Query 042910
Match_columns 234
No_of_seqs 121 out of 205
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 10:51:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042910.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042910hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1161 Protein involved in va 100.0 1.4E-28 3E-33 224.9 10.9 155 1-174 1-168 (310)
2 PF03105 SPX: SPX domain; Int 99.9 3E-28 6.5E-33 210.2 8.6 87 1-88 1-120 (275)
3 KOG1162 Predicted small molecu 99.9 5.6E-24 1.2E-28 209.4 7.6 143 1-150 1-172 (617)
4 COG5036 SPX domain-containing 99.6 9.7E-16 2.1E-20 145.2 11.8 159 1-178 1-164 (509)
5 COG5408 SPX domain-containing 99.3 5.8E-12 1.3E-16 115.5 9.6 79 1-80 1-99 (296)
6 KOG2026 Spindle pole body prot 39.2 12 0.00027 36.5 0.6 42 128-177 302-344 (442)
7 PHA02929 N1R/p28-like protein; 28.0 9.2 0.0002 34.7 -2.1 36 193-228 149-184 (238)
8 PF13639 zf-RING_2: Ring finge 27.3 24 0.00051 22.8 0.3 10 220-229 2-11 (44)
9 cd07635 BAR_GRAF2 The Bin/Amph 27.0 53 0.0012 29.2 2.5 26 119-144 97-122 (207)
10 TIGR00134 gatE_arch glutamyl-t 26.5 30 0.00065 35.5 1.0 17 188-204 22-38 (620)
11 PRK11193 hypothetical protein; 25.3 37 0.00081 28.5 1.2 20 211-230 63-82 (172)
12 KOG1281 Na+/dicarboxylate, Na+ 24.0 67 0.0014 32.9 2.9 48 118-171 12-60 (586)
13 KOG0823 Predicted E3 ubiquitin 23.9 27 0.0006 31.7 0.2 11 218-228 47-57 (230)
14 PHA02926 zinc finger-like prot 22.5 32 0.00069 31.4 0.3 27 202-228 154-180 (242)
15 KOG0320 Predicted E3 ubiquitin 22.0 33 0.00072 30.2 0.3 13 219-231 132-144 (187)
16 PF02909 TetR_C: Tetracyclin r 20.7 87 0.0019 24.1 2.4 28 147-174 5-36 (139)
17 PF15389 DUF4612: Domain of un 20.6 48 0.001 27.1 0.9 19 56-74 86-104 (115)
18 PRK04028 glutamyl-tRNA(Gln) am 20.2 49 0.0011 34.2 1.1 16 188-203 25-40 (630)
No 1
>KOG1161 consensus Protein involved in vacuolar polyphosphate accumulation, contains SPX domain [Inorganic ion transport and metabolism]
Probab=99.95 E-value=1.4e-28 Score=224.93 Aligned_cols=155 Identities=23% Similarity=0.197 Sum_probs=110.8
Q ss_pred CchhhhhHHhhhccccCCCccchHHHHHHHHhhhhcccchhhhccCCCCCCCCCCCCCcccccchHHHHhHHHHHHHHHH
Q 042910 1 MKFCKKYQEYMQGQERKLPGVGFKKLKKILKMCRKEFQSQKEINKGVVDTQTCPHQCPVCDGTFFPSLLNEMSAIVGCFN 80 (234)
Q Consensus 1 MKFGK~l~~~~~~e~~~~~YInYK~LKK~LK~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~FF~~L~~EieKIngFf~ 80 (234)
|||||.|++...| +|+++|||||.|||.||+++.+...+... . ..+..|+..|++|||||++|+.
T Consensus 1 MkFGk~L~~~~l~-ew~~~yinYk~LKK~lK~~~~~~~~~~~~--------~------~~e~dFv~~Ld~ELEKv~~F~l 65 (310)
T KOG1161|consen 1 MKFGKYLKEELLP-EWKDKYINYKELKKLLKQYSIQTADSSPD--------S------RDESDFVRLLDAELEKVNGFQL 65 (310)
T ss_pred CchhHHHHHhhhh-hHhhhhcCHHHHHHHHHHhccccccCCcc--------c------chHHHHHHHHHHHHHHHHHHHH
Confidence 9999999988888 58889999999999999987754332110 0 1478999999999999999977
Q ss_pred HHH-------HHHHHHHHh----ccCchhhhhhhcccccchHHHHHhhhhHHHHHHhHHHHHHHHHhhhhcccccchhhh
Q 042910 81 ERA-------QKLLELHLA----SGFSKCLIWFKGKLHGTHGALIQEGKDLVTYALINAIAIRKILKKYDKVHYSKQGQA 149 (234)
Q Consensus 81 eRl-------~~Ll~~~~a----s~~~~~~~~ir~~l~~~~~~l~qeg~~L~nYveLNatG~RKILKK~DK~~~S~~G~~ 149 (234)
+|. ++|-+++.+ +-....+..++.++++.+++|+ +|.||++||+|||+||||||||++|..-.-.
T Consensus 66 ek~~el~~Rl~~L~e~~~~~~~~~~~~~~~~~lr~~l~~~~~em~----~L~~fs~LN~tGf~KILKK~DKrtg~~l~~~ 141 (310)
T KOG1161|consen 66 EKESELIIRLKELEEKIDALSLEPPSAEEMKELREELVDFHGEMV----LLENFSRLNYTGFAKILKKHDKRTGYRLRPY 141 (310)
T ss_pred HHHHHHHHHHHHHHHHhhccccCCcchhHHHHHHHHHHHHHHHHH----HHHHHHHHhHHHHHHHHHHHhcccccccccH
Confidence 764 444444432 1122234556777766666666 9999999999999999999999999766666
Q ss_pred hHHHHHHHhH--HHhhchHHHHHhhhh
Q 042910 150 FKSQAQSMHV--EILQSPWLCELMAFH 174 (234)
Q Consensus 150 ~~~~~~~~~~--e~l~~p~~~e~~a~~ 174 (234)
|..++..... -=..+|.+-|..+++
T Consensus 142 f~~~l~~~Pf~~~e~~~~Lv~e~~~l~ 168 (310)
T KOG1161|consen 142 FQVRLLHQPFFTTEQLFRLVYEISILL 168 (310)
T ss_pred HHHHHHhCCCchhhhHHHHHHHHHHHH
Confidence 6444422211 112345566666554
No 2
>PF03105 SPX: SPX domain; InterPro: IPR004331 The SPX domain is named after SYG1/Pho81/XPR1 proteins. This 180 residue length domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1, the N terminus directly binds to the G- protein beta subunit and inhibits transduction of the mating pheromone signal [] suggesting that all the members of this family are involved in G-protein associated signal transduction. The C-terminal of these proteins often have an EXS domain (IPR004342 from INTERPRO) []. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family [, ]. NUC-2 contains several ankyrin repeats (IPR002110 from INTERPRO). Several members of this family are the XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with Murine leukemia virus (MLV) []. The similarity between SYG1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae [, ]. In addition, given the similarities between XPR1 and SYG1 and phosphate regulatory proteins, it has been proposed that XPR1 might be involved in G-protein associated signal transduction [, , ] and may itself function as a phosphate sensor [].
Probab=99.95 E-value=3e-28 Score=210.20 Aligned_cols=87 Identities=23% Similarity=0.288 Sum_probs=62.1
Q ss_pred CchhhhhHHhhhccccCCCccchHHHHHHHHhhhhcccchhhh---------------------------ccCC----CC
Q 042910 1 MKFCKKYQEYMQGQERKLPGVGFKKLKKILKMCRKEFQSQKEI---------------------------NKGV----VD 49 (234)
Q Consensus 1 MKFGK~l~~~~~~e~~~~~YInYK~LKK~LK~~~~~~~~~~~~---------------------------~~~~----~d 49 (234)
|||||+|+.++.|| |+++||+||.|||+||++.......... ..+. ..
T Consensus 1 MKFgk~L~~~~vpE-W~~~YidYk~LKk~ik~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (275)
T PF03105_consen 1 MKFGKQLQENAVPE-WRDKYIDYKQLKKLIKRIQNEKESLGLSAETLSSISISSSSSSSSRSSSNSFESTSPSSSNTSPS 79 (275)
T ss_pred CCchHHHHHhcCHH-HHHHhCCHHHHHHHHHHHHhhhhcccccccccchhhhhhhhhccccccccccccccccccccccc
Confidence 99999999999995 7679999999999999998865543100 0000 00
Q ss_pred --CCCCCCCCCcccccchHHHHhHHHHHHHHHHHHHHHHHH
Q 042910 50 --TQTCPHQCPVCDGTFFPSLLNEMSAIVGCFNERAQKLLE 88 (234)
Q Consensus 50 --~~~~~~~~~~~~~~FF~~L~~EieKIngFf~eRl~~Ll~ 88 (234)
...........+..||..|+.|++|||.||.+++.++.+
T Consensus 80 ~~~~~~~~~~~~~~~~F~~~L~~El~KVn~Fy~~k~~el~~ 120 (275)
T PF03105_consen 80 SSNSEQNEDNEESEEEFFELLDEELEKVNDFYKEKEKELRE 120 (275)
T ss_pred ccccchhhhhhhhHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 000111223468899999999999999999998765554
No 3
>KOG1162 consensus Predicted small molecule transporter [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.89 E-value=5.6e-24 Score=209.36 Aligned_cols=143 Identities=25% Similarity=0.322 Sum_probs=102.9
Q ss_pred CchhhhhHHhhhccccCCCccchHHHHHHHHhhhhcccchhhhccCCCCCCCCCCCCCcccccchHHHHhHHHHHHHHHH
Q 042910 1 MKFCKKYQEYMQGQERKLPGVGFKKLKKILKMCRKEFQSQKEINKGVVDTQTCPHQCPVCDGTFFPSLLNEMSAIVGCFN 80 (234)
Q Consensus 1 MKFGK~l~~~~~~e~~~~~YInYK~LKK~LK~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~FF~~L~~EieKIngFf~ 80 (234)
|||||.|.++++|| |+.+||+|+.|||+||++....++..+.+ .....++....++.||.+||.|+.|||.||.
T Consensus 1 MKFgk~~~~q~~pE-W~~ay~dY~~lK~~l~~i~~~~~~~~~t~-----~~~~~~~~~~~~~~Ff~~ld~el~Kvn~Fy~ 74 (617)
T KOG1162|consen 1 MKFGKELESQLVPE-WRQAYIDYKYLKKLLKEIIENKPSSEETT-----FLMVSEEGGEFEEVFFRRLDEELNKVNKFYK 74 (617)
T ss_pred CcchHHHHHhcCHH-HHHHhhhHHHHHHHHHHHHhcCCCcCccH-----HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999997 55599999999999999999887654321 1111224556799999999999999999999
Q ss_pred HHHHHHHHHHHhc--c---------------------------CchhhhhhhcccccchHHHHHhhhhHHHHHHhHHHHH
Q 042910 81 ERAQKLLELHLAS--G---------------------------FSKCLIWFKGKLHGTHGALIQEGKDLVTYALINAIAI 131 (234)
Q Consensus 81 eRl~~Ll~~~~as--~---------------------------~~~~~~~ir~~l~~~~~~l~qeg~~L~nYveLNatG~ 131 (234)
+++.+..+.+... | +.+...+.+..+..+..++-+-++.|+||+.||.|||
T Consensus 75 ~k~~e~~~~~~~L~~ql~~~~~~r~~~~~~~~~~~~~~~~~~~f~~~~~~~e~~lk~af~Efy~~L~llk~y~~lN~~~f 154 (617)
T KOG1162|consen 75 EKVKEAREEAEELNKQLDALIALRVKSRSSVDISDRAARLRGKFTKVLRKAEEKLKLAFSEFYLKLRLLKNYQFLNVTAF 154 (617)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9976554433110 0 0000011111122222244444458999999999999
Q ss_pred HHHHhhhhcccccchhhhh
Q 042910 132 RKILKKYDKVHYSKQGQAF 150 (234)
Q Consensus 132 RKILKK~DK~~~S~~G~~~ 150 (234)
|||+|||||..+++. ..|
T Consensus 155 ~KI~KKyDK~~~~~~-~~~ 172 (617)
T KOG1162|consen 155 RKILKKYDKITSRDA-KRY 172 (617)
T ss_pred HHHHHHHHhhcccch-HHH
Confidence 999999999999988 888
No 4
>COG5036 SPX domain-containing protein involved in vacuolar polyphosphate accumulation [Inorganic ion transport and metabolism]
Probab=99.65 E-value=9.7e-16 Score=145.21 Aligned_cols=159 Identities=19% Similarity=0.235 Sum_probs=104.3
Q ss_pred CchhhhhHHhhhccccCCCccchHHHHHHHHhhhhcccchhhhccCCCCCCCCCCCCCcccccchHHHHhHHHHHHHHHH
Q 042910 1 MKFCKKYQEYMQGQERKLPGVGFKKLKKILKMCRKEFQSQKEINKGVVDTQTCPHQCPVCDGTFFPSLLNEMSAIVGCFN 80 (234)
Q Consensus 1 MKFGK~l~~~~~~e~~~~~YInYK~LKK~LK~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~FF~~L~~EieKIngFf~ 80 (234)
|+||++|.+-+-+ +|+.+||||..||+.||.-..++.=+ ...+.+|..+|++||+||-||=.
T Consensus 1 M~Fg~~L~~~ly~-p~k~~YinYe~LK~~lK~~~~~~~w~-----------------e~dEsdFVe~Ld~eLeKVY~F~~ 62 (509)
T COG5036 1 MRFGKKLKNNLYP-PYKYSYINYENLKKLLKESEEEGSWS-----------------ESDESDFVEELDKELEKVYGFQL 62 (509)
T ss_pred CchhHHHHhccCc-ccccccCCHHHHHHHHhhccccCCCc-----------------ccchHHHHHHHHHHHHHHHHHHH
Confidence 9999999999888 58889999999999999822111111 12367999999999999999944
Q ss_pred HHHHHHHHHHH--hccCchhhhhhh-cccccchHHHHHhhhhHHHHHHhHHHHHHHHHhhhhcccccchhhhhHHHHHHH
Q 042910 81 ERAQKLLELHL--ASGFSKCLIWFK-GKLHGTHGALIQEGKDLVTYALINAIAIRKILKKYDKVHYSKQGQAFKSQAQSM 157 (234)
Q Consensus 81 eRl~~Ll~~~~--as~~~~~~~~ir-~~l~~~~~~l~qeg~~L~nYveLNatG~RKILKK~DK~~~S~~G~~~~~~~~~~ 157 (234)
++...+.++-+ ..+.+..+..+- ..+....++-..+..+|-+|..||+|||.||+|||||..|..-.-.|.-|+.+.
T Consensus 63 ~k~~ev~erl~~leeq~~~~i~~~ds~~~~~~LeE~L~~v~~l~kF~RLN~tGF~KIvKKHDK~~~y~lkpvfqvrLk~~ 142 (509)
T COG5036 63 SKYSEVMERLRTLEEQTDEAIQELDSDNFPKILEEELDTVHDLAKFSRLNFTGFKKIVKKHDKHTGYSLKPVFQVRLKAK 142 (509)
T ss_pred HHHHHHHHHHHHHHhccHHHhhcccCCcchhHHHHHHHHHHHHHhhhhhhhHHHHHHHHhhcCCCCceechhHHHHhccC
Confidence 44332222111 111110100000 011111222223445899999999999999999999998888888886666432
Q ss_pred --hHHHhhchHHHHHhhhhhccc
Q 042910 158 --HVEILQSPWLCELMAFHINLR 178 (234)
Q Consensus 158 --~~e~l~~p~~~e~~a~~~n~~ 178 (234)
+.| -.+|.|.++.-+|==+|
T Consensus 143 p~~se-~yd~Ll~kis~LY~~lR 164 (509)
T COG5036 143 PFFSE-QYDPLLYKISSLYNILR 164 (509)
T ss_pred Ccchh-hhcHHHHHHHHHHHHHH
Confidence 333 35899999988764333
No 5
>COG5408 SPX domain-containing protein [Signal transduction mechanisms]
Probab=99.32 E-value=5.8e-12 Score=115.50 Aligned_cols=79 Identities=18% Similarity=0.170 Sum_probs=54.1
Q ss_pred CchhhhhHHhhhccccCCCccchHHHHHHHHhhhhcccchhhh-ccC--CCCC-------CC---------CCCCCCccc
Q 042910 1 MKFCKKYQEYMQGQERKLPGVGFKKLKKILKMCRKEFQSQKEI-NKG--VVDT-------QT---------CPHQCPVCD 61 (234)
Q Consensus 1 MKFGK~l~~~~~~e~~~~~YInYK~LKK~LK~~~~~~~~~~~~-~~~--~~d~-------~~---------~~~~~~~~~ 61 (234)
||||+.|+.+..|| |+.+||+||.|||+|+.+...+..++.+ ++. ..+. .. ..+..+...
T Consensus 1 MKF~~~L~~naVPE-Wss~Y~dYk~lKKlI~~l~~~~~~~~~~~~~~~e~~~~~~~~~~~~dr~~~~l~~~~s~~~~~~v 79 (296)
T COG5408 1 MKFGHSLQFNAVPE-WSSKYIDYKQLKKLIYSLQKDQLSSYHGVSDNDETRDEAGEPSNWRDRFNHALKKELSPLQANYV 79 (296)
T ss_pred Ccchhhhhhccchh-hHHhhhhHHHHHHHHHHHhcchhhhhccCCccccccccccCCCChhhhhcchhhhhhhhHHHHHH
Confidence 99999999999996 6669999999999999998866544322 111 1110 00 001112335
Q ss_pred ccchHH-HHhHHHHHHHHHH
Q 042910 62 GTFFPS-LLNEMSAIVGCFN 80 (234)
Q Consensus 62 ~~FF~~-L~~EieKIngFf~ 80 (234)
+.||.. +..|+.|++.|++
T Consensus 80 ~~f~e~~i~~e~~k~~e~~~ 99 (296)
T COG5408 80 AKFFENYISEEAIKLDEFYS 99 (296)
T ss_pred HHHHHHhhhHHHHHHHhhhc
Confidence 678888 8899999997743
No 6
>KOG2026 consensus Spindle pole body protein - Sad1p [Cytoskeleton]
Probab=39.18 E-value=12 Score=36.54 Aligned_cols=42 Identities=24% Similarity=0.425 Sum_probs=32.7
Q ss_pred HHHHHHHHhhhhcccccchhhhhHHHHHHHhHHHhhch-HHHHHhhhhhcc
Q 042910 128 AIAIRKILKKYDKVHYSKQGQAFKSQAQSMHVEILQSP-WLCELMAFHINL 177 (234)
Q Consensus 128 atG~RKILKK~DK~~~S~~G~~~~~~~~~~~~e~l~~p-~~~e~~a~~~n~ 177 (234)
-.++.+||||||+.+-+....-. -+|..+++++| ||| ||++-
T Consensus 302 QV~l~~lL~Kf~g~t~~e~~~~~----~~~rf~l~k~P~yli----fh~~r 344 (442)
T KOG2026|consen 302 QVALFDLLKKFDGETVTEVVTPK----LAMRFRLTKLPRYLI----FHMKR 344 (442)
T ss_pred cchHHHHHHHhcCceeeeecchh----hhhheeeecCCceEE----EEeee
Confidence 46899999999999888766555 34888999998 444 77764
No 7
>PHA02929 N1R/p28-like protein; Provisional
Probab=28.03 E-value=9.2 Score=34.67 Aligned_cols=36 Identities=28% Similarity=0.391 Sum_probs=22.4
Q ss_pred cceeeecCCCCeeEEeeccceeeeeceecccccchh
Q 042910 193 GCYLKFNDDKPSLSCELFDSVKLDIDLTCSICLVSQ 228 (234)
Q Consensus 193 ~~~~~~~~~~~~~~~~l~~s~~~~~~ltc~icl~~~ 228 (234)
++|=+|-++-|++.-+.-+-....-+.+||||++.+
T Consensus 149 ~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~ 184 (238)
T PHA02929 149 KNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKV 184 (238)
T ss_pred chhHHHHHhcchhhhhhhhhhcCCCCCCCccCCccc
Confidence 345556666666654444444445578999999974
No 8
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=27.30 E-value=24 Score=22.80 Aligned_cols=10 Identities=40% Similarity=0.906 Sum_probs=8.2
Q ss_pred ecccccchhh
Q 042910 220 TCSICLVSQS 229 (234)
Q Consensus 220 tc~icl~~~~ 229 (234)
+|+||++.+.
T Consensus 2 ~C~IC~~~~~ 11 (44)
T PF13639_consen 2 ECPICLEEFE 11 (44)
T ss_dssp CETTTTCBHH
T ss_pred CCcCCChhhc
Confidence 6999999763
No 9
>cd07635 BAR_GRAF2 The Bin/Amphiphysin/Rvs (BAR) domain of GTPase Regulator Associated with Focal adhesion 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. GTPase Regulator Associated with Focal adhesion kinase 2 (GRAF2), also called Rho GTPase activating protein 10 (ARHGAP10) or PS-GAP, is a GAP with activity towards Cdc42 and RhoA which regulates caspase-activated p21-activated protein kinase-2 (PAK-2p34). GRAF2 interacts with PAK-2p34, leading to its stabilization and decrease of cell death. It is highly expressed in skeletal muscle and also interacts with PKNbeta, which is a target of Rho. GRAF2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of the related prote
Probab=27.00 E-value=53 Score=29.23 Aligned_cols=26 Identities=23% Similarity=0.195 Sum_probs=19.5
Q ss_pred hHHHHHHhHHHHHHHHHhhhhccccc
Q 042910 119 DLVTYALINAIAIRKILKKYDKVHYS 144 (234)
Q Consensus 119 ~L~nYveLNatG~RKILKK~DK~~~S 144 (234)
-|++|+.==-.+++--=|+|||.+-.
T Consensus 97 pL~~F~kedl~~~Ke~KK~FdK~se~ 122 (207)
T cd07635 97 PLERFRKEQLGAVKEEKKKFDKETEK 122 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence 47788777777777777888887554
No 10
>TIGR00134 gatE_arch glutamyl-tRNA(Gln) amidotransferase, subunit E. The Archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp--tRNA ligase, but the genes have not been identified. It is likely that this protein replaces gatB in Asp-tRNA(Asn) amidotransferase but that both enzymes share gatA.
Probab=26.48 E-value=30 Score=35.54 Aligned_cols=17 Identities=24% Similarity=0.579 Sum_probs=14.4
Q ss_pred CCccCcceeeecCCCCe
Q 042910 188 PAFFEGCYLKFNDDKPS 204 (234)
Q Consensus 188 ~~~~~~~~~~~~~~~~~ 204 (234)
+.+|++|+-+|.++.|-
T Consensus 22 ~KlFc~c~~~~~~~~p~ 38 (620)
T TIGR00134 22 SKLFCPCPTELRDSEPD 38 (620)
T ss_pred CCccCCCCcccccCCCc
Confidence 44999999999888884
No 11
>PRK11193 hypothetical protein; Provisional
Probab=25.35 E-value=37 Score=28.55 Aligned_cols=20 Identities=15% Similarity=0.421 Sum_probs=16.5
Q ss_pred cceeeeeceecccccchhhh
Q 042910 211 DSVKLDIDLTCSICLVSQSF 230 (234)
Q Consensus 211 ~s~~~~~~ltc~icl~~~~~ 230 (234)
=+++.++.++|.-||+.+.+
T Consensus 63 g~v~~~v~l~C~RCL~~~~~ 82 (172)
T PRK11193 63 GKAVVEVTLECQRCNEPFTH 82 (172)
T ss_pred EEEEEEEEEECCCCCccCce
Confidence 35778889999999998764
No 12
>KOG1281 consensus Na+/dicarboxylate, Na+/tricarboxylate and phosphate transporters [Inorganic ion transport and metabolism]
Probab=24.03 E-value=67 Score=32.94 Aligned_cols=48 Identities=17% Similarity=0.304 Sum_probs=35.1
Q ss_pred hhHHHHHHhHHHHHHHHHhhhhcccccch-hhhhHHHHHHHhHHHhhchHHHHHh
Q 042910 118 KDLVTYALINAIAIRKILKKYDKVHYSKQ-GQAFKSQAQSMHVEILQSPWLCELM 171 (234)
Q Consensus 118 ~~L~nYveLNatG~RKILKK~DK~~~S~~-G~~~~~~~~~~~~e~l~~p~~~e~~ 171 (234)
-.+.+|..+|.+++.|+.||+||.++++. ++- .--+..+..=|..|..
T Consensus 12 ~~~~~~~~~~~~~ll~~p~~~~~~l~~~~e~~c------~y~~~vm~~yw~~Eal 60 (586)
T KOG1281|consen 12 LQYRSLLVLNRTPLLLLPKKLDKLLHSSEEARC------AYVILVMAVYWVTEAL 60 (586)
T ss_pred HHhhhhheeehhhhhhcchhhhhhcCCcHHHHH------HHHHHHHHHHHHHhhc
Confidence 36789999999999999999999999975 222 1234455555666643
No 13
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.93 E-value=27 Score=31.66 Aligned_cols=11 Identities=36% Similarity=0.733 Sum_probs=8.9
Q ss_pred ceecccccchh
Q 042910 218 DLTCSICLVSQ 228 (234)
Q Consensus 218 ~ltc~icl~~~ 228 (234)
.-+|.||||++
T Consensus 47 ~FdCNICLd~a 57 (230)
T KOG0823|consen 47 FFDCNICLDLA 57 (230)
T ss_pred ceeeeeecccc
Confidence 34699999986
No 14
>PHA02926 zinc finger-like protein; Provisional
Probab=22.48 E-value=32 Score=31.41 Aligned_cols=27 Identities=15% Similarity=0.239 Sum_probs=19.0
Q ss_pred CCeeEEeeccceeeeeceecccccchh
Q 042910 202 KPSLSCELFDSVKLDIDLTCSICLVSQ 228 (234)
Q Consensus 202 ~~~~~~~l~~s~~~~~~ltc~icl~~~ 228 (234)
=|.+--+--|..+..-+.+|+||+|.+
T Consensus 154 i~~il~~ye~~~~~SkE~eCgICmE~I 180 (242)
T PHA02926 154 IIKILDKYEDVYRVSKEKECGICYEVV 180 (242)
T ss_pred hhHHHHHHHHHHhccCCCCCccCcccc
Confidence 344434445666677789999999986
No 15
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.95 E-value=33 Score=30.20 Aligned_cols=13 Identities=46% Similarity=0.654 Sum_probs=10.8
Q ss_pred eecccccchhhhh
Q 042910 219 LTCSICLVSQSFI 231 (234)
Q Consensus 219 ltc~icl~~~~~~ 231 (234)
-.||||||.|+=.
T Consensus 132 ~~CPiCl~~~sek 144 (187)
T KOG0320|consen 132 YKCPICLDSVSEK 144 (187)
T ss_pred cCCCceecchhhc
Confidence 6799999998754
No 16
>PF02909 TetR_C: Tetracyclin repressor, C-terminal all-alpha domain; InterPro: IPR004111 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification [, ]: Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria []. There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity []. The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain found in the tetracycline transcriptional repressor TetR, which binds to the Tet(A) gene to repress its expression in the absence of tetracycline []. Tet(A) is a membrane-associated efflux protein that exports tetracycline from the cell before it can attach to ribosomes and inhibit polypeptide chain growth. TetR occurs as a homodimer and uses two helix-turn-helix (HTH) motifs to bind tandem DNA operators, thereby blocking the expression of the associated genes, TetA and TetR. The structure of the class D TetR repressor protein [] involves 10 alpha-helices, with connecting turns and loops. The three N-terminal helices constitute the DNA-binding HTH domain, which has an inverse orientation compared with HTH motifs in other DNA-binding proteins. The core of the protein, formed by helices 5-10, is responsible for dimerisation and contains, for each monomer, a binding pocket that accommodates tetracycline in the presence of a divalent cation.; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 2Y30_B 3ZQL_C 2Y31_B 2Y2Z_A 2VPR_A 3B6A_A 3B6C_A 2OPT_A 2NS7_B 2NS8_C ....
Probab=20.70 E-value=87 Score=24.15 Aligned_cols=28 Identities=25% Similarity=0.703 Sum_probs=21.5
Q ss_pred hhhhHHHH----HHHhHHHhhchHHHHHhhhh
Q 042910 147 GQAFKSQA----QSMHVEILQSPWLCELMAFH 174 (234)
Q Consensus 147 G~~~~~~~----~~~~~e~l~~p~~~e~~a~~ 174 (234)
|..|+.++ .+.+--++..||+.++++=+
T Consensus 5 ~~~W~~~l~~~a~~~r~~~~~hP~~~~~~~~~ 36 (139)
T PF02909_consen 5 GDDWRERLRALARAYRAALLRHPWLAELLLAR 36 (139)
T ss_dssp TSEHHHHHHHHHHHHHHHHHTSTTHHHHHHTS
T ss_pred CCCHHHHHHHHHHHHHHHHHHCcCHHHHHHhc
Confidence 33566555 77888999999999998754
No 17
>PF15389 DUF4612: Domain of unknown function (DUF4612)
Probab=20.59 E-value=48 Score=27.11 Aligned_cols=19 Identities=16% Similarity=0.260 Sum_probs=15.3
Q ss_pred CCCcccccchHHHHhHHHH
Q 042910 56 QCPVCDGTFFPSLLNEMSA 74 (234)
Q Consensus 56 ~~~~~~~~FF~~L~~EieK 74 (234)
++..-.+.||++||+-|++
T Consensus 86 ~iS~SQqdFFRMLDeKIek 104 (115)
T PF15389_consen 86 HISESQQDFFRMLDEKIEK 104 (115)
T ss_pred hhhHHHHHHHHHHHHHHHc
Confidence 4455678999999998876
No 18
>PRK04028 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated
Probab=20.25 E-value=49 Score=34.15 Aligned_cols=16 Identities=31% Similarity=0.706 Sum_probs=12.8
Q ss_pred CCccCcceeeecCCCC
Q 042910 188 PAFFEGCYLKFNDDKP 203 (234)
Q Consensus 188 ~~~~~~~~~~~~~~~~ 203 (234)
..+|++|+-+|+++.|
T Consensus 25 ~KlFc~c~~~~~~~~~ 40 (630)
T PRK04028 25 RKLFCNCPTELRDDEP 40 (630)
T ss_pred CCccCCCCccccCccc
Confidence 4499999999987554
Done!