Query 017036
Match_columns 378
No_of_seqs 196 out of 516
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 05:02:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017036.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017036hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00261 traB pheromone shutd 100.0 8.6E-62 1.9E-66 486.0 24.0 254 88-371 2-261 (380)
2 COG1916 Uncharacterized homolo 100.0 1.1E-57 2.5E-62 445.5 23.5 257 88-371 10-270 (388)
3 KOG2860 Uncharacterized conser 100.0 1.1E-53 2.4E-58 410.4 5.7 338 8-376 10-355 (359)
4 PF01963 TraB: TraB family; I 99.9 4.4E-26 9.4E-31 215.7 10.3 225 88-324 8-247 (259)
5 COG3735 Uncharacterized protei 99.4 2.1E-13 4.6E-18 132.2 8.4 229 81-322 33-284 (299)
6 PF04187 DUF399: Protein of un 95.9 0.039 8.6E-07 51.9 8.6 29 287-317 174-202 (213)
7 KOG2860 Uncharacterized conser 94.2 0.0055 1.2E-07 60.8 -2.7 105 183-325 129-234 (359)
8 PHA03049 IMV membrane protein; 69.9 6.4 0.00014 30.6 3.5 27 349-375 2-28 (68)
9 PF03808 Glyco_tran_WecB: Glyc 60.9 22 0.00047 32.1 5.9 41 91-131 74-116 (172)
10 PF05961 Chordopox_A13L: Chord 60.4 12 0.00026 29.2 3.4 26 350-375 3-28 (68)
11 cd05013 SIS_RpiR RpiR-like pro 51.3 61 0.0013 26.6 6.7 37 89-126 13-49 (139)
12 PF11044 TMEMspv1-c74-12: Plec 50.8 37 0.0008 24.6 4.3 30 346-375 2-34 (49)
13 PF14582 Metallophos_3: Metall 42.5 23 0.0005 34.4 3.0 59 64-122 139-212 (255)
14 PF01212 Beta_elim_lyase: Beta 38.9 1.1E+02 0.0025 30.0 7.4 41 86-126 89-134 (290)
15 PF14202 TnpW: Transposon-enco 36.1 40 0.00088 23.2 2.6 20 89-109 8-27 (37)
16 TIGR00228 ruvC crossover junct 35.7 33 0.00072 31.0 2.8 32 92-123 25-64 (156)
17 cd05014 SIS_Kpsf KpsF-like pro 34.6 1.5E+02 0.0033 24.3 6.6 32 90-122 1-32 (128)
18 TIGR00696 wecB_tagA_cpsF bacte 34.0 96 0.0021 28.4 5.6 39 92-131 75-115 (177)
19 PF02075 RuvC: Crossover junct 33.7 38 0.00082 30.0 2.8 31 95-125 28-67 (149)
20 PRK00039 ruvC Holliday junctio 33.4 39 0.00084 30.6 2.8 21 105-125 50-70 (164)
21 KOG2629 Peroxisomal membrane a 33.0 52 0.0011 32.8 3.8 32 345-376 76-107 (300)
22 PF10945 DUF2629: Protein of u 30.9 48 0.001 23.9 2.4 28 36-63 16-43 (44)
23 PF02571 CbiJ: Precorrin-6x re 30.5 41 0.0009 32.5 2.7 32 186-220 200-231 (249)
24 PRK08057 cobalt-precorrin-6x r 30.1 42 0.00092 32.4 2.7 31 186-219 196-226 (248)
25 cd00529 RuvC_resolvase Hollida 27.0 1.1E+02 0.0024 27.0 4.7 22 104-125 47-68 (154)
26 COG3016 PhuW Uncharacterized i 26.7 1.1E+02 0.0023 30.3 4.7 57 268-324 189-251 (295)
27 cd02067 B12-binding B12 bindin 26.4 89 0.0019 25.8 3.7 31 88-122 26-56 (119)
28 cd06533 Glyco_transf_WecG_TagA 25.3 96 0.0021 27.9 4.0 39 91-129 72-112 (171)
29 COG0817 RuvC Holliday junction 24.3 52 0.0011 30.0 2.0 19 105-123 46-64 (160)
30 PF15361 RIC3: Resistance to i 24.1 73 0.0016 28.6 2.9 26 349-374 78-103 (152)
31 PF06724 DUF1206: Domain of Un 23.1 1E+02 0.0022 23.7 3.2 21 356-376 49-69 (73)
32 PRK14762 membrane protein; Pro 22.8 1.2E+02 0.0025 19.4 2.7 23 351-373 2-26 (27)
33 PF08727 P3A: Poliovirus 3A pr 20.4 50 0.0011 25.1 0.9 15 24-38 4-19 (57)
No 1
>TIGR00261 traB pheromone shutdown-related protein TraB. traB is a plasmid encoded gene that functions in the shutdown of the peptide sex pheromone cPD1 which is produced by the plasmid free recipient cell prior to conjugative transfer in Enterococcus faecalis. Once the recipient acquires the plasmid, production of cPD1 is shut down. The gene product may play another role in the other species in the family.
Probab=100.00 E-value=8.6e-62 Score=486.01 Aligned_cols=254 Identities=27% Similarity=0.450 Sum_probs=224.1
Q ss_pred CCceEEEEeecCCChhhHHHHHHHHHHcCCCeEEEeeccchhccccCCC--CCCChhhhhhhhccccCCccccccccccc
Q 017036 88 EPENIWLIGTTHLSQDSAADVERVVRAIKPDNVVVELCRSRAGIMYTSN--GGENDQQLRSNMFSLSGTGFFGAVGRSID 165 (378)
Q Consensus 88 ~~~~VyLVGTaHvS~~Sa~~V~~vI~~vkPD~V~VELc~~R~~~L~~~~--~~~l~~~l~~~~~~~~~~~~~~~~~~si~ 165 (378)
++++||||||||+|++|+++|+++|+++|||+||||||++|++.|.... +.++.++++
T Consensus 2 ~~~~i~lvGTAHvS~~S~~eV~~~I~~~~PD~VaVELd~~R~~~l~~~~~~~~di~~vlk-------------------- 61 (380)
T TIGR00261 2 HEKTIYILGTAHVSKKSSEEVANLIEILKPDYIAVELDERRYHSLLNTKWRNLDIDKVLK-------------------- 61 (380)
T ss_pred CCcEEEEEecccCCHHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHhhhhhccCCHHHHhh--------------------
Confidence 5799999999999999999999999999999999999999999887652 334455544
Q ss_pred ccchhHHHHHHHHHHHHhhhhccCCCCChHHHHHHHHHHHHhCCeEeecCchhHHHHHHHHccCChHHHHHHHHHHHHhc
Q 017036 166 LGGQTALALRLLLALFSSKISSDVNRPFGDEFRAARKVAEEVGAQIVLGDRPIEITLERAWNSLKWNEKLNLLINVIRGI 245 (378)
Q Consensus 166 ~gg~~~l~~~llL~~~q~~l~~~lg~~PG~Efr~Ai~~A~~~ga~VvLgDR~i~iTl~R~~~~ls~~eklkl~~~ll~~~ 245 (378)
.|+...++.+++|++||+++++++|++||+||++|+++|++.||+|+|+||||++|++|+|++|++|+|+|++++++.+.
T Consensus 62 ~g~~~~~l~~~~La~~q~~l~~~~gi~PG~Em~~Ai~~A~e~g~~v~LiDRdI~iTl~R~w~~~~~~eK~kl~~~l~~~~ 141 (380)
T TIGR00261 62 QGNAFFLIINLILANFQKKLGEEQGIKPGSEMKTAIEKAKKHGIPLILIDRDIETTLKRAWISITFFEKAKIISSLFSST 141 (380)
T ss_pred cCchHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCcEEEeCCCHhHHHHHHHHhCCHHHHHHHHHHHHhcc
Confidence 34445678899999999999999999999999999999999999999999999999999999999999999999998766
Q ss_pred cCCCCCChhhhcCCCCchHHHHHHHHHHhhCCCcccchhhhccHHHHHHHHHhhhhCCCCeEEEEECCCchhhhHhhhhh
Q 017036 246 TSPSDMSLDNLKEPSPDDSTFQLYKKLSFSCPSLLLPLIHERDKYLAWSLKRSKAVNNSKKVVGVIGKGHMNGVIYALVS 325 (378)
Q Consensus 246 ~~~~~~s~eevE~~k~~D~l~~l~~el~~~~P~l~~~LidERD~yma~~L~~~~~~~~~~~vVaVVGagHl~GI~~~L~~ 325 (378)
+ +.+++++|+++++|.++++++|+++.+|.++++|++|||+|||++|.+.. .+++++|+||||||++||+++|.+
T Consensus 142 ~---~~~e~~ie~l~~~d~L~~~~~e~~~~~P~l~~~LIdERD~ymA~~L~~l~--~~~~~VvaVVGAGHl~GI~~~l~~ 216 (380)
T TIGR00261 142 D---AKIEDEIEKLLEQDALSKIMKELSKISPKVKKVLIDERDEFMANKLLEGE--GNKNIIVAVVGAGHVSGIMRTLKK 216 (380)
T ss_pred c---cCCHHHHHHhhhhhHHHHHHHHHhhhCCchhhHHHHHHHHHHHHHHHHhh--cCCCcEEEEECcchhhhHHHHHhC
Confidence 5 46789999999999999999999999999999999999999999999874 345799999999999999999987
Q ss_pred cCC--CCCcccccCCCCCCCCCChhH-HHHHHHHHHHHHHHHHH-HHHHH
Q 017036 326 DQG--NLRFRDLAGKRPSGDGSNGWI-ASLLKSLVRDTVIGILL-WALYE 371 (378)
Q Consensus 326 ~~~--~~~~~~l~~~~~~~~~~~~~~-~k~~~~~~~~~~ig~~~-~~~~~ 371 (378)
++. .+++.+|.++| +++++ .|+++|+|+++++++++ |+||.
T Consensus 217 ~~~~~~~~~~~L~~~p-----~~~~~~~k~~~~~i~~~i~~~~~~~~~~~ 261 (380)
T TIGR00261 217 LQNKNIINLEELEKVK-----KKHFSFSKVLSYLIAISIILLFVMISFYL 261 (380)
T ss_pred ccccCCCChHHHhcCC-----CCCccHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 643 33456666665 44444 49999999999999888 99886
No 2
>COG1916 Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown]
Probab=100.00 E-value=1.1e-57 Score=445.55 Aligned_cols=257 Identities=30% Similarity=0.436 Sum_probs=223.6
Q ss_pred CCceEEEEeecCCChhhHHHHHHHHHHcCCCeEEEeeccchhccccCCCC--CCChhhhhhhhccccCCccccccccccc
Q 017036 88 EPENIWLIGTTHLSQDSAADVERVVRAIKPDNVVVELCRSRAGIMYTSNG--GENDQQLRSNMFSLSGTGFFGAVGRSID 165 (378)
Q Consensus 88 ~~~~VyLVGTaHvS~~Sa~~V~~vI~~vkPD~V~VELc~~R~~~L~~~~~--~~l~~~l~~~~~~~~~~~~~~~~~~si~ 165 (378)
+.++|||+||||+|++|.++|+++|++.+||+|+||||+.|+..|..... .++.+++|+
T Consensus 10 ~~~~v~iiGTAHVS~~SveeVrr~I~~~~PDaVAVELd~~R~~sLl~~~~~~ldl~~vlk~------------------- 70 (388)
T COG1916 10 EEKEVYILGTAHVSKDSVEEVRRIILEEKPDAVAVELDEARLLSLLGGSREELDLAQVLKE------------------- 70 (388)
T ss_pred ccceEEEEeeeecCHhHHHHHHHHHHhcCCCeEEEEecHHHHHHHhcCCcccCCHHHHHHc-------------------
Confidence 45699999999999999999999999999999999999999988877655 444566654
Q ss_pred ccchhHHHHHHHHHHHHhhhhccCCCCChHHHHHHHHHHHHhCCeEeecCchhHHHHHHHHccCChHHHHHHHHHHHHhc
Q 017036 166 LGGQTALALRLLLALFSSKISSDVNRPFGDEFRAARKVAEEVGAQIVLGDRPIEITLERAWNSLKWNEKLNLLINVIRGI 245 (378)
Q Consensus 166 ~gg~~~l~~~llL~~~q~~l~~~lg~~PG~Efr~Ai~~A~~~ga~VvLgDR~i~iTl~R~~~~ls~~eklkl~~~ll~~~ 245 (378)
|+...++.+++|++||+++++++|++||+||++||+.|++.|+||+++||||++||+|+|.+|++|||+|++++++.++
T Consensus 71 -Gk~~~~l~~~lLa~~Qrklg~~~Gv~PGsEmk~AIe~A~e~ga~V~lIDRdI~vTl~R~~~~~~~~EKlK~~~~L~~~~ 149 (388)
T COG1916 71 -GKAFFLLAGLLLAYFQRKLGKELGVKPGSEMKAAIEAARELGAPVALIDRDIGVTLRRAWAKMPFWEKLKLISSLISGL 149 (388)
T ss_pred -CchHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCCEEEecccHHHHHHHHHHhCCHHHHHHHHHHHHHhc
Confidence 4445678899999999999999999999999999999999999999999999999999999999999999999999873
Q ss_pred cCCCCCChhhhcCCCCchHHHHHHHHHHhhCCCcccchhhhccHHHHHHHHHhhhhCCCCeEEEEECCCchhhhHhhhhh
Q 017036 246 TSPSDMSLDNLKEPSPDDSTFQLYKKLSFSCPSLLLPLIHERDKYLAWSLKRSKAVNNSKKVVGVIGKGHMNGVIYALVS 325 (378)
Q Consensus 246 ~~~~~~s~eevE~~k~~D~l~~l~~el~~~~P~l~~~LidERD~yma~~L~~~~~~~~~~~vVaVVGagHl~GI~~~L~~ 325 (378)
..+ ..++.++++++..|+++.+|+|+++.+|++|++||||||+|||++|.+.. +...+|||||||||..||+++|++
T Consensus 150 ~~~-g~~e~ei~~l~~~D~~~al~~efr~~~P~~~~vLIDERd~ymA~nll~~~--~~~~~vvAVVGAGH~~GI~~~L~~ 226 (388)
T COG1916 150 LFP-GQSEIEIDELKQEDVLSALMQEFRRFSPTVYKVLIDERDRYMARNLLEIV--SILNDVVAVVGAGHVRGIERYLKN 226 (388)
T ss_pred ccC-CCchHHHHHHhhhhHHHHHHHHHHHhChhHHHHHHHHHHHHHHHHHHHHH--cccCcEEEEEccccHHHHHHHHhc
Confidence 322 23788999999999999999999999999999999999999999999875 344569999999999999999988
Q ss_pred cCCCCC-cccccCCCCCCCCCChhHHHHH-HHHHHHHHHHHHHHHHHH
Q 017036 326 DQGNLR-FRDLAGKRPSGDGSNGWIASLL-KSLVRDTVIGILLWALYE 371 (378)
Q Consensus 326 ~~~~~~-~~~l~~~~~~~~~~~~~~~k~~-~~~~~~~~ig~~~~~~~~ 371 (378)
+++..+ ..||+++++ ..++..|++ .|++.++++++++-+||.
T Consensus 227 ~~~~p~~l~el~~~~~----~~~s~~k~~~g~~~~~l~~~~iv~~~~~ 270 (388)
T COG1916 227 SDSAPPHLEELTELEK----KGSSLGKVLLGILLAALLIFLIVICFGL 270 (388)
T ss_pred cccCCccHHHHhcccc----cccchhhhHHHHHHHHHHHHHHHHHHhc
Confidence 665554 688888876 345666666 888888888888777653
No 3
>KOG2860 consensus Uncharacterized conserved protein, contains TraB domain [Signal transduction mechanisms]
Probab=100.00 E-value=1.1e-53 Score=410.42 Aligned_cols=338 Identities=30% Similarity=0.374 Sum_probs=287.1
Q ss_pred CCCcccCCCCCCCCCCCCccccccCCCCCCchhhhhhhhhhHHHHHhhchhhhhhhccCceeeeccccCCCCCccccccc
Q 017036 8 TFPIFSANPNLLSTKPIKPFKVSIKPPPQDFDFRTEILSDSQATIAKACPELLNLADDGTLVLIQKRQFGPVPAWRSEFV 87 (378)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~ 87 (378)
.||+|+++ .+++. .+ ++.++..|||+|++|..|..+++++++..+|+ .|++.+ + .++..++|.++|+- +.
T Consensus 10 ~~~~~~~~--e~~~~-~~-~~~~~~g~~~~~~~r~di~~~~~~a~a~~~~e-~dla~~-~---~~~~~~~~d~~~~k-~l 79 (359)
T KOG2860|consen 10 DYELEQAP--EATED-AV-VNNPVCGGYHFGRKRADIFVPNANAVAVLKWE-TDLAIP-P---RNPVLSDSDEEWKK-AI 79 (359)
T ss_pred cccccCCh--Hhhhh-hh-ccCcccCCcccchhhhhccchhhhhhhccCCc-hhcccC-C---CCCcccCCcHHHHH-hh
Confidence 37888776 55555 33 67889999999999999999999999999999 999977 4 67778889999998 66
Q ss_pred CCceEEEEeecCCChhhHHHHHHHHHHcCCCeEEEeeccchhccccCCCCCCChhhhhhhhccccCCccccccccccccc
Q 017036 88 EPENIWLIGTTHLSQDSAADVERVVRAIKPDNVVVELCRSRAGIMYTSNGGENDQQLRSNMFSLSGTGFFGAVGRSIDLG 167 (378)
Q Consensus 88 ~~~~VyLVGTaHvS~~Sa~~V~~vI~~vkPD~V~VELc~~R~~~L~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~si~~g 167 (378)
.+++||||||+|+|++|+++|..+|+.+|||.|+||||++|..++..++. .+.++.-.+.|.+|.+...++.+.+
T Consensus 80 ~~s~i~lVgTah~S~Es~~~v~~virtv~pd~V~vElCrsr~sIis~~ep-----~l~se~evl~g~~f~~~~~~~~~~g 154 (359)
T KOG2860|consen 80 LDSTIYLVGTAHFSKESQEDVSNVIRAVQPDFVMVELCRSRISIISADEP-----QLLSEAEVLNGAKFRGIFEEAGKIG 154 (359)
T ss_pred ccceeEEEEeeecCccccccHHHHhhccCcceeehhhccchhhcccccCh-----hhhccCcccCCcceeeeeccccccC
Confidence 78999999999999999999999999999999999999999888765543 2333344456888999888888888
Q ss_pred chhHHHHHHHHHHHHhhhhccCCCCChHHHHHHHHHHHH-hCCeEeecCchhHHHHHHHHccCChHHHHHHHHHHHHhcc
Q 017036 168 GQTALALRLLLALFSSKISSDVNRPFGDEFRAARKVAEE-VGAQIVLGDRPIEITLERAWNSLKWNEKLNLLINVIRGIT 246 (378)
Q Consensus 168 g~~~l~~~llL~~~q~~l~~~lg~~PG~Efr~Ai~~A~~-~ga~VvLgDR~i~iTl~R~~~~ls~~eklkl~~~ll~~~~ 246 (378)
|...+ ++..++.+..+++++.||+||+.|.+++-+ .||.++||||||++||+|+|++|++|++.++++++....
T Consensus 155 G~~~L----~lrsv~a~~~~dLdmaa~gefr~a~~efs~~~g~~v~lgDrpieitLqRa~~eLs~~~a~~lv~~vt~s~- 229 (359)
T KOG2860|consen 155 GIVFL----LLRSVSAKDLGDLDMAAGGEFRRASREFSTLMGCLVVLGDRPIEITLQRALSELSSWQAVVLVGHVTFSK- 229 (359)
T ss_pred ceEeh----hhhhhhhhhccccccccchhHHHHhhhhccCCCceEEecCCcceeeHHHHHHhcchhheeeEEEEEEEee-
Confidence 88654 566677778888999999999999998854 599999999999999999999999999999888764322
Q ss_pred CCCCCChhhhcCCCCchHHHHHHHHHHhhCCCcccchhhhccHHHHHHHHHhhhh--C-----CCCeEEEEECCCchhhh
Q 017036 247 SPSDMSLDNLKEPSPDDSTFQLYKKLSFSCPSLLLPLIHERDKYLAWSLKRSKAV--N-----NSKKVVGVIGKGHMNGV 319 (378)
Q Consensus 247 ~~~~~s~eevE~~k~~D~l~~l~~el~~~~P~l~~~LidERD~yma~~L~~~~~~--~-----~~~~vVaVVGagHl~GI 319 (378)
++.++.+++|.|++.|.+++++.+|...+|.+..+|+.|||.||++.|+.+..+ . .+-.+|+|||.||.+||
T Consensus 230 -~~s~~t~eve~c~q~~Lveql~~~~a~~vp~~~lvlv~eRd~yl~~slelif~v~~~~gq~~~~~mvvvVvgi~~~sG~ 308 (359)
T KOG2860|consen 230 -KNSIQTEEVENCKQTDLVEQLTIEMANFVPALSLVLVQERDLYLCHSLELIFTVWLRGGQQILPYMVVVVVGIGHVSGI 308 (359)
T ss_pred -ccccchhhhhhhhHHhHHHHHHHHHHhhHHHHHHHHHHHHHhhhccchhheeeecccCCccccceEEEEEEEEEecchh
Confidence 345667899999999999999999999999999999999999999999876432 1 23579999999999999
Q ss_pred HhhhhhcCCCCCcccccCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 017036 320 IYALVSDQGNLRFRDLAGKRPSGDGSNGWIASLLKSLVRDTVIGILLWALYEQVKGT 376 (378)
Q Consensus 320 ~~~L~~~~~~~~~~~l~~~~~~~~~~~~~~~k~~~~~~~~~~ig~~~~~~~~~~~~~ 376 (378)
-..|+. +++..++++| +++|..|++|+.+++++||+ +|+.||..+..
T Consensus 309 ~~~~~~----~~~d~~~~~~-----~~~~~qkv~k~~vr~~~igl-~~l~~r~~~~~ 355 (359)
T KOG2860|consen 309 YLAWNT----IDFDPLMNIP-----PPSLGQKVFKTGVRIVVIGL-GYLAYRGGRAI 355 (359)
T ss_pred hhhhcc----cCCCCcCCCC-----ChHHHHHHHhhchheeeeeh-HHHHHhhchhh
Confidence 998864 3444577776 78999999999999999994 49999976543
No 4
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=99.93 E-value=4.4e-26 Score=215.73 Aligned_cols=225 Identities=25% Similarity=0.247 Sum_probs=165.1
Q ss_pred CCceEEEEeecCCChhhHHHHHHHHHH--cCCCeEEEeeccch-------hccccCCCCCCChhhhhhhhccccCCcccc
Q 017036 88 EPENIWLIGTTHLSQDSAADVERVVRA--IKPDNVVVELCRSR-------AGIMYTSNGGENDQQLRSNMFSLSGTGFFG 158 (378)
Q Consensus 88 ~~~~VyLVGTaHvS~~Sa~~V~~vI~~--vkPD~V~VELc~~R-------~~~L~~~~~~~l~~~l~~~~~~~~~~~~~~ 158 (378)
++.++||+||+|+++.+...+...|++ .+||+|+||++..- ...+..+++..+.+.+....+.. ...++.
T Consensus 8 ~g~~~yL~GT~H~~~~~~~~~~~~i~~a~~~sd~v~~E~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~~~~~~-l~~~~~ 86 (259)
T PF01963_consen 8 NGKTVYLLGTIHVSPKSFYPLPDAIEEALKKSDVVVVELDMSDPEAQAQMQQAMMLPDGKTLKDLLSPEEYAR-LEELLA 86 (259)
T ss_pred CCeEEEEEeccCCCchhhhhhHHHHHHHHhcCCEEEEecccccHHHHHHHHhhccCCCcccHHHhcCHHHHHH-HHHHHH
Confidence 478999999999999999999999999 99999999991111 11122222233333322221111 001111
Q ss_pred cc---cccccccchhHHHHHHHHHHHHhhhhccCCCCChHHHHHHHHHHHHhCCeEe-ecCchhHHHHHHHHccCChHHH
Q 017036 159 AV---GRSIDLGGQTALALRLLLALFSSKISSDVNRPFGDEFRAARKVAEEVGAQIV-LGDRPIEITLERAWNSLKWNEK 234 (378)
Q Consensus 159 ~~---~~si~~gg~~~l~~~llL~~~q~~l~~~lg~~PG~Efr~Ai~~A~~~ga~Vv-LgDR~i~iTl~R~~~~ls~~ek 234 (378)
.. ...++..++|.+++.+....+++.+..+.|+.++.+++ |++.|++|. |+|++.|+++. ++++.+++
T Consensus 87 ~~~~~~~~~~~~~p~~~~~~l~~~~~~~~~~~~~gvd~~l~~~-----A~~~~~~v~~Le~~~~q~~~~---~~~~~~~q 158 (259)
T PF01963_consen 87 EYGLPLEMLRKLKPWAAAFLLSLSAFQKGYSPEYGVDPYLEQR-----AAEEGKPVVGLETREEQITLL---RSLPLDEQ 158 (259)
T ss_pred hcCCCHHHHHcCCHHHHHHHHHHHHHhccccccccccHHHHHH-----HHHhCCCcccccCHHHHHHHH---hcCCHHHH
Confidence 11 14566788899888888888988888888999998888 555666655 89999999955 56699999
Q ss_pred HHHHHHHHHhccCCCCCChhhhcCCCCchHHHHHHHHHHh--hCCCcccchhhhccHHHHHHHHHhhhhCCCCeEEEEEC
Q 017036 235 LNLLINVIRGITSPSDMSLDNLKEPSPDDSTFQLYKKLSF--SCPSLLLPLIHERDKYLAWSLKRSKAVNNSKKVVGVIG 312 (378)
Q Consensus 235 lkl~~~ll~~~~~~~~~s~eevE~~k~~D~l~~l~~el~~--~~P~l~~~LidERD~yma~~L~~~~~~~~~~~vVaVVG 312 (378)
.+++..++..+........+.++.|+++|. +.+++.+.+ .+|.+++.|+++||++|+.+|.++. +..+++|+|||
T Consensus 159 ~~~L~~~l~~~~~~~~~~~~~~~~~~~gd~-~~l~~~~~~~~~~p~~~~~ll~~RN~~~~~~i~~~l--~~~~~~fvvVG 235 (259)
T PF01963_consen 159 VKMLRETLDDIEDGEKMLEQLIEAWKNGDL-DALMELMKEDESFPELYEVLLDERNRRWAEKIEELL--KEGGTVFVVVG 235 (259)
T ss_pred HHHHHHHHhccccchHHHHHHHHHHHccCH-HHHHHHHHhcccCHHHHHHHHHHHhHHHHHHHHHHH--hcCCCEEEEEc
Confidence 999988886654333334456666888886 778888887 8999999999999999999999875 34579999999
Q ss_pred CCchhhhHhhhh
Q 017036 313 KGHMNGVIYALV 324 (378)
Q Consensus 313 agHl~GI~~~L~ 324 (378)
|||+.|....+.
T Consensus 236 a~HL~G~~gvl~ 247 (259)
T PF01963_consen 236 AGHLPGEDGVLD 247 (259)
T ss_pred chhccchhhHHH
Confidence 999998777653
No 5
>COG3735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.44 E-value=2.1e-13 Score=132.17 Aligned_cols=229 Identities=15% Similarity=0.137 Sum_probs=135.4
Q ss_pred cccccccCCceEEEEeecCCChhh----HHHHHHHHHHcCCCeEEEeeccc--------h--hccccCCCCCCChhhhhh
Q 017036 81 AWRSEFVEPENIWLIGTTHLSQDS----AADVERVVRAIKPDNVVVELCRS--------R--AGIMYTSNGGENDQQLRS 146 (378)
Q Consensus 81 ~~~~~~~~~~~VyLVGTaHvS~~S----a~~V~~vI~~vkPD~V~VELc~~--------R--~~~L~~~~~~~l~~~l~~ 146 (378)
.|..+--.++.+||+||.|++..- ...+.++++. -+.++||+|.. + -......+..++.+.+++
T Consensus 33 ~~~i~~~G~s~~yL~GTiHvg~~~~~~lp~~~~~a~~~--A~tLivE~d~~~~~~~a~i~~~~~l~~~~~~~~l~~~Ls~ 110 (299)
T COG3735 33 FWKIEKPGNSPLYLLGTIHVGSPRVLPLPDKLLKALDQ--ADTLIVEADDIVKKNTAVILKQPMLTGFTDGENLEDRLSP 110 (299)
T ss_pred ceeeecCCCCceEEeeeeecCCCccccCCHHHHHHHhh--cCceEEEeccccccchHHHhcccccccCCCCcchhhhcCH
Confidence 666666566779999999998765 5667777776 99999999951 1 111222333344443333
Q ss_pred hhccccCCccc---ccccccccccchhHHHHHHHHHHHHhhhhccCCCCChHHHHHHHHHHHHhCCeEeecCc-hhHHHH
Q 017036 147 NMFSLSGTGFF---GAVGRSIDLGGQTALALRLLLALFSSKISSDVNRPFGDEFRAARKVAEEVGAQIVLGDR-PIEITL 222 (378)
Q Consensus 147 ~~~~~~~~~~~---~~~~~si~~gg~~~l~~~llL~~~q~~l~~~lg~~PG~Efr~Ai~~A~~~ga~VvLgDR-~i~iTl 222 (378)
.-+.. ..... |..-..++...+|.+.+.+.+..+++. + +.-..|-|.. -.+.|++.|.||+--+- ..|+.
T Consensus 111 e~~~~-le~~~~~lGi~~~~~~~~~pW~la~~L~~~~~~~~-~--~~~~~giD~~-L~q~A~~~~k~I~gLEt~~~Ql~- 184 (299)
T COG3735 111 EQLAR-LEMILQELGIPLQALSKMPPWQLASVLAATQCEKA-G--LRGEYGIDYQ-LLQAAKAQNKPILGLETAEEQLA- 184 (299)
T ss_pred HHHHH-HHHHHHHcCCCHHHHhcCCcHHHHHHHHHHHHHHc-C--cCcccchhHH-HHHHHHHcCCCccchhhHHHHHH-
Confidence 11110 00001 111245677788887777666666543 1 2334466655 56789999999887544 44544
Q ss_pred HHHHccCChHHHHHHHHHHHHhccCCCCCChhhhcCCCCch--HHHHHHH---HHHhhCCCcccchhhhccHHHHHHHHH
Q 017036 223 ERAWNSLKWNEKLNLLINVIRGITSPSDMSLDNLKEPSPDD--STFQLYK---KLSFSCPSLLLPLIHERDKYLAWSLKR 297 (378)
Q Consensus 223 ~R~~~~ls~~eklkl~~~ll~~~~~~~~~s~eevE~~k~~D--~l~~l~~---el~~~~P~l~~~LidERD~yma~~L~~ 297 (378)
+++.++...-++++..++..--+..+.-+-.+.-+.+.| ++...+. .+...++.++++|+.+||..|+.+ +.
T Consensus 185 --~l~~LP~d~~i~~L~~tl~~~~~~~d~l~tmi~~~l~gD~~~~~~~~~~~~~~~~~~~~~~~~li~~RN~~wad~-~~ 261 (299)
T COG3735 185 --ALASLPLDFGIELLIDTLALGDTNADLLETMIDLWLNGDVGMFMPNLQAILPNKTFYADLYDVLITQRNRAWADK-KT 261 (299)
T ss_pred --HHHcCChHHHHHHHHHHHHccccHHHHHHHHHHHHHcCCcchhhHHHhhhCccccchHHHHHHHHHHHHHHHHHh-hc
Confidence 788888666666666554310000001111122233333 1222221 222456778999999999999997 22
Q ss_pred hhhhCCCCeEEEEECCCchhhhHhh
Q 017036 298 SKAVNNSKKVVGVIGKGHMNGVIYA 322 (378)
Q Consensus 298 ~~~~~~~~~vVaVVGagHl~GI~~~ 322 (378)
.. -.+++.|++|||||+.|-+..
T Consensus 262 ~~--l~~G~~fvaVGAlHL~G~e~L 284 (299)
T COG3735 262 PL--LQGGRYFVAVGALHLPGPEGL 284 (299)
T ss_pred cc--cCCCCEEEEeccccccCcccH
Confidence 21 268999999999999996543
No 6
>PF04187 DUF399: Protein of unknown function, DUF399; InterPro: IPR007314 No function is known for any member of this family.; PDB: 2G5G_X.
Probab=95.90 E-value=0.039 Score=51.92 Aligned_cols=29 Identities=28% Similarity=0.406 Sum_probs=22.9
Q ss_pred ccHHHHHHHHHhhhhCCCCeEEEEECCCchh
Q 017036 287 RDKYLAWSLKRSKAVNNSKKVVGVIGKGHMN 317 (378)
Q Consensus 287 RD~yma~~L~~~~~~~~~~~vVaVVGagHl~ 317 (378)
||..||.+|.+.. .++.++|+|+|.||+.
T Consensus 174 ~D~~MA~~i~~~~--~~~~~vv~i~G~gH~~ 202 (213)
T PF04187_consen 174 WDATMAESIAAAL--HPGRPVVVIAGNGHVR 202 (213)
T ss_dssp HHHHHHHHHHH-S-----SEEEEEEEHHHH-
T ss_pred HHHHHHHHHHHHH--hccCeEEEEeCcchhc
Confidence 9999999998875 4589999999999985
No 7
>KOG2860 consensus Uncharacterized conserved protein, contains TraB domain [Signal transduction mechanisms]
Probab=94.16 E-value=0.0055 Score=60.77 Aligned_cols=105 Identities=17% Similarity=0.164 Sum_probs=79.8
Q ss_pred hhhhccCCCCChHHHHHHHHHHHHhCCeEeecCchhHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCChhhhcCCCCc
Q 017036 183 SKISSDVNRPFGDEFRAARKVAEEVGAQIVLGDRPIEITLERAWNSLKWNEKLNLLINVIRGITSPSDMSLDNLKEPSPD 262 (378)
Q Consensus 183 ~~l~~~lg~~PG~Efr~Ai~~A~~~ga~VvLgDR~i~iTl~R~~~~ls~~eklkl~~~ll~~~~~~~~~s~eevE~~k~~ 262 (378)
..+.++...-+|.+|+.+++.|.+.|-.+.|+||-++.-.-+-.
T Consensus 129 p~l~se~evl~g~~f~~~~~~~~~~gG~~~L~lrsv~a~~~~dL------------------------------------ 172 (359)
T KOG2860|consen 129 PQLLSEAEVLNGAKFRGIFEEAGKIGGIVFLLLRSVSAKDLGDL------------------------------------ 172 (359)
T ss_pred hhhhccCcccCCcceeeeeccccccCceEehhhhhhhhhhcccc------------------------------------
Confidence 44566677889999999999999999999999997764321111
Q ss_pred hHHH-HHHHHHHhhCCCcccchhhhccHHHHHHHHHhhhhCCCCeEEEEECCCchhhhHhhhhh
Q 017036 263 DSTF-QLYKKLSFSCPSLLLPLIHERDKYLAWSLKRSKAVNNSKKVVGVIGKGHMNGVIYALVS 325 (378)
Q Consensus 263 D~l~-~l~~el~~~~P~l~~~LidERD~yma~~L~~~~~~~~~~~vVaVVGagHl~GI~~~L~~ 325 (378)
|++. .-+..+..+|+++...++++||++|.-+|+++.+ .-.-.+++++-+|+.++.+.+..
T Consensus 173 dmaa~gefr~a~~efs~~~g~~v~lgDrpieitLqRa~~--eLs~~~a~~lv~~vt~s~~~s~~ 234 (359)
T KOG2860|consen 173 DMAAGGEFRRASREFSTLMGCLVVLGDRPIEITLQRALS--ELSSWQAVVLVGHVTFSKKNSIQ 234 (359)
T ss_pred ccccchhHHHHhhhhccCCCceEEecCCcceeeHHHHHH--hcchhheeeEEEEEEEeeccccc
Confidence 1111 1134556788999999999999999999998863 56777888888999999877643
No 8
>PHA03049 IMV membrane protein; Provisional
Probab=69.95 E-value=6.4 Score=30.65 Aligned_cols=27 Identities=15% Similarity=0.548 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 017036 349 IASLLKSLVRDTVIGILLWALYEQVKG 375 (378)
Q Consensus 349 ~~k~~~~~~~~~~ig~~~~~~~~~~~~ 375 (378)
++-++-.+|=.+|+|+|+||.|.--++
T Consensus 2 I~d~~l~iICVaIi~lIvYgiYnkk~~ 28 (68)
T PHA03049 2 IGDIILVIICVVIIGLIVYGIYNKKTT 28 (68)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 344556677788999999999986544
No 9
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=60.92 E-value=22 Score=32.09 Aligned_cols=41 Identities=20% Similarity=0.299 Sum_probs=30.1
Q ss_pred eEEEEeecCC--ChhhHHHHHHHHHHcCCCeEEEeeccchhcc
Q 017036 91 NIWLIGTTHL--SQDSAADVERVVRAIKPDNVVVELCRSRAGI 131 (378)
Q Consensus 91 ~VyLVGTaHv--S~~Sa~~V~~vI~~vkPD~V~VELc~~R~~~ 131 (378)
.+-++|+.|- .++..+.+.+.|.+.+||+|+|=+-..+.+.
T Consensus 74 ~l~ivg~~~g~f~~~~~~~i~~~I~~~~pdiv~vglG~PkQE~ 116 (172)
T PF03808_consen 74 GLRIVGYHHGYFDEEEEEAIINRINASGPDIVFVGLGAPKQER 116 (172)
T ss_pred CeEEEEecCCCCChhhHHHHHHHHHHcCCCEEEEECCCCHHHH
Confidence 5677887774 5667788888888888888888776655443
No 10
>PF05961 Chordopox_A13L: Chordopoxvirus A13L protein; InterPro: IPR009236 This family consists of A13L proteins from the Chordopoxviruses. A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus [].
Probab=60.41 E-value=12 Score=29.21 Aligned_cols=26 Identities=19% Similarity=0.572 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc
Q 017036 350 ASLLKSLVRDTVIGILLWALYEQVKG 375 (378)
Q Consensus 350 ~k~~~~~~~~~~ig~~~~~~~~~~~~ 375 (378)
.-++-.+|=.+++|+|+||.|.-.++
T Consensus 3 ~d~iLi~ICVaii~lIlY~iYnr~~~ 28 (68)
T PF05961_consen 3 GDFILIIICVAIIGLILYGIYNRKKT 28 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 44555677788999999999986554
No 11
>cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
Probab=51.30 E-value=61 Score=26.59 Aligned_cols=37 Identities=14% Similarity=0.094 Sum_probs=29.9
Q ss_pred CceEEEEeecCCChhhHHHHHHHHHHcCCCeEEEeecc
Q 017036 89 PENIWLIGTTHLSQDSAADVERVVRAIKPDNVVVELCR 126 (378)
Q Consensus 89 ~~~VyLVGTaHvS~~Sa~~V~~vI~~vkPD~V~VELc~ 126 (378)
.+.|+++|+-+ |...+......++...+++.++.-..
T Consensus 13 ~~~i~i~g~g~-s~~~a~~~~~~l~~~~~~~~~~~~~~ 49 (139)
T cd05013 13 ARRIYIFGVGS-SGLVAEYLAYKLLRLGKPVVLLSDPH 49 (139)
T ss_pred CCEEEEEEcCc-hHHHHHHHHHHHHHcCCceEEecCHH
Confidence 47899999976 77889999999999888777764433
No 12
>PF11044 TMEMspv1-c74-12: Plectrovirus spv1-c74 ORF 12 transmembrane protein; InterPro: IPR022743 This is a group of proteins expressed by Plectroviruses. The Plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. This entry represents putative transmembrane proteins of unknown function.
Probab=50.82 E-value=37 Score=24.55 Aligned_cols=30 Identities=17% Similarity=0.589 Sum_probs=20.7
Q ss_pred ChhHHHHHHHHHHHHH---HHHHHHHHHHHhhc
Q 017036 346 NGWIASLLKSLVRDTV---IGILLWALYEQVKG 375 (378)
Q Consensus 346 ~~~~~k~~~~~~~~~~---ig~~~~~~~~~~~~ 375 (378)
|+|++-++...|.+.+ +|+.+|-=.+++++
T Consensus 2 p~wlt~iFsvvIil~If~~iGl~IyQkikqIrg 34 (49)
T PF11044_consen 2 PTWLTTIFSVVIILGIFAWIGLSIYQKIKQIRG 34 (49)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4688888887777767 66666666666654
No 13
>PF14582 Metallophos_3: Metallophosphoesterase, calcineurin superfamily; PDB: 1UF3_B 2YVT_A.
Probab=42.51 E-value=23 Score=34.36 Aligned_cols=59 Identities=25% Similarity=0.360 Sum_probs=39.3
Q ss_pred ccCceeeeccccCCC--CCccc--------ccccCCceEEEEeecC-C----ChhhHHHHHHHHHHcCCCeEEE
Q 017036 64 DDGTLVLIQKRQFGP--VPAWR--------SEFVEPENIWLIGTTH-L----SQDSAADVERVVRAIKPDNVVV 122 (378)
Q Consensus 64 ~~~~~~~~~~~~~~p--~~~~~--------~~~~~~~~VyLVGTaH-v----S~~Sa~~V~~vI~~vkPD~V~V 122 (378)
..|++..-++.++-+ +|.|. .++-+...|.|+.|.- + ....++.|+.+|+..+|++|+.
T Consensus 139 ~GGeI~~~~~~~~~~LrYP~weaey~lk~l~elk~~r~IlLfhtpPd~~kg~~h~GS~~V~dlIk~~~P~ivl~ 212 (255)
T PF14582_consen 139 MGGEITDDQREEEFKLRYPAWEAEYSLKFLRELKDYRKILLFHTPPDLHKGLIHVGSAAVRDLIKTYNPDIVLC 212 (255)
T ss_dssp E-SEEESSS-BCSSS-EEEHHHHHHHHGGGGGCTSSEEEEEESS-BTBCTCTBTTSBHHHHHHHHHH--SEEEE
T ss_pred cCccccCCCccccccccchHHHHHHHHHHHHhcccccEEEEEecCCccCCCcccccHHHHHHHHHhcCCcEEEe
Confidence 456777667777666 89987 4444567888877755 1 2234789999999999999987
No 14
>PF01212 Beta_elim_lyase: Beta-eliminating lyase; InterPro: IPR001597 This domain is found in many tryptophanases (tryptophan indole-lyase, TNase), tyrosine phenol-lyases (TPL) and threonine aldolases. It is involved in the degradation of amino acids. The glycine cleavage system is composed of four proteins: P, T, L and H. In Bacillus subtilis, the P 'protein' is an heterodimer of two subunits. The glycine cleavage system catalyses the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein; GO: 0016829 lyase activity, 0006520 cellular amino acid metabolic process; PDB: 3PJ0_C 2C44_C 2V0Y_A 2OQX_A 2V1P_A 1AX4_B 3LWS_A 1C7G_A 1V72_A 2YHK_B ....
Probab=38.86 E-value=1.1e+02 Score=29.99 Aligned_cols=41 Identities=12% Similarity=0.132 Sum_probs=34.1
Q ss_pred ccCCceEEEEeecCCChhhHHHHHHHHHH-----cCCCeEEEeecc
Q 017036 86 FVEPENIWLIGTTHLSQDSAADVERVVRA-----IKPDNVVVELCR 126 (378)
Q Consensus 86 ~~~~~~VyLVGTaHvS~~Sa~~V~~vI~~-----vkPD~V~VELc~ 126 (378)
...+.++.-|++.+..+-+.++++++|++ .+|-+|++|.+.
T Consensus 89 ~~~G~~~~~l~~~~~G~l~~~~l~~~~~~~~~h~~~~~~v~le~t~ 134 (290)
T PF01212_consen 89 ELSGAKLIPLPSDDDGKLTPEDLEAAIEEHGAHHPQPAVVSLENTT 134 (290)
T ss_dssp HHTTCEEEEEBECTGTBB-HHHHHHHHHHHTGTSGGEEEEEEESSB
T ss_pred HhcCcEEEECCCcccCCCCHHHHHHHhhhccccCCCccEEEEEecC
Confidence 33678899999987688889999999999 788999999877
No 15
>PF14202 TnpW: Transposon-encoded protein TnpW
Probab=36.10 E-value=40 Score=23.15 Aligned_cols=20 Identities=15% Similarity=0.413 Sum_probs=15.4
Q ss_pred CceEEEEeecCCChhhHHHHH
Q 017036 89 PENIWLIGTTHLSQDSAADVE 109 (378)
Q Consensus 89 ~~~VyLVGTaHvS~~Sa~~V~ 109 (378)
|++.|+|.+ |+|+.|.+-.+
T Consensus 8 G~Tty~V~~-~F~~~s~et~~ 27 (37)
T PF14202_consen 8 GKTTYVVEV-HFSETSKETMQ 27 (37)
T ss_pred CCEEEEEEE-EECCCccccHH
Confidence 688999987 99988844333
No 16
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=35.67 E-value=33 Score=31.02 Aligned_cols=32 Identities=19% Similarity=0.300 Sum_probs=24.3
Q ss_pred EEEEeecCCChhh--------HHHHHHHHHHcCCCeEEEe
Q 017036 92 IWLIGTTHLSQDS--------AADVERVVRAIKPDNVVVE 123 (378)
Q Consensus 92 VyLVGTaHvS~~S--------a~~V~~vI~~vkPD~V~VE 123 (378)
+.=.|+.+.+..+ -+.++++|++.+||.|+||
T Consensus 25 ~v~~G~I~t~~~~~~~RL~~I~~~l~~~i~~y~P~~~aiE 64 (156)
T TIGR00228 25 YLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPNYFAIE 64 (156)
T ss_pred EEEeeEEECCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEe
Confidence 3445676654333 5788999999999999998
No 17
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=34.60 E-value=1.5e+02 Score=24.34 Aligned_cols=32 Identities=9% Similarity=0.125 Sum_probs=25.6
Q ss_pred ceEEEEeecCCChhhHHHHHHHHHHcCCCeEEE
Q 017036 90 ENIWLIGTTHLSQDSAADVERVVRAIKPDNVVV 122 (378)
Q Consensus 90 ~~VyLVGTaHvS~~Sa~~V~~vI~~vkPD~V~V 122 (378)
+.||++|+- .|.-.++..+..+......++++
T Consensus 1 ~~I~i~G~G-~S~~~a~~~~~~l~~~g~~~~~~ 32 (128)
T cd05014 1 GKVVVTGVG-KSGHIARKIAATLSSTGTPAFFL 32 (128)
T ss_pred CeEEEEeCc-HhHHHHHHHHHHhhcCCCceEEc
Confidence 369999998 66777888888888888887776
No 18
>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.
Probab=34.01 E-value=96 Score=28.37 Aligned_cols=39 Identities=15% Similarity=0.186 Sum_probs=25.3
Q ss_pred EEEEeecC--CChhhHHHHHHHHHHcCCCeEEEeeccchhcc
Q 017036 92 IWLIGTTH--LSQDSAADVERVVRAIKPDNVVVELCRSRAGI 131 (378)
Q Consensus 92 VyLVGTaH--vS~~Sa~~V~~vI~~vkPD~V~VELc~~R~~~ 131 (378)
+.++|. | ++++-.+++.+.|.+-+||+|+|=|-.-|.+.
T Consensus 75 l~i~g~-~g~f~~~~~~~i~~~I~~s~~dil~VglG~PkQE~ 115 (177)
T TIGR00696 75 LKIVGA-FGPLEPEERKAALAKIARSGAGIVFVGLGCPKQEI 115 (177)
T ss_pred CEEEEE-CCCCChHHHHHHHHHHHHcCCCEEEEEcCCcHhHH
Confidence 344555 4 23333466778888888888888777766554
No 19
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []. RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.
Probab=33.68 E-value=38 Score=30.02 Aligned_cols=31 Identities=29% Similarity=0.468 Sum_probs=20.2
Q ss_pred EeecCCChh-h--------HHHHHHHHHHcCCCeEEEeec
Q 017036 95 IGTTHLSQD-S--------AADVERVVRAIKPDNVVVELC 125 (378)
Q Consensus 95 VGTaHvS~~-S--------a~~V~~vI~~vkPD~V~VELc 125 (378)
.||.+.++. + .+.+.++|++.+||.|++|--
T Consensus 28 ~G~I~t~~~~~~~~Rl~~I~~~l~~li~~~~P~~vaiE~~ 67 (149)
T PF02075_consen 28 YGTIKTSSKDSLPERLKEIYEELEELIEEYNPDEVAIEEI 67 (149)
T ss_dssp EEEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEEE-
T ss_pred eCeEECCCCCCHHHHHHHHHHHHHHHHHhhCCCEEEeehh
Confidence 466776655 2 678899999999999999964
No 20
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=33.37 E-value=39 Score=30.62 Aligned_cols=21 Identities=19% Similarity=0.414 Sum_probs=18.7
Q ss_pred HHHHHHHHHHcCCCeEEEeec
Q 017036 105 AADVERVVRAIKPDNVVVELC 125 (378)
Q Consensus 105 a~~V~~vI~~vkPD~V~VELc 125 (378)
.+.+.++|++.+||.|+||-.
T Consensus 50 ~~~l~~~i~~~~Pd~vaiE~~ 70 (164)
T PRK00039 50 YDGLSELIDEYQPDEVAIEEV 70 (164)
T ss_pred HHHHHHHHHHhCCCEEEEehh
Confidence 588999999999999999953
No 21
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=32.95 E-value=52 Score=32.78 Aligned_cols=32 Identities=16% Similarity=0.203 Sum_probs=25.4
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 017036 345 SNGWIASLLKSLVRDTVIGILLWALYEQVKGT 376 (378)
Q Consensus 345 ~~~~~~k~~~~~~~~~~ig~~~~~~~~~~~~~ 376 (378)
+...+.+|--|++-+++.+-|+||+|++++.-
T Consensus 76 ~~~~~~rwrdy~vmAvi~aGi~y~~y~~~K~Y 107 (300)
T KOG2629|consen 76 QQNVLRRWRDYFVMAVILAGIAYAAYRFVKSY 107 (300)
T ss_pred CccchhhHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 34456777778888888889999999998753
No 22
>PF10945 DUF2629: Protein of unknown function (DUF2629); InterPro: IPR024487 Some members in this family of proteins are annotated as YhjR however currently no function is known.
Probab=30.86 E-value=48 Score=23.87 Aligned_cols=28 Identities=18% Similarity=0.208 Sum_probs=23.1
Q ss_pred CCchhhhhhhhhhHHHHHhhchhhhhhh
Q 017036 36 QDFDFRTEILSDSQATIAKACPELLNLA 63 (378)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (378)
|+++|+.=..++-...+-++||.|.++.
T Consensus 16 p~~~Y~DIsr~e~l~~~~~RWPLLaEl~ 43 (44)
T PF10945_consen 16 PDINYIDISREERLNQALQRWPLLAELA 43 (44)
T ss_pred CCccHHHHHHHHHHHHHHHHChhHHHHh
Confidence 7899997666666689999999988775
No 23
>PF02571 CbiJ: Precorrin-6x reductase CbiJ/CobK; InterPro: IPR003723 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y [, ].; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process, 0055114 oxidation-reduction process
Probab=30.47 E-value=41 Score=32.48 Aligned_cols=32 Identities=22% Similarity=0.357 Sum_probs=25.0
Q ss_pred hccCCCCChHHHHHHHHHHHHhCCeEeecCchhHH
Q 017036 186 SSDVNRPFGDEFRAARKVAEEVGAQIVLGDRPIEI 220 (378)
Q Consensus 186 ~~~lg~~PG~Efr~Ai~~A~~~ga~VvLgDR~i~i 220 (378)
.++.|-. |.+=+ +++|++.|++|++++||..-
T Consensus 200 tK~SG~~-g~~eK--i~AA~~lgi~vivI~RP~~~ 231 (249)
T PF02571_consen 200 TKESGGS-GFDEK--IEAARELGIPVIVIKRPPEP 231 (249)
T ss_pred EcCCCch-hhHHH--HHHHHHcCCeEEEEeCCCCC
Confidence 5566666 65444 88999999999999998763
No 24
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=30.09 E-value=42 Score=32.42 Aligned_cols=31 Identities=26% Similarity=0.382 Sum_probs=22.9
Q ss_pred hccCCCCChHHHHHHHHHHHHhCCeEeecCchhH
Q 017036 186 SSDVNRPFGDEFRAARKVAEEVGAQIVLGDRPIE 219 (378)
Q Consensus 186 ~~~lg~~PG~Efr~Ai~~A~~~ga~VvLgDR~i~ 219 (378)
.++.|-. | +.+=+++|++.|++|++++||..
T Consensus 196 tK~SG~~-g--~~eKi~AA~~lgi~vivI~RP~~ 226 (248)
T PRK08057 196 TKNSGGA-G--TEAKLEAARELGIPVVMIARPAL 226 (248)
T ss_pred EcCCCch-h--hHHHHHHHHHcCCeEEEEeCCCC
Confidence 4455544 4 34447899999999999999863
No 25
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=27.02 E-value=1.1e+02 Score=27.01 Aligned_cols=22 Identities=23% Similarity=0.388 Sum_probs=19.3
Q ss_pred hHHHHHHHHHHcCCCeEEEeec
Q 017036 104 SAADVERVVRAIKPDNVVVELC 125 (378)
Q Consensus 104 Sa~~V~~vI~~vkPD~V~VELc 125 (378)
..+.++++|+..+||.|++|--
T Consensus 47 I~~~l~~~i~~~~Pd~vaiE~~ 68 (154)
T cd00529 47 IYDGLNEVIDQFQPDVVAIERV 68 (154)
T ss_pred HHHHHHHHHHHhCCCEEEEEEh
Confidence 3789999999999999999943
No 26
>COG3016 PhuW Uncharacterized iron-regulated protein [Function unknown]
Probab=26.71 E-value=1.1e+02 Score=30.29 Aligned_cols=57 Identities=25% Similarity=0.328 Sum_probs=32.6
Q ss_pred HHHHHHhhCCCcccchhh---hccHHHHHHHHHhhhhCCCCeEEEEECCCchh---hhHhhhh
Q 017036 268 LYKKLSFSCPSLLLPLIH---ERDKYLAWSLKRSKAVNNSKKVVGVIGKGHMN---GVIYALV 324 (378)
Q Consensus 268 l~~el~~~~P~l~~~Lid---ERD~yma~~L~~~~~~~~~~~vVaVVGagHl~---GI~~~L~ 324 (378)
.+++|..-.|.-.+-+++ +=|+.|++++.+....++..+|..|.|.+|.. |+--++.
T Consensus 189 ~ls~~H~gnp~~nk~~l~aqvt~dq~marrma~~L~~~p~rkvlliAGsfHt~kglGvp~hl~ 251 (295)
T COG3016 189 LLSELHRGNPSSNKSFLDAQVTWDQAMARRMAKTLILHPDRKVLLIAGSFHTYKGLGVPYHLK 251 (295)
T ss_pred HHHHHhcCCcchhhhHHHHHHHHHHHHHHHHHHHHHhCCCcceEEEeccchhhccCCcceeHH
Confidence 445565555554332222 24555555554443335669999999999985 4444443
No 27
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=26.36 E-value=89 Score=25.83 Aligned_cols=31 Identities=6% Similarity=0.132 Sum_probs=24.4
Q ss_pred CCceEEEEeecCCChhhHHHHHHHHHHcCCCeEEE
Q 017036 88 EPENIWLIGTTHLSQDSAADVERVVRAIKPDNVVV 122 (378)
Q Consensus 88 ~~~~VyLVGTaHvS~~Sa~~V~~vI~~vkPD~V~V 122 (378)
.|-+|+-+|. .-+.+++.+.+++.+||+|++
T Consensus 26 ~G~~V~~lg~----~~~~~~l~~~~~~~~pdvV~i 56 (119)
T cd02067 26 AGFEVIDLGV----DVPPEEIVEAAKEEDADAIGL 56 (119)
T ss_pred CCCEEEECCC----CCCHHHHHHHHHHcCCCEEEE
Confidence 3567777883 345678888999999999998
No 28
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=25.33 E-value=96 Score=27.89 Aligned_cols=39 Identities=15% Similarity=0.199 Sum_probs=20.9
Q ss_pred eEEEEeecCCChhh--HHHHHHHHHHcCCCeEEEeeccchh
Q 017036 91 NIWLIGTTHLSQDS--AADVERVVRAIKPDNVVVELCRSRA 129 (378)
Q Consensus 91 ~VyLVGTaHvS~~S--a~~V~~vI~~vkPD~V~VELc~~R~ 129 (378)
.+.++|+.|..-.. .+++.+.|.+.+||+|+|=|-..+.
T Consensus 72 ~l~i~g~~~g~~~~~~~~~i~~~I~~~~pdiv~vglG~PkQ 112 (171)
T cd06533 72 GLKIVGYHHGYFGPEEEEEIIERINASGADILFVGLGAPKQ 112 (171)
T ss_pred CcEEEEecCCCCChhhHHHHHHHHHHcCCCEEEEECCCCHH
Confidence 35556655533222 2335666666666666666555443
No 29
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=24.33 E-value=52 Score=29.97 Aligned_cols=19 Identities=26% Similarity=0.511 Sum_probs=17.8
Q ss_pred HHHHHHHHHHcCCCeEEEe
Q 017036 105 AADVERVVRAIKPDNVVVE 123 (378)
Q Consensus 105 a~~V~~vI~~vkPD~V~VE 123 (378)
-+.+.++|++.+||.|+||
T Consensus 46 ~~~l~~vl~~~~P~~~AIE 64 (160)
T COG0817 46 YDGLSEVLDEYQPDEVAIE 64 (160)
T ss_pred HHHHHHHHHHhCCCeeehh
Confidence 6789999999999999998
No 30
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=24.14 E-value=73 Score=28.62 Aligned_cols=26 Identities=31% Similarity=0.457 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 017036 349 IASLLKSLVRDTVIGILLWALYEQVK 374 (378)
Q Consensus 349 ~~k~~~~~~~~~~ig~~~~~~~~~~~ 374 (378)
..-+..+++|+=-||+++|.+|.++|
T Consensus 78 ~~g~~~~imPlYtiGI~~f~lY~l~K 103 (152)
T PF15361_consen 78 GKGLMGQIMPLYTIGIVLFILYTLFK 103 (152)
T ss_pred CCchhhhHhHHHHHHHHHHHHHHHHH
Confidence 44566688888888888888888776
No 31
>PF06724 DUF1206: Domain of Unknown Function (DUF1206); InterPro: IPR009597 This region consists of two a pair of transmembrane helices and occurs three times in each of the family member proteins.
Probab=23.13 E-value=1e+02 Score=23.68 Aligned_cols=21 Identities=19% Similarity=0.469 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcc
Q 017036 356 LVRDTVIGILLWALYEQVKGT 376 (378)
Q Consensus 356 ~~~~~~ig~~~~~~~~~~~~~ 376 (378)
++-++-+|+++|++|+++++.
T Consensus 49 ll~~vg~gli~~gi~~~~~a~ 69 (73)
T PF06724_consen 49 LLGAVGLGLIGYGIWQFVKAV 69 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 444556778888888777654
No 32
>PRK14762 membrane protein; Provisional
Probab=22.78 E-value=1.2e+02 Score=19.41 Aligned_cols=23 Identities=13% Similarity=0.319 Sum_probs=14.9
Q ss_pred HHHHHHHHHH-HHH-HHHHHHHHHh
Q 017036 351 SLLKSLVRDT-VIG-ILLWALYEQV 373 (378)
Q Consensus 351 k~~~~~~~~~-~ig-~~~~~~~~~~ 373 (378)
|++.|.+-.+ ++| +++.|.|+++
T Consensus 2 ki~lw~i~iifligllvvtgvfkli 26 (27)
T PRK14762 2 KIILWAVLIIFLIGLLVVTGVFKMI 26 (27)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4566666543 466 6678888865
No 33
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=20.39 E-value=50 Score=25.07 Aligned_cols=15 Identities=33% Similarity=0.638 Sum_probs=4.5
Q ss_pred CCcccccc-CCCCCCc
Q 017036 24 IKPFKVSI-KPPPQDF 38 (378)
Q Consensus 24 ~~~~~~~~-~~~~~~~ 38 (378)
+|++++++ ..|||+|
T Consensus 4 ~k~l~I~~~~~P~P~~ 19 (57)
T PF08727_consen 4 YKDLKISVEETPPPPA 19 (57)
T ss_dssp -SS-S--SSS--SS-T
T ss_pred CcceeeeccCCCCCHH
Confidence 45555666 5555554
Done!