Query 046619
Match_columns 239
No_of_seqs 108 out of 223
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 02:42:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046619.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046619hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14144 DOG1: Seed dormancy c 100.0 4.4E-37 9.6E-42 230.9 8.6 78 22-99 1-79 (80)
2 PF13801 Metal_resist: Heavy-m 97.2 0.0088 1.9E-07 45.7 11.5 85 112-210 40-124 (125)
3 COG3678 CpxP P pilus assembly/ 96.7 0.031 6.6E-07 47.3 11.3 87 113-216 57-143 (160)
4 PRK12750 cpxP periplasmic repr 96.6 0.11 2.4E-06 44.3 14.5 101 113-227 52-160 (170)
5 PRK10455 periplasmic protein; 96.1 0.076 1.7E-06 44.9 10.2 84 113-214 56-140 (161)
6 PRK12751 cpxP periplasmic stre 95.1 0.46 9.9E-06 40.3 11.5 95 113-225 56-151 (162)
7 PRK10363 cpxP periplasmic repr 94.9 0.24 5.3E-06 42.2 9.3 83 113-213 50-133 (166)
8 PF07813 LTXXQ: LTXXQ motif fa 92.1 0.79 1.7E-05 34.1 7.0 83 109-212 11-96 (100)
9 COG4323 Predicted membrane pro 71.5 6 0.00013 30.6 3.6 77 1-102 1-90 (105)
10 PRK11546 zraP zinc resistance 58.9 1.1E+02 0.0023 25.6 11.4 74 108-195 38-111 (143)
11 PRK14563 ribosome modulation f 58.3 4.4 9.4E-05 28.6 0.6 15 76-91 33-47 (55)
12 TIGR02302 aProt_lowcomp conser 43.5 4.4E+02 0.0096 28.2 14.3 132 25-200 510-646 (851)
13 cd00223 TOPRIM_TopoIIB_SPO TOP 43.4 34 0.00073 28.2 3.8 39 81-130 89-127 (160)
14 PF11239 DUF3040: Protein of u 43.3 24 0.00051 26.2 2.6 30 113-142 2-31 (82)
15 PF11459 DUF2893: Protein of u 41.7 59 0.0013 23.9 4.4 42 179-220 20-61 (69)
16 PF11172 DUF2959: Protein of u 40.2 88 0.0019 27.6 6.0 129 36-192 58-196 (201)
17 PF13586 DDE_Tnp_1_2: Transpos 40.1 14 0.00029 27.4 0.9 19 72-90 44-62 (88)
18 COG3130 Rmf Ribosome modulatio 38.7 11 0.00023 26.2 0.1 18 76-93 32-49 (55)
19 PF14644 DUF4456: Domain of un 36.7 50 0.0011 28.7 4.0 41 6-46 94-134 (208)
20 PF00589 Phage_integrase: Phag 36.3 17 0.00037 28.5 0.9 19 81-99 28-46 (173)
21 PF06698 DUF1192: Protein of u 34.5 77 0.0017 22.6 3.9 34 108-141 15-49 (59)
22 PLN02796 D-glycerate 3-kinase 33.0 86 0.0019 29.8 5.2 43 13-58 278-320 (347)
23 PF10552 ORF6C: ORF6C domain; 33.0 1.6E+02 0.0035 23.0 6.1 21 76-96 93-113 (116)
24 COG4898 Uncharacterized protei 32.1 48 0.001 26.1 2.8 17 81-97 34-50 (115)
25 KOG4100 Uncharacterized conser 31.9 2.8E+02 0.0061 22.5 7.2 94 7-131 10-110 (125)
26 PF04957 RMF: Ribosome modulat 31.2 8.7 0.00019 27.0 -1.3 13 78-90 34-46 (55)
27 PF13628 DUF4142: Domain of un 31.1 2.2E+02 0.0047 22.6 6.6 53 3-55 80-133 (139)
28 PF03371 PRP38: PRP38 family; 30.5 51 0.0011 28.1 2.9 24 89-121 62-85 (172)
29 COG4240 Predicted kinase [Gene 29.9 1.6E+02 0.0035 27.1 6.1 50 14-66 231-280 (300)
30 PLN03046 D-glycerate 3-kinase; 28.0 99 0.0021 30.6 4.7 43 13-58 390-432 (460)
31 PF11221 Med21: Subunit 21 of 27.0 3.1E+02 0.0068 22.3 7.0 40 108-147 92-131 (144)
32 smart00533 MUTSd DNA-binding d 26.5 1.7E+02 0.0037 25.8 5.8 65 18-91 224-288 (308)
33 COG4755 Uncharacterized protei 26.2 1.7E+02 0.0036 24.4 5.1 25 6-30 13-37 (151)
34 PF11897 DUF3417: Protein of u 26.1 61 0.0013 26.0 2.5 46 13-58 41-90 (118)
35 PF04918 DltD_M: DltD central 25.8 29 0.00064 29.0 0.7 39 48-94 9-47 (163)
36 PF06013 WXG100: Proteins of 1 25.4 2.3E+02 0.005 19.4 5.8 25 3-27 43-67 (86)
37 PF03232 COQ7: Ubiquinone bios 25.0 2.1E+02 0.0045 24.4 5.7 44 4-49 87-131 (172)
38 PF04678 DUF607: Protein of un 24.5 3E+02 0.0065 23.3 6.6 53 89-150 34-86 (180)
39 COG1510 Predicted transcriptio 24.2 2.5E+02 0.0055 24.3 6.0 60 11-70 97-170 (177)
40 cd01189 INT_phiLC3_C phiLC3 ph 23.3 1.2E+02 0.0026 24.1 3.8 18 81-98 28-45 (191)
41 PRK15366 type III secretion sy 22.8 1.6E+02 0.0034 22.3 4.0 26 112-137 38-63 (80)
42 cd01182 INT_REC_C DNA breaking 22.5 56 0.0012 24.6 1.7 19 81-99 22-40 (162)
43 cd00068 GGL G protein gamma su 22.4 2E+02 0.0043 19.9 4.2 46 18-74 2-47 (57)
44 PF09236 AHSP: Alpha-haemoglob 21.9 2.1E+02 0.0045 22.0 4.5 24 35-58 28-51 (89)
45 PRK15354 type III secretion sy 21.7 4.1E+02 0.0088 23.8 7.0 45 177-223 64-109 (224)
46 PF10234 Cluap1: Clusterin-ass 21.0 6.5E+02 0.014 23.1 8.6 28 172-200 192-219 (267)
47 PF10925 DUF2680: Protein of u 20.7 2.5E+02 0.0055 19.7 4.5 27 114-151 1-27 (59)
No 1
>PF14144 DOG1: Seed dormancy control
Probab=100.00 E-value=4.4e-37 Score=230.92 Aligned_cols=78 Identities=37% Similarity=0.696 Sum_probs=76.1
Q ss_pred hhHHHHHHhhhhCC-ChHHHHHHHHHHHHhHHHHHHHHHhhhcccchhhcCCCCCchHHHHHHHhcCCChhHHHHHHHH
Q 046619 22 DYSQQLIRISKESS-SEAEQQALVSKLTSHYKEYYTVKWALAHEDVLVFYCPVWVSTFEMAYSWVTGWKPSIIFRLVDS 99 (239)
Q Consensus 22 ~~~~eLr~al~~~~-~d~~L~~LV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W~sp~Er~flWiGG~RPS~~l~Llys 99 (239)
|+++|||+|++++. +|.+|+.||+++++||++||++|+.||++|||++|+|+|+||+||||+||||||||++|+||||
T Consensus 1 ~~l~eLr~al~~~~~~~~~L~~lV~~~~~Hy~~y~~~K~~aa~~DV~~~~s~~W~sp~Er~flWiGG~RPS~~~~ll~s 79 (80)
T PF14144_consen 1 RQLNELRAALQSHADSDDELRSLVDKVMSHYDEYYRAKSAAAKADVFHLLSPPWKSPLERCFLWIGGWRPSELFKLLYS 79 (80)
T ss_pred CcHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHhCCCCCCHHHHHHHHHhcCCHHHHHHHHhc
Confidence 57999999999997 8999999999999999999999999999999999999999999999999999999999999986
No 2
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=97.21 E-value=0.0088 Score=45.74 Aligned_cols=85 Identities=25% Similarity=0.269 Sum_probs=68.2
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhhcCCCCChhhHHHHHHHHhHHhHHHHHHHHhH
Q 046619 112 AELTEQQLRKIEELRLKIRLEEEKVEREMERQQVALADRKMVELARLTSRLSNGEVDGLVEVALKGLLSGLEKVMKAADC 191 (239)
Q Consensus 112 ~~Ls~~Ql~~i~~Lq~~~~~~E~aLs~~ma~lQ~slad~~~~~~~~~~~~~~g~~~~~~~~~a~~~~l~~L~~~l~~AD~ 191 (239)
-+||++|..+|..+......+-..+-+.+......+..... ....+ ..++...++.+...-.+...
T Consensus 40 l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~ll~-----------~~~~D---~~~i~a~~~~~~~~~~~l~~ 105 (125)
T PF13801_consen 40 LNLTPEQQAKLRALMDEFRQEMRALRQELRAARQELRALLA-----------APPPD---EAAIEALLEEIREAQAELRQ 105 (125)
T ss_dssp S-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----------CSSS----HHHHHHHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----------CCCCC---HHHHHHHHHHHHHHHHHHHH
Confidence 36999999999999999999999999999999888877653 11222 44555667777888888888
Q ss_pred HHHHHHHhhhhcCChHHHH
Q 046619 192 VRLKTLKGILDVLSTKQSV 210 (239)
Q Consensus 192 LR~~TL~~~~~iLt~~QaA 210 (239)
.|.+++.++..+|||.|=+
T Consensus 106 ~~~~~~~~~~~~LtpeQR~ 124 (125)
T PF13801_consen 106 ERLEHLLEIRAVLTPEQRA 124 (125)
T ss_dssp HHHHHHHHHHHTT-GGGHH
T ss_pred HHHHHHHHHHHcCCHHHhC
Confidence 9999999999999999965
No 3
>COG3678 CpxP P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein [Intracellular trafficking and secretion / Cell motility and secretio / Signal transduction mechanisms / Inorganic ion transport and metabolism]
Probab=96.69 E-value=0.031 Score=47.34 Aligned_cols=87 Identities=20% Similarity=0.243 Sum_probs=61.2
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhhcCCCCChhhHHHHHHHHhHHhHHHHHHHHhHH
Q 046619 113 ELTEQQLRKIEELRLKIRLEEEKVEREMERQQVALADRKMVELARLTSRLSNGEVDGLVEVALKGLLSGLEKVMKAADCV 192 (239)
Q Consensus 113 ~Ls~~Ql~~i~~Lq~~~~~~E~aLs~~ma~lQ~slad~~~~~~~~~~~~~~g~~~~~~~~~a~~~~l~~L~~~l~~AD~L 192 (239)
+||++|..+|.++...-+ .+..+-+..-...+-+.+. .++.+ +.++....+.++..-.+.+.+
T Consensus 57 ~lT~~Qrqqi~~i~~~~~---~a~~~~~~~~r~~l~~li~-----------a~~~D---~aka~a~~~~m~~~~~~~~~~ 119 (160)
T COG3678 57 DLTRAQRQQIRDLMQAQR---RAQREQLRSKRRALHELIA-----------ADQFD---EAKARAQAEKMENQRQALREL 119 (160)
T ss_pred cccHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHh-----------cCCcC---HHHHHHHHHHHHHHHHHHHHH
Confidence 699999999999887766 3333333333333333322 11223 446667888899999999999
Q ss_pred HHHHHHhhhhcCChHHHHHHHHHH
Q 046619 193 RLKTLKGILDVLSTKQSVDFLAGT 216 (239)
Q Consensus 193 R~~TL~~~~~iLt~~QaA~fL~A~ 216 (239)
|.++-.++..||||.|.+.|=--.
T Consensus 120 r~k~~~~m~~vLTPEQr~~l~~~~ 143 (160)
T COG3678 120 RVKSDNQMYQVLTPEQRAKLQELL 143 (160)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHH
Confidence 999999999999999997664433
No 4
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=96.65 E-value=0.11 Score=44.31 Aligned_cols=101 Identities=18% Similarity=0.200 Sum_probs=60.2
Q ss_pred CchHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHhhhHHHHHHHHHhhcCCCCChhhHHHHHHHHhHHhHHH
Q 046619 113 ELTEQQLRKIEELRLKIRLEEEK--------VEREMERQQVALADRKMVELARLTSRLSNGEVDGLVEVALKGLLSGLEK 184 (239)
Q Consensus 113 ~Ls~~Ql~~i~~Lq~~~~~~E~a--------Ls~~ma~lQ~slad~~~~~~~~~~~~~~g~~~~~~~~~a~~~~l~~L~~ 184 (239)
+||++|...|..++...+.+=.+ ....|....+.+.+.+. .+..+ +.++....+.+..
T Consensus 52 ~LTdeQk~qik~i~~~~r~~~k~~~~~~r~~~~~~m~a~~~~~~~Ll~-----------a~~FD---eaavral~~~~~~ 117 (170)
T PRK12750 52 DLTDAQKEQLKEMREANRAEMKAKYSGNREQSHAEMKAHHAKVQALVL-----------ADDFD---EAAANDLAKQMVE 117 (170)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHh-----------cCCCC---HHHHHHHHHHHHH
Confidence 59999999999998877765444 23334434433333332 11223 2222222222222
Q ss_pred HHHHHhHHHHHHHHhhhhcCChHHHHHHHHHHHHHHHHHhhhc
Q 046619 185 VMKAADCVRLKTLKGILDVLSTKQSVDFLAGTSILQIQMSIRG 227 (239)
Q Consensus 185 ~l~~AD~LR~~TL~~~~~iLt~~QaA~fL~A~~e~~~~lr~~g 227 (239)
.-.+.---|.++.++++.||||-|=+.|-.-..+.....++-+
T Consensus 118 ~~~e~~v~~~~~~~~~~~vLTpEQRak~~e~~~~r~~~~~~~~ 160 (170)
T PRK12750 118 KQVERRVKMLEKRHQMLSILTPEQKAKFQELQQERMQECQDKM 160 (170)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 2222223467899999999999999999888666666665554
No 5
>PRK10455 periplasmic protein; Reviewed
Probab=96.07 E-value=0.076 Score=44.89 Aligned_cols=84 Identities=20% Similarity=0.222 Sum_probs=52.5
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhhHHHHHHHHHhhcCCCCChhhHHHHHHHHhHHhHHHHHHHHhH
Q 046619 113 ELTEQQLRKIEELRLKIRLEEEKVE-REMERQQVALADRKMVELARLTSRLSNGEVDGLVEVALKGLLSGLEKVMKAADC 191 (239)
Q Consensus 113 ~Ls~~Ql~~i~~Lq~~~~~~E~aLs-~~ma~lQ~slad~~~~~~~~~~~~~~g~~~~~~~~~a~~~~l~~L~~~l~~AD~ 191 (239)
+||++|...|..|.+..+..-...+ ++...++. .+. .+..+ +.++...++.+...-.+.-.
T Consensus 56 ~LT~~Qrqqir~im~~~r~~~~~~~~~~r~~l~~----li~-----------ad~FD---eaavra~~~k~~~~~~~~~~ 117 (161)
T PRK10455 56 NLTDAQKQQIRDIMKAQRDQMKRPPLEERRAMHD----IIA-----------SDTFD---KAKAEAQITKMEAQRKARML 117 (161)
T ss_pred CCCHHHHHHHHHHHHHHHHhhccccHHHHHHHHH----HHc-----------cCccC---HHHHHHHHHHHHHHHHHHHH
Confidence 5999999999999877666533322 22222221 111 11222 33444445555555555555
Q ss_pred HHHHHHHhhhhcCChHHHHHHHH
Q 046619 192 VRLKTLKGILDVLSTKQSVDFLA 214 (239)
Q Consensus 192 LR~~TL~~~~~iLt~~QaA~fL~ 214 (239)
.|.++-.+|..||||-|-+.|=-
T Consensus 118 ~~~~~~~qiy~vLTPEQr~q~~~ 140 (161)
T PRK10455 118 AHMETQNKIYNVLTPEQKKQFNA 140 (161)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHH
Confidence 78899999999999999998753
No 6
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=95.13 E-value=0.46 Score=40.33 Aligned_cols=95 Identities=14% Similarity=0.151 Sum_probs=58.2
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHhhhHHHHHHHHHhhcCCCCChhhHHHHHHHHhHHhHHHHHHHHhH
Q 046619 113 ELTEQQLRKIEELRLKIRLEEEKV-EREMERQQVALADRKMVELARLTSRLSNGEVDGLVEVALKGLLSGLEKVMKAADC 191 (239)
Q Consensus 113 ~Ls~~Ql~~i~~Lq~~~~~~E~aL-s~~ma~lQ~slad~~~~~~~~~~~~~~g~~~~~~~~~a~~~~l~~L~~~l~~AD~ 191 (239)
+||++|...|-.+....+...... -.+++.++..+. .+..+ +.++...++.+...-..---
T Consensus 56 ~LTd~QR~qmr~im~~~r~~~~~~~~~~~~~m~~Li~---------------Ad~FD---eaAvra~~~kma~~~~e~~v 117 (162)
T PRK12751 56 NLTEQQRQQMRDLMRQSHQSQPRLDLEDREAMHKLIT---------------ADKFD---EAAVRAQAEKMSQNQIERHV 117 (162)
T ss_pred CCCHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHh---------------cCCCC---HHHHHHHHHHHHHHHHHHHH
Confidence 599999999999988877753211 112222222111 12233 33333444444444444444
Q ss_pred HHHHHHHhhhhcCChHHHHHHHHHHHHHHHHHhh
Q 046619 192 VRLKTLKGILDVLSTKQSVDFLAGTSILQIQMSI 225 (239)
Q Consensus 192 LR~~TL~~~~~iLt~~QaA~fL~A~~e~~~~lr~ 225 (239)
-+.++..+++.+|||-|-+.|---.-+-...++.
T Consensus 118 ~~~~~~~qmy~lLTPEQra~l~~~~e~r~~~~~~ 151 (162)
T PRK12751 118 EMAKVRNQMYNLLTPEQKEALNKKHQERIEKLQQ 151 (162)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence 6789999999999999999997766665555554
No 7
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=94.91 E-value=0.24 Score=42.21 Aligned_cols=83 Identities=22% Similarity=0.227 Sum_probs=50.9
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhhhHHHHHHHHHhhcCCCCChhhHHHHHHHHhHHhHHHHHHHHhH
Q 046619 113 ELTEQQLRKIEELRLKIRLEEEKVER-EMERQQVALADRKMVELARLTSRLSNGEVDGLVEVALKGLLSGLEKVMKAADC 191 (239)
Q Consensus 113 ~Ls~~Ql~~i~~Lq~~~~~~E~aLs~-~ma~lQ~slad~~~~~~~~~~~~~~g~~~~~~~~~a~~~~l~~L~~~l~~AD~ 191 (239)
+||++|...|.+|.+.-+.+.+.++. +++.++ +.+. .++.+ +.|+...++.+..-=.+.-=
T Consensus 50 dLTdaQRqQmRdLm~~~r~~~~~~~~~er~amh----~LI~-----------ad~FD---Eaavra~a~kma~~~~e~~V 111 (166)
T PRK10363 50 SLTEHQRQQMRDLMQQARHEQPPVNVSEMETMH----RLVT-----------AENFD---ENAVRAQAEKMAQEQVARQV 111 (166)
T ss_pred CCCHHHHHHHHHHHHHHHhcccccCHHHHHHHH----HHHh-----------cCCCC---HHHHHHHHHHHHHHHHHHHH
Confidence 59999999999999888876554432 222222 1111 12233 33333333433333333333
Q ss_pred HHHHHHHhhhhcCChHHHHHHH
Q 046619 192 VRLKTLKGILDVLSTKQSVDFL 213 (239)
Q Consensus 192 LR~~TL~~~~~iLt~~QaA~fL 213 (239)
-|.++-++|..||||-|-+.|=
T Consensus 112 em~k~~nqmy~lLTPEQKaq~~ 133 (166)
T PRK10363 112 EMAKVRNQMYRLLTPEQQAVLN 133 (166)
T ss_pred HHHHHHHHHHHhCCHHHHHHHH
Confidence 5678999999999999999983
No 8
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=92.10 E-value=0.79 Score=34.09 Aligned_cols=83 Identities=18% Similarity=0.241 Sum_probs=45.0
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHhhhHHHHHHHHHhhcCCCCChhhHHHHHHHHhHHhHHHH
Q 046619 109 GSLAELTEQQLRKIEELRLKIRLEEEKV---EREMERQQVALADRKMVELARLTSRLSNGEVDGLVEVALKGLLSGLEKV 185 (239)
Q Consensus 109 ~~l~~Ls~~Ql~~i~~Lq~~~~~~E~aL---s~~ma~lQ~slad~~~~~~~~~~~~~~g~~~~~~~~~a~~~~l~~L~~~ 185 (239)
..|+ ||++|...+..|....+..-..+ .+.+.++.. + . .+..-..++ ...+.+...
T Consensus 11 ~~L~-LT~eQ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-----~------------~--~~~~~~~~~-~~~~~~~~~ 69 (100)
T PF07813_consen 11 EELN-LTDEQKAKWRAIRQAMKAKMKPLKAMREQLRALRD-----P------------S--FDEAAPEAL-AAMAEMMEL 69 (100)
T ss_dssp TTS---THHHHHHHHHHHHHHCTTS------HHHHHHHHH-----S------------S----HHHHHHH-H--HHCHHH
T ss_pred hhCC-CCHHHHHHHHHHHHHHHHHHHhhcccHHHHHHhcc-----c------------c--CChhHHHHH-HHHHHHHHH
Confidence 3454 99999999999998887776666 222222212 0 0 000001111 111344444
Q ss_pred HHHHhHHHHHHHHhhhhcCChHHHHHH
Q 046619 186 MKAADCVRLKTLKGILDVLSTKQSVDF 212 (239)
Q Consensus 186 l~~AD~LR~~TL~~~~~iLt~~QaA~f 212 (239)
-.+.-..|..+...+..||||-|=+.|
T Consensus 70 ~~~~~~~~~~~~~~~~~vLt~eQk~~~ 96 (100)
T PF07813_consen 70 RAEMMEERAKAQHALYAVLTPEQKEKF 96 (100)
T ss_dssp HHHHHHHHHHHHHHHHTTS-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHH
Confidence 445555678999999999999998776
No 9
>COG4323 Predicted membrane protein [Function unknown]
Probab=71.54 E-value=6 Score=30.62 Aligned_cols=77 Identities=19% Similarity=0.310 Sum_probs=48.9
Q ss_pred CCChHH---HHHHHHHHHHHHHHhhhHHHHHHhhhhCCChHHHHHHHHHHHHhHHHHHHHHHhhhcccchhhcCCCCC--
Q 046619 1 MKNQVE---EKFAEFFEKWVCQLDDYSQQLIRISKESSSEAEQQALVSKLTSHYKEYYTVKWALAHEDVLVFYCPVWV-- 75 (239)
Q Consensus 1 ~~~~~~---~~F~~~Y~~W~~e~~~~~~eLr~al~~~~~d~~L~~LV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W~-- 75 (239)
|+||.+ .+|..||.-.+.||.+-+..=-+..-+ ---|--||.. +++|.|.
T Consensus 1 m~~tda~Rf~SFAeFYPyYl~EH~N~vcRRLH~vGs---~LvlvcL~~~----------------------Vf~~~w~wl 55 (105)
T COG4323 1 MPNTDAARFKSFAEFYPYYLTEHANPVCRRLHVVGS---SLVLVCLVLG----------------------VFRGDWRWL 55 (105)
T ss_pred CCCchHHHhhhHHHhchHHHHhccchhHhhhhhhhh---HHHHHHHHHH----------------------HHhcchHHH
Confidence 778886 577889999999997655432222111 1123333332 2334443
Q ss_pred --chHHH-HHHHhcCC-----ChhHHHHHHHHhhh
Q 046619 76 --STFEM-AYSWVTGW-----KPSIIFRLVDSLRK 102 (239)
Q Consensus 76 --sp~Er-~flWiGG~-----RPS~~l~Llys~~g 102 (239)
.|+-- .|.|+|-| ||..+-.=+||+||
T Consensus 56 lAapv~GYgFAWvGHFvFEKNRPATFkyPvySlMG 90 (105)
T COG4323 56 LAAPVIGYGFAWVGHFVFEKNRPATFKYPVYSLMG 90 (105)
T ss_pred HHhhhhcccceeeeeeeeecCCCccccccHHHhhc
Confidence 23333 79999987 99999999999998
No 10
>PRK11546 zraP zinc resistance protein; Provisional
Probab=58.88 E-value=1.1e+02 Score=25.61 Aligned_cols=74 Identities=14% Similarity=0.129 Sum_probs=44.4
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhhcCCCCChhhHHHHHHHHhHHhHHHHHH
Q 046619 108 GGSLAELTEQQLRKIEELRLKIRLEEEKVEREMERQQVALADRKMVELARLTSRLSNGEVDGLVEVALKGLLSGLEKVMK 187 (239)
Q Consensus 108 ~~~l~~Ls~~Ql~~i~~Lq~~~~~~E~aLs~~ma~lQ~slad~~~~~~~~~~~~~~g~~~~~~~~~a~~~~l~~L~~~l~ 187 (239)
.+-..+||++|...++.|+++-...=..|-+.+-.-+..+-.... ++.++...-.++..++..|..
T Consensus 38 ~~~~~~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnALl~-----------~~~pD~~kI~aL~kEI~~Lr~--- 103 (143)
T PRK11546 38 QQNAAPLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLT-----------ANPPDSSKINAVAKEMENLRQ--- 103 (143)
T ss_pred ccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----------CCCCCHHHHHHHHHHHHHHHH---
Confidence 445668999999999999888777666666666555554444322 223444434444455555554
Q ss_pred HHhHHHHH
Q 046619 188 AADCVRLK 195 (239)
Q Consensus 188 ~AD~LR~~ 195 (239)
+-+.+|.+
T Consensus 104 kL~e~r~~ 111 (143)
T PRK11546 104 SLDELRVK 111 (143)
T ss_pred HHHHHHHH
Confidence 44555553
No 11
>PRK14563 ribosome modulation factor; Provisional
Probab=58.29 E-value=4.4 Score=28.56 Aligned_cols=15 Identities=20% Similarity=0.762 Sum_probs=10.8
Q ss_pred chHHHHHHHhcCCChh
Q 046619 76 STFEMAYSWVTGWKPS 91 (239)
Q Consensus 76 sp~Er~flWiGG~RPS 91 (239)
++--|+ .||||||-.
T Consensus 33 ~~~~r~-~Wl~GWReg 47 (55)
T PRK14563 33 TLDARS-QWLGGWREA 47 (55)
T ss_pred CcHHHH-HHHHHHHHH
Confidence 444455 899999954
No 12
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=43.54 E-value=4.4e+02 Score=28.21 Aligned_cols=132 Identities=16% Similarity=0.165 Sum_probs=77.5
Q ss_pred HHHHHhhhhCCChHHHHHHHHHHHHhHHHHHHHHHhhhcccchhhcCCCCCchHHHHHHHhcCCChhHHHHHHHHhhhcc
Q 046619 25 QQLIRISKESSSEAEQQALVSKLTSHYKEYYTVKWALAHEDVLVFYCPVWVSTFEMAYSWVTGWKPSIIFRLVDSLRKTM 104 (239)
Q Consensus 25 ~eLr~al~~~~~d~~L~~LV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W~sp~Er~flWiGG~RPS~~l~Llys~~gl~ 104 (239)
..|+.||...++|.|+..|.+..-.--++|.+..+.-+.++.-. +-.|.
T Consensus 510 ~aL~eAL~~gAsdeEI~~Lm~eLR~Am~~ym~~LAeq~~~~~~~------------------~~~~~------------- 558 (851)
T TIGR02302 510 DALKDALERGASDEEIKQLTDKLRAAMQTYMRQLAQQLRNNPQQ------------------LARPL------------- 558 (851)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCccc------------------ccccC-------------
Confidence 45777777778999999999999999999999887666554210 11111
Q ss_pred CCCCCCCCCchHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhhcCC-CCChhhHHHHHHHHhH
Q 046619 105 VPGGGSLAELTEQQL----RKIEELRLKIRLEEEKVEREMERQQVALADRKMVELARLTSRLS-NGEVDGLVEVALKGLL 179 (239)
Q Consensus 105 g~~~~~l~~Ls~~Ql----~~i~~Lq~~~~~~E~aLs~~ma~lQ~slad~~~~~~~~~~~~~~-g~~~~~~~~~a~~~~l 179 (239)
.+....+|++.| .+|.+|-++=..+|. -+-|+.+|+.+-..-+ +++. |++..++ ...|+..+
T Consensus 559 ---~~~~~~l~~~dLq~Mmd~ieela~~G~~~~A--~qlL~qlq~mmenlq~-------~q~~~g~~~~~~-~~~~~q~m 625 (851)
T TIGR02302 559 ---DPNTKVLRQQDLQNMMDQIENLARSGDRDQA--KQLLSQLQQMMNNLQM-------GQPGQGQQMGDQ-SGDMEQQM 625 (851)
T ss_pred ---CccccccCHHHHHHHHHHHHHHHHcCCHHHH--HHHHHHHHHHHHHHhc-------cCcCCCcccccc-hHHHHHHH
Confidence 111123555544 445555444333333 4445555555444322 1211 2110011 11345677
Q ss_pred HhHHHHHHHHhHHHHHHHHhh
Q 046619 180 SGLEKVMKAADCVRLKTLKGI 200 (239)
Q Consensus 180 ~~L~~~l~~AD~LR~~TL~~~ 200 (239)
++|..++++=..|+=+|.++.
T Consensus 626 ~~L~e~lr~QQ~L~D~tfr~~ 646 (851)
T TIGR02302 626 NKLGELMRKQQQLRDETFKLD 646 (851)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 888999999999999999875
No 13
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=43.41 E-value=34 Score=28.23 Aligned_cols=39 Identities=33% Similarity=0.567 Sum_probs=30.3
Q ss_pred HHHHhcCCChhHHHHHHHHhhhccCCCCCCCCCchHHHHHHHHHHHHHHH
Q 046619 81 AYSWVTGWKPSIIFRLVDSLRKTMVPGGGSLAELTEQQLRKIEELRLKIR 130 (239)
Q Consensus 81 ~flWiGG~RPS~~l~Llys~~gl~g~~~~~l~~Ls~~Ql~~i~~Lq~~~~ 130 (239)
.+.|+ |.+||.+.++- .....|||+..+..+.+|.....
T Consensus 89 ~l~~~-G~~~~d~~~~~----------~~~~~~Ls~~d~~~l~~ll~~~~ 127 (160)
T cd00223 89 DLRWL-GLRPSDIIRLP----------DLPLLPLSERDLKRAKSLLRRPR 127 (160)
T ss_pred CcEEc-cCCHHHHhhcc----------ccccCCCCHHHHHHHHHHHhccc
Confidence 46676 58899988733 45677999999999999888754
No 14
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=43.31 E-value=24 Score=26.16 Aligned_cols=30 Identities=20% Similarity=0.519 Sum_probs=27.6
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046619 113 ELTEQQLRKIEELRLKIRLEEEKVEREMER 142 (239)
Q Consensus 113 ~Ls~~Ql~~i~~Lq~~~~~~E~aLs~~ma~ 142 (239)
||||+..+.++++++....+.+.+.+.|..
T Consensus 2 ~LSe~E~r~L~eiEr~L~~~DP~fa~~l~~ 31 (82)
T PF11239_consen 2 PLSEHEQRRLEEIERQLRADDPRFAARLRS 31 (82)
T ss_pred CCCHHHHHHHHHHHHHHHhcCcHHHHHhcc
Confidence 699999999999999999999999998886
No 15
>PF11459 DUF2893: Protein of unknwon function (DUF2893); InterPro: IPR021561 This is a bacterial family of uncharacterised proteins.
Probab=41.73 E-value=59 Score=23.86 Aligned_cols=42 Identities=10% Similarity=0.157 Sum_probs=36.5
Q ss_pred HHhHHHHHHHHhHHHHHHHHhhhhcCChHHHHHHHHHHHHHH
Q 046619 179 LSGLEKVMKAADCVRLKTLKGILDVLSTKQSVDFLAGTSILQ 220 (239)
Q Consensus 179 l~~L~~~l~~AD~LR~~TL~~~~~iLt~~QaA~fL~A~~e~~ 220 (239)
++....++.-..+||-+.|+++.+--|-.++.+-++.+++.+
T Consensus 20 ~e~a~~l~egL~nLrp~~lq~LL~~C~svKvkRLfl~lA~~~ 61 (69)
T PF11459_consen 20 FEEADELMEGLRNLRPRVLQELLEHCTSVKVKRLFLYLAERA 61 (69)
T ss_pred HHHHHHHHHHHhhcCHHHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 455566777788899999999999999999999999999865
No 16
>PF11172 DUF2959: Protein of unknown function (DUF2959); InterPro: IPR021342 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=40.25 E-value=88 Score=27.61 Aligned_cols=129 Identities=20% Similarity=0.213 Sum_probs=78.6
Q ss_pred ChHHHHHHHHHHHHhHHHHHHHHH-----hhhcccchhhcCCCCCchHHHHHHHhcCCChhHHHHHHHHhhhccCCCCCC
Q 046619 36 SEAEQQALVSKLTSHYKEYYTVKW-----ALAHEDVLVFYCPVWVSTFEMAYSWVTGWKPSIIFRLVDSLRKTMVPGGGS 110 (239)
Q Consensus 36 ~d~~L~~LV~~~~~Hy~~y~~~K~-----~aA~~DV~~~~s~~W~sp~Er~flWiGG~RPS~~l~Llys~~gl~g~~~~~ 110 (239)
++.+|..--+..-..|+.-=.+-. ..+=+||..-+--.|..-++ .|+ .|+
T Consensus 58 ~ggdLe~~Y~~ln~~ye~s~~~A~~V~~RI~~vE~Va~ALF~EWe~EL~-----------------~Y~--------~~s 112 (201)
T PF11172_consen 58 DGGDLEDKYNALNDEYESSEDAAEEVSDRIDAVEDVADALFDEWEQELD-----------------QYS--------NAS 112 (201)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------HHc--------CHH
Confidence 345676666666666654221111 22346777777777766543 244 777
Q ss_pred CCCchHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH-HHHhhcCCCCChhhHHHHHHHHhHHhHHHH
Q 046619 111 LAELTEQQLR----KIEELRLKIRLEEEKVEREMERQQVALADRKMVEL-ARLTSRLSNGEVDGLVEVALKGLLSGLEKV 185 (239)
Q Consensus 111 l~~Ls~~Ql~----~i~~Lq~~~~~~E~aLs~~ma~lQ~slad~~~~~~-~~~~~~~~g~~~~~~~~~a~~~~l~~L~~~ 185 (239)
|---|++||. +-.+|-...+++|+++..-+..+++.+-=... ++ |+.++.+. |....+...|...+..|+.-
T Consensus 113 LR~~S~~kL~~tr~~Y~~L~~aM~~Ae~km~PVL~~~~D~vL~LKH-NLNA~AI~sL~--~e~~~~~~di~~Li~~m~~s 189 (201)
T PF11172_consen 113 LRRASEQKLAETRRRYAQLIKAMRRAESKMQPVLAAFRDQVLYLKH-NLNAQAIASLQ--GEFSSIESDISQLIKEMERS 189 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHhc-cccHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Confidence 7778888874 45678888888888777766666554321111 11 12222332 34567788888888999999
Q ss_pred HHHHhHH
Q 046619 186 MKAADCV 192 (239)
Q Consensus 186 l~~AD~L 192 (239)
+.+||..
T Consensus 190 I~ead~F 196 (201)
T PF11172_consen 190 IAEADAF 196 (201)
T ss_pred HHHHHHH
Confidence 9999853
No 17
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=40.06 E-value=14 Score=27.39 Aligned_cols=19 Identities=11% Similarity=0.310 Sum_probs=15.4
Q ss_pred CCCCchHHHHHHHhcCCCh
Q 046619 72 PVWVSTFEMAYSWVTGWKP 90 (239)
Q Consensus 72 ~~W~sp~Er~flWiGG~RP 90 (239)
.+.+.-.||+|-||.+||-
T Consensus 44 ~~~Rw~VEr~f~wlk~~Rr 62 (88)
T PF13586_consen 44 YKRRWVVERTFAWLKRFRR 62 (88)
T ss_pred hccceehhhhhHHHHHcCc
Confidence 4455569999999999984
No 18
>COG3130 Rmf Ribosome modulation factor [Translation, ribosomal structure and biogenesis]
Probab=38.68 E-value=11 Score=26.25 Aligned_cols=18 Identities=22% Similarity=0.796 Sum_probs=12.5
Q ss_pred chHHHHHHHhcCCChhHH
Q 046619 76 STFEMAYSWVTGWKPSII 93 (239)
Q Consensus 76 sp~Er~flWiGG~RPS~~ 93 (239)
+.++.--.|+||||--.-
T Consensus 32 q~~~~Rs~WLgGWRea~~ 49 (55)
T COG3130 32 QTLNQRSQWLGGWREAMA 49 (55)
T ss_pred cCchHHHHHHHHHHHHhh
Confidence 344555679999997543
No 19
>PF14644 DUF4456: Domain of unknown function (DUF4456)
Probab=36.65 E-value=50 Score=28.70 Aligned_cols=41 Identities=24% Similarity=0.335 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHhhhhCCChHHHHHHHHH
Q 046619 6 EEKFAEFFEKWVCQLDDYSQQLIRISKESSSEAEQQALVSK 46 (239)
Q Consensus 6 ~~~F~~~Y~~W~~e~~~~~~eLr~al~~~~~d~~L~~LV~~ 46 (239)
...|...+..|...-+.+..+||-.|-.+....+|..|.+.
T Consensus 94 ~~~f~~~~~~~~~~k~~h~~~LrP~LghP~~~~eL~~L~~~ 134 (208)
T PF14644_consen 94 QEEFEQQQKQWEQQKDQHEQQLRPNLGHPDNRQELESLCER 134 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCcCCCCCCHHHHHHHHHH
Confidence 35699999999999999999999999776666778877653
No 20
>PF00589 Phage_integrase: Phage integrase family; InterPro: IPR002104 Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The catalytic site residues in CRE recombinase (P06956 from SWISSPROT) are Arg-173, His-289, Arg-292 and Tyr-324.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration; PDB: 1A0P_A 1Z1G_B 1Z19_A 1AE9_A 1Z1B_A 1P7D_B 2A3V_C 1Q3V_E 1Q3U_A 1OUQ_F ....
Probab=36.35 E-value=17 Score=28.54 Aligned_cols=19 Identities=32% Similarity=0.351 Sum_probs=13.0
Q ss_pred HHHHhcCCChhHHHHHHHH
Q 046619 81 AYSWVTGWKPSIIFRLVDS 99 (239)
Q Consensus 81 ~flWiGG~RPS~~l~Llys 99 (239)
.+++.+|+||++++.|=+.
T Consensus 28 ~l~~~tG~R~~El~~l~~~ 46 (173)
T PF00589_consen 28 LLLLYTGLRPSELLRLRWD 46 (173)
T ss_dssp HHHHHHT--HHHHHT-BGG
T ss_pred HHHHHHccchhhhhhhhhh
Confidence 5788999999999987644
No 21
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=34.52 E-value=77 Score=22.57 Aligned_cols=34 Identities=24% Similarity=0.349 Sum_probs=27.2
Q ss_pred CCCCCCchHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q 046619 108 GGSLAELTEQQL-RKIEELRLKIRLEEEKVEREME 141 (239)
Q Consensus 108 ~~~l~~Ls~~Ql-~~i~~Lq~~~~~~E~aLs~~ma 141 (239)
+.+|++||-..| .+|..|+.++.+.|.++...-+
T Consensus 15 g~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~~K~a 49 (59)
T PF06698_consen 15 GEDLSLLSVEELEERIALLEAEIARLEAAIAKKSA 49 (59)
T ss_pred CCCchhcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567888988776 6889999998888888877654
No 22
>PLN02796 D-glycerate 3-kinase
Probab=33.04 E-value=86 Score=29.81 Aligned_cols=43 Identities=23% Similarity=0.283 Sum_probs=32.9
Q ss_pred HHHHHHHHhhhHHHHHHhhhhCCChHHHHHHHHHHHHhHHHHHHHH
Q 046619 13 FEKWVCQLDDYSQQLIRISKESSSEAEQQALVSKLTSHYKEYYTVK 58 (239)
Q Consensus 13 Y~~W~~e~~~~~~eLr~al~~~~~d~~L~~LV~~~~~Hy~~y~~~K 58 (239)
--+|..+|++.+. ..-...++|+++...|+.+|=-|..||..-
T Consensus 278 v~~WR~qQE~~l~---~~~~~gMsde~v~~FV~~~mP~y~~y~~~l 320 (347)
T PLN02796 278 VYEWRLQAEIAMR---AKGKPGMSDEEVADFVSRYMPAYKAYLPGL 320 (347)
T ss_pred HHHHHHHHHHHHH---HhCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3478888887554 332345899999999999999999998766
No 23
>PF10552 ORF6C: ORF6C domain; InterPro: IPR018878 This entry represents the carboxy-terminal domain from ORF6 (Q9B012 from SWISSPROT), an antirepressor protein from Lactococcus phage bIL285 [].
Probab=32.99 E-value=1.6e+02 Score=23.02 Aligned_cols=21 Identities=24% Similarity=0.782 Sum_probs=17.6
Q ss_pred chHHHHHHHhcCCChhHHHHH
Q 046619 76 STFEMAYSWVTGWKPSIIFRL 96 (239)
Q Consensus 76 sp~Er~flWiGG~RPS~~l~L 96 (239)
.=+|.++-+|-+|+||..+..
T Consensus 93 kdfd~A~~~I~~W~p~~~l~~ 113 (116)
T PF10552_consen 93 KDFDEALEFINNWEPSTALKM 113 (116)
T ss_pred HHHHHHHHHHHHcCCCHHHHH
Confidence 347889999999999987754
No 24
>COG4898 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.12 E-value=48 Score=26.15 Aligned_cols=17 Identities=29% Similarity=0.649 Sum_probs=14.9
Q ss_pred HHHHhcCCChhHHHHHH
Q 046619 81 AYSWVTGWKPSIIFRLV 97 (239)
Q Consensus 81 ~flWiGG~RPS~~l~Ll 97 (239)
-..|+.|+-||.+..-|
T Consensus 34 vi~WLTGY~~~~l~~~l 50 (115)
T COG4898 34 VISWLTGYEVSDLLACL 50 (115)
T ss_pred HHHHHhcCCHHHHHHHH
Confidence 56799999999998877
No 25
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.87 E-value=2.8e+02 Score=22.52 Aligned_cols=94 Identities=11% Similarity=0.135 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHhhhhCCChHHHH-------HHHHHHHHhHHHHHHHHHhhhcccchhhcCCCCCchHH
Q 046619 7 EKFAEFFEKWVCQLDDYSQQLIRISKESSSEAEQQ-------ALVSKLTSHYKEYYTVKWALAHEDVLVFYCPVWVSTFE 79 (239)
Q Consensus 7 ~~F~~~Y~~W~~e~~~~~~eLr~al~~~~~d~~L~-------~LV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W~sp~E 79 (239)
..|..-|.+=+..|.-+-.++|..=..-. -+|.+ ..+..+++-+..|..+-+.-+. ..|.|+-.
T Consensus 10 ~rvrlLYkriLrlHr~lp~~~R~lGD~YV-kdEFrrHk~vnp~~~~~FlteW~~Ya~~l~qql~------~~g~~K~~-- 80 (125)
T KOG4100|consen 10 PRVRLLYKRILRLHRGLPAELRALGDQYV-KDEFRRHKTVNPLEAQGFLTEWERYAVALSQQLS------SAGKWKGE-- 80 (125)
T ss_pred chHHHHHHHHHHHHccCChHHHHHHHHHH-HHHHHHhccCChHHHHHHHHHHHHHHHHHHHHhh------hcCccccc--
Confidence 34555677777766667777765421100 01111 2356778888888877764333 46778765
Q ss_pred HHHHHhcCCChhHHHHHHHHhhhccCCCCCCCCCchHHHHHHHHHHHHHHHH
Q 046619 80 MAYSWVTGWKPSIIFRLVDSLRKTMVPGGGSLAELTEQQLRKIEELRLKIRL 131 (239)
Q Consensus 80 r~flWiGG~RPS~~l~Llys~~gl~g~~~~~l~~Ls~~Ql~~i~~Lq~~~~~ 131 (239)
+|-+=||+. ++.|+++|+..+++|-++++.
T Consensus 81 -----~g~~ld~d~-----------------le~l~deqi~QLyELm~ea~k 110 (125)
T KOG4100|consen 81 -----IGSDLDSDK-----------------LEQLSDEQIGQLYELMKEAQK 110 (125)
T ss_pred -----ccccCCHHH-----------------HHHcCHHHHHHHHHHHHHHHh
Confidence 355556643 457899999999999888876
No 26
>PF04957 RMF: Ribosome modulation factor; InterPro: IPR007040 This entry contains ribosome modulation factors (RMF). They associate with 70s ribosomes and converts them to a dimeric form (100S ribosomes) which appear during the transition from the exponential growth phase to the stationary phase of Escherichia colicells [, ]. It has been proposed that RMF mediates the formation of a 'storage ribosome', the 100S particle, in stationary phase by inactivating excess ribosomes to protect them from degradation and to maintain the required balance between the concentrations of ribosomes and protein synthesis factors in order to maintain translational elongation efficiency [, ]. ; PDB: 2JRM_A 3V24_V 3V22_V.
Probab=31.24 E-value=8.7 Score=27.03 Aligned_cols=13 Identities=23% Similarity=0.831 Sum_probs=9.9
Q ss_pred HHHHHHHhcCCCh
Q 046619 78 FEMAYSWVTGWKP 90 (239)
Q Consensus 78 ~Er~flWiGG~RP 90 (239)
.+-.-.||||||-
T Consensus 34 ~~~r~~Wl~GWre 46 (55)
T PF04957_consen 34 GDARSQWLGGWRE 46 (55)
T ss_dssp CHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHH
Confidence 3447789999984
No 27
>PF13628 DUF4142: Domain of unknown function (DUF4142)
Probab=31.08 E-value=2.2e+02 Score=22.59 Aligned_cols=53 Identities=8% Similarity=0.024 Sum_probs=35.1
Q ss_pred ChHHHHHHHHHHHHHHHHhh-hHHHHHHhhhhCCChHHHHHHHHHHHHhHHHHH
Q 046619 3 NQVEEKFAEFFEKWVCQLDD-YSQQLIRISKESSSEAEQQALVSKLTSHYKEYY 55 (239)
Q Consensus 3 ~~~~~~F~~~Y~~W~~e~~~-~~~eLr~al~~~~~d~~L~~LV~~~~~Hy~~y~ 55 (239)
+.+...|+..|-..+..-++ .+..+.........|.+|+.++.+.+.-...+.
T Consensus 80 ~~~g~~FD~~yl~~~i~~h~~~l~~~~~~~~~~~~~~~lk~~a~~~lp~l~~hl 133 (139)
T PF13628_consen 80 KLSGSAFDRAYLDAQIKAHEKALALFEKQLAASGKDPELKAFAQETLPVLEAHL 133 (139)
T ss_pred cCchhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHhHHHHHHH
Confidence 34568999999888766555 555555524444567888888877765555443
No 28
>PF03371 PRP38: PRP38 family; InterPro: IPR005037 Members of this family are related to the pre mRNA splicing factor PRP38 from yeast [], therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation [].
Probab=30.47 E-value=51 Score=28.13 Aligned_cols=24 Identities=33% Similarity=0.497 Sum_probs=17.9
Q ss_pred ChhHHHHHHHHhhhccCCCCCCCCCchHHHHHH
Q 046619 89 KPSIIFRLVDSLRKTMVPGGGSLAELTEQQLRK 121 (239)
Q Consensus 89 RPS~~l~Llys~~gl~g~~~~~l~~Ls~~Ql~~ 121 (239)
|||.+|=|+|.+. ++. +|.+|+..
T Consensus 62 ~Ps~f~CLL~KLl--------~l~-pt~~~v~~ 85 (172)
T PF03371_consen 62 RPSPFFCLLYKLL--------QLR-PTKEQVKE 85 (172)
T ss_pred CCchHHHHHHHHH--------hcc-cCHHHHHH
Confidence 6999999998753 565 67777655
No 29
>COG4240 Predicted kinase [General function prediction only]
Probab=29.94 E-value=1.6e+02 Score=27.12 Aligned_cols=50 Identities=16% Similarity=0.183 Sum_probs=39.2
Q ss_pred HHHHHHHhhhHHHHHHhhhhCCChHHHHHHHHHHHHhHHHHHHHHHhhhcccc
Q 046619 14 EKWVCQLDDYSQQLIRISKESSSEAEQQALVSKLTSHYKEYYTVKWALAHEDV 66 (239)
Q Consensus 14 ~~W~~e~~~~~~eLr~al~~~~~d~~L~~LV~~~~~Hy~~y~~~K~~aA~~DV 66 (239)
-.|.-+|+ .+|++.+...++|++...-|+..|..|.-|+..-+.-+.-|.
T Consensus 231 y~WRlQqE---hkliAr~~kgmsdeqv~efvn~ymrsl~lylq~ls~~~al~~ 280 (300)
T COG4240 231 YAWRLQQE---HKLIARLAKGMSDEQVSEFVNAYMRSLELYLQRLSEWIALDL 280 (300)
T ss_pred HHHHHHHH---HHHHHHHhccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 36887775 356666777789999999999999999889888876666553
No 30
>PLN03046 D-glycerate 3-kinase; Provisional
Probab=27.96 E-value=99 Score=30.59 Aligned_cols=43 Identities=23% Similarity=0.286 Sum_probs=32.2
Q ss_pred HHHHHHHHhhhHHHHHHhhhhCCChHHHHHHHHHHHHhHHHHHHHH
Q 046619 13 FEKWVCQLDDYSQQLIRISKESSSEAEQQALVSKLTSHYKEYYTVK 58 (239)
Q Consensus 13 Y~~W~~e~~~~~~eLr~al~~~~~d~~L~~LV~~~~~Hy~~y~~~K 58 (239)
--+|..+|++.+. ..-...++|+++..-|+..|-.|+.|+..-
T Consensus 390 Vy~WRlqQE~kLr---~~gg~GMsdeqV~~FV~~YmPaY~~y~~~L 432 (460)
T PLN03046 390 VYQWRLQAEIAMR---ADGKPGMSDEEVMDFVSRYLPAYKAYLPTL 432 (460)
T ss_pred HHHHHHHHHHHHH---HcCCCCCCHHHHHHHHHHhhhHHHHHHHHH
Confidence 3457777776443 322334899999999999999999999876
No 31
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=27.04 E-value=3.1e+02 Score=22.31 Aligned_cols=40 Identities=23% Similarity=0.292 Sum_probs=31.5
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 046619 108 GGSLAELTEQQLRKIEELRLKIRLEEEKVEREMERQQVAL 147 (239)
Q Consensus 108 ~~~l~~Ls~~Ql~~i~~Lq~~~~~~E~aLs~~ma~lQ~sl 147 (239)
.|.++.-.+.|..+|.+|+.+...+|..+-+.+.+-..-+
T Consensus 92 LPg~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll 131 (144)
T PF11221_consen 92 LPGIEVSEEEQLKRIKELEEENEEAEEELQEAVKEAEELL 131 (144)
T ss_dssp STTSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6777767778999999999999999998887776554433
No 32
>smart00533 MUTSd DNA-binding domain of DNA mismatch repair MUTS family.
Probab=26.47 E-value=1.7e+02 Score=25.79 Aligned_cols=65 Identities=17% Similarity=0.075 Sum_probs=44.5
Q ss_pred HHHhhhHHHHHHhhhhCCChHHHHHHHHHHHHhHHHHHHHHHhhhcccchhhcCCCCCchHHHHHHHhcCCChh
Q 046619 18 CQLDDYSQQLIRISKESSSEAEQQALVSKLTSHYKEYYTVKWALAHEDVLVFYCPVWVSTFEMAYSWVTGWKPS 91 (239)
Q Consensus 18 ~e~~~~~~eLr~al~~~~~d~~L~~LV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W~sp~Er~flWiGG~RPS 91 (239)
.+.+..+.++...... ....-++.+++.+.+|+..++..-..++.=|++.-++ ..-.+.+++||.
T Consensus 224 ~~l~~~~~~~~~~~~~-~~~~i~~~l~~~i~~~~~~l~~~~~~i~~lD~l~s~a--------~~a~~~~~~~P~ 288 (308)
T smart00533 224 KELENELLEAKEEIER-LEKEILRELLEKVLEYLEELRALAEALAELDVLLSLA--------TLAAEGNYVRPE 288 (308)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHCCCcCCe
Confidence 3455555555554433 1234588999999999999999998999999875432 222466888887
No 33
>COG4755 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.17 E-value=1.7e+02 Score=24.36 Aligned_cols=25 Identities=28% Similarity=0.340 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHh
Q 046619 6 EEKFAEFFEKWVCQLDDYSQQLIRI 30 (239)
Q Consensus 6 ~~~F~~~Y~~W~~e~~~~~~eLr~a 30 (239)
..+|-.-.++|+..|++++.+|.+.
T Consensus 13 ~~sf~~~Le~WvklQk~~l~~lk~~ 37 (151)
T COG4755 13 LESFMERLEQWVKLQKRQLKELKSH 37 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 4789999999999999999999765
No 34
>PF11897 DUF3417: Protein of unknown function (DUF3417); InterPro: IPR024517 This domain of unknown function is found at the N terminus of members of the glycogen phosphorylase family.
Probab=26.06 E-value=61 Score=25.95 Aligned_cols=46 Identities=22% Similarity=0.307 Sum_probs=33.7
Q ss_pred HHHHHHHHhhhHHHHHHhhhhC----CChHHHHHHHHHHHHhHHHHHHHH
Q 046619 13 FEKWVCQLDDYSQQLIRISKES----SSEAEQQALVSKLTSHYKEYYTVK 58 (239)
Q Consensus 13 Y~~W~~e~~~~~~eLr~al~~~----~~d~~L~~LV~~~~~Hy~~y~~~K 58 (239)
.+.|-+-.++=+.-|+....++ ..|.+....++.+++.|++|...|
T Consensus 41 p~lW~~~~~NPv~~L~~vs~~rL~~la~D~~fl~~~~~v~~~f~~Ym~~~ 90 (118)
T PF11897_consen 41 PELWEESGHNPVRLLQEVSQERLEELAQDPEFLARYDRVYARFEEYMSQK 90 (118)
T ss_pred HHHHHHcCCCHHHHHHHCCHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCC
Confidence 5678774444444555444332 568899999999999999999987
No 35
>PF04918 DltD_M: DltD central region; InterPro: IPR007002 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the central region of DltD.; PDB: 3BMA_C.
Probab=25.78 E-value=29 Score=28.96 Aligned_cols=39 Identities=13% Similarity=0.246 Sum_probs=23.8
Q ss_pred HHhHHHHHHHHHhhhcccchhhcCCCCCchHHHHHHHhcCCChhHHH
Q 046619 48 TSHYKEYYTVKWALAHEDVLVFYCPVWVSTFEMAYSWVTGWKPSIIF 94 (239)
Q Consensus 48 ~~Hy~~y~~~K~~aA~~DV~~~~s~~W~sp~Er~flWiGG~RPS~~l 94 (239)
+.||...=..-..+.+.-|..++||-|.++ +|-.|..+-
T Consensus 9 L~q~~~m~s~~~~lk~KK~V~iiSPQWF~k--------~G~~~~aF~ 47 (163)
T PF04918_consen 9 LIQAFNMGSIGDQLKNKKAVFIISPQWFTK--------KGVDPDAFQ 47 (163)
T ss_dssp HHHHHHHTTSHHHHTT-EEEEE--GGG--T--------T-S-HHHHH
T ss_pred HHHHHHHHhhhccccCCcEEEEECCcccCC--------CCcCHHHHH
Confidence 456666655666778889999999999999 888887543
No 36
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=25.35 E-value=2.3e+02 Score=19.38 Aligned_cols=25 Identities=20% Similarity=0.546 Sum_probs=16.2
Q ss_pred ChHHHHHHHHHHHHHHHHhhhHHHH
Q 046619 3 NQVEEKFAEFFEKWVCQLDDYSQQL 27 (239)
Q Consensus 3 ~~~~~~F~~~Y~~W~~e~~~~~~eL 27 (239)
+.++..|...|..|-....+....|
T Consensus 43 G~a~~af~~~~~~~~~~~~~~~~~L 67 (86)
T PF06013_consen 43 GEAADAFQDKFEEWNQAFRQLNEAL 67 (86)
T ss_dssp SSTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455677777777777666655555
No 37
>PF03232 COQ7: Ubiquinone biosynthesis protein COQ7; InterPro: IPR011566 Coq7 (also known as Clk-1) is a di-iron carboxylate protein occuring in both prokaryotes and eukaryotes that is essential for ubiquinone biosynthesis [, ]. It has been implicated in the aging process as mutations in the Caenorhabditis elegans gene lead to increased lifespan []. Coq7 is a membrane-bound protein that functions as a monooxygenase to hydroxylate demethoxyubiquinone (2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone) in the penultimate step of ubiquinone biosynthesis []. Biochemical studies indicate that NADH can serve directly as a reductant for catalytic activation of dioxygen and substrate oxidation by the enzyme, with no requirement for an additional reductase protein component []. This direct reaction with NADH is so far unique amongst members of the di-iron carboxylate protein family. This entry is specific for the bacterial Coq7 proteins.; GO: 0006744 ubiquinone biosynthetic process, 0055114 oxidation-reduction process
Probab=24.98 E-value=2.1e+02 Score=24.39 Aligned_cols=44 Identities=14% Similarity=0.210 Sum_probs=33.8
Q ss_pred hHHHHHHHHHHHHHHHH-hhhHHHHHHhhhhCCChHHHHHHHHHHHH
Q 046619 4 QVEEKFAEFFEKWVCQL-DDYSQQLIRISKESSSEAEQQALVSKLTS 49 (239)
Q Consensus 4 ~~~~~F~~~Y~~W~~e~-~~~~~eLr~al~~~~~d~~L~~LV~~~~~ 49 (239)
..+..|...-+.++.+| +.|+.+|...- ...|.+|+..|.++..
T Consensus 87 ~~~~a~t~avE~~V~~Hy~~Ql~~L~~~~--~~~d~~l~~~i~~~r~ 131 (172)
T PF03232_consen 87 KAAMACTAAVETVVEEHYNDQLRELPAMG--EEEDPELRAIIEQFRD 131 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcc--ccchHHHHHHHHHHHH
Confidence 34678899999999998 77999987533 2357788888888765
No 38
>PF04678 DUF607: Protein of unknown function, DUF607; InterPro: IPR006769 This entry represents the C-terminal domain of coiled-coil domain containing protein 109.
Probab=24.46 E-value=3e+02 Score=23.29 Aligned_cols=53 Identities=17% Similarity=0.278 Sum_probs=34.1
Q ss_pred ChhHHHHHHHHhhhccCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 046619 89 KPSIIFRLVDSLRKTMVPGGGSLAELTEQQLRKIEELRLKIRLEEEKVEREMERQQVALADR 150 (239)
Q Consensus 89 RPS~~l~Llys~~gl~g~~~~~l~~Ls~~Ql~~i~~Lq~~~~~~E~aLs~~ma~lQ~slad~ 150 (239)
||+.+..++... .+ ..+..+.|..+...|+......+.+| +.|++.+..+...
T Consensus 34 ~P~~v~~~v~~~-------~~-~~~~~~~~~~~~~~l~~~l~~~~~el-~~le~~k~~id~~ 86 (180)
T PF04678_consen 34 RPKQVKEAVHRL-------LP-LLNVEEYQNSRERQLRKRLEELRQEL-APLEKIKQEIDEK 86 (180)
T ss_pred CHHHHHHHHHHH-------hc-cccchhhhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 488877777553 22 23456667777788888887777777 5555555555443
No 39
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=24.21 E-value=2.5e+02 Score=24.29 Aligned_cols=60 Identities=23% Similarity=0.381 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhhhHHHHHHhhhhC--------C-C-hHHHHHHHHHHHHhHHHHHHHHHhhh----cccchhhc
Q 046619 11 EFFEKWVCQLDDYSQQLIRISKES--------S-S-EAEQQALVSKLTSHYKEYYTVKWALA----HEDVLVFY 70 (239)
Q Consensus 11 ~~Y~~W~~e~~~~~~eLr~al~~~--------~-~-d~~L~~LV~~~~~Hy~~y~~~K~~aA----~~DV~~~~ 70 (239)
-|+++|-.+-.....-|+.++..- . + -.+....+...+.+|..||+.-..+. ..+||.++
T Consensus 97 ~f~ek~~ReId~t~e~l~k~~~e~~~~~~~~~~~~~~ke~~~~l~~~l~~~~~~~~ll~~l~e~~~~~ev~k~l 170 (177)
T COG1510 97 LFEEKWKREIDPTKEALKKLLEELNEDLDDRDLTERIKEIKSKLERLLKWSEDYYELLTRLLEFLESEEVFKYL 170 (177)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 488999999999888888887431 1 1 13456778888999999998876433 55677665
No 40
>cd01189 INT_phiLC3_C phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus phage phiLC3, TPW22, Tuc2009, BK5-T, A2, bIL285, bIL286, bIL311, ul36 and phi g1e; Staphylococcus aureus phage phi13 and phi42; Oenococcus oeni phage fOg44; Streptococcus thermophilus phage O1205 and Sfi21; and Streptococcus pyogenes phage T12 and T270.
Probab=23.28 E-value=1.2e+02 Score=24.10 Aligned_cols=18 Identities=17% Similarity=-0.042 Sum_probs=14.8
Q ss_pred HHHHhcCCChhHHHHHHH
Q 046619 81 AYSWVTGWKPSIIFRLVD 98 (239)
Q Consensus 81 ~flWiGG~RPS~~l~Lly 98 (239)
.+++.+|.||++++.|-.
T Consensus 28 ~l~~~~G~R~~Ei~~l~~ 45 (191)
T cd01189 28 LLLAYTGLRIGEALALTW 45 (191)
T ss_pred HHHHHhccHHHHHhhcee
Confidence 467779999999998753
No 41
>PRK15366 type III secretion system chaperone SsaE; Provisional
Probab=22.77 E-value=1.6e+02 Score=22.26 Aligned_cols=26 Identities=19% Similarity=0.069 Sum_probs=22.7
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHHH
Q 046619 112 AELTEQQLRKIEELRLKIRLEEEKVE 137 (239)
Q Consensus 112 ~~Ls~~Ql~~i~~Lq~~~~~~E~aLs 137 (239)
.|=|++|-..+.-|..++.++|+-|.
T Consensus 38 ~P~sp~qYqq~t~l~ea~lqA~~IIn 63 (80)
T PRK15366 38 KLQDPQQYQQNTLLLEAIEQAENIIN 63 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999999775
No 42
>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family include the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many intergrase/recombinases also have N-terminal domains, which show little sequence or structure similarity.
Probab=22.55 E-value=56 Score=24.58 Aligned_cols=19 Identities=26% Similarity=0.123 Sum_probs=16.3
Q ss_pred HHHHhcCCChhHHHHHHHH
Q 046619 81 AYSWVTGWKPSIIFRLVDS 99 (239)
Q Consensus 81 ~flWiGG~RPS~~l~Llys 99 (239)
.++..+|.||+++.++-+.
T Consensus 22 ~l~~~~G~R~~ei~~l~~~ 40 (162)
T cd01182 22 LLLLYTGLRVSELLALRWS 40 (162)
T ss_pred HHHHHhCCCHHHHhhhehh
Confidence 6778899999999998863
No 43
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=22.35 E-value=2e+02 Score=19.90 Aligned_cols=46 Identities=22% Similarity=0.137 Sum_probs=32.6
Q ss_pred HHHhhhHHHHHHhhhhCCChHHHHHHHHHHHHhHHHHHHHHHhhhcccchhhcCCCC
Q 046619 18 CQLDDYSQQLIRISKESSSEAEQQALVSKLTSHYKEYYTVKWALAHEDVLVFYCPVW 74 (239)
Q Consensus 18 ~e~~~~~~eLr~al~~~~~d~~L~~LV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W 74 (239)
+.+++.+..||..+.-. |.-|.++..-+..|++.. +..|. +++|.|
T Consensus 2 ~~~~~~veqLr~el~~~------RikvS~a~~~l~~y~e~~---~~~Dp--ll~g~~ 47 (57)
T cd00068 2 DQLKKEVEQLRKELSRE------RLKVSKAAAELLKYCEQN---AENDP--LLTGPP 47 (57)
T ss_pred HHHHHHHHHHHHHHCCc------hhhHHHHHHHHHHHHHhc---CCCCC--CCCCCC
Confidence 35677888898887542 556777777788888766 67785 457777
No 44
>PF09236 AHSP: Alpha-haemoglobin stabilising protein; InterPro: IPR015317 Alpha-haemoglobin stabilising protein (AHSP) acts a molecular chaperone for free alpha-haemoglobin, preventing the harmful aggregation of alpha-haemoglobin during normal erythroid cell development: it specifically protects free alpha-haemoglobin from precipitation. AHSP adopts a helical secondary structure consisting of an elongated antiparallel three alpha-helix bundle []. ; GO: 0030492 hemoglobin binding, 0006457 protein folding, 0020027 hemoglobin metabolic process, 0030097 hemopoiesis, 0050821 protein stabilization; PDB: 1Y01_A 1XZY_A 3OVU_A 1W0A_A 3IA3_C 1Z8U_A 1W0B_A 1W09_A.
Probab=21.95 E-value=2.1e+02 Score=22.01 Aligned_cols=24 Identities=25% Similarity=0.430 Sum_probs=21.7
Q ss_pred CChHHHHHHHHHHHHhHHHHHHHH
Q 046619 35 SSEAEQQALVSKLTSHYKEYYTVK 58 (239)
Q Consensus 35 ~~d~~L~~LV~~~~~Hy~~y~~~K 58 (239)
.+++.+..+|+.-++-|-+||+.+
T Consensus 28 i~ee~MvtvV~DwvnfYINYy~~~ 51 (89)
T PF09236_consen 28 ISEEAMVTVVNDWVNFYINYYKKQ 51 (89)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHTT
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 578899999999999999999988
No 45
>PRK15354 type III secretion system protein SsaK; Provisional
Probab=21.75 E-value=4.1e+02 Score=23.82 Aligned_cols=45 Identities=18% Similarity=0.166 Sum_probs=34.7
Q ss_pred HhHHhHHHHHHHHhHHHHHHHHhh-hhcCChHHHHHHHHHHHHHHHHH
Q 046619 177 GLLSGLEKVMKAADCVRLKTLKGI-LDVLSTKQSVDFLAGTSILQIQM 223 (239)
Q Consensus 177 ~~l~~L~~~l~~AD~LR~~TL~~~-~~iLt~~QaA~fL~A~~e~~~~l 223 (239)
.+-.-+...-.+||+||.+|+.++ .++| .|=+.+|++..++...|
T Consensus 64 ~~~~ll~qaqqqad~L~~~~~~~~E~~~L--~qHV~wLve~e~lE~sL 109 (224)
T PRK15354 64 YQREQKVEQQQELACLRKNTLEKMEVEWL--EQHVKHLQEDENQFRSL 109 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhHHHHHHH
Confidence 444456677789999999999998 6776 46688888888877655
No 46
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=20.98 E-value=6.5e+02 Score=23.08 Aligned_cols=28 Identities=18% Similarity=0.366 Sum_probs=14.1
Q ss_pred HHHHHHhHHhHHHHHHHHhHHHHHHHHhh
Q 046619 172 EVALKGLLSGLEKVMKAADCVRLKTLKGI 200 (239)
Q Consensus 172 ~~a~~~~l~~L~~~l~~AD~LR~~TL~~~ 200 (239)
+.+++.|++.-..=+.++. =|++||+.+
T Consensus 192 e~~Le~KIekkk~ELER~q-KRL~sLq~v 219 (267)
T PF10234_consen 192 EANLEAKIEKKKQELERNQ-KRLQSLQSV 219 (267)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHhc
Confidence 3344445544444444443 267777764
No 47
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=20.69 E-value=2.5e+02 Score=19.72 Aligned_cols=27 Identities=26% Similarity=0.364 Sum_probs=19.0
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 046619 114 LTEQQLRKIEELRLKIRLEEEKVEREMERQQVALADRK 151 (239)
Q Consensus 114 Ls~~Ql~~i~~Lq~~~~~~E~aLs~~ma~lQ~slad~~ 151 (239)
||++|...|.+|.. .|-+++..+.|.-
T Consensus 1 lT~~Qk~el~~l~~-----------qm~e~kK~~idk~ 27 (59)
T PF10925_consen 1 LTDQQKKELKALYK-----------QMLELKKQIIDKY 27 (59)
T ss_pred CCHHHHHHHHHHHH-----------HHHHHHHHHHHHH
Confidence 78999888877654 4556666666654
Done!