Query psy9354
Match_columns 308
No_of_seqs 122 out of 136
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 17:00:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9354.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9354hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2829|consensus 100.0 9.4E-82 2E-86 590.4 22.9 221 24-251 19-269 (326)
2 PF08781 DP: Transcription fac 100.0 5.7E-53 1.2E-57 363.2 16.2 140 112-253 1-141 (142)
3 PF02319 E2F_TDP: E2F/DP famil 97.6 2.1E-05 4.6E-10 60.4 1.7 55 50-105 1-71 (71)
4 KOG2577|consensus 92.8 4 8.7E-05 40.9 14.6 146 46-200 64-234 (354)
5 PF11315 Med30: Mediator compl 50.0 31 0.00067 30.8 4.7 31 112-142 104-134 (150)
6 KOG2264|consensus 47.4 38 0.00082 36.8 5.6 16 185-200 190-205 (907)
7 PF07106 TBPIP: Tat binding pr 47.0 1.5E+02 0.0032 25.8 8.5 61 67-127 12-87 (169)
8 PF13404 HTH_AsnC-type: AsnC-t 46.5 29 0.00063 24.3 3.2 24 58-81 4-27 (42)
9 PF14931 IFT20: Intraflagellar 46.2 37 0.0008 29.1 4.5 73 72-148 37-109 (120)
10 PF08880 QLQ: QLQ; InterPro: 40.2 32 0.0007 23.9 2.7 19 132-150 5-23 (37)
11 PF10481 CENP-F_N: Cenp-F N-te 39.6 33 0.00071 33.9 3.5 37 103-139 8-45 (307)
12 PRK11179 DNA-binding transcrip 36.7 43 0.00093 28.7 3.5 29 53-81 5-33 (153)
13 KOG3088|consensus 36.6 89 0.0019 31.1 6.0 49 111-165 59-107 (313)
14 cd00890 Prefoldin Prefoldin is 29.3 3E+02 0.0066 22.1 7.6 56 94-149 65-124 (129)
15 PF10473 CENP-F_leu_zip: Leuci 29.0 2E+02 0.0043 25.4 6.4 41 112-152 73-113 (140)
16 TIGR00325 lpxC UDP-3-0-acyl N- 28.0 1.2E+02 0.0026 29.9 5.4 47 174-220 144-206 (297)
17 cd06445 ATase The DNA repair p 26.9 70 0.0015 24.7 2.9 23 60-82 3-28 (79)
18 PF09766 FimP: Fms-interacting 26.8 1.6E+02 0.0034 29.3 6.0 34 114-147 110-143 (355)
19 PF03392 OS-D: Insect pheromon 26.5 28 0.00061 28.5 0.6 27 215-242 23-49 (95)
20 PRK11169 leucine-responsive tr 26.4 69 0.0015 27.7 3.1 30 52-81 9-38 (164)
21 PF08501 Shikimate_dh_N: Shiki 24.7 22 0.00047 27.7 -0.3 17 10-26 1-17 (83)
22 PF01035 DNA_binding_1: 6-O-me 23.7 67 0.0015 25.4 2.3 24 58-81 3-29 (85)
23 PF11594 Med28: Mediator compl 23.5 2.4E+02 0.0052 24.1 5.7 35 116-150 39-73 (106)
24 COG1522 Lrp Transcriptional re 23.4 82 0.0018 26.1 2.9 25 57-81 8-32 (154)
25 PF07904 Eaf7: Chromatin modif 23.3 1.1E+02 0.0024 24.8 3.5 32 55-86 19-58 (91)
26 PF02050 FliJ: Flagellar FliJ 23.2 3.4E+02 0.0075 20.7 7.3 44 114-157 61-104 (123)
27 PHA03188 UL14 tegument protein 23.1 2.8E+02 0.0061 26.1 6.5 43 114-156 58-102 (199)
28 PRK03947 prefoldin subunit alp 22.9 4.6E+02 0.0099 22.0 7.5 15 93-107 71-85 (140)
29 PF08317 Spc7: Spc7 kinetochor 22.7 2.5E+02 0.0053 27.3 6.4 38 116-153 234-271 (325)
30 PF04568 IATP: Mitochondrial A 22.5 2.4E+02 0.0051 23.7 5.4 29 113-141 70-98 (100)
31 PTZ00481 Membrane attack compl 22.3 2.5E+02 0.0054 29.7 6.5 116 96-216 319-438 (524)
32 PF03331 LpxC: UDP-3-O-acyl N- 22.3 1.8E+02 0.004 28.2 5.4 49 172-220 142-207 (277)
33 cd00024 CHROMO Chromatin organ 22.1 73 0.0016 21.9 2.0 19 100-118 23-43 (55)
34 PF09278 MerR-DNA-bind: MerR, 22.0 2.3E+02 0.0049 20.4 4.7 32 112-143 32-63 (65)
35 CHL00081 chlI Mg-protoporyphyr 21.9 1.8E+02 0.0038 29.1 5.3 86 166-254 182-285 (350)
36 smart00298 CHROMO Chromatin or 21.8 1.3E+02 0.0028 20.5 3.2 19 100-118 21-41 (55)
37 smart00787 Spc7 Spc7 kinetocho 20.7 2.8E+02 0.006 27.3 6.3 37 117-153 230-266 (312)
38 PRK07720 fliJ flagellar biosyn 20.5 4E+02 0.0087 22.4 6.6 41 117-157 83-123 (146)
39 PF08678 Rsbr_N: Rsbr N termin 20.2 96 0.0021 27.1 2.7 24 52-75 78-101 (129)
40 PF10828 DUF2570: Protein of u 20.2 5E+02 0.011 21.4 7.1 46 112-157 25-70 (110)
41 TIGR00589 ogt O-6-methylguanin 20.0 1.2E+02 0.0026 24.0 3.0 24 58-81 3-29 (80)
No 1
>KOG2829|consensus
Probab=100.00 E-value=9.4e-82 Score=590.38 Aligned_cols=221 Identities=49% Similarity=0.792 Sum_probs=209.0
Q ss_pred cccccccccCCCCCC-CCCCcccccccccCcchhhhhHHHHHHHhhcCCcchHHHHHHHHHhhhcccC------------
Q psy9354 24 ATVKYAKKRSSAGLG-DEGGAYKRSREKASKGLRHFSMKVCEKVRRKGVTTYNEVADELVQEFSEDHN------------ 90 (308)
Q Consensus 24 ~tq~~~~kr~~~~~s-~~~~~krk~~ek~~kGLRhfSmKVcEKVqeKg~TTYnEVADELV~E~~~~~~------------ 90 (308)
|.++.+ +.+. .|++++.++++++++|||||||+|||||++||+|||||||||||++|...++
T Consensus 19 ~~~~~~-----s~~~~~~~a~~~~ks~k~g~gLRhfs~kVCeKve~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd 93 (326)
T KOG2829|consen 19 VLGNQP-----SDSGSSWSAGRKRKSDKAGGGLRHFSMKVCEKVERKGTTTYNEVADELVAEFAGANNYSHICPNEQEYD 93 (326)
T ss_pred cccCCc-----CCCCCccccccCCCCCCCCcchhhhhHHHHHHHHhcCCccHHHHHHHHHHHHhccccccccCccccccc
Confidence 555544 4444 8999989999999999999999999999999999999999999999988761
Q ss_pred -----------------cccccccCccEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q psy9354 91 -----------------TASSEQEKKEIKWLGLPTNSLQESLNLNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKNI 153 (308)
Q Consensus 91 -----------------i~IIsKeKKeIkWiGLPtns~qe~~~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~RNk 153 (308)
++||+|+||+|+|+|||+|+.++|++|++|++++++||++|+++||||++|++||||||+||+
T Consensus 94 ~KNIRRRVYDALNVlmAmnIIsKdKKEIrW~GLP~~ss~dv~~le~Er~k~~erI~kK~a~lqEl~~q~~~fknLV~RN~ 173 (326)
T KOG2829|consen 94 QKNIRRRVYDALNVLMAMNIISKDKKEIRWIGLPATSSQDVSELEEERKKRMERIKKKAAQLQELIEQVSAFKNLVQRNR 173 (326)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcccceeeeeccCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 369999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhcCCCCCCCccccceEEEEcCCCCeEEeeeecCcceEEEEcCCceeeeccHHHHHHhhccCCCCCCCCCHHHHHHH
Q psy9354 154 DSEKIHGEPAPSSAIQLPFLIVSTDKKTVIDCSMSNDKTEYLFVFDNKFEIHDDIEILKRMGLGMGLDKGEWTEEDLQEA 233 (308)
Q Consensus 154 ~~e~~~~~~~~~~~I~LPFIlV~Tsk~t~IdCeiS~Dk~ey~F~F~~~FEIhDD~eILK~Mgl~~gLe~g~~s~edl~~a 233 (308)
.++..+++|+++ |+||||||+|+++|+|+|+||+|+++|+|+||+||+||||++|||+||++|||+.|.||++|++.|
T Consensus 174 ~~e~~~~~P~~~--i~LPFiiinT~k~a~IeceiseDks~~~F~FnktFevHDD~eILK~m~~~~~le~~~~saed~~~~ 251 (326)
T KOG2829|consen 174 HAESQGQPPSEN--IHLPFIIINTSKKAVIECEISEDKSEYLFKFNKTFEVHDDIEILKRMGENCGLEQGNCSAEDLKIA 251 (326)
T ss_pred hhhhccCCCCcc--cccceEEEecCCCceEEEEecccceeeeeecCCceeeccHHHHHHHHHhhcccccCCCCHHHHHHH
Confidence 999976666554 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhccchhhHHHHHHHhhc
Q psy9354 234 KRLVAPCMEKYVNQIAYN 251 (308)
Q Consensus 234 k~lvPk~l~~yv~~~~~~ 251 (308)
++|+|++|++|++.|++|
T Consensus 252 ~s~~p~~~e~~~~~~~~~ 269 (326)
T KOG2829|consen 252 KSLVPEALEKYVENINTG 269 (326)
T ss_pred HhhCcccccccccccccc
Confidence 999999999999999999
No 2
>PF08781 DP: Transcription factor DP; InterPro: IPR014889 DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer [] and negatively regulates the G1-S transition. ; PDB: 2AZE_A.
Probab=100.00 E-value=5.7e-53 Score=363.15 Aligned_cols=140 Identities=48% Similarity=0.813 Sum_probs=125.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhcCCCCCCCccccceEEEEcCCCCeEEeeeecCc
Q psy9354 112 QESLNLNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKNIDSEKIHGEPAPSSAIQLPFLIVSTDKKTVIDCSMSNDK 191 (308)
Q Consensus 112 qe~~~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~RNk~~e~~~~~~~~~~~I~LPFIlV~Tsk~t~IdCeiS~Dk 191 (308)
|+|++|++|++++++||++|+++||||++|++||||||+||+++++.++.|+ ++|+||||||+|+++|+|+|+||+|+
T Consensus 1 q~~~~Le~ek~~~~~rI~~K~~~LqEL~~Q~va~knLv~RN~~~~~~~~~p~--~~i~LPFIlV~T~~~a~I~ceiS~D~ 78 (142)
T PF08781_consen 1 QECEELEEEKQRRRERIKKKKEQLQELILQQVAFKNLVQRNRQLEQSGNAPS--SGIQLPFILVNTSKKAVIECEISEDK 78 (142)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSS----GEEESS-EEEEEESS--EEEEE-TTS
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCC--CeeecCEEEEEecCCcEEEEEEcCCc
Confidence 6899999999999999999999999999999999999999999999755544 89999999999999999999999999
Q ss_pred ceEEEEcCCc-eeeeccHHHHHHhhccCCCCCCCCCHHHHHHHHhccchhhHHHHHHHhhcCC
Q psy9354 192 TEYLFVFDNK-FEIHDDIEILKRMGLGMGLDKGEWTEEDLQEAKRLVAPCMEKYVNQIAYNDG 253 (308)
Q Consensus 192 ~ey~F~F~~~-FEIhDD~eILK~Mgl~~gLe~g~~s~edl~~ak~lvPk~l~~yv~~~~~~~~ 253 (308)
++|+|+||++ ||||||++|||+|||++||++|.|++++++.|++++|++|++||++||.|+.
T Consensus 79 ~~~~F~Fn~~pFeIhDD~eVLK~m~~~~~~~~~~~~~~~~~~~~s~~p~~l~~yv~~~~~~~~ 141 (142)
T PF08781_consen 79 SEYHFDFNSTPFEIHDDIEVLKRMGLAFGLESGSCTPEDLAKAKSLVPKALEPYVDEMAQGTS 141 (142)
T ss_dssp SEEEEEESS--EEEEEHHHHHHHTTTTTTGGGT---HHHHHHHHHTS-GGGHHHHHHHHHSTT
T ss_pred cEEEEEcCCCceeeechHHHHHHHHhhcCCCCCCCCccchhcccccCCccchhhhHHHhhcCC
Confidence 9999999998 9999999999999999999999999999999999999999999999999975
No 3
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=97.65 E-value=2.1e-05 Score=60.44 Aligned_cols=55 Identities=25% Similarity=0.462 Sum_probs=43.2
Q ss_pred ccCcchhhhhHH---HHHHHhhcCCcchHHHHHHHHHhhhccc------------Ccccccc-cCccEEEec
Q psy9354 50 KASKGLRHFSMK---VCEKVRRKGVTTYNEVADELVQEFSEDH------------NTASSEQ-EKKEIKWLG 105 (308)
Q Consensus 50 k~~kGLRhfSmK---VcEKVqeKg~TTYnEVADELV~E~~~~~------------~i~IIsK-eKKeIkWiG 105 (308)
++.+||.+++.+ +|+..+. +.+++++||++|+.+-.... +++||.| .|+.++|+|
T Consensus 1 r~~~sL~~lt~~fi~~~~~~~~-~~i~l~~ia~~l~~~~~k~~~RRlYDI~NVLealgli~K~~k~~~~W~G 71 (71)
T PF02319_consen 1 RKEKSLKLLTQRFIQLFESSPD-KSISLNEIADKLISENVKTQRRRLYDIINVLEALGLIEKQSKNSYKWIG 71 (71)
T ss_dssp TTTTHHHHHHHHHHHHHHHCCC-TEEEHHHHHHHCHHHCCHHHCHHHHHHHHHHHHCTSEEEEETTEEEE--
T ss_pred CCcCCHHHHHHHHHHHHHHCCC-CcccHHHHHHHHcccccccccchhhHHHHHHHHhCceeecCCCceEecC
Confidence 467899999999 7777766 99999999999998822111 4689999 888999998
No 4
>KOG2577|consensus
Probab=92.80 E-value=4 Score=40.91 Aligned_cols=146 Identities=18% Similarity=0.245 Sum_probs=79.8
Q ss_pred ccccccCcchhhhhHHHHHHHhhc--CCcchHHHHHHHHHhhhccc--------Ccccccc-cCccEEEecCCCCC----
Q psy9354 46 RSREKASKGLRHFSMKVCEKVRRK--GVTTYNEVADELVQEFSEDH--------NTASSEQ-EKKEIKWLGLPTNS---- 110 (308)
Q Consensus 46 k~~ek~~kGLRhfSmKVcEKVqeK--g~TTYnEVADELV~E~~~~~--------~i~IIsK-eKKeIkWiGLPtns---- 110 (308)
.++-+..+.|-.+..|-...|++- |.-.-|++|+.|=-- +-.- .|++|.| .|..|+|+|--.++
T Consensus 64 ~~~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L~Vq-KRRIYDITNVLEGI~LIeKksKN~IqW~G~~~~~~~~~ 142 (354)
T KOG2577|consen 64 SESTRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVLNVQ-KRRIYDITNVLEGIGLIEKKSKNNIQWIGGDFNSTGGV 142 (354)
T ss_pred CCcccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHhccc-cceeeehhhhhhcccceeeccccceeeecCCCcccccc
Confidence 455667778999999999999876 599999999998322 1111 3567766 45679999987664
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH---HhHhhhhh----cCCCCCCCccccc-eEEEEcCCCC
Q psy9354 111 LQESLNLNKERKQLIQRINQKTRHLHDLL-LQQISLKKLIQ---KNIDSEKI----HGEPAPSSAIQLP-FLIVSTDKKT 181 (308)
Q Consensus 111 ~qe~~~Le~ek~k~~erIkqKk~~LqELi-~Q~iA~KnLV~---RNk~~e~~----~~~~~~~~~I~LP-FIlV~Tsk~t 181 (308)
...++.|+.|... +.+....|-+|+ .-+..|++|.+ .++.++-. ..-+ .++-= .|+|.....+
T Consensus 143 ~e~~~~l~~e~~~----L~~~E~~LD~~i~~~q~~L~~lted~~n~~laYVT~eDI~~i~----~f~~q~vi~vkap~et 214 (354)
T KOG2577|consen 143 PERLNGLEAEVED----LSQEEDDLDQLIRDCQQNLRLLTEDVENRRLAYVTYEDIRSIP----GFDEQTVIAVKAPPET 214 (354)
T ss_pred HHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHhcchhcccceeeeHHHHhhcc----ccCCceEEEEecCCcc
Confidence 2334444444332 222222332222 12223333322 22222111 1111 11222 2467777778
Q ss_pred eEEeeee-cCcceEEEEcCC
Q psy9354 182 VIDCSMS-NDKTEYLFVFDN 200 (308)
Q Consensus 182 ~IdCeiS-~Dk~ey~F~F~~ 200 (308)
..+|-+. .++..+...-++
T Consensus 215 ~levp~~~~~~~~i~L~s~~ 234 (354)
T KOG2577|consen 215 RLEVPDPDEDRYQIRLKSNQ 234 (354)
T ss_pred eEecccCCCCceEEEeccCC
Confidence 8887777 555555555443
No 5
>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.
Probab=49.95 E-value=31 Score=30.85 Aligned_cols=31 Identities=35% Similarity=0.554 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9354 112 QESLNLNKERKQLIQRINQKTRHLHDLLLQQ 142 (308)
Q Consensus 112 qe~~~Le~ek~k~~erIkqKk~~LqELi~Q~ 142 (308)
.+...+.+|+.++.+++.+|.++|.+++.|.
T Consensus 104 ~~~~~~~~er~el~e~v~~KN~qLk~iid~l 134 (150)
T PF11315_consen 104 EEYRQLLEERKELIEQVKQKNQQLKEIIDQL 134 (150)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555688999999999999999999999884
No 6
>KOG2264|consensus
Probab=47.35 E-value=38 Score=36.79 Aligned_cols=16 Identities=25% Similarity=0.517 Sum_probs=10.3
Q ss_pred eeeecCcceEEEEcCC
Q psy9354 185 CSMSNDKTEYLFVFDN 200 (308)
Q Consensus 185 CeiS~Dk~ey~F~F~~ 200 (308)
|+++.-.--|.++-|.
T Consensus 190 CsltSgfPVYvyd~D~ 205 (907)
T KOG2264|consen 190 CSLTSGFPVYVYDSDI 205 (907)
T ss_pred ccccCCceeEEeccce
Confidence 6666666667666654
No 7
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=47.02 E-value=1.5e+02 Score=25.84 Aligned_cols=61 Identities=20% Similarity=0.220 Sum_probs=33.4
Q ss_pred hhcCCcchHHHHHHHHHhhhccc----------Cccccccc-CccEEE-e---cCCCCCHHHHHHHHHHHHHHHHH
Q psy9354 67 RRKGVTTYNEVADELVQEFSEDH----------NTASSEQE-KKEIKW-L---GLPTNSLQESLNLNKERKQLIQR 127 (308)
Q Consensus 67 qeKg~TTYnEVADELV~E~~~~~----------~i~IIsKe-KKeIkW-i---GLPtns~qe~~~Le~ek~k~~er 127 (308)
+..+--|.++|.|.|=..+.+.. .-.|+.|. ||...| . +++..+..+...+..+...+++.
T Consensus 12 ~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~~~~~~s~eel~~ld~ei~~L~~e 87 (169)
T PF07106_consen 12 EQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFANQDELEVPSPEELAELDAEIKELREE 87 (169)
T ss_pred HcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeecceEEEeeCccccCCCCchhHHHHHHHHHHHHHH
Confidence 34566678899999988887765 12377776 444444 2 44433444433333333333333
No 8
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=46.47 E-value=29 Score=24.26 Aligned_cols=24 Identities=29% Similarity=0.551 Sum_probs=19.1
Q ss_pred hhHHHHHHHhhcCCcchHHHHHHH
Q psy9354 58 FSMKVCEKVRRKGVTTYNEVADEL 81 (308)
Q Consensus 58 fSmKVcEKVqeKg~TTYnEVADEL 81 (308)
+=.++...+++.++++|.+||.++
T Consensus 4 ~D~~Il~~Lq~d~r~s~~~la~~l 27 (42)
T PF13404_consen 4 LDRKILRLLQEDGRRSYAELAEEL 27 (42)
T ss_dssp HHHHHHHHHHH-TTS-HHHHHHHH
T ss_pred HHHHHHHHHHHcCCccHHHHHHHH
Confidence 456788999999999999999885
No 9
>PF14931 IFT20: Intraflagellar transport complex B, subunit 20
Probab=46.21 E-value=37 Score=29.10 Aligned_cols=73 Identities=19% Similarity=0.253 Sum_probs=46.3
Q ss_pred cchHHHHHHHHHhhhcccCcccccccCccEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9354 72 TTYNEVADELVQEFSEDHNTASSEQEKKEIKWLGLPTNSLQESLNLNKERKQLIQRINQKTRHLHDLLLQQISLKKL 148 (308)
Q Consensus 72 TTYnEVADELV~E~~~~~~i~IIsKeKKeIkWiGLPtns~qe~~~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnL 148 (308)
+.++.|...++..+..-. .-| |+.+++-||+-+--......-+.+.+.+...|..|+.+|.-|-.++.+|+.+
T Consensus 37 ~~F~~iv~~~~~~~~~~A--~~V--E~eKlkAIG~RN~l~s~~k~R~~~~q~lq~~I~Ek~~eLERl~~E~~sL~kv 109 (120)
T PF14931_consen 37 SEFQKIVKGFIEILDELA--KRV--ENEKLKAIGARNLLKSEAKQREAQQQQLQALIAEKKMELERLRSEYESLQKV 109 (120)
T ss_pred HHHHHHHHHHHHHHHHHH--HHH--HHHHHHHHHhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356665555555443222 112 3444666775532223334456677888999999999999999999998765
No 10
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=40.17 E-value=32 Score=23.89 Aligned_cols=19 Identities=26% Similarity=0.347 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy9354 132 TRHLHDLLLQQISLKKLIQ 150 (308)
Q Consensus 132 k~~LqELi~Q~iA~KnLV~ 150 (308)
..||++|..|..|||.|..
T Consensus 5 ~~Ql~~L~~Qi~ayK~l~~ 23 (37)
T PF08880_consen 5 PAQLQELRAQILAYKYLAR 23 (37)
T ss_pred HHHHHHHHHHHHHHHHHHc
Confidence 4689999999999999765
No 11
>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []. Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].
Probab=39.57 E-value=33 Score=33.89 Aligned_cols=37 Identities=32% Similarity=0.527 Sum_probs=0.0
Q ss_pred E-ecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9354 103 W-LGLPTNSLQESLNLNKERKQLIQRINQKTRHLHDLL 139 (308)
Q Consensus 103 W-iGLPtns~qe~~~Le~ek~k~~erIkqKk~~LqELi 139 (308)
| .|||+...+.++.|+...++++..=+||+=+|.-|.
T Consensus 8 WKeGL~~~aLqKIqelE~QldkLkKE~qQrQfQleSlE 45 (307)
T PF10481_consen 8 WKEGLPTRALQKIQELEQQLDKLKKERQQRQFQLESLE 45 (307)
T ss_pred HhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
No 12
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=36.65 E-value=43 Score=28.65 Aligned_cols=29 Identities=17% Similarity=0.312 Sum_probs=25.5
Q ss_pred cchhhhhHHHHHHHhhcCCcchHHHHHHH
Q psy9354 53 KGLRHFSMKVCEKVRRKGVTTYNEVADEL 81 (308)
Q Consensus 53 kGLRhfSmKVcEKVqeKg~TTYnEVADEL 81 (308)
..|-.+=.++.+.++..+++||.|+|.+|
T Consensus 5 ~~lD~~D~~Il~~Lq~d~R~s~~eiA~~l 33 (153)
T PRK11179 5 YQIDNLDRGILEALMENARTPYAELAKQF 33 (153)
T ss_pred cccCHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 34667778899999999999999999986
No 13
>KOG3088|consensus
Probab=36.59 E-value=89 Score=31.12 Aligned_cols=49 Identities=16% Similarity=0.191 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhcCCCCCC
Q psy9354 111 LQESLNLNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKNIDSEKIHGEPAPS 165 (308)
Q Consensus 111 ~qe~~~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~RNk~~e~~~~~~~~~ 165 (308)
.++...-++|.+++++.|++|.+.|. +.+.+++++ |..-+.++.||-|+
T Consensus 59 a~~~~~kq~eL~~rqeEL~Rke~ELd---RREr~~a~~---g~~~~~nNWPPLP~ 107 (313)
T KOG3088|consen 59 AKDLAKKQAELLKKQEELRRKEQELD---RRERALARA---GIVIRENNWPPLPS 107 (313)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHh---HHHHHHhhc---cCcccccCCCCCCC
Confidence 56666667888888888888876554 456666663 33333345555443
No 14
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=29.34 E-value=3e+02 Score=22.13 Aligned_cols=56 Identities=25% Similarity=0.251 Sum_probs=27.4
Q ss_pred ccccCccEEEecCCCC---CHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9354 94 SEQEKKEIKWLGLPTN---SLQE-SLNLNKERKQLIQRINQKTRHLHDLLLQQISLKKLI 149 (308)
Q Consensus 94 IsKeKKeIkWiGLPtn---s~qe-~~~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV 149 (308)
|..+++-+.|+|...- +..+ ...|+.....+..+++.=.+.+.++..+...++.-+
T Consensus 65 i~~~~~v~v~iG~~~~ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l 124 (129)
T cd00890 65 VKDDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEEL 124 (129)
T ss_pred ECCCCEEEEEecCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3477888999997532 1222 223333334444444444444444444444444433
No 15
>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding
Probab=28.96 E-value=2e+02 Score=25.43 Aligned_cols=41 Identities=24% Similarity=0.332 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy9354 112 QESLNLNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKN 152 (308)
Q Consensus 112 qe~~~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~RN 152 (308)
.+...+..++..+...+++|+....+|..-...|.+||+.=
T Consensus 73 ~EL~~l~sEk~~L~k~lq~~q~kv~eLE~~~~~~~~~l~~~ 113 (140)
T PF10473_consen 73 LELDTLRSEKENLDKELQKKQEKVSELESLNSSLENLLQEK 113 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 45666778888899999999999999999999999999853
No 16
>TIGR00325 lpxC UDP-3-0-acyl N-acetylglucosamine deacetylase. UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase from E. coli, LpxC, was previously designated EnvA. This enzyme is involved in lipid-A precursor biosynthesis. It is essential for cell viability.
Probab=28.04 E-value=1.2e+02 Score=29.88 Aligned_cols=47 Identities=28% Similarity=0.343 Sum_probs=34.2
Q ss_pred EEEcCCCCeEEeeeecC-----cceEEEEcC-----------CceeeeccHHHHHHhhccCCC
Q psy9354 174 IVSTDKKTVIDCSMSND-----KTEYLFVFD-----------NKFEIHDDIEILKRMGLGMGL 220 (308)
Q Consensus 174 lV~Tsk~t~IdCeiS~D-----k~ey~F~F~-----------~~FEIhDD~eILK~Mgl~~gL 220 (308)
.+--+..-.|.|.|.=+ ++.|.|.++ .||-+..|+|-|+++||+.|-
T Consensus 144 ~~~P~~~~~i~~~Idf~~~~ig~Q~~~~~~~~~~f~~eIA~ARTFgf~~eve~L~~~GLa~Gg 206 (297)
T TIGR00325 144 EFKPYNGFRLDFTIDFNHPAIGKQWYTMNFSAEAFATQIARARTFGFMDDIEYLRSAGLIKGG 206 (297)
T ss_pred EEEcCCCcEEEEEEECCCCcccceEEEEeCCHHHHHHHhcCCceEEcHHHHHHHHHCCccccc
Confidence 33334557788887654 466666654 579999999999999998864
No 17
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=26.95 E-value=70 Score=24.75 Aligned_cols=23 Identities=35% Similarity=0.384 Sum_probs=16.5
Q ss_pred HHHHHHHh---hcCCcchHHHHHHHH
Q psy9354 60 MKVCEKVR---RKGVTTYNEVADELV 82 (308)
Q Consensus 60 mKVcEKVq---eKg~TTYnEVADELV 82 (308)
.+|++.|. .=.++||.+||+.+=
T Consensus 3 ~~V~~~v~~IP~G~v~TYg~iA~~~g 28 (79)
T cd06445 3 RRVWEALRQIPYGEVTTYGQIAKLAG 28 (79)
T ss_pred HHHHHHHhcCCCCCcCcHHHHHHHHC
Confidence 34555554 667899999998763
No 18
>PF09766 FimP: Fms-interacting protein; InterPro: IPR019163 This entry represents Thoc5 which is one of the subunits of the THO complex, which additionally contains: HPR1, Thoc2, Thoc6 and Thoc7. The evolutionarily conserved multisubunit THO complex, which is recruited to actively transcribed genes is required for the efficient expression of genes that have internal tandem repeats. It is suggested that the THO complex functions to rectify aberrant structures that arise during transcription [, ] and is required for cell proliferation and for proper export of heat-shock mRNAs under heat stress []. This entry also identifies the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes [].
Probab=26.84 E-value=1.6e+02 Score=29.28 Aligned_cols=34 Identities=35% Similarity=0.368 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9354 114 SLNLNKERKQLIQRINQKTRHLHDLLLQQISLKK 147 (308)
Q Consensus 114 ~~~Le~ek~k~~erIkqKk~~LqELi~Q~iA~Kn 147 (308)
++.|+.+++++...++.|++.|..|-.+..+|+.
T Consensus 110 ~~el~~~k~~l~~~~~~k~~~L~~l~~~L~~l~~ 143 (355)
T PF09766_consen 110 LKELEQRKKKLQQENKKKKKFLDSLPPQLKSLKK 143 (355)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 4556667777777888888888777766665543
No 19
>PF03392 OS-D: Insect pheromone-binding family, A10/OS-D; InterPro: IPR005055 A class of small (14-20 Kd) water-soluble proteins, called odorant binding proteins (OBPs), first discovered in the insect sensillar lymph but also in the mucus of vertebrates, is postulated to mediate the solubilisation of hydrophobic odorant molecules, and thereby to facilitate their transport to the receptor neurons. The product of a gene expressed in the olfactory system of Drosophila melanogaster (Fruit fly), OS-D, shares features common to vertebrate odorant-binding proteins, but has a primary structure unlike odorant-binding proteins []. OS-D derivatives have subsequently been found in chemosensory organs of phylogenetically distinct insects, including cockroaches, phasmids and moths, suggesting that OS-D-like proteins seem to be conserved in the insect phylum.; PDB: 1KX9_A 1N8U_A 1KX8_A 1K19_A 1N8V_A 2GVS_A 2JNT_A.
Probab=26.49 E-value=28 Score=28.52 Aligned_cols=27 Identities=26% Similarity=0.370 Sum_probs=21.0
Q ss_pred hccCCCCCCCCCHHHHHHHHhccchhhH
Q psy9354 215 GLGMGLDKGEWTEEDLQEAKRLVAPCME 242 (308)
Q Consensus 215 gl~~gLe~g~~s~edl~~ak~lvPk~l~ 242 (308)
.+.|=|+.|.||+ +-+..|.++|.+|+
T Consensus 23 y~~ClldkgpCt~-~~~~lK~~ipeal~ 49 (95)
T PF03392_consen 23 YIDCLLDKGPCTP-EGKELKKVIPEALK 49 (95)
T ss_dssp HHHHHTSSSTSHH-HHHHHHHHHHHHHH
T ss_pred HHHHHhcCCCCCH-HHHHHHHHHHHHHH
Confidence 3456699999976 46677999999886
No 20
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=26.41 E-value=69 Score=27.75 Aligned_cols=30 Identities=13% Similarity=0.334 Sum_probs=26.9
Q ss_pred CcchhhhhHHHHHHHhhcCCcchHHHHHHH
Q psy9354 52 SKGLRHFSMKVCEKVRRKGVTTYNEVADEL 81 (308)
Q Consensus 52 ~kGLRhfSmKVcEKVqeKg~TTYnEVADEL 81 (308)
.+.|-.+=.++...+++.++.||.|+|.+|
T Consensus 9 ~~~lD~~D~~IL~~Lq~d~R~s~~eiA~~l 38 (164)
T PRK11169 9 GKDLDRIDRNILNELQKDGRISNVELSKRV 38 (164)
T ss_pred hhhHHHHHHHHHHHhccCCCCCHHHHHHHH
Confidence 456888889999999999999999999985
No 21
>PF08501 Shikimate_dh_N: Shikimate dehydrogenase substrate binding domain; InterPro: IPR013708 This domain is the substrate binding domain of shikimate dehydrogenase []. Shikimate dehydrogenase catalyses the fourth step of the mycobacterial Shikimate pathway, which results in the biosynthesis of chorismate. Chorismate is a precursor of aromatic amino acids, naphthoquinones, menaquinones and mycobactins [, ]. This pathway is an important target for antibacterial agents, especially against Mycobacterium tuberculosis, since it does not occur in mammals.; GO: 0004764 shikimate 3-dehydrogenase (NADP+) activity, 0055114 oxidation-reduction process; PDB: 3U62_A 2EGG_A 1P74_B 1P77_A 3O8Q_A 3TNL_C 3TOZ_G 1NYT_C 1VI2_B 1NPD_A ....
Probab=24.74 E-value=22 Score=27.68 Aligned_cols=17 Identities=29% Similarity=0.501 Sum_probs=12.5
Q ss_pred EeeCCCCCCCCCccccc
Q psy9354 10 VVASPVEYSPEPLPATV 26 (308)
Q Consensus 10 ~igsp~~~~p~~~~~tq 26 (308)
|||.|+.|+.+|.|-..
T Consensus 1 viG~pi~hS~SP~~hn~ 17 (83)
T PF08501_consen 1 VIGNPISHSLSPLIHNA 17 (83)
T ss_dssp EEESSSTT-SHHHHHHH
T ss_pred CcCCCcccccCHHHHHH
Confidence 68888888888877655
No 22
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=23.67 E-value=67 Score=25.35 Aligned_cols=24 Identities=50% Similarity=0.650 Sum_probs=18.1
Q ss_pred hhHHHHHHHhhc---CCcchHHHHHHH
Q psy9354 58 FSMKVCEKVRRK---GVTTYNEVADEL 81 (308)
Q Consensus 58 fSmKVcEKVqeK---g~TTYnEVADEL 81 (308)
|..+|++.|++= .+|||.+||..+
T Consensus 3 f~~~V~~~v~~IP~G~v~TYg~iA~~~ 29 (85)
T PF01035_consen 3 FQRRVWEAVRQIPYGKVTTYGEIARLL 29 (85)
T ss_dssp HHHHHHHHHTTS-TT-BEEHHHHHHHT
T ss_pred HHHHHHHHHHcCCCCceEeHHHHHHHH
Confidence 667788877653 689999999875
No 23
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=23.50 E-value=2.4e+02 Score=24.10 Aligned_cols=35 Identities=20% Similarity=0.238 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9354 116 NLNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQ 150 (308)
Q Consensus 116 ~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~ 150 (308)
-|++|...+++.+.+|.+.++.+......+++|+.
T Consensus 39 ~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~ 73 (106)
T PF11594_consen 39 VLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLS 73 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778888888889999999999999999999854
No 24
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=23.37 E-value=82 Score=26.08 Aligned_cols=25 Identities=8% Similarity=0.234 Sum_probs=21.8
Q ss_pred hhhHHHHHHHhhcCCcchHHHHHHH
Q psy9354 57 HFSMKVCEKVRRKGVTTYNEVADEL 81 (308)
Q Consensus 57 hfSmKVcEKVqeKg~TTYnEVADEL 81 (308)
-+=.++.+.++..++++|+|+|++|
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l 32 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV 32 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH
Confidence 3456799999999999999999986
No 25
>PF07904 Eaf7: Chromatin modification-related protein EAF7; InterPro: IPR012423 The Saccharomyces cerevisiae (Baker's yeast) member of this family P53911 from SWISSPROT is part of NuA4, the only essential histone acetyltransferase complex in S. cerevisiae involved in global histone acetylation []. ; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0043189 H4/H2A histone acetyltransferase complex
Probab=23.29 E-value=1.1e+02 Score=24.79 Aligned_cols=32 Identities=19% Similarity=0.360 Sum_probs=27.3
Q ss_pred hhhhhHH-HHHHHhhc-------CCcchHHHHHHHHHhhh
Q psy9354 55 LRHFSMK-VCEKVRRK-------GVTTYNEVADELVQEFS 86 (308)
Q Consensus 55 LRhfSmK-VcEKVqeK-------g~TTYnEVADELV~E~~ 86 (308)
=|||.|. +++.+.+. ..+|..+|.+.|=.-|.
T Consensus 19 ~KHF~M~~I~~~l~~~~~~~~~~~~~t~~~IW~kL~~~Yd 58 (91)
T PF07904_consen 19 HKHFHMICIVERLNNPGFDPKLNKHFTIDDIWKKLRTLYD 58 (91)
T ss_pred chHHHHHHHHHHHhccccCCccCCcCCHHHHHHHHHHhcC
Confidence 4899998 88999887 88999999999877764
No 26
>PF02050 FliJ: Flagellar FliJ protein; InterPro: IPR012823 Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects []. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export. The sequences of fliH, fliI and the adjacent gene, fliJ, have been deduced. FliJ was shown to encode a protein of molecular mass 17,302 Da []. It is a membrane-associated protein that affects chemotactic events, mutations in FliJ result in failure to respond to chemotactic stimuli.; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 bacterial-type flagellum, 0016020 membrane, 0044461 bacterial-type flagellum part; PDB: 3AJW_A.
Probab=23.15 E-value=3.4e+02 Score=20.67 Aligned_cols=44 Identities=18% Similarity=0.237 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh
Q psy9354 114 SLNLNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKNIDSEK 157 (308)
Q Consensus 114 ~~~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~RNk~~e~ 157 (308)
+..++.+.......+..++..|.+.......+..|.+|-.....
T Consensus 61 i~~~~~~~~~~~~~~~~~r~~l~~a~~~~k~~e~L~e~~~~~~~ 104 (123)
T PF02050_consen 61 IQQQQQELERLEQEVEQAREELQEARRERKKLEKLKERRREEYQ 104 (123)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44456677778888899999999999999999999998877654
No 27
>PHA03188 UL14 tegument protein; Provisional
Probab=23.12 E-value=2.8e+02 Score=26.10 Aligned_cols=43 Identities=21% Similarity=0.290 Sum_probs=37.3
Q ss_pred HHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhh
Q psy9354 114 SLNLNKER--KQLIQRINQKTRHLHDLLLQQISLKKLIQKNIDSE 156 (308)
Q Consensus 114 ~~~Le~ek--~k~~erIkqKk~~LqELi~Q~iA~KnLV~RNk~~e 156 (308)
+.+|+... ..|.+.++||-+.+|.-+.-|.+.+.++.+|+.--
T Consensus 58 ~~dl~rqLrs~aRve~veQK~r~Iq~rVeeQ~a~r~iL~~nRRfL 102 (199)
T PHA03188 58 CADLNNNIRSAARIAAVEQKIADIQEKVEEQTSIQKILNANRRYI 102 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Confidence 45666665 67899999999999999999999999999998753
No 28
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=22.88 E-value=4.6e+02 Score=21.99 Aligned_cols=15 Identities=27% Similarity=0.246 Sum_probs=12.1
Q ss_pred cccccCccEEEecCC
Q psy9354 93 SSEQEKKEIKWLGLP 107 (308)
Q Consensus 93 IIsKeKKeIkWiGLP 107 (308)
-|....|-+-|+|..
T Consensus 71 ~v~~~~kV~v~lG~g 85 (140)
T PRK03947 71 KVKDKDKVIVSLGAG 85 (140)
T ss_pred EecCCCeEEEEcCCC
Confidence 566778899999976
No 29
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=22.74 E-value=2.5e+02 Score=27.30 Aligned_cols=38 Identities=18% Similarity=0.290 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q psy9354 116 NLNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKNI 153 (308)
Q Consensus 116 ~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~RNk 153 (308)
.|+.+++.+.+.|+..+++.+++..+...++..++.++
T Consensus 234 el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~r 271 (325)
T PF08317_consen 234 ELQEELEELEEKIEELEEQKQELLAEIAEAEKIREECR 271 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34555556666666666666666666666666666554
No 30
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=22.51 E-value=2.4e+02 Score=23.69 Aligned_cols=29 Identities=21% Similarity=0.369 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9354 113 ESLNLNKERKQLIQRINQKTRHLHDLLLQ 141 (308)
Q Consensus 113 e~~~Le~ek~k~~erIkqKk~~LqELi~Q 141 (308)
+.+.|+.-++++.+.+...+++|.+|..+
T Consensus 70 EkEqL~~Lk~kl~~e~~~~~k~i~~le~~ 98 (100)
T PF04568_consen 70 EKEQLKKLKEKLKEEIEHHRKEIDELEKH 98 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34445555566666666677777777654
No 31
>PTZ00481 Membrane attack complex/ Perforin (MACPF) Superfamily; Provisional
Probab=22.29 E-value=2.5e+02 Score=29.74 Aligned_cols=116 Identities=16% Similarity=0.209 Sum_probs=66.6
Q ss_pred ccCccEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh--hcCCCCCCCccccceE
Q psy9354 96 QEKKEIKWLGLPTNSLQESLNLNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKNIDSEK--IHGEPAPSSAIQLPFL 173 (308)
Q Consensus 96 KeKKeIkWiGLPtns~qe~~~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~RNk~~e~--~~~~~~~~~~I~LPFI 173 (308)
|=.+-..|.-+|.+. |-.+||+.-..+|.|+.+++++.-|.-++ =+.-|+||..+-. .+|....+..+.+|.-
T Consensus 319 K~n~ipiW~afpagp-qvk~NlqqaI~nriesM~qr~~~~q~qv~----eqRrie~~~P~ta~Aiqgng~~~~~~~~p~~ 393 (524)
T PTZ00481 319 KINRFLSWDNLTANP-QVKANLQQAIMNRIESMKQRQISYQQQVR----EQRRIERNGPRTAWAIQGNGNCNGQLPLPLN 393 (524)
T ss_pred eeeeeeehhhcccCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhcCCcceEEEccCccccCcccCCcc
Confidence 334556898888766 66778998888899999998888776444 4566788877655 3443333344555554
Q ss_pred EEEcCCCCeEEeeeecCcceEEEEc--CCceeeeccHHHHHHhhc
Q psy9354 174 IVSTDKKTVIDCSMSNDKTEYLFVF--DNKFEIHDDIEILKRMGL 216 (308)
Q Consensus 174 lV~Tsk~t~IdCeiS~Dk~ey~F~F--~~~FEIhDD~eILK~Mgl 216 (308)
+.-++.=..=+.++......+-+.- -..=++|+=++++|...-
T Consensus 394 ~~i~~~f~~~~a~~c~~~~~~~~~~~~c~s~~~~~~~~~~~evry 438 (524)
T PTZ00481 394 YSISRQFQMKAASVCPPGLDFNYSKSRCSSGPFHTLLDIPKEVRY 438 (524)
T ss_pred eeecccccccccccCCCCCchhHHhcccCCCcccchhhhhhhhcc
Confidence 4333332222333333333332222 112344455677776554
No 32
>PF03331 LpxC: UDP-3-O-acyl N-acetylglycosamine deacetylase; InterPro: IPR004463 UDP-3-O-N-acetylglucosamine deacetylases are zinc-dependent metalloamidases that catalyse the second and committed step in the biosynthesis of lipid A. Lipid A anchors lipopolysaccharide (the major constituent of the outer membrane) into the membrane in Gram negative bacteria. LpxC shows no homology to mammalian metalloamidases and is essential for cell viability, making it an important target for the development of novel antibacterial compounds []. The structure of UDP-3-O-N-acetylglucosamine deacetylase (LpxC) from Aquifex aeolicus has a two-layer alpha/beta structure similar to that of the second domain of ribosomal protein S5, only in LpxC there is a duplication giving two structural repeats of this fold, each repeat being elaborated with additional structures forming the active site. LpxC contains a zinc-binding motif, which resides at the base of an active site cleft and adjacent to a hydrophobic tunnel occupied by a fatty acid []. This tunnel accounts for the specificity of LpxC toward substrates and inhibitors bearing appropriately positioned 3-O-fatty acid substituents []. This entry represents the UDP-3-O-N-acetylglucosamine deacetylase family of proteins.; GO: 0008759 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity, 0009245 lipid A biosynthetic process; PDB: 2VES_C 3U1Y_A 3P3E_A 3UHM_A 1XXE_A 2IER_A 1YH8_B 2GO4_A 2O3Z_B 2GO3_B ....
Probab=22.27 E-value=1.8e+02 Score=28.25 Aligned_cols=49 Identities=18% Similarity=0.370 Sum_probs=33.0
Q ss_pred eEEEEcCCCCeEEeeeecCc------ceEEEEcC-----------CceeeeccHHHHHHhhccCCC
Q psy9354 172 FLIVSTDKKTVIDCSMSNDK------TEYLFVFD-----------NKFEIHDDIEILKRMGLGMGL 220 (308)
Q Consensus 172 FIlV~Tsk~t~IdCeiS~Dk------~ey~F~F~-----------~~FEIhDD~eILK~Mgl~~gL 220 (308)
||.+.-+..-.|.|.|.=+. +.|.|.++ .||-+..|++-|+++||+.|-
T Consensus 142 ~i~~~P~~~l~i~~~idf~~~~ig~~Q~~~~~~~~~~f~~eIa~ARTF~f~~eve~L~~~GL~~Gg 207 (277)
T PF03331_consen 142 FIRALPSDGLKITYTIDFPHPAIGRTQSFSFELTPETFKREIAPARTFGFLEEVEYLRKRGLAKGG 207 (277)
T ss_dssp EEEEEE-SSEEEEEEEE-SSTTTTGGCEEEEETTHHHHHHHTTT--EEEEHHHHHHHHHTT-STT-
T ss_pred EEEEEeCCCcEEEEEEECCCCCcCCceEEEEEeCHHHHHHHhhccCccCcHHHHHHHHHCCCcccc
Confidence 44444456677888886554 67778764 578999999999999998764
No 33
>cd00024 CHROMO Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
Probab=22.11 E-value=73 Score=21.86 Aligned_cols=19 Identities=26% Similarity=0.545 Sum_probs=11.8
Q ss_pred cEEEecCCC--CCHHHHHHHH
Q psy9354 100 EIKWLGLPT--NSLQESLNLN 118 (308)
Q Consensus 100 eIkWiGLPt--ns~qe~~~Le 118 (308)
.|+|.|+|. ++.....+|.
T Consensus 23 ~VkW~g~~~~~~tWe~~~~l~ 43 (55)
T cd00024 23 LVKWKGYSYSEDTWEPEENLE 43 (55)
T ss_pred EEEECCCCCccCccccHHHhC
Confidence 479999984 4444444443
No 34
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=22.02 E-value=2.3e+02 Score=20.36 Aligned_cols=32 Identities=13% Similarity=0.106 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9354 112 QESLNLNKERKQLIQRINQKTRHLHDLLLQQI 143 (308)
Q Consensus 112 qe~~~Le~ek~k~~erIkqKk~~LqELi~Q~i 143 (308)
..|.....-.....+.|.++-+.|+.+..+..
T Consensus 32 ~~~~~~~~~l~~~~~~i~~~i~~L~~~~~~L~ 63 (65)
T PF09278_consen 32 PPCADRRALLEEKLEEIEEQIAELQALRAQLE 63 (65)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44555555556666777777777776655443
No 35
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=21.92 E-value=1.8e+02 Score=29.07 Aligned_cols=86 Identities=10% Similarity=0.106 Sum_probs=59.7
Q ss_pred CccccceEEEEcCCCCeEEeeeec---CcceEEEEcCCceeeeccHHHHHHhhccCCC----------CCCCCCHHHHHH
Q psy9354 166 SAIQLPFLIVSTDKKTVIDCSMSN---DKTEYLFVFDNKFEIHDDIEILKRMGLGMGL----------DKGEWTEEDLQE 232 (308)
Q Consensus 166 ~~I~LPFIlV~Tsk~t~IdCeiS~---Dk~ey~F~F~~~FEIhDD~eILK~Mgl~~gL----------e~g~~s~edl~~ 232 (308)
.....|||++.|..-. +-++.+ |++-+.+.++.+-.--...+||++- +.+.- +....+.+++..
T Consensus 182 ~~~p~rfiviaT~np~--eg~l~~~LldRf~l~i~l~~~~~~~~e~~il~~~-~~~~~~~~~~~~~~~~~~~~~~~~I~~ 258 (350)
T CHL00081 182 IRHPARFVLVGSGNPE--EGELRPQLLDRFGMHAEIRTVKDPELRVKIVEQR-TSFDKNPQEFREKYEESQEELRSKIVA 258 (350)
T ss_pred eecCCCEEEEeccCcc--cCCCCHHHHHHhCceeecCCCCChHHHHHHHHhh-hccccChhhhhhhhccccccCHHHHHH
Confidence 4567799999887643 223433 6666667777776667788999985 22211 113457899999
Q ss_pred HHhccc-----hhhHHHHHHHhhcCCC
Q psy9354 233 AKRLVA-----PCMEKYVNQIAYNDGL 254 (308)
Q Consensus 233 ak~lvP-----k~l~~yv~~~~~~~~~ 254 (308)
|+..|| ..+..|+.+++..++.
T Consensus 259 ar~~~~~V~v~~~~~~yi~~l~~~~~~ 285 (350)
T CHL00081 259 AQNLLPKVEIDYDLRVKISQICSELDV 285 (350)
T ss_pred HHHhcCCCccCHHHHHHHHHHHHHHCC
Confidence 998766 6789999999988765
No 36
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=21.80 E-value=1.3e+02 Score=20.46 Aligned_cols=19 Identities=26% Similarity=0.476 Sum_probs=12.1
Q ss_pred cEEEecCCC--CCHHHHHHHH
Q psy9354 100 EIKWLGLPT--NSLQESLNLN 118 (308)
Q Consensus 100 eIkWiGLPt--ns~qe~~~Le 118 (308)
.|+|.|++. ++.....+|.
T Consensus 21 lVkW~g~~~~~~tW~~~~~l~ 41 (55)
T smart00298 21 LVKWKGYSYSEDTWEPEENLL 41 (55)
T ss_pred EEEECCCCCccCceeeHHHHH
Confidence 489999986 4544444443
No 37
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=20.68 E-value=2.8e+02 Score=27.30 Aligned_cols=37 Identities=19% Similarity=0.220 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q psy9354 117 LNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKNI 153 (308)
Q Consensus 117 Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~RNk 153 (308)
++.+.+.+..+|+..++..+++..+.....+.++.++
T Consensus 230 ~~~~l~~l~~~I~~~~~~k~e~~~~I~~ae~~~~~~r 266 (312)
T smart00787 230 LEEELQELESKIEDLTNKKSELNTEIAEAEKKLEQCR 266 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3444555555555555566666666666666555554
No 38
>PRK07720 fliJ flagellar biosynthesis chaperone; Validated
Probab=20.47 E-value=4e+02 Score=22.44 Aligned_cols=41 Identities=15% Similarity=0.131 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh
Q psy9354 117 LNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKNIDSEK 157 (308)
Q Consensus 117 Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~RNk~~e~ 157 (308)
.+.........+++++..+++-.....+|..|++|-.....
T Consensus 83 q~~~v~~~~~~ve~~r~~~~ea~~~~k~~ekLker~~~~~~ 123 (146)
T PRK07720 83 YQLLVMQAREQMNRKQQDLTEKNIEVKKYEKMKEKKQEMFA 123 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455667888999999999999999999999999776554
No 39
>PF08678 Rsbr_N: Rsbr N terminal; InterPro: IPR014792 Rsbr is a regulator of the RNA polymerase sigma factor subunit sigma(B). The structure of the N-terminal domain belongs to the globin fold superfamily []. ; PDB: 2BNL_A.
Probab=20.21 E-value=96 Score=27.10 Aligned_cols=24 Identities=25% Similarity=0.450 Sum_probs=17.5
Q ss_pred CcchhhhhHHHHHHHhhcCCcchH
Q psy9354 52 SKGLRHFSMKVCEKVRRKGVTTYN 75 (308)
Q Consensus 52 ~kGLRhfSmKVcEKVqeKg~TTYn 75 (308)
.+||+.|..-|.+.+.+.+.+..+
T Consensus 78 T~GL~~F~kvvy~~m~~~~~~~~~ 101 (129)
T PF08678_consen 78 TKGLQEFRKVVYETMNEEEIDDQQ 101 (129)
T ss_dssp HHHHHHHHHHHHHHHHHT--TT--
T ss_pred HHHHHHHHHHHHHHHHhcccchHH
Confidence 369999999999999999955543
No 40
>PF10828 DUF2570: Protein of unknown function (DUF2570); InterPro: IPR022538 This entry is represented by Bacteriophage IME08, pseT.3. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of proteins with unknown function.
Probab=20.17 E-value=5e+02 Score=21.39 Aligned_cols=46 Identities=22% Similarity=0.200 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh
Q psy9354 112 QESLNLNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKNIDSEK 157 (308)
Q Consensus 112 qe~~~Le~ek~k~~erIkqKk~~LqELi~Q~iA~KnLV~RNk~~e~ 157 (308)
+.++.|+.+.+...+.|.+.....++|..+...-+.++..++..++
T Consensus 25 ~~i~~L~a~n~~q~~tI~qq~~~~~~L~~~~~~~r~~~~~~~~~~q 70 (110)
T PF10828_consen 25 QRIDRLRAENKAQAQTIQQQEDANQELKAQLQQNRQAVEEQQKREQ 70 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788888888888888888788877776666666666665444
No 41
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.03 E-value=1.2e+02 Score=24.00 Aligned_cols=24 Identities=21% Similarity=0.495 Sum_probs=18.7
Q ss_pred hhHHHHHHHhh---cCCcchHHHHHHH
Q psy9354 58 FSMKVCEKVRR---KGVTTYNEVADEL 81 (308)
Q Consensus 58 fSmKVcEKVqe---Kg~TTYnEVADEL 81 (308)
|-.+|++.|.+ =.++||.+||..+
T Consensus 3 f~~~V~~~l~~IP~G~v~TYg~iA~~~ 29 (80)
T TIGR00589 3 FQQRVWQALRTIPYGETKSYGQLAARI 29 (80)
T ss_pred HHHHHHHHHhCCCCCCcCCHHHHHHHh
Confidence 66778877765 4679999999875
Done!