Query psy9276
Match_columns 583
No_of_seqs 105 out of 113
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 23:19:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9276.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9276hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06584 DIRP: DIRP; InterPro 100.0 6.4E-44 1.4E-48 318.4 9.8 105 175-279 1-109 (109)
2 KOG1019|consensus 100.0 8.6E-40 1.9E-44 363.0 13.2 409 147-571 145-637 (837)
3 KOG1019|consensus 99.8 1.1E-19 2.3E-24 203.6 7.2 230 143-448 523-758 (837)
4 PF09465 LBR_tudor: Lamin-B re 92.1 0.72 1.6E-05 37.8 6.9 40 265-306 4-44 (55)
5 PF15057 DUF4537: Domain of un 91.2 0.46 9.9E-06 44.0 5.7 49 270-323 1-50 (124)
6 smart00333 TUDOR Tudor domain. 90.5 0.9 1.9E-05 35.3 6.0 49 266-318 2-50 (57)
7 smart00743 Agenet Tudor-like d 87.5 1.7 3.8E-05 34.5 5.8 38 266-305 2-39 (61)
8 PF15057 DUF4537: Domain of un 87.0 1.1 2.3E-05 41.6 4.9 56 264-321 53-112 (124)
9 PF07039 DUF1325: SGF29 tudor- 85.9 1.8 3.9E-05 40.6 5.9 53 265-318 70-125 (130)
10 PLN03094 Substrate binding sub 76.2 43 0.00094 36.8 12.9 33 267-305 130-162 (370)
11 PF09038 53-BP1_Tudor: Tumour 74.7 6.7 0.00014 36.9 5.4 45 269-316 5-50 (122)
12 KOG0995|consensus 73.7 5.7 0.00012 45.5 5.6 58 143-200 65-142 (581)
13 PF11717 Tudor-knot: RNA bindi 73.7 6.8 0.00015 31.2 4.6 37 267-305 1-39 (55)
14 PF06003 SMN: Survival motor n 73.6 8.9 0.00019 39.9 6.6 54 265-322 67-122 (264)
15 cd04508 TUDOR Tudor domains ar 70.8 13 0.00028 27.8 5.4 42 270-314 1-42 (48)
16 PF10241 KxDL: Uncharacterized 44.2 1.1E+02 0.0023 26.9 7.1 63 391-453 21-83 (88)
17 COG4251 Bacteriophytochrome (l 43.3 3.7E+02 0.008 32.2 13.0 45 395-453 508-552 (750)
18 smart00561 MBT Present in Dros 43.2 72 0.0015 28.5 6.0 44 261-306 22-65 (96)
19 PF10591 SPARC_Ca_bdg: Secrete 42.5 6.1 0.00013 36.0 -0.8 29 201-229 67-95 (113)
20 PF08605 Rad9_Rad53_bind: Fung 37.2 56 0.0012 31.0 4.6 27 281-307 21-47 (131)
21 KOG3038|consensus 36.0 46 0.00099 35.1 4.1 41 265-306 197-239 (264)
22 PF04717 Phage_base_V: Phage-r 35.3 41 0.00088 28.2 3.1 17 287-303 1-17 (79)
23 COG4985 ABC-type phosphate tra 35.0 2.6E+02 0.0056 29.6 9.2 70 380-449 163-246 (289)
24 PRK02507 proton extrusion prot 31.8 1.5E+02 0.0033 33.3 7.5 115 432-557 241-361 (422)
25 TIGR02266 gmx_TIGR02266 Myxoco 30.9 1.6E+02 0.0035 24.8 6.1 45 263-307 33-84 (96)
26 PF03040 CemA: CemA family; I 30.8 1.7E+02 0.0036 30.4 7.2 76 463-547 79-154 (230)
27 KOG3026|consensus 30.6 59 0.0013 34.1 3.9 42 266-308 90-131 (262)
28 CHL00043 cemA envelope membran 30.4 1.6E+02 0.0035 31.2 7.1 83 464-555 111-198 (261)
29 PLN00104 MYST -like histone ac 30.3 86 0.0019 35.5 5.4 41 264-305 51-97 (450)
30 PF05641 Agenet: Agenet domain 28.9 1.4E+02 0.003 24.7 5.2 38 267-305 1-40 (68)
31 KOG4578|consensus 28.3 23 0.00051 38.6 0.6 28 202-229 347-377 (421)
32 cd06080 MUM1_like Mutated mela 27.2 1.3E+02 0.0028 26.4 4.8 38 267-306 1-38 (80)
33 cd01735 LSm12_N LSm12 belongs 26.6 1.4E+02 0.0031 25.0 4.8 31 266-298 2-32 (61)
34 PF07238 PilZ: PilZ domain; I 25.2 1.6E+02 0.0035 24.0 5.0 38 264-301 42-81 (102)
35 KOG4515|consensus 23.9 2E+02 0.0043 29.4 6.0 50 391-445 116-165 (217)
36 PF13437 HlyD_3: HlyD family s 23.4 1.8E+02 0.004 24.8 5.2 46 259-304 42-92 (105)
37 smart00557 IG_FLMN Filamin-typ 22.5 2.3E+02 0.0049 24.4 5.6 42 270-313 31-72 (93)
38 KOG4485|consensus 21.3 1.3E+03 0.029 26.8 16.9 82 202-307 259-354 (724)
39 PLN03217 transcription factor 21.3 1.3E+02 0.0028 27.2 3.8 45 490-537 15-60 (93)
40 CHL00141 rpl24 ribosomal prote 20.7 2.3E+02 0.0051 24.8 5.2 37 264-304 6-42 (83)
41 PF02470 MCE: mce related prot 20.5 2.2E+02 0.0047 23.7 4.9 33 267-305 15-49 (81)
No 1
>PF06584 DIRP: DIRP; InterPro: IPR010561 DIRP (Domain in Rb-related Pathway) is postulated to be involved in the Rb-related pathway, which is encoded by multiple eukaryotic genomes and is present in proteins including lin-9 of Caenorhabditis elegans, aly of Drosophila melanogaster and mustard weed. Studies of lin-9 and aly of fruit fly proteins containing DIRP suggest that this domain might be involved in development. Aly, lin-9, act in parallel to, or downstream of, activation of MAPK by the RTK-Ras signalling pathway.
Probab=100.00 E-value=6.4e-44 Score=318.39 Aligned_cols=105 Identities=55% Similarity=0.935 Sum_probs=101.5
Q ss_pred ccccCCccccccchHHHHHHHhCCCCcccccchhHHHHHHhhhCCCCCCChhhHHHHHHHHHHHHHHHHHHhhccCCC--
Q psy9276 175 FYSNIDRPLFNDNDFITCMKESFPQLKKYVFSRTEWSMVRRMVGKPRRCSSSFFTEERINLERRRNVIRYLQQGKCGD-- 252 (583)
Q Consensus 175 FYS~IDkp~F~~nEF~~~L~e~fP~l~trkLtR~EW~~IRr~mGKPRRfS~aFl~eER~kLe~~R~~IR~lqq~~~~d-- 252 (583)
|||+||+|||..|||++||+++||+++|++|||+||+.|||+||||||||++||+|||++||+||++||++|++++++
T Consensus 1 FYS~iDk~~f~~neF~~~L~e~~p~l~t~~ltR~eW~~IRr~mGKPRRfS~aF~~eER~~Le~~R~~iR~lQ~~~~~~~~ 80 (109)
T PF06584_consen 1 FYSFIDKPLFEDNEFQECLRESFPLLKTRKLTRVEWQKIRRSMGKPRRFSPAFLEEEREELERKRQKIRQLQQRKFHDTE 80 (109)
T ss_pred CCccccHHHHhhhHHHHHHHHhCCcccCCccCHHHHHHHHHHcCCCCcCcHHHHHHHHHHHHHHHHHHHHHhhccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred --CCccCCCCCCCCccccCCCEEEEEecC
Q psy9276 253 --QTTVKDIPSEIPIQLVVGTKVTARVRS 279 (583)
Q Consensus 253 --~~~~~~LP~~IP~PL~VG~kV~Arl~~ 279 (583)
...+++||++||+||+|||||||+||+
T Consensus 81 ~~~~~~~~lP~~iP~pL~vG~kV~arl~~ 109 (109)
T PF06584_consen 81 LNSDLLEDLPDEIPLPLSVGTKVTARLPK 109 (109)
T ss_pred cchhhhhcCchhcCCcCCCCCEEEEecCC
Confidence 556899999999999999999999984
No 2
>KOG1019|consensus
Probab=100.00 E-value=8.6e-40 Score=363.01 Aligned_cols=409 Identities=19% Similarity=0.152 Sum_probs=320.2
Q ss_pred chhhhHHHHHHHHhhcCccccccceeecccccCCccccc-cchHHHHHHHhCCCCcccccchhHHHHHHhhhCCCCCCCh
Q psy9276 147 RNLGQRVGMKLRNLLKLPKAYRFVCYEFFYSNIDRPLFN-DNDFITCMKESFPQLKKYVFSRTEWSMVRRMVGKPRRCSS 225 (583)
Q Consensus 147 ~~~~q~~g~rL~n~Lk~pka~RW~~~EwFYS~IDkp~F~-~nEF~~~L~e~fP~l~trkLtR~EW~~IRr~mGKPRRfS~ 225 (583)
+...+..|.+++|+++++.+|+|+|+|||||..|++.|. ..+|++..++.+|.+ ++-+.|+.|+.+|+- ||+||||.
T Consensus 145 ~~~D~~eg~~l~n~~~s~~~~~~~~~q~~~~~~~k~~~~~~~~~~~~~aed~~~~-s~~n~r~~~ql~r~~-~ksRr~~~ 222 (837)
T KOG1019|consen 145 KRSDFDEGLRLTNEAKSLSGHLWFFKQFRTSQADKPTLKQFLVYKNQTAEDAPTL-SRPNIRALWQLDRRD-GKSRRGSA 222 (837)
T ss_pred ccccccccccchhhhccccchHHHHHHHHhhhhccccchhhhHHHhhhhhhhhhc-cchhhhhhhhhhccc-ccchhccc
Confidence 667789999999999999999999999999999999999 999999999999998 999999999999999 99999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHhhcc-CC---CCCccCCCCCCCCccccCCCEEEEEecCCCCcc-eeeEEEEEeCCCCeeE
Q psy9276 226 SFFTEERINLERRRNVIRYLQQGK-CG---DQTTVKDIPSEIPIQLVVGTKVTARVRSPQDGL-FTGVVDAYDTSNNTYR 300 (583)
Q Consensus 226 aFl~eER~kLe~~R~~IR~lqq~~-~~---d~~~~~~LP~~IP~PL~VG~kV~Arl~~~~~gL-~~G~Vlavd~~~~~Yr 300 (583)
-||.+|+.++..+|..++..|++. +. +.+.++.+|.+||.||.-+++|+++|....++. -.|+|+-++. ..+|.
T Consensus 223 ~~f~~e~~E~~~~~~~~~~~~sr~~~~~~~nss~~~~~~~~i~~~l~~~~~~Ss~L~~~er~~~~~~kv~~~e~-ae~sy 301 (837)
T KOG1019|consen 223 PFFREELSEQIPKRERIKTSQSREKFSKLKNSSMLRIGPRSIPKPLGKPDRVSSLLMDMERMGLEEAKVVKDEL-AEGSY 301 (837)
T ss_pred hhhHhHHhhhhHHHHhhhhhhhhcccCCCCchHHhhhhhhhcccccccCccchhhhhchhhcccccceeEeech-hhhhh
Confidence 999999999999999888766653 32 444579999999999999999999998877775 4555555555 56666
Q ss_pred EEecCCCCceeeecCcccccCCCcccchhhhhhhhhc----------cC-----------CCCC-------------CCC
Q psy9276 301 ITFDRQGLGTQSIPDYEVLSNDTPETLNRQSFLQMFF----------AS-----------VPND-------------HTN 346 (583)
Q Consensus 301 V~Fdr~~lgv~~VpD~evms~~~~e~l~lssi~~~~~----------~s-----------p~~~-------------sp~ 346 (583)
|.| +||....||+++.|..+...+...+.....- ++ |..+ +..
T Consensus 302 ~~d---~~~~~~~~ae~~~s~~p~~~l~S~~~t~~~~~~s~~i~d~~ss~~~iv~~~~~~~~~nv~~~ke~L~~~l~a~~ 378 (837)
T KOG1019|consen 302 LDD---GLDALKLPAEESVSMLPGNRLESESSTHYKEERSGIIMDVNSSGFEIVETSPHIPKNNVSDTKELLDGKLRALS 378 (837)
T ss_pred hhh---hhhhhccchhhcccccccccchhhcccccccccccceeccCcCCceeeccCcCCccccchhhhhhhhhhhhhhh
Confidence 777 9999999999999999988887665544331 00 0000 000
Q ss_pred ----CCC---------------------CCCCCcccccchhhhhhhccC---CccHHHHH--H-------------HHHH
Q psy9276 347 ----RTG---------------------KPEPEAMDANHIDKELEGMLG---EYPVELLE--Q-------------VVRF 383 (583)
Q Consensus 347 ----~~~---------------------dPl~g~~~~~~~~~~~~~~iG---~~p~~lL~--~-------------lv~L 383 (583)
... +++++.|.. ..+.+++..+ ++....++ + +.++
T Consensus 379 ~~k~k~~k~~s~d~~~v~~~il~~ls~~~~~~v~D~e--t~~ei~q~~S~~~~~~~~~~e~~s~v~~~r~~~~~a~~q~~ 456 (837)
T KOG1019|consen 379 KRKIKPSKPLSTDGVRVSVAILMDLSRKRKLLVLDVE--TPKEISQSKSRNRGESTERLEKKSLVKGRRYSAVPANLQRL 456 (837)
T ss_pred hhcccccccccCCCccchhHHhhhhcccCcccccccc--chhhhhcccccccccchhhhhhhhhhhhhhhhhhhHHHHHh
Confidence 000 111111110 0011111111 23333444 3 4555
Q ss_pred HHHHHHHHHHHHHHHhhcHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhccccccccccccc
Q psy9276 384 KKLLKFKKTEVYQIRDMNSEAERRQLYGEPYDRAFQKKYAGHILRLEKINKDVNTVLASLSVNLKKLSVTSENMSSQLYA 463 (583)
Q Consensus 384 sKlL~~Ke~lV~~L~~MN~EAE~~~s~g~~~~e~FQrrYA~vvi~Le~vN~~L~~~L~~Lq~~~~~la~~~~~~~~~~~~ 463 (583)
.+.+..+..++.++...+..+......-..+...||++||-+++++++.|..++..|.+.+.+..+++++ ...+.+
T Consensus 457 t~~i~~~~~l~~d~~~~~~d~~~~~~q~s~~~~~~~~Qk~~n~rd~elk~a~~e~~~~~e~~h~~~~s~n----~~Sq~~ 532 (837)
T KOG1019|consen 457 TKKIGEESRLTRDKKELGADADIQPRQVSKSGPAFQEQKAPNIRDIELKNALQEKALSGEQDHHMYFSRN----DLSQSE 532 (837)
T ss_pred hhhccchhhhhhhhhhcccccccccchhcccchhhhhhhcchhHHHHHHhHHHHHHhhcccchhhhcccc----chhHHH
Confidence 5555555555555555554444433333346788999999999999999999999999999999999999 888899
Q ss_pred CCchHHHHHHHHHHHHHHHHHHhhcCCcccCcchHHHHHHHHHHHHHHHhhcCcCCCchhhHHHHHHHHHHHH-hcCCCC
Q psy9276 464 LSPSDLQQETYIAAQEIVDTVNKKNGNKIVDDQPVVSLITDLTALVLQIKTLSHSSRSAYEVEVLNKTMSDIY-KKLSPN 542 (583)
Q Consensus 464 ~~ps~lre~Cr~~A~e~~~~v~~~n~~~v~~~~~~~~LI~~LttLLlq~~~Lg~~~~na~e~~vL~d~l~eIk-~~l~p~ 542 (583)
+-|.+.|+.|..+| ..+|+++|.+...+...+.-++...|..|.+++--|....++.+..+|.+||.+++ ..+.++
T Consensus 533 l~~~~kre~c~~~~---~~~vd~i~~~~~~~~~~l~~~k~~~Td~L~~v~lg~~p~~s~V~~~vl~~~lqeprs~~~~~~ 609 (837)
T KOG1019|consen 533 LLPKAKREECSSQA---GRTVDHINEGFYSANPHLGFLKMEFTDYLNHVRLGGTPRLSAVEWSVLKSSLQEPRSTRILQE 609 (837)
T ss_pred hcchhHHHhhhccC---chhHHHHHhHHhhcCcchhHHHhhhhhhhhccccccccchhhhhHHHHHHHhhcchhhhhhhh
Confidence 99999999999999 99999999987655444888899999999999988888878888899999999999 555999
Q ss_pred hHHHHhHHHHHHHHHHHHhhhhcccCCcC
Q psy9276 543 NQSVFENCIGVHMEQIKAALAGERGSLAT 571 (583)
Q Consensus 543 N~~~Fq~~Veih~~~i~~~l~~~~~~l~~ 571 (583)
|.+.||.+||+|++|++..+ +..|++.+
T Consensus 610 er~~lq~yvE~~~k~~~~l~-s~~~~~~~ 637 (837)
T KOG1019|consen 610 EREKLQDYVESVRKTYHELR-SEAGELLG 637 (837)
T ss_pred HHHHHHHHHHhhhcchhhhh-cccccccc
Confidence 99999999999999999999 88777654
No 3
>KOG1019|consensus
Probab=99.78 E-value=1.1e-19 Score=203.63 Aligned_cols=230 Identities=17% Similarity=0.154 Sum_probs=197.6
Q ss_pred CCCCchhhhHH--HHHHHHhhcCccccccceeecccccCCccccccchHHHHHHHhCCCCcccccchhHHHHHHhhhCCC
Q psy9276 143 SSPDRNLGQRV--GMKLRNLLKLPKAYRFVCYEFFYSNIDRPLFNDNDFITCMKESFPQLKKYVFSRTEWSMVRRMVGKP 220 (583)
Q Consensus 143 ~~pd~~~~q~~--g~rL~n~Lk~pka~RW~~~EwFYS~IDkp~F~~nEF~~~L~e~fP~l~trkLtR~EW~~IRr~mGKP 220 (583)
-++..-+.+.| ...+.+|+.++-..+||++||||+++|.+||..-+|..||.+ .++.++.++++++|.+|-.++|.|
T Consensus 523 ~s~n~~Sq~~l~~~~kre~c~~~~~~~vd~i~~~~~~~~~~l~~~k~~~Td~L~~-v~lg~~p~~s~V~~~vl~~~lqep 601 (837)
T KOG1019|consen 523 FSRNDLSQSELLPKAKREECSSQAGRTVDHINEGFYSANPHLGFLKMEFTDYLNH-VRLGGTPRLSAVEWSVLKSSLQEP 601 (837)
T ss_pred ccccchhHHHhcchhHHHhhhccCchhHHHHHhHHhhcCcchhHHHhhhhhhhhc-cccccccchhhhhHHHHHHHhhcc
Confidence 35555555555 357899999999999999999999999999999999999986 688899999999999999999999
Q ss_pred CCCChhhHHHHHHHHHHHHHHHHHHhhccCCCCCccCCCCCCCCccccCCCEEEEEecCCCCcceeeEEEEEeCCCCeeE
Q psy9276 221 RRCSSSFFTEERINLERRRNVIRYLQQGKCGDQTTVKDIPSEIPIQLVVGTKVTARVRSPQDGLFTGVVDAYDTSNNTYR 300 (583)
Q Consensus 221 RRfS~aFl~eER~kLe~~R~~IR~lqq~~~~d~~~~~~LP~~IP~PL~VG~kV~Arl~~~~~gL~~G~Vlavd~~~~~Yr 300 (583)
| |..|..+||++|+.|++.+|.++..... .....++.+..+|+.|| |.||.+ +++|+|.|+++|+ +.|-
T Consensus 602 r--s~~~~~~er~~lq~yvE~~~k~~~~l~s--~~~~~~~t~~~r~~d~~----~s~p~t-~e~~d~~~~~~~~--n~~~ 670 (837)
T KOG1019|consen 602 R--STRILQEEREKLQDYVESVRKTYHELRS--EAGELLGTDLARKLDVG----ASHPKT-REIHDGKILTVDH--NKCN 670 (837)
T ss_pred h--hhhhhhhHHHHHHHHHHhhhcchhhhhc--cccccccchhccccccc----cCCcch-hhhhhhhhhhccc--ccCc
Confidence 9 9999999999999999999998764221 23578899999999999 999997 7999999999998 6899
Q ss_pred EEecCCCCceeeecCcccccCCCcccchhhhhhhhhccCCCCCCCCCCCCCCCCcccccchhhhhhhccCCccHHHHHHH
Q psy9276 301 ITFDRQGLGTQSIPDYEVLSNDTPETLNRQSFLQMFFASVPNDHTNRTGKPEPEAMDANHIDKELEGMLGEYPVELLEQV 380 (583)
Q Consensus 301 V~Fdr~~lgv~~VpD~evms~~~~e~l~lssi~~~~~~sp~~~sp~~~~dPl~g~~~~~~~~~~~~~~iG~~p~~lL~~l 380 (583)
|-|| .+|++.|||.+||++++
T Consensus 671 ~~~~--~~~a~~~~~q~~~~ln~--------------------------------------------------------- 691 (837)
T KOG1019|consen 671 VLFD--KLGAELVMDQDCMPLNP--------------------------------------------------------- 691 (837)
T ss_pred cchh--hhcccccchhhccccCh---------------------------------------------------------
Confidence 9998 67799999999988743
Q ss_pred HHHHHHHHHHHHHHHHHHhhcHHHHHHhhcCCC---C-CHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhh
Q psy9276 381 VRFKKLLKFKKTEVYQIRDMNSEAERRQLYGEP---Y-DRAFQKKYAGHILRLEKINKDVNTVLASLSVNLK 448 (583)
Q Consensus 381 v~LsKlL~~Ke~lV~~L~~MN~EAE~~~s~g~~---~-~e~FQrrYA~vvi~Le~vN~~L~~~L~~Lq~~~~ 448 (583)
++++++.+..+|..||++.++.++.|.. + .+-|+..|+.+..++...|..+...|.+..++..
T Consensus 692 -----~~dk~e~~~r~~d~~~~~~~e~q~~g~~na~~~s~~~~~~~~~v~fq~~~~~d~~~~~L~g~~q~~~ 758 (837)
T KOG1019|consen 692 -----LEDKPEGLRRQIDKCLEKEKEAQLGGHENAGYSSLFRPDELENVEFQMNQQLDPEEPHLDGKVQHNT 758 (837)
T ss_pred -----hhhhhhhhhhhhhHHHHHHHHHHhCCCCCcCchhhcCchhHHHHHHHHHhccCchhhhhhhhhhccc
Confidence 3345666777788889888888887753 2 3889999999999999999999999988888654
No 4
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=92.09 E-value=0.72 Score=37.77 Aligned_cols=40 Identities=23% Similarity=0.516 Sum_probs=31.4
Q ss_pred ccccCCCEEEEEecCCCCcc-eeeEEEEEeCCCCeeEEEecCC
Q psy9276 265 IQLVVGTKVTARVRSPQDGL-FTGVVDAYDTSNNTYRITFDRQ 306 (583)
Q Consensus 265 ~PL~VG~kV~Arl~~~~~gL-~~G~Vlavd~~~~~YrV~Fdr~ 306 (583)
+-+..|.+|.++-|. +.+ |.|.|+++|.....|.|+|+-.
T Consensus 4 ~k~~~Ge~V~~rWP~--s~lYYe~kV~~~d~~~~~y~V~Y~DG 44 (55)
T PF09465_consen 4 RKFAIGEVVMVRWPG--SSLYYEGKVLSYDSKSDRYTVLYEDG 44 (55)
T ss_dssp SSS-SS-EEEEE-TT--TS-EEEEEEEEEETTTTEEEEEETTS
T ss_pred ccccCCCEEEEECCC--CCcEEEEEEEEecccCceEEEEEcCC
Confidence 557899999999876 455 5999999999999999999863
No 5
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=91.17 E-value=0.46 Score=44.03 Aligned_cols=49 Identities=31% Similarity=0.547 Sum_probs=38.2
Q ss_pred CCEEEEEecCCCCcc-eeeEEEEEeCCCCeeEEEecCCCCceeeecCcccccCCC
Q psy9276 270 GTKVTARVRSPQDGL-FTGVVDAYDTSNNTYRITFDRQGLGTQSIPDYEVLSNDT 323 (583)
Q Consensus 270 G~kV~Arl~~~~~gL-~~G~Vlavd~~~~~YrV~Fdr~~lgv~~VpD~evms~~~ 323 (583)
||+|+||... ||+ |.|+|...- ...+|.|.|+... +..|+..++++...
T Consensus 1 g~~VlAR~~~--DG~YY~GtV~~~~-~~~~~lV~f~~~~--~~~v~~~~iI~~~~ 50 (124)
T PF15057_consen 1 GQKVLARREE--DGFYYPGTVKKCV-SSGQFLVEFDDGD--TQEVPISDIIALSD 50 (124)
T ss_pred CCeEEEeeCC--CCcEEeEEEEEcc-CCCEEEEEECCCC--EEEeChHHeEEccC
Confidence 8999999753 775 999999876 6789999995443 67777777766653
No 6
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=90.54 E-value=0.9 Score=35.31 Aligned_cols=49 Identities=22% Similarity=0.386 Sum_probs=36.7
Q ss_pred cccCCCEEEEEecCCCCcceeeEEEEEeCCCCeeEEEecCCCCceeeecCccc
Q psy9276 266 QLVVGTKVTARVRSPQDGLFTGVVDAYDTSNNTYRITFDRQGLGTQSIPDYEV 318 (583)
Q Consensus 266 PL~VG~kV~Arl~~~~~gL~~G~Vlavd~~~~~YrV~Fdr~~lgv~~VpD~ev 318 (583)
++.+|+.|.|+. . ...-|.|+|+.++.. ..|.|.|.--| ..+.|+=.++
T Consensus 2 ~~~~G~~~~a~~-~-d~~wyra~I~~~~~~-~~~~V~f~D~G-~~~~v~~~~l 50 (57)
T smart00333 2 TFKVGDKVAARW-E-DGEWYRARIIKVDGE-QLYEVFFIDYG-NEEVVPPSDL 50 (57)
T ss_pred CCCCCCEEEEEe-C-CCCEEEEEEEEECCC-CEEEEEEECCC-ccEEEeHHHe
Confidence 468999999997 3 456899999999986 89999998644 1344443333
No 7
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=87.46 E-value=1.7 Score=34.53 Aligned_cols=38 Identities=16% Similarity=0.294 Sum_probs=33.1
Q ss_pred cccCCCEEEEEecCCCCcceeeEEEEEeCCCCeeEEEecC
Q psy9276 266 QLVVGTKVTARVRSPQDGLFTGVVDAYDTSNNTYRITFDR 305 (583)
Q Consensus 266 PL~VG~kV~Arl~~~~~gL~~G~Vlavd~~~~~YrV~Fdr 305 (583)
-+.+|+.|-|+.+. .++-+.|+|+.++. ++.|.|.|+.
T Consensus 2 ~~~~G~~Ve~~~~~-~~~W~~a~V~~~~~-~~~~~V~~~~ 39 (61)
T smart00743 2 DFKKGDRVEVFSKE-EDSWWEAVVTKVLG-DGKYLVRYLT 39 (61)
T ss_pred CcCCCCEEEEEECC-CCEEEEEEEEEECC-CCEEEEEECC
Confidence 36899999999865 57889999999987 5789999987
No 8
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=86.98 E-value=1.1 Score=41.65 Aligned_cols=56 Identities=27% Similarity=0.239 Sum_probs=42.4
Q ss_pred CccccCCCEEEEEecCCCCcceeeEEEEE----eCCCCeeEEEecCCCCceeeecCcccccC
Q psy9276 264 PIQLVVGTKVTARVRSPQDGLFTGVVDAY----DTSNNTYRITFDRQGLGTQSIPDYEVLSN 321 (583)
Q Consensus 264 P~PL~VG~kV~Arl~~~~~gL~~G~Vlav----d~~~~~YrV~Fdr~~lgv~~VpD~evms~ 321 (583)
-.||.+|++|+|.++.....-..|+|++. ...+..|.|.|-... ...||.-+|.-+
T Consensus 53 ~~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng~--~~~vp~~~~~~I 112 (124)
T PF15057_consen 53 RHSLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYNGK--TAKVPRGEVIWI 112 (124)
T ss_pred cCcCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEECCC--CCccchhhEEEC
Confidence 67999999999998654445667999963 445689999998766 566777666544
No 9
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=85.92 E-value=1.8 Score=40.55 Aligned_cols=53 Identities=19% Similarity=0.306 Sum_probs=35.3
Q ss_pred ccccCCCEEEEEecCCCCcceeeEEEEE-eCCCCeeEEEecCCCCc--eeeecCccc
Q psy9276 265 IQLVVGTKVTARVRSPQDGLFTGVVDAY-DTSNNTYRITFDRQGLG--TQSIPDYEV 318 (583)
Q Consensus 265 ~PL~VG~kV~Arl~~~~~gL~~G~Vlav-d~~~~~YrV~Fdr~~lg--v~~VpD~ev 318 (583)
.-+..|++|+|+-|.| ..+|.|+|.+. ......|++.|+-.+-. .+.||.--|
T Consensus 70 ~~f~~g~~VLAlYP~T-T~FY~A~V~~~p~~~~~~y~l~Fedd~~~~~~~~V~~r~V 125 (130)
T PF07039_consen 70 AEFPKGTKVLALYPDT-TCFYPATVVSPPKKKSGEYKLKFEDDEDADGYREVPQRYV 125 (130)
T ss_dssp GS--TT-EEEEE-TTS-SEEEEEEEEEE-SSTTS-EEEEECTTTSTTSBEEE-GGGE
T ss_pred hhCCCCCEEEEECCCC-ceEEEEEEEeCCCCCCCcEEEEEeCCCCcCCcEEEccceE
Confidence 5578999999999996 59999999987 23567999999976632 255554433
No 10
>PLN03094 Substrate binding subunit of ER-derived-lipid transporter; Provisional
Probab=76.22 E-value=43 Score=36.81 Aligned_cols=33 Identities=24% Similarity=0.295 Sum_probs=28.6
Q ss_pred ccCCCEEEEEecCCCCcceeeEEEEEeCCCCeeEEEecC
Q psy9276 267 LVVGTKVTARVRSPQDGLFTGVVDAYDTSNNTYRITFDR 305 (583)
Q Consensus 267 L~VG~kV~Arl~~~~~gL~~G~Vlavd~~~~~YrV~Fdr 305 (583)
|.+|+.|.. .|+--|+|.++.+..+..+|.|.-
T Consensus 130 L~~Gs~Vr~------~GV~VG~V~~I~l~~~~V~V~~~I 162 (370)
T PLN03094 130 ICVGTPVRI------RGVTVGNVVRVRPSLEKIDVVVEV 162 (370)
T ss_pred CCCCCceEE------cCEEeeEEEEEEecCCeEEEEEEE
Confidence 578998887 599999999999988889998864
No 11
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=74.68 E-value=6.7 Score=36.92 Aligned_cols=45 Identities=24% Similarity=0.427 Sum_probs=31.6
Q ss_pred CCCEEEEEecCCCCcc-eeeEEEEEeCCCCeeEEEecCCCCceeeecCc
Q psy9276 269 VGTKVTARVRSPQDGL-FTGVVDAYDTSNNTYRITFDRQGLGTQSIPDY 316 (583)
Q Consensus 269 VG~kV~Arl~~~~~gL-~~G~Vlavd~~~~~YrV~Fdr~~lgv~~VpD~ 316 (583)
||-+|.|+-. .++- |.|+|.. |..++.|.|.||-..--....+|+
T Consensus 5 iG~rV~AkWS--~n~yyY~G~I~~-~~~~~kykv~FdDG~~~~v~~~di 50 (122)
T PF09038_consen 5 IGLRVFAKWS--DNGYYYPGKITS-DKGKNKYKVLFDDGYECRVLGKDI 50 (122)
T ss_dssp TT-EEEEESS--TTSEEEEEEEEE-EETTTEEEEEETTS-EEEEECCCE
T ss_pred cccEEEEEEc--cCCcccCceEee-cCCCCeEEEEecCCccceeccCcE
Confidence 8999999865 3555 7999998 677899999999764222334443
No 12
>KOG0995|consensus
Probab=73.72 E-value=5.7 Score=45.51 Aligned_cols=58 Identities=19% Similarity=0.385 Sum_probs=43.1
Q ss_pred CCCCchhhhHHHHHHHHhhcC--------------cccccc-ceeecccccCCccccc----cchHHHHHHHh-CCCC
Q psy9276 143 SSPDRNLGQRVGMKLRNLLKL--------------PKAYRF-VCYEFFYSNIDRPLFN----DNDFITCMKES-FPQL 200 (583)
Q Consensus 143 ~~pd~~~~q~~g~rL~n~Lk~--------------pka~RW-~~~EwFYS~IDkp~F~----~nEF~~~L~e~-fP~l 200 (583)
.+-|++-.|..+..++|||.- |...-+ ++|.|.|+++|.+|+. .+|-.+||+.. +|-+
T Consensus 65 pl~dk~~~s~c~~~I~~fL~engf~~~iS~k~l~~PS~KdF~~iFkfLY~~Ldp~y~f~~r~EeEV~~ilK~L~YPf~ 142 (581)
T KOG0995|consen 65 PLSDKRYRSQCIRQIYNFLVENGFSHPISIKLLMKPSVKDFIAIFKFLYGFLDPDYEFPERIEEEVVQILKNLKYPFL 142 (581)
T ss_pred CcccHHHHHHHHHHHHHHHHHcCCCCChhhhhcCCCccccHHHHHHHHHhccCCCcccchhHHHHHHHHHHhCCCCcc
Confidence 455766677788888888752 333333 4789999999999988 78888888875 5654
No 13
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=73.68 E-value=6.8 Score=31.23 Aligned_cols=37 Identities=16% Similarity=0.310 Sum_probs=28.8
Q ss_pred ccCCCEEEEEecCCCCcceeeEEEEEeCCC--CeeEEEecC
Q psy9276 267 LVVGTKVTARVRSPQDGLFTGVVDAYDTSN--NTYRITFDR 305 (583)
Q Consensus 267 L~VG~kV~Arl~~~~~gL~~G~Vlavd~~~--~~YrV~Fdr 305 (583)
|.||++|.+.+ .....|.++|+.+...+ ..|.|-|..
T Consensus 1 ~~vG~~v~~~~--~~~~~y~A~I~~~r~~~~~~~YyVHY~g 39 (55)
T PF11717_consen 1 FEVGEKVLCKY--KDGQWYEAKILDIREKNGEPEYYVHYQG 39 (55)
T ss_dssp --TTEEEEEEE--TTTEEEEEEEEEEEECTTCEEEEEEETT
T ss_pred CCcCCEEEEEE--CCCcEEEEEEEEEEecCCCEEEEEEcCC
Confidence 57999999998 23578999999988754 479999974
No 14
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=73.59 E-value=8.9 Score=39.93 Aligned_cols=54 Identities=19% Similarity=0.379 Sum_probs=37.4
Q ss_pred ccccCCCEEEEEecCCCCc-ceeeEEEEEeCCCCeeEEEecCCCCc-eeeecCcccccCC
Q psy9276 265 IQLVVGTKVTARVRSPQDG-LFTGVVDAYDTSNNTYRITFDRQGLG-TQSIPDYEVLSND 322 (583)
Q Consensus 265 ~PL~VG~kV~Arl~~~~~g-L~~G~Vlavd~~~~~YrV~Fdr~~lg-v~~VpD~evms~~ 322 (583)
....||++..|.-- .|| +|.++|.+|+..+.+|.|+|+- .| .+.|.=.++++..
T Consensus 67 ~~WkvGd~C~A~~s--~Dg~~Y~A~I~~i~~~~~~~~V~f~g--Ygn~e~v~l~dL~~~~ 122 (264)
T PF06003_consen 67 KKWKVGDKCMAVYS--EDGQYYPATIESIDEEDGTCVVVFTG--YGNEEEVNLSDLKPSE 122 (264)
T ss_dssp T---TT-EEEEE-T--TTSSEEEEEEEEEETTTTEEEEEETT--TTEEEEEEGGGEEETT
T ss_pred cCCCCCCEEEEEEC--CCCCEEEEEEEEEcCCCCEEEEEEcc--cCCeEeeehhhhcccc
Confidence 46789999999863 355 7999999999988899999984 34 4555555555543
No 15
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=70.78 E-value=13 Score=27.79 Aligned_cols=42 Identities=14% Similarity=0.271 Sum_probs=31.4
Q ss_pred CCEEEEEecCCCCcceeeEEEEEeCCCCeeEEEecCCCCceeeec
Q psy9276 270 GTKVTARVRSPQDGLFTGVVDAYDTSNNTYRITFDRQGLGTQSIP 314 (583)
Q Consensus 270 G~kV~Arl~~~~~gL~~G~Vlavd~~~~~YrV~Fdr~~lgv~~Vp 314 (583)
|+.|.|+... ....|.|+|+.+++ +..|.|.|.-=|. ++.|+
T Consensus 1 G~~c~a~~~~-d~~wyra~V~~~~~-~~~~~V~f~DyG~-~~~v~ 42 (48)
T cd04508 1 GDLCLAKYSD-DGKWYRAKITSILS-DGKVEVFFVDYGN-TEVVP 42 (48)
T ss_pred CCEEEEEECC-CCeEEEEEEEEECC-CCcEEEEEEcCCC-cEEEe
Confidence 7889998764 24579999999987 6899999985442 34444
No 16
>PF10241 KxDL: Uncharacterized conserved protein; InterPro: IPR019371 This entry represents a conserved region of 80 residues which defines a family of short proteins. There is a characteristic KxDL motif towards the C terminus. The function is unknown.
Probab=44.24 E-value=1.1e+02 Score=26.94 Aligned_cols=63 Identities=14% Similarity=0.178 Sum_probs=40.9
Q ss_pred HHHHHHHHhhcHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhccc
Q psy9276 391 KTEVYQIRDMNSEAERRQLYGEPYDRAFQKKYAGHILRLEKINKDVNTVLASLSVNLKKLSVT 453 (583)
Q Consensus 391 e~lV~~L~~MN~EAE~~~s~g~~~~e~FQrrYA~vvi~Le~vN~~L~~~L~~Lq~~~~~la~~ 453 (583)
..++..|..-|.+.......++.-=..++.+|+...-.|..+.+||+..-..|+..-..++..
T Consensus 21 ~~~l~~ln~tn~~L~~~n~~s~~rl~~~~~~f~~~~~~l~~mK~DLd~i~krir~lk~kl~~~ 83 (88)
T PF10241_consen 21 AQTLGRLNKTNEELLNLNDLSQQRLAEARERFARHTKLLKEMKKDLDYIFKRIRSLKAKLAKQ 83 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 333444444444443333322211256888999999999999999999988888877666644
No 17
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=43.26 E-value=3.7e+02 Score=32.25 Aligned_cols=45 Identities=20% Similarity=0.199 Sum_probs=37.0
Q ss_pred HHHHhhcHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhccc
Q psy9276 395 YQIRDMNSEAERRQLYGEPYDRAFQKKYAGHILRLEKINKDVNTVLASLSVNLKKLSVT 453 (583)
Q Consensus 395 ~~L~~MN~EAE~~~s~g~~~~e~FQrrYA~vvi~Le~vN~~L~~~L~~Lq~~~~~la~~ 453 (583)
.+|++||-+.|+.+. =+++||.++ +-+|..+|+++..|.+-++..
T Consensus 508 eela~l~r~lersn~--------el~~f~yv~------sHdlqePl~~I~~~a~lL~~~ 552 (750)
T COG4251 508 EELAQLRRELERSNA--------ELRAFAYVA------SHDLQEPLRQISNYAQLLSER 552 (750)
T ss_pred HHHHHHHHHHhhhhH--------HHHHHHHHh------hhhhhHHHHHHHHHHHhhhhc
Confidence 467888888887753 578888876 999999999999999977755
No 18
>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
Probab=43.15 E-value=72 Score=28.48 Aligned_cols=44 Identities=18% Similarity=0.134 Sum_probs=35.3
Q ss_pred CCCCccccCCCEEEEEecCCCCcceeeEEEEEeCCCCeeEEEecCC
Q psy9276 261 SEIPIQLVVGTKVTARVRSPQDGLFTGVVDAYDTSNNTYRITFDRQ 306 (583)
Q Consensus 261 ~~IP~PL~VG~kV~Arl~~~~~gL~~G~Vlavd~~~~~YrV~Fdr~ 306 (583)
......|.||+|+-|.-+.....++-++|..|. +...+|.||--
T Consensus 22 ~~~~~~F~vGmkLEavD~~~~~~i~vAtV~~v~--g~~l~v~~dg~ 65 (96)
T smart00561 22 DSPPNGFKVGMKLEAVDPRNPSLICVATVVEVK--GYRLLLHFDGW 65 (96)
T ss_pred CCccCcccCCCEEEEECCCCCceEEEEEEEEEE--CCEEEEEEccC
Confidence 344567999999999988754678999999987 46889999943
No 19
>PF10591 SPARC_Ca_bdg: Secreted protein acidic and rich in cysteine Ca binding region; InterPro: IPR019577 This entry represents the calcium-binding domain found in SPARC (Secreted Protein Acidic and Rich in Cysteine) and Testican (also known as SPOCK; or SParc/Osteonectin, Cwcv and Kazal-like domains) proteins. SPARC proteins are down-regulated in various tumours and may have a tumour-suppressor function [, ]. Testican-3 appears to be a novel regulator that reduces the activity of matrix metalloproteinase (MMP) in adult T-cell leukemia (ATL) []. This cysteine-rich domain is responsible for the anti-spreading activity of human urothelial cells. This extracellular calcium-binding domain is rich in alpha-helices and contains two EF-hands that each coordinates one Ca2+ ion, forming a helix-loop-helix structure that not only drives the conformation of the protein but is also necessary for biological activity. The anti-spreading activity was dependent on the coordination of Ca2+ by a Glu residue at the Z position of EF-hand 2 []. ; GO: 0005509 calcium ion binding, 0007165 signal transduction, 0005578 proteinaceous extracellular matrix; PDB: 1BMO_A 1SRA_A 2V53_A 1NUB_B.
Probab=42.51 E-value=6.1 Score=36.01 Aligned_cols=29 Identities=34% Similarity=0.622 Sum_probs=25.4
Q ss_pred cccccchhHHHHHHhhhCCCCCCChhhHH
Q psy9276 201 KKYVFSRTEWSMVRRMVGKPRRCSSSFFT 229 (583)
Q Consensus 201 ~trkLtR~EW~~IRr~mGKPRRfS~aFl~ 229 (583)
+-..|++.||..||+.|-++++|...||.
T Consensus 67 ~d~~L~~~El~~l~~~l~~~e~C~~~F~~ 95 (113)
T PF10591_consen 67 KDGVLDRSELKPLRRPLMPPEHCARPFFR 95 (113)
T ss_dssp -SSEE-TTTTGGGGSTTSTTGGGHHHHHH
T ss_pred CCCccCHHHHHHHHHHHhhhHHHHHHHHH
Confidence 35799999999999999999999999985
No 20
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=37.16 E-value=56 Score=31.03 Aligned_cols=27 Identities=4% Similarity=0.076 Sum_probs=23.6
Q ss_pred CCcceeeEEEEEeCCCCeeEEEecCCC
Q psy9276 281 QDGLFTGVVDAYDTSNNTYRITFDRQG 307 (583)
Q Consensus 281 ~~gL~~G~Vlavd~~~~~YrV~Fdr~~ 307 (583)
..+.|.|++++.+....+|.|.|+-..
T Consensus 21 ~~~yYPa~~~~~~~~~~~~~V~Fedg~ 47 (131)
T PF08605_consen 21 NLKYYPATCVGSGVDRDRSLVRFEDGT 47 (131)
T ss_pred CCeEeeEEEEeecCCCCeEEEEEecCc
Confidence 468999999999888788999999766
No 21
>KOG3038|consensus
Probab=35.98 E-value=46 Score=35.13 Aligned_cols=41 Identities=20% Similarity=0.282 Sum_probs=29.6
Q ss_pred ccccCCCEEEEEecCCCCcceeeEEEEEeCC-CCeeEE-EecCC
Q psy9276 265 IQLVVGTKVTARVRSPQDGLFTGVVDAYDTS-NNTYRI-TFDRQ 306 (583)
Q Consensus 265 ~PL~VG~kV~Arl~~~~~gL~~G~Vlavd~~-~~~YrV-~Fdr~ 306 (583)
++|+.|+.|+|+-|.+ .-+|.|.|.+--.. .+.|.| .||-.
T Consensus 197 ~~fpp~~~VLA~YP~T-TcFY~aiVh~tp~d~s~~y~vlffD~~ 239 (264)
T KOG3038|consen 197 ALFPPGTIVLAVYPGT-TCFYKAIVHSTPRDGSCDYYVLFFDDE 239 (264)
T ss_pred cCCCCCCEEEEEcCCc-ceeeeeEeecCCCCCCCcceeeeecCc
Confidence 7789999999999997 48999999975322 123444 45543
No 22
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=35.25 E-value=41 Score=28.19 Aligned_cols=17 Identities=35% Similarity=0.610 Sum_probs=15.4
Q ss_pred eEEEEEeCCCCeeEEEe
Q psy9276 287 GVVDAYDTSNNTYRITF 303 (583)
Q Consensus 287 G~Vlavd~~~~~YrV~F 303 (583)
|+|.+||+.+.+|||+|
T Consensus 1 G~V~~v~~~~grvrV~~ 17 (79)
T PF04717_consen 1 GTVTAVDPDKGRVRVRF 17 (79)
T ss_dssp EEEEEEETTTTEEEEE-
T ss_pred CeEEEEECCCCEEEEEE
Confidence 89999999999999999
No 23
>COG4985 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]
Probab=34.96 E-value=2.6e+02 Score=29.60 Aligned_cols=70 Identities=29% Similarity=0.320 Sum_probs=50.6
Q ss_pred HHHHHHHHHHHHHHHHH--------HHhhcHHHHHHhh------cCCCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Q psy9276 380 VVRFKKLLKFKKTEVYQ--------IRDMNSEAERRQL------YGEPYDRAFQKKYAGHILRLEKINKDVNTVLASLSV 445 (583)
Q Consensus 380 lv~LsKlL~~Ke~lV~~--------L~~MN~EAE~~~s------~g~~~~e~FQrrYA~vvi~Le~vN~~L~~~L~~Lq~ 445 (583)
.-+|+|-|-+=+++..+ ++-+|...|+... ....++.+||.+|++-.=.|++--+.|...|+.||+
T Consensus 163 ~~eLqkr~~~v~~l~~q~~k~~~~qv~~in~qlErLRL~krrlQl~g~Ld~~~q~~~~ae~seLq~r~~~l~~~L~~L~~ 242 (289)
T COG4985 163 ERELQKRLLEVETLRDQVDKMVEQQVRVINSQLERLRLEKRRLQLNGQLDDEFQQHYVAEKSELQKRLAQLQTELDALRA 242 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34556655555555544 4556887775532 122588999999999999999999999999999998
Q ss_pred Hhhh
Q psy9276 446 NLKK 449 (583)
Q Consensus 446 ~~~~ 449 (583)
-.+.
T Consensus 243 e~~r 246 (289)
T COG4985 243 ELER 246 (289)
T ss_pred hhhh
Confidence 4443
No 24
>PRK02507 proton extrusion protein PcxA; Provisional
Probab=31.81 E-value=1.5e+02 Score=33.33 Aligned_cols=115 Identities=20% Similarity=0.274 Sum_probs=73.2
Q ss_pred hhHHH-HHHHHHHHHHhhhhcccccccccccccCCchHHHHHHHHHHHHHHHHHHhhcCCcccCcchHHHHHHHHHHHHH
Q psy9276 432 INKDV-NTVLASLSVNLKKLSVTSENMSSQLYALSPSDLQQETYIAAQEIVDTVNKKNGNKIVDDQPVVSLITDLTALVL 510 (583)
Q Consensus 432 vN~~L-~~~L~~Lq~~~~~la~~~~~~~~~~~~~~ps~lre~Cr~~A~e~~~~v~~~n~~~v~~~~~~~~LI~~LttLLl 510 (583)
+|... +.+|..++++=..+--+ ++-+..+-+.++.++++-+++| .++++..|...+ +.+..+++++.++..
T Consensus 241 ln~~qee~al~~l~~~EE~l~fd--~li~~~p~~~~~~~~~~i~~ka---ieL~~~~n~~si---~~i~nl~tDli~~~~ 312 (422)
T PRK02507 241 INPELEEEALEELRRFKEELEFE--ALLGLAPPLSPEEIEEKLKEKA---EELAEEARYESL---NAIKNVFADLFSLIA 312 (422)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHH--HHhccCCCCCHHHHHHHHHHHH---HHHHHHHHHhhH---HHHHHHHHHHHHHHH
Confidence 45554 34566666543333222 1111123345678899999999 666666666443 337789999998888
Q ss_pred HHhhcCcCCCchhhHHHHHHHHHHHHhcCCCChHHHHh-----HHHHHHHHH
Q psy9276 511 QIKTLSHSSRSAYEVEVLNKTMSDIYKKLSPNNQSVFE-----NCIGVHMEQ 557 (583)
Q Consensus 511 q~~~Lg~~~~na~e~~vL~d~l~eIk~~l~p~N~~~Fq-----~~Veih~~~ 557 (583)
.+.-+--++ .++.+|+.-++|+-=+|+..--+.+- -+|+-|=-|
T Consensus 313 f~~l~i~~k---~~l~IL~s~~~E~~Y~LSDt~KAF~IIL~TDlfVGFHSph 361 (422)
T PRK02507 313 FAVVLIFSR---EEIEVLKSFLDEIVYGLSDSAKAFIIILFTDIFVGFHSPH 361 (422)
T ss_pred HHHHHHhCc---chhhHHHHHHHHHHhcCcHHHHHHHHHHHHHHHhcCCCch
Confidence 877554432 27889999999999998776666553 456655444
No 25
>TIGR02266 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266. This domain is related to Type IV pilus assembly protein PilZ (Pfam model pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622.
Probab=30.89 E-value=1.6e+02 Score=24.77 Aligned_cols=45 Identities=22% Similarity=0.361 Sum_probs=32.4
Q ss_pred CCccccCCCEEEEEecCCCC--cc-eeeEEEEEeCCCC----eeEEEecCCC
Q psy9276 263 IPIQLVVGTKVTARVRSPQD--GL-FTGVVDAYDTSNN----TYRITFDRQG 307 (583)
Q Consensus 263 IP~PL~VG~kV~Arl~~~~~--gL-~~G~Vlavd~~~~----~YrV~Fdr~~ 307 (583)
.+.|+.+|++|...+..|.. .+ ..|.|+-+.+... .|.|+|....
T Consensus 33 ~~~~~~~g~~v~l~l~l~~~~~~i~~~g~Vv~~~~~~~~~~~~~Gv~F~~~~ 84 (96)
T TIGR02266 33 TRKPLAVGTRVELKLTLPGGERPVELKGVVAWVRPAADGGPPGMGVRFEDLD 84 (96)
T ss_pred cCCCcCCCCEEEEEEEcCCCCeEEEEEEEEEEeCCCCCCCCCeeEEEeccCC
Confidence 35778999999999977642 24 6899998876543 4778886443
No 26
>PF03040 CemA: CemA family; InterPro: IPR004282 Members of this family are probable integral membrane proteins. Their molecular function is unknown. CemA proteins are found in the inner envelope membrane of chloroplasts but not in the thylakoid membrane []. A cyanobacterial member of this family (proton extrusion protein PcxA) is involved in light-induced Na(+)-dependent proton extrusion and has been implicated in CO2 transport, but is probably not a CO2 transporter itself [].; GO: 0016021 integral to membrane
Probab=30.83 E-value=1.7e+02 Score=30.35 Aligned_cols=76 Identities=20% Similarity=0.346 Sum_probs=57.9
Q ss_pred cCCchHHHHHHHHHHHHHHHHHHhhcCCcccCcchHHHHHHHHHHHHHHHhhcCcCCCchhhHHHHHHHHHHHHhcCCCC
Q psy9276 463 ALSPSDLQQETYIAAQEIVDTVNKKNGNKIVDDQPVVSLITDLTALVLQIKTLSHSSRSAYEVEVLNKTMSDIYKKLSPN 542 (583)
Q Consensus 463 ~~~ps~lre~Cr~~A~e~~~~v~~~n~~~v~~~~~~~~LI~~LttLLlq~~~Lg~~~~na~e~~vL~d~l~eIk~~l~p~ 542 (583)
-+.+..++++-+++| .++++..|...+ +.+..+.++++++...+.-+--++ .++.+|+.-++|+-=+|+..
T Consensus 79 ~ls~q~l~~~I~~ka---~~l~~~~~~~~~---~~i~n~~~d~i~~~~~~~~~~~~~---~~l~il~s~~~e~~y~LsDt 149 (230)
T PF03040_consen 79 ELSSQELRIEIHEKA---IELAKEYNEESI---HAILNLFTDIISFIIFSGLLILGK---EQLAILNSWIQEFFYSLSDT 149 (230)
T ss_pred ccchhHHHHHHHHHH---HHHHHHHHHhhH---HHHHHHHHHHHHHHHHHHHHHhcc---chhHHHHHHHHHHhhCccHH
Confidence 446678899999999 677777776543 337889999999988888665543 26889999999999998766
Q ss_pred hHHHH
Q psy9276 543 NQSVF 547 (583)
Q Consensus 543 N~~~F 547 (583)
--+.+
T Consensus 150 ~KaF~ 154 (230)
T PF03040_consen 150 AKAFL 154 (230)
T ss_pred HHHHH
Confidence 66554
No 27
>KOG3026|consensus
Probab=30.62 E-value=59 Score=34.09 Aligned_cols=42 Identities=21% Similarity=0.331 Sum_probs=35.8
Q ss_pred cccCCCEEEEEecCCCCcceeeEEEEEeCCCCeeEEEecCCCC
Q psy9276 266 QLVVGTKVTARVRSPQDGLFTGVVDAYDTSNNTYRITFDRQGL 308 (583)
Q Consensus 266 PL~VG~kV~Arl~~~~~gL~~G~Vlavd~~~~~YrV~Fdr~~l 308 (583)
-+.||+||+|.++. ...+|+.+|.++++...+--|.|+..+.
T Consensus 90 ~w~vg~K~~A~~~d-dg~~y~AtIe~ita~~~~~ai~f~s~~~ 131 (262)
T KOG3026|consen 90 GWKVGDKVQAVFSD-DGQIYDATIEHITAMEGTVAIIFASYGT 131 (262)
T ss_pred ccccCCEEEEeecC-CCceEEeehhhccCCCCceeEEEeeccc
Confidence 37899999999875 3569999999999988899999987664
No 28
>CHL00043 cemA envelope membrane protein
Probab=30.37 E-value=1.6e+02 Score=31.18 Aligned_cols=83 Identities=17% Similarity=0.198 Sum_probs=60.4
Q ss_pred CCchHHHHHHHHHHHHHHHHHHhhcCCcccCcchHHHHHHHHHHHHHHHhhcCcCCCchhhHHHHHHHHHHHHhcCCCCh
Q psy9276 464 LSPSDLQQETYIAAQEIVDTVNKKNGNKIVDDQPVVSLITDLTALVLQIKTLSHSSRSAYEVEVLNKTMSDIYKKLSPNN 543 (583)
Q Consensus 464 ~~ps~lre~Cr~~A~e~~~~v~~~n~~~v~~~~~~~~LI~~LttLLlq~~~Lg~~~~na~e~~vL~d~l~eIk~~l~p~N 543 (583)
+.+..++++-+++| .++++..|...+. ....+.+++.++...+.-+--++ .++.+|+..++|+-=+|+-.-
T Consensus 111 ~~~~~~~~~i~~ka---ieL~~~~n~~~i~---~i~n~~td~i~~~~~~~~~i~~k---~~l~il~s~~~E~~Y~LSDt~ 181 (261)
T CHL00043 111 THLQKLRIGIHKET---IQLAKIYNEDSIH---TILHLSTNIISFAILSGLSILGK---EELVILNSWLQEFLYNLSDTI 181 (261)
T ss_pred CCHHHHHHHHHHHH---HHHHHHHHHHhHH---HHHHHHHHHHHHHHHHHHHHhCc---chHHHHHHHHHHHHhcCcHHH
Confidence 45677889999999 6777777765543 37789999998888887555543 278899999999999987665
Q ss_pred HHHHh-----HHHHHHH
Q psy9276 544 QSVFE-----NCIGVHM 555 (583)
Q Consensus 544 ~~~Fq-----~~Veih~ 555 (583)
-+.+- -+|+-|=
T Consensus 182 KAF~IiL~TDlfvGFHS 198 (261)
T CHL00043 182 KAFSILLLTDLCIGFHS 198 (261)
T ss_pred HHHHHHHHHHHHhcCCC
Confidence 55543 3555553
No 29
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=30.35 E-value=86 Score=35.51 Aligned_cols=41 Identities=22% Similarity=0.237 Sum_probs=31.9
Q ss_pred CccccCCCEEEEEecCCCCcceeeEEEEEeCCC------CeeEEEecC
Q psy9276 264 PIQLVVGTKVTARVRSPQDGLFTGVVDAYDTSN------NTYRITFDR 305 (583)
Q Consensus 264 P~PL~VG~kV~Arl~~~~~gL~~G~Vlavd~~~------~~YrV~Fdr 305 (583)
..+|.||++|.|++... ..+|.+.|+.+.... ..|-|.|..
T Consensus 51 ~~~~~VGekVla~~~~D-g~~~~A~VI~~R~~~~~~~~~~~YYVHY~g 97 (450)
T PLN00104 51 MLPLEVGTRVMCRWRFD-GKYHPVKVIERRRGGSGGPNDYEYYVHYTE 97 (450)
T ss_pred cceeccCCEEEEEECCC-CCEEEEEEEEEeccCCCCCCCceEEEEEec
Confidence 36799999999998642 457799999988633 469998874
No 30
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=28.89 E-value=1.4e+02 Score=24.65 Aligned_cols=38 Identities=16% Similarity=0.282 Sum_probs=25.0
Q ss_pred ccCCCEEEEEecC--CCCcceeeEEEEEeCCCCeeEEEecC
Q psy9276 267 LVVGTKVTARVRS--PQDGLFTGVVDAYDTSNNTYRITFDR 305 (583)
Q Consensus 267 L~VG~kV~Arl~~--~~~gL~~G~Vlavd~~~~~YrV~Fdr 305 (583)
|.+|++|-++--. ....=|.|+|+.....+ .|.|.++.
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~-~~~V~Y~~ 40 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD-KYLVEYDD 40 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT--EEEEEETT
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc-EEEEEECC
Confidence 4689999998633 22235999999988743 99999963
No 31
>KOG4578|consensus
Probab=28.29 E-value=23 Score=38.63 Aligned_cols=28 Identities=39% Similarity=0.891 Sum_probs=24.6
Q ss_pred ccccchhHHHHHHhhh---CCCCCCChhhHH
Q psy9276 202 KYVFSRTEWSMVRRMV---GKPRRCSSSFFT 229 (583)
Q Consensus 202 trkLtR~EW~~IRr~m---GKPRRfS~aFl~ 229 (583)
...+.|.||.-.|+.+ -|||+||..||+
T Consensus 347 nn~i~rrEwKpFK~~l~k~s~~rkC~rk~~~ 377 (421)
T KOG4578|consen 347 NNDIERREWKPFKRVLLKKSKPRKCSRKFFK 377 (421)
T ss_pred cCccchhhcchHHHHHHhhccHHHHhhhcch
Confidence 4678999999999987 589999999985
No 32
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=27.16 E-value=1.3e+02 Score=26.40 Aligned_cols=38 Identities=13% Similarity=0.213 Sum_probs=29.7
Q ss_pred ccCCCEEEEEecCCCCcceeeEEEEEeCCCCeeEEEecCC
Q psy9276 267 LVVGTKVTARVRSPQDGLFTGVVDAYDTSNNTYRITFDRQ 306 (583)
Q Consensus 267 L~VG~kV~Arl~~~~~gL~~G~Vlavd~~~~~YrV~Fdr~ 306 (583)
+.+|+-|-|.+.+. ---.|.|.++...+..|+|.|=-.
T Consensus 1 f~~gdlVWaK~~g~--P~WPa~I~~~~~~~~k~~V~FfG~ 38 (80)
T cd06080 1 FEKNDLVWAKIQGY--PWWPAVIKSISRKKQKARVNFIGD 38 (80)
T ss_pred CCCCCEEEEeCCCC--CCCCEEEeeecCCCCEEEEEEeCC
Confidence 46899999987651 346789999888788999999533
No 33
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=26.60 E-value=1.4e+02 Score=24.96 Aligned_cols=31 Identities=26% Similarity=0.388 Sum_probs=24.8
Q ss_pred cccCCCEEEEEecCCCCcceeeEEEEEeCCCCe
Q psy9276 266 QLVVGTKVTARVRSPQDGLFTGVVDAYDTSNNT 298 (583)
Q Consensus 266 PL~VG~kV~Arl~~~~~gL~~G~Vlavd~~~~~ 298 (583)
++++|.+|-.. .+.+.-+.|.|++||+....
T Consensus 2 ~f~iGs~V~~k--Tc~g~~ieGEV~afD~~tk~ 32 (61)
T cd01735 2 CFSVGSQVSCR--TCFEQRLQGEVVAFDYPSKM 32 (61)
T ss_pred ccccccEEEEE--ecCCceEEEEEEEecCCCcE
Confidence 47899999876 34578999999999996433
No 34
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=25.16 E-value=1.6e+02 Score=24.00 Aligned_cols=38 Identities=29% Similarity=0.486 Sum_probs=26.2
Q ss_pred CccccCCCEEEEEecCCCCcc--eeeEEEEEeCCCCeeEE
Q psy9276 264 PIQLVVGTKVTARVRSPQDGL--FTGVVDAYDTSNNTYRI 301 (583)
Q Consensus 264 P~PL~VG~kV~Arl~~~~~gL--~~G~Vlavd~~~~~YrV 301 (583)
+.++.+|++|...+..+..+. ..|+|+.+....+.|.+
T Consensus 42 ~~~~~~~~~v~l~~~~~~~~~~~~~~~V~~~~~~~~~~~~ 81 (102)
T PF07238_consen 42 PKPLEPGDRVRLSFSLPGGGFPIVTGRVVRIQKDSDGYRV 81 (102)
T ss_dssp CTG--TTSEEEEEEECTTTSCEEEEEEEEEEEEESSEEEE
T ss_pred CCCCCCCCEEEEEEEeCCCCeeEEEEEEEEEECCCCceEE
Confidence 449999999998887765554 89999987775444443
No 35
>KOG4515|consensus
Probab=23.86 E-value=2e+02 Score=29.42 Aligned_cols=50 Identities=24% Similarity=0.304 Sum_probs=34.4
Q ss_pred HHHHHHHHhhcHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Q psy9276 391 KTEVYQIRDMNSEAERRQLYGEPYDRAFQKKYAGHILRLEKINKDVNTVLASLSV 445 (583)
Q Consensus 391 e~lV~~L~~MN~EAE~~~s~g~~~~e~FQrrYA~vvi~Le~vN~~L~~~L~~Lq~ 445 (583)
-++|.+.+.|-...++..+ .--+.|++||.-+-+|..+|. |..-|..+|-
T Consensus 116 n~lv~r~K~v~~s~~tLf~----~~~~~qk~ya~yaeq~~k~n~-ls~~l~riq~ 165 (217)
T KOG4515|consen 116 NKLVARCKSVEASMITLFE----ETRAHQKQYAGYAEQLSKLNQ-LSDDLCRIQI 165 (217)
T ss_pred HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 4567777777766666554 235689999999999999885 4444444443
No 36
>PF13437 HlyD_3: HlyD family secretion protein
Probab=23.40 E-value=1.8e+02 Score=24.83 Aligned_cols=46 Identities=24% Similarity=0.420 Sum_probs=31.6
Q ss_pred CCCCCCcccc-CCCEEEEEecCCCCcceeeEEEEEeC----CCCeeEEEec
Q psy9276 259 IPSEIPIQLV-VGTKVTARVRSPQDGLFTGVVDAYDT----SNNTYRITFD 304 (583)
Q Consensus 259 LP~~IP~PL~-VG~kV~Arl~~~~~gL~~G~Vlavd~----~~~~YrV~Fd 304 (583)
+|..--.-+. +|++|+..+......-+.|+|..+.+ .+.+|+|++.
T Consensus 42 v~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~~~~~~~~~~~v~~~ 92 (105)
T PF13437_consen 42 VPEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISPSPDPQGGTYRVEIS 92 (105)
T ss_pred EChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeCcccCCCcEEEEEEE
Confidence 3444445665 99999999973234589999998866 3346666654
No 37
>smart00557 IG_FLMN Filamin-type immunoglobulin domains. These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).
Probab=22.51 E-value=2.3e+02 Score=24.37 Aligned_cols=42 Identities=19% Similarity=0.395 Sum_probs=31.0
Q ss_pred CCEEEEEecCCCCcceeeEEEEEeCCCCeeEEEecCCCCceeee
Q psy9276 270 GTKVTARVRSPQDGLFTGVVDAYDTSNNTYRITFDRQGLGTQSI 313 (583)
Q Consensus 270 G~kV~Arl~~~~~gL~~G~Vlavd~~~~~YrV~Fdr~~lgv~~V 313 (583)
|..+.+.+..|.......+|. |..+.+|.|.|.-..-|.+.|
T Consensus 31 ~~~~~v~i~~p~g~~~~~~v~--d~~dGty~v~y~P~~~G~~~i 72 (93)
T smart00557 31 GGELEVEVTGPSGKKVPVEVK--DNGDGTYTVSYTPTEPGDYTV 72 (93)
T ss_pred CCcEEEEEECCCCCeeEeEEE--eCCCCEEEEEEEeCCCEeEEE
Confidence 566777777774335666775 777789999999888887765
No 38
>KOG4485|consensus
Probab=21.32 E-value=1.3e+03 Score=26.83 Aligned_cols=82 Identities=18% Similarity=0.286 Sum_probs=51.9
Q ss_pred ccccchhHHHHHHhhhCCCCCC------------ChhhHHHHHHHHHHHH--HHHHHHhhccCCCCCccCCCCCCCCccc
Q psy9276 202 KYVFSRTEWSMVRRMVGKPRRC------------SSSFFTEERINLERRR--NVIRYLQQGKCGDQTTVKDIPSEIPIQL 267 (583)
Q Consensus 202 trkLtR~EW~~IRr~mGKPRRf------------S~aFl~eER~kLe~~R--~~IR~lqq~~~~d~~~~~~LP~~IP~PL 267 (583)
...+|+-||..|.|.---|=|+ |.+|+.-|-++|-.+- ..|-.|.. ++.. =|.+
T Consensus 259 N~HiTaEEWevihr~d~dplrlpldfsaqggdgas~a~aaTeaQ~lf~~Dia~AiHkLfa----eldI---diad----- 326 (724)
T KOG4485|consen 259 NPHITAEEWEVIHRIDMDPLRLPLDFSAQGGDGASEAFAATEAQELFHSDIAHAIHKLFA----ELDI---DIAD----- 326 (724)
T ss_pred CCccCHHHHHHHHHhcCCcccCcccccccCCCccccchhhHHHHHHHHHHHHHHHHHHHH----hcCC---Cccc-----
Confidence 5789999999999987666665 5789998888876552 23333322 2200 0111
Q ss_pred cCCCEEEEEecCCCCcceeeEEEEEeCCCCeeEEEecCCC
Q psy9276 268 VVGTKVTARVRSPQDGLFTGVVDAYDTSNNTYRITFDRQG 307 (583)
Q Consensus 268 ~VG~kV~Arl~~~~~gL~~G~Vlavd~~~~~YrV~Fdr~~ 307 (583)
.|...||+.-|+..|+ +-++.+.--|.+
T Consensus 327 -----------a~~hRLYdaEiiehd~-disfilicP~ad 354 (724)
T KOG4485|consen 327 -----------APGHRLYDAEIIEHDD-DISFILICPRAD 354 (724)
T ss_pred -----------CCcceeeeeeeeccCC-CceEEEEecCcc
Confidence 1235688888887776 346666555554
No 39
>PLN03217 transcription factor ATBS1; Provisional
Probab=21.27 E-value=1.3e+02 Score=27.16 Aligned_cols=45 Identities=24% Similarity=0.361 Sum_probs=33.0
Q ss_pred CcccCcchHHHHHHHHHHHHHHHhh-cCcCCCchhhHHHHHHHHHHHHh
Q psy9276 490 NKIVDDQPVVSLITDLTALVLQIKT-LSHSSRSAYEVEVLNKTMSDIYK 537 (583)
Q Consensus 490 ~~v~~~~~~~~LI~~LttLLlq~~~-Lg~~~~na~e~~vL~d~l~eIk~ 537 (583)
..+.+++ +.+||..|++||=-++. -+.+. +---++|+++-+.||+
T Consensus 15 ~risddq-i~dLvsKLq~llPe~r~~r~s~k--~saskvLqEtC~YIrs 60 (93)
T PLN03217 15 SRISEDQ-INDLIIKLQQLLPELRDSRRSDK--VSAARVLQDTCNYIRN 60 (93)
T ss_pred CCCCHHH-HHHHHHHHHHHChHHHhhhcccc--ccHHHHHHHHHHHHHH
Confidence 3567777 99999999999999875 33322 2134688888888875
No 40
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=20.74 E-value=2.3e+02 Score=24.82 Aligned_cols=37 Identities=14% Similarity=0.199 Sum_probs=28.7
Q ss_pred CccccCCCEEEEEecCCCCcceeeEEEEEeCCCCeeEEEec
Q psy9276 264 PIQLVVGTKVTARVRSPQDGLFTGVVDAYDTSNNTYRITFD 304 (583)
Q Consensus 264 P~PL~VG~kV~Arl~~~~~gL~~G~Vlavd~~~~~YrV~Fd 304 (583)
-+++.+|++|..+- ++..| ..|+|+.|++.+ ++|.-+
T Consensus 6 ~~~I~~GD~V~Vi~-G~dKG-K~G~V~~V~~~~--~~V~Ve 42 (83)
T CHL00141 6 KMHVKIGDTVKIIS-GSDKG-KIGEVLKIIKKS--NKVIVK 42 (83)
T ss_pred eCcccCCCEEEEeE-cCCCC-cEEEEEEEEcCC--CEEEEc
Confidence 35889999999976 55566 569999999954 567766
No 41
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=20.49 E-value=2.2e+02 Score=23.69 Aligned_cols=33 Identities=33% Similarity=0.462 Sum_probs=25.5
Q ss_pred ccCCCEEEEEecCCCCcceeeEEEEE--eCCCCeeEEEecC
Q psy9276 267 LVVGTKVTARVRSPQDGLFTGVVDAY--DTSNNTYRITFDR 305 (583)
Q Consensus 267 L~VG~kV~Arl~~~~~gL~~G~Vlav--d~~~~~YrV~Fdr 305 (583)
|.+|+.|.. .|+--|+|.++ ++..+..+|.+.-
T Consensus 15 L~~gs~V~~------~Gv~VG~V~~i~l~~~~~~v~v~~~i 49 (81)
T PF02470_consen 15 LSVGSPVRY------RGVEVGKVTSIELDPDGNRVRVTLRI 49 (81)
T ss_pred CCCcCEEEE------CCEEEEEEEEEEEcCCCCEEEEEEEE
Confidence 568988887 69999999999 6666666666643
Done!