Query 002329
Match_columns 936
No_of_seqs 74 out of 76
Neff 3.5
Searched_HMMs 46136
Date Thu Mar 28 21:37:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002329.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002329hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4329 DNA-binding protein [G 99.7 1.3E-18 2.8E-23 188.4 3.9 154 34-218 168-332 (445)
2 KOG3554 Histone deacetylase co 98.8 9.1E-10 2E-14 123.1 0.4 179 16-215 135-337 (693)
3 KOG4167 Predicted DNA-binding 98.8 1.7E-09 3.8E-14 125.7 0.7 51 163-214 619-669 (907)
4 KOG1194 Predicted DNA-binding 98.5 3.6E-08 7.7E-13 110.6 3.0 61 163-224 187-249 (534)
5 smart00717 SANT SANT SWI3, AD 97.3 0.00022 4.7E-09 54.8 2.8 43 164-206 2-45 (49)
6 PF00249 Myb_DNA-binding: Myb- 97.1 0.00037 8.1E-09 56.2 2.5 43 164-206 2-46 (48)
7 PF01448 ELM2: ELM2 domain; I 96.9 0.0006 1.3E-08 56.9 2.4 26 40-65 1-26 (55)
8 cd00167 SANT 'SWI3, ADA2, N-Co 96.8 0.001 2.2E-08 50.5 2.5 42 165-206 1-43 (45)
9 PF12174 RST: RCD1-SRO-TAF4 (R 93.7 0.073 1.6E-06 47.7 3.7 52 242-293 13-64 (70)
10 PF13921 Myb_DNA-bind_6: Myb-l 93.0 0.081 1.7E-06 44.1 2.7 41 166-206 1-41 (60)
11 TIGR01557 myb_SHAQKYF myb-like 92.2 0.096 2.1E-06 45.1 2.2 41 164-204 4-50 (57)
12 KOG4468 Polycomb-group transcr 91.1 0.23 5E-06 59.1 4.4 246 163-468 88-360 (782)
13 cd04709 BAH_MTA BAH, or Bromo 90.5 0.1 2.2E-06 53.3 0.8 26 33-58 136-161 (164)
14 KOG2133 Transcriptional corepr 78.9 1.4 3.1E-05 55.0 2.9 121 34-193 72-193 (1229)
15 KOG1878 Nuclear receptor coreg 66.7 1.9 4.1E-05 55.9 0.1 54 162-216 224-277 (1672)
16 PLN03212 Transcription repress 54.5 7.7 0.00017 42.6 2.0 59 150-208 65-123 (249)
17 PLN03091 hypothetical protein; 53.8 9.6 0.00021 44.8 2.7 57 150-206 54-110 (459)
18 KOG4076 Regulator of ATP-sensi 44.4 7.1 0.00015 38.8 -0.1 30 389-418 45-74 (121)
19 COG2456 Uncharacterized conser 44.3 10 0.00022 37.4 0.9 21 344-364 30-51 (121)
20 PF11888 DUF3408: Protein of u 43.3 31 0.00067 34.2 4.1 39 222-280 76-114 (136)
21 KOG0457 Histone acetyltransfer 39.2 24 0.00051 41.6 2.9 54 162-215 71-125 (438)
22 COG3896 Chloramphenicol 3-O-ph 39.1 20 0.00044 37.8 2.2 33 352-391 56-93 (205)
23 COG5259 RSC8 RSC chromatin rem 38.6 25 0.00053 41.9 2.9 41 163-203 279-319 (531)
24 PF13833 EF-hand_8: EF-hand do 33.9 77 0.0017 25.6 4.4 41 242-282 12-53 (54)
25 COG5118 BDP1 Transcription ini 33.4 42 0.00091 39.2 3.6 39 163-201 365-403 (507)
26 cd06145 REX1_like DEDDh 3'-5' 32.8 35 0.00076 33.7 2.6 62 290-365 5-71 (150)
27 PF08044 DUF1707: Domain of un 28.1 70 0.0015 27.5 3.3 37 251-287 3-40 (53)
28 KOG4622 Predicted nucleotide k 27.0 22 0.00048 38.6 0.2 35 208-246 104-138 (291)
29 PF09454 Vps23_core: Vps23 cor 25.9 96 0.0021 27.7 3.9 35 255-289 24-58 (65)
30 cd05030 calgranulins Calgranul 24.7 71 0.0015 29.1 3.0 42 241-282 33-79 (88)
31 PF00036 EF-hand_1: EF hand; 23.3 88 0.0019 23.6 2.7 23 260-282 3-28 (29)
32 cd00052 EH Eps15 homology doma 21.3 1.7E+02 0.0037 23.9 4.3 26 258-283 34-62 (67)
33 cd00051 EFh EF-hand, calcium b 20.8 1.5E+02 0.0032 22.5 3.7 38 243-280 25-62 (63)
No 1
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=99.73 E-value=1.3e-18 Score=188.41 Aligned_cols=154 Identities=19% Similarity=0.308 Sum_probs=98.7
Q ss_pred CCCCCCcccCCcccccCCCCCchhhhhhhccCCCCccccccccccccccceeeeeeccccCCCCC--c----cchh-hhc
Q 002329 34 GDRQVNPRIGDEFQVEIPPMITGSEYIQLLMNPTDSEYIFHASHSFLMGLAIPIMWLHNELNNPD--E----SVKY-TKR 106 (936)
Q Consensus 34 gdp~v~PRVGdEYQaEIP~LiTes~~~~l~~np~d~e~i~~~~~~f~vGLpIPImW~~~e~~~~~--~----~~kS-~~~ 106 (936)
+|=.-.++||..|||+||.++.. ....+.+-+.. +.++|-+...-..+ + +.+- .+.
T Consensus 168 d~wKk~ImVg~~fQAdip~~~~~---------~~e~~~~yene--------dqllwDps~lpedEVie~l~k~v~~~~~~ 230 (445)
T KOG4329|consen 168 DDWKKEIMVGVLFQADIPLGNEA---------TVEEEKRYENE--------DQLLWDPSNLPEDEVIEFLLKAVVRLRKE 230 (445)
T ss_pred chhhhheeeccchhccccchhhh---------hhhhccccccc--------ceeeeccccCchHHHHHHHHHHHHhhhcc
Confidence 44566789999999999999874 22223322222 67888765321110 1 0111 111
Q ss_pred ccccccCCCCCCCCCccccCCCcccCCc--cchhhhccccccccccccCCCCCCCCCCC-CCCCHHHHHHHHHHHHHhcc
Q 002329 107 KKIRTNTGKKSSEPNFSELNDGEEMKPK--NREAKVAGMTNLDQLSKCTSCSPVPGFLR-DPWKDSEKDIFLLGLYIFGK 183 (936)
Q Consensus 107 ~~~~~~~~~~~~~~~ve~~dd~ke~~~a--~l~~~~~~~~~~~q~~k~~~~~pvPg~~~-~~Wse~E~~~F~lGL~ifGK 183 (936)
+...|.. -|+.++-. .|+.-+..+++...+.+++-+--.|--.. ..|+|+||++|+.||..|||
T Consensus 231 ~~~p~~P-------------~gt~vkDnEqAL~~LvkcnfDteeAlrr~rfnvk~~rd~l~~wsEeEcr~FEegl~~yGK 297 (445)
T KOG4329|consen 231 HDQPCPP-------------EGTEVKDNEQALYELVKCNFDTEEALRRLRFNVKTVRDDLSGWSEEECRNFEEGLELYGK 297 (445)
T ss_pred cCCCCCC-------------ccccccccHHHHHHHHHcCCcHHHHHHhcCCcceecccccccCCHHHHHHHHHHHHHhcc
Confidence 1111111 12222111 24444445566655555543333333222 79999999999999999999
Q ss_pred chHHHHh-hhccccccchheeeccccccCccCcchh
Q 002329 184 NFFQIKR-FIETKEMGDILSFYYGEFYRSPAHRRWT 218 (936)
Q Consensus 184 Nf~~Ikk-fv~~K~~gEil~FYYgkf~ks~~y~rWS 218 (936)
|||+||+ .|++++|||||.|||+ |+||++|+.|.
T Consensus 298 DF~lIr~nkvrtRsvgElVeyYYl-WKkSeryd~~~ 332 (445)
T KOG4329|consen 298 DFHLIRANKVRTRSVGELVEYYYL-WKKSERYDVFA 332 (445)
T ss_pred cHHHHHhcccccchHHHHHHHHHH-hhcCcchhhHh
Confidence 9999999 9999999999999999 99999999875
No 2
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=98.80 E-value=9.1e-10 Score=123.12 Aligned_cols=179 Identities=17% Similarity=0.213 Sum_probs=108.1
Q ss_pred ccccccCCCCCCCcccccCCC--------CCCcccCCcccccCCCCCchhhhhhhccCCCCccccccccccccccceeee
Q 002329 16 TSLKQLVPSDSVDINDLFGDR--------QVNPRIGDEFQVEIPPMITGSEYIQLLMNPTDSEYIFHASHSFLMGLAIPI 87 (936)
Q Consensus 16 ~s~~q~~~~~s~~~~~~~gdp--------~v~PRVGdEYQaEIP~LiTes~~~~l~~np~d~e~i~~~~~~f~vGLpIPI 87 (936)
+++.+-++.+-.-..-.+=|| +..+|||.-|||+||.++.|-|-. | .-+... .-.
T Consensus 135 e~~~~YL~~eDtFfySLVyDP~~kTLLADkGeIRVG~kYQA~i~e~l~EgEeD-------~-req~kl---------Ev~ 197 (693)
T KOG3554|consen 135 ESLQSYLEKEDTFFYSLVYDPNQKTLLADKGEIRVGEKYQADIPEWLEEGEED-------D-REQSKL---------EVK 197 (693)
T ss_pred HHHHhhccccceeEEEeeeccchhhhhccCcceeecccccccchHHHHhcccc-------c-cccccc---------eeE
Confidence 344444444443333344454 578999999999999999875421 1 111100 234
Q ss_pred eeccc-c--CCCCCcc---chhhhccccc--ccCCCCCCC----CCccccCCCcccCCccchhhhccccccccccccCCC
Q 002329 88 MWLHN-E--LNNPDES---VKYTKRKKIR--TNTGKKSSE----PNFSELNDGEEMKPKNREAKVAGMTNLDQLSKCTSC 155 (936)
Q Consensus 88 mW~~~-e--~~~~~~~---~kS~~~~~~~--~~~~~~~~~----~~ve~~dd~ke~~~a~l~~~~~~~~~~~q~~k~~~~ 155 (936)
.|-+. . ...++.. +++...++-- |.+-..-+. ..++++|-+-.-+-+.||- ..|+..|+-..+++
T Consensus 198 VW~ph~pLTDrqIDQflvVARsVGtFARAlDcsSsvrqPsLhmsAAaASRDiTlFHAmdtLhr---~~YDl~~Ais~LVP 274 (693)
T KOG3554|consen 198 VWDPHNPLTDRQIDQFLVVARSVGTFARALDCSSSVRQPSLHMSAAAASRDITLFHAMDTLHR---NNYDLSKAISYLVP 274 (693)
T ss_pred eecCCCCcchhcchhhehhhhhhhHHHHhhcccccccCcchhhhhhhhcccchhhhHHHHHHH---ccccHHHHHHHhhc
Confidence 67643 2 2222221 5555433322 333222221 1234554222223444443 45777765443333
Q ss_pred CCCCCCCC---CCCCHHHHHHHHHHHHHhccchHHHHh-hhccccccchheeeccccccCccCc
Q 002329 156 SPVPGFLR---DPWKDSEKDIFLLGLYIFGKNFFQIKR-FIETKEMGDILSFYYGEFYRSPAHR 215 (936)
Q Consensus 156 ~pvPg~~~---~~Wse~E~~~F~lGL~ifGKNf~~Ikk-fv~~K~~gEil~FYYgkf~ks~~y~ 215 (936)
.-=|-+.+ .-||-.|...|+-+|=-|||+|.-|+. ||+=|++.+|+.|||+ |+-+++|-
T Consensus 275 lGGPvLCRDemEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYm-wKttdRYv 337 (693)
T KOG3554|consen 275 LGGPVLCRDEMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYM-WKTTDRYV 337 (693)
T ss_pred CCCceeehhhhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHH-HhhhhHHH
Confidence 22233333 579999999999999999999999999 9999999999999999 99998874
No 3
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=98.76 E-value=1.7e-09 Score=125.73 Aligned_cols=51 Identities=22% Similarity=0.613 Sum_probs=47.0
Q ss_pred CCCCCHHHHHHHHHHHHHhccchHHHHhhhccccccchheeeccccccCccC
Q 002329 163 RDPWKDSEKDIFLLGLYIFGKNFFQIKRFIETKEMGDILSFYYGEFYRSPAH 214 (936)
Q Consensus 163 ~~~Wse~E~~~F~lGL~ifGKNf~~Ikkfv~~K~~gEil~FYYgkf~ks~~y 214 (936)
+..||-.|.+-|-++||.|-|||..|++-|.+|||.+||.|||. |+|-.+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt-WKK~~~~ 669 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT-WKKIMRL 669 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH-HHHhccc
Confidence 37999999999999999999999999999999999999999998 8875443
No 4
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=98.54 E-value=3.6e-08 Score=110.65 Aligned_cols=61 Identities=16% Similarity=0.503 Sum_probs=50.8
Q ss_pred CCCCCHHHHHHHHHHHHHhccchHHHHhhhccccccchheeeccccccCccCcch--hcccCCC
Q 002329 163 RDPWKDSEKDIFLLGLYIFGKNFFQIKRFIETKEMGDILSFYYGEFYRSPAHRRW--TDCRKPR 224 (936)
Q Consensus 163 ~~~Wse~E~~~F~lGL~ifGKNf~~Ikkfv~~K~~gEil~FYYgkf~ks~~y~rW--S~cRk~r 224 (936)
-+-|+.+|.-.|+.++.+|||+|++|++-|++|++.+|+-|||- |+|.-.|.-- ..||+.+
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~-~KK~~~~~s~~~~h~~~~~ 249 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYS-WKKTREYDSQMNRHRNETK 249 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHH-HHHHhhHHHHHHHHHhhhh
Confidence 37899999999999999999999999999999999999999996 6665555433 2344444
No 5
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=97.25 E-value=0.00022 Score=54.81 Aligned_cols=43 Identities=12% Similarity=0.323 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHHhc-cchHHHHhhhccccccchheeecc
Q 002329 164 DPWKDSEKDIFLLGLYIFG-KNFFQIKRFIETKEMGDILSFYYG 206 (936)
Q Consensus 164 ~~Wse~E~~~F~lGL~ifG-KNf~~Ikkfv~~K~~gEil~FYYg 206 (936)
..||++|...|+.++..|| ++|..|.+.+++|+..+|..+||.
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~ 45 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNN 45 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHH
Confidence 5799999999999999999 999999999999999999999985
No 6
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=97.06 E-value=0.00037 Score=56.25 Aligned_cols=43 Identities=21% Similarity=0.448 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHHHhccc-hHHHHhhhc-cccccchheeecc
Q 002329 164 DPWKDSEKDIFLLGLYIFGKN-FFQIKRFIE-TKEMGDILSFYYG 206 (936)
Q Consensus 164 ~~Wse~E~~~F~lGL~ifGKN-f~~Ikkfv~-~K~~gEil~FYYg 206 (936)
..||++|...|+.++..||++ |..|.+.|+ +||..+|..+||-
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~ 46 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQN 46 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHh
Confidence 479999999999999999999 999999988 9999999999873
No 7
>PF01448 ELM2: ELM2 domain; InterPro: IPR000949 The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex []. The domain is usually found to the N terminus of a myb-like DNA binding domain and a GATA binding domain. ELM2, in some instances, is also found associated with the ARID DNA binding domain IPR001606 from INTERPRO. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.
Probab=96.89 E-value=0.0006 Score=56.88 Aligned_cols=26 Identities=35% Similarity=0.492 Sum_probs=21.0
Q ss_pred cccCCcccccCCCCCchhhhhhhccC
Q 002329 40 PRIGDEFQVEIPPMITGSEYIQLLMN 65 (936)
Q Consensus 40 PRVGdEYQaEIP~LiTes~~~~l~~n 65 (936)
+|||++|||+||.|.+...+..-..+
T Consensus 1 IrVG~~yQA~IP~~~~~~~~~~~~~~ 26 (55)
T PF01448_consen 1 IRVGPEYQAEIPELLPDSERDEDQEE 26 (55)
T ss_pred CCcCCccCCcCCCCcccccccccccc
Confidence 69999999999999998765544443
No 8
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=96.75 E-value=0.001 Score=50.51 Aligned_cols=42 Identities=17% Similarity=0.423 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHHHhc-cchHHHHhhhccccccchheeecc
Q 002329 165 PWKDSEKDIFLLGLYIFG-KNFFQIKRFIETKEMGDILSFYYG 206 (936)
Q Consensus 165 ~Wse~E~~~F~lGL~ifG-KNf~~Ikkfv~~K~~gEil~FYYg 206 (936)
.||++|.+.|+.++..|| ++|..|.+++++|+..+|..+||-
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~ 43 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRN 43 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHH
Confidence 599999999999999999 999999999999999999998874
No 9
>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=93.72 E-value=0.073 Score=47.66 Aligned_cols=52 Identities=27% Similarity=0.367 Sum_probs=49.0
Q ss_pred HHHHhhcCCCChhhHHHHHHHHHHhhcCCccHHHHHHHHhhhhhhhhhheee
Q 002329 242 ELVSRLLPHIPEESHNSLLEVSKSFAEGRTSLESYVFSLQAAVGVHALVESV 293 (936)
Q Consensus 242 ELlsRL~~~v~~e~~~~L~evsksF~EGk~sLEeYVfsLKstVGl~~lveaV 293 (936)
-||+=|.++||..-.+.|..-+..|.+++|+=||||-.|+.+||=++|+.|+
T Consensus 13 ~L~~~l~~~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVGD~lL~s~I 64 (70)
T PF12174_consen 13 MLFSALSKHLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVGDQLLRSAI 64 (70)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 5888899999999999999999999999999999999999999999999875
No 10
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=92.98 E-value=0.081 Score=44.13 Aligned_cols=41 Identities=12% Similarity=0.335 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHHHhccchHHHHhhhccccccchheeecc
Q 002329 166 WKDSEKDIFLLGLYIFGKNFFQIKRFIETKEMGDILSFYYG 206 (936)
Q Consensus 166 Wse~E~~~F~lGL~ifGKNf~~Ikkfv~~K~~gEil~FYYg 206 (936)
||++|-+..+.+...||.|+..|.++|++|+...|...|+-
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHH
Confidence 99999999999999999999999999988999999988876
No 11
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=92.24 E-value=0.096 Score=45.10 Aligned_cols=41 Identities=17% Similarity=0.321 Sum_probs=33.5
Q ss_pred CCCCHHHHHHHHHHHHHhcc-ch---HHHHhhh-ccc-cccchheee
Q 002329 164 DPWKDSEKDIFLLGLYIFGK-NF---FQIKRFI-ETK-EMGDILSFY 204 (936)
Q Consensus 164 ~~Wse~E~~~F~lGL~ifGK-Nf---~~Ikkfv-~~K-~~gEil~FY 204 (936)
-.||++|...|+.|+..||. |. ..|.+.+ .++ |...|-+++
T Consensus 4 ~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~ 50 (57)
T TIGR01557 4 VVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHL 50 (57)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHH
Confidence 47999999999999999999 99 9998844 455 666666654
No 12
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=91.06 E-value=0.23 Score=59.06 Aligned_cols=246 Identities=18% Similarity=0.171 Sum_probs=119.9
Q ss_pred CCCCCHHHHHHHHHHHHHhccchHHHHh----------hhccccccchheeeccccccCccCcchhcccCCCCccccccc
Q 002329 163 RDPWKDSEKDIFLLGLYIFGKNFFQIKR----------FIETKEMGDILSFYYGEFYRSPAHRRWTDCRKPRSRKCVYGR 232 (936)
Q Consensus 163 ~~~Wse~E~~~F~lGL~ifGKNf~~Ikk----------fv~~K~~gEil~FYYgkf~ks~~y~rWS~cRk~r~rrCi~G~ 232 (936)
...|+-.|..+|.-||.+|||||-.|=+ .+..||---+-+|||--.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~------------------------ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV------------------------ 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH------------------------
Confidence 6899999999999999999999999933 334444444444444211
Q ss_pred ccccchhHHHHHHhhcCCCChhhHHHHHHHHHHhhcCC-ccHHHHHHHHhhhhhhhhh-heeeecCCCCCCCcccccccC
Q 002329 233 KIFSGWRQQELVSRLLPHIPEESHNSLLEVSKSFAEGR-TSLESYVFSLQAAVGVHAL-VESVGIGKGKEDLTSLTIEPV 310 (936)
Q Consensus 233 kiftG~RQqELlsRL~~~v~~e~~~~L~evsksF~EGk-~sLEeYVfsLKstVGl~~l-veaVgIGKgK~DLT~~~~ep~ 310 (936)
.|--.++ .-+.++..+|+..+-+-..-..-+ ..+|.|+-.||-.|=-+-+ |-+ -||--+=+|-.-.---
T Consensus 144 -----~~m~k~~--F~~~l~~dAkel~tliNa~e~rrk~fl~ek~~~Klk~Lv~~Gqi~VR~--~~k~I~iktp~c~alr 214 (782)
T KOG4468|consen 144 -----RRMNKLL--FGPDLSLDAKELKTLINAAELRRKSFLLEKYSCKLKKLVLKGQIPVRR--FKKFIEIKTPQCLALR 214 (782)
T ss_pred -----HHHHhhh--cccccCcchhhHHHHhhHHHHHHHHHHHHHHHHHHHHHhhcceeeeee--ccceeEecCCccHHHH
Confidence 1111222 234477778874433222111122 3799999999988733211 111 1111111111000000
Q ss_pred cCCCcccccCCC-CCCcccCCCChhhhHhhhccccccccccccchhhhhhhh---------hhhhccccccCCCCCCccc
Q 002329 311 KTNPVSSVFPTM-PSGKACSSLTSTDIIKFLTGDFRLSKARCNDIFWEAVWP---------RLLARGWRSEQPRDEGYVS 380 (936)
Q Consensus 311 k~~~v~Sv~pei-P~GKacSSLts~dIIKfLTGdFRLSKARsNDLFWEAVWP---------RLLARGWHSEQPkd~~~~~ 380 (936)
+ .+.+--.+ -+|+-.++++|+-|=.| =.-..+-+.-|=.-.-| --+|.-||++-----.-+.
T Consensus 215 R---~~~~k~~~~lP~~~~~~~~p~n~~~h-----~r~r~l~qnPfgr~il~~~~~v~kl~~~~~~kw~~a~~S~p~~~~ 286 (782)
T KOG4468|consen 215 R---KSIRKRTCQLPGENLSSASPGNISSH-----SRERGLDQNPFGRLILSDGQNVKKLGPGRASKWHGASLSVPLGDE 286 (782)
T ss_pred H---HHhhhhhccCCccceeeecccccchh-----hhhhhhccCcceeEEecCchhHHHhccchhhhcccccccCccccc
Confidence 0 01111111 23666777777654221 11111111111000000 0257779988621111112
Q ss_pred CCceEEEeccccccccc---cccccc--CcccccHHHHHHhhccCCceeeeeccccccccccccchhhhhccccCCCCCC
Q 002329 381 SKDCLVFLMPGVKKFSR---RKLVKG--DHYFDSVSDILKKVASEPKLLELEAEEPRVSRCNEEDQWVLEELSDQDNSSN 455 (936)
Q Consensus 381 sK~~LVflvPGVkKFSR---rKLvKg--~hYFDSvsdvL~kV~sep~llele~~~~~~~~~~ee~gw~~e~~~~~~~~sd 455 (936)
=+-...|++|+.-.=+| |++.+- +-..|-|++|.-||+||- ||+ -+. .-.-|+..+
T Consensus 287 L~pd~a~~~~s~c~q~~A~~rp~~s~Sisi~i~~vee~~fK~~ae~--le~--tgi---------------~va~d~~~~ 347 (782)
T KOG4468|consen 287 LKPDTAFGRGSRCRQKQAGYRPWESASISIAIDGVEEVAFKDAAEH--LER--TGI---------------DVAMDDQTD 347 (782)
T ss_pred cCcccccccccceeccccccCchhhhHHHHHHHHHHHHHHHHHHhh--hhh--ccc---------------eeecccccc
Confidence 25667788888765554 222222 112344566777777763 233 222 223455666
Q ss_pred CCCccccCCCCCC
Q 002329 456 HRPHCYLKPLTSN 468 (936)
Q Consensus 456 ~~~~~ylkp~~s~ 468 (936)
.++.+|+-++.+-
T Consensus 348 tkP~~~~t~p~p~ 360 (782)
T KOG4468|consen 348 TKPTRYLTGPSPL 360 (782)
T ss_pred cCCcccccCCCCc
Confidence 6788888877664
No 13
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=90.47 E-value=0.1 Score=53.29 Aligned_cols=26 Identities=19% Similarity=0.307 Sum_probs=22.3
Q ss_pred cCCCCCCcccCCcccccCCCCCchhh
Q 002329 33 FGDRQVNPRIGDEFQVEIPPMITGSE 58 (936)
Q Consensus 33 ~gdp~v~PRVGdEYQaEIP~LiTes~ 58 (936)
+-..+.++|||..|||+||+|+..++
T Consensus 136 l~~~~geirvg~~~qa~~p~~~~~~~ 161 (164)
T cd04709 136 LLADQGEIRVGPSYQAKLPDLQPFPS 161 (164)
T ss_pred ecccceeEEecCcccccCCcccCCCC
Confidence 44678999999999999999998654
No 14
>KOG2133 consensus Transcriptional corepressor Atrophin-1/DRPLA [General function prediction only]
Probab=78.90 E-value=1.4 Score=55.04 Aligned_cols=121 Identities=12% Similarity=0.020 Sum_probs=82.8
Q ss_pred CCCCCCcccCCcccccCCCCCchhhhhhhccCCCCccccccccccccccceeeeeeccccCCCCCccchhhhcccccccC
Q 002329 34 GDRQVNPRIGDEFQVEIPPMITGSEYIQLLMNPTDSEYIFHASHSFLMGLAIPIMWLHNELNNPDESVKYTKRKKIRTNT 113 (936)
Q Consensus 34 gdp~v~PRVGdEYQaEIP~LiTes~~~~l~~np~d~e~i~~~~~~f~vGLpIPImW~~~e~~~~~~~~kS~~~~~~~~~~ 113 (936)
+-.+..++++...++..| +-|..|-+.+.....|.+... +.|+++ ++
T Consensus 72 ~~~e~s~se~~s~~~~~P-~~t~hEE~~~~qk~~d~Ds~~---------------------------~~Sl~~-----dg 118 (1229)
T KOG2133|consen 72 DECEPSISEDSSDGVSSP-METNHEELEFSQKHYDIDSLY---------------------------SRSLTG-----DG 118 (1229)
T ss_pred cccccccccCcccccCCC-CcccccccccccccCCccchh---------------------------cccccC-----CC
Confidence 334557888999999999 333333233333322221110 234443 44
Q ss_pred CCCCCCCCccccCCCcccCCccchhhhccccccccccccCCCCCCCCCCCCCCCHHHHHHHHHHHHHhccchHHHHh-hh
Q 002329 114 GKKSSEPNFSELNDGEEMKPKNREAKVAGMTNLDQLSKCTSCSPVPGFLRDPWKDSEKDIFLLGLYIFGKNFFQIKR-FI 192 (936)
Q Consensus 114 ~~~~~~~~ve~~dd~ke~~~a~l~~~~~~~~~~~q~~k~~~~~pvPg~~~~~Wse~E~~~F~lGL~ifGKNf~~Ikk-fv 192 (936)
++-+.++..+.++|++++++. ++.+..++.......+..-+.|..+...|.+.+.++ . +.|++|+|+.++. -+
T Consensus 119 ~sn~~g~v~a~rqdT~ls~~~---s~~e~~y~~~~~l~~~v~~~~p~lia~~~~~~~~Kr-~--~~~~~k~s~~~r~~d~ 192 (1229)
T KOG2133|consen 119 GSNCRGIVYAYRQDTDLSGFQ---SHDETLYDLRDSLFVEVSQPEPYLIAAICGFKYTKR-D--DRQVVKLSFYFRADDI 192 (1229)
T ss_pred CCCCccchhhhhccccchhhc---cccchhhhhhhhhhhhhccCCccccccccCcccccc-c--cccccccccccccccC
Confidence 455556777777788877665 455667777777778888889999999999999998 3 9999999999999 65
Q ss_pred c
Q 002329 193 E 193 (936)
Q Consensus 193 ~ 193 (936)
.
T Consensus 193 P 193 (1229)
T KOG2133|consen 193 P 193 (1229)
T ss_pred c
Confidence 5
No 15
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=66.67 E-value=1.9 Score=55.94 Aligned_cols=54 Identities=28% Similarity=0.436 Sum_probs=47.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhccchHHHHhhhccccccchheeeccccccCccCcc
Q 002329 162 LRDPWKDSEKDIFLLGLYIFGKNFFQIKRFIETKEMGDILSFYYGEFYRSPAHRR 216 (936)
Q Consensus 162 ~~~~Wse~E~~~F~lGL~ifGKNf~~Ikkfv~~K~~gEil~FYYgkf~ks~~y~r 216 (936)
..+.|+++|-.-|--=|-+.=|||+.|-.|++-|++.||+.|||+ =+|.+-|+-
T Consensus 224 ~~n~Ws~~Ek~~fk~rf~~H~knf~~~as~~erkSv~d~vlfyy~-nkkte~yk~ 277 (1672)
T KOG1878|consen 224 RMNEWSPEEKELFKSRFAQHVKNFGLIASFFERKSVSDCVLFYYL-NKKTENYKK 277 (1672)
T ss_pred HhhhccccccccccchhhhcCcchhhhhhhhcccchhhceeeeee-cccchhHHh
Confidence 457899999999999999999999999999999999999999999 566665553
No 16
>PLN03212 Transcription repressor MYB5; Provisional
Probab=54.49 E-value=7.7 Score=42.58 Aligned_cols=59 Identities=15% Similarity=0.150 Sum_probs=49.8
Q ss_pred cccCCCCCCCCCCCCCCCHHHHHHHHHHHHHhccchHHHHhhhccccccchheeecccc
Q 002329 150 SKCTSCSPVPGFLRDPWKDSEKDIFLLGLYIFGKNFFQIKRFIETKEMGDILSFYYGEF 208 (936)
Q Consensus 150 ~k~~~~~pvPg~~~~~Wse~E~~~F~lGL~ifGKNf~~Ikkfv~~K~~gEil~FYYgkf 208 (936)
+++=..++-|+.-...||++|-+..+.....||..+..|.++|+.+|--.|-.+||...
T Consensus 65 ReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~L 123 (249)
T PLN03212 65 RLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHL 123 (249)
T ss_pred HHHHHHhhchhcccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHH
Confidence 34455677899999999999988888888899999999999999999888888887633
No 17
>PLN03091 hypothetical protein; Provisional
Probab=53.75 E-value=9.6 Score=44.83 Aligned_cols=57 Identities=12% Similarity=0.179 Sum_probs=50.1
Q ss_pred cccCCCCCCCCCCCCCCCHHHHHHHHHHHHHhccchHHHHhhhccccccchheeecc
Q 002329 150 SKCTSCSPVPGFLRDPWKDSEKDIFLLGLYIFGKNFFQIKRFIETKEMGDILSFYYG 206 (936)
Q Consensus 150 ~k~~~~~pvPg~~~~~Wse~E~~~F~lGL~ifGKNf~~Ikkfv~~K~~gEil~FYYg 206 (936)
+++=..++-|+.....||.+|-+..+.....||..+..|.++|+.|+--.|-.+||.
T Consensus 54 RERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWns 110 (459)
T PLN03091 54 RLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNS 110 (459)
T ss_pred hHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHH
Confidence 345566788999999999999999999999999999999999999998888877775
No 18
>KOG4076 consensus Regulator of ATP-sensitive K+ channels Alpha-endosulfine/ARPP-19 and related cAMP-regulated phosphoproteins [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=44.35 E-value=7.1 Score=38.80 Aligned_cols=30 Identities=40% Similarity=0.695 Sum_probs=26.5
Q ss_pred cccccccccccccccCcccccHHHHHHhhc
Q 002329 389 MPGVKKFSRRKLVKGDHYFDSVSDILKKVA 418 (936)
Q Consensus 389 vPGVkKFSRrKLvKg~hYFDSvsdvL~kV~ 418 (936)
+||=+-|=|+||-||-.||||=.=.|.|--
T Consensus 45 lP~~sd~l~krlQkgrKyFDSGDYam~KAk 74 (121)
T KOG4076|consen 45 LPGGSDFLRKRLQKGRKYFDSGDYAMAKAK 74 (121)
T ss_pred CCcccHHHHHHHHhcccccccchHHHHHhh
Confidence 688899999999999999999888888753
No 19
>COG2456 Uncharacterized conserved protein [Function unknown]
Probab=44.27 E-value=10 Score=37.37 Aligned_cols=21 Identities=38% Similarity=0.846 Sum_probs=15.7
Q ss_pred cccccccccc-hhhhhhhhhhh
Q 002329 344 FRLSKARCND-IFWEAVWPRLL 364 (936)
Q Consensus 344 FRLSKARsND-LFWEAVWPRLL 364 (936)
||.+|.--|| |||||+|--+|
T Consensus 30 ~k~~k~s~~~ll~W~~~wv~vl 51 (121)
T COG2456 30 LKRRKLSLSDLLFWEAFWVFVL 51 (121)
T ss_pred HHHhcCCccchHHHHHHHHHHH
Confidence 5667766666 69999997654
No 20
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=43.32 E-value=31 Score=34.20 Aligned_cols=39 Identities=31% Similarity=0.566 Sum_probs=35.6
Q ss_pred CCCCcccccccccccchhHHHHHHhhcCCCChhhHHHHHHHHHHhhcCCccHHHHHHHH
Q 002329 222 KPRSRKCVYGRKIFSGWRQQELVSRLLPHIPEESHNSLLEVSKSFAEGRTSLESYVFSL 280 (936)
Q Consensus 222 k~r~rrCi~G~kiftG~RQqELlsRL~~~v~~e~~~~L~evsksF~EGk~sLEeYVfsL 280 (936)
+.+.|+||| |+.|.|+.|..|-.-.++++||+--||.++
T Consensus 76 ~~~~R~~vy--------------------I~~e~h~~l~~Iv~~ig~~~~si~~yidNI 114 (136)
T PF11888_consen 76 KIKARKGVY--------------------ISRETHERLSRIVRVIGERKMSISGYIDNI 114 (136)
T ss_pred CCCCCeeeE--------------------ECHHHHHHHHHHHHHHCCCCCcHHHHHHHH
Confidence 477888887 999999999999999999999999999875
No 21
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=39.17 E-value=24 Score=41.57 Aligned_cols=54 Identities=26% Similarity=0.420 Sum_probs=49.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhc-cchHHHHhhhccccccchheeeccccccCccCc
Q 002329 162 LRDPWKDSEKDIFLLGLYIFG-KNFFQIKRFIETKEMGDILSFYYGEFYRSPAHR 215 (936)
Q Consensus 162 ~~~~Wse~E~~~F~lGL~ifG-KNf~~Ikkfv~~K~~gEil~FYYgkf~ks~~y~ 215 (936)
....|+-+|.=.|+.|+-+|| =|+--|-+.|++|+--||..+|+-.|-.+.-|.
T Consensus 71 ~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~ 125 (438)
T KOG0457|consen 71 LDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVNSPIFP 125 (438)
T ss_pred CCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhcCcccc
Confidence 347899999999999999999 599999999999999999999998888888665
No 22
>COG3896 Chloramphenicol 3-O-phosphotransferase [Defense mechanisms]
Probab=39.07 E-value=20 Score=37.83 Aligned_cols=33 Identities=45% Similarity=0.766 Sum_probs=24.3
Q ss_pred cchhhhhhhhhh--hhcc--ccc-cCCCCCCcccCCceEEEeccc
Q 002329 352 NDIFWEAVWPRL--LARG--WRS-EQPRDEGYVSSKDCLVFLMPG 391 (936)
Q Consensus 352 NDLFWEAVWPRL--LARG--WHS-EQPkd~~~~~sK~~LVflvPG 391 (936)
=|+|||+|=|++ +||| |-+ +.|. --.+|-|.||
T Consensus 56 iD~f~e~lpp~~~d~a~g~~~~~~v~~d-------g~~~v~v~~g 93 (205)
T COG3896 56 IDLFWEALPPEQLDLARGYTWDSAVEAD-------GLEWVTVHPG 93 (205)
T ss_pred HHHHHHhCCHHhhccccccccccccccC-------CceeeEeech
Confidence 399999999996 5899 766 4332 3456777777
No 23
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=38.59 E-value=25 Score=41.90 Aligned_cols=41 Identities=20% Similarity=0.445 Sum_probs=38.4
Q ss_pred CCCCCHHHHHHHHHHHHHhccchHHHHhhhccccccchhee
Q 002329 163 RDPWKDSEKDIFLLGLYIFGKNFFQIKRFIETKEMGDILSF 203 (936)
Q Consensus 163 ~~~Wse~E~~~F~lGL~ifGKNf~~Ikkfv~~K~~gEil~F 203 (936)
+..||..|.-..+.|+-.||-++..|-+-|++|+..+||--
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~ 319 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILH 319 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHH
Confidence 36999999999999999999999999999999999999853
No 24
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=33.87 E-value=77 Score=25.56 Aligned_cols=41 Identities=20% Similarity=0.300 Sum_probs=31.9
Q ss_pred HHHHhhcCC-CChhhHHHHHHHHHHhhcCCccHHHHHHHHhh
Q 002329 242 ELVSRLLPH-IPEESHNSLLEVSKSFAEGRTSLESYVFSLQA 282 (936)
Q Consensus 242 ELlsRL~~~-v~~e~~~~L~evsksF~EGk~sLEeYVfsLKs 282 (936)
..|+.+--. ++++.-+.|+..+=.=..|.++++||+..++.
T Consensus 12 ~~l~~~g~~~~s~~e~~~l~~~~D~~~~G~I~~~EF~~~~~~ 53 (54)
T PF13833_consen 12 RALSKLGIKDLSEEEVDRLFREFDTDGDGYISFDEFISMMQR 53 (54)
T ss_dssp HHHHHTTSSSSCHHHHHHHHHHHTTSSSSSEEHHHHHHHHHH
T ss_pred HHHHHhCCCCCCHHHHHHHHHhcccCCCCCCCHHHHHHHHHh
Confidence 344444344 78888888888888889999999999998864
No 25
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=33.36 E-value=42 Score=39.20 Aligned_cols=39 Identities=26% Similarity=0.440 Sum_probs=34.0
Q ss_pred CCCCCHHHHHHHHHHHHHhccchHHHHhhhccccccchh
Q 002329 163 RDPWKDSEKDIFLLGLYIFGKNFFQIKRFIETKEMGDIL 201 (936)
Q Consensus 163 ~~~Wse~E~~~F~lGL~ifGKNf~~Ikkfv~~K~~gEil 201 (936)
...|+-.|...|-++|-|+|-+|.+|....++|.-..|-
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIK 403 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIK 403 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHH
Confidence 368999999999999999999999999987877666554
No 26
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=32.81 E-value=35 Score=33.74 Aligned_cols=62 Identities=23% Similarity=0.154 Sum_probs=40.9
Q ss_pred heeeecCCCCCCCcccccccCcCCCccc--ccCCCCCC---cccCCCChhhhHhhhccccccccccccchhhhhhhhhhh
Q 002329 290 VESVGIGKGKEDLTSLTIEPVKTNPVSS--VFPTMPSG---KACSSLTSTDIIKFLTGDFRLSKARCNDIFWEAVWPRLL 364 (936)
Q Consensus 290 veaVgIGKgK~DLT~~~~ep~k~~~v~S--v~peiP~G---KacSSLts~dIIKfLTGdFRLSKARsNDLFWEAVWPRLL 364 (936)
+|.||+|+| ..|..+++-..+.+.+|. |.|+.|+- -..+-+|++++..- -.-|+.|||+++
T Consensus 5 ~E~~g~~~g-~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a-------------~~~~~~v~~~~~ 70 (150)
T cd06145 5 CEMCYTTDG-LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENV-------------TTTLEDVQKKLL 70 (150)
T ss_pred eeeeeecCC-CEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccC-------------CCCHHHHHHHHH
Confidence 588999988 778888887776665655 44766652 44455555554321 026788999887
Q ss_pred h
Q 002329 365 A 365 (936)
Q Consensus 365 A 365 (936)
.
T Consensus 71 ~ 71 (150)
T cd06145 71 S 71 (150)
T ss_pred H
Confidence 5
No 27
>PF08044 DUF1707: Domain of unknown function (DUF1707); InterPro: IPR012551 This domain is found in a variety of actinomycetales proteins. All of the proteins containing this domain are hypothetical and probably membrane bound or associated. Currently, it is unclear to the function of this domain.
Probab=28.08 E-value=70 Score=27.53 Aligned_cols=37 Identities=27% Similarity=0.386 Sum_probs=26.9
Q ss_pred CChhhHH-HHHHHHHHhhcCCccHHHHHHHHhhhhhhh
Q 002329 251 IPEESHN-SLLEVSKSFAEGRTSLESYVFSLQAAVGVH 287 (936)
Q Consensus 251 v~~e~~~-~L~evsksF~EGk~sLEeYVfsLKstVGl~ 287 (936)
|++.-++ .+-.....|++|+++++||---+-......
T Consensus 3 ~sd~dR~~~~~~L~~a~a~GrL~~~Ef~~R~~~a~~A~ 40 (53)
T PF08044_consen 3 ASDADRERAVDLLRAAFAEGRLSLDEFDERLDAAYAAR 40 (53)
T ss_pred CcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcC
Confidence 5555565 445578899999999999987766555443
No 28
>KOG4622 consensus Predicted nucleotide kinase [General function prediction only]
Probab=26.96 E-value=22 Score=38.60 Aligned_cols=35 Identities=20% Similarity=0.376 Sum_probs=25.9
Q ss_pred cccCccCcchhcccCCCCcccccccccccchhHHHHHHh
Q 002329 208 FYRSPAHRRWTDCRKPRSRKCVYGRKIFSGWRQQELVSR 246 (936)
Q Consensus 208 f~ks~~y~rWS~cRk~r~rrCi~G~kiftG~RQqELlsR 246 (936)
||||++|+..--||.. -||+|+ ||--.---|-|.|
T Consensus 104 Y~kSMR~k~~ki~kd~---GciFG~-Iflas~ide~Lqa 138 (291)
T KOG4622|consen 104 YLKSMRHKFQKIAKDH---GCIFGI-IFLASGIDEALQA 138 (291)
T ss_pred HHHHhhhHHHHHHHHc---CCeeee-eehhhhHHHHHHh
Confidence 3589999999888754 799998 6665555565554
No 29
>PF09454 Vps23_core: Vps23 core domain; InterPro: IPR017916 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ]. This entry represents the Steadiness box domain.; PDB: 2CAZ_A 2F66_D 2F6M_A 2P22_A.
Probab=25.92 E-value=96 Score=27.73 Aligned_cols=35 Identities=9% Similarity=0.309 Sum_probs=27.2
Q ss_pred hHHHHHHHHHHhhcCCccHHHHHHHHhhhhhhhhh
Q 002329 255 SHNSLLEVSKSFAEGRTSLESYVFSLQAAVGVHAL 289 (936)
Q Consensus 255 ~~~~L~evsksF~EGk~sLEeYVfsLKstVGl~~l 289 (936)
..+++.-+.++|..|+|+|+.|+-..+..--=+.+
T Consensus 24 ieDtiy~L~~al~~g~I~~d~~lK~vR~LaReQF~ 58 (65)
T PF09454_consen 24 IEDTIYYLDRALQRGSIDLDTFLKQVRSLAREQFL 58 (65)
T ss_dssp HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence 34688889999999999999999888876544433
No 30
>cd05030 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth.
Probab=24.71 E-value=71 Score=29.11 Aligned_cols=42 Identities=19% Similarity=0.400 Sum_probs=0.0
Q ss_pred HHHHHhhcCCCC-----hhhHHHHHHHHHHhhcCCccHHHHHHHHhh
Q 002329 241 QELVSRLLPHIP-----EESHNSLLEVSKSFAEGRTSLESYVFSLQA 282 (936)
Q Consensus 241 qELlsRL~~~v~-----~e~~~~L~evsksF~EGk~sLEeYVfsLKs 282 (936)
..+|.+.++... ++.-+.++..+..-..|+++++||+..+..
T Consensus 33 ~~ll~~~~g~~~t~~~~~~~v~~i~~~~D~d~dG~I~f~eF~~~~~~ 79 (88)
T cd05030 33 KQLVEKELPNFLKKEKNQKAIDKIFEDLDTNQDGQLSFEEFLVLVIK 79 (88)
T ss_pred HHHHHHHhhHhhccCCCHHHHHHHHHHcCCCCCCcCcHHHHHHHHHH
No 31
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=23.32 E-value=88 Score=23.60 Aligned_cols=23 Identities=17% Similarity=0.420 Sum_probs=18.1
Q ss_pred HHHHHHh---hcCCccHHHHHHHHhh
Q 002329 260 LEVSKSF---AEGRTSLESYVFSLQA 282 (936)
Q Consensus 260 ~evsksF---~EGk~sLEeYVfsLKs 282 (936)
-++++.| +.|.|+++||+..|++
T Consensus 3 ~~~F~~~D~d~dG~I~~~Ef~~~~~~ 28 (29)
T PF00036_consen 3 KEAFREFDKDGDGKIDFEEFKEMMKK 28 (29)
T ss_dssp HHHHHHHSTTSSSEEEHHHHHHHHHH
T ss_pred HHHHHHHCCCCCCcCCHHHHHHHHHh
Confidence 4455555 6899999999998886
No 32
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=21.31 E-value=1.7e+02 Score=23.87 Aligned_cols=26 Identities=12% Similarity=0.273 Sum_probs=18.7
Q ss_pred HHHHHHHHh---hcCCccHHHHHHHHhhh
Q 002329 258 SLLEVSKSF---AEGRTSLESYVFSLQAA 283 (936)
Q Consensus 258 ~L~evsksF---~EGk~sLEeYVfsLKst 283 (936)
.+-++++.| ..|+++++||+..+..+
T Consensus 34 ~~~~i~~~~d~~~~g~i~~~ef~~~~~~~ 62 (67)
T cd00052 34 VLAQIWDLADTDKDGKLDKEEFAIAMHLI 62 (67)
T ss_pred HHHHHHHHhcCCCCCcCCHHHHHHHHHHH
Confidence 344555555 57999999999887654
No 33
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=20.84 E-value=1.5e+02 Score=22.54 Aligned_cols=38 Identities=13% Similarity=0.266 Sum_probs=22.3
Q ss_pred HHHhhcCCCChhhHHHHHHHHHHhhcCCccHHHHHHHH
Q 002329 243 LVSRLLPHIPEESHNSLLEVSKSFAEGRTSLESYVFSL 280 (936)
Q Consensus 243 LlsRL~~~v~~e~~~~L~evsksF~EGk~sLEeYVfsL 280 (936)
+|.++....+.+.-..+++.+-.-.+|.+++++|+..+
T Consensus 25 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ef~~~~ 62 (63)
T cd00051 25 ALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLELM 62 (63)
T ss_pred HHHHhCCCCCHHHHHHHHHHhCCCCCCeEeHHHHHHHh
Confidence 44555555555544444444433467889999987543
Done!