Query gi|254781075|ref|YP_003065488.1| hypothetical protein CLIBASIA_04885 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 266
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 04:43:04 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781075.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02396 diverge_rpsU rpsU-di 85.4 1.7 4.2E-05 24.0 4.5 41 22-62 119-162 (195)
2 pfam08511 COQ9 COQ9. COQ9 is a 82.6 2.8 7.2E-05 22.6 4.7 42 22-63 5-49 (79)
3 PRK13943 protein-L-isoaspartat 75.9 3 7.7E-05 22.4 3.1 66 92-157 230-304 (317)
4 pfam11014 DUF2852 Protein of u 59.0 10 0.00025 19.0 2.9 24 134-157 66-89 (115)
5 COG2911 Uncharacterized protei 54.5 8.8 0.00023 19.4 2.1 12 65-76 39-50 (1278)
6 pfam04699 P16-Arc ARP2/3 compl 36.8 22 0.00057 16.8 1.8 13 205-217 100-112 (153)
7 KOG1465 consensus 34.4 28 0.00072 16.1 2.0 29 22-50 67-95 (353)
8 KOG0995 consensus 33.1 39 0.001 15.2 5.1 48 64-112 121-172 (581)
9 KOG3860 consensus 31.8 25 0.00065 16.4 1.5 20 68-87 344-363 (494)
10 KOG2504 consensus 31.4 36 0.00092 15.4 2.2 42 41-83 290-331 (509)
11 pfam02942 Flu_B_NS1 Influenza 29.8 27 0.00069 16.2 1.3 10 195-204 216-225 (247)
12 COG3274 Predicted O-acyltransf 29.6 45 0.0011 14.8 4.0 21 54-74 120-140 (332)
13 TIGR02919 TIGR02919 conserved 29.5 45 0.0011 14.8 2.7 12 131-142 364-375 (448)
14 TIGR02211 LolD_lipo_ex lipopro 29.1 24 0.00062 16.5 1.0 52 201-259 94-155 (221)
15 KOG1089 consensus 27.7 32 0.00081 15.8 1.4 77 34-114 421-498 (573)
16 TIGR01068 thioredoxin thioredo 27.4 14 0.00036 18.1 -0.5 20 204-223 53-72 (101)
17 TIGR02673 FtsE cell division A 27.3 26 0.00067 16.3 0.9 16 244-259 136-151 (215)
18 KOG3560 consensus 26.6 23 0.0006 16.6 0.5 26 164-191 131-157 (712)
19 pfam10925 DUF2680 Protein of u 25.5 53 0.0013 14.4 3.9 52 146-200 4-55 (59)
20 COG3947 Response regulator con 25.4 53 0.0013 14.4 3.6 73 132-204 243-346 (361)
21 KOG3226 consensus 24.8 28 0.00072 16.1 0.7 30 155-184 479-508 (508)
22 PRK11546 zraP zinc resistance 23.1 59 0.0015 14.1 4.5 37 179-215 44-80 (139)
23 pfam05411 Peptidase_C32 Equine 22.9 26 0.00067 16.3 0.2 37 9-50 10-46 (128)
24 TIGR02470 sucr_synth sucrose s 21.6 63 0.0016 13.9 2.5 11 160-170 552-562 (790)
25 TIGR00806 rfc reduced folate c 20.4 66 0.0017 13.7 4.0 48 70-121 381-429 (542)
26 pfam05203 Hom_end_hint Hom_end 20.2 12 0.00032 18.4 -1.9 76 125-209 103-179 (438)
No 1
>TIGR02396 diverge_rpsU rpsU-divergently transcribed protein; InterPro: IPR012762 COQ9 is an protein that is required for the biosynthesis of coenzyme Q , which functions in the respiratory electron transport chain and serves as a lipophilic antioxidant. In Saccharomyces cerevisiae, Q biosynthesis requires nine Coq proteins (Coq1-Coq9), with the COQ9 product acting subsequent to the prenylation of 4-hydroxybenzoic acid. ; GO: 0006744 ubiquinone biosynthetic process.
Probab=85.37 E-value=1.7 Score=24.03 Aligned_cols=41 Identities=27% Similarity=0.458 Sum_probs=29.9
Q ss_pred HCCHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10878887899999999843---334566667999999999999
Q gi|254781075|r 22 ILSPTEVYNVHRRIWHLLRD---DFGYFTKRTFFCFAFFITIIY 62 (266)
Q Consensus 22 ilsptevynvhrriwhllrd---dfgyftkrtffcfaffitiiy 62 (266)
+.|-.+++..--.|||+..| ||+|+|||.-..=-+--|++|
T Consensus 119 ~~s~~~~~~l~D~Iwy~~GD~S~Df~wYtKRa~L~gvy~~~elf 162 (195)
T TIGR02396 119 ATSLRLLAELVDEIWYLAGDKSTDFNWYTKRAILSGVYSSTELF 162 (195)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 58999999999999998766003763389999999999999999
No 2
>pfam08511 COQ9 COQ9. COQ9 is an enzyme that is required for the biosynthesis of coenzyme Q. It may either catalyse a reaction in the coenzyme Q biosynthetic pathway or have a regulatory role.
Probab=82.56 E-value=2.8 Score=22.56 Aligned_cols=42 Identities=26% Similarity=0.475 Sum_probs=33.6
Q ss_pred HCCHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10878887899999999843---3345666679999999999999
Q gi|254781075|r 22 ILSPTEVYNVHRRIWHLLRD---DFGYFTKRTFFCFAFFITIIYV 63 (266)
Q Consensus 22 ilsptevynvhrriwhllrd---dfgyftkrtffcfaffitiiyv 63 (266)
..+..++|+.--.|||+..| ||.|+|||.-.+-.+--|.+|-
T Consensus 5 ~~~~~~l~~~~D~IW~~aGD~StD~n~YtKR~~L~~vY~st~l~~ 49 (79)
T pfam08511 5 PTSLKLLWRLADDIWYAAGDTSTDFNWYTKRATLSAVYSSTELYM 49 (79)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999981897667227999999999999999999
No 3
>PRK13943 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=75.92 E-value=3 Score=22.35 Aligned_cols=66 Identities=14% Similarity=0.091 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHEECCCCEEEEECC---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1200654999999999865641117741333102---------25999999999999987558888878899999
Q gi|254781075|r 92 TEYTWHDIETFLALLYMSCILVATDDRKLRMIED---------GDRIIEIIQSIRRAFDQYKEEERKALSDIQEQ 157 (266)
Q Consensus 92 teytwhdietflallymscilvatddrklrmied---------gdriieiiqsirrafdqykeeerkalsdiqeq 157 (266)
.|-+|-++.-|+.|+|.+.--.|+-|+..--|++ --||-.+++.++|.++|+++.....+.++|-.
T Consensus 230 ~~~~~~~~~if~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~w~~~~~~s~~~~~~~ 304 (317)
T PRK13943 230 REILLVRSHIFVELVDLLTRRLTEIDGTFYYAGPNGVVEFLDDRMRIYGDAPEIENLLTQWESCGYRSFEYLQLH 304 (317)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCEEEEECCHHHHHHHHHHHHHCCCCCHHHHHEE
T ss_conf 333268889999999999864564156178765881699966835663244999999999987288667784112
No 4
>pfam11014 DUF2852 Protein of unknown function (DUF2852). This bacterial family of proteins has no known function.
Probab=58.99 E-value=10 Score=19.01 Aligned_cols=24 Identities=33% Similarity=0.493 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999987558888878899999
Q gi|254781075|r 134 QSIRRAFDQYKEEERKALSDIQEQ 157 (266)
Q Consensus 134 qsirrafdqykeeerkalsdiqeq 157 (266)
.|=..|||.|++++.+-|.+.|++
T Consensus 66 ssGN~AFD~Yr~~tL~RLEeEq~~ 89 (115)
T pfam11014 66 SSGNEAFDEYRAETLRRLEEEQRA 89 (115)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 961167899999999999999999
No 5
>COG2911 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.48 E-value=8.8 Score=19.35 Aligned_cols=12 Identities=17% Similarity=0.213 Sum_probs=6.1
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999999
Q gi|254781075|r 65 FPIFINFLISYI 76 (266)
Q Consensus 65 fpifinflisyi 76 (266)
.+.+++++-++.
T Consensus 39 ~~~~~~~~~~~~ 50 (1278)
T COG2911 39 LRYGLNAIDSWL 50 (1278)
T ss_pred HHHHHHHHHHHC
T ss_conf 468999998657
No 6
>pfam04699 P16-Arc ARP2/3 complex 16 kDa subunit (p16-Arc). The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices.
Probab=36.83 E-value=22 Score=16.78 Aligned_cols=13 Identities=31% Similarity=0.585 Sum_probs=5.4
Q ss_pred HHHHHHHHHHCCC
Q ss_conf 4569999854030
Q gi|254781075|r 205 SDELEDILSRYSI 217 (266)
Q Consensus 205 sdeledilsrysi 217 (266)
+.+-.|+|-.|--
T Consensus 100 ~~~~~D~LMKYiY 112 (153)
T pfam04699 100 DSEQQDVLMKYLY 112 (153)
T ss_pred CHHHHHHHHHHHH
T ss_conf 9887506899998
No 7
>KOG1465 consensus
Probab=34.36 E-value=28 Score=16.12 Aligned_cols=29 Identities=28% Similarity=0.270 Sum_probs=24.4
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10878887899999999843334566667
Q gi|254781075|r 22 ILSPTEVYNVHRRIWHLLRDDFGYFTKRT 50 (266)
Q Consensus 22 ilsptevynvhrriwhllrddfgyftkrt 50 (266)
--+.+-+-|+-|||-+++||.++-.++++
T Consensus 67 ~psE~~~gNiirrIlkliReE~~~l~~~~ 95 (353)
T KOG1465 67 QPSELSCGNIIRRILKLIREEVLELTGGA 95 (353)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 87300056899999999999999974567
No 8
>KOG0995 consensus
Probab=33.15 E-value=39 Score=15.20 Aligned_cols=48 Identities=31% Similarity=0.309 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHCCC----EECCCEEEHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999853142----002222201120065499999999986564
Q gi|254781075|r 64 FFPIFINFLISYIYKNIGY----KISSQYYSLTEYTWHDIETFLALLYMSCIL 112 (266)
Q Consensus 64 ffpifinflisyiyknigy----kissqyyslteytwhdietflallymscil 112 (266)
+||.-+.=-++.|.||.|| .|||++-.-+.-+|+.|-..|.-|- +||-
T Consensus 121 ~f~~r~EeEV~~ilK~L~YPf~~siSs~~a~gspH~WP~iL~mlhWlv-dlI~ 172 (581)
T KOG0995 121 EFPERIEEEVVQILKNLKYPFLLSISSLQAAGSPHNWPHILGMLHWLV-DLIR 172 (581)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCCCHHHHCCCCCCCCCHHHHHHHHHHH-HHHH
T ss_conf 650658889999998179986531444215889986289999999999-9999
No 9
>KOG3860 consensus
Probab=31.82 E-value=25 Score=16.41 Aligned_cols=20 Identities=40% Similarity=0.634 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHCCCEECCC
Q ss_conf 99999999985314200222
Q gi|254781075|r 68 FINFLISYIYKNIGYKISSQ 87 (266)
Q Consensus 68 finflisyiyknigykissq 87 (266)
|-+||+-|+|-.+|.+-++-
T Consensus 344 fn~wLiryvYiplgGs~~~~ 363 (494)
T KOG3860 344 FNKWLIRYVYIPLGGSRSSL 363 (494)
T ss_pred HHHHHHHHEEECCCCCCCHH
T ss_conf 99999998001358872379
No 10
>KOG2504 consensus
Probab=31.43 E-value=36 Score=15.43 Aligned_cols=42 Identities=21% Similarity=0.356 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCE
Q ss_conf 3334566667999999999999999999999999998531420
Q gi|254781075|r 41 DDFGYFTKRTFFCFAFFITIIYVFFPIFINFLISYIYKNIGYK 83 (266)
Q Consensus 41 ddfgyftkrtffcfaffitiiyvffpifinflisyiyknigyk 83 (266)
-|+..|..++|.++++..++.++-|.++.-+|.+|-- +.|+.
T Consensus 290 ~d~~ll~~~~fl~~~~~~~~~~~g~~~p~~~l~~~~~-~~g~~ 331 (509)
T KOG2504 290 LDLSLLKDPKFLLLALSNLFAYLGFNVPFVYLPSYAK-SLGLS 331 (509)
T ss_pred CHHHHHCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHH-HCCCC
T ss_conf 2078861558999999999999987633444087785-55984
No 11
>pfam02942 Flu_B_NS1 Influenza B non-structural protein (NS1). A specific region of the influenza B virus NS1 protein, which includes part of its effector domain, blocks the covalent linkage of ISG15 to its target proteins both in vitro and in infected cells. Of the several hundred proteins induced by interferon (IFN) alpha/beta, the ubiquitin-like ISG15 protein is one of the most predominant. Influenza A virus employs a different strategy: its NS1 protein does not bind the ISG15 protein, but little or no ISG15 protein is produced during infection.
Probab=29.81 E-value=27 Score=16.23 Aligned_cols=10 Identities=40% Similarity=0.574 Sum_probs=3.9
Q ss_pred HHHHHHHHHH
Q ss_conf 9986665202
Q gi|254781075|r 195 ARMKNQLVAE 204 (266)
Q Consensus 195 armknqlvae 204 (266)
.|.-..|||.
T Consensus 216 grlvaklvat 225 (247)
T pfam02942 216 GRLVAKLVAT 225 (247)
T ss_pred CCHHHHEECC
T ss_conf 5333301103
No 12
>COG3274 Predicted O-acyltransferase [General function prediction only]
Probab=29.57 E-value=45 Score=14.82 Aligned_cols=21 Identities=38% Similarity=0.605 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999999999
Q gi|254781075|r 54 FAFFITIIYVFFPIFINFLIS 74 (266)
Q Consensus 54 faffitiiyvffpifinflis 74 (266)
|-|-|.++|.+-|+..--+++
T Consensus 120 flf~i~~iYLi~pLi~~~~v~ 140 (332)
T COG3274 120 FLFAILGIYLISPLIQVILVS 140 (332)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999999976
No 13
>TIGR02919 TIGR02919 conserved hypothetical protein TIGR02919; InterPro: IPR014268 Members of this entry are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus..
Probab=29.48 E-value=45 Score=14.81 Aligned_cols=12 Identities=50% Similarity=0.974 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999987
Q gi|254781075|r 131 EIIQSIRRAFDQ 142 (266)
Q Consensus 131 eiiqsirrafdq 142 (266)
||.+.|||||++
T Consensus 364 Eil~AvR~AF~y 375 (448)
T TIGR02919 364 EILNAVRRAFEY 375 (448)
T ss_pred CHHHHHHHHHHH
T ss_conf 378899887564
No 14
>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein; InterPro: IPR011924 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions 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 hydrolyze 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 polarize 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 , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents LolD, a member of the ABC transporter family. LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on the residue immediately following the modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. Excluded from this entry are homologs from the archaeal genus Methanosarcina .; GO: 0005524 ATP binding, 0006810 transport, 0016020 membrane.
Probab=29.13 E-value=24 Score=16.54 Aligned_cols=52 Identities=35% Similarity=0.463 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHH----HHHHHHHHHHHH------HHHHHHHHHHHHHHH
Q ss_conf 52024569999854030126656411276678----887778888776------641324348887777
Q gi|254781075|r 201 LVAESDELEDILSRYSIESIPLDLPEMSQDEA----IKYINHVYLLGK------WISRGEIQRSQIARR 259 (266)
Q Consensus 201 lvaesdeledilsrysiesipldlpemsqdea----ikyinhvyllgk------wisrgeiqrsqiarr 259 (266)
|.+|=.-||.+ ++|+=.-.+|..|| -+-...|-|--+ =+|-||=||.-|||-
T Consensus 94 LL~dFtaLENV-------aMP~LIg~~s~~ea~~~A~~mL~~VgL~~R~~h~PSELSGGERQRvAIARA 155 (221)
T TIGR02211 94 LLPDFTALENV-------AMPLLIGKKSKKEAKERAYEMLEKVGLEHRINHRPSELSGGERQRVAIARA 155 (221)
T ss_pred CCCCCCHHHHH-------HHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 03000026887-------777753589988999999999886073344555777345633799999998
No 15
>KOG1089 consensus
Probab=27.67 E-value=32 Score=15.79 Aligned_cols=77 Identities=26% Similarity=0.298 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCEECCCEEEHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999843334566667999999999999-99999999999999853142002222201120065499999999986564
Q gi|254781075|r 34 RIWHLLRDDFGYFTKRTFFCFAFFITIIY-VFFPIFINFLISYIYKNIGYKISSQYYSLTEYTWHDIETFLALLYMSCIL 112 (266)
Q Consensus 34 riwhllrddfgyftkrtffcfaffitiiy-vffpifinflisyiyknigykissqyyslteytwhdietflallymscil 112 (266)
-+|+|++.--+-|- |--+|.|.+.+ ++.+.|.+||-.---.----+++++-+|+-.|-+++.+.|+-.+|-.--.
T Consensus 421 cvwQl~~QfP~~FE----Fne~fLi~L~~h~ys~qfGtFl~NsekeR~e~~~~~kt~slW~~~~~~~~~f~Nply~~~~~ 496 (573)
T KOG1089 421 CVWQLLEQFPCAFE----FNERFLIKLHEHAYSSQFGTFLGNSEKERRELNLSEKTTSLWDYLLPRKEEFVNPLYDPRYL 496 (573)
T ss_pred HHHHHHHHCCCCEE----HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCEEHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 99999853875320----10799999997667764034334678889983555342227877765234304755445666
Q ss_pred EE
Q ss_conf 11
Q gi|254781075|r 113 VA 114 (266)
Q Consensus 113 va 114 (266)
++
T Consensus 497 ~~ 498 (573)
T KOG1089 497 VI 498 (573)
T ss_pred CE
T ss_conf 40
No 16
>TIGR01068 thioredoxin thioredoxin; InterPro: IPR005746 Thioredoxins , , , are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of 2 cysteine thiol groups to a disulphide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulphide and a dithiol. TR-S_2 + NADPH + H^+ -> TR-(SH)_2 + NADP^+ (1) trx-S_2 + TR-(SH)_2 -> trx-(SH)_2 + TR-S_2 (2) Protein-S_2 + trx-(SH)_2 -> Protein-(SH)_2 + trx-S_2 (3) In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide (steps 1 and 2). Reduced thioredoxin then directly reduces the disulphide in the substrate protein (step 3) . Protein disulphide isomerase (PDI), a resident foldase of the endoplasmic recticulum, is a multi-functional protein that catalyses the formation and isomerisation of disulphide bonds during protein folding , . PDI contains 2 redox active domains, near the N- and C-termini, that are similar to thioredoxin: both contribute to disulphide isomerase activity, but are functionally non-equivalent . Interestingly, a mutant PDI, with all 4 of the active cysteines replaced by serine, displays a low but detectable level of disulphide isomerase activity . Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity . A number of endoplasmic reticulum proteins that differ from the PDI major isozyme contain 2 (ERp60, ERp5) or 3 (ERp72 ) thioredoxin domains; all of them seem to be PDIs. 3D-structures have been determined for a number of thioredoxins . The molecule has a doubly-wound alternating alpha/beta fold, consisting of a 5-stranded parallel beta-sheet core, enclosed by 4 alpha-helices. The active site disulphide is located at the N-terminus of helix 2 in a short segment that is separated from the rest of the helix by a kink caused by a conserved proline. The 4-membered disulphide ring is located on the surface of the protein. A flat hydrophobic surface lies adjacent to the disulphide, which presumably facilitates interaction with other proteins. One invariant feature of all thioredoxins is a cis-proline located in a loop preceding beta-strand 4. This residue is positioned in van der Waals contact with the active site cysteines and is important both for stability and function . Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase . Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0006662 glycerol ether metabolic process, 0045454 cell redox homeostasis.
Probab=27.37 E-value=14 Score=18.06 Aligned_cols=20 Identities=45% Similarity=0.619 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHCCCCCCCCC
Q ss_conf 24569999854030126656
Q gi|254781075|r 204 ESDELEDILSRYSIESIPLD 223 (266)
Q Consensus 204 esdeledilsrysiesipld 223 (266)
.-||-.++-++|.|.|||-=
T Consensus 53 nvD~~~~~A~~ygi~SIPTl 72 (101)
T TIGR01068 53 NVDENPDIAAKYGIRSIPTL 72 (101)
T ss_pred ECCCCCCCHHHCCCCCCCEE
T ss_conf 34788341445285405637
No 17
>TIGR02673 FtsE cell division ATP-binding protein FtsE; InterPro: IPR005286 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions 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 hydrolyze 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 polarize 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 , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). FtsE is an ABC transporter ATP-binding protein. This protein and its permease partner FtsX, localize to the cell division site. In a number of species, the ftsEX gene pair is located next to ftsY, which encodes the signal recognition particle-docki ng protein.; GO: 0005524 ATP binding, 0051301 cell division.
Probab=27.25 E-value=26 Score=16.29 Aligned_cols=16 Identities=50% Similarity=0.574 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 6641324348887777
Q gi|254781075|r 244 KWISRGEIQRSQIARR 259 (266)
Q Consensus 244 kwisrgeiqrsqiarr 259 (266)
.-.|.||=||--|||-
T Consensus 136 ~~LSGGEQQRvaIARA 151 (215)
T TIGR02673 136 EQLSGGEQQRVAIARA 151 (215)
T ss_pred CCCCCCHHHHHHHHHH
T ss_conf 1004725788888765
No 18
>KOG3560 consensus
Probab=26.58 E-value=23 Score=16.63 Aligned_cols=26 Identities=38% Similarity=0.813 Sum_probs=17.6
Q ss_pred HEEEE-CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 00253-14647764124887899997588
Q gi|254781075|r 164 KKIVF-SSDREEYIGLHQKQIDLIHQNID 191 (266)
Q Consensus 164 kkivf-ssdreeyiglhqkqidlihqnid 191 (266)
..|.| |+.-|.|.|.||. |.+||++-
T Consensus 131 g~ifyAS~tIedYLGFhQS--DV~HQsVY 157 (712)
T KOG3560 131 GEIFYASATIEDYLGFHQS--DVMHQSVY 157 (712)
T ss_pred CEEEEEHHHHHHHHCCCCC--CHHHHHHH
T ss_conf 3699740017765352300--10104588
No 19
>pfam10925 DUF2680 Protein of unknown function (DUF2680). Members in this family of proteins are annotated as yckD however currently no function is known.
Probab=25.54 E-value=53 Score=14.37 Aligned_cols=52 Identities=23% Similarity=0.390 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHCCHHHEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8888788999997300310025314647764124887899997588999998666
Q gi|254781075|r 146 EERKALSDIQEQLLNDASKKIVFSSDREEYIGLHQKQIDLIHQNIDRHLARMKNQ 200 (266)
Q Consensus 146 eerkalsdiqeqllndaskkivfssdreeyiglhqkqidlihqnidrhlarmknq 200 (266)
+..+.+.+++.|.+. .-|++| +-.-+|--+.+.|-|.|-+|||.+...|+..
T Consensus 4 qQk~ei~~l~kqi~e-l~Kqii--~KyVe~G~iT~eQa~~i~~~id~r~~~~~qN 55 (59)
T pfam10925 4 QQKKEIEALYKQIAE-LRKQVI--DKYVEAGVITKEQADHIKKNIDKRVEYMKQN 55 (59)
T ss_pred HHHHHHHHHHHHHHH-HHHHHH--HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 889999999999999-999999--9999827564999999999999999999986
No 20
>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]
Probab=25.41 E-value=53 Score=14.35 Aligned_cols=73 Identities=29% Similarity=0.419 Sum_probs=48.9
Q ss_pred HHHHHHHHHHHHH------------HHHHHHHHHHHHHHHCCHHHEEEECCCHHHHHHHHHHHHHHHH---------HH-
Q ss_conf 9999999998755------------8888878899999730031002531464776412488789999---------75-
Q gi|254781075|r 132 IIQSIRRAFDQYK------------EEERKALSDIQEQLLNDASKKIVFSSDREEYIGLHQKQIDLIH---------QN- 189 (266)
Q Consensus 132 iiqsirrafdqyk------------eeerkalsdiqeqllndaskkivfssdreeyiglhqkqidlih---------qn- 189 (266)
-|.+.++-..||| |.||+-++..+-.+++-+.+--.-+.--.|-|.+||+-+.+-. ++
T Consensus 243 tide~kelv~~ykgdyl~e~~y~Waedererle~ly~kllgkva~~yle~g~~neAi~l~qr~ltldpL~e~~nk~lm~~ 322 (361)
T COG3947 243 TIDELKELVGQYKGDYLPEADYPWAEDERERLEQLYMKLLGKVARAYLEAGKPNEAIQLHQRALTLDPLSEQDNKGLMAS 322 (361)
T ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf 77899999998537767744465100368999999999999999999975992789999987720270446789999999
Q ss_pred ---------HHHHHHHHHHHHHHH
Q ss_conf ---------889999986665202
Q gi|254781075|r 190 ---------IDRHLARMKNQLVAE 204 (266)
Q Consensus 190 ---------idrhlarmknqlvae 204 (266)
.-.|-+||+.+|-||
T Consensus 323 la~~gD~is~~khyerya~vleae 346 (361)
T COG3947 323 LATLGDEISAIKHYERYAEVLEAE 346 (361)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 998065043423899999999999
No 21
>KOG3226 consensus
Probab=24.79 E-value=28 Score=16.13 Aligned_cols=30 Identities=37% Similarity=0.471 Sum_probs=16.0
Q ss_pred HHHHHCCHHHEEEECCCHHHHHHHHHHHHH
Q ss_conf 999730031002531464776412488789
Q gi|254781075|r 155 QEQLLNDASKKIVFSSDREEYIGLHQKQID 184 (266)
Q Consensus 155 qeqllndaskkivfssdreeyiglhqkqid 184 (266)
.+|++--...-.--|.|.|.|..+||||||
T Consensus 479 ~~~~~~~~QD~Y~~STDE~~~~E~~k~~~D 508 (508)
T KOG3226 479 IDQLAILSQDIYEVSTDEEDYLELKKKQID 508 (508)
T ss_pred HHHCCCCCCCCCCCCCCCCHHHHHHCCCCC
T ss_conf 543057777863234664114676413899
No 22
>PRK11546 zraP zinc resistance protein; Provisional
Probab=23.10 E-value=59 Score=14.07 Aligned_cols=37 Identities=22% Similarity=0.346 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 4887899997588999998666520245699998540
Q gi|254781075|r 179 HQKQIDLIHQNIDRHLARMKNQLVAESDELEDILSRY 215 (266)
Q Consensus 179 hqkqidlihqnidrhlarmknqlvaesdeledilsry 215 (266)
.|+..+-||++.-...+-++.||.+...|++-+|+.-
T Consensus 44 QQa~~qkL~~eF~~eTa~LRqqL~aKr~ElNALL~at 80 (139)
T PRK11546 44 QQAAAQKIHNDFYAQTSALRQQLVSKRYEYNALLTAN 80 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 9999999999999999999999999899999998069
No 23
>pfam05411 Peptidase_C32 Equine arteritis virus putative proteinase. These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication.
Probab=22.93 E-value=26 Score=16.30 Aligned_cols=37 Identities=41% Similarity=0.401 Sum_probs=27.0
Q ss_pred HHHCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 652143210032010878887899999999843334566667
Q gi|254781075|r 9 IVATSKKWSFLFAILSPTEVYNVHRRIWHLLRDDFGYFTKRT 50 (266)
Q Consensus 9 ivatskkwsflfailsptevynvhrriwhllrddfgyftkrt 50 (266)
-|..+|-|--+| -.+|.||-+-.-+ +.|.|||-||-.
T Consensus 10 tvp~g~CW~~lF-~~~~~~v~~~E~~----~A~~fGYqtk~G 46 (128)
T pfam05411 10 TVPEGKCWLKLF-DHSGWEVPCCELT----LADTFGYQTKCG 46 (128)
T ss_pred CCCCCCEEHHEC-CCCCCCCCHHHHH----HHHHHCCCCCCC
T ss_conf 478876543000-5997112236776----777637535656
No 24
>TIGR02470 sucr_synth sucrose synthase; InterPro: IPR012820 This entry represents sucrose synthase an enzyme that despite its name, generally uses rather produces sucrose. Sucrose plus UDP (or ADP) becomes D-fructose plus UDP-glucose (or ADP-glucose), which is then available for cell wall (or starch) biosynthesis. The enzyme is homologous to sucrose phosphate synthase, which catalyses the penultimate step in sucrose synthesis. Sucrose synthase is found, so far, exclusively in plants and cyanobacteria.; GO: 0016157 sucrose synthase activity.
Probab=21.57 E-value=63 Score=13.88 Aligned_cols=11 Identities=45% Similarity=0.733 Sum_probs=3.9
Q ss_pred CCHHHEEEECC
Q ss_conf 00310025314
Q gi|254781075|r 160 NDASKKIVFSS 170 (266)
Q Consensus 160 ndaskkivfss 170 (266)
.|.+|.|.||-
T Consensus 552 ~d~~KPiiFsM 562 (790)
T TIGR02470 552 KDPNKPIIFSM 562 (790)
T ss_pred CCCCCCCEEEE
T ss_conf 07687826630
No 25
>TIGR00806 rfc reduced folate carrier; InterPro: IPR002666 The reduced folate carrier (a transmembrane glycoprotein) transports reduced folate into mammalian cells via the carrier mediated mechanism (as opposed to the receptor mediated mechanism) it also transports cytotoxic folate analogues used in chemotherapy , such as methotrexate (MTX). Mammalian cells have an absolute requirement for exogenous folates which are needed for growth, and biosynthesis of macromolecules .; GO: 0005542 folic acid binding, 0008518 reduced folate carrier activity, 0006810 transport, 0016020 membrane.
Probab=20.38 E-value=66 Score=13.72 Aligned_cols=48 Identities=33% Similarity=0.457 Sum_probs=23.3
Q ss_pred HHHHHHHHHHCCCEECCCEEEHHHHHHHHHHHHHHHHHHHHH-HEECCCCEEE
Q ss_conf 999999985314200222220112006549999999998656-4111774133
Q gi|254781075|r 70 NFLISYIYKNIGYKISSQYYSLTEYTWHDIETFLALLYMSCI-LVATDDRKLR 121 (266)
Q Consensus 70 nflisyiyknigykissqyyslteytwhdietflallymsci-lvatddrklr 121 (266)
.|+..----.|....++.-..|- -.|.||+|+.--++| +|..|.|||.
T Consensus 381 Q~~~~IA~~~~A~sL~~~L~aL~----FGiNTF~A~~l~~~~T~vV~D~~~LG 429 (542)
T TIGR00806 381 QLLVPIATFQIASSLSKELCALV----FGINTFLALALKTIITLVVSDKRGLG 429 (542)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHEEEECCCCCC
T ss_conf 98878998999886647789999----76999999999876440014410046
No 26
>pfam05203 Hom_end_hint Hom_end-associated Hint. Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a a second domain containing the protein-splicing active site. This Domain corresponds to the latter protein-splicing domain.
Probab=20.22 E-value=12 Score=18.39 Aligned_cols=76 Identities=20% Similarity=0.255 Sum_probs=29.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH-HEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 225999999999999987558888878899999730031-0025314647764124887899997588999998666520
Q gi|254781075|r 125 DGDRIIEIIQSIRRAFDQYKEEERKALSDIQEQLLNDAS-KKIVFSSDREEYIGLHQKQIDLIHQNIDRHLARMKNQLVA 203 (266)
Q Consensus 125 dgdriieiiqsirrafdqykeeerkalsdiqeqllndas-kkivfssdreeyiglhqkqidlihqnidrhlarmknqlva 203 (266)
...|.|++.......|..-.. +.+|.....+-....++ ..+.+.-.-.+|+.|. .+.-+....+.+....
T Consensus 103 ~~~r~i~~vk~~~k~f~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~iea~d~~~L~--------~~vr~~~~~~~~Pvl~ 173 (438)
T pfam05203 103 TDGRIIEIVKEHHKSFPHTEG-EERAKEFAKEFASVIATGEYIEWEIEARDLAKLS--------PQVRVASKQFRNPVLY 173 (438)
T ss_pred CCCCEEEECCCCCCCCCCCCC-HHHHHHHHHHHHHHCCCCCCCEEEEEHHHHHHCC--------HHHHHCEEEEECCCCC
T ss_conf 467244300000234554333-1567777777664025667855998859945278--------5443131147765334
Q ss_pred HHHHHH
Q ss_conf 245699
Q gi|254781075|r 204 ESDELE 209 (266)
Q Consensus 204 esdele 209 (266)
++++|-
T Consensus 174 ~~~~l~ 179 (438)
T pfam05203 174 ENGILS 179 (438)
T ss_pred CCCCCC
T ss_conf 553210
Done!