Query psy2644
Match_columns 119
No_of_seqs 104 out of 264
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 21:29:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2644.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2644hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02149 KA1: Kinase associate 99.9 3.6E-22 7.8E-27 119.4 6.5 46 74-119 2-47 (47)
2 KOG0586|consensus 97.7 8.2E-06 1.8E-10 70.1 0.0 60 42-112 536-595 (596)
3 PF03822 NAF: NAF domain; Int 71.3 6.2 0.00014 24.7 3.1 27 31-57 36-62 (63)
4 PF00120 Gln-synt_C: Glutamine 66.3 13 0.00028 28.6 4.6 66 35-119 64-129 (259)
5 PF12949 HeH: HeH/LEM domain; 63.4 3.4 7.3E-05 23.0 0.6 17 42-58 6-22 (35)
6 PRK13009 succinyl-diaminopimel 61.4 30 0.00065 27.4 6.0 49 9-57 235-283 (375)
7 PF05046 Img2: Mitochondrial l 56.7 12 0.00026 24.6 2.5 25 91-115 26-50 (87)
8 PF01193 RNA_pol_L: RNA polyme 51.5 50 0.0011 20.0 4.6 32 20-51 32-63 (66)
9 TIGR01246 dapE_proteo succinyl 48.7 63 0.0014 25.6 6.0 49 9-57 232-280 (370)
10 KOG1283|consensus 46.3 13 0.00027 31.0 1.6 73 30-105 93-166 (414)
11 PF00924 MS_channel: Mechanose 44.3 58 0.0012 23.5 4.8 64 18-85 112-176 (206)
12 cd00460 RNAP_RPB11_RPB3 RPB11 43.6 43 0.00094 21.6 3.6 28 24-51 54-81 (86)
13 PF06135 DUF965: Bacterial pro 43.1 28 0.0006 22.8 2.5 38 28-66 7-46 (79)
14 PF03698 UPF0180: Uncharacteri 43.0 59 0.0013 21.2 4.1 17 33-49 63-79 (80)
15 PF07137 VDE: Violaxanthin de- 42.8 17 0.00038 27.7 1.8 29 30-58 152-180 (198)
16 cd03030 GRX_SH3BGR Glutaredoxi 42.8 37 0.0008 22.4 3.2 30 31-60 8-37 (92)
17 PF04908 SH3BGR: SH3-binding, 41.6 30 0.00064 23.4 2.6 30 30-59 8-37 (99)
18 PF04502 DUF572: Family of unk 41.1 28 0.00062 28.0 2.9 41 59-99 36-76 (324)
19 PLN03036 glutamine synthetase; 39.8 37 0.00079 28.8 3.4 63 38-119 228-290 (432)
20 PF09553 RE_Eco47II: Eco47II r 39.0 20 0.00044 27.7 1.6 20 94-113 176-204 (214)
21 PLN02284 glutamine synthetase 38.6 56 0.0012 26.7 4.3 64 37-119 167-230 (354)
22 PF00101 RuBisCO_small: Ribulo 38.3 51 0.0011 22.3 3.4 30 27-56 47-76 (99)
23 smart00596 PRE_C2HC PRE_C2HC d 37.6 1.1E+02 0.0024 19.5 5.3 54 43-102 2-55 (69)
24 COG4972 PilM Tfp pilus assembl 37.1 33 0.00072 28.4 2.7 23 36-58 55-77 (354)
25 PRK08652 acetylornithine deace 36.9 81 0.0018 24.5 4.8 48 10-58 209-256 (347)
26 PRK14543 nucleoside diphosphat 36.8 42 0.00092 24.8 3.0 43 12-54 98-155 (169)
27 TIGR03105 gln_synth_III glutam 36.2 44 0.00096 28.1 3.4 67 34-119 152-218 (435)
28 PF11979 DUF3480: Domain of un 36.1 1.9E+02 0.0041 24.1 6.9 51 8-70 158-211 (356)
29 PRK05473 hypothetical protein; 35.8 36 0.00077 22.7 2.2 37 28-65 10-48 (86)
30 COG0174 GlnA Glutamine synthet 35.4 39 0.00083 28.7 2.9 80 19-119 147-226 (443)
31 PRK05417 glutathione-dependent 35.0 1.1E+02 0.0023 23.1 5.0 53 3-55 113-165 (191)
32 cd05860 Ig4_SCFR Fourth immuno 34.7 31 0.00068 23.4 1.9 26 56-83 74-99 (101)
33 PF10847 DUF2656: Protein of u 33.1 63 0.0014 23.1 3.3 31 27-57 44-74 (132)
34 PF07687 M20_dimer: Peptidase 32.8 25 0.00054 22.6 1.1 43 9-52 65-107 (111)
35 PRK03094 hypothetical protein; 32.3 94 0.002 20.3 3.8 42 7-49 38-79 (80)
36 PF01514 YscJ_FliF: Secretory 31.2 42 0.00091 25.3 2.3 25 34-59 33-57 (206)
37 cd03527 RuBisCO_small Ribulose 30.6 72 0.0016 21.6 3.1 33 21-53 39-74 (99)
38 PHA00458 single-stranded DNA-b 30.4 2.7E+02 0.0058 21.8 7.6 28 25-52 36-66 (233)
39 PTZ00039 40S ribosomal protein 30.2 1.9E+02 0.0041 20.0 5.8 62 24-85 17-85 (115)
40 TIGR00106 uncharacterized prot 30.0 85 0.0018 20.9 3.4 28 34-62 13-40 (97)
41 PRK15348 type III secretion sy 27.8 1.1E+02 0.0024 24.0 4.2 33 33-66 24-59 (249)
42 PRK00933 ribosomal biogenesis 27.4 60 0.0013 23.9 2.5 32 32-63 4-35 (165)
43 cd06218 DHOD_e_trans FAD/NAD b 26.9 1.2E+02 0.0025 22.9 4.1 20 38-57 188-207 (246)
44 cd07032 RNAP_I_II_AC40 AC40 su 26.7 80 0.0017 25.3 3.3 27 25-51 257-283 (291)
45 COG4472 Uncharacterized protei 26.4 53 0.0012 21.7 1.8 38 28-66 10-49 (88)
46 COG4309 Uncharacterized conser 26.3 79 0.0017 21.5 2.7 38 29-66 36-74 (98)
47 TIGR02554 PrgH type III secret 26.1 2.7E+02 0.0059 23.4 6.3 82 22-106 278-385 (389)
48 TIGR02017 hutG_amidohyd N-form 25.8 2.2E+02 0.0047 22.2 5.5 58 26-85 162-225 (263)
49 cd07031 RNAP_II_RPB3 RPB3 subu 25.3 94 0.002 24.4 3.4 27 25-51 227-253 (265)
50 PF07927 YcfA: YcfA-like prote 25.2 81 0.0017 18.1 2.4 16 43-58 2-17 (56)
51 PRK06222 ferredoxin-NADP(+) re 25.0 1.2E+02 0.0027 23.4 4.0 22 37-58 188-209 (281)
52 PF13989 YejG: YejG-like prote 24.5 1.9E+02 0.0041 19.9 4.3 36 35-70 48-86 (106)
53 PRK15327 type III secretion sy 24.3 3.1E+02 0.0067 23.1 6.4 80 24-106 285-390 (393)
54 PF05413 Peptidase_C34: Putati 24.0 38 0.00082 22.5 0.8 31 21-51 2-37 (92)
55 PF09480 PrgH: Type III secret 23.9 3E+02 0.0064 22.9 6.2 54 29-84 275-349 (375)
56 PF08621 RPAP1_N: RPAP1-like, 23.9 48 0.0011 19.6 1.2 24 31-54 10-33 (49)
57 COG4277 Predicted DNA-binding 23.8 1E+02 0.0022 25.6 3.3 62 23-85 101-170 (404)
58 PRK06446 hypothetical protein; 23.7 2.6E+02 0.0057 22.8 5.9 37 17-53 296-332 (436)
59 PF08915 tRNA-Thr_ED: Archaea- 23.4 1.8E+02 0.0039 21.0 4.2 30 38-67 93-127 (138)
60 PRK07079 hypothetical protein; 23.1 2.4E+02 0.0052 23.3 5.6 44 10-53 309-354 (469)
61 PF05013 FGase: N-formylglutam 23.0 97 0.0021 23.2 3.0 60 24-85 152-217 (222)
62 cd06407 PB1_NLP A PB1 domain i 22.5 1.3E+02 0.0027 19.4 3.1 27 93-119 8-35 (82)
63 cd03063 TRX_Fd_FDH_beta TRX-li 22.1 1.5E+02 0.0032 19.6 3.4 33 35-68 13-47 (92)
64 PF12046 DUF3529: Protein of u 22.1 1.7E+02 0.0036 21.9 4.0 35 19-57 27-61 (173)
65 PLN02320 seryl-tRNA synthetase 22.0 2.2E+02 0.0048 24.7 5.2 46 38-89 361-406 (502)
66 TIGR03526 selenium_YgeY putati 22.0 3E+02 0.0065 22.0 5.8 37 17-53 245-281 (395)
67 TIGR03320 ygeY M20/DapE family 21.9 2.8E+02 0.0061 22.1 5.7 37 17-53 245-281 (395)
68 PF01890 CbiG_C: Cobalamin syn 21.7 1.1E+02 0.0024 21.0 2.8 30 29-58 5-34 (121)
69 cd00307 RuBisCO_small_like Rib 21.7 1.5E+02 0.0033 19.4 3.3 32 22-53 26-59 (84)
70 PLN02372 violaxanthin de-epoxi 21.7 81 0.0017 26.9 2.5 28 30-57 320-347 (455)
71 COG0011 Uncharacterized conser 21.7 1.5E+02 0.0032 20.2 3.4 27 35-62 16-42 (100)
72 PF11305 DUF3107: Protein of u 21.3 1.3E+02 0.0028 19.4 2.8 23 30-52 14-36 (74)
73 PF01910 DUF77: Domain of unkn 20.8 1.1E+02 0.0024 20.1 2.6 27 35-62 12-38 (92)
74 PRK08596 acetylornithine deace 20.8 2.9E+02 0.0063 22.4 5.6 43 9-52 259-301 (421)
75 PRK07205 hypothetical protein; 20.8 2.1E+02 0.0045 23.5 4.7 38 20-57 315-352 (444)
76 TIGR02544 III_secr_YscJ type I 20.4 1.4E+02 0.003 22.3 3.4 32 34-66 24-59 (193)
77 PF00731 AIRC: AIR carboxylase 20.0 1.5E+02 0.0032 21.5 3.3 24 35-58 9-32 (150)
No 1
>PF02149 KA1: Kinase associated domain 1; InterPro: IPR001772 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Eukaryotic protein kinases [, , , , ] are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. There are a number of conserved regions in the catalytic domain of protein kinases. In the N-terminal extremity of the catalytic domain there is a glycine-rich stretch of residues in the vicinity of a lysine residue, which has been shown to be involved in ATP binding. In the central part of the catalytic domain there is a conserved aspartic acid residue which is important for the catalytic activity of the enzyme []. Members of the KIN2/PAR-1/MARK kinase subfamily are conserved from yeast to human and share the same domain organisation: an N-terminal kinase domain (IPR000719 from INTERPRO) and a C-terminal kinase associated domain 1 (KA1). Some members of the KIN1/PAR-1/MARK family also contain an UBA domain (IPR000449 from INTERPRO). Members of this kinase subfamily are involved in various biological processes such as cell polarity, cell cycle control, intracellular signalling, microtubule stability and protein stability []. The function of the KA1 domain is not yet known. Some proteins known to contain a KA1 domain are listed below: Mammalian MAP/microtubule affinity-regulating kinases (MARK 1,2,3). They regulate polarity in neuronal cell models and appear to function redundantly in phosphorylating MT-associated proteins and in regulating MT stability []. Mammalian maternal embryonic leucine zipper kinase (MELK). It phosphorylates ZNF622 and may contribute to its redirection to the nucleus. It may be involved in the inhibition of spliceosome assembly during mitosis. Caenorhabditis elegans and drosophila PAR-1 protein. It is required for establishing polarity in embryos where it is asymmetrically distributed []. Fungal Kin1 and Kin2 protein kinases involved in regulation of exocytosis. They localise to the cytoplasmic face of the plasma membrane []. Plant KIN10 and KIN11 proteins, catalytic subunits of the putative trimeric SNF1-related protein kinase (SnRK) complex. This entry represents the KA1 domain.; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 3OSE_A 1V5S_A 1UL7_A.
Probab=99.87 E-value=3.6e-22 Score=119.40 Aligned_cols=46 Identities=63% Similarity=1.017 Sum_probs=41.4
Q ss_pred CcceEEEEEEEeecCCCcceeeEEEecCCchhHHHHHHHHHHhcCC
Q psy2644 74 DSLVQWEIEVCKLPRLSLNGVRFKRISGTSIGFKNIASKIANELKL 119 (119)
Q Consensus 74 ~~~v~fEiEVcrl~~l~l~gi~fkRl~Gd~~~Yk~lc~~il~~l~L 119 (119)
+..|+||||||++|++++|||+|||++||+|+||++|++|+++|+|
T Consensus 2 ~~~v~fEieV~kl~~~~l~Gv~~kRi~Gd~~~yk~lc~~il~~l~L 47 (47)
T PF02149_consen 2 KEVVKFEIEVCKLPRLGLYGVDFKRISGDSWQYKDLCSKILNELRL 47 (47)
T ss_dssp CC-EEEEEEEEEECCCTCEEEEEEEEES-HHHHHHHHHHHHHHTT-
T ss_pred CcceEEEEEEEEecCCCeeEEEEEEeeCCHHHHHHHHHHHHHHccC
Confidence 3579999999999999999999999999999999999999999987
No 2
>KOG0586|consensus
Probab=97.70 E-value=8.2e-06 Score=70.14 Aligned_cols=60 Identities=82% Similarity=1.327 Sum_probs=52.7
Q ss_pred HHHHHHHHhhCCCceEEeCcEEEEeeeCCCCCCcceEEEEEEEeecCCCcceeeEEEecCCchhHHHHHHH
Q psy2644 42 MAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKRISGTSIGFKNIASK 112 (119)
Q Consensus 42 m~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~~~~~v~fEiEVcrl~~l~l~gi~fkRl~Gd~~~Yk~lc~~ 112 (119)
|.|++.+++.+++++++.+ .+.|+.....++|++++|++|.++.+|+||+|++ ++.++++
T Consensus 536 ~~~~~~v~~~~~~~~~~~~------~~~~~~a~a~~~~~~~~~~~~~~s~~g~r~~r~s-----~~~~~s~ 595 (596)
T KOG0586|consen 536 MREIRKVLDANGCDYEQLR------YHGDPGADAMVQWEMEVCKLPRLSLNGVRFRRIS-----FKNIASK 595 (596)
T ss_pred hhhhhhccccccccccccc------cCCCCCcccccccccceeecCcccccceeecccc-----CCCccCC
Confidence 9999999999999999776 4667667788999999999999999999999998 7776654
No 3
>PF03822 NAF: NAF domain; InterPro: IPR004041 The NAF domain is a 24 amino acid domain that is found in a plant-specific subgroup of serine-threonine protein kinases (CIPKs), that interact with calcineurin B-like calcium sensor proteins (CBLs). Whereas the N-terminal part of CIPKs comprises a conserved catalytic domain typical of Ser-Thr kinases, the much less conserved C-terminal domain appears to be unique to this subgroup of kinases. The only exception is the NAF domain that forms an 'island of conservation' in this otherwise variable region. The NAF domain has been named after the prominent conserved amino acids Asn-Ala-Phe. It represents a minimum protein interaction module that is both necessary and sufficient to mediate the interaction with the CBL calcium sensor proteins []. The secondary structure of the NAF domain is currently not known, but secondary structure computation of the C-terminal region of Arabidopsis thaliana CBL-interacting protein kinase 1 revealed a long helical structure [].; GO: 0007165 signal transduction; PDB: 2ZFD_B 2EHB_D.
Probab=71.30 E-value=6.2 Score=24.68 Aligned_cols=27 Identities=15% Similarity=0.252 Sum_probs=22.4
Q ss_pred eeecCCCHHHHHHHHHHHHhhCCCceE
Q psy2644 31 KTTSSRDPNEIMAEIRKVLDANNCDYE 57 (119)
Q Consensus 31 ~ttSsk~P~eIm~ei~rvL~~~~i~~~ 57 (119)
.-||..+|++|+..|..+....|...+
T Consensus 36 RF~S~~~~~~Ii~klEe~a~~~~~~V~ 62 (63)
T PF03822_consen 36 RFTSKEPASEIIEKLEEIAKKLGFRVK 62 (63)
T ss_dssp EEEESS-HHHHHHHHHHHHHHTTEEEE
T ss_pred eEecCCCHHHHHHHHHHHHHhcCceee
Confidence 446899999999999999999887765
No 4
>PF00120 Gln-synt_C: Glutamine synthetase, catalytic domain; InterPro: IPR008146 Glutamine synthetase (6.3.1.2 from EC) (GS) [] plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. There seem to be three different classes of GS [, , ]: Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see IPR001637 from INTERPRO). Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast. Class III enzymes (GSIII) have been found in Bacteroides fragilis. in Butyrivibrio fibrisolvens. It is a hexamer of identical chains and in some protozoa. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes. While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.; GO: 0004356 glutamate-ammonia ligase activity, 0006807 nitrogen compound metabolic process; PDB: 2J9I_E 3ZXV_D 1HTQ_D 1HTO_F 2BVC_F 2WGS_G 3ZXR_B 2WHI_D 3NG0_A 1LGR_C ....
Probab=66.32 E-value=13 Score=28.64 Aligned_cols=66 Identities=23% Similarity=0.261 Sum_probs=46.1
Q ss_pred CCCHHHHHHHHHHHHhhCCCceEEeCcEEEEeeeCCCCCCcceEEEEEEEeecCCCcceeeEEEecCCchhHHHHHHHHH
Q psy2644 35 SRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKRISGTSIGFKNIASKIA 114 (119)
Q Consensus 35 sk~P~eIm~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~~~~~v~fEiEVcrl~~l~l~gi~fkRl~Gd~~~Yk~lc~~il 114 (119)
.....+++.+|.+.|.++||+.+... ++. ..-|||+.+--.+.+ ...-+.|.||.++++|.
T Consensus 64 ~~~~~~~~~~i~~~l~~~Gi~ve~~h-------~E~----gpgQ~Ei~~~~~~~l--------~aaD~~~~~k~~ik~vA 124 (259)
T PF00120_consen 64 LDAGEDFLEEIVDALEQAGIPVEQIH-------HEV----GPGQYEINLGPCDPL--------EAADNLVLFKEIIKEVA 124 (259)
T ss_dssp TSTTHHHHHHHHHHHHHCT--EEEEE-------EES----STTEEEEEEEEEECH--------HHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHhhccccccc-------ccc----chHhhccccccCcHH--------HHHHHHHHHHHHHHHHH
Confidence 45789999999999999999886422 111 124899887765543 24556789999999998
Q ss_pred HhcCC
Q psy2644 115 NELKL 119 (119)
Q Consensus 115 ~~l~L 119 (119)
.+.+|
T Consensus 125 ~~~Gl 129 (259)
T PF00120_consen 125 RKHGL 129 (259)
T ss_dssp HHTTE
T ss_pred HHcCC
Confidence 77653
No 5
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=63.43 E-value=3.4 Score=22.97 Aligned_cols=17 Identities=18% Similarity=0.661 Sum_probs=11.9
Q ss_pred HHHHHHHHhhCCCceEE
Q psy2644 42 MAEIRKVLDANNCDYEQ 58 (119)
Q Consensus 42 m~ei~rvL~~~~i~~~~ 58 (119)
+.||+++|.++||+|..
T Consensus 6 V~~Lk~iL~~~~I~~ps 22 (35)
T PF12949_consen 6 VAQLKRILDEHGIEFPS 22 (35)
T ss_dssp SHHHHHHHHHHT---SS
T ss_pred HHHHHHHHHHcCCCCCC
Confidence 57899999999999953
No 6
>PRK13009 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=61.43 E-value=30 Score=27.35 Aligned_cols=49 Identities=16% Similarity=0.379 Sum_probs=38.3
Q ss_pred eeeCCCCCCCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCCCceE
Q psy2644 9 VVSNAVNDDQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYE 57 (119)
Q Consensus 9 ~~~~~~~~~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~ 57 (119)
.|+|.......-|-.....+++......++++++++|++.+++.++.++
T Consensus 235 ~i~~G~~~~nvip~~~~~~~diR~~~~~~~e~i~~~i~~~~~~~~~~~~ 283 (375)
T PRK13009 235 NIDAGTGATNVIPGELEAQFNFRFSTEHTAESLKARVEAILDKHGLDYT 283 (375)
T ss_pred EEecCCCCCcccCCcEEEEEEEecCCCCCHHHHHHHHHHHHHhcCCCeE
Confidence 3454432234578889999999999999999999999999998766554
No 7
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 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 family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=56.65 E-value=12 Score=24.56 Aligned_cols=25 Identities=16% Similarity=0.141 Sum_probs=18.9
Q ss_pred cceeeEEEecCCchhHHHHHHHHHH
Q psy2644 91 LNGVRFKRISGTSIGFKNIASKIAN 115 (119)
Q Consensus 91 l~gi~fkRl~Gd~~~Yk~lc~~il~ 115 (119)
..---+|++.||.|++++=-.+.|.
T Consensus 26 ~~~T~IrkI~GD~~aL~~dL~~~l~ 50 (87)
T PF05046_consen 26 RKITVIRKIEGDIWALKKDLRKFLG 50 (87)
T ss_pred EeEEEEEeecCCHHHHHHHHHHHhh
Confidence 4445699999999999876666654
No 8
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=51.53 E-value=50 Score=20.04 Aligned_cols=32 Identities=25% Similarity=0.480 Sum_probs=26.3
Q ss_pred CCeEeceeeeeeeecCCCHHHHHHHHHHHHhh
Q psy2644 20 KPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDA 51 (119)
Q Consensus 20 kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~ 51 (119)
.|..-+..|.+.|..+.+|.+++.+=.+.|.+
T Consensus 32 ~~~~~~~~~~IeT~g~~~p~~~l~~A~~~l~~ 63 (66)
T PF01193_consen 32 HPNEDKFVFRIETDGSLTPKEALLKAIKILKE 63 (66)
T ss_dssp SSEEEEEEEEEEEBSSS-HHHHHHHHHHHHHH
T ss_pred cCCCCEEEEEEEECCCCCHHHHHHHHHHHHHH
Confidence 55667889999999999999999988888764
No 9
>TIGR01246 dapE_proteo succinyl-diaminopimelate desuccinylase, proteobacterial clade. This model describes a proteobacterial subset of succinyl-diaminopimelate desuccinylases. An experimentally confirmed Gram-positive lineage succinyl-diaminopimelate desuccinylase has been described for Corynebacterium glutamicum, and a neighbor-joining tree shows the seed members, SP:Q59284, and putative archaeal members such as TrEMBL:O58003 in a single clade. However, the archaeal members differ substantially, share a number of motifs with acetylornithine deacetylases rather than succinyl-diaminopimelate desuccinylases, and are not taken as trusted examples of succinyl-diaminopimelate desuccinylases. This model is limited to proteobacterial members for this reason.
Probab=48.70 E-value=63 Score=25.55 Aligned_cols=49 Identities=14% Similarity=0.361 Sum_probs=37.7
Q ss_pred eeeCCCCCCCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCCCceE
Q psy2644 9 VVSNAVNDDQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYE 57 (119)
Q Consensus 9 ~~~~~~~~~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~ 57 (119)
.|+|.......-|-.....+++.+....++++|..+|++.++..++.++
T Consensus 232 ~i~~g~~~~nvvP~~~~~~~diR~~~~~~~~~v~~~i~~~~~~~~~~~~ 280 (370)
T TIGR01246 232 NIHAGTGANNVIPGELYVQFNLRFSTEVSDEILKQRVEAILDQHGLDYD 280 (370)
T ss_pred eeecCCCCCcccCCceEEEEEEecCCCCCHHHHHHHHHHHHHHcCCCEE
Confidence 3444322234568888999999999999999999999999998766554
No 10
>KOG1283|consensus
Probab=46.35 E-value=13 Score=31.03 Aligned_cols=73 Identities=14% Similarity=0.157 Sum_probs=47.0
Q ss_pred eeeecCCCHHHHHHHHHHHHhhCCCceEEeCcEEEEeeeCCCCCCcceEEEEEEEeecCCCcceeeEEEec-CCchh
Q psy2644 30 MKTTSSRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKRIS-GTSIG 105 (119)
Q Consensus 30 v~ttSsk~P~eIm~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~~~~~v~fEiEVcrl~~l~l~gi~fkRl~-Gd~~~ 105 (119)
.-||+.+....=|-++.+-+-.++-+|+ +-||.+.|.+.. ++-..+|-+|+.....-+..-..|.++. ||+|.
T Consensus 93 ~Y~~~~~qia~Dl~~llk~f~~~h~e~~-t~P~~If~ESYG--GKma~k~al~l~~aIk~G~i~~nf~~VaLGDSWI 166 (414)
T KOG1283|consen 93 AYTTNNKQIALDLVELLKGFFTNHPEFK-TVPLYIFCESYG--GKMAAKFALELDDAIKRGEIKLNFIGVALGDSWI 166 (414)
T ss_pred cccccHHHHHHHHHHHHHHHHhcCcccc-ccceEEEEhhcc--cchhhhhhhhHHHHHhcCceeecceeEEccCccc
Confidence 3455555555556677777888999997 458999998754 3445677777665544333334455554 99984
No 11
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=44.30 E-value=58 Score=23.51 Aligned_cols=64 Identities=17% Similarity=0.231 Sum_probs=37.1
Q ss_pred CCCCeEeceeeeeeeecC-CCHHHHHHHHHHHHhhCCCceEEeCcEEEEeeeCCCCCCcceEEEEEEEe
Q psy2644 18 QVKPRSLRFTWSMKTTSS-RDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCK 85 (119)
Q Consensus 18 ~~kpR~lk~~~~v~ttSs-k~P~eIm~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~~~~~v~fEiEVcr 85 (119)
.++.+.+...+.+...+. ..++++.+++.+.+++..-......++.......+ ..+.+.+.+.-
T Consensus 112 ~~~~~~~~v~~~v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~i~~~~ 176 (206)
T PF00924_consen 112 SSPYRRVVVEIPVDYDTDPEKIEELREKIEEALRSNPYIFKEPEPRVVVDEIGD----SSLEFRIRVYV 176 (206)
T ss_dssp -SSEEEEEEEEEE-TTS----HHHHHHHHHHHHHH-TTC-TTS-EEEEEEEE-S----SSEEEEEEEEE
T ss_pred cCCceeeeeeeeEecCCCchHHHHHHHHHHHHHhcCchhhcCCCCeEEEccccC----CceEEEEEEEE
Confidence 455677777777766655 67999999999999887655443344554554433 45677665443
No 12
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=43.60 E-value=43 Score=21.58 Aligned_cols=28 Identities=21% Similarity=0.342 Sum_probs=24.0
Q ss_pred eceeeeeeeecCCCHHHHHHHHHHHHhh
Q psy2644 24 LRFTWSMKTTSSRDPNEIMAEIRKVLDA 51 (119)
Q Consensus 24 lk~~~~v~ttSsk~P~eIm~ei~rvL~~ 51 (119)
-++.|.+.|+.+.+|.+++.+-.+.|.+
T Consensus 54 d~~~~~VeT~Gs~~P~~al~~Ai~~L~~ 81 (86)
T cd00460 54 DKFILRIETVGSIPPEEALRRAVEILRK 81 (86)
T ss_pred CeEEEEEEECCCCCHHHHHHHHHHHHHH
Confidence 4788999999999999999888887765
No 13
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=43.12 E-value=28 Score=22.84 Aligned_cols=38 Identities=16% Similarity=0.343 Sum_probs=27.4
Q ss_pred eeeeeecCCCHHHHHHHHHHHHhhCCCce-EE-eCcEEEEe
Q psy2644 28 WSMKTTSSRDPNEIMAEIRKVLDANNCDY-EQ-RERFLLLC 66 (119)
Q Consensus 28 ~~v~ttSsk~P~eIm~ei~rvL~~~~i~~-~~-~g~y~l~C 66 (119)
|+..-.-..+..+++.++.++|.+.|-.= .| .| |.|..
T Consensus 7 F~~~~~~~~~~~~iL~~Vy~AL~EKGYnPinQivG-YllSG 46 (79)
T PF06135_consen 7 FKFEKEKEKEIREILKQVYAALEEKGYNPINQIVG-YLLSG 46 (79)
T ss_pred eeCCCcchhhHHHHHHHHHHHHHHcCCChHHHHHh-heecC
Confidence 44544556789999999999999998753 33 45 76653
No 14
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=43.02 E-value=59 Score=21.21 Aligned_cols=17 Identities=29% Similarity=0.423 Sum_probs=14.7
Q ss_pred ecCCCHHHHHHHHHHHH
Q psy2644 33 TSSRDPNEIMAEIRKVL 49 (119)
Q Consensus 33 tSsk~P~eIm~ei~rvL 49 (119)
-+.++|+||.++|.+-|
T Consensus 63 A~G~T~eEI~~~v~~rl 79 (80)
T PF03698_consen 63 ASGLTAEEIVQEVEERL 79 (80)
T ss_pred cCCCCHHHHHHHHHHhh
Confidence 36899999999999866
No 15
>PF07137 VDE: Violaxanthin de-epoxidase (VDE); InterPro: IPR010788 This family represents a conserved region approximately 350 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage [].; GO: 0046422 violaxanthin de-epoxidase activity, 0055114 oxidation-reduction process, 0009507 chloroplast; PDB: 3CQN_B 3CQR_A.
Probab=42.82 E-value=17 Score=27.68 Aligned_cols=29 Identities=24% Similarity=0.439 Sum_probs=21.0
Q ss_pred eeeecCCCHHHHHHHHHHHHhhCCCceEE
Q psy2644 30 MKTTSSRDPNEIMAEIRKVLDANNCDYEQ 58 (119)
Q Consensus 30 v~ttSsk~P~eIm~ei~rvL~~~~i~~~~ 58 (119)
|-|+|+.=|++++-||.+++++.|++|.+
T Consensus 152 VYtrs~~lP~s~~p~l~~aa~k~G~d~~~ 180 (198)
T PF07137_consen 152 VYTRSPTLPESIVPELRRAAKKAGIDFSK 180 (198)
T ss_dssp EEESSSS--GGGHHHHHHHHHHTT--GGG
T ss_pred EEeCCCCCChHHhHHHHHHHHHhCCCHHH
Confidence 44566667999999999999999999863
No 16
>cd03030 GRX_SH3BGR Glutaredoxin (GRX) family, SH3BGR (SH3 domain binding glutamic acid-rich protein) subfamily; a recently-identified subfamily composed of SH3BGR and similar proteins possessing significant sequence similarity to GRX, but without a redox active CXXC motif. The SH3BGR gene was cloned in an effort to identify genes mapping to chromosome 21, which could be involved in the pathogenesis of congenital heart disease affecting Down syndrome newborns. Several human SH3BGR-like (SH3BGRL) genes have been identified since, mapping to different locations in the chromosome. Of these, SH3BGRL3 was identified as a tumor necrosis factor (TNF) alpha inhibitory protein and was also named TIP-B1. Upregulation of expression of SH3BGRL3 is associated with differentiation. It has been suggested that it functions as a regulator of differentiation-related signal transduction pathways.
Probab=42.80 E-value=37 Score=22.37 Aligned_cols=30 Identities=17% Similarity=0.345 Sum_probs=21.1
Q ss_pred eeecCCCHHHHHHHHHHHHhhCCCceEEeC
Q psy2644 31 KTTSSRDPNEIMAEIRKVLDANNCDYEQRE 60 (119)
Q Consensus 31 ~ttSsk~P~eIm~ei~rvL~~~~i~~~~~g 60 (119)
++++++.-.+=-+++++.|++++|+|++..
T Consensus 8 s~~g~~~~k~~~~~v~~lL~~k~I~f~eiD 37 (92)
T cd03030 8 SSSGSTEIKKRQQEVLGFLEAKKIEFEEVD 37 (92)
T ss_pred cccccHHHHHHHHHHHHHHHHCCCceEEEe
Confidence 444444444445688999999999998754
No 17
>PF04908 SH3BGR: SH3-binding, glutamic acid-rich protein; InterPro: IPR006993 This family of proteins, which contains SH3BGRL3, is functionally uncharacterised. SH3BGRL3 is a highly conserved small protein, which is widely expressed and shows a significant similarity to glutaredoxin 1 (GRX1) of Escherichia coli which is predicted to belong to the thioredoxin superfamily. However, SH3BGRL3 lacks both conserved cysteine residues, which characterise the enzymatic active site of GRX. This structural feature raises the possibility that SH3BGRL3 and its homologues could function as endogenous modulators of GRX activity []. ; PDB: 1SJ6_A 1U6T_A 1WRY_A 1T1V_B 1J0F_A 2CT6_A.
Probab=41.63 E-value=30 Score=23.36 Aligned_cols=30 Identities=17% Similarity=0.287 Sum_probs=18.1
Q ss_pred eeeecCCCHHHHHHHHHHHHhhCCCceEEe
Q psy2644 30 MKTTSSRDPNEIMAEIRKVLDANNCDYEQR 59 (119)
Q Consensus 30 v~ttSsk~P~eIm~ei~rvL~~~~i~~~~~ 59 (119)
.+++++..-..=-++|.+.|++++|+|+..
T Consensus 8 ss~sg~~~ikk~q~~v~~iL~a~kI~fe~v 37 (99)
T PF04908_consen 8 SSISGSREIKKRQQRVLMILEAKKIPFEEV 37 (99)
T ss_dssp -SS-SSHHHHHHHHHHHHHHHHTT--EEEE
T ss_pred ecccCCHHHHHHHHHHHHHHHHcCCCcEEE
Confidence 344444444444578999999999999863
No 18
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=41.12 E-value=28 Score=28.03 Aligned_cols=41 Identities=12% Similarity=0.046 Sum_probs=31.5
Q ss_pred eCcEEEEeeeCCCCCCcceEEEEEEEeecCCCcceeeEEEe
Q psy2644 59 RERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKRI 99 (119)
Q Consensus 59 ~g~y~l~C~~~~~~~~~~v~fEiEVcrl~~l~l~gi~fkRl 99 (119)
--||.+.|.+++..-..+++|-.+--++.+..-||+.+=|.
T Consensus 36 ~~Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF 76 (324)
T PF04502_consen 36 MMPFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRF 76 (324)
T ss_pred cCCccCcCCCCccccccceeeeeeeEecCCCccccceEEEE
Confidence 35999999998876677899999999888755666655443
No 19
>PLN03036 glutamine synthetase; Provisional
Probab=39.76 E-value=37 Score=28.75 Aligned_cols=63 Identities=13% Similarity=-0.002 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHHhhCCCceEEeCcEEEEeeeCCCCCCcceEEEEEEEeecCCCcceeeEEEecCCchhHHHHHHHHHHhc
Q psy2644 38 PNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKRISGTSIGFKNIASKIANEL 117 (119)
Q Consensus 38 P~eIm~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~~~~~v~fEiEVcrl~~l~l~gi~fkRl~Gd~~~Yk~lc~~il~~l 117 (119)
..+++.++.++|...||..+... ++. ..-|||+.+-.-. --...-+.|.||.+.++|..+.
T Consensus 228 ~~~i~~~i~~a~~~~GI~Ie~~~-------~E~----gpGQ~Ei~l~~~d--------~L~aAD~~~l~R~ivk~VA~~~ 288 (432)
T PLN03036 228 GRDISDAHYKACLYAGINISGTN-------GEV----MPGQWEYQVGPSV--------GIDAGDHIWCSRYILERITEQA 288 (432)
T ss_pred HHHHHHHHHHHHHHCCCCeEEEE-------cCc----CCCceEEecCCCh--------HHHHHHHHHHHHHHHHHHHHHh
Confidence 58999999999999999987422 111 2348988864422 2245677899999999998876
Q ss_pred CC
Q psy2644 118 KL 119 (119)
Q Consensus 118 ~L 119 (119)
++
T Consensus 289 Gl 290 (432)
T PLN03036 289 GV 290 (432)
T ss_pred CC
Confidence 54
No 20
>PF09553 RE_Eco47II: Eco47II restriction endonuclease; InterPro: IPR019057 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes Eco47II which recognises GGNCC but the cleavage site is not known. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=39.01 E-value=20 Score=27.68 Aligned_cols=20 Identities=35% Similarity=0.687 Sum_probs=16.7
Q ss_pred eeEEEecCCch---------hHHHHHHHH
Q psy2644 94 VRFKRISGTSI---------GFKNIASKI 113 (119)
Q Consensus 94 i~fkRl~Gd~~---------~Yk~lc~~i 113 (119)
-+++|++||.+ +|++||..|
T Consensus 176 ~~IR~Is~d~FY~lvtG~~dAf~~Lc~~L 204 (214)
T PF09553_consen 176 PRIRRISGDQFYELVTGDEDAFKELCMAL 204 (214)
T ss_pred cceEEecHHHHHHHHhCChhHHHHHHHHh
Confidence 46899998877 999999865
No 21
>PLN02284 glutamine synthetase
Probab=38.64 E-value=56 Score=26.66 Aligned_cols=64 Identities=13% Similarity=0.003 Sum_probs=44.8
Q ss_pred CHHHHHHHHHHHHhhCCCceEEeCcEEEEeeeCCCCCCcceEEEEEEEeecCCCcceeeEEEecCCchhHHHHHHHHHHh
Q psy2644 37 DPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKRISGTSIGFKNIASKIANE 116 (119)
Q Consensus 37 ~P~eIm~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~~~~~v~fEiEVcrl~~l~l~gi~fkRl~Gd~~~Yk~lc~~il~~ 116 (119)
.-.+++.+|.++|++.||..+... |+. ..-|||+.+-..+. -+..-+.|.||.+.+.|..+
T Consensus 167 ~~~~~~~~l~~~l~~~Gi~ve~~h-------~E~----apGQ~Ei~l~~~d~--------l~aAD~~~~~K~vvk~vA~~ 227 (354)
T PLN02284 167 FGRDIVDAHYKACLYAGINISGIN-------GEV----MPGQWEFQVGPVVG--------ISAGDQLWVARYILERITEI 227 (354)
T ss_pred HHHHHHHHHHHHHHHCCCCeEEEE-------cCc----CCCceEEEecCCcH--------HHHHHHHHHHHHHHHHHHHH
Confidence 347999999999999999987422 211 12489887655332 24566778899999998877
Q ss_pred cCC
Q psy2644 117 LKL 119 (119)
Q Consensus 117 l~L 119 (119)
.++
T Consensus 228 ~Gl 230 (354)
T PLN02284 228 AGV 230 (354)
T ss_pred hCC
Confidence 653
No 22
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=38.29 E-value=51 Score=22.28 Aligned_cols=30 Identities=23% Similarity=0.604 Sum_probs=23.9
Q ss_pred eeeeeeecCCCHHHHHHHHHHHHhhCCCce
Q psy2644 27 TWSMKTTSSRDPNEIMAEIRKVLDANNCDY 56 (119)
Q Consensus 27 ~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~ 56 (119)
+|...+--..+|.+|+.||...+.+.-=.|
T Consensus 47 mW~~p~~~~~~~~~Vl~el~~c~~~~p~~y 76 (99)
T PF00101_consen 47 MWKLPMFGCTDPAQVLAELEACLAEHPGEY 76 (99)
T ss_dssp EESSEBTTBSSHHHHHHHHHHHHHHSTTSE
T ss_pred cCCCCCcCCCCHHHHHHHHHHHHHhCCCce
Confidence 466777788999999999999999643333
No 23
>smart00596 PRE_C2HC PRE_C2HC domain.
Probab=37.59 E-value=1.1e+02 Score=19.51 Aligned_cols=54 Identities=11% Similarity=0.089 Sum_probs=33.0
Q ss_pred HHHHHHHhhCCCceEEeCcEEEEeeeCCCCCCcceEEEEEEEeecCCCcceeeEEEecCC
Q psy2644 43 AEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKRISGT 102 (119)
Q Consensus 43 ~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~~~~~v~fEiEVcrl~~l~l~gi~fkRl~Gd 102 (119)
.+|...|...|.+.... .|..........-=|++||..-+.. ...+.+|+|.|-
T Consensus 2 ~~I~~~L~~~G~~v~~i-----~~m~~~~~r~P~nmf~vel~~~~~~-~~Il~ik~Lg~~ 55 (69)
T smart00596 2 SQIEEALKDIGFPVLFI-----HNMLNRDTKNPQNMFEVELVPAANG-KEILNIKTLGGQ 55 (69)
T ss_pred HHHHHHHHHcCCceeEE-----EcccccCCCCcceeEEEEeeecCCC-cceEeehhhCCe
Confidence 47889999999887643 2433222123344588888877653 345666666653
No 24
>COG4972 PilM Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=37.07 E-value=33 Score=28.39 Aligned_cols=23 Identities=9% Similarity=0.200 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHHHHhhCCCceEE
Q psy2644 36 RDPNEIMAEIRKVLDANNCDYEQ 58 (119)
Q Consensus 36 k~P~eIm~ei~rvL~~~~i~~~~ 58 (119)
-+|+.|-..|+++|.++|+..++
T Consensus 55 vd~~av~~~Lk~ala~~gi~~k~ 77 (354)
T COG4972 55 VDYDAVASALKRALAKLGIKSKN 77 (354)
T ss_pred ccHHHHHHHHHHHHHhcCcchhh
Confidence 47999999999999999998875
No 25
>PRK08652 acetylornithine deacetylase; Provisional
Probab=36.85 E-value=81 Score=24.47 Aligned_cols=48 Identities=17% Similarity=0.320 Sum_probs=39.2
Q ss_pred eeCCCCCCCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCCCceEE
Q psy2644 10 VSNAVNDDQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQ 58 (119)
Q Consensus 10 ~~~~~~~~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~~ 58 (119)
|+|... ...-|-.....+++......+++++.++|.+.+...++.++.
T Consensus 209 i~gg~~-~nviP~~~~~~~diR~~~~~~~~~v~~~i~~~~~~~~v~~~~ 256 (347)
T PRK08652 209 IIGGSP-EYSIPALCRLRLDARIPPEVEVEDVLDEIDPILDEYTVKYEY 256 (347)
T ss_pred eecCCC-CCccCCcEEEEEEEEcCCCCCHHHHHHHHHHHHHhcCceEEE
Confidence 555432 246688889999999999999999999999999988877754
No 26
>PRK14543 nucleoside diphosphate kinase; Provisional
Probab=36.80 E-value=42 Score=24.78 Aligned_cols=43 Identities=16% Similarity=0.256 Sum_probs=33.3
Q ss_pred CCCCCCCCCCeEeceeeeee---------------eecCCCHHHHHHHHHHHHhhCCC
Q psy2644 12 NAVNDDQVKPRSLRFTWSMK---------------TTSSRDPNEIMAEIRKVLDANNC 54 (119)
Q Consensus 12 ~~~~~~~~kpR~lk~~~~v~---------------ttSsk~P~eIm~ei~rvL~~~~i 54 (119)
|++....+.|.++|+.|..+ .-.|.+|+....||.-.+....+
T Consensus 98 Gpt~p~~a~p~tIR~~fg~~~~~~~~~~~~~~rN~vH~SDs~esA~rEi~~fF~~~e~ 155 (169)
T PRK14543 98 GSTEPKLAIPGTIRGDFSYHSFNYANEKGFSVYNVIHASANEDDALREIPIWFKDNEI 155 (169)
T ss_pred CCCCccccCCCcchhhhcccccccccccccceeeEEECCCCHHHHHHHHHHhCCcccc
Confidence 66555677899999999875 34677899999999998876444
No 27
>TIGR03105 gln_synth_III glutamine synthetase, type III. This family consists of the type III isozyme of glutamine synthetase, originally described in Rhizobium meliloti, where types I and II also occur.
Probab=36.17 E-value=44 Score=28.06 Aligned_cols=67 Identities=15% Similarity=0.154 Sum_probs=45.8
Q ss_pred cCCCHHHHHHHHHHHHhhCCCceEEeCcEEEEeeeCCCCCCcceEEEEEEEeecCCCcceeeEEEecCCchhHHHHHHHH
Q psy2644 34 SSRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKRISGTSIGFKNIASKI 113 (119)
Q Consensus 34 Ssk~P~eIm~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~~~~~v~fEiEVcrl~~l~l~gi~fkRl~Gd~~~Yk~lc~~i 113 (119)
+......++.+|.++|+++||..+... ... ..-|||+.+--.+ --+..-+.+.||.+.++|
T Consensus 152 ~~~~~~~~~~~i~~~l~~~gi~ve~~~-----~E~------gpGQ~Ei~l~~~~--------~l~aaD~~~~~k~~vk~v 212 (435)
T TIGR03105 152 GLMRRYDVLTEISDAMNALGWDPYQND-----HED------ANGQFEMNFTYAD--------ALTTADRHAFFRYMVKEI 212 (435)
T ss_pred chhhhhHHHHHHHHHHHHCCCCeEEee-----cCc------CCCceEEecCcch--------HHHHHHHHHHHHHHHHHH
Confidence 345678999999999999999987422 111 1248887754332 223566778889999888
Q ss_pred HHhcCC
Q psy2644 114 ANELKL 119 (119)
Q Consensus 114 l~~l~L 119 (119)
..+.+|
T Consensus 213 A~~~Gl 218 (435)
T TIGR03105 213 AEKHGM 218 (435)
T ss_pred HHHhCC
Confidence 877654
No 28
>PF11979 DUF3480: Domain of unknown function (DUF3480); InterPro: IPR022557 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 350 to 362 amino acids in length. This domain is found C-terminal to PF01363 from PFAM.
Probab=36.08 E-value=1.9e+02 Score=24.07 Aligned_cols=51 Identities=22% Similarity=0.264 Sum_probs=31.2
Q ss_pred eeeeCCCC--C-CCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCCCceEEeCcEEEEeeeCC
Q psy2644 8 NVVSNAVN--D-DQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGD 70 (119)
Q Consensus 8 ~~~~~~~~--~-~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~~~g~y~l~C~~~~ 70 (119)
+|.+|+-+ . -.+|--.+.....|.++ .|-|.+|+++|+++ + .|.+.|-..|
T Consensus 158 vVfnGaLKssSg~~aKsSIVEDGlmVQi~-----~e~m~~Lr~ALr~~------k-Df~I~cg~~d 211 (356)
T PF11979_consen 158 VVFNGALKSSSGFLAKSSIVEDGLMVQIT-----PETMESLRQALREM------K-DFTITCGKVD 211 (356)
T ss_pred EEEcccccccccccccceEEeeeeEEEec-----HHHHHHHHHHHHhC------C-CeEEecCCcc
Confidence 45556622 1 22244455555566554 67999999999963 2 4777786544
No 29
>PRK05473 hypothetical protein; Provisional
Probab=35.76 E-value=36 Score=22.67 Aligned_cols=37 Identities=19% Similarity=0.413 Sum_probs=25.9
Q ss_pred eeeeeecCCCHHHHHHHHHHHHhhCCCc-eEE-eCcEEEE
Q psy2644 28 WSMKTTSSRDPNEIMAEIRKVLDANNCD-YEQ-RERFLLL 65 (119)
Q Consensus 28 ~~v~ttSsk~P~eIm~ei~rvL~~~~i~-~~~-~g~y~l~ 65 (119)
|++..-...+..+|+..+..||.+.|-. ..| .| |.|.
T Consensus 10 F~~~~~~~~~v~eiL~~Vy~AL~EKGYNPinQiVG-YllS 48 (86)
T PRK05473 10 FDFDDEKKKDVREILTTVYDALEEKGYNPINQIVG-YLLS 48 (86)
T ss_pred eeCCcccHHHHHHHHHHHHHHHHHcCCChHHHHHh-hhcc
Confidence 4444444557899999999999998864 233 44 7655
No 30
>COG0174 GlnA Glutamine synthetase [Amino acid transport and metabolism]
Probab=35.41 E-value=39 Score=28.74 Aligned_cols=80 Identities=16% Similarity=0.184 Sum_probs=55.3
Q ss_pred CCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCCCceEEeCcEEEEeeeCCCCCCcceEEEEEEEeecCCCcceeeEEE
Q psy2644 19 VKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKR 98 (119)
Q Consensus 19 ~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~~~~~v~fEiEVcrl~~l~l~gi~fkR 98 (119)
..|..-.+.|++.- ...-+++++||..+|++.|+.-+... |+. ..-||||.+- +-+.-+
T Consensus 147 ~~~~~~~~yf~~~~--~~~~~~~~~di~~~l~~~Gi~ie~~h-------hEv----a~gQ~EI~~~--------~~~~l~ 205 (443)
T COG0174 147 GRPADKGGYFDVAP--LDEAEDFRRDIVEALEAAGIEIEAIH-------HEV----APGQFEINLR--------FDDALK 205 (443)
T ss_pred CccCCCCcccCccc--cccHHHHHHHHHHHHHHCCCCcEecc-------ccc----cCCceEEecC--------CCCHHH
Confidence 34555567777754 36678999999999999999886422 221 1138886643 223446
Q ss_pred ecCCchhHHHHHHHHHHhcCC
Q psy2644 99 ISGTSIGFKNIASKIANELKL 119 (119)
Q Consensus 99 l~Gd~~~Yk~lc~~il~~l~L 119 (119)
..-+.|.||.+++.|..+.++
T Consensus 206 ~AD~~~~~K~vvk~vA~~hG~ 226 (443)
T COG0174 206 AADQIVIFKYVVKEVAEKHGL 226 (443)
T ss_pred HHHHHHHHHHHHHHHHHHhCC
Confidence 778889999999999877654
No 31
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=35.02 E-value=1.1e+02 Score=23.13 Aligned_cols=53 Identities=17% Similarity=0.096 Sum_probs=37.6
Q ss_pred CCCcceeeeCCCCCCCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCCCc
Q psy2644 3 PVPKHNVVSNAVNDDQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCD 55 (119)
Q Consensus 3 ~~~~~~~~~~~~~~~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~ 55 (119)
|.|-...|+-...++....+.-.-.|.-+...+--+.+-|.+|+.-|+++|.+
T Consensus 113 ~~pgl~fV~~gllDd~~~~~P~~~ifvsS~~e~~~~~~~~~~~~~~~~~~~~~ 165 (191)
T PRK05417 113 PFYGLDFVHTELSQEQGWSAPGFAAFVSSIIESGTDPEQMDGIRARLKELGLE 165 (191)
T ss_pred CCCCeEEEehhhcCCCCCCCceEEeeeeeccccCCChHHhHHHHHHHHHcCCC
Confidence 45566666644445555455566677777777777777799999999999875
No 32
>cd05860 Ig4_SCFR Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR). Ig4_SCFR: The fourth Immunoglobulin (Ig)-like domain in stem cell factor receptor (SCFR). SCFR is organized as an extracellular component having five IG-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. SCFR and its ligand SCF are critical for normal hematopoiesis, mast cell development, melanocytes and gametogenesis. SCF binds to the second and third Ig-like domains of SCFR. This fourth Ig-like domain participates in SCFR dimerization, which follows ligand binding. Deletion of this fourth domain abolishes the ligand-induced dimerization of SCFR and completely inhibits signal transduction.
Probab=34.65 E-value=31 Score=23.38 Aligned_cols=26 Identities=15% Similarity=0.286 Sum_probs=20.1
Q ss_pred eEEeCcEEEEeeeCCCCCCcceEEEEEE
Q psy2644 56 YEQRERFLLLCVHGDPNTDSLVQWEIEV 83 (119)
Q Consensus 56 ~~~~g~y~l~C~~~~~~~~~~v~fEiEV 83 (119)
..+.|.|.+.+.+.+. ...+.|+++|
T Consensus 74 ~~E~G~YTf~a~N~~~--~~s~tF~l~v 99 (101)
T cd05860 74 GTEGGTYTFLVSNSDA--SASVTFNVYV 99 (101)
T ss_pred hhhCcEEEEEEECCCC--eEEEEEEEEE
Confidence 3456999999988774 4569999886
No 33
>PF10847 DUF2656: Protein of unknown function (DUF2656); InterPro: IPR020325 This entry contains uncharacterised proteins from the cpeY 3'-region. They have no known function, but are found in the phycobilisome.
Probab=33.07 E-value=63 Score=23.14 Aligned_cols=31 Identities=16% Similarity=0.371 Sum_probs=27.0
Q ss_pred eeeeeeecCCCHHHHHHHHHHHHhhCCCceE
Q psy2644 27 TWSMKTTSSRDPNEIMAEIRKVLDANNCDYE 57 (119)
Q Consensus 27 ~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~ 57 (119)
-|.|.+.|..+|++|-.|+-|++.+......
T Consensus 44 HW~v~i~s~lsp~~~~~~~v~aw~~~R~~~g 74 (132)
T PF10847_consen 44 HWMVEIESDLSPDEMAEELVRAWKQYRNSLG 74 (132)
T ss_pred ceEEEecccCCHHHHHHHHHHHHHHHHHhhc
Confidence 4999999999999999999999998665553
No 34
>PF07687 M20_dimer: Peptidase dimerisation domain This family only corresponds to M20 family; InterPro: IPR011650 This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the MEROPS peptidase family M20 []. This family includes a range of zinc exopeptidases: carboxypeptidases, dipeptidases and specialised aminopeptidases [].; GO: 0016787 hydrolase activity; PDB: 3GB0_A 2F7V_A 1R3N_C 2VL1_D 2V8V_C 1R43_B 2V8G_B 2V8H_D 2V8D_A 3PFE_A ....
Probab=32.78 E-value=25 Score=22.55 Aligned_cols=43 Identities=21% Similarity=0.298 Sum_probs=33.1
Q ss_pred eeeCCCCCCCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhC
Q psy2644 9 VVSNAVNDDQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDAN 52 (119)
Q Consensus 9 ~~~~~~~~~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~ 52 (119)
.+.|.. ....=|-.....+++......+++++.++|++.+++.
T Consensus 65 ~i~gG~-~~n~ip~~a~~~~~~R~~p~~~~~~i~~~i~~~~~~~ 107 (111)
T PF07687_consen 65 SIEGGT-APNVIPDEATLTVDIRYPPGEDLEEIKAEIEAAVEKI 107 (111)
T ss_dssp EEEEES-STTEESSEEEEEEEEEESTCHHHHHHHHHHHHHHHHH
T ss_pred ecccCC-cCCEECCEEEEEEEEECCCcchHHHHHHHHHHHHHHh
Confidence 344433 3345567778889999888999999999999999874
No 35
>PRK03094 hypothetical protein; Provisional
Probab=32.33 E-value=94 Score=20.34 Aligned_cols=42 Identities=14% Similarity=0.055 Sum_probs=23.6
Q ss_pred ceeeeCCCCCCCCCCeEeceeeeeeeecCCCHHHHHHHHHHHH
Q psy2644 7 HNVVSNAVNDDQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVL 49 (119)
Q Consensus 7 ~~~~~~~~~~~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL 49 (119)
.+||+|.+.+-..--.+.-+.+-+. -+-+.|+||..+|..-|
T Consensus 38 a~VitG~d~n~mgi~d~~t~~pVI~-A~G~TaeEI~~~ve~r~ 79 (80)
T PRK03094 38 CCVVTGQDSNVMGIADTSTKGSVIT-ASGLTADEICQQVESRL 79 (80)
T ss_pred EEEEeCCCcceecccccccCCcEEE-cCCCCHHHHHHHHHHhh
Confidence 3678887432222111222233333 36899999999998654
No 36
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=31.22 E-value=42 Score=25.27 Aligned_cols=25 Identities=32% Similarity=0.412 Sum_probs=19.1
Q ss_pred cCCCHHHHHHHHHHHHhhCCCceEEe
Q psy2644 34 SSRDPNEIMAEIRKVLDANNCDYEQR 59 (119)
Q Consensus 34 Ssk~P~eIm~ei~rvL~~~~i~~~~~ 59 (119)
+..++.+ ..+|..+|+++||+|+..
T Consensus 33 ~~l~~~d-a~~i~~~L~~~gI~y~~~ 57 (206)
T PF01514_consen 33 SGLDEED-ANEIVAALDENGIPYKLS 57 (206)
T ss_dssp EEE-HHH-HHHHHHHHHHTT--EEEE
T ss_pred cCCCHHH-HHHHHHHHHHCCCCcEec
Confidence 4567888 899999999999999874
No 37
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=30.58 E-value=72 Score=21.62 Aligned_cols=33 Identities=18% Similarity=0.302 Sum_probs=23.8
Q ss_pred CeEeceeee---eeeecCCCHHHHHHHHHHHHhhCC
Q psy2644 21 PRSLRFTWS---MKTTSSRDPNEIMAEIRKVLDANN 53 (119)
Q Consensus 21 pR~lk~~~~---v~ttSsk~P~eIm~ei~rvL~~~~ 53 (119)
+|.--..|. +-+-...++++||.||...+.+.-
T Consensus 39 ~~~~~~yW~mwklP~f~~~d~~~Vl~ei~~C~~~~p 74 (99)
T cd03527 39 EHYDNRYWTMWKLPMFGCTDPAQVLREIEACRKAYP 74 (99)
T ss_pred CCCCCCEEeeccCCCCCCCCHHHHHHHHHHHHHHCC
Confidence 344444555 455557899999999999999743
No 38
>PHA00458 single-stranded DNA-binding protein
Probab=30.40 E-value=2.7e+02 Score=21.83 Aligned_cols=28 Identities=29% Similarity=0.356 Sum_probs=21.7
Q ss_pred ceeeeeeeecCC-C--HHHHHHHHHHHHhhC
Q psy2644 25 RFTWSMKTTSSR-D--PNEIMAEIRKVLDAN 52 (119)
Q Consensus 25 k~~~~v~ttSsk-~--P~eIm~ei~rvL~~~ 52 (119)
+|.+.|..|-++ + .+.++.+|.++.+++
T Consensus 36 rG~Ykv~lt~~~d~P~~qkmid~I~~~hee~ 66 (233)
T PHA00458 36 RGVYKVSLTVSNDDPRCQKMIDEIVKAHEEN 66 (233)
T ss_pred CceeEEEEEecCCChHHHHHHHHHHHHHHHH
Confidence 789999888666 4 356888888888776
No 39
>PTZ00039 40S ribosomal protein S20; Provisional
Probab=30.17 E-value=1.9e+02 Score=20.05 Aligned_cols=62 Identities=11% Similarity=0.135 Sum_probs=41.0
Q ss_pred eceeeeeeeecCCCHHHHHHHHHHHHhhCCCceEE-------eCcEEEEeeeCCCCCCcceEEEEEEEe
Q psy2644 24 LRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQ-------RERFLLLCVHGDPNTDSLVQWEIEVCK 85 (119)
Q Consensus 24 lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~~-------~g~y~l~C~~~~~~~~~~v~fEiEVcr 85 (119)
.+-...+.....+.-+.+.++|.+.....|...+- .-.|.++.+-.....+.+=+|||-+.+
T Consensus 17 ~kirI~L~S~d~~~Ld~~~~~Ii~~ak~~g~~v~GPipLPtK~~~~tvlrSPhg~~kksreqfE~RiHK 85 (115)
T PTZ00039 17 HKIRITLTSKNLKSIEKVCADIITGAKEKNLKVTGPVRMPVKTLRITTRKSPCGEGTNTWDRFEMRIYK 85 (115)
T ss_pred eEEEEEEEECCHHHHHHHHHHHHHHHHHcCCEeECCccCCceeEEEEeeeCCCCCCCchHHHheeeeee
Confidence 34455555566778899999999999999998741 122544444332223456789988876
No 40
>TIGR00106 uncharacterized protein, MTH1187 family. This protein has been crystallized in both Methanobacterium thermoautotrophicum and yeast, but its function remains unknown. Both crystal structures showed sulfate ions bound at the interface of two dimers to form a tetramer.
Probab=30.05 E-value=85 Score=20.91 Aligned_cols=28 Identities=18% Similarity=0.228 Sum_probs=23.0
Q ss_pred cCCCHHHHHHHHHHHHhhCCCceEEeCcE
Q psy2644 34 SSRDPNEIMAEIRKVLDANNCDYEQRERF 62 (119)
Q Consensus 34 Ssk~P~eIm~ei~rvL~~~~i~~~~~g~y 62 (119)
.+-+..+..+++.++|++.|+.|.. ||+
T Consensus 13 ~~~s~s~yVa~~i~~l~~sGl~y~~-~pm 40 (97)
T TIGR00106 13 VGASVSSYVAAAIEVLKESGLKYEL-HPM 40 (97)
T ss_pred CCCcHHHHHHHHHHHHHHcCCCeEe-cCC
Confidence 3457888999999999999999974 444
No 41
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=27.76 E-value=1.1e+02 Score=24.00 Aligned_cols=33 Identities=18% Similarity=0.177 Sum_probs=24.9
Q ss_pred ecCCCHHHHHHHHHHHHhhCCCceEE---eCcEEEEe
Q psy2644 33 TSSRDPNEIMAEIRKVLDANNCDYEQ---RERFLLLC 66 (119)
Q Consensus 33 tSsk~P~eIm~ei~rvL~~~~i~~~~---~g~y~l~C 66 (119)
-|..+++| .++|...|+++||+|+. .+++.+.-
T Consensus 24 ysgL~~~d-A~~I~a~L~~~gI~y~~~~~~~G~tI~V 59 (249)
T PRK15348 24 YRSLPEDE-ANQMLALLMQHHIDAEKKQEEDGVTLRV 59 (249)
T ss_pred HcCCCHHH-HHHHHHHHHHcCCCceEeeCCCCeEEEe
Confidence 35567777 78999999999999975 34466554
No 42
>PRK00933 ribosomal biogenesis protein; Validated
Probab=27.43 E-value=60 Score=23.90 Aligned_cols=32 Identities=22% Similarity=0.379 Sum_probs=21.2
Q ss_pred eecCCCHHHHHHHHHHHHhhCCCceEEeCcEE
Q psy2644 32 TTSSRDPNEIMAEIRKVLDANNCDYEQRERFL 63 (119)
Q Consensus 32 ttSsk~P~eIm~ei~rvL~~~~i~~~~~g~y~ 63 (119)
|||.++-+....-.+......|+.|-.+|.+.
T Consensus 4 TTSrkPs~~t~~fAkeLa~~ln~~yv~Rgk~S 35 (165)
T PRK00933 4 TTSRKPSQRTRSLVKDLARFLNCKYVNRGKMS 35 (165)
T ss_pred ECCCCCCHHHHHHHHHHHHHhCCEEEccCCcc
Confidence 45555555566666666677899987776554
No 43
>cd06218 DHOD_e_trans FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as 3 cofactors: FMN, FAD, and an [2Fe-2S] cluster.
Probab=26.85 E-value=1.2e+02 Score=22.88 Aligned_cols=20 Identities=5% Similarity=0.303 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHhhCCCceE
Q psy2644 38 PNEIMAEIRKVLDANNCDYE 57 (119)
Q Consensus 38 P~eIm~ei~rvL~~~~i~~~ 57 (119)
|..++..+.+.|++.|++..
T Consensus 188 p~~mv~~~~~~L~~~Gv~~~ 207 (246)
T cd06218 188 PEPMLKAVAELAAERGVPCQ 207 (246)
T ss_pred CHHHHHHHHHHHHhcCCCEE
Confidence 77899999999999999854
No 44
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=26.73 E-value=80 Score=25.34 Aligned_cols=27 Identities=26% Similarity=0.512 Sum_probs=24.9
Q ss_pred ceeeeeeeecCCCHHHHHHHHHHHHhh
Q psy2644 25 RFTWSMKTTSSRDPNEIMAEIRKVLDA 51 (119)
Q Consensus 25 k~~~~v~ttSsk~P~eIm~ei~rvL~~ 51 (119)
+|.|++.+|-+.+|++|+.+=.++|.+
T Consensus 257 ~fiF~VES~G~l~p~~i~~~Ai~iL~~ 283 (291)
T cd07032 257 HFIFSIESTGALPPDVLFLEAIKILKE 283 (291)
T ss_pred EEEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence 789999999999999999999999886
No 45
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.39 E-value=53 Score=21.75 Aligned_cols=38 Identities=16% Similarity=0.362 Sum_probs=26.5
Q ss_pred eeeeeecCCCHHHHHHHHHHHHhhCCCc-eEE-eCcEEEEe
Q psy2644 28 WSMKTTSSRDPNEIMAEIRKVLDANNCD-YEQ-RERFLLLC 66 (119)
Q Consensus 28 ~~v~ttSsk~P~eIm~ei~rvL~~~~i~-~~~-~g~y~l~C 66 (119)
|++.-.-.++-.+++.++.++|++.|-- ..| .| |+|..
T Consensus 10 f~~~d~~~~~v~e~L~~VY~sL~ekGYNpiNQiVG-YllSG 49 (88)
T COG4472 10 FDVGDSDKKDVKETLNDVYNSLEEKGYNPINQIVG-YLLSG 49 (88)
T ss_pred eecCCChHHHHHHHHHHHHHHHHHcCCChHHHHHh-hhccC
Confidence 4444445678999999999999998864 233 34 76553
No 46
>COG4309 Uncharacterized conserved protein [Function unknown]
Probab=26.28 E-value=79 Score=21.46 Aligned_cols=38 Identities=13% Similarity=0.182 Sum_probs=28.9
Q ss_pred eeeeecCCCHHHHHHHHHH-HHhhCCCceEEeCcEEEEe
Q psy2644 29 SMKTTSSRDPNEIMAEIRK-VLDANNCDYEQRERFLLLC 66 (119)
Q Consensus 29 ~v~ttSsk~P~eIm~ei~r-vL~~~~i~~~~~g~y~l~C 66 (119)
.+.++|.-||.-++.++.- --.+.+.+|.++||++.+.
T Consensus 36 ~leiisDHdP~pL~~~L~~~~pg~f~wey~e~Gp~vwRv 74 (98)
T COG4309 36 SLEIISDHDPRPLRYQLSTEFPGKFGWEYLENGPEVWRV 74 (98)
T ss_pred ceEeecCCCcHHHHHHhhhcCCccceeEEecCCCeEEEE
Confidence 4678899999999998876 4455677788888876554
No 47
>TIGR02554 PrgH type III secretion system protein PrgH/EprH. In Samonella, this gene is part of a four-gene operon PrgHIJK and in general is found in type III secretion operons. PrgH has been shown to be required for secretion, as well as being a structural component of the needle complex.
Probab=26.09 E-value=2.7e+02 Score=23.37 Aligned_cols=82 Identities=15% Similarity=0.164 Sum_probs=51.5
Q ss_pred eEeceeeeeeeecCCCHHHHHHHHHHHHhhCCCceEEe---CcEEEEee--eCC---------------CCCCcceEEEE
Q psy2644 22 RSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQR---ERFLLLCV--HGD---------------PNTDSLVQWEI 81 (119)
Q Consensus 22 R~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~~~---g~y~l~C~--~~~---------------~~~~~~v~fEi 81 (119)
+.+.++-++... .++.+++..+=+..|++.+|.|++. +.+.+--. -.| .+|...|+|.+
T Consensus 278 ~~~pya~~v~I~-~~s~~~l~~~Ae~GL~~~ni~yr~i~~~~~vtFiI~~aL~D~~l~~l~~Fv~~F~~~WG~~~VqFsI 356 (389)
T TIGR02554 278 RLMPYARDVRII-DADDGAAEQQAENGLDKQALPYRRLARRGGVTFVIAGALDDEELARARQFVDSYYRKWGGRYVQFAI 356 (389)
T ss_pred HhCCccceeEEE-EcCHHHHHHHHHhhHHhcCCceEEEecCCcEEEEEcCCCCHHHHHHHHHHHHHHHHhhCccEEEEEE
Confidence 344555566654 7899999999999999999999872 33443321 111 13677899998
Q ss_pred EEEeecCC------CcceeeEEEecCCchhH
Q psy2644 82 EVCKLPRL------SLNGVRFKRISGTSIGF 106 (119)
Q Consensus 82 EVcrl~~l------~l~gi~fkRl~Gd~~~Y 106 (119)
++--=.-. +-.| +-.+....|-|
T Consensus 357 ~L~~nwL~gKSf~~g~~G--Yv~l~~~HWYF 385 (389)
T TIGR02554 357 ELKDDWLKGKSFRYGGDG--YVKLDHGHWYF 385 (389)
T ss_pred EeCcccccCcceeeCCCC--eEEeCCCcccc
Confidence 86431100 1223 55666666655
No 48
>TIGR02017 hutG_amidohyd N-formylglutamate amidohydrolase. In some species, histidine is converted to via urocanate and then formimino-L-glutamate to glutamate in four steps, where the fourth step is conversion of N-formimino-L-glutamate to L-glutamate and formamide. In others, that pathway from formimino-L-glutamate may differ, with the next enzyme being formiminoglutamate hydrolase (HutF) yielding N-formyl-L-glutamate. This model represents the enzyme N-formylglutamate deformylase, also called N-formylglutamate amidohydrolase, which then produces glutamate.
Probab=25.83 E-value=2.2e+02 Score=22.23 Aligned_cols=58 Identities=14% Similarity=0.221 Sum_probs=36.3
Q ss_pred eeeeeeeecCC-CHHHHHHHHHHHHh-hCCCceEEeCcE----EEEeeeCCCCCCcceEEEEEEEe
Q psy2644 26 FTWSMKTTSSR-DPNEIMAEIRKVLD-ANNCDYEQRERF----LLLCVHGDPNTDSLVQWEIEVCK 85 (119)
Q Consensus 26 ~~~~v~ttSsk-~P~eIm~ei~rvL~-~~~i~~~~~g~y----~l~C~~~~~~~~~~v~fEiEVcr 85 (119)
-.|++++-... .+.++.+-+.++|+ +.|..+..++|| ..+ .++.+. ...=.++|||.|
T Consensus 162 pd~~lG~~~G~s~~~~l~~~l~~~l~~~~g~~v~~N~Py~Gg~itr-~yg~p~-~~vhaiQiEi~r 225 (263)
T TIGR02017 162 PDFNIGTNDGASCDPALTDAVEAVCAKATGYSHVLNGRFKGGWITR-HYGQPQ-NGVHAVQMELAQ 225 (263)
T ss_pred CCEEEeCCCCCCCCHHHHHHHHHHHHhcCCceEEeCCCCCCcceec-ccCCCC-CCCceEeeeEch
Confidence 35899887655 36777888889996 677777666554 433 333321 123336677775
No 49
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=25.25 E-value=94 Score=24.38 Aligned_cols=27 Identities=19% Similarity=0.423 Sum_probs=24.4
Q ss_pred ceeeeeeeecCCCHHHHHHHHHHHHhh
Q psy2644 25 RFTWSMKTTSSRDPNEIMAEIRKVLDA 51 (119)
Q Consensus 25 k~~~~v~ttSsk~P~eIm~ei~rvL~~ 51 (119)
++.|+|-+|-+.+|++|+.+=.++|.+
T Consensus 227 ~fiF~VES~Gsl~p~~Iv~~Al~iL~~ 253 (265)
T cd07031 227 KFYFNVESTGALPPEQIVLSGLEILKK 253 (265)
T ss_pred EEEEEEEecCCCCHHHHHHHHHHHHHH
Confidence 688999999999999999998888875
No 50
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=25.19 E-value=81 Score=18.10 Aligned_cols=16 Identities=19% Similarity=0.285 Sum_probs=13.3
Q ss_pred HHHHHHHhhCCCceEE
Q psy2644 43 AEIRKVLDANNCDYEQ 58 (119)
Q Consensus 43 ~ei~rvL~~~~i~~~~ 58 (119)
.|+.++|.+.|+....
T Consensus 2 ~el~k~L~~~G~~~~r 17 (56)
T PF07927_consen 2 RELIKLLEKAGFEEVR 17 (56)
T ss_dssp HHHHHHHHHTT-EEEE
T ss_pred hHHHHHHHHCCCEEec
Confidence 6899999999998875
No 51
>PRK06222 ferredoxin-NADP(+) reductase subunit alpha; Reviewed
Probab=24.97 E-value=1.2e+02 Score=23.38 Aligned_cols=22 Identities=9% Similarity=0.042 Sum_probs=18.6
Q ss_pred CHHHHHHHHHHHHhhCCCceEE
Q psy2644 37 DPNEIMAEIRKVLDANNCDYEQ 58 (119)
Q Consensus 37 ~P~eIm~ei~rvL~~~~i~~~~ 58 (119)
-|..+|..+.+.|.+.|+.+..
T Consensus 188 GP~~M~~~v~~~l~~~gv~~~~ 209 (281)
T PRK06222 188 GPVIMMKFVAELTKPYGIKTIV 209 (281)
T ss_pred CCHHHHHHHHHHHHhcCCCEEE
Confidence 4788999999999999997643
No 52
>PF13989 YejG: YejG-like protein
Probab=24.54 E-value=1.9e+02 Score=19.95 Aligned_cols=36 Identities=17% Similarity=0.188 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHHHHhhCCCceEE---eCcEEEEeeeCC
Q psy2644 35 SRDPNEIMAEIRKVLDANNCDYEQ---RERFLLLCVHGD 70 (119)
Q Consensus 35 sk~P~eIm~ei~rvL~~~~i~~~~---~g~y~l~C~~~~ 70 (119)
..+.-+||.+|..+|.+..|+... .|.=.|+-...|
T Consensus 48 g~~aw~im~~L~~sL~eiqv~~~vvE~eGepCLFv~~~D 86 (106)
T PF13989_consen 48 GESAWQIMQQLSQSLAEIQVDCAVVEWEGEPCLFVHRED 86 (106)
T ss_pred ChHHHHHHHHHHHHHHHhcccceEEEecCCceEEEeccc
Confidence 346889999999999999998754 344444444444
No 53
>PRK15327 type III secretion system needle complex protein PrgH; Provisional
Probab=24.30 E-value=3.1e+02 Score=23.11 Aligned_cols=80 Identities=18% Similarity=0.154 Sum_probs=50.2
Q ss_pred eceeeeeeeecCCCHHHHHHHHHHHHhhCCCceEEe---CcEEEEee--eCC---------------CCCCcceEEEEEE
Q psy2644 24 LRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQR---ERFLLLCV--HGD---------------PNTDSLVQWEIEV 83 (119)
Q Consensus 24 lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~~~---g~y~l~C~--~~~---------------~~~~~~v~fEiEV 83 (119)
+.++-++... +.+.+++..+=+..|++.+|.|++. +.+.+--. -.| .+|...|+|.+++
T Consensus 285 ~pya~~v~I~-~~s~~~l~~~Ae~GL~~~nv~yr~i~~~~~vtFiI~~sL~D~~l~~l~~fv~~F~~~WG~~~IqFsI~L 363 (393)
T PRK15327 285 MPYADSVNIT-LMDDVTAAGQAEAGLKQQALPYSRRDHKGSVTFVIQGALDDGEIQRARQFVDSYYRTWGGRYVQFAIEL 363 (393)
T ss_pred CCccceeEEE-EcCHHHHHHHHHhhHHhcCCceEEEecCCcEEEEEcCCCCHHHHHHHHHHHHHHHHhhCccEEEEEEEe
Confidence 3445555553 7899999999999999999999872 33443321 111 1366789999886
Q ss_pred EeecCC------CcceeeEEEecCCchhH
Q psy2644 84 CKLPRL------SLNGVRFKRISGTSIGF 106 (119)
Q Consensus 84 crl~~l------~l~gi~fkRl~Gd~~~Y 106 (119)
--=.-- +-.| +-.+....|-|
T Consensus 364 ~~nwL~gKSf~~~~~G--Yv~l~~~HWYF 390 (393)
T PRK15327 364 KDDWLKGKSFQYGAQG--YVKMSPGHWYF 390 (393)
T ss_pred ccccccCcceeeCCCc--eEEecCCcccc
Confidence 431100 1223 55666666655
No 54
>PF05413 Peptidase_C34: Putative closterovirus papain-like endopeptidase; InterPro: IPR008744 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This signature is found in the RNA-direct RNA polymerase of apple chlorotic leaf spot virus and cherry mottle virus.; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0005524 ATP binding, 0019079 viral genome replication
Probab=23.99 E-value=38 Score=22.48 Aligned_cols=31 Identities=19% Similarity=0.337 Sum_probs=22.8
Q ss_pred CeEeceeeee-----eeecCCCHHHHHHHHHHHHhh
Q psy2644 21 PRSLRFTWSM-----KTTSSRDPNEIMAEIRKVLDA 51 (119)
Q Consensus 21 pR~lk~~~~v-----~ttSsk~P~eIm~ei~rvL~~ 51 (119)
.+.++|.|+- ...-+|.|+|||.-+-.+|+.
T Consensus 2 ~kFikGk~DClf~s~a~~I~Kkpeevm~~~phvldR 37 (92)
T PF05413_consen 2 VKFIKGKYDCLFVSVAEIIHKKPEEVMMFLPHVLDR 37 (92)
T ss_pred cceeccccccHHHHHHHHHhcCHHHHHHhChHHHHH
Confidence 3556666662 333489999999999999886
No 55
>PF09480 PrgH: Type III secretion system protein PrgH-EprH (PrgH); InterPro: IPR019029 In Salmonella, the gene encoding this protein is part of a four-gene operon PrgHIJK, while in other organisms it is found in type III secretion operons. PrgH has been shown to be required for type III secretion and is a structural component of the needle complex, which is the core component of type III secretion systems. ; GO: 0016021 integral to membrane; PDB: 4A4Y_A 2XXS_A 2Y9J_C 3GR1_F 3GR0_D.
Probab=23.95 E-value=3e+02 Score=22.92 Aligned_cols=54 Identities=15% Similarity=0.243 Sum_probs=32.6
Q ss_pred eeeeecCCCHHHHHHHHHHHHhhCCCceEEe---CcEEEEeeeCC------------------CCCCcceEEEEEEE
Q psy2644 29 SMKTTSSRDPNEIMAEIRKVLDANNCDYEQR---ERFLLLCVHGD------------------PNTDSLVQWEIEVC 84 (119)
Q Consensus 29 ~v~ttSsk~P~eIm~ei~rvL~~~~i~~~~~---g~y~l~C~~~~------------------~~~~~~v~fEiEVc 84 (119)
++.. -..+.+++..+-+..|++.+|.|++. +.+.+-- .+. .+|...|+|.+++-
T Consensus 275 ~v~i-~~~s~~~l~~~Ae~GL~~~ni~yr~i~~~~~vtFiI-~~~L~D~~l~~l~~fi~~f~~~WG~~~IqFsI~L~ 349 (375)
T PF09480_consen 275 DVKI-KSKSDEELLQQAENGLTRLNIPYRRINKNNGVTFII-RDALNDKELSSLRRFIDEFYQQWGTRYIQFSINLK 349 (375)
T ss_dssp --EE-EEE-HHHHHHHHHHHHHHTT--EEEEEETTEEEEEE--S---HHHHHHHHHHHHHHHHHH-SSSEEEEEEE-
T ss_pred cceE-EEcCHHHHHHHHHHHHHhcCCceEEEecCCeEEEEE-eCCCCHHHHHHHHHHHHHHHHhhCccEEEEEEEec
Confidence 3443 36789999999999999999999872 3343332 221 02567899998864
No 56
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=23.86 E-value=48 Score=19.56 Aligned_cols=24 Identities=25% Similarity=0.318 Sum_probs=19.3
Q ss_pred eeecCCCHHHHHHHHHHHHhhCCC
Q psy2644 31 KTTSSRDPNEIMAEIRKVLDANNC 54 (119)
Q Consensus 31 ~ttSsk~P~eIm~ei~rvL~~~~i 54 (119)
...++++|++|..|=...+..++-
T Consensus 10 ~rL~~MS~eEI~~er~eL~~~LdP 33 (49)
T PF08621_consen 10 ARLASMSPEEIEEEREELLESLDP 33 (49)
T ss_pred HHHHhCCHHHHHHHHHHHHHhCCH
Confidence 345789999999998888887764
No 57
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=23.84 E-value=1e+02 Score=25.63 Aligned_cols=62 Identities=16% Similarity=0.124 Sum_probs=43.5
Q ss_pred EeceeeeeeeecCCCHHHHHHHHHHHHhhCCCceEEeCcEEEEeeeCCCC--------CCcceEEEEEEEe
Q psy2644 23 SLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPN--------TDSLVQWEIEVCK 85 (119)
Q Consensus 23 ~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~--------~~~~v~fEiEVcr 85 (119)
.+.|.|-.+- -.++|++-|.|+.+|++.+..+++-.|=-.++-..+.+. -.+.|...||.-.
T Consensus 101 YIeGLFLSSG-vi~~~DyTmE~mi~var~LRle~~f~GYIHlK~IPgas~~li~eaglyadRvSiNIElp~ 170 (404)
T COG4277 101 YIEGLFLSSG-VIKNPDYTMEEMIEVARILRLEHKFRGYIHLKIIPGASPDLIKEAGLYADRVSINIELPT 170 (404)
T ss_pred hhhhheeccc-cccCcchHHHHHHHHHHHHhhccccCcEEEEEecCCCCHHHHHHHhhhhheeEEeEecCC
Confidence 4566665543 479999999999999999999998777335665544321 1246777777544
No 58
>PRK06446 hypothetical protein; Provisional
Probab=23.70 E-value=2.6e+02 Score=22.82 Aligned_cols=37 Identities=16% Similarity=0.293 Sum_probs=33.0
Q ss_pred CCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCC
Q psy2644 17 DQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANN 53 (119)
Q Consensus 17 ~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~ 53 (119)
...-|-.....+++.+....++++++++|++.+.+.+
T Consensus 296 ~nvvP~~a~~~~d~R~~p~~~~~~v~~~l~~~~~~~~ 332 (436)
T PRK06446 296 KTIVPSRAFAKLDFRLVPNQDPYKIFELLKKHLQKVG 332 (436)
T ss_pred CcEecCceEEEEEEEcCCCCCHHHHHHHHHHHHHHcC
Confidence 3667888899999999999999999999999999854
No 59
>PF08915 tRNA-Thr_ED: Archaea-specific editing domain of threonyl-tRNA synthetase; InterPro: IPR015011 Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet []. ; GO: 0004829 threonine-tRNA ligase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0005737 cytoplasm; PDB: 3PD4_B 3PD3_A 2HL0_A 2HL1_A 2HKZ_A 3PD5_B 2HL2_A 3PD2_B 1Y2Q_A.
Probab=23.44 E-value=1.8e+02 Score=20.96 Aligned_cols=30 Identities=17% Similarity=0.349 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHhhCCCceEEe--C---cEEEEee
Q psy2644 38 PNEIMAEIRKVLDANNCDYEQR--E---RFLLLCV 67 (119)
Q Consensus 38 P~eIm~ei~rvL~~~~i~~~~~--g---~y~l~C~ 67 (119)
+.+|+.++...|.+.|++.... | .|.+.|.
T Consensus 93 A~~iL~~le~~L~~~g~eV~raPFGwyK~F~i~ck 127 (138)
T PF08915_consen 93 AVEILKKLEERLKSRGFEVYRAPFGWYKEFEISCK 127 (138)
T ss_dssp HHHHHHHHHHHHHHTT-EEEE--TTEEEEEEEEE-
T ss_pred HHHHHHHHHHHHHhCCCeEEEeCCccceeEEEEec
Confidence 4578888999999999987642 1 2678885
No 60
>PRK07079 hypothetical protein; Provisional
Probab=23.07 E-value=2.4e+02 Score=23.32 Aligned_cols=44 Identities=18% Similarity=0.206 Sum_probs=34.5
Q ss_pred eeCCCC--CCCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCC
Q psy2644 10 VSNAVN--DDQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANN 53 (119)
Q Consensus 10 ~~~~~~--~~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~ 53 (119)
|.|.+. ....=|-.....+++......+|++|+.+|.+.+++.+
T Consensus 309 i~gG~~~~~~NvVP~~a~~~vdiR~~P~~~~e~v~~~l~~~i~~~~ 354 (469)
T PRK07079 309 FKTGNPDAPVNAIPGSARAVCQLRFVVGTDWENLAPHLRAHLDAHG 354 (469)
T ss_pred eecCCCCCcceEecCceEEEEEEEcCCCCCHHHHHHHHHHHHHhcC
Confidence 555532 23556667788899999999999999999999999854
No 61
>PF05013 FGase: N-formylglutamate amidohydrolase; InterPro: IPR007709 Formylglutamate amidohydrolase (FGase) catalyzes the terminal reaction in the five-step pathway for histidine utilization in Pseudomonas putida. By this action, N-formyl-L-glutamate (FG) is hydrolyzed to produce L-glutamate plus formate [].; PDB: 2ODF_G 2Q7S_A.
Probab=23.05 E-value=97 Score=23.21 Aligned_cols=60 Identities=15% Similarity=0.215 Sum_probs=37.2
Q ss_pred eceeeeeeeecCCC-HHHHHHHHHHHHh-hCCCceEEeCcEEEEe----eeCCCCCCcceEEEEEEEe
Q psy2644 24 LRFTWSMKTTSSRD-PNEIMAEIRKVLD-ANNCDYEQRERFLLLC----VHGDPNTDSLVQWEIEVCK 85 (119)
Q Consensus 24 lk~~~~v~ttSsk~-P~eIm~ei~rvL~-~~~i~~~~~g~y~l~C----~~~~~~~~~~v~fEiEVcr 85 (119)
-...|.+++..... +.+++.-+.++|+ +.|..+..+.||.- + .++.+ ....-.++|||.+
T Consensus 152 ~~~~~~lG~~~~~s~~~~l~~~~~~~l~~~~g~~v~~N~Py~G-g~~~~~~~~~-~~~v~~iqiEi~~ 217 (222)
T PF05013_consen 152 PRPDIVLGTLHGPSCDPELVDALAEALEASDGYSVRVNEPYSG-GYITRYYGRP-ARGVHAIQIEINR 217 (222)
T ss_dssp ---SECEECCTTTSS-HHHHHHHHHHCC-CTTS-EEETSS--G-GHCCCHHHCC-CCTEEEEEEEEEG
T ss_pred CCCCeEEEcCCCCCCCHHHHHHHHHHhhcccCcEEeeCCCCCC-cchhcEEecC-CCCceEEEEEEEH
Confidence 45678999887755 8899999999999 78888888878742 1 01111 2334557777765
No 62
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=22.54 E-value=1.3e+02 Score=19.43 Aligned_cols=27 Identities=33% Similarity=0.486 Sum_probs=19.5
Q ss_pred eeeEEEec-CCchhHHHHHHHHHHhcCC
Q psy2644 93 GVRFKRIS-GTSIGFKNIASKIANELKL 119 (119)
Q Consensus 93 gi~fkRl~-Gd~~~Yk~lc~~il~~l~L 119 (119)
|=+..|+. -.+|.|.+|+++|-+.+++
T Consensus 8 ~~d~~r~~l~~~~~~~~L~~~i~~r~~~ 35 (82)
T cd06407 8 GEEKIRFRLPPSWGFTELKQEIAKRFKL 35 (82)
T ss_pred CCeEEEEEcCCCCCHHHHHHHHHHHhCC
Confidence 33455555 4578999999999887653
No 63
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=22.15 E-value=1.5e+02 Score=19.64 Aligned_cols=33 Identities=9% Similarity=-0.017 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHHhhCCC--ceEEeCcEEEEeee
Q psy2644 35 SRDPNEIMAEIRKVLDANNC--DYEQRERFLLLCVH 68 (119)
Q Consensus 35 sk~P~eIm~ei~rvL~~~~i--~~~~~g~y~l~C~~ 68 (119)
+.-.++|+++|.+.+.+.|+ ..+++|.+.+ |..
T Consensus 13 AaGA~~V~~al~~ei~~~gl~v~v~~tGC~G~-C~~ 47 (92)
T cd03063 13 ALGADEVAEAIEAEAAARGLAATIVRNGSRGM-YWL 47 (92)
T ss_pred hhCHHHHHHHHHHHHHHcCCeEEEEEecCcee-cCC
Confidence 44689999999999999996 5566786663 754
No 64
>PF12046 DUF3529: Protein of unknown function (DUF3529); InterPro: IPR021919 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.
Probab=22.11 E-value=1.7e+02 Score=21.92 Aligned_cols=35 Identities=23% Similarity=0.441 Sum_probs=25.3
Q ss_pred CCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCCCceE
Q psy2644 19 VKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYE 57 (119)
Q Consensus 19 ~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~ 57 (119)
+|-|+-+-. ..|..+|++++.+|..-|++.|-.-.
T Consensus 27 ~KdRt~~~~----~~s~~p~~~~~~~l~~yf~~r~y~v~ 61 (173)
T PF12046_consen 27 VKDRTEQVT----FESPQPPDEVLEQLKAYFEQRNYRVA 61 (173)
T ss_pred ccccEEEEE----EEcCCCHHHHHHHHHHHHHhcCceec
Confidence 344444433 35789999999999999998765544
No 65
>PLN02320 seryl-tRNA synthetase
Probab=22.00 E-value=2.2e+02 Score=24.70 Aligned_cols=46 Identities=13% Similarity=0.283 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhhCCCceEEeCcEEEEeeeCCCCCCcceEEEEEEEeecCC
Q psy2644 38 PNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRL 89 (119)
Q Consensus 38 P~eIm~ei~rvL~~~~i~~~~~g~y~l~C~~~~~~~~~~v~fEiEVcrl~~l 89 (119)
-++++..+..+|..+|+.|... ..|. +|-+-....+++||+. +|..
T Consensus 361 ~e~ll~~~e~i~~~LgLpyrvv----~l~t-gDLg~~a~kkyDiEvW-~P~~ 406 (502)
T PLN02320 361 HEELIQIEEDLFTSLGLHFKTL----DMAT-ADLGAPAYRKFDIEAW-MPGL 406 (502)
T ss_pred HHHHHHHHHHHHHHcCCCeEEE----EecC-CccchhhhheEEEEEE-ecCC
Confidence 3455666677888999998643 2454 4433345678888865 3543
No 66
>TIGR03526 selenium_YgeY putative selenium metabolism hydrolase. SelD, selenophosphate synthase, is the selenium donor protein for both selenocysteine and selenouridine biosynthesis systems, but it occurs also in a few prokaryotes that have neither of those pathways. The method of partial phylogenetic profiling, starting from such orphan-selD genomes, identifies this protein as one of those most strongly correlated to SelD occurrence. Its distribution is also well correlated with that of family TIGR03309, a putative accessory protein of labile selenium (non-selenocysteine) enzyme maturation. This family includes the uncharacterized YgeY of Escherichia coli, and belongs to a larger family of metalloenzymes in which some are known peptidases, others enzymes of different types.
Probab=21.98 E-value=3e+02 Score=22.04 Aligned_cols=37 Identities=8% Similarity=0.021 Sum_probs=31.0
Q ss_pred CCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCC
Q psy2644 17 DQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANN 53 (119)
Q Consensus 17 ~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~ 53 (119)
...=|-..+..+++.+....++++++.+|++++...+
T Consensus 245 ~nviP~~~~~~~d~R~~~~~~~~~~~~~i~~~~~~~~ 281 (395)
T TIGR03526 245 RCAVADGCTISIDRRLTWGETWEYALEQIRNLPAVQG 281 (395)
T ss_pred CCccCCeEEEEEEEecCCCCCHHHHHHHHHHHHHhcC
Confidence 3456777888999998889999999999999988654
No 67
>TIGR03320 ygeY M20/DapE family protein YgeY. Members of this protein family, including the YgeY protein of Escherichia coli, typically are found in extended genomic regions associated with purine catabolism. Homologs include peptidases and deacylases of the M20/M25 /M40 and DapE/ArgE families. The function is unknown.
Probab=21.90 E-value=2.8e+02 Score=22.15 Aligned_cols=37 Identities=8% Similarity=0.021 Sum_probs=31.3
Q ss_pred CCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCC
Q psy2644 17 DQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANN 53 (119)
Q Consensus 17 ~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~ 53 (119)
...-|-.....+++......++++++++|++.+...+
T Consensus 245 ~NviP~~~~~~~diR~~p~~~~~~i~~~i~~~~~~~~ 281 (395)
T TIGR03320 245 RCAVADGCTISIDRRLTWGETWEYALEQIRNLPAVQG 281 (395)
T ss_pred cCccCCEEEEEEEEecCCCCCHHHHHHHHHHHHhhcC
Confidence 3467888899999999889999999999999987643
No 68
>PF01890 CbiG_C: Cobalamin synthesis G C-terminus; InterPro: IPR002750 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CbiG proteins are specific for anaerobic cobalamin biosynthesis. CbiG, which shows homology with CobE of the aerobic pathway, participates in the conversion of cobalt-precorrin 5 into cobalt-precorrin 6 []. CbiG is responsible for the opening of the delta-lactone ring and extrusion of the C2-unit []. The aerobic pathway uses molecular oxygen to trigger the events at C-20 leading to contraction and expulsion of the C2-unit as acetic acid from a metal-free intermediate, whereas the anaerobic route involves the internal delivery of oxygen from a carboxylic acid terminus to C-20 followed by extrusion of the C2-unit as acetaldehyde, using cobalt complexes as substrates []. This entry represents the core domain of CibG.; GO: 0009236 cobalamin biosynthetic process; PDB: 3BY5_A 2W6K_A 2W6L_A 3EEQ_B.
Probab=21.74 E-value=1.1e+02 Score=21.00 Aligned_cols=30 Identities=13% Similarity=0.148 Sum_probs=21.2
Q ss_pred eeeeecCCCHHHHHHHHHHHHhhCCCceEE
Q psy2644 29 SMKTTSSRDPNEIMAEIRKVLDANNCDYEQ 58 (119)
Q Consensus 29 ~v~ttSsk~P~eIm~ei~rvL~~~~i~~~~ 58 (119)
.++..+.-++++|...|.++|++.|+....
T Consensus 5 GiGcrr~~~~~~i~~ai~~~l~~~~~~~~~ 34 (121)
T PF01890_consen 5 GIGCRRGAPAEEIEEAIEQALAEAGLSPRS 34 (121)
T ss_dssp EEEE-SS--HHHHHHHHHHHHHHCT--GGG
T ss_pred EeCcCCCCCHHHHHHHHHHHHHHcCCChhh
Confidence 356667778999999999999999998754
No 69
>cd00307 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome t
Probab=21.71 E-value=1.5e+02 Score=19.42 Aligned_cols=32 Identities=16% Similarity=0.223 Sum_probs=24.5
Q ss_pred eEeceeeeeeeecC--CCHHHHHHHHHHHHhhCC
Q psy2644 22 RSLRFTWSMKTTSS--RDPNEIMAEIRKVLDANN 53 (119)
Q Consensus 22 R~lk~~~~v~ttSs--k~P~eIm~ei~rvL~~~~ 53 (119)
|.-+-+|-+.+-.- .+|.+||.||...+.+.-
T Consensus 26 ~rywt~w~lp~f~~~~~~~~~Vl~el~~c~~~~p 59 (84)
T cd00307 26 RRFRTSSWQSCGPIEGRSEAQVLAALEACLAEHP 59 (84)
T ss_pred CccHhhhcCCCCCCCCCCHHHHHHHHHHHHHHCC
Confidence 55566666665555 899999999999999643
No 70
>PLN02372 violaxanthin de-epoxidase
Probab=21.68 E-value=81 Score=26.94 Aligned_cols=28 Identities=29% Similarity=0.377 Sum_probs=25.0
Q ss_pred eeeecCCCHHHHHHHHHHHHhhCCCceE
Q psy2644 30 MKTTSSRDPNEIMAEIRKVLDANNCDYE 57 (119)
Q Consensus 30 v~ttSsk~P~eIm~ei~rvL~~~~i~~~ 57 (119)
|-|+|..=|+++.-+|.+++++.|++|.
T Consensus 320 vyTrs~~lP~~~~p~L~~Aa~kvG~df~ 347 (455)
T PLN02372 320 VYTRSSTLPESIVPELEKAAKKVGRDFS 347 (455)
T ss_pred EEecCCCCChhhhHHHHHHHHHcCCCHH
Confidence 5677778789999999999999999986
No 71
>COG0011 Uncharacterized conserved protein [Function unknown]
Probab=21.67 E-value=1.5e+02 Score=20.18 Aligned_cols=27 Identities=15% Similarity=0.252 Sum_probs=22.5
Q ss_pred CCCHHHHHHHHHHHHhhCCCceEEeCcE
Q psy2644 35 SRDPNEIMAEIRKVLDANNCDYEQRERF 62 (119)
Q Consensus 35 sk~P~eIm~ei~rvL~~~~i~~~~~g~y 62 (119)
+-+-....+++.++|++.|+.|. .||+
T Consensus 16 ~~svs~yVa~~i~~lk~~glky~-~~pm 42 (100)
T COG0011 16 GPSVSKYVAEAIEILKESGLKYQ-LGPM 42 (100)
T ss_pred CCCHHHHHHHHHHHHHHcCCcee-ecCc
Confidence 44568999999999999999997 4555
No 72
>PF11305 DUF3107: Protein of unknown function (DUF3107); InterPro: IPR021456 Some members in this family of proteins are annotated as ATP-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=21.26 E-value=1.3e+02 Score=19.39 Aligned_cols=23 Identities=17% Similarity=0.320 Sum_probs=20.0
Q ss_pred eeeecCCCHHHHHHHHHHHHhhC
Q psy2644 30 MKTTSSRDPNEIMAEIRKVLDAN 52 (119)
Q Consensus 30 v~ttSsk~P~eIm~ei~rvL~~~ 52 (119)
+...|..++++|...|..+|..-
T Consensus 14 l~ies~~s~dev~~~v~~Al~~~ 36 (74)
T PF11305_consen 14 LVIESDQSADEVEAAVTDALADG 36 (74)
T ss_pred EEEecCCCHHHHHHHHHHHHhCC
Confidence 35568899999999999999976
No 73
>PF01910 DUF77: Domain of unknown function DUF77; InterPro: IPR002767 This entry contains several hypothetical proteins of unknown function found in archaebacteria, eukaryotes and eubacteria. The structures of YBL001c from Saccharomyces cerevisiae and its homologue MTH1187 from the archaea Methanobacterium thermoautotrophicum have been determined []. These proteins have a ferredoxin-like alpha/beta sandwich structure with anti-parallel beta-sheets. Generally, they have two domains that form a single beta-sheet dimer, where two dimers pack sheet-to-sheet into a tetramer, some proteins having an extra C-terminal helix. ; PDB: 1LXJ_A 1YQH_A 2EKY_G 2EPI_A 1VK8_D 2IBO_C 1LXN_B.
Probab=20.85 E-value=1.1e+02 Score=20.11 Aligned_cols=27 Identities=19% Similarity=0.274 Sum_probs=23.0
Q ss_pred CCCHHHHHHHHHHHHhhCCCceEEeCcE
Q psy2644 35 SRDPNEIMAEIRKVLDANNCDYEQRERF 62 (119)
Q Consensus 35 sk~P~eIm~ei~rvL~~~~i~~~~~g~y 62 (119)
+-+....++++.++|++.|+.|.. ||+
T Consensus 12 ~~s~~~~V~~~i~~i~~sgl~y~v-~pm 38 (92)
T PF01910_consen 12 GESVSAYVAEAIEVIKESGLKYEV-GPM 38 (92)
T ss_dssp SSHHHHHHHHHHHHHHTSSSEEEE-ETT
T ss_pred CCCHHHHHHHHHHHHHHcCCceEE-cCC
Confidence 567888999999999999999974 444
No 74
>PRK08596 acetylornithine deacetylase; Validated
Probab=20.83 E-value=2.9e+02 Score=22.44 Aligned_cols=43 Identities=9% Similarity=0.142 Sum_probs=34.2
Q ss_pred eeeCCCCCCCCCCeEeceeeeeeeecCCCHHHHHHHHHHHHhhC
Q psy2644 9 VVSNAVNDDQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDAN 52 (119)
Q Consensus 9 ~~~~~~~~~~~kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~ 52 (119)
.|.|.. ....-|-.....+++.+....++++|+++|+++++..
T Consensus 259 ~i~gG~-~~nvvP~~~~~~~d~R~~p~~~~~~v~~~i~~~~~~~ 301 (421)
T PRK08596 259 VIEGGR-HAAFIADECRLWITVHFYPNETYEQVIKEIEEYIGKV 301 (421)
T ss_pred eeeCCC-CCCccCceEEEEEEeeeCCCCCHHHHHHHHHHHHHHH
Confidence 355542 2246677889999999999999999999999999863
No 75
>PRK07205 hypothetical protein; Provisional
Probab=20.81 E-value=2.1e+02 Score=23.46 Aligned_cols=38 Identities=8% Similarity=0.194 Sum_probs=32.5
Q ss_pred CCeEeceeeeeeeecCCCHHHHHHHHHHHHhhCCCceE
Q psy2644 20 KPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYE 57 (119)
Q Consensus 20 kpR~lk~~~~v~ttSsk~P~eIm~ei~rvL~~~~i~~~ 57 (119)
-|-.....+++.+....++++++++|.+.+++.++.+.
T Consensus 315 vP~~a~~~ld~R~~p~~~~e~v~~~i~~~~~~~~v~~~ 352 (444)
T PRK07205 315 TKEKSEIRIDIRIPVLADKEKLVQQLSQKAQEYGLTYE 352 (444)
T ss_pred ECCEEEEEEEEeCCCCCCHHHHHHHHHHHHHHcCcEEE
Confidence 46667888888888889999999999999998888765
No 76
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=20.44 E-value=1.4e+02 Score=22.29 Aligned_cols=32 Identities=22% Similarity=0.214 Sum_probs=23.4
Q ss_pred cCCCHHHHHHHHHHHHhhCCCceEE---e-CcEEEEe
Q psy2644 34 SSRDPNEIMAEIRKVLDANNCDYEQ---R-ERFLLLC 66 (119)
Q Consensus 34 Ssk~P~eIm~ei~rvL~~~~i~~~~---~-g~y~l~C 66 (119)
+..++++ .++|...|+++||.|+. . +.+.+..
T Consensus 24 ~~L~~~d-a~~I~~~L~~~gI~y~~~~~~~~g~~I~V 59 (193)
T TIGR02544 24 SGLSERE-ANEMLAVLMRHGIDAEKEGSGKGGYTISV 59 (193)
T ss_pred cCCCHHH-HHHHHHHHHHCCCCeEEeecCCCCeEEEE
Confidence 4456666 78999999999999986 1 2355555
No 77
>PF00731 AIRC: AIR carboxylase; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process; PDB: 3TRH_O 2YWX_A 2NSL_A 1D7A_A 2NSJ_A 1QCZ_A 2ATE_A 2NSH_A 3RG8_C 3RGG_D ....
Probab=20.01 E-value=1.5e+02 Score=21.52 Aligned_cols=24 Identities=29% Similarity=0.267 Sum_probs=19.1
Q ss_pred CCCHHHHHHHHHHHHhhCCCceEE
Q psy2644 35 SRDPNEIMAEIRKVLDANNCDYEQ 58 (119)
Q Consensus 35 sk~P~eIm~ei~rvL~~~~i~~~~ 58 (119)
|.+=..++.|+..+|++.||.|+.
T Consensus 9 s~SD~~~~~~a~~~L~~~gi~~~~ 32 (150)
T PF00731_consen 9 STSDLPIAEEAAKTLEEFGIPYEV 32 (150)
T ss_dssp SGGGHHHHHHHHHHHHHTT-EEEE
T ss_pred CHHHHHHHHHHHHHHHHcCCCEEE
Confidence 445567899999999999999973
Done!