Query 034128
Match_columns 103
No_of_seqs 106 out of 1037
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 10:04:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034128.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034128hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11628 transcriptional regul 100.0 1.8E-35 3.9E-40 200.6 9.8 87 10-102 1-87 (105)
2 PF01722 BolA: BolA-like prote 100.0 9.6E-35 2.1E-39 186.9 9.0 76 19-100 1-76 (76)
3 KOG2313 Stress-induced protein 100.0 1.3E-34 2.9E-39 193.1 9.7 98 3-100 2-100 (100)
4 COG0271 BolA Stress-induced mo 100.0 3E-34 6.4E-39 190.0 9.3 85 14-103 6-90 (90)
5 KOG3348 BolA (bacterial stress 100.0 1.5E-30 3.4E-35 169.3 8.1 81 9-102 1-81 (85)
6 COG5007 Predicted transcriptio 99.9 1.2E-27 2.6E-32 154.2 8.2 76 12-103 2-78 (80)
7 PF06183 DinI: DinI-like famil 73.0 6.6 0.00014 24.3 3.5 31 5-35 2-32 (65)
8 cd05403 NT_KNTase_like Nucleot 70.2 21 0.00046 21.5 8.0 77 11-101 2-79 (93)
9 TIGR02174 CXXU_selWTH selT/sel 65.6 29 0.00063 21.3 5.5 30 5-34 7-36 (72)
10 cd05402 NT_PAP_TUTase Nucleoti 56.6 51 0.0011 21.2 8.2 62 12-82 5-66 (114)
11 PF12543 DUF3738: Protein of u 49.6 46 0.001 24.4 4.9 60 17-89 2-61 (189)
12 PF10330 Stb3: Putative Sin3 b 49.4 21 0.00045 23.8 2.7 22 59-80 33-54 (92)
13 TIGR03435 Soli_TIGR03435 Solib 49.1 34 0.00073 26.3 4.2 69 6-88 27-95 (237)
14 KOG3490 Transcription elongati 48.1 31 0.00067 23.7 3.5 40 56-100 44-91 (111)
15 PF06233 Usg: Usg-like family; 46.6 40 0.00086 22.0 3.6 29 73-101 42-73 (82)
16 PF14824 Sirohm_synth_M: Siroh 44.9 14 0.00031 19.7 1.2 21 4-24 10-30 (30)
17 PF01909 NTP_transf_2: Nucleot 44.9 65 0.0014 19.5 4.5 44 14-65 2-45 (93)
18 PF06006 DUF905: Bacterial pro 42.2 24 0.00053 22.4 2.1 17 28-59 22-38 (70)
19 COG5425 Usg protein, probable 39.8 35 0.00076 22.4 2.6 37 60-102 43-82 (90)
20 PRK10597 DNA damage-inducible 39.5 55 0.0012 21.2 3.5 31 5-35 14-46 (81)
21 PRK00777 phosphopantetheine ad 38.4 1.1E+02 0.0024 21.5 5.3 59 8-74 51-110 (153)
22 PF12685 SpoIIIAH: SpoIIIAH-li 38.3 66 0.0014 23.4 4.2 50 10-77 134-184 (196)
23 PF12170 DNA_pol3_tau_5: DNA p 36.0 1.5E+02 0.0032 20.8 5.6 49 52-102 52-106 (142)
24 cd02164 PPAT_CoAS phosphopante 32.1 1.1E+02 0.0023 21.4 4.3 71 8-94 51-122 (143)
25 PF01877 RNA_binding: RNA bind 31.4 1.7E+02 0.0036 19.7 5.2 24 12-35 14-38 (120)
26 PF06649 DUF1161: Protein of u 30.2 1.1E+02 0.0023 18.4 3.4 24 11-34 3-27 (52)
27 KOG3125 Thymidine kinase [Nucl 29.7 41 0.00089 25.8 2.0 18 57-74 31-50 (234)
28 COG5204 SPT4 Transcription elo 28.3 44 0.00095 22.7 1.7 36 59-99 48-91 (112)
29 COG1019 Predicted nucleotidylt 27.0 2.5E+02 0.0055 20.4 5.8 72 6-95 53-126 (158)
30 PF06042 DUF925: Bacterial pro 24.9 1.5E+02 0.0033 21.4 4.2 34 7-40 48-81 (163)
31 TIGR00090 iojap_ybeB iojap-lik 24.7 2.1E+02 0.0045 18.6 5.0 70 13-100 2-72 (99)
32 PF10262 Rdx: Rdx family; Int 23.8 1.8E+02 0.0039 17.7 5.3 27 6-32 10-38 (76)
33 cd07973 Spt4 Transcription elo 23.3 41 0.00089 22.4 0.9 30 66-100 58-87 (98)
34 smart00542 FYRC "FY-rich" doma 22.8 1.6E+02 0.0035 18.7 3.6 32 53-84 1-35 (86)
35 PRK00447 hypothetical protein; 22.7 2E+02 0.0042 20.3 4.3 21 13-33 17-37 (144)
36 PF07498 Rho_N: Rho terminatio 20.4 97 0.0021 17.2 1.9 20 64-83 20-39 (43)
No 1
>PRK11628 transcriptional regulator BolA; Provisional
Probab=100.00 E-value=1.8e-35 Score=200.63 Aligned_cols=87 Identities=37% Similarity=0.575 Sum_probs=80.9
Q ss_pred hhHHHHHHHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhcCCcce
Q 034128 10 IARAMRMETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDELNSGLHA 89 (103)
Q Consensus 10 ~~~~~~I~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~~~iHA 89 (103)
|+.+++|+++|+++|+|..|+|.|+|++|+||. | |+ +||+|+|||+.|+|||+|+||||||++|+++|+++|||
T Consensus 1 mm~~~~I~~~L~~~l~~~~l~V~d~S~~H~~~~----g-~~-~Hf~v~IVS~~F~G~s~v~RHRlVy~~L~~~i~~~IHA 74 (105)
T PRK11628 1 MMIREQIEEKLRAAFQPVFLEVVDESYRHNVPA----G-SE-SHFKVVLVSDRFTGERFLNRHRMIYSTLAEELSTTVHA 74 (105)
T ss_pred CCcHHHHHHHHHhhCCCcEEEEEECcccccCCC----C-CC-ceEEEEEEChHhCCCCHHHHHHHHHHHHHHHHhCCccc
Confidence 567899999999999999999999999998854 2 24 89999999999999999999999999999999978999
Q ss_pred EEEEecChhHHhh
Q 034128 90 LSIVAKTPQEAAL 102 (103)
Q Consensus 90 lsi~t~tp~Ew~~ 102 (103)
|+|+||||+||+.
T Consensus 75 Lsi~t~tp~Ew~~ 87 (105)
T PRK11628 75 LALHTYTIKEWEG 87 (105)
T ss_pred eeeecCCHHHHHH
Confidence 9999999999975
No 2
>PF01722 BolA: BolA-like protein; InterPro: IPR002634 This family consist of the morpho-protein BolA from Escherichia coli and its various homologs. In E. coli, over-expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division []. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase []. BolA is also induced by stress during early stages of growth [] and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5 [, ].; PDB: 1XS3_A 1V60_A 3O2E_A 1NY8_A 3TR3_A 2KZ0_A 2DHM_A 2KDN_A 1V9J_A.
Probab=100.00 E-value=9.6e-35 Score=186.94 Aligned_cols=76 Identities=57% Similarity=0.911 Sum_probs=68.4
Q ss_pred HHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhcCCcceEEEEecChh
Q 034128 19 KLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDELNSGLHALSIVAKTPQ 98 (103)
Q Consensus 19 ~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~~~iHAlsi~t~tp~ 98 (103)
||+++|+|+.|+|.|+|++|+||. + |++||+|+|||+.|+|||+|+||||||++|+++|+++||||+|+|+||+
T Consensus 1 Kl~~~l~~~~l~V~d~S~~H~~h~----~--g~sHf~i~IvS~~F~g~s~i~rhr~V~~~L~~~i~~~iHAlsi~t~tp~ 74 (76)
T PF01722_consen 1 KLKAALPPTHLEVEDESHKHAGHA----G--GGSHFKIIIVSDEFEGKSRIKRHRLVYKALKDEIKDGIHALSIKTYTPE 74 (76)
T ss_dssp HHHHHHTTSEEEEEE-SSSSSS-C----C--SSSEEEEEEECGGGTTS-HHHHHHHHHHHTHHHHGCTCSEEEEEEE-HH
T ss_pred ChhHhCCCcEEEEEECcccccCCC----C--CCceEEEEEEcHHhCCCCHHHHHHHHHHHHHHHhcCCceEEEEEcCCcc
Confidence 688999999999999999999999 3 2499999999999999999999999999999999978999999999999
Q ss_pred HH
Q 034128 99 EA 100 (103)
Q Consensus 99 Ew 100 (103)
||
T Consensus 75 Ew 76 (76)
T PF01722_consen 75 EW 76 (76)
T ss_dssp HH
T ss_pred cC
Confidence 99
No 3
>KOG2313 consensus Stress-induced protein UVI31+ [Signal transduction mechanisms]
Probab=100.00 E-value=1.3e-34 Score=193.07 Aligned_cols=98 Identities=48% Similarity=0.706 Sum_probs=93.4
Q ss_pred CCCCcchhhHHHHHHHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHH
Q 034128 3 SRGANAVIARAMRMETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDE 82 (103)
Q Consensus 3 ~~~~~~~~~~~~~I~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~ 82 (103)
+++++.++++..+|+++|..+|.|..+++.|+|++|+||+..+|...+|+||+|.|||++|+|+|+++||||||++|+||
T Consensus 2 ~~~~~~~g~~~~ri~~~l~~~lkp~~le~~n~S~~hagH~~~kg~~~~EtHFrv~vVS~~FeG~s~v~RHRlVy~~L~eE 81 (100)
T KOG2313|consen 2 SAPSGIYGPRESRIREKLFEALKPLNLELYNESHQHAGHAVPKGMDGAETHFRVEVVSSAFEGLSLVKRHRLVYKALKEE 81 (100)
T ss_pred CCcccccCcHHHHHHHHhHhhcCcceEEEeeccccccccccccCCCCCccEEEEEEechhhCCccHHHHHHHHHHHHHHH
Confidence 56789999999999999999999999999999999999999998555789999999999999999999999999999999
Q ss_pred hcC-CcceEEEEecChhHH
Q 034128 83 LNS-GLHALSIVAKTPQEA 100 (103)
Q Consensus 83 i~~-~iHAlsi~t~tp~Ew 100 (103)
+.+ ++|||+|.++||+||
T Consensus 82 l~~~gvHAL~i~aKTP~e~ 100 (100)
T KOG2313|consen 82 LAGTGVHALSIMAKTPSEV 100 (100)
T ss_pred hhccceeEEEeeccCCCCC
Confidence 998 699999999999998
No 4
>COG0271 BolA Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]
Probab=100.00 E-value=3e-34 Score=190.00 Aligned_cols=85 Identities=52% Similarity=0.813 Sum_probs=79.9
Q ss_pred HHHHHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhcCCcceEEEE
Q 034128 14 MRMETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDELNSGLHALSIV 93 (103)
Q Consensus 14 ~~I~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~~~iHAlsi~ 93 (103)
.+|+++|+++|+|..++|.|+|+.|+||++ +|+ +||+|+|||+.|+|||+|+|||+||.+|+++|.++||||+|+
T Consensus 6 ~~Ie~~l~~~f~p~~l~i~deS~~h~~~~~----g~~-~Hf~i~IVS~~F~G~s~v~rHr~V~~~L~del~~~iHALal~ 80 (90)
T COG0271 6 ERIEKKLRAAFPPSFLEIIDESHRHHGHAG----GGG-SHFKVVIVSEAFQGKSLVARHRLVYSALKDELSGGIHALALH 80 (90)
T ss_pred HHHHHHHHhcCCCceEEEEecccccccCCC----CCC-CeEEEEEEchhhCCccHHHHHHHHHHHHHHHHhccceeeEeE
Confidence 689999999999999999999999999996 335 999999999999999999999999999999999779999999
Q ss_pred ecChhHHhhC
Q 034128 94 AKTPQEAALK 103 (103)
Q Consensus 94 t~tp~Ew~~~ 103 (103)
|+||+||..+
T Consensus 81 t~t~~e~~~~ 90 (90)
T COG0271 81 TYTPEEWKGK 90 (90)
T ss_pred eeccchhccC
Confidence 9999999753
No 5
>KOG3348 consensus BolA (bacterial stress-induced morphogen)-related protein [Signal transduction mechanisms]
Probab=99.97 E-value=1.5e-30 Score=169.33 Aligned_cols=81 Identities=42% Similarity=0.665 Sum_probs=76.8
Q ss_pred hhhHHHHHHHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhcCCcc
Q 034128 9 VIARAMRMETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDELNSGLH 88 (103)
Q Consensus 9 ~~~~~~~I~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~~~iH 88 (103)
++..+++|+++|+++|.|.+|+|+|.| |||| +.|+|+|||+.|+|||+|+|||+||++|+++|+ .||
T Consensus 1 m~~~e~~l~~~L~~~l~p~~v~V~D~S-----------gGCG-~~F~v~IvS~~FeGKs~L~rHRlVN~~L~Eeik-~iH 67 (85)
T KOG3348|consen 1 MTVTEERLEELLTEALEPEHVEVQDVS-----------GGCG-SMFDVVIVSAAFEGKSLLARHRLVNSILAEEIK-EIH 67 (85)
T ss_pred CcchHHHHHHHHHhhcCceEEEEEEcC-----------CCcc-ceEEEEEEccccCChHHHHHHHHHHHHHHHHHH-HHh
Confidence 356789999999999999999999998 6699 999999999999999999999999999999998 899
Q ss_pred eEEEEecChhHHhh
Q 034128 89 ALSIVAKTPQEAAL 102 (103)
Q Consensus 89 Alsi~t~tp~Ew~~ 102 (103)
||+++||||++|..
T Consensus 68 alt~kt~t~~~w~~ 81 (85)
T KOG3348|consen 68 ALTIKTYTPEEWSK 81 (85)
T ss_pred hheeeecChhhhcc
Confidence 99999999999974
No 6
>COG5007 Predicted transcriptional regulator, BolA superfamily [Transcription]
Probab=99.95 E-value=1.2e-27 Score=154.16 Aligned_cols=76 Identities=34% Similarity=0.503 Sum_probs=71.0
Q ss_pred HHHHHHHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhc-CCcceE
Q 034128 12 RAMRMETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDELN-SGLHAL 90 (103)
Q Consensus 12 ~~~~I~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~-~~iHAl 90 (103)
..++|+..|+++||.++++|+.+ | +||.+++||+.|+|||+|+|||+||..|.++|. +.||||
T Consensus 2 ~~e~Ik~ll~~~L~~e~v~V~Gd---------------g-~Hf~vi~Vs~~F~g~srvkrqq~vYApL~~~i~~~~IHAl 65 (80)
T COG5007 2 DNEEIKSLLENALPLEEVEVEGD---------------G-SHFQVIAVSEEFAGKSRVKRQQLVYAPLMAYIADNEIHAL 65 (80)
T ss_pred CHHHHHHHHHhcCCccEEEEecC---------------C-ceEEEEEehHhhcCccHHHHHHHHHHHHHHHhhcCceEEE
Confidence 35899999999999999999976 4 899999999999999999999999999999998 569999
Q ss_pred EEEecChhHHhhC
Q 034128 91 SIVAKTPQEAALK 103 (103)
Q Consensus 91 si~t~tp~Ew~~~ 103 (103)
+|+||||+||.++
T Consensus 66 sikt~Tp~eW~~~ 78 (80)
T COG5007 66 SIKTYTPAEWARD 78 (80)
T ss_pred EeeecCHHHhhhc
Confidence 9999999999864
No 7
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=72.95 E-value=6.6 Score=24.27 Aligned_cols=31 Identities=16% Similarity=0.139 Sum_probs=25.4
Q ss_pred CCcchhhHHHHHHHHHHhcCCCceEEEEecC
Q 034128 5 GANAVIARAMRMETKLRSALEATVLEIDDVS 35 (103)
Q Consensus 5 ~~~~~~~~~~~I~~~L~~~l~~~~v~V~d~S 35 (103)
+.|.+.....++.++|...||...|.|...|
T Consensus 2 p~ga~~AL~~EL~kRl~~~yPd~~v~Vr~~s 32 (65)
T PF06183_consen 2 PAGALEALESELTKRLHRQYPDAEVRVRPGS 32 (65)
T ss_dssp -TTHHHHHHHHHHHHHHHH-SS-EEEEEEES
T ss_pred CccHHHHHHHHHHHHHHHHCCCceEeeeecc
Confidence 4677888899999999999999999999775
No 8
>cd05403 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is
Probab=70.24 E-value=21 Score=21.51 Aligned_cols=77 Identities=12% Similarity=0.025 Sum_probs=49.2
Q ss_pred hHHHHHHHHHHhcCC-CceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhcCCcce
Q 034128 11 ARAMRMETKLRSALE-ATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDELNSGLHA 89 (103)
Q Consensus 11 ~~~~~I~~~L~~~l~-~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~~~iHA 89 (103)
...++|.+.|++.+. ...+-+...- ++|+....|.++|.|+.+.........+ ....+... ....
T Consensus 2 ~~~~~i~~~l~~~~~~i~~i~LfGS~--------arg~~~~~SDiDl~vi~~~~~~~~~~~~---~~~~~~~~---~~~~ 67 (93)
T cd05403 2 EILEEILEILRELLGGVEKVYLFGSY--------ARGDARPDSDIDLLVIFDDPLDPLELAR---LLEELELL---LGRP 67 (93)
T ss_pred hhHHHHHHHHHHHhCCccEEEEEeee--------ecCCCCCCCCeeEEEEeCCCCCHHHHHH---HHHHHHHH---hCCc
Confidence 346788888888887 7788888763 2233224599999999999987666554 22222222 2455
Q ss_pred EEEEecChhHHh
Q 034128 90 LSIVAKTPQEAA 101 (103)
Q Consensus 90 lsi~t~tp~Ew~ 101 (103)
+.+..+++.++.
T Consensus 68 vDi~~~~~~~~~ 79 (93)
T cd05403 68 VDLVVLNALELE 79 (93)
T ss_pred EEEEECCccchh
Confidence 666666666553
No 9
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=65.61 E-value=29 Score=21.35 Aligned_cols=30 Identities=17% Similarity=0.227 Sum_probs=25.2
Q ss_pred CCcchhhHHHHHHHHHHhcCCCceEEEEec
Q 034128 5 GANAVIARAMRMETKLRSALEATVLEIDDV 34 (103)
Q Consensus 5 ~~~~~~~~~~~I~~~L~~~l~~~~v~V~d~ 34 (103)
+.+.++.++..+++.|.+.||...+.+...
T Consensus 7 ~~C~y~~Ra~~l~q~L~~~Fp~~~v~~~~~ 36 (72)
T TIGR02174 7 GSCGYKPRAAWLKQELLEEFPDLEIEGENT 36 (72)
T ss_pred CCCCChHHHHHHHHHHHHHCCCCeeEEeee
Confidence 356689999999999999999887777665
No 10
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=56.56 E-value=51 Score=21.18 Aligned_cols=62 Identities=11% Similarity=0.071 Sum_probs=43.0
Q ss_pred HHHHHHHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHH
Q 034128 12 RAMRMETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDE 82 (103)
Q Consensus 12 ~~~~I~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~ 82 (103)
..++|++.++..+|...+.+...+.. |-+...|..++.|..+.. .......-+.+.++|+..
T Consensus 5 i~~~l~~~i~~~~~~~~v~~fGS~~~--------g~~~~~SDiDl~i~~~~~-~~~~~~~l~~l~~~l~~~ 66 (114)
T cd05402 5 VLDRLQELIKEWFPGAKLYPFGSYVT--------GLGLPGSDIDLCLLGPNH-RVDREDFLRKLAKLLKKS 66 (114)
T ss_pred HHHHHHHHHHHHCCCCEEEEeccccc--------CCCCCCCCeeEEEEeCCC-CccHHHHHHHHHHHHHhC
Confidence 45788888888788889999987632 211233899999999977 345555556666666543
No 11
>PF12543 DUF3738: Protein of unknown function (DUF3738); InterPro: IPR017801 This entry describes a paralogous family of about 40 proteins first found in Solibacter usitatus (strain Ellin6076), one of the first three members of the Acidobacteria to be sequenced. The family is well-diversified, with few protein pairs showing greater than 50 % pairwise identity. A few members of the family are longer, multidomain proteins.
Probab=49.61 E-value=46 Score=24.35 Aligned_cols=60 Identities=13% Similarity=0.165 Sum_probs=41.4
Q ss_pred HHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhcCCcce
Q 034128 17 ETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDELNSGLHA 89 (103)
Q Consensus 17 ~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~~~iHA 89 (103)
+.+|..++.-..-.|..- ++|-...+|+|....|. +-+.-+...|+-++|++.|.-.+|-
T Consensus 2 ~~lI~~Ay~v~~~qiv~~-----------P~W~~~~ryDI~Ak~p~--~~~~~q~~~MLq~lLaeRF~L~~H~ 61 (189)
T PF12543_consen 2 KDLIQFAYGVQPYQIVGG-----------PDWLDSERYDIVAKVPP--GSTRDQLRLMLQALLAERFKLKVHR 61 (189)
T ss_pred HHHHHHHHCCChhhcccC-----------CCCCccCceeEEEECCC--CCCHHHHHHHHHHHHHHHhCcEEEe
Confidence 455666666554443322 36666689999987764 5666778999999999999744553
No 12
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=49.42 E-value=21 Score=23.82 Aligned_cols=22 Identities=18% Similarity=0.376 Sum_probs=20.2
Q ss_pred ECCCCCCCCHHHHHHHHHHHHH
Q 034128 59 VSPKFEGKNLVNRHRMVYQVLS 80 (103)
Q Consensus 59 vS~~F~G~s~l~RhrlVy~~L~ 80 (103)
--|.|++.|.=++-|+|..+|.
T Consensus 33 ~vPgF~~ls~sKqRRLi~~ALE 54 (92)
T PF10330_consen 33 SVPGFSDLSPSKQRRLIMAALE 54 (92)
T ss_pred cCCCcccCCHHHHHHHHHHHHh
Confidence 3488999999999999999997
No 13
>TIGR03435 Soli_TIGR03435 Solibacter paralogous family TIGR03435. This model describes a paralogous family of about 40 proteins found in Solibacter usitatus Ellin6076, one of the first three members of the Acidobacteria to be sequenced, and nowhere else. The family is well-diversified, with few pairs showing greater than 50 % pairwise identity. Two members of the family are longer, multidomain proteins with (two different) fused peptidase domains.
Probab=49.14 E-value=34 Score=26.32 Aligned_cols=69 Identities=12% Similarity=0.240 Sum_probs=51.9
Q ss_pred CcchhhHHHHHHHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhcC
Q 034128 6 ANAVIARAMRMETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDELNS 85 (103)
Q Consensus 6 ~~~~~~~~~~I~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~~ 85 (103)
.|.+...--.++++|..++.-....|..- +|-...+|+|...-| .|-++=+.-.|.-.+|++-|.-
T Consensus 27 ~g~~~~~~~tL~~lI~~AY~v~~~qv~GP------------~Wl~serfDi~Ak~p--~g~~~~q~~~MLQ~LLaeRF~L 92 (237)
T TIGR03435 27 GGRLTITNVTLRDLIQAAYGVKPYQVSGP------------DWLDSERFDIVAKAP--AGATREQVRLMLQTLLAERFKL 92 (237)
T ss_pred CCEEEEcCCCHHHHHHHHhCCCHHheeCC------------CcCCccceeEEEeCC--CCCCHHHHHHHHHHHHHHhhCe
Confidence 34444455678899999988776666643 455568999999998 6778888888999999999974
Q ss_pred Ccc
Q 034128 86 GLH 88 (103)
Q Consensus 86 ~iH 88 (103)
.+|
T Consensus 93 ~~H 95 (237)
T TIGR03435 93 AVH 95 (237)
T ss_pred EEe
Confidence 444
No 14
>KOG3490 consensus Transcription elongation factor SPT4 [Transcription]
Probab=48.11 E-value=31 Score=23.69 Aligned_cols=40 Identities=25% Similarity=0.497 Sum_probs=31.0
Q ss_pred EEEECCCCCCC--------CHHHHHHHHHHHHHHHhcCCcceEEEEecChhHH
Q 034128 56 LKIVSPKFEGK--------NLVNRHRMVYQVLSDELNSGLHALSIVAKTPQEA 100 (103)
Q Consensus 56 i~IvS~~F~G~--------s~l~RhrlVy~~L~~~i~~~iHAlsi~t~tp~Ew 100 (103)
....||.|+|+ ||+.+.+.|- .|..|++|+++.-.=|+|.
T Consensus 44 ~ecTS~nF~GiIa~m~Pt~SWVakWqri~-----~f~~G~YAi~VsG~Lpe~~ 91 (111)
T KOG3490|consen 44 YECTSPNFDGIIAMMSPTESWVAKWQRIG-----RFTPGMYAISVSGVLPEEV 91 (111)
T ss_pred EEecCCCccceeeeeCccHHHHHHHHhhc-----cccCceEEEEecccCCHHH
Confidence 35679999985 8899988873 4545999999987777764
No 15
>PF06233 Usg: Usg-like family; InterPro: IPR009354 This is a family of bacterial proteins, referred to as Usg. Usg is found in the same operon as trpF, trpB, and trpA and is expressed in a coupled transcription-translation system [].
Probab=46.61 E-value=40 Score=22.03 Aligned_cols=29 Identities=21% Similarity=0.257 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhcCCcceEEEE---ecChhHHh
Q 034128 73 RMVYQVLSDELNSGLHALSIV---AKTPQEAA 101 (103)
Q Consensus 73 rlVy~~L~~~i~~~iHAlsi~---t~tp~Ew~ 101 (103)
+.-.+-+.++|.+.+|++.+. ...|.||.
T Consensus 42 ~~Fl~fW~~~leG~LHSVrvah~~LI~p~E~r 73 (82)
T PF06233_consen 42 FKFLDFWQRELEGPLHSVRVAHRKLIRPAEWR 73 (82)
T ss_pred HHHHHHHHHhccCceeEEEeecccccChHHhh
Confidence 445678899999889999885 57799996
No 16
>PF14824 Sirohm_synth_M: Sirohaem biosynthesis protein central; PDB: 1KYQ_B.
Probab=44.88 E-value=14 Score=19.67 Aligned_cols=21 Identities=10% Similarity=0.010 Sum_probs=16.3
Q ss_pred CCCcchhhHHHHHHHHHHhcC
Q 034128 4 RGANAVIARAMRMETKLRSAL 24 (103)
Q Consensus 4 ~~~~~~~~~~~~I~~~L~~~l 24 (103)
+++|.....+..|++.|++.|
T Consensus 10 STnG~sP~la~~iR~~ie~~l 30 (30)
T PF14824_consen 10 STNGKSPRLARLIRKEIERLL 30 (30)
T ss_dssp EESSS-HHHHHHHHHHHHHHH
T ss_pred ECCCCChHHHHHHHHHHHHhC
Confidence 567888889999999998654
No 17
>PF01909 NTP_transf_2: Nucleotidyltransferase domain A subset of this Pfam family; InterPro: IPR002934 A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [, ]. Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analogue of the fingers domain found in many polymerases.; GO: 0016779 nucleotidyltransferase activity; PDB: 4EBK_B 4EBJ_A 1KNY_A 2B4V_A 2B56_A 2B51_A 1NO5_B 1Q79_A 1Q78_A 1F5A_A ....
Probab=44.86 E-value=65 Score=19.54 Aligned_cols=44 Identities=11% Similarity=0.153 Sum_probs=32.8
Q ss_pred HHHHHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCC
Q 034128 14 MRMETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEG 65 (103)
Q Consensus 14 ~~I~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G 65 (103)
++|.+.|+..++...+.+..... .|.....|.+++.|+.+....
T Consensus 2 ~~i~~~l~~~~~~~~v~lfGS~a--------~g~~~~~SDIDl~i~~~~~~~ 45 (93)
T PF01909_consen 2 EEIKEILKELFGVAEVYLFGSYA--------RGDATPDSDIDLLIILDEPED 45 (93)
T ss_dssp HHHHHHHHHHHTTEEEEEEHHHH--------HTSSCTTSCEEEEEEESSTSC
T ss_pred HHHHHHHHHHCCCCEEEEECCcc--------cCcCCCCCCEEEEEEeCCccc
Confidence 57888888888888888887642 232223389999999999876
No 18
>PF06006 DUF905: Bacterial protein of unknown function (DUF905); InterPro: IPR009253 This family consists of several short hypothetical proteobacterial proteins of unknown function.; PDB: 2HJJ_A.
Probab=42.25 E-value=24 Score=22.35 Aligned_cols=17 Identities=41% Similarity=0.581 Sum_probs=10.8
Q ss_pred eEEEEecCccccCCccccCCCCccceeEEEEE
Q 034128 28 VLEIDDVSHKHAGHAAVKDSNSGETHFDLKIV 59 (103)
Q Consensus 28 ~v~V~d~S~~H~gH~~~~~~~~~esHf~i~Iv 59 (103)
.|-|+|+. | +||+++|-
T Consensus 22 NV~IeDdq--------------g-~HfRlvvR 38 (70)
T PF06006_consen 22 NVFIEDDQ--------------G-THFRLVVR 38 (70)
T ss_dssp TEEEES-S--------------S-S--EEEEE
T ss_pred ceeeccCC--------------C-CeEEEEEE
Confidence 47788873 3 89999998
No 19
>COG5425 Usg protein, probable subunit of phosphoribosylanthranilate isomerase [Amino acid transport and metabolism]
Probab=39.84 E-value=35 Score=22.42 Aligned_cols=37 Identities=22% Similarity=0.319 Sum_probs=27.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHhcCCcceEEEE---ecChhHHhh
Q 034128 60 SPKFEGKNLVNRHRMVYQVLSDELNSGLHALSIV---AKTPQEAAL 102 (103)
Q Consensus 60 S~~F~G~s~l~RhrlVy~~L~~~i~~~iHAlsi~---t~tp~Ew~~ 102 (103)
+|.|--| +-..+-+++++.+.+|++... ...|+||..
T Consensus 43 AP~FP~l------~~Fl~fWq~~ldGpLHsVry~H~~li~p~eWr~ 82 (90)
T COG5425 43 APEFPVL------KGFLDFWQRELDGPLHSVRYTHRRLISPSEWRA 82 (90)
T ss_pred CcccHHH------HHHHHHHHHhccCCceeeehhhhhhcCHHHHhh
Confidence 5666443 345678899999889999864 678999973
No 20
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=39.48 E-value=55 Score=21.17 Aligned_cols=31 Identities=16% Similarity=0.171 Sum_probs=27.1
Q ss_pred CCcchhhHHHHHHHHHHhcCCCce--EEEEecC
Q 034128 5 GANAVIARAMRMETKLRSALEATV--LEIDDVS 35 (103)
Q Consensus 5 ~~~~~~~~~~~I~~~L~~~l~~~~--v~V~d~S 35 (103)
+.|.+.....+|..+|...||... |.|.-.|
T Consensus 14 p~ga~~AL~~EL~kRl~~~fPd~~~~v~Vr~~s 46 (81)
T PRK10597 14 PAGAIDALAGELSRRIQYAFPDNEGHVSVRYAA 46 (81)
T ss_pred ChhHHHHHHHHHHHHHHhhCCCCCccEEEeecC
Confidence 457888899999999999999987 9998775
No 21
>PRK00777 phosphopantetheine adenylyltransferase; Provisional
Probab=38.36 E-value=1.1e+02 Score=21.49 Aligned_cols=59 Identities=22% Similarity=0.255 Sum_probs=31.0
Q ss_pred chhhHHHHHHHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCC-CCCCCHHHHHHH
Q 034128 8 AVIARAMRMETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPK-FEGKNLVNRHRM 74 (103)
Q Consensus 8 ~~~~~~~~I~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~-F~G~s~l~Rhrl 74 (103)
++..+.+.++..+....+...+.+...+... .+. ....++++|+|++ ..|-..+++.|.
T Consensus 51 ~~e~R~~~v~~~~~~~~~~~~~~i~~i~d~~------gp~--~~~~~d~ivvs~et~~~~~~in~~r~ 110 (153)
T PRK00777 51 PYEVRLKNLKKFLKAVEYDREYEIVKIDDPY------GPA--LEDDFDAIVVSPETYPGALKINEIRR 110 (153)
T ss_pred CHHHHHHHHHHHHHhcCCCCcEEEEeccccC------CCc--cccCCCEEEEChhhhhhHHHHHHHHH
Confidence 3344445555555443344456655433211 112 1235999999997 666655554443
No 22
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=38.34 E-value=66 Score=23.41 Aligned_cols=50 Identities=20% Similarity=0.347 Sum_probs=29.6
Q ss_pred hhHHHHHHHHHHhc-CCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHH
Q 034128 10 IARAMRMETKLRSA-LEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQ 77 (103)
Q Consensus 10 ~~~~~~I~~~L~~~-l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~ 77 (103)
+..+..|+.+|+++ |+.+.|.+.|. .++|+|-++.....-..+--.+|.+
T Consensus 134 ~~kE~~iE~llkakGf~davv~~~~~------------------~v~VvV~~~~L~~~~~~~I~diV~~ 184 (196)
T PF12685_consen 134 MEKEMEIENLLKAKGFEDAVVFIEDD------------------SVDVVVKADKLSDAEAAQIIDIVMR 184 (196)
T ss_dssp HHHHHHHHHHHHTTS-SEEEEE-SSS------------------EEEEEEE-S---HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCceEEEeeCC------------------EEEEEEeCCCCCHHHHHHHHHHHHH
Confidence 44567899999988 88877777643 6899999998444433433333333
No 23
>PF12170 DNA_pol3_tau_5: DNA polymerase III tau subunit V interacting with alpha; InterPro: IPR021029 This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with PF00004 from PFAM. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. The extreme C-terminal region of this domain 5 is the part which interacts with the alpha subunit of the DNA polymerase III holoenzyme [, ]. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 2AYA_A.
Probab=36.00 E-value=1.5e+02 Score=20.79 Aligned_cols=49 Identities=24% Similarity=0.209 Sum_probs=32.7
Q ss_pred ceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhcCCcceEEEE------ecChhHHhh
Q 034128 52 THFDLKIVSPKFEGKNLVNRHRMVYQVLSDELNSGLHALSIV------AKTPQEAAL 102 (103)
Q Consensus 52 sHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~~~iHAlsi~------t~tp~Ew~~ 102 (103)
..+. ..+.|++.-+..=..+..+..+|.+.+...+. |+|. ..||-||..
T Consensus 52 ~~v~-L~L~~~q~HL~~~~a~~~L~~ALs~~~g~~i~-L~I~~~~~~~~~TP~e~r~ 106 (142)
T PF12170_consen 52 DQVC-LHLRPSQKHLNNDSAQEQLQQALSEYLGEPIK-LSIEEGDNPARETPLEIRQ 106 (142)
T ss_dssp SEEE-EEE-GGGTTT--HHHHHHHHHHHHHHHSS--E-EEEEE---TTS--HHHHHH
T ss_pred CEEE-EEEChhhHhhCCHHHHHHHHHHHHHHhCCCEE-EEEEECCCCCCCCHHHHHH
Confidence 4564 45788999999999999999999999975555 4442 369999974
No 24
>cd02164 PPAT_CoAS phosphopantetheine adenylyltransferase domain of eukaryotic and archaeal bifunctional enzymes. The PPAT domain of the bifunctional enzyme with PPAT and DPCK functions. The final two steps of the CoA biosynthesis pathway are catalyzed by phosphopantetheine adenylyltransferase (PPAT) and dephospho-CoA (dPCoA) kinase (DPCK). The PPAT reaction involves the reversible adenylation of 4'-phosphopantetheine to form 3'-dPCoA and PPi, and DPCK catalyses phosphorylation of the 3'-hydroxy group of the ribose moiety of dPCoA. In eukaryotes the two enzymes are part of a large multienzyme complex . Studies in Corynebacterium ammoniagenes suggested that separate enzymes were present, and this was confirmed through identification of the bacterial PPAT/CoAD.
Probab=32.09 E-value=1.1e+02 Score=21.39 Aligned_cols=71 Identities=20% Similarity=0.248 Sum_probs=36.8
Q ss_pred chhhHHHHHHHHHHhcCCC-ceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhcCC
Q 034128 8 AVIARAMRMETKLRSALEA-TVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDELNSG 86 (103)
Q Consensus 8 ~~~~~~~~I~~~L~~~l~~-~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~~~ 86 (103)
+...+.+.+++.|.. +.+ ..++|...+.. .| +. ..+..|+.+|||++... .-..||+.=++ .+
T Consensus 51 s~e~R~~~l~~~l~~-~~~~~~~~i~~i~d~-~G-----pt-~~~~~~d~lVVS~ET~~-----~~~~iN~~R~~---~g 114 (143)
T cd02164 51 PYEERIANLHEFLVD-LKPTLKYEIVPIDDP-YG-----PT-GTDPDLEAIVVSPETYP-----GALKINRKREE---NG 114 (143)
T ss_pred CHHHHHHHHHHHHHh-cCCCceEEEEEccCC-CC-----Cc-ccCCCCCEEEEcHHHhh-----hHHHHHHHHHH---CC
Confidence 344555666666643 443 35555544311 11 11 12357999999998643 34455554442 25
Q ss_pred cceEEEEe
Q 034128 87 LHALSIVA 94 (103)
Q Consensus 87 iHAlsi~t 94 (103)
+..|.|..
T Consensus 115 l~pl~i~~ 122 (143)
T cd02164 115 LSPLEIVV 122 (143)
T ss_pred CCceeEEE
Confidence 55555543
No 25
>PF01877 RNA_binding: RNA binding; InterPro: IPR002739 The proteins in this entry are functionally uncharacterised.; PDB: 2WNY_B 2NWU_A 2NRQ_A 2OGK_A 3D7A_B 3C9G_B 2PZZ_D.
Probab=31.37 E-value=1.7e+02 Score=19.75 Aligned_cols=24 Identities=13% Similarity=0.285 Sum_probs=19.0
Q ss_pred HHHHHHHHHHhcC-CCceEEEEecC
Q 034128 12 RAMRMETKLRSAL-EATVLEIDDVS 35 (103)
Q Consensus 12 ~~~~I~~~L~~~l-~~~~v~V~d~S 35 (103)
..+++.+.|.+-| +...+++....
T Consensus 14 D~eKV~~Al~nlf~~~~~~~~~~~~ 38 (120)
T PF01877_consen 14 DEEKVKKALSNLFPPDAEIEIEEEE 38 (120)
T ss_dssp -HHHHHHHHHHHSCTTSEEEEEEEE
T ss_pred CHHHHHHHHHHHhCCCCceEEEEec
Confidence 3678889999999 67788888774
No 26
>PF06649 DUF1161: Protein of unknown function (DUF1161); InterPro: IPR010595 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=30.24 E-value=1.1e+02 Score=18.37 Aligned_cols=24 Identities=21% Similarity=0.200 Sum_probs=15.0
Q ss_pred hHHHHHHHHHHhc-CCCceEEEEec
Q 034128 11 ARAMRMETKLRSA-LEATVLEIDDV 34 (103)
Q Consensus 11 ~~~~~I~~~L~~~-l~~~~v~V~d~ 34 (103)
...++|..||.+. .+...|+|.+.
T Consensus 3 ~lk~eI~~KI~anGV~~ftLeiV~n 27 (52)
T PF06649_consen 3 ELKAEIEQKIIANGVSSFTLEIVPN 27 (52)
T ss_pred HHHHHHHHHHHHcCCCceEEEEeeC
Confidence 4567888888654 34446666655
No 27
>KOG3125 consensus Thymidine kinase [Nucleotide transport and metabolism]
Probab=29.71 E-value=41 Score=25.81 Aligned_cols=18 Identities=39% Similarity=0.639 Sum_probs=14.4
Q ss_pred EEECCCCCCCCH--HHHHHH
Q 034128 57 KIVSPKFEGKNL--VNRHRM 74 (103)
Q Consensus 57 ~IvS~~F~G~s~--l~Rhrl 74 (103)
+|.+|.|.||+. |.|+|.
T Consensus 31 vI~gPMfSGKTt~LLrr~r~ 50 (234)
T KOG3125|consen 31 VILGPMFSGKTTELLRRIRR 50 (234)
T ss_pred EEeccccCcchHHHHHHHHH
Confidence 478999999985 777764
No 28
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=28.26 E-value=44 Score=22.73 Aligned_cols=36 Identities=33% Similarity=0.600 Sum_probs=27.1
Q ss_pred ECCCCCCC--------CHHHHHHHHHHHHHHHhcCCcceEEEEecChhH
Q 034128 59 VSPKFEGK--------NLVNRHRMVYQVLSDELNSGLHALSIVAKTPQE 99 (103)
Q Consensus 59 vS~~F~G~--------s~l~RhrlVy~~L~~~i~~~iHAlsi~t~tp~E 99 (103)
.||.|+|. ||+.+.+.| +++..+|+|..+.-.-+++
T Consensus 48 TSp~FeGvvam~~Pt~SWVakWqri-----d~f~~GlYA~~V~G~L~ed 91 (112)
T COG5204 48 TSPKFEGVVAMLQPTNSWVAKWQRI-----DEFRKGLYAMVVEGALSED 91 (112)
T ss_pred cCcchHHHHHHhcccHHHHHHHhhh-----cccccceeEEEEcccCCHH
Confidence 79999984 788888877 4554589998887655554
No 29
>COG1019 Predicted nucleotidyltransferase [General function prediction only]
Probab=26.97 E-value=2.5e+02 Score=20.44 Aligned_cols=72 Identities=19% Similarity=0.226 Sum_probs=38.5
Q ss_pred CcchhhHHHHHHHHHHhcCCCce--EEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHh
Q 034128 6 ANAVIARAMRMETKLRSALEATV--LEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDEL 83 (103)
Q Consensus 6 ~~~~~~~~~~I~~~L~~~l~~~~--v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i 83 (103)
-.++..+...+.+.|...-+... +.+.|.. |....+.+|+++||||+=.- +=..||++=.
T Consensus 53 i~p~~~R~~~l~~fl~~~~~~~~~iv~i~Dp~----------G~t~~~~~~e~iVVS~ET~~-----~Al~IN~~R~--- 114 (158)
T COG1019 53 IEPYEVRLRNLRNFLESIKADYEEIVPIDDPY----------GPTVEDPDFEAIVVSPETYP-----GALKINEIRE--- 114 (158)
T ss_pred CCcHHHHHHHHHHHHHHhcCCcceEEEecCCC----------CCCCCcCceeEEEEccccch-----hHHHHHHHHH---
Confidence 34566666777777754444333 3343332 12123459999999997443 2333444322
Q ss_pred cCCcceEEEEec
Q 034128 84 NSGLHALSIVAK 95 (103)
Q Consensus 84 ~~~iHAlsi~t~ 95 (103)
+.|+-.|+|.+.
T Consensus 115 ~~Gl~pL~I~~i 126 (158)
T COG1019 115 KRGLPPLEIIVI 126 (158)
T ss_pred HCCCCCeEEEEE
Confidence 235666666553
No 30
>PF06042 DUF925: Bacterial protein of unknown function (DUF925); InterPro: IPR009267 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 2LA3_A.
Probab=24.93 E-value=1.5e+02 Score=21.41 Aligned_cols=34 Identities=15% Similarity=0.195 Sum_probs=27.2
Q ss_pred cchhhHHHHHHHHHHhcCCCceEEEEecCccccC
Q 034128 7 NAVIARAMRMETKLRSALEATVLEIDDVSHKHAG 40 (103)
Q Consensus 7 ~~~~~~~~~I~~~L~~~l~~~~v~V~d~S~~H~g 40 (103)
...-....++++.|++.++...++|.|.-..|.-
T Consensus 48 d~s~e~e~~~e~~l~~~~p~~~weVkNQArmHl~ 81 (163)
T PF06042_consen 48 DLSYEAEDAIEARLRALFPGYPWEVKNQARMHLW 81 (163)
T ss_dssp TS-HHHHHHHHHHHHHH-TTSEEEEEESTTTTSS
T ss_pred CCCHHHHHHHHHHHHHhCCCCCEEEEeeeeeeee
Confidence 4455577899999999999999999999888864
No 31
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=24.65 E-value=2.1e+02 Score=18.63 Aligned_cols=70 Identities=14% Similarity=0.133 Sum_probs=36.0
Q ss_pred HHHHHHHHHhcCCCceEEEEecCccccCCccccCCCCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHHhc-CCcceEE
Q 034128 13 AMRMETKLRSALEATVLEIDDVSHKHAGHAAVKDSNSGETHFDLKIVSPKFEGKNLVNRHRMVYQVLSDELN-SGLHALS 91 (103)
Q Consensus 13 ~~~I~~~L~~~l~~~~v~V~d~S~~H~gH~~~~~~~~~esHf~i~IvS~~F~G~s~l~RhrlVy~~L~~~i~-~~iHAls 91 (103)
++.|.+.|.++ ....+.|.|.+. -|.-+.|-|+....+. -+-. .+...+.+.++ .++.-+.
T Consensus 2 ~~~i~~~l~~k-ka~dI~vldv~~-----------~~~~~dy~VI~Tg~S~-----rh~~-aia~~v~~~~k~~~~~~~~ 63 (99)
T TIGR00090 2 LELIVEALDDK-KAEDIVVLDVRG-----------KSSIADYFVIASGTSS-----RHVK-AIADNVEEELKEAGLKPLG 63 (99)
T ss_pred HHHHHHHHHHc-CCCCEEEEECCC-----------CCcccCEEEEEEeCCH-----HHHH-HHHHHHHHHHHHcCCCccc
Confidence 34566666544 667899999962 1233566665554433 2222 23333333333 2455555
Q ss_pred EEecChhHH
Q 034128 92 IVAKTPQEA 100 (103)
Q Consensus 92 i~t~tp~Ew 100 (103)
+.-....+|
T Consensus 64 ~EG~~~~~W 72 (99)
T TIGR00090 64 VEGLEEGDW 72 (99)
T ss_pred ccCCCCCCE
Confidence 555555555
No 32
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=23.79 E-value=1.8e+02 Score=17.68 Aligned_cols=27 Identities=15% Similarity=0.274 Sum_probs=21.5
Q ss_pred CcchhhHHHHHHHHHHhcCCC--ceEEEE
Q 034128 6 ANAVIARAMRMETKLRSALEA--TVLEID 32 (103)
Q Consensus 6 ~~~~~~~~~~I~~~L~~~l~~--~~v~V~ 32 (103)
.+.+-..+..+++.|.+.||. ..++..
T Consensus 10 ~C~~~~~a~~l~~~l~~~fp~~~~~v~~~ 38 (76)
T PF10262_consen 10 SCGYRPRALELAQELLQTFPDRIAEVELS 38 (76)
T ss_dssp TTTCHHHHHHHHHHHHHHSTTTCSEEEEE
T ss_pred CCCCHHHHHHHHHHHHHHCCCcceEEEEE
Confidence 456677899999999999999 555554
No 33
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=23.28 E-value=41 Score=22.45 Aligned_cols=30 Identities=23% Similarity=0.436 Sum_probs=22.3
Q ss_pred CCHHHHHHHHHHHHHHHhcCCcceEEEEecChhHH
Q 034128 66 KNLVNRHRMVYQVLSDELNSGLHALSIVAKTPQEA 100 (103)
Q Consensus 66 ~s~l~RhrlVy~~L~~~i~~~iHAlsi~t~tp~Ew 100 (103)
+|++.|...+. ... .|++||++.=.-|++-
T Consensus 58 ~SwVAk~l~i~----~~~-pG~YAi~V~g~lp~~i 87 (98)
T cd07973 58 KSWVARWQRID----KFV-PGIYAISVSGRLPEDI 87 (98)
T ss_pred hhHHHHHhCCC----CCC-CCeEEEEecCcCCHHH
Confidence 58998888774 223 4999999987777653
No 34
>smart00542 FYRC "FY-rich" domain, C-terminal region. is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.
Probab=22.83 E-value=1.6e+02 Score=18.65 Aligned_cols=32 Identities=22% Similarity=0.292 Sum_probs=25.9
Q ss_pred eeEEEEEC---CCCCCCCHHHHHHHHHHHHHHHhc
Q 034128 53 HFDLKIVS---PKFEGKNLVNRHRMVYQVLSDELN 84 (103)
Q Consensus 53 Hf~i~IvS---~~F~G~s~l~RhrlVy~~L~~~i~ 84 (103)
+|+|++-+ -.|.|-|.=+=|++|++.+.+...
T Consensus 1 lF~v~~~~~~~~~~~~~S~~~~W~~vl~~v~~~r~ 35 (86)
T smart00542 1 LFRVEIESDPDEVFKGESPEKCWEMVLERVQEARI 35 (86)
T ss_pred CeEEEEecCCCCeEEeCCHHHHHHHHHHHHHHHHH
Confidence 35666665 368999999999999999998874
No 35
>PRK00447 hypothetical protein; Provisional
Probab=22.66 E-value=2e+02 Score=20.35 Aligned_cols=21 Identities=10% Similarity=0.243 Sum_probs=17.0
Q ss_pred HHHHHHHHHhcCCCceEEEEe
Q 034128 13 AMRMETKLRSALEATVLEIDD 33 (103)
Q Consensus 13 ~~~I~~~L~~~l~~~~v~V~d 33 (103)
.+++.+.|.+-||...+++.+
T Consensus 17 ~eKV~~Ai~Nifp~~~ie~~~ 37 (144)
T PRK00447 17 EEKVKKAILNFFDFEKFEAED 37 (144)
T ss_pred HHHHHHHHHhhCCcceEEEEe
Confidence 467888999999998888654
No 36
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=20.40 E-value=97 Score=17.16 Aligned_cols=20 Identities=15% Similarity=0.522 Sum_probs=15.4
Q ss_pred CCCCHHHHHHHHHHHHHHHh
Q 034128 64 EGKNLVNRHRMVYQVLSDEL 83 (103)
Q Consensus 64 ~G~s~l~RhrlVy~~L~~~i 83 (103)
.|-+.++++.+|+++|+..-
T Consensus 20 ~~~~~~~K~eLI~~Il~~q~ 39 (43)
T PF07498_consen 20 EGYSKMRKQELIFAILKAQA 39 (43)
T ss_dssp TTGCCS-HHHHHHHHHHHHC
T ss_pred CCCCcCCHHHHHHHHHHHHH
Confidence 36678899999999998654
Done!