Query 032138
Match_columns 146
No_of_seqs 104 out of 200
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 10:06:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032138.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032138hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00658 RPOL8c RNA polymera 100.0 5.1E-68 1.1E-72 408.9 16.8 141 4-145 2-143 (143)
2 PF03870 RNA_pol_Rpb8: RNA pol 100.0 4.2E-67 9E-72 401.9 16.6 137 8-145 1-138 (138)
3 PTZ00167 RNA polymerase subuni 100.0 3.4E-66 7.4E-71 398.9 16.5 139 1-146 2-140 (144)
4 KOG3400 RNA polymerase subunit 100.0 8.9E-66 1.9E-70 391.3 14.7 143 1-145 1-143 (143)
5 PRK14980 DNA-directed RNA poly 99.0 1.8E-08 3.8E-13 76.6 13.4 118 4-145 6-125 (127)
6 PF03459 TOBE: TOBE domain; I 80.4 7.2 0.00016 24.8 5.4 50 91-144 6-58 (64)
7 PF08530 PepX_C: X-Pro dipepti 76.2 11 0.00024 29.6 6.4 54 11-65 115-181 (218)
8 PF10246 MRP-S35: Mitochondria 41.8 36 0.00079 25.4 3.3 50 87-144 22-72 (104)
9 PRK05371 x-prolyl-dipeptidyl a 41.4 83 0.0018 30.3 6.5 28 38-65 712-739 (767)
10 TIGR00976 /NonD putative hydro 41.0 74 0.0016 28.8 5.8 54 12-66 446-506 (550)
11 KOG4078 Putative mitochondrial 39.7 29 0.00063 27.6 2.7 28 89-124 83-110 (173)
12 PRK06763 F0F1 ATP synthase sub 37.1 2.1E+02 0.0046 23.9 7.4 29 29-60 56-84 (213)
13 PF13745 HxxPF_rpt: HxxPF-repe 35.4 70 0.0015 20.9 3.8 30 19-50 55-84 (91)
14 PF11183 PmrD: Polymyxin resis 33.0 91 0.002 22.3 4.1 30 28-58 17-47 (82)
15 PF08292 RNA_pol_Rbc25: RNA po 32.5 50 0.0011 24.8 2.9 49 6-63 25-73 (122)
16 TIGR00638 Mop molybdenum-pteri 31.7 1.4E+02 0.0029 18.8 6.0 51 91-145 8-61 (69)
17 PF10871 DUF2748: Protein of u 27.4 42 0.0009 30.0 1.9 17 104-120 171-187 (447)
18 PRK05659 sulfur carrier protei 27.3 81 0.0018 20.2 2.9 23 39-61 31-61 (66)
19 TIGR02722 lp_ uncharacterized 25.5 98 0.0021 24.5 3.6 29 86-117 140-168 (189)
20 PF13670 PepSY_2: Peptidase pr 23.4 61 0.0013 21.9 1.8 21 26-46 55-76 (83)
21 cd03576 NTR_PCOLCE NTR domain, 23.3 3E+02 0.0065 20.7 5.7 53 89-144 24-89 (124)
22 cd02847 Chitobiase_C_term Chit 23.2 71 0.0015 22.2 2.1 21 8-28 57-77 (78)
23 PRK13444 atpC F0F1 ATP synthas 22.9 1.9E+02 0.004 21.5 4.5 31 10-40 5-36 (127)
24 PF02823 ATP-synt_DE_N: ATP sy 22.6 1.3E+02 0.0028 20.2 3.3 30 11-40 1-31 (80)
25 PF11485 DUF3211: Protein of u 21.6 70 0.0015 24.8 2.0 13 87-99 52-64 (136)
26 PF06257 DUF1021: Protein of u 20.2 88 0.0019 21.9 2.1 20 7-27 42-61 (76)
No 1
>smart00658 RPOL8c RNA polymerase subunit 8. subunit of RNA polymerase I, II and III
Probab=100.00 E-value=5.1e-68 Score=408.90 Aligned_cols=141 Identities=59% Similarity=0.971 Sum_probs=132.5
Q ss_pred ccceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCCC-Cc
Q 032138 4 IVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGA-RK 82 (146)
Q Consensus 4 ~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~~-~~ 82 (146)
.+||||+|+|++|||+||||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++||+++++.|++.+ .+
T Consensus 2 ~~lfeD~F~V~~iDp~gKkfdrVSRi~~~S~~~~~~l~LDiNtelyPv~~gd~~~l~La~tL~~dg~~d~~~~~~~~~~~ 81 (143)
T smart00658 2 IILFDDIFKVKSVDPDGKKFDKVSRIFAESEYLQMELTLDINSEIYPLAVGDKFTLVIASTLNEDGTPDSGENNPIALIK 81 (143)
T ss_pred ceeeeeEEEEEEECCCCCeEccEEEEEEEcCCCceEEEEEecceEEeccCCCEEEEEEecccccCCCCcccccccccccc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999998653 36
Q ss_pred cccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEee
Q 032138 83 TLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK 145 (146)
Q Consensus 83 slad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk 145 (146)
+|||+|||||||||||||++++ +..+++||||||||||+|+|++++|++|++|++|||||||
T Consensus 82 ~Lad~ydYVM~GkvYk~e~~~~-~~~~~~vy~SFGGLLm~L~G~~~~L~~~~~d~~vYLLirk 143 (143)
T smart00658 82 SLADKYEYVMYGKVYRIEEDKT-ETEKLSVYVSFGGLLMRLKGDANNLKGFELDSNLYLLMRK 143 (143)
T ss_pred chhhcCCEEeeeEEEEEEecCC-CceEEEEEEEeccEeEEEEeCHHHCccccCCCEEEEEEeC
Confidence 7999999999999999998642 1259999999999999999999999999999999999997
No 2
>PF03870 RNA_pol_Rpb8: RNA polymerase Rpb8; InterPro: IPR005570 Rpb8 is a subunit common to the three yeast RNA polymerases, pol I, II and III. Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits.; GO: 0006351 transcription, DNA-dependent; PDB: 1TWH_H 1R9T_H 1I3Q_H 2B8K_H 1TWA_H 2NVY_H 4A3E_H 1Y77_H 3GTK_H 2E2J_H ....
Probab=100.00 E-value=4.2e-67 Score=401.92 Aligned_cols=137 Identities=58% Similarity=1.006 Sum_probs=125.7
Q ss_pred eeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCC-CCccccc
Q 032138 8 EDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPG-ARKTLAD 86 (146)
Q Consensus 8 ed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~-~~~slad 86 (146)
||+|+|++||||||||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++||+++++.|++. +++||||
T Consensus 1 eD~F~V~~vD~dGkkfdrVSRi~~~S~~~~m~l~LDiNtelyPl~~~d~~~l~La~tL~~dg~~d~~~~~~~~~~~slad 80 (138)
T PF03870_consen 1 EDIFTVTDVDPDGKKFDRVSRIFAKSESFDMELTLDINTELYPLKVGDKFTLALASTLNLDGTPDDGSWRPKGGEPSLAD 80 (138)
T ss_dssp EEEEEEEEEE---SSSSSEEEEEEEESSSS-EEEEEEETTTSSSTSSEEEEEEECSSS-SSSSSTTTSSSSTTCTTCCCT
T ss_pred CCeEEEEEECCCCCeeccEEEEEEEeCCCceEEEEEccccEEccCCCCEEEEEEecccccCCCCCccccccCCCCcchhh
Confidence 799999999999999999999999999999999999999999999999999999999999999999999874 5679999
Q ss_pred cccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEee
Q 032138 87 KYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK 145 (146)
Q Consensus 87 ~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk 145 (146)
+|||||||||||+++.+ +.+++++||||||||||+|+|++++|++|++|+||||||||
T Consensus 81 ~ydYVMyGkvYk~ee~~-~~~~~~~vY~SFGGLLM~L~G~~~~l~~l~~d~~vYLLirK 138 (138)
T PF03870_consen 81 DYDYVMYGKVYKFEEGS-GGSDKVKVYASFGGLLMRLEGDPRHLSDLEVDSRVYLLIRK 138 (138)
T ss_dssp SSSEEEEEEEEEEEESS-S-TSCEEEEEEETTEEEEEEESSCCCTSTSTSSTCCEEEEE
T ss_pred heeeEeeeEEEeeeccC-CCCceEEEEEEecceeEEEEeCHHHCccccCCCEEEEEEeC
Confidence 99999999999999653 35789999999999999999999999999999999999998
No 3
>PTZ00167 RNA polymerase subunit 8c; Provisional
Probab=100.00 E-value=3.4e-66 Score=398.91 Aligned_cols=139 Identities=40% Similarity=0.736 Sum_probs=131.8
Q ss_pred CCcccceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCCC
Q 032138 1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGA 80 (146)
Q Consensus 1 ms~~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~~ 80 (146)
|++++||||+|+|++|||+| |||||||.|+|++++|+|+|||||||||+++||+|+|+||+|| +|| ++++.|+|.+
T Consensus 2 ~~~~~LfeD~F~V~~iD~~g--fdrVSRI~a~S~~~~~~l~LDiNtelyPv~~gd~~~l~LastL-~dg-~d~~~~~~~~ 77 (144)
T PTZ00167 2 SLPSCLFEDRFVVRSVDNSK--FERVSRIKAKSTGFDAELILDINSDLFPVREKQSLYIGLTNQL-SSG-PDDNVWESSE 77 (144)
T ss_pred CCCceEEEeeEEEEecCCCC--CceEEEEEEEeCCCceEEEEEecccEEeccCCCEEEEEEeccc-cCC-CCcccccccc
Confidence 45689999999999999986 9999999999999999999999999999999999999999999 999 7888899888
Q ss_pred CccccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEeeC
Q 032138 81 RKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRKL 146 (146)
Q Consensus 81 ~~slad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk~ 146 (146)
++||||+|||||||||||||+++ +++++||||||||||+|+|++++|++|++|+||||||||+
T Consensus 78 ~~tLad~ydYVM~GkvYk~ee~~---s~~~~vy~SFGGLLM~L~G~~~~L~~~~~d~~vYLLirk~ 140 (144)
T PTZ00167 78 PQSLMDQYEYVMYGKIFKFEEKS---SERRTLYASFGGLLMALTADKQVVGDLELDMRIYLLVRRS 140 (144)
T ss_pred cccccccCCEEcceEEEEeeecC---CCcEEEEEEcccEeEEEEcCHHHCccccCCCEEEEEEEec
Confidence 99999999999999999999753 4699999999999999999999999999999999999995
No 4
>KOG3400 consensus RNA polymerase subunit 8 [Transcription]
Probab=100.00 E-value=8.9e-66 Score=391.34 Aligned_cols=143 Identities=60% Similarity=1.032 Sum_probs=136.7
Q ss_pred CCcccceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCCC
Q 032138 1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGA 80 (146)
Q Consensus 1 ms~~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~~ 80 (146)
|| ++||+|||+|++||||||||+||||++|+|++++|+|+||||++|||++.||+|+|+||+||++||+||+++|+|.+
T Consensus 1 Ma-~ilfdDiF~V~~vDpeGkkydrVsR~~~~S~~~~m~l~LDiNt~lyPl~~gdkf~l~iastL~eDgtpd~g~~~p~a 79 (143)
T KOG3400|consen 1 MA-GILFDDIFKVSDVDPEGKKYDRVSRIEAKSESFKMDLILDINTQLYPLATGDKFTLVIASTLNEDGTPDTGEYTPGA 79 (143)
T ss_pred Cc-chhhhhceeeeecCcccchhhheEeEEeeCCCceEEEEEecccEEEeeccCCEEEEEEecccccCCCccccccCccc
Confidence 55 69999999999999999999999999999999999999999999999999999999999999999999999999887
Q ss_pred CccccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEee
Q 032138 81 RKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK 145 (146)
Q Consensus 81 ~~slad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk 145 (146)
...|||+|||||||||||+|.++ +..+..++|+|||||||+|+|++++|.+|++|+++||||||
T Consensus 80 ~~~~ad~~eYvMyGkvYriE~~e-~~~~~~~~YvSFGGLLMrl~G~~~nl~~fe~d~~~yLLmrk 143 (143)
T KOG3400|consen 80 KKPLADEYEYVMYGKVYRIEYDE-GKTEKASAYVSFGGLLMRLQGDARNLHGFELDQRLYLLMRK 143 (143)
T ss_pred cccccceeeEEEeeEEEEEeccC-CccceeeEEEeeceEEEEecCChhhccccccccEEEEEeeC
Confidence 77799999999999999999764 56788899999999999999999999999999999999997
No 5
>PRK14980 DNA-directed RNA polymerase subunit G; Provisional
Probab=99.00 E-value=1.8e-08 Score=76.64 Aligned_cols=118 Identities=13% Similarity=0.240 Sum_probs=97.0
Q ss_pred ccceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCCCCcc
Q 032138 4 IVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKT 83 (146)
Q Consensus 4 ~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~~~~s 83 (146)
+.-+.-.=+|++|.| |+ +-.-.++.+.+ .+.++++|+|.+|-+..+||.+.+.|.+.- |.
T Consensus 6 ~~~~~~~cKI~SIEk-g~-l~~l~i~~~~C--~~~~v~fDi~~~L~~fsege~v~iiIS~ek----------------P~ 65 (127)
T PRK14980 6 AQEIILSCKINSIEK-GS-LKNLSIIHMSC--NDFNISFDIIDSINIFSQKEKVKAIISKER----------------PS 65 (127)
T ss_pred hhheeeEEeeeeecc-cc-cCCcEEEEEec--CCeEEEEEehhhhheecCCCcEEEEEeccC----------------cc
Confidence 455677789999999 53 77777877777 459999999999999999999999987652 23
Q ss_pred ccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCC--CCCCCCCeEEEEEee
Q 032138 84 LADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYV--SHFELDQRLFLLMRK 145 (146)
Q Consensus 84 lad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l--~~l~~d~~vYLL~rk 145 (146)
. .+.|+.-||-|...+- ..+++..+-+|++|||.++.-..+-| ++|++=+++|+..||
T Consensus 66 ~-~~~dFCghGyvV~~~k---~~~~~y~~iISl~GlLv~I~sk~~~~~~s~~~~Md~vY~cV~K 125 (127)
T PRK14980 66 Y-TNDDFCAHGYIVTESS---NNGNRYTTIISLFGLLVKIISKESFLKTHQLNVMDHVYFCVKK 125 (127)
T ss_pred c-ccceeecCcEEEEEEe---cCCCeEEEEEEeeeEEEEEEehhhcccccccccccEEEEEEEc
Confidence 3 3388999999998853 34789999999999999999988744 678877899999997
No 6
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=80.38 E-value=7.2 Score=24.78 Aligned_cols=50 Identities=12% Similarity=0.240 Sum_probs=35.7
Q ss_pred EEeeEEEEeecCCCCCcceEEEEEEecc---eeeEEEcCCCCCCCCCCCCeEEEEEe
Q 032138 91 IMHGKLFKIGDEGSGKSLKAEIYVSYGG---LLMMLKGDPSYVSHFELDQRLFLLMR 144 (146)
Q Consensus 91 VMyGkVYk~e~~~~~~~~~~~vy~SFGG---LLM~L~G~~~~l~~l~~d~~vYLL~r 144 (146)
...|+|..++.. +....+++-.|| |..+++.+...-=+|+.++.||+.+|
T Consensus 6 ~l~g~V~~ie~~----g~~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ik 58 (64)
T PF03459_consen 6 QLPGTVESIENL----GSEVEVTLDLGGGETLTARITPESAEELGLKPGDEVYASIK 58 (64)
T ss_dssp EEEEEEEEEEES----SSEEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEEE-
T ss_pred EEEEEEEEEEEC----CCeEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEEEe
Confidence 356999999964 578889999999 66666664443345889999999987
No 7
>PF08530 PepX_C: X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; InterPro: IPR013736 This domain is found at the C terminus of cocaine esterase CocE, several glutaryl-7-ACA acylases, and the putative diester hydrolase NonD of Streptomyces griseus (all hydrolases). The domain, which is a beta sandwich, is also found in serine peptidases belonging to MEROPS peptidase family S15: Xaa-Pro dipeptidyl-peptidases. Members of this entry, that are not characterised as peptidases, show extensive low-level similarity to the Xaa-Pro dipeptidyl-peptidases. ; GO: 0008239 dipeptidyl-peptidase activity; PDB: 2B4K_D 1RYY_F 2B9V_O 1NX9_B 3PUH_B 3I2I_A 3I2G_A 1JU4_A 3I2K_A 1L7R_A ....
Probab=76.22 E-value=11 Score=29.57 Aligned_cols=54 Identities=13% Similarity=0.308 Sum_probs=39.4
Q ss_pred EEEeeeCCCCCccceEeeEEEEe------------c-CCceEEEEEecccceecccCCEEEEEEeeec
Q 032138 11 FVVEKIDPDGKKFDKVSRIEAHS------------Q-NCDMYMLLDVNSELYPMRVGDKFTMALAHTL 65 (146)
Q Consensus 11 F~V~~iD~dgKkfdrVSRi~~~S------------~-~~~~~l~LDiNtelypl~~~d~~~l~LassL 65 (146)
-.+.+++|+|+ =..|++-.++- + +--..+.+.++.--|-+++|.+++|.|+++=
T Consensus 115 v~L~dv~pdG~-~~~it~G~l~~s~r~~~~~~~~~~pg~~~~~~i~L~p~~~~~~~GhrLrl~I~~~d 181 (218)
T PF08530_consen 115 VRLSDVDPDGT-STLITRGWLRASHRESDEKPEPLEPGEPYDVTIELQPTAYVFPAGHRLRLSISSSD 181 (218)
T ss_dssp EEEEEEETTSS-EEEEEEEEEEGGGSSCSSST----TT-EEEEEEEEEEEEEEE-TT-EEEEEEESSB
T ss_pred EEEEEeCCCCC-EEEccceEEEcccccCccccccCCCCcEEEEEEEEchhccEECCCCEEEEEEEecC
Confidence 35679999997 35667755553 1 2235889999999999999999999999873
No 8
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=41.84 E-value=36 Score=25.36 Aligned_cols=50 Identities=20% Similarity=0.414 Sum_probs=35.6
Q ss_pred cccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEc-CCCCCCCCCCCCeEEEEEe
Q 032138 87 KYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKG-DPSYVSHFELDQRLFLLMR 144 (146)
Q Consensus 87 ~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G-~~~~l~~l~~d~~vYLL~r 144 (146)
-.+=+..||||++-++ ..||=|||=-=+.-- +..+-+.+..+.+|-+.++
T Consensus 22 ~~gk~V~G~I~hvv~d--------dLYIDfG~KFhcVc~rp~~~~~~y~~G~rV~lrLk 72 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDD--------DLYIDFGGKFHCVCKRPAVNGEKYVRGSRVRLRLK 72 (104)
T ss_pred ccCCEEEEEEEEEecC--------ceEEEeCCceeEEEecccccccccccCCEEEEEEC
Confidence 3556889999999753 399999996655433 3345566778888877664
No 9
>PRK05371 x-prolyl-dipeptidyl aminopeptidase; Provisional
Probab=41.38 E-value=83 Score=30.34 Aligned_cols=28 Identities=18% Similarity=0.278 Sum_probs=26.3
Q ss_pred eEEEEEecccceecccCCEEEEEEeeec
Q 032138 38 MYMLLDVNSELYPMRVGDKFTMALAHTL 65 (146)
Q Consensus 38 ~~l~LDiNtelypl~~~d~~~l~LassL 65 (146)
++++++.+.-.|-+++|.+++|.|++|=
T Consensus 712 ~~v~i~L~pt~~~~~~GHRLrL~I~ssd 739 (767)
T PRK05371 712 YDVTFDLQPTDYVLPAGHQLGLVLYSTD 739 (767)
T ss_pred EEEEEecccceeeeCCCCEEEEEEEecC
Confidence 7899999999999999999999999884
No 10
>TIGR00976 /NonD putative hydrolase, CocE/NonD family. This model represents a protein subfamily that includes the cocaine esterase CocE, several glutaryl-7-ACA acylases, and the putative diester hydrolase NonD of Streptomyces griseus (all hydrolases). This family shows extensive, low-level similarity to a family of xaa-pro dipeptidyl-peptidases, and local similarity by PSI-BLAST to many other hydrolases.
Probab=40.97 E-value=74 Score=28.80 Aligned_cols=54 Identities=11% Similarity=0.194 Sum_probs=37.7
Q ss_pred EEeeeCCCCCccceEeeEEEE-e------cCCceEEEEEecccceecccCCEEEEEEeeecC
Q 032138 12 VVEKIDPDGKKFDKVSRIEAH-S------QNCDMYMLLDVNSELYPMRVGDKFTMALAHTLN 66 (146)
Q Consensus 12 ~V~~iD~dgKkfdrVSRi~~~-S------~~~~~~l~LDiNtelypl~~~d~~~l~LassL~ 66 (146)
++.+++|||+.. .|+.-..+ + .+.-.++++++..--|-+++|.+++|.|+++=.
T Consensus 446 ~L~dV~pdG~~~-~i~~g~lr~~~r~~~~~G~~~~v~i~l~~~~~~f~~Ghrlrl~I~ssd~ 506 (550)
T TIGR00976 446 KLTDVDPDGRAI-ALDEGICRVRYRRTSVNGEIYEVDIDLGATANLFAPGHRLRVEVGSSNF 506 (550)
T ss_pred EEEEECCCCeEE-ecccceeeeecccccCCCceEEEEEeccccceEECCCCEEEEEEEccCC
Confidence 456899999642 23321111 1 123467889999999999999999999998754
No 11
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=39.71 E-value=29 Score=27.61 Aligned_cols=28 Identities=29% Similarity=0.616 Sum_probs=21.7
Q ss_pred cEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEE
Q 032138 89 EYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLK 124 (146)
Q Consensus 89 dYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~ 124 (146)
+=+.-||||++-++ + +||-|||=.=+.-
T Consensus 83 gklV~GkIfhiV~~-----D---lYIDFG~KFhcVC 110 (173)
T KOG4078|consen 83 GKLVIGKIFHIVEE-----D---LYIDFGGKFHCVC 110 (173)
T ss_pred CcEEEeeeeeeecc-----c---eEEecCCeEEEEE
Confidence 46788999999753 2 8999999776653
No 12
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=37.07 E-value=2.1e+02 Score=23.86 Aligned_cols=29 Identities=21% Similarity=0.358 Sum_probs=21.6
Q ss_pred EEEEecCCceEEEEEecccceecccCCEEEEE
Q 032138 29 IEAHSQNCDMYMLLDVNSELYPMRVGDKFTMA 60 (146)
Q Consensus 29 i~~~S~~~~~~l~LDiNtelypl~~~d~~~l~ 60 (146)
|+++.-+..+.+.+|.++.. ++||.+...
T Consensus 56 iesk~yn~~v~i~~d~~~nv---KVGD~VKaT 84 (213)
T PRK06763 56 IKSKQYEEPVSVYIDSLSNV---KVGDEVKAT 84 (213)
T ss_pred EEeccCCCceEEEecCCCCc---ccCcEEEEc
Confidence 34443344699999999987 999999874
No 13
>PF13745 HxxPF_rpt: HxxPF-repeated domain; PDB: 2JGP_A.
Probab=35.44 E-value=70 Score=20.93 Aligned_cols=30 Identities=23% Similarity=0.465 Sum_probs=16.2
Q ss_pred CCCccceEeeEEEEecCCceEEEEEeccccee
Q 032138 19 DGKKFDKVSRIEAHSQNCDMYMLLDVNSELYP 50 (146)
Q Consensus 19 dgKkfdrVSRi~~~S~~~~~~l~LDiNtelyp 50 (146)
.+-+||=.=. +......+.+.+++|++||-
T Consensus 55 ~~~~~DL~l~--~~~~~~~l~~~~~Y~~~lf~ 84 (91)
T PF13745_consen 55 GGAKFDLTLE--VREDGDGLRLQLEYNTDLFS 84 (91)
T ss_dssp SB-SSSEEEE--EEE-SS-EEEEEEEETTT--
T ss_pred cceeeeEEEE--EEecCCeEEEEEEEEhHhCC
Confidence 3445665433 33333568888999998884
No 14
>PF11183 PmrD: Polymyxin resistance protein PmrD; InterPro: IPR020146 The Salmonella PmrA/PmrB two-component system is required for resistance to the cationic peptide antibiotic olymyxin B, resistance to Fe(3+)-mediated killing, growth in soil, virulence in mice, and infection of chicken macrophages. PmrA-activated genes encode periplasmic and integral membrane proteins as well as cytoplasmic products mediating the modification of the lipopolysaccharide, suggesting a role for the PmrA/PmrB system in remodeling of the Gram-negative envelope. The PmrA/PmrB two-component system of Salmonella enterica is activated by Fe(3+), which is sensed by the PmrB protein, and by low Mg(2+), which is sensed by the PhoQ protein. The low Mg(2+) activation requires pmrD, a PhoPPhoQ-activated gene that activates the response regulator PmrA at a posttranscriptional level. However, under conditions that activate the PmrA protein independently of pmrD, such as exposure to Fe3, lower levels of pmrD transcription occur. It has been demonstrated that PmrA binds to the pmrD promoter, suppressing transcription. Negative regulation of the PhoP/PhoQ-activated pmrD gene by the PmrA/ PmrB system closes a regulatory circuit designed to maintain proper cellular levels of activated PmrA protein, and constitutes a singular example of a multicomponent feedback loop []. ; PDB: 2RQX_A 2JSO_A.
Probab=33.00 E-value=91 Score=22.33 Aligned_cols=30 Identities=23% Similarity=0.366 Sum_probs=20.9
Q ss_pred eEEEEe-cCCceEEEEEecccceecccCCEEE
Q 032138 28 RIEAHS-QNCDMYMLLDVNSELYPMRVGDKFT 58 (146)
Q Consensus 28 Ri~~~S-~~~~~~l~LDiNtelypl~~~d~~~ 58 (146)
.+.+.+ ....+.|+.-|++ -++++.||+++
T Consensus 17 ~~l~l~~a~g~LkmIAEv~s-~~~l~~GD~Lt 47 (82)
T PF11183_consen 17 HVLLLCDAGGALKMIAEVTS-DFRLQEGDKLT 47 (82)
T ss_dssp EEEEEEETTTTCEEEEEEEE-SS---TT-EEE
T ss_pred EEEEEecCCCCeEEEEEeec-CcccCCCCCcc
Confidence 555666 4567999999999 89999999996
No 15
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=32.46 E-value=50 Score=24.77 Aligned_cols=49 Identities=16% Similarity=0.414 Sum_probs=30.4
Q ss_pred ceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEee
Q 032138 6 LFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAH 63 (146)
Q Consensus 6 Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~Las 63 (146)
.|+|||.-.+.=|++..||.-.++..=.-. ..+-+.+..|+.+++-+.+
T Consensus 25 FFddI~IP~~~L~~ps~fd~~~~~W~W~~~---------~~~~l~~d~ge~IRFRV~~ 73 (122)
T PF08292_consen 25 FFDDIFIPPSLLPEPSRFDEEEQAWVWEYD---------EEQELFFDIGEEIRFRVES 73 (122)
T ss_dssp CEEEEEEECCCC-TTEEEECCCTEEEEEES---------SSEEEEE-TT-EEEEEEEE
T ss_pred ccccEEECHHHCCCCCccCccCCEEEEECC---------CCceeEccCCCEEEEEEeE
Confidence 689999999998988888766655443322 4455555566666664443
No 16
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=31.70 E-value=1.4e+02 Score=18.82 Aligned_cols=51 Identities=18% Similarity=0.273 Sum_probs=33.2
Q ss_pred EEeeEEEEeecCCCCCcceEEEEEEecce-eeEEEcCCCCC--CCCCCCCeEEEEEee
Q 032138 91 IMHGKLFKIGDEGSGKSLKAEIYVSYGGL-LMMLKGDPSYV--SHFELDQRLFLLMRK 145 (146)
Q Consensus 91 VMyGkVYk~e~~~~~~~~~~~vy~SFGGL-LM~L~G~~~~l--~~l~~d~~vYLL~rk 145 (146)
...|+|=+++.. +....+.+..||- -+.-.=+.+.+ -.|+.++++|+.+|.
T Consensus 8 ~l~g~I~~i~~~----g~~~~v~l~~~~~~~l~a~i~~~~~~~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 8 QLKGKVVAIEDG----DVNAEVDLLLGGGTKLTAVITLESVAELGLKPGKEVYAVIKA 61 (69)
T ss_pred EEEEEEEEEEEC----CCeEEEEEEECCCCEEEEEecHHHHhhCCCCCCCEEEEEEEC
Confidence 456999999753 4567777777443 33333333443 357789999999884
No 17
>PF10871 DUF2748: Protein of unknown function (DUF2748); InterPro: IPR020183 This entry represents proteins that are mainly confined to Rickettsia and Orientia. The proteins, which include RP364 and RC0048, are currently uncharacterised.
Probab=27.44 E-value=42 Score=29.97 Aligned_cols=17 Identities=35% Similarity=0.450 Sum_probs=13.9
Q ss_pred CCCcceEEEEEEeccee
Q 032138 104 SGKSLKAEIYVSYGGLL 120 (146)
Q Consensus 104 ~~~~~~~~vy~SFGGLL 120 (146)
+.++..+.+|+|+||==
T Consensus 171 S~NGkdvAIfVSCGGNP 187 (447)
T PF10871_consen 171 STNGKDVAIFVSCGGNP 187 (447)
T ss_pred ccCCCcEEEEEecCCCc
Confidence 45688999999999843
No 18
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=27.26 E-value=81 Score=20.16 Aligned_cols=23 Identities=30% Similarity=0.573 Sum_probs=17.4
Q ss_pred EEEEEeccccee--------cccCCEEEEEE
Q 032138 39 YMLLDVNSELYP--------MRVGDKFTMAL 61 (146)
Q Consensus 39 ~l~LDiNtelyp--------l~~~d~~~l~L 61 (146)
.+.+.+|-++.| ++.||++.+.=
T Consensus 31 ~vav~vNg~iv~r~~~~~~~l~~gD~vei~~ 61 (66)
T PRK05659 31 RVAVEVNGEIVPRSQHASTALREGDVVEIVH 61 (66)
T ss_pred eEEEEECCeEeCHHHcCcccCCCCCEEEEEE
Confidence 345668887777 89999998864
No 19
>TIGR02722 lp_ uncharacterized proteobacterial lipoprotein. Members of this protein family are restricted to the Proteobacteria, and all are predicted lipoproteins. In genomes that contain the thiK gene for the salvage enzyme thiamin kinase, the member of this family is encoded nearby.
Probab=25.49 E-value=98 Score=24.46 Aligned_cols=29 Identities=17% Similarity=0.307 Sum_probs=19.9
Q ss_pred ccccEEEeeEEEEeecCCCCCcceEEEEEEec
Q 032138 86 DKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYG 117 (146)
Q Consensus 86 d~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFG 117 (146)
-.-||++||+|-.+... .+....+|+.|-
T Consensus 140 ~gADy~L~G~I~~~~~~---~~~~~~~~~~~~ 168 (189)
T TIGR02722 140 VGADYSLYGKISSIVKS---DGSRKLVYYKFT 168 (189)
T ss_pred hCCCEEEEEEEEEEEee---cCCCceEEEEEE
Confidence 35689999999999754 233356666553
No 20
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=23.39 E-value=61 Score=21.90 Aligned_cols=21 Identities=14% Similarity=0.235 Sum_probs=10.6
Q ss_pred EeeEEEEec-CCceEEEEEecc
Q 032138 26 VSRIEAHSQ-NCDMYMLLDVNS 46 (146)
Q Consensus 26 VSRi~~~S~-~~~~~l~LDiNt 46 (146)
+-.+.+... +..+++.+|-+|
T Consensus 55 ~yev~~~~~dG~~~ev~vD~~t 76 (83)
T PF13670_consen 55 CYEVEARDKDGKKVEVYVDPAT 76 (83)
T ss_pred EEEEEEEECCCCEEEEEEcCCC
Confidence 345554433 334666666554
No 21
>cd03576 NTR_PCOLCE NTR domain, PCOLCE subfamily; Procollagen C-endopeptidase enhancers (PCOLCEs) are extracellular matrix proteins that enhance the activity of procollagen C-proteases, by binding to the procollagen I C-peptide. They contain a C-terminal NTR domain, which have been suggested to possess inhibitory functions towards specific serine proteases but not towards metzincins, which are inhibited by the related TIMPs.
Probab=23.34 E-value=3e+02 Score=20.71 Aligned_cols=53 Identities=19% Similarity=0.323 Sum_probs=31.8
Q ss_pred cEEEeeEEEEeecCCCCCcceEE-----EE------EEecceeeE--EEcCCCCCCCCCCCCeEEEEEe
Q 032138 89 EYIMHGKLFKIGDEGSGKSLKAE-----IY------VSYGGLLMM--LKGDPSYVSHFELDQRLFLLMR 144 (146)
Q Consensus 89 dYVMyGkVYk~e~~~~~~~~~~~-----vy------~SFGGLLM~--L~G~~~~l~~l~~d~~vYLL~r 144 (146)
|||-.|+|...+..+ +.-+++ || +.+||--|. +..-......|+.+ +=||+|=
T Consensus 24 dfaI~g~V~~~~~~~--~~~~~tv~i~~vyK~g~l~l~~~~~~l~V~~~~~~~~CP~lr~g-~~YliMG 89 (124)
T cd03576 24 EFVITGTVISMTRGP--GSLHATVSIIKLYKEGRLAITQAGKTMSVKITVVCKQCPLLRRG-LNYILMG 89 (124)
T ss_pred CceEEEEEEEEEEcC--CeEEEEEEeeeeeecCCcccCcCCceEEEEecccccCCCCcccC-CEEEEEe
Confidence 899999999998653 222222 22 345553333 33444455778886 6677773
No 22
>cd02847 Chitobiase_C_term Chitobiase C-terminus domain. Chitobiase (AKA N-acetylglucosaminidase) digests the beta, 1-4 glycosidic bonds of the N-acetylglucosamine (NAG) oligomers found in chitin, an important structural element of fungal cell wall and arthropod exoskeletons. It is thought to proceed through an acid-base reaction mechanism, in which one protein carboxylate acts as catalytic acid, while the nucleophile is the polar acetamido group of the sugar in a substrate-assisted reaction with retention of the anomeric configuration. The C-terminus of chitobiase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chit
Probab=23.24 E-value=71 Score=22.22 Aligned_cols=21 Identities=19% Similarity=0.378 Sum_probs=17.0
Q ss_pred eeeEEEeeeCCCCCccceEee
Q 032138 8 EDIFVVEKIDPDGKKFDKVSR 28 (146)
Q Consensus 8 ed~F~V~~iD~dgKkfdrVSR 28 (146)
.+.+.|..+.++||.+.|+..
T Consensus 57 ~~~v~vr~~s~~G~r~sR~~~ 77 (78)
T cd02847 57 SGDVQIRSVSFDGKRVSRVTS 77 (78)
T ss_pred cccEEEEEEcCCCCeecceee
Confidence 467889999999998777654
No 23
>PRK13444 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=22.92 E-value=1.9e+02 Score=21.50 Aligned_cols=31 Identities=13% Similarity=0.174 Sum_probs=26.3
Q ss_pred eEEEeeeCCCCCccc-eEeeEEEEecCCceEE
Q 032138 10 IFVVEKIDPDGKKFD-KVSRIEAHSQNCDMYM 40 (146)
Q Consensus 10 ~F~V~~iD~dgKkfd-rVSRi~~~S~~~~~~l 40 (146)
.|.++=+.|++..|+ .|.++.+.+..+++.+
T Consensus 5 ~~~l~IvtP~~~~~~~~v~~V~~p~~~G~~gI 36 (127)
T PRK13444 5 KLTVSVISPEKILYKGEVDSLIVPGSEGFFGI 36 (127)
T ss_pred ceEEEEEcCCceEEeceEEEEEEECCccCeEe
Confidence 588999999998887 7999999988877664
No 24
>PF02823 ATP-synt_DE_N: ATP synthase, Delta/Epsilon chain, beta-sandwich domain; InterPro: IPR020546 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This family represents subunits called delta (in mitochondrial ATPase) or epsilon (in bacteria or chloroplast ATPase). The interaction site of subunit C of the F0 complex with the delta or epsilon subunit of the F1 complex may be important for connecting the rotor of F1 (gamma subunit) to the rotor of F0 (C subunit) []. In bacterial species, the delta subunit is the equivalent of the Oligomycin sensitive subunit (OSCP, IPR000711 from INTERPRO) in metazoans. The C-terminal domain of the epsilon subunit appears to act as an inhibitor of ATPase activity []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015986 ATP synthesis coupled proton transport, 0045261 proton-transporting ATP synthase complex, catalytic core F(1); PDB: 2WSS_H 1E79_H 2JDI_H 2W6I_H 2W6H_H 2W6J_H 2CK3_H 2V7Q_H 1H8E_H 2XND_H ....
Probab=22.60 E-value=1.3e+02 Score=20.15 Aligned_cols=30 Identities=17% Similarity=0.396 Sum_probs=23.7
Q ss_pred EEEeeeCCCCCccc-eEeeEEEEecCCceEE
Q 032138 11 FVVEKIDPDGKKFD-KVSRIEAHSQNCDMYM 40 (146)
Q Consensus 11 F~V~~iD~dgKkfd-rVSRi~~~S~~~~~~l 40 (146)
|+++=+.|++..|+ .|.++.+.+..+++.+
T Consensus 1 l~l~IvtP~~~~~~~~v~~v~~~t~~G~~gI 31 (80)
T PF02823_consen 1 LKLKIVTPDGIFFEGEVESVVLPTTDGEFGI 31 (80)
T ss_dssp EEEEEEESSSEEEEEEESEEEEEBSSSEEEE
T ss_pred CEEEEEcCCceEEeeEEEEEEEECCCcChhh
Confidence 56777889888777 7999999988876664
No 25
>PF11485 DUF3211: Protein of unknown function (DUF3211); InterPro: IPR021578 This archaeal family of proteins has no known function. ; PDB: 2EJX_A.
Probab=21.61 E-value=70 Score=24.79 Aligned_cols=13 Identities=15% Similarity=0.554 Sum_probs=11.4
Q ss_pred cccEEEeeEEEEe
Q 032138 87 KYEYIMHGKLFKI 99 (146)
Q Consensus 87 ~ydYVMyGkVYk~ 99 (146)
.+.|.|||+||+=
T Consensus 52 ~~~~~~~G~vy~s 64 (136)
T PF11485_consen 52 GFPFEMKGNVYVS 64 (136)
T ss_dssp TEEEEEEEEEEEE
T ss_pred eEEEEEEEEEEEc
Confidence 4889999999975
No 26
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=20.18 E-value=88 Score=21.91 Aligned_cols=20 Identities=40% Similarity=0.918 Sum_probs=11.9
Q ss_pred eeeeEEEeeeCCCCCccceEe
Q 032138 7 FEDIFVVEKIDPDGKKFDKVS 27 (146)
Q Consensus 7 fed~F~V~~iD~dgKkfdrVS 27 (146)
|-.+|.|. +|.+...|+|||
T Consensus 42 YPsvFvV~-l~~~~~~~~rvS 61 (76)
T PF06257_consen 42 YPSVFVVE-LDQEENQFERVS 61 (76)
T ss_dssp -SSEEEEE-ES-S-SS-EEEE
T ss_pred cCcEEEEE-EccCCCceEEEE
Confidence 55678876 888666688887
Done!