Query 033373
Match_columns 120
No_of_seqs 163 out of 1109
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 13:06:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033373.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033373hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0721 GatC Asp-tRNAAsn/Glu-t 99.8 1.9E-18 4.1E-23 121.9 6.7 64 56-120 1-64 (96)
2 TIGR00135 gatC glutamyl-tRNA(G 99.8 3.2E-18 7E-23 118.2 7.4 62 58-120 1-62 (93)
3 PRK00034 gatC aspartyl/glutamy 99.7 3.8E-18 8.2E-23 117.7 7.4 64 56-120 1-64 (95)
4 PRK12821 aspartyl/glutamyl-tRN 99.7 4.5E-17 9.7E-22 140.7 7.7 65 56-120 387-451 (477)
5 PRK12820 bifunctional aspartyl 99.4 3.6E-13 7.7E-18 121.5 6.9 61 57-119 611-671 (706)
6 PF02686 Glu-tRNAGln: Glu-tRNA 99.2 6.4E-12 1.4E-16 82.1 3.7 46 74-120 1-46 (72)
7 TIGR01827 gatC_rel Asp-tRNA(As 96.7 0.0019 4.2E-08 43.7 3.2 34 83-119 3-37 (73)
8 KOG4247 Mitochondrial DNA poly 95.7 0.019 4.1E-07 43.7 4.4 60 52-114 42-101 (175)
9 PF13318 DUF4089: Protein of u 84.1 5.1 0.00011 25.2 5.5 41 63-103 2-42 (50)
10 COG3079 Uncharacterized protei 71.5 6.1 0.00013 31.3 3.7 37 60-96 128-165 (186)
11 PRK02166 hypothetical protein; 68.0 6 0.00013 30.9 3.1 37 59-95 126-162 (184)
12 PF13499 EF-hand_7: EF-hand do 66.2 2.5 5.4E-05 25.9 0.5 40 44-84 4-43 (66)
13 PRK07235 amidase; Provisional 62.1 13 0.00028 32.6 4.3 51 56-107 4-54 (502)
14 PF13833 EF-hand_8: EF-hand do 60.4 13 0.00027 22.0 2.9 31 56-86 3-34 (54)
15 PRK04758 hypothetical protein; 60.1 12 0.00025 29.2 3.3 37 59-95 124-161 (181)
16 PRK01736 hypothetical protein; 59.0 13 0.00027 28.9 3.4 36 60-95 129-165 (190)
17 PF07128 DUF1380: Protein of u 58.7 12 0.00027 28.4 3.2 44 46-89 13-58 (139)
18 PF05397 Med15_fungi: Mediator 51.9 10 0.00023 27.4 1.8 33 67-99 20-54 (115)
19 PF11181 YflT: Heat induced st 45.4 20 0.00043 24.8 2.3 23 66-88 74-96 (103)
20 KOG0030 Myosin essential light 42.3 20 0.00043 27.7 2.0 46 41-87 89-134 (152)
21 PF09677 TrbI_Ftype: Type-F co 39.0 61 0.0013 23.3 4.1 28 65-92 45-72 (111)
22 TIGR03279 cyano_FeS_chp putati 38.8 43 0.00093 29.6 3.8 81 14-99 85-176 (433)
23 PRK13717 conjugal transfer pro 38.2 63 0.0014 24.3 4.1 29 64-92 58-86 (128)
24 PF06580 His_kinase: Histidine 35.3 93 0.002 20.5 4.3 32 61-94 16-47 (82)
25 PF04201 TPD52: Tumour protein 34.3 67 0.0014 25.0 3.8 30 70-99 22-51 (162)
26 PF10256 Erf4: Golgin subfamil 32.9 93 0.002 21.6 4.2 23 69-92 26-48 (118)
27 TIGR02744 TrbI_Ftype type-F co 32.5 87 0.0019 22.9 4.0 27 65-91 46-72 (112)
28 TIGR00268 conserved hypothetic 32.4 29 0.00062 27.4 1.6 42 56-97 177-238 (252)
29 PF09754 PAC2: PAC2 family; I 31.8 86 0.0019 23.6 4.1 40 59-98 180-219 (219)
30 PRK06474 hypothetical protein; 31.8 46 0.00099 25.3 2.6 26 70-95 132-157 (178)
31 PF07308 DUF1456: Protein of u 31.8 67 0.0014 21.2 3.1 29 56-84 12-40 (68)
32 PF02969 TAF: TATA box binding 31.7 1.4E+02 0.0031 19.6 4.6 37 55-91 1-38 (66)
33 TIGR03798 ocin_TIGR03798 bacte 29.5 80 0.0017 20.0 3.1 30 58-87 25-54 (64)
34 TIGR03544 DivI1A_domain DivIVA 29.1 83 0.0018 17.8 2.8 30 59-88 2-32 (34)
35 PF02413 Caudo_TAP: Caudoviral 28.6 1.1E+02 0.0025 21.8 4.1 33 74-110 94-126 (130)
36 PTZ00373 60S Acidic ribosomal 28.4 1.3E+02 0.0027 22.0 4.3 44 56-99 18-67 (112)
37 PRK09706 transcriptional repre 28.0 89 0.0019 22.2 3.4 39 57-97 84-122 (135)
38 PRK10870 transcriptional repre 28.0 1E+02 0.0022 23.2 3.9 28 73-100 142-169 (176)
39 cd04411 Ribosomal_P1_P2_L12p R 26.3 1.2E+02 0.0026 21.6 3.8 31 57-87 16-46 (105)
40 COG1103 Archaea-specific pyrid 25.9 46 0.00099 28.8 1.8 45 33-91 331-379 (382)
41 PF00034 Cytochrom_C: Cytochro 24.9 69 0.0015 19.4 2.1 12 85-96 79-90 (91)
42 COG1071 AcoA Pyruvate/2-oxoglu 24.5 3E+02 0.0064 23.8 6.5 61 47-107 265-337 (358)
43 PF14842 FliG_N: FliG N-termin 24.0 1.8E+02 0.004 20.1 4.4 34 57-90 29-64 (108)
44 PF14069 SpoVIF: Stage VI spor 23.8 1.6E+02 0.0034 20.2 3.9 25 61-85 35-59 (79)
45 cd05832 Ribosomal_L12p Ribosom 23.6 93 0.002 22.5 2.8 33 56-88 15-47 (106)
46 CHL00123 rps6 ribosomal protei 23.3 55 0.0012 22.6 1.5 45 69-113 13-58 (97)
47 PRK01546 hypothetical protein; 23.1 1.3E+02 0.0028 20.8 3.3 24 58-81 2-29 (79)
48 COG2047 Uncharacterized protei 23.1 1.8E+02 0.0039 24.3 4.7 38 61-98 203-240 (258)
49 cd05027 S-100B S-100B: S-100B 22.3 81 0.0018 21.2 2.2 41 46-86 14-60 (88)
50 smart00685 DM14 Repeats in fly 22.1 1.4E+02 0.003 19.4 3.2 27 80-106 31-57 (59)
51 PRK02539 hypothetical protein; 22.1 1.3E+02 0.0029 21.1 3.2 23 59-81 2-28 (85)
52 cd05832 Ribosomal_L12p Ribosom 22.1 1.5E+02 0.0033 21.4 3.7 39 66-104 9-53 (106)
53 PRK14981 DNA-directed RNA poly 21.7 2E+02 0.0043 20.5 4.2 12 39-50 37-48 (112)
54 cd00051 EFh EF-hand, calcium b 21.2 1.6E+02 0.0034 16.0 4.2 31 56-86 15-45 (63)
55 cd05833 Ribosomal_P2 Ribosomal 20.8 1.9E+02 0.004 20.8 3.9 33 56-88 16-48 (109)
56 KOG0031 Myosin regulatory ligh 20.2 1.4E+02 0.0031 23.5 3.4 45 56-101 47-99 (171)
No 1
>COG0721 GatC Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit [Translation, ribosomal structure and biogenesis]
Probab=99.75 E-value=1.9e-18 Score=121.92 Aligned_cols=64 Identities=27% Similarity=0.506 Sum_probs=60.2
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCccccccccccccCC
Q 033373 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRADLSALSQRRK 120 (120)
Q Consensus 56 m~I~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~eVDTe~VePm~hp~e~~~~~~r~ 120 (120)
|.|++++|+|||+||||+++|+|++.|..+|++|++||++|++|||+||+||+||.+.. +.+|+
T Consensus 1 ~~i~~e~v~~la~LarL~lseee~e~~~~~l~~Il~~veql~evD~~~vep~~~~~~~~-~~lRe 64 (96)
T COG0721 1 MAIDREEVKHLAKLARLELSEEELEKFATQLEDILGYVEQLNEVDTEGVEPTTHPLEVS-NVLRE 64 (96)
T ss_pred CccCHHHHHHHHHHhhcccCHHHHHHHHHHHHHHHHHHHHHHhccccCCCccccccccc-ccccC
Confidence 68999999999999999999999999999999999999999999999999999999887 55553
No 2
>TIGR00135 gatC glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, C subunit. This model has been revised to remove the candidate sequence from Methanococcus jannaschii, now part of a related model.
Probab=99.75 E-value=3.2e-18 Score=118.18 Aligned_cols=62 Identities=27% Similarity=0.471 Sum_probs=58.7
Q ss_pred CChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCccccccccccccCC
Q 033373 58 LEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRADLSALSQRRK 120 (120)
Q Consensus 58 I~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~eVDTe~VePm~hp~e~~~~~~r~ 120 (120)
|++++|+|||+||||+|+++|++.+.++|++|++||++|++|||+||+||+|+.+.. +.||+
T Consensus 1 i~~~~v~~lA~La~L~l~eee~~~~~~~l~~il~~~~~L~~vdt~~v~p~~~~~~~~-~~lRe 62 (93)
T TIGR00135 1 ISDEEVKHLAKLARLELSEEEAESFAGDLDKILGFVEQLNEVDTENVEPMTHPLEIS-NVLRE 62 (93)
T ss_pred CCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHhcCccCCCCcccCccccc-cCCCC
Confidence 689999999999999999999999999999999999999999999999999998776 67774
No 3
>PRK00034 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed
Probab=99.75 E-value=3.8e-18 Score=117.72 Aligned_cols=64 Identities=28% Similarity=0.485 Sum_probs=60.6
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCccccccccccccCC
Q 033373 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRADLSALSQRRK 120 (120)
Q Consensus 56 m~I~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~eVDTe~VePm~hp~e~~~~~~r~ 120 (120)
|+|++++|++||+||||+++++|++.+.++|++|++||++|+++||++|+||+|+.+ ..+.||+
T Consensus 1 M~i~~e~i~~la~La~l~l~~ee~~~~~~~l~~il~~~~~l~~vd~~~vep~~~~~~-~~~~lRe 64 (95)
T PRK00034 1 MAITREEVKHLAKLARLELSEEELEKFAGQLNKILDFVEQLNEVDTEGVEPTTHPLD-MKNVLRE 64 (95)
T ss_pred CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCcccCccc-ccCCCCC
Confidence 689999999999999999999999999999999999999999999999999999987 4677774
No 4
>PRK12821 aspartyl/glutamyl-tRNA amidotransferase subunit C-like protein; Provisional
Probab=99.69 E-value=4.5e-17 Score=140.69 Aligned_cols=65 Identities=20% Similarity=0.339 Sum_probs=62.2
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCccccccccccccCC
Q 033373 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRADLSALSQRRK 120 (120)
Q Consensus 56 m~I~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~eVDTe~VePm~hp~e~~~~~~r~ 120 (120)
+++++|+|+|+|+||||+++|||++++.+||++|++|+|+|++|||+|||||.||.+...+++|+
T Consensus 387 ~~ItkEeVkKLAkLARLeLSEEElEkl~~dLn~ILdyVEkLnEVDTegVEPM~hp~e~~~nvLRE 451 (477)
T PRK12821 387 QQLNKDELKKLARLVMFDLDDAELEKLQVEFKDITSSFKQVEKIDTTNVKPMYAPFSNSPTPLRK 451 (477)
T ss_pred ccCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHcccCcCCCCCcccCcccccCCCCC
Confidence 68999999999999999999999999999999999999999999999999999999777778885
No 5
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=99.41 E-value=3.6e-13 Score=121.51 Aligned_cols=61 Identities=15% Similarity=0.195 Sum_probs=56.5
Q ss_pred CCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCccccccccccccC
Q 033373 57 SLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRADLSALSQRR 119 (120)
Q Consensus 57 ~I~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~eVDTe~VePm~hp~e~~~~~~r 119 (120)
+=.+++|+|||+||||+|+|+|++.++++|++||+||++|++||| +|+||+||++..+ .+|
T Consensus 611 ~~~~~~V~~iA~LARL~l~eeE~~~~~~~L~~IL~~ve~L~evdt-~VeP~~~~~~~~~-~lR 671 (706)
T PRK12820 611 AEKEDLIDHLSWVSRIGFAEAERAAIESALADAEELAAQLEDIAC-DEEPLFSPAPAAN-RMG 671 (706)
T ss_pred ccchHHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhccC-CCCCCcCcccccc-CCC
Confidence 568999999999999999999999999999999999999999999 5999999987665 555
No 6
>PF02686 Glu-tRNAGln: Glu-tRNAGln amidotransferase C subunit; InterPro: IPR003837 Glu-tRNAGln amidotransferase is a heterotrimeric enzyme that is required for correct decoding of glutamine codons during translation. The Glu-tRNA Gln amidotransferase enzyme is an important translational fidelity mechanism replacing incorrectly charged Glu-tRNAGln with the correct Gln-tRANGln via transmidation of the misacylated Glu-tRNAGln []. This activity supplements the lack of glutaminyl-tRNA synthetase activity in Gram-positive eubacteria, cyanobacteria, archaea, and organelles [].; GO: 0006450 regulation of translational fidelity; PDB: 2DQN_C 3IP4_C 2G5I_C 2F2A_C 2G5H_C 2DF4_C 3AL0_C 3KFU_G 3H0R_I 3H0L_U ....
Probab=99.24 E-value=6.4e-12 Score=82.12 Aligned_cols=46 Identities=26% Similarity=0.499 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCccccccccccccCC
Q 033373 74 LTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRADLSALSQRRK 120 (120)
Q Consensus 74 LsEeEle~~~~qLn~IL~~~d~L~eVDTe~VePm~hp~e~~~~~~r~ 120 (120)
|+|+|++.+.++|++|++||++|++|||+||+||+|+.+ ..+.||.
T Consensus 1 l~eeE~~~~~~~l~~il~~~~~l~~vdt~~v~p~~~~~~-~~~~lRe 46 (72)
T PF02686_consen 1 LTEEELEKLTKQLNDILDYVEKLQEVDTEGVEPMYHPVE-MSNPLRE 46 (72)
T ss_dssp --HHHHHHHHHHHHHHHHHHTTGGGS--TT----S-SS--SS--EB-
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCccccccc-ccCCCCC
Confidence 689999999999999999999999999999999999987 6677773
No 7
>TIGR01827 gatC_rel Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase, subunit C, putative. This model represents a family small family related to GatC, the third subunit of an enzyme for completing the charging of tRNA(Gln) by amidating the Glu-tRNA(Gln). The few known archaea that contain a member of this family appear to produce Asn-tRNA(Asn) by an analogous amidotransferase reaction. This protein is proposed to substitute for GatC in the charging of both tRNAs.
Probab=96.69 E-value=0.0019 Score=43.72 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=24.7
Q ss_pred HHHHHHHHH-HHHHhccCCCCCCCCccccccccccccC
Q 033373 83 APKIRQVID-WFGQLQDVDLDSVDPALRADLSALSQRR 119 (120)
Q Consensus 83 ~~qLn~IL~-~~d~L~eVDTe~VePm~hp~e~~~~~~r 119 (120)
.++-..|++ |-++|++|| ||+||+|+.+..+ .||
T Consensus 3 ~~~~~~~~~~~~e~L~evd--~VeP~~~~~~~~n-~lR 37 (73)
T TIGR01827 3 LKEAEEILEEFSERLEDVD--EEEETYYISDGSN-KFR 37 (73)
T ss_pred HHHHHHHHHHHHHHHHccC--CCCCccccccccc-CCC
Confidence 345555654 348899999 9999999986555 555
No 8
>KOG4247 consensus Mitochondrial DNA polymerase accessory subunit [Replication, recombination and repair]
Probab=95.68 E-value=0.019 Score=43.73 Aligned_cols=60 Identities=13% Similarity=0.218 Sum_probs=51.2
Q ss_pred CCCCCCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccccccc
Q 033373 52 TTTRSSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRADLSA 114 (120)
Q Consensus 52 ~~~~m~I~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~eVDTe~VePm~hp~e~~ 114 (120)
.+.|.+|+.+.+.|+..|+-..++.|+. ...|..-+.....|.-||++||+||..+.+..
T Consensus 42 lspmpqidaklinhlerlslvrfdseqa---vanlrssirvakrlelvdvegvepmhtvwedq 101 (175)
T KOG4247|consen 42 LSPMPQIDAKLINHLERLSLVRFDSEQA---VANLRSSIRVAKRLELVDVEGVEPMHTVWEDQ 101 (175)
T ss_pred cCCcchhhHHHHHHHHhhhheeecHHHH---HHHHHHHHhHHhheeeeeccCccchhhhcccc
Confidence 4577889999999999999999988765 56777888888999999999999998776644
No 9
>PF13318 DUF4089: Protein of unknown function (DUF4089)
Probab=84.12 E-value=5.1 Score=25.20 Aligned_cols=41 Identities=10% Similarity=0.101 Sum_probs=37.5
Q ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCC
Q 033373 63 VPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDS 103 (120)
Q Consensus 63 V~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~eVDTe~ 103 (120)
|...+.+--|.|+|+-.+.+..+|..|..+.+.+.+...++
T Consensus 2 v~~~a~llgL~l~~~~r~~V~~n~~ri~~mA~~v~~fpL~~ 42 (50)
T PF13318_consen 2 VDQMAALLGLPLDEEWRPGVVANFERIAAMAQLVMEFPLPD 42 (50)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHcCCCCc
Confidence 56789999999999999999999999999999999988754
No 10
>COG3079 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.48 E-value=6.1 Score=31.32 Aligned_cols=37 Identities=16% Similarity=0.336 Sum_probs=32.0
Q ss_pred hhHHHHHHHHcCCCCCH-HHHHHHHHHHHHHHHHHHHh
Q 033373 60 PPDVPRLAQTARISLTP-HEVEEFAPKIRQVIDWFGQL 96 (120)
Q Consensus 60 keeV~kLA~LARL~LsE-eEle~~~~qLn~IL~~~d~L 96 (120)
.|-++-++++|.+..+| +..++....|.+|++|+...
T Consensus 128 ~EaldDL~~iaQlg~Deded~EE~~~~leEiiEyvRva 165 (186)
T COG3079 128 GEALDDLANIAQLGYDEDEDQEELEESLEEIIEYVRVA 165 (186)
T ss_pred HHHHHHHHHHHHhcCCccccHHHHHHHHHHHHHHHHHH
Confidence 46688899999999988 78889999999999998753
No 11
>PRK02166 hypothetical protein; Reviewed
Probab=67.99 E-value=6 Score=30.86 Aligned_cols=37 Identities=14% Similarity=0.176 Sum_probs=30.1
Q ss_pred ChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033373 59 EPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQ 95 (120)
Q Consensus 59 ~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~ 95 (120)
.+|-++-++..|+++.++++-+.-...+.+|++|+..
T Consensus 126 ~~E~l~Dl~~Iaql~~d~dd~ee~E~al~Ei~EyvRv 162 (184)
T PRK02166 126 AKEVLQDLAAISQVQDALEESEDGETDYMEVMEYLRV 162 (184)
T ss_pred HHHHHHHHHHHHccCCCCCCCchHHHHHHHHHHHHHH
Confidence 4566888999999998877777788889999999863
No 12
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=66.21 E-value=2.5 Score=25.94 Aligned_cols=40 Identities=8% Similarity=0.141 Sum_probs=28.8
Q ss_pred ccccCCCCCCCCCCCChhHHHHHHHHcCCCCCHHHHHHHHH
Q 033373 44 NRTRNCSTTTTRSSLEPPDVPRLAQTARISLTPHEVEEFAP 84 (120)
Q Consensus 44 ~~~r~~s~~~~~m~I~keeV~kLA~LARL~LsEeEle~~~~ 84 (120)
+.++.+.+... ..|+.+|+..+........++++.+....
T Consensus 4 ~~F~~~D~d~~-G~i~~~el~~~~~~~~~~~~~~~~~~~~~ 43 (66)
T PF13499_consen 4 EAFKKFDKDGD-GYISKEELRRALKHLGRDMSDEESDEMID 43 (66)
T ss_dssp HHHHHHSTTSS-SEEEHHHHHHHHHHTTSHSTHHHHHHHHH
T ss_pred HHHHHHcCCcc-CCCCHHHHHHHHHHhcccccHHHHHHHHH
Confidence 33444555443 48999999999999998888777766433
No 13
>PRK07235 amidase; Provisional
Probab=62.14 E-value=13 Score=32.62 Aligned_cols=51 Identities=14% Similarity=0.330 Sum_probs=42.3
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCc
Q 033373 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPA 107 (120)
Q Consensus 56 m~I~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~eVDTe~VePm 107 (120)
...++++++.+|.--.++|.+++++.+..-++.-++-+|.++++ .+-+++.
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 54 (502)
T PRK07235 4 KRPTLEQLREIAAQFGLDLTDEELASYLSLMQASLDAYDRIDEL-PDEIPPV 54 (502)
T ss_pred CCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHhccCHHHHHHHH-hhccccc
Confidence 45789999999999999999999999999999888888887777 3444443
No 14
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=60.42 E-value=13 Score=22.02 Aligned_cols=31 Identities=16% Similarity=0.267 Sum_probs=25.8
Q ss_pred CCCChhHHHHHHHHcCCC-CCHHHHHHHHHHH
Q 033373 56 SSLEPPDVPRLAQTARIS-LTPHEVEEFAPKI 86 (120)
Q Consensus 56 m~I~keeV~kLA~LARL~-LsEeEle~~~~qL 86 (120)
..|+.+++.++...-.+. ++++|++.+...+
T Consensus 3 G~i~~~~~~~~l~~~g~~~~s~~e~~~l~~~~ 34 (54)
T PF13833_consen 3 GKITREEFRRALSKLGIKDLSEEEVDRLFREF 34 (54)
T ss_dssp SEEEHHHHHHHHHHTTSSSSCHHHHHHHHHHH
T ss_pred CEECHHHHHHHHHHhCCCCCCHHHHHHHHHhc
Confidence 368899999999777888 9999998887655
No 15
>PRK04758 hypothetical protein; Validated
Probab=60.13 E-value=12 Score=29.24 Aligned_cols=37 Identities=16% Similarity=0.174 Sum_probs=29.6
Q ss_pred ChhHHHHHHHHcCCCCCH-HHHHHHHHHHHHHHHHHHH
Q 033373 59 EPPDVPRLAQTARISLTP-HEVEEFAPKIRQVIDWFGQ 95 (120)
Q Consensus 59 ~keeV~kLA~LARL~LsE-eEle~~~~qLn~IL~~~d~ 95 (120)
.+|-++-++..|++++++ ++-+.-...+.+|++|+..
T Consensus 124 ~~E~L~Dl~~Iaql~~d~~ed~ee~E~al~El~EyvRv 161 (181)
T PRK04758 124 GEEALQDLARLAQASSDDFDAAEEDDTALAEIEEFVRV 161 (181)
T ss_pred HHHHHHHHHHHHccCCCcccCchHHHHHHHHHHHHHHH
Confidence 456788899999999874 4557788899999999863
No 16
>PRK01736 hypothetical protein; Reviewed
Probab=59.03 E-value=13 Score=28.94 Aligned_cols=36 Identities=19% Similarity=0.368 Sum_probs=29.7
Q ss_pred hhHHHHHHHHcCCCCCH-HHHHHHHHHHHHHHHHHHH
Q 033373 60 PPDVPRLAQTARISLTP-HEVEEFAPKIRQVIDWFGQ 95 (120)
Q Consensus 60 keeV~kLA~LARL~LsE-eEle~~~~qLn~IL~~~d~ 95 (120)
+|-|+-++.+|++++++ ++-+.....+.+|++|+..
T Consensus 129 ~E~l~Dl~~Ia~~~~d~~ed~ee~e~~~~Ei~EyvR~ 165 (190)
T PRK01736 129 GEAIDDLRNIAQLGYDEDEDQEELAQSLEEVIEYVRV 165 (190)
T ss_pred HHHHHHHHHHHhcCCCccccchHHHHHHHHHHHHHHH
Confidence 67788999999999874 4567888899999999863
No 17
>PF07128 DUF1380: Protein of unknown function (DUF1380); InterPro: IPR009811 This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be specific to Enterobacteria. The function of this family is unknown.
Probab=58.68 E-value=12 Score=28.36 Aligned_cols=44 Identities=20% Similarity=0.237 Sum_probs=34.4
Q ss_pred ccCCCCCCCC--CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Q 033373 46 TRNCSTTTTR--SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQV 89 (120)
Q Consensus 46 ~r~~s~~~~~--m~I~keeV~kLA~LARL~LsEeEle~~~~qLn~I 89 (120)
.+-|...+.- --.|++||..+|.=.-.+++|+|++.+..++.++
T Consensus 13 ~~~y~~dE~l~LlIWT~eDV~~~a~gme~~lTd~E~~aVL~~I~~~ 58 (139)
T PF07128_consen 13 KRDYPNDEPLALLIWTREDVRALADGMEYNLTDDEARAVLARIGDI 58 (139)
T ss_pred HHhCCCCCeeEEEEecHHHHHHHHhcCCCCCCHHHHHHHHHHHhcC
Confidence 3455555533 3469999999999778999999999999888776
No 18
>PF05397 Med15_fungi: Mediator complex subunit 15; InterPro: IPR008626 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family represents subunit 15 of the Mediator complex in fungi. It contains Saccharomyces cerevisiae GAL11 (Med15) protein. Gal11 (Med15) and Sin4 (Med16) proteins are S. cerevisiae global transcription factors that regulate transcription of a variety of genes, both positively and negatively. Gal11, in a major part, functions in the activation of transcription, whereas Sin4 has an opposite role [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=51.95 E-value=10 Score=27.36 Aligned_cols=33 Identities=12% Similarity=0.426 Sum_probs=27.0
Q ss_pred HHHcCCC--CCHHHHHHHHHHHHHHHHHHHHhccC
Q 033373 67 AQTARIS--LTPHEVEEFAPKIRQVIDWFGQLQDV 99 (120)
Q Consensus 67 A~LARL~--LsEeEle~~~~qLn~IL~~~d~L~eV 99 (120)
-.|.-+. +++||...+.+++.++.+++..++.+
T Consensus 20 ~~l~~v~~~ls~eeK~~i~~~l~~~~~m~~~vd~l 54 (115)
T PF05397_consen 20 VRLSPVTNSLSPEEKAAIRQQLQEIQDMLARVDSL 54 (115)
T ss_pred CCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666 99999999999999999998887653
No 19
>PF11181 YflT: Heat induced stress protein YflT
Probab=45.43 E-value=20 Score=24.76 Aligned_cols=23 Identities=17% Similarity=0.381 Sum_probs=20.4
Q ss_pred HHHHcCCCCCHHHHHHHHHHHHH
Q 033373 66 LAQTARISLTPHEVEEFAPKIRQ 88 (120)
Q Consensus 66 LA~LARL~LsEeEle~~~~qLn~ 88 (120)
-+.|.+++|+++|.+.+.+++.+
T Consensus 74 ~~~l~~lGl~~~ea~~y~~~l~~ 96 (103)
T PF11181_consen 74 RSKLESLGLSEDEAERYEEELDQ 96 (103)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHC
Confidence 38899999999999999998863
No 20
>KOG0030 consensus Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=42.25 E-value=20 Score=27.70 Aligned_cols=46 Identities=20% Similarity=0.215 Sum_probs=37.6
Q ss_pred cccccccCCCCCCCCCCCChhHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 033373 41 DYNNRTRNCSTTTTRSSLEPPDVPRLAQTARISLTPHEVEEFAPKIR 87 (120)
Q Consensus 41 ~~~~~~r~~s~~~~~m~I~keeV~kLA~LARL~LsEeEle~~~~qLn 87 (120)
++-+++|+|++.++. .|.-.+++||.---==.++|+|++.+..--.
T Consensus 89 dfvegLrvFDkeg~G-~i~~aeLRhvLttlGekl~eeEVe~Llag~e 134 (152)
T KOG0030|consen 89 DFVEGLRVFDKEGNG-TIMGAELRHVLTTLGEKLTEEEVEELLAGQE 134 (152)
T ss_pred HHHHHHHhhcccCCc-ceeHHHHHHHHHHHHhhccHHHHHHHHcccc
Confidence 567889999998877 6788899999877777899999998875433
No 21
>PF09677 TrbI_Ftype: Type-F conjugative transfer system protein (TrbI_Ftype); InterPro: IPR014115 This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm [, ].
Probab=38.96 E-value=61 Score=23.33 Aligned_cols=28 Identities=36% Similarity=0.472 Sum_probs=23.9
Q ss_pred HHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 033373 65 RLAQTARISLTPHEVEEFAPKIRQVIDW 92 (120)
Q Consensus 65 kLA~LARL~LsEeEle~~~~qLn~IL~~ 92 (120)
.+..+++-+++|+|.+....+|+..|+-
T Consensus 45 f~~~~a~~~lt~~q~~a~t~~F~~aL~~ 72 (111)
T PF09677_consen 45 FVQQLARSSLTPEQVEALTQRFMQALEA 72 (111)
T ss_pred HHHHHhccCCCHHHHHHHHHHHHHHHHH
Confidence 4666889999999999999999888853
No 22
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase. Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Probab=38.79 E-value=43 Score=29.65 Aligned_cols=81 Identities=14% Similarity=0.146 Sum_probs=53.7
Q ss_pred CCceeecccCCccCCCCCCcccccc--cccccccccCCCCCCCCCCCChhHHHHHHH--HcCCCC-----CHHHHHHHHH
Q 033373 14 PKHHIFNNTKGSIFSSKMPTRYYYY--DYDYNNRTRNCSTTTTRSSLEPPDVPRLAQ--TARISL-----TPHEVEEFAP 84 (120)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~r~~s~~~~~m~I~keeV~kLA~--LARL~L-----sEeEle~~~~ 84 (120)
.|+|+|-+=--= .+-|-+--|-+ ||.+-=..=+|-|.|+| +++|+++|.+ |+.|.+ +++-..++..
T Consensus 85 ~N~C~FCFidQl--P~gmR~sLY~KDDDyRLSFL~GnyiTLTNl---~~~d~~RI~~~~lspl~iSVhat~p~lR~~ll~ 159 (433)
T TIGR03279 85 NNRCPFCFIDQQ--PPGKRESLYLKDDDYRLSFLYGSYLTLTNL---PPAEWQRIEQLRLSPLYVSVHATEPSLRARLLK 159 (433)
T ss_pred CCcCceEeccCC--CCCCcCcceeccCcchhhhhccceeeecCC---CHHHHHHHHHcCCCCEEEEEecCCHHHHHHHhC
Confidence 488886433222 22333345555 66666677788888887 9999999985 666665 5777777764
Q ss_pred H--HHHHHHHHHHhccC
Q 033373 85 K--IRQVIDWFGQLQDV 99 (120)
Q Consensus 85 q--Ln~IL~~~d~L~eV 99 (120)
. -.++++.++.|.+-
T Consensus 160 n~~a~~il~~l~~l~~~ 176 (433)
T TIGR03279 160 NPRAGLILEQLKWFQER 176 (433)
T ss_pred CCCHHHHHHHHHHHHHc
Confidence 3 66777777777554
No 23
>PRK13717 conjugal transfer protein TrbI; Provisional
Probab=38.24 E-value=63 Score=24.29 Aligned_cols=29 Identities=3% Similarity=0.183 Sum_probs=24.4
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 033373 64 PRLAQTARISLTPHEVEEFAPKIRQVIDW 92 (120)
Q Consensus 64 ~kLA~LARL~LsEeEle~~~~qLn~IL~~ 92 (120)
..+..++..+++|++.+.+++.|+..|+-
T Consensus 58 ~F~~Q~~~~~lte~q~e~lt~rF~~aL~~ 86 (128)
T PRK13717 58 AFFDSASQKQLSEAQSKALSARFNTALEA 86 (128)
T ss_pred HHHHHHhccCCCHHHHHHHHHHHHHHHHH
Confidence 34667789999999999999999888763
No 24
>PF06580 His_kinase: Histidine kinase; InterPro: IPR010559 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This family represents a region within bacterial histidine kinase enzymes. Two-component signal transduction systems such as those mediated by histidine kinase are integral parts of bacterial cellular regulatory processes, and are used to regulate the expression of genes involved in virulence. Members of this family often contain IPR003594 from INTERPRO and/or IPR003660 from INTERPRO.; GO: 0000155 two-component sensor activity, 0000160 two-component signal transduction system (phosphorelay), 0016021 integral to membrane
Probab=35.27 E-value=93 Score=20.52 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=26.3
Q ss_pred hHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHH
Q 033373 61 PDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFG 94 (120)
Q Consensus 61 eeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d 94 (120)
..+..|..+++.+ .++...+...|.+++.|.=
T Consensus 16 NtLn~I~~l~~~~--~~~~~~~i~~ls~~lRy~l 47 (82)
T PF06580_consen 16 NTLNSISWLARID--PEKASEMILSLSDLLRYSL 47 (82)
T ss_pred HHHHHHHHHHHcC--HHHHHHHHHHHHHHHHHHh
Confidence 4567788888888 8888899999999888864
No 25
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=34.27 E-value=67 Score=25.01 Aligned_cols=30 Identities=23% Similarity=0.324 Sum_probs=25.5
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHhccC
Q 033373 70 ARISLTPHEVEEFAPKIRQVIDWFGQLQDV 99 (120)
Q Consensus 70 ARL~LsEeEle~~~~qLn~IL~~~d~L~eV 99 (120)
+.-.|+|+|.+++..+|.++-+-+..|.+|
T Consensus 22 ~~~~LsEeE~eeLr~EL~KvEeEI~TLrqv 51 (162)
T PF04201_consen 22 SEEGLSEEEREELRSELAKVEEEIQTLRQV 51 (162)
T ss_pred CcccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346899999999999999998888887765
No 26
>PF10256 Erf4: Golgin subfamily A member 7/ERF4 family; InterPro: IPR019383 Proteins in this entry include Golgin subfamily A member 7 and the Ras modification protein ERF4.
Probab=32.92 E-value=93 Score=21.64 Aligned_cols=23 Identities=26% Similarity=0.433 Sum_probs=18.9
Q ss_pred HcCCCCCHHHHHHHHHHHHHHHHH
Q 033373 69 TARISLTPHEVEEFAPKIRQVIDW 92 (120)
Q Consensus 69 LARL~LsEeEle~~~~qLn~IL~~ 92 (120)
|... ++++|-+.+..++|+++.-
T Consensus 26 L~~~-is~~ef~~iI~~IN~~l~~ 48 (118)
T PF10256_consen 26 LSGY-ISPEEFEEIINTINQILKE 48 (118)
T ss_pred hcCC-CCHHHHHHHHHHHHHHHHH
Confidence 5555 9999999999999998653
No 27
>TIGR02744 TrbI_Ftype type-F conjugative transfer system protein TrbI. This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm.
Probab=32.54 E-value=87 Score=22.88 Aligned_cols=27 Identities=4% Similarity=0.197 Sum_probs=23.3
Q ss_pred HHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 033373 65 RLAQTARISLTPHEVEEFAPKIRQVID 91 (120)
Q Consensus 65 kLA~LARL~LsEeEle~~~~qLn~IL~ 91 (120)
.+..++.-+++|+|.+.+.+.|+..|+
T Consensus 46 F~~q~~~~~lte~q~~~~~~rF~~~L~ 72 (112)
T TIGR02744 46 FFDSASQKKLSEAQQKALLGRFNALLE 72 (112)
T ss_pred HHHHHhhcCCCHHHHHHHHHHHHHHHH
Confidence 345578999999999999999999884
No 28
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=32.40 E-value=29 Score=27.44 Aligned_cols=42 Identities=14% Similarity=0.254 Sum_probs=32.6
Q ss_pred CCCChhHHHHHH--------------------HHcCCCCCHHHHHHHHHHHHHHHHHHHHhc
Q 033373 56 SSLEPPDVPRLA--------------------QTARISLTPHEVEEFAPKIRQVIDWFGQLQ 97 (120)
Q Consensus 56 m~I~keeV~kLA--------------------~LARL~LsEeEle~~~~qLn~IL~~~d~L~ 97 (120)
..||++.+..+. .+|||+++++|...+......|.+.+..+.
T Consensus 177 ~~it~~~l~~v~~~E~~l~~~g~~~~rvr~~~~~a~ie~~~~~~~~~~~~~~~i~~~~~~~g 238 (252)
T TIGR00268 177 REIDEEKLKMVDEAEEVLRNAGVGQVRVRNYDNLAVIEVPEDELSKLLNEAEEVRDKFKDIG 238 (252)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCeEEEEecCCeEEEEECHHHHHHHHhhHHHHHHHHHHcC
Confidence 568877776654 479999999999999988777777766553
No 29
>PF09754 PAC2: PAC2 family; InterPro: IPR019151 This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome, which is about 2000 kilodaltons (kDa) in molecular mass and contains one 20S core particle structure and two 19S regulatory caps. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits [, , , ].; PDB: 3MNF_A 2P90_B 3E35_A 3GAA_D 2WAM_C.
Probab=31.84 E-value=86 Score=23.61 Aligned_cols=40 Identities=18% Similarity=0.238 Sum_probs=32.0
Q ss_pred ChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhcc
Q 033373 59 EPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQD 98 (120)
Q Consensus 59 ~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~e 98 (120)
...-++.+.++..+.++=+++++-.+++.+|.+++++|+|
T Consensus 180 A~~ll~~l~~~~~~~id~~~l~~ead~~~e~~~~~~~l~e 219 (219)
T PF09754_consen 180 AARLLEALSKLLGLKIDLSDLEEEADNIEEAEEMVEQLEE 219 (219)
T ss_dssp HHHHHHHHHHHHT---HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhCceeeHHHHHHhcCCHHHHHHHHHHhcC
Confidence 4567899999999999989999999888899999998875
No 30
>PRK06474 hypothetical protein; Provisional
Probab=31.84 E-value=46 Score=25.34 Aligned_cols=26 Identities=19% Similarity=0.388 Sum_probs=21.8
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033373 70 ARISLTPHEVEEFAPKIRQVIDWFGQ 95 (120)
Q Consensus 70 ARL~LsEeEle~~~~qLn~IL~~~d~ 95 (120)
..|.+++||.++|.++|.++++=...
T Consensus 132 ~~L~Lt~ee~~el~~el~~ll~~y~~ 157 (178)
T PRK06474 132 VELKLDEEEFEEFQSELNELMIKYYN 157 (178)
T ss_pred eeEecCHHHHHHHHHHHHHHHHHHHh
Confidence 35779999999999999998876643
No 31
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=31.75 E-value=67 Score=21.22 Aligned_cols=29 Identities=14% Similarity=0.196 Sum_probs=25.8
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHH
Q 033373 56 SSLEPPDVPRLAQTARISLTPHEVEEFAP 84 (120)
Q Consensus 56 m~I~keeV~kLA~LARL~LsEeEle~~~~ 84 (120)
..++.+++..|-.|+-+.++.+|+..+..
T Consensus 12 l~l~d~~m~~if~l~~~~vs~~el~a~lr 40 (68)
T PF07308_consen 12 LDLKDDDMIEIFALAGFEVSKAELSAWLR 40 (68)
T ss_pred HcCChHHHHHHHHHcCCccCHHHHHHHHC
Confidence 46789999999999999999999988764
No 32
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=31.69 E-value=1.4e+02 Score=19.64 Aligned_cols=37 Identities=16% Similarity=0.257 Sum_probs=24.5
Q ss_pred CCCCChhHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHH
Q 033373 55 RSSLEPPDVPRLAQTARI-SLTPHEVEEFAPKIRQVID 91 (120)
Q Consensus 55 ~m~I~keeV~kLA~LARL-~LsEeEle~~~~qLn~IL~ 91 (120)
|..++.+.|+-+|.-.-| +++|+-...++++.+--+.
T Consensus 1 ~s~~~~esvk~iAes~Gi~~l~de~a~~La~dveyrlr 38 (66)
T PF02969_consen 1 MSVFSQESVKDIAESLGISNLSDEAAKALAEDVEYRLR 38 (66)
T ss_dssp -----HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHH
T ss_pred CCcCCHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Confidence 345788999999999999 8999999998888765443
No 33
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=29.53 E-value=80 Score=20.01 Aligned_cols=30 Identities=20% Similarity=0.341 Sum_probs=23.9
Q ss_pred CChhHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 033373 58 LEPPDVPRLAQTARISLTPHEVEEFAPKIR 87 (120)
Q Consensus 58 I~keeV~kLA~LARL~LsEeEle~~~~qLn 87 (120)
.+.+++-.||+=.-++++++|++....+|+
T Consensus 25 ~~~e~~~~lA~~~Gf~ft~~el~~~~~els 54 (64)
T TIGR03798 25 EDPEDRVAIAKEAGFEFTGEDLKEAGEELS 54 (64)
T ss_pred CCHHHHHHHHHHcCCCCCHHHHHHHHhhCC
Confidence 367889999999999999999987554443
No 34
>TIGR03544 DivI1A_domain DivIVA domain. This model describes a domain found in Bacillus subtilis cell division initiation protein DivIVA, and homologs, toward the N-terminus. It is also found as a repeated domain in certain other proteins, including family TIGR03543.
Probab=29.14 E-value=83 Score=17.75 Aligned_cols=30 Identities=17% Similarity=0.389 Sum_probs=18.2
Q ss_pred ChhHHHHHHHHcCC-CCCHHHHHHHHHHHHH
Q 033373 59 EPPDVPRLAQTARI-SLTPHEVEEFAPKIRQ 88 (120)
Q Consensus 59 ~keeV~kLA~LARL-~LsEeEle~~~~qLn~ 88 (120)
++++|+...-=..+ +.+++|++.+..++.+
T Consensus 2 t~~dIr~~~F~~~~rGY~~~eVD~fLd~v~~ 32 (34)
T TIGR03544 2 TPEDIRNKRFKKKLRGYDAAEVDAFLDRVAD 32 (34)
T ss_pred CHHHHhhCcCCCCCCCCCHHHHHHHHHHHHH
Confidence 44444444332222 6788888888887754
No 35
>PF02413 Caudo_TAP: Caudovirales tail fibre assembly protein; InterPro: IPR003458 This family contains Bacteriophage T4 gp38 and related bacterial prophage and phage proteins. Gene 38 of phage T4 codes for a protein containing 183 amino acid residues with molecular weight of 22.3 kDa. Together with genes 36 and 37, whose products are structural proteins of the fibre distal part, gene 38 forms one transcription unit. Gp38, is a chaperone, which is required for assembly of the distal part of the long fibres and which is absent from the mature phage particle. In the absence of gp38 gp37, which is a component of the distal part of the long tail fibre, fails to oligomerise. The carboxy-terminal region of gp37 forms the tip of the distal fibre that interacts with the cell receptors. Functionally the role of gp38 can be replaced by pTfa of Bacteriophage lambda [, , ]. The function of many of the other members of this family remain to be elucidated.
Probab=28.62 E-value=1.1e+02 Score=21.80 Aligned_cols=33 Identities=15% Similarity=0.105 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccc
Q 033373 74 LTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRA 110 (120)
Q Consensus 74 LsEeEle~~~~qLn~IL~~~d~L~eVDTe~VePm~hp 110 (120)
++++|. ..|..-..|...|+.||++..+-...|
T Consensus 94 atd~e~----~~L~~Wk~Yrv~L~rvD~s~apdI~WP 126 (130)
T PF02413_consen 94 ATDEEK----ARLKAWKKYRVALNRVDTSTAPDIDWP 126 (130)
T ss_pred CChHHH----HHHHHHHHHHHHHhccCCCCCCCCCCC
Confidence 356663 677788899999999999886544444
No 36
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=28.36 E-value=1.3e+02 Score=21.97 Aligned_cols=44 Identities=9% Similarity=0.215 Sum_probs=35.1
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHH--HHHH----HHHhccC
Q 033373 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQ--VIDW----FGQLQDV 99 (120)
Q Consensus 56 m~I~keeV~kLA~LARL~LsEeEle~~~~qLn~--IL~~----~d~L~eV 99 (120)
-.+|.++|++|.+-+-++++++.++.|.+.|+. |-+. .++|..|
T Consensus 18 ~~pTaddI~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~sv 67 (112)
T PTZ00373 18 ENPTKKEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNI 67 (112)
T ss_pred CCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcc
Confidence 468999999999999999999999999987643 3333 3566666
No 37
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=28.05 E-value=89 Score=22.16 Aligned_cols=39 Identities=18% Similarity=0.194 Sum_probs=28.8
Q ss_pred CCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhc
Q 033373 57 SLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQ 97 (120)
Q Consensus 57 ~I~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~ 97 (120)
.++.++.+-+..+.. +++++.+.+...+...+++++.+-
T Consensus 84 ~l~~~~~~ll~~~~~--L~~~~~~~~l~~l~~~~~~~~~~~ 122 (135)
T PRK09706 84 ELSEDQKELLELFDA--LPESEQDAQLSEMRARVENFNKLF 122 (135)
T ss_pred CCCHHHHHHHHHHHH--CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 456655444444443 789999999999999999998763
No 38
>PRK10870 transcriptional repressor MprA; Provisional
Probab=27.96 E-value=1e+02 Score=23.17 Aligned_cols=28 Identities=14% Similarity=0.346 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHhccCC
Q 033373 73 SLTPHEVEEFAPKIRQVIDWFGQLQDVD 100 (120)
Q Consensus 73 ~LsEeEle~~~~qLn~IL~~~d~L~eVD 100 (120)
.++++|.+.+..-|+.+.+.++.+.+-|
T Consensus 142 ~ls~~e~~~l~~~L~kl~~~l~~~~~~~ 169 (176)
T PRK10870 142 ALSTTEKDQLEQITRKLLSRLDQMEQDG 169 (176)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHhhCCCc
Confidence 6899999999999999998888765543
No 39
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=26.30 E-value=1.2e+02 Score=21.61 Aligned_cols=31 Identities=19% Similarity=0.351 Sum_probs=28.6
Q ss_pred CCChhHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 033373 57 SLEPPDVPRLAQTARISLTPHEVEEFAPKIR 87 (120)
Q Consensus 57 ~I~keeV~kLA~LARL~LsEeEle~~~~qLn 87 (120)
.+|.++|++|.+-+-++++++-+..|.+.|.
T Consensus 16 ~~ta~~I~~IL~aaGveVe~~~~~~~~~aLa 46 (105)
T cd04411 16 ELTEDKIKELLSAAGAEIEPERVKLFLSALN 46 (105)
T ss_pred CCCHHHHHHHHHHcCCCcCHHHHHHHHHHHc
Confidence 4899999999999999999999999998853
No 40
>COG1103 Archaea-specific pyridoxal phosphate-dependent enzymes [General function prediction only]
Probab=25.93 E-value=46 Score=28.82 Aligned_cols=45 Identities=11% Similarity=0.202 Sum_probs=34.8
Q ss_pred cccccc----cccccccccCCCCCCCCCCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 033373 33 TRYYYY----DYDYNNRTRNCSTTTTRSSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVID 91 (120)
Q Consensus 33 ~~~~~~----~~~~~~~~r~~s~~~~~m~I~keeV~kLA~LARL~LsEeEle~~~~qLn~IL~ 91 (120)
++||-| .++||-+.|+++-- -+|+-..+++||++.....|.+|++
T Consensus 331 ~gyFlY~ELK~RgI~GI~~G~Tk~--------------~K~svyGl~~Eqve~V~~afkeI~e 379 (382)
T COG1103 331 KGYFLYEELKKRGIHGIQPGQTKY--------------FKLSVYGLSWEQVEYVVDAFKEIAE 379 (382)
T ss_pred CceeeHHHHHhcCccccccCceeE--------------EEEEeecCCHHHHHHHHHHHHHHHH
Confidence 478877 89999999998641 2356677888888888888888875
No 41
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=24.93 E-value=69 Score=19.41 Aligned_cols=12 Identities=17% Similarity=0.432 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHh
Q 033373 85 KIRQVIDWFGQL 96 (120)
Q Consensus 85 qLn~IL~~~d~L 96 (120)
|+.+|++|+..|
T Consensus 79 e~~~l~ayl~sl 90 (91)
T PF00034_consen 79 EIADLAAYLRSL 90 (91)
T ss_dssp HHHHHHHHHHHT
T ss_pred HHHHHHHHHHHh
Confidence 345566666655
No 42
>COG1071 AcoA Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]
Probab=24.46 E-value=3e+02 Score=23.84 Aligned_cols=61 Identities=10% Similarity=0.112 Sum_probs=38.2
Q ss_pred cCCCCCCCCCCCChhHHHHHHH----------HcCCC-CCHHHHHHHHHHHHHHHHH-HHHhccCCCCCCCCc
Q 033373 47 RNCSTTTTRSSLEPPDVPRLAQ----------TARIS-LTPHEVEEFAPKIRQVIDW-FGQLQDVDLDSVDPA 107 (120)
Q Consensus 47 r~~s~~~~~m~I~keeV~kLA~----------LARL~-LsEeEle~~~~qLn~IL~~-~d~L~eVDTe~VePm 107 (120)
++++++....--++++++.-.. |-... ++|+|++.+.++..++++- ++.-....--+++.+
T Consensus 265 ~HS~sDd~~~YRskeE~~~~~~~DPi~r~~~~L~~~g~~see~~~~i~~e~~~~V~ea~e~a~~~p~P~~~~~ 337 (358)
T COG1071 265 GHSTSDDPSKYRSKEEVEEWKKRDPIVRLRKYLIEAGILSEEELEAIEAEAKAEVDEAVEFAEASPYPDVSEL 337 (358)
T ss_pred CCCCCCCccccCCHHHHHHHhccChHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCChhHh
Confidence 3444444233347888776653 44444 8999999999999888876 555555443333333
No 43
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=24.00 E-value=1.8e+02 Score=20.15 Aligned_cols=34 Identities=26% Similarity=0.549 Sum_probs=22.4
Q ss_pred CCChhHHHHHHH-HcCCC-CCHHHHHHHHHHHHHHH
Q 033373 57 SLEPPDVPRLAQ-TARIS-LTPHEVEEFAPKIRQVI 90 (120)
Q Consensus 57 ~I~keeV~kLA~-LARL~-LsEeEle~~~~qLn~IL 90 (120)
.+++++|++|+. .++|. ++.++++.+..+|.+..
T Consensus 29 ~l~~~ei~~i~~~ma~l~~v~~~~~~~Vl~EF~~~~ 64 (108)
T PF14842_consen 29 HLDEEEIERISREMAKLGSVSPEEVEEVLEEFYDEI 64 (108)
T ss_dssp HS-HHHHHHHHHHHHT-----HHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 467888888864 67776 78999999888888743
No 44
>PF14069 SpoVIF: Stage VI sporulation protein F
Probab=23.77 E-value=1.6e+02 Score=20.22 Aligned_cols=25 Identities=8% Similarity=0.183 Sum_probs=18.9
Q ss_pred hHHHHHHHHcCCCCCHHHHHHHHHH
Q 033373 61 PDVPRLAQTARISLTPHEVEEFAPK 85 (120)
Q Consensus 61 eeV~kLA~LARL~LsEeEle~~~~q 85 (120)
.-|+.+|.+|.-.++++..+.+.+.
T Consensus 35 ~lIk~vs~~an~~Vs~~~ed~IV~~ 59 (79)
T PF14069_consen 35 QLIKQVSQIANKPVSKEQEDQIVQA 59 (79)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 4467778888888888888777654
No 45
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=23.56 E-value=93 Score=22.47 Aligned_cols=33 Identities=9% Similarity=0.305 Sum_probs=29.6
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 033373 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQ 88 (120)
Q Consensus 56 m~I~keeV~kLA~LARL~LsEeEle~~~~qLn~ 88 (120)
..||.++|+.|..-+-+++++.....|...|+.
T Consensus 15 ~eITae~I~~IL~AAGveVd~~~~~ala~aL~g 47 (106)
T cd05832 15 KEINEENLKKVLEAAGIEVDEARVKALVAALEE 47 (106)
T ss_pred CCCCHHHHHHHHHHhCCcccHHHHHHHHHHHcC
Confidence 379999999999999999999999999888764
No 46
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=23.31 E-value=55 Score=22.64 Aligned_cols=45 Identities=9% Similarity=0.008 Sum_probs=36.3
Q ss_pred HcCCCCCHHHHHHHHHHHHHHHHHHH-HhccCCCCCCCCccccccc
Q 033373 69 TARISLTPHEVEEFAPKIRQVIDWFG-QLQDVDLDSVDPALRADLS 113 (120)
Q Consensus 69 LARL~LsEeEle~~~~qLn~IL~~~d-~L~eVDTe~VePm~hp~e~ 113 (120)
+.+=+++|++++.+.+.+.+++.-.. .+.++|.=|...+++|+..
T Consensus 13 Il~p~l~e~~~~~~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~I~k 58 (97)
T CHL00123 13 LLKPDLNEEELLKWIENYKKLLRKRGAKNISVQNRGKRKLSYKINK 58 (97)
T ss_pred EECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecCeeeeEEcCC
Confidence 34567899999999999999987764 6777888888888888764
No 47
>PRK01546 hypothetical protein; Provisional
Probab=23.15 E-value=1.3e+02 Score=20.84 Aligned_cols=24 Identities=33% Similarity=0.289 Sum_probs=15.5
Q ss_pred CChhHHHHHHHHcCC----CCCHHHHHH
Q 033373 58 LEPPDVPRLAQTARI----SLTPHEVEE 81 (120)
Q Consensus 58 I~keeV~kLA~LARL----~LsEeEle~ 81 (120)
++++.+.+|=.||+. +|+++|.++
T Consensus 2 ~~~~~i~RINeLakK~K~~gLT~eEk~E 29 (79)
T PRK01546 2 LSHELVERINFLAKKAKAEGLTEEEQRE 29 (79)
T ss_pred CcHHHHHHHHHHHHhhcccCCCHHHHHH
Confidence 455666666666665 578887653
No 48
>COG2047 Uncharacterized protein (ATP-grasp superfamily) [General function prediction only]
Probab=23.08 E-value=1.8e+02 Score=24.25 Aligned_cols=38 Identities=16% Similarity=0.303 Sum_probs=33.3
Q ss_pred hHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhcc
Q 033373 61 PDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQD 98 (120)
Q Consensus 61 eeV~kLA~LARL~LsEeEle~~~~qLn~IL~~~d~L~e 98 (120)
.-++.+++.--|+++.+.++.=++++.+|++-++.+.+
T Consensus 203 aVL~vl~k~lgiEid~~~Le~RAke~E~ii~k~~emee 240 (258)
T COG2047 203 AVLEVLCKMLGIEIDMEALEERAKEMEEIIEKLKEMEE 240 (258)
T ss_pred HHHHHHHHHhCceecHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999999999999988877743
No 49
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=22.33 E-value=81 Score=21.20 Aligned_cols=41 Identities=10% Similarity=0.098 Sum_probs=28.8
Q ss_pred ccCCCCCCCCC-CCChhHHHHHHHH-----cCCCCCHHHHHHHHHHH
Q 033373 46 TRNCSTTTTRS-SLEPPDVPRLAQT-----ARISLTPHEVEEFAPKI 86 (120)
Q Consensus 46 ~r~~s~~~~~m-~I~keeV~kLA~L-----ARL~LsEeEle~~~~qL 86 (120)
++-|+...+.- .|+.++++.+..- .-...++++++.+.+++
T Consensus 14 F~~fD~~dgdG~~I~~~eL~~ll~~~~~~~lg~~~~~~~v~~~i~~~ 60 (88)
T cd05027 14 FHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETL 60 (88)
T ss_pred HHHhcccCCCcCEECHHHHHHHHHHHhHHHhcCCCCHHHHHHHHHHh
Confidence 34455322333 5999999999986 66678888888887755
No 50
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=22.11 E-value=1.4e+02 Score=19.43 Aligned_cols=27 Identities=22% Similarity=0.235 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHhccCCCCCCCC
Q 033373 80 EEFAPKIRQVIDWFGQLQDVDLDSVDP 106 (120)
Q Consensus 80 e~~~~qLn~IL~~~d~L~eVDTe~VeP 106 (120)
.++.++|++.++....=..||++.++|
T Consensus 31 ~R~~K~~~~~I~~~~aG~pVd~~~lP~ 57 (59)
T smart00685 31 LRIAKQFDDAIKAARAGRPVDLSELPP 57 (59)
T ss_pred HHHHhhHHHHHHHHHCCCCCChhcCCC
Confidence 345678888888888888999999886
No 51
>PRK02539 hypothetical protein; Provisional
Probab=22.08 E-value=1.3e+02 Score=21.09 Aligned_cols=23 Identities=30% Similarity=0.486 Sum_probs=15.1
Q ss_pred ChhHHHHHHHHcCC----CCCHHHHHH
Q 033373 59 EPPDVPRLAQTARI----SLTPHEVEE 81 (120)
Q Consensus 59 ~keeV~kLA~LARL----~LsEeEle~ 81 (120)
+++.|.+|=.||+. +|+++|.++
T Consensus 2 ~~~~I~RINeLakK~K~~gLT~eEk~E 28 (85)
T PRK02539 2 DPKKIARINELAKKKKTEGLTGEEKVE 28 (85)
T ss_pred CHHHHHHHHHHHHHhcccCCCHHHHHH
Confidence 45666666666665 578888654
No 52
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=22.06 E-value=1.5e+02 Score=21.38 Aligned_cols=39 Identities=15% Similarity=0.259 Sum_probs=32.9
Q ss_pred HHHHcCCCCCHHHHHHHHHHHH------HHHHHHHHhccCCCCCC
Q 033373 66 LAQTARISLTPHEVEEFAPKIR------QVIDWFGQLQDVDLDSV 104 (120)
Q Consensus 66 LA~LARL~LsEeEle~~~~qLn------~IL~~~d~L~eVDTe~V 104 (120)
|++++..+++++.+..+.+.-+ .+.-++..|+.+|++++
T Consensus 9 LL~~~G~eITae~I~~IL~AAGveVd~~~~~ala~aL~gkdIeEl 53 (106)
T cd05832 9 LLHYAGKEINEENLKKVLEAAGIEVDEARVKALVAALEEVNIDEA 53 (106)
T ss_pred HHHhcCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHH
Confidence 5677888999999999999887 78888899999887654
No 53
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=21.68 E-value=2e+02 Score=20.47 Aligned_cols=12 Identities=33% Similarity=0.429 Sum_probs=7.1
Q ss_pred cccccccccCCC
Q 033373 39 DYDYNNRTRNCS 50 (120)
Q Consensus 39 ~~~~~~~~r~~s 50 (120)
..+|.+.+-.++
T Consensus 37 tl~y~~kFsk~~ 48 (112)
T PRK14981 37 TLDYLNRFSKLD 48 (112)
T ss_pred HHHHHHHHhCCC
Confidence 566666655554
No 54
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=21.24 E-value=1.6e+02 Score=15.99 Aligned_cols=31 Identities=10% Similarity=0.287 Sum_probs=24.9
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHH
Q 033373 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKI 86 (120)
Q Consensus 56 m~I~keeV~kLA~LARL~LsEeEle~~~~qL 86 (120)
..|+.+++..+........+++++..+...+
T Consensus 15 g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 45 (63)
T cd00051 15 GTISADELKAALKSLGEGLSEEEIDEMIREV 45 (63)
T ss_pred CcCcHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence 4789999999999888889988887655443
No 55
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=20.80 E-value=1.9e+02 Score=20.81 Aligned_cols=33 Identities=9% Similarity=0.266 Sum_probs=29.7
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 033373 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQ 88 (120)
Q Consensus 56 m~I~keeV~kLA~LARL~LsEeEle~~~~qLn~ 88 (120)
-.+|.++|++|.+=+-+++++.....|...|+.
T Consensus 16 ~~pTa~dI~~IL~AaGveVe~~~~~lf~~~L~G 48 (109)
T cd05833 16 ASPSAADVKKILGSVGVEVDDEKLNKVISELEG 48 (109)
T ss_pred CCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcC
Confidence 478999999999999999999999999987753
No 56
>KOG0031 consensus Myosin regulatory light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=20.24 E-value=1.4e+02 Score=23.46 Aligned_cols=45 Identities=18% Similarity=0.325 Sum_probs=33.0
Q ss_pred CCCChhHHHH-HHHHcCCCCCHHHHHHHHHHH------HHHHHHH-HHhccCCC
Q 033373 56 SSLEPPDVPR-LAQTARISLTPHEVEEFAPKI------RQVIDWF-GQLQDVDL 101 (120)
Q Consensus 56 m~I~keeV~k-LA~LARL~LsEeEle~~~~qL------n~IL~~~-d~L~eVDT 101 (120)
--|+++|++. +|.|-++ .+|+|++.+.++- -..|.+| +.|...|-
T Consensus 47 G~IdkeDL~d~~aSlGk~-~~d~elDaM~~Ea~gPINft~FLTmfGekL~gtdp 99 (171)
T KOG0031|consen 47 GFIDKEDLRDMLASLGKI-ASDEELDAMMKEAPGPINFTVFLTMFGEKLNGTDP 99 (171)
T ss_pred CcccHHHHHHHHHHcCCC-CCHHHHHHHHHhCCCCeeHHHHHHHHHHHhcCCCH
Confidence 3589999875 6889999 9999999999873 4455555 45554444
Done!