Query 027209
Match_columns 226
No_of_seqs 94 out of 96
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 06:35:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027209.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027209hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13266 DUF4057: Protein of u 100.0 1.4E-83 3E-88 578.1 11.4 199 25-224 104-302 (302)
2 PF13266 DUF4057: Protein of u 100.0 6.7E-38 1.5E-42 282.7 4.4 156 11-204 16-179 (302)
3 PRK14463 ribosomal RNA large s 22.5 46 0.001 31.2 1.3 29 190-222 319-348 (349)
4 PF07623 PEGSRP: Protein of un 14.4 73 0.0016 20.5 0.5 8 213-220 4-11 (27)
5 KOG2178 Predicted sugar kinase 13.7 1.5E+02 0.0033 29.4 2.6 43 3-45 307-358 (409)
6 PF14493 HTH_40: Helix-turn-he 12.8 93 0.002 23.2 0.7 19 52-70 12-30 (91)
7 PF01960 ArgJ: ArgJ family; I 7.8 2.1E+02 0.0045 28.1 1.3 44 4-48 168-214 (388)
8 PF14996 RMP: Retinal Maintena 7.0 4.4E+02 0.0095 22.7 2.7 53 171-223 8-61 (146)
9 PF09571 RE_XcyI: XcyI restric 6.8 95 0.0021 29.7 -1.4 63 130-192 194-262 (318)
10 COG5622 Protein required for a 6.4 82 0.0018 27.0 -1.9 57 111-167 33-93 (139)
No 1
>PF13266 DUF4057: Protein of unknown function (DUF4057)
Probab=100.00 E-value=1.4e-83 Score=578.11 Aligned_cols=199 Identities=81% Similarity=1.136 Sum_probs=196.4
Q ss_pred cccccccccCCCcceeeecCCCcCCCCCCCChhHhhhhhhhccccCCccccccccccchhhhhhhhcCccCCCCCCCCcc
Q 027209 25 FWRLNFQQAMNGISQISFSAEETVSPKKPTSVPEVAKQRELSGSLQSESDLKTKKQISDAKFKEISGHDIFSPAPEIQPR 104 (226)
Q Consensus 25 ~~~r~~qq~~~g~SqIsFg~e~~~spkKp~s~~EvAKqrELsGt~~~~~~~~~~K~~S~aK~KEmsGs~IFa~p~e~~pr 104 (226)
-++|||||+++|+|||||++||+++||||||++|||||||||||+++++|.+.+||+|+||+|||+|||||++|+++.||
T Consensus 104 t~vr~yQq~~~giSqISF~~eesvsPKKpts~~EVAKQRELSGTlese~D~k~kkq~S~AK~KELSGhdIFapp~~~~pr 183 (302)
T PF13266_consen 104 TGVRMYQQAINGISQISFSEEESVSPKKPTSLPEVAKQRELSGTLESEADSKMKKQISNAKSKELSGHDIFAPPPEIKPR 183 (302)
T ss_pred cccceecccccccceeeecCCCCcCCCCccchHHHHHHhhhcCccccchhhHHHhhhhhhhhhhcccCcccCCCccCCCC
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHhhhhhhhhcccCCCCCCCCCccceeeeecCCCCCcceecCCCCccccccccchhhhhhhcCCcccCCCCCCCCCCCC
Q 027209 105 SLAAARSLESKESKDMGEPAPRNVRTSVKVSNPAGGQSNILFGEEPVVKTSKKIHNQKFAELTGNDIFKGDVPPGSAEKP 184 (226)
Q Consensus 105 ~~~~a~~~~~k~~~~~~~~~p~n~~t~~~v~~~~~g~S~IsFsee~~vkt~Kkis~~K~aELSGndIFk~D~~p~~aeK~ 184 (226)
.++ +|.||+|||++++||+|+|.+|++++.++++|+|+|.|++|+++||+||||++||+||+|||||++|.++.++||+
T Consensus 184 ~~~-~r~le~k~~~~~~e~~~~~~~ts~~~~n~a~~~s~~~~~~~~~~Ktakki~~~K~aeltGN~IFk~d~p~~saek~ 262 (302)
T PF13266_consen 184 SLT-ARSLELKENKDRGEPAPRNVRTSVKVSNPAGGQSNIEFGEDSVVKTAKKISNQKFAELTGNNIFKGDVPPASAEKP 262 (302)
T ss_pred cch-hhhhhhcccccccCCCCCcccccccccCCcCcccccccccCcchhhhhhhhhhhhhhcccCcccCCCCCCCCcccc
Confidence 994 8999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhhhhccCCCCCCCCCcccccccCCCcccCCCCCCCcc
Q 027209 185 LSNAKLREMSGSNIFADEKVESRDYFGGVRKPPGGESSIS 224 (226)
Q Consensus 185 lS~AKlkEmSGsDIFADgK~~~Rd~~ggvrkPPGGeSSIa 224 (226)
||.||||||+|+|||||||+++|||+|||||||||+||||
T Consensus 263 lS~AKlrEmsGsdIFaDgk~~~rd~~gg~rkPPGG~SSIa 302 (302)
T PF13266_consen 263 LSSAKLREMSGSDIFADGKAESRDYLGGVRKPPGGESSIA 302 (302)
T ss_pred hhhhhHhhcccccccccCCcccchhcCCccCCCCCCCcCC
Confidence 9999999999999999999999999999999999999997
No 2
>PF13266 DUF4057: Protein of unknown function (DUF4057)
Probab=100.00 E-value=6.7e-38 Score=282.71 Aligned_cols=156 Identities=31% Similarity=0.353 Sum_probs=133.6
Q ss_pred eEEEeecCCCCc----cccccccccccCCCcceeeecCCCcCCCCCCCChhHhhhhhhhccccCCccccccccccchhhh
Q 027209 11 LAIVITEHPCAF----ISFWRLNFQQAMNGISQISFSAEETVSPKKPTSVPEVAKQRELSGSLQSESDLKTKKQISDAKF 86 (226)
Q Consensus 11 ~~~~~~~~~~~~----~~~~~r~~qq~~~g~SqIsFg~e~~~spkKp~s~~EvAKqrELsGt~~~~~~~~~~K~~S~aK~ 86 (226)
|.+--+++|+.. .+.+.|+..||.+|||.|.||++ -|.|...+|++||+||++||
T Consensus 16 ltWse~~~~~~~~~~~~~~~a~RshQPs~giskv~fGgQ---------------------vT~EEAEsL~KRKpCS~~K~ 74 (302)
T PF13266_consen 16 LTWSETPPPDSPAASSTSRPARRSHQPSDGISKVVFGGQ---------------------VTEEEAESLNKRKPCSGYKM 74 (302)
T ss_pred ccccCCCCcccccccCCCCCCCCCCCCcccccccccCCc---------------------CCHHHHHHHhccCcCccccc
Confidence 344444444444 55666667789999999999997 56666668999999999999
Q ss_pred hhhhcCccCCCCCCCCcchhHhhhhhhhhcccCCCCCCCCCccceeeeec-CCCCCcceecCCCCccccccccchhhhh-
Q 027209 87 KEISGHDIFSPAPEIQPRSLAAARSLESKESKDMGEPAPRNVRTSVKVSN-PAGGQSNILFGEEPVVKTSKKIHNQKFA- 164 (226)
Q Consensus 87 KEmsGs~IFa~p~e~~pr~~~~a~~~~~k~~~~~~~~~p~n~~t~~~v~~-~~~g~S~IsFsee~~vkt~Kkis~~K~a- 164 (226)
|||+|+|||++++++...+.++| +|...+|.+++|| +.+|+|||||++|++|.++|+++.++||
T Consensus 75 KEmTGSGIF~~~~e~~~se~~sa--------------n~~~~rt~vr~yQq~~~giSqISF~~eesvsPKKpts~~EVAK 140 (302)
T PF13266_consen 75 KEMTGSGIFSANGEDDASESGSA--------------NPTPNRTGVRMYQQAINGISQISFSEEESVSPKKPTSLPEVAK 140 (302)
T ss_pred eecccccccccCCCCcccccccC--------------CCCccccccceecccccccceeeecCCCCcCCCCccchHHHHH
Confidence 99999999999999999888755 5655688888777 6689999999999999999999999998
Q ss_pred --hhcCCcccCCCCCCCCCCCCCchhhhhccCCCCCCCCCcc
Q 027209 165 --ELTGNDIFKGDVPPGSAEKPLSNAKLREMSGSNIFADEKV 204 (226)
Q Consensus 165 --ELSGndIFk~D~~p~~aeK~lS~AKlkEmSGsDIFADgK~ 204 (226)
||||+.....|.+.+ |++|+||.||||||||||++..
T Consensus 141 QRELSGTlese~D~k~k---kq~S~AK~KELSGhdIFapp~~ 179 (302)
T PF13266_consen 141 QRELSGTLESEADSKMK---KQISNAKSKELSGHDIFAPPPE 179 (302)
T ss_pred HhhhcCccccchhhHHH---hhhhhhhhhhcccCcccCCCcc
Confidence 999999999999888 9999999999999999998654
No 3
>PRK14463 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=22.47 E-value=46 Score=31.25 Aligned_cols=29 Identities=38% Similarity=0.559 Sum_probs=18.7
Q ss_pred hhccCCCCCCCC-CcccccccCCCcccCCCCCCC
Q 027209 190 LREMSGSNIFAD-EKVESRDYFGGVRKPPGGESS 222 (226)
Q Consensus 190 lkEmSGsDIFAD-gK~~~Rd~~ggvrkPPGGeSS 222 (226)
+|.=-|.||.|- |.... -.+|-||||||-
T Consensus 319 vR~~~G~di~aaCGqL~~----~~~~~~~~~~~~ 348 (349)
T PRK14463 319 TRSSRGSDISAACGQLKG----KLDKAPPGGESC 348 (349)
T ss_pred EeCCCCcchhhccCcccc----cccCCCCCCCCC
Confidence 344468888874 33322 257999999983
No 4
>PF07623 PEGSRP: Protein of unknown function (DUF1584); InterPro: IPR011477 This sequence motif is highly conserved in several short hypothetical proteins from Rhodopirellula baltica. It is also associated with IPR011476 from INTERPRO in Q7UJJ9 from SWISSPROT.
Probab=14.39 E-value=73 Score=20.46 Aligned_cols=8 Identities=75% Similarity=1.244 Sum_probs=5.8
Q ss_pred cccCCCCC
Q 027209 213 VRKPPGGE 220 (226)
Q Consensus 213 vrkPPGGe 220 (226)
-|||||-+
T Consensus 4 ~RkppG~~ 11 (27)
T PF07623_consen 4 WRKPPGEE 11 (27)
T ss_pred cccCCCCC
Confidence 48999853
No 5
>KOG2178 consensus Predicted sugar kinase [Carbohydrate transport and metabolism]
Probab=13.75 E-value=1.5e+02 Score=29.35 Aligned_cols=43 Identities=19% Similarity=0.208 Sum_probs=29.5
Q ss_pred hhhhcce--eeEEEeecCCCCcccc------cccccc-ccCCCcceeeecCC
Q 027209 3 KMVHQNL--MLAIVITEHPCAFISF------WRLNFQ-QAMNGISQISFSAE 45 (226)
Q Consensus 3 ~~~~~~~--~~~~~~~~~~~~~~~~------~~r~~q-q~~~g~SqIsFg~e 45 (226)
-|||+++ ||.-.|.||-+.|-+| -+|+-- +-+-..+.+||-|-
T Consensus 307 SlvhP~vpAIlvTPICPhSLSFRPIIlPds~~L~I~i~~dsR~~awvSfDG~ 358 (409)
T KOG2178|consen 307 SLVHPSVPAILVTPICPHSLSFRPIILPDSSELRVEVPLDSRSTAWVSFDGR 358 (409)
T ss_pred ceecCCCCeEEEeccCCCcccccceEccCccEEEEEeCccccccceEEecCc
Confidence 3899988 8888899999998776 222221 12234577999985
No 6
>PF14493 HTH_40: Helix-turn-helix domain
Probab=12.82 E-value=93 Score=23.22 Aligned_cols=19 Identities=42% Similarity=0.382 Sum_probs=14.7
Q ss_pred CCCChhHhhhhhhhccccC
Q 027209 52 KPTSVPEVAKQRELSGSLQ 70 (226)
Q Consensus 52 Kp~s~~EvAKqrELsGt~~ 70 (226)
+-.|+.|||++|.|+=+-+
T Consensus 12 ~G~si~eIA~~R~L~~sTI 30 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTI 30 (91)
T ss_pred cCCCHHHHHHHcCCCHHHH
Confidence 3468999999999975544
No 7
>PF01960 ArgJ: ArgJ family; InterPro: IPR002813 ArgJ is a bifunctional protein that catalyses the first 2.3.1.35 from EC and fifth steps 2.3.1.1 from EC in arginine biosynthesis []. The structure has been determined for glutamate N-acetyltransferase 2 (ornithine acetyltransferase; 2.3.1.35 from EC), an ArgJ-like protein from Streptomyces clavuligerus [].; GO: 0004358 glutamate N-acetyltransferase activity, 0006526 arginine biosynthetic process; PDB: 1VRA_A 1VZ7_A 1VZ8_D 2VZK_H 2V4I_A 2YEP_E 1VZ6_A 3IT4_A 3IT6_D.
Probab=7.81 E-value=2.1e+02 Score=28.05 Aligned_cols=44 Identities=23% Similarity=0.453 Sum_probs=17.4
Q ss_pred hhhcce--eeEEEeecCCCCccccccccccccCC-CcceeeecCCCcC
Q 027209 4 MVHQNL--MLAIVITEHPCAFISFWRLNFQQAMN-GISQISFSAEETV 48 (226)
Q Consensus 4 ~~~~~~--~~~~~~~~~~~~~~~~~~r~~qq~~~-g~SqIsFg~e~~~ 48 (226)
|+|+|+ ||+++.|.-+-.+--+ -++..+.+. -+..||..++.|.
T Consensus 168 MI~PnMATML~fi~TDA~i~~~~L-~~~L~~av~~SFN~IsVDGDtST 214 (388)
T PF01960_consen 168 MIHPNMATMLAFITTDAAISPDAL-QKALRRAVDRSFNRISVDGDTST 214 (388)
T ss_dssp S----EE--EEEEEEECB--HHHH-HHHHHHHHHHTGGGBESSS---S
T ss_pred ccCCchhhhheeeeeCCCCCHHHH-HHHHHHHHHhccCCceecCCCCc
Confidence 999998 9999999533222211 122222222 3566776665443
No 8
>PF14996 RMP: Retinal Maintenance
Probab=6.96 E-value=4.4e+02 Score=22.68 Aligned_cols=53 Identities=28% Similarity=0.276 Sum_probs=28.9
Q ss_pred ccCCCCCCCCCC-CCCchhhhhccCCCCCCCCCcccccccCCCcccCCCCCCCc
Q 027209 171 IFKGDVPPGSAE-KPLSNAKLREMSGSNIFADEKVESRDYFGGVRKPPGGESSI 223 (226)
Q Consensus 171 IFk~D~~p~~ae-K~lS~AKlkEmSGsDIFADgK~~~Rd~~ggvrkPPGGeSSI 223 (226)
||..+.+..... +..+.......+-.-++.-+|-=.-=|+||.+-|.|-++++
T Consensus 8 i~e~~~~~~~~~~~~~~~~~~~~~~~ss~~~~~kkC~~v~lgGs~~~~G~~t~~ 61 (146)
T PF14996_consen 8 IFEDPNPDKKPPRKKSSQSSGSTSSRSSSQPSSKKCSPVYLGGSSDPRGIGTSS 61 (146)
T ss_pred HhcCCCccccCcccccccCCCCcCcccccCCCCCccCCEEECCCcCCCcccccc
Confidence 555543333211 22233333344444445434444444999999999998875
No 9
>PF09571 RE_XcyI: XcyI restriction endonuclease; InterPro: IPR019071 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the restriction endonuclease XcyI, which recognises and cleaves the double-stranded sequence C^CCGGG. ; GO: 0000287 magnesium ion binding, 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=6.82 E-value=95 Score=29.72 Aligned_cols=63 Identities=29% Similarity=0.363 Sum_probs=44.0
Q ss_pred ceeeeecCCCCCcceecCCCCccccccccchhhhh-----hh-cCCcccCCCCCCCCCCCCCchhhhhc
Q 027209 130 TSVKVSNPAGGQSNILFGEEPVVKTSKKIHNQKFA-----EL-TGNDIFKGDVPPGSAEKPLSNAKLRE 192 (226)
Q Consensus 130 t~~~v~~~~~g~S~IsFsee~~vkt~Kkis~~K~a-----EL-SGndIFk~D~~p~~aeK~lS~AKlkE 192 (226)
+...+.+++|.+--|-|+.||-+--.++..++++. |. .|.|...--..-+.|||.+..||..-
T Consensus 194 n~i~l~naAGR~v~I~Fa~DPDIiI~E~~~~~~~k~~vAIEVKgGtD~snihnRlGeAeKShqKak~~~ 262 (318)
T PF09571_consen 194 NRIVLNNAAGRQVLIEFASDPDIIIREKLGNRNYKNVVAIEVKGGTDPSNIHNRLGEAEKSHQKAKKSG 262 (318)
T ss_pred ceEEEecCCCCEEEEEECCCCCeEeeeccccccCceEEEEEEecCCChhHHHHHHHHHHHHHHHHHhcC
Confidence 45666777777778999999999888888877655 55 44444332233357888888887654
No 10
>COG5622 Protein required for attachment to host cells [Cell motility and secretion]
Probab=6.38 E-value=82 Score=26.99 Aligned_cols=57 Identities=18% Similarity=0.215 Sum_probs=33.5
Q ss_pred hhhhhcccCCCCCCCCCccceeeeecCCCC----CcceecCCCCccccccccchhhhhhhc
Q 027209 111 SLESKESKDMGEPAPRNVRTSVKVSNPAGG----QSNILFGEEPVVKTSKKIHNQKFAELT 167 (226)
Q Consensus 111 ~~~~k~~~~~~~~~p~n~~t~~~v~~~~~g----~S~IsFsee~~vkt~Kkis~~K~aELS 167 (226)
+|+.+-..|..+++++...+..+++.-.+- +-+-+|.++..-...|..+..||++|.
T Consensus 33 nl~~~~~~di~~~~~~~~~r~~h~s~~~~pd~~~e~~~~fa~~~a~~l~r~v~~g~~~~Lv 93 (139)
T COG5622 33 NLPAKLVLDIDNDHHGRGARQSHSSSSSNPDSSREEEDSFAAEIAKELNRSVHGGKFKNLV 93 (139)
T ss_pred CcccchhhhhccCCCCcccchhhhhccCCCccccccchhHHHHHHHHHHHHHhhcccceeE
Confidence 455565666666665544443333332222 235677776666778888888887763
Done!