Query psy10450
Match_columns 111
No_of_seqs 102 out of 1087
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 18:30:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10450.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10450hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4171|consensus 99.9 6.7E-27 1.5E-31 190.4 10.1 95 9-110 467-562 (671)
2 PF00211 Guanylate_cyc: Adenyl 99.9 3.7E-21 8E-26 134.8 10.1 96 9-110 33-128 (184)
3 KOG3619|consensus 99.8 5.3E-21 1.2E-25 160.3 10.6 95 9-109 137-231 (867)
4 KOG3618|consensus 99.8 2.5E-21 5.4E-26 159.8 6.5 89 8-101 364-452 (1318)
5 KOG1023|consensus 99.8 4.3E-20 9.4E-25 147.8 5.6 91 8-102 320-412 (484)
6 cd07302 CHD cyclase homology d 99.8 6.9E-18 1.5E-22 115.7 13.0 96 9-110 26-123 (177)
7 smart00044 CYCc Adenylyl- / gu 99.8 6.4E-18 1.4E-22 119.7 13.1 97 9-110 61-158 (194)
8 KOG3619|consensus 99.8 1.3E-18 2.7E-23 146.1 7.8 93 9-102 679-780 (867)
9 COG2114 CyaA Adenylate cyclase 99.7 8.1E-17 1.8E-21 117.9 11.4 90 9-111 71-160 (227)
10 KOG3618|consensus 99.7 4E-18 8.8E-23 141.1 1.9 99 3-102 1102-1209(1318)
11 cd07556 Nucleotidyl_cyc_III Cl 98.2 0.00012 2.6E-09 47.4 12.0 81 9-99 26-106 (133)
12 TIGR02578 cas_TM1811_Csm1 CRIS 68.6 67 0.0015 27.4 9.5 68 11-89 557-625 (648)
13 COG3887 Predicted signaling pr 68.4 45 0.00098 28.5 8.3 78 4-91 194-271 (655)
14 PF05165 GGDN: GGDN family; I 64.4 36 0.00078 25.7 6.4 32 11-46 155-186 (246)
15 COG2429 Archaeal GTP cyclohydr 64.1 40 0.00087 25.4 6.5 37 10-50 158-194 (250)
16 TIGR02577 cas_TM1794_Crm2 CRIS 55.2 1.2E+02 0.0025 24.9 9.2 65 10-87 390-457 (482)
17 PF10664 NdhM: Cyanobacterial 51.7 21 0.00046 23.4 2.9 21 7-27 40-60 (108)
18 PRK14538 putative bifunctional 50.3 81 0.0018 27.9 7.1 75 6-90 226-300 (838)
19 PHA02102 hypothetical protein 47.8 30 0.00065 20.8 3.0 49 57-111 5-54 (72)
20 TIGR00612 ispG_gcpE 1-hydroxy- 46.4 23 0.0005 28.0 3.0 14 79-92 120-133 (346)
21 PF15530 Toxin_50: Putative to 46.1 14 0.0003 26.0 1.5 30 81-110 85-114 (168)
22 KOG0173|consensus 45.9 29 0.00062 26.4 3.3 80 30-111 67-167 (271)
23 PRK00366 ispG 4-hydroxy-3-meth 43.6 27 0.00059 27.7 3.0 14 79-92 129-142 (360)
24 PRK08474 F0F1 ATP synthase sub 43.4 1.1E+02 0.0024 21.3 5.9 24 3-26 78-101 (176)
25 cd00424 PolY Y-family of DNA p 40.1 1.7E+02 0.0036 22.4 6.9 80 6-97 70-149 (343)
26 PRK01220 malonate decarboxylas 39.9 22 0.00047 23.2 1.7 12 90-101 16-27 (99)
27 PRK02240 GTP cyclohydrolase II 39.4 1.6E+02 0.0034 22.4 6.4 61 10-87 161-222 (254)
28 PRK02406 DNA polymerase IV; Va 38.5 1.8E+02 0.0039 22.2 7.1 79 6-98 66-145 (343)
29 TIGR03130 malonate_delta malon 38.4 23 0.00049 23.0 1.5 11 91-101 18-28 (98)
30 PF04551 GcpE: GcpE protein; 37.2 38 0.00082 27.0 2.9 13 80-92 131-143 (359)
31 PF11969 DcpS_C: Scavenger mRN 36.2 95 0.0021 20.1 4.4 25 67-91 68-92 (116)
32 PF00990 GGDEF: GGDEF domain; 35.1 1.2E+02 0.0026 19.2 7.6 78 9-90 53-132 (161)
33 COG4066 Uncharacterized protei 34.6 1.5E+02 0.0032 20.9 5.2 59 4-65 70-158 (165)
34 PRK03103 DNA polymerase IV; Re 28.7 2.6E+02 0.0057 21.9 6.5 79 7-98 77-155 (409)
35 PF12108 SF3a60_bindingd: Spli 28.6 71 0.0015 15.9 2.1 21 8-28 6-26 (28)
36 PF15151 RGCC: Response gene t 27.4 70 0.0015 21.4 2.5 18 8-25 18-35 (121)
37 PRK03858 DNA polymerase IV; Va 26.5 3.1E+02 0.0067 21.3 7.4 78 6-97 71-149 (396)
38 cd03468 PolY_like DNA Polymera 25.7 2.8E+02 0.006 20.8 5.9 78 6-97 69-146 (335)
39 PRK02048 4-hydroxy-3-methylbut 25.4 48 0.001 28.2 1.8 14 79-92 153-166 (611)
40 PRK03348 DNA polymerase IV; Pr 25.2 3.7E+02 0.008 21.7 7.2 78 7-96 78-155 (454)
41 PRK00694 4-hydroxy-3-methylbut 25.1 45 0.00098 28.3 1.6 15 79-93 157-171 (606)
42 PF09749 HVSL: Uncharacterised 25.1 93 0.002 22.8 3.1 27 5-32 150-176 (239)
43 TIGR03471 HpnJ hopanoid biosyn 24.9 3.3E+02 0.0072 21.8 6.5 54 2-66 304-365 (472)
44 PF13113 DUF3970: Protein of u 24.5 70 0.0015 18.9 1.9 18 5-22 7-24 (60)
45 PRK03352 DNA polymerase IV; Va 24.5 3.2E+02 0.007 20.8 6.2 74 6-97 80-153 (346)
46 PLN02925 4-hydroxy-3-methylbut 24.2 57 0.0012 28.3 2.1 15 78-92 221-235 (733)
47 COG3400 Uncharacterized protei 24.0 2E+02 0.0043 23.4 4.9 61 5-74 206-266 (471)
48 PRK02103 malonate decarboxylas 23.8 55 0.0012 21.5 1.5 12 90-101 19-30 (105)
49 PF01025 GrpE: GrpE; InterPro 23.7 1.1E+02 0.0023 20.8 3.1 29 9-41 92-120 (165)
50 COG0821 gcpE 1-hydroxy-2-methy 23.6 68 0.0015 25.5 2.2 14 79-92 122-135 (361)
51 cd06246 M14_CPB2 Peptidase M14 23.1 1.1E+02 0.0024 23.4 3.3 29 10-41 7-35 (300)
52 PF14459 Prok-E2_C: Prokaryoti 22.7 2.5E+02 0.0054 18.8 4.5 22 82-103 54-78 (131)
53 PF01250 Ribosomal_S6: Ribosom 22.6 1.3E+02 0.0028 18.4 3.1 32 7-40 14-45 (92)
54 PRK14133 DNA polymerase IV; Pr 22.5 3.6E+02 0.0078 20.6 7.3 77 6-99 74-151 (347)
55 PF14492 EFG_II: Elongation Fa 22.4 1.6E+02 0.0034 17.5 3.3 44 2-46 9-52 (75)
56 KOG4700|consensus 22.3 1.5E+02 0.0032 21.7 3.5 32 9-40 92-123 (207)
57 PRK13436 F0F1 ATP synthase sub 22.1 1.7E+02 0.0038 20.4 4.0 24 3-26 83-106 (179)
58 PF02268 TFIIA_gamma_N: Transc 21.4 1.4E+02 0.0031 16.8 2.7 18 7-24 29-46 (49)
59 TIGR00256 D-tyrosyl-tRNA(Tyr) 20.9 1.3E+02 0.0029 20.8 3.0 22 4-25 95-116 (145)
60 COG5049 XRN1 5'-3' exonuclease 20.6 3.8E+02 0.0083 23.9 6.2 38 7-53 55-93 (953)
61 PF07342 DUF1474: Protein of u 20.3 1.2E+02 0.0027 19.7 2.6 22 9-33 66-87 (100)
No 1
>KOG4171|consensus
Probab=99.94 E-value=6.7e-27 Score=190.42 Aligned_cols=95 Identities=26% Similarity=0.348 Sum_probs=86.9
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcC-CCCceeEEEE
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQH-KPDAQLKSGM 87 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~-~~~l~lRIGI 87 (111)
.+||++|++||+++..| +||||+||||+||+++|+|..++. ||+.++++||+|++..+++-.+. +.++++||||
T Consensus 467 ~~LN~lyt~fD~~i~~~----~VYKVETIGDaYm~vsG~P~~~~~-HAe~i~~~AL~Mm~~ak~v~~p~~~~pi~iRiGI 541 (671)
T KOG4171|consen 467 NMLNELYTRFDRIIDTH----DVYKVETIGDAYMVVSGLPDASDY-HAEHIADLALGMMEEAKEVVSPVTGEPIQIRIGI 541 (671)
T ss_pred HHHHHHHHHHHHhhccc----CeEEEeeccchheeecCCCCCChh-HHHHHHHHHHHHHHHhhhhcCcCCCCceEEEEEe
Confidence 78999999999999866 799999999999999999999999 99999999999999999988664 7889999999
Q ss_pred ecccEeEEeecCCCccceecccC
Q psy10450 88 IEFPHHPKLIRDERALSSSQISP 110 (111)
Q Consensus 88 htGpvv~GvIG~~~~l~~~~i~~ 110 (111)
|||||+|||||.+-| .+|.++
T Consensus 542 HsG~VvAGVVG~kmP--RYCLFG 562 (671)
T KOG4171|consen 542 HSGPVVAGVVGVKMP--RYCLFG 562 (671)
T ss_pred ccCCeeeeeeccccc--ceeecC
Confidence 999999999998655 566554
No 2
>PF00211 Guanylate_cyc: Adenylate and Guanylate cyclase catalytic domain; InterPro: IPR001054 Guanylate cyclases (4.6.1.2 from EC) catalyse the formation of cyclic GMP (cGMP) from GTP. cGMP acts as an intracellular messenger, activating cGMP-dependent kinases and regulating cGMP-sensitive ion channels. The role of cGMP as a second messenger in vascular smooth muscle relaxation and retinal photo-transduction is well established. Guanylate cyclase is found both in the soluble and particulate fractions of eukaryotic cells. The soluble and plasma membrane-bound forms differ in structure, regulation and other properties [, , , ]. Most currently known plasma membrane-bound forms are receptors for small polypeptides. The soluble forms of guanylate cyclase are cytoplasmic heterodimers having alpha and beta subunits. In all characterised eukaryote guanylyl- and adenylyl cyclases, cyclic nucleotide synthesis is carried out by the conserved class III cyclase domain. ; GO: 0016849 phosphorus-oxygen lyase activity, 0009190 cyclic nucleotide biosynthetic process, 0035556 intracellular signal transduction; PDB: 3UVJ_A 1FX4_A 1WC4_B 2BW7_D 1WC1_A 1WC0_A 1WC3_A 1WC5_A 1WC6_A 3ET6_B ....
Probab=99.86 E-value=3.7e-21 Score=134.83 Aligned_cols=96 Identities=24% Similarity=0.317 Sum_probs=88.2
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEEEEe
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKSGMI 88 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRIGIh 88 (111)
+.||++|+.+++++.+| ++++++++||+||++||.|.+..+ ++.+++++|++|++.++.++....+++.+|||||
T Consensus 33 ~~l~~~~~~~~~~v~~~----~g~~~~~~Gd~~~~~f~~~~~~~~-~~~~a~~~al~~~~~~~~~~~~~~~~~~~rIGI~ 107 (184)
T PF00211_consen 33 RLLNDFFSSLDRIVKQH----GGEIIKFIGDGVMAVFGLPEPDED-AAERAVQFALALLEALERLNKESGPPLSVRIGIH 107 (184)
T ss_dssp HHHHHHHHHHHHHHHHT----TEEEEEEETTEEEEEESSSSCHCH-HHHHHHHHHHHHHHHHHHHHHHHHSS-EEEEEEE
T ss_pred HHHHHHHHHhhhccccc----cccccccccceeEEEecccccccc-ccccccccccchhhcccccccccceeeeeecccc
Confidence 78999999999999999 499999999999999999977666 9999999999999999998877778899999999
Q ss_pred cccEeEEeecCCCccceecccC
Q psy10450 89 EFPHHPKLIRDERALSSSQISP 110 (111)
Q Consensus 89 tGpvv~GvIG~~~~l~~~~i~~ 110 (111)
+|||++|++| .++..|+++|+
T Consensus 108 ~G~v~~g~~G-~~~~~~~v~G~ 128 (184)
T PF00211_consen 108 TGPVVVGVVG-SRRPEYDVFGD 128 (184)
T ss_dssp EEEEEEEEEE-SSSEEEEEESH
T ss_pred cccccccccc-Ccccceeeeeh
Confidence 9999999999 88888999985
No 3
>KOG3619|consensus
Probab=99.85 E-value=5.3e-21 Score=160.29 Aligned_cols=95 Identities=22% Similarity=0.303 Sum_probs=87.9
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEEEEe
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKSGMI 88 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRIGIh 88 (111)
.+||+||++||+++.++ .+.+||..||||.|++|+|.+++| ||..++++.++|.++++.++..++.+++||||||
T Consensus 137 ~~LneLf~rfd~lA~~~----~clRiKiLGdcyyCvsglp~~~~d-HA~~~v~mgl~Mi~aI~~vr~at~~dvnmrvGih 211 (867)
T KOG3619|consen 137 KVLNELFARFDRLAAEN----HCLRIKILGDCYYCVSGLPEARPD-HAVCCVEMGLDMIKAIKQVREATGVDVNMRVGIH 211 (867)
T ss_pred HHHHHHHHHHHHHHHhc----ceEeeeeecceeEEecCCCCCChh-HHHHHHHHHHHHHHHHHHHHHHhCCCCceEEEEe
Confidence 78999999999999999 599999999999999999999999 9999999999999999999999999999999999
Q ss_pred cccEeEEeecCCCccceeccc
Q psy10450 89 EFPHHPKLIRDERALSSSQIS 109 (111)
Q Consensus 89 tGpvv~GvIG~~~~l~~~~i~ 109 (111)
||+|.|||+|..+ ..|-+.+
T Consensus 212 sG~Vl~GvlG~~k-wq~DVws 231 (867)
T KOG3619|consen 212 SGSVLCGVLGLRK-WQYDVWS 231 (867)
T ss_pred cCceeecccccce-eeeeecc
Confidence 9999999999765 3444443
No 4
>KOG3618|consensus
Probab=99.84 E-value=2.5e-21 Score=159.85 Aligned_cols=89 Identities=24% Similarity=0.345 Sum_probs=85.4
Q ss_pred hHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEEEE
Q psy10450 8 EEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKSGM 87 (111)
Q Consensus 8 ~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRIGI 87 (111)
+++||+||.+||.+|+.- +++||.|+||||.|++|+|+++.| ||.++++|.|.|+.+++.|.....+.++||+||
T Consensus 364 V~lLNDLFgRFD~LC~l~----gcEKISTLGDCYYCVaGCPEPraD-HA~ccvEMGLgMI~AirqFd~~r~e~VnMRVGv 438 (1318)
T KOG3618|consen 364 VGLLNDLFGRFDRLCELT----GCEKISTLGDCYYCVAGCPEPRAD-HAYCCVEMGLGMIKAIRQFDQERKEMVNMRVGV 438 (1318)
T ss_pred HHHHHHHHHHHHHHHHhc----CcchhccccceeeeecCCCCCccc-ceeeehhhcchHHHHHHHHHHHhhcccceEEEE
Confidence 489999999999999887 599999999999999999999999 999999999999999999999999999999999
Q ss_pred ecccEeEEeecCCC
Q psy10450 88 IEFPHHPKLIRDER 101 (111)
Q Consensus 88 htGpvv~GvIG~~~ 101 (111)
|||.|.||++|..|
T Consensus 439 HTGtVlCGivGtrR 452 (1318)
T KOG3618|consen 439 HTGTVLCGIVGTRR 452 (1318)
T ss_pred ecceEEeeeeecce
Confidence 99999999999865
No 5
>KOG1023|consensus
Probab=99.80 E-value=4.3e-20 Score=147.78 Aligned_cols=91 Identities=40% Similarity=0.532 Sum_probs=85.0
Q ss_pred hHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCC--ceeEE
Q psy10450 8 EEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPD--AQLKS 85 (111)
Q Consensus 8 ~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~--l~lRI 85 (111)
+..||.+|+.||.++++| ++|||+|+||+||+++|+|..+...|+..++.+|++++..+..+..++.|. +++||
T Consensus 320 v~~lNdlyt~Fd~ii~~~----d~yKVetiGDaYmvvSglp~~n~~~H~~eia~msl~~~~~~~~f~i~H~P~~~l~iRi 395 (484)
T KOG1023|consen 320 VTLLNDLYTTFDRIIDKH----DVYKVETIGDAYMVVSGLPIRNGYRHAREIASMALGLRSFLESFSLPHRPWEKLRLRI 395 (484)
T ss_pred eeeccchHHhhhhccccc----CCeeEeccCcceeecccCceecHhHHHHHHHHHHHHHHHHHhccCCCCCCchhhheee
Confidence 367999999999999999 699999999999999999999988899999999999999999999888764 99999
Q ss_pred EEecccEeEEeecCCCc
Q psy10450 86 GMIEFPHHPKLIRDERA 102 (111)
Q Consensus 86 GIhtGpvv~GvIG~~~~ 102 (111)
|+|+|||++||+|.+-|
T Consensus 396 g~~sg~~~agVvgl~mP 412 (484)
T KOG1023|consen 396 GFHSGPVVAGVVGLKMP 412 (484)
T ss_pred ccccCCceecccccCCC
Confidence 99999999999998755
No 6
>cd07302 CHD cyclase homology domain. Catalytic domains of the mononucleotidyl cyclases (MNC's), also called cyclase homology domains (CHDs), are part of the class III nucleotidyl cyclases. This class includes eukaryotic and prokaryotic adenylate cyclases (AC's) and guanylate cyclases (GC's). They seem to share a common catalytic mechanism in their requirement for two magnesium ions to bind the polyphosphate moiety of the nucleotide.
Probab=99.78 E-value=6.9e-18 Score=115.66 Aligned_cols=96 Identities=28% Similarity=0.351 Sum_probs=88.4
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhc--CCCCceeEEE
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQ--HKPDAQLKSG 86 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~--~~~~l~lRIG 86 (111)
+.||.+++.+++++.+| +.+++++.||++|++|+.|....+ ++.+++++|++|++.++.++.. ....+.+|||
T Consensus 26 ~~l~~~~~~~~~~~~~~----~g~~~~~~gd~~~~~f~~~~~~~~-~~~~A~~~a~~i~~~~~~~~~~~~~~~~~~~riG 100 (177)
T cd07302 26 ELLNEYFSAFDEIIERH----GGTVDKTIGDAVMAVFGLPGAHED-HAERAVRAALEMQEALAELNAEREGGPPLRLRIG 100 (177)
T ss_pred HHHHHHHHHHHHHHHHc----CCEEEEEeCceEEEEeCCCCCchh-HHHHHHHHHHHHHHHHHHHhhcccCCCCeEEEEE
Confidence 67899999999999998 588999999999999999988777 9999999999999999998865 6678999999
Q ss_pred EecccEeEEeecCCCccceecccC
Q psy10450 87 MIEFPHHPKLIRDERALSSSQISP 110 (111)
Q Consensus 87 IhtGpvv~GvIG~~~~l~~~~i~~ 110 (111)
||+||+++|.+|+. .-.|+++|+
T Consensus 101 i~~G~~~~g~~g~~-~~~~~~~G~ 123 (177)
T cd07302 101 IHTGPVVAGVVGSE-RPEYTVIGD 123 (177)
T ss_pred EecceEEEEecCCC-CcceeEecc
Confidence 99999999999999 888888886
No 7
>smart00044 CYCc Adenylyl- / guanylyl cyclase, catalytic domain. Present in two copies in mammalian adenylyl cyclases. Eubacterial homologues are known. Two residues (Asn, Arg) are thought to be involved in catalysis. These cyclases have important roles in a diverse range of cellular processes.
Probab=99.78 E-value=6.4e-18 Score=119.69 Aligned_cols=97 Identities=25% Similarity=0.322 Sum_probs=86.7
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcC-CCCceeEEEE
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQH-KPDAQLKSGM 87 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~-~~~l~lRIGI 87 (111)
+.||.+|..+++++.+|+ .+.+|++||++|++|+.|.....+|+.+++.+|+++++.+..++.+. ..++++||||
T Consensus 61 ~~l~~~~~~~~~~i~~~g----g~v~~~~Gd~~l~~F~~~~~~~~~~a~~a~~~al~l~~~~~~~~~~~~~~~l~~riGi 136 (194)
T smart00044 61 TLLNDLYSRFDRIIDRHG----GYKVKTIGDAYMVVSGLPTEALVDHAELAADEALDMVESLKTVLSQHRGNGLRVRIGI 136 (194)
T ss_pred HHHHHHHHHHHHHHHhcC----eEEEEEeCCEEEEEECCCCCcchHHHHHHHHHHHHHHHHHHHHHhhccCCCeeEEEEE
Confidence 678999999999999994 88889999999999999988753499999999999999999887653 5679999999
Q ss_pred ecccEeEEeecCCCccceecccC
Q psy10450 88 IEFPHHPKLIRDERALSSSQISP 110 (111)
Q Consensus 88 htGpvv~GvIG~~~~l~~~~i~~ 110 (111)
|+|+|++|.+|...+ .|+++|+
T Consensus 137 h~G~v~~~~~g~~~~-~~~~~G~ 158 (194)
T smart00044 137 HTGPVVAGVVGITMP-RYCLFGD 158 (194)
T ss_pred eccceEEEecCCCCc-eeEEeCh
Confidence 999999999999986 6999886
No 8
>KOG3619|consensus
Probab=99.76 E-value=1.3e-18 Score=146.14 Aligned_cols=93 Identities=24% Similarity=0.384 Sum_probs=83.3
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCC-CCC--CCc------hHHHHHHHHHHHHHHHHHHhhhcCCC
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGL-PER--NGD------NHAREISRMALAILEAVQSFSIQHKP 79 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Gl-p~~--~~~------~~a~~~~~~Al~m~~~~~~~~~~~~~ 79 (111)
..||++++.||++..+. .|.+++||||+|-+|||++|+ |.. +.+ +|+-.+++||++|.+.+++.|.....
T Consensus 679 RlLNEIIaDFDeLL~~p-kF~~IEKIKTIGSTYMAAsGL~~~~~~~~~~~~~~~~h~~~l~eFAlal~~~L~~IN~~SfN 757 (867)
T KOG3619|consen 679 RLLNEIIADFDELLSKP-KFSGVEKIKTIGSTYMAASGLNPTSAQENDQSLRQWSHLGALVEFALALMHKLDEINRHSFN 757 (867)
T ss_pred HHHHHHHhhHHHhcCcc-ccccceeEEEecchhhhhhCCChhhhhccCcchhHHhhHHHHHHHHHHHHHHHHhhhHHhhc
Confidence 78999999999999954 667999999999999999999 332 121 47888999999999999999998889
Q ss_pred CceeEEEEecccEeEEeecCCCc
Q psy10450 80 DAQLKSGMIEFPHHPKLIRDERA 102 (111)
Q Consensus 80 ~l~lRIGIhtGpvv~GvIG~~~~ 102 (111)
.+.+||||+.|||+|||||.++|
T Consensus 758 nF~LrIGin~GpvvAGVIGArKP 780 (867)
T KOG3619|consen 758 NFELRIGINHGPVVAGVIGARKP 780 (867)
T ss_pred cceeeeceeccceeeeEecCCCC
Confidence 99999999999999999999988
No 9
>COG2114 CyaA Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]
Probab=99.72 E-value=8.1e-17 Score=117.86 Aligned_cols=90 Identities=14% Similarity=0.144 Sum_probs=72.3
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEEEEe
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKSGMI 88 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRIGIh 88 (111)
++||.+|..++..+.+|+ ...+|++||++|++||.|.+..+ ....+..++++|.+..+.++.+. +++|||||
T Consensus 71 ~ll~~~~~~~~~~v~~~g----G~v~k~iGD~~la~F~~p~~~~~-A~~~a~~~~~~~~~~~~~~~~~~---l~~riGi~ 142 (227)
T COG2114 71 ELLNLYFDAVAEVVARHG----GRVVKFIGDGFLAVFGRPSPLED-AVACALDLQLALRNPLARLRRES---LRVRIGIH 142 (227)
T ss_pred HHHHHHHHHHHHHHHHcC----CEEEEEecceEEEEeCCCCCcHH-HHHHHHHHHHHHHHHHhhccCcC---eeEEEEEE
Confidence 789999999999999995 77888999999999999987662 22333335556666666555433 99999999
Q ss_pred cccEeEEeecCCCccceecccCC
Q psy10450 89 EFPHHPKLIRDERALSSSQISPG 111 (111)
Q Consensus 89 tGpvv~GvIG~~~~l~~~~i~~~ 111 (111)
+|+|+.|.+|+ ||++|+.
T Consensus 143 ~G~vv~~~~g~-----~~~~G~~ 160 (227)
T COG2114 143 TGEVVVGNTGG-----YTVVGSA 160 (227)
T ss_pred eecEEEEeecC-----eeEechH
Confidence 99999999999 9999873
No 10
>KOG3618|consensus
Probab=99.70 E-value=4e-18 Score=141.10 Aligned_cols=99 Identities=24% Similarity=0.336 Sum_probs=87.6
Q ss_pred cccCCh--HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCC-CCCCC-----chHHHHHHHHHHHHHHHHHHhh
Q psy10450 3 IELGRE--EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGL-PERNG-----DNHAREISRMALAILEAVQSFS 74 (111)
Q Consensus 3 ~~~~~~--e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Gl-p~~~~-----~~~a~~~~~~Al~m~~~~~~~~ 74 (111)
-|+|++ ..||+++..||++..+. +|..++||||||-+|||++|+ |+... ++|...+.+||++||++++.||
T Consensus 1102 yeGGkEflRVLNElIGDFDELLsrP-df~~iEKIKTIG~tyMAASGLnp~~~~~~~hp~EHl~~l~eFa~amq~Vvd~FN 1180 (1318)
T KOG3618|consen 1102 YEGGKEFLRVLNELIGDFDELLSRP-DFSSIEKIKTIGATYMAASGLNPAQAQDGSHPQEHLQILFEFAKAMQRVVDDFN 1180 (1318)
T ss_pred hhchHHHHHHHHHHhccHHHHhccc-cchhhHHHhhhhHHHHHhcCCChHHccCCCChHHHHHHHHHHHHHHHHHHHHhh
Confidence 477887 88999999999999988 677999999999999999999 54432 3688999999999999999999
Q ss_pred hcC-CCCceeEEEEecccEeEEeecCCCc
Q psy10450 75 IQH-KPDAQLKSGMIEFPHHPKLIRDERA 102 (111)
Q Consensus 75 ~~~-~~~l~lRIGIhtGpvv~GvIG~~~~ 102 (111)
... ..++.+|||+|.|||+|||||..+.
T Consensus 1181 ~dlL~Fnf~lrvG~NiGpvTAGVIGTtKL 1209 (1318)
T KOG3618|consen 1181 NDLLWFNFKLRVGFNIGPVTAGVIGTTKL 1209 (1318)
T ss_pred hhhhheeeeEEeeccccCcccccccccee
Confidence 764 4679999999999999999999874
No 11
>cd07556 Nucleotidyl_cyc_III Class III nucleotidyl cyclases. Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's). The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways.
Probab=98.17 E-value=0.00012 Score=47.38 Aligned_cols=81 Identities=27% Similarity=0.359 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEEEEe
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKSGMI 88 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRIGIh 88 (111)
+.|.++...+.+.+..++ .....+-||.+++++.. + ...++..++.++.+.+..........+.++||++
T Consensus 26 ~~l~~~~~~l~~~~~~~~----~~~~r~~~d~f~~l~~~-----~-~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~ig~~ 95 (133)
T cd07556 26 ELLNELAGRFDSLIRRSG----DLKIKTIGDEFMVVSGL-----D-HPAAAVAFAEDMREAVSALNQSEGNPVRVRIGIH 95 (133)
T ss_pred HHHHHHHHHHHHHHHHcC----cEEEEeecceEEEEECc-----h-HHHHHHHHHHHHHHHHHHHHhccCCceEEEEEEe
Confidence 566777777777777753 34445889999999853 2 4567788888888888765544555689999999
Q ss_pred cccEeEEeecC
Q psy10450 89 EFPHHPKLIRD 99 (111)
Q Consensus 89 tGpvv~GvIG~ 99 (111)
+|++..+..|.
T Consensus 96 ~g~~~~~~~~~ 106 (133)
T cd07556 96 TGPVVVGVIGS 106 (133)
T ss_pred cccEEEEeccC
Confidence 99999998775
No 12
>TIGR02578 cas_TM1811_Csm1 CRISPR-associated protein, Csm1 family. The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2. A typical example is TM1811 from Thermotoga maritima. CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats. This protein family belongs to a conserved gene cluster regularly found near CRISPR repeats.
Probab=68.56 E-value=67 Score=27.41 Aligned_cols=68 Identities=16% Similarity=0.170 Sum_probs=45.6
Q ss_pred HHHHHHH-HHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEEEEec
Q psy10450 11 EDKVFKS-FKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKSGMIE 89 (111)
Q Consensus 11 Ln~lf~~-fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRIGIht 89 (111)
|+.+|+. ...+++++...++++-|-.=||-++++. ....++++|.++.+...++... +.+.+..||..
T Consensus 557 l~~fF~~~v~~i~~~~~~~~~~~~VYaGGDDv~~ig---------~~~~~l~~A~~i~~~F~~~~~~--~~~TlSaGi~i 625 (648)
T TIGR02578 557 LELFFKLYLLHLAEDKRNKRNLYVVYSGGDDLFLIG---------PWNAVLELASDIREYFEKFTCR--DKITISAGVVV 625 (648)
T ss_pred HHHHHHHHHHHHHhhhccCCCEEEEEEccccEEEEc---------cHHHHHHHHHHHHHHHHHHhCC--CCeeEEEEEEE
Confidence 3333442 3345555433446888888888888887 4567889999999999887533 56777777654
No 13
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=68.36 E-value=45 Score=28.48 Aligned_cols=78 Identities=12% Similarity=0.014 Sum_probs=56.3
Q ss_pred ccCChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCcee
Q psy10450 4 ELGREEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQL 83 (111)
Q Consensus 4 ~~~~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~l 83 (111)
|+.|..+-+.+-+-.++.+++| +++-=++.+|-|+++... .-...+.+-=..+++.+++......-++.+
T Consensus 194 d~~rs~inS~V~s~l~~~a~~~----~if~rr~s~drf~~~~~~------~~L~~l~~~kF~iLd~~RE~s~~~~ipLTL 263 (655)
T COG3887 194 DSDRSQINSFVTSFLEEWATEY----NIFLRRYSSDRFYAFTNY------KILEKLEEDKFSILDEFREESSQKNIPLTL 263 (655)
T ss_pred hhhHHHHHHHHHHHHHHHHHHh----hhhheeecCCeEEEEecH------HHHHHHHHhhhHHHHHHHHHhhccCcceEE
Confidence 3445555555556677888888 566667999999999853 244566666677777777777677778999
Q ss_pred EEEEeccc
Q psy10450 84 KSGMIEFP 91 (111)
Q Consensus 84 RIGIhtGp 91 (111)
.||+..|.
T Consensus 264 SiGvg~g~ 271 (655)
T COG3887 264 SIGVGYGE 271 (655)
T ss_pred EEEeccCc
Confidence 99998874
No 14
>PF05165 GGDN: GGDN family; InterPro: IPR007839 GTP cyclohydrolase III catalyses the formation of 2-amino-5-formylamino-6- ribofuranosylamino-4(3H)-pyrimidinone ribonucleotide monophosphate and inorganic phosphate from GTP. The enzyme also has an independent pyrophosphate phosphohydrolase activity. The proteins are 200-270 amino acids in length.; GO: 0003933 GTP cyclohydrolase activity, 0009058 biosynthetic process; PDB: 2QV6_B.
Probab=64.45 E-value=36 Score=25.66 Aligned_cols=32 Identities=16% Similarity=0.115 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeC
Q psy10450 11 EDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSG 46 (111)
Q Consensus 11 Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~G 46 (111)
.++++..+-+.+.+|+.. .+ -.-||-+|+++.
T Consensus 155 I~~l~~~l~~~~~~~G~L--~f--ylGGDNi~~v~p 186 (246)
T PF05165_consen 155 IEDLYAKLMKYLEKYGSL--AF--YLGGDNIMAVCP 186 (246)
T ss_dssp HHHHHHHHHHHHHTTT-----E--EEETTEEEEE-T
T ss_pred HHHHHHHHHHHHHhcCCE--EE--EecCceEEEECC
Confidence 456666666666777533 33 367999999884
No 15
>COG2429 Archaeal GTP cyclohydrolase III [Nucleotide transport and metabolism]
Probab=64.15 E-value=40 Score=25.36 Aligned_cols=37 Identities=16% Similarity=0.108 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCC
Q psy10450 10 DEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPER 50 (111)
Q Consensus 10 ~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~ 50 (111)
..+..+..+++-+.+++ .--.-.=||-+|+++..-++
T Consensus 158 ~I~~~~~~L~~~l~k~g----al~fflGGDN~ma~~p~~s~ 194 (250)
T COG2429 158 EIQRVYATLMRFLEKIG----ALLFFLGGDNIMAVCPGLSA 194 (250)
T ss_pred HHHHHHHHHHHHHHhcC----cEEEEecCcceEEECCCCCc
Confidence 56788889999999985 22223568999999866443
No 16
>TIGR02577 cas_TM1794_Crm2 CRISPR-associated protein, Crm2 family. This model represent a Crm2 family of the CRISPR-associated RAMP module, a set of six genes recurring found together in prokaryotic genomes. This gene cluster is found only in species with CRISPR repeats, usually near the repeats themselves. Because most of the six (but not this family) contain RAMP domains, and because its appearance in a genome appears to depend on other CRISPR-associated Cas genes, the set is designated the CRISPR RAMP module. This protein, typified by TM1794 from Thermotoga maritima, is designated Crm2, for CRISPR RAMP Module protein 2.
Probab=55.22 E-value=1.2e+02 Score=24.94 Aligned_cols=65 Identities=8% Similarity=0.009 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhc---CCCCceeEEE
Q psy10450 10 DEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQ---HKPDAQLKSG 86 (111)
Q Consensus 10 ~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~---~~~~l~lRIG 86 (111)
.|+.++...-..+.++ +.+-|-.=||-++++. .+..++++|.++.+.....-.. ..+.+.+-.|
T Consensus 390 aL~~f~~~~~~~v~~~----~g~~VYaGGDDvlai~---------p~~~al~~a~~l~~~F~~~~~~~~~~~~~~T~SaG 456 (482)
T TIGR02577 390 ALAEFSLKAVKIVVNE----HGELVYAGGDDVLALL---------PVDTALDVAKELRKEFRESLEKSLGGERGPTMSAG 456 (482)
T ss_pred HHHHHHHHHHHHhhhh----CeEEEEEccCcEEEEc---------cHHHHHHHHHHHHHHHHHHhhcccccCCCceEEEE
Confidence 3444454444444444 3666667888888887 4567899999999888765433 2334555544
Q ss_pred E
Q psy10450 87 M 87 (111)
Q Consensus 87 I 87 (111)
|
T Consensus 457 I 457 (482)
T TIGR02577 457 L 457 (482)
T ss_pred E
Confidence 4
No 17
>PF10664 NdhM: Cyanobacterial and plastid NDH-1 subunit M; InterPro: IPR018922 The NADH dehydrogenase I complex shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in plants is believed to be plastoquinone. The NADH dehydrogenase I complex couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. This entry represents subunit M of the NADH dehydrogenase I complex in cyanobacteria and plant chloroplasts []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=51.70 E-value=21 Score=23.39 Aligned_cols=21 Identities=29% Similarity=0.368 Sum_probs=18.2
Q ss_pred ChHHHHHHHHHHHHHHHhhCC
Q psy10450 7 REEDEDKVFKSFKFLTLKVSP 27 (111)
Q Consensus 7 ~~e~Ln~lf~~fd~l~~~~~~ 27 (111)
.++.|+++++.||++++.|.|
T Consensus 40 ~~~~l~kVy~~F~eLVe~~~G 60 (108)
T PF10664_consen 40 NEEALQKVYRKFDELVESYAG 60 (108)
T ss_pred CHHHHHHHHHHHHHHHHhhcC
Confidence 468899999999999998853
No 18
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=50.26 E-value=81 Score=27.87 Aligned_cols=75 Identities=9% Similarity=0.180 Sum_probs=55.1
Q ss_pred CChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEE
Q psy10450 6 GREEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKS 85 (111)
Q Consensus 6 ~~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRI 85 (111)
-+..+...+-+.+++.+.+|+ .+-=++-.|-|++++.- +..+.+.+--..+++.++..+.....++.+.|
T Consensus 226 ~~s~l~~~i~~~l~~~~~~~~----~~~r~~~~dry~~~~~~------~~l~~~~~~kF~iLd~ir~~~~~~~~~vTLSi 295 (838)
T PRK14538 226 EQSQIQGEYLSALSDFIEPYE----GYLKQLIDDRFLLLINR------QNLDKMIENKFSILDTIRNISHKYQLKVTLSM 295 (838)
T ss_pred HHHHHHHHHHHHHHHHHHhCC----EEEEEecCCcEEEEEEH------HHHHHHHHhCCcHHHHHHHhhcCCCCceEEEE
Confidence 344555666667777777775 43346789999999842 35666777777888888888777778899999
Q ss_pred EEecc
Q psy10450 86 GMIEF 90 (111)
Q Consensus 86 GIhtG 90 (111)
||..|
T Consensus 296 Gig~g 300 (838)
T PRK14538 296 GIACW 300 (838)
T ss_pred EEeCC
Confidence 99987
No 19
>PHA02102 hypothetical protein
Probab=47.81 E-value=30 Score=20.82 Aligned_cols=49 Identities=22% Similarity=0.194 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHhhhc-CCCCceeEEEEecccEeEEeecCCCccceecccCC
Q psy10450 57 REISRMALAILEAVQSFSIQ-HKPDAQLKSGMIEFPHHPKLIRDERALSSSQISPG 111 (111)
Q Consensus 57 ~~~~~~Al~m~~~~~~~~~~-~~~~l~lRIGIhtGpvv~GvIG~~~~l~~~~i~~~ 111 (111)
..+++.|+++++.+..++.- ..++..+.| +. . +-|.-++-|++||-|.|
T Consensus 5 neLvekA~eLqkLl~eV~dlAse~~yGvei--n~-~---nev~f~DWLsSSCYGEg 54 (72)
T PHA02102 5 NELVEKALELQKLLKEVKDLASEQDYGVEI--ND-D---NEVRFEDWLSSSCYGEG 54 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhccceee--CC-C---CcEeHHHhhcccccccc
Confidence 45788999999998887732 344444444 32 1 34566777777777654
No 20
>TIGR00612 ispG_gcpE 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase. Chlamydial members of the family have a long insert. The family is largely restricted to Bacteria, where it is widely but not universally distributed. No homology can be detected between the GcpE family and other proteins.
Probab=46.43 E-value=23 Score=27.97 Aligned_cols=14 Identities=7% Similarity=0.031 Sum_probs=12.0
Q ss_pred CCceeEEEEecccE
Q psy10450 79 PDAQLKSGMIEFPH 92 (111)
Q Consensus 79 ~~l~lRIGIhtGpv 92 (111)
..+.+|||+|+|++
T Consensus 120 ~~ipIRIGVN~GSL 133 (346)
T TIGR00612 120 HGKAMRIGVNHGSL 133 (346)
T ss_pred CCCCEEEecCCCCC
Confidence 45889999999986
No 21
>PF15530 Toxin_50: Putative toxin 50
Probab=46.13 E-value=14 Score=26.04 Aligned_cols=30 Identities=20% Similarity=0.093 Sum_probs=23.5
Q ss_pred ceeEEEEecccEeEEeecCCCccceecccC
Q psy10450 81 AQLKSGMIEFPHHPKLIRDERALSSSQISP 110 (111)
Q Consensus 81 l~lRIGIhtGpvv~GvIG~~~~l~~~~i~~ 110 (111)
....|||..||-.-|++|+..+=.++-||-
T Consensus 85 a~asiGi~FGPYfpg~~gd~~rdyS~~~g~ 114 (168)
T PF15530_consen 85 AGASIGISFGPYFPGVFGDPDRDYSINLGF 114 (168)
T ss_pred ecceEeeecCCcCccccCCCCccceecccc
Confidence 344599999999999999988766665553
No 22
>KOG0173|consensus
Probab=45.87 E-value=29 Score=26.42 Aligned_cols=80 Identities=16% Similarity=0.144 Sum_probs=43.9
Q ss_pred CCeEEeeeCcEEEEEeCCCCCCCchHHHHH-----------------HHHHHHHHHHHHHhhhcCCCCceeEE-EEe-cc
Q psy10450 30 LPSQVETIGDAYMVVSGLPERNGDNHAREI-----------------SRMALAILEAVQSFSIQHKPDAQLKS-GMI-EF 90 (111)
Q Consensus 30 ~v~KiktiGd~yma~~Glp~~~~~~~a~~~-----------------~~~Al~m~~~~~~~~~~~~~~l~lRI-GIh-tG 90 (111)
++.||..+-+-++|+.+-..++.+ .+..+ +-+|+.|++.. -|+.+..-..-+=| |+. +|
T Consensus 67 nC~KIH~ia~~IyccGAGtAADte-~vt~m~ss~l~Lh~l~t~R~~rVv~A~~mlkQ~-LFrYqG~IgA~LiiGGvD~TG 144 (271)
T KOG0173|consen 67 NCEKIHFIAPNIYCCGAGTAADTE-MVTRMISSNLELHRLNTGRKPRVVTALRMLKQH-LFRYQGHIGAALILGGVDPTG 144 (271)
T ss_pred hhHHHhhcccceEEccCCchhhHH-HHHHHHHHHHHHHHhccCCCCceeeHHHHHHHH-HHHhcCcccceeEEccccCCC
Confidence 378888888888887665555333 22111 11233333221 12222222222222 454 48
Q ss_pred cEeEEe--ecCCCccceecccCC
Q psy10450 91 PHHPKL--IRDERALSSSQISPG 111 (111)
Q Consensus 91 pvv~Gv--IG~~~~l~~~~i~~~ 111 (111)
|-+-.+ =||.+.+.|+.+|+|
T Consensus 145 pHLy~i~phGStd~~Pf~alGSG 167 (271)
T KOG0173|consen 145 PHLYSIHPHGSTDKLPFTALGSG 167 (271)
T ss_pred CceEEEcCCCCcCccceeeeccc
Confidence 866554 599999999999987
No 23
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=43.63 E-value=27 Score=27.75 Aligned_cols=14 Identities=7% Similarity=-0.035 Sum_probs=12.0
Q ss_pred CCceeEEEEecccE
Q psy10450 79 PDAQLKSGMIEFPH 92 (111)
Q Consensus 79 ~~l~lRIGIhtGpv 92 (111)
..+.+|||+|+|++
T Consensus 129 ~~ipIRIGvN~GSL 142 (360)
T PRK00366 129 YGIPIRIGVNAGSL 142 (360)
T ss_pred CCCCEEEecCCccC
Confidence 45889999999985
No 24
>PRK08474 F0F1 ATP synthase subunit delta; Validated
Probab=43.41 E-value=1.1e+02 Score=21.28 Aligned_cols=24 Identities=17% Similarity=-0.086 Sum_probs=21.8
Q ss_pred cccCChHHHHHHHHHHHHHHHhhC
Q psy10450 3 IELGREEDEDKVFKSFKFLTLKVS 26 (111)
Q Consensus 3 ~~~~~~e~Ln~lf~~fd~l~~~~~ 26 (111)
++.+|...|.+++..|.++..++.
T Consensus 78 i~n~R~~~L~~I~~~f~~~~~~~~ 101 (176)
T PRK08474 78 AENKRLELIPAIAKELERQIALKE 101 (176)
T ss_pred HHCChHHHHHHHHHHHHHHHHHHc
Confidence 578999999999999999999884
No 25
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=40.13 E-value=1.7e+02 Score=22.44 Aligned_cols=80 Identities=16% Similarity=0.097 Sum_probs=51.3
Q ss_pred CChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEE
Q psy10450 6 GREEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKS 85 (111)
Q Consensus 6 ~~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRI 85 (111)
-+++...++..++-+++.+|. ....+-.+..+||=++|......+ ....|.++++.+... .+ .+..+|
T Consensus 70 ~~~~~y~~~s~~i~~~l~~~s---p~ve~~siDE~~ldvt~~~~~~~~-----~~~la~~i~~~i~~~---~g-gl~~si 137 (343)
T cd00424 70 ARLDLYRRLSERLLSELEEVA---PLVEVASIDELFLDLTGSARLLGL-----GSEVALRIKRHIAEQ---LG-GITASI 137 (343)
T ss_pred CCcHHHHHHHHHHHHHHHHhC---CcEEEccCCEEEEECCCchhccCC-----HHHHHHHHHHHHHHH---hC-CceEEE
Confidence 456777777778888888774 233345678899999987533222 334666776666531 11 257788
Q ss_pred EEecccEeEEee
Q psy10450 86 GMIEFPHHPKLI 97 (111)
Q Consensus 86 GIhtGpvv~GvI 97 (111)
||...+.+|-+.
T Consensus 138 Gia~n~~lAKlA 149 (343)
T cd00424 138 GIASNKLLAKLA 149 (343)
T ss_pred eecccHHHHHHH
Confidence 988877766544
No 26
>PRK01220 malonate decarboxylase subunit delta; Provisional
Probab=39.91 E-value=22 Score=23.16 Aligned_cols=12 Identities=0% Similarity=-0.230 Sum_probs=10.6
Q ss_pred ccEeEEeecCCC
Q psy10450 90 FPHHPKLIRDER 101 (111)
Q Consensus 90 Gpvv~GvIG~~~ 101 (111)
+++.+||+||.+
T Consensus 16 ~~~lvGVVGSGd 27 (99)
T PRK01220 16 GRALVGVVGSGD 27 (99)
T ss_pred CCEEEEEEccCc
Confidence 599999999976
No 27
>PRK02240 GTP cyclohydrolase III; Provisional
Probab=39.41 E-value=1.6e+02 Score=22.41 Aligned_cols=61 Identities=13% Similarity=0.181 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHh-hCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEEEE
Q psy10450 10 DEDKVFKSFKFLTLK-VSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKSGM 87 (111)
Q Consensus 10 ~Ln~lf~~fd~l~~~-~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRIGI 87 (111)
..++++..+-+.+.+ |+.. .+- .=||-+|++| |.-... +..+.+..++...+-+++..||+
T Consensus 161 ~i~~~~~~l~~~~~~~~g~l--~ff--~GGDN~~~~~--~~l~~~-----------~~~~~i~~i~~~~~v~lkvGIG~ 222 (254)
T PRK02240 161 EIEQAYLALMRELRKAHDAL--SFF--VGGDNFMAPC--PGLSEG-----------DFLDAIEHVREEVGVELKVGIGR 222 (254)
T ss_pred HHHHHHHHHHHHHHHhcCcE--EEE--ecCceEEEEC--CCCCHH-----------HHHHHHHHHhhccCeeEEeeecc
No 28
>PRK02406 DNA polymerase IV; Validated
Probab=38.53 E-value=1.8e+02 Score=22.23 Aligned_cols=79 Identities=15% Similarity=0.182 Sum_probs=49.1
Q ss_pred CChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHH-HHhhhcCCCCceeE
Q psy10450 6 GREEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAV-QSFSIQHKPDAQLK 84 (111)
Q Consensus 6 ~~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~-~~~~~~~~~~l~lR 84 (111)
-+++.-.+...++-+++.+|. +.++ +..+..+||-+.|......+ ...+|..+++.+ +.+ .+..+
T Consensus 66 ~d~~~y~~~s~~i~~~l~~~s--p~ve-~~siDe~~ldvt~~~~~~~~-----~~~la~~i~~~i~~~~------gl~~s 131 (343)
T PRK02406 66 GRFDVYKEVSRQIREIFRRYT--DLIE-PLSLDEAYLDVTDNKLCIGS-----ATLIAQEIRQDIFEEL------GLTAS 131 (343)
T ss_pred CChHHHHHHHHHHHHHHHHhC--CceE-EccCCeEEEeccCccccCCC-----HHHHHHHHHHHHHHHH------CCCeE
Confidence 355566666667777777774 2233 45677899999987544333 234566666665 333 26778
Q ss_pred EEEecccEeEEeec
Q psy10450 85 SGMIEFPHHPKLIR 98 (111)
Q Consensus 85 IGIhtGpvv~GvIG 98 (111)
|||...+..|-+.-
T Consensus 132 iGia~n~~lAklas 145 (343)
T PRK02406 132 AGVAPNKFLAKIAS 145 (343)
T ss_pred EEeccCHHHHHHHh
Confidence 88888777665543
No 29
>TIGR03130 malonate_delta malonate decarboxylase acyl carrier protein. Members of this protein family are the acyl carrier protein, also called the delta subunit, of malonate decarboxylase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=38.39 E-value=23 Score=23.05 Aligned_cols=11 Identities=9% Similarity=0.163 Sum_probs=9.5
Q ss_pred cEeEEeecCCC
Q psy10450 91 PHHPKLIRDER 101 (111)
Q Consensus 91 pvv~GvIG~~~ 101 (111)
|+.+||+||.+
T Consensus 18 ~~lvGVVGSGd 28 (98)
T TIGR03130 18 PALVGVVGSGD 28 (98)
T ss_pred cEEEEEEccCc
Confidence 49999999975
No 30
>PF04551 GcpE: GcpE protein; InterPro: IPR004588 This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is largely restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.; GO: 0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity, 0016114 terpenoid biosynthetic process, 0055114 oxidation-reduction process; PDB: 2Y0F_C 3NOY_A.
Probab=37.22 E-value=38 Score=26.97 Aligned_cols=13 Identities=8% Similarity=0.046 Sum_probs=10.6
Q ss_pred CceeEEEEecccE
Q psy10450 80 DAQLKSGMIEFPH 92 (111)
Q Consensus 80 ~l~lRIGIhtGpv 92 (111)
.+.+|||+|+|+.
T Consensus 131 ~ipIRIGvN~GSL 143 (359)
T PF04551_consen 131 GIPIRIGVNSGSL 143 (359)
T ss_dssp T-EEEEEEEGGGS
T ss_pred CCCEEEecccccC
Confidence 4789999999985
No 31
>PF11969 DcpS_C: Scavenger mRNA decapping enzyme C-term binding; PDB: 1VLR_B 1XMM_D 1XML_B 1ST0_A 3BLA_B 3BL9_B 3BL7_B 1ST4_B 1XQU_B.
Probab=36.19 E-value=95 Score=20.11 Aligned_cols=25 Identities=12% Similarity=0.049 Sum_probs=14.1
Q ss_pred HHHHHHhhhcCCCCceeEEEEeccc
Q psy10450 67 LEAVQSFSIQHKPDAQLKSGMIEFP 91 (111)
Q Consensus 67 ~~~~~~~~~~~~~~l~lRIGIhtGp 91 (111)
.+.+++..........+++|+|..|
T Consensus 68 ~~~~~~~~~~~~~~~~~~~gfH~~P 92 (116)
T PF11969_consen 68 RELLKEEYPGDLDSDDIRLGFHYPP 92 (116)
T ss_dssp HHHHHHHH-TT-EGGGEEEEEESS-
T ss_pred HHHHHHhcccccchhhhcccccCCC
Confidence 3334333322345578999999999
No 32
>PF00990 GGDEF: GGDEF domain; InterPro: IPR000160 This domain appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria [,]. Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation. Structural studies of PleD from Caulobacter crescentus show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase [].; PDB: 3IGN_A 3BRE_B 3EZU_A 3ICL_B 3PJX_A 3PJW_A 3HVW_A 3HVA_B 3I5C_B 3I5B_B ....
Probab=35.13 E-value=1.2e+02 Score=19.17 Aligned_cols=78 Identities=10% Similarity=0.093 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCC--CceeEEE
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKP--DAQLKSG 86 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~--~l~lRIG 86 (111)
+..++++..+-+.+.+.-.. .-.-..+-+|.++++.- ....+ .+..+.+...++.+.+.......+. .+.+.+|
T Consensus 53 ~~~~~~l~~i~~~L~~~~~~-~~~~~r~~~~~f~il~~--~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G 128 (161)
T PF00990_consen 53 EVGDEILRQIAKRLKKQLRE-SDILARLGDDEFAILLP--DTDSE-EAEELAERLERLIDELNEPIDIDGIEVHLTLSIG 128 (161)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-TSEEEEEETTEEEEEEE--TCTHH-HHHHHHHHHHHHHHHHCCEEESTTEEEECEEEEE
T ss_pred cccccccccccccccccccc-ccccccccchheeeccc--ccccc-cchhhhhhhhhhhhhcccccccccccccccccce
Confidence 44556666666666655322 23333477888877653 33222 3444555544444444332111222 2566677
Q ss_pred Eecc
Q psy10450 87 MIEF 90 (111)
Q Consensus 87 IhtG 90 (111)
+...
T Consensus 129 ~~~~ 132 (161)
T PF00990_consen 129 IAVY 132 (161)
T ss_dssp EEEE
T ss_pred EEEe
Confidence 6654
No 33
>COG4066 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.59 E-value=1.5e+02 Score=20.93 Aligned_cols=59 Identities=19% Similarity=0.277 Sum_probs=39.6
Q ss_pred ccCChHHHHHHHHHHHHHHHhh------------------------------CCCCCCeEEeeeCcEEEEEeCCCCCCCc
Q psy10450 4 ELGREEDEDKVFKSFKFLTLKV------------------------------SPFPLPSQVETIGDAYMVVSGLPERNGD 53 (111)
Q Consensus 4 ~~~~~e~Ln~lf~~fd~l~~~~------------------------------~~~~~v~KiktiGd~yma~~Glp~~~~~ 53 (111)
|+|.+|.+|++++..++....+ -.||++.||.-=|++|.|---. ...+
T Consensus 70 ~eg~~E~~D~~l~~~~~~k~~~~~de~~f~~i~~i~~~Y~tfvrkEPlHPpgt~FPGgfkVrkkgnvyYCPVKd--kq~n 147 (165)
T COG4066 70 EEGDEEKLDEMLNRIERFKKYYTPDEERFINISKILCPYLTFVRKEPLHPPGTTFPGGFKVRKKGNVYYCPVKD--KQLN 147 (165)
T ss_pred cccCHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHHhCCCCCCCCCcCCCceEEEeeCCEEeccccc--cccC
Confidence 6788999999988888776652 1247899999999998764432 2222
Q ss_pred hHHHHHHHHHHH
Q psy10450 54 NHAREISRMALA 65 (111)
Q Consensus 54 ~~a~~~~~~Al~ 65 (111)
.....|++...
T Consensus 148 -~pgslC~fCva 158 (165)
T COG4066 148 -QPGSLCEFCVA 158 (165)
T ss_pred -CCcchhheeec
Confidence 34455555443
No 34
>PRK03103 DNA polymerase IV; Reviewed
Probab=28.74 E-value=2.6e+02 Score=21.93 Aligned_cols=79 Identities=14% Similarity=0.069 Sum_probs=48.5
Q ss_pred ChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEEE
Q psy10450 7 REEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKSG 86 (111)
Q Consensus 7 ~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRIG 86 (111)
+++.-.++..++-+++.+|.+ .++ +-.+..+|+-++|...-..+ ...+|.+|++.+... ..+..+||
T Consensus 77 d~~~y~~~s~~i~~~l~~~sp--~ve-~~siDe~~lDvt~~~~~~~~-----~~~la~~ir~~i~~~-----~gl~~svG 143 (409)
T PRK03103 77 RMQRYIDVSLQITRILEDFTD--LVE-PFSIDEQFLDVTGSQKLFGS-----PLEIAQKIQQRIMRE-----TGVYARVG 143 (409)
T ss_pred CHHHHHHHHHHHHHHHHHhCc--cce-ecCCCeeEeeccchhhcCCC-----HHHHHHHHHHHHHHH-----HCceEEEe
Confidence 455556666666677777742 233 34678899999987533222 234566666666331 13678899
Q ss_pred EecccEeEEeec
Q psy10450 87 MIEFPHHPKLIR 98 (111)
Q Consensus 87 IhtGpvv~GvIG 98 (111)
|...+..|-+..
T Consensus 144 ia~n~~lAklas 155 (409)
T PRK03103 144 IGPNKLLAKMAC 155 (409)
T ss_pred ecCCHHHHHHHh
Confidence 888877666553
No 35
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=28.59 E-value=71 Score=15.92 Aligned_cols=21 Identities=5% Similarity=0.105 Sum_probs=15.0
Q ss_pred hHHHHHHHHHHHHHHHhhCCC
Q psy10450 8 EEDEDKVFKSFKFLTLKVSPF 28 (111)
Q Consensus 8 ~e~Ln~lf~~fd~l~~~~~~~ 28 (111)
+..+.++|+++.++-+-|..+
T Consensus 6 ~d~f~eFY~rlk~Ike~Hrr~ 26 (28)
T PF12108_consen 6 GDPFSEFYERLKEIKEYHRRY 26 (28)
T ss_dssp --HHHHHHHHHHHHHHHHHS-
T ss_pred CChHHHHHHHHHHHHHHHHhC
Confidence 457889999999998877433
No 36
>PF15151 RGCC: Response gene to complement 32 protein family
Probab=27.43 E-value=70 Score=21.39 Aligned_cols=18 Identities=6% Similarity=0.230 Sum_probs=16.2
Q ss_pred hHHHHHHHHHHHHHHHhh
Q psy10450 8 EEDEDKVFKSFKFLTLKV 25 (111)
Q Consensus 8 ~e~Ln~lf~~fd~l~~~~ 25 (111)
..+|+++.+.||.+++.+
T Consensus 18 ~~eL~d~L~EFd~Vvedf 35 (121)
T PF15151_consen 18 DDELSDLLCEFDAVVEDF 35 (121)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 378999999999999987
No 37
>PRK03858 DNA polymerase IV; Validated
Probab=26.48 E-value=3.1e+02 Score=21.32 Aligned_cols=78 Identities=18% Similarity=0.210 Sum_probs=50.0
Q ss_pred CChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHH-HhhhcCCCCceeE
Q psy10450 6 GREEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQ-SFSIQHKPDAQLK 84 (111)
Q Consensus 6 ~~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~-~~~~~~~~~l~lR 84 (111)
.+++.-.++..++-+++.++. +.++ +-.+..+|+-+.|...-..+ ...+|.++++.+. .+ .+..+
T Consensus 71 ~d~~~y~~~s~~i~~~l~~~s--~~ve-~~siDe~~ldvt~~~~~~~~-----~~~la~~ir~~i~~~~------gl~~s 136 (396)
T PRK03858 71 PRMSAYSRASKAVFEVFRDTT--PLVE-GLSIDEAFLDVGGLRRISGT-----PVQIAARLRRRVREEV------GLPIT 136 (396)
T ss_pred CCHHHHHHHHHHHHHHHHHhC--CceE-EecCCeEEEEccccccccCC-----HHHHHHHHHHHHHHHH------CCCeE
Confidence 466666677777777777774 2233 34678899999987432222 3346667777664 33 26778
Q ss_pred EEEecccEeEEee
Q psy10450 85 SGMIEFPHHPKLI 97 (111)
Q Consensus 85 IGIhtGpvv~GvI 97 (111)
|||..-+..|-+.
T Consensus 137 vGia~n~~lAkla 149 (396)
T PRK03858 137 VGVARTKFLAKVA 149 (396)
T ss_pred EEEcCChHHHHHh
Confidence 8888877766555
No 38
>cd03468 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=25.65 E-value=2.8e+02 Score=20.81 Aligned_cols=78 Identities=15% Similarity=0.271 Sum_probs=44.4
Q ss_pred CChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEE
Q psy10450 6 GREEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKS 85 (111)
Q Consensus 6 ~~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRI 85 (111)
.+++.-.+.+.++-+++.+|.. .++ +..++.+|+=++|......+ ....|..+++.+.. ..+..+|
T Consensus 69 ~~~~~y~~~s~~i~~~l~~~s~--~ve-~~s~de~~ldvs~~~~~~~~-----~~~~a~~i~~~~~~------~gl~~si 134 (335)
T cd03468 69 YDPEADARALQELALWLLRFTP--LVA-LDGPDGLLLDVTGCLHLFGG-----EDALAASLRAALAT------LGLSARA 134 (335)
T ss_pred CChHHHHHHHHHHHHHHHhcCC--ccc-cCCCCeEEEEcccchhhcCC-----HHHHHHHHHHHHHH------cCCeEEE
Confidence 3455555555555566666642 233 34678899999987433222 22345555554422 2467888
Q ss_pred EEecccEeEEee
Q psy10450 86 GMIEFPHHPKLI 97 (111)
Q Consensus 86 GIhtGpvv~GvI 97 (111)
||...+..|-+.
T Consensus 135 Gia~n~~~Akla 146 (335)
T cd03468 135 GIADTPGAAWLL 146 (335)
T ss_pred EecCCHHHHHHH
Confidence 888877665443
No 39
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=25.42 E-value=48 Score=28.22 Aligned_cols=14 Identities=7% Similarity=0.067 Sum_probs=12.0
Q ss_pred CCceeEEEEecccE
Q psy10450 79 PDAQLKSGMIEFPH 92 (111)
Q Consensus 79 ~~l~lRIGIhtGpv 92 (111)
....+|||+|+|++
T Consensus 153 ~~~~iRIGvN~GSL 166 (611)
T PRK02048 153 NHTAIRIGVNHGSL 166 (611)
T ss_pred CCCCEEEecCCcCc
Confidence 45789999999986
No 40
>PRK03348 DNA polymerase IV; Provisional
Probab=25.16 E-value=3.7e+02 Score=21.72 Aligned_cols=78 Identities=12% Similarity=0.014 Sum_probs=47.8
Q ss_pred ChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEEE
Q psy10450 7 REEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKSG 86 (111)
Q Consensus 7 ~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRIG 86 (111)
|++.-.+...++-+++.+|. ....+..+..+||-+.++...... .+..+|.++++.+..-. .+..+||
T Consensus 78 d~~~Y~~~s~~i~~~l~~~s---p~VE~~SiDE~flD~~~l~~~~~~----~~~~~a~~lr~~I~~~~-----Gl~~SvG 145 (454)
T PRK03348 78 RFVVYRAASRRVFDTLRELS---PVVEQLSFDEAFVEPAELAGASAE----EVEAFAERLRARVREET-----GLPASVG 145 (454)
T ss_pred ChHHHHHHHHHHHHHHHHhC---CceEEecCCeEEEEccccccccCC----CHHHHHHHHHHHHHHHH-----CCCeEEE
Confidence 45555566666667777774 233345678889987776543221 23446677777764321 3678899
Q ss_pred EecccEeEEe
Q psy10450 87 MIEFPHHPKL 96 (111)
Q Consensus 87 IhtGpvv~Gv 96 (111)
|...+.+|-+
T Consensus 146 Ia~nk~lAKl 155 (454)
T PRK03348 146 AGSGKQIAKI 155 (454)
T ss_pred EcCCHHHHHH
Confidence 8888877654
No 41
>PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated
Probab=25.13 E-value=45 Score=28.29 Aligned_cols=15 Identities=7% Similarity=-0.002 Sum_probs=12.4
Q ss_pred CCceeEEEEecccEe
Q psy10450 79 PDAQLKSGMIEFPHH 93 (111)
Q Consensus 79 ~~l~lRIGIhtGpvv 93 (111)
....+|||+|+|++-
T Consensus 157 ~~~~IRIGvN~GSL~ 171 (606)
T PRK00694 157 LGKAMRIGVNHGSLS 171 (606)
T ss_pred CCCCEEEecCCcCch
Confidence 457899999999863
No 42
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=25.12 E-value=93 Score=22.77 Aligned_cols=27 Identities=7% Similarity=0.128 Sum_probs=20.7
Q ss_pred cCChHHHHHHHHHHHHHHHhhCCCCCCe
Q psy10450 5 LGREEDEDKVFKSFKFLTLKVSPFPLPS 32 (111)
Q Consensus 5 ~~~~e~Ln~lf~~fd~l~~~~~~~~~v~ 32 (111)
.+..+.|+.+....|++..+| +.+..|
T Consensus 150 ~~~~~~l~~l~~~i~~~l~~~-~lp~~Y 176 (239)
T PF09749_consen 150 EGSNNELKRLLDRINEVLKEF-GLPPFY 176 (239)
T ss_pred ccccHHHHHHHHHHHHHHHHh-CCCccc
Confidence 344444999999999999999 555666
No 43
>TIGR03471 HpnJ hopanoid biosynthesis associated radical SAM protein HpnJ. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift.
Probab=24.86 E-value=3.3e+02 Score=21.84 Aligned_cols=54 Identities=20% Similarity=0.213 Sum_probs=33.7
Q ss_pred ccccCChHHHHHHHH--------HHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHH
Q psy10450 2 KIELGREEDEDKVFK--------SFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAI 66 (111)
Q Consensus 2 ~~~~~~~e~Ln~lf~--------~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m 66 (111)
-+||+.++.|+.+-. +.-+.+.++ ++. ..+ --+.|+|....+ +.++.++++.++
T Consensus 304 GiES~s~~~L~~~~K~~~~~~~~~~i~~~~~~----Gi~---v~~---~~IiGlPget~e-~~~~ti~~~~~l 365 (472)
T TIGR03471 304 GYESGDQQILKNIKKGLTVEIARRFTRDCHKL----GIK---VHG---TFILGLPGETRE-TIRKTIDFAKEL 365 (472)
T ss_pred cCCCCCHHHHHHhcCCCCHHHHHHHHHHHHHC----CCe---EEE---EEEEeCCCCCHH-HHHHHHHHHHhc
Confidence 379999999987632 333444455 232 222 124699988766 777777777664
No 44
>PF13113 DUF3970: Protein of unknown function (DUF3970)
Probab=24.54 E-value=70 Score=18.90 Aligned_cols=18 Identities=33% Similarity=0.529 Sum_probs=14.7
Q ss_pred cCChHHHHHHHHHHHHHH
Q psy10450 5 LGREEDEDKVFKSFKFLT 22 (111)
Q Consensus 5 ~~~~e~Ln~lf~~fd~l~ 22 (111)
+|..|++.++...|.++-
T Consensus 7 ~G~~eEi~~fi~~~~~~~ 24 (60)
T PF13113_consen 7 SGTKEEIEEFIKSFEKLK 24 (60)
T ss_pred cCCHHHHHHHHHhhhhcC
Confidence 467789999999998864
No 45
>PRK03352 DNA polymerase IV; Validated
Probab=24.52 E-value=3.2e+02 Score=20.82 Aligned_cols=74 Identities=15% Similarity=0.024 Sum_probs=45.9
Q ss_pred CChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhhhcCCCCceeEE
Q psy10450 6 GREEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFSIQHKPDAQLKS 85 (111)
Q Consensus 6 ~~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~~~~~~~l~lRI 85 (111)
-+++.-.+....+-+++.+|. +.++ +..+..+|+-+.+. + ...+|..+++.+... ..+..+|
T Consensus 80 ~~~~~y~~~s~~i~~~l~~~s--~~ve-~~siDe~~ld~t~~-----~-----~~~la~~ir~~i~~~-----~gl~~si 141 (346)
T PRK03352 80 SDPAAYDAASEEVMATLRDLG--VPVE-VWGWDEAFLGVDTD-----D-----PEALAEEIRAAVLER-----TGLSCSV 141 (346)
T ss_pred CCcHHHHHHHHHHHHHHHHhC--CceE-EecCccEEEeCCCC-----C-----HHHHHHHHHHHHHHH-----HCCCEEE
Confidence 355666666666777777774 2233 34578899988885 1 223566666666541 1267788
Q ss_pred EEecccEeEEee
Q psy10450 86 GMIEFPHHPKLI 97 (111)
Q Consensus 86 GIhtGpvv~GvI 97 (111)
||...+..|-+.
T Consensus 142 Gia~nk~lAkla 153 (346)
T PRK03352 142 GIGDNKLRAKIA 153 (346)
T ss_pred eecCCHHHHHHH
Confidence 888877666544
No 46
>PLN02925 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
Probab=24.18 E-value=57 Score=28.35 Aligned_cols=15 Identities=13% Similarity=0.002 Sum_probs=12.3
Q ss_pred CCCceeEEEEecccE
Q psy10450 78 KPDAQLKSGMIEFPH 92 (111)
Q Consensus 78 ~~~l~lRIGIhtGpv 92 (111)
.....+|||+|+|++
T Consensus 221 ~~~~~iRIGvN~GSL 235 (733)
T PLN02925 221 KYGRAMRIGTNHGSL 235 (733)
T ss_pred HCCCCEEEecCCcCc
Confidence 345789999999986
No 47
>COG3400 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.01 E-value=2e+02 Score=23.40 Aligned_cols=61 Identities=16% Similarity=0.191 Sum_probs=43.6
Q ss_pred cCChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHHHHhh
Q psy10450 5 LGREEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAVQSFS 74 (111)
Q Consensus 5 ~~~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~~~~~ 74 (111)
.|+|+.||.+|-....-+.++ |- -.|.++.|...-...+.. .-.+-++-||...+-+++.+
T Consensus 206 vG~P~~ln~~~H~v~~~vgqF---P~-----pfGs~Vy~~idmk~~n~~-~~~r~v~~~L~l~~k~~~~~ 266 (471)
T COG3400 206 VGNPEILNAVYHQVKSNVGQF---PA-----PFGSSVYLYIDMKLQNRK-AMMRDVYQALFLHKKLKSYK 266 (471)
T ss_pred eCChHHHHHHHHHHhcccccC---CC-----CCCceEEEEechhhhhHH-HHHHHHHHHHHHHHHHHHhh
Confidence 489999999998877777655 22 247776665554455444 55778999999988887765
No 48
>PRK02103 malonate decarboxylase subunit delta; Provisional
Probab=23.82 E-value=55 Score=21.49 Aligned_cols=12 Identities=0% Similarity=-0.089 Sum_probs=10.3
Q ss_pred ccEeEEeecCCC
Q psy10450 90 FPHHPKLIRDER 101 (111)
Q Consensus 90 Gpvv~GvIG~~~ 101 (111)
-++++||+||.+
T Consensus 19 ~~~lvGVVgSGd 30 (105)
T PRK02103 19 AAALVGVVASGN 30 (105)
T ss_pred CceEEEEEccCc
Confidence 489999999975
No 49
>PF01025 GrpE: GrpE; InterPro: IPR000740 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes the grpE protein. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold []. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. The X-ray crystal structure of GrpE in complex with the ATPase domain of DnaK revealed that GrpE is an asymmetric homodimer, bent in a manner that favours extensive contacts with only one DnaKATPase monomer []. GrpE does not actively compete for the atomic positions occupied by the nucleotide. GrpE and ADP mutually reduce one another's affinity for DnaK 200-fold, and ATP instantly dissociates GrpE from DnaK.; GO: 0000774 adenyl-nucleotide exchange factor activity, 0042803 protein homodimerization activity, 0051087 chaperone binding, 0006457 protein folding; PDB: 3A6M_A 4ANI_A 1DKG_B.
Probab=23.71 E-value=1.1e+02 Score=20.80 Aligned_cols=29 Identities=17% Similarity=0.339 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEE
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAY 41 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~y 41 (111)
+-++.+...|.++..++ ++.+|...|+.|
T Consensus 92 ~g~~~~~~~l~~~L~~~----Gv~~i~~~G~~F 120 (165)
T PF01025_consen 92 EGLEMILKQLEDILEKN----GVEEIEPVGEPF 120 (165)
T ss_dssp HHHHHHHHHHHHHHHTT----TEEEE--TSSB-
T ss_pred HHHHHHHHHHHHHHHHC----CCEecCCCCCCC
Confidence 55788889999999999 599999988764
No 50
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=23.58 E-value=68 Score=25.49 Aligned_cols=14 Identities=7% Similarity=0.024 Sum_probs=11.5
Q ss_pred CCceeEEEEecccE
Q psy10450 79 PDAQLKSGMIEFPH 92 (111)
Q Consensus 79 ~~l~lRIGIhtGpv 92 (111)
....+|||+|.|+.
T Consensus 122 ~g~piRIGVN~GSL 135 (361)
T COG0821 122 KGIPIRIGVNAGSL 135 (361)
T ss_pred cCCCEEEecccCch
Confidence 35789999999974
No 51
>cd06246 M14_CPB2 Peptidase M14 Carboxypeptidase (CP) B2 (CPB2, also known as plasma carboxypeptidase B, carboxypeptidase U, and CPU), belongs to the carboxpeptidase A/B subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPB2 enzyme displays B-like activity; it only cleaves the basic residues lysine or arginine. It is produced and secreted by the liver as the inactive precursor, procarboxypeptidase U or PCPB2, commonly referred to as thrombin-activatable fibrinolysis inhibitor (TAFI). It circulates in plasma as a zymogen bound to plasminogen, and the active enzyme, TAFIa, inhibits fibrinolysis. It is highly regulated, increased TAFI concentrations are thought to increase the risk of thrombosis and coronary artery disease by reducing fibrinolytic activity whil
Probab=23.08 E-value=1.1e+02 Score=23.42 Aligned_cols=29 Identities=14% Similarity=0.285 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEE
Q psy10450 10 DEDKVFKSFKFLTLKVSPFPLPSQVETIGDAY 41 (111)
Q Consensus 10 ~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~y 41 (111)
.++++.+-+++++.+| |+..++..||.++
T Consensus 7 ~~~ei~~~l~~l~~~~---p~~v~~~~iG~S~ 35 (300)
T cd06246 7 SLNEIYSWIEFITERH---SDMLEKIHIGSSF 35 (300)
T ss_pred CHHHHHHHHHHHHHHC---CCcEEEEecccCC
Confidence 4678889999999888 4788888899875
No 52
>PF14459 Prok-E2_C: Prokaryotic E2 family C
Probab=22.70 E-value=2.5e+02 Score=18.83 Aligned_cols=22 Identities=18% Similarity=0.140 Sum_probs=15.0
Q ss_pred eeEEEE---ecccEeEEeecCCCcc
Q psy10450 82 QLKSGM---IEFPHHPKLIRDERAL 103 (111)
Q Consensus 82 ~lRIGI---htGpvv~GvIG~~~~l 103 (111)
+-||+| -.-|.++=|+|+.||-
T Consensus 54 Np~I~i~r~G~s~~~clV~G~trp~ 78 (131)
T PF14459_consen 54 NPRIEIRRSGSSPMHCLVIGSTRPK 78 (131)
T ss_pred CCCeEEEecCCCceEEEEecCCCCC
Confidence 335555 2337889999999874
No 53
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=22.61 E-value=1.3e+02 Score=18.36 Aligned_cols=32 Identities=25% Similarity=0.254 Sum_probs=26.0
Q ss_pred ChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcE
Q psy10450 7 REEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDA 40 (111)
Q Consensus 7 ~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~ 40 (111)
.++.+.++...+.+++.++++. +.+++..|.-
T Consensus 14 ~~~~~~~~~~~~~~~i~~~gg~--v~~~~~~G~r 45 (92)
T PF01250_consen 14 SEEEIKKLIERVKKIIEKNGGV--VRSVENWGKR 45 (92)
T ss_dssp CHHHHHHHHHHHHHHHHHTTEE--EEEEEEEEEE
T ss_pred CHHHHHHHHHHHHHHHHHCCCE--EEEEEEEeec
Confidence 4679999999999999999766 7777666654
No 54
>PRK14133 DNA polymerase IV; Provisional
Probab=22.49 E-value=3.6e+02 Score=20.61 Aligned_cols=77 Identities=22% Similarity=0.261 Sum_probs=48.4
Q ss_pred CChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCCCCCCCchHHHHHHHHHHHHHHHH-HHhhhcCCCCceeE
Q psy10450 6 GREEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGLPERNGDNHAREISRMALAILEAV-QSFSIQHKPDAQLK 84 (111)
Q Consensus 6 ~~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Glp~~~~~~~a~~~~~~Al~m~~~~-~~~~~~~~~~l~lR 84 (111)
-+++.-.++...+-+++.+|.+ .++ +-.+..+|+-++|.. .+ ....|..+++.+ +.+ .+..+
T Consensus 74 ~d~~~y~~~s~~i~~~l~~~s~--~ve-~~siDe~~ldv~~~~---~~-----~~~la~~i~~~i~~~~------gl~~s 136 (347)
T PRK14133 74 VRHERYKEVSKNIFKILYEVTP--IVE-PVSIDEAYLDITNIK---EE-----PIKIAKYIKKKVKKET------GLTLS 136 (347)
T ss_pred CCHHHHHHHHHHHHHHHHHhCC--ceE-EccCCeEEEEccCCC---CC-----HHHHHHHHHHHHHHHH------CCcEE
Confidence 3566666777777777777742 243 345677899999875 12 233556666655 333 26778
Q ss_pred EEEecccEeEEeecC
Q psy10450 85 SGMIEFPHHPKLIRD 99 (111)
Q Consensus 85 IGIhtGpvv~GvIG~ 99 (111)
|||...+..|-+..+
T Consensus 137 iGia~n~~~Aklas~ 151 (347)
T PRK14133 137 VGISYNKFLAKLASD 151 (347)
T ss_pred EEEcCcHHHHHHHhc
Confidence 898888777665543
No 55
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=22.41 E-value=1.6e+02 Score=17.48 Aligned_cols=44 Identities=23% Similarity=0.201 Sum_probs=29.9
Q ss_pred ccccCChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeC
Q psy10450 2 KIELGREEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSG 46 (111)
Q Consensus 2 ~~~~~~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~G 46 (111)
.||..++++..++.+.+.+++..-. .-.++.-+--|..++...|
T Consensus 9 ~i~p~~~~d~~kl~~aL~~l~~eDP-~l~~~~d~et~e~~l~g~G 52 (75)
T PF14492_consen 9 AIEPKNKEDEPKLSEALQKLSEEDP-SLRVERDEETGELILSGMG 52 (75)
T ss_dssp EEEESSHHHHHHHHHHHHHHHHH-T-TSEEEEETTTSEEEEEESS
T ss_pred EEEECCHhHHHHHHHHHHHHHhcCC-eEEEEEcchhceEEEEECC
Confidence 5788899999999999999998762 2233333334665555555
No 56
>KOG4700|consensus
Probab=22.30 E-value=1.5e+02 Score=21.66 Aligned_cols=32 Identities=6% Similarity=0.064 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcE
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQVETIGDA 40 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~ 40 (111)
..|++--..+.....+-.+..+|-+|||+||-
T Consensus 92 ~~L~rs~~~~rh~l~~~~~~g~vP~IkFV~DK 123 (207)
T KOG4700|consen 92 DFLERSKHQIRHRLEESIGIGTVPEIKFVGDK 123 (207)
T ss_pred HHHHHHHHHHHHHHHHHhccccCCceEEecch
Confidence 56666666777777766566689999999886
No 57
>PRK13436 F0F1 ATP synthase subunit delta; Provisional
Probab=22.07 E-value=1.7e+02 Score=20.36 Aligned_cols=24 Identities=13% Similarity=-0.056 Sum_probs=21.8
Q ss_pred cccCChHHHHHHHHHHHHHHHhhC
Q psy10450 3 IELGREEDEDKVFKSFKFLTLKVS 26 (111)
Q Consensus 3 ~~~~~~e~Ln~lf~~fd~l~~~~~ 26 (111)
+|.+|...|.+++..|.++..++.
T Consensus 83 ~~~~R~~~l~~I~~~f~~~~~~~~ 106 (179)
T PRK13436 83 AKNNLFIYIKQILKKFVKLSNEKL 106 (179)
T ss_pred HHCChHHHHHHHHHHHHHHHHHHc
Confidence 578999999999999999999884
No 58
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=21.39 E-value=1.4e+02 Score=16.80 Aligned_cols=18 Identities=17% Similarity=0.071 Sum_probs=14.5
Q ss_pred ChHHHHHHHHHHHHHHHh
Q psy10450 7 REEDEDKVFKSFKFLTLK 24 (111)
Q Consensus 7 ~~e~Ln~lf~~fd~l~~~ 24 (111)
.|++-+++...||+.+.+
T Consensus 29 ~p~La~kVL~~FDksi~~ 46 (49)
T PF02268_consen 29 TPQLAMKVLEQFDKSINE 46 (49)
T ss_dssp -HHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 478889999999998764
No 59
>TIGR00256 D-tyrosyl-tRNA(Tyr) deacylase. This homodimeric enzyme appears able to cleave any D-amino acid (and glycine, which does not have distinct D/L forms) from charged tRNA. The name reflects characterization with respect to D-Tyr on tRNA(Tyr) as established in the literature, but substrate specificity seems much broader.
Probab=20.88 E-value=1.3e+02 Score=20.78 Aligned_cols=22 Identities=9% Similarity=0.173 Sum_probs=19.9
Q ss_pred ccCChHHHHHHHHHHHHHHHhh
Q psy10450 4 ELGREEDEDKVFKSFKFLTLKV 25 (111)
Q Consensus 4 ~~~~~e~Ln~lf~~fd~l~~~~ 25 (111)
.++.||.-+++|..|-+.+.++
T Consensus 95 ~a~~~~~A~~ly~~fv~~l~~~ 116 (145)
T TIGR00256 95 KGASPDRAEELYEYFVELCREK 116 (145)
T ss_pred ccCCHHHHHHHHHHHHHHHHhc
Confidence 5788999999999999999876
No 60
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=20.59 E-value=3.8e+02 Score=23.87 Aligned_cols=38 Identities=32% Similarity=0.566 Sum_probs=27.7
Q ss_pred ChHHHHHHHHHHHHHHHhhCCCCCCeEEeeeCcEEEEEeCC-CCCCCc
Q psy10450 7 REEDEDKVFKSFKFLTLKVSPFPLPSQVETIGDAYMVVSGL-PERNGD 53 (111)
Q Consensus 7 ~~e~Ln~lf~~fd~l~~~~~~~~~v~KiktiGd~yma~~Gl-p~~~~~ 53 (111)
++|++-.+|.-.|.+..+- .-.| .+ |||+-|+ |.+.-+
T Consensus 55 EeEm~~aVf~Yidhil~~i----rPrK--ll---ymAVDGvAPRAKMN 93 (953)
T COG5049 55 EEEMYKAVFEYIDHILLKI----RPRK--LL---YMAVDGVAPRAKMN 93 (953)
T ss_pred HHHHHHHHHHHHHHHHHhc----Ccce--EE---EEEecccCchhhhh
Confidence 4588888899999998876 2444 44 9999999 655433
No 61
>PF07342 DUF1474: Protein of unknown function (DUF1474); InterPro: IPR009942 This entry is represented by Bacteriophage PT1028, Orf16. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins of around 100 residues in length. Members of this family seem to be found exclusively in Staphylococcus aureus. The function of this family is unknown.
Probab=20.26 E-value=1.2e+02 Score=19.68 Aligned_cols=22 Identities=18% Similarity=0.061 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCeE
Q psy10450 9 EDEDKVFKSFKFLTLKVSPFPLPSQ 33 (111)
Q Consensus 9 e~Ln~lf~~fd~l~~~~~~~~~v~K 33 (111)
++|.-|..+||.+++++. .+.|
T Consensus 66 dL~~~Ylkefd~li~kF~---eiEK 87 (100)
T PF07342_consen 66 DLMHMYLKEFDELIEKFK---EIEK 87 (100)
T ss_pred HHHHHHHHHHHHHHHHHH---HHHH
Confidence 677888899999998873 5666
Done!