Query 032478
Match_columns 140
No_of_seqs 142 out of 332
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 14:36:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032478.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032478hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3262 H/ACA small nucleolar 100.0 3.6E-56 7.8E-61 354.2 8.8 138 1-139 1-142 (215)
2 PRK13149 H/ACA RNA-protein com 99.9 4E-27 8.6E-32 162.3 8.2 72 50-125 1-73 (73)
3 COG3277 GAR1 RNA-binding prote 99.9 9.5E-27 2.1E-31 169.0 8.5 91 50-140 1-91 (98)
4 PF04410 Gar1: Gar1/Naf1 RNA b 99.9 6E-26 1.3E-30 174.5 7.2 97 41-140 14-113 (154)
5 KOG1596 Fibrillarin and relate 99.6 1.9E-15 4.1E-20 126.4 7.3 67 45-126 79-156 (317)
6 PTZ00146 fibrillarin; Provisio 99.6 1E-14 2.3E-19 123.0 8.1 67 44-121 52-135 (293)
7 KOG2236 Uncharacterized conser 98.7 1.2E-08 2.7E-13 90.7 4.2 78 49-126 207-287 (483)
8 PF01269 Fibrillarin: Fibrilla 98.2 4.8E-07 1E-11 74.6 0.4 63 57-126 3-82 (229)
9 COG1889 NOP1 Fibrillarin-like 97.6 2.5E-05 5.4E-10 64.3 2.2 62 57-125 8-84 (231)
10 PTZ00146 fibrillarin; Provisio 94.2 0.081 1.8E-06 45.2 4.7 16 52-67 64-80 (293)
11 PRK04266 fibrillarin; Provisio 93.7 0.056 1.2E-06 43.8 2.9 61 55-122 3-76 (226)
12 KOG3262 H/ACA small nucleolar 89.4 0.37 8.1E-06 39.4 3.1 12 115-126 107-118 (215)
13 PF05239 PRC: PRC-barrel domai 81.4 2.6 5.6E-05 27.6 3.7 33 76-108 10-45 (79)
14 PF02470 MCE: mce related prot 68.7 31 0.00068 22.8 7.2 60 71-135 14-75 (81)
15 COG3881 PRC-barrel domain cont 67.9 2.8 6E-05 33.6 1.2 34 76-109 8-43 (176)
16 TIGR02273 16S_RimM 16S rRNA pr 56.0 17 0.00037 27.8 3.6 33 75-107 100-132 (165)
17 KOG1596 Fibrillarin and relate 55.6 22 0.00047 30.7 4.5 18 51-68 89-107 (317)
18 PRK13828 rimM 16S rRNA-process 46.8 29 0.00062 26.6 3.6 33 75-107 85-117 (161)
19 PRK00122 rimM 16S rRNA-process 46.4 33 0.00071 26.4 3.9 31 76-106 106-136 (172)
20 PRK14592 rimM 16S rRNA-process 46.2 32 0.0007 26.4 3.8 32 76-107 98-129 (165)
21 PRK13829 rimM 16S rRNA-process 45.4 35 0.00075 26.3 3.9 33 76-109 95-127 (162)
22 PF08669 GCV_T_C: Glycine clea 40.1 1.2E+02 0.0025 20.5 6.3 54 69-125 28-82 (95)
23 PRK14591 rimM 16S rRNA-process 39.2 44 0.00096 25.8 3.6 32 76-107 106-137 (169)
24 PF09939 DUF2171: Uncharacteri 38.5 69 0.0015 21.9 4.0 28 77-110 5-32 (67)
25 PF14578 GTP_EFTU_D4: Elongati 38.2 1.2E+02 0.0026 21.3 5.4 72 46-124 3-81 (81)
26 COG0809 QueA S-adenosylmethion 37.4 83 0.0018 27.9 5.4 59 61-127 52-113 (348)
27 COG5436 Predicted integral mem 37.1 19 0.00041 28.9 1.3 31 71-101 86-127 (182)
28 PRK12442 translation initiatio 37.0 71 0.0015 23.0 4.1 21 89-112 11-31 (87)
29 PRK14593 rimM 16S rRNA-process 36.0 1E+02 0.0022 24.1 5.2 33 75-108 109-141 (184)
30 PF13953 PapC_C: PapC C-termin 32.7 49 0.0011 21.6 2.5 22 72-93 9-30 (68)
31 TIGR00008 infA translation ini 32.1 89 0.0019 21.3 3.8 22 88-112 8-29 (68)
32 COG0806 RimM RimM protein, req 31.2 68 0.0015 25.4 3.6 32 76-107 107-138 (174)
33 cd03698 eRF3_II_like eRF3_II_l 28.8 1E+02 0.0022 20.5 3.7 10 117-126 28-37 (83)
34 COG4353 Uncharacterized conser 26.9 19 0.0004 29.2 -0.3 60 64-124 16-91 (192)
35 PRK14594 rimM 16S rRNA-process 26.7 93 0.002 24.0 3.6 31 76-107 103-133 (166)
36 COG2850 Uncharacterized conser 25.2 42 0.00091 30.1 1.5 47 80-126 146-193 (383)
37 PRK03760 hypothetical protein; 24.3 1.8E+02 0.0038 21.4 4.5 52 73-126 59-116 (117)
38 KOG4745 Metalloproteinase inhi 24.3 64 0.0014 25.2 2.2 36 89-124 9-49 (141)
39 PHA02110 hypothetical protein 24.1 43 0.00093 24.2 1.1 10 79-88 7-16 (98)
40 PF10246 MRP-S35: Mitochondria 23.8 72 0.0016 23.7 2.3 25 43-67 18-42 (104)
41 PF13865 FoP_duplication: C-te 23.3 89 0.0019 21.2 2.6 9 45-53 37-45 (74)
42 PRK14590 rimM 16S rRNA-process 23.3 1.4E+02 0.003 23.2 4.0 31 76-106 103-134 (171)
43 PRK13922 rod shape-determining 23.3 3.9E+02 0.0084 21.7 6.8 64 49-124 205-269 (276)
44 PF01176 eIF-1a: Translation i 22.8 1.6E+02 0.0035 19.1 3.7 40 84-126 2-52 (65)
45 PLN03138 Protein TOC75; Provis 22.3 78 0.0017 30.9 2.8 13 116-128 221-233 (796)
46 cd04717 BAH_polybromo BAH, or 22.2 1.1E+02 0.0024 21.9 3.1 22 85-106 20-42 (121)
47 PF03459 TOBE: TOBE domain; I 20.9 2.1E+02 0.0045 17.7 3.8 11 115-125 46-56 (64)
48 KOG0105 Alternative splicing f 20.6 1.2E+02 0.0025 25.4 3.1 34 88-125 152-185 (241)
49 COG5489 Uncharacterized conser 20.5 1.6E+02 0.0036 21.9 3.6 58 50-109 3-76 (107)
No 1
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.6e-56 Score=354.19 Aligned_cols=138 Identities=67% Similarity=1.148 Sum_probs=117.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCC-CCCCCCCCCCceEEEceeeeeccCCeEEEeccCCCCCCC
Q 032478 1 MRPPRGGGGFRGGRDGGRGGRGGG---RFGGGGRGGGGRG-GFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYF 76 (140)
Q Consensus 1 ~~~~~~~~~~~g~~~~~~g~~~~g---~~~gg~~ggrgg~-~~g~~~~Gpp~~v~~lG~f~H~~eg~lV~k~t~~~VPyf 76 (140)
|+|||+++++++++ ++|++.+++ ++++++..||+++ .++.+|++||++|+|||+|+|+||+|||||+++++||||
T Consensus 1 ~~~~rgggg~~g~~-gfRgg~ggg~~gg~rgg~g~grgg~~~~~~~d~gpp~evvelg~flh~Cegd~Vck~~~~kIPyf 79 (215)
T KOG3262|consen 1 GGGPRGGGGGGGGG-GFRGGGGGGRGGGFRGGNGFGRGGRGGRGFQDQGPPEEVVELGKFLHMCEGDLVCKLTNKKIPYF 79 (215)
T ss_pred CCCCcCCCCCCCCC-CcccCCCCCCCCCcccCcccccCCcccCCcccCCCchhhhhhhhhhhhcCCceEEeeccccCCCC
Confidence 78899887776664 455544432 2333322224332 223579999999999999999999999999999999999
Q ss_pred CCceeeccceeeeeeeeeeCCCCcccEEEEecCCcccCCCCCCCEEEecCCCcccccCCCCCC
Q 032478 77 NAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQP 139 (140)
Q Consensus 77 na~Vy~enK~~IGKVdeIfGPi~~~yfsvKl~~gi~a~sfk~gdk~yI~p~kllPl~rFlp~p 139 (140)
|||||+|||+|||||||||+||||+||||||+++|+|+|||++|||||||+|||||+||||+|
T Consensus 80 NAPIylenk~qIGKVDEIfG~i~d~~fsIK~~dgv~assfk~g~k~fi~p~KllPl~RFLP~p 142 (215)
T KOG3262|consen 80 NAPIYLENKEQIGKVDEIFGPINDVHFSIKPSDGVQASSFKPGDKLFIDPDKLLPLDRFLPQP 142 (215)
T ss_pred CCceeecchhhhcchhhhcccccccEEEEecCCCceeecccCCCeEEecccccCcHhhcCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999997
No 2
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=99.94 E-value=4e-27 Score=162.26 Aligned_cols=72 Identities=29% Similarity=0.560 Sum_probs=68.7
Q ss_pred EEEceeeeecc-CCeEEEeccCCCCCCCCCceeeccceeeeeeeeeeCCCCcccEEEEecCCcccCCCCCCCEEEec
Q 032478 50 VVEVSSFLHAC-EGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYID 125 (140)
Q Consensus 50 v~~lG~f~H~~-eg~lV~k~t~~~VPyfna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl~~gi~a~sfk~gdk~yI~ 125 (140)
|.++|+|+|.| ++++|||+ +++|+||++||+||+++||||+|||||++++||+||+++++.++ +.||+|||.
T Consensus 1 Mk~~G~~~h~~~~g~lI~~~--~~~P~~n~~V~~~~~~~IGkV~dIfGPV~~pY~~Vk~~~~~~~~--~~g~k~yi~ 73 (73)
T PRK13149 1 MKRLGKVLHYAPKGKLIIRL--DKQPPIGSVVYDKKLKKIGKVVDVFGPVKEPYVLVKPDKKDPPE--LVGEKLYVR 73 (73)
T ss_pred CcEeEEEEEEcCCCCEEEEc--CCCCCCCCEeECCCCCEeEEEEEEECCCCCcEEEEEeCCCCCcc--ccCCEEEeC
Confidence 47899999999 89999999 78999999999999999999999999999999999999999997 889999984
No 3
>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=9.5e-27 Score=168.99 Aligned_cols=91 Identities=38% Similarity=0.647 Sum_probs=86.7
Q ss_pred EEEceeeeeccCCeEEEeccCCCCCCCCCceeeccceeeeeeeeeeCCCCcccEEEEecCCcccCCCCCCCEEEecCCCc
Q 032478 50 VVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKL 129 (140)
Q Consensus 50 v~~lG~f~H~~eg~lV~k~t~~~VPyfna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl~~gi~a~sfk~gdk~yI~p~kl 129 (140)
+++||+++|.|+..+||..++..+|++|++||+++.++||+|+|||||++++|+.||+++.+...++.++|++||.++++
T Consensus 1 m~~lG~vlh~~~~g~vi~~~~~~iP~l~~~V~~~~~k~IG~V~dVfGPv~~PY~~Vkp~~~~~~~~~~vg~~lYi~~~k~ 80 (98)
T COG3277 1 MKRLGKVLHVCGTGMVIVRDNDRIPPLNAPVYDANLKRIGKVVDVFGPVDEPYILVKPDDRDVKLESLVGDTLYIPPDKL 80 (98)
T ss_pred CccceeEEEecCCceEEEeCCCCCCCCCCeeEecCCCEEEEEEEEEccCCCCEEEEeccccccccccccceEEEeccccc
Confidence 46899999999999999998779999999999999999999999999999999999999999888899999999999999
Q ss_pred ccccCCCCCCC
Q 032478 130 LPLARFLPQPK 140 (140)
Q Consensus 130 lPl~rFlp~p~ 140 (140)
++.+||+|++|
T Consensus 81 ~~~~r~~~~~k 91 (98)
T COG3277 81 IRKKRKLPRKK 91 (98)
T ss_pred CcccccCcccc
Confidence 99999999875
No 4
>PF04410 Gar1: Gar1/Naf1 RNA binding region; InterPro: IPR007504 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. This entry represents Gar1 and Naf1. Naf1 is an RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex, disappearing during maturation of the complex being replaced by GAR1 to yield mature H/ACA snoRNPs complex. Naf1 reveals a striking structural homology with the core domain of archaeal Gar1 [].; GO: 0030515 snoRNA binding, 0031120 snRNA pseudouridine synthesis, 0042254 ribosome biogenesis; PDB: 2EY4_C 3MQK_C 2RFK_C 2HVY_B 3HAY_B 3U28_C 3UAI_C 2EQN_A 2V3M_F.
Probab=99.93 E-value=6e-26 Score=174.45 Aligned_cols=97 Identities=44% Similarity=0.774 Sum_probs=81.8
Q ss_pred CCCCCCCceEEEceeeeeccCCeEEEeccCC-CCCCCCCceeeccceeeeeeeeeeCCCCcccEEEE--ecCCcccCCCC
Q 032478 41 FRDEGPPAEVVEVSSFLHACEGDAVTKLTNE-KIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVK--MMEGIVATSYS 117 (140)
Q Consensus 41 ~~~~Gpp~~v~~lG~f~H~~eg~lV~k~t~~-~VPyfna~Vy~enK~~IGKVdeIfGPi~~~yfsvK--l~~gi~a~sfk 117 (140)
..+.+|+.++++||+++|+|++.+||+++.+ .||++|+.||+|+++.||+|+|||||++++||+|| +++.+.+.+++
T Consensus 14 ~~~~~~~~~i~~lG~v~~i~~~~vVvk~~~~~~vl~~~s~v~~edr~~iG~V~eiFGpV~~P~y~Vr~~~~~~~~~~~~~ 93 (154)
T PF04410_consen 14 DVEIGPPEEIKPLGTVSHIVENLVVVKSTPSKQVLDFGSVVCLEDRTKIGKVDEIFGPVNNPYYSVRFNSSEGIKAKSLK 93 (154)
T ss_dssp T-B--TTSSEEEEEEEEEEETTEEEEEE-SS-CEEBTT-EEEETTSBEEEEEEEEESESSS-EEEEE-SCHHHHHHHCCC
T ss_pred CcccCCCceEEEeeeEEEEeCCcEEEEeCCCCcCCCCCCEEECCCCCEeEEEeeEeCCCCceEEEEEeCCcccccccccc
Confidence 3467899999999999999999999999877 89999999999999999999999999999999999 88899999999
Q ss_pred CCCEEEecCCCcccccCCCCCCC
Q 032478 118 LGDKFYIDPSKLLPLARFLPQPK 140 (140)
Q Consensus 118 ~gdk~yI~p~kllPl~rFlp~p~ 140 (140)
++++||+++. |+++|||+|+
T Consensus 94 ~g~~vy~~~~---~~~~~~~~~~ 113 (154)
T PF04410_consen 94 VGDKVYYDPD---PTSRFLPEPL 113 (154)
T ss_dssp TTSEEEEECC----GGGG-----
T ss_pred ccceEEECCC---chheeccccc
Confidence 9999999999 9999998863
No 5
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=99.60 E-value=1.9e-15 Score=126.43 Aligned_cols=67 Identities=27% Similarity=0.506 Sum_probs=56.7
Q ss_pred CCCceEEEceeeeeccCCeEEEec------cCCCCCCCCCceeeccceeee----eeee-eeCCCCcccEEEEecCCccc
Q 032478 45 GPPAEVVEVSSFLHACEGDAVTKL------TNEKIPYFNAPIYLQNKTQIG----KVDE-IFGPINESYFSVKMMEGIVA 113 (140)
Q Consensus 45 Gpp~~v~~lG~f~H~~eg~lV~k~------t~~~VPyfna~Vy~enK~~IG----KVde-IfGPi~~~yfsvKl~~gi~a 113 (140)
+....++| +|++.+++|+|. |+|+|| +++||+|++..|. ||++ ||+| |++||+++|..
T Consensus 79 gG~~v~vE----PHRh~GVfi~rgkeDaLvTkNlvp--ge~vYgEkRisv~~~~~kvEyRVWnP-----frSKLAA~I~g 147 (317)
T KOG1596|consen 79 GGSKVLVE----PHRHAGVFIARGKEDALVTKNLVP--GESVYGEKRISVENEDGKVEYRVWNP-----FRSKLAAGILG 147 (317)
T ss_pred CCceEEec----cccccceEEEcCchhheeecccCC--cccccCceEEEeecCCCcEEEEEeCh-----HHHHHHHHhhc
Confidence 46677888 999999999996 889999 9999999999994 7887 9999 99999999887
Q ss_pred CCCCCCCEEEecC
Q 032478 114 TSYSLGDKFYIDP 126 (140)
Q Consensus 114 ~sfk~gdk~yI~p 126 (140)
. -|.|+|.|
T Consensus 148 G----vdnihikp 156 (317)
T KOG1596|consen 148 G----VDNIHIKP 156 (317)
T ss_pred C----ccceeecC
Confidence 6 44444443
No 6
>PTZ00146 fibrillarin; Provisional
Probab=99.55 E-value=1e-14 Score=123.00 Aligned_cols=67 Identities=24% Similarity=0.502 Sum_probs=54.8
Q ss_pred CCCCceEEEceeeeeccCCeEEEe------ccCCCCCCCCCceeeccceeee------eeee-eeCCCCcccEEEEecCC
Q 032478 44 EGPPAEVVEVSSFLHACEGDAVTK------LTNEKIPYFNAPIYLQNKTQIG------KVDE-IFGPINESYFSVKMMEG 110 (140)
Q Consensus 44 ~Gpp~~v~~lG~f~H~~eg~lV~k------~t~~~VPyfna~Vy~enK~~IG------KVde-IfGPi~~~yfsvKl~~g 110 (140)
.++.+.+++ +|.++++++++ +|.|++| +.+||.|++.++. ++++ +|+| |++||+++
T Consensus 52 ~~~~~~~~~----~~~~~gv~~~~~~~~~l~t~n~~p--g~~vygek~~~~~~~~~~~~~eyR~w~p-----~rSKlaa~ 120 (293)
T PTZ00146 52 GGPGKVIVV----PHRFPGVFIAKGKSDALVTKNMVP--GESVYGEKRISVEDAEGGEKIEYRVWNP-----FRSKLAAA 120 (293)
T ss_pred CCCCceEEe----eeeecCEEEeecCCceeEeecCCC--CcccccceEEeeccCCCCCcceeeeeCC-----cccHHHHH
Confidence 345677777 99999999998 3889999 9999999999998 5555 9999 99999987
Q ss_pred cccC----CCCCCCE
Q 032478 111 IVAT----SYSLGDK 121 (140)
Q Consensus 111 i~a~----sfk~gdk 121 (140)
|... .++++++
T Consensus 121 i~~g~~~l~IkpG~~ 135 (293)
T PTZ00146 121 IIGGVANIPIKPGSK 135 (293)
T ss_pred HHCCcceeccCCCCE
Confidence 7654 4556654
No 7
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.70 E-value=1.2e-08 Score=90.74 Aligned_cols=78 Identities=22% Similarity=0.484 Sum_probs=69.2
Q ss_pred eEEEceeeeeccCCeEEEeccCCCCC-CCCCceeeccceeeeeeeeeeCCCCcccEEEEecCCcccC--CCCCCCEEEec
Q 032478 49 EVVEVSSFLHACEGDAVTKLTNEKIP-YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVAT--SYSLGDKFYID 125 (140)
Q Consensus 49 ~v~~lG~f~H~~eg~lV~k~t~~~VP-yfna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl~~gi~a~--sfk~gdk~yI~ 125 (140)
++++||.++-+.+...|+++|.++.+ -+.+.+|+|+++.||+|+|||||+.++||.|+....-.+. .++.|+++|+-
T Consensus 207 ~~~plG~V~svv~~~VII~s~~~~~vlde~Svlf~edR~~lG~I~EiFGpV~~P~YvvRFnS~~e~~~~gi~ig~~vy~a 286 (483)
T KOG2236|consen 207 ELLPLGKVSSVVDQQVIIESTCNKEVLDEDSVLFLEDRTALGQIFEIFGPVKNPYYVVRFNSEEEISFLGICIGEKVYYA 286 (483)
T ss_pred ceechhHHHHHhhhceEEEeccCcccccccceEEeeccccchhhhhhhcccCCceEEEecCchhhhhhhccccCCeeEec
Confidence 68899999999999999999888655 6899999999999999999999999999999997654444 67889999998
Q ss_pred C
Q 032478 126 P 126 (140)
Q Consensus 126 p 126 (140)
|
T Consensus 287 p 287 (483)
T KOG2236|consen 287 P 287 (483)
T ss_pred C
Confidence 7
No 8
>PF01269 Fibrillarin: Fibrillarin; InterPro: IPR000692 Fibrillarin is a component of a nucleolar small nuclear ribonucleoprotein (SnRNP), functioning in vivo in ribosomal RNA processing [, ]. It is associated with U3, U8 and U13 small nuclear RNAs in mammals [] and is similar to the yeast NOP1 protein []. Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.; GO: 0003723 RNA binding, 0008168 methyltransferase activity, 0006364 rRNA processing, 0008033 tRNA processing; PDB: 3PLA_E 3ID6_C 3ID5_B 1NT2_A 3NVK_J 2NNW_B 3NVM_B 3NMU_J 1PRY_A 1G8A_A ....
Probab=98.15 E-value=4.8e-07 Score=74.59 Aligned_cols=63 Identities=21% Similarity=0.451 Sum_probs=44.0
Q ss_pred ee-ccCCeEEEec------cCCCCCCCCCceeeccceeeeee----ee-eeCCCCcccEEEEecCCcccC----CCCCCC
Q 032478 57 LH-ACEGDAVTKL------TNEKIPYFNAPIYLQNKTQIGKV----DE-IFGPINESYFSVKMMEGIVAT----SYSLGD 120 (140)
Q Consensus 57 ~H-~~eg~lV~k~------t~~~VPyfna~Vy~enK~~IGKV----de-IfGPi~~~yfsvKl~~gi~a~----sfk~gd 120 (140)
+| .++|.++++. |.|++| +.+||+|++..+... ++ +|+| |++||+++|..+ .+++|+
T Consensus 3 ~h~~~~gvy~~~~~~~~l~T~n~~p--g~~vYGEk~i~~~~~~~~~eYR~W~P-----~RSKLaAai~~Gl~~~~ik~gs 75 (229)
T PF01269_consen 3 PHERFEGVYIARGKGDALATKNLVP--GESVYGEKRISVEGEGKKVEYRVWNP-----FRSKLAAAILKGLENIPIKPGS 75 (229)
T ss_dssp EEESSTTEEEEETTSTEEEEE-SST--T--SSSSEEEEETTE---EEEEEE-T-----TT-HHHHHHHTT-S--S--TT-
T ss_pred ceeeecCEEEEecCCCeEEEecCCC--CCcccCceeEeecCCCCccceeecCc-----hhhHHHHHHHcCccccCCCCCC
Confidence 78 8899999983 889999 999999999998643 44 9999 999999977554 667776
Q ss_pred E-EEecC
Q 032478 121 K-FYIDP 126 (140)
Q Consensus 121 k-~yI~p 126 (140)
| ||+..
T Consensus 76 kVLYLGA 82 (229)
T PF01269_consen 76 KVLYLGA 82 (229)
T ss_dssp EEEEETT
T ss_pred EEEEecc
Confidence 5 46654
No 9
>COG1889 NOP1 Fibrillarin-like rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.65 E-value=2.5e-05 Score=64.29 Aligned_cols=62 Identities=19% Similarity=0.360 Sum_probs=48.9
Q ss_pred ee-ccCCeEEEec--------cCCCCCCCCCceeeccceeeeeeee-eeCCCCcccEEEEecCCcccC----CCCCCCEE
Q 032478 57 LH-ACEGDAVTKL--------TNEKIPYFNAPIYLQNKTQIGKVDE-IFGPINESYFSVKMMEGIVAT----SYSLGDKF 122 (140)
Q Consensus 57 ~H-~~eg~lV~k~--------t~~~VPyfna~Vy~enK~~IGKVde-IfGPi~~~yfsvKl~~gi~a~----sfk~gdk~ 122 (140)
+| .++++++++. |.|.+| +.+||+|+.+++.--++ +|+| +++||+++|..+ .+++++++
T Consensus 8 ~~~~~~gvy~~~~~dg~~~l~T~nl~p--g~~VYGE~ii~~~~~eYR~Wnp-----~RSKLaAaIl~Gl~~~pi~~g~~V 80 (231)
T COG1889 8 PHERFEGVYIVRFKDGSDRLATKNLVP--GERVYGERIIKVEGEEYREWNP-----RRSKLAAAILKGLKNFPIKEGSKV 80 (231)
T ss_pred cccccCCeEEEEcccccceeeeecCCC--CccccCceeEEecCcceeeeCc-----chhHHHHHHHcCcccCCcCCCCEE
Confidence 45 4677777764 678999 99999999999987655 9999 999999988865 55677763
Q ss_pred -Eec
Q 032478 123 -YID 125 (140)
Q Consensus 123 -yI~ 125 (140)
|..
T Consensus 81 LYLG 84 (231)
T COG1889 81 LYLG 84 (231)
T ss_pred EEee
Confidence 553
No 10
>PTZ00146 fibrillarin; Provisional
Probab=94.18 E-value=0.081 Score=45.16 Aligned_cols=16 Identities=25% Similarity=0.173 Sum_probs=7.1
Q ss_pred Eceeeeecc-CCeEEEe
Q 032478 52 EVSSFLHAC-EGDAVTK 67 (140)
Q Consensus 52 ~lG~f~H~~-eg~lV~k 67 (140)
.-|.|.... ++.|+-+
T Consensus 64 ~~gv~~~~~~~~~l~t~ 80 (293)
T PTZ00146 64 FPGVFIAKGKSDALVTK 80 (293)
T ss_pred ecCEEEeecCCceeEee
Confidence 335555442 2345444
No 11
>PRK04266 fibrillarin; Provisional
Probab=93.73 E-value=0.056 Score=43.80 Aligned_cols=61 Identities=16% Similarity=0.177 Sum_probs=45.7
Q ss_pred eeeeccCCeEEEec--------cCCCCCCCCCceeeccceeee-eeeeeeCCCCcccEEEEecCCccc----CCCCCCCE
Q 032478 55 SFLHACEGDAVTKL--------TNEKIPYFNAPIYLQNKTQIG-KVDEIFGPINESYFSVKMMEGIVA----TSYSLGDK 121 (140)
Q Consensus 55 ~f~H~~eg~lV~k~--------t~~~VPyfna~Vy~enK~~IG-KVdeIfGPi~~~yfsvKl~~gi~a----~sfk~gdk 121 (140)
+++|.+++.+++|. |.|++| +..+|++.-...- .-..+|-| ++.|+++.+.+ -.++++++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~g~~~~~~~~~~~~~~~~-----~r~~~~~~ll~~~~~l~i~~g~~ 75 (226)
T PRK04266 3 KKKEIFEGVYEVEFEDGSKRLATKNLVP--GKRVYGERLIKWEGVEYREWNP-----RRSKLAAAILKGLKNFPIKKGSK 75 (226)
T ss_pred ccccccCCEEEEecCCCcceEeeecCCC--CCCCCCceEEecCCcEEEEECC-----CccchHHHHHhhHhhCCCCCCCE
Confidence 46899999999994 778999 9999987765542 22358999 78899887776 45566765
Q ss_pred E
Q 032478 122 F 122 (140)
Q Consensus 122 ~ 122 (140)
+
T Consensus 76 V 76 (226)
T PRK04266 76 V 76 (226)
T ss_pred E
Confidence 3
No 12
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=89.43 E-value=0.37 Score=39.40 Aligned_cols=12 Identities=17% Similarity=0.052 Sum_probs=6.3
Q ss_pred CCCCCCEEEecC
Q 032478 115 SYSLGDKFYIDP 126 (140)
Q Consensus 115 sfk~gdk~yI~p 126 (140)
|+|+.|-|+...
T Consensus 107 sIK~~dgv~ass 118 (215)
T KOG3262|consen 107 SIKPSDGVQASS 118 (215)
T ss_pred EEecCCCceeec
Confidence 455566555443
No 13
>PF05239 PRC: PRC-barrel domain; InterPro: IPR007903 The PRC-barrel is an all beta barrel domain found in photosynthetic reaction centre subunit H of the purple bacteria. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the C terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain [].; PDB: 2QGG_A 3H9N_A 2WJN_H 2PRC_H 5PRC_H 2X5V_H 1DXR_H 1R2C_H 3G7F_H 1PRC_H ....
Probab=81.39 E-value=2.6 Score=27.64 Aligned_cols=33 Identities=21% Similarity=0.287 Sum_probs=24.9
Q ss_pred CCCceeeccceeeeeeeee-eCCCCcc--cEEEEec
Q 032478 76 FNAPIYLQNKTQIGKVDEI-FGPINES--YFSVKMM 108 (140)
Q Consensus 76 fna~Vy~enK~~IGKVdeI-fGPi~~~--yfsvKl~ 108 (140)
.+.+||+++-.++|+|++| +.+.+.- ++.++..
T Consensus 10 ~g~~V~~~~G~~iG~V~di~id~~~~~i~~i~v~~~ 45 (79)
T PF05239_consen 10 IGKEVIDRDGEKIGKVKDIVIDPKTGKIVGIVVSSG 45 (79)
T ss_dssp TTSEEEETTSCEEEEEEEEEEETTTTEEEEEEEEET
T ss_pred cCCEEEcCCCCEEEEEEEEEEeCCCCCEEEEEEcCC
Confidence 4789999999999999997 8874433 3555543
No 14
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=68.70 E-value=31 Score=22.83 Aligned_cols=60 Identities=17% Similarity=0.195 Sum_probs=42.3
Q ss_pred CCCCCCCCceeeccceeeeeeeee-e-CCCCcccEEEEecCCcccCCCCCCCEEEecCCCcccccCC
Q 032478 71 EKIPYFNAPIYLQNKTQIGKVDEI-F-GPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARF 135 (140)
Q Consensus 71 ~~VPyfna~Vy~enK~~IGKVdeI-f-GPi~~~yfsvKl~~gi~a~sfk~gdk~yI~p~kllPl~rF 135 (140)
...+ +++|.. +-.+||+|++| | -..+.+.+++++++... ..+..+.++-|....|| =+.|
T Consensus 14 GL~~--gs~V~~-~Gv~VG~V~~i~l~~~~~~v~v~~~i~~~~~-~~i~~~s~a~i~~~~ll-G~~~ 75 (81)
T PF02470_consen 14 GLSV--GSPVRY-RGVEVGKVTSIELDPDGNRVRVTLRIDPDYW-HRIPDDSRASIRSSGLL-GEKY 75 (81)
T ss_pred CCCC--cCEEEE-CCEEEEEEEEEEEcCCCCEEEEEEEEcCCcc-eecCCCcEEEEEeCCch-hheE
Confidence 3466 888888 68899999997 4 43456778888877662 24566888888877776 4433
No 15
>COG3881 PRC-barrel domain containing protein [General function prediction only]
Probab=67.85 E-value=2.8 Score=33.57 Aligned_cols=34 Identities=24% Similarity=0.440 Sum_probs=26.5
Q ss_pred CCCceeecc-ceeeeeeee-eeCCCCcccEEEEecC
Q 032478 76 FNAPIYLQN-KTQIGKVDE-IFGPINESYFSVKMME 109 (140)
Q Consensus 76 fna~Vy~en-K~~IGKVde-IfGPi~~~yfsvKl~~ 109 (140)
.+.|||.++ -.++|.|++ ||++.-+..--++.++
T Consensus 8 eG~pVys~~tg~~lg~V~Dvif~~~gdrvl~flvnk 43 (176)
T COG3881 8 EGAPVYSTKTGEKLGAVDDVIFNFSGDRVLGFLVNK 43 (176)
T ss_pred cCCceEEecccccccceeeEEEecCCCeEEEEEEec
Confidence 388999988 899999999 8999766655555443
No 16
>TIGR02273 16S_RimM 16S rRNA processing protein RimM. This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide.
Probab=56.02 E-value=17 Score=27.78 Aligned_cols=33 Identities=18% Similarity=0.271 Sum_probs=28.5
Q ss_pred CCCCceeeccceeeeeeeeeeCCCCcccEEEEe
Q 032478 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (140)
Q Consensus 75 yfna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl 107 (140)
.++..|++++...+|+|.+|+..-.+..+.||.
T Consensus 100 LiG~~V~d~~~~~lG~V~~v~~~~a~dll~V~~ 132 (165)
T TIGR02273 100 LIGLEVVTEEGEELGKVVEILETGANDVLVVRS 132 (165)
T ss_pred hCCcEEEcCCCcEEEEEEEEecCCCccEEEEEE
Confidence 357899999989999999999877777799986
No 17
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=55.58 E-value=22 Score=30.74 Aligned_cols=18 Identities=28% Similarity=0.235 Sum_probs=9.3
Q ss_pred EEceeeeecc-CCeEEEec
Q 032478 51 VEVSSFLHAC-EGDAVTKL 68 (140)
Q Consensus 51 ~~lG~f~H~~-eg~lV~k~ 68 (140)
-.-|.|.-+- |+-||.|.
T Consensus 89 Rh~GVfi~rgkeDaLvTkN 107 (317)
T KOG1596|consen 89 RHAGVFIARGKEDALVTKN 107 (317)
T ss_pred cccceEEEcCchhheeecc
Confidence 3455555443 45566653
No 18
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=46.79 E-value=29 Score=26.65 Aligned_cols=33 Identities=6% Similarity=0.055 Sum_probs=26.5
Q ss_pred CCCCceeeccceeeeeeeeeeCCCCcccEEEEe
Q 032478 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (140)
Q Consensus 75 yfna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl 107 (140)
.++..|++++...+|+|.+|+..-.+-.+.||.
T Consensus 85 LiG~~V~d~~g~~lG~V~~V~~~ga~dvlvV~~ 117 (161)
T PRK13828 85 LIGLAAVDTGGALLGRVKAVHNFGAGDILEIAP 117 (161)
T ss_pred ccCCEEEeCCCCEEEEEEEEccCCCccEEEEEE
Confidence 358899999999999999998855555578884
No 19
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=46.38 E-value=33 Score=26.41 Aligned_cols=31 Identities=16% Similarity=0.259 Sum_probs=26.4
Q ss_pred CCCceeeccceeeeeeeeeeCCCCcccEEEE
Q 032478 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVK 106 (140)
Q Consensus 76 fna~Vy~enK~~IGKVdeIfGPi~~~yfsvK 106 (140)
++..||+++...+|+|.+|+..-.+..+.||
T Consensus 106 iG~~V~d~~g~~lG~V~~v~~~~a~dll~I~ 136 (172)
T PRK00122 106 IGLEVVDEDGEELGKVTDILETGANDVLVVL 136 (172)
T ss_pred CCcEEEeCCCcEEEEEEEEccCCCceEEEEE
Confidence 5889999988999999999887666678886
No 20
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=46.19 E-value=32 Score=26.40 Aligned_cols=32 Identities=13% Similarity=0.264 Sum_probs=26.3
Q ss_pred CCCceeeccceeeeeeeeeeCCCCcccEEEEe
Q 032478 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (140)
Q Consensus 76 fna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl 107 (140)
.+..|++++...+|+|.+|+-.-.+-.+.|+.
T Consensus 98 iG~~V~~~~g~~lG~V~~v~~~ga~dvlvI~~ 129 (165)
T PRK14592 98 IGMEVKLEDNTIYGYIKKIYNFGSCDIIEISL 129 (165)
T ss_pred CCcEEEcCCCCEEEEEEEEccCCCccEEEEEE
Confidence 58899999999999999988765555688883
No 21
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=45.36 E-value=35 Score=26.26 Aligned_cols=33 Identities=12% Similarity=0.314 Sum_probs=26.2
Q ss_pred CCCceeeccceeeeeeeeeeCCCCcccEEEEecC
Q 032478 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKMME 109 (140)
Q Consensus 76 fna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl~~ 109 (140)
.+..|| ++...+|+|.+|+..-.+-.+.||..+
T Consensus 95 iG~~V~-~~g~~lG~V~~v~~~ga~dvlvV~~~~ 127 (162)
T PRK13829 95 RGLPVY-VDGEPLGEVVDVEDAGAQDLLVIRHVG 127 (162)
T ss_pred cCeEEE-ECCEeeEEEEEEecCCCceEEEEEeCC
Confidence 477899 888999999999886655567888644
No 22
>PF08669 GCV_T_C: Glycine cleavage T-protein C-terminal barrel domain; InterPro: IPR013977 This entry shows glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. ; PDB: 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 3GIR_A 1WOO_A 1WOS_A 1WOR_A ....
Probab=40.12 E-value=1.2e+02 Score=20.53 Aligned_cols=54 Identities=13% Similarity=0.313 Sum_probs=36.1
Q ss_pred cCCCCCCCCCceeeccceeeeeeee-eeCCCCcccEEEEecCCcccCCCCCCCEEEec
Q 032478 69 TNEKIPYFNAPIYLQNKTQIGKVDE-IFGPINESYFSVKMMEGIVATSYSLGDKFYID 125 (140)
Q Consensus 69 t~~~VPyfna~Vy~enK~~IGKVde-IfGPi~~~yfsvKl~~gi~a~sfk~gdk~yI~ 125 (140)
+.+..|.-+++||.++.++||.|-. .|.|..+-.+.+=+ |.....++++.|.|+
T Consensus 28 ~~~~~~~~g~~v~~~~g~~vG~vTS~~~sp~~~~~Iala~---v~~~~~~~g~~l~v~ 82 (95)
T PF08669_consen 28 DGDAPPRGGEPVYDEDGKPVGRVTSGAYSPTLGKNIALAY---VDREYAEPGTELEVE 82 (95)
T ss_dssp SSSS--STTCEEEETTTEEEEEEEEEEEETTTTEEEEEEE---EEGGGGSTTSEEEEE
T ss_pred CCccCCCCCCEEEECCCcEEeEEEEEeECCCCCceEEEEE---ECHHHcCCCCEEEEE
Confidence 3345778899999999999999998 78887554332221 113345668888886
No 23
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=39.18 E-value=44 Score=25.80 Aligned_cols=32 Identities=16% Similarity=0.148 Sum_probs=25.8
Q ss_pred CCCceeeccceeeeeeeeeeCCCCcccEEEEe
Q 032478 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (140)
Q Consensus 76 fna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl 107 (140)
++..||+++...+|+|.+|+-.-.+..+.||.
T Consensus 106 iG~~V~d~~g~~lG~V~~v~~~ga~dll~I~~ 137 (169)
T PRK14591 106 IGCSVKNINNDSFGVVVDIIETGANEVLVCKE 137 (169)
T ss_pred cCcEEEeCCCCEEEEEEEEeecCCceEEEEEc
Confidence 57899999999999999988766555567874
No 24
>PF09939 DUF2171: Uncharacterized protein conserved in bacteria (DUF2171); InterPro: IPR018684 This family of various hypothetical prokaryotic proteins has no known function.
Probab=38.55 E-value=69 Score=21.88 Aligned_cols=28 Identities=18% Similarity=0.400 Sum_probs=23.9
Q ss_pred CCceeeccceeeeeeeeeeCCCCcccEEEEecCC
Q 032478 77 NAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEG 110 (140)
Q Consensus 77 na~Vy~enK~~IGKVdeIfGPi~~~yfsvKl~~g 110 (140)
...|+..+-..||+||.+=|. +|||...
T Consensus 5 hmeVi~sdG~~vGtVDhveGd------~IKLtk~ 32 (67)
T PF09939_consen 5 HMEVIGSDGVHVGTVDHVEGD------RIKLTKD 32 (67)
T ss_pred CCEEEeCCCCEEEEEeeEeCC------EEEEecc
Confidence 457899999999999999897 8998653
No 25
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=38.21 E-value=1.2e+02 Score=21.28 Aligned_cols=72 Identities=15% Similarity=0.220 Sum_probs=36.9
Q ss_pred CCceEEEceeeeeccCCeEEEeccCCCCCCCCCceeeccceeeeeeeeeeCCCCcc-------cEEEEecCCcccCCCCC
Q 032478 46 PPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINES-------YFSVKMMEGIVATSYSL 118 (140)
Q Consensus 46 pp~~v~~lG~f~H~~eg~lV~k~t~~~VPyfna~Vy~enK~~IGKVdeIfGPi~~~-------yfsvKl~~gi~a~sfk~ 118 (140)
||..+.-|=.|.....+.+|.+. ..-+-+.+.++ +-..||+|..|=-.-+++ =+.++++..+ .+++
T Consensus 3 ~p~ki~Ilp~~vFr~~~~IvG~V-~~G~ik~G~~l---~G~~iG~I~sIe~~~k~v~~A~~G~eVai~Ieg~~---~i~e 75 (81)
T PF14578_consen 3 RPGKIRILPVCVFRQSDAIVGEV-LEGIIKPGYPL---DGRKIGRIKSIEDNGKNVDEAKKGDEVAISIEGPT---QIKE 75 (81)
T ss_dssp -SEEEEEEEEEEECTCCEEEEEE-EEEEEETT-EE---CSSCEEEEEEEEETTEEESEEETT-EEEEEEET-----TB-T
T ss_pred CceEEEECCcCEEecCCeEEEEE-eeeEEeCCCcc---CCEEEEEEEEeEECCcCccccCCCCEEEEEEeCCc---cCCC
Confidence 56776666555544445444422 11233447777 333488877653332222 2677776643 7889
Q ss_pred CCEEEe
Q 032478 119 GDKFYI 124 (140)
Q Consensus 119 gdk~yI 124 (140)
||.||+
T Consensus 76 GDiLyV 81 (81)
T PF14578_consen 76 GDILYV 81 (81)
T ss_dssp T-EEEE
T ss_pred CCEEeC
Confidence 999996
No 26
>COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis]
Probab=37.43 E-value=83 Score=27.89 Aligned_cols=59 Identities=22% Similarity=0.256 Sum_probs=37.1
Q ss_pred CCeEEEeccCCCCCCCCCceeeccceeeeeeeee---eCCCCcccEEEEecCCcccCCCCCCCEEEecCC
Q 032478 61 EGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEI---FGPINESYFSVKMMEGIVATSYSLGDKFYIDPS 127 (140)
Q Consensus 61 eg~lV~k~t~~~VPyfna~Vy~enK~~IGKVdeI---fGPi~~~yfsvKl~~gi~a~sfk~gdk~yI~p~ 127 (140)
+|+++|-....-+| |.+|..+...-++|+=. +=..+..-..+|++. .+|+||+||.+.+
T Consensus 52 ~GD~LVfNdTrVIp---ARl~G~k~~~g~~vEvll~~~~~~~~w~al~~~~k-----r~k~G~~i~f~~~ 113 (348)
T COG0809 52 PGDLLVFNDTRVIP---ARLFGRKHESGGKVEVLLERRLDDNRWLALIKPSK-----RLKAGDEIYFGDG 113 (348)
T ss_pred CCCEEEEecCeeec---hheeeccCCCCceEEEEEEeecCCCcEEEEecccc-----CCCCCCEEEeCCC
Confidence 36666655333344 88888776666677632 222344456777654 6677899999875
No 27
>COG5436 Predicted integral membrane protein [Function unknown]
Probab=37.14 E-value=19 Score=28.93 Aligned_cols=31 Identities=32% Similarity=0.625 Sum_probs=21.8
Q ss_pred CCCCCCCCceeeccceee----------eeeee-eeCCCCcc
Q 032478 71 EKIPYFNAPIYLQNKTQI----------GKVDE-IFGPINES 101 (140)
Q Consensus 71 ~~VPyfna~Vy~enK~~I----------GKVde-IfGPi~~~ 101 (140)
-+|||..-+||+.|-..+ ||.|- |.-|+...
T Consensus 86 ~nvpyWSvsiyds~~nn~fS~ND~ta~~gkLDlVvatPiqmi 127 (182)
T COG5436 86 GNVPYWSVSIYDSNGNNFFSINDRTAKGGKLDLVVATPIQMI 127 (182)
T ss_pred CCCceEEEEEEcCCCCceEEeccccccCCccceEEecchhhe
Confidence 489999999999887765 45564 45555433
No 28
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=36.98 E-value=71 Score=22.97 Aligned_cols=21 Identities=38% Similarity=0.623 Sum_probs=12.7
Q ss_pred eeeeeeeCCCCcccEEEEecCCcc
Q 032478 89 GKVDEIFGPINESYFSVKMMEGIV 112 (140)
Q Consensus 89 GKVdeIfGPi~~~yfsvKl~~gi~ 112 (140)
|+|.|++.- -.|+|+|+++..
T Consensus 11 G~V~e~Lp~---~~frV~LenG~~ 31 (87)
T PRK12442 11 GIVDEVLPD---SRFRVTLENGVE 31 (87)
T ss_pred EEEEEECCC---CEEEEEeCCCCE
Confidence 667776552 357777765543
No 29
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=35.95 E-value=1e+02 Score=24.12 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=24.7
Q ss_pred CCCCceeeccceeeeeeeeeeCCCCcccEEEEec
Q 032478 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMM 108 (140)
Q Consensus 75 yfna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl~ 108 (140)
.++..||++ ...+|+|.+|+..-.+-.+.|+..
T Consensus 109 LiGl~V~~~-g~~lG~V~~v~~~ga~dvlvV~~~ 141 (184)
T PRK14593 109 LVGLSVVEE-NEILGKVIEIQRISQTDYFMVETT 141 (184)
T ss_pred ccCcEEEEC-CEEeEEEEEEccCCCceEEEEEec
Confidence 357889986 578999999988555555788753
No 30
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=32.70 E-value=49 Score=21.65 Aligned_cols=22 Identities=27% Similarity=0.309 Sum_probs=15.3
Q ss_pred CCCCCCCceeeccceeeeeeee
Q 032478 72 KIPYFNAPIYLQNKTQIGKVDE 93 (140)
Q Consensus 72 ~VPyfna~Vy~enK~~IGKVde 93 (140)
+.+-|+|.|++++...+|-|.+
T Consensus 9 ~~lPfGA~v~~~~g~~~g~Vg~ 30 (68)
T PF13953_consen 9 KPLPFGASVSDEDGNNIGIVGQ 30 (68)
T ss_dssp EE--TT-EEEETTSSEEEEB-G
T ss_pred CcCCCCcEEEcCCCCEEEEEcC
Confidence 3345999999999999988875
No 31
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=32.14 E-value=89 Score=21.29 Aligned_cols=22 Identities=32% Similarity=0.430 Sum_probs=15.5
Q ss_pred eeeeeeeeCCCCcccEEEEecCCcc
Q 032478 88 IGKVDEIFGPINESYFSVKMMEGIV 112 (140)
Q Consensus 88 IGKVdeIfGPi~~~yfsvKl~~gi~ 112 (140)
.|+|.|.++- -+|+|+|+++..
T Consensus 8 ~G~V~e~L~~---~~f~V~l~ng~~ 29 (68)
T TIGR00008 8 EGKVTESLPN---AMFRVELENGHE 29 (68)
T ss_pred EEEEEEECCC---CEEEEEECCCCE
Confidence 3778887663 468888887654
No 32
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=31.20 E-value=68 Score=25.41 Aligned_cols=32 Identities=22% Similarity=0.302 Sum_probs=27.6
Q ss_pred CCCceeeccceeeeeeeeeeCCCCcccEEEEe
Q 032478 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (140)
Q Consensus 76 fna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl 107 (140)
.+..||+++-..+|+|.+|+-+-++-.+-||.
T Consensus 107 iG~~V~~~~g~~lG~V~~i~~~Ga~Dvl~V~~ 138 (174)
T COG0806 107 IGLEVVTEDGELLGKVTEILETGANDVLVVKA 138 (174)
T ss_pred cCcEEEcCCCcEEEEEEEEeeCCCccEEEEEe
Confidence 47889999999999999999988766678886
No 33
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=28.76 E-value=1e+02 Score=20.54 Aligned_cols=10 Identities=30% Similarity=0.640 Sum_probs=4.5
Q ss_pred CCCCEEEecC
Q 032478 117 SLGDKFYIDP 126 (140)
Q Consensus 117 k~gdk~yI~p 126 (140)
++||+++|-|
T Consensus 28 ~~Gd~v~i~P 37 (83)
T cd03698 28 QKGDTLLVMP 37 (83)
T ss_pred eCCCEEEEeC
Confidence 3344444444
No 34
>COG4353 Uncharacterized conserved protein [Function unknown]
Probab=26.85 E-value=19 Score=29.15 Aligned_cols=60 Identities=27% Similarity=0.440 Sum_probs=33.5
Q ss_pred EEEeccCCCCC-CCCCceeeccceeeeeee------------eeeCCCCcccEEEEecCC---cccCCCCCCCEEEe
Q 032478 64 AVTKLTNEKIP-YFNAPIYLQNKTQIGKVD------------EIFGPINESYFSVKMMEG---IVATSYSLGDKFYI 124 (140)
Q Consensus 64 lV~k~t~~~VP-yfna~Vy~enK~~IGKVd------------eIfGPi~~~yfsvKl~~g---i~a~sfk~gdk~yI 124 (140)
+++|+.....- -||-.+++||-.+++++. |||| ++.+++-+-+... +.+..+.+++++|+
T Consensus 16 l~vk~~qgrfkeef~~dl~Le~ge~l~~l~vF~GR~yytPW~Eifn-v~Pv~~gs~~E~~l~~~l~~~lspg~~lfV 91 (192)
T COG4353 16 LVVKNLQGRFKEEFNFDLLLENGEQLGKLKVFKGRDYYTPWLEIFN-VNPVFRGSELEVKLYKVLYNFLSPGGKLFV 91 (192)
T ss_pred eeeeccccccceeeeeEEeecCCceeeEEEEEcCCccccchhhccc-cCCccCCCHHHHHHHHHHHHhcCCCCceEE
Confidence 45554322222 467788888888888766 3443 3333333322221 22346788999987
No 35
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=26.65 E-value=93 Score=23.97 Aligned_cols=31 Identities=23% Similarity=0.352 Sum_probs=25.2
Q ss_pred CCCceeeccceeeeeeeeeeCCCCcccEEEEe
Q 032478 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (140)
Q Consensus 76 fna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl 107 (140)
.|..|+++ ...+|+|.+|+-.-.+..+.||.
T Consensus 103 iG~~V~~~-g~~lG~V~~v~~~ga~dll~V~~ 133 (166)
T PRK14594 103 IGYAIVND-GKELGEVVSFFECLNSVLLEVKV 133 (166)
T ss_pred cCeEEEEC-CEEEEEEEEEeeCCCcEEEEEEe
Confidence 47789986 78899999998876666688884
No 36
>COG2850 Uncharacterized conserved protein [Function unknown]
Probab=25.23 E-value=42 Score=30.07 Aligned_cols=47 Identities=17% Similarity=0.155 Sum_probs=28.3
Q ss_pred eeeccceeeeeeeeeeCCCCcccE-EEEecCCcccCCCCCCCEEEecC
Q 032478 80 IYLQNKTQIGKVDEIFGPINESYF-SVKMMEGIVATSYSLGDKFYIDP 126 (140)
Q Consensus 80 Vy~enK~~IGKVdeIfGPi~~~yf-svKl~~gi~a~sfk~gdk~yI~p 126 (140)
.|++++.+|+|-++.-.+..+++- .+-+.+-+....+.+||.+||.|
T Consensus 146 g~G~RRW~v~~~~~~~~~~~~~d~~~~~~f~~~~d~vlepGDiLYiPp 193 (383)
T COG2850 146 GQGRRRWRVGKKCNMSTLCPHPDLLILAPFEPDIDEVLEPGDILYIPP 193 (383)
T ss_pred ecccceeecCCcccccCcCCCcchhhcCCCCchhhhhcCCCceeecCC
Confidence 467888888887654444333321 11122333344678899999998
No 37
>PRK03760 hypothetical protein; Provisional
Probab=24.33 E-value=1.8e+02 Score=21.41 Aligned_cols=52 Identities=13% Similarity=0.224 Sum_probs=35.1
Q ss_pred CCCCCCceeeccceeeeeeee-----eeCCCCcccEEEEecCCcccC-CCCCCCEEEecC
Q 032478 73 IPYFNAPIYLQNKTQIGKVDE-----IFGPINESYFSVKMMEGIVAT-SYSLGDKFYIDP 126 (140)
Q Consensus 73 VPyfna~Vy~enK~~IGKVde-----IfGPi~~~yfsvKl~~gi~a~-sfk~gdk~yI~p 126 (140)
+| =+.||..+.-+|=.|.+ +..|.....+.+.+.++..+. .+++||+|.+..
T Consensus 59 ~p--LDiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 59 SS--IDVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKIRVLKVEVGDEIEWID 116 (117)
T ss_pred Ce--eEEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCChHHHcCCCCCCEEEEee
Confidence 55 78888877766666654 334444555777777776643 689999997754
No 38
>KOG4745 consensus Metalloproteinase inhibitor TIMP and related proteins [General function prediction only]
Probab=24.30 E-value=64 Score=25.16 Aligned_cols=36 Identities=25% Similarity=0.334 Sum_probs=27.2
Q ss_pred eeeeeeeCCCCcccEEEEecCC-----cccCCCCCCCEEEe
Q 032478 89 GKVDEIFGPINESYFSVKMMEG-----IVATSYSLGDKFYI 124 (140)
Q Consensus 89 GKVdeIfGPi~~~yfsvKl~~g-----i~a~sfk~gdk~yI 124 (140)
-.+++|+-|.++...=+|++.+ +.|+++.-++++||
T Consensus 9 ~~~~~i~Tp~~es~CG~~l~~~~~keYLlaGrv~~dg~l~i 49 (141)
T KOG4745|consen 9 TDPEFIYTPADESACGLKLDVGGKKEYLLAGRVEGDGKLLI 49 (141)
T ss_pred CCcceecCcccccccceeeecCCcEEEEEeeeecCCCcEEE
Confidence 3457788888888888888776 56677766778877
No 39
>PHA02110 hypothetical protein
Probab=24.06 E-value=43 Score=24.23 Aligned_cols=10 Identities=40% Similarity=0.833 Sum_probs=8.2
Q ss_pred ceeeccceee
Q 032478 79 PIYLQNKTQI 88 (140)
Q Consensus 79 ~Vy~enK~~I 88 (140)
.||+|.|.|+
T Consensus 7 kvylesk~q~ 16 (98)
T PHA02110 7 KVYLESKIQL 16 (98)
T ss_pred eeeeehhhhh
Confidence 4889998886
No 40
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=23.78 E-value=72 Score=23.68 Aligned_cols=25 Identities=16% Similarity=0.376 Sum_probs=21.0
Q ss_pred CCCCCceEEEceeeeeccCCeEEEe
Q 032478 43 DEGPPAEVVEVSSFLHACEGDAVTK 67 (140)
Q Consensus 43 ~~Gpp~~v~~lG~f~H~~eg~lV~k 67 (140)
+.|+|+-.+-+|++.|..++++-+-
T Consensus 18 ~lG~~~gk~V~G~I~hvv~ddLYID 42 (104)
T PF10246_consen 18 QLGDPEGKIVIGKIFHVVDDDLYID 42 (104)
T ss_pred hcCCccCCEEEEEEEEEecCceEEE
Confidence 5688899999999999998887654
No 41
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=23.33 E-value=89 Score=21.20 Aligned_cols=9 Identities=33% Similarity=0.637 Sum_probs=4.2
Q ss_pred CCCceEEEc
Q 032478 45 GPPAEVVEV 53 (140)
Q Consensus 45 Gpp~~v~~l 53 (140)
-||....+|
T Consensus 37 ~~~kT~EeL 45 (74)
T PF13865_consen 37 KPPKTAEEL 45 (74)
T ss_pred CCCCCHHHH
Confidence 444444443
No 42
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=23.31 E-value=1.4e+02 Score=23.22 Aligned_cols=31 Identities=3% Similarity=0.027 Sum_probs=22.9
Q ss_pred CCCceeeccceeee-eeeeeeCCCCcccEEEE
Q 032478 76 FNAPIYLQNKTQIG-KVDEIFGPINESYFSVK 106 (140)
Q Consensus 76 fna~Vy~enK~~IG-KVdeIfGPi~~~yfsvK 106 (140)
.+..|++++...+| +|.+|+-.-.+..+.|+
T Consensus 103 iG~~V~d~~g~~lGG~V~~v~~~~a~dllvV~ 134 (171)
T PRK14590 103 IGLQAIDETGKPLNWKLTDVQDNPAHPILVFI 134 (171)
T ss_pred cCcEEEeCCCCEeeeEEEEEecCCCceEEEEE
Confidence 57889999999997 99997655444445654
No 43
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=23.26 E-value=3.9e+02 Score=21.72 Aligned_cols=64 Identities=13% Similarity=0.045 Sum_probs=38.2
Q ss_pred eEEEceeeeeccCCeEEEeccC-CCCCCCCCceeeccceeeeeeeeeeCCCCcccEEEEecCCcccCCCCCCCEEEe
Q 032478 49 EVVEVSSFLHACEGDAVTKLTN-EKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYI 124 (140)
Q Consensus 49 ~v~~lG~f~H~~eg~lV~k~t~-~~VPyfna~Vy~enK~~IGKVdeIfGPi~~~yfsvKl~~gi~a~sfk~gdk~yI 124 (140)
.+..+-......+||.|+-+-. ...| .-..||+|.+|--..+..|.++++... ..+..-+.+||
T Consensus 205 ~l~~i~~~~~i~~GD~VvTSGl~g~fP---------~Gi~VG~V~~v~~~~~~~~~~~~v~p~---~d~~~l~~V~V 269 (276)
T PRK13922 205 KLEFIPRSADIKVGDLVVTSGLGGIFP---------AGLPVGKVTSVERDDYGLFKTVYVKPA---ADLDRLRYVLV 269 (276)
T ss_pred EEEecCCCCCCCCCCEEEECCCCCcCC---------CCCEEEEEEEEEeCCCCCeeEEEEEEC---cccCCCcEEEE
Confidence 4555444455667888887643 3455 567899999995555555644444332 23334577777
No 44
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=22.78 E-value=1.6e+02 Score=19.14 Aligned_cols=40 Identities=28% Similarity=0.473 Sum_probs=23.9
Q ss_pred cceeeeeeeeeeCCCCcccEEEEecCCcccC-----------CCCCCCEEEecC
Q 032478 84 NKTQIGKVDEIFGPINESYFSVKMMEGIVAT-----------SYSLGDKFYIDP 126 (140)
Q Consensus 84 nK~~IGKVdeIfGPi~~~yfsvKl~~gi~a~-----------sfk~gdk~yI~p 126 (140)
.-+.+++|-+.+|- -+|.|+++++...- .+++||.+-+++
T Consensus 2 e~e~~~~V~~~lG~---~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 2 EGEVIGRVTEMLGN---NLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp TTEEEEEEEEEESS---SEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEE
T ss_pred CcEEEEEEEEECCC---CEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEe
Confidence 44567777777764 44788887765421 456677776664
No 45
>PLN03138 Protein TOC75; Provisional
Probab=22.28 E-value=78 Score=30.91 Aligned_cols=13 Identities=8% Similarity=0.013 Sum_probs=5.4
Q ss_pred CCCCCEEEecCCC
Q 032478 116 YSLGDKFYIDPSK 128 (140)
Q Consensus 116 fk~gdk~yI~p~k 128 (140)
|+++++.+|+.-+
T Consensus 221 i~Eg~~~~I~~I~ 233 (796)
T PLN03138 221 FTESTWQSADSFR 233 (796)
T ss_pred EEeCCceeeeeee
Confidence 3444444444333
No 46
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=22.24 E-value=1.1e+02 Score=21.91 Aligned_cols=22 Identities=18% Similarity=0.279 Sum_probs=12.6
Q ss_pred ceeeeeeeeeeCCC-CcccEEEE
Q 032478 85 KTQIGKVDEIFGPI-NESYFSVK 106 (140)
Q Consensus 85 K~~IGKVdeIfGPi-~~~yfsvK 106 (140)
+..|++|++||--. .+.+|++-
T Consensus 20 ~~~i~~I~~i~~~~~g~~~~~~~ 42 (121)
T cd04717 20 KPIIFRIERLWKDEDGEKFFFGC 42 (121)
T ss_pred CCEEEEEeEEEECCCCCEEEEEE
Confidence 34477788777654 34444443
No 47
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=20.95 E-value=2.1e+02 Score=17.67 Aligned_cols=11 Identities=27% Similarity=0.555 Sum_probs=6.7
Q ss_pred CCCCCCEEEec
Q 032478 115 SYSLGDKFYID 125 (140)
Q Consensus 115 sfk~gdk~yI~ 125 (140)
.+++||++|+-
T Consensus 46 ~L~~G~~V~~~ 56 (64)
T PF03459_consen 46 GLKPGDEVYAS 56 (64)
T ss_dssp T-STT-EEEEE
T ss_pred CCCCCCEEEEE
Confidence 57889998763
No 48
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=20.62 E-value=1.2e+02 Score=25.36 Aligned_cols=34 Identities=24% Similarity=0.323 Sum_probs=15.9
Q ss_pred eeeeeeeeCCCCcccEEEEecCCcccCCCCCCCEEEec
Q 032478 88 IGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYID 125 (140)
Q Consensus 88 IGKVdeIfGPi~~~yfsvKl~~gi~a~sfk~gdk~yI~ 125 (140)
+|-||++ .-.+.-|.--||++...- .+|+.+||.
T Consensus 152 ~GvV~~~-r~eDMkYAvr~ld~~~~~---seGe~~yir 185 (241)
T KOG0105|consen 152 VGVVEYL-RKEDMKYAVRKLDDQKFR---SEGETAYIR 185 (241)
T ss_pred ceeeeee-ehhhHHHHHHhhcccccc---CcCcEeeEE
Confidence 5666643 222333433444442222 257777774
No 49
>COG5489 Uncharacterized conserved protein [Function unknown]
Probab=20.45 E-value=1.6e+02 Score=21.92 Aligned_cols=58 Identities=19% Similarity=0.340 Sum_probs=30.6
Q ss_pred EEEceeeeeccCCeEE-------EeccCCCCCCCCCceeecc----ceeeeeee--eeeCCC---CcccEEEEecC
Q 032478 50 VVEVSSFLHACEGDAV-------TKLTNEKIPYFNAPIYLQN----KTQIGKVD--EIFGPI---NESYFSVKMME 109 (140)
Q Consensus 50 v~~lG~f~H~~eg~lV-------~k~t~~~VPyfna~Vy~en----K~~IGKVd--eIfGPi---~~~yfsvKl~~ 109 (140)
+..+|+|...-++.+. +......|| |+..-.+| +..+|.+| .-|.-+ -+-|+||||++
T Consensus 3 ma~IGtf~~~~~~~~~G~irTL~vnakv~lvP--n~~~s~~~aPdfRV~~gg~eiGAaW~k~s~~G~dYlsvkLdd 76 (107)
T COG5489 3 MATIGTFTKNGNGGFEGTIRTLTVNAKVRLVP--NESKSGDNAPDFRVTAGGVEIGAAWNKTSNSGRDYLSVKLDD 76 (107)
T ss_pred eEEEEEEeecCCCceEEEEEEEEEcceEEEcc--cCCCCCCCCCcEEEEecCcchhhhhhhhcccCcceEEEEecC
Confidence 5677888765333322 222223466 54444333 34455554 235444 34499999986
Done!