Query 043203
Match_columns 613
No_of_seqs 211 out of 528
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 02:32:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043203.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043203hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10440 WIYLD: Ubiquitin-bind 99.9 3.4E-26 7.3E-31 188.8 5.8 59 2-60 7-65 (65)
2 PF05033 Pre-SET: Pre-SET moti 99.9 4.1E-23 8.8E-28 179.6 7.4 102 450-598 1-103 (103)
3 smart00468 PreSET N-terminal t 99.8 1.3E-21 2.9E-26 170.0 6.8 80 448-532 1-81 (98)
4 KOG1082 Histone H3 (Lys9) meth 99.8 4.1E-19 8.9E-24 186.6 8.3 128 441-613 54-183 (364)
5 KOG1141 Predicted histone meth 99.7 3.3E-18 7.2E-23 191.0 0.9 137 440-613 666-806 (1262)
6 KOG1141 Predicted histone meth 98.4 2.6E-07 5.6E-12 105.4 5.8 127 448-611 877-1010(1262)
7 smart00466 SRA SET and RING fi 91.8 0.05 1.1E-06 52.7 0.0 24 412-436 132-155 (155)
8 smart00570 AWS associated with 85.9 0.28 6E-06 39.8 0.4 26 578-603 24-49 (51)
9 PF07499 RuvA_C: RuvA, C-termi 84.8 1.4 3E-05 34.5 3.8 27 6-32 3-29 (47)
10 PF02182 SAD_SRA: SAD/SRA doma 83.5 0.31 6.8E-06 47.0 -0.3 25 411-436 131-155 (155)
11 KOG3813 Uncharacterized conser 60.9 4.3 9.3E-05 46.3 1.5 20 498-520 307-326 (640)
12 KOG4442 Clathrin coat binding 54.9 6.2 0.00013 46.4 1.5 34 580-613 92-127 (729)
13 smart00165 UBA Ubiquitin assoc 54.7 16 0.00034 26.5 3.1 23 7-29 2-24 (37)
14 cd00194 UBA Ubiquitin Associat 51.7 19 0.00041 26.2 3.1 22 7-28 2-23 (38)
15 PF00627 UBA: UBA/TS-N domain; 39.3 36 0.00078 25.0 3.0 21 8-28 4-24 (37)
16 PF14490 HHH_4: Helix-hairpin- 37.0 16 0.00035 32.1 1.0 44 3-50 5-49 (94)
17 PF09288 UBA_3: Fungal ubiquit 29.0 47 0.001 27.7 2.3 23 8-30 11-33 (55)
18 KOG0164 Myosin class I heavy c 26.7 70 0.0015 38.6 4.0 40 6-45 246-286 (1001)
19 KOG0162 Myosin class I heavy c 25.6 56 0.0012 39.5 3.0 49 4-52 252-301 (1106)
20 PF02637 GatB_Yqey: GatB domai 21.1 2.3E+02 0.0051 26.6 5.8 56 4-60 43-108 (148)
No 1
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=99.92 E-value=3.4e-26 Score=188.76 Aligned_cols=59 Identities=46% Similarity=0.753 Sum_probs=57.1
Q ss_pred ChHHHHHHHHHHHhcCCChhhHHHHHHHHHHHhccCccccccchhHHHHHhhhhhcccc
Q 043203 2 DRERAVRAANAMKAIGIVDKQVQTVLVNLLELFNWNWEYIEAEDYRALKDTYFDFKENQ 60 (613)
Q Consensus 2 ~~~r~~~A~~am~~lG~~~~~v~~vlk~Ll~~y~~nW~~iEe~~Yr~l~dai~d~~e~~ 60 (613)
.++||+||+|||++|||++++|+|||++||++||+||+||||+|||+|+|||||.|+++
T Consensus 7 ~~~R~daA~dam~~lG~~~~~v~~vl~~LL~lY~~nW~lIEed~Y~~L~dai~e~~e~q 65 (65)
T PF10440_consen 7 GNERIDAALDAMRQLGFSKKQVRPVLKNLLKLYDGNWELIEEDNYRVLADAIFEEQEEQ 65 (65)
T ss_pred CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCchhhhcccHHHHHHHHHHHhhcC
Confidence 37999999999999999999999999999999999999999999999999999999875
No 2
>PF05033 Pre-SET: Pre-SET motif; InterPro: IPR007728 This region is found in a number of histone lysine methyltransferases (HMTase), N-terminal to the SET domain; it is generally described as the pre-SET domain. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils and stabilising the SET domain. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site [] when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity []. ; GO: 0008270 zinc ion binding, 0018024 histone-lysine N-methyltransferase activity, 0034968 histone lysine methylation, 0005634 nucleus; PDB: 3K5K_A 2O8J_D 3RJW_B 1ML9_A 1PEG_B 1MVH_A 1MVX_A 3BO5_A 2RFI_B 3MO5_B ....
Probab=99.88 E-value=4.1e-23 Score=179.65 Aligned_cols=102 Identities=41% Similarity=0.797 Sum_probs=70.9
Q ss_pred cccCCCCCCceEEEeCCCCCCC-CCceEeeccccCCCcccccccccccCCCCCcCCCCCCCCCCCCcccccccCCccccC
Q 043203 450 DIAKGLENVRIPLVDETCNEDL-PKFTYIPQNVIYQSAYVHISLARISDEDCCSNCSGDCLSLSIPCACTRETGGEFAYT 528 (613)
Q Consensus 450 DISkG~E~vPIpvVNeVDde~P-P~F~YI~~ni~~q~a~vnisla~i~~~~gC~dC~g~Cls~s~~CaC~~~ngg~faYt 528 (613)
|||+|+|++||+++|+||++.| +.|+||+++++.+++. ++. ..+..+| +|.++|... ..|+|++++++.++|+
T Consensus 1 Dis~g~e~~pI~~~N~vd~~~~p~~F~Yi~~~~~~~~~~-~~~---~~~~~~C-~C~~~C~~~-~~C~C~~~~~~~~~Y~ 74 (103)
T PF05033_consen 1 DISRGKENVPIPVVNDVDDEPPPPNFEYIPENIYGEGVP-DID---PEFLQGC-DCSGDCSNP-SNCECLQRNGGIFAYD 74 (103)
T ss_dssp -TTCTSSSS-EEEEESSSS--SSTSSEE-SS-EESTTSS--TB---GGGTS-----SSSSTCT-TTSHHHCCTSSS-SB-
T ss_pred CCCCCccCCCEEEEeCCCCCCCCCCeEEeeeEEcCCCcc-ccc---cccCccC-ccCCCCCCC-CCCcCccccCcccccc
Confidence 8999999999999999999985 7999999999888765 322 3456799 999999544 4899999999899999
Q ss_pred CCCcchHHHHHhhhhccCCCCccccccccCCCccccCCCCCCccccCCccccceeecCCCCCCCCCCCCc
Q 043203 529 QQGLLKEEFLSACMSMKKGPCEEHLVYCQDCPIERSNNEYCPEKCKGHIVRKFIKECWRKCGCSMQCQNR 598 (613)
Q Consensus 529 ~~GlL~~~fl~~ciS~~r~P~~~~~~yc~~cpler~kn~~~~epckGhL~r~~IyECn~~CgC~~~C~NR 598 (613)
.+|+|... ...+|||||+.|+|+++|+||
T Consensus 75 ~~g~l~~~-----------------------------------------~~~~i~EC~~~C~C~~~C~NR 103 (103)
T PF05033_consen 75 SNGRLRIP-----------------------------------------DKPPIFECNDNCGCSPSCRNR 103 (103)
T ss_dssp TTSSBSSS-----------------------------------------STSEEE---TTSSS-TTSTT-
T ss_pred CCCcCccC-----------------------------------------CCCeEEeCCCCCCCCCCCCCC
Confidence 99999620 247999999999999999998
No 3
>smart00468 PreSET N-terminal to some SET domains. A Cys-rich putative Zn2+-binding domain that occurs N-terminal to some SET domains. Function is unknown. Unpublished.
Probab=99.85 E-value=1.3e-21 Score=170.04 Aligned_cols=80 Identities=41% Similarity=0.734 Sum_probs=66.8
Q ss_pred eccccCCCCCCceEEEeCCCCCCC-CCceEeeccccCCCcccccccccccCCCCCcCCCCCCCCCCCCcccccccCCccc
Q 043203 448 ITDIAKGLENVRIPLVDETCNEDL-PKFTYIPQNVIYQSAYVHISLARISDEDCCSNCSGDCLSLSIPCACTRETGGEFA 526 (613)
Q Consensus 448 ~~DISkG~E~vPIpvVNeVDde~P-P~F~YI~~ni~~q~a~vnisla~i~~~~gC~dC~g~Cls~s~~CaC~~~ngg~fa 526 (613)
..|||+|+|++||++||+||++.| +.|+||++++.++++.+. ....+..|| +|.++|.+.. .|.|++++++.|+
T Consensus 1 ~~Dis~G~E~~pI~~vN~vD~~~~p~~F~Yi~~~~~~~gv~~~---~~~~~~~gC-~C~~~C~~~~-~C~C~~~~~~~~~ 75 (98)
T smart00468 1 CLDISNGKENVPVPLVNEVDEDPPPPDFEYISEYIYGQGVPID---RSPSPLVGC-SCSGDCSSSN-KCECARKNGGEFA 75 (98)
T ss_pred CccccCCccCCCcceEecCCCCCCCCCcEECcceEcCCCcccc---cCCCCCCCC-cCCCCCCCCC-cCCcHhhcCCccC
Confidence 369999999999999999999885 699999999988775432 235677899 9999999973 5999999999999
Q ss_pred cCCCCc
Q 043203 527 YTQQGL 532 (613)
Q Consensus 527 Yt~~Gl 532 (613)
|+..+.
T Consensus 76 Y~~~~~ 81 (98)
T smart00468 76 YELNGG 81 (98)
T ss_pred cccCCC
Confidence 953333
No 4
>KOG1082 consensus Histone H3 (Lys9) methyltransferase SUV39H1/Clr4, required for transcriptional silencing [Chromatin structure and dynamics; Transcription]
Probab=99.77 E-value=4.1e-19 Score=186.61 Aligned_cols=128 Identities=31% Similarity=0.575 Sum_probs=102.4
Q ss_pred cccccee-eccccCCCCCCceEEEeCCCCCCCCCceEeeccccCCCcccccccccccCCCCCcCCCCCCCCCCC-Ccccc
Q 043203 441 NEKRSIR-ITDIAKGLENVRIPLVDETCNEDLPKFTYIPQNVIYQSAYVHISLARISDEDCCSNCSGDCLSLSI-PCACT 518 (613)
Q Consensus 441 ~~~r~~~-~~DISkG~E~vPIpvVNeVDde~PP~F~YI~~ni~~q~a~vnisla~i~~~~gC~dC~g~Cls~s~-~CaC~ 518 (613)
..++... ..||+.|.|++||+++|+||+..+..|.|++..++.++ .. . ......+| .|.+.|..... .|.|.
T Consensus 54 ~~~~~~~~~~d~~~~~e~~~v~~~n~id~~~~~~f~y~~~~~~~~~-~~--~--~~~~~~~c-~C~~~~~~~~~~~C~C~ 127 (364)
T KOG1082|consen 54 DKLEAKSELEDIALGSENLPVPLVNRIDEDAPLYFQYIATEIVDPG-EL--S--DCENSTGC-RCCSSCSSVLPLTCLCE 127 (364)
T ss_pred cccccccccccccCccccCceeeeeeccCCccccceeccccccCcc-cc--c--cCccccCC-CccCCCCCCCCccccCh
Confidence 3344444 99999999999999999999887899999999988775 11 1 22334678 78877766422 29999
Q ss_pred cccCCccccCCCCcchHHHHHhhhhccCCCCccccccccCCCccccCCCCCCccccCCccccceeecCCCCCCCCCCCCc
Q 043203 519 RETGGEFAYTQQGLLKEEFLSACMSMKKGPCEEHLVYCQDCPIERSNNEYCPEKCKGHIVRKFIKECWRKCGCSMQCQNR 598 (613)
Q Consensus 519 ~~ngg~faYt~~GlL~~~fl~~ciS~~r~P~~~~~~yc~~cpler~kn~~~~epckGhL~r~~IyECn~~CgC~~~C~NR 598 (613)
+.+++.++|+.+|.... +|..+..|||||..|+|+.+|.||
T Consensus 128 ~~n~~~~~~~~~~~~~~---------------------------------------~~~~~~~i~EC~~~C~C~~~C~nR 168 (364)
T KOG1082|consen 128 RHNGGLVAYTCDGDCGT---------------------------------------LGKFKEPVFECSVACGCHPDCANR 168 (364)
T ss_pred HhhCCccccccCCcccc---------------------------------------ccccCccccccccCCCCCCcCcch
Confidence 99999999987775421 122467899999999999999999
Q ss_pred eeeeCCeeeEEEeeC
Q 043203 599 IVQQGITCKLQVRMT 613 (613)
Q Consensus 599 VVQrGIk~~LEVFkT 613 (613)
|||+|++.+||||+|
T Consensus 169 v~q~g~~~~leIfrt 183 (364)
T KOG1082|consen 169 VVQKGLQFHLEVFRT 183 (364)
T ss_pred hhccccccceEEEec
Confidence 999999999999998
No 5
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=99.69 E-value=3.3e-18 Score=191.02 Aligned_cols=137 Identities=26% Similarity=0.381 Sum_probs=108.0
Q ss_pred ccccccee-eccccCCCCCCceEEEeCCCCCCCCCceEeeccccCCCcccccccccccCCCCCcCCCCCCCCCCCCcccc
Q 043203 440 CNEKRSIR-ITDIAKGLENVRIPLVDETCNEDLPKFTYIPQNVIYQSAYVHISLARISDEDCCSNCSGDCLSLSIPCACT 518 (613)
Q Consensus 440 ~~~~r~~~-~~DISkG~E~vPIpvVNeVDde~PP~F~YI~~ni~~q~a~vnisla~i~~~~gC~dC~g~Cls~s~~CaC~ 518 (613)
+...+++. +.||+.|.|.+||.++|++|+.+||.|.|-.+.+..-+.-.| .+..+.++| +|..+|.+. ++|+|.
T Consensus 666 ~~p~kp~~~~~Di~~g~e~vpis~~neids~~lpq~ay~K~~ip~~~nl~n---~~~~fl~sc-dc~~gcid~-~kcach 740 (1262)
T KOG1141|consen 666 PNPLKPGNRCTDIPCGREHVPISEKNEIDSHRLPQAAYKKHMIPTNNNLSN---RRKDFLQSC-DCPTGCIDS-MKCACH 740 (1262)
T ss_pred CCCcCCcceeccccCCccccccceeecccCcCCccchhheeeccCCCcccc---cChhhhhcC-CCCcchhhh-hhhhHH
Confidence 33457777 999999999999999999999999999999998655443233 345678999 999999997 599999
Q ss_pred cccCCccccCCCCcchHHHHHhhhhccCCCCccccccccCCCccccCCCCCCccccC--CccccceeecCCCCCCCCC-C
Q 043203 519 RETGGEFAYTQQGLLKEEFLSACMSMKKGPCEEHLVYCQDCPIERSNNEYCPEKCKG--HIVRKFIKECWRKCGCSMQ-C 595 (613)
Q Consensus 519 ~~ngg~faYt~~GlL~~~fl~~ciS~~r~P~~~~~~yc~~cpler~kn~~~~epckG--hL~r~~IyECn~~CgC~~~-C 595 (613)
|++...-+-++.|-+.. ...| .+|. ...++.||||+..|+|.++ |
T Consensus 741 Qltvk~~~t~p~~~v~~--------------t~gy------------------kyKRl~e~~ptg~yEc~k~ckc~~~~C 788 (1262)
T KOG1141|consen 741 QLTVKKKTTGPNQNVAS--------------TNGY------------------KYKRLIEIRPTGPYECLKACKCCGPDC 788 (1262)
T ss_pred HHHHHhhccCCCccccc--------------Ccch------------------hhHHHHHhcCCCHHHHHHhhccCcHHH
Confidence 99866555555555543 1111 1121 1246889999999999987 9
Q ss_pred CCceeeeCCeeeEEEeeC
Q 043203 596 QNRIVQQGITCKLQVRMT 613 (613)
Q Consensus 596 ~NRVVQrGIk~~LEVFkT 613 (613)
.||+||+|.+++||+|+|
T Consensus 789 ~nrmvqhg~qvRlq~fkt 806 (1262)
T KOG1141|consen 789 LNRMVQHGYQVRLQRFKT 806 (1262)
T ss_pred HHHHhhcCceeEeeeccc
Confidence 999999999999999998
No 6
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=98.42 E-value=2.6e-07 Score=105.40 Aligned_cols=127 Identities=26% Similarity=0.427 Sum_probs=91.2
Q ss_pred eccccCCCCCCceEEEeCCCCCCCCCceEeeccccCCCcccccccccccCCCCCcCCCCCCCCCCCCcccccccCC---c
Q 043203 448 ITDIAKGLENVRIPLVDETCNEDLPKFTYIPQNVIYQSAYVHISLARISDEDCCSNCSGDCLSLSIPCACTRETGG---E 524 (613)
Q Consensus 448 ~~DISkG~E~vPIpvVNeVDde~PP~F~YI~~ni~~q~a~vnisla~i~~~~gC~dC~g~Cls~s~~CaC~~~ngg---~ 524 (613)
++|.+.|.+.+|||+||.+|+..||.-.|....+.+ .+.+.++.-.-++..+| +|-+.|.+.+ +|.|.+...- .
T Consensus 877 ~~d~~~g~sg~~~p~~~~~d~~~~~~c~d~~~~~~~-~~~~~~s~~~~~~~~~~-s~d~hp~d~~-~~~~~~~~~~~~~~ 953 (1262)
T KOG1141|consen 877 VADFSLGTSGIPIPLVNSVDNDEPPSCEDSKRRFQY-NDQVDISSVSRDFCSGC-SCDGHPSDAS-KCECQQLSIEAMKR 953 (1262)
T ss_pred hhhhhccccCCCCccccccccCCCccccccceeecc-cccchhhhhcccccccc-ccCCCCcccC-cccCCCCChhhhcC
Confidence 899999999999999999999999988888777544 23445554455778899 8999999986 9999987521 1
Q ss_pred cc--cCCCC--cchHHHHHhhhhccCCCCccccccccCCCccccCCCCCCccccCCccccceeecCCCCCCCCCCCCcee
Q 043203 525 FA--YTQQG--LLKEEFLSACMSMKKGPCEEHLVYCQDCPIERSNNEYCPEKCKGHIVRKFIKECWRKCGCSMQCQNRIV 600 (613)
Q Consensus 525 fa--Yt~~G--lL~~~fl~~ciS~~r~P~~~~~~yc~~cpler~kn~~~~epckGhL~r~~IyECn~~CgC~~~C~NRVV 600 (613)
++ ...+| .+.+ ..+.|--. .+-+.|||+..|.|...|+||||
T Consensus 954 cpp~~s~d~~~~~~e---------------------------------S~~~~ns~-~~~~f~e~~~hss~~~~e~~~~v 999 (1262)
T KOG1141|consen 954 CPPNLSFDGHDELYE---------------------------------SSEKQNSF-LKLFFFECNDHSSCHRKEYNRVV 999 (1262)
T ss_pred CCCccccCchhhhhh---------------------------------hhhhcchh-hhccceeccccchhcccccchhh
Confidence 11 11111 1111 00111111 24688999999999999999999
Q ss_pred eeCCeeeEEEe
Q 043203 601 QQGITCKLQVR 611 (613)
Q Consensus 601 QrGIk~~LEVF 611 (613)
|.|++++.+|-
T Consensus 1000 ~~~~~~~me~~ 1010 (1262)
T KOG1141|consen 1000 QNNIKYPMEVS 1010 (1262)
T ss_pred hcCCccceeee
Confidence 99999987753
No 7
>smart00466 SRA SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. Domain in SET domain containing proteins and in Deinococcus radiodurans DRA1533.
Probab=91.78 E-value=0.05 Score=52.75 Aligned_cols=24 Identities=8% Similarity=-0.008 Sum_probs=22.9
Q ss_pred chhhhcCCCCCccccCccccccCCC
Q 043203 412 RDLNKKSSNRSNCLNSSNLATVQQQ 436 (613)
Q Consensus 412 ~~w~e~g~~g~~v~k~~~L~r~p~q 436 (613)
++|.++|++|+.||||+ |+|+|||
T Consensus 132 ~~w~e~g~~G~~v~kfk-L~R~~gQ 155 (155)
T smart00466 132 DYWREVGKSGFLVFKFK-LVRIPGQ 155 (155)
T ss_pred EEEEecCCCCcEEEEEE-EEeCCCC
Confidence 57999999999999999 9999998
No 8
>smart00570 AWS associated with SET domains. subdomain of PRESET
Probab=85.90 E-value=0.28 Score=39.77 Aligned_cols=26 Identities=31% Similarity=0.673 Sum_probs=23.1
Q ss_pred cccceeecCCCCCCCCCCCCceeeeC
Q 043203 578 VRKFIKECWRKCGCSMQCQNRIVQQG 603 (613)
Q Consensus 578 ~r~~IyECn~~CgC~~~C~NRVVQrG 603 (613)
-|-..+||.+.|.|+..|.||.-|+.
T Consensus 24 NR~l~~EC~~~C~~G~~C~NqrFqk~ 49 (51)
T smart00570 24 NRMLLIECSSDCPCGSYCSNQRFQKR 49 (51)
T ss_pred HHHHhhhcCCCCCCCcCccCcccccC
Confidence 36678999999999999999999874
No 9
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=84.83 E-value=1.4 Score=34.47 Aligned_cols=27 Identities=26% Similarity=0.354 Sum_probs=23.9
Q ss_pred HHHHHHHHHhcCCChhhHHHHHHHHHH
Q 043203 6 AVRAANAMKAIGIVDKQVQTVLVNLLE 32 (613)
Q Consensus 6 ~~~A~~am~~lG~~~~~v~~vlk~Ll~ 32 (613)
.+-|+.|+..|||+++++..+|++++.
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~~ 29 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLLE 29 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhc
Confidence 356899999999999999999999997
No 10
>PF02182 SAD_SRA: SAD/SRA domain; InterPro: IPR003105 This domain has been termed SRA-YDG, for SET and Ring finger Associated, and because of the conserved YDG motif within the domain. Further characteristics of the domain are the conservation of up to 13 evenly spaced glycine residues and a VRV(I/V)RG motif. The domain is mainly found in plants and animals and in bacteria. In animals, this domain is associated with the Np95-like ring finger protein and the related gene product Np97, which contains PHD and RING FINGER domains and which is an important determinant in cell cycle progression. Np95 is a chromatin-associated ubiquitin ligase, binding to histones is direct and shows a remarkable preference for histone H3 and its N-terminal tail. The SRA-YDG domain contained in Np95 is indispensable both for the interaction with histones and for chromatin binding in vivo [, ]. In plants the SRA-YDG domain is associated with the SET domain, found in a family of histone methyl transferases, and in bacteria it is found in association with HNH, a non-specific nuclease motif [, ].; GO: 0042393 histone binding; PDB: 2ZO1_B 2ZKD_A 2ZO0_B 2ZKF_A 2ZKG_B 3FDE_A 3F8I_A 2ZO2_B 3F8J_B 2ZKE_A ....
Probab=83.53 E-value=0.31 Score=47.02 Aligned_cols=25 Identities=12% Similarity=0.105 Sum_probs=21.5
Q ss_pred cchhhhcCCCCCccccCccccccCCC
Q 043203 411 ERDLNKKSSNRSNCLNSSNLATVQQQ 436 (613)
Q Consensus 411 ~~~w~e~g~~g~~v~k~~~L~r~p~q 436 (613)
.++|.+++++|+.||||+ |+|+|||
T Consensus 131 ~~~w~~~g~~G~~v~kF~-L~R~~gQ 155 (155)
T PF02182_consen 131 VKYWREKGKSGFKVFKFK-LVRLPGQ 155 (155)
T ss_dssp EEEEEEE-TTSSEEEEEE-EEE-TSS
T ss_pred EEEEEEeCCCCcEEEEEE-EEECCCC
Confidence 368999999999999999 9999998
No 11
>KOG3813 consensus Uncharacterized conserved protein (tumor-suppressor AXUD1 in humans) [General function prediction only]
Probab=60.92 E-value=4.3 Score=46.33 Aligned_cols=20 Identities=40% Similarity=0.989 Sum_probs=17.6
Q ss_pred CCCCcCCCCCCCCCCCCcccccc
Q 043203 498 EDCCSNCSGDCLSLSIPCACTRE 520 (613)
Q Consensus 498 ~~gC~dC~g~Cls~s~~CaC~~~ 520 (613)
+.|| +|.+-|.+. .|+|.+.
T Consensus 307 eCGC-sCr~~CdPE--TCaCSqa 326 (640)
T KOG3813|consen 307 ECGC-SCRGVCDPE--TCACSQA 326 (640)
T ss_pred hhCC-cccceeChh--hcchhcc
Confidence 5889 999999986 7999884
No 12
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=54.94 E-value=6.2 Score=46.41 Aligned_cols=34 Identities=29% Similarity=0.539 Sum_probs=31.3
Q ss_pred cceeecCC-CCC-CCCCCCCceeeeCCeeeEEEeeC
Q 043203 580 KFIKECWR-KCG-CSMQCQNRIVQQGITCKLQVRMT 613 (613)
Q Consensus 580 ~~IyECn~-~Cg-C~~~C~NRVVQrGIk~~LEVFkT 613 (613)
-...||++ .|. |+..|.|+--|+---.+++||+|
T Consensus 92 ~t~iECs~~~C~~cg~~C~NQRFQkkqyA~vevF~T 127 (729)
T KOG4442|consen 92 MTSIECSDRECPRCGVYCKNQRFQKKQYAKVEVFLT 127 (729)
T ss_pred hhhcccCCccCCCccccccchhhhhhccCceeEEEe
Confidence 34569999 999 99999999999999999999998
No 13
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=54.69 E-value=16 Score=26.48 Aligned_cols=23 Identities=9% Similarity=0.177 Sum_probs=19.1
Q ss_pred HHHHHHHHhcCCChhhHHHHHHH
Q 043203 7 VRAANAMKAIGIVDKQVQTVLVN 29 (613)
Q Consensus 7 ~~A~~am~~lG~~~~~v~~vlk~ 29 (613)
..++..|..|||++.+++..|+.
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~ 24 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRA 24 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 35688999999999998887764
No 14
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=51.67 E-value=19 Score=26.16 Aligned_cols=22 Identities=9% Similarity=0.211 Sum_probs=17.7
Q ss_pred HHHHHHHHhcCCChhhHHHHHH
Q 043203 7 VRAANAMKAIGIVDKQVQTVLV 28 (613)
Q Consensus 7 ~~A~~am~~lG~~~~~v~~vlk 28 (613)
+.+++.|..|||++.+++..|+
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~ 23 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALR 23 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHH
Confidence 3578899999999888877654
No 15
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=39.34 E-value=36 Score=25.04 Aligned_cols=21 Identities=14% Similarity=0.292 Sum_probs=15.9
Q ss_pred HHHHHHHhcCCChhhHHHHHH
Q 043203 8 RAANAMKAIGIVDKQVQTVLV 28 (613)
Q Consensus 8 ~A~~am~~lG~~~~~v~~vlk 28 (613)
..+..+..|||++.+++..|+
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~ 24 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALR 24 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHH
Confidence 467788888999998877664
No 16
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=37.05 E-value=16 Score=32.10 Aligned_cols=44 Identities=14% Similarity=0.259 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHHhcCCChhhHHHHHHHHHHHhccC-ccccccchhHHHH
Q 043203 3 RERAVRAANAMKAIGIVDKQVQTVLVNLLELFNWN-WEYIEAEDYRALK 50 (613)
Q Consensus 3 ~~r~~~A~~am~~lG~~~~~v~~vlk~Ll~~y~~n-W~~iEe~~Yr~l~ 50 (613)
+..+.+++..+..+||+.+.+ ++|++.|+.+ ++-|+++-|+++.
T Consensus 5 ~~~~~~~~~~L~~~gl~~~~a----~kl~~~yg~~ai~~l~~nPY~L~~ 49 (94)
T PF14490_consen 5 NRGLRELMAFLQEYGLSPKLA----MKLYKKYGDDAIEILKENPYRLIE 49 (94)
T ss_dssp ----HHHHHHHHHTT--HHHH----HHHHHHH-TTHHHHHHH-STCCCB
T ss_pred HHHHHHHHHHHHHcCCCHHHH----HHHHHHHhHHHHHHHHHChHHHHH
Confidence 345677889999999998655 5677889875 9999999999876
No 17
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=29.01 E-value=47 Score=27.74 Aligned_cols=23 Identities=22% Similarity=0.356 Sum_probs=18.0
Q ss_pred HHHHHHHhcCCChhhHHHHHHHH
Q 043203 8 RAANAMKAIGIVDKQVQTVLVNL 30 (613)
Q Consensus 8 ~A~~am~~lG~~~~~v~~vlk~L 30 (613)
..++.|-.|||+...|-.||++|
T Consensus 11 ~lVd~F~~mGF~~dkVvevlrrl 33 (55)
T PF09288_consen 11 DLVDQFENMGFERDKVVEVLRRL 33 (55)
T ss_dssp HHHHHHHHHT--HHHHHHHHHHS
T ss_pred HHHHHHHHcCCcHHHHHHHHHHh
Confidence 34688899999999999999987
No 18
>KOG0164 consensus Myosin class I heavy chain [Cytoskeleton]
Probab=26.66 E-value=70 Score=38.59 Aligned_cols=40 Identities=28% Similarity=0.454 Sum_probs=31.2
Q ss_pred HHHHHHHHHhcCCChhhHHHHHHHHHHHhc-cCccccccch
Q 043203 6 AVRAANAMKAIGIVDKQVQTVLVNLLELFN-WNWEYIEAED 45 (613)
Q Consensus 6 ~~~A~~am~~lG~~~~~v~~vlk~Ll~~y~-~nW~~iEe~~ 45 (613)
.++--+||+.+||++.+|+.|++-+-.+-- ||-+||++|.
T Consensus 246 fk~V~~Am~vIgFs~eEVe~v~~iiAavLhLGNv~f~~~ed 286 (1001)
T KOG0164|consen 246 FKAVQKAMRVIGFSEEEVESVLSIIAAVLHLGNVEFADNED 286 (1001)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccceEEeecCc
Confidence 445678999999999999998876554433 8988887764
No 19
>KOG0162 consensus Myosin class I heavy chain [Cytoskeleton]
Probab=25.59 E-value=56 Score=39.46 Aligned_cols=49 Identities=31% Similarity=0.383 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHhcCCChhhHHHHHHHHHH-HhccCccccccchhHHHHHh
Q 043203 4 ERAVRAANAMKAIGIVDKQVQTVLVNLLE-LFNWNWEYIEAEDYRALKDT 52 (613)
Q Consensus 4 ~r~~~A~~am~~lG~~~~~v~~vlk~Ll~-~y~~nW~~iEe~~Yr~l~da 52 (613)
.-...-|.||+.+||....-..||+=|-- |.=||--||||++|.++-|.
T Consensus 252 kdfq~Tl~AM~vIGi~~~eQ~~v~rmva~IL~lGNIsF~Ee~~~a~V~~~ 301 (1106)
T KOG0162|consen 252 KDFQETLHAMKVIGINQEEQDEVLRMVAGILHLGNISFIEEGNYAAVSDK 301 (1106)
T ss_pred HHHHHHHHHheeccCChHHHHHHHHHHHHHHhccceeEEeeCCcceeccc
Confidence 34556799999999999877777765543 33489999999999887653
No 20
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=21.14 E-value=2.3e+02 Score=26.56 Aligned_cols=56 Identities=21% Similarity=0.186 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHhcCCChhhHHHHHHHHHHHhcc---------Ccccccc-chhHHHHHhhhhhcccc
Q 043203 4 ERAVRAANAMKAIGIVDKQVQTVLVNLLELFNW---------NWEYIEA-EDYRALKDTYFDFKENQ 60 (613)
Q Consensus 4 ~r~~~A~~am~~lG~~~~~v~~vlk~Ll~~y~~---------nW~~iEe-~~Yr~l~dai~d~~e~~ 60 (613)
.++..-++.+..=-|+.+.++.+|..|++- ++ ||..|.+ +.++.+++.++++....
T Consensus 43 ~~l~~li~l~~~~~Is~~~ak~ll~~~~~~-~~~~~~ii~~~~l~~i~d~~el~~~v~~vi~~n~~~ 108 (148)
T PF02637_consen 43 EHLAELINLLEDGKISKKSAKELLRELLEN-GKSPEEIIEENGLWQISDEEELEALVEEVIAENPKE 108 (148)
T ss_dssp HHHHHHHHHHHTTSSGHHHHHHHHHHHHHH-TS-HHHHHHHTT---B--CCHHHHHHHHHHHC-HHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHHHc-CCCHHHHHHHcCCCcCCCHHHHHHHHHHHHHHCHHH
Confidence 456666777778889999999999999876 43 5888876 89999999999876543
Done!