Query gi|254780740|ref|YP_003065153.1| peptidase S16 lon domain protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 221
No_of_seqs 129 out of 2186
Neff 8.3
Searched_HMMs 39220
Date Sun May 29 21:14:18 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780740.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10787 DNA-binding ATP-depen 100.0 1.1E-40 2.8E-45 275.2 20.0 206 15-221 8-218 (784)
2 COG2802 Uncharacterized protei 100.0 2.6E-37 6.7E-42 254.0 17.0 203 8-211 2-210 (221)
3 pfam02190 LON ATP-dependent pr 100.0 7.6E-35 2E-39 238.6 20.0 187 17-206 1-192 (193)
4 COG0466 Lon ATP-dependent Lon 100.0 9.7E-35 2.5E-39 237.9 19.2 204 17-221 9-219 (782)
5 TIGR00763 lon ATP-dependent pr 100.0 1.7E-28 4.4E-33 198.7 15.6 203 19-221 1-300 (941)
6 KOG2004 consensus 99.6 2.2E-13 5.5E-18 103.9 16.2 208 12-220 63-305 (906)
7 KOG4159 consensus 99.5 1.7E-13 4.4E-18 104.5 8.8 111 12-128 171-282 (398)
8 smart00464 LON Found in ATP-de 98.7 1.7E-08 4.3E-13 73.1 5.5 90 17-203 1-91 (92)
9 KOG1400 consensus 96.7 0.0027 7E-08 40.4 4.5 188 15-209 63-318 (371)
10 TIGR02885 spore_sigF RNA polym 81.1 0.59 1.5E-05 25.8 0.8 159 43-213 9-209 (231)
11 smart00755 Grip golgin-97, Ran 43.5 23 0.00059 15.8 2.8 25 167-191 22-46 (46)
12 TIGR02272 gentisate_1_2 gentis 43.4 24 0.00061 15.7 3.4 92 20-113 197-299 (343)
13 pfam01465 GRIP GRIP domain. Th 27.6 43 0.0011 14.1 2.1 22 168-189 24-45 (45)
14 TIGR00506 ribB 3,4-dihydroxy-2 27.3 27 0.0007 15.3 1.0 20 99-118 77-97 (230)
15 cd03169 GATase1_PfpI_1 Type 1 25.3 47 0.0012 13.8 3.0 38 25-62 78-116 (180)
No 1
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=100.00 E-value=1.1e-40 Score=275.24 Aligned_cols=206 Identities=20% Similarity=0.262 Sum_probs=177.8
Q ss_pred CCCCCEEECCCCEECCCCCCCEEECCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCHHHEEEEEEEECCCCCCCCC
Q ss_conf 43155333087357888512343183899999999997099326620123433446643521100132421013466662
Q gi|254780740|r 15 PCLLPIFPLLGMLLLPGSRFSFSVFERRYIAMFDSVLAGDRLIGLVQPAISGFLANSDNGLSQIGCIGRITSFVETDDGH 94 (221)
Q Consensus 15 p~~lPi~PL~~~VlFP~~~~pL~Ife~ry~~~i~~~l~~~~~igiv~~~~~~~~~~~~~~l~~vGt~a~I~~~~~~~dG~ 94 (221)
+-.||++||||+|+|||+++||+|++++|++++++|+++++.+++++|+++..++|+.+++|+|||+|+|+++.++|||+
T Consensus 8 ~l~LPvLPLRd~VvFPgmviPL~VGR~kSI~AlE~A~~~d~~I~LVaQKD~~~deP~~eDLY~VGTlAkI~QviklPDG~ 87 (784)
T PRK10787 8 RIEIPVLPLRDVVVYPHMVIPLFVGREKSIRCLEAAMDHDKKIMLVAQKEASTDEPGVNDLFTVGTVASILQMLKLPDGT 87 (784)
T ss_pred CCEEEEEEECCCCCCCCCCEEEEECCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCHHHCCCCCEEEEEEEEEECCCCC
T ss_conf 62467998589102799205899688899999999996499799997568887999814522562799999967879994
Q ss_pred EEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCH-H-HHHH-HHCCHHHHH
Q ss_conf 489875421111010002454068999952222254102456788865788998865103201-3-5777-630535799
Q gi|254780740|r 95 YIMTVIGVCRFRLLEEAYQLNSWRCFYIAPFISDLAGNDNDGVDRVALLEVFRNYLTVNNLDA-D-WESI-EEASNEILV 171 (221)
Q Consensus 95 ~~i~v~G~~R~kI~~~~~~~~py~~a~v~~~~~d~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-~-~~~i-~~~~~~~l~ 171 (221)
++|+++|++||||.+ +.+.+||+.|+++.+.+....+.+.++....+.+.|++|...+...+ + ...+ +..+++.++
T Consensus 88 vkVLVeGl~RvkI~~-~~~~~pyl~A~Ve~l~~~~~d~~E~EAL~r~li~~f~~~v~l~~~ip~E~l~~l~~iddp~kLA 166 (784)
T PRK10787 88 VKVLVEGLQRARISA-LSDNGEHFSAKAEYLESPTIDEREQEVLVRTAISQFEGYIKLNKKIPPEVLTSLNSIDDPARLA 166 (784)
T ss_pred EEEEEEEEEEEEEEE-EECCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHH
T ss_conf 899999877899999-9747896899999806888896689999999999999999857679999999998378889999
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHH--HHHHHHHHHHHHCCCC
Q ss_conf 9999867999899999853689899999999999--9999997423210349
Q gi|254780740|r 172 NSLAMLSPFSEEEKQALLEAPDFRARAQTLIAIM--KIVLARAYTHCENRLQ 221 (221)
Q Consensus 172 d~iA~~l~~~~~eKQ~lLE~~~~~~Rl~~l~~~L--e~el~~~~~~~~~~vq 221 (221)
|++|++++++.++||++||+.|+.+|+++++++| +.++.+.+++++++||
T Consensus 167 D~IAs~L~ls~eeKQeLLE~~dvkeRLekll~lL~kElEileLe~kI~~kVk 218 (784)
T PRK10787 167 DTIAAHMPLKLADKQSVLEMSDVNERLEYLMAMMESEIDLLQVEKRIRNRVK 218 (784)
T ss_pred HHHHHCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9987327999999999986389999999999999999999999999999999
No 2
>COG2802 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]
Probab=100.00 E-value=2.6e-37 Score=254.04 Aligned_cols=203 Identities=44% Similarity=0.676 Sum_probs=175.1
Q ss_pred HCCHHHCCCCCCEEECCCCEECCCCCCCEEECCHHHHHHHHHHHHCCCCEEEEECCCCC-CCCCCCCCHHHEEEEEEEEC
Q ss_conf 07966784315533308735788851234318389999999999709932662012343-34466435211001324210
Q gi|254780740|r 8 YKNREDLPCLLPIFPLLGMLLLPGSRFSFSVFERRYIAMFDSVLAGDRLIGLVQPAISG-FLANSDNGLSQIGCIGRITS 86 (221)
Q Consensus 8 ~~~~~~lp~~lPi~PL~~~VlFP~~~~pL~Ife~ry~~~i~~~l~~~~~igiv~~~~~~-~~~~~~~~l~~vGt~a~I~~ 86 (221)
|....++|.+||+|||+++|+|||..+||||||+||+.|+++|+++++.||+|...... ...+....++.|||+|+|++
T Consensus 2 ~~~~~~~p~~LplFPL~~~vLlPg~~LpL~IFEpRY~~Mv~~~~~~~r~fGvv~i~~~~~~~~~~~~~ls~VGcla~I~~ 81 (221)
T COG2802 2 YSSPDDLPLELPLFPLPGAVLLPGGLLPLNIFEPRYLAMVRTCLAEGRRFGVVLIDRGREVGGGLPPELSDVGCLARITE 81 (221)
T ss_pred CCCCCCCCCEEECCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHCCCEEEEEEE
T ss_conf 88767765233313466610368987726552699999999987348851478742564446788650110450478867
Q ss_pred CCCCCCCCEEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCCCHHH--HHHHHH---HHHHHHHHHHHHCCCCHHHHH
Q ss_conf 134666624898754211110100024540689999522222541024--567888---657889988651032013577
Q gi|254780740|r 87 FVETDDGHYIMTVIGVCRFRLLEEAYQLNSWRCFYIAPFISDLAGNDN--DGVDRV---ALLEVFRNYLTVNNLDADWES 161 (221)
Q Consensus 87 ~~~~~dG~~~i~v~G~~R~kI~~~~~~~~py~~a~v~~~~~d~~~~~~--~~~~~~---~l~~~~~~~~~~~~~~~~~~~ 161 (221)
+.+++||++.|.++|.+||||.++...++||+.+.+.. ..|.....- .+.... .+...++.|........+|..
T Consensus 82 ~~~~~DGr~~I~~~G~~RFRv~~~~~~~~pyr~~~~~~-~~D~~~~~~~a~evdr~~~~~l~~~~r~~~~~~~l~~d~~~ 160 (221)
T COG2802 82 FEELGDGRYLILVRGGQRFRVLEELADDDPYRRARVPF-WPDLPSDPDGAEEVDRRLDALLMRAARAYLQRLELLADWES 160 (221)
T ss_pred EEECCCCCEEEEEEEEEEEEEEEEECCCCCCEEECCCC-CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHCC
T ss_conf 35758982899997578899887760567504402046-78876671068999999999999999987652231333014
Q ss_pred HHHCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 76305357999999867999899999853689899999999999999999
Q gi|254780740|r 162 IEEASNEILVNSLAMLSPFSEEEKQALLEAPDFRARAQTLIAIMKIVLAR 211 (221)
Q Consensus 162 i~~~~~~~l~d~iA~~l~~~~~eKQ~lLE~~~~~~Rl~~l~~~Le~el~~ 211 (221)
.+..++.++++.+++.+|++..+||.+||+.|...|++.+..+++.-.+.
T Consensus 161 ~~~~~~~~l~n~L~~llp~~~~~k~~ll~a~d~~~r~~~L~~~~e~l~a~ 210 (221)
T COG2802 161 YERASNADLANRLYMLLPFDPAEKQALLEAPDLPTRAERLIRLLEQLLAR 210 (221)
T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf 66536799999999857888467888872665677999999999998887
No 3
>pfam02190 LON ATP-dependent protease La (LON) domain.
Probab=100.00 E-value=7.6e-35 Score=238.56 Aligned_cols=187 Identities=29% Similarity=0.391 Sum_probs=144.6
Q ss_pred CCCEEECCCCEECCCCCCCEEECCHHHHHHHHHHHHCCCCEE-EEECCCCCCCCCCCCCHHHEEEEEEEECCCCCCCCCE
Q ss_conf 155333087357888512343183899999999997099326-6201234334466435211001324210134666624
Q gi|254780740|r 17 LLPIFPLLGMLLLPGSRFSFSVFERRYIAMFDSVLAGDRLIG-LVQPAISGFLANSDNGLSQIGCIGRITSFVETDDGHY 95 (221)
Q Consensus 17 ~lPi~PL~~~VlFP~~~~pL~Ife~ry~~~i~~~l~~~~~ig-iv~~~~~~~~~~~~~~l~~vGt~a~I~~~~~~~dG~~ 95 (221)
.||+|||+|+|+|||+.+||+||||||++|+++|+++++.++ ++.+ ...+.++.+++|+|||+|+|.++.+++||++
T Consensus 1 ~lPl~pl~~~vlfPg~~~pl~i~e~r~~~~i~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~vG~~~~I~~~~~~~dg~~ 78 (193)
T pfam02190 1 ELPLLPLRNVVLFPGMVLPLHVFEPRYIAAIEEALESDRPFFGLVLV--SQKDPPSPDDLYEVGTLARIIQIVKLPDGRL 78 (193)
T ss_pred CCCEEECCCCEECCCCCEEEEECCHHHHHHHHHHHHCCCCEEEEEEE--CCCCCCCCCCHHHEEEEEEEEEEEECCCCEE
T ss_conf 98889748900179966747989789999999998459978999984--6778888433422768999999650699729
Q ss_pred EEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHH---H-HHHCCHHHHH
Q ss_conf 89875421111010002454068999952222254102456788865788998865103201357---7-7630535799
Q gi|254780740|r 96 IMTVIGVCRFRLLEEAYQLNSWRCFYIAPFISDLAGNDNDGVDRVALLEVFRNYLTVNNLDADWE---S-IEEASNEILV 171 (221)
Q Consensus 96 ~i~v~G~~R~kI~~~~~~~~py~~a~v~~~~~d~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~---~-i~~~~~~~l~ 171 (221)
.|.++|.+||||.++..+++||+.|++++..++........ ....+.+..+.+....+...++. . ....++..++
T Consensus 79 ~v~v~G~~R~kI~~~~~~~~~~~~a~v~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 157 (193)
T pfam02190 79 KILVEGLERFRILELEEQEEPYLVAEVEDLPEEESEELEEA-LEALVKELIELLKELLPLLLPLELLLKIDNIEDPGRLA 157 (193)
T ss_pred EEEEEEEEEEEEEEEECCCCCEEEEEEEECCCCCCCCCHHH-HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHH
T ss_conf 99999899899988750578708999986577787545799-99999999999999734269888998776658999999
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf 99998679998999998536898999999999999
Q gi|254780740|r 172 NSLAMLSPFSEEEKQALLEAPDFRARAQTLIAIMK 206 (221)
Q Consensus 172 d~iA~~l~~~~~eKQ~lLE~~~~~~Rl~~l~~~Le 206 (221)
|++|++++++.++||+|||+.|+.+|+++++++|+
T Consensus 158 ~~~a~~l~~~~~~kq~lLe~~~~~~Rl~~l~~~L~ 192 (193)
T pfam02190 158 DLIASLLPLSPEEKQELLETLDVKERLEKLLELLK 192 (193)
T ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf 99998389899999998847999999999999967
No 4
>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.7e-35 Score=237.91 Aligned_cols=204 Identities=20% Similarity=0.315 Sum_probs=175.1
Q ss_pred CCCEEECCCCEECCCCCCCEEECCHHHHHHHHHHHHCC-CCEEEEECCCCCCCCCCCCCHHHEEEEEEEECCCCCCCCCE
Q ss_conf 15533308735788851234318389999999999709-93266201234334466435211001324210134666624
Q gi|254780740|r 17 LLPIFPLLGMLLLPGSRFSFSVFERRYIAMFDSVLAGD-RLIGLVQPAISGFLANSDNGLSQIGCIGRITSFVETDDGHY 95 (221)
Q Consensus 17 ~lPi~PL~~~VlFP~~~~pL~Ife~ry~~~i~~~l~~~-~~igiv~~~~~~~~~~~~~~l~~vGt~a~I~~~~~~~dG~~ 95 (221)
.||++|||+.|+||++++||+|++++|+++++.+++++ +.+++++|++...+.+..+++|+|||+|+|.+..++|||++
T Consensus 9 ~lpvlplr~~vvfP~m~~pl~vgr~~si~ale~a~~~~~k~i~l~~qk~~~~d~p~~~dly~vGt~a~I~q~~~lpdg~~ 88 (782)
T COG0466 9 ELPVLPLRDVVVFPGMVIPLFVGREKSIKALEEAMKNDQKYILLVTQKDASTDEPTEDDLYEVGTLAKILQILKLPDGTV 88 (782)
T ss_pred CCEEEEECCCEECCCCEEEEECCCHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCHHHHHHCCCCEEEEEEEECCCCCE
T ss_conf 63068715852078851668727753799999997278877999981376657997011331200116345355799847
Q ss_pred EEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCCC-HHHHHHHHHHHHHHHHHHHHHCCC-CHH-HHHHH-HCCHHHHH
Q ss_conf 898754211110100024540689999522222541-024567888657889988651032-013-57776-30535799
Q gi|254780740|r 96 IMTVIGVCRFRLLEEAYQLNSWRCFYIAPFISDLAG-NDNDGVDRVALLEVFRNYLTVNNL-DAD-WESIE-EASNEILV 171 (221)
Q Consensus 96 ~i~v~G~~R~kI~~~~~~~~py~~a~v~~~~~d~~~-~~~~~~~~~~l~~~~~~~~~~~~~-~~~-~~~i~-~~~~~~l~ 171 (221)
+|+++|.+|++|.+ +.....|..|.++...++... ..+..+....+...|++|...+.. ..+ +..+. ..++..++
T Consensus 89 kvlveg~~R~~I~~-~~~~~~~~~a~~~~i~~~~~~~~~~~~al~~~i~~~~~~~~~l~~~~~~e~l~~~~~i~~~~kla 167 (782)
T COG0466 89 KVLVEGLQRVRISK-LSDEEEFFEAEIELLPDEPIDEEREIEALVRSILSEFEEYAKLNKKIPPEELQSLNSIDDPGKLA 167 (782)
T ss_pred EEEEEEEEEEEEEE-ECCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHH
T ss_conf 99997641689875-42677716999886377765432679999999999999999845578999997775156457899
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHH--HHHHHHHHHHHCCCC
Q ss_conf 99998679998999998536898999999999999--999997423210349
Q gi|254780740|r 172 NSLAMLSPFSEEEKQALLEAPDFRARAQTLIAIMK--IVLARAYTHCENRLQ 221 (221)
Q Consensus 172 d~iA~~l~~~~~eKQ~lLE~~~~~~Rl~~l~~~Le--~el~~~~~~~~~~vq 221 (221)
|++|++++++.++||++||+.|+.+|+++++.+++ .++.+.+++|.++|+
T Consensus 168 d~iaa~l~~~~~~kQ~iLe~~~v~~Rlek~l~~l~~ei~~~~~ek~I~~kVk 219 (782)
T COG0466 168 DTIAAHLPLKLEEKQEILETLDVKERLEKLLDLLEKEIDLLQLEKRIRKKVK 219 (782)
T ss_pred HHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999857787899999987188999999999999999999999999999999
No 5
>TIGR00763 lon ATP-dependent protease La; InterPro: IPR004815 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This signature defines the bacterial and eukaryotic lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). This family of sequences does not include the archaeal lon homologs, IPR004663 from INTERPRO. In the eukaryotes the majority of the proteins are located in the mitochondrial matrix , . In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response .; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0006510 ATP-dependent proteolysis.
Probab=99.96 E-value=1.7e-28 Score=198.68 Aligned_cols=203 Identities=16% Similarity=0.241 Sum_probs=169.4
Q ss_pred CEEECCCCEECCCCCCCEEEC--CHHHHHHHHHHHHCCCCEE---EEECCCCCCCCC-----CCCCHHHEEEEEEEECCC
Q ss_conf 533308735788851234318--3899999999997099326---620123433446-----643521100132421013
Q gi|254780740|r 19 PIFPLLGMLLLPGSRFSFSVF--ERRYIAMFDSVLAGDRLIG---LVQPAISGFLAN-----SDNGLSQIGCIGRITSFV 88 (221)
Q Consensus 19 Pi~PL~~~VlFP~~~~pL~If--e~ry~~~i~~~l~~~~~ig---iv~~~~~~~~~~-----~~~~l~~vGt~a~I~~~~ 88 (221)
|++|+++.|+|||+++||.|+ +++++++|++++.....++ ++.+++...+.+ +..++|++||+|+|++..
T Consensus 1 p~Lp~~~~~lFPg~~~~i~v~~D~~~~~~~i~~~~~~~~~~~G~~~f~~kd~~~~~~~~~i~~~~d~Y~~Gv~a~I~~~~ 80 (941)
T TIGR00763 1 PLLPLRRRPLFPGMIKPIVVGSDREKSIKLIKEALRLKQPYLGIVVFLQKDDDNEEPKLVITEEDDIYSVGVVAQILEML 80 (941)
T ss_pred CCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHCCCHHHHHHEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEEE
T ss_conf 95411782016844189986058789999999998721100102110010056667432014621100676215445420
Q ss_pred CCCC-----CCEEEEEEEEEEEEECCCCC---------------------------------------------------
Q ss_conf 4666-----62489875421111010002---------------------------------------------------
Q gi|254780740|r 89 ETDD-----GHYIMTVIGVCRFRLLEEAY--------------------------------------------------- 112 (221)
Q Consensus 89 ~~~d-----G~~~i~v~G~~R~kI~~~~~--------------------------------------------------- 112 (221)
+++| ++|.++++|.+|++|.+.+.
T Consensus 81 ~~~~~~~~~~~~~~~v~Gl~R~~i~e~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~v~~eL~~~~~~e~~~~ 160 (941)
T TIGR00763 81 KLPDEKSGTATYKVVVEGLRRIRIKELVDPDEEVDPEEEEAEDARKPRDKKSASKKSPKLEDAEVESELSAKEPKEEKEE 160 (941)
T ss_pred CCCCCCCCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCEECHHHHCCCCCCCCCC
T ss_conf 26777656551689986033057743268887888766650113311013341777887244201503311367875568
Q ss_pred ----------CCCCEEEEEEEECC---CCC-CCH-HHHHHHHHHHHHHHHHHHHHCCCCH----HHHHHHH-----CCHH
Q ss_conf ----------45406899995222---225-410-2456788865788998865103201----3577763-----0535
Q gi|254780740|r 113 ----------QLNSWRCFYIAPFI---SDL-AGN-DNDGVDRVALLEVFRNYLTVNNLDA----DWESIEE-----ASNE 168 (221)
Q Consensus 113 ----------~~~py~~a~v~~~~---~d~-~~~-~~~~~~~~~l~~~~~~~~~~~~~~~----~~~~i~~-----~~~~ 168 (221)
++.+|+.++|+... ++. ..+ .+..+....+.+.++++++.+.+.- .+..+.. .++.
T Consensus 161 ~~~~~~~~~~~~~~~~~v~v~~l~m~~~~~~~~~~~~~~Al~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~S~~v~~~P~ 240 (941)
T TIGR00763 161 ESEELPEITLQKEEYLVVRVDNLKMEKDEPFDKDDEEIKALTREIKETFRELISLSKLFREQPALLSALEDSANVIDEPG 240 (941)
T ss_pred CCCCCCCHHHHCCCEEEEEEEEEECCCCCCCCHHCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCH
T ss_conf 87544300110167558986421001024530002023478999999999998523120003777432544475104622
Q ss_pred HHHHHHHHHCCCC-HHHHHHHHCCCCHH-HHHHHHHHHH--HH---HHHHHHHHHHCCCC
Q ss_conf 7999999867999-89999985368989-9999999999--99---99997423210349
Q gi|254780740|r 169 ILVNSLAMLSPFS-EEEKQALLEAPDFR-ARAQTLIAIM--KI---VLARAYTHCENRLQ 221 (221)
Q Consensus 169 ~l~d~iA~~l~~~-~~eKQ~lLE~~~~~-~Rl~~l~~~L--e~---el~~~~~~~~~~vq 221 (221)
.|||++|+.+++. ..++|.+||+.|+. +||++++.+| |+ ++++.++.|.++|+
T Consensus 241 ~LaD~~Aa~~~~~e~~e~Q~vLe~~n~~h~RL~k~l~l~~~E~Ghi~~~kl~~~I~~~V~ 300 (941)
T TIGR00763 241 RLADLVAASLQLKEIEELQEVLETVNIEHKRLKKALELLKKELGHIELLKLQNKIAKKVE 300 (941)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 588899986320362689999874085257899999998863104678999999889999
No 6
>KOG2004 consensus
Probab=99.58 E-value=2.2e-13 Score=103.87 Aligned_cols=208 Identities=19% Similarity=0.200 Sum_probs=138.9
Q ss_pred HHCCCCCCEEECCCCEECCCCCCCEEECCHHHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCCCH---------------
Q ss_conf 678431553330873578885123431838999999999970-9932662012343344664352---------------
Q gi|254780740|r 12 EDLPCLLPIFPLLGMLLLPGSRFSFSVFERRYIAMFDSVLAG-DRLIGLVQPAISGFLANSDNGL--------------- 75 (221)
Q Consensus 12 ~~lp~~lPi~PL~~~VlFP~~~~pL~Ife~ry~~~i~~~l~~-~~~igiv~~~~~~~~~~~~~~l--------------- 75 (221)
-+.|..+|++|++.-|+|||..+++.|-.++.++++++.+.. .-++|+...++..........+
T Consensus 63 ~~~~~~l~~Lpi~~~pLfPGf~~~i~v~~~~~~~~i~~~l~~~qpyiG~fl~kdd~~~~~~~t~~~~vyi~~~~~~~~~~ 142 (906)
T KOG2004 63 PDVPPRLPALPITRGPLFPGFYKRIEVKSPKVLALIREKLRRQQPYIGAFLLKDDSSGDSVITSINEVYILEVFPGKDKL 142 (906)
T ss_pred CCCCCCCCEEECCCCCCCCCCEEEEEECCHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCEEECCCCCEEEEECCCCCH
T ss_conf 65575452433367776777236888268889999999997308641214303677787404441533124541277612
Q ss_pred ------HHEEEEE---EEECCCCCCCCCEEEEEEEEEEEEECCCCCCCCCEE--EEEEEECCCC-CCCHHHHHHHHHHHH
Q ss_conf ------1100132---421013466662489875421111010002454068--9999522222-541024567888657
Q gi|254780740|r 76 ------SQIGCIG---RITSFVETDDGHYIMTVIGVCRFRLLEEAYQLNSWR--CFYIAPFISD-LAGNDNDGVDRVALL 143 (221)
Q Consensus 76 ------~~vGt~a---~I~~~~~~~dG~~~i~v~G~~R~kI~~~~~~~~py~--~a~v~~~~~d-~~~~~~~~~~~~~l~ 143 (221)
++.+.++ .|..-.+-..+.+.+.+.|.+|+++.. ..+..++. ..++....+. ...+++..+....+.
T Consensus 143 ~~~l~~hRr~~~~~~~~~~~g~~~~~~~~~~~~~~~~r~~i~e-~~~e~~~~vl~v~v~~v~~e~~~~~~~~ka~~~ei~ 221 (906)
T KOG2004 143 RMVLYPHRRIRITELAPISEGKEDAEVEYSLLVTGLSRLNITE-MKEEKEAEVLSVEVENVKDEPFKKDEEIKALTSEIL 221 (906)
T ss_pred HHHHHHHHEEEEEEECCCCCCCCCCCCCEEECCCCCCCCCCHH-HHCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHH
T ss_conf 3334033303422211455444456664432356521245012-102466774256531056776676537789999999
Q ss_pred HHHHHHHHHCCCCHH-----HHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH--HHHHHHHH
Q ss_conf 889988651032013-----57776305357999999867999899999853689899999999999999--99974232
Q gi|254780740|r 144 EVFRNYLTVNNLDAD-----WESIEEASNEILVNSLAMLSPFSEEEKQALLEAPDFRARAQTLIAIMKIV--LARAYTHC 216 (221)
Q Consensus 144 ~~~~~~~~~~~~~~~-----~~~i~~~~~~~l~d~iA~~l~~~~~eKQ~lLE~~~~~~Rl~~l~~~Le~e--l~~~~~~~ 216 (221)
..+++....+.+.-. ...+...++..|+|+.|+.+..+..+.|++|++.|+.+|+++.+.+++.+ +++..+.+
T Consensus 222 ~t~rdii~~n~l~r~~v~~~~~~~~~~~~~~LaD~~aai~~~~~~elq~vL~~~di~~Rl~~al~llkke~e~~klq~ki 301 (906)
T KOG2004 222 KTLRDIIAVNSLFREQVATLSQLIVEDNPIKLADFGAAISGAEFHELQEVLEETDIEKRLEKALELLKKELELAKLQQKI 301 (906)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999997527789999999987344675678899888851477899999874387889999999999999999999885
Q ss_pred HCCC
Q ss_conf 1034
Q gi|254780740|r 217 ENRL 220 (221)
Q Consensus 217 ~~~v 220 (221)
...|
T Consensus 302 ~k~v 305 (906)
T KOG2004 302 GKEV 305 (906)
T ss_pred HHHH
T ss_conf 3677
No 7
>KOG4159 consensus
Probab=99.49 E-value=1.7e-13 Score=104.47 Aligned_cols=111 Identities=27% Similarity=0.451 Sum_probs=95.1
Q ss_pred HHCCCCCCEEECCCCEECCCCCCCEEECCHHHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCCCHHHEEEEEEEECCCCC
Q ss_conf 678431553330873578885123431838999999999970-9932662012343344664352110013242101346
Q gi|254780740|r 12 EDLPCLLPIFPLLGMLLLPGSRFSFSVFERRYIAMFDSVLAG-DRLIGLVQPAISGFLANSDNGLSQIGCIGRITSFVET 90 (221)
Q Consensus 12 ~~lp~~lPi~PL~~~VlFP~~~~pL~Ife~ry~~~i~~~l~~-~~~igiv~~~~~~~~~~~~~~l~~vGt~a~I~~~~~~ 90 (221)
.+.-...|+||+ .+..||...+||++||+||..|++.|+.. ++.||++.+.... +....+++||+.+|.++..+
T Consensus 171 ~~~e~~~p~f~v-~~~~~p~v~cpl~vfe~~y~lm~~r~~~~~~~rf~i~~sd~~~----~~~~~~e~g~i~ei~~v~~l 245 (398)
T KOG4159 171 SSRECESPLFPV-CTLAFPEVPCPLQVFEPRYRLMIRRLLETGDKRFGICLSDSSK----GSGQAAEIGCILEIRKVESL 245 (398)
T ss_pred CCCCCCCCCCCC-CCCCCCCCCCCHHHCCCHHHHHHHHHHHHCCEEEEEECCCCCC----CCCHHHHCCCHHHHCCCCCC
T ss_conf 332024776330-4000335667178706429999999986255022124266557----86314333310433035002
Q ss_pred CCCCEEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCC
Q ss_conf 66624898754211110100024540689999522222
Q gi|254780740|r 91 DDGHYIMTVIGVCRFRLLEEAYQLNSWRCFYIAPFISD 128 (221)
Q Consensus 91 ~dG~~~i~v~G~~R~kI~~~~~~~~py~~a~v~~~~~d 128 (221)
+||+..+...|..||++.. ...+++|..|.+++.++.
T Consensus 246 ~dgrsv~~~~gk~r~r~~~-~~~~d~y~~~~ve~l~d~ 282 (398)
T KOG4159 246 GDGRSVVDSIGKSRFRVLL-FSQTDGYPVADVEYLEDR 282 (398)
T ss_pred CCCCHHHHHHCCCCEEEEE-ECCCCCCEEEEEEEEECC
T ss_conf 5640456542576514565-217876314443223074
No 8
>smart00464 LON Found in ATP-dependent protease La (LON). N-terminal domain of the ATP-dependent protease La (LON), present also in other bacterial ORFs.
Probab=98.74 E-value=1.7e-08 Score=73.14 Aligned_cols=90 Identities=24% Similarity=0.308 Sum_probs=76.3
Q ss_pred CCCEEECCCCEECCCCCCCEEECCHHHHHHHHHHHHCC-CCEEEEECCCCCCCCCCCCCHHHEEEEEEEECCCCCCCCCE
Q ss_conf 15533308735788851234318389999999999709-93266201234334466435211001324210134666624
Q gi|254780740|r 17 LLPIFPLLGMLLLPGSRFSFSVFERRYIAMFDSVLAGD-RLIGLVQPAISGFLANSDNGLSQIGCIGRITSFVETDDGHY 95 (221)
Q Consensus 17 ~lPi~PL~~~VlFP~~~~pL~Ife~ry~~~i~~~l~~~-~~igiv~~~~~~~~~~~~~~l~~vGt~a~I~~~~~~~dG~~ 95 (221)
.+|++|+++.++|||...++.+.+++..+++.+.+... ..+|+..+++...+.
T Consensus 1 ~~~~lpi~~~~lfpg~~~~i~v~~~~~v~ai~e~~~~~qp~v~~~l~~d~~~~~-------------------------- 54 (92)
T smart00464 1 TLPLLPIRRRPLFPGFVLPIPVKRPKSVAAIKEALRRSQPYVIVFLLQDDPTET-------------------------- 54 (92)
T ss_pred CCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCCCCCC--------------------------
T ss_conf 975212567766887557788388889999999998169825688853689998--------------------------
Q ss_pred EEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHH
Q ss_conf 89875421111010002454068999952222254102456788865788998865103201357776305357999999
Q gi|254780740|r 96 IMTVIGVCRFRLLEEAYQLNSWRCFYIAPFISDLAGNDNDGVDRVALLEVFRNYLTVNNLDADWESIEEASNEILVNSLA 175 (221)
Q Consensus 96 ~i~v~G~~R~kI~~~~~~~~py~~a~v~~~~~d~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~l~d~iA 175 (221)
+..++++++
T Consensus 55 -----------------------------------------------------------------------~~~~s~~~~ 63 (92)
T smart00464 55 -----------------------------------------------------------------------PEPLSDTIA 63 (92)
T ss_pred -----------------------------------------------------------------------CCCCCHHHH
T ss_conf -----------------------------------------------------------------------864410066
Q ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 8679998999998536898999999999
Q gi|254780740|r 176 MLSPFSEEEKQALLEAPDFRARAQTLIA 203 (221)
Q Consensus 176 ~~l~~~~~eKQ~lLE~~~~~~Rl~~l~~ 203 (221)
+.+++...+||.+||+.+++.|+++.++
T Consensus 64 ~~~~~~~~~~q~lL~~~~~~~R~~~~i~ 91 (92)
T smart00464 64 ALMPLELHEKQELLELEGTNKRLEKVIK 91 (92)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHC
T ss_conf 7616889888899986160177888742
No 9
>KOG1400 consensus
Probab=96.67 E-value=0.0027 Score=40.42 Aligned_cols=188 Identities=14% Similarity=0.144 Sum_probs=95.9
Q ss_pred CCCCCEEECCCCEECCCCCCCEEECCHHHHHHHHHHHHC--CCCEEEEECCCCCCCCCCCCCHHHEEEEEEEECCCCCC-
Q ss_conf 431553330873578885123431838999999999970--99326620123433446643521100132421013466-
Q gi|254780740|r 15 PCLLPIFPLLGMLLLPGSRFSFSVFERRYIAMFDSVLAG--DRLIGLVQPAISGFLANSDNGLSQIGCIGRITSFVETD- 91 (221)
Q Consensus 15 p~~lPi~PL~~~VlFP~~~~pL~Ife~ry~~~i~~~l~~--~~~igiv~~~~~~~~~~~~~~l~~vGt~a~I~~~~~~~- 91 (221)
-..+|++++-.+|+|||..+||.++.|+-+.+++.-... ++.|.+....+. .+....-+|.+.|-. -+.|
T Consensus 63 ~~~~p~~~~~~~v~~PgqtLPl~~i~~~~~s~~r~lvs~ar~~~F~vl~r~~v------~~re~~r~tt~evd~-~R~p~ 135 (371)
T KOG1400 63 TNWIPICGQVMAVLFPGQTLPLKFIDPQERSIVRRLVSSARDNGFVVLFRSDV------PERESLRYTTTEVDA-YRVPQ 135 (371)
T ss_pred EEEECCCCCEEEEECCCCCCCCHHCCHHHHHHHHHHHHHHCCCCEEEEECCCC------HHHHHCCCCCEECCC-CCCCH
T ss_conf 02631467204686476668600059889999999987611796589850424------677634660000035-65603
Q ss_pred C--CC--EEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCC----CCH--HHHHH---------------------H-H
Q ss_conf 6--62--48987542111101000245406899995222225----410--24567---------------------8-8
Q gi|254780740|r 92 D--GH--YIMTVIGVCRFRLLEEAYQLNSWRCFYIAPFISDL----AGN--DNDGV---------------------D-R 139 (221)
Q Consensus 92 d--G~--~~i~v~G~~R~kI~~~~~~~~py~~a~v~~~~~d~----~~~--~~~~~---------------------~-~ 139 (221)
| |. .++...|.-|+++.+.-.+..+--.+++.-.|.+. ... ...+. . .
T Consensus 136 d~Fgn~l~~~~~~G~y~~~vl~lR~qs~g~~e~~~qL~P~~~i~~~~~Sf~~~~avq~~~~n~~~ia~~~n~~p~s~e~d 215 (371)
T KOG1400 136 DNFGNALSMVKAMGRYRCKVLKLRTQSLGRGEAEVQLLPDVEIPCLLPSFIPKSAVQLPAHNKCSIATRINGYPFSAERD 215 (371)
T ss_pred HHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCEEEECCCCCCCCCCCCCCCHHHHEECCCCCCEECCCCCCCCCCCCCC
T ss_conf 44410202226426410232441135877666347744655322246553422341102457603214788885564432
Q ss_pred HHHHHHHHH--------------------------HHHHCCCCH--HHHHHHHC-----CHHHHHHHHHHHCCCCHHHHH
Q ss_conf 865788998--------------------------865103201--35777630-----535799999986799989999
Q gi|254780740|r 140 VALLEVFRN--------------------------YLTVNNLDA--DWESIEEA-----SNEILVNSLAMLSPFSEEEKQ 186 (221)
Q Consensus 140 ~~l~~~~~~--------------------------~~~~~~~~~--~~~~i~~~-----~~~~l~d~iA~~l~~~~~eKQ 186 (221)
..-...|+. ++..+.... -|.++.+. .+..+++.+|..++..-.-++
T Consensus 216 m~sla~f~~i~sls~~h~~~ll~~~~was~tyqSy~la~rivenarl~yE~lk~ds~~~kpivlSf~~a~kihv~e~~~~ 295 (371)
T KOG1400 216 MTSLAVFRQIGSLSGFHGDDLLSWPKWASLTYQSYFLAKRIVENARLWYELLKEDSAPGKPIVLSFKYAWKIHVCERCRE 295 (371)
T ss_pred HHHHHHHEEHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHHHH
T ss_conf 22344421105454321454003433412778899999999988888987506333678855753254444126289999
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 98536898999999999999999
Q gi|254780740|r 187 ALLEAPDFRARAQTLIAIMKIVL 209 (221)
Q Consensus 187 ~lLE~~~~~~Rl~~l~~~Le~el 209 (221)
.||...++..|+.+....++.+.
T Consensus 296 hL~~~g~v~tRlq~e~~~~~k~t 318 (371)
T KOG1400 296 HLLWEGSVMTRLQREFFGIQKET 318 (371)
T ss_pred HHHHHCCCCCCHHEEEECCCCHH
T ss_conf 98862354301110340302001
No 10
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=81.05 E-value=0.59 Score=25.78 Aligned_cols=159 Identities=14% Similarity=0.092 Sum_probs=78.4
Q ss_pred HHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCHHHEEEEEEEECCCCCCCCCEEEEEEEEEEEEECCCCCCCCCEEEEEE
Q ss_conf 99999999970993266201234334466435211001324210134666624898754211110100024540689999
Q gi|254780740|r 43 YIAMFDSVLAGDRLIGLVQPAISGFLANSDNGLSQIGCIGRITSFVETDDGHYIMTVIGVCRFRLLEEAYQLNSWRCFYI 122 (221)
Q Consensus 43 y~~~i~~~l~~~~~igiv~~~~~~~~~~~~~~l~~vGt~a~I~~~~~~~dG~~~i~v~G~~R~kI~~~~~~~~py~~a~v 122 (221)
-.+|.+.-.+.|-...-...+.=..-+=+.+|+|.+||+|-|..+.+++. .|.|-.-. -.=|--+++|
T Consensus 9 Dk~A~dkLi~~N~~LV~siv~rF~nRGYe~eDlFQIGciGLvKAidkFD~-~y~VKFST-----------YAVPmI~GEI 76 (231)
T TIGR02885 9 DKEARDKLIEENLRLVSSIVKRFLNRGYEYEDLFQIGCIGLVKAIDKFDL-SYDVKFST-----------YAVPMIMGEI 76 (231)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCC-CCCEEEEE-----------CCCCHHHHHH
T ss_conf 48999999872334689999985206887000022211556665542176-77701552-----------1222022122
Q ss_pred EECCCCCCCHHHH----------HHHHHHHHHHHHHHH------HHCCCC--------------HH-HHHH--HHCCHHH
Q ss_conf 5222225410245----------678886578899886------510320--------------13-5777--6305357
Q gi|254780740|r 123 APFISDLAGNDND----------GVDRVALLEVFRNYL------TVNNLD--------------AD-WESI--EEASNEI 169 (221)
Q Consensus 123 ~~~~~d~~~~~~~----------~~~~~~l~~~~~~~~------~~~~~~--------------~~-~~~i--~~~~~~~ 169 (221)
..|..|...-.-. ...++.|...+.+=+ +..|+. .. .+.+ +..+|-.
T Consensus 77 kRFLRDDG~ikVSRSlK~la~k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~~~sly~tvh~dDGdPi~ 156 (231)
T TIGR02885 77 KRFLRDDGIIKVSRSLKELARKIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARSLQSLYDTVHEDDGDPIL 156 (231)
T ss_pred HHHHCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHCCEEECCCCCHHH
T ss_conf 23102688557515278999999877999999838998889998875878878664420257610110011417946446
Q ss_pred HHHHHHHH--CCCCHHHH---HHHHCCCCHHHHHHHHHHHH----HHHHHHHH
Q ss_conf 99999986--79998999---99853689899999999999----99999974
Q gi|254780740|r 170 LVNSLAML--SPFSEEEK---QALLEAPDFRARAQTLIAIM----KIVLARAY 213 (221)
Q Consensus 170 l~d~iA~~--l~~~~~eK---Q~lLE~~~~~~Rl~~l~~~L----e~el~~~~ 213 (221)
|+|.+|.. -.-++.+| ++.|...+.++|.-.++.+. +.|.|+.-
T Consensus 157 LlD~i~d~~~~~~~~~~ki~Lke~i~~Ld~rer~ii~LRYFKDkTQ~eVA~~L 209 (231)
T TIGR02885 157 LLDQIADKGSEDSDLLEKIALKEAISKLDERERQIIMLRYFKDKTQTEVAKML 209 (231)
T ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHC
T ss_conf 76652125771368999899999986125226789774101400179999771
No 11
>smart00755 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245.
Probab=43.49 E-value=23 Score=15.78 Aligned_cols=25 Identities=36% Similarity=0.470 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCC
Q ss_conf 3579999998679998999998536
Q gi|254780740|r 167 NEILVNSLAMLSPFSEEEKQALLEA 191 (221)
Q Consensus 167 ~~~l~d~iA~~l~~~~~eKQ~lLE~ 191 (221)
...++-.+++.+.++++++|.+++.
T Consensus 22 ~~~ll~vist~L~fs~~e~q~l~~~ 46 (46)
T smart00755 22 RETLLKVISTVLQLSPEEMQKLLEV 46 (46)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHCC
T ss_conf 8889999999983599999767339
No 12
>TIGR02272 gentisate_1_2 gentisate 1,2-dioxygenase; InterPro: IPR011960 This family consists of gentisate 1,2-dioxygenases. This ring-opening enzyme acts in salicylate degradation that goes via gentisate rather than via catechol. It converts gentisate to maleylpyruvate. Some putative gentisate 1,2-dioxygenases may be excluded from this entry..
Probab=43.45 E-value=24 Score=15.68 Aligned_cols=92 Identities=13% Similarity=0.112 Sum_probs=56.0
Q ss_pred EEECCCCEECC-CCCCCEEECC-HHHHHHHHHHHHC---CCCEEEEECCCCCCCCCCCCCHHHEEEEEEEE------CCC
Q ss_conf 33308735788-8512343183-8999999999970---99326620123433446643521100132421------013
Q gi|254780740|r 20 IFPLLGMLLLP-GSRFSFSVFE-RRYIAMFDSVLAG---DRLIGLVQPAISGFLANSDNGLSQIGCIGRIT------SFV 88 (221)
Q Consensus 20 i~PL~~~VlFP-~~~~pL~Ife-~ry~~~i~~~l~~---~~~igiv~~~~~~~~~~~~~~l~~vGt~a~I~------~~~ 88 (221)
++|++...-=+ -+..|++=.. .|++.++++..+. |..-|+-... .....+....-+||+-.+.+ +..
T Consensus 197 l~P~r~~~~~~rp~ssPiF~YpY~~~ReAL~~l~~~~~~D~~~G~kL~y--~NP~~G~~~Mpti~~f~qllP~gf~t~~~ 274 (343)
T TIGR02272 197 LLPVRHKRSDKRPTSSPIFSYPYERSREALDKLKRTGEVDPWHGLKLRY--VNPATGGFAMPTISAFIQLLPKGFRTATY 274 (343)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHCCEEEEE--ECCCCCCCCCHHHHHHHHHCCHHHCCCCC
T ss_conf 5520000167876668731277000068999999734885114743686--47767785503489999860321147755
Q ss_pred CCCCCCEEEEEEEEEEEEECCCCCC
Q ss_conf 4666624898754211110100024
Q gi|254780740|r 89 ETDDGHYIMTVIGVCRFRLLEEAYQ 113 (221)
Q Consensus 89 ~~~dG~~~i~v~G~~R~kI~~~~~~ 113 (221)
+.-|+|+.+.|+|..+++|.+....
T Consensus 275 RSTDaTvf~vvEG~G~~~Ig~~~f~ 299 (343)
T TIGR02272 275 RSTDATVFCVVEGRGQVRIGDAVFE 299 (343)
T ss_pred CCCCCEEEEEECCCCEEEECCEEEE
T ss_conf 5446406888717733677882776
No 13
>pfam01465 GRIP GRIP domain. The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi. The GRIP domain contains a completely conserved tyrosine residue. At least some of these domains have been shown to bind to GTPase Arl1, see structures in.
Probab=27.62 E-value=43 Score=14.08 Aligned_cols=22 Identities=45% Similarity=0.582 Sum_probs=18.2
Q ss_pred HHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 5799999986799989999985
Q gi|254780740|r 168 EILVNSLAMLSPFSEEEKQALL 189 (221)
Q Consensus 168 ~~l~d~iA~~l~~~~~eKQ~lL 189 (221)
..++..+++.+.|+.+++|.++
T Consensus 24 ~~llpvi~tlL~fs~~e~~~i~ 45 (45)
T pfam01465 24 EQLLPVISTLLKFSPEEKQKIL 45 (45)
T ss_pred HHHHHHHHHHHCCCHHHHHCCC
T ss_conf 9889999999828999984019
No 14
>TIGR00506 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; InterPro: IPR000422 3,4-Dihydroxy-2-butanone 4-phosphate is biosynthesized from ribulose 5-phosphate and serves as the biosynthetic precursor for the xylene ring of riboflavin . It 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 34-dihydroxy-2-butanone-4-phosphate synthase activity, 0009231 riboflavin biosynthetic process.
Probab=27.33 E-value=27 Score=15.32 Aligned_cols=20 Identities=5% Similarity=0.021 Sum_probs=10.5
Q ss_pred EEEEEEEEECCCCC-CCCCEE
Q ss_conf 75421111010002-454068
Q gi|254780740|r 99 VIGVCRFRLLEEAY-QLNSWR 118 (221)
Q Consensus 99 v~G~~R~kI~~~~~-~~~py~ 118 (221)
-..-+||++++.+. .+.||-
T Consensus 77 ~~~~~k~pvlrkl~p~Di~Yd 97 (230)
T TIGR00506 77 TSASEKLPVLRKLTPDDIPYD 97 (230)
T ss_pred HHHHCCCCCCCCCCCCCCCCC
T ss_conf 022113550100067867877
No 15
>cd03169 GATase1_PfpI_1 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.
Probab=25.33 E-value=47 Score=13.82 Aligned_cols=38 Identities=13% Similarity=0.301 Sum_probs=26.1
Q ss_pred CCEECCCCCCCEEEC-CHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf 735788851234318-38999999999970993266201
Q gi|254780740|r 25 GMLLLPGSRFSFSVF-ERRYIAMFDSVLAGDRLIGLVQP 62 (221)
Q Consensus 25 ~~VlFP~~~~pL~If-e~ry~~~i~~~l~~~~~igiv~~ 62 (221)
+.+++||..-|-++. .+.-++++++..+.++.++.+|.
T Consensus 78 Dai~iPGG~g~~~l~~d~~~~~li~~~~~~gK~iaaICh 116 (180)
T cd03169 78 DALVIPGGRAPEYLRLDEKVLAIVRHFAEANKPVAAICH 116 (180)
T ss_pred CEEEECCCCCHHHHHCCHHHHHHHHHHHHCCCEEEEECC
T ss_conf 999989982287771197999999999981996997781
Done!