Query 019465
Match_columns 340
No_of_seqs 170 out of 675
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 09:41:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019465.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019465hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00777 Glyco_transf_29: Glyc 100.0 4.8E-52 1E-56 391.9 8.9 190 27-219 33-265 (266)
2 KOG2692 Sialyltransferase [Car 100.0 1.7E-42 3.8E-47 342.9 13.3 199 18-219 121-369 (376)
3 PF06002 CST-I: Alpha-2,3-sial 96.5 0.035 7.6E-07 54.2 12.0 164 49-217 2-210 (291)
4 PF01973 MAF_flag10: Protein o 64.8 18 0.00039 31.8 5.9 122 49-176 25-163 (170)
5 PF10143 PhosphMutase: 2,3-bis 13.2 65 0.0014 29.2 -0.0 25 60-84 42-66 (172)
6 PF06422 PDR_CDR: CDR ABC tran 12.0 1.1E+02 0.0024 25.2 1.0 22 36-57 2-25 (103)
7 PF12434 Malate_DH: Malate deh 10.5 1.5E+02 0.0032 19.5 1.0 14 297-310 13-26 (28)
8 COG1634 Uncharacterized Rossma 10.4 1.7E+02 0.0036 28.2 1.7 122 48-179 52-183 (232)
9 PF03826 OAR: OAR domain; Int 10.4 1.7E+02 0.0036 18.1 1.1 14 296-309 6-19 (21)
10 KOG3994 Uncharacterized conser 10.3 61 0.0013 31.6 -1.2 22 158-179 193-214 (291)
No 1
>PF00777 Glyco_transf_29: Glycosyltransferase family 29 (sialyltransferase); InterPro: IPR001675 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 29 (GT29 from CAZY) comprises enzymes with a number of known activities; sialyltransferase (2.4.99 from EC), beta-galactosamide alpha-2,6-sialyltransferase (2.4.99.1 from EC), alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase (2.4.99.3 from EC), beta-galactoside alpha-2,3-sialyltransferase (2.4.99.4 from EC), N-acetyllactosaminide alpha-2,3-sialyltransferase (2.4.99.6 from EC), alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase (2.4.99.8 from EC); lactosylceramide alpha-2,3-sialyltransferase (2.4.99.9 from EC). These enzymes use a nucleotide monophosphosugar as the donor (CMP-NeuA) instead of a nucleotide diphosphosugar. Sialyltransferase may be responsible for the synthesis of the sequence NEUAC-Alpha-2,3-GAL-Beta-1,3-GALNAC-, found on sugar chains O-linked to thr or ser and also as a terminal sequenec on certain gagnliosides. These enzymes catalyse sialyltransfer reactions during glycosylation, and are type II membrane proteins.; GO: 0008373 sialyltransferase activity, 0006486 protein glycosylation, 0030173 integral to Golgi membrane; PDB: 2WNF_A 2WML_A 2WNB_A.
Probab=100.00 E-value=4.8e-52 Score=391.89 Aligned_cols=190 Identities=33% Similarity=0.481 Sum_probs=110.1
Q ss_pred hhhHHHHhccCCCCCCCCCCC----cceEEEEcCCCCCCCCcCCccccccceeeecCCCcccccccCCCCcCceeEeecc
Q 019465 27 TLCEEHLNLILPAKPPFRPRQ----FKKCAVVGNSGDLLKTEFGEEIDSHDAVIRDNEAPVNQRYAKHVGLKRDFRLVVR 102 (340)
Q Consensus 27 s~~~~~L~~~lP~~sP~~~~~----c~~CAVVGNSGiL~gS~cG~EIDs~D~VIR~N~APv~~gye~DVGsKTt~~~~n~ 102 (340)
..+.+.|+.++|..+|+...+ |+|||||||||||+||+||+|||+||||||||+||+ .|||+|||+|||++++|+
T Consensus 33 ~~i~~~l~~l~~~~~p~~~~~~~~~~~~CAVVGNsGiL~~S~~G~eID~~D~ViR~N~aP~-~gfe~DVG~kT~~~~~n~ 111 (266)
T PF00777_consen 33 FKISKELYKLLPESSPFSLKHFKRRCRTCAVVGNSGILLGSGCGKEIDSHDFVIRMNLAPV-KGFEKDVGSKTTLRTMNP 111 (266)
T ss_dssp --HHHHHHHHTTT-S-S---TTTTG--EEEEE--BGGGTT---HHHHHTSSEEEEETT----TT-HHHH-S--SEEEEBT
T ss_pred hhHHHHHHHhCcccCccccccccCCCCeEEEEcCChHhccCccccccccCeeEEecCCccc-cccccccCccccccccCh
Confidence 678999999999999986655 999999999999999999999999999999999999 799999999999999999
Q ss_pred chhhhHHhhhcCCCCeEEE-Ee----------ccchhhH-----------H---HHHh-hcCCcceeehh--hhh----c
Q 019465 103 GAARNMVAILKGSTDEVLI-IK----------SVTHKDF-----------N---AMIK-SIPNPVYLFQG--IVL----R 150 (340)
Q Consensus 103 ~~~~~~~~~L~~~~~~~l~-ik----------~~~~~d~-----------~---~~~k-~i~nP~~l~~~--~~~----r 150 (340)
+++...... .. .+..+. +. .+..... . ...+ .+.||.++... .+. +
T Consensus 112 ~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~ 189 (266)
T PF00777_consen 112 SSLQRRYNL-LD-KDTFLVLLPFKGSDLVWLPAFSSKKNTRKSFWAYKALEKKYPNQKVRILHPEFLRYIWRFWLRRGGR 189 (266)
T ss_dssp TB-----------TT-EEEE--SSHHHHHHHHHHTTT-----BSSSB--S-----GGGEEEB-HHHHHHHHHHTSTT---
T ss_pred hHhhhhccc-cc-cccceeccccccchhhhhhhhhccccccccccchhhhhhccCcceeeecCHHHHhhHHHHhhhhhcc
Confidence 998432221 11 111111 11 1110000 0 0001 34567665422 122 2
Q ss_pred cCCCCcHHHHHHHHHhcCCeEEEeeeeeCCCCCccccccCCC-------CCCCCchhHHHHHHHHHhcCcEEEEcC
Q 019465 151 RGAKGTGMKSIELALSMCDIVDIYGFTVDPGYTEWTRYFSTP-------RKGHNPLQGRAYYQLLECLGVIRIHSP 219 (340)
Q Consensus 151 ~~~pSTGll~i~lAL~lCDeV~lYGF~pd~~~~~~~HYYd~~-------~~~H~~~~E~~~~q~Lh~~GvIrlh~~ 219 (340)
..+||||++++++||++||||+||||||..+.+.+|||||+. ...|+|.+|++++++||++|+|++|++
T Consensus 190 ~~~pSTG~~~~~~Al~~CD~V~lYGF~p~~~~~~~~HYyd~~~~~~~~~~~~H~~~~E~~~~~~L~~~Gvi~l~~g 265 (266)
T PF00777_consen 190 GNRPSTGLMAVSLALHFCDEVHLYGFWPPDNRTVPYHYYDNVKPKPCFFYKNHDMPAEFRLLKRLHKQGVIKLHTG 265 (266)
T ss_dssp SSS--HHHHHHHHHHHH-SEEEEES-S---TTS---BTTB------------S-HHHHHHHHHHHHHTTSSEEE--
T ss_pred ccCCCccHHHHHHHhcCCCeEEEEEEEecCCCCCccccccCccccccCCCCCCCCHHHHHHHHHHHHCCCeEEecC
Confidence 357999999999999999999999999955668899999983 245999999999999999999999986
No 2
>KOG2692 consensus Sialyltransferase [Carbohydrate transport and metabolism]
Probab=100.00 E-value=1.7e-42 Score=342.95 Aligned_cols=199 Identities=28% Similarity=0.406 Sum_probs=138.9
Q ss_pred ccccc-ccchhhhHHHHhccCCCCCCCCC---CCcceEEEEcCCCCCCCCcCCccccccceeeecCCCcccccccCCCCc
Q 019465 18 RGADK-CYNRTLCEEHLNLILPAKPPFRP---RQFKKCAVVGNSGDLLKTEFGEEIDSHDAVIRDNEAPVNQRYAKHVGL 93 (340)
Q Consensus 18 ~~~~~-c~~~s~~~~~L~~~lP~~sP~~~---~~c~~CAVVGNSGiL~gS~cG~EIDs~D~VIR~N~APv~~gye~DVGs 93 (340)
..... |.+.....+ ++..+|+.+|+.+ ..|++||||||||+|+||+||+|||+||||||||+||| +|||+|||+
T Consensus 121 ~~~~~~~~~~~~~~~-~~~~~p~~~p~~~~~~~~c~~CAVVGNsG~L~~S~~G~eID~~D~ViR~N~APt-~gye~DVGs 198 (376)
T KOG2692|consen 121 YSRSRWRRLEVIDPP-LFLLLPGVSPLFPLLFKRCRRCAVVGNSGILLNSRLGREIDSHDFVIRLNLAPT-KGYEKDVGS 198 (376)
T ss_pred ecccccccccccCcc-hhhhccccCCCcccccccCceEEEECCcceeCCCccccccccccEEEECCCCCc-cchhccccc
Confidence 33444 544433323 6788888887432 33888999999999999999999999999999999999 899999999
Q ss_pred CceeEeeccchhhhHH-hhhc--CCCCeEEEEecc-chhhHH------H-------------------HHhhcCCcceee
Q 019465 94 KRDFRLVVRGAARNMV-AILK--GSTDEVLIIKSV-THKDFN------A-------------------MIKSIPNPVYLF 144 (340)
Q Consensus 94 KTt~~~~n~~~~~~~~-~~L~--~~~~~~l~ik~~-~~~d~~------~-------------------~~k~i~nP~~l~ 144 (340)
|||++++||+++.... ..+. ... ..++++.. ...++. . ...++++|.|+.
T Consensus 199 KTt~r~~n~~Sv~~~~~~~~~~~~~~-~~~vv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~ 277 (376)
T KOG2692|consen 199 KTTLRTVNPPSVPTLLRNYLLDEPKR-VTFVVWLPFKNMSLLWLPAFYNTVNLRTGYWPVPRLYPVKPDKILLLDPLFIL 277 (376)
T ss_pred ceeEEEEcchhhhhcccccccccccc-ceEEEEcCccchhhhhhhhhccccccccceeecceeccCCcCeEeecChHHHH
Confidence 9999999987764321 1111 111 22222211 100000 0 000234444432
Q ss_pred h---hhhhcc----CCCCcHHHHHHHHHhcCCeEEEeeeeeCCCCC----ccccccCCC------CCCCCchhHHHHHHH
Q 019465 145 Q---GIVLRR----GAKGTGMKSIELALSMCDIVDIYGFTVDPGYT----EWTRYFSTP------RKGHNPLQGRAYYQL 207 (340)
Q Consensus 145 ~---~~~~r~----~~pSTGll~i~lAL~lCDeV~lYGF~pd~~~~----~~~HYYd~~------~~~H~~~~E~~~~q~ 207 (340)
. .++... .+||||++++++||++|||||+|||||++... ..+||||+. ...|++..|...++.
T Consensus 278 ~~~~~~~~s~~~~~~~pSTG~l~~~lAl~lCdeV~lyGF~~~~~~~~~~~~~~hYyd~~~~~~~~~~~H~~~~e~~~~~~ 357 (376)
T KOG2692|consen 278 YTVDRYLKSHGVQPKRPSTGLLAVTLALHLCDEVHLYGFGPDNRCRNSHYVPYHYYDNAKPDELFYGLHDMPLEGEALRK 357 (376)
T ss_pred HHHHHHhhCCCCCCCCCChhHHHHHHHHhhcCeEEEEEecCCCCCccCCCCccccccccccchhhhhhhhchhHHHHHHH
Confidence 1 223223 37999999999999999999999999986432 257999974 257999999999999
Q ss_pred HHhcCcEEEEcC
Q 019465 208 LECLGVIRIHSP 219 (340)
Q Consensus 208 Lh~~GvIrlh~~ 219 (340)
||++|+|.+-..
T Consensus 358 l~~~g~~~~~~~ 369 (376)
T KOG2692|consen 358 LHEKGVIILLLR 369 (376)
T ss_pred HHhccccccccc
Confidence 999997765443
No 3
>PF06002 CST-I: Alpha-2,3-sialyltransferase (CST-I); InterPro: IPR009251 This entry represents several alpha-2,3-sialyltransferase (2.4.99 from EC) proteins, most of which are found in the food-borne pathogen Campylobacter jejuni. Sialyltransferases transfer a sialic acid moiety from cytidine-5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to terminal positions of various key glycoconjugates, which play critical roles in cell recognition and adherence []. The structure of Cst-II alpha-2,3-sialyltransferase from C. jejuni consists of a 3-layer alpha/beta/alpha topology. Cst-II catalytic mechanism involves an essential histidine (general base) and two tyrosine residues (coordination of the phosphate leaving group) to carry out substrate binding and glycosyl transfer. ; PDB: 2X63_A 2X61_B 1RO7_B 2WQQ_A 2X62_B 1RO8_A 2DRJ_A 2P56_A 2P2V_A.
Probab=96.53 E-value=0.035 Score=54.21 Aligned_cols=164 Identities=15% Similarity=0.207 Sum_probs=85.0
Q ss_pred ceEEEEcCCCCCCCCcCCccccccceeeecCCCcccccccCCCCcCceeEeeccchhhhHH----hhhcC--CCCeEEEE
Q 019465 49 KKCAVVGNSGDLLKTEFGEEIDSHDAVIRDNEAPVNQRYAKHVGLKRDFRLVVRGAARNMV----AILKG--STDEVLII 122 (340)
Q Consensus 49 ~~CAVVGNSGiL~gS~cG~EIDs~D~VIR~N~APv~~gye~DVGsKTt~~~~n~~~~~~~~----~~L~~--~~~~~l~i 122 (340)
++|.|.|||.+|..-..|. +-.-+.|||||.-=-...| -.|.+..-+++|+..+.... ..... +.-+-++.
T Consensus 2 k~~~i~gngps~~~~~~~~-~~~~~~~fr~n~fy~e~~~--~lg~~~~~VFFn~~vf~~Qy~T~~~Li~n~EY~~e~i~c 78 (291)
T PF06002_consen 2 KPAIIAGNGPSLKEIDYSL-LPKDFDVFRCNQFYFEDKY--YLGKKVKAVFFNPCVFFEQYYTAKQLIQNGEYEIENIYC 78 (291)
T ss_dssp SEEEEE-SSGGGGC--GGG-S-SSEEEEEETTGGG-SBE--TT-SEECEEEE-GGGHHHHHHHHHHHHHTTS-EECEEEE
T ss_pred CceEEeCCCCchhhcchhh-CCCcccEEEecceecchhh--hcccceeEEEechHHHHHHHHHHHHHHhcCceeeeeeEE
Confidence 5799999999998887776 5555669999996543333 48999999999998864321 11111 11122333
Q ss_pred eccchhh-----HHHHHh-hcCCcc----eeeh-----h-h----hhccCCCCcHHHHHHHHHhc-CCeEEEeeeeeCCC
Q 019465 123 KSVTHKD-----FNAMIK-SIPNPV----YLFQ-----G-I----VLRRGAKGTGMKSIELALSM-CDIVDIYGFTVDPG 181 (340)
Q Consensus 123 k~~~~~d-----~~~~~k-~i~nP~----~l~~-----~-~----~~r~~~pSTGll~i~lAL~l-CDeV~lYGF~pd~~ 181 (340)
+.+-..+ +....+ .++.-. ++.+ . . .....+.|||.+|+.+|+.+ -.||-|.|... .
T Consensus 79 s~~~~~~~e~~~f~~~~~~~yp~~~~~y~~l~~l~~f~~~~ky~~~y~~q~~TSGVyM~~vAIAlGYKEIYLaGIDF--Y 156 (291)
T PF06002_consen 79 STINFEDFENKYFDDYFDKHYPDARLTYSYLKKLKPFYAHIKYNEIYYNQRITSGVYMCAVAIALGYKEIYLAGIDF--Y 156 (291)
T ss_dssp ---S-TTTS-HHHHHHHHHHSTT-EETHHHHTTSHHHHHHHHHHHHHH-----HHHHHHHHHHHCT--EEEEES--T--T
T ss_pred eccccccccchhhhhHHHHhCCCchhHHHHHHhcHHHHHHHHHHHhhcCCCcchHHHHHHHHHHcCcceEEEeeeee--e
Confidence 3332111 222111 122111 0100 0 0 01134679999999999998 67899999831 1
Q ss_pred CCccccc-cCCC-----------------CCCCCchhHHHHHHHHHhcCcEEEE
Q 019465 182 YTEWTRY-FSTP-----------------RKGHNPLQGRAYYQLLECLGVIRIH 217 (340)
Q Consensus 182 ~~~~~HY-Yd~~-----------------~~~H~~~~E~~~~q~Lh~~GvIrlh 217 (340)
...+.|| |+.. ...|+....-+.++.|.+.+-++++
T Consensus 157 ~~~~~hy~fe~k~~ni~~l~~~~~~~~~~~~~Hsk~~Dlqal~~lqk~y~v~iY 210 (291)
T PF06002_consen 157 QNGGGHYAFENKSENIINLLPDFENRKSSDIQHSKDYDLQALEFLQKYYDVKIY 210 (291)
T ss_dssp -TTSSSSSS-SSTHHHHHHSGGGGSS--STTT--HHHHHHHHHHHHHHHT-EEE
T ss_pred cCCCCcccccccccchhhhCcccccccccccccchhhCHHHHHHHHHhcCeeEE
Confidence 2446677 5442 2578888888888888888777776
No 4
>PF01973 MAF_flag10: Protein of unknown function DUF115; InterPro: IPR002826 The prokaryotic proteins in this family have no known function.
Probab=64.78 E-value=18 Score=31.75 Aligned_cols=122 Identities=19% Similarity=0.192 Sum_probs=69.6
Q ss_pred ceEEEEcCCCCCCCC-cCCccccccceeeecCCCcccccccCCCCcCceeEeeccchhhhHH--hhhcCCCCeEEEEecc
Q 019465 49 KKCAVVGNSGDLLKT-EFGEEIDSHDAVIRDNEAPVNQRYAKHVGLKRDFRLVVRGAARNMV--AILKGSTDEVLIIKSV 125 (340)
Q Consensus 49 ~~CAVVGNSGiL~gS-~cG~EIDs~D~VIR~N~APv~~gye~DVGsKTt~~~~n~~~~~~~~--~~L~~~~~~~l~ik~~ 125 (340)
++|.|||||-+|... ..=++.-..-++|=+|.+-. -..+-|-+-++++.......... ..+....+..++....
T Consensus 25 ~~~~IvgaGPSL~~~i~~lk~~~~~~~iia~~sa~~---~L~~~gI~Pd~~v~~D~~~~~~~~~~~~~~~~~i~l~~~~~ 101 (170)
T PF01973_consen 25 KPAIIVGAGPSLDKNIELLKENRNKAIIIAVNSALK---ALLKNGIKPDFVVSIDPQFWNYEHFKEINKEFDIPLFFASS 101 (170)
T ss_pred CeEEEEecCCCHHHHHHHHHhcccCcEEEEecHHHH---HHHHcCceEEEEEEcCCCcchHHHHhhcccccceEEEEecc
Confidence 699999999998764 12233334567778888743 23467888888887654332211 1111111334444433
Q ss_pred chhhHHHHHhhcCCccee-eh------hhhh------ccCCCCcHHHHHHHHHhc-CCeEEEeee
Q 019465 126 THKDFNAMIKSIPNPVYL-FQ------GIVL------RRGAKGTGMKSIELALSM-CDIVDIYGF 176 (340)
Q Consensus 126 ~~~d~~~~~k~i~nP~~l-~~------~~~~------r~~~pSTGll~i~lAL~l-CDeV~lYGF 176 (340)
.++.... .+..+.+. +. .+.. -...+|.+..++.+|+++ |++|-+.|.
T Consensus 102 ~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~sV~~~a~~lA~~lG~~~I~L~G~ 163 (170)
T PF01973_consen 102 ANPNILR---KFKGPKIFFFSNSYQYFAWFSKDFGYILYSGGSVANTALQLAYYLGFKPIYLIGQ 163 (170)
T ss_pred cCHHHHH---HcCCceEEEecCCccchhhhhccccccCCCCccHHHHHHHHHHHHCCCcEEEEee
Confidence 3333322 23333321 11 1110 122468899999999988 999999998
No 5
>PF10143 PhosphMutase: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; InterPro: IPR004456 This family represents 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGAM), it is a metalloenzyme found particularly in archaea and some eubacteria. It is responsble for the interconversion of 2-phosphoglycerate and 3-phosphoglycerate []. It is distantly related to the iPGAM (IPR005995 from INTERPRO) characteristic of plants and many eubacteria. The common active site and metal-binding residues of the phosphatase domain are easily identified, but the putative phosphotransferase domain is highly diverged. These proteins are unrelated to the cofactor-dependent PGAM (PIRSF001490 from PIRSF). Activity has been demonstrated for proteins from Methanocaldococcus jannaschii (Methanococcus jannaschii) [, ], Pyrococcus furiosus [], and Sulfolobus solfataricus []. These proteins were initially misidentified as phosphonopyruvate decarboxylase.; GO: 0003824 catalytic activity, 0046872 metal ion binding; PDB: 2ZKT_A 3KD8_A 3IDD_B.
Probab=13.20 E-value=65 Score=29.21 Aligned_cols=25 Identities=28% Similarity=0.274 Sum_probs=15.8
Q ss_pred CCCCcCCccccccceeeecCCCccc
Q 019465 60 LLKTEFGEEIDSHDAVIRDNEAPVN 84 (340)
Q Consensus 60 L~gS~cG~EIDs~D~VIR~N~APv~ 84 (340)
|-.-+.|-+++.-|++||+|++.++
T Consensus 42 lEAlg~Gi~l~~~dvafR~Nl~tv~ 66 (172)
T PF10143_consen 42 LEALGAGIELKPGDVAFRCNLVTVD 66 (172)
T ss_dssp HHHHHTT----TT-EEEEEEEEEEC
T ss_pred HHhccCCCCCCCCCEEEEEEEEEec
Confidence 3334678899999999999999884
No 6
>PF06422 PDR_CDR: CDR ABC transporter; InterPro: IPR010929 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). In yeast, the PDR and CDR ABC transporters display extensive sequence homology, and confer resistance to several anti-fungal compounds by actively transporting their substrates out of the cell. These transporters have two homologous halves, each with an N-terminal intracellular hydrophilic region that contains an ATP-binding site, followed by a C-terminal membrane-associated region containing six transmembrane segments []. This entry represents a domain of the PDR/CDR ABC transporter comprising extracellular loop 3, transmembrane segment 6 and a linker region.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane
Probab=11.99 E-value=1.1e+02 Score=25.22 Aligned_cols=22 Identities=32% Similarity=0.696 Sum_probs=16.6
Q ss_pred cCCCCCCCCC--CCcceEEEEcCC
Q 019465 36 ILPAKPPFRP--RQFKKCAVVGNS 57 (340)
Q Consensus 36 ~lP~~sP~~~--~~c~~CAVVGNS 57 (340)
++|.-+.+.+ ...+.|+|+|.-
T Consensus 2 ~iP~Gp~Y~~~~~~~q~C~~~Ga~ 25 (103)
T PF06422_consen 2 LIPSGPGYDNISPANQVCAVVGAQ 25 (103)
T ss_pred cCCCCCCCCCCCCCcCccCCCCCC
Confidence 5777776765 459999998874
No 7
>PF12434 Malate_DH: Malate dehydrogenase enzyme
Probab=10.47 E-value=1.5e+02 Score=19.50 Aligned_cols=14 Identities=21% Similarity=0.036 Sum_probs=10.7
Q ss_pred cchhhHHHHHHHhh
Q 019465 297 PFKSLRKEAQDHYF 310 (340)
Q Consensus 297 ~~~~~r~~a~~h~~ 310 (340)
....||++|.++..
T Consensus 13 ~r~~lR~AALeYHe 26 (28)
T PF12434_consen 13 KRAQLRQAALEYHE 26 (28)
T ss_pred HHHHHHHHHHHhcc
Confidence 34679999998764
No 8
>COG1634 Uncharacterized Rossmann fold enzyme [General function prediction only]
Probab=10.44 E-value=1.7e+02 Score=28.25 Aligned_cols=122 Identities=20% Similarity=0.193 Sum_probs=65.0
Q ss_pred cceEEEEcCCCCCCCCcCCccccccceeeecCCCcccccccCCCCcCceeEeeccchhhhHHhhhc-CCCCeEEEEeccc
Q 019465 48 FKKCAVVGNSGDLLKTEFGEEIDSHDAVIRDNEAPVNQRYAKHVGLKRDFRLVVRGAARNMVAILK-GSTDEVLIIKSVT 126 (340)
Q Consensus 48 c~~CAVVGNSGiL~gS~cG~EIDs~D~VIR~N~APv~~gye~DVGsKTt~~~~n~~~~~~~~~~L~-~~~~~~l~ik~~~ 126 (340)
-++|+||||+..|....-| .+.++||==-.|-. .--+.|-.-++++.--.-- +...+. ....+++++.+
T Consensus 52 g~~v~vvG~gP~l~e~~~~---~~~~~vi~AdgA~~---~l~~~gi~pDiiVTDlDgd--~e~~~~~~~~g~i~VVHA-- 121 (232)
T COG1634 52 GREVAVVGAGPSLEEEIKG---LSSEVVIAADGAVS---ALLERGIRPDIIVTDLDGD--PEDLLSCTAKGSIVVVHA-- 121 (232)
T ss_pred CCEEEEECCCCcHhhhhcc---cccceEEeccHHHH---HHHHcCCCCcEEEecCCCC--HHHHHHhhccCCEEEEEe--
Confidence 6799999999998776555 66778876444432 2225677777666532111 111111 22334555542
Q ss_pred hhhHHHHHh-hcCCcc-e--eehhhhhc----cCCCCcHHHHHHHHHhc-CCeEEEeeeeeC
Q 019465 127 HKDFNAMIK-SIPNPV-Y--LFQGIVLR----RGAKGTGMKSIELALSM-CDIVDIYGFTVD 179 (340)
Q Consensus 127 ~~d~~~~~k-~i~nP~-~--l~~~~~~r----~~~pSTGll~i~lAL~l-CDeV~lYGF~pd 179 (340)
|.|--..+. ..+... + ..|....+ -+-.|-|==++.+|.++ ..+|.++||++.
T Consensus 122 HGDNi~~i~~~~~~~~~vigTtQ~~P~~~v~NfgGFTDGDRAa~LA~~lgA~~I~l~GfdF~ 183 (232)
T COG1634 122 HGDNIWRIPKVVPVLDRVIGTTQVRPFDRVYNFGGFTDGDRAAFLAYYLGAEKIRLVGFDFG 183 (232)
T ss_pred cCcCHHHhhccccccceeecccccCCCcceeccCCCCCchHHHHHHHHhCCCeEEEeeecCC
Confidence 333111111 111110 0 01111111 12236777899999999 788999999754
No 9
>PF03826 OAR: OAR domain; InterPro: IPR003654 This 14 amino acid motif has been identified within the C-terminal region of several Paired-like homeodomain (HD) containing proteins [, ]. It was named OAR domain after the initials of otp, aristaless, and rax []. Although it has been proposed that this domain could be important for transactivation and be involved in protein-protein interactions or DNA binding [, ], is function is not yet known. Some proteins known to contain a OAR domain include human RIEG, defects in which are the cause of Rieger syndrome []; human OG12X and Mus musculus (Mouse) Og12x, whose function is not yet known []; vertebrate Rax, which plays a role in the proliferation and/or differentiation of retinal cells []; Drosophila DRX, which appears to be important in brain development []; and human SHOX, encoded by the short stature homeobox-containing gene. Defects or lack of this protein are the cause of short stature associated with the Turner syndrome [].; GO: 0003677 DNA binding, 0007275 multicellular organismal development, 0005634 nucleus
Probab=10.42 E-value=1.7e+02 Score=18.11 Aligned_cols=14 Identities=29% Similarity=0.458 Sum_probs=12.0
Q ss_pred ccchhhHHHHHHHh
Q 019465 296 MPFKSLRKEAQDHY 309 (340)
Q Consensus 296 ~~~~~~r~~a~~h~ 309 (340)
-.|.+||-.|++|-
T Consensus 6 sSIa~LRlKAkeH~ 19 (21)
T PF03826_consen 6 SSIAALRLKAKEHS 19 (21)
T ss_pred hhHHHHHHHHHHhc
Confidence 37899999999995
No 10
>KOG3994 consensus Uncharacterized conserved protein [Function unknown]
Probab=10.29 E-value=61 Score=31.56 Aligned_cols=22 Identities=36% Similarity=0.504 Sum_probs=18.5
Q ss_pred HHHHHHHHhcCCeEEEeeeeeC
Q 019465 158 MKSIELALSMCDIVDIYGFTVD 179 (340)
Q Consensus 158 ll~i~lAL~lCDeV~lYGF~pd 179 (340)
.-.|..|-++||..+-||+|.|
T Consensus 193 akFI~~A~eiC~~L~~~GYWAD 214 (291)
T KOG3994|consen 193 AKFILAAREICDRLLSYGYWAD 214 (291)
T ss_pred HHHHHHHHHHHHHHHhcchHhh
Confidence 3457788999999999999965
Done!