Query 030998
Match_columns 167
No_of_seqs 134 out of 860
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 07:42:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030998hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06280 DUF1034: Fn3-like dom 95.3 0.25 5.3E-06 36.1 9.1 82 63-149 10-111 (112)
2 PF10633 NPCBM_assoc: NPCBM-as 95.0 0.32 7E-06 33.3 8.5 58 60-117 4-62 (78)
3 PF11614 FixG_C: IG-like fold 86.1 4.2 9.2E-05 29.7 6.9 54 64-118 34-87 (118)
4 COG1470 Predicted membrane pro 76.8 25 0.00055 32.8 9.6 104 45-160 381-491 (513)
5 smart00635 BID_2 Bacterial Ig- 69.5 22 0.00049 24.2 6.0 39 90-139 4-42 (81)
6 PF14874 PapD-like: Flagellar- 67.5 39 0.00085 23.5 12.1 79 62-151 21-99 (102)
7 PF09244 DUF1964: Domain of un 67.1 19 0.00041 24.7 4.9 44 97-144 15-58 (68)
8 PF00345 PapD_N: Pili and flag 59.3 65 0.0014 23.3 7.4 51 63-115 16-73 (122)
9 TIGR02745 ccoG_rdxA_fixG cytoc 57.6 44 0.00095 30.6 7.1 53 64-117 349-401 (434)
10 PF00347 Ribosomal_L6: Ribosom 52.2 37 0.0008 22.6 4.5 26 86-111 2-27 (77)
11 COG1470 Predicted membrane pro 51.5 1.4E+02 0.003 28.2 9.2 110 5-117 221-345 (513)
12 PF00635 Motile_Sperm: MSP (Ma 50.2 84 0.0018 21.8 8.2 53 62-117 19-71 (109)
13 PF07718 Coatamer_beta_C: Coat 44.3 1.2E+02 0.0027 23.7 6.8 50 81-138 90-139 (140)
14 cd00237 p23 p23 binds heat sho 43.9 91 0.002 22.8 5.8 22 82-103 18-39 (106)
15 PF13195 DUF4011: Protein of u 36.9 53 0.0011 25.9 3.8 27 129-155 120-147 (176)
16 PF14874 PapD-like: Flagellar- 35.2 1.1E+02 0.0023 21.2 4.9 28 90-117 3-32 (102)
17 PF12180 EABR: TSG101 and ALIX 31.7 6.5 0.00014 23.8 -1.6 16 5-20 15-30 (35)
18 PLN03080 Probable beta-xylosid 31.3 1.7E+02 0.0037 28.8 7.0 53 62-115 685-744 (779)
19 PF12970 DUF3858: Domain of Un 30.8 87 0.0019 23.8 3.9 36 76-111 36-71 (116)
20 PF15496 DUF4646: Domain of un 30.8 26 0.00056 26.5 1.1 16 7-22 45-60 (123)
21 PF07610 DUF1573: Protein of u 30.8 1.3E+02 0.0028 18.3 5.2 12 102-113 34-45 (45)
22 PF00635 Motile_Sperm: MSP (Ma 30.3 1.8E+02 0.004 20.1 5.5 53 90-152 1-55 (109)
23 PF08310 LGFP: LGFP repeat; I 21.5 47 0.001 21.1 0.9 24 130-153 22-45 (54)
No 1
>PF06280 DUF1034: Fn3-like domain (DUF1034); InterPro: IPR010435 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain of unknown function is present in bacterial and plant peptidases belonging to MEROPS peptidase family S8 (subfamily S8A subtilisin, clan SB). It is C-terminal to and adjacent to the S8 peptidase domain and can be found in conjunction with the PA (Protease associated) domain (IPR003137 from INTERPRO) and additionally in Gram-positive bacteria with the surface protein anchor domain (IPR001899 from INTERPRO).; GO: 0004252 serine-type endopeptidase activity, 0005618 cell wall, 0016020 membrane; PDB: 3EIF_A 1XF1_B.
Probab=95.26 E-value=0.25 Score=36.14 Aligned_cols=82 Identities=23% Similarity=0.336 Sum_probs=48.8
Q ss_pred EEEEEEEEecCCCCcceEEEEEC--------CCC----------c-EEEEEcCEEEEeecCceEEEEEEEEEccccccCC
Q 030998 63 FTFKRVLTNVADTRSTYTAAVKA--------PVG----------M-TVTVEPATLSFAGKFSKAEFSLTVNINLGNAFSP 123 (167)
Q Consensus 63 ~tv~RTVTNVg~~~stY~a~V~~--------P~g----------v-~V~V~P~~L~F~~~gqk~sf~Vt~~~~~~~~~~~ 123 (167)
.+++=+++|.|+..-+|+.+... ..| . .++..|..++. ++||++.++|+|...... ...
T Consensus 10 ~~~~itl~N~~~~~~ty~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~vTV-~ag~s~~v~vti~~p~~~-~~~ 87 (112)
T PF06280_consen 10 FSFTITLHNYGDKPVTYTLSHVPVLTDKTDTEEGYSILVPPVPSISTVSFSPDTVTV-PAGQSKTVTVTITPPSGL-DAS 87 (112)
T ss_dssp EEEEEEEEE-SSS-EEEEEEEE-EEEEEE--ETTEEEEEEEE----EEE---EEEEE--TTEEEEEEEEEE--GGG-HHT
T ss_pred eEEEEEEEECCCCCEEEEEeeEEEEeeEeeccCCcccccccccceeeEEeCCCeEEE-CCCCEEEEEEEEEehhcC-Ccc
Confidence 56666777777777777665541 112 1 56777888888 789999999999984420 002
Q ss_pred CCCccceEEEEEEEeCCCce-EEEceE
Q 030998 124 KSNFLGNFGYLTWYEVKRKH-TVRSPI 149 (167)
Q Consensus 124 ~~~~~~~fGsl~W~d~~g~h-~VRSPI 149 (167)
...+ ..|.|..+++ ..+ .++.|.
T Consensus 88 ~~~~--~eG~I~~~~~-~~~~~lsIPy 111 (112)
T PF06280_consen 88 NGPF--YEGFITFKSS-DGEPDLSIPY 111 (112)
T ss_dssp T-EE--EEEEEEEESS-TTSEEEEEEE
T ss_pred cCCE--EEEEEEEEcC-CCCEEEEeee
Confidence 2345 8899999986 444 777774
No 2
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=94.96 E-value=0.32 Score=33.27 Aligned_cols=58 Identities=19% Similarity=0.260 Sum_probs=38.2
Q ss_pred CeeEEEEEEEEecCCCC-cceEEEEECCCCcEEEEEcCEEEEeecCceEEEEEEEEEcc
Q 030998 60 TASFTFKRVLTNVADTR-STYTAAVKAPVGMTVTVEPATLSFAGKFSKAEFSLTVNINL 117 (167)
Q Consensus 60 ~~~~tv~RTVTNVg~~~-stY~a~V~~P~gv~V~V~P~~L~F~~~gqk~sf~Vt~~~~~ 117 (167)
....+++=+|+|-|... ...++++..|.|-.+...|..+.--++||+++++++|+...
T Consensus 4 G~~~~~~~tv~N~g~~~~~~v~~~l~~P~GW~~~~~~~~~~~l~pG~s~~~~~~V~vp~ 62 (78)
T PF10633_consen 4 GETVTVTLTVTNTGTAPLTNVSLSLSLPEGWTVSASPASVPSLPPGESVTVTFTVTVPA 62 (78)
T ss_dssp TEEEEEEEEEE--SSS-BSS-EEEEE--TTSE---EEEEE--B-TTSEEEEEEEEEE-T
T ss_pred CCEEEEEEEEEECCCCceeeEEEEEeCCCCccccCCccccccCCCCCEEEEEEEEECCC
Confidence 35678888999999754 56889999999999999999887668999999999998764
No 3
>PF11614 FixG_C: IG-like fold at C-terminal of FixG, putative oxidoreductase; PDB: 2R39_A.
Probab=86.14 E-value=4.2 Score=29.72 Aligned_cols=54 Identities=20% Similarity=0.197 Sum_probs=37.5
Q ss_pred EEEEEEEecCCCCcceEEEEECCCCcEEEEEcCEEEEeecCceEEEEEEEEEccc
Q 030998 64 TFKRVLTNVADTRSTYTAAVKAPVGMTVTVEPATLSFAGKFSKAEFSLTVNINLG 118 (167)
Q Consensus 64 tv~RTVTNVg~~~stY~a~V~~P~gv~V~V~P~~L~F~~~gqk~sf~Vt~~~~~~ 118 (167)
..+=.++|-+...-+|+.++..++|+++......+.. ++|++..+.+.+.+...
T Consensus 34 ~Y~lkl~Nkt~~~~~~~i~~~g~~~~~l~~~~~~i~v-~~g~~~~~~v~v~~p~~ 87 (118)
T PF11614_consen 34 QYTLKLTNKTNQPRTYTISVEGLPGAELQGPENTITV-PPGETREVPVFVTAPPD 87 (118)
T ss_dssp EEEEEEEE-SSS-EEEEEEEES-SS-EE-ES--EEEE--TT-EEEEEEEEEE-GG
T ss_pred EEEEEEEECCCCCEEEEEEEecCCCeEEECCCcceEE-CCCCEEEEEEEEEECHH
Confidence 3556789999999999999999999999654478888 78999999999987654
No 4
>COG1470 Predicted membrane protein [Function unknown]
Probab=76.85 E-value=25 Score=32.85 Aligned_cols=104 Identities=12% Similarity=0.144 Sum_probs=70.3
Q ss_pred CCCcce--EEEEecCCCCeeEEEEEEEEecCCCC-cceEEEEECCCCcEEEEEcCEEEEeecCceEEEEEEEEEcccccc
Q 030998 45 DLNYPS--FIIILNNSNTASFTFKRVLTNVADTR-STYTAAVKAPVGMTVTVEPATLSFAGKFSKAEFSLTVNINLGNAF 121 (167)
Q Consensus 45 dLNYPS--i~v~~~~~~~~~~tv~RTVTNVg~~~-stY~a~V~~P~gv~V~V~P~~L~F~~~gqk~sf~Vt~~~~~~~~~ 121 (167)
+|+.++ +.+... .....++.=.++|-|+.+ .-=+.+|.+|.|-++.|.|+++---++|+.++..+++++...
T Consensus 381 ~v~l~~g~~~lt~t--aGee~~i~i~I~NsGna~LtdIkl~v~~PqgWei~Vd~~~I~sL~pge~~tV~ltI~vP~~--- 455 (513)
T COG1470 381 LVKLDNGPYRLTIT--AGEEKTIRISIENSGNAPLTDIKLTVNGPQGWEIEVDESTIPSLEPGESKTVSLTITVPED--- 455 (513)
T ss_pred eEEccCCcEEEEec--CCccceEEEEEEecCCCccceeeEEecCCccceEEECcccccccCCCCcceEEEEEEcCCC---
Confidence 566666 444432 233567777789999754 456899999999999999999887799999999999998764
Q ss_pred CCCCCccce----EEEEEEEeCCCceEEEceEEEEEeeCCCcc
Q 030998 122 SPKSNFLGN----FGYLTWYEVKRKHTVRSPIVAAFANNSRGV 160 (167)
Q Consensus 122 ~~~~~~~~~----fGsl~W~d~~g~h~VRSPIaV~~~~~~~~~ 160 (167)
+..++|... --..+|.| +.-|.|...+.++.+
T Consensus 456 a~aGdY~i~i~~ksDq~s~e~-------tlrV~V~~sS~st~i 491 (513)
T COG1470 456 AGAGDYRITITAKSDQASSED-------TLRVVVGQSSTSTYI 491 (513)
T ss_pred CCCCcEEEEEEEeeccccccc-------eEEEEEeccccchhh
Confidence 145555200 11345665 444566655555544
No 5
>smart00635 BID_2 Bacterial Ig-like domain 2.
Probab=69.47 E-value=22 Score=24.21 Aligned_cols=39 Identities=33% Similarity=0.364 Sum_probs=29.1
Q ss_pred EEEEEcCEEEEeecCceEEEEEEEEEccccccCCCCCccceEEEEEEEeC
Q 030998 90 TVTVEPATLSFAGKFSKAEFSLTVNINLGNAFSPKSNFLGNFGYLTWYEV 139 (167)
Q Consensus 90 ~V~V~P~~L~F~~~gqk~sf~Vt~~~~~~~~~~~~~~~~~~fGsl~W~d~ 139 (167)
.|++.|..+.+ ..|+++.|++++..... . ....++|+.+
T Consensus 4 ~i~i~p~~~~l-~~G~~~~l~a~~~~~~~-----~-----~~~~v~w~Ss 42 (81)
T smart00635 4 SVTVTPTTASV-KKGLTLQLTATVTPSSA-----K-----VTGKVTWTSS 42 (81)
T ss_pred EEEEeCCeeEE-eCCCeEEEEEEEECCCC-----C-----ccceEEEEEC
Confidence 67889999998 58999999999764332 1 1366889874
No 6
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=67.52 E-value=39 Score=23.52 Aligned_cols=79 Identities=18% Similarity=0.258 Sum_probs=50.7
Q ss_pred eEEEEEEEEecCCCCcceEEEEECCCCcEEEEEcCEEEEeecCceEEEEEEEEEccccccCCCCCccceEEEEEEEeCCC
Q 030998 62 SFTFKRVLTNVADTRSTYTAAVKAPVGMTVTVEPATLSFAGKFSKAEFSLTVNINLGNAFSPKSNFLGNFGYLTWYEVKR 141 (167)
Q Consensus 62 ~~tv~RTVTNVg~~~stY~a~V~~P~gv~V~V~P~~L~F~~~gqk~sf~Vt~~~~~~~~~~~~~~~~~~fGsl~W~d~~g 141 (167)
..+.+=+++|.|.....|++.......-..+|.|..= +-++|++..++|+|.... ..+.+ -+.|.-.- .
T Consensus 21 ~~~~~v~l~N~s~~p~~f~v~~~~~~~~~~~v~~~~g-~l~PG~~~~~~V~~~~~~-----~~g~~---~~~l~i~~--e 89 (102)
T PF14874_consen 21 TYSRTVTLTNTSSIPARFRVRQPESLSSFFSVEPPSG-FLAPGESVELEVTFSPTK-----PLGDY---EGSLVITT--E 89 (102)
T ss_pred EEEEEEEEEECCCCCEEEEEEeCCcCCCCEEEECCCC-EECCCCEEEEEEEEEeCC-----CCceE---EEEEEEEE--C
Confidence 3444556799999999999876432344566676653 337899999999999543 22333 46665555 3
Q ss_pred ceEEEceEEE
Q 030998 142 KHTVRSPIVA 151 (167)
Q Consensus 142 ~h~VRSPIaV 151 (167)
...+..|+-.
T Consensus 90 ~~~~~i~v~a 99 (102)
T PF14874_consen 90 GGSFEIPVKA 99 (102)
T ss_pred CeEEEEEEEE
Confidence 4455555543
No 7
>PF09244 DUF1964: Domain of unknown function (DUF1964); InterPro: IPR015325 This domain is C-terminal to the catalytic sucrose phosphorylase beta/alpha barrel domain. It adopts a beta-sandwich fold, with Greek-key topology and is functionally uncharacterised []. ; PDB: 1R7A_B 2GDU_A 2GDV_A.
Probab=67.07 E-value=19 Score=24.65 Aligned_cols=44 Identities=16% Similarity=0.243 Sum_probs=25.6
Q ss_pred EEEEeecCceEEEEEEEEEccccccCCCCCccceEEEEEEEeCCCceE
Q 030998 97 TLSFAGKFSKAEFSLTVNINLGNAFSPKSNFLGNFGYLTWYEVKRKHT 144 (167)
Q Consensus 97 ~L~F~~~gqk~sf~Vt~~~~~~~~~~~~~~~~~~fGsl~W~d~~g~h~ 144 (167)
.|+|+=.|++-+=+++|+....- -..... .-.+|.|+|+.|.|.
T Consensus 15 Sitf~W~g~~t~atLtFePg~Gl--g~~n~~--pVatl~W~DsaG~H~ 58 (68)
T PF09244_consen 15 SITFTWTGATTSATLTFEPGRGL--GVDNTT--PVATLAWTDSAGDHR 58 (68)
T ss_dssp EEEEEEE-SS-EEEEEE-GGGC---STT--S----EEEEEEETTEEEE
T ss_pred EEEEEEeccccEEEEEEccCccc--CccCCc--ceeEEEEeccCCCcc
Confidence 56788788888888999864320 011122 458999999877776
No 8
>PF00345 PapD_N: Pili and flagellar-assembly chaperone, PapD N-terminal domain; InterPro: IPR016147 Most Gram-negative bacteria possess a supramolecular structure - the pili - on their surface, which mediates attachment to specific receptors. Many interactive subunits are required to assemble pili, but their assembly only takes place after translocation across the cytoplasmic membrane. Periplasmic chaperones assist pili assembly by binding to the subunits, thereby preventing premature aggregation [, ]. Pili chaperones are structurally, and possibly evolutionarily, related to the immunoglobulin superfamily [, ]: they contain two globular domains, with a topology identical to an immunoglobulin fold. This entry represents the N-terminal domain of pili assembly chaperone, and has a beta-sandwich fold consisting of seven strands in two sheets with a Greek key topology.; GO: 0007047 cellular cell wall organization, 0030288 outer membrane-bounded periplasmic space; PDB: 2CO6_B 2CO7_B 1L4I_B 3GFU_A 3F65_F 3F6L_A 3F6I_A 3GEW_B 3DSN_D 2OS7_B ....
Probab=59.26 E-value=65 Score=23.29 Aligned_cols=51 Identities=12% Similarity=-0.033 Sum_probs=38.4
Q ss_pred EEEEEEEEecCCCCcceEEEEEC---CCC----cEEEEEcCEEEEeecCceEEEEEEEEE
Q 030998 63 FTFKRVLTNVADTRSTYTAAVKA---PVG----MTVTVEPATLSFAGKFSKAEFSLTVNI 115 (167)
Q Consensus 63 ~tv~RTVTNVg~~~stY~a~V~~---P~g----v~V~V~P~~L~F~~~gqk~sf~Vt~~~ 115 (167)
.+..=+|+|-|+..-.+.+.+.- ..+ -.+-|.|..+.. ++|+++.+.| +..
T Consensus 16 ~~~~i~v~N~~~~~~~vq~~v~~~~~~~~~~~~~~~~vsPp~~~L-~pg~~q~vRv-~~~ 73 (122)
T PF00345_consen 16 RSASITVTNNSDQPYLVQVWVYDQDDEDEDEPTDPFIVSPPIFRL-EPGESQTVRV-YRG 73 (122)
T ss_dssp SEEEEEEEESSSSEEEEEEEEEETTSTTSSSSSSSEEEESSEEEE-ETTEEEEEEE-EEC
T ss_pred CEEEEEEEcCCCCcEEEEEEEEcCCCcccccccccEEEeCCceEe-CCCCcEEEEE-Eec
Confidence 35567889988877777777763 111 257799999999 7899999999 663
No 9
>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.
Probab=57.61 E-value=44 Score=30.61 Aligned_cols=53 Identities=13% Similarity=0.149 Sum_probs=43.8
Q ss_pred EEEEEEEecCCCCcceEEEEECCCCcEEEEEcCEEEEeecCceEEEEEEEEEcc
Q 030998 64 TFKRVLTNVADTRSTYTAAVKAPVGMTVTVEPATLSFAGKFSKAEFSLTVNINL 117 (167)
Q Consensus 64 tv~RTVTNVg~~~stY~a~V~~P~gv~V~V~P~~L~F~~~gqk~sf~Vt~~~~~ 117 (167)
..+=.+.|-+..+.+|+.+++.++|.++...++.+.. ++||+.++.|.+....
T Consensus 349 ~Y~~~i~Nk~~~~~~~~l~v~g~~~~~~~~~~~~i~v-~~g~~~~~~v~v~~~~ 401 (434)
T TIGR02745 349 TYTLKILNKTEQPHEYYLSVLGLPGIKIEGPGAPIHV-KAGEKVKLPVFLRTPP 401 (434)
T ss_pred EEEEEEEECCCCCEEEEEEEecCCCcEEEcCCceEEE-CCCCEEEEEEEEEech
Confidence 3555689999889999999999999998876557777 7899999999988754
No 10
>PF00347 Ribosomal_L6: Ribosomal protein L6; InterPro: IPR020040 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 [, ]. L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites []. This entry represents the alpha-beta domain found duplicated in ribosomal L6 proteins. This domain consists of two beta-sheets and one alpha-helix packed around single core [].; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 2HGJ_H 2HGQ_H 2HGU_H 1S1I_H 3O5H_I 3O58_I 3J16_F 3IZS_F 2V47_H 2WDJ_H ....
Probab=52.24 E-value=37 Score=22.56 Aligned_cols=26 Identities=19% Similarity=0.373 Sum_probs=19.2
Q ss_pred CCCcEEEEEcCEEEEeecCceEEEEE
Q 030998 86 PVGMTVTVEPATLSFAGKFSKAEFSL 111 (167)
Q Consensus 86 P~gv~V~V~P~~L~F~~~gqk~sf~V 111 (167)
|.|++|+++...+.|..+.-++++.+
T Consensus 2 P~gV~v~~~~~~i~v~G~~g~l~~~~ 27 (77)
T PF00347_consen 2 PEGVKVTIKGNIITVKGPKGELSRPI 27 (77)
T ss_dssp STTCEEEEETTEEEEESSSSEEEEEE
T ss_pred CCcEEEEEeCcEEEEECCCEeEEEEC
Confidence 78899999998888866555555543
No 11
>COG1470 Predicted membrane protein [Function unknown]
Probab=51.53 E-value=1.4e+02 Score=28.17 Aligned_cols=110 Identities=17% Similarity=0.232 Sum_probs=69.9
Q ss_pred eeeeCChhhHHHhhhcCC-CCcceeeeeeccccccc-C------CCC--CCCCcceEEEEecCCCCeeEEEEEEEEecCC
Q 030998 5 LVYDIEIQDYLNYLCAMN-YTSQQIRVVTGTSDFTC-E------HGN--LDLNYPSFIIILNNSNTASFTFKRVLTNVAD 74 (167)
Q Consensus 5 LVYD~~~~DYi~fLC~lg-y~~~~i~~it~~~~~~C-~------~~~--~dLNYPSi~v~~~~~~~~~~tv~RTVTNVg~ 74 (167)
+...+++.+|+--+-.-| |... .+.+......+- . +.. ..||--++..-... .....++=++-|-|.
T Consensus 221 ~~~e~t~g~y~~~i~~~g~ye~~-~~av~l~d~~t~dLkls~~~k~~~ftEl~~s~~~~~i~~--~~t~sf~V~IeN~g~ 297 (513)
T COG1470 221 LEVEITPGKYVVLIAKKGIYEKK-KRAVKLNDGETKDLKLSVTEKKSYFTELNSSDIYLEISP--STTASFTVSIENRGK 297 (513)
T ss_pred eeEEecCcceEEEeccccceecc-eEEEEcCCCcccceeEEEEeccceEEEeecccceeEEcc--CCceEEEEEEccCCC
Confidence 345678888888887778 5443 333332111111 0 111 46776666554431 234567777899999
Q ss_pred CCcceEEEEE-CCCCcEEEEEcCEEEEe----ecCceEEEEEEEEEcc
Q 030998 75 TRSTYTAAVK-APVGMTVTVEPATLSFA----GKFSKAEFSLTVNINL 117 (167)
Q Consensus 75 ~~stY~a~V~-~P~gv~V~V~P~~L~F~----~~gqk~sf~Vt~~~~~ 117 (167)
..-.|.-++. .|+|....-.=..++.+ ++||++.++|.+....
T Consensus 298 ~~d~y~Le~~g~pe~w~~~Fteg~~~vt~vkL~~gE~kdvtleV~ps~ 345 (513)
T COG1470 298 QDDEYALELSGLPEGWTAEFTEGELRVTSVKLKPGEEKDVTLEVYPSL 345 (513)
T ss_pred CCceeEEEeccCCCCcceEEeeCceEEEEEEecCCCceEEEEEEecCC
Confidence 9999999998 89887765554433333 5799999999998754
No 12
>PF00635 Motile_Sperm: MSP (Major sperm protein) domain; InterPro: IPR000535 Major sperm proteins (MSP) are central components in molecular interactions underlying sperm motility in Caenorhabditis elegans, whose sperm employ an amoebae-like crawling motion using a MSP-containing lamellipod, rather than the flagellar-based swimming motion associated with other sperm. These proteins oligomerise to form an extensive filament system that extends from sperm villipoda, along the leading edge of the pseudopod. About 30 MSP isoforms may exist in C. elegans. MSPs form a fibrous network, whereby MSP dimers form helical subfilaments that coil around one another to produce filaments, which in turn form supercoils to produce bundles. The crystal structure of MSP from C. elegans reveals an immunoglobulin (Ig)-like seven-stranded beta sandwich fold []. ; GO: 0005198 structural molecule activity; PDB: 1MSP_A 3MSP_B 2BVU_B 2MSP_C 1Z9O_F 1Z9L_A 3IKK_A 1WIC_A 2CRI_A 2RR3_A ....
Probab=50.22 E-value=84 Score=21.84 Aligned_cols=53 Identities=17% Similarity=0.127 Sum_probs=38.7
Q ss_pred eEEEEEEEEecCCCCcceEEEEECCCCcEEEEEcCEEEEeecCceEEEEEEEEEcc
Q 030998 62 SFTFKRVLTNVADTRSTYTAAVKAPVGMTVTVEPATLSFAGKFSKAEFSLTVNINL 117 (167)
Q Consensus 62 ~~tv~RTVTNVg~~~stY~a~V~~P~gv~V~V~P~~L~F~~~gqk~sf~Vt~~~~~ 117 (167)
.....=+++|.++..-.|++.-..|..+. |.|..=.. ++|++....|++....
T Consensus 19 ~~~~~l~l~N~s~~~i~fKiktt~~~~y~--v~P~~G~i-~p~~~~~i~I~~~~~~ 71 (109)
T PF00635_consen 19 QQSCELTLTNPSDKPIAFKIKTTNPNRYR--VKPSYGII-EPGESVEITITFQPFD 71 (109)
T ss_dssp -EEEEEEEEE-SSSEEEEEEEES-TTTEE--EESSEEEE--TTEEEEEEEEE-SSS
T ss_pred eEEEEEEEECCCCCcEEEEEEcCCCceEE--ecCCCEEE-CCCCEEEEEEEEEecc
Confidence 34555689999999899999999998776 57997544 7899999999988643
No 13
>PF07718 Coatamer_beta_C: Coatomer beta C-terminal region; InterPro: IPR011710 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C-terminal domain of the beta subunit from coatomer proteins (Beta-coat proteins). The C-terminal domain probably adapts the function of the N-terminal IPR002553 from INTERPRO domain. Coatomer protein complex I (COPI)-coated vesicles are involved in transport between the endoplasmic reticulum and the Golgi but also participate in transport from early to late endosomes within the endocytic pathway []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat
Probab=44.32 E-value=1.2e+02 Score=23.68 Aligned_cols=50 Identities=10% Similarity=0.244 Sum_probs=37.8
Q ss_pred EEEECCCCcEEEEEcCEEEEeecCceEEEEEEEEEccccccCCCCCccceEEEEEEEe
Q 030998 81 AAVKAPVGMTVTVEPATLSFAGKFSKAEFSLTVNINLGNAFSPKSNFLGNFGYLTWYE 138 (167)
Q Consensus 81 a~V~~P~gv~V~V~P~~L~F~~~gqk~sf~Vt~~~~~~~~~~~~~~~~~~fGsl~W~d 138 (167)
+....-.++++.=+|...+. .+++....+.+|+.... ..+. .||.|+|..
T Consensus 90 vElat~gdLklve~p~~~tL-~P~~~~~i~~~iKVsSt-----etGv--IfG~I~Yd~ 139 (140)
T PF07718_consen 90 VELATLGDLKLVERPQPITL-APHGFARIKATIKVSST-----ETGV--IFGNIVYDG 139 (140)
T ss_pred EEEEecCCcEEccCCCceee-CCCcEEEEEEEEEEEec-----cCCE--EEEEEEEec
Confidence 33344456888889998887 78999999999988763 3456 899999853
No 14
>cd00237 p23 p23 binds heat shock protein (Hsp)90 and participates in the folding of a number of Hsp90 clients, including the progesterone receptor. p23 also has a passive chaperoning activity and in addition may participate in prostaglandin synthesis.
Probab=43.94 E-value=91 Score=22.78 Aligned_cols=22 Identities=23% Similarity=0.342 Sum_probs=16.6
Q ss_pred EEECCCCcEEEEEcCEEEEeec
Q 030998 82 AVKAPVGMTVTVEPATLSFAGK 103 (167)
Q Consensus 82 ~V~~P~gv~V~V~P~~L~F~~~ 103 (167)
.+.-+..+.|.++|..|.|+..
T Consensus 18 ~v~d~~d~~v~l~~~~l~f~~~ 39 (106)
T cd00237 18 CVEDSKDVKVDFEKSKLTFSCL 39 (106)
T ss_pred EeCCCCCcEEEEecCEEEEEEE
Confidence 3333578899999999999863
No 15
>PF13195 DUF4011: Protein of unknown function (DUF4011)
Probab=36.86 E-value=53 Score=25.87 Aligned_cols=27 Identities=30% Similarity=0.682 Sum_probs=21.4
Q ss_pred ceEEEEEEEeC-CCceEEEceEEEEEee
Q 030998 129 GNFGYLTWYEV-KRKHTVRSPIVAAFAN 155 (167)
Q Consensus 129 ~~fGsl~W~d~-~g~h~VRSPIaV~~~~ 155 (167)
.+||.|.|.+. ......++|+...+..
T Consensus 120 La~G~L~W~~~~~~~~~~~APLlL~PV~ 147 (176)
T PF13195_consen 120 LAFGFLEWYESDDSDKPRRAPLLLIPVE 147 (176)
T ss_pred eeeeEEEeccCCCCCCEEECCEEEEeEE
Confidence 38999999974 4578999999987643
No 16
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=35.25 E-value=1.1e+02 Score=21.22 Aligned_cols=28 Identities=21% Similarity=0.230 Sum_probs=21.3
Q ss_pred EEEEEcCEEEEeec--CceEEEEEEEEEcc
Q 030998 90 TVTVEPATLSFAGK--FSKAEFSLTVNINL 117 (167)
Q Consensus 90 ~V~V~P~~L~F~~~--gqk~sf~Vt~~~~~ 117 (167)
.++++|+.|.|... |++.+.+|+++..+
T Consensus 3 ~l~v~P~~ldFG~v~~g~~~~~~v~l~N~s 32 (102)
T PF14874_consen 3 TLEVSPKELDFGNVFVGQTYSRTVTLTNTS 32 (102)
T ss_pred EEEEeCCEEEeeEEccCCEEEEEEEEEECC
Confidence 67899999999854 67777777776654
No 17
>PF12180 EABR: TSG101 and ALIX binding domain of CEP55; InterPro: IPR022008 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. This domain is the active domain of CEP55. CEP55 is a protein involved in cytokinesis, specifically in abscission of the plasma membrane at the midbody. To perform this function, CEP55 complexes with ESCRT-I (by a Proline rich sequence in its TSG101 domain) and ALIX. This is the domain on CEP55 which binds to both TSG101 and ALIX. It also acts as a hinge between the N and C termini. This domain is called EABR. ; PDB: 3E1R_A.
Probab=31.69 E-value=6.5 Score=23.82 Aligned_cols=16 Identities=31% Similarity=0.393 Sum_probs=14.5
Q ss_pred eeeeCChhhHHHhhhc
Q 030998 5 LVYDIEIQDYLNYLCA 20 (167)
Q Consensus 5 LVYD~~~~DYi~fLC~ 20 (167)
|.||.+-++|+.-||+
T Consensus 15 q~YD~qRE~YV~~L~~ 30 (35)
T PF12180_consen 15 QKYDQQREAYVRGLLA 30 (35)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHhHHHHHHHHHH
Confidence 5799999999999997
No 18
>PLN03080 Probable beta-xylosidase; Provisional
Probab=31.34 E-value=1.7e+02 Score=28.80 Aligned_cols=53 Identities=17% Similarity=0.225 Sum_probs=33.6
Q ss_pred eEEEEEEEEecCCCCcceEEE--EECCCCcEEEEEcCEEE-Ee----ecCceEEEEEEEEE
Q 030998 62 SFTFKRVLTNVADTRSTYTAA--VKAPVGMTVTVEPATLS-FA----GKFSKAEFSLTVNI 115 (167)
Q Consensus 62 ~~tv~RTVTNVg~~~stY~a~--V~~P~gv~V~V~P~~L~-F~----~~gqk~sf~Vt~~~ 115 (167)
..+|+=+|||.|+......+- +..|.+- +..-+..|. |. ++||++..++++..
T Consensus 685 ~~~v~v~VtNtG~~~G~evvQlYv~~p~~~-~~~P~k~L~gF~kv~L~~Ges~~V~~~l~~ 744 (779)
T PLN03080 685 RFNVHISVSNVGEMDGSHVVMLFSRSPPVV-PGVPEKQLVGFDRVHTASGRSTETEIVVDP 744 (779)
T ss_pred eEEEEEEEEECCcccCcEEEEEEEecCccC-CCCcchhccCcEeEeeCCCCEEEEEEEeCc
Confidence 477889999999866655544 4556431 111223443 33 67899988888865
No 19
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=30.78 E-value=87 Score=23.85 Aligned_cols=36 Identities=25% Similarity=0.432 Sum_probs=20.3
Q ss_pred CcceEEEEECCCCcEEEEEcCEEEEeecCceEEEEE
Q 030998 76 RSTYTAAVKAPVGMTVTVEPATLSFAGKFSKAEFSL 111 (167)
Q Consensus 76 ~stY~a~V~~P~gv~V~V~P~~L~F~~~gqk~sf~V 111 (167)
.++|+-.|..|+|.++...|..-..+.+-.|.+++|
T Consensus 36 ~E~ytyti~~pegm~l~t~~~~K~I~N~~Gk~~isv 71 (116)
T PF12970_consen 36 DETYTYTIELPEGMKLVTPPMEKKIDNPVGKVSISV 71 (116)
T ss_dssp EEEEEEEEEE-TT-EE-S--S-EEEEETTEEEEEEE
T ss_pred CcceEEEEEcCCCCeeecCccceeccCCcceEEEEE
Confidence 357888888899999988887666655544544433
No 20
>PF15496 DUF4646: Domain of unknown function (DUF4646)
Probab=30.78 E-value=26 Score=26.47 Aligned_cols=16 Identities=19% Similarity=0.486 Sum_probs=13.6
Q ss_pred eeCChhhHHHhhhcCC
Q 030998 7 YDIEIQDYLNYLCAMN 22 (167)
Q Consensus 7 YD~~~~DYi~fLC~lg 22 (167)
||.+++||..||-.+.
T Consensus 45 ~DVs~eDW~~F~~dl~ 60 (123)
T PF15496_consen 45 HDVSEEDWTRFLNDLS 60 (123)
T ss_pred cCCCHHHHHHHHHHHH
Confidence 7999999999986543
No 21
>PF07610 DUF1573: Protein of unknown function (DUF1573); InterPro: IPR011467 These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Probab=30.76 E-value=1.3e+02 Score=18.33 Aligned_cols=12 Identities=8% Similarity=0.030 Sum_probs=8.9
Q ss_pred ecCceEEEEEEE
Q 030998 102 GKFSKAEFSLTV 113 (167)
Q Consensus 102 ~~gqk~sf~Vt~ 113 (167)
++||+...+|++
T Consensus 34 ~PGes~~i~v~y 45 (45)
T PF07610_consen 34 APGESGKIKVTY 45 (45)
T ss_pred CCCCEEEEEEEC
Confidence 678888777764
No 22
>PF00635 Motile_Sperm: MSP (Major sperm protein) domain; InterPro: IPR000535 Major sperm proteins (MSP) are central components in molecular interactions underlying sperm motility in Caenorhabditis elegans, whose sperm employ an amoebae-like crawling motion using a MSP-containing lamellipod, rather than the flagellar-based swimming motion associated with other sperm. These proteins oligomerise to form an extensive filament system that extends from sperm villipoda, along the leading edge of the pseudopod. About 30 MSP isoforms may exist in C. elegans. MSPs form a fibrous network, whereby MSP dimers form helical subfilaments that coil around one another to produce filaments, which in turn form supercoils to produce bundles. The crystal structure of MSP from C. elegans reveals an immunoglobulin (Ig)-like seven-stranded beta sandwich fold []. ; GO: 0005198 structural molecule activity; PDB: 1MSP_A 3MSP_B 2BVU_B 2MSP_C 1Z9O_F 1Z9L_A 3IKK_A 1WIC_A 2CRI_A 2RR3_A ....
Probab=30.34 E-value=1.8e+02 Score=20.06 Aligned_cols=53 Identities=19% Similarity=0.237 Sum_probs=30.8
Q ss_pred EEEEEcC-EEEEeecC-ceEEEEEEEEEccccccCCCCCccceEEEEEEEeCCCceEEEceEEEE
Q 030998 90 TVTVEPA-TLSFAGKF-SKAEFSLTVNINLGNAFSPKSNFLGNFGYLTWYEVKRKHTVRSPIVAA 152 (167)
Q Consensus 90 ~V~V~P~-~L~F~~~g-qk~sf~Vt~~~~~~~~~~~~~~~~~~fGsl~W~d~~g~h~VRSPIaV~ 152 (167)
++.|.|. .|.|.... +...-.+++..... ... +|---+... ..+.|+-+.++-
T Consensus 1 ~l~v~P~~~i~F~~~~~~~~~~~l~l~N~s~------~~i--~fKiktt~~--~~y~v~P~~G~i 55 (109)
T PF00635_consen 1 DLSVEPSELIFFNAPFNKQQSCELTLTNPSD------KPI--AFKIKTTNP--NRYRVKPSYGII 55 (109)
T ss_dssp -CEEESSSEEEEESSTSS-EEEEEEEEE-SS------SEE--EEEEEES-T--TTEEEESSEEEE
T ss_pred CeEEeCCcceEEcCCCCceEEEEEEEECCCC------CcE--EEEEEcCCC--ceEEecCCCEEE
Confidence 3678999 88887754 55666667765542 233 554443333 567787776654
No 23
>PF08310 LGFP: LGFP repeat; InterPro: IPR013207 This 54 amino acid repeat is found in many hypothetical proteins. Several hypothetical proteins from Corynebacterium glutamicum (Brevibacterium flavum) and Corynebacterium efficiens along with PS1 protein contain this repeat region. The N-terminal region of PS1 contains an esterase domain which transfers corynomycolic acid. The C-terminal region consists of 4 tandem LGFP repeats. It is hypothesised that the PS1 proteins in Corynebacterium, when associated with the cell wall, may be anchored via the LGFP tandem repeats that may be important for maintaining cell wall integrity. Deletion of Q01377 from SWISSPROT protein results in a 10-fold increase in the cell volume of the organism and infers the corresponding involvement of the protein in the cell shape formation []. The secondary structure of each repeat is predicted to comprise two beta-strands and one alpha-helix.
Probab=21.54 E-value=47 Score=21.14 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=18.2
Q ss_pred eEEEEEEEeCCCceEEEceEEEEE
Q 030998 130 NFGYLTWYEVKRKHTVRSPIVAAF 153 (167)
Q Consensus 130 ~fGsl~W~d~~g~h~VRSPIaV~~ 153 (167)
.-|.|.|+...|.|.|+-+|.-++
T Consensus 22 ~~G~Iywsp~tGa~~v~G~I~~~w 45 (54)
T PF08310_consen 22 QNGTIYWSPATGAHAVHGAILDKW 45 (54)
T ss_pred CCeEEEEeCCCCcEEECHHHHHHH
Confidence 569999998656799987765444
Done!