Query psy1670
Match_columns 68
No_of_seqs 26 out of 28
Neff 2.1
Searched_HMMs 46136
Date Fri Aug 16 19:47:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1670.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1670hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3977|consensus 99.9 6.6E-22 1.4E-26 146.1 6.4 67 1-67 1-67 (221)
2 PF00992 Troponin: Troponin; 93.8 0.11 2.3E-06 35.0 3.8 24 44-67 1-24 (132)
3 PF03457 HA: Helicase associat 68.2 7.4 0.00016 22.1 2.7 19 32-50 47-65 (68)
4 PF07946 DUF1682: Protein of u 60.6 39 0.00084 25.1 5.9 17 31-47 294-310 (321)
5 KOG3088|consensus 50.0 27 0.00059 27.7 3.9 25 6-30 68-92 (313)
6 PF08278 DnaG_DnaB_bind: DNA p 35.9 87 0.0019 19.3 3.9 15 36-51 113-127 (127)
7 PF08035 Op_neuropeptide: Opio 34.0 14 0.00031 20.6 0.1 9 36-44 2-12 (31)
8 PLN02316 synthase/transferase 31.9 1.2E+02 0.0026 27.1 5.3 45 9-53 263-309 (1036)
9 PF00645 zf-PARP: Poly(ADP-rib 31.6 51 0.0011 19.3 2.2 17 35-51 63-81 (82)
10 PRK14600 ruvA Holliday junctio 29.3 47 0.001 23.4 2.1 18 35-52 60-77 (186)
11 COG2118 DNA-binding protein [G 27.8 2.1E+02 0.0046 19.8 6.2 27 24-50 35-61 (116)
12 COG0632 RuvA Holliday junction 26.2 59 0.0013 23.6 2.2 19 34-52 59-77 (201)
13 PRK14605 ruvA Holliday junctio 24.7 64 0.0014 22.6 2.1 18 35-52 60-77 (194)
14 PF10057 DUF2294: Uncharacteri 24.3 2E+02 0.0043 18.4 4.4 27 36-62 45-83 (118)
15 KOG1029|consensus 23.5 5.7E+02 0.012 23.8 8.0 35 11-46 336-370 (1118)
16 PRK14601 ruvA Holliday junctio 23.3 71 0.0015 22.6 2.1 18 35-52 60-77 (183)
17 TIGR00084 ruvA Holliday juncti 22.9 75 0.0016 22.2 2.1 18 35-52 59-76 (191)
18 KOG2357|consensus 21.5 4.8E+02 0.01 21.8 7.7 48 11-65 382-429 (440)
19 PF10003 DUF2244: Integral mem 21.0 1.1E+02 0.0024 20.2 2.5 17 36-52 121-137 (140)
No 1
>KOG3977|consensus
Probab=99.86 E-value=6.6e-22 Score=146.13 Aligned_cols=67 Identities=58% Similarity=0.738 Sum_probs=64.2
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy1670 1 MADDAAKKAKQAEIDRKRAEVRKRMEEASKAKKAKKGFMTPERKKKLRLLLRKKAAEELKKEQERKV 67 (68)
Q Consensus 1 m~d~~~~~rk~~E~erKkAEvrkrleea~~~kK~kkGflTpErKKkLr~Llm~KAAEelK~eq~~k~ 67 (68)
|.|+++.+|+.++++.+++|||+||++|+..++.|+||+||+||++||+|||++|||||++||++++
T Consensus 1 ~~dg~~~~rka~~re~kk~evrkrleeA~~~~~~KKgfltpeRKkkLrkLlm~kAaedLkqqq~~kE 67 (221)
T KOG3977|consen 1 EVDGDDAARKAQEREAKKAEVRKRLEEAGMPKKEKKGFLTPERKKKLRKLLMQKAAEDLKQQQELKE 67 (221)
T ss_pred CCccchhhhhccchhHHHHHHHHHHHHhcccchhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788889999999999999999999999999999999999999999999999999999999999875
No 2
>PF00992 Troponin: Troponin; InterPro: IPR001978 The troponin (Tn) complex regulates Ca2+ induced muscle contraction. Tn contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). This family includes troponin T and troponin I. Troponin I binds to actin and troponin T binds to tropomyosin [, , ].; PDB: 1J1D_C 1MXL_I 1LXF_I 2KRD_I 1J1E_F 2L1R_B 2KGB_I 1YTZ_I 1YV0_I 1VDJ_A ....
Probab=93.79 E-value=0.11 Score=34.98 Aligned_cols=24 Identities=46% Similarity=0.404 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhh
Q psy1670 44 KKKLRLLLRKKAAEELKKEQERKV 67 (68)
Q Consensus 44 KKkLr~Llm~KAAEelK~eq~~k~ 67 (68)
|++|+.|++.+|+++|..+|+.++
T Consensus 1 K~~lK~L~~~kA~~el~~e~~~ke 24 (132)
T PF00992_consen 1 KRMLKDLLLLKAKIELHFEQRKKE 24 (132)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred CchHHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999999998765
No 3
>PF03457 HA: Helicase associated domain; InterPro: IPR005114 This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid.; PDB: 2KTA_A.
Probab=68.17 E-value=7.4 Score=22.13 Aligned_cols=19 Identities=47% Similarity=0.744 Sum_probs=12.1
Q ss_pred HhhhccCCCHHHHHHHHHH
Q psy1670 32 KKAKKGFMTPERKKKLRLL 50 (68)
Q Consensus 32 kK~kkGflTpErKKkLr~L 50 (68)
.+.++|-|||++...|..|
T Consensus 47 ~~~r~g~L~~er~~~L~~l 65 (68)
T PF03457_consen 47 RKYRKGKLTPERIERLDAL 65 (68)
T ss_dssp HHHHHT---HHHHHHHHHH
T ss_pred HHHHcCCCCHHHHHHHHcC
Confidence 4445577999999999876
No 4
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=60.63 E-value=39 Score=25.10 Aligned_cols=17 Identities=24% Similarity=0.487 Sum_probs=10.5
Q ss_pred HHhhhccCCCHHHHHHH
Q psy1670 31 AKKAKKGFMTPERKKKL 47 (68)
Q Consensus 31 ~kK~kkGflTpErKKkL 47 (68)
.+..+-.=||||..+|+
T Consensus 294 e~~~~~~~lspeeQrK~ 310 (321)
T PF07946_consen 294 ERERKLSKLSPEEQRKY 310 (321)
T ss_pred HHHHHHhcCCHHHHHHH
Confidence 33343334999987775
No 5
>KOG3088|consensus
Probab=49.96 E-value=27 Score=27.71 Aligned_cols=25 Identities=28% Similarity=0.388 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1670 6 AKKAKQAEIDRKRAEVRKRMEEASK 30 (68)
Q Consensus 6 ~~~rk~~E~erKkAEvrkrleea~~ 30 (68)
|-+++|+|-+||.+|.-+|-++...
T Consensus 68 eL~~rqeEL~Rke~ELdRREr~~a~ 92 (313)
T KOG3088|consen 68 ELLKKQEELRRKEQELDRRERALAR 92 (313)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHhh
Confidence 4567778888888888777777665
No 6
>PF08278 DnaG_DnaB_bind: DNA primase DnaG DnaB-binding ; InterPro: IPR013173 Eubacterial DnaG primases interact with several factors to form the replisome. One of these factors is DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB []. This domain has a multi-helical structure that forms an orthogonal bundle [].; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 2HAJ_A 1T3W_B.
Probab=35.89 E-value=87 Score=19.32 Aligned_cols=15 Identities=53% Similarity=0.767 Sum_probs=10.8
Q ss_pred ccCCCHHHHHHHHHHH
Q psy1670 36 KGFMTPERKKKLRLLL 51 (68)
Q Consensus 36 kGflTpErKKkLr~Ll 51 (68)
.| +|++.|+-|+.||
T Consensus 113 ~~-Lt~eEk~el~~Ll 127 (127)
T PF08278_consen 113 GG-LTDEEKQELRRLL 127 (127)
T ss_dssp T----HHHHHHHHHHH
T ss_pred CC-cCHHHHHHHHHhC
Confidence 55 9999999999986
No 7
>PF08035 Op_neuropeptide: Opioids neuropeptide; InterPro: IPR013532 Pro-opiomelanocortin is present in high levels in the pituitary and is processed into 3 major peptide families: adrenocorticotrophin (ACTH); alpha-, beta- and gamma-melanocyte- stimulating hormones (MSH); and beta-endorphin []. ACTH regulates the synthesis and release of glucocorticoids and, to some extent, aldosterone in the adrenal cortex. It is synthesised and released in response to corticotrophin-releasing factor at times of stress (i.e. heat, cold, infection, etc.), its release leading to increased metabolism. The action of MSH in man is poorly understood, but it may be involved in temperature regulation []. Full activity of ACTH resides in the first 20 N-terminal amino acids, the first 13 of which are identical to alpha-MSH [, ]. This region corresponds to the conserved YGG motif that is found in a wide variety of opioid neuropeptides such as enkephalin
Probab=33.96 E-value=14 Score=20.56 Aligned_cols=9 Identities=56% Similarity=0.951 Sum_probs=6.9
Q ss_pred ccCCCH--HHH
Q psy1670 36 KGFMTP--ERK 44 (68)
Q Consensus 36 kGflTp--ErK 44 (68)
+|||++ |+-
T Consensus 2 GGFM~s~~e~s 12 (31)
T PF08035_consen 2 GGFMKSWDERS 12 (31)
T ss_pred Ccccccccccc
Confidence 699998 653
No 8
>PLN02316 synthase/transferase
Probab=31.92 E-value=1.2e+02 Score=27.10 Aligned_cols=45 Identities=36% Similarity=0.507 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH--HHHhhhccCCCHHHHHHHHHHHHH
Q psy1670 9 AKQAEIDRKRAEVRKRMEEAS--KAKKAKKGFMTPERKKKLRLLLRK 53 (68)
Q Consensus 9 rk~~E~erKkAEvrkrleea~--~~kK~kkGflTpErKKkLr~Llm~ 53 (68)
+.++|++|...|.+++-++.+ .+..+.-.--+.+++++|+.|+..
T Consensus 263 ~e~ae~~~~~ee~~r~~~~kaa~~a~~a~akae~~~~~~~~~~~~~~ 309 (1036)
T PLN02316 263 KEEAERERQAEEQRRREEEKAAMEADRAQAKAEVEKRREKLQNLLKK 309 (1036)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHHHHHHhh
Confidence 345677777777777765532 112221121455667777776643
No 9
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=31.56 E-value=51 Score=19.34 Aligned_cols=17 Identities=47% Similarity=0.913 Sum_probs=13.4
Q ss_pred hccC--CCHHHHHHHHHHH
Q psy1670 35 KKGF--MTPERKKKLRLLL 51 (68)
Q Consensus 35 kkGf--lTpErKKkLr~Ll 51 (68)
-.|| |+|+-+.+|+.+|
T Consensus 63 i~G~~~L~~~Dq~~i~~~i 81 (82)
T PF00645_consen 63 IKGFDELKPEDQEKIRKLI 81 (82)
T ss_dssp CETCCCS-HHHHHHHHHHH
T ss_pred CCChHHCCHHHHHHHHHHh
Confidence 4577 9999999999886
No 10
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.27 E-value=47 Score=23.39 Aligned_cols=18 Identities=33% Similarity=0.648 Sum_probs=15.7
Q ss_pred hccCCCHHHHHHHHHHHH
Q psy1670 35 KKGFMTPERKKKLRLLLR 52 (68)
Q Consensus 35 kkGflTpErKKkLr~Llm 52 (68)
.-||.|++.+...+.|+-
T Consensus 60 LyGF~~~~Er~lF~~Lis 77 (186)
T PRK14600 60 LYGFLNREEQDCLRMLVK 77 (186)
T ss_pred eeCCCCHHHHHHHHHHhC
Confidence 469999999999999874
No 11
>COG2118 DNA-binding protein [General function prediction only]
Probab=27.79 E-value=2.1e+02 Score=19.84 Aligned_cols=27 Identities=26% Similarity=0.488 Sum_probs=18.1
Q ss_pred HHHHHHHHHhhhccCCCHHHHHHHHHH
Q psy1670 24 RMEEASKAKKAKKGFMTPERKKKLRLL 50 (68)
Q Consensus 24 rleea~~~kK~kkGflTpErKKkLr~L 50 (68)
|.+..++..-...-||||+-+.-|..+
T Consensus 35 r~~~eaqkqaiLrqiLtpeAreRL~~i 61 (116)
T COG2118 35 RQEEEAQKQAILRQILTPEARERLARV 61 (116)
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHHh
Confidence 333334444458889999999888754
No 12
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=26.22 E-value=59 Score=23.56 Aligned_cols=19 Identities=37% Similarity=0.634 Sum_probs=16.8
Q ss_pred hhccCCCHHHHHHHHHHHH
Q psy1670 34 AKKGFMTPERKKKLRLLLR 52 (68)
Q Consensus 34 ~kkGflTpErKKkLr~Llm 52 (68)
..-||.|.+.|...|.||-
T Consensus 59 ~LyGF~~~~ER~lF~~Lis 77 (201)
T COG0632 59 LLYGFLTEEERELFRLLIS 77 (201)
T ss_pred HHcCCCCHHHHHHHHHHHc
Confidence 4679999999999999985
No 13
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.74 E-value=64 Score=22.64 Aligned_cols=18 Identities=28% Similarity=0.327 Sum_probs=15.5
Q ss_pred hccCCCHHHHHHHHHHHH
Q psy1670 35 KKGFMTPERKKKLRLLLR 52 (68)
Q Consensus 35 kkGflTpErKKkLr~Llm 52 (68)
.-||.|++.+...+.|+-
T Consensus 60 LyGF~~~~Er~lF~~Li~ 77 (194)
T PRK14605 60 LFGFATTEELSLFETLID 77 (194)
T ss_pred eeCCCCHHHHHHHHHHhC
Confidence 459999999999998873
No 14
>PF10057 DUF2294: Uncharacterized conserved protein (DUF2294); InterPro: IPR018745 This domain of unknown function is found in a family of hypothetical bacterial proteins with no known function. It is also found at the C terminus of proteins provisionally annotated as response regulators.
Probab=24.33 E-value=2e+02 Score=18.37 Aligned_cols=27 Identities=37% Similarity=0.455 Sum_probs=17.3
Q ss_pred ccCCCHHHHHHH------------HHHHHHHHHHHHHHH
Q psy1670 36 KGFMTPERKKKL------------RLLLRKKAAEELKKE 62 (68)
Q Consensus 36 kGflTpErKKkL------------r~Llm~KAAEelK~e 62 (68)
.|||||.-+-.+ |..|+...-++++..
T Consensus 45 ~g~LTp~Ek~L~~~~~g~~lv~~~R~~l~~~~~~~l~~~ 83 (118)
T PF10057_consen 45 EGFLTPAEKFLAETEEGRELVKQVRTSLIESLKPELKEM 83 (118)
T ss_pred ECCCCHHHHHHHhCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 589999877544 455665555555543
No 15
>KOG1029|consensus
Probab=23.50 E-value=5.7e+02 Score=23.75 Aligned_cols=35 Identities=23% Similarity=0.306 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccCCCHHHHHH
Q psy1670 11 QAEIDRKRAEVRKRMEEASKAKKAKKGFMTPERKKK 46 (68)
Q Consensus 11 ~~E~erKkAEvrkrleea~~~kK~kkGflTpErKKk 46 (68)
..|.+++++|-+.+.|.....||-+-- .-.|||+-
T Consensus 336 leeqqqreree~eqkEreE~ekkerer-qEqErk~q 370 (1118)
T KOG1029|consen 336 LEEQQQREREEVEQKEREEEEKKERER-QEQERKAQ 370 (1118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH
Confidence 344444444444444444433333222 33444443
No 16
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.33 E-value=71 Score=22.55 Aligned_cols=18 Identities=28% Similarity=0.628 Sum_probs=15.6
Q ss_pred hccCCCHHHHHHHHHHHH
Q psy1670 35 KKGFMTPERKKKLRLLLR 52 (68)
Q Consensus 35 kkGflTpErKKkLr~Llm 52 (68)
.-||.|++.+...+.|+-
T Consensus 60 LyGF~~~~Er~lF~~Li~ 77 (183)
T PRK14601 60 LYGFLDKDEQKMFEMLLK 77 (183)
T ss_pred eeCCCCHHHHHHHHHHhc
Confidence 469999999999998874
No 17
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=22.90 E-value=75 Score=22.25 Aligned_cols=18 Identities=28% Similarity=0.434 Sum_probs=15.5
Q ss_pred hccCCCHHHHHHHHHHHH
Q psy1670 35 KKGFMTPERKKKLRLLLR 52 (68)
Q Consensus 35 kkGflTpErKKkLr~Llm 52 (68)
.-||.|++.+...+.|+.
T Consensus 59 LyGF~~~~Er~lF~~L~~ 76 (191)
T TIGR00084 59 LFGFNTLEERELFKELIK 76 (191)
T ss_pred eeCCCCHHHHHHHHHHhC
Confidence 469999999999998874
No 18
>KOG2357|consensus
Probab=21.52 E-value=4.8e+02 Score=21.78 Aligned_cols=48 Identities=25% Similarity=0.384 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy1670 11 QAEIDRKRAEVRKRMEEASKAKKAKKGFMTPERKKKLRLLLRKKAAEELKKEQER 65 (68)
Q Consensus 11 ~~E~erKkAEvrkrleea~~~kK~kkGflTpErKKkLr~Llm~KAAEelK~eq~~ 65 (68)
.-...|.+|.-.+|.|..-..+..-+.-..||+-+ ++=|++++++.+.
T Consensus 382 ~th~~rqEaaQ~kk~Ek~Ka~kekl~a~~d~Ek~r-------r~EakerkR~~K~ 429 (440)
T KOG2357|consen 382 LTHAARQEAAQEKKAEKKKAEKEKLKASGDPEKQR-------RKEAKERKRQAKK 429 (440)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHH-------HHHHHHHHHHHHh
Confidence 33445666666667666654555555557887633 3445555555443
No 19
>PF10003 DUF2244: Integral membrane protein (DUF2244); InterPro: IPR019253 This entry consists of various bacterial putative membrane proteins with no known function.
Probab=20.95 E-value=1.1e+02 Score=20.17 Aligned_cols=17 Identities=35% Similarity=0.628 Sum_probs=13.8
Q ss_pred ccCCCHHHHHHHHHHHH
Q psy1670 36 KGFMTPERKKKLRLLLR 52 (68)
Q Consensus 36 kGflTpErKKkLr~Llm 52 (68)
+-||||+.+..|-..|.
T Consensus 121 G~fL~~~eR~~la~~L~ 137 (140)
T PF10003_consen 121 GRFLNPEEREELARELR 137 (140)
T ss_pred ccCCCHHHHHHHHHHHH
Confidence 56999999998876664
Done!