Query 041187
Match_columns 189
No_of_seqs 120 out of 189
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:37:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041187.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041187hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00570 cdk7 CDK-activating 100.0 6.9E-47 1.5E-51 335.8 12.7 182 5-189 64-306 (309)
2 COG5220 TFB3 Cdk activating ki 100.0 1.3E-35 2.8E-40 257.7 5.7 183 6-189 75-308 (314)
3 PF06391 MAT1: CDK-activating 100.0 6.3E-33 1.4E-37 234.2 0.0 93 7-99 14-109 (200)
4 KOG3800 Predicted E3 ubiquitin 100.0 4.1E-31 8.9E-36 232.9 6.5 183 7-189 63-299 (300)
5 KOG3800 Predicted E3 ubiquitin 96.9 0.00012 2.6E-09 65.8 -1.8 152 23-189 25-177 (300)
6 KOG1924 RhoA GTPase effector D 62.4 69 0.0015 33.5 9.9 31 19-49 407-438 (1102)
7 PF08073 CHDNT: CHDNT (NUC034) 45.2 29 0.00063 24.3 3.1 48 23-70 3-54 (55)
8 PF07807 RED_C: RED-like prote 40.3 19 0.00041 28.8 1.7 21 26-46 37-57 (118)
9 PF05008 V-SNARE: Vesicle tran 33.2 1.4E+02 0.0031 20.7 5.2 59 14-72 7-72 (79)
10 PTZ00233 variable surface prot 31.4 1.4E+02 0.003 29.3 6.3 58 18-80 10-67 (509)
11 smart00150 SPEC Spectrin repea 31.4 1.4E+02 0.0031 20.2 4.9 40 32-71 6-45 (101)
12 PF03705 CheR_N: CheR methyltr 29.4 78 0.0017 20.5 3.1 29 10-40 23-51 (57)
13 COG3310 Uncharacterized protei 29.2 43 0.00094 28.6 2.2 37 14-50 61-108 (196)
14 PHA03141 helicase-primase prim 28.3 1.3E+02 0.0028 23.6 4.5 34 35-68 61-96 (101)
15 PRK00888 ftsB cell division pr 25.9 2.3E+02 0.005 21.6 5.6 38 46-83 15-56 (105)
16 PF13434 K_oxygenase: L-lysine 22.7 57 0.0012 29.4 2.0 35 10-45 72-106 (341)
17 PF13904 DUF4207: Domain of un 21.8 1.3E+02 0.0028 26.5 3.9 17 57-73 180-196 (264)
18 PHA03369 capsid maturational p 21.2 7.4E+02 0.016 25.2 9.3 56 22-77 280-338 (663)
19 PF14284 PcfJ: PcfJ-like prote 20.2 4.5E+02 0.0097 21.4 6.6 19 36-54 2-20 (169)
No 1
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=6.9e-47 Score=335.76 Aligned_cols=182 Identities=31% Similarity=0.418 Sum_probs=139.9
Q ss_pred CCCchhHHHHHHHHHHHHhcccCCCCCChHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 041187 5 SSNPQNRELAIRKRIASIYNKREEDFPSLKEYNDYLEEVEDMIFNLVEGVNVHEFEEKIQEYQKENAEQIMINQARKAEE 84 (189)
Q Consensus 5 ~~~~~ekEv~iRkrv~~ifNk~e~DF~~l~~YNdYLE~vEdiifnL~~g~d~~~te~~l~~y~~~n~~~I~~n~~~~~ee 84 (189)
.+..+||||+|||||++||||+++||+||++||||||+||||||||+||+|+++||++|++|+++|+.+|.+|+++..++
T Consensus 64 ~D~~vekEV~iRkrv~~i~Nk~e~dF~~l~~yNdYLE~vEdii~nL~~~~d~~~te~~l~~y~~~n~~~I~~n~~~~~~e 143 (309)
T TIGR00570 64 EDPTVEKEVDIRKRVLKIYNKREEDFPSLREYNDYLEEVEDIVYNLTNNIDLENTKKKIETYQKENKDVIQKNKEKSTRE 143 (309)
T ss_pred ccHHHHHHHHHHHHHHHHHccchhccCCHHHHHHHHHHHHHHHHHhhcCCcHHHHHHHHHHHHHHhHHHHHHHHHHHHhH
Confidence 35556999999999999999999999999999999999999999999999999999999999999999999999988777
Q ss_pred HHHH---HHHhccccccc-------CcCCCC------------CccccCCC----cc-------CCCCCCcc--------
Q 041187 85 LAAA---LAASKGISAQD-------DTNGDP------------SQSALGGI----GV-------GGTQGQYV-------- 123 (189)
Q Consensus 85 ~~~~---~~~ek~~~~q~-------~~ee~~------------~~~~~~~~----~~-------~~~~g~~~-------- 123 (189)
.+.. +++|++.++++ +.+|++ |+++..+. +. +++++..+
T Consensus 144 ~~~~~~~~~~E~~~~~~rr~~~~~~e~ee~~~~~~~~~~~ld~L~~s~~~~~~~i~~~~~~~~~~k~~~~r~~~~~~~~~ 223 (309)
T TIGR00570 144 QEELEEALEFEKEEEEQRRLLLQKEEEEQQMNKRKNKQALLDELETSTLPAAELIAQHKKNSVKLEMQVEKPKPEKPNTF 223 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhhhhhccccchhhh
Confidence 7766 56666666553 222221 44433221 10 11111111
Q ss_pred ------ccccCC-----CCCCCCCCCCcccCCCCCCC--------CCCcHHHHHHHh-hccccccccchHHHHHHHHHHH
Q 041187 124 ------PTLAGG-----QPRPTGIPQPIAHAGGMDLH--------SYDNEAMMKLRA-ERGGRAAGWSMELSKKRALEEA 183 (189)
Q Consensus 124 ------~~i~g~-----~~~~~~~~~P~P~~GG~~~~--------~y~d~~~~~~R~-~~~~~AGGys~~~~~~RaL~EA 183 (189)
|...++ .+.|..||+|| ||.... .|.+.|+..+|. ++.++||||++++|+.|||+||
T Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~py~Pf---~g~~~~p~~y~~~~~~~~~y~~~~r~~~~~~~aGGy~~~~~~~RaL~EA 300 (309)
T TIGR00570 224 STGIKMGYQISLVPVQKSEEALYPYQPL---NIETEGPPVPTLEELVRQGYLNHVRAASPQDIAGGYTSNLACERALQEA 300 (309)
T ss_pred hhcccccccccccccCCCCCCCCCcCCC---CCCCCCCCCCCccccccccHHHHHhccCcccccCCcCHHHHHHHHHHHH
Confidence 211111 12245689988 776643 358999999988 8899999999999999999999
Q ss_pred hhccCC
Q 041187 184 FASIWI 189 (189)
Q Consensus 184 Fsgl~~ 189 (189)
|+||+|
T Consensus 301 F~GL~~ 306 (309)
T TIGR00570 301 FSGLFW 306 (309)
T ss_pred HccCCc
Confidence 999987
No 2
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=100.00 E-value=1.3e-35 Score=257.65 Aligned_cols=183 Identities=27% Similarity=0.393 Sum_probs=127.2
Q ss_pred CCchhHHHHHHHHHHHHhcccCCCCC-ChHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 041187 6 SNPQNRELAIRKRIASIYNKREEDFP-SLKEYNDYLEEVEDMIFNLVEGVNVHEFEEKIQEYQKENAEQIMINQARKAEE 84 (189)
Q Consensus 6 ~~~~ekEv~iRkrv~~ifNk~e~DF~-~l~~YNdYLE~vEdiifnL~~g~d~~~te~~l~~y~~~n~~~I~~n~~~~~ee 84 (189)
+.++||||||||||+.+|||+++||. ||.+||||||+||+|||+|+++|||+.||.|+++|++.|+++|+.|-+|..-|
T Consensus 75 D~~vEkEvdvRkr~~r~Fnk~~~eF~gdl~~YNdYLEevE~l~f~l~~~idv~~teEKvk~yee~n~dsI~nN~~R~~~e 154 (314)
T COG5220 75 DITVEKEVDVRKRLLRAFNKEEEEFGGDLAKYNDYLEEVEELVFELLELIDVSLTEEKVKKYEEMNQDSILNNLERPTPE 154 (314)
T ss_pred hhhhhhhhhHHHHHHHHhccchhhhCccHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHhhccccCCcc
Confidence 56789999999999999999999998 99999999999999999999999999999999999999999999986543332
Q ss_pred HH---------HHHHHhcccc-cccCcCCCC--CccccCCC---cc---------------CCCCCCccc----------
Q 041187 85 LA---------AALAASKGIS-AQDDTNGDP--SQSALGGI---GV---------------GGTQGQYVP---------- 124 (189)
Q Consensus 85 ~~---------~~~~~ek~~~-~q~~~ee~~--~~~~~~~~---~~---------------~~~~g~~~~---------- 124 (189)
.+ .++..++.++ +|.+.+|+. .|+.++.+ ++ .+.+....|
T Consensus 155 ~~~~~q~~~l~kr~K~kkR~~~~q~~eeEr~~kE~~kkeI~~~l~t~~~D~Nkti~~~~~s~k~~~e~~~r~v~e~~rnn 234 (314)
T COG5220 155 VMPGKQKNVLQKRMKLKKRQLERQIEEEERMNKEWTKKEIGNRLGTASEDGNKTIKIGIISDKFDPEELPRIVVEPTRNN 234 (314)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccCcchhhhhcccccccCHHHHhHHHhccccCC
Confidence 22 2222222222 222333322 22222211 11 111111111
Q ss_pred --cccCCCCCCCCCCCCcccCCCCCCC--------CCCcHHHHHHHhhccccccccchHHHHHHHHHHHhhccCC
Q 041187 125 --TLAGGQPRPTGIPQPIAHAGGMDLH--------SYDNEAMMKLRAERGGRAAGWSMELSKKRALEEAFASIWI 189 (189)
Q Consensus 125 --~i~g~~~~~~~~~~P~P~~GG~~~~--------~y~d~~~~~~R~~~~~~AGGys~~~~~~RaL~EAFsgl~~ 189 (189)
...+.+.......++.|+.|..+.| .|.||.++++-+ ..++|+||.+.++|.|+|+|||+||-|
T Consensus 235 ~i~lsnVq~~~kD~~Pf~P~~g~~~~~~~fsl~~s~y~dp~ik~l~H-k~~~~~GF~~~~~~~R~L~EAF~Gl~~ 308 (314)
T COG5220 235 KIYLSNVQGFLKDLQPFAPGGGSYNAHTIFSLAISSYGDPNIKDLEH-KEFIASGFNTNYAYERVLTEAFMGLGC 308 (314)
T ss_pred ceechhhhhhHhhcCCCCCCCCCcCCceeEEEeccccCCcchhhhcc-chhhhcCcccHHHHHHHHHHHHccCCe
Confidence 1112222222222334445666555 479999999999 459999999999999999999999965
No 3
>PF06391 MAT1: CDK-activating kinase assembly factor MAT1; InterPro: IPR015877 MAT1 (menage a trois 1) is a RING finger protein with a characteristic C3HC4 motif located in the N-terminal domain. This entry represents the central region of MAT1. MAT1 stabilises the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex which then goes on to activate many of the CDK enzymes intimately involved in the cell cycle []. CDK7 forms a stable complex with cyclin H and MAT1 in vivo only when phosphorylated on either one of two residues (Ser164 or Thr170) in its T-loop. The requirement for MAT1 for the activation of CAK can be by-passed by the phosphorylation of CDK7 on the T-loop. The two mechanisms for CDK7 complex stabilisation and activation (MAT1 addition and T-loop phosphorylation), which can operate independently in vitro, actually cooperate under physiological conditions to maintain complex integrity. With prolonged exposure to elevated temperature, dissociation to monomeric subunits occurs in vivo when CDK7 is dephosphorylated, even in the presence of MAT1 []. The Cyclin H-MAT1-CDK7 complex also forms part of TFIIH, a multiprotein complex required for both transcription and DNA repair.; GO: 0007049 cell cycle, 0005634 nucleus; PDB: 1G25_A.
Probab=99.97 E-value=6.3e-33 Score=234.17 Aligned_cols=93 Identities=51% Similarity=0.779 Sum_probs=0.0
Q ss_pred CchhHHHHHHHHHHHHhcccCCCCCChHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 041187 7 NPQNRELAIRKRIASIYNKREEDFPSLKEYNDYLEEVEDMIFNLVEGVNVHEFEEKIQEYQKENAEQIMINQARKAEELA 86 (189)
Q Consensus 7 ~~~ekEv~iRkrv~~ifNk~e~DF~~l~~YNdYLE~vEdiifnL~~g~d~~~te~~l~~y~~~n~~~I~~n~~~~~ee~~ 86 (189)
..|||||+|||||++||||+++||+||++||||||+||||||||++|+|+++|+++|++|+++|+++|.+|+++..++..
T Consensus 14 ~~VekEv~iRkrV~~ifNk~eeDF~~l~~YNdYLE~vE~iifnL~~~idv~~te~~l~~y~~~n~~~I~~N~~~~~~e~~ 93 (200)
T PF06391_consen 14 LGVEKEVDIRKRVLKIFNKREEDFESLREYNDYLEEVEDIIFNLVNGIDVEETEAKLAQYERENKDEIERNKARASEEQE 93 (200)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhHHHHHHHHHHHHHHHccChhhcCCHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 45699999999999999999999999999999999999999999999999999999999999999999999988777766
Q ss_pred HH---HHHhccccccc
Q 041187 87 AA---LAASKGISAQD 99 (189)
Q Consensus 87 ~~---~~~ek~~~~q~ 99 (189)
.. +..|+..+.++
T Consensus 94 ~~~~~~~~Ek~~~~~r 109 (200)
T PF06391_consen 94 ELEQQQEAEKEQKEER 109 (200)
T ss_dssp ----------------
T ss_pred HHHHHHHHHHHHHHHH
Confidence 66 44455554333
No 4
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=4.1e-31 Score=232.85 Aligned_cols=183 Identities=29% Similarity=0.396 Sum_probs=125.2
Q ss_pred CchhHHHHHHHHHHHHhcccCCCCC-ChHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhHHHHHHHHHHH---H
Q 041187 7 NPQNRELAIRKRIASIYNKREEDFP-SLKEYNDYLEEVEDMIFNLVEGVNVHEFEEKIQEYQKENAEQIMINQARK---A 82 (189)
Q Consensus 7 ~~~ekEv~iRkrv~~ifNk~e~DF~-~l~~YNdYLE~vEdiifnL~~g~d~~~te~~l~~y~~~n~~~I~~n~~~~---~ 82 (189)
.++||||+|||||++||||+++||. ||.+||||||+||||||||++++|+..|+++++.|++.|+++|..|..|. +
T Consensus 63 ~~vekEv~iRrri~~~~nk~~eeF~~~LaeyndylEe~Ediv~nl~~~~dv~~t~~k~~~ye~~nk~~I~~n~~R~~~~~ 142 (300)
T KOG3800|consen 63 PTVEKEVDIRRRILRIFNKKEEEFTGSLAEYNDYLEEVEDIVFNLGNNIDVTETKEKVKTYEEPNKDSIQNNKERVHREQ 142 (300)
T ss_pred hHHHHHHHHHHHHHHHhccchhhhhhhHHHHhcccHHHHHHHHHhhcccchhHHHHHHHHhhccCcccccCChhhcchHH
Confidence 3459999999999999999999999 99999999999999999999999999999999999999999999997653 3
Q ss_pred HHHHHHHHHhccccccc------CcCCCC--------------CccccCC-C--cc----CCCCCCccc-c------cc-
Q 041187 83 EELAAALAASKGISAQD------DTNGDP--------------SQSALGG-I--GV----GGTQGQYVP-T------LA- 127 (189)
Q Consensus 83 ee~~~~~~~ek~~~~q~------~~ee~~--------------~~~~~~~-~--~~----~~~~g~~~~-~------i~- 127 (189)
+..+.++..+|.+..++ ++.+.. |..+.+. + .+ .+++....| + |+
T Consensus 143 e~~e~~l~~ekr~~~~~r~~~~r~~~ee~~~s~~~~~~ei~~~L~~s~qd~~~~i~~~~~~~~qq~~~~~~~s~nt~ir~ 222 (300)
T KOG3800|consen 143 EDLEQRLELEKRQKEFRREELEREAQEEEIASAWVDKQEIIDELYTSDQDPNKVITLSKHKKKQQARKPASTSFNTIIRV 222 (300)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhccHHHHHHHHhcCCCchhhhhhhhhhhhhccCCCccccchhheeec
Confidence 33444444444444222 111100 2222211 0 00 111111111 1 11
Q ss_pred ---CCCCCC---CC-CCCCcccCCCCCCCC--------CCcHHHHHHHhhccccccccchHHHHHHHHHHHhhccCC
Q 041187 128 ---GGQPRP---TG-IPQPIAHAGGMDLHS--------YDNEAMMKLRAERGGRAAGWSMELSKKRALEEAFASIWI 189 (189)
Q Consensus 128 ---g~~~~~---~~-~~~P~P~~GG~~~~~--------y~d~~~~~~R~~~~~~AGGys~~~~~~RaL~EAFsgl~~ 189 (189)
++-+.+ .+ .+++-|+.|....+. |.+....+.-+.+..+||||.....+.|||+|||+||++
T Consensus 223 ~~~s~~~~~n~~~~~~~pf~pl~~~~~g~~~~~~~~~v~~~~~~~~r~~~~~~~aggf~~~~~~~r~l~ea~~Gl~~ 299 (300)
T KOG3800|consen 223 SSISLEPNENSEESAAFPFEPLRGEKEGPPMPGTKKIVARGYFAHIRAHTPEELAGGFTSNLACERALQEAFSGLFY 299 (300)
T ss_pred cccccccchhhhhccccccccccccccCCCCcChhhhhhhhhhHHhhcCChHHhhcCCcchHHHHHHHHHHhccccc
Confidence 111221 22 344445566555442 356666666668899999999999999999999999985
No 5
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=96.90 E-value=0.00012 Score=65.81 Aligned_cols=152 Identities=16% Similarity=0.101 Sum_probs=108.0
Q ss_pred hcccCCCCCChHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhcccccccCcC
Q 041187 23 YNKREEDFPSLKEYNDYLEEVEDMIFNLVEGVNVHEFEEKIQEYQKENAEQIMINQARKAEELAAALAASKGISAQDDTN 102 (189)
Q Consensus 23 fNk~e~DF~~l~~YNdYLE~vEdiifnL~~g~d~~~te~~l~~y~~~n~~~I~~n~~~~~ee~~~~~~~ek~~~~q~~~e 102 (189)
+|.++.-|++|-.||+|+.. |++++-+.++..+...|..+.+|+.+++..|.++-.|++++....+++-.....+- +
T Consensus 25 H~lCEsCvd~iF~~g~~~Cp-eC~~iLRk~nfr~q~fED~~vekEv~iRrri~~~~nk~~eeF~~~LaeyndylEe~--E 101 (300)
T KOG3800|consen 25 HRLCESCVDRIFSLGPAQCP-ECMVILRKNNFRVQTFEDPTVEKEVDIRRRILRIFNKKEEEFTGSLAEYNDYLEEV--E 101 (300)
T ss_pred chHHHHHHHHHHhcCCCCCC-cccchhhhcccchhhcchhHHHHHHHHHHHHHHHhccchhhhhhhHHHHhcccHHH--H
Confidence 56778889999999999999 99999999999999999999999999999999999999999886666554443321 0
Q ss_pred CCCCccccCCCccCCCCCCccccccCCCCCCCC-CCCCcccCCCCCCCCCCcHHHHHHHhhccccccccchHHHHHHHHH
Q 041187 103 GDPSQSALGGIGVGGTQGQYVPTLAGGQPRPTG-IPQPIAHAGGMDLHSYDNEAMMKLRAERGGRAAGWSMELSKKRALE 181 (189)
Q Consensus 103 e~~~~~~~~~~~~~~~~g~~~~~i~g~~~~~~~-~~~P~P~~GG~~~~~y~d~~~~~~R~~~~~~AGGys~~~~~~RaL~ 181 (189)
+ -+.+.+. ..-...+-..+++. .+.|.|+.++.....|+-+|+...+.. .=++||++.+..-+++..
T Consensus 102 d---iv~nl~~--------~~dv~~t~~k~~~ye~~nk~~I~~n~~R~~~~~e~~e~~l~~-ekr~~~~~r~~~~r~~~e 169 (300)
T KOG3800|consen 102 D---IVFNLGN--------NIDVTETKEKVKTYEEPNKDSIQNNKERVHREQEDLEQRLEL-EKRQKEFRREELEREAQE 169 (300)
T ss_pred H---HHHHhhc--------ccchhHHHHHHHHhhccCcccccCChhhcchHHHHHHHHHHH-HHHhhhHHHHHHHHHHHH
Confidence 0 0111111 00011111222221 234445578888777876666543332 235889999999999999
Q ss_pred HHhhccCC
Q 041187 182 EAFASIWI 189 (189)
Q Consensus 182 EAFsgl~~ 189 (189)
|+|.+.|+
T Consensus 170 e~~~s~~~ 177 (300)
T KOG3800|consen 170 EEIASAWV 177 (300)
T ss_pred HHHHHHhc
Confidence 99999994
No 6
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=62.39 E-value=69 Score=33.54 Aligned_cols=31 Identities=16% Similarity=0.306 Sum_probs=21.8
Q ss_pred HHHHhcccCCCCCChHHHHHHHHH-HHHHHHH
Q 041187 19 IASIYNKREEDFPSLKEYNDYLEE-VEDMIFN 49 (189)
Q Consensus 19 v~~ifNk~e~DF~~l~~YNdYLE~-vEdiifn 49 (189)
|++-+=..++||..-+.|-.-.|+ |-+||+.
T Consensus 407 ILQhlllirnDy~~rpqYykLIEecISqIvlH 438 (1102)
T KOG1924|consen 407 ILQHLLLIRNDYYIRPQYYKLIEECISQIVLH 438 (1102)
T ss_pred HHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHh
Confidence 455566788899988888777755 5566653
No 7
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=45.20 E-value=29 Score=24.27 Aligned_cols=48 Identities=23% Similarity=0.450 Sum_probs=39.9
Q ss_pred hcccCCCCCChHHHHHHHHHHHHHHHHhccCCCHHH----HHHHHHHHHHHh
Q 041187 23 YNKREEDFPSLKEYNDYLEEVEDMIFNLVEGVNVHE----FEEKIQEYQKEN 70 (189)
Q Consensus 23 fNk~e~DF~~l~~YNdYLE~vEdiifnL~~g~d~~~----te~~l~~y~~~n 70 (189)
++-+++||.+|.-|..|-.-|-=+|-+---|+-+.+ ..+|.++|+..|
T Consensus 3 ~~y~~ed~~~lt~yK~Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~~~n 54 (55)
T PF08073_consen 3 IDYTEEDFQNLTNYKAFSQHVRPLLAKANPKAPMSKLMMLLQAKWREFQEHN 54 (55)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHHhcC
Confidence 455789999999999999999999988888887755 577888888765
No 8
>PF07807 RED_C: RED-like protein C-terminal region; InterPro: IPR012492 This family contains sequences that are similar to the C-terminal region of Red protein (Q13123 from SWISSPROT). This and related proteins are thought to be localised to the nucleus, and contain a RED repeat which consists of a number of RE and RD sequence elements []. The region in question has several conserved NLS sequences []. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated or that the protein self-aggregates extremely efficiently [].
Probab=40.30 E-value=19 Score=28.85 Aligned_cols=21 Identities=33% Similarity=0.621 Sum_probs=19.2
Q ss_pred cCCCCCChHHHHHHHHHHHHH
Q 041187 26 REEDFPSLKEYNDYLEEVEDM 46 (189)
Q Consensus 26 ~e~DF~~l~~YNdYLE~vEdi 46 (189)
.+=||+|..+|.+|.+..|-|
T Consensus 37 ~RwDFdT~EEy~~Y~~~kEal 57 (118)
T PF07807_consen 37 GRWDFDTEEEYSKYMEQKEAL 57 (118)
T ss_pred ccCCCCCHHHHHHHHhhhhhC
Confidence 677999999999999999984
No 9
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=33.23 E-value=1.4e+02 Score=20.74 Aligned_cols=59 Identities=19% Similarity=0.385 Sum_probs=43.7
Q ss_pred HHHHHHHHHhcccCCCCC-ChHHHHHHHHHHHHHHHHhc---cCCCH---HHHHHHHHHHHHHhHH
Q 041187 14 AIRKRIASIYNKREEDFP-SLKEYNDYLEEVEDMIFNLV---EGVNV---HEFEEKIQEYQKENAE 72 (189)
Q Consensus 14 ~iRkrv~~ifNk~e~DF~-~l~~YNdYLE~vEdiifnL~---~g~d~---~~te~~l~~y~~~n~~ 72 (189)
+|.+++..+.+...++.. .++....+|++.+++|-.|- ++++. .....+|+.|+.+-..
T Consensus 7 ~i~~~l~~~~~~~~~~r~~~i~~~e~~l~ea~~~l~qMe~E~~~~p~s~r~~~~~kl~~yr~~l~~ 72 (79)
T PF05008_consen 7 EIKSKLERIKNLSGEQRKSLIREIERDLDEAEELLKQMELEVRSLPPSERNQYKSKLRSYRSELKK 72 (79)
T ss_dssp HHHHHHHHGGGS-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence 688889999887776664 67889999999999998774 45543 3467788888877654
No 10
>PTZ00233 variable surface protein Vir18; Provisional
Probab=31.39 E-value=1.4e+02 Score=29.31 Aligned_cols=58 Identities=16% Similarity=0.297 Sum_probs=43.9
Q ss_pred HHHHHhcccCCCCCChHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhHHHHHHHHHH
Q 041187 18 RIASIYNKREEDFPSLKEYNDYLEEVEDMIFNLVEGVNVHEFEEKIQEYQKENAEQIMINQAR 80 (189)
Q Consensus 18 rv~~ifNk~e~DF~~l~~YNdYLE~vEdiifnL~~g~d~~~te~~l~~y~~~n~~~I~~n~~~ 80 (189)
|++..| ++-....-+..|+.|+.+||.-|=+|-.-.. ..--++|.+-|+..|.+|...
T Consensus 10 ~~~n~y-q~~~~~~Cin~Y~~~K~EIEqkId~f~k~~~----~nFykew~~I~k~I~~KN~EL 67 (509)
T PTZ00233 10 RIINLY-QTYKTAPCMNTYSTLKSDIEQKIDDFNKATH----TNIYTQWDQLNKYIITKDAEL 67 (509)
T ss_pred hHHHHH-HhhcccchhHhHHHHHHHHHHHHHHHhhccc----hhHHHHHHHHHHHHHhhhhhh
Confidence 377777 5667788999999999999999988865443 234467888888888888643
No 11
>smart00150 SPEC Spectrin repeats.
Probab=31.37 E-value=1.4e+02 Score=20.15 Aligned_cols=40 Identities=18% Similarity=0.247 Sum_probs=31.7
Q ss_pred ChHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhH
Q 041187 32 SLKEYNDYLEEVEDMIFNLVEGVNVHEFEEKIQEYQKENA 71 (189)
Q Consensus 32 ~l~~YNdYLE~vEdiifnL~~g~d~~~te~~l~~y~~~n~ 71 (189)
++.+-.+.|++.|.++-....|.|++.++..+++++.-..
T Consensus 6 ~~~~l~~Wl~~~e~~l~~~~~~~d~~~~~~~~~~~~~~~~ 45 (101)
T smart00150 6 DADELEAWLSEKEALLASEDLGKDLESVEALLKKHEALEA 45 (101)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHH
Confidence 5667788899999887777788899999999987765443
No 12
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=29.38 E-value=78 Score=20.53 Aligned_cols=29 Identities=24% Similarity=0.453 Sum_probs=17.7
Q ss_pred hHHHHHHHHHHHHhcccCCCCCChHHHHHHH
Q 041187 10 NRELAIRKRIASIYNKREEDFPSLKEYNDYL 40 (189)
Q Consensus 10 ekEv~iRkrv~~ifNk~e~DF~~l~~YNdYL 40 (189)
-|..-|.+||.+..... .++|..+|-++|
T Consensus 23 ~K~~~l~rRl~~rm~~~--~~~~~~~y~~~L 51 (57)
T PF03705_consen 23 YKRSLLERRLARRMRAL--GLPSFAEYYELL 51 (57)
T ss_dssp GGHHHHHHHHHHHHHHH--T---HHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHc--CCCCHHHHHHHH
Confidence 67788999999888754 344444444444
No 13
>COG3310 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.24 E-value=43 Score=28.64 Aligned_cols=37 Identities=16% Similarity=0.432 Sum_probs=23.7
Q ss_pred HHHHHHHHHhcccCCC-----------CCChHHHHHHHHHHHHHHHHh
Q 041187 14 AIRKRIASIYNKREED-----------FPSLKEYNDYLEEVEDMIFNL 50 (189)
Q Consensus 14 ~iRkrv~~ifNk~e~D-----------F~~l~~YNdYLE~vEdiifnL 50 (189)
++++.++..=|+--.. |++..+|||||+.+|-+|-.+
T Consensus 61 hl~~ell~L~~tpa~eleTTLlV~P~ll~DF~d~n~~ld~~dA~i~~~ 108 (196)
T COG3310 61 HLDEELLRLRNTPATELETTLLVHPTLLPDFDDFNDMLDIADAAIVEN 108 (196)
T ss_pred HHHHHHHHhcCCchhhhceeEEeeccccchhhHHHHHHHHHHHHHHhc
Confidence 4555555554544333 345568999999999887543
No 14
>PHA03141 helicase-primase primase subunit; Provisional
Probab=28.27 E-value=1.3e+02 Score=23.59 Aligned_cols=34 Identities=21% Similarity=0.439 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHh--ccCCCHHHHHHHHHHHHH
Q 041187 35 EYNDYLEEVEDMIFNL--VEGVNVHEFEEKIQEYQK 68 (189)
Q Consensus 35 ~YNdYLE~vEdiifnL--~~g~d~~~te~~l~~y~~ 68 (189)
.|+.||++.=+++..+ -++.+-.++..+|+.|.+
T Consensus 61 ~y~~Yl~~~L~~~~~v~g~~~~~~~~~~~~le~~~~ 96 (101)
T PHA03141 61 DFAAYLHEALSVFSKVGGEAGTINKETDHKLEGFKK 96 (101)
T ss_pred cHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHH
Confidence 6999999998887777 233444677889988875
No 15
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=25.93 E-value=2.3e+02 Score=21.60 Aligned_cols=38 Identities=24% Similarity=0.245 Sum_probs=28.6
Q ss_pred HHHHhccCCC----HHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 041187 46 MIFNLVEGVN----VHEFEEKIQEYQKENAEQIMINQARKAE 83 (189)
Q Consensus 46 iifnL~~g~d----~~~te~~l~~y~~~n~~~I~~n~~~~~e 83 (189)
+.|.|+.|.. ..+.++++..-+++|+..-.+|...+.+
T Consensus 15 l~y~l~~g~~G~~~~~~l~~q~~~~~~e~~~l~~~n~~L~~e 56 (105)
T PRK00888 15 LQYSLWFGKNGILDYWRVNDQVAAQQQTNAKLKARNDQLFAE 56 (105)
T ss_pred HHHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567776655 5778889999999999988888765443
No 16
>PF13434 K_oxygenase: L-lysine 6-monooxygenase (NADPH-requiring); PDB: 3S61_B 3S5W_B.
Probab=22.70 E-value=57 Score=29.41 Aligned_cols=35 Identities=37% Similarity=0.533 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHHHhcccCCCCCChHHHHHHHHHHHH
Q 041187 10 NRELAIRKRIASIYNKREEDFPSLKEYNDYLEEVED 45 (189)
Q Consensus 10 ekEv~iRkrv~~ifNk~e~DF~~l~~YNdYLE~vEd 45 (189)
-.=+.-+.|+..-||. +..|++..+|||||..|=+
T Consensus 72 lnYL~~~~rl~~f~~~-~~~~p~R~ef~dYl~Wva~ 106 (341)
T PF13434_consen 72 LNYLHEHGRLYEFYNR-GYFFPSRREFNDYLRWVAE 106 (341)
T ss_dssp HHHHHHTT-HHHHHHH---SS-BHHHHHHHHHHHHC
T ss_pred HHHHHHcCChhhhhhc-CCCCCCHHHHHHHHHHHHH
Confidence 4445556788888884 4667899999999988643
No 17
>PF13904 DUF4207: Domain of unknown function (DUF4207)
Probab=21.78 E-value=1.3e+02 Score=26.45 Aligned_cols=17 Identities=24% Similarity=0.556 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHhHHH
Q 041187 57 HEFEEKIQEYQKENAEQ 73 (189)
Q Consensus 57 ~~te~~l~~y~~~n~~~ 73 (189)
+++...+..|...-..+
T Consensus 180 e~a~~~~q~W~~kK~~e 196 (264)
T PF13904_consen 180 EEAKQRYQEWERKKKEE 196 (264)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 55666777776554443
No 18
>PHA03369 capsid maturational protease; Provisional
Probab=21.21 E-value=7.4e+02 Score=25.25 Aligned_cols=56 Identities=20% Similarity=0.213 Sum_probs=40.2
Q ss_pred HhcccCCCCCChHHHHHHHHHHHHHHHHhccCCCH---HHHHHHHHHHHHHhHHHHHHH
Q 041187 22 IYNKREEDFPSLKEYNDYLEEVEDMIFNLVEGVNV---HEFEEKIQEYQKENAEQIMIN 77 (189)
Q Consensus 22 ifNk~e~DF~~l~~YNdYLE~vEdiifnL~~g~d~---~~te~~l~~y~~~n~~~I~~n 77 (189)
+-|.++.+|+.-++|-.++|+.=+-|++|..-.-+ .+=+.-++.|-.+..+.-..-
T Consensus 280 ~~n~s~~ss~es~E~~~~~e~~~~ql~~~~k~l~~~~~~kde~v~~~yl~~G~~~F~~I 338 (663)
T PHA03369 280 TLNPSFGSSDESPEWKTFYEALADQLNNLYKLLRTIYKHKDETVIEQYLIEGRKLFSTI 338 (663)
T ss_pred ccCCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHhccCccchHHHHHHHHHHHHHHHH
Confidence 46999999999999999999999999998743311 112445566666666665444
No 19
>PF14284 PcfJ: PcfJ-like protein
Probab=20.24 E-value=4.5e+02 Score=21.39 Aligned_cols=19 Identities=26% Similarity=0.490 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHhccCC
Q 041187 36 YNDYLEEVEDMIFNLVEGV 54 (189)
Q Consensus 36 YNdYLE~vEdiifnL~~g~ 54 (189)
|.|||.+.+.+=.+|.+..
T Consensus 2 w~DYl~m~~~l~~d~~~~~ 20 (169)
T PF14284_consen 2 WKDYLRMLEKLGKDLNNEI 20 (169)
T ss_pred hHHHHHHHHHhCccccccc
Confidence 8999999999977777664
Done!