Query 026365
Match_columns 239
No_of_seqs 135 out of 294
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 07:05:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026365.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026365hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03195 DUF260: Protein of un 100.0 1.5E-45 3.2E-50 290.9 7.4 101 2-107 1-101 (101)
2 COG3416 Uncharacterized protei 21.5 87 0.0019 29.0 2.8 48 52-99 16-63 (233)
3 PF15300 INT_SG_DDX_CT_C: INTS 19.1 70 0.0015 24.1 1.4 27 46-72 23-51 (65)
4 PF03242 LEA_3: Late embryogen 15.9 56 0.0012 26.1 0.3 20 68-87 58-77 (93)
5 PF04706 Dickkopf_N: Dickkopf 15.6 73 0.0016 22.9 0.8 15 2-16 22-36 (52)
6 PRK00451 glycine dehydrogenase 14.4 76 0.0017 29.6 0.8 33 24-59 3-35 (447)
7 PF14623 Vint: Hint-domain 12.8 55 0.0012 28.7 -0.6 39 38-82 121-159 (162)
8 PF05965 FYRC: F/Y rich C-term 11.3 1.7E+02 0.0037 21.8 1.7 24 37-60 51-76 (86)
9 cd07920 Pumilio Pumilio-family 10.4 2.2E+02 0.0047 25.2 2.4 40 43-83 164-203 (322)
10 PF10431 ClpB_D2-small: C-term 10.2 5.4E+02 0.012 18.5 4.1 41 61-105 32-72 (81)
No 1
>PF03195 DUF260: Protein of unknown function DUF260; InterPro: IPR004883 The lateral organ boundaries (LOB) gene is expressed at the adaxial base of initiating lateral organs and encodes a plant-specific protein of unknown function. The N-terminal one half of the LOB protein contains a conserved approximately 100-amino acid domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins and in proteins from a variety of other plant species. Genes encoding LOB domain (LBD) proteins are expressed in a variety of temporal- and tissue-specific patterns, suggesting that they may function in diverse processes [] The LOB domain contains conserved blocks of amino acids that identify the LBD gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is defining feature of the LOB domain, is present in all LBD proteins. It is possible that this motif forms a new zinc finger [].
Probab=100.00 E-value=1.5e-45 Score=290.85 Aligned_cols=101 Identities=33% Similarity=0.593 Sum_probs=96.5
Q ss_pred CccchhhcccCCCCCCcccccCCCCCCCcccchhhHHHHhhhccccHHHHhhcCCCCChHHHHHHHHHHHhccccCCCCc
Q 026365 2 SCNGCRVLRKGCSESCILRPCLQWIESPESQGHATVFVAKFFGRAGLMSFISAVPESQRPALFQSLLYEACGRTVNPVNG 81 (239)
Q Consensus 2 ~CAACK~lRRrC~~dCilAPYFp~ipa~~~q~fa~~~VhKvFG~sNV~kmL~~lp~~qR~da~~SLlYEA~aR~rDPVyG 81 (239)
+|||||||||+|+++|+||||| |++++++|. +||||||++||+|||+++|+++|+++|+||+|||++|.+|||||
T Consensus 1 ~CaaCk~lRr~C~~~C~laPyF---P~~~~~~F~--~vhkvFG~sni~k~L~~~~~~~R~~a~~Sl~yEA~~R~~dPv~G 75 (101)
T PF03195_consen 1 PCAACKHLRRRCSPDCVLAPYF---PADQPQRFA--NVHKVFGVSNISKMLQELPPEQREDAMRSLVYEANARARDPVYG 75 (101)
T ss_pred CChHHHHHhCCCCCCCcCCCCC---ChhHHHHHH--HHHHHHchhHHHHHHHhCCccchhhHHHHHHHHHHhhccCCCcc
Confidence 7999999999999999999999 678888876 79999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhHHHHHHHHHHHHHcCCCC
Q 026365 82 AVGLLWTGNWHVCQAAVETVLRGGTL 107 (239)
Q Consensus 82 cvGiI~~Lq~qI~q~avE~vL~g~~l 107 (239)
|+|+||.|+|||+++++|+++.+..|
T Consensus 76 c~G~i~~L~~ql~~~~~el~~~~~~l 101 (101)
T PF03195_consen 76 CVGIISQLQQQLQQLQAELALVRAQL 101 (101)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHccC
Confidence 99999999999999999999888765
No 2
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.45 E-value=87 Score=29.02 Aligned_cols=48 Identities=10% Similarity=0.109 Sum_probs=38.1
Q ss_pred hhcCCCCChHHHHHHHHHHHhccccCCCCchhhhhhhhHHHHHHHHHH
Q 026365 52 ISAVPESQRPALFQSLLYEACGRTVNPVNGAVGLLWTGNWHVCQAAVE 99 (239)
Q Consensus 52 L~~lp~~qR~da~~SLlYEA~aR~rDPVyGcvGiI~~Lq~qI~q~avE 99 (239)
|+......|+..++.||-||-++.-|--|=-+-.|..+.+-|..++.+
T Consensus 16 lk~a~~~~rD~~Ae~lI~~~~~~qP~a~Y~laQ~vliqE~ALk~a~~~ 63 (233)
T COG3416 16 LKKAEANERDPQAEALIAEAVAKQPDAAYYLAQRVLIQEQALKKASTQ 63 (233)
T ss_pred HhhcccCCCChHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHH
Confidence 677777899999999999999999999888887777666655544333
No 3
>PF15300 INT_SG_DDX_CT_C: INTS6/SAGE1/DDX26B/CT45 C-terminus
Probab=19.07 E-value=70 Score=24.12 Aligned_cols=27 Identities=19% Similarity=0.389 Sum_probs=23.2
Q ss_pred ccHHHHhhcC--CCCChHHHHHHHHHHHh
Q 026365 46 AGLMSFISAV--PESQRPALFQSLLYEAC 72 (239)
Q Consensus 46 sNV~kmL~~l--p~~qR~da~~SLlYEA~ 72 (239)
+.|.++|+.| |.+.|...+..++.||.
T Consensus 23 e~iF~lL~~vqG~~~~r~~fv~~~IkEA~ 51 (65)
T PF15300_consen 23 EKIFKLLEQVQGPLEVRKQFVEMIIKEAA 51 (65)
T ss_pred HHHHHHHHHccCCHHHHHHHHHHHHHHHH
Confidence 3677889987 78899999999999995
No 4
>PF03242 LEA_3: Late embryogenesis abundant protein; InterPro: IPR004926 Late-embryogenesis abundant (LEA) genes encode a diverse group of proteins that accumulate to high levels during the maturation phase of seed development []. This group includes LEA-5 [], whose expression is induced by salt, drought and heat stress [], and related proteins. ; GO: 0006950 response to stress
Probab=15.93 E-value=56 Score=26.08 Aligned_cols=20 Identities=20% Similarity=0.049 Sum_probs=15.8
Q ss_pred HHHHhccccCCCCchhhhhh
Q 026365 68 LYEACGRTVNPVNGAVGLLW 87 (239)
Q Consensus 68 lYEA~aR~rDPVyGcvGiI~ 87 (239)
-.|-..|..|||-|++--..
T Consensus 58 ~~~~~~W~pDPvTGyyrPen 77 (93)
T PF03242_consen 58 SKEKSSWMPDPVTGYYRPEN 77 (93)
T ss_pred cccccccccCCCCccccCCC
Confidence 56778999999999875543
No 5
>PF04706 Dickkopf_N: Dickkopf N-terminal cysteine-rich region; InterPro: IPR006796 Dickkopf proteins are a class of Wnt antagonists. They possess two conserved cysteine-rich regions. This family represents the N-terminal conserved region []. The C-terminal region has been found to share significant sequence similarity to the colipase fold (IPR001981 from INTERPRO) [].; GO: 0007275 multicellular organismal development, 0030178 negative regulation of Wnt receptor signaling pathway, 0005576 extracellular region
Probab=15.65 E-value=73 Score=22.93 Aligned_cols=15 Identities=40% Similarity=0.891 Sum_probs=13.1
Q ss_pred CccchhhcccCCCCC
Q 026365 2 SCNGCRVLRKGCSES 16 (239)
Q Consensus 2 ~CAACK~lRRrC~~d 16 (239)
.|..||-++++|..|
T Consensus 22 ~C~~Cr~~~~rC~Rd 36 (52)
T PF04706_consen 22 KCLPCRKRRKRCTRD 36 (52)
T ss_pred cChhhccCCCCCCCC
Confidence 489999999999865
No 6
>PRK00451 glycine dehydrogenase subunit 1; Validated
Probab=14.45 E-value=76 Score=29.64 Aligned_cols=33 Identities=15% Similarity=0.273 Sum_probs=20.8
Q ss_pred CCCCCCcccchhhHHHHhhhccccHHHHhhcCCCCC
Q 026365 24 QWIESPESQGHATVFVAKFFGRAGLMSFISAVPESQ 59 (239)
Q Consensus 24 p~ipa~~~q~fa~~~VhKvFG~sNV~kmL~~lp~~q 59 (239)
||||+.+ +.-. .+-+.||.++|-.+++.+|.+.
T Consensus 3 ~~~~~~~-~~~~--~~~~~~~~~~~~~~~~~~p~~~ 35 (447)
T PRK00451 3 PYIPHTE-EDIR--EMLDAIGVKSIDELFADIPEEL 35 (447)
T ss_pred CCCCCCH-HHHH--HHHHHhCCCCHHHHHHhCCHHH
Confidence 3446653 3322 3678999999977776666443
No 7
>PF14623 Vint: Hint-domain
Probab=12.77 E-value=55 Score=28.66 Aligned_cols=39 Identities=21% Similarity=0.371 Sum_probs=28.6
Q ss_pred HHHhhhccccHHHHhhcCCCCChHHHHHHHHHHHhccccCCCCch
Q 026365 38 FVAKFFGRAGLMSFISAVPESQRPALFQSLLYEACGRTVNPVNGA 82 (239)
Q Consensus 38 ~VhKvFG~sNV~kmL~~lp~~qR~da~~SLlYEA~aR~rDPVyGc 82 (239)
-+|.|||...|.+-|..|+.-.-. +.+...-.|||..|-
T Consensus 121 raH~fFG~~~V~~~L~~L~~~~~G------~v~~~g~~Rd~~Tgl 159 (162)
T PF14623_consen 121 RAHAFFGDNAVVRDLASLPGFANG------VVECRGVKRDPETGL 159 (162)
T ss_pred EeecccCcHHHHHHHHhCCCCCCC------EEEecceEECccccc
Confidence 479999999999999999874322 345555578887663
No 8
>PF05965 FYRC: F/Y rich C-terminus; InterPro: IPR003889 The "FY-rich" domain C-terminal region is sometimes closely juxtaposed with the N-terminal region (IPR003888 from INTERPRO), but sometimes is far distant. It is of unknown function, but occurs frequently in chromatin-associated proteins like trithorax and its homologues.; GO: 0005634 nucleus; PDB: 2WZO_A.
Probab=11.26 E-value=1.7e+02 Score=21.82 Aligned_cols=24 Identities=17% Similarity=0.476 Sum_probs=18.0
Q ss_pred HHHHhhhcccc--HHHHhhcCCCCCh
Q 026365 37 VFVAKFFGRAG--LMSFISAVPESQR 60 (239)
Q Consensus 37 ~~VhKvFG~sN--V~kmL~~lp~~qR 60 (239)
+.-+.+||.++ |+++|++||-.++
T Consensus 51 isG~~~FGls~p~V~~lie~Lp~a~~ 76 (86)
T PF05965_consen 51 ISGPEMFGLSNPAVQRLIESLPGADK 76 (86)
T ss_dssp --HHHHHSTTSHHHHHHHTTSTTGGG
T ss_pred CCHhHhcCCCCHHHHHHHHhCCCcch
Confidence 45688999875 8999999996543
No 9
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=10.38 E-value=2.2e+02 Score=25.16 Aligned_cols=40 Identities=20% Similarity=0.276 Sum_probs=30.8
Q ss_pred hccccHHHHhhcCCCCChHHHHHHHHHHHhccccCCCCchh
Q 026365 43 FGRAGLMSFISAVPESQRPALFQSLLYEACGRTVNPVNGAV 83 (239)
Q Consensus 43 FG~sNV~kmL~~lp~~qR~da~~SLlYEA~aR~rDPVyGcv 83 (239)
+|-.-|.++|+..++++|..+++.|+-+...=..|| ||.+
T Consensus 164 ~G~~vvq~~l~~~~~~~~~~l~~~l~~~~~~L~~d~-~Gn~ 203 (322)
T cd07920 164 YGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQ-FGNY 203 (322)
T ss_pred cccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCC-chhh
Confidence 677778888888888888888888887777666674 6654
No 10
>PF10431 ClpB_D2-small: C-terminal, D2-small domain, of ClpB protein ; InterPro: IPR019489 Most Clp ATPases form complexes with peptidase subunits and are involved in protein degradation, though some, such as ClpB, do not associate with peptidases and are involved in protein disaggregation []. This entry represents the C-terminal domain of Clp ATPases, often referred to as the D2-small domain, which forms a mixed alpha-beta structure. Compared with the adjacent AAA D1-small domain (IPR003959 from INTERPRO) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit, thereby providing enough binding energy to stabilise the functional assembly [].; PDB: 3HWS_A 3HTE_F 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 3PXI_A 1R6B_X ....
Probab=10.24 E-value=5.4e+02 Score=18.50 Aligned_cols=41 Identities=20% Similarity=0.204 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhccccCCCCchhhhhhhhHHHHHHHHHHHHHcCC
Q 026365 61 PALFQSLLYEACGRTVNPVNGAVGLLWTGNWHVCQAAVETVLRGG 105 (239)
Q Consensus 61 ~da~~SLlYEA~aR~rDPVyGcvGiI~~Lq~qI~q~avE~vL~g~ 105 (239)
+++++-|+-++ .||-||+=++-..++.+|...-.+..|.|.
T Consensus 32 ~~~~~~l~~~~----~~~~~GAR~l~r~i~~~i~~~la~~il~~~ 72 (81)
T PF10431_consen 32 DAVVDYLAEKG----YDPEYGARPLRRIIEREIEPPLADAILSGK 72 (81)
T ss_dssp HHHHHHHHHHH----HHTTTTTTCHHHHHHHHHHHHHHHHHHHSC
T ss_pred HHHHHHHHHhC----cccCCCHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 44555555444 679999999999999999988888888775
Done!