Query psy16395
Match_columns 157
No_of_seqs 108 out of 118
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 20:14:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16395.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16395hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10255 Paf67: RNA polymerase 100.0 4E-50 8.6E-55 356.7 10.6 128 4-146 268-404 (404)
2 KOG3677|consensus 100.0 1.4E-43 3.1E-48 317.4 7.1 142 3-156 375-523 (525)
3 PF01399 PCI: PCI domain; Int 89.3 0.76 1.6E-05 31.7 4.2 48 26-88 37-84 (105)
4 smart00753 PAM PCI/PINT associ 87.5 1.4 3.1E-05 30.2 4.7 33 29-61 4-36 (88)
5 smart00088 PINT motif in prote 87.5 1.4 3.1E-05 30.2 4.7 33 29-61 4-36 (88)
6 PF09012 FeoC: FeoC like trans 84.8 1.4 3.1E-05 29.8 3.5 45 36-95 1-45 (69)
7 PRK15431 ferrous iron transpor 65.9 26 0.00056 25.4 5.8 44 36-94 3-46 (78)
8 PF08220 HTH_DeoR: DeoR-like h 54.7 26 0.00057 22.9 3.9 41 39-94 4-44 (57)
9 PF03586 Herpes_UL36: Herpesvi 54.2 5.9 0.00013 34.5 0.9 78 42-156 104-181 (253)
10 PF10075 PCI_Csn8: COP9 signal 53.5 15 0.00033 27.7 3.0 33 25-61 77-109 (143)
11 KOG1076|consensus 46.1 37 0.00081 33.9 5.0 31 31-61 700-730 (843)
12 PRK09649 RNA polymerase sigma 38.0 48 0.001 25.7 3.7 49 37-102 132-182 (185)
13 PRK10681 DNA-binding transcrip 37.6 44 0.00094 27.9 3.6 44 33-91 5-48 (252)
14 cd05397 NT_Pol-beta-like Nucle 37.2 30 0.00064 22.0 2.0 18 102-119 25-42 (49)
15 smart00265 BH4 BH4 Bcl-2 homol 36.4 31 0.00066 20.4 1.8 24 77-100 4-27 (27)
16 cd05403 NT_KNTase_like Nucleot 34.9 24 0.00053 23.4 1.4 19 102-120 26-44 (93)
17 KOG4023|consensus 32.2 41 0.00089 25.9 2.3 32 10-47 65-99 (108)
18 PF04666 Glyco_transf_54: N-Ac 31.9 64 0.0014 28.3 3.8 39 42-90 212-250 (297)
19 PHA03247 large tegument protei 31.2 22 0.00047 40.1 0.9 78 42-156 1418-1495(3151)
20 PF10772 DUF2597: Protein of u 30.9 36 0.00079 27.1 1.9 16 113-128 2-17 (134)
21 PF06565 DUF1126: Repeat of un 30.6 35 0.00077 20.7 1.4 17 114-130 2-18 (33)
22 cd05402 NT_PAP_TUTase Nucleoti 30.2 39 0.00085 24.0 1.9 21 102-122 27-47 (114)
23 PF11055 Gsf2: Glucose signall 30.0 22 0.00048 32.6 0.7 11 4-14 128-138 (377)
24 PF08880 QLQ: QLQ; InterPro: 27.8 40 0.00087 21.0 1.4 18 78-95 8-25 (37)
25 PRK10906 DNA-binding transcrip 27.0 1E+02 0.0022 25.9 4.1 52 35-101 5-56 (252)
26 KOG1497|consensus 26.8 45 0.00097 30.7 2.0 23 39-61 307-329 (399)
27 PRK12537 RNA polymerase sigma 25.3 83 0.0018 24.1 3.1 35 45-94 145-179 (182)
28 TIGR02985 Sig70_bacteroi1 RNA 25.3 96 0.0021 22.4 3.3 43 37-94 115-159 (161)
29 PRK06759 RNA polymerase factor 24.8 1.1E+02 0.0023 22.4 3.5 46 35-95 106-153 (154)
30 PRK10434 srlR DNA-bindng trans 24.5 1.1E+02 0.0025 25.5 4.0 51 36-101 6-56 (256)
31 cd06171 Sigma70_r4 Sigma70, re 22.0 1.7E+02 0.0037 16.7 5.3 39 39-92 15-54 (55)
32 PF12793 SgrR_N: Sugar transpo 22.0 2.2E+02 0.0049 21.4 4.8 60 40-120 3-69 (115)
33 PF02180 BH4: Bcl-2 homology r 21.8 46 0.00099 19.8 0.8 23 77-99 4-26 (27)
34 cd07749 NT_Pol-beta-like_1 Nuc 21.4 49 0.0011 26.8 1.1 37 85-121 8-47 (156)
35 TIGR02983 SigE-fam_strep RNA p 21.2 1.2E+02 0.0025 22.5 3.1 44 36-94 111-156 (162)
36 PRK09642 RNA polymerase sigma 21.1 1.1E+02 0.0024 22.6 2.9 44 37-95 108-153 (160)
37 KOG0687|consensus 21.1 2.5E+02 0.0055 26.0 5.7 87 25-150 297-392 (393)
38 KOG2582|consensus 21.1 1.7E+02 0.0036 27.4 4.6 24 38-61 306-329 (422)
39 cd06867 PX_SNX41_42 The phosph 21.1 48 0.001 24.2 0.9 18 122-139 22-39 (112)
40 PRK09644 RNA polymerase sigma 21.0 83 0.0018 23.6 2.3 48 35-97 108-157 (165)
41 PF03902 Gal4_dimer: Gal4-like 20.9 76 0.0016 21.9 1.8 29 28-56 28-57 (57)
42 KOG2790|consensus 20.3 74 0.0016 29.0 2.1 52 7-60 294-363 (370)
43 TIGR02952 Sig70_famx2 RNA poly 20.3 1.9E+02 0.004 21.4 4.0 45 35-94 122-168 (170)
44 PRK12524 RNA polymerase sigma 20.1 1.3E+02 0.0028 23.4 3.2 51 35-100 136-188 (196)
No 1
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=100.00 E-value=4e-50 Score=356.74 Aligned_cols=128 Identities=56% Similarity=0.941 Sum_probs=122.9
Q ss_pred cccccccc-CCCCCC----CCchHHH---HHHHHHHHhhhhchhhHhHHhhhccCChHHHHHHhhccccCCCcccccccc
Q psy16395 4 LNKLIVVK-PGLFYS----HFISPFR---QVFMDEVNQQKMLPTIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVD 75 (157)
Q Consensus 4 ~~~fi~~~-~~~f~n----~~~ep~~---~~Fl~eV~~Q~~lp~iRSYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~ 75 (157)
-||||||+ ||.+.+ .+.||++ ++||+||++|+.+|+|||||||||||+++|||+||++
T Consensus 268 cPKFIsp~~pp~~~~~~~~~~~e~~~~Ql~~Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~v-------------- 333 (404)
T PF10255_consen 268 CPKFISPVSPPDYDGPSQNKNKEPYRRQLKLFLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLDV-------------- 333 (404)
T ss_pred CCCccCCCCCCCcccccchhhhhHHHHHHHHHHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcCC--------------
Confidence 49999999 888777 3448999 9999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHhhhcceee-eecCCCCCCCcceeeccceeEEEeCCeEEEeeccchhhhhhHHHHHHHHHH
Q psy16395 76 KETKSLITHLLAFKHKMKNV-VWTRGPSGLEGTFQSGSELDFYIDNEMIHIADTKVAHRYGDFFIRKIIKFE 146 (157)
Q Consensus 76 ~d~e~lr~~Ll~~K~k~rql-~w~~G~~~l~Ge~~~~sDlDFyID~DmIhIaetk~~rrygd~Fir~I~K~e 146 (157)
|+++||++|||+|||+||+ +|++|+++++|++++++|+|||||+|||||+|+|++|||||||+|||+|||
T Consensus 334 -d~~~lr~~Ll~~K~k~~ql~~w~~g~sll~G~~~~~~dlDf~Id~D~IhI~e~k~~r~~~d~F~r~i~k~e 404 (404)
T PF10255_consen 334 -DEEELRSQLLCFKHKSRQLVRWSGGASLLDGEFQSSSDLDFYIDGDMIHIAETKVARRYGDFFIRQINKFE 404 (404)
T ss_pred -CHHHHHHHHHHHHHHHHHHhhccCCCcccccceeecCceEEEEeCCEEEEeeccccchhHHHHHHHHHhcC
Confidence 9999999999999999999 999999999999999999999999999999999999999999999999985
No 2
>KOG3677|consensus
Probab=100.00 E-value=1.4e-43 Score=317.38 Aligned_cols=142 Identities=58% Similarity=0.889 Sum_probs=132.5
Q ss_pred cccccccccCCCCCC----CCchHHH---HHHHHHHHhhhhchhhHhHHhhhccCChHHHHHHhhccccCCCcccccccc
Q psy16395 3 LLNKLIVVKPGLFYS----HFISPFR---QVFMDEVNQQKMLPTIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVD 75 (157)
Q Consensus 3 ~~~~fi~~~~~~f~n----~~~ep~~---~~Fl~eV~~Q~~lp~iRSYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~ 75 (157)
+-|||.||++|..++ +..||+. ++||+||.||..+|++|||||||||+|++|||+|||+...
T Consensus 375 ~cpkflsp~~~~~dgv~~~y~kePl~~qlq~fld~v~qq~dl~~~rsylklyTt~P~kkla~F~D~~d~----------- 443 (525)
T KOG3677|consen 375 LCPKFLSPVVPNYDGVLPNYHKEPLLQQLQVFLDEVSQQADLPTIRSYLKLYTTLPVKKLASFLDLTDQ----------- 443 (525)
T ss_pred cCccccCCCCcccccccccccccHHHHHHHHHhHHHhhhccchHHHHHHHHHHhccHHHhhhccCCchh-----------
Confidence 458999999999887 6789998 8999999999999999999999999999999999999211
Q ss_pred CChHHHHHHHHHhhhcceeeeecCCCCCCCcceeeccceeEEEeCCeEEEeeccchhhhhhHHHHHHHHHHHHHHHHhhc
Q psy16395 76 KETKSLITHLLAFKHKMKNVVWTRGPSGLEGTFQSGSELDFYIDNEMIHIADTKVAHRYGDFFIRKIIKFEELNKKLQAI 155 (157)
Q Consensus 76 ~d~e~lr~~Ll~~K~k~rql~w~~G~~~l~Ge~~~~sDlDFyID~DmIhIaetk~~rrygd~Fir~I~K~e~l~~~L~~~ 155 (157)
..+.++.+|+|||||++|++|+.|++.++|++.+++++|||||.|||||+|||++|||||+|||+|+||+|++|.|+.+
T Consensus 444 -~~dk~li~Ll~~khkm~nlv~~sg~s~~d~~f~~~s~idfyid~dmi~iaDtkv~r~~gd~fir~i~kf~El~~vLK~i 522 (525)
T KOG3677|consen 444 -ERDKFLIQLLVFKHKMKNLVWTSGPSDLDDAFFSRSEIDFYIDKDMIHIADTKVARRYGDIFIRQIHKFEELNRVLKLI 522 (525)
T ss_pred -hhhhhHHHHHHHHHHHHHHHHhcCCccccccccCcceeeEEechhHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 2335999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred c
Q psy16395 156 K 156 (157)
Q Consensus 156 ~ 156 (157)
.
T Consensus 523 ~ 523 (525)
T KOG3677|consen 523 T 523 (525)
T ss_pred c
Confidence 4
No 3
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=89.29 E-value=0.76 Score=31.69 Aligned_cols=48 Identities=13% Similarity=0.317 Sum_probs=38.6
Q ss_pred HHHHHHHhhhhchhhHhHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHh
Q psy16395 26 VFMDEVNQQKMLPTIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAF 88 (157)
Q Consensus 26 ~Fl~eV~~Q~~lp~iRSYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~ 88 (157)
.-.+.+......-.|++|.+-|++++++.+|..+++ +++++...|+.+
T Consensus 37 ~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~---------------~~~~vE~~l~~~ 84 (105)
T PF01399_consen 37 EYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQL---------------SEEEVESILIDL 84 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTC---------------CHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhcc---------------chHHHHHHHHHH
Confidence 344667777777889999999999999999999999 777777777655
No 4
>smart00753 PAM PCI/PINT associated module.
Probab=87.52 E-value=1.4 Score=30.25 Aligned_cols=33 Identities=21% Similarity=0.431 Sum_probs=28.5
Q ss_pred HHHHhhhhchhhHhHHhhhccCChHHHHHHhhc
Q psy16395 29 DEVNQQKMLPTIRSYLKLYTTLPLSKLATFMGN 61 (157)
Q Consensus 29 ~eV~~Q~~lp~iRSYLKLYtti~l~KLAsfmdv 61 (157)
+.+......-.|++|.+-|++++++.||..+++
T Consensus 4 ~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l 36 (88)
T smart00753 4 ERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGL 36 (88)
T ss_pred HHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCc
Confidence 445566667789999999999999999999999
No 5
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=87.52 E-value=1.4 Score=30.25 Aligned_cols=33 Identities=21% Similarity=0.431 Sum_probs=28.5
Q ss_pred HHHHhhhhchhhHhHHhhhccCChHHHHHHhhc
Q psy16395 29 DEVNQQKMLPTIRSYLKLYTTLPLSKLATFMGN 61 (157)
Q Consensus 29 ~eV~~Q~~lp~iRSYLKLYtti~l~KLAsfmdv 61 (157)
+.+......-.|++|.+-|++++++.||..+++
T Consensus 4 ~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l 36 (88)
T smart00088 4 ERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGL 36 (88)
T ss_pred HHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCc
Confidence 445566667789999999999999999999999
No 6
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=84.81 E-value=1.4 Score=29.75 Aligned_cols=45 Identities=27% Similarity=0.278 Sum_probs=36.5
Q ss_pred hchhhHhHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceee
Q psy16395 36 MLPTIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNV 95 (157)
Q Consensus 36 ~lp~iRSYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql 95 (157)
+|-.||.|++.-.+++++-||.-+++ +++.++..|-...++++--
T Consensus 1 ~L~~i~~~l~~~~~~S~~eLa~~~~~---------------s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 1 MLQEIRDYLRERGRVSLAELAREFGI---------------SPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp -CHHHHHHHHHS-SEEHHHHHHHTT-----------------HHHHHHHHHHHHCCTSCE
T ss_pred CHHHHHHHHHHcCCcCHHHHHHHHCc---------------CHHHHHHHHHHHHHCCcEE
Confidence 35689999999999999999999999 9999999998888876543
No 7
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=65.90 E-value=26 Score=25.45 Aligned_cols=44 Identities=14% Similarity=0.168 Sum_probs=37.1
Q ss_pred hchhhHhHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhccee
Q psy16395 36 MLPTIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKN 94 (157)
Q Consensus 36 ~lp~iRSYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rq 94 (157)
.|-.||.||-++..+++.-||.-++. +++.++..|-..-.++|-
T Consensus 3 ~L~qlRd~l~~~gr~s~~~Ls~~~~~---------------p~~~VeaMLe~l~~kGkv 46 (78)
T PRK15431 3 SLIQVRDLLALRGRMEAAQISQTLNT---------------PQPMINAMLQQLESMGKA 46 (78)
T ss_pred cHHHHHHHHHHcCcccHHHHHHHHCc---------------CHHHHHHHHHHHHHCCCe
Confidence 35689999999999999999999999 899998888666555443
No 8
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=54.72 E-value=26 Score=22.89 Aligned_cols=41 Identities=17% Similarity=0.126 Sum_probs=36.8
Q ss_pred hhHhHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhccee
Q psy16395 39 TIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKN 94 (157)
Q Consensus 39 ~iRSYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rq 94 (157)
.|-.||+=-..++++.||..++| .+.++|-.|..+.....-
T Consensus 4 ~Il~~l~~~~~~s~~ela~~~~V---------------S~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 4 QILELLKEKGKVSVKELAEEFGV---------------SEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHcCCEEHHHHHHHHCc---------------CHHHHHHHHHHHHHCCCE
Confidence 46778888999999999999999 999999999999888763
No 9
>PF03586 Herpes_UL36: Herpesvirus UL36 tegument protein; InterPro: IPR005210 The UL36 open reading frame (ORF) encodes the largest Human herpesvirus 1 (HHV-1) protein, a 270 kDa polypeptide designated VP1/2, which is also a component of the virion tegument. A null mutation in the UL36 gene of herpes simplex virus type 1 results in accumulation of unenveloped DNA-filled capsids in the cytoplasm of infected cells []. The region which defines these sequences only covers a small central part of this large protein.; GO: 0004197 cysteine-type endopeptidase activity, 0008242 omega peptidase activity
Probab=54.16 E-value=5.9 Score=34.46 Aligned_cols=78 Identities=19% Similarity=0.332 Sum_probs=51.3
Q ss_pred hHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceeeeecCCCCCCCcceeeccceeEEEeCC
Q psy16395 42 SYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNVVWTRGPSGLEGTFQSGSELDFYIDNE 121 (157)
Q Consensus 42 SYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql~w~~G~~~l~Ge~~~~sDlDFyID~D 121 (157)
-|-+|+ .++++.|.++|.+ -.+ +|.+=. ..+|. +.--|+=+.|.+|
T Consensus 104 ~y~~LF-gv~ve~L~~L~rI---------------~~~-----iL~~A~------------a~~G~-idy~~~V~~l~~d 149 (253)
T PF03586_consen 104 YYTTLF-GVDVEPLLRLMRI---------------AEG-----ILEHAA------------AGGGN-IDYYDAVGRLSGD 149 (253)
T ss_pred HHHHHH-cccHHHHHHHHHH---------------HHH-----HHHHHH------------ccCCC-CcHHHHHHHHHHH
Confidence 377888 9999999999999 233 333211 01121 1111222245567
Q ss_pred eEEEeeccchhhhhhHHHHHHHHHHHHHHHHhhcc
Q psy16395 122 MIHIADTKVAHRYGDFFIRKIIKFEELNKKLQAIK 156 (157)
Q Consensus 122 mIhIaetk~~rrygd~Fir~I~K~e~l~~~L~~~~ 156 (157)
+-+|-+ =.+|.|||-|--.+|++....|+.++
T Consensus 150 L~~vP~---L~kYVdFYrrgy~~F~~~~~~L~~lR 181 (253)
T PF03586_consen 150 LMQVPE---LAKYVDFYRRGYEEFEEERARLSALR 181 (253)
T ss_pred HHhChh---HHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 765533 37899999999999999999998764
No 10
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=53.49 E-value=15 Score=27.73 Aligned_cols=33 Identities=27% Similarity=0.445 Sum_probs=21.9
Q ss_pred HHHHHHHHhhhhchhhHhHHhhhccCChHHHHHHhhc
Q psy16395 25 QVFMDEVNQQKMLPTIRSYLKLYTTLPLSKLATFMGN 61 (157)
Q Consensus 25 ~~Fl~eV~~Q~~lp~iRSYLKLYtti~l~KLAsfmdv 61 (157)
..|.+.|+.. .++.--+-|++|+++.||.+|++
T Consensus 77 ~~~~~~iR~~----i~~~i~~aY~sIs~~~la~~Lg~ 109 (143)
T PF10075_consen 77 PGFEDTIRER----IAHLISKAYSSISLSDLAEMLGL 109 (143)
T ss_dssp TTHHHHHHHH----HHHHHHHH-SEE-HHHHHHHTTS
T ss_pred HHHHHHHHHH----HHHHHHHHHhHcCHHHHHHHhCC
Confidence 4444444443 34455678999999999999999
No 11
>KOG1076|consensus
Probab=46.14 E-value=37 Score=33.92 Aligned_cols=31 Identities=19% Similarity=0.445 Sum_probs=22.6
Q ss_pred HHhhhhchhhHhHHhhhccCChHHHHHHhhc
Q psy16395 31 VNQQKMLPTIRSYLKLYTTLPLSKLATFMGN 61 (157)
Q Consensus 31 V~~Q~~lp~iRSYLKLYtti~l~KLAsfmdv 61 (157)
|+.-.+=.-+-+|-..|+|++++|||...|+
T Consensus 700 IqEEsLRTYLftYss~Y~SvSl~~LA~mFdL 730 (843)
T KOG1076|consen 700 IQEESLRTYLFTYSSVYDSVSLAKLADMFDL 730 (843)
T ss_pred HHHHHHHHHHHHhhhhhhhccHHHHHHHhCC
Confidence 3333333344566688999999999999998
No 12
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=37.96 E-value=48 Score=25.72 Aligned_cols=49 Identities=10% Similarity=0.062 Sum_probs=39.5
Q ss_pred chhhHhHH--hhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceeeeecCCCC
Q psy16395 37 LPTIRSYL--KLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNVVWTRGPS 102 (157)
Q Consensus 37 lp~iRSYL--KLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql~w~~G~~ 102 (157)
-|.-|.=+ +-|.-++.+-+|.-|++ ++.++++.|.--+.+.|+ |-.|.+
T Consensus 132 p~~~r~v~~L~~~~g~s~~EIA~~lgi---------------s~~tVk~~l~Rar~~Lr~--~~~~~~ 182 (185)
T PRK09649 132 TTDQREALLLTQLLGLSYADAAAVCGC---------------PVGTIRSRVARARDALLA--DAEPDD 182 (185)
T ss_pred CHHHhHHhhhHHHcCCCHHHHHHHHCC---------------CHHHHHHHHHHHHHHHHh--hCCccc
Confidence 34555544 44689999999999999 999999999999999887 666644
No 13
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=37.62 E-value=44 Score=27.88 Aligned_cols=44 Identities=18% Similarity=0.200 Sum_probs=37.5
Q ss_pred hhhhchhhHhHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhc
Q psy16395 33 QQKMLPTIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHK 91 (157)
Q Consensus 33 ~Q~~lp~iRSYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k 91 (157)
.++..-.|..||+-+..+.++.||..++| .+++.|.-|-..-..
T Consensus 5 ~~eR~~~I~~~l~~~~~v~v~eLa~~~~V---------------S~~TIRRDL~~Le~~ 48 (252)
T PRK10681 5 RDERIGQLLQALKRSDKLHLKDAAALLGV---------------SEMTIRRDLNAHSAP 48 (252)
T ss_pred HHHHHHHHHHHHHHcCCCcHHHHHHHhCC---------------CHHHHHHHHHHhhcC
Confidence 34455678899999999999999999999 999999999887643
No 14
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=37.21 E-value=30 Score=22.04 Aligned_cols=18 Identities=22% Similarity=0.326 Sum_probs=15.5
Q ss_pred CCCCcceeeccceeEEEe
Q psy16395 102 SGLEGTFQSGSELDFYID 119 (157)
Q Consensus 102 ~~l~Ge~~~~sDlDFyID 119 (157)
|...|+....||+|+.+.
T Consensus 25 S~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 25 SLVRGLLKKSSDIDLACV 42 (49)
T ss_pred CcCCCCCCCCCCEEEEEE
Confidence 566799888999999987
No 15
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=36.38 E-value=31 Score=20.44 Aligned_cols=24 Identities=17% Similarity=0.555 Sum_probs=21.0
Q ss_pred ChHHHHHHHHHhhhcceeeeecCC
Q psy16395 77 ETKSLITHLLAFKHKMKNVVWTRG 100 (157)
Q Consensus 77 d~e~lr~~Ll~~K~k~rql~w~~G 100 (157)
|-.+|....+++|-+.|...|..|
T Consensus 4 ~nRelV~~yv~yKLsQrgy~w~~~ 27 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYEWDAG 27 (27)
T ss_pred chHHHHHHHHHHHHhhcCCCCCCC
Confidence 667899999999999999999754
No 16
>cd05403 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is
Probab=34.86 E-value=24 Score=23.36 Aligned_cols=19 Identities=21% Similarity=0.253 Sum_probs=15.7
Q ss_pred CCCCcceeeccceeEEEeC
Q psy16395 102 SGLEGTFQSGSELDFYIDN 120 (157)
Q Consensus 102 ~~l~Ge~~~~sDlDFyID~ 120 (157)
|...|+....||+|+.|-.
T Consensus 26 S~arg~~~~~SDiDl~vi~ 44 (93)
T cd05403 26 SYARGDARPDSDIDLLVIF 44 (93)
T ss_pred eeecCCCCCCCCeeEEEEe
Confidence 6678998889999998753
No 17
>KOG4023|consensus
Probab=32.18 E-value=41 Score=25.91 Aligned_cols=32 Identities=22% Similarity=0.417 Sum_probs=24.5
Q ss_pred ccCCCCCCCCchHHH---HHHHHHHHhhhhchhhHhHHhhh
Q psy16395 10 VKPGLFYSHFISPFR---QVFMDEVNQQKMLPTIRSYLKLY 47 (157)
Q Consensus 10 ~~~~~f~n~~~ep~~---~~Fl~eV~~Q~~lp~iRSYLKLY 47 (157)
|.||.+- |.|-|. ..|++.|++ -+|-+||||=
T Consensus 65 plPPqif--n~d~Y~Gdye~F~ea~E~----ntl~eFL~la 99 (108)
T KOG4023|consen 65 PLPPQIF--NGDQYCGDYELFFEAVEQ----NTLQEFLGLA 99 (108)
T ss_pred CCCcccc--cCccccccHHHHHHHHHH----HHHHHHHccC
Confidence 5778754 556677 999999976 4788999874
No 18
>PF04666 Glyco_transf_54: N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region; InterPro: IPR006759 The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyse the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (2.4.1.145 from EC) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms a GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminal end of the protein [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0005975 carbohydrate metabolic process, 0016020 membrane
Probab=31.92 E-value=64 Score=28.30 Aligned_cols=39 Identities=23% Similarity=0.249 Sum_probs=30.7
Q ss_pred hHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhh
Q psy16395 42 SYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKH 90 (157)
Q Consensus 42 SYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~ 90 (157)
-.=|||.+-++..||+|+-+--++. +.+-|..+.+..|.
T Consensus 212 ~iGKlf~s~dL~~l~~fl~~fy~~~----------P~D~Ll~~~~~~~~ 250 (297)
T PF04666_consen 212 FIGKLFRSSDLPRLARFLLMFYKDK----------PIDWLLDHFFWLKV 250 (297)
T ss_pred chhheeccccHHHHHHHHHHHhhcC----------cHHHHHHHHHHHhc
Confidence 3458999999999999998754444 77888888777766
No 19
>PHA03247 large tegument protein UL36; Provisional
Probab=31.17 E-value=22 Score=40.14 Aligned_cols=78 Identities=22% Similarity=0.360 Sum_probs=53.9
Q ss_pred hHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceeeeecCCCCCCCcceeeccceeEEEeCC
Q psy16395 42 SYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNVVWTRGPSGLEGTFQSGSELDFYIDNE 121 (157)
Q Consensus 42 SYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql~w~~G~~~l~Ge~~~~sDlDFyID~D 121 (157)
-|-+|+ ..+++-|+.+|.+ +.-||.+=.. | .|. ..--|+=.+|.+|
T Consensus 1418 ~~~~LF-gVdve~L~~LmrI--------------------a~giL~~a~a--------~----~G~-~dY~d~V~~l~~D 1463 (3151)
T PHA03247 1418 TYAEMF-RVDTEPLARLLRL--------------------AGGLLELAQA--------G----GGF-IDYHEAVSRLAED 1463 (3151)
T ss_pred HHHHHh-cccHHHHHHHHHH--------------------HHHHHHHHhh--------c----CCC-CcHHHHHHHHHHH
Confidence 377888 7999999999999 4456655331 1 111 1112222346677
Q ss_pred eEEEeeccchhhhhhHHHHHHHHHHHHHHHHhhcc
Q psy16395 122 MIHIADTKVAHRYGDFFIRKIIKFEELNKKLQAIK 156 (157)
Q Consensus 122 mIhIaetk~~rrygd~Fir~I~K~e~l~~~L~~~~ 156 (157)
|-+|-. =++|.|||-|--.+|++....|++++
T Consensus 1464 L~~vP~---L~kYVdFYrrg~~~F~~~~~~L~~lR 1495 (3151)
T PHA03247 1464 LNGVPS---LRRYVPFFRRGHAEYLELCDRLDALR 1495 (3151)
T ss_pred Hhhchh---HHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 766532 48899999999999999999998764
No 20
>PF10772 DUF2597: Protein of unknown function (DUF2597); InterPro: IPR019708 This entry is represented by Bacteriophage HP1, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents proteins with unknown function and is restricted to Proteobacteria. One of the proteins is annotated to a predictive tail tube protein.
Probab=30.91 E-value=36 Score=27.12 Aligned_cols=16 Identities=25% Similarity=0.520 Sum_probs=13.9
Q ss_pred ceeEEEeCCeEEEeec
Q psy16395 113 ELDFYIDNEMIHIADT 128 (157)
Q Consensus 113 DlDFyID~DmIhIaet 128 (157)
++|++|++.+|||...
T Consensus 2 ~fD~~ig~~~vhve~~ 17 (134)
T PF10772_consen 2 SFDVNIGGLMVHVEKA 17 (134)
T ss_pred ceeEEeCCEEEEEEEE
Confidence 5899999999999754
No 21
>PF06565 DUF1126: Repeat of unknown function (DUF1126); InterPro: IPR010554 This group contains several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.; PDB: 2Z14_A 2Z13_A.
Probab=30.58 E-value=35 Score=20.65 Aligned_cols=17 Identities=24% Similarity=0.669 Sum_probs=11.9
Q ss_pred eeEEEeCCeEEEeeccc
Q psy16395 114 LDFYIDNEMIHIADTKV 130 (157)
Q Consensus 114 lDFyID~DmIhIaetk~ 130 (157)
+-||+.+|+|.|.|..+
T Consensus 2 i~y~L~DdTi~I~E~~~ 18 (33)
T PF06565_consen 2 ISYYLADDTISIFEPPV 18 (33)
T ss_dssp EEEETTTTEEEEE----
T ss_pred EEEEccCCCEEEEEecc
Confidence 56999999999999654
No 22
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=30.23 E-value=39 Score=24.02 Aligned_cols=21 Identities=24% Similarity=0.253 Sum_probs=17.1
Q ss_pred CCCCcceeeccceeEEEeCCe
Q psy16395 102 SGLEGTFQSGSELDFYIDNEM 122 (157)
Q Consensus 102 ~~l~Ge~~~~sDlDFyID~Dm 122 (157)
|...|.....||+|+.|..+-
T Consensus 27 S~~~g~~~~~SDiDl~i~~~~ 47 (114)
T cd05402 27 SYVTGLGLPGSDIDLCLLGPN 47 (114)
T ss_pred ccccCCCCCCCCeeEEEEeCC
Confidence 566788888999999988653
No 23
>PF11055 Gsf2: Glucose signalling factor 2; InterPro: IPR022757 This entry represents fungal Glucose singalling factor 2. Gsf2 is localised to the ER and functions to promote the secretion of certain hexose transporters [].
Probab=29.96 E-value=22 Score=32.57 Aligned_cols=11 Identities=36% Similarity=0.724 Sum_probs=10.0
Q ss_pred ccccccccCCC
Q psy16395 4 LNKLIVVKPGL 14 (157)
Q Consensus 4 ~~~fi~~~~~~ 14 (157)
||-||||+|+-
T Consensus 128 LPD~ISPTPGI 138 (377)
T PF11055_consen 128 LPDFISPTPGI 138 (377)
T ss_pred CCcccCCCCch
Confidence 79999999984
No 24
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=27.76 E-value=40 Score=21.00 Aligned_cols=18 Identities=28% Similarity=0.396 Sum_probs=14.9
Q ss_pred hHHHHHHHHHhhhcceee
Q psy16395 78 TKSLITHLLAFKHKMKNV 95 (157)
Q Consensus 78 ~e~lr~~Ll~~K~k~rql 95 (157)
-.+||.|+++||+-.|+.
T Consensus 8 l~~L~~Qi~ayK~l~~~~ 25 (37)
T PF08880_consen 8 LQELRAQILAYKYLARNQ 25 (37)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 458999999999987753
No 25
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=27.04 E-value=1e+02 Score=25.87 Aligned_cols=52 Identities=12% Similarity=0.100 Sum_probs=42.3
Q ss_pred hhchhhHhHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceeeeecCCC
Q psy16395 35 KMLPTIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNVVWTRGP 101 (157)
Q Consensus 35 ~~lp~iRSYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql~w~~G~ 101 (157)
...-.|..||+=...+.+.-||..++| +++++|..|-.+-..+.-.+..+|+
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~v---------------S~~TiRRdL~~Le~~g~l~r~~GGa 56 (252)
T PRK10906 5 QRHDAIIELVKQQGYVSTEELVEHFSV---------------SPQTIRRDLNDLAEQNKILRHHGGA 56 (252)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHhCC---------------CHHHHHHHHHHHHHCCCEEEecCCE
Confidence 344578899999999999999999999 9999999998888876544444553
No 26
>KOG1497|consensus
Probab=26.78 E-value=45 Score=30.71 Aligned_cols=23 Identities=22% Similarity=0.401 Sum_probs=20.9
Q ss_pred hhHhHHhhhccCChHHHHHHhhc
Q psy16395 39 TIRSYLKLYTTLPLSKLATFMGN 61 (157)
Q Consensus 39 ~iRSYLKLYtti~l~KLAsfmdv 61 (157)
.|=|--|||++|+.+.|+.++++
T Consensus 307 Nlls~Skly~nisf~~Lg~ll~i 329 (399)
T KOG1497|consen 307 NLLSASKLYNNISFEELGALLKI 329 (399)
T ss_pred hHHHHHHHHHhccHHHHHHHhCC
Confidence 46677899999999999999999
No 27
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=25.27 E-value=83 Score=24.11 Aligned_cols=35 Identities=6% Similarity=0.076 Sum_probs=31.3
Q ss_pred hhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhccee
Q psy16395 45 KLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKN 94 (157)
Q Consensus 45 KLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rq 94 (157)
+.|..++.+..|.-|++ ++.+++.+|..-+++.|.
T Consensus 145 ~~~~~~s~~eIA~~lgi---------------s~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 145 AYVDGCSHAEIAQRLGA---------------PLGTVKAWIKRSLKALRE 179 (182)
T ss_pred HHHcCCCHHHHHHHHCC---------------ChhhHHHHHHHHHHHHHH
Confidence 34689999999999999 999999999999888775
No 28
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=25.26 E-value=96 Score=22.37 Aligned_cols=43 Identities=14% Similarity=0.215 Sum_probs=35.4
Q ss_pred chhhHhHHhh--hccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhccee
Q psy16395 37 LPTIRSYLKL--YTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKN 94 (157)
Q Consensus 37 lp~iRSYLKL--Ytti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rq 94 (157)
-|.-|.-+.| +..++.+.+|.-|++ ++.+++..+..-|.+.|+
T Consensus 115 ~~~~r~il~l~~~~~~~~~eIA~~lgi---------------s~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 115 PEQCRKIFILSRFEGKSYKEIAEELGI---------------SVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCC---------------CHHHHHHHHHHHHHHHHh
Confidence 4555666665 579999999999999 999999999988887764
No 29
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=24.82 E-value=1.1e+02 Score=22.44 Aligned_cols=46 Identities=9% Similarity=0.008 Sum_probs=36.7
Q ss_pred hhchhhHhHH--hhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceee
Q psy16395 35 KMLPTIRSYL--KLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNV 95 (157)
Q Consensus 35 ~~lp~iRSYL--KLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql 95 (157)
.+-|.=|.-+ ..|..++.+-.|.-|++ ++.++++++-.-+.+.|..
T Consensus 106 ~L~~~~r~ii~l~~~~~~s~~EIA~~l~i---------------s~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGKTMGEIALETEM---------------TYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHHCC---------------CHHHHHHHHHHHHHHHhhc
Confidence 4445566644 45689999999999999 9999999999888887753
No 30
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=24.54 E-value=1.1e+02 Score=25.50 Aligned_cols=51 Identities=16% Similarity=0.218 Sum_probs=40.5
Q ss_pred hchhhHhHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceeeeecCCC
Q psy16395 36 MLPTIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNVVWTRGP 101 (157)
Q Consensus 36 ~lp~iRSYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql~w~~G~ 101 (157)
..-.|..+|+-+..++++-||..++| .++.+|..|-.+-....-.+..+|+
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~V---------------S~~TIRRDL~~Le~~g~l~r~~Gga 56 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDT---------------TGTTIRKDLVILEHAGTVIRTYGGV 56 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCC---------------CHHHHHHHHHHHHHCCCEEEEECCE
Confidence 44567889999999999999999999 9999999998887664433334443
No 31
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=22.01 E-value=1.7e+02 Score=16.67 Aligned_cols=39 Identities=15% Similarity=0.204 Sum_probs=29.1
Q ss_pred hhHhHHhhh-ccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcc
Q psy16395 39 TIRSYLKLY-TTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKM 92 (157)
Q Consensus 39 ~iRSYLKLY-tti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~ 92 (157)
.-+-+.-+| ..++...+|.-|++ +...+..++-..+.+.
T Consensus 15 ~~~~~~~~~~~~~~~~~ia~~~~~---------------s~~~i~~~~~~~~~~l 54 (55)
T cd06171 15 EREVILLRFGEGLSYEEIAEILGI---------------SRSTVRQRLHRALKKL 54 (55)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHCc---------------CHHHHHHHHHHHHHHc
Confidence 344444455 88999999999999 8888888876665543
No 32
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=21.96 E-value=2.2e+02 Score=21.35 Aligned_cols=60 Identities=22% Similarity=0.395 Sum_probs=39.1
Q ss_pred hHhHHhhhc-------cCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceeeeecCCCCCCCcceeecc
Q psy16395 40 IRSYLKLYT-------TLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNVVWTRGPSGLEGTFQSGS 112 (157)
Q Consensus 40 iRSYLKLYt-------ti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql~w~~G~~~l~Ge~~~~s 112 (157)
++-|..||. .++++.||..+.. .+-+++.-|-.+=. --=+.|.+|.+- |. .|
T Consensus 3 ~~~y~~L~~~~~~~~~~vtl~elA~~l~c---------------S~Rn~r~lLkkm~~-~gWi~W~pg~GR--G~---~S 61 (115)
T PF12793_consen 3 LEQYQRLWQHYGGQPVEVTLDELAELLFC---------------SRRNARTLLKKMQE-EGWITWQPGRGR--GN---RS 61 (115)
T ss_pred HHHHHHHHHHcCCCCcceeHHHHHHHhCC---------------CHHHHHHHHHHHHH-CCCeeeeCCCCC--CC---CC
Confidence 355666664 5789999999999 77776665544432 344789888542 22 36
Q ss_pred ceeEEEeC
Q psy16395 113 ELDFYIDN 120 (157)
Q Consensus 113 DlDFyID~ 120 (157)
-+-|.++-
T Consensus 62 ~L~~l~~~ 69 (115)
T PF12793_consen 62 QLTFLKSP 69 (115)
T ss_pred eeEEeeCH
Confidence 66666553
No 33
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=21.85 E-value=46 Score=19.76 Aligned_cols=23 Identities=17% Similarity=0.621 Sum_probs=19.6
Q ss_pred ChHHHHHHHHHhhhcceeeeecC
Q psy16395 77 ETKSLITHLLAFKHKMKNVVWTR 99 (157)
Q Consensus 77 d~e~lr~~Ll~~K~k~rql~w~~ 99 (157)
+-.+|....+++|-+.|...|.+
T Consensus 4 ~nR~lV~~yi~yKLsQrgy~w~~ 26 (27)
T PF02180_consen 4 DNRELVEDYISYKLSQRGYVWEE 26 (27)
T ss_dssp HHHHHHHHHHHHHHHHTTSTSTT
T ss_pred cHHHHHHHHHHHHhhhcCCCCCC
Confidence 45678889999999999999975
No 34
>cd07749 NT_Pol-beta-like_1 Nucleotidyltransferase (NT) domain of an uncharacterized subgroup of the Pol beta-like NT superfamily. The Pol beta-like NT superfamily includes DNA polymerase beta and other family X DNA Polymerases, as well as Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly(A) polymerases, terminal uridylyl transferases, Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. Proteins belonging to this subgroup are uncharacterized. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.
Probab=21.42 E-value=49 Score=26.81 Aligned_cols=37 Identities=30% Similarity=0.295 Sum_probs=29.6
Q ss_pred HHHhhhcceeeeecCCCCC---CCcceeeccceeEEEeCC
Q psy16395 85 LLAFKHKMKNVVWTRGPSG---LEGTFQSGSELDFYIDNE 121 (157)
Q Consensus 85 Ll~~K~k~rql~w~~G~~~---l~Ge~~~~sDlDFyID~D 121 (157)
.+|-|-...++.|-=|+|+ +.|-...-.|+|.++|..
T Consensus 8 ~i~~~ln~~~i~W~lgGS~~L~l~Gl~~~p~DIDI~~D~~ 47 (156)
T cd07749 8 KFYERLKNINVNWALTGSLSFALQGVPVEPHDIDIQTDNE 47 (156)
T ss_pred HHHHHhccCCceEEehhhHHHHHcCCCCCCCcceEEEchh
Confidence 4566778899999877664 678877789999999964
No 35
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=21.19 E-value=1.2e+02 Score=22.48 Aligned_cols=44 Identities=14% Similarity=0.273 Sum_probs=36.2
Q ss_pred hchhhHhHH--hhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhccee
Q psy16395 36 MLPTIRSYL--KLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKN 94 (157)
Q Consensus 36 ~lp~iRSYL--KLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rq 94 (157)
+-|.-|.-+ +.+..++.+..|.-|++ ++.+++++|.--+.+.|.
T Consensus 111 L~~~~r~i~~l~~~~g~s~~eIA~~lgi---------------s~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 111 LPARQRAVVVLRYYEDLSEAQVAEALGI---------------SVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHhhhHHHhcCCHHHHHHHhCC---------------CHHHHHHHHHHHHHHHHH
Confidence 445666655 44689999999999999 999999999998888765
No 36
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=21.15 E-value=1.1e+02 Score=22.65 Aligned_cols=44 Identities=14% Similarity=0.067 Sum_probs=36.1
Q ss_pred chhhHhHHh--hhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceee
Q psy16395 37 LPTIRSYLK--LYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNV 95 (157)
Q Consensus 37 lp~iRSYLK--LYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql 95 (157)
-|.-|.=+. .|.-++.+..|.-|++ ++.+++++|.--+.+.|..
T Consensus 108 p~~~r~v~~l~~~~g~s~~EIA~~lgi---------------s~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 108 PENYRDVVLAHYLEEKSYQEIALQEKI---------------EVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CHHHHHHHHHHHHhCCCHHHHHHHHCC---------------CHHHHHHHHHHHHHHHHHH
Confidence 344455444 4789999999999999 9999999999999888865
No 37
>KOG0687|consensus
Probab=21.14 E-value=2.5e+02 Score=25.98 Aligned_cols=87 Identities=21% Similarity=0.384 Sum_probs=56.2
Q ss_pred HHHHHHHHhhhhchhhHhHHhhhccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceeeeecCCCCCC
Q psy16395 25 QVFMDEVNQQKMLPTIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNVVWTRGPSGL 104 (157)
Q Consensus 25 ~~Fl~eV~~Q~~lp~iRSYLKLYtti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql~w~~G~~~l 104 (157)
+-|..|++..--. .+|.=|.++.++-.|.=..| ..+=+-..|
T Consensus 297 ~yyvREMR~rvY~----QlLESYrsl~l~~MA~aFgV---------------SVefiDreL------------------- 338 (393)
T KOG0687|consen 297 RYYVREMRRRVYA----QLLESYRSLTLESMAKAFGV---------------SVEFIDREL------------------- 338 (393)
T ss_pred HHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhCc---------------hHHHHHhHH-------------------
Confidence 5666666543221 34555889999999988888 555333322
Q ss_pred CcceeeccceeEEEeC--CeEEEee--ccc-----hhhhhhHHHHHHHHHHHHHH
Q psy16395 105 EGTFQSGSELDFYIDN--EMIHIAD--TKV-----AHRYGDFFIRKIIKFEELNK 150 (157)
Q Consensus 105 ~Ge~~~~sDlDFyID~--DmIhIae--tk~-----~rrygd~Fir~I~K~e~l~~ 150 (157)
|+|+..+.|..-||. .+|-+.- .|- .=.+||..++.|+|+..+++
T Consensus 339 -~rFI~~grL~ckIDrVnGVVEtNrpD~KN~qyq~vikqGd~LLnriQK~~rvi~ 392 (393)
T KOG0687|consen 339 -GRFIAAGRLHCKIDRVNGVVETNRPDEKNAQYQAVIKQGDLLLNRIQKLSRVIN 392 (393)
T ss_pred -HHhhccCceeeeeecccceeecCCccccchHHHHHHhhhHHHHHHHHHHHHHhc
Confidence 556677778888884 4444421 222 12489999999999988764
No 38
>KOG2582|consensus
Probab=21.13 E-value=1.7e+02 Score=27.38 Aligned_cols=24 Identities=25% Similarity=0.325 Sum_probs=20.2
Q ss_pred hhhHhHHhhhccCChHHHHHHhhc
Q psy16395 38 PTIRSYLKLYTTLPLSKLATFMGN 61 (157)
Q Consensus 38 p~iRSYLKLYtti~l~KLAsfmdv 61 (157)
-+|.+..|-|+|+.++-.|+...+
T Consensus 306 ~nI~rltktF~sLsL~dIA~~vQL 329 (422)
T KOG2582|consen 306 KNIQRLTKTFLSLSLSDIASRVQL 329 (422)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHh
Confidence 578899999999999999994433
No 39
>cd06867 PX_SNX41_42 The phosphoinositide binding Phox Homology domain of fungal Sorting Nexins 41 and 42. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX41 and SNX42 (also called Atg20p) form dimers with SNX4, and are required in protein recycling from the sorting endosome (post-Golgi endosome) back
Probab=21.09 E-value=48 Score=24.24 Aligned_cols=18 Identities=28% Similarity=0.608 Sum_probs=14.0
Q ss_pred eEEEeeccchhhhhhHHH
Q psy16395 122 MIHIADTKVAHRYGDFFI 139 (157)
Q Consensus 122 mIhIaetk~~rrygd~Fi 139 (157)
.|++....+.|||.||--
T Consensus 22 ~I~~~~~~V~RRYsdF~~ 39 (112)
T cd06867 22 VIRLGGSEVKRRYSEFES 39 (112)
T ss_pred EEEeeeEEEEeccHHHHH
Confidence 466777788999999853
No 40
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=20.96 E-value=83 Score=23.58 Aligned_cols=48 Identities=13% Similarity=0.168 Sum_probs=39.2
Q ss_pred hhchhhHhHHhh--hccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceeeee
Q psy16395 35 KMLPTIRSYLKL--YTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNVVW 97 (157)
Q Consensus 35 ~~lp~iRSYLKL--Ytti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql~w 97 (157)
.+-|.-|.-+.| +.-++.+.+|.-|++ ++.+++++|--.|.+.|...-
T Consensus 108 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---------------s~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 108 TLPVIEAQAILLCDVHELTYEEAASVLDL---------------KLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred hCCHHHHHHHHhHHHhcCCHHHHHHHHCC---------------CHHHHHHHHHHHHHHHHHHHH
Confidence 344555655554 589999999999999 999999999999999887653
No 41
>PF03902 Gal4_dimer: Gal4-like dimerisation domain; InterPro: IPR005600 The DNA binding domain (residues 1 to 147) of the yeast transcriptional activator GAL4 exists in solution in dimeric form, with the region responsible for dimerisation somewhere between residues 74 and 147. Experimental studies confirmed that the 'hydrophobic region' of the protein (residues 54-97, which contains a larger proportion of alpha-helix), is essential for dimerisation []. ; PDB: 1HBW_B 1D66_A 3COQ_A.
Probab=20.88 E-value=76 Score=21.91 Aligned_cols=29 Identities=24% Similarity=0.501 Sum_probs=17.6
Q ss_pred HHHHHhhhhchhhHhHHh-hhccCChHHHH
Q psy16395 28 MDEVNQQKMLPTIRSYLK-LYTTLPLSKLA 56 (157)
Q Consensus 28 l~eV~~Q~~lp~iRSYLK-LYtti~l~KLA 56 (157)
++++-++...+.||-.++ |+.+.++.|+|
T Consensus 28 id~lL~~~~~~~l~~il~~l~~~~~~~~~~ 57 (57)
T PF03902_consen 28 IDDLLNDRDASDLKPILKKLFPQVNVPKLA 57 (57)
T ss_dssp HHHHHHHHSCHHHHHHHHHH--S--SS---
T ss_pred HHHHHHcccHHHHHHHHHHhccccCCCCCC
Confidence 455666778899999997 99999998876
No 42
>KOG2790|consensus
Probab=20.34 E-value=74 Score=28.98 Aligned_cols=52 Identities=27% Similarity=0.409 Sum_probs=35.0
Q ss_pred cccccCCCCCCCCchH-------HHHHHHHHHHhhhhc--------hhhHhHHhhhccCChH---HHHHHhh
Q psy16395 7 LIVVKPGLFYSHFISP-------FRQVFMDEVNQQKML--------PTIRSYLKLYTTLPLS---KLATFMG 60 (157)
Q Consensus 7 fi~~~~~~f~n~~~ep-------~~~~Fl~eV~~Q~~l--------p~iRSYLKLYtti~l~---KLAsfmd 60 (157)
|++|+.|.--+--+=| ++.-|+.|-....++ ..|| .-||+.|+++ +||.||.
T Consensus 294 y~cpVe~~~RS~MNV~Fri~~d~Le~eFLkeA~~~~mv~LKGhRSVGGiR--ASlYNAisv~~~q~L~~~m~ 363 (370)
T KOG2790|consen 294 YRCPVEPSVRSRMNVPFRIEKDELEAEFLKEAAKEHMVQLKGHRSVGGIR--ASLYNAISVEEVQKLAAFMK 363 (370)
T ss_pred EEcccchhhhhhcccceeecchHHHHHHHHHHHHhhhhccccccccccch--hhhhccccHHHHHHHHHHHH
Confidence 5677777655533333 338899987665543 3444 4689999975 8999986
No 43
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=20.28 E-value=1.9e+02 Score=21.38 Aligned_cols=45 Identities=16% Similarity=0.291 Sum_probs=37.7
Q ss_pred hhchhhHhHHhh--hccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhccee
Q psy16395 35 KMLPTIRSYLKL--YTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKN 94 (157)
Q Consensus 35 ~~lp~iRSYLKL--Ytti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rq 94 (157)
.+.|.=|.=+.| |.-++.+.+|.-|++ ++.+++..|..-+.+.|.
T Consensus 122 ~L~~~~r~vl~l~~~~g~s~~eIA~~l~i---------------s~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQNLPIAEVARILGK---------------TEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHHCC---------------CHHHHHHHHHHHHHHHHH
Confidence 555777777777 589999999999999 999999999888877653
No 44
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=20.12 E-value=1.3e+02 Score=23.43 Aligned_cols=51 Identities=12% Similarity=0.055 Sum_probs=40.9
Q ss_pred hhchhhHhHHhh--hccCChHHHHHHhhccccCCCccccccccCChHHHHHHHHHhhhcceeeeecCC
Q psy16395 35 KMLPTIRSYLKL--YTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITHLLAFKHKMKNVVWTRG 100 (157)
Q Consensus 35 ~~lp~iRSYLKL--Ytti~l~KLAsfmdv~~~~~~~~~~~~~~~d~e~lr~~Ll~~K~k~rql~w~~G 100 (157)
.+-|.=|.=+.| |..++.+.+|.-|++ ++.++++.|-.-+++.|......+
T Consensus 136 ~L~~~~r~i~~L~~~~g~s~~eIA~~lgi---------------s~~tV~~~l~Ra~~~Lr~~l~~~~ 188 (196)
T PRK12524 136 ALPERQRQAVVLRHIEGLSNPEIAEVMEI---------------GVEAVESLTARGKRALAALLAGQR 188 (196)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCc---------------CHHHHHHHHHHHHHHHHHHHHhcc
Confidence 344555655555 589999999999999 999999999999999888765544
Done!