Query 009379
Match_columns 536
No_of_seqs 155 out of 1123
Neff 3.7
Searched_HMMs 46136
Date Thu Mar 28 12:24:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009379.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009379hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0290 InfC Translation initi 100.0 1.3E-54 2.7E-59 406.7 18.5 165 79-253 8-175 (176)
2 CHL00199 infC translation init 100.0 1.8E-51 4E-56 389.5 19.5 167 75-246 10-179 (182)
3 TIGR00168 infC translation ini 100.0 1.2E-50 2.5E-55 378.9 19.7 159 83-246 1-163 (165)
4 PRK00028 infC translation init 100.0 1.6E-50 3.4E-55 381.4 19.6 163 79-246 9-174 (177)
5 PF05198 IF3_N: Translation in 99.9 9.2E-25 2E-29 182.1 6.8 72 79-150 2-75 (76)
6 PF00707 IF3_C: Translation in 99.9 7.5E-24 1.6E-28 179.1 8.3 85 163-247 3-88 (88)
7 PF14877 mIF3: Mitochondrial t 98.1 2.2E-05 4.7E-10 76.0 11.4 116 89-204 32-169 (181)
8 PRK15108 biotin synthase; Prov 23.0 4.4E+02 0.0095 28.0 8.8 45 174-220 166-211 (345)
9 PF10881 DUF2726: Protein of u 22.8 2.2E+02 0.0047 25.3 5.6 86 95-183 36-123 (126)
10 TIGR00620 sporelyase spore pho 22.2 2.1E+02 0.0045 28.8 5.8 57 165-224 46-117 (199)
11 PRK10560 hofQ outer membrane p 21.3 8.7E+02 0.019 26.1 10.7 101 81-198 22-123 (386)
12 PRK00513 minC septum formation 20.9 1.4E+02 0.003 29.7 4.3 35 176-212 33-67 (214)
13 PF00926 DHBP_synthase: 3,4-di 20.9 82 0.0018 31.3 2.8 33 90-123 156-188 (194)
14 PF04627 ATP-synt_Eps: Mitocho 20.7 41 0.00089 26.8 0.5 17 1-17 1-17 (50)
15 cd06396 PB1_NBR1 The PB1 domai 20.5 1.5E+02 0.0033 25.9 4.0 34 89-123 39-77 (81)
No 1
>COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-54 Score=406.69 Aligned_cols=165 Identities=38% Similarity=0.620 Sum_probs=159.9
Q ss_pred CCCCCCCCCCCceEEEEeCCCC--ccccHHHHHHHHHhcCCcEEEecCCCCCCeEEEecchhHHHHHHHHHHHHHhhccc
Q 009379 79 SGPRLNDKINAQFVRLVLDEGH--KVVSRHEALALARSLQCDLVEVDRKANPPVCKIMDFHKEKYQKELKEKDRAKAKSD 156 (536)
Q Consensus 79 d~~riNEeI~a~~VRLIdedG~--GVms~~EAL~lAk~~~LDLVeVsp~a~PPVCKImDYgK~kYEqqKKeKEaKKkqkk 156 (536)
+.+++|++|++++|||||++|+ |++++.|||++|++.+||||+|+++++||||||||||||+||++||++|++|+|+.
T Consensus 8 ~~~~iN~~Ir~~evrlIg~~GeqlGiv~~~eAL~lA~e~~LDLV~Ispna~PPVcKImDYGKfkye~~KK~kEakKkQk~ 87 (176)
T COG0290 8 KEPLINEEIRAREVRLIGEDGEQLGIVSIEEALKLAEEAGLDLVEISPNAKPPVCKIMDYGKFKYEQKKKAKEAKKKQKQ 87 (176)
T ss_pred ccccccccccccEEEEECCCCcEEcceeHHHHHHHHHHcCCCEEEECCCCCCCeeEeeeccchHHHHHHHHHHHhhcCce
Confidence 4689999999999999999996 99999999999999999999999999999999999999999999999999999887
Q ss_pred cccccccceeEEEeecCCcchHHHHHHHHHHHHhcCCeEEEEEEecCCcccchHHHH-HHHHHHHHhhhccccccCcccC
Q 009379 157 ITLKKGDCKEVRFSGKIEQKDLQMKADTVKRLMDKGYRVKCMALPVGKKEETEDLGG-YLSRLIDLIEDISVVESGPHVE 235 (536)
Q Consensus 157 ~~~r~~k~KEIrLs~~IdeHDL~~KlKQakkFLeKG~KVKVtI~fRGRE~~~qElge-lL~RV~e~LeEVg~VE~kPk~E 235 (536)
+ .+|||+|+++|++|||++|++++++||++|++|||+|+|||||++|+|+|. +|++|.++|+|+|.+|+.|+++
T Consensus 88 i-----~vKEik~rp~Id~hD~~~K~k~~~rFLe~GdkVKvtirfrGRe~~h~elG~~~l~r~~~~~~~~~~ve~~pk~e 162 (176)
T COG0290 88 I-----QVKEIKLRPKIDEHDYETKLKNARRFLEKGDKVKVTIRFRGREMAHQELGVKVLERVAEDLEDIAKVESEPKME 162 (176)
T ss_pred E-----EEEEEEeecCcCcchHHHHHHHHHHHHHCCCeEEEEEEEechhhhhHHHHHHHHHHHHHHhhhhheeecccccC
Confidence 7 799999999999999999999999999999999999999999999999998 9999999999999999999999
Q ss_pred CceEEEEEecCCCCCCCC
Q 009379 236 RKQAYAIIRHVKFGPSKK 253 (536)
Q Consensus 236 GK~m~miL~P~k~~P~kK 253 (536)
|++|+|+| +|+++
T Consensus 163 gr~m~m~l-----aPkkk 175 (176)
T COG0290 163 GRQMIMVL-----APKKK 175 (176)
T ss_pred CceEEEEE-----cccCC
Confidence 99999998 77765
No 2
>CHL00199 infC translation initiation factor 3; Provisional
Probab=100.00 E-value=1.8e-51 Score=389.52 Aligned_cols=167 Identities=25% Similarity=0.436 Sum_probs=158.8
Q ss_pred ccccCCCCCCCCCCCceEEEEeCCCC--ccccHHHHHHHHHhcCCcEEEecCCCCCCeEEEecchhHHHHHHHHHHHHHh
Q 009379 75 EKETSGPRLNDKINAQFVRLVLDEGH--KVVSRHEALALARSLQCDLVEVDRKANPPVCKIMDFHKEKYQKELKEKDRAK 152 (536)
Q Consensus 75 ~~d~d~~riNEeI~a~~VRLIdedG~--GVms~~EAL~lAk~~~LDLVeVsp~a~PPVCKImDYgK~kYEqqKKeKEaKK 152 (536)
+.+.+++++|++|++++|||||++|+ |+|++.|||++|++.+||||+|+++++|||||||||+||+||++||+++++|
T Consensus 10 ~~~~~~~~iNe~I~~~~VrlI~~~G~~lGv~~~~eAl~~A~~~~lDLVeVs~~a~PPVCKImdygK~kye~~KK~keakK 89 (182)
T CHL00199 10 KLSRDLPLINERIRFPKVRVIDDSGEQLGIFTSEQAIQLAANQGLDLVLVSEKSDPPVCRIIDYGKYKFTQEKRAKEAKK 89 (182)
T ss_pred hcccccCCcCcccCCCEEEEECCCCcCCCceeHHHHHHHHHHcCCCEEEECCCCCCCeEEEeehHHHHHHHHHHHHHHHh
Confidence 34446799999999999999999996 9999999999999999999999999999999999999999999999999998
Q ss_pred hccccccccccceeEEEeecCCcchHHHHHHHHHHHHhcCCeEEEEEEecCCcccchHHHH-HHHHHHHHhhhccccccC
Q 009379 153 AKSDITLKKGDCKEVRFSGKIEQKDLQMKADTVKRLMDKGYRVKCMALPVGKKEETEDLGG-YLSRLIDLIEDISVVESG 231 (536)
Q Consensus 153 kqkk~~~r~~k~KEIrLs~~IdeHDL~~KlKQakkFLeKG~KVKVtI~fRGRE~~~qElge-lL~RV~e~LeEVg~VE~k 231 (536)
+|+.+ .+|||+|+|+|++|||++|++||++||++||+|+|+|+|||||++|.|+|. +|++|.++|+++|.+|..
T Consensus 90 kq~~~-----~~KEirl~~~I~~hDl~~K~k~~~kFL~~G~kVkv~i~frGRE~~~~e~g~~ll~r~~~~l~~~a~ve~~ 164 (182)
T CHL00199 90 KQHNS-----SIKEVKMRYKIEEHDYKVRINQAFKFLQAGDKVKATLTFRGREIQHLNLAINLLNKMAADLSSIAEIQQP 164 (182)
T ss_pred ccCCc-----cceEEEecCCCCccHHHHHHHHHHHHHHCCCEEEEEEEEchhHHhhHHHHHHHHHHHHHHhhhhheeecC
Confidence 87655 799999999999999999999999999999999999999999999999997 999999999999999999
Q ss_pred cccCCceEEEEEecC
Q 009379 232 PHVERKQAYAIIRHV 246 (536)
Q Consensus 232 Pk~EGK~m~miL~P~ 246 (536)
|+++|++|.|+|.|.
T Consensus 165 pk~eGr~m~~~l~P~ 179 (182)
T CHL00199 165 PSQDGRNMIMILSPK 179 (182)
T ss_pred ccccCCEEEEEEecC
Confidence 999999999999554
No 3
>TIGR00168 infC translation initiation factor IF-3. render its expression particularly sensitive to excess of its gene product IF-3 thereby regulating its own expression
Probab=100.00 E-value=1.2e-50 Score=378.87 Aligned_cols=159 Identities=35% Similarity=0.547 Sum_probs=152.9
Q ss_pred CCCCCCCceEEEEeCCCC--ccccHHHHHHHHHhcCCcEEEecCCCCCCeEEEecchhHHHHHHHHHHHHHhhccccccc
Q 009379 83 LNDKINAQFVRLVLDEGH--KVVSRHEALALARSLQCDLVEVDRKANPPVCKIMDFHKEKYQKELKEKDRAKAKSDITLK 160 (536)
Q Consensus 83 iNEeI~a~~VRLIdedG~--GVms~~EAL~lAk~~~LDLVeVsp~a~PPVCKImDYgK~kYEqqKKeKEaKKkqkk~~~r 160 (536)
+|++|++++|||||+||+ |+|++.|||++|++.+||||+|+++++|||||||||+||+||++||+|+++|+++.+
T Consensus 1 iNe~I~~~~Vrli~~dG~~lgv~~~~eAl~~A~~~~lDLVev~~~a~PPVckImdy~k~~ye~~KK~ke~kkkq~~~--- 77 (165)
T TIGR00168 1 INERIRFNEVRLIDENGEQLGIVSREEALEIAEEAGLDLVLISPNAKPPVCKIMDYGKYKYEQEKKKKEAKKNQKII--- 77 (165)
T ss_pred CCcCcCCCEEEEECCCCcCCCcccHHHHHHHHHHcCCcEEEECCCCCCCEEEEeeHHHHHHHHHHHHHHHHhcCCCC---
Confidence 699999999999999996 999999999999999999999999999999999999999999999999998877654
Q ss_pred cccceeEEEeecCCcchHHHHHHHHHHHHhcCCeEEEEEEecCCcccchHHHH-HHHHHHHHhhhccccccCc-ccCCce
Q 009379 161 KGDCKEVRFSGKIEQKDLQMKADTVKRLMDKGYRVKCMALPVGKKEETEDLGG-YLSRLIDLIEDISVVESGP-HVERKQ 238 (536)
Q Consensus 161 ~~k~KEIrLs~~IdeHDL~~KlKQakkFLeKG~KVKVtI~fRGRE~~~qElge-lL~RV~e~LeEVg~VE~kP-k~EGK~ 238 (536)
.+|||+|+|+|++|||++|++||++||++||+|+|+|+||||++++.|+|. +|++|.+.|+|+|.++..| +++|++
T Consensus 78 --~~KEi~~~~~I~~hDl~~K~k~~~~FL~kG~kVkv~l~frgRe~~~~e~g~~ll~~i~~~l~~~~~~e~~p~~~eG~~ 155 (165)
T TIGR00168 78 --QVKEVKMRPTIDEHDLQFKLKQAIRFLEKGDKVKFTVRFRGRESTHIELGEKVLDRFYTDVADVAEVEKPPTKSEGRM 155 (165)
T ss_pred --cceeEEEcCCCChhhHHHHHHHHHHHHHCCCeEEEEEEEcCCcccCHHHHHHHHHHHHHHhhhhhheecCcccccCCE
Confidence 799999999999999999999999999999999999999999999999997 9999999999999999999 999999
Q ss_pred EEEEEecC
Q 009379 239 AYAIIRHV 246 (536)
Q Consensus 239 m~miL~P~ 246 (536)
|+|+|.|.
T Consensus 156 ~~~~l~P~ 163 (165)
T TIGR00168 156 MSMLLAPK 163 (165)
T ss_pred EEEEEEeC
Confidence 99999664
No 4
>PRK00028 infC translation initiation factor IF-3; Reviewed
Probab=100.00 E-value=1.6e-50 Score=381.44 Aligned_cols=163 Identities=38% Similarity=0.618 Sum_probs=156.3
Q ss_pred CCCCCCCCCCCceEEEEeCCCC--ccccHHHHHHHHHhcCCcEEEecCCCCCCeEEEecchhHHHHHHHHHHHHHhhccc
Q 009379 79 SGPRLNDKINAQFVRLVLDEGH--KVVSRHEALALARSLQCDLVEVDRKANPPVCKIMDFHKEKYQKELKEKDRAKAKSD 156 (536)
Q Consensus 79 d~~riNEeI~a~~VRLIdedG~--GVms~~EAL~lAk~~~LDLVeVsp~a~PPVCKImDYgK~kYEqqKKeKEaKKkqkk 156 (536)
+++++||+|++++|||||+||+ |+|++.|||++|++.+||||+|+++++|||||||||+||+||++||+++++|+++.
T Consensus 9 ~~~~iNe~I~~~~Vrli~~dG~~lgv~~~~eAl~~A~~~~lDLV~v~~~~~PPVckI~dy~k~~ye~~kK~ke~kkkq~~ 88 (177)
T PRK00028 9 KEPRINEQIRAREVRLIGDDGEQLGIVSTREALELAEEAGLDLVEISPNAKPPVCKIMDYGKFKYEQKKKQKEAKKKQKV 88 (177)
T ss_pred ccCCcCcCcCCCEEEEECCCCcCCCceeHHHHHHHHHHcCCCEEEECCCCCCCEEEEEeHHHHHHHHHHHHHHhhhccCc
Confidence 5699999999999999999996 99999999999999999999999999999999999999999999999999887765
Q ss_pred cccccccceeEEEeecCCcchHHHHHHHHHHHHhcCCeEEEEEEecCCcccchHHHH-HHHHHHHHhhhccccccCcccC
Q 009379 157 ITLKKGDCKEVRFSGKIEQKDLQMKADTVKRLMDKGYRVKCMALPVGKKEETEDLGG-YLSRLIDLIEDISVVESGPHVE 235 (536)
Q Consensus 157 ~~~r~~k~KEIrLs~~IdeHDL~~KlKQakkFLeKG~KVKVtI~fRGRE~~~qElge-lL~RV~e~LeEVg~VE~kPk~E 235 (536)
+ .+|||+|+|+|++|||++|+++|++||++||+|+|+|+||||++++.|+|. +|++|.+.|+|+|.++.+|+++
T Consensus 89 ~-----~~KEirl~~~I~~hDl~~K~k~~~kFL~kG~kVkv~l~frgre~~~~e~g~~vl~~v~~~l~~~~~~e~~p~~~ 163 (177)
T PRK00028 89 I-----EVKEIKFRPKIDEHDYETKLKHARRFLEKGDKVKVTLRFRGREIAHKELGMELLERVAEDLEDIAKVEQEPKME 163 (177)
T ss_pred c-----ceeEEEEccCCChhHHHHHHHHHHHHHHCCCEEEEEEEEcCCcccCHHHHHHHHHHHHHHcchhhheecccccc
Confidence 4 799999999999999999999999999999999999999999999999997 9999999999999999999999
Q ss_pred CceEEEEEecC
Q 009379 236 RKQAYAIIRHV 246 (536)
Q Consensus 236 GK~m~miL~P~ 246 (536)
|++|+|+|.|.
T Consensus 164 G~~~~~~l~P~ 174 (177)
T PRK00028 164 GRQMIMVLAPK 174 (177)
T ss_pred CCEEEEEEEeC
Confidence 99999999553
No 5
>PF05198 IF3_N: Translation initiation factor IF-3, N-terminal domain; InterPro: IPR019814 Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit []. The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 []. ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1TIF_A.
Probab=99.91 E-value=9.2e-25 Score=182.06 Aligned_cols=72 Identities=49% Similarity=0.756 Sum_probs=58.6
Q ss_pred CCCCCCCCCCCceEEEEeCCCC--ccccHHHHHHHHHhcCCcEEEecCCCCCCeEEEecchhHHHHHHHHHHHH
Q 009379 79 SGPRLNDKINAQFVRLVLDEGH--KVVSRHEALALARSLQCDLVEVDRKANPPVCKIMDFHKEKYQKELKEKDR 150 (536)
Q Consensus 79 d~~riNEeI~a~~VRLIdedG~--GVms~~EAL~lAk~~~LDLVeVsp~a~PPVCKImDYgK~kYEqqKKeKEa 150 (536)
+++++|++|++++|||||++|+ |+|+++|||++|++.+||||+|+++++|||||||||+||+||++||+||+
T Consensus 2 ~~~~iNe~I~~~~VrlI~~~g~~lGv~~~~eAl~~A~~~~lDLV~v~~~~~PPVcKi~dy~k~~ye~~kk~ke~ 75 (76)
T PF05198_consen 2 DKPRINEEIRAPEVRLIDEDGEQLGVMSLREALRLAKEKGLDLVEVSPNADPPVCKIMDYGKYKYEQKKKAKEA 75 (76)
T ss_dssp ----BGGG---SEEEEE-TTS-EEEEEEHHHHHHHHHHTT-EEEEEETTSSS-EEEEE-HHHHHHHHHHHHHHT
T ss_pred CCCCCCCCcCCCEEEEECCCCcEeceEEHHHHHHHHHHcCCcEEEEcCCCCCCeEEEechHHHHHHHHHHHHhc
Confidence 4689999999999999999996 99999999999999999999999999999999999999999999998875
No 6
>PF00707 IF3_C: Translation initiation factor IF-3, C-terminal domain; InterPro: IPR019815 Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit []. The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 []. ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2IFE_A 1TIG_A 2CRQ_A.
Probab=99.90 E-value=7.5e-24 Score=179.15 Aligned_cols=85 Identities=34% Similarity=0.554 Sum_probs=78.2
Q ss_pred cceeEEEeecCCcchHHHHHHHHHHHHhcCCeEEEEEEecCCcccchHHHH-HHHHHHHHhhhccccccCcccCCceEEE
Q 009379 163 DCKEVRFSGKIEQKDLQMKADTVKRLMDKGYRVKCMALPVGKKEETEDLGG-YLSRLIDLIEDISVVESGPHVERKQAYA 241 (536)
Q Consensus 163 k~KEIrLs~~IdeHDL~~KlKQakkFLeKG~KVKVtI~fRGRE~~~qElge-lL~RV~e~LeEVg~VE~kPk~EGK~m~m 241 (536)
.+|||+|+|+|++|||++|+++|++||++||+|+|+|.||||++.+.|.+. +|++|.+.|+++|.++..|+++|++|+|
T Consensus 3 ~~KEi~~~~~I~~hDl~~K~k~~~~fL~kG~~Vkv~i~~rgr~~~~~e~~~~~l~~i~~~l~~~~~~~~~~~~~g~~~~~ 82 (88)
T PF00707_consen 3 KVKEIRFSPNIDEHDLETKLKQAKKFLEKGHKVKVVIRFRGREMAHPELGEEVLERIIEELKDVGKVEKKPKMEGKQMSM 82 (88)
T ss_dssp EEEEEEEETT--HHHHHHHHHHHHHHHHTTEEEEEEEE-SSTTTTHHHHHHHHHHHHHHHCTTTEEEEEEEEECCCCEEE
T ss_pred eEEEEEEecCcChhHHHHHHHHHHHHHHCCCEEEEEEEecCccccchHHHHHHHHHHHHHHhhhcEEeecccccCCEEEE
Confidence 689999999999999999999999999999999999999999999999887 9999999999999999999999999999
Q ss_pred EEecCC
Q 009379 242 IIRHVK 247 (536)
Q Consensus 242 iL~P~k 247 (536)
+|.|.|
T Consensus 83 ~l~P~k 88 (88)
T PF00707_consen 83 ILSPKK 88 (88)
T ss_dssp EEEES-
T ss_pred EEEeCC
Confidence 997764
No 7
>PF14877 mIF3: Mitochondrial translation initiation factor
Probab=98.14 E-value=2.2e-05 Score=76.01 Aligned_cols=116 Identities=20% Similarity=0.239 Sum_probs=81.6
Q ss_pred CceEEEEeCCC--CccccHHHHHHHH--HhcCCcEEEecCCC---CCCeEEEecchh----HH-HHHHHHHHHH------
Q 009379 89 AQFVRLVLDEG--HKVVSRHEALALA--RSLQCDLVEVDRKA---NPPVCKIMDFHK----EK-YQKELKEKDR------ 150 (536)
Q Consensus 89 a~~VRLIdedG--~GVms~~EAL~lA--k~~~LDLVeVsp~a---~PPVCKImDYgK----~k-YEqqKKeKEa------ 150 (536)
...|.+|++.. .+.+++.+.++-. +.+||-||-+.... +-|++||++-.. |- |-.+.|++|.
T Consensus 32 ~g~Vk~inp~t~~Le~~~l~~~~~~lDL~~~Gl~iV~~~~~~~~~~lPLVK~v~~~~alk~YSd~LAk~Ke~ELl~~G~~ 111 (181)
T PF14877_consen 32 NGKVKFINPETNKLEESNLRDIAKGLDLSKHGLQIVNSEKDQKGRDLPLVKIVEVREALKQYSDELAKQKEKELLEMGKA 111 (181)
T ss_pred CCeEEEEcCCCCcceeeeHHHHHHhCCccccceEEecccccCCCCcCceEEEecHHHHHHHHHHHHHHHHHHHHHHhchh
Confidence 46899997655 4899999998877 47888888887665 669999998421 11 1122233322
Q ss_pred -Hhh--ccccccccccceeEEEeecCCcchHHH-HHHHHHHHHhcCCeEEEEEEecCC
Q 009379 151 -AKA--KSDITLKKGDCKEVRFSGKIEQKDLQM-KADTVKRLMDKGYRVKCMALPVGK 204 (536)
Q Consensus 151 -KKk--qkk~~~r~~k~KEIrLs~~IdeHDL~~-KlKQakkFLeKG~KVKVtI~fRGR 204 (536)
++. +.....+...+|.|+|+|.|..+||.. |..-+..-|+||++|-|.|--+++
T Consensus 112 ~k~~~~k~~~ekkks~~K~i~isW~Is~~DL~~QK~~EI~~~LkKG~kv~iyi~dK~~ 169 (181)
T PF14877_consen 112 LKKLDKKLKAEKKKSSTKQIKISWQISPDDLKNQKANEIEKRLKKGEKVNIYIDDKDN 169 (181)
T ss_pred HHHhhhhchhhhcccccceEEEEEeechHHHHHHHHHHHHHHHhCCCeEEEEEcCCCC
Confidence 110 001111234789999999999999964 888899999999999998865544
No 8
>PRK15108 biotin synthase; Provisional
Probab=23.01 E-value=4.4e+02 Score=27.97 Aligned_cols=45 Identities=24% Similarity=0.434 Sum_probs=34.4
Q ss_pred CcchHHHHHHHHHHHHhcCCeEEEEEEe-cCCcccchHHHHHHHHHHH
Q 009379 174 EQKDLQMKADTVKRLMDKGYRVKCMALP-VGKKEETEDLGGYLSRLID 220 (536)
Q Consensus 174 deHDL~~KlKQakkFLeKG~KVKVtI~f-RGRE~~~qElgelL~RV~e 220 (536)
..|+|+.+++-++...+.|.+|-..+.+ -|- +.+|..+++..+.+
T Consensus 166 ~~~~~~~rl~~i~~a~~~G~~v~sg~i~GlgE--t~ed~v~~~~~l~~ 211 (345)
T PRK15108 166 TTRTYQERLDTLEKVRDAGIKVCSGGIVGLGE--TVKDRAGLLLQLAN 211 (345)
T ss_pred CCCCHHHHHHHHHHHHHcCCceeeEEEEeCCC--CHHHHHHHHHHHHh
Confidence 6899999999999999999999888775 343 44565555555553
No 9
>PF10881 DUF2726: Protein of unknown function (DUF2726); InterPro: IPR024402 This domain found in bacterial proteins has no known function.
Probab=22.84 E-value=2.2e+02 Score=25.34 Aligned_cols=86 Identities=24% Similarity=0.278 Sum_probs=50.4
Q ss_pred EeCCCCccccHHHHHHHHHhcCCcEEEecCCCCCCeEEEecchhHHHHHHHHHHHHHhhccccccccccceeEEEee--c
Q 009379 95 VLDEGHKVVSRHEALALARSLQCDLVEVDRKANPPVCKIMDFHKEKYQKELKEKDRAKAKSDITLKKGDCKEVRFSG--K 172 (536)
Q Consensus 95 IdedG~GVms~~EAL~lAk~~~LDLVeVsp~a~PPVCKImDYgK~kYEqqKKeKEaKKkqkk~~~r~~k~KEIrLs~--~ 172 (536)
|+.++...-...++.......-+|.|.++....-|||-|---+........+++++.|.+ .+....+.-|+|+. .
T Consensus 36 l~~~~~~~~~~~~~~~~~~~~~vDFvv~d~~~~~p~~vIEld~~~h~~~~~~~rD~~k~~---~l~~agiplir~~~~~~ 112 (126)
T PF10881_consen 36 LRPEGPSRRERKEAFNRINQKHVDFVVCDKRDGRPVAVIELDGSSHDQEKRQERDEFKDR---VLKKAGIPLIRISPKDS 112 (126)
T ss_pred hCccCCCchhHHHHHHHhcCCCccEEEEECCCCcEEEEEEecCccccchhhHHHHHHHHH---HHHHCCCCEEEEeCCCC
Confidence 344444555667888888899999999997766788888744443333333334433321 11223556667743 4
Q ss_pred CCcchHHHHHH
Q 009379 173 IEQKDLQMKAD 183 (536)
Q Consensus 173 IdeHDL~~KlK 183 (536)
.+...|...+.
T Consensus 113 ~~~~~l~~~l~ 123 (126)
T PF10881_consen 113 YSVEELRRDLR 123 (126)
T ss_pred CCHHHHHHHHH
Confidence 45555554443
No 10
>TIGR00620 sporelyase spore photoproduct lyase. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.18 E-value=2.1e+02 Score=28.83 Aligned_cols=57 Identities=21% Similarity=0.369 Sum_probs=40.3
Q ss_pred eeEEEeecCCcc-----------hHHHHHHHHHHHHhcCCeEEEEEEe----cCCcccchHHHHHHHHHHHHhhh
Q 009379 165 KEVRFSGKIEQK-----------DLQMKADTVKRLMDKGYRVKCMALP----VGKKEETEDLGGYLSRLIDLIED 224 (536)
Q Consensus 165 KEIrLs~~IdeH-----------DL~~KlKQakkFLeKG~KVKVtI~f----RGRE~~~qElgelL~RV~e~LeE 224 (536)
.-++|+|.+... -|.-|++.|+++.++||+|.+.+.. -|=+ ++-.++|++|.+.|..
T Consensus 46 ~~t~~rfSlnp~~Ii~~~E~~T~sl~~Rl~Aa~k~a~aGy~Vg~~~~PIi~~egW~---e~Y~~l~~~l~~~l~~ 117 (199)
T TIGR00620 46 GKTRFRFSINADYVIKNFEPGTSPLDKRIEAAVKVAKAGYPLGFIIAPIYIHEGWK---EGYRNLLEKLDEALPQ 117 (199)
T ss_pred CCEEEEEEeCHHHHHHHhcCCCCCHHHHHHHHHHHHHcCCeEEEEeeceEeeCChH---HHHHHHHHHHHHhCCH
Confidence 445666665433 4677999999999999999998763 4432 2334578888777765
No 11
>PRK10560 hofQ outer membrane porin HofQ; Provisional
Probab=21.26 E-value=8.7e+02 Score=26.06 Aligned_cols=101 Identities=13% Similarity=0.137 Sum_probs=54.5
Q ss_pred CCCCCCCCCceEEEEeCCCCccccHHHHHHHH-HhcCCcEEEecCCCCCCeEEEecchhHHHHHHHHHHHHHhhcccccc
Q 009379 81 PRLNDKINAQFVRLVLDEGHKVVSRHEALALA-RSLQCDLVEVDRKANPPVCKIMDFHKEKYQKELKEKDRAKAKSDITL 159 (536)
Q Consensus 81 ~riNEeI~a~~VRLIdedG~GVms~~EAL~lA-k~~~LDLVeVsp~a~PPVCKImDYgK~kYEqqKKeKEaKKkqkk~~~ 159 (536)
+.++.++.. .|.|.-. .++.++||..+ +.++|.++... -+++|.-.........+.+-+..+.+...
T Consensus 22 iVidp~V~G-~VTl~~~----~V~~~qal~~iL~~~gl~~~~~g-----~i~~I~p~~~~~~~~a~~~~~~~~~~~~~-- 89 (386)
T PRK10560 22 LVVSPDVSG-TVSLHLT----DVPWKQALQTVVKSAGLILRQEG-----NILSVHSQAWQNENIARQEAEQARAQANL-- 89 (386)
T ss_pred EEECCCCcc-eEEEEEe----CCCHHHHHHHHHHhCCCcEEEeC-----CEEEEEchhhhhhHHHHHHHHHHhhcccC--
Confidence 444555542 3444442 48999999877 67788888864 38888875322222211111111111111
Q ss_pred ccccceeEEEeecCCcchHHHHHHHHHHHHhcCCeEEEE
Q 009379 160 KKGDCKEVRFSGKIEQKDLQMKADTVKRLMDKGYRVKCM 198 (536)
Q Consensus 160 r~~k~KEIrLs~~IdeHDL~~KlKQakkFLeKG~KVKVt 198 (536)
...++.+.|+. ++..|+. +.++.||..+-+|.+.
T Consensus 90 -~~~t~vi~L~y-a~A~el~---~~l~~ll~~~g~v~~d 123 (386)
T PRK10560 90 -PLENRSITLQY-ADAGELA---KAGEKLLSAKGSMTVD 123 (386)
T ss_pred -CcEEEEEEecC-CCHHHHH---hhhcccccCCcEEEEE
Confidence 23567788865 3444553 3356788776565443
No 12
>PRK00513 minC septum formation inhibitor; Reviewed
Probab=20.93 E-value=1.4e+02 Score=29.75 Aligned_cols=35 Identities=14% Similarity=0.113 Sum_probs=25.6
Q ss_pred chHHHHHHHHHHHHhcCCeEEEEEEecCCcccchHHH
Q 009379 176 KDLQMKADTVKRLMDKGYRVKCMALPVGKKEETEDLG 212 (536)
Q Consensus 176 HDL~~KlKQakkFLeKG~KVKVtI~fRGRE~~~qElg 212 (536)
.+|..|+.++..|+.. ++.|+|.+.+|.....|+.
T Consensus 33 ~~L~~kl~~~~~ff~~--~~~v~l~~~~r~l~~~~~~ 67 (214)
T PRK00513 33 QELKEKLSKGKYFWKG--KATVHVKVGNRLLDEEQLQ 67 (214)
T ss_pred HHHHHHHHhCchhcCC--CeEEEEEECCCCCCHHHHH
Confidence 4588889999999854 6788888888865544443
No 13
>PF00926 DHBP_synthase: 3,4-dihydroxy-2-butanone 4-phosphate synthase; InterPro: IPR000422 3,4-dihydroxy-2-butanone 4-phosphate synthase (4.1.99.12 from EC) (DHBP synthase) (RibB) catalyses the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate, the latter serving as the biosynthetic precursor for the xylene ring of riboflavin []. In Photobacterium leiognathi, the riboflavin synthesis genes ribB (DHBP synthase), ribE (riboflavin synthase), ribH (lumazone synthase) and ribA (GTP cyclohydrolase II) all reside in the lux operon []. RibB is sometimes found as a bifunctional enzyme with GTP cyclohydrolase II that catalyses the first committed step in the biosynthesis of riboflavin (IPR000926 from INTERPRO). No sequences with significant homology to DHBP synthase are found in the metazoa.; GO: 0008686 3,4-dihydroxy-2-butanone-4-phosphate synthase activity, 0009231 riboflavin biosynthetic process; PDB: 1K4O_A 1K4L_A 1K4P_A 1K49_A 1K4I_A 1TKU_A 1TKS_B 2RIS_A 2RIU_A 3MIO_A ....
Probab=20.87 E-value=82 Score=31.34 Aligned_cols=33 Identities=18% Similarity=0.360 Sum_probs=26.9
Q ss_pred ceEEEEeCCCCccccHHHHHHHHHhcCCcEEEec
Q 009379 90 QFVRLVLDEGHKVVSRHEALALARSLQCDLVEVD 123 (536)
Q Consensus 90 ~~VRLIdedG~GVms~~EAL~lAk~~~LDLVeVs 123 (536)
=.+.|+++|| ..++..++.+.|++++|-+|.|+
T Consensus 156 vi~eil~~dG-~~~~~~~~~~fA~~~~l~~vsi~ 188 (194)
T PF00926_consen 156 VICEILDDDG-DMARRDELEEFAKKHGLPIVSIE 188 (194)
T ss_dssp EEEEBBETTS-SBHCHHHHHHHHHHTT-EEEEHH
T ss_pred EEEEEeCCCC-CcCCHHHHHHHHHHcCCcEEEHH
Confidence 3567778877 78999999999999999998875
No 14
>PF04627 ATP-synt_Eps: Mitochondrial ATP synthase epsilon chain; InterPro: IPR006721 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This family constitutes the mitochondrial ATP synthase epsilon subunit, which is distinct from the bacterial epsilon subunit (the latter being homologous to the mitochondrial delta subunit, IPR001469 from INTERPRO). The mitochondrial epsilon subunit is located in the stalk region of the F1 complex, and acts as an inhibitor of the ATPase catalytic core. The epsilon subunit can assume two conformations, contracted and extended, where the latter inhibits ATP hydrolysis. The conformation of the epsilon subunit is determined by the direction of rotation of the gamma subunit, and possibly by the presence of ADP. The extended epsilon subunit is thought to become extended in the presence of ADP, thereby acting as a safety lock to prevent wasteful ATP hydrolysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015986 ATP synthesis coupled proton transport, 0000275 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1); PDB: 3OEH_R 3OE7_1 3OFN_R 3OEE_I 2HLD_I 3FKS_I 2WPD_I 3ZRY_I 2V7Q_I 1H8E_I ....
Probab=20.69 E-value=41 Score=26.84 Aligned_cols=17 Identities=18% Similarity=-0.174 Sum_probs=11.8
Q ss_pred Ccccccccccchhhhhh
Q 009379 1 MAFSCRTNQSRLKHLTH 17 (536)
Q Consensus 1 ma~~~~~n~~~l~~l~~ 17 (536)
|+||+.-.=++|+|+++
T Consensus 1 m~~WR~AGlsY~~Ys~i 17 (50)
T PF04627_consen 1 MSAWRAAGLSYNKYSNI 17 (50)
T ss_dssp --SSTTSS--HHHHHHH
T ss_pred ChHHHHhCcCHHHHHHH
Confidence 89999999999998876
No 15
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=20.48 E-value=1.5e+02 Score=25.92 Aligned_cols=34 Identities=21% Similarity=0.200 Sum_probs=26.2
Q ss_pred CceEEEEeCCCC-----ccccHHHHHHHHHhcCCcEEEec
Q 009379 89 AQFVRLVLDEGH-----KVVSRHEALALARSLQCDLVEVD 123 (536)
Q Consensus 89 a~~VRLIdedG~-----GVms~~EAL~lAk~~~LDLVeVs 123 (536)
.=.|.-+|+||. -.+.++||+++|.+.+ .++.++
T Consensus 39 ~f~lKYlDde~e~v~lssd~eLeE~~rl~~~~~-~~l~~~ 77 (81)
T cd06396 39 DIQIKYVDEENEEVSVNSQGEYEEALKSAVRQG-NLLQMN 77 (81)
T ss_pred cceeEEEcCCCCEEEEEchhhHHHHHHHHHhCC-CEEEEE
Confidence 336777899996 4678999999998887 566553
Done!