Query psy2782
Match_columns 147
No_of_seqs 139 out of 226
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 16:45:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2782.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2782hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2239|consensus 100.0 1.7E-44 3.6E-49 295.2 12.4 130 14-143 15-144 (209)
2 PF01849 NAC: NAC domain; Int 99.9 1E-23 2.2E-28 140.6 5.7 58 65-122 1-58 (58)
3 PRK06369 nac nascent polypepti 99.8 3.9E-19 8.5E-24 135.0 6.4 61 64-126 6-70 (115)
4 KOG2240|consensus 98.9 3.9E-10 8.5E-15 90.4 2.4 63 62-124 38-100 (162)
5 TIGR00264 alpha-NAC-related pr 98.8 1.1E-08 2.4E-13 78.3 5.9 58 65-122 11-70 (116)
6 COG1308 EGD2 Transcription fac 98.0 9E-06 2E-10 63.0 5.1 53 65-118 8-64 (122)
7 PF10411 DsbC_N: Disulfide bon 77.0 3.4 7.5E-05 27.2 3.1 31 78-118 20-50 (57)
8 COG2428 Uncharacterized conser 63.9 5.2 0.00011 33.5 2.1 51 68-118 40-93 (196)
9 PF00403 HMA: Heavy-metal-asso 62.5 24 0.00053 22.2 4.7 34 65-103 13-46 (62)
10 cd06587 Glo_EDI_BRP_like This 60.3 40 0.00086 21.1 6.2 57 64-123 8-72 (112)
11 TIGR03757 conj_TIGR03757 integ 56.7 9.8 0.00021 29.2 2.4 26 74-122 79-104 (113)
12 TIGR00632 vsr DNA mismatch end 56.1 17 0.00038 27.8 3.6 40 57-96 16-61 (117)
13 PF07511 DUF1525: Protein of u 52.7 12 0.00027 28.6 2.3 25 74-121 78-102 (114)
14 KOG3198|consensus 50.9 32 0.0007 27.9 4.5 46 56-101 37-95 (152)
15 PF11699 CENP-C_C: Mif2/CENP-C 48.4 44 0.00095 24.1 4.5 33 80-115 40-72 (85)
16 PF08503 DapH_N: Tetrahydrodip 45.3 36 0.00077 24.9 3.7 31 84-118 19-50 (83)
17 PRK10877 protein disulfide iso 44.9 73 0.0016 26.1 5.9 42 66-118 24-72 (232)
18 PRK13839 conjugal transfer pro 38.6 73 0.0016 27.6 5.1 57 58-119 29-88 (277)
19 PRK14897 unknown domain/DNA-di 38.3 39 0.00085 31.9 3.7 28 66-93 330-357 (509)
20 cd02736 RNAP_III_Rpc1_C Larges 37.0 45 0.00097 29.1 3.7 26 67-92 133-158 (300)
21 PF08002 DUF1697: Protein of u 35.4 32 0.00069 26.3 2.3 27 66-97 22-48 (137)
22 PHA02131 hypothetical protein 35.2 79 0.0017 22.4 4.0 33 78-122 10-42 (70)
23 PF14242 DUF4342: Domain of un 33.2 94 0.002 22.4 4.3 27 66-98 20-46 (84)
24 TIGR02389 RNA_pol_rpoA2 DNA-di 31.3 70 0.0015 28.8 4.0 29 65-93 195-223 (367)
25 TIGR01955 RfaH transcriptional 30.1 1.6E+02 0.0034 22.1 5.2 57 61-117 7-80 (159)
26 cd03020 DsbA_DsbC_DsbG DsbA fa 29.9 71 0.0015 24.7 3.4 30 78-118 9-38 (197)
27 cd02735 RNAP_I_Rpa1_C Largest 29.9 41 0.00088 29.3 2.3 27 67-93 137-163 (309)
28 cd06528 RNAP_A'' A'' subunit o 29.6 60 0.0013 29.1 3.3 28 66-93 191-218 (363)
29 PRK13885 conjugal transfer pro 28.6 1.1E+02 0.0024 26.8 4.7 55 58-119 37-99 (299)
30 COG0490 Putative regulatory, l 26.9 84 0.0018 25.6 3.4 52 66-119 97-148 (162)
31 PF13276 HTH_21: HTH-like doma 26.8 54 0.0012 21.0 1.9 19 62-80 37-55 (60)
32 PF13535 ATP-grasp_4: ATP-gras 26.2 1.7E+02 0.0038 21.1 4.8 35 62-98 138-173 (184)
33 PF13893 RRM_5: RNA recognitio 25.6 1.2E+02 0.0026 18.6 3.3 19 69-92 2-20 (56)
34 KOG1329|consensus 25.5 1.9E+02 0.0041 29.4 6.1 66 57-125 651-726 (887)
35 KOG3003|consensus 25.3 1.1E+02 0.0025 26.3 4.1 37 64-100 163-212 (236)
36 smart00481 POLIIIAc DNA polyme 24.8 59 0.0013 20.9 1.9 21 64-84 42-62 (67)
37 PF03852 Vsr: DNA mismatch end 24.2 77 0.0017 22.9 2.5 21 58-78 17-37 (75)
38 KOG3705|consensus 24.1 92 0.002 29.6 3.6 31 61-93 344-374 (580)
39 PF03471 CorC_HlyC: Transporte 24.0 55 0.0012 22.2 1.6 21 108-128 4-24 (81)
40 PF14137 DUF4304: Domain of un 23.5 2.3E+02 0.005 19.8 4.9 27 70-99 3-29 (117)
41 PF11455 DUF3018: Protein of 22.8 61 0.0013 22.8 1.7 16 66-81 6-21 (65)
42 cd04438 DEP_dishevelled DEP (D 22.6 60 0.0013 23.2 1.7 22 93-117 63-84 (84)
43 PF07478 Dala_Dala_lig_C: D-al 22.4 2E+02 0.0042 23.0 4.7 35 61-98 134-169 (203)
44 PRK11657 dsbG disulfide isomer 21.3 2.2E+02 0.0049 23.5 5.0 33 94-127 50-87 (251)
45 TIGR01310 L7 60S ribosomal pro 20.8 38 0.00082 28.8 0.4 49 66-125 88-137 (235)
46 PF07717 OB_NTP_bind: Oligonuc 20.6 1.6E+02 0.0034 20.7 3.5 49 65-119 34-89 (114)
47 smart00738 NGN In Spt5p, this 20.5 2.7E+02 0.0058 19.1 4.6 14 62-75 9-22 (106)
48 cd01657 Ribosomal_L7_archeal_e 20.5 50 0.0011 26.2 1.0 49 66-125 15-64 (159)
49 PRK04309 DNA-directed RNA poly 20.3 1.3E+02 0.0028 27.2 3.6 27 67-93 209-235 (383)
50 PRK14571 D-alanyl-alanine synt 20.3 2.2E+02 0.0048 23.4 4.8 32 65-99 229-260 (299)
No 1
>KOG2239|consensus
Probab=100.00 E-value=1.7e-44 Score=295.16 Aligned_cols=130 Identities=62% Similarity=0.893 Sum_probs=119.3
Q ss_pred CCCCcccCCCCCCCCCCCCccccccCCCCCCcccccCCchhhhhhhhhChhHHHHHHHHHHhCCeecCCeeEEEEEecCc
Q psy2782 14 GGEAELHDDSGTESDSEDSIPELEASGDPLGSAGASGLANDLVSKAKQSRGEKKARKIMSKLGLKQIQGVSRVTIRKSKN 93 (147)
Q Consensus 14 ~~~~~~~~~s~~~sdsd~~~PeLe~~~~~~~~~~~~~~~~~~~~~~kqsr~EKKaRKaL~KLGLk~V~gI~RVtirKskn 93 (147)
........+++++|+++|++|+|++++.....+.++++++++..++||||+|||+||+|.|||||+|+||+||||||+||
T Consensus 15 a~~~~~~~~~~~~~~~~ed~~d~~e~d~~~~~~~~~~~~~~~~~~akqsrsekKark~m~KLGlk~v~gV~RVti~ksKN 94 (209)
T KOG2239|consen 15 APQPQAETGSGTESDSDEDVPELEEQDSTETTDEAAEIDEEPVAKAKQSRSEKKARKAMLKLGLKQVTGVTRVTIRKSKN 94 (209)
T ss_pred ccchhhccccCCCCcccccccccccccccccchhhhcccccchhhhhcchHHHHHHHHHHhcCCccccceeEEEEEeccc
Confidence 33445568999999999999999999854333888899999999999999999999999999999999999999999999
Q ss_pred eEEEEeCCeeeecCCCCcEEEEccccccchHHHHHHHHHHhcCCCCCCCC
Q psy2782 94 ILFVINKPDVFKNPASDTYIVFGEAKIEDLSQQAQVAAAEKFKAPEISPA 143 (147)
Q Consensus 94 ~lfvI~~PdVyksp~SnTYIVFGEak~eDlsqqaq~~Aae~~~~~~~~~~ 143 (147)
+||+|++|||||+|+|||||||||++++||+||+|.+|+++|+.+..++.
T Consensus 95 ilfvI~kPdVyKsp~sdtYiiFGeakiedls~q~q~~aae~fk~~~~~~~ 144 (209)
T KOG2239|consen 95 ILFVITKPDVYKSPASDTYIIFGEAKIEDLSQQAQMQAAERFKVPQEAPG 144 (209)
T ss_pred EEEEecCCceeccCCCceEEEecccccchhHHHHHHHHHHhccCCccccc
Confidence 99999999999999999999999999999999999999999999876654
No 2
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=99.89 E-value=1e-23 Score=140.57 Aligned_cols=58 Identities=57% Similarity=0.936 Sum_probs=49.0
Q ss_pred HHHHHHHHHHhCCeecCCeeEEEEEecCceEEEEeCCeeeecCCCCcEEEEccccccc
Q psy2782 65 EKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKIED 122 (147)
Q Consensus 65 EKKaRKaL~KLGLk~V~gI~RVtirKskn~lfvI~~PdVyksp~SnTYIVFGEak~eD 122 (147)
|||+|++|+||||++|+||.||+|++++|.+|||++|+||+++++|||+|||+++.+|
T Consensus 1 ekk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~~~~P~V~~~~~~~tyvV~G~~~~~~ 58 (58)
T PF01849_consen 1 EKKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFVFNNPEVQKSPGSNTYVVFGEAEEED 58 (58)
T ss_dssp -------GHHCT-EEETTEEEEEEEETTTEEEEEESEEEEEETTCCEEEEESEEEEEE
T ss_pred CHHHHHHHHHcCCcccCCcEEEEEEECCceEEEEcCCeEEEcCCCCEEEEEeeeEEcC
Confidence 6999999999999999999999999999999999999999999999999999999876
No 3
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=99.77 E-value=3.9e-19 Score=135.03 Aligned_cols=61 Identities=23% Similarity=0.455 Sum_probs=57.9
Q ss_pred hHHHHHHHHHHhCCe--ecCCeeEEEEEecCceEEEEeCCeee--ecCCCCcEEEEccccccchHHH
Q psy2782 64 GEKKARKIMSKLGLK--QIQGVSRVTIRKSKNILFVINKPDVF--KNPASDTYIVFGEAKIEDLSQQ 126 (147)
Q Consensus 64 ~EKKaRKaL~KLGLk--~V~gI~RVtirKskn~lfvI~~PdVy--ksp~SnTYIVFGEak~eDlsqq 126 (147)
++||+|++|+||||+ +| ||+||+||+++ .+|+|++|+|| ++++++||+|||+++.+|++++
T Consensus 6 nprk~rkmmkkmGik~e~i-~v~~V~Ir~~~-~~~Vi~~P~V~~m~~~g~~tY~I~Ge~~~e~~~~~ 70 (115)
T PRK06369 6 NPRKMKQMMKQMGIDVEEL-DVEEVIIRLKD-KEIVFENPQVTVMDAQGQKTYQIVGEPEEVEKEAE 70 (115)
T ss_pred CHHHHHHHHHHcCCcchhc-CeEEEEEEeCC-EEEEEcCCeEEEEecCCCcEEEEEeccEEeecccc
Confidence 579999999999999 99 99999999999 99999999999 8999999999999999997654
No 4
>KOG2240|consensus
Probab=98.93 E-value=3.9e-10 Score=90.39 Aligned_cols=63 Identities=27% Similarity=0.504 Sum_probs=59.7
Q ss_pred ChhHHHHHHHHHHhCCeecCCeeEEEEEecCceEEEEeCCeeeecCCCCcEEEEccccccchH
Q psy2782 62 SRGEKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKIEDLS 124 (147)
Q Consensus 62 sr~EKKaRKaL~KLGLk~V~gI~RVtirKskn~lfvI~~PdVyksp~SnTYIVFGEak~eDls 124 (147)
..++||++--|+||++.+++||.+|+|+|.++.++||++|.|++|.+.|||.|.|+++.+-++
T Consensus 38 ~~ddkKlqs~lkkl~v~~i~~i~evn~~k~~g~Vihf~~~~vqasl~~nTf~ItG~~~~k~l~ 100 (162)
T KOG2240|consen 38 TADDKKLQSSLKKLGVNNIPGIEEVNMFKNDGTVIHFNNPKVQASLAANTFTITGHAETKQLT 100 (162)
T ss_pred CcccchhhhhhhhhccccccchhHhhhccccceeEecCCccccccccCCeEEEecCCcccchh
Confidence 556899999999999999999999999999999999999999999999999999999988654
No 5
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=98.79 E-value=1.1e-08 Score=78.30 Aligned_cols=58 Identities=26% Similarity=0.336 Sum_probs=50.6
Q ss_pred HHHHHHHHHHhCCeec-CCeeEEEEEe-cCceEEEEeCCeeeecCCCCcEEEEccccccc
Q psy2782 65 EKKARKIMSKLGLKQI-QGVSRVTIRK-SKNILFVINKPDVFKNPASDTYIVFGEAKIED 122 (147)
Q Consensus 65 EKKaRKaL~KLGLk~V-~gI~RVtirK-skn~lfvI~~PdVyksp~SnTYIVFGEak~eD 122 (147)
=|++|++|++||++.. .+|.+|+|+. ++.++|...++.|++.++..||.|||+++.++
T Consensus 11 ~~~mkkmMk~MGi~~~eidV~~ViIk~~~k~ivf~~p~V~~m~~~G~~tYqI~G~~~~~~ 70 (116)
T TIGR00264 11 LKQMQKMMKQMGMEMEDLDVEEVIIVFDDEEWIFENPKVQVMDILGVKTYQITGKPKKEK 70 (116)
T ss_pred HHHHHHHHHHcCCCccccccEEEEEEeCCceEEEecCeeEEEecCCcEEEEEecccEEee
Confidence 3699999999998765 4599999999 56788777777889999999999999999877
No 6
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=98.02 E-value=9e-06 Score=62.96 Aligned_cols=53 Identities=30% Similarity=0.594 Sum_probs=46.9
Q ss_pred HHHHHHHHHHhC--CeecCCeeEEEEEecCceEEEEeCCeeeec--CCCCcEEEEccc
Q psy2782 65 EKKARKIMSKLG--LKQIQGVSRVTIRKSKNILFVINKPDVFKN--PASDTYIVFGEA 118 (147)
Q Consensus 65 EKKaRKaL~KLG--Lk~V~gI~RVtirKskn~lfvI~~PdVyks--p~SnTYIVFGEa 118 (147)
=++++++|+.|| +++++||.||.|+..++. ++|++|.||.- .+.-||=|.|..
T Consensus 8 pr~l~k~mkqmGi~~eeld~v~~V~i~~kd~e-~vi~~P~V~~~~~~g~~~yqi~g~~ 64 (122)
T COG1308 8 PRKLKKLMKQMGIDVEELDGVERVIIKLKDTE-YVIENPQVTVMKAMGQKTYQISGDP 64 (122)
T ss_pred HHHHHHHHHHhCCCceeccCceEEEEEcCCce-EEeeCCcEEeehhcchhHHHHhcch
Confidence 378889999998 999999999999999999 99999999963 566788888884
No 7
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=77.05 E-value=3.4 Score=27.20 Aligned_cols=31 Identities=23% Similarity=0.530 Sum_probs=20.1
Q ss_pred eecCCeeEEEEEecCceEEEEeCCeeeecCCCCcEEEEccc
Q psy2782 78 KQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEA 118 (147)
Q Consensus 78 k~V~gI~RVtirKskn~lfvI~~PdVyksp~SnTYIVFGEa 118 (147)
.+++|+.+|.+ +++++ +|-++ ...|+|+|+.
T Consensus 20 spi~GlyeV~~-~~~~i--------~Y~~~-dg~yli~G~l 50 (57)
T PF10411_consen 20 SPIPGLYEVVL-KGGGI--------LYVDE-DGRYLIQGQL 50 (57)
T ss_dssp -SSTTEEEEEE--TTEE--------EEEET-TSSEEEES-E
T ss_pred CCCCCeEEEEE-CCCeE--------EEEcC-CCCEEEEeEE
Confidence 46899999998 44442 34443 6689999975
No 8
>COG2428 Uncharacterized conserved protein [Function unknown]
Probab=63.93 E-value=5.2 Score=33.46 Aligned_cols=51 Identities=27% Similarity=0.568 Sum_probs=38.4
Q ss_pred HHHHHHHhCCeecCC-eeEEEEEecCceEEEEeCCeeeec--CCCCcEEEEccc
Q psy2782 68 ARKIMSKLGLKQIQG-VSRVTIRKSKNILFVINKPDVFKN--PASDTYIVFGEA 118 (147)
Q Consensus 68 aRKaL~KLGLk~V~g-I~RVtirKskn~lfvI~~PdVyks--p~SnTYIVFGEa 118 (147)
.+..|.|+|+.-||- ++|.-+++++=+++-...++=.+- ..++||||||-.
T Consensus 40 ~p~vlak~g~~~i~e~~~~~~l~r~rvivLDl~a~~~L~PEdas~~~~ivvGGI 93 (196)
T COG2428 40 EPEVLAKIGLSGIPESITRLPLDRSRVIVLDLQAEEELKPEDASEDTYIVVGGI 93 (196)
T ss_pred hhHHHHHhccccCchhHhhcccCCCCEEEecCCCCCCCCcccCCcccEEEECcc
Confidence 678999999987775 788778888877776666554442 257899999964
No 9
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=62.50 E-value=24 Score=22.19 Aligned_cols=34 Identities=32% Similarity=0.460 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhCCeecCCeeEEEEEecCceEEEEeCCee
Q psy2782 65 EKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDV 103 (147)
Q Consensus 65 EKKaRKaL~KLGLk~V~gI~RVtirKskn~lfvI~~PdV 103 (147)
.++.+++|.+ ++||..|.+--..+.+-+.-+|+.
T Consensus 13 ~~~v~~~l~~-----~~GV~~v~vd~~~~~v~v~~~~~~ 46 (62)
T PF00403_consen 13 AKKVEKALSK-----LPGVKSVKVDLETKTVTVTYDPDK 46 (62)
T ss_dssp HHHHHHHHHT-----STTEEEEEEETTTTEEEEEESTTT
T ss_pred HHHHHHHHhc-----CCCCcEEEEECCCCEEEEEEecCC
Confidence 5778888887 799999999888887777666653
No 10
>cd06587 Glo_EDI_BRP_like This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain clas
Probab=60.25 E-value=40 Score=21.12 Aligned_cols=57 Identities=11% Similarity=0.129 Sum_probs=38.5
Q ss_pred hHHHHHHHHHH-hCCeecCCe----eEEEEEecCceEEEEeCCeeeec---CCCCcEEEEccccccch
Q psy2782 64 GEKKARKIMSK-LGLKQIQGV----SRVTIRKSKNILFVINKPDVFKN---PASDTYIVFGEAKIEDL 123 (147)
Q Consensus 64 ~EKKaRKaL~K-LGLk~V~gI----~RVtirKskn~lfvI~~PdVyks---p~SnTYIVFGEak~eDl 123 (147)
+=.++++-..+ ||++.+... .+..+....+..|.|..+.-... +.....+.|. ++|+
T Consensus 8 d~~~~~~fy~~~lg~~~~~~~~~~~~~~~~~~~~~~~i~l~~~~~~~~~~~~~~~~~~~~~---v~~~ 72 (112)
T cd06587 8 DLEAAVAFYEEVLGFEVLFRNGNGGAEFAVLGLGGTRLELFEGDEPAPAPSGGGGVHLAFE---VDDV 72 (112)
T ss_pred CHHHHHHHHHhccCCEEEEeeccCCEEEEEEecCCceEEEecCCCCCCcccCCCeeEEEEE---CCCH
Confidence 34677778887 999988887 47777776678888888765543 2333455555 4565
No 11
>TIGR03757 conj_TIGR03757 integrating conjugative element protein, PFL_4709 family. Members of this protein belong to extended genomic regions that appear to be spread by conjugative transfer.
Probab=56.72 E-value=9.8 Score=29.22 Aligned_cols=26 Identities=35% Similarity=0.832 Sum_probs=19.5
Q ss_pred HhCCeecCCeeEEEEEecCceEEEEeCCeeeecCCCCcEEEEccccccc
Q psy2782 74 KLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKIED 122 (147)
Q Consensus 74 KLGLk~V~gI~RVtirKskn~lfvI~~PdVyksp~SnTYIVFGEak~eD 122 (147)
-||++.+|-| ||+ +.|||+|++.+.-
T Consensus 79 ~lGi~k~PAV-------------V~D----------~~~VVYG~~DV~~ 104 (113)
T TIGR03757 79 QLGVTKIPAV-------------VVD----------RRYVVYGETDVAR 104 (113)
T ss_pred HcCCccCCEE-------------EEc----------CCeEEecCccHHH
Confidence 5899999883 444 5699999986543
No 12
>TIGR00632 vsr DNA mismatch endonuclease Vsr. All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase.
Probab=56.08 E-value=17 Score=27.84 Aligned_cols=40 Identities=20% Similarity=0.507 Sum_probs=29.0
Q ss_pred hhhhhChhHHHHHHHHHHhCCe------ecCCeeEEEEEecCceEE
Q psy2782 57 SKAKQSRGEKKARKIMSKLGLK------QIQGVSRVTIRKSKNILF 96 (147)
Q Consensus 57 ~~~kqsr~EKKaRKaL~KLGLk------~V~gI~RVtirKskn~lf 96 (147)
-+.+..+.|.++|++|-.+|++ .+||+--+.+.+-+=.||
T Consensus 16 iR~~~T~pE~~lr~~L~~~G~rfR~q~~~lpg~pD~~~~~~klaIf 61 (117)
T TIGR00632 16 IRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIF 61 (117)
T ss_pred HhcCCCHHHHHHHHHHHhCCCEEEEecCCCCCcccEEecCCCEEEE
Confidence 3677889999999999999986 256665555555554444
No 13
>PF07511 DUF1525: Protein of unknown function (DUF1525); InterPro: IPR011090 This family of proteins is restricted to the Gammaproteobacteria. Members belong to extended genomic regions that appear to be spread by conjugative transfer.
Probab=52.66 E-value=12 Score=28.57 Aligned_cols=25 Identities=36% Similarity=0.840 Sum_probs=18.7
Q ss_pred HhCCeecCCeeEEEEEecCceEEEEeCCeeeecCCCCcEEEEcccccc
Q psy2782 74 KLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKIE 121 (147)
Q Consensus 74 KLGLk~V~gI~RVtirKskn~lfvI~~PdVyksp~SnTYIVFGEak~e 121 (147)
.||++.+|-| ||+ +.|||+|++.+.
T Consensus 78 ~lgi~k~PAV-------------VfD----------~~~VVYG~tDV~ 102 (114)
T PF07511_consen 78 SLGITKYPAV-------------VFD----------DRYVVYGETDVA 102 (114)
T ss_pred HhCccccCEE-------------EEc----------CCeEEecccHHH
Confidence 5899998873 344 689999998543
No 14
>KOG3198|consensus
Probab=50.90 E-value=32 Score=27.92 Aligned_cols=46 Identities=26% Similarity=0.385 Sum_probs=37.6
Q ss_pred hhhhhhChhHHHHHHHHHHhCCeec-------------CCeeEEEEEecCceEEEEeCC
Q psy2782 56 VSKAKQSRGEKKARKIMSKLGLKQI-------------QGVSRVTIRKSKNILFVINKP 101 (147)
Q Consensus 56 ~~~~kqsr~EKKaRKaL~KLGLk~V-------------~gI~RVtirKskn~lfvI~~P 101 (147)
..++-+|-.-+-.+.+++.|||.-. +|=.||.+++.+|.+|+|+-|
T Consensus 37 ke~aVeNP~a~eI~Dvl~~lgl~~~~E~~K~hPrD~~n~GRVRvqlk~edG~l~~~~~~ 95 (152)
T KOG3198|consen 37 KEKAVENPLAKEIADVLRALGLNCLLEPNKKHPRDFVNPGRVRVQLKNEDGTLYVIAFI 95 (152)
T ss_pred HHHhhcCcchhHHHHHHHHhCCcccccccccCchhcCCCceEEEEeeccCCcEEeecch
Confidence 3556666677889999999998764 567799999999999999874
No 15
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=48.39 E-value=44 Score=24.07 Aligned_cols=33 Identities=33% Similarity=0.536 Sum_probs=25.1
Q ss_pred cCCeeEEEEEecCceEEEEeCCeeeecCCCCcEEEE
Q psy2782 80 IQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVF 115 (147)
Q Consensus 80 V~gI~RVtirKskn~lfvI~~PdVyksp~SnTYIVF 115 (147)
+.|..+||| .+.-|++..-++|..|..|.|-|=
T Consensus 40 ~~G~v~Vti---~~~~f~v~~G~~F~VP~gN~Y~i~ 72 (85)
T PF11699_consen 40 IKGKVEVTI---HETSFVVTKGGSFQVPRGNYYSIK 72 (85)
T ss_dssp EESEEEEEE---TTEEEEEETT-EEEE-TT-EEEEE
T ss_pred EeCEEEEEE---cCcEEEEeCCCEEEECCCCEEEEE
Confidence 578888988 456799999999999999999763
No 16
>PF08503 DapH_N: Tetrahydrodipicolinate succinyltransferase N-terminal; InterPro: IPR013710 This domain is found at the N terminus of tetrahydrodipicolinate N-acetyltransferase (DapH) which catalyses the acylation of L-2-amino-6-oxopimelate to 2-N-acetyl-6-oxopimelate in the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants []. The N-terminal domain as defined here contains three alpha-helices and two twisted hairpin loops []. ; GO: 0047200 tetrahydrodipicolinate N-acetyltransferase activity; PDB: 3CJ8_A 3BV8_A 3R8Y_F.
Probab=45.25 E-value=36 Score=24.87 Aligned_cols=31 Identities=26% Similarity=0.445 Sum_probs=21.3
Q ss_pred eEEEEEec-CceEEEEeCCeeeecCCCCcEEEEccc
Q psy2782 84 SRVTIRKS-KNILFVINKPDVFKNPASDTYIVFGEA 118 (147)
Q Consensus 84 ~RVtirKs-kn~lfvI~~PdVyksp~SnTYIVFGEa 118 (147)
.+|.++-. .++-| ..-++|.+ .+.+||||+.
T Consensus 19 VKvYv~G~l~~~~~--~~~~~fg~--~~~~vvfGd~ 50 (83)
T PF08503_consen 19 VKVYVKGDLAGIDF--EDVKVFGS--GNFGVVFGDW 50 (83)
T ss_dssp EEEEEEESCTC-----TTSEEEEE--SSEEEEEEEH
T ss_pred EEEEEeeeecCCCh--hheEEEeC--CCcEEEEecH
Confidence 35666665 55544 78888887 6789999996
No 17
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=44.87 E-value=73 Score=26.11 Aligned_cols=42 Identities=17% Similarity=0.395 Sum_probs=27.9
Q ss_pred HHHHHHHHHhCC-------eecCCeeEEEEEecCceEEEEeCCeeeecCCCCcEEEEccc
Q psy2782 66 KKARKIMSKLGL-------KQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEA 118 (147)
Q Consensus 66 KKaRKaL~KLGL-------k~V~gI~RVtirKskn~lfvI~~PdVyksp~SnTYIVFGEa 118 (147)
..++++|.++|+ .|++|+.+|.+ +++ + +|-+ ..+.|+|+|+.
T Consensus 24 ~~~~~~l~~~~~~v~~v~~sp~~Gl~ev~~--~~~-i-------~Y~~-~dg~y~i~G~l 72 (232)
T PRK10877 24 AAIQQTLAKLGIQSADIQPSPVAGMKTVLT--ESG-V-------LYIT-DDGKHIIQGPM 72 (232)
T ss_pred HHHHHHHHHcCCceeEEccCCCCCeEEEEE--CCe-E-------EEEc-CCCCEEEeeee
Confidence 566677777765 35788888876 222 3 3444 46679999986
No 18
>PRK13839 conjugal transfer protein TrbG; Provisional
Probab=38.61 E-value=73 Score=27.64 Aligned_cols=57 Identities=14% Similarity=0.231 Sum_probs=39.3
Q ss_pred hhhhChhHHHHHHHHHHhCCeecCCeeEEEEEecCc-eEEEE--eCCeeeecCCCCcEEEEcccc
Q psy2782 58 KAKQSRGEKKARKIMSKLGLKQIQGVSRVTIRKSKN-ILFVI--NKPDVFKNPASDTYIVFGEAK 119 (147)
Q Consensus 58 ~~kqsr~EKKaRKaL~KLGLk~V~gI~RVtirKskn-~lfvI--~~PdVyksp~SnTYIVFGEak 119 (147)
.+..+..|+++.++-+|--=. .+..++..++ +.|.+ .+|-|+.+|..-|.|.|++-+
T Consensus 29 ~~~l~~~e~~~~~~~~~w~~~-----~~~~~~~~dg~v~f~yg~~~p~v~~apg~vt~I~L~pgE 88 (277)
T PRK13839 29 AQSMTANEAKGTGISGQWRGS-----PGLVTKGPDGKVIFLFGETQPSVVCSPLQVCDIELQGGE 88 (277)
T ss_pred CCCCCHHHHHHHHHHHHhhcC-----CCceEEcCCCCEEEEcCCCCcEEEEeCCcEEEEEECCCC
Confidence 446677888888776664322 1223666554 55554 689999999999999998654
No 19
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=38.25 E-value=39 Score=31.93 Aligned_cols=28 Identities=25% Similarity=0.389 Sum_probs=22.7
Q ss_pred HHHHHHHHHhCCeecCCeeEEEEEecCc
Q psy2782 66 KKARKIMSKLGLKQIQGVSRVTIRKSKN 93 (147)
Q Consensus 66 KKaRKaL~KLGLk~V~gI~RVtirKskn 93 (147)
+++++.|..+-++-+|||.||.|++.++
T Consensus 330 ~~l~~~l~~i~I~GipgI~r~~i~~~~~ 357 (509)
T PRK14897 330 YLLAEKVKSLTIKGIKGIKRAIARKEND 357 (509)
T ss_pred HHHHHHhhccEEeCCCCccEEEEecCCC
Confidence 4556677788899999999999997653
No 20
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=37.04 E-value=45 Score=29.10 Aligned_cols=26 Identities=23% Similarity=0.358 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCeecCCeeEEEEEecC
Q psy2782 67 KARKIMSKLGLKQIQGVSRVTIRKSK 92 (147)
Q Consensus 67 KaRKaL~KLGLk~V~gI~RVtirKsk 92 (147)
+.++.|..+-++-+|||.|+.|++.+
T Consensus 133 ~l~~~l~~~~v~Gi~gI~r~~i~~~~ 158 (300)
T cd02736 133 SLKRKLPDVVVSGIPEVKRAVINKDK 158 (300)
T ss_pred HHHHHhccceEeCCCCceEEEEecCC
Confidence 34455666669999999999998865
No 21
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=35.42 E-value=32 Score=26.26 Aligned_cols=27 Identities=26% Similarity=0.519 Sum_probs=20.3
Q ss_pred HHHHHHHHHhCCeecCCeeEEEEEecCceEEE
Q psy2782 66 KKARKIMSKLGLKQIQGVSRVTIRKSKNILFV 97 (147)
Q Consensus 66 KKaRKaL~KLGLk~V~gI~RVtirKskn~lfv 97 (147)
+-+|.+|.++|+..|. |.-.|+|++|-
T Consensus 22 aeLr~~l~~~Gf~~V~-----Tyi~SGNvvf~ 48 (137)
T PF08002_consen 22 AELREALEDLGFTNVR-----TYIQSGNVVFE 48 (137)
T ss_dssp HHHHHHHHHCT-EEEE-----EETTTTEEEEE
T ss_pred HHHHHHHHHcCCCCce-----EEEeeCCEEEe
Confidence 5689999999988664 67777777765
No 22
>PHA02131 hypothetical protein
Probab=35.15 E-value=79 Score=22.40 Aligned_cols=33 Identities=15% Similarity=0.404 Sum_probs=21.3
Q ss_pred eecCCeeEEEEEecCceEEEEeCCeeeecCCCCcEEEEccccccc
Q psy2782 78 KQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKIED 122 (147)
Q Consensus 78 k~V~gI~RVtirKskn~lfvI~~PdVyksp~SnTYIVFGEak~eD 122 (147)
-.|.||++|.|.+.-.. -+-.+||.|-.-++-|
T Consensus 10 akvngitkvdmirgh~~------------~g~~c~imfk~~~v~d 42 (70)
T PHA02131 10 AKVNGITKVDMIRGHYR------------FGISCWIMFKNDQVID 42 (70)
T ss_pred hhhcCceEEEEecccee------------cceEEEEEEcCCCEEE
Confidence 34889999999876311 1223677777666554
No 23
>PF14242 DUF4342: Domain of unknown function (DUF4342)
Probab=33.19 E-value=94 Score=22.42 Aligned_cols=27 Identities=30% Similarity=0.557 Sum_probs=21.3
Q ss_pred HHHHHHHHHhCCeecCCeeEEEEEecCceEEEE
Q psy2782 66 KKARKIMSKLGLKQIQGVSRVTIRKSKNILFVI 98 (147)
Q Consensus 66 KKaRKaL~KLGLk~V~gI~RVtirKskn~lfvI 98 (147)
.|.+..+.| -+++|+.++|++.+++-|
T Consensus 20 ~~iK~li~k------GNv~Ri~Ikk~~~tll~i 46 (84)
T PF14242_consen 20 DKIKELIKK------GNVTRIIIKKDDKTLLDI 46 (84)
T ss_pred HHHHHHHHh------cCeEEEEEEcCCeEEEEe
Confidence 456666666 468999999999888776
No 24
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=31.35 E-value=70 Score=28.78 Aligned_cols=29 Identities=34% Similarity=0.590 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhCCeecCCeeEEEEEecCc
Q psy2782 65 EKKARKIMSKLGLKQIQGVSRVTIRKSKN 93 (147)
Q Consensus 65 EKKaRKaL~KLGLk~V~gI~RVtirKskn 93 (147)
=+++++.|..+-++-+|||.||.|++.++
T Consensus 195 l~~l~~~l~~~~v~Gi~gI~r~~i~~~~~ 223 (367)
T TIGR02389 195 LRKLKEKIKNLHIKGIKGIKRVVIRKEGD 223 (367)
T ss_pred HHHHHHHhhhceEeCCCCceEEEEECCCC
Confidence 35566677788899999999999986544
No 25
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=30.09 E-value=1.6e+02 Score=22.06 Aligned_cols=57 Identities=18% Similarity=0.318 Sum_probs=32.6
Q ss_pred hChhHHHHHHHHHHhCCeecCCeeEEEEEec-----------CceEEEEeCCe------eeecCCCCcEEEEcc
Q psy2782 61 QSRGEKKARKIMSKLGLKQIQGVSRVTIRKS-----------KNILFVINKPD------VFKNPASDTYIVFGE 117 (147)
Q Consensus 61 qsr~EKKaRKaL~KLGLk~V~gI~RVtirKs-----------kn~lfvI~~Pd------Vyksp~SnTYIVFGE 117 (147)
.++.|+|++..|.+.|+.-.-=..++..+++ .|.||+=..++ |...++--.|+-||.
T Consensus 7 ~~~~E~~v~~~L~~~gi~~~~P~~~~~~~~~g~~~~~~~plfpgYvFv~~~~~~~~~~~i~~~~gv~~~v~~~~ 80 (159)
T TIGR01955 7 KPRQEQRAQEHLERQAVECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVRFGG 80 (159)
T ss_pred cCchHHHHHHHHHHCCCEEEccCEEEEEEECCcEEEEEEecCCCeEEEEEccCCCceEEEecCCCcCEEECCCC
Confidence 4678999999999999544322222222222 35667654443 333454455565665
No 26
>cd03020 DsbA_DsbC_DsbG DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins. DsbC and DsbG are kept in their reduced state by the cytoplasmic membrane protein DsbD, which utilizes the TRX/TRX reductase system in the cytosol as a source of reducing equivalents. DsbG differ from DsbC in that it has a more limited substrate specificity, and it may preferentially act later in the folding process to catalyze disulfide rearrangements in folded or partially folded proteins. Also included in the alignment is the predicted protein TrbB, whose gene was sequenced from the enterohemorrhagic E. coli type IV pilus gene cluster, which is required for efficient plasmid transfer.
Probab=29.91 E-value=71 Score=24.72 Aligned_cols=30 Identities=13% Similarity=0.400 Sum_probs=20.5
Q ss_pred eecCCeeEEEEEecCceEEEEeCCeeeecCCCCcEEEEccc
Q psy2782 78 KQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEA 118 (147)
Q Consensus 78 k~V~gI~RVtirKskn~lfvI~~PdVyksp~SnTYIVFGEa 118 (147)
.+++|+..|.+. +.+ +|-+ ..+.|+|+|+.
T Consensus 9 sp~~Gl~~v~~~---~~~-------~y~~-~dg~~~i~G~l 38 (197)
T cd03020 9 TPVAGLYEVVTG---GGV-------LYTD-DDGRYLIQGNL 38 (197)
T ss_pred CCCCCeEEEEEC---CEE-------EEEc-CCCCEEEEeEE
Confidence 468888888875 122 3444 46689999984
No 27
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=29.88 E-value=41 Score=29.34 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCeecCCeeEEEEEecCc
Q psy2782 67 KARKIMSKLGLKQIQGVSRVTIRKSKN 93 (147)
Q Consensus 67 KaRKaL~KLGLk~V~gI~RVtirKskn 93 (147)
..++.|.++-++.+|||.|+.|++.++
T Consensus 137 ~~~~~l~~~~i~gi~gI~r~~i~~~~~ 163 (309)
T cd02735 137 IVEKLARKAVIREIPGITRCFVVEEDK 163 (309)
T ss_pred HHHHHhcccEEeCCCCccEEEEecCcC
Confidence 356778888999999999999987753
No 28
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=29.57 E-value=60 Score=29.10 Aligned_cols=28 Identities=29% Similarity=0.529 Sum_probs=22.2
Q ss_pred HHHHHHHHHhCCeecCCeeEEEEEecCc
Q psy2782 66 KKARKIMSKLGLKQIQGVSRVTIRKSKN 93 (147)
Q Consensus 66 KKaRKaL~KLGLk~V~gI~RVtirKskn 93 (147)
++.++.|..+-++-+|||.||.|++.++
T Consensus 191 ~~l~~~l~~~~v~Gi~gI~r~~i~~~~~ 218 (363)
T cd06528 191 RKLAEKILNTKIKGIKGIKRVIVRKEED 218 (363)
T ss_pred HHHHHhhcccEEeCCCCceEEEEecCCc
Confidence 4455566677799999999999987765
No 29
>PRK13885 conjugal transfer protein TrbG; Provisional
Probab=28.59 E-value=1.1e+02 Score=26.77 Aligned_cols=55 Identities=20% Similarity=0.318 Sum_probs=37.2
Q ss_pred hhhhChhHHHHHHHHHHh------CCeecCCeeEEEEEecCceEEEE--eCCeeeecCCCCcEEEEcccc
Q psy2782 58 KAKQSRGEKKARKIMSKL------GLKQIQGVSRVTIRKSKNILFVI--NKPDVFKNPASDTYIVFGEAK 119 (147)
Q Consensus 58 ~~kqsr~EKKaRKaL~KL------GLk~V~gI~RVtirKskn~lfvI--~~PdVyksp~SnTYIVFGEak 119 (147)
.++.+..|+++.++-+|. |++|++| .+..+.|++ +.|.|++.|..-|.|.|++-+
T Consensus 37 ~~~l~~~e~~~~~~~~~w~~~~~~~~~p~~g-------~DgrV~~~Yg~~~~~I~~apg~vt~I~L~pgE 99 (299)
T PRK13885 37 NPTLTAQERAALAIAKRWQAGSATGIKPVAG-------SDGSIKFVYGAQQPSIVCAVLQVCDIALQPGE 99 (299)
T ss_pred CCCcCHHHHHHHHHHHHHhhCCCcCCCceEC-------CCCcEEEECCCCeEEEEEeCCcEEEEEECCCC
Confidence 445666778877665543 5677776 233344554 457899999999999998653
No 30
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=26.88 E-value=84 Score=25.63 Aligned_cols=52 Identities=23% Similarity=0.296 Sum_probs=38.4
Q ss_pred HHHHHHHHHhCCeecCCeeEEEEEecCceEEEEeCCeeeecCCCCcEEEEcccc
Q psy2782 66 KKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAK 119 (147)
Q Consensus 66 KKaRKaL~KLGLk~V~gI~RVtirKskn~lfvI~~PdVyksp~SnTYIVFGEak 119 (147)
...-|.|--|++.+=+|++=|-|.|+ +-+++=.-|+ +.--+.||+||.|+..
T Consensus 97 ~~~GksiGdl~irq~TGaTIIAI~r~-~e~I~SPgPy-~vle~gDtlvviG~~~ 148 (162)
T COG0490 97 PFIGKTIGDLNIRQNTGATVIAIVRN-EEKILSPGPY-TVLEAGDTLVVIGEET 148 (162)
T ss_pred cccCcchhhcccccccCcEEEEEEec-CcEecCCCch-hhhcCCCEEEEEecch
Confidence 36677888999999999999999994 4443434443 2234699999999863
No 31
>PF13276 HTH_21: HTH-like domain
Probab=26.80 E-value=54 Score=20.95 Aligned_cols=19 Identities=26% Similarity=0.602 Sum_probs=16.3
Q ss_pred ChhHHHHHHHHHHhCCeec
Q psy2782 62 SRGEKKARKIMSKLGLKQI 80 (147)
Q Consensus 62 sr~EKKaRKaL~KLGLk~V 80 (147)
.-+.|+.+.+|..+||...
T Consensus 37 ~v~~krV~RlM~~~gL~~~ 55 (60)
T PF13276_consen 37 RVSRKRVRRLMREMGLRSK 55 (60)
T ss_pred cccHHHHHHHHHHcCCccc
Confidence 5678999999999999754
No 32
>PF13535 ATP-grasp_4: ATP-grasp domain; PDB: 3VMM_A 3LN6_A 3LN7_B 2PN1_A 4DIM_A.
Probab=26.18 E-value=1.7e+02 Score=21.12 Aligned_cols=35 Identities=23% Similarity=0.378 Sum_probs=26.1
Q ss_pred ChhHHHHHHHHHHhCCeecCCeeEEEEEecC-ceEEEE
Q psy2782 62 SRGEKKARKIMSKLGLKQIQGVSRVTIRKSK-NILFVI 98 (147)
Q Consensus 62 sr~EKKaRKaL~KLGLk~V~gI~RVtirKsk-n~lfvI 98 (147)
.+-+..+++++..||+. .|+..|-++... |.+++|
T Consensus 138 ~~~~~~~~~~~~~~g~~--~G~~~id~~~~~~g~~~~i 173 (184)
T PF13535_consen 138 EELRDLARKLLRALGYR--NGFFHIDFIVDPDGELYFI 173 (184)
T ss_dssp HHHHHHHHHHHHHHT----SEEEEEEEEEETCCEEEEE
T ss_pred HHHHHHHHHHHHHcCCc--eEEEEEEEEEeCCCCEEEE
Confidence 55578899999999987 899999999876 444444
No 33
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=25.62 E-value=1.2e+02 Score=18.56 Aligned_cols=19 Identities=42% Similarity=0.627 Sum_probs=12.4
Q ss_pred HHHHHHhCCeecCCeeEEEEEecC
Q psy2782 69 RKIMSKLGLKQIQGVSRVTIRKSK 92 (147)
Q Consensus 69 RKaL~KLGLk~V~gI~RVtirKsk 92 (147)
++.++++| .|.+|.|.+.+
T Consensus 2 ~~~f~~fG-----~V~~i~~~~~~ 20 (56)
T PF13893_consen 2 YKLFSKFG-----EVKKIKIFKKK 20 (56)
T ss_dssp HHHHTTTS------EEEEEEETTS
T ss_pred hHHhCCcc-----cEEEEEEEeCC
Confidence 55666766 47777777765
No 34
>KOG1329|consensus
Probab=25.48 E-value=1.9e+02 Score=29.44 Aligned_cols=66 Identities=21% Similarity=0.321 Sum_probs=49.9
Q ss_pred hhhhhChhHHHHHHHHHHhCCeecCCeeEEEEEecCce----------EEEEeCCeeeecCCCCcEEEEccccccchHH
Q psy2782 57 SKAKQSRGEKKARKIMSKLGLKQIQGVSRVTIRKSKNI----------LFVINKPDVFKNPASDTYIVFGEAKIEDLSQ 125 (147)
Q Consensus 57 ~~~kqsr~EKKaRKaL~KLGLk~V~gI~RVtirKskn~----------lfvI~~PdVyksp~SnTYIVFGEak~eDlsq 125 (147)
+..-++++|+-.-++|.++|+.+-.=|.-.++|+=.+. +++|.- ++.- ..|+|||.|-|.|.|-|+
T Consensus 651 QyrTms~g~~sI~~~Lka~g~d~~~yi~f~~lr~~g~~e~~~~~~~~emIYVHs-K~mI--vDD~~vIIGSANINqRSm 726 (887)
T KOG1329|consen 651 QYRTMSMGYKSIYKALKAVGLDPADYIDFLGLRCLGNREEQAQRLRREMIYVHS-KLMI--VDDEYVIIGSANINQRSM 726 (887)
T ss_pred HHHHHhhhHHHHHHHHHHhcCCccccceeeeeeeeeccccccccceEEEEEEee-eeEE--ecCCEEEEeecccchhhc
Confidence 55667999999999999999998667888888876554 222221 2333 489999999999987653
No 35
>KOG3003|consensus
Probab=25.33 E-value=1.1e+02 Score=26.33 Aligned_cols=37 Identities=16% Similarity=0.410 Sum_probs=27.5
Q ss_pred hHHHHHHHHHHhCCeecCCe--------eEEEEE-----ecCceEEEEeC
Q psy2782 64 GEKKARKIMSKLGLKQIQGV--------SRVTIR-----KSKNILFVINK 100 (147)
Q Consensus 64 ~EKKaRKaL~KLGLk~V~gI--------~RVtir-----Kskn~lfvI~~ 100 (147)
-|+++.+.+.|+||-++..| .+..|+ +..|+++++.+
T Consensus 163 te~ql~~vf~KhGLekldPigekFDPn~HEAvfq~p~~~k~pgtV~~v~k 212 (236)
T KOG3003|consen 163 TEAQLKEVFAKHGLEKLDPIGEKFDPNEHEAVFQVPDAAKEPGTVALVTK 212 (236)
T ss_pred HHHHHHHHHHHcCceecCCCCCCCCcchhheeEeccccCCCCCeEEEEec
Confidence 57899999999999988665 456666 55577766544
No 36
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=24.79 E-value=59 Score=20.90 Aligned_cols=21 Identities=33% Similarity=0.460 Sum_probs=16.6
Q ss_pred hHHHHHHHHHHhCCeecCCee
Q psy2782 64 GEKKARKIMSKLGLKQIQGVS 84 (147)
Q Consensus 64 ~EKKaRKaL~KLGLk~V~gI~ 84 (147)
+--.++....+.|++.++||+
T Consensus 42 ~~~~~~~~~~~~gi~~i~G~E 62 (67)
T smart00481 42 GAVEFYKAAKKAGIKPIIGLE 62 (67)
T ss_pred CHHHHHHHHHHcCCeEEEEEE
Confidence 345677777889999999983
No 37
>PF03852 Vsr: DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine []. GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine []. The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology []. ; GO: 0004519 endonuclease activity, 0006298 mismatch repair; PDB: 1ODG_A 1VSR_A 1CW0_A.
Probab=24.24 E-value=77 Score=22.85 Aligned_cols=21 Identities=29% Similarity=0.580 Sum_probs=15.4
Q ss_pred hhhhChhHHHHHHHHHHhCCe
Q psy2782 58 KAKQSRGEKKARKIMSKLGLK 78 (147)
Q Consensus 58 ~~kqsr~EKKaRKaL~KLGLk 78 (147)
+.|-++-|..+|++|-.+|++
T Consensus 17 r~k~TkpE~~lr~~L~~~G~R 37 (75)
T PF03852_consen 17 RSKDTKPELALRRALHALGLR 37 (75)
T ss_dssp -SSS-HHHHHHHHHHHHTT--
T ss_pred cCCCChHHHHHHHHHHhcCCE
Confidence 556678899999999999965
No 38
>KOG3705|consensus
Probab=24.13 E-value=92 Score=29.65 Aligned_cols=31 Identities=26% Similarity=0.473 Sum_probs=26.3
Q ss_pred hChhHHHHHHHHHHhCCeecCCeeEEEEEecCc
Q psy2782 61 QSRGEKKARKIMSKLGLKQIQGVSRVTIRKSKN 93 (147)
Q Consensus 61 qsr~EKKaRKaL~KLGLk~V~gI~RVtirKskn 93 (147)
|+.-++|+-++|++||++. -|.-|.+|+.+.
T Consensus 344 qp~t~~~l~~a~k~lg~~~--PivGvhvRRTDK 374 (580)
T KOG3705|consen 344 QPATQEKLDKALKSLGLDK--PIVGVHVRRTDK 374 (580)
T ss_pred ChhhHHHHHHHHHhCCCCC--ceeeEEEEeccc
Confidence 5788999999999999987 577788888763
No 39
>PF03471 CorC_HlyC: Transporter associated domain; InterPro: IPR005170 This small domain is found in a family of proteins with the CBS IPR002550 from INTERPRO domain and two CBS domains with this domain found at the C terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates.; PDB: 3DED_F 2PLI_C 2R2Z_A 2P4P_A 2O3G_A 2P3H_A 3LLB_A 3LAE_A 2P13_B 2NQW_A ....
Probab=24.04 E-value=55 Score=22.20 Aligned_cols=21 Identities=33% Similarity=0.556 Sum_probs=17.6
Q ss_pred CCCcEEEEccccccchHHHHH
Q psy2782 108 ASDTYIVFGEAKIEDLSQQAQ 128 (147)
Q Consensus 108 ~SnTYIVFGEak~eDlsqqaq 128 (147)
..++|+|-|...++|++....
T Consensus 4 ~~~~~~v~G~~~l~~l~~~~~ 24 (81)
T PF03471_consen 4 DDGTYIVSGSTPLDDLNELLG 24 (81)
T ss_dssp TTSEEEEETTSBHHHHHHHHT
T ss_pred cCCEEEEEecCCHHHHHHHHC
Confidence 368999999999999987653
No 40
>PF14137 DUF4304: Domain of unknown function (DUF4304)
Probab=23.48 E-value=2.3e+02 Score=19.80 Aligned_cols=27 Identities=33% Similarity=0.698 Sum_probs=16.7
Q ss_pred HHHHHhCCeecCCeeEEEEEecCceEEEEe
Q psy2782 70 KIMSKLGLKQIQGVSRVTIRKSKNILFVIN 99 (147)
Q Consensus 70 KaL~KLGLk~V~gI~RVtirKskn~lfvI~ 99 (147)
..|+.+|.+. .|.+... +.++++++|+
T Consensus 3 ~~Lk~~GFkk-~~~~~~~--~~~~~~~~i~ 29 (117)
T PF14137_consen 3 PLLKELGFKK-KGNNFYR--KNDDLIFVIN 29 (117)
T ss_pred hhhhhhCeec-cCCeEEE--ECCCeEEEEE
Confidence 5688899888 6654333 4455555553
No 41
>PF11455 DUF3018: Protein of unknown function (DUF3018); InterPro: IPR021558 This is a bacterial family of uncharacterised proteins.
Probab=22.82 E-value=61 Score=22.82 Aligned_cols=16 Identities=31% Similarity=0.594 Sum_probs=14.0
Q ss_pred HHHHHHHHHhCCeecC
Q psy2782 66 KKARKIMSKLGLKQIQ 81 (147)
Q Consensus 66 KKaRKaL~KLGLk~V~ 81 (147)
+|-|..|..-||+||+
T Consensus 6 ~khR~~lRa~GLRPVq 21 (65)
T PF11455_consen 6 RKHRERLRAAGLRPVQ 21 (65)
T ss_pred HHHHHHHHHcCCCcce
Confidence 6889999999999974
No 42
>cd04438 DEP_dishevelled DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in dishevelled-like proteins. Dishevelled-like proteins play a key role in the transduction of the Wnt signal from the cell surface to the nucleus, which in turn is an important regulatory pathway for cellular development and growth. They contain an N-terminal DIX domain, a central PDZ domain, and a C-terminal DEP domain.
Probab=22.55 E-value=60 Score=23.16 Aligned_cols=22 Identities=23% Similarity=0.386 Sum_probs=18.6
Q ss_pred ceEEEEeCCeeeecCCCCcEEEEcc
Q psy2782 93 NILFVINKPDVFKNPASDTYIVFGE 117 (147)
Q Consensus 93 n~lfvI~~PdVyksp~SnTYIVFGE 117 (147)
|+++|+.+--.|+ ...|-|||+
T Consensus 63 G~i~HV~~~h~F~---d~~yy~~~~ 84 (84)
T cd04438 63 GYIRHTVNKITFS---EQCYYVFGD 84 (84)
T ss_pred CcEEecCCCcccc---CCeEEecCC
Confidence 6889999988887 359999996
No 43
>PF07478 Dala_Dala_lig_C: D-ala D-ala ligase C-terminus; InterPro: IPR011095 This entry represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme 6.3.2.4 from EC. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine: D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [].; GO: 0008716 D-alanine-D-alanine ligase activity; PDB: 3Q1K_D 3I12_C 1IOV_A 1IOW_A 2DLN_A 4EG0_B 3LWB_A 1EHI_B 2FB9_A 3V4Z_A ....
Probab=22.35 E-value=2e+02 Score=23.02 Aligned_cols=35 Identities=23% Similarity=0.433 Sum_probs=26.4
Q ss_pred hChhHHHHHHHHHHhCCeecCCeeEEEEEec-CceEEEE
Q psy2782 61 QSRGEKKARKIMSKLGLKQIQGVSRVTIRKS-KNILFVI 98 (147)
Q Consensus 61 qsr~EKKaRKaL~KLGLk~V~gI~RVtirKs-kn~lfvI 98 (147)
+++=.+=++++..-||++ |+.||-||-+ +|.++++
T Consensus 134 ~~~i~~~a~~a~~~lg~~---~~~RiD~rv~~~g~~~~l 169 (203)
T PF07478_consen 134 QEKIKEIAKKAFKALGCR---GYARIDFRVDEDGKPYFL 169 (203)
T ss_dssp HHHHHHHHHHHHHHTTTC---SEEEEEEEEETTTEEEEE
T ss_pred HHHHHHHHHHHHHHHcCC---CceeEEEEeccCCceEEE
Confidence 344457788999999976 8899999977 5655554
No 44
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=21.32 E-value=2.2e+02 Score=23.55 Aligned_cols=33 Identities=12% Similarity=0.023 Sum_probs=19.0
Q ss_pred eEEEEe-CCe-eeecCCCCcEEEEcccc---ccchHHHH
Q psy2782 94 ILFVIN-KPD-VFKNPASDTYIVFGEAK---IEDLSQQA 127 (147)
Q Consensus 94 ~lfvI~-~Pd-Vyksp~SnTYIVFGEak---~eDlsqqa 127 (147)
++.+.. ++. +|-+ ..+.|+|+|..= -.||+.+.
T Consensus 50 ~~~~~~~~~~i~Y~t-~dg~y~i~G~l~d~~~~nlT~~~ 87 (251)
T PRK11657 50 YAAKYQDMGVTIYLT-PDGKHAISGYMYDEKGENLSEAL 87 (251)
T ss_pred EEEEeCCCceEEEEc-CCCCEEEEEEEEcCCCCccCHHH
Confidence 333433 443 4444 467899999753 34666544
No 45
>TIGR01310 L7 60S ribosomal protein L7, eukaryotic. Members of this family average ~ 250 residues in length, somewhat longer than the archaeal L30P/L7E homolog (~ 155 residues) and much longer than the related bacterial/organellar form (~ 60 residues).
Probab=20.80 E-value=38 Score=28.84 Aligned_cols=49 Identities=22% Similarity=0.447 Sum_probs=33.7
Q ss_pred HHHHHHHHHhCCeecCCeeEEEEEecCceEEEEeCCeeeec-CCCCcEEEEccccccchHH
Q psy2782 66 KKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKN-PASDTYIVFGEAKIEDLSQ 125 (147)
Q Consensus 66 KKaRKaL~KLGLk~V~gI~RVtirKskn~lfvI~~PdVyks-p~SnTYIVFGEak~eDlsq 125 (147)
.+.|++|.-|+|.++.. -+|+-.+|....- ---..||++|++..+-+..
T Consensus 88 p~v~k~L~lLRL~~in~-----------~Vfvk~~~~~~~ML~~VepYVt~G~p~l~tvr~ 137 (235)
T TIGR01310 88 PKPRKVLRLLRLKQVHN-----------GVFVKVNKATLQMLRIVEPYVAYGYPNLKSVRE 137 (235)
T ss_pred HHHHHHHHHhCCCccce-----------EEEEECCHHHHHHHHhcCCeEEEecCCHHHHHH
Confidence 67999999999987654 5666666654321 1134699999998765544
No 46
>PF07717 OB_NTP_bind: Oligonucleotide/oligosaccharide-binding (OB)-fold; InterPro: IPR011709 This domain is found towards the C terminus of the DEAD-box helicases (IPR011545 from INTERPRO). In these helicases it appears to be always found in association with IPR007502 from INTERPRO. ; PDB: 3I4U_A 2XAU_B 3KX2_B.
Probab=20.60 E-value=1.6e+02 Score=20.67 Aligned_cols=49 Identities=24% Similarity=0.354 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhCCeecCCeeEEEEEecCceEEEE-eCCeeeecCCCC------cEEEEcccc
Q psy2782 65 EKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVI-NKPDVFKNPASD------TYIVFGEAK 119 (147)
Q Consensus 65 EKKaRKaL~KLGLk~V~gI~RVtirKskn~lfvI-~~PdVyksp~Sn------TYIVFGEak 119 (147)
...+|++|.. || .++|.+.. .++....+ .+..||-.|.|- .||||+|.-
T Consensus 34 ~~~i~~~l~a-G~--~~nvA~~~---~~~~y~~~~~~~~v~iHPsS~l~~~~p~~vvy~e~~ 89 (114)
T PF07717_consen 34 WELIRAALCA-GF--YPNVARRD---NKGSYKTLSNGQPVFIHPSSVLFKKPPKWVVYHELV 89 (114)
T ss_dssp CHHHHHHHHH-HH--CCCEEEE----TTSSEEETTTG-EEEE-TTSTTTTTT-SEEEEEEEE
T ss_pred HHHHHHHHHH-hh--hhheEEeC---CCCCEEEecCCCEEEEecCccccccccccchhhhhe
Confidence 3666666654 32 45666444 45556666 555677777654 699999863
No 47
>smart00738 NGN In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. In Spt5p, this domain may confer affinity for Spt4p.Spt4p
Probab=20.53 E-value=2.7e+02 Score=19.07 Aligned_cols=14 Identities=21% Similarity=0.268 Sum_probs=11.5
Q ss_pred ChhHHHHHHHHHHh
Q psy2782 62 SRGEKKARKIMSKL 75 (147)
Q Consensus 62 sr~EKKaRKaL~KL 75 (147)
++.|+++.+.|.+.
T Consensus 9 ~g~E~~v~~~L~~~ 22 (106)
T smart00738 9 SGQEKRVAENLERK 22 (106)
T ss_pred CCcHHHHHHHHHHH
Confidence 56789999988886
No 48
>cd01657 Ribosomal_L7_archeal_euk Ribosomal protein L7, which is found in archaea and eukaryotes but not in prokaryotes, binds domain II of the 23S rRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L7 members have an N-terminal extension not found in the archeal L7 orthologs. L7 is closely related to the ribosomal L30 protein found in eukaryotes and prokaryotes.
Probab=20.47 E-value=50 Score=26.15 Aligned_cols=49 Identities=27% Similarity=0.452 Sum_probs=33.9
Q ss_pred HHHHHHHHHhCCeecCCeeEEEEEecCceEEEEeCCeeeecC-CCCcEEEEccccccchHH
Q psy2782 66 KKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNP-ASDTYIVFGEAKIEDLSQ 125 (147)
Q Consensus 66 KKaRKaL~KLGLk~V~gI~RVtirKskn~lfvI~~PdVyksp-~SnTYIVFGEak~eDlsq 125 (147)
.+.|++|..|||+.+.. .+|+-++|.+..-. .-..||.+|++..+-+..
T Consensus 15 ~~~r~tL~~LgL~k~~~-----------~v~~~~t~~~~gmL~kV~~~V~~ge~~~~tv~~ 64 (159)
T cd01657 15 PKIRKTLQLLRLRRINN-----------AVFVKLTKATIGMLKKVEPYVTWGEPNLETLRE 64 (159)
T ss_pred HHHHHHHHHcCCCcCCC-----------EEEEeCCHHHHHHHHHhhhheEeccCcHHHHHH
Confidence 68999999999987654 56666667654311 123599999987665443
No 49
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=20.33 E-value=1.3e+02 Score=27.20 Aligned_cols=27 Identities=33% Similarity=0.572 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCeecCCeeEEEEEecCc
Q psy2782 67 KARKIMSKLGLKQIQGVSRVTIRKSKN 93 (147)
Q Consensus 67 KaRKaL~KLGLk~V~gI~RVtirKskn 93 (147)
+++..|..+-++-+|||.||.|++.++
T Consensus 209 ~l~~~l~~~~vkGi~gI~r~~i~~~~~ 235 (383)
T PRK04309 209 KLAEKIRNIKIKGIKGIKRVIIRKEGD 235 (383)
T ss_pred HHHHHhcccEEECCCCceEEEEecCCC
Confidence 445556666799999999999998755
No 50
>PRK14571 D-alanyl-alanine synthetase A; Provisional
Probab=20.30 E-value=2.2e+02 Score=23.37 Aligned_cols=32 Identities=22% Similarity=0.315 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhCCeecCCeeEEEEEecCceEEEEe
Q psy2782 65 EKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVIN 99 (147)
Q Consensus 65 EKKaRKaL~KLGLk~V~gI~RVtirKskn~lfvI~ 99 (147)
.+-++++...||+. |+.||-|+-.++.+++|.
T Consensus 229 ~~~a~~~~~~lg~~---g~~rvD~~~~~~~~~viE 260 (299)
T PRK14571 229 KETALKAFVEAGCR---GFGRVDGIFSDGRFYFLE 260 (299)
T ss_pred HHHHHHHHHHhCCC---ceEEEEEEEECCcEEEEE
Confidence 46688899999975 899998887766666653
Done!