Query 032225
Match_columns 145
No_of_seqs 108 out of 169
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 11:15:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032225.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032225hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11708 Slu7: Pre-mRNA splici 100.0 8.5E-57 1.8E-61 372.0 12.0 127 10-145 66-193 (239)
2 KOG2560 RNA splicing factor - 100.0 5.4E-52 1.2E-56 368.8 10.0 139 7-145 219-357 (529)
3 COG2947 Uncharacterized conser 80.0 0.88 1.9E-05 36.5 1.1 13 42-54 77-89 (156)
4 TIGR02647 DNA conserved hypoth 36.4 26 0.00056 25.3 1.7 38 83-120 8-45 (77)
5 PF07443 HARP: HepA-related pr 35.4 17 0.00038 24.4 0.7 11 45-55 19-29 (55)
6 PF10384 Scm3: Centromere prot 30.3 1.1E+02 0.0025 20.5 4.0 12 129-140 16-27 (58)
7 PF03789 ELK: ELK domain ; In 27.5 34 0.00075 19.2 0.9 12 130-141 2-13 (22)
8 PF05835 Synaphin: Synaphin pr 26.3 1.4E+02 0.0031 23.4 4.5 22 120-141 54-75 (139)
9 PF13100 OstA_2: OstA-like pro 23.7 18 0.0004 28.1 -0.9 29 27-59 56-85 (158)
10 KOG3539 Spondins, extracellula 22.2 48 0.001 31.2 1.3 32 24-57 293-324 (508)
11 KOG3383 Uncharacterized conser 21.8 44 0.00096 27.4 1.0 11 44-54 96-106 (187)
No 1
>PF11708 Slu7: Pre-mRNA splicing Prp18-interacting factor; InterPro: IPR021715 The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyses the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3'ss from targeted RNase H cleavage. This change, which probably reflects binding of the 3'ss PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain.
Probab=100.00 E-value=8.5e-57 Score=372.01 Aligned_cols=127 Identities=43% Similarity=0.662 Sum_probs=120.7
Q ss_pred ccccceecCCCCCCccccccccccChHHHhhcCCCCCCCCCCCCcccccCCCCCCCCCcccccCCCceeccccHHHHHHH
Q 032225 10 QVKKGVCGNGSGITGTNRDLRIREDIPKYLLNLDENSAYYDPKIRSMREDLNPDDNPNEKFYAGYNRYRMGGQALEWKQV 89 (145)
Q Consensus 10 ~~d~~~r~~~~~~~~t~rnLRiREDtAkYL~NLd~nsa~YDPKSRsmRd~p~~~~~~~~~~fagdnF~R~sGe~~e~~~l 89 (145)
+.+.++|| |+|||||||||||||+|||+|||+|||||||||++|+ .++.+.+|+|+||||+|||+.+|++|
T Consensus 66 ~~~~k~~~-------t~rnLRiREDtAkYL~NLd~nsa~YDPKSRsmrd~p~--~~~~~~~~~gdnFvR~sGea~e~~~l 136 (239)
T PF11708_consen 66 KKDSKTRI-------TVRNLRIREDTAKYLLNLDSNSAYYDPKSRSMRDNPA--KDPGDVLFAGDNFVRLSGEAQEFEKL 136 (239)
T ss_pred cccccccc-------ccccccccccHHHHHHhCCCCCccCCCCccccccCCC--CChhhccccccCceeccccHHHHHHH
Confidence 35566666 9999999999999999999999999999999999996 78889999999999999999999999
Q ss_pred HHHHHHHhcCCC-ccccccCcCHHHHHhhhHHHHHHHHHHHHHHHHHHHhcCcCCCC
Q 032225 90 NIHAWKASGRGQ-DIHPEAALTQAELHYRWEKDIEEKKRLCKKEKIMEKYGNAASED 145 (145)
Q Consensus 90 q~fAWea~~kG~-~~hl~AnPT~~ell~k~~~~kke~~k~~~k~~ilekYGg~e~l~ 145 (145)
|+||||++++|. +||||||||++|+|+|+++++|++++.+.+++||+||||++|+.
T Consensus 137 q~FAWea~~kg~~~~hl~AnPT~~E~l~k~~~~kk~~~~~~~k~~ll~kYGg~e~~~ 193 (239)
T PF11708_consen 137 QRFAWEAAKKGGLDVHLQANPTKAELLRKEFKEKKEELKEEKKQSLLEKYGGEEHLD 193 (239)
T ss_pred HHHHHHHHhccCCceeeeeCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccc
Confidence 999999999998 99999999999999999999999999999999999999999863
No 2
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=100.00 E-value=5.4e-52 Score=368.84 Aligned_cols=139 Identities=45% Similarity=0.658 Sum_probs=134.3
Q ss_pred cCcccccceecCCCCCCccccccccccChHHHhhcCCCCCCCCCCCCcccccCCCCCCCCCcccccCCCceeccccHHHH
Q 032225 7 ILPQVKKGVCGNGSGITGTNRDLRIREDIPKYLLNLDENSAYYDPKIRSMREDLNPDDNPNEKFYAGYNRYRMGGQALEW 86 (145)
Q Consensus 7 ~~~~~d~~~r~~~~~~~~t~rnLRiREDtAkYL~NLd~nsa~YDPKSRsmRd~p~~~~~~~~~~fagdnF~R~sGe~~e~ 86 (145)
.+..+-+++|.+++|+++|||||||||||||||+|||+||+||||||||||++|+++.++.+..|.|+||||+|||+.+|
T Consensus 219 D~a~~~k~v~~~d~~s~iTvrnLRiRED~AkYL~nld~Nsa~YDPKSRsMReep~~~~~~~e~~~~gdnfvr~SGe~~~~ 298 (529)
T KOG2560|consen 219 DFADMLKTVRDTDDGSRITVRNLRIREDTAKYLRNLDVNSAYYDPKSRSMREEPLPGKDPNEDEYSGDNFVRNSGEALEF 298 (529)
T ss_pred hhhcccccccccCCCceeeeecceechhHHHHHHhcCCcccccCccccccccCCCCCCChhhhhhcccceeeccchhhhH
Confidence 35567788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCccccccCcCHHHHHhhhHHHHHHHHHHHHHHHHHHHhcCcCCCC
Q 032225 87 KQVNIHAWKASGRGQDIHPEAALTQAELHYRWEKDIEEKKRLCKKEKIMEKYGNAASED 145 (145)
Q Consensus 87 ~~lq~fAWea~~kG~~~hl~AnPT~~ell~k~~~~kke~~k~~~k~~ilekYGg~e~l~ 145 (145)
++||+|||||..+|+++|+||+||++|++++.++.+++.++.++++.||+||||.+|++
T Consensus 299 ~qlq~FAweA~~kG~~~H~~A~Ptk~Ell~k~~k~kke~lK~q~kq~il~kYG~~~~~d 357 (529)
T KOG2560|consen 299 NQLQMFAWEAFDKGVDVHMQADPTKLELLYKENKVKKETLKKQTKQEILDKYGGGEHKD 357 (529)
T ss_pred HHHHHHHHHHhcccceeeeecCcHHHHHHHHHhHHHHHHHHHHHHHHHHhhcCCccccc
Confidence 99999999999999999999999999999999999999999999999999999999874
No 3
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=80.02 E-value=0.88 Score=36.53 Aligned_cols=13 Identities=54% Similarity=0.986 Sum_probs=11.3
Q ss_pred CCCCCCCCCCCCc
Q 032225 42 LDENSAYYDPKIR 54 (145)
Q Consensus 42 Ld~nsa~YDPKSR 54 (145)
.||+|.|||||+-
T Consensus 77 ~d~~spYyDPka~ 89 (156)
T COG2947 77 FDPASPYYDPKAT 89 (156)
T ss_pred cCCCCcccCcccc
Confidence 6899999999974
No 4
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=36.44 E-value=26 Score=25.31 Aligned_cols=38 Identities=13% Similarity=0.208 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHhcCCCccccccCcCHHHHHhhhHH
Q 032225 83 ALEWKQVNIHAWKASGRGQDIHPEAALTQAELHYRWEK 120 (145)
Q Consensus 83 ~~e~~~lq~fAWea~~kG~~~hl~AnPT~~ell~k~~~ 120 (145)
..|++-|-+|=-+....|+.||--|+|..-+.+.|=++
T Consensus 8 i~ElnlL~~F~~~S~~~GIKvH~dA~p~~i~a~~RLhe 45 (77)
T TIGR02647 8 IAELELLALFNLSSTQEGIKVHSTASPAAVAAAARLHE 45 (77)
T ss_pred HHHHHHHHhCCchhhhcCccccccCCHHHHHHHHHHHH
Confidence 46788888899999999999999999999888877664
No 5
>PF07443 HARP: HepA-related protein (HARP); InterPro: IPR010003 This entry represents a conserved region approximately 60 residues long within eukaryotic HepA-related protein (HARP). This exhibits single-stranded DNA-dependent ATPase activity, and is ubiquitously expressed in human and mouse tissues []. Family members may contain more than one copy of this region.; GO: 0004386 helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0016568 chromatin modification, 0005634 nucleus
Probab=35.44 E-value=17 Score=24.44 Aligned_cols=11 Identities=55% Similarity=0.812 Sum_probs=8.5
Q ss_pred CCCCCCCCCcc
Q 032225 45 NSAYYDPKIRS 55 (145)
Q Consensus 45 nsa~YDPKSRs 55 (145)
.|-.|||+||.
T Consensus 19 pSr~YD~~Tr~ 29 (55)
T PF07443_consen 19 PSRNYDPKTRK 29 (55)
T ss_pred cccccCcccee
Confidence 34679999995
No 6
>PF10384 Scm3: Centromere protein Scm3; InterPro: IPR018465 The centromere protein Scm3 is a non-histone component of centromeric chromatin that binds to CenH3-H4 histones, which are required for kinetochore assembly. Scm3 is required for Cse4 localisation and is required for its centromeric association [, ]. The histone H3 variant Cse4 replaces conventional histone H3 in centromeric chromatin and helps direct the assembly of the kinetochore. In addition, Scm3 has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for G2/M progression []. Scm3 is required to maintain kinetochore function throughout the cell cycle. Scm3 contains a nuclear export signal (NES). The N-terminal region of Scm3 is well conserved and functions as the CenH3-interacting domain, while the C-terminal region is variable in size and sometimes consists of DNA binding motifs [].; GO: 0005634 nucleus; PDB: 3R45_C 2YFV_C 2L5A_A.
Probab=30.32 E-value=1.1e+02 Score=20.54 Aligned_cols=12 Identities=50% Similarity=0.872 Sum_probs=10.3
Q ss_pred HHHHHHHHHhcC
Q 032225 129 CKKEKIMEKYGN 140 (145)
Q Consensus 129 ~~k~~ilekYGg 140 (145)
..-++|++|||.
T Consensus 16 ~~~e~I~~KY~~ 27 (58)
T PF10384_consen 16 SRWESIIEKYGQ 27 (58)
T ss_dssp HHHHHHHHHHCS
T ss_pred HHHHHHHHHhcC
Confidence 467899999997
No 7
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=27.54 E-value=34 Score=19.16 Aligned_cols=12 Identities=25% Similarity=0.517 Sum_probs=9.4
Q ss_pred HHHHHHHHhcCc
Q 032225 130 KKEKIMEKYGNA 141 (145)
Q Consensus 130 ~k~~ilekYGg~ 141 (145)
-|..|+.||||.
T Consensus 2 LK~~LlrkY~g~ 13 (22)
T PF03789_consen 2 LKHQLLRKYSGY 13 (22)
T ss_pred HHHHHHHHHhHh
Confidence 367899999973
No 8
>PF05835 Synaphin: Synaphin protein; InterPro: IPR008849 This family consists of several eukaryotic synaphin 1 and 2 proteins. Synaphin/complexin is a cytosolic protein that preferentially binds to syntaxin within the SNARE complex. Synaphin promotes SNAREs to form precomplexes that oligomerise into higher order structures. A peptide from the central, syntaxin binding domain of synaphin competitively inhibits these two proteins from interacting and prevents SNARE complexes from oligomerising. It is thought that oligomerisation of SNARE complexes into a higher order structure creates a SNARE scaffold for efficient, regulated fusion of synaptic vesicles []. Synaphin promotes neuronal exocytosis by promoting interaction between the complementary syntaxin and synaptobrevin transmembrane regions that reside in opposing membranes prior to fusion [].; GO: 0019905 syntaxin binding, 0006836 neurotransmitter transport; PDB: 3RL0_m 3RK3_E 1L4A_E 1KIL_E.
Probab=26.25 E-value=1.4e+02 Score=23.38 Aligned_cols=22 Identities=27% Similarity=0.342 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHhcCc
Q 032225 120 KDIEEKKRLCKKEKIMEKYGNA 141 (145)
Q Consensus 120 ~~kke~~k~~~k~~ilekYGg~ 141 (145)
-.++++.+...|+.|-+|||-.
T Consensus 54 ~~k~eaERe~mRq~IRdKY~l~ 75 (139)
T PF05835_consen 54 HAKMEAEREKMRQHIRDKYGLK 75 (139)
T ss_dssp HHHHHHHHHHHHHHHHHHHT--
T ss_pred HHHHHHHHHHHHHHHHhhcccc
Confidence 3356677888999999999954
No 9
>PF13100 OstA_2: OstA-like protein
Probab=23.70 E-value=18 Score=28.14 Aligned_cols=29 Identities=21% Similarity=0.376 Sum_probs=21.4
Q ss_pred ccccccc-ChHHHhhcCCCCCCCCCCCCcccccC
Q 032225 27 RDLRIRE-DIPKYLLNLDENSAYYDPKIRSMRED 59 (145)
Q Consensus 27 rnLRiRE-DtAkYL~NLd~nsa~YDPKSRsmRd~ 59 (145)
=|+||.+ |+ ..|.++.++||+.|+.++-.
T Consensus 56 GnV~i~qgDt----~~i~~d~~~Y~~~t~~a~~~ 85 (158)
T PF13100_consen 56 GNVRITQGDT----LTITSDYLEYDGNTKIAEAR 85 (158)
T ss_pred cCEEEEcCCc----EEEEeCeEEEECCccEEEEE
Confidence 3677766 65 56778888999999887543
No 10
>KOG3539 consensus Spondins, extracellular matrix proteins [Extracellular structures]
Probab=22.17 E-value=48 Score=31.22 Aligned_cols=32 Identities=28% Similarity=0.383 Sum_probs=25.6
Q ss_pred ccccccccccChHHHhhcCCCCCCCCCCCCcccc
Q 032225 24 GTNRDLRIREDIPKYLLNLDENSAYYDPKIRSMR 57 (145)
Q Consensus 24 ~t~rnLRiREDtAkYL~NLd~nsa~YDPKSRsmR 57 (145)
-|+..-+|++=|-.|+ ++|-|.+||||++.|.
T Consensus 293 pteP~~~i~~ITs~~p--~~P~s~FY~pks~~lp 324 (508)
T KOG3539|consen 293 PTEPQDVIYRITSPYP--LHPASPFYDPKSKCLP 324 (508)
T ss_pred CCCCCCCceEeccCCC--CCCcccccCcccccCC
Confidence 4666777777777764 7899999999999984
No 11
>KOG3383 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.85 E-value=44 Score=27.43 Aligned_cols=11 Identities=55% Similarity=1.069 Sum_probs=8.4
Q ss_pred CCCCCCCCCCc
Q 032225 44 ENSAYYDPKIR 54 (145)
Q Consensus 44 ~nsa~YDPKSR 54 (145)
.|..||||+|-
T Consensus 96 ~ndp~ydp~st 106 (187)
T KOG3383|consen 96 ENDPYYDPEST 106 (187)
T ss_pred cCCCCcCcccc
Confidence 45579999975
Done!