Query gi|254781221|ref|YP_003065634.1| hypothetical protein CLIBASIA_05640 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 68
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 06:28:07 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781221.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5567 Predicted small peripl 57.7 8 0.0002 19.9 2.3 27 3-30 5-31 (58)
2 TIGR00706 SppA_dom signal pept 52.4 16 0.0004 18.3 3.1 24 37-60 148-171 (224)
3 TIGR02689 ars_reduc_gluta arse 48.8 3.4 8.7E-05 21.9 -0.8 19 12-30 75-93 (126)
4 PRK11372 lysozyme inhibitor; P 38.6 25 0.00064 17.2 2.3 22 1-22 1-22 (109)
5 COG5248 TAF19 Transcription in 31.6 25 0.00065 17.2 1.4 49 19-68 69-117 (126)
6 pfam02530 Porin_2 Porin subfam 30.5 18 0.00046 18.0 0.5 35 1-35 1-42 (378)
7 pfam04771 CAV_VP3 Chicken anae 27.2 12 0.00031 18.9 -0.8 13 12-24 43-55 (121)
8 TIGR01158 SUI1_rel translation 26.5 36 0.00091 16.4 1.5 15 7-21 65-79 (111)
9 PRK10796 LPS-assembly lipoprot 26.3 52 0.0013 15.5 2.3 19 3-21 4-22 (196)
10 KOG1440 consensus 25.4 63 0.0016 15.1 4.0 32 28-59 400-431 (432)
11 pfam10264 Stork_head Winged he 24.8 58 0.0015 15.3 2.3 30 29-58 13-42 (80)
12 COG2063 FlgH Flagellar basal b 24.7 58 0.0015 15.3 2.3 27 4-30 4-32 (230)
13 pfam06932 DUF1283 Protein of u 24.6 64 0.0016 15.1 2.5 22 41-62 50-71 (109)
14 pfam05788 Orbi_VP1 Orbivirus R 23.4 69 0.0018 14.9 4.3 56 2-64 359-426 (1301)
15 PRK10263 DNA translocase FtsK; 23.3 42 0.0011 16.1 1.3 26 3-32 112-137 (1355)
16 cd00225 API3 Ascaris pepsin in 21.6 63 0.0016 15.1 2.0 23 37-59 29-53 (159)
17 TIGR02211 LolD_lipo_ex lipopro 20.8 78 0.002 14.6 2.6 40 4-43 148-187 (221)
No 1
>COG5567 Predicted small periplasmic lipoprotein [Cell motility and secretion]
Probab=57.71 E-value=8 Score=19.89 Aligned_cols=27 Identities=44% Similarity=0.797 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHH
Q ss_conf 7899999999998336323681118889
Q gi|254781221|r 3 IKKVLIASTLLSLCGCGLADEPKKLNPD 30 (68)
Q Consensus 3 ikkvliastllslcgcgladepkklnpd 30 (68)
++-.+...+|+||.|||+-. |--+-|+
T Consensus 5 ~~s~~ala~l~sLA~CG~KG-PLy~Ppa 31 (58)
T COG5567 5 FKSLLALATLFSLAGCGLKG-PLYFPPA 31 (58)
T ss_pred HHHHHHHHHHHHHHHCCCCC-CCCCCHH
T ss_conf 99999999999998526678-7627824
No 2
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type; InterPro: IPR004635 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. This group of sequences represent both long and short forms of the bacterial SppA and homologs found in the archaea and plants. Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signaling function. During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . ; GO: 0008233 peptidase activity, 0006508 proteolysis.
Probab=52.42 E-value=16 Score=18.33 Aligned_cols=24 Identities=46% Similarity=0.573 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 865288899999999889999964
Q gi|254781221|r 37 CRLTLEEQKELQTKVNQRYEEHLT 60 (68)
Q Consensus 37 crltleeqkelqtkvnqryeehlt 60 (68)
-.||-||+.-||+-||..|+..+.
T Consensus 148 R~lt~eE~~~lQ~~v~~~Y~~F~~ 171 (224)
T TIGR00706 148 RELTPEERKILQSLVNESYEQFVQ 171 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 776299999999988888757899
No 3
>TIGR02689 ars_reduc_gluta arsenate reductase, glutathione/glutaredoxin type; InterPro: IPR014062 Members of this protein family represent a novel form of arsenate reductase, for example Synechocystis sp. (strain PCC 6803) slr0946, which use glutathione and glutaredoxin. Homologs that use thioredoxin for reducing equivalents are excluded from this entry. Both families are among the subset of arsenate reductases that belong the low-molecular-weight protein-tyrosine phosphatase superfamily..
Probab=48.77 E-value=3.4 Score=21.88 Aligned_cols=19 Identities=32% Similarity=0.767 Sum_probs=12.1
Q ss_pred HHHHHCCCCCCCCCCCCHH
Q ss_conf 9998336323681118889
Q gi|254781221|r 12 LLSLCGCGLADEPKKLNPD 30 (68)
Q Consensus 12 llslcgcgladepkklnpd 30 (68)
.+||||||+.-.+.-+..+
T Consensus 75 vislCGCG~nlP~~W~~~~ 93 (126)
T TIGR02689 75 VISLCGCGVNLPEAWVTRE 93 (126)
T ss_pred EEEECCCCCCCCHHHHHHH
T ss_conf 7763057765637788888
No 4
>PRK11372 lysozyme inhibitor; Provisional
Probab=38.58 E-value=25 Score=17.22 Aligned_cols=22 Identities=36% Similarity=0.617 Sum_probs=19.2
Q ss_pred CHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 9178999999999983363236
Q gi|254781221|r 1 MTIKKVLIASTLLSLCGCGLAD 22 (68)
Q Consensus 1 mtikkvliastllslcgcglad 22 (68)
|..||.+++...+-|.||.+-.
T Consensus 1 ~~MKkll~~~~~llLsGCs~~~ 22 (109)
T PRK11372 1 MSMKKLLIICLPVLLTGCSAYN 22 (109)
T ss_pred CCHHHHHHHHHHHHHHCCCCCC
T ss_conf 9548899999999970454322
No 5
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=31.55 E-value=25 Score=17.20 Aligned_cols=49 Identities=24% Similarity=0.234 Sum_probs=24.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 32368111888999999986528889999999988999996402101369
Q gi|254781221|r 19 GLADEPKKLNPDQLCDAVCRLTLEEQKELQTKVNQRYEEHLTKGAKLSSD 68 (68)
Q Consensus 19 gladepkklnpdqlcdavcrltleeqkelqtkvnqryeehltkgaklssd 68 (68)
.|-+.||||.--.---+.-..--+..|..|.+-| ||++.+.-|.|..|+
T Consensus 69 aLr~DpkKlgRveeLl~tn~~i~~Akk~F~~~ds-Ryr~e~~~~~kM~s~ 117 (126)
T COG5248 69 ALRRDPKKLGRVEELLITNEEIKLAKKAFEPKDS-RYRKELRINTKMHSF 117 (126)
T ss_pred HHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCHHH-HHHHHHHHCCHHHHH
T ss_conf 9962968771799999710788887224672247-999999834247666
No 6
>pfam02530 Porin_2 Porin subfamily. This family consists of porins from the alpha subdivision of Proteobacteria the members of this family are related to pfam00267. The porins form large aqueous channels in the cell membrane allowing the selective entry of hydrophilic compounds this so called 'molecular sieve' is found in the cell walls of gram negative bacteria.
Probab=30.53 E-value=18 Score=18.00 Aligned_cols=35 Identities=37% Similarity=0.641 Sum_probs=27.6
Q ss_pred CHHHHHHHHHH--HHHHHCCCCCCCCCCCCHHH-----HHHH
Q ss_conf 91789999999--99983363236811188899-----9999
Q gi|254781221|r 1 MTIKKVLIAST--LLSLCGCGLADEPKKLNPDQ-----LCDA 35 (68)
Q Consensus 1 mtikkvliast--llslcgcgladepkklnpdq-----lcda 35 (68)
|.||..|+.|. |...-|.--||-|-+-.|.. .|||
T Consensus 1 MNiKsLlLgSaaalvA~sgA~AAD~iV~aePEpvEYVrVCda 42 (378)
T pfam02530 1 MNIKSLLLGSAAALAAVSGAQAADAIVAAEPEPVEYVRVCDA 42 (378)
T ss_pred CCHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCEEEECCC
T ss_conf 956788888899999840020136533478776325898666
No 7
>pfam04771 CAV_VP3 Chicken anaemia virus VP-3 protein. This protein is found in the nucleus of infected cells and may act as a transcriptional regulator. It induces apoptosis, and is also known as apoptin.
Probab=27.18 E-value=12 Score=18.94 Aligned_cols=13 Identities=62% Similarity=1.170 Sum_probs=9.7
Q ss_pred HHHHHCCCCCCCC
Q ss_conf 9998336323681
Q gi|254781221|r 12 LLSLCGCGLADEP 24 (68)
Q Consensus 12 llslcgcgladep 24 (68)
-||||||.-|..|
T Consensus 43 tlslcgcanarap 55 (121)
T pfam04771 43 TLSLCGCANARAP 55 (121)
T ss_pred EEEEECCCCCCCC
T ss_conf 8875032455785
No 8
>TIGR01158 SUI1_rel translation initation factor SUI1, putative; InterPro: IPR005872 This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met.; GO: 0003743 translation initiation factor activity, 0006412 translation.
Probab=26.53 E-value=36 Score=16.41 Aligned_cols=15 Identities=40% Similarity=0.682 Sum_probs=12.9
Q ss_pred HHHHHHHHHHCCCCC
Q ss_conf 999999998336323
Q gi|254781221|r 7 LIASTLLSLCGCGLA 21 (68)
Q Consensus 7 liastllslcgcgla 21 (68)
-+|+.|=+.||||=+
T Consensus 65 ~LAk~LK~~cacGGT 79 (111)
T TIGR01158 65 ELAKELKSKCACGGT 79 (111)
T ss_pred HHHHHHHHHHCCCCC
T ss_conf 999987788468974
No 9
>PRK10796 LPS-assembly lipoprotein RlpB; Provisional
Probab=26.27 E-value=52 Score=15.52 Aligned_cols=19 Identities=26% Similarity=0.665 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHCCCCC
Q ss_conf 7899999999998336323
Q gi|254781221|r 3 IKKVLIASTLLSLCGCGLA 21 (68)
Q Consensus 3 ikkvliastllslcgcgla 21 (68)
++..+++-..|-+||||..
T Consensus 4 l~~l~l~lavll~agCGFh 22 (196)
T PRK10796 4 LATLLLSLAVLVTAGCGWH 22 (196)
T ss_pred HHHHHHHHHHHHHCCCCCE
T ss_conf 9999999999997476715
No 10
>KOG1440 consensus
Probab=25.36 E-value=63 Score=15.10 Aligned_cols=32 Identities=28% Similarity=0.312 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 88999999986528889999999988999996
Q gi|254781221|r 28 NPDQLCDAVCRLTLEEQKELQTKVNQRYEEHL 59 (68)
Q Consensus 28 npdqlcdavcrltleeqkelqtkvnqryeehl 59 (68)
++..+-|..|+|+.|||.+|-.+.+++.+++.
T Consensus 400 ~~s~ll~qi~~l~~~qq~~l~~~L~~~l~~~~ 431 (432)
T KOG1440 400 GVSKLLDQILTLTPEQQLNLFEKLQRRLSSKG 431 (432)
T ss_pred CHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC
T ss_conf 77899999981798999999999999998605
No 11
>pfam10264 Stork_head Winged helix Storkhead-box1 domain. This is the conserved N-terminal winged helix domain of Storkhead-box1 protein which is likely to be a DNA binding domain. In humans the full-length protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia.
Probab=24.80 E-value=58 Score=15.29 Aligned_cols=30 Identities=30% Similarity=0.506 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 899999998652888999999998899999
Q gi|254781221|r 29 PDQLCDAVCRLTLEEQKELQTKVNQRYEEH 58 (68)
Q Consensus 29 pdqlcdavcrltleeqkelqtkvnqryeeh 58 (68)
||-||+|+-.|+-..+---|...-+..-.|
T Consensus 13 ~EvlC~aI~dln~~~~~at~e~l~~~L~~~ 42 (80)
T pfam10264 13 GEVLCDAISDLNAQGQSATQEAIRQHLTTH 42 (80)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 999999999985668810599999999985
No 12
>COG2063 FlgH Flagellar basal body L-ring protein [Cell motility and secretion]
Probab=24.67 E-value=58 Score=15.28 Aligned_cols=27 Identities=30% Similarity=0.482 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHC--CCCCCCCCCCCHH
Q ss_conf 89999999999833--6323681118889
Q gi|254781221|r 4 KKVLIASTLLSLCG--CGLADEPKKLNPD 30 (68)
Q Consensus 4 kkvliastllslcg--cgladepkklnpd 30 (68)
++.+.+-.+|++|| |+-...++.++|.
T Consensus 4 ~~~~~~l~~la~c~~e~~~~p~~~p~~~~ 32 (230)
T COG2063 4 LYALLALGLLAGCGTECAKVPPLSPIVPG 32 (230)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf 37999999998732653168875546788
No 13
>pfam06932 DUF1283 Protein of unknown function (DUF1283). This family consists of several hypothetical proteins of around 115 residues in length which seem to be specific to Enterobacteria. The function of the family is unknown.
Probab=24.62 E-value=64 Score=15.05 Aligned_cols=22 Identities=32% Similarity=0.563 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 8889999999988999996402
Q gi|254781221|r 41 LEEQKELQTKVNQRYEEHLTKG 62 (68)
Q Consensus 41 leeqkelqtkvnqryeehltkg 62 (68)
-.+.+.|..|||.|-|....|-
T Consensus 50 W~~tr~LR~KVN~R~EKefDK~ 71 (109)
T pfam06932 50 WNDTRSLRNKVNKRAEKEFDKA 71 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8788999999868887620378
No 14
>pfam05788 Orbi_VP1 Orbivirus RNA-dependent RNA polymerase (VP1). This family consists of the RNA-dependent RNA polymerase protein VP1 from the Orbiviruses. VP1 may have both enzymatic and structural roles in the virus life cycle.
Probab=23.42 E-value=69 Score=14.89 Aligned_cols=56 Identities=38% Similarity=0.564 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHH---HCCCCC------CCC---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 17899999999998---336323------681---1188899999998652888999999998899999640210
Q gi|254781221|r 2 TIKKVLIASTLLSL---CGCGLA------DEP---KKLNPDQLCDAVCRLTLEEQKELQTKVNQRYEEHLTKGAK 64 (68)
Q Consensus 2 tikkvliastllsl---cgcgla------dep---kklnpdqlcdavcrltleeqkelqtkvnqryeehltkgak 64 (68)
.++.|..||-|||+ -|.|-| +++ -|-+|+.+-+-||..|-+ -+-|.|+|...+|-.
T Consensus 359 ~~~hv~lAS~lLSiQtiTGYGRAWVkN~~~d~EkqmkP~~~Nli~rV~d~T~~-------~f~qAY~EA~~~gee 426 (1301)
T pfam05788 359 KISHVILASYLLSIQTITGYGRAWVKNVGDDPEKQMKPDPSNLITRVSDMTRN-------NFIQAYNEAREHGEE 426 (1301)
T ss_pred CHHHHHHHHHHHHHEEECCCCCEEEECCCCCHHHHCCCCCCCHHHHHHHHHHH-------HHHHHHHHHHHCCCC
T ss_conf 21488999998771120255502210278898995499975478999999999-------999999999966787
No 15
>PRK10263 DNA translocase FtsK; Provisional
Probab=23.31 E-value=42 Score=16.06 Aligned_cols=26 Identities=35% Similarity=0.622 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf 789999999999833632368111888999
Q gi|254781221|r 3 IKKVLIASTLLSLCGCGLADEPKKLNPDQL 32 (68)
Q Consensus 3 ikkvliastllslcgcgladepkklnpdql 32 (68)
+---||....|-|..||||+ ||.|.+
T Consensus 112 ~slRLiG~LaLiLTSCGLAa----lN~DDi 137 (1355)
T PRK10263 112 VSLRIIGVLALILTSCGLAA----INADDI 137 (1355)
T ss_pred HHHHHHHHHHHHHHHHHHHH----CCCCCC
T ss_conf 99999999999997004654----174111
No 16
>cd00225 API3 Ascaris pepsin inhibitor-3 (API3); protein inhibitor that reversibly inhibits aspartic proteinase cathepsin E, and gastric enzymes pepsin and gastricsin.
Probab=21.64 E-value=63 Score=15.07 Aligned_cols=23 Identities=39% Similarity=0.525 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHH--HHHHH
Q ss_conf 865288899999999889--99996
Q gi|254781221|r 37 CRLTLEEQKELQTKVNQR--YEEHL 59 (68)
Q Consensus 37 crltleeqkelqtkvnqr--yeehl 59 (68)
-.||-+||+||.+.+++- |.+.+
T Consensus 29 ReLt~~Eq~Ela~y~~e~~~yK~~~ 53 (159)
T cd00225 29 RELTPDEQQELAQYVEDVADYKEEV 53 (159)
T ss_pred HHCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 2188889999999999999999999
No 17
>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=20.76 E-value=78 Score=14.58 Aligned_cols=40 Identities=30% Similarity=0.321 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 8999999999983363236811188899999998652888
Q gi|254781221|r 4 KKVLIASTLLSLCGCGLADEPKKLNPDQLCDAVCRLTLEE 43 (68)
Q Consensus 4 kkvliastllslcgcgladepkklnpdqlcdavcrltlee 43 (68)
..|-||-.|..---|=|||||.-==-..-...|-.|-.|=
T Consensus 148 QRvAIARALvN~P~lvlADEPTGNLD~~~a~~iF~L~~eL 187 (221)
T TIGR02211 148 QRVAIARALVNQPSLVLADEPTGNLDNNNAKSIFELMLEL 187 (221)
T ss_pred HHHHHHHHHHCCCCEEECCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 9999999861897658612988532377799999999998
Done!