Query 022999
Match_columns 289
No_of_seqs 132 out of 591
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 07:43:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022999.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022999hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00051 RNA-binding S4 domain 100.0 9.2E-64 2E-68 463.9 22.1 223 61-284 6-229 (267)
2 TIGR03069 PS_II_S4 photosystem 100.0 6.8E-61 1.5E-65 442.6 21.5 220 64-286 2-224 (257)
3 COG2302 Uncharacterized conser 100.0 7.7E-61 1.7E-65 436.0 19.9 215 67-284 3-218 (257)
4 KOG4837 Uncharacterized conser 99.8 1.7E-21 3.6E-26 173.9 1.9 210 58-286 6-215 (248)
5 TIGR01017 rpsD_bact ribosomal 98.6 2.5E-08 5.4E-13 89.7 2.5 69 195-282 57-126 (200)
6 PRK05327 rpsD 30S ribosomal pr 98.5 2.8E-08 6.2E-13 89.5 1.4 69 194-281 59-128 (203)
7 PF01479 S4: S4 domain; Inter 98.5 2.6E-07 5.6E-12 64.1 5.1 36 247-282 1-37 (48)
8 TIGR02988 YaaA_near_RecF S4 do 98.1 5.8E-06 1.3E-10 60.1 4.8 42 243-285 5-49 (59)
9 PF03880 DbpA: DbpA RNA bindin 97.7 8.5E-05 1.8E-09 56.4 5.2 60 164-224 11-73 (74)
10 cd00165 S4 S4/Hsp/ tRNA synthe 97.3 0.00044 9.5E-09 48.9 4.6 39 247-285 1-41 (70)
11 PRK10348 ribosome-associated h 97.1 0.00062 1.4E-08 58.0 4.6 43 245-287 7-50 (133)
12 smart00363 S4 S4 RNA-binding d 97.1 0.0011 2.3E-08 45.6 4.6 37 247-283 1-39 (60)
13 CHL00113 rps4 ribosomal protei 96.8 0.0015 3.2E-08 59.1 4.3 36 247-282 89-125 (201)
14 COG1188 Ribosome-associated he 96.7 0.0015 3.3E-08 53.1 3.5 43 245-287 7-50 (100)
15 PF06353 DUF1062: Protein of u 96.3 0.0073 1.6E-07 52.0 5.3 34 245-278 101-134 (142)
16 PRK11180 rluD 23S rRNA pseudou 96.1 0.0061 1.3E-07 58.2 4.3 38 244-281 15-53 (325)
17 PRK11025 23S rRNA pseudouridyl 95.9 0.017 3.7E-07 55.1 6.2 49 236-284 7-58 (317)
18 COG4332 Uncharacterized protei 95.9 0.014 3.1E-07 52.2 5.0 77 202-278 85-170 (203)
19 PRK04051 rps4p 30S ribosomal p 95.6 0.015 3.4E-07 51.7 4.5 38 248-285 104-142 (177)
20 COG0522 RpsD Ribosomal protein 93.9 0.066 1.4E-06 48.8 3.9 35 248-282 95-130 (205)
21 TIGR01018 rpsD_arch ribosomal 92.1 0.17 3.8E-06 44.5 3.8 42 241-282 95-140 (162)
22 PLN00189 40S ribosomal protein 88.3 0.19 4.2E-06 45.4 0.8 42 241-282 100-145 (194)
23 PTZ00155 40S ribosomal protein 88.3 0.41 8.9E-06 42.9 2.9 36 247-282 107-143 (181)
24 KOG4837 Uncharacterized conser 79.9 0.68 1.5E-05 42.6 0.5 49 236-284 129-177 (248)
25 cd02644 R3H_jag R3H domain fou 75.9 24 0.00052 26.4 7.8 59 78-138 6-64 (67)
26 PRK05912 tyrosyl-tRNA syntheta 73.8 4.2 9.1E-05 40.5 4.2 33 249-281 346-378 (408)
27 TIGR01764 excise DNA binding d 73.6 3.2 7E-05 27.3 2.4 21 253-273 7-27 (49)
28 PRK11634 ATP-dependent RNA hel 73.1 6.7 0.00014 41.2 5.7 73 152-226 486-561 (629)
29 PRK13354 tyrosyl-tRNA syntheta 71.7 5 0.00011 40.1 4.2 33 249-281 346-378 (410)
30 PRK11507 ribosome-associated p 70.4 5.8 0.00013 30.4 3.4 33 247-279 12-45 (70)
31 COG2501 S4-like RNA binding pr 61.0 8.9 0.00019 29.6 2.8 39 249-287 14-54 (73)
32 COG0529 CysC Adenylylsulfate k 60.8 19 0.0004 32.8 5.2 86 49-134 31-136 (197)
33 PF13275 S4_2: S4 domain; PDB: 56.1 2.4 5.2E-05 31.9 -1.0 42 246-287 7-50 (65)
34 PF12728 HTH_17: Helix-turn-he 49.3 13 0.00029 25.3 1.9 21 253-273 7-27 (51)
35 COG1847 Jag Predicted RNA-bind 48.3 77 0.0017 29.2 7.1 54 80-134 149-202 (208)
36 cd02638 R3H_unknown_1 R3H doma 47.0 1E+02 0.0022 23.2 6.4 40 88-127 11-50 (62)
37 COG0162 TyrS Tyrosyl-tRNA synt 43.1 25 0.00054 35.3 3.4 32 249-280 339-370 (401)
38 cd04762 HTH_MerR-trunc Helix-T 41.0 22 0.00048 23.0 1.9 22 253-274 6-27 (49)
39 COG0481 LepA Membrane GTPase L 40.7 54 0.0012 34.2 5.4 172 99-275 344-532 (603)
40 PF01424 R3H: R3H domain; Int 37.9 1.5E+02 0.0032 21.1 7.5 39 96-138 22-60 (63)
41 TIGR00234 tyrS tyrosyl-tRNA sy 34.6 52 0.0011 32.5 4.2 38 250-287 334-371 (377)
42 PRK10377 PTS system glucitol/s 34.2 69 0.0015 26.8 4.3 44 184-230 53-96 (120)
43 TIGR00849 gutA PTS system, glu 33.5 72 0.0016 26.8 4.3 44 184-230 53-96 (121)
44 cd02639 R3H_RRM R3H domain of 29.4 1.2E+02 0.0025 22.4 4.3 40 94-136 17-56 (60)
45 cd02640 R3H_NRF R3H domain of 28.0 1.8E+02 0.0038 21.4 5.1 42 93-137 16-57 (60)
46 KOG4469 Uncharacterized conser 26.5 13 0.00029 34.9 -1.4 45 18-63 278-322 (391)
47 PRK04313 30S ribosomal protein 26.4 62 0.0013 30.3 3.0 36 246-281 37-74 (237)
48 PF13613 HTH_Tnp_4: Helix-turn 25.3 51 0.0011 23.1 1.7 21 250-270 22-42 (53)
49 cd06007 R3H_DEXH_helicase R3H 25.0 2.4E+02 0.0052 20.6 5.3 41 94-137 16-56 (59)
50 smart00393 R3H Putative single 23.6 3.2E+02 0.0069 20.4 7.5 47 89-139 30-77 (79)
51 PF03610 EIIA-man: PTS system 23.2 2.1E+02 0.0046 22.7 5.2 72 50-121 10-85 (116)
52 TIGR02675 tape_meas_nterm tape 23.2 80 0.0017 23.9 2.6 29 248-276 45-73 (75)
53 PF10809 DUF2732: Protein of u 22.5 57 0.0012 25.5 1.6 30 243-272 35-66 (77)
54 PF06115 DUF956: Domain of unk 22.5 40 0.00088 28.4 0.9 39 184-223 23-61 (118)
55 COG1471 RPS4A Ribosomal protei 21.9 80 0.0017 29.7 2.7 36 246-281 40-77 (241)
56 cd04761 HTH_MerR-SF Helix-Turn 21.0 78 0.0017 20.8 1.9 22 253-274 6-27 (49)
57 PTZ00118 40S ribosomal protein 20.4 96 0.0021 29.5 3.0 36 246-281 41-78 (262)
No 1
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=100.00 E-value=9.2e-64 Score=463.86 Aligned_cols=223 Identities=65% Similarity=0.967 Sum_probs=203.5
Q ss_pred hhccH-HHHhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEEEe
Q 022999 61 VKGNF-DDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSV 139 (289)
Q Consensus 61 ~~~~~-~~ll~~~~~~e~k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl~i 139 (289)
-.++. ..+++|+.+ +++.++++++||+++|.+++.+++|+||||+||.++.+++++.+++++.++|||++|||+|++|
T Consensus 6 ~~~~~~~~i~~h~~~-ee~~~~~~~~d~~~~a~~~~~~~~T~FL~p~e~~i~~~~~~~~~~i~~~~~GGy~~AER~r~~~ 84 (267)
T PLN00051 6 AAGDADSALLGVVDP-AHREEVKRILEMAERASDRWEVEHTDFLTPPIVKDSMAALEKLADVKAVAWGGYAQAERCRLSI 84 (267)
T ss_pred hccchhhHHHhhcCh-hhHHHHHHHHHHHHHHHhcCCEEECccCCHHHHHHHHHHhcccCCeEEEEecCCchHeEEEEEE
Confidence 33444 368999875 5599999999999999999999999999999999999999888899999999999999999999
Q ss_pred eCCCCCCCCcCceEEEEEecCCCCCCCCchhhHHHHHhCCCCCCccccEEEecCCeEEEEecchHHHHHHHhhchhcceE
Q 022999 140 GHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVS 219 (289)
Q Consensus 140 ~~p~y~~~~~~~i~~L~I~~~~kF~~LsHRD~LGaLmgLGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~ 219 (289)
+|+++++.+++++++++|++++||.+|+|||||||||||||+|+++|||++.++++||++|+++|++||++||+|||+++
T Consensus 85 ~p~~~~~~~~f~i~~l~i~~~~kF~~l~HrD~LGaLm~LGIkRe~iGDIlv~~~~~~~v~v~~~i~~fi~~nl~kIg~~~ 164 (267)
T PLN00051 85 GRPEVLTSQPDIVAALSVSGNFMFDPASHGDFLGAILGTGITRDKVGDILVQGERGAQVLVVPELVEFLSSSLTKVRTVP 164 (267)
T ss_pred echHhccccCCcEEEEEEEcccCCCCCCHHHHHHHHHHcCCcHhhcCCEEEcCCCcEEEEEcHHHHHHHHHHhhhcccee
Confidence 86665533336899999999999999999999999999999999999999855456999999999999999999999999
Q ss_pred EEEEEecCCcccCCCCCeeEEEEeecccchHHHHHccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999 220 VSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKAS 284 (289)
Q Consensus 220 V~v~ei~~~~l~~~~~~~ke~~~tVsSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~~~~ 284 (289)
|++++++++++.+|+++|+++.++|||+|||+++|++|++||++++++|++|+|+|||+++.++|
T Consensus 165 V~~~~~~~~~~~~~~~~~~e~~~~vas~RLD~vla~~~~~SRsk~~~lI~~g~V~vN~~~v~~~s 229 (267)
T PLN00051 165 VECRAIPLSALEVEPPRVESFKSVEASLRLDALASAGFRMSRSKLVDLISSGDVRVNWREVTKNG 229 (267)
T ss_pred EEEEEecHHHcCCCccceEEccCCcCcccHHHHHHHHhccCHHHHHHHHHcCcEEECCEEcCCCC
Confidence 99999999998888889999999999999999999999999999999999999999999765444
No 2
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=100.00 E-value=6.8e-61 Score=442.61 Aligned_cols=220 Identities=43% Similarity=0.670 Sum_probs=198.1
Q ss_pred cHHHHhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEEEeeCCC
Q 022999 64 NFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPE 143 (289)
Q Consensus 64 ~~~~ll~~~~~~e~k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl~i~~p~ 143 (289)
+++.++++++++|+ +++++||+++|.++|.+++|+||||+||.++.+++++..++++.++|||++|||+|++|+|++
T Consensus 2 ~~~~~~~~~~~~ee---~~~~~d~~~~~~~~~~~~~T~FL~p~e~~i~~~~~~~~~~~~~~~~GG~~~AER~r~~~~p~~ 78 (257)
T TIGR03069 2 PREELLKGANYPEE---LERLLDLAEQALRTWEPVWSDFLSAPLQEEILKRFSNLTDLKWLAWGGYPQAERQRIACARSD 78 (257)
T ss_pred ChHHHHHhCCCHHH---HHHHHHHHHHHHhhCCEEECCCCCHHHHHHHHHHhcccCCcEEEEecCCcHHhEEEEEEeccc
Confidence 45678999886342 999999999999999999999999999999999998888999999999999999999998665
Q ss_pred CCCCC-cCceEEEEEecCCCCCCCCchhhHHHHHhCCCCCCccccEEEecCCeEEEEecchHHHHHHHhhchhcceEEEE
Q 022999 144 ALTSD-PDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSC 222 (289)
Q Consensus 144 y~~~~-~~~i~~L~I~~~~kF~~LsHRD~LGaLmgLGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~V~v 222 (289)
++.+. ++++++++|++++||.+|+|||||||||||||+|+++|||++.++++||++|+++|++||.+||+|||+++|++
T Consensus 79 ~~~~~~df~i~~l~i~~~~kF~~l~Hrd~LGalm~lGi~R~~iGDI~v~~~~~~~v~v~~~i~~~i~~~l~kIg~~~V~~ 158 (257)
T TIGR03069 79 NPLDPDIIPIQGLLIEGNFLFDPASHEDFRGALLGTGIVREKIGDIWVLGDRGAQALCTPELAEFLQEKLGQVRDVEVKC 158 (257)
T ss_pred ccCCcccCceEEEEEEcccccCCCCHHHHHHHHHHcCCcHhhcCCEEEecCCcEEEEECHHHHHHHHHHhhhccceeEEE
Confidence 54322 35899999999999999999999999999999999999998776656999999999999999999999999999
Q ss_pred EEecCCcccCCCCCe-eEEEEeecccchHHHHHccccccHHHHHHHHHcCCeEECcEEe-cccccc
Q 022999 223 TRIPLLALEYEPPRT-KSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQIS-AKASAI 286 (289)
Q Consensus 223 ~ei~~~~l~~~~~~~-ke~~~tVsSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~-~~~~~~ 286 (289)
++++++++..+++++ +++.++|+|+|||+++++++++||++++++|++|+|+|||+++ .++..+
T Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~v~s~RLD~lls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v 224 (257)
T TIGR03069 159 KAIPLEELQIPAPRTPKELTTVEASLRIDAIASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSREL 224 (257)
T ss_pred EEeCHHHcCCCCcccceEecCCCccccHHHHHHhhhhhhHHHHHHHHHCCeEEECCEEcCCCCCcC
Confidence 999999875555555 9999999999999999999999999999999999999999976 444333
No 3
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=100.00 E-value=7.7e-61 Score=436.01 Aligned_cols=215 Identities=33% Similarity=0.446 Sum_probs=199.6
Q ss_pred HHhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEEEeeCCCCCC
Q 022999 67 DLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 146 (289)
Q Consensus 67 ~ll~~~~~~e~k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl~i~~p~y~~ 146 (289)
.++.|+. .|++.+++|++||+++++++|++..||||||+|+.+....++ ..++++.++||||+|||+|++++|++|..
T Consensus 3 ~iyqhf~-~eer~fidr~l~~~~~ve~~y~v~~T~Fl~P~e~~i~~~l~~-~~~v~~~~~Gg~~~aEr~r~~l~P~y~~~ 80 (257)
T COG2302 3 GIYQHFR-AEERPFIDRVLEWIKQVEKTYTVVVTDFLDPREQAILKTLAG-LEDVKVSFSGGYPRAERKRLILYPAYYPL 80 (257)
T ss_pred cHhhhcC-chhHHHHHHHHHHHHHHhcCceEEEccCcCcHHHHHHHHHhC-ccceeEEeecCCchhheeEEEEcccccCh
Confidence 4677866 567999999999999999999999999999999999888777 78999999999999999999998555543
Q ss_pred C-CcCceEEEEEecCCCCCCCCchhhHHHHHhCCCCCCccccEEEecCCeEEEEecchHHHHHHHhhchhcceEEEEEEe
Q 022999 147 S-DPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRI 225 (289)
Q Consensus 147 ~-~~~~i~~L~I~~~~kF~~LsHRD~LGaLmgLGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei 225 (289)
+ .++++++++|.|++||.+++||||||+||||||+|+++|||++.+ ++||++|.+++++|+..+|+|||+++|+++++
T Consensus 81 ~~~df~l~l~eI~y~~kF~~l~H~~~LGtll~lGikRe~~GDIiv~~-~~aQliv~~~~~~f~~~~Ltkig~~~V~l~ei 159 (257)
T COG2302 81 EESDFELTLLEISYASKFVSLTHRDILGTLLSLGIKREKFGDIIVEG-EGAQLIVATELADFFLLHLTKIGKAPVKLEEI 159 (257)
T ss_pred hhcccceEEEEEEcccccccccHHHHHHHHHhccCcHHhhccEEEeC-CeeEEEEehhHHHHHHHHHHhhcCcceEEEEc
Confidence 3 345899999999999999999999999999999999999999876 69999999999999999999999999999999
Q ss_pred cCCcccCCCCCeeEEEEeecccchHHHHHccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999 226 PLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKAS 284 (289)
Q Consensus 226 ~~~~l~~~~~~~ke~~~tVsSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~~~~ 284 (289)
+++++..+.++|++..++|||||||+|+|++||+||++|+++|++|+|+||++++.++|
T Consensus 160 ~~~~l~~~~~~~~e~~~~vsSlRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s 218 (257)
T COG2302 160 DLEELKESTEKWKELDVTVSSLRLDVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKAS 218 (257)
T ss_pred CHHHcccCccceeEEeeeeehhhHHHHHHHHHhhhHHHHHHHHHcCceEEeeEEecccc
Confidence 99999988889999999999999999999999999999999999999999999777444
No 4
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.82 E-value=1.7e-21 Score=173.86 Aligned_cols=210 Identities=54% Similarity=0.839 Sum_probs=188.8
Q ss_pred HHHhhccHHHHhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEE
Q 022999 58 IQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (289)
Q Consensus 58 ~~~~~~~~~~ll~~~~~~e~k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl 137 (289)
..|+|++.+.+++.+.+...-..+.+++++|.++.......+|+||.|. .+..++++.....|||+.||+|++
T Consensus 6 ~~~i~g~~~~~~~~vg~~~v~k~~~~~~~m~~~~~~~r~f~~t~~l~ps-------l~t~F~~v~s~~lpgl~~a~ec~~ 78 (248)
T KOG4837|consen 6 SEAIKGDVDFLLKGVGDQAVAKEVKQILEMARRASSKREFLHTDFLTPS-------LLTKFADVKSVALPGLPEAEECRI 78 (248)
T ss_pred hhHhhhhhhhhhhcccHHHHHhhcHHHHHHHHHHHhhHHHHhhhhhCch-------hhhccccchhhhcCCCCCChheEe
Confidence 3789999999999999988889999999999999999999999999994 345778999999999999999999
Q ss_pred EeeCCCCCCCCcCceEEEEEecCCCCCCCCchhhHHHHHhCCCCCCccccEEEecCCeEEEEecchHHHHHHHhhchhcc
Q 022999 138 SVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGN 217 (289)
Q Consensus 138 ~i~~p~y~~~~~~~i~~L~I~~~~kF~~LsHRD~LGaLmgLGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr 217 (289)
-|+.|+....+++..+.+.+..++.|++.+|.||||+++ ||+.|||.++.+ |+.+.+++.+|..+-|.|+|
T Consensus 79 pi~~~~~~ts~k~~kksl~~td~~dsd~esh~Df~~e~~-----~e~~~D~~Vvk~---~~~i~~~v~sfr~d~llK~G- 149 (248)
T KOG4837|consen 79 PIGHPDVLTSDKDIKKSLSITDNFDSDPESHGDFLGEIL-----REKLGDILVVKE---KVLIVPEVVSFRVDALLKVG- 149 (248)
T ss_pred eccCccccccchhHHHHhhhccccCCCcccchhHHHHHH-----HHhcCCceeeeh---hhhhhhHHHHHHHHHHHHhc-
Confidence 999998766666667889999999999999999999998 999999998864 58888999999999999999
Q ss_pred eEEEEEEecCCcccCCCCCeeEEEEeecccchHHHHHccccccHHHHHHHHHcCCeEECcEEecccccc
Q 022999 218 VSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKASAI 286 (289)
Q Consensus 218 ~~V~v~ei~~~~l~~~~~~~ke~~~tVsSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~~~~~~ 286 (289)
..|.+..+++.-+.+. ++.-+++..-.|+|+|+.-++.|.++|+ .++|....|+||-..+.+++.|
T Consensus 150 lgv~rnKVel~fye~e-~R~N~~Kl~kkS~~i~vgds~d~~ig~~--~~~~s~~~~rV~~~tV~~~~t~ 215 (248)
T KOG4837|consen 150 LGVTRNKVELLFYEYE-PRTNSFKLVKKSLRIDVGDSADFKIGRS--VDLISSKDVRVNWATVTKNGTI 215 (248)
T ss_pred cccccchhhHhhhhcc-cccCcccccccceeeecccccceeeecc--cccCCcceEEEeeeeecccceE
Confidence 9999999988766655 6888899999999999999999999999 8899999999998877766654
No 5
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=98.57 E-value=2.5e-08 Score=89.69 Aligned_cols=69 Identities=16% Similarity=0.143 Sum_probs=60.2
Q ss_pred eEEEEecchHHHHHHHhhchhcceEEEEEEecCCcccCCCCCeeEEEEeecccchHHHH-HccccccHHHHHHHHHcCCe
Q 022999 195 GAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALA-SAGFKLSRSKLVNLIRYSSL 273 (289)
Q Consensus 195 ~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei~~~~l~~~~~~~ke~~~tVsSlRLDaVv-s~~f~lSRska~~lI~~GkV 273 (289)
.+|.++.+++.+|+..++.++|++.+.+ +.+.+ +|||.++ +.+|..||++|.++|+.|+|
T Consensus 57 ~~Yg~~e~q~~~~~~~a~~~~g~t~~~l--l~~le-----------------~RLD~~L~~~g~~~SR~~ArqlI~~G~V 117 (200)
T TIGR01017 57 FMYGITEKQFRKYFKEAKKLKGNTGENL--LRLLE-----------------SRLDNVVYRLGFAPTRFAARQLVSHGHI 117 (200)
T ss_pred HHHhchHHHHHHHHHHHhccCCCchhHH--HHHHH-----------------HHHHHHHHHcCCCCCHHHHHHHHHCCCE
Confidence 6899999999999999999999999877 32211 7999998 77889999999999999999
Q ss_pred EECcEEecc
Q 022999 274 ASLVQISAK 282 (289)
Q Consensus 274 ~vn~~~~~~ 282 (289)
.|||+++..
T Consensus 118 ~VNgk~v~~ 126 (200)
T TIGR01017 118 LVNGKKVDI 126 (200)
T ss_pred EECCEEeCC
Confidence 999997643
No 6
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=98.52 E-value=2.8e-08 Score=89.50 Aligned_cols=69 Identities=16% Similarity=0.235 Sum_probs=60.6
Q ss_pred CeEEEEecchHHHHHHHhhchhcceEEEEEEecCCcccCCCCCeeEEEEeecccchHHHH-HccccccHHHHHHHHHcCC
Q 022999 194 KGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALA-SAGFKLSRSKLVNLIRYSS 272 (289)
Q Consensus 194 ~~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei~~~~l~~~~~~~ke~~~tVsSlRLDaVv-s~~f~lSRska~~lI~~Gk 272 (289)
..+|.++.+++.+|+..++.++|++.+.+ +.+.| +|||.++ +.+|..||++|.++|..|+
T Consensus 59 ~~~Y~~~e~q~~~~~~~a~~~~g~t~~~l--l~~lE-----------------~RLD~iL~~~g~~~SR~~arqlI~~G~ 119 (203)
T PRK05327 59 RRIYGVLEKQFRRYFKEAARRKGNTGENL--LQLLE-----------------SRLDNVVYRLGFAPTRRQARQLVSHGH 119 (203)
T ss_pred HHHhcCcHHHHHHHHHHHHhccCCcHhHH--HHHHH-----------------HHHHHHHHHcCccCCHHHHHHHHHCCc
Confidence 36899999999999999999999999877 33212 8999998 7789999999999999999
Q ss_pred eEECcEEec
Q 022999 273 LASLVQISA 281 (289)
Q Consensus 273 V~vn~~~~~ 281 (289)
|.|||+.+.
T Consensus 120 V~VNgk~v~ 128 (203)
T PRK05327 120 ILVNGKKVN 128 (203)
T ss_pred EEECCEEEC
Confidence 999999765
No 7
>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=98.48 E-value=2.6e-07 Score=64.11 Aligned_cols=36 Identities=25% Similarity=0.334 Sum_probs=33.5
Q ss_pred cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999 247 LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK 282 (289)
Q Consensus 247 lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~ 282 (289)
+|||.+++ .++..||++|+++|++|.|+|||+++..
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~ 37 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKD 37 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESS
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcC
Confidence 69999999 8899999999999999999999997774
No 8
>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=98.08 E-value=5.8e-06 Score=60.06 Aligned_cols=42 Identities=5% Similarity=0.043 Sum_probs=35.8
Q ss_pred eecccchHHHHHccccc--cHHHHHHHHHcCCeEECcEEe-ccccc
Q 022999 243 IEASLRVDALASAGFKL--SRSKLVNLIRYSSLASLVQIS-AKASA 285 (289)
Q Consensus 243 tVsSlRLDaVvs~~f~l--SRska~~lI~~GkV~vn~~~~-~~~~~ 285 (289)
.....|||.+++.. ++ ||+.++.+|+.|.|+|||++. +++.-
T Consensus 5 ~~~~~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~ 49 (59)
T TIGR02988 5 FTEYITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKK 49 (59)
T ss_pred cchHHHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCEEccCCCCC
Confidence 34668999999998 88 999999999999999999976 44443
No 9
>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins [].; PDB: 2G0C_A 3MOJ_B.
Probab=97.66 E-value=8.5e-05 Score=56.44 Aligned_cols=60 Identities=25% Similarity=0.339 Sum_probs=43.3
Q ss_pred CCCCchhhHHHHHh-CCCCCCccccEEEecCCeEEEEecchHHHHHHHhhc--hhcceEEEEEE
Q 022999 164 QPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLE--KVGNVSVSCTR 224 (289)
Q Consensus 164 ~~LsHRD~LGaLmg-LGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLt--KIgr~~V~v~e 224 (289)
+.++++|++|+|.+ .||.++.||+|-+.+ +..+|-|.++.++-+++.|. ++++.+|++++
T Consensus 11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~-~~S~vev~~~~a~~v~~~l~~~~~~gk~v~ve~ 73 (74)
T PF03880_consen 11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD-NFSFVEVPEEVAEKVLEALNGKKIKGKKVRVER 73 (74)
T ss_dssp GT--HHHHHHHHHTCTTB-GGGEEEEEE-S-S-EEEEE-TT-HHHHHHHHTT--SSS----EEE
T ss_pred cCCCHHHHHHHHHhccCCCHHhEEEEEEee-eEEEEEECHHHHHHHHHHhcCCCCCCeeEEEEE
Confidence 56799999999998 599999999998765 58999999999999999998 77888888864
No 10
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=97.29 E-value=0.00044 Score=48.89 Aligned_cols=39 Identities=18% Similarity=0.188 Sum_probs=33.1
Q ss_pred cchHHHHHcc-ccccHHHHHHHHHcCCeEECcEEe-ccccc
Q 022999 247 LRVDALASAG-FKLSRSKLVNLIRYSSLASLVQIS-AKASA 285 (289)
Q Consensus 247 lRLDaVvs~~-f~lSRska~~lI~~GkV~vn~~~~-~~~~~ 285 (289)
+|||.++... +..||+.++.+|++|.|+|||+.. .++..
T Consensus 1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~ 41 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYK 41 (70)
T ss_pred CcHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCccC
Confidence 4899998877 678999999999999999999976 55443
No 11
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=97.13 E-value=0.00062 Score=57.96 Aligned_cols=43 Identities=19% Similarity=0.147 Sum_probs=36.3
Q ss_pred cccchHHH-HHccccccHHHHHHHHHcCCeEECcEEeccccccc
Q 022999 245 ASLRVDAL-ASAGFKLSRSKLVNLIRYSSLASLVQISAKASAIR 287 (289)
Q Consensus 245 sSlRLDaV-vs~~f~lSRska~~lI~~GkV~vn~~~~~~~~~~~ 287 (289)
.++|||.. .++.|=-||+.|+++|++|+|.|||+..+++.++.
T Consensus 7 ~~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~~Kps~~V~ 50 (133)
T PRK10348 7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVE 50 (133)
T ss_pred ccccHHHHHHHcCccccHHHHHHHHHCCCEEECCEECCCCCccC
Confidence 36799975 56789999999999999999999999977665543
No 12
>smart00363 S4 S4 RNA-binding domain.
Probab=97.06 E-value=0.0011 Score=45.55 Aligned_cols=37 Identities=19% Similarity=0.115 Sum_probs=32.1
Q ss_pred cchHHHHHcc-ccccHHHHHHHHHcCCeEECcEEe-ccc
Q 022999 247 LRVDALASAG-FKLSRSKLVNLIRYSSLASLVQIS-AKA 283 (289)
Q Consensus 247 lRLDaVvs~~-f~lSRska~~lI~~GkV~vn~~~~-~~~ 283 (289)
+|||.++... +..||+.++.+|++|.|.|||+.. .++
T Consensus 1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~~~~~~~ 39 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPS 39 (60)
T ss_pred CcHHHHHHHcCcccCHHHHHHHHHcCCEEECCEEecCCC
Confidence 4899998876 679999999999999999999977 443
No 13
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=96.78 E-value=0.0015 Score=59.14 Aligned_cols=36 Identities=14% Similarity=0.167 Sum_probs=32.2
Q ss_pred cchHHHH-HccccccHHHHHHHHHcCCeEECcEEecc
Q 022999 247 LRVDALA-SAGFKLSRSKLVNLIRYSSLASLVQISAK 282 (289)
Q Consensus 247 lRLDaVv-s~~f~lSRska~~lI~~GkV~vn~~~~~~ 282 (289)
+|||.++ ..+|..||+.|.++|..|+|.|||+++..
T Consensus 89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ 125 (201)
T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDI 125 (201)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecC
Confidence 7999999 46778999999999999999999997644
No 14
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=96.73 E-value=0.0015 Score=53.07 Aligned_cols=43 Identities=19% Similarity=0.166 Sum_probs=36.6
Q ss_pred cccchHHHHHcc-ccccHHHHHHHHHcCCeEECcEEeccccccc
Q 022999 245 ASLRVDALASAG-FKLSRSKLVNLIRYSSLASLVQISAKASAIR 287 (289)
Q Consensus 245 sSlRLDaVvs~~-f~lSRska~~lI~~GkV~vn~~~~~~~~~~~ 287 (289)
.-+|||.-+-.. |=-+|+-|++++++|+|+|||+.++++.++.
T Consensus 7 ~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~aKpS~~VK 50 (100)
T COG1188 7 DRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRAKPSKEVK 50 (100)
T ss_pred cceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEcccccccC
Confidence 358999987654 7789999999999999999999998877654
No 15
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=96.32 E-value=0.0073 Score=52.00 Aligned_cols=34 Identities=35% Similarity=0.382 Sum_probs=31.6
Q ss_pred cccchHHHHHccccccHHHHHHHHHcCCeEECcE
Q 022999 245 ASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQ 278 (289)
Q Consensus 245 sSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~ 278 (289)
.++|||++++..+++||++.+.++++|.+..+-.
T Consensus 101 ~~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~~~~ 134 (142)
T PF06353_consen 101 FPLRLDRLLARQLGLSRSRLKRLIEQGLIRSDPD 134 (142)
T ss_pred CCccHHHHHHHHhCcCHHHHHHHHHCCCEEecCc
Confidence 5799999999999999999999999999998843
No 16
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=96.13 E-value=0.0061 Score=58.25 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=33.9
Q ss_pred ecccchHHHHHccc-cccHHHHHHHHHcCCeEECcEEec
Q 022999 244 EASLRVDALASAGF-KLSRSKLVNLIRYSSLASLVQISA 281 (289)
Q Consensus 244 VsSlRLDaVvs~~f-~lSRska~~lI~~GkV~vn~~~~~ 281 (289)
-+++|||.+++..| ..||+.++.+|++|+|+|||+.+.
T Consensus 15 ~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~ 53 (325)
T PRK11180 15 QLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVIN 53 (325)
T ss_pred cCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEcc
Confidence 35789999999987 589999999999999999999653
No 17
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=95.89 E-value=0.017 Score=55.06 Aligned_cols=49 Identities=14% Similarity=0.162 Sum_probs=39.1
Q ss_pred CeeEEEEe--ecccchHHHHHccc-cccHHHHHHHHHcCCeEECcEEecccc
Q 022999 236 RTKSFKTI--EASLRVDALASAGF-KLSRSKLVNLIRYSSLASLVQISAKAS 284 (289)
Q Consensus 236 ~~ke~~~t--VsSlRLDaVvs~~f-~lSRska~~lI~~GkV~vn~~~~~~~~ 284 (289)
..+++.+. -++.|||.+++..+ ++||+.++.+|++|+|+|||+.+.++.
T Consensus 7 ~~~~~~v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v~~~~ 58 (317)
T PRK11025 7 SVKIVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEY 58 (317)
T ss_pred ccEEEEECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEcCccc
Confidence 34444444 36799999999777 689999999999999999999775543
No 18
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.85 E-value=0.014 Score=52.16 Aligned_cols=77 Identities=21% Similarity=0.230 Sum_probs=55.3
Q ss_pred chHHHHHHHhhchhcceEEEEEEecCCcccC----CCCCee--EEEEe---ecccchHHHHHccccccHHHHHHHHHcCC
Q 022999 202 PELADYLITSLEKVGNVSVSCTRIPLLALEY----EPPRTK--SFKTI---EASLRVDALASAGFKLSRSKLVNLIRYSS 272 (289)
Q Consensus 202 ~eia~fi~~nLtKIgr~~V~v~ei~~~~l~~----~~~~~k--e~~~t---VsSlRLDaVvs~~f~lSRska~~lI~~Gk 272 (289)
++.+.+..-++.-+++..-++++.|.-.++. ....++ |..+. -+|+|||+++++-+|+|||..|.+|+.|+
T Consensus 85 a~larr~afdla~lRr~~~r~~g~pd~~i~krilge~~~~~~vel~l~~~~p~qlrl~~Ll~seL~LSrS~lq~lie~g~ 164 (203)
T COG4332 85 AALARRFAFDLAILRRNNARLSGFPDFHIQKRILGEIASHAAVELSLRISRPFQLRLDRLLASELGLSRSELQRLIETGQ 164 (203)
T ss_pred HHHHHHHHhhHHHHHhccccccCCCchhhhhheecCcccceeEEEEEcccCcchhHHHHHHHHHhCcCHHHHHHHHHcCc
Confidence 5677777778888887776776666533221 111222 22222 36899999999999999999999999999
Q ss_pred eEECcE
Q 022999 273 LASLVQ 278 (289)
Q Consensus 273 V~vn~~ 278 (289)
+..+-.
T Consensus 165 Irgdtd 170 (203)
T COG4332 165 IRGDTD 170 (203)
T ss_pred eeecch
Confidence 998754
No 19
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=95.64 E-value=0.015 Score=51.70 Aligned_cols=38 Identities=13% Similarity=0.134 Sum_probs=33.0
Q ss_pred chHHHH-HccccccHHHHHHHHHcCCeEECcEEeccccc
Q 022999 248 RVDALA-SAGFKLSRSKLVNLIRYSSLASLVQISAKASA 285 (289)
Q Consensus 248 RLDaVv-s~~f~lSRska~~lI~~GkV~vn~~~~~~~~~ 285 (289)
|||.++ ..+|--||+.|+++|.+|+|.|||+++.+.|-
T Consensus 104 RLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~ 142 (177)
T PRK04051 104 RLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142 (177)
T ss_pred HHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCe
Confidence 999865 57999999999999999999999997666553
No 20
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=93.88 E-value=0.066 Score=48.76 Aligned_cols=35 Identities=17% Similarity=0.199 Sum_probs=31.5
Q ss_pred chHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999 248 RVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK 282 (289)
Q Consensus 248 RLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~ 282 (289)
|||+||= .+|.-||..|.++|..|.|.|||+.+.-
T Consensus 95 RLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~i 130 (205)
T COG0522 95 RLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNI 130 (205)
T ss_pred HHHHHHHHhcccccHHHHHHHhhcceEEECCEEecc
Confidence 8999986 6999999999999999999999995543
No 21
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=92.12 E-value=0.17 Score=44.48 Aligned_cols=42 Identities=12% Similarity=0.005 Sum_probs=35.0
Q ss_pred EEeecc---cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999 241 KTIEAS---LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK 282 (289)
Q Consensus 241 ~~tVsS---lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~ 282 (289)
+++|++ -|||.|+- .+|--|...|.++|..|.|.|||+++..
T Consensus 95 ~Ltv~~~leRRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~ 140 (162)
T TIGR01018 95 GLTVEDFLERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTS 140 (162)
T ss_pred hccHHHHHHHhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEecc
Confidence 455555 49999876 6899999999999999999999995544
No 22
>PLN00189 40S ribosomal protein S9; Provisional
Probab=88.31 E-value=0.19 Score=45.44 Aligned_cols=42 Identities=21% Similarity=0.120 Sum_probs=35.1
Q ss_pred EEeecc---cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999 241 KTIEAS---LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK 282 (289)
Q Consensus 241 ~~tVsS---lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~ 282 (289)
.++|++ -|||+|+- .+|--|+..|.++|..|.|.|||+++..
T Consensus 100 ~Ltvs~~leRRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~ 145 (194)
T PLN00189 100 ALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNV 145 (194)
T ss_pred hccHHHHHHhhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEec
Confidence 456666 69999875 6889999999999999999999995543
No 23
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=88.26 E-value=0.41 Score=42.86 Aligned_cols=36 Identities=22% Similarity=0.092 Sum_probs=31.5
Q ss_pred cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999 247 LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK 282 (289)
Q Consensus 247 lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~ 282 (289)
-|||+|+- .+|--|...|.++|..|.|.|||+++..
T Consensus 107 RRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~ 143 (181)
T PTZ00155 107 RRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDI 143 (181)
T ss_pred HhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEecc
Confidence 38999886 5889999999999999999999996543
No 24
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.85 E-value=0.68 Score=42.56 Aligned_cols=49 Identities=24% Similarity=0.153 Sum_probs=42.3
Q ss_pred CeeEEEEeecccchHHHHHccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999 236 RTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKAS 284 (289)
Q Consensus 236 ~~ke~~~tVsSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~~~~ 284 (289)
+++.+..-|-|+|.|++.-.+.++-|+|...+.=.+..++|++..-++|
T Consensus 129 ~~~~i~~~v~sfr~d~llK~Glgv~rnKVel~fye~e~R~N~~Kl~kkS 177 (248)
T KOG4837|consen 129 EKVLIVPEVVSFRVDALLKVGLGVTRNKVELLFYEYEPRTNSFKLVKKS 177 (248)
T ss_pred hhhhhhhHHHHHHHHHHHHhccccccchhhHhhhhcccccCcccccccc
Confidence 4555666789999999999999999999999999999999998665544
No 25
>cd02644 R3H_jag R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=75.86 E-value=24 Score=26.41 Aligned_cols=59 Identities=14% Similarity=0.050 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEEE
Q 022999 78 IEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLS 138 (289)
Q Consensus 78 k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl~ 138 (289)
..+.....++++++..++.++.-+=+++.|..++..++.+++++.-...|-=+ .|.+++
T Consensus 6 ~~L~~~A~~~a~~v~~tg~~~~l~PM~~~eRrivH~~~~~~~~l~T~S~G~~~--~R~vvI 64 (67)
T cd02644 6 ETLIRLAERAAEKVRRTGKPVKLEPMNAYERRIIHDALANDEDVETESEGEGP--YRRVVI 64 (67)
T ss_pred HHHHHHHHHHHHHHHHHCCeeEeCCCCHHHHHHHHHHHHhCCCceEEeecCCC--CeEEEE
Confidence 45566677888999999999999999999999999999998889888777432 454443
No 26
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=73.80 E-value=4.2 Score=40.49 Aligned_cols=33 Identities=21% Similarity=0.202 Sum_probs=30.2
Q ss_pred hHHHHHccccccHHHHHHHHHcCCeEECcEEec
Q 022999 249 VDALASAGFKLSRSKLVNLIRYSSLASLVQISA 281 (289)
Q Consensus 249 LDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~ 281 (289)
+|.++.+++--|++.|..+|++|-|+|||+.+.
T Consensus 346 ~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~ 378 (408)
T PRK05912 346 LALLVEAGLVPSKSEARRLIKQGGVKINGEKVS 378 (408)
T ss_pred HHHHHHhCCCCCHHHHHHHHHcCCEEECCEEec
Confidence 499999999999999999999999999999653
No 27
>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=73.57 E-value=3.2 Score=27.35 Aligned_cols=21 Identities=24% Similarity=0.306 Sum_probs=18.8
Q ss_pred HHccccccHHHHHHHHHcCCe
Q 022999 253 ASAGFKLSRSKLVNLIRYSSL 273 (289)
Q Consensus 253 vs~~f~lSRska~~lI~~GkV 273 (289)
+|+.+|+||+....++++|.+
T Consensus 7 ~a~~lgis~~ti~~~~~~g~i 27 (49)
T TIGR01764 7 AAEYLGVSKDTVYRLIHEGEL 27 (49)
T ss_pred HHHHHCCCHHHHHHHHHcCCC
Confidence 568899999999999999973
No 28
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=73.11 E-value=6.7 Score=41.19 Aligned_cols=73 Identities=12% Similarity=0.152 Sum_probs=57.3
Q ss_pred eEEEEEecCCCCCCCCchhhHHHHHh-CCCCCCccccEEEecCCeEEEEecchHHHHHHHhhch--hcceEEEEEEec
Q 022999 152 VAALSITGNFGFQPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEK--VGNVSVSCTRIP 226 (289)
Q Consensus 152 i~~L~I~~~~kF~~LsHRD~LGaLmg-LGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtK--Igr~~V~v~ei~ 226 (289)
+.-+.|+-- +-+.++.++++|+|-+ .||++..||+|=+.+ +..+|=+.+++++-+...|.+ |.+.+|.++...
T Consensus 486 ~~~~~~~~g-~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~-~~s~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 (629)
T PRK11634 486 MQLYRIEVG-RDDGVEVRHIVGAIANEGDISSRYIGNIKLFA-SHSTIELPKGMPGEVLQHFTRTRILNKPMNMQLLG 561 (629)
T ss_pred CEEEEEecc-cccCCCHHHHHHHHHhhcCCChhhCCcEEEeC-CceEEEcChhhHHHHHHHhccccccCCceEEEECC
Confidence 444555431 2256799999999998 999999999996664 578899999999999999976 557788877653
No 29
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=71.67 E-value=5 Score=40.08 Aligned_cols=33 Identities=21% Similarity=0.243 Sum_probs=30.2
Q ss_pred hHHHHHccccccHHHHHHHHHcCCeEECcEEec
Q 022999 249 VDALASAGFKLSRSKLVNLIRYSSLASLVQISA 281 (289)
Q Consensus 249 LDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~ 281 (289)
+|.++++++--|++.|..+|++|-|+|||+.+.
T Consensus 346 ~~~l~~~~~~~S~~earrli~~ggv~in~~~v~ 378 (410)
T PRK13354 346 VDLLVDLGLEPSKREARRLIQNGAIKINGEKVT 378 (410)
T ss_pred HHHHHHhCCCCCHHHHHHHHHcCCEEECCEEcc
Confidence 389999999999999999999999999999653
No 30
>PRK11507 ribosome-associated protein; Provisional
Probab=70.40 E-value=5.8 Score=30.39 Aligned_cols=33 Identities=12% Similarity=0.054 Sum_probs=25.4
Q ss_pred cchHHHHH-ccccccHHHHHHHHHcCCeEECcEE
Q 022999 247 LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQI 279 (289)
Q Consensus 247 lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~ 279 (289)
.+||-++- +.+==|=..|+.+|+.|.|+|||++
T Consensus 12 I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGev 45 (70)
T PRK11507 12 VELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAV 45 (70)
T ss_pred EEHHHHHhhhCcccChHHHHHHHHcCceEECCEE
Confidence 34676664 2344577899999999999999994
No 31
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=60.96 E-value=8.9 Score=29.64 Aligned_cols=39 Identities=15% Similarity=0.158 Sum_probs=27.2
Q ss_pred hHHHHH-ccccccHHHHHHHHHcCCeEECcE-Eeccccccc
Q 022999 249 VDALAS-AGFKLSRSKLVNLIRYSSLASLVQ-ISAKASAIR 287 (289)
Q Consensus 249 LDaVvs-~~f~lSRska~~lI~~GkV~vn~~-~~~~~~~~~ 287 (289)
|+.++- .+.-=|=..|+.+|..|.|+|||+ +.++.--||
T Consensus 14 L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr 54 (73)
T COG2501 14 LGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLR 54 (73)
T ss_pred HHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEee
Confidence 555543 244457789999999999999999 444444444
No 32
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=60.84 E-value=19 Score=32.79 Aligned_cols=86 Identities=17% Similarity=0.237 Sum_probs=58.6
Q ss_pred cccchhhHHHHHhhccHH------HHhcc------------CCCcchHHHHHHHHHHHHHHhcCCCeEEecCCCHHH--H
Q 022999 49 HTASGIRHLIQAVKGNFD------DLLKG------------VGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPV--L 108 (289)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~------~ll~~------------~~~~e~k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e--~ 108 (289)
+..+|....|.|+....- .+|++ +.+++-.+.+.|+-+.+.+..+.+.++.|.|.+|.- .
T Consensus 31 LSGsGKSTiA~ale~~L~~~G~~~y~LDGDnvR~gL~~dLgFs~edR~eniRRvaevAkll~daG~iviva~ISP~r~~R 110 (197)
T COG0529 31 LSGSGKSTIANALEEKLFAKGYHVYLLDGDNVRHGLNRDLGFSREDRIENIRRVAEVAKLLADAGLIVIVAFISPYREDR 110 (197)
T ss_pred CCCCCHHHHHHHHHHHHHHcCCeEEEecChhHhhcccCCCCCChHHHHHHHHHHHHHHHHHHHCCeEEEEEeeCccHHHH
Confidence 467899999988832211 12221 444555677999999999999999999999999984 4
Q ss_pred HHHHHHHhccCCeeEEEeCCCcccce
Q 022999 109 KESMMALEKLADVKAVAQGGYPQAER 134 (289)
Q Consensus 109 ~i~~~il~~~~~v~~~~~GGy~~AER 134 (289)
+.+..++++-..+.+...--.+.+|+
T Consensus 111 ~~aR~~~~~~~FiEVyV~~pl~vce~ 136 (197)
T COG0529 111 QMARELLGEGEFIEVYVDTPLEVCER 136 (197)
T ss_pred HHHHHHhCcCceEEEEeCCCHHHHHh
Confidence 45566666544566655544444444
No 33
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=56.10 E-value=2.4 Score=31.93 Aligned_cols=42 Identities=14% Similarity=0.163 Sum_probs=23.4
Q ss_pred ccchHHHHHc-cccccHHHHHHHHHcCCeEECcE-Eeccccccc
Q 022999 246 SLRVDALASA-GFKLSRSKLVNLIRYSSLASLVQ-ISAKASAIR 287 (289)
Q Consensus 246 SlRLDaVvs~-~f~lSRska~~lI~~GkV~vn~~-~~~~~~~~~ 287 (289)
..+||-++-. ++=-|=..|+.+|++|.|+|||+ +..+..-||
T Consensus 7 ~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~ 50 (65)
T PF13275_consen 7 YITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLR 50 (65)
T ss_dssp ---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----
T ss_pred cEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCC
Confidence 3456666642 33346678999999999999998 444433333
No 34
>PF12728 HTH_17: Helix-turn-helix domain
Probab=49.28 E-value=13 Score=25.34 Aligned_cols=21 Identities=29% Similarity=0.360 Sum_probs=19.3
Q ss_pred HHccccccHHHHHHHHHcCCe
Q 022999 253 ASAGFKLSRSKLVNLIRYSSL 273 (289)
Q Consensus 253 vs~~f~lSRska~~lI~~GkV 273 (289)
++..+|+|++.+.+++++|.+
T Consensus 7 ~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 7 AAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHCcCHHHHHHHHHcCCC
Confidence 578899999999999999987
No 35
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=48.29 E-value=77 Score=29.19 Aligned_cols=54 Identities=19% Similarity=0.121 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccce
Q 022999 80 EVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAER 134 (289)
Q Consensus 80 ~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AER 134 (289)
+++=...++++|.+.++++..+=++|+|.+++...++..+++.-..- |.+..-|
T Consensus 149 L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH~~l~~~~~V~T~Se-G~ep~R~ 202 (208)
T COG1847 149 LIKLAERAAERVLETGRSVELEPMPPFERKIVHTALSANPGVETYSE-GEEPNRR 202 (208)
T ss_pred HHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHHHHHHhcCCcceeec-CCCCceE
Confidence 34444556688999999999999999999999999999999976554 4444444
No 36
>cd02638 R3H_unknown_1 R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=46.99 E-value=1e+02 Score=23.20 Aligned_cols=40 Identities=15% Similarity=-0.071 Sum_probs=32.3
Q ss_pred HHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeC
Q 022999 88 ARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQG 127 (289)
Q Consensus 88 ~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~G 127 (289)
+-.....+++...+=++|+|.+++...+.+.+++.-...|
T Consensus 11 f~~~~~~~r~v~LePM~~~ERkIIH~~Lq~~~~v~T~S~G 50 (62)
T cd02638 11 FLLSFQRYRVLLFPPLNSRRRYLIHQTVENRFLLSTFSVG 50 (62)
T ss_pred HHHhcccCCeEecCCCChHHHHHHHHHHhcCCCceEEEcc
Confidence 3444556789999999999999999999998888766554
No 37
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=43.05 E-value=25 Score=35.28 Aligned_cols=32 Identities=31% Similarity=0.290 Sum_probs=29.6
Q ss_pred hHHHHHccccccHHHHHHHHHcCCeEECcEEe
Q 022999 249 VDALASAGFKLSRSKLVNLIRYSSLASLVQIS 280 (289)
Q Consensus 249 LDaVvs~~f~lSRska~~lI~~GkV~vn~~~~ 280 (289)
+|.++.+++.-||+.|..+|++|-|++||+.+
T Consensus 339 ~~~lv~~~L~psr~earr~i~~g~v~in~~~v 370 (401)
T COG0162 339 VDLLVDAGLAPSRSEARRLIQQGGVKINGEKV 370 (401)
T ss_pred HHHHHHhCCcccHHHHHhhcccCCEEECCEec
Confidence 68899999999999999999999999999843
No 38
>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=40.97 E-value=22 Score=22.96 Aligned_cols=22 Identities=23% Similarity=0.217 Sum_probs=19.6
Q ss_pred HHccccccHHHHHHHHHcCCeE
Q 022999 253 ASAGFKLSRSKLVNLIRYSSLA 274 (289)
Q Consensus 253 vs~~f~lSRska~~lI~~GkV~ 274 (289)
+|..+|+|++....++++|.+.
T Consensus 6 ~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 6 AAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHCcCHHHHHHHHHcCCCC
Confidence 5678999999999999999864
No 39
>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]
Probab=40.66 E-value=54 Score=34.17 Aligned_cols=172 Identities=17% Similarity=0.185 Sum_probs=90.7
Q ss_pred EecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccce-------eEEEeeCCCCCCCCcCceEEEEEecCC-CCCCCCchh
Q 022999 99 HSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAER-------CRLSVGHPEALTSDPDIVAALSITGNF-GFQPCSHGD 170 (289)
Q Consensus 99 ~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AER-------krl~i~~p~y~~~~~~~i~~L~I~~~~-kF~~LsHRD 170 (289)
.-.||-.-...++...+++-.++.....- |.-.. ..+.+-+|..++ ++-..-+|.-++ +-.-++..+
T Consensus 344 RcGFLGlLHmeiiqERLeREf~ldlI~Ta--PsV~Y~v~~~~g~~~~i~NPs~~P---~~~~I~~i~EP~v~~~ii~P~e 418 (603)
T COG0481 344 RCGFLGLLHMEIIQERLEREFDLDLITTA--PSVVYKVELTDGEEIEVDNPSDLP---DPNKIEEIEEPYVKATIITPQE 418 (603)
T ss_pred eehhhhHHHHHHHHHHHHHhhCcceEecC--CceEEEEEEcCCcEEEecChHhCC---ChhhhheeeCceeEEEEeCcHH
Confidence 34799887777776666554444433321 11111 123333443321 111111221111 112247779
Q ss_pred hHHHHHhCCC-CCCccccEEEecCCeEEEEecchHHHHHHHhhchhcceEEEEEEecCCcccCCCCCeeEEEEeecccch
Q 022999 171 FLGSILGTGI-AREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRV 249 (289)
Q Consensus 171 ~LGaLmgLGI-~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei~~~~l~~~~~~~ke~~~tVsSlRL 249 (289)
|||++|.|=. +|....|+-..+++++.+...=.+++.+.+=+.|.+.++==.--.+.+...+.+...-...+.|.+-++
T Consensus 419 ylG~vm~Lcq~kRG~~~~m~yl~~~rv~l~Y~lPl~Eiv~DFfDkLKS~skGYAS~DYe~~~y~~~~lVK~dIlvNge~V 498 (603)
T COG0481 419 YLGNVMELCQEKRGIQIDMEYLDQNRVMLTYELPLAEIVFDFFDKLKSISKGYASFDYEFIGYRESDLVKVDILVNGEKV 498 (603)
T ss_pred HHHHHHHHHHHhcCceecceEecCceEEEEEecchHHHHHHHhHhhhccccceeeeccccccccccceEEEEEEecCccc
Confidence 9999999654 788888886666567877776666665555455544322111112222333344455668899999999
Q ss_pred HHHHHccc-----cccH---HHHHHHHHcCCeEE
Q 022999 250 DALASAGF-----KLSR---SKLVNLIRYSSLAS 275 (289)
Q Consensus 250 DaVvs~~f-----~lSR---ska~~lI~~GkV~v 275 (289)
||+..-+. .-.| .|.+++|-..+-.|
T Consensus 499 DALs~ivHrd~A~~rgr~~~~KlKelIPrq~Fei 532 (603)
T COG0481 499 DALSFIVHRDNAYERGRELVEKLKELIPRQQFEI 532 (603)
T ss_pred cceeeeechhHHHHHHHHHHHHHHhhccHhheee
Confidence 99854332 2222 24566666655433
No 40
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=37.87 E-value=1.5e+02 Score=21.07 Aligned_cols=39 Identities=13% Similarity=0.035 Sum_probs=26.9
Q ss_pred CeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEEE
Q 022999 96 EVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLS 138 (289)
Q Consensus 96 ~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl~ 138 (289)
...+-+ +++.+..++..++. ..++.....| ++..|..++
T Consensus 22 ~~~f~p-m~~~~R~~iH~~a~-~~gL~s~S~g--~~~~R~vvv 60 (63)
T PF01424_consen 22 SLEFPP-MNSFERKLIHELAE-YYGLKSKSEG--EGPNRRVVV 60 (63)
T ss_dssp EEEEEC---SHHHHHHHHHHH-HCTEEEEEES--SSSSSEEEE
T ss_pred EEEECC-CCHHHHHHHHHHHH-HCCCEEEEec--CCCCeEEEE
Confidence 555555 99999998888776 6789888887 555665544
No 41
>TIGR00234 tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples.
Probab=34.56 E-value=52 Score=32.49 Aligned_cols=38 Identities=21% Similarity=0.142 Sum_probs=31.8
Q ss_pred HHHHHccccccHHHHHHHHHcCCeEECcEEeccccccc
Q 022999 250 DALASAGFKLSRSKLVNLIRYSSLASLVQISAKASAIR 287 (289)
Q Consensus 250 DaVvs~~f~lSRska~~lI~~GkV~vn~~~~~~~~~~~ 287 (289)
|....++.--|++.+..+|++|-|+||++.+.--..+|
T Consensus 334 ~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~ 371 (377)
T TIGR00234 334 DLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDLEPIR 371 (377)
T ss_pred HHHHHcCCCcChHHHHHHHHhCCEEECCEeccCchhhh
Confidence 67777888899999999999999999999766545444
No 42
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=34.23 E-value=69 Score=26.84 Aligned_cols=44 Identities=11% Similarity=0.133 Sum_probs=34.0
Q ss_pred ccccEEEecCCeEEEEecchHHHHHHHhhchhcceEEEEEEecCCcc
Q 022999 184 KIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLAL 230 (289)
Q Consensus 184 kiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei~~~~l 230 (289)
+.||.+.-++ ..|.+. .+.+-...||..+|++.+.+...+..++
T Consensus 53 ~~Gd~l~i~~-~~Y~It--aVG~~a~~NL~~LGHiTi~F~g~~~~~l 96 (120)
T PRK10377 53 QPGLQFELGQ-HRYPVT--AVGSVAEDNLRELGHVTLRFDGLNEAEF 96 (120)
T ss_pred CCCCEEEECC-EEEEEE--EEhHHHHHHHHhcCCEEEEECCCCCccc
Confidence 7899998864 455444 4788888999999999999987665444
No 43
>TIGR00849 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.
Probab=33.51 E-value=72 Score=26.79 Aligned_cols=44 Identities=18% Similarity=0.275 Sum_probs=33.9
Q ss_pred ccccEEEecCCeEEEEecchHHHHHHHhhchhcceEEEEEEecCCcc
Q 022999 184 KIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLAL 230 (289)
Q Consensus 184 kiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei~~~~l 230 (289)
+.||.+.-++ ..|.+. .+.+-...||..+|++.+.+...+..++
T Consensus 53 ~~Gd~l~i~~-~~Y~It--aVG~~a~~NL~~LGHiTi~F~g~~~~~l 96 (121)
T TIGR00849 53 KPGQVFMIGG-IAYPVT--AVGDVAEKNLRSLGHITVRFDGSNVAEF 96 (121)
T ss_pred CCCCEEEECC-EEEEEE--EEhHHHHHHHHhcCCEEEEECCCCCccc
Confidence 7899998864 455544 4788888999999999999986555444
No 44
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=29.41 E-value=1.2e+02 Score=22.45 Aligned_cols=40 Identities=20% Similarity=0.251 Sum_probs=30.2
Q ss_pred CCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeE
Q 022999 94 RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCR 136 (289)
Q Consensus 94 ~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkr 136 (289)
.+...+.+-|+|.|..++..+..++ ++.....|+.+ .|++
T Consensus 17 ~~eL~Fp~~ls~~eRriih~la~~l-GL~~~s~G~g~--~R~v 56 (60)
T cd02639 17 RDELAFPSSLSPAERRIVHLLASRL-GLNHVSDGTGE--RRQV 56 (60)
T ss_pred ceEEEcCCCCCHHHHHHHHHHHHHc-CCceEEeCCCc--eEEE
Confidence 4577888889999999888776665 68788888854 4443
No 45
>cd02640 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=28.05 E-value=1.8e+02 Score=21.39 Aligned_cols=42 Identities=14% Similarity=0.112 Sum_probs=31.2
Q ss_pred cCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEE
Q 022999 93 SRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (289)
Q Consensus 93 ~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl 137 (289)
......+.+-|++.|..++..+..+ .+++....|- +.+|..+
T Consensus 16 ~~~~l~f~p~lt~~eR~~vH~~a~~-~gL~s~S~G~--g~~R~v~ 57 (60)
T cd02640 16 DIRDMVFSPEFSKEERALIHQIAQK-YGLKSRSYGS--GNDRYLV 57 (60)
T ss_pred ccceEEcCCCCCHHHHHHHHHHHHH-cCCceeeEeC--CCCeEEE
Confidence 3667888899999999998888766 5788877665 3356443
No 46
>KOG4469 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.53 E-value=13 Score=34.95 Aligned_cols=45 Identities=24% Similarity=0.376 Sum_probs=33.0
Q ss_pred ccCCCCcccccCCCCccCccccccccCcccccccchhhHHHHHhhc
Q 022999 18 TFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKG 63 (289)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (289)
++...|.+|--.+.||.|+|.+.+++|.++. ..+|.|.+...+|-
T Consensus 278 vpsvshvtharhqesclhttrtsfslpipls-stpgfctaivslkw 322 (391)
T KOG4469|consen 278 VPSVSHVTHARHQESCLHTTRTSFSLPIPLS-STPGFCTAIVSLKW 322 (391)
T ss_pred CCcchhhhhhhhhhhhhhcccceeeeccccC-CCCccEeeEeeeee
Confidence 3444555565668899999999999988863 45689988766654
No 47
>PRK04313 30S ribosomal protein S4e; Validated
Probab=26.45 E-value=62 Score=30.30 Aligned_cols=36 Identities=6% Similarity=-0.028 Sum_probs=28.6
Q ss_pred ccchHHHHHcccc--ccHHHHHHHHHcCCeEECcEEec
Q 022999 246 SLRVDALASAGFK--LSRSKLVNLIRYSSLASLVQISA 281 (289)
Q Consensus 246 SlRLDaVvs~~f~--lSRska~~lI~~GkV~vn~~~~~ 281 (289)
|+=|=.++...++ .++..|+..+.+|+|+|||+++.
T Consensus 37 siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~ 74 (237)
T PRK04313 37 SIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRK 74 (237)
T ss_pred ccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEc
Confidence 4556566666555 68899999999999999999764
No 48
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=25.31 E-value=51 Score=23.06 Aligned_cols=21 Identities=14% Similarity=0.090 Sum_probs=17.6
Q ss_pred HHHHHccccccHHHHHHHHHc
Q 022999 250 DALASAGFKLSRSKLVNLIRY 270 (289)
Q Consensus 250 DaVvs~~f~lSRska~~lI~~ 270 (289)
...+|..||+|++.+...+..
T Consensus 22 ~~~La~~FgIs~stvsri~~~ 42 (53)
T PF13613_consen 22 FQDLAYRFGISQSTVSRIFHE 42 (53)
T ss_pred HhHHhhheeecHHHHHHHHHH
Confidence 456889999999999988763
No 49
>cd06007 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=24.98 E-value=2.4e+02 Score=20.64 Aligned_cols=41 Identities=17% Similarity=0.028 Sum_probs=30.8
Q ss_pred CCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEE
Q 022999 94 RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (289)
Q Consensus 94 ~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl 137 (289)
.....+.+=||+.|...+..+..+ .+++....|- +.+|..+
T Consensus 16 ~~~l~Fpp~ls~~eR~~vH~~a~~-~gL~s~S~G~--g~~R~v~ 56 (59)
T cd06007 16 NEEYEFPSSLTNHERAVIHRLCRK-LGLKSKSKGK--GSNRRLS 56 (59)
T ss_pred ccEEEcCCCCCHHHHHHHHHHHHH-cCCCceeecC--CCCeEEE
Confidence 667788889999999988888766 5788876665 3366544
No 50
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=23.61 E-value=3.2e+02 Score=20.45 Aligned_cols=47 Identities=17% Similarity=0.068 Sum_probs=32.4
Q ss_pred HHHhc-CCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEEEe
Q 022999 89 RRASS-RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSV 139 (289)
Q Consensus 89 ~~a~~-~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl~i 139 (289)
+.+.. +....+.+ +++.+..++..++.++ ++.....|- +..|.+++.
T Consensus 30 ~~v~~~~~~~~~~p-m~~~~R~~iH~~a~~~-~l~s~S~g~--g~~R~vvv~ 77 (79)
T smart00393 30 RFVKSTKESVELPP-MNSYERKIVHELAEKY-GLESESFGE--GPKRRVVIS 77 (79)
T ss_pred HHHhccCCeEEcCC-CCHHHHHHHHHHHHHc-CCEEEEEcC--CCCcEEEEE
Confidence 33433 34556666 9999999999998887 888887775 334655543
No 51
>PF03610 EIIA-man: PTS system fructose IIA component; InterPro: IPR004701 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for IIA and IIB components.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane; PDB: 3GDW_B 2JZN_A 1VSQ_A 2JZO_B 1VRC_A 1PDO_A 3GX1_A 3B48_B 3BED_B 3IPR_C ....
Probab=23.17 E-value=2.1e+02 Score=22.73 Aligned_cols=72 Identities=11% Similarity=0.089 Sum_probs=48.5
Q ss_pred ccchhhHHHHHhhcc-H--HHHhccCCCcchHHHHHHHHHHHHHHh-cCCCeEEecCCCHHHHHHHHHHHhccCCe
Q 022999 50 TASGIRHLIQAVKGN-F--DDLLKGVGDKNAIEEVKHILEMARRAS-SRREVLHSDFLTPPVLKESMMALEKLADV 121 (289)
Q Consensus 50 ~~~~~~~~~~~~~~~-~--~~ll~~~~~~e~k~~v~ri~D~~~~a~-~~~~~~~TdFLdP~e~~i~~~il~~~~~v 121 (289)
.+.|...++..+-++ . -..+....+.+...+.+++.+.++... ......+||...-.-.+.+...+.+.+.+
T Consensus 10 ~A~g~~~~~~~i~G~~~~~i~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~vlil~Dl~ggsp~n~a~~~~~~~~~~ 85 (116)
T PF03610_consen 10 LAEGLLESAEMILGEDQDNIEAVDLYPDESIEDFEEKLEEAIEELDEGDGVLILTDLGGGSPFNEAARLLLDKPNI 85 (116)
T ss_dssp HHHHHHHHHHHHHTSTCSSEEEEEETTTSCHHHHHHHHHHHHHHCCTTSEEEEEESSTTSHHHHHHHHHHCTSTTE
T ss_pred HHHHHHHHHHHHcCCCcccEEEEECcCCCCHHHHHHHHHHHHHhccCCCcEEEEeeCCCCccchHHHHHhccCCCE
Confidence 456677777777666 2 233444556667788899999997764 56689999999866666655555554443
No 52
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=23.16 E-value=80 Score=23.94 Aligned_cols=29 Identities=10% Similarity=0.133 Sum_probs=25.0
Q ss_pred chHHHHHccccccHHHHHHHHHcCCeEEC
Q 022999 248 RVDALASAGFKLSRSKLVNLIRYSSLASL 276 (289)
Q Consensus 248 RLDaVvs~~f~lSRska~~lI~~GkV~vn 276 (289)
++-..++..+|+|..+.+++.+.|+|..+
T Consensus 45 ~~~~~lAk~~G~t~~~l~~~~~~Gkit~~ 73 (75)
T TIGR02675 45 GALQALAKAMGVTRGELRKMLSDGKLTAD 73 (75)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHCCCCccc
Confidence 46667788999999999999999999754
No 53
>PF10809 DUF2732: Protein of unknown function (DUF2732); InterPro: IPR020126 This entry represents a group of proteins with no known function
Probab=22.54 E-value=57 Score=25.46 Aligned_cols=30 Identities=33% Similarity=0.279 Sum_probs=24.7
Q ss_pred eecccchHHHHHcccc--ccHHHHHHHHHcCC
Q 022999 243 IEASLRVDALASAGFK--LSRSKLVNLIRYSS 272 (289)
Q Consensus 243 tVsSlRLDaVvs~~f~--lSRska~~lI~~Gk 272 (289)
..-|.|||+++..+.+ +|...+.+++.+.-
T Consensus 35 ~~~S~RL~~LA~hi~~~~ls~~E~~ELLrqEA 66 (77)
T PF10809_consen 35 DAFSSRLDALAAHIANEELSAVEAAELLRQEA 66 (77)
T ss_pred HHHHHHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence 4568999999998874 99999999987643
No 54
>PF06115 DUF956: Domain of unknown function (DUF956); InterPro: IPR010360 This is a family of bacterial sequences with undetermined function.
Probab=22.48 E-value=40 Score=28.36 Aligned_cols=39 Identities=28% Similarity=0.509 Sum_probs=31.4
Q ss_pred ccccEEEecCCeEEEEecchHHHHHHHhhchhcceEEEEE
Q 022999 184 KIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCT 223 (289)
Q Consensus 184 kiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~V~v~ 223 (289)
+-|+|++ ||++.-++-++...+||.-=++.|-.+..++.
T Consensus 23 ~yGkimi-GDkaFEFyn~~n~~dyIQIPW~eI~~V~a~V~ 61 (118)
T PF06115_consen 23 KYGKIMI-GDKAFEFYNDRNVEDYIQIPWEEIDYVIASVS 61 (118)
T ss_pred ccCeEEE-cccceEeecCCChhhcEEeChhheeEEEEEEE
Confidence 8899986 66677888888999999887777777766664
No 55
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=21.86 E-value=80 Score=29.67 Aligned_cols=36 Identities=8% Similarity=0.047 Sum_probs=24.6
Q ss_pred ccchHHHHHccccccH--HHHHHHHHcCCeEECcEEec
Q 022999 246 SLRVDALASAGFKLSR--SKLVNLIRYSSLASLVQISA 281 (289)
Q Consensus 246 SlRLDaVvs~~f~lSR--ska~~lI~~GkV~vn~~~~~ 281 (289)
|+=|=.|+.-.++.+= ..|+..|..|+|+|||++++
T Consensus 40 slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRk 77 (241)
T COG1471 40 SLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRK 77 (241)
T ss_pred cccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEec
Confidence 3334445555544432 46889999999999998765
No 56
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.00 E-value=78 Score=20.82 Aligned_cols=22 Identities=23% Similarity=0.040 Sum_probs=20.1
Q ss_pred HHccccccHHHHHHHHHcCCeE
Q 022999 253 ASAGFKLSRSKLVNLIRYSSLA 274 (289)
Q Consensus 253 vs~~f~lSRska~~lI~~GkV~ 274 (289)
+|..+|+|.+....+++.|.+.
T Consensus 6 ~a~~~gv~~~tlr~~~~~g~l~ 27 (49)
T cd04761 6 LAKLTGVSPSTLRYYERIGLLS 27 (49)
T ss_pred HHHHHCcCHHHHHHHHHCCCCC
Confidence 5789999999999999999876
No 57
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=20.41 E-value=96 Score=29.52 Aligned_cols=36 Identities=11% Similarity=0.081 Sum_probs=28.2
Q ss_pred ccchHHHHHcccc--ccHHHHHHHHHcCCeEECcEEec
Q 022999 246 SLRVDALASAGFK--LSRSKLVNLIRYSSLASLVQISA 281 (289)
Q Consensus 246 SlRLDaVvs~~f~--lSRska~~lI~~GkV~vn~~~~~ 281 (289)
|+=|=-++...++ .+...|+..+.+|+|+|||+++.
T Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~ 78 (262)
T PTZ00118 41 CLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRT 78 (262)
T ss_pred ccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEc
Confidence 4555567776666 46679999999999999999764
Done!