Query psy12771
Match_columns 160
No_of_seqs 130 out of 312
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 19:16:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12771.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12771hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3611|consensus 100.0 4.1E-30 8.9E-35 243.0 8.1 131 1-159 77-226 (737)
2 PF01403 Sema: Sema domain; I 99.6 1.3E-16 2.9E-21 140.4 4.0 112 33-159 34-175 (433)
3 smart00630 Sema semaphorin dom 99.4 3.4E-13 7.4E-18 119.5 7.6 86 48-159 57-147 (390)
4 PF05253 zf-U11-48K: U11-48K-l 61.9 3.5 7.7E-05 23.8 0.6 10 79-88 3-12 (27)
5 PF12304 BCLP: Beta-casein lik 22.8 37 0.0008 28.6 0.7 15 75-89 123-137 (188)
6 KOG4376|consensus 19.7 49 0.0011 27.2 0.8 14 78-91 14-27 (161)
7 KOG3768|consensus 15.4 1E+02 0.0022 30.9 1.9 23 75-97 111-133 (888)
8 PRK08298 cytidine deaminase; V 13.9 1.6E+02 0.0035 23.0 2.4 27 78-112 17-43 (136)
9 PF13915 DUF4210: Domain of un 12.6 1.8E+02 0.004 20.6 2.1 21 75-95 31-51 (66)
10 PRK05578 cytidine deaminase; V 11.3 2.2E+02 0.0047 22.0 2.4 30 78-113 16-45 (131)
No 1
>KOG3611|consensus
Probab=99.96 E-value=4.1e-30 Score=242.99 Aligned_cols=131 Identities=34% Similarity=0.520 Sum_probs=108.0
Q ss_pred CcccCCCCCCCc-cccccCCCCCccchhhcccccccchhhHHHHhhhcccccceEEeeecCcccccCCCc----------
Q psy12771 1 MYSFLGLPPLSF-ENQHNFPAVPPQLATFFGVKKVVEEEEEEEKKKERGFTKVFFWKILENNLTHLGRHE---------- 69 (160)
Q Consensus 1 ~~~~~~~~~~~~-~~~~~~p~~~~~~~~~~~~~~~i~~~~~~~kk~~~~~~~nfirvL~~~N~ThL~~~e---------- 69 (160)
||++. |.+++. .+.+.|+++.+.+ .+|.-+.|+ ..+|.||||+|+..|.+||+.|.
T Consensus 77 vf~l~-l~~~~~~~~~~~W~~~~~~~-----------~~C~~kgk~-~~eC~N~irvL~~~~~~~L~vCGT~Af~P~C~~ 143 (737)
T KOG3611|consen 77 VFRLS-LENISEVQAKLEWKSSESDR-----------EECRMKGKD-ETECRNYIRVLAPRNNGHLYVCGTNAFNPVCRN 143 (737)
T ss_pred EEEEe-cCccccccceeeccCChhhh-----------hhhcccCCC-hhHccceeEEEeecCCCeEEEeecccCCcchhh
Confidence 46666 777775 6667777777666 344333333 46789999999999999996221
Q ss_pred -------c-CCccCcccccCCCCCCCCCeeEEecCCCCCCCCccceeecccccCCCceEeecccccccCCCCccccceec
Q psy12771 70 -------H-VPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTI 141 (160)
Q Consensus 70 -------~-v~~~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~l~~~~~G~~~~~~LRTe 141 (160)
. +.+.++|+|+|||||++|+||+++++ +|||||++||+|+|++|||++ |++ +.|||+
T Consensus 144 ~~~~~~~~~~~~~~~g~g~CP~dP~~nstav~~~~-------~Lys~t~~dF~g~d~~I~Rs~------g~~--~~lrT~ 208 (737)
T KOG3611|consen 144 YNVTTLQESVQRLESGIGRCPYDPKHNSTAVFVDG-------ELYSGTVADFLGSDALIYRSL------GKN--PTLRTV 208 (737)
T ss_pred hccccccccCccccCCceeCCCCCCcCceEEEECC-------EEEEEecccccCCCceEEEec------CCC--CCceec
Confidence 1 35689999999999999999999998 899999999999999999987 765 679999
Q ss_pred cCccCCCCCCCeeEEEec
Q psy12771 142 KYDSKWLDSFKSLIAKII 159 (160)
Q Consensus 142 ~~dskWLneP~FV~S~~I 159 (160)
++|++|||||+||+|+.|
T Consensus 209 ~~dskwLneP~FV~a~~i 226 (737)
T KOG3611|consen 209 KYDSKWLNEPNFVGAFDI 226 (737)
T ss_pred cCCchhccCCcEEEeeee
Confidence 999999999999999987
No 2
>PF01403 Sema: Sema domain; InterPro: IPR001627 The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in a hepatocyte growth factor receptor, in SEX protein [] and in viral proteins. CD100 (also called SEMA4D) is associated with PTPase and serine kinase activity. CD100 increases PMA, CD3 and CD2 induced T cell proliferation, increases CD45 induced T cell adhesion, induces B cell homotypic adhesion and down-regulates B cell expression of CD23. The Sema domain is characterised by a conserved set of cysteine residues, which form four disulphide bonds to stabilise the structure. The Sema domain fold is a variation of the beta propeller topology, with seven blades radially arranged around a central axis. Each blade contains a four- stranded (strands A to D) antiparallel beta sheet. The inner strand of each blade (A) lines the channel at the centre of the propeller, with strands B and C of the same repeat radiating outward, and strand D of the next repeat forming the outer edge of the blade. The large size of the Sema domain is not due to a single inserted domain but results from the presence of additional secondary structure elements inserted in most of the blades. The Sema domain uses a 'loop and hook' system to close the circle between the first and the last blades. The blades are constructed sequentially with an N-terminal beta- strand closing the circle by providing the outermost strand (D) of the seventh (C-terminal) blade. The beta-propeller is further stabilised by an extension of the N terminus, providing an additional, fifth beta-strand on the outer edge of blade 6 [, , ]. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0005515 protein binding; PDB: 3NVX_A 3NVQ_A 3OL2_A 1OLZ_B 3OKT_A 3AL9_B 3OKY_A 3AL8_B 3NVN_A 3OKW_A ....
Probab=99.63 E-value=1.3e-16 Score=140.39 Aligned_cols=112 Identities=29% Similarity=0.364 Sum_probs=90.2
Q ss_pred cccchhhHHHHhhhc--------ccccceEEeeecCcccccCCC--------------cc--------CCccCcccccCC
Q psy12771 33 KVVEEEEEEEKKKER--------GFTKVFFWKILENNLTHLGRH--------------EH--------VPGIGSGIAKCP 82 (160)
Q Consensus 33 ~~i~~~~~~~kk~~~--------~~~~nfirvL~~~N~ThL~~~--------------e~--------v~~~esG~gkCP 82 (160)
..+.|..+.+.+++| ..|.|||++|+..|.+||..| .. .....+|.++||
T Consensus 34 ~~~~~~~~~~~~~~C~~~~~~~~~~c~N~i~vL~~~~~~~Li~CGT~~~~p~C~~~~l~~~~~l~~~~~~~~~~~~~~~~ 113 (433)
T PF01403_consen 34 QRTGWTSDCEDCEECQPKGKSNETECNNYIKVLLVYNDNRLIVCGTNAFQPICRLRNLSNISCLFSLSPDESPSGQGVCP 113 (433)
T ss_dssp EEEEEEEEHHHCHHHCSTTTTTTTTSSEBEEEEEEESSSEEEEEESTTTSCEEEEEETTTCEEEEEEEECCEEEGTTTS-
T ss_pred ccccCccccccccccCCCcccccccCcceeEEEEecCCCEEEEcCccccccCccEeccccccceeeeecccccCCeeecc
Confidence 345566555555554 468899999999999888522 11 134579999999
Q ss_pred CCCCCCCeeEEecCCCCCCCCccceeecccccCCCceEeecccccccCCCCccccceeccCccCCCCCCCeeEEEec
Q psy12771 83 YDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKII 159 (160)
Q Consensus 83 ydP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~l~~~~~G~~~~~~LRTe~~dskWLneP~FV~S~~I 159 (160)
|+|..+.+++++++ +||+|+..||.|.+++|+|.+ +.+ ..++|+.++++||++|+||+++.|
T Consensus 114 ~~p~~~~~~~~~~~-------~lyvgt~~~~~~~~~~i~R~~------~~~--~~l~~~~~~~~~~~~p~fv~~~~~ 175 (433)
T PF01403_consen 114 YDPNQSSVALVVNG-------ELYVGTTYDFSGSSPIISRSL------GSQ--PPLRTEQYDSKWLNEPSFVSSFEI 175 (433)
T ss_dssp SSTTSCEEEEEETT-------EEEEEEESSTTSSSEEEEEEE------TSS--STEESCCCCTTSSSSTEEEEEEEE
T ss_pred cccCCCcceecccc-------cEEEeeeccccCCCcceeecc------ccc--cccccccccccccccccccccccc
Confidence 99999999999965 899999999999999999987 443 689999999999999999999875
No 3
>smart00630 Sema semaphorin domain.
Probab=99.42 E-value=3.4e-13 Score=119.48 Aligned_cols=86 Identities=26% Similarity=0.230 Sum_probs=67.4
Q ss_pred ccccceEEeeecCcccccCCCccCCccCcccccCCCCCCCCCeeEEecCCCCCCCCccceeecccccCCCceEeeccccc
Q psy12771 48 GFTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLN 127 (160)
Q Consensus 48 ~~~~nfirvL~~~N~ThL~~~e~v~~~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~l~~ 127 (160)
..|.||||+|+.+|.+||+.|.. -.-.++|-+-.- + +||+||+.||.|++++|+|++
T Consensus 57 ~dc~N~irll~~~~~~~L~~CGT----~a~~p~C~~~~l---------~-------~ly~gt~~~~~~~~~~i~r~~--- 113 (390)
T smart00630 57 TDCVNYIRLLLDYNDDRLLVCGT----NAFQPVCRLINL---------G-------ELYVGTVADFSGSDPAIPRSL--- 113 (390)
T ss_pred ccCcceEEEEEEcCCCEEEEeCC----CCCCCceeEEec---------C-------ceEEEEecccCCCCcceeccc---
Confidence 46789999999999999998752 122455654322 1 599999999999999999997
Q ss_pred ccCCCCc-----cccceeccCccCCCCCCCeeEEEec
Q psy12771 128 FTTGKKE-----YTFKRTIKYDSKWLDSFKSLIAKII 159 (160)
Q Consensus 128 ~~~G~~~-----~~~LRTe~~dskWLneP~FV~S~~I 159 (160)
|.+. ...|||++++++|||+|+||+||.+
T Consensus 114 ---~~r~l~~~~~~~l~t~~~~~~~l~~~~FV~sf~~ 147 (390)
T smart00630 114 ---SVRRLKGTSGVSLRTVLYDSKWLNEPNFVYAFES 147 (390)
T ss_pred ---cccccccccCceeeccccCcccccCCcEEEEEEc
Confidence 3321 1379999999999999999999853
No 4
>PF05253 zf-U11-48K: U11-48K-like CHHC zinc finger; InterPro: IPR022776 This zinc binding domain [] has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function []. ; PDB: 2VY5_A 2VY4_A.
Probab=61.87 E-value=3.5 Score=23.85 Aligned_cols=10 Identities=40% Similarity=1.368 Sum_probs=6.3
Q ss_pred ccCCCCCCCC
Q psy12771 79 AKCPYDPNDN 88 (160)
Q Consensus 79 gkCPydP~~n 88 (160)
..|||||.+.
T Consensus 3 v~CPyn~~H~ 12 (27)
T PF05253_consen 3 VRCPYNPSHR 12 (27)
T ss_dssp EE-TTTSS-E
T ss_pred eeCCCCCCcC
Confidence 4699999764
No 5
>PF12304 BCLP: Beta-casein like protein; InterPro: IPR020977 This entry represents eukaryotic proteins that are typically between 216 to 240 amino acids in length which have two conserved sequence motifs: VLR and TRIY. Beta-casein-like protein is associated with cell morphology and a regulation of growth pattern of tumours. It is found in adenocarcinomas of uterine cervical tissues[].
Probab=22.80 E-value=37 Score=28.59 Aligned_cols=15 Identities=33% Similarity=0.660 Sum_probs=10.5
Q ss_pred CcccccCCCCCCCCC
Q psy12771 75 GSGIAKCPYDPNDNS 89 (160)
Q Consensus 75 esG~gkCPydP~~ns 89 (160)
......|||||..=+
T Consensus 123 ~~it~dCPFDpTRIY 137 (188)
T PF12304_consen 123 SSITNDCPFDPTRIY 137 (188)
T ss_pred cCCCCCCCCCcchHH
Confidence 345567999997544
No 6
>KOG4376|consensus
Probab=19.68 E-value=49 Score=27.18 Aligned_cols=14 Identities=29% Similarity=0.660 Sum_probs=10.8
Q ss_pred cccCCCCCCCCCee
Q psy12771 78 IAKCPYDPNDNSTA 91 (160)
Q Consensus 78 ~gkCPydP~~nsTa 91 (160)
-+.||||+.+....
T Consensus 14 ~~iCPYdk~HrI~l 27 (161)
T KOG4376|consen 14 SIICPYDKDHRISL 27 (161)
T ss_pred ceeCCCCCcceecH
Confidence 45799999987654
No 7
>KOG3768|consensus
Probab=15.37 E-value=1e+02 Score=30.88 Aligned_cols=23 Identities=17% Similarity=0.450 Sum_probs=18.3
Q ss_pred CcccccCCCCCCCCCeeEEecCC
Q psy12771 75 GSGIAKCPYDPNDNSTAIWVEKG 97 (160)
Q Consensus 75 esG~gkCPydP~~nsTal~vdgg 97 (160)
.-|+|||||.=.-...-+++|||
T Consensus 111 ~yGqGR~pf~lEP~~iI~iTDG~ 133 (888)
T KOG3768|consen 111 GYGQGRLPFNLEPVTIILITDGG 133 (888)
T ss_pred ccccccCccccCceEEEEEecCC
Confidence 46899999997666677778885
No 8
>PRK08298 cytidine deaminase; Validated
Probab=13.90 E-value=1.6e+02 Score=23.04 Aligned_cols=27 Identities=19% Similarity=0.134 Sum_probs=20.1
Q ss_pred cccCCCCCCCCCeeEEecCCCCCCCCccceeeccc
Q psy12771 78 IAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAE 112 (160)
Q Consensus 78 ~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~tD 112 (160)
...|||+ +=.+|++.+.| ++|+|...+
T Consensus 17 ~aY~PYS--~VgAAllt~dG------~i~tG~NvE 43 (136)
T PRK08298 17 QRYPNGW--GGAAAMRVEDG------TILTSVAPE 43 (136)
T ss_pred hccCCCC--ceeEEEEeCCC------CEEEEEeec
Confidence 4469999 56677777666 699998854
No 9
>PF13915 DUF4210: Domain of unknown function (DUF4210)
Probab=12.63 E-value=1.8e+02 Score=20.59 Aligned_cols=21 Identities=24% Similarity=0.292 Sum_probs=17.2
Q ss_pred CcccccCCCCCCCCCeeEEec
Q psy12771 75 GSGIAKCPYDPNDNSTAIWVE 95 (160)
Q Consensus 75 esG~gkCPydP~~nsTal~vd 95 (160)
.+|.++||-.=+.+.++++-+
T Consensus 31 vsG~~~cP~h~~lpf~a~fy~ 51 (66)
T PF13915_consen 31 VSGSGFCPPHVKLPFSAVFYS 51 (66)
T ss_pred ccccccCCCcEEeeeEEEEee
Confidence 478889999888888887766
No 10
>PRK05578 cytidine deaminase; Validated
Probab=11.29 E-value=2.2e+02 Score=22.02 Aligned_cols=30 Identities=30% Similarity=0.494 Sum_probs=23.4
Q ss_pred cccCCCCCCCCCeeEEecCCCCCCCCccceeecccc
Q psy12771 78 IAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEF 113 (160)
Q Consensus 78 ~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~tDF 113 (160)
+..|||+-.+-.+++..+.| .+|+|...+-
T Consensus 16 ~ay~PyS~f~Vgaa~~~~~G------~i~~G~nvEn 45 (131)
T PRK05578 16 KAYAPYSKFPVGAALLTDDG------RIYTGCNIEN 45 (131)
T ss_pred hcCCCcCCCceEEEEEeCCC------CEEEEEEeeC
Confidence 34689998877788888776 6999988774
Done!