Query 043281
Match_columns 234
No_of_seqs 111 out of 169
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 03:19:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043281.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043281hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06884 DUF1264: Protein of u 100.0 4E-103 8E-108 666.1 14.8 171 29-199 1-171 (171)
2 smart00136 LamNT Laminin N-ter 36.9 8.2 0.00018 34.9 -0.9 79 58-147 33-131 (238)
3 PF04934 Med6: MED6 mediator s 34.7 13 0.00029 30.9 0.1 35 79-120 59-93 (140)
4 TIGR03646 YtoQ_fam YtoQ family 30.2 8 0.00017 33.2 -2.0 58 96-162 47-109 (144)
5 PF01435 Peptidase_M48: Peptid 29.0 17 0.00038 30.1 -0.1 40 64-103 47-90 (226)
6 PF09022 Staphostatin_A: Staph 27.1 61 0.0013 26.6 2.6 33 54-89 47-79 (105)
7 PF01221 Dynein_light: Dynein 26.4 51 0.0011 24.9 2.0 18 128-145 40-57 (89)
8 PF01082 Cu2_monooxygen: Coppe 24.6 70 0.0015 25.9 2.6 75 64-148 16-94 (132)
9 TIGR00787 dctP tripartite ATP- 24.5 26 0.00056 30.6 0.1 24 83-106 205-228 (257)
10 COG0518 GuaA GMP synthase - Gl 22.6 42 0.00091 29.4 1.0 52 92-144 121-175 (198)
11 KOG1194 Predicted DNA-binding 22.2 25 0.00054 35.6 -0.5 73 71-146 131-213 (534)
12 COG4741 Predicted secreted end 21.5 1.3E+02 0.0028 26.7 3.7 54 74-136 103-158 (175)
No 1
>PF06884 DUF1264: Protein of unknown function (DUF1264); InterPro: IPR010686 This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins.
Probab=100.00 E-value=3.7e-103 Score=666.12 Aligned_cols=171 Identities=59% Similarity=1.082 Sum_probs=169.7
Q ss_pred CCCchHHHHhhhhhcccccCCCCCceeecccccccCcccceeEeeeCCCCCcceeeeeeeechhhhcCCCCcccccCccc
Q 043281 29 GFVPTNKIHQHLCAFHFYGDDMTRQVEAHHFCGHQNDEMRQCLIYNSAEADARLIGLEYIISENLFLTLPDEEKPLWHTH 108 (234)
Q Consensus 29 ~~~Pv~~i~~hL~aFH~ya~d~~rqvEAHHYC~~vneD~~QCliyDs~~~~ArLIGIEYiISe~lf~tLP~eEkklWHsH 108 (234)
+|+||++||+||||||+|++||+|||||||||+|||+||+||+|||||++|||||||||||||+||+|||+|||||||||
T Consensus 1 nf~Pv~~i~~hl~~fH~y~~d~~rqveahHyC~~vned~~QC~iyDs~~~~ArLIGvEYiISe~lf~tLP~eEkklWHsH 80 (171)
T PF06884_consen 1 NFKPVKQICQHLCAFHFYADDPTRQVEAHHYCSHVNEDFRQCLIYDSNEPNARLIGVEYIISEKLFETLPEEEKKLWHSH 80 (171)
T ss_pred CCCchHHHHhHhhhhhcccCCCCceeeeeeeeeecCCcceEEEEecCCCCCcceeeeeEEEcHHHHhhCCHHHHhccCCc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceecceeeeCCCCChHhHhHHHHHhhhhcCceEEeeccCCCCCCCCCcCccccccCCCCccChHHHHHHHhhhCCChHH
Q 043281 109 EFEVKSGVLFMPGIPGPVQRLDLEKVCKTYGKTVHFWQVDKGDNLPLGLPQIMMALTRDGQLYENLAQDVEKSYGVSFDK 188 (234)
Q Consensus 109 ~yEVkSG~L~~p~vP~~ae~~~M~~l~~tYGKt~HtWq~Drgd~LPlG~P~LMmsft~dgq~~~~lv~~RD~r~gi~t~~ 188 (234)
+||||||+|++|+||+++|+++|++|++|||||||||||||||+||||+|+||||||+|||++++||++||+||||||++
T Consensus 81 ~~EVkSG~L~~p~vP~~ae~~~m~~l~~tYGKt~HtWq~Drgd~LPlG~P~LM~sft~dgq~~~~lv~~RD~r~gv~t~~ 160 (171)
T PF06884_consen 81 VYEVKSGMLVMPGVPEAAEKAEMEKLVKTYGKTWHTWQVDRGDKLPLGPPQLMMSFTRDGQVDPELVKERDERFGVDTEE 160 (171)
T ss_pred ceeeeeeeEecCCCCHHHHHHHHHHHHhhhCCeEEeccCCCCCCCCCCCCeeccccCCcccCCHHHHHHHHHhcCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhccCCCC
Q 043281 189 ERVNRAYMNGP 199 (234)
Q Consensus 189 kr~~R~~i~~p 199 (234)
||++|++|++|
T Consensus 161 kr~~R~~i~~~ 171 (171)
T PF06884_consen 161 KRESRADIPEP 171 (171)
T ss_pred HHHHhcccccC
Confidence 99999999876
No 2
>smart00136 LamNT Laminin N-terminal domain (domain VI). N-terminal domain of laminins and laminin-related protein such as Unc-6/ netrins.
Probab=36.89 E-value=8.2 Score=34.87 Aligned_cols=79 Identities=22% Similarity=0.392 Sum_probs=47.2
Q ss_pred ccccc--cCcccceeEeeeCCCCCcceeeeeeeechhhhcCCCCcccccCcccc-----------------ceecceeee
Q 043281 58 HFCGH--QNDEMRQCLIYNSAEADARLIGLEYIISENLFLTLPDEEKPLWHTHE-----------------FEVKSGVLF 118 (234)
Q Consensus 58 HYC~~--vneD~~QCliyDs~~~~ArLIGIEYiISe~lf~tLP~eEkklWHsH~-----------------yEVkSG~L~ 118 (234)
.||.. ..+.-.+|-+=|+..++ +=-.+|||+.-.. +.....|-|-. |||--=.|.
T Consensus 33 ~yC~~~~~~~~~~~C~~CDa~~p~-~~Hp~~~l~D~~~-----~~~~TwWQS~~~~~~~~~VtitLdL~k~fevtyi~l~ 106 (238)
T smart00136 33 RYCKLVGHTEQGKKCDYCDARNPR-RSHPAENLTDGNN-----PNNPTWWQSEPLSNGPQNVNLTLDLGKEFHVTYVILK 106 (238)
T ss_pred ceeEeccccCcCCcCCCCCCCCcc-ccCCHHHhhccCC-----CCCCceecCCCcCCCCccEEEEEecCCEEEEEEEEEE
Confidence 45554 24556789888988773 5567888885332 23456777765 666543333
Q ss_pred CC-CCChHhHhHHHHHhhhhcCceEEeecc
Q 043281 119 MP-GIPGPVQRLDLEKVCKTYGKTVHFWQV 147 (234)
Q Consensus 119 ~p-~vP~~ae~~~M~~l~~tYGKt~HtWq~ 147 (234)
.- .-|.+ ..+|+- .|||||.-||.
T Consensus 107 F~s~RPa~---~i~erS--d~G~tW~p~qy 131 (238)
T smart00136 107 FCSPRPSL---WILERS--DFGKTWQPWQY 131 (238)
T ss_pred ecCCCCce---EEEeec--CCCCCCcEeee
Confidence 32 13321 122222 79999999995
No 3
>PF04934 Med6: MED6 mediator sub complex component; InterPro: IPR007018 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Regulation of mRNA synthesis requires intermediary proteins that transduce regulatory signals from upstream transcriptional activator proteins to basal transcription machinery at the core promoter. Three types of intermediary factors that enable the basal transcription machinery to respond to transcriptional activator proteins bound to regulatory DNA sequences have been identified: (i) TAFIIs, which associate with TATA-binding protein (TBP) to form TFIID; (ii) mediator, which associates with RNA polymerase II to form a holo-polymerase; and (iii) coactivators such as human upstream stimulatory activity (USA), mammalian CBP/P300, yeast ADA complex, and HMG proteins. The interaction of these multiprotein complexes with activators and general transcription factors is essential for transcriptional regulation. This family of proteins represent the transcriptional mediator protein subunit 6 that is required for activation of many RNA polymerase II promoters and which are conserved from yeast to humans []..; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3RJ1_N.
Probab=34.72 E-value=13 Score=30.95 Aligned_cols=35 Identities=20% Similarity=0.302 Sum_probs=1.7
Q ss_pred CcceeeeeeeechhhhcCCCCcccccCccccceecceeeeCC
Q 043281 79 DARLIGLEYIISENLFLTLPDEEKPLWHTHEFEVKSGVLFMP 120 (234)
Q Consensus 79 ~ArLIGIEYiISe~lf~tLP~eEkklWHsH~yEVkSG~L~~p 120 (234)
-.++.||||+|... .|-.+|..++.+..|+.-+.|
T Consensus 59 L~~m~GiEY~l~~~-------~eP~l~vI~Kq~r~~~~~~~~ 93 (140)
T PF04934_consen 59 LRNMKGIEYVLAHV-------QEPGLFVIRKQRRQSPDEVTP 93 (140)
T ss_dssp TTS---------------------------------------
T ss_pred HhhcCCeEEEEecc-------CCCCEEEEEEeeccCCCcceE
Confidence 45778999988754 455999999999988766654
No 4
>TIGR03646 YtoQ_fam YtoQ family protein. Members of this family are uncharacterized proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship.
Probab=30.18 E-value=8 Score=33.19 Aligned_cols=58 Identities=26% Similarity=0.470 Sum_probs=47.4
Q ss_pred CCCCcccccCccccceecceeeeCCCCChHhHhHHHHH---hhhhcCceEEeec--cCCCCCCCCCcCcccc
Q 043281 96 TLPDEEKPLWHTHEFEVKSGVLFMPGIPGPVQRLDLEK---VCKTYGKTVHFWQ--VDKGDNLPLGLPQIMM 162 (234)
Q Consensus 96 tLP~eEkklWHsH~yEVkSG~L~~p~vP~~ae~~~M~~---l~~tYGKt~HtWq--~Drgd~LPlG~P~LMm 162 (234)
-|-+|+++|||.|.- ..|-...-+..|++ ++-.||--|--|+ +|-|-..-||-|.+.+
T Consensus 47 iLG~e~~~fw~D~k~---------a~iNaiRT~~li~~aDvvVvrFGekYKQWNaAfDAg~aaAlgKplI~l 109 (144)
T TIGR03646 47 ILGKQPSNFWRDDAA---------ASINNIRTRKLIEKADVVIALFGEKYKQWNAAFDAGYAAALGKPLIIL 109 (144)
T ss_pred HhCCCCccccccccc---------cchhhHHHHHHHhhCCEEEEEechHHHHHHHHhhHHHHHHcCCCeEEe
Confidence 577889999999973 34555666666766 6778999999999 5999999999999988
No 5
>PF01435 Peptidase_M48: Peptidase family M48 This is family M48 in the peptidase classification. ; InterPro: IPR001915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: 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-, N-, 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. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; 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. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. 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 []. This group of metallopeptidases belong to MEROPS peptidase family M48 (Ste24 endopeptidase family, clan M-); members of both subfamily are represented. The members of this set of proteins are mostly described as probable protease htpX homologue (3.4.24 from EC) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit. In Saccharomyces cerevisiae (Baker's yeast) Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification is complete. The Ste24p contains multiple predicted membrane spans, a zinc metalloprotease motif (HEXXH), and a COOH-terminal ER retrieval signal (KKXX). The HEXXH protease motif is critical for Ste24p activity, since Ste24p fails to function when conserved residues within this motif are mutated. The Ste24p homologues occur in a diverse group of organisms, including Escherichia coli, Schizosaccharomyces pombe (Fission yeast), Haemophilus influenzae, and Homo sapiens (Human), which indicates that the gene is highly conserved throughout evolution. Ste24p and the proteins related to it define a subfamily of proteins that are likely to function as intracellular, membrane-associated zinc metalloproteases []. HtpX is a zinc-dependent endoprotease member of the membrane-localized proteolytic system in E. coli, which participates in the proteolytic quality control of membrane proteins in conjunction with FtsH, a membrane-bound and ATP-dependent protease. Biochemical characterisation revealed that HtpX undergoes self-degradation upon cell disruption or membrane solubilization. It can also degraded casein and cleaves solubilized membrane proteins, for example, SecY []. Expression of HtpX in the plasma membrane is under the control of CpxR, with the metalloproteinase active site of HtpX located on the cytosolic side of the membrane. This suggests a potential role for HtpX in the response to mis-folded proteins [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 3CQB_A 3C37_B.
Probab=28.98 E-value=17 Score=30.11 Aligned_cols=40 Identities=15% Similarity=0.205 Sum_probs=30.8
Q ss_pred CcccceeEeeeCCCCCcceeeeee----eechhhhcCCCCcccc
Q 043281 64 NDEMRQCLIYNSAEADARLIGLEY----IISENLFLTLPDEEKP 103 (234)
Q Consensus 64 neD~~QCliyDs~~~~ArLIGIEY----iISe~lf~tLP~eEkk 103 (234)
+-....-.|+|++..||-.+|.-. +|+..+++.|+++|-.
T Consensus 47 ~~~~~~v~v~~~~~~NA~~~g~~~~~~I~v~~~ll~~~~~~el~ 90 (226)
T PF01435_consen 47 GIPPPRVYVIDSPSPNAFATGGGPRKRIVVTSGLLESLSEDELA 90 (226)
T ss_dssp TSS--EEEEE--SSEEEEEETTTC--EEEEEHHHHHHSSHHHHH
T ss_pred CCCCCeEEEEcCCCCcEEEEccCCCcEEEEeChhhhcccHHHHH
Confidence 333456788999999999999987 8999999999999965
No 6
>PF09022 Staphostatin_A: Staphostatin A; InterPro: IPR015112 The staphostatin A polypeptide chain folds into a slightly deformed, eight-stranded beta-barrel, with strands beta-4 through beta-8 forming an antiparallel sheet while the N terminus forms a psi-loop motif. Members of this family constitute a class of cysteine protease inhibitors distinct in the fold and the mechanism of action from any known inhibitors of these enzymes []. ; PDB: 1OH1_A.
Probab=27.14 E-value=61 Score=26.60 Aligned_cols=33 Identities=30% Similarity=0.565 Sum_probs=23.8
Q ss_pred eeecccccccCcccceeEeeeCCCCCcceeeeeeee
Q 043281 54 VEAHHFCGHQNDEMRQCLIYNSAEADARLIGLEYII 89 (234)
Q Consensus 54 vEAHHYC~~vneD~~QCliyDs~~~~ArLIGIEYiI 89 (234)
+-..-||+-+|+|-||-++|.-+.++ |=||-+|
T Consensus 47 ~~p~YiC~~in~~~r~iiL~n~~n~s---IvIEi~i 79 (105)
T PF09022_consen 47 IQPDYICKYINTDSRQIILYNKDNSS---IVIEIII 79 (105)
T ss_dssp TT--EEEEEEETTTTEEEEEETTTS----EEEEEE-
T ss_pred CCcceeeeeecCCceEEEEEcCCCCc---EEEEEEE
Confidence 34567999999999999999887776 4566554
No 7
>PF01221 Dynein_light: Dynein light chain type 1 ; InterPro: IPR001372 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits (see IPR004273 from INTERPRO), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, ]. Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer alpha-beta core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].; GO: 0007017 microtubule-based process, 0005875 microtubule associated complex; PDB: 1F95_A 1F96_A 1F3C_A 3P8M_B 2XQQ_C 1RE6_A 1CMI_A 1PWK_A 1PWJ_A 4DS1_C ....
Probab=26.41 E-value=51 Score=24.90 Aligned_cols=18 Identities=28% Similarity=0.342 Sum_probs=12.7
Q ss_pred hHHHHHhhhhcCceEEee
Q 043281 128 RLDLEKVCKTYGKTVHFW 145 (234)
Q Consensus 128 ~~~M~~l~~tYGKt~HtW 145 (234)
+..=+.+-++||++||-.
T Consensus 40 ~~iK~~lD~~yG~~Wh~I 57 (89)
T PF01221_consen 40 EFIKQELDKKYGPTWHCI 57 (89)
T ss_dssp HHHHHHHHHHHSS-EEEE
T ss_pred HHHHHHHhcccCCceEEE
Confidence 344456788999999985
No 8
>PF01082 Cu2_monooxygen: Copper type II ascorbate-dependent monooxygenase, N-terminal domain; InterPro: IPR000323 Copper type II, ascorbate-dependent monooxygenases [] are a class of enzymes that requires copper as a cofactor and which uses ascorbate as an electron donor. This family contains two related enzymes, Dopamine-beta-monooxygenase (1.14.17.1 from EC) and Peptidyl-glycine alpha-amidating monooxygenase (1.14.17.3 from EC). There are a few regions of sequence similarities between these two enzymes, two of these regions contain clusters of conserved histidine residues which are most probably involved in binding copper.; GO: 0004497 monooxygenase activity, 0005507 copper ion binding, 0016715 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen, 0055114 oxidation-reduction process; PDB: 1YI9_A 3MLL_A 1SDW_A 3MID_A 1YIP_A 3PHM_A 3MIC_A 3MIB_A 1OPM_A 3MIG_A ....
Probab=24.65 E-value=70 Score=25.92 Aligned_cols=75 Identities=12% Similarity=0.220 Sum_probs=38.8
Q ss_pred CcccceeEeeeCCC--CCcceeeeeeeechhhhcCCCCcccccCccccceecceeeeC--CCCChHhHhHHHHHhhhhcC
Q 043281 64 NDEMRQCLIYNSAE--ADARLIGLEYIISENLFLTLPDEEKPLWHTHEFEVKSGVLFM--PGIPGPVQRLDLEKVCKTYG 139 (234)
Q Consensus 64 neD~~QCliyDs~~--~~ArLIGIEYiISe~lf~tLP~eEkklWHsH~yEVkSG~L~~--p~vP~~ae~~~M~~l~~tYG 139 (234)
++|...|.+++-+. .+..+||+|-+|+.. +-.=|.-.|+-.++.-.. ....+.. ...+......-.
T Consensus 16 ~~t~Y~C~~~~lp~~~~~~hIi~~ep~~~~~---------~~VHHmlly~C~~~~~~~~~~~~~~C~-~~~~~~~~~~C~ 85 (132)
T PF01082_consen 16 QDTTYWCFVFKLPDLTEKHHIIGFEPIITNG---------EVVHHMLLYGCDGDNDPLSRESGGECY-SANMPGDFGSCS 85 (132)
T ss_dssp SSSEEEEEEEE-S-S-S-EEEEEEEEE--T----------TTEEEEEEEEES---SBSSSSSSEEG--------GG-SB-
T ss_pred CCCeEEEEEEECCcccccceEEEeeeeeccC---------CcEEEEEEEEECCCCccCcccCCCccc-ceeccccccccc
Confidence 47899999999887 789999999999985 345566667776651111 1111111 223333444448
Q ss_pred ceEEeeccC
Q 043281 140 KTVHFWQVD 148 (234)
Q Consensus 140 Kt~HtWq~D 148 (234)
.++..|-..
T Consensus 86 ~ii~aWA~G 94 (132)
T PF01082_consen 86 TIIAAWAPG 94 (132)
T ss_dssp EEEEEEETT
T ss_pred ceEEEEcCC
Confidence 899999864
No 9
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=24.52 E-value=26 Score=30.58 Aligned_cols=24 Identities=13% Similarity=0.430 Sum_probs=19.8
Q ss_pred eeeeeeechhhhcCCCCcccccCc
Q 043281 83 IGLEYIISENLFLTLPDEEKPLWH 106 (234)
Q Consensus 83 IGIEYiISe~lf~tLP~eEkklWH 106 (234)
.+.-++||.+.|++||+|.|+.=.
T Consensus 205 ~~~~~~~n~~~~~~L~~e~q~~i~ 228 (257)
T TIGR00787 205 LGYLVVVNKAFWKSLPPDLQAVVK 228 (257)
T ss_pred cceEEEEeHHHHhcCCHHHHHHHH
Confidence 445689999999999999998533
No 10
>COG0518 GuaA GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]
Probab=22.56 E-value=42 Score=29.38 Aligned_cols=52 Identities=21% Similarity=0.310 Sum_probs=32.9
Q ss_pred hhhcCCCCcccccCccccceec---ceeeeCCCCChHhHhHHHHHhhhhcCceEEe
Q 043281 92 NLFLTLPDEEKPLWHTHEFEVK---SGVLFMPGIPGPVQRLDLEKVCKTYGKTVHF 144 (234)
Q Consensus 92 ~lf~tLP~eEkklWHsH~yEVk---SG~L~~p~vP~~ae~~~M~~l~~tYGKt~Ht 144 (234)
.+|+.||+.+...||||.-+|. .|--+... .+....+.|+.=.+.||=-||.
T Consensus 121 ~l~~gl~~~~~~v~~sH~D~v~~lP~g~~vlA~-s~~cp~qa~~~~~~~~gvQFHp 175 (198)
T COG0518 121 PLFAGLPDLFTTVFMSHGDTVVELPEGAVVLAS-SETCPNQAFRYGKRAYGVQFHP 175 (198)
T ss_pred ccccCCccccCccccchhCccccCCCCCEEEec-CCCChhhheecCCcEEEEeeee
Confidence 4899999988889999987775 33333222 3334455555445666655553
No 11
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=22.19 E-value=25 Score=35.58 Aligned_cols=73 Identities=27% Similarity=0.387 Sum_probs=49.1
Q ss_pred EeeeCCC--CCcceeeeeeeechhhhcCCCCcccc----cCccccceecceeee----CCCCChHhHhHHHHHhhhhcCc
Q 043281 71 LIYNSAE--ADARLIGLEYIISENLFLTLPDEEKP----LWHTHEFEVKSGVLF----MPGIPGPVQRLDLEKVCKTYGK 140 (234)
Q Consensus 71 liyDs~~--~~ArLIGIEYiISe~lf~tLP~eEkk----lWHsH~yEVkSG~L~----~p~vP~~ae~~~M~~l~~tYGK 140 (234)
|||--+. ++++|- ||| ++.-=.-+=+.||. +||.|+++----.|. .|..|-+.++-++++--.-|||
T Consensus 131 liWsp~~~i~D~kL~--EYI-~~A~~rY~i~ieqAL~iL~~h~~d~d~A~~~l~rr~~~~d~WT~Ed~vlFe~aF~~~GK 207 (534)
T KOG1194|consen 131 LIWSPPLEIQDDKLE--EYI-SEAKERYGIPIEQALFILFWHKHDFDLAHADLARRTEFPDEWTAEDIVLFEQAFQFFGK 207 (534)
T ss_pred eeecCcccCcHHHHH--HHH-HHHHHhcCCcHHHHHHHHHhhcccchHHHHHHhhcCCCcccchHHHHHHHHHHHHHhcc
Confidence 5776555 355653 554 33322223345554 599999987544443 3678889999999999999999
Q ss_pred eEEeec
Q 043281 141 TVHFWQ 146 (234)
Q Consensus 141 t~HtWq 146 (234)
.||-=+
T Consensus 208 ~F~kIr 213 (534)
T KOG1194|consen 208 DFHKIR 213 (534)
T ss_pred cHHHHH
Confidence 998554
No 12
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=21.50 E-value=1.3e+02 Score=26.72 Aligned_cols=54 Identities=22% Similarity=0.356 Sum_probs=36.2
Q ss_pred eCCCCCcceee--eeeeechhhhcCCCCcccccCccccceecceeeeCCCCChHhHhHHHHHhhh
Q 043281 74 NSAEADARLIG--LEYIISENLFLTLPDEEKPLWHTHEFEVKSGVLFMPGIPGPVQRLDLEKVCK 136 (234)
Q Consensus 74 Ds~~~~ArLIG--IEYiISe~lf~tLP~eEkklWHsH~yEVkSG~L~~p~vP~~ae~~~M~~l~~ 136 (234)
.=|-+|||.|| |.||| |+.|++.+-. -.--.|||||- +..+. ..|++.|+.+.+
T Consensus 103 ~ynPkD~RfIGTPvD~iV----FdGLs~G~i~--~IvFvEVKtGk--t~~Ls-eREk~Vr~ai~~ 158 (175)
T COG4741 103 KYNPKDARFIGTPVDFIV----FDGLSEGNIE--SIVFVEVKTGK--TSSLS-EREKAVRDAIEN 158 (175)
T ss_pred CcCCccceeeCCCceEEE----EcCCCcCcee--EEEEEEEecCC--cCCcc-HHHHHHHHHHhc
Confidence 34667899998 67886 7788775421 22236999995 22333 568888888765
Done!