Query psy12684
Match_columns 163
No_of_seqs 109 out of 963
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 16:58:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12684.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12684hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03028 Dynein_heavy: Dynein 99.9 1.2E-26 2.6E-31 214.6 12.3 122 6-161 301-425 (707)
2 COG5245 DYN1 Dynein, heavy cha 97.7 4E-05 8.7E-10 76.8 4.6 100 11-149 3054-3162(3164)
3 PF06115 DUF956: Domain of unk 73.9 0.61 1.3E-05 34.9 -1.3 19 17-35 47-65 (118)
4 KOG0936|consensus 38.3 22 0.00048 28.0 1.8 31 18-48 111-141 (182)
5 PF06200 tify: tify domain; I 32.5 15 0.00032 21.8 0.0 9 29-37 9-17 (36)
6 PF05491 RuvB_C: Holliday junc 22.0 53 0.0011 22.7 1.2 17 38-54 7-23 (76)
7 PF13559 DUF4129: Domain of un 18.5 1.3E+02 0.0029 18.9 2.6 32 19-50 39-70 (72)
8 PF13404 HTH_AsnC-type: AsnC-t 17.0 1.2E+02 0.0027 18.0 2.0 14 38-51 2-15 (42)
9 cd08340 DED_c-FLIP_repeat2 Dea 15.8 2.3E+02 0.0049 19.4 3.3 39 2-40 1-39 (81)
10 cd01790 Herp_N Homocysteine-re 14.6 86 0.0019 21.6 0.9 21 29-51 47-67 (79)
No 1
>PF03028 Dynein_heavy: Dynein heavy chain and region D6 of dynein motor; InterPro: IPR004273 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits, intermediate size subunits and small subunits (see IPR001372 from INTERPRO). This family represents the C-terminal region of dynein heavy chain. The dynein heavy chain also exhibits ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. ; GO: 0003777 microtubule motor activity, 0007018 microtubule-based movement, 0030286 dynein complex; PDB: 3VKG_A 3VKH_C 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A.
Probab=99.94 E-value=1.2e-26 Score=214.61 Aligned_cols=122 Identities=39% Similarity=0.713 Sum_probs=100.9
Q ss_pred HHHHHHHhcc--CCCchhHHHHhhhcccccccccCHhHHHHHHHHHHHhcCccccccccccCCCCCCCcccchhhhhhhh
Q psy12684 6 STYLTYLNQL--TDVQFEALRYLTGECNYGGRVTDDWDRRTLNTILYKFFCPAALEDENYLFDPSVTDDWDRRTLNTILY 83 (163)
Q Consensus 6 ~~l~~~l~~~--~~ipw~~L~ylig~i~YGGrVtD~~Drr~L~t~l~~~f~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 83 (163)
.+|.+|+++. +++||++|+|++|+|+|||||||+||+|+|.+|+++||++++++.++.+
T Consensus 301 ~~l~~~~~~~~~~~ipw~~l~~l~~~i~YGGrv~d~~D~r~l~~~~~~~f~~~~~~~~~~l------------------- 361 (707)
T PF03028_consen 301 DILDNWLDESSPESIPWDALRYLIGEIVYGGRVDDEWDRRLLNTLLNQFFNPEIFDPDFQL------------------- 361 (707)
T ss_dssp HHHHHHHHHCSCCCTTHHHHHHHHHHTTTTTT-SSHHHHHHHHHHHHHHSSGGGGSTT-EE-------------------
T ss_pred HHHHHHHhhccccCCcHHHHHHHhhhceecCeeccHHHHHHHHHHHHHHcCchhhcchhhc-------------------
Confidence 5677888887 8999999999999999999999999999999999999998777664433
Q ss_pred hccccccccCCCcccCC-CCceeCCCCCCHHHHHHHHhcCCCCCCCccccCChHHHHHHHHHHHHHHHHHHhhcccCcc
Q psy12684 84 KFFCPAALEDENYLFDP-SGFYYTPNEPDYDGYLNYIKNLPLVASPIIFGMNENADILKDQQETNLVLGNVLLTQERTV 161 (163)
Q Consensus 84 ~~~~~~~~~~~~~~~~~-~~~~~~P~~~~~~~~~~~I~~lP~~d~P~~fGL~~NA~~~~~~~~a~~il~~ll~lqp~~~ 161 (163)
.+ +..+.+|...++++|.+||+++|..++|+|||||+||++.++++++++++++++.+||+..
T Consensus 362 ---------------~~~~~~~~~P~~~~~~~~~~~i~~lp~~~~p~~~GL~~na~~~~~~~~s~~ll~~l~~l~~~~~ 425 (707)
T PF03028_consen 362 ---------------SPDSGSYSIPDSNSLEDYIEWIEQLPDEDPPEWFGLPPNAEISLQQQESRELLSSLLSLQPRES 425 (707)
T ss_dssp ---------------ET-TTTEE----SSHHHHHHHHCTS-SS--CCCCTS-TTHHHHHHHHHHHHHHHHHHHCCCTTT
T ss_pred ---------------ccCCCCccCCccccHHHHHHHHHhCCCCCCccccCCCccHHHHHHHHHHHHHHhhhhhcccccc
Confidence 22 2458899999999999999999999999999999999999999999999999999999863
No 2
>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]
Probab=97.69 E-value=4e-05 Score=76.84 Aligned_cols=100 Identities=15% Similarity=0.058 Sum_probs=74.6
Q ss_pred HHhccCCCchhHHHHhhhcccccccccCHhHHHHHHHHHHHhcCccccccccccCCCCCCCcccchhhhhhhhhcccccc
Q psy12684 11 YLNQLTDVQFEALRYLTGECNYGGRVTDDWDRRTLNTILYKFFCPAALEDENYLFDPSVTDDWDRRTLNTILYKFFCPAA 90 (163)
Q Consensus 11 ~l~~~~~ipw~~L~ylig~i~YGGrVtD~~Drr~L~t~l~~~f~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (163)
|++..+.+||...|-+|..|+|||||+-..|..++..||+++++-+ .
T Consensus 3054 ~~nhln~~~wg~~rDlI~tIvyG~K~s~~~D~~vvdK~c~~~~a~~------------~--------------------- 3100 (3164)
T COG5245 3054 FLNHLNARKWGNNRDLIFTIVYGKKHSLMEDSKVVDKYCRGYGAHE------------T--------------------- 3100 (3164)
T ss_pred hccccccccccchhhheeEeeecCccchhhhHHHHHHHHHHhccCc------------c---------------------
Confidence 3444489999999999999999999999999999999999999832 0
Q ss_pred ccCCCcccCCCCceeCCCC--C-------CHHHHHHHHhcCCCCCCCccccCChHHHHHHHHHHHHHH
Q psy12684 91 LEDENYLFDPSGFYYTPNE--P-------DYDGYLNYIKNLPLVASPIIFGMNENADILKDQQETNLV 149 (163)
Q Consensus 91 ~~~~~~~~~~~~~~~~P~~--~-------~~~~~~~~I~~lP~~d~P~~fGL~~NA~~~~~~~~a~~i 149 (163)
+-++.++ .+.|+. . ....-...|..+|+..+|.|+-+|.|.+..+..-++.++
T Consensus 3101 ----~sQi~~~--V~~~dp~l~~~~~ee~~rsSa~~vigqlpd~~l~~wl~~p~~s~~~~~~vy~s~i 3162 (3164)
T COG5245 3101 ----SSQILAS--VPGGDPELVKFHMEEMCRSSAFGVIGQLPDLALCAWLMGPCDSEYLKAIVYSSRI 3162 (3164)
T ss_pred ----cchhccC--CcCCChHHHHhhHHHHHHHhhhhhcccCcccccchhhcCchhHHHHHHHHHHHhh
Confidence 1123332 333331 1 111222344569999999999999999999999888765
No 3
>PF06115 DUF956: Domain of unknown function (DUF956); InterPro: IPR010360 This is a family of bacterial sequences with undetermined function.
Probab=73.85 E-value=0.61 Score=34.91 Aligned_cols=19 Identities=16% Similarity=0.656 Sum_probs=18.1
Q ss_pred CCchhHHHHhhhccccccc
Q psy12684 17 DVQFEALRYLTGECNYGGR 35 (163)
Q Consensus 17 ~ipw~~L~ylig~i~YGGr 35 (163)
+|||+.+.+..+.+.++||
T Consensus 47 QIPW~eI~~V~a~V~fkgk 65 (118)
T PF06115_consen 47 QIPWEEIDYVIASVSFKGK 65 (118)
T ss_pred EeChhheeEEEEEEEECCC
Confidence 6999999999999999988
No 4
>KOG0936|consensus
Probab=38.29 E-value=22 Score=28.02 Aligned_cols=31 Identities=13% Similarity=0.249 Sum_probs=26.4
Q ss_pred CchhHHHHhhhcccccccccCHhHHHHHHHH
Q psy12684 18 VQFEALRYLTGECNYGGRVTDDWDRRTLNTI 48 (163)
Q Consensus 18 ipw~~L~ylig~i~YGGrVtD~~Drr~L~t~ 48 (163)
+.|+.+++++.||+.||-|-...=-++..++
T Consensus 111 F~~~k~h~iL~EiV~GGmVlETn~neIv~av 141 (182)
T KOG0936|consen 111 FNWQKVHAILAEIVMGGMVLETNMNEIVAAV 141 (182)
T ss_pred eeHHHHHHHHHHHHhCCeEEeccHHHHHHHH
Confidence 6799999999999999999877766666654
No 5
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=32.50 E-value=15 Score=21.79 Aligned_cols=9 Identities=44% Similarity=0.782 Sum_probs=6.7
Q ss_pred ccccccccc
Q psy12684 29 ECNYGGRVT 37 (163)
Q Consensus 29 ~i~YGGrVt 37 (163)
.|-|||+|-
T Consensus 9 TIfY~G~V~ 17 (36)
T PF06200_consen 9 TIFYGGQVC 17 (36)
T ss_pred EEEECCEEE
Confidence 578999863
No 6
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=21.96 E-value=53 Score=22.71 Aligned_cols=17 Identities=41% Similarity=0.620 Sum_probs=14.1
Q ss_pred CHhHHHHHHHHHHHhcC
Q psy12684 38 DDWDRRTLNTILYKFFC 54 (163)
Q Consensus 38 D~~Drr~L~t~l~~~f~ 54 (163)
|..||++|.++.+.|=.
T Consensus 7 d~~D~~yL~~l~~~f~g 23 (76)
T PF05491_consen 7 DELDRRYLKTLIENFKG 23 (76)
T ss_dssp BHHHHHHHHHHHHCSTT
T ss_pred CHHHHHHHHHHHHHcCC
Confidence 78899999999886553
No 7
>PF13559 DUF4129: Domain of unknown function (DUF4129)
Probab=18.51 E-value=1.3e+02 Score=18.88 Aligned_cols=32 Identities=25% Similarity=0.324 Sum_probs=22.3
Q ss_pred chhHHHHhhhcccccccccCHhHHHHHHHHHH
Q psy12684 19 QFEALRYLTGECNYGGRVTDDWDRRTLNTILY 50 (163)
Q Consensus 19 pw~~L~ylig~i~YGGrVtD~~Drr~L~t~l~ 50 (163)
++..|.-+...+.|||+--+.-|.+-+...++
T Consensus 39 ~~~~lt~~ye~~~Yg~~~~~~~~~~~~~~~~~ 70 (72)
T PF13559_consen 39 ALEELTRLYERARYGGRPPSAEEFQRAREALR 70 (72)
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHh
Confidence 46677777888899999766666655555443
No 8
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=16.96 E-value=1.2e+02 Score=18.03 Aligned_cols=14 Identities=29% Similarity=0.482 Sum_probs=10.5
Q ss_pred CHhHHHHHHHHHHH
Q psy12684 38 DDWDRRTLNTILYK 51 (163)
Q Consensus 38 D~~Drr~L~t~l~~ 51 (163)
|+.|+++|..+-..
T Consensus 2 D~~D~~Il~~Lq~d 15 (42)
T PF13404_consen 2 DELDRKILRLLQED 15 (42)
T ss_dssp -HHHHHHHHHHHH-
T ss_pred CHHHHHHHHHHHHc
Confidence 78999999988664
No 9
>cd08340 DED_c-FLIP_repeat2 Death Effector Domain, repeat 2, of cellular FLICE-Inhibitory Protein. Death Effector Domain (DED), repeat 2, similar to that found in cellular FLICE-inhibitory protein (c-FLIP/CASH, also known as Casper/iFLICE/FLAME-1/CLARP/MRIT/usurpin). c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of the Death Inducing Signalling Complex (DISC). At low levels, c-FLIP has been shown to enhance apoptotic signaling by allosterically activating caspase-8. As a modulator of the initiator caspases, c-FLIP regulates life and death in various types of cells and tissues. All members contain two N-terminal DEDs and a C-terminal pseudo-caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-as
Probab=15.79 E-value=2.3e+02 Score=19.43 Aligned_cols=39 Identities=21% Similarity=0.263 Sum_probs=29.2
Q ss_pred chHHHHHHHHHhccCCCchhHHHHhhhcccccccccCHh
Q psy12684 2 SGYRSTYLTYLNQLTDVQFEALRYLTGECNYGGRVTDDW 40 (163)
Q Consensus 2 ~~~~~~l~~~l~~~~~ipw~~L~ylig~i~YGGrVtD~~ 40 (163)
|.||..|...=++..+-.-++++|+....+==++..+..
T Consensus 1 s~yr~lL~~Ise~L~~~dl~~lkFL~~d~i~~~kle~~~ 39 (81)
T cd08340 1 SDYRVLMVEVGEELDKSDLRSLIFLLKDLMPSGSKAKDK 39 (81)
T ss_pred CcHHHHHHHHHHHcCHHHHHHHHHHhhcccccccccccC
Confidence 789999988777777778899999998766444444443
No 10
>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein. Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.
Probab=14.61 E-value=86 Score=21.60 Aligned_cols=21 Identities=29% Similarity=0.468 Sum_probs=16.1
Q ss_pred cccccccccCHhHHHHHHHHHHH
Q psy12684 29 ECNYGGRVTDDWDRRTLNTILYK 51 (163)
Q Consensus 29 ~i~YGGrVtD~~Drr~L~t~l~~ 51 (163)
..||.|||-. |-..|..+++.
T Consensus 47 rLIy~GKiLk--D~~tL~~~~~~ 67 (79)
T cd01790 47 RLIYSGKLLP--DHLKLRDVLRK 67 (79)
T ss_pred EEEEcCeecc--chhhHHHHhhc
Confidence 4689999996 55778777654
Done!