Query 031659
Match_columns 155
No_of_seqs 185 out of 870
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 03:36:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031659.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031659hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0898 40S ribosomal protein 100.0 7.9E-75 1.7E-79 452.8 5.7 143 13-155 10-152 (152)
2 PTZ00096 40S ribosomal protein 100.0 8.5E-71 1.8E-75 431.1 9.1 140 14-153 4-143 (143)
3 TIGR01025 rpsS_arch ribosomal 100.0 1E-66 2.2E-71 405.1 8.8 135 21-155 1-135 (135)
4 PRK04038 rps19p 30S ribosomal 100.0 1.1E-65 2.4E-70 398.9 10.4 133 20-155 2-134 (134)
5 COG0185 RpsS Ribosomal protein 100.0 3E-42 6.6E-47 253.4 5.7 92 52-148 2-93 (93)
6 CHL00050 rps19 ribosomal prote 100.0 1.3E-35 2.8E-40 218.0 6.8 81 55-139 1-84 (92)
7 TIGR01050 rpsS_bact ribosomal 100.0 6.7E-35 1.4E-39 214.3 6.2 82 55-140 1-85 (92)
8 PRK00357 rpsS 30S ribosomal pr 100.0 7.9E-35 1.7E-39 214.0 5.9 82 55-140 1-85 (92)
9 PF00203 Ribosomal_S19: Riboso 100.0 8E-35 1.7E-39 208.9 5.5 81 57-138 1-81 (81)
10 PLN03147 ribosomal protein S19 100.0 3.6E-32 7.8E-37 200.0 6.2 78 57-141 1-81 (92)
11 KOG0899 Mitochondrial/chloropl 100.0 2.7E-31 5.8E-36 193.6 3.5 80 54-140 9-91 (93)
12 PF03131 bZIP_Maf: bZIP Maf tr 74.9 2.1 4.4E-05 30.9 1.8 33 30-71 1-33 (92)
13 cd06101 citrate_synt Citrate s 72.2 3.4 7.3E-05 35.2 2.7 24 24-47 22-46 (265)
14 PRK12350 citrate synthase 2; P 70.3 4.1 8.8E-05 36.4 2.9 24 24-47 24-48 (353)
15 cd06116 CaCS_like Chloroflexus 66.7 5.2 0.00011 36.0 2.8 24 24-47 28-52 (384)
16 TIGR03738 PRTRC_C PRTRC system 66.4 4.1 8.8E-05 28.8 1.6 28 22-49 6-34 (66)
17 cd06113 citrate_synt_like_1_2 66.0 5 0.00011 36.4 2.6 24 24-47 37-67 (406)
18 cd06109 BsCS-I_like Bacillus s 65.4 5.9 0.00013 35.2 2.9 24 24-47 22-46 (349)
19 cd06108 Ec2MCS_like Escherichi 64.8 6.1 0.00013 35.4 2.9 24 24-47 22-46 (363)
20 PRK14034 citrate synthase; Pro 63.8 6.4 0.00014 35.3 2.8 24 24-47 24-48 (372)
21 cd06118 citrate_synt_like_1 Ci 62.4 6.5 0.00014 34.7 2.6 24 24-47 22-46 (358)
22 PRK14036 citrate synthase; Pro 62.1 7.4 0.00016 35.0 2.9 24 24-47 27-51 (377)
23 PF13543 KSR1-SAM: SAM like do 61.5 6.8 0.00015 30.7 2.3 22 28-49 89-110 (129)
24 PRK12351 methylcitrate synthas 60.7 8.1 0.00018 34.8 2.9 26 22-47 29-55 (378)
25 PRK14037 citrate synthase; Pro 60.7 8.1 0.00018 34.7 2.9 23 25-47 28-51 (377)
26 cd06115 AthCS_per_like Arabido 60.5 7.8 0.00017 35.3 2.8 24 24-47 48-72 (410)
27 cd06111 DsCS_like Cold-active 60.3 7.5 0.00016 34.6 2.6 24 24-47 22-46 (362)
28 PF00285 Citrate_synt: Citrate 60.1 5.7 0.00012 34.9 1.8 23 25-47 22-45 (356)
29 TIGR01798 cit_synth_I citrate 59.8 8.3 0.00018 35.2 2.8 24 24-47 55-79 (412)
30 cd06117 Ec2MCS_like_1 Subgroup 59.3 8.9 0.00019 34.3 2.9 25 23-47 21-46 (366)
31 cd06107 EcCS_AthCS-per_like Es 59.2 8.5 0.00018 34.7 2.8 24 24-47 28-52 (382)
32 PRK14033 citrate synthase; Pro 58.8 9.1 0.0002 34.3 2.9 24 24-47 32-56 (375)
33 PRK09569 type I citrate syntha 58.8 7.3 0.00016 35.9 2.3 23 25-47 61-93 (437)
34 PRK12349 citrate synthase 3; P 58.1 9.5 0.00021 34.1 2.9 24 24-47 28-52 (369)
35 TIGR01800 cit_synth_II 2-methy 57.8 8.9 0.00019 34.2 2.7 23 25-47 23-46 (368)
36 cd06110 BSuCS-II_like Bacillus 57.5 9.2 0.0002 33.8 2.7 23 25-47 23-46 (356)
37 cd06112 citrate_synt_like_1_1 57.3 10 0.00022 34.0 2.9 24 24-47 24-48 (373)
38 PLN02456 citrate synthase 57.0 8.8 0.00019 35.5 2.5 24 24-47 87-111 (455)
39 PRK14035 citrate synthase; Pro 56.5 10 0.00022 34.1 2.8 24 24-47 24-48 (371)
40 cd06114 EcCS_like Escherichia 55.9 11 0.00023 34.2 2.9 24 24-47 50-74 (400)
41 PRK14032 citrate synthase; Pro 55.1 10 0.00022 34.9 2.6 24 24-47 67-97 (447)
42 PRK05614 gltA type II citrate 54.6 10 0.00022 34.6 2.5 24 24-47 68-92 (419)
43 PRK06224 citrate synthase; Pro 51.1 15 0.00032 31.2 2.8 23 24-46 20-43 (263)
44 PRK00635 excinuclease ABC subu 50.5 14 0.00031 39.7 3.1 33 23-55 1646-1680(1809)
45 cd06105 ScCit1-2_like Saccharo 44.7 17 0.00037 33.4 2.3 23 25-47 59-91 (427)
46 cd06103 ScCS-like Saccharomyce 44.7 17 0.00037 33.4 2.3 22 26-47 60-91 (426)
47 cd06102 citrate_synt_like_2 Ci 40.5 25 0.00055 30.5 2.7 26 23-48 31-57 (282)
48 cd06106 ScCit3_like Saccharomy 40.0 20 0.00043 33.0 2.1 23 25-47 59-91 (428)
49 PF14454 Prok_Ub: Prokaryotic 39.2 21 0.00045 25.0 1.6 28 22-49 7-35 (65)
50 PF12936 Kri1_C: KRI1-like fam 37.2 37 0.00081 25.1 2.8 29 23-51 27-62 (93)
51 TIGR00630 uvra excinuclease AB 35.2 32 0.0007 34.5 2.8 27 23-49 775-801 (924)
52 PF05361 PP1_inhibitor: PKC-ac 34.4 14 0.00029 29.7 0.1 40 29-76 73-120 (144)
53 COG0178 UvrA Excinuclease ATPa 32.5 38 0.00083 34.3 2.8 35 21-55 767-803 (935)
54 smart00540 LEM in nuclear memb 32.2 83 0.0018 20.3 3.5 35 33-74 1-41 (44)
55 PF06528 Phage_P2_GpE: Phage P 29.8 90 0.002 19.8 3.3 20 29-48 9-28 (39)
56 PF01783 Ribosomal_L32p: Ribos 27.2 38 0.00083 22.4 1.3 49 49-115 8-56 (56)
57 TIGR01689 EcbF-BcbF capsule bi 26.0 53 0.0011 25.2 2.1 22 28-49 100-121 (126)
58 TIGR01793 cit_synth_euk citrat 25.6 55 0.0012 30.1 2.4 23 25-47 62-94 (427)
59 cd00166 SAM Sterile alpha moti 25.3 52 0.0011 20.3 1.6 19 28-46 26-44 (63)
60 COG0372 GltA Citrate synthase 24.9 58 0.0013 29.7 2.4 22 25-46 40-62 (390)
61 PF08921 DUF1904: Domain of un 24.5 40 0.00087 25.3 1.1 27 25-51 4-33 (108)
62 PF09597 IGR: IGR protein moti 24.4 46 0.001 22.6 1.3 26 32-57 23-49 (57)
63 PF10109 FluMu_gp41: Mu-like p 24.1 88 0.0019 20.9 2.7 22 28-49 55-76 (82)
64 PRK00349 uvrA excinuclease ABC 22.6 82 0.0018 31.8 3.2 28 21-48 775-802 (943)
65 PF07647 SAM_2: SAM domain (St 22.5 37 0.0008 21.9 0.5 33 23-55 23-58 (66)
66 PRK01110 rpmF 50S ribosomal pr 22.4 54 0.0012 22.3 1.3 21 94-115 36-56 (60)
67 TIGR00630 uvra excinuclease AB 21.5 72 0.0016 32.2 2.5 27 23-49 420-446 (924)
No 1
>KOG0898 consensus 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.9e-75 Score=452.83 Aligned_cols=143 Identities=82% Similarity=1.276 Sum_probs=140.6
Q ss_pred hhcCCcccceeeeeeecCChhHHhcCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHhhhcCCCCCCCCceEeccCC
Q 031659 13 AAGQPKKRTFKKFSFRGVDLDALLDMSTDELAKLFSARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRN 92 (155)
Q Consensus 13 ~~~~~Kkrtf~kFtYRG~~ld~L~~ms~eel~~L~~ar~RR~~~Rgl~k~~~~Llkklrkak~~~~~~~kp~~Ikt~~R~ 92 (155)
++.++|||||++|||||+|||||+|||.|||++|+|||+||+++|||+++|+.||++||+|+++++++++|++|+||+||
T Consensus 10 ~~~~kKKRTFrkftyrGVdld~Lldms~~~~~~l~~ar~rrR~~RGL~~k~~~liKklrkAkk~A~~~ekpe~VkTHlR~ 89 (152)
T KOG0898|consen 10 AAVLKKKRTFRKFTYRGVDLDQLLDMSTEQLVKLFPARQRRRLNRGLTRKPHSLIKKLRKAKKEAPPMEKPEVVKTHLRN 89 (152)
T ss_pred HHHHhhhhhhhhccccCCCHHHHhcCCHHHHHHHHHHHHHHHHHcccccchHHHHHHHHHHHhhcCcccCcHHHHHHhhc
Confidence 34688999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeccCccccEEEEecCCcccccccCCCcceeeeeeeeeeeecccCCCCCCCCCCCcCcccCC
Q 031659 93 MIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIGATHSSRFIPLK 155 (155)
Q Consensus 93 ~~IlP~mVG~~v~VyNGK~f~~v~I~~eMIGhkLGEFa~Trk~~~Hg~pGigAT~sS~FvplK 155 (155)
|||+|||||+.|||||||+|++|||+||||||||||||+||||++||+|||||||||+|+|||
T Consensus 90 mII~PEMvGs~VGVyNGK~FnqvEiKPEMIGhYL~eFsiTykpvkHgrpgigat~SsrfipLk 152 (152)
T KOG0898|consen 90 MIIVPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGIGATHSSRFIPLK 152 (152)
T ss_pred ceeeHhhhcceEEEecCcccceeeccHHHHhhhhhhccccccccccCCCCCCcccccccccCC
Confidence 999999999999999999999999999999999999999999999999999999999999997
No 2
>PTZ00096 40S ribosomal protein S15; Provisional
Probab=100.00 E-value=8.5e-71 Score=431.09 Aligned_cols=140 Identities=69% Similarity=1.189 Sum_probs=137.4
Q ss_pred hcCCcccceeeeeeecCChhHHhcCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHhhhcCCCCCCCCceEeccCCc
Q 031659 14 AGQPKKRTFKKFSFRGVDLDALLDMSTDELAKLFSARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNM 93 (155)
Q Consensus 14 ~~~~Kkrtf~kFtYRG~~ld~L~~ms~eel~~L~~ar~RR~~~Rgl~k~~~~Llkklrkak~~~~~~~kp~~Ikt~~R~~ 93 (155)
++++|+|+|++|+|||+|||||++||+|||++|+||||||+++|||..++.+||++|++++++++++++|++|+||+|+|
T Consensus 4 ~~~~k~r~~k~f~yRG~~l~~L~~m~~~e~~~L~~aR~RR~~~RGl~~~~~~LlkKirk~~~~~~~~~k~~~ikT~~R~~ 83 (143)
T PTZ00096 4 EQLKKKRTFKKFTYRGVELEKLLALPEEELVELFRARQRRRINRGIKRKHPTLLKKLRKAKKATKPGEKPKAVKTHLRDM 83 (143)
T ss_pred cccccccccceeeeecCCHHHHHcCCHHHHHHHcCcccccccccCCCHHHHHHHHHHHHHhhhcccccCCcceeEecccC
Confidence 47789999999999999999999999999999999999999999999999999999999999888899999999999999
Q ss_pred eeccCccccEEEEecCCcccccccCCCcceeeeeeeeeeeecccCCCCCCCCCCCcCccc
Q 031659 94 IIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIGATHSSRFIP 153 (155)
Q Consensus 94 ~IlP~mVG~~v~VyNGK~f~~v~I~~eMIGhkLGEFa~Trk~~~Hg~pGigAT~sS~Fvp 153 (155)
+|+|+|||++|+|||||+|++|+|+||||||||||||+||+++.||+|||||||||+|||
T Consensus 84 ~IlP~mVG~ti~VyNGK~fv~V~I~~eMIGhkLGEFa~Trk~~~Hg~pGigATrSS~fvp 143 (143)
T PTZ00096 84 IIVPEMVGSVVGVYNGKQFNNVEIKPEMIGHYLGEFSITYKPVRHGKPGVGATHSSRFIP 143 (143)
T ss_pred eeCccccCcEEEEEcCCeeEeeEeccCeeceeeccccCCcccccCCCCCcCcccccccCC
Confidence 999999999999999999999999999999999999999999999999999999999998
No 3
>TIGR01025 rpsS_arch ribosomal protein S19(archaeal)/S15(eukaryotic). This model represents eukaryotic ribosomal protein S15 and its archaeal equivalent. It excludes bacterial and organellar ribosomal protein S19. The nomenclature for the archaeal members is unresolved and given variously as S19 (after the more distant bacterial homologs) or S15.
Probab=100.00 E-value=1e-66 Score=405.06 Aligned_cols=135 Identities=71% Similarity=1.132 Sum_probs=130.9
Q ss_pred ceeeeeeecCChhHHhcCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHhhhcCCCCCCCCceEeccCCceeccCcc
Q 031659 21 TFKKFSFRGVDLDALLDMSTDELAKLFSARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMI 100 (155)
Q Consensus 21 tf~kFtYRG~~ld~L~~ms~eel~~L~~ar~RR~~~Rgl~k~~~~Llkklrkak~~~~~~~kp~~Ikt~~R~~~IlP~mV 100 (155)
+|++|+|||++||+|++||++||++|+||||||++.||+...+.+||++++++++...++++|++|+||+|+|+|+|+||
T Consensus 1 ~~~~f~yrG~~l~~L~~m~~~e~~~l~~ar~RRs~~RG~~~~~~~Llkki~k~~~~~~~g~k~~~IKT~sR~s~IlP~~V 80 (135)
T TIGR01025 1 TFKEFRYRGYTLEELQDMSLEELAKLLPARQRRRLKRGLTPKQKKLLKKLRKAKKEAPKGEKPEVIRTHCRDMIILPEMV 80 (135)
T ss_pred CCceEeecccCHHHHHcCCHHHHHHHcCcccCcccccCCchhhHHHHHHHHHHHhccccccCCcceEEeccCCeeChhhc
Confidence 68999999999999999999999999999999999999999999999999998876666778899999999999999999
Q ss_pred ccEEEEecCCcccccccCCCcceeeeeeeeeeeecccCCCCCCCCCCCcCcccCC
Q 031659 101 GSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIGATHSSRFIPLK 155 (155)
Q Consensus 101 G~~v~VyNGK~f~~v~I~~eMIGhkLGEFa~Trk~~~Hg~pGigAT~sS~FvplK 155 (155)
|++|+|||||+|++|+|+||||||||||||+||+++.||+||||||+||+|||||
T Consensus 81 G~ti~VyNGk~fv~v~I~~eMVGhklGEFa~Trk~~~Hg~pGigAt~ss~fvplK 135 (135)
T TIGR01025 81 GSTVGVYNGKEFVQVEIKPEMIGHYLGEFSITRKPVKHGRPGIGATRSSMFVPLK 135 (135)
T ss_pred CcEEEEEcCCeeEEEEecCCeeceeecccccCcccCcCCCCCcCccccccceeCc
Confidence 9999999999999999999999999999999999999999999999999999997
No 4
>PRK04038 rps19p 30S ribosomal protein S19P; Provisional
Probab=100.00 E-value=1.1e-65 Score=398.86 Aligned_cols=133 Identities=55% Similarity=0.967 Sum_probs=127.5
Q ss_pred cceeeeeeecCChhHHhcCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHhhhcCCCCCCCCceEeccCCceeccCc
Q 031659 20 RTFKKFSFRGVDLDALLDMSTDELAKLFSARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEM 99 (155)
Q Consensus 20 rtf~kFtYRG~~ld~L~~ms~eel~~L~~ar~RR~~~Rgl~k~~~~Llkklrkak~~~~~~~kp~~Ikt~~R~~~IlP~m 99 (155)
++|++|+|||++||||++||+|||++|+||||||++.||+...+.+||++++++++.. ++|++|+||+|+|+|+|+|
T Consensus 2 ~~~~~f~yrG~~l~~L~~m~~~~~~~l~~ar~RRsl~KGp~~~~~~LlkKi~k~~~~~---~k~~~ikT~sR~s~IlP~~ 78 (134)
T PRK04038 2 KRWKEFTYRGYTLEELQEMSLEEFAELLPARQRRSLKRGLTPEQRKLLEKIRKARREK---KKGRVIRTHVRDMIILPEM 78 (134)
T ss_pred CccceeeecccCHHHHHcCCHHHHHHHcchhhhhhhccCCCcchHHHHHHHHHHHhcc---cCCcceeEeccCCeeChhh
Confidence 6899999999999999999999999999999999999999988999999999987633 4567899999999999999
Q ss_pred cccEEEEecCCcccccccCCCcceeeeeeeeeeeecccCCCCCCCCCCCcCcccCC
Q 031659 100 IGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIGATHSSRFIPLK 155 (155)
Q Consensus 100 VG~~v~VyNGK~f~~v~I~~eMIGhkLGEFa~Trk~~~Hg~pGigAT~sS~FvplK 155 (155)
||++|+|||||+|++|+|+||||||||||||+||+++.||+|||||||||+|||||
T Consensus 79 VG~ti~VyNGk~fv~v~I~~eMVGhklGEFa~Trk~~~Hg~pGigAT~sS~fvplK 134 (134)
T PRK04038 79 VGLTIAVYNGKEFVEVEIVPEMIGHYLGEFALTRKRVQHGSPGIGATRSSKFVPLK 134 (134)
T ss_pred cCeEEEEecCceeEeEEeccCccceeeccccCCcccCcCCCCCcCccccccceeCc
Confidence 99999999999999999999999999999999999999999999999999999997
No 5
>COG0185 RpsS Ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-42 Score=253.41 Aligned_cols=92 Identities=47% Similarity=0.681 Sum_probs=81.8
Q ss_pred hhhhhcCCCCCcchHHHHHHHhhhcCCCCCCCCceEeccCCceeccCccccEEEEecCCcccccccCCCcceeeeeeeee
Q 031659 52 RRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSI 131 (155)
Q Consensus 52 RR~~~Rgl~k~~~~Llkklrkak~~~~~~~kp~~Ikt~~R~~~IlP~mVG~~v~VyNGK~f~~v~I~~eMIGhkLGEFa~ 131 (155)
||++.||.. .+.+||+++++++... ++ ++||||||+|+|||+|||++|+|||||+|+||+|+|||||||||||||
T Consensus 2 ~RSlkkGp~-~~~~Ll~Kv~~~~~~~---~k-~~IkT~sR~stIlPemVG~ti~VhNGk~~vpV~I~~eMVGHkLGEFap 76 (93)
T COG0185 2 RRSLKKGPF-VDKHLLKKVRKAKESG---KK-KPIKTWSRRSTILPEMVGLTIAVHNGKKFVPVEITEEMVGHKLGEFAP 76 (93)
T ss_pred CcccccCcc-ccHHHHHHHHHHHhcc---CC-CcceeeecccEechhhcCcEEEEEcCceEEEEEechhhcceecccccc
Confidence 455555555 4469999999988632 33 689999999999999999999999999999999999999999999999
Q ss_pred eeecccCCCCCCCCCCC
Q 031659 132 SYKPVKHGRPGIGATHS 148 (155)
Q Consensus 132 Trk~~~Hg~pGigAT~s 148 (155)
||+++.|+.||+|||+|
T Consensus 77 TR~~~~H~~~~~~atr~ 93 (93)
T COG0185 77 TRTFVGHGADGIKATRS 93 (93)
T ss_pred eecccccCCCCcCcccC
Confidence 99999999999999986
No 6
>CHL00050 rps19 ribosomal protein S19
Probab=100.00 E-value=1.3e-35 Score=218.03 Aligned_cols=81 Identities=37% Similarity=0.552 Sum_probs=74.4
Q ss_pred hhcCCCCCcc---hHHHHHHHhhhcCCCCCCCCceEeccCCceeccCccccEEEEecCCcccccccCCCcceeeeeeeee
Q 031659 55 FQRGLKRKPM---ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSI 131 (155)
Q Consensus 55 ~~Rgl~k~~~---~Llkklrkak~~~~~~~kp~~Ikt~~R~~~IlP~mVG~~v~VyNGK~f~~v~I~~eMIGhkLGEFa~ 131 (155)
|.||+||+|+ +||++++++.. .+++++|+||+|+|+|||+|||++|+|||||+|++|+|+||||||||||||+
T Consensus 1 M~RS~wKgpfv~~~Ll~ki~~~~~----~~~~~~ikT~sR~s~IlP~~vg~t~~VyNGk~fv~v~I~~eMVGhklGEFa~ 76 (92)
T CHL00050 1 MTRSLKKNPFVANHLLKKIEKLNT----KEEKEIIVTWSRASTIIPTMIGHTIAVHNGKEHIPIYITDQMVGHKLGEFAP 76 (92)
T ss_pred CCCccccCcccCHHHHHHHHHhhh----ccCCccceEEccccEeChhhcCcEEEEEcCceEEEEEEccccccceeeeEee
Confidence 7899999997 89999987653 2345689999999999999999999999999999999999999999999999
Q ss_pred eeecccCC
Q 031659 132 SYKPVKHG 139 (155)
Q Consensus 132 Trk~~~Hg 139 (155)
||+++.|+
T Consensus 77 TRk~~~h~ 84 (92)
T CHL00050 77 TRNFRGHA 84 (92)
T ss_pred eecccccc
Confidence 99999995
No 7
>TIGR01050 rpsS_bact ribosomal protein S19, bacterial/organelle. the Archaea may be designated S15 or S19.
Probab=100.00 E-value=6.7e-35 Score=214.35 Aligned_cols=82 Identities=39% Similarity=0.608 Sum_probs=75.1
Q ss_pred hhcCCCCCcc---hHHHHHHHhhhcCCCCCCCCceEeccCCceeccCccccEEEEecCCcccccccCCCcceeeeeeeee
Q 031659 55 FQRGLKRKPM---ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSI 131 (155)
Q Consensus 55 ~~Rgl~k~~~---~Llkklrkak~~~~~~~kp~~Ikt~~R~~~IlP~mVG~~v~VyNGK~f~~v~I~~eMIGhkLGEFa~ 131 (155)
|+||+|++|+ +||+++++++. .+++++|+||+|+|+|+|+|||++|+||||++|++|+|++|||||||||||+
T Consensus 1 MsRS~wKgpfv~~~Ll~ki~k~~~----~~~~~~ikT~sR~s~IlP~~vg~~i~VynGk~fv~v~I~~~MvGhklGEFa~ 76 (92)
T TIGR01050 1 MSRSLKKGPFVDHHLLKKVEKLNE----SGKKKVIKTWSRRSTIIPEMIGHTIAVHNGKKFIPVYITEDMVGHKLGEFAP 76 (92)
T ss_pred CCcccccCccccHHHHHHHHHhhc----ccCCCceEEEecccEEChHHCCcEEEEEcCceEEEEEeCcCeecceeeeeec
Confidence 6899999996 89999988752 2346789999999999999999999999999999999999999999999999
Q ss_pred eeecccCCC
Q 031659 132 SYKPVKHGR 140 (155)
Q Consensus 132 Trk~~~Hg~ 140 (155)
||+++.|++
T Consensus 77 TRk~~~h~~ 85 (92)
T TIGR01050 77 TRTFKGHAK 85 (92)
T ss_pred eeecccccc
Confidence 999999975
No 8
>PRK00357 rpsS 30S ribosomal protein S19; Reviewed
Probab=100.00 E-value=7.9e-35 Score=214.00 Aligned_cols=82 Identities=33% Similarity=0.528 Sum_probs=74.5
Q ss_pred hhcCCCCCcc---hHHHHHHHhhhcCCCCCCCCceEeccCCceeccCccccEEEEecCCcccccccCCCcceeeeeeeee
Q 031659 55 FQRGLKRKPM---ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSI 131 (155)
Q Consensus 55 ~~Rgl~k~~~---~Llkklrkak~~~~~~~kp~~Ikt~~R~~~IlP~mVG~~v~VyNGK~f~~v~I~~eMIGhkLGEFa~ 131 (155)
|.||+|++|+ +||+++++++.. .++++|+||+|+|+|+|+|||++|+||||++|++|+|+|||||||||||++
T Consensus 1 M~RS~~Kgp~v~~~Ll~ki~k~~~~----~~~~~ikT~sR~s~IlP~~vg~~i~VyNGk~fv~v~I~~emiGhklGEFa~ 76 (92)
T PRK00357 1 MARSLKKGPFVDGHLLKKVEKANES----GDKKVIKTWSRRSTILPEFVGLTIAVHNGRKHVPVYVTENMVGHKLGEFAP 76 (92)
T ss_pred CCcccccCccccHHHHHHHHHHhhc----cCCCceEEeeccCCcCHHHCCceEEEEcCCeeEeEEeccCccceeeeeecc
Confidence 6899999986 899999987532 235679999999999999999999999999999999999999999999999
Q ss_pred eeecccCCC
Q 031659 132 SYKPVKHGR 140 (155)
Q Consensus 132 Trk~~~Hg~ 140 (155)
||++++|+.
T Consensus 77 Tr~~~~H~~ 85 (92)
T PRK00357 77 TRTFRGHAA 85 (92)
T ss_pred eeccccccc
Confidence 999999973
No 9
>PF00203 Ribosomal_S19: Ribosomal protein S19; InterPro: IPR002222 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The small subunit ribosomal proteins can be categorised as: primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S19 contains 88-144 amino acid residues. In Escherichia coli, S19 is known to form a complex with S13 that binds strongly to 16S ribosomal RNA. Experimental evidence [] has revealed that S19 is moderately exposed on the ribosomal surface, and is designated a secondary rRNA binding protein. S19 belongs to a family of ribosomal proteins [, ] that includes: eubacterial S19; algal and plant chloroplast S19; cyanelle S19; archaebacterial S19; plant mitochondrial S19; and eukaryotic S15 ('rig' protein).; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 2XZM_S 2XZN_S 2ZKQ_s 3U5C_P 3O30_I 3U5G_P 3O2Z_I 3IZB_R 1S1H_S 1XMO_S ....
Probab=100.00 E-value=8e-35 Score=208.90 Aligned_cols=81 Identities=51% Similarity=0.838 Sum_probs=74.1
Q ss_pred cCCCCCcchHHHHHHHhhhcCCCCCCCCceEeccCCceeccCccccEEEEecCCcccccccCCCcceeeeeeeeeeeecc
Q 031659 57 RGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPV 136 (155)
Q Consensus 57 Rgl~k~~~~Llkklrkak~~~~~~~kp~~Ikt~~R~~~IlP~mVG~~v~VyNGK~f~~v~I~~eMIGhkLGEFa~Trk~~ 136 (155)
||+|++|+.+...++++++..+.+++ ++|+||+|+|+|+|+|||++|+|||||+|++|+|+|||||||||||++||+++
T Consensus 1 Rs~~K~~~~~~~~l~k~~~~~~~~~k-~~ikt~~R~s~IlP~~vg~~i~VyNGk~f~~i~I~~~miG~klGEF~~Trk~~ 79 (81)
T PF00203_consen 1 RSLWKGPFVLKKLLKKIKKLNPSKKK-KVIKTHSRSSTILPEMVGKTIGVYNGKKFVPIKITPEMIGHKLGEFAPTRKPV 79 (81)
T ss_dssp CCSSSSTHHHHHHHHHHHHHHCTTST-SEEEESSTTSBBSGTGTTSEEEEESSSSEEEEECSSTGTSSBCGCGSSSSSTS
T ss_pred CCCCcccchhHHHHHHHHHHhhcCCC-cceEEEeCCCCcccceeceEEEEecCceEEEEEecccccceEeeceeeecccC
Confidence 89999999888778777665554554 79999999999999999999999999999999999999999999999999999
Q ss_pred cC
Q 031659 137 KH 138 (155)
Q Consensus 137 ~H 138 (155)
.|
T Consensus 80 ~H 81 (81)
T PF00203_consen 80 KH 81 (81)
T ss_dssp CT
T ss_pred CC
Confidence 98
No 10
>PLN03147 ribosomal protein S19; Provisional
Probab=99.97 E-value=3.6e-32 Score=200.00 Aligned_cols=78 Identities=21% Similarity=0.347 Sum_probs=69.1
Q ss_pred cCCCCCcc---hHHHHHHHhhhcCCCCCCCCceEeccCCceeccCccccEEEEecCCcccccccCCCcceeeeeeeeeee
Q 031659 57 RGLKRKPM---ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISY 133 (155)
Q Consensus 57 Rgl~k~~~---~Llkklrkak~~~~~~~kp~~Ikt~~R~~~IlP~mVG~~v~VyNGK~f~~v~I~~eMIGhkLGEFa~Tr 133 (155)
||+|++|+ +|+ ++.+++.. ..+|+||||+|+|+|+|||++|+|||||+|++|+|+|||||||||||++||
T Consensus 1 RS~wKGPfv~~~L~-k~~~~~~~------~~~iktwSR~S~IlP~~vg~ti~VyNGk~fv~v~It~~MVGhKlGEFa~Tr 73 (92)
T PLN03147 1 QAIWKGAFVDAFLA-RIKKKRDL------LLGKKIWSHRSSILPDFVDCSVLIYNGKTHIRCKITEGKVGHKFGEFAFTR 73 (92)
T ss_pred CCCccCccccHHHH-HHHHHHhc------CCceeEEcccceECHHHcCCEEEEeCCCceEEEEecCCccceeeeccccEe
Confidence 89999997 664 57765531 147999999999999999999999999999999999999999999999999
Q ss_pred ecccCCCC
Q 031659 134 KPVKHGRP 141 (155)
Q Consensus 134 k~~~Hg~p 141 (155)
+++.|..-
T Consensus 74 k~~~hk~~ 81 (92)
T PLN03147 74 KRRPHRAI 81 (92)
T ss_pred cccCCCCc
Confidence 99999754
No 11
>KOG0899 consensus Mitochondrial/chloroplast ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2.7e-31 Score=193.55 Aligned_cols=80 Identities=33% Similarity=0.575 Sum_probs=71.1
Q ss_pred hhhcCCCCCcc---hHHHHHHHhhhcCCCCCCCCceEeccCCceeccCccccEEEEecCCcccccccCCCcceeeeeeee
Q 031659 54 RFQRGLKRKPM---ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFS 130 (155)
Q Consensus 54 ~~~Rgl~k~~~---~Llkklrkak~~~~~~~kp~~Ikt~~R~~~IlP~mVG~~v~VyNGK~f~~v~I~~eMIGhkLGEFa 130 (155)
+|.||+||+|+ .|+++..+++. ..+|+||+|+++|||+|||++|.|||||+|++|+|+++|||||||||+
T Consensus 9 Sm~RSvwK~P~V~~~~~rk~~~~~~-------~~pikt~sRasTIlP~~Vg~~~~IhNGk~~v~vkIte~mVGHKlGEFa 81 (93)
T KOG0899|consen 9 SMTRSVWKGPFVVKFLLRKIEKLKG-------KAPIKTWSRASTILPTMVGHTFAIHNGKEHVPVKITEDMVGHKLGEFA 81 (93)
T ss_pred HHHHHhhcCcchhHHHHHHHHHhcC-------CCceeehhhhcchhhhhhCceEEEecCcceeeEEeecchhcccccccc
Confidence 49999999997 56666655442 235999999999999999999999999999999999999999999999
Q ss_pred eeeecccCCC
Q 031659 131 ISYKPVKHGR 140 (155)
Q Consensus 131 ~Trk~~~Hg~ 140 (155)
+|||...|.+
T Consensus 82 pTrk~~~~ak 91 (93)
T KOG0899|consen 82 PTRKFFGHAK 91 (93)
T ss_pred chhhhhcccc
Confidence 9999999975
No 12
>PF03131 bZIP_Maf: bZIP Maf transcription factor; InterPro: IPR004826 There are several different types of Maf transcription factors with different roles in the cell. MafG and MafH are small Mafs which lack a putative transactivation domain. They behave as transcriptional repressors when they dimerize among themselves. However they also serve as transcriptional activators by dimerizing with other (usually larger) basic-zipper proteins and recruiting them to specific DNA-binding sites. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Neural retina-specific leucine zipper proteins also belong to this family. Together with the basic region, the Maf extended homology region (EHR), conserved only within the Maf family, defines the DNA binding specific to Mafs. This structure enables Mafs to make a broader area of contact with DNA and to recognise longer DNA sequences. In particular, the two residues at the beginning of helix H2 are positioned to recognise the flanking region []. Small Maf proteins heterodimerize with Fos and may act as competitive repressors of the NF2-E2 transcription factor. In mouse, Maf1 may play an early role in axial patterning. Defects in these proteins are a cause of autosomal dominant retinitis pigmentosa. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2KZ5_A 3A5T_A 1K1V_A 1SKN_P 2WT7_B 2WTY_B.
Probab=74.92 E-value=2.1 Score=30.86 Aligned_cols=33 Identities=33% Similarity=0.553 Sum_probs=20.8
Q ss_pred CChhHHhcCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHH
Q 031659 30 VDLDALLDMSTDELAKLFSARARRRFQRGLKRKPMALIKKLR 71 (155)
Q Consensus 30 ~~ld~L~~ms~eel~~L~~ar~RR~~~Rgl~k~~~~Llkklr 71 (155)
++-|+|..||.+||-.++ +|++..+...|+.+|
T Consensus 1 ~s~eeL~~m~v~efn~~L---------~~lt~~q~~~lK~~R 33 (92)
T PF03131_consen 1 FSDEELVSMSVREFNRLL---------RGLTEEQIAELKQRR 33 (92)
T ss_dssp --HHHHHHS-HHHHHHHC---------TTS-HHHHHHHHHHH
T ss_pred CCHHHHhhCCHHHHHHHH---------HcCCHHHHHHHHHHH
Confidence 367899999999986665 566656555555554
No 13
>cd06101 citrate_synt Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the
Probab=72.23 E-value=3.4 Score=35.21 Aligned_cols=24 Identities=29% Similarity=0.540 Sum_probs=20.9
Q ss_pred eeeeecCChhHHh-cCCHHHHHHHH
Q 031659 24 KFSFRGVDLDALL-DMSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~-~ms~eel~~L~ 47 (155)
+..|||++++||. ++|++|.+-||
T Consensus 22 ~l~yRGy~i~dL~~~~~f~ev~~LL 46 (265)
T cd06101 22 GLRYRGYPIEELAENSSFEEVAYLL 46 (265)
T ss_pred EEEECCeeHHHHHhcCCHHHHHHHH
Confidence 4789999999998 88899987764
No 14
>PRK12350 citrate synthase 2; Provisional
Probab=70.28 E-value=4.1 Score=36.45 Aligned_cols=24 Identities=25% Similarity=0.609 Sum_probs=20.4
Q ss_pred eeeeecCChhHHhcC-CHHHHHHHH
Q 031659 24 KFSFRGVDLDALLDM-STDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~m-s~eel~~L~ 47 (155)
..+|||++++||-+- |+||.+-||
T Consensus 24 ~L~YRGy~i~dLa~~~sFeEva~LL 48 (353)
T PRK12350 24 ALRYRGVDIEDLVGRVTFEDVWALL 48 (353)
T ss_pred EEEECCccHHHHhccCCHHHHHHHH
Confidence 489999999999965 789987774
No 15
>cd06116 CaCS_like Chloroflexus aurantiacus (Ca) citrate synthase (CS)_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). This group is similar to gram-negative Escherichia coli (Ec) CS (type II, gltA) and Arabidopsis thaliana (Ath) peroxisomal (Per) CS. However EcCS and AthPerCS are not found in this group. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers w
Probab=66.73 E-value=5.2 Score=36.03 Aligned_cols=24 Identities=29% Similarity=0.441 Sum_probs=20.3
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||++++||.+ -++||.+-||
T Consensus 28 ~L~YRGy~I~dL~~~~~feEv~yLL 52 (384)
T cd06116 28 ILRYRGYPIEQLAEQSSYLEVAYLL 52 (384)
T ss_pred eEEECCccHHHHhccCCHHHHHHHH
Confidence 58999999999996 6888877664
No 16
>TIGR03738 PRTRC_C PRTRC system protein C. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated PRTRC system protein C.
Probab=66.37 E-value=4.1 Score=28.80 Aligned_cols=28 Identities=29% Similarity=0.533 Sum_probs=24.4
Q ss_pred eeeeeeecCChhHH-hcCCHHHHHHHHHH
Q 031659 22 FKKFSFRGVDLDAL-LDMSTDELAKLFSA 49 (155)
Q Consensus 22 f~kFtYRG~~ld~L-~~ms~eel~~L~~a 49 (155)
-|.|.|.|+.|++- -.||.||.+.++.+
T Consensus 6 ~RvF~~~gi~L~DP~p~~spe~V~dfYs~ 34 (66)
T TIGR03738 6 SRVFTYNGVRLADPSPAMSPEQVRDFYSA 34 (66)
T ss_pred EEEEEECCeEcCCCCCCCCHHHHHHHHhc
Confidence 36799999999988 88999999888876
No 17
>cd06113 citrate_synt_like_1_2 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) a carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) h
Probab=66.03 E-value=5 Score=36.39 Aligned_cols=24 Identities=33% Similarity=0.577 Sum_probs=19.9
Q ss_pred eeeeecCChhHHhcC-------CHHHHHHHH
Q 031659 24 KFSFRGVDLDALLDM-------STDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~m-------s~eel~~L~ 47 (155)
+..|||++++||.+- ++||.+-||
T Consensus 37 ~L~yRGy~I~dLa~~~p~~~~~sFEev~yLL 67 (406)
T cd06113 37 KLYYRGYDVEDLVNGAQKENRFGFEETAYLL 67 (406)
T ss_pred eeeECCCcHHHHHhhcccccCCCHHHHHHHH
Confidence 589999999999975 788876664
No 18
>cd06109 BsCS-I_like Bacillus subtilis (Bs) citrate synthase CS-I_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains proteins similar to BsCS-I, one of two CS isozymes in the gram-positive B. subtilis. The majority of CS activity in B. subtilis is provided by the other isozyme, BsCS-II (not included in this group). BsCS-
Probab=65.40 E-value=5.9 Score=35.19 Aligned_cols=24 Identities=25% Similarity=0.504 Sum_probs=20.4
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||++++||.+ -+.||.+-||
T Consensus 22 ~L~YRGy~i~dL~~~~~feev~~LL 46 (349)
T cd06109 22 RLIIRGYSVEDLAGSASFEDVAALL 46 (349)
T ss_pred eEEECCccHHHHHhhCCHHHHHHHH
Confidence 48899999999996 6799987765
No 19
>cd06108 Ec2MCS_like Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and OAA to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). This group contains proteins similar to the E. coli 2MCS, EcPrpC. EcPrpC is one of two CS isozymes in the gram-negative E. coli. EcPrpC is a dimeric (type I ) CS; it is induced during growth on propionate and prefers PrCoA as a substrate though it has partial CS activity with AcCoA. This group also includes Salmonella typhimurium PrpC and Ralstonia eutropha (Re) 2-MCS1 which are also induced during growth on propionate and prefer PrCoA as substrate, but can also use AcCoA. Re 2-MCS1 can use butyryl-CoA and valeryl-CoA at a lower rate. A second Ralstonia eutropha 2MC
Probab=64.79 E-value=6.1 Score=35.36 Aligned_cols=24 Identities=29% Similarity=0.641 Sum_probs=20.6
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||++++||.+ -+.||++-||
T Consensus 22 ~L~yRGy~i~dLa~~~sfeeva~LL 46 (363)
T cd06108 22 GLTYRGYDIEDLAENATFEEVAYLL 46 (363)
T ss_pred EEEECCccHHHHHhcCCHHHHHHHH
Confidence 58999999999996 6799987765
No 20
>PRK14034 citrate synthase; Provisional
Probab=63.78 E-value=6.4 Score=35.33 Aligned_cols=24 Identities=25% Similarity=0.535 Sum_probs=20.6
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||++++||.+ -+.||.+-||
T Consensus 24 ~L~YRGy~i~dLa~~~~fEeva~LL 48 (372)
T PRK14034 24 TLTYVGYNIDDLAENASFEEVVYLL 48 (372)
T ss_pred eEEECCccHHHHhccCCHHHHHHHH
Confidence 59999999999996 6899987665
No 21
>cd06118 citrate_synt_like_1 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and
Probab=62.39 E-value=6.5 Score=34.73 Aligned_cols=24 Identities=33% Similarity=0.607 Sum_probs=20.7
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
.-.|||++++||.+ .++||.+-|+
T Consensus 22 ~l~YRG~~i~dL~~~~~feeva~LL 46 (358)
T cd06118 22 ILRYRGYDIEELAEKSSFEEVAYLL 46 (358)
T ss_pred eEEECCccHHHHHhcCCHHHHHHHH
Confidence 48999999999996 7899988765
No 22
>PRK14036 citrate synthase; Provisional
Probab=62.09 E-value=7.4 Score=34.96 Aligned_cols=24 Identities=29% Similarity=0.403 Sum_probs=20.2
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||++++||.+ .+.||.+-|+
T Consensus 27 ~L~yRGy~i~dL~~~~~Feev~~LL 51 (377)
T PRK14036 27 ILEYRGYPIEELAEKSSFLETAYLL 51 (377)
T ss_pred EEEECCccHHHHHccCCHHHHHHHH
Confidence 47899999999996 7899977665
No 23
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=61.51 E-value=6.8 Score=30.72 Aligned_cols=22 Identities=36% Similarity=0.662 Sum_probs=18.8
Q ss_pred ecCChhHHhcCCHHHHHHHHHH
Q 031659 28 RGVDLDALLDMSTDELAKLFSA 49 (155)
Q Consensus 28 RG~~ld~L~~ms~eel~~L~~a 49 (155)
+..+||+|++||-+|+-+++..
T Consensus 89 ~~~tLe~Llemsd~el~~~l~~ 110 (129)
T PF13543_consen 89 KVLTLEALLEMSDEELKEILNR 110 (129)
T ss_pred hhcCHHHHHhCCHHHHHHHHHH
Confidence 3569999999999999888864
No 24
>PRK12351 methylcitrate synthase; Provisional
Probab=60.71 E-value=8.1 Score=34.80 Aligned_cols=26 Identities=27% Similarity=0.464 Sum_probs=21.7
Q ss_pred eeeeeeecCChhHHhc-CCHHHHHHHH
Q 031659 22 FKKFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 22 f~kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
.....|||++++||.+ -+.||.+-||
T Consensus 29 ~g~L~YRGy~I~dLa~~~~feeva~LL 55 (378)
T PRK12351 29 GNDLHYRGYDILDLAEHCEFEEVAHLL 55 (378)
T ss_pred CCEEEECCccHHHHHhcCCHHHHHHHH
Confidence 4579999999999996 6789977665
No 25
>PRK14037 citrate synthase; Provisional
Probab=60.65 E-value=8.1 Score=34.71 Aligned_cols=23 Identities=26% Similarity=0.537 Sum_probs=19.7
Q ss_pred eeeecCChhHHhc-CCHHHHHHHH
Q 031659 25 FSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 25 FtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
..|||++++||.. .+++|.+-|+
T Consensus 28 L~yRGy~i~dL~~~~~Feev~~LL 51 (377)
T PRK14037 28 LRYRGYNIEDLVNYGSYEETIYLM 51 (377)
T ss_pred EEECCccHHHHHccCCHHHHHHHH
Confidence 7899999999994 7899977665
No 26
>cd06115 AthCS_per_like Arabidopsis thaliana (Ath) peroxisomal (Per) CS_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains three Arabidopsis peroxisomal CS proteins, CYS1, -2, and -3 which are involved in the glyoxylate cycle. AthCYS1, in addition to a peroxisomal targeting sequence, has a predicted secretory signal peptide; it may be targeted to both the secretory pathway and the peroxisomes and is thought to be located in the extracellular matrix. AthCSY1 is expr
Probab=60.52 E-value=7.8 Score=35.30 Aligned_cols=24 Identities=25% Similarity=0.430 Sum_probs=19.9
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||++++||.+ -++||.+-||
T Consensus 48 ~L~YRGy~I~dLa~~~~feEv~~LL 72 (410)
T cd06115 48 ILRYRGYPIEELAEKSTFLEVAYLL 72 (410)
T ss_pred eEEECCccHHHHHhcCCHHHHHHHH
Confidence 47899999999997 5788876664
No 27
>cd06111 DsCS_like Cold-active citrate synthase (CS) from an Antarctic bacterial strain DS2-3R (Ds)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. DsCS, compared with CS from the hyperthermophile Pyrococcus furiosus (not included in this group), has an increase in the size of surface loops, a higher proline content in the loop regions, a more accessible active site, and a highe
Probab=60.30 E-value=7.5 Score=34.63 Aligned_cols=24 Identities=29% Similarity=0.544 Sum_probs=20.0
Q ss_pred eeeeecCChhHHh-cCCHHHHHHHH
Q 031659 24 KFSFRGVDLDALL-DMSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~-~ms~eel~~L~ 47 (155)
...|||+|++||. +.++||.+-|+
T Consensus 22 ~L~yRG~di~dLa~~~~feeva~LL 46 (362)
T cd06111 22 SLTYRGYPVQDLAENCSFEEVAYLL 46 (362)
T ss_pred eEEECCccHHHHHccCCHHHHHHHH
Confidence 4789999999999 55899987664
No 28
>PF00285 Citrate_synt: Citrate synthase; InterPro: IPR002020 Citrate synthase 2.3.3.1 from EC is a member of a small family of enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors. It catalyses the first reaction in the Krebs' cycle, namely the conversion of oxaloacetate and acetyl-coenzyme A into citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The reaction proceeds via a non-covalently bound citryl-coenzyme A intermediate in a 2-step process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA). Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a conformational change upon binding of the oxaloacetate ligand, whereby the active site cleft closes over in order to form the acetyl-CoA binding site []. The energy required for domain closure comes from the interaction of the enzyme with the substrate. Type II enzymes possess an extra N-terminal beta-sheet domain, and some type II enzymes are allosterically inhibited by NADH []. This entry represents types I and II citrate synthase enzymes, as well as the related enzymes 2-methylcitrate synthase and ATP citrate synthase. 2-methylcitrate (2.3.3.5 from EC) synthase catalyses the conversion of oxaloacetate and propanoyl-CoA into (2R,3S)-2-hydroxybutane-1,2,3-tricarboxylate and coenzyme A. This enzyme is induced during bacterial growth on propionate, while type II hexameric citrate synthase is constitutive []. ATP citrate synthase (2.3.3.8 from EC) (also known as ATP citrate lyase) catalyses the MgATP-dependent, CoA-dependent cleavage of citrate into oxaloacetate and acetyl-CoA, a key step in the reductive tricarboxylic acid pathway of CO2 assimilation used by a variety of autotrophic bacteria and archaea to fix carbon dioxide []. ATP citrate synthase is composed of two distinct subunits. In eukaryotes, ATP citrate synthase is a homotetramer of a single large polypeptide, and is used to produce cytosolic acetyl-CoA from mitochondrial produced citrate [].; GO: 0046912 transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer, 0044262 cellular carbohydrate metabolic process; PDB: 2C6X_D 3L96_B 1OWB_B 1NXG_A 1K3P_A 1OWC_B 3L97_B 1NXE_A 3L98_A 3L99_A ....
Probab=60.10 E-value=5.7 Score=34.95 Aligned_cols=23 Identities=35% Similarity=0.670 Sum_probs=20.2
Q ss_pred eeeecCChhHHhc-CCHHHHHHHH
Q 031659 25 FSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 25 FtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
-.|||++++||.+ -++||.+-||
T Consensus 22 L~YRGy~i~dL~~~~sfeeva~LL 45 (356)
T PF00285_consen 22 LRYRGYDIEDLAENASFEEVAYLL 45 (356)
T ss_dssp EEETTEEHHHHHHHSBHHHHHHHH
T ss_pred EEEcCeEHHHHHhcCCHHHHHHHH
Confidence 7899999999999 7788877765
No 29
>TIGR01798 cit_synth_I citrate synthase I (hexameric type). This model describes one of several distinct but closely homologous classes of citrate synthase, the protein that brings carbon (from acetyl-CoA) into the TCA cycle. This form, class I, is known to be hexameric and allosterically inhibited by NADH in Escherichia coli, Acinetobacter anitratum, Azotobacter vinelandii, Pseudomonas aeruginosa, etc. In most species with a class I citrate synthase, a dimeric class II isozyme is found. The class II enzyme may act primarily on propionyl-CoA to make 2-methylcitrate or be bifunctional, may be found among propionate utilization enzymes, and may be constitutive or induced by propionate. Some members of this model group as class I enzymes, and may be hexameric, but have shown regulatory properties more like class II enzymes.
Probab=59.85 E-value=8.3 Score=35.16 Aligned_cols=24 Identities=25% Similarity=0.355 Sum_probs=19.9
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
..+|||++++||.+ -++||.+-||
T Consensus 55 ~L~YRGy~I~dL~~~~~feEv~yLL 79 (412)
T TIGR01798 55 ILLYRGYPIDQLATKSDYLEVCYLL 79 (412)
T ss_pred EEEECCccHHHHhccCCHHHHHHHH
Confidence 47999999999998 5788876664
No 30
>cd06117 Ec2MCS_like_1 Subgroup of Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and OAA to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). This group contains proteins similar to the E. coli 2MCS, EcPrpC. EcPrpC is one of two CS isozymes in the gram-negative E. coli. EcPrpC is a dimeric (type I ) CS; it is induced during growth on propionate and prefers PrCoA as a substrate, but has a partial CS activity with AcCoA. This group also includes Salmonella typhimurium PrpC and Ralstonia eutropha (Re) 2-MCS1 which are also induced during growth on propionate, prefer PrCoA as substrate, but can also can use AcCoA. Re 2-MCS1 at a low rate can use butyryl-CoA and valeryl-CoA. A second Ralstonia eu
Probab=59.27 E-value=8.9 Score=34.31 Aligned_cols=25 Identities=28% Similarity=0.522 Sum_probs=20.6
Q ss_pred eeeeeecCChhHHh-cCCHHHHHHHH
Q 031659 23 KKFSFRGVDLDALL-DMSTDELAKLF 47 (155)
Q Consensus 23 ~kFtYRG~~ld~L~-~ms~eel~~L~ 47 (155)
-...|||++++||. +-+.||.+-||
T Consensus 21 g~L~YRGy~i~dLa~~~~FEeva~LL 46 (366)
T cd06117 21 NDLHYRGYDILDLAEKCEFEEVAHLL 46 (366)
T ss_pred CEEEECCccHHHHHhcCCHHHHHHHH
Confidence 36899999999997 55799987765
No 31
>cd06107 EcCS_AthCS-per_like Escherichia coli (Ec) citrate synthase (CS) gltA and Arabidopsis thaliana (Ath) peroxisomal (Per) CS_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of ide
Probab=59.19 E-value=8.5 Score=34.69 Aligned_cols=24 Identities=25% Similarity=0.498 Sum_probs=19.4
Q ss_pred eeeeecCChhHHhcC-CHHHHHHHH
Q 031659 24 KFSFRGVDLDALLDM-STDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~m-s~eel~~L~ 47 (155)
...|||++++||.+- +.||.+-||
T Consensus 28 ~L~YRGy~I~dLa~~~~feev~yLL 52 (382)
T cd06107 28 ILLYRGYPIEQLAESSTYEEVAYLL 52 (382)
T ss_pred eEEECCccHHHHHhcCCHHHHHHHH
Confidence 479999999999966 478876664
No 32
>PRK14033 citrate synthase; Provisional
Probab=58.83 E-value=9.1 Score=34.31 Aligned_cols=24 Identities=29% Similarity=0.509 Sum_probs=20.1
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||+|++||.+ .++||.+-|+
T Consensus 32 ~L~yRG~di~dLa~~~sfeeva~LL 56 (375)
T PRK14033 32 SLTYRGYPVQDLAARCSFEEVAYLL 56 (375)
T ss_pred eEEECCccHHHHHhcCCHHHHHHHH
Confidence 47899999999996 7899987654
No 33
>PRK09569 type I citrate synthase; Reviewed
Probab=58.78 E-value=7.3 Score=35.85 Aligned_cols=23 Identities=13% Similarity=0.391 Sum_probs=19.1
Q ss_pred eeeecCChhHHhcC----------CHHHHHHHH
Q 031659 25 FSFRGVDLDALLDM----------STDELAKLF 47 (155)
Q Consensus 25 FtYRG~~ld~L~~m----------s~eel~~L~ 47 (155)
-.|||++++||.+- +.||.+-||
T Consensus 61 l~YRGy~I~dL~~~~p~~~~~~~~~fEev~~LL 93 (437)
T PRK09569 61 IRFRGKTIPETFEALPKAPGSEYPTVESFWYFL 93 (437)
T ss_pred eeECCccHHHHHhhCccccccCCCCHHHHHHHH
Confidence 47999999999977 688877664
No 34
>PRK12349 citrate synthase 3; Provisional
Probab=58.06 E-value=9.5 Score=34.10 Aligned_cols=24 Identities=21% Similarity=0.302 Sum_probs=20.4
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||+|++||.+ .|+||.+-|+
T Consensus 28 ~L~YRGydi~dLa~~~sFeeva~LL 52 (369)
T PRK12349 28 EIVIQGYDLIELSKTKEYLDIVHLL 52 (369)
T ss_pred EEEECCccHHHHHccCCHHHHHHHH
Confidence 48999999999996 6899987765
No 35
>TIGR01800 cit_synth_II 2-methylcitrate synthase/citrate synthase II. Members of this family are dimeric enzymes with activity as 2-methylcitrate synthase, citrate synthase, or both. Many Gram-negative species have a hexameric citrate synthase, termed citrate synthase I (TIGR01798). Members of this family (TIGR01800) appear as a second citrate synthase isozyme but typically are associated with propionate metabolism and synthesize 2-methylcitrate from propionyl-CoA; citrate synthase activity may be incidental. A number of species, including Thermoplasma acidophilum, Pyrococcus furiosus, and the Antarctic bacterium DS2-3R have a bifunctional member of this family as the only citrate synthase isozyme.
Probab=57.84 E-value=8.9 Score=34.16 Aligned_cols=23 Identities=35% Similarity=0.694 Sum_probs=19.9
Q ss_pred eeeecCChhHHhc-CCHHHHHHHH
Q 031659 25 FSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 25 FtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
..|||+|++||.. .++||.+-|+
T Consensus 23 l~yRG~~i~dL~~~~~feeva~LL 46 (368)
T TIGR01800 23 LTYRGYDIEDLAEHASFEEVAYLL 46 (368)
T ss_pred EEECCeeHHHHHhcCCHHHHHHHH
Confidence 7899999999995 7899987654
No 36
>cd06110 BSuCS-II_like Bacillus subtilis (Bs) citrate synthase (CS)-II_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains proteins similar to BsCS-II, the major CS of the gram-positive bacterium Bacillus subtilis. A mutation in the gene which encodes BsCS-II (citZ gene) has been described which resulted in a significant loss of CS activity, partial glutamate auxotrophy, and a sporulation deficiency, a
Probab=57.53 E-value=9.2 Score=33.83 Aligned_cols=23 Identities=30% Similarity=0.593 Sum_probs=19.7
Q ss_pred eeeecCChhHHhc-CCHHHHHHHH
Q 031659 25 FSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 25 FtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
..|||+|++||.. .+.||.+-|+
T Consensus 23 L~yRG~di~dL~~~~~feeva~LL 46 (356)
T cd06110 23 LIYRGYDIHDLAENSTFEEVAYLL 46 (356)
T ss_pred EEECCeeHHHHHhcCCHHHHHHHH
Confidence 6899999999995 7899987665
No 37
>cd06112 citrate_synt_like_1_1 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, an
Probab=57.33 E-value=10 Score=34.00 Aligned_cols=24 Identities=33% Similarity=0.613 Sum_probs=20.0
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||++++||.. .+.||.+-|+
T Consensus 24 ~L~yRGy~i~dL~~~~~Feev~~LL 48 (373)
T cd06112 24 ILEYRGYDIEELAEYSSFEEVALLL 48 (373)
T ss_pred EEEECCccHHHHhcCCCHHHHHHHH
Confidence 47999999999996 5788977665
No 38
>PLN02456 citrate synthase
Probab=57.00 E-value=8.8 Score=35.47 Aligned_cols=24 Identities=29% Similarity=0.534 Sum_probs=19.9
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||++++||.+ .+.||.+-||
T Consensus 87 ~L~YRGy~I~dLa~~~~feevayLL 111 (455)
T PLN02456 87 ILRFRGYPIEELAEKSPFEEVAYLL 111 (455)
T ss_pred EEEECCccHHHHHhcCCHHHHHHHH
Confidence 46999999999997 6788877665
No 39
>PRK14035 citrate synthase; Provisional
Probab=56.55 E-value=10 Score=34.05 Aligned_cols=24 Identities=29% Similarity=0.580 Sum_probs=20.5
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
+..|||++++||.+ -+.||.+-||
T Consensus 24 ~L~YRGy~i~dLa~~~~Feeva~LL 48 (371)
T PRK14035 24 QLTYAGYDIDDLAENASFEEVIFLL 48 (371)
T ss_pred EeEECCccHHHHHhcCCHHHHHHHH
Confidence 48999999999997 5799987765
No 40
>cd06114 EcCS_like Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some typ
Probab=55.89 E-value=11 Score=34.21 Aligned_cols=24 Identities=25% Similarity=0.411 Sum_probs=20.3
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||++++||.+ -++||.+-||
T Consensus 50 ~L~YRGy~i~dLa~~~sfEEva~LL 74 (400)
T cd06114 50 ILRYRGYPIEQLAEKSSFLEVCYLL 74 (400)
T ss_pred EEEECCccHHHHHhcCCHHHHHHHH
Confidence 47899999999997 5799987765
No 41
>PRK14032 citrate synthase; Provisional
Probab=55.11 E-value=10 Score=34.95 Aligned_cols=24 Identities=33% Similarity=0.603 Sum_probs=19.6
Q ss_pred eeeeecCChhHHhcC-------CHHHHHHHH
Q 031659 24 KFSFRGVDLDALLDM-------STDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~m-------s~eel~~L~ 47 (155)
..+|||++++||.+- ++||.+-||
T Consensus 67 ~L~YRGy~I~dLa~~~~~~~~~~FeEv~~LL 97 (447)
T PRK14032 67 KLYYRGYDIKDLVNGFLKEKRFGFEEVAYLL 97 (447)
T ss_pred ceeECCccHHHHHhhcccccCCCHHHHHHHH
Confidence 388999999999977 788866554
No 42
>PRK05614 gltA type II citrate synthase; Reviewed
Probab=54.65 E-value=10 Score=34.61 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=20.2
Q ss_pred eeeeecCChhHHhc-CCHHHHHHHH
Q 031659 24 KFSFRGVDLDALLD-MSTDELAKLF 47 (155)
Q Consensus 24 kFtYRG~~ld~L~~-ms~eel~~L~ 47 (155)
...|||++++||.+ -++||.+-||
T Consensus 68 ~L~YRGy~i~dLa~~~~feEva~LL 92 (419)
T PRK05614 68 ILLYRGYPIEQLAEKSDFLEVCYLL 92 (419)
T ss_pred EEEECCccHHHHHhcCCHHHHHHHH
Confidence 37899999999998 5788877775
No 43
>PRK06224 citrate synthase; Provisional
Probab=51.14 E-value=15 Score=31.16 Aligned_cols=23 Identities=30% Similarity=0.540 Sum_probs=18.3
Q ss_pred eeeeecCChhHHh-cCCHHHHHHH
Q 031659 24 KFSFRGVDLDALL-DMSTDELAKL 46 (155)
Q Consensus 24 kFtYRG~~ld~L~-~ms~eel~~L 46 (155)
+..|||++++||. ++|++|..=|
T Consensus 20 ~l~yrG~~~~dL~~~~sf~e~~~l 43 (263)
T PRK06224 20 EIYVRGYDLEDLIGKLSFTDMIFL 43 (263)
T ss_pred eeEECCccHHHHhhcCCHHHHHHH
Confidence 4899999999994 7888885443
No 44
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=50.50 E-value=14 Score=39.70 Aligned_cols=33 Identities=18% Similarity=0.459 Sum_probs=27.5
Q ss_pred eeeeeecCChhHHhcCCHHHHHHHHHH--HHhhhh
Q 031659 23 KKFSFRGVDLDALLDMSTDELAKLFSA--RARRRF 55 (155)
Q Consensus 23 ~kFtYRG~~ld~L~~ms~eel~~L~~a--r~RR~~ 55 (155)
-+.+|+|+++.|+++|+.+|.++.|.. +..+.+
T Consensus 1646 L~v~~~gk~I~dvL~mtv~ea~~~F~~~~~i~~~L 1680 (1809)
T PRK00635 1646 QEVVYEGKHFGQLLQTPIEEVAETFPFLKKIQKPL 1680 (1809)
T ss_pred HhheeCCCCHHHHhcCCHHHHHHHhhccHHHHHHH
Confidence 458999999999999999999999965 444444
No 45
>cd06105 ScCit1-2_like Saccharomyces cerevisiae (Sc) citrate synthases Cit1-2_like. Citrate synthases (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-neg
Probab=44.73 E-value=17 Score=33.42 Aligned_cols=23 Identities=22% Similarity=0.404 Sum_probs=18.3
Q ss_pred eeeecCChhHHhcCC----------HHHHHHHH
Q 031659 25 FSFRGVDLDALLDMS----------TDELAKLF 47 (155)
Q Consensus 25 FtYRG~~ld~L~~ms----------~eel~~L~ 47 (155)
-.|||++++||.+-+ .||++-||
T Consensus 59 l~YRGy~I~dLa~~~~~~~~~~~~~fEev~yLL 91 (427)
T cd06105 59 IRFRGLSIPECQKLLPKAPGGEEPLPEGLFWLL 91 (427)
T ss_pred eEECCccHHHHHhhCcccccccccCHHHHHHHH
Confidence 479999999998764 68877664
No 46
>cd06103 ScCS-like Saccharomyces cerevisiae (Sc) citrate synthase (CS)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homo
Probab=44.70 E-value=17 Score=33.37 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=18.1
Q ss_pred eeecCChhHHhcCC----------HHHHHHHH
Q 031659 26 SFRGVDLDALLDMS----------TDELAKLF 47 (155)
Q Consensus 26 tYRG~~ld~L~~ms----------~eel~~L~ 47 (155)
.|||++++||.+-+ .||.+-||
T Consensus 60 ~YRGy~I~dLa~~~~~~~~~~~~~fEev~yLL 91 (426)
T cd06103 60 RFRGKTIPECQELLPKADGGGEPLPEGLFWLL 91 (426)
T ss_pred EECCccHHHHHhhCccccccCcCcHHHHHHHH
Confidence 69999999999863 88877665
No 47
>cd06102 citrate_synt_like_2 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and
Probab=40.53 E-value=25 Score=30.49 Aligned_cols=26 Identities=27% Similarity=0.397 Sum_probs=21.7
Q ss_pred eeeeeecCChhHHh-cCCHHHHHHHHH
Q 031659 23 KKFSFRGVDLDALL-DMSTDELAKLFS 48 (155)
Q Consensus 23 ~kFtYRG~~ld~L~-~ms~eel~~L~~ 48 (155)
....|||+|+.||. +.++||.+.|+=
T Consensus 31 ~~~~yRG~da~~L~~~~~~e~va~LLw 57 (282)
T cd06102 31 GRLFYRGRDAVELAETATLEEVAALLW 57 (282)
T ss_pred CeeEEcCccHHHHHhcCCHHHHHHHHH
Confidence 34789999999997 788999888763
No 48
>cd06106 ScCit3_like Saccharomyces cerevisiae (Sc) 2-methylcitrate synthase Cit3-like. 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxaloacetate (OAA) to form 2-methylcitrate and CoA. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) with OAA to form citrate and CoA, the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the a
Probab=40.00 E-value=20 Score=32.96 Aligned_cols=23 Identities=13% Similarity=0.254 Sum_probs=17.9
Q ss_pred eeeecCChhHHhcC--------CH--HHHHHHH
Q 031659 25 FSFRGVDLDALLDM--------ST--DELAKLF 47 (155)
Q Consensus 25 FtYRG~~ld~L~~m--------s~--eel~~L~ 47 (155)
-.|||++++||.+- +. ||.+-||
T Consensus 59 l~YRGy~I~dLa~~~~~~~~~~~f~~Eev~yLL 91 (428)
T cd06106 59 IRFHGKTIPECQKELPKAPIGGEMLPESMLWLL 91 (428)
T ss_pred eeECCCcHHHHHhhCccccccCCccHHHHHHHH
Confidence 46999999999885 44 7776664
No 49
>PF14454 Prok_Ub: Prokaryotic Ubiquitin
Probab=39.21 E-value=21 Score=24.96 Aligned_cols=28 Identities=21% Similarity=0.508 Sum_probs=22.2
Q ss_pred eeeeeeecCChhH-HhcCCHHHHHHHHHH
Q 031659 22 FKKFSFRGVDLDA-LLDMSTDELAKLFSA 49 (155)
Q Consensus 22 f~kFtYRG~~ld~-L~~ms~eel~~L~~a 49 (155)
-|.|.|-|++|++ =-.||.||+..++.+
T Consensus 7 ~R~F~~~g~~L~DP~p~~spe~V~~~ya~ 35 (65)
T PF14454_consen 7 TRVFRYNGITLPDPNPSLSPEEVRDFYAA 35 (65)
T ss_pred EEEEEECCEECCCCCCCCCHHHHHHHHhh
Confidence 3678999999887 458999998777754
No 50
>PF12936 Kri1_C: KRI1-like family C-terminal; InterPro: IPR024626 The yeast member of the Kri1-like family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus []. This entry represents the C-terminal domain of this protein family.
Probab=37.19 E-value=37 Score=25.09 Aligned_cols=29 Identities=24% Similarity=0.519 Sum_probs=24.3
Q ss_pred eeeeee-------cCChhHHhcCCHHHHHHHHHHHH
Q 031659 23 KKFSFR-------GVDLDALLDMSTDELAKLFSARA 51 (155)
Q Consensus 23 ~kFtYR-------G~~ld~L~~ms~eel~~L~~ar~ 51 (155)
..|.|| |.|.+|+|.++-.||-+.++-..
T Consensus 27 ~RFkYr~V~p~~fGLt~~eIL~adDkeLNq~vsLKk 62 (93)
T PF12936_consen 27 TRFKYREVPPNSFGLTTEEILMADDKELNQWVSLKK 62 (93)
T ss_pred CceeeeecCcccCCCCHHHHHhCCHHHHHHHhhHHh
Confidence 449998 78999999999999988887643
No 51
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.17 E-value=32 Score=34.53 Aligned_cols=27 Identities=26% Similarity=0.598 Sum_probs=23.9
Q ss_pred eeeeeecCChhHHhcCCHHHHHHHHHH
Q 031659 23 KKFSFRGVDLDALLDMSTDELAKLFSA 49 (155)
Q Consensus 23 ~kFtYRG~~ld~L~~ms~eel~~L~~a 49 (155)
-+.+|+|+++.|+++|+.+|..+.+..
T Consensus 775 l~v~~~g~~i~dvl~~tv~e~~~f~~~ 801 (924)
T TIGR00630 775 LEVKYKGKNIADVLDMTVEEAYEFFEA 801 (924)
T ss_pred HhceeCCCCHHHHhCCcHHHHHHHHHh
Confidence 458999999999999999998888753
No 52
>PF05361 PP1_inhibitor: PKC-activated protein phosphatase-1 inhibitor; InterPro: IPR008025 Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction [].; GO: 0042325 regulation of phosphorylation, 0005737 cytoplasm; PDB: 2RLT_A 1J2M_A 1K5O_A 1J2N_A.
Probab=34.36 E-value=14 Score=29.74 Aligned_cols=40 Identities=35% Similarity=0.625 Sum_probs=23.1
Q ss_pred cCChhHHhcCCHHHHHHHHHHHHhhh-hh---c--CCCCCcc--hHHHHHHHhhhc
Q 031659 29 GVDLDALLDMSTDELAKLFSARARRR-FQ---R--GLKRKPM--ALIKKLRKAKRE 76 (155)
Q Consensus 29 G~~ld~L~~ms~eel~~L~~ar~RR~-~~---R--gl~k~~~--~Llkklrkak~~ 76 (155)
-+|+|+|++|+.|| +|++ +. + +-....| .||.+++...+.
T Consensus 73 EIDIDeLLDl~sde--------eR~~~LqelL~~C~~ptE~FI~ELL~kLkgL~k~ 120 (144)
T PF05361_consen 73 EIDIDELLDLESDE--------ERRRKLQELLQDCPKPTEDFIQELLSKLKGLRKL 120 (144)
T ss_dssp SSHHHHHHCTSSTT--------HHHHHHHHHHTTCSSTTHHHHHHHHHHCTTT---
T ss_pred cccHHHHhcCCchH--------HHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC
Confidence 36889999999887 5555 32 1 2222223 677777766553
No 53
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=32.51 E-value=38 Score=34.31 Aligned_cols=35 Identities=23% Similarity=0.503 Sum_probs=27.9
Q ss_pred ceeeeeeecCChhHHhcCCHHHHHHHHHHH--Hhhhh
Q 031659 21 TFKKFSFRGVDLDALLDMSTDELAKLFSAR--ARRRF 55 (155)
Q Consensus 21 tf~kFtYRG~~ld~L~~ms~eel~~L~~ar--~RR~~ 55 (155)
.-=+.+|+|+++.+.|+|+.||-.+.|.+- ..|++
T Consensus 767 EtLev~ykGK~IadVL~MTveEA~~FF~~~p~I~rkL 803 (935)
T COG0178 767 ETLEVKYKGKNIADVLDMTVEEALEFFEAIPKIARKL 803 (935)
T ss_pred ceEEEEECCccHHHHHhccHHHHHHHHhcchHHHHHH
Confidence 344689999999999999999988888763 34444
No 54
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=32.25 E-value=83 Score=20.30 Aligned_cols=35 Identities=37% Similarity=0.409 Sum_probs=23.9
Q ss_pred hHHhcCCHHHHHHHHHHHHhhhhhcCCCCCcc------hHHHHHHHhh
Q 031659 33 DALLDMSTDELAKLFSARARRRFQRGLKRKPM------ALIKKLRKAK 74 (155)
Q Consensus 33 d~L~~ms~eel~~L~~ar~RR~~~Rgl~k~~~------~Llkklrkak 74 (155)
+++..+|.+|| .+.-..-|+..+|. .+.+||+++.
T Consensus 1 ~d~~~LSd~eL-------~~~L~~~G~~~gPIt~sTR~vy~kkL~~~~ 41 (44)
T smart00540 1 DDVDRLSDAEL-------RAELKQYGLPPGPITDTTRKLYEKKLRKLR 41 (44)
T ss_pred CchhHcCHHHH-------HHHHHHcCCCCCCcCcchHHHHHHHHHHHH
Confidence 35677888887 34445679999995 4566777653
No 55
>PF06528 Phage_P2_GpE: Phage P2 GpE; InterPro: IPR009493 This entry is represented by Burkholderia phage phiE202, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins which are closely related to the GpE tail protein from Phage P2.
Probab=29.83 E-value=90 Score=19.81 Aligned_cols=20 Identities=25% Similarity=0.096 Sum_probs=16.2
Q ss_pred cCChhHHhcCCHHHHHHHHH
Q 031659 29 GVDLDALLDMSTDELAKLFS 48 (155)
Q Consensus 29 G~~ld~L~~ms~eel~~L~~ 48 (155)
|-+.+++..||++||+.-..
T Consensus 9 hW~Pse~~~m~l~El~~Wre 28 (39)
T PF06528_consen 9 HWPPSEMDAMSLDELMDWRE 28 (39)
T ss_pred CCCHHHHhcCCHHHHHHHHH
Confidence 45789999999999876543
No 56
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=27.16 E-value=38 Score=22.39 Aligned_cols=49 Identities=22% Similarity=0.375 Sum_probs=27.5
Q ss_pred HHHhhhhhcCCCCCcchHHHHHHHhhhcCCCCCCCCceEeccCCceeccCccccEEEEecCCccccc
Q 031659 49 ARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQV 115 (155)
Q Consensus 49 ar~RR~~~Rgl~k~~~~Llkklrkak~~~~~~~kp~~Ikt~~R~~~IlP~mVG~~v~VyNGK~f~~v 115 (155)
|+.|++++|+.|+- + .|.++.--.=....+|-.|-..-|.|+|++.+.|
T Consensus 8 Sksr~~~Rrs~~~l-----~-------------~~~l~~c~~cg~~~~~H~vc~~cG~y~~r~v~~~ 56 (56)
T PF01783_consen 8 SKSRKRMRRSHWKL-----K-------------APNLVKCPNCGEPKLPHRVCPSCGYYKGRQVIEV 56 (56)
T ss_dssp CHHHHHHHTTTTS--------------------TTSEEESSSSSSEESTTSBCTTTBBSSSSSSST-
T ss_pred ChhHccchhccccc-----c-------------ccceeeeccCCCEecccEeeCCCCeECCEEEeeC
Confidence 46788888887722 1 1112222222345666666555579999987754
No 57
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=26.04 E-value=53 Score=25.15 Aligned_cols=22 Identities=18% Similarity=0.320 Sum_probs=19.1
Q ss_pred ecCChhHHhcCCHHHHHHHHHH
Q 031659 28 RGVDLDALLDMSTDELAKLFSA 49 (155)
Q Consensus 28 RG~~ld~L~~ms~eel~~L~~a 49 (155)
|++--+++.+||+||+-+|+..
T Consensus 100 ~~ir~~~~~~~~~~~~~~~~~~ 121 (126)
T TIGR01689 100 RAIRPSEFSSLTYDEINTLTKI 121 (126)
T ss_pred hhhCHHHHHhcCHHHHHHHHhh
Confidence 6777899999999999988854
No 58
>TIGR01793 cit_synth_euk citrate (Si)-synthase, eukaryotic. This model includes both mitochondrial and peroxisomal forms of citrate synthase. Citrate synthase is the entry point to the TCA cycle from acetyl-CoA. Peroxisomal forms, such as SP:P08679 from yeast (recognized by the C-terminal targeting motif SKL) act in the glyoxylate cycle. Eukaryotic homologs excluded by the high trusted cutoff of this model include a Tetrahymena thermophila citrate synthase that doubles as a filament protein, a putative citrate synthase from Plasmodium falciparum (no TCA cycle), and a methylcitrate synthase from Aspergillus nidulans.
Probab=25.60 E-value=55 Score=30.14 Aligned_cols=23 Identities=22% Similarity=0.401 Sum_probs=16.6
Q ss_pred eeeecCChhHHhc----CC------HHHHHHHH
Q 031659 25 FSFRGVDLDALLD----MS------TDELAKLF 47 (155)
Q Consensus 25 FtYRG~~ld~L~~----ms------~eel~~L~ 47 (155)
-.|||++++||++ -+ .||++-||
T Consensus 62 l~yRGy~I~dl~~~~~~~~~~~~~~fEev~~LL 94 (427)
T TIGR01793 62 IRFRGLSIPECQKLLPKAKGGEEPLPEGLLWLL 94 (427)
T ss_pred eEECCeeHHHHHHHhccCCccccCCHHHHHHHH
Confidence 5799999999843 33 67766654
No 59
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=25.28 E-value=52 Score=20.33 Aligned_cols=19 Identities=37% Similarity=0.636 Sum_probs=15.0
Q ss_pred ecCChhHHhcCCHHHHHHH
Q 031659 28 RGVDLDALLDMSTDELAKL 46 (155)
Q Consensus 28 RG~~ld~L~~ms~eel~~L 46 (155)
.|+|.+.|+.|+.++|.++
T Consensus 26 ~~i~g~~L~~l~~~dL~~l 44 (63)
T cd00166 26 NGIDGDLLLLLTEEDLKEL 44 (63)
T ss_pred cCCCHHHHhHCCHHHHHHc
Confidence 4678999999999887643
No 60
>COG0372 GltA Citrate synthase [Energy production and conversion]
Probab=24.88 E-value=58 Score=29.71 Aligned_cols=22 Identities=36% Similarity=0.659 Sum_probs=17.3
Q ss_pred eeeecCChhHHhcCC-HHHHHHH
Q 031659 25 FSFRGVDLDALLDMS-TDELAKL 46 (155)
Q Consensus 25 FtYRG~~ld~L~~ms-~eel~~L 46 (155)
-+|||++++||.+-+ .+|..-|
T Consensus 40 L~yrGy~i~dla~~~~feev~~L 62 (390)
T COG0372 40 LRYRGYDIEDLAEKSSFEEVAYL 62 (390)
T ss_pred EEECCccHHHHHhhcCHHHHHHH
Confidence 789999999999884 5664444
No 61
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=24.54 E-value=40 Score=25.34 Aligned_cols=27 Identities=30% Similarity=0.629 Sum_probs=19.2
Q ss_pred eeeecCChhHHhcCCH---HHHHHHHHHHH
Q 031659 25 FSFRGVDLDALLDMST---DELAKLFSARA 51 (155)
Q Consensus 25 FtYRG~~ld~L~~ms~---eel~~L~~ar~ 51 (155)
..+||++-+++..+|- |+|++|+.+.+
T Consensus 4 lr~rGi~~e~v~~~S~~LideLa~i~~~p~ 33 (108)
T PF08921_consen 4 LRFRGIEEEQVQELSKELIDELAEICGCPR 33 (108)
T ss_dssp EEEESS-HHHHHHHHHHHHHHHHHHHT--G
T ss_pred EEEecCCHHHHHHHhHHHHHHHHHHHCCCc
Confidence 4689999999999985 57777776543
No 62
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=24.42 E-value=46 Score=22.62 Aligned_cols=26 Identities=31% Similarity=0.506 Sum_probs=17.2
Q ss_pred hhHHhcCCHHHHHHH-HHHHHhhhhhc
Q 031659 32 LDALLDMSTDELAKL-FSARARRRFQR 57 (155)
Q Consensus 32 ld~L~~ms~eel~~L-~~ar~RR~~~R 57 (155)
.|+|..++..+|-++ +|+++||-+-|
T Consensus 23 w~~lf~~~s~~LK~~GIp~r~RryiL~ 49 (57)
T PF09597_consen 23 WEKLFTTSSKQLKELGIPVRQRRYILR 49 (57)
T ss_pred HHHHHhcCHHHHHHCCCCHHHHHHHHH
Confidence 577777777666554 47777776643
No 63
>PF10109 FluMu_gp41: Mu-like prophage FluMu protein gp41; InterPro: IPR019289 Members of this family of prokaryotic proteins include various Gp41 proteins and related sequences [].
Probab=24.15 E-value=88 Score=20.90 Aligned_cols=22 Identities=18% Similarity=0.323 Sum_probs=17.4
Q ss_pred ecCChhHHhcCCHHHHHHHHHH
Q 031659 28 RGVDLDALLDMSTDELAKLFSA 49 (155)
Q Consensus 28 RG~~ld~L~~ms~eel~~L~~a 49 (155)
-|++.++|.+|+..++.++...
T Consensus 55 ~gl~~~~l~~L~~~D~~~l~~~ 76 (82)
T PF10109_consen 55 TGLPPEDLDQLDARDYNRLQEA 76 (82)
T ss_pred cCCCHHHHHcCCHHHHHHHHHH
Confidence 3688899999999888777543
No 64
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=22.64 E-value=82 Score=31.84 Aligned_cols=28 Identities=21% Similarity=0.533 Sum_probs=24.5
Q ss_pred ceeeeeeecCChhHHhcCCHHHHHHHHH
Q 031659 21 TFKKFSFRGVDLDALLDMSTDELAKLFS 48 (155)
Q Consensus 21 tf~kFtYRG~~ld~L~~ms~eel~~L~~ 48 (155)
.-...+|+|.++.|+++|+.+|..+++.
T Consensus 775 e~l~v~~~g~~i~dvl~ltv~E~l~~f~ 802 (943)
T PRK00349 775 ETLEVKYKGKNIADVLDMTVEEALEFFE 802 (943)
T ss_pred cceEEEECCCCHHHHhcCcHHHHHHHHH
Confidence 3456899999999999999999888874
No 65
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=22.46 E-value=37 Score=21.89 Aligned_cols=33 Identities=27% Similarity=0.578 Sum_probs=23.6
Q ss_pred eeeeeecCCh-hHHhcCCHHHHHHH-H-HHHHhhhh
Q 031659 23 KKFSFRGVDL-DALLDMSTDELAKL-F-SARARRRF 55 (155)
Q Consensus 23 ~kFtYRG~~l-d~L~~ms~eel~~L-~-~ar~RR~~ 55 (155)
..|...|++- +.|..|+.++|.++ + +...|+++
T Consensus 23 ~~f~~~~i~g~~~L~~l~~~~L~~lGI~~~~~r~kl 58 (66)
T PF07647_consen 23 DNFRENGIDGLEDLLQLTEEDLKELGITNLGHRRKL 58 (66)
T ss_dssp HHHHHTTCSHHHHHTTSCHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHcCCcHHHHHhhCCHHHHHHcCCCCHHHHHHH
Confidence 3477788898 99999999998765 2 33444444
No 66
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=22.39 E-value=54 Score=22.27 Aligned_cols=21 Identities=19% Similarity=0.442 Sum_probs=16.1
Q ss_pred eeccCccccEEEEecCCccccc
Q 031659 94 IIVPEMIGSIIGVYNGKTFNQV 115 (155)
Q Consensus 94 ~IlP~mVG~~v~VyNGK~f~~v 115 (155)
.++|--|-. -|.|+|++.+.+
T Consensus 36 ~~~pH~vc~-cG~Y~gr~v~~~ 56 (60)
T PRK01110 36 YHLPHHVSP-KGYYKGRKVLKK 56 (60)
T ss_pred eeccceecC-CcccCCeEeecc
Confidence 467777766 789999988764
No 67
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.46 E-value=72 Score=32.16 Aligned_cols=27 Identities=15% Similarity=0.290 Sum_probs=23.4
Q ss_pred eeeeeecCChhHHhcCCHHHHHHHHHH
Q 031659 23 KKFSFRGVDLDALLDMSTDELAKLFSA 49 (155)
Q Consensus 23 ~kFtYRG~~ld~L~~ms~eel~~L~~a 49 (155)
...+|.|+++.|+.+|+.+|+.+.+..
T Consensus 420 l~v~i~g~~I~e~~~~~v~~~~~~~~~ 446 (924)
T TIGR00630 420 LAVKVGGKSIADVSELSIREAHEFFNQ 446 (924)
T ss_pred heeEECCEEHHHHhcCCHHHHHHHHHh
Confidence 458899999999999999998887754
Done!