Query psy15424
Match_columns 153
No_of_seqs 46 out of 48
Neff 2.7
Searched_HMMs 46136
Date Fri Aug 16 20:39:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15424.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15424hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3600|consensus 99.9 2.5E-26 5.5E-31 224.3 4.8 71 38-143 20-91 (2238)
2 PF11597 Med13_N: Mediator com 99.9 4.8E-26 1E-30 197.6 5.5 83 39-149 15-97 (401)
3 PLN02705 beta-amylase 81.4 4.4 9.5E-05 39.6 6.4 48 3-50 66-144 (681)
4 PF15127 DUF4565: Protein of u 27.0 22 0.00047 27.1 0.1 20 67-86 48-67 (91)
5 PF05704 Caps_synth: Capsular 26.5 47 0.001 28.1 2.0 14 124-137 43-57 (276)
6 PF11705 RNA_pol_3_Rpc31: DNA- 25.2 45 0.00097 27.3 1.6 10 1-10 1-10 (233)
7 KOG1346|consensus 23.4 47 0.001 32.3 1.5 21 115-137 212-232 (659)
8 PF15125 TMEM238: TMEM238 prot 22.6 11 0.00025 27.0 -2.0 8 129-136 49-56 (65)
9 PF08344 TRP_2: Transient rece 21.4 51 0.0011 23.1 1.0 13 67-79 37-49 (63)
10 smart00774 WRKY DNA binding do 17.7 20 0.00043 24.8 -1.6 26 45-81 4-29 (59)
No 1
>KOG3600|consensus
Probab=99.92 E-value=2.5e-26 Score=224.30 Aligned_cols=71 Identities=45% Similarity=0.845 Sum_probs=63.8
Q ss_pred CCcccccCceeeeeecCCCCCCCCCCCCCCC-CchHHHHHHHHhhCCceeEEeecCCCCCCCCCCCCCCcccccCCCCcC
Q psy15424 38 GGDTDLCGIKWRKLVHGDSAGTGYSPGSEPL-EDPVLASYAKCLAGDILCVWRRVGTPQNGGSGGGGGGLFDSIGLPQVT 116 (153)
Q Consensus 38 ~~lTDL~GIKWRkyv~~~~~~~~~~p~~~pL-~DPVL~SYSRCL~adILCVWRR~~~p~~~~~~~~~~~~f~~~~~~~~~ 116 (153)
-.|.||+|||||||+|+.++ |++.++ +|+||+||||||.+||||||||++.+
T Consensus 20 ~~l~el~gikwk~y~~k~~a-----p~~~~~t~d~vl~a~skcl~~~il~~wrr~~~~---------------------- 72 (2238)
T KOG3600|consen 20 YALLELPGIKWKCYRTKPNA-----PRGVALTADFVLKAYSKCLLDGILCTWRRKPND---------------------- 72 (2238)
T ss_pred HHhhcCCCcceeEEeccCCC-----cceeeechhHHHHHHHHHHhhCceeeeecCCCC----------------------
Confidence 36899999999999998865 788888 99999999999999999999998753
Q ss_pred CCCCccccccceeEEEecCCCCCCCcc
Q psy15424 117 SVPPLSLQAAKELWIFWYGEEPDLSSI 143 (153)
Q Consensus 117 ~~PplSl~~aKELWIFWYGeEPdLs~l 143 (153)
++||||||||||||.|..+
T Consensus 73 --------~~kelwvfw~~dep~ll~~ 91 (2238)
T KOG3600|consen 73 --------APKELWVFWYDDEPALLQK 91 (2238)
T ss_pred --------CcceeEEEEeCCCcHHHHh
Confidence 7799999999999988654
No 2
>PF11597 Med13_N: Mediator complex subunit 13 N-terminal; InterPro: IPR021643 Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood [].
Probab=99.92 E-value=4.8e-26 Score=197.58 Aligned_cols=83 Identities=51% Similarity=0.824 Sum_probs=71.7
Q ss_pred CcccccCceeeeeecCCCCCCCCCCCCCCCCchHHHHHHHHhhCCceeEEeecCCCCCCCCCCCCCCcccccCCCCcCCC
Q psy15424 39 GDTDLCGIKWRKLVHGDSAGTGYSPGSEPLEDPVLASYAKCLAGDILCVWRRVGTPQNGGSGGGGGGLFDSIGLPQVTSV 118 (153)
Q Consensus 39 ~lTDL~GIKWRkyv~~~~~~~~~~p~~~pL~DPVL~SYSRCL~adILCVWRR~~~p~~~~~~~~~~~~f~~~~~~~~~~~ 118 (153)
.++||+|||||+|++..+++ ....+++||||+||+||++++|||+|||++.+...
T Consensus 15 ~l~~lsgI~WR~Y~~~~~~~----~~~~~~~dpvl~s~~~~~~~~~l~~~lR~~~~lv~--------------------- 69 (401)
T PF11597_consen 15 ALDDLSGIKWRIYVWEPNAS----RSPGPLEDPVLSSYSRCLAADILEVWLRNQGCLVS--------------------- 69 (401)
T ss_pred eeccCCcceEEEeecCCCCC----CCCCCCCChHHHHHHHhhhhhHHHHHhhcCCCCCC---------------------
Confidence 58999999999999977653 45678899999999999999999999998887432
Q ss_pred CCccccccceeEEEecCCCCCCCcccchhhh
Q psy15424 119 PPLSLQAAKELWIFWYGEEPDLSSIVTPELF 149 (153)
Q Consensus 119 PplSl~~aKELWIFWYGeEPdLs~lV~pEL~ 149 (153)
....+|||||||||+|||+.+++++|+.
T Consensus 70 ---~~~~rkeLWvF~~~~ep~~~~~~~~~~~ 97 (401)
T PF11597_consen 70 ---YDADRKELWVFWYGPEPDLLDPVHPEDE 97 (401)
T ss_pred ---CCCCCcEEEEEecCCCcccccceeeccc
Confidence 1238999999999999999999998854
No 3
>PLN02705 beta-amylase
Probab=81.42 E-value=4.4 Score=39.57 Aligned_cols=48 Identities=33% Similarity=0.562 Sum_probs=31.5
Q ss_pred CCCCCCCCcccCcccccchHHHHHHHHHHH-------------------------------HhhccCCcccccCceeee
Q psy15424 3 GRGGGGGGEREGGKVRETEEEEEEEVEKWE-------------------------------RLGERGGDTDLCGIKWRK 50 (153)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------~~~~~~~lTDL~GIKWRk 50 (153)
+.||||||.+.|.+-||.|.|....-|.=. ++-|+|-+.++.|.+.|+
T Consensus 66 ~~~~~~~~~~~~~~~~~~e~e~~~~rer~rrai~~ki~aglr~~g~~~lp~~~d~n~vl~al~~eagw~v~~dg~~yr~ 144 (681)
T PLN02705 66 SSGGGGGGGGKGKREREKEKERTKLRERHRRAITSRMLAGLRQYGNFPLPARADMNDVLAALAREAGWTVEADGTTYRQ 144 (681)
T ss_pred cCCCCCCCCCCCCCcchhhhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCcccchHHHHHHHHHhcCcEEcCCCCcccC
Confidence 456666777777777766665544444332 234677788999999984
No 4
>PF15127 DUF4565: Protein of unknown function (DUF4565)
Probab=27.00 E-value=22 Score=27.05 Aligned_cols=20 Identities=40% Similarity=0.650 Sum_probs=17.6
Q ss_pred CCCchHHHHHHHHhhCCcee
Q psy15424 67 PLEDPVLASYAKCLAGDILC 86 (153)
Q Consensus 67 pL~DPVL~SYSRCL~adILC 86 (153)
|..-|||.-||-||+.+||.
T Consensus 48 ~~a~~vvlEyA~rLSqEIl~ 67 (91)
T PF15127_consen 48 PGASPVVLEYAHRLSQEILS 67 (91)
T ss_pred CCCCchhHHHHHHHHHHHHH
Confidence 44779999999999999985
No 5
>PF05704 Caps_synth: Capsular polysaccharide synthesis protein; InterPro: IPR008441 This entry consists of several capsular polysaccharide proteins. Capsular polysaccharide (CPS) is a major virulence factor in Streptococcus pneumoniae. This family is often transcribed with putative glycosyl transferases to give rise to bifunctional proteins [].
Probab=26.49 E-value=47 Score=28.14 Aligned_cols=14 Identities=43% Similarity=1.227 Sum_probs=10.2
Q ss_pred cccceeEEEec-CCC
Q psy15424 124 QAAKELWIFWY-GEE 137 (153)
Q Consensus 124 ~~aKELWIFWY-GeE 137 (153)
...|-.|+||+ |.|
T Consensus 43 ~~~k~IW~~W~QG~e 57 (276)
T PF05704_consen 43 TNEKIIWVCWWQGEE 57 (276)
T ss_pred CCCCcEEEEECCCcc
Confidence 35566999999 453
No 6
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=25.20 E-value=45 Score=27.28 Aligned_cols=10 Identities=80% Similarity=1.577 Sum_probs=5.9
Q ss_pred CCCCCCCCCC
Q psy15424 1 MRGRGGGGGG 10 (153)
Q Consensus 1 ~~~~~~~~~~ 10 (153)
|-|||||+||
T Consensus 1 MSgRGggrg~ 10 (233)
T PF11705_consen 1 MSGRGGGRGG 10 (233)
T ss_pred CCCCCCCCCC
Confidence 5566666554
No 7
>KOG1346|consensus
Probab=23.36 E-value=47 Score=32.28 Aligned_cols=21 Identities=38% Similarity=0.960 Sum_probs=13.6
Q ss_pred cCCCCCccccccceeEEEecCCC
Q psy15424 115 VTSVPPLSLQAAKELWIFWYGEE 137 (153)
Q Consensus 115 ~~~~PplSl~~aKELWIFWYGeE 137 (153)
-|-+|.....-+|||| ||||+
T Consensus 212 epelPYmRPPLSKELW--~~~dp 232 (659)
T KOG1346|consen 212 EPELPYMRPPLSKELW--WYGDP 232 (659)
T ss_pred CccCcccCCCcchhce--ecCCC
Confidence 3455555555679998 77763
No 8
>PF15125 TMEM238: TMEM238 protein family
Probab=22.61 E-value=11 Score=27.04 Aligned_cols=8 Identities=50% Similarity=1.817 Sum_probs=6.5
Q ss_pred eEEEecCC
Q psy15424 129 LWIFWYGE 136 (153)
Q Consensus 129 LWIFWYGe 136 (153)
.|||||.-
T Consensus 49 ~Wv~WYtg 56 (65)
T PF15125_consen 49 WWVFWYTG 56 (65)
T ss_pred HHHHHHhc
Confidence 59999965
No 9
>PF08344 TRP_2: Transient receptor ion channel II; InterPro: IPR013555 TRP (transient receptor potential) channels can be described as tetramers formed by subunits with six transmembrane domains and containing cation-selective pores, which in several cases show high calcium permeability. The molecular architecture of TRP channels is reminiscent of voltage-gated channels and comprises six putative transmembrane segments (S1-S6), intracellular N- and C-termini, and a pore-forming reentrant loop between S5 and S6 []. TRP channels represent a superfamily conserved from worms to humans that comprise seven subfamilies []: TRPC (canonical), TRPV (vanilloid), TRPM (melastatin or long TRPs), TRPA (ankyrin), whose only member is the transmembrane protein 1, TRPP(polycystin), TRPML (mucolipin) and TRPN (Nomp-C homologues), which has a single member that can be found in worms, flies, and zebrafish. TRPs are classified essentially according to their primary amino acid sequence rather than selectivity or ligand affinity, due to their heterogenous properties and complex regulation. TRP channels are involved in many physiological functions, ranging from pure sensory functions, such as pheromone signalling, taste transduction, nociception, and temperature sensation, over homeostatic functions, such as Ca2+ and Mg2+ reabsorption and osmoregulation, to many other motile functions, such as muscle contraction and vaso-motor control []. This domain is found in Trp proteins, generally located to the C terminus of the Ankyrin repeats (IPR002110 from INTERPRO).
Probab=21.40 E-value=51 Score=23.12 Aligned_cols=13 Identities=23% Similarity=0.639 Sum_probs=10.5
Q ss_pred CCCchHHHHHHHH
Q psy15424 67 PLEDPVLASYAKC 79 (153)
Q Consensus 67 pL~DPVL~SYSRC 79 (153)
.-+||||++|--+
T Consensus 37 ts~DPi~~AF~Ls 49 (63)
T PF08344_consen 37 TSDDPILTAFELS 49 (63)
T ss_pred cCccHHHHHHHHH
Confidence 4599999999754
No 10
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=17.73 E-value=20 Score=24.79 Aligned_cols=26 Identities=35% Similarity=0.675 Sum_probs=19.1
Q ss_pred CceeeeeecCCCCCCCCCCCCCCCCchHHHHHHHHhh
Q psy15424 45 GIKWRKLVHGDSAGTGYSPGSEPLEDPVLASYAKCLA 81 (153)
Q Consensus 45 GIKWRkyv~~~~~~~~~~p~~~pL~DPVL~SYSRCL~ 81 (153)
|-+||||-.....+. |-.+||=||-.
T Consensus 4 Gy~WRKYGQK~ikgs-----------~~pRsYYrCt~ 29 (59)
T smart00774 4 GYQWRKYGQKVIKGS-----------PFPRSYYRCTY 29 (59)
T ss_pred cccccccCcEecCCC-----------cCcceEEeccc
Confidence 789999988765422 33478999988
Done!