Query psy4851
Match_columns 62
No_of_seqs 114 out of 421
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 19:18:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4851.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4851hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2102|consensus 99.5 7.1E-15 1.5E-19 112.3 4.8 61 1-62 401-462 (941)
2 TIGR00358 3_prime_RNase VacB a 99.4 6.6E-13 1.4E-17 98.2 5.9 58 1-60 125-182 (654)
3 PRK11642 exoribonuclease R; Pr 99.3 1.2E-11 2.5E-16 93.7 6.3 58 1-60 191-248 (813)
4 TIGR02063 RNase_R ribonuclease 99.3 1.1E-11 2.5E-16 92.1 5.9 57 1-59 177-233 (709)
5 COG0557 VacB Exoribonuclease R 99.0 8.8E-10 1.9E-14 82.3 5.8 58 1-60 179-236 (706)
6 TIGR02062 RNase_B exoribonucle 99.0 1.2E-09 2.6E-14 81.1 6.2 57 1-58 124-180 (639)
7 PRK05054 exoribonuclease II; P 98.9 5.3E-09 1.1E-13 77.7 5.7 53 1-55 127-180 (644)
8 PF08206 OB_RNB: Ribonuclease 86.6 0.51 1.1E-05 25.0 1.6 21 2-24 38-58 (58)
9 TIGR02063 RNase_R ribonuclease 85.0 1.2 2.7E-05 33.8 3.4 28 2-30 109-136 (709)
10 KOG3110|consensus 72.7 4.7 0.0001 25.7 2.8 32 18-59 16-47 (153)
11 PF12949 HeH: HeH/LEM domain; 67.9 3.6 7.8E-05 20.2 1.2 14 33-46 7-20 (35)
12 smart00357 CSP Cold shock prot 65.9 15 0.00032 18.4 3.4 22 2-25 43-64 (64)
13 PRK13149 H/ACA RNA-protein com 55.5 13 0.00029 20.6 2.2 19 13-31 33-51 (73)
14 PF03843 Slp: Outer membrane l 55.1 5.9 0.00013 25.1 0.8 30 2-32 78-107 (160)
15 TIGR00752 slp outer membrane l 51.6 7.9 0.00017 25.3 1.0 29 2-32 92-120 (182)
16 PF12434 Malate_DH: Malate deh 47.4 7.8 0.00017 18.2 0.3 21 30-50 8-28 (28)
17 COG0394 Wzb Protein-tyrosine-p 42.6 25 0.00054 21.6 2.1 32 18-49 29-64 (139)
18 KOG3861|consensus 38.7 26 0.00057 25.5 2.0 28 18-45 80-109 (438)
19 COG2053 RPS28A Ribosomal prote 38.3 19 0.00042 20.2 1.1 17 13-30 3-19 (69)
20 PF01191 RNA_pol_Rpb5_C: RNA p 36.0 46 0.001 18.7 2.4 20 31-50 16-35 (74)
21 cd04910 ACT_AK-Ectoine_1 ACT d 35.8 27 0.00059 19.4 1.4 21 25-46 12-32 (71)
22 TIGR02717 AcCoA-syn-alpha acet 35.5 73 0.0016 23.0 3.9 44 14-57 290-333 (447)
23 PF08940 DUF1918: Domain of un 35.3 30 0.00064 18.8 1.5 14 18-31 22-35 (58)
24 COG2117 Predicted subunit of t 33.9 38 0.00081 22.5 2.0 25 27-51 160-185 (198)
25 COG3830 ACT domain-containing 32.3 74 0.0016 18.7 2.9 36 21-56 5-41 (90)
26 COG3840 ThiQ ABC-type thiamine 30.0 85 0.0018 21.4 3.3 32 15-46 21-52 (231)
27 smart00540 LEM in nuclear memb 29.5 75 0.0016 16.1 2.4 19 31-49 7-25 (44)
28 PF01200 Ribosomal_S28e: Ribos 29.0 51 0.0011 18.5 1.8 14 17-30 9-22 (69)
29 smart00513 SAP Putative DNA-bi 29.0 70 0.0015 14.8 2.1 16 32-47 6-21 (35)
30 TIGR02237 recomb_radB DNA repa 28.7 67 0.0015 20.0 2.6 28 14-41 7-34 (209)
31 PF03683 UPF0175: Uncharacteri 28.3 1.1E+02 0.0024 16.7 3.3 24 30-54 46-69 (76)
32 PF01451 LMWPc: Low molecular 27.7 41 0.00088 19.8 1.4 25 27-51 42-66 (138)
33 PF02291 TFIID-31kDa: Transcri 26.0 36 0.00077 21.1 0.9 21 35-57 18-38 (129)
34 COG4046 Uncharacterized protei 25.3 56 0.0012 23.7 1.9 35 25-59 289-328 (368)
35 PF11472 DUF3206: Protein of u 24.6 18 0.00039 22.3 -0.6 13 47-59 36-48 (128)
36 PRK04007 rps28e 30S ribosomal 24.5 59 0.0013 18.3 1.5 13 18-30 8-20 (70)
37 KOG0673|consensus 24.2 88 0.0019 21.9 2.6 34 18-51 225-258 (293)
38 PRK07080 hypothetical protein; 23.4 72 0.0016 22.7 2.1 28 30-57 287-314 (317)
39 PF02037 SAP: SAP domain; Int 23.3 96 0.0021 14.5 2.0 16 32-47 6-21 (35)
40 COG0384 Predicted epimerase, P 23.0 99 0.0021 21.5 2.7 33 14-49 18-50 (291)
41 PHA02723 hypothetical protein; 21.7 12 0.00027 21.0 -1.6 24 15-38 4-27 (77)
42 PTZ00085 40S ribosomal protein 21.5 71 0.0015 18.1 1.5 16 15-30 9-24 (73)
43 cd01123 Rad51_DMC1_radA Rad51_ 21.3 1.3E+02 0.0029 18.9 3.0 29 14-42 14-42 (235)
44 COG1086 Predicted nucleoside-d 20.8 1.2E+02 0.0027 23.4 3.0 44 14-59 297-340 (588)
45 PRK14561 hypothetical protein; 20.6 87 0.0019 20.0 2.0 24 27-50 158-182 (194)
46 KOG2792|consensus 20.4 89 0.0019 22.0 2.0 26 16-41 249-274 (280)
47 TIGR01016 sucCoAbeta succinyl- 20.4 1E+02 0.0022 21.6 2.4 19 31-49 4-22 (386)
48 cd04457 S1_S28E S1_S28E: S28E, 20.3 75 0.0016 17.4 1.4 12 19-30 3-14 (60)
No 1
>KOG2102|consensus
Probab=99.53 E-value=7.1e-15 Score=112.35 Aligned_cols=61 Identities=51% Similarity=0.828 Sum_probs=58.9
Q ss_pred CEEEEEeecCCCCCCCCceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcHHHHhhCCC-CCC
Q psy4851 1 MIFALIKPLIIHHMRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPP-MPW 62 (62)
Q Consensus 1 ~~~a~I~~W~~~~s~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~~vl~~lp~-~~w 62 (62)
+|+|.|++|+. +|+||.||+++.||..|+.++|+++||.+|++++.+|+++++.|||+ .||
T Consensus 401 ~~~~~I~~W~~-ts~~p~g~~v~~lG~i~~~~~e~~aLL~en~v~~~~f~~~~~~~lp~~~~~ 462 (941)
T KOG2102|consen 401 RIVAAIDRWPR-TSLYPFGHLVRELGTIGDTETETEALLLENGVPHKPFSQALLDCLPRSHPW 462 (941)
T ss_pred eEEEEeccccc-CCcccCceehhhccCcCCccchhhhhhhcCCCcccccCHHHHhcCCccCCC
Confidence 47999999998 99999999999999999999999999999999999999999999999 887
No 2
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=99.39 E-value=6.6e-13 Score=98.18 Aligned_cols=58 Identities=19% Similarity=0.209 Sum_probs=54.3
Q ss_pred CEEEEEeecCCCCCCCCceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcHHHHhhCCCC
Q psy4851 1 MIFALIKPLIIHHMRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPM 60 (62)
Q Consensus 1 ~~~a~I~~W~~~~s~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~~vl~~lp~~ 60 (62)
+|+|+|++||. .+..|.|+|+++||..||+.+|+.+||.+|||+. +||++|++|++..
T Consensus 125 ~V~v~i~~~p~-~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i~~-~f~~~v~~~a~~~ 182 (654)
T TIGR00358 125 KVVVELTEYPL-RRNLFYGEITQILGNNDDPLIPWWVTLARHEIPF-EFPDGVEQQAAKL 182 (654)
T ss_pred EEEEEEccCCC-CCCCceEEEEEEEcCCCCcccHHHHHHHHcCcCC-CCCHHHHHHHHhc
Confidence 47899999998 8999999999999999999999999999999997 6999999998753
No 3
>PRK11642 exoribonuclease R; Provisional
Probab=99.26 E-value=1.2e-11 Score=93.75 Aligned_cols=58 Identities=14% Similarity=0.206 Sum_probs=54.1
Q ss_pred CEEEEEeecCCCCCCCCceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcHHHHhhCCCC
Q psy4851 1 MIFALIKPLIIHHMRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPM 60 (62)
Q Consensus 1 ~~~a~I~~W~~~~s~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~~vl~~lp~~ 60 (62)
+|+|+|++||. ....|.|+|+++||..+|+.+|+.+||++|+|+. +||++|++++...
T Consensus 191 ~V~v~I~~~p~-~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~-~Fp~~v~~ea~~~ 248 (813)
T PRK11642 191 VVVVELTQRPT-RRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPY-IWPQAVEQQVAGL 248 (813)
T ss_pred EEEEEEecCCC-cCCCCCEEEEEEecCCCCcchHHHHHHHHcCCCC-CCCHHHHHHHHhc
Confidence 47899999998 8999999999999999999999999999999998 5999999998753
No 4
>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=99.25 E-value=1.1e-11 Score=92.06 Aligned_cols=57 Identities=21% Similarity=0.299 Sum_probs=53.6
Q ss_pred CEEEEEeecCCCCCCCCceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcHHHHhhCCC
Q psy4851 1 MIFALIKPLIIHHMRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPP 59 (62)
Q Consensus 1 ~~~a~I~~W~~~~s~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~~vl~~lp~ 59 (62)
.|+|+|++||. .+.+|.|+|+++||..||..+|+.++|.+|||+. +||++|++++..
T Consensus 177 ~v~v~i~~~p~-~~~~~~g~i~~~lg~~~d~~~~~~~il~~~~i~~-~f~~~v~~~a~~ 233 (709)
T TIGR02063 177 KVLVEITKYPD-RNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY-EFPEEVLDEAAK 233 (709)
T ss_pred EEEEEEccCCC-CCCCceEEEEEEeCCCCcccchHHHHHHHcCcCC-CCCHHHHHHHHh
Confidence 47899999998 8999999999999999999999999999999998 699999998764
No 5
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.99 E-value=8.8e-10 Score=82.27 Aligned_cols=58 Identities=28% Similarity=0.475 Sum_probs=54.4
Q ss_pred CEEEEEeecCCCCCCCCceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcHHHHhhCCCC
Q psy4851 1 MIFALIKPLIIHHMRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPM 60 (62)
Q Consensus 1 ~~~a~I~~W~~~~s~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~~vl~~lp~~ 60 (62)
+++++|++|+. ++.+|.|+++++||..++..+++.++|++|++++. ||++|++|+...
T Consensus 179 ~v~~~i~~~~~-~~~~~~g~v~~~lG~~~~~~~~~~~il~~~~i~~~-f~~~v~~~a~~~ 236 (706)
T COG0557 179 LVVVEITRWPD-TSRPPFGEVVEVLGDLGDPGADIEAILRDHGIPSE-FPEKVLDEAAAL 236 (706)
T ss_pred EEEEEecccCC-cCCCCceeEEEeecCCCCcchhHHHHHHHcCCCCC-CCHHHHHHHHhc
Confidence 47899999998 89999999999999999999999999999999995 999999998753
No 6
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=98.98 E-value=1.2e-09 Score=81.09 Aligned_cols=57 Identities=14% Similarity=0.009 Sum_probs=50.5
Q ss_pred CEEEEEeecCCCCCCCCceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcHHHHhhCC
Q psy4851 1 MIFALIKPLIIHHMRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLP 58 (62)
Q Consensus 1 ~~~a~I~~W~~~~s~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~~vl~~lp 58 (62)
+++|+|++||....+.|.|+|+++||..+|+.+++.+||++|+|+. +||+++++++.
T Consensus 124 ~V~v~I~~~p~~~~~~~~~~I~~vLG~~~d~~~d~~~il~~~~l~~-~f~~~v~~ea~ 180 (639)
T TIGR02062 124 WAVAELRRHPLKGDRSFYAELTQYITFADDHLAPWWVTLARHNLER-EEPDGVADEML 180 (639)
T ss_pred EEEEEEeccCCCCCCCceEEEEEEeCCCCCCccHHHHHHHHcCcCC-CCCHHHHHhhh
Confidence 3789999999732356999999999999999999999999999998 59999998764
No 7
>PRK05054 exoribonuclease II; Provisional
Probab=98.85 E-value=5.3e-09 Score=77.70 Aligned_cols=53 Identities=11% Similarity=0.009 Sum_probs=48.1
Q ss_pred CEEEEEeecCCCCC-CCCceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcHHHHh
Q psy4851 1 MIFALIKPLIIHHM-RYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLS 55 (62)
Q Consensus 1 ~~~a~I~~W~~~~s-~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~~vl~ 55 (62)
+++|+|++||. .. +.|.|+|+++||..+|+.+|+.+||++|+|+. +||+++++
T Consensus 127 ~V~v~i~~~p~-~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l~~-~f~~~~~~ 180 (644)
T PRK05054 127 WVVAELRRHPL-KGDRGFYAEITQFITDADDHFAPWWVTLARHNLER-EAPAGGVA 180 (644)
T ss_pred EEEEEEecCCC-CCCCCceEEEEEEECCCCCCccHHHHHHHHcCCCC-CCCchhhh
Confidence 47899999997 43 45999999999999999999999999999998 59999986
No 8
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=86.65 E-value=0.51 Score=25.00 Aligned_cols=21 Identities=24% Similarity=0.455 Sum_probs=17.8
Q ss_pred EEEEEeecCCCCCCCCceEEEee
Q psy4851 2 IFALIKPLIIHHMRYPQGHFVRA 24 (62)
Q Consensus 2 ~~a~I~~W~~~~s~~P~G~iv~~ 24 (62)
++|+|.. +. ..+.|.|+|+++
T Consensus 38 V~v~i~~-~~-~~~~~eg~vv~V 58 (58)
T PF08206_consen 38 VLVRITP-PS-RGKRPEGEVVEV 58 (58)
T ss_dssp EEEEEEE-SS-SEEEEEEEEEE-
T ss_pred EEEEEec-CC-CCCCCCEEEEeC
Confidence 6889998 76 889999999985
No 9
>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=85.02 E-value=1.2 Score=33.80 Aligned_cols=28 Identities=11% Similarity=0.011 Sum_probs=23.7
Q ss_pred EEEEEeecCCCCCCCCceEEEeecCCCCC
Q psy4851 2 IFALIKPLIIHHMRYPQGHFVRALGPIGD 30 (62)
Q Consensus 2 ~~a~I~~W~~~~s~~P~G~iv~~LG~~gd 30 (62)
|+|+|..|+. ..+.|.|+|+++||...+
T Consensus 109 Vlv~I~~~~~-~~~~~eg~Vv~Il~r~~~ 136 (709)
T TIGR02063 109 VLVRITGKPD-GGDRFEARVIKILERAND 136 (709)
T ss_pred EEEEEecccC-CCCCceEEEEEEEeeCCC
Confidence 6799999975 567789999999998764
No 10
>KOG3110|consensus
Probab=72.71 E-value=4.7 Score=25.75 Aligned_cols=32 Identities=31% Similarity=0.542 Sum_probs=28.7
Q ss_pred ceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcHHHHhhCCC
Q psy4851 18 QGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPP 59 (62)
Q Consensus 18 ~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~~vl~~lp~ 59 (62)
.|.|++=+|+.+ .|-|||+..||..+++.||.
T Consensus 16 ~g~VVrGFGRGs----------keLGiPTAN~~~~~v~~l~~ 47 (153)
T KOG3110|consen 16 GGEVVRGFGRGS----------KELGIPTANFPENVVPKLPE 47 (153)
T ss_pred cCeEEEecCCCc----------cccCCccCCCCHHHHhcccc
Confidence 589999999987 47899999999999999985
No 11
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=67.93 E-value=3.6 Score=20.15 Aligned_cols=14 Identities=21% Similarity=0.323 Sum_probs=10.2
Q ss_pred HHHHHHHHhCCCCC
Q psy4851 33 TENEVLLLEHDVPH 46 (62)
Q Consensus 33 ~E~~aIL~e~~i~~ 46 (62)
+|..+||.+|||.+
T Consensus 7 ~~Lk~iL~~~~I~~ 20 (35)
T PF12949_consen 7 AQLKRILDEHGIEF 20 (35)
T ss_dssp HHHHHHHHHHT---
T ss_pred HHHHHHHHHcCCCC
Confidence 68899999999975
No 12
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=65.91 E-value=15 Score=18.39 Aligned_cols=22 Identities=14% Similarity=-0.058 Sum_probs=16.4
Q ss_pred EEEEEeecCCCCCCCCceEEEeec
Q psy4851 2 IFALIKPLIIHHMRYPQGHFVRAL 25 (62)
Q Consensus 2 ~~a~I~~W~~~~s~~P~G~iv~~L 25 (62)
+.++|..+. ....|.++++++|
T Consensus 43 V~~~i~~~~--~~~~~~a~~v~~~ 64 (64)
T smart00357 43 VEFKVVSPR--GGGKPEAENVVKL 64 (64)
T ss_pred EEEEEEEcc--CCCCcEEEEEEeC
Confidence 678888873 3456899999875
No 13
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=55.55 E-value=13 Score=20.60 Aligned_cols=19 Identities=21% Similarity=0.408 Sum_probs=16.2
Q ss_pred CCCCCceEEEeecCCCCCh
Q psy4851 13 HMRYPQGHFVRALGPIGDK 31 (62)
Q Consensus 13 ~s~~P~G~iv~~LG~~gd~ 31 (62)
.++...|+|.+++|+..++
T Consensus 33 ~~~~~IGkV~dIfGPV~~p 51 (73)
T PRK13149 33 KKLKKIGKVVDVFGPVKEP 51 (73)
T ss_pred CCCCEeEEEEEEECCCCCc
Confidence 4678899999999998765
No 14
>PF03843 Slp: Outer membrane lipoprotein Slp family; InterPro: IPR004658 Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli (which also contains a close paralog), Haemophilus influenzae and Pasteurella multocida and Vibrio cholerae. The known members of the family to date share a motif LX[GA]C near the N terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N terminus. Slp from E. coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.; GO: 0019867 outer membrane
Probab=55.06 E-value=5.9 Score=25.12 Aligned_cols=30 Identities=17% Similarity=0.370 Sum_probs=26.4
Q ss_pred EEEEEeecCCCCCCCCceEEEeecCCCCChH
Q psy4851 2 IFALIKPLIIHHMRYPQGHFVRALGPIGDKD 32 (62)
Q Consensus 2 ~~a~I~~W~~~~s~~P~G~iv~~LG~~gd~e 32 (62)
|+|++...-+ ...|..|+.+.++|.....+
T Consensus 78 Fla~~~gFLD-P~~y~~Gr~vTV~G~v~g~~ 107 (160)
T PF03843_consen 78 FLARVPGFLD-PAIYAPGRLVTVVGTVTGME 107 (160)
T ss_pred EEEEeCCCcC-HHHcCCCCEEEEEEEecceE
Confidence 7899999987 89999999999999887655
No 15
>TIGR00752 slp outer membrane lipoprotein, Slp family. Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli, which also contains a close paralog, Haemophilus influenzae and Pasteurella multocida and Vibrio cholera. The known members of the family to date share a motif LX[GA]C near the N-terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N-terminus. Slp from Escherichia coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.
Probab=51.58 E-value=7.9 Score=25.31 Aligned_cols=29 Identities=14% Similarity=0.295 Sum_probs=24.6
Q ss_pred EEEEEeecCCCCCCCCceEEEeecCCCCChH
Q psy4851 2 IFALIKPLIIHHMRYPQGHFVRALGPIGDKD 32 (62)
Q Consensus 2 ~~a~I~~W~~~~s~~P~G~iv~~LG~~gd~e 32 (62)
|+|++..+-+ ...| .|+.+.++|.....+
T Consensus 92 Fla~~~gFLD-P~~y-~Gr~VTVvG~i~G~e 120 (182)
T TIGR00752 92 FIAYFNGFLD-PVNL-RERYVTVGGQIAGTE 120 (182)
T ss_pred EEEEeCCCcC-hhhc-CCCEEEEEEEecceE
Confidence 7899999998 8999 699999999765544
No 16
>PF12434 Malate_DH: Malate dehydrogenase enzyme
Probab=47.40 E-value=7.8 Score=18.18 Aligned_cols=21 Identities=14% Similarity=0.290 Sum_probs=17.3
Q ss_pred ChHHHHHHHHHhCCCCCCCCc
Q psy4851 30 DKDTENEVLLLEHDVPHSKFS 50 (62)
Q Consensus 30 d~e~E~~aIL~e~~i~~~~F~ 50 (62)
|+..+..+-|++..+.+.+||
T Consensus 8 d~~~~~r~~lR~AALeYHefP 28 (28)
T PF12434_consen 8 DNKEDKRAQLRQAALEYHEFP 28 (28)
T ss_pred cchHHHHHHHHHHHHHhccCC
Confidence 556788889999888888886
No 17
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=42.55 E-value=25 Score=21.65 Aligned_cols=32 Identities=25% Similarity=0.237 Sum_probs=24.5
Q ss_pred ceEEEeecC----CCCChHHHHHHHHHhCCCCCCCC
Q psy4851 18 QGHFVRALG----PIGDKDTENEVLLLEHDVPHSKF 49 (62)
Q Consensus 18 ~G~iv~~LG----~~gd~e~E~~aIL~e~~i~~~~F 49 (62)
.+--+.+=| ..+.++..+.++|.|+||+.+..
T Consensus 29 ~~~~v~SAGt~~~~g~~~~~~a~~vl~e~Gid~~~~ 64 (139)
T COG0394 29 DNVEVDSAGTGGHPGEPPDPRAVEVLAEHGIDISGH 64 (139)
T ss_pred CCeEEECCccCCCCCCCCCHHHHHHHHHcCCCcCCc
Confidence 345566667 45559999999999999998753
No 18
>KOG3861|consensus
Probab=38.68 E-value=26 Score=25.54 Aligned_cols=28 Identities=25% Similarity=0.318 Sum_probs=24.8
Q ss_pred ceEEEeecCCCCChH--HHHHHHHHhCCCC
Q psy4851 18 QGHFVRALGPIGDKD--TENEVLLLEHDVP 45 (62)
Q Consensus 18 ~G~iv~~LG~~gd~e--~E~~aIL~e~~i~ 45 (62)
-|.++=.||..|+.+ +-++-.|.+|||-
T Consensus 80 GGsl~vllGEGGE~rf~tnvNf~le~YGI~ 109 (438)
T KOG3861|consen 80 GGSLVVLLGEGGEPRFNTNVNFFLEQYGIY 109 (438)
T ss_pred CCeEEEEecCCCCccccccHHHHHHHhCeE
Confidence 378899999999988 8899999999983
No 19
>COG2053 RPS28A Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]
Probab=38.31 E-value=19 Score=20.18 Aligned_cols=17 Identities=24% Similarity=0.409 Sum_probs=12.8
Q ss_pred CCCCCceEEEeecCCCCC
Q psy4851 13 HMRYPQGHFVRALGPIGD 30 (62)
Q Consensus 13 ~s~~P~G~iv~~LG~~gd 30 (62)
++.+| ++++++||.-|-
T Consensus 3 e~~~~-aeVi~vlgRTG~ 19 (69)
T COG2053 3 EEATP-AEVIEVLGRTGM 19 (69)
T ss_pred ccccc-hheeeeecccCc
Confidence 34566 999999998764
No 20
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=36.01 E-value=46 Score=18.74 Aligned_cols=20 Identities=15% Similarity=0.318 Sum_probs=13.9
Q ss_pred hHHHHHHHHHhCCCCCCCCc
Q psy4851 31 KDTENEVLLLEHDVPHSKFS 50 (62)
Q Consensus 31 ~e~E~~aIL~e~~i~~~~F~ 50 (62)
.+.|.+.+|.+|++....+|
T Consensus 16 s~eE~~~lL~~y~i~~~qLP 35 (74)
T PF01191_consen 16 SEEEKKELLKKYNIKPEQLP 35 (74)
T ss_dssp -HHHHHHHHHHTT--TTCSS
T ss_pred CHHHHHHHHHHhCCChhhCC
Confidence 36799999999999875553
No 21
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=35.80 E-value=27 Score=19.38 Aligned_cols=21 Identities=33% Similarity=0.379 Sum_probs=18.0
Q ss_pred cCCCCChHHHHHHHHHhCCCCC
Q psy4851 25 LGPIGDKDTENEVLLLEHDVPH 46 (62)
Q Consensus 25 LG~~gd~e~E~~aIL~e~~i~~ 46 (62)
+|..| .+.++-.+|.+|++..
T Consensus 12 vG~~g-~d~~i~~~l~~~~v~i 32 (71)
T cd04910 12 VGEVG-YDLEILELLQRFKVSI 32 (71)
T ss_pred cCChh-HHHHHHHHHHHcCCeE
Confidence 57777 9999999999999864
No 22
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=35.54 E-value=73 Score=23.03 Aligned_cols=44 Identities=16% Similarity=0.165 Sum_probs=39.2
Q ss_pred CCCCceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcHHHHhhC
Q psy4851 14 MRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYL 57 (62)
Q Consensus 14 s~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~~vl~~l 57 (62)
.+.|.|.=+-++...|-.-.-+.-.+.++|+...+|+++..+.|
T Consensus 290 ~~~~~g~rvaivs~sGG~g~l~aD~~~~~Gl~lp~ls~~t~~~L 333 (447)
T TIGR02717 290 QPLPKGNRVAIITNAGGPGVIATDACEENGLELAELSEATKNKL 333 (447)
T ss_pred CCCCCCCeEEEEECCchHHHHHHHHHHHcCCCcCCCCHHHHHHH
Confidence 45778999999999999999999999999999999999887654
No 23
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=35.25 E-value=30 Score=18.84 Aligned_cols=14 Identities=36% Similarity=0.662 Sum_probs=9.5
Q ss_pred ceEEEeecCCCCCh
Q psy4851 18 QGHFVRALGPIGDK 31 (62)
Q Consensus 18 ~G~iv~~LG~~gd~ 31 (62)
.|.|+++.|..|.+
T Consensus 22 ~GeIveV~g~dG~P 35 (58)
T PF08940_consen 22 HGEIVEVRGPDGSP 35 (58)
T ss_dssp EEEEEE-S-SSS-S
T ss_pred EeEEEEEECCCCCC
Confidence 59999999998864
No 24
>COG2117 Predicted subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]
Probab=33.89 E-value=38 Score=22.51 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=20.9
Q ss_pred CCCChHHHHHHHHHhCCCCCCC-CcH
Q psy4851 27 PIGDKDTENEVLLLEHDVPHSK-FSD 51 (62)
Q Consensus 27 ~~gd~e~E~~aIL~e~~i~~~~-F~~ 51 (62)
+.+|-|+|...+|.+.|..... ||.
T Consensus 160 ~k~DYEaElR~lL~erg~~~~~~FP~ 185 (198)
T COG2117 160 EKADYEAELRYLLRERGTAPEDIFPE 185 (198)
T ss_pred cccchHHHHHHHHHHcCCChHHhcch
Confidence 5689999999999999987655 664
No 25
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=32.27 E-value=74 Score=18.69 Aligned_cols=36 Identities=19% Similarity=0.141 Sum_probs=26.1
Q ss_pred EEeecCCC-CChHHHHHHHHHhCCCCCCCCcHHHHhh
Q psy4851 21 FVRALGPI-GDKDTENEVLLLEHDVPHSKFSDLVLSY 56 (62)
Q Consensus 21 iv~~LG~~-gd~e~E~~aIL~e~~i~~~~F~~~vl~~ 56 (62)
++.++|+. -.+=+-.-.+|++||+...+-|+.++++
T Consensus 5 vITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~ 41 (90)
T COG3830 5 VITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDG 41 (90)
T ss_pred EEEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhh
Confidence 56677732 2455677889999999877777777765
No 26
>COG3840 ThiQ ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]
Probab=29.99 E-value=85 Score=21.41 Aligned_cols=32 Identities=28% Similarity=0.478 Sum_probs=27.8
Q ss_pred CCCceEEEeecCCCCChHHHHHHHHHhCCCCC
Q psy4851 15 RYPQGHFVRALGPIGDKDTENEVLLLEHDVPH 46 (62)
Q Consensus 15 ~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~ 46 (62)
..|.|+++-++|++|.-..-.-.+++-+..|.
T Consensus 21 ~v~~ge~vAi~GpSGaGKSTLLnLIAGF~~P~ 52 (231)
T COG3840 21 TVPAGEIVAILGPSGAGKSTLLNLIAGFETPA 52 (231)
T ss_pred eecCCcEEEEECCCCccHHHHHHHHHhccCCC
Confidence 46889999999999999998888888877664
No 27
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=29.55 E-value=75 Score=16.13 Aligned_cols=19 Identities=21% Similarity=0.253 Sum_probs=15.7
Q ss_pred hHHHHHHHHHhCCCCCCCC
Q psy4851 31 KDTENEVLLLEHDVPHSKF 49 (62)
Q Consensus 31 ~e~E~~aIL~e~~i~~~~F 49 (62)
.+.|..+-|.+||++..|-
T Consensus 7 Sd~eL~~~L~~~G~~~gPI 25 (44)
T smart00540 7 SDAELRAELKQYGLPPGPI 25 (44)
T ss_pred CHHHHHHHHHHcCCCCCCc
Confidence 4689999999999987653
No 28
>PF01200 Ribosomal_S28e: Ribosomal protein S28e; InterPro: IPR000289 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. Examples are: Mammalian S28 [] Plant S28 [] Fungi S33 [] Archaebacterial S28e. These proteins have from 64 to 78 amino acids and a highly conserved C-terminal region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_Y 2XZN_1 2XZM_1 1NY4_A 1NE3_A 3U5C_c 3U5G_c 3O30_R 3O2Z_R 3IZB_Y.
Probab=29.01 E-value=51 Score=18.50 Aligned_cols=14 Identities=21% Similarity=0.503 Sum_probs=11.6
Q ss_pred CceEEEeecCCCCC
Q psy4851 17 PQGHFVRALGPIGD 30 (62)
Q Consensus 17 P~G~iv~~LG~~gd 30 (62)
-.++++++||..|.
T Consensus 9 ~~A~V~kVlgRtGs 22 (69)
T PF01200_consen 9 KLARVIKVLGRTGS 22 (69)
T ss_dssp EEEEEEEEECCCTS
T ss_pred eeEEEEEEcccccC
Confidence 35899999998875
No 29
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=28.95 E-value=70 Score=14.81 Aligned_cols=16 Identities=19% Similarity=0.057 Sum_probs=14.1
Q ss_pred HHHHHHHHHhCCCCCC
Q psy4851 32 DTENEVLLLEHDVPHS 47 (62)
Q Consensus 32 e~E~~aIL~e~~i~~~ 47 (62)
..|..+++.++|++..
T Consensus 6 ~~~Lk~~l~~~gl~~~ 21 (35)
T smart00513 6 VSELKDELKKRGLSTS 21 (35)
T ss_pred HHHHHHHHHHcCCCCC
Confidence 5789999999999975
No 30
>TIGR02237 recomb_radB DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).
Probab=28.74 E-value=67 Score=19.99 Aligned_cols=28 Identities=21% Similarity=0.292 Sum_probs=23.5
Q ss_pred CCCCceEEEeecCCCCChHHHHHHHHHh
Q psy4851 14 MRYPQGHFVRALGPIGDKDTENEVLLLE 41 (62)
Q Consensus 14 s~~P~G~iv~~LG~~gd~e~E~~aIL~e 41 (62)
.-.|.|+++.+.|+.|.-.+....-+..
T Consensus 7 GGi~~g~i~~i~G~~GsGKT~l~~~~~~ 34 (209)
T TIGR02237 7 GGVERGTITQIYGPPGSGKTNICMILAV 34 (209)
T ss_pred CCCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence 4689999999999999999988655553
No 31
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=28.34 E-value=1.1e+02 Score=16.74 Aligned_cols=24 Identities=25% Similarity=0.232 Sum_probs=18.9
Q ss_pred ChHHHHHHHHHhCCCCCCCCcHHHH
Q psy4851 30 DKDTENEVLLLEHDVPHSKFSDLVL 54 (62)
Q Consensus 30 d~e~E~~aIL~e~~i~~~~F~~~vl 54 (62)
=...|+..+|.++||+ ..++.+=+
T Consensus 46 ~s~~eF~~~L~~~gI~-~~~~~eel 69 (76)
T PF03683_consen 46 MSRWEFLELLKERGIP-INYDEEEL 69 (76)
T ss_pred CCHHHHHHHHHHCCCC-CCCCHHHH
Confidence 3678999999999999 46866543
No 32
>PF01451 LMWPc: Low molecular weight phosphotyrosine protein phosphatase; InterPro: IPR023485 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents the low molecular weight (LMW) protein-tyrosine phosphatases (or acid phosphatase), which act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates [, ]. The structure of a LMW PTPase has been solved by X-ray crystallography [] and is found to form a single structural domain. It belongs to the alpha/beta class, with 6 alpha-helices and 4 beta-strands forming a 3-layer alpha-beta-alpha sandwich architecture.; PDB: 3RH0_B 1JL3_B 2IPA_B 1Z2D_A 1Z2E_A 2CWD_D 2L18_A 2L17_A 2L19_A 1BVH_A ....
Probab=27.66 E-value=41 Score=19.78 Aligned_cols=25 Identities=24% Similarity=0.230 Sum_probs=20.2
Q ss_pred CCCChHHHHHHHHHhCCCCCCCCcH
Q psy4851 27 PIGDKDTENEVLLLEHDVPHSKFSD 51 (62)
Q Consensus 27 ~~gd~e~E~~aIL~e~~i~~~~F~~ 51 (62)
..+.++..+.++|.++|++.+.+..
T Consensus 42 ~~~~~~~~a~~~l~~~gid~~~~~s 66 (138)
T PF01451_consen 42 PGEPVDPRAIAVLKEHGIDISGHRS 66 (138)
T ss_dssp TTSSSTHHHHHHHHHTTSSCTTSBB
T ss_pred ccccccchHHHHHHHhCCCccccee
Confidence 4567889999999999999876643
No 33
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=25.97 E-value=36 Score=21.06 Aligned_cols=21 Identities=19% Similarity=0.297 Sum_probs=13.7
Q ss_pred HHHHHHhCCCCCCCCcHHHHhhC
Q psy4851 35 NEVLLLEHDVPHSKFSDLVLSYL 57 (62)
Q Consensus 35 ~~aIL~e~~i~~~~F~~~vl~~l 57 (62)
++.||.+.||. +|.+.|..+|
T Consensus 18 i~~iL~~~Gv~--~yeprVv~qL 38 (129)
T PF02291_consen 18 IHLILKSMGVT--EYEPRVVNQL 38 (129)
T ss_dssp HHHHHHHTT-----B-THHHHHH
T ss_pred HHHHHHHcCCc--ccCHHHHHHH
Confidence 67899999997 3888887654
No 34
>COG4046 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.28 E-value=56 Score=23.68 Aligned_cols=35 Identities=14% Similarity=0.289 Sum_probs=26.0
Q ss_pred cCCCCChHHHHHHHHHhCCCCCCCC-----cHHHHhhCCC
Q psy4851 25 LGPIGDKDTENEVLLLEHDVPHSKF-----SDLVLSYLPP 59 (62)
Q Consensus 25 LG~~gd~e~E~~aIL~e~~i~~~~F-----~~~vl~~lp~ 59 (62)
.|.+|--..-++.|..+|||+.+.| +++++-++|.
T Consensus 289 mGd~G~EK~~iE~ia~kygi~l~Av~IKMs~eEAit~M~~ 328 (368)
T COG4046 289 MGDPGVEKIFIERIAVKYGIPLDAVIIKMSPEEAITQMPE 328 (368)
T ss_pred cCCCCcceeeHHHHHHHhCCcchheeeecCHHHHhhhCcH
Confidence 4556666666899999999998766 5667777663
No 35
>PF11472 DUF3206: Protein of unknown function (DUF3206); InterPro: IPR021571 This bacterial family of proteins has no known function. ; PDB: 2AU5_A.
Probab=24.65 E-value=18 Score=22.27 Aligned_cols=13 Identities=38% Similarity=0.580 Sum_probs=8.6
Q ss_pred CCCcHHHHhhCCC
Q psy4851 47 SKFSDLVLSYLPP 59 (62)
Q Consensus 47 ~~F~~~vl~~lp~ 59 (62)
+.|+|+||+.+..
T Consensus 36 S~F~P~VL~~ME~ 48 (128)
T PF11472_consen 36 SHFSPIVLKIMEK 48 (128)
T ss_dssp TT--HHHHHHHHH
T ss_pred ccCCHHHHHHHhh
Confidence 3599999998865
No 36
>PRK04007 rps28e 30S ribosomal protein S28e; Validated
Probab=24.46 E-value=59 Score=18.32 Aligned_cols=13 Identities=15% Similarity=0.386 Sum_probs=10.9
Q ss_pred ceEEEeecCCCCC
Q psy4851 18 QGHFVRALGPIGD 30 (62)
Q Consensus 18 ~G~iv~~LG~~gd 30 (62)
.++++++||..|.
T Consensus 8 ~A~VikVlGRTG~ 20 (70)
T PRK04007 8 PAEVIEIIGRTGM 20 (70)
T ss_pred eEEEEEEeccccc
Confidence 4899999998775
No 37
>KOG0673|consensus
Probab=24.17 E-value=88 Score=21.91 Aligned_cols=34 Identities=21% Similarity=0.332 Sum_probs=30.8
Q ss_pred ceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcH
Q psy4851 18 QGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSD 51 (62)
Q Consensus 18 ~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~ 51 (62)
.|.++.+||++--....++++-.+-..+.++||.
T Consensus 225 pgdfiH~lGdahvy~~Hv~al~~Ql~r~PrpFPk 258 (293)
T KOG0673|consen 225 PGDFIHVLGDAHVYKDHVDALQEQLQRPPRPFPK 258 (293)
T ss_pred CCceEEecchhhhhHHHHHHHHHHHhcCCCCCCc
Confidence 5999999999999999999999998888888985
No 38
>PRK07080 hypothetical protein; Validated
Probab=23.35 E-value=72 Score=22.74 Aligned_cols=28 Identities=14% Similarity=0.154 Sum_probs=24.0
Q ss_pred ChHHHHHHHHHhCCCCCCCCcHHHHhhC
Q psy4851 30 DKDTENEVLLLEHDVPHSKFSDLVLSYL 57 (62)
Q Consensus 30 d~e~E~~aIL~e~~i~~~~F~~~vl~~l 57 (62)
.+|-=+.|+|..||++...+|+.|-+.|
T Consensus 287 GlER~a~All~~hG~d~~~WP~~Vr~~l 314 (317)
T PRK07080 287 GLERLALALFRHHGLDPAAWPAAVRDVL 314 (317)
T ss_pred CHHHHHHHHHHHhCCChhhccHHHHHHh
Confidence 4666788999999999989999998765
No 39
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=23.29 E-value=96 Score=14.51 Aligned_cols=16 Identities=25% Similarity=0.108 Sum_probs=12.9
Q ss_pred HHHHHHHHHhCCCCCC
Q psy4851 32 DTENEVLLLEHDVPHS 47 (62)
Q Consensus 32 e~E~~aIL~e~~i~~~ 47 (62)
-.|...++.++|++..
T Consensus 6 v~eLk~~l~~~gL~~~ 21 (35)
T PF02037_consen 6 VAELKEELKERGLSTS 21 (35)
T ss_dssp HHHHHHHHHHTTS-ST
T ss_pred HHHHHHHHHHCCCCCC
Confidence 4688999999999975
No 40
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=22.99 E-value=99 Score=21.53 Aligned_cols=33 Identities=15% Similarity=0.219 Sum_probs=27.3
Q ss_pred CCCCceEEEeecCCCCChHHHHHHHHHhCCCCCCCC
Q psy4851 14 MRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKF 49 (62)
Q Consensus 14 s~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F 49 (62)
.-+|.|-+. ...+-.+.+|++|..|.|.+..-|
T Consensus 18 ~GNp~aVv~---~a~~Lsd~~MQ~IA~e~n~SET~F 50 (291)
T COG0384 18 GGNPLAVVL---DADGLSDEQMQAIAREFNLSETAF 50 (291)
T ss_pred CCCceEEEe---CCCCCCHHHHHHHHHHhCCceeEE
Confidence 457788776 677888999999999999987656
No 41
>PHA02723 hypothetical protein; Provisional
Probab=21.71 E-value=12 Score=21.00 Aligned_cols=24 Identities=29% Similarity=0.441 Sum_probs=20.6
Q ss_pred CCCceEEEeecCCCCChHHHHHHH
Q psy4851 15 RYPQGHFVRALGPIGDKDTENEVL 38 (62)
Q Consensus 15 ~~P~G~iv~~LG~~gd~e~E~~aI 38 (62)
.|=.|.+.++||-..|..+|..+|
T Consensus 4 ~yysgnlesvlgyvsdmht~lasi 27 (77)
T PHA02723 4 AYYSGNLESVLGYVSDMHTELASI 27 (77)
T ss_pred ccccCCHHHHHHHHHHHHHHHHHH
Confidence 455788999999999999998776
No 42
>PTZ00085 40S ribosomal protein S28; Provisional
Probab=21.52 E-value=71 Score=18.14 Aligned_cols=16 Identities=19% Similarity=0.407 Sum_probs=12.4
Q ss_pred CCCceEEEeecCCCCC
Q psy4851 15 RYPQGHFVRALGPIGD 30 (62)
Q Consensus 15 ~~P~G~iv~~LG~~gd 30 (62)
.--.++++++||..|.
T Consensus 9 ~~~~A~VikVlGRTG~ 24 (73)
T PTZ00085 9 QPKLAKVIKVLGRTGS 24 (73)
T ss_pred CceeEEEEEEeccccC
Confidence 3346999999998875
No 43
>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
Probab=21.34 E-value=1.3e+02 Score=18.87 Aligned_cols=29 Identities=17% Similarity=0.141 Sum_probs=24.8
Q ss_pred CCCCceEEEeecCCCCChHHHHHHHHHhC
Q psy4851 14 MRYPQGHFVRALGPIGDKDTENEVLLLEH 42 (62)
Q Consensus 14 s~~P~G~iv~~LG~~gd~e~E~~aIL~e~ 42 (62)
.-.|.|+++.+.|+.|.-.+....-+.-+
T Consensus 14 GGi~~g~i~~i~G~~GsGKT~l~~~l~~~ 42 (235)
T cd01123 14 GGIETGSITEIFGEFGSGKTQLCHQLAVT 42 (235)
T ss_pred CCCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence 56899999999999999999988766543
No 44
>COG1086 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]
Probab=20.81 E-value=1.2e+02 Score=23.40 Aligned_cols=44 Identities=23% Similarity=0.348 Sum_probs=37.6
Q ss_pred CCCCceEEEeecCCCCChHHHHHHHHHhCCCCCCCCcHHHHhhCCC
Q psy4851 14 MRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPP 59 (62)
Q Consensus 14 s~~P~G~iv~~LG~~gd~e~E~~aIL~e~~i~~~~F~~~vl~~lp~ 59 (62)
.++|..++.-.||+..|.+. +..++.+|.++. -|-.+++|..|-
T Consensus 297 ~~~~~~~~~~~igdVrD~~~-~~~~~~~~kvd~-VfHAAA~KHVPl 340 (588)
T COG1086 297 EKFPELKLRFYIGDVRDRDR-VERAMEGHKVDI-VFHAAALKHVPL 340 (588)
T ss_pred hhCCCcceEEEecccccHHH-HHHHHhcCCCce-EEEhhhhccCcc
Confidence 46788999999999999876 455788999998 599999999995
No 45
>PRK14561 hypothetical protein; Provisional
Probab=20.64 E-value=87 Score=20.00 Aligned_cols=24 Identities=33% Similarity=0.339 Sum_probs=19.2
Q ss_pred CCCChHHHHHHHHHhCCCCCCC-Cc
Q psy4851 27 PIGDKDTENEVLLLEHDVPHSK-FS 50 (62)
Q Consensus 27 ~~gd~e~E~~aIL~e~~i~~~~-F~ 50 (62)
..||-|+|+..+|.+-+.+... ||
T Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~ 182 (194)
T PRK14561 158 PKSDYETELRELLRERGGDPLEIFP 182 (194)
T ss_pred CccchHHHHHHHHHHhCCChhHhCC
Confidence 3578999999999998887543 66
No 46
>KOG2792|consensus
Probab=20.44 E-value=89 Score=21.98 Aligned_cols=26 Identities=31% Similarity=0.423 Sum_probs=22.5
Q ss_pred CCceEEEeecCCCCChHHHHHHHHHh
Q psy4851 16 YPQGHFVRALGPIGDKDTENEVLLLE 41 (62)
Q Consensus 16 ~P~G~iv~~LG~~gd~e~E~~aIL~e 41 (62)
.|.|++++.+|+.-+.+.=.++|+.+
T Consensus 249 dPeg~Fvd~~GrN~~~~~~~~~I~~~ 274 (280)
T KOG2792|consen 249 DPEGEFVDYYGRNYDADELADSILKH 274 (280)
T ss_pred CCCcceehhhcccCCHHHHHHHHHHH
Confidence 59999999999999988888777754
No 47
>TIGR01016 sucCoAbeta succinyl-CoA synthetase, beta subunit. This family contains a split seen both in a maximum parsimony tree (which ignores gaps) and in the gap pattern near position 85 of the seed alignment. Eukaryotic and most bacterial sequences are longer and contain a region similar to TXQTXXXG. Sequences from Deinococcus radiodurans, Mycobacterium tuberculosis, Streptomyces coelicolor, and the Archaea are 6 amino acids shorter in that region and contain a motif resembling [KR]G
Probab=20.37 E-value=1e+02 Score=21.60 Aligned_cols=19 Identities=5% Similarity=0.209 Sum_probs=16.3
Q ss_pred hHHHHHHHHHhCCCCCCCC
Q psy4851 31 KDTENEVLLLEHDVPHSKF 49 (62)
Q Consensus 31 ~e~E~~aIL~e~~i~~~~F 49 (62)
.|.+.+.+|.+|||++.+|
T Consensus 4 ~E~~aK~ll~~~GIpvp~~ 22 (386)
T TIGR01016 4 HEYQAKQIFAKYGIPVPRG 22 (386)
T ss_pred cHHHHHHHHHHcCCCCCCc
Confidence 3678899999999998765
No 48
>cd04457 S1_S28E S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28E might be involved in protein synthesis.
Probab=20.27 E-value=75 Score=17.39 Aligned_cols=12 Identities=25% Similarity=0.642 Sum_probs=9.4
Q ss_pred eEEEeecCCCCC
Q psy4851 19 GHFVRALGPIGD 30 (62)
Q Consensus 19 G~iv~~LG~~gd 30 (62)
++++++||..|.
T Consensus 3 A~V~kvlGRtG~ 14 (60)
T cd04457 3 AEVIKVLGRTGS 14 (60)
T ss_pred eEEEEEeccccC
Confidence 678888887765
Done!