Query psy10139
Match_columns 106
No_of_seqs 105 out of 113
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 18:49:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10139.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10139hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10390 ELL: RNA polymerase I 100.0 1.2E-34 2.5E-39 230.4 6.4 84 2-86 199-283 (284)
2 KOG4796|consensus 100.0 2E-29 4.4E-34 215.9 7.8 97 2-99 212-308 (604)
3 KOG1140|consensus 98.8 4.2E-09 9E-14 100.1 4.4 95 2-99 781-890 (1738)
4 PRK00117 recX recombination re 87.2 1.4 2.9E-05 31.6 4.5 42 2-46 13-54 (157)
5 PRK14136 recX recombination re 86.7 1.4 3.1E-05 36.6 4.9 42 2-46 164-205 (309)
6 PRK14137 recX recombination re 84.0 2.1 4.6E-05 32.8 4.5 42 2-46 42-83 (195)
7 PF05793 TFIIF_alpha: Transcri 79.0 2.6 5.6E-05 36.7 3.8 50 4-53 467-523 (527)
8 PRK14135 recX recombination re 78.3 5 0.00011 31.0 4.8 41 3-46 60-100 (263)
9 PRK14134 recX recombination re 77.6 4.8 0.0001 32.3 4.7 41 3-46 64-104 (283)
10 PF02270 TFIIF_beta: Transcrip 62.2 7.9 0.00017 30.8 2.8 24 35-58 245-273 (275)
11 smart00096 UTG Uteroglobin. 54.2 25 0.00054 23.2 3.7 37 10-46 23-65 (69)
12 PRK02363 DNA-directed RNA poly 50.0 37 0.0008 24.7 4.4 54 13-77 18-81 (129)
13 cd02639 R3H_RRM R3H domain of 47.5 11 0.00024 24.1 1.1 8 4-11 31-38 (60)
14 PRK11031 guanosine pentaphosph 47.2 56 0.0012 28.0 5.7 59 20-78 337-398 (496)
15 KOG4603|consensus 46.9 37 0.00079 26.7 4.1 34 11-47 19-52 (201)
16 PF13907 DUF4208: Domain of un 46.7 9 0.00019 26.2 0.7 49 21-69 29-89 (100)
17 PF01022 HTH_5: Bacterial regu 44.9 21 0.00045 20.7 2.0 23 2-24 3-25 (47)
18 cd00090 HTH_ARSR Arsenical Res 43.4 63 0.0014 18.4 5.1 58 3-66 9-77 (78)
19 PF08197 TT_ORF2a: pORF2a trun 43.2 11 0.00023 23.6 0.5 8 64-71 40-47 (49)
20 PF07205 DUF1413: Domain of un 42.5 35 0.00076 21.7 2.9 38 39-79 3-41 (70)
21 KOG2905|consensus 40.6 22 0.00047 29.1 2.1 24 35-58 215-243 (254)
22 PF11387 DUF2795: Protein of u 39.7 49 0.0011 19.6 3.1 33 14-53 7-39 (44)
23 PRK00199 ihfB integration host 39.5 83 0.0018 20.7 4.5 32 15-46 1-35 (94)
24 COG0776 HimA Bacterial nucleoi 37.9 91 0.002 21.6 4.6 43 14-56 1-55 (94)
25 PF05973 Gp49: Phage derived p 35.9 54 0.0012 21.2 3.1 33 28-60 5-50 (91)
26 PF04801 Sin_N: Sin-like prote 35.4 80 0.0017 26.3 4.8 55 2-59 271-326 (421)
27 PF04510 DUF577: Family of unk 34.4 61 0.0013 25.0 3.6 47 17-63 5-56 (174)
28 PF10826 DUF2551: Protein of u 33.9 1.6E+02 0.0034 20.3 6.1 57 2-58 12-79 (83)
29 TIGR00988 hip integration host 32.8 1.2E+02 0.0027 19.7 4.6 32 15-46 1-35 (94)
30 PF05066 HARE-HTH: HB1, ASXL, 30.5 77 0.0017 19.7 3.1 54 3-56 4-71 (72)
31 COG2137 OraA Uncharacterized p 30.1 74 0.0016 24.1 3.4 41 3-46 23-63 (174)
32 PF00325 Crp: Bacterial regula 30.0 35 0.00076 19.3 1.3 29 1-29 3-31 (32)
33 KOG2616|consensus 29.5 66 0.0014 26.4 3.2 40 3-42 104-144 (266)
34 COG1777 Predicted transcriptio 29.5 35 0.00076 27.2 1.7 34 2-40 16-49 (217)
35 PRK10854 exopolyphosphatase; P 28.7 1.6E+02 0.0034 25.4 5.6 60 20-79 343-407 (513)
36 smart00346 HTH_ICLR helix_turn 26.5 1.7E+02 0.0036 18.2 5.7 59 5-69 9-76 (91)
37 COG1321 TroR Mn-dependent tran 26.5 57 0.0012 24.0 2.2 29 4-32 28-56 (154)
38 PF11417 Inhibitor_G39P: Loade 26.3 38 0.00083 22.2 1.2 12 1-12 1-12 (71)
39 COG3343 RpoE DNA-directed RNA 25.1 74 0.0016 24.7 2.7 49 13-75 29-90 (175)
40 PF03874 RNA_pol_Rpb4: RNA pol 25.0 1.2E+02 0.0026 20.5 3.5 43 3-46 73-115 (117)
41 TIGR00678 holB DNA polymerase 24.4 85 0.0018 22.5 2.8 38 3-44 144-181 (188)
42 PHA03335 hypothetical protein; 24.3 42 0.0009 28.7 1.3 67 5-71 189-269 (385)
43 TIGR00987 himA integration hos 24.1 1.7E+02 0.0037 19.3 4.1 32 15-46 2-35 (96)
44 TIGR03853 matur_matur probable 24.1 96 0.0021 21.0 2.8 50 5-54 6-69 (77)
45 PF00216 Bac_DNA_binding: Bact 24.0 1.5E+02 0.0032 18.8 3.6 27 15-44 1-28 (90)
46 PF13331 DUF4093: Domain of un 22.9 2.1E+02 0.0045 19.3 4.3 37 2-41 50-86 (87)
47 smart00657 RPOL4c DNA-directed 22.6 2E+02 0.0043 20.0 4.3 45 3-48 71-115 (118)
48 cd02643 R3H_NF-X1 R3H domain o 22.4 56 0.0012 21.2 1.4 10 2-11 43-52 (74)
49 PRK10664 transcriptional regul 22.0 2.2E+02 0.0048 18.9 4.3 32 15-46 1-34 (90)
50 TIGR02063 RNase_R ribonuclease 21.6 2.4E+02 0.0053 25.3 5.6 54 2-57 3-65 (709)
51 PF01638 HxlR: HxlR-like helix 21.4 1E+02 0.0022 20.1 2.4 37 5-46 9-45 (90)
52 PF15061 DUF4538: Domain of un 21.1 96 0.0021 20.0 2.2 23 10-32 25-50 (58)
53 PF15141 DUF4574: Domain of un 20.6 1.4E+02 0.0031 20.5 3.1 37 17-53 34-75 (84)
54 PRK13916 plasmid segregation p 20.3 1.7E+02 0.0037 20.6 3.5 46 1-46 1-49 (97)
55 KOG4327|consensus 20.0 58 0.0013 26.0 1.2 15 88-102 172-186 (218)
No 1
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=100.00 E-value=1.2e-34 Score=230.45 Aligned_cols=84 Identities=43% Similarity=0.865 Sum_probs=71.1
Q ss_pred hhHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhccC-CCeEEechhhhhhccCCCCCCCHHHHHHHHHH
Q psy10139 2 LQDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAFAR-DNTYHLQRHVWNDVQDDWPFYSQQDKNMLKSR 80 (106)
Q Consensus 2 lr~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~~~-~~~Y~Lk~~~~~evq~dWp~Yse~er~~~krr 80 (106)
||+|||||||||||+++||++||++||++++|++.|++||++||++. +|+|+||++||+|||.||||||++|||+++|+
T Consensus 199 lReRvIHLLALkpykK~ELl~rL~~dg~~~~dk~~l~~iL~~Va~l~~~~~y~Lk~~~ykevq~dWP~yse~erq~l~r~ 278 (284)
T PF10390_consen 199 LRERVIHLLALKPYKKPELLLRLQKDGLSPKDKDELDSILQEVANLNKDNSYTLKDHFYKEVQKDWPGYSEEERQLLKRR 278 (284)
T ss_dssp HHHHHHHHHHHS-EEHHHHHHHHHHH---HHHHHHHHHHHHHCCEEETTTEEEE-STHHHHS-TT-TT--TCHHHHHHHH
T ss_pred ccccchhhhhcCccccHHHHHHHHhcCCChHHHHHHHHHHHHHhccCcCCeEEehHHHHhhhccCCCCCCHHHHHHHHHH
Confidence 79999999999999999999999999999999999999999999995 99999999999999999999999999999997
Q ss_pred Hhhhhc
Q psy10139 81 ELLQNF 86 (106)
Q Consensus 81 k~~q~~ 86 (106)
+ ++++
T Consensus 279 l-~~~l 283 (284)
T PF10390_consen 279 L-SRKL 283 (284)
T ss_dssp H-HHHS
T ss_pred H-Hhhc
Confidence 7 5444
No 2
>KOG4796|consensus
Probab=99.96 E-value=2e-29 Score=215.92 Aligned_cols=97 Identities=36% Similarity=0.642 Sum_probs=90.4
Q ss_pred hhHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhccCCCeEEechhhhhhccCCCCCCCHHHHHHHHHHH
Q psy10139 2 LQDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAFARDNTYHLQRHVWNDVQDDWPFYSQQDKNMLKSRE 81 (106)
Q Consensus 2 lr~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~~~~~~Y~Lk~~~~~evq~dWp~Yse~er~~~krrk 81 (106)
||+||||||||++|+++||++||++||+.++|++.|++||++..+.++|+|+|++++|+||+.+||||||+|+|+++|++
T Consensus 212 ir~RviHLlalk~ykk~El~~rLk~dGl~~~e~~~i~~il~~~~~~~~~t~~Lrd~~~~evdq~Wp~yse~d~~~lkr~~ 291 (604)
T KOG4796|consen 212 IRDRVIHLLALKAYKKPELLARLKKDGLPQEEKNKIRSILQQNSRSKDGTYTLRDSMLKEVDQNWPGYSEGDKQHLKRVL 291 (604)
T ss_pred hHHHHHHHHHhhhcccHHHHHHHhhcCCcHHHHHHHHHHHHhhcccccccchHHHHhhhHHHhcCCCcchHHHHHHHHHh
Confidence 79999999999999999999999999999999999999999977789999999999999999999999999999999877
Q ss_pred hhhhcCCCCCCCCCCchh
Q psy10139 82 LLQNFSENHSITPFYSQQ 99 (106)
Q Consensus 82 ~~q~~~pP~s~p~~~~~~ 99 (106)
.++++||++.-.|.+-.
T Consensus 292 -~~~l~~~~s~~n~~~~~ 308 (604)
T KOG4796|consen 292 -NRKLRPPQSDNNFAGTS 308 (604)
T ss_pred -hccCCCCCCCccccCcc
Confidence 78899998776665543
No 3
>KOG1140|consensus
Probab=98.79 E-value=4.2e-09 Score=100.10 Aligned_cols=95 Identities=14% Similarity=0.222 Sum_probs=80.1
Q ss_pred hhHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhcc-------CCCeEEechhhhhhccCCCCCCCHHHH
Q psy10139 2 LQDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAFA-------RDNTYHLQRHVWNDVQDDWPFYSQQDK 74 (106)
Q Consensus 2 lr~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~~-------~~~~Y~Lk~~~~~evq~dWp~Yse~er 74 (106)
+|.+|||+||.+|.+.+.|+..++.|-. +..+++.++++||.| ..|+|.||+++|++|+.++.|||..+|
T Consensus 781 ~k~~iIh~L~~~~lays~lv~s~~~dl~---~~l~~d~~~e~Va~~~~p~~~~~~gvf~lK~~~~~~~dpy~~~~s~s~q 857 (1738)
T KOG1140|consen 781 IKSEIIHILCFKPLSYSQLVRKIPHDLT---KTLSFDEALEEVAVFKKPKGLADNGVFVLKESYYDEVDPYYKHLSKSEQ 857 (1738)
T ss_pred HHHHHHHHHHhcchhHHHHHHhchhhhh---hcccchHHHHHHHhhccCCccccceEEEechhhhhhcCchhhhhhHhHH
Confidence 6889999999999999999999999987 358999999999997 569999999999999999999999999
Q ss_pred HHHHH------HHh-hhh-cCCCCCCCCCCchh
Q psy10139 75 NMLKS------REL-LQN-FSENHSITPFYSQQ 99 (106)
Q Consensus 75 ~~~kr------rk~-~q~-~~pP~s~p~~~~~~ 99 (106)
....+ .+. .+. |++|+.+|.|++.-
T Consensus 858 ~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll 890 (1738)
T KOG1140|consen 858 SESEATIRKSRLAKKKDVIALVPPILPKFIKLL 890 (1738)
T ss_pred hhhhHHHHHHHHHHhhccccccCCCcHHHHHHH
Confidence 84332 221 233 67777788887765
No 4
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=87.17 E-value=1.4 Score=31.63 Aligned_cols=42 Identities=26% Similarity=0.392 Sum_probs=35.3
Q ss_pred hhHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhc
Q psy10139 2 LQDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAF 46 (106)
Q Consensus 2 lr~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~ 46 (106)
.+...+++|+-++++..||..+|.+-|..+ +.++.+|+....
T Consensus 13 a~~~al~~L~~r~~s~~el~~kL~~kg~~~---~~i~~vl~~l~~ 54 (157)
T PRK00117 13 ARARALRLLARREHSRAELRRKLAAKGFSE---EVIEAVLDRLKE 54 (157)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHhcCCCH---HHHHHHHHHHHH
Confidence 356889999999999999999999999986 577777766543
No 5
>PRK14136 recX recombination regulator RecX; Provisional
Probab=86.67 E-value=1.4 Score=36.57 Aligned_cols=42 Identities=21% Similarity=0.346 Sum_probs=36.3
Q ss_pred hhHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhc
Q psy10139 2 LQDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAF 46 (106)
Q Consensus 2 lr~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~ 46 (106)
++.+.+++|+-+.++..||..+|.+-|..+ +.++.||+.+-.
T Consensus 164 lk~kAL~lLSrReRSe~ELr~KL~kkG~~e---e~IE~VIerLke 205 (309)
T PRK14136 164 LKGRALGYLSRREYSRAELARKLAPYADES---DSVEPLLDALER 205 (309)
T ss_pred HHHHHHHHhhcccccHHHHHHHHHHcCCCH---HHHHHHHHHHHH
Confidence 578899999999999999999999999976 577888776654
No 6
>PRK14137 recX recombination regulator RecX; Provisional
Probab=84.04 E-value=2.1 Score=32.85 Aligned_cols=42 Identities=24% Similarity=0.260 Sum_probs=35.7
Q ss_pred hhHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhc
Q psy10139 2 LQDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAF 46 (106)
Q Consensus 2 lr~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~ 46 (106)
++...+++|+-+.++..||..+|.+.|..+ ..++.||+..-.
T Consensus 42 ~~~~Al~~Ls~R~rS~~ELr~KL~~kg~~~---e~Ie~vI~rL~e 83 (195)
T PRK14137 42 LLAYAFRALAARAMTAAELRAKLERRSEDE---ALVTEVLERVQE 83 (195)
T ss_pred HHHHHHHHHhcchhhHHHHHHHHHhcCCCH---HHHHHHHHHHHH
Confidence 456789999999999999999999999976 677777776654
No 7
>PF05793 TFIIF_alpha: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); InterPro: IPR008851 Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II [].; GO: 0003677 DNA binding, 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1F3U_F 1NHA_A 1I27_A 1J2X_A 2K7L_A 1ONV_A.
Probab=79.05 E-value=2.6 Score=36.74 Aligned_cols=50 Identities=18% Similarity=0.288 Sum_probs=38.3
Q ss_pred HHHHHHHhcCCCCcHHHHHHHHhc---CCChHhHhHHHHHHHHhhcc----CCCeEE
Q psy10139 4 DRIIHLLAVRPYKKPELYAALTRD---GIRDRDRNQMMAILNGIAFA----RDNTYH 53 (106)
Q Consensus 4 ~RIIHLLAlkPy~k~EL~~rL~kd---g~~~~dk~~l~~iL~eVA~~----~~~~Y~ 53 (106)
+.|+..|.-+||+--||+.++..- ..++.+++.|..||..|+.. +++.|.
T Consensus 467 e~VrryL~rkPmTTkdLL~kFk~k~~~l~s~~~~~~~~~ILkki~p~~k~~~~~~~~ 523 (527)
T PF05793_consen 467 EEVRRYLRRKPMTTKDLLKKFKSKKTGLSSEEDKNVFAQILKKINPIQKTIGGKMYL 523 (527)
T ss_dssp HHHHHHHHHS-B-HHHHHHHTSHHHHSS-HHHHHHHHHHHHHHH--EEEEETTEEEE
T ss_pred HHHHHHHhcCCccHHHHHHHHHhccCCCCcHHHHHHHHHHHHHhChHheeccCceEE
Confidence 679999999999999999999876 56788999999999999975 444554
No 8
>PRK14135 recX recombination regulator RecX; Provisional
Probab=78.31 E-value=5 Score=30.96 Aligned_cols=41 Identities=10% Similarity=0.188 Sum_probs=35.1
Q ss_pred hHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhc
Q psy10139 3 QDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAF 46 (106)
Q Consensus 3 r~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~ 46 (106)
+...+++|+-++++..||..+|.+-|..+ +.++.+|+....
T Consensus 60 ~~~Al~~L~~r~~s~~el~~kL~~kg~~~---~~Ie~vl~~l~~ 100 (263)
T PRK14135 60 KNLALYYLSYQMRTEKEVRDYLKKHEISE---EIISEVIDKLKE 100 (263)
T ss_pred HHHHHHHhhhccccHHHHHHHHHHCCCCH---HHHHHHHHHHHH
Confidence 56789999999999999999999999976 678888776643
No 9
>PRK14134 recX recombination regulator RecX; Provisional
Probab=77.56 E-value=4.8 Score=32.28 Aligned_cols=41 Identities=2% Similarity=0.022 Sum_probs=35.2
Q ss_pred hHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhc
Q psy10139 3 QDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAF 46 (106)
Q Consensus 3 r~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~ 46 (106)
+..-+|+|+-++++..||..+|.+.|..+ +.++.||+.+-.
T Consensus 64 ~~~AL~~Ls~r~rSe~Elr~KL~~k~~~~---~~Ie~vI~~L~e 104 (283)
T PRK14134 64 KGYALKYIEKSYKTEKQIKEKLYLKEYDE---DAVNRVIRFLKE 104 (283)
T ss_pred HHHHHHHhccCcchHHHHHHHHHhCCCCH---HHHHHHHHHHHH
Confidence 45678999999999999999999999977 688888777654
No 10
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=62.24 E-value=7.9 Score=30.79 Aligned_cols=24 Identities=25% Similarity=0.355 Sum_probs=13.4
Q ss_pred hHHHHHHHHhhcc-----CCCeEEechhh
Q psy10139 35 NQMMAILNGIAFA-----RDNTYHLQRHV 58 (106)
Q Consensus 35 ~~l~~iL~eVA~~-----~~~~Y~Lk~~~ 58 (106)
+=|-.||++||.+ -.|.|+||+++
T Consensus 245 ~yLKeiL~eIa~~~k~g~~~~~w~LKpey 273 (275)
T PF02270_consen 245 AYLKEILEEIAVLNKRGPHKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHH--EE--TT---EE----SS
T ss_pred HHHHHHHHHHHHHhccCCcCCcEecchHH
Confidence 6899999999998 22899999975
No 11
>smart00096 UTG Uteroglobin.
Probab=54.21 E-value=25 Score=23.25 Aligned_cols=37 Identities=16% Similarity=0.390 Sum_probs=28.4
Q ss_pred HhcCCCCc-HHHHHHHHh-----cCCChHhHhHHHHHHHHhhc
Q psy10139 10 LAVRPYKK-PELYAALTR-----DGIRDRDRNQMMAILNGIAF 46 (106)
Q Consensus 10 LAlkPy~k-~EL~~rL~k-----dg~~~~dk~~l~~iL~eVA~ 46 (106)
.++++|+- ||++....+ |++++++|+.+.++|.+|..
T Consensus 23 ~~l~~y~~~~~~~ea~~~lK~cvD~L~~~~k~~i~~ll~kI~~ 65 (69)
T smart00096 23 ASLKQFKPDPDMLEAGRQLKKLVDTLPQETRENILKLTEKIYT 65 (69)
T ss_pred HHHHhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHc
Confidence 46788885 676654332 77999999999999999863
No 12
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=49.96 E-value=37 Score=24.66 Aligned_cols=54 Identities=13% Similarity=0.225 Sum_probs=37.0
Q ss_pred CCCCcHHHHHHHHhcCCChHhHhHHHHHHHHh-------hcc---CCCeEEechhhhhhccCCCCCCCHHHHHHH
Q psy10139 13 RPYKKPELYAALTRDGIRDRDRNQMMAILNGI-------AFA---RDNTYHLQRHVWNDVQDDWPFYSQQDKNML 77 (106)
Q Consensus 13 kPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eV-------A~~---~~~~Y~Lk~~~~~evq~dWp~Yse~er~~~ 77 (106)
+||...+|+....+...... ..+.+.|.++ +.| ++|.|.|+. |++|...+....
T Consensus 18 ~~m~f~dL~~ev~~~~~~s~--e~~~~~iaq~YtdLn~DGRFi~lG~n~WgLr~---------w~p~d~i~e~~~ 81 (129)
T PRK02363 18 EPMSFYDLVNEIQKYLGKSD--EEIRERIAQFYTDLNLDGRFISLGDNKWGLRS---------WYPVDEIDEEII 81 (129)
T ss_pred CcccHHHHHHHHHHHhCCCH--HHHHHHHHHHHHHHhccCCeeEcCCCceeccc---------ccChhhhhhhhh
Confidence 69999999999888655321 2333333332 233 889999987 999988777633
No 13
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=47.47 E-value=11 Score=24.06 Aligned_cols=8 Identities=75% Similarity=1.161 Sum_probs=6.7
Q ss_pred HHHHHHHh
Q psy10139 4 DRIIHLLA 11 (106)
Q Consensus 4 ~RIIHLLA 11 (106)
++|||.||
T Consensus 31 Rriih~la 38 (60)
T cd02639 31 RRIVHLLA 38 (60)
T ss_pred HHHHHHHH
Confidence 68888888
No 14
>PRK11031 guanosine pentaphosphate phosphohydrolase; Provisional
Probab=47.25 E-value=56 Score=28.02 Aligned_cols=59 Identities=17% Similarity=0.266 Sum_probs=37.9
Q ss_pred HHHHHHhc-CCChHhHhHHH--HHHHHhhccCCCeEEechhhhhhccCCCCCCCHHHHHHHH
Q psy10139 20 LYAALTRD-GIRDRDRNQMM--AILNGIAFARDNTYHLQRHVWNDVQDDWPFYSQQDKNMLK 78 (106)
Q Consensus 20 L~~rL~kd-g~~~~dk~~l~--~iL~eVA~~~~~~Y~Lk~~~~~evq~dWp~Yse~er~~~k 78 (106)
|...|... ++.+.|+.-|+ ++|.+|+.+=+-..+-+-.+|-=.+.+|+|+|..|+..+-
T Consensus 337 Lf~~l~~~~~l~~~~~~LL~~Aa~LhdiG~~I~~~~~~~Hs~yiI~~s~l~G~s~~E~~~iA 398 (496)
T PRK11031 337 FLQQVENEWHLEPRSRELLISACQLHEIGLSVDFKQAPQHAAYLVRNLDLPGFTPAQKKLLA 398 (496)
T ss_pred HHHhhhhhcCCChHHHHHHHHHHHHHhcCCccCCCccchHHHHHHhcCCCCCCCHHHHHHHH
Confidence 44444432 45455454444 4477887764334445666777778999999999999655
No 15
>KOG4603|consensus
Probab=46.94 E-value=37 Score=26.75 Aligned_cols=34 Identities=21% Similarity=0.486 Sum_probs=30.1
Q ss_pred hcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhcc
Q psy10139 11 AVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAFA 47 (106)
Q Consensus 11 AlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~~ 47 (106)
+=|||+.++++..|++..+. ++.+.++|++.|.-
T Consensus 19 qNrP~ssq~v~~~lq~e~lg---ktavqk~Ld~La~~ 52 (201)
T KOG4603|consen 19 QNRPYSSQDVFGNLQREHLG---KTAVQKTLDQLAQQ 52 (201)
T ss_pred hcCCCchHHHHHHHHHHhcc---chHHHHHHHHHHHc
Confidence 56899999999999999875 48999999999974
No 16
>PF13907 DUF4208: Domain of unknown function (DUF4208)
Probab=46.70 E-value=9 Score=26.18 Aligned_cols=49 Identities=22% Similarity=0.470 Sum_probs=30.9
Q ss_pred HHHHHh--cCCChHhHhH-HHHHHHHhhcc-----CC----CeEEechhhhhhccCCCCCC
Q psy10139 21 YAALTR--DGIRDRDRNQ-MMAILNGIAFA-----RD----NTYHLQRHVWNDVQDDWPFY 69 (106)
Q Consensus 21 ~~rL~k--dg~~~~dk~~-l~~iL~eVA~~-----~~----~~Y~Lk~~~~~evq~dWp~Y 69 (106)
+++|.. .|+..+++.. |...|-.||++ +. ..=.|+.++|.-|..+||.=
T Consensus 29 LkkL~~~~~~l~~~e~a~~lk~~L~~IG~~I~~~l~~~~~~~~~~l~~~LW~fvs~fwp~~ 89 (100)
T PF13907_consen 29 LKKLKKPKKGLPRKERAKILKKELLKIGDFIDSILKEYKDDEPEKLRKHLWSFVSKFWPNK 89 (100)
T ss_pred HHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHcCCCC
Confidence 444444 3454444433 45557777775 11 23478999999999999975
No 17
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=44.91 E-value=21 Score=20.69 Aligned_cols=23 Identities=35% Similarity=0.440 Sum_probs=20.6
Q ss_pred hhHHHHHHHhcCCCCcHHHHHHH
Q psy10139 2 LQDRIIHLLAVRPYKKPELYAAL 24 (106)
Q Consensus 2 lr~RIIHLLAlkPy~k~EL~~rL 24 (106)
.|-+|+.+|+=+|+.-.||...+
T Consensus 3 ~R~~Il~~L~~~~~~~~el~~~l 25 (47)
T PF01022_consen 3 TRLRILKLLSEGPLTVSELAEEL 25 (47)
T ss_dssp HHHHHHHHHTTSSEEHHHHHHHH
T ss_pred HHHHHHHHHHhCCCchhhHHHhc
Confidence 47899999999999999998876
No 18
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=43.40 E-value=63 Score=18.44 Aligned_cols=58 Identities=22% Similarity=0.282 Sum_probs=37.9
Q ss_pred hHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhc---c------CCCeEEec--hhhhhhccCCC
Q psy10139 3 QDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAF---A------RDNTYHLQ--RHVWNDVQDDW 66 (106)
Q Consensus 3 r~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~---~------~~~~Y~Lk--~~~~~evq~dW 66 (106)
+..|++.+.-.+.+..||...+ |++. ..+..+|+.... + +.+.|.+. ++++..+...|
T Consensus 9 ~~~il~~l~~~~~~~~ei~~~~---~i~~---~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~g~~~~~~~~~~~ 77 (78)
T cd00090 9 RLRILRLLLEGPLTVSELAERL---GLSQ---STVSRHLKKLEEAGLVESRREGRRVYYSLTDAERLLALLESLL 77 (78)
T ss_pred HHHHHHHHHHCCcCHHHHHHHH---CcCH---hHHHHHHHHHHHCCCeEEEEeccEEEEEeCCchHHHHHHHHhh
Confidence 4578888887888889988876 5544 566666666543 1 23577777 67776665433
No 19
>PF08197 TT_ORF2a: pORF2a truncated protein; InterPro: IPR013267 Most isolated ORF2 of TT virus (TTV) encode a 49 amino acid protein (pORF2a) because of an in-frame stop codon. ORF2s isolated from G1 TTV encode a 202 amino acid protein (pORF2ab) [].
Probab=43.22 E-value=11 Score=23.60 Aligned_cols=8 Identities=63% Similarity=1.327 Sum_probs=6.6
Q ss_pred CCCCCCCH
Q psy10139 64 DDWPFYSQ 71 (106)
Q Consensus 64 ~dWp~Yse 71 (106)
+|||||-.
T Consensus 40 rdwpg~gq 47 (49)
T PF08197_consen 40 RDWPGYGQ 47 (49)
T ss_pred ccCCCcCC
Confidence 69999964
No 20
>PF07205 DUF1413: Domain of unknown function (DUF1413); InterPro: IPR010813 This family consists of several hypothetical bacterial proteins, which seem to be specific to Staphylococcus species. Members of this family are typically around 100 residues in length. The function of this family is unknown.
Probab=42.48 E-value=35 Score=21.66 Aligned_cols=38 Identities=11% Similarity=0.369 Sum_probs=28.5
Q ss_pred HHHHHhhccCCC-eEEechhhhhhccCCCCCCCHHHHHHHHH
Q psy10139 39 AILNGIAFARDN-TYHLQRHVWNDVQDDWPFYSQQDKNMLKS 79 (106)
Q Consensus 39 ~iL~eVA~~~~~-~Y~Lk~~~~~evq~dWp~Yse~er~~~kr 79 (106)
.++..+-++..| +|+|+ .+|.+ ..|-.-|..||+.+.|
T Consensus 3 ~~i~~~~~l~~gt~F~l~-dLf~~--~~w~~~s~~~r~~~g~ 41 (70)
T PF07205_consen 3 EAIAKLKNLPPGTVFTLK-DLFGK--EEWNTLSRAERQSLGR 41 (70)
T ss_pred HHHHHHHcCCCCCEEeeh-HhcCh--HhhhhCCHHHHHHHHH
Confidence 455666667555 99999 45544 4899999999998887
No 21
>KOG2905|consensus
Probab=40.65 E-value=22 Score=29.05 Aligned_cols=24 Identities=29% Similarity=0.451 Sum_probs=19.5
Q ss_pred hHHHHHHHHhhcc--C---CCeEEechhh
Q psy10139 35 NQMMAILNGIAFA--R---DNTYHLQRHV 58 (106)
Q Consensus 35 ~~l~~iL~eVA~~--~---~~~Y~Lk~~~ 58 (106)
.-|-.||++||.+ + .|+|+||++.
T Consensus 215 ~fLKEiL~~icv~NkKg~~k~tyeLKPEY 243 (254)
T KOG2905|consen 215 AFLKEILKDICVLNKKGPYKNTYELKPEY 243 (254)
T ss_pred HHHHHHHHHHHHHhccCcccCceecCHHH
Confidence 5677899999987 2 3899999985
No 22
>PF11387 DUF2795: Protein of unknown function (DUF2795); InterPro: IPR021527 This family of proteins has no known function.
Probab=39.68 E-value=49 Score=19.58 Aligned_cols=33 Identities=30% Similarity=0.493 Sum_probs=23.3
Q ss_pred CCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhccCCCeEE
Q psy10139 14 PYKKPELYAALTRDGIRDRDRNQMMAILNGIAFARDNTYH 53 (106)
Q Consensus 14 Py~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~~~~~~Y~ 53 (106)
|-++.+|+....+.|..+ .||+.+..+.++.|.
T Consensus 7 Pa~k~~Lv~~A~~~gA~~-------~vl~~L~~lP~~~Y~ 39 (44)
T PF11387_consen 7 PADKDELVRHARRNGAPD-------DVLDALERLPDREYE 39 (44)
T ss_pred CCCHHHHHHHHHHcCCCH-------HHHHHHHHCCccCCC
Confidence 667899999999999864 355555555555553
No 23
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=39.50 E-value=83 Score=20.66 Aligned_cols=32 Identities=25% Similarity=0.318 Sum_probs=20.9
Q ss_pred CCcHHHHHHHHh--cCCChHhH-hHHHHHHHHhhc
Q psy10139 15 YKKPELYAALTR--DGIRDRDR-NQMMAILNGIAF 46 (106)
Q Consensus 15 y~k~EL~~rL~k--dg~~~~dk-~~l~~iL~eVA~ 46 (106)
|.+.||+.++.+ .|++..|- ..++.+++.++.
T Consensus 1 mtk~eli~~ia~~~~~~s~~~~~~vv~~~~~~i~~ 35 (94)
T PRK00199 1 MTKSELIERLAARNPHLSAKDVENAVKEILEEMSD 35 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence 678999999975 36775432 345555666654
No 24
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=37.87 E-value=91 Score=21.57 Aligned_cols=43 Identities=21% Similarity=0.321 Sum_probs=27.8
Q ss_pred CCCcHHHHHHHHhcC-CChHh-HhHHHHHHHHhhc-c---------CCCeEEech
Q psy10139 14 PYKKPELYAALTRDG-IRDRD-RNQMMAILNGIAF-A---------RDNTYHLQR 56 (106)
Q Consensus 14 Py~k~EL~~rL~kdg-~~~~d-k~~l~~iL~eVA~-~---------~~~~Y~Lk~ 56 (106)
+|.++||+..+-+.. ++.+| ++.++.+++.|.. + +=|+|+++.
T Consensus 1 ~mtKseli~~ia~~~~l~k~~a~~~v~~~~~~i~~aL~~G~~V~l~gFG~F~v~~ 55 (94)
T COG0776 1 TMTKSELIDAIAEKAGLSKKDAEEAVDAFLEEITEALAKGERVELRGFGTFEVRE 55 (94)
T ss_pred CCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEeeeeeeEeec
Confidence 478999999998755 44422 3456667777764 2 336777654
No 25
>PF05973 Gp49: Phage derived protein Gp49-like (DUF891); InterPro: IPR009241 This entry consists of several hypothetical viral and bacterial proteins some are annotated as addiction module killer proteins.
Probab=35.87 E-value=54 Score=21.18 Aligned_cols=33 Identities=21% Similarity=0.397 Sum_probs=22.3
Q ss_pred CCChHhHhHHHHHHHHhhcc------------C-CCeEEechhhhh
Q psy10139 28 GIRDRDRNQMMAILNGIAFA------------R-DNTYHLQRHVWN 60 (106)
Q Consensus 28 g~~~~dk~~l~~iL~eVA~~------------~-~~~Y~Lk~~~~~ 60 (106)
+++..++..+...|+.++.. + +|.|+|+-..-+
T Consensus 5 ~L~~~~~~~i~~~l~~l~~~G~~l~~~~~k~l~~~~i~ElR~~~~~ 50 (91)
T PF05973_consen 5 SLPDKERAKILAQLERLEEHGPSLGEPLFKHLKGDGIYELRVRGGS 50 (91)
T ss_pred hCCHHHHHHHHHHHHHHHhcCCccCCCcccccCcCCeEEEEEeecC
Confidence 34455567777777777553 5 899999985544
No 26
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=35.43 E-value=80 Score=26.30 Aligned_cols=55 Identities=20% Similarity=0.299 Sum_probs=41.0
Q ss_pred hhHHHHHHHhc-CCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhccCCCeEEechhhh
Q psy10139 2 LQDRIIHLLAV-RPYKKPELYAALTRDGIRDRDRNQMMAILNGIAFARDNTYHLQRHVW 59 (106)
Q Consensus 2 lr~RIIHLLAl-kPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~~~~~~Y~Lk~~~~ 59 (106)
+.++|..+|.- +-++.++|..-|+....+. +.|-.+|++||.+=.|.|.+|.++.
T Consensus 271 l~eqi~~ll~~~~v~~Fs~L~~ll~~~~~~~---~~lL~~L~~~AvLV~G~WV~kS~ll 326 (421)
T PF04801_consen 271 LEEQIKALLKKARVISFSELRKLLPSNSDTD---EELLRALQQVAVLVQGNWVVKSELL 326 (421)
T ss_pred HHHHHHHHHHhCCcccHHHHHHHhccccchH---HHHHHHHHhheEEEeeeEEEehhhc
Confidence 45678888874 4456799988876655322 5777799999999888999998764
No 27
>PF04510 DUF577: Family of unknown function (DUF577); InterPro: IPR007598 This is a family of Arabidopsis thaliana (Mouse-ear cress) proteins. Many of these members contain a repeated region.
Probab=34.44 E-value=61 Score=25.00 Aligned_cols=47 Identities=19% Similarity=0.246 Sum_probs=39.4
Q ss_pred cHHHHHHHHhcCCChHhHhHHHHHHHHhhc--c---CCCeEEechhhhhhcc
Q psy10139 17 KPELYAALTRDGIRDRDRNQMMAILNGIAF--A---RDNTYHLQRHVWNDVQ 63 (106)
Q Consensus 17 k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~--~---~~~~Y~Lk~~~~~evq 63 (106)
+|=|+.-|+..|.++.|-.-|..|...||. + .++=|+|.+++.....
T Consensus 5 kplLIsCL~~q~~k~s~~KiL~~iVs~Va~~v~~~~~~~W~eL~d~Ils~~~ 56 (174)
T PF04510_consen 5 KPLLISCLTMQETKESDFKILRRIVSHVAYEVFDLQEGGWDELSDCILSLSE 56 (174)
T ss_pred HHHHHHHHHhhcccHhHHHHHHHHHHHHHHHHHhcCCCCchhHHHHHHHhhc
Confidence 466899999999999888899999999995 2 6678899999887554
No 28
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=33.86 E-value=1.6e+02 Score=20.27 Aligned_cols=57 Identities=16% Similarity=0.432 Sum_probs=35.4
Q ss_pred hhHHHHHH-HhcCCCCcHHHHHHHHhc-CCChHhHhHHHHHHH-Hhhcc--------CCCeEEechhh
Q psy10139 2 LQDRIIHL-LAVRPYKKPELYAALTRD-GIRDRDRNQMMAILN-GIAFA--------RDNTYHLQRHV 58 (106)
Q Consensus 2 lr~RIIHL-LAlkPy~k~EL~~rL~kd-g~~~~dk~~l~~iL~-eVA~~--------~~~~Y~Lk~~~ 58 (106)
+|+.|..+ |--++++-++|..+|.+. .++-+--++|-.++. ..+-+ ..++|+||++.
T Consensus 12 iRr~vL~~fl~~~~~T~~di~e~L~~~f~vs~~~VasMVG~i~SrlGIL~~~k~~~g~~~~Y~LKe~Y 79 (83)
T PF10826_consen 12 IRRAVLKLFLKGKKFTTDDIYERLKEKFDVSYRGVASMVGLIHSRLGILSIHKDSYGDHNVYSLKEKY 79 (83)
T ss_pred HHHHHHHHHHhCCCeeHHHHHHHHHHHcCchHHHHHHHHHHHHHhhhheeecccccCCccEEEecHHh
Confidence 56777765 567899999999999987 333321222222222 22222 45899999875
No 29
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=32.85 E-value=1.2e+02 Score=19.70 Aligned_cols=32 Identities=19% Similarity=0.343 Sum_probs=19.8
Q ss_pred CCcHHHHHHHHhc--CCChHh-HhHHHHHHHHhhc
Q psy10139 15 YKKPELYAALTRD--GIRDRD-RNQMMAILNGIAF 46 (106)
Q Consensus 15 y~k~EL~~rL~kd--g~~~~d-k~~l~~iL~eVA~ 46 (106)
|.+.||+..+.+. +++..| +..++.+++.++.
T Consensus 1 m~k~eli~~i~~~~~~~s~~~v~~vv~~~~~~i~~ 35 (94)
T TIGR00988 1 MTKSELIERIATQQSHLPAKDVEDAVKTMLEHMAS 35 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence 5788999999863 466533 2344555555554
No 30
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=30.51 E-value=77 Score=19.73 Aligned_cols=54 Identities=17% Similarity=0.308 Sum_probs=30.4
Q ss_pred hHHHHHHHh--cCCCCcHHHHHHHHhcCCChH-hH---hHHHHHHH-Hhh----cc---CCCeEEech
Q psy10139 3 QDRIIHLLA--VRPYKKPELYAALTRDGIRDR-DR---NQMMAILN-GIA----FA---RDNTYHLQR 56 (106)
Q Consensus 3 r~RIIHLLA--lkPy~k~EL~~rL~kdg~~~~-dk---~~l~~iL~-eVA----~~---~~~~Y~Lk~ 56 (106)
.+-++++|. =+|++..||.....+.|+-.. .+ +.|.+.|. .+- .| ++|.|.|+.
T Consensus 4 ~eaa~~vL~~~~~pm~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~~~d~~F~~vg~~~~~L~~ 71 (72)
T PF05066_consen 4 KEAAYEVLEEAGRPMTFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIKNEDSRFVKVGPGRWGLRS 71 (72)
T ss_dssp HHHHHHHHHHH-S-EEHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH-T-SS-EESSSSEEE-GG
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcccCCCCEEEeCCCcEEeee
Confidence 444555553 379999999999999887542 22 34543322 231 34 678888864
No 31
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=30.11 E-value=74 Score=24.14 Aligned_cols=41 Identities=20% Similarity=0.336 Sum_probs=34.1
Q ss_pred hHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhc
Q psy10139 3 QDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAF 46 (106)
Q Consensus 3 r~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~ 46 (106)
+.+-+++|+-+-.+..||...|.+-|.++ ..++.||.-++.
T Consensus 23 ~~~Al~~Ls~R~rse~ELr~kL~k~~~~~---~~Ie~Vi~~l~~ 63 (174)
T COG2137 23 LNRALRLLSRRDRSEKELRRKLAKKEFSE---EIIEEVIDRLAE 63 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCH---HHHHHHHHHHHH
Confidence 45678999999999999999999999987 567888766654
No 32
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=30.00 E-value=35 Score=19.28 Aligned_cols=29 Identities=21% Similarity=0.361 Sum_probs=19.7
Q ss_pred ChhHHHHHHHhcCCCCcHHHHHHHHhcCC
Q psy10139 1 MLQDRIIHLLAVRPYKKPELYAALTRDGI 29 (106)
Q Consensus 1 ~lr~RIIHLLAlkPy~k~EL~~rL~kdg~ 29 (106)
|-|..|--.|.+-+-+-|-++++|.++|+
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~gl 31 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGL 31 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCC
Confidence 44667777777777777888888888775
No 33
>KOG2616|consensus
Probab=29.54 E-value=66 Score=26.37 Aligned_cols=40 Identities=18% Similarity=0.199 Sum_probs=31.3
Q ss_pred hHHHHHHHhcCCCCc-HHHHHHHHhcCCChHhHhHHHHHHH
Q psy10139 3 QDRIIHLLAVRPYKK-PELYAALTRDGIRDRDRNQMMAILN 42 (106)
Q Consensus 3 r~RIIHLLAlkPy~k-~EL~~rL~kdg~~~~dk~~l~~iL~ 42 (106)
.||+.||||.+--.- .+|..++.++|--+-++.-++++=+
T Consensus 104 ~ER~lwlla~~d~qi~~~l~nefe~~~~~qv~kel~ekls~ 144 (266)
T KOG2616|consen 104 FERVLWLLAGSDSQITRALMNEFERTGSVQVPKELHEKLSE 144 (266)
T ss_pred HHHHHHHHhCChHHHHHHHHHHHhhCCceecCHHHHHHHHH
Confidence 489999999987664 8888889999977667777776633
No 34
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=29.50 E-value=35 Score=27.24 Aligned_cols=34 Identities=26% Similarity=0.493 Sum_probs=25.9
Q ss_pred hhHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHH
Q psy10139 2 LQDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAI 40 (106)
Q Consensus 2 lr~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~i 40 (106)
.|+|||.||+=+||=-+|+...| |+++ ++.++.+
T Consensus 16 tRR~Il~lLt~~p~yvsEiS~~l---gvsq--kAVl~HL 49 (217)
T COG1777 16 TRRRILQLLTRRPCYVSEISREL---GVSQ--KAVLKHL 49 (217)
T ss_pred HHHHHHHHHhcCchHHHHHHhhc---CcCH--HHHHHHH
Confidence 58999999999997678887654 7776 3555544
No 35
>PRK10854 exopolyphosphatase; Provisional
Probab=28.67 E-value=1.6e+02 Score=25.37 Aligned_cols=60 Identities=15% Similarity=0.228 Sum_probs=39.1
Q ss_pred HHHHHHhc--C-CChHhHhHHH--HHHHHhhccCCCeEEechhhhhhccCCCCCCCHHHHHHHHH
Q psy10139 20 LYAALTRD--G-IRDRDRNQMM--AILNGIAFARDNTYHLQRHVWNDVQDDWPFYSQQDKNMLKS 79 (106)
Q Consensus 20 L~~rL~kd--g-~~~~dk~~l~--~iL~eVA~~~~~~Y~Lk~~~~~evq~dWp~Yse~er~~~kr 79 (106)
|...|.+. + ..+.|+.-|+ ++|.+|+.+=+-.+.=+-.+|-=-+.|++|+|..|+..+-.
T Consensus 343 LFd~l~~~h~~~~~~~~~~LL~~Aa~LhdiG~~I~~~~~~~Hs~yiI~~s~l~G~s~~E~~~iA~ 407 (513)
T PRK10854 343 LYEQWREQNPKLAHPQLEALLKWAAMLHEVGLNINHSGLHRHSAYILQNTDLPGFNQEQQLMLAT 407 (513)
T ss_pred HHHhhhhhhcccCCHHHHHHHHHHHHHHhcCCccCCCCcchhHHHHHhcCCCCCCCHHHHHHHHH
Confidence 44444443 2 2444454443 45888887744455556667777889999999999996554
No 36
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=26.50 E-value=1.7e+02 Score=18.22 Aligned_cols=59 Identities=20% Similarity=0.220 Sum_probs=41.1
Q ss_pred HHHHHHhcC--CCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhcc-------CCCeEEechhhhhhccCCCCCC
Q psy10139 5 RIIHLLAVR--PYKKPELYAALTRDGIRDRDRNQMMAILNGIAFA-------RDNTYHLQRHVWNDVQDDWPFY 69 (106)
Q Consensus 5 RIIHLLAlk--Py~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~~-------~~~~Y~Lk~~~~~evq~dWp~Y 69 (106)
.|+.+|+-. |++-+||...+ |++. ..+..+|+..... .+|.|.+-..++.--...+...
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l---~i~~---~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~~~~~~~~~~~ 76 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERL---GLSK---STAHRLLNTLQELGYVEQDGQNGRYRLGPKVLELGQSYLSSL 76 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHh---CCCH---HHHHHHHHHHHHCCCeeecCCCCceeecHHHHHHHHHHHhcC
Confidence 577888764 78899999998 6654 6777777766532 3568999888876555444333
No 37
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=26.45 E-value=57 Score=24.00 Aligned_cols=29 Identities=28% Similarity=0.343 Sum_probs=25.5
Q ss_pred HHHHHHHhcCCCCcHHHHHHHHhcCCChH
Q psy10139 4 DRIIHLLAVRPYKKPELYAALTRDGIRDR 32 (106)
Q Consensus 4 ~RIIHLLAlkPy~k~EL~~rL~kdg~~~~ 32 (106)
..|-+.|-+.|.+-++.+++|.+.|+-+.
T Consensus 28 ~diA~~L~Vsp~sVt~ml~rL~~~GlV~~ 56 (154)
T COG1321 28 KDIAERLKVSPPSVTEMLKRLERLGLVEY 56 (154)
T ss_pred HHHHHHhCCCcHHHHHHHHHHHHCCCeEE
Confidence 46889999999999999999999998643
No 38
>PF11417 Inhibitor_G39P: Loader and inhibitor of phage G40P; InterPro: IPR024424 G39P inhibits the initiation of DNA replication by blocking G40P replicative helicase. G39P has a bipartite stricture consisting of a folded N-terminal domain and an unfolded C-terminal domain. The C-terminal is essential for helicase interaction [].; PDB: 1NO1_B.
Probab=26.26 E-value=38 Score=22.18 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=7.7
Q ss_pred ChhHHHHHHHhc
Q psy10139 1 MLQDRIIHLLAV 12 (106)
Q Consensus 1 ~lr~RIIHLLAl 12 (106)
|.|+++++||++
T Consensus 1 Mtk~E~~~ll~~ 12 (71)
T PF11417_consen 1 MTKEETAKLLKL 12 (71)
T ss_dssp --HHHHHHHHHH
T ss_pred CCHHHHHHHHHH
Confidence 677888888775
No 39
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=25.11 E-value=74 Score=24.69 Aligned_cols=49 Identities=16% Similarity=0.243 Sum_probs=33.1
Q ss_pred CCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhcc-------------CCCeEEechhhhhhccCCCCCCCHHHHH
Q psy10139 13 RPYKKPELYAALTRDGIRDRDRNQMMAILNGIAFA-------------RDNTYHLQRHVWNDVQDDWPFYSQQDKN 75 (106)
Q Consensus 13 kPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~~-------------~~~~Y~Lk~~~~~evq~dWp~Yse~er~ 75 (106)
+||..++|++-.++-+.. +.+.|-+.|+.| |++.|-| ++|+++-+-+.-
T Consensus 29 ~~~~F~dii~EI~~~~~~-----s~~ei~~~i~~FYTdln~DgrFi~LGdn~WgL---------Rswy~~Deidee 90 (175)
T COG3343 29 KPFNFSDIINEIQKLLGV-----SKEEIRSRIGQFYTDLNIDGRFISLGDNKWGL---------RSWYPLDEIDEE 90 (175)
T ss_pred CCccHHHHHHHHHHHhCc-----CHHHHHHHHHHHHHHhccCCceeeccccccch---------hhccchhHHHHH
Confidence 689999999999997653 233444445544 5555555 469988776655
No 40
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=24.96 E-value=1.2e+02 Score=20.46 Aligned_cols=43 Identities=21% Similarity=0.271 Sum_probs=30.6
Q ss_pred hHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhc
Q psy10139 3 QDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAF 46 (106)
Q Consensus 3 r~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~ 46 (106)
+.+++.++=+.|-+-.|+..=++..+..- +.+.++.||+.|+.
T Consensus 73 ~~E~~qi~Nl~P~~~~El~~ii~~~~~r~-~ee~l~~iL~~v~~ 115 (117)
T PF03874_consen 73 EFEILQIINLRPTTAVELRAIIESLESRF-SEEDLEEILDLVSK 115 (117)
T ss_dssp HHHHHHHHHH--SSHHHHHHHSTTGTTTS-THHHHHHHHHHHHH
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHhccCC-CHHHHHHHHHHHHH
Confidence 45788888899998899988888877432 12678888887765
No 41
>TIGR00678 holB DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
Probab=24.42 E-value=85 Score=22.47 Aligned_cols=38 Identities=24% Similarity=0.360 Sum_probs=27.2
Q ss_pred hHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHh
Q psy10139 3 QDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGI 44 (106)
Q Consensus 3 r~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eV 44 (106)
+.|. +.+-+.|++..|+..+|.+.|+.+ +.++.+++.+
T Consensus 144 ~sr~-~~~~~~~~~~~~~~~~l~~~gi~~---~~~~~i~~~~ 181 (188)
T TIGR00678 144 RSRC-QVLPFPPLSEEALLQWLIRQGISE---EAAELLLALA 181 (188)
T ss_pred Hhhc-EEeeCCCCCHHHHHHHHHHcCCCH---HHHHHHHHHc
Confidence 4444 467899999999999999998653 4455555444
No 42
>PHA03335 hypothetical protein; Provisional
Probab=24.28 E-value=42 Score=28.66 Aligned_cols=67 Identities=12% Similarity=0.305 Sum_probs=48.0
Q ss_pred HHHHHHhcCCCCcH-------HHHHHHHhcC--CChHhHhHHHHHHHHhhccCCCeEEech---hhhhhccC--CCCCCC
Q psy10139 5 RIIHLLAVRPYKKP-------ELYAALTRDG--IRDRDRNQMMAILNGIAFARDNTYHLQR---HVWNDVQD--DWPFYS 70 (106)
Q Consensus 5 RIIHLLAlkPy~k~-------EL~~rL~kdg--~~~~dk~~l~~iL~eVA~~~~~~Y~Lk~---~~~~evq~--dWp~Ys 70 (106)
-+-|=|++-|+=.| .|..+|++|- ..+.-++.+..++++||.++.|+=++.. =+|.-+|. .|.-|.
T Consensus 189 ~~~~PL~~ip~i~pWTlPilrgimsqLqrniWagGQNRkekitelve~l~~v~~~~~~~~htmcLIYhvLNayiNWf~fn 268 (385)
T PHA03335 189 TVEDPLDLIPTIYPWTLPILRGIMSQLQRNIWAGGQNRKEKITELVEELAKVKRGAANLEHTMCLIYHVLNAYINWFAFN 268 (385)
T ss_pred hccCcHHHhhhhhhcccHHHHHHHHHHhhhhhhcccchHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHhHHHhh
Confidence 34456666665444 7888999975 2344578899999999999887777765 35777775 588886
Q ss_pred H
Q psy10139 71 Q 71 (106)
Q Consensus 71 e 71 (106)
.
T Consensus 269 ~ 269 (385)
T PHA03335 269 R 269 (385)
T ss_pred h
Confidence 4
No 43
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=24.11 E-value=1.7e+02 Score=19.30 Aligned_cols=32 Identities=16% Similarity=0.209 Sum_probs=18.0
Q ss_pred CCcHHHHHHHHhcC-CChHh-HhHHHHHHHHhhc
Q psy10139 15 YKKPELYAALTRDG-IRDRD-RNQMMAILNGIAF 46 (106)
Q Consensus 15 y~k~EL~~rL~kdg-~~~~d-k~~l~~iL~eVA~ 46 (106)
|.+.||+.++.+.. ++..| +..++.+++.++.
T Consensus 2 mtk~eli~~ia~~~~~s~~~v~~vv~~~~~~i~~ 35 (96)
T TIGR00987 2 LTKAEMSEYLFDELGLSKREAKELVELFFEEIRR 35 (96)
T ss_pred CCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 67889998887754 44322 1233444444443
No 44
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=24.11 E-value=96 Score=20.99 Aligned_cols=50 Identities=18% Similarity=0.375 Sum_probs=31.8
Q ss_pred HHHHHH--hcCCCCcHHHHHHHHhc-C---------CChHhHhHHHHHHHHhhcc--CCCeEEe
Q psy10139 5 RIIHLL--AVRPYKKPELYAALTRD-G---------IRDRDRNQMMAILNGIAFA--RDNTYHL 54 (106)
Q Consensus 5 RIIHLL--AlkPy~k~EL~~rL~kd-g---------~~~~dk~~l~~iL~eVA~~--~~~~Y~L 54 (106)
.|.|++ .=+||++++|...+.+. | ...=+-+.|-..|.+=+.| .+|-|+.
T Consensus 6 eVL~mml~~~~~~t~~~L~~~i~~~FG~~arFhTCSa~~m~a~~Li~FL~~kgKfi~~~~gft~ 69 (77)
T TIGR03853 6 EVLNLMLASGEPYTRESLKAAIEQKFGEDARFHTCSAEGMTADELLQFLLKKGKFIESDGGFTT 69 (77)
T ss_pred HHHHHHHHcCCCcCHHHHHHHHHHHhCCCceEeecccccCCHHHHHHHHHHCCCEeecCCcEEE
Confidence 588999 88999999998887652 1 1112335555556555555 4555544
No 45
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=24.04 E-value=1.5e+02 Score=18.75 Aligned_cols=27 Identities=22% Similarity=0.502 Sum_probs=15.1
Q ss_pred CCcHHHHHHHHhc-CCChHhHhHHHHHHHHh
Q psy10139 15 YKKPELYAALTRD-GIRDRDRNQMMAILNGI 44 (106)
Q Consensus 15 y~k~EL~~rL~kd-g~~~~dk~~l~~iL~eV 44 (106)
|++.||+.++.+. |++.. ....+|+.+
T Consensus 1 Mtk~eli~~ia~~~~~s~~---~v~~vl~~~ 28 (90)
T PF00216_consen 1 MTKKELIKRIAEKTGLSKK---DVEAVLDAL 28 (90)
T ss_dssp EBHHHHHHHHHHHHTSSHH---HHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCCCHH---HHHHHHHHH
Confidence 4567777777664 56653 444444433
No 46
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=22.85 E-value=2.1e+02 Score=19.31 Aligned_cols=37 Identities=16% Similarity=0.193 Sum_probs=28.7
Q ss_pred hhHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHH
Q psy10139 2 LQDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAIL 41 (106)
Q Consensus 2 lr~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL 41 (106)
.|++|-..|-|.-...-.|++||.-=|++. +.++.+|
T Consensus 50 rR~~l~~~L~iGy~N~KqllkrLN~f~it~---~e~~~al 86 (87)
T PF13331_consen 50 RREKLGEYLGIGYGNAKQLLKRLNMFGITR---EEFEEAL 86 (87)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHcCCCH---HHHHHHh
Confidence 478888999995555689999999999975 5666654
No 47
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=22.55 E-value=2e+02 Score=19.97 Aligned_cols=45 Identities=18% Similarity=0.161 Sum_probs=34.0
Q ss_pred hHHHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhccC
Q psy10139 3 QDRIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAFAR 48 (106)
Q Consensus 3 r~RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~~~ 48 (106)
+-++..+.-+.|-+-.|+..-++..+..- +...++.||+.|+.++
T Consensus 71 k~E~~~i~Nl~P~s~~E~~~lI~sl~~r~-~ee~l~~iL~~i~~~~ 115 (118)
T smart00657 71 KFEIAQLGNLRPETAEEAQLLIPSLEERI-DEEELEELLDDLSSLL 115 (118)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhhhhhccC-CHHHHHHHHHHHHHhc
Confidence 45678888889999899888888876432 2367888888888753
No 48
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=22.40 E-value=56 Score=21.21 Aligned_cols=10 Identities=50% Similarity=0.660 Sum_probs=7.5
Q ss_pred hhHHHHHHHh
Q psy10139 2 LQDRIIHLLA 11 (106)
Q Consensus 2 lr~RIIHLLA 11 (106)
..++|||.||
T Consensus 43 ~eR~iIH~la 52 (74)
T cd02643 43 EKRRIVHELA 52 (74)
T ss_pred HHHHHHHHHH
Confidence 3578899876
No 49
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=22.02 E-value=2.2e+02 Score=18.86 Aligned_cols=32 Identities=16% Similarity=0.244 Sum_probs=19.3
Q ss_pred CCcHHHHHHHHhc-CCChHhH-hHHHHHHHHhhc
Q psy10139 15 YKKPELYAALTRD-GIRDRDR-NQMMAILNGIAF 46 (106)
Q Consensus 15 y~k~EL~~rL~kd-g~~~~dk-~~l~~iL~eVA~ 46 (106)
|.+.||+..|.+. |++.+|- ..++.+++.|..
T Consensus 1 MtK~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~ 34 (90)
T PRK10664 1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTE 34 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5788888888775 4555432 234455555544
No 50
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=21.58 E-value=2.4e+02 Score=25.26 Aligned_cols=54 Identities=22% Similarity=0.367 Sum_probs=37.9
Q ss_pred hhHHHHHHHhc---CCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhcc------CCCeEEechh
Q psy10139 2 LQDRIIHLLAV---RPYKKPELYAALTRDGIRDRDRNQMMAILNGIAFA------RDNTYHLQRH 57 (106)
Q Consensus 2 lr~RIIHLLAl---kPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~~------~~~~Y~Lk~~ 57 (106)
.++.|+.+|-- +|++..||.+.|.-.+. .++..|..+|+....- +.|.|.+++.
T Consensus 3 ~~~~il~~l~~~~~~~~~~~~l~~~l~~~~~--~~~~~l~~~l~~l~~~g~l~~~~~~~~~~~~~ 65 (709)
T TIGR02063 3 LRELILEFLKSKKGKPISLKELAKAFHLKGA--DEKKALRKRLRALEDDGLVKKNRRGLYALPES 65 (709)
T ss_pred cHHHHHHHHHhCCCCCCCHHHHHHHhCCCCh--HHHHHHHHHHHHHHHCCCEEEcCCceEecCCC
Confidence 35678888863 78899999999944332 3678888888876542 5577777653
No 51
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=21.35 E-value=1e+02 Score=20.06 Aligned_cols=37 Identities=24% Similarity=0.271 Sum_probs=26.9
Q ss_pred HHHHHHhcCCCCcHHHHHHHHhcCCChHhHhHHHHHHHHhhc
Q psy10139 5 RIIHLLAVRPYKKPELYAALTRDGIRDRDRNQMMAILNGIAF 46 (106)
Q Consensus 5 RIIHLLAlkPy~k~EL~~rL~kdg~~~~dk~~l~~iL~eVA~ 46 (106)
.|+..|.-.|...+||..+++ |+++ ..|..-|.+.-.
T Consensus 9 ~IL~~l~~g~~rf~el~~~l~--~is~---~~L~~~L~~L~~ 45 (90)
T PF01638_consen 9 LILRALFQGPMRFSELQRRLP--GISP---KVLSQRLKELEE 45 (90)
T ss_dssp HHHHHHTTSSEEHHHHHHHST--TS-H---HHHHHHHHHHHH
T ss_pred HHHHHHHhCCCcHHHHHHhcc--hhHH---HHHHHHHHHHHH
Confidence 478888889999999999985 6765 466666555443
No 52
>PF15061 DUF4538: Domain of unknown function (DUF4538)
Probab=21.08 E-value=96 Score=20.02 Aligned_cols=23 Identities=30% Similarity=0.606 Sum_probs=17.6
Q ss_pred HhcCCCCcHHHHHHHHh---cCCChH
Q psy10139 10 LAVRPYKKPELYAALTR---DGIRDR 32 (106)
Q Consensus 10 LAlkPy~k~EL~~rL~k---dg~~~~ 32 (106)
..++||=++|=+++.|+ +|++++
T Consensus 25 i~~~Pmm~~eeYk~~Q~~nR~gI~qe 50 (58)
T PF15061_consen 25 IYFRPMMNPEEYKKEQKINRAGIKQE 50 (58)
T ss_pred hhcccccChHHHHHHHHHHHhcccHh
Confidence 35789999999998765 667664
No 53
>PF15141 DUF4574: Domain of unknown function (DUF4574)
Probab=20.60 E-value=1.4e+02 Score=20.53 Aligned_cols=37 Identities=19% Similarity=0.287 Sum_probs=27.2
Q ss_pred cHHHHHHHHhcCCCh-----HhHhHHHHHHHHhhccCCCeEE
Q psy10139 17 KPELYAALTRDGIRD-----RDRNQMMAILNGIAFARDNTYH 53 (106)
Q Consensus 17 k~EL~~rL~kdg~~~-----~dk~~l~~iL~eVA~~~~~~Y~ 53 (106)
+-|+++.+++..-.. +-+.-+.+.|+|.|....++|-
T Consensus 34 K~e~lK~~pe~~p~~~~E~~~~kaL~m~~LqEAA~T~enia~ 75 (84)
T PF15141_consen 34 KQEMLKEMPEQNPRRRDEAAKRKALVMQTLQEAAETQENIAR 75 (84)
T ss_pred HHHHHHHccccCchhhhHHHHHhHHHHHHHHHHHccCCCeee
Confidence 457899998765431 2356788999999998887774
No 54
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=20.35 E-value=1.7e+02 Score=20.58 Aligned_cols=46 Identities=20% Similarity=0.341 Sum_probs=33.9
Q ss_pred ChhHHHHHHHhcCCCCcHHHHHHHHh--cCCC-hHhHhHHHHHHHHhhc
Q psy10139 1 MLQDRIIHLLAVRPYKKPELYAALTR--DGIR-DRDRNQMMAILNGIAF 46 (106)
Q Consensus 1 ~lr~RIIHLLAlkPy~k~EL~~rL~k--dg~~-~~dk~~l~~iL~eVA~ 46 (106)
|=++..-|+|-|+--++|||..-|.. +|-. --=++.|+.-|++++.
T Consensus 1 ~~K~~~r~~L~i~r~~~~~iF~FL~~~P~GT~~~~iR~~L~rYI~~~G~ 49 (97)
T PRK13916 1 MDKKETKHLLKIKKEDYPQIFDFLENVPRGTKTAHIREALRRYIEEIGE 49 (97)
T ss_pred CchhhhhHHHHhcccccHHHHHHHHHCCCCCccHHHHHHHHHHHHhcCC
Confidence 44678889999999999999877654 4432 2235678888888875
No 55
>KOG4327|consensus
Probab=20.03 E-value=58 Score=26.03 Aligned_cols=15 Identities=7% Similarity=0.016 Sum_probs=11.1
Q ss_pred CCCCCCCCCchhhhh
Q psy10139 88 ENHSITPFYSQQDKN 102 (106)
Q Consensus 88 pP~s~p~~~~~~~~~ 102 (106)
|||.||+.||..+..
T Consensus 172 pPP~pp~i~p~~~de 186 (218)
T KOG4327|consen 172 PPPMPPPICPDSLDE 186 (218)
T ss_pred CCCCCcccCCCCchH
Confidence 456688999987665
Done!