Query gi|254780203|ref|YP_003064616.1| hypothetical protein CLIBASIA_00440 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 82
No_of_seqs 3 out of 5
Neff 1.7
Searched_HMMs 39220
Date Mon May 23 12:01:32 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780203.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00740 MeTr MeTr subgroup of 63.3 16 0.00041 19.3 5.6 63 2-64 128-194 (252)
2 COG4003 Uncharacterized protei 58.3 20 0.00051 18.7 4.4 56 9-65 4-61 (98)
3 TIGR00501 met_pdase_II methion 49.6 13 0.00032 19.9 2.2 61 3-66 122-204 (327)
4 KOG1855 consensus 48.1 12 0.00032 19.9 2.0 54 19-78 247-305 (484)
5 TIGR01742 SA_tandem_lipo Staph 43.0 7.5 0.00019 21.2 0.2 21 19-42 46-66 (267)
6 cd00181 TarH Taxis toward Aspa 42.3 24 0.0006 18.3 2.7 27 43-69 86-112 (140)
7 PHA01632 hypothetical protein 42.1 24 0.00062 18.2 2.7 25 6-30 26-50 (64)
8 PTZ00053 methionine aminopepti 39.0 14 0.00036 19.6 1.1 63 3-65 226-307 (435)
9 pfam04507 DUF576 Protein of un 35.8 17 0.00043 19.2 1.1 21 19-42 35-55 (257)
10 PRK13015 3-dehydroquinate dehy 31.5 41 0.001 16.9 2.5 24 42-65 124-147 (148)
11 TIGR02257 cobalto_cobN cobalto 29.9 26 0.00067 18.0 1.3 29 13-41 1019-1050(1310)
12 pfam09249 tRNA_NucTransf2 tRNA 29.2 50 0.0013 16.4 2.6 30 19-58 4-33 (114)
13 pfam02203 TarH Tar ligand bind 27.5 61 0.0015 15.9 2.8 27 43-69 77-103 (133)
14 pfam06154 YagB_YeeU_YfjZ YagB/ 27.2 46 0.0012 16.6 2.2 25 12-36 46-70 (104)
15 cd04440 DEP_2_P-Rex DEP (Dishe 26.7 36 0.00092 17.2 1.5 52 12-66 1-53 (93)
16 pfam06953 ArsD Arsenical resis 26.2 21 0.00055 18.5 0.3 29 48-81 23-51 (119)
17 TIGR02995 ectoine_ehuB ectoine 25.0 51 0.0013 16.3 2.0 27 5-31 234-266 (285)
18 pfam08558 TRF Telomere repeat 23.4 76 0.0019 15.3 4.8 52 12-63 37-89 (235)
19 TIGR03671 cca_archaeal CCA-add 22.1 74 0.0019 15.4 2.4 38 19-67 154-191 (408)
20 PRK13300 tRNA CCA-pyrophosphor 21.1 80 0.002 15.2 2.4 40 19-69 159-198 (446)
21 pfam05499 DMAP1 DNA methyltran 20.1 89 0.0023 14.9 3.7 52 17-68 103-157 (176)
No 1
>cd00740 MeTr MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent methyltransferases catalyze the transfer of a methyl group via a methyl- cob(III)amide intermediate. These include MeTr, a functional heterodimer, and the folate binding domain of MetH.
Probab=63.31 E-value=16 Score=19.26 Aligned_cols=63 Identities=19% Similarity=0.326 Sum_probs=42.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHH-HH-HCCHHC--CCCCCCHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf 83001401899999979999999-83-103001--25322478620022899999999999999718
Q gi|254780203|r 2 DDRKYRPSKEEVRDAFPELIKAL-EK-GLSTFD--VEPLKNPVKSHGKGYESYISHVCELIELLKNK 64 (82)
Q Consensus 2 ~d~kYRPs~eevR~afPkl~K~~-Ek-~ls~y~--VdPL~~Pv~i~~~g~e~Y~~H~CaLi~lLen~ 64 (82)
|+.----+.++--.++-+++... |+ |+++-| +|||.-|+-.|.+....+-....+.|++++..
T Consensus 128 de~Gip~t~e~R~~ia~~i~~~~~~~~Gi~~edI~~DpLv~pi~tg~e~~~~~~~~tleaI~~ik~~ 194 (252)
T cd00740 128 DEQGQAKTRDKKVEIAERAYEALTEFVGFPPEDIIFDPLILPIATGIEEHRPYALETIDAIRMIKER 194 (252)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHEEEECCHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 8999989999999999999999998569988997886635776457467888999999999999987
No 2
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=58.33 E-value=20 Score=18.74 Aligned_cols=56 Identities=27% Similarity=0.318 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHCCCCCC--CHHHHCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 18999999799999998310300125322--4786200228999999999999997188
Q gi|254780203|r 9 SKEEVRDAFPELIKALEKGLSTFDVEPLK--NPVKSHGKGYESYISHVCELIELLKNKD 65 (82)
Q Consensus 9 s~eevR~afPkl~K~~Ek~ls~y~VdPL~--~Pv~i~~~g~e~Y~~H~CaLi~lLen~~ 65 (82)
-+++.+..||.|.|-+| |+.+-+-+|+- ||.-+.--.--.-+-.+-+.|+||+++.
T Consensus 4 ~~~~fkk~fp~l~~ele-g~~l~~~~~~~gy~PtV~D~L~rCdT~EEAlEii~yleKrG 61 (98)
T COG4003 4 DKEEFKKKFPALAKELE-GIRLEPKIDFSGYNPTVIDFLRRCDTEEEALEIINYLEKRG 61 (98)
T ss_pred CHHHHHHHHHHHHHHHH-CCCCCCCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHC
T ss_conf 38999998289998861-45267567756789639999998264999999999999927
No 3
>TIGR00501 met_pdase_II methionine aminopeptidase, type II; InterPro: IPR002468 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . 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 metallopeptidases belong to MEROPS peptidase family M24 (clan MG), subfamily M24A. Methionine aminopeptidase (3.4.11.18 from EC) (MAP) is responsible for the removal of the amino-terminal (initiator) methionine from nascent eukaryotic cytosolic and cytoplasmic prokaryotic proteins if the penultimate amino acid is small and uncharged. All MAP studied to date are monomeric proteins that require cobalt ions for activity. Two subfamilies of MAP enzymes are known to exist , . While being evolutionary related, they only share a limited amount of sequence similarity mostly clustered around the residues shown, in the Escherichia coli MAP , to be involved in cobalt-binding. The first family consists of enzymes from prokaryotes as well as eukaryotic MAP-1, while the second group (IPR002467 from INTERPRO) is made up of archaeal MAP and eukaryotic MAP-2 and includes proteins which do not seem to be MAP, but that are clearly evolutionary related such as mouse proliferation-associated protein 1 and fission yeast curved DNA-binding protein. ; GO: 0004239 methionyl aminopeptidase activity, 0006508 proteolysis.
Probab=49.56 E-value=13 Score=19.92 Aligned_cols=61 Identities=26% Similarity=0.441 Sum_probs=45.0
Q ss_pred CCCCCCHHHHHHHHHHH-------------HHHHHHHHCCH---------HCCCCCCCHHHHCCHHHHHHHHHHHHHHHH
Q ss_conf 30014018999999799-------------99999831030---------012532247862002289999999999999
Q gi|254780203|r 3 DRKYRPSKEEVRDAFPE-------------LIKALEKGLST---------FDVEPLKNPVKSHGKGYESYISHVCELIEL 60 (82)
Q Consensus 3 d~kYRPs~eevR~afPk-------------l~K~~Ek~ls~---------y~VdPL~~Pv~i~~~g~e~Y~~H~CaLi~l 60 (82)
|.||.-+-+++++|.-- +=|+||.+++- |.+.|. +-.-|.||.-|+.|.--=|--
T Consensus 122 ddky~~L~~A~~dAl~~~i~~~~~~v~v~eiG~~I~e~i~syeveinGetYg~kP~---~NL~GHs~~rY~~H~G~SiPn 198 (327)
T TIGR00501 122 DDKYKELVKAAKDALYTAIKEIRAGVEVGEIGKAIEEVIESYEVEINGETYGVKPI---SNLTGHSMARYLLHAGLSIPN 198 (327)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHHCCEEEEECCCCCCCCCC---CCCCCCCCCHHHHCCCCCCEE
T ss_conf 01589999999999887775006981260020776653221357765720143342---227356400154358950003
Q ss_pred HHCCCC
Q ss_conf 971885
Q gi|254780203|r 61 LKNKDF 66 (82)
Q Consensus 61 Len~~f 66 (82)
..+++-
T Consensus 199 ~~~~~~ 204 (327)
T TIGR00501 199 VKERDT 204 (327)
T ss_pred EECCCC
T ss_conf 427987
No 4
>KOG1855 consensus
Probab=48.08 E-value=12 Score=19.94 Aligned_cols=54 Identities=28% Similarity=0.341 Sum_probs=31.1
Q ss_pred HHHHHHHHHCCHHCCCCCCC---HHHH--CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 99999983103001253224---7862--002289999999999999971885501578876532
Q gi|254780203|r 19 ELIKALEKGLSTFDVEPLKN---PVKS--HGKGYESYISHVCELIELLKNKDFDGVEIERKSYNL 78 (82)
Q Consensus 19 kl~K~~Ek~ls~y~VdPL~~---Pv~i--~~~g~e~Y~~H~CaLi~lLen~~f~~~~i~rk~~n~ 78 (82)
.|+|+|-..=+.--|--++- |.++ ..++|-.---.+||||+ |+++++++|+-.+
T Consensus 247 nl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvE------ye~~~~A~KA~e~ 305 (484)
T KOG1855 247 NLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVE------YEEVEAARKAREL 305 (484)
T ss_pred HHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHH------HHHHHHHHHHHHH
T ss_conf 8999853255413566407887784323477644045545666654------3124888999986
No 5
>TIGR01742 SA_tandem_lipo Staphylococcus tandem lipoproteins; InterPro: IPR007595 This family contains several uncharacterised staphylococcal proteins..
Probab=42.96 E-value=7.5 Score=21.24 Aligned_cols=21 Identities=38% Similarity=0.583 Sum_probs=16.2
Q ss_pred HHHHHHHHHCCHHCCCCCCCHHHH
Q ss_conf 999999831030012532247862
Q gi|254780203|r 19 ELIKALEKGLSTFDVEPLKNPVKS 42 (82)
Q Consensus 19 kl~K~~Ek~ls~y~VdPL~~Pv~i 42 (82)
.|=|+|+|+||.| |.+|==+.
T Consensus 46 ~~Kksf~KtL~mY---PIKNLE~L 66 (267)
T TIGR01742 46 QIKKSFEKTLSMY---PIKNLEDL 66 (267)
T ss_pred HHCCCHHHCCCCC---CCCCCHHH
T ss_conf 4211011002578---83442123
No 6
>cd00181 TarH Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane signalers monitor the chemical environment by means of specific ligand-binding sites arrayed on the periplasmic side of the membrane, and in turn control cytoplasmic signals that modulate the flagellar rotational machinery. Aspartate is detected through direct binding to Tar molecules, whereas maltose is detected indirectly when complexed with the periplasmic maltose-binding protein.
Probab=42.32 E-value=24 Score=18.29 Aligned_cols=27 Identities=19% Similarity=0.497 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf 002289999999999999971885501
Q gi|254780203|r 43 HGKGYESYISHVCELIELLKNKDFDGV 69 (82)
Q Consensus 43 ~~~g~e~Y~~H~CaLi~lLen~~f~~~ 69 (82)
-+++|..|....-+|+.+|+++++++.
T Consensus 86 l~~~Y~~~~~aL~el~~~L~~~~l~~F 112 (140)
T cd00181 86 LKEKFKQYFQALAELIQILASGNMNAF 112 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 999999999999999999886998899
No 7
>PHA01632 hypothetical protein
Probab=42.13 E-value=24 Score=18.23 Aligned_cols=25 Identities=24% Similarity=0.610 Sum_probs=20.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf 1401899999979999999831030
Q gi|254780203|r 6 YRPSKEEVRDAFPELIKALEKGLST 30 (82)
Q Consensus 6 YRPs~eevR~afPkl~K~~Ek~ls~ 30 (82)
-.|+.||.|.+.||++|-+..-++-
T Consensus 26 ~kpteeelrkvlpkilkdyanmie~ 50 (64)
T PHA01632 26 QKPTEEELRKVLPKILKDYANMIEN 50 (64)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9977999999999999999999861
No 8
>PTZ00053 methionine aminopeptidase II; Provisional
Probab=39.02 E-value=14 Score=19.59 Aligned_cols=63 Identities=22% Similarity=0.472 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHH-------------HHHHHHHHHCCHHCCC------CCCCHHHHCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 3001401899999979-------------9999998310300125------32247862002289999999999999971
Q gi|254780203|r 3 DRKYRPSKEEVRDAFP-------------ELIKALEKGLSTFDVE------PLKNPVKSHGKGYESYISHVCELIELLKN 63 (82)
Q Consensus 3 d~kYRPs~eevR~afP-------------kl~K~~Ek~ls~y~Vd------PL~~Pv~i~~~g~e~Y~~H~CaLi~lLen 63 (82)
|.+|.|+-+++++|-- ++-++++..++-|.|+ |.+--+...|.+..+|..|.---|-...+
T Consensus 226 ~~kyd~Ll~A~keAt~taIk~agidvrl~eIG~aIqEvieSyevei~gk~y~vKPI~NL~GH~I~~Y~IHggksIP~v~~ 305 (435)
T PTZ00053 226 NEKYDPLLEATKEATNEGIKQAGIDARLCDIGEAIQEVIESYEVELNGKVYPVKSIRNLTGHNIGPYIIHSGKSVPIVRG 305 (435)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHEEEECCCCCCCCCCCCCCCCCCCCEEECCCCEECCCCC
T ss_conf 87537899999999999999851686188899999999975234433633167404677766530235116855321168
Q ss_pred CC
Q ss_conf 88
Q gi|254780203|r 64 KD 65 (82)
Q Consensus 64 ~~ 65 (82)
++
T Consensus 306 ~~ 307 (435)
T PTZ00053 306 GE 307 (435)
T ss_pred CC
T ss_conf 86
No 9
>pfam04507 DUF576 Protein of unknown function, DUF576. This family contains several uncharacterized staphylococcal proteins.
Probab=35.76 E-value=17 Score=19.16 Aligned_cols=21 Identities=29% Similarity=0.499 Sum_probs=16.6
Q ss_pred HHHHHHHHHCCHHCCCCCCCHHHH
Q ss_conf 999999831030012532247862
Q gi|254780203|r 19 ELIKALEKGLSTFDVEPLKNPVKS 42 (82)
Q Consensus 19 kl~K~~Ek~ls~y~VdPL~~Pv~i 42 (82)
+|-|+|+|+|+.| |.+|--+.
T Consensus 35 qIKksF~KtL~mY---PiKNLEDl 55 (257)
T pfam04507 35 QIKKSFAKTLDMY---PIKNLEDL 55 (257)
T ss_pred HHHHHHHHHHHCC---CCCCHHHH
T ss_conf 9999998776226---64447776
No 10
>PRK13015 3-dehydroquinate dehydratase; Reviewed
Probab=31.53 E-value=41 Score=16.89 Aligned_cols=24 Identities=29% Similarity=0.324 Sum_probs=20.1
Q ss_pred HCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 200228999999999999997188
Q gi|254780203|r 42 SHGKGYESYISHVCELIELLKNKD 65 (82)
Q Consensus 42 i~~~g~e~Y~~H~CaLi~lLen~~ 65 (82)
|-|.|..||.+-+-+|+++|+.+.
T Consensus 124 I~G~G~~gY~lAl~~l~~ll~~~~ 147 (148)
T PRK13015 124 ICGLGTEGYRLALRRLATLFKAGA 147 (148)
T ss_pred EECCCHHHHHHHHHHHHHHHHHCC
T ss_conf 971777889999999999997356
No 11
>TIGR02257 cobalto_cobN cobaltochelatase, CobN subunit; InterPro: IPR011953 This family of proteins catalyzes the insertion of cobalt into the corrin ring of hydrogenobyrinic acid a,c-diamide. This aerobic branch of corrin ring synthesis is part of the adenosylcobalamin biosynthetic pathway ..
Probab=29.88 E-value=26 Score=18.01 Aligned_cols=29 Identities=38% Similarity=0.641 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHCC---HHCCCCCCCHHH
Q ss_conf 99997999999983103---001253224786
Q gi|254780203|r 13 VRDAFPELIKALEKGLS---TFDVEPLKNPVK 41 (82)
Q Consensus 13 vR~afPkl~K~~Ek~ls---~y~VdPL~~Pv~ 41 (82)
-|||||.||.-|.+++. .-|=++-.||.-
T Consensus 1019 FRDAFP~LI~L~d~A~~~Va~lDE~~~~NPLA 1050 (1310)
T TIGR02257 1019 FRDAFPNLIALVDKAVQAVAQLDEPEELNPLA 1050 (1310)
T ss_pred HHHCCHHHHHHHHHHHHHHHHCCCCHHCCCHH
T ss_conf 33001789999999999997306882007467
No 12
>pfam09249 tRNA_NucTransf2 tRNA nucleotidyltransferase, second domain. Members of this family adopt a structure consisting of a five helical bundle core. They are predominantly found in Archaeal tRNA nucleotidyltransferase, following the catalytic nucleotidyltransferase domain.
Probab=29.16 E-value=50 Score=16.36 Aligned_cols=30 Identities=30% Similarity=0.783 Sum_probs=21.9
Q ss_pred HHHHHHHHHCCHHCCCCCCCHHHHCCHHHHHHHHHHHHHH
Q ss_conf 9999998310300125322478620022899999999999
Q gi|254780203|r 19 ELIKALEKGLSTFDVEPLKNPVKSHGKGYESYISHVCELI 58 (82)
Q Consensus 19 kl~K~~Ek~ls~y~VdPL~~Pv~i~~~g~e~Y~~H~CaLi 58 (82)
.|+|.|-|++..|. -++-.+||-|| +|+|.
T Consensus 4 rLlK~FlK~igvYG-------aE~~~~GFSGY---l~ElL 33 (114)
T pfam09249 4 RLLKQFLKGIGVYG-------SELKTQGFSGY---LCELL 33 (114)
T ss_pred HHHHHHHHHCCCCC-------HHHHCCCCHHH---HHHHH
T ss_conf 89999998658552-------66751662289---99999
No 13
>pfam02203 TarH Tar ligand binding domain homologue.
Probab=27.47 E-value=61 Score=15.87 Aligned_cols=27 Identities=33% Similarity=0.620 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf 002289999999999999971885501
Q gi|254780203|r 43 HGKGYESYISHVCELIELLKNKDFDGV 69 (82)
Q Consensus 43 ~~~g~e~Y~~H~CaLi~lLen~~f~~~ 69 (82)
-++.|++|..-.-+|+.+|+++++++.
T Consensus 77 l~~~y~~y~~aL~el~~~l~~~~~~~F 103 (133)
T pfam02203 77 LKEKYKQYISALAELIQILEAGNIDAF 103 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 999999999999999999877985789
No 14
>pfam06154 YagB_YeeU_YfjZ YagB/YeeU/YfjZ family. This family of proteins includes three proteins from E. coli YagB, YeeU and YfjZ. The function of these proteins is unknown. They are about 120 amino acids in length.
Probab=27.22 E-value=46 Score=16.56 Aligned_cols=25 Identities=36% Similarity=0.561 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHCCHHCCCCC
Q ss_conf 9999979999999831030012532
Q gi|254780203|r 12 EVRDAFPELIKALEKGLSTFDVEPL 36 (82)
Q Consensus 12 evR~afPkl~K~~Ek~ls~y~VdPL 36 (82)
..-.+||.+||-+|..+..=..+|-
T Consensus 46 ~Ld~aFP~~i~qlE~ml~sGeL~pr 70 (104)
T pfam06154 46 HLDEAFPHFIKQLELMLLSGELNPR 70 (104)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 9999999999999998645998857
No 15
>cd04440 DEP_2_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity.
Probab=26.70 E-value=36 Score=17.20 Aligned_cols=52 Identities=23% Similarity=0.308 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHCCHHCCCCCCCHHHHCCHHHHHHHHHHHHHHHHH-HCCCC
Q ss_conf 99999799999998310300125322478620022899999999999999-71885
Q gi|254780203|r 12 EVRDAFPELIKALEKGLSTFDVEPLKNPVKSHGKGYESYISHVCELIELL-KNKDF 66 (82)
Q Consensus 12 evR~afPkl~K~~Ek~ls~y~VdPL~~Pv~i~~~g~e~Y~~H~CaLi~lL-en~~f 66 (82)
||-++|-+=-+..++--|.+ .|||-.++-|.+.|.+- --.++||.|| ++++-
T Consensus 1 ~~~~v~~~G~~ly~rl~~~~--~~lIkdR~~~l~tY~~c-F~GselVdWLv~~ge~ 53 (93)
T cd04440 1 EMEDIMSKGVRLYCRLHSLF--TPVVKDRDYHLKTYKSV-VPASKLVDWLLAQGDC 53 (93)
T ss_pred CHHHHHHHHHHHHHHHHHCC--CCCCCCCHHHCCCCCCE-EEHHHHHHHHHHCCCC
T ss_conf 97899874099999998115--65011007521066522-1728999999977886
No 16
>pfam06953 ArsD Arsenical resistance operon trans-acting repressor ArsD. This family consists of several bacterial arsenical resistance operon trans-acting repressor ArsD proteins. ArsD is a trans-acting repressor of the arsRDABC operon that confers resistance to arsenicals and antimonials in Escherichia coli. It possesses two-pairs of vicinal cysteine residues, Cys(12)-Cys(13) and Cys(112)-Cys(113), that potentially form separate binding sites for the metalloids that trigger dissociation of ArsD from the operon. However, as a homodimer it has four vicinal cysteine pairs.
Probab=26.24 E-value=21 Score=18.54 Aligned_cols=29 Identities=34% Similarity=0.650 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCC
Q ss_conf 9999999999999971885501578876532215
Q gi|254780203|r 48 ESYISHVCELIELLKNKDFDGVEIERKSYNLRKN 81 (82)
Q Consensus 48 e~Y~~H~CaLi~lLen~~f~~~~i~rk~~n~r~~ 81 (82)
.+--..+-+.++||++ +|++|+| ||+..+
T Consensus 23 D~~L~~~aa~~~~lk~---~gv~v~R--~NL~~~ 51 (119)
T pfam06953 23 DPELVRFAADLDWLKQ---NGVEVER--YNLAQQ 51 (119)
T ss_pred CHHHHHHHHHHHHHHH---CCCEEEE--CCCCCC
T ss_conf 9899999999999996---7947997--166328
No 17
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein; InterPro: IPR014337 Members of this entry are the extracellular solute-binding proteins of ABC transporters and they closely resemble amino acid transporters. The member from Sinorhizobium meliloti (Rhizobium meliloti) is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes..
Probab=25.04 E-value=51 Score=16.30 Aligned_cols=27 Identities=41% Similarity=0.753 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHHHH-HHHHH-----HHHHCCHH
Q ss_conf 01401899999979-99999-----98310300
Q gi|254780203|r 5 KYRPSKEEVRDAFP-ELIKA-----LEKGLSTF 31 (82)
Q Consensus 5 kYRPs~eevR~afP-kl~K~-----~Ek~ls~y 31 (82)
-+||--||.||+|- +|.|- +.|.|.+|
T Consensus 234 AFRpeDkeLRDafn~~L~k~~~s~e~~Ki~apy 266 (285)
T TIGR02995 234 AFRPEDKELRDAFNVELAKLKESDEFKKIVAPY 266 (285)
T ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCHHHHCCC
T ss_conf 116666777879989999862465401122136
No 18
>pfam08558 TRF Telomere repeat binding factor (TRF). Telomere repeat binding factor (TRF) family proteins are important for the regulation of telomere stability. The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain pfam00249 at the carboxy terminus. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres. This domain is composed of multiple alpha helices arranged in a solenoid conformation similar to TPR repeats. The fungal members have now also been found to carry two double strand telomeric repeat binding factors.
Probab=23.35 E-value=76 Score=15.30 Aligned_cols=52 Identities=15% Similarity=0.074 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHCCHH-CCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999799999998310300-12532247862002289999999999999971
Q gi|254780203|r 12 EVRDAFPELIKALEKGLSTF-DVEPLKNPVKSHGKGYESYISHVCELIELLKN 63 (82)
Q Consensus 12 evR~afPkl~K~~Ek~ls~y-~VdPL~~Pv~i~~~g~e~Y~~H~CaLi~lLen 63 (82)
+...+|-.|...|+.+...| ..+|+..|....-.+.++|+--.--.+|+.+.
T Consensus 37 ~~~~~f~~L~~lF~~~k~~ys~~~~~L~~~~~~~~~~e~~i~~tirkaNlatf 89 (235)
T pfam08558 37 ERGEDFRTLRDLFEALKKRYSEKSPFLSVDPLIIRDPEQRIMQTLRRANLATF 89 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 87899999999999999983789976688843146899999999999999999
No 19
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=22.12 E-value=74 Score=15.37 Aligned_cols=38 Identities=26% Similarity=0.710 Sum_probs=23.3
Q ss_pred HHHHHHHHHCCHHCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 9999998310300125322478620022899999999999999718855
Q gi|254780203|r 19 ELIKALEKGLSTFDVEPLKNPVKSHGKGYESYISHVCELIELLKNKDFD 67 (82)
Q Consensus 19 kl~K~~Ek~ls~y~VdPL~~Pv~i~~~g~e~Y~~H~CaLi~lLen~~f~ 67 (82)
.|+|.|-|++..|. -++-.+||-|| +|+|.- ++-|.|.
T Consensus 154 rLlK~Flk~~gvYG-------ae~~~~GFSGY---l~ELLi-i~YGsF~ 191 (408)
T TIGR03671 154 RLLKQFLKGIGVYG-------SELKTRGFSGY---LCELLV-IHYGSFE 191 (408)
T ss_pred HHHHHHHHHCCCCC-------HHHHCCCCHHH---HHHHHH-HHHCCHH
T ss_conf 99999987478453-------56660673478---999999-9964699
No 20
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=21.08 E-value=80 Score=15.16 Aligned_cols=40 Identities=28% Similarity=0.654 Sum_probs=24.9
Q ss_pred HHHHHHHHHCCHHCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf 999999831030012532247862002289999999999999971885501
Q gi|254780203|r 19 ELIKALEKGLSTFDVEPLKNPVKSHGKGYESYISHVCELIELLKNKDFDGV 69 (82)
Q Consensus 19 kl~K~~Ek~ls~y~VdPL~~Pv~i~~~g~e~Y~~H~CaLi~lLen~~f~~~ 69 (82)
.|+|.|-|++..|. -++-.+||-|| +|+|.- ++-|.|..+
T Consensus 159 rLlK~FlK~igvYG-------aE~~~~GFSGY---l~ElLi-i~yGsF~~~ 198 (446)
T PRK13300 159 RLLKQFLKGIGVYG-------AELKTGGFSGY---LCELLI-IYYGSFENV 198 (446)
T ss_pred HHHHHHHHHCCCCC-------HHHHCCCCHHH---HHHHHH-HHHCCHHHH
T ss_conf 99999987468354-------56650773578---999999-996469999
No 21
>pfam05499 DMAP1 DNA methyltransferase 1-associated protein 1 (DMAP1). DNA methylation can contribute to transcriptional silencing through several transcriptionally repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone deacetylases (HDACs). The chief enzyme that maintains mammalian DNA methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic amino terminus of DNMT1 binds to HDAC2 and DMAP1 (for DNMT1 associated protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted to replication foci through interaction with the far N terminus of DNMT1 throughout S phase, whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how histones may become deacetylated in heterochromatin following replication.
Probab=20.07 E-value=89 Score=14.90 Aligned_cols=52 Identities=25% Similarity=0.277 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHCCHHCCCCCCCHHHHCCHHHHHHHHHHH---HHHHHHHCCCCCH
Q ss_conf 799999998310300125322478620022899999999---9999997188550
Q gi|254780203|r 17 FPELIKALEKGLSTFDVEPLKNPVKSHGKGYESYISHVC---ELIELLKNKDFDG 68 (82)
Q Consensus 17 fPkl~K~~Ek~ls~y~VdPL~~Pv~i~~~g~e~Y~~H~C---aLi~lLen~~f~~ 68 (82)
--|.+|++|-.|+-+.||+--.|.+---..|..+++.+- +|--.+-|-.|.-
T Consensus 103 GqKK~K~iE~~L~el~v~~~P~ptEeIcq~FNeLRsdiVLL~ELK~Al~ncefEl 157 (176)
T pfam05499 103 GQKKIKALEQALEELKVDLNPMPTEEICQMFNELRSDMVLLYELKQALGTCEFEL 157 (176)
T ss_pred CCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 6146778999999739999999779999999999999999999999998617899
Done!