIGR00416 163 CANIE----EENP-QACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIV-GHVTKEGSIAGP-KVLEH 235 (454)
T ss_pred HHHHH----hcCC-cEEEEecchhhcccccccCCCCHHHHHHHHHHHHHHHHHhCCEEEEE-eccccCCccCCc-ccEee
Confidence 11122 1233 369999999986431 13334333 333322233333322 2422211 122 46899
Q ss_pred hheeEEEeec
Q 023377 203 LSSMVASVEP 212 (283)
Q Consensus 203 LSstvvtv~P 212 (283)
++.+++.++-
T Consensus 236 lvD~VI~Le~ 245 (454)
T TIGR00416 236 MVDTVLYFEG 245 (454)
T ss_pred eceEEEEEec
Confidence 9999999874
No 45
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=54.31 E-value=13 Score=31.40 Aligned_cols=26 Identities=12% Similarity=0.061 Sum_probs=17.0
Q ss_pred cccceeEEEEeecChHHHHHHHhhcC
Q 023377 53 SQSRGLVVVAYSRSPSFYVDLLKRRG 78 (283)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G 78 (283)
.+...|..+.+|.++++...-+++.+
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 37789999999999988888777653
No 46
>PF14417 MEDS: MEDS: MEthanogen/methylotroph, DcmR Sensory domain
Probab=53.73 E-value=46 Score=29.05 Aligned_cols=137 Identities=15% Similarity=0.174 Sum_probs=80.6
Q ss_pred HHHHHHHHHHHHhhccccceeEEEEe-ecChHHHHHHHhhcCcCccC--CCCeEEEEeccC--CCCCCcccccCCccccc
Q 023377 38 NYVLTQLSNYILAGKSQSRGLVVVAY-SRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYT--DPLGWKNWLIDKDISQE 112 (283)
Q Consensus 38 ~h~~~~l~s~i~a~~~q~~~Vhvl~f-e~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~yS--DPLGW~~~~~~~~~~~~ 112 (283)
..++..+.++|++|-.+++.+.++.= ....+...+.|++.|.|.+. -...+.++|... -+-|+-+
T Consensus 30 ~e~~~~~~~Fi~~GL~~ge~~l~v~~~~~~~~~l~~~L~~~~~d~~~~~~~gqL~~~~~~~~Y~~~g~f~---------- 99 (191)
T PF14417_consen 30 EELLEVLVPFIREGLARGERCLYVAPDPRRVEELRDELRKAGPDVEQYLDSGQLELLDAEEWYLPDGRFD---------- 99 (191)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEECCCCCHHHHHHHHHhcCCchhhcccCCCEEEecchhhhccCCCcC----------
Confidence 56677789999999999999999998 78899999999999887655 234687887421 1111111
Q ss_pred cccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHH---HHhhhcCCceeEEEeeecc
Q 023377 113 ASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGI---LSNLRSHDQVSSIFWLLHS 189 (283)
Q Consensus 113 ~s~~~~~~~~v~~L~sl~~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~l---L~~Lr~~~~vssVl~LLHs 189 (283)
...+-+.+...++... .+|-+.+-++-| .+|.++. +...+.+. +..+-. ..-...++.-..
T Consensus 100 ----------~~~~i~~~~~~~~~a~---~~G~~~lRv~ge-~~w~~~~-~~~~l~~yE~~ln~~~~-~~~~~~lC~Yd~ 163 (191)
T PF14417_consen 100 ----------PARMIAFWRAALEQAL---AEGYRGLRVIGE-MTWALRS-GWEELLRYEALLNRLFA-EHPFTALCAYDR 163 (191)
T ss_pred ----------HHHHHHHHHHHHHHHH---hCCCCcEEEEEe-chhhccc-cHHHHHHHHHHHHHHhc-CCCEEEEeccch
Confidence 1111111122222222 123334788888 7888887 55544322 222222 234445566666
Q ss_pred cccchhhHhHH
Q 023377 190 DLHEIKFTSVL 200 (283)
Q Consensus 190 DLHe~~~v~AL 200 (283)
+.-.+.++..+
T Consensus 164 ~~~~~~~~~~~ 174 (191)
T PF14417_consen 164 RRFSPEVLADA 174 (191)
T ss_pred HhCCHHHHHHH
Confidence 55555555444
No 47
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=50.76 E-value=3.9 Score=27.39 Aligned_cols=14 Identities=57% Similarity=1.217 Sum_probs=11.2
Q ss_pred hhhccchhhhhhcc
Q 023377 260 YFCGECADLLYRKS 273 (283)
Q Consensus 260 ~~~~~~~~~~~~~~ 273 (283)
-||.+|+.+||-+.
T Consensus 2 ~FCp~C~nlL~p~~ 15 (35)
T PF02150_consen 2 RFCPECGNLLYPKE 15 (35)
T ss_dssp -BETTTTSBEEEEE
T ss_pred eeCCCCCccceEcC
Confidence 59999999998653
No 48
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=50.44 E-value=51 Score=32.24 Aligned_cols=67 Identities=12% Similarity=0.155 Sum_probs=38.6
Q ss_pred EEEEEechhHHHH------hcChHHHHHHHHhhhcC-CceeEEEeeecccc----------cchhhHhHHhhhheeEEEe
Q 023377 148 FSIAIDSVSEMVR------HASISSVAGILSNLRSH-DQVSSIFWLLHSDL----------HEIKFTSVLEYLSSMVASV 210 (283)
Q Consensus 148 ~tVaIDSLS~LL~------h~s~~~vc~lL~~Lr~~-~~vssVl~LLHsDL----------He~~~v~ALe~LSstvvtv 210 (283)
-.|+||+|..|-- +.....+++.|..|-+. ....=++.-+.-+. ..-+-.+++|+-|.+++-+
T Consensus 307 ~lvvIDyLql~~~~~~~~~~~~~~~i~~~Lk~lAke~~i~Vi~lsQlnr~~~~r~~krp~lsdlr~Sg~Ieq~AD~v~~l 386 (421)
T TIGR03600 307 DLIVVDYIQLMAPTRGRDRNEELGGISRGLKALAKELDVPVVLLAQLNRGSEKRTDKRPIMSDLRDSGAIEQDADVIGLI 386 (421)
T ss_pred CEEEEecccccCCCCCCCHHHHHHHHHHHHHHHHHHhCCcEEEecccCcchhhcCCCCCChHHHhhcCCccccCcEEEEe
Confidence 4899999977642 12233456666666542 22222222222222 2344567899999999999
Q ss_pred ecCC
Q 023377 211 EPFN 214 (283)
Q Consensus 211 ~P~~ 214 (283)
....
T Consensus 387 ~R~~ 390 (421)
T TIGR03600 387 HREG 390 (421)
T ss_pred cccc
Confidence 7543
No 49
>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=48.72 E-value=1.4e+02 Score=28.90 Aligned_cols=91 Identities=18% Similarity=0.146 Sum_probs=51.6
Q ss_pred ccceeEEEEeecChHHHHHHHhhcCcC-ccCCCCeEE-EEeccCCCCCCcccccCCcccccccccccccc------chhh
Q 023377 54 QSRGLVVVAYSRSPSFYVDLLKRRGID-IASSHDWIH-ILDCYTDPLGWKNWLIDKDISQEASSLSSFCQ------DVRN 125 (283)
Q Consensus 54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d-~~s~~~ri~-i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~------~v~~ 125 (283)
+++.++-+++|+|.+...+..++- . .+.++-.+. +.--|+||+.|-.+... .+.+..+.+++ ...+
T Consensus 101 ~~~~~~Y~plDIS~~~L~~a~~~L--~~~~~p~l~v~~l~gdy~~~l~~l~~~~~----~~~~r~~~flGSsiGNf~~~e 174 (319)
T TIGR03439 101 QKKSVDYYALDVSRSELQRTLAEL--PLGNFSHVRCAGLLGTYDDGLAWLKRPEN----RSRPTTILWLGSSIGNFSRPE 174 (319)
T ss_pred cCCCceEEEEECCHHHHHHHHHhh--hhccCCCeEEEEEEecHHHHHhhcccccc----cCCccEEEEeCccccCCCHHH
Confidence 456799999999999998887754 3 222222332 56679999998753110 01111122222 1223
Q ss_pred hhHHHHHHHH-hccCccCCCCCcEEEEEech
Q 023377 126 LDKLYSLIIE-QGKGLIGQGKDRFSIAIDSV 155 (283)
Q Consensus 126 L~sl~~si~e-~~r~~~~~~k~~~tVaIDSL 155 (283)
-..++..+.+ ..+ ++..+.|.+|..
T Consensus 175 a~~fL~~~~~~~l~-----~~d~lLiG~D~~ 200 (319)
T TIGR03439 175 AAAFLAGFLATALS-----PSDSFLIGLDGC 200 (319)
T ss_pred HHHHHHHHHHhhCC-----CCCEEEEecCCC
Confidence 3334444444 333 456699999976
No 50
>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=45.69 E-value=1.5e+02 Score=23.28 Aligned_cols=64 Identities=16% Similarity=0.176 Sum_probs=38.9
Q ss_pred EEEEEechhHHHHhcC------hHHHHHHHHhhhcC--CceeEEEeeecccccc------hhhHhHHhhhheeEEEee
Q 023377 148 FSIAIDSVSEMVRHAS------ISSVAGILSNLRSH--DQVSSIFWLLHSDLHE------IKFTSVLEYLSSMVASVE 211 (283)
Q Consensus 148 ~tVaIDSLS~LL~h~s------~~~vc~lL~~Lr~~--~~vssVl~LLHsDLHe------~~~v~ALe~LSstvvtv~ 211 (283)
-.++||+++.++.... ...+.+.|.+|... ..=..++...|.+-=+ .+...++++++.+++.+.
T Consensus 87 ~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~l~ 164 (165)
T cd01120 87 DLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSGDKGDPRLTRGAQNLEDIADTVIVLS 164 (165)
T ss_pred EEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEEEecCCccccCcccccCccceeeecceEEEEe
Confidence 6899999999887532 23445566655542 1234455566644211 113467899998888763
No 51
>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=40.59 E-value=62 Score=24.89 Aligned_cols=57 Identities=21% Similarity=0.203 Sum_probs=45.0
Q ss_pred CCceeecccCCCCchhh------HHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHh
Q 023377 19 APALTIKDSKASPFGFD------VFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLK 75 (283)
Q Consensus 19 ap~l~i~Dsl~~~~g~~------~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk 75 (283)
.|.+++-|.++.-++.. ....++..|.+.+.....+...+.|++....++.....+.
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 58999999997765444 5677888888888887777778888888888887777665
No 52
>PRK09519 recA DNA recombination protein RecA; Reviewed
Probab=38.27 E-value=1.7e+02 Score=32.23 Aligned_cols=122 Identities=14% Similarity=0.137 Sum_probs=65.2
Q ss_pred hccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHH
Q 023377 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY 130 (283)
Q Consensus 51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~ 130 (283)
+..+++.+..+.+|-+++ .+-+++.|+|.+ ++.+.. |. +.++ .+
T Consensus 84 a~~~G~~v~yId~E~t~~--~~~A~~lGvDl~----~llv~~----~~-----------------------~~E~---~l 127 (790)
T PRK09519 84 AQAAGGVAAFIDAEHALD--PDYAKKLGVDTD----SLLVSQ----PD-----------------------TGEQ---AL 127 (790)
T ss_pred HHHcCCcEEEECCccchh--HHHHHHcCCChh----HeEEec----CC-----------------------CHHH---HH
Confidence 335678888888888777 345667788843 343221 21 0111 11
Q ss_pred HHHHHhccCccCCCCCcEEEEEechhHHHHh------cChH-------HHHHHHHhhhcC-----------CceeEEEee
Q 023377 131 SLIIEQGKGLIGQGKDRFSIAIDSVSEMVRH------ASIS-------SVAGILSNLRSH-----------DQVSSIFWL 186 (283)
Q Consensus 131 ~si~e~~r~~~~~~k~~~tVaIDSLS~LL~h------~s~~-------~vc~lL~~Lr~~-----------~~vssVl~L 186 (283)
..+.+..+ ++++ -.|+|||++.|..+ .+-. .+.+.|+.|.+. .|+...++.
T Consensus 128 ~~i~~lv~----~~~~-~LVVIDSI~aL~~r~E~~g~~g~~~~~~q~rl~~q~L~~L~~~l~~~nvtvi~TNQv~~~~g~ 202 (790)
T PRK09519 128 EIADMLIR----SGAL-DIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALNNSGTTAIFINQLRDKIGV 202 (790)
T ss_pred HHHHHHhh----cCCC-eEEEEcchhhhcchhhccCCCCcccHHHHHHHHHHHHHHHHHHHHhCCCEEEEEecceecCCC
Confidence 12222222 2333 57999999999952 1111 124556655553 233332221
Q ss_pred ecccccchhhHhHHhhhheeEEEeecC
Q 023377 187 LHSDLHEIKFTSVLEYLSSMVASVEPF 213 (283)
Q Consensus 187 LHsDLHe~~~v~ALe~LSstvvtv~P~ 213 (283)
.=+|=..+--=.+|.|-||+-+.|.-.
T Consensus 203 ~fg~p~~~~GG~~l~h~ss~Ri~lrk~ 229 (790)
T PRK09519 203 MFGSPETTTGGKALKFYASVRMDVRRV 229 (790)
T ss_pred cCCCCCcCCCCcccceeccEEEEeeec
Confidence 112333344456899999999998753
No 53
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=35.55 E-value=12 Score=33.04 Aligned_cols=22 Identities=27% Similarity=0.724 Sum_probs=17.9
Q ss_pred eccCCceehhhhhHHHhhhccchh
Q 023377 244 KRRNGRVRVMVISMFLYFCGECAD 267 (283)
Q Consensus 244 KrRnGRV~~~~e~~~~~~~~~~~~ 267 (283)
+..+|+. .+.|||-|.|+-|+.
T Consensus 33 ~p~~~~~--~VvEffdy~CphC~~ 54 (207)
T PRK10954 33 KPVAGEP--QVLEFFSFYCPHCYQ 54 (207)
T ss_pred CcCCCCC--eEEEEeCCCCccHHH
Confidence 4457865 478999999999997
No 54
>PF13466 STAS_2: STAS domain
Probab=31.25 E-value=97 Score=22.60 Aligned_cols=34 Identities=21% Similarity=0.252 Sum_probs=24.1
Q ss_pred HHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcC
Q 023377 44 LSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGID 80 (283)
Q Consensus 44 l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d 80 (283)
|.+..+..+.++..+++.+ .++..+.+++..|+|
T Consensus 47 L~~~~~~~~~~g~~~~l~~---~~~~~~~ll~~~gld 80 (80)
T PF13466_consen 47 LLAAARRARARGRQLRLTG---PSPALRRLLELLGLD 80 (80)
T ss_pred HHHHHHHHHHCCCeEEEEc---CCHHHHHHHHHhCcC
Confidence 4444556677888888876 445588888888876
No 55
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=30.74 E-value=48 Score=26.17 Aligned_cols=44 Identities=20% Similarity=0.236 Sum_probs=27.5
Q ss_pred HHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCC
Q 023377 44 LSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPL 98 (283)
Q Consensus 44 l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPL 98 (283)
|++...+-.+.+-.+++|+++-.+. -.++++.++++ .+.|.||-
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 3444444555677788898887755 55555556665 24678883
No 56
>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=30.34 E-value=2.3e+02 Score=25.31 Aligned_cols=33 Identities=12% Similarity=0.005 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHhhccccceeEEEEeecChHHH
Q 023377 37 FNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFY 70 (283)
Q Consensus 37 ~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y 70 (283)
...+...|++.+.+. .+.--+..+|-|||--+-
T Consensus 9 ~~~l~~~L~~~~~~~-~~~iv~lCIGTDRstGDs 41 (163)
T PF06866_consen 9 PEKLANFLYSLIPKH-NREIVFLCIGTDRSTGDS 41 (163)
T ss_pred HHHHHHHHHHHHhhc-CCCEEEEEECCCCCcccc
Confidence 345555567766655 444455556667766543
No 57
>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=29.91 E-value=1.8e+02 Score=28.37 Aligned_cols=22 Identities=5% Similarity=0.045 Sum_probs=18.0
Q ss_pred cccceeEEEEeecChHHHHHHH
Q 023377 53 SQSRGLVVVAYSRSPSFYVDLL 74 (283)
Q Consensus 53 ~q~~~Vhvl~fe~Spe~y~~~l 74 (283)
.++..|.++.+|-++++...=+
T Consensus 222 ~~g~~vl~~SlEm~~~~i~~R~ 243 (434)
T TIGR00665 222 KEGKPVAFFSLEMSAEQLAMRM 243 (434)
T ss_pred hCCCeEEEEeCcCCHHHHHHHH
Confidence 3578899999999999987633
No 58
>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=29.47 E-value=21 Score=33.37 Aligned_cols=25 Identities=28% Similarity=0.353 Sum_probs=19.3
Q ss_pred eecccccchhhHhHHhhhheeEEEeecC
Q 023377 186 LLHSDLHEIKFTSVLEYLSSMVASVEPF 213 (283)
Q Consensus 186 LLHsDLHe~~~v~ALe~LSstvvtv~P~ 213 (283)
+||+|||...++.+=. ..++-+-|-
T Consensus 162 lLHGDLH~~NIL~~~~---~~WlaIDPk 186 (253)
T PF04655_consen 162 LLHGDLHHGNILAAGR---RGWLAIDPK 186 (253)
T ss_pred eeccccchHhhhccCC---CCceEeCCc
Confidence 8999999999987664 556666553
No 59
>KOG1406 consensus Peroxisomal 3-ketoacyl-CoA-thiolase P-44/SCP2 [Lipid transport and metabolism]
Probab=25.64 E-value=46 Score=32.78 Aligned_cols=39 Identities=13% Similarity=0.292 Sum_probs=31.2
Q ss_pred eeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCC
Q 023377 57 GLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTD 96 (283)
Q Consensus 57 ~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySD 96 (283)
.+-+++||-+...-+.+..+.|+.++. -+-|..||||+-
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 455677888877777888888998888 677899999984
No 60
>smart00455 RBD Raf-like Ras-binding domain.
Probab=25.61 E-value=46 Score=25.24 Aligned_cols=36 Identities=19% Similarity=0.244 Sum_probs=24.5
Q ss_pred hHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCccccc
Q 023377 67 PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLI 105 (283)
Q Consensus 67 pe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~ 105 (283)
-|.....|+++|++++. ..+++-.=..|+.|++...
T Consensus 23 ~e~L~~~~~kr~l~~~~---~~v~~~g~~k~ldl~~~~~ 58 (70)
T smart00455 23 RDALAKALKKRGLNPEC---CVVRLRGEKKPLDLNQPIS 58 (70)
T ss_pred HHHHHHHHHHcCCCHHH---EEEEEcCCCcceecCCccc
Confidence 45677889999999766 2333323348999998643
No 61
>KOG3124 consensus Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]
Probab=24.86 E-value=39 Score=32.46 Aligned_cols=42 Identities=31% Similarity=0.364 Sum_probs=27.3
Q ss_pred ccCCCCCceeecccCCCCchhhH-HHHHHHH------HHHHHHhhccccc
Q 023377 14 LEGEHAPALTIKDSKASPFGFDV-FNYVLTQ------LSNYILAGKSQSR 56 (283)
Q Consensus 14 l~ge~ap~l~i~Dsl~~~~g~~~-~~h~~~~------l~s~i~a~~~q~~ 56 (283)
++.++-|+ .++|+++||+|+.+ +.|++.+ +...+.++..|.+
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 34444444 46999999999887 5677765 4555555555544
No 62
>PF11382 DUF3186: Protein of unknown function (DUF3186); InterPro: IPR021522 This bacterial family of proteins has no known function.
Probab=24.52 E-value=1.4e+02 Score=28.72 Aligned_cols=61 Identities=20% Similarity=0.336 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHHhhccccceeEEEEeecCh----HHHHHHHhhcCcCccCCCCeEEEEeccCCCCCC
Q 023377 37 FNYVLTQLSNYILAGKSQSRGLVVVAYSRSP----SFYVDLLKRRGIDIASSHDWIHILDCYTDPLGW 100 (283)
Q Consensus 37 ~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Sp----e~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW 100 (283)
.+.|+.++...+.+++..++.|.||...... +.-.+++++.|-.. ..++.+-|-|.||-.=
T Consensus 65 ~d~f~~~~~~~lv~g~L~g~~V~vV~~p~a~~~~~~~v~~~L~~AGA~v---~g~i~lt~~~~d~~~~ 129 (308)
T PF11382_consen 65 ADQFIAAVAPRLVAGRLTGRSVAVVTLPGADDEDVDAVRELLEQAGATV---TGRITLTDKFLDPEQA 129 (308)
T ss_pred HHHHHHHHHHHHhcCccCCCEEEEEEcCCCChHHHHHHHHHHHHCCCeE---EEEEEEchhhcChhhH
Confidence 5677888888888999999999999965433 45667788887774 4479999999999853
No 63
>PRK08114 cystathionine beta-lyase; Provisional
Probab=24.47 E-value=37 Score=33.66 Aligned_cols=60 Identities=13% Similarity=0.184 Sum_probs=33.8
Q ss_pred cCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeec----ChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcc
Q 023377 27 SKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSR----SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKN 102 (283)
Q Consensus 27 sl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~----Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~ 102 (283)
.+..++|....+.++..| + ..++. ||..+. +...+.+.+++.|++ ++++|. .||-.+.+
T Consensus 80 a~~~~SGmaAi~~~~~~l---l----~~GD~--Vv~~~~~Yg~t~~l~~~~l~~~Gi~-------v~~vd~-~d~~~l~~ 142 (395)
T PRK08114 80 CALYPCGAAAVANAILAF---V----EQGDH--VLMTGTAYEPTQDFCSKILSKLGVT-------TTWFDP-LIGADIAK 142 (395)
T ss_pred EEEEhHHHHHHHHHHHHH---c----CCCCE--EEEeCCCcHHHHHHHHHHHHhcCcE-------EEEECC-CCHHHHHH
Confidence 344667888777765433 2 23443 443322 224555667888665 777884 56665554
Q ss_pred c
Q 023377 103 W 103 (283)
Q Consensus 103 ~ 103 (283)
.
T Consensus 143 ~ 143 (395)
T PRK08114 143 L 143 (395)
T ss_pred h
Confidence 3
No 64
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.03 E-value=27 Score=24.01 Aligned_cols=13 Identities=38% Similarity=1.048 Sum_probs=11.5
Q ss_pred hhccchhhhhhcc
Q 023377 261 FCGECADLLYRKS 273 (283)
Q Consensus 261 ~~~~~~~~~~~~~ 273 (283)
||.+|..+||.+.
T Consensus 2 FCp~Cg~~l~~~~ 14 (52)
T smart00661 2 FCPKCGNMLIPKE 14 (52)
T ss_pred CCCCCCCcccccc
Confidence 8999999999874
No 65
>PRK04296 thymidine kinase; Provisional
Probab=22.72 E-value=3.6e+02 Score=23.41 Aligned_cols=98 Identities=17% Similarity=0.156 Sum_probs=63.8
Q ss_pred EEEEEechhHHHHhcChHHHHHHHHhhhcCCceeEEEeeecccccc--hhhHhHHhhhheeEEEeecCCcccccccccch
Q 023377 148 FSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHE--IKFTSVLEYLSSMVASVEPFNQAAFGQRVDLE 225 (283)
Q Consensus 148 ~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~~~vssVl~LLHsDLHe--~~~v~ALe~LSstvvtv~P~~~~~~~~~~~~~ 225 (283)
-+|+||.+-. .+..++-.+++.|+. ..+.-|+.-+-+|.-+ -.....|..+|-.+..+..-... |.+
T Consensus 80 dvviIDEaq~----l~~~~v~~l~~~l~~-~g~~vi~tgl~~~~~~~~f~~~~~L~~~aD~V~~l~~vC~~--Cg~---- 148 (190)
T PRK04296 80 DCVLIDEAQF----LDKEQVVQLAEVLDD-LGIPVICYGLDTDFRGEPFEGSPYLLALADKVTELKAICVH--CGR---- 148 (190)
T ss_pred CEEEEEcccc----CCHHHHHHHHHHHHH-cCCeEEEEecCcccccCcCchHHHHHHhcCeEEEeeEEccc--cCC----
Confidence 5899999943 233446667777665 4566677777777654 23556888899999999886632 433
Q ss_pred hhhhhhccccceeEEEEEec-----cCC-ceehhhhhHHHhhhccch
Q 023377 226 NLSMLEQNFRKGKFHVRFKR-----RNG-RVRVMVISMFLYFCGECA 266 (283)
Q Consensus 226 ~~~~l~~n~~k~~~~vr~Kr-----RnG-RV~~~~e~~~~~~~~~~~ 266 (283)
++.++.|+-. .+| +|..=-.+.|.--|..|-
T Consensus 149 ----------~a~~~~r~~~~~~~~~~~~~~~ig~~e~Y~~~Cr~c~ 185 (190)
T PRK04296 149 ----------KATMNQRLIDGGPAVYEGPQVLVGGNESYEAVCRKHY 185 (190)
T ss_pred ----------ccceEEEEeCCCCccCCCCEEEECCcCcEEehhHHhh
Confidence 4677778773 233 444444456666677774
No 66
>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=22.68 E-value=1.3e+02 Score=28.29 Aligned_cols=38 Identities=21% Similarity=0.370 Sum_probs=26.6
Q ss_pred ccceeEEE-EeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCC
Q 023377 54 QSRGLVVV-AYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGW 100 (283)
Q Consensus 54 q~~~Vhvl-~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW 100 (283)
|++.+|+- ..--+++++..+++..||. +.+.|+||.+|
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 34444432 2346788999999977655 67889999887
No 67
>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=21.82 E-value=4.4e+02 Score=24.65 Aligned_cols=92 Identities=13% Similarity=-0.059 Sum_probs=46.8
Q ss_pred eeEEEEeecChHHHHHHHhhcCcCccCCCCeEE-EEeccCCCCCCcccccCCccccccc-cccccccchhhhhHHHHHHH
Q 023377 57 GLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIH-ILDCYTDPLGWKNWLIDKDISQEAS-SLSSFCQDVRNLDKLYSLII 134 (283)
Q Consensus 57 ~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~-i~D~ySDPLGW~~~~~~~~~~~~~s-~~~~~~~~v~~L~sl~~si~ 134 (283)
+.+++++|+|++......++. ....++-++. +.--|.|++.|.......+..--.+ ..+..+ +..+...++..+.
T Consensus 88 ~~~~~~iDiS~~mL~~a~~~l--~~~~p~~~v~~i~gD~~~~~~~~~~~~~~~~~~~~~gs~~~~~-~~~e~~~~L~~i~ 164 (301)
T TIGR03438 88 PARYVPIDISADALKESAAAL--AADYPQLEVHGICADFTQPLALPPEPAAGRRLGFFPGSTIGNF-TPEEAVAFLRRIR 164 (301)
T ss_pred CCeEEEEECCHHHHHHHHHHH--HhhCCCceEEEEEEcccchhhhhcccccCCeEEEEecccccCC-CHHHHHHHHHHHH
Confidence 688999999999766554432 1101122343 3344567776654321000000000 011111 2445566667766
Q ss_pred HhccCccCCCCCcEEEEEechh
Q 023377 135 EQGKGLIGQGKDRFSIAIDSVS 156 (283)
Q Consensus 135 e~~r~~~~~~k~~~tVaIDSLS 156 (283)
+..+ ++..+.|.+|..-
T Consensus 165 ~~L~-----pgG~~lig~d~~~ 181 (301)
T TIGR03438 165 QLLG-----PGGGLLIGVDLVK 181 (301)
T ss_pred HhcC-----CCCEEEEeccCCC
Confidence 6665 4556888888764
No 68
>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....
Probab=21.16 E-value=5.3e+02 Score=23.47 Aligned_cols=78 Identities=15% Similarity=0.162 Sum_probs=41.6
Q ss_pred ccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHH--H
Q 023377 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY--S 131 (283)
Q Consensus 54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ySDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~--~ 131 (283)
+++.++++++.-.++|..++.+.. -......+.+++..-..||. +.+....+ .
T Consensus 40 ~~d~~V~~~iGer~~Ev~~~~~~~-~~~~~~~~t~vv~~t~~~~~------------------------~~r~~~~~~a~ 94 (215)
T PF00006_consen 40 DADVVVYALIGERGREVTEFIEEL-KGEGALERTVVVAATSDEPP------------------------AARYRAPYTAL 94 (215)
T ss_dssp TTTEEEEEEESECHHHHHHHHHHH-HHTTGGGGEEEEEEETTS-H------------------------HHHHHHHHHHH
T ss_pred cccceeeeeccccchhHHHHHHHH-hhcccccccccccccchhhH------------------------HHHhhhhccch
Confidence 466668888877777666655432 01112134466665444443 11112111 2
Q ss_pred HHHHhccCccCCCCCcEEEEEechhHHHH
Q 023377 132 LIIEQGKGLIGQGKDRFSIAIDSVSEMVR 160 (283)
Q Consensus 132 si~e~~r~~~~~~k~~~tVaIDSLS~LL~ 160 (283)
.+.|..+ .+|+. +.+++|+++-+-+
T Consensus 95 t~AEyfr---d~G~d-Vlli~Dsltr~a~ 119 (215)
T PF00006_consen 95 TIAEYFR---DQGKD-VLLIIDSLTRWAQ 119 (215)
T ss_dssp HHHHHHH---HTTSE-EEEEEETHHHHHH
T ss_pred hhhHHHh---hcCCc-eeehhhhhHHHHH
Confidence 3444444 45675 9999999986653
No 69
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=20.59 E-value=2.4e+02 Score=23.35 Aligned_cols=39 Identities=10% Similarity=0.107 Sum_probs=28.3
Q ss_pred eecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeec
Q 023377 23 TIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSR 65 (283)
Q Consensus 23 ~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~ 65 (283)
..-|+-.|.. ...+..|++++++..+.. ...|+|+.||-
T Consensus 3 vaiDtSGSis-~~~l~~fl~ev~~i~~~~---~~~v~vi~~D~ 41 (126)
T PF09967_consen 3 VAIDTSGSIS-DEELRRFLSEVAGILRRF---PAEVHVIQFDA 41 (126)
T ss_pred EEEECCCCCC-HHHHHHHHHHHHHHHHhC---CCCEEEEEECC
Confidence 4567777775 567888888888765554 45599999974
No 70
>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=20.18 E-value=95 Score=21.99 Aligned_cols=18 Identities=39% Similarity=0.650 Sum_probs=14.1
Q ss_pred ceeEEEEEeccCCceehh
Q 023377 236 KGKFHVRFKRRNGRVRVM 253 (283)
Q Consensus 236 k~~~~vr~KrRnGRV~~~ 253 (283)
.|+++.|+|-.||.|.-.
T Consensus 3 ~g~~~f~L~a~ng~vias 20 (49)
T PF07411_consen 3 DGQFRFRLKAGNGEVIAS 20 (49)
T ss_dssp TSEEEEEEE-TTS-EEEE
T ss_pred CCCEEEEEEcCCCCEEEe
Confidence 589999999999999873
Done!