Query 024646
Match_columns 265
No_of_seqs 66 out of 68
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 06:19:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024646.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024646hhsearch_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 1.4E-25 3E-30 206.5 10.1 184 17-253 10-206 (280)
2 PF09807 DUF2348: Uncharacteri 99.2 2E-09 4.3E-14 98.3 17.9 185 18-215 18-213 (249)
3 PF06745 KaiC: KaiC; InterPro 98.2 4.7E-06 1E-10 73.0 8.5 137 50-212 42-185 (226)
4 TIGR03877 thermo_KaiC_1 KaiC d 97.9 0.00013 2.8E-09 65.2 10.8 143 51-211 45-193 (237)
5 PRK06067 flagellar accessory p 97.8 0.00059 1.3E-08 60.3 13.3 136 52-213 50-188 (234)
6 PRK04328 hypothetical protein; 97.7 0.00048 1E-08 62.3 11.0 144 50-211 46-195 (249)
7 COG2874 FlaH Predicted ATPases 97.4 0.0083 1.8E-07 55.1 15.0 137 51-213 52-191 (235)
8 PRK09302 circadian clock prote 97.3 0.0021 4.5E-08 63.6 10.6 131 51-212 297-434 (509)
9 PRK09302 circadian clock prote 96.8 0.011 2.5E-07 58.4 10.8 136 51-211 55-200 (509)
10 TIGR02655 circ_KaiC circadian 96.2 0.081 1.8E-06 52.5 12.9 131 50-211 286-423 (484)
11 TIGR03881 KaiC_arch_4 KaiC dom 96.1 0.17 3.8E-06 44.2 13.2 135 53-212 46-189 (229)
12 cd01124 KaiC KaiC is a circadi 96.0 0.11 2.3E-06 43.5 10.8 136 51-213 23-165 (187)
13 TIGR02655 circ_KaiC circadian 95.8 0.096 2.1E-06 52.0 11.1 138 50-211 44-190 (484)
14 COG0467 RAD55 RecA-superfamily 95.4 0.069 1.5E-06 48.1 7.9 145 50-215 46-196 (260)
15 TIGR03878 thermo_KaiC_2 KaiC d 95.3 0.13 2.8E-06 46.9 9.6 133 51-211 60-203 (259)
16 PRK08533 flagellar accessory p 94.8 0.29 6.3E-06 43.9 10.0 130 53-212 50-185 (230)
17 TIGR03880 KaiC_arch_3 KaiC dom 94.3 0.56 1.2E-05 41.1 10.5 130 51-211 40-177 (224)
18 KOG4723 Uncharacterized conser 94.3 0.26 5.5E-06 45.3 8.3 72 16-95 16-89 (248)
19 PRK05973 replicative DNA helic 93.3 1.8 3.9E-05 39.8 12.2 62 15-83 59-120 (237)
20 TIGR02237 recomb_radB DNA repa 93.0 0.89 1.9E-05 39.1 9.4 38 53-93 38-76 (209)
21 PF05625 PAXNEB: PAXNEB protei 91.7 0.39 8.4E-06 46.4 6.0 69 148-216 202-280 (363)
22 PRK04301 radA DNA repair and r 90.7 3.9 8.5E-05 38.2 11.5 39 56-94 137-177 (317)
23 cd01121 Sms Sms (bacterial rad 90.2 9.1 0.0002 37.3 13.9 115 54-212 109-233 (372)
24 PRK11823 DNA repair protein Ra 90.1 8.2 0.00018 38.3 13.8 116 53-212 106-231 (446)
25 cd01393 recA_like RecA is a b 89.3 9.7 0.00021 32.9 12.2 127 56-214 54-202 (226)
26 TIGR02236 recomb_radA DNA repa 88.8 5.1 0.00011 37.0 10.6 38 57-94 131-170 (310)
27 PRK09361 radB DNA repair and r 88.2 9.5 0.00021 33.2 11.4 65 148-212 109-190 (225)
28 cd01123 Rad51_DMC1_radA Rad51_ 87.3 5.4 0.00012 34.7 9.3 40 55-94 53-94 (235)
29 cd01122 GP4d_helicase GP4d_hel 85.6 26 0.00056 31.3 14.9 21 55-75 59-79 (271)
30 PTZ00035 Rad51 protein; Provis 83.8 23 0.0005 33.9 12.4 40 55-94 152-193 (337)
31 cd00984 DnaB_C DnaB helicase C 83.3 1.6 3.4E-05 38.3 4.0 67 148-214 125-209 (242)
32 PF03192 DUF257: Pyrococcus pr 81.7 34 0.00073 30.9 12.0 153 21-213 13-187 (210)
33 TIGR02238 recomb_DMC1 meiotic 81.1 22 0.00048 33.7 11.1 41 54-94 129-171 (313)
34 TIGR02239 recomb_RAD51 DNA rep 80.3 49 0.0011 31.3 13.2 125 56-212 131-281 (316)
35 cd01394 radB RadB. The archaea 80.0 31 0.00067 29.8 11.0 64 148-211 105-185 (218)
36 PF05763 DUF835: Protein of un 79.9 8 0.00017 32.6 7.0 50 123-177 57-106 (136)
37 PLN03187 meiotic recombination 76.2 22 0.00049 34.4 9.7 39 56-94 161-201 (344)
38 PF08423 Rad51: Rad51; InterP 65.1 33 0.00072 31.4 7.8 41 55-95 72-114 (256)
39 PLN03186 DNA repair protein RA 65.0 1.4E+02 0.003 28.9 15.4 124 57-212 159-307 (342)
40 TIGR00416 sms DNA repair prote 63.8 90 0.002 31.2 11.2 114 54-212 121-245 (454)
41 PRK09354 recA recombinase A; P 63.8 61 0.0013 31.6 9.7 43 30-81 70-112 (349)
42 cd01125 repA Hexameric Replica 60.8 1.2E+02 0.0026 26.8 13.2 141 54-217 40-195 (239)
43 cd00983 recA RecA is a bacter 59.0 44 0.00096 32.2 7.8 121 53-214 81-225 (325)
44 TIGR02012 tigrfam_recA protein 58.0 57 0.0012 31.4 8.3 48 30-90 65-112 (321)
45 cd01120 RecA-like_NTPases RecA 51.1 1.2E+02 0.0025 23.7 13.8 64 148-211 87-164 (165)
46 PF14417 MEDS: MEDS: MEthanoge 49.6 58 0.0013 28.1 6.4 137 38-200 30-174 (191)
47 PF13481 AAA_25: AAA domain; P 47.8 19 0.00042 30.1 3.1 25 54-78 69-93 (193)
48 PF00004 AAA: ATPase family as 37.5 77 0.0017 24.2 4.8 57 19-75 58-120 (132)
49 PF05301 Mec-17: Touch recepto 33.9 68 0.0015 27.0 4.1 70 17-96 42-120 (120)
50 KOG3124 Pyrroline-5-carboxylat 31.2 26 0.00056 33.2 1.4 42 14-56 214-262 (267)
51 PRK09519 recA DNA recombinatio 31.1 2.1E+02 0.0045 31.2 8.1 66 148-213 140-229 (790)
52 PF00154 RecA: recA bacterial 27.2 1.5E+02 0.0032 28.7 5.8 51 29-92 62-112 (322)
53 PF13911 AhpC-TSA_2: AhpC/TSA 27.1 59 0.0013 25.4 2.6 43 45-98 3-45 (115)
54 cd04754 Commd6 COMM_Domain con 26.4 54 0.0012 26.1 2.2 34 230-265 41-79 (86)
55 PF11633 SUD-M: Single-strande 25.8 25 0.00054 30.4 0.2 64 25-94 6-69 (142)
56 PF13466 STAS_2: STAS domain 24.5 1.6E+02 0.0034 21.2 4.4 34 44-80 47-80 (80)
57 smart00455 RBD Raf-like Ras-bi 23.2 55 0.0012 24.5 1.7 36 67-105 23-58 (70)
58 KOG1406 Peroxisomal 3-ketoacyl 23.1 55 0.0012 31.7 2.0 40 56-96 264-303 (408)
59 PF09967 DUF2201: VWA-like dom 22.9 2E+02 0.0043 23.5 5.1 39 22-64 2-40 (126)
60 COG4544 Uncharacterized conser 22.7 1.3E+02 0.0028 28.4 4.3 55 34-95 64-118 (260)
61 PF11382 DUF3186: Protein of u 22.6 1.5E+02 0.0033 28.0 4.9 60 37-99 65-128 (308)
62 PF04655 APH_6_hur: Aminoglyco 22.1 34 0.00074 31.6 0.4 27 186-215 162-188 (253)
63 KOG3444 Uncharacterized conser 20.4 55 0.0012 27.4 1.2 35 142-176 75-109 (121)
64 PF06866 DUF1256: Protein of u 20.2 6E+02 0.013 22.4 9.1 32 36-68 8-39 (163)
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=1.4e-25 Score=206.50 Aligned_cols=184 Identities=22% Similarity=0.230 Sum_probs=110.5
Q ss_pred CCCCceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccCC
Q 024646 17 EHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTD 96 (265)
Q Consensus 17 e~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ysD 96 (265)
|..|+++|.||++.|+ ..+++++ |+..+.++..||+|+||.+++ .+ |+|... +|-
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 3789999999999985 6666664 445688899999999999876 44 665333 222
Q ss_pred CCCCcccccCccccccccccccccccchhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc
Q 024646 97 PLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS 176 (265)
Q Consensus 97 PlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~ 176 (265)
+|+- .+++..+.........+++.+++|+|||||||+.|+++ +++++|++|++
T Consensus 65 --~~~~------------------------~~i~~~i~s~~~~~~~~~~~~~lVvIDSLn~ll~~~~~-~l~~fLssl~~ 117 (280)
T PF10483_consen 65 --GKSL------------------------QDIVKEIKSHLPSSSSSPTKKFLVVIDSLNYLLNHHPC-QLSQFLSSLLS 117 (280)
T ss_dssp --SS-H------------------------HHHHHHHHHTS--SS-SS---EEEEES-GGGS-GG----GHHHHHHHH--
T ss_pred --CCCH------------------------HHHHHHHHhhcccccccCCCCeEEEEEcchHHHHHHHH-HHHHHHHhccc
Confidence 3321 11112222221111222344599999999999999999 99999999998
Q ss_pred CCceeEEEEeecccc-------cchhHHHHHHhhheeEEEeeeCCcccccccchhhhhhhhh------hccccceEEEEe
Q 024646 177 HDQVSSIFWLLHSDL-------HEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLE------QNFRKGKFHVRF 243 (265)
Q Consensus 177 ~~~vssVl~LLHsDL-------He~~vv~ALe~LAs~vv~v~P~~~~~~~~~~~~~~~~~l~------~n~~kg~~~vr~ 243 (265)
+++ ++|||++|+|+ |+|+++.+|+|||||+++|+|........+++.+++.-++ .|..+.++++++
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 888 78999999999 9999999999999999999999998888877777766554 445577899999
Q ss_pred ecCCCchhhh
Q 024646 244 KRRNGRVRVM 253 (265)
Q Consensus 244 KrrnGRV~~~ 253 (265)
|||+||+...
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 9999998654
No 2
>PF09807 DUF2348: Uncharacterized conserved protein (DUF2348); InterPro: IPR018627 Members of this family of putative uncharacterised proteins have no known function.
Probab=99.18 E-value=2e-09 Score=98.31 Aligned_cols=185 Identities=18% Similarity=0.244 Sum_probs=128.9
Q ss_pred CCCceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccC
Q 024646 18 HAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYT 95 (265)
Q Consensus 18 ~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ys 95 (265)
..-+++|+|+ .+++ .=+..|++. .+++ .+..|.+|+|..+.+.|...++|-|++-... +.+++++|..+
T Consensus 18 ~g~~ili~d~-~~dg-sFLlh~~L~---~~Lk----~~~~V~fv~~~q~~~HY~~v~~KLG~NL~~~~~~gql~fiD~l~ 88 (249)
T PF09807_consen 18 PGKLILIEDC-ETDG-SFLLHHFLS---QYLK----AGCKVCFVAFSQSFSHYNNVAQKLGVNLSAAKEKGQLVFIDGLK 88 (249)
T ss_pred CCeEEEEEcC-CCCc-hhHHHHHHH---HHhc----CCCcEEEEEccCCHHHHHHHHHhhEecchHhccCCcEEEeehhh
Confidence 3447999999 8875 556666553 3333 4558999999999999999999999987652 34799999999
Q ss_pred CCCCCcccccCccccccccccccccccchhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHH-hcChHHHHHHHHhh
Q 024646 96 DPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR-HASISSVAGILSNL 174 (265)
Q Consensus 96 DPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~-h~s~~~vc~lL~~L 174 (265)
++++|--....++... +..+.--.+...|.+++..+.+..+...+ .++ ++|+||-||.|+- ..+..+|..+++.+
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 8887743211000000 11111111234578887777665552222 233 8999999999997 34556889999999
Q ss_pred hc---CCceeEEEEeecccccc----hh-HHHHHHhhheeEEEeeeCCc
Q 024646 175 RS---HDQVSSIFWLLHSDLHE----IK-FTSVLEYLSSMVASVEPFNQ 215 (265)
Q Consensus 175 r~---~~~vssVl~LLHsDLHe----~~-vv~ALe~LAs~vv~v~P~~~ 215 (265)
|. ...-.+++.+.|.|-.. .. ....|+|+|..+|+++|...
T Consensus 165 ra~l~~~~~~~lVvl~h~d~~~~~e~~~~l~~~L~h~a~l~i~v~~L~T 213 (249)
T PF09807_consen 165 RATLCSESNGSLVVLVHCDIDDEDEENDLLLNSLAHMADLVITVEPLPT 213 (249)
T ss_pred HHHhccccCCCEEEEEecCCCCccchHHHHHHHHHHHhcEEEEecCCCC
Confidence 84 23346899999998652 22 78999999999999999654
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=98.24 E-value=4.7e-06 Score=72.99 Aligned_cols=137 Identities=20% Similarity=0.243 Sum_probs=90.5
Q ss_pred hhccc-cceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhh
Q 024646 50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (265)
Q Consensus 50 a~~~q-~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (265)
++..+ ++.+..+.+|.+|+++.+-++..|+|.+.. +.++.++|+++...+|.. . ++..+
T Consensus 42 ~~~~~~ge~vlyvs~ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~~~~~~--~----------------~~~~l 103 (226)
T PF06745_consen 42 NGLKNFGEKVLYVSFEEPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERIGWSP--N----------------DLEEL 103 (226)
T ss_dssp HHHHHHT--EEEEESSS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGST-TS--C----------------CHHHH
T ss_pred HhhhhcCCcEEEEEecCCHHHHHHHHHHcCCcHHHHhhcCCEEEEecccccccccc--c----------------CHHHH
Confidence 45666 899999999999999999999999875541 336999999999988872 1 12232
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEEeecccccchhHHHHHHh-
Q 024646 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLHSDLHEIKFTSVLEY- 202 (265)
Q Consensus 127 ~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LLHsDLHe~~vv~ALe~- 202 (265)
...+...++.. ++ -.|+||||+.|....+...+-.+|+.|.+. ..+..++..-..+-+++.....+++
T Consensus 104 ~~~i~~~i~~~-------~~-~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~llt~~~~~~~~~~~~~~i~~~ 175 (226)
T PF06745_consen 104 LSKIREAIEEL-------KP-DRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTLLTSEMPSGSEDDGTFGIEHY 175 (226)
T ss_dssp HHHHHHHHHHH-------TS-SEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEEEEEEESSSSSSSSSTSHHHH
T ss_pred HHHHHHHHHhc-------CC-CEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEEEEEccccCcccccccchhhh
Confidence 22223333322 22 589999999997777777666666666652 4455555544344555666666766
Q ss_pred hheeEEEeee
Q 024646 203 LSSMVASVEP 212 (265)
Q Consensus 203 LAs~vv~v~P 212 (265)
++.++|.+.-
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 9999999965
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=97.89 E-value=0.00013 Score=65.18 Aligned_cols=143 Identities=17% Similarity=0.181 Sum_probs=83.9
Q ss_pred hccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhH
Q 024646 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (265)
Q Consensus 51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (265)
+..+++.+..+.+|-+|+++.+-++..|+|... -..++.++|||++-.++...... + +..+..++..
T Consensus 45 ~~~~ge~~lyvs~ee~~~~i~~~~~~~g~~~~~~~~~g~l~~~d~~~~~~~~~~~~~~----------~-~~~~~~~~~~ 113 (237)
T TIGR03877 45 GLQMGEPGIYVALEEHPVQVRRNMAQFGWDVRKYEEEGKFAIVDAFTGGIGEAAEREK----------Y-VVKDPTDVRE 113 (237)
T ss_pred HHHcCCcEEEEEeeCCHHHHHHHHHHhCCCHHHHhhcCCEEEEecccccccccccccc----------c-cccCcccHHH
Confidence 445689999999999999999999999987532 13479999999986554431110 0 1112224444
Q ss_pred HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh---HHHHHHHHhhhcCCceeEEEEeecccccchhH-HHHHHhhh
Q 024646 129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKF-TSVLEYLS 204 (265)
Q Consensus 129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~---~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~v-v~ALe~LA 204 (265)
++..+.+..+ +.++ -.|+||||+.++...+. ..+.++.+.+++.. +..++ .-|.+..+... ...++|++
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 4344333221 1123 37999999998764432 22344444555433 33333 23332222111 12478999
Q ss_pred eeEEEee
Q 024646 205 SMVASVE 211 (265)
Q Consensus 205 s~vv~v~ 211 (265)
-++|.+.
T Consensus 187 D~vI~L~ 193 (237)
T TIGR03877 187 DGIIRLD 193 (237)
T ss_pred eEEEEEE
Confidence 9999986
No 5
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=97.79 E-value=0.00059 Score=60.30 Aligned_cols=136 Identities=17% Similarity=0.236 Sum_probs=93.9
Q ss_pred ccccceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHH
Q 024646 52 KSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKL 129 (265)
Q Consensus 52 ~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl 129 (265)
..+++.+..+.+|.+|+++.+-+.+.|+|.... ...+.++|.+..+..|... +.+++-..
T Consensus 50 ~~~g~~~~y~~~e~~~~~~~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~------------------~~~~ll~~ 111 (234)
T PRK06067 50 LKQGKKVYVITTENTSKSYLKQMESVKIDISDFFLWGYLRIFPLNTEGFEWNST------------------LANKLLEL 111 (234)
T ss_pred HhCCCEEEEEEcCCCHHHHHHHHHHCCCChhHHHhCCCceEEeccccccccCcc------------------hHHHHHHH
Confidence 346899999999999999999999999876541 3357778877766665541 11222222
Q ss_pred HHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC-CceeEEEEeecccccchhHHHHHHhhheeEE
Q 024646 130 YSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH-DQVSSIFWLLHSDLHEIKFTSVLEYLSSMVA 208 (265)
Q Consensus 130 ~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~~-~~vssVl~LLHsDLHe~~vv~ALe~LAs~vv 208 (265)
+...++. .++ -.|+|||++.++...+...+..++..|+.. ..=..++...|.+.+.......+++++-.++
T Consensus 112 l~~~i~~-------~~~-~~iviDs~t~~~~~~~~~~~~~~l~~l~~l~~~g~tvllt~~~~~~~~~~~~~~~~l~DgvI 183 (234)
T PRK06067 112 IIEFIKS-------KRE-DVIIIDSLTIFATYAEEDDILNFLTEAKNLVDLGKTILITLHPYAFSEELLSRIRSICDVYL 183 (234)
T ss_pred HHHHHHh-------cCC-CEEEEecHHHHHhcCCHHHHHHHHHHHHHHHhCCCEEEEEecCCcCCHHHHHHHHhheEEEE
Confidence 2222321 233 379999999998888888888876655432 1124567777877776777788999999999
Q ss_pred EeeeC
Q 024646 209 SVEPF 213 (265)
Q Consensus 209 ~v~P~ 213 (265)
.+...
T Consensus 184 ~L~~~ 188 (234)
T PRK06067 184 KLRAE 188 (234)
T ss_pred EEEee
Confidence 99764
No 6
>PRK04328 hypothetical protein; Provisional
Probab=97.67 E-value=0.00048 Score=62.33 Aligned_cols=144 Identities=19% Similarity=0.171 Sum_probs=84.6
Q ss_pred hhccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhh
Q 024646 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (265)
Q Consensus 50 a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (265)
.+..+++.+..+.+|-+|+.+.+-+++.|+|... -+.++.++|+|+.-.+...... .+ +..+..++.
T Consensus 46 ~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~~~l~iid~~~~~~~~~~~~~----------~~-~~~~~~~~~ 114 (249)
T PRK04328 46 NGLQMGEPGVYVALEEHPVQVRRNMRQFGWDVRKYEEEGKFAIVDAFTGGIGSAAKRE----------KY-VVKDPDDVR 114 (249)
T ss_pred HHHhcCCcEEEEEeeCCHHHHHHHHHHcCCCHHHHhhcCCEEEEeccccccccccccc----------cc-cccCcccHH
Confidence 3456789999999999999999999999987533 1347999999998776543111 01 111223344
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh---HHHHHHHHhhhcCCceeEEEEeecccccchhH-HHHHHhh
Q 024646 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKF-TSVLEYL 203 (265)
Q Consensus 128 sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~---~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~v-v~ALe~L 203 (265)
.++..+.+..+ +.++ -.||||||+.|....+- ..+.++.+.|++.. +..++. .|.+..+... -..++|+
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 44333333221 1123 37999999998764321 22344555566543 333322 2333222111 1246899
Q ss_pred heeEEEee
Q 024646 204 SSMVASVE 211 (265)
Q Consensus 204 As~vv~v~ 211 (265)
+-++|.++
T Consensus 188 ~D~vI~L~ 195 (249)
T PRK04328 188 VDGIIRLD 195 (249)
T ss_pred EEEEEEEE
Confidence 99999886
No 7
>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=97.39 E-value=0.0083 Score=55.08 Aligned_cols=137 Identities=16% Similarity=0.163 Sum_probs=106.3
Q ss_pred hccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhH
Q 024646 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (265)
Q Consensus 51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (265)
.-.++..|..+.-|.+--+|..-|..-+.|..- ++.++.|.-.-.+|.+|+.... ++
T Consensus 52 ~L~~g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G~l~~~~~~~~~~~~~~~~~---------------------~~ 110 (235)
T COG2874 52 FLMNGYRVTYVSTELTVREFIKQMESLSYDVSDFLLSGRLLFFPVNLEPVNWGRRSA---------------------RK 110 (235)
T ss_pred HHhCCceEEEEEechhHHHHHHHHHhcCCCchHHHhcceeEEEEecccccccChHHH---------------------HH
Confidence 456788999999999999999999988777543 4567777777779999998443 11
Q ss_pred HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc-CCceeEEEEeecccccchhHHHHHHhhheeE
Q 024646 129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS-HDQVSSIFWLLHSDLHEIKFTSVLEYLSSMV 207 (265)
Q Consensus 129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~-~~~vssVl~LLHsDLHe~~vv~ALe~LAs~v 207 (265)
++..+++..| ..-+ =+|.|||||..+.+.+..+|-+++..+|+ ++.=.-|+--+|.+.-.+.++.-++..+++-
T Consensus 111 ~L~~l~~~~k---~~~~--dViIIDSls~~~~~~~~~~vl~fm~~~r~l~d~gKvIilTvhp~~l~e~~~~rirs~~d~~ 185 (235)
T COG2874 111 LLDLLLEFIK---RWEK--DVIIIDSLSAFATYDSEDAVLNFMTFLRKLSDLGKVIILTVHPSALDEDVLTRIRSACDVY 185 (235)
T ss_pred HHHHHHhhHH---hhcC--CEEEEecccHHhhcccHHHHHHHHHHHHHHHhCCCEEEEEeChhhcCHHHHHHHHHhhhee
Confidence 2223333222 1113 48999999999999999999999999998 4566678888999999999999999999999
Q ss_pred EEeeeC
Q 024646 208 ASVEPF 213 (265)
Q Consensus 208 v~v~P~ 213 (265)
+.++-.
T Consensus 186 l~L~~~ 191 (235)
T COG2874 186 LRLRLE 191 (235)
T ss_pred EEEEhh
Confidence 988643
No 8
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=97.26 E-value=0.0021 Score=63.64 Aligned_cols=131 Identities=18% Similarity=0.252 Sum_probs=84.3
Q ss_pred hccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhH
Q 024646 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (265)
Q Consensus 51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (265)
+..+++.+..+.||-+|+.+.+-++..|+|.+. -...+.++|.+.++.+|+. .+..
T Consensus 297 ~~~~g~~~~yis~e~~~~~i~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~----------------------~~~~ 354 (509)
T PRK09302 297 ACRRGERCLLFAFEESRAQLIRNARSWGIDLEKMEEKGLLKIICARPESYGLED----------------------HLII 354 (509)
T ss_pred HHhCCCcEEEEEecCCHHHHHHHHHHcCCChHHHhhcCCceeecCCcccCCHHH----------------------HHHH
Confidence 456789999999999999999999988887543 1235778887776665543 1122
Q ss_pred HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEEeecccc--cchhHHHHHHhh
Q 024646 129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLHSDL--HEIKFTSVLEYL 203 (265)
Q Consensus 129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LLHsDL--He~~vv~ALe~L 203 (265)
+ ...++. .++ -.|+||||+.+....+...+-+.|..|.+. -.+..++...-.+. +.+.....++|+
T Consensus 355 i-~~~i~~-------~~~-~~vVIDslt~l~~~~~~~~~~~~l~~l~~~~k~~~~t~l~t~~~~~~~g~~~~~~~~~~~l 425 (509)
T PRK09302 355 I-KREIEE-------FKP-SRVAIDPLSALARGGSLNEFRQFVIRLTDYLKSEEITGLFTNLTPDFMGSHSITESHISSL 425 (509)
T ss_pred H-HHHHHH-------cCC-CEEEEcCHHHHHHhCCHHHHHHHHHHHHHHHHhCCCeEEEEeccccccCCCCCCcCceEEe
Confidence 2 222331 234 379999999999877776655555544331 34555555332222 233333458999
Q ss_pred heeEEEeee
Q 024646 204 SSMVASVEP 212 (265)
Q Consensus 204 As~vv~v~P 212 (265)
+-++|.+.=
T Consensus 426 ~D~vI~L~~ 434 (509)
T PRK09302 426 TDTWILLQY 434 (509)
T ss_pred eeEEEEEEE
Confidence 999999963
No 9
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=96.77 E-value=0.011 Score=58.44 Aligned_cols=136 Identities=18% Similarity=0.160 Sum_probs=84.8
Q ss_pred hccc-cceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhhh
Q 024646 51 GKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (265)
Q Consensus 51 ~~~q-~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (265)
+..+ ++.+..+.+|-+++++.+-++.-|+|.+.. +.++.++|.+.+|..|.. .. -.++.
T Consensus 55 ~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~g~l~~~~~~~~~~~~~~-~~-----------------~~~~~ 116 (509)
T PRK09302 55 GIKRFDEPGVFVTFEESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSEQEE-AG-----------------EYDLE 116 (509)
T ss_pred HHHhcCCCEEEEEccCCHHHHHHHHHHcCCCHHHHhhCCeEEEEecCcccccccc-cc-----------------cccHH
Confidence 4445 889999999999999999999999886542 346999999999988864 11 01233
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH-----HHHHHHHhhhcCCceeEEEEeecccccch--hHHHHH
Q 024646 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS-----SVAGILSNLRSHDQVSSIFWLLHSDLHEI--KFTSVL 200 (265)
Q Consensus 128 sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~-----~vc~lL~~Lr~~~~vssVl~LLHsDLHe~--~vv~AL 200 (265)
.++..+.+..+ +.++ -.|+|||++.+....... .+.+++..|++. .+..++. -|..-... ...+..
T Consensus 117 ~l~~~l~~~i~----~~~~-~~vVIDSls~l~~~~d~~~~~r~~l~~L~~~Lk~~-g~TvLlt-~~~~~~~~~~~~~~~~ 189 (509)
T PRK09302 117 ALFIRIEYAID----KIGA-KRVVLDSIEALFSGFSNEAVVRRELRRLFAWLKQK-GVTAVIT-GERGDEYGPLTRYGVE 189 (509)
T ss_pred HHHHHHHHHHH----hhCC-CEEEECCHHHHHhhccCHHHHHHHHHHHHHHHHhC-CCEEEEE-ECCccCcCCccccCce
Confidence 33333333221 1233 479999999987654332 345555556543 3333333 34332111 112245
Q ss_pred HhhheeEEEee
Q 024646 201 EYLSSMVASVE 211 (265)
Q Consensus 201 e~LAs~vv~v~ 211 (265)
++++..++.++
T Consensus 190 ~~laDgVI~L~ 200 (509)
T PRK09302 190 EFVSDCVIILR 200 (509)
T ss_pred EEEeeEEEEEe
Confidence 88999999886
No 10
>TIGR02655 circ_KaiC circadian clock protein KaiC. Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.
Probab=96.22 E-value=0.081 Score=52.53 Aligned_cols=131 Identities=18% Similarity=0.260 Sum_probs=77.8
Q ss_pred hhccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhh
Q 024646 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (265)
Q Consensus 50 a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (265)
+++.+++.+..++||-|++++..-+++-|+|.+. ...++.+++.+....+... .+.
T Consensus 286 ~~~~~ge~~~y~s~eEs~~~i~~~~~~lg~~~~~~~~~g~l~~~~~~p~~~~~~~----------------------~~~ 343 (484)
T TIGR02655 286 NACANKERAILFAYEESRAQLLRNAYSWGIDFEEMEQQGLLKIICAYPESAGLED----------------------HLQ 343 (484)
T ss_pred HHHHCCCeEEEEEeeCCHHHHHHHHHHcCCChHHHhhCCcEEEEEcccccCChHH----------------------HHH
Confidence 3456789999999999999999999999987433 1235888887643332111 122
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc---CCceeEEEEeecccccc--hhHHHHHHh
Q 024646 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS---HDQVSSIFWLLHSDLHE--IKFTSVLEY 202 (265)
Q Consensus 128 sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~---~~~vssVl~LLHsDLHe--~~vv~ALe~ 202 (265)
.+...+.+ .++ -.|+||||+.+....+..++-..++.|.+ ...|..++...=.++=+ +-.-.-++|
T Consensus 344 ~i~~~i~~--------~~~-~~vvIDsi~~~~~~~~~~~~r~~~~~l~~~lk~~~it~~~t~~~~~~~~~~~~~~~~~s~ 414 (484)
T TIGR02655 344 IIKSEIAD--------FKP-ARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGFFTNTSDQFMGSHSITDSHIST 414 (484)
T ss_pred HHHHHHHH--------cCC-CEEEEcCHHHHHHhcCHHHHHHHHHHHHHHHhhCCCeEEEeecccccccCCccCCCCeeE
Confidence 33222222 123 38999999999876666655444443333 24455554433222111 111134688
Q ss_pred hheeEEEee
Q 024646 203 LSSMVASVE 211 (265)
Q Consensus 203 LAs~vv~v~ 211 (265)
|+-.+|.+.
T Consensus 415 l~D~ii~l~ 423 (484)
T TIGR02655 415 ITDTILMLQ 423 (484)
T ss_pred eeeEEEEEE
Confidence 888888774
No 11
>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family. Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.
Probab=96.12 E-value=0.17 Score=44.20 Aligned_cols=135 Identities=12% Similarity=0.047 Sum_probs=76.0
Q ss_pred cccceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCC--CCcccccCccccccccccccccccchhhhH
Q 024646 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPL--GWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (265)
Q Consensus 53 ~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPl--gW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (265)
.+++.+..+.+|.+++.+.+-+++.|++.... +.++.+.|.+.... .|.- .. + ++.++..
T Consensus 46 ~~g~~~~~is~e~~~~~i~~~~~~~g~~~~~~~~~~~l~i~d~~~~~~~~~~~~-~~-----------~----~~~~~~~ 109 (229)
T TIGR03881 46 RDGDPVIYVTTEESRESIIRQAAQFGMDFEKAIEEGKLVIIDALMKEKEDEWSL-RE-----------L----SIEELLN 109 (229)
T ss_pred hcCCeEEEEEccCCHHHHHHHHHHhCCCHHHHhhcCCEEEEEcccccccccccc-cc-----------C----CHHHHHH
Confidence 45789999999999999988888889876542 34688888775431 1221 00 1 2223322
Q ss_pred HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHH----hhhcCCceeEEEEeecc-cccchhHHHHHHhh
Q 024646 129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILS----NLRSHDQVSSIFWLLHS-DLHEIKFTSVLEYL 203 (265)
Q Consensus 129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~----~Lr~~~~vssVl~LLHs-DLHe~~vv~ALe~L 203 (265)
-+....+.. + .++ -.|+|||++.++...+.. .-..+. .++. ..+..++. -|- +.-++.....++|+
T Consensus 110 ~i~~~~~~~----~-~~~-~~vvIDsl~~l~~~~~~~-~r~~~~~l~~~l~~-~~~tvil~-~~~~~~~~~~~~~~~~~l 180 (229)
T TIGR03881 110 KVIEAKKYL----G-YGH-ARLVIDSMSAFWLDKPAM-ARKYSYYLKRVLNR-WNFTILLT-SQYAITTSQAFGFGIEHV 180 (229)
T ss_pred HHHHHHHhh----c-cCc-eEEEecCchhhhccChHH-HHHHHHHHHHHHHh-CCCEEEEE-ecccccCCCCcccceEEE
Confidence 212222211 0 022 478999999998755432 122222 2333 23444443 342 22222222458999
Q ss_pred heeEEEeee
Q 024646 204 SSMVASVEP 212 (265)
Q Consensus 204 As~vv~v~P 212 (265)
+-.+|.++-
T Consensus 181 ~D~vI~L~~ 189 (229)
T TIGR03881 181 ADGIIRFRK 189 (229)
T ss_pred EeEEEEEEE
Confidence 999999874
No 12
>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=0.11 Score=43.46 Aligned_cols=136 Identities=19% Similarity=0.121 Sum_probs=81.6
Q ss_pred hccccceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhH
Q 024646 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (265)
Q Consensus 51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (265)
+..+++.+.++.+|-+++.+.+-+++.|++.+.+ ...+.+.|.+...+..... . ...++..
T Consensus 23 ~~~~g~~v~~~s~e~~~~~~~~~~~~~g~~~~~l~~~g~l~~~d~~~~~~s~~~~-~----------------~~~~~~~ 85 (187)
T cd01124 23 GLARGEPGLYVTLEESPEELIENAESLGWDLERLEDEGLLAIVDADPDEIGPAES-S----------------LRLELIQ 85 (187)
T ss_pred HHHCCCcEEEEECCCCHHHHHHHHHHcCCChHHHHhcCCeEEEecCccccchhhh-h----------------hhHHHHH
Confidence 3456889999999999999999999888875431 2346777755544421110 0 0001111
Q ss_pred HHHHHHHhccCccCCCCCcEEEEEechhHHHH---hcChHHHHHHHHhhhcCCceeEEEEeeccccc-c-hhHHHHHHhh
Q 024646 129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR---HASISSVAGILSNLRSHDQVSSIFWLLHSDLH-E-IKFTSVLEYL 203 (265)
Q Consensus 129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~---h~s~~~vc~lL~~Lr~~~~vssVl~LLHsDLH-e-~~vv~ALe~L 203 (265)
.+...+.. .++ -.|+||+++.++. ......+-.++..|++. .+. ++..-|..-. + ......++++
T Consensus 86 ~i~~~~~~-------~~~-~~lviD~~~~~~~~~~~~~~~~i~~l~~~l~~~-g~t-vi~v~~~~~~~~~~~~~~~~~~~ 155 (187)
T cd01124 86 RLKDAIEE-------FKA-KRVVIDSVSGLLLMEQSTARLEIRRLLFALKRF-GVT-TLLTSEQSGLEGTGFGGGDVEYL 155 (187)
T ss_pred HHHHHHHH-------hCC-CEEEEeCcHHHhhcChHHHHHHHHHHHHHHHHC-CCE-EEEEeccccCCCcccCcCceeEe
Confidence 11222221 123 5899999999987 44455566777787764 333 3333443222 1 2334678999
Q ss_pred heeEEEeeeC
Q 024646 204 SSMVASVEPF 213 (265)
Q Consensus 204 As~vv~v~P~ 213 (265)
+..++.++-.
T Consensus 156 aD~ii~l~~~ 165 (187)
T cd01124 156 VDGVIRLRLD 165 (187)
T ss_pred eeEEEEEEEE
Confidence 9999988754
No 13
>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=95.77 E-value=0.096 Score=52.02 Aligned_cols=138 Identities=19% Similarity=0.174 Sum_probs=83.2
Q ss_pred hhccc-cceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhh
Q 024646 50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (265)
Q Consensus 50 a~~~q-~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (265)
++..+ ++.+..++||-+|+++.+-+++.|+|-+.. ..++.++|.+..+ |..... + --++
T Consensus 44 ~g~~~~ge~~lyvs~eE~~~~l~~~~~~~G~~~~~~~~~g~l~~~~~~~~~--~~~~~~---------------~-~~~l 105 (484)
T TIGR02655 44 NGIIHFDEPGVFVTFEESPQDIIKNARSFGWDLQKLVDEGKLFILDASPDP--EGQDVV---------------G-GFDL 105 (484)
T ss_pred HHHHhCCCCEEEEEEecCHHHHHHHHHHcCCCHHHHhhcCceEEEecCchh--cccccc---------------c-cCCH
Confidence 45556 899999999999999999999999986531 3468888875433 222110 0 0123
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh-----HHHHHHHHhhhcCCceeEEEEeecccccchh-HHHHH
Q 024646 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-----SSVAGILSNLRSHDQVSSIFWLLHSDLHEIK-FTSVL 200 (265)
Q Consensus 127 ~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~-----~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~-vv~AL 200 (265)
..++..+.+... + +++ --|+|||++.+....+. ..+..+++.|++. .+..++.--+.+...+. ..+..
T Consensus 106 ~~~l~~i~~~ls---~-g~~-qRVvIDSl~aL~~~~~~~~~~r~~l~~Li~~L~~~-g~TvLLtsh~~~~~~~~~~~~~~ 179 (484)
T TIGR02655 106 SALIERINYAIR---K-YKA-KRVSIDSVTAVFQQYDAVSVVRREIFRLVARLKQI-GVTTVMTTERIEEYGPIARYGVE 179 (484)
T ss_pred HHHHHHHHHHHH---H-hCC-cEEEEeehhHhhhhcCchHHHHHHHHHHHHHHHHC-CCEEEEEecCcccccccccCCce
Confidence 333333333211 1 233 47999999998766554 2456677777653 45545543333332221 12234
Q ss_pred HhhheeEEEee
Q 024646 201 EYLSSMVASVE 211 (265)
Q Consensus 201 e~LAs~vv~v~ 211 (265)
+|++-.+|.+.
T Consensus 180 e~laDgVI~L~ 190 (484)
T TIGR02655 180 EFVSDNVVILR 190 (484)
T ss_pred eEeeeeEEEEE
Confidence 99999999886
No 14
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=95.40 E-value=0.069 Score=48.11 Aligned_cols=145 Identities=19% Similarity=0.240 Sum_probs=88.0
Q ss_pred hhccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhh
Q 024646 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (265)
Q Consensus 50 a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (265)
.++..++.+..+++|-+|+++.+-+++.|.|.+. -+..+.++|.++.+.+=..... .+..++.
T Consensus 46 ~~~~~ge~vlyvs~~e~~~~l~~~~~~~g~d~~~~~~~g~l~i~d~~~~~~~~~~~~~---------------~~~~~~~ 110 (260)
T COG0467 46 EGAREGEPVLYVSTEESPEELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLVSIVV---------------GDPLDLE 110 (260)
T ss_pred HHHhcCCcEEEEEecCCHHHHHHHHHHcCCCHHHHhhcCCEEEEEccccccccccccc---------------cCCccHH
Confidence 4555599999999999999999999999988753 2346889998888774322000 0112333
Q ss_pred HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHH-HHHHhhhcC-CceeEEEEeecccccchhHH--HHHHhh
Q 024646 128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVA-GILSNLRSH-DQVSSIFWLLHSDLHEIKFT--SVLEYL 203 (265)
Q Consensus 128 sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc-~lL~~Lr~~-~~vssVl~LLHsDLHe~~vv--~ALe~L 203 (265)
++...+.+..+ .-++ ..++|||++.+......+... ..+..|.+. ..-. +.+++.+|....... +-.+++
T Consensus 111 ~l~~~I~~~~~----~~~~-~~~ViDsi~~~~~~~~~~~~~r~~~~~l~~~~~~~~-~t~~~~~~~~~~~~~~~~~~~~~ 184 (260)
T COG0467 111 ELLDRIREIVE----KEGA-DRVVIDSITELTLYLNDPALVRRILLLLKRFLKKLG-VTSLLTTEAPVEERGESGVEEYI 184 (260)
T ss_pred HHHHHHHHHHH----HhCC-CEEEEeCCchHhhhcCchHHHHHHHHHHHHHHHhCC-CEEEEEecccccCCCccceEEEE
Confidence 33333333222 1122 689999999766666655553 444444442 1222 455555554332221 455668
Q ss_pred heeEEEeeeCCc
Q 024646 204 SSMVASVEPFNQ 215 (265)
Q Consensus 204 As~vv~v~P~~~ 215 (265)
+..+|.+.....
T Consensus 185 vdgvI~l~~~~~ 196 (260)
T COG0467 185 VDGVIRLDLKEI 196 (260)
T ss_pred EEEEEEEeeecc
Confidence 888888877544
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=95.35 E-value=0.13 Score=46.89 Aligned_cols=133 Identities=14% Similarity=0.107 Sum_probs=70.3
Q ss_pred hccccceeEEEEeeCChHH----HHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhh
Q 024646 51 GKSQSRGLVVVAYSRSPSF----YVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (265)
Q Consensus 51 ~~~q~~~Vhvl~fe~spe~----y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (265)
+..+++.+..+.+|-++++ +..-.++.|+|.+...++++++|..+.+.- . .++
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 4457899999999976654 333345667775544567888887653210 0 012
Q ss_pred hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH---HHHHHHHhhhcCCceeEEEEeeccccc---c-hhHHHH
Q 024646 127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS---SVAGILSNLRSHDQVSSIFWLLHSDLH---E-IKFTSV 199 (265)
Q Consensus 127 ~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~---~vc~lL~~Lr~~~~vssVl~LLHsDLH---e-~~vv~A 199 (265)
..++..+.+..+ +.++ =.||||||+.+.+..... .+.++++.|++...-.=++.-.+.+.. . +..-..
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 222222222111 1223 379999999876543221 223344555543332223333333221 1 111125
Q ss_pred HHhhheeEEEee
Q 024646 200 LEYLSSMVASVE 211 (265)
Q Consensus 200 Le~LAs~vv~v~ 211 (265)
++|++-.+|.+.
T Consensus 192 ~~~l~D~vI~L~ 203 (259)
T TIGR03878 192 VSHIVDGTIVLA 203 (259)
T ss_pred eeEeeccEEEEe
Confidence 899999999887
No 16
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=94.77 E-value=0.29 Score=43.93 Aligned_cols=130 Identities=13% Similarity=0.194 Sum_probs=74.7
Q ss_pred cccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHH
Q 024646 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY 130 (265)
Q Consensus 53 ~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~ 130 (265)
.+++.+..+.+|.+++++.+.+++.|+|.+. ....+.++++|..-.++. +.+..+
T Consensus 50 ~~g~~~~yi~~e~~~~~~~~~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~~-----------------------~~~~~l 106 (230)
T PRK08533 50 QNGYSVSYVSTQLTTTEFIKQMMSLGYDINKKLISGKLLYIPVYPLLSGNS-----------------------EKRKFL 106 (230)
T ss_pred hCCCcEEEEeCCCCHHHHHHHHHHhCCchHHHhhcCcEEEEEecccccChH-----------------------HHHHHH
Confidence 3568889999999999999999988887543 234677777763211111 111111
Q ss_pred HHHHHhccCccCCCCCcEEEEEechhHHHHhcC----hHHHHHHHHhhhcCCceeEEEEeecccccchhHHHHHHhhhee
Q 024646 131 SLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHAS----ISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSM 206 (265)
Q Consensus 131 ~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s----~~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~vv~ALe~LAs~ 206 (265)
..+.+..+ ..++ -.++||+++.++.... ...+.++|+.|++... .++-..|.+.-......-++|++-+
T Consensus 107 ~~il~~~~----~~~~-~~lVIDe~t~~l~~~~d~~~~~~l~~~l~~l~~~g~--tvi~t~~~~~~~~~~~~~~~~~~Dg 179 (230)
T PRK08533 107 KKLMNTRR----FYEK-DVIIIDSLSSLISNDASEVAVNDLMAFFKRISSLNK--VIILTANPKELDESVLTILRTAATM 179 (230)
T ss_pred HHHHHHHH----hcCC-CEEEEECccHHhcCCcchHHHHHHHHHHHHHHhCCC--EEEEEecccccccccceeEEEeeeE
Confidence 22222111 1123 3799999999985432 2456677777755322 2222222221112222357999999
Q ss_pred EEEeee
Q 024646 207 VASVEP 212 (265)
Q Consensus 207 vv~v~P 212 (265)
+|.+.-
T Consensus 180 vI~L~~ 185 (230)
T PRK08533 180 LIRLEV 185 (230)
T ss_pred EEEEEE
Confidence 998864
No 17
>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=94.33 E-value=0.56 Score=41.06 Aligned_cols=130 Identities=14% Similarity=0.194 Sum_probs=75.4
Q ss_pred hccccceeEEEEeeCChHHHHHHHhhcCCCccC-CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHH
Q 024646 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS-SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKL 129 (265)
Q Consensus 51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~-~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl 129 (265)
+..+++.+..+.+|-+++.+.+-++..|++.+. .++++.++|....-. ...+..+...
T Consensus 40 ~~~~g~~~~y~s~e~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---------------------~~~~~~l~~~ 98 (224)
T TIGR03880 40 GLKNGEKAMYISLEEREERILGYAKSKGWDLEDYIDKSLYIVRLDPSDF---------------------KTSLNRIKNE 98 (224)
T ss_pred HHhCCCeEEEEECCCCHHHHHHHHHHcCCChHHHHhCCeEEEecCHHHH---------------------HhhHHHHHHH
Confidence 345689999999999999999999888876543 122466776321100 0011222211
Q ss_pred HHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh-----HHHHHHHHhhhcCCceeEEEEeecccccch--hHHHHHHh
Q 024646 130 YSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-----SSVAGILSNLRSHDQVSSIFWLLHSDLHEI--KFTSVLEY 202 (265)
Q Consensus 130 ~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~-----~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~--~vv~ALe~ 202 (265)
+...++. .++ -.|+|||++.+-.-.+. ..+..++..|++. .+ .++..-|.+-..+ .....+++
T Consensus 99 ~~~~i~~-------~~~-~~vVIDsls~l~~~~~~~~~~r~~l~~l~~~lk~~-~~-tvll~s~~~~~~~~~~~~~~~~~ 168 (224)
T TIGR03880 99 LPILIKE-------LGA-SRVVIDPISLLETLFDDDAERRTELFRFYSSLRET-GV-TTILTSEADKTNVFASKYGLIEY 168 (224)
T ss_pred HHHHHHH-------hCC-CEEEEcChHHHhhhcCCHHHHHHHHHHHHHHHHhC-CC-EEEEEEcccCCCCCccCCCceEE
Confidence 1222221 123 36789999987221222 3566788888764 33 3444455443322 22355899
Q ss_pred hheeEEEee
Q 024646 203 LSSMVASVE 211 (265)
Q Consensus 203 LAs~vv~v~ 211 (265)
++..++.+.
T Consensus 169 l~D~vI~L~ 177 (224)
T TIGR03880 169 LADGVIILK 177 (224)
T ss_pred EEeEEEEEe
Confidence 999999994
No 18
>KOG4723 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.26 E-value=0.26 Score=45.28 Aligned_cols=72 Identities=19% Similarity=0.343 Sum_probs=56.0
Q ss_pred CCCCCceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEec
Q 024646 16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDC 93 (265)
Q Consensus 16 ge~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ 93 (265)
.|+--..+++|+..+|+ .-+|-|++. -..+++ +.+.+++|.++.+.|--.+++-|.|-.. .+.+++++|.
T Consensus 16 ~EqgkltLl~d~~eT~g-sFl~H~~l~---~~Lkan----~~~cFlaf~k~fshy~i~~rKlG~~l~t~k~rgqlvF~dg 87 (248)
T KOG4723|consen 16 PEQGKLTLLLDTRETPG-SFLFHYYLY---HALKAN----ESTCFLAFSKTFSHYAISMRKLGMDLKTKKNRGQLVFIDG 87 (248)
T ss_pred CCCccEEEEeecccCCc-eeeHHHHHH---HHHhcC----CcEEEEEeecchhHHHHHHHHhCCceeecccCCcEEEEhh
Confidence 46667899999999985 666666442 222222 8999999999999999999999998776 2335999998
Q ss_pred cC
Q 024646 94 YT 95 (265)
Q Consensus 94 ys 95 (265)
++
T Consensus 88 l~ 89 (248)
T KOG4723|consen 88 LS 89 (248)
T ss_pred hh
Confidence 87
No 19
>PRK05973 replicative DNA helicase; Provisional
Probab=93.33 E-value=1.8 Score=39.75 Aligned_cols=62 Identities=13% Similarity=-0.025 Sum_probs=40.1
Q ss_pred cCCCCCceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccC
Q 024646 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS 83 (265)
Q Consensus 15 ~ge~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~ 83 (265)
.|=.++.+++---=...|=+.+..+++. .+..+++.|.++.||-+++++.+=++..|+|.+.
T Consensus 59 GGl~~Gsl~LIaG~PG~GKT~lalqfa~-------~~a~~Ge~vlyfSlEes~~~i~~R~~s~g~d~~~ 120 (237)
T PRK05973 59 SQLKPGDLVLLGARPGHGKTLLGLELAV-------EAMKSGRTGVFFTLEYTEQDVRDRLRALGADRAQ 120 (237)
T ss_pred CCCCCCCEEEEEeCCCCCHHHHHHHHHH-------HHHhcCCeEEEEEEeCCHHHHHHHHHHcCCChHH
Confidence 4555554444322233333444444332 2345688999999999999999999999988655
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=93.02 E-value=0.89 Score=39.09 Aligned_cols=38 Identities=13% Similarity=0.261 Sum_probs=26.5
Q ss_pred cccceeEEEEeeC-ChHHHHHHHhhcCCCccCCCCeEEEEec
Q 024646 53 SQSRGLVVVAYSR-SPSFYVDLLKRRGIDIASSHDWIHILDC 93 (265)
Q Consensus 53 ~q~~~Vhvl~fe~-spe~y~~~lk~~G~d~~~~~~~v~i~D~ 93 (265)
.+++.+..+.+|. +++.+.+.++.. ++ ....+++++++
T Consensus 38 ~~g~~v~yi~~e~~~~~rl~~~~~~~-~~--~~~~~i~~~~~ 76 (209)
T TIGR02237 38 RQGKKVVYIDTEGLSPERFKQIAEDR-PE--RALSNFIVFEV 76 (209)
T ss_pred hCCCeEEEEECCCCCHHHHHHHHHhC-hH--HHhcCEEEEEC
Confidence 3478899999996 888888866643 11 11456888776
No 21
>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=91.66 E-value=0.39 Score=46.42 Aligned_cols=69 Identities=23% Similarity=0.228 Sum_probs=49.1
Q ss_pred EEEEEechhHHHHhcC----hHHHHHHHHhhhc----CCceeEEEEeeccccc--chhHHHHHHhhheeEEEeeeCCcc
Q 024646 148 FSIAIDSVSEMVRHAS----ISSVAGILSNLRS----HDQVSSIFWLLHSDLH--EIKFTSVLEYLSSMVASVEPFNQA 216 (265)
Q Consensus 148 ~~VaIDSLS~LL~h~s----~~~vc~lL~~Lr~----~~~vssVl~LLHsDLH--e~~vv~ALe~LAs~vv~v~P~~~~ 216 (265)
.=|+|-||..-+-..+ ...+.+||+.||. +..-..++.-+=.+|- .+..+..|++++-++|.|+|....
T Consensus 202 ~RI~I~sl~SP~w~~~~~~~~~~ll~FL~~LR~LlR~~~s~~v~~iTlP~~L~~~~~~~~~~l~~l~D~vi~Le~F~~~ 280 (363)
T PF05625_consen 202 LRIVIPSLGSPLWYPPSASQPSELLRFLHSLRALLRKYSSNAVAMITLPSHLYPRSPSLVRRLEHLADGVIELESFAGS 280 (363)
T ss_dssp EEEEETTTT-TTTS-GGGGBHHHHHHHHHHHHHHHHHTTTTEEEEEEEEGTTS---HHHHHHHHHHSSEEEEEEE--HH
T ss_pred EEEEEcCCCCcccCCcccccHHHHHHHHHHHHHHHhccCCCEEEEEEECHHHhccChHHHHHHHHhCCEEEEeecCCCc
Confidence 6788887766443322 2248999999987 3445555556678887 799999999999999999999876
No 22
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=90.71 E-value=3.9 Score=38.17 Aligned_cols=39 Identities=21% Similarity=0.269 Sum_probs=30.4
Q ss_pred ceeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (265)
Q Consensus 56 ~~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~y 94 (265)
..+..+.+|. +|+.+.+.+++.|+|.+..-+++++++++
T Consensus 137 ~~~~yi~te~~f~~~rl~~~~~~~g~~~~~~l~~i~~~~~~ 177 (317)
T PRK04301 137 GKAVYIDTEGTFRPERIEQMAEALGLDPDEVLDNIHVARAY 177 (317)
T ss_pred ceEEEEeCCCCcCHHHHHHHHHHcCCChHhhhccEEEEeCC
Confidence 5889999998 68999999988888865544567777654
No 23
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=90.22 E-value=9.1 Score=37.27 Aligned_cols=115 Identities=21% Similarity=0.177 Sum_probs=62.6
Q ss_pred ccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHHH
Q 024646 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (265)
Q Consensus 54 q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~ 133 (265)
+++.|..+.+|-+++....-.++-|++. .++.+.+. .++..++..+
T Consensus 109 ~g~~VlYvs~EEs~~qi~~Ra~rlg~~~----~~l~l~~e------------------------------~~le~I~~~i 154 (372)
T cd01121 109 RGGKVLYVSGEESPEQIKLRADRLGIST----ENLYLLAE------------------------------TNLEDILASI 154 (372)
T ss_pred cCCeEEEEECCcCHHHHHHHHHHcCCCc----ccEEEEcc------------------------------CcHHHHHHHH
Confidence 4568888999999888776666666652 23333210 0122222222
Q ss_pred HHhccCccCCCCCcEEEEEechhHHHHhc------ChHHHHHHHHhhhc---CCceeEE-EEeecccccchhHHHHHHhh
Q 024646 134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA------SISSVAGILSNLRS---HDQVSSI-FWLLHSDLHEIKFTSVLEYL 203 (265)
Q Consensus 134 ~e~~~~~~~~~k~r~~VaIDSLS~LL~h~------s~~~vc~lL~~Lr~---~~~vssV-l~LLHsDLHe~~vv~ALe~L 203 (265)
.+ .++ -.|+|||++.+.... +..++-..+..|.+ ...+.-+ ++-+..|-+-.+ .+.|+|+
T Consensus 155 ~~--------~~~-~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~lak~~~itvilvghvtk~g~~aG-~~~leh~ 224 (372)
T cd01121 155 EE--------LKP-DLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMRFAKERNIPIFIVGHVTKEGSIAG-PKVLEHM 224 (372)
T ss_pred Hh--------cCC-cEEEEcchHHhhccccccCCCCHHHHHHHHHHHHHHHHHcCCeEEEEeeccCCCcccC-cccchhh
Confidence 21 234 479999999986532 23444444444433 2223322 222333322222 2579999
Q ss_pred heeEEEeee
Q 024646 204 SSMVASVEP 212 (265)
Q Consensus 204 As~vv~v~P 212 (265)
+.+++.++-
T Consensus 225 vD~Vi~le~ 233 (372)
T cd01121 225 VDTVLYFEG 233 (372)
T ss_pred ceEEEEEEc
Confidence 999998874
No 24
>PRK11823 DNA repair protein RadA; Provisional
Probab=90.12 E-value=8.2 Score=38.29 Aligned_cols=116 Identities=22% Similarity=0.176 Sum_probs=63.6
Q ss_pred cccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHH
Q 024646 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (265)
Q Consensus 53 ~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~ 132 (265)
.+++.|..+.+|-+++.+..-.++.|++. +++.+.+ + .++..+...
T Consensus 106 ~~g~~vlYvs~Ees~~qi~~ra~rlg~~~----~~l~~~~----e--------------------------~~l~~i~~~ 151 (446)
T PRK11823 106 AAGGKVLYVSGEESASQIKLRAERLGLPS----DNLYLLA----E--------------------------TNLEAILAT 151 (446)
T ss_pred hcCCeEEEEEccccHHHHHHHHHHcCCCh----hcEEEeC----C--------------------------CCHHHHHHH
Confidence 35778999999999988877677777752 2333211 0 012222222
Q ss_pred HHHhccCccCCCCCcEEEEEechhHHHHh------cChHHHHHHHHhhhc---CCceeEEE-EeecccccchhHHHHHHh
Q 024646 133 IIEQGKGLIGQGKDRFSIAIDSVSEMVRH------ASISSVAGILSNLRS---HDQVSSIF-WLLHSDLHEIKFTSVLEY 202 (265)
Q Consensus 133 ~~e~~~~~~~~~k~r~~VaIDSLS~LL~h------~s~~~vc~lL~~Lr~---~~~vssVl-~LLHsDLHe~~vv~ALe~ 202 (265)
+.+ .++ -.|+|||++.+... .+..++-..+..|.+ ...+.-++ +-+..|-+-.+. ..++|
T Consensus 152 i~~--------~~~-~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~~ak~~~itvilv~hvtk~~~~ag~-~~leh 221 (446)
T PRK11823 152 IEE--------EKP-DLVVIDSIQTMYSPELESAPGSVSQVRECAAELMRLAKQRGIAVFLVGHVTKEGAIAGP-RVLEH 221 (446)
T ss_pred HHh--------hCC-CEEEEechhhhccccccCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEeeccCCCCcCCc-chhhh
Confidence 222 234 47999999998652 123444444444443 12233222 223333222222 56999
Q ss_pred hheeEEEeee
Q 024646 203 LSSMVASVEP 212 (265)
Q Consensus 203 LAs~vv~v~P 212 (265)
++.+++.++-
T Consensus 222 lvD~Vi~le~ 231 (446)
T PRK11823 222 MVDTVLYFEG 231 (446)
T ss_pred hCeEEEEEEc
Confidence 9999998873
No 25
>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=89.31 E-value=9.7 Score=32.90 Aligned_cols=127 Identities=15% Similarity=0.114 Sum_probs=67.0
Q ss_pred ceeEEEEeeCC--hHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHHH
Q 024646 56 RGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (265)
Q Consensus 56 ~~Vhvl~fe~s--pe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~ 133 (265)
..|..+..|.+ ++.+.+.....+.+.+...+++.+.++++ + .++...+..+
T Consensus 54 ~~v~yi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~~-~--------------------------~~~~~~l~~~ 106 (226)
T cd01393 54 GKVVYIDTEGAFRPERLVQLAVRFGLDPEEVLDNIYVARPYN-G--------------------------EQQLEIVEEL 106 (226)
T ss_pred ceEEEEecCCCCCHHHHHHHHHHhccchhhhhccEEEEeCCC-H--------------------------HHHHHHHHHH
Confidence 67888888876 66777767776666544345677777631 1 1222222222
Q ss_pred HHhccCccCCCCCcEEEEEechhHHHHhc--Ch-------HHHHHHHHhhhc----CCceeEEEEeeccccc-----chh
Q 024646 134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA--SI-------SSVAGILSNLRS----HDQVSSIFWLLHSDLH-----EIK 195 (265)
Q Consensus 134 ~e~~~~~~~~~k~r~~VaIDSLS~LL~h~--s~-------~~vc~lL~~Lr~----~~~vssVl~LLHsDLH-----e~~ 195 (265)
.+.. ...+. -.|+||||+.+.+.. +- ..+.++++.|++ +....=++.-+..+.- ...
T Consensus 107 ~~~~----~~~~~-~lvVIDsis~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~~~vi~tnq~~~~~~~~~~~~~~ 181 (226)
T cd01393 107 ERIM----SSGRV-DLVVVDSVAALFRKEFIGRGMLAERARLLSQALRKLLRLADKFNVAVVFTNQVRAKVDVMFGDPET 181 (226)
T ss_pred HHHh----hcCCe-eEEEEcCcchhhhhhhcCCchHHHHHHHHHHHHHHHHHHHHHhCcEEEEEEEEeeecccccCCCcc
Confidence 2211 11233 589999999987642 11 233444444443 2211111222222221 122
Q ss_pred HH--HHHHhhheeEEEeeeCC
Q 024646 196 FT--SVLEYLSSMVASVEPFN 214 (265)
Q Consensus 196 vv--~ALe~LAs~vv~v~P~~ 214 (265)
+. .+++|.+++.+.++...
T Consensus 182 p~~G~~~~~~~~~ri~l~~~~ 202 (226)
T cd01393 182 PAGGNALAHASTTRLDLRKGR 202 (226)
T ss_pred ccCchhhhCcccEEEEEEecC
Confidence 33 68899999988887533
No 26
>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=88.80 E-value=5.1 Score=37.04 Aligned_cols=38 Identities=18% Similarity=0.279 Sum_probs=28.9
Q ss_pred eeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646 57 GLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (265)
Q Consensus 57 ~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~y 94 (265)
.++.+.+|- +|+.+.+.++..|++.+...+++.+..++
T Consensus 131 ~~~yi~te~~f~~~rl~~~~~~~gl~~~~~~~~i~i~~~~ 170 (310)
T TIGR02236 131 KAVYIDTENTFRPERIMQMAEARGLDPDEVLKNIYVARAY 170 (310)
T ss_pred eEEEEECCCCCCHHHHHHHHHHcCCCHHHHhhceEEEecC
Confidence 788888888 78899999988888764434567776653
No 27
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=88.23 E-value=9.5 Score=33.24 Aligned_cols=65 Identities=23% Similarity=0.176 Sum_probs=38.1
Q ss_pred EEEEEechhHHHHhc-----C----hHHHHHHHHhhhc----CCceeEEEEeecccccc----hhHHHHHHhhheeEEEe
Q 024646 148 FSIAIDSVSEMVRHA-----S----ISSVAGILSNLRS----HDQVSSIFWLLHSDLHE----IKFTSVLEYLSSMVASV 210 (265)
Q Consensus 148 ~~VaIDSLS~LL~h~-----s----~~~vc~lL~~Lr~----~~~vssVl~LLHsDLHe----~~vv~ALe~LAs~vv~v 210 (265)
=.|+||||+.+.+.. . ...+.+.++.|++ +....=+..-++.+.+. +---..++|++++++.+
T Consensus 109 ~lvVIDsi~al~~~~~~~~~~~~~~~~~l~~~l~~L~~~a~~~~v~vi~tnq~~~~~~~~~~~~~gg~~~~~~~d~ii~l 188 (225)
T PRK09361 109 GLIVLDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHDLAVVITNQVYSDIDSDGLRPLGGHTLEHWSKTILRL 188 (225)
T ss_pred cEEEEeCcHHHhHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhCCEEEEEccceecCCCCcccCCCcchhhhhccEEEEE
Confidence 489999999987642 1 1234554444433 33333333444445442 21123789999999999
Q ss_pred ee
Q 024646 211 EP 212 (265)
Q Consensus 211 ~P 212 (265)
+.
T Consensus 189 ~~ 190 (225)
T PRK09361 189 EK 190 (225)
T ss_pred EE
Confidence 76
No 28
>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
Probab=87.26 E-value=5.4 Score=34.69 Aligned_cols=40 Identities=23% Similarity=0.284 Sum_probs=30.6
Q ss_pred cceeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (265)
Q Consensus 55 ~~~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~y 94 (265)
.+++..+.+|. +++.+.+.+++.|.+....-+++++.++|
T Consensus 53 ~~~viyi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~ 94 (235)
T cd01123 53 EGKAVYIDTEGTFRPERLVQIAERFGLDPEEVLDNIYVARAY 94 (235)
T ss_pred CccEEEEeCCCCcCHHHHHHHHHHhccChHhHhcCEEEEecC
Confidence 36888888888 57888888888888766556678877764
No 29
>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=85.63 E-value=26 Score=31.27 Aligned_cols=21 Identities=5% Similarity=-0.113 Sum_probs=17.7
Q ss_pred cceeEEEEeeCChHHHHHHHh
Q 024646 55 SRGLVVVAYSRSPSFYVDLLK 75 (265)
Q Consensus 55 ~~~Vhvl~fe~spe~y~~~lk 75 (265)
+..|.++.+|-++++...-+.
T Consensus 59 g~~vl~iS~E~~~~~~~~r~~ 79 (271)
T cd01122 59 GVRVGTISLEEPVVRTARRLL 79 (271)
T ss_pred CceEEEEEcccCHHHHHHHHH
Confidence 789999999999988877553
No 30
>PTZ00035 Rad51 protein; Provisional
Probab=83.76 E-value=23 Score=33.93 Aligned_cols=40 Identities=20% Similarity=0.272 Sum_probs=28.4
Q ss_pred cceeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (265)
Q Consensus 55 ~~~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~y 94 (265)
+..+..+..|. +|+...+..++.|++.+..-.++.+.++|
T Consensus 152 ~g~vvyIdtE~~f~~eri~~ia~~~g~~~~~~l~nI~~~~~~ 193 (337)
T PTZ00035 152 EGKVLYIDTEGTFRPERIVQIAERFGLDPEDVLDNIAYARAY 193 (337)
T ss_pred CceEEEEEccCCCCHHHHHHHHHHhCCChHhHhhceEEEccC
Confidence 44677888887 48888888888888766544566666544
No 31
>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=83.26 E-value=1.6 Score=38.29 Aligned_cols=67 Identities=18% Similarity=0.119 Sum_probs=39.1
Q ss_pred EEEEEechhHHHHhc----ChHHHHHHHHhhhcC-CceeEEEEeecc------c-------ccchhHHHHHHhhheeEEE
Q 024646 148 FSIAIDSVSEMVRHA----SISSVAGILSNLRSH-DQVSSIFWLLHS------D-------LHEIKFTSVLEYLSSMVAS 209 (265)
Q Consensus 148 ~~VaIDSLS~LL~h~----s~~~vc~lL~~Lr~~-~~vssVl~LLHs------D-------LHe~~vv~ALe~LAs~vv~ 209 (265)
-.|+||+|+.+-... .-..+..++..|+.- .+....+++++. + ++.-+-.+++++.|.+++.
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 123445556666641 223333444441 1 2233344788999999999
Q ss_pred eeeCC
Q 024646 210 VEPFN 214 (265)
Q Consensus 210 v~P~~ 214 (265)
+.+..
T Consensus 205 l~~~~ 209 (242)
T cd00984 205 LYRDE 209 (242)
T ss_pred Eeccc
Confidence 98753
No 32
>PF03192 DUF257: Pyrococcus protein of unknown function, DUF257; InterPro: IPR005489 This family of proteins is of unknown function.; PDB: 2EKD_C.
Probab=81.67 E-value=34 Score=30.91 Aligned_cols=153 Identities=17% Similarity=0.265 Sum_probs=89.6
Q ss_pred ceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEE----------
Q 024646 21 ALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHI---------- 90 (265)
Q Consensus 21 ~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i---------- 90 (265)
+++||-+-.++ +.++ ++..+..++.++-.|.|..+=-+-..|..-|+..|+|.+. -+++.+
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 56787766333 3333 4455666777888899988888888999999999999765 122333
Q ss_pred -----EeccCCCCCCcccccCccccccccccccccccchhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHH--HhcC
Q 024646 91 -----LDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMV--RHAS 163 (265)
Q Consensus 91 -----~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL--~h~s 163 (265)
++..+||--|. +.+..+.+.. .. +.+++..+=-+.-++ ...+
T Consensus 84 nVv~ri~~~~d~~~~~--------------------------k~Y~~~~~~~---~~--~~~~i~ivlGiekl~~~~~~~ 132 (210)
T PF03192_consen 84 NVVGRIPITSDPSVYL--------------------------KEYEEILEKV---LE--KEKVINIVLGIEKLFYFFENS 132 (210)
T ss_dssp EEEEEE-----BBTTB--------------------------HHHHHHHTT--------S-SEEEEEE-HHHHH-HH-S-
T ss_pred eEEEEEecccChHHHH--------------------------HHHHHHHHHH---hc--cCCeEEEEecHHHHHHHHhcc
Confidence 33333333222 2223333321 11 222455555666666 4478
Q ss_pred hHHHHHHHHhhhcC--CceeEEEEeecccccch---hHHHHHHhhheeEEEeeeC
Q 024646 164 ISSVAGILSNLRSH--DQVSSIFWLLHSDLHEI---KFTSVLEYLSSMVASVEPF 213 (265)
Q Consensus 164 ~~~vc~lL~~Lr~~--~~vssVl~LLHsDLHe~---~vv~ALe~LAs~vv~v~P~ 213 (265)
..++..++..+.+. ..=..-|..++.|+-+. .+...||-+||+|+.++..
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 23345688999999986 8888999999999999875
No 33
>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=81.14 E-value=22 Score=33.72 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=31.8
Q ss_pred ccceeEEEEeeCC--hHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646 54 QSRGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCY 94 (265)
Q Consensus 54 q~~~Vhvl~fe~s--pe~y~~~lk~~G~d~~~~~~~v~i~D~y 94 (265)
.+..+..+..|-+ |+.+.+.+++.|+|++..-+++.+.++|
T Consensus 129 ~~~~vvYIdtE~~f~~eRi~~~a~~~g~d~~~~l~~i~~~~~~ 171 (313)
T TIGR02238 129 GNGKVAYIDTEGTFRPDRIRAIAERFGVDPDAVLDNILYARAY 171 (313)
T ss_pred CCCeEEEEEcCCCCCHHHHHHHHHHcCCChHHhcCcEEEecCC
Confidence 3568899999995 9999999999999876645667766554
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=80.31 E-value=49 Score=31.33 Aligned_cols=125 Identities=12% Similarity=0.113 Sum_probs=67.8
Q ss_pred ceeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHHH
Q 024646 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (265)
Q Consensus 56 ~~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~ 133 (265)
..+..+.+|. +|+-+.+..++.|++++..-.++++.++|+ + .++..++...
T Consensus 131 ~~vvyIdtE~~f~~~Rl~~ia~~~~~~~~~~l~~i~~~~~~~-~--------------------------~~~~~~l~~~ 183 (316)
T TIGR02239 131 GKALYIDTEGTFRPERLLAIAERYGLNPEDVLDNVAYARAYN-T--------------------------DHQLQLLQQA 183 (316)
T ss_pred ceEEEEECCCCCCHHHHHHHHHHcCCChHHhhccEEEEecCC-h--------------------------HHHHHHHHHH
Confidence 3677888888 687788888888887655445566665431 0 1111111222
Q ss_pred HHhccCccCCCCCcEEEEEechhHHHHhcC-----h----HHHHHHHHhhhc----CCceeEEEEeeccccc--------
Q 024646 134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHAS-----I----SSVAGILSNLRS----HDQVSSIFWLLHSDLH-------- 192 (265)
Q Consensus 134 ~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s-----~----~~vc~lL~~Lr~----~~~vssVl~LLHsDLH-------- 192 (265)
.+... ..+. -.|+|||++.+.+..- . ..+.++++.|++ +....=+..-+.+|.-
T Consensus 184 ~~~~~----~~~~-~LvVIDSI~al~r~~~~~~~~~~~rq~~l~~~~~~L~~la~~~~vavv~tNqv~~~~~~~~~~~~g 258 (316)
T TIGR02239 184 AAMMS----ESRF-ALLIVDSATALYRTDFSGRGELSARQMHLARFLRSLQRLADEFGVAVVITNQVVAQVDGAGSMFAG 258 (316)
T ss_pred HHhhc----cCCc-cEEEEECcHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHHHHhCCEEEEECceEEecCCccccccC
Confidence 22111 1233 4799999999976421 1 123455556654 2222222222222222
Q ss_pred ---chhHHHHHHhhheeEEEeee
Q 024646 193 ---EIKFTSVLEYLSSMVASVEP 212 (265)
Q Consensus 193 ---e~~vv~ALe~LAs~vv~v~P 212 (265)
.|--=.+++|.+++.+.++-
T Consensus 259 ~~~~p~gG~~~~h~~~~ri~l~k 281 (316)
T TIGR02239 259 DPKKPIGGNIMAHASTTRLSLRK 281 (316)
T ss_pred CCCcCCchHHHHhhccEEEEEEe
Confidence 12223588999999999984
No 35
>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=80.04 E-value=31 Score=29.77 Aligned_cols=64 Identities=23% Similarity=0.127 Sum_probs=35.9
Q ss_pred EEEEEechhHHHHhcCh---------HHHHHHHHhhhc----CCceeEEEEeeccccc----chhHHHHHHhhheeEEEe
Q 024646 148 FSIAIDSVSEMVRHASI---------SSVAGILSNLRS----HDQVSSIFWLLHSDLH----EIKFTSVLEYLSSMVASV 210 (265)
Q Consensus 148 ~~VaIDSLS~LL~h~s~---------~~vc~lL~~Lr~----~~~vssVl~LLHsDLH----e~~vv~ALe~LAs~vv~v 210 (265)
-.|+|||++.+.+..-. ..+.+.++.|+. +....=+.+-+..+.. .|.--..++|++.+++.+
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 48999999999653211 144555544443 3333323333333332 122223689999999999
Q ss_pred e
Q 024646 211 E 211 (265)
Q Consensus 211 ~ 211 (265)
+
T Consensus 185 ~ 185 (218)
T cd01394 185 E 185 (218)
T ss_pred E
Confidence 6
No 36
>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=79.89 E-value=8 Score=32.61 Aligned_cols=50 Identities=22% Similarity=0.271 Sum_probs=36.3
Q ss_pred chhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC
Q 024646 123 VRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH 177 (265)
Q Consensus 123 v~~L~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~~ 177 (265)
+.+|..+...+.+-- .+.+. -+|+||++=-|+.++|+..+..+|+.|+-+
T Consensus 57 Pt~L~~l~~~i~~fl----~~~~~-~vViiD~lEYL~l~NgF~~v~KFL~~LkD~ 106 (136)
T PF05763_consen 57 PTNLHKLLDTIVRFL----KENGN-GVVIIDGLEYLILENGFESVLKFLASLKDY 106 (136)
T ss_pred chhhHHHHHHHHHHH----HhCCC-cEEEEecHHHHHHHcCHHHHHHHHHHhHHH
Confidence 345555545555422 22111 499999999999999999999999999964
No 37
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=76.22 E-value=22 Score=34.36 Aligned_cols=39 Identities=21% Similarity=0.256 Sum_probs=31.0
Q ss_pred ceeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (265)
Q Consensus 56 ~~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~y 94 (265)
..+..+.+|. +|+-+.+..++.|+|++..-++|.+.++|
T Consensus 161 ~~vvyIdTE~tF~peRl~~ia~~~g~d~~~~l~~I~~~~~~ 201 (344)
T PLN03187 161 GKVAYIDTEGTFRPDRIVPIAERFGMDADAVLDNIIYARAY 201 (344)
T ss_pred ceEEEEEcCCCCCHHHHHHHHHHcCCChhhhcCeEEEecCC
Confidence 5789999998 69999999999999876645667766654
No 38
>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=65.07 E-value=33 Score=31.38 Aligned_cols=41 Identities=20% Similarity=0.300 Sum_probs=29.1
Q ss_pred cceeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEeccC
Q 024646 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYT 95 (265)
Q Consensus 55 ~~~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~ys 95 (265)
+..|+.+..|. +++-+.+.+++++++.+..-++|++..+|+
T Consensus 72 ~~~vvyidTe~~f~~~Rl~~i~~~~~~~~~~~l~~I~v~~~~~ 114 (256)
T PF08423_consen 72 GGKVVYIDTEGTFSPERLQQIAERFGLDPEEILDNIFVIRVFD 114 (256)
T ss_dssp SSEEEEEESSSSS-HHHHHHHHHHTTS-HHHHHHTEEEEE-SS
T ss_pred CCceEEEeCCCCCCHHHHHHHhhccccccchhhhceeeeecCC
Confidence 45688888887 688899999998887665456788877653
No 39
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=64.99 E-value=1.4e+02 Score=28.91 Aligned_cols=124 Identities=10% Similarity=0.134 Sum_probs=70.0
Q ss_pred eeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHHHH
Q 024646 57 GLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLII 134 (265)
Q Consensus 57 ~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~~ 134 (265)
.+..+.+|. +|+-..+..++.|+|.+..-+++++.++|+ .. ++..++....
T Consensus 159 ~vlyIdtE~~f~~eRl~qia~~~~~~~~~~l~~i~~~~~~~----~e-----------------------~~~~ll~~~~ 211 (342)
T PLN03186 159 KAMYIDTEGTFRPQRLIQIAERFGLNGADVLENVAYARAYN----TD-----------------------HQSELLLEAA 211 (342)
T ss_pred eEEEEECCCCccHHHHHHHHHHcCCChhhhccceEEEecCC----HH-----------------------HHHHHHHHHH
Confidence 689999999 688899999988888655445676666541 11 1111111111
Q ss_pred HhccCccCCCCCcEEEEEechhHHHHhc--C---h----HHHHHHHHhhhc----CCceeEEEEeeccccc------chh
Q 024646 135 EQGKGLIGQGKDRFSIAIDSVSEMVRHA--S---I----SSVAGILSNLRS----HDQVSSIFWLLHSDLH------EIK 195 (265)
Q Consensus 135 e~~~~~~~~~k~r~~VaIDSLS~LL~h~--s---~----~~vc~lL~~Lr~----~~~vssVl~LLHsDLH------e~~ 195 (265)
... .+.+. -.|+|||++.+.+.. + . ..+.++++.|++ +....=+..-+.++.. .|+
T Consensus 212 ~~~----~~~~~-~LIVIDSI~alfr~~~~~~g~l~~r~~~L~~~l~~L~~lA~~~~vaVviTNqv~~~~~~~~~~~~~~ 286 (342)
T PLN03186 212 SMM----AETRF-ALMIVDSATALYRTEFSGRGELSARQMHLGKFLRSLQRLADEFGVAVVITNQVVAQVDGSAFFAGPQ 286 (342)
T ss_pred HHh----hccCC-CEEEEeCcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHcCCEEEEEcCEEEccCCccccCCCc
Confidence 110 11233 479999999998742 1 1 124566666665 3222222233333332 222
Q ss_pred HH----HHHHhhheeEEEeee
Q 024646 196 FT----SVLEYLSSMVASVEP 212 (265)
Q Consensus 196 vv----~ALe~LAs~vv~v~P 212 (265)
+. .+++|.+++.+.++-
T Consensus 287 ~~P~gG~~~~h~~~tRl~L~k 307 (342)
T PLN03186 287 LKPIGGNIMAHASTTRLALRK 307 (342)
T ss_pred cccchhHHHHhhccEEEEEEe
Confidence 11 388999999999974
No 40
>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=63.77 E-value=90 Score=31.19 Aligned_cols=114 Identities=18% Similarity=0.119 Sum_probs=60.9
Q ss_pred ccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHHH
Q 024646 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (265)
Q Consensus 54 q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~ 133 (265)
+++.|..+.+|-+++.+..-.++.|++ .+++.+++. . ++..+...+
T Consensus 121 ~g~kvlYvs~EEs~~qi~~ra~rlg~~----~~~l~~~~e----~--------------------------~~~~I~~~i 166 (454)
T TIGR00416 121 NQMKVLYVSGEESLQQIKMRAIRLGLP----EPNLYVLSE----T--------------------------NWEQICANI 166 (454)
T ss_pred cCCcEEEEECcCCHHHHHHHHHHcCCC----hHHeEEcCC----C--------------------------CHHHHHHHH
Confidence 456788899998888777655566665 233444331 0 112221222
Q ss_pred HHhccCccCCCCCcEEEEEechhHHHHhc------ChHHHHHHHHhhhc---CCceeEEEEeecccccc--hhHHHHHHh
Q 024646 134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA------SISSVAGILSNLRS---HDQVSSIFWLLHSDLHE--IKFTSVLEY 202 (265)
Q Consensus 134 ~e~~~~~~~~~k~r~~VaIDSLS~LL~h~------s~~~vc~lL~~Lr~---~~~vssVl~LLHsDLHe--~~vv~ALe~ 202 (265)
.+ .++ -.|+|||++.+.... +..++-..+..|.+ ...+..++- -|-.-.+ .++ ..++|
T Consensus 167 ~~--------~~~-~~vVIDSIq~l~~~~~~~~~g~~~q~r~~~~~L~~~ak~~giTvllt-~hvtkeg~~aG~-~~le~ 235 (454)
T TIGR00416 167 EE--------ENP-QACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIV-GHVTKEGSIAGP-KVLEH 235 (454)
T ss_pred Hh--------cCC-cEEEEecchhhcccccccCCCCHHHHHHHHHHHHHHHHHhCCEEEEE-eccccCCccCCc-ccEee
Confidence 22 234 369999999986421 23444443333333 233443332 2322111 122 46899
Q ss_pred hheeEEEeee
Q 024646 203 LSSMVASVEP 212 (265)
Q Consensus 203 LAs~vv~v~P 212 (265)
++.+++.++-
T Consensus 236 lvD~VI~Le~ 245 (454)
T TIGR00416 236 MVDTVLYFEG 245 (454)
T ss_pred eceEEEEEec
Confidence 9999999874
No 41
>PRK09354 recA recombinase A; Provisional
Probab=63.76 E-value=61 Score=31.60 Aligned_cols=43 Identities=12% Similarity=0.062 Sum_probs=28.2
Q ss_pred CCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCc
Q 024646 30 SPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDI 81 (265)
Q Consensus 30 ~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~ 81 (265)
..+=+.+..|++.+ ...++..+..+.+|-+++. +.+++.|+|.
T Consensus 70 GsGKTtLal~~~~~-------~~~~G~~~~yId~E~s~~~--~~a~~lGvdl 112 (349)
T PRK09354 70 SSGKTTLALHAIAE-------AQKAGGTAAFIDAEHALDP--VYAKKLGVDI 112 (349)
T ss_pred CCCHHHHHHHHHHH-------HHHcCCcEEEECCccchHH--HHHHHcCCCH
Confidence 33445566665432 2346788999999998874 5567778873
No 42
>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=60.83 E-value=1.2e+02 Score=26.81 Aligned_cols=141 Identities=14% Similarity=0.068 Sum_probs=69.9
Q ss_pred ccceeEEEEeeCChHHHHHHHhhcCCCc--cCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHH
Q 024646 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDI--ASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYS 131 (265)
Q Consensus 54 q~~~Vhvl~fe~spe~y~~~lk~~G~d~--~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~ 131 (265)
+...|.+++.|-++++..+=++..+..- +....++.+.+....|+.+..... . .....+.
T Consensus 40 ~~~~Vlyi~~Ed~~~~i~~Rl~~i~~~~~~~~~~~rl~~~~g~~~~l~~~~~~~-----------~---~~~~~~~---- 101 (239)
T cd01125 40 EPGRVVYLSAEDPREEIHRRLEAILQHLEPDDAGDRLFIDSGRIQPISIAREGR-----------I---IVVPEFE---- 101 (239)
T ss_pred CCceEEEEECCCCHHHHHHHHHHHHhhcCCcCcccceEEeccCCCceecccCCc-----------c---cccHHHH----
Confidence 5668999999999987776555443321 111244544432222222211000 0 0112333
Q ss_pred HHHHhccCccCCCCCcEEEEEechhHHHH--hcChHHHHHHHHhhhcC-CceeEEEEeecccccc----------hhHHH
Q 024646 132 LIIEQGKGLIGQGKDRFSIAIDSVSEMVR--HASISSVAGILSNLRSH-DQVSSIFWLLHSDLHE----------IKFTS 198 (265)
Q Consensus 132 ~~~e~~~~~~~~~k~r~~VaIDSLS~LL~--h~s~~~vc~lL~~Lr~~-~~vssVl~LLHsDLHe----------~~vv~ 198 (265)
.+++..+ ..++ -+|+||+++.+-. .......-.++..|++. .+-...+.++|.+-.. .+=..
T Consensus 102 ~l~~~~~----~~~~-~lvviDpl~~~~~~~~~d~~~~~~~~~~L~~~a~~~g~avl~v~H~~K~~~~~~~~~~~~rGss 176 (239)
T cd01125 102 RIIEQLL----IRRI-DLVVIDPLVSFHGVSENDNGAMDAVIKALRRIAAQTGAAILLVHHVRKGSAKDGDTQEAARGAS 176 (239)
T ss_pred HHHHHHH----hcCC-CEEEECChHHhCCCCcCCHHHHHHHHHHHHHHHHHhCCEEEEEeccCcccccCcccccccCcHH
Confidence 3333221 1233 5899999988711 12233344444444431 1223344455555532 22266
Q ss_pred HHHhhheeEEEeeeCCccc
Q 024646 199 VLEYLSSMVASVEPFNQAA 217 (265)
Q Consensus 199 ALe~LAs~vv~v~P~~~~~ 217 (265)
||...+-.+..+.|.....
T Consensus 177 al~~~~r~~~~l~~~~~~~ 195 (239)
T cd01125 177 ALVDGARWVRALTRMTSEE 195 (239)
T ss_pred HHhcccceEEEEeeCCHHH
Confidence 7777788888888776544
No 43
>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=58.97 E-value=44 Score=32.19 Aligned_cols=121 Identities=17% Similarity=0.199 Sum_probs=63.6
Q ss_pred cccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHH
Q 024646 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (265)
Q Consensus 53 ~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~ 132 (265)
.++..+.++.+|-+++. +.+++.|+|. +++++.+ |... .++......
T Consensus 81 ~~g~~~vyId~E~~~~~--~~a~~lGvd~----~~l~v~~----p~~~-----------------------eq~l~i~~~ 127 (325)
T cd00983 81 KLGGTVAFIDAEHALDP--VYAKKLGVDL----DNLLISQ----PDTG-----------------------EQALEIADS 127 (325)
T ss_pred HcCCCEEEECccccHHH--HHHHHcCCCH----HHheecC----CCCH-----------------------HHHHHHHHH
Confidence 45778889999887763 4566777763 3455332 3211 111111122
Q ss_pred HHHhccCccCCCCCcEEEEEechhHHHHhcCh-------------HHHHHHHHhhhc----CCceeEEEEeeccccc---
Q 024646 133 IIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-------------SSVAGILSNLRS----HDQVSSIFWLLHSDLH--- 192 (265)
Q Consensus 133 ~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~-------------~~vc~lL~~Lr~----~~~vssVl~LLHsDLH--- 192 (265)
.+. .+.. -.|+|||++.|..+... -.+.+.|+.|.. +....=++.-++.+.=
T Consensus 128 li~-------s~~~-~lIVIDSvaal~~~~E~~~~~~~~~~~~qaR~l~~~Lr~L~~~~~k~~~~vI~tNQvr~~ig~~~ 199 (325)
T cd00983 128 LVR-------SGAV-DLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSINKSNTTVIFINQLREKIGVMF 199 (325)
T ss_pred HHh-------ccCC-CEEEEcchHhhcccccccccccccchHHHHHHHHHHHHHHHHHHHhCCCEEEEEEcccccccccc
Confidence 222 1233 58999999999865321 123455555543 3222222222333321
Q ss_pred -chhH---HHHHHhhheeEEEeeeCC
Q 024646 193 -EIKF---TSVLEYLSSMVASVEPFN 214 (265)
Q Consensus 193 -e~~v---v~ALe~LAs~vv~v~P~~ 214 (265)
.|.. =.+|+|.|++.+.+.-..
T Consensus 200 g~~e~~~GG~~L~~~ss~rl~lrk~~ 225 (325)
T cd00983 200 GNPETTTGGNALKFYSSVRLDIRRIE 225 (325)
T ss_pred CCCccCCCchHHhhhcceEEEEEeec
Confidence 1212 247999999999996543
No 44
>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=57.99 E-value=57 Score=31.39 Aligned_cols=48 Identities=10% Similarity=0.088 Sum_probs=29.4
Q ss_pred CCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEE
Q 024646 30 SPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHI 90 (265)
Q Consensus 30 ~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i 90 (265)
..+=+.+..|++.. ...++..+.++.+|-+++. ..+++.|+|. +++++
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 33445555665443 2345778889999887764 3466778873 34654
No 45
>cd01120 RecA-like_NTPases RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Probab=51.07 E-value=1.2e+02 Score=23.69 Aligned_cols=64 Identities=16% Similarity=0.176 Sum_probs=38.6
Q ss_pred EEEEEechhHHHHhcC------hHHHHHHHHhhhcC--CceeEEEEeecccccc------hhHHHHHHhhheeEEEee
Q 024646 148 FSIAIDSVSEMVRHAS------ISSVAGILSNLRSH--DQVSSIFWLLHSDLHE------IKFTSVLEYLSSMVASVE 211 (265)
Q Consensus 148 ~~VaIDSLS~LL~h~s------~~~vc~lL~~Lr~~--~~vssVl~LLHsDLHe------~~vv~ALe~LAs~vv~v~ 211 (265)
-.|+||+++.++.... ...+...|.+|... ..=..|+...|.+-=+ .....++++++.+++.+.
T Consensus 87 ~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~l~ 164 (165)
T cd01120 87 DLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSGDKGDPRLTRGAQNLEDIADTVIVLS 164 (165)
T ss_pred EEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEEEecCCccccCcccccCccceeeecceEEEEe
Confidence 6899999999887532 23445555555542 1233455555544211 114467899988888764
No 46
>PF14417 MEDS: MEDS: MEthanogen/methylotroph, DcmR Sensory domain
Probab=49.63 E-value=58 Score=28.14 Aligned_cols=137 Identities=14% Similarity=0.120 Sum_probs=80.6
Q ss_pred HHHHHHHHHHHHhhccccceeEEEEe-eCChHHHHHHHhhcCCCccC--CCCeEEEEeccC--CCCCCcccccCcccccc
Q 024646 38 NYVLTQLSNYILAGKSQSRGLVVVAY-SRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYT--DPLGWKNWLIDKDISQE 112 (265)
Q Consensus 38 ~h~~~~l~s~i~a~~~q~~~Vhvl~f-e~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ys--DPlgW~~~~~~~~~~~~ 112 (265)
..++..+.++|++|-.+++.+.+++= ....+...+.|++.|+|.+. -...+.++|... -+-|+.+...
T Consensus 30 ~e~~~~~~~Fi~~GL~~ge~~l~v~~~~~~~~~l~~~L~~~~~d~~~~~~~gqL~~~~~~~~Y~~~g~f~~~~------- 102 (191)
T PF14417_consen 30 EELLEVLVPFIREGLARGERCLYVAPDPRRVEELRDELRKAGPDVEQYLDSGQLELLDAEEWYLPDGRFDPAR------- 102 (191)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEECCCCCHHHHHHHHHhcCCchhhcccCCCEEEecchhhhccCCCcCHHH-------
Confidence 55677899999999999999999998 78888999999988887655 245688887521 1222222111
Q ss_pred ccccccccccchhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHH---HHhhhcCCceeEEEEeecc
Q 024646 113 ASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGI---LSNLRSHDQVSSIFWLLHS 189 (265)
Q Consensus 113 ~s~~~~~~~~v~~L~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~l---L~~Lr~~~~vssVl~LLHs 189 (265)
-+..+...+..... +|-..+-++-| .+|.++. +..++... +..+-. ..--..++.-..
T Consensus 103 ---------~i~~~~~~~~~a~~-------~G~~~lRv~ge-~~w~~~~-~~~~l~~yE~~ln~~~~-~~~~~~lC~Yd~ 163 (191)
T PF14417_consen 103 ---------MIAFWRAALEQALA-------EGYRGLRVIGE-MTWALRS-GWEELLRYEALLNRLFA-EHPFTALCAYDR 163 (191)
T ss_pred ---------HHHHHHHHHHHHHh-------CCCCcEEEEEe-chhhccc-cHHHHHHHHHHHHHHhc-CCCEEEEeccch
Confidence 12223322222222 12334777788 7888877 55554332 222222 224445566665
Q ss_pred cccchhHHHHH
Q 024646 190 DLHEIKFTSVL 200 (265)
Q Consensus 190 DLHe~~vv~AL 200 (265)
+.-.+.++..+
T Consensus 164 ~~~~~~~~~~~ 174 (191)
T PF14417_consen 164 RRFSPEVLADA 174 (191)
T ss_pred HhCCHHHHHHH
Confidence 55555555444
No 47
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=47.83 E-value=19 Score=30.09 Aligned_cols=25 Identities=12% Similarity=0.058 Sum_probs=16.8
Q ss_pred ccceeEEEEeeCChHHHHHHHhhcC
Q 024646 54 QSRGLVVVAYSRSPSFYVDLLKRRG 78 (265)
Q Consensus 54 q~~~Vhvl~fe~spe~y~~~lk~~G 78 (265)
+...|..+.+|.+++++..-++..+
T Consensus 69 ~~~~Vl~i~~E~~~~~~~~rl~~~~ 93 (193)
T PF13481_consen 69 RPGRVLYISLEDSESQIARRLRALL 93 (193)
T ss_dssp ----EEEEESSS-HHHHHHHHHHHH
T ss_pred cCceEEEEeccCCHHHHHHHHHHHh
Confidence 6789999999999988888777553
No 48
>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=37.52 E-value=77 Score=24.17 Aligned_cols=57 Identities=21% Similarity=0.203 Sum_probs=43.8
Q ss_pred CCceeeccCCCCCchhh------HHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHh
Q 024646 19 APALTIKDSKASPFGFD------VFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLK 75 (265)
Q Consensus 19 ap~l~i~Dsl~~~~g~~------~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk 75 (265)
.|.+++-|.++.-++.. ....++..|.+.+.....+...+.+++....++..-..+.
T Consensus 58 ~~~vl~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~ 120 (132)
T PF00004_consen 58 KPCVLFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALL 120 (132)
T ss_dssp TSEEEEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHH
T ss_pred cceeeeeccchhcccccccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHH
Confidence 58999999997765443 5677788888888887777777888888888877666555
No 49
>PF05301 Mec-17: Touch receptor neuron protein Mec-17; InterPro: IPR007965 Mec-17 is the protein product of one of the 18 genes required for the development and function of the touch receptor neuron for gentle touch. Mec-17 is specifically required for maintaining the differentiation of the touch receptor []. This family is conserved to higher eukaryotes.; GO: 0019799 tubulin N-acetyltransferase activity
Probab=33.86 E-value=68 Score=27.02 Aligned_cols=70 Identities=21% Similarity=0.372 Sum_probs=42.7
Q ss_pred CCCCceeecc-----CC-CCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhh-cCCCccC--CCCe
Q 024646 17 EHAPALTIKD-----SK-ASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKR-RGIDIAS--SHDW 87 (265)
Q Consensus 17 e~ap~l~i~D-----sl-~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~-~G~d~~~--~~~~ 87 (265)
|.-|+++|-| |. -.=.|-.+|.|.+. ...-..+=+|+|+|.+-++.+|++ +|+.... .|+=
T Consensus 42 e~~~~~cvLDFyVhes~QR~G~Gk~LF~~ML~----------~e~~~p~~~a~DrPS~Kll~Fl~Khy~L~~~ipQ~NNF 111 (120)
T PF05301_consen 42 EIEPLLCVLDFYVHESRQRRGYGKRLFDHMLQ----------EENVSPHQLAIDRPSPKLLSFLKKHYGLQRYIPQSNNF 111 (120)
T ss_pred EecccceeeeEEEEeceeccCchHHHHHHHHH----------HcCCCcccceecCCcHHHHHHHHHhcCCCcCCCCCccE
Confidence 3346555444 44 22347889999874 222345678999999999998876 3443322 2545
Q ss_pred EEEEeccCC
Q 024646 88 IHILDCYTD 96 (265)
Q Consensus 88 v~i~D~ysD 96 (265)
+++-.+|.|
T Consensus 112 VVf~~fF~d 120 (120)
T PF05301_consen 112 VVFEGFFDD 120 (120)
T ss_pred EEehHhcCC
Confidence 566666655
No 50
>KOG3124 consensus Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]
Probab=31.19 E-value=26 Score=33.19 Aligned_cols=42 Identities=31% Similarity=0.364 Sum_probs=27.5
Q ss_pred ccCCCCCceeeccCCCCCchhhH-HHHHHHH------HHHHHHhhccccc
Q 024646 14 LEGEHAPALTIKDSKASPFGFDV-FNYVLTQ------LSNYILAGKSQSR 56 (265)
Q Consensus 14 ~~ge~ap~l~i~Dsl~~~~g~~~-~~h~~~~------l~s~i~a~~~q~~ 56 (265)
++.++-|+ .++|+++||+|+.+ +-|++.+ +.+.+.++..|++
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 34454454 46999999999887 6677765 4555555554443
No 51
>PRK09519 recA DNA recombination protein RecA; Reviewed
Probab=31.09 E-value=2.1e+02 Score=31.19 Aligned_cols=66 Identities=15% Similarity=0.196 Sum_probs=37.2
Q ss_pred EEEEEechhHHHHh------cC-----hH--HHHHHHHhhhcC---CceeE-EEEeecc-------cccchhHHHHHHhh
Q 024646 148 FSIAIDSVSEMVRH------AS-----IS--SVAGILSNLRSH---DQVSS-IFWLLHS-------DLHEIKFTSVLEYL 203 (265)
Q Consensus 148 ~~VaIDSLS~LL~h------~s-----~~--~vc~lL~~Lr~~---~~vss-Vl~LLHs-------DLHe~~vv~ALe~L 203 (265)
-.|+|||++.|..+ .+ .+ .+.+.|+.|.+. -.+.. +.-.+++ |=..+--=.+|.|-
T Consensus 140 ~LVVIDSI~aL~~r~E~~g~~g~~~~~~q~rl~~q~L~~L~~~l~~~nvtvi~TNQv~~~~g~~fg~p~~~~GG~~l~h~ 219 (790)
T PRK09519 140 DIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALNNSGTTAIFINQLRDKIGVMFGSPETTTGGKALKFY 219 (790)
T ss_pred eEEEEcchhhhcchhhccCCCCcccHHHHHHHHHHHHHHHHHHHHhCCCEEEEEecceecCCCcCCCCCcCCCCccccee
Confidence 57999999999952 11 11 124566656553 12222 2222333 22333344679999
Q ss_pred heeEEEeeeC
Q 024646 204 SSMVASVEPF 213 (265)
Q Consensus 204 As~vv~v~P~ 213 (265)
||+-+.|.-.
T Consensus 220 ss~Ri~lrk~ 229 (790)
T PRK09519 220 ASVRMDVRRV 229 (790)
T ss_pred ccEEEEeeec
Confidence 9999888753
No 52
>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []. In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....
Probab=27.16 E-value=1.5e+02 Score=28.67 Aligned_cols=51 Identities=10% Similarity=0.121 Sum_probs=25.8
Q ss_pred CCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEe
Q 024646 29 ASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILD 92 (265)
Q Consensus 29 ~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D 92 (265)
.+.+-+.++.|++++. ..++.-+.++ |.....+.+.+++.|+|. +++.+..
T Consensus 62 ~ssGKttLaL~~ia~~-------q~~g~~~a~I--D~e~~ld~~~a~~lGvdl----~rllv~~ 112 (322)
T PF00154_consen 62 ESSGKTTLALHAIAEA-------QKQGGICAFI--DAEHALDPEYAESLGVDL----DRLLVVQ 112 (322)
T ss_dssp TTSSHHHHHHHHHHHH-------HHTT-EEEEE--ESSS---HHHHHHTT--G----GGEEEEE
T ss_pred CCCchhhhHHHHHHhh-------hcccceeEEe--cCcccchhhHHHhcCccc----cceEEec
Confidence 4556777777866532 1234444444 444445667777889984 3466554
No 53
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=27.14 E-value=59 Score=25.36 Aligned_cols=43 Identities=19% Similarity=0.210 Sum_probs=26.6
Q ss_pred HHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccCCCC
Q 024646 45 SNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPL 98 (265)
Q Consensus 45 ~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPl 98 (265)
++...+-.+.+-.+++|+++..+. -.++++.++++ .+.|.||-
T Consensus 3 ~~~~~~l~~~gv~lv~I~~g~~~~-~~~f~~~~~~p----------~~ly~D~~ 45 (115)
T PF13911_consen 3 SRRKPELEAAGVKLVVIGCGSPEG-IEKFCELTGFP----------FPLYVDPE 45 (115)
T ss_pred hHhHHHHHHcCCeEEEEEcCCHHH-HHHHHhccCCC----------CcEEEeCc
Confidence 333334445667789999887754 55555556664 24678884
No 54
>cd04754 Commd6 COMM_Domain containing protein 6. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=26.40 E-value=54 Score=26.14 Aligned_cols=34 Identities=15% Similarity=0.345 Sum_probs=24.2
Q ss_pred hhhccccceEEEEeecCCCchhh-----hHHHHHHHhhhcC
Q 024646 230 LEQNFRKGKFHVRFKRRNGRVRV-----MASNLHQFCLKMK 265 (265)
Q Consensus 230 l~~n~~kg~~~vr~KrrnGRV~~-----~~E~~~~~~~~~~ 265 (265)
+..+|-. +.+-.+++||.+.. ..++|+.|+..||
T Consensus 41 l~~Pfl~--l~L~V~~~~G~~~~~~~EmTlpEFq~f~~~~~ 79 (86)
T cd04754 41 LNSPYVA--VTLKVADPSGQVVTKSFEMTIPEFQNFSRQFK 79 (86)
T ss_pred cCCceEE--EEEEEEccCCCccceEEEEcHHHHHHHHHHHH
Confidence 4444522 55667778999976 4699999998774
No 55
>PF11633 SUD-M: Single-stranded poly(A) binding domain; InterPro: IPR024375 This domain identifies non-structural protein 3 (Nsp3). It is found in human SARS coronavirus polyprotein 1a and 1ab, and in related coronavirus polyproteins [].; PDB: 2KQV_A 2W2G_A 2WCT_D 2JZE_A 2JZF_A 2RNK_A 2JZD_A.
Probab=25.79 E-value=25 Score=30.37 Aligned_cols=64 Identities=19% Similarity=0.229 Sum_probs=30.9
Q ss_pred ccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646 25 KDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (265)
Q Consensus 25 ~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~y 94 (265)
..+.+.+....+...+.-.++.-++-++.++ -+..+..|.++ +..+||++|++. ...+.-+|.|
T Consensus 6 ~~~~~~~~~~~ll~~v~~~~r~ml~~ak~~g-~~~pvc~D~~A--~~k~lkr~gv~~---~egl~t~~G~ 69 (142)
T PF11633_consen 6 YNSAADNSKEELLGVVSWNFRAMLQHAKETG-LLCPVCIDYPA--FCKTLKRKGVDP---KEGLQTVDGV 69 (142)
T ss_dssp ---S-------GGCEE---CHHHHHHHHHHT--EEEEETT-HH--HHHHHHHTTS------SEEEES-SS
T ss_pred ccCCCCCCCCceeeeeehhHHHHHHHHHhcC-cEEEEEeccHH--HHHHHhccCccc---ccceEEecce
Confidence 3344444444444444444455444455555 57788889888 999999999985 5567776544
No 56
>PF13466 STAS_2: STAS domain
Probab=24.54 E-value=1.6e+02 Score=21.19 Aligned_cols=34 Identities=21% Similarity=0.252 Sum_probs=23.4
Q ss_pred HHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCC
Q 024646 44 LSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGID 80 (265)
Q Consensus 44 l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d 80 (265)
|.+..+..+.++..+.+.+ .++....+++..|+|
T Consensus 47 L~~~~~~~~~~g~~~~l~~---~~~~~~~ll~~~gld 80 (80)
T PF13466_consen 47 LLAAARRARARGRQLRLTG---PSPALRRLLELLGLD 80 (80)
T ss_pred HHHHHHHHHHCCCeEEEEc---CCHHHHHHHHHhCcC
Confidence 4445555666777777766 444588888888875
No 57
>smart00455 RBD Raf-like Ras-binding domain.
Probab=23.22 E-value=55 Score=24.46 Aligned_cols=36 Identities=19% Similarity=0.244 Sum_probs=24.5
Q ss_pred hHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCccccc
Q 024646 67 PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLI 105 (265)
Q Consensus 67 pe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~ 105 (265)
.|.....|++||++++. ...++-.-..|+.|++...
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 45677899999998655 3333333448999998443
No 58
>KOG1406 consensus Peroxisomal 3-ketoacyl-CoA-thiolase P-44/SCP2 [Lipid transport and metabolism]
Probab=23.06 E-value=55 Score=31.74 Aligned_cols=40 Identities=13% Similarity=0.283 Sum_probs=31.7
Q ss_pred ceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccCC
Q 024646 56 RGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTD 96 (265)
Q Consensus 56 ~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ysD 96 (265)
..+-+++||-+...-+.+..+.|+.++. -+-|..||||+-
T Consensus 264 s~ikm~gfdm~~~aa~~l~aksgltpnd-vqvielhdcfs~ 303 (408)
T KOG1406|consen 264 SLIKMAGFDMTRLAAKRLFAKSGLTPND-VQVIELHDCFSA 303 (408)
T ss_pred hhhhhhcchHHHHHHHHHHHHcCCCccc-ceEEEeecccch
Confidence 3456778888877778888888998877 667899999984
No 59
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=22.94 E-value=2e+02 Score=23.50 Aligned_cols=39 Identities=10% Similarity=0.128 Sum_probs=28.9
Q ss_pred eeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEee
Q 024646 22 LTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYS 64 (265)
Q Consensus 22 l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe 64 (265)
+..-|+-.|.. ...+..|++++++..+.. ...|+|+.||
T Consensus 2 ~vaiDtSGSis-~~~l~~fl~ev~~i~~~~---~~~v~vi~~D 40 (126)
T PF09967_consen 2 VVAIDTSGSIS-DEELRRFLSEVAGILRRF---PAEVHVIQFD 40 (126)
T ss_pred EEEEECCCCCC-HHHHHHHHHHHHHHHHhC---CCCEEEEEEC
Confidence 34567777775 567888888888766555 4459999999
No 60
>COG4544 Uncharacterized conserved protein [Function unknown]
Probab=22.69 E-value=1.3e+02 Score=28.44 Aligned_cols=55 Identities=11% Similarity=0.135 Sum_probs=39.5
Q ss_pred hhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccC
Q 024646 34 FDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYT 95 (265)
Q Consensus 34 ~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ys 95 (265)
.....=|+..|.+..++.+..+.-||++..+ +-|.--|+..||| ..|++|+.|++
T Consensus 64 ~ga~~GaAaAl~~~g~~~r~~gpVvWi~tr~---dlf~paL~~~Gl~----~~RlifVea~~ 118 (260)
T COG4544 64 AGAADGAAAALAVLGLAARRGGPVVWILTRE---DLFPPALAAFGLD----PERLIFVEARK 118 (260)
T ss_pred ccchhhHHHHHHHHhhhcccCCCEEEEEecc---cccchhHhhcCCC----hhhEEEEeCCc
Confidence 3334456677888888888888899998843 3333338889999 57799998764
No 61
>PF11382 DUF3186: Protein of unknown function (DUF3186); InterPro: IPR021522 This bacterial family of proteins has no known function.
Probab=22.62 E-value=1.5e+02 Score=28.05 Aligned_cols=60 Identities=20% Similarity=0.356 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHHHhhccccceeEEEEeeCC----hHHHHHHHhhcCCCccCCCCeEEEEeccCCCCC
Q 024646 37 FNYVLTQLSNYILAGKSQSRGLVVVAYSRS----PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLG 99 (265)
Q Consensus 37 ~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~s----pe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlg 99 (265)
.+.|+..+...+.+++..++.|.||..... .+...++|++.|-.. ..++.+-|-|.||-.
T Consensus 65 ~d~f~~~~~~~lv~g~L~g~~V~vV~~p~a~~~~~~~v~~~L~~AGA~v---~g~i~lt~~~~d~~~ 128 (308)
T PF11382_consen 65 ADQFIAAVAPRLVAGRLTGRSVAVVTLPGADDEDVDAVRELLEQAGATV---TGRITLTDKFLDPEQ 128 (308)
T ss_pred HHHHHHHHHHHHhcCccCCCEEEEEEcCCCChHHHHHHHHHHHHCCCeE---EEEEEEchhhcChhh
Confidence 466778888888899999999999996543 446777888888764 558999999999985
No 62
>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=22.11 E-value=34 Score=31.60 Aligned_cols=27 Identities=26% Similarity=0.313 Sum_probs=20.8
Q ss_pred eecccccchhHHHHHHhhheeEEEeeeCCc
Q 024646 186 LLHSDLHEIKFTSVLEYLSSMVASVEPFNQ 215 (265)
Q Consensus 186 LLHsDLHe~~vv~ALe~LAs~vv~v~P~~~ 215 (265)
+||+|||...++.+=. ..++-+.|...
T Consensus 162 lLHGDLH~~NIL~~~~---~~WlaIDPkgl 188 (253)
T PF04655_consen 162 LLHGDLHHGNILAAGR---RGWLAIDPKGL 188 (253)
T ss_pred eeccccchHhhhccCC---CCceEeCCccc
Confidence 8999999998887653 66777777543
No 63
>KOG3444 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.36 E-value=55 Score=27.44 Aligned_cols=35 Identities=34% Similarity=0.378 Sum_probs=30.5
Q ss_pred CCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc
Q 024646 142 GQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS 176 (265)
Q Consensus 142 ~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~ 176 (265)
.-.|-.|++|+||=..-+|....-++|+.||.|-.
T Consensus 75 tNTkVKFIlvvdssd~avreteiRsv~r~~h~l~t 109 (121)
T KOG3444|consen 75 TNTKVKFILVVDSSDYAVRETEIRSVFRILHLLYT 109 (121)
T ss_pred eccEEEEEEEEcCCcceehhHHHHHHHHHHHHHHH
Confidence 33566699999999999999999999999998764
No 64
>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=20.25 E-value=6e+02 Score=22.39 Aligned_cols=32 Identities=13% Similarity=0.073 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHhhccccceeEEEEeeCChH
Q 024646 36 VFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPS 68 (265)
Q Consensus 36 ~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe 68 (265)
....+...|++.+.+. .+.--+..+|-|||--
T Consensus 8 a~~~l~~~L~~~~~~~-~~~iv~lCIGTDRstG 39 (163)
T PF06866_consen 8 APEKLANFLYSLIPKH-NREIVFLCIGTDRSTG 39 (163)
T ss_pred HHHHHHHHHHHHHhhc-CCCEEEEEECCCCCcc
Confidence 3445555666766655 4444555666777743
Done!