Query psy4238
Match_columns 67
No_of_seqs 105 out of 232
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 20:21:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4238.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4238hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00189 40S ribosomal protein 99.9 1.4E-23 3E-28 148.9 5.4 64 2-65 130-193 (194)
2 KOG3301|consensus 99.9 6.1E-23 1.3E-27 144.7 4.0 66 2-67 118-183 (183)
3 PTZ00155 40S ribosomal protein 99.8 1.5E-20 3.2E-25 132.0 4.8 53 2-54 128-180 (181)
4 TIGR01018 rpsD_arch ribosomal 99.6 1.1E-15 2.5E-20 105.8 3.5 38 2-39 125-162 (162)
5 PRK04051 rps4p 30S ribosomal p 99.5 4.4E-14 9.5E-19 98.9 3.4 47 2-48 124-171 (177)
6 COG0522 RpsD Ribosomal protein 99.4 1.7E-13 3.7E-18 97.5 2.2 44 2-45 115-159 (205)
7 CHL00113 rps4 ribosomal protei 97.5 5.2E-05 1.1E-09 53.9 1.8 33 2-36 110-142 (201)
8 TIGR01017 rpsD_bact ribosomal 97.3 0.00015 3.3E-09 51.0 1.9 33 2-36 111-143 (200)
9 PRK05327 rpsD 30S ribosomal pr 97.2 0.00021 4.5E-09 50.4 1.8 32 2-35 114-145 (203)
10 PF01479 S4: S4 domain; Inter 97.0 0.0002 4.4E-09 39.0 0.3 23 3-25 23-45 (48)
11 KOG4655|consensus 96.7 0.00021 4.5E-09 51.1 -1.5 35 3-37 129-163 (181)
12 cd00165 S4 S4/Hsp/ tRNA synthe 96.2 0.0039 8.4E-08 33.6 1.9 31 3-35 23-53 (70)
13 smart00363 S4 S4 RNA-binding d 95.4 0.019 4E-07 30.1 2.5 30 3-34 23-52 (60)
14 TIGR02988 YaaA_near_RecF S4 do 95.4 0.0061 1.3E-07 34.7 0.7 24 3-26 31-54 (59)
15 PF11736 DUF3299: Protein of u 93.1 0.063 1.4E-06 36.6 1.9 25 9-33 52-78 (146)
16 COG1188 Ribosome-associated he 92.9 0.076 1.7E-06 34.8 1.9 29 4-33 32-60 (100)
17 TIGR00478 tly hemolysin TlyA f 90.2 0.16 3.5E-06 36.4 1.4 34 3-38 22-55 (228)
18 PRK10348 ribosome-associated h 89.2 0.19 4.2E-06 34.1 1.1 29 3-32 31-59 (133)
19 TIGR03069 PS_II_S4 photosystem 85.1 0.62 1.3E-05 34.0 1.9 29 3-33 205-233 (257)
20 COG1189 Predicted rRNA methyla 81.2 0.98 2.1E-05 33.7 1.6 36 3-40 25-61 (245)
21 PRK10700 23S rRNA pseudouridyl 78.9 1.5 3.3E-05 32.2 2.0 30 3-33 24-53 (289)
22 PF05949 DUF881: Bacterial pro 75.9 1.5 3.2E-05 29.5 1.1 28 7-34 60-87 (149)
23 PLN00051 RNA-binding S4 domain 73.9 1.5 3.3E-05 32.4 0.9 24 3-26 213-236 (267)
24 PRK10839 16S rRNA pseudouridyl 73.8 2.4 5.2E-05 29.5 1.8 29 3-33 22-50 (232)
25 TIGR00005 rluA_subfam pseudour 71.3 2.7 5.9E-05 30.0 1.6 30 3-34 28-57 (299)
26 COG0564 RluA Pseudouridylate s 68.4 3.7 8.1E-05 30.3 1.9 31 3-34 34-64 (289)
27 PRK11180 rluD 23S rRNA pseudou 66.8 4.1 8.9E-05 29.9 1.8 29 3-33 40-68 (325)
28 PHA01635 hypothetical protein 62.8 4.9 0.00011 29.9 1.6 18 7-24 64-81 (231)
29 PRK10475 23S rRNA pseudouridin 62.0 6.1 0.00013 29.3 2.0 28 3-33 28-55 (290)
30 PF14451 Ub-Mut7C: Mut7-C ubiq 59.7 13 0.00028 23.0 2.9 27 6-35 50-76 (81)
31 PRK11025 23S rRNA pseudouridyl 51.0 9.3 0.0002 28.1 1.4 28 3-33 42-69 (317)
32 COG3879 Uncharacterized protei 41.7 25 0.00054 26.3 2.4 34 6-39 154-188 (247)
33 PRK14352 glmU bifunctional N-a 39.1 38 0.00081 25.8 3.1 52 3-54 413-465 (482)
34 COG1187 RsuA 16S rRNA uridine- 38.5 30 0.00064 25.5 2.4 24 3-26 24-47 (248)
35 COG2302 Uncharacterized conser 33.7 23 0.00051 26.7 1.2 33 3-37 202-234 (257)
36 COG2129 Predicted phosphoester 33.5 32 0.00069 25.4 1.9 19 2-20 178-203 (226)
37 PF00498 FHA: FHA domain; Int 31.8 86 0.0019 17.1 3.1 24 8-32 44-67 (68)
38 PF01324 Diphtheria_R: Diphthe 31.7 33 0.00071 23.8 1.6 12 6-17 68-79 (154)
39 TIGR00024 SbcD_rel_arch putati 30.3 69 0.0015 22.6 3.1 31 12-42 153-184 (225)
40 cd00754 MoaD Ubiquitin domain 29.8 67 0.0015 18.1 2.5 25 7-34 51-75 (80)
41 cd01764 Urm1 Urm1-like ubuitin 29.5 70 0.0015 19.8 2.7 32 7-40 61-93 (94)
42 COG4525 TauB ABC-type taurine 27.0 44 0.00095 25.3 1.7 25 4-34 58-82 (259)
43 PF05965 FYRC: F/Y rich C-term 26.0 30 0.00065 20.7 0.6 23 17-39 3-25 (86)
44 COG3495 Uncharacterized protei 24.6 47 0.001 23.7 1.4 21 9-29 68-88 (166)
45 PRK06437 hypothetical protein; 23.9 1.2E+02 0.0025 17.6 2.8 24 7-33 38-61 (67)
46 KOG1057|consensus 23.5 91 0.002 27.7 3.1 42 7-49 169-211 (1018)
47 PF11343 DUF3145: Protein of u 23.2 44 0.00096 23.6 1.0 16 1-16 90-105 (158)
48 PF14541 TAXi_C: Xylanase inhi 23.1 1.2E+02 0.0025 19.6 3.0 32 8-39 9-41 (161)
49 PF08288 PIGA: PIGA (GPI ancho 21.8 44 0.00096 21.6 0.8 8 2-9 52-59 (90)
50 PRK05659 sulfur carrier protei 21.6 80 0.0017 17.6 1.8 13 7-19 2-14 (66)
51 PRK15287 putative minor fimbri 21.4 90 0.002 20.7 2.2 28 6-33 20-47 (158)
52 PF08844 DUF1815: Domain of un 21.4 69 0.0015 21.3 1.6 23 11-33 40-62 (105)
53 PRK09968 serine/threonine-spec 21.1 88 0.0019 21.6 2.2 31 2-42 182-212 (218)
54 COG1703 ArgK Putative periplas 20.4 79 0.0017 24.6 2.0 24 30-53 85-109 (323)
55 PF11160 DUF2945: Protein of u 20.1 2.1E+02 0.0045 16.9 3.6 32 7-38 24-59 (62)
56 PF03308 ArgK: ArgK protein; 20.0 56 0.0012 24.6 1.1 24 30-53 63-87 (266)
57 PRK01777 hypothetical protein; 20.0 2.4E+02 0.0053 17.7 4.3 43 4-52 48-90 (95)
No 1
>PLN00189 40S ribosomal protein S9; Provisional
Probab=99.89 E-value=1.4e-23 Score=148.87 Aligned_cols=64 Identities=56% Similarity=0.828 Sum_probs=57.6
Q ss_pred ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCCcchhhhhhhhhhhccCCCCCCcc
Q psy4238 2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEED 65 (67)
Q Consensus 2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~pgRvkrk~~k~~~~~~~~~~~~~ 65 (67)
.|+||||+|||++||+|||+|++++|++|+|+.+|||+++.|+|+|||+++++++++++++|||
T Consensus 130 lI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~~Sp~~~~~p~r~~~k~~~~~~~~~~~~~~~~ 193 (194)
T PLN00189 130 LIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSLTSPLGGGRPGRVKRKNQKAASGGGDGDEEDE 193 (194)
T ss_pred heeCCCEeECCEEEecCcEEEecCCEEEEEEecCCcccCCChhHHHHHHHHhccCCCCcccccc
Confidence 5999999999999999999999999999999999999997799999999999877655555443
No 2
>KOG3301|consensus
Probab=99.87 E-value=6.1e-23 Score=144.73 Aligned_cols=66 Identities=61% Similarity=0.818 Sum_probs=58.4
Q ss_pred ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCCcchhhhhhhhhhhccCCCCCCcccC
Q psy4238 2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67 (67)
Q Consensus 2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~pgRvkrk~~k~~~~~~~~~~~~~~~ 67 (67)
.|.|+||+|++|+||+|||||+.|+|++|||+++|||++++|+|+|+|+++++.++.++.+++||+
T Consensus 118 Li~~rhI~V~~qiV~IPsf~vrldsqk~iD~s~~s~~g~~~pg~~krk~~~k~~~~~g~~~~~Ee~ 183 (183)
T KOG3301|consen 118 LIRQRHIRVGKQIVNIPSFMVRLDSQKHIDFSLPSPYGGARPGRVKRKNNQKADAKGGGLDENEEE 183 (183)
T ss_pred HhcCccEEecCeEeeccceeEeechhhhccccccccCCCCCcchhhhhhhhhhhcccCCccccccC
Confidence 588999999999999999999999999999999999999999999999877776666655555543
No 3
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=99.81 E-value=1.5e-20 Score=131.98 Aligned_cols=53 Identities=58% Similarity=0.834 Sum_probs=50.0
Q ss_pred ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCCcchhhhhhhhhh
Q psy4238 2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKA 54 (67)
Q Consensus 2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~pgRvkrk~~k~~ 54 (67)
.|+||||+|||++||+|||+|++++|++|+|+.+|||+++.|+|++||+++++
T Consensus 128 lI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S~~~~~~~~r~~~~~~~~~ 180 (181)
T PTZ00155 128 LIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTSPFGNGRPGRVKRKAAKAA 180 (181)
T ss_pred heeCCCEEECCEEeccCceEeccCccCceeeecCCCccCCChHHHHHHhhhhc
Confidence 59999999999999999999999999999999999999977999999988764
No 4
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=99.58 E-value=1.1e-15 Score=105.81 Aligned_cols=38 Identities=39% Similarity=0.537 Sum_probs=36.7
Q ss_pred ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCC
Q psy4238 2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFG 39 (67)
Q Consensus 2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~ 39 (67)
.|+||||+|||++||+|||+|++++|++|+|+.+|||+
T Consensus 125 lI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S~~~ 162 (162)
T TIGR01018 125 LIVHGHIAVDGRRVTSPSYIVRREEEKKIDFAPSSPFK 162 (162)
T ss_pred HhhCCCeeECCEEeccCceEecCCCCCeeeeecCCCCC
Confidence 58999999999999999999999999999999999985
No 5
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=99.45 E-value=4.4e-14 Score=98.90 Aligned_cols=47 Identities=26% Similarity=0.318 Sum_probs=43.2
Q ss_pred ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCC-cchhhh
Q psy4238 2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-AGRVKR 48 (67)
Q Consensus 2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~-pgRvkr 48 (67)
.|.||||+|||++|+.|||+|+.++|++|+|+++||++... |+|..-
T Consensus 124 lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~S~i~~~~~~~r~~~ 171 (177)
T PRK04051 124 FIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPLADELHPERAEA 171 (177)
T ss_pred HHHcCCEEECCEEeCCCCeECCCCCcceEEEeCCCCCCCCCCcchhhh
Confidence 48999999999999999999999999999999999999855 887654
No 6
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=99.38 E-value=1.7e-13 Score=97.53 Aligned_cols=44 Identities=20% Similarity=0.115 Sum_probs=40.7
Q ss_pred ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCC-cch
Q psy4238 2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-AGR 45 (67)
Q Consensus 2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~-pgR 45 (67)
.|+||||+|||++||+|||+|+.+.|..|.+..+||+.... +++
T Consensus 115 lV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~~~~~~~~~ 159 (205)
T COG0522 115 LVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEALEL 159 (205)
T ss_pred HhhcceEEECCEEeccCcEEecCCCEEEeeecccchhhhhhhhhh
Confidence 48999999999999999999999999999999999999876 544
No 7
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=97.50 E-value=5.2e-05 Score=53.91 Aligned_cols=33 Identities=18% Similarity=0.165 Sum_probs=28.1
Q ss_pred ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCC
Q psy4238 2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNS 36 (67)
Q Consensus 2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~S 36 (67)
.|.||||.|||++|++|||.|..+ +.|.+...|
T Consensus 110 lI~~G~V~VNGk~v~~ps~~Vk~G--D~I~V~~~~ 142 (201)
T CHL00113 110 LVNHGHILVNGRIVDIPSYRCKPK--DIITVKDKQ 142 (201)
T ss_pred HHHCCcEEECCEEecCccccCCCC--CEEEEcccc
Confidence 378999999999999999999876 788886544
No 8
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=97.27 E-value=0.00015 Score=50.97 Aligned_cols=33 Identities=27% Similarity=0.230 Sum_probs=28.1
Q ss_pred ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCC
Q psy4238 2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNS 36 (67)
Q Consensus 2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~S 36 (67)
.|.||||.|||++|+.|||.|..+ +.|.+...+
T Consensus 111 lI~~G~V~VNgk~v~~ps~~V~~G--D~I~V~~~~ 143 (200)
T TIGR01017 111 LVSHGHILVNGKKVDIPSYQVRPG--DIISIKEKS 143 (200)
T ss_pred HHHCCCEEECCEEeCCCCCCCCCC--CEEEEeeCc
Confidence 378999999999999999999866 678887554
No 9
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=97.17 E-value=0.00021 Score=50.42 Aligned_cols=32 Identities=25% Similarity=0.217 Sum_probs=27.4
Q ss_pred ceeeeeEEECCEEeccCCeeEEcCCCCceEeecC
Q psy4238 2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLN 35 (67)
Q Consensus 2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~ 35 (67)
.|.||||.|||+.|++|||.|..+ +.|.+...
T Consensus 114 lI~~G~V~VNgk~v~~ps~~v~~G--D~I~v~~~ 145 (203)
T PRK05327 114 LVSHGHILVNGKKVNIPSYRVKPG--DVIEVREK 145 (203)
T ss_pred HHHCCcEEECCEEECCCCcCCCCC--CEEEECCc
Confidence 378999999999999999998765 66888765
No 10
>PF01479 S4: S4 domain; InterPro: IPR002942 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 S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=96.99 E-value=0.0002 Score=39.00 Aligned_cols=23 Identities=30% Similarity=0.372 Sum_probs=20.8
Q ss_pred eeeeeEEECCEEeccCCeeEEcC
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLD 25 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~d 25 (67)
|-+|+|.|||++|+-|+|.|..+
T Consensus 23 I~~g~V~VNg~~v~~~~~~v~~~ 45 (48)
T PF01479_consen 23 IKQGRVKVNGKVVKDPSYIVKPG 45 (48)
T ss_dssp HHTTTEEETTEEESSTTSBESTT
T ss_pred cCCCEEEECCEEEcCCCCCCCCc
Confidence 67899999999999999999754
No 11
>KOG4655|consensus
Probab=96.70 E-value=0.00021 Score=51.06 Aligned_cols=35 Identities=23% Similarity=0.265 Sum_probs=32.3
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEeecCCC
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSP 37 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SP 37 (67)
|=|||++||-.+||=|+|||.+..|+.|.+-.+|-
T Consensus 129 vEqGHVRvGp~~vtDPa~lvtr~mEDfvtWvd~SK 163 (181)
T KOG4655|consen 129 VEQGHVRVGPKVVTDPAFLVTRSMEDFVTWVDSSK 163 (181)
T ss_pred HHcCceeeCCeeccCchHHhhhhhhhhhhhhhhHH
Confidence 56999999999999999999999999999887774
No 12
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=96.17 E-value=0.0039 Score=33.65 Aligned_cols=31 Identities=26% Similarity=0.234 Sum_probs=25.7
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEeecC
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLN 35 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~ 35 (67)
|-+|+|.|||++++.|++.|..+ +.|.+...
T Consensus 23 i~~g~V~vn~~~~~~~~~~v~~~--d~i~i~~~ 53 (70)
T cd00165 23 IKHGHVLVNGKVVTKPSYKVKPG--DVIEVDGK 53 (70)
T ss_pred HHcCCEEECCEEccCCccCcCCC--CEEEEcCC
Confidence 67899999999998899998876 56777753
No 13
>smart00363 S4 S4 RNA-binding domain.
Probab=95.38 E-value=0.019 Score=30.12 Aligned_cols=30 Identities=23% Similarity=0.214 Sum_probs=24.1
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEeec
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSL 34 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~ 34 (67)
|-+|+|.|||+.++.|++.|.. .+.|.+..
T Consensus 23 i~~g~i~vng~~~~~~~~~l~~--gd~i~~~~ 52 (60)
T smart00363 23 IEQGRVKVNGKKVTKPSYIVKP--GDVISVRG 52 (60)
T ss_pred HHcCCEEECCEEecCCCeEeCC--CCEEEEcc
Confidence 5689999999999779988754 46777765
No 14
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=95.38 E-value=0.0061 Score=34.74 Aligned_cols=24 Identities=8% Similarity=-0.162 Sum_probs=20.6
Q ss_pred eeeeeEEECCEEeccCCeeEEcCC
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDS 26 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~de 26 (67)
|-.|+|.|||++|+.|+|.|...+
T Consensus 31 i~~G~V~VNg~~~~~~~~~l~~Gd 54 (59)
T TIGR02988 31 LQENEVLVNGELENRRGKKLYPGD 54 (59)
T ss_pred HHcCCEEECCEEccCCCCCCCCCC
Confidence 678999999999999999877654
No 15
>PF11736 DUF3299: Protein of unknown function (DUF3299); InterPro: IPR021727 This is a family of bacterial proteins of unknown function.
Probab=93.12 E-value=0.063 Score=36.59 Aligned_cols=25 Identities=28% Similarity=0.636 Sum_probs=20.1
Q ss_pred EECCEEeccCCeeEEcCCCC-ce-Eee
Q psy4238 9 RVRKQVVNIPSFVVRLDSQK-HI-DFS 33 (67)
Q Consensus 9 aV~gq~V~~PsylVr~deE~-~I-df~ 33 (67)
+++||.|.+|||||.++.+. .| +|-
T Consensus 52 ~L~Gk~V~i~Gf~vPle~~~~~v~eFl 78 (146)
T PF11736_consen 52 ALDGKQVRIPGFMVPLEQEEGKVTEFL 78 (146)
T ss_pred HhCCCEEEEeeEEEeeccCCCcEEEEE
Confidence 46899999999999999864 34 553
No 16
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=92.89 E-value=0.076 Score=34.83 Aligned_cols=29 Identities=24% Similarity=0.134 Sum_probs=24.8
Q ss_pred eeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238 4 VWEIGRVRKQVVNIPSFVVRLDSQKHIDFS 33 (67)
Q Consensus 4 vHGHIaV~gq~V~~PsylVr~deE~~Idf~ 33 (67)
-=|||.|||+++ .||+.|+.+..=.|.|.
T Consensus 32 ~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~ 60 (100)
T COG1188 32 EGGRVKVNGQRA-KPSKEVKVGDILTIRFG 60 (100)
T ss_pred HCCeEEECCEEc-ccccccCCCCEEEEEeC
Confidence 359999999998 69999999988777765
No 17
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=90.17 E-value=0.16 Score=36.36 Aligned_cols=34 Identities=29% Similarity=0.355 Sum_probs=27.1
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCC
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPF 38 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl 38 (67)
|..|+|.|||++++.|++.|..+ +.|.+....+|
T Consensus 22 I~~G~V~Vng~~v~k~s~~V~~~--d~I~v~~~~~~ 55 (228)
T TIGR00478 22 ILKGFVLVNGKKVDKPSALVDFD--AKIELLQNPLF 55 (228)
T ss_pred HHCCcEEECCEEeCCCCCCCCCC--CEEeccCccch
Confidence 67899999999999999988654 67877654333
No 18
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=89.22 E-value=0.19 Score=34.07 Aligned_cols=29 Identities=21% Similarity=0.098 Sum_probs=23.8
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEe
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDF 32 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf 32 (67)
|-.|+|.|||++ ..||..|..+.+=.|.|
T Consensus 31 I~~G~V~vnG~~-~Kps~~V~~gd~l~v~~ 59 (133)
T PRK10348 31 IEGGKVHYNGQR-SKPSKIVELNATLTLRQ 59 (133)
T ss_pred HHCCCEEECCEE-CCCCCccCCCCEEEEEE
Confidence 667999999999 78999998776655544
No 19
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=85.12 E-value=0.62 Score=33.96 Aligned_cols=29 Identities=17% Similarity=0.181 Sum_probs=23.7
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS 33 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~ 33 (67)
|-.|+|.|||+.|+.|++.|... +.|.+.
T Consensus 205 I~~G~V~VNg~~v~~~s~~v~~g--D~Isvr 233 (257)
T TIGR03069 205 IKAGRLRLNWKTVTQPSRELKVG--DRLQLR 233 (257)
T ss_pred HHCCeEEECCEEcCCCCCcCCCC--CEEEEc
Confidence 66899999999999999988544 566665
No 20
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=81.17 E-value=0.98 Score=33.65 Aligned_cols=36 Identities=25% Similarity=0.307 Sum_probs=27.0
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEee-cCCCCCC
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS-LNSPFGG 40 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~-~~SPl~~ 40 (67)
|--|-+.|||++|+.||++|..+. .|+.. +-.||-.
T Consensus 25 I~~G~V~Vng~~v~KP~~~V~~~~--~i~v~~~~~~yVS 61 (245)
T COG1189 25 ILAGNVLVNGEKVTKPSQLVDIDD--EIEVKGEEQPYVS 61 (245)
T ss_pred HHcCeEEECCEEecCcceecCCCc--eEEEcccCcCccc
Confidence 556899999999999999998554 45555 5555543
No 21
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=78.87 E-value=1.5 Score=32.21 Aligned_cols=30 Identities=13% Similarity=-0.017 Sum_probs=24.0
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS 33 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~ 33 (67)
|-.|.|.|||+++ .|++.|.....+.|.+.
T Consensus 24 I~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~ 53 (289)
T PRK10700 24 IEAGRVSVDGKIA-TLGDRVEVTPGLKIRID 53 (289)
T ss_pred HHcCCEEECCEec-cCCCEeCCCCCeEEEEC
Confidence 6789999999998 49999987655666664
No 22
>PF05949 DUF881: Bacterial protein of unknown function (DUF881); InterPro: IPR010273 This family consists of a series of hypothetical bacterial proteins. One of the family members Q45543 from SWISSPROT from Bacillus subtilis is thought to be involved in cell division and sporulation [].; PDB: 3GMG_B.
Probab=75.85 E-value=1.5 Score=29.49 Aligned_cols=28 Identities=7% Similarity=-0.123 Sum_probs=15.9
Q ss_pred eEEECCEEeccCCeeEEcCCCCceEeec
Q psy4238 7 IGRVRKQVVNIPSFVVRLDSQKHIDFSL 34 (67)
Q Consensus 7 HIaV~gq~V~~PsylVr~deE~~Idf~~ 34 (67)
.|+||||||+.=|++.-...-=.|++.+
T Consensus 60 AIsINg~Ri~~~S~Ir~~g~~i~Vng~~ 87 (149)
T PF05949_consen 60 AISINGQRIVATSAIRCAGGTILVNGRP 87 (149)
T ss_dssp EEEEE-EE--TT--EEEETTEEEETTEE
T ss_pred EEEECCEEEcCcEEEEEeCCEEEECCEE
Confidence 5888888888888777776655555543
No 23
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=73.90 E-value=1.5 Score=32.35 Aligned_cols=24 Identities=17% Similarity=-0.008 Sum_probs=20.8
Q ss_pred eeeeeEEECCEEeccCCeeEEcCC
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDS 26 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~de 26 (67)
|-.|+|.||++.|+.|+|.|....
T Consensus 213 I~~g~V~vN~~~v~~~s~~v~~gD 236 (267)
T PLN00051 213 ISSGDVRVNWREVTKNGTTLKTGD 236 (267)
T ss_pred HHcCcEEECCEEcCCCCCCCCCCC
Confidence 567999999999999999887654
No 24
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=73.79 E-value=2.4 Score=29.45 Aligned_cols=29 Identities=10% Similarity=0.170 Sum_probs=23.2
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS 33 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~ 33 (67)
|-.|.|.|||++++.|++.|... +.|.++
T Consensus 22 i~~g~V~VNg~~~~~~~~~l~~g--d~I~l~ 50 (232)
T PRK10839 22 LRANRVTVDGEIVKNGAFKLLPE--HDVAYD 50 (232)
T ss_pred HHcCeEEECCEEeccCCcCcCCC--CEEEEC
Confidence 45799999999998899988654 457665
No 25
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=71.28 E-value=2.7 Score=30.03 Aligned_cols=30 Identities=20% Similarity=0.186 Sum_probs=23.1
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEeec
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSL 34 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~ 34 (67)
|-.|.|.|||+++..|++.|... +.|.++.
T Consensus 28 i~~G~V~VNg~~~~~~~~~v~~g--d~I~i~~ 57 (299)
T TIGR00005 28 IENGQVKVNGKVTANPKLKVKDG--DRITVRV 57 (299)
T ss_pred HHCCcEEECCEeccCcccCCCCC--CEEEEec
Confidence 56899999998777799988755 5676653
No 26
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=68.41 E-value=3.7 Score=30.28 Aligned_cols=31 Identities=23% Similarity=0.213 Sum_probs=25.1
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEeec
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSL 34 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~ 34 (67)
|--|.|.|||++|+ |+|.|..+..=.+.+..
T Consensus 34 i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~ 64 (289)
T COG0564 34 IRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPE 64 (289)
T ss_pred HHCCCEEECCEEcc-CCeeeCCCCEEEEeccc
Confidence 34589999999999 99999888776666644
No 27
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=66.85 E-value=4.1 Score=29.93 Aligned_cols=29 Identities=21% Similarity=0.145 Sum_probs=23.3
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS 33 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~ 33 (67)
|-.|.|.|||++|+.|++.|... +.|.++
T Consensus 40 I~~G~V~VNg~~v~~~~~~v~~g--D~I~v~ 68 (325)
T PRK11180 40 ILDQRVLVNGKVINKPKEKVLGG--EQVAID 68 (325)
T ss_pred HHCCCEEECCEEccCCCcCcCCC--CEEEEe
Confidence 56799999999998899998755 456665
No 28
>PHA01635 hypothetical protein
Probab=62.78 E-value=4.9 Score=29.88 Aligned_cols=18 Identities=17% Similarity=0.300 Sum_probs=15.4
Q ss_pred eEEECCEEeccCCeeEEc
Q psy4238 7 IGRVRKQVVNIPSFVVRL 24 (67)
Q Consensus 7 HIaV~gq~V~~PsylVr~ 24 (67)
-|.+|||.|++|+|+-..
T Consensus 64 ~l~ingq~v~vP~YiFG~ 81 (231)
T PHA01635 64 ELNINGQQVTVPDYIFGN 81 (231)
T ss_pred EEEEcCcEeeccceeccc
Confidence 488999999999998653
No 29
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=61.99 E-value=6.1 Score=29.28 Aligned_cols=28 Identities=7% Similarity=-0.110 Sum_probs=21.8
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS 33 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~ 33 (67)
|-.|.|.|||++++ |++.|.. .+.|.++
T Consensus 28 I~~G~V~VNGk~v~-~~~~V~~--gD~V~v~ 55 (290)
T PRK10475 28 IEQGNVFINGKRAT-IGDQVKA--GDVVKVN 55 (290)
T ss_pred HHCCcEEECCEEcc-CCCCcCC--CCEEEEC
Confidence 56899999999985 8988743 4667765
No 30
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=59.74 E-value=13 Score=22.97 Aligned_cols=27 Identities=7% Similarity=0.059 Sum_probs=21.1
Q ss_pred eeEEECCEEeccCCeeEEcCCCCceEeecC
Q psy4238 6 EIGRVRKQVVNIPSFVVRLDSQKHIDFSLN 35 (67)
Q Consensus 6 GHIaV~gq~V~~PsylVr~deE~~Idf~~~ 35 (67)
|-|.|||+-|+ ++|+++ .-+.|.+++.
T Consensus 50 ~~i~vNG~~v~-~~~~~~--~Gd~v~V~P~ 76 (81)
T PF14451_consen 50 GLILVNGRPVD-FDYRLK--DGDRVAVYPV 76 (81)
T ss_pred EEEEECCEECC-CcccCC--CCCEEEEEec
Confidence 67899999998 788765 5667777764
No 31
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=51.00 E-value=9.3 Score=28.05 Aligned_cols=28 Identities=14% Similarity=0.274 Sum_probs=22.3
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS 33 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~ 33 (67)
|-.|.|.|||++++ |++.|... +.|.+.
T Consensus 42 i~~G~V~VNg~~v~-~~~~v~~G--D~I~i~ 69 (317)
T PRK11025 42 LRKGEVRVNKKRIK-PEYKLEAG--DEVRIP 69 (317)
T ss_pred HHcCCEEECCEEcC-cccccCCC--CEEEeC
Confidence 56899999999985 89988766 567764
No 32
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.72 E-value=25 Score=26.30 Aligned_cols=34 Identities=15% Similarity=0.182 Sum_probs=23.3
Q ss_pred eeEEECCEEeccCCeeEEcCCCCceEee-cCCCCC
Q psy4238 6 EIGRVRKQVVNIPSFVVRLDSQKHIDFS-LNSPFG 39 (67)
Q Consensus 6 GHIaV~gq~V~~PsylVr~deE~~Idf~-~~SPl~ 39 (67)
.+|+||||||..=+++.-+..--.||=. ..+||.
T Consensus 154 EaIsIn~~RI~~~t~Ir~v~g~~~vdg~~~~~P~T 188 (247)
T COG3879 154 EAISINGQRIGSNTTIRCVGGTLLVDGRRLSAPYT 188 (247)
T ss_pred hheeECCEEeecceEEEecCCeEEECCeecCCCeE
Confidence 3799999999998888777664444322 344554
No 33
>PRK14352 glmU bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional
Probab=39.08 E-value=38 Score=25.83 Aligned_cols=52 Identities=15% Similarity=-0.064 Sum_probs=39.1
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCC-cchhhhhhhhhh
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-AGRVKRKNLRKA 54 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~-pgRvkrk~~k~~ 54 (67)
++.+++.|+...+--++-+|..+-....-+...+|...-+ =.+.|+++.+.+
T Consensus 413 ~i~~~~~Ig~~~~igags~v~~~v~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 465 (482)
T PRK14352 413 MFVAPVTVGDGAYTGAGTVIREDVPPGALAVSEGPQRNIEGWVQRKRPGTPAA 465 (482)
T ss_pred EEeCCCEECCCcEECCCCEEcCCCCCCcEEEecccccccccccccccccchhh
Confidence 5678899998888889999999988777666667777665 455566655554
No 34
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=38.47 E-value=30 Score=25.53 Aligned_cols=24 Identities=25% Similarity=0.145 Sum_probs=19.9
Q ss_pred eeeeeEEECCEEeccCCeeEEcCC
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDS 26 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~de 26 (67)
|-=|.|.|||++++.|+..|.-+.
T Consensus 24 I~~G~V~VnG~v~~~~~~~v~~~~ 47 (248)
T COG1187 24 IEEGRVTVNGKVATLGGVVVDPDD 47 (248)
T ss_pred HHcCCEEECCEEeccCCeEeCCCC
Confidence 456889999999999998877665
No 35
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=33.65 E-value=23 Score=26.69 Aligned_cols=33 Identities=21% Similarity=0.067 Sum_probs=25.5
Q ss_pred eeeeeEEECCEEeccCCeeEEcCCCCceEeecCCC
Q psy4238 3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSP 37 (67)
Q Consensus 3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SP 37 (67)
|.-|-+.||.+.|+.|||-|.. .+.|..-..--
T Consensus 202 Ie~g~VkVN~k~v~~~s~~v~~--GDliSirG~GR 234 (257)
T COG2302 202 IEKGKVKVNWKVVDKASYEVQE--GDLISIRGFGR 234 (257)
T ss_pred HHcCceEEeeEEeccccceecc--CCEEEEecccc
Confidence 5568899999999999998764 56777654433
No 36
>COG2129 Predicted phosphoesterases, related to the Icc protein [General function prediction only]
Probab=33.51 E-value=32 Score=25.41 Aligned_cols=19 Identities=11% Similarity=-0.106 Sum_probs=16.1
Q ss_pred ceeeeeEE-------ECCEEeccCCe
Q psy4238 2 GIVWEIGR-------VRKQVVNIPSF 20 (67)
Q Consensus 2 ~IvHGHIa-------V~gq~V~~Psy 20 (67)
..+||||- ||..+|.-|+-
T Consensus 178 l~i~GHIHEs~G~d~iG~TivVNPG~ 203 (226)
T COG2129 178 LGLHGHIHESRGIDKIGNTIVVNPGP 203 (226)
T ss_pred eEEEeeecccccccccCCeEEECCCC
Confidence 57899996 99999888984
No 37
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=31.84 E-value=86 Score=17.08 Aligned_cols=24 Identities=29% Similarity=0.266 Sum_probs=13.5
Q ss_pred EEECCEEeccCCeeEEcCCCCceEe
Q psy4238 8 GRVRKQVVNIPSFVVRLDSQKHIDF 32 (67)
Q Consensus 8 IaV~gq~V~~PsylVr~deE~~Idf 32 (67)
+.|||+++. |+..+++...+.|.|
T Consensus 44 t~vng~~l~-~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 44 TFVNGQRLG-PGEPVPLKDGDIIRF 67 (68)
T ss_dssp EEETTEEES-STSEEEE-TTEEEEE
T ss_pred EEECCEEcC-CCCEEECCCCCEEEc
Confidence 456777766 555555555555543
No 38
>PF01324 Diphtheria_R: Diphtheria toxin, R domain; InterPro: IPR022404 This entry represents the C-terminal receptor-binding domain, also known as the R domain. This domain has a beta-sandwich fold consisiting of nine strands in two sheet with greek-key topology; it is a subclass of immunoglobin-like fold []. The R domain binds to cell surface receptor, permitting the toxin to enter the cell by receptor mediated endocytosis [, ]. Diphtheria toxin (2.4.2.36 from EC) is a 58 kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae. The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis []. The mechanism of inhibition involves transfer of the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. The catalysed reaction is as follows: NAD+ + peptide diphthamide = nicotinamide + peptide N-(ADP-D-ribosyl)diphthamide The crystal structure of the diphtheria toxin homodimer has been determined to 2.5A resolution []. The structure reveals a Y-shaped molecule of 3 domains, a catalytic domain (fragment A), whose fold is of the alpha + beta type; a transmembrane (TM) domain, which consists of 9 alpha-helices, 2 pairs of which may participate in pH-triggered membrane insertion and translocation; and a receptor-binding domain, which forms a flattened beta-barrel with a jelly-roll-like topology []. The TM- and receptor binding-domains together constitute fragment B.; PDB: 1MDT_B 1SGK_A 1F0L_B 1DDT_A 1TOX_B 4AE0_A 1XDT_T 4AE1_A.
Probab=31.66 E-value=33 Score=23.78 Aligned_cols=12 Identities=8% Similarity=0.039 Sum_probs=9.7
Q ss_pred eeEEECCEEecc
Q psy4238 6 EIGRVRKQVVNI 17 (67)
Q Consensus 6 GHIaV~gq~V~~ 17 (67)
-||+|||+.+..
T Consensus 68 thisvngrkirm 79 (154)
T PF01324_consen 68 THISVNGRKIRM 79 (154)
T ss_dssp -EEEETTEEEEE
T ss_pred eeEEEcCeEEEE
Confidence 489999999874
No 39
>TIGR00024 SbcD_rel_arch putative phosphoesterase, SbcD/Mre11-related. Members of this uncharacterized family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11. SbcD is a subunit of the SbcCD nuclease of E. coli that can cleave DNA hairpins to unblock stalled DNA replication. All members of this family are archaeal.
Probab=30.33 E-value=69 Score=22.64 Aligned_cols=31 Identities=16% Similarity=0.344 Sum_probs=20.6
Q ss_pred CEEeccCCeeEEc-CCCCceEeecCCCCCCCC
Q psy4238 12 KQVVNIPSFVVRL-DSQKHIDFSLNSPFGGGG 42 (67)
Q Consensus 12 gq~V~~PsylVr~-deE~~Idf~~~SPl~~~~ 42 (67)
++.++.|-|+... +....+=.=..|+|+++.
T Consensus 153 ~~~~r~pcf~~~~~~~~~~lvLPAF~~~~gG~ 184 (225)
T TIGR00024 153 AAGYKFPCFLLGEVEDKRVIVLPAFNPLCAGS 184 (225)
T ss_pred cceEEeeEEEEeccCCCCEEEECCCCCccCCc
Confidence 3567779998852 224455555778888876
No 40
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=29.84 E-value=67 Score=18.12 Aligned_cols=25 Identities=12% Similarity=-0.009 Sum_probs=17.8
Q ss_pred eEEECCEEeccCCeeEEcCCCCceEeec
Q psy4238 7 IGRVRKQVVNIPSFVVRLDSQKHIDFSL 34 (67)
Q Consensus 7 HIaV~gq~V~~PsylVr~deE~~Idf~~ 34 (67)
.++|||+.|+ ..+ .+.+.+.|.|.+
T Consensus 51 ~v~vNg~~v~-~~~--~l~~gD~v~i~p 75 (80)
T cd00754 51 RIAVNGEYVR-LDT--PLKDGDEVAIIP 75 (80)
T ss_pred EEEECCeEcC-CCc--ccCCCCEEEEeC
Confidence 5899999998 554 456667777654
No 41
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=29.46 E-value=70 Score=19.85 Aligned_cols=32 Identities=16% Similarity=0.122 Sum_probs=18.8
Q ss_pred eEEECCEEeccC-CeeEEcCCCCceEeecCCCCCC
Q psy4238 7 IGRVRKQVVNIP-SFVVRLDSQKHIDFSLNSPFGG 40 (67)
Q Consensus 7 HIaV~gq~V~~P-sylVr~deE~~Idf~~~SPl~~ 40 (67)
.|.|||+.+..- +.=-.+...+.|.|.| |+++
T Consensus 61 ~VlvN~~di~~l~g~~t~L~dgD~v~i~P--~v~G 93 (94)
T cd01764 61 IVLINDTDWELLGEEDYILEDGDHVVFIS--TLHG 93 (94)
T ss_pred EEEECCccccccCCcccCCCCcCEEEEEC--CCCC
Confidence 467788776543 2334456666777765 5544
No 42
>COG4525 TauB ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=27.00 E-value=44 Score=25.30 Aligned_cols=25 Identities=8% Similarity=0.113 Sum_probs=19.3
Q ss_pred eeeeEEECCEEeccCCeeEEcCCCCceEeec
Q psy4238 4 VWEIGRVRKQVVNIPSFVVRLDSQKHIDFSL 34 (67)
Q Consensus 4 vHGHIaV~gq~V~~PsylVr~deE~~Idf~~ 34 (67)
.+|.|.+||++++-|+ .|.-+=|-.
T Consensus 58 ~~G~i~l~~r~i~gPg------aergvVFQ~ 82 (259)
T COG4525 58 SRGSIQLNGRRIEGPG------AERGVVFQN 82 (259)
T ss_pred ccceEEECCEeccCCC------ccceeEecc
Confidence 5899999999999998 444455543
No 43
>PF05965 FYRC: F/Y rich C-terminus; InterPro: IPR003889 The "FY-rich" domain C-terminal region is sometimes closely juxtaposed with the N-terminal region (IPR003888 from INTERPRO), but sometimes is far distant. It is of unknown function, but occurs frequently in chromatin-associated proteins like trithorax and its homologues.; GO: 0005634 nucleus; PDB: 2WZO_A.
Probab=26.04 E-value=30 Score=20.67 Aligned_cols=23 Identities=26% Similarity=0.208 Sum_probs=17.6
Q ss_pred cCCeeEEcCCCCceEeecCCCCC
Q psy4238 17 IPSFVVRLDSQKHIDFSLNSPFG 39 (67)
Q Consensus 17 ~PsylVr~deE~~Idf~~~SPl~ 39 (67)
.|-|.|..++...+.|..+||-+
T Consensus 3 ~P~F~Vt~~d~p~~~~~g~s~~~ 25 (86)
T PF05965_consen 3 GPLFEVTSEDDPGEVFEGSSPTE 25 (86)
T ss_dssp SEEEEEEETT-GGG-EEESSHHH
T ss_pred CCEEEEEECCCCCCEEEeCCHHH
Confidence 58899998887788899888865
No 44
>COG3495 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.65 E-value=47 Score=23.66 Aligned_cols=21 Identities=14% Similarity=0.434 Sum_probs=17.3
Q ss_pred EECCEEeccCCeeEEcCCCCc
Q psy4238 9 RVRKQVVNIPSFVVRLDSQKH 29 (67)
Q Consensus 9 aV~gq~V~~PsylVr~deE~~ 29 (67)
+.||..+..|+|.|.++....
T Consensus 68 ~LdG~~~klpGy~vPle~d~k 88 (166)
T COG3495 68 ELDGSATKLPGYAVPLERDGK 88 (166)
T ss_pred hcccceeccCcceeecccCcc
Confidence 468999999999999986543
No 45
>PRK06437 hypothetical protein; Provisional
Probab=23.90 E-value=1.2e+02 Score=17.59 Aligned_cols=24 Identities=13% Similarity=0.018 Sum_probs=16.4
Q ss_pred eEEECCEEeccCCeeEEcCCCCceEee
Q psy4238 7 IGRVRKQVVNIPSFVVRLDSQKHIDFS 33 (67)
Q Consensus 7 HIaV~gq~V~~PsylVr~deE~~Idf~ 33 (67)
.|.|||+.|. +.+.+ .+.+.|++.
T Consensus 38 aV~vNg~iv~-~~~~L--~dgD~Veiv 61 (67)
T PRK06437 38 VVIVNGSPVL-EDHNV--KKEDDVLIL 61 (67)
T ss_pred EEEECCEECC-CceEc--CCCCEEEEE
Confidence 4668999987 66644 466777665
No 46
>KOG1057|consensus
Probab=23.49 E-value=91 Score=27.67 Aligned_cols=42 Identities=29% Similarity=0.351 Sum_probs=27.8
Q ss_pred eEEECCEEeccCCeeEEcCCCCc-eEeecCCCCCCCCcchhhhh
Q psy4238 7 IGRVRKQVVNIPSFVVRLDSQKH-IDFSLNSPFGGGGAGRVKRK 49 (67)
Q Consensus 7 HIaV~gq~V~~PsylVr~deE~~-Idf~~~SPl~~~~pgRvkrk 49 (67)
|+.|||.+.+.|.-==+++.|+| |-.|-.|.-+|+ -.|-=||
T Consensus 169 ~vEVnGevf~KPFVEKPVs~EDHNIYIYYPsSaGGG-sqrLFRK 211 (1018)
T KOG1057|consen 169 HVEVNGEVFQKPFVEKPVSAEDHNIYIYYPSSAGGG-SQRLFRK 211 (1018)
T ss_pred eEEEcceeccCCcccCCCCcccccEEEEecCCCCcc-HHHHHHH
Confidence 89999999999986667788887 444444443433 3344444
No 47
>PF11343 DUF3145: Protein of unknown function (DUF3145); InterPro: IPR021491 This family of proteins with unknown function appear to be restricted to Actinobacteria.
Probab=23.17 E-value=44 Score=23.62 Aligned_cols=16 Identities=31% Similarity=0.322 Sum_probs=14.0
Q ss_pred CceeeeeEEECCEEec
Q psy4238 1 LGIVWEIGRVRKQVVN 16 (67)
Q Consensus 1 ~~IvHGHIaV~gq~V~ 16 (67)
|||-|+.+..+|.+|=
T Consensus 90 LGi~~a~t~a~Gdvvv 105 (158)
T PF11343_consen 90 LGIFHAQTDANGDVVV 105 (158)
T ss_pred CcceeeeecCCCCEec
Confidence 7999999999998863
No 48
>PF14541 TAXi_C: Xylanase inhibitor C-terminal; PDB: 3AUP_D 3HD8_A 1T6G_A 1T6E_X 2B42_A 3VLB_A 3VLA_A.
Probab=23.09 E-value=1.2e+02 Score=19.62 Aligned_cols=32 Identities=16% Similarity=0.136 Sum_probs=17.6
Q ss_pred EEECCEEeccCCeeEE-cCCCCceEeecCCCCC
Q psy4238 8 GRVRKQVVNIPSFVVR-LDSQKHIDFSLNSPFG 39 (67)
Q Consensus 8 IaV~gq~V~~PsylVr-~deE~~Idf~~~SPl~ 39 (67)
|+|+|+++.+|...-. .+....+-++..++|+
T Consensus 9 Isvg~~~l~~~~~~~~~~~~~g~~iiDSGT~~T 41 (161)
T PF14541_consen 9 ISVGGKRLPIPPSVFQLSDGSGGTIIDSGTTYT 41 (161)
T ss_dssp EEETTEEE---TTCSCETTSTCSEEE-SSSSSE
T ss_pred EEECCEEecCChHHhhccCCCCCEEEECCCCcc
Confidence 8999999999985411 3344555566666654
No 49
>PF08288 PIGA: PIGA (GPI anchor biosynthesis); InterPro: IPR013234 This domain is found on phosphatidylinositol N-acetylglucosaminyltransferase proteins. These proteins are involved in GPI anchor biosynthesis and are associated with the disease paroxysmal nocturnal haemoglobinuria [].; GO: 0006506 GPI anchor biosynthetic process
Probab=21.82 E-value=44 Score=21.58 Aligned_cols=8 Identities=25% Similarity=0.090 Sum_probs=6.3
Q ss_pred ceeeeeEE
Q psy4238 2 GIVWEIGR 9 (67)
Q Consensus 2 ~IvHGHIa 9 (67)
-|||||-+
T Consensus 52 ~IVHgH~a 59 (90)
T PF08288_consen 52 DIVHGHQA 59 (90)
T ss_pred eEEEeehh
Confidence 48999965
No 50
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=21.64 E-value=80 Score=17.57 Aligned_cols=13 Identities=8% Similarity=0.128 Sum_probs=9.6
Q ss_pred eEEECCEEeccCC
Q psy4238 7 IGRVRKQVVNIPS 19 (67)
Q Consensus 7 HIaV~gq~V~~Ps 19 (67)
.|.|||+.++.|.
T Consensus 2 ~i~vNG~~~~~~~ 14 (66)
T PRK05659 2 NIQLNGEPRELPD 14 (66)
T ss_pred EEEECCeEEEcCC
Confidence 4788888877664
No 51
>PRK15287 putative minor fimbrial subunit StfF; Provisional
Probab=21.41 E-value=90 Score=20.75 Aligned_cols=28 Identities=11% Similarity=0.279 Sum_probs=21.2
Q ss_pred eeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238 6 EIGRVRKQVVNIPSFVVRLDSQKHIDFS 33 (67)
Q Consensus 6 GHIaV~gq~V~~PsylVr~deE~~Idf~ 33 (67)
+.|.+.|.+|..|...|.-++.-.|+|-
T Consensus 20 ~~i~f~G~Iv~~p~C~i~~~~~i~V~fG 47 (158)
T PRK15287 20 DNLKFHGTLISPPNCTINNDQTIDVKFG 47 (158)
T ss_pred ceEEEEEEEEcCCCCEEcCCccEEEEcc
Confidence 5789999999988888876554455554
No 52
>PF08844 DUF1815: Domain of unknown function (DUF1815); InterPro: IPR014943 This entry is about 100 amino acids in length and is functionally uncharacterised.
Probab=21.38 E-value=69 Score=21.30 Aligned_cols=23 Identities=30% Similarity=0.403 Sum_probs=19.6
Q ss_pred CCEEeccCCeeEEcCCCCceEee
Q psy4238 11 RKQVVNIPSFVVRLDSQKHIDFS 33 (67)
Q Consensus 11 ~gq~V~~PsylVr~deE~~Idf~ 33 (67)
+|.--+..||||.+.+.-.|-|-
T Consensus 40 dG~~~~~ASFmv~lg~~HliRFL 62 (105)
T PF08844_consen 40 DGRDMNSASFMVSLGDNHLIRFL 62 (105)
T ss_pred CCCCCCceeEEEEcCCCcEEEEE
Confidence 46667899999999999999885
No 53
>PRK09968 serine/threonine-specific protein phosphatase 2; Provisional
Probab=21.07 E-value=88 Score=21.63 Aligned_cols=31 Identities=13% Similarity=0.121 Sum_probs=20.2
Q ss_pred ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCC
Q psy4238 2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG 42 (67)
Q Consensus 2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~ 42 (67)
.|||||.-+.. +...+ ..|-+.+.|.+++..
T Consensus 182 ~vv~GHTh~~~--------~~~~~--~~i~IDtGs~~gG~L 212 (218)
T PRK09968 182 YFIFGHMMFDN--------IQTFA--NQIYIDTGSPKSGRL 212 (218)
T ss_pred EEEECCCCcCc--------ceeEC--CEEEEECCCCCCCce
Confidence 37999976643 22222 378888999887643
No 54
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=20.36 E-value=79 Score=24.63 Aligned_cols=24 Identities=29% Similarity=0.434 Sum_probs=20.5
Q ss_pred eEeecCCCCCCCC-cchhhhhhhhh
Q psy4238 30 IDFSLNSPFGGGG-AGRVKRKNLRK 53 (67)
Q Consensus 30 Idf~~~SPl~~~~-pgRvkrk~~k~ 53 (67)
|..+|+|||.++. -|-+-|++...
T Consensus 85 lAVDPSSp~TGGsiLGDRiRM~~~~ 109 (323)
T COG1703 85 LAVDPSSPFTGGSILGDRIRMQRLA 109 (323)
T ss_pred EEECCCCCCCCccccccHhhHHhhc
Confidence 6788999999998 99888887665
No 55
>PF11160 DUF2945: Protein of unknown function (DUF2945); InterPro: IPR021331 This family of proteins has no known function.
Probab=20.06 E-value=2.1e+02 Score=16.95 Aligned_cols=32 Identities=16% Similarity=0.230 Sum_probs=22.2
Q ss_pred eEEECCEEecc----CCeeEEcCCCCceEeecCCCC
Q psy4238 7 IGRVRKQVVNI----PSFVVRLDSQKHIDFSLNSPF 38 (67)
Q Consensus 7 HIaV~gq~V~~----PsylVr~deE~~Idf~~~SPl 38 (67)
.+.|.|+.|+. |-|+|+-|.-..+.....|-|
T Consensus 24 ~~~~~G~~v~AS~ddP~Y~I~sd~tgk~a~hk~~al 59 (62)
T PF11160_consen 24 PTEIKGRTVNASKDDPRYEIESDKTGKRAAHKPSAL 59 (62)
T ss_pred ceeECCEEecCCCCCCEEEEEEcCCCCeEEEchhHh
Confidence 34578887764 889999888777766544433
No 56
>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.
Probab=20.03 E-value=56 Score=24.64 Aligned_cols=24 Identities=29% Similarity=0.434 Sum_probs=14.2
Q ss_pred eEeecCCCCCCCC-cchhhhhhhhh
Q psy4238 30 IDFSLNSPFGGGG-AGRVKRKNLRK 53 (67)
Q Consensus 30 Idf~~~SPl~~~~-pgRvkrk~~k~ 53 (67)
+..+|+|||.++. -|-+-|++.-.
T Consensus 63 lAVDPSSp~tGGAlLGDRiRM~~~~ 87 (266)
T PF03308_consen 63 LAVDPSSPFTGGALLGDRIRMQELS 87 (266)
T ss_dssp EEE-GGGGCC---SS--GGGCHHHH
T ss_pred EEECCCCCCCCCcccccHHHhcCcC
Confidence 6678999999998 88888876543
No 57
>PRK01777 hypothetical protein; Validated
Probab=20.02 E-value=2.4e+02 Score=17.71 Aligned_cols=43 Identities=9% Similarity=0.081 Sum_probs=27.9
Q ss_pred eeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCCcchhhhhhhh
Q psy4238 4 VWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLR 52 (67)
Q Consensus 4 vHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~pgRvkrk~~k 52 (67)
.++.+-|+|+.|+ +.. .+.+-+.|++|+ ||.-. |-..+|++..
T Consensus 48 ~~~~vgI~Gk~v~-~d~--~L~dGDRVeIyr--PL~~D-Pk~~Rr~ra~ 90 (95)
T PRK01777 48 AKNKVGIYSRPAK-LTD--VLRDGDRVEIYR--PLLAD-PKELRRKRAE 90 (95)
T ss_pred ccceEEEeCeECC-CCC--cCCCCCEEEEec--CCCCC-HHHHHHHHHH
Confidence 3578899999998 554 466788999986 44422 5444444443
Done!