Query gi|254781028|ref|YP_003065441.1| putative Mg2+ chelatase family protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 87
No_of_seqs 100 out of 998
Neff 4.1
Searched_HMMs 39220
Date Mon May 30 03:13:26 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781028.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00368 TIGR00368 Mg chelata 100.0 1.5E-30 3.7E-35 200.9 4.2 70 5-79 1-70 (505)
2 PRK09862 putative ATP-dependen 100.0 3.7E-29 9.6E-34 192.6 8.3 73 2-79 3-75 (506)
3 COG0606 Predicted ATPase with 99.9 5E-23 1.3E-27 156.7 4.6 61 14-79 1-61 (490)
4 pfam05362 Lon_C Lon protease ( 69.7 11 0.00029 19.7 6.7 53 1-53 26-78 (205)
5 TIGR02405 trehalos_R_Ecol treh 49.9 10 0.00027 20.0 1.8 21 41-67 29-49 (311)
6 pfam07837 FTCD_N Formiminotran 48.7 27 0.00069 17.5 4.4 52 15-66 31-82 (178)
7 TIGR00395 leuS_arch leucyl-tRN 42.1 25 0.00063 17.8 2.7 41 25-65 490-530 (1109)
8 pfam11130 TraC_F_IV F pilus as 39.8 37 0.00094 16.7 5.1 40 37-87 140-179 (236)
9 PRK10178 D-alanyl-D-alanine di 39.7 34 0.00087 16.9 3.2 27 38-64 137-163 (188)
10 TIGR01239 galT_2 galactose-1-p 37.7 16 0.0004 18.9 1.2 25 46-75 123-151 (502)
11 COG3643 Glutamate formiminotra 35.8 43 0.0011 16.3 5.3 52 15-66 33-84 (302)
12 pfam01427 Peptidase_M15 D-ala- 32.4 49 0.0012 16.0 3.2 28 37-64 151-178 (198)
13 TIGR00960 3a0501s02 Type II (G 31.2 30 0.00075 17.3 1.7 33 32-67 106-138 (216)
14 TIGR02040 PpsR-CrtJ transcript 29.0 54 0.0014 15.8 2.7 35 37-76 42-95 (453)
15 cd02201 FtsZ_type1 FtsZ is a G 28.0 36 0.00091 16.8 1.7 28 36-63 66-93 (304)
16 TIGR00097 HMP-P_kinase phospho 27.8 48 0.0012 16.1 2.3 18 38-55 231-248 (264)
17 PRK09330 cell division protein 25.9 42 0.0011 16.4 1.7 26 36-61 78-103 (387)
18 PRK09568 DNA primase large sub 25.3 50 0.0013 16.0 2.0 29 25-53 22-50 (306)
19 PRK13018 cell division protein 22.3 55 0.0014 15.7 1.8 26 36-61 93-118 (387)
20 pfam00356 LacI Bacterial regul 20.8 76 0.0019 14.9 2.2 18 40-57 26-43 (46)
21 pfam02064 MAS20 MAS20 protein 20.3 52 0.0013 15.9 1.3 16 69-84 121-136 (184)
No 1
>TIGR00368 TIGR00368 Mg chelatase homolog; InterPro: IPR004482 This family of bacterial proteins are variously described as 'hypothetical protein yifB', 'competence protein', 'hypothetical protein' or 'Mg chelatase-related protein'. These proteins are a subset of the magnesium chelatase, ChlI subunit family and either belong to or show significant homology to the non-peptidase homologs of the MEROPS peptidase family S16 (lon protease family, clan SF), IPR001984 from INTERPRO. .
Probab=99.96 E-value=1.5e-30 Score=200.85 Aligned_cols=70 Identities=33% Similarity=0.529 Sum_probs=68.5
Q ss_pred EEEEEEEEEEEEEEEEEEECCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECHHHHH
Q ss_conf 999999733017899999846897437996162588899989999999977984421128940479963758899
Q gi|254781028|r 5 ISTIAFQGIKGIPVEVQVMVSPGRVGVQIVGLPDKAVIESRERIQSHFIHAGLLFLVNELPSIYLQLIYQKKDLI 79 (87)
Q Consensus 5 i~S~al~Gi~a~~V~VEv~is~GlP~f~iVGLpD~aVkESreRVrsAl~nsGl~F~~~~~p~~~~tinl~p~dl~ 79 (87)
|||.+..|++|.+|+||||++.|+|+++||||||++||||||||||||+|+|| +||.+||||||+||||-
T Consensus 1 vyS~s~lG~~a~~v~vEvdis~G~pg~~~VGLp~~~vkEsreRVksAl~Ns~F-----~fP~~rI~iNLAPAdl~ 70 (505)
T TIGR00368 1 VYSRSSLGVEAPLVTVEVDISKGLPGITIVGLPETTVKESRERVKSALKNSGF-----KFPAKRITINLAPADLP 70 (505)
T ss_pred CCCCHHHCCCCCEEEEEEEECCCCCCCEEECCCCCCHHHHHHHHHHHHHHCCC-----CCCCCEEEEECCCCCCC
T ss_conf 90201106364034798873077872134338863105667899999861576-----68854016653888876
No 2
>PRK09862 putative ATP-dependent protease; Provisional
Probab=99.96 E-value=3.7e-29 Score=192.60 Aligned_cols=73 Identities=34% Similarity=0.582 Sum_probs=71.2
Q ss_pred EEEEEEEEEEEEEEEEEEEEEECCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECHHHHH
Q ss_conf 369999999733017899999846897437996162588899989999999977984421128940479963758899
Q gi|254781028|r 2 ISRISTIAFQGIKGIPVEVQVMVSPGRVGVQIVGLPDKAVIESRERIQSHFIHAGLLFLVNELPSIYLQLIYQKKDLI 79 (87)
Q Consensus 2 lski~S~al~Gi~a~~V~VEv~is~GlP~f~iVGLpD~aVkESreRVrsAl~nsGl~F~~~~~p~~~~tinl~p~dl~ 79 (87)
+++++|+++.|++|++|+||||+++|+|+|+||||||++|||||||||+|++|+|| +||.+||||||+|||+-
T Consensus 3 ~a~v~s~al~Gi~~~~V~VEv~i~~GlP~f~iVGLpd~av~EsreRVrsAl~nsg~-----~~P~~rItVNLaPAdl~ 75 (506)
T PRK09862 3 LSIVHTRAALGVNAPPITVEVHISKGLPGLTMVGLPETTVKEARDRVRSAIINSGY-----EYPAKKITINLAPADLP 75 (506)
T ss_pred CEEEEEEEEECCEEEEEEEEEEECCCCCCEEEECCCHHHHHHHHHHHHHHHHHCCC-----CCCCCCEEEECCCCCCC
T ss_conf 35676642307501699999982599862278378469999999999999983899-----99988089970787888
No 3
>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=5e-23 Score=156.70 Aligned_cols=61 Identities=43% Similarity=0.662 Sum_probs=59.1
Q ss_pred EEEEEEEEEECCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECHHHHH
Q ss_conf 017899999846897437996162588899989999999977984421128940479963758899
Q gi|254781028|r 14 KGIPVEVQVMVSPGRVGVQIVGLPDKAVIESRERIQSHFIHAGLLFLVNELPSIYLQLIYQKKDLI 79 (87)
Q Consensus 14 ~a~~V~VEv~is~GlP~f~iVGLpD~aVkESreRVrsAl~nsGl~F~~~~~p~~~~tinl~p~dl~ 79 (87)
+|.+|+||+|+++|+|+|+||||||++|+|||||||+|++|+|| +||.+|||+||+||||-
T Consensus 1 ~a~~V~VEv~~s~glp~~~iVGL~d~av~EsreRVraal~nsgf-----~~P~~ritiNLaPadl~ 61 (490)
T COG0606 1 EAPPVEVEVDISNGLPGFTIVGLPDTAVKESRERVRAALTNSGF-----EFPAKRITINLAPADLP 61 (490)
T ss_pred CCCCCCEEEEECCCCCCCEEEECCCHHHHHHHHHHHHHHHHCCC-----CCCHHHEEECCCCCCCC
T ss_conf 99742238873389765036406817789999999989874678-----88767803115710025
No 4
>pfam05362 Lon_C Lon protease (S16) C-terminal proteolytic domain. The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops.
Probab=69.68 E-value=11 Score=19.74 Aligned_cols=53 Identities=15% Similarity=0.277 Sum_probs=41.7
Q ss_pred CEEEEEEEEEEEEEEEEEEEEEECCCCCCEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf 93699999997330178999998468974379961625888999899999999
Q gi|254781028|r 1 MISRISTIAFQGIKGIPVEVQVMVSPGRVGVQIVGLPDKAVIESRERIQSHFI 53 (87)
Q Consensus 1 Mlski~S~al~Gi~a~~V~VEv~is~GlP~f~iVGLpD~aVkESreRVrsAl~ 53 (87)
++..++..+..+..+.+..+|+...+|-..+.+.|......|||-.=-.+-++
T Consensus 26 ~iG~vnGLa~t~~GG~il~IE~~~~~g~g~l~lTG~lg~vmkES~~~A~s~~k 78 (205)
T pfam05362 26 QVGVVTGLAWTEVGGDLLTIEATIMPGKGKLTLTGQLGDVMKESAQAALSYVR 78 (205)
T ss_pred CCEEEEEEEEECCCCEEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 87199998992799788999999955888400347557899999999999999
No 5
>TIGR02405 trehalos_R_Ecol trehalose operon repressor; InterPro: IPR012771 Trehalose is a non-reducing disaccharide which can be used as both a carbon source and an osmoprotectant in bacteria. Trehalose uptake into the cytoplasm occurs via a trehalose-specific phosphotransferase system which phosphorylates trehalase to trehalose-6-phosphate (Tre6P) during transport into the cytoplasm, and a hydrolase which hydrolyses Tre6P to glucose and glucose-6-phophate. This entry represents LacI-type TreR, a transcriptional repressor of trehalose uptake found mainly within the gamma-proteobacteria. It does not include the GntR-type TreR's such as those found in Bacillus species. It is capable of binding both the inducer Tre6P and trehalose. Binding of trehalose does not affect the repressor's affinity for its DNA binding site, while binding Tre6P substantially reduces its affinity. The repression activity of TreR is therefore regulated by the ratio of trehalose to Tre6P within the cell . The protein is composed of two domains, an N-terminal DNA-binding helix-turn-helix domain, and a C-terminal effector-binding domain which is homologous to that of LacI. The effector-binding domain is composed of two subdomains, both of which form an alpha-beta-alpha sandwhich, with the effector binding site located at the interface of these subdomains . Tre6P and trehalose bind competitively to this site, with the affinty for trehalose substantially lower than that for Tre6P.; GO: 0003677 DNA binding, 0016566 specific transcriptional repressor activity, 0005991 trehalose metabolic process, 0016481 negative regulation of transcription.
Probab=49.91 E-value=10 Score=19.96 Aligned_cols=21 Identities=38% Similarity=0.706 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCE
Q ss_conf 899989999999977984421128940
Q gi|254781028|r 41 VIESRERIQSHFIHAGLLFLVNELPSI 67 (87)
Q Consensus 41 VkESreRVrsAl~nsGl~F~~~~~p~~ 67 (87)
-.|.||||.+-+...|| .||+
T Consensus 29 ~~~tRERVE~viq~~gF------~PSk 49 (311)
T TIGR02405 29 SIETRERVEAVIQQSGF------VPSK 49 (311)
T ss_pred CCHHHHHHHHHHHHCCC------CCCH
T ss_conf 72033688888751588------8642
No 6
>pfam07837 FTCD_N Formiminotransferase domain, N-terminal subdomain. The formiminotransferase (FT) domain of formiminotransferase- cyclodeaminase (FTCD) forms a homodimer, and each protomer comprises two subdomains. The N-terminal subdomain is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains.
Probab=48.69 E-value=27 Score=17.54 Aligned_cols=52 Identities=15% Similarity=0.063 Sum_probs=44.8
Q ss_pred EEEEEEEEECCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 1789999984689743799616258889998999999997798442112894
Q gi|254781028|r 15 GIPVEVQVMVSPGRVGVQIVGLPDKAVIESRERIQSHFIHAGLLFLVNELPS 66 (87)
Q Consensus 15 a~~V~VEv~is~GlP~f~iVGLpD~aVkESreRVrsAl~nsGl~F~~~~~p~ 66 (87)
...++|+.|..-.-..|+++|-|+.-.+-+..=++.|+....+..|.-+-|-
T Consensus 31 v~lLdv~~d~d~NRtV~T~vG~p~~v~~aa~~~~~~A~e~IDm~~H~G~HPR 82 (178)
T pfam07837 31 VKLLDYSSDADHNRSVVTFVGEPEPVKEAALEMVKKAAELIDMRKHKGEHPR 82 (178)
T ss_pred CEEEECCCCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCHHHCCCCCCC
T ss_conf 3797446898767425885378299999999999999986036643587887
No 7
>TIGR00395 leuS_arch leucyl-tRNA synthetase; InterPro: IPR004493 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Leucyl tRNA synthetase (6.1.1.4 from EC) is an alpha monomer that belongs to class Ia. There are two different families of leucyl-tRNA synthetases. This family includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases.; GO: 0000166 nucleotide binding, 0004823 leucine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006429 leucyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=42.05 E-value=25 Score=17.76 Aligned_cols=41 Identities=22% Similarity=0.354 Sum_probs=32.5
Q ss_pred CCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 68974379961625888999899999999779844211289
Q gi|254781028|r 25 SPGRVGVQIVGLPDKAVIESRERIQSHFIHAGLLFLVNELP 65 (87)
Q Consensus 25 s~GlP~f~iVGLpD~aVkESreRVrsAl~nsGl~F~~~~~p 65 (87)
.+|...-++.-....-|+|+||||..-|...|+.+--+||-
T Consensus 490 ~~Gvm~~~~~~Y~G~kV~eak~~v~~dL~~~GlA~v~yEFs 530 (1109)
T TIGR00395 490 HTGVMIENILDYKGMKVSEAKEKVKEDLIDKGLADVMYEFS 530 (1109)
T ss_pred CCEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEECCCC
T ss_conf 50032047757886117999999999998537860201657
No 8
>pfam11130 TraC_F_IV F pilus assembly Type-IV secretion system for plasmid transfer. This family of TraC proteins is conserved in Proteobacteria. TraC is a cytoplasmic, peripheral membrane protein and is one of the proteins encoded by the F transfer region of the conjugative plasmid that is required for the assembly of F pilin into the mature F pilus structure. F pili are filamentous appendages that help establish the physical contact between donor and recipient cells involved in the conjugation process.
Probab=39.85 E-value=37 Score=16.72 Aligned_cols=40 Identities=28% Similarity=0.382 Sum_probs=31.1
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECHHHHHHHHHHHHC
Q ss_conf 258889998999999997798442112894047996375889998888619
Q gi|254781028|r 37 PDKAVIESRERIQSHFIHAGLLFLVNELPSIYLQLIYQKKDLIMIYLSFLH 87 (87)
Q Consensus 37 pD~aVkESreRVrsAl~nsGl~F~~~~~p~~~~tinl~p~dl~~~~~~~~~ 87 (87)
+.....+-+++++++|+++|+ -+-.+.|.||+-....+++
T Consensus 140 ~~~~l~~~~~~l~~~L~~agl-----------~~~~~~~~~l~~~l~~~~N 179 (236)
T pfam11130 140 PIEELNELRERLEASLASAGL-----------AARRLDPEDLIDWLRRWFN 179 (236)
T ss_pred HHHHHHHHHHHHHHHHHHCCC-----------CCEECCHHHHHHHHHHHCC
T ss_conf 899999999999999986898-----------4376699999999999809
No 9
>PRK10178 D-alanyl-D-alanine dipeptidase; Provisional
Probab=39.71 E-value=34 Score=16.93 Aligned_cols=27 Identities=22% Similarity=0.261 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 588899989999999977984421128
Q gi|254781028|r 38 DKAVIESRERIQSHFIHAGLLFLVNEL 64 (87)
Q Consensus 38 D~aVkESreRVrsAl~nsGl~F~~~~~ 64 (87)
+...++-|...+.++...||..+..||
T Consensus 137 ~~~~~~nR~lL~~~M~~~GF~~~~~EW 163 (188)
T PRK10178 137 PPAVQRNRLLLLGIMHAAGFVHIASEW 163 (188)
T ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 999999999999999983997798826
No 10
>TIGR01239 galT_2 galactose-1-phosphate uridylyltransferase; InterPro: IPR000766 Galactose-1-phosphate uridyl transferase 2.7.7.12 from EC (galT) catalyzes the transfer of an uridyldiphosphate group on galactose (or glucose) 1-phosphate. During the reaction, the uridyl moiety links to a histidine residue. In the Escherichia coli enzyme, it has been shown that two histidine residues separated by a single proline residue are essential for enzyme activity. On the basis of sequence similarities, two apparently unrelated families seem to exist. Class-I enzymes are found in eukaryotes as well as some bacteria such as E. coli or Streptomyces lividans, while class-II enzymes have been found so far only in bacteria such as Bacillus subtilis or Lactobacillus helveticus .; GO: 0008108 UDP-glucose:hexose-1-phosphate uridylyltransferase activity, 0006012 galactose metabolic process, 0005737 cytoplasm.
Probab=37.72 E-value=16 Score=18.94 Aligned_cols=25 Identities=12% Similarity=0.267 Sum_probs=19.0
Q ss_pred HHHHHHHHHCCCCCCCCCCCCEE----EEEEECH
Q ss_conf 99999999779844211289404----7996375
Q gi|254781028|r 46 ERIQSHFIHAGLLFLVNELPSIY----LQLIYQK 75 (87)
Q Consensus 46 eRVrsAl~nsGl~F~~~~~p~~~----~tinl~p 75 (87)
-|.++-=+|..| .-|++| ||||||+
T Consensus 123 vk~~~IAkNi~y-----~~~T~YG~LEiTINLSK 151 (502)
T TIGR01239 123 VKTDAIAKNIAY-----KVPTEYGDLEITINLSK 151 (502)
T ss_pred CCHHHHHCCCCC-----CCCCCCCCEEEEEECCC
T ss_conf 001144323221-----36752165456630788
No 11
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=35.82 E-value=43 Score=16.35 Aligned_cols=52 Identities=19% Similarity=0.137 Sum_probs=46.4
Q ss_pred EEEEEEEEECCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 1789999984689743799616258889998999999997798442112894
Q gi|254781028|r 15 GIPVEVQVMVSPGRVGVQIVGLPDKAVIESRERIQSHFIHAGLLFLVNELPS 66 (87)
Q Consensus 15 a~~V~VEv~is~GlP~f~iVGLpD~aVkESreRVrsAl~nsGl~F~~~~~p~ 66 (87)
-..++||-|....-..|++||=|.+.+.-+.+-++.|-.+..+.-|--|-|-
T Consensus 33 v~ildve~danhNRsViT~vgdp~~~~~A~f~~ik~AaelIDM~~H~GeHpR 84 (302)
T COG3643 33 VKILDVEMDANHNRSVITLVGDPSKVVNAAFALIKKAAELIDMRNHKGEHPR 84 (302)
T ss_pred EEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHHHCHHCCCCCCCC
T ss_conf 3899714678877238999569389999999999988886040202788877
No 12
>pfam01427 Peptidase_M15 D-ala-D-ala dipeptidase.
Probab=32.40 E-value=49 Score=16.01 Aligned_cols=28 Identities=14% Similarity=0.172 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 2588899989999999977984421128
Q gi|254781028|r 37 PDKAVIESRERIQSHFIHAGLLFLVNEL 64 (87)
Q Consensus 37 pD~aVkESreRVrsAl~nsGl~F~~~~~ 64 (87)
.+...+.-|...|.++...||..+..||
T Consensus 151 is~~~~~NR~lL~~~M~~~GF~~y~~EW 178 (198)
T pfam01427 151 VSPNAQRNRRLLRAIMESGGFLRYSGEW 178 (198)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 9999999999999999983897798827
No 13
>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein; InterPro: IPR013505 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=31.19 E-value=30 Score=17.30 Aligned_cols=33 Identities=27% Similarity=0.472 Sum_probs=26.0
Q ss_pred EEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCE
Q ss_conf 996162588899989999999977984421128940
Q gi|254781028|r 32 QIVGLPDKAVIESRERIQSHFIHAGLLFLVNELPSI 67 (87)
Q Consensus 32 ~iVGLpD~aVkESreRVrsAl~nsGl~F~~~~~p~~ 67 (87)
.|+|.+- ++..+||++||...|+.=-.+.+|..
T Consensus 106 ~iiG~~~---~~~~~rv~~aL~~VGL~~K~~~lP~~ 138 (216)
T TIGR00960 106 RIIGVPG---RDINERVSAALEKVGLKGKAHALPVQ 138 (216)
T ss_pred HHCCCCC---CCHHHHHHHHHHHCCCCCHHHCCCCC
T ss_conf 5228997---42678999998730611212407620
No 14
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR; InterPro: IPR011785 This entry represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor . These proteins contain a Helix-Turn-Helix motif of the "fis" type..
Probab=29.04 E-value=54 Score=15.79 Aligned_cols=35 Identities=20% Similarity=0.350 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHHHHHH-------------------CCCCCCCCCCCCEEEEEEECHH
Q ss_conf 258889998999999997-------------------7984421128940479963758
Q gi|254781028|r 37 PDKAVIESRERIQSHFIH-------------------AGLLFLVNELPSIYLQLIYQKK 76 (87)
Q Consensus 37 pD~aVkESreRVrsAl~n-------------------sGl~F~~~~~p~~~~tinl~p~ 76 (87)
-|--..|||||++.++.. +++ |+|..++++-|.-+
T Consensus 42 ~ei~~~es~~k~~~~l~~a~~~g~~a~r~~~~~~~~P~~~-----ElP~~F~~~~L~~s 95 (453)
T TIGR02040 42 EEIVTEESKEKVEALLSEAKRTGVGAVRVELNRFVLPSDL-----ELPMEFVLVRLGAS 95 (453)
T ss_pred HHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCC-----CCCEEEEEECCCCC
T ss_conf 4413577899999999714688885777766541179997-----24403467616787
No 15
>cd02201 FtsZ_type1 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells.
Probab=27.98 E-value=36 Score=16.82 Aligned_cols=28 Identities=32% Similarity=0.430 Sum_probs=22.6
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 6258889998999999997798442112
Q gi|254781028|r 36 LPDKAVIESRERIQSHFIHAGLLFLVNE 63 (87)
Q Consensus 36 LpD~aVkESreRVrsAl~nsGl~F~~~~ 63 (87)
....|..|++|.++.++.++.+-|..--
T Consensus 66 ~G~~AA~e~~~~I~~~l~~~d~vfi~AG 93 (304)
T cd02201 66 VGRKAAEESREEIKEALEGADMVFITAG 93 (304)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf 9999999889999999736876999942
No 16
>TIGR00097 HMP-P_kinase phosphomethylpyrimidine kinase; InterPro: IPR004399 Phosphomethylpyrimidine kinase (2.7.4.7 from EC), also known as HMP-phosphate kinase, catalyses the phosphorylation of HMP-P to HMP-PP in the reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine during the biosynthesis of thiamine.; GO: 0008972 phosphomethylpyrimidine kinase activity, 0009228 thiamin biosynthetic process.
Probab=27.80 E-value=48 Score=16.08 Aligned_cols=18 Identities=22% Similarity=0.242 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHC
Q ss_conf 588899989999999977
Q gi|254781028|r 38 DKAVIESRERIQSHFIHA 55 (87)
Q Consensus 38 D~aVkESreRVrsAl~ns 55 (87)
..||+++|+-|+.||+++
T Consensus 231 ~~Av~~AK~fv~~Ai~~~ 248 (264)
T TIGR00097 231 KDAVKEAKEFVTGAIKYS 248 (264)
T ss_pred HHHHHHHHHHHHHHHHCC
T ss_conf 899999999999997478
No 17
>PRK09330 cell division protein FtsZ; Validated
Probab=25.86 E-value=42 Score=16.41 Aligned_cols=26 Identities=35% Similarity=0.477 Sum_probs=21.8
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 62588899989999999977984421
Q gi|254781028|r 36 LPDKAVIESRERIQSHFIHAGLLFLV 61 (87)
Q Consensus 36 LpD~aVkESreRVrsAl~nsGl~F~~ 61 (87)
....|..||+|.++.++..+.+-|..
T Consensus 78 ~G~~AA~es~~~I~~~l~g~dmvFIt 103 (387)
T PRK09330 78 VGRKAAEESREEIREALEGADMVFIT 103 (387)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf 88999999999999997789879996
No 18
>PRK09568 DNA primase large subunit; Reviewed
Probab=25.28 E-value=50 Score=15.98 Aligned_cols=29 Identities=17% Similarity=0.177 Sum_probs=23.5
Q ss_pred CCCCCEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf 68974379961625888999899999999
Q gi|254781028|r 25 SPGRVGVQIVGLPDKAVIESRERIQSHFI 53 (87)
Q Consensus 25 s~GlP~f~iVGLpD~aVkESreRVrsAl~ 53 (87)
+.|+-.+.++-.+..++..++|||++|+.
T Consensus 22 g~~l~l~~~~~~~~~~verA~eRi~~al~ 50 (306)
T PRK09568 22 GGGVTLNDLLTTDSKYIDQAKERIRKIVK 50 (306)
T ss_pred CCCCCHHHHCCCCHHHHHHHHHHHHHHHC
T ss_conf 67731544215652799999999999862
No 19
>PRK13018 cell division protein FtsZ; Provisional
Probab=22.35 E-value=55 Score=15.72 Aligned_cols=26 Identities=35% Similarity=0.460 Sum_probs=20.9
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 62588899989999999977984421
Q gi|254781028|r 36 LPDKAVIESRERIQSHFIHAGLLFLV 61 (87)
Q Consensus 36 LpD~aVkESreRVrsAl~nsGl~F~~ 61 (87)
....|..||++.|+.++..+.+-|..
T Consensus 93 iG~~AAees~~~I~~~l~g~DmVFIt 118 (387)
T PRK13018 93 VGRKAAEESRDEIKEVLKGADLVFVT 118 (387)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf 99999998299999997589869999
No 20
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=20.77 E-value=76 Score=14.90 Aligned_cols=18 Identities=22% Similarity=0.414 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHCCC
Q ss_conf 889998999999997798
Q gi|254781028|r 40 AVIESRERIQSHFIHAGL 57 (87)
Q Consensus 40 aVkESreRVrsAl~nsGl 57 (87)
--.|.|+||+.|++..||
T Consensus 26 vs~~tr~rI~~~a~~lgY 43 (46)
T pfam00356 26 VSEETREKVEAAMEELGY 43 (46)
T ss_pred CCHHHHHHHHHHHHHHCC
T ss_conf 999999999999999789
No 21
>pfam02064 MAS20 MAS20 protein import receptor.
Probab=20.29 E-value=52 Score=15.85 Aligned_cols=16 Identities=44% Similarity=0.465 Sum_probs=12.2
Q ss_pred EEEEECHHHHHHHHHH
Q ss_conf 7996375889998888
Q gi|254781028|r 69 LQLIYQKKDLIMIYLS 84 (87)
Q Consensus 69 ~tinl~p~dl~~~~~~ 84 (87)
|.+-=+|+||+.||-.
T Consensus 121 L~VYPqP~dLL~IYq~ 136 (184)
T pfam02064 121 LKVYPQPADLIGIYDK 136 (184)
T ss_pred HHHCCCHHHHHHHHHH
T ss_conf 8608988999999981
Done!