Query psy13301
Match_columns 194
No_of_seqs 114 out of 217
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 15:59:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13301.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13301hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3533|consensus 100.0 6E-61 1.3E-65 472.0 8.4 185 1-185 2432-2661(2706)
2 KOG2243|consensus 100.0 6.1E-52 1.3E-56 406.6 9.5 190 1-190 4829-5019(5019)
3 PLN03223 Polycystin cation cha 96.8 0.00098 2.1E-08 69.6 3.5 86 2-100 1341-1429(1634)
4 KOG3599|consensus 92.9 0.41 9E-06 48.4 8.0 66 29-102 621-688 (798)
5 TIGR00870 trp transient-recept 90.8 1.1 2.4E-05 44.0 8.2 68 30-102 557-624 (743)
6 PF08016 PKD_channel: Polycyst 90.3 0.76 1.7E-05 42.3 6.3 76 5-95 349-424 (425)
7 PF00520 Ion_trans: Ion transp 85.2 0.4 8.6E-06 37.2 1.0 84 3-89 109-200 (200)
8 PHA02565 49 recombination endo 76.3 2.3 5.1E-05 35.1 2.6 39 93-136 5-43 (157)
9 KOG2302|consensus 57.4 41 0.00088 36.0 7.4 99 3-104 1272-1399(1956)
10 KOG3676|consensus 54.5 47 0.001 33.9 7.3 31 70-100 624-654 (782)
11 PRK09174 F0F1 ATP synthase sub 44.6 93 0.002 26.3 6.7 39 61-99 50-88 (204)
12 PHA03023 hypothetical protein; 41.6 70 0.0015 25.1 5.0 36 80-119 13-51 (112)
13 KOG3609|consensus 39.8 33 0.00072 35.2 3.7 68 28-100 547-618 (822)
14 PF14147 Spore_YhaL: Sporulati 39.8 34 0.00073 23.4 2.6 25 84-108 8-32 (52)
15 PF03904 DUF334: Domain of unk 39.4 59 0.0013 28.5 4.8 18 132-149 191-208 (230)
16 PF05803 Chordopox_L2: Chordop 39.2 33 0.00071 25.8 2.8 19 64-82 40-58 (87)
17 KOG2301|consensus 38.7 12 0.00025 41.0 0.4 89 2-95 576-664 (1592)
18 smart00265 BH4 BH4 Bcl-2 homol 38.5 24 0.00052 21.0 1.5 18 159-176 9-26 (27)
19 PHA02706 hypothetical protein; 36.3 40 0.00088 23.0 2.6 23 70-92 4-26 (58)
20 PHA02690 hypothetical protein; 34.6 44 0.00095 25.0 2.8 18 63-80 40-57 (90)
21 PF02945 Endonuclease_7: Recom 34.2 8.7 0.00019 28.2 -1.0 20 97-116 11-30 (81)
22 COG3238 Uncharacterized protei 33.1 36 0.00079 27.9 2.4 22 75-96 98-119 (150)
23 PF00653 BIR: Inhibitor of Apo 33.0 12 0.00025 26.0 -0.5 30 106-135 34-63 (70)
24 KOG2301|consensus 33.0 32 0.00069 37.8 2.5 38 64-101 1371-1408(1592)
25 KOG1101|consensus 31.9 28 0.00061 28.3 1.5 28 108-135 51-78 (147)
26 cd00350 rubredoxin_like Rubred 31.9 14 0.00031 22.3 -0.1 16 108-123 17-32 (33)
27 PF13314 DUF4083: Domain of un 30.2 86 0.0019 21.9 3.5 23 68-90 3-27 (58)
28 COG3763 Uncharacterized protei 29.5 1.1E+02 0.0024 22.2 4.1 31 75-105 5-35 (71)
29 cd00729 rubredoxin_SM Rubredox 29.3 18 0.00039 22.2 -0.0 16 108-123 18-33 (34)
30 PF04657 DUF606: Protein of un 29.0 55 0.0012 25.9 2.7 28 74-101 92-119 (138)
31 KOG2302|consensus 27.8 97 0.0021 33.4 4.8 43 68-110 364-410 (1956)
32 PRK08476 F0F1 ATP synthase sub 27.7 2E+02 0.0042 22.7 5.7 40 64-103 7-46 (141)
33 PF02180 BH4: Bcl-2 homology r 26.8 40 0.00087 20.1 1.2 18 159-176 9-26 (27)
34 PRK06231 F0F1 ATP synthase sub 26.5 1.8E+02 0.0038 24.6 5.5 40 64-103 48-87 (205)
35 PRK13461 F0F1 ATP synthase sub 26.3 2.1E+02 0.0047 22.6 5.8 40 63-102 4-43 (159)
36 PRK13453 F0F1 ATP synthase sub 25.0 2.3E+02 0.0049 23.0 5.8 38 64-101 18-55 (173)
37 PHA02845 hypothetical protein; 25.0 73 0.0016 24.2 2.6 19 64-82 41-59 (91)
38 TIGR01710 typeII_sec_gspG gene 24.7 1.3E+02 0.0028 23.4 4.1 30 75-104 8-37 (134)
39 PRK14473 F0F1 ATP synthase sub 24.5 2.4E+02 0.0053 22.4 5.8 42 64-105 8-49 (164)
40 PF08653 DASH_Dam1: DASH compl 22.9 34 0.00075 23.7 0.5 27 88-114 2-28 (58)
41 PRK10537 voltage-gated potassi 22.9 3.2E+02 0.0068 25.5 6.9 13 107-119 239-251 (393)
42 COG2165 PulG Type II secretory 22.9 1.6E+02 0.0036 21.6 4.3 26 75-100 15-40 (149)
43 PRK07352 F0F1 ATP synthase sub 22.4 3E+02 0.0065 22.2 6.0 34 67-100 22-55 (174)
44 PF00253 Ribosomal_S14: Riboso 22.0 46 0.00099 22.5 0.9 18 107-124 15-32 (55)
45 smart00238 BIR Baculoviral inh 22.0 52 0.0011 22.4 1.2 27 108-134 36-62 (71)
46 COG1773 Rubredoxin [Energy pro 20.7 42 0.0009 23.2 0.5 17 109-125 37-53 (55)
No 1
>KOG3533|consensus
Probab=100.00 E-value=6e-61 Score=472.01 Aligned_cols=185 Identities=35% Similarity=0.777 Sum_probs=173.2
Q ss_pred CEEEehhHHHHHhHHhhhcc--------------------------------------------cccccccCccchHHHH
Q psy13301 1 MLYIYTVIAFNFFRKFYVQE--------------------------------------------EDDVVDKKCHDMMTCF 36 (194)
Q Consensus 1 iiYifsii~f~~f~~~~~~~--------------------------------------------~~~~~~~~C~tl~~Cf 36 (194)
++|+|||+||.||+++|.-+ +++..+..|+|||+|+
T Consensus 2432 LvYlFSIiGflffkdDF~leVD~l~n~~~~~~~l~~~~~~~~~~~tc~~enC~~~~p~~~~~~~~~e~kersCdtLlMCI 2511 (2706)
T KOG3533|consen 2432 LVYLFSILGFLFFKDDFYLEVDRLENDSAVPSPLSATISSGIPSETCPSENCPGLQPSEKPDDNDDEKKERSCETLLMCI 2511 (2706)
T ss_pred HHHHHHHHHHHhcccceEEEecccccCCCCCCccccccccCCccccCCCCCCCCCCCCCCCCcccccchhhhhhHHHHHH
Confidence 47999999999999877531 0123456799999999
Q ss_pred HHhhhhccccCCcccccCCCCCCCC-cchhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHHHHHHHhhccCceeec
Q psy13301 37 VFHLYKGVRAGGGIGDEIGDPDGDD-YEVYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQLESVKEDMESNCFICG 115 (194)
Q Consensus 37 ~~~~~~glr~gGGig~~l~~~~~~~-~~~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~~~~~~d~~~~CFICg 115 (194)
++++++||||||||||+|+.|++++ ...+|++||++||++|+||+||+|||+||||||+||.|||++|+..|+.|||||
T Consensus 2512 vt~lnqGLRnGGGiGDvLR~Psk~E~lF~aRV~YDllFffivIiIVLNLIFGVIIDTFaDLRsEKqkKEeILKttCFICg 2591 (2706)
T KOG3533|consen 2512 VTTLNQGLRNGGGIGDVLRNPSKWEDLFIARVAYDLLFFFIVIIIVLNLIFGVIIDTFADLRSEKQKKEEILKTTCFICG 2591 (2706)
T ss_pred HHHHhhhcccCCChhhhhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHhhhhHHHHHHhcceeEee
Confidence 9999999999999999999999765 468899999999999999999999999999999999999999999999999999
Q ss_pred CCccccccCCCChhhhhhhhcchhhHHHHHHHhccCCCCCCChhhHHHHHHHhcCCCCeeechhHHhhhc
Q psy13301 116 IGKDYFDKVPHGFDTHVQQEHNLANYMFFLMHLINKPDTEFTGQETYVWNMYQQRCWDFFPVGDCFRKQY 185 (194)
Q Consensus 116 i~r~~fd~~~~gF~~Hi~~eHnmWnYl~fi~yL~~K~~te~tg~E~yV~~~i~~~d~swfP~~~~~~~~~ 185 (194)
++|+.||++.-.|++|||.|||||||+|||+-++-|++|||||+||||+++++++.++|||..||+||+.
T Consensus 2592 LeR~kFDNktVsFEeHik~EHNmWhYLyfIVlvkvKd~Te~TGPESYVaqmvk~~nLdWFPRmrAmSLvs 2661 (2706)
T KOG3533|consen 2592 LERSKFDNKTVTFEEHIKTEHNMWHYLYFIVLVKVKDETEFTGPESYVAQMVKDRNLDWFPRMRAMSLVS 2661 (2706)
T ss_pred cchhhccCceeeHHHhhhhhhhhHHhhheeEEEEecCCccccChHHHHHHHHHhcccchhhhhHhhhhhc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999874
No 2
>KOG2243|consensus
Probab=100.00 E-value=6.1e-52 Score=406.56 Aligned_cols=190 Identities=78% Similarity=1.447 Sum_probs=186.3
Q ss_pred CEEEehhHHHHHhHHhhhccc-ccccccCccchHHHHHHhhhhccccCCcccccCCCCCCCCcchhhHhhHHHHHHHHHH
Q psy13301 1 MLYIYTVIAFNFFRKFYVQEE-DDVVDKKCHDMMTCFVFHLYKGVRAGGGIGDEIGDPDGDDYEVYRIIFDITFFFFVIV 79 (194)
Q Consensus 1 iiYifsii~f~~f~~~~~~~~-~~~~~~~C~tl~~Cf~~~~~~glr~gGGig~~l~~~~~~~~~~~R~~fDl~ffiiv~i 79 (194)
|+|+|+|+||.||+++|+.++ +++++..|+.+.+|.+++++-|+|+||||||.+.+|.+++|+.+|.+||++||++|++
T Consensus 4829 vvylytvvafnffrkfynksed~d~pdmkcddmltcylfhmyvgvragggigdeiedpagd~yeiyriifditffffviv 4908 (5019)
T KOG2243|consen 4829 VVYLYTVVAFNFFRKFYNKSEDDDEPDMKCDDMLTCYLFHMYVGVRAGGGIGDEIEDPAGDEYEIYRIIFDITFFFFVIV 4908 (5019)
T ss_pred HHHHHHHHHHHHHHHHhcccccCCCCCccchhhHHHHhhheeeeeecCCcccccccCCCCCcceeeeeeehhhHHHHHHH
Confidence 579999999999999999887 6778889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcchHHhHHHHHHHHHhhccCceeecCCccccccCCCChhhhhhhhcchhhHHHHHHHhccCCCCCCChh
Q psy13301 80 ILLAIIQGLIIDAFGELRDQLESVKEDMESNCFICGIGKDYFDKVPHGFDTHVQQEHNLANYMFFLMHLINKPDTEFTGQ 159 (194)
Q Consensus 80 i~lnIi~GIIIDtF~eLR~e~~~~~~d~~~~CFICgi~r~~fd~~~~gF~~Hi~~eHnmWnYl~fi~yL~~K~~te~tg~ 159 (194)
|+|.||.|.|||+|+||||++++..+||+.+||||||..+.||..++||+.|..+|||+-||+||++||..|++||+||.
T Consensus 4909 illaiiqgliidafgelrdqqeqvkedmetkcficgigndyfdt~phgfethtlqehnlanylfflmylinkdetehtgq 4988 (5019)
T KOG2243|consen 4909 ILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFICGIGNDYFDTTPHGFETHTLQEHNLANYLFFLMYLINKDETEHTGQ 4988 (5019)
T ss_pred HHHHHHHHHhHHHHHhhHhHHHHHHhhhhcceEEeccccccccCCCCcccccchhhhhHHHHHHHHHHHhcccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHhcCCCCeeechhHHhhhchhhhC
Q psy13301 160 ETYVWNMYQQRCWDFFPVGDCFRKQYEEDLG 190 (194)
Q Consensus 160 E~yV~~~i~~~d~swfP~~~~~~~~~~~~~~ 190 (194)
||||+++.|++.++|||-+.|+++|+|+|+|
T Consensus 4989 esyvwkmyqercwdffpagdcfrkqyedql~ 5019 (5019)
T KOG2243|consen 4989 ESYVWKMYQERCWDFFPAGDCFRKQYEDQLG 5019 (5019)
T ss_pred hhHHHHHHHHHHHhhCCchhhHHHHHHhhcC
Confidence 9999999999999999999999999999987
No 3
>PLN03223 Polycystin cation channel protein; Provisional
Probab=96.79 E-value=0.00098 Score=69.57 Aligned_cols=86 Identities=23% Similarity=0.383 Sum_probs=57.0
Q ss_pred EEEehhHHHHHhHHhhhcccccccccCccchHHHHHHhhhhccccCCccc---ccCCCCCCCCcchhhHhhHHHHHHHHH
Q psy13301 2 LYIYTVIAFNFFRKFYVQEEDDVVDKKCHDMMTCFVFHLYKGVRAGGGIG---DEIGDPDGDDYEVYRIIFDITFFFFVI 78 (194)
Q Consensus 2 iYifsii~f~~f~~~~~~~~~~~~~~~C~tl~~Cf~~~~~~glr~gGGig---~~l~~~~~~~~~~~R~~fDl~ffiiv~ 78 (194)
++.||++|+..|... ...-.|+..++.+.+...+ |.+. +.+.+....+ .+.--+|=.+|.++++
T Consensus 1341 F~AFAqLG~LLFGt~---------ve~FSTf~sSL~TLFqMLL---GDfdYF~eDLk~l~e~n-rVLGPIYFfSFILLV~ 1407 (1634)
T PLN03223 1341 FVGYAFIGHVIFGNA---------SVHFSDMTDSINSLFENLL---GDITYFNEDLKNLTGLQ-FVVGMIYFYSYNIFVF 1407 (1634)
T ss_pred HHHHHHHHHHHhccC---------chhhcCHHHHHHHHHHHHH---cCchHHHHHHHhhhccc-chHHHHHHHHHHHHHH
Confidence 467888888887542 2356788888888886554 2221 1121111111 1233345577889999
Q ss_pred HHHHHHHHHHhhcchHHhHHHH
Q psy13301 79 VILLAIIQGLIIDAFGELRDQL 100 (194)
Q Consensus 79 ii~lnIi~GIIIDtF~eLR~e~ 100 (194)
+|+|||+.|||.|+|++.|++.
T Consensus 1408 FILLNMFIAII~DSFsEVK~d~ 1429 (1634)
T PLN03223 1408 MILFNFLLAIICDAFGEVKANA 1429 (1634)
T ss_pred HHHHHHHHHHHHHHHHHHHhhh
Confidence 9999999999999999998764
No 4
>KOG3599|consensus
Probab=92.89 E-value=0.41 Score=48.38 Aligned_cols=66 Identities=24% Similarity=0.401 Sum_probs=47.0
Q ss_pred ccchHHHHHHhhhhccccCCcccccCCCCCCC-Cc-chhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHHHH
Q psy13301 29 CHDMMTCFVFHLYKGVRAGGGIGDEIGDPDGD-DY-EVYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQLES 102 (194)
Q Consensus 29 C~tl~~Cf~~~~~~glr~gGGig~~l~~~~~~-~~-~~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~~~ 102 (194)
=.|+.+|+.+.+...+ |+ + .|..- .. .+.=.++=.++-+++..|++||+-+||.|+|+|.|++..+
T Consensus 621 f~~f~~s~~t~~~~~~------G~-~-~~~~i~~~~r~LG~~~~~~~v~~v~~illnmF~aiI~~~~~evk~~~~~ 688 (798)
T KOG3599|consen 621 FRTFVASIVTLLRYIL------GD-F-CPAEIFHANRILGPLLFLTYVFVVSFILLNLFVAIINDTYGEVKADLAK 688 (798)
T ss_pred hHHHHHHHHHHHHHHh------cc-C-CccccccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhHHHhh
Confidence 3678899988887765 22 1 12211 11 1233456677888899999999999999999999998866
No 5
>TIGR00870 trp transient-receptor-potential calcium channel protein. after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
Probab=90.80 E-value=1.1 Score=43.99 Aligned_cols=68 Identities=10% Similarity=0.244 Sum_probs=42.2
Q ss_pred cchHHHHHHhhhhccccCCcccccCCCCCCCCcchhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHHHH
Q psy13301 30 HDMMTCFVFHLYKGVRAGGGIGDEIGDPDGDDYEVYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQLES 102 (194)
Q Consensus 30 ~tl~~Cf~~~~~~glr~gGGig~~l~~~~~~~~~~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~~~ 102 (194)
.++...+.+.+...+ |.++.. .+......+.-.++=.+|-++++||++||..+++-|||.+..++.++
T Consensus 557 ~~~~~s~~~lf~~~~----G~~~~~-~~~~~~~~~~~~il~~~y~~i~~ilLlNlLIAmm~~t~~~v~~~~~~ 624 (743)
T TIGR00870 557 STLFETSQELFWAII----GLGDLL-ANEHKFTEFVGLLLFGAYNVIMYILLLNMLIAMMGNTYQLIADDADE 624 (743)
T ss_pred cCHHHHHHHHHHHHc----CCcccc-cccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhhHH
Confidence 345556666555544 234432 12211112233344566888999999999999999999988877443
No 6
>PF08016 PKD_channel: Polycystin cation channel; InterPro: IPR013122 Polycystic kidney diseases (PKD) are disorders characterised by large numbers of cysts distributed throughout grossly-enlarged kidneys. Cyst development is associated with impairment of kidney function, and ultimately kidney failure and death []. Most cases of autosomal dominant PKD result from mutations in the PKD1 gene that cause premature protein termination. A second gene for autosomal dominant polycystic kidney disease has been identified by positional cloning []. The predicted 968-amino acid sequence of the PKD2 gene product (polycystin-2) contains 6 transmembrane domains, with intracellular N- and C-termini. Polycystin-2 shares some similarity with the family of voltage-activated calcium (and sodium) channels, and contains a potential calcium-binding domain. Polycystin-2 is strongly expressed in ovary, foetal and adult kidney, testis, and small intestine. Polycystin-1 requires the presence of this protein for stable expression and is believed to interact with it via its C terminus. All mutations between exons 1 and 11 result in a truncated polycystin-2 that lacks a calcium-binding EF-hand domain and the cytoplasmic domains required for the interaction of polycystin-2 with polycystin-1 []. PKD2, although clinically milder than PKD1, has a deleterious impact on life expectancy. This entry contains proteins belonging to the polycystin family including Mucolipin and Polycystin-1 and -2 (PKD1 and PKD2). The domain contains the cation channel region of PKD1 and PKD2 proteins. PKD1 and PKD2 may function through a common signalling pathway that is necessary for normal tubulogenesis. The PKD2 gene product has six transmembrane spans with intracellular amino- and carboxyl-termini []. Mucolipin is a cationic channel which probably plays a role in the endocytic pathway and in the control of membrane trafficking of proteins and lipids. It could play a major role in the calcium ion transport regulating lysosomal exocytosis [, , ].
Probab=90.32 E-value=0.76 Score=42.25 Aligned_cols=76 Identities=17% Similarity=0.318 Sum_probs=45.6
Q ss_pred ehhHHHHHhHHhhhcccccccccCccchHHHHHHhhhhccccCCcccccCCCCCCCCcchhhHhhHHHHHHHHHHHHHHH
Q psy13301 5 YTVIAFNFFRKFYVQEEDDVVDKKCHDMMTCFVFHLYKGVRAGGGIGDEIGDPDGDDYEVYRIIFDITFFFFVIVILLAI 84 (194)
Q Consensus 5 fsii~f~~f~~~~~~~~~~~~~~~C~tl~~Cf~~~~~~glr~gGGig~~l~~~~~~~~~~~R~~fDl~ffiiv~ii~lnI 84 (194)
||..++..|.. ....-.|+...+.+.+..-+- +-+.. .+..+ +...+.+++ .+|.+++.++++|+
T Consensus 349 fa~~g~l~fG~---------~~~~f~s~~~s~~tl~~~l~g-~~~~~-~~~~~---~~~lg~l~~-~~~~~~~~~illNl 413 (425)
T PF08016_consen 349 FAQAGYLLFGS---------YSEDFSSFSSSLVTLFRMLLG-DFDYD-ELYQA---NPVLGPLFF-FSFMFLVFFILLNL 413 (425)
T ss_pred HHHHHHHhhcC---------CccccCCHHHHHHHHHHHhcC-CCchh-hhhcc---cccHHHHHH-HHHHHHHHHHHHHH
Confidence 55566655532 123456777777666544331 11111 11111 122455555 88889999999999
Q ss_pred HHHHhhcchHH
Q psy13301 85 IQGLIIDAFGE 95 (194)
Q Consensus 85 i~GIIIDtF~e 95 (194)
+.+||.|+|.+
T Consensus 414 ~iaIi~~~y~~ 424 (425)
T PF08016_consen 414 FIAIINDSYEE 424 (425)
T ss_pred HHHHHHHHhhc
Confidence 99999999985
No 7
>PF00520 Ion_trans: Ion transport protein calcium channel signature potassium channel signature sodium channel signature; InterPro: IPR005821 This group of proteins is found in sodium, potassium, and calcium ion channels proteins. The proteins have 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some Na channels proteins the domain is repeated four times, whereas in others (e.g. K channels) the protein forms a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not included in the Pfam family due to it lacking the first four helices. ; GO: 0005216 ion channel activity, 0006811 ion transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 3VMX_B 1QG9_A 1UJL_A 2LE7_A 2LCM_A 3A2A_A 3RW0_A 4EKW_A 3RVY_B 3RVZ_B ....
Probab=85.24 E-value=0.4 Score=37.23 Aligned_cols=84 Identities=18% Similarity=0.274 Sum_probs=48.9
Q ss_pred EEehhHHHHHhHHhhhcc--------cccccccCccchHHHHHHhhhhccccCCcccccCCCCCCCCcchhhHhhHHHHH
Q psy13301 3 YIYTVIAFNFFRKFYVQE--------EDDVVDKKCHDMMTCFVFHLYKGVRAGGGIGDEIGDPDGDDYEVYRIIFDITFF 74 (194)
Q Consensus 3 Yifsii~f~~f~~~~~~~--------~~~~~~~~C~tl~~Cf~~~~~~glr~gGGig~~l~~~~~~~~~~~R~~fDl~ff 74 (194)
+.||++++..|......+ ++....+.+++...++.+.+.-.. +-|-++.+.+.. ......-.+|-.+|.
T Consensus 109 ~~~a~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~f~~~~~s~~~~~~~~t--~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 185 (200)
T PF00520_consen 109 LFFACIGYQLFGGSDNSCCDPTWDSENDIYGYENFDSFGESLYWLFQTMT--GEGWGDVMPSCM-SARSWLAVIFFISFI 185 (200)
T ss_dssp HHHHHHHHHHHTTTS-------SS----SSTHHHHSSHHHHHHHHHHHHT--TTTCCCCHHHHH-HTTSTTHHHHHHHHH
T ss_pred ccccchhheecccccccccccccccccccccccccccccccccccccccc--cCCccccccccc-cccchhHhHHhhhhh
Confidence 457778887776543221 012233445667777766663322 223344332100 011356788889999
Q ss_pred HHHHHHHHHHHHHHh
Q psy13301 75 FFVIVILLAIIQGLI 89 (194)
Q Consensus 75 iiv~ii~lnIi~GII 89 (194)
+++.++++|++.|+|
T Consensus 186 ~i~~~~l~nlliavi 200 (200)
T PF00520_consen 186 IIVSILLLNLLIAVI 200 (200)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHhcC
Confidence 999999999999987
No 8
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=76.33 E-value=2.3 Score=35.14 Aligned_cols=39 Identities=15% Similarity=0.313 Sum_probs=28.6
Q ss_pred hHHhHHHHHHHHHhhccCceeecCCccccccCCCChhhhhhhhc
Q psy13301 93 FGELRDQLESVKEDMESNCFICGIGKDYFDKVPHGFDTHVQQEH 136 (194)
Q Consensus 93 F~eLR~e~~~~~~d~~~~CFICgi~r~~fd~~~~gF~~Hi~~eH 136 (194)
=+++++.++++-+.+..+|-||+.. ++....+ .|+-++|
T Consensus 5 ~k~~~~~k~~l~e~Q~G~CaiC~~~---l~~~~~~--~~vDHDH 43 (157)
T PHA02565 5 GKSYKEEKQKLFEAQNGICPLCKRE---LDGDVSK--NHLDHDH 43 (157)
T ss_pred HHHHHHHHHHHHHHhCCcCCCCCCc---cCCCccc--cccCCCC
Confidence 3689999999999999999999854 2211111 3777777
No 9
>KOG2302|consensus
Probab=57.39 E-value=41 Score=35.99 Aligned_cols=99 Identities=15% Similarity=0.330 Sum_probs=62.3
Q ss_pred EEehhHHHHHhHH-hhhcccc-------------ccc-----ccCccchHHHHHHhhhhccccCCcccccCCC-------
Q psy13301 3 YIYTVIAFNFFRK-FYVQEED-------------DVV-----DKKCHDMMTCFVFHLYKGVRAGGGIGDEIGD------- 56 (194)
Q Consensus 3 Yifsii~f~~f~~-~~~~~~~-------------~~~-----~~~C~tl~~Cf~~~~~~glr~gGGig~~l~~------- 56 (194)
.||++++-+.|+. +|.-... +.. ...-+++.|-.++.+...-+ -|..+.+.+
T Consensus 1272 iiFgilgvqLFkgkfy~c~g~dtrnitnKSdc~aa~yRwvrhkyNfdnlgqalmSLFvLaSk--DgWv~ImyDgldavav 1349 (1956)
T KOG2302|consen 1272 IIFGILGVQLFKGKFYHCLGVDTRNITNKSDCMAAPYRWVRHKYNFDNLGQALMSLFVLASK--DGWVNIMYDGLDAVAV 1349 (1956)
T ss_pred HHHHHHHHHHhcccceeccccccccccchhhhcccchhhhhhhcccchHHHHHHHHHHHhcc--cchhhhhccchhhcee
Confidence 4788889888884 4432110 000 12346777777666544333 233333321
Q ss_pred ---CCCCCcchhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHHHHHH
Q psy13301 57 ---PDGDDYEVYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQLESVK 104 (194)
Q Consensus 57 ---~~~~~~~~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~~~~~ 104 (194)
|- -+...|-.+|=.+|++||..++|||+.|..+..|-.=|+++++-+
T Consensus 1350 dqqPI-~nhnpwmllYfIsfllIvsffVlnmfVgvvvenfhKcrqhqe~Ee 1399 (1956)
T KOG2302|consen 1350 DQQPI-LNHNPWMLLYFISFLLIVSFFVLNMFVGVVVENFHKCRQHQEAEE 1399 (1956)
T ss_pred eeecc-ccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11 122357788999999999999999999999999988887665443
No 10
>KOG3676|consensus
Probab=54.48 E-value=47 Score=33.91 Aligned_cols=31 Identities=10% Similarity=0.417 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcchHHhHHHH
Q psy13301 70 DITFFFFVIVILLAIIQGLIIDAFGELRDQL 100 (194)
Q Consensus 70 Dl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~ 100 (194)
=++|-|++.|+++||.....-+|....=.++
T Consensus 624 fv~y~ilv~ILllNMLIAMMg~Ty~~Va~~s 654 (782)
T KOG3676|consen 624 FVAYMILVTILLLNMLIAMMGNTYETVAQES 654 (782)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHhH
Confidence 3567788889999999999999976554443
No 11
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=44.60 E-value=93 Score=26.33 Aligned_cols=39 Identities=13% Similarity=0.103 Sum_probs=28.3
Q ss_pred CcchhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHH
Q psy13301 61 DYEVYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQ 99 (194)
Q Consensus 61 ~~~~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e 99 (194)
+...+.+++-++-|+++.+++-.++..-|.+...+-++.
T Consensus 50 ~~~~~~l~w~~I~FliL~~lL~k~~~~pI~~vLe~R~~~ 88 (204)
T PRK09174 50 THYASQLLWLAITFGLFYLFMSRVILPRIGGIIETRRDR 88 (204)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334678888888888888888888877777766544433
No 12
>PHA03023 hypothetical protein; Provisional
Probab=41.62 E-value=70 Score=25.15 Aligned_cols=36 Identities=14% Similarity=0.225 Sum_probs=22.1
Q ss_pred HHHHHHHHHhhcchHHhHHHHHHHHH---hhccCceeecCCcc
Q psy13301 80 ILLAIIQGLIIDAFGELRDQLESVKE---DMESNCFICGIGKD 119 (194)
Q Consensus 80 i~lnIi~GIIIDtF~eLR~e~~~~~~---d~~~~CFICgi~r~ 119 (194)
+..|||.--|.+. ||-|.+.-++ +.+++ |+|=-+|.
T Consensus 13 LIfNIIvp~I~eK---Lr~E~~ay~~y~~~L~~~-~~Cv~d~l 51 (112)
T PHA03023 13 LIINIIFNKELNK---LELDKKIFENAEDDLKTT-ISCINDHW 51 (112)
T ss_pred HHHHHHHHHHHHH---HHHHHHHHHHHHHhcCCc-EEEECCEE
Confidence 3457777777664 6666654333 45666 99965554
No 13
>KOG3609|consensus
Probab=39.80 E-value=33 Score=35.16 Aligned_cols=68 Identities=12% Similarity=0.195 Sum_probs=44.3
Q ss_pred CccchHHHHHHhhhhccccCCcccccCCCC-CCCCcchhhHhhH---HHHHHHHHHHHHHHHHHHhhcchHHhHHHH
Q psy13301 28 KCHDMMTCFVFHLYKGVRAGGGIGDEIGDP-DGDDYEVYRIIFD---ITFFFFVIVILLAIIQGLIIDAFGELRDQL 100 (194)
Q Consensus 28 ~C~tl~~Cf~~~~~~glr~gGGig~~l~~~-~~~~~~~~R~~fD---l~ffiiv~ii~lnIi~GIIIDtF~eLR~e~ 100 (194)
.+.|+.+-+-+.+..-| |+.+ +.++ -+.+..+.+++.- =+|.++.+|++|||...+|-++|.+.-|+.
T Consensus 547 ~fsti~eS~~tLFWsiF----glv~-~~~~~l~~~Hkf~e~ig~~lfG~Y~vi~vIVLLNmLIAMmnnSyQeIeD~A 618 (822)
T KOG3609|consen 547 SFSTIGESSKTLFWSIF----GLVV-LGSVVLPYKHKFTEFIGEVLFGVYNVILIIVLLNLLIAMMSNSYQEIEDDA 618 (822)
T ss_pred ccccHHHHHHHHHHHHH----hccc-ccceecccchhHHHHHHHHHHHhhheeeHHHHHHHHHHHHHhHHHHHhhcc
Confidence 46777777777776665 4444 2221 1222234444332 347889999999999999999999887654
No 14
>PF14147 Spore_YhaL: Sporulation protein YhaL
Probab=39.76 E-value=34 Score=23.41 Aligned_cols=25 Identities=24% Similarity=0.450 Sum_probs=19.7
Q ss_pred HHHHHhhcchHHhHHHHHHHHHhhc
Q psy13301 84 IIQGLIIDAFGELRDQLESVKEDME 108 (194)
Q Consensus 84 Ii~GIIIDtF~eLR~e~~~~~~d~~ 108 (194)
+|.|||+-.+-.+|.-+.+.+.|++
T Consensus 8 vi~gI~~S~ym~v~t~~eE~~~dq~ 32 (52)
T PF14147_consen 8 VIAGIIFSGYMAVKTAKEEREIDQE 32 (52)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 4678888888888888888777764
No 15
>PF03904 DUF334: Domain of unknown function (DUF334); InterPro: IPR005602 This is a family of proteins found in Staphylococcus aureus plasmid with no characterised function.
Probab=39.42 E-value=59 Score=28.52 Aligned_cols=18 Identities=11% Similarity=0.576 Sum_probs=15.4
Q ss_pred hhhhcchhhHHHHHHHhc
Q psy13301 132 VQQEHNLANYMFFLMHLI 149 (194)
Q Consensus 132 i~~eHnmWnYl~fi~yL~ 149 (194)
|+..|..|-||+|++|+-
T Consensus 191 ik~se~~~~~lwyi~Y~v 208 (230)
T PF03904_consen 191 IKASESFWTYLWYIAYLV 208 (230)
T ss_pred HhhhHhHHHHHHHHHHhh
Confidence 566788999999999984
No 16
>PF05803 Chordopox_L2: Chordopoxvirus L2 protein; InterPro: IPR008447 This family consists of several Chordopoxvirus L2 proteins.
Probab=39.21 E-value=33 Score=25.78 Aligned_cols=19 Identities=37% Similarity=0.772 Sum_probs=15.5
Q ss_pred hhhHhhHHHHHHHHHHHHH
Q psy13301 64 VYRIIFDITFFFFVIVILL 82 (194)
Q Consensus 64 ~~R~~fDl~ffiiv~ii~l 82 (194)
..|++||++.+++|+..++
T Consensus 40 ~~RLlfDlli~~~Vi~~~~ 58 (87)
T PF05803_consen 40 FLRLLFDLLITVIVIIIFL 58 (87)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6899999999888776643
No 17
>KOG2301|consensus
Probab=38.71 E-value=12 Score=41.04 Aligned_cols=89 Identities=20% Similarity=0.318 Sum_probs=51.0
Q ss_pred EEEehhHHHHHhHHhhhcccccccccCccchHHHHHHhhhhccccCCcccccCCCCCCCCcchhhHhhHHHHHHHHHHHH
Q psy13301 2 LYIYTVIAFNFFRKFYVQEEDDVVDKKCHDMMTCFVFHLYKGVRAGGGIGDEIGDPDGDDYEVYRIIFDITFFFFVIVIL 81 (194)
Q Consensus 2 iYifsii~f~~f~~~~~~~~~~~~~~~C~tl~~Cf~~~~~~glr~gGGig~~l~~~~~~~~~~~R~~fDl~ffiiv~ii~ 81 (194)
+.|||++|...|-..|+.. .+.. ..=+++.+-|++++. -.+|+.-+++.+-........=.+|=+..+++-+.++
T Consensus 576 i~Ifa~~gmqlFg~~~n~~-~~~~-~~~~~fp~sfl~vFq---lt~e~W~evm~~~~~~~~~~~~~i~Fi~~~l~gn~vv 650 (1592)
T KOG2301|consen 576 IFIFAAIGMQLFGGVYNLH-CDIH-WHFTDFPHSFLSVFQ---ITCEEWTDVMWDCMEAAGQPLCAIYFIAYFLFGNLVV 650 (1592)
T ss_pred HHHHHHhhHHhhCcccCCC-CCCc-cchhhCHHHHHHHHH---HcCCchHHHHHHHHHHhccchhhhHHHHHHHHHHHHH
Confidence 5689999999998888652 1111 123455666666665 3344444444211000001111123344556667789
Q ss_pred HHHHHHHhhcchHH
Q psy13301 82 LAIIQGLIIDAFGE 95 (194)
Q Consensus 82 lnIi~GIIIDtF~e 95 (194)
||++-.+++|.|+.
T Consensus 651 LnlFlAl~~~n~~~ 664 (1592)
T KOG2301|consen 651 LNLFLALILDNFES 664 (1592)
T ss_pred HHHHHHHHHhhchh
Confidence 99999999999974
No 18
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=38.49 E-value=24 Score=21.01 Aligned_cols=18 Identities=17% Similarity=0.167 Sum_probs=16.1
Q ss_pred hhHHHHHHHhcCCCCeee
Q psy13301 159 QETYVWNMYQQRCWDFFP 176 (194)
Q Consensus 159 ~E~yV~~~i~~~d~swfP 176 (194)
+|.||.-||.++...|.|
T Consensus 9 V~~yv~yKLsQrgy~w~~ 26 (27)
T smart00265 9 VVDYVTYKLSQNGYEWDA 26 (27)
T ss_pred HHHHHHHHHhhcCCCCCC
Confidence 688999999999999976
No 19
>PHA02706 hypothetical protein; Provisional
Probab=36.34 E-value=40 Score=23.01 Aligned_cols=23 Identities=30% Similarity=0.560 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcc
Q psy13301 70 DITFFFFVIVILLAIIQGLIIDA 92 (194)
Q Consensus 70 Dl~ffiiv~ii~lnIi~GIIIDt 92 (194)
..+--++-++.||==|..|||||
T Consensus 4 e~tllviaiimmllgi~siiidt 26 (58)
T PHA02706 4 ENTLLVIAIIMMLLGIASIIIDT 26 (58)
T ss_pred hhhhHHHHHHHHHHhhHHHhhhe
Confidence 34444555666777788999999
No 20
>PHA02690 hypothetical protein; Provisional
Probab=34.61 E-value=44 Score=24.98 Aligned_cols=18 Identities=28% Similarity=0.837 Sum_probs=14.1
Q ss_pred chhhHhhHHHHHHHHHHH
Q psy13301 63 EVYRIIFDITFFFFVIVI 80 (194)
Q Consensus 63 ~~~R~~fDl~ffiiv~ii 80 (194)
..+|++||+.+-++|++-
T Consensus 40 ~~~RlLfDL~lTvfV~my 57 (90)
T PHA02690 40 QMWRLLFDLLLTVFVVMY 57 (90)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 378999999997776553
No 21
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=34.19 E-value=8.7 Score=28.22 Aligned_cols=20 Identities=30% Similarity=0.705 Sum_probs=14.0
Q ss_pred HHHHHHHHHhhccCceeecC
Q psy13301 97 RDQLESVKEDMESNCFICGI 116 (194)
Q Consensus 97 R~e~~~~~~d~~~~CFICgi 116 (194)
.++.+++.+.+..+|-|||.
T Consensus 11 ~~~~~~l~~~q~~~C~iC~~ 30 (81)
T PF02945_consen 11 PEEYEALLEEQGGRCAICGK 30 (81)
T ss_dssp HHHHHCCHHHTTTE-TTT-S
T ss_pred HHHHHHHHHHhCCcCcCCCC
Confidence 45666777788899999997
No 22
>COG3238 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.11 E-value=36 Score=27.87 Aligned_cols=22 Identities=41% Similarity=0.632 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHhhcchHHh
Q psy13301 75 FFVIVILLAIIQGLIIDAFGEL 96 (194)
Q Consensus 75 iiv~ii~lnIi~GIIIDtF~eL 96 (194)
.++.++.-+++.|.+||.|+-.
T Consensus 98 t~~l~i~gQli~glliD~fG~~ 119 (150)
T COG3238 98 TIALVIAGQLIMGLLIDHFGWF 119 (150)
T ss_pred HHHHHHHHHHHHHHHHHhhccc
Confidence 3466778899999999999865
No 23
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=33.04 E-value=12 Score=25.99 Aligned_cols=30 Identities=20% Similarity=0.566 Sum_probs=21.5
Q ss_pred hhccCceeecCCccccccCCCChhhhhhhh
Q psy13301 106 DMESNCFICGIGKDYFDKVPHGFDTHVQQE 135 (194)
Q Consensus 106 d~~~~CFICgi~r~~fd~~~~gF~~Hi~~e 135 (194)
+-+-+||-||+.-+..+..+.-+++|.+..
T Consensus 34 ~d~v~C~~C~~~l~~w~~~Ddp~~~H~~~s 63 (70)
T PF00653_consen 34 GDRVRCFYCGLELDNWEPNDDPWEEHKRHS 63 (70)
T ss_dssp TTEEEETTTTEEEES-STT--HHHHHHHHS
T ss_pred CCEEEEeccCCEEeCCCCCCCHHHHHHHHC
Confidence 346789999999988888777788887653
No 24
>KOG2301|consensus
Probab=33.00 E-value=32 Score=37.83 Aligned_cols=38 Identities=13% Similarity=0.364 Sum_probs=33.7
Q ss_pred hhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHHH
Q psy13301 64 VYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQLE 101 (194)
Q Consensus 64 ~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~~ 101 (194)
.+-++|=.+|+++...|++|+.-++|+|-|+-+.++..
T Consensus 1371 ~~Ai~YF~Sf~iIs~~IvvNLfVAVImeNFs~~t~~~s 1408 (1592)
T KOG2301|consen 1371 TVAIIYFVSWILISSYIVVNLFVAVILENFSYATEDSS 1408 (1592)
T ss_pred CcceehhhHHHHHHHHHHHHHHHHHHHhhhhhhccccc
Confidence 45677889999999999999999999999999887764
No 25
>KOG1101|consensus
Probab=31.92 E-value=28 Score=28.27 Aligned_cols=28 Identities=21% Similarity=0.500 Sum_probs=25.0
Q ss_pred ccCceeecCCccccccCCCChhhhhhhh
Q psy13301 108 ESNCFICGIGKDYFDKVPHGFDTHVQQE 135 (194)
Q Consensus 108 ~~~CFICgi~r~~fd~~~~gF~~Hi~~e 135 (194)
.-+||-||..=...|..+.-|.+|-|.-
T Consensus 51 ~~~Cf~C~~~L~~We~~DDPW~EH~k~~ 78 (147)
T KOG1101|consen 51 CVKCFFCSGGLDDWEPGDDPWEEHAKWS 78 (147)
T ss_pred ceECcccCcccccCCCCCCcHHHHHhhC
Confidence 5689999999999999999999999763
No 26
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.92 E-value=14 Score=22.25 Aligned_cols=16 Identities=44% Similarity=0.816 Sum_probs=13.2
Q ss_pred ccCceeecCCcccccc
Q psy13301 108 ESNCFICGIGKDYFDK 123 (194)
Q Consensus 108 ~~~CFICgi~r~~fd~ 123 (194)
..+|-+||..++.|..
T Consensus 17 ~~~CP~Cg~~~~~F~~ 32 (33)
T cd00350 17 PWVCPVCGAPKDKFEK 32 (33)
T ss_pred CCcCcCCCCcHHHcEE
Confidence 4589999999988864
No 27
>PF13314 DUF4083: Domain of unknown function (DUF4083)
Probab=30.19 E-value=86 Score=21.90 Aligned_cols=23 Identities=30% Similarity=0.605 Sum_probs=15.4
Q ss_pred hhHHHHHHHHH--HHHHHHHHHHhh
Q psy13301 68 IFDITFFFFVI--VILLAIIQGLII 90 (194)
Q Consensus 68 ~fDl~ffiiv~--ii~lnIi~GIII 90 (194)
++|++|+++|+ ++++-+.||.+|
T Consensus 3 i~~~Iy~~~Vi~l~vl~~~~Ftl~I 27 (58)
T PF13314_consen 3 IGDLIYYILVIILIVLFGASFTLFI 27 (58)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67889998444 445566777665
No 28
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.47 E-value=1.1e+02 Score=22.18 Aligned_cols=31 Identities=26% Similarity=0.461 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHhhcchHHhHHHHHHHHH
Q psy13301 75 FFVIVILLAIIQGLIIDAFGELRDQLESVKE 105 (194)
Q Consensus 75 iiv~ii~lnIi~GIIIDtF~eLR~e~~~~~~ 105 (194)
+-++++.+.+++|+|+-.|=.-|.-+.++.+
T Consensus 5 lail~ivl~ll~G~~~G~fiark~~~k~lk~ 35 (71)
T COG3763 5 LAILLIVLALLAGLIGGFFIARKQMKKQLKD 35 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3457778899999999999887776666554
No 29
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=29.29 E-value=18 Score=22.17 Aligned_cols=16 Identities=38% Similarity=0.887 Sum_probs=13.1
Q ss_pred ccCceeecCCcccccc
Q psy13301 108 ESNCFICGIGKDYFDK 123 (194)
Q Consensus 108 ~~~CFICgi~r~~fd~ 123 (194)
-.+|-+||-.++.|++
T Consensus 18 p~~CP~Cg~~~~~F~~ 33 (34)
T cd00729 18 PEKCPICGAPKEKFEE 33 (34)
T ss_pred CCcCcCCCCchHHcEE
Confidence 3689999999888864
No 30
>PF04657 DUF606: Protein of unknown function, DUF606; InterPro: IPR006750 This family contains uncharacterised bacterial proteins.
Probab=29.02 E-value=55 Score=25.87 Aligned_cols=28 Identities=21% Similarity=0.420 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHhhcchHHhHHHHH
Q psy13301 74 FFFVIVILLAIIQGLIIDAFGELRDQLE 101 (194)
Q Consensus 74 fiiv~ii~lnIi~GIIIDtF~eLR~e~~ 101 (194)
..++.++.-+++.|++||.|+-+-.++.
T Consensus 92 ~~~~l~~~GQl~~sl~iD~fG~fg~~~~ 119 (138)
T PF04657_consen 92 LTTILIVAGQLIASLLIDHFGLFGAPKR 119 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHccccCCCCC
Confidence 3456677789999999999987655543
No 31
>KOG2302|consensus
Probab=27.79 E-value=97 Score=33.37 Aligned_cols=43 Identities=12% Similarity=0.454 Sum_probs=34.9
Q ss_pred hhHHHHHHHHHHH----HHHHHHHHhhcchHHhHHHHHHHHHhhccC
Q psy13301 68 IFDITFFFFVIVI----LLAIIQGLIIDAFGELRDQLESVKEDMESN 110 (194)
Q Consensus 68 ~fDl~ffiiv~ii----~lnIi~GIIIDtF~eLR~e~~~~~~d~~~~ 110 (194)
+|.++|||+++|+ |+|+-.=+|.-.|+|-++...++...++-+
T Consensus 364 fynfiyfilliivgsffminKOGvviatqfsetkqresqlmreqr~r 410 (1956)
T KOG2302|consen 364 FYNFIYFILLIIVGSFFMINLCLVVIATQFSETKQRESQLMREQRQR 410 (1956)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHH
Confidence 6888899988876 789999999999999877777776666543
No 32
>PRK08476 F0F1 ATP synthase subunit B'; Validated
Probab=27.73 E-value=2e+02 Score=22.69 Aligned_cols=40 Identities=15% Similarity=0.306 Sum_probs=31.4
Q ss_pred hhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHHHHH
Q psy13301 64 VYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQLESV 103 (194)
Q Consensus 64 ~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~~~~ 103 (194)
++-+++-++.|+++.+++--++++-|.....+-++.-++-
T Consensus 7 ~~~~~~qli~Flil~~~l~kfl~kPi~~~l~~R~~~I~~~ 46 (141)
T PRK08476 7 PYLMLATFVVFLLLIVILNSWLYKPLLKFMDNRNASIKND 46 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5678899999999999988899999988877655554433
No 33
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=26.83 E-value=40 Score=20.09 Aligned_cols=18 Identities=22% Similarity=0.240 Sum_probs=15.8
Q ss_pred hhHHHHHHHhcCCCCeee
Q psy13301 159 QETYVWNMYQQRCWDFFP 176 (194)
Q Consensus 159 ~E~yV~~~i~~~d~swfP 176 (194)
+|.||.-||.++...|.|
T Consensus 9 V~~yi~yKLsQrgy~w~~ 26 (27)
T PF02180_consen 9 VEDYISYKLSQRGYVWEE 26 (27)
T ss_dssp HHHHHHHHHHHTTSTSTT
T ss_pred HHHHHHHHhhhcCCCCCC
Confidence 688999999999999865
No 34
>PRK06231 F0F1 ATP synthase subunit B; Validated
Probab=26.48 E-value=1.8e+02 Score=24.56 Aligned_cols=40 Identities=8% Similarity=0.161 Sum_probs=32.9
Q ss_pred hhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHHHHH
Q psy13301 64 VYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQLESV 103 (194)
Q Consensus 64 ~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~~~~ 103 (194)
++-+++-++.|++++.|+--++.+-|.+.+.+-|+.-.+-
T Consensus 48 ~~~~i~qlInFlIlv~lL~k~l~kPi~~~L~~R~~~I~~~ 87 (205)
T PRK06231 48 FWVFIAHLIAFSILLLLGIFLFWKPTQRFLNKRKELIEAE 87 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788899999999999999999999999988766554433
No 35
>PRK13461 F0F1 ATP synthase subunit B; Provisional
Probab=26.35 E-value=2.1e+02 Score=22.58 Aligned_cols=40 Identities=18% Similarity=0.297 Sum_probs=30.6
Q ss_pred chhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHHHH
Q psy13301 63 EVYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQLES 102 (194)
Q Consensus 63 ~~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~~~ 102 (194)
+++-+++-++.|+++..|+--.+.+-|.+.+.+-++.-..
T Consensus 4 ~~~~~~~~~inF~il~~iL~~f~~kpi~~~l~~R~~~I~~ 43 (159)
T PRK13461 4 NIPTIIATIINFIILLLILKHFFFDKIKAVIDSRQSEIDN 43 (159)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 3567888888888888888888889998888765554433
No 36
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=25.05 E-value=2.3e+02 Score=22.99 Aligned_cols=38 Identities=13% Similarity=0.263 Sum_probs=29.9
Q ss_pred hhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHHH
Q psy13301 64 VYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQLE 101 (194)
Q Consensus 64 ~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~~ 101 (194)
++-+++-++.|++++.++--++.+-|.+...+-++.-.
T Consensus 18 ~~t~~~~iInFliL~~lL~~~l~~pi~~~l~~R~~~I~ 55 (173)
T PRK13453 18 WGTVIVTVLTFIVLLALLKKFAWGPLKDVMDKRERDIN 55 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56688888888888888888888999988776665543
No 37
>PHA02845 hypothetical protein; Provisional
Probab=25.03 E-value=73 Score=24.16 Aligned_cols=19 Identities=21% Similarity=0.649 Sum_probs=14.9
Q ss_pred hhhHhhHHHHHHHHHHHHH
Q psy13301 64 VYRIIFDITFFFFVIVILL 82 (194)
Q Consensus 64 ~~R~~fDl~ffiiv~ii~l 82 (194)
..|.+||++..++|+..++
T Consensus 41 ~~RLlfDl~i~viVi~~~~ 59 (91)
T PHA02845 41 FIRLTIDLILLIIVMIFLM 59 (91)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5799999998887776543
No 38
>TIGR01710 typeII_sec_gspG general secretion pathway protein G. This model represents GspG, protein G of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=24.75 E-value=1.3e+02 Score=23.41 Aligned_cols=30 Identities=13% Similarity=0.349 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHhhcchHHhHHHHHHHH
Q psy13301 75 FFVIVILLAIIQGLIIDAFGELRDQLESVK 104 (194)
Q Consensus 75 iiv~ii~lnIi~GIIIDtF~eLR~e~~~~~ 104 (194)
++|++.++-|+.++++-++....++.++.+
T Consensus 8 llivlaIigil~~i~~p~~~~~~~~a~~~~ 37 (134)
T TIGR01710 8 IMVVLVILGLLAALVAPKLFSQADKAKAQV 37 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456777778888888877766555444433
No 39
>PRK14473 F0F1 ATP synthase subunit B; Provisional
Probab=24.53 E-value=2.4e+02 Score=22.39 Aligned_cols=42 Identities=14% Similarity=0.292 Sum_probs=32.5
Q ss_pred hhhHhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHHHHHHH
Q psy13301 64 VYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQLESVKE 105 (194)
Q Consensus 64 ~~R~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~~~~~~ 105 (194)
++-+++-++-|+|+++|+--++.+-|.+...+-++.-.+..+
T Consensus 8 ~~~~~~~~inflil~~lL~~fl~kpi~~~l~~R~~~I~~~l~ 49 (164)
T PRK14473 8 LGLLIAQLINFLLLIFLLRTFLYRPVLNLLNERTRRIEESLR 49 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466788888899998888899999999988876655444333
No 40
>PF08653 DASH_Dam1: DASH complex subunit Dam1; InterPro: IPR013962 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=22.91 E-value=34 Score=23.75 Aligned_cols=27 Identities=30% Similarity=0.470 Sum_probs=23.9
Q ss_pred HhhcchHHhHHHHHHHHHhhccCceee
Q psy13301 88 LIIDAFGELRDQLESVKEDMESNCFIC 114 (194)
Q Consensus 88 IIIDtF~eLR~e~~~~~~d~~~~CFIC 114 (194)
.++++|++|.|....++..+.+-+.|+
T Consensus 2 ~l~~~f~eL~D~~~~L~~n~~~L~~ih 28 (58)
T PF08653_consen 2 FLEPQFAELSDSMETLDKNMEQLNQIH 28 (58)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367899999999999999999888877
No 41
>PRK10537 voltage-gated potassium channel; Provisional
Probab=22.90 E-value=3.2e+02 Score=25.45 Aligned_cols=13 Identities=23% Similarity=0.440 Sum_probs=9.9
Q ss_pred hccCceeecCCcc
Q psy13301 107 MESNCFICGIGKD 119 (194)
Q Consensus 107 ~~~~CFICgi~r~ 119 (194)
.++.--|||..+-
T Consensus 239 ~k~HvII~G~g~l 251 (393)
T PRK10537 239 RKDHFIICGHSPL 251 (393)
T ss_pred cCCeEEEECCChH
Confidence 3688899998764
No 42
>COG2165 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.86 E-value=1.6e+02 Score=21.57 Aligned_cols=26 Identities=15% Similarity=0.409 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHhhcchHHhHHHH
Q psy13301 75 FFVIVILLAIIQGLIIDAFGELRDQL 100 (194)
Q Consensus 75 iiv~ii~lnIi~GIIIDtF~eLR~e~ 100 (194)
++|+++++-|+.++++-++..-+++.
T Consensus 15 lLVvl~Iigil~~~~~p~~~~~~~~~ 40 (149)
T COG2165 15 LLVVLAIIGILAALALPSLQGSIDKA 40 (149)
T ss_pred HHHHHHHHHHHHHHHHhhhhhHHHHH
Confidence 46777788888888888877666555
No 43
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=22.44 E-value=3e+02 Score=22.15 Aligned_cols=34 Identities=18% Similarity=0.255 Sum_probs=19.0
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHhhcchHHhHHHH
Q psy13301 67 IIFDITFFFFVIVILLAIIQGLIIDAFGELRDQL 100 (194)
Q Consensus 67 ~~fDl~ffiiv~ii~lnIi~GIIIDtF~eLR~e~ 100 (194)
+++-++-|+|++.|+--.+...|.+.+.+-++.-
T Consensus 22 ~~~~iinflIl~~lL~~fl~kpI~~~l~~R~~~I 55 (174)
T PRK07352 22 LETNLINLAIVIGLLYYFGRGFLGKILEERREAI 55 (174)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 3444445555555555555577777766555443
No 44
>PF00253 Ribosomal_S14: Ribosomal protein S14p/S29e; InterPro: IPR001209 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 [, ]. S14 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S14 is known to be required for the assembly of 30S particles and may also be responsible for determining the conformation of 16S rRNA at the A site. It belongs to a family of ribosomal proteins [, ] that include, bacterial, algal and plant chloroplast, yeast mitochondrial, cyanelle and archael, Methanococcus vannielii S14's, as well as yeast mitochondrial MRP2, yeast YS29A/B and mammalian S29.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_N 2XZM_N 1S1H_N 3IZ6_N 2YKR_N 2QBB_N 3I1Z_N 3OAQ_N 3R8O_N 2Z4K_N ....
Probab=22.01 E-value=46 Score=22.46 Aligned_cols=18 Identities=22% Similarity=0.562 Sum_probs=15.3
Q ss_pred hccCceeecCCccccccC
Q psy13301 107 MESNCFICGIGKDYFDKV 124 (194)
Q Consensus 107 ~~~~CFICgi~r~~fd~~ 124 (194)
.+|.|.+||-.|..+-+-
T Consensus 15 ~~nrC~~tGR~rgv~r~f 32 (55)
T PF00253_consen 15 IKNRCVITGRSRGVIRKF 32 (55)
T ss_dssp SCSSBSSSCSSSSBETTT
T ss_pred CCeecccCCCceeeeccc
Confidence 579999999999888664
No 45
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=21.97 E-value=52 Score=22.41 Aligned_cols=27 Identities=26% Similarity=0.577 Sum_probs=20.5
Q ss_pred ccCceeecCCccccccCCCChhhhhhh
Q psy13301 108 ESNCFICGIGKDYFDKVPHGFDTHVQQ 134 (194)
Q Consensus 108 ~~~CFICgi~r~~fd~~~~gF~~Hi~~ 134 (194)
.-+|+-||..=+..+..+.-+++|.+.
T Consensus 36 ~v~C~~C~~~l~~w~~~d~p~~~H~~~ 62 (71)
T smart00238 36 EVKCFFCGGELDNWEPGDDPWEEHKKW 62 (71)
T ss_pred EEEeCCCCCCcCCCCCCCCHHHHHhHh
Confidence 578999999877766666677787653
No 46
>COG1773 Rubredoxin [Energy production and conversion]
Probab=20.73 E-value=42 Score=23.18 Aligned_cols=17 Identities=35% Similarity=0.762 Sum_probs=14.1
Q ss_pred cCceeecCCccccccCC
Q psy13301 109 SNCFICGIGKDYFDKVP 125 (194)
Q Consensus 109 ~~CFICgi~r~~fd~~~ 125 (194)
=.|-.||..|+.|++.+
T Consensus 37 w~CP~Cg~~K~~F~~~~ 53 (55)
T COG1773 37 WVCPECGVGKKDFEMID 53 (55)
T ss_pred cCCCCCCCCHhHeeecc
Confidence 47999999999998754
Done!