Query 029944
Match_columns 185
No_of_seqs 137 out of 286
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 06:05:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029944.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029944hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1696 60s ribosomal protein 100.0 2.9E-82 6.3E-87 522.9 16.6 183 1-183 1-183 (193)
2 PTZ00097 60S ribosomal protein 100.0 9E-80 2E-84 507.8 18.7 174 3-176 1-174 (175)
3 cd01417 Ribosomal_L19e_E Ribos 100.0 2.3E-78 5.1E-83 495.4 17.4 164 4-167 1-164 (164)
4 PTZ00436 60S ribosomal protein 100.0 1.8E-76 3.9E-81 522.6 20.0 170 1-170 1-170 (357)
5 PF01280 Ribosomal_L19e: Ribos 100.0 3.3E-74 7.2E-79 464.9 14.2 148 2-149 1-148 (148)
6 PRK08570 rpl19e 50S ribosomal 100.0 4.4E-73 9.5E-78 459.0 15.6 147 1-147 1-147 (150)
7 cd00481 Ribosomal_L19e Ribosom 100.0 7.3E-73 1.6E-77 455.6 14.9 145 4-148 1-145 (145)
8 cd01418 Ribosomal_L19e_A Ribos 100.0 2.9E-71 6.2E-76 446.2 15.5 142 4-145 1-142 (145)
9 COG2147 RPL19A Ribosomal prote 100.0 1.4E-68 3E-73 431.2 14.9 149 1-149 1-149 (150)
10 TIGR01764 excise DNA binding d 70.6 2.7 5.9E-05 25.8 1.4 30 23-53 1-30 (49)
11 PF12728 HTH_17: Helix-turn-he 69.8 3 6.5E-05 26.9 1.5 29 23-52 1-29 (51)
12 PF13453 zf-TFIIB: Transcripti 58.9 4.2 9.1E-05 25.9 0.6 15 20-34 26-40 (41)
13 PF13880 Acetyltransf_13: ESCO 58.6 3.1 6.7E-05 30.3 -0.1 14 16-29 5-18 (70)
14 PF14468 DUF4427: Protein of u 51.1 12 0.00025 30.5 2.1 33 12-53 30-62 (132)
15 TIGR02075 pyrH_bact uridylate 46.5 22 0.00047 30.0 3.2 48 5-52 77-125 (233)
16 PRK00247 putative inner membra 40.8 3.1E+02 0.0067 26.3 10.1 69 92-167 291-363 (429)
17 PRK05920 aromatic acid decarbo 37.7 38 0.00082 28.9 3.3 47 9-58 121-167 (204)
18 PF09851 SHOCT: Short C-termin 37.7 40 0.00087 20.4 2.5 20 104-123 6-25 (31)
19 PF01479 S4: S4 domain; Inter 36.7 26 0.00057 22.1 1.7 25 31-55 9-33 (48)
20 smart00345 HTH_GNTR helix_turn 35.1 30 0.00064 21.8 1.8 25 32-56 32-56 (60)
21 PF12802 MarR_2: MarR family; 34.3 29 0.00062 22.5 1.6 52 7-60 7-61 (62)
22 cd04254 AAK_UMPK-PyrH-Ec UMP k 33.7 42 0.0009 28.2 2.9 44 9-52 81-124 (231)
23 COG3592 Uncharacterized conser 32.5 22 0.00047 26.4 0.9 19 11-30 35-53 (74)
24 PRK11548 outer membrane biogen 32.5 31 0.00068 26.4 1.8 26 22-47 36-61 (113)
25 PRK06029 3-octaprenyl-4-hydrox 31.7 58 0.0013 27.3 3.4 47 9-58 106-152 (185)
26 PHA00616 hypothetical protein 30.9 28 0.00061 23.3 1.1 20 129-148 8-27 (44)
27 PF08535 KorB: KorB domain; I 30.0 46 0.00099 24.2 2.3 39 6-51 5-43 (93)
28 TIGR01610 phage_O_Nterm phage 29.9 32 0.00069 25.4 1.4 38 16-54 40-81 (95)
29 PF03428 RP-C: Replication pro 29.9 1.9E+02 0.0042 24.2 6.2 56 90-145 71-139 (177)
30 PF06353 DUF1062: Protein of u 26.8 48 0.001 27.0 2.0 23 34-56 113-135 (142)
31 PF00392 GntR: Bacterial regul 25.6 55 0.0012 21.9 1.9 28 31-58 35-62 (64)
32 PF00096 zf-C2H2: Zinc finger, 25.6 54 0.0012 17.5 1.5 16 129-144 7-22 (23)
33 PRK00083 frr ribosome recyclin 25.2 3.8E+02 0.0082 22.5 7.2 85 22-126 69-159 (185)
34 smart00099 btg1 tob/btg1 famil 24.8 27 0.00059 27.4 0.2 10 21-30 93-102 (108)
35 COG5104 PRP40 Splicing factor 24.0 3E+02 0.0066 27.2 7.1 50 6-56 426-488 (590)
36 TIGR02988 YaaA_near_RecF S4 do 23.6 59 0.0013 21.7 1.7 19 36-54 22-40 (59)
37 cd04762 HTH_MerR-trunc Helix-T 23.4 67 0.0015 19.1 1.8 17 36-52 12-28 (49)
38 KOG1596 Fibrillarin and relate 23.2 52 0.0011 30.1 1.7 56 6-71 137-204 (317)
39 smart00420 HTH_DEOR helix_turn 21.9 75 0.0016 19.3 1.9 25 32-56 26-50 (53)
40 TIGR00421 ubiX_pad polyprenyl 21.9 1.1E+02 0.0024 25.3 3.4 47 9-58 103-149 (181)
41 COG3664 XynB Beta-xylosidase [ 21.1 35 0.00075 32.7 0.2 46 10-56 23-68 (428)
42 PF07742 BTG: BTG family; Int 21.0 29 0.00063 27.3 -0.2 10 21-30 95-104 (118)
43 PF04355 SmpA_OmlA: SmpA / Oml 20.8 49 0.0011 22.6 0.9 27 24-50 4-30 (71)
44 cd04261 AAK_AKii-LysC-BS AAK_A 20.8 92 0.002 26.2 2.7 43 10-53 79-131 (239)
45 PF06014 DUF910: Bacterial pro 20.7 78 0.0017 22.7 1.9 22 101-122 29-50 (62)
46 cd01145 TroA_c Periplasmic bin 20.4 50 0.0011 27.2 1.0 19 19-37 107-125 (203)
47 PF13412 HTH_24: Winged helix- 20.3 72 0.0016 20.0 1.6 20 32-51 29-48 (48)
48 PF02736 Myosin_N: Myosin N-te 20.2 41 0.00088 21.5 0.4 10 19-28 1-11 (42)
49 PRK10079 phosphonate metabolis 20.2 67 0.0014 26.8 1.7 46 8-58 23-73 (241)
50 PF15319 RHINO: RAD9, RAD1, HU 20.1 39 0.00084 30.0 0.3 33 84-120 202-234 (236)
No 1
>KOG1696 consensus 60s ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-82 Score=522.88 Aligned_cols=183 Identities=75% Similarity=1.141 Sum_probs=181.4
Q ss_pred CCchhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCC
Q 029944 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (185)
Q Consensus 1 M~~l~~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~SR~R~r~~~~~r~kGR~~G~Gk 80 (185)
|++|++|||||||||+||+.+|||||||+++|++|||||+|++||+||+||.+|+++|||+||+++.+++++|||+|+|+
T Consensus 1 Ms~lrlqKRLAssVl~cGKkKvWlDpNE~~eI~~ansRq~irkLikdg~iI~Kp~~vhsr~r~rk~~~akrkgrH~G~GK 80 (193)
T KOG1696|consen 1 MSNLRLQKRLAASVLKCGKKKVWLDPNEISEISGANSRQNIRKLIKDGLIIRKPVTVHSRSRCRKRLEAKRKGRHMGYGK 80 (193)
T ss_pred CchHHHHHHHHHHHHHhcccceeeCccHHHHhcccchHHHHHHHHhCCeEeecchhhhHHHHHHHHHHHHHhccccCccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHhhhHHHHhhhhhHHHH
Q 029944 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFE 160 (185)
Q Consensus 81 RkGt~~AR~p~K~~Wm~riR~lRr~Lk~~re~~kID~~~Yr~lY~kaKGn~Fknk~~L~e~i~~~k~e~~r~k~l~dQae 160 (185)
|+||+|||||+|++||++||+||++|++|||+|+||+|+||.||+++|||+|+|+.+|+||||+.++|++++|+|+||||
T Consensus 81 RkGTanArmP~k~~Wmrr~RvlRrlL~kyR~skKIdkh~YH~lY~k~KGnvFKnK~~LmE~I~K~KAe~~r~K~LadQae 160 (193)
T KOG1696|consen 81 RKGTANARMPSKVLWMRRMRVLRRLLKKYRDSKKIDKHMYHDLYLKVKGNVFKNKRVLMEHIHKSKAEKAREKLLADQAE 160 (193)
T ss_pred ccccccccCchhHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhchHHHHHHHHHHHHHHHhh
Q 029944 161 AKRAKNKASRERKLARREERLAQ 183 (185)
Q Consensus 161 A~r~k~k~~r~rr~~~~~~kk~~ 183 (185)
|++.++++++++++|++++++++
T Consensus 161 Arr~k~k~ar~rreer~~~k~~~ 183 (193)
T KOG1696|consen 161 ARRLKNKAARKRREERLAAKPQE 183 (193)
T ss_pred HHHhhhHHHhhhHHHHHhhchhh
Confidence 99999999999999999998864
No 2
>PTZ00097 60S ribosomal protein L19; Provisional
Probab=100.00 E-value=9e-80 Score=507.78 Aligned_cols=174 Identities=71% Similarity=1.152 Sum_probs=171.3
Q ss_pred chhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCCcc
Q 029944 3 SLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRK 82 (185)
Q Consensus 3 ~l~~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~SR~R~r~~~~~r~kGR~~G~GkRk 82 (185)
+|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||||++++++++++|||+|||||+
T Consensus 1 ~l~~QKRLAA~vL~cG~~rVWiDP~~~~eI~~A~tR~dIR~LIkdG~I~~kp~kg~SR~R~r~~~~~k~kGR~~G~G~RK 80 (175)
T PTZ00097 1 NLRLQKRLAASVLKCGKNRVWLDPNEASEISLANSRFSIRKLIKDGLIIRKPVAVHSRARARRFHEAKRKGRHTGIGKRR 80 (175)
T ss_pred CchHHHHHHHHHHCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCCCCCChHHHHHHHHHHHhCCCCCCCCCc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHhhhHHHHhhhhhHHHHHH
Q 029944 83 GTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAK 162 (185)
Q Consensus 83 Gt~~AR~p~K~~Wm~riR~lRr~Lk~~re~~kID~~~Yr~lY~kaKGn~Fknk~~L~e~i~~~k~e~~r~k~l~dQaeA~ 162 (185)
||+|||+|+|+.||.+||+||++|++|||+|+||+|+||.||++||||+|+|++||++||++.++|++++++|+||+||+
T Consensus 81 Gtk~AR~p~K~~W~~riR~lRr~Lk~~R~~~kIdk~~Yr~lY~kaKGn~Fknk~~L~~~I~~~kae~~r~k~l~~q~~a~ 160 (175)
T PTZ00097 81 GTREARMPTKVLWMRRQRVLRRLLRKYRAAKKIDRHMYHEFYLKSKGNQFKNKRVLIEAIHKTKNEKVKEKKIQDQLEAR 160 (175)
T ss_pred CcccccCcHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhchHHHHHHHHHH
Q 029944 163 RAKNKASRERKLAR 176 (185)
Q Consensus 163 r~k~k~~r~rr~~~ 176 (185)
+.+++++++++.++
T Consensus 161 r~k~~~~~~~r~~~ 174 (175)
T PTZ00097 161 RAKAKALRNKRKAK 174 (175)
T ss_pred HHHHHHHHHHHhhc
Confidence 99999999987653
No 3
>cd01417 Ribosomal_L19e_E Ribosomal protein L19e, eukaryotic. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=100.00 E-value=2.3e-78 Score=495.37 Aligned_cols=164 Identities=79% Similarity=1.221 Sum_probs=161.9
Q ss_pred hhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCCccc
Q 029944 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (185)
Q Consensus 4 l~~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~SR~R~r~~~~~r~kGR~~G~GkRkG 83 (185)
|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||||++++++++++|||+|+|||+|
T Consensus 1 l~~QKRLAA~vL~cG~~rVW~DP~~~~eI~~A~tR~dIR~LIkdG~I~~kp~kg~SR~R~r~~~~~k~kGR~~G~G~RkG 80 (164)
T cd01417 1 LRLQKRLAASVLKCGKRKVWLDPNEISEISNANSRQSIRKLIKDGLIIKKPVKVHSRSRARKRHEAKRKGRHMGYGKRKG 80 (164)
T ss_pred CcHHHHHHHHHHCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCCCcCCHHHHHHHHHHHHhCCCCCCCCCcC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHhhhHHHHhhhhhHHHHHHH
Q 029944 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFEAKR 163 (185)
Q Consensus 84 t~~AR~p~K~~Wm~riR~lRr~Lk~~re~~kID~~~Yr~lY~kaKGn~Fknk~~L~e~i~~~k~e~~r~k~l~dQaeA~r 163 (185)
|+|||+|+|+.||++||+||++|++|||+|+||+|+||.||++||||+|+|++||++||++.++|+++++.|+||+||++
T Consensus 81 t~~AR~p~K~~W~~riR~lRr~Lk~~R~~~kIdk~~Yr~lY~kaKGn~Fknk~~L~~~I~~~kae~~r~k~l~~q~~a~r 160 (164)
T cd01417 81 TANARMPSKVLWMRRQRVLRRLLKKYRESKKIDKHLYHELYLKAKGNVFKNKRVLMEHIHKAKAEKAREKELADQAEARR 160 (164)
T ss_pred cccccCcHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hchH
Q 029944 164 AKNK 167 (185)
Q Consensus 164 ~k~k 167 (185)
++++
T Consensus 161 ~~~~ 164 (164)
T cd01417 161 AKNK 164 (164)
T ss_pred hccC
Confidence 8863
No 4
>PTZ00436 60S ribosomal protein L19-like protein; Provisional
Probab=100.00 E-value=1.8e-76 Score=522.57 Aligned_cols=170 Identities=67% Similarity=1.101 Sum_probs=168.0
Q ss_pred CCchhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCC
Q 029944 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (185)
Q Consensus 1 M~~l~~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~SR~R~r~~~~~r~kGR~~G~Gk 80 (185)
|++|++||||||+||+||++|||||||+++||++||||+|||+||+||+|+++|++||||||+|++++++++|||+|+||
T Consensus 1 M~dLklQKRLAAsVL~cGk~RVWiDPnel~eIa~AiTReDIRkLIkdGlIikKp~KGhSRgRaRkr~eaKrKGRhrG~Gs 80 (357)
T PTZ00436 1 MVSLKLQARLAADILRCGRHRVWLDPNEASEISNANSRKSVRKLIKDGLIIRKPVKVHSRSRWRHMKEAKSMGRHEGAGR 80 (357)
T ss_pred CcchHHHHHHHHHHhCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCcccCChHHHHHHHHHHHhCcCCCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHhhhHHHHhhhhhHHHH
Q 029944 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQFE 160 (185)
Q Consensus 81 RkGt~~AR~p~K~~Wm~riR~lRr~Lk~~re~~kID~~~Yr~lY~kaKGn~Fknk~~L~e~i~~~k~e~~r~k~l~dQae 160 (185)
|+||+|||+|+|++||++||+||++|++|||+|+||+|+||.||+++|||+|+|++||++||++.++|+.++++|.||++
T Consensus 81 RKGTk~AR~P~K~~WIrRIRaLRRlLKklRd~gKIDkh~YR~LYrKAKGn~FKNK~~L~e~I~k~KaE~~R~K~L~dQ~e 160 (357)
T PTZ00436 81 REGTREARMPSKELWMRRLRILRRLLRKYREEKKIDRHIYRELYVKAKGNVFRNKRNLMEHIHKVKNEKKKERQLAEQLA 160 (357)
T ss_pred CcCcccccCcHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCccCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhchHHHH
Q 029944 161 AKRAKNKASR 170 (185)
Q Consensus 161 A~r~k~k~~r 170 (185)
|+|.++++.|
T Consensus 161 ArR~k~~~~r 170 (357)
T PTZ00436 161 AKRLKDEQHR 170 (357)
T ss_pred HHHHHhhhhh
Confidence 9999988654
No 5
>PF01280 Ribosomal_L19e: Ribosomal protein L19e; InterPro: IPR000196 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 entry represents structural domain of the ribosomal protein L19 from eukaryotes, as well as L19e from archaea []. L19/L19e is absent in bacteria. L19/L19e is part of the large ribosomal subunit, whose structure has been determined in a number of eukaryotic and archaeal species []. L19/L19e is a multi-helical protein consisting of two different 3-helical domains connected by a long, partly helical linker.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_T 3O58_S 3O5H_S 3IZS_T 2WWA_J 1S1I_P 2WW9_J 2ZKR_7 4A1A_O 4A1C_O ....
Probab=100.00 E-value=3.3e-74 Score=464.89 Aligned_cols=148 Identities=68% Similarity=1.093 Sum_probs=130.9
Q ss_pred CchhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCCc
Q 029944 2 VSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKR 81 (185)
Q Consensus 2 ~~l~~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~SR~R~r~~~~~r~kGR~~G~GkR 81 (185)
|||++||||||+||+||+++|||||||++||++||||+|||+||+||+|+++|++|||||||+++++++++|||+|||+|
T Consensus 1 m~l~~QKRLAa~vL~~G~~rVw~DP~~~~eI~~A~tR~~IR~LIk~G~I~~k~~k~~Sr~R~r~~~~~r~kGr~~G~G~R 80 (148)
T PF01280_consen 1 MDLKLQKRLAASVLGCGKNRVWIDPNELEEIANAITREDIRKLIKDGLIIKKPVKGHSRGRARKRKEARRKGRHRGPGKR 80 (148)
T ss_dssp -STHHHHHHHHHHHTS-GGGEEE-STTHHHHHH--SHHHHHHHHHTTSEEE---S--STHHHHHHHHHHHCTTS-SSTTS
T ss_pred CccHHHHHHHHHHHCCCCCcEEeCHHHHHHHHhhhhHHHHHHHHHCCCeEeCCCCCCchHHHHHHHHHHhhccccccccc
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHhhhHH
Q 029944 82 KGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEK 149 (185)
Q Consensus 82 kGt~~AR~p~K~~Wm~riR~lRr~Lk~~re~~kID~~~Yr~lY~kaKGn~Fknk~~L~e~i~~~k~e~ 149 (185)
+||+|||+|+|+.||.+||+||++|++|||+|+||+|+||.||++||||+|+|++||++||+++++|+
T Consensus 81 kGt~~AR~~~K~~W~~riR~lRr~Lk~~r~~~kID~~~Yr~lY~kaKGn~Fkn~~~L~~~i~~~k~e~ 148 (148)
T PF01280_consen 81 KGTKNARMPEKELWMRRIRALRRLLKRLRDSGKIDRHMYRSLYRKAKGNVFKNKRHLMEHIHKLKAEK 148 (148)
T ss_dssp -S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTTS-SSHHHHHHHHHHHHHCH
T ss_pred cccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCcccCHHHHHHHHHHhccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999875
No 6
>PRK08570 rpl19e 50S ribosomal protein L19e; Reviewed
Probab=100.00 E-value=4.4e-73 Score=458.96 Aligned_cols=147 Identities=42% Similarity=0.736 Sum_probs=145.4
Q ss_pred CCchhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCC
Q 029944 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (185)
Q Consensus 1 M~~l~~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~SR~R~r~~~~~r~kGR~~G~Gk 80 (185)
|++|++|+||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||||++++++++++|||+||||
T Consensus 1 M~~l~~qkRLAA~iL~~G~~rVw~DP~~~~eI~~A~tR~dIR~LI~~G~I~~kp~kg~Sr~R~r~~~~~r~kGr~~G~G~ 80 (150)
T PRK08570 1 MMDLSAQKRLAADILGVGVSRVWIDPEALEDVAEAITREDIRELIKEGVIKAKPKKGISRGRARERHEKRKKGRRRGPGS 80 (150)
T ss_pred CcchHHHHHHHHHHHCCCccceeeCHHHHHHHHHHhhHHHHHHHHHCCCeeecCccCCChHHHHHHHHHHHhCCCCCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHhhh
Q 029944 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKA 147 (185)
Q Consensus 81 RkGt~~AR~p~K~~Wm~riR~lRr~Lk~~re~~kID~~~Yr~lY~kaKGn~Fknk~~L~e~i~~~k~ 147 (185)
|+||+|||+|+|+.||.+||+||++|++|||+|+||+|+||.||++||||+|+|++||++||+....
T Consensus 81 RkGt~~AR~p~K~~W~~riR~lRr~Lk~lR~~~kId~~~Yr~lY~kaKGn~Fkn~~~L~~~i~~~~~ 147 (150)
T PRK08570 81 RKGKKGARTPKKERWINRIRALRRYLRELRDEGKIDRKTYRKLYRKAKGGEFRSVSHLKTYIEEHGL 147 (150)
T ss_pred CCCcccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCccCCHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999999999999999999998764
No 7
>cd00481 Ribosomal_L19e Ribosomal protein L19e. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=100.00 E-value=7.3e-73 Score=455.58 Aligned_cols=145 Identities=66% Similarity=1.102 Sum_probs=142.9
Q ss_pred hhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCCccc
Q 029944 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (185)
Q Consensus 4 l~~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~SR~R~r~~~~~r~kGR~~G~GkRkG 83 (185)
|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||||++++++++++|||+|||||+|
T Consensus 1 l~~QkRLAA~vL~~G~~rVW~DP~~~~eI~~A~tR~dIR~LIkdG~I~~kp~kg~Sr~R~r~~~~~r~kGr~~G~G~RkG 80 (145)
T cd00481 1 LRLQKRLAADILKCGKNRVWIDPNELEEIANANTREDIRKLIKDGLIIKKPKKGHSRGRARKRHEARRKGRHRGPGSRKG 80 (145)
T ss_pred CcHHHHHHHHHHCCCCCceeeCHHHHHHHHHhhhHHHHHHHHHCCCeeecCCCCCChHHHHHHHHHHHhCcCCCCCCccC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHhhhH
Q 029944 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAE 148 (185)
Q Consensus 84 t~~AR~p~K~~Wm~riR~lRr~Lk~~re~~kID~~~Yr~lY~kaKGn~Fknk~~L~e~i~~~k~e 148 (185)
|++||+|+|+.||.+||+||++|++|||+|+||+|+||.||++||||+|+|++||++||++.++|
T Consensus 81 t~~AR~p~K~~W~~riR~lRr~Lk~~R~~~kIdk~~Yr~lY~kaKG~~Fknk~~L~~~i~~~~~~ 145 (145)
T cd00481 81 TKGARMPSKELWIRRIRALRRLLKKLRDSGKIDKHTYRELYLKAKGNVFKNKRHLKEYIHKAKAE 145 (145)
T ss_pred ccccCCcHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCCHHHHHHHHHHhccC
Confidence 99999999999999999999999999999999999999999999999999999999999998764
No 8
>cd01418 Ribosomal_L19e_A Ribosomal protein L19e, archaeal. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=100.00 E-value=2.9e-71 Score=446.18 Aligned_cols=142 Identities=40% Similarity=0.723 Sum_probs=140.5
Q ss_pred hhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCCccc
Q 029944 4 LKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKG 83 (185)
Q Consensus 4 l~~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~SR~R~r~~~~~r~kGR~~G~GkRkG 83 (185)
|++||||||+||+||+++||||||+++||++||||+|||+||+||+|+++|++||||||++++++++++|||+|||||+|
T Consensus 1 l~~QkRLAA~iL~~G~~rVw~DP~~~~eI~~A~tR~dIR~LI~~G~I~~kp~kg~Sr~R~r~~~~~r~kGr~~G~G~RkG 80 (145)
T cd01418 1 LSSQRRLAADILGVGINRVWIDPERLEEVAEAITRDDIRALIKEGVIKAKPKKGISRGRLKERHEKRKKGRRRGPGSRKG 80 (145)
T ss_pred CcHHHHHHHHHHCCCCCeeeeChHHHHHHHHhhhHHHHHHHHHCCCeeecCCCCCCHHHHHHHHHHHHhCcCCCCCCCCC
Confidence 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHh
Q 029944 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKS 145 (185)
Q Consensus 84 t~~AR~p~K~~Wm~riR~lRr~Lk~~re~~kID~~~Yr~lY~kaKGn~Fknk~~L~e~i~~~ 145 (185)
|+|||+|+|+.||.+||+||++|++|||+|+||+|+||.||++||||+|+|++||++||..+
T Consensus 81 t~~AR~p~K~~W~~riR~lRr~Lk~~R~~~kId~~~Yr~lY~kaKGn~Fkn~~~L~~~I~~~ 142 (145)
T cd01418 81 KKGARTPKKERWIKTIRALRRYLKELRDKGKIDKKTYRKLYRKAKGGSFRSLSHLKSYLKQH 142 (145)
T ss_pred ccccCCCHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCCcCCHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999876
No 9
>COG2147 RPL19A Ribosomal protein L19E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-68 Score=431.16 Aligned_cols=149 Identities=50% Similarity=0.809 Sum_probs=146.6
Q ss_pred CCchhhhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHhcCcCCCCCC
Q 029944 1 MVSLKLQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGK 80 (185)
Q Consensus 1 M~~l~~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~SR~R~r~~~~~r~kGR~~G~Gk 80 (185)
|+||++|+||||+||+||++|||||||+++||++|+||+|||.||+||+|+++|++|+|+||+++++++++||||+||||
T Consensus 1 M~nl~~qkRLAA~il~vG~~Rvwidp~~~eei~~A~TR~dIr~LIk~g~I~~k~~kg~SrgR~rkr~~qkkkgr~rG~Gs 80 (150)
T COG2147 1 MSNLRTQKRLAADILGVGENRVWIDPNEIEEIASAITREDIRALIKDGVIKAKPKKGISRGRARKRHAQKKKGRRRGPGS 80 (150)
T ss_pred CchHHHHHHHHHHHHccCcceeeeChHHHHHHHHhhhHHHHHHHHHCCCeeeccccccchHHHHHHHHHHhcccCCCCCc
Confidence 88999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhhHHHHhhhcCCccccHHHHHHHHHHhhhHH
Q 029944 81 RKGTREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEK 149 (185)
Q Consensus 81 RkGt~~AR~p~K~~Wm~riR~lRr~Lk~~re~~kID~~~Yr~lY~kaKGn~Fknk~~L~e~i~~~k~e~ 149 (185)
|+||++||+|+|+.||.+||+||++|++|+|+|+||+|+||.||+++|||.|++++||.+||.+++.++
T Consensus 81 RKG~k~AR~p~K~~Wi~~IRalR~~Lr~lrd~gkIdk~~YR~lY~~aKGg~fk~~~~L~~~i~~~~~~k 149 (150)
T COG2147 81 RKGTKGARMPSKERWIKRIRALRRELRKLRDDGKIDKHTYRKLYRMAKGGAFKSKSHLKSYIEEAKLLK 149 (150)
T ss_pred cccccccCCCHHHHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHcCCccccHHHHHHHHHHhcccc
Confidence 999999999999999999999999999999999999999999999999999999999999999987653
No 10
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=70.58 E-value=2.7 Score=25.81 Aligned_cols=30 Identities=20% Similarity=0.297 Sum_probs=24.7
Q ss_pred ecCccchhHHHhhhhhHHHHhhhhcCceeec
Q 029944 23 WLDPNEVNEISMANSRQNIRKLVKDGFIIRK 53 (185)
Q Consensus 23 WlDP~e~~eIa~A~sR~~IRkLIkdG~I~~k 53 (185)
||++.|+.++-. +|+..|+.|+++|.|-.-
T Consensus 1 ~lt~~e~a~~lg-is~~ti~~~~~~g~i~~~ 30 (49)
T TIGR01764 1 YLTVEEAAEYLG-VSKDTVYRLIHEGELPAY 30 (49)
T ss_pred CCCHHHHHHHHC-CCHHHHHHHHHcCCCCeE
Confidence 677788888775 799999999999987653
No 11
>PF12728 HTH_17: Helix-turn-helix domain
Probab=69.77 E-value=3 Score=26.86 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=24.8
Q ss_pred ecCccchhHHHhhhhhHHHHhhhhcCceee
Q 029944 23 WLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (185)
Q Consensus 23 WlDP~e~~eIa~A~sR~~IRkLIkdG~I~~ 52 (185)
||++.|+-++-. +|+..|+.+++.|.|..
T Consensus 1 ~lt~~e~a~~l~-is~~tv~~~~~~g~i~~ 29 (51)
T PF12728_consen 1 YLTVKEAAELLG-ISRSTVYRWIRQGKIPP 29 (51)
T ss_pred CCCHHHHHHHHC-cCHHHHHHHHHcCCCCe
Confidence 678888888888 79999999999997743
No 12
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=58.86 E-value=4.2 Score=25.87 Aligned_cols=15 Identities=27% Similarity=0.809 Sum_probs=12.4
Q ss_pred CceecCccchhHHHh
Q 029944 20 GKVWLDPNEVNEISM 34 (185)
Q Consensus 20 ~rVWlDP~e~~eIa~ 34 (185)
.-||||++|++.|.+
T Consensus 26 ~G~W~d~~el~~~~e 40 (41)
T PF13453_consen 26 GGIWFDAGELEKLLE 40 (41)
T ss_pred CeEEccHHHHHHHHh
Confidence 469999999998754
No 13
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=58.58 E-value=3.1 Score=30.28 Aligned_cols=14 Identities=29% Similarity=1.037 Sum_probs=12.0
Q ss_pred ccCCCceecCccch
Q 029944 16 KCGRGKVWLDPNEV 29 (185)
Q Consensus 16 ~cG~~rVWlDP~e~ 29 (185)
-||++|||..|..-
T Consensus 5 ~~GI~RIWV~~~~R 18 (70)
T PF13880_consen 5 VCGISRIWVSPSHR 18 (70)
T ss_pred EEEeEEEEeChhhh
Confidence 59999999999763
No 14
>PF14468 DUF4427: Protein of unknown function (DUF4427)
Probab=51.15 E-value=12 Score=30.54 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=25.2
Q ss_pred HHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeec
Q 029944 12 ASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRK 53 (185)
Q Consensus 12 a~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~k 53 (185)
.-++.-|...||| |+ |+.+=+|.||+.|.|+.-
T Consensus 30 ~~~~e~G~~wvWi-~D--------N~~~~vRALl~~grV~v~ 62 (132)
T PF14468_consen 30 DYDREFGNAWVWI-HD--------NQSEVVRALLQAGRVKVN 62 (132)
T ss_pred cchhhcCceEEEE-ec--------CcCHHHHHHHHcCceeec
Confidence 3456789999999 33 455668999999998754
No 15
>TIGR02075 pyrH_bact uridylate kinase. This protein, also called UMP kinase, converts UMP to UDP by adding a phosphate from ATP. It is the first step in pyrimidine biosynthesis. GTP is an allosteric activator. In a large fraction of all bacterial genomes, the gene tends to be located immediately downstream of elongation factor Ts and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function and found in the archaea and in spirochetes, is described by a separate model, TIGR02076.
Probab=46.49 E-value=22 Score=30.03 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=38.1
Q ss_pred hhhHHH-HHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceee
Q 029944 5 KLQKRL-SASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (185)
Q Consensus 5 ~~QKRL-Aa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~ 52 (185)
.++-+| +..+...|.+-++++|.....+..-.+.+.+..|++.|.|..
T Consensus 77 ~l~~~l~~~~L~~~Gi~a~~l~~~~~~~~~~~~~~~~i~~ll~~g~VpV 125 (233)
T TIGR02075 77 VINGLALRDALEKLGVKTRVLSAISMPQICESYIRRKAIKHLEKGKVVI 125 (233)
T ss_pred HHHHHHHHHHHHhCCCCcEEeccccCCCCccccCHHHHHHHHHCCCEEE
Confidence 455665 677778999999999998765555567899999999999854
No 16
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=40.79 E-value=3.1e+02 Score=26.28 Aligned_cols=69 Identities=16% Similarity=0.254 Sum_probs=36.2
Q ss_pred hHHHHHHHHHHHHHHHHHHhcC---CCChHhhHHHHhhhcCCccccHHHHHHHHHHhhhHHHHhhhhhHH-HHHHHhchH
Q 029944 92 KILWMRRMRVLRRLLRKYRESK---KIDKHMYHDMYMKVKGNVFKNKRVLMESIHKSKAEKAREKTLSDQ-FEAKRAKNK 167 (185)
Q Consensus 92 K~~Wm~riR~lRr~Lk~~re~~---kID~~~Yr~lY~kaKGn~Fknk~~L~e~i~~~k~e~~r~k~l~dQ-aeA~r~k~k 167 (185)
+..|..+.+..+..++..|... .|.+..+..|..- +...=.+.=...+++++++|.++.+ -||.|.-++
T Consensus 291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~-------~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~~~~~~ 363 (429)
T PRK00247 291 RAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAE-------NAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINR 363 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccCCcccHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456666666665555555544 7888877777442 1222223333345566666666543 233333344
No 17
>PRK05920 aromatic acid decarboxylase; Validated
Probab=37.68 E-value=38 Score=28.91 Aligned_cols=47 Identities=32% Similarity=0.289 Sum_probs=36.5
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCC
Q 029944 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIH 58 (185)
Q Consensus 9 RLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~ 58 (185)
+.|...|+.+. .|.|=|.+... +++++++|..|-..|.++.-|..|.
T Consensus 121 ~~a~~~L~~~~-pvvi~P~~m~~--~~~~~~nl~~L~~~G~~ii~P~~g~ 167 (204)
T PRK05920 121 RAADVVLKERR-KLILVPRETPL--SLIHLENMLKLAEAGAIILPAIPAF 167 (204)
T ss_pred HHHHHHHhcCC-CEEEEeCCCCC--CHHHHHHHHHHHHCCCEEeCCcccc
Confidence 55567788777 45555765443 7889999999999999999999875
No 18
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=37.66 E-value=40 Score=20.41 Aligned_cols=20 Identities=15% Similarity=0.320 Sum_probs=17.2
Q ss_pred HHHHHHHhcCCCChHhhHHH
Q 029944 104 RLLRKYRESKKIDKHMYHDM 123 (185)
Q Consensus 104 r~Lk~~re~~kID~~~Yr~l 123 (185)
..|+.+.+.|.|+...|...
T Consensus 6 ~~L~~l~~~G~IseeEy~~~ 25 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYEQK 25 (31)
T ss_pred HHHHHHHHcCCCCHHHHHHH
Confidence 46889999999999999764
No 19
>PF01479 S4: S4 domain; InterPro: IPR002942 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 [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=36.72 E-value=26 Score=22.13 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=19.6
Q ss_pred HHHhhhhhHHHHhhhhcCceeecCC
Q 029944 31 EISMANSRQNIRKLVKDGFIIRKPT 55 (185)
Q Consensus 31 eIa~A~sR~~IRkLIkdG~I~~kp~ 55 (185)
+.-.+.||.++++||+.|-|..--.
T Consensus 9 ~~~~~~sr~~a~~~I~~g~V~VNg~ 33 (48)
T PF01479_consen 9 RLGLASSRSEARRLIKQGRVKVNGK 33 (48)
T ss_dssp HTTSSSSHHHHHHHHHTTTEEETTE
T ss_pred HcCCcCCHHHHHHhcCCCEEEECCE
Confidence 3445779999999999999876443
No 20
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=35.12 E-value=30 Score=21.81 Aligned_cols=25 Identities=24% Similarity=0.578 Sum_probs=18.1
Q ss_pred HHhhhhhHHHHhhhhcCceeecCCC
Q 029944 32 ISMANSRQNIRKLVKDGFIIRKPTK 56 (185)
Q Consensus 32 Ia~A~sR~~IRkLIkdG~I~~kp~~ 56 (185)
|+.+.-+..+..|.++|+|...|-.
T Consensus 32 vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 32 VSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCC
Confidence 3345556777789999999877654
No 21
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=34.26 E-value=29 Score=22.53 Aligned_cols=52 Identities=21% Similarity=0.242 Sum_probs=30.3
Q ss_pred hHHHHHHHhccCCCceecCccchhHH---HhhhhhHHHHhhhhcCceeecCCCCCCh
Q 029944 7 QKRLSASVLKCGRGKVWLDPNEVNEI---SMANSRQNIRKLVKDGFIIRKPTKIHSR 60 (185)
Q Consensus 7 QKRLAa~vL~cG~~rVWlDP~e~~eI---a~A~sR~~IRkLIkdG~I~~kp~~~~SR 60 (185)
|-++-..|..+|.. ++-+.++.+. +-...-.-|..|++.|+|.+.+.....|
T Consensus 7 q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D~R 61 (62)
T PF12802_consen 7 QFRVLMALARHPGE--ELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGDRR 61 (62)
T ss_dssp HHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSSTT
T ss_pred HHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCCCC
Confidence 44444555555554 3333333332 2233345688999999999998877665
No 22
>cd04254 AAK_UMPK-PyrH-Ec UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). The UMP kinase of E. coli (Ec) is known to function as a homohexamer, with GTP and UTP being allosteric effectors. Like other related enzymes (carbamate kinase, aspartokinase, and N-acetylglutamate kinase) the E. coli and most bacterial and chloroplast UMPKs (this CD) have a conserved, N-terminal, lysine residue proposed to function in the catalysis of the phosphoryl group transfer, whereas most archaeal UMPKs appear to lack this residue and the Pyrococcus furiosus structure has an additional Mg ion bound to the ATP molecule which is proposed to function as the catalysis instead. Members of this CD be
Probab=33.68 E-value=42 Score=28.25 Aligned_cols=44 Identities=9% Similarity=0.130 Sum_probs=35.8
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceee
Q 029944 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIR 52 (185)
Q Consensus 9 RLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~ 52 (185)
-|++.+...|.+-++|+|-+++.+.....-+.+..+++.|.|..
T Consensus 81 ll~~~L~~~Gv~a~~l~~~~~~~~~~~~~~~~l~~~l~~g~ipV 124 (231)
T cd04254 81 ALQDALESLGVKTRVMSAIPMQGVAEPYIRRRAIRHLEKGRVVI 124 (231)
T ss_pred HHHHHHHHcCCCeEEEcHHHhhhhhcccCHHHHHHHHHCCCEEE
Confidence 35667778999999999998876655566799999999998743
No 23
>COG3592 Uncharacterized conserved protein [Function unknown]
Probab=32.49 E-value=22 Score=26.39 Aligned_cols=19 Identities=32% Similarity=0.789 Sum_probs=14.8
Q ss_pred HHHHhccCCCceecCccchh
Q 029944 11 SASVLKCGRGKVWLDPNEVN 30 (185)
Q Consensus 11 Aa~vL~cG~~rVWlDP~e~~ 30 (185)
+++|+++|..= ||+|+..+
T Consensus 35 n~~vF~~~rkP-WI~Pd~~~ 53 (74)
T COG3592 35 NPKVFNLGRKP-WIMPDAVD 53 (74)
T ss_pred CHhhcccCCCC-ccCCCCCC
Confidence 56788888765 99998754
No 24
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=32.47 E-value=31 Score=26.38 Aligned_cols=26 Identities=23% Similarity=0.440 Sum_probs=23.3
Q ss_pred eecCccchhHHHhhhhhHHHHhhhhc
Q 029944 22 VWLDPNEVNEISMANSRQNIRKLVKD 47 (185)
Q Consensus 22 VWlDP~e~~eIa~A~sR~~IRkLIkd 47 (185)
-++||+.+.+|.--.|+++|+.|+-.
T Consensus 36 ~~~~~~~l~~l~~GmTk~qV~~lLGt 61 (113)
T PRK11548 36 NYLTPNDVAKIHVGMTQQQVAYTLGT 61 (113)
T ss_pred ccCCHHHHHHhcCCCCHHHHHHHcCC
Confidence 37899999999999999999999854
No 25
>PRK06029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
Probab=31.72 E-value=58 Score=27.31 Aligned_cols=47 Identities=26% Similarity=0.248 Sum_probs=36.1
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCC
Q 029944 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIH 58 (185)
Q Consensus 9 RLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~ 58 (185)
+.|...|.+++ .|.|=|. +--.+.++.+++..|-+.|.++..|..|.
T Consensus 106 ~~a~~~L~~~~-pvii~P~--~M~~~p~~~~Nl~~L~~~G~~vi~P~~g~ 152 (185)
T PRK06029 106 RAADVMLKERR-RLVLCVR--ETPLHLGHLRNMTKLAEMGAIIMPPVPAF 152 (185)
T ss_pred HHHHHHHhcCC-CEEEEec--cccCCHHHHHHHHHHHHCcCEEECCCccc
Confidence 44556778765 4555574 45668999999999999999999998763
No 26
>PHA00616 hypothetical protein
Probab=30.89 E-value=28 Score=23.30 Aligned_cols=20 Identities=20% Similarity=0.571 Sum_probs=16.6
Q ss_pred CCccccHHHHHHHHHHhhhH
Q 029944 129 GNVFKNKRVLMESIHKSKAE 148 (185)
Q Consensus 129 Gn~Fknk~~L~e~i~~~k~e 148 (185)
|..|.++++|..|+.+.-.+
T Consensus 8 G~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 8 GGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred hHHHhhHHHHHHHHHHhcCC
Confidence 78999999999999765443
No 27
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=30.01 E-value=46 Score=24.22 Aligned_cols=39 Identities=23% Similarity=0.600 Sum_probs=23.9
Q ss_pred hhHHHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCcee
Q 029944 6 LQKRLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFII 51 (185)
Q Consensus 6 ~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~ 51 (185)
+|..||..| |+++-|+ .+-++-+.-=++|+.|+.+|.|.
T Consensus 5 tq~eIA~~l---Gks~s~V----s~~l~Ll~lP~~i~~~v~~g~~~ 43 (93)
T PF08535_consen 5 TQEEIAKRL---GKSRSWV----SNHLALLDLPEEIKELVRSGRIS 43 (93)
T ss_dssp -HHHHHHHT---T--HHHH----HHHHGGGS--HHHHHHHHTTS--
T ss_pred CHHHHHHHH---CCCHHHH----HHHHHHHcCCHHHHHHHHcCCCc
Confidence 467778766 9999887 34445555667899999999774
No 28
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=29.91 E-value=32 Score=25.39 Aligned_cols=38 Identities=18% Similarity=0.305 Sum_probs=25.4
Q ss_pred ccCCCceecCccchhHHHhhhhhHH----HHhhhhcCceeecC
Q 029944 16 KCGRGKVWLDPNEVNEISMANSRQN----IRKLVKDGFIIRKP 54 (185)
Q Consensus 16 ~cG~~rVWlDP~e~~eIa~A~sR~~----IRkLIkdG~I~~kp 54 (185)
|.+...+++.+.|+.++... ||+. |..|.+.|+|....
T Consensus 40 G~~~~~~~is~~eLa~~~g~-sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 40 GWNKKQDRVTATVIAELTGL-SRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred CccccCCccCHHHHHHHHCc-CHHHHHHHHHHHHHCCCeeeec
Confidence 34456677777766666544 4544 55799999998655
No 29
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=29.89 E-value=1.9e+02 Score=24.22 Aligned_cols=56 Identities=21% Similarity=0.254 Sum_probs=39.6
Q ss_pred cchHHHHHHH-----HHHHHHHHHHHhcCCCC---hHhhHHHHhhhcCCc----cc-cHHHHHHHHHHh
Q 029944 90 PTKILWMRRM-----RVLRRLLRKYRESKKID---KHMYHDMYMKVKGNV----FK-NKRVLMESIHKS 145 (185)
Q Consensus 90 p~K~~Wm~ri-----R~lRr~Lk~~re~~kID---~~~Yr~lY~kaKGn~----Fk-nk~~L~e~i~~~ 145 (185)
|+...-..++ +-+|+.|..|-|.|.|- +..++-+..+-.+|. |= |.+-|..-..+.
T Consensus 71 pSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrDS~NgkRy~~R~~~G~I~~A~GfdLsPL~~R~~El 139 (177)
T PF03428_consen 71 PSNAQLAERLNGMSERTLRRHLARLVEAGLIVRRDSPNGKRYARRDRGGRIVEAFGFDLSPLIARAEEL 139 (177)
T ss_pred cCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeeccCCCCCccCccCCCCCEEeEeCcCHHHHHHHHHHH
Confidence 4455555566 89999999999999994 466888777766554 33 667666655543
No 30
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=26.78 E-value=48 Score=27.03 Aligned_cols=23 Identities=30% Similarity=0.673 Sum_probs=20.7
Q ss_pred hhhhhHHHHhhhhcCceeecCCC
Q 029944 34 MANSRQNIRKLVKDGFIIRKPTK 56 (185)
Q Consensus 34 ~A~sR~~IRkLIkdG~I~~kp~~ 56 (185)
--+||.+|..|+++|.|...|.+
T Consensus 113 L~lSrs~l~~l~~~G~I~~~~~~ 135 (142)
T PF06353_consen 113 LGLSRSRLKRLIEQGLIRSDPDK 135 (142)
T ss_pred hCcCHHHHHHHHHCCCEEecCcc
Confidence 45899999999999999998877
No 31
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=25.58 E-value=55 Score=21.94 Aligned_cols=28 Identities=29% Similarity=0.540 Sum_probs=21.6
Q ss_pred HHHhhhhhHHHHhhhhcCceeecCCCCC
Q 029944 31 EISMANSRQNIRKLVKDGFIIRKPTKIH 58 (185)
Q Consensus 31 eIa~A~sR~~IRkLIkdG~I~~kp~~~~ 58 (185)
+|+-..-|+-+..|..+|+|...|-.|.
T Consensus 35 ~vsr~tvr~al~~L~~~g~i~~~~~~G~ 62 (64)
T PF00392_consen 35 GVSRTTVREALRRLEAEGLIERRPGRGT 62 (64)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred ccCCcHHHHHHHHHHHCCcEEEECCceE
Confidence 3455666778889999999999987763
No 32
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=25.57 E-value=54 Score=17.51 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=13.3
Q ss_pred CCccccHHHHHHHHHH
Q 029944 129 GNVFKNKRVLMESIHK 144 (185)
Q Consensus 129 Gn~Fknk~~L~e~i~~ 144 (185)
|-.|.+...|..||..
T Consensus 7 ~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 7 GKSFSSKSNLKRHMRR 22 (23)
T ss_dssp TEEESSHHHHHHHHHH
T ss_pred CCccCCHHHHHHHHhH
Confidence 5679999999999864
No 33
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=25.17 E-value=3.8e+02 Score=22.48 Aligned_cols=85 Identities=22% Similarity=0.304 Sum_probs=56.2
Q ss_pred eecCccchhHHHhhhhhHHHH-hhhhcCceeecCCCCCChhHH-HHHHHHHhcCcCCCCCCcccccccCCcchHHHHHHH
Q 029944 22 VWLDPNEVNEISMANSRQNIR-KLVKDGFIIRKPTKIHSRSRA-RRMKEAKRKGRHSGYGKRKGTREARLPTKILWMRRM 99 (185)
Q Consensus 22 VWlDP~e~~eIa~A~sR~~IR-kLIkdG~I~~kp~~~~SR~R~-r~~~~~r~kGR~~G~GkRkGt~~AR~p~K~~Wm~ri 99 (185)
+| ||+-+..|..|+.-.++- .=+.||-.++-|+---+.-|- ---+.++..+ +.+-..|
T Consensus 69 p~-D~~~i~~I~kAI~~s~lgl~P~~dg~~Iri~iP~lT~E~R~elvK~~k~~~-------------------E~aKv~i 128 (185)
T PRK00083 69 PW-DKSMLKAIEKAIRASDLGLNPSNDGTVIRLPIPPLTEERRKELVKQVKKEA-------------------EEAKVAI 128 (185)
T ss_pred eC-CHhHHHHHHHHHHHCCCCCCcccCCCEEEecCCCCCHHHHHHHHHHHHHHH-------------------HHHHHHH
Confidence 44 999999999999876653 224588888877765555433 3333333322 2344678
Q ss_pred HHHHHH----HHHHHhcCCCChHhhHHHHhh
Q 029944 100 RVLRRL----LRKYRESKKIDKHMYHDMYMK 126 (185)
Q Consensus 100 R~lRr~----Lk~~re~~kID~~~Yr~lY~k 126 (185)
|.+|+- |+.+...|.|.....+.+...
T Consensus 129 RniRr~~~~~iKk~~k~~~iseD~~k~~e~e 159 (185)
T PRK00083 129 RNIRRDANDKLKKLEKDKEISEDELKRAEDE 159 (185)
T ss_pred HHHHHHHHHHHHHHhhcCCCChHHHHHHHHH
Confidence 888886 666666788888887776653
No 34
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=24.78 E-value=27 Score=27.43 Aligned_cols=10 Identities=50% Similarity=1.165 Sum_probs=8.2
Q ss_pred ceecCccchh
Q 029944 21 KVWLDPNEVN 30 (185)
Q Consensus 21 rVWlDP~e~~ 30 (185)
.||+||.|+.
T Consensus 93 tiwvDP~eVs 102 (108)
T smart00099 93 TLWVDPFEVS 102 (108)
T ss_pred EEEECCCEEE
Confidence 5899999864
No 35
>COG5104 PRP40 Splicing factor [RNA processing and modification]
Probab=23.99 E-value=3e+02 Score=27.19 Aligned_cols=50 Identities=24% Similarity=0.264 Sum_probs=37.5
Q ss_pred hhHHHHHHHhccCCCceecCccchhHHHhhhhh-------------HHHHhhhhcCceeecCCC
Q 029944 6 LQKRLSASVLKCGRGKVWLDPNEVNEISMANSR-------------QNIRKLVKDGFIIRKPTK 56 (185)
Q Consensus 6 ~QKRLAa~vL~cG~~rVWlDP~e~~eIa~A~sR-------------~~IRkLIkdG~I~~kp~~ 56 (185)
.-+|+.+..+-+|..-+| |...+++|-.+++= +++-.||-||+|..+..+
T Consensus 426 ~~r~~~~~~~~~~qis~~-d~~~vdei~~~~~Ek~eE~e~~~d~v~kE~is~i~D~~I~qr~Ek 488 (590)
T COG5104 426 FARRSYERETRTGQISPT-DRRAVDEIFEAIAEKKEEGEIKFDKVDKEDISLIVDGLIKQRNEK 488 (590)
T ss_pred HHHHHHHHHHHhccCCCc-cccchHHHHHHHHHHHhhcchhhhhhhHHHHHHHHHHHHHHhHHH
Confidence 346778888889999999 88889999888763 233468888888765443
No 36
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=23.64 E-value=59 Score=21.66 Aligned_cols=19 Identities=5% Similarity=0.162 Sum_probs=16.6
Q ss_pred hhhHHHHhhhhcCceeecC
Q 029944 36 NSRQNIRKLVKDGFIIRKP 54 (185)
Q Consensus 36 ~sR~~IRkLIkdG~I~~kp 54 (185)
.||..+++||++|.|..--
T Consensus 22 ~SR~~~k~li~~G~V~VNg 40 (59)
T TIGR02988 22 DSGGQAKWFLQENEVLVNG 40 (59)
T ss_pred cCHHHHHHHHHcCCEEECC
Confidence 4999999999999998743
No 37
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=23.35 E-value=67 Score=19.13 Aligned_cols=17 Identities=29% Similarity=0.432 Sum_probs=14.5
Q ss_pred hhhHHHHhhhhcCceee
Q 029944 36 NSRQNIRKLVKDGFIIR 52 (185)
Q Consensus 36 ~sR~~IRkLIkdG~I~~ 52 (185)
+|+..|+.++++|.|..
T Consensus 12 vs~~tl~~~~~~g~~~~ 28 (49)
T cd04762 12 VSPSTLRRWVKEGKLKA 28 (49)
T ss_pred cCHHHHHHHHHcCCCCc
Confidence 68899999999998753
No 38
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=23.17 E-value=52 Score=30.13 Aligned_cols=56 Identities=21% Similarity=0.353 Sum_probs=34.5
Q ss_pred hhHHHHHHHhccCCCceecCccc------------hhHHHhhhhhHHHHhhhhcCceeecCCCCCChhHHHHHHHHHh
Q 029944 6 LQKRLSASVLKCGRGKVWLDPNE------------VNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKR 71 (185)
Q Consensus 6 ~QKRLAa~vL~cG~~rVWlDP~e------------~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~SR~R~r~~~~~r~ 71 (185)
.|-.|||.||+ |..-+||.|-. ++.|++-.- .+|++.+--.. |-.||--.+.++|+
T Consensus 137 frSKLAA~I~g-GvdnihikpGsKVLYLGAasGttVSHvSDiVG--------peG~VYAVEfs-~rsGRdL~nmAkkR 204 (317)
T KOG1596|consen 137 FRSKLAAGILG-GVDNIHIKPGSKVLYLGAASGTTVSHVSDIVG--------PEGCVYAVEFS-HRSGRDLINMAKKR 204 (317)
T ss_pred HHHHHHHHhhc-CccceeecCCceEEEeeccCCceeehhhcccC--------CCceEEEEEec-ccchHHHHHHhhcc
Confidence 46789999986 99999999853 233333322 45676664433 33356555555543
No 39
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=21.90 E-value=75 Score=19.31 Aligned_cols=25 Identities=24% Similarity=0.411 Sum_probs=18.0
Q ss_pred HHhhhhhHHHHhhhhcCceeecCCC
Q 029944 32 ISMANSRQNIRKLVKDGFIIRKPTK 56 (185)
Q Consensus 32 Ia~A~sR~~IRkLIkdG~I~~kp~~ 56 (185)
++.+.-...|..|.+.|+|...+.-
T Consensus 26 ~s~~tv~~~l~~L~~~g~i~~~~~~ 50 (53)
T smart00420 26 VSEMTIRRDLNKLEEQGLLTRVHGG 50 (53)
T ss_pred CCHHHHHHHHHHHHHCCCEEEeecC
Confidence 3445557778899999999876543
No 40
>TIGR00421 ubiX_pad polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases. In E.coli, the protein UbiX (3-octaprenyl-4-hydroxybenzoate carboxy-lyase) has been shown to be involved in the third step of ubiquinone biosynthesis. It catalyzes the reaction [3-octaprenyl-4-hydroxybenzoate = 2-octaprenylphenol + CO2]. The knockout of the homologous protein in yeast confers sensitivity to phenylacrylic acid. Members are not restricted to ubiquinone-synthesizing species. This family represents a distinct clade within the flavoprotein family of Pfam model pfam02441.
Probab=21.87 E-value=1.1e+02 Score=25.29 Aligned_cols=47 Identities=30% Similarity=0.295 Sum_probs=35.3
Q ss_pred HHHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCCCC
Q 029944 9 RLSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTKIH 58 (185)
Q Consensus 9 RLAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~~~ 58 (185)
+.|...|+++. .|.|=|.+. -.++.+.+++..|-+.|.++.-|..|.
T Consensus 103 ~~a~~~L~~~~-pv~i~P~~m--~~~~~~~~Nl~~L~~~G~~ii~P~~g~ 149 (181)
T TIGR00421 103 RAADVCLKERR-KLVLVPRET--PLNSIHLENMLRLSRMGAIILPPMPAF 149 (181)
T ss_pred HHHHHHHhcCC-CEEEEeCCC--cCCHHHHHHHHHHHHCCCEEECCCCcc
Confidence 44555788776 455557544 458888999999999999999998764
No 41
>COG3664 XynB Beta-xylosidase [Carbohydrate transport and metabolism]
Probab=21.08 E-value=35 Score=32.73 Aligned_cols=46 Identities=13% Similarity=0.034 Sum_probs=38.4
Q ss_pred HHHHHhccCCCceecCccchhHHHhhhhhHHHHhhhhcCceeecCCC
Q 029944 10 LSASVLKCGRGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPTK 56 (185)
Q Consensus 10 LAa~vL~cG~~rVWlDP~e~~eIa~A~sR~~IRkLIkdG~I~~kp~~ 56 (185)
.++.|+.+-..+.|++|+++++|.++..=-. ..||..|+|...+..
T Consensus 23 ~~~~v~h~~~q~~~~~~t~~d~i~d~~~~~~-~~~ie~~l~~~~l~~ 68 (428)
T COG3664 23 RRHGVWHVNAQKLFYPFTYIDEIIDTLLDLG-LDLIELFLIWNNLNT 68 (428)
T ss_pred hhcceeeeeeccccCChHHHHHHHHHHHHhc-cHHHHHhhcccchhh
Confidence 3556777777789999999999999988767 899999999887654
No 42
>PF07742 BTG: BTG family; InterPro: IPR002087 Anti-proliferative proteins have been shown to include mammalian and avian protein BTG1 (which appears to be involved in negative regulation of cell proliferation) and rat/mouse NGF-inducible protein PC3/TIS21 (BTG2) [, , ]. These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain. The sequence of the N-terminal half of these proteins is well conserved.; PDB: 3DJU_B 3E9V_A 2Z15_D 2D5R_B 3DJN_B.
Probab=21.02 E-value=29 Score=27.28 Aligned_cols=10 Identities=50% Similarity=1.282 Sum_probs=8.1
Q ss_pred ceecCccchh
Q 029944 21 KVWLDPNEVN 30 (185)
Q Consensus 21 rVWlDP~e~~ 30 (185)
-||+||.|+.
T Consensus 95 tlWvDPgeVs 104 (118)
T PF07742_consen 95 TLWVDPGEVS 104 (118)
T ss_dssp EEEEETTEEE
T ss_pred EEEECCCEEE
Confidence 5899998864
No 43
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=20.81 E-value=49 Score=22.64 Aligned_cols=27 Identities=15% Similarity=0.327 Sum_probs=21.2
Q ss_pred cCccchhHHHhhhhhHHHHhhhhcCce
Q 029944 24 LDPNEVNEISMANSRQNIRKLVKDGFI 50 (185)
Q Consensus 24 lDP~e~~eIa~A~sR~~IRkLIkdG~I 50 (185)
+|++.+++|.--.|+++|+.|+-.=..
T Consensus 4 ~~~~~~~~i~~GmTk~qV~~lLG~P~~ 30 (71)
T PF04355_consen 4 LTQEQLAQIKPGMTKDQVRALLGSPSL 30 (71)
T ss_dssp TTSHHHTTT-TTSBHHHHHHHHTS-SE
T ss_pred CCHHHHHhhcCCCCHHHHHHhcCCCCc
Confidence 688899999999999999999865333
No 44
>cd04261 AAK_AKii-LysC-BS AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine, and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase isoenzyme type, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In this organism and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regulated by the concerted action of lysine and
Probab=20.75 E-value=92 Score=26.20 Aligned_cols=43 Identities=19% Similarity=0.253 Sum_probs=31.6
Q ss_pred HHHHHhccCCCceecCccchh----------HHHhhhhhHHHHhhhhcCceeec
Q 029944 10 LSASVLKCGRGKVWLDPNEVN----------EISMANSRQNIRKLVKDGFIIRK 53 (185)
Q Consensus 10 LAa~vL~cG~~rVWlDP~e~~----------eIa~A~sR~~IRkLIkdG~I~~k 53 (185)
+++.+...|.+-+||+|.+.. ++... +.+.|..|++.|.|-.-
T Consensus 79 ~~~~l~~~g~~a~~l~~~~~~l~~~~~~~~~~i~~~-~~~~l~~ll~~~~ipVi 131 (239)
T cd04261 79 LAMALNRLGIKAISLTGWQAGILTDGHHGKARIIDI-DPDRIRELLEEGDVVIV 131 (239)
T ss_pred HHHHHHhCCCCeEEechhhCCEEecCCCCcceechh-hHHHHHHHHHcCCeEEE
Confidence 466677899999999998752 23222 34889999999976554
No 45
>PF06014 DUF910: Bacterial protein of unknown function (DUF910); InterPro: IPR009256 This family consists of several short bacterial proteins of unknown function.; PDB: 2NN4_A.
Probab=20.69 E-value=78 Score=22.69 Aligned_cols=22 Identities=27% Similarity=0.342 Sum_probs=17.2
Q ss_pred HHHHHHHHHHhcCCCChHhhHH
Q 029944 101 VLRRLLRKYRESKKIDKHMYHD 122 (185)
Q Consensus 101 ~lRr~Lk~~re~~kID~~~Yr~ 122 (185)
.+--.|+.|-++|.||+++|-.
T Consensus 29 lM~~El~~Ly~~~lidk~~y~~ 50 (62)
T PF06014_consen 29 LMEIELKELYKSGLIDKKEYLT 50 (62)
T ss_dssp HHHHHHHHHHHTTSS-HHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHH
Confidence 4556899999999999988754
No 46
>cd01145 TroA_c Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=20.42 E-value=50 Score=27.15 Aligned_cols=19 Identities=37% Similarity=0.704 Sum_probs=15.7
Q ss_pred CCceecCccchhHHHhhhh
Q 029944 19 RGKVWLDPNEVNEISMANS 37 (185)
Q Consensus 19 ~~rVWlDP~e~~eIa~A~s 37 (185)
---||+||+....++.++.
T Consensus 107 dPH~Wldp~~~~~~a~~I~ 125 (203)
T cd01145 107 NPHVWLDPNNAPALAKALA 125 (203)
T ss_pred CcCeecCHHHHHHHHHHHH
Confidence 4468999999988888776
No 47
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=20.28 E-value=72 Score=20.03 Aligned_cols=20 Identities=30% Similarity=0.466 Sum_probs=15.2
Q ss_pred HHhhhhhHHHHhhhhcCcee
Q 029944 32 ISMANSRQNIRKLVKDGFII 51 (185)
Q Consensus 32 Ia~A~sR~~IRkLIkdG~I~ 51 (185)
|+.+....-|++|+++|+|.
T Consensus 29 is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 29 ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp S-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHHHCcCcC
Confidence 45566778889999999984
No 48
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=20.24 E-value=41 Score=21.55 Aligned_cols=10 Identities=50% Similarity=1.139 Sum_probs=6.2
Q ss_pred CCceec-Cccc
Q 029944 19 RGKVWL-DPNE 28 (185)
Q Consensus 19 ~~rVWl-DP~e 28 (185)
++.||+ ||++
T Consensus 1 K~~vWvpD~~e 11 (42)
T PF02736_consen 1 KKWVWVPDPKE 11 (42)
T ss_dssp TTEEEEEESSS
T ss_pred CCEEEEeCCcc
Confidence 456888 5544
No 49
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=20.20 E-value=67 Score=26.82 Aligned_cols=46 Identities=28% Similarity=0.487 Sum_probs=29.3
Q ss_pred HHHHHHHhccCCCceecCccchh-----HHHhhhhhHHHHhhhhcCceeecCCCCC
Q 029944 8 KRLSASVLKCGRGKVWLDPNEVN-----EISMANSRQNIRKLVKDGFIIRKPTKIH 58 (185)
Q Consensus 8 KRLAa~vL~cG~~rVWlDP~e~~-----eIa~A~sR~~IRkLIkdG~I~~kp~~~~ 58 (185)
.++.+ .|..|.. | |.|.+ .|+-..-|+-|..|+.+|+|.+++-+|.
T Consensus 23 ~~I~~-~~~~G~~---L-PsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~Gt 73 (241)
T PRK10079 23 QELRQ-HYRCGDY---L-PAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGV 73 (241)
T ss_pred HHHhc-ccCCCCc---C-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCEE
Confidence 34443 4555552 4 44443 2344555677779999999999998763
No 50
>PF15319 RHINO: RAD9, RAD1, HUS1-interacting nuclear orphan protein
Probab=20.08 E-value=39 Score=30.02 Aligned_cols=33 Identities=36% Similarity=0.640 Sum_probs=25.1
Q ss_pred ccccCCcchHHHHHHHHHHHHHHHHHHhcCCCChHhh
Q 029944 84 TREARLPTKILWMRRMRVLRRLLRKYRESKKIDKHMY 120 (185)
Q Consensus 84 t~~AR~p~K~~Wm~riR~lRr~Lk~~re~~kID~~~Y 120 (185)
|-.--..-|+.|-+| +-||..|||.|++++..|
T Consensus 202 TPE~~YGiKvTWRRR----~hL~~yLrerGkL~~sq~ 234 (236)
T PF15319_consen 202 TPEEKYGIKVTWRRR----RHLLAYLRERGKLSRSQF 234 (236)
T ss_pred CCcccccceeeeecc----HHHHHHHHHhCccchhhc
Confidence 333345569999766 578999999999998764
Done!