Query psy934
Match_columns 143
No_of_seqs 102 out of 773
Neff 7.1
Searched_HMMs 46136
Date Sat Aug 17 00:47:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy934.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/934hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3717|consensus 100.0 9.5E-41 2.1E-45 282.2 13.4 130 2-134 472-604 (612)
2 PF00755 Carn_acyltransf: Chol 100.0 8.3E-38 1.8E-42 272.1 12.3 126 2-130 463-591 (591)
3 KOG3718|consensus 100.0 2.1E-31 4.6E-36 222.7 11.4 129 3-132 473-603 (609)
4 KOG3719|consensus 100.0 4E-31 8.6E-36 222.8 12.4 129 4-138 505-636 (638)
5 KOG3716|consensus 100.0 3E-30 6.6E-35 222.2 9.4 129 2-137 616-761 (764)
6 PF06974 DUF1298: Protein of u 95.5 0.18 4E-06 36.8 9.0 65 65-130 78-152 (153)
7 TIGR02681 phage_pRha phage reg 58.6 32 0.00069 23.8 5.1 43 90-135 65-107 (108)
8 PF15560 Imm8: Immunity protei 56.0 32 0.0007 24.9 4.7 36 98-133 77-114 (133)
9 TIGR02946 acyl_WS_DGAT acyltra 48.8 55 0.0012 27.4 5.9 45 85-130 400-444 (446)
10 PF13222 DUF4030: Protein of u 41.4 77 0.0017 23.2 4.8 50 80-129 66-117 (142)
11 PF09228 Prok-TraM: Prokaryoti 39.7 58 0.0012 22.6 3.8 25 1-25 24-48 (102)
12 KOG3438|consensus 38.4 35 0.00075 23.7 2.6 41 86-132 42-85 (105)
13 PF13774 Longin: Regulated-SNA 35.4 67 0.0015 20.4 3.6 42 85-127 21-62 (83)
14 PRK12729 fliE flagellar hook-b 31.8 65 0.0014 23.2 3.2 24 111-134 52-75 (127)
15 PRK12566 glycine dehydrogenase 31.1 1.1E+02 0.0023 29.3 5.3 43 94-138 845-887 (954)
16 PF01193 RNA_pol_L: RNA polyme 28.2 90 0.0019 19.2 3.1 40 87-132 26-65 (66)
17 KOG3222|consensus 27.9 28 0.00062 26.7 0.8 37 70-106 139-176 (195)
18 PF09564 RE_NgoBV: NgoBV restr 27.7 84 0.0018 24.8 3.4 39 88-127 163-201 (240)
19 PF02954 HTH_8: Bacterial regu 27.6 23 0.0005 19.9 0.2 30 7-36 7-36 (42)
20 cd01207 Ena-Vasp Enabled-VASP- 27.5 78 0.0017 22.2 3.0 18 111-128 93-110 (111)
21 PF03220 Tombus_P19: Tombusvir 27.1 1E+02 0.0022 22.7 3.5 48 87-141 107-154 (170)
22 PF02662 FlpD: Methyl-viologen 23.2 1.5E+02 0.0033 20.7 3.9 33 94-131 91-123 (124)
23 cd00460 RNAP_RPB11_RPB3 RPB11 23.2 2.2E+02 0.0048 18.5 5.5 32 96-133 53-84 (86)
24 PF01797 Y1_Tnp: Transposase I 23.1 2.3E+02 0.0049 18.8 4.7 35 90-127 43-77 (121)
25 COG1908 FrhD Coenzyme F420-red 22.6 2E+02 0.0043 20.7 4.3 32 94-131 92-124 (132)
26 PF07687 M20_dimer: Peptidase 22.3 2.3E+02 0.0049 18.3 4.6 38 91-129 71-108 (111)
27 PF09669 Phage_pRha: Phage reg 22.1 1E+02 0.0022 20.3 2.7 39 90-131 54-92 (93)
28 PF14483 Cut8_M: Cut8 dimerisa 21.6 1.5E+02 0.0032 16.7 2.8 25 1-25 10-34 (38)
29 PRK14012 cysteine desulfurase; 20.2 1.2E+02 0.0027 24.9 3.4 43 87-131 341-383 (404)
30 TIGR01821 5aminolev_synth 5-am 20.2 1.4E+02 0.0029 24.6 3.6 30 97-128 368-397 (402)
No 1
>KOG3717|consensus
Probab=100.00 E-value=9.5e-41 Score=282.25 Aligned_cols=130 Identities=46% Similarity=0.890 Sum_probs=126.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhCCCCC-CCcCchhHHhhcCCCCcee--ccCCCCCCCcc
Q psy934 2 KDKKKLDLFDAAIKKQTQIMTENIQGEGIDLHLLGLRQTALEHNIPC-ELFQDEAYKLSNEDNDFFF--QEVACKSDSFM 78 (143)
Q Consensus 2 s~~ek~~ll~~A~~~H~~~~~~a~~G~G~DRHL~gL~~~a~~~~~~~-~lF~d~~~~~~~~~~~~~l--S~~~~~~~~~~ 78 (143)
+.+||+++|+.|+++|+.+++.|++|.||||||+|||++|++.+.++ +||.||.|..+++ |.| ||+++..+.++
T Consensus 472 ~~~ek~~llr~Av~~h~~yt~~ai~G~gvDrHLlgLk~~a~e~~~~iPelF~dp~y~~s~~---F~lSTSQV~t~~d~~m 548 (612)
T KOG3717|consen 472 PKSEKLELLRKAVQAHTKYTKRAIRGNGVDRHLLGLKLMAIENCKPIPELFKDPSYAISMH---FLLSTSQVPTKTDIFM 548 (612)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhCCCcchhhcCcHhhHhhe---eeeecccCccccceee
Confidence 56899999999999999999999999999999999999999999999 9999999999999 999 68999999999
Q ss_pred ccccccCCCceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHHhhc
Q psy934 79 GYGPVVPDGYGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNLVES 134 (143)
Q Consensus 79 gfgp~~~dGyGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ll~~ 134 (143)
|||||+||||||||+++++.|.|+||+|++|+.|++.+|+..|++|+.||+++|+.
T Consensus 549 ~yGpvv~dGYG~cYNp~~~~i~f~isaf~sc~~Ts~~rfak~L~~al~dmkdll~~ 604 (612)
T KOG3717|consen 549 GYGPVVPDGYGCCYNPQEEHIIFAISAFRSCPETSASRFAKYLEQALDDMRDLLSN 604 (612)
T ss_pred eecCcCCCCcccccCCCcceEEEEeeccccCccccHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999985
No 2
>PF00755 Carn_acyltransf: Choline/Carnitine o-acyltransferase; InterPro: IPR000542 A number of eukaryotic acetyltransferases can, on the basis of sequence similarities, be grouped together into a family. These enzymes include: Choline o-acetyltransferase 2.3.1.6 from EC, an enzyme that catalyses the biosynthesis of the neurotransmitter acetylcholine []. Carnitine o-acetyltransferase 2.3.1.7 from EC []. Peroxisomal carnitine octanoyltransferase 2.3.1.137 from EC, a fatty acid beta-oxidation pathway enzyme which is involved in the transport of medium-chain acyl-coenzyme A's from peroxisome to mitochondria []. Mitochondrial carnitine palmitoyltransferases I and II 2.3.1.21 from EC (CPT), enzymes involved in fatty acid metabolism and transport []. Mycoplasma pneumoniae putative acetyltransferase C09_orf600. ; GO: 0016746 transferase activity, transferring acyl groups; PDB: 2DEB_B 2H4T_A 2FW3_A 2RCU_B 2FYO_A 1S5O_A 1NM8_A 1T7Q_B 2H3W_B 1NDI_B ....
Probab=100.00 E-value=8.3e-38 Score=272.07 Aligned_cols=126 Identities=43% Similarity=0.726 Sum_probs=113.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhCCCCC-CCcCchhHHhhcCCCCceec--cCCCCCCCcc
Q psy934 2 KDKKKLDLFDAAIKKQTQIMTENIQGEGIDLHLLGLRQTALEHNIPC-ELFQDEAYKLSNEDNDFFFQ--EVACKSDSFM 78 (143)
Q Consensus 2 s~~ek~~ll~~A~~~H~~~~~~a~~G~G~DRHL~gL~~~a~~~~~~~-~lF~d~~~~~~~~~~~~~lS--~~~~~~~~~~ 78 (143)
+.+||++||++|+++|++++++|++|+||||||+||+++|++.|.++ +||+||+|+++++ |.|| +++......+
T Consensus 463 ~~~e~~~ll~~A~~~H~~~~~~a~~G~G~dRHL~~L~~~a~~~~~~~P~lf~d~~~~~~~~---~~lsTS~~~~~~~~~~ 539 (591)
T PF00755_consen 463 SKEEKRELLRAAVKAHKQYIKEAMRGKGFDRHLFGLRCLAKENGIELPELFSDPAYKRSSN---FVLSTSQVPSPALSGG 539 (591)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHTTTSSHHHHHHHHHHHHHTTSS--HHHHSHHHHHHTS----SEEEEEEEESSSEEE
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhhccchhhhccChHHHhcCC---ceeecccccccccccc
Confidence 56899999999999999999999999999999999999999989999 8999999999999 9995 4666667789
Q ss_pred ccccccCCCceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHH
Q psy934 79 GYGPVVPDGYGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGN 130 (143)
Q Consensus 79 gfgp~~~dGyGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ 130 (143)
|||||+||||||+|+|.+|+|.|+||+|++|+.|++++|+++|++||+||++
T Consensus 540 gfgpv~~dGyGi~Y~i~~~~i~f~iss~~~~~~t~~~~f~~~l~~al~dm~d 591 (591)
T PF00755_consen 540 GFGPVVPDGYGICYNIQPDSISFSISSFKSCPETSSERFAKALEQALRDMRD 591 (591)
T ss_dssp E---SSTTSEEEEEEEESSEEEEEEEEETTSTTS-HHHHHHHHHHHHHHHHH
T ss_pred cccCCCCcceEEEEEecCCeEEEEEEecCCCCcccHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999999999999999999999999999999985
No 3
>KOG3718|consensus
Probab=99.97 E-value=2.1e-31 Score=222.74 Aligned_cols=129 Identities=26% Similarity=0.443 Sum_probs=112.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhCCCCC-CCcCchhHHhhcCCCCceeccCCCCCCCcccc-
Q psy934 3 DKKKLDLFDAAIKKQTQIMTENIQGEGIDLHLLGLRQTALEHNIPC-ELFQDEAYKLSNEDNDFFFQEVACKSDSFMGY- 80 (143)
Q Consensus 3 ~~ek~~ll~~A~~~H~~~~~~a~~G~G~DRHL~gL~~~a~~~~~~~-~lF~d~~~~~~~~~~~~~lS~~~~~~~~~~gf- 80 (143)
.+++..+|+.|+.+|+.+|++|+.|+||||||+||++++.+.+.++ +||.||.|.++.++|||+||++.......+||
T Consensus 473 ~e~lk~lf~~A~n~Hn~lM~d~~~GkG~DRHl~GL~laa~e~~~~iPefl~dp~fskSGGgGNFvLSTSf~Gy~~tfG~V 552 (609)
T KOG3718|consen 473 DESLKRLFRRAVNEHNHLMNDARKGKGIDRHLFGLWLAAYESKMDIPEFLDDPMFSKSGGGGNFVLSTSFLGYTATFGFV 552 (609)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHhcCCchhhhcCccccccCCCCcEEEEeehhcchhcccee
Confidence 3678899999999999999999999999999999999999999999 89999999999999999998766555567788
Q ss_pred ccccCCCceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHHh
Q psy934 81 GPVVPDGYGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNLV 132 (143)
Q Consensus 81 gp~~~dGyGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ll 132 (143)
+|+++||||+.|.|.+++|.+.+|+|++|++|+.+ |+..|..++..+...|
T Consensus 553 apMv~dGYG~FY~I~~~r~~va~Saw~ds~~t~ae-k~~ni~~~lf~~~~~L 603 (609)
T KOG3718|consen 553 APMVFDGYGVFYSITSERVFVATSAWRDSLKTSAE-KFNNIFKDLFRRISVL 603 (609)
T ss_pred eeecccCcceEEEeccceEEEehhhhhccchhhHH-HHHHHHHHHHhhHHHh
Confidence 79999999999999999999999999999876555 5555555555554444
No 4
>KOG3719|consensus
Probab=99.97 E-value=4e-31 Score=222.84 Aligned_cols=129 Identities=31% Similarity=0.516 Sum_probs=115.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhCCCCC-CCcCchhHHhhcCCCCceec--cCCCCCCCcccc
Q psy934 4 KKKLDLFDAAIKKQTQIMTENIQGEGIDLHLLGLRQTALEHNIPC-ELFQDEAYKLSNEDNDFFFQ--EVACKSDSFMGY 80 (143)
Q Consensus 4 ~ek~~ll~~A~~~H~~~~~~a~~G~G~DRHL~gL~~~a~~~~~~~-~lF~d~~~~~~~~~~~~~lS--~~~~~~~~~~gf 80 (143)
.+.+.++.+|.+.|.+++|+|..|+|+||||+|||++++..++++ +||.||+|.+.++ +.|| +++++....+||
T Consensus 505 ~kl~~li~~Cs~~H~qltKeasmGqG~DRHl~ALk~la~~e~~~~pdlf~dp~y~~~~~---nvLstStlgn~a~~~gGf 581 (638)
T KOG3719|consen 505 GKLQQLIDTCSKTHGQLTKEASMGQGYDRHLFALKHLAQKESIPLPDLFEDPAYTRMNN---NVLSTSTLGNPALTAGGF 581 (638)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHhcCCCCchhhcCcccccccC---ceEeeccCCchhhhccCc
Confidence 355666777777999999999999999999999999999889999 9999999999999 9995 455555667999
Q ss_pred ccccCCCceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHHhhccccc
Q psy934 81 GPVVPDGYGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNLVESRKIS 138 (143)
Q Consensus 81 gp~~~dGyGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ll~~~~~~ 138 (143)
||||+|||||+|+|.||.+...|||+++ ..+.+|..+|+++|.+|+..++.++..
T Consensus 582 gPvv~~GFGIGY~I~d~~vg~vVsS~~~---q~~~~f~~~leksL~ei~~~~~~~ks~ 636 (638)
T KOG3719|consen 582 GPVVPNGFGIGYIIKDDQVGAVVSSYKR---QRGARFMFMLEKSLDEIRSYLRMSKST 636 (638)
T ss_pred cccccCCcceeeEeecCccceEEecccc---ccHHHHHHHHHHHHHHHHHHHhccccc
Confidence 9999999999999999999999999975 349999999999999999999876543
No 5
>KOG3716|consensus
Probab=99.96 E-value=3e-30 Score=222.23 Aligned_cols=129 Identities=29% Similarity=0.450 Sum_probs=108.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhCCCCCCCcC---chhHHhhcCCCCceeccCCCC-----
Q psy934 2 KDKKKLDLFDAAIKKQTQIMTENIQGEGIDLHLLGLRQTALEHNIPCELFQ---DEAYKLSNEDNDFFFQEVACK----- 73 (143)
Q Consensus 2 s~~ek~~ll~~A~~~H~~~~~~a~~G~G~DRHL~gL~~~a~~~~~~~~lF~---d~~~~~~~~~~~~~lS~~~~~----- 73 (143)
+.++|++||++||++|+.+.++||.|+|||||||+|+++++..+.+-+|+. .+.|..|+ ||+|..
T Consensus 616 T~~~rl~llk~Acd~Hq~~yk~aM~G~GvDRHLF~LyVvskyL~~~SPFL~~v~s~~W~LST-------Sq~P~~q~~~~ 688 (764)
T KOG3716|consen 616 TKQERLQLLKKACDKHQLNYKEAMTGQGVDRHLFALYVVSKYLGVQSPFLDEVLSEKWLLST-------SQTPNMQENSF 688 (764)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHhhcCCccceeeeeeeehhhcccCChHHHhhcCCceeecc-------cCCcccchhcc
Confidence 457999999999999999999999999999999999999998776533222 24343333 344433
Q ss_pred --------CCCccccccccCCCceeeeccc-CCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHHhhcccc
Q psy934 74 --------SDSFMGYGPVVPDGYGCSYNPR-EATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNLVESRKI 137 (143)
Q Consensus 74 --------~~~~~gfgp~~~dGyGi~Y~i~-~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ll~~~~~ 137 (143)
...++|||||..|||||||.+. ++.|.|+|||++|++.||+.||.++|.+|+.||++|++..+.
T Consensus 689 d~~~~p~~i~~GggFGpvaddGYGVsY~~~G~~~I~fHIsSk~Ss~~TDS~Rfg~hl~eal~di~~Lf~~~~~ 761 (764)
T KOG3716|consen 689 DEDKSPDNISLGGGFGPVADDGYGVSYIFAGENAIFFHISSKHSSENTDSHRFGQHLKEALHDIADLFEDATA 761 (764)
T ss_pred CcccCccccccCCccCCccCCCceeEEEEecCceEEEEeecccccccccHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 1266899999999999999997 779999999999999999999999999999999999987654
No 6
>PF06974 DUF1298: Protein of unknown function (DUF1298); InterPro: IPR009721 This entry represents the C terminus (approximately 170 residues) of a number of hypothetical plant proteins. O-acyltransferase WSD1 is a bifunctional wax ester synthase/diacylglycerol acyltransferase, which is involved in cuticular wax biosynthesis [].; GO: 0004144 diacylglycerol O-acyltransferase activity
Probab=95.48 E-value=0.18 Score=36.85 Aligned_cols=65 Identities=11% Similarity=0.202 Sum_probs=44.6
Q ss_pred ceeccCCCCCC---------Ccccccc-ccCCCceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHH
Q psy934 65 FFFQEVACKSD---------SFMGYGP-VVPDGYGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGN 130 (143)
Q Consensus 65 ~~lS~~~~~~~---------~~~gfgp-~~~dGyGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ 130 (143)
..+|++|.+.. ..+.+.| ..+.|.+|+..=..+++.|.|.+-++- --|.++|.+++++++.+|++
T Consensus 78 ~viSNVPGP~~~l~~~G~~v~~i~~~~~~~~~~L~itv~SY~g~l~~gi~ad~~~-vpD~~~l~~~~~~~l~eL~~ 152 (153)
T PF06974_consen 78 LVISNVPGPQEPLYFAGARVEYIYPSPLGDGQALNITVFSYAGKLDFGIVADRDA-VPDPQRLADCFEEALEELKE 152 (153)
T ss_pred EEEecCCCChhheEECCeeeEEEEeeeecCCcceEEEEEEeCCEEEEEEEEcccc-CCCHHHHHHHHHHHHHHHHc
Confidence 55599887731 1111222 234455565555699999999987653 34899999999999999985
No 7
>TIGR02681 phage_pRha phage regulatory protein, rha family. Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that pRha is a phage regulatory protein.
Probab=58.62 E-value=32 Score=23.83 Aligned_cols=43 Identities=12% Similarity=0.186 Sum_probs=36.1
Q ss_pred eeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHHhhcc
Q psy934 90 CSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNLVESR 135 (143)
Q Consensus 90 i~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ll~~~ 135 (143)
-+|.+..|...+.|..+. ...+..|...+-+++.+|.+-|+..
T Consensus 65 ~~Y~ltkdgf~lLvmg~t---g~ka~~fK~~yI~~Fn~ME~~l~~~ 107 (108)
T TIGR02681 65 PMFNLTEDGFTIVAMGYT---TPKAMKMKEKFIKEFNEMKEHLQKV 107 (108)
T ss_pred EEEEEcCCceEEEEecCC---hHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 589999998998888873 2357889999999999999988754
No 8
>PF15560 Imm8: Immunity protein 8
Probab=56.02 E-value=32 Score=24.85 Aligned_cols=36 Identities=22% Similarity=0.513 Sum_probs=30.9
Q ss_pred eEEEEEEe--ccCCCCCcHHHHHHHHHHHHHHHHHHhh
Q psy934 98 TIVFCVSA--FKSCLTTSAAKFATSLDESLSAIGNLVE 133 (143)
Q Consensus 98 ~i~f~iss--~~~~~~t~~~~F~~~L~~al~~m~~ll~ 133 (143)
-..||+.. |.+++..++.+|...++..+.++-.|+.
T Consensus 77 v~~fcid~~~W~s~k~~dv~kFL~~~~~~li~lg~lI~ 114 (133)
T PF15560_consen 77 VVEFCIDRNYWTSEKLEDVNKFLLFIEDLLIQLGDLIK 114 (133)
T ss_pred eEEEEeccccccCCccccHHHHHHHHHHHHHHhHHHHH
Confidence 35677766 8888888999999999999999999885
No 9
>TIGR02946 acyl_WS_DGAT acyltransferase, WS/DGAT/MGAT. This bacteria-specific protein family includes a characterized, homodimeric, broad specificity acyltransferase from Acinetobacter sp. strain ADP1, active as wax ester synthase, as acyl coenzyme A:diacylglycerol acyltransferase, and as acyl-CoA:monoacylglycerol acyltransferase.
Probab=48.79 E-value=55 Score=27.37 Aligned_cols=45 Identities=13% Similarity=0.249 Sum_probs=34.5
Q ss_pred CCCceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHH
Q psy934 85 PDGYGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGN 130 (143)
Q Consensus 85 ~dGyGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ 130 (143)
+.|.+|+-.-.++.+.++|++-++. -.+.++|.+.+++++.+|.+
T Consensus 400 ~~~l~~~~~sy~g~l~~~~~~d~~~-~~d~~~l~~~~~~~l~~l~~ 444 (446)
T TIGR02946 400 GQGLNITVTSYNGQLDFGLLADRDA-VPDPQELADALEAALEELEA 444 (446)
T ss_pred CCeEEEEEEecCCeEEEEEeechhh-CCCHHHHHHHHHHHHHHHHh
Confidence 3455555555689999999886543 34799999999999999975
No 10
>PF13222 DUF4030: Protein of unknown function (DUF4030)
Probab=41.39 E-value=77 Score=23.17 Aligned_cols=50 Identities=12% Similarity=0.311 Sum_probs=35.0
Q ss_pred cccccCCCceee-ecccCCe-EEEEEEeccCCCCCcHHHHHHHHHHHHHHHH
Q psy934 80 YGPVVPDGYGCS-YNPREAT-IVFCVSAFKSCLTTSAAKFATSLDESLSAIG 129 (143)
Q Consensus 80 fgp~~~dGyGi~-Y~i~~~~-i~f~iss~~~~~~t~~~~F~~~L~~al~~m~ 129 (143)
|+--.-.|+||. |++..+. +.+.|-+.-++..-.+..|.+-++.-.+++.
T Consensus 66 f~Kn~Y~~~gI~~~n~k~~qp~~v~I~t~in~~d~~AKE~g~kiEkei~~~l 117 (142)
T PF13222_consen 66 FGKNGYKGFGIQQINVKSSQPVTVTIKTKINSSDPGAKEFGKKIEKEINEVL 117 (142)
T ss_pred hhccCccccceeEeeecCCCcEEEEEeccccccccchHHHHHHHHHHHHHHH
Confidence 333345789999 9998664 4777776444444568889999998776654
No 11
>PF09228 Prok-TraM: Prokaryotic Transcriptional repressor TraM; InterPro: IPR015309 Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel alpha-helices. These proteins can be divided into two parts, a globular head and an elongated tail, and they negatively regulate conjugation and the expression of tra genes by antagonising traR/AAI-dependent activation []. ; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 2Q0O_D 2HJD_D 1UPG_A 1US6_B 1RFY_B.
Probab=39.68 E-value=58 Score=22.59 Aligned_cols=25 Identities=12% Similarity=0.178 Sum_probs=19.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhh
Q psy934 1 MKDKKKLDLFDAAIKKQTQIMTENI 25 (143)
Q Consensus 1 ~s~~ek~~ll~~A~~~H~~~~~~a~ 25 (143)
|+.++...|=..|++.|.+++.++-
T Consensus 24 l~~seLE~Ltv~AIRehR~lv~~ae 48 (102)
T PF09228_consen 24 LPKSELETLTVSAIREHRRLVEAAE 48 (102)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5667777788899999999998764
No 12
>KOG3438|consensus
Probab=38.44 E-value=35 Score=23.73 Aligned_cols=41 Identities=17% Similarity=0.192 Sum_probs=23.3
Q ss_pred CCceeeecc---cCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHHh
Q psy934 86 DGYGCSYNP---REATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNLV 132 (143)
Q Consensus 86 dGyGi~Y~i---~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ll 132 (143)
+-=-|+|.| .++.+.|.|.+..+.+ -. +.|.++|.++.+++
T Consensus 42 eVefcGYtIPHPse~k~niRIQt~~~~~--A~----evl~kgl~el~~~c 85 (105)
T KOG3438|consen 42 EVEFCGYTIPHPSEDKINIRIQTRDGDP--AV----EVLKKGLEELMQLC 85 (105)
T ss_pred ceEEEeccCCCCchhhheEEEEecCCCc--ch----HHHHHHHHHHHHHH
Confidence 333456664 3678999998874322 23 44455555555544
No 13
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D ....
Probab=35.38 E-value=67 Score=20.43 Aligned_cols=42 Identities=17% Similarity=0.203 Sum_probs=23.9
Q ss_pred CCCceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHH
Q psy934 85 PDGYGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSA 127 (143)
Q Consensus 85 ~dGyGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~ 127 (143)
.++|=++|.+.++ +.+.+-+-++.|..-+-.|.+.|.+....
T Consensus 21 ~~~~~fh~~~~~~-i~~~citd~~~~~r~aF~fL~~i~~~F~~ 62 (83)
T PF13774_consen 21 SGNYVFHYLVEDG-IAYLCITDKSYPKRVAFAFLEEIKQEFIQ 62 (83)
T ss_dssp ETTEEEEEEEETT-EEEEEEEETTS-HHHHHHHHHHHHHHHHH
T ss_pred ECCEEEEEEEcCC-eEEEEEEcCCCCcchHHHHHHHHHHHHHH
Confidence 5668888888555 55544445555544455566555554443
No 14
>PRK12729 fliE flagellar hook-basal body protein FliE; Provisional
Probab=31.82 E-value=65 Score=23.20 Aligned_cols=24 Identities=17% Similarity=0.378 Sum_probs=19.0
Q ss_pred CCcHHHHHHHHHHHHHHHHHHhhc
Q psy934 111 TTSAAKFATSLDESLSAIGNLVES 134 (143)
Q Consensus 111 ~t~~~~F~~~L~~al~~m~~ll~~ 134 (143)
.....-|.+.|..|+.++-+.-..
T Consensus 52 ~~~~~sF~d~Lk~Al~~VN~~Q~~ 75 (127)
T PRK12729 52 DYVAESFSEAMKNALTSVNDLQVE 75 (127)
T ss_pred CcccCCHHHHHHHHHHHHHHHHHH
Confidence 445677999999999999877643
No 15
>PRK12566 glycine dehydrogenase; Provisional
Probab=31.10 E-value=1.1e+02 Score=29.33 Aligned_cols=43 Identities=16% Similarity=0.213 Sum_probs=34.6
Q ss_pred ccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHHhhccccc
Q psy934 94 PREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNLVESRKIS 138 (143)
Q Consensus 94 i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ll~~~~~~ 138 (143)
+.++.+.+++|=+++ ..+..+|++.|.....++.++-......
T Consensus 845 Pv~~~LmIepTE~es--keEIDrf~eAL~~I~~e~~~v~~g~~~~ 887 (954)
T PRK12566 845 PVPGTLMVEPTESES--KAELDRFVEAMLSIRAEIGKVQEGNWPA 887 (954)
T ss_pred ccCCEEEEEeeeeCC--HHHHHHHHHHHHHHHHHHHHHHcCCCCc
Confidence 457889998887765 5689999999999999999987655433
No 16
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=28.23 E-value=90 Score=19.16 Aligned_cols=40 Identities=18% Similarity=0.228 Sum_probs=27.5
Q ss_pred CceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHHh
Q psy934 87 GYGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNLV 132 (143)
Q Consensus 87 GyGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ll 132 (143)
|+.|.+...++.+.|.|-+..+. + =.+.|.+|+..+.+.+
T Consensus 26 ~~ai~~~~~~~~~~~~IeT~g~~---~---p~~~l~~A~~~l~~~~ 65 (66)
T PF01193_consen 26 GVAIDGHPNEDKFVFRIETDGSL---T---PKEALLKAIKILKEKL 65 (66)
T ss_dssp EEEEEESSEEEEEEEEEEEBSSS-------HHHHHHHHHHHHHHHH
T ss_pred CceEEecCCCCEEEEEEEECCCC---C---HHHHHHHHHHHHHHhc
Confidence 34444466788999999987432 2 3467888888887765
No 17
>KOG3222|consensus
Probab=27.89 E-value=28 Score=26.68 Aligned_cols=37 Identities=24% Similarity=0.409 Sum_probs=25.9
Q ss_pred CCCCCCCccccccc-cCCCceeeecccCCeEEEEEEec
Q psy934 70 VACKSDSFMGYGPV-VPDGYGCSYNPREATIVFCVSAF 106 (143)
Q Consensus 70 ~~~~~~~~~gfgp~-~~dGyGi~Y~i~~~~i~f~iss~ 106 (143)
+|...+..+||-|+ .||||.-+|.=.+....=.||.+
T Consensus 139 Vp~rG~~~fGwd~iFqP~g~~~tyaEMpk~ekN~iSHR 176 (195)
T KOG3222|consen 139 VPPRGPTDFGWDPIFQPDGYEQTYAEMPKDEKNAISHR 176 (195)
T ss_pred cCCCCCCCCCCCcccCCCccccchhhCChhHhhhhhHH
Confidence 45555667888777 67999999987766665455543
No 18
>PF09564 RE_NgoBV: NgoBV restriction endonuclease; InterPro: IPR019064 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the restriction endonuclease NgoBV, which recognises the sequence GGNNCC, but whose cleavage site is unknown.
Probab=27.72 E-value=84 Score=24.84 Aligned_cols=39 Identities=21% Similarity=0.298 Sum_probs=24.6
Q ss_pred ceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHH
Q psy934 88 YGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSA 127 (143)
Q Consensus 88 yGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~ 127 (143)
+|+.|+|+|.. -|.+.-.....-.+.+.|..+|++++..
T Consensus 163 r~~iyniRP~~-~f~~~k~~~~~Fes~edfI~Ai~et~~~ 201 (240)
T PF09564_consen 163 RGVIYNIRPGS-WFKTNKTNASVFESLEDFISAIYETVYQ 201 (240)
T ss_pred cceeEEecCCc-eeeecCCCchhhhhHHHHHHHHHHHHHh
Confidence 45889999885 3333321111235788899999888764
No 19
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=27.59 E-value=23 Score=19.93 Aligned_cols=30 Identities=17% Similarity=0.122 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCChHHHHHH
Q psy934 7 LDLFDAAIKKQTQIMTENIQGEGIDLHLLG 36 (143)
Q Consensus 7 ~~ll~~A~~~H~~~~~~a~~G~G~DRHL~g 36 (143)
.+++++|.+.|.....+|..=.|+.|.=+-
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~ 36 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLLGISRRTLY 36 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHH
Confidence 478999999999888999888888886543
No 20
>cd01207 Ena-Vasp Enabled-VASP-type homology (EVH1) domain. Enabled-VASP-type homology (EVH1) domain. The EVH1 domain binds to other proteins at proline rich sequences. It is found in proteins involved in cytoskeletal reorganization such as Enabled and VASP. Ena-VASP type EVH1 domains specifically recognize FPPPP motifs in the focal adhesion proteins zyxin and vinculin, and the ActA surface protein of Listeria monocytogenes. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=27.53 E-value=78 Score=22.19 Aligned_cols=18 Identities=22% Similarity=0.396 Sum_probs=16.0
Q ss_pred CCcHHHHHHHHHHHHHHH
Q psy934 111 TTSAAKFATSLDESLSAI 128 (143)
Q Consensus 111 ~t~~~~F~~~L~~al~~m 128 (143)
+.++.+|...++.||.++
T Consensus 93 e~eA~~F~~~v~~Al~~L 110 (111)
T cd01207 93 KEDATMFASAMLSALEVL 110 (111)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 468999999999999987
No 21
>PF03220 Tombus_P19: Tombusvirus P19 core protein; InterPro: IPR004905 This family represents the Tombusvirus P19 core protein.; GO: 0019012 virion; PDB: 1RPU_A 1R9F_A.
Probab=27.07 E-value=1e+02 Score=22.71 Aligned_cols=48 Identities=13% Similarity=0.255 Sum_probs=28.8
Q ss_pred CceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHHhhcccccccc
Q psy934 87 GYGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNLVESRKISTEN 141 (143)
Q Consensus 87 GyGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ll~~~~~~~~~ 141 (143)
-.||.|.|.=-.+.++||.-. .. +...++-|.+.-+.+|+-.+..-++
T Consensus 107 QigCTYsIRfRG~~~TlSGGS----rt---Lqrl~eMAiR~K~~~LQl~p~evE~ 154 (170)
T PF03220_consen 107 QIGCTYSIRFRGVSVTLSGGS----RT---LQRLIEMAIRTKRTMLQLTPSEVES 154 (170)
T ss_dssp --EEEEEEEETTEEEEEEEEG----GG---HHHHHHHHHHHHHHHCTSS-S----
T ss_pred ccceeEEEEEeeeEEEecCCh----HH---HHHHHHHHHHHHHHHhccCcHhhhc
Confidence 358999998777888888741 22 4445566777777778776665444
No 22
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=23.22 E-value=1.5e+02 Score=20.74 Aligned_cols=33 Identities=15% Similarity=0.160 Sum_probs=25.2
Q ss_pred ccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHH
Q psy934 94 PREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNL 131 (143)
Q Consensus 94 i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~l 131 (143)
+.+++|.+.-.+- .+..+|.+.+++-..++++|
T Consensus 91 i~~eRv~~~~~~~-----~~~~~fa~~~~~f~~~i~~l 123 (124)
T PF02662_consen 91 IEPERVRLYWISA-----PEGKRFAEIVNEFTERIKEL 123 (124)
T ss_pred CChhHeEEEEeCc-----ccHHHHHHHHHHHHHHHHHc
Confidence 5678998854332 47899999999988888765
No 23
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=23.17 E-value=2.2e+02 Score=18.47 Aligned_cols=32 Identities=13% Similarity=0.270 Sum_probs=22.1
Q ss_pred CCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHHhh
Q psy934 96 EATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNLVE 133 (143)
Q Consensus 96 ~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~ll~ 133 (143)
.+.+.|.|.+..+ .++ .++|.+|+..+.+-++
T Consensus 53 ~d~~~~~VeT~Gs---~~P---~~al~~Ai~~L~~~~~ 84 (86)
T cd00460 53 EDKFILRIETVGS---IPP---EEALRRAVEILRKKLE 84 (86)
T ss_pred CCeEEEEEEECCC---CCH---HHHHHHHHHHHHHHHh
Confidence 6689999988633 233 3677788888777654
No 24
>PF01797 Y1_Tnp: Transposase IS200 like; InterPro: IPR002686 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This entry represents a domain found in transposases for IS200 from Escherichia coli []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2F5G_B 2F4F_B 2EC2_F 2XM3_C 2XQC_D 2XO6_A 2XMA_E 2VJV_B 2VIH_B 2VJU_A ....
Probab=23.05 E-value=2.3e+02 Score=18.84 Aligned_cols=35 Identities=20% Similarity=0.147 Sum_probs=25.1
Q ss_pred eeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHH
Q psy934 90 CSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSA 127 (143)
Q Consensus 90 i~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~ 127 (143)
+.|.+.||.+.+.|+... ..+..+|...|......
T Consensus 43 ~~~~vm~nHvHllv~~~~---~~~is~~~~~lK~~~s~ 77 (121)
T PF01797_consen 43 IAFVVMPNHVHLLVSIPP---KQSISKFMQRLKGRSSR 77 (121)
T ss_dssp EEEEEETTEEEEEEEE-T---TS-HHHHHHHHHHHHHH
T ss_pred eeecccCcccceeeeecc---cccchheeecccccccc
Confidence 568899999999999863 44677888777765443
No 25
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=22.59 E-value=2e+02 Score=20.75 Aligned_cols=32 Identities=25% Similarity=0.369 Sum_probs=24.8
Q ss_pred ccCCeEEE-EEEeccCCCCCcHHHHHHHHHHHHHHHHHH
Q psy934 94 PREATIVF-CVSAFKSCLTTSAAKFATSLDESLSAIGNL 131 (143)
Q Consensus 94 i~~~~i~f-~iss~~~~~~t~~~~F~~~L~~al~~m~~l 131 (143)
|.++++.+ .||+ .+.++|.+.+.+-..++++|
T Consensus 92 ie~eRv~~~wiSa------~E~ekf~e~~~efv~~i~~l 124 (132)
T COG1908 92 IEPERVRVLWISA------AEGEKFAETINEFVERIKEL 124 (132)
T ss_pred CCcceEEEEEEeh------hhHHHHHHHHHHHHHHHHHh
Confidence 56788876 4554 37899999999888888775
No 26
>PF07687 M20_dimer: Peptidase dimerisation domain This family only corresponds to M20 family; InterPro: IPR011650 This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the MEROPS peptidase family M20 []. This family includes a range of zinc exopeptidases: carboxypeptidases, dipeptidases and specialised aminopeptidases [].; GO: 0016787 hydrolase activity; PDB: 3GB0_A 2F7V_A 1R3N_C 2VL1_D 2V8V_C 1R43_B 2V8G_B 2V8H_D 2V8D_A 3PFE_A ....
Probab=22.32 E-value=2.3e+02 Score=18.28 Aligned_cols=38 Identities=8% Similarity=0.061 Sum_probs=28.3
Q ss_pred eecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHH
Q psy934 91 SYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIG 129 (143)
Q Consensus 91 ~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~ 129 (143)
.-++-|+...+.++.+-. |..+.+...+.+++.+.++.
T Consensus 71 ~~n~ip~~a~~~~~~R~~-p~~~~~~i~~~i~~~~~~~~ 108 (111)
T PF07687_consen 71 APNVIPDEATLTVDIRYP-PGEDLEEIKAEIEAAVEKIA 108 (111)
T ss_dssp STTEESSEEEEEEEEEES-TCHHHHHHHHHHHHHHHHHH
T ss_pred cCCEECCEEEEEEEEECC-CcchHHHHHHHHHHHHHHhh
Confidence 446778888888887643 46678888888888887764
No 27
>PF09669 Phage_pRha: Phage regulatory protein Rha (Phage_pRha); InterPro: IPR019104 This entry represents a family of proteins which are encoded in temperate phages and bacterial prophage regions. They include the product of the late operon rha gene from lambdoid phage phi-80. The presence of this gene interferes with the infection of bacterial strains lacking the integration host factor that regulates the rha gene. Rha is thought to function as a phage regulatory protein.
Probab=22.15 E-value=1e+02 Score=20.33 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=32.4
Q ss_pred eeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHH
Q psy934 90 CSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNL 131 (143)
Q Consensus 90 i~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~l 131 (143)
=+|.+..+.+.+-++.+. ...+.+|...+-+++.+|.+-
T Consensus 54 ~~y~Ltk~g~~lL~~~~~---g~~a~~~k~~~I~~f~~me~~ 92 (93)
T PF09669_consen 54 PCYLLTKDGFTLLVMGYS---GKKAVEFKAAYIERFNEMEEE 92 (93)
T ss_pred EEEEEccChhheehhhhc---cchHHHHHHHHHHHHHHHHhc
Confidence 378899998999999885 235889999999999999864
No 28
>PF14483 Cut8_M: Cut8 dimerisation domain; PDB: 3Q5W_A 3Q5X_A.
Probab=21.64 E-value=1.5e+02 Score=16.65 Aligned_cols=25 Identities=12% Similarity=0.223 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhh
Q psy934 1 MKDKKKLDLFDAAIKKQTQIMTENI 25 (143)
Q Consensus 1 ~s~~ek~~ll~~A~~~H~~~~~~a~ 25 (143)
|+.++.+.+|+..+++|-+...+..
T Consensus 10 Ld~~qL~~lL~~l~~~HPei~~~i~ 34 (38)
T PF14483_consen 10 LDKDQLQSLLQSLCERHPEIQQEIR 34 (38)
T ss_dssp S-HHHHHHHHHHHHHHSTHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhChhHHHHHH
Confidence 5778889999999999988776654
No 29
>PRK14012 cysteine desulfurase; Provisional
Probab=20.19 E-value=1.2e+02 Score=24.91 Aligned_cols=43 Identities=14% Similarity=0.234 Sum_probs=33.2
Q ss_pred CceeeecccCCeEEEEEEeccCCCCCcHHHHHHHHHHHHHHHHHH
Q psy934 87 GYGCSYNPREATIVFCVSAFKSCLTTSAAKFATSLDESLSAIGNL 131 (143)
Q Consensus 87 GyGi~Y~i~~~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m~~l 131 (143)
.+|+.+.+.+..|++++..+.+ ..+..++++.|.+.+.+++.+
T Consensus 341 ~~~~~~~~~~~~iRls~~~~~t--~~dvd~~~~~l~~~~~~~~~~ 383 (404)
T PRK14012 341 ALGLNDELAHSSIRFSLGRFTT--EEEIDYAIELVRKSIGKLREL 383 (404)
T ss_pred HcCCChhhcCceEEEEecCCCC--HHHHHHHHHHHHHHHHHHHhh
Confidence 4566666777888988887743 568999999999988887654
No 30
>TIGR01821 5aminolev_synth 5-aminolevulinic acid synthase. This model represents 5-aminolevulinic acid synthase, an enzyme for one of two routes to the heme precursor 5-aminolevulinate. The protein is a pyridoxal phosphate-dependent enzyme related to 2-amino-3-ketobutyrate CoA tranferase and 8-amino-7-oxononanoate synthase. This enzyme appears restricted to the alpha Proteobacteria and mitochondrial derivatives.
Probab=20.18 E-value=1.4e+02 Score=24.64 Aligned_cols=30 Identities=3% Similarity=0.006 Sum_probs=23.5
Q ss_pred CeEEEEEEeccCCCCCcHHHHHHHHHHHHHHH
Q psy934 97 ATIVFCVSAFKSCLTTSAAKFATSLDESLSAI 128 (143)
Q Consensus 97 ~~i~f~iss~~~~~~t~~~~F~~~L~~al~~m 128 (143)
+.|+|+++...+ ..+..+|.+.|.+++.++
T Consensus 368 ~~lRis~~~~~t--~edi~~~~~~l~~~~~~~ 397 (402)
T TIGR01821 368 ERLRITPTPAHT--DKMIDDLVEALLLVWDRL 397 (402)
T ss_pred ceEEEEeCCCCC--HHHHHHHHHHHHHHHHHc
Confidence 579999988754 467899999998887654
Done!