Query psy5528
Match_columns 182
No_of_seqs 60 out of 62
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 19:51:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5528.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5528hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1974|consensus 99.4 6.9E-13 1.5E-17 133.5 9.6 129 12-145 345-477 (1229)
2 KOG1974|consensus 98.3 7.7E-07 1.7E-11 90.7 6.4 117 1-133 537-653 (1229)
3 PRK05339 PEP synthetase regula 56.5 12 0.00027 33.4 3.3 93 2-96 59-172 (269)
4 PF12091 DUF3567: Protein of u 55.5 5.8 0.00013 30.3 0.9 22 2-23 55-76 (85)
5 KOG0183|consensus 55.1 15 0.00032 32.9 3.5 38 90-129 165-202 (249)
6 PF06777 DUF1227: Protein of u 50.0 38 0.00082 28.0 4.9 87 24-123 12-119 (146)
7 PTZ00296 choline kinase; Provi 41.8 88 0.0019 29.3 6.6 86 7-103 345-430 (442)
8 PF03618 Kinase-PPPase: Kinase 41.4 28 0.00061 30.9 3.1 93 2-96 53-166 (255)
9 PF14058 PcfK: PcfK-like prote 39.5 46 0.001 27.1 3.9 37 26-62 35-71 (140)
10 PF09702 Cas_Csa5: CRISPR-asso 37.6 63 0.0014 25.7 4.2 31 4-37 68-98 (105)
11 KOG1125|consensus 37.2 84 0.0018 31.4 5.9 108 18-128 356-492 (579)
12 PF02197 RIIa: Regulatory subu 36.3 87 0.0019 19.9 4.0 33 13-65 2-34 (38)
13 PF12663 DUF3788: Protein of u 34.1 43 0.00094 26.5 2.9 13 6-18 3-15 (133)
14 KOG3500|consensus 33.2 32 0.0007 26.3 1.9 22 51-72 44-65 (84)
15 PF08542 Rep_fac_C: Replicatio 31.3 1.8E+02 0.0039 20.2 6.0 36 9-44 3-51 (89)
16 PF08229 SHR3_chaperone: ER me 28.3 65 0.0014 27.7 3.2 36 112-147 124-170 (196)
17 PF10852 DUF2651: Protein of u 28.0 38 0.00083 25.8 1.5 13 48-60 47-59 (82)
18 KOG2686|consensus 26.6 91 0.002 29.4 4.0 76 7-99 275-354 (366)
19 KOG2573|consensus 24.6 47 0.001 32.3 1.9 37 120-156 420-456 (498)
20 PLN02236 choline kinase 24.2 3.3E+02 0.0072 24.1 7.0 76 8-100 262-337 (344)
21 cd00353 Ribosomal_S15p_S13e Ri 24.2 2.1E+02 0.0045 20.8 4.8 43 84-131 23-65 (80)
22 PF00312 Ribosomal_S15: Riboso 23.2 2.7E+02 0.0059 20.2 5.3 45 85-134 25-69 (83)
23 COG4084 Uncharacterized protei 23.0 72 0.0016 26.3 2.4 48 53-100 29-76 (135)
24 PF00489 IL6: Interleukin-6/G- 22.3 75 0.0016 25.7 2.4 28 108-135 51-78 (154)
No 1
>KOG1974|consensus
Probab=99.41 E-value=6.9e-13 Score=133.54 Aligned_cols=129 Identities=12% Similarity=0.166 Sum_probs=119.3
Q ss_pred HHHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhccc--cccchHHHHHHHHHHHHhhhhcCCcccceecceeeeehhhhhh
Q psy5528 12 DDIAHLLKEFTVDFLLKGYGRLVSQLYDLLVTDLH--SQIDTSHFFWLVTYFLKFVVQLELDIDHVSSVISFDIISYLSF 89 (182)
Q Consensus 12 ~dIrlfLKEFcvdFL~~gYN~LV~~l~~~Llr~~~--~~~DeSyflWavtfFl~Fnr~l~f~le~VsevlSidif~yLt~ 89 (182)
-+++-.|+.||++|++.|||.||+-.+..++++.+ ++|++.+++|..+||+.|.|+..|..- +++++|.+.||++.
T Consensus 345 l~v~g~lr~~~~ev~e~~~n~l~~s~k~~~~~~~~~a~e~~~~sll~t~s~f~~f~r~s~~~~~-~se~~~~~~f~~~~- 422 (1229)
T KOG1974|consen 345 LNVHGSLRNFEDEVLEECYNQLMKSSKPHLLRQQPVAAEIVENSLLPTQSFFQGFFRNSSFKPP-ASETISDRMFHFNE- 422 (1229)
T ss_pred hhhhhHHHHHHHHHHHHHHHHhhhhhhhhHhhcCccccccccchhhHHHHHHHHHhccccCCCc-hhhhhHHHHHHHHH-
Confidence 36788999999999999999999999999999875 899999999999999999999999988 99999999999999
Q ss_pred hhhhHHHHHHHHhhccCCCCCchhHHHHHH--HHHHHHHHHHHHHHhhhhhHHHhhhh
Q psy5528 90 EGINLCEHLQIVKQHKGINLDPYVRRLHLI--IHTMVRLFNQHKIYTTSLRRRMRKKK 145 (182)
Q Consensus 90 E~v~~~E~le~~~~~~~~dl~~w~RRLHLa--vkAirElL~tl~~y~ks~d~~~res~ 145 (182)
.++++|++++.... +....|.++||.+ |+||+|++.....++-+...+++++.
T Consensus 423 --~s~t~y~~~~~~~~-k~~ea~e~~l~~~~~~k~~~ell~l~~~l~~~~~~e~~e~~ 477 (1229)
T KOG1974|consen 423 --SSVTNYVEAAKDGR-KEVEAFELLLTAAKCVKQYLELLSLVNELDDCGSEEAVESQ 477 (1229)
T ss_pred --HHHHHHHHHHHhcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchhHHHHHH
Confidence 68899999998875 5799999999999 99999999999999988888776654
No 2
>KOG1974|consensus
Probab=98.33 E-value=7.7e-07 Score=90.75 Aligned_cols=117 Identities=26% Similarity=0.455 Sum_probs=108.4
Q ss_pred CcccCCCCCChHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhccccccchHHHHHHHHHHHHhhhhcCCcccceeccee
Q psy5528 1 MKALLHYTPSEDDIAHLLKEFTVDFLLKGYGRLVSQLYDLLVTDLHSQIDTSHFFWLVTYFLKFVVQLELDIDHVSSVIS 80 (182)
Q Consensus 1 ~~~l~~~~pt~~dIrlfLKEFcvdFL~~gYN~LV~~l~~~Llr~~~~~~DeSyflWavtfFl~Fnr~l~f~le~VsevlS 80 (182)
|||.+++.|+...+.+-++++.++|...||-..|-.++.++.. ++++|.+|+.+.+..+.+.+.+++
T Consensus 537 ~~~~vq~~~r~~kkk~~~~~~~~~~~~~~ls~~v~~~~~e~s~-------------~~~l~~e~~~~~~~~~~i~~~vlt 603 (1229)
T KOG1974|consen 537 MKGVVQKKRRKRKKKNSLKEETVEFELKGLSYNVLSVLEELSD-------------LVTLFLEFASRRQLNPEISSTVLT 603 (1229)
T ss_pred hhhhhhccccccchhccchhhhHHHHHHHhhhcchhhHHHhhh-------------hHHHHHHHHHHhhcCcccccchhh
Confidence 5899999999999999999999999999998888888888776 789999999999999999999999
Q ss_pred eeehhhhhhhhhhHHHHHHHHhhccCCCCCchhHHHHHHHHHHHHHHHHHHHH
Q psy5528 81 FDIISYLSFEGINLCEHLQIVKQHKGINLDPYVRRLHLIIHTMVRLFNQHKIY 133 (182)
Q Consensus 81 idif~yLt~E~v~~~E~le~~~~~~~~dl~~w~RRLHLavkAirElL~tl~~y 133 (182)
+|+.+++..++ |+..+.++.+.+.+.++..++||..++|+||++++=-+|
T Consensus 604 ~d~~~~~~~~~---~~~~~a~s~~~s~~~~~q~~q~~~~l~~~re~~~~d~a~ 653 (1229)
T KOG1974|consen 604 YDALSDLPYEG---EQQLEAASRQESIDVKDQLQQMHYLLKAIREFLQADKAH 653 (1229)
T ss_pred hhhhhhcCchh---hhhhhHHhhhcccchhHHHHHHHHHHHHHHHHhhhhhhh
Confidence 99999999888 778999999988899999999999999999999984444
No 3
>PRK05339 PEP synthetase regulatory protein; Provisional
Probab=56.50 E-value=12 Score=33.38 Aligned_cols=93 Identities=20% Similarity=0.298 Sum_probs=60.7
Q ss_pred cccCCCCCChHHHHHHHHHHHHHH---HhhhhhhHHHHHHHHHhhcc------ccccchHHHHHHHHHHHHhhhhc--CC
Q psy5528 2 KALLHYTPSEDDIAHLLKEFTVDF---LLKGYGRLVSQLYDLLVTDL------HSQIDTSHFFWLVTYFLKFVVQL--EL 70 (182)
Q Consensus 2 ~~l~~~~pt~~dIrlfLKEFcvdF---L~~gYN~LV~~l~~~Llr~~------~~~~DeSyflWavtfFl~Fnr~l--~f 70 (182)
.|++-||=.+.++|.+|++||-.+ ..+-.++++..+-..|-... ....|+.||=..=+ |+|+-.+ |-
T Consensus 59 ~~iV~~Tlv~~elr~~l~~~~~~~~i~~vdll~p~i~~le~~lg~~p~~~pG~~~~ld~~Yf~RIeA--iefal~hDDG~ 136 (269)
T PRK05339 59 RPIVFYTLVDPELREILEERCAEFGIPCIDILGPLIAPLEQELGLKPTPEPGRTHGLDEEYFKRIEA--IEFALAHDDGQ 136 (269)
T ss_pred CCEEEEeCCCHHHHHHHHHHHHHcCCCEEeccHHHHHHHHHHHCcCCCCCCCcccCCcHHHHHHHHH--HHHHHHcCCCC
Confidence 467788999999999999999998 77788899999988876653 22478877755322 3444333 13
Q ss_pred cccc----------eecceeeeehhhhhhhhhhHHH
Q psy5528 71 DIDH----------VSSVISFDIISYLSFEGINLCE 96 (182)
Q Consensus 71 ~le~----------VsevlSidif~yLt~E~v~~~E 96 (182)
++.. ||-|=-..+==||-.-|....+
T Consensus 137 ~~~~l~~ADIiLvGVSRtsKTPlS~YLA~~G~KvAN 172 (269)
T PRK05339 137 DPRGLDEADVILVGVSRTSKTPTSLYLANKGIKAAN 172 (269)
T ss_pred CcCCcccCCEEEECcCCCCCcHHHHHHHccCCceEe
Confidence 3322 3444334444566665555444
No 4
>PF12091 DUF3567: Protein of unknown function (DUF3567); InterPro: IPR021951 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved EIVDK sequence motif.
Probab=55.48 E-value=5.8 Score=30.31 Aligned_cols=22 Identities=18% Similarity=0.555 Sum_probs=19.1
Q ss_pred cccCCCCCChHHHHHHHHHHHH
Q psy5528 2 KALLHYTPSEDDIAHLLKEFTV 23 (182)
Q Consensus 2 ~~l~~~~pt~~dIrlfLKEFcv 23 (182)
++|..-+||.|+|-.||..||.
T Consensus 55 ~~li~~~Pt~EevDdfL~~y~~ 76 (85)
T PF12091_consen 55 QALIASEPTQEEVDDFLGGYDA 76 (85)
T ss_pred HHHHhcCCCHHHHHHHHHHHHH
Confidence 4677889999999999999984
No 5
>KOG0183|consensus
Probab=55.08 E-value=15 Score=32.87 Aligned_cols=38 Identities=11% Similarity=0.183 Sum_probs=28.7
Q ss_pred hhhhHHHHHHHHhhccCCCCCchhHHHHHHHHHHHHHHHH
Q psy5528 90 EGINLCEHLQIVKQHKGINLDPYVRRLHLIIHTMVRLFNQ 129 (182)
Q Consensus 90 E~v~~~E~le~~~~~~~~dl~~w~RRLHLavkAirElL~t 129 (182)
.....+|+||-+-.++ .+..=.=-++|+++|.-|..|+
T Consensus 165 ~sk~VrEflEK~y~e~--~~~~~~~~ikL~ir~LleVvqs 202 (249)
T KOG0183|consen 165 SSKTVREFLEKNYKEE--AIATEGETIKLAIRALLEVVQS 202 (249)
T ss_pred ccHHHHHHHHHhcccc--cccccccHHHHHHHHHHHHhhc
Confidence 3457889999988864 4444455689999999998885
No 6
>PF06777 DUF1227: Protein of unknown function (DUF1227); InterPro: IPR010643 This domain represents a conserved region within a number of eukaryotic DNA repair helicases.; GO: 0005634 nucleus
Probab=50.03 E-value=38 Score=27.98 Aligned_cols=87 Identities=25% Similarity=0.376 Sum_probs=58.9
Q ss_pred HHHhhhhhhHHHHHHHH------------------Hhhccccc---cchHHHHHHHHHHHHhhhhcCCcccceecceeee
Q psy5528 24 DFLLKGYGRLVSQLYDL------------------LVTDLHSQ---IDTSHFFWLVTYFLKFVVQLELDIDHVSSVISFD 82 (182)
Q Consensus 24 dFL~~gYN~LV~~l~~~------------------Llr~~~~~---~DeSyflWavtfFl~Fnr~l~f~le~VsevlSid 82 (182)
+=|.+-|+.||.-|+.. ++.+ +.| -.-.||+=.|.-|.+|-+.. +++.| |.|-.
T Consensus 12 ~rLq~EY~rLV~GL~~~~~~~~~d~~~~npvLp~dil~e-aVPGnIR~AeHFv~flkR~veylk~r-lrv~~---v~~e~ 86 (146)
T PF06777_consen 12 QRLQDEYDRLVEGLREAEIARETDEILANPVLPDDILKE-AVPGNIRRAEHFVAFLKRFVEYLKTR-LRVQH---VISES 86 (146)
T ss_pred HHHHHHHHHHHHHHHHhccccccchhhcCCCCchhhhhh-cCCchHHhHHHHHHHHHHHHHHHHHH-hhhcc---eeecC
Confidence 45788999999999954 2222 122 23459999999999998766 55555 45557
Q ss_pred ehhhhhhhhhhHHHHHHHHhhccCCCCCchhHHHHHHHHHH
Q psy5528 83 IISYLSFEGINLCEHLQIVKQHKGINLDPYVRRLHLIIHTM 123 (182)
Q Consensus 83 if~yLt~E~v~~~E~le~~~~~~~~dl~~w~RRLHLavkAi 123 (182)
-.+||+ .+++.--++ .+-++-|.-|||.-+++.
T Consensus 87 P~sFL~----~~~~~~~id----~k~LrFc~eRL~sLl~TL 119 (146)
T PF06777_consen 87 PLSFLQ----HLKDETFID----RKPLRFCSERLSSLLRTL 119 (146)
T ss_pred HHHHHH----HHHHHhCCC----cHHHHHHHHHHHHHHHHH
Confidence 788887 333322222 236788999999877664
No 7
>PTZ00296 choline kinase; Provisional
Probab=41.78 E-value=88 Score=29.27 Aligned_cols=86 Identities=10% Similarity=0.101 Sum_probs=45.8
Q ss_pred CCCChHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhccccccchHHHHHHHHHHHHhhhhcCCcccceecceeeeehhh
Q psy5528 7 YTPSEDDIAHLLKEFTVDFLLKGYGRLVSQLYDLLVTDLHSQIDTSHFFWLVTYFLKFVVQLELDIDHVSSVISFDIISY 86 (182)
Q Consensus 7 ~~pt~~dIrlfLKEFcvdFL~~gYN~LV~~l~~~Llr~~~~~~DeSyflWavtfFl~Fnr~l~f~le~VsevlSidif~y 86 (182)
..||.+..+.|++.+.-.++.++-..--....+.|+.+-..--=-||+||++--.+. |.+. ...+. |-|
T Consensus 345 ~yPs~e~q~~Fi~~Yl~~~~~~~~~~~~~~~v~~l~~ev~~f~l~shl~W~lWaiiq-a~~~-------~s~id---FDy 413 (442)
T PTZ00296 345 KYISYENRKLFITAYLSNYLDKSLVVPNPKIIDQILEAVEVQALGAHLLWGFWSIIR-GYQT-------KSYNE---FDF 413 (442)
T ss_pred cCcCHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHHHHHhhhhHHHHHHHHHHh-CCcc-------cCCCC---CCH
Confidence 468888888888888766543211110111223344432223335799999877665 2111 11233 445
Q ss_pred hhhhhhhHHHHHHHHhh
Q psy5528 87 LSFEGINLCEHLQIVKQ 103 (182)
Q Consensus 87 Lt~E~v~~~E~le~~~~ 103 (182)
+.|-..++.+|++.-..
T Consensus 414 ~~Ya~~R~~~Y~~~k~~ 430 (442)
T PTZ00296 414 FLYAKERFKMYDEQKEY 430 (442)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 55555677777665433
No 8
>PF03618 Kinase-PPPase: Kinase/pyrophosphorylase; InterPro: IPR005177 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.; GO: 0005524 ATP binding, 0016772 transferase activity, transferring phosphorus-containing groups
Probab=41.38 E-value=28 Score=30.86 Aligned_cols=93 Identities=22% Similarity=0.303 Sum_probs=62.3
Q ss_pred cccCCCCCChHHHHHHHHHHHHHH---HhhhhhhHHHHHHHHHhhcc------ccccchHHHHH--HHHHHHHhhhhcCC
Q psy5528 2 KALLHYTPSEDDIAHLLKEFTVDF---LLKGYGRLVSQLYDLLVTDL------HSQIDTSHFFW--LVTYFLKFVVQLEL 70 (182)
Q Consensus 2 ~~l~~~~pt~~dIrlfLKEFcvdF---L~~gYN~LV~~l~~~Llr~~------~~~~DeSyflW--avtfFl~Fnr~l~f 70 (182)
.|++-||=.+.++|..|++||-++ ..+-.++++..+-+.|-... ....|+.||=. ||-|-+++--. -
T Consensus 53 ~~iV~~Tlv~~~lr~~l~~~~~~~~i~~~Dll~~~l~~l~~~lg~~p~~~pg~~~~ld~~Yf~RIeAiefav~~DDG--~ 130 (255)
T PF03618_consen 53 NAIVFYTLVDPELREYLEEFCREHGIPCVDLLGPLLSALEEFLGQKPSRKPGLQHQLDEDYFKRIEAIEFAVKHDDG--K 130 (255)
T ss_pred CCEEEEeCCCHHHHHHHHHHHHhcCCCEEeccHHHHHHHHHHHCcCcccccCccccchHHHHHHHHHHHHHHHccCC--C
Confidence 367778899999999999999998 77788899999988887654 22588887754 45555544322 2
Q ss_pred cccc----------eecceeeeehhhhhhhhhhHHH
Q psy5528 71 DIDH----------VSSVISFDIISYLSFEGINLCE 96 (182)
Q Consensus 71 ~le~----------VsevlSidif~yLt~E~v~~~E 96 (182)
++.. ||-|=-..+==||-..|....+
T Consensus 131 ~~~~l~~ADivLvGVSRtsKTPlS~YLA~~G~KvAN 166 (255)
T PF03618_consen 131 NPRGLDEADIVLVGVSRTSKTPLSMYLANKGYKVAN 166 (255)
T ss_pred CccccccCCEEEEcccccCCCchhHHHHhcCcceee
Confidence 2222 4444444455577666655544
No 9
>PF14058 PcfK: PcfK-like protein
Probab=39.49 E-value=46 Score=27.06 Aligned_cols=37 Identities=14% Similarity=0.205 Sum_probs=26.8
Q ss_pred HhhhhhhHHHHHHHHHhhccccccchHHHHHHHHHHH
Q psy5528 26 LLKGYGRLVSQLYDLLVTDLHSQIDTSHFFWLVTYFL 62 (182)
Q Consensus 26 L~~gYN~LV~~l~~~Llr~~~~~~DeSyflWavtfFl 62 (182)
|..|+++.++.++.+=-..-+---|..-|=||+-||.
T Consensus 35 i~~c~~Yi~~~a~k~~~~g~~~v~DdeVf~wa~~Yy~ 71 (140)
T PF14058_consen 35 IDDCVTYILNKAQKQKNSGCNGVSDDEVFSWAVHYYD 71 (140)
T ss_pred HHHHHHHHHHHHHHHHcCCCCccChHHHHHHHHHHHc
Confidence 4568888888888653222233567789999999998
No 10
>PF09702 Cas_Csa5: CRISPR-associated protein (Cas_Csa5); InterPro: IPR010157 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a minor family of Cas protein found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus.
Probab=37.56 E-value=63 Score=25.68 Aligned_cols=31 Identities=26% Similarity=0.622 Sum_probs=25.9
Q ss_pred cCCCCCChHHHHHHHHHHHHHHHhhhhhhHHHHH
Q psy5528 4 LLHYTPSEDDIAHLLKEFTVDFLLKGYGRLVSQL 37 (182)
Q Consensus 4 l~~~~pt~~dIrlfLKEFcvdFL~~gYN~LV~~l 37 (182)
++-+.||++||-.||..-.-|. +|-..|+.|
T Consensus 68 ~~g~lPt~~eVe~Fl~~v~~di---~~Arkvgal 98 (105)
T PF09702_consen 68 IVGYLPTDEEVEDFLDDVERDI---YYARKVGAL 98 (105)
T ss_pred ecCCCCChHHHHHHHHHHHHHH---HHHHHHHHH
Confidence 4668899999999999988888 777777765
No 11
>KOG1125|consensus
Probab=37.24 E-value=84 Score=31.36 Aligned_cols=108 Identities=23% Similarity=0.210 Sum_probs=79.2
Q ss_pred HHHHHHHHHhhhhhh-HHHHHHHHHhhc------------cc-----cccchHHHHHHHHHHHHhhhhcCC--cccceec
Q psy5528 18 LKEFTVDFLLKGYGR-LVSQLYDLLVTD------------LH-----SQIDTSHFFWLVTYFLKFVVQLEL--DIDHVSS 77 (182)
Q Consensus 18 LKEFcvdFL~~gYN~-LV~~l~~~Llr~------------~~-----~~~DeSyflWavtfFl~Fnr~l~f--~le~Vse 77 (182)
|.-.-|.+.+-|++. -+..|++=|... .. ...|.+|+.=.-.+||+-+++++. |.+ |-.
T Consensus 356 LmaLAVSytNeg~q~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~Dpd-vQ~ 434 (579)
T KOG1125|consen 356 LMALAVSYTNEGLQNQALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPD-VQS 434 (579)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChh-HHh
Confidence 445556666666653 344444433322 01 347889999999999999999994 333 222
Q ss_pred ceeeeehhhhhhhhhhHHHHHHHHhhccCCCCCchhH---------HHHHHHHHHHHHHH
Q psy5528 78 VISFDIISYLSFEGINLCEHLQIVKQHKGINLDPYVR---------RLHLIIHTMVRLFN 128 (182)
Q Consensus 78 vlSidif~yLt~E~v~~~E~le~~~~~~~~dl~~w~R---------RLHLavkAirElL~ 128 (182)
+ .-|+-|+..|-.+-..-|+.....+..|...|-| |-|-||-||++-|+
T Consensus 435 ~--LGVLy~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALq 492 (579)
T KOG1125|consen 435 G--LGVLYNLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQ 492 (579)
T ss_pred h--hHHHHhcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHh
Confidence 3 4578899998888888999999988899999977 78999999999886
No 12
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=36.27 E-value=87 Score=19.95 Aligned_cols=33 Identities=33% Similarity=0.528 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhccccccchHHHHHHHHHHHHhh
Q psy5528 13 DIAHLLKEFTVDFLLKGYGRLVSQLYDLLVTDLHSQIDTSHFFWLVTYFLKFV 65 (182)
Q Consensus 13 dIrlfLKEFcvdFL~~gYN~LV~~l~~~Llr~~~~~~DeSyflWavtfFl~Fn 65 (182)
++..+|++|+++.| ++ +|-|- +-|+..||-+..
T Consensus 2 ~l~~lL~~~~~~vl----------------~~--qP~Di--~~F~a~yF~~L~ 34 (38)
T PF02197_consen 2 GLQELLKEFTREVL----------------RE--QPDDI--LQFAADYFEKLE 34 (38)
T ss_dssp THHHHHHHHHHHHH----------------HH----S-H--HHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHH----------------HH--CCCcH--HHHHHHHHHHHH
Confidence 34556666666664 32 46664 456777775544
No 13
>PF12663 DUF3788: Protein of unknown function (DUF3788); InterPro: IPR024265 This family of functionally uncharacterised proteins is found in bacteria and archaea. Proteins in this family are typically between 137 and 149 amino acids in length and may be distantly related to RelE proteins.
Probab=34.06 E-value=43 Score=26.48 Aligned_cols=13 Identities=31% Similarity=0.677 Sum_probs=11.0
Q ss_pred CCCCChHHHHHHH
Q psy5528 6 HYTPSEDDIAHLL 18 (182)
Q Consensus 6 ~~~pt~~dIrlfL 18 (182)
+..||+++|+.+|
T Consensus 3 ~~~Pt~~~i~~~l 15 (133)
T PF12663_consen 3 DQKPTEEEISEYL 15 (133)
T ss_pred CCCcCHHHHHHHH
Confidence 4689999999876
No 14
>KOG3500|consensus
Probab=33.21 E-value=32 Score=26.34 Aligned_cols=22 Identities=18% Similarity=0.591 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHHHhhhhcCCcc
Q psy5528 51 TSHFFWLVTYFLKFVVQLELDI 72 (182)
Q Consensus 51 eSyflWavtfFl~Fnr~l~f~l 72 (182)
-+|.||++.|-++.|...+=++
T Consensus 44 CCwlfWli~ylaQlNPLigP~l 65 (84)
T KOG3500|consen 44 CCWLFWLIVYLAQLNPLIGPQL 65 (84)
T ss_pred HHHHHHHHHHHHHhCccccccc
Confidence 3699999999999998776443
No 15
>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=31.27 E-value=1.8e+02 Score=20.17 Aligned_cols=36 Identities=28% Similarity=0.583 Sum_probs=21.4
Q ss_pred CChHHHHHHHH-----------HHHHHHHhhhhh--hHHHHHHHHHhhc
Q psy5528 9 PSEDDIAHLLK-----------EFTVDFLLKGYG--RLVSQLYDLLVTD 44 (182)
Q Consensus 9 pt~~dIrlfLK-----------EFcvdFL~~gYN--~LV~~l~~~Llr~ 44 (182)
|+++.|..+++ ..+-+++..||. .++.++++.++..
T Consensus 3 p~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~G~s~~~Il~~l~~~l~~~ 51 (89)
T PF08542_consen 3 PPPEVIEEILESCLNGDFKEARKKLYELLVEGYSASDILKQLHEVLVES 51 (89)
T ss_dssp --HHHHHHHHHHHHHTCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHTS
T ss_pred CCHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 66666666653 334556666665 4788888888886
No 16
>PF08229 SHR3_chaperone: ER membrane protein SH3 ; InterPro: IPR013248 This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs) []. Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER.
Probab=28.34 E-value=65 Score=27.73 Aligned_cols=36 Identities=8% Similarity=0.026 Sum_probs=22.4
Q ss_pred hhHHHHHHHHHHHH-----------HHHHHHHHhhhhhHHHhhhhhh
Q psy5528 112 YVRRLHLIIHTMVR-----------LFNQHKIYTTSLRRRMRKKKKV 147 (182)
Q Consensus 112 w~RRLHLavkAirE-----------lL~tl~~y~ks~d~~~res~~v 147 (182)
-.|..+|.|-|=-. +||+=.-|....|+...+.-..
T Consensus 124 v~r~~~l~VlAASn~Ii~~~LvGVLvLQaG~~YAe~~~~~~~~~~~~ 170 (196)
T PF08229_consen 124 VDREDGLRVLAASNTIIALVLVGVLVLQAGQWYAERKDAKELEEFEK 170 (196)
T ss_pred ccHHHHHHHHHHhhHHHHHHHHHHHHHHhhHHHHhhhhHHHHHHHHH
Confidence 36778887766332 4566677877777665554433
No 17
>PF10852 DUF2651: Protein of unknown function (DUF2651) ; InterPro: IPR020258 This entry contains transmembrane proteins with no known function.
Probab=27.98 E-value=38 Score=25.79 Aligned_cols=13 Identities=46% Similarity=1.152 Sum_probs=11.8
Q ss_pred ccchHHHHHHHHH
Q psy5528 48 QIDTSHFFWLVTY 60 (182)
Q Consensus 48 ~~DeSyflWavtf 60 (182)
-.|.|.|+|++.|
T Consensus 47 ~fn~SFf~WvvvY 59 (82)
T PF10852_consen 47 LFNPSFFFWVVVY 59 (82)
T ss_pred hhChHHHHHHHHH
Confidence 5799999999998
No 18
>KOG2686|consensus
Probab=26.63 E-value=91 Score=29.38 Aligned_cols=76 Identities=16% Similarity=0.253 Sum_probs=44.0
Q ss_pred CCCChHHHHHHHHHHHHHHHhhhhh----hHHHHHHHHHhhccccccchHHHHHHHHHHHHhhhhcCCcccceecceeee
Q psy5528 7 YTPSEDDIAHLLKEFTVDFLLKGYG----RLVSQLYDLLVTDLHSQIDTSHFFWLVTYFLKFVVQLELDIDHVSSVISFD 82 (182)
Q Consensus 7 ~~pt~~dIrlfLKEFcvdFL~~gYN----~LV~~l~~~Llr~~~~~~DeSyflWavtfFl~Fnr~l~f~le~VsevlSid 82 (182)
..|++++++. ||..+|...+| +--.+|.. |+.+-..-.=.||+||++-=-+.+-.... .
T Consensus 275 ~~p~~e~~~~----F~~sYl~~~~~~~~~~~~~ev~~-L~~e~~~~~p~shlfW~LWsi~q~~~~~~------------i 337 (366)
T KOG2686|consen 275 LYPGEEQRQR----FIESYLDSAAVKRKEPREKEVEK-LLKEIRFFTPASHLFWGLWSILQALVLHK------------I 337 (366)
T ss_pred hCCCcHHHHH----HHHHHHHHhhccccCchHHHHHH-HHHHHHHHhhhhHHHHHHHHHHHhhhccc------------c
Confidence 4788998865 56677777774 34444443 33333334556799998854444332211 4
Q ss_pred ehhhhhhhhhhHHHHHH
Q psy5528 83 IISYLSFEGINLCEHLQ 99 (182)
Q Consensus 83 if~yLt~E~v~~~E~le 99 (182)
-|.|..+...+..-++.
T Consensus 338 ~fdy~~y~r~rf~~y~~ 354 (366)
T KOG2686|consen 338 EFDYMEYARDRFAVYFH 354 (366)
T ss_pred ccChHHHHHHHHHHHhc
Confidence 45666666666554443
No 19
>KOG2573|consensus
Probab=24.61 E-value=47 Score=32.25 Aligned_cols=37 Identities=16% Similarity=0.114 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHhhhhhHHHhhhhhhchHHHHHHH
Q psy5528 120 IHTMVRLFNQHKIYTTSLRRRMRKKKKVEKEEEEEKK 156 (182)
Q Consensus 120 vkAirElL~tl~~y~ks~d~~~res~~v~~~~~~~~~ 156 (182)
+.+++|...+.+.-+.-.++..-.+.+...+..+|++
T Consensus 420 ~~vmkea~e~~~~~~~~~~~e~e~~~~e~~ek~~ek~ 456 (498)
T KOG2573|consen 420 SDVMKEAMEAYNGISRDSAPEDEASAKEKPEKDEEKE 456 (498)
T ss_pred hHHHHHHHHHhcccccccchhhhhhhhhhhhhhhhhh
Confidence 3455555444444444444445444444333333333
No 20
>PLN02236 choline kinase
Probab=24.19 E-value=3.3e+02 Score=24.12 Aligned_cols=76 Identities=17% Similarity=0.337 Sum_probs=37.6
Q ss_pred CCChHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhccccccchHHHHHHHHHHHHhhhhcCCcccceecceeeeehhhh
Q psy5528 8 TPSEDDIAHLLKEFTVDFLLKGYGRLVSQLYDLLVTDLHSQIDTSHFFWLVTYFLKFVVQLELDIDHVSSVISFDIISYL 87 (182)
Q Consensus 8 ~pt~~dIrlfLKEFcvdFL~~gYN~LV~~l~~~Llr~~~~~~DeSyflWavtfFl~Fnr~l~f~le~VsevlSidif~yL 87 (182)
.|+.+..+.|++.|+-.. | ...-..-.+.|..+-..-.=-||+||++-=.+. + .+|+ +| |-|+
T Consensus 262 ~~~~~~~~~fi~~Yl~~~---g-~~~~~~~~~~l~~~v~~~~~~~~l~W~lWa~iq-~--------~~s~---~~-fdy~ 324 (344)
T PLN02236 262 YPGEEERRRFIRTYLSSS---G-EEPSDEEVEQLLDDVEKYTLASHLFWGLWGIIS-G--------HVNK---ID-FDYM 324 (344)
T ss_pred CcCHHHHHHHHHHHHhhc---C-CCchHHHHHHHHHHHHHHhhHhHHHHHHHHHHh-c--------ccCC---CC-CCHH
Confidence 578888888888887421 0 111112222333222222223588887755432 1 1222 23 5566
Q ss_pred hhhhhhHHHHHHH
Q psy5528 88 SFEGINLCEHLQI 100 (182)
Q Consensus 88 t~E~v~~~E~le~ 100 (182)
.|-..++..|+.+
T Consensus 325 ~Ya~~R~~~y~~~ 337 (344)
T PLN02236 325 EYARQRFEQYWLR 337 (344)
T ss_pred HHHHHHHHHHHHH
Confidence 5555566666654
No 21
>cd00353 Ribosomal_S15p_S13e Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome. S15 also plays an important autoregulatory role by binding and preventing its own mRNA from being translated. S15 has a predominantly alpha-helical fold that is highly structured except for the N-terminal alpha helix.
Probab=24.18 E-value=2.1e+02 Score=20.80 Aligned_cols=43 Identities=33% Similarity=0.384 Sum_probs=36.4
Q ss_pred hhhhhhhhhhHHHHHHHHhhccCCCCCchhHHHHHHHHHHHHHHHHHH
Q psy5528 84 ISYLSFEGINLCEHLQIVKQHKGINLDPYVRRLHLIIHTMVRLFNQHK 131 (182)
Q Consensus 84 f~yLt~E~v~~~E~le~~~~~~~~dl~~w~RRLHLavkAirElL~tl~ 131 (182)
+-.||....++++.++.+.+|. ...|.|...|--.+-||..+.
T Consensus 23 ia~LT~rI~~L~~Hl~~~~KD~-----~~krgL~~lv~kRrrLL~YLk 65 (80)
T cd00353 23 LALLTERIVNLTEHLEKNKKDK-----HSKRGLLLLVSKRRRLLKYLK 65 (80)
T ss_pred HHHHHHHHHHHHHHHHHccccc-----hHHHhHHHHHHHHHHHHHHHH
Confidence 3456889999999999999984 678999999999999998774
No 22
>PF00312 Ribosomal_S15: Ribosomal protein S15; InterPro: IPR000589 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ,], groups bacterial and plant chloroplast S15; archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YSH_E 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 1S1H_O 3MR8_O 3D5C_O 3MS0_O ....
Probab=23.22 E-value=2.7e+02 Score=20.24 Aligned_cols=45 Identities=27% Similarity=0.203 Sum_probs=38.4
Q ss_pred hhhhhhhhhHHHHHHHHhhccCCCCCchhHHHHHHHHHHHHHHHHHHHHh
Q psy5528 85 SYLSFEGINLCEHLQIVKQHKGINLDPYVRRLHLIIHTMVRLFNQHKIYT 134 (182)
Q Consensus 85 ~yLt~E~v~~~E~le~~~~~~~~dl~~w~RRLHLavkAirElL~tl~~y~ 134 (182)
-.||....++.+.++.+.+|. ...|.|-..|...+-+|..+...+
T Consensus 25 a~LT~rI~~L~~Hl~~~kkD~-----~skr~L~~lv~kRrrlL~YLrr~~ 69 (83)
T PF00312_consen 25 AILTERIRNLQEHLKKNKKDK-----HSKRGLLKLVSKRRRLLKYLRRKD 69 (83)
T ss_dssp HHHHHHHHHHHHHHHHTTTSH-----HHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHhcccc-----ccceehhHHHHHHHHHHHHHHhCC
Confidence 356888899999999988874 788999999999999999887765
No 23
>COG4084 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.02 E-value=72 Score=26.26 Aligned_cols=48 Identities=10% Similarity=0.109 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhhhhcCCcccceecceeeeehhhhhhhhhhHHHHHHH
Q psy5528 53 HFFWLVTYFLKFVVQLELDIDHVSSVISFDIISYLSFEGINLCEHLQI 100 (182)
Q Consensus 53 yflWavtfFl~Fnr~l~f~le~VsevlSidif~yLt~E~v~~~E~le~ 100 (182)
-|+|-=--|-+.|+.++.++++|-+++|=..=+==-++.-...|+-++
T Consensus 29 sy~~~~DVv~pla~~L~IdveevidIl~~kld~ssly~LH~~~EqA~~ 76 (135)
T COG4084 29 SYAYRRDVVHPLAELLNIDVEEVIDILSRKLDCSSLYGLHSEVEQAER 76 (135)
T ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHHHhcchhHHHHhhHHHHHHhh
Confidence 478888899999999999999998888643322222333344445444
No 24
>PF00489 IL6: Interleukin-6/G-CSF/MGF family; InterPro: IPR003573 Interleukin-6 (IL6), also refered to as B-cell stimulatory factor-2 (BSF-2) and interferon beta-2, is a cytokine involved in a wide variety of biological functions []. It plays an essential role in the final differentiation of B-cells into IG-secreting cells, as well as inducing myeloma/plasmacytoma growth, nerve cell differentiation and, in hepatocytes, acute phase reactants [, ]. A number of other cytokines may be grouped with IL6 on the basis of sequence similarity [, , ]: these include granulocyte colony-stimulating factor (GCSF) and myelomonocytic growth factor (MGF). GCSF acts in hematopoiesis by affecting the production, differentiation and function of 2 related white cell groups in the blood []. MGF also acts in hematopoiesis, stimulating proliferation and colony formation of normal and transformed avian cells of the myeloid lineage. Cytokines of the IL6/GCSF/MGF family are glycoproteins of about 170 to 180 amino acid residues that contains four conserved cysteine residues involved in two disulphide bonds []. They have a compact, globular fold (similar to other interleukins), stabilised by the 2 disulphide bonds. One half of the structure is dominated by a 4 alpha-helix bundle with a left-handed twist []: the helices are anti-parallel, with 2 overhand connections, which fall into a 2-stranded anti-parallel beta-sheet. The fourth alpha-helix is important to the biological activity of the molecule []. It has been said [] that this family can be extended by the adjunction of LIF and OSM (see the relevant entry IPR001581 from INTERPRO) which seem to be structurally related.; GO: 0005125 cytokine activity, 0006955 immune response, 0005576 extracellular region; PDB: 1P9M_B 2IL6_A 1IL6_A 1ALU_A 3QWR_B 3DUH_C 3D85_C 3D87_C 1BGC_A 2L3Y_A ....
Probab=22.31 E-value=75 Score=25.74 Aligned_cols=28 Identities=14% Similarity=0.094 Sum_probs=23.6
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHHHhh
Q psy5528 108 NLDPYVRRLHLIIHTMVRLFNQHKIYTT 135 (182)
Q Consensus 108 dl~~w~RRLHLavkAirElL~tl~~y~k 135 (182)
+...|.+|||-++..|+-||+.|..-..
T Consensus 51 n~e~CL~ri~~GL~~yq~lL~~l~~~~~ 78 (154)
T PF00489_consen 51 NKETCLSRIHSGLQEYQILLKYLQGEFP 78 (154)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHTTTSST
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhhCc
Confidence 4578999999999999999998877544
Done!