Query 027063
Match_columns 229
No_of_seqs 115 out of 1094
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 04:26:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027063.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027063hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00029 60S ribosomal protein 100.0 1.1E-56 2.3E-61 381.1 23.1 215 1-216 1-216 (216)
2 PTZ00225 60S ribosomal protein 100.0 1.4E-53 3E-58 361.0 24.2 211 1-214 1-212 (214)
3 PRK04203 rpl1P 50S ribosomal p 100.0 1.5E-50 3.2E-55 343.5 24.0 211 4-217 2-215 (215)
4 cd00403 Ribosomal_L1 Ribosomal 100.0 1E-45 2.2E-50 312.3 22.3 203 10-215 2-208 (208)
5 CHL00129 rpl1 ribosomal protei 100.0 5E-43 1.1E-47 299.1 21.9 193 13-215 22-223 (229)
6 PF00687 Ribosomal_L1: Ribosom 100.0 6.9E-43 1.5E-47 297.1 19.3 200 13-212 1-220 (220)
7 COG0081 RplA Ribosomal protein 100.0 2.5E-42 5.5E-47 290.4 21.7 196 11-215 21-225 (228)
8 TIGR01169 rplA_bact ribosomal 100.0 2.5E-42 5.4E-47 294.9 21.8 190 13-212 21-219 (227)
9 PRK05424 rplA 50S ribosomal pr 100.0 2.5E-42 5.4E-47 295.4 21.7 192 13-214 22-222 (230)
10 KOG1570 60S ribosomal protein 100.0 7.4E-37 1.6E-41 251.8 11.9 212 1-212 2-214 (218)
11 KOG1685 Uncharacterized conser 100.0 2E-36 4.2E-41 267.6 11.0 219 2-224 17-267 (343)
12 KOG1569 50S ribosomal protein 100.0 8E-28 1.7E-32 207.9 15.8 190 12-210 91-298 (323)
13 TIGR01170 rplA_mito ribosomal 100.0 1.5E-27 3.2E-32 189.8 14.1 131 13-154 3-141 (141)
14 PF13003 MRL1: Ribosomal prote 97.1 0.00088 1.9E-08 52.4 5.2 55 13-68 72-133 (133)
15 PRK02228 V-type ATP synthase s 71.9 11 0.00024 28.0 5.2 85 64-153 2-95 (100)
16 PRK01395 V-type ATP synthase s 62.6 28 0.0006 26.2 5.7 70 63-139 4-76 (104)
17 PRK04203 rpl1P 50S ribosomal p 47.9 12 0.00026 31.8 1.8 21 117-137 117-139 (215)
18 COG1436 NtpG Archaeal/vacuolar 45.9 39 0.00085 25.5 4.1 85 63-153 3-99 (104)
19 PRK01189 V-type ATP synthase s 44.2 79 0.0017 23.7 5.6 84 63-153 3-98 (104)
20 PF04481 DUF561: Protein of un 36.9 80 0.0017 27.3 5.1 113 63-194 62-179 (242)
21 KOG0780 Signal recognition par 34.9 49 0.0011 31.2 3.7 81 29-115 100-192 (483)
22 COG4844 Uncharacterized protei 34.3 35 0.00075 23.9 2.1 17 173-189 58-74 (78)
23 PF01400 Astacin: Astacin (Pep 32.4 1E+02 0.0022 25.4 5.0 46 177-228 18-64 (191)
24 TIGR00853 pts-lac PTS system, 27.9 2E+02 0.0043 20.9 5.4 53 62-124 3-68 (95)
25 PF01990 ATP-synt_F: ATP synth 26.0 88 0.0019 22.6 3.2 69 65-138 1-73 (95)
26 PF00281 Ribosomal_L5: Ribosom 25.8 1.9E+02 0.0042 19.0 4.5 31 163-195 11-41 (56)
27 KOG0180 20S proteasome, regula 24.5 1.2E+02 0.0027 25.2 4.0 37 171-207 154-192 (204)
28 PRK03957 V-type ATP synthase s 24.4 2.9E+02 0.0063 20.3 6.5 56 64-125 2-63 (100)
29 TIGR03260 met_CoM_red_D methyl 24.4 63 0.0014 26.0 2.3 30 163-192 67-98 (150)
30 PLN02331 phosphoribosylglycina 22.3 86 0.0019 26.5 2.8 23 64-86 29-54 (207)
31 PF09291 DUF1968: Domain of un 21.8 80 0.0017 22.9 2.2 19 53-71 4-22 (85)
32 PRK13958 N-(5'-phosphoribosyl) 20.7 46 0.001 28.0 0.9 26 63-88 3-28 (207)
33 PF15585 Imm46: Immunity prote 20.3 3.5E+02 0.0076 21.3 5.6 44 161-204 48-91 (129)
No 1
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=1.1e-56 Score=381.11 Aligned_cols=215 Identities=67% Similarity=1.057 Sum_probs=206.7
Q ss_pred CCcCCHHHHHHHHHHHHHHhhhhccCCCCccEEEEEEEcccCCCCCCcceeeEEcCCCCCCCcEEEEEeCcccHHHHHHc
Q 027063 1 MSKLQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKI 80 (229)
Q Consensus 1 ~~~~~~~~v~~av~~l~~~~k~~~~~~~~e~I~l~i~lk~~~~kk~~~~~~~I~LPh~~~~~~kIcvf~~~~~~~~a~~~ 80 (229)
|++++++++++||++|++|.+ .+.++|+|+|+++|+|++++|++++++|+.|.|||+.+++.+||||++++.+++|+++
T Consensus 1 m~~~~~~~~~~av~~~~~~~~-~~~~~f~esv~~~i~Lk~id~~~~~~ir~~v~LP~~~gk~~~v~V~a~~~~~~~Ak~a 79 (216)
T PTZ00029 1 MSKLSSEALRKAIAEILEGSE-EKKRKFVETVELQIGLKDYDTQKDKRFSGSVKLPNVPKPNLKVCVLGDAVHCDEAKKL 79 (216)
T ss_pred CCcCCHHHHHHHHHHHHhhcc-ccccCCceEEEEEEEcCCCCCCcCcccceeEecCCCCCCCcEEEEECCcHHHHHHHHc
Confidence 888999999999999998743 3678999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCCCCccccCcccHHHHHHHhhccceeEec
Q 027063 81 GLDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKFPTLVTHQESLESKVNETKATVKFQLK 160 (229)
Q Consensus 81 g~~vig~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K~p~~v~~~~~l~~~i~~~~~~~~~~~~ 160 (229)
||+++|.++|++.+++++++|+|+.+||+||||+++||.|||+|||+|||++|+|++++.++|+.+.|++++++++||++
T Consensus 80 Ga~vvg~edL~~~~k~~k~~kkl~~~fD~flA~~~im~~l~riLGp~l~p~~K~P~~v~~~~d~~~~i~~~k~~v~~r~~ 159 (216)
T PTZ00029 80 GLDFMDIEGLKKFNKNKKLVKKLAKKYDAFLASQSLLPQIPRLLGPGLNKAGKFPTLITHNDDIEDKINELKSSVKFQLK 159 (216)
T ss_pred CCCEecHHHHHHhhhhHHHHhcccccCCEEEECHHHHHHHHHHhccccccCCCCCCcccCccCHHHHHHHHHheEEEEEC
Confidence 99999999999999999999999999999999999999999999999999999999987778999999999999999999
Q ss_pred ccceEEEEEecCCCCHHHHHHHHHHHHHHHHHhccCCcccE-EEEeecCCCccccee
Q 027063 161 KVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQNV-PLSEEYHGSFKPHLL 216 (229)
Q Consensus 161 ~~~~i~v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg~~nI-~l~~k~~~S~~~~~~ 216 (229)
+++|++++||+++|+++||+|||.+++++|.+.+|+||.|| ++|+|++.|.+.+||
T Consensus 160 k~~~i~v~VG~~~~~~e~l~eNi~avl~~i~~~~~kg~~~Iksv~lktTmgp~v~v~ 216 (216)
T PTZ00029 160 KVLCLGVAVGNVEMTEEQLRQNIVLSINFLVSLLKKNWQNIKTLHIKSTMGKPQRIY 216 (216)
T ss_pred CCCEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHhccccccEeEEEEECCCCCCEeCC
Confidence 99999999999999999999999999999999999999999 999999999999886
No 2
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=1.4e-53 Score=360.96 Aligned_cols=211 Identities=55% Similarity=0.868 Sum_probs=199.6
Q ss_pred CCcCCHHHHHHHHHHHHHHhhhhccCCCCccEEEEEEEcccCCCCCCcceeeEEcCCCCCCCcEEEEEeCcccHHHHHHc
Q 027063 1 MSKLQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKI 80 (229)
Q Consensus 1 ~~~~~~~~v~~av~~l~~~~k~~~~~~~~e~I~l~i~lk~~~~kk~~~~~~~I~LPh~~~~~~kIcvf~~~~~~~~a~~~ 80 (229)
|++++++++++||+.|+++. +.++|+|||+++|+|||+||++++++|+.|.|||+.++..+||||++++.+++|+++
T Consensus 1 m~k~~~~~i~~Av~~~lk~~---~~~kF~Etvdl~v~Lk~iDp~kd~~irg~v~LPhg~gk~~kV~v~~~~~~~~~Ak~a 77 (214)
T PTZ00225 1 MSKIPPQTLSEAIQAVLKVD---KERKFKESIDLQVNLKNYDPQKDKRFSGSLKLPNVCRPRMTVCLLCDLVHEDIAKKE 77 (214)
T ss_pred CCcCCHHHHHHHHHHHHHhc---ccCCCCceEEEEEeccCcCCCcCcccceeEECCCCCCCCcEEEEECChHHHHHHHHC
Confidence 88999999999999988665 556899999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCCCCccccCcccHHHHHHHhhccceeEec
Q 027063 81 GLDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKFPTLVTHQESLESKVNETKATVKFQLK 160 (229)
Q Consensus 81 g~~vig~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K~p~~v~~~~~l~~~i~~~~~~~~~~~~ 160 (229)
||+++|.++|++.+++++.+|+|+.+||+|||++++||.|||+|||.|+|++|+|++++.++|+.+.|+++++++.||++
T Consensus 78 Gad~v~~e~l~~l~k~~~~~kkl~~~fD~fiA~~~~m~~lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~ 157 (214)
T PTZ00225 78 GVPTMNQEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLK 157 (214)
T ss_pred CCCEECHHHHHHHHhccHHHHHHHhhCCEEEECHHHHHhhhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEec
Confidence 99999999999999999999999999999999999999999999998889999999988778999999999999999999
Q ss_pred ccceEEEEEecCCCCHHHHHHHHHHHHHHHHHhccCCcccE-EEEeecCCCcccc
Q 027063 161 KVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQNV-PLSEEYHGSFKPH 214 (229)
Q Consensus 161 ~~~~i~v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg~~nI-~l~~k~~~S~~~~ 214 (229)
+.++++++||+++|+++||+||+.++++.|.+.+|++|+|| ++++|++=+.+.-
T Consensus 158 k~~~~~~~VGk~~m~~e~i~eNi~a~l~~l~~~~p~k~~nIksv~iktTMGp~~~ 212 (214)
T PTZ00225 158 KVLCLGTCVGHVEMTEEQLRQNVVMAINFLVSLLKKNWQNLKSAYIKSTMGKPQR 212 (214)
T ss_pred CccEEEeEEccCCCCHHHHHHHHHHHHHHHHHhCCcCCceEeEEEEECCCCCCEe
Confidence 99999999999999999999999999999999999999999 8887776655433
No 3
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=100.00 E-value=1.5e-50 Score=343.52 Aligned_cols=211 Identities=28% Similarity=0.430 Sum_probs=197.7
Q ss_pred CCHHHHHHHHHHHHHHhhhhccCCCCccEEEEEEEcccCCCC-CCcceeeEEcCCCCCCCcEEEEEeCcccHHHHHHcCC
Q 027063 4 LQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGL 82 (229)
Q Consensus 4 ~~~~~v~~av~~l~~~~k~~~~~~~~e~I~l~i~lk~~~~kk-~~~~~~~I~LPh~~~~~~kIcvf~~~~~~~~a~~~g~ 82 (229)
+++|++.+||+.+.++. +.++|+|+|+++|+||++++++ ++++||.|.|||+++++.+|||||+++..++|+++||
T Consensus 2 ~~~~~~~eai~~~k~~~---~~~kf~esvel~v~Lk~id~~k~~~~irg~i~LP~~~~k~~~V~vf~~~~~~~~Ak~aGa 78 (215)
T PRK04203 2 MDREKIEEAVKEALEEA---PKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIAKGELALQAKEAGA 78 (215)
T ss_pred CcHHHHHHHHHHHHHhc---ccCCCCceEEEEEEecCCCCCccCceeeEEEECCCCCCCCcEEEEEcChHhHHHHHHcCC
Confidence 58899999988887643 5579999999999999999987 8899999999999999999999999988999999999
Q ss_pred C-eeChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCCCCccccCcccHHHHHHHhhccceeEecc
Q 027063 83 D-YMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKFPTLVTHQESLESKVNETKATVKFQLKK 161 (229)
Q Consensus 83 ~-vig~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K~p~~v~~~~~l~~~i~~~~~~~~~~~~~ 161 (229)
+ ++|.++|.+.+..++.+|+|+.+||+||||++|||.|+++||+.|+|++|+|.+++.+.|+.++|++++++++|+.++
T Consensus 79 ~~v~~~e~L~~i~~~~k~~rkl~~~fD~~lA~~~im~~l~k~LGk~lgprgkmP~p~~~t~di~~~i~~~~~~~~~r~~k 158 (215)
T PRK04203 79 DYVITREELEELGGDKRAAKKLANEYDFFIAEADLMPLIGRYLGPVLGPRGKMPTPLPPNADIKPLVERLKNTVRIRTKD 158 (215)
T ss_pred CEEeCHHHHHHHhcChHHHhhhhhcCCEEEECHHHHHHHHHHHhhhcCcCCCCCCCcCCCCCHHHHHHHHhhceEEEeCC
Confidence 9 778888877777899999999999999999999999999999999999999999986669999999999999999999
Q ss_pred cceEEEEEecCCCCHHHHHHHHHHHHHHHHHhccCCcccE-EEEeecCCCcccceec
Q 027063 162 VLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQNV-PLSEEYHGSFKPHLLR 217 (229)
Q Consensus 162 ~~~i~v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg~~nI-~l~~k~~~S~~~~~~~ 217 (229)
+++++++||+++|+++||+||+.+++++|.+.+|+||+|| ++|++++.|.+.+|+.
T Consensus 159 ~~~i~v~VG~~~m~~e~l~eNi~avl~~i~~~~p~g~~~Iksi~lktTmgp~i~i~~ 215 (215)
T PRK04203 159 QPTFHVRVGTEDMSPEELAENIDAVLNRIESKLEKGRQNIKSVYVKTTMGPAVKVEL 215 (215)
T ss_pred CCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCccccccEEEEEEECCCCCCEEeeC
Confidence 9999999999999999999999999999999999999999 9999999999999873
No 4
>cd00403 Ribosomal_L1 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA. Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity. L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site.
Probab=100.00 E-value=1e-45 Score=312.30 Aligned_cols=203 Identities=37% Similarity=0.542 Sum_probs=188.4
Q ss_pred HHHHHHHHHHhhhhccCCCCccEEEEEEEcccCCCCCCcceeeEEcCCCCCCCcEEEEEeCcccHHHHHHcCCCeeChHH
Q 027063 10 REAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDYMDVEG 89 (229)
Q Consensus 10 ~~av~~l~~~~k~~~~~~~~e~I~l~i~lk~~~~kk~~~~~~~I~LPh~~~~~~kIcvf~~~~~~~~a~~~g~~vig~~~ 89 (229)
.+|+++|.++.. ...+++|+|+|+|+++.++.+++.++++.|.|||+++++.+||||+++++.++|+++|++++|+++
T Consensus 2 ~~Ai~~l~~~~~--~~~~~~~~v~l~i~l~~~~~~~~~~~~~~i~LPh~~~~~~~i~v~~~d~~~~~a~~~~a~vig~~~ 79 (208)
T cd00403 2 EEAIKALKKTSV--KKRKFDETVELQINLKKDDRKKDQRIRGTVILPHGLGKDVKVCVFAKDEQAKEAKAAGADVVGGED 79 (208)
T ss_pred HHHHHHHHHhcc--ccCCCCceEEEEEEeCCCCCccccccceeEECCCCCCCCeEEEEEcChHhHHHHHHcCCCEEcHHH
Confidence 467777766653 355788999999999764435578899999999999999999999999888899999999999999
Q ss_pred HHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCCCCccccC--cccHHHHHHHhhccceeEecccceEEE
Q 027063 90 LKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKFPTLVTH--QESLESKVNETKATVKFQLKKVLCMGV 167 (229)
Q Consensus 90 L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K~p~~v~~--~~~l~~~i~~~~~~~~~~~~~~~~i~v 167 (229)
|+++|++++.+ +|+.+||+||||+++++.+++.||+.|++++|+|++++. .+|+.++|++++++++|+.++++++++
T Consensus 80 L~~~~~~~~~~-~l~~~~D~fla~~~~~~~~~~~lgk~~~~k~k~P~~~~~t~~~~l~~~i~~~~~~~~~~~~~~~~~~v 158 (208)
T cd00403 80 LKKKIKNGEAK-KLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKMPNPKTGTVTEDLAKAIEEAKSSVEFRLDKGGCIHV 158 (208)
T ss_pred HHHHhhcchhh-hhhhcCCEEEECHHHHHHHHHHhccccccCCCCCcCCCCCCcccHHHHHHHHHhCeEEEECCCCEEEE
Confidence 99999999999 999999999999999999999999999999999999975 689999999999999999999999999
Q ss_pred EEecCCCCHHHHHHHHHHHHHHHHHhcc-CCcccE-EEEeecCCCcccce
Q 027063 168 AVGNLSMEEKQIFQNVQMSVNFLVSLLK-KNWQNV-PLSEEYHGSFKPHL 215 (229)
Q Consensus 168 ~VG~~~m~~~ei~eNi~a~l~~l~~~~p-kg~~nI-~l~~k~~~S~~~~~ 215 (229)
+||+++|+++||+|||.++++.+.+++| +||.|| +++++++.|.++||
T Consensus 159 ~VG~~~m~~~~l~eNi~~vi~~i~~~~~~~~~~~i~~v~lktt~~~~lpI 208 (208)
T cd00403 159 PVGKVSMSPEQLVENIEAVINALVKKLPSKKGQNIKSIYLKTTMGPSLPI 208 (208)
T ss_pred EEeCCCCCHHHHHHHHHHHHHHHHHhCCcccCeEEEEEEEECCCCCCeEC
Confidence 9999999999999999999999999999 999999 99999999999986
No 5
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=100.00 E-value=5e-43 Score=299.11 Aligned_cols=193 Identities=22% Similarity=0.333 Sum_probs=172.5
Q ss_pred HHHHHHHhhhhccCCCCccEEEEEEEcccCCCC-CCcceeeEEcCCCCCCCcEEEEEeCcccHHHHHHcCCCeeChHHHH
Q 027063 13 VSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDYMDVEGLK 91 (229)
Q Consensus 13 v~~l~~~~k~~~~~~~~e~I~l~i~lk~~~~kk-~~~~~~~I~LPh~~~~~~kIcvf~~~~~~~~a~~~g~~vig~~~L~ 91 (229)
+.++++++++.+.++|+|+|+++|+| ++++++ ++++||.|.|||+++++.+|||||+++.+++|+++||+++|++||+
T Consensus 22 l~eAi~~~k~~~~~kF~esvel~i~L-~id~kk~~~~irg~v~LP~~~gk~~kV~Vfa~~~~~~eAk~aGad~vg~edLi 100 (229)
T CHL00129 22 PEEAINLLKETATAKFIETAEAHISL-NIDPKYADQQLRTTVTLPKGTGKTIRIAVLTNEEKITEAKNAGADIVGSDDLI 100 (229)
T ss_pred HHHHHHHHHHhCcCCCCccEEEEEEE-CCCCCCCCCceeeEEECCCCCCCCcEEEEECChHhHHHHHHcCCCEeCHHHHH
Confidence 45566666666778999999999999 899987 8999999999999999999999999999999999999999999999
Q ss_pred HhhhCHHHHHHHhhcccEEEEehhhhhh---hhhhhcC-CCCCCCCCCccccCcccHHHHHHHhhc-cceeEecccceEE
Q 027063 92 KLNKNKKLVKKLAKKYHAFLASESVIKQ---IPRLLGP-GLNKAGKFPTLVTHQESLESKVNETKA-TVKFQLKKVLCMG 166 (229)
Q Consensus 92 ~~~~~~e~~rkL~~~yd~flad~~i~~~---l~~~LG~-~~~p~~K~p~~v~~~~~l~~~i~~~~~-~~~~~~~~~~~i~ 166 (229)
+.++++.. +||+|||++++||. |+++||| |+||+.|.||++ +|+.+.|+++++ ++.||.++.++++
T Consensus 101 ~~ik~~~~------~fd~~iAt~d~m~~l~kLgriLGprGlMP~pk~gTvt---~di~~~V~~~k~G~v~~r~dk~g~i~ 171 (229)
T CHL00129 101 EEITKGNL------DFDLLIATPDMMPKLAKLGRVLGPRGLMPSPKSGTVT---TDLASAINEFKKGKLEYRADKTGIVH 171 (229)
T ss_pred HHHHcCcc------cCCEEEECHHHHHHHHHhcCcccccCCCCCCCCCCcc---ccHHHHHHHHhcCcEEEEecCCcEEE
Confidence 98877664 89999999999986 5588888 899999999988 699999999997 7999999999999
Q ss_pred EEEecCCCCHHHHHHHHHHHHHHHHHhccCCcc--cE-EEEeecCCCcccce
Q 027063 167 VAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQ--NV-PLSEEYHGSFKPHL 215 (229)
Q Consensus 167 v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg~~--nI-~l~~k~~~S~~~~~ 215 (229)
++||+++|+++||.||+.+++++|.++.|.+|+ +| +++++++-+.+..|
T Consensus 172 ~~VG~~~m~~~~l~eNi~a~l~~i~~~~p~~~kg~~ik~v~issTMGp~v~i 223 (229)
T CHL00129 172 VLFGKSNFTEEDLLENLQAIYESIEQNRPSGVKGKYWKSFYICSTMGPSIQI 223 (229)
T ss_pred EEEeCCCCCHHHHHHHHHHHHHHHHHhCcccccCceEEEEEEECCCCCCEEe
Confidence 999999999999999999999999999999988 77 66666555554443
No 6
>PF00687 Ribosomal_L1: Ribosomal protein L1p/L10e family; InterPro: IPR002143 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L1 is the largest protein from the large ribosomal subunit. The L1 protein contains two domains: 2-layer alpha/beta domain and a 3-layer alpha/beta domain (interrupts the first domain). In Escherichia coli, L1 is known to bind to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L1. Algal and plant chloroplast L1. Cyanelle L1. Archaebacterial L1. Vertebrate L10A. Yeast SSM1. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3QOY_A 3BBO_D 1VSA_A 1VSP_A 2NOQ_G 3IZS_A 1S1I_A 3O5H_A 3O58_A 2WRL_C ....
Probab=100.00 E-value=6.9e-43 Score=297.09 Aligned_cols=200 Identities=35% Similarity=0.554 Sum_probs=179.3
Q ss_pred HHHHHHHhhhh----ccCCCCccEEEEEEEcccCCCCCCcc-eeeEEcCCCCC-CCcEEEEEeCcccHH---------HH
Q 027063 13 VSSIVQYSKET----KKRNFTETIELQIGLKNYDPQKDKRF-SGSVKLPHIPR-PKMKVCMLGDAQHVE---------EA 77 (229)
Q Consensus 13 v~~l~~~~k~~----~~~~~~e~I~l~i~lk~~~~kk~~~~-~~~I~LPh~~~-~~~kIcvf~~~~~~~---------~a 77 (229)
|+||++|+++. ...+++++|+|+|+++++..+++.++ ++.|.||||++ ++.+||||+++++.+ ++
T Consensus 1 ~~aL~k~~~~~~~~~~~~~~~~~v~l~i~~~~~~~~~~~~~~~~~i~LPh~~~~~~~~vcli~~d~~~~~~~~~~~~~~~ 80 (220)
T PF00687_consen 1 IKALKKYIKKKKEENEDDNFDESVYLQITLKKIPKKKDKSFKPGRIPLPHPLYIKNSKVCLIVKDPQKKAKEKEKLEEKA 80 (220)
T ss_dssp HTCHHHHHHHHHHCCCCSSSSTEEEEEEEESSSTTSSCTST-EEEEEBSTSSS-SSSBEEEEESCHHHHHH-------HH
T ss_pred ChHHHHHHHHHHhhcccCCCCcEEEEEEEeCcCCCccccccccceeeecCCCCCCccEEEEEecCcchhhhhhhhhhhhh
Confidence 56788888774 34567899999999986444445667 99999999998 899999999775533 34
Q ss_pred HHcCCCeeChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCC-CCCCCCCccccC-cccHHHHHHHhhccc
Q 027063 78 EKIGLDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGL-NKAGKFPTLVTH-QESLESKVNETKATV 155 (229)
Q Consensus 78 ~~~g~~vig~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~-~p~~K~p~~v~~-~~~l~~~i~~~~~~~ 155 (229)
.+.|++++|+++|+++|++++.+|+|+.+||+||||++|++.|++.||+.| .|++|+|++++. ++++.++|+++++++
T Consensus 81 ~~~~~~vi~~~~L~~~~~~~~~~r~l~~~~d~flad~~i~~~l~~~Lgk~~~~~k~k~P~~v~~~~~~l~~~i~~~~~~~ 160 (220)
T PF00687_consen 81 VEAGAKVIGGEELKKKYKTIEAKRKLAKSYDFFLADPRIMPKLPKLLGKIFYGKKGKMPIPVTLSKEDLKEQIEKALNST 160 (220)
T ss_dssp HHTTCSEEECHHHHHHHCHHHHCHHHHHCSSEEEEEGGGHHHHHHHTHHHH-CCTTTSCEEBSSHTSCHHHHHHHHHTEE
T ss_pred hhcccceecHHHHHHHHHHHHHHHHHHhhcCEEEECHHHHHHHHHhhhhheecccCCcceEEeccchhHHHHHHHHHCCE
Confidence 678999999999999999999999999999999999999999999999977 678899999986 479999999999999
Q ss_pred eeEec-ccceEEEEEecCCCCHHHHHHHHHHHHHHHHHh-ccCCcccE-EEEeecCCCcc
Q 027063 156 KFQLK-KVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSL-LKKNWQNV-PLSEEYHGSFK 212 (229)
Q Consensus 156 ~~~~~-~~~~i~v~VG~~~m~~~ei~eNi~a~l~~l~~~-~pkg~~nI-~l~~k~~~S~~ 212 (229)
.|+.. ++++++++||+++|+++||+|||.++++.+.++ +|+||.|| +++++++.|.+
T Consensus 161 ~~~~~~~~~~~~v~VG~~~~~~~~i~eNi~~~i~~i~~~~~~~g~~~I~~i~ikst~s~~ 220 (220)
T PF00687_consen 161 KFRLSGKGGCISVKVGHLSMTDEQIVENIKAVIKAIVSKPLPKGWKNIKSIYIKSTMSPS 220 (220)
T ss_dssp EEEETBTSSEEEEEEEETTSCHHHHHHHHHHHHHHHHHTTTSSSSGSEEEEEEEESSSEE
T ss_pred EEEeeccCCeeecCccCCCCCHHHHHHHHHHHHHHHHHhhhccCcceEEEEEEECCCCCC
Confidence 99988 999999999999999999999999999999999 99999999 99999999864
No 7
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-42 Score=290.39 Aligned_cols=196 Identities=31% Similarity=0.477 Sum_probs=174.4
Q ss_pred HHHHHHHHHhhhhccCCCCccEEEEEEEcccCCCC-CCcceeeEEcCCCCCCCcEEEEEeCcccHHHHHHcCCCeeChHH
Q 027063 11 EAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDYMDVEG 89 (229)
Q Consensus 11 ~av~~l~~~~k~~~~~~~~e~I~l~i~lk~~~~kk-~~~~~~~I~LPh~~~~~~kIcvf~~~~~~~~a~~~g~~vig~~~ 89 (229)
..+.++++.+|+.+.++|+|||+++++|+ +||++ ++++||.+.|||..++..+||||++++.+++|+++||+++|.+|
T Consensus 21 ~~i~eai~~~ke~~~~kF~etVevav~L~-vD~~k~dq~vrg~VvLP~g~gk~vrV~Vfa~g~~~~~A~~AGad~Vg~ed 99 (228)
T COG0081 21 YSLEEAVKLLKETSKRKFDETVEVAVNLK-VDPRKPDQRVRGSVVLPNGTGKTVRVAVFADGEKAEEAKAAGADYVGGED 99 (228)
T ss_pred hhHHHHHHHHHhccccCcceEEEEEEEcc-cCCCCcccccceeEECCCCCCCccEEEEEcChHhHHHHHHcCCCEecHHH
Confidence 45666777777777889999999999995 99976 99999999999999999999999999999999999999999999
Q ss_pred HHHhhhCHHHHHHHhhcccEEEEehhhhhh---hhhhhcC-CCCCCCCCCccccCcccHHHHHHHhhc-cceeEecccce
Q 027063 90 LKKLNKNKKLVKKLAKKYHAFLASESVIKQ---IPRLLGP-GLNKAGKFPTLVTHQESLESKVNETKA-TVKFQLKKVLC 164 (229)
Q Consensus 90 L~~~~~~~e~~rkL~~~yd~flad~~i~~~---l~~~LG~-~~~p~~K~p~~v~~~~~l~~~i~~~~~-~~~~~~~~~~~ 164 (229)
|.+.+++++ ...||+|+|+|++||. |+++||| |+||+.|.||+. .|+.+.|+++++ ++.||+++.++
T Consensus 100 l~e~ik~~r-----~~~fD~~IAtpdmM~~v~~LG~vLGPRGlMP~Pk~gTvt---~Dv~~av~~~K~g~v~~R~dk~g~ 171 (228)
T COG0081 100 LIELIKNGR-----AKDFDVFIATPDMMPLVGKLGKVLGPRGLMPNPKTGTVT---DDVAKAVEELKKGTVEFRADKAGV 171 (228)
T ss_pred HHHHHhCcc-----hhcCCEEEECchHHHHHHHHhhhcCCCCCCCCCCCCCCC---cCHHHHHHHHhcCcEEEEECCCce
Confidence 999999985 2389999999999995 6788888 888888888887 699999999999 99999999999
Q ss_pred EEEEEecCCCCHHHHHHHHHHHHHHHHHhccCC--cccE-EEEeecCCCcccce
Q 027063 165 MGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKN--WQNV-PLSEEYHGSFKPHL 215 (229)
Q Consensus 165 i~v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg--~~nI-~l~~k~~~S~~~~~ 215 (229)
+|+.||+.+|++++|.||+.++++.|.+.+|.+ |++| +++++++-+.+..|
T Consensus 172 ih~~iGk~sf~~e~L~eNi~a~l~~i~~~~p~~~kg~~ik~v~vstTMGP~v~v 225 (228)
T COG0081 172 IHVPIGKVSFDDEKLAENIEALLNAIVKAKPAGAKGQYIKSVYVSTTMGPGVKV 225 (228)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHhCcCCcccceEeEEEEecCCCCCEEe
Confidence 999999999999999999999999999999987 7777 55555544444433
No 8
>TIGR01169 rplA_bact ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model.
Probab=100.00 E-value=2.5e-42 Score=294.93 Aligned_cols=190 Identities=24% Similarity=0.403 Sum_probs=170.8
Q ss_pred HHHHHHHhhhhccCCCCccEEEEEEEcccCCCC-CCcceeeEEcCCCCCCCcEEEEEeCcccHHHHHHcCCCeeChHHHH
Q 027063 13 VSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDYMDVEGLK 91 (229)
Q Consensus 13 v~~l~~~~k~~~~~~~~e~I~l~i~lk~~~~kk-~~~~~~~I~LPh~~~~~~kIcvf~~~~~~~~a~~~g~~vig~~~L~ 91 (229)
+.++++++++.+.++|+|+|+++|+| ++++++ +++++|.|.|||+++++.+|||||+++.+++|+++||+++|++||+
T Consensus 21 l~eAi~~lk~~~~~~f~esvel~i~L-~id~kK~~~~irg~v~LP~~~gk~~kV~Vfa~~~~~~~Ak~aGa~~vg~~eLi 99 (227)
T TIGR01169 21 LDEAIALLKETATAKFDETVEVAIRL-GIDPRKSDQQVRGTVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADYVGSDDLI 99 (227)
T ss_pred HHHHHHHHHhhccCCCCCCEEEEEEE-CcCCCcCCCeeeEEEECCCCCCCCcEEEEEcCchhHHHHHHcCCCEeCHHHHH
Confidence 45556666666778999999999999 899988 8999999999999999999999999988999999999999999999
Q ss_pred HhhhCHHHHHHHhhcccEEEEehhhhhh---hhhhhcC-CCCCCCCCCccccCcccHHHHHHHhhc-cceeEecccceEE
Q 027063 92 KLNKNKKLVKKLAKKYHAFLASESVIKQ---IPRLLGP-GLNKAGKFPTLVTHQESLESKVNETKA-TVKFQLKKVLCMG 166 (229)
Q Consensus 92 ~~~~~~e~~rkL~~~yd~flad~~i~~~---l~~~LG~-~~~p~~K~p~~v~~~~~l~~~i~~~~~-~~~~~~~~~~~i~ 166 (229)
+.++++.. +||+|||++++||. |+++||| ++||+.|.||++ +|+.+.|+++++ ++.||.++.++++
T Consensus 100 ~~ik~~~~------~fd~~iat~~~m~~l~~Lg~iLGPrGlMP~~k~gtv~---~di~~~I~~~k~g~v~~r~~k~g~i~ 170 (227)
T TIGR01169 100 EKIKKGWL------DFDVVIATPDMMRVVGKLGRILGPRGLMPNPKTGTVT---ADVAKAVKNAKKGQVEFRADKAGNIH 170 (227)
T ss_pred HHHHcCCc------cCCEEEECHHHHHHHHHhccccccccCCCCCCCCCcc---ccHHHHHHHHHcCcEEEEeCCCCEEE
Confidence 98877654 89999999999986 5789999 999999999998 699999999997 7999999999999
Q ss_pred EEEecCCCCHHHHHHHHHHHHHHHHHhccCCc--ccE-EEEeecCCCcc
Q 027063 167 VAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNW--QNV-PLSEEYHGSFK 212 (229)
Q Consensus 167 v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg~--~nI-~l~~k~~~S~~ 212 (229)
++||+++|+++||.|||.++++++.++.|.+| .+| +++++++-+.+
T Consensus 171 ~~VG~~~m~~e~i~eNi~a~l~~i~~~~p~~~kg~~Ik~v~lssTmGp~ 219 (227)
T TIGR01169 171 ASIGKVSFDSEKLKENLEALLDAIKKAKPSGAKGQYIKNIALSSTMGPG 219 (227)
T ss_pred EEEecCCCCHHHHHHHHHHHHHHHHHhCccccCCCEEEEEEEECCCCCC
Confidence 99999999999999999999999999999998 677 56655544444
No 9
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=100.00 E-value=2.5e-42 Score=295.45 Aligned_cols=192 Identities=24% Similarity=0.387 Sum_probs=170.6
Q ss_pred HHHHHHHhhhhccCCCCccEEEEEEEcccCCCC-CCcceeeEEcCCCCCCCcEEEEEeCcccHHHHHHcCCCeeChHHHH
Q 027063 13 VSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDYMDVEGLK 91 (229)
Q Consensus 13 v~~l~~~~k~~~~~~~~e~I~l~i~lk~~~~kk-~~~~~~~I~LPh~~~~~~kIcvf~~~~~~~~a~~~g~~vig~~~L~ 91 (229)
+.++++++++.+.++|+|+|+++|+| ++++++ +++++|.|.|||+++++.+|||||+++.+++|+++||+++|++||+
T Consensus 22 l~eAi~~lk~~~~~kF~esvel~v~L-~id~kK~~~~irg~v~LP~~~gk~~kI~Vfa~~~~~~~Ak~aGa~~vg~eeLi 100 (230)
T PRK05424 22 LEEAIALVKETATAKFDETVDVAVNL-GVDPRKADQQVRGAVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADIVGGEDLI 100 (230)
T ss_pred HHHHHHHHHhhccCCCCCcEEEEEEe-CCCCCCCCCeeeEEEECCCCCCCCcEEEEECChHhHHHHHHcCCCEeCHHHHH
Confidence 34445555555678999999999999 899988 8999999999999999999999999888999999999999999999
Q ss_pred HhhhCHHHHHHHhhcccEEEEehhhhhh---hhhhhcC-CCCCCCCCCccccCcccHHHHHHHhhc-cceeEecccceEE
Q 027063 92 KLNKNKKLVKKLAKKYHAFLASESVIKQ---IPRLLGP-GLNKAGKFPTLVTHQESLESKVNETKA-TVKFQLKKVLCMG 166 (229)
Q Consensus 92 ~~~~~~e~~rkL~~~yd~flad~~i~~~---l~~~LG~-~~~p~~K~p~~v~~~~~l~~~i~~~~~-~~~~~~~~~~~i~ 166 (229)
+.++++.. +||+|||++++||. |+++||| |+||+.|.||++ +|+.+.|+++++ ++.||.++.++++
T Consensus 101 ~~ik~~~~------~fd~~iat~~~m~~l~~Lg~iLGPrGlMP~pk~gTv~---~di~~~I~~~k~g~v~~r~~k~g~i~ 171 (230)
T PRK05424 101 EKIKGGWL------DFDVVIATPDMMGKVGKLGRILGPRGLMPNPKTGTVT---MDVAKAVKEAKAGKVEFRVDKAGIIH 171 (230)
T ss_pred HHHhcCCC------cCCEEEECHHHHHHHHHhccccccccCCCCCCCCCcc---hhHHHHHHHHhcCcEEEEecCCCEEE
Confidence 99886654 89999999999987 6788888 889999999988 699999999997 7999999999999
Q ss_pred EEEecCCCCHHHHHHHHHHHHHHHHHhccCCc--ccE-EEEeecCCCcccc
Q 027063 167 VAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNW--QNV-PLSEEYHGSFKPH 214 (229)
Q Consensus 167 v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg~--~nI-~l~~k~~~S~~~~ 214 (229)
++||+++|+++||.|||.++++++.++.|.+| .+| +++++++-+.+..
T Consensus 172 ~~IG~~~m~~e~i~eNi~a~l~~i~~~~p~~~kg~~Ik~v~lssTmGp~~~ 222 (230)
T PRK05424 172 APIGKVSFDAEKLKENLKALIDAIKKAKPATAKGTYIKSVSLSSTMGPGVK 222 (230)
T ss_pred EEEeCCCCCHHHHHHHHHHHHHHHHHhCccccCCCEEEEEEEECCCCCCEE
Confidence 99999999999999999999999999999999 777 6666665555433
No 10
>KOG1570 consensus 60S ribosomal protein L10A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.4e-37 Score=251.79 Aligned_cols=212 Identities=67% Similarity=1.007 Sum_probs=204.3
Q ss_pred CCcCCHHHHHHHHHHHHHHhhhhccCCCCccEEEEEEEcccCCCCCCcceeeEEcCCCCCCCcEEEEEeCcccHHHHHHc
Q 027063 1 MSKLQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKI 80 (229)
Q Consensus 1 ~~~~~~~~v~~av~~l~~~~k~~~~~~~~e~I~l~i~lk~~~~kk~~~~~~~I~LPh~~~~~~kIcvf~~~~~~~~a~~~ 80 (229)
|+++.++++..||.+++.+.+..+.++|.+||++|++|+|++|.++.++.+.+.|||.+++..++|+|.|..+.++|.+.
T Consensus 2 ~sk~~~~~l~~~v~~i~~~~~~~k~~~~~~tielQi~Lk~ydp~Kdkr~s~~~~l~~~~~p~~k~cv~gd~~h~~~ak~~ 81 (218)
T KOG1570|consen 2 SSKVEEEALREAVAEILLRSKEFKNRNFVETIELQINLKNYDPQKDKRFSGSVKLPHAPRPKMKVCVIGDQQHCDEAKAI 81 (218)
T ss_pred CcchhHHHHHHHHHHHHhccccccCccceeeeeeeecccccChhHhCcccceEecCCCCCccceeeeechHHHHHHhhcC
Confidence 57789999999999999999888889999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCCCCccccCcccHHHHHHHhhccceeEec
Q 027063 81 GLDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKFPTLVTHQESLESKVNETKATVKFQLK 160 (229)
Q Consensus 81 g~~vig~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K~p~~v~~~~~l~~~i~~~~~~~~~~~~ 160 (229)
|.+.+..++|++.-++.+.++++++.||.|||..+++.+|||+|||++-..+|.|+++.+++++.+.+++.+++..|+.+
T Consensus 82 ~~p~m~~d~lkklnk~Kklvkklakky~~flase~~ikQlpr~lgp~l~kaGkfps~l~~~d~l~akv~evk~t~k~q~k 161 (218)
T KOG1570|consen 82 DLPAMDIDALKKLNKNKKLVKKLAKKYDAFLASESLIKQLPRILGPGLSKAGKFPSLLVHGDSLYAKVEEVKSTIKFQMK 161 (218)
T ss_pred CCCCcCHHHHhcCcccchHHHHHHHHhhhHHhhHHHHHHhhhhhcccccccccCCccccchHHHHHHHHHHHhhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999889999999999999999999
Q ss_pred ccceEEEEEecCCCCHHHHHHHHHHHHHHHHHhccCCcccE-EEEeecCCCcc
Q 027063 161 KVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQNV-PLSEEYHGSFK 212 (229)
Q Consensus 161 ~~~~i~v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg~~nI-~l~~k~~~S~~ 212 (229)
+--|++|.|||+.|+++|+++||.-.++++++.+.++|+|+ ++++|++-+..
T Consensus 162 kvKOGavaVGhv~M~d~el~~nI~l~vnFlVSlLKknwQNvral~iKst~g~p 214 (218)
T KOG1570|consen 162 KVLCLAVAVGHVGMTDEELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKP 214 (218)
T ss_pred hhhheeeeecCCCCCHHHHHHhhhhhhhhHHHHHhhcccchhheeeccCCCCc
Confidence 99999999999999999999999999999999999999999 99999877654
No 11
>KOG1685 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2e-36 Score=267.61 Aligned_cols=219 Identities=21% Similarity=0.301 Sum_probs=178.7
Q ss_pred CcCCHHHHHHHHHHHHHHhhhhc---------cCCCCccEEEEEEEcccCCCCCCcceeeEEcCCCC----C--CCcEEE
Q 027063 2 SKLQSDALREAVSSIVQYSKETK---------KRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIP----R--PKMKVC 66 (229)
Q Consensus 2 ~~~~~~~v~~av~~l~~~~k~~~---------~~~~~e~I~l~i~lk~~~~kk~~~~~~~I~LPh~~----~--~~~kIc 66 (229)
.+++...++.|++++.++.-... ...+...++++.++ +......+-.|++||++ - .+.+||
T Consensus 17 ~~v~~~~~e~~~k~~~~~~~~~~k~~~~~~~~~~k~~~~~~~~k~~----~~~~~~n~~~IP~k~~~~~~~~~~~~~~vc 92 (343)
T KOG1685|consen 17 ESVSPKNVESAVKALDKEREKKSKAENPQLLEALKNVYKVVLQKNT----PQKVGTNKLKIPLKHLLKKLLLKHDDTDVC 92 (343)
T ss_pred cccCchhhhHHHhhhhhhhHHHHHhhhhhhhhhhhhhHHHHHHHhc----ccccccccccccCcchhcccccCCCCCceE
Confidence 34566666667766665532221 11233445555554 22222233356666664 2 478999
Q ss_pred EEeCccc--------H-HHHHHcCCC----eeChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCC
Q 027063 67 MLGDAQH--------V-EEAEKIGLD----YMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGK 133 (229)
Q Consensus 67 vf~~~~~--------~-~~a~~~g~~----vig~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K 133 (229)
||++|.+ + +...++|++ ||++.+|+..|+.||++|+|+++||+||||+||+|+||++||+.|+..+|
T Consensus 93 LIvkD~~~~~~t~~~~~d~l~~~gi~~itkVI~~~~LK~~yksyeaKr~L~~sfDlflaD~RV~~~LP~llGK~f~q~kk 172 (343)
T KOG1685|consen 93 LIVKDLQQSYLTEEDAEDLLESEGIKSITKVISLSKLKRDYKSYEAKRKLLSSFDLFLADDRVIPLLPKLLGKEFYQKKK 172 (343)
T ss_pred EEecCchhccccHHHHHHHHHHcCCccceeeeehHHHHHHHHHHHHHHHHHhhccEEEEcchhHhHHHHHhhhhhccccc
Confidence 9997632 1 455788987 89999999999999999999999999999999999999999999999999
Q ss_pred CCccccC-ccc--HHHHHHHhhccceeEecccceEEEEEecCCCCHHHHHHHHHHHHHHHHHhccCCcccE-EEEeecCC
Q 027063 134 FPTLVTH-QES--LESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQNV-PLSEEYHG 209 (229)
Q Consensus 134 ~p~~v~~-~~~--l~~~i~~~~~~~~~~~~~~~~i~v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg~~nI-~l~~k~~~ 209 (229)
.|++++. .++ |.++|++++++++|++..|.|+.++|||++|+.+||.|||.++++.+...+|+||.|| ++|+|+..
T Consensus 173 ~Pv~i~l~k~~~~l~~qi~~a~~~t~~~~~~g~~~~i~vg~l~~~~~~l~ENv~~vlk~l~e~~P~~~~~Irsl~lKt~~ 252 (343)
T KOG1685|consen 173 VPVSIRLSKKNELLKQQIENACGSTYFRLRKGTSSAIKVGHLGNTSEELAENVVAVLKGLSEILPGGWKNIRSLHLKTSR 252 (343)
T ss_pred CceEEEecccchHHHHHHHHHhhhheeeccCCceeEEEeccccccHHHHHHHHHHHHHHHHHHccchHhHhHHHhhhccC
Confidence 9999985 344 9999999999999999999999999999999999999999999999999999999999 99999999
Q ss_pred Ccccceecccccccc
Q 027063 210 SFKPHLLRNSALCWS 224 (229)
Q Consensus 210 S~~~~~~~~~~~~~~ 224 (229)
|.+||+|.++.+.++
T Consensus 253 s~aLPly~s~~~~~~ 267 (343)
T KOG1685|consen 253 SPALPLYVSVISLKE 267 (343)
T ss_pred Ccccceeecccchhh
Confidence 999999999988765
No 12
>KOG1569 consensus 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=8e-28 Score=207.94 Aligned_cols=190 Identities=23% Similarity=0.301 Sum_probs=156.5
Q ss_pred HHHHHHHHhhhhccC----CCCccEEEEEEEcccCCCC----CCcceeeEEcCCCCCC--CcEEEEEeCc-ccHHHHHHc
Q 027063 12 AVSSIVQYSKETKKR----NFTETIELQIGLKNYDPQK----DKRFSGSVKLPHIPRP--KMKVCMLGDA-QHVEEAEKI 80 (229)
Q Consensus 12 av~~l~~~~k~~~~~----~~~e~I~l~i~lk~~~~kk----~~~~~~~I~LPh~~~~--~~kIcvf~~~-~~~~~a~~~ 80 (229)
+|.++++..|+.... ...+++.+.+.+ +|...+ ..++++.+.+|||++. ..+|+||+++ ...++|+++
T Consensus 91 ~vq~a~~~~ke~~~~sa~~~pk~~~~l~i~l-~~~a~~~~k~~~~~~~~v~vP~Pf~~ge~r~IavFtn~~~kveeArEa 169 (323)
T KOG1569|consen 91 EVQKAVHLHKELQILSAYNVPKQPVNLRIEL-NMLAEKETKGVAPLQGSVTVPHPFAHGEIRKIAVFTNDASKVEEAREA 169 (323)
T ss_pred hHHHHHHHHHHhccchhhhCCCCceeeeEEe-eeeeeeeccccCCCceeEeccccCCCCceEEEEEecCChHHHHHHHhc
Confidence 466777777776533 235888888888 665532 5567889999999954 6789999977 677899999
Q ss_pred CCCeeChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhh---hhhhhcCCCCCCCCCCccccCcccHHHHHHHhhcc--c
Q 027063 81 GLDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQ---IPRLLGPGLNKAGKFPTLVTHQESLESKVNETKAT--V 155 (229)
Q Consensus 81 g~~vig~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~---l~~~LG~~~~p~~K~p~~v~~~~~l~~~i~~~~~~--~ 155 (229)
||.++|+.+|+++|+++++ .. +||+++|+|+|||. |.++||+. ||+.|.||+. +||+++|++++++ +
T Consensus 170 GA~l~GG~dLIkkI~~Gei---~~-Dyd~~vA~Pdim~~l~~Lr~iL~~r-~Pn~k~gtvg---~nipemieeFk~G~~i 241 (323)
T KOG1569|consen 170 GAALAGGTDLIKKIKSGEI---VA-DYDFYVAHPDIMPELNRLRKILGPR-FPNPKRGTVG---RNIPEMIEEFKNGHEI 241 (323)
T ss_pred cccccccHHHHHHhhcCeE---EE-eeceeeecchHHHHHHHHHHHhccc-CCCcccCccc---cchHHHHHHhhCCccc
Confidence 9999999999999999997 23 48899999999985 66888886 9999999998 7999999999998 8
Q ss_pred eeEecccceEEEEEecCCCCHHHHHHHHHHHHHHHHHhccCCcccE--EEEeecCCC
Q 027063 156 KFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQNV--PLSEEYHGS 210 (229)
Q Consensus 156 ~~~~~~~~~i~v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg~~nI--~l~~k~~~S 210 (229)
.|+..+.+.++++||+++|+.+||.+||.+++.+++.+.|+...++ +.++.++.|
T Consensus 242 ~~d~~~~~~~~~~vGkl~mt~e~i~~Ni~a~i~av~t~rp~~~G~fv~ra~L~Ss~g 298 (323)
T KOG1569|consen 242 KFDEERENILQIKVGKLDMTSEQILANIQAVIAAVCTHRPKALGPFVVRALLRSSPG 298 (323)
T ss_pred ccccccCceeeeeeeeecCCHHHHHHHHHHHHHHHHhcCCcccCceeeeeEeecCCC
Confidence 8887777888999999999999999999999999999998765554 444444333
No 13
>TIGR01170 rplA_mito ribosomal protein L1, mitochondrial. This model represents the mitochondrial homolog of bacterial ribosomal protein L1. Unlike chloroplast L1, this form was not sufficiently similar to bacterial forms to include in a single bacterial/organellar L1.
Probab=99.95 E-value=1.5e-27 Score=189.77 Aligned_cols=131 Identities=27% Similarity=0.393 Sum_probs=115.7
Q ss_pred HHHHHHHhhhhccC--CCCccEEEEEEEcccCCCCCCcceeeEEcCCCCCCCcEEEEEeCccc-HHHHHHcCCCeeChHH
Q 027063 13 VSSIVQYSKETKKR--NFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQH-VEEAEKIGLDYMDVEG 89 (229)
Q Consensus 13 v~~l~~~~k~~~~~--~~~e~I~l~i~lk~~~~kk~~~~~~~I~LPh~~~~~~kIcvf~~~~~-~~~a~~~g~~vig~~~ 89 (229)
+.++++++|+.+.. +|+|+|+++|+| ++++++ .++||.|.|||+++++.+||||+++++ .++|+++||+++|++|
T Consensus 3 i~eA~~~lk~~~~~~~~~~etvel~i~L-~~~~~~-~~irg~v~LP~~~~k~~kV~Vf~~~~~~~~~Ak~aGa~~vg~ed 80 (141)
T TIGR01170 3 VIKAFVYLKTKSISMYVPKQSVNLDIGL-LMELGK-ESVQGMFSFPHPFGKEPKIAVFTKGASEVEEAREAGADYVGGDD 80 (141)
T ss_pred HHHHHHHHHHhcccCCCCCceEEEEEEE-CCCCCC-CCceEEEECCCCCCCCCEEEEECCChHHHHHHHHcCCCEeCHHH
Confidence 45677888887766 899999999999 676654 349999999999999999999998877 5789999999999999
Q ss_pred HHHhhhCHHHHHHHhhc-ccEEEEehhhhhh---hhhhhcC-CCCCCCCCCccccCcccHHHHHHHhhcc
Q 027063 90 LKKLNKNKKLVKKLAKK-YHAFLASESVIKQ---IPRLLGP-GLNKAGKFPTLVTHQESLESKVNETKAT 154 (229)
Q Consensus 90 L~~~~~~~e~~rkL~~~-yd~flad~~i~~~---l~~~LG~-~~~p~~K~p~~v~~~~~l~~~i~~~~~~ 154 (229)
|++++++++. . ||+|||++++||. |+++||| ++||+.|.||++ +|+.++|++++++
T Consensus 81 Li~~i~~g~~------~~fd~~iA~~~~m~~l~~Lg~iLGprGlMP~~k~gTv~---~di~~~I~~~k~G 141 (141)
T TIGR01170 81 LIKKIEDGEI------KPFDYLIAHPDIVPELAQLRRLLGPKGLMPSPKRGTVG---DNLLSMIETFKKG 141 (141)
T ss_pred HHHHHhcCCc------ccccEEEECHHHHHHHHHhhcccccCcCCCCCCCCCcc---cCHHHHHHHHhCc
Confidence 9999998886 5 9999999999985 7799999 999999999998 6999999998763
No 14
>PF13003 MRL1: Ribosomal protein L1; InterPro: IPR024663 This entry represents a ribosomal protein L1 domain found mainly in chordates.
Probab=97.15 E-value=0.00088 Score=52.43 Aligned_cols=55 Identities=22% Similarity=0.282 Sum_probs=44.8
Q ss_pred HHHHHHHhhhhccCCCC---ccEEEEEEEcccCCCC---CCcceeeEEcCCCCC-CCcEEEEE
Q 027063 13 VSSIVQYSKETKKRNFT---ETIELQIGLKNYDPQK---DKRFSGSVKLPHIPR-PKMKVCML 68 (229)
Q Consensus 13 v~~l~~~~k~~~~~~~~---e~I~l~i~lk~~~~kk---~~~~~~~I~LPh~~~-~~~kIcvf 68 (229)
|+.++.++|+.+..+|. |.|++.++| +|...| ..|+...|.||||+- +-.+|+||
T Consensus 72 ve~Ai~mLKkfQ~lDfT~pkQ~VYldL~L-dm~l~KKkkVePF~s~i~lPypF~~eiNKv~VF 133 (133)
T PF13003_consen 72 VEKAIDMLKKFQILDFTSPKQPVYLDLTL-DMKLEKKKKVEPFASVILLPYPFTSEINKVLVF 133 (133)
T ss_pred HHHHHHHHHhcccccCCCCCCcEEEeeee-hhhhccccccCCCccceecccccccccceeeeC
Confidence 67778889998887775 899999999 776632 678999999999994 46788886
No 15
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=71.87 E-value=11 Score=27.97 Aligned_cols=85 Identities=16% Similarity=0.268 Sum_probs=55.5
Q ss_pred EEEEEeCcccHHHHHHcCCC--e-eCh-HHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCCCCcccc
Q 027063 64 KVCMLGDAQHVEEAEKIGLD--Y-MDV-EGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKFPTLVT 139 (229)
Q Consensus 64 kIcvf~~~~~~~~a~~~g~~--v-ig~-~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K~p~~v~ 139 (229)
+|+|++|.+..--.+-+|+. + +.. +++.+.+++.-. .++|.+++.+.++...++..+-. .+.+...|.++.
T Consensus 2 kIaVIGD~dtv~GFrLaGi~~~~~~~~~ee~~~~l~~l~~----~~d~gII~Ite~~~~~i~e~i~~-~~~~~~~P~ii~ 76 (100)
T PRK02228 2 EIAVIGSPEFTTGFRLAGIRKVYEVPDDEKLDEAVEEVLE----DDDVGILVMHDDDLEKLPRRLRR-TLEESVEPTVVT 76 (100)
T ss_pred EEEEEeCHHHHHHHHHcCCceEEeeCCHHHHHHHHHHHhh----CCCEEEEEEehhHhHhhHHHHHH-HHhcCCCCEEEE
Confidence 78999997665556678886 2 233 445544443211 23688999999998888766553 566777888874
Q ss_pred -C----cccHHHHHHHhhc
Q 027063 140 -H----QESLESKVNETKA 153 (229)
Q Consensus 140 -~----~~~l~~~i~~~~~ 153 (229)
+ ++.+.+.++++.+
T Consensus 77 IP~~~~~~~i~~~v~raIG 95 (100)
T PRK02228 77 LGGGGGSGGLREKIKRAIG 95 (100)
T ss_pred ECCCccchHHHHHHHHHhC
Confidence 2 2356666766655
No 16
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=62.55 E-value=28 Score=26.17 Aligned_cols=70 Identities=17% Similarity=0.372 Sum_probs=46.6
Q ss_pred cEEEEEeCcccHHHHHHcCCC---eeChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCCCCcccc
Q 027063 63 MKVCMLGDAQHVEEAEKIGLD---YMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKFPTLVT 139 (229)
Q Consensus 63 ~kIcvf~~~~~~~~a~~~g~~---vig~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K~p~~v~ 139 (229)
.+|+|++|.+..-=.+-+|++ +.+.+++.+.+.. . ..++|-.++.+.++...++..+-. + .+...|.++.
T Consensus 4 ~kIaVIGD~dtv~GFrLaGi~~~~v~~~ee~~~~i~~--l---~~~d~gII~Ite~~a~~i~~~i~~-~-~~~~~P~Il~ 76 (104)
T PRK01395 4 YKIGVVGDKDSILPFKALGIDVFPVIDEQEAINTLRK--L---AMEDYGIIYITEQIAADIPETIER-Y-DNQVLPAIIL 76 (104)
T ss_pred eeEEEEECHHHHHHHHHcCCeeEEecChHHHHHHHHH--H---hcCCcEEEEEcHHHHHHhHHHHHH-h-cCCCCCEEEE
Confidence 489999997665545667877 3355665554443 1 134688999999999988876653 2 4556777763
No 17
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=47.93 E-value=12 Score=31.83 Aligned_cols=21 Identities=29% Similarity=0.369 Sum_probs=17.4
Q ss_pred hh-hhhhhhcC-CCCCCCCCCcc
Q 027063 117 IK-QIPRLLGP-GLNKAGKFPTL 137 (229)
Q Consensus 117 ~~-~l~~~LG~-~~~p~~K~p~~ 137 (229)
++ .|+++||| ++||+.+.++.
T Consensus 117 l~k~LGk~lgprgkmP~p~~~t~ 139 (215)
T PRK04203 117 IGRYLGPVLGPRGKMPTPLPPNA 139 (215)
T ss_pred HHHHHhhhcCcCCCCCCCcCCCC
Confidence 45 48999999 99999888774
No 18
>COG1436 NtpG Archaeal/vacuolar-type H+-ATPase subunit F [Energy production and conversion]
Probab=45.93 E-value=39 Score=25.48 Aligned_cols=85 Identities=19% Similarity=0.288 Sum_probs=51.6
Q ss_pred cEEEEEeCcccHHHHHHcCCC---eeChHH--HHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCCCCcc
Q 027063 63 MKVCMLGDAQHVEEAEKIGLD---YMDVEG--LKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKFPTL 137 (229)
Q Consensus 63 ~kIcvf~~~~~~~~a~~~g~~---vig~~~--L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K~p~~ 137 (229)
.+|||+.|.+..---+=+|+. ++...+ +.+.+..... ..|+..+-+.+++..++..+-. .....-.|++
T Consensus 3 ~~I~VIGd~dtvtGFrLaGv~~~~v~~~~~~~~~~~~~~l~~-----~~~~iIiite~~a~~i~~~i~~-~~~~~~~P~i 76 (104)
T COG1436 3 MKIAVIGDRDTVTGFRLAGVRVVYVADDEEDELRAALRVLAE-----DDVGIILITEDLAEKIREEIRR-IIRSSVLPAI 76 (104)
T ss_pred eEEEEEEccchhhceeeecceeEEEecChhHHHHHHHHhhcc-----CCceEEEEeHHHHhhhHHHHHH-HhhccCccEE
Confidence 589999988764333335655 244432 4444444332 2688999999999988877664 3323334665
Q ss_pred cc-Cc------ccHHHHHHHhhc
Q 027063 138 VT-HQ------ESLESKVNETKA 153 (229)
Q Consensus 138 v~-~~------~~l~~~i~~~~~ 153 (229)
+. ++ ..+++.|+++.+
T Consensus 77 v~IPs~~~~~~~~~~~~I~k~vG 99 (104)
T COG1436 77 VEIPSPGKEEEEPLRELIRRAVG 99 (104)
T ss_pred EEeCCCCCCccchHHHHHHHHHh
Confidence 53 11 467777777665
No 19
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=44.18 E-value=79 Score=23.70 Aligned_cols=84 Identities=19% Similarity=0.248 Sum_probs=52.8
Q ss_pred cEEEEEeCcccHHHHHHcCCC-eeCh--HHHHHhhhCHHHHHHHhh-cccEEEEehhhhhhhh-hhhcCCCCCCCCCCcc
Q 027063 63 MKVCMLGDAQHVEEAEKIGLD-YMDV--EGLKKLNKNKKLVKKLAK-KYHAFLASESVIKQIP-RLLGPGLNKAGKFPTL 137 (229)
Q Consensus 63 ~kIcvf~~~~~~~~a~~~g~~-vig~--~~L~~~~~~~e~~rkL~~-~yd~flad~~i~~~l~-~~LG~~~~p~~K~p~~ 137 (229)
.+|+|+.|.+..-=-+-+|++ +... ++.. .+..+.|+. +|-.++.+.++...++ ..+- .+++...|.+
T Consensus 3 ~kIaVvGd~DtilGFrlaGi~~v~~~~~~e~~-----~~~~~~l~~~~~gII~iTE~~a~~i~~~~i~--~~~~~~~P~I 75 (104)
T PRK01189 3 SCITVIGERDVVLGFRLLGIGDTIEAEGKDLV-----KKFLEIFNNPKCKYIFVSESTKNMFDKNTLR--SLESSSKPLV 75 (104)
T ss_pred ceEEEEcCHHHHHHHHHcCCceEEEcCCHHHH-----HHHHHHHhcCCeEEEEEEHHHHhhCCHHHHH--HHhccCCCeE
Confidence 379999987765445667885 4322 2222 122334433 4888999999999888 4544 4557888888
Q ss_pred c---cCc----ccHHHHHHHhhc
Q 027063 138 V---THQ----ESLESKVNETKA 153 (229)
Q Consensus 138 v---~~~----~~l~~~i~~~~~ 153 (229)
+ .++ +.+.+.++++.+
T Consensus 76 I~Ipipg~~~~~~i~~~ik~aiG 98 (104)
T PRK01189 76 VFIPLPGISEEESIEEMAKRILG 98 (104)
T ss_pred EEEeCCCCccchhHHHHHHHHhc
Confidence 8 221 356666666654
No 20
>PF04481 DUF561: Protein of unknown function (DUF561); InterPro: IPR007570 Protein in this entry are of unknown function and are found in cyanobacteria and the chloroplasts of algae. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=36.91 E-value=80 Score=27.27 Aligned_cols=113 Identities=13% Similarity=0.177 Sum_probs=60.6
Q ss_pred cEEEEEe-CcccHHHHHHcCCCeeChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCCCCccccCc
Q 027063 63 MKVCMLG-DAQHVEEAEKIGLDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKFPTLVTHQ 141 (229)
Q Consensus 63 ~kIcvf~-~~~~~~~a~~~g~~vig~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K~p~~v~~~ 141 (229)
.-|||=+ +++..-.|.++||+.|-.-.....|.++. .+...+++..--+. +.++|..-.-+-|++.
T Consensus 62 lPICVSaVep~~f~~aV~AGAdliEIGNfDsFY~qGr-----------~f~a~eVL~Lt~~t--R~LLP~~~LsVTVPHi 128 (242)
T PF04481_consen 62 LPICVSAVEPELFVAAVKAGADLIEIGNFDSFYAQGR-----------RFSAEEVLALTRET--RSLLPDITLSVTVPHI 128 (242)
T ss_pred CCeEeecCCHHHHHHHHHhCCCEEEecchHHHHhcCC-----------eecHHHHHHHHHHH--HHhCCCCceEEecCcc
Confidence 3489986 77776788999999775444333333332 23333343322211 1344443322222322
Q ss_pred ccHHHHHHHhh----ccceeEecccceEEEEEecCCCCHHHHHHHHHHHHHHHHHhc
Q 027063 142 ESLESKVNETK----ATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLL 194 (229)
Q Consensus 142 ~~l~~~i~~~~----~~~~~~~~~~~~i~v~VG~~~m~~~ei~eNi~a~l~~l~~~~ 194 (229)
=.+.++++-+. .+..+-+..|+..+.+ ...-+..+|+.+...+...+
T Consensus 129 L~ld~Qv~LA~~L~~~GaDiIQTEGgtss~p------~~~g~lglIekaapTLAaay 179 (242)
T PF04481_consen 129 LPLDQQVQLAEDLVKAGADIIQTEGGTSSKP------TSPGILGLIEKAAPTLAAAY 179 (242)
T ss_pred ccHHHHHHHHHHHHHhCCcEEEcCCCCCCCC------CCcchHHHHHHHhHHHHHHH
Confidence 24444444443 2566665566665554 34557778888888776655
No 21
>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.87 E-value=49 Score=31.17 Aligned_cols=81 Identities=15% Similarity=0.222 Sum_probs=44.8
Q ss_pred CccEEEEEEEcccCCCCCCcceeeEEcCCCC-CCCcEEEEEeCc--------ccHHHHHHcCCCeeCh-HHHHH-hhhCH
Q 027063 29 TETIELQIGLKNYDPQKDKRFSGSVKLPHIP-RPKMKVCMLGDA--------QHVEEAEKIGLDYMDV-EGLKK-LNKNK 97 (229)
Q Consensus 29 ~e~I~l~i~lk~~~~kk~~~~~~~I~LPh~~-~~~~kIcvf~~~--------~~~~~a~~~g~~vig~-~~L~~-~~~~~ 97 (229)
..+|-+-+.|-+ .-|.... -.|-|-. ++..++|++|-| +..+.|.+++++|.|. ++..- ++..
T Consensus 100 kpsVimfVGLqG--~GKTTtc---~KlA~y~kkkG~K~~LvcaDTFRagAfDQLkqnA~k~~iP~ygsyte~dpv~ia~- 173 (483)
T KOG0780|consen 100 KPSVIMFVGLQG--SGKTTTC---TKLAYYYKKKGYKVALVCADTFRAGAFDQLKQNATKARVPFYGSYTEADPVKIAS- 173 (483)
T ss_pred CCcEEEEEeccC--CCcceeH---HHHHHHHHhcCCceeEEeecccccchHHHHHHHhHhhCCeeEecccccchHHHHH-
Confidence 367777777743 2232222 2233333 467899999843 2235688899996653 44332 1111
Q ss_pred HHHHHH-hhcccEEEEehh
Q 027063 98 KLVKKL-AKKYHAFLASES 115 (229)
Q Consensus 98 e~~rkL-~~~yd~flad~~ 115 (229)
+-..++ ...||++|+|.+
T Consensus 174 egv~~fKke~fdvIIvDTS 192 (483)
T KOG0780|consen 174 EGVDRFKKENFDVIIVDTS 192 (483)
T ss_pred HHHHHHHhcCCcEEEEeCC
Confidence 111111 136999999987
No 22
>COG4844 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.34 E-value=35 Score=23.85 Aligned_cols=17 Identities=6% Similarity=0.143 Sum_probs=14.2
Q ss_pred CCCHHHHHHHHHHHHHH
Q 027063 173 SMEEKQIFQNVQMSVNF 189 (229)
Q Consensus 173 ~m~~~ei~eNi~a~l~~ 189 (229)
+-+++|++|||-+.++.
T Consensus 58 Get~eeLv~NIY~~i~E 74 (78)
T COG4844 58 GETPEELVENIYTFIEE 74 (78)
T ss_pred CCCHHHHHHHHHHHHhc
Confidence 45899999999988764
No 23
>PF01400 Astacin: Astacin (Peptidase family M12A) This Prosite motif covers only the active site.; InterPro: IPR001506 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12A (astacin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The astacin () family of metalloendopeptidases encompasses a range of proteins found in hydra to humans, in mature and developmental systems []. Their functions include activation of growth factors, degradation of polypeptides, and processing of extracellular proteins []. The proteins are synthesised with N-terminal signal and pro-enzyme sequences, and many contain multiple domains C-terminal to the protease domain. They are either secreted from cells, or are associated with the plasma membrane. The astacin molecule adopts a kidney shape, with a deep active-site cleft between its N- and C-terminal domains []. The zinc ion, which lies at the bottom of the cleft, exhibits a unique penta-coordinated mode of binding, involving 3 histidine residues, a tyrosine and a water molecule (which is also bound to the carboxylate side chain of Glu93) []. The N-terminal domain comprises 2 alpha-helices and a 5-stranded beta-sheet. The overall topology of this domain is shared by the archetypal zinc-endopeptidase thermolysin. Astacin protease domains also share common features with serralysins, matrix metalloendopeptidases, and snake venom proteases; they cleave peptide bonds in polypeptides such as insulin B chain and bradykinin, and in proteins such as casein and gelatin; and they have arylamidase activity [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3LQB_A 3EDH_A 3EDG_A 3EDI_A 1IAE_A 1IAB_A 1IAA_A 1AST_A 1IAC_A 1QJJ_A ....
Probab=32.41 E-value=1e+02 Score=25.44 Aligned_cols=46 Identities=15% Similarity=0.244 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHhccCCcccE-EEEeecCCCcccceecccccccccccC
Q 027063 177 KQIFQNVQMSVNFLVSLLKKNWQNV-PLSEEYHGSFKPHLLRNSALCWSFVGK 228 (229)
Q Consensus 177 ~ei~eNi~a~l~~l~~~~pkg~~nI-~l~~k~~~S~~~~~~~~~~~~~~~~~~ 228 (229)
....+.|..+++.+.+.- +| .+..+ .....--.....-.|||+||.
T Consensus 18 ~~~~~~I~~Am~~~e~~T-----cI~F~~~~-~~~~~~i~~~~~~gC~S~vG~ 64 (191)
T PF01400_consen 18 SSQRQRIRKAMDEWEKNT-----CIRFVERT-ENEDDYISFSNGSGCWSYVGR 64 (191)
T ss_dssp HHHHHHHHHHHHHHHHHS-----SEEEEE-S-SSSSSEEEEESSSSEEEESS-
T ss_pred HHHHHHHHHHHHHHHhCC-----CEEEEECC-CCCceEEEeecCccccchhhh
Confidence 445588999999998764 56 33333 233333345667789999996
No 24
>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family.
Probab=27.89 E-value=2e+02 Score=20.90 Aligned_cols=53 Identities=17% Similarity=0.162 Sum_probs=34.7
Q ss_pred CcEEEEEeCcc---------cHHHHHHcCCCe----eChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhh
Q 027063 62 KMKVCMLGDAQ---------HVEEAEKIGLDY----MDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLL 124 (229)
Q Consensus 62 ~~kIcvf~~~~---------~~~~a~~~g~~v----ig~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~L 124 (229)
..+|+++|..- ..+.+++.|.++ .+..++... ...||++|..|.+-..+..+-
T Consensus 3 ~~~ILl~C~~G~sSS~l~~k~~~~~~~~gi~~~v~a~~~~~~~~~----------~~~~Dvill~pqi~~~~~~i~ 68 (95)
T TIGR00853 3 ETNILLLCAAGMSTSLLVNKMNKAAEEYGVPVKIAAGSYGAAGEK----------LDDADVVLLAPQVAYMLPDLK 68 (95)
T ss_pred ccEEEEECCCchhHHHHHHHHHHHHHHCCCcEEEEEecHHHHHhh----------cCCCCEEEECchHHHHHHHHH
Confidence 46888888541 135677888873 455554322 347999999999876666553
No 25
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=26.00 E-value=88 Score=22.57 Aligned_cols=69 Identities=19% Similarity=0.319 Sum_probs=43.7
Q ss_pred EEEEeCcccHHHHHHcCCC--ee--ChHHHHHhhhCHHHHHHHhhcccEEEEehhhhhhhhhhhcCCCCCCCCCCccc
Q 027063 65 VCMLGDAQHVEEAEKIGLD--YM--DVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKFPTLV 138 (229)
Q Consensus 65 Icvf~~~~~~~~a~~~g~~--vi--g~~~L~~~~~~~e~~rkL~~~yd~flad~~i~~~l~~~LG~~~~p~~K~p~~v 138 (229)
|+|++|.+...--+=+|++ ++ ..+++.+.++..-. ...+-+++.+.+++..++..+-. +..+...|+++
T Consensus 1 IavIGd~~~v~gFrLaGv~~~~~~~~~ee~~~~l~~l~~----~~~~gIIii~e~~~~~~~~~l~~-~~~~~~~P~iv 73 (95)
T PF01990_consen 1 IAVIGDRDTVLGFRLAGVEGVYVNTDPEEAEEALKELLK----DEDVGIIIITEDLAEKIRDELDE-YREESSLPLIV 73 (95)
T ss_dssp EEEEE-HHHHHHHHHTTSEEEEESHSHHHHHHHHHHHHH----HTTEEEEEEEHHHHTTHHHHHHH-HHHTSSSSEEE
T ss_pred CEEEeCHHHHHHHHHcCCCCccCCCCHHHHHHHHHHHhc----CCCccEEEeeHHHHHHHHHHHHH-HHhccCCceEE
Confidence 5778877665555667887 33 55666665544321 24788999999998887766653 33334556666
No 26
>PF00281 Ribosomal_L5: Ribosomal protein L5; InterPro: IPR002132 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , , ], groups: Eubacterial L5. Algal chloroplast L5. Cyanelle L5. Archaebacterial L5. Mammalian L11. Tetrahymena thermophila L21. Dictyostelium discoideum (Slime mold) L5 Saccharomyces cerevisiae (Baker's yeast) L16 (39A). Plant mitochondrial L5. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1IQ4_B 4A1A_D 4A1C_D 4A17_D 4A1E_D 3BBO_H 3O5H_K 1S1I_J 3O58_K 3IZS_E ....
Probab=25.84 E-value=1.9e+02 Score=19.01 Aligned_cols=31 Identities=6% Similarity=0.298 Sum_probs=24.2
Q ss_pred ceEEEEEecCCCCHHHHHHHHHHHHHHHHHhcc
Q 027063 163 LCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLK 195 (229)
Q Consensus 163 ~~i~v~VG~~~m~~~ei~eNi~a~l~~l~~~~p 195 (229)
-++++.+|..... ..+++....++.|....|
T Consensus 11 Ivin~gvg~~~~~--k~l~~a~~~L~~ItGQkp 41 (56)
T PF00281_consen 11 IVINIGVGEAGDD--KVLEKAKKELEQITGQKP 41 (56)
T ss_dssp EEEEEESSTTSST--HHHHHHHHHHHHHHSS--
T ss_pred EEEECCCCccccc--hHHHHHHHHHHHHhCCce
Confidence 3567788877776 788999999999998887
No 27
>KOG0180 consensus 20S proteasome, regulatory subunit beta type PSMB3/PUP3 [Posttranslational modification, protein turnover, chaperones]
Probab=24.49 E-value=1.2e+02 Score=25.15 Aligned_cols=37 Identities=19% Similarity=0.288 Sum_probs=29.2
Q ss_pred cCCCCHHHHHHHH-HHHHHHHHHhccCCcccE-EEEeec
Q 027063 171 NLSMEEKQIFQNV-QMSVNFLVSLLKKNWQNV-PLSEEY 207 (229)
Q Consensus 171 ~~~m~~~ei~eNi-~a~l~~l~~~~pkg~~nI-~l~~k~ 207 (229)
+-+|.++||.|-| +++++++-...-.||.-+ |+-.|.
T Consensus 154 ~pnmepd~LFetisQa~Lna~DRDalSGwGa~vyiI~kd 192 (204)
T KOG0180|consen 154 EPNMEPDELFETISQALLNAVDRDALSGWGAVVYIITKD 192 (204)
T ss_pred CCCCCHHHHHHHHHHHHHhHhhhhhhccCCeEEEEEccc
Confidence 3479999999987 567788877778999988 776553
No 28
>PRK03957 V-type ATP synthase subunit F; Provisional
Probab=24.45 E-value=2.9e+02 Score=20.29 Aligned_cols=56 Identities=25% Similarity=0.417 Sum_probs=35.8
Q ss_pred EEEEEeCcccHHHHHHcCCC--e-eC-hHHHHHhhhCHHHHHHHh--hcccEEEEehhhhhhhhhhhc
Q 027063 64 KVCMLGDAQHVEEAEKIGLD--Y-MD-VEGLKKLNKNKKLVKKLA--KKYHAFLASESVIKQIPRLLG 125 (229)
Q Consensus 64 kIcvf~~~~~~~~a~~~g~~--v-ig-~~~L~~~~~~~e~~rkL~--~~yd~flad~~i~~~l~~~LG 125 (229)
+|+|++|.+..-=-+-+|++ + +. .+++.+.++ ++. ++|-+++.+.+++..+...+-
T Consensus 2 kIaVIgD~dtv~GFrLaGi~~~~~v~~~ee~~~~l~------~l~~~~d~gII~ite~~~~~i~~~i~ 63 (100)
T PRK03957 2 KIAVVGDRDTVTGFRLAGLTEVYEVKNPEEAKNAIK------ELVENDEIGIIIITERIAEEIRDLIS 63 (100)
T ss_pred EEEEEeCHHHHHHHHHcCCCceEEeCCHHHHHHHHH------HHhhCCCeEEEEEcHHHHHHHHHHHh
Confidence 78999987655444567874 2 22 245444433 343 468899999999888765543
No 29
>TIGR03260 met_CoM_red_D methyl-coenzyme M reductase operon protein D. Members of this protein family are protein D, a non-structural protein, of the operon for methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). That enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis; it has several modified sites, so accessory proteins are expected. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes. Proteins in this family are expressed at much lower levels than the methyl-coenzyme M reductase itself and associate and have been shown to form at least transient associations. The precise function is unknown.
Probab=24.39 E-value=63 Score=26.00 Aligned_cols=30 Identities=17% Similarity=0.400 Sum_probs=25.0
Q ss_pred ceEEEEEecCCCC--HHHHHHHHHHHHHHHHH
Q 027063 163 LCMGVAVGNLSME--EKQIFQNVQMSVNFLVS 192 (229)
Q Consensus 163 ~~i~v~VG~~~m~--~~ei~eNi~a~l~~l~~ 192 (229)
--+.|.||++-.+ .++..++|.++++.+..
T Consensus 67 veL~V~VGrI~le~~~~~~i~~I~eiC~e~~p 98 (150)
T TIGR03260 67 VELRVQVGRIILELEDEDIVEEIEEICKEMLP 98 (150)
T ss_pred EEEEEEEeEEEEEecCHHHHHHHHHHHHhhCC
Confidence 3568999999877 99999999999988743
No 30
>PLN02331 phosphoribosylglycinamide formyltransferase
Probab=22.26 E-value=86 Score=26.46 Aligned_cols=23 Identities=17% Similarity=0.203 Sum_probs=15.2
Q ss_pred EEEEEeCccc---HHHHHHcCCCeeC
Q 027063 64 KVCMLGDAQH---VEEAEKIGLDYMD 86 (229)
Q Consensus 64 kIcvf~~~~~---~~~a~~~g~~vig 86 (229)
-++||++.+. .+.|++.|+++.-
T Consensus 29 i~~visn~~~~~~~~~A~~~gIp~~~ 54 (207)
T PLN02331 29 VVVVVTNKPGCGGAEYARENGIPVLV 54 (207)
T ss_pred EEEEEEeCCCChHHHHHHHhCCCEEE
Confidence 4566676543 3678889998654
No 31
>PF09291 DUF1968: Domain of unknown function (DUF1968); InterPro: IPR015370 This domain is found in mammalian T-cell antigen receptors, it adopts an immunoglobulin-like beta-sandwich fold, with seven strands in two beta-sheets in a Greek-key topology. Their exact function of members of this entry have not, as yet, been determined. ; PDB: 2NW2_A 2NX5_N 2EYT_C 2ESV_D 3DXA_I 1ZGL_S 3KPR_I 2IAL_A 3QEQ_D 3O6F_G ....
Probab=21.83 E-value=80 Score=22.90 Aligned_cols=19 Identities=21% Similarity=0.375 Sum_probs=13.3
Q ss_pred EEcCCCCCCCcEEEEEeCc
Q 027063 53 VKLPHIPRPKMKVCMLGDA 71 (229)
Q Consensus 53 I~LPh~~~~~~kIcvf~~~ 71 (229)
.+|--|--.+..||+|+|=
T Consensus 4 YQLr~pkss~tSVCLFTDF 22 (85)
T PF09291_consen 4 YQLRSPKSSDTSVCLFTDF 22 (85)
T ss_dssp EEEEESSSSSSEEEEEESE
T ss_pred eecCCCCCCCceEEEEecc
Confidence 4454455568899999973
No 32
>PRK13958 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=20.68 E-value=46 Score=27.96 Aligned_cols=26 Identities=19% Similarity=0.386 Sum_probs=22.8
Q ss_pred cEEEEEeCcccHHHHHHcCCCeeChH
Q 027063 63 MKVCMLGDAQHVEEAEKIGLDYMDVE 88 (229)
Q Consensus 63 ~kIcvf~~~~~~~~a~~~g~~vig~~ 88 (229)
.|||=+++.++++.|.++|++++|.-
T Consensus 3 vKICGit~~eda~~~~~~GaD~iGfI 28 (207)
T PRK13958 3 LKFCGFTTIKDVTAASQLPIDAIGFI 28 (207)
T ss_pred EEEcCCCcHHHHHHHHHcCCCEEEEe
Confidence 58999998888889999999988884
No 33
>PF15585 Imm46: Immunity protein 46
Probab=20.32 E-value=3.5e+02 Score=21.26 Aligned_cols=44 Identities=9% Similarity=-0.019 Sum_probs=38.3
Q ss_pred ccceEEEEEecCCCCHHHHHHHHHHHHHHHHHhccCCcccEEEE
Q 027063 161 KVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQNVPLS 204 (229)
Q Consensus 161 ~~~~i~v~VG~~~m~~~ei~eNi~a~l~~l~~~~pkg~~nI~l~ 204 (229)
..|+..+.+|-.+--.-+-.++|..+.+.|....|+++.=++++
T Consensus 48 ~NG~~~l~~~g~~NHr~~~~~eii~lf~~i~e~aPGSYGlLy~r 91 (129)
T PF15585_consen 48 MNGSYFLHFGGLSNHRGQEAPEIIELFERIAEIAPGSYGLLYIR 91 (129)
T ss_pred cCCcEEEEEccccCCCccchHHHHHHHHHHHHhCCCceeEEEEe
Confidence 46788899999998888999999999999999999998865554
Done!