Query psy12658
Match_columns 67
No_of_seqs 100 out of 455
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 16:11:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12658.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12658hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00155 histone H2A; Provisio 99.9 4.2E-27 9.2E-32 140.8 1.0 53 11-64 1-53 (58)
2 PLN00153 histone H2A; Provisio 99.9 4.2E-24 9.1E-29 143.8 1.1 53 11-64 1-53 (129)
3 PLN00157 histone H2A; Provisio 99.9 7E-24 1.5E-28 143.2 1.1 54 11-64 1-55 (132)
4 PTZ00017 histone H2A; Provisio 99.8 2.1E-22 4.5E-27 136.3 1.5 54 11-64 1-56 (134)
5 PLN00156 histone H2AX; Provisi 99.8 7.3E-22 1.6E-26 134.4 0.9 44 21-64 15-58 (139)
6 PLN00154 histone H2A; Provisio 99.8 7.6E-22 1.7E-26 133.9 0.6 60 5-64 3-68 (136)
7 PTZ00252 histone H2A; Provisio 99.8 2.6E-21 5.6E-26 131.1 0.4 41 24-64 13-54 (134)
8 KOG1756|consensus 99.8 1.4E-20 2.9E-25 127.3 0.0 54 11-64 1-56 (131)
9 cd00074 H2A Histone 2A; H2A is 99.8 5.5E-20 1.2E-24 121.1 0.2 47 19-65 4-50 (115)
10 smart00414 H2A Histone 2A. 99.7 3.1E-19 6.8E-24 116.1 -0.4 38 27-64 1-38 (106)
11 COG5262 HTA1 Histone H2A [Chro 99.6 1.2E-16 2.6E-21 107.9 0.4 44 21-64 12-55 (132)
12 KOG1757|consensus 99.6 2E-16 4.3E-21 106.5 -1.7 43 22-64 17-60 (131)
13 PF00125 Histone: Core histone 94.8 0.00096 2.1E-08 39.1 -3.9 36 29-64 2-38 (75)
14 PLN00035 histone H4; Provision 86.5 0.11 2.4E-06 34.0 -1.3 45 11-58 1-51 (103)
15 PF00808 CBFD_NFYB_HMF: Histon 66.7 0.46 9.9E-06 27.2 -2.6 28 35-62 2-29 (65)
16 COG5247 BUR6 Class 2 transcrip 61.8 1.9 4E-05 28.9 -0.7 27 35-61 23-49 (113)
17 COG5208 HAP5 CCAAT-binding fac 39.9 8.7 0.00019 29.0 -0.2 31 33-63 107-137 (286)
18 KOG1657|consensus 37.7 7.1 0.00015 28.6 -1.0 35 29-63 68-102 (236)
19 PF10931 DUF2735: Protein of u 35.5 14 0.00031 21.3 0.3 8 34-41 5-12 (51)
20 PF11850 DUF3370: Protein of u 31.3 17 0.00037 29.2 0.2 38 27-64 175-212 (441)
21 PF11705 RNA_pol_3_Rpc31: DNA- 30.0 28 0.00061 24.5 1.1 10 11-20 1-10 (233)
22 PF09377 SBDS_C: SBDS protein 28.5 13 0.00029 24.2 -0.7 21 31-51 18-38 (125)
23 PTZ00015 histone H4; Provision 20.1 29 0.00063 22.6 -0.4 22 36-58 31-52 (102)
No 1
>PLN00155 histone H2A; Provisional
Probab=99.93 E-value=4.2e-27 Score=140.77 Aligned_cols=53 Identities=47% Similarity=0.690 Sum_probs=47.3
Q ss_pred cccCCcccccccCCCccccccceeeeehhhhhhhccCCCccceeccCCceeeee
Q psy12658 11 LSTNGKEQIKAKKAPKSRSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGI 64 (67)
Q Consensus 11 msg~gk~~~k~k~k~~SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa 64 (67)
|||+|+++ +.+++++|+|++|||||||+||||+|++|+|++|||++|||||||
T Consensus 1 msg~g~g~-~~~~k~~srS~rAgL~FPVgri~r~Lr~g~~a~Rvga~apVYlAA 53 (58)
T PLN00155 1 MAGRGKGK-TSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAA 53 (58)
T ss_pred CCCCCCCC-ccccCccCcccccccccchHHHHHHHhcCChhhcccCCcHHHHHH
Confidence 88777643 344577999999999999999999999999999999999999998
No 2
>PLN00153 histone H2A; Provisional
Probab=99.88 E-value=4.2e-24 Score=143.80 Aligned_cols=53 Identities=47% Similarity=0.690 Sum_probs=47.7
Q ss_pred cccCCcccccccCCCccccccceeeeehhhhhhhccCCCccceeccCCceeeee
Q psy12658 11 LSTNGKEQIKAKKAPKSRSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGI 64 (67)
Q Consensus 11 msg~gk~~~k~k~k~~SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa 64 (67)
|||+|+++ +.+++.+|+|+|||||||||||||+|++|+|++|||++|||||||
T Consensus 1 m~g~~~~~-~~~~k~~srS~ragL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAA 53 (129)
T PLN00153 1 MAGRGKGK-TSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAA 53 (129)
T ss_pred CCCCCCCC-ccccCccCcccccCcccchHHHHHHHhcCchhhccCCCchHHHHH
Confidence 89887743 345578999999999999999999999999999999999999997
No 3
>PLN00157 histone H2A; Provisional
Probab=99.88 E-value=7e-24 Score=143.19 Aligned_cols=54 Identities=43% Similarity=0.613 Sum_probs=48.3
Q ss_pred cccCCccc-ccccCCCccccccceeeeehhhhhhhccCCCccceeccCCceeeee
Q psy12658 11 LSTNGKEQ-IKAKKAPKSRSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGI 64 (67)
Q Consensus 11 msg~gk~~-~k~k~k~~SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa 64 (67)
|||+|+.. ++.+++..|+|+|||||||||||||+|++|+|++||+++|||||||
T Consensus 1 ms~~g~~~~~~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAA 55 (132)
T PLN00157 1 MSGRGKRKGGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAA 55 (132)
T ss_pred CCCCCCCCCCccCcCCcCcccccCcccchHHHHHHHhcCchhhhcCCCcHhHHHH
Confidence 88877642 3456678999999999999999999999999999999999999997
No 4
>PTZ00017 histone H2A; Provisional
Probab=99.85 E-value=2.1e-22 Score=136.26 Aligned_cols=54 Identities=50% Similarity=0.708 Sum_probs=45.9
Q ss_pred cccCCccccc--ccCCCccccccceeeeehhhhhhhccCCCccceeccCCceeeee
Q psy12658 11 LSTNGKEQIK--AKKAPKSRSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGI 64 (67)
Q Consensus 11 msg~gk~~~k--~k~k~~SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa 64 (67)
|||+|+.+++ .++++.|+|+||||||||+||||+|++|+|++||+++|||||||
T Consensus 1 ~~~~~~~~~~~~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAA 56 (134)
T PTZ00017 1 KGGKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAA 56 (134)
T ss_pred CCCCCcCCCCcccCcCcccccccCCcccchHHHHHHHhccchhccccccchhhhHH
Confidence 4555543322 35678999999999999999999999999999999999999997
No 5
>PLN00156 histone H2AX; Provisional
Probab=99.83 E-value=7.3e-22 Score=134.39 Aligned_cols=44 Identities=48% Similarity=0.681 Sum_probs=42.0
Q ss_pred ccCCCccccccceeeeehhhhhhhccCCCccceeccCCceeeee
Q psy12658 21 AKKAPKSRSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGI 64 (67)
Q Consensus 21 ~k~k~~SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa 64 (67)
.++++.|+|+||||||||+||||+|++|+|++||+++|||||||
T Consensus 15 ~~~k~~srS~rAgL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAA 58 (139)
T PLN00156 15 KATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSA 58 (139)
T ss_pred cccCCcCcccccCcccchHHHHHHHhcCChhhccCCccHHHHHH
Confidence 46778999999999999999999999999999999999999997
No 6
>PLN00154 histone H2A; Provisional
Probab=99.83 E-value=7.6e-22 Score=133.95 Aligned_cols=60 Identities=40% Similarity=0.451 Sum_probs=48.9
Q ss_pred cccccccccCCccc-----ccccCCCccccccceeeeehhhhhhhccCCC-ccceeccCCceeeee
Q psy12658 5 KKAVHGLSTNGKEQ-----IKAKKAPKSRSQRANLVFPVSRCHRFLKKGR-YAERIGLGAWSINGI 64 (67)
Q Consensus 5 ~~~~~~msg~gk~~-----~k~k~k~~SrS~rAgLqFPVgRv~r~Lr~g~-ya~Rvga~ApVYlaa 64 (67)
.+....|+|..... .+.+++..|+|+||||||||+||||+|++|+ |++|||++|||||||
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~k~~srS~rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAA 68 (136)
T PLN00154 3 GKGGKGLLAAKTTAAAAKKDKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAA 68 (136)
T ss_pred CccccccccCCcCCcccccccCCcCCcCcccccCccCchHHHHHHHHhhhhhccccccchHHHHHH
Confidence 45567888743211 2245678999999999999999999999998 568999999999997
No 7
>PTZ00252 histone H2A; Provisional
Probab=99.81 E-value=2.6e-21 Score=131.14 Aligned_cols=41 Identities=39% Similarity=0.644 Sum_probs=38.8
Q ss_pred CCcc-ccccceeeeehhhhhhhccCCCccceeccCCceeeee
Q psy12658 24 APKS-RSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGI 64 (67)
Q Consensus 24 k~~S-rS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa 64 (67)
+..+ +|+|||||||||||||+|++|+|++|||++|||||||
T Consensus 13 ~~~~~rS~rAGL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAA 54 (134)
T PTZ00252 13 KSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAA 54 (134)
T ss_pred ccccccccccCccCchHHHHHHHHcCCcccccCCccHHHHHH
Confidence 4555 9999999999999999999999999999999999997
No 8
>KOG1756|consensus
Probab=99.78 E-value=1.4e-20 Score=127.30 Aligned_cols=54 Identities=52% Similarity=0.753 Sum_probs=46.8
Q ss_pred cccCCccc-cccc-CCCccccccceeeeehhhhhhhccCCCccceeccCCceeeee
Q psy12658 11 LSTNGKEQ-IKAK-KAPKSRSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGI 64 (67)
Q Consensus 11 msg~gk~~-~k~k-~k~~SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa 64 (67)
||++++++ ++.+ ++..|+|.+||||||||||||+||+|+|++||+++|||||||
T Consensus 1 ~s~~~k~gk~~~~~~~~~srs~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laa 56 (131)
T KOG1756|consen 1 MSGRGKGGKAKPRAKAKSSRSSRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAA 56 (131)
T ss_pred CCccCCCCcccchhhhhcchhhhcccccCHHHHHHHHHccchhhhccCCChHHHHH
Confidence 67777665 3333 567799999999999999999999999999999999999987
No 9
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=99.76 E-value=5.5e-20 Score=121.15 Aligned_cols=47 Identities=55% Similarity=0.753 Sum_probs=43.5
Q ss_pred ccccCCCccccccceeeeehhhhhhhccCCCccceeccCCceeeeee
Q psy12658 19 IKAKKAPKSRSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGIQ 65 (67)
Q Consensus 19 ~k~k~k~~SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa~ 65 (67)
+|.++++.|+|+||||||||+||||+|++++|++||+++|||||||-
T Consensus 4 ~k~~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAv 50 (115)
T cd00074 4 GKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAV 50 (115)
T ss_pred CccCcCccccccccCccCcHHHHHHHHHcCccccccccchHHHHHHH
Confidence 46667788999999999999999999999999999999999999973
No 10
>smart00414 H2A Histone 2A.
Probab=99.73 E-value=3.1e-19 Score=116.10 Aligned_cols=38 Identities=55% Similarity=0.820 Sum_probs=37.1
Q ss_pred cccccceeeeehhhhhhhccCCCccceeccCCceeeee
Q psy12658 27 SRSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGI 64 (67)
Q Consensus 27 SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa 64 (67)
|+|+|||||||||||||+|++++|++||+++|||||||
T Consensus 1 srS~ragL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaA 38 (106)
T smart00414 1 SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAA 38 (106)
T ss_pred CccccCCccCchHHHHHHHHcCccccccccccHHHHHH
Confidence 68999999999999999999999999999999999997
No 11
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=99.60 E-value=1.2e-16 Score=107.91 Aligned_cols=44 Identities=45% Similarity=0.693 Sum_probs=40.8
Q ss_pred ccCCCccccccceeeeehhhhhhhccCCCccceeccCCceeeee
Q psy12658 21 AKKAPKSRSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGI 64 (67)
Q Consensus 21 ~k~k~~SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa 64 (67)
.-+...|+|++|||+||||||+|+|++++|..|||++|||||+|
T Consensus 12 ~~r~~~s~sa~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~A 55 (132)
T COG5262 12 DARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAA 55 (132)
T ss_pred cchhccchhhhcCccccHHHHHHHHHcCccceeecCCcHHHHHH
Confidence 34556899999999999999999999999999999999999987
No 12
>KOG1757|consensus
Probab=99.56 E-value=2e-16 Score=106.48 Aligned_cols=43 Identities=42% Similarity=0.528 Sum_probs=39.9
Q ss_pred cCCCccccccceeeeehhhhhhhccCCCccc-eeccCCceeeee
Q psy12658 22 KKAPKSRSQRANLVFPVSRCHRFLKKGRYAE-RIGLGAWSINGI 64 (67)
Q Consensus 22 k~k~~SrS~rAgLqFPVgRv~r~Lr~g~ya~-Rvga~ApVYlaa 64 (67)
+.+..|+|+||||||||+||||+|+....+. |||+.|.||+||
T Consensus 17 ~~k~vs~s~raGlqFpVgRihr~LK~r~t~h~rVGataavy~aa 60 (131)
T KOG1757|consen 17 KAKAVSRSARAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAA 60 (131)
T ss_pred hhhhhhHHHhcccccchHHHHHHHHHhcccccccchHHHHHHHH
Confidence 4778999999999999999999999998885 999999999987
No 13
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=94.79 E-value=0.00096 Score=39.07 Aligned_cols=36 Identities=25% Similarity=0.196 Sum_probs=31.7
Q ss_pred cccceeeeehhhhhhhccCCCccc-eeccCCceeeee
Q psy12658 29 SQRANLVFPVSRCHRFLKKGRYAE-RIGLGAWSINGI 64 (67)
Q Consensus 29 S~rAgLqFPVgRv~r~Lr~g~ya~-Rvga~ApVYlaa 64 (67)
+....+.||+.||.+.+....+.+ ||++.|++||.+
T Consensus 2 ~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~ 38 (75)
T PF00125_consen 2 TRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQS 38 (75)
T ss_dssp HSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHH
T ss_pred cccccCceEEeeeeehhhcccccccccccccchhhhh
Confidence 456778999999999999999997 999999999864
No 14
>PLN00035 histone H4; Provisional
Probab=86.47 E-value=0.11 Score=34.05 Aligned_cols=45 Identities=22% Similarity=0.239 Sum_probs=28.3
Q ss_pred cccCCccccc-----ccC-CCccccccceeeeehhhhhhhccCCCccceeccCC
Q psy12658 11 LSTNGKEQIK-----AKK-APKSRSQRANLVFPVSRCHRFLKKGRYAERIGLGA 58 (67)
Q Consensus 11 msg~gk~~~k-----~k~-k~~SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~A 58 (67)
|||+||++.+ .|+ +...+-+-++ +|..-|.|+++.+- ++||+..+
T Consensus 1 m~~~~k~~~g~g~~g~kr~~k~~~d~i~~--ipk~~IrRLARr~G-vkRIS~~a 51 (103)
T PLN00035 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQG--ITKPAIRRLARRGG-VKRISGLI 51 (103)
T ss_pred CCCCCCCCCCCCCCcchHHHHHHHhhhcc--CCHHHHHHHHHHcC-cccchHHH
Confidence 7777765321 111 1122333344 88889999999877 88998764
No 15
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=66.70 E-value=0.46 Score=27.24 Aligned_cols=28 Identities=21% Similarity=0.297 Sum_probs=20.0
Q ss_pred eeehhhhhhhccCCCccceeccCCceee
Q psy12658 35 VFPVSRCHRFLKKGRYAERIGLGAWSIN 62 (67)
Q Consensus 35 qFPVgRv~r~Lr~g~ya~Rvga~ApVYl 62 (67)
.||+++|.+.++.-.-..+|+..|+..+
T Consensus 2 ~lP~a~vkri~k~~~~~~~vs~ea~~~i 29 (65)
T PF00808_consen 2 SLPLARVKRIMKSDPDVMRVSKEAVEAI 29 (65)
T ss_dssp SS-HHHHHHHHHHTSTTSEE-HHHHHHH
T ss_pred CCChHHHHHHhccCCCccchhHHHHHHH
Confidence 4899999999998745567887776554
No 16
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=61.80 E-value=1.9 Score=28.92 Aligned_cols=27 Identities=19% Similarity=0.401 Sum_probs=23.3
Q ss_pred eeehhhhhhhccCCCccceeccCCcee
Q psy12658 35 VFPVSRCHRFLKKGRYAERIGLGAWSI 61 (67)
Q Consensus 35 qFPVgRv~r~Lr~g~ya~Rvga~ApVY 61 (67)
.||++||.+.+....-...|++..||.
T Consensus 23 rFP~ar~KkIMQ~deDiGKV~q~tPVI 49 (113)
T COG5247 23 RFPIARLKKIMQLDEDIGKVGQSTPVI 49 (113)
T ss_pred cCCHHHHHHHHHhhhhhhhhhhcchHH
Confidence 499999999998877777889999985
No 17
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=39.86 E-value=8.7 Score=29.02 Aligned_cols=31 Identities=16% Similarity=0.217 Sum_probs=26.9
Q ss_pred eeeeehhhhhhhccCCCccceeccCCceeee
Q psy12658 33 NLVFPVSRCHRFLKKGRYAERIGLGAWSING 63 (67)
Q Consensus 33 gLqFPVgRv~r~Lr~g~ya~Rvga~ApVYla 63 (67)
.+..|..||.+.+|...=.+=|++.|||.+|
T Consensus 107 ~h~LPlARIkkvMKtdedVkMisaEaPvlFa 137 (286)
T COG5208 107 DHNLPLARIKKVMKTDEDVKMISAEAPVLFA 137 (286)
T ss_pred hccCcHHHHHHHHhcccchhheecccchHHH
Confidence 3568999999999988777899999999775
No 18
>KOG1657|consensus
Probab=37.68 E-value=7.1 Score=28.57 Aligned_cols=35 Identities=17% Similarity=0.197 Sum_probs=28.6
Q ss_pred cccceeeeehhhhhhhccCCCccceeccCCceeee
Q psy12658 29 SQRANLVFPVSRCHRFLKKGRYAERIGLGAWSING 63 (67)
Q Consensus 29 S~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYla 63 (67)
..-....||++||.+.+|...-..-|.+.|||.++
T Consensus 68 ~d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~a 102 (236)
T KOG1657|consen 68 LDFKNHILPLARIKKIMKSDEDVSMITAEAPVLFA 102 (236)
T ss_pred cchhhccCcHhhccccccccccccccchhHHHHHH
Confidence 33445789999999999998888899999998654
No 19
>PF10931 DUF2735: Protein of unknown function (DUF2735); InterPro: IPR021232 Some members in this family of proteins are annotated as glutamine synthetase translation inhibitor however this function can not be confirmed.
Probab=35.53 E-value=14 Score=21.32 Aligned_cols=8 Identities=38% Similarity=0.571 Sum_probs=5.9
Q ss_pred eeeehhhh
Q psy12658 34 LVFPVSRC 41 (67)
Q Consensus 34 LqFPVgRv 41 (67)
+||||+=-
T Consensus 5 YQFPvggr 12 (51)
T PF10931_consen 5 YQFPVGGR 12 (51)
T ss_pred eecccccc
Confidence 79999543
No 20
>PF11850 DUF3370: Protein of unknown function (DUF3370); InterPro: IPR021801 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 452 to 532 amino acids in length.
Probab=31.30 E-value=17 Score=29.22 Aligned_cols=38 Identities=16% Similarity=-0.014 Sum_probs=28.3
Q ss_pred cccccceeeeehhhhhhhccCCCccceeccCCceeeee
Q psy12658 27 SRSQRANLVFPVSRCHRFLKKGRYAERIGLGAWSINGI 64 (67)
Q Consensus 27 SrS~rAgLqFPVgRv~r~Lr~g~ya~Rvga~ApVYlaa 64 (67)
+..-=..|.+||.-+...|--++.--|+.++.|||+|.
T Consensus 175 ~~~mL~nlpIPv~gl~p~lNGRstllRl~S~Gpvy~As 212 (441)
T PF11850_consen 175 QSRMLLNLPIPVRGLDPPLNGRSTLLRLRSSGPVYMAS 212 (441)
T ss_pred CceEEEeccccCCCCCCCCCcceeEEEEecCCcchHHH
Confidence 33444578889988887774445556999999999984
No 21
>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=29.95 E-value=28 Score=24.53 Aligned_cols=10 Identities=20% Similarity=0.162 Sum_probs=6.4
Q ss_pred cccCCccccc
Q psy12658 11 LSTNGKEQIK 20 (67)
Q Consensus 11 msg~gk~~~k 20 (67)
|||+|+++++
T Consensus 1 MSgRGggrg~ 10 (233)
T PF11705_consen 1 MSGRGGGRGG 10 (233)
T ss_pred CCCCCCCCCC
Confidence 8877765443
No 22
>PF09377 SBDS_C: SBDS protein C-terminal domain; InterPro: IPR018978 This entry represents the C-terminal domain of proteins that are highly conserved in species ranging from archaea to vertebrates and plants []. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS, OMIM 260400) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterised by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism [, ]. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. Together with the EF-2-like GTPase RIA1 (EfI1), it triggers the GTP-dependent release of TIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating TIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition []. A number of uncharacterised hydrophilic proteins of about 30 kDa share regions of similarity. These include, Mouse protein 22A3. Saccharomyces cerevisiae chromosome XII hypothetical protein YLR022c. Caenorhabditis elegans hypothetical protein W06E11.4. Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ0592. ; GO: 0042254 ribosome biogenesis; PDB: 2KDO_A 2L9N_A 2WBM_B 1P9Q_C 1T95_A.
Probab=28.46 E-value=13 Score=24.19 Aligned_cols=21 Identities=24% Similarity=0.578 Sum_probs=16.6
Q ss_pred cceeeeehhhhhhhccCCCcc
Q psy12658 31 RANLVFPVSRCHRFLKKGRYA 51 (67)
Q Consensus 31 rAgLqFPVgRv~r~Lr~g~ya 51 (67)
+.++.+|+++|++.|++-+|+
T Consensus 18 ~T~rP~p~~~IE~Am~e~~~~ 38 (125)
T PF09377_consen 18 RTNRPYPPTRIEKAMKEAHFS 38 (125)
T ss_dssp TTTBTT-HHHHHHHHHHTTS-
T ss_pred CCCCCCCHHHHHHHHHhCCcc
Confidence 457889999999999988876
No 23
>PTZ00015 histone H4; Provisional
Probab=20.11 E-value=29 Score=22.57 Aligned_cols=22 Identities=18% Similarity=0.267 Sum_probs=15.4
Q ss_pred eehhhhhhhccCCCccceeccCC
Q psy12658 36 FPVSRCHRFLKKGRYAERIGLGA 58 (67)
Q Consensus 36 FPVgRv~r~Lr~g~ya~Rvga~A 58 (67)
+|..-|.|+++.+ =++||+.++
T Consensus 31 I~k~~IrRLarr~-GvkRIS~d~ 52 (102)
T PTZ00015 31 ITKGAIRRLARRG-GVKRISGDI 52 (102)
T ss_pred CCHHHHHHHHHHc-CCccchHHH
Confidence 6667788888875 357887654
Done!