Query 020816
Match_columns 321
No_of_seqs 155 out of 323
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:23:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020816.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020816hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3077 Uncharacterized conser 100.0 6.2E-46 1.3E-50 347.2 12.2 182 6-187 60-254 (260)
2 PF03556 Cullin_binding: Culli 100.0 8.9E-43 1.9E-47 292.5 8.9 114 69-182 1-117 (117)
3 KOG3077 Uncharacterized conser 98.0 6.5E-07 1.4E-11 85.1 -0.9 166 83-253 74-251 (260)
4 cd05024 S-100A10 S-100A10: A s 41.3 1.1E+02 0.0023 25.2 6.3 68 10-99 8-78 (91)
5 cd05026 S-100Z S-100Z: S-100Z 39.7 1.3E+02 0.0028 23.9 6.5 69 10-96 10-80 (93)
6 PF04659 Arch_fla_DE: Archaeal 37.4 63 0.0014 27.0 4.4 53 127-179 21-87 (99)
7 PF04444 Dioxygenase_N: Catech 34.3 55 0.0012 25.9 3.5 45 126-180 11-56 (74)
8 PF06535 RGM_N: Repulsive guid 33.3 12 0.00026 34.0 -0.5 21 155-176 111-131 (161)
9 PF08671 SinI: Anti-repressor 33.1 59 0.0013 21.7 2.9 28 128-155 3-30 (30)
10 PRK10391 oriC-binding nucleoid 32.0 67 0.0014 25.6 3.5 33 61-93 8-41 (71)
11 cd05030 calgranulins Calgranul 29.0 2.6E+02 0.0056 21.9 6.6 72 10-98 8-80 (88)
12 cd05023 S-100A11 S-100A11: S-1 27.2 2.9E+02 0.0064 21.9 6.7 71 10-99 9-82 (89)
13 KOG2223 Uncharacterized conser 25.3 1.2E+02 0.0025 32.2 4.9 29 91-123 476-504 (586)
14 PRK10945 gene expression modul 23.2 1.3E+02 0.0028 24.1 3.8 38 47-93 7-45 (72)
15 cd03462 1,2-CCD chlorocatechol 20.0 3.2E+02 0.007 26.3 6.5 50 126-185 12-61 (247)
No 1
>KOG3077 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=6.2e-46 Score=347.23 Aligned_cols=182 Identities=26% Similarity=0.493 Sum_probs=161.3
Q ss_pred CCChhHHHHHHHHHhccccc-------ccccccccCccCCCCCCcccccHHHHH-----HHHhhhhhhhhccccchHHHH
Q 020816 6 LSNPLDIFEIYRRFCEIKSQ-------NADVCIEDSYREDKESPKAKFSREALA-----ELFNLVELTVHIRIFVFDELF 73 (321)
Q Consensus 6 ~~~~~dL~~lF~rY~D~~s~-------i~~lC~dLgv~~d~dVm~a~iSre~~t-----~L~~~~dg~~~lgc~tiDsLk 73 (321)
..+...++++|.+|+|+..+ +.+||+||||+|++.+++.-.++.+++ ..-+|..|+..+||+|+|+|+
T Consensus 60 ~~s~~~l~~~f~~y~d~~d~~~i~~dgi~~fc~dlg~~p~~i~~LvlAwkl~A~~m~~Fsr~ef~~g~~~l~~dS~d~lq 139 (260)
T KOG3077|consen 60 RVSEKRLEELFNQYKDPDDDNLIGPDGIEKFCEDLGVEPEDISVLVLAWKLGAATMCEFSREEFLKGMTALGCDSIDKLQ 139 (260)
T ss_pred cccHHHHHHHHHHhcCcccccccChHHHHHHHHHhCCCchhHHHHHHHHHhccchhhhhhHHHHHHHHHHcCCCcHHHHH
Confidence 35567899999999999884 999999999999654443322222211 122469999999999999999
Q ss_pred HHHHhcc-ccCChhhhhhhhhhhhhcccccCcccccHHHHHHHHHHhhcCccccHHHHHHHHHhhcCCccCHHhHHHHHH
Q 020816 74 KLMSQLD-LMGDFSEFSRFYDFVFFMCRENGQKNITVSRAVTAWRLVLAGRFRLLNQWCDFVERNQRHNISEDTWQQVLA 152 (321)
Q Consensus 74 kLl~~L~-l~~D~~~Fk~fY~FtF~fare~gQKsL~letAIa~W~LLL~~~f~~Ld~W~~FL~~~~~k~ISkDtW~q~l~ 152 (321)
..++.+. .++|.++|+.+|+|||+|++++|||+|++++||+||+|||+.++|+|++|++||++++++.|+||||+|+|+
T Consensus 140 ~~l~~l~~~l~d~~~Fk~iY~faf~fa~e~~qk~Ld~~~ai~~w~ll~~~~~pll~~w~~FL~~~~~~~~~KDtW~~~l~ 219 (260)
T KOG3077|consen 140 QRLDFLRSVLKDLEKFKSIYRFAFNFAKEPGQKSLDLETAISLWKLLFGQTPPLLDQWIQFLKDSPNRAISKDTWNLLLD 219 (260)
T ss_pred HHHHHHHHHHccHHHhhHHHHhhhhhccCcCcCcCCHHHHHHHHHHHhCCCCchHHHHHHHHHhCcCcccCcccHHHHHH
Confidence 9999998 566999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcccCCCCCCCCCCchHHHHHHHHHHHhhCC
Q 020816 153 FSRCVHENLEGYDPEGAWPVLIDDFVEHMYRVSGS 187 (321)
Q Consensus 153 F~~~v~~dls~YDe~gAWP~LIDEFVE~~r~~~gs 187 (321)
|++++++|+|||||+||||+||||||||.|.+...
T Consensus 220 Fs~~i~~dlSnYDeegAWP~liDeFVe~~r~~~~~ 254 (260)
T KOG3077|consen 220 FSKTIDPDLSNYDEEGAWPVLIDEFVEYLRDKQSN 254 (260)
T ss_pred HHHhcCccccCccccccchHHHHHHHHHHHHhccC
Confidence 99999999999999999999999999999988754
No 2
>PF03556 Cullin_binding: Cullin binding; InterPro: IPR005176 The eukaryotic defective in cullin neddylation (DCN) protein family, may contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes. These multi-protein complexes are required for polyubiquitination and subsequent degradation of target proteins by the 26S proteasome []. Proteins in the DCN family include: Yeast DCN1. Vertebrate DCN1-like protein 1. Vertebrate DCN1-like protein 2. Vertebrate DCN1-like protein 4. This entry represents a domain found within DCN family proteins. Its function is unknown but it has been suggested that it has the features of a basic helix-loop-helix leucine zipper (bHLH-ZIP) domain [].It is often found in association with a UBA-like domain (IPR009060 from INTERPRO).; PDB: 3TDI_A 2IS9_A 3O6B_E 3O2P_A 3BQ3_A 3TDZ_A 3TDU_B.
Probab=100.00 E-value=8.9e-43 Score=292.55 Aligned_cols=114 Identities=44% Similarity=0.880 Sum_probs=102.8
Q ss_pred hHHHHHHHHhcc--ccCChhhhhhhhhhhhhcccccCcccccHHHHHHHHHHhhcCc-cccHHHHHHHHHhhcCCccCHH
Q 020816 69 FDELFKLMSQLD--LMGDFSEFSRFYDFVFFMCRENGQKNITVSRAVTAWRLVLAGR-FRLLNQWCDFVERNQRHNISED 145 (321)
Q Consensus 69 iDsLkkLl~~L~--l~~D~~~Fk~fY~FtF~fare~gQKsL~letAIa~W~LLL~~~-f~~Ld~W~~FL~~~~~k~ISkD 145 (321)
|++|++.+++|. +.+|+++|++||+|||+|+|++|||+|++|+||+||+|||+++ ++++++|++||+++++++||||
T Consensus 1 I~~lk~~l~~l~~~l~~d~~~F~~~Y~f~F~~~~~~~qr~l~~e~Ai~~W~llf~~~~~~~l~~w~~Fl~~~~~k~IskD 80 (117)
T PF03556_consen 1 IDKLKQKLPELRKELRSDPEYFKKFYRFTFDFAREEGQRSLPLETAIAYWRLLFSGRFFPLLDSWIEFLEEKYKKAISKD 80 (117)
T ss_dssp HHHHHHCHHHHHHHCCHSHHHHHHHHHHHHHHHS-TT-SSEEHHHHHHHHHHHTTTTSSCCHHHHHHHHHHCT-SEEEHH
T ss_pred CHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHhCCcccCCCCHHHHHHHHHHHcCCCCcHHHHHHHHHHHHcCCcCcChh
Confidence 678888899887 6779999999999999999999999999999999999999988 8999999999999999999999
Q ss_pred hHHHHHHHHhhhcccCCCCCCCCCCchHHHHHHHHHH
Q 020816 146 TWQQVLAFSRCVHENLEGYDPEGAWPVLIDDFVEHMY 182 (321)
Q Consensus 146 tW~q~l~F~~~v~~dls~YDe~gAWP~LIDEFVE~~r 182 (321)
||+|+++|++++++++++|||+||||+||||||||+|
T Consensus 81 ~W~~~l~F~~~~~~dls~Yde~~AWP~liDeFVe~~r 117 (117)
T PF03556_consen 81 TWNQFLDFFKTVDEDLSNYDEEGAWPSLIDEFVEWLR 117 (117)
T ss_dssp HHHHHHHHHHH-HCCHCC--TTSSS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCccccCCCCCCCCcHHHHHHHHHhC
Confidence 9999999999999999999999999999999999997
No 3
>KOG3077 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.05 E-value=6.5e-07 Score=85.12 Aligned_cols=166 Identities=16% Similarity=0.021 Sum_probs=111.6
Q ss_pred CCh-hhhhhhhhhhhhcccccCcccccHHHHHHHHHHhhcCccccHHHHHHHHHhhcCCccCHHhHHHHHHHHhhhcccC
Q 020816 83 GDF-SEFSRFYDFVFFMCRENGQKNITVSRAVTAWRLVLAGRFRLLNQWCDFVERNQRHNISEDTWQQVLAFSRCVHENL 161 (321)
Q Consensus 83 ~D~-~~Fk~fY~FtF~fare~gQKsL~letAIa~W~LLL~~~f~~Ld~W~~FL~~~~~k~ISkDtW~q~l~F~~~v~~dl 161 (321)
.|| +.+.-+|...+.||.+-|+...++.++|-+|++. ++++..+..|.-+-.-+....+|-|+|++.|+|.+++..|+
T Consensus 74 ~d~~d~~~i~~dgi~~fc~dlg~~p~~i~~LvlAwkl~-A~~m~~Fsr~ef~~g~~~l~~dS~d~lq~~l~~l~~~l~d~ 152 (260)
T KOG3077|consen 74 KDPDDDNLIGPDGIEKFCEDLGVEPEDISVLVLAWKLG-AATMCEFSREEFLKGMTALGCDSIDKLQQRLDFLRSVLKDL 152 (260)
T ss_pred cCcccccccChHHHHHHHHHhCCCchhHHHHHHHHHhc-cchhhhhhHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHccH
Confidence 454 2389999999999999999999999999999999 88877787876665556678999999999999999998899
Q ss_pred CCCCCCCCCchHHHHHHHHHHHhhCCCCCCCcccCCCCCCCCccccC---------CCCCCCccCCCccccCCCCCcccc
Q 020816 162 EGYDPEGAWPVLIDDFVEHMYRVSGSKENPGLFCSCGDSESQSCGYE---------DSLPGLKIFPGLKRKSSGIEQDEM 232 (321)
Q Consensus 162 s~YDe~gAWP~LIDEFVE~~r~~~gs~~~~~~~~~~~~~~~~~~~~~---------~~~~g~~~~~g~~~~~~~~~~~~~ 232 (321)
+.|+.-.+||..|+. |..++..+....-...|-|+ .++..|... ++.-| +-++++++..+...+.++
T Consensus 153 ~~Fk~iY~faf~fa~--e~~qk~Ld~~~ai~~w~ll~-~~~~pll~~w~~FL~~~~~~~~~-KDtW~~~l~Fs~~i~~dl 228 (260)
T KOG3077|consen 153 EKFKSIYRFAFNFAK--EPGQKSLDLETAISLWKLLF-GQTPPLLDQWIQFLKDSPNRAIS-KDTWNLLLDFSKTIDPDL 228 (260)
T ss_pred HHhhHHHHhhhhhcc--CcCcCcCCHHHHHHHHHHHh-CCCCchHHHHHHHHHhCcCcccC-cccHHHHHHHHHhcCccc
Confidence 999888777766554 32222222111122223333 222222210 22333 788899888877666666
Q ss_pred ccccCCCccccchhhH--hhhhh
Q 020816 233 ESSDAHIPELTDHNHI--SKRSR 253 (321)
Q Consensus 233 ~~~~~~~~~~~~~~~~--~k~~~ 253 (321)
+.-|.+-.-....-.+ .+|.|
T Consensus 229 SnYDeegAWP~liDeFVe~~r~~ 251 (260)
T KOG3077|consen 229 SNYDEEGAWPVLIDEFVEYLRDK 251 (260)
T ss_pred cCccccccchHHHHHHHHHHHHh
Confidence 6655433222222222 77777
No 4
>cd05024 S-100A10 S-100A10: A subgroup of the S-100A10 domain found in proteins similar to S100A10. S100A10 is a member of the S100 family of EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A10 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. A unique feature of S100A10 is that it contains mutation in both of the calcium binding sites, making it calcium insensitive. S100A10 has been detected in brain, heart, gastrointestinal tract, kidney, liver, lung, spleen, testes, epidermis, aorta, and thymus. Structural data supports the homo- and hetero-dimeric as well as hetero-tetrameric nature of the protein. S100A10 has multiple binding partners in its calcium free state and is therefore involved in many diverse biological functions.
Probab=41.31 E-value=1.1e+02 Score=25.24 Aligned_cols=68 Identities=19% Similarity=0.251 Sum_probs=47.6
Q ss_pred hHHHHHHHHHhcccccccccccccCccCCCCCCcccccHHHHHHHH--hhhhhhhhccccchHHHHHHHHhccccCCh-h
Q 020816 10 LDIFEIYRRFCEIKSQNADVCIEDSYREDKESPKAKFSREALAELF--NLVELTVHIRIFVFDELFKLMSQLDLMGDF-S 86 (321)
Q Consensus 10 ~dL~~lF~rY~D~~s~i~~lC~dLgv~~d~dVm~a~iSre~~t~L~--~~~dg~~~lgc~tiDsLkkLl~~L~l~~D~-~ 86 (321)
..|..+|.+|++.. ..++|.++.+|. +++..... ...-+.+.+++..|+.-.|. -
T Consensus 8 ~~lI~~FhkYaG~~--------------------~tLsk~Elk~Ll~~Elp~~l~~--~~d~~~vd~im~~LD~n~Dg~v 65 (91)
T cd05024 8 EKMMLTFHKFAGEK--------------------NYLNRDDLQKLMEKEFSEFLKN--QNDPMAVDKIMKDLDDCRDGKV 65 (91)
T ss_pred HHHHHHHHHHcCCC--------------------CcCCHHHHHHHHHHHhHHHHcC--CCCHHHHHHHHHHhCCCCCCcC
Confidence 45899999999321 247788888885 46655433 34677888999999865553 6
Q ss_pred hhhhhhhhhhhcc
Q 020816 87 EFSRFYDFVFFMC 99 (321)
Q Consensus 87 ~Fk~fY~FtF~fa 99 (321)
.|.+|-.+.+..+
T Consensus 66 dF~EF~~Lv~~l~ 78 (91)
T cd05024 66 GFQSFFSLIAGLL 78 (91)
T ss_pred cHHHHHHHHHHHH
Confidence 7988888776544
No 5
>cd05026 S-100Z S-100Z: S-100Z domain found in proteins similar to S100Z. S100Z is a member of the S100 domain family within the EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100Z group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately.S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control. S100Z is normally expressed in various tissues, with its highest level of expression being in spleen and leukocytes. The function of S100Z remains unclear. Preliminary structural data suggests that S100Z is homodimer, however a heterodimer with S100P has been reported. S100Z is capable of binding calcium ions. When calcium binds to S110Z, the protein experiences a conformational change, which exposes hydrophobic surfac
Probab=39.68 E-value=1.3e+02 Score=23.90 Aligned_cols=69 Identities=20% Similarity=0.187 Sum_probs=41.8
Q ss_pred hHHHHHHHHHhcccccccccccccCccCCCCCCcc-cccHHHHHHHHhhhhhhhhccccchHHHHHHHHhccccCCh-hh
Q 020816 10 LDIFEIYRRFCEIKSQNADVCIEDSYREDKESPKA-KFSREALAELFNLVELTVHIRIFVFDELFKLMSQLDLMGDF-SE 87 (321)
Q Consensus 10 ~dL~~lF~rY~D~~s~i~~lC~dLgv~~d~dVm~a-~iSre~~t~L~~~~dg~~~lgc~tiDsLkkLl~~L~l~~D~-~~ 87 (321)
..|.++|.+|.+.+.. + .||+.++.++.+-.-+....+..+-+.+.+++..++...|. -.
T Consensus 10 ~~~~~~F~~~dd~dgd------------------g~~Is~~EL~~ll~~~~~~~~~~~~~~~~v~~i~~elD~n~dG~Id 71 (93)
T cd05026 10 DTLIRIFHNYSGKEGD------------------RYKLSKGELKELLQRELTDFLSSQKDPMLVDKIMNDLDSNKDNEVD 71 (93)
T ss_pred HHHHHHHHHHHccCCC------------------CCEECHHHHHHHHHHHhHHhcccccCHHHHHHHHHHhCCCCCCCCC
Confidence 4567779999976442 2 37788886665432222223334667899999998753332 45
Q ss_pred hhhhhhhhh
Q 020816 88 FSRFYDFVF 96 (321)
Q Consensus 88 Fk~fY~FtF 96 (321)
|.+|.....
T Consensus 72 f~EF~~l~~ 80 (93)
T cd05026 72 FNEFVVLVA 80 (93)
T ss_pred HHHHHHHHH
Confidence 666655443
No 6
>PF04659 Arch_fla_DE: Archaeal flagella protein ; InterPro: IPR006752 Archaeal flagella are unique motility structures, and the absence of bacterial structural motility genes in the complete genome sequences of flagellated archaeal species has always suggested that archaeal flagellar biogenesis is likely mediated by novel components. FlaD and FlaE, are present in the cell as membrane-associated proteins but are not major components of isolated flagellar filaments. Interestingly, flaD was found to encode two proteins, each translated from a separate ribosome binding site. This group of sequences contain the archaeal flaD and flaE proteins. The conserved region that defines these sequences is found in the N-teminal region of flaE but towards the C-terminal region of flaD [].; GO: 0001539 ciliary or flagellar motility
Probab=37.37 E-value=63 Score=27.01 Aligned_cols=53 Identities=21% Similarity=0.474 Sum_probs=39.7
Q ss_pred HHHHHHHHHhhc--------------CCccCHHhHHHHHHHHhhhcccCCCCCCCCCCchHHHHHHH
Q 020816 127 LNQWCDFVERNQ--------------RHNISEDTWQQVLAFSRCVHENLEGYDPEGAWPVLIDDFVE 179 (321)
Q Consensus 127 Ld~W~~FL~~~~--------------~k~ISkDtW~q~l~F~~~v~~dls~YDe~gAWP~LIDEFVE 179 (321)
+=.|++||-++. ...||.+.=.+++.|++-+..+-...+..+.|...+|+=+.
T Consensus 21 ~~eWLefLve~~G~~~~~~~L~YY~~igWISe~V~~~L~~~~~G~~~~~~~~~~~~~~~Lt~~DH~~ 87 (99)
T PF04659_consen 21 VFEWLEFLVERVGHNNAADALDYYESIGWISEEVREQLLKYLKGFKYDHDDFEWKPSWKLTIDDHIK 87 (99)
T ss_pred HHHHHHHHHHHcccccHHHHHHHHHHcCCcCHHHHHHHHHHHhCCCCCccccccCCCCCCCHHHHHH
Confidence 457999986541 35799999999999999876554444447889989987554
No 7
>PF04444 Dioxygenase_N: Catechol dioxygenase N terminus; InterPro: IPR007535 This domain is the N-terminal region of catechol, chlorocatechol or hydroxyquinol 1,2-dioxygenase proteins. This region is always found adjacent to the dioxygenase domain (IPR000627 from INTERPRO). Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes (IPR000486 from INTERPRO) use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) []. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Enzymes that belong to the intradiol family include catechol 1,2-dioxygenase (1,2-CTD) (1.13.11.1 from EC); protocatechuate 3,4-dioxygenase (3,4-PCD) (1.13.11.3 from EC); and chlorocatechol 1,2-dioxygenase (1.13.11.1 from EC) [].; GO: 0005506 iron ion binding, 0018576 catechol 1,2-dioxygenase activity, 0009712 catechol-containing compound metabolic process, 0055114 oxidation-reduction process; PDB: 3O6R_B 1S9A_A 3O6J_A 3O5U_B 3O32_B 3HHY_A 3HHX_A 3HJS_A 3HJQ_A 3HKP_A ....
Probab=34.28 E-value=55 Score=25.88 Aligned_cols=45 Identities=27% Similarity=0.550 Sum_probs=36.3
Q ss_pred cHHHHHHHHHhhcCCccCHHhHHHHHHHHhhhcccCCCCCCCCCCchHHHHH-HHH
Q 020816 126 LLNQWCDFVERNQRHNISEDTWQQVLAFSRCVHENLEGYDPEGAWPVLIDDF-VEH 180 (321)
Q Consensus 126 ~Ld~W~~FL~~~~~k~ISkDtW~q~l~F~~~v~~dls~YDe~gAWP~LIDEF-VE~ 180 (321)
++..-.+|+.+ ..||.|.|..-.+|+..+.. .+-||.|.|=| ++.
T Consensus 11 lv~~lh~~i~e---~~lT~~E~~~av~~L~~~G~-------~~E~~Ll~DvlGle~ 56 (74)
T PF04444_consen 11 LVRHLHDFIRE---VDLTEDEWWAAVDFLNRVGQ-------RNEFILLSDVLGLEH 56 (74)
T ss_dssp HHHHHHHHHHH---CT--HHHHHHHHHHHHHHHH-------TTHHHHHHHHTTHHH
T ss_pred HHHHHHHHHHH---hCCCHHHHHHHHHHHHHhcC-------CCchhhhhhhhccch
Confidence 45666777776 46999999999999999976 78899999999 888
No 8
>PF06535 RGM_N: Repulsive guidance molecule (RGM) N-terminus; InterPro: IPR010536 This entry represents the N-terminal region of several mammalian and one bird sequence from Gallus gallus (Chicken). All of the mammalian proteins are hypothetical and have no known function but Q8JG54 from SWISSPROT from the chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum [].
Probab=33.32 E-value=12 Score=33.99 Aligned_cols=21 Identities=38% Similarity=0.904 Sum_probs=14.3
Q ss_pred hhhcccCCCCCCCCCCchHHHH
Q 020816 155 RCVHENLEGYDPEGAWPVLIDD 176 (321)
Q Consensus 155 ~~v~~dls~YDe~gAWP~LIDE 176 (321)
+++++++.-=-.+||||+ ||.
T Consensus 111 RTF~~~fqTC~v~GAWPL-IdN 131 (161)
T PF06535_consen 111 RTFNDEFQTCKVEGAWPL-IDN 131 (161)
T ss_pred hhccCCceeeeeecceee-ecC
Confidence 455566666668999995 453
No 9
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=33.08 E-value=59 Score=21.74 Aligned_cols=28 Identities=14% Similarity=0.630 Sum_probs=22.1
Q ss_pred HHHHHHHHhhcCCccCHHhHHHHHHHHh
Q 020816 128 NQWCDFVERNQRHNISEDTWQQVLAFSR 155 (321)
Q Consensus 128 d~W~~FL~~~~~k~ISkDtW~q~l~F~~ 155 (321)
..|++.+.+-..-+||++.=+.||.|.+
T Consensus 3 ~EW~~Li~eA~~~Gls~eeir~FL~~~k 30 (30)
T PF08671_consen 3 EEWVELIKEAKESGLSKEEIREFLEFNK 30 (30)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 4799999888888999999999998853
No 10
>PRK10391 oriC-binding nucleoid-associated protein; Provisional
Probab=31.98 E-value=67 Score=25.64 Aligned_cols=33 Identities=24% Similarity=0.326 Sum_probs=24.4
Q ss_pred hhhccccchHHHHHHHHhcc-ccCChhhhhhhhh
Q 020816 61 TVHIRIFVFDELFKLMSQLD-LMGDFSEFSRFYD 93 (321)
Q Consensus 61 ~~~lgc~tiDsLkkLl~~L~-l~~D~~~Fk~fY~ 93 (321)
+.+-+|+|.|+|.+++.++. -++|++.-..||.
T Consensus 8 lkfRkcss~eTLEkv~e~~~y~L~~~~e~~~f~~ 41 (71)
T PRK10391 8 LKFRKISSLESLEKLFDHLNYTLTDDQEIINMYR 41 (71)
T ss_pred HHHHhcCcHHHHHHHHHHhhcccCCHHHHHHHHH
Confidence 45668999999999999997 3456555555554
No 11
>cd05030 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth.
Probab=28.97 E-value=2.6e+02 Score=21.91 Aligned_cols=72 Identities=14% Similarity=0.183 Sum_probs=42.0
Q ss_pred hHHHHHHHHHhcccccccccccccCccCCCCCCcccccHHHHHHHHhhhhhhhhccccchHHHHHHHHhccccCC-hhhh
Q 020816 10 LDIFEIYRRFCEIKSQNADVCIEDSYREDKESPKAKFSREALAELFNLVELTVHIRIFVFDELFKLMSQLDLMGD-FSEF 88 (321)
Q Consensus 10 ~dL~~lF~rY~D~~s~i~~lC~dLgv~~d~dVm~a~iSre~~t~L~~~~dg~~~lgc~tiDsLkkLl~~L~l~~D-~~~F 88 (321)
..|..+|.+|+..... . ..|++.++..+....-+-...++..-+.+..++..++...| .-.|
T Consensus 8 ~~~~~~f~~y~~~~~~-~----------------~~Is~~El~~ll~~~~g~~~t~~~~~~~v~~i~~~~D~d~dG~I~f 70 (88)
T cd05030 8 ETIINVFHQYSVRKGH-P----------------DTLYKKEFKQLVEKELPNFLKKEKNQKAIDKIFEDLDTNQDGQLSF 70 (88)
T ss_pred HHHHHHHHHHhccCCC-c----------------ccCCHHHHHHHHHHHhhHhhccCCCHHHHHHHHHHcCCCCCCcCcH
Confidence 4588999999987532 1 34778777666542111111144456778888888874333 2456
Q ss_pred hhhhhhhhhc
Q 020816 89 SRFYDFVFFM 98 (321)
Q Consensus 89 k~fY~FtF~f 98 (321)
.+|..+.-.+
T Consensus 71 ~eF~~~~~~~ 80 (88)
T cd05030 71 EEFLVLVIKV 80 (88)
T ss_pred HHHHHHHHHH
Confidence 6665554443
No 12
>cd05023 S-100A11 S-100A11: S-100A11 domain found in proteins similar to S100A11. S100A11 is a member of the S-100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A11 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100 proteins have also been associated with a variety of pathological events, including neoplastic transformation and neurodegenerative diseases such as Alzheimer's, usually via over expression of the protein. S100A11 is expressed in smooth muscle and other tissues and involves in calcium-dependent membrane aggregation, which is important for cell vesiculation . As is the case for many other S100 proteins, S
Probab=27.19 E-value=2.9e+02 Score=21.93 Aligned_cols=71 Identities=17% Similarity=0.303 Sum_probs=44.7
Q ss_pred hHHHHHHHHHhcccccccccccccCccCCCCCCcccccHHHHHHHHh--hhhhhhhccccchHHHHHHHHhccccCCh-h
Q 020816 10 LDIFEIYRRFCEIKSQNADVCIEDSYREDKESPKAKFSREALAELFN--LVELTVHIRIFVFDELFKLMSQLDLMGDF-S 86 (321)
Q Consensus 10 ~dL~~lF~rY~D~~s~i~~lC~dLgv~~d~dVm~a~iSre~~t~L~~--~~dg~~~lgc~tiDsLkkLl~~L~l~~D~-~ 86 (321)
..|.++|.+|.+.+..- ..+|+.++.++.+ ++..+. ...+-..+.+++..++...|. -
T Consensus 9 ~~l~~~F~~y~~~dg~~-----------------~~Ls~~Elk~ll~~e~~~~~~--~~~~~~~~~~ll~~~D~d~DG~I 69 (89)
T cd05023 9 ESLIAVFQKYAGKDGDS-----------------YQLSKTEFLSFMNTELASFTK--NQKDPGVLDRMMKKLDLNSDGQL 69 (89)
T ss_pred HHHHHHHHHHhccCCCc-----------------CeECHHHHHHHHHHhhhHhhc--CCCCHHHHHHHHHHcCCCCCCcC
Confidence 45889999998774421 2477888876653 333331 122346788888888754443 5
Q ss_pred hhhhhhhhhhhcc
Q 020816 87 EFSRFYDFVFFMC 99 (321)
Q Consensus 87 ~Fk~fY~FtF~fa 99 (321)
.|.+|.+.....+
T Consensus 70 ~f~EF~~l~~~l~ 82 (89)
T cd05023 70 DFQEFLNLIGGLA 82 (89)
T ss_pred cHHHHHHHHHHHH
Confidence 6888877666554
No 13
>KOG2223 consensus Uncharacterized conserved protein, contains TBC domain [Signal transduction mechanisms; General function prediction only]
Probab=25.34 E-value=1.2e+02 Score=32.23 Aligned_cols=29 Identities=17% Similarity=0.462 Sum_probs=22.2
Q ss_pred hhhhhhhcccccCcccccHHHHHHHHHHhhcCc
Q 020816 91 FYDFVFFMCRENGQKNITVSRAVTAWRLVLAGR 123 (321)
Q Consensus 91 fY~FtF~fare~gQKsL~letAIa~W~LLL~~~ 123 (321)
+|..+|.+- .|+|++|.|+..|.+++...
T Consensus 476 lidwiftly----skslpldlacRIwDvy~rdg 504 (586)
T KOG2223|consen 476 LIDWIFTLY----SKSLPLDLACRIWDVYCRDG 504 (586)
T ss_pred hHHHHHHHH----hccCChHHhhhhhheeeecc
Confidence 456666543 38999999999999988753
No 14
>PRK10945 gene expression modulator; Provisional
Probab=23.18 E-value=1.3e+02 Score=24.08 Aligned_cols=38 Identities=21% Similarity=0.347 Sum_probs=26.7
Q ss_pred cHHHHHHHHhhhhhhhhccccchHHHHHHHHhcc-ccCChhhhhhhhh
Q 020816 47 SREALAELFNLVELTVHIRIFVFDELFKLMSQLD-LMGDFSEFSRFYD 93 (321)
Q Consensus 47 Sre~~t~L~~~~dg~~~lgc~tiDsLkkLl~~L~-l~~D~~~Fk~fY~ 93 (321)
+++++ ++.+-+|.|.|+|.+++.++. -+.+ +.+..||.
T Consensus 7 tk~dy--------L~~fRrcss~eTLEkvie~~~~~L~~-~E~~~f~~ 45 (72)
T PRK10945 7 TKTDY--------LMRLRRCQTIDTLERVIEKNKYELSD-DELAVFYS 45 (72)
T ss_pred cHHHH--------HHHHHhcCcHHHHHHHHHHhhccCCH-HHHHHHHH
Confidence 66766 345568999999999999987 2333 55655554
No 15
>cd03462 1,2-CCD chlorocatechol 1,2-dioxygenases (1,2-CCDs) (type II enzymes) are homodimeric intradiol dioxygenases that degrade chlorocatechols via the addition of molecular oxygen and the subsequent cleavage between two adjacent hydroxyl groups. This reaction is part of the modified ortho-cleavage pathway which is a central oxidative bacterial pathway that channels chlorocatechols, derived from the degradation of chlorinated benzoic acids, phenoxyacetic acids, phenols, benzenes, and other aromatics into the energy-generating tricarboxylic acid pathway.
Probab=20.05 E-value=3.2e+02 Score=26.33 Aligned_cols=50 Identities=22% Similarity=0.484 Sum_probs=40.2
Q ss_pred cHHHHHHHHHhhcCCccCHHhHHHHHHHHhhhcccCCCCCCCCCCchHHHHHHHHHHHhh
Q 020816 126 LLNQWCDFVERNQRHNISEDTWQQVLAFSRCVHENLEGYDPEGAWPVLIDDFVEHMYRVS 185 (321)
Q Consensus 126 ~Ld~W~~FL~~~~~k~ISkDtW~q~l~F~~~v~~dls~YDe~gAWP~LIDEFVE~~r~~~ 185 (321)
++..-.+|+++ ..+|.|.|..-++|+..+.. .+-|+.|.|=+|+-+-+..
T Consensus 12 lv~~lh~f~re---~~lt~~E~~~~~~~l~~~G~-------r~E~~Ll~Dvl~~~~vd~~ 61 (247)
T cd03462 12 IVDAIRDVLLK---HEVTYDEYRAGVQYLIKVGE-------AGEWPLLLDVFFNSTIEEV 61 (247)
T ss_pred HHHHHHHHHHH---hCCCHHHHHHHHHHHHHHhc-------cCchhHhHHHHHHHHHHHH
Confidence 34555677766 46999999999999999875 7889999999988765554
Done!