Query 048420
Match_columns 386
No_of_seqs 163 out of 286
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 09:22:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048420.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048420hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2613 NMD protein affecting 100.0 2E-131 5E-136 980.7 26.0 368 4-380 4-492 (502)
2 COG1499 NMD3 NMD protein affec 100.0 2.8E-51 6E-56 408.8 20.4 270 10-285 3-353 (355)
3 PF04981 NMD3: NMD3 family ; 100.0 3.4E-43 7.3E-48 333.2 13.5 159 16-180 1-236 (236)
4 PF13248 zf-ribbon_3: zinc-rib 76.6 1.4 3.1E-05 28.4 1.1 22 13-35 2-23 (26)
5 PF13240 zinc_ribbon_2: zinc-r 76.5 1.4 3.1E-05 27.9 1.1 20 15-35 1-20 (23)
6 cd04467 S1_aIF5A S1_aIF5A: Arc 64.7 11 0.00023 29.2 3.8 27 195-221 7-33 (57)
7 PF09889 DUF2116: Uncharacteri 64.6 3.2 7E-05 32.3 0.9 20 15-35 5-25 (59)
8 TIGR03054 photo_alph_chp1 puta 53.8 21 0.00046 32.1 4.4 34 186-219 89-122 (135)
9 COG1734 DksA DnaK suppressor p 53.3 4.4 9.6E-05 35.7 -0.0 23 13-35 80-108 (120)
10 PF09297 zf-NADH-PPase: NADH p 48.9 4.4 9.5E-05 27.2 -0.6 24 13-36 3-29 (32)
11 PF14260 zf-C4pol: C4-type zin 48.3 8.5 0.00018 30.1 0.9 23 16-38 1-23 (73)
12 cd05705 S1_Rrp5_repeat_hs14 S1 44.3 70 0.0015 25.1 5.6 52 196-247 10-67 (74)
13 PF05810 NinF: NinF protein; 43.4 9.1 0.0002 29.7 0.4 23 15-37 19-41 (58)
14 smart00259 ZnF_A20 A20-like zi 43.0 13 0.00027 24.5 0.9 23 14-36 2-26 (26)
15 TIGR03826 YvyF flagellar opero 42.9 15 0.00032 33.1 1.7 25 11-37 79-103 (137)
16 PF12647 RNHCP: RNHCP domain; 41.8 13 0.00027 31.6 1.0 41 14-58 5-51 (92)
17 PRK11019 hypothetical protein; 37.1 18 0.00039 30.3 1.2 25 13-37 36-66 (88)
18 COG3809 Uncharacterized protei 35.5 11 0.00024 31.3 -0.3 12 14-25 2-13 (88)
19 PF10571 UPF0547: Uncharacteri 35.4 14 0.00029 24.2 0.2 19 15-34 2-20 (26)
20 PRK11595 DNA utilization prote 35.4 22 0.00047 33.8 1.6 23 15-37 7-29 (227)
21 PRK12495 hypothetical protein; 35.2 9.7 0.00021 37.0 -0.8 22 14-35 43-65 (226)
22 PF07754 DUF1610: Domain of un 35.1 17 0.00036 23.6 0.6 19 16-34 1-22 (24)
23 PF06677 Auto_anti-p27: Sjogre 34.7 13 0.00028 26.9 0.0 20 15-34 19-40 (41)
24 TIGR02890 spore_yteA sporulati 34.5 16 0.00035 33.5 0.6 24 13-36 86-115 (159)
25 PF01258 zf-dskA_traR: Prokary 33.1 12 0.00025 25.8 -0.5 22 16-37 6-33 (36)
26 TIGR03826 YvyF flagellar opero 32.5 17 0.00036 32.8 0.3 29 15-43 5-33 (137)
27 PF14471 DUF4428: Domain of un 32.2 23 0.0005 26.6 1.0 24 15-38 1-30 (51)
28 TIGR02420 dksA RNA polymerase- 32.0 17 0.00038 30.9 0.3 23 13-35 80-108 (110)
29 PHA00080 DksA-like zinc finger 31.4 22 0.00047 28.5 0.8 24 13-36 31-60 (72)
30 TIGR02276 beta_rpt_yvtn 40-res 31.1 65 0.0014 21.4 3.1 24 192-215 4-27 (42)
31 PRK00420 hypothetical protein; 30.6 20 0.00044 31.3 0.5 23 14-36 24-48 (112)
32 TIGR00201 comF comF family pro 29.9 24 0.00052 32.4 0.9 21 16-37 1-21 (190)
33 PF12773 DZR: Double zinc ribb 28.1 28 0.00062 25.0 0.9 24 13-36 12-37 (50)
34 PRK13715 conjugal transfer pro 27.9 21 0.00046 28.7 0.2 22 15-36 36-63 (73)
35 TIGR01031 rpmF_bact ribosomal 26.3 35 0.00076 26.0 1.1 25 9-35 22-46 (55)
36 cd02549 Peptidase_C39A A sub-f 24.7 77 0.0017 26.5 3.1 37 188-224 90-128 (141)
37 TIGR02419 C4_traR_proteo phage 24.1 42 0.0009 26.2 1.2 24 13-36 31-60 (63)
38 COG2174 RPL34A Ribosomal prote 23.7 40 0.00087 28.6 1.1 26 14-39 35-82 (93)
39 PF15644 Tox-PL: Papain fold t 23.7 95 0.0021 26.2 3.4 23 192-214 88-110 (111)
40 COG5324 Uncharacterized conser 23.7 19 0.00042 39.1 -1.0 66 129-202 528-593 (758)
41 PF03884 DUF329: Domain of unk 22.8 33 0.00072 26.6 0.4 34 13-48 2-40 (57)
42 smart00661 RPOL9 RNA polymeras 22.6 38 0.00082 24.4 0.7 21 15-35 2-27 (52)
43 PRK08359 transcription factor; 22.4 59 0.0013 30.5 2.1 22 14-35 7-37 (176)
44 TIGR00270 conserved hypothetic 22.3 47 0.001 30.3 1.3 21 15-35 2-31 (154)
45 PF01783 Ribosomal_L32p: Ribos 22.0 56 0.0012 24.8 1.5 21 12-34 25-45 (56)
46 PTZ00218 40S ribosomal protein 21.6 50 0.0011 25.4 1.1 29 13-41 16-47 (54)
47 COG4068 Uncharacterized protei 21.3 43 0.00093 26.4 0.7 19 13-32 8-26 (64)
48 PTZ00074 60S ribosomal protein 21.3 45 0.00097 30.2 0.9 26 14-39 42-89 (135)
49 COG3024 Uncharacterized protei 21.3 58 0.0013 26.0 1.5 40 9-50 3-47 (65)
50 PRK12286 rpmF 50S ribosomal pr 20.8 50 0.0011 25.4 1.0 24 10-35 24-47 (57)
51 TIGR00100 hypA hydrogenase nic 20.4 52 0.0011 28.4 1.2 33 12-44 69-102 (115)
No 1
>KOG2613 consensus NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-131 Score=980.67 Aligned_cols=368 Identities=44% Similarity=0.715 Sum_probs=343.0
Q ss_pred ccCcCCCCC-eeeeecCCCCCCCCCcccchHhhhccccccccccceeEEeecCc--------------------------
Q 048420 4 AAGIFAVRK-TVSCCKCGITMVSNASNMCVTCLKSEVDITESLQKHANITPCPK-------------------------- 56 (386)
Q Consensus 4 ~~~~~~~~~-~ilCc~CG~~i~pn~~nmC~~Cl~~~vdItegIpk~~~i~~Cr~-------------------------- 56 (386)
++..+..++ +||||.||+||+||++|||++||+++||||+||||+++|.|||+
T Consensus 4 ~~~~p~~~~~~ILCCeCGvpi~Pn~anMC~~Clrs~VDITegipr~~~i~~Cr~CeRYlqPP~~Wi~a~leSrELLaicl 83 (502)
T KOG2613|consen 4 ESIDPNVQGATILCCECGVPIEPNPANMCVDCLRSEVDITEGIPRQATISFCRECERYLQPPKTWIRAELESRELLAICL 83 (502)
T ss_pred cCCCccCCCcEEEEecCCCcCCCchHHHHHHHhheeeehhcCCcchhhhhhccccceecCCcHHHhhhhhccHHHHHHHH
Confidence 344444344 89999999999999999999999999999999999999999999
Q ss_pred -------------------------eEEEEEEEEEeecCeeEEEEEEEEE--eeeccCCCCccccccCCCcchhhhhhH-
Q 048420 57 -------------------------IKLKLTVQKEVLEGVIVEQSDVVMS--RNITCVNLVPGFMQTGPDHWDAAVQLE- 108 (386)
Q Consensus 57 -------------------------ikVkltVqkEv~~g~ilqQ~~vVe~--~~~~C~~~~C~r~~a~~~~w~A~VQvR- 108 (386)
||||||||||+|+|+||||+|+||| +++|||| |+|.+| +++|+|+||||
T Consensus 84 kklK~L~~VrLvDA~FVwTEpHSkRIkVKLTVq~E~~~~tilqQ~f~Vey~V~~~~C~D--C~R~ea-kdfW~a~vQvRQ 160 (502)
T KOG2613|consen 84 KKLKGLNKVRLVDANFVWTEPHSKRIKVKLTVQKEVFTNTILQQSFVVEYTVRNQQCPD--CARVEA-KDFWRALVQVRQ 160 (502)
T ss_pred HhhcCcceeEEeccceEeccCCCceEEEEEEEEhhhcCCceeeeeEEEEEEEecccCch--hhhhhh-hHHHHHHHHHHh
Confidence 9999999999999999999999999 9999999 999998 89999999999
Q ss_pred -------------HHhhccccccccCeeeeCCceeEEecChhhHHHHHHhhccccCeEEeeeceeeccccCCCcceeEEE
Q 048420 109 -------------LIQKHDAPARATKIKKMDHGIEFFFSGRSHAVKFVEFVGEVVPAQSRHEKQLVSRGTKSRNCKCKYT 175 (386)
Q Consensus 109 -------------lIlKh~a~~~~~~I~~~~dGlDFyf~~r~~A~k~v~fl~sv~P~~~k~S~qLis~D~~sn~~~yK~T 175 (386)
+||||+||.++++|++.++||||||++++||+|||+||++++|+++|.|++|||||+|||+||||||
T Consensus 161 r~~hkrTF~YLEQLILKh~ah~~t~~Ik~~~~GlDFyy~~k~hA~kmVeFL~~vvP~ryk~se~LIS~D~hsn~ynYK~t 240 (502)
T KOG2613|consen 161 RAEHKRTFFYLEQLILKHNAHGNTINIKEVKDGLDFYYANKNHAVKMVEFLQTVVPIRYKVSERLISHDVHSNTYNYKFT 240 (502)
T ss_pred hcccchhhHHHHHHHHhcchhhcccccccccCCcceeeccHHHHHHHHHHHHhhceeEEecchhhhhhhcccCcccceee
Confidence 8999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeecee-----------hhccCCCCCeEEEEeeCCcEEEEcCCCCceeEeccccccccCCcccCCCCCceEEEEEee
Q 048420 176 CSVEISAIS-----------AHNLGNLGPFVICTKVTNSIALLDPFTLRHCYLDADQYWRSPFKALHTSRQLVEYIVLDV 244 (386)
Q Consensus 176 ~SVeI~pic-----------a~~lG~i~~l~lc~kV~~~I~liDP~Tl~~~~l~~~~Ywr~pF~~l~~~~~LvefiVldi 244 (386)
|||||+||| |++|||||||+||+||+++|+||||.|+|+++|++..|||+||++|++++||+||+|+|+
T Consensus 241 ~SVEIvPiCkDdlVcLpkkva~~lGNi~qlvvc~kVs~~I~llDP~tlq~adl~~s~yWr~pF~sl~~~kqL~ef~V~dv 320 (502)
T KOG2613|consen 241 YSVEIVPICKDDLVCLPKKVAQSLGNISQLVVCTKVSNTITLLDPRTLQTADLTGSVYWRAPFNSLCDPKQLTEFIVLDV 320 (502)
T ss_pred eEEEEeeeccCceEEcCHHHHHhcCCccceEEEEEecCceEEeCCcceeeeecccceeecCcchhhcChhhheEEEEEEE
Confidence 999999999 999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccc----------------------cCCcEEEEEeecCCccCCCCeEeeecccccCCCchHhhccCCCCCCCeEEEec
Q 048420 245 KVAST----------------------ENDTILSTRTHLGHLLILGDYAIGYDLHEANQNDIELENYKSLVPPDTIKIKK 302 (386)
Q Consensus 245 e~~~~----------------------~nd~~~~~rTHLG~iL~~GD~vlGYdl~~~n~n~~~~~~~~~~~~PdviLVkK 302 (386)
++.+. +||..+++||||||+|+|||+||||||+++|+||++||++..+.+||||||||
T Consensus 321 ~~v~~~~~~g~kh~l~dv~v~r~sd~g~nd~~~~~RtHLGhil~~gD~vlgydl~~~N~N~~~~d~~~~d~vPdvvlVkK 400 (502)
T KOG2613|consen 321 DPVGEAGGKGQKHALADVWVARSSDLGMNDKFHYARTHLGHILKPGDLVLGYDLANANLNDEEFDKLNIDGVPDVVLVKK 400 (502)
T ss_pred ecccccCCccceeeeeeEEEEEcCccCcccceeeehhhccccCCCCCeeeeeeeccCccchhhhhhhcccCCCcEEEEEc
Confidence 98753 67889999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhhccCCCCCCccccccccccCCCCccchhhhHHHHHHHHHHHh-------------------ccCCC-CCCCCC
Q 048420 303 SYKEKNQRKHRKPNPPKLKPLEMEVDGSKCGADREKVNNEYEEFLRDLM-------------------ASVTD-KEDVPS 362 (386)
Q Consensus 303 ~y~~~~~~~~~~~R~wkLk~l~~e~~~~~~~~~~~~~e~dye~Fl~dl~-------------------~~~~~-~~~~p~ 362 (386)
+|+++ +++.|+||||+|++|. ..++.+.++.++||++||+||+ ++++| ++|+|+
T Consensus 401 ~y~r~----~r~~r~WKlK~l~~e~--~~~~~~~~~~~~eY~~FledlEEd~elr~~vnlyrd~~~~~~~d~d~~ed~p~ 474 (502)
T KOG2613|consen 401 MYDRT----KRKSRNWKLKRLAMEM--SRGKNESERTEKEYELFLEDLEEDPELRQGVNLYRDKEKPTESDTDDAEDAPQ 474 (502)
T ss_pred ccccc----chhccceehhhhhhhh--ccccccchhhHHHHHHHHHhhhcCHHHHhcceeeeccCCCCccccccccCCCC
Confidence 99843 2356999999999986 3466778889999999999992 13333 488999
Q ss_pred CChhhhhccCCCCCCCCC
Q 048420 363 VPLDYLLADLDSSDKEEG 380 (386)
Q Consensus 363 i~l~ellddl~~~~~~~~ 380 (386)
|+|+||||||+++.+||+
T Consensus 475 i~ldElLedl~~~~~e~~ 492 (502)
T KOG2613|consen 475 ITLDELLEDLKLSFEEDD 492 (502)
T ss_pred CCHHHHHhhhhcchhhcc
Confidence 999999999988766444
No 2
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-51 Score=408.78 Aligned_cols=270 Identities=19% Similarity=0.266 Sum_probs=246.0
Q ss_pred CCCeeeeecCCCCCCCCCcccchHhhhccccccccccceeEEeecCc---------------------------------
Q 048420 10 VRKTVSCCKCGITMVSNASNMCVTCLKSEVDITESLQKHANITPCPK--------------------------------- 56 (386)
Q Consensus 10 ~~~~ilCc~CG~~i~pn~~nmC~~Cl~~~vdItegIpk~~~i~~Cr~--------------------------------- 56 (386)
...+++||.||++++|+..+||.+|+..+..+. +||..+++.+|++
T Consensus 3 ~~~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~-~ip~~~~v~~C~~Cga~~~~~~W~~~~~~~~~l~~~~~~~~~~~~~ 81 (355)
T COG1499 3 DASTILCVRCGRSVDPLIDGLCGDCYVETTPLI-EIPDEVNVEVCRHCGAYRIRGRWVDEEGANRLLEALEDEVLRRLEK 81 (355)
T ss_pred CCcccEeccCCCcCchhhccccHHHHhccCccc-cCCCceEEEECCcCCCccCCCcceeccccchHHHHHHHHHhhhhhh
Confidence 457899999999999999999999999966665 8999999999998
Q ss_pred ------------------eEEEEEEEEEeec-CeeEEEEEEEEE--eeeccCCCCccccccCCCcchhhhhhH-------
Q 048420 57 ------------------IKLKLTVQKEVLE-GVIVEQSDVVMS--RNITCVNLVPGFMQTGPDHWDAAVQLE------- 108 (386)
Q Consensus 57 ------------------ikVkltVqkEv~~-g~ilqQ~~vVe~--~~~~C~~~~C~r~~a~~~~w~A~VQvR------- 108 (386)
+.++++|+++-.- |+.+||.+.|+| ++.+||+ |+| ++ ++||+|+||||
T Consensus 82 ~~~~~~~~~~~~~~~~~r~~~~~~i~~~~~~~~~~~~~~~~v~~~v~~~~Cp~--C~r-~~-~~y~eAivQvR~~~r~~~ 157 (355)
T COG1499 82 VNEAVEVEFAFEEPKSRRLTVRVTIKGRGHVRGTPRTQLVEVTVEVRRTLCPR--CSR-FT-GGYYEAIVQVRAKGRELT 157 (355)
T ss_pred hccccccceeeeccCCCceEEEEEEEEeeecCCCceeEEEEEEEEEEEeEChh--hhc-cc-cceeEEEEEEEeccCccc
Confidence 6789999977655 999999999999 9999999 999 45 79999999999
Q ss_pred ------------HHhhcc---ccccccCeeeeCCceeEEecChhhHHHHHHhhccccCeEEeeeceeeccccCCCcceeE
Q 048420 109 ------------LIQKHD---APARATKIKKMDHGIEFFFSGRSHAVKFVEFVGEVVPAQSRHEKQLVSRGTKSRNCKCK 173 (386)
Q Consensus 109 ------------lIlKh~---a~~~~~~I~~~~dGlDFyf~~r~~A~k~v~fl~sv~P~~~k~S~qLis~D~~sn~~~yK 173 (386)
.++|+. ..++++++++.++||||||+|+++|+|+++||.+++|+++++|++|+|.|.++|+.+||
T Consensus 158 ~eee~~~~~ve~~v~k~~~~d~~~fIs~~~ek~eGiD~y~gs~~~arkva~~i~~~~~~~v~eS~~Lvg~d~~tgk~~yR 237 (355)
T COG1499 158 EEEEEAFLFVEEIVLKRKKRDRMAFISDTEEKKEGIDIYLGSRNAARKVARFILEKFGGEVKESEKLVGRDRFTGKRVYR 237 (355)
T ss_pred chhHHHHHHHHHHHHhhhccccccchhhhcccccceEEEEeccchHHHHHHHHHHHcCcEEEecceeEEEecCCCceEEE
Confidence 344554 45689999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEeeceeh---hccCCCCCeEEEEeeCCcEEEEcCCCCceeEeccccccccCCcccCCCCCceEEEEEeeeeccc-
Q 048420 174 YTCSVEISAISA---HNLGNLGPFVICTKVTNSIALLDPFTLRHCYLDADQYWRSPFKALHTSRQLVEYIVLDVKVAST- 249 (386)
Q Consensus 174 ~T~SVeI~pica---~~lG~i~~l~lc~kV~~~I~liDP~Tl~~~~l~~~~Ywr~pF~~l~~~~~LvefiVldie~~~~- 249 (386)
|||||+|||+|. -++.+ +++++|.+.++.|.++|+.|++..+++.+.||+++|..+....+|++|+|++.++...
T Consensus 238 ~t~Svrip~~~~gDiV~~~~-~~~~~v~~~~~~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~~~~~~~vvs~~~~~~~ 316 (355)
T COG1499 238 FTYSVRIPEFRPGDIVSVRG-RQLVLVRSIGKGIVVLDLETGEPVEITWSVYKRNEGKVAVKEPRLKKAVVVSRDPSAIQ 316 (355)
T ss_pred EEEEEECCCCCCCCEEEECC-CeEEEEEEecCceEEEecccCCccccChhhcccCcceeeeccccceEEEEEecCCCceE
Confidence 999999999992 22222 6999999999999999999999999999999999999999999999999999998753
Q ss_pred -cCCcEEEEEeecCCccCCCCeEeeecccccCCCchH
Q 048420 250 -ENDTILSTRTHLGHLLILGDYAIGYDLHEANQNDIE 285 (386)
Q Consensus 250 -~nd~~~~~rTHLG~iL~~GD~vlGYdl~~~n~n~~~ 285 (386)
...++|.++||+|..|++||+|++|.+++.||+.++
T Consensus 317 v~d~et~e~~~~~~~~~~~g~~v~v~~~~~~~~~~~~ 353 (355)
T COG1499 317 VLDPETYEARTVKGPSLEEGDEVKVFKVRGRNYVVEE 353 (355)
T ss_pred EEecceEEEEeccCCCCCCCCEEEEEEEeceEEeecc
Confidence 556889999999999999999999999999987654
No 3
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=100.00 E-value=3.4e-43 Score=333.23 Aligned_cols=159 Identities=31% Similarity=0.518 Sum_probs=154.3
Q ss_pred eecCCCCCCCCCcccchHhhhccccccccccceeEEeecCc---------------------------------------
Q 048420 16 CCKCGITMVSNASNMCVTCLKSEVDITESLQKHANITPCPK--------------------------------------- 56 (386)
Q Consensus 16 Cc~CG~~i~pn~~nmC~~Cl~~~vdItegIpk~~~i~~Cr~--------------------------------------- 56 (386)
||.||++++|+++|||.+|++++++|++ ||+++++.+||.
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~e-i~~~i~v~~C~~Cg~~~~~~~W~~~~~~el~~~~lk~v~~~l~~~~~~~~d 79 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIE-IPDRIEVTICPKCGRYRIGGRWVDPESRELEELCLKKVERGLKKNIKVHVD 79 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeee-cCCccCceECCCCCCEECCCEeeecCcccHHHHHHHHHHHHHHHhhccccc
Confidence 9999999999999999999999999998 999999999999
Q ss_pred ------------eEEEEEEEEEeecCeeEEEEEEEEE--eeeccCCCCccccccCCCcchhhhhhH--------------
Q 048420 57 ------------IKLKLTVQKEVLEGVIVEQSDVVMS--RNITCVNLVPGFMQTGPDHWDAAVQLE-------------- 108 (386)
Q Consensus 57 ------------ikVkltVqkEv~~g~ilqQ~~vVe~--~~~~C~~~~C~r~~a~~~~w~A~VQvR-------------- 108 (386)
++++++||+++++|+.+||++.|+| ++++||+ |+|.+ ++||+|+||||
T Consensus 80 ~~~v~~e~~~~r~~v~v~v~~~v~~~~~~~~~~~v~~~v~~~~C~~--C~r~~--~~~~eaiVQvR~~~r~~~~~e~~~~ 155 (236)
T PF04981_consen 80 AEFVWTEPHSKRIKVKVTVQGEVHGGTPVEQEYEVEVRVKRQQCPD--CSRIA--GGYYEAIVQVRQRGRKLTEEEKEVI 155 (236)
T ss_pred ccEEEEEeeCCEEEEEEEEEEEEcccceEEEEEEEEEEEEcCCChh--HHhhh--CCCccEEEEEEecCCCCCHHHHHHH
Confidence 6789999999999999999999999 9999999 99986 69999999999
Q ss_pred ----------HHhhccccccccCeeeeCCceeEEecChhhHHHHHHhhccccCeEEeeeceeeccccCCCcceeEEEEEE
Q 048420 109 ----------LIQKHDAPARATKIKKMDHGIEFFFSGRSHAVKFVEFVGEVVPAQSRHEKQLVSRGTKSRNCKCKYTCSV 178 (386)
Q Consensus 109 ----------lIlKh~a~~~~~~I~~~~dGlDFyf~~r~~A~k~v~fl~sv~P~~~k~S~qLis~D~~sn~~~yK~T~SV 178 (386)
+++|+++++++++|++.++||||||+++++|+||++||++.+|+++++|++|||+|.+ |+++|||||||
T Consensus 156 ~~~~~~~le~l~~k~~~~~~i~~i~e~keGlD~y~~s~~~Arki~~~i~~~~~~~v~eS~klvg~~~~-gk~~yr~T~sV 234 (236)
T PF04981_consen 156 HKIVFEILEQLILKGDRHAFISDIEEVKEGLDFYFGSKNAARKIVSFIHSKFGGRVKESYKLVGRDDS-GKDVYRYTISV 234 (236)
T ss_pred HHHHHHHHHHHHhhccchhcccceEECCCCEEEEECCHHHHHHHHHHHHHhcCeEEEECceeeeEeCC-CCeEEEEEEEE
Confidence 5678899999999999999999999999999999999999999999999999999999 99999999999
Q ss_pred Ee
Q 048420 179 EI 180 (386)
Q Consensus 179 eI 180 (386)
+|
T Consensus 235 rl 236 (236)
T PF04981_consen 235 RL 236 (236)
T ss_pred EC
Confidence 97
No 4
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=76.58 E-value=1.4 Score=28.43 Aligned_cols=22 Identities=23% Similarity=0.671 Sum_probs=17.2
Q ss_pred eeeeecCCCCCCCCCcccchHhh
Q 048420 13 TVSCCKCGITMVSNASNMCVTCL 35 (386)
Q Consensus 13 ~ilCc~CG~~i~pn~~nmC~~Cl 35 (386)
++.|..||.+++ ..+..|..|=
T Consensus 2 ~~~Cp~Cg~~~~-~~~~fC~~CG 23 (26)
T PF13248_consen 2 EMFCPNCGAEID-PDAKFCPNCG 23 (26)
T ss_pred cCCCcccCCcCC-cccccChhhC
Confidence 467999999765 5578999884
No 5
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=76.47 E-value=1.4 Score=27.90 Aligned_cols=20 Identities=25% Similarity=0.796 Sum_probs=16.1
Q ss_pred eeecCCCCCCCCCcccchHhh
Q 048420 15 SCCKCGITMVSNASNMCVTCL 35 (386)
Q Consensus 15 lCc~CG~~i~pn~~nmC~~Cl 35 (386)
.|..||..++ ..++.|..|=
T Consensus 1 ~Cp~CG~~~~-~~~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIE-DDAKFCPNCG 20 (23)
T ss_pred CCcccCCCCC-CcCcchhhhC
Confidence 4899999987 4678899884
No 6
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=64.70 E-value=11 Score=29.20 Aligned_cols=27 Identities=11% Similarity=0.123 Sum_probs=22.5
Q ss_pred EEEEeeCCcEEEEcCCCCceeEecccc
Q 048420 195 VICTKVTNSIALLDPFTLRHCYLDADQ 221 (386)
Q Consensus 195 ~lc~kV~~~I~liDP~Tl~~~~l~~~~ 221 (386)
.|++-.++.++|+||.|..+.++..+.
T Consensus 7 qVisi~g~~vQlMD~eTYeT~ev~~p~ 33 (57)
T cd04467 7 QVLSIMGDVVQLMDLETYETFEVPIPE 33 (57)
T ss_pred EEEEEcCCEEEEeccccceeEEEecch
Confidence 355566779999999999999999874
No 7
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=64.56 E-value=3.2 Score=32.31 Aligned_cols=20 Identities=25% Similarity=0.795 Sum_probs=15.3
Q ss_pred eeecCCCCCCCCCcccc-hHhh
Q 048420 15 SCCKCGITMVSNASNMC-VTCL 35 (386)
Q Consensus 15 lCc~CG~~i~pn~~nmC-~~Cl 35 (386)
-|..||.||+|+ ..-| ..|-
T Consensus 5 HC~~CG~~Ip~~-~~fCS~~C~ 25 (59)
T PF09889_consen 5 HCPVCGKPIPPD-ESFCSPKCR 25 (59)
T ss_pred cCCcCCCcCCcc-hhhhCHHHH
Confidence 499999999876 4577 4674
No 8
>TIGR03054 photo_alph_chp1 putative photosynthetic complex assembly protein. In twenty or so anoxygenic photosynthetic alpha-Proteobacteria known so far, a gene for a member of this protein family is present and is found in the vicinity of puhA, which encodes a component of the photosynthetic reaction center, and other genes associated with photosynthesis. This protein family is suggested, consequently, as a probable assembly factor for the photosynthetic reaction center, but its seems its actual function has not yet been demonstrated.
Probab=53.83 E-value=21 Score=32.13 Aligned_cols=34 Identities=24% Similarity=0.245 Sum_probs=29.4
Q ss_pred hccCCCCCeEEEEeeCCcEEEEcCCCCceeEecc
Q 048420 186 HNLGNLGPFVICTKVTNSIALLDPFTLRHCYLDA 219 (386)
Q Consensus 186 ~~lG~i~~l~lc~kV~~~I~liDP~Tl~~~~l~~ 219 (386)
+.+|.-.|+.|.-+-+..+.|.||.|++.++|.+
T Consensus 89 ~gv~~~~Pf~L~r~~dGrltL~Dp~Tg~~i~L~a 122 (135)
T TIGR03054 89 AGVAAEPPFRLTRYDNGRLTLTDPATGWSIELNA 122 (135)
T ss_pred cCCCCCCCEEEEEEeCCcEEEEcCCCCcEEEEee
Confidence 3356668999999999999999999999999975
No 9
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=53.31 E-value=4.4 Score=35.67 Aligned_cols=23 Identities=22% Similarity=0.700 Sum_probs=17.6
Q ss_pred eeeeecCCCCCCC-----CC-cccchHhh
Q 048420 13 TVSCCKCGITMVS-----NA-SNMCVTCL 35 (386)
Q Consensus 13 ~ilCc~CG~~i~p-----n~-~nmC~~Cl 35 (386)
+..|..||.||.+ .| +.||++|-
T Consensus 80 YG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ 108 (120)
T COG1734 80 YGICEECGEPIPEARLEARPTARLCIECQ 108 (120)
T ss_pred ccchhccCCcCCHHHHhhCcchHHHHHHH
Confidence 3579999999964 23 47999995
No 10
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=48.90 E-value=4.4 Score=27.18 Aligned_cols=24 Identities=21% Similarity=0.565 Sum_probs=13.8
Q ss_pred eeeeecCCCCCCCCCcc---cchHhhh
Q 048420 13 TVSCCKCGITMVSNASN---MCVTCLK 36 (386)
Q Consensus 13 ~ilCc~CG~~i~pn~~n---mC~~Cl~ 36 (386)
+-+|..||.+..+..++ .|.+|=.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 35799999999887664 5777743
No 11
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=48.25 E-value=8.5 Score=30.09 Aligned_cols=23 Identities=26% Similarity=0.706 Sum_probs=19.7
Q ss_pred eecCCCCCCCCCcccchHhhhcc
Q 048420 16 CCKCGITMVSNASNMCVTCLKSE 38 (386)
Q Consensus 16 Cc~CG~~i~pn~~nmC~~Cl~~~ 38 (386)
|..||.++..+...+|.+|+...
T Consensus 1 C~~C~~~~~~~~~~lC~~C~~~~ 23 (73)
T PF14260_consen 1 CLVCGAKTQEGESPLCSNCRSDP 23 (73)
T ss_pred CCCCCCcCCCCCCCcCcccCcCh
Confidence 88999999877779999999643
No 12
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=44.28 E-value=70 Score=25.11 Aligned_cols=52 Identities=13% Similarity=0.116 Sum_probs=37.5
Q ss_pred EEEeeCCcEEEEcCCCCceeEec----cccccccC--CcccCCCCCceEEEEEeeeec
Q 048420 196 ICTKVTNSIALLDPFTLRHCYLD----ADQYWRSP--FKALHTSRQLVEYIVLDVKVA 247 (386)
Q Consensus 196 lc~kV~~~I~liDP~Tl~~~~l~----~~~Ywr~p--F~~l~~~~~LvefiVldie~~ 247 (386)
-+.++++.-.+++...+-.+.|. +..+|++| +...+...+.+++.|+++++.
T Consensus 10 ~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~ 67 (74)
T cd05705 10 YVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSE 67 (74)
T ss_pred EEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECC
Confidence 34666676566776666666666 34566776 456788999999999999874
No 13
>PF05810 NinF: NinF protein; InterPro: IPR008712 This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
Probab=43.42 E-value=9.1 Score=29.70 Aligned_cols=23 Identities=22% Similarity=0.782 Sum_probs=21.1
Q ss_pred eeecCCCCCCCCCcccchHhhhc
Q 048420 15 SCCKCGITMVSNASNMCVTCLKS 37 (386)
Q Consensus 15 lCc~CG~~i~pn~~nmC~~Cl~~ 37 (386)
+|+.||....|...-.|..|...
T Consensus 19 lCa~C~~~L~~~E~h~Ce~C~~E 41 (58)
T PF05810_consen 19 LCANCGQKLHPDETHVCEECCAE 41 (58)
T ss_pred HHhccCcccccchhhHHHHHHHH
Confidence 59999999999999999999876
No 14
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=43.03 E-value=13 Score=24.48 Aligned_cols=23 Identities=26% Similarity=0.782 Sum_probs=18.9
Q ss_pred eeee--cCCCCCCCCCcccchHhhh
Q 048420 14 VSCC--KCGITMVSNASNMCVTCLK 36 (386)
Q Consensus 14 ilCc--~CG~~i~pn~~nmC~~Cl~ 36 (386)
++|- .||-.-.|...|||..|++
T Consensus 2 ~~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 2 IKCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred CccccCCCCCcCChhhcccCHhhcC
Confidence 4677 7998877788899999985
No 15
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=42.93 E-value=15 Score=33.09 Aligned_cols=25 Identities=20% Similarity=0.668 Sum_probs=20.8
Q ss_pred CCeeeeecCCCCCCCCCcccchHhhhc
Q 048420 11 RKTVSCCKCGITMVSNASNMCVTCLKS 37 (386)
Q Consensus 11 ~~~ilCc~CG~~i~pn~~nmC~~Cl~~ 37 (386)
...++|-.||.+|. .+.+|.+|...
T Consensus 79 nl~~~CE~CG~~I~--~Gr~C~~C~~~ 103 (137)
T TIGR03826 79 NLGYPCERCGTSIR--EGRLCDSCAGE 103 (137)
T ss_pred CCcCcccccCCcCC--CCCccHHHHHH
Confidence 34689999999995 66999999864
No 16
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=41.79 E-value=13 Score=31.57 Aligned_cols=41 Identities=34% Similarity=0.681 Sum_probs=27.6
Q ss_pred eeeecCCCCCCCCCc-----ccchHhhhcc-ccccccccceeEEeecCceE
Q 048420 14 VSCCKCGITMVSNAS-----NMCVTCLKSE-VDITESLQKHANITPCPKIK 58 (386)
Q Consensus 14 ilCc~CG~~i~pn~~-----nmC~~Cl~~~-vdItegIpk~~~i~~Cr~ik 58 (386)
-.|..||..+.|... |-|..||-+. ||+. |-. .-.-|+++-
T Consensus 5 F~C~~CG~~V~p~~~g~~~RNHCP~CL~S~Hvd~~---pGD-Ras~C~g~M 51 (92)
T PF12647_consen 5 FTCVHCGLTVSPLAAGSAHRNHCPSCLSSLHVDIV---PGD-RASDCGGRM 51 (92)
T ss_pred cCccccCCCcccCCCCCCccCcCcccccccccCCC---CCC-ccccCCCee
Confidence 459999999877433 7899999875 5654 332 122488843
No 17
>PRK11019 hypothetical protein; Provisional
Probab=37.08 E-value=18 Score=30.33 Aligned_cols=25 Identities=24% Similarity=0.692 Sum_probs=18.6
Q ss_pred eeeeecCCCCCCC-----C-CcccchHhhhc
Q 048420 13 TVSCCKCGITMVS-----N-ASNMCVTCLKS 37 (386)
Q Consensus 13 ~ilCc~CG~~i~p-----n-~~nmC~~Cl~~ 37 (386)
.-+|..||.+|.. . ....|+.|-..
T Consensus 36 yg~C~~CG~~Ip~~Rl~A~P~a~~Cv~Cq~~ 66 (88)
T PRK11019 36 LTECEECGEPIPEARRKAIPGVRLCVACQQE 66 (88)
T ss_pred CCeeCcCCCcCcHHHHhhcCCccccHHHHHH
Confidence 3589999999964 1 34689999754
No 18
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.47 E-value=11 Score=31.28 Aligned_cols=12 Identities=33% Similarity=0.885 Sum_probs=8.6
Q ss_pred eeeecCCCCCCC
Q 048420 14 VSCCKCGITMVS 25 (386)
Q Consensus 14 ilCc~CG~~i~p 25 (386)
++|++||+.+.+
T Consensus 2 llCP~C~v~l~~ 13 (88)
T COG3809 2 LLCPICGVELVM 13 (88)
T ss_pred cccCcCCceeee
Confidence 468888887654
No 19
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=35.44 E-value=14 Score=24.23 Aligned_cols=19 Identities=26% Similarity=0.994 Sum_probs=13.9
Q ss_pred eeecCCCCCCCCCcccchHh
Q 048420 15 SCCKCGITMVSNASNMCVTC 34 (386)
Q Consensus 15 lCc~CG~~i~pn~~nmC~~C 34 (386)
-|+.||..+ |..+..|..|
T Consensus 2 ~CP~C~~~V-~~~~~~Cp~C 20 (26)
T PF10571_consen 2 TCPECGAEV-PESAKFCPHC 20 (26)
T ss_pred cCCCCcCCc-hhhcCcCCCC
Confidence 388888866 3667788777
No 20
>PRK11595 DNA utilization protein GntX; Provisional
Probab=35.43 E-value=22 Score=33.83 Aligned_cols=23 Identities=17% Similarity=0.632 Sum_probs=19.1
Q ss_pred eeecCCCCCCCCCcccchHhhhc
Q 048420 15 SCCKCGITMVSNASNMCVTCLKS 37 (386)
Q Consensus 15 lCc~CG~~i~pn~~nmC~~Cl~~ 37 (386)
.|..||.++..+...+|..|...
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~ 29 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRA 29 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhh
Confidence 49999999876666799999764
No 21
>PRK12495 hypothetical protein; Provisional
Probab=35.21 E-value=9.7 Score=37.00 Aligned_cols=22 Identities=27% Similarity=0.786 Sum_probs=16.5
Q ss_pred eeeecCCCCCCCCCcc-cchHhh
Q 048420 14 VSCCKCGITMVSNASN-MCVTCL 35 (386)
Q Consensus 14 ilCc~CG~~i~pn~~n-mC~~Cl 35 (386)
-.|..||.||...+.- .|+.|-
T Consensus 43 ~hC~~CG~PIpa~pG~~~Cp~CQ 65 (226)
T PRK12495 43 AHCDECGDPIFRHDGQEFCPTCQ 65 (226)
T ss_pred hhcccccCcccCCCCeeECCCCC
Confidence 4699999999866543 588885
No 22
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=35.13 E-value=17 Score=23.60 Aligned_cols=19 Identities=26% Similarity=0.833 Sum_probs=11.7
Q ss_pred eecCCCCCCCCC-c--ccchHh
Q 048420 16 CCKCGITMVSNA-S--NMCVTC 34 (386)
Q Consensus 16 Cc~CG~~i~pn~-~--nmC~~C 34 (386)
|-.||++|.|-. + =.|.+|
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnC 22 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNC 22 (24)
T ss_pred CccCCCcccCcccCceEeCCCC
Confidence 667777777654 2 256665
No 23
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=34.74 E-value=13 Score=26.89 Aligned_cols=20 Identities=30% Similarity=0.969 Sum_probs=14.5
Q ss_pred eeecCCCCCCCC--CcccchHh
Q 048420 15 SCCKCGITMVSN--ASNMCVTC 34 (386)
Q Consensus 15 lCc~CG~~i~pn--~~nmC~~C 34 (386)
.|..||.|.-.+ ..-.|+.|
T Consensus 19 ~Cp~C~~PL~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMRDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEEecCCCEECCCC
Confidence 499999988553 33578877
No 24
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=34.49 E-value=16 Score=33.50 Aligned_cols=24 Identities=25% Similarity=0.589 Sum_probs=18.5
Q ss_pred eeeeecCCCCCCCC-----C-cccchHhhh
Q 048420 13 TVSCCKCGITMVSN-----A-SNMCVTCLK 36 (386)
Q Consensus 13 ~ilCc~CG~~i~pn-----~-~nmC~~Cl~ 36 (386)
+-.|..||.+|.+. | +..|+.|-.
T Consensus 86 YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~ 115 (159)
T TIGR02890 86 YGICEVCGKPIPYERLEAIPTATTCVECQN 115 (159)
T ss_pred CCeecccCCcccHHHHhhCCCcchhHHHHH
Confidence 46899999999652 3 478999954
No 25
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=33.11 E-value=12 Score=25.75 Aligned_cols=22 Identities=27% Similarity=0.862 Sum_probs=15.3
Q ss_pred eecCCCCCCCC------CcccchHhhhc
Q 048420 16 CCKCGITMVSN------ASNMCVTCLKS 37 (386)
Q Consensus 16 Cc~CG~~i~pn------~~nmC~~Cl~~ 37 (386)
|-.||-+|... .+.+|+.|...
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 99999998653 56799999653
No 26
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=32.51 E-value=17 Score=32.79 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=23.0
Q ss_pred eeecCCCCCCCCCcccchHhhhccccccc
Q 048420 15 SCCKCGITMVSNASNMCVTCLKSEVDITE 43 (386)
Q Consensus 15 lCc~CG~~i~pn~~nmC~~Cl~~~vdIte 43 (386)
-|..||.+...+....|..|+...-+.=+
T Consensus 5 nC~~CgklF~~~~~~iCp~C~~~~e~~f~ 33 (137)
T TIGR03826 5 NCPKCGRLFVKTGRDVCPSCYEEEEREFE 33 (137)
T ss_pred cccccchhhhhcCCccCHHHhHHHHHHHH
Confidence 59999999987777899999976554433
No 27
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=32.19 E-value=23 Score=26.56 Aligned_cols=24 Identities=29% Similarity=0.653 Sum_probs=17.3
Q ss_pred eeecCCCCCCCCC------cccchHhhhcc
Q 048420 15 SCCKCGITMVSNA------SNMCVTCLKSE 38 (386)
Q Consensus 15 lCc~CG~~i~pn~------~nmC~~Cl~~~ 38 (386)
.|+.||..+--.. ..+|.+|+..=
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHh
Confidence 4999998664322 36999999664
No 28
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=32.00 E-value=17 Score=30.91 Aligned_cols=23 Identities=22% Similarity=0.638 Sum_probs=17.5
Q ss_pred eeeeecCCCCCCC-----CC-cccchHhh
Q 048420 13 TVSCCKCGITMVS-----NA-SNMCVTCL 35 (386)
Q Consensus 13 ~ilCc~CG~~i~p-----n~-~nmC~~Cl 35 (386)
+-.|-.||.||.+ .| +..|+.|-
T Consensus 80 yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 80 YGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred CCchhccCCcccHHHHhhCCCccccHHhH
Confidence 4689999999964 33 46799994
No 29
>PHA00080 DksA-like zinc finger domain containing protein
Probab=31.38 E-value=22 Score=28.54 Aligned_cols=24 Identities=25% Similarity=0.706 Sum_probs=17.7
Q ss_pred eeeeecCCCCCCC-----CC-cccchHhhh
Q 048420 13 TVSCCKCGITMVS-----NA-SNMCVTCLK 36 (386)
Q Consensus 13 ~ilCc~CG~~i~p-----n~-~nmC~~Cl~ 36 (386)
.-.|-.||.+|++ .| ...|+.|-.
T Consensus 31 ~~~C~~Cg~~Ip~~Rl~a~P~~~~Cv~Cq~ 60 (72)
T PHA00080 31 ATHCEECGDPIPEARREAVPGCRTCVSCQE 60 (72)
T ss_pred CCEecCCCCcCcHHHHHhCCCccCcHHHHH
Confidence 3579999999964 23 467999954
No 30
>TIGR02276 beta_rpt_yvtn 40-residue YVTN family beta-propeller repeat. This repeat of about 40 amino acids is found in up to 14 copies per protein. Archaea Methanosarcina mazei and Methanosarcina acetivorans each have over 10 genes that encode tandem copies of this repeat, which is also found in other species. PSIPRED predicts with high confidence that each 40-residue repeats contains four beta strands. This model overlaps somewhat with the NHL repeat (Pfam pfam01436) and also shows sequence similarity to the WD domain, G-beta repeat (Pfam pfam00400).
Probab=31.13 E-value=65 Score=21.40 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=19.5
Q ss_pred CCeEEEEeeCCcEEEEcCCCCcee
Q 048420 192 GPFVICTKVTNSIALLDPFTLRHC 215 (386)
Q Consensus 192 ~~l~lc~kV~~~I~liDP~Tl~~~ 215 (386)
+.+++..+-+++|.++|+.|++..
T Consensus 4 ~~lyv~~~~~~~v~~id~~~~~~~ 27 (42)
T TIGR02276 4 TKLYVTNSGSNTVSVIDTATNKVI 27 (42)
T ss_pred CEEEEEeCCCCEEEEEECCCCeEE
Confidence 457787888889999999987763
No 31
>PRK00420 hypothetical protein; Validated
Probab=30.61 E-value=20 Score=31.27 Aligned_cols=23 Identities=22% Similarity=0.557 Sum_probs=17.6
Q ss_pred eeeecCCCCCCC--CCcccchHhhh
Q 048420 14 VSCCKCGITMVS--NASNMCVTCLK 36 (386)
Q Consensus 14 ilCc~CG~~i~p--n~~nmC~~Cl~ 36 (386)
-.|+.||.|.-. +....|+.|=.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCC
Confidence 459999999875 45568999865
No 32
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=29.87 E-value=24 Score=32.45 Aligned_cols=21 Identities=29% Similarity=0.624 Sum_probs=17.2
Q ss_pred eecCCCCCCCCCcccchHhhhc
Q 048420 16 CCKCGITMVSNASNMCVTCLKS 37 (386)
Q Consensus 16 Cc~CG~~i~pn~~nmC~~Cl~~ 37 (386)
|..||.++.+. ..+|.+|...
T Consensus 1 C~~C~~~~~~~-~~~C~~C~~~ 21 (190)
T TIGR00201 1 CSLCGRPYQSV-HALCRQCGSW 21 (190)
T ss_pred CCccccccccc-cCCchhhCCc
Confidence 88999998754 5799999765
No 33
>PF12773 DZR: Double zinc ribbon
Probab=28.05 E-value=28 Score=25.00 Aligned_cols=24 Identities=21% Similarity=0.643 Sum_probs=13.2
Q ss_pred eeeeecCCCCCC--CCCcccchHhhh
Q 048420 13 TVSCCKCGITMV--SNASNMCVTCLK 36 (386)
Q Consensus 13 ~ilCc~CG~~i~--pn~~nmC~~Cl~ 36 (386)
.-+|..||.++. +.....|..|-.
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcC
Confidence 445666666665 233345666654
No 34
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=27.90 E-value=21 Score=28.69 Aligned_cols=22 Identities=27% Similarity=0.699 Sum_probs=16.5
Q ss_pred eeecCCCCCCC-----CC-cccchHhhh
Q 048420 15 SCCKCGITMVS-----NA-SNMCVTCLK 36 (386)
Q Consensus 15 lCc~CG~~i~p-----n~-~nmC~~Cl~ 36 (386)
.|..||.+|++ .| ...|+.|-.
T Consensus 36 ~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~ 63 (73)
T PRK13715 36 LCEACGNPIPEARRKIFPGVTLCVECQA 63 (73)
T ss_pred cHhhcCCcCCHHHHhcCCCcCCCHHHHH
Confidence 79999999964 23 467999943
No 35
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=26.28 E-value=35 Score=26.01 Aligned_cols=25 Identities=24% Similarity=0.525 Sum_probs=19.6
Q ss_pred CCCCeeeeecCCCCCCCCCcccchHhh
Q 048420 9 AVRKTVSCCKCGITMVSNASNMCVTCL 35 (386)
Q Consensus 9 ~~~~~ilCc~CG~~i~pn~~nmC~~Cl 35 (386)
..++.+.|..||.+. .+..+|..|-
T Consensus 22 ~~p~l~~C~~cG~~~--~~H~vc~~cG 46 (55)
T TIGR01031 22 TAPTLVVCPNCGEFK--LPHRVCPSCG 46 (55)
T ss_pred cCCcceECCCCCCcc--cCeeECCccC
Confidence 344567899999987 4788999985
No 36
>cd02549 Peptidase_C39A A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=24.71 E-value=77 Score=26.51 Aligned_cols=37 Identities=14% Similarity=0.173 Sum_probs=29.0
Q ss_pred cCCCCCeEEEEeeC--CcEEEEcCCCCceeEeccccccc
Q 048420 188 LGNLGPFVICTKVT--NSIALLDPFTLRHCYLDADQYWR 224 (386)
Q Consensus 188 lG~i~~l~lc~kV~--~~I~liDP~Tl~~~~l~~~~Ywr 224 (386)
.+..|..+|+.... ..+.+.||.+++...++.+.|.+
T Consensus 90 ~~~~gH~vVv~g~~~~~~~~i~DP~~~~~~~~~~~~f~~ 128 (141)
T cd02549 90 ITPSGHAMVVIGYDRKGNVYVNDPGGGRRLVVSFDEFEK 128 (141)
T ss_pred cCCCCeEEEEEEEcCCCCEEEECCCCCcCEEEeHHHHHH
Confidence 45568899999987 48999999998877777765543
No 37
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=24.06 E-value=42 Score=26.17 Aligned_cols=24 Identities=25% Similarity=0.624 Sum_probs=17.5
Q ss_pred eeeeecCCCCCCC-----CC-cccchHhhh
Q 048420 13 TVSCCKCGITMVS-----NA-SNMCVTCLK 36 (386)
Q Consensus 13 ~ilCc~CG~~i~p-----n~-~nmC~~Cl~ 36 (386)
.-.|..||.+|.+ .| ...|+.|-.
T Consensus 31 ~g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~ 60 (63)
T TIGR02419 31 LRECEDCGEPIPEARREALPGVTRCVSCQE 60 (63)
T ss_pred CCeeccCCCcChHHHHhhcCCcCCcHHHHh
Confidence 4689999999964 23 357888843
No 38
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=23.71 E-value=40 Score=28.60 Aligned_cols=26 Identities=19% Similarity=0.698 Sum_probs=18.4
Q ss_pred eeeecCCCCCCCCCc----------------------ccchHhhhccc
Q 048420 14 VSCCKCGITMVSNAS----------------------NMCVTCLKSEV 39 (386)
Q Consensus 14 ilCc~CG~~i~pn~~----------------------nmC~~Cl~~~v 39 (386)
-.|..||.|+..-+. -+|.+|++..+
T Consensus 35 p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~~~i 82 (93)
T COG2174 35 PKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVRERI 82 (93)
T ss_pred CcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHHHHH
Confidence 369999998754332 47999987653
No 39
>PF15644 Tox-PL: Papain fold toxin 1; PDB: 3B21_A.
Probab=23.70 E-value=95 Score=26.18 Aligned_cols=23 Identities=22% Similarity=0.268 Sum_probs=18.8
Q ss_pred CCeEEEEeeCCcEEEEcCCCCce
Q 048420 192 GPFVICTKVTNSIALLDPFTLRH 214 (386)
Q Consensus 192 ~~l~lc~kV~~~I~liDP~Tl~~ 214 (386)
|..+.+......|+++||.|++.
T Consensus 88 gHa~nvv~~~G~i~~~D~Q~G~~ 110 (111)
T PF15644_consen 88 GHAFNVVNQNGKIVFLDPQSGKV 110 (111)
T ss_dssp TTEEEEEEE-SSEEEEBTTTTBS
T ss_pred ceEEEEEeCCCeEEEEeCCCCCC
Confidence 77777778888899999999875
No 40
>COG5324 Uncharacterized conserved protein [Function unknown]
Probab=23.65 E-value=19 Score=39.09 Aligned_cols=66 Identities=17% Similarity=0.286 Sum_probs=55.0
Q ss_pred eeEEecChhhHHHHHHhhccccCeEEeeeceeeccccCCCcceeEEEEEEEeeceehhccCCCCCeEEEEeeCC
Q 048420 129 IEFFFSGRSHAVKFVEFVGEVVPAQSRHEKQLVSRGTKSRNCKCKYTCSVEISAISAHNLGNLGPFVICTKVTN 202 (386)
Q Consensus 129 lDFyf~~r~~A~k~v~fl~sv~P~~~k~S~qLis~D~~sn~~~yK~T~SVeI~pica~~lG~i~~l~lc~kV~~ 202 (386)
|||-.+|...|++++..++.-.|. ||..|++...+-.-+.||||-+|--.+.+||-++- |=++++.
T Consensus 528 ld~~~~sl~nar~i~n~~~k~~p~-------lip~~p~ddd~~~a~~~a~ey~pt~rk~~gn~~kk-ik~~ita 593 (758)
T COG5324 528 LDPLIGSLENARRIVNYFKKNIPE-------LIPNDPSDDDYAAALNYAVEYVPTYRKTFGNDSKK-IKNKITA 593 (758)
T ss_pred cccccchhhhHHHHHHHHHhhCcc-------ccCCCCCchHHHHHHhhhhhcCchhhhhhCCchHH-hhhheeh
Confidence 788999999999999999998885 77999999999999999999999887778876554 3244433
No 41
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=22.83 E-value=33 Score=26.58 Aligned_cols=34 Identities=26% Similarity=0.551 Sum_probs=16.6
Q ss_pred eeeeecCCCCCCCCCcc----cch-Hhhhccccccccccce
Q 048420 13 TVSCCKCGITMVSNASN----MCV-TCLKSEVDITESLQKH 48 (386)
Q Consensus 13 ~ilCc~CG~~i~pn~~n----mC~-~Cl~~~vdItegIpk~ 48 (386)
|+.|+.||.+....+.| .|. .|- .+|+-..+..+
T Consensus 2 ~v~CP~C~k~~~~~~~n~~rPFCS~RCk--~iDLg~W~~e~ 40 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPFRPFCSERCK--LIDLGRWANEE 40 (57)
T ss_dssp EEE-TTT--EEE-SSSSS--SSSSHHHH--HHHHS-SSSSS
T ss_pred cccCCCCCCeecccCCCCcCCcccHhhc--ccCHHHHhcCC
Confidence 68899999988774443 443 232 45555444443
No 42
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.62 E-value=38 Score=24.37 Aligned_cols=21 Identities=29% Similarity=0.724 Sum_probs=13.6
Q ss_pred eeecCCCCCCCCC-----cccchHhh
Q 048420 15 SCCKCGITMVSNA-----SNMCVTCL 35 (386)
Q Consensus 15 lCc~CG~~i~pn~-----~nmC~~Cl 35 (386)
+|..||..+.+.. ...|..|=
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg 27 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCG 27 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCC
Confidence 7999998775542 23466664
No 43
>PRK08359 transcription factor; Validated
Probab=22.45 E-value=59 Score=30.48 Aligned_cols=22 Identities=23% Similarity=0.555 Sum_probs=16.8
Q ss_pred eeeecCCCCCCCCC---------cccchHhh
Q 048420 14 VSCCKCGITMVSNA---------SNMCVTCL 35 (386)
Q Consensus 14 ilCc~CG~~i~pn~---------~nmC~~Cl 35 (386)
+.|=+||++|...+ -..|.+|.
T Consensus 7 ~~CEiCG~~i~g~~~~v~ieGael~VC~~Ca 37 (176)
T PRK08359 7 RYCEICGAEIRGPGHRIRIEGAELLVCDRCY 37 (176)
T ss_pred ceeecCCCccCCCCeEEEEcCeEEehHHHHH
Confidence 45999999987552 25799999
No 44
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=22.26 E-value=47 Score=30.31 Aligned_cols=21 Identities=24% Similarity=0.694 Sum_probs=13.4
Q ss_pred eeecCCCCCCCCC---------cccchHhh
Q 048420 15 SCCKCGITMVSNA---------SNMCVTCL 35 (386)
Q Consensus 15 lCc~CG~~i~pn~---------~nmC~~Cl 35 (386)
-|=+||++|...+ -+.|.+|.
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~ 31 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECR 31 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHH
Confidence 4777777775442 25677777
No 45
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=21.97 E-value=56 Score=24.78 Aligned_cols=21 Identities=29% Similarity=0.762 Sum_probs=17.7
Q ss_pred CeeeeecCCCCCCCCCcccchHh
Q 048420 12 KTVSCCKCGITMVSNASNMCVTC 34 (386)
Q Consensus 12 ~~ilCc~CG~~i~pn~~nmC~~C 34 (386)
+.+.|..||.+. .+..+|..|
T Consensus 25 ~l~~c~~cg~~~--~~H~vc~~c 45 (56)
T PF01783_consen 25 NLVKCPNCGEPK--LPHRVCPSC 45 (56)
T ss_dssp SEEESSSSSSEE--STTSBCTTT
T ss_pred ceeeeccCCCEe--cccEeeCCC
Confidence 568899999876 477999999
No 46
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=21.56 E-value=50 Score=25.44 Aligned_cols=29 Identities=17% Similarity=0.535 Sum_probs=20.4
Q ss_pred eeeeecCCCCCC---CCCcccchHhhhccccc
Q 048420 13 TVSCCKCGITMV---SNASNMCVTCLKSEVDI 41 (386)
Q Consensus 13 ~ilCc~CG~~i~---pn~~nmC~~Cl~~~vdI 41 (386)
.-.|..||.+-. .-.-|||-.|+|+...-
T Consensus 16 sr~C~vCg~~~gliRkygL~~CRqCFRe~A~~ 47 (54)
T PTZ00218 16 SRQCRVCSNRHGLIRKYGLNVCRQCFRENAEL 47 (54)
T ss_pred CCeeecCCCcchhhhhcCcchhhHHHHHhhHh
Confidence 467999999632 12237999999986543
No 47
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=21.29 E-value=43 Score=26.42 Aligned_cols=19 Identities=21% Similarity=0.702 Sum_probs=13.2
Q ss_pred eeeeecCCCCCCCCCcccch
Q 048420 13 TVSCCKCGITMVSNASNMCV 32 (386)
Q Consensus 13 ~ilCc~CG~~i~pn~~nmC~ 32 (386)
+--|..||++|+|.. ..|.
T Consensus 8 H~HC~VCg~aIp~de-~~CS 26 (64)
T COG4068 8 HRHCVVCGKAIPPDE-QVCS 26 (64)
T ss_pred CccccccCCcCCCcc-chHH
Confidence 345999999998653 3443
No 48
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=21.27 E-value=45 Score=30.17 Aligned_cols=26 Identities=19% Similarity=0.717 Sum_probs=19.3
Q ss_pred eeeecCCCCCCCC----------------------CcccchHhhhccc
Q 048420 14 VSCCKCGITMVSN----------------------ASNMCVTCLKSEV 39 (386)
Q Consensus 14 ilCc~CG~~i~pn----------------------~~nmC~~Cl~~~v 39 (386)
-.|..||.++..- ...+|..|++.++
T Consensus 42 pkC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CVr~rI 89 (135)
T PTZ00074 42 PKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCVRDRI 89 (135)
T ss_pred CCCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHHHHHH
Confidence 4599999987542 2369999998765
No 49
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.26 E-value=58 Score=26.01 Aligned_cols=40 Identities=28% Similarity=0.565 Sum_probs=23.3
Q ss_pred CCCCeeeeecCCCCCCCCCcc----cch-HhhhccccccccccceeE
Q 048420 9 AVRKTVSCCKCGITMVSNASN----MCV-TCLKSEVDITESLQKHAN 50 (386)
Q Consensus 9 ~~~~~ilCc~CG~~i~pn~~n----mC~-~Cl~~~vdItegIpk~~~ 50 (386)
....++.|..||++.+-.+.+ .|. .| +.+|+-+....+..
T Consensus 3 ~~~~~v~CP~Cgkpv~w~~~s~frPFCSkRC--klIDLg~Wa~eey~ 47 (65)
T COG3024 3 SLRITVPCPTCGKPVVWGEESPFRPFCSKRC--KLIDLGEWAAEEYA 47 (65)
T ss_pred CccccccCCCCCCcccccccCCcCcchhHhh--hhcchhhhhccCcc
Confidence 345689999999998653222 332 33 34666555544433
No 50
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=20.79 E-value=50 Score=25.40 Aligned_cols=24 Identities=25% Similarity=0.636 Sum_probs=18.4
Q ss_pred CCCeeeeecCCCCCCCCCcccchHhh
Q 048420 10 VRKTVSCCKCGITMVSNASNMCVTCL 35 (386)
Q Consensus 10 ~~~~ilCc~CG~~i~pn~~nmC~~Cl 35 (386)
.+..+.|..||...- +...|..|-
T Consensus 24 ~~~l~~C~~CG~~~~--~H~vC~~CG 47 (57)
T PRK12286 24 APGLVECPNCGEPKL--PHRVCPSCG 47 (57)
T ss_pred CCcceECCCCCCccC--CeEECCCCC
Confidence 344578999999874 678888884
No 51
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=20.36 E-value=52 Score=28.36 Aligned_cols=33 Identities=12% Similarity=0.334 Sum_probs=25.9
Q ss_pred CeeeeecCCCCCCCCC-cccchHhhhcccccccc
Q 048420 12 KTVSCCKCGITMVSNA-SNMCVTCLKSEVDITES 44 (386)
Q Consensus 12 ~~ilCc~CG~~i~pn~-~nmC~~Cl~~~vdIteg 44 (386)
....|-.||....+.. .-.|+.|=-..++|+.|
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~~i~~G 102 (115)
T TIGR00100 69 VECECEDCSEEVSPEIDLYRCPKCHGIMLQVRAG 102 (115)
T ss_pred cEEEcccCCCEEecCCcCccCcCCcCCCcEEecC
Confidence 3578999998776643 45599999999999874
Done!