Query 047612
Match_columns 238
No_of_seqs 113 out of 225
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 12:54:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047612.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047612hhsearch_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 8.9E-36 1.9E-40 223.7 8.7 80 31-111 1-80 (80)
2 PF13801 Metal_resist: Heavy-m 97.2 0.0091 2E-07 45.6 11.7 87 111-211 38-124 (125)
3 COG3678 CpxP P pilus assembly/ 96.6 0.035 7.6E-07 47.0 11.1 107 94-219 39-145 (160)
4 PRK12750 cpxP periplasmic repr 96.4 0.18 3.9E-06 43.0 14.4 104 110-228 49-160 (170)
5 PRK10455 periplasmic protein; 96.2 0.067 1.5E-06 45.2 10.7 109 93-227 37-149 (161)
6 PRK12751 cpxP periplasmic stre 95.4 0.34 7.3E-06 41.1 11.6 98 111-227 54-152 (162)
7 PRK10363 cpxP periplasmic repr 95.0 0.16 3.5E-06 43.2 8.5 97 111-226 48-145 (166)
8 PF07813 LTXXQ: LTXXQ motif fa 93.0 0.61 1.3E-05 34.7 7.4 81 110-213 11-96 (100)
9 cd00223 TOPRIM_TopoIIB_SPO TOP 54.3 18 0.00039 29.8 3.8 52 92-144 89-141 (160)
10 PRK14563 ribosome modulation f 53.0 6.3 0.00014 27.7 0.7 15 87-102 33-47 (55)
11 PF07889 DUF1664: Protein of u 51.7 62 0.0014 26.4 6.4 23 92-114 21-43 (126)
12 PF11459 DUF2893: Protein of u 45.0 56 0.0012 24.0 4.7 41 181-221 21-61 (69)
13 PF13586 DDE_Tnp_1_2: Transpos 40.7 13 0.00028 27.5 0.8 19 83-101 44-62 (88)
14 PF14644 DUF4456: Domain of un 40.2 35 0.00076 29.7 3.6 40 16-57 95-134 (208)
15 PF06698 DUF1192: Protein of u 39.9 61 0.0013 23.0 4.1 37 106-142 12-49 (59)
16 PF11239 DUF3040: Protein of u 38.0 31 0.00067 25.5 2.5 30 114-143 2-31 (82)
17 COG3130 Rmf Ribosome modulatio 37.6 12 0.00025 26.0 0.2 17 87-103 32-48 (55)
18 PF05227 CHASE3: CHASE3 domain 37.4 1.8E+02 0.0039 22.2 7.0 50 13-67 35-84 (138)
19 PF00589 Phage_integrase: Phag 35.9 20 0.00043 28.1 1.3 20 92-111 28-47 (173)
20 PF12355 Dscam_C: Down syndrom 34.0 17 0.00036 29.2 0.5 17 3-20 66-82 (124)
21 PF10552 ORF6C: ORF6C domain; 33.0 1.2E+02 0.0025 23.8 5.2 20 88-107 94-113 (116)
22 COG1510 Predicted transcriptio 32.1 2.3E+02 0.0049 24.6 7.1 62 20-81 97-170 (177)
23 PF04957 RMF: Ribosome modulat 31.7 9.8 0.00021 26.8 -1.0 13 89-101 34-46 (55)
24 TIGR02889 spore_YpeB germinati 29.7 5.4E+02 0.012 25.2 11.7 118 19-150 34-153 (435)
25 PF10234 Cluap1: Clusterin-ass 27.2 4.3E+02 0.0094 24.2 8.5 28 123-150 160-187 (267)
26 smart00533 MUTSd DNA-binding d 27.0 1.9E+02 0.0042 25.4 6.2 67 26-103 223-289 (308)
27 PLN02796 D-glycerate 3-kinase 26.8 1.4E+02 0.003 28.4 5.4 43 22-69 278-320 (347)
28 PF05531 NPV_P10: Nucleopolyhe 26.0 2.8E+02 0.0061 20.7 7.5 61 128-207 7-67 (75)
29 PF03735 ENT: ENT domain; Int 25.8 1.2E+02 0.0027 22.3 3.9 31 27-61 28-58 (73)
30 PRK15354 type III secretion sy 25.7 3.4E+02 0.0073 24.3 7.2 50 173-224 59-109 (224)
31 KOG4100 Uncharacterized conser 25.1 2.2E+02 0.0047 23.1 5.4 93 17-132 11-110 (125)
32 COG3407 MVD1 Mevalonate pyroph 24.0 1.9E+02 0.004 27.4 5.7 45 19-69 203-247 (329)
33 PLN03217 transcription factor 23.5 2.1E+02 0.0045 22.1 4.8 35 117-152 48-82 (93)
34 TIGR01062 parC_Gneg DNA topois 23.5 5.2E+02 0.011 27.1 9.2 91 50-152 338-444 (735)
35 cd01182 INT_REC_C DNA breaking 23.3 54 0.0012 24.7 1.7 22 92-113 22-43 (162)
36 COG4710 Predicted DNA-binding 23.1 3.3E+02 0.0071 20.4 6.1 24 172-195 35-58 (80)
37 PF04918 DltD_M: DltD central 22.8 35 0.00076 28.5 0.6 39 59-105 9-47 (163)
38 cd01189 INT_phiLC3_C phiLC3 ph 22.4 1.2E+02 0.0025 24.1 3.6 21 92-112 28-48 (191)
39 KOG3759 Uncharacterized RUN do 21.8 1.8E+02 0.0038 29.2 5.1 66 25-96 178-246 (621)
40 PHA03395 p10 fibrous body prot 21.7 3.8E+02 0.0082 20.6 7.2 61 128-207 7-67 (87)
41 CHL00132 psaF photosystem I su 21.7 2.9E+02 0.0063 24.0 5.9 79 13-99 33-120 (185)
42 PRK15366 type III secretion sy 21.5 1.7E+02 0.0037 22.1 3.9 27 113-139 38-64 (80)
43 TIGR01834 PHA_synth_III_E poly 21.3 7E+02 0.015 23.5 10.0 127 15-145 155-316 (320)
44 KOG2202 U2 snRNP splicing fact 21.2 1.4E+02 0.0031 27.2 4.2 61 16-87 76-136 (260)
45 COG4755 Uncharacterized protei 21.2 2.3E+02 0.005 23.5 5.0 27 14-40 12-38 (151)
46 PRK06975 bifunctional uroporph 20.3 9.4E+02 0.02 24.6 10.9 50 173-224 380-429 (656)
47 PLN00060 meiotic recombination 20.3 1.8E+02 0.0038 28.1 4.8 66 80-147 283-353 (384)
No 1
>PF14144 DOG1: Seed dormancy control
Probab=100.00 E-value=8.9e-36 Score=223.74 Aligned_cols=80 Identities=38% Similarity=0.850 Sum_probs=74.5
Q ss_pred hHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHHHHHhhhhhchhhhcCCCCCChhHHHHHHhhCCChhhHHHhhhc
Q 047612 31 HLLDELISAQENHHQSRDEDLKELVKRVLAHYQQYYQEKSKVAQHNVFLLFAPTWFTPFEQTFFWIAGFNPTLAFRVVNE 110 (238)
Q Consensus 31 ~~l~eLr~al~~~~~~~d~eL~~LV~~~l~Hy~~y~~~K~~aA~~DV~~~~s~~W~tp~Er~flWiGG~RPS~~l~Ll~~ 110 (238)
+++.|||++++ ++..+|.+|+.||++|++||++||++|+.||++|||++|+|+|+||+||||+||||||||++|+||.+
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 RQLNELRAALQ-SHADSDDELRSLVDKVMSHYDEYYRAKSAAAKADVFHLLSPPWKSPLERCFLWIGGWRPSELFKLLYS 79 (80)
T ss_pred CcHHHHHHHHH-hcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHhCCCCCCHHHHHHHHHhcCCHHHHHHHHhc
Confidence 57899999997 33348999999999999999999999999999999999999999999999999999999999999965
Q ss_pred c
Q 047612 111 S 111 (238)
Q Consensus 111 ~ 111 (238)
+
T Consensus 80 ~ 80 (80)
T PF14144_consen 80 Q 80 (80)
T ss_pred C
Confidence 3
No 2
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=97.22 E-value=0.0091 Score=45.62 Aligned_cols=87 Identities=20% Similarity=0.195 Sum_probs=70.6
Q ss_pred cCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhchhhHHHHHhhhCCCCccchhhhHHHHHHHHHHHHHHHHHHH
Q 047612 111 SVKDLADEQRQRMDSLSVETRVEEKLLNDELARIQESVAGPTIMELARRRGRLGEWEMTEGVEVTESNLRASLESLVANA 190 (238)
Q Consensus 111 ~l~~Lt~~Ql~~i~~Lq~~t~~~E~aLs~~ma~lQ~slad~~~~~~~~~~g~~g~~~~~~~~~~am~~kl~~L~~~l~qA 190 (238)
..-+||++|..+|..+......+-..+-+.+......+...... ... -..+++..++.+...-.+.
T Consensus 38 ~~l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~ll~~------~~~--------D~~~i~a~~~~~~~~~~~l 103 (125)
T PF13801_consen 38 DMLNLTPEQQAKLRALMDEFRQEMRALRQELRAARQELRALLAA------PPP--------DEAAIEALLEEIREAQAEL 103 (125)
T ss_dssp HHS-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------SSS---------HHHHHHHHHHHHHHHHHH
T ss_pred hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC------CCC--------CHHHHHHHHHHHHHHHHHH
Confidence 34569999999999999999999999999999999988877641 111 2456667778888888899
Q ss_pred hHHHHHHHHHHhhcCCHHHHH
Q 047612 191 DMLRTTTTAKVVEILDPLQNV 211 (238)
Q Consensus 191 D~LR~~TL~~~~~iLtp~Qaa 211 (238)
+..|.+++.++..+|||.|=+
T Consensus 104 ~~~~~~~~~~~~~~LtpeQR~ 124 (125)
T PF13801_consen 104 RQERLEHLLEIRAVLTPEQRA 124 (125)
T ss_dssp HHHHHHHHHHHHHTT-GGGHH
T ss_pred HHHHHHHHHHHHHcCCHHHhC
Confidence 999999999999999999965
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=96.62 E-value=0.035 Score=46.96 Aligned_cols=107 Identities=18% Similarity=0.224 Sum_probs=69.9
Q ss_pred HHhhCCChhhHHHhhhccCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhchhhHHHHHhhhCCCCccchhhhHH
Q 047612 94 FWIAGFNPTLAFRVVNESVKDLADEQRQRMDSLSVETRVEEKLLNDELARIQESVAGPTIMELARRRGRLGEWEMTEGVE 173 (238)
Q Consensus 94 lWiGG~RPS~~l~Ll~~~l~~Lt~~Ql~~i~~Lq~~t~~~E~aLs~~ma~lQ~slad~~~~~~~~~~g~~g~~~~~~~~~ 173 (238)
+|.|+|-|=--= ..-+.+ +||++|..+|..+...-+ .+..+-+..-..++-+.+. .+.. -+
T Consensus 39 ~~~g~~~~~~~~-~~~~~l-~lT~~Qrqqi~~i~~~~~---~a~~~~~~~~r~~l~~li~------a~~~--------D~ 99 (160)
T COG3678 39 HHGGQFGPRHQG-GMFKGL-DLTRAQRQQIRDLMQAQR---RAQREQLRSKRRALHELIA------ADQF--------DE 99 (160)
T ss_pred ccCCCCCccccc-cccccc-cccHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHh------cCCc--------CH
Confidence 477766664210 011223 499999999998887766 3333333333344443332 1211 25
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 047612 174 VTESNLRASLESLVANADMLRTTTTAKVVEILDPLQNVKFFTAVAR 219 (238)
Q Consensus 174 ~am~~kl~~L~~~l~qAD~LR~~TL~~~~~iLtp~Qaa~fL~A~~e 219 (238)
.++....+.++..-.+.+.+|.++-.++..||||.|.+.|=--.++
T Consensus 100 aka~a~~~~m~~~~~~~~~~r~k~~~~m~~vLTPEQr~~l~~~~~~ 145 (160)
T COG3678 100 AKARAQAEKMENQRQALRELRVKSDNQMYQVLTPEQRAKLQELLAQ 145 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 5677888999999999999999999999999999999776544433
No 4
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=96.42 E-value=0.18 Score=42.95 Aligned_cols=104 Identities=15% Similarity=0.207 Sum_probs=63.0
Q ss_pred ccCCCCcHHHHHHHHHHhHHHHHHHHH--------HHHHHHHHHHHhchhhHHHHHhhhCCCCccchhhhHHHHHHHHHH
Q 047612 110 ESVKDLADEQRQRMDSLSVETRVEEKL--------LNDELARIQESVAGPTIMELARRRGRLGEWEMTEGVEVTESNLRA 181 (238)
Q Consensus 110 ~~l~~Lt~~Ql~~i~~Lq~~t~~~E~a--------Ls~~ma~lQ~slad~~~~~~~~~~g~~g~~~~~~~~~~am~~kl~ 181 (238)
..|+ ||++|...|..++...+.+=.+ ....|....+.+.+.+. ..+ +. +.++....+
T Consensus 49 ~~L~-LTdeQk~qik~i~~~~r~~~k~~~~~~r~~~~~~m~a~~~~~~~Ll~------a~~-----FD---eaavral~~ 113 (170)
T PRK12750 49 RQLD-LTDAQKEQLKEMREANRAEMKAKYSGNREQSHAEMKAHHAKVQALVL------ADD-----FD---EAAANDLAK 113 (170)
T ss_pred hhCC-CCHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHh------cCC-----CC---HHHHHHHHH
Confidence 3455 9999999999998877764444 33444444444444443 121 11 223322222
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHh
Q 047612 182 SLESLVANADMLRTTTTAKVVEILDPLQNVKFFTAVARLQLRIRRWA 228 (238)
Q Consensus 182 ~L~~~l~qAD~LR~~TL~~~~~iLtp~Qaa~fL~A~~e~~~~lr~lg 228 (238)
.+...-.+.---|.++.++++.||||-|=+.|-.-..+......+-+
T Consensus 114 ~~~~~~~e~~v~~~~~~~~~~~vLTpEQRak~~e~~~~r~~~~~~~~ 160 (170)
T PRK12750 114 QMVEKQVERRVKMLEKRHQMLSILTPEQKAKFQELQQERMQECQDKM 160 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 22222222223467889999999999999999888666665555544
No 5
>PRK10455 periplasmic protein; Reviewed
Probab=96.23 E-value=0.067 Score=45.21 Aligned_cols=109 Identities=16% Similarity=0.239 Sum_probs=65.2
Q ss_pred HHHhh---CCChhhHHHhhhccCCCCcHHHHHHHHHHhHHHHHHHHHHH-HHHHHHHHHhchhhHHHHHhhhCCCCccch
Q 047612 93 FFWIA---GFNPTLAFRVVNESVKDLADEQRQRMDSLSVETRVEEKLLN-DELARIQESVAGPTIMELARRRGRLGEWEM 168 (238)
Q Consensus 93 flWiG---G~RPS~~l~Ll~~~l~~Lt~~Ql~~i~~Lq~~t~~~E~aLs-~~ma~lQ~slad~~~~~~~~~~g~~g~~~~ 168 (238)
.++-| |..+...|+ .|. ||++|...|..|.+..+..-...+ ++...++.- +. .+. +
T Consensus 37 ~~~~~~~~g~~~~~m~~----~L~-LT~~Qrqqir~im~~~r~~~~~~~~~~r~~l~~l----i~------ad~-----F 96 (161)
T PRK10455 37 MMHHKGKFGPHHDMMFK----GLN-LTDAQKQQIRDIMKAQRDQMKRPPLEERRAMHDI----IA------SDT-----F 96 (161)
T ss_pred cccCCCCCCchhhhhhh----hCC-CCHHHHHHHHHHHHHHHHhhccccHHHHHHHHHH----Hc------cCc-----c
Confidence 45544 344444443 455 999999999999777666533322 222333221 11 111 1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHH
Q 047612 169 TEGVEVTESNLRASLESLVANADMLRTTTTAKVVEILDPLQNVKFFTAVARLQLRIRRW 227 (238)
Q Consensus 169 ~~~~~~am~~kl~~L~~~l~qAD~LR~~TL~~~~~iLtp~Qaa~fL~A~~e~~~~lr~l 227 (238)
-+.++...++.+...-.+.-..|.++-.+|..||||-|-+.|=. .+..|+.++
T Consensus 97 ---Deaavra~~~k~~~~~~~~~~~~~~~~~qiy~vLTPEQr~q~~~---~~ekr~~~~ 149 (161)
T PRK10455 97 ---DKAKAEAQITKMEAQRKARMLAHMETQNKIYNVLTPEQKKQFNA---NFEKRLTER 149 (161)
T ss_pred ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH---HHHHHHHhc
Confidence 14445455555655556666688999999999999999998753 334444443
No 6
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=95.42 E-value=0.34 Score=41.10 Aligned_cols=98 Identities=11% Similarity=0.160 Sum_probs=62.1
Q ss_pred cCCCCcHHHHHHHHHHhHHHHHHHHHH-HHHHHHHHHHhchhhHHHHHhhhCCCCccchhhhHHHHHHHHHHHHHHHHHH
Q 047612 111 SVKDLADEQRQRMDSLSVETRVEEKLL-NDELARIQESVAGPTIMELARRRGRLGEWEMTEGVEVTESNLRASLESLVAN 189 (238)
Q Consensus 111 ~l~~Lt~~Ql~~i~~Lq~~t~~~E~aL-s~~ma~lQ~slad~~~~~~~~~~g~~g~~~~~~~~~~am~~kl~~L~~~l~q 189 (238)
.+. ||++|...|-.+....+...... -.+++.++.-+...+ + -+.++...++.+...-..
T Consensus 54 ~l~-LTd~QR~qmr~im~~~r~~~~~~~~~~~~~m~~Li~Ad~---------------F---DeaAvra~~~kma~~~~e 114 (162)
T PRK12751 54 GIN-LTEQQRQQMRDLMRQSHQSQPRLDLEDREAMHKLITADK---------------F---DEAAVRAQAEKMSQNQIE 114 (162)
T ss_pred cCC-CCHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhcCC---------------C---CHHHHHHHHHHHHHHHHH
Confidence 444 99999999999888777653111 123333333222211 1 144444445555544444
Q ss_pred HhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHH
Q 047612 190 ADMLRTTTTAKVVEILDPLQNVKFFTAVARLQLRIRRW 227 (238)
Q Consensus 190 AD~LR~~TL~~~~~iLtp~Qaa~fL~A~~e~~~~lr~l 227 (238)
---.+.++..+++.+|||-|-+.|=--.-+-...+|..
T Consensus 115 ~~v~~~~~~~qmy~lLTPEQra~l~~~~e~r~~~~~~~ 152 (162)
T PRK12751 115 RHVEMAKVRNQMYNLLTPEQKEALNKKHQERIEKLQQK 152 (162)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhc
Confidence 44577899999999999999999987777766666654
No 7
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=95.02 E-value=0.16 Score=43.23 Aligned_cols=97 Identities=15% Similarity=0.181 Sum_probs=57.7
Q ss_pred cCCCCcHHHHHHHHHHhHHHHHHHHHHHH-HHHHHHHHhchhhHHHHHhhhCCCCccchhhhHHHHHHHHHHHHHHHHHH
Q 047612 111 SVKDLADEQRQRMDSLSVETRVEEKLLND-ELARIQESVAGPTIMELARRRGRLGEWEMTEGVEVTESNLRASLESLVAN 189 (238)
Q Consensus 111 ~l~~Lt~~Ql~~i~~Lq~~t~~~E~aLs~-~ma~lQ~slad~~~~~~~~~~g~~g~~~~~~~~~~am~~kl~~L~~~l~q 189 (238)
.|. ||++|...|-.|.+.-+.+...++. +++.++ +.+. .+. + -+.++....+.+...=..
T Consensus 48 gLd-LTdaQRqQmRdLm~~~r~~~~~~~~~er~amh----~LI~------ad~-----F---DEaavra~a~kma~~~~e 108 (166)
T PRK10363 48 GIS-LTEHQRQQMRDLMQQARHEQPPVNVSEMETMH----RLVT------AEN-----F---DENAVRAQAEKMAQEQVA 108 (166)
T ss_pred CCC-CCHHHHHHHHHHHHHHHhcccccCHHHHHHHH----HHHh------cCC-----C---CHHHHHHHHHHHHHHHHH
Confidence 344 9999999999999888876554432 333333 1111 111 1 144444444444443333
Q ss_pred HhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHH
Q 047612 190 ADMLRTTTTAKVVEILDPLQNVKFFTAVARLQLRIRR 226 (238)
Q Consensus 190 AD~LR~~TL~~~~~iLtp~Qaa~fL~A~~e~~~~lr~ 226 (238)
.-=-|.++-.+|..||||-|-+.|=--.-+....+|+
T Consensus 109 ~~Vem~k~~nqmy~lLTPEQKaq~~~~~~~rm~~~~~ 145 (166)
T PRK10363 109 RQVEMAKVRNQMYRLLTPEQQAVLNEKHQQRMEQLRD 145 (166)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence 3346778899999999999999994433333333333
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=92.99 E-value=0.61 Score=34.71 Aligned_cols=81 Identities=22% Similarity=0.317 Sum_probs=46.2
Q ss_pred ccCCCCcHHHHHHHHHHhHHHHHHHHHH---HHHHHHHHHHhchhhHHHHHhhhCCCCccchhhhHHHHHHH--HHHHHH
Q 047612 110 ESVKDLADEQRQRMDSLSVETRVEEKLL---NDELARIQESVAGPTIMELARRRGRLGEWEMTEGVEVTESN--LRASLE 184 (238)
Q Consensus 110 ~~l~~Lt~~Ql~~i~~Lq~~t~~~E~aL---s~~ma~lQ~slad~~~~~~~~~~g~~g~~~~~~~~~~am~~--kl~~L~ 184 (238)
..|. ||++|...|..+....+..-..+ .+.+.++.. +.. -..+++. ..+.+.
T Consensus 11 ~~L~-LT~eQ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~--------------~~~--------~~~~~~~~~~~~~~~ 67 (100)
T PF07813_consen 11 EELN-LTDEQKAKWRAIRQAMKAKMKPLKAMREQLRALRD--------------PSF--------DEAAPEALAAMAEMM 67 (100)
T ss_dssp TTS---THHHHHHHHHHHHHHCTTS------HHHHHHHHH--------------SS----------HHHHHHHH--HHCH
T ss_pred hhCC-CCHHHHHHHHHHHHHHHHHHHhhcccHHHHHHhcc--------------ccC--------ChhHHHHHHHHHHHH
Confidence 4555 99999999999998887766666 222222222 000 0111111 114444
Q ss_pred HHHHHHhHHHHHHHHHHhhcCCHHHHHHH
Q 047612 185 SLVANADMLRTTTTAKVVEILDPLQNVKF 213 (238)
Q Consensus 185 ~~l~qAD~LR~~TL~~~~~iLtp~Qaa~f 213 (238)
..-.+.-..|..+...+..||||-|=..|
T Consensus 68 ~~~~~~~~~~~~~~~~~~~vLt~eQk~~~ 96 (100)
T PF07813_consen 68 ELRAEMMEERAKAQHALYAVLTPEQKEKF 96 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHTTS-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHH
Confidence 55555566788999999999999998776
No 9
>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=54.33 E-value=18 Score=29.83 Aligned_cols=52 Identities=23% Similarity=0.378 Sum_probs=36.6
Q ss_pred HHHHhhCCChhhHHHhhhccCCCCcHHHHHHHHHHhHHHHH-HHHHHHHHHHHH
Q 047612 92 TFFWIAGFNPTLAFRVVNESVKDLADEQRQRMDSLSVETRV-EEKLLNDELARI 144 (238)
Q Consensus 92 ~flWiGG~RPS~~l~Ll~~~l~~Lt~~Ql~~i~~Lq~~t~~-~E~aLs~~ma~l 144 (238)
.+.|+ |.+||.+.++-.....|||+..+..+.+|..+..- .++.+..++...
T Consensus 89 ~l~~~-G~~~~d~~~~~~~~~~~Ls~~d~~~l~~ll~~~~~~~~~~~~~el~~m 141 (160)
T cd00223 89 DLRWL-GLRPSDIIRLPDLPLLPLSERDLKRAKSLLRRPRFKELPEWKRELQLM 141 (160)
T ss_pred CcEEc-cCCHHHHhhccccccCCCCHHHHHHHHHHHhccccccCHHHHHHHHHH
Confidence 45666 68899998755677889999999999999887543 233344444333
No 10
>PRK14563 ribosome modulation factor; Provisional
Probab=53.00 E-value=6.3 Score=27.74 Aligned_cols=15 Identities=20% Similarity=0.539 Sum_probs=10.5
Q ss_pred ChhHHHHHHhhCCChh
Q 047612 87 TPFEQTFFWIAGFNPT 102 (238)
Q Consensus 87 tp~Er~flWiGG~RPS 102 (238)
++--|. .||||||=.
T Consensus 33 ~~~~r~-~Wl~GWReg 47 (55)
T PRK14563 33 TLDARS-QWLGGWREA 47 (55)
T ss_pred CcHHHH-HHHHHHHHH
Confidence 444455 899999953
No 11
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=51.66 E-value=62 Score=26.37 Aligned_cols=23 Identities=22% Similarity=0.469 Sum_probs=17.1
Q ss_pred HHHHhhCCChhhHHHhhhccCCC
Q 047612 92 TFFWIAGFNPTLAFRVVNESVKD 114 (238)
Q Consensus 92 ~flWiGG~RPS~~l~Ll~~~l~~ 114 (238)
+++|.=||.=|.+.=+-..+|.+
T Consensus 21 ~Y~wwKGws~sD~M~vTrr~m~~ 43 (126)
T PF07889_consen 21 GYMWWKGWSFSDLMFVTRRSMSD 43 (126)
T ss_pred eeeeecCCchhHHHHHHHHhHHH
Confidence 68999999988877666555544
No 12
>PF11459 DUF2893: Protein of unknwon function (DUF2893); InterPro: IPR021561 This is a bacterial family of uncharacterised proteins.
Probab=45.02 E-value=56 Score=23.98 Aligned_cols=41 Identities=15% Similarity=0.215 Sum_probs=34.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHH
Q 047612 181 ASLESLVANADMLRTTTTAKVVEILDPLQNVKFFTAVARLQ 221 (238)
Q Consensus 181 ~~L~~~l~qAD~LR~~TL~~~~~iLtp~Qaa~fL~A~~e~~ 221 (238)
+....++.-..+||-+.|+++.+--|-.++.+-++.+|+.+
T Consensus 21 e~a~~l~egL~nLrp~~lq~LL~~C~svKvkRLfl~lA~~~ 61 (69)
T PF11459_consen 21 EEADELMEGLRNLRPRVLQELLEHCTSVKVKRLFLYLAERA 61 (69)
T ss_pred HHHHHHHHHHhhcCHHHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 34455666667899999999999999999999999999875
No 13
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=40.66 E-value=13 Score=27.46 Aligned_cols=19 Identities=26% Similarity=0.375 Sum_probs=15.4
Q ss_pred CCCCChhHHHHHHhhCCCh
Q 047612 83 PTWFTPFEQTFFWIAGFNP 101 (238)
Q Consensus 83 ~~W~tp~Er~flWiGG~RP 101 (238)
.+.+.-.||+|-||.+||-
T Consensus 44 ~~~Rw~VEr~f~wlk~~Rr 62 (88)
T PF13586_consen 44 YKRRWVVERTFAWLKRFRR 62 (88)
T ss_pred hccceehhhhhHHHHHcCc
Confidence 3455569999999999984
No 14
>PF14644 DUF4456: Domain of unknown function (DUF4456)
Probab=40.21 E-value=35 Score=29.66 Aligned_cols=40 Identities=20% Similarity=0.402 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHHHhhhHHHHHHHHhhhcCCCChhhHHHHHHH
Q 047612 16 ASFETFFRAWLVRQEHLLDELISAQENHHQSRDEDLKELVKR 57 (238)
Q Consensus 16 ~~F~~~Y~~W~~eq~~~l~eLr~al~~~~~~~d~eL~~LV~~ 57 (238)
..|..++..|...-+.+..+||-.|- ++....+|..|++.
T Consensus 95 ~~f~~~~~~~~~~k~~h~~~LrP~Lg--hP~~~~eL~~L~~~ 134 (208)
T PF14644_consen 95 EEFEQQQKQWEQQKDQHEQQLRPNLG--HPDNRQELESLCER 134 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCcCC--CCCCHHHHHHHHHH
Confidence 56999999999999999999999984 55567888888764
No 15
>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=39.87 E-value=61 Score=23.05 Aligned_cols=37 Identities=22% Similarity=0.222 Sum_probs=30.3
Q ss_pred HhhhccCCCCcHHHH-HHHHHHhHHHHHHHHHHHHHHH
Q 047612 106 RVVNESVKDLADEQR-QRMDSLSVETRVEEKLLNDELA 142 (238)
Q Consensus 106 ~Ll~~~l~~Lt~~Ql-~~i~~Lq~~t~~~E~aLs~~ma 142 (238)
+++..+|++||-..| .+|..|+.++.+.|.++...-+
T Consensus 12 ~~ig~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~~K~a 49 (59)
T PF06698_consen 12 HEIGEDLSLLSVEELEERIALLEAEIARLEAAIAKKSA 49 (59)
T ss_pred cccCCCchhcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566778999998887 5699999999999998887644
No 16
>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=37.99 E-value=31 Score=25.51 Aligned_cols=30 Identities=13% Similarity=0.406 Sum_probs=27.4
Q ss_pred CCcHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 047612 114 DLADEQRQRMDSLSVETRVEEKLLNDELAR 143 (238)
Q Consensus 114 ~Lt~~Ql~~i~~Lq~~t~~~E~aLs~~ma~ 143 (238)
||||+..+.++++++....+...+.+.|..
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 689999999999999999999999988877
No 17
>COG3130 Rmf Ribosome modulation factor [Translation, ribosomal structure and biogenesis]
Probab=37.61 E-value=12 Score=26.03 Aligned_cols=17 Identities=18% Similarity=0.608 Sum_probs=12.1
Q ss_pred ChhHHHHHHhhCCChhh
Q 047612 87 TPFEQTFFWIAGFNPTL 103 (238)
Q Consensus 87 tp~Er~flWiGG~RPS~ 103 (238)
+.++.--.|+||||--.
T Consensus 32 q~~~~Rs~WLgGWRea~ 48 (55)
T COG3130 32 QTLNQRSQWLGGWREAM 48 (55)
T ss_pred cCchHHHHHHHHHHHHh
Confidence 34455567999999654
No 18
>PF05227 CHASE3: CHASE3 domain; InterPro: IPR007891 CHASE3 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are upstream of signal transduction pathways in bacteria. Specifically, CHASE3 domains are found in histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognised by CHASE3 domains are not known at this time [].; PDB: 3VA9_A.
Probab=37.41 E-value=1.8e+02 Score=22.20 Aligned_cols=50 Identities=14% Similarity=0.167 Sum_probs=37.2
Q ss_pred chhhhHHHHHHHHHHHhhhHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHH
Q 047612 13 DNVASFETFFRAWLVRQEHLLDELISAQENHHQSRDEDLKELVKRVLAHYQQYYQ 67 (238)
Q Consensus 13 ~~~~~F~~~Y~~W~~eq~~~l~eLr~al~~~~~~~d~eL~~LV~~~l~Hy~~y~~ 67 (238)
++...|-.-|..........+.+|+..+. .+.+.+..|+.+-.-+..|+.
T Consensus 35 tgd~~~l~~y~~~~~~~~~~l~~L~~l~~-----~~p~q~~~l~~l~~~~~~~~~ 84 (138)
T PF05227_consen 35 TGDPEFLEPYQEARARLEKALAQLRQLVQ-----DNPEQQERLDQLEELIDQWRE 84 (138)
T ss_dssp H--HHHHHHHHHHHHHHHHHHHHHHHHTT-----T-HHHHHHHHHHHHHHHHHHH
T ss_pred cCCHhhhchHHHHHHHHHHHHHHHHHHhc-----CCHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999999998874 345666677777777776664
No 19
>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=35.88 E-value=20 Score=28.12 Aligned_cols=20 Identities=15% Similarity=0.368 Sum_probs=13.4
Q ss_pred HHHHhhCCChhhHHHhhhcc
Q 047612 92 TFFWIAGFNPTLAFRVVNES 111 (238)
Q Consensus 92 ~flWiGG~RPS~~l~Ll~~~ 111 (238)
.+++.+|+||++++.|=..+
T Consensus 28 ~l~~~tG~R~~El~~l~~~~ 47 (173)
T PF00589_consen 28 LLLLYTGLRPSELLRLRWDD 47 (173)
T ss_dssp HHHHHHT--HHHHHT-BGGG
T ss_pred HHHHHHccchhhhhhhhhhh
Confidence 56889999999999876444
No 20
>PF12355 Dscam_C: Down syndrome cell adhesion molecule C terminal ; InterPro: IPR021012 This entry is specific to the insecta, predominantly Drosophila spp. This entry is found in association with PF00047 from PFAM, PF07679 from PFAM and PF00041 from PFAM. The Down syndrome cell adhesion molecule (Dscam) belongs to a family of cell membrane molecules involved in the differentiation of the nervous system. This is the C-terminal cytoplasmic tail region of Dscam. In Drosophila melanogaster (Fruit fly) the gene has at least 59 different transcripts. Dscam may play a role in the nervous and immune systems [].
Probab=34.01 E-value=17 Score=29.25 Aligned_cols=17 Identities=29% Similarity=0.489 Sum_probs=10.3
Q ss_pred CCCCCCCCCCchhhhHHH
Q 047612 3 ENPRARYNNDDNVASFET 20 (238)
Q Consensus 3 ~~~~~~~~~~~~~~~F~~ 20 (238)
|+||||++.+++ .+|.+
T Consensus 66 PpPPPRn~D~~n-sSfND 82 (124)
T PF12355_consen 66 PPPPPRNHDVSN-SSFND 82 (124)
T ss_pred CCcCCCCCCCCC-ccccc
Confidence 556777776643 55543
No 21
>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=33.03 E-value=1.2e+02 Score=23.83 Aligned_cols=20 Identities=20% Similarity=0.635 Sum_probs=17.0
Q ss_pred hhHHHHHHhhCCChhhHHHh
Q 047612 88 PFEQTFFWIAGFNPTLAFRV 107 (238)
Q Consensus 88 p~Er~flWiGG~RPS~~l~L 107 (238)
=+|.++-+|-+|+||..+..
T Consensus 94 dfd~A~~~I~~W~p~~~l~~ 113 (116)
T PF10552_consen 94 DFDEALEFINNWEPSTALKM 113 (116)
T ss_pred HHHHHHHHHHHcCCCHHHHH
Confidence 47889999999999987653
No 22
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=32.14 E-value=2.3e+02 Score=24.56 Aligned_cols=62 Identities=18% Similarity=0.347 Sum_probs=43.0
Q ss_pred HHHHHHHHHhhhHHHHHHHHhhhcCCC-------C-hhhHHHHHHHHHHHHHHHHHHHHhh----hhhchhhhc
Q 047612 20 TFFRAWLVRQEHLLDELISAQENHHQS-------R-DEDLKELVKRVLAHYQQYYQEKSKV----AQHNVFLLF 81 (238)
Q Consensus 20 ~~Y~~W~~eq~~~l~eLr~al~~~~~~-------~-d~eL~~LV~~~l~Hy~~y~~~K~~a----A~~DV~~~~ 81 (238)
-|+++|-.+-.....-|+.++...... + -.+....+...+.+|..||+.-... -..+||.++
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 378899988888888888886411111 1 1346678888999999999976633 255777765
No 23
>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=31.68 E-value=9.8 Score=26.78 Aligned_cols=13 Identities=15% Similarity=0.493 Sum_probs=9.8
Q ss_pred hHHHHHHhhCCCh
Q 047612 89 FEQTFFWIAGFNP 101 (238)
Q Consensus 89 ~Er~flWiGG~RP 101 (238)
.+-.-.||||||=
T Consensus 34 ~~~r~~Wl~GWre 46 (55)
T PF04957_consen 34 GDARSQWLGGWRE 46 (55)
T ss_dssp CHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHH
Confidence 3446789999984
No 24
>TIGR02889 spore_YpeB germination protein YpeB. Members of this family are YpeB, a protein usually encoded with the putative spore-cortex-lytic enzyme SleB and required, together with SleB, for normal germination. This family is retricted to endospore-forming species in the Firmicutes lineage of bacteria, and found in all such species to date except Clostridium perfringens. The matching phenotypes of mutants in SleB (called a lytic transglycosylase) and YpeB suggests that YpeB is necessary to allow SleB to function.
Probab=29.70 E-value=5.4e+02 Score=25.18 Aligned_cols=118 Identities=10% Similarity=0.162 Sum_probs=79.1
Q ss_pred HHHHHHHHHHhhhHHHHHHHHhhhcCCC-ChhhHHHHHHHHHHHHHHHHHHHHhhhhhchhhh-cCCCCCChhHHHHHHh
Q 047612 19 ETFFRAWLVRQEHLLDELISAQENHHQS-RDEDLKELVKRVLAHYQQYYQEKSKVAQHNVFLL-FAPTWFTPFEQTFFWI 96 (238)
Q Consensus 19 ~~~Y~~W~~eq~~~l~eLr~al~~~~~~-~d~eL~~LV~~~l~Hy~~y~~~K~~aA~~DV~~~-~s~~W~tp~Er~flWi 96 (238)
+-.|.+=+.++-.++..|+..+.....+ ++..+. .++.+.++. +.+|++|+-.+ ++.+=.+-.|.++.=|
T Consensus 34 en~YqRaf~dL~~~vd~l~~~L~k~l~~~s~~q~~-------~~l~~vwr~-as~A~~~l~qLPl~~~~~~~T~kFLsqi 105 (435)
T TIGR02889 34 QAQYQRAFYELTYHVEQIEAQLGKTLAMGSQRQNT-------PVLADVWRH-ASAANESLSQLPLTQESLEKTSKFLSQV 105 (435)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHhhhCCHHHHH-------HHHHHHHHH-HHHHHHHHhcCCCCCcchhhHHHHHHHH
Confidence 4456666666666666666665311111 222233 344444443 34577787776 3555567778899999
Q ss_pred hCCChhhHHHhhhccCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhch
Q 047612 97 AGFNPTLAFRVVNESVKDLADEQRQRMDSLSVETRVEEKLLNDELARIQESVAG 150 (238)
Q Consensus 97 GG~RPS~~l~Ll~~~l~~Lt~~Ql~~i~~Lq~~t~~~E~aLs~~ma~lQ~slad 150 (238)
|+|==+...+.+.+. |||+++...|.+|...+.. |.+.|..+|..+..
T Consensus 106 GDfsy~la~~~~~g~--~lt~~e~~tL~~L~~~a~~----l~~~L~~~q~~v~~ 153 (435)
T TIGR02889 106 GDFTYTLSVKDAEGK--SLSDKEYKTLTTLYNQAVK----LENQLRKVQNIVMQ 153 (435)
T ss_pred HHHHHHHHhhhccCC--CCCHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHc
Confidence 999999888888665 8999999999999887754 66777777777744
No 25
>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=27.25 E-value=4.3e+02 Score=24.24 Aligned_cols=28 Identities=11% Similarity=0.259 Sum_probs=12.3
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHhch
Q 047612 123 MDSLSVETRVEEKLLNDELARIQESVAG 150 (238)
Q Consensus 123 i~~Lq~~t~~~E~aLs~~ma~lQ~slad 150 (238)
|+.+++.++.+=.++.++++..++.+..
T Consensus 160 ~~~iE~~l~~ai~~~~~~~~~~~~~l~~ 187 (267)
T PF10234_consen 160 LNEIEKALKEAIKAVQQQLQQTQQQLNN 187 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444444444443
No 26
>smart00533 MUTSd DNA-binding domain of DNA mismatch repair MUTS family.
Probab=27.01 E-value=1.9e+02 Score=25.43 Aligned_cols=67 Identities=24% Similarity=0.183 Sum_probs=48.3
Q ss_pred HHHhhhHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHHHHHhhhhhchhhhcCCCCCChhHHHHHHhhCCChhh
Q 047612 26 LVRQEHLLDELISAQENHHQSRDEDLKELVKRVLAHYQQYYQEKSKVAQHNVFLLFAPTWFTPFEQTFFWIAGFNPTL 103 (238)
Q Consensus 26 ~~eq~~~l~eLr~al~~~~~~~d~eL~~LV~~~l~Hy~~y~~~K~~aA~~DV~~~~s~~W~tp~Er~flWiGG~RPS~ 103 (238)
+.+.+..+.++....... ...-++.+++.+..|+..++..-..++.=|++.-++ ++-.+.+++||.-
T Consensus 223 ~~~l~~~~~~~~~~~~~~---~~~i~~~l~~~i~~~~~~l~~~~~~i~~lD~l~s~a--------~~a~~~~~~~P~i 289 (308)
T smart00533 223 LKELENELLEAKEEIERL---EKEILRELLEKVLEYLEELRALAEALAELDVLLSLA--------TLAAEGNYVRPEF 289 (308)
T ss_pred HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHCCCcCCee
Confidence 456677777776665411 245688999999999999999999999999876443 2224667888873
No 27
>PLN02796 D-glycerate 3-kinase
Probab=26.83 E-value=1.4e+02 Score=28.45 Aligned_cols=43 Identities=19% Similarity=0.412 Sum_probs=31.4
Q ss_pred HHHHHHHhhhHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHHHH
Q 047612 22 FRAWLVRQEHLLDELISAQENHHQSRDEDLKELVKRVLAHYQQYYQEK 69 (238)
Q Consensus 22 Y~~W~~eq~~~l~eLr~al~~~~~~~d~eL~~LV~~~l~Hy~~y~~~K 69 (238)
--+|..+|++.+. +.- ..-++|+++..-|+.+|=-|+.||..-
T Consensus 278 v~~WR~qQE~~l~---~~~--~~gMsde~v~~FV~~~mP~y~~y~~~l 320 (347)
T PLN02796 278 VYEWRLQAEIAMR---AKG--KPGMSDEEVADFVSRYMPAYKAYLPGL 320 (347)
T ss_pred HHHHHHHHHHHHH---HhC--CCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3467777776554 222 234789999999999999999998765
No 28
>PF05531 NPV_P10: Nucleopolyhedrovirus P10 protein; InterPro: IPR008702 This family consists of several nucleopolyhedrovirus P10 proteins which are thought to be involved in the morphogenesis of the polyhedra [].; GO: 0019028 viral capsid
Probab=25.96 E-value=2.8e+02 Score=20.66 Aligned_cols=61 Identities=16% Similarity=0.224 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhchhhHHHHHhhhCCCCccchhhhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCH
Q 047612 128 VETRVEEKLLNDELARIQESVAGPTIMELARRRGRLGEWEMTEGVEVTESNLRASLESLVANADMLRTTTTAKVVEILDP 207 (238)
Q Consensus 128 ~~t~~~E~aLs~~ma~lQ~slad~~~~~~~~~~g~~g~~~~~~~~~~am~~kl~~L~~~l~qAD~LR~~TL~~~~~iLtp 207 (238)
.-+++.-.++++.+..+|+.+.+... ... --..+.+|++++..-+..-+ .++..+.+||+|
T Consensus 7 l~Ir~dIk~vd~KVdaLq~~V~~l~~--------~~~-------~v~~l~~klDa~~~~l~~l~----~~V~~I~~iL~~ 67 (75)
T PF05531_consen 7 LVIRQDIKAVDDKVDALQTQVDDLES--------NLP-------DVTELNKKLDAQSAQLTTLN----TKVNEIQDILNP 67 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh--------cCC-------chHHHHHHHHHHHHHHHHHH----HHHHHHHHHhCC
Confidence 34677778888999999998866442 111 01233345555544443333 377788888885
No 29
>PF03735 ENT: ENT domain; InterPro: IPR005491 This entry represents a protein regulator which is able to repress transcription, possibly via its interaction with a multi protein chromatin re-modeling complex that modifies the chromatin. Its interaction with BRCA2 suggests that it may play a central role in the DNA repair function of BRCA2 []. ; PDB: 1UZ3_B 1UTU_B 2FMM_E.
Probab=25.78 E-value=1.2e+02 Score=22.30 Aligned_cols=31 Identities=29% Similarity=0.424 Sum_probs=23.0
Q ss_pred HHhhhHHHHHHHHhhhcCCCChhhHHHHHHHHHHH
Q 047612 27 VRQEHLLDELISAQENHHQSRDEDLKELVKRVLAH 61 (238)
Q Consensus 27 ~eq~~~l~eLr~al~~~~~~~d~eL~~LV~~~l~H 61 (238)
.++...+.+||..++ +++++.+..+.++.+.
T Consensus 28 weke~lLt~Lr~~L~----IS~e~H~~~l~~~~~D 58 (73)
T PF03735_consen 28 WEKEKLLTELRKELN----ISDEEHREELRRAVSD 58 (73)
T ss_dssp HHHHHHHHHHHHHTT------HHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHhC----CCcHHHHHHHHHHhcc
Confidence 367888999999995 7888888888887653
No 30
>PRK15354 type III secretion system protein SsaK; Provisional
Probab=25.66 E-value=3.4e+02 Score=24.32 Aligned_cols=50 Identities=22% Similarity=0.110 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHH-hhcCCHHHHHHHHHHHHHHHHHH
Q 047612 173 EVTESNLRASLESLVANADMLRTTTTAKV-VEILDPLQNVKFFTAVARLQLRI 224 (238)
Q Consensus 173 ~~am~~kl~~L~~~l~qAD~LR~~TL~~~-~~iLtp~Qaa~fL~A~~e~~~~l 224 (238)
..|-..+-.-+...-.+||+||.+|+.++ .++| .|=+.+|++..++...|
T Consensus 59 q~A~~~~~~ll~qaqqqad~L~~~~~~~~E~~~L--~qHV~wLve~e~lE~sL 109 (224)
T PRK15354 59 RDAYRYQREQKVEQQQELACLRKNTLEKMEVEWL--EQHVKHLQEDENQFRSL 109 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhHHHHHHH
Confidence 33333555567777889999999999999 6776 46788888888876554
No 31
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.08 E-value=2.2e+02 Score=23.12 Aligned_cols=93 Identities=17% Similarity=0.210 Sum_probs=62.2
Q ss_pred hHHHHHHHHHHHhhhHHHHHHHHhhhcCCCChhhHH-------HHHHHHHHHHHHHHHHHHhhhhhchhhhcCCCCCChh
Q 047612 17 SFETFFRAWLVRQEHLLDELISAQENHHQSRDEDLK-------ELVKRVLAHYQQYYQEKSKVAQHNVFLLFAPTWFTPF 89 (238)
Q Consensus 17 ~F~~~Y~~W~~eq~~~l~eLr~al~~~~~~~d~eL~-------~LV~~~l~Hy~~y~~~K~~aA~~DV~~~~s~~W~tp~ 89 (238)
.|-.-|.+=+.-|.-.-.++|+-=- . --.+|.+ .-+..+++-+..|..+-+.-+. ..|.|+-.
T Consensus 11 rvrlLYkriLrlHr~lp~~~R~lGD-~--YVkdEFrrHk~vnp~~~~~FlteW~~Ya~~l~qql~------~~g~~K~~- 80 (125)
T KOG4100|consen 11 RVRLLYKRILRLHRGLPAELRALGD-Q--YVKDEFRRHKTVNPLEAQGFLTEWERYAVALSQQLS------SAGKWKGE- 80 (125)
T ss_pred hHHHHHHHHHHHHccCChHHHHHHH-H--HHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHhh------hcCccccc-
Confidence 4555777777777766677776521 0 0001111 2467888999999888765433 56888865
Q ss_pred HHHHHHhhCCChhhHHHhhhccCCCCcHHHHHHHHHHhHHHHH
Q 047612 90 EQTFFWIAGFNPTLAFRVVNESVKDLADEQRQRMDSLSVETRV 132 (238)
Q Consensus 90 Er~flWiGG~RPS~~l~Ll~~~l~~Lt~~Ql~~i~~Lq~~t~~ 132 (238)
+|-+=||+ .|+.|+++|+-.+++|.++++.
T Consensus 81 ------~g~~ld~d-------~le~l~deqi~QLyELm~ea~k 110 (125)
T KOG4100|consen 81 ------IGSDLDSD-------KLEQLSDEQIGQLYELMKEAQK 110 (125)
T ss_pred ------ccccCCHH-------HHHHcCHHHHHHHHHHHHHHHh
Confidence 46666664 4567899999999999888776
No 32
>COG3407 MVD1 Mevalonate pyrophosphate decarboxylase [Lipid metabolism]
Probab=23.98 E-value=1.9e+02 Score=27.41 Aligned_cols=45 Identities=20% Similarity=0.342 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhhhHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHHHH
Q 047612 19 ETFFRAWLVRQEHLLDELISAQENHHQSRDEDLKELVKRVLAHYQQYYQEK 69 (238)
Q Consensus 19 ~~~Y~~W~~eq~~~l~eLr~al~~~~~~~d~eL~~LV~~~l~Hy~~y~~~K 69 (238)
..||..|++....++.+.+.+.+ +.+...+.+..+.+..++...-
T Consensus 203 S~~y~~w~~~~~~~~~~m~~~~~------~~Df~~i~~~~e~dsl~mHA~l 247 (329)
T COG3407 203 SPFYDAWLEHSEEDLEEMKEAIR------EKDFEKIGELAENDSLEMHATL 247 (329)
T ss_pred ChHHHHHHHHHHHhHHHHHHHHh------ccCHHHHHHHHHhhHHHHHHHH
Confidence 45999999999999999999985 3457778888888888877643
No 33
>PLN03217 transcription factor ATBS1; Provisional
Probab=23.48 E-value=2.1e+02 Score=22.08 Aligned_cols=35 Identities=11% Similarity=0.060 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhchhh
Q 047612 117 DEQRQRMDSLSVETRVEEKLLNDELARIQESVAGPT 152 (238)
Q Consensus 117 ~~Ql~~i~~Lq~~t~~~E~aLs~~ma~lQ~slad~~ 152 (238)
..=|..-|+--++..++.|.|++++++|-.+ .+.+
T Consensus 48 skvLqEtC~YIrsLhrEvDdLSerLs~LL~t-~~s~ 82 (93)
T PLN03217 48 ARVLQDTCNYIRNLHREVDDLSERLSELLAN-SDTA 82 (93)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cCCc
Confidence 3445788999999999999999999999987 4433
No 34
>TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit, proteobacterial. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason.
Probab=23.46 E-value=5.2e+02 Score=27.14 Aligned_cols=91 Identities=15% Similarity=0.183 Sum_probs=59.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhhhchhhhcCCCCCChhHHHHHHhhCCC-----hhhHHHhhhccCCC---------C
Q 047612 50 DLKELVKRVLAHYQQYYQEKSKVAQHNVFLLFAPTWFTPFEQTFFWIAGFN-----PTLAFRVVNESVKD---------L 115 (238)
Q Consensus 50 eL~~LV~~~l~Hy~~y~~~K~~aA~~DV~~~~s~~W~tp~Er~flWiGG~R-----PS~~l~Ll~~~l~~---------L 115 (238)
.|+.+++..+.|=.++|..+....-.. +|.-+..+.|+- =-++++++..+-+| |
T Consensus 338 ~l~~il~~~~~~R~~~~~rR~~~~l~k------------~~~rl~il~Gl~ia~~~iDevI~iIR~s~~~k~~L~~~f~l 405 (735)
T TIGR01062 338 NLLEILQEWLVFRRNTVIRRLTYRLNK------------VLQRLHILEGLRIAFLNIDEVIEIIREEDEPKTILMERFKL 405 (735)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHhHHHHHHHHHcChhhHHHHHHhcCC
Confidence 488888889999888888776432111 223333344432 14456666554333 9
Q ss_pred cHHHHHHHHH--HhHHHHHHHHHHHHHHHHHHHHhchhh
Q 047612 116 ADEQRQRMDS--LSVETRVEEKLLNDELARIQESVAGPT 152 (238)
Q Consensus 116 t~~Ql~~i~~--Lq~~t~~~E~aLs~~ma~lQ~slad~~ 152 (238)
|+.|...|=+ |++=++-+|.+|.+|.++|+...++..
T Consensus 406 s~~QaeaIL~mrL~~L~~le~~~i~~E~~~l~~e~~~l~ 444 (735)
T TIGR01062 406 SAIQAEAILNLRLRHLAKLEEHAIIDEQSELEKERAILE 444 (735)
T ss_pred CHHHHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 9999988854 455667788888888888887777644
No 35
>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=23.29 E-value=54 Score=24.67 Aligned_cols=22 Identities=5% Similarity=0.129 Sum_probs=17.5
Q ss_pred HHHHhhCCChhhHHHhhhccCC
Q 047612 92 TFFWIAGFNPTLAFRVVNESVK 113 (238)
Q Consensus 92 ~flWiGG~RPS~~l~Ll~~~l~ 113 (238)
.++..+|.||+++.++-..++.
T Consensus 22 ~l~~~~G~R~~ei~~l~~~~v~ 43 (162)
T cd01182 22 LLLLYTGLRVSELLALRWSDID 43 (162)
T ss_pred HHHHHhCCCHHHHhhhehhccc
Confidence 5778899999999988755444
No 36
>COG4710 Predicted DNA-binding protein with an HTH domain [General function prediction only]
Probab=23.13 E-value=3.3e+02 Score=20.41 Aligned_cols=24 Identities=13% Similarity=0.135 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHH
Q 047612 172 VEVTESNLRASLESLVANADMLRT 195 (238)
Q Consensus 172 ~~~am~~kl~~L~~~l~qAD~LR~ 195 (238)
+..|++..++.|+.|...+|.|+.
T Consensus 35 vrEaIE~~ieemED~ylA~~aler 58 (80)
T COG4710 35 VREAIEAYIEEMEDFYLAVNALER 58 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 799999999999999999998764
No 37
>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=22.82 E-value=35 Score=28.47 Aligned_cols=39 Identities=18% Similarity=0.393 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhhhhhchhhhcCCCCCChhHHHHHHhhCCChhhHH
Q 047612 59 LAHYQQYYQEKSKVAQHNVFLLFAPTWFTPFEQTFFWIAGFNPTLAF 105 (238)
Q Consensus 59 l~Hy~~y~~~K~~aA~~DV~~~~s~~W~tp~Er~flWiGG~RPS~~l 105 (238)
+.||...=.+-..+...-|..++||-|.++ +|..|..+-
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 456666555656678899999999999999 888887653
No 38
>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=22.41 E-value=1.2e+02 Score=24.13 Aligned_cols=21 Identities=10% Similarity=0.116 Sum_probs=16.3
Q ss_pred HHHHhhCCChhhHHHhhhccC
Q 047612 92 TFFWIAGFNPTLAFRVVNESV 112 (238)
Q Consensus 92 ~flWiGG~RPS~~l~Ll~~~l 112 (238)
.+++.+|.||++++.|-..++
T Consensus 28 ~l~~~~G~R~~Ei~~l~~~dv 48 (191)
T cd01189 28 LLLAYTGLRIGEALALTWSDI 48 (191)
T ss_pred HHHHHhccHHHHHhhceeccc
Confidence 467779999999998864444
No 39
>KOG3759 consensus Uncharacterized RUN domain protein [Signal transduction mechanisms]
Probab=21.78 E-value=1.8e+02 Score=29.17 Aligned_cols=66 Identities=24% Similarity=0.330 Sum_probs=46.8
Q ss_pred HHHHhhhHHHHHHHHhhhc---CCCChhhHHHHHHHHHHHHHHHHHHHHhhhhhchhhhcCCCCCChhHHHHHHh
Q 047612 25 WLVRQEHLLDELISAQENH---HQSRDEDLKELVKRVLAHYQQYYQEKSKVAQHNVFLLFAPTWFTPFEQTFFWI 96 (238)
Q Consensus 25 W~~eq~~~l~eLr~al~~~---~~~~d~eL~~LV~~~l~Hy~~y~~~K~~aA~~DV~~~~s~~W~tp~Er~flWi 96 (238)
=++.|+-.+.+||..+.-+ ...+-.+|+.-||.++..+-.-|.+|.-+-..=- +=.|-+||+.-+|
T Consensus 178 iLekQk~ilDeLr~Kl~lnl~i~~lsteelr~qVD~A~~q~VnP~k~KeQLV~QLk------TQItDLErFInFl 246 (621)
T KOG3759|consen 178 ILEKQKAILDELREKLELNLDIDKLSTEELRRQVDDALKQLVNPFKEKEQLVDQLK------TQITDLERFINFL 246 (621)
T ss_pred HHHHHHHHHHHHHHHhhccCCcccccHHHHHHHHHHHHHHHhChHHHHHHHHHHHH------HHHHHHHHHHHHH
Confidence 3577888899999997522 2346789999999999999999999985432111 1235677766655
No 40
>PHA03395 p10 fibrous body protein; Provisional
Probab=21.74 E-value=3.8e+02 Score=20.60 Aligned_cols=61 Identities=15% Similarity=0.220 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhchhhHHHHHhhhCCCCccchhhhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCH
Q 047612 128 VETRVEEKLLNDELARIQESVAGPTIMELARRRGRLGEWEMTEGVEVTESNLRASLESLVANADMLRTTTTAKVVEILDP 207 (238)
Q Consensus 128 ~~t~~~E~aLs~~ma~lQ~slad~~~~~~~~~~g~~g~~~~~~~~~~am~~kl~~L~~~l~qAD~LR~~TL~~~~~iLtp 207 (238)
.-++.+-.++++.+..+|+.+.+... ... --.++.+++.++-.-+.-. ..++..|.+||+|
T Consensus 7 l~Ir~dIkavd~KVdalQ~~V~~l~~--------nlp-------dv~~l~~kLdaq~~~Ltti----~tkv~~I~diLnp 67 (87)
T PHA03395 7 LLIRQDIKAVSDKVDALQAAVDDVRA--------NLP-------DVTEINEKLDAQSASLDTI----SSAVDNITDILNP 67 (87)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHh--------cCC-------cHHHHHHHHHhHHHHHHHH----HHHHHHHHHccCC
Confidence 34677888999999999998888643 111 1233445555555544222 3567777888886
No 41
>CHL00132 psaF photosystem I subunit III; Validated
Probab=21.72 E-value=2.9e+02 Score=24.02 Aligned_cols=79 Identities=15% Similarity=0.310 Sum_probs=49.3
Q ss_pred chhhhHHHHHHHHHHHhhhHHHHHHHHhh--hcCCCChhhHHHHHHHHHHHHHHHHHHHHhhhhhc-hhhhc-CCCCCCh
Q 047612 13 DNVASFETFFRAWLVRQEHLLDELISAQE--NHHQSRDEDLKELVKRVLAHYQQYYQEKSKVAQHN-VFLLF-APTWFTP 88 (238)
Q Consensus 13 ~~~~~F~~~Y~~W~~eq~~~l~eLr~al~--~~~~~~d~eL~~LV~~~l~Hy~~y~~~K~~aA~~D-V~~~~-s~~W~tp 88 (238)
+++..|. ...+..+..|.+-++ +....+.-.|+.-|++.-..|+.|-.. ..++..| .+|++ .|.|.-.
T Consensus 33 ses~aF~-------kR~~~~~k~Le~rlk~Y~~~s~p~lal~~qi~~tk~RFe~Y~~~-~lLCG~DGLPHLI~dG~~~Ha 104 (185)
T CHL00132 33 SESPAFQ-------KRLNNSVKKLENRLAKYEANSPPALALQQQIDKTKARFDKYGRS-GLLCGTDGLPHLITDGRWSHA 104 (185)
T ss_pred ccCHHHH-------HHHHHHHHHHHhhhhccCCCCChHHHHHHHHHHHHHHHHHhccc-ccccCCCCCceeecCCCcccc
Confidence 7778887 334444555544444 111122346899999999999988553 2346555 45665 8999765
Q ss_pred hHH-----HHHHhhCC
Q 047612 89 FEQ-----TFFWIAGF 99 (238)
Q Consensus 89 ~Er-----~flWiGG~ 99 (238)
-|= .|++|.||
T Consensus 105 GeF~IPgllFLYIAGw 120 (185)
T CHL00132 105 GEFTIPGLLFLYITGW 120 (185)
T ss_pred hhhhhhhHHHHHHhhh
Confidence 443 57777776
No 42
>PRK15366 type III secretion system chaperone SsaE; Provisional
Probab=21.50 E-value=1.7e+02 Score=22.11 Aligned_cols=27 Identities=22% Similarity=0.094 Sum_probs=23.5
Q ss_pred CCCcHHHHHHHHHHhHHHHHHHHHHHH
Q 047612 113 KDLADEQRQRMDSLSVETRVEEKLLND 139 (238)
Q Consensus 113 ~~Lt~~Ql~~i~~Lq~~t~~~E~aLs~ 139 (238)
.|=|++|-.++.-|..++.++|+.|.-
T Consensus 38 ~P~sp~qYqq~t~l~ea~lqA~~IIn~ 64 (80)
T PRK15366 38 KLQDPQQYQQNTLLLEAIEQAENIINI 64 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356899999999999999999998864
No 43
>TIGR01834 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit. This model represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. This model must be designated subfamily to indicate the heterogeneity of PHAs.
Probab=21.29 E-value=7e+02 Score=23.53 Aligned_cols=127 Identities=13% Similarity=0.101 Sum_probs=62.9
Q ss_pred hhhHHHHHHHHHH--------HhhhHHHHHHHH-hhhcCCCChhhHHHHHHHHHHHHHHHHHHHHhh-hh--h--chhhh
Q 047612 15 VASFETFFRAWLV--------RQEHLLDELISA-QENHHQSRDEDLKELVKRVLAHYQQYYQEKSKV-AQ--H--NVFLL 80 (238)
Q Consensus 15 ~~~F~~~Y~~W~~--------eq~~~l~eLr~a-l~~~~~~~d~eL~~LV~~~l~Hy~~y~~~K~~a-A~--~--DV~~~ 80 (238)
...|..-|+.|+. |++.++.+|-.+ +. -...-.+...+...+..+..+-+..+-.. ++ . +-+.=
T Consensus 155 ~~~~~~~~~~~L~~P~lG~~Re~q~~~~~l~~a~~~--yq~a~~ey~~~~~~~~~ks~e~~~~~l~~~~~~g~~v~s~re 232 (320)
T TIGR01834 155 DQLYRKNLSSFLSMPALGYSREMQSQLQRLFRDWME--YQQAMADYQLLEADIGYKSFAALMSDLLARAKSGKPVKTAKA 232 (320)
T ss_pred HHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCchhHHH
Confidence 4677888888874 444454444333 21 00111233333444443333333333221 11 2 33455
Q ss_pred cCCCCCChhHHHHHHhhCCChhhHHHhh---------------------hccCCCCcHHHHHHHHHHhHHHHHHHHHHHH
Q 047612 81 FAPTWFTPFEQTFFWIAGFNPTLAFRVV---------------------NESVKDLADEQRQRMDSLSVETRVEEKLLND 139 (238)
Q Consensus 81 ~s~~W~tp~Er~flWiGG~RPS~~l~Ll---------------------~~~l~~Lt~~Ql~~i~~Lq~~t~~~E~aLs~ 139 (238)
|...|...+|.+|.=+ +.-.++.++. ...|.=.|..++..+..--.+++++-++|.+
T Consensus 233 ~~d~W~~~ae~~~~e~--~~S~efak~~G~lvna~m~lr~~~qe~~e~~L~~LnlPTRsElDe~~krL~ELrR~vr~L~k 310 (320)
T TIGR01834 233 LYDLWVIAAEEAYAEV--FASEENAKVHGKFINALMRLRIQQQEIVEALLKMLNLPTRSELDEAHQRIQQLRREVKSLKK 310 (320)
T ss_pred HHHHHHHHHHHHHHHH--HcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6777888888877533 2233333333 2344445666666555555555555556666
Q ss_pred HHHHHH
Q 047612 140 ELARIQ 145 (238)
Q Consensus 140 ~ma~lQ 145 (238)
+++++.
T Consensus 311 ~l~~l~ 316 (320)
T TIGR01834 311 RLGDLE 316 (320)
T ss_pred HHHHhh
Confidence 665554
No 44
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=21.23 E-value=1.4e+02 Score=27.25 Aligned_cols=61 Identities=15% Similarity=0.201 Sum_probs=40.0
Q ss_pred hhHHHHHHHHHHHhhhHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHHHHHhhhhhchhhhcCCCCCC
Q 047612 16 ASFETFFRAWLVRQEHLLDELISAQENHHQSRDEDLKELVKRVLAHYQQYYQEKSKVAQHNVFLLFAPTWFT 87 (238)
Q Consensus 16 ~~F~~~Y~~W~~eq~~~l~eLr~al~~~~~~~d~eL~~LV~~~l~Hy~~y~~~K~~aA~~DV~~~~s~~W~t 87 (238)
..|+.||+.|+.|+.....|+..--. .++-=..||..|.-+|..--.+ .+|. ..|.+.|.+
T Consensus 76 ~~~defyEd~f~E~~~kygEiee~~V-----c~Nl~~hl~GNVYV~f~~Ee~a--e~a~----~~lnnRw~~ 136 (260)
T KOG2202|consen 76 RHEDEFYEDVFTELEDKYGEIEELNV-----CDNLGDHLVGNVYVKFRSEEDA--EAAL----EDLNNRWYN 136 (260)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhhhh-----hcccchhhhhhhhhhcccHHHH--HHHH----HHHcCcccc
Confidence 68999999999999988888766621 2333346788887777643222 2232 346677654
No 45
>COG4755 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.16 E-value=2.3e+02 Score=23.54 Aligned_cols=27 Identities=30% Similarity=0.395 Sum_probs=23.6
Q ss_pred hhhhHHHHHHHHHHHhhhHHHHHHHHh
Q 047612 14 NVASFETFFRAWLVRQEHLLDELISAQ 40 (238)
Q Consensus 14 ~~~~F~~~Y~~W~~eq~~~l~eLr~al 40 (238)
.-.+|-.-.++|+..|++++.+|.+-=
T Consensus 12 ~~~sf~~~Le~WvklQk~~l~~lk~~~ 38 (151)
T COG4755 12 YLESFMERLEQWVKLQKRQLKELKSHG 38 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 347899999999999999999997764
No 46
>PRK06975 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed
Probab=20.29 E-value=9.4e+02 Score=24.63 Aligned_cols=50 Identities=14% Similarity=0.054 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHH
Q 047612 173 EVTESNLRASLESLVANADMLRTTTTAKVVEILDPLQNVKFFTAVARLQLRI 224 (238)
Q Consensus 173 ~~am~~kl~~L~~~l~qAD~LR~~TL~~~~~iLtp~Qaa~fL~A~~e~~~~l 224 (238)
...+..+++.|+.-+.+.+ ..++.|++.+.-|+- .--.+++|=+||.+++
T Consensus 380 ~~~~~~~l~~le~~l~~~~-~~~~~L~~~~~~l~~-~r~dW~laEae~Ll~l 429 (656)
T PRK06975 380 VHQLDSQFAQLDGKLADAQ-SAQQALEQQYQDLSR-NRDDWMIAEVEQMLSS 429 (656)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhc-ChhhhHHHHHHHHHHH
Confidence 3445577888888666655 567778888777763 3478888888888877
No 47
>PLN00060 meiotic recombination protein SPO11-2; Provisional
Probab=20.26 E-value=1.8e+02 Score=28.12 Aligned_cols=66 Identities=15% Similarity=0.121 Sum_probs=43.6
Q ss_pred hcCCCCCChhHHH-----HHHhhCCChhhHHHhhhccCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 047612 80 LFAPTWFTPFEQT-----FFWIAGFNPTLAFRVVNESVKDLADEQRQRMDSLSVETRVEEKLLNDELARIQES 147 (238)
Q Consensus 80 ~~s~~W~tp~Er~-----flWiGG~RPS~~l~Ll~~~l~~Lt~~Ql~~i~~Lq~~t~~~E~aLs~~ma~lQ~s 147 (238)
+..|..+..+|.. ..|| |.|||.+.++=...+-|||+....++.+|-....-.. ...+|+...++.
T Consensus 283 YkyGS~~~a~es~~la~~i~WL-Gl~~sDi~~l~~~~~i~Lt~rD~~~~~~lL~~~~~~~-~w~~EL~~Ml~~ 353 (384)
T PLN00060 283 YKFGSIGMGLEAYRYACNVKWL-GLRGDDLQLIPPEAFVELKPRDLQIAKSLLSSKFLQN-RYREELTLMVQT 353 (384)
T ss_pred hhcCchhhhhcccccccCCeEe-cCCHHHHhcCCHhhcCCCCHHHHHHHHHHhhChhHHH-HHHHHHHHHHHh
Confidence 3456666666643 6788 5899998873334567899999999988877643322 455555554443
Done!