Query psy17102
Match_columns 412
No_of_seqs 138 out of 229
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 21:57:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17102.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17102hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00301 DM Doublesex DNA-bi 99.9 3.7E-27 8.1E-32 180.4 4.5 54 55-108 1-54 (54)
2 KOG3815|consensus 99.9 5.4E-26 1.2E-30 221.0 5.9 73 49-121 29-101 (322)
3 PF00751 DM: DM DNA binding do 99.9 7.5E-24 1.6E-28 158.1 0.5 47 55-101 1-47 (47)
4 PF03474 DMA: DMRTA motif; In 99.8 3.9E-21 8.4E-26 139.0 4.2 39 292-330 1-39 (39)
5 PF02845 CUE: CUE domain; Int 97.1 0.00065 1.4E-08 48.7 4.1 38 295-332 4-41 (42)
6 smart00546 CUE Domain that may 96.7 0.0029 6.4E-08 45.3 4.4 38 295-332 5-42 (43)
7 cd00194 UBA Ubiquitin Associat 80.5 2.1 4.5E-05 29.4 3.0 23 308-330 15-37 (38)
8 smart00165 UBA Ubiquitin assoc 72.3 4.1 9E-05 27.8 2.7 23 308-330 15-37 (37)
9 PF00627 UBA: UBA/TS-N domain; 72.1 7.4 0.00016 27.1 3.9 25 305-329 13-37 (37)
10 PF02954 HTH_8: Bacterial regu 51.8 19 0.00041 25.8 3.1 22 308-329 7-28 (42)
11 PRK06369 nac nascent polypepti 42.5 24 0.00053 31.5 2.9 33 296-329 80-112 (115)
12 KOG3450|consensus 35.9 36 0.00078 30.7 2.9 24 308-331 95-118 (119)
13 KOG4588|consensus 35.4 37 0.00081 34.1 3.2 32 302-333 1-32 (267)
14 KOG3815|consensus 34.7 12 0.00026 37.6 -0.2 57 52-108 145-201 (322)
15 TIGR00264 alpha-NAC-related pr 34.6 38 0.00082 30.5 2.8 22 308-329 93-114 (116)
16 KOG4317|consensus 34.1 22 0.00048 37.1 1.5 22 43-64 6-27 (383)
17 PLN03166 60S ribosomal protein 30.8 51 0.0011 28.7 2.9 39 51-89 36-87 (96)
18 TIGR00927 2A1904 K+-dependent 29.1 17 0.00036 42.6 -0.3 9 58-66 921-929 (1096)
19 PF14555 UBA_4: UBA-like domai 28.9 86 0.0019 22.6 3.5 28 307-334 14-41 (43)
20 PTZ00074 60S ribosomal protein 27.7 1.5E+02 0.0032 27.4 5.5 39 51-89 36-85 (135)
21 KOG4215|consensus 25.7 14 0.00031 39.0 -1.4 50 41-90 17-79 (432)
22 PLN03086 PRLI-interacting fact 25.6 16 0.00034 40.1 -1.2 40 56-95 407-448 (567)
23 KOG4167|consensus 25.2 2E+02 0.0042 33.5 6.9 30 83-112 793-822 (907)
24 COG1308 EGD2 Transcription fac 24.7 60 0.0013 29.5 2.4 22 308-329 99-120 (122)
25 COG2174 RPL34A Ribosomal prote 23.8 52 0.0011 28.7 1.8 39 51-89 29-78 (93)
26 PF09026 CENP-B_dimeris: Centr 22.5 27 0.00059 30.8 -0.1 13 21-33 33-45 (101)
27 PF08600 Rsm1: Rsm1-like; Int 22.3 45 0.00098 27.9 1.1 18 67-84 47-64 (91)
28 PF07967 zf-C3HC: C3HC zinc fi 21.9 45 0.00098 29.1 1.1 49 38-86 23-96 (133)
29 PF10669 Phage_Gp23: Protein g 21.1 60 0.0013 29.0 1.7 21 92-112 78-98 (121)
No 1
>smart00301 DM Doublesex DNA-binding motif.
Probab=99.93 E-value=3.7e-27 Score=180.38 Aligned_cols=54 Identities=54% Similarity=1.089 Sum_probs=52.8
Q ss_pred CCCCCccccCCCCccccCCCCccCCCCCCCCCCchhHHHHHHhHHHHHHHhHhh
Q psy17102 55 RTPKCARCRNHGVVSALKGHKRYCRWRDCVCAKCTLIAERQRVMAAQVALRRQQ 108 (412)
Q Consensus 55 R~P~CaRCRNHGv~s~lKGHKr~Cpfr~C~C~kC~Li~ERqRVmAaQvALRRqQ 108 (412)
|.|+|+||+|||++++|||||++|+|++|.|++|.||+|||+|||+||||||+|
T Consensus 1 r~p~C~rCrnHg~~~~lKGHKr~C~~r~C~C~kC~Li~~Rq~vma~qvalrR~q 54 (54)
T smart00301 1 RIPYCQKCENHGVKVPLKGHKPECPFRDCECEKCTLVEKRRALMALQIKLKREQ 54 (54)
T ss_pred CCCcChhHhcCCCeeccCCcCCCCCCCCCcCCCCcChHHHHHHHHHHHHHHhcC
Confidence 679999999999999999999999999999999999999999999999999987
No 2
>KOG3815|consensus
Probab=99.92 E-value=5.4e-26 Score=220.97 Aligned_cols=73 Identities=62% Similarity=0.997 Sum_probs=67.9
Q ss_pred hhhcCCCCCCCccccCCCCccccCCCCccCCCCCCCCCCchhHHHHHHhHHHHHHHhHhhHHHHHHHHHhccc
Q psy17102 49 TVHRYQRTPKCARCRNHGVVSALKGHKRYCRWRDCVCAKCTLIAERQRVMAAQVALRRQQAQEENEARELGLI 121 (412)
Q Consensus 49 a~~~~~R~P~CaRCRNHGv~s~lKGHKr~Cpfr~C~C~kC~Li~ERqRVmAaQvALRRqQaqEe~e~relgl~ 121 (412)
+.++..|.|+|+||||||++++|||||++|+|++|.|+||.||+||||||++||+|||+|++|+.+++++.+.
T Consensus 29 ~~~~~~r~p~CaRCrnHG~~~~LKGHk~~C~~~~C~C~kC~li~eRqrvmaaqvaLrRqqa~ee~~a~~~~~~ 101 (322)
T KOG3815|consen 29 PPAPSARGPKCARCENHGVLSRLKGHKRSCPYRDCPCEKCGLVEERRRVMAAQVALRRQQDGEEAGAKERPPM 101 (322)
T ss_pred ccccccccchhhhhhccCcceeccCCCCCCCCCCCCchHhcchHHHHHHHHHHHHHHHhhhhhhhhhcccCCC
Confidence 4678899999999999999999999999999999999999999999999999999999999999888744444
No 3
>PF00751 DM: DM DNA binding domain; InterPro: IPR001275 This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans []. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides []. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [, ]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [, , ]. The NMR analysis of the DSX DM domain [] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.; GO: 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007548 sex differentiation, 0005634 nucleus; PDB: 1LPV_A.
Probab=99.87 E-value=7.5e-24 Score=158.08 Aligned_cols=47 Identities=79% Similarity=1.471 Sum_probs=31.9
Q ss_pred CCCCCccccCCCCccccCCCCccCCCCCCCCCCchhHHHHHHhHHHH
Q psy17102 55 RTPKCARCRNHGVVSALKGHKRYCRWRDCVCAKCTLIAERQRVMAAQ 101 (412)
Q Consensus 55 R~P~CaRCRNHGv~s~lKGHKr~Cpfr~C~C~kC~Li~ERqRVmAaQ 101 (412)
|.|+|+||+|||+++++||||++|+|++|.|++|.||+|||+|||+|
T Consensus 1 R~p~C~RCrnHG~~~~lKgHk~~C~~~~C~C~kC~li~eRq~vma~q 47 (47)
T PF00751_consen 1 RSPTCARCRNHGVIVPLKGHKRYCPFRDCQCDKCALIAERQRVMAAQ 47 (47)
T ss_dssp --SS-HHHHTTT---TTTT-GGG-TTTT--SHHHHHHHHHH--S---
T ss_pred CCCcCcchhcCCcccchhhhccccCcCCCcCCCCcCcHHHHHHHhcC
Confidence 67999999999999999999999999999999999999999999997
No 4
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=99.83 E-value=3.9e-21 Score=139.04 Aligned_cols=39 Identities=56% Similarity=1.042 Sum_probs=37.9
Q ss_pred CCChhhhHHhhcCCCchhHHHHHHHhhCchHHHHHHHHH
Q psy17102 292 GRSPVDVLRRVFPNRRRGEVETVLQRCKGDVLQAIEMMV 330 (412)
Q Consensus 292 ~Rsp~DiL~RVFP~~kRs~LE~iLq~C~GDVVqAIE~~L 330 (412)
+|+|+|||+||||++||++||+|||+|+||||||||++|
T Consensus 1 ~r~pidiL~rvFP~~kr~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 1 QRSPIDILTRVFPHQKRSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred CCCHHHHHHHHCCCCChHHHHHHHHHcCCcHHHHHHHhC
Confidence 589999999999999999999999999999999999986
No 5
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=97.14 E-value=0.00065 Score=48.69 Aligned_cols=38 Identities=37% Similarity=0.532 Sum_probs=34.5
Q ss_pred hhhhHHhhcCCCchhHHHHHHHhhCchHHHHHHHHHhc
Q psy17102 295 PVDVLRRVFPNRRRGEVETVLQRCKGDVLQAIEMMVYS 332 (412)
Q Consensus 295 p~DiL~RVFP~~kRs~LE~iLq~C~GDVVqAIE~~L~s 332 (412)
-++.|.-+||+-.+.+|+.+|+.++|||-.||+.+|.+
T Consensus 4 ~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 4 MVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 46889999999999999999999999999999999964
No 6
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=96.69 E-value=0.0029 Score=45.35 Aligned_cols=38 Identities=24% Similarity=0.426 Sum_probs=35.7
Q ss_pred hhhhHHhhcCCCchhHHHHHHHhhCchHHHHHHHHHhc
Q psy17102 295 PVDVLRRVFPNRRRGEVETVLQRCKGDVLQAIEMMVYS 332 (412)
Q Consensus 295 p~DiL~RVFP~~kRs~LE~iLq~C~GDVVqAIE~~L~s 332 (412)
-++.|.-+||+-.+..++.+|+.|+|||-.||+.+|.+
T Consensus 5 ~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 5 ALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 57889999999999999999999999999999999964
No 7
>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=80.53 E-value=2.1 Score=29.41 Aligned_cols=23 Identities=26% Similarity=0.447 Sum_probs=21.0
Q ss_pred hhHHHHHHHhhCchHHHHHHHHH
Q psy17102 308 RGEVETVLQRCKGDVLQAIEMMV 330 (412)
Q Consensus 308 Rs~LE~iLq~C~GDVVqAIE~~L 330 (412)
+......|+.|+|||-+||+.++
T Consensus 15 ~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 15 REEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHh
Confidence 77888899999999999999886
No 8
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=72.34 E-value=4.1 Score=27.84 Aligned_cols=23 Identities=30% Similarity=0.460 Sum_probs=19.0
Q ss_pred hhHHHHHHHhhCchHHHHHHHHH
Q psy17102 308 RGEVETVLQRCKGDVLQAIEMMV 330 (412)
Q Consensus 308 Rs~LE~iLq~C~GDVVqAIE~~L 330 (412)
+...-..|+.|+|||-+||+.++
T Consensus 15 ~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 15 REEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHC
Confidence 34666789999999999999764
No 9
>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=72.12 E-value=7.4 Score=27.11 Aligned_cols=25 Identities=24% Similarity=0.550 Sum_probs=19.5
Q ss_pred CCchhHHHHHHHhhCchHHHHHHHH
Q psy17102 305 NRRRGEVETVLQRCKGDVLQAIEMM 329 (412)
Q Consensus 305 ~~kRs~LE~iLq~C~GDVVqAIE~~ 329 (412)
.-.+......|+.|+|||-+||+.+
T Consensus 13 Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 13 GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 3345577788999999999999864
No 10
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=51.81 E-value=19 Score=25.79 Aligned_cols=22 Identities=27% Similarity=0.644 Sum_probs=18.0
Q ss_pred hhHHHHHHHhhCchHHHHHHHH
Q psy17102 308 RGEVETVLQRCKGDVLQAIEMM 329 (412)
Q Consensus 308 Rs~LE~iLq~C~GDVVqAIE~~ 329 (412)
+..|+..|+.|+|++.+|-+.+
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHH
Confidence 5678999999999999997654
No 11
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=42.46 E-value=24 Score=31.50 Aligned_cols=33 Identities=18% Similarity=0.341 Sum_probs=22.0
Q ss_pred hhhHHhhcCCCchhHHHHHHHhhCchHHHHHHHH
Q psy17102 296 VDVLRRVFPNRRRGEVETVLQRCKGDVLQAIEMM 329 (412)
Q Consensus 296 ~DiL~RVFP~~kRs~LE~iLq~C~GDVVqAIE~~ 329 (412)
|++++.=+ +-.|..--..|..|+||+|.||-.+
T Consensus 80 I~lv~~q~-gvs~~~A~~AL~~~~gDl~~AI~~L 112 (115)
T PRK06369 80 IELVAEQT-GVSEEEARKALEEANGDLAEAILKL 112 (115)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHcCCcHHHHHHHH
Confidence 44444333 2234555667999999999999765
No 12
>KOG3450|consensus
Probab=35.94 E-value=36 Score=30.66 Aligned_cols=24 Identities=25% Similarity=0.458 Sum_probs=19.7
Q ss_pred hhHHHHHHHhhCchHHHHHHHHHh
Q psy17102 308 RGEVETVLQRCKGDVLQAIEMMVY 331 (412)
Q Consensus 308 Rs~LE~iLq~C~GDVVqAIE~~L~ 331 (412)
+.+.|..|+-.+||||.|++.+++
T Consensus 95 k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 95 KAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred HHHHHHHHHHhcccHHHHHHHHhc
Confidence 345667789999999999999874
No 13
>KOG4588|consensus
Probab=35.39 E-value=37 Score=34.11 Aligned_cols=32 Identities=25% Similarity=0.344 Sum_probs=29.8
Q ss_pred hcCCCchhHHHHHHHhhCchHHHHHHHHHhcC
Q psy17102 302 VFPNRRRGEVETVLQRCKGDVLQAIEMMVYSE 333 (412)
Q Consensus 302 VFP~~kRs~LE~iLq~C~GDVVqAIE~~L~s~ 333 (412)
.||+--+.++|.||+.--|+|-++|..+|...
T Consensus 1 Mfp~~Dye~ie~VlranlgavD~tid~llaM~ 32 (267)
T KOG4588|consen 1 MFPYDDYEDIEGVLRANLGAVDRTIDDLLAMF 32 (267)
T ss_pred CCCcchHHHHHHHHHHhcchHHHHHHHHHHhc
Confidence 49999999999999999999999999999755
No 14
>KOG3815|consensus
Probab=34.69 E-value=12 Score=37.56 Aligned_cols=57 Identities=37% Similarity=0.458 Sum_probs=49.9
Q ss_pred cCCCCCCCccccCCCCccccCCCCccCCCCCCCCCCchhHHHHHHhHHHHHHHhHhh
Q psy17102 52 RYQRTPKCARCRNHGVVSALKGHKRYCRWRDCVCAKCTLIAERQRVMAAQVALRRQQ 108 (412)
Q Consensus 52 ~~~R~P~CaRCRNHGv~s~lKGHKr~Cpfr~C~C~kC~Li~ERqRVmAaQvALRRqQ 108 (412)
......++..|++||......+|...+++.+|.+..+.+..++..++.+...+....
T Consensus 145 ~~~~~~~s~~~~~~~s~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (322)
T KOG3815|consen 145 NSRLTPKSGSSRNHGSVSLMKGLSPSEEDRDCASSNSLLPSERSRVDEADGSLSPSP 201 (322)
T ss_pred cccccccccCCCCCCcceeecccccCcccccccccCCcccccCCCccccccCcCCCC
Confidence 355567999999999999999999999999999999999999998888877655554
No 15
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=34.62 E-value=38 Score=30.48 Aligned_cols=22 Identities=32% Similarity=0.634 Sum_probs=16.8
Q ss_pred hhHHHHHHHhhCchHHHHHHHH
Q psy17102 308 RGEVETVLQRCKGDVLQAIEMM 329 (412)
Q Consensus 308 Rs~LE~iLq~C~GDVVqAIE~~ 329 (412)
|..--..|.-|+||+|.||-.+
T Consensus 93 ~e~A~~AL~~~~gDl~~AI~~L 114 (116)
T TIGR00264 93 KEEARRALEECGGDLAEAIMKL 114 (116)
T ss_pred HHHHHHHHHHcCCCHHHHHHHh
Confidence 4455567889999999998654
No 16
>KOG4317|consensus
Probab=34.11 E-value=22 Score=37.06 Aligned_cols=22 Identities=18% Similarity=0.239 Sum_probs=16.6
Q ss_pred chhhhhhhhcCCCCCCCccccC
Q psy17102 43 NCRFLTTVHRYQRTPKCARCRN 64 (412)
Q Consensus 43 ~~~~l~a~~~~~R~P~CaRCRN 64 (412)
+.+|-.++..-+|.|+|-||.-
T Consensus 6 ~~~~C~ic~vq~~~YtCPRCn~ 27 (383)
T KOG4317|consen 6 SFLACGICGVQKREYTCPRCNL 27 (383)
T ss_pred ceeeccccccccccccCCCCCc
Confidence 3455567888889999999953
No 17
>PLN03166 60S ribosomal protein L34; Provisional
Probab=30.78 E-value=51 Score=28.66 Aligned_cols=39 Identities=10% Similarity=0.318 Sum_probs=29.7
Q ss_pred hcCCCCCCCccccC--CCCcc----cc------CCCCc-cCCCCCCCCCCch
Q psy17102 51 HRYQRTPKCARCRN--HGVVS----AL------KGHKR-YCRWRDCVCAKCT 89 (412)
Q Consensus 51 ~~~~R~P~CaRCRN--HGv~s----~l------KGHKr-~Cpfr~C~C~kC~ 89 (412)
++-...|+|+.|.. |||.. .+ |..|+ .-.|.-+-|++|+
T Consensus 36 kK~~~~pkC~~cg~~L~Gi~~~Rp~~~~~~~lsK~~K~vsRaYGG~lc~~cv 87 (96)
T PLN03166 36 KKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYGGVLSGSAV 87 (96)
T ss_pred ccCCCCCcCCCCCCccCCccCCChhhhhhhhcccCcCccccCcCCcccHHHH
Confidence 67778899999988 89843 12 24444 5899999999997
No 18
>TIGR00927 2A1904 K+-dependent Na+/Ca+ exchanger.
Probab=29.13 E-value=17 Score=42.60 Aligned_cols=9 Identities=11% Similarity=0.206 Sum_probs=5.0
Q ss_pred CCccccCCC
Q psy17102 58 KCARCRNHG 66 (412)
Q Consensus 58 ~CaRCRNHG 66 (412)
+|-.||...
T Consensus 921 TIPDcrk~~ 929 (1096)
T TIGR00927 921 TVPDVRRQE 929 (1096)
T ss_pred ecCCCCccc
Confidence 566666543
No 19
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=28.89 E-value=86 Score=22.56 Aligned_cols=28 Identities=11% Similarity=0.031 Sum_probs=22.3
Q ss_pred chhHHHHHHHhhCchHHHHHHHHHhcCC
Q psy17102 307 RRGEVETVLQRCKGDVLQAIEMMVYSEQ 334 (412)
Q Consensus 307 kRs~LE~iLq~C~GDVVqAIE~~L~s~e 334 (412)
...+-..+|+.|++||-.||...+...+
T Consensus 14 ~~~~A~~~L~~~~wdle~Av~~y~~~~~ 41 (43)
T PF14555_consen 14 DEDVAIQYLEANNWDLEAAVNAYFDDGE 41 (43)
T ss_dssp SHHHHHHHHHHTTT-HHHHHHHHHHSS-
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence 5577788999999999999999986543
No 20
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=27.74 E-value=1.5e+02 Score=27.38 Aligned_cols=39 Identities=21% Similarity=0.592 Sum_probs=29.5
Q ss_pred hcCCCCCCCccccC--CCCccc--------cCCCCc-cCCCCCCCCCCch
Q psy17102 51 HRYQRTPKCARCRN--HGVVSA--------LKGHKR-YCRWRDCVCAKCT 89 (412)
Q Consensus 51 ~~~~R~P~CaRCRN--HGv~s~--------lKGHKr-~Cpfr~C~C~kC~ 89 (412)
++-...|+|+.|.. |||... -|..++ .-.|.-+-|++|+
T Consensus 36 KK~~~~pkC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CV 85 (135)
T PTZ00074 36 KKKSSGPKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCV 85 (135)
T ss_pred ccCCCCCCCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHH
Confidence 56677889999987 887432 344444 5899999999997
No 21
>KOG4215|consensus
Probab=25.72 E-value=14 Score=39.04 Aligned_cols=50 Identities=18% Similarity=0.276 Sum_probs=34.3
Q ss_pred CCchhhhhhhhc----CCCCCCCccccCCCCccccCCCCccCCCCC---------CCCCCchh
Q psy17102 41 LPNCRFLTTVHR----YQRTPKCARCRNHGVVSALKGHKRYCRWRD---------CVCAKCTL 90 (412)
Q Consensus 41 ~p~~~~l~a~~~----~~R~P~CaRCRNHGv~s~lKGHKr~Cpfr~---------C~C~kC~L 90 (412)
--+.+|.--.+| --..-.|.-|+.--..+-+|.|+..|+|.. |.|-.|.|
T Consensus 17 ~~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRf 79 (432)
T KOG4215|consen 17 GVAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRF 79 (432)
T ss_pred cccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhH
Confidence 344555543333 233458999998888899999999999953 45666654
No 22
>PLN03086 PRLI-interacting factor K; Provisional
Probab=25.58 E-value=16 Score=40.13 Aligned_cols=40 Identities=23% Similarity=0.632 Sum_probs=33.3
Q ss_pred CCCCccccCCCCccccCCCCccCCCCCCCCCC--chhHHHHH
Q psy17102 56 TPKCARCRNHGVVSALKGHKRYCRWRDCVCAK--CTLIAERQ 95 (412)
Q Consensus 56 ~P~CaRCRNHGv~s~lKGHKr~Cpfr~C~C~k--C~Li~ERq 95 (412)
.-+|..|...+-...+.-|..+|.|....|.+ |..+..|.
T Consensus 407 ~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~ 448 (567)
T PLN03086 407 TVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVE 448 (567)
T ss_pred eEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeecc
Confidence 34799999999999999999999999988864 77666443
No 23
>KOG4167|consensus
Probab=25.24 E-value=2e+02 Score=33.45 Aligned_cols=30 Identities=20% Similarity=0.385 Sum_probs=19.4
Q ss_pred CCCCCchhHHHHHHhHHHHHHHhHhhHHHH
Q psy17102 83 CVCAKCTLIAERQRVMAAQVALRRQQAQEE 112 (412)
Q Consensus 83 C~C~kC~Li~ERqRVmAaQvALRRqQaqEe 112 (412)
=.|..|.-+-++=+...|-....|+|+..+
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr~q~~~~ 822 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHRQQEEQQ 822 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 346666666677777777777667666444
No 24
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=24.74 E-value=60 Score=29.53 Aligned_cols=22 Identities=32% Similarity=0.456 Sum_probs=17.1
Q ss_pred hhHHHHHHHhhCchHHHHHHHH
Q psy17102 308 RGEVETVLQRCKGDVLQAIEMM 329 (412)
Q Consensus 308 Rs~LE~iLq~C~GDVVqAIE~~ 329 (412)
|...-..|.-|+||+++||=.+
T Consensus 99 reeA~kAL~e~~GDlaeAIm~L 120 (122)
T COG1308 99 REEAIKALEEAGGDLAEAIMKL 120 (122)
T ss_pred HHHHHHHHHHcCCcHHHHHHHh
Confidence 5555667889999999998554
No 25
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=23.77 E-value=52 Score=28.73 Aligned_cols=39 Identities=31% Similarity=0.629 Sum_probs=31.8
Q ss_pred hcCCCCCCCccccC--CCCccc--------cCCCCc-cCCCCCCCCCCch
Q psy17102 51 HRYQRTPKCARCRN--HGVVSA--------LKGHKR-YCRWRDCVCAKCT 89 (412)
Q Consensus 51 ~~~~R~P~CaRCRN--HGv~s~--------lKGHKr-~Cpfr~C~C~kC~ 89 (412)
++.+..++|+.|-. |||... -|-||+ .-+|.-|-|.+|+
T Consensus 29 kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~ 78 (93)
T COG2174 29 KKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCV 78 (93)
T ss_pred eccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHH
Confidence 66778899999987 887533 467777 5999999999997
No 26
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=22.50 E-value=27 Score=30.80 Aligned_cols=13 Identities=23% Similarity=0.578 Sum_probs=0.0
Q ss_pred hhccccCCCCCcc
Q psy17102 21 EGEEKKDGPTTPK 33 (412)
Q Consensus 21 ~~~~~~~~~~~~~ 33 (412)
++++..++-..|+
T Consensus 33 dddee~de~p~p~ 45 (101)
T PF09026_consen 33 DDDEEEDEVPVPE 45 (101)
T ss_dssp -------------
T ss_pred ccccccccccchh
Confidence 3333334333333
No 27
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=22.32 E-value=45 Score=27.93 Aligned_cols=18 Identities=28% Similarity=0.765 Sum_probs=15.1
Q ss_pred CccccCCCCccCCCCCCC
Q psy17102 67 VVSALKGHKRYCRWRDCV 84 (412)
Q Consensus 67 v~s~lKGHKr~Cpfr~C~ 84 (412)
.+.+++.|..+|||.+-+
T Consensus 47 ~~d~~~eHr~~CPwv~~~ 64 (91)
T PF08600_consen 47 PFDPLEEHREYCPWVNPS 64 (91)
T ss_pred CCCCcccccccCCccCCc
Confidence 467899999999998753
No 28
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 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 zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=21.94 E-value=45 Score=29.14 Aligned_cols=49 Identities=24% Similarity=0.448 Sum_probs=31.1
Q ss_pred ccCCCchhhhhhh--hcCCCCCCCccccCCCCcc-----------------------ccCCCCccCCCCCCCCC
Q psy17102 38 FSHLPNCRFLTTV--HRYQRTPKCARCRNHGVVS-----------------------ALKGHKRYCRWRDCVCA 86 (412)
Q Consensus 38 ~~~~p~~~~l~a~--~~~~R~P~CaRCRNHGv~s-----------------------~lKGHKr~Cpfr~C~C~ 86 (412)
...|-|..+++-+ =...-.-+|.-|...=++. -..||+..|+|+.-.|.
T Consensus 23 p~~lspl~cA~~GW~~~~~d~l~C~~C~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~H~~~CpWr~~~cp 96 (133)
T PF07967_consen 23 PPWLSPLECARRGWICVSKDMLKCESCGARLCVKLSDSPPDLDSEVYKKLVEKYSEQLVTGHKESCPWRNNSCP 96 (133)
T ss_pred CcccCHHHHHHcCCCcCCCCEEEeCCCCCEEEEeccccchHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCC
Confidence 4456666666531 1123445788787643333 12799999999999997
No 29
>PF10669 Phage_Gp23: Protein gp23 (Bacteriophage A118); InterPro: IPR018926 This entry is represented by the major tail subunit protein, Gp23 of Listeria phage A118 and prophage found in Bacilli. The function is currently unknown.
Probab=21.13 E-value=60 Score=29.05 Aligned_cols=21 Identities=29% Similarity=0.311 Sum_probs=12.5
Q ss_pred HHHHHhHHHHHHHhHhhHHHH
Q psy17102 92 AERQRVMAAQVALRRQQAQEE 112 (412)
Q Consensus 92 ~ERqRVmAaQvALRRqQaqEe 112 (412)
.+-+++|..|-.+--+|+|-.
T Consensus 78 ~~~q~Lm~rQN~mm~~qqqsi 98 (121)
T PF10669_consen 78 NKQQSLMNRQNNMMKQQQQSI 98 (121)
T ss_pred hHHHHHHHHHhHHHHHHHHhH
Confidence 355666666666665555543
Done!