Query psy7794
Match_columns 139
No_of_seqs 211 out of 297
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 19:00:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7794.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7794hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2140|consensus 100.0 2E-30 4.4E-35 234.0 6.0 73 67-139 122-194 (739)
2 KOG2140|consensus 99.7 5.6E-18 1.2E-22 153.8 2.2 49 1-53 611-659 (739)
3 KOG2141|consensus 96.9 0.0019 4.2E-08 61.4 5.9 53 73-133 291-343 (822)
4 PF00619 CARD: Caspase recruit 70.2 6.8 0.00015 26.1 3.4 31 106-138 1-31 (85)
5 PF15359 CDV3: Carnitine defic 56.1 9.3 0.0002 29.3 2.2 16 74-89 83-98 (129)
6 PF09055 Sod_Ni: Nickel-contai 53.0 26 0.00056 27.1 4.2 38 76-113 11-60 (128)
7 TIGR01110 mdcA malonate decarb 41.2 5.5 0.00012 37.2 -1.3 19 69-87 523-541 (543)
8 PF15586 Imm47: Immunity prote 37.8 51 0.0011 24.6 3.6 53 81-133 50-105 (116)
9 PF05214 Baculo_p33: Baculovir 35.8 21 0.00046 30.5 1.4 18 96-113 231-248 (250)
10 PF07159 DUF1394: Protein of u 34.6 52 0.0011 28.6 3.7 35 75-117 41-75 (303)
11 PRK15091 ABC transporter outer 33.8 8.9 0.00019 32.4 -1.1 20 10-31 98-117 (251)
12 PF11712 Vma12: Endoplasmic re 33.7 80 0.0017 23.7 4.2 16 103-118 69-84 (142)
13 PF02637 GatB_Yqey: GatB domai 25.6 90 0.0019 23.2 3.2 57 79-136 38-105 (148)
14 PF08542 Rep_fac_C: Replicatio 24.2 1.5E+02 0.0033 19.6 3.9 44 81-134 3-46 (89)
15 cd08806 CARD_CARD14_CARMA2 Cas 24.0 68 0.0015 23.4 2.2 30 106-138 2-31 (86)
16 PF07817 GLE1: GLE1-like prote 22.8 96 0.0021 25.6 3.1 23 102-124 22-44 (256)
17 PF02607 B12-binding_2: B12 bi 21.8 1.6E+02 0.0034 19.1 3.5 30 106-135 1-30 (79)
18 TIGR02209 ftsL_broad cell divi 21.7 99 0.0021 20.6 2.5 45 86-133 26-71 (85)
19 PF04333 VacJ: VacJ like lipop 21.6 34 0.00073 27.9 0.2 19 10-30 74-92 (200)
20 PF11159 DUF2939: Protein of u 21.2 1E+02 0.0022 21.4 2.6 39 82-120 13-52 (95)
21 PF01390 SEA: SEA domain; Int 21.0 2.1E+02 0.0045 19.4 4.1 31 90-121 18-48 (107)
22 PF02757 YLP: YLP motif; Inte 20.9 34 0.00073 15.4 0.1 7 78-84 2-8 (9)
No 1
>KOG2140|consensus
Probab=99.96 E-value=2e-30 Score=233.95 Aligned_cols=73 Identities=60% Similarity=1.000 Sum_probs=69.9
Q ss_pred CCCCccCCCCCCCCCCHHHHHHHhhhccCCCchHHHHHHHHHHHHHHhhhhhhccCCcHHHHHHHHHHhhcCC
Q psy7794 67 TSTNILSSKTGGAYIPPAKLKLMQQSISDKSSVEYQRISWETLKKSIHGSVNKVNTGNIGIIARKLFQENIFD 139 (139)
Q Consensus 67 sssdslsSr~GG~YIpp~kl~~~~~~~~d~~s~eyQR~~We~LkksInglvNkvn~sNI~~iv~ELF~eNlir 139 (139)
++.+++.+|+||+|||||||++||++++|++|.+||||+||+|||+|||||||||.+||++|++|||+|||||
T Consensus 122 ~P~~l~~trtGG~YIPPaKL~~mq~qi~Dk~s~~yQRmnWEalkksInglInkvn~sNi~~ii~eLfqeNiir 194 (739)
T KOG2140|consen 122 DPLDLLRTRTGGAYIPPAKLRMMQAQITDKNSIEYQRMNWEALKKSINGLINKVNASNIQEIIRELFQENIIR 194 (739)
T ss_pred CHHHHhhccCCCeecCHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHh
Confidence 3446788999999999999999999999999999999999999999999999999999999999999999997
No 2
>KOG2140|consensus
Probab=99.69 E-value=5.6e-18 Score=153.82 Aligned_cols=49 Identities=57% Similarity=0.966 Sum_probs=44.2
Q ss_pred CCCCCCCCCCCCcceechhhhhcccccccccccCcchhhhhhhcccCCccccc
Q psy7794 1 MEGVFPRDNPKNTRFAINFFTSIGLGGLTRYYGDSGRKDQRDSTKQTPQNKQK 53 (139)
Q Consensus 1 ~~glfp~d~~~~~rfaiN~ft~iglg~lt~~~~~~~~~~~~~~~~~~~~~k~~ 53 (139)
|.||||.|||+|+||||||||+||||+||+ +||++|...+|...+.++.
T Consensus 611 l~glFP~dnp~n~RfsINfFTsIGLGgLTe----elRe~L~~~pk~~~a~~eq 659 (739)
T KOG2140|consen 611 LEGLFPRDNPRNTRFSINFFTSIGLGGLTE----ELREYLKNMPKVEDAEKEQ 659 (739)
T ss_pred hhccCcCCCcccceeeeehhhhhccccchH----HHHHHHHhcchhhhhhHHH
Confidence 689999999999999999999999999997 6899999998888766643
No 3
>KOG2141|consensus
Probab=96.88 E-value=0.0019 Score=61.40 Aligned_cols=53 Identities=28% Similarity=0.498 Sum_probs=43.5
Q ss_pred CCCCCCCCCCHHHHHHHhhhccCCCchHHHHHHHHHHHHHHhhhhhhccCCcHHHHHHHHH
Q psy7794 73 SSKTGGAYIPPAKLKLMQQSISDKSSVEYQRISWETLKKSIHGSVNKVNTGNIGIIARKLF 133 (139)
Q Consensus 73 sSr~GG~YIpp~kl~~~~~~~~d~~s~eyQR~~We~LkksInglvNkvn~sNI~~iv~ELF 133 (139)
.+-+|..||||+=-+.|. +++++++.|| |++.+||++||++.+||-.|+.+|=
T Consensus 291 ~~~s~sKYvPPslRkkl~---~~~~sE~l~r-----l~rkv~g~LNKLSdaNi~~I~~~i~ 343 (822)
T KOG2141|consen 291 KINSSSKYVPPSLRKKLE---TSSESEQLQR-----LRRKVNGSLNKLSDANIIKIIAGIA 343 (822)
T ss_pred ccccccccCCHHHHHHhc---CccchHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355677899999655554 6778888887 6899999999999999999988763
No 4
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=70.23 E-value=6.8 Score=26.08 Aligned_cols=31 Identities=19% Similarity=0.341 Sum_probs=28.6
Q ss_pred HHHHHHHHhhhhhhccCCcHHHHHHHHHHhhcC
Q psy7794 106 WETLKKSIHGSVNKVNTGNIGIIARKLFQENIF 138 (139)
Q Consensus 106 We~LkksInglvNkvn~sNI~~iv~ELF~eNli 138 (139)
|+.|++.=..||..++ ++..++..|++.|++
T Consensus 1 ~~~L~~~r~~Lv~~l~--~~~~ild~L~~~~vl 31 (85)
T PF00619_consen 1 QELLRKNRQELVEDLD--DLDDILDHLLSRGVL 31 (85)
T ss_dssp HHHHHHTHHHHHHHSS--HHHHHHHHHHHTTSS
T ss_pred CHHHHHhHHHHHHHhC--cHHHHHHHHHHCCCC
Confidence 8889999999999999 999999999999886
No 5
>PF15359 CDV3: Carnitine deficiency-associated protein 3
Probab=56.09 E-value=9.3 Score=29.35 Aligned_cols=16 Identities=38% Similarity=0.627 Sum_probs=12.1
Q ss_pred CCCCCCCCCHHHHHHH
Q psy7794 74 SKTGGAYIPPAKLKLM 89 (139)
Q Consensus 74 Sr~GG~YIpp~kl~~~ 89 (139)
..+||+|+||+..-+.
T Consensus 83 ~~~~gvY~PP~~R~~~ 98 (129)
T PF15359_consen 83 ATTSGVYRPPAARNTT 98 (129)
T ss_pred CCCCceecCccccccc
Confidence 5689999999874443
No 6
>PF09055 Sod_Ni: Nickel-containing superoxide dismutase; InterPro: IPR014123 This entry represents nickel-dependent superoxide dismutase (NiSOD) (1.15.1.1 from EC), a SOD enzyme that uses nickel, rather than iron, manganese, copper, or zinc. All SOD enzymes catalyse the dismutation of toxic superoxide radical anions to oxygen and hydrogen peroxide in order to protect cells from oxidative damage. The catalytic cycle of NiSOD consists of two half-reactions, each initiated by the successive approach of substrate to the metal centre. The first (reductive) phase involves Ni(III) reduction to Ni(II), and the second (oxidative) phase involves the metal reoxidation back to its resting state []. NiSOD has a novel SOD fold and assembly, consisting of a hexameric assembly of 4-helix bundles of up-and-down topology, which contains a 9-residue nickel-hook structural motif that is critical for metal binding and catalysis []. A gene for a required protease (NiSOD maturation protease; IPR014124 from INTERPRO) is adjacent to the NiSOD gene. ; GO: 0004784 superoxide dismutase activity, 0016151 nickel ion binding, 0016209 antioxidant activity; PDB: 1T6U_K 1T6I_C 1T6Q_C 3G50_A 3G4Z_C 3G4X_A 1Q0D_G 1Q0F_K 1Q0G_H 1Q0K_L ....
Probab=53.05 E-value=26 Score=27.06 Aligned_cols=38 Identities=21% Similarity=0.401 Sum_probs=21.8
Q ss_pred CCCCCCC-HHHHHHH-----hhhccCCCch------HHHHHHHHHHHHHH
Q psy7794 76 TGGAYIP-PAKLKLM-----QQSISDKSSV------EYQRISWETLKKSI 113 (139)
Q Consensus 76 ~GG~YIp-p~kl~~~-----~~~~~d~~s~------eyQR~~We~LkksI 113 (139)
.+|+|-| ++|..++ .+.+.+.+.. ..|+..|-..|..=
T Consensus 11 PCGIYDp~~Ari~a~ti~k~~~~i~~l~~~~~~~~~~nq~~R~i~~KE~h 60 (128)
T PF09055_consen 11 PCGIYDPAQARIAALTIKKMMKKINELEDKSTDAQDQNQLTRWIMIKEEH 60 (128)
T ss_dssp S-S---THHHHHHHHHHHHHHHHHCC---H-------HHHHHHHHHHHHH
T ss_pred CCcCCCcHHHHHHHHHHHHHHHHHHHcCCccchhhhHHHHHHHHHHHHHH
Confidence 6899999 9998774 4555543322 27899998887653
No 7
>TIGR01110 mdcA malonate decarboxylase, alpha subunit. This model describes malonate decarboxylase alpha subunit, from both the water-soluble form as found in Klebsiella pneumoniae and the form couple to sodium ion pumping in Malonomonas rubra. Malonate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases. Essentially, it couples the energy derived from decarboxylation of a carboxylic acid substrate to move Na+ ion across the bilayer. Functional malonate decarboylase is a multi subunit protein. The alpha subunit enzymatically performs the transfer of malonate (substrate) to an acyl carrier protein subunit for subsequent decarboxylation, hence the name: acetyl-S-acyl carrier protein:malonate carrier protein-SH transferase.
Probab=41.24 E-value=5.5 Score=37.25 Aligned_cols=19 Identities=37% Similarity=0.706 Sum_probs=15.4
Q ss_pred CCccCCCCCCCCCCHHHHH
Q psy7794 69 TNILSSKTGGAYIPPAKLK 87 (139)
Q Consensus 69 sdslsSr~GG~YIpp~kl~ 87 (139)
...+-.++||-|-||+|.|
T Consensus 523 ~~~l~~~s~gly~pp~~fr 541 (543)
T TIGR01110 523 VKDLVEWSGGLYNPPARFR 541 (543)
T ss_pred HHHHHHhcCCCcCChhhcc
Confidence 3455579999999999976
No 8
>PF15586 Imm47: Immunity protein 47
Probab=37.83 E-value=51 Score=24.61 Aligned_cols=53 Identities=17% Similarity=0.181 Sum_probs=36.4
Q ss_pred CCHHHHHHHhhhcc---CCCchHHHHHHHHHHHHHHhhhhhhccCCcHHHHHHHHH
Q psy7794 81 IPPAKLKLMQQSIS---DKSSVEYQRISWETLKKSIHGSVNKVNTGNIGIIARKLF 133 (139)
Q Consensus 81 Ipp~kl~~~~~~~~---d~~s~eyQR~~We~LkksInglvNkvn~sNI~~iv~ELF 133 (139)
.-|.-|..+...-. ....--.=+-.|+++++.|+.+|++.+.++-..++..|-
T Consensus 50 cTP~wL~~~~~~~~~~~gr~~LIv~~yd~~~I~~~i~~~i~~c~~~~W~~~~~kLs 105 (116)
T PF15586_consen 50 CTPKWLSKNCWKPGILWGRHMLIVEEYDYDEIKKTIERIIESCEGDDWDEIAEKLS 105 (116)
T ss_pred EcHHHHHHhhcCCcceeccceEEEecCCHHHHHHHHHHHHHHccCCCHHHHHHHHH
Confidence 45777776554311 111111122389999999999999999999999988774
No 9
>PF05214 Baculo_p33: Baculovirus P33; InterPro: IPR007879 This family consists of a series of baculoviral 33 kDa early protein homologues.; PDB: 3QZY_B 3P0K_A.
Probab=35.81 E-value=21 Score=30.48 Aligned_cols=18 Identities=39% Similarity=0.780 Sum_probs=8.5
Q ss_pred CCchHHHHHHHHHHHHHH
Q psy7794 96 KSSVEYQRISWETLKKSI 113 (139)
Q Consensus 96 ~~s~eyQR~~We~LkksI 113 (139)
+....||||.|...||..
T Consensus 231 k~~~~~qrM~W~~YKklL 248 (250)
T PF05214_consen 231 KPPNNYQRMEWSDYKKLL 248 (250)
T ss_dssp ---TT-----HHHHHHHH
T ss_pred CChhhcccccHHHHHHHh
Confidence 455679999999999975
No 10
>PF07159 DUF1394: Protein of unknown function (DUF1394); InterPro: IPR009828 This family consists of several hypothetical eukaryotic proteins of around 320 residues in length. The function of this family is unknown.
Probab=34.62 E-value=52 Score=28.59 Aligned_cols=35 Identities=26% Similarity=0.356 Sum_probs=25.1
Q ss_pred CCCCCCCCHHHHHHHhhhccCCCchHHHHHHHHHHHHHHhhhh
Q psy7794 75 KTGGAYIPPAKLKLMQQSISDKSSVEYQRISWETLKKSIHGSV 117 (139)
Q Consensus 75 r~GG~YIpp~kl~~~~~~~~d~~s~eyQR~~We~LkksInglv 117 (139)
+.+|.-||- .+++.+.++.|+.+|++|.-.|..|-
T Consensus 41 rgas~~Ir~--------Ai~~Ps~ee~qe~aw~al~P~V~kLk 75 (303)
T PF07159_consen 41 RGASREIRQ--------AISNPSDEELQEKAWEALEPLVKKLK 75 (303)
T ss_pred cCchHHHHH--------HHcCCChHHHHHHHHHHHhhHHHHHH
Confidence 445556653 34667778899999999987776654
No 11
>PRK15091 ABC transporter outer membrane lipoprotein; Provisional
Probab=33.78 E-value=8.9 Score=32.42 Aligned_cols=20 Identities=45% Similarity=0.700 Sum_probs=16.9
Q ss_pred CCCcceechhhhhccccccccc
Q psy7794 10 PKNTRFAINFFTSIGLGGLTRY 31 (139)
Q Consensus 10 ~~~~rfaiN~ft~iglg~lt~~ 31 (139)
.+..||.|| |-+|+|+|-+-
T Consensus 98 ~~~~RF~vN--TT~Gi~Gl~Dv 117 (251)
T PRK15091 98 VHFTRFFLN--TLLGMGGLIDV 117 (251)
T ss_pred hhcceeEee--cccccceeeeh
Confidence 347899999 99999998864
No 12
>PF11712 Vma12: Endoplasmic reticulum-based factor for assembly of V-ATPase; InterPro: IPR021013 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterised member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum [].
Probab=33.66 E-value=80 Score=23.73 Aligned_cols=16 Identities=13% Similarity=0.252 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHhhhhh
Q psy7794 103 RISWETLKKSIHGSVN 118 (139)
Q Consensus 103 R~~We~LkksInglvN 118 (139)
...|...|+.|--++|
T Consensus 69 ~~~~k~~~~qls~v~N 84 (142)
T PF11712_consen 69 AQELKSVKRQLSTVFN 84 (142)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3457777777766655
No 13
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=25.57 E-value=90 Score=23.24 Aligned_cols=57 Identities=25% Similarity=0.275 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHh-----hhccCCCchHHHHHHHHHHHHHHhhhhhhcc------CCcHHHHHHHHHHhh
Q psy7794 79 AYIPPAKLKLMQ-----QSISDKSSVEYQRISWETLKKSIHGSVNKVN------TGNIGIIARKLFQEN 136 (139)
Q Consensus 79 ~YIpp~kl~~~~-----~~~~d~~s~eyQR~~We~LkksInglvNkvn------~sNI~~iv~ELF~eN 136 (139)
..|+|..+..+- ..++.+...+.=+..|+. .+++..+|.+.+ .+-|..+|.+.+.+|
T Consensus 38 ~~i~~~~l~~li~l~~~~~Is~~~ak~ll~~~~~~-~~~~~~ii~~~~l~~i~d~~el~~~v~~vi~~n 105 (148)
T PF02637_consen 38 SPISPEHLAELINLLEDGKISKKSAKELLRELLEN-GKSPEEIIEENGLWQISDEEELEALVEEVIAEN 105 (148)
T ss_dssp SSSTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH-TS-HHHHHHHTT---B--CCHHHHHHHHHHHC-
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHc-CCCHHHHHHHcCCCcCCCHHHHHHHHHHHHHHC
Confidence 479999998863 345555566777788888 999999998863 345778888888776
No 14
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=24.16 E-value=1.5e+02 Score=19.61 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=28.7
Q ss_pred CCHHHHHHHhhhccCCCchHHHHHHHHHHHHHHhhhhhhccCCcHHHHHHHHHH
Q psy7794 81 IPPAKLKLMQQSISDKSSVEYQRISWETLKKSIHGSVNKVNTGNIGIIARKLFQ 134 (139)
Q Consensus 81 Ipp~kl~~~~~~~~d~~s~eyQR~~We~LkksInglvNkvn~sNI~~iv~ELF~ 134 (139)
.||..++.+-+.+ +...|++.++.++.++.. -=+..+|+.+|+.
T Consensus 3 p~~~~i~~i~~~~--------~~~~~~~~~~~~~~l~~~--G~s~~~Il~~l~~ 46 (89)
T PF08542_consen 3 PPPEVIEEILESC--------LNGDFKEARKKLYELLVE--GYSASDILKQLHE 46 (89)
T ss_dssp --HHHHHHHHHHH--------HHTCHHHHHHHHHHHHHT--T--HHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--------HhCCHHHHHHHHHHHHHc--CCCHHHHHHHHHH
Confidence 4666666655433 233888999999999887 5567778877764
No 15
>cd08806 CARD_CARD14_CARMA2 Caspase activation and recruitment domain of CARD14-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD14, also known as BIMP2 or CARMA2 (caspase recruitment domain-containing membrane-associated guanylate kinase protein 2). CARD14 has been identified as a novel member of the MAGUK (membrane-associated guanylate kinase) family that functions as upstream activators of BCL10 (B-cell lymphoma 10) and NF-kB signaling. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways
Probab=24.05 E-value=68 Score=23.35 Aligned_cols=30 Identities=20% Similarity=0.403 Sum_probs=25.7
Q ss_pred HHHHHHHHhhhhhhccCCcHHHHHHHHHHhhcC
Q psy7794 106 WETLKKSIHGSVNKVNTGNIGIIARKLFQENIF 138 (139)
Q Consensus 106 We~LkksInglvNkvn~sNI~~iv~ELF~eNli 138 (139)
|+.|+..=..|+.-++++ .+++.|.+|.|+
T Consensus 2 w~~le~~R~~L~~~l~p~---~l~pYLrQ~~IL 31 (86)
T cd08806 2 WEMMEDHRHRIVRGIRPS---RLTPYLRQAKVL 31 (86)
T ss_pred hHHHHHHHHHHHHhhcHh---hccHHHHHcCCC
Confidence 999999999999888854 488999999875
No 16
>PF07817 GLE1: GLE1-like protein; InterPro: IPR012476 The members of this family are sequences that are similar to the human protein GLE1 (O75458 from SWISSPROT). This protein is localised at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm []. ; GO: 0016973 poly(A)+ mRNA export from nucleus, 0005643 nuclear pore; PDB: 3PEV_B 3RRN_B 3PEU_B 3RRM_B.
Probab=22.78 E-value=96 Score=25.60 Aligned_cols=23 Identities=17% Similarity=0.218 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHhhhhhhccCCc
Q psy7794 102 QRISWETLKKSIHGSVNKVNTGN 124 (139)
Q Consensus 102 QR~~We~LkksInglvNkvn~sN 124 (139)
=+..|..+||.||.-||.++.++
T Consensus 22 lKk~~~~~kr~I~~~vgQls~~~ 44 (256)
T PF07817_consen 22 LKKLRFDLKRKINPKVGQLSNSS 44 (256)
T ss_dssp HHHHHHHHHHHHCCHHHC--SBH
T ss_pred HHHHHHHhhhhCcCcHhhccCcH
Confidence 46689999999999999999876
No 17
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=21.79 E-value=1.6e+02 Score=19.09 Aligned_cols=30 Identities=10% Similarity=0.258 Sum_probs=23.4
Q ss_pred HHHHHHHHhhhhhhccCCcHHHHHHHHHHh
Q psy7794 106 WETLKKSIHGSVNKVNTGNIGIIARKLFQE 135 (139)
Q Consensus 106 We~LkksInglvNkvn~sNI~~iv~ELF~e 135 (139)
|+.+.+.+-..|-..+...+..++.+++..
T Consensus 1 ~~~~~~~l~~al~~~d~~~~~~~~~~~l~~ 30 (79)
T PF02607_consen 1 WEELIERLLDALLAGDEEEAEALLEEALAQ 30 (79)
T ss_dssp -HHHHHHHHHHHHTT-CCHHHHHHHHHHHC
T ss_pred ChHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence 888888888888888888888888888754
No 18
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=21.74 E-value=99 Score=20.63 Aligned_cols=45 Identities=13% Similarity=0.290 Sum_probs=29.9
Q ss_pred HHHHhhhccC-CCchHHHHHHHHHHHHHHhhhhhhccCCcHHHHHHHHH
Q psy7794 86 LKLMQQSISD-KSSVEYQRISWETLKKSIHGSVNKVNTGNIGIIARKLF 133 (139)
Q Consensus 86 l~~~~~~~~d-~~s~eyQR~~We~LkksInglvNkvn~sNI~~iv~ELF 133 (139)
.+.++.++.+ ..-.+.++..|++|+..|..+-+ .+.|..++++-|
T Consensus 26 ~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~---~~rIe~~Ar~~l 71 (85)
T TIGR02209 26 TRQLNNELQKLQLEIDKLQKEWRDLQLEVAELSR---HERIEKIAKKQL 71 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC---HHHHHHHHHHhc
Confidence 3444444333 22245678999999999998764 677888887644
No 19
>PF04333 VacJ: VacJ like lipoprotein; InterPro: IPR007428 Lipoproteins in Gram-negative microbes also act as structural stabilisers, forming non-covalent bonds with peptidoglycan on the outer membrane of the cell []. Following completion of the genomes of several Gram-negative prokaryotes, a putative lipoprotein, VacJ, has been discovered in the raw sequence open reading frames. Biochemical analysis of the Shigella flexneri VacJ protein revealed it to be essential for virulence, promoting spread of bacterial cells through the intercellular space of tissues []. Upon expression in the facultative intracellular microbe, host cells form membranous protrusions containing the pathogen, allowing it to move to the cytoplasm of the next target cell. As homologues of this lipoprotein have largely been found in obligate or facultative intracellular microbial genomes, it appears to be specific for that particular lifestyle []. ; GO: 0016020 membrane
Probab=21.62 E-value=34 Score=27.93 Aligned_cols=19 Identities=47% Similarity=0.805 Sum_probs=15.6
Q ss_pred CCCcceechhhhhcccccccc
Q psy7794 10 PKNTRFAINFFTSIGLGGLTR 30 (139)
Q Consensus 10 ~~~~rfaiN~ft~iglg~lt~ 30 (139)
..-.||+|| |.+|+|+|-+
T Consensus 74 ~~~~RF~iN--sT~Gl~Gl~D 92 (200)
T PF04333_consen 74 NELGRFLIN--STVGLGGLFD 92 (200)
T ss_pred Hhhhheeee--cchhccccee
Confidence 346799999 7889999876
No 20
>PF11159 DUF2939: Protein of unknown function (DUF2939); InterPro: IPR021330 This bacterial family of proteins has no known function.
Probab=21.20 E-value=1e+02 Score=21.36 Aligned_cols=39 Identities=15% Similarity=0.295 Sum_probs=28.7
Q ss_pred CHHHHHHHhhhccCCCchH-HHHHHHHHHHHHHhhhhhhc
Q psy7794 82 PPAKLKLMQQSISDKSSVE-YQRISWETLKKSIHGSVNKV 120 (139)
Q Consensus 82 pp~kl~~~~~~~~d~~s~e-yQR~~We~LkksInglvNkv 120 (139)
|=.=+.++++.+.+.+... -++..|.++|.||..-+++.
T Consensus 13 Py~al~~i~~Ai~~~D~~~l~~~VD~~avr~slk~ql~~~ 52 (95)
T PF11159_consen 13 PYYALYQIRQAIQAHDAAALARYVDFPAVRASLKDQLNAE 52 (95)
T ss_pred HHHHHHHHHHHHHHcCHHHHHHHcCHHHHHHHHHHHHHHH
Confidence 3344677777777766666 47789999999998877654
No 21
>PF01390 SEA: SEA domain; InterPro: IPR000082 SEA is an extracellular domain associated with O-glycosylation []. Proteins found to contain SEA-modules include, agrin, enterokinase, 63 kDa Strongylocentrotus purpuratus (Purple sea urchin) sperm protein, perlecan (heparan sulphate proteoglycan core, mucin 1 and the cell surface antigen, 114/A10, and two functionally uncharacterised, probably extracellular, Caenorhabditis elegans proteins. Despite the functional diversity of these adhesive proteins, a common denominator seems to be their existence in heavily glycosylated environments. In addition, the better characterised proteins all contain O-glycosidic-linked carbohydrates such as heparan sulphate that contribute considerably to their molecular masses. The common module might regulate or assist binding to neighbouring carbohydrate moieties. Enterokinase, the initiator of intestinal digestion, is a mosaic protease composed of a distinctive assortment of domains []. ; PDB: 2ACM_B 1IVZ_A 2E7V_A.
Probab=20.96 E-value=2.1e+02 Score=19.37 Aligned_cols=31 Identities=16% Similarity=0.339 Sum_probs=22.5
Q ss_pred hhhccCCCchHHHHHHHHHHHHHHhhhhhhcc
Q psy7794 90 QQSISDKSSVEYQRISWETLKKSIHGSVNKVN 121 (139)
Q Consensus 90 ~~~~~d~~s~eyQR~~We~LkksInglvNkvn 121 (139)
..+..|++|.+||-+ ...+...|+.+..+..
T Consensus 18 ~~~l~d~~S~~f~~l-~~~i~~~i~~~~~~~~ 48 (107)
T PF01390_consen 18 TPDLADPNSPEFQEL-ARDIEDQINSVFRNSS 48 (107)
T ss_dssp -GGGG-TTSHHHHHH-HHHHHHHHHHHHHTST
T ss_pred chhcCCCCCHHHHHH-HHHHHHHHHHhhccCc
Confidence 456789999999988 4567777887777653
No 22
>PF02757 YLP: YLP motif; InterPro: IPR004019 The YLP motif is found in one or several copies in various Drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues and its presence in the human Erbb-2 and ErbB-4 receptor protein-tyrosine kinases (2.7.10.1 from EC) may suggest it could be a substrate for tyrosine kinases. ErbBs (1-4) are single-pass transmembrane proteins that activate a wide variety of signalling pathways, including those involved in proliferation, migration, differentiation, survival, and apoptosis; they are frequently misregulated in cancer []. ErbB-2 is an essential component of a neuregulin-receptor complex, although neuregulins do not interact with it alone. ErbB-4 specifically binds and is activated by neuregulins, NRG-2, NRG-3, heparin-binding EGF-like growth factor, betacellulin and NTAK [].
Probab=20.89 E-value=34 Score=15.40 Aligned_cols=7 Identities=43% Similarity=1.251 Sum_probs=5.1
Q ss_pred CCCCCHH
Q psy7794 78 GAYIPPA 84 (139)
Q Consensus 78 G~YIpp~ 84 (139)
..|.||.
T Consensus 2 ~eYLpP~ 8 (9)
T PF02757_consen 2 NEYLPPV 8 (9)
T ss_pred ccccCCC
Confidence 4688884
Done!