Query 022012
Match_columns 304
No_of_seqs 147 out of 994
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 07:21:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022012.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022012hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00129 rpl1 ribosomal protei 100.0 1.5E-40 3.3E-45 303.5 14.4 126 177-304 15-140 (229)
2 PRK05424 rplA 50S ribosomal pr 100.0 1.3E-39 2.9E-44 297.1 14.6 128 176-304 13-140 (230)
3 COG0081 RplA Ribosomal protein 100.0 6.4E-40 1.4E-44 299.8 12.0 129 175-304 13-142 (228)
4 TIGR01169 rplA_bact ribosomal 100.0 3.2E-39 7E-44 294.0 14.5 128 176-304 12-139 (227)
5 TIGR01170 rplA_mito ribosomal 100.0 1.5E-38 3.2E-43 272.5 14.1 119 183-304 1-123 (141)
6 PRK04203 rpl1P 50S ribosomal p 100.0 3.1E-33 6.7E-38 252.3 13.5 120 184-304 6-135 (215)
7 PTZ00225 60S ribosomal protein 100.0 7.1E-31 1.5E-35 237.9 12.3 118 184-303 8-134 (214)
8 PTZ00029 60S ribosomal protein 100.0 1.7E-29 3.6E-34 228.6 12.4 119 184-303 8-136 (216)
9 cd00403 Ribosomal_L1 Ribosomal 99.9 4.6E-25 1E-29 194.6 12.5 119 185-304 1-127 (208)
10 KOG1569 50S ribosomal protein 99.9 5.6E-23 1.2E-27 194.7 11.1 127 175-304 82-220 (323)
11 PF00687 Ribosomal_L1: Ribosom 99.8 4.9E-19 1.1E-23 157.0 11.0 106 197-303 17-141 (220)
12 KOG1570 60S ribosomal protein 99.6 2.2E-16 4.7E-21 143.8 4.6 121 182-304 7-139 (218)
13 PF13003 MRL1: Ribosomal prote 96.6 0.0043 9.4E-08 53.9 5.9 64 177-240 64-133 (133)
14 KOG1685 Uncharacterized conser 85.8 1.1 2.5E-05 44.4 4.7 70 233-302 87-175 (343)
15 PTZ00029 60S ribosomal protein 82.7 0.58 1.3E-05 43.1 1.1 16 288-304 117-132 (216)
16 COG1064 AdhP Zn-dependent alco 67.7 8.8 0.00019 38.1 4.9 61 235-300 191-255 (339)
17 TIGR00853 pts-lac PTS system, 64.5 17 0.00036 29.3 5.1 65 233-298 2-75 (95)
18 PRK01189 V-type ATP synthase s 60.5 15 0.00032 30.5 4.2 52 235-288 3-60 (104)
19 PTZ00225 60S ribosomal protein 58.5 5.4 0.00012 36.9 1.4 16 288-304 115-130 (214)
20 PRK02228 V-type ATP synthase s 54.9 25 0.00055 28.6 4.7 60 235-294 1-66 (100)
21 PRK01395 V-type ATP synthase s 51.6 48 0.001 27.4 5.8 65 235-301 4-72 (104)
22 PRK13958 N-(5'-phosphoribosyl) 47.2 12 0.00026 34.1 1.7 25 235-259 3-27 (207)
23 cd05565 PTS_IIB_lactose PTS_II 45.8 41 0.00089 27.6 4.6 59 236-299 2-73 (99)
24 PRK09590 celB cellobiose phosp 43.3 77 0.0017 26.2 5.8 60 236-298 3-75 (104)
25 COG0135 TrpF Phosphoribosylant 40.6 17 0.00037 33.7 1.8 25 234-258 3-27 (208)
26 PF00697 PRAI: N-(5'phosphorib 40.4 21 0.00046 31.9 2.3 59 235-295 1-71 (197)
27 cd05564 PTS_IIB_chitobiose_lic 38.6 60 0.0013 25.9 4.4 60 236-296 1-69 (96)
28 PRK01222 N-(5'-phosphoribosyl) 38.5 18 0.00038 33.0 1.5 26 234-259 4-29 (210)
29 PLN02363 phosphoribosylanthran 37.5 19 0.00042 34.1 1.6 27 233-259 47-73 (256)
30 PRK04148 hypothetical protein; 35.8 92 0.002 27.1 5.4 62 234-295 17-102 (134)
31 cd00405 PRAI Phosphoribosylant 32.2 29 0.00062 30.7 1.7 25 235-259 1-25 (203)
32 PF00107 ADH_zinc_N: Zinc-bind 32.0 76 0.0017 25.0 4.0 64 235-298 15-83 (130)
33 PF05991 NYN_YacP: YacP-like N 31.8 74 0.0016 28.0 4.2 35 234-268 94-129 (166)
34 PRK03957 V-type ATP synthase s 31.2 90 0.002 25.4 4.4 55 235-289 1-60 (100)
35 KOG1198 Zinc-binding oxidoredu 30.9 91 0.002 30.7 5.1 46 234-279 183-231 (347)
36 COG1436 NtpG Archaeal/vacuolar 30.2 63 0.0014 27.0 3.4 58 235-293 3-67 (104)
37 PF12270 Cyt_c_ox_IV: Cytochro 27.2 36 0.00077 30.1 1.4 16 117-132 60-75 (137)
38 KOG1588 RNA-binding protein Sa 26.1 26 0.00056 33.9 0.4 10 290-299 109-118 (259)
39 cd01140 FatB Siderophore bindi 25.4 1.8E+02 0.0039 26.1 5.7 33 223-259 4-36 (270)
40 COG1544 Ribosome-associated pr 22.1 2.5E+02 0.0053 23.7 5.5 51 180-230 7-61 (110)
41 PLN02331 phosphoribosylglycina 21.5 1.5E+02 0.0032 27.3 4.4 41 236-279 29-84 (207)
42 KOG2523 Predicted RNA-binding 21.3 1E+02 0.0022 28.5 3.2 39 227-268 123-161 (181)
43 TIGR00078 nadC nicotinate-nucl 21.2 1.1E+02 0.0024 29.0 3.6 27 233-259 177-204 (265)
44 PRK09427 bifunctional indole-3 20.2 52 0.0011 33.8 1.3 26 234-259 258-283 (454)
45 PRK15452 putative protease; Pr 20.1 1.8E+02 0.0038 29.9 5.0 26 235-260 4-32 (443)
No 1
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=100.00 E-value=1.5e-40 Score=303.55 Aligned_cols=126 Identities=41% Similarity=0.671 Sum_probs=122.1
Q ss_pred cCCCCccCHHHHHHHHHHHcccCCCccEEEEEEEccCCCCCCceeeeEEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCe
Q 022012 177 KESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADI 256 (304)
Q Consensus 177 ~ek~~~ysl~EAIr~lke~a~rkF~ETVEL~I~LnvD~kK~d~~~rGsV~LPh~~gK~~KIlVFadgd~aeeAkeAGAd~ 256 (304)
.+ ...|++.|||+.+++.+.++|+||||++|+||+|++|++++|||+|.|||++|++.||||||+++++++|++|||++
T Consensus 15 ~~-~~~y~l~eAi~~~k~~~~~kF~esvel~i~L~id~kk~~~~irg~v~LP~~~gk~~kV~Vfa~~~~~~eAk~aGad~ 93 (229)
T CHL00129 15 IE-KKLYSPEEAINLLKETATAKFIETAEAHISLNIDPKYADQQLRTTVTLPKGTGKTIRIAVLTNEEKITEAKNAGADI 93 (229)
T ss_pred cc-ccccCHHHHHHHHHHhCcCCCCccEEEEEEECCCCCCCCCceeeEEECCCCCCCCcEEEEECChHhHHHHHHcCCCE
Confidence 44 67899999999999988999999999999999999999999999999999999999999999999999999999999
Q ss_pred echHHHHHHHHhCCcccccEEEEcCcchhHHHhhhhccCCCCCCCCCC
Q 022012 257 VGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPK 304 (304)
Q Consensus 257 VGgeELIeKIkk~gkLdFD~~IATpdmMpkL~kLGriLGPRGLMPnpK 304 (304)
||++|||++|+ ++|++||+||||+|||++|++|||+|||||||||||
T Consensus 94 vg~edLi~~ik-~~~~~fd~~iAt~d~m~~l~kLgriLGprGlMP~pk 140 (229)
T CHL00129 94 VGSDDLIEEIT-KGNLDFDLLIATPDMMPKLAKLGRVLGPRGLMPSPK 140 (229)
T ss_pred eCHHHHHHHHH-cCcccCCEEEECHHHHHHHHHhcCcccccCCCCCCC
Confidence 99999999998 699999999999999999999999999999999997
No 2
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=100.00 E-value=1.3e-39 Score=297.06 Aligned_cols=128 Identities=51% Similarity=0.770 Sum_probs=123.4
Q ss_pred ccCCCCccCHHHHHHHHHHHcccCCCccEEEEEEEccCCCCCCceeeeEEEcCCCCCCCcEEEEEcCchhHHHHHHcCCC
Q 022012 176 KKESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGAD 255 (304)
Q Consensus 176 k~ek~~~ysl~EAIr~lke~a~rkF~ETVEL~I~LnvD~kK~d~~~rGsV~LPh~~gK~~KIlVFadgd~aeeAkeAGAd 255 (304)
..++...|++.|||+.+++.+.++|+||||++|+|++|++|++++|||+|.|||++|++.||||||+++++++|+++||+
T Consensus 13 ~~~~~~~y~l~eAi~~lk~~~~~kF~esvel~v~L~id~kK~~~~irg~v~LP~~~gk~~kI~Vfa~~~~~~~Ak~aGa~ 92 (230)
T PRK05424 13 KVDRTKLYSLEEAIALVKETATAKFDETVDVAVNLGVDPRKADQQVRGAVVLPHGTGKTVRVAVFAKGEKAEEAKAAGAD 92 (230)
T ss_pred hccccCccCHHHHHHHHHhhccCCCCCcEEEEEEeCCCCCCCCCeeeEEEECCCCCCCCcEEEEECChHhHHHHHHcCCC
Confidence 34667899999999999998899999999999999999999999999999999999999999999999999999999999
Q ss_pred eechHHHHHHHHhCCcccccEEEEcCcchhHHHhhhhccCCCCCCCCCC
Q 022012 256 IVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPK 304 (304)
Q Consensus 256 ~VGgeELIeKIkk~gkLdFD~~IATpdmMpkL~kLGriLGPRGLMPnpK 304 (304)
+|||+|||++|+ +||++||+||||++||++|++|||+||||||||++|
T Consensus 93 ~vg~eeLi~~ik-~~~~~fd~~iat~~~m~~l~~Lg~iLGPrGlMP~pk 140 (230)
T PRK05424 93 IVGGEDLIEKIK-GGWLDFDVVIATPDMMGKVGKLGRILGPRGLMPNPK 140 (230)
T ss_pred EeCHHHHHHHHh-cCCCcCCEEEECHHHHHHHHHhccccccccCCCCCC
Confidence 999999999998 799999999999999999999999999999999997
No 3
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.4e-40 Score=299.76 Aligned_cols=129 Identities=48% Similarity=0.739 Sum_probs=123.8
Q ss_pred cccCCCCccCHHHHHHHHHHHcccCCCccEEEEEEEccCCCCCCceeeeEEEcCCCCCCCcEEEEEcCchhHHHHHHcCC
Q 022012 175 KKKESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGA 254 (304)
Q Consensus 175 ~k~ek~~~ysl~EAIr~lke~a~rkF~ETVEL~I~LnvD~kK~d~~~rGsV~LPh~~gK~~KIlVFadgd~aeeAkeAGA 254 (304)
.+......|++.|||+++++.+.++|+||||++|+|++|++|++++|||+|.|||++|+..||||||+++.+++|++|||
T Consensus 13 ~~~d~~~~~~i~eai~~~ke~~~~kF~etVevav~L~vD~~k~dq~vrg~VvLP~g~gk~vrV~Vfa~g~~~~~A~~AGa 92 (228)
T COG0081 13 EKVDRNKLYSLEEAVKLLKETSKRKFDETVEVAVNLKVDPRKPDQRVRGSVVLPNGTGKTVRVAVFADGEKAEEAKAAGA 92 (228)
T ss_pred HhhhhhhhhhHHHHHHHHHhccccCcceEEEEEEEcccCCCCcccccceeEECCCCCCCccEEEEEcChHhHHHHHHcCC
Confidence 44566678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeechHHHHHHHHhCC-cccccEEEEcCcchhHHHhhhhccCCCCCCCCCC
Q 022012 255 DIVGGLELIEEIASSG-KLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPK 304 (304)
Q Consensus 255 d~VGgeELIeKIkk~g-kLdFD~~IATpdmMpkL~kLGriLGPRGLMPnpK 304 (304)
||||++||+++|+ +| |++||+||||||||+.|++||++|||||||||||
T Consensus 93 d~Vg~edl~e~ik-~~r~~~fD~~IAtpdmM~~v~~LG~vLGPRGlMP~Pk 142 (228)
T COG0081 93 DYVGGEDLIELIK-NGRAKDFDVFIATPDMMPLVGKLGKVLGPRGLMPNPK 142 (228)
T ss_pred CEecHHHHHHHHh-CcchhcCCEEEECchHHHHHHHHhhhcCCCCCCCCCC
Confidence 9999999999998 68 8999999999999999988999999999999997
No 4
>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=3.2e-39 Score=294.02 Aligned_cols=128 Identities=51% Similarity=0.745 Sum_probs=123.1
Q ss_pred ccCCCCccCHHHHHHHHHHHcccCCCccEEEEEEEccCCCCCCceeeeEEEcCCCCCCCcEEEEEcCchhHHHHHHcCCC
Q 022012 176 KKESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGAD 255 (304)
Q Consensus 176 k~ek~~~ysl~EAIr~lke~a~rkF~ETVEL~I~LnvD~kK~d~~~rGsV~LPh~~gK~~KIlVFadgd~aeeAkeAGAd 255 (304)
+.+....|++.|||+.+++.+.++|+||||++|+||+|++|++++|||+|.|||++|++.||||||+++++++|+++||+
T Consensus 12 ~~~~~~~y~l~eAi~~lk~~~~~~f~esvel~i~L~id~kK~~~~irg~v~LP~~~gk~~kV~Vfa~~~~~~~Ak~aGa~ 91 (227)
T TIGR01169 12 KVDRNKLYSLDEAIALLKETATAKFDETVEVAIRLGIDPRKSDQQVRGTVVLPHGTGKTVRVAVFAKGEKAEEAKAAGAD 91 (227)
T ss_pred hcccCCccCHHHHHHHHHhhccCCCCCCEEEEEEECcCCCcCCCeeeEEEECCCCCCCCcEEEEEcCchhHHHHHHcCCC
Confidence 44566799999999999998899999999999999999999999999999999999999999999999999999999999
Q ss_pred eechHHHHHHHHhCCcccccEEEEcCcchhHHHhhhhccCCCCCCCCCC
Q 022012 256 IVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPK 304 (304)
Q Consensus 256 ~VGgeELIeKIkk~gkLdFD~~IATpdmMpkL~kLGriLGPRGLMPnpK 304 (304)
+|||+|||++|+ +++++||+||||++||++|++|||+|||||||||+|
T Consensus 92 ~vg~~eLi~~ik-~~~~~fd~~iat~~~m~~l~~Lg~iLGPrGlMP~~k 139 (227)
T TIGR01169 92 YVGSDDLIEKIK-KGWLDFDVVIATPDMMRVVGKLGRILGPRGLMPNPK 139 (227)
T ss_pred EeCHHHHHHHHH-cCCccCCEEEECHHHHHHHHHhccccccccCCCCCC
Confidence 999999999998 689999999999999999999999999999999997
No 5
>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=100.00 E-value=1.5e-38 Score=272.47 Aligned_cols=119 Identities=32% Similarity=0.561 Sum_probs=112.7
Q ss_pred cCHHHHHHHHHHHccc--CCCccEEEEEEEccCCCCCCceeeeEEEcCCCCCCCcEEEEEcCchh-HHHHHHcCCCeech
Q 022012 183 LDLMDAIKQVKANAKA--TFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGAD-AEEARAAGADIVGG 259 (304)
Q Consensus 183 ysl~EAIr~lke~a~r--kF~ETVEL~I~LnvD~kK~d~~~rGsV~LPh~~gK~~KIlVFadgd~-aeeAkeAGAd~VGg 259 (304)
|++.|||++||+.+.. +|+||||++|+|+++..+ ..|||+|.|||+++++.||||||++++ +++|+++||++|||
T Consensus 1 y~i~eA~~~lk~~~~~~~~~~etvel~i~L~~~~~~--~~irg~v~LP~~~~k~~kV~Vf~~~~~~~~~Ak~aGa~~vg~ 78 (141)
T TIGR01170 1 YKVIKAFVYLKTKSISMYVPKQSVNLDIGLLMELGK--ESVQGMFSFPHPFGKEPKIAVFTKGASEVEEAREAGADYVGG 78 (141)
T ss_pred CCHHHHHHHHHHhcccCCCCCceEEEEEEECCCCCC--CCceEEEECCCCCCCCCEEEEECCChHHHHHHHHcCCCEeCH
Confidence 7899999999999977 999999999999988765 349999999999999999999999987 68899999999999
Q ss_pred HHHHHHHHhCCccc-ccEEEEcCcchhHHHhhhhccCCCCCCCCCC
Q 022012 260 LELIEEIASSGKLD-VEKCFSTRQFMPRLFKISKILNQHGLMPNPK 304 (304)
Q Consensus 260 eELIeKIkk~gkLd-FD~~IATpdmMpkL~kLGriLGPRGLMPnpK 304 (304)
+|||++|+ ++|++ ||+||||++||++|++|||+|||||||||+|
T Consensus 79 edLi~~i~-~g~~~~fd~~iA~~~~m~~l~~Lg~iLGprGlMP~~k 123 (141)
T TIGR01170 79 DDLIKKIE-DGEIKPFDYLIAHPDIVPELAQLRRLLGPKGLMPSPK 123 (141)
T ss_pred HHHHHHHh-cCCcccccEEEECHHHHHHHHHhhcccccCcCCCCCC
Confidence 99999998 79999 9999999999999999999999999999997
No 6
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=100.00 E-value=3.1e-33 Score=252.29 Aligned_cols=120 Identities=30% Similarity=0.458 Sum_probs=112.8
Q ss_pred CHHHHHHHHHHH-cccCCCccEEEEEEE-ccCCCCCCceeeeEEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCeechHH
Q 022012 184 DLMDAIKQVKAN-AKATFDETVEAHVRL-AIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADIVGGLE 261 (304)
Q Consensus 184 sl~EAIr~lke~-a~rkF~ETVEL~I~L-nvD~kK~d~~~rGsV~LPh~~gK~~KIlVFadgd~aeeAkeAGAd~VGgeE 261 (304)
.+.|||+.+++. ..++|+||||++|+| ++|++|+++++||+|.|||++|+..+|||||+++.+++|+++||++|||.|
T Consensus 6 ~~~eai~~~k~~~~~~kf~esvel~v~Lk~id~~k~~~~irg~i~LP~~~~k~~~V~vf~~~~~~~~Ak~aGa~~v~~~e 85 (215)
T PRK04203 6 KIEEAVKEALEEAPKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIAKGELALQAKEAGADYVITRE 85 (215)
T ss_pred HHHHHHHHHHHhcccCCCCceEEEEEEecCCCCCccCceeeEEEECCCCCCCCcEEEEEcChHhHHHHHHcCCCEEeCHH
Confidence 378999999985 599999999999999 999999999999999999999999999999999999999999999888888
Q ss_pred HHHHHHhCC-------cccccEEEEcCcchhHHHh-hhhccCCCCCCCCCC
Q 022012 262 LIEEIASSG-------KLDVEKCFSTRQFMPRLFK-ISKILNQHGLMPNPK 304 (304)
Q Consensus 262 LIeKIkk~g-------kLdFD~~IATpdmMpkL~k-LGriLGPRGLMPnpK 304 (304)
+|++|.+ + +.+||+||||++||+.|++ ||++||||||||+||
T Consensus 86 ~L~~i~~-~~k~~rkl~~~fD~~lA~~~im~~l~k~LGk~lgprgkmP~p~ 135 (215)
T PRK04203 86 ELEELGG-DKRAAKKLANEYDFFIAEADLMPLIGRYLGPVLGPRGKMPTPL 135 (215)
T ss_pred HHHHHhc-ChHHHhhhhhcCCEEEECHHHHHHHHHHHhhhcCcCCCCCCCc
Confidence 8999973 4 3499999999999999998 999999999999986
No 7
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=99.97 E-value=7.1e-31 Score=237.86 Aligned_cols=118 Identities=18% Similarity=0.326 Sum_probs=110.0
Q ss_pred CHHHHHHHHH-HHcccCCCccEEEEEEE-ccCCCCCCceeeeEEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCeechHH
Q 022012 184 DLMDAIKQVK-ANAKATFDETVEAHVRL-AIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADIVGGLE 261 (304)
Q Consensus 184 sl~EAIr~lk-e~a~rkF~ETVEL~I~L-nvD~kK~d~~~rGsV~LPh~~gK~~KIlVFadgd~aeeAkeAGAd~VGgeE 261 (304)
.+.|||+.++ ....++|+||||++|+| |+|+++ ++++||+|.|||+.|+..+|||||+++++++|+++||+++|.+|
T Consensus 8 ~i~~Av~~~lk~~~~~kF~Etvdl~v~Lk~iDp~k-d~~irg~v~LPhg~gk~~kV~v~~~~~~~~~Ak~aGad~v~~e~ 86 (214)
T PTZ00225 8 TLSEAIQAVLKVDKERKFKESIDLQVNLKNYDPQK-DKRFSGSLKLPNVCRPRMTVCLLCDLVHEDIAKKEGVPTMNQEE 86 (214)
T ss_pred HHHHHHHHHHHhcccCCCCceEEEEEeccCcCCCc-CcccceeEECCCCCCCCcEEEEECChHHHHHHHHCCCCEECHHH
Confidence 4889999966 55599999999999999 999998 99999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCc------ccccEEEEcCcchhHHHh-hhhccCCCCCCCCC
Q 022012 262 LIEEIASSGK------LDVEKCFSTRQFMPRLFK-ISKILNQHGLMPNP 303 (304)
Q Consensus 262 LIeKIkk~gk------LdFD~~IATpdmMpkL~k-LGriLGPRGLMPnp 303 (304)
|++.++ ++| .+||+||||++||+.|++ ||+.|||+|+||++
T Consensus 87 l~~l~k-~~~~~kkl~~~fD~fiA~~~~m~~lgk~LGp~~~p~gK~P~~ 134 (214)
T PTZ00225 87 LKKLNK-NKKLVKKMCNQYDAFLCSESIIKTVPRLVGPHMHRMGKFPTV 134 (214)
T ss_pred HHHHHh-ccHHHHHHHhhCCEEEECHHHHHhhhhhcCCCCCcCCCCCcc
Confidence 998887 565 589999999999999999 99999999999986
No 8
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=99.96 E-value=1.7e-29 Score=228.60 Aligned_cols=119 Identities=22% Similarity=0.348 Sum_probs=106.9
Q ss_pred CHHHHHHHHHH--Hc-ccCCCccEEEEEEE-ccCCCCCCceeeeEEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCeech
Q 022012 184 DLMDAIKQVKA--NA-KATFDETVEAHVRL-AIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADIVGG 259 (304)
Q Consensus 184 sl~EAIr~lke--~a-~rkF~ETVEL~I~L-nvD~kK~d~~~rGsV~LPh~~gK~~KIlVFadgd~aeeAkeAGAd~VGg 259 (304)
.+.+||+.+++ .. .++|+||||++|+| ++|+++ ++++||+|.|||++|+..+|||||+++.+++|+++||++||+
T Consensus 8 ~~~~av~~~~~~~~~~~~~f~esv~~~i~Lk~id~~~-~~~ir~~v~LP~~~gk~~~v~V~a~~~~~~~Ak~aGa~vvg~ 86 (216)
T PTZ00029 8 ALRKAIAEILEGSEEKKRKFVETVELQIGLKDYDTQK-DKRFSGSVKLPNVPKPNLKVCVLGDAVHCDEAKKLGLDFMDI 86 (216)
T ss_pred HHHHHHHHHHhhccccccCCceEEEEEEEcCCCCCCc-CcccceeEecCCCCCCCcEEEEECCcHHHHHHHHcCCCEecH
Confidence 47899999996 33 99999999999999 899998 999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHh----CCc-ccccEEEEcCcchhHHHh-hhhccCCCCCCCCC
Q 022012 260 LELIEEIAS----SGK-LDVEKCFSTRQFMPRLFK-ISKILNQHGLMPNP 303 (304)
Q Consensus 260 eELIeKIkk----~gk-LdFD~~IATpdmMpkL~k-LGriLGPRGLMPnp 303 (304)
+||++.+++ +++ .+||+||||+++|+.|++ ||+.|+|+|+||.+
T Consensus 87 edL~~~~k~~k~~kkl~~~fD~flA~~~im~~l~riLGp~l~p~~K~P~~ 136 (216)
T PTZ00029 87 EGLKKFNKNKKLVKKLAKKYDAFLASQSLLPQIPRLLGPGLNKAGKFPTL 136 (216)
T ss_pred HHHHHhhhhHHHHhcccccCCEEEECHHHHHHHHHHhccccccCCCCCCc
Confidence 999984331 344 389999999999999988 88888888888865
No 9
>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=99.92 E-value=4.6e-25 Score=194.59 Aligned_cols=119 Identities=45% Similarity=0.673 Sum_probs=109.5
Q ss_pred HHHHHHHHHHHc--ccCCCccEEEEEEEccCCCCCCceeeeEEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCeechHHH
Q 022012 185 LMDAIKQVKANA--KATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADIVGGLEL 262 (304)
Q Consensus 185 l~EAIr~lke~a--~rkF~ETVEL~I~LnvD~kK~d~~~rGsV~LPh~~gK~~KIlVFadgd~aeeAkeAGAd~VGgeEL 262 (304)
+.+||+.+++.+ ...|+++|+|+|+|+....+++.+++|.|.|||++++..+|||||++.++++|+++||++||+++|
T Consensus 1 ~~~Ai~~l~~~~~~~~~~~~~v~l~i~l~~~~~~~~~~~~~~i~LPh~~~~~~~i~v~~~d~~~~~a~~~~a~vig~~~L 80 (208)
T cd00403 1 LEEAIKALKKTSVKKRKFDETVELQINLKKDDRKKDQRIRGTVILPHGLGKDVKVCVFAKDEQAKEAKAAGADVVGGEDL 80 (208)
T ss_pred CHHHHHHHHHhccccCCCCceEEEEEEeCCCCCccccccceeEECCCCCCCCeEEEEEcChHhHHHHHHcCCCEEcHHHH
Confidence 368999999988 889999999999997665566889999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCc-----ccccEEEEcCcchhHHHh-hhhccCCCCCCCCCC
Q 022012 263 IEEIASSGK-----LDVEKCFSTRQFMPRLFK-ISKILNQHGLMPNPK 304 (304)
Q Consensus 263 IeKIkk~gk-----LdFD~~IATpdmMpkL~k-LGriLGPRGLMPnpK 304 (304)
+++++ .++ .+||+|||++++|+.+.+ ||++||+||+||+++
T Consensus 81 ~~~~~-~~~~~~l~~~~D~fla~~~~~~~~~~~lgk~~~~k~k~P~~~ 127 (208)
T cd00403 81 KKKIK-NGEAKKLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKMPNPK 127 (208)
T ss_pred HHHhh-cchhhhhhhcCCEEEECHHHHHHHHHHhccccccCCCCCcCC
Confidence 99998 455 489999999999999987 999999999999985
No 10
>KOG1569 consensus 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=5.6e-23 Score=194.70 Aligned_cols=127 Identities=29% Similarity=0.493 Sum_probs=112.5
Q ss_pred cccCCCCccCHHHHHHHHHHHc----ccCCCccEEEEEEEccCCC---CCCceeeeEEEcCCCCC--CCcEEEEEcCc-h
Q 022012 175 KKKESRPVLDLMDAIKQVKANA----KATFDETVEAHVRLAIPPR---KTELIVRGTMNLPHGDK--KAVRVAFFAEG-A 244 (304)
Q Consensus 175 ~k~ek~~~ysl~EAIr~lke~a----~rkF~ETVEL~I~LnvD~k---K~d~~~rGsV~LPh~~g--K~~KIlVFadg-d 244 (304)
+...+++.|++.+|+..+|++. ....++++.+.|.||+... |+...+.|++..||+++ ..++|+||++| .
T Consensus 82 Kr~~kr~~y~vq~a~~~~ke~~~~sa~~~pk~~~~l~i~l~~~a~~~~k~~~~~~~~v~vP~Pf~~ge~r~IavFtn~~~ 161 (323)
T KOG1569|consen 82 KRLYKRQIYEVQKAVHLHKELQILSAYNVPKQPVNLRIELNMLAEKETKGVAPLQGSVTVPHPFAHGEIRKIAVFTNDAS 161 (323)
T ss_pred hhhcCcchhhHHHHHHHHHHhccchhhhCCCCceeeeEEeeeeeeeeccccCCCceeEeccccCCCCceEEEEEecCChH
Confidence 3446779999999999999987 4456799999999987643 45678999999999994 46789999999 7
Q ss_pred hHHHHHHcCCCeechHHHHHHHHhCCcc--cccEEEEcCcchhHHHhhhhccCCCCCCCCCC
Q 022012 245 DAEEARAAGADIVGGLELIEEIASSGKL--DVEKCFSTRQFMPRLFKISKILNQHGLMPNPK 304 (304)
Q Consensus 245 ~aeeAkeAGAd~VGgeELIeKIkk~gkL--dFD~~IATpdmMpkL~kLGriLGPRGLMPnpK 304 (304)
..++|+++||++|||.|||++|. +|.| |||+||||||||+.|..|+++|||| |||+|
T Consensus 162 kveeArEaGA~l~GG~dLIkkI~-~Gei~~Dyd~~vA~Pdim~~l~~Lr~iL~~r--~Pn~k 220 (323)
T KOG1569|consen 162 KVEEAREAGAALAGGTDLIKKIK-SGEIVADYDFYVAHPDIMPELNRLRKILGPR--FPNPK 220 (323)
T ss_pred HHHHHHhccccccccHHHHHHhh-cCeEEEeeceeeecchHHHHHHHHHHHhccc--CCCcc
Confidence 89999999999999999999998 6887 8889999999999999999999998 99997
No 11
>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=99.79 E-value=4.9e-19 Score=157.00 Aligned_cols=106 Identities=31% Similarity=0.535 Sum_probs=92.8
Q ss_pred ccCCCccEEEEEEEccCCCCCCcee-eeEEEcCCCCC-CCcEEEEEcCchhHH---------HHHHcCCCeechHHHHHH
Q 022012 197 KATFDETVEAHVRLAIPPRKTELIV-RGTMNLPHGDK-KAVRVAFFAEGADAE---------EARAAGADIVGGLELIEE 265 (304)
Q Consensus 197 ~rkF~ETVEL~I~LnvD~kK~d~~~-rGsV~LPh~~g-K~~KIlVFadgd~ae---------eAkeAGAd~VGgeELIeK 265 (304)
..+++++|+|+|.+...+.+.+.++ +|.|.|||++. +..+||||+++.++. ++.++|++++|+++|+++
T Consensus 17 ~~~~~~~v~l~i~~~~~~~~~~~~~~~~~i~LPh~~~~~~~~vcli~~d~~~~~~~~~~~~~~~~~~~~~vi~~~~L~~~ 96 (220)
T PF00687_consen 17 DDNFDESVYLQITLKKIPKKKDKSFKPGRIPLPHPLYIKNSKVCLIVKDPQKKAKEKEKLEEKAVEAGAKVIGGEELKKK 96 (220)
T ss_dssp CSSSSTEEEEEEEESSSTTSSCTST-EEEEEBSTSSS-SSSBEEEEESCHHHHHH-------HHHHTTCSEEECHHHHHH
T ss_pred cCCCCcEEEEEEEeCcCCCccccccccceeeecCCCCCCccEEEEEecCcchhhhhhhhhhhhhhhcccceecHHHHHHH
Confidence 7789999999999976666656777 99999999998 899999999875543 356789999999999999
Q ss_pred ---HHhCCc-c--cccEEEEcCcchhHHHh-hhhcc-CCCCCCCCC
Q 022012 266 ---IASSGK-L--DVEKCFSTRQFMPRLFK-ISKIL-NQHGLMPNP 303 (304)
Q Consensus 266 ---Ikk~gk-L--dFD~~IATpdmMpkL~k-LGriL-GPRGLMPnp 303 (304)
+. +++ + +||+|||++++|+.|.+ ||++| |++|+||++
T Consensus 97 ~~~~~-~~r~l~~~~d~flad~~i~~~l~~~Lgk~~~~~k~k~P~~ 141 (220)
T PF00687_consen 97 YKTIE-AKRKLAKSYDFFLADPRIMPKLPKLLGKIFYGKKGKMPIP 141 (220)
T ss_dssp HCHHH-HCHHHHHCSSEEEEEGGGHHHHHHHTHHHH-CCTTTSCEE
T ss_pred HHHHH-HHHHHHhhcCEEEECHHHHHHHHHhhhhheecccCCcceE
Confidence 66 455 3 89999999999999999 99999 999999975
No 12
>KOG1570 consensus 60S ribosomal protein L10A [Translation, ribosomal structure and biogenesis]
Probab=99.62 E-value=2.2e-16 Score=143.81 Aligned_cols=121 Identities=19% Similarity=0.360 Sum_probs=108.0
Q ss_pred ccCHHHHHHHHHHHc----ccCCCccEEEEEEE-ccCCCCCCceeeeEEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCe
Q 022012 182 VLDLMDAIKQVKANA----KATFDETVEAHVRL-AIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADI 256 (304)
Q Consensus 182 ~ysl~EAIr~lke~a----~rkF~ETVEL~I~L-nvD~kK~d~~~rGsV~LPh~~gK~~KIlVFadgd~aeeAkeAGAd~ 256 (304)
.+++.+||..+.-.+ .++|.+||+++|+| |+|+.| +.+|.|++.|||...+..+||||+|..++++|++.|.++
T Consensus 7 ~~~l~~~v~~i~~~~~~~k~~~~~~tielQi~Lk~ydp~K-dkr~s~~~~l~~~~~p~~k~cv~gd~~h~~~ak~~~~p~ 85 (218)
T KOG1570|consen 7 EEALREAVAEILLRSKEFKNRNFVETIELQINLKNYDPQK-DKRFSGSVKLPHAPRPKMKVCVIGDQQHCDEAKAIDLPA 85 (218)
T ss_pred HHHHHHHHHHHHhccccccCccceeeeeeeecccccChhH-hCcccceEecCCCCCccceeeeechHHHHHHhhcCCCCC
Confidence 456778887777544 78899999999999 999999 899999999999999999999999999999999999999
Q ss_pred echHHHHHHHHhCCcc------cccEEEEcCcchhHHHh-hhhccCCCCCCCCCC
Q 022012 257 VGGLELIEEIASSGKL------DVEKCFSTRQFMPRLFK-ISKILNQHGLMPNPK 304 (304)
Q Consensus 257 VGgeELIeKIkk~gkL------dFD~~IATpdmMpkL~k-LGriLGPRGLMPnpK 304 (304)
+--++ ++++.++++| .||+|||+.+++.+|.+ ||+.|...|++|++.
T Consensus 86 m~~d~-lkklnk~Kklvkklakky~~flase~~ikQlpr~lgp~l~kaGkfps~l 139 (218)
T KOG1570|consen 86 MDIDA-LKKLNKNKKLVKKLAKKYDAFLASESLIKQLPRILGPGLSKAGKFPSLL 139 (218)
T ss_pred cCHHH-HhcCcccchHHHHHHHHhhhHHhhHHHHHHhhhhhcccccccccCCccc
Confidence 99665 4888765665 79999999999999998 999999999999864
No 13
>PF13003 MRL1: Ribosomal protein L1; InterPro: IPR024663 This entry represents a ribosomal protein L1 domain found mainly in chordates.
Probab=96.64 E-value=0.0043 Score=53.92 Aligned_cols=64 Identities=20% Similarity=0.232 Sum_probs=50.4
Q ss_pred cCCCCccCHHHHHHHHHHHcccCC---CccEEEEEEEccC--CCCCCceeeeEEEcCCCCCC-CcEEEEE
Q 022012 177 KESRPVLDLMDAIKQVKANAKATF---DETVEAHVRLAIP--PRKTELIVRGTMNLPHGDKK-AVRVAFF 240 (304)
Q Consensus 177 ~ek~~~ysl~EAIr~lke~a~rkF---~ETVEL~I~LnvD--~kK~d~~~rGsV~LPh~~gK-~~KIlVF 240 (304)
-...+.|.+++||.+|+.+..-.| .+.|.+.++||+- .+|...+|-+.|.|||++.. -.+|+||
T Consensus 64 lyPr~Iyeve~Ai~mLKkfQ~lDfT~pkQ~VYldL~Ldm~l~KKkkVePF~s~i~lPypF~~eiNKv~VF 133 (133)
T PF13003_consen 64 LYPRPIYEVEKAIDMLKKFQILDFTSPKQPVYLDLTLDMKLEKKKKVEPFASVILLPYPFTSEINKVLVF 133 (133)
T ss_pred eccccHHHHHHHHHHHHhcccccCCCCCCcEEEeeeehhhhccccccCCCccceecccccccccceeeeC
Confidence 355688999999999999886666 4678888888664 34446799999999999944 4689987
No 14
>KOG1685 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.83 E-value=1.1 Score=44.43 Aligned_cols=70 Identities=19% Similarity=0.278 Sum_probs=52.8
Q ss_pred CCcEEEEEcCchh--------H-HHHHHcCCC----eechHHHHHHHHh---CCcc--cccEEEEcCcchhHHHh-hhhc
Q 022012 233 KAVRVAFFAEGAD--------A-EEARAAGAD----IVGGLELIEEIAS---SGKL--DVEKCFSTRQFMPRLFK-ISKI 293 (304)
Q Consensus 233 K~~KIlVFadgd~--------a-eeAkeAGAd----~VGgeELIeKIkk---~gkL--dFD~~IATpdmMpkL~k-LGri 293 (304)
.+..||+|.++.+ + +.-.++|.. ++++..|=.+.+. ..+| +||+|||.-.+++.|.+ ||+.
T Consensus 87 ~~~~vcLIvkD~~~~~~t~~~~~d~l~~~gi~~itkVI~~~~LK~~yksyeaKr~L~~sfDlflaD~RV~~~LP~llGK~ 166 (343)
T KOG1685|consen 87 DDTDVCLIVKDLQQSYLTEEDAEDLLESEGIKSITKVISLSKLKRDYKSYEAKRKLLSSFDLFLADDRVIPLLPKLLGKE 166 (343)
T ss_pred CCCceEEEecCchhccccHHHHHHHHHHcCCccceeeeehHHHHHHHHHHHHHHHHHhhccEEEEcchhHhHHHHHhhhh
Confidence 4678999998732 2 445678987 7888887444433 2235 79999999999999999 9998
Q ss_pred cCCCCCCCC
Q 022012 294 LNQHGLMPN 302 (304)
Q Consensus 294 LGPRGLMPn 302 (304)
.-.+.+.|-
T Consensus 167 f~q~kk~Pv 175 (343)
T KOG1685|consen 167 FYQKKKVPV 175 (343)
T ss_pred hcccccCce
Confidence 887777764
No 15
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=82.67 E-value=0.58 Score=43.05 Aligned_cols=16 Identities=31% Similarity=0.436 Sum_probs=14.1
Q ss_pred HhhhhccCCCCCCCCCC
Q 022012 288 FKISKILNQHGLMPNPK 304 (304)
Q Consensus 288 ~kLGriLGPRGLMPnpK 304 (304)
..||++||| ||||++|
T Consensus 117 ~~l~riLGp-~l~p~~K 132 (216)
T PTZ00029 117 PQIPRLLGP-GLNKAGK 132 (216)
T ss_pred HHHHHHhcc-ccccCCC
Confidence 348999999 9999987
No 16
>COG1064 AdhP Zn-dependent alcohol dehydrogenases [General function prediction only]
Probab=67.74 E-value=8.8 Score=38.10 Aligned_cols=61 Identities=21% Similarity=0.218 Sum_probs=42.1
Q ss_pred cEEEEEcCc-hhHHHHHHcCCCeech---HHHHHHHHhCCcccccEEEEcCcchhHHHhhhhccCCCCCC
Q 022012 235 VRVAFFAEG-ADAEEARAAGADIVGG---LELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLM 300 (304)
Q Consensus 235 ~KIlVFadg-d~aeeAkeAGAd~VGg---eELIeKIkk~gkLdFD~~IATpdmMpkL~kLGriLGPRGLM 300 (304)
-+|.+|..+ +..+.|++.||+++-. ++.++++++ + ||.+|-|-. -..+...-+.|.+.|.|
T Consensus 191 a~Via~~~~~~K~e~a~~lGAd~~i~~~~~~~~~~~~~---~-~d~ii~tv~-~~~~~~~l~~l~~~G~~ 255 (339)
T COG1064 191 AEVIAITRSEEKLELAKKLGADHVINSSDSDALEAVKE---I-ADAIIDTVG-PATLEPSLKALRRGGTL 255 (339)
T ss_pred CeEEEEeCChHHHHHHHHhCCcEEEEcCCchhhHHhHh---h-CcEEEECCC-hhhHHHHHHHHhcCCEE
Confidence 566667665 5567788888886654 556666652 2 999999988 66676666777776643
No 17
>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=64.55 E-value=17 Score=29.31 Aligned_cols=65 Identities=11% Similarity=0.074 Sum_probs=39.3
Q ss_pred CCcEEEEEcCch---------hHHHHHHcCCCeechHHHHHHHHhCCcccccEEEEcCcchhHHHhhhhccCCCC
Q 022012 233 KAVRVAFFAEGA---------DAEEARAAGADIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHG 298 (304)
Q Consensus 233 K~~KIlVFadgd---------~aeeAkeAGAd~VGgeELIeKIkk~gkLdFD~~IATpdmMpkL~kLGriLGPRG 298 (304)
+..+|+++|.+- ..+.|++.|.++--..-=+.++.. .--+||++|.+|.+--.+..+-..+...|
T Consensus 2 ~~~~ILl~C~~G~sSS~l~~k~~~~~~~~gi~~~v~a~~~~~~~~-~~~~~Dvill~pqi~~~~~~i~~~~~~~~ 75 (95)
T TIGR00853 2 NETNILLLCAAGMSTSLLVNKMNKAAEEYGVPVKIAAGSYGAAGE-KLDDADVVLLAPQVAYMLPDLKKETDKKG 75 (95)
T ss_pred CccEEEEECCCchhHHHHHHHHHHHHHHCCCcEEEEEecHHHHHh-hcCCCCEEEECchHHHHHHHHHHHhhhcC
Confidence 346899998751 234466677764211111223321 11279999999999888877777665543
No 18
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=60.52 E-value=15 Score=30.50 Aligned_cols=52 Identities=12% Similarity=0.098 Sum_probs=41.6
Q ss_pred cEEEEEcCchhHHHHHHcCCC---eechHHHHHHHHhCCcc---cccEEEEcCcchhHHH
Q 022012 235 VRVAFFAEGADAEEARAAGAD---IVGGLELIEEIASSGKL---DVEKCFSTRQFMPRLF 288 (304)
Q Consensus 235 ~KIlVFadgd~aeeAkeAGAd---~VGgeELIeKIkk~gkL---dFD~~IATpdmMpkL~ 288 (304)
.||+|+++.+.+---+.+|.+ .+..++..+++.+ .+ +|=+++.|.++...+.
T Consensus 3 ~kIaVvGd~DtilGFrlaGi~~v~~~~~~e~~~~~~~--~l~~~~~gII~iTE~~a~~i~ 60 (104)
T PRK01189 3 SCITVIGERDVVLGFRLLGIGDTIEAEGKDLVKKFLE--IFNNPKCKYIFVSESTKNMFD 60 (104)
T ss_pred ceEEEEcCHHHHHHHHHcCCceEEEcCCHHHHHHHHH--HHhcCCeEEEEEEHHHHhhCC
Confidence 379999999988888889996 5566666666653 34 6999999999988887
No 19
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=58.47 E-value=5.4 Score=36.93 Aligned_cols=16 Identities=13% Similarity=0.146 Sum_probs=13.6
Q ss_pred HhhhhccCCCCCCCCCC
Q 022012 288 FKISKILNQHGLMPNPK 304 (304)
Q Consensus 288 ~kLGriLGPRGLMPnpK 304 (304)
..|||+|||+|+ |+.|
T Consensus 115 ~~lgk~LGp~~~-p~gK 130 (214)
T PTZ00225 115 KTVPRLVGPHMH-RMGK 130 (214)
T ss_pred HhhhhhcCCCCC-cCCC
Confidence 348999999997 9987
No 20
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=54.93 E-value=25 Score=28.57 Aligned_cols=60 Identities=18% Similarity=0.153 Sum_probs=42.4
Q ss_pred cEEEEEcCchhHHHHHHcCCC--e-ech-HHHHHHHHh-CCcccccEEEEcCcchhHHHh-hhhcc
Q 022012 235 VRVAFFAEGADAEEARAAGAD--I-VGG-LELIEEIAS-SGKLDVEKCFSTRQFMPRLFK-ISKIL 294 (304)
Q Consensus 235 ~KIlVFadgd~aeeAkeAGAd--~-VGg-eELIeKIkk-~gkLdFD~~IATpdmMpkL~k-LGriL 294 (304)
.||+|++|.+.+.--+-+|+. + +.. +|+.+.|++ -..=+|-.++.|.++...+.. +.+.+
T Consensus 1 mkIaVIGD~dtv~GFrLaGi~~~~~~~~~ee~~~~l~~l~~~~d~gII~Ite~~~~~i~e~i~~~~ 66 (100)
T PRK02228 1 MEIAVIGSPEFTTGFRLAGIRKVYEVPDDEKLDEAVEEVLEDDDVGILVMHDDDLEKLPRRLRRTL 66 (100)
T ss_pred CEEEEEeCHHHHHHHHHcCCceEEeeCCHHHHHHHHHHHhhCCCEEEEEEehhHhHhhHHHHHHHH
Confidence 489999998888888999996 3 355 344444432 011279999999999888876 65533
No 21
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=51.55 E-value=48 Score=27.39 Aligned_cols=65 Identities=15% Similarity=0.274 Sum_probs=44.9
Q ss_pred cEEEEEcCchhHHHHHHcCCCe---echHHHHHHHHhCCcccccEEEEcCcchhHHHh-hhhccCCCCCCC
Q 022012 235 VRVAFFAEGADAEEARAAGADI---VGGLELIEEIASSGKLDVEKCFSTRQFMPRLFK-ISKILNQHGLMP 301 (304)
Q Consensus 235 ~KIlVFadgd~aeeAkeAGAd~---VGgeELIeKIkk~gkLdFD~~IATpdmMpkL~k-LGriLGPRGLMP 301 (304)
.||+|++|.+.+.=-+-+|++. .+.+++.+.|.+-..=+|-+++.|.++...+.. +.+. . +..+|
T Consensus 4 ~kIaVIGD~dtv~GFrLaGi~~~~v~~~ee~~~~i~~l~~~d~gII~Ite~~a~~i~~~i~~~-~-~~~~P 72 (104)
T PRK01395 4 YKIGVVGDKDSILPFKALGIDVFPVIDEQEAINTLRKLAMEDYGIIYITEQIAADIPETIERY-D-NQVLP 72 (104)
T ss_pred eeEEEEECHHHHHHHHHcCCeeEEecChHHHHHHHHHHhcCCcEEEEEcHHHHHHhHHHHHHh-c-CCCCC
Confidence 4899999988888888899873 344555554542001179999999999999976 5544 3 44444
No 22
>PRK13958 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=47.19 E-value=12 Score=34.08 Aligned_cols=25 Identities=20% Similarity=0.189 Sum_probs=23.0
Q ss_pred cEEEEEcCchhHHHHHHcCCCeech
Q 022012 235 VRVAFFAEGADAEEARAAGADIVGG 259 (304)
Q Consensus 235 ~KIlVFadgd~aeeAkeAGAd~VGg 259 (304)
.|||=+.+.+++..|.++|||++|-
T Consensus 3 vKICGit~~eda~~~~~~GaD~iGf 27 (207)
T PRK13958 3 LKFCGFTTIKDVTAASQLPIDAIGF 27 (207)
T ss_pred EEEcCCCcHHHHHHHHHcCCCEEEE
Confidence 6899999999999999999999984
No 23
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=45.84 E-value=41 Score=27.64 Aligned_cols=59 Identities=17% Similarity=0.225 Sum_probs=39.0
Q ss_pred EEEEEcCc---------hhHHHHHHcCCCee---chHHHHHHHHhCCcc-cccEEEEcCcchhHHHhhhhccCCCCC
Q 022012 236 RVAFFAEG---------ADAEEARAAGADIV---GGLELIEEIASSGKL-DVEKCFSTRQFMPRLFKISKILNQHGL 299 (304)
Q Consensus 236 KIlVFadg---------d~aeeAkeAGAd~V---GgeELIeKIkk~gkL-dFD~~IATpdmMpkL~kLGriLGPRGL 299 (304)
+|+++|.+ ...+.|++.|.++- .+. .++.. .+ +||.++.+|.+--.+..+-..+++.|.
T Consensus 2 ~Ill~C~~GaSSs~la~km~~~a~~~gi~~~i~a~~~---~e~~~--~~~~~Dvill~PQv~~~~~~i~~~~~~~~i 73 (99)
T cd05565 2 NVLVLCAGGGTSGLLANALNKGAKERGVPLEAAAGAY---GSHYD--MIPDYDLVILAPQMASYYDELKKDTDRLGI 73 (99)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeeH---HHHHH--hccCCCEEEEcChHHHHHHHHHHHhhhcCC
Confidence 68888864 12355777787642 222 22321 22 799999999998888888887777653
No 24
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=43.30 E-value=77 Score=26.19 Aligned_cols=60 Identities=13% Similarity=0.150 Sum_probs=37.8
Q ss_pred EEEEEcCch---------hHHHHHHcCCCe----echHHHHHHHHhCCcccccEEEEcCcchhHHHhhhhccCCCC
Q 022012 236 RVAFFAEGA---------DAEEARAAGADI----VGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHG 298 (304)
Q Consensus 236 KIlVFadgd---------~aeeAkeAGAd~----VGgeELIeKIkk~gkLdFD~~IATpdmMpkL~kLGriLGPRG 298 (304)
||+++|.+- ..+.|++.|.++ ++..++ +... ..-+||.+|.+|.+--.+..+-.++.++|
T Consensus 3 kILlvCg~G~STSlla~k~k~~~~e~gi~~~i~a~~~~e~-~~~~--~~~~~DvIll~PQi~~~~~~i~~~~~~~~ 75 (104)
T PRK09590 3 KALIICAAGMSSSMMAKKTTEYLKEQGKDIEVDAITATEG-EKAI--AAAEYDLYLVSPQTKMYFKQFEEAGAKVG 75 (104)
T ss_pred EEEEECCCchHHHHHHHHHHHHHHHCCCceEEEEecHHHH-HHhh--ccCCCCEEEEChHHHHHHHHHHHHhhhcC
Confidence 688888751 234466677764 444443 3221 12369999999998777776766665544
No 25
>COG0135 TrpF Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism]
Probab=40.57 E-value=17 Score=33.71 Aligned_cols=25 Identities=36% Similarity=0.501 Sum_probs=22.9
Q ss_pred CcEEEEEcCchhHHHHHHcCCCeec
Q 022012 234 AVRVAFFAEGADAEEARAAGADIVG 258 (304)
Q Consensus 234 ~~KIlVFadgd~aeeAkeAGAd~VG 258 (304)
..|||=++..++++.|-++||||+|
T Consensus 3 ~vKICGlt~~eda~~a~~~gad~iG 27 (208)
T COG0135 3 KVKICGLTRLEDAKAAAKAGADYIG 27 (208)
T ss_pred ceEECCCCCHHHHHHHHHcCCCEEE
Confidence 4789999999999999999999987
No 26
>PF00697 PRAI: N-(5'phosphoribosyl)anthranilate (PRA) isomerase; InterPro: IPR001240 Indole-3-glycerol phosphate synthase (IGPS) (see IPR001468 from INTERPRO) catalyzes the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyzes N-(5-phosphoribosyl)anthranilate isomerase (PRAI) activity, the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (GATase) N-terminal domain (see IPR000991 from INTERPRO). Phosphoribosylanthranilate isomerase (PRAI) is monomeric and labile in most mesophilic microorganisms, but dimeric and stable in the hyperthermophile Thermotoga maritima (tPRAI) []. The comparison to the known 2.0 A structure of PRAI from Escherichia coli (ePRAI) shows that tPRAI has the complete TIM- or (beta alp ha)8-barrel fold, whereas helix alpha5 in ePRAI is replaced by a loop. The subunits of tPRAI associate via the N-terminal faces of their central beta-barrels. Two long, symmetry-related loops that protrude reciprocally into cavities of the other subunit provide for multiple hydrophobic interactions. Moreover, the side chains of the N-terminal methionines and the C-terminal leucines of both subunits are immobilized in a hydrophobic cluster, and the number of salt bridges is increased in tPRAI. These features appear to be mainly responsible for the high thermostability of tPRAI []. ; GO: 0004640 phosphoribosylanthranilate isomerase activity, 0006568 tryptophan metabolic process; PDB: 1V5X_A 1PII_A 1JCM_P 2KZH_A 1LBM_A 1DL3_A 1NSJ_A.
Probab=40.44 E-value=21 Score=31.86 Aligned_cols=59 Identities=20% Similarity=0.178 Sum_probs=34.4
Q ss_pred cEEEEEcCchhHHHHHHcCCCeech-----------HHHHHHHHhCCccc-ccEEEEcCcchhHHHhhhhccC
Q 022012 235 VRVAFFAEGADAEEARAAGADIVGG-----------LELIEEIASSGKLD-VEKCFSTRQFMPRLFKISKILN 295 (304)
Q Consensus 235 ~KIlVFadgd~aeeAkeAGAd~VGg-----------eELIeKIkk~gkLd-FD~~IATpdmMpkL~kLGriLG 295 (304)
+|||=+.+.+++..|.++|+|++|- .+.+.+|. .++. .-+.+.....+..+..+...++
T Consensus 1 vKICGi~~~~da~~~~~~g~d~~Gfi~~~~S~R~v~~~~a~~l~--~~~~~~~VgVf~~~~~~~I~~~~~~~~ 71 (197)
T PF00697_consen 1 VKICGITRPEDARLAAELGADYLGFIFYPKSPRYVSPDQARELV--SAVPPKIVGVFVNQSPEEILEIVEELG 71 (197)
T ss_dssp EEEE---SHHHHHHHHHHTSSEEEEE--TTCTTB--HHHHHHHH--CCSSSSEEEEESSS-HHHHHHHHHHCT
T ss_pred CeECCCCcHHHHHHHHHcCCCEEeeecCCCCCCccCHHHHHHHH--HhcCCCEEEEEcCCCHHHHHHHHHHcC
Confidence 4899999999999999999999984 23334443 2332 2334444445555655555444
No 27
>cd05564 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins from chbA, chbB, and chbC of the chb operon (formerly the cel (cellulose) operon). In the lichenan system, these subunits are expressed from licA, licB, and licC of the lic operon. The lic operon of Bacillus subtilis is required for the transport and degradation of oligomeric beta-glucosides, which are produced by extracellular enzymes on substrates such as lichenan or barley glucan. The lic operon is transcribed from a gammaA-dependent promoter and is inducible by lichenan, lichenan hydrolysate, and cellobiose. The IIB d
Probab=38.62 E-value=60 Score=25.93 Aligned_cols=60 Identities=13% Similarity=0.021 Sum_probs=33.7
Q ss_pred EEEEEcCc---------hhHHHHHHcCCCeechHHHHHHHHhCCcccccEEEEcCcchhHHHhhhhccCC
Q 022012 236 RVAFFAEG---------ADAEEARAAGADIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQ 296 (304)
Q Consensus 236 KIlVFadg---------d~aeeAkeAGAd~VGgeELIeKIkk~gkLdFD~~IATpdmMpkL~kLGriLGP 296 (304)
||+++|.+ ...+.+++.|.++--..-=+.++.. .--+||.+|.+|.+.-.+..+-+.+.+
T Consensus 1 kIl~~Cg~G~sTS~~~~ki~~~~~~~~~~~~v~~~~~~~~~~-~~~~~Diil~~Pqv~~~~~~i~~~~~~ 69 (96)
T cd05564 1 KILLVCSAGMSTSILVKKMKKAAEKRGIDAEIEAVPESELEE-YIDDADVVLLGPQVRYMLDEVKKKAAE 69 (96)
T ss_pred CEEEEcCCCchHHHHHHHHHHHHHHCCCceEEEEecHHHHHH-hcCCCCEEEEChhHHHHHHHHHHHhcc
Confidence 46777764 1224455567653111111233431 123799999999998888777655443
No 28
>PRK01222 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=38.51 E-value=18 Score=32.96 Aligned_cols=26 Identities=35% Similarity=0.418 Sum_probs=23.3
Q ss_pred CcEEEEEcCchhHHHHHHcCCCeech
Q 022012 234 AVRVAFFAEGADAEEARAAGADIVGG 259 (304)
Q Consensus 234 ~~KIlVFadgd~aeeAkeAGAd~VGg 259 (304)
..|||=+.+.++++.|.++|||++|-
T Consensus 4 ~vKICGi~~~eda~~~~~~Gad~iGf 29 (210)
T PRK01222 4 RVKICGITTPEDAEAAAELGADAIGF 29 (210)
T ss_pred eEEECCCCcHHHHHHHHHcCCCEEEE
Confidence 37899899989999999999999985
No 29
>PLN02363 phosphoribosylanthranilate isomerase
Probab=37.47 E-value=19 Score=34.07 Aligned_cols=27 Identities=33% Similarity=0.393 Sum_probs=24.2
Q ss_pred CCcEEEEEcCchhHHHHHHcCCCeech
Q 022012 233 KAVRVAFFAEGADAEEARAAGADIVGG 259 (304)
Q Consensus 233 K~~KIlVFadgd~aeeAkeAGAd~VGg 259 (304)
...|||=+.+.+++..|.++|||++|-
T Consensus 47 ~~VKICGit~~eda~~a~~~GaD~iGf 73 (256)
T PLN02363 47 PLVKMCGITSARDAAMAVEAGADFIGM 73 (256)
T ss_pred ceEEECCCCcHHHHHHHHHcCCCEEEE
Confidence 458999999999999999999999985
No 30
>PRK04148 hypothetical protein; Provisional
Probab=35.84 E-value=92 Score=27.09 Aligned_cols=62 Identities=18% Similarity=0.353 Sum_probs=40.4
Q ss_pred CcEEEEEcCc---hhHHHHHHcCCCeechH---HHHHHHHhCC-------------cc--cccEEEE---cCcchhHHHh
Q 022012 234 AVRVAFFAEG---ADAEEARAAGADIVGGL---ELIEEIASSG-------------KL--DVEKCFS---TRQFMPRLFK 289 (304)
Q Consensus 234 ~~KIlVFadg---d~aeeAkeAGAd~VGge---ELIeKIkk~g-------------kL--dFD~~IA---TpdmMpkL~k 289 (304)
..+|++++-| +.+....+.|.++++.| +.+++++..+ .+ ++|.+.+ .++|++-|.+
T Consensus 17 ~~kileIG~GfG~~vA~~L~~~G~~ViaIDi~~~aV~~a~~~~~~~v~dDlf~p~~~~y~~a~liysirpp~el~~~~~~ 96 (134)
T PRK04148 17 NKKIVELGIGFYFKVAKKLKESGFDVIVIDINEKAVEKAKKLGLNAFVDDLFNPNLEIYKNAKLIYSIRPPRDLQPFILE 96 (134)
T ss_pred CCEEEEEEecCCHHHHHHHHHCCCEEEEEECCHHHHHHHHHhCCeEEECcCCCCCHHHHhcCCEEEEeCCCHHHHHHHHH
Confidence 3567777665 34555566777777665 4455444311 12 6788776 6899999999
Q ss_pred hhhccC
Q 022012 290 ISKILN 295 (304)
Q Consensus 290 LGriLG 295 (304)
|++-+|
T Consensus 97 la~~~~ 102 (134)
T PRK04148 97 LAKKIN 102 (134)
T ss_pred HHHHcC
Confidence 888776
No 31
>cd00405 PRAI Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric, monofunctional and thermolabile, but in some thermophile organisms PRAI is dimeric for reasons of stability and in others it is fused to other components of the tryptophan biosynthesis pathway to form multifunctional enzymes.
Probab=32.17 E-value=29 Score=30.71 Aligned_cols=25 Identities=36% Similarity=0.368 Sum_probs=21.8
Q ss_pred cEEEEEcCchhHHHHHHcCCCeech
Q 022012 235 VRVAFFAEGADAEEARAAGADIVGG 259 (304)
Q Consensus 235 ~KIlVFadgd~aeeAkeAGAd~VGg 259 (304)
.|||=+.+.++++.|.++||+++|-
T Consensus 1 vKiCGi~~~ed~~~a~~~Gvd~ig~ 25 (203)
T cd00405 1 VKICGITTLEDALAAAEAGADAIGF 25 (203)
T ss_pred CEECCCCCHHHHHHHHHcCCCEEEE
Confidence 4788888889999999999999874
No 32
>PF00107 ADH_zinc_N: Zinc-binding dehydrogenase; InterPro: IPR013149 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of alcohols to their corresponding acetaldehyde or ketone with the concomitant reduction of NAD: alcohol + NAD = aldehyde or ketone + NADH Currently three structurally and catalytically different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Zinc-containing ADH's [, ] are dimeric or tetrameric enzymes that bind two atoms of zinc per subunit. One of the zinc atom is essential for catalytic activity while the other is not. Both zinc atoms are coordinated by either cysteine or histidine residues; the catalytic zinc is coordinated by two cysteines and one histidine. Zinc-containing ADH's are found in bacteria, mammals, plants, and in fungi. In many species there is more than one isozyme (for example, humans have at least six isozymes, yeast have three, etc.). A number of other zinc-dependent dehydrogenases are closely related to zinc ADH [] and are included in this family. Sorbitol dehydrogenase (1.1.1.14 from EC) L-threonine 3-dehydrogenase (1.1.1.103 from EC) Glutathione-dependent formaldehyde dehydrogenase (1.1.1.284 from EC) Mannitol dehydrogenase (1.1.1.255 from EC) In addition, this family includes NADP-dependent quinone oxidoreductase (1.6.5.5 from EC), an enzyme found in bacteria (gene qor), in yeast and in mammals where, in some species such as rodents, it has been recruited as an eye lens protein and is known as zeta-crystallin []. The sequence of quinone oxidoreductase is distantly related to that other zinc-containing alcohol dehydrogenases and it lacks the zinc-ligand residues. The torpedo fish and mammalian synaptic vesicle membrane protein vat-1 is related to qor. This entry represents the cofactor-binding domain of these enzymes, which is normally found towards the C terminus. Structural studies indicate that it forms a classical Rossman fold that reversibly binds NAD(H) [, , ].; GO: 0008270 zinc ion binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3PI7_A 3COS_D 1VJ1_A 2ZB3_A 1PIW_B 1Q1N_A 1PS0_A 2EER_B 3KRT_A 1ZSY_A ....
Probab=32.05 E-value=76 Score=24.97 Aligned_cols=64 Identities=23% Similarity=0.231 Sum_probs=38.5
Q ss_pred cEEEEEcCc-hhHHHHHHcCCCeech---HHHHHHHHh-CCcccccEEEEcCcchhHHHhhhhccCCCC
Q 022012 235 VRVAFFAEG-ADAEEARAAGADIVGG---LELIEEIAS-SGKLDVEKCFSTRQFMPRLFKISKILNQHG 298 (304)
Q Consensus 235 ~KIlVFadg-d~aeeAkeAGAd~VGg---eELIeKIkk-~gkLdFD~~IATpdmMpkL~kLGriLGPRG 298 (304)
.+|.+++.. +..+.|++.||+++-. +++.++|.+ .+.-.+|++|=+...-..+...-..|++.|
T Consensus 15 ~~vi~~~~~~~k~~~~~~~Ga~~~~~~~~~~~~~~i~~~~~~~~~d~vid~~g~~~~~~~~~~~l~~~G 83 (130)
T PF00107_consen 15 AKVIATDRSEEKLELAKELGADHVIDYSDDDFVEQIRELTGGRGVDVVIDCVGSGDTLQEAIKLLRPGG 83 (130)
T ss_dssp SEEEEEESSHHHHHHHHHTTESEEEETTTSSHHHHHHHHTTTSSEEEEEESSSSHHHHHHHHHHEEEEE
T ss_pred CEEEEEECCHHHHHHHHhhcccccccccccccccccccccccccceEEEEecCcHHHHHHHHHHhccCC
Confidence 466666665 5778899999987633 246777764 222358888766554344433334444433
No 33
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=31.82 E-value=74 Score=27.97 Aligned_cols=35 Identities=20% Similarity=0.310 Sum_probs=29.7
Q ss_pred CcEEEEEcCc-hhHHHHHHcCCCeechHHHHHHHHh
Q 022012 234 AVRVAFFAEG-ADAEEARAAGADIVGGLELIEEIAS 268 (304)
Q Consensus 234 ~~KIlVFadg-d~aeeAkeAGAd~VGgeELIeKIkk 268 (304)
...|+|.+++ .....|+..||..+..++++..|..
T Consensus 94 ~~~v~VVTSD~~iq~~~~~~GA~~iss~ef~~~l~~ 129 (166)
T PF05991_consen 94 PRQVTVVTSDREIQRAARGRGAKRISSEEFLRELKA 129 (166)
T ss_pred CCeEEEEeCCHHHHHHHhhCCCEEEcHHHHHHHHHH
Confidence 3689999987 5567788999999999999999875
No 34
>PRK03957 V-type ATP synthase subunit F; Provisional
Probab=31.23 E-value=90 Score=25.41 Aligned_cols=55 Identities=15% Similarity=0.142 Sum_probs=38.2
Q ss_pred cEEEEEcCchhHHHHHHcCCC---eech-HHHHHHHHh-CCcccccEEEEcCcchhHHHh
Q 022012 235 VRVAFFAEGADAEEARAAGAD---IVGG-LELIEEIAS-SGKLDVEKCFSTRQFMPRLFK 289 (304)
Q Consensus 235 ~KIlVFadgd~aeeAkeAGAd---~VGg-eELIeKIkk-~gkLdFD~~IATpdmMpkL~k 289 (304)
.||+|++|.+.+.==+-+|+. .+.. +|..+.|.+ -..=+|-.++.|.++...+..
T Consensus 1 mkIaVIgD~dtv~GFrLaGi~~~~~v~~~ee~~~~l~~l~~~~d~gII~ite~~~~~i~~ 60 (100)
T PRK03957 1 MKIAVVGDRDTVTGFRLAGLTEVYEVKNPEEAKNAIKELVENDEIGIIIITERIAEEIRD 60 (100)
T ss_pred CEEEEEeCHHHHHHHHHcCCCceEEeCCHHHHHHHHHHHhhCCCeEEEEEcHHHHHHHHH
Confidence 389999998888778889985 3444 444333432 011169999999999988865
No 35
>KOG1198 consensus Zinc-binding oxidoreductase [Energy production and conversion; General function prediction only]
Probab=30.94 E-value=91 Score=30.68 Aligned_cols=46 Identities=22% Similarity=0.218 Sum_probs=32.9
Q ss_pred CcEEEEEcCchhHHHHHHcCCCee---chHHHHHHHHhCCcccccEEEE
Q 022012 234 AVRVAFFAEGADAEEARAAGADIV---GGLELIEEIASSGKLDVEKCFS 279 (304)
Q Consensus 234 ~~KIlVFadgd~aeeAkeAGAd~V---GgeELIeKIkk~gkLdFD~~IA 279 (304)
-.+|.+.|..+..+.+++.|||.| ..+++++++++..--.||++|-
T Consensus 183 ~~~v~t~~s~e~~~l~k~lGAd~vvdy~~~~~~e~~kk~~~~~~DvVlD 231 (347)
T KOG1198|consen 183 AIKVVTACSKEKLELVKKLGADEVVDYKDENVVELIKKYTGKGVDVVLD 231 (347)
T ss_pred CcEEEEEcccchHHHHHHcCCcEeecCCCHHHHHHHHhhcCCCccEEEE
Confidence 368888999999999999999876 3466777776411115777664
No 36
>COG1436 NtpG Archaeal/vacuolar-type H+-ATPase subunit F [Energy production and conversion]
Probab=30.23 E-value=63 Score=27.02 Aligned_cols=58 Identities=19% Similarity=0.297 Sum_probs=40.0
Q ss_pred cEEEEEcCchhHHHHHHcCCCee---chHH-HHHHHHh--CCcccccEEEEcCcchhHHHh-hhhc
Q 022012 235 VRVAFFAEGADAEEARAAGADIV---GGLE-LIEEIAS--SGKLDVEKCFSTRQFMPRLFK-ISKI 293 (304)
Q Consensus 235 ~KIlVFadgd~aeeAkeAGAd~V---GgeE-LIeKIkk--~gkLdFD~~IATpdmMpkL~k-LGri 293 (304)
.+|||++|.+.+.-=+=+|+..+ ..++ ++.+..+ .+. +|.++|-|.+++..|.. +.++
T Consensus 3 ~~I~VIGd~dtvtGFrLaGv~~~~v~~~~~~~~~~~~~~l~~~-~~~iIiite~~a~~i~~~i~~~ 67 (104)
T COG1436 3 MKIAVIGDRDTVTGFRLAGVRVVYVADDEEDELRAALRVLAED-DVGIILITEDLAEKIREEIRRI 67 (104)
T ss_pred eEEEEEEccchhhceeeecceeEEEecChhHHHHHHHHhhccC-CceEEEEeHHHHhhhHHHHHHH
Confidence 58999999987766666777633 3332 2333332 223 89999999999999987 6655
No 37
>PF12270 Cyt_c_ox_IV: Cytochrome c oxidase subunit IV; InterPro: IPR021050 This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. This family is the fourth subunit of the cytochrome c oxidase complex. This subunit does not have a catalytic capacity but instead, is required for assembly and/or stability of the complex []. ; GO: 0004129 cytochrome-c oxidase activity, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=27.16 E-value=36 Score=30.05 Aligned_cols=16 Identities=38% Similarity=0.509 Sum_probs=13.8
Q ss_pred CcccCCCCCCCCCCCC
Q 022012 117 SRVAPLPEAGEPASGE 132 (304)
Q Consensus 117 ~r~~plp~~~~~~~~~ 132 (304)
.|+-++|||++.+|.+
T Consensus 60 rr~~~rPED~~daEI~ 75 (137)
T PF12270_consen 60 RRIGPRPEDREDAEIA 75 (137)
T ss_pred hhCCCCCccccccccc
Confidence 4688999999999877
No 38
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=26.12 E-value=26 Score=33.90 Aligned_cols=10 Identities=30% Similarity=0.620 Sum_probs=8.9
Q ss_pred hhhccCCCCC
Q 022012 290 ISKILNQHGL 299 (304)
Q Consensus 290 LGriLGPRGL 299 (304)
+||||||||.
T Consensus 109 VGRILGPrGn 118 (259)
T KOG1588|consen 109 VGRILGPRGN 118 (259)
T ss_pred ccccccCCcc
Confidence 5999999995
No 39
>cd01140 FatB Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=25.37 E-value=1.8e+02 Score=26.08 Aligned_cols=33 Identities=24% Similarity=0.445 Sum_probs=16.1
Q ss_pred eEEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCeech
Q 022012 223 GTMNLPHGDKKAVRVAFFAEGADAEEARAAGADIVGG 259 (304)
Q Consensus 223 GsV~LPh~~gK~~KIlVFadgd~aeeAkeAGAd~VGg 259 (304)
|.|+||+.. .||.++.. ...+.....|+.+||.
T Consensus 4 g~vtl~~~p---~RIv~l~~-~~~~~l~~Lg~~ivgv 36 (270)
T cd01140 4 GETKVPKNP---EKVVVFDV-GALDTLDALGVKVVGV 36 (270)
T ss_pred CceeccCCC---ceEEEecc-cchhHHHHcCCceEEe
Confidence 456666554 24554432 2234444455555554
No 40
>COG1544 Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
Probab=22.12 E-value=2.5e+02 Score=23.69 Aligned_cols=51 Identities=22% Similarity=0.447 Sum_probs=33.7
Q ss_pred CCccCHHHHHHHHHHHc----ccCCCccEEEEEEEccCCCCCCceeeeEEEcCCC
Q 022012 180 RPVLDLMDAIKQVKANA----KATFDETVEAHVRLAIPPRKTELIVRGTMNLPHG 230 (304)
Q Consensus 180 ~~~ysl~EAIr~lke~a----~rkF~ETVEL~I~LnvD~kK~d~~~rGsV~LPh~ 230 (304)
...+++.+||+..-+.. .+.|..-+++++.|++...+....+.-++.|+++
T Consensus 7 G~nieit~a~r~~Ve~Kl~kl~r~~~~~~~~~v~l~~e~~~~~~~ve~ti~~~~g 61 (110)
T COG1544 7 GKNVEITEAIREYVEEKLAKLERYFDDIINVDVTLSKEKNRSRFKVEATIHLPGG 61 (110)
T ss_pred eeeeeeCHHHHHHHHHHHHHHHhhhccCccEEEEEEeeccccceEEEEEEEcCCc
Confidence 45578889999877654 6677777788888876553223455555666554
No 41
>PLN02331 phosphoribosylglycinamide formyltransferase
Probab=21.53 E-value=1.5e+02 Score=27.32 Aligned_cols=41 Identities=22% Similarity=0.244 Sum_probs=22.8
Q ss_pred EEEEEcCchh---HHHHHHcCCCeec------------hHHHHHHHHhCCcccccEEEE
Q 022012 236 RVAFFAEGAD---AEEARAAGADIVG------------GLELIEEIASSGKLDVEKCFS 279 (304)
Q Consensus 236 KIlVFadgd~---aeeAkeAGAd~VG------------geELIeKIkk~gkLdFD~~IA 279 (304)
-++|+++... .+.|.++|+.+.- .+++++.+. .+++|+++.
T Consensus 29 i~~visn~~~~~~~~~A~~~gIp~~~~~~~~~~~~~~~~~~~~~~l~---~~~~Dliv~ 84 (207)
T PLN02331 29 VVVVVTNKPGCGGAEYARENGIPVLVYPKTKGEPDGLSPDELVDALR---GAGVDFVLL 84 (207)
T ss_pred EEEEEEeCCCChHHHHHHHhCCCEEEeccccCCCcccchHHHHHHHH---hcCCCEEEE
Confidence 3566666533 3667777876542 345555554 345565544
No 42
>KOG2523 consensus Predicted RNA-binding protein with PUA domain [Translation, ribosomal structure and biogenesis]
Probab=21.30 E-value=1e+02 Score=28.51 Aligned_cols=39 Identities=36% Similarity=0.488 Sum_probs=29.8
Q ss_pred cCCCCCCCcEEEEEcCchhHHHHHHcCCCeechHHHHHHHHh
Q 022012 227 LPHGDKKAVRVAFFAEGADAEEARAAGADIVGGLELIEEIAS 268 (304)
Q Consensus 227 LPh~~gK~~KIlVFadgd~aeeAkeAGAd~VGgeELIeKIkk 268 (304)
||.++-+..-|+|.|+|.. -|.+.|-..+|.+| |+.+++
T Consensus 123 l~~~~ekd~~V~i~aeGK~--~alAiG~~~ms~ke-i~s~nK 161 (181)
T KOG2523|consen 123 LPPGVEKDTIVAIMAEGKE--HALAIGLTKMSAKE-IKSVNK 161 (181)
T ss_pred CCCCccCCCEEEEEecCch--hhhhhhhhhhcHHH-HHhhcc
Confidence 5556667788999999863 36777999999888 577763
No 43
>TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase. Synonym: quinolinate phosphoribosyltransferase (decarboxylating)
Probab=21.19 E-value=1.1e+02 Score=29.05 Aligned_cols=27 Identities=41% Similarity=0.450 Sum_probs=22.1
Q ss_pred CCcEEEEEcCc-hhHHHHHHcCCCeech
Q 022012 233 KAVRVAFFAEG-ADAEEARAAGADIVGG 259 (304)
Q Consensus 233 K~~KIlVFadg-d~aeeAkeAGAd~VGg 259 (304)
...+|.|=|+. +++.+|.++||||++-
T Consensus 177 ~~~~Igvev~t~eea~~A~~~gaDyI~l 204 (265)
T TIGR00078 177 FALKIEVEVESLEEAEEAAEAGADIIML 204 (265)
T ss_pred CCCeEEEEeCCHHHHHHHHHcCCCEEEE
Confidence 35679998887 7788999999999953
No 44
>PRK09427 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional
Probab=20.19 E-value=52 Score=33.79 Aligned_cols=26 Identities=31% Similarity=0.203 Sum_probs=23.8
Q ss_pred CcEEEEEcCchhHHHHHHcCCCeech
Q 022012 234 AVRVAFFAEGADAEEARAAGADIVGG 259 (304)
Q Consensus 234 ~~KIlVFadgd~aeeAkeAGAd~VGg 259 (304)
..|||=+.+.+++..|.++|||++|-
T Consensus 258 ~vKICGit~~eda~~a~~~GaD~lGf 283 (454)
T PRK09427 258 ENKVCGLTRPQDAKAAYDAGAVYGGL 283 (454)
T ss_pred ccccCCCCCHHHHHHHHhCCCCEEee
Confidence 58999999999999999999999885
No 45
>PRK15452 putative protease; Provisional
Probab=20.13 E-value=1.8e+02 Score=29.89 Aligned_cols=26 Identities=27% Similarity=0.101 Sum_probs=20.4
Q ss_pred cEEEEEcCc-hhHHHHHHcCCC--eechH
Q 022012 235 VRVAFFAEG-ADAEEARAAGAD--IVGGL 260 (304)
Q Consensus 235 ~KIlVFadg-d~aeeAkeAGAd--~VGge 260 (304)
..++|-|.. +.+..|.++||| |+|++
T Consensus 4 peLlapag~~e~l~aAi~~GADaVY~G~~ 32 (443)
T PRK15452 4 PELLSPAGTLKNMRYAFAYGADAVYAGQP 32 (443)
T ss_pred cEEEEECCCHHHHHHHHHCCCCEEEECCC
Confidence 468888877 788899999999 55663
Done!