Query psy18189
Match_columns 119
No_of_seqs 142 out of 203
Neff 3.3
Searched_HMMs 46136
Date Sat Aug 17 01:06:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18189.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18189hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2239|consensus 100.0 5E-38 1.1E-42 249.7 9.7 106 12-117 13-119 (209)
2 PF01849 NAC: NAC domain; Int 99.8 6.4E-19 1.4E-23 113.7 5.8 53 65-117 1-54 (58)
3 PRK06369 nac nascent polypepti 99.7 1.6E-16 3.4E-21 117.1 6.7 52 64-117 6-62 (115)
4 TIGR00264 alpha-NAC-related pr 98.5 3.7E-07 8E-12 67.9 5.7 52 65-116 11-65 (116)
5 COG1308 EGD2 Transcription fac 98.0 1.2E-05 2.6E-10 60.4 5.0 40 66-106 9-50 (122)
6 PF10411 DsbC_N: Disulfide bon 90.9 0.25 5.5E-06 31.6 2.7 32 79-119 21-52 (57)
7 KOG2240|consensus 88.6 0.28 6.1E-06 38.6 1.8 52 63-114 39-90 (162)
8 PRK10877 protein disulfide iso 82.4 3.5 7.6E-05 32.6 5.2 44 66-119 24-74 (232)
9 PF11699 CENP-C_C: Mif2/CENP-C 74.6 5 0.00011 28.0 3.6 37 79-118 39-75 (85)
10 TIGR01955 RfaH transcriptional 68.4 22 0.00047 25.7 5.9 19 61-79 7-25 (159)
11 TIGR00632 vsr DNA mismatch end 62.9 13 0.00027 27.7 3.8 41 57-97 16-62 (117)
12 PF00403 HMA: Heavy-metal-asso 57.7 35 0.00076 20.7 4.6 34 65-103 13-46 (62)
13 PRK09014 rfaH transcriptional 57.5 35 0.00076 25.0 5.3 18 61-78 10-27 (162)
14 COG2428 Uncharacterized conser 54.9 8.8 0.00019 31.2 1.9 51 68-118 40-94 (196)
15 cd03020 DsbA_DsbC_DsbG DsbA fa 47.3 21 0.00046 26.6 2.9 32 78-119 9-40 (197)
16 PRK11657 dsbG disulfide isomer 45.5 64 0.0014 25.8 5.5 46 70-119 28-77 (251)
17 PF07845 DUF1636: Protein of u 44.2 16 0.00034 26.9 1.7 31 86-117 41-73 (116)
18 PF13276 HTH_21: HTH-like doma 38.9 26 0.00057 21.6 1.9 19 62-80 37-55 (60)
19 PF08002 DUF1697: Protein of u 37.1 32 0.0007 25.3 2.4 27 66-97 22-48 (137)
20 KOG3571|consensus 34.1 42 0.00092 31.4 3.1 23 66-89 443-468 (626)
21 smart00738 NGN In Spt5p, this 33.7 1.3E+02 0.0027 20.0 4.7 15 61-75 8-22 (106)
22 PF03852 Vsr: DNA mismatch end 30.5 59 0.0013 22.7 2.7 40 58-97 17-62 (75)
23 PF09401 NSP10: RNA synthesis 27.8 68 0.0015 24.5 2.9 46 66-115 17-62 (124)
24 PLN02875 4-hydroxyphenylpyruva 27.3 1.4E+02 0.0029 26.3 5.0 36 66-101 12-56 (398)
25 KOG4037|consensus 27.2 78 0.0017 26.3 3.3 31 74-104 65-111 (240)
26 PF11455 DUF3018: Protein of 26.7 46 0.001 22.7 1.6 15 66-80 6-20 (65)
27 KOG3198|consensus 26.3 1.3E+02 0.0027 23.8 4.1 46 56-101 37-95 (152)
28 cd02735 RNAP_I_Rpa1_C Largest 25.9 53 0.0012 27.6 2.2 26 68-93 138-163 (309)
29 KOG3169|consensus 25.8 77 0.0017 26.1 3.0 44 74-117 58-105 (208)
30 KOG2852|consensus 25.3 43 0.00094 29.7 1.6 21 97-117 250-270 (380)
31 TIGR03783 Bac_Flav_CT_G Bacter 24.9 23 0.00051 33.4 -0.1 52 63-116 2-55 (829)
32 PF13535 ATP-grasp_4: ATP-gras 24.8 1.5E+02 0.0033 20.6 4.0 35 62-98 138-173 (184)
33 TIGR00922 nusG transcription t 24.7 1.8E+02 0.0039 21.3 4.6 17 61-77 7-27 (172)
34 PF14242 DUF4342: Domain of un 24.6 92 0.002 21.7 2.9 27 66-98 20-46 (84)
35 smart00481 POLIIIAc DNA polyme 23.5 70 0.0015 19.8 1.9 21 63-83 41-61 (67)
36 PF05565 Sipho_Gp157: Siphovir 22.9 1.3E+02 0.0028 22.6 3.6 29 69-97 85-114 (162)
37 PRK14571 D-alanyl-alanine synt 22.5 1.8E+02 0.0038 23.0 4.5 33 63-98 227-259 (299)
38 PRK05609 nusG transcription an 22.3 1.5E+02 0.0032 21.8 3.7 18 61-78 14-35 (181)
39 PF08394 Arc_trans_TRASH: Arch 22.0 61 0.0013 19.8 1.4 16 98-114 9-24 (37)
40 cd02409 KH-II KH-II (K homolo 22.0 1.4E+02 0.003 17.6 3.0 19 82-100 12-33 (68)
41 cd07758 ThTPase Thiamine Triph 21.5 2.3E+02 0.005 21.8 4.8 35 68-102 104-140 (196)
42 PF00327 Ribosomal_L30: Riboso 21.5 70 0.0015 19.8 1.6 15 66-80 15-29 (52)
43 smart00577 CPDc catalytic doma 21.0 75 0.0016 22.8 1.9 54 63-118 69-125 (148)
44 cd00221 Vsr Very Short Patch R 20.9 1.2E+02 0.0025 22.0 2.9 23 57-79 13-35 (115)
45 TIGR02389 RNA_pol_rpoA2 DNA-di 20.8 1.3E+02 0.0028 26.2 3.6 28 66-93 196-223 (367)
46 PF07530 PRE_C2HC: Associated 20.6 1.3E+02 0.0027 20.0 2.8 21 69-90 5-25 (68)
No 1
>KOG2239|consensus
Probab=100.00 E-value=5e-38 Score=249.66 Aligned_cols=106 Identities=52% Similarity=0.725 Sum_probs=94.9
Q ss_pred cCCCCCcccCCCCCCCCCCCCccccccCCCCCCccccCCCCcccchhhccChhHHHHHHHHHhcCCeeecCeeEEEEEec
Q psy18189 12 SSGGEAELHDDSGTESDSEDSIPELEASGDPLGSAGASGLANDLVSKAKQSRGEKKARKIMSKLGLKQIQGVSRVTIRKS 91 (119)
Q Consensus 12 ~~~~~~~~~~~s~~~sdsdd~vPeLee~~~~~q~~~~~~~~~~~~~~~KqSR~EKKARKam~KLGLK~V~gI~RVtirKs 91 (119)
..+..+....+++++|+++|++|+|++++.....++++++++++..++||||+||||||+|+|||||+|+||+||||||+
T Consensus 13 ~~a~~~~~~~~~~~~~~~~ed~~d~~e~d~~~~~~~~~~~~~~~~~~akqsrsekKark~m~KLGlk~v~gV~RVti~ks 92 (209)
T KOG2239|consen 13 QEAPQPQAETGSGTESDSDEDVPELEEQDSTETTDEAAEIDEEPVAKAKQSRSEKKARKAMLKLGLKQVTGVTRVTIRKS 92 (209)
T ss_pred hhccchhhccccCCCCcccccccccccccccccchhhhcccccchhhhhcchHHHHHHHHHHhcCCccccceeEEEEEec
Confidence 33444455689999999999999999998543337788999999999999999999999999999999999999999999
Q ss_pred CcEEEEEcCCeeeeCCCCCcEE-Eeec
Q psy18189 92 KNILFVINKPDVFKNPPLSGSG-FKDI 117 (119)
Q Consensus 92 knilFvI~~PdVyKsp~sdtyV-Fg~~ 117 (119)
|||||||++|||||+|+||||| |||.
T Consensus 93 KNilfvI~kPdVyKsp~sdtYiiFGea 119 (209)
T KOG2239|consen 93 KNILFVITKPDVYKSPASDTYIIFGEA 119 (209)
T ss_pred ccEEEEecCCceeccCCCceEEEeccc
Confidence 9999999999999999999997 9985
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=99.77 E-value=6.4e-19 Score=113.69 Aligned_cols=53 Identities=45% Similarity=0.715 Sum_probs=43.3
Q ss_pred HHHHHHHHHhcCCeeecCeeEEEEEecCcEEEEEcCCeeeeCCCCCcEE-Eeec
Q psy18189 65 EKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPPLSGSG-FKDI 117 (119)
Q Consensus 65 EKKARKam~KLGLK~V~gI~RVtirKsknilFvI~~PdVyKsp~sdtyV-Fg~~ 117 (119)
|||+|++|.||||++++||.||+|+++++.+|+|++|+||++++++||+ ||+.
T Consensus 1 ekk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~~~~P~V~~~~~~~tyvV~G~~ 54 (58)
T PF01849_consen 1 EKKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFVFNNPEVQKSPGSNTYVVFGEA 54 (58)
T ss_dssp -------GHHCT-EEETTEEEEEEEETTTEEEEEESEEEEEETTCCEEEEESEE
T ss_pred CHHHHHHHHHcCCcccCCcEEEEEEECCceEEEEcCCeEEEcCCCCEEEEEeee
Confidence 7999999999999999999999999999999999999999999999888 8874
No 3
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=99.66 E-value=1.6e-16 Score=117.11 Aligned_cols=52 Identities=19% Similarity=0.341 Sum_probs=48.5
Q ss_pred hHHHHHHHHHhcCCe--eecCeeEEEEEecCcEEEEEcCCeee--eCCCCCcEE-Eeec
Q psy18189 64 GEKKARKIMSKLGLK--QIQGVSRVTIRKSKNILFVINKPDVF--KNPPLSGSG-FKDI 117 (119)
Q Consensus 64 ~EKKARKam~KLGLK--~V~gI~RVtirKsknilFvI~~PdVy--Ksp~sdtyV-Fg~~ 117 (119)
++||+||+|.||||+ ++ ||.|||||+++ .+|||++|+|| ++++++||+ ||+-
T Consensus 6 nprk~rkmmkkmGik~e~i-~v~~V~Ir~~~-~~~Vi~~P~V~~m~~~g~~tY~I~Ge~ 62 (115)
T PRK06369 6 NPRKMKQMMKQMGIDVEEL-DVEEVIIRLKD-KEIVFENPQVTVMDAQGQKTYQIVGEP 62 (115)
T ss_pred CHHHHHHHHHHcCCcchhc-CeEEEEEEeCC-EEEEEcCCeEEEEecCCCcEEEEEecc
Confidence 579999999999999 99 99999999999 99999999999 899999776 9973
No 4
>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=98.46 E-value=3.7e-07 Score=67.89 Aligned_cols=52 Identities=19% Similarity=0.189 Sum_probs=45.4
Q ss_pred HHHHHHHHHhcCCeee-cCeeEEEEEe-cCcEEEEEcCCeeeeCCCCCcEE-Eee
Q psy18189 65 EKKARKIMSKLGLKQI-QGVSRVTIRK-SKNILFVINKPDVFKNPPLSGSG-FKD 116 (119)
Q Consensus 65 EKKARKam~KLGLK~V-~gI~RVtirK-sknilFvI~~PdVyKsp~sdtyV-Fg~ 116 (119)
=|+.|++|.+|||+.. .+|.+|+||. ++.++|...++.||+.++..||. ||+
T Consensus 11 ~~~mkkmMk~MGi~~~eidV~~ViIk~~~k~ivf~~p~V~~m~~~G~~tYqI~G~ 65 (116)
T TIGR00264 11 LKQMQKMMKQMGMEMEDLDVEEVIIVFDDEEWIFENPKVQVMDILGVKTYQITGK 65 (116)
T ss_pred HHHHHHHHHHcCCCccccccEEEEEEeCCceEEEecCeeEEEecCCcEEEEEecc
Confidence 3699999999998876 5699999999 68899888888999999998776 886
No 5
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=97.98 E-value=1.2e-05 Score=60.38 Aligned_cols=40 Identities=33% Similarity=0.649 Sum_probs=37.0
Q ss_pred HHHHHHHHhcC--CeeecCeeEEEEEecCcEEEEEcCCeeeeC
Q psy18189 66 KKARKIMSKLG--LKQIQGVSRVTIRKSKNILFVINKPDVFKN 106 (119)
Q Consensus 66 KKARKam~KLG--LK~V~gI~RVtirKsknilFvI~~PdVyKs 106 (119)
++.+|+|..|| ++++.||.||.|+..++. +||++|.||.-
T Consensus 9 r~l~k~mkqmGi~~eeld~v~~V~i~~kd~e-~vi~~P~V~~~ 50 (122)
T COG1308 9 RKLKKLMKQMGIDVEELDGVERVIIKLKDTE-YVIENPQVTVM 50 (122)
T ss_pred HHHHHHHHHhCCCceeccCceEEEEEcCCce-EEeeCCcEEee
Confidence 67789999998 999999999999999998 99999999964
No 6
>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=90.90 E-value=0.25 Score=31.57 Aligned_cols=32 Identities=16% Similarity=0.177 Sum_probs=22.8
Q ss_pred eecCeeEEEEEecCcEEEEEcCCeeeeCCCCCcEEEeecCC
Q psy18189 79 QIQGVSRVTIRKSKNILFVINKPDVFKNPPLSGSGFKDILN 119 (119)
Q Consensus 79 ~V~gI~RVtirKsknilFvI~~PdVyKsp~sdtyVFg~~~~ 119 (119)
+++|+..|++ +++++ +|-++.+.++++|++++
T Consensus 21 pi~GlyeV~~-~~~~i--------~Y~~~dg~yli~G~l~d 52 (57)
T PF10411_consen 21 PIPGLYEVVL-KGGGI--------LYVDEDGRYLIQGQLYD 52 (57)
T ss_dssp SSTTEEEEEE--TTEE--------EEEETTSSEEEES-EEE
T ss_pred CCCCeEEEEE-CCCeE--------EEEcCCCCEEEEeEEEe
Confidence 5788888888 55554 46678899999999863
No 7
>KOG2240|consensus
Probab=88.61 E-value=0.28 Score=38.61 Aligned_cols=52 Identities=23% Similarity=0.376 Sum_probs=47.4
Q ss_pred hhHHHHHHHHHhcCCeeecCeeEEEEEecCcEEEEEcCCeeeeCCCCCcEEE
Q psy18189 63 RGEKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPPLSGSGF 114 (119)
Q Consensus 63 R~EKKARKam~KLGLK~V~gI~RVtirKsknilFvI~~PdVyKsp~sdtyVF 114 (119)
..-||..--|.||++.+++||..|.|-|.+.-..-+++|-|-++.+.+|+.|
T Consensus 39 ~ddkKlqs~lkkl~v~~i~~i~evn~~k~~g~Vihf~~~~vqasl~~nTf~I 90 (162)
T KOG2240|consen 39 ADDKKLQSSLKKLGVNNIPGIEEVNMFKNDGTVIHFNNPKVQASLAANTFTI 90 (162)
T ss_pred cccchhhhhhhhhccccccchhHhhhccccceeEecCCccccccccCCeEEE
Confidence 3457888889999999999999999999999999999999999999998875
No 8
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=82.41 E-value=3.5 Score=32.60 Aligned_cols=44 Identities=11% Similarity=0.237 Sum_probs=30.2
Q ss_pred HHHHHHHHhcCCe-------eecCeeEEEEEecCcEEEEEcCCeeeeCCCCCcEEEeecCC
Q psy18189 66 KKARKIMSKLGLK-------QIQGVSRVTIRKSKNILFVINKPDVFKNPPLSGSGFKDILN 119 (119)
Q Consensus 66 KKARKam~KLGLK-------~V~gI~RVtirKsknilFvI~~PdVyKsp~sdtyVFg~~~~ 119 (119)
...+++|.++|++ |++|+..|.+ ++++ +|-++.+.++++|++++
T Consensus 24 ~~~~~~l~~~~~~v~~v~~sp~~Gl~ev~~--~~~i--------~Y~~~dg~y~i~G~l~d 74 (232)
T PRK10877 24 AAIQQTLAKLGIQSADIQPSPVAGMKTVLT--ESGV--------LYITDDGKHIIQGPMYD 74 (232)
T ss_pred HHHHHHHHHcCCceeEEccCCCCCeEEEEE--CCeE--------EEEcCCCCEEEeeeeEe
Confidence 4556667776654 4678877765 2332 56778889999999875
No 9
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=74.60 E-value=5 Score=27.98 Aligned_cols=37 Identities=32% Similarity=0.398 Sum_probs=27.5
Q ss_pred eecCeeEEEEEecCcEEEEEcCCeeeeCCCCCcEEEeecC
Q psy18189 79 QIQGVSRVTIRKSKNILFVINKPDVFKNPPLSGSGFKDIL 118 (119)
Q Consensus 79 ~V~gI~RVtirKsknilFvI~~PdVyKsp~sdtyVFg~~~ 118 (119)
-+.|..+|||-.. -|+|..-+.|..|.+|+|-|--+.
T Consensus 39 V~~G~v~Vti~~~---~f~v~~G~~F~VP~gN~Y~i~N~~ 75 (85)
T PF11699_consen 39 VIKGKVEVTIHET---SFVVTKGGSFQVPRGNYYSIKNIG 75 (85)
T ss_dssp EEESEEEEEETTE---EEEEETT-EEEE-TT-EEEEEE-S
T ss_pred EEeCEEEEEEcCc---EEEEeCCCEEEECCCCEEEEEECC
Confidence 3689999999654 499999999999999999886543
No 10
>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=68.43 E-value=22 Score=25.73 Aligned_cols=19 Identities=16% Similarity=0.379 Sum_probs=15.9
Q ss_pred cChhHHHHHHHHHhcCCee
Q psy18189 61 QSRGEKKARKIMSKLGLKQ 79 (119)
Q Consensus 61 qSR~EKKARKam~KLGLK~ 79 (119)
.++.|+|+++.|.+.|+.-
T Consensus 7 ~~~~E~~v~~~L~~~gi~~ 25 (159)
T TIGR01955 7 KPRQEQRAQEHLERQAVEC 25 (159)
T ss_pred cCchHHHHHHHHHHCCCEE
Confidence 4688999999999999543
No 11
>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=62.90 E-value=13 Score=27.69 Aligned_cols=41 Identities=20% Similarity=0.519 Sum_probs=34.9
Q ss_pred hhhccChhHHHHHHHHHhcCCe------eecCeeEEEEEecCcEEEE
Q psy18189 57 SKAKQSRGEKKARKIMSKLGLK------QIQGVSRVTIRKSKNILFV 97 (119)
Q Consensus 57 ~~~KqSR~EKKARKam~KLGLK------~V~gI~RVtirKsknilFv 97 (119)
-+++.++.|.+-|++|-.+||+ .+||+--+.+.+-+=++||
T Consensus 16 iR~~~T~pE~~lr~~L~~~G~rfR~q~~~lpg~pD~~~~~~klaIfV 62 (117)
T TIGR00632 16 IRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFI 62 (117)
T ss_pred HhcCCCHHHHHHHHHHHhCCCEEEEecCCCCCcccEEecCCCEEEEE
Confidence 3678889999999999999986 3788888889888877776
No 12
>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=57.69 E-value=35 Score=20.66 Aligned_cols=34 Identities=32% Similarity=0.460 Sum_probs=27.4
Q ss_pred HHHHHHHHHhcCCeeecCeeEEEEEecCcEEEEEcCCee
Q psy18189 65 EKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDV 103 (119)
Q Consensus 65 EKKARKam~KLGLK~V~gI~RVtirKsknilFvI~~PdV 103 (119)
+++.+++|++ ++||..|.+--..+.+-|.-.|+.
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 5677888887 799999999998887777776654
No 13
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=57.47 E-value=35 Score=24.98 Aligned_cols=18 Identities=11% Similarity=0.322 Sum_probs=15.4
Q ss_pred cChhHHHHHHHHHhcCCe
Q psy18189 61 QSRGEKKARKIMSKLGLK 78 (119)
Q Consensus 61 qSR~EKKARKam~KLGLK 78 (119)
.++.|+|+++.|.+.|+.
T Consensus 10 ~~~~E~~v~~~L~~~gi~ 27 (162)
T PRK09014 10 KRGQLQRAQEHLERQGVE 27 (162)
T ss_pred cCchHHHHHHHHHHCCCE
Confidence 468999999999999943
No 14
>COG2428 Uncharacterized conserved protein [Function unknown]
Probab=54.88 E-value=8.8 Score=31.20 Aligned_cols=51 Identities=20% Similarity=0.350 Sum_probs=38.8
Q ss_pred HHHHHHhcCCeeecC-eeEEEEEecCcEEEEEcCCeeeeCC--CCC-cEEEeecC
Q psy18189 68 ARKIMSKLGLKQIQG-VSRVTIRKSKNILFVINKPDVFKNP--PLS-GSGFKDIL 118 (119)
Q Consensus 68 ARKam~KLGLK~V~g-I~RVtirKsknilFvI~~PdVyKsp--~sd-tyVFg~~~ 118 (119)
-++.+.|+|++-||- ++|.-+++++-|++=...++=.+-- ..+ ++|||-||
T Consensus 40 ~p~vlak~g~~~i~e~~~~~~l~r~rvivLDl~a~~~L~PEdas~~~~ivvGGIl 94 (196)
T COG2428 40 EPEVLAKIGLSGIPESITRLPLDRSRVIVLDLQAEEELKPEDASEDTYIVVGGIL 94 (196)
T ss_pred hhHHHHHhccccCchhHhhcccCCCCEEEecCCCCCCCCcccCCcccEEEECccc
Confidence 578999999988875 8899999999888877766655532 345 55699887
No 15
>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=47.27 E-value=21 Score=26.58 Aligned_cols=32 Identities=6% Similarity=0.044 Sum_probs=23.3
Q ss_pred eeecCeeEEEEEecCcEEEEEcCCeeeeCCCCCcEEEeecCC
Q psy18189 78 KQIQGVSRVTIRKSKNILFVINKPDVFKNPPLSGSGFKDILN 119 (119)
Q Consensus 78 K~V~gI~RVtirKsknilFvI~~PdVyKsp~sdtyVFg~~~~ 119 (119)
.+++|+..|.+. .+ -+|-++.+.+.++|++++
T Consensus 9 sp~~Gl~~v~~~--~~--------~~y~~~dg~~~i~G~l~d 40 (197)
T cd03020 9 TPVAGLYEVVTG--GG--------VLYTDDDGRYLIQGNLYD 40 (197)
T ss_pred CCCCCeEEEEEC--CE--------EEEEcCCCCEEEEeEEEE
Confidence 357788888765 22 357788889999999874
No 16
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=45.53 E-value=64 Score=25.80 Aligned_cols=46 Identities=11% Similarity=0.047 Sum_probs=27.3
Q ss_pred HHHHhcCCeeecCeeEEEEEecC--cEEEEEc-CC-eeeeCCCCCcEEEeecCC
Q psy18189 70 KIMSKLGLKQIQGVSRVTIRKSK--NILFVIN-KP-DVFKNPPLSGSGFKDILN 119 (119)
Q Consensus 70 Kam~KLGLK~V~gI~RVtirKsk--nilFvI~-~P-dVyKsp~sdtyVFg~~~~ 119 (119)
+.|.++|++-+. +-..-+. .++.+++ ++ =+|-++.++++++|++++
T Consensus 28 ~~l~~~g~~v~~----~~~~p~~l~g~~~~~~~~~~i~Y~t~dg~y~i~G~l~d 77 (251)
T PRK11657 28 KALEKQGITIIK----TFDAPGGLKGYAAKYQDMGVTIYLTPDGKHAISGYMYD 77 (251)
T ss_pred HHHHhCCCEEEE----eecCCCCceEEEEEeCCCceEEEEcCCCCEEEEEEEEc
Confidence 667888886421 1001111 2333333 45 378888899999999875
No 17
>PF07845 DUF1636: Protein of unknown function (DUF1636); InterPro: IPR012863 The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
Probab=44.17 E-value=16 Score=26.89 Aligned_cols=31 Identities=23% Similarity=0.313 Sum_probs=20.9
Q ss_pred EEEEecCcEEEEEcCCe--eeeCCCCCcEEEeec
Q psy18189 86 VTIRKSKNILFVINKPD--VFKNPPLSGSGFKDI 117 (119)
Q Consensus 86 VtirKsknilFvI~~Pd--VyKsp~sdtyVFg~~ 117 (119)
|+|+.-. -|..=++|= .|..|+--+|||||+
T Consensus 41 v~v~~v~-CL~~C~r~CtVA~~~~gK~tYlfGdl 73 (116)
T PF07845_consen 41 VEVRPVE-CLSACDRPCTVALQAPGKWTYLFGDL 73 (116)
T ss_pred eEEEecc-HHhcCCCceEEEEEcCCCcEEEEecC
Confidence 5665443 345556663 466788889999997
No 18
>PF13276 HTH_21: HTH-like domain
Probab=38.94 E-value=26 Score=21.65 Aligned_cols=19 Identities=26% Similarity=0.602 Sum_probs=16.1
Q ss_pred ChhHHHHHHHHHhcCCeee
Q psy18189 62 SRGEKKARKIMSKLGLKQI 80 (119)
Q Consensus 62 SR~EKKARKam~KLGLK~V 80 (119)
.-|+|+.+++|..+||...
T Consensus 37 ~v~~krV~RlM~~~gL~~~ 55 (60)
T PF13276_consen 37 RVSRKRVRRLMREMGLRSK 55 (60)
T ss_pred cccHHHHHHHHHHcCCccc
Confidence 4568999999999999754
No 19
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=37.08 E-value=32 Score=25.32 Aligned_cols=27 Identities=26% Similarity=0.519 Sum_probs=22.1
Q ss_pred HHHHHHHHhcCCeeecCeeEEEEEecCcEEEE
Q psy18189 66 KKARKIMSKLGLKQIQGVSRVTIRKSKNILFV 97 (119)
Q Consensus 66 KKARKam~KLGLK~V~gI~RVtirKsknilFv 97 (119)
+-=|.++.++|+..|. |.=.|+|++|-
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 4567899999998874 88899999997
No 20
>KOG3571|consensus
Probab=34.10 E-value=42 Score=31.43 Aligned_cols=23 Identities=35% Similarity=0.426 Sum_probs=17.2
Q ss_pred HHHHH---HHHhcCCeeecCeeEEEEE
Q psy18189 66 KKARK---IMSKLGLKQIQGVSRVTIR 89 (119)
Q Consensus 66 KKARK---am~KLGLK~V~gI~RVtir 89 (119)
|+||+ .|+|+||- -+.|.++||-
T Consensus 443 keAR~yAs~lLk~g~I-rHtVnK~TFt 468 (626)
T KOG3571|consen 443 KEARKYASRLLKAGYI-RHTVNKLTFT 468 (626)
T ss_pred HHHHHHHHHHHHhCch-hhcccceeee
Confidence 67776 58899976 3678888875
No 21
>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=33.72 E-value=1.3e+02 Score=19.96 Aligned_cols=15 Identities=20% Similarity=0.251 Sum_probs=12.1
Q ss_pred cChhHHHHHHHHHhc
Q psy18189 61 QSRGEKKARKIMSKL 75 (119)
Q Consensus 61 qSR~EKKARKam~KL 75 (119)
.++.|+++++.|.+.
T Consensus 8 ~~g~E~~v~~~L~~~ 22 (106)
T smart00738 8 TSGQEKRVAENLERK 22 (106)
T ss_pred eCCcHHHHHHHHHHH
Confidence 356799999988886
No 22
>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=30.50 E-value=59 Score=22.71 Aligned_cols=40 Identities=28% Similarity=0.520 Sum_probs=24.1
Q ss_pred hhccChhHHHHHHHHHhcCCe------eecCeeEEEEEecCcEEEE
Q psy18189 58 KAKQSRGEKKARKIMSKLGLK------QIQGVSRVTIRKSKNILFV 97 (119)
Q Consensus 58 ~~KqSR~EKKARKam~KLGLK------~V~gI~RVtirKsknilFv 97 (119)
++|-++-|..-|++|-.+|++ .+||=--+.|.+-+-.+||
T Consensus 17 r~k~TkpE~~lr~~L~~~G~RyR~~~~~lpG~PDiv~~~~k~aIFV 62 (75)
T PF03852_consen 17 RSKDTKPELALRRALHALGLRYRLNRKDLPGKPDIVFPKYKIAIFV 62 (75)
T ss_dssp -SSS-HHHHHHHHHHHHTT--EEES-TTSTT--SEEEGGGTEEEEE
T ss_pred cCCCChHHHHHHHHHHhcCCEEEEccCcCCCCCCEEECCCCEEEEE
Confidence 466788999999999999964 4555444555555544443
No 23
>PF09401 NSP10: RNA synthesis protein NSP10; InterPro: IPR018995 Non-structural protein 10 (NSP10) is involved in RNA synthesis. It is synthesised as part of a replicase polyprotein, whose cleavage generates many non-structural proteins []. NSP10 contains two zinc binding motifs and forms two anti-parallel helices which are stacked against an irregular beta sheet []. A cluster of basic residues on the protein surface suggests a nucleic acid-binding function. ; GO: 0003723 RNA binding, 0008270 zinc ion binding, 0019079 viral genome replication, 0048471 perinuclear region of cytoplasm; PDB: 2XYQ_B 2XYR_B 2XYV_B 3R24_B 2GA6_I 2G9T_V 2FYG_A.
Probab=27.77 E-value=68 Score=24.54 Aligned_cols=46 Identities=24% Similarity=0.197 Sum_probs=23.4
Q ss_pred HHHHHHHHhcCCeeecCeeEEEEEecCcEEEEEcCCeeeeCCCCCcEEEe
Q psy18189 66 KKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPPLSGSGFK 115 (119)
Q Consensus 66 KKARKam~KLGLK~V~gI~RVtirKsknilFvI~~PdVyKsp~sdtyVFg 115 (119)
+||-.-.-+-|-++|.++.++-.-++++-.|+-.+|| ++-+-.+||
T Consensus 17 ~~~Yld~V~~G~~pi~ncvkMl~~~sG~g~ait~~p~----~~~~q~syg 62 (124)
T PF09401_consen 17 AKAYLDYVKPGGKPIVNCVKMLFYKSGEGYAITVKPE----ANLNQDSYG 62 (124)
T ss_dssp HHHHHHHHHTT--------BEE-SSBS---SEESS-------BTTEEEEE
T ss_pred hHhHHHHhccCCccEEEEEEeeecCCCCcEEEEcCCC----CcccccccC
Confidence 5666667788999999999999999999999999998 334444444
No 24
>PLN02875 4-hydroxyphenylpyruvate dioxygenase
Probab=27.26 E-value=1.4e+02 Score=26.30 Aligned_cols=36 Identities=17% Similarity=0.373 Sum_probs=27.5
Q ss_pred HHHHHHHH-hcCCeeec--------CeeEEEEEecCcEEEEEcCC
Q psy18189 66 KKARKIMS-KLGLKQIQ--------GVSRVTIRKSKNILFVINKP 101 (119)
Q Consensus 66 KKARKam~-KLGLK~V~--------gI~RVtirKsknilFvI~~P 101 (119)
+.++.... +||++.+- ..+..++-|.++|.|+++.|
T Consensus 12 ~~~~~~f~~~~GF~~~a~~~~~tg~~~~~s~~~r~g~i~fv~~~~ 56 (398)
T PLN02875 12 TNTARRFSWGLGMPLVAKSDLTTGNTTYASYLLRSGDLVFLFTAP 56 (398)
T ss_pred HHHHHHHHHhcCCCeEeecCCCCCCcceEEEEEEeCCEEEEEeCC
Confidence 55566665 89998764 23567777899999999998
No 25
>KOG4037|consensus
Probab=27.17 E-value=78 Score=26.28 Aligned_cols=31 Identities=48% Similarity=0.745 Sum_probs=24.6
Q ss_pred hcCCeeecC--------------eeEEEEEe--cCcEEEEEcCCeee
Q psy18189 74 KLGLKQIQG--------------VSRVTIRK--SKNILFVINKPDVF 104 (119)
Q Consensus 74 KLGLK~V~g--------------I~RVtirK--sknilFvI~~PdVy 104 (119)
-|||..++| .+|..||- ++.+||-|.+|.|-
T Consensus 65 VL~L~~IT~dyLCSp~aNvy~IdFtrFkIRDldsg~VLFEIaKPp~e 111 (240)
T KOG4037|consen 65 VLGLQRITGDYLCSPEANVYKIDFTRFKIRDLDSGTVLFEIAKPPVE 111 (240)
T ss_pred hhccccccCCceeCcccceEEeeeEEEEEeeccCCcEEEEecCCCCc
Confidence 478887775 56777776 57899999999875
No 26
>PF11455 DUF3018: Protein of unknown function (DUF3018); InterPro: IPR021558 This is a bacterial family of uncharacterised proteins.
Probab=26.68 E-value=46 Score=22.68 Aligned_cols=15 Identities=27% Similarity=0.574 Sum_probs=13.7
Q ss_pred HHHHHHHHhcCCeee
Q psy18189 66 KKARKIMSKLGLKQI 80 (119)
Q Consensus 66 KKARKam~KLGLK~V 80 (119)
+|-|..|...||+||
T Consensus 6 ~khR~~lRa~GLRPV 20 (65)
T PF11455_consen 6 RKHRERLRAAGLRPV 20 (65)
T ss_pred HHHHHHHHHcCCCcc
Confidence 678999999999997
No 27
>KOG3198|consensus
Probab=26.26 E-value=1.3e+02 Score=23.83 Aligned_cols=46 Identities=26% Similarity=0.385 Sum_probs=36.1
Q ss_pred chhhccChhHHHHHHHHHhcCCeee-------------cCeeEEEEEecCcEEEEEcCC
Q psy18189 56 VSKAKQSRGEKKARKIMSKLGLKQI-------------QGVSRVTIRKSKNILFVINKP 101 (119)
Q Consensus 56 ~~~~KqSR~EKKARKam~KLGLK~V-------------~gI~RVtirKsknilFvI~~P 101 (119)
..++.++-.-+--+.++..|||.-. +|=.||.|++-.+.||+|+-|
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 3455556666778899999998753 567899999999999999874
No 28
>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=25.85 E-value=53 Score=27.63 Aligned_cols=26 Identities=19% Similarity=0.422 Sum_probs=21.8
Q ss_pred HHHHHHhcCCeeecCeeEEEEEecCc
Q psy18189 68 ARKIMSKLGLKQIQGVSRVTIRKSKN 93 (119)
Q Consensus 68 ARKam~KLGLK~V~gI~RVtirKskn 93 (119)
.++++.++-++.+|||.|+.|++.++
T Consensus 138 ~~~~l~~~~i~gi~gI~r~~i~~~~~ 163 (309)
T cd02735 138 VEKLARKAVIREIPGITRCFVVEEDK 163 (309)
T ss_pred HHHHhcccEEeCCCCccEEEEecCcC
Confidence 45777888899999999999987653
No 29
>KOG3169|consensus
Probab=25.83 E-value=77 Score=26.14 Aligned_cols=44 Identities=23% Similarity=0.161 Sum_probs=32.0
Q ss_pred hcCCeeecCeeEEEEEecCcEEEEEcCCee----eeCCCCCcEEEeec
Q psy18189 74 KLGLKQIQGVSRVTIRKSKNILFVINKPDV----FKNPPLSGSGFKDI 117 (119)
Q Consensus 74 KLGLK~V~gI~RVtirKsknilFvI~~PdV----yKsp~sdtyVFg~~ 117 (119)
+--|..+.||.=|-+--..-+||||.|--= =-.|=.+|||+|..
T Consensus 58 ~e~L~~m~GieYvl~~~~~P~LfVIrKQ~R~n~tev~PLa~YYII~g~ 105 (208)
T KOG3169|consen 58 EEHLFSMVGIEYVLLHSREPILFVIRKQRRHNPTEVIPLADYYIINGN 105 (208)
T ss_pred HHHHhhCcCeEEEEEecCCCeEEEEehhhcCCCccceeeeeEEEECce
Confidence 334788999999999888889999976321 12345688998764
No 30
>KOG2852|consensus
Probab=25.30 E-value=43 Score=29.66 Aligned_cols=21 Identities=14% Similarity=0.067 Sum_probs=18.5
Q ss_pred EEcCCeeeeCCCCCcEEEeec
Q psy18189 97 VINKPDVFKNPPLSGSGFKDI 117 (119)
Q Consensus 97 vI~~PdVyKsp~sdtyVFg~~ 117 (119)
-|-+|++|-.+...-||||+-
T Consensus 250 ei~~pe~y~rkd~Evyicg~~ 270 (380)
T KOG2852|consen 250 EICKPEEYARKDREVYICGET 270 (380)
T ss_pred cccCcceeecCCceEEEecCC
Confidence 377999999999999999973
No 31
>TIGR03783 Bac_Flav_CT_G Bacteroides conjugation system ATPase, TraG family. Members of this family include the predicted ATPase, TraG, encoded by transfer region genes of conjugative transposons of Bacteroides, such as CTnDOT, found on the main chromosome. Members also include TraG homologs borne on plasmids in Bacteroides. The protein family is related to the conjugative transfer system ATPase VirB4.
Probab=24.93 E-value=23 Score=33.42 Aligned_cols=52 Identities=17% Similarity=0.325 Sum_probs=40.5
Q ss_pred hhHHHHHHHHHhcCCeeecCeeEEEEEecCc--EEEEEcCCeeeeCCCCCcEEEee
Q psy18189 63 RGEKKARKIMSKLGLKQIQGVSRVTIRKSKN--ILFVINKPDVFKNPPLSGSGFKD 116 (119)
Q Consensus 63 R~EKKARKam~KLGLK~V~gI~RVtirKskn--ilFvI~~PdVyKsp~sdtyVFg~ 116 (119)
|+.+|+--+.++++|..|.+ -|.+-|.++ +.|-+.+||+|....++|+-|..
T Consensus 2 ~~~~k~~~~~~~~~~~~~~~--~~i~~~~g~~~v~~~~~~pe~~s~~~~~y~~~~~ 55 (829)
T TIGR03783 2 RNVLKATTLESRFPLLAVEN--GCIVSKDADITVAFRVELPELFTVTSAEYEAIHS 55 (829)
T ss_pred CchhhhhhhhcccChheecC--ceEEecCCCEEEEEEEeCCeEEecCHHHHHHHHH
Confidence 34566666889999998888 488888886 67889999999987777776544
No 32
>PF13535 ATP-grasp_4: ATP-grasp domain; PDB: 3VMM_A 3LN6_A 3LN7_B 2PN1_A 4DIM_A.
Probab=24.77 E-value=1.5e+02 Score=20.58 Aligned_cols=35 Identities=23% Similarity=0.395 Sum_probs=25.9
Q ss_pred ChhHHHHHHHHHhcCCeeecCeeEEEEEecCc-EEEEE
Q psy18189 62 SRGEKKARKIMSKLGLKQIQGVSRVTIRKSKN-ILFVI 98 (119)
Q Consensus 62 SR~EKKARKam~KLGLK~V~gI~RVtirKskn-ilFvI 98 (119)
.+-+..+++++..||+. .|+..|-++...+ -+++|
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 56778999999999987 8999999888763 24444
No 33
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=24.67 E-value=1.8e+02 Score=21.30 Aligned_cols=17 Identities=35% Similarity=0.483 Sum_probs=14.0
Q ss_pred cChhHHHHHHHHHh----cCC
Q psy18189 61 QSRGEKKARKIMSK----LGL 77 (119)
Q Consensus 61 qSR~EKKARKam~K----LGL 77 (119)
.++.|+++.+.|.+ .|+
T Consensus 7 ~~~~E~~v~~~L~~~~~~~g~ 27 (172)
T TIGR00922 7 YSGYEKKVKQNLEELIELLGM 27 (172)
T ss_pred ECChHHHHHHHHHHHHHHCCC
Confidence 46889999999987 575
No 34
>PF14242 DUF4342: Domain of unknown function (DUF4342)
Probab=24.63 E-value=92 Score=21.73 Aligned_cols=27 Identities=30% Similarity=0.557 Sum_probs=20.2
Q ss_pred HHHHHHHHhcCCeeecCeeEEEEEecCcEEEEE
Q psy18189 66 KKARKIMSKLGLKQIQGVSRVTIRKSKNILFVI 98 (119)
Q Consensus 66 KKARKam~KLGLK~V~gI~RVtirKsknilFvI 98 (119)
.+.+.++.| -+++|+.|||....++-|
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 355666665 568999999999887755
No 35
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=23.50 E-value=70 Score=19.80 Aligned_cols=21 Identities=33% Similarity=0.406 Sum_probs=17.0
Q ss_pred hhHHHHHHHHHhcCCeeecCe
Q psy18189 63 RGEKKARKIMSKLGLKQIQGV 83 (119)
Q Consensus 63 R~EKKARKam~KLGLK~V~gI 83 (119)
.+.-.+++++.+.|++.++|+
T Consensus 41 ~~~~~~~~~~~~~gi~~i~G~ 61 (67)
T smart00481 41 FGAVEFYKAAKKAGIKPIIGL 61 (67)
T ss_pred cCHHHHHHHHHHcCCeEEEEE
Confidence 345677788888999999997
No 36
>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].
Probab=22.89 E-value=1.3e+02 Score=22.65 Aligned_cols=29 Identities=24% Similarity=0.378 Sum_probs=22.5
Q ss_pred HHHHHhcCCeeecC-eeEEEEEecCcEEEE
Q psy18189 69 RKIMSKLGLKQIQG-VSRVTIRKSKNILFV 97 (119)
Q Consensus 69 RKam~KLGLK~V~g-I~RVtirKsknilFv 97 (119)
..+|..+|++.|.+ ...|++|++..-+.|
T Consensus 85 ~~~m~~~g~~ki~t~~~tisirk~~~sv~I 114 (162)
T PF05565_consen 85 LDAMEAAGIKKIKTPLFTISIRKNPPSVEI 114 (162)
T ss_pred HHHHHHcCCceeecCceEEEEecCCCCeEe
Confidence 35788999999876 788999998854444
No 37
>PRK14571 D-alanyl-alanine synthetase A; Provisional
Probab=22.51 E-value=1.8e+02 Score=23.00 Aligned_cols=33 Identities=21% Similarity=0.241 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHhcCCeeecCeeEEEEEecCcEEEEE
Q psy18189 63 RGEKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVI 98 (119)
Q Consensus 63 R~EKKARKam~KLGLK~V~gI~RVtirKsknilFvI 98 (119)
+=++-|+++...||+. |+.||-|+-..+-++||
T Consensus 227 ~i~~~a~~~~~~lg~~---g~~rvD~~~~~~~~~vi 259 (299)
T PRK14571 227 LVKETALKAFVEAGCR---GFGRVDGIFSDGRFYFL 259 (299)
T ss_pred HHHHHHHHHHHHhCCC---ceEEEEEEEECCcEEEE
Confidence 4456789999999974 88999988765555555
No 38
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=22.27 E-value=1.5e+02 Score=21.84 Aligned_cols=18 Identities=28% Similarity=0.351 Sum_probs=14.3
Q ss_pred cChhHHHHHHHHHhc----CCe
Q psy18189 61 QSRGEKKARKIMSKL----GLK 78 (119)
Q Consensus 61 qSR~EKKARKam~KL----GLK 78 (119)
.++.|+++++.|.+- |+.
T Consensus 14 ~~~~E~~v~~~L~~~~~~~~i~ 35 (181)
T PRK05609 14 YSGYEKKVKENLENRIETLGME 35 (181)
T ss_pred ECCcHHHHHHHHHHHHHHCCCc
Confidence 468899999998875 765
No 39
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=22.04 E-value=61 Score=19.82 Aligned_cols=16 Identities=25% Similarity=0.044 Sum_probs=12.3
Q ss_pred EcCCeeeeCCCCCcEEE
Q psy18189 98 INKPDVFKNPPLSGSGF 114 (119)
Q Consensus 98 I~~PdVyKsp~sdtyVF 114 (119)
..+|-|||. ++..|+|
T Consensus 9 ~~eP~~~k~-~~~~y~f 24 (37)
T PF08394_consen 9 TGEPIVVKI-GNKVYYF 24 (37)
T ss_pred cCCEEEEEE-CCeEEEE
Confidence 568999998 5667766
No 40
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=21.95 E-value=1.4e+02 Score=17.60 Aligned_cols=19 Identities=32% Similarity=0.672 Sum_probs=13.8
Q ss_pred CeeEEEEEec---CcEEEEEcC
Q psy18189 82 GVSRVTIRKS---KNILFVINK 100 (119)
Q Consensus 82 gI~RVtirKs---knilFvI~~ 100 (119)
||.+|.|.+. ..+.+++.+
T Consensus 12 ~i~~i~i~~~~~~~~~~i~~~~ 33 (68)
T cd02409 12 GISGVEIERTPDRIEIIIVVAR 33 (68)
T ss_pred CCCeEEEEEcCCcEEEEEEECC
Confidence 7889999984 556666665
No 41
>cd07758 ThTPase Thiamine Triphosphatase. ThTPase is a soluble cytosolic enzyme which converts thiamine triphosphate (ThTP) to thiamine diphosphate. This catalytic activity depends on a divalent metal cofactor, for example Mg++. ThTPase regulates the intracellular concentration of ThTP, maintaining it at a low concentration in vivo. ThTP acts as a messenger in cell signaling in response to cellular stress, and in addition, can phosphorylate proteins in certain tissues. There is another class of membrane-associated enzymes in animal tissues which also convert ThTP to thiamine diphosphate, however they do not belong to this subgroup. This subgroup belongs to the CYTH/triphosphate tunnel metalloenzyme (TTM)-like superfamily, whose enzymes have a unique active site located within an eight-stranded beta barrel.
Probab=21.52 E-value=2.3e+02 Score=21.84 Aligned_cols=35 Identities=11% Similarity=0.221 Sum_probs=25.0
Q ss_pred HHHHHHhcCCeeecCeeEEEE--EecCcEEEEEcCCe
Q psy18189 68 ARKIMSKLGLKQIQGVSRVTI--RKSKNILFVINKPD 102 (119)
Q Consensus 68 ARKam~KLGLK~V~gI~RVti--rKsknilFvI~~Pd 102 (119)
.+++|.+||++++-.+++..- +-..++.+++++=+
T Consensus 104 ~~~~L~~lgf~~~~~~~k~R~~y~~~~g~~v~LD~~~ 140 (196)
T cd07758 104 LGDELANLGLREFASFVTKRESWKLDGAFRVDLDRTD 140 (196)
T ss_pred HHHHHhhCCCeEEEEEEEEEEEEEcCCCcEEEEeccc
Confidence 678999999999987765432 22336788887755
No 42
>PF00327 Ribosomal_L30: Ribosomal protein L30p/L7e; InterPro: IPR016082 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L30 is one of the proteins from the large ribosomal subunit. L30 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups bacteria and archaea L30, yeast mitochondrial L33, and Drosophila melanogaster, Dictyostelium discoideum (Slime mold), fungal and mammalian L7 ribosomal proteins. L30 from bacteria are small proteins of about 60 residues, those from archaea are proteins of about 150 residues, and eukaryotic L7 are proteins of about 250 to 270 residues. This entry represents a domain with a ferredoxin-like fold, with a core structure consisting of core: beta-alpha-beta-alpha-beta. This domain is found in prokaryotic ribosomal protein L30 (short-chain member of the family), as well as in archaeal L30 (L30a) (long-chain member of the family), the later containing an additional C-terminal (sub)domain).; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3DF2_Y 3DF4_Y 3O5H_G 3O58_G 1S1I_F 3IZS_e 1M1K_X 1M90_X 1QVG_V 1YIT_W ....
Probab=21.47 E-value=70 Score=19.77 Aligned_cols=15 Identities=47% Similarity=0.784 Sum_probs=12.2
Q ss_pred HHHHHHHHhcCCeee
Q psy18189 66 KKARKIMSKLGLKQI 80 (119)
Q Consensus 66 KKARKam~KLGLK~V 80 (119)
.+.|+.|.-|||+++
T Consensus 15 ~~~~~tl~~LgL~k~ 29 (52)
T PF00327_consen 15 PKVRKTLKALGLRKI 29 (52)
T ss_dssp HHHHHHHHHTT-SST
T ss_pred HHHHHHHHHcCCCcC
Confidence 678999999999866
No 43
>smart00577 CPDc catalytic domain of ctd-like phosphatases.
Probab=20.99 E-value=75 Score=22.76 Aligned_cols=54 Identities=11% Similarity=-0.061 Sum_probs=27.5
Q ss_pred hhHHHHHHHHHhcCCee-e-cC-eeEEEEEecCcEEEEEcCCeeeeCCCCCcEEEeecC
Q psy18189 63 RGEKKARKIMSKLGLKQ-I-QG-VSRVTIRKSKNILFVINKPDVFKNPPLSGSGFKDIL 118 (119)
Q Consensus 63 R~EKKARKam~KLGLK~-V-~g-I~RVtirKsknilFvI~~PdVyKsp~sdtyVFg~~~ 118 (119)
....-++.++..+|+.. . .. +++=.+...|.. .+..-+.+..+..++++|||-.
T Consensus 69 ~~~~~~~~il~~l~~~~~~f~~i~~~~d~~~~KP~--~~k~l~~l~~~p~~~i~i~Ds~ 125 (148)
T smart00577 69 GLRMYADPVLDLLDPKKYFGYRRLFRDECVFVKGK--YVKDLSLLGRDLSNVIIIDDSP 125 (148)
T ss_pred CcHHHHHHHHHHhCcCCCEeeeEEECccccccCCe--EeecHHHcCCChhcEEEEECCH
Confidence 44567888899998743 1 11 111112222211 1111233344567899999864
No 44
>cd00221 Vsr Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches.
Probab=20.88 E-value=1.2e+02 Score=22.03 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=20.0
Q ss_pred hhhccChhHHHHHHHHHhcCCee
Q psy18189 57 SKAKQSRGEKKARKIMSKLGLKQ 79 (119)
Q Consensus 57 ~~~KqSR~EKKARKam~KLGLK~ 79 (119)
-+.++|..|...|++|..+||+.
T Consensus 13 ~r~~~s~~E~~lr~~L~~~Gl~~ 35 (115)
T cd00221 13 IRSKDTKPERAVRSALWELGYRF 35 (115)
T ss_pred hhcCCCHHHHHHHHHHHHCCCEE
Confidence 35679999999999999999963
No 45
>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=20.82 E-value=1.3e+02 Score=26.20 Aligned_cols=28 Identities=36% Similarity=0.644 Sum_probs=21.6
Q ss_pred HHHHHHHHhcCCeeecCeeEEEEEecCc
Q psy18189 66 KKARKIMSKLGLKQIQGVSRVTIRKSKN 93 (119)
Q Consensus 66 KKARKam~KLGLK~V~gI~RVtirKskn 93 (119)
++-++.+..+=++-+|||.|+.|+..++
T Consensus 196 ~~l~~~l~~~~v~Gi~gI~r~~i~~~~~ 223 (367)
T TIGR02389 196 RKLKEKIKNLHIKGIKGIKRVVIRKEGD 223 (367)
T ss_pred HHHHHHhhhceEeCCCCceEEEEECCCC
Confidence 4445566778899999999999986544
No 46
>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth. These proteins are possibly involved in RNA binding or single strand DNA binding.
Probab=20.64 E-value=1.3e+02 Score=20.02 Aligned_cols=21 Identities=10% Similarity=0.189 Sum_probs=17.3
Q ss_pred HHHHHhcCCeeecCeeEEEEEe
Q psy18189 69 RKIMSKLGLKQIQGVSRVTIRK 90 (119)
Q Consensus 69 RKam~KLGLK~V~gI~RVtirK 90 (119)
+.+|.++|+... .|.|++-|+
T Consensus 5 ~~~L~~~G~~v~-~i~~~~~~~ 25 (68)
T PF07530_consen 5 KEELKDQGHPVR-NIHNMHSRN 25 (68)
T ss_pred HHHHHHcCCceE-EEEccccCC
Confidence 578999999855 889988883
Done!