Query 034565
Match_columns 91
No_of_seqs 85 out of 87
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 04:10:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034565.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034565hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3213 Transcription factor I 100.0 4.1E-38 8.9E-43 242.4 5.8 83 8-90 107-189 (238)
2 PF05018 DUF667: Protein of un 100.0 1.2E-37 2.7E-42 230.5 6.4 83 8-90 107-189 (190)
3 PRK00153 hypothetical protein; 61.1 30 0.00065 23.1 5.1 43 33-75 15-62 (104)
4 PF11606 AlcCBM31: Family 31 c 57.1 4.6 0.0001 28.1 0.6 28 7-36 12-39 (93)
5 PF02575 YbaB_DNA_bd: YbaB/Ebf 52.9 20 0.00042 22.9 3.0 42 34-75 8-54 (93)
6 PF09103 BRCA-2_OB1: BRCA2, ol 37.7 18 0.00039 25.3 1.1 19 20-38 33-51 (118)
7 COG2954 Uncharacterized protei 36.7 23 0.0005 26.7 1.6 65 1-89 1-71 (156)
8 PF03478 DUF295: Protein of un 36.7 31 0.00067 20.2 1.9 11 57-71 30-40 (54)
9 PF08381 BRX: Transcription fa 32.5 27 0.00059 22.3 1.2 23 55-77 20-42 (59)
10 PF12565 DUF3747: Protein of u 32.1 16 0.00034 28.0 0.1 22 19-48 147-168 (181)
11 PF14619 SnAC: Snf2-ATP coupli 31.7 13 0.00028 23.8 -0.4 16 69-84 17-32 (74)
12 TIGR00251 conserved hypothetic 30.6 1.2E+02 0.0027 20.2 4.2 38 37-82 50-87 (87)
13 PRK14626 hypothetical protein; 27.4 1.9E+02 0.0041 20.0 4.8 26 52-77 41-66 (110)
14 PRK14627 hypothetical protein; 25.8 79 0.0017 21.4 2.7 26 52-77 37-62 (100)
15 TIGR00103 DNA_YbaB_EbfC DNA-bi 25.4 1.8E+02 0.0039 19.5 4.4 42 33-74 17-63 (102)
16 PF08478 POTRA_1: POTRA domain 23.5 65 0.0014 18.8 1.7 33 25-57 24-56 (69)
17 PRK14625 hypothetical protein; 23.1 2.7E+02 0.0058 19.4 5.0 45 33-77 14-63 (109)
18 PRK14622 hypothetical protein; 22.2 1.1E+02 0.0023 20.9 2.8 26 52-77 37-62 (103)
19 PF10361 DUF2434: Protein of u 21.3 29 0.00064 28.4 -0.2 15 1-15 107-121 (296)
20 smart00135 LY Low-density lipo 20.7 45 0.00097 17.1 0.5 10 64-73 21-30 (43)
21 PF02033 RBFA: Ribosome-bindin 20.6 1.4E+02 0.003 19.5 3.0 23 48-70 27-49 (104)
22 KOG4699 Preprotein translocase 20.2 45 0.00097 25.6 0.6 12 25-36 127-138 (180)
23 COG5538 SEC66 Endoplasmic reti 20.2 45 0.00097 25.6 0.6 12 25-36 127-138 (180)
No 1
>KOG3213 consensus Transcription factor IIB [Transcription]
Probab=100.00 E-value=4.1e-38 Score=242.35 Aligned_cols=83 Identities=72% Similarity=1.206 Sum_probs=81.1
Q ss_pred ceeeeeeeeceeEeeccccCccchhhhhcHHHHHHHHhCcceeEEEEEEEecceeeEEeeeccccCCCcCCcccceeecc
Q 034565 8 TIQAVTRVKPYICTMPLRLDDGWNQIQLNLADFTRRAYGTNYVETLRVQVHANCRLRRIYFSDRLYSEEELPPEFKLYLP 87 (91)
Q Consensus 8 ~fq~~trVkp~~c~mPL~L~~GWN~i~~nL~d~t~~aygT~yvet~rv~I~ANCRlRRIYFsDrlYs~~ELP~e~kl~~p 87 (91)
|||++++|+|++|+|||.|++||||||+||+|||+++||++|.||++||||||||||||||+|++|+++|+|.+||++.+
T Consensus 107 n~~ke~~~kp~~~~mPl~m~~~W~~iqlnL~dft~~~~~~~y~etl~iql~AncriRriyf~~kl~~~~e~~~~frlm~r 186 (238)
T KOG3213|consen 107 NFQKETSVKPFICTMPLVMDAGWNQIQLNLADFTRRAYGTNYGETLSIQLHANCRIRRIYFADKLYSEAELPLEFRLMLR 186 (238)
T ss_pred ccchhhcccceEEecceEecCcceeEEeeHHHHHHHHhccceeeEEEEEEecceEEEEEEeccccCChhhCCCcceEccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred ccC
Q 034565 88 MQK 90 (91)
Q Consensus 88 ~~~ 90 (91)
.++
T Consensus 187 f~~ 189 (238)
T KOG3213|consen 187 FQV 189 (238)
T ss_pred ccC
Confidence 764
No 2
>PF05018 DUF667: Protein of unknown function (DUF667); InterPro: IPR007714 This family of proteins are highly conserved in eukaryotes. Some proteins in the family are annotated as transcription factors. However, there is currently no support for this in the literature.
Probab=100.00 E-value=1.2e-37 Score=230.51 Aligned_cols=83 Identities=70% Similarity=1.273 Sum_probs=81.4
Q ss_pred ceeeeeeeeceeEeeccccCccchhhhhcHHHHHHHHhCcceeEEEEEEEecceeeEEeeeccccCCCcCCcccceeecc
Q 034565 8 TIQAVTRVKPYICTMPLRLDDGWNQIQLNLADFTRRAYGTNYVETLRVQVHANCRLRRIYFSDRLYSEEELPPEFKLYLP 87 (91)
Q Consensus 8 ~fq~~trVkp~~c~mPL~L~~GWN~i~~nL~d~t~~aygT~yvet~rv~I~ANCRlRRIYFsDrlYs~~ELP~e~kl~~p 87 (91)
|||+.++++|++|+|||.|++|||+|+|||+++|+++|||+|+||++|+||||||||||||||++|++||||+||||++|
T Consensus 107 n~~k~~~~~~~~~~iPl~l~~~W~~l~idL~~~~~~~y~~~~~~sl~i~I~ancrlRrIyfsD~ly~~~elp~~~~l~~~ 186 (190)
T PF05018_consen 107 NFQKETKVTPFHCQIPLRLSPGWNNLQIDLADLTRRAYGTNYFESLRIQICANCRLRRIYFSDRLYSEDELPPEFKLYLP 186 (190)
T ss_pred eeeccccccccEEEcccccCCCcEEEEEEHHHHHHHHhccCceEEEEEEEecCEEEEEEEecCccCChhhCchhhEEccc
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccC
Q 034565 88 MQK 90 (91)
Q Consensus 88 ~~~ 90 (91)
.+.
T Consensus 187 ~~~ 189 (190)
T PF05018_consen 187 KQE 189 (190)
T ss_pred cCC
Confidence 875
No 3
>PRK00153 hypothetical protein; Validated
Probab=61.10 E-value=30 Score=23.14 Aligned_cols=43 Identities=9% Similarity=0.176 Sum_probs=32.4
Q ss_pred hhhcHHHHHHHHhCcceeEE-----EEEEEecceeeEEeeeccccCCC
Q 034565 33 IQLNLADFTRRAYGTNYVET-----LRVQVHANCRLRRIYFSDRLYSE 75 (91)
Q Consensus 33 i~~nL~d~t~~aygT~yvet-----~rv~I~ANCRlRRIYFsDrlYs~ 75 (91)
+|=.++++-.+.=...+-.+ ++|.|++++.|.+|-+.++++..
T Consensus 15 ~q~~~~~~q~~l~~~~~~~~s~~G~V~V~v~G~~~v~~i~Id~~ll~~ 62 (104)
T PRK00153 15 MQEKMQKMQEELAQMEVEGEAGGGLVKVTMTGKKEVKRVKIDPSLVDP 62 (104)
T ss_pred HHHHHHHHHHHHhccEEEEEECCCeEEEEEecCceEEEEEECHHHcCC
Confidence 45556666666555555443 89999999999999999999954
No 4
>PF11606 AlcCBM31: Family 31 carbohydrate binding protein; InterPro: IPR021016 Beta-1,3-xylan is a homopolymer of b-1,3-linked D-xylose and is a polysaccharide peculiar to marine algae. Beta-1,3-xylanase is a beta-1,3-xylan hydrolyzing enzyme [].; GO: 0033905 xylan endo-1,3-beta-xylosidase activity; PDB: 2COV_F.
Probab=57.09 E-value=4.6 Score=28.06 Aligned_cols=28 Identities=14% Similarity=0.299 Sum_probs=17.2
Q ss_pred cceeeeeeeeceeEeeccccCccchhhhhc
Q 034565 7 RTIQAVTRVKPYICTMPLRLDDGWNQIQLN 36 (91)
Q Consensus 7 ~~fq~~trVkp~~c~mPL~L~~GWN~i~~n 36 (91)
=+|.+.+-+.-|.... .-+.|||+|++|
T Consensus 12 ~~Yvsds~ievfH~d~--gWsAgwnY~CLd 39 (93)
T PF11606_consen 12 YNYVSDSEIEVFHKDN--GWSAGWNYLCLD 39 (93)
T ss_dssp EEEEETTEEEEEEE--------SSEEEEET
T ss_pred eeeecCceEEEEEecC--CccceeeEEEec
Confidence 3567777777776654 789999999987
No 5
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=52.87 E-value=20 Score=22.89 Aligned_cols=42 Identities=14% Similarity=0.107 Sum_probs=28.1
Q ss_pred hhcHHHHHHHHhCcceeEE-----EEEEEecceeeEEeeeccccCCC
Q 034565 34 QLNLADFTRRAYGTNYVET-----LRVQVHANCRLRRIYFSDRLYSE 75 (91)
Q Consensus 34 ~~nL~d~t~~aygT~yvet-----~rv~I~ANCRlRRIYFsDrlYs~ 75 (91)
+=.++++-.+.=...+-.+ ++|.|+++.++..|-|.++++.+
T Consensus 8 ~~~~~~~~~~l~~~~~~~~s~~g~V~V~v~g~g~v~~i~i~~~~~~~ 54 (93)
T PF02575_consen 8 QEKMEEAQEELAEIEVTGTSGDGLVTVTVNGNGEVVDIEIDPSALRP 54 (93)
T ss_dssp HHHHHHHHHHHHHSEEEEEETCCTEEEEEETTS-EEEEEE-GGGGCT
T ss_pred HHHHHHHHHHHhcCEEEEEECCCEEEEEEecCceEEEEEEehHhhcc
Confidence 3344555555433444433 89999999999999999999974
No 6
>PF09103 BRCA-2_OB1: BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; InterPro: IPR015187 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome []. ; GO: 0000724 double-strand break repair via homologous recombination; PDB: 1IYJ_D 1MIU_A.
Probab=37.67 E-value=18 Score=25.28 Aligned_cols=19 Identities=37% Similarity=0.642 Sum_probs=8.1
Q ss_pred EeeccccCccchhhhhcHH
Q 034565 20 CTMPLRLDDGWNQIQLNLA 38 (91)
Q Consensus 20 c~mPL~L~~GWN~i~~nL~ 38 (91)
...-+.|.+||-.|..-|.
T Consensus 33 ~~~~lelTDGWY~Ika~lD 51 (118)
T PF09103_consen 33 ESAILELTDGWYSIKAQLD 51 (118)
T ss_dssp ----EEEE-SS-EEEE---
T ss_pred ccCEEEEecCCEEEEEEeC
Confidence 4556788999998765444
No 7
>COG2954 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.71 E-value=23 Score=26.66 Aligned_cols=65 Identities=29% Similarity=0.554 Sum_probs=39.0
Q ss_pred CccccccceeeeeeeeceeEeeccccCccchhhhhcHHHHHHHHhCcc-e-----eEEEEEEEecceeeEEeeeccccCC
Q 034565 1 MAIDVDRTIQAVTRVKPYICTMPLRLDDGWNQIQLNLADFTRRAYGTN-Y-----VETLRVQVHANCRLRRIYFSDRLYS 74 (91)
Q Consensus 1 ~~~~~~~~fq~~trVkp~~c~mPL~L~~GWN~i~~nL~d~t~~aygT~-y-----vet~rv~I~ANCRlRRIYFsDrlYs 74 (91)
|||.+.|-| |.-+++|.+.. ...+|-.. | ..|+||+|+.+ |-|.+=+-++
T Consensus 1 Ma~EIERKF--------------LV~~d~WR~~a------~~~i~~~q~y~at~~~~tVRVRi~g~----~A~LTiK~~~ 56 (156)
T COG2954 1 MAIEIERKF--------------LVAGDGWRQLA------DGSIYRRQGYLATEQGRTVRVRIVGD----RAYLTIKGGA 56 (156)
T ss_pred Ccceeeeee--------------eecCccHHHhh------ccceeecceeeecCCCcEEEEEEecc----eEEEEEEccc
Confidence 788888877 44588999852 12223322 4 45899999984 5666655555
Q ss_pred CcCCcccceeecccc
Q 034565 75 EEELPPEFKLYLPMQ 89 (91)
Q Consensus 75 ~~ELP~e~kl~~p~~ 89 (91)
-.=--.||..-+|+.
T Consensus 57 ~~~~R~EfEY~iPl~ 71 (156)
T COG2954 57 SGLSRSEFEYEIPLA 71 (156)
T ss_pred cceeeeeeeeccccc
Confidence 444444555555543
No 8
>PF03478 DUF295: Protein of unknown function (DUF295); InterPro: IPR005174 This family of proteins are found in plants. The function of the proteins is unknown.
Probab=36.65 E-value=31 Score=20.25 Aligned_cols=11 Identities=55% Similarity=1.189 Sum_probs=8.7
Q ss_pred EecceeeEEeeeccc
Q 034565 57 VHANCRLRRIYFSDR 71 (91)
Q Consensus 57 I~ANCRlRRIYFsDr 71 (91)
+.+|| |||.|.
T Consensus 30 ~~~n~----IYf~~~ 40 (54)
T PF03478_consen 30 LKGNC----IYFLDD 40 (54)
T ss_pred ccCCE----EEEecC
Confidence 44676 999998
No 9
>PF08381 BRX: Transcription factor regulating root and shoot growth via Pin3; InterPro: IPR013591 This is a short domain, approximately 35 residues in length that is found near the C terminus in a number of plant proteins, being repeated in some members. It is found in Brevis radix-like proteins. These may act as a regulator of cell proliferation and elongation in the root []. It is also found in proteins annotated as involved in disease resistance and in the regulation of chromosome condensation, which also contain other domains with varied functions, such as TIR (IPR000157 from INTERPRO) and FYVE (IPR000306 from INTERPRO) respectively.
Probab=32.47 E-value=27 Score=22.30 Aligned_cols=23 Identities=26% Similarity=0.333 Sum_probs=17.4
Q ss_pred EEEecceeeEEeeeccccCCCcC
Q 034565 55 VQVHANCRLRRIYFSDRLYSEEE 77 (91)
Q Consensus 55 v~I~ANCRlRRIYFsDrlYs~~E 77 (91)
..-+..-.||||=||-+.|++.+
T Consensus 20 ~~p~G~~~LkRVRFSR~~F~e~q 42 (59)
T PF08381_consen 20 SLPDGGNDLKRVRFSRERFSEWQ 42 (59)
T ss_pred ECCCCCeeEEEEEEhhhhcCHHH
Confidence 33344667999999999998654
No 10
>PF12565 DUF3747: Protein of unknown function (DUF3747); InterPro: IPR022222 This family of proteins is found in bacteria. Proteins in this family are typically between 215 and 413 amino acids in length. There is a conserved DSNGYS sequence motif.
Probab=32.12 E-value=16 Score=27.97 Aligned_cols=22 Identities=32% Similarity=0.703 Sum_probs=17.9
Q ss_pred eEeeccccCccchhhhhcHHHHHHHHhCcc
Q 034565 19 ICTMPLRLDDGWNQIQLNLADFTRRAYGTN 48 (91)
Q Consensus 19 ~c~mPL~L~~GWN~i~~nL~d~t~~aygT~ 48 (91)
..-|.+.|++||. |+||+|+-+
T Consensus 147 ~GF~ki~LePGW~--------l~rRty~gk 168 (181)
T PF12565_consen 147 NGFLKINLEPGWR--------LTRRTYQGK 168 (181)
T ss_pred CceEEEEeCCCce--------eeehhcCCc
Confidence 3468899999995 899999764
No 11
>PF14619 SnAC: Snf2-ATP coupling, chromatin remodelling complex
Probab=31.68 E-value=13 Score=23.81 Aligned_cols=16 Identities=38% Similarity=0.601 Sum_probs=13.2
Q ss_pred ccccCCCcCCccccee
Q 034565 69 SDRLYSEEELPPEFKL 84 (91)
Q Consensus 69 sDrlYs~~ELP~e~kl 84 (91)
..||.+++|||.-|.-
T Consensus 17 p~RLm~e~ELPe~~~~ 32 (74)
T PF14619_consen 17 PSRLMEESELPEWYRE 32 (74)
T ss_pred CccccchhhchHHHHh
Confidence 3689999999998754
No 12
>TIGR00251 conserved hypothetical protein TIGR00251.
Probab=30.63 E-value=1.2e+02 Score=20.19 Aligned_cols=38 Identities=21% Similarity=0.452 Sum_probs=29.9
Q ss_pred HHHHHHHHhCcceeEEEEEEEecceeeEEeeeccccCCCcCCcccc
Q 034565 37 LADFTRRAYGTNYVETLRVQVHANCRLRRIYFSDRLYSEEELPPEF 82 (91)
Q Consensus 37 L~d~t~~aygT~yvet~rv~I~ANCRlRRIYFsDrlYs~~ELP~e~ 82 (91)
|-.|..+.||. .+.+.=++..|.+.|...+ .+++|+|+
T Consensus 50 li~~La~~l~v----~I~i~~G~tsR~K~v~I~~----~~~~~~~~ 87 (87)
T TIGR00251 50 LIKFFGEIFGV----DVEIVSGELSRQKTIKIIN----PRDIPPEI 87 (87)
T ss_pred HHHHHHHHhCc----eEEEEecCCCCceEEEEeC----cccccccC
Confidence 44788888997 6677778999999998766 56788763
No 13
>PRK14626 hypothetical protein; Provisional
Probab=27.41 E-value=1.9e+02 Score=19.95 Aligned_cols=26 Identities=15% Similarity=0.310 Sum_probs=22.6
Q ss_pred EEEEEEecceeeEEeeeccccCCCcC
Q 034565 52 TLRVQVHANCRLRRIYFSDRLYSEEE 77 (91)
Q Consensus 52 t~rv~I~ANCRlRRIYFsDrlYs~~E 77 (91)
.++|.++.+..|.+|-..+.+...++
T Consensus 41 ~VkV~~nG~~ev~~i~Id~~ll~~ed 66 (110)
T PRK14626 41 MVKVVSNGLGEIKDVEIDKSLLNEDE 66 (110)
T ss_pred EEEEEEECCccEEEEEECHHHcCccc
Confidence 38999999999999999999987543
No 14
>PRK14627 hypothetical protein; Provisional
Probab=25.83 E-value=79 Score=21.43 Aligned_cols=26 Identities=12% Similarity=0.322 Sum_probs=23.0
Q ss_pred EEEEEEecceeeEEeeeccccCCCcC
Q 034565 52 TLRVQVHANCRLRRIYFSDRLYSEEE 77 (91)
Q Consensus 52 t~rv~I~ANCRlRRIYFsDrlYs~~E 77 (91)
.++|.+..+..|.+|-+.+.+..+|+
T Consensus 37 ~VkV~~~G~~~v~~i~Idp~ll~~ed 62 (100)
T PRK14627 37 AITVKMNGHREVQSITISPEVVDPDD 62 (100)
T ss_pred eEEEEEEcCccEEEEEECHHHcCccc
Confidence 48999999999999999999997554
No 15
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=25.40 E-value=1.8e+02 Score=19.54 Aligned_cols=42 Identities=14% Similarity=0.215 Sum_probs=30.6
Q ss_pred hhhcHHHHHHHHhCcceeEE-----EEEEEecceeeEEeeeccccCC
Q 034565 33 IQLNLADFTRRAYGTNYVET-----LRVQVHANCRLRRIYFSDRLYS 74 (91)
Q Consensus 33 i~~nL~d~t~~aygT~yvet-----~rv~I~ANCRlRRIYFsDrlYs 74 (91)
+|-.++++-.+.=.+.+..+ ++|.+.++..+.+|-+.++++.
T Consensus 17 mQ~k~~~~q~eL~~~~v~g~sggGlV~V~~~G~~~v~~v~Id~~~l~ 63 (102)
T TIGR00103 17 MQEKMKKLQEEIAQFEVTGKSGAGLVTVTINGNLELKSIEIDPSLLE 63 (102)
T ss_pred HHHHHHHHHHHHhccEEEEEECCCEEEEEEEcCceEEEEEECHHHHh
Confidence 34455555555544444433 8999999999999999999997
No 16
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=23.50 E-value=65 Score=18.84 Aligned_cols=33 Identities=21% Similarity=0.338 Sum_probs=28.2
Q ss_pred ccCccchhhhhcHHHHHHHHhCcceeEEEEEEE
Q 034565 25 RLDDGWNQIQLNLADFTRRAYGTNYVETLRVQV 57 (91)
Q Consensus 25 ~L~~GWN~i~~nL~d~t~~aygT~yvet~rv~I 57 (91)
.+..|.|-+.+|+.++-.+.-.-.+++.+.|.-
T Consensus 24 ~~~~~~~~~~~~~~~~~~~l~~~p~V~~v~V~r 56 (69)
T PF08478_consen 24 GIQKGKNLFSLDLKKIEQRLEKLPWVKSVSVSR 56 (69)
T ss_dssp CTTSTTTCCCSHHHHHHHCCCCTTTEEEEEEEE
T ss_pred CcCCCCeEEEECHHHHHHHHHcCCCEEEEEEEE
Confidence 456689999999999999998899999888763
No 17
>PRK14625 hypothetical protein; Provisional
Probab=23.13 E-value=2.7e+02 Score=19.36 Aligned_cols=45 Identities=29% Similarity=0.318 Sum_probs=32.3
Q ss_pred hhhcHHHHHHHHhCcceeEE-----EEEEEecceeeEEeeeccccCCCcC
Q 034565 33 IQLNLADFTRRAYGTNYVET-----LRVQVHANCRLRRIYFSDRLYSEEE 77 (91)
Q Consensus 33 i~~nL~d~t~~aygT~yvet-----~rv~I~ANCRlRRIYFsDrlYs~~E 77 (91)
+|=.+++.-...-.+.+..+ ++|.+..|..+.+|-..+.+..+++
T Consensus 14 mQ~km~~~Q~el~~~~v~g~sggG~VkV~~~G~~~v~~I~Idp~ll~~eD 63 (109)
T PRK14625 14 MQQKLADAQARLAETTVEGTSGGGMVTVTLMGNGELVRVLMDESLVQPGE 63 (109)
T ss_pred HHHHHHHHHHHHhccEEEEEECCCeEEEEEecCceEEEEEECHHHcCCcc
Confidence 44455555555444555544 8999999999999999999887554
No 18
>PRK14622 hypothetical protein; Provisional
Probab=22.16 E-value=1.1e+02 Score=20.93 Aligned_cols=26 Identities=12% Similarity=0.431 Sum_probs=22.5
Q ss_pred EEEEEEecceeeEEeeeccccCCCcC
Q 034565 52 TLRVQVHANCRLRRIYFSDRLYSEEE 77 (91)
Q Consensus 52 t~rv~I~ANCRlRRIYFsDrlYs~~E 77 (91)
.++|.+..+..|.+|-..+.+..+++
T Consensus 37 ~VkV~~nG~~~v~~i~Idp~~l~~ed 62 (103)
T PRK14622 37 LVKVAMNGKCEVTRLTVDPKAVDPND 62 (103)
T ss_pred eEEEEEEcCceEEEEEECHHHcCccc
Confidence 48999999999999999999886443
No 19
>PF10361 DUF2434: Protein of unknown function (DUF2434); InterPro: IPR018830 This entry represents a family of proteins conserved in fungi. Their function is not known.
Probab=21.29 E-value=29 Score=28.41 Aligned_cols=15 Identities=40% Similarity=0.448 Sum_probs=11.3
Q ss_pred Cccccccceeeeeee
Q 034565 1 MAIDVDRTIQAVTRV 15 (91)
Q Consensus 1 ~~~~~~~~fq~~trV 15 (91)
|+|||||+|-..+.+
T Consensus 107 ~~IDVDR~yl~~~pi 121 (296)
T PF10361_consen 107 MSIDVDRYYLQGLPI 121 (296)
T ss_pred eeeeecHHhcccccH
Confidence 679999998765544
No 20
>smart00135 LY Low-density lipoprotein-receptor YWTD domain. Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Probab=20.71 E-value=45 Score=17.15 Aligned_cols=10 Identities=30% Similarity=0.604 Sum_probs=7.7
Q ss_pred EEeeeccccC
Q 034565 64 RRIYFSDRLY 73 (91)
Q Consensus 64 RRIYFsDrlY 73 (91)
+++||+|..-
T Consensus 21 ~~lYw~D~~~ 30 (43)
T smart00135 21 GRLYWTDWGL 30 (43)
T ss_pred CEEEEEeCCC
Confidence 5899999654
No 21
>PF02033 RBFA: Ribosome-binding factor A; InterPro: IPR000238 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosome-binding factor A [] (gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most bacteria. A putative chloroplastic form seems to exist in plants.; GO: 0006364 rRNA processing; PDB: 2R1C_A 2DYJ_B 2KZF_A 2E7G_A 1JOS_A 1KKG_A 1PA4_A.
Probab=20.58 E-value=1.4e+02 Score=19.45 Aligned_cols=23 Identities=22% Similarity=0.349 Sum_probs=20.9
Q ss_pred ceeEEEEEEEecceeeEEeeecc
Q 034565 48 NYVETLRVQVHANCRLRRIYFSD 70 (91)
Q Consensus 48 ~yvet~rv~I~ANCRlRRIYFsD 70 (91)
..++..+|.+.++++.-+||++-
T Consensus 27 ~~vtIt~V~ls~Dl~~a~Vy~~~ 49 (104)
T PF02033_consen 27 KLVTITRVELSPDLSHAKVYVSI 49 (104)
T ss_dssp HCEEEEEEEECTTSSEEEEEEEE
T ss_pred ceEEEEEEEECCCCCEEEEEEEE
Confidence 67899999999999999999963
No 22
>KOG4699 consensus Preprotein translocase subunit Sec66 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.18 E-value=45 Score=25.63 Aligned_cols=12 Identities=33% Similarity=0.664 Sum_probs=9.4
Q ss_pred ccCccchhhhhc
Q 034565 25 RLDDGWNQIQLN 36 (91)
Q Consensus 25 ~L~~GWN~i~~n 36 (91)
+|.|||+|.-|-
T Consensus 127 ~lqPGw~q~if~ 138 (180)
T KOG4699|consen 127 ILQPGWGQEIFK 138 (180)
T ss_pred hcCCchhHHHHH
Confidence 578999996653
No 23
>COG5538 SEC66 Endoplasmic reticulum translocation complex, subunit SEC66 [Cell motility and secretion]
Probab=20.18 E-value=45 Score=25.63 Aligned_cols=12 Identities=33% Similarity=0.664 Sum_probs=9.4
Q ss_pred ccCccchhhhhc
Q 034565 25 RLDDGWNQIQLN 36 (91)
Q Consensus 25 ~L~~GWN~i~~n 36 (91)
+|.|||+|.-|-
T Consensus 127 ~lqPGw~q~if~ 138 (180)
T COG5538 127 ILQPGWGQEIFK 138 (180)
T ss_pred hcCCchhHHHHH
Confidence 578999996653
Done!