Query psy5915
Match_columns 89
No_of_seqs 128 out of 1019
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 21:42:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5915.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5915hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2057 AtoA Acyl CoA:acetate/ 99.9 1.1E-21 2.4E-26 147.7 7.1 67 20-86 156-222 (225)
2 KOG3822|consensus 99.8 1E-20 2.3E-25 151.9 4.8 71 19-89 446-516 (516)
3 TIGR02428 pcaJ_scoB_fam 3-oxoa 99.6 1.8E-15 3.8E-20 111.6 6.8 57 20-77 151-207 (207)
4 COG4670 Acyl CoA:acetate/3-ket 98.9 1.5E-09 3.2E-14 89.8 5.0 49 37-86 458-507 (527)
5 PF01144 CoA_trans: Coenzyme A 94.2 0.0086 1.9E-07 43.3 -1.0 48 23-70 167-217 (217)
6 PF13014 KH_3: KH domain 61.5 6.7 0.00015 21.5 1.7 19 61-79 10-28 (43)
7 cd02410 archeal_CPSF_KH The ar 56.3 24 0.00053 25.4 4.2 32 46-77 72-111 (145)
8 PF13336 AcetylCoA_hyd_C: Acet 46.8 22 0.00047 25.7 2.7 29 19-47 95-126 (154)
9 PRK05354 arginine decarboxylas 46.0 43 0.00093 29.0 4.8 37 40-76 557-593 (634)
10 cd02393 PNPase_KH Polynucleoti 42.6 19 0.00041 21.4 1.6 20 61-80 21-40 (61)
11 cd01760 RBD Ubiquitin-like dom 41.4 70 0.0015 20.0 4.1 23 49-71 7-29 (72)
12 TIGR01273 speA arginine decarb 40.6 59 0.0013 28.1 4.8 37 40-76 550-586 (624)
13 cd02394 vigilin_like_KH K homo 39.1 32 0.00069 19.7 2.2 20 61-80 19-38 (62)
14 PF11994 DUF3489: Protein of u 38.3 23 0.0005 22.7 1.6 18 59-76 22-39 (72)
15 COG1782 Predicted metal-depend 37.8 23 0.0005 30.8 1.9 65 3-78 63-135 (637)
16 cd01818 TIAM1_RBD Ubiquitin do 36.2 59 0.0013 21.2 3.3 23 49-71 7-29 (77)
17 PF04312 DUF460: Protein of un 34.1 1.1E+02 0.0024 21.8 4.7 46 39-86 42-90 (138)
18 cd02396 PCBP_like_KH K homolog 33.8 30 0.00065 20.4 1.5 22 60-81 18-39 (65)
19 PF02196 RBD: Raf-like Ras-bin 32.4 1.1E+02 0.0023 18.8 3.9 22 49-70 8-29 (71)
20 smart00455 RBD Raf-like Ras-bi 31.4 1.3E+02 0.0028 18.5 4.2 23 49-71 7-29 (70)
21 TIGR01584 citF citrate lyase, 30.2 42 0.00091 28.5 2.3 51 20-70 401-455 (492)
22 TIGR00768 rimK_fam alpha-L-glu 29.8 83 0.0018 22.5 3.5 28 48-75 242-269 (277)
23 TIGR03458 YgfH_subfam succinat 29.3 47 0.001 27.8 2.4 29 19-47 399-427 (485)
24 PF12936 Kri1_C: KRI1-like fam 29.1 35 0.00077 22.6 1.4 27 50-76 26-55 (93)
25 PLN02439 arginine decarboxylas 28.6 1.2E+02 0.0026 25.9 4.7 34 43-76 486-520 (559)
26 PRK01966 ddl D-alanyl-alanine 27.8 1E+02 0.0022 23.6 3.9 29 48-76 287-321 (333)
27 TIGR03675 arCOG00543 arCOG0054 27.4 1.1E+02 0.0023 26.5 4.2 33 46-78 89-129 (630)
28 PF14783 BBS2_Mid: Ciliary BBS 26.9 48 0.001 22.7 1.7 16 39-54 2-17 (111)
29 PRK12491 pyrroline-5-carboxyla 25.6 77 0.0017 23.9 2.9 23 52-74 90-112 (272)
30 smart00322 KH K homology RNA-b 24.5 66 0.0014 17.5 1.8 20 60-79 21-40 (69)
31 cd00105 KH-I K homology RNA-bi 24.5 57 0.0012 18.3 1.6 21 60-80 18-38 (64)
32 PF14454 Prok_Ub: Prokaryotic 24.4 77 0.0017 19.8 2.2 26 43-71 8-33 (65)
33 COG0345 ProC Pyrroline-5-carbo 24.2 75 0.0016 24.6 2.6 26 52-78 88-113 (266)
34 PF00013 KH_1: KH domain syndr 23.9 34 0.00074 19.5 0.5 20 61-80 19-38 (60)
35 PF01008 IF-2B: Initiation fac 23.0 39 0.00084 25.1 0.8 18 29-46 264-281 (282)
36 COG5270 PUA domain (predicted 22.5 41 0.0009 25.5 0.8 14 22-35 17-30 (202)
37 PF02655 ATP-grasp_3: ATP-gras 22.1 67 0.0015 22.0 1.8 33 21-63 127-159 (161)
38 COG0450 AhpC Peroxiredoxin [Po 21.5 1.3E+02 0.0028 22.6 3.3 35 39-73 122-159 (194)
39 cd02395 SF1_like-KH Splicing f 21.5 65 0.0014 22.0 1.6 20 61-80 25-44 (120)
40 PF14795 Leucyl-specific: Leuc 21.4 73 0.0016 19.5 1.6 38 40-79 2-47 (56)
41 COG3642 Mn2+-dependent serine/ 20.9 1.6E+02 0.0034 22.4 3.6 29 43-71 65-93 (204)
42 KOG0854|consensus 20.7 1.7E+02 0.0036 22.4 3.8 33 39-71 129-164 (224)
43 cd06472 ACD_ScHsp26_like Alpha 20.4 97 0.0021 19.3 2.1 31 49-79 7-39 (92)
44 PF04355 SmpA_OmlA: SmpA / Oml 20.1 80 0.0017 18.7 1.6 23 55-77 9-31 (71)
No 1
>COG2057 AtoA Acyl CoA:acetate/3-ketoacid CoA transferase, beta subunit [Lipid metabolism]
Probab=99.85 E-value=1.1e-21 Score=147.71 Aligned_cols=67 Identities=27% Similarity=0.396 Sum_probs=61.9
Q ss_pred CccCCCCCCCCCCCCccEEEcCceEEEeccCCcEEEEEecCCCCHHHHHHhhCCceeecCCCCCCCc
Q psy5915 20 DALPTKPTRLGLTALSSDVLSRDCVFEVDKERGLTLIEIAEGVEVPEIIVSTGCDFAVSPDLKPMGQ 86 (89)
Q Consensus 20 ~~~~~CtlPLTg~~~V~~IITdlaVf~~d~~~~l~L~ei~pGvt~eeV~~~Tg~~l~va~~l~~m~~ 86 (89)
|++++|+||||+.+||++||||||||+|+++++|+|.|+|||+|+|||+++|||+|++++.+.+|+.
T Consensus 156 ki~~~ctlplt~~~~v~~iiTdl~V~~~~~~~~~~l~el~pgvT~e~V~~~T~~~~~~~~~~~~~~~ 222 (225)
T COG2057 156 KILKECTLPLTGNGCVDRVITDLAVFEFDPGGELTLVELAPGVTIEDVVEKTGAEFKVADAVEETRA 222 (225)
T ss_pred cccCcccccccCCCCceEEEeccEEEEecCCCeEEEEEeCCCCCHHHHHhhcCceEEeccccccccc
Confidence 5899999999999999999999999999555569999999999999999999999999998877654
No 2
>KOG3822|consensus
Probab=99.81 E-value=1e-20 Score=151.88 Aligned_cols=71 Identities=42% Similarity=0.680 Sum_probs=67.8
Q ss_pred cCccCCCCCCCCCCCCccEEEcCceEEEeccCCcEEEEEecCCCCHHHHHHhhCCceeecCCCCCCCcccC
Q psy5915 19 ADALPTKPTRLGLTALSSDVLSRDCVFEVDKERGLTLIEIAEGVEVPEIIVSTGCDFAVSPDLKPMGQVET 89 (89)
Q Consensus 19 ~~~~~~CtlPLTg~~~V~~IITdlaVf~~d~~~~l~L~ei~pGvt~eeV~~~Tg~~l~va~~l~~m~~~~~ 89 (89)
++|+.+|+|||||++||++||||+|||++|...+|+|+|+..|.|+|||+..||++|.||++++.|+|++.
T Consensus 446 pKIme~C~lPLTGK~~v~rIItekAVFdV~~k~gLTLiE~~eglTVDDi~ksTgc~F~vSpnLkpM~Qi~~ 516 (516)
T KOG3822|consen 446 PKIMEKCTLPLTGKGCVDRIITEKAVFDVDKKKGLTLIELWEGLTVDDIKKSTGCKFAVSPNLKPMQQIAP 516 (516)
T ss_pred chhhhhccccccCcchHhhhhhhheeEEeecCCCcEEeeeccCCcHHHHHhccCcceeeCCCccccccCCC
Confidence 56888999999999999999999999999888899999999999999999999999999999999999863
No 3
>TIGR02428 pcaJ_scoB_fam 3-oxoacid CoA-transferase, B subunit. Various members of this family are characterized as the B subunits of succinyl-CoA:3-ketoacid-CoA transferase (EC 2.8.3.5), beta-ketoadipate:succinyl-CoA transferase (EC 2.8.3.6), acetyl-CoA:acetoacetate CoA transferase (EC 2.8.3.8), and butyrate-acetoacetate CoA-transferase (EC 2.8.3.9). This represents a very distinct clade with strong sequence conservation within the larger family defined by Pfam model pfam01144. The A subunit represents a different clade in pfam01144.
Probab=99.60 E-value=1.8e-15 Score=111.58 Aligned_cols=57 Identities=30% Similarity=0.377 Sum_probs=53.3
Q ss_pred CccCCCCCCCCCCCCccEEEcCceEEEeccCCcEEEEEecCCCCHHHHHHhhCCceee
Q psy5915 20 DALPTKPTRLGLTALSSDVLSRDCVFEVDKERGLTLIEIAEGVEVPEIIVSTGCDFAV 77 (89)
Q Consensus 20 ~~~~~CtlPLTg~~~V~~IITdlaVf~~d~~~~l~L~ei~pGvt~eeV~~~Tg~~l~v 77 (89)
+|+++|++|+|+.++++.||||+|||++++ .+|+|.|+|||+|+|||+++|||+|.+
T Consensus 151 ~iv~~~~~~~t~~~~v~~vVTe~gV~~l~~-~~l~L~~~~pgv~~~dv~~~tg~~l~~ 207 (207)
T TIGR02428 151 KILKECTLPLTGAGCVDRIVTELAVFEVTD-GGLILRELAPGVTVEELQAKTEADLII 207 (207)
T ss_pred EEcccCCCccCCCCcccEEECCCEEEEEeC-CcEEEEEECCCCCHHHHHHhcCCceeC
Confidence 588999999999999999999999999954 499999999999999999999999974
No 4
>COG4670 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]
Probab=98.91 E-value=1.5e-09 Score=89.80 Aligned_cols=49 Identities=35% Similarity=0.544 Sum_probs=46.9
Q ss_pred EEEcCceEEEeccCCcEEEEEecCCCCHH-HHHHhhCCceeecCCCCCCCc
Q psy5915 37 DVLSRDCVFEVDKERGLTLIEIAEGVEVP-EIIVSTGCDFAVSPDLKPMGQ 86 (89)
Q Consensus 37 ~IITdlaVf~~d~~~~l~L~ei~pGvt~e-eV~~~Tg~~l~va~~l~~m~~ 86 (89)
..|||+|||++ ++++|.|+|+|||++++ ||+.+++|++.|+++++.|++
T Consensus 458 ~YVTERaVF~L-t~~GL~L~EIAPGvDlekDIL~qmef~piia~~Lk~MD~ 507 (527)
T COG4670 458 LYVTERAVFKL-TPDGLTLIEIAPGVDLEKDILDQMEFEPIIADDLKEMDE 507 (527)
T ss_pred EEEEeeEEEEE-cCCCEEEEEecCCCChhhhHHhccCCCccccccccccCH
Confidence 79999999999 88999999999999998 999999999999999999964
No 5
>PF01144 CoA_trans: Coenzyme A transferase; InterPro: IPR004165 Coenzyme A (CoA) transferases belong to an evolutionary conserved [, ] family of enzymes catalyzing the reversible transfer of CoA from one carboxylic acid to another. They have been identified in many prokaryotes and in mammalian tissues. The bacterial enzymes are heterodimer of two subunits (A and B) of about 25 Kd each while eukaryotic SCOT consist of a single chain which is colinear with the two bacterial subunits.; GO: 0008410 CoA-transferase activity, 0008152 metabolic process; PDB: 3DLX_C 1K6D_A 3OXO_H 1M3E_D 3K6M_C 2NRC_A 1OOY_B 1O9L_C 1OOZ_A 1OPE_B ....
Probab=94.20 E-value=0.0086 Score=43.30 Aligned_cols=48 Identities=17% Similarity=0.023 Sum_probs=36.4
Q ss_pred CCCCCCCCCCCCcc--EEEcCceEEEeccC-CcEEEEEecCCCCHHHHHHh
Q psy5915 23 PTKPTRLGLTALSS--DVLSRDCVFEVDKE-RGLTLIEIAEGVEVPEIIVS 70 (89)
Q Consensus 23 ~~CtlPLTg~~~V~--~IITdlaVf~~d~~-~~l~L~ei~pGvt~eeV~~~ 70 (89)
-.++.+......+. ..+|.++|+++++. +.+.+..++||+++|+|.++
T Consensus 167 ~~~~~~~~~~~~~a~a~~~tiv~ve~iv~~~~~~~~~~~iPg~~Vd~Vvea 217 (217)
T PF01144_consen 167 FEGSPGHFDDPAIAMAAKITIVTVEEIVEEGRRDPLRVVIPGVLVDAVVEA 217 (217)
T ss_dssp SSGSSHTTHSHHHHHCEEEEEEEEEEEECTTTSEEEEEEBTGGGHSEEEET
T ss_pred EeCCCCccccccccccceEEEEEEEEEeccCCccceEEEeCCCchHHeEeC
Confidence 34455555544443 89999999999655 48999999999999988653
No 6
>PF13014 KH_3: KH domain
Probab=61.51 E-value=6.7 Score=21.50 Aligned_cols=19 Identities=32% Similarity=0.588 Sum_probs=17.8
Q ss_pred CCCHHHHHHhhCCceeecC
Q psy5915 61 GVEVPEIIVSTGCDFAVSP 79 (89)
Q Consensus 61 Gvt~eeV~~~Tg~~l~va~ 79 (89)
|.++.+|++.||+.+.+++
T Consensus 10 G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 10 GSTIKEIREETGAKIQIPP 28 (43)
T ss_pred ChHHHHHHHHhCcEEEECC
Confidence 7889999999999999987
No 7
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=56.31 E-value=24 Score=25.35 Aligned_cols=32 Identities=22% Similarity=0.208 Sum_probs=23.7
Q ss_pred EeccC-CcEEEEEecC-------CCCHHHHHHhhCCceee
Q psy5915 46 EVDKE-RGLTLIEIAE-------GVEVPEIIVSTGCDFAV 77 (89)
Q Consensus 46 ~~d~~-~~l~L~ei~p-------Gvt~eeV~~~Tg~~l~v 77 (89)
.||++ |+.++..--| |.++.+|...|||...+
T Consensus 72 ~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 72 YFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKV 111 (145)
T ss_pred EecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEE
Confidence 46666 4555554445 67889999999999887
No 8
>PF13336 AcetylCoA_hyd_C: Acetyl-CoA hydrolase/transferase C-terminal domain; PDB: 3EH7_A 3D3U_A 2OAS_A 3GK7_B 3QDQ_A 2G39_A 2NVV_C 3S8D_B 3QLI_B 3QLK_B ....
Probab=46.76 E-value=22 Score=25.70 Aligned_cols=29 Identities=14% Similarity=0.156 Sum_probs=20.3
Q ss_pred cCccCCCC--CCCCC-CCCccEEEcCceEEEe
Q psy5915 19 ADALPTKP--TRLGL-TALSSDVLSRDCVFEV 47 (89)
Q Consensus 19 ~~~~~~Ct--lPLTg-~~~V~~IITdlaVf~~ 47 (89)
.+||...+ -|.|. ...|+.||||.||-++
T Consensus 95 S~Iv~~l~~g~~vt~~r~dvd~VVTEyGvA~L 126 (154)
T PF13336_consen 95 SRIVPRLPPGAPVTTPRHDVDYVVTEYGVADL 126 (154)
T ss_dssp ESEESS-STTSSESB-TTT-SEEEETTEEEE-
T ss_pred cceeeeecCCCCcccCcccCCEEEcCCEEEEe
Confidence 35777777 45554 6789999999999998
No 9
>PRK05354 arginine decarboxylase; Provisional
Probab=46.00 E-value=43 Score=28.99 Aligned_cols=37 Identities=19% Similarity=0.317 Sum_probs=32.1
Q ss_pred cCceEEEeccCCcEEEEEecCCCCHHHHHHhhCCcee
Q psy5915 40 SRDCVFEVDKERGLTLIEIAEGVEVPEIIVSTGCDFA 76 (89)
Q Consensus 40 TdlaVf~~d~~~~l~L~ei~pGvt~eeV~~~Tg~~l~ 76 (89)
|+-.-+.+|+++++.+..+.+|-|+++|+..++++..
T Consensus 557 ~~~v~v~~~~~g~~~i~~~~~g~~~~~vL~~v~y~~~ 593 (634)
T PRK05354 557 TNAVHVRVDEDGGYEIEHVIEGDTVADVLEYVQYDPK 593 (634)
T ss_pred CCEEEEEECCCCCEEEEEecCCCCHHHHHHHcCCCHH
Confidence 6667777877789999999999999999999998754
No 10
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=42.59 E-value=19 Score=21.37 Aligned_cols=20 Identities=30% Similarity=0.541 Sum_probs=18.0
Q ss_pred CCCHHHHHHhhCCceeecCC
Q psy5915 61 GVEVPEIIVSTGCDFAVSPD 80 (89)
Q Consensus 61 Gvt~eeV~~~Tg~~l~va~~ 80 (89)
|.++.+|++.||+.+.++++
T Consensus 21 G~~ik~I~~~tg~~I~i~~~ 40 (61)
T cd02393 21 GKTIKKIIEETGVKIDIEDD 40 (61)
T ss_pred chHHHHHHHHHCCEEEeCCC
Confidence 88999999999999999763
No 11
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=41.38 E-value=70 Score=20.04 Aligned_cols=23 Identities=13% Similarity=0.368 Sum_probs=20.5
Q ss_pred cCCcEEEEEecCCCCHHHHHHhh
Q psy5915 49 KERGLTLIEIAEGVEVPEIIVST 71 (89)
Q Consensus 49 ~~~~l~L~ei~pGvt~eeV~~~T 71 (89)
++|+-.+..+-||.|+.|+.+..
T Consensus 7 Png~~t~V~vrpg~ti~d~L~~~ 29 (72)
T cd01760 7 PNGQRTVVPVRPGMSVRDVLAKA 29 (72)
T ss_pred cCCCeEEEEECCCCCHHHHHHHH
Confidence 78999999999999999987753
No 12
>TIGR01273 speA arginine decarboxylase, biosynthetic. A distinct biodegradative form is also pyridoxal phosphate-dependent but is not similar in sequence.
Probab=40.61 E-value=59 Score=28.07 Aligned_cols=37 Identities=16% Similarity=0.219 Sum_probs=30.7
Q ss_pred cCceEEEeccCCcEEEEEecCCCCHHHHHHhhCCcee
Q psy5915 40 SRDCVFEVDKERGLTLIEIAEGVEVPEIIVSTGCDFA 76 (89)
Q Consensus 40 TdlaVf~~d~~~~l~L~ei~pGvt~eeV~~~Tg~~l~ 76 (89)
|+-.-+.+|++|++.+..+.+|-|++||+...+++..
T Consensus 550 ~~~v~v~~~~~g~~~~~~~~~g~~~~~vL~~v~y~~~ 586 (624)
T TIGR01273 550 TSAVRVVFDGDGGYEVEDIREGDTTEDMLRYVQYDPK 586 (624)
T ss_pred CCEEEEEECCCCCEEEEEecCCCCHHHHHHHcCCCHH
Confidence 5555666767778999999999999999999998743
No 13
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=39.13 E-value=32 Score=19.74 Aligned_cols=20 Identities=20% Similarity=0.398 Sum_probs=18.0
Q ss_pred CCCHHHHHHhhCCceeecCC
Q psy5915 61 GVEVPEIIVSTGCDFAVSPD 80 (89)
Q Consensus 61 Gvt~eeV~~~Tg~~l~va~~ 80 (89)
|.++.+|++.||+.+.+++.
T Consensus 19 G~~i~~i~~~~g~~I~i~~~ 38 (62)
T cd02394 19 GSNIRKIMEETGVKIRFPDP 38 (62)
T ss_pred CCcHHHHHHHhCCEEEcCCC
Confidence 78999999999999999763
No 14
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=38.33 E-value=23 Score=22.69 Aligned_cols=18 Identities=33% Similarity=0.446 Sum_probs=15.4
Q ss_pred cCCCCHHHHHHhhCCcee
Q psy5915 59 AEGVEVPEIIVSTGCDFA 76 (89)
Q Consensus 59 ~pGvt~eeV~~~Tg~~l~ 76 (89)
-.|.|+++|-++|||.-+
T Consensus 22 p~GATi~ei~~atGWq~H 39 (72)
T PF11994_consen 22 PEGATIAEICEATGWQPH 39 (72)
T ss_pred CCCCCHHHHHHhhCCchh
Confidence 469999999999999754
No 15
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=37.77 E-value=23 Score=30.82 Aligned_cols=65 Identities=18% Similarity=0.224 Sum_probs=40.3
Q ss_pred ccCCCCCCCCCccccccCccCCCCCCCCCCCCccEEEcCceEEEeccC-CcEEEEEecC-------CCCHHHHHHhhCCc
Q psy5915 3 QIRPGRESNPRPSAYKADALPTKPTRLGLTALSSDVLSRDCVFEVDKE-RGLTLIEIAE-------GVEVPEIIVSTGCD 74 (89)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~CtlPLTg~~~V~~IITdlaVf~~d~~-~~l~L~ei~p-------Gvt~eeV~~~Tg~~ 74 (89)
-|||++...--|+--.+.|++--| -..-||| +.||.+ |+.++..--| |.++.+|.++|||.
T Consensus 63 ~iR~dPsvl~~~e~A~~~I~eivP--------~ea~i~~---i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~ 131 (637)
T COG1782 63 IIRPDPSVLKPPEEARKIILEIVP--------EEAGITD---IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWA 131 (637)
T ss_pred EeccCchhcCCHHHHHHHHHHhCc--------cccCcee---EEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCc
Confidence 467777666555543333332111 1345677 446566 5666655556 67999999999999
Q ss_pred eeec
Q psy5915 75 FAVS 78 (89)
Q Consensus 75 l~va 78 (89)
..+-
T Consensus 132 p~iv 135 (637)
T COG1782 132 PKIV 135 (637)
T ss_pred ceee
Confidence 8874
No 16
>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor. Tiam1 (T lymphoma invasion and metastasis 1) a guanine nucleotide exchange factor that activates Rac, is an important regulator of Rho GTPase functions in tumor cells including regulation of cell shape and invasiveness in epithelial cells and fibroblasts. TIAM1 has an RBD (Ras-binding domain) similar to that of Raf kinase as well as PH (pleckstrin homology), PDZ, and RhoGEF domains.
Probab=36.17 E-value=59 Score=21.18 Aligned_cols=23 Identities=17% Similarity=0.294 Sum_probs=21.0
Q ss_pred cCCcEEEEEecCCCCHHHHHHhh
Q psy5915 49 KERGLTLIEIAEGVEVPEIIVST 71 (89)
Q Consensus 49 ~~~~l~L~ei~pGvt~eeV~~~T 71 (89)
++++-....+-||.|++||++.+
T Consensus 7 Pn~~~~~v~vrp~~tv~dvLe~a 29 (77)
T cd01818 7 PDNQPVLTYLRPGMSVEDFLESA 29 (77)
T ss_pred CCCceEEEEECCCCCHHHHHHHH
Confidence 78889999999999999999876
No 17
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=34.12 E-value=1.1e+02 Score=21.85 Aligned_cols=46 Identities=15% Similarity=0.265 Sum_probs=37.0
Q ss_pred EcCceEEEeccCCcEEEEEecCCCCHHHHH---HhhCCceeecCCCCCCCc
Q psy5915 39 LSRDCVFEVDKERGLTLIEIAEGVEVPEII---VSTGCDFAVSPDLKPMGQ 86 (89)
Q Consensus 39 ITdlaVf~~d~~~~l~L~ei~pGvt~eeV~---~~Tg~~l~va~~l~~m~~ 86 (89)
.|-.|++++ +|++....-.-+.+..||. .+.|-++.|+.|+..|+.
T Consensus 42 ttgiAildL--~G~~l~l~S~R~~~~~evi~~I~~~G~PviVAtDV~p~P~ 90 (138)
T PF04312_consen 42 TTGIAILDL--DGELLDLKSSRNMSRSEVIEWISEYGKPVIVATDVSPPPE 90 (138)
T ss_pred eeEEEEEec--CCcEEEEEeecCCCHHHHHHHHHHcCCEEEEEecCCCCcH
Confidence 466688877 8888888888899998774 568999999999887754
No 18
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=33.77 E-value=30 Score=20.39 Aligned_cols=22 Identities=32% Similarity=0.433 Sum_probs=18.9
Q ss_pred CCCCHHHHHHhhCCceeecCCC
Q psy5915 60 EGVEVPEIIVSTGCDFAVSPDL 81 (89)
Q Consensus 60 pGvt~eeV~~~Tg~~l~va~~l 81 (89)
.|-.+.+|++.||+.+.++++-
T Consensus 18 ~G~~i~~i~~~tga~I~i~~~~ 39 (65)
T cd02396 18 GGSTIKEIREETGAKIRVSKSV 39 (65)
T ss_pred CcHHHHHHHHHHCCEEEEcCCC
Confidence 4788999999999999998654
No 19
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=32.35 E-value=1.1e+02 Score=18.84 Aligned_cols=22 Identities=9% Similarity=0.324 Sum_probs=18.8
Q ss_pred cCCcEEEEEecCCCCHHHHHHh
Q psy5915 49 KERGLTLIEIAEGVEVPEIIVS 70 (89)
Q Consensus 49 ~~~~l~L~ei~pGvt~eeV~~~ 70 (89)
++++-.+..+-||.|+.|..+.
T Consensus 8 P~~q~t~V~vrpg~ti~d~L~~ 29 (71)
T PF02196_consen 8 PNGQRTVVQVRPGMTIRDALSK 29 (71)
T ss_dssp TTTEEEEEEE-TTSBHHHHHHH
T ss_pred CCCCEEEEEEcCCCCHHHHHHH
Confidence 7899999999999999988764
No 20
>smart00455 RBD Raf-like Ras-binding domain.
Probab=31.39 E-value=1.3e+02 Score=18.47 Aligned_cols=23 Identities=13% Similarity=0.329 Sum_probs=20.1
Q ss_pred cCCcEEEEEecCCCCHHHHHHhh
Q psy5915 49 KERGLTLIEIAEGVEVPEIIVST 71 (89)
Q Consensus 49 ~~~~l~L~ei~pGvt~eeV~~~T 71 (89)
++++.....+-||.|+.|+.+..
T Consensus 7 P~~~~~~V~vrpg~tl~e~L~~~ 29 (70)
T smart00455 7 PDNQRTVVKVRPGKTVRDALAKA 29 (70)
T ss_pred CCCCEEEEEECCCCCHHHHHHHH
Confidence 78899999999999999887653
No 21
>TIGR01584 citF citrate lyase, alpha subunit. This is a model of the alpha subunit of the holoenzyme citrate lyase (EC 4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC 4.1.3.34), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The alpha subunit catalyzes the reaction Acetyl-CoA + citrate = acetate + (3S)-citryl-CoA. The seed contains an experimentally characterized member from Lactococcus lactis subsp. lactis. The model covers both Gram positive and Gram negative bacteria. It is quite robust with queries scoring either quite well or quite poorly against the model. There are currently no hits in between the noise cutoff and trusted cutoff.
Probab=30.20 E-value=42 Score=28.54 Aligned_cols=51 Identities=6% Similarity=-0.078 Sum_probs=32.5
Q ss_pred CccCCCCCCCCCCCCccEEEcCceEE-EeccC---CcEEEEEecCCCCHHHHHHh
Q psy5915 20 DALPTKPTRLGLTALSSDVLSRDCVF-EVDKE---RGLTLIEIAEGVEVPEIIVS 70 (89)
Q Consensus 20 ~~~~~CtlPLTg~~~V~~IITdlaVf-~~d~~---~~l~L~ei~pGvt~eeV~~~ 70 (89)
+|+.+.+-=-|....|+.||||.|+- ..-.. .++.+..=.|=+|+||+++.
T Consensus 401 ~IV~~v~~VtTpr~~Vd~VVTEyGIAvnlrg~~l~eR~~~~~~l~~~~i~~l~~~ 455 (492)
T TIGR01584 401 TVVEKVTTVITPGESIDVLVTEIGIAINPKRKDLIEKLSNKPGIPLYTIEELQEI 455 (492)
T ss_pred eEeCCCCCEECChhhCCEEEccCEEecCCCCCCHHHHHhhcCCCCcccHHHHHHH
Confidence 45666643334577899999999998 54111 13444455667778887764
No 22
>TIGR00768 rimK_fam alpha-L-glutamate ligases, RimK family. This family, related to bacterial glutathione synthetases, contains at least two different alpha-L-glutamate ligases. One is RimK, as in E. coli, which adds additional Glu residues to the native Glu-Glu C-terminus of ribosomal protein S6, but not to Lys-Glu mutants. Most species with a member of this subfamily lack an S6 homolog ending in Glu-Glu, however. Members in Methanococcus jannaschii act instead as a tetrahydromethanopterin:alpha-l-glutamate ligase (MJ0620) and a gamma-F420-2:alpha-l-glutamate ligase (MJ1001).
Probab=29.85 E-value=83 Score=22.48 Aligned_cols=28 Identities=25% Similarity=0.469 Sum_probs=21.6
Q ss_pred ccCCcEEEEEecCCCCHHHHHHhhCCce
Q psy5915 48 DKERGLTLIEIAEGVEVPEIIVSTGCDF 75 (89)
Q Consensus 48 d~~~~l~L~ei~pGvt~eeV~~~Tg~~l 75 (89)
|++|++++.|+.|-.....+...||.++
T Consensus 242 ~~~g~~~viEiN~~p~~~~~~~~~g~~l 269 (277)
T TIGR00768 242 SEDRGLLVNEVNPNPEFKNSVKTTGVNI 269 (277)
T ss_pred cCCCCeEEEEEcCCcchhhhHHHHCCCH
Confidence 4566899999999777777777777665
No 23
>TIGR03458 YgfH_subfam succinate CoA transferases. A closely related clade not included in this family are the Ach1p proteins of fungi which are acetyl-CoA hydrolases. This name has been applied to many of the proteins detected by this model, possibly erroneously.
Probab=29.33 E-value=47 Score=27.80 Aligned_cols=29 Identities=3% Similarity=-0.011 Sum_probs=22.7
Q ss_pred cCccCCCCCCCCCCCCccEEEcCceEEEe
Q psy5915 19 ADALPTKPTRLGLTALSSDVLSRDCVFEV 47 (89)
Q Consensus 19 ~~~~~~CtlPLTg~~~V~~IITdlaVf~~ 47 (89)
.+||+.++---|...-|+.||||.|+.++
T Consensus 399 S~Ivp~l~~vt~~r~dv~~vVTE~G~A~L 427 (485)
T TIGR03458 399 SSIVPMVSHVDHTEHDVMVIVTEQGLADL 427 (485)
T ss_pred eeEeecCCCcCCchhhCCEEEecCEEEEe
Confidence 34888886334457788999999999998
No 24
>PF12936 Kri1_C: KRI1-like family C-terminal; InterPro: IPR024626 The yeast member of the Kri1-like family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus []. This entry represents the C-terminal domain of this protein family.
Probab=29.08 E-value=35 Score=22.61 Aligned_cols=27 Identities=15% Similarity=0.336 Sum_probs=23.0
Q ss_pred CCcEEEEEecC---CCCHHHHHHhhCCcee
Q psy5915 50 ERGLTLIEIAE---GVEVPEIIVSTGCDFA 76 (89)
Q Consensus 50 ~~~l~L~ei~p---Gvt~eeV~~~Tg~~l~ 76 (89)
..+|.=+++.| |.|.+||+.+++.+|.
T Consensus 26 p~RFkYr~V~p~~fGLt~~eIL~adDkeLN 55 (93)
T PF12936_consen 26 PTRFKYREVPPNSFGLTTEEILMADDKELN 55 (93)
T ss_pred CCceeeeecCcccCCCCHHHHHhCCHHHHH
Confidence 34788899999 9999999999887765
No 25
>PLN02439 arginine decarboxylase
Probab=28.60 E-value=1.2e+02 Score=25.92 Aligned_cols=34 Identities=6% Similarity=0.149 Sum_probs=27.4
Q ss_pred eEEEeccCC-cEEEEEecCCCCHHHHHHhhCCcee
Q psy5915 43 CVFEVDKER-GLTLIEIAEGVEVPEIIVSTGCDFA 76 (89)
Q Consensus 43 aVf~~d~~~-~l~L~ei~pGvt~eeV~~~Tg~~l~ 76 (89)
.-+.+++++ ++.+..+.+|-|+++|....+++..
T Consensus 486 v~v~~~~~~~~~~~~~~~~g~~~~~vl~~~~y~~~ 520 (559)
T PLN02439 486 VRVSQSDGPGGFAVTRAVPGQSCADVLRAMQHEPE 520 (559)
T ss_pred EEEEEcCCCCceEEEEecCCCCHHHHHHHcCCCHH
Confidence 334555566 6999999999999999999998754
No 26
>PRK01966 ddl D-alanyl-alanine synthetase A; Reviewed
Probab=27.77 E-value=1e+02 Score=23.59 Aligned_cols=29 Identities=21% Similarity=0.430 Sum_probs=20.0
Q ss_pred ccCCcEEEEEec--CCCCH----HHHHHhhCCcee
Q psy5915 48 DKERGLTLIEIA--EGVEV----PEIIVSTGCDFA 76 (89)
Q Consensus 48 d~~~~l~L~ei~--pGvt~----eeV~~~Tg~~l~ 76 (89)
|.++.+++.|+. ||.|. .+..++.|+++.
T Consensus 287 ~~~g~~~vlEiNt~Pg~t~~s~~p~~~~~~G~~~~ 321 (333)
T PRK01966 287 TEDGEIYLNEINTMPGFTPISMYPKLWEASGLSYP 321 (333)
T ss_pred cCCCCEEEEEeeCCCCCCcccHHHHHHHHcCCCHH
Confidence 445679999988 88764 355667777653
No 27
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=27.42 E-value=1.1e+02 Score=26.47 Aligned_cols=33 Identities=21% Similarity=0.178 Sum_probs=23.5
Q ss_pred EeccCC-cEEEEEecC-------CCCHHHHHHhhCCceeec
Q psy5915 46 EVDKER-GLTLIEIAE-------GVEVPEIIVSTGCDFAVS 78 (89)
Q Consensus 46 ~~d~~~-~l~L~ei~p-------Gvt~eeV~~~Tg~~l~va 78 (89)
.||++. +..+..--| |.++.+|..+|||...|-
T Consensus 89 ~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~ 129 (630)
T TIGR03675 89 YFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVV 129 (630)
T ss_pred EecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEE
Confidence 466674 444444434 678999999999998873
No 28
>PF14783 BBS2_Mid: Ciliary BBSome complex subunit 2, middle region
Probab=26.93 E-value=48 Score=22.74 Aligned_cols=16 Identities=19% Similarity=0.484 Sum_probs=11.9
Q ss_pred EcCceEEEeccCCcEE
Q psy5915 39 LSRDCVFEVDKERGLT 54 (89)
Q Consensus 39 ITdlaVf~~d~~~~l~ 54 (89)
||-||+++||.+|.-.
T Consensus 2 V~al~~~d~d~dg~~e 17 (111)
T PF14783_consen 2 VTALCLFDFDGDGENE 17 (111)
T ss_pred eeEEEEEecCCCCcce
Confidence 5778999997776533
No 29
>PRK12491 pyrroline-5-carboxylate reductase; Reviewed
Probab=25.62 E-value=77 Score=23.90 Aligned_cols=23 Identities=13% Similarity=0.164 Sum_probs=20.1
Q ss_pred cEEEEEecCCCCHHHHHHhhCCc
Q psy5915 52 GLTLIEIAEGVEVPEIIVSTGCD 74 (89)
Q Consensus 52 ~l~L~ei~pGvt~eeV~~~Tg~~ 74 (89)
+-.+++++.|++++++++..+..
T Consensus 90 ~~lvISi~AGi~i~~l~~~l~~~ 112 (272)
T PRK12491 90 DVIVVTIAAGKSIKSTENEFDRK 112 (272)
T ss_pred CcEEEEeCCCCcHHHHHHhcCCC
Confidence 46899999999999999988753
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=24.54 E-value=66 Score=17.47 Aligned_cols=20 Identities=20% Similarity=0.356 Sum_probs=17.7
Q ss_pred CCCCHHHHHHhhCCceeecC
Q psy5915 60 EGVEVPEIIVSTGCDFAVSP 79 (89)
Q Consensus 60 pGvt~eeV~~~Tg~~l~va~ 79 (89)
.|.++.+|+..||+.+.+..
T Consensus 21 ~G~~i~~i~~~~~~~i~~~~ 40 (69)
T smart00322 21 GGSTIKKIEEETGVKIDIPE 40 (69)
T ss_pred CchHHHHHHHHHCCEEEECC
Confidence 57889999999999999865
No 31
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=24.50 E-value=57 Score=18.28 Aligned_cols=21 Identities=24% Similarity=0.393 Sum_probs=18.1
Q ss_pred CCCCHHHHHHhhCCceeecCC
Q psy5915 60 EGVEVPEIIVSTGCDFAVSPD 80 (89)
Q Consensus 60 pGvt~eeV~~~Tg~~l~va~~ 80 (89)
-|..+.+|++.||+.+.+.+.
T Consensus 18 ~G~~i~~I~~~s~~~I~i~~~ 38 (64)
T cd00105 18 GGSTIKEIREETGAKIKIPDS 38 (64)
T ss_pred CCHHHHHHHHHHCCEEEEcCC
Confidence 388899999999999999753
No 32
>PF14454 Prok_Ub: Prokaryotic Ubiquitin
Probab=24.38 E-value=77 Score=19.80 Aligned_cols=26 Identities=23% Similarity=0.222 Sum_probs=21.1
Q ss_pred eEEEeccCCcEEEEEecCCCCHHHHHHhh
Q psy5915 43 CVFEVDKERGLTLIEIAEGVEVPEIIVST 71 (89)
Q Consensus 43 aVf~~d~~~~l~L~ei~pGvt~eeV~~~T 71 (89)
-+|.+ +++.|..=.|..|+|+|++--
T Consensus 8 R~F~~---~g~~L~DP~p~~spe~V~~~y 33 (65)
T PF14454_consen 8 RVFRY---NGITLPDPNPSLSPEEVRDFY 33 (65)
T ss_pred EEEEE---CCEECCCCCCCCCHHHHHHHH
Confidence 46777 568899999999999998743
No 33
>COG0345 ProC Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]
Probab=24.19 E-value=75 Score=24.59 Aligned_cols=26 Identities=27% Similarity=0.348 Sum_probs=21.6
Q ss_pred cEEEEEecCCCCHHHHHHhhCCceeec
Q psy5915 52 GLTLIEIAEGVEVPEIIVSTGCDFAVS 78 (89)
Q Consensus 52 ~l~L~ei~pGvt~eeV~~~Tg~~l~va 78 (89)
+=.+++++.|+++++++...| ...+.
T Consensus 88 ~~lvISiaAGv~~~~l~~~l~-~~~vv 113 (266)
T COG0345 88 DKLVISIAAGVSIETLERLLG-GLRVV 113 (266)
T ss_pred CCEEEEEeCCCCHHHHHHHcC-CCceE
Confidence 456889999999999999998 55553
No 34
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=23.92 E-value=34 Score=19.48 Aligned_cols=20 Identities=30% Similarity=0.503 Sum_probs=17.1
Q ss_pred CCCHHHHHHhhCCceeecCC
Q psy5915 61 GVEVPEIIVSTGCDFAVSPD 80 (89)
Q Consensus 61 Gvt~eeV~~~Tg~~l~va~~ 80 (89)
|..+.+|++.||+.+.++++
T Consensus 19 G~~i~~I~~~t~~~I~i~~~ 38 (60)
T PF00013_consen 19 GSNIKEIEEETGVKIQIPDD 38 (60)
T ss_dssp GHHHHHHHHHHTSEEEEEST
T ss_pred CCcHHHhhhhcCeEEEEcCC
Confidence 56788999999999999764
No 35
>PF01008 IF-2B: Initiation factor 2 subunit family; InterPro: IPR000649 Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. The eukaryotic translation initiation factor EIF-2B is a complex made up of five different subunits, alpha, beta, gamma, delta and epsilon, and catalyses the exchange of EIF-2-bound GDP for GTP. This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes; related proteins from archaebacteria and IF-2 from prokaryotes and also contains a subfamily of proteins in eukaryotes, archaeae (e.g. Pyrococcus furiosus), or eubacteria such as Bacillus subtilis and Thermotoga maritima. Many of these proteins were initially annotated as putative translation initiation factors despite the fact that there is no evidence for the requirement of an IF2 recycling factor in prokaryotic translation initiation. Recently, one of these proteins from B. subtilis has been functionally characterised as a 5-methylthioribose-1-phosphate isomerase (MTNA) []. This enzyme participates in the methionine salvage pathway catalysing the isomerisation of 5-methylthioribose-1-phosphate to 5-methylthioribulose-1-phosphate []. The methionine salvage pathway leads to the synthesis of methionine from methylthioadenosine, the end product of the spermidine and spermine anabolism in many species.; GO: 0044237 cellular metabolic process; PDB: 1VB5_A 1T5O_D 3A11_E 3VM6_C 1W2W_A 1T9K_A 3ECS_B 2YRF_A 2YVK_B 2A0U_A ....
Probab=23.04 E-value=39 Score=25.14 Aligned_cols=18 Identities=6% Similarity=0.049 Sum_probs=13.3
Q ss_pred CCCCCCccEEEcCceEEE
Q psy5915 29 LGLTALSSDVLSRDCVFE 46 (89)
Q Consensus 29 LTg~~~V~~IITdlaVf~ 46 (89)
+|-...++++|||+|+|.
T Consensus 264 ~tP~~~It~~iTe~G~~~ 281 (282)
T PF01008_consen 264 YTPPDLITLIITELGILP 281 (282)
T ss_dssp EEEGGG-SEEEETTEEE-
T ss_pred ecCHHHCCEEEcCCCCCC
Confidence 455667899999999985
No 36
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=22.48 E-value=41 Score=25.50 Aligned_cols=14 Identities=14% Similarity=-0.299 Sum_probs=12.1
Q ss_pred cCCCCCCCCCCCCc
Q psy5915 22 LPTKPTRLGLTALS 35 (89)
Q Consensus 22 ~~~CtlPLTg~~~V 35 (89)
-++|.+||++..|+
T Consensus 17 Ce~cNlPl~~~~c~ 30 (202)
T COG5270 17 CEKCNLPLLGRRCS 30 (202)
T ss_pred hhhCCCcccccccc
Confidence 47899999999885
No 37
>PF02655 ATP-grasp_3: ATP-grasp domain; InterPro: IPR003806 The ATP-grasp fold is one of several distinct ATP-binding folds, and is found in enzymes that catalyze the formation of amide bonds, catalyzing the ATP-dependent ligation of a carboxylate-containing molecule to an amino or thiol group-containing molecule []. This fold is found in many different enzyme families, including various peptide synthetases, biotin carboxylase, synapsin, succinyl-CoA synthetase, pyruvate phosphate dikinase, and glutathione synthetase, amongst others []. These enzymes contribute predominantly to macromolecular synthesis, using ATP-hydrolysis to activate their substrates. The ATP-grasp fold shares functional and structural similarities with the PIPK (phosphatidylinositol phosphate kinase) and protein kinase superfamilies. The ATP-grasp domain consists of two subdomains with different alpha+beta folds, which grasp the ATP molecule between them. Each subdomain provides a variable loop that forms part of the active site, with regions from other domains also contributing to the active site, even though these other domains are not conserved between the various ATP-grasp enzymes []. This entry describes a type of ATP-grasp fold that is found in a set of proteins of unknown function.; GO: 0005524 ATP binding, 0046872 metal ion binding; PDB: 3DF7_A.
Probab=22.08 E-value=67 Score=22.00 Aligned_cols=33 Identities=21% Similarity=0.098 Sum_probs=20.8
Q ss_pred ccCCCCCCCCCCCCccEEEcCceEEEeccCCcEEEEEecCCCC
Q psy5915 21 ALPTKPTRLGLTALSSDVLSRDCVFEVDKERGLTLIEIAEGVE 63 (89)
Q Consensus 21 ~~~~CtlPLTg~~~V~~IITdlaVf~~d~~~~l~L~ei~pGvt 63 (89)
+.+..+ .|.|.-+||.|++| +++++.||-|=.|
T Consensus 127 i~~~l~-gl~G~~giD~I~~~---------~~~~viEINPR~t 159 (161)
T PF02655_consen 127 IAEALP-GLRGYVGIDFILDD---------GGPYVIEINPRFT 159 (161)
T ss_dssp HHTTST-T--EEEEEEEEESS----------SEEEEEEESS--
T ss_pred HHHHcC-CCeeeEeEEEEEeC---------CcEEEEEEcCCCC
Confidence 444444 88888899988765 6788888888543
No 38
>COG0450 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=21.49 E-value=1.3e+02 Score=22.61 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=27.8
Q ss_pred EcCceEEEeccCCcEEEEEecC---CCCHHHHHHhhCC
Q psy5915 39 LSRDCVFEVDKERGLTLIEIAE---GVEVPEIIVSTGC 73 (89)
Q Consensus 39 ITdlaVf~~d~~~~l~L~ei~p---Gvt~eeV~~~Tg~ 73 (89)
+|-+|+|=+|+++..+...++| |-+++|+.+...+
T Consensus 122 ~a~R~~FIIDp~g~ir~~~v~~~~iGRn~dEilR~idA 159 (194)
T COG0450 122 LALRGTFIIDPDGVIRHILVNPLTIGRNVDEILRVIDA 159 (194)
T ss_pred cceeEEEEECCCCeEEEEEEecCCCCcCHHHHHHHHHH
Confidence 3889999999999888888877 6678888765543
No 39
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=21.48 E-value=65 Score=21.95 Aligned_cols=20 Identities=15% Similarity=0.331 Sum_probs=17.8
Q ss_pred CCCHHHHHHhhCCceeecCC
Q psy5915 61 GVEVPEIIVSTGCDFAVSPD 80 (89)
Q Consensus 61 Gvt~eeV~~~Tg~~l~va~~ 80 (89)
|.|+.+|++.||+.+.+.++
T Consensus 25 G~tiK~i~~eTg~kI~Irg~ 44 (120)
T cd02395 25 GNTLKQLEKETGAKISIRGK 44 (120)
T ss_pred ChHHHHHHHHHCCEEEEecC
Confidence 78889999999999999754
No 40
>PF14795 Leucyl-specific: Leucine-tRNA synthetase-specific domain; PDB: 1OBC_A 2BTE_A 2V0G_A 2BYT_A 1OBH_A 1H3N_A 2V0C_A.
Probab=21.40 E-value=73 Score=19.55 Aligned_cols=38 Identities=21% Similarity=0.313 Sum_probs=22.6
Q ss_pred cCceEEEeccCCcEEEE-------EecCC-CCHHHHHHhhCCceeecC
Q psy5915 40 SRDCVFEVDKERGLTLI-------EIAEG-VEVPEIIVSTGCDFAVSP 79 (89)
Q Consensus 40 TdlaVf~~d~~~~l~L~-------ei~pG-vt~eeV~~~Tg~~l~va~ 79 (89)
||.|=.++ ..++++|. |+..| .|++|++ ++|++++-.+
T Consensus 2 Td~GpVeV-eg~rvrL~e~~R~rLel~~~~Ls~ee~~-KmGAELR~he 47 (56)
T PF14795_consen 2 TDFGPVEV-EGERVRLPEPTRIRLELEEGELSLEEVK-KMGAELRPHE 47 (56)
T ss_dssp EEEEEEEE-ETTEEE--HHHHHHHT-S-SEEEHHHHH-HTT-EEEE-T
T ss_pred CcccceEE-eCCEEEcCcchhheeecccccccHHHHH-hhchhcccCC
Confidence 56666677 55666665 35566 7889886 6899988643
No 41
>COG3642 Mn2+-dependent serine/threonine protein kinase [Signal transduction mechanisms]
Probab=20.88 E-value=1.6e+02 Score=22.44 Aligned_cols=29 Identities=28% Similarity=0.544 Sum_probs=24.3
Q ss_pred eEEEeccCCcEEEEEecCCCCHHHHHHhh
Q psy5915 43 CVFEVDKERGLTLIEIAEGVEVPEIIVST 71 (89)
Q Consensus 43 aVf~~d~~~~l~L~ei~pGvt~eeV~~~T 71 (89)
.||++|++.++.+.|..+|-.+.|.....
T Consensus 65 ~v~dvD~~~~~I~me~I~G~~lkd~l~~~ 93 (204)
T COG3642 65 IVYDVDPDNGLIVMEYIEGELLKDALEEA 93 (204)
T ss_pred eEEEEcCCCCEEEEEEeCChhHHHHHHhc
Confidence 58999999999999999999997655544
No 42
>KOG0854|consensus
Probab=20.74 E-value=1.7e+02 Score=22.44 Aligned_cols=33 Identities=21% Similarity=0.308 Sum_probs=27.2
Q ss_pred EcCceEEEeccCCcEEEEEecC---CCCHHHHHHhh
Q psy5915 39 LSRDCVFEVDKERGLTLIEIAE---GVEVPEIIVST 71 (89)
Q Consensus 39 ITdlaVf~~d~~~~l~L~ei~p---Gvt~eeV~~~T 71 (89)
.|-+|||-+|++..+.|.=++| |-..+||+...
T Consensus 129 ~T~Ravfvi~pdkKirLs~lYP~ttGRN~dEiLRvi 164 (224)
T KOG0854|consen 129 KTVRAVFVIDPDKKIRLSFLYPSTTGRNFDEILRVI 164 (224)
T ss_pred ceEEEEEEECCCceEEEEEEcccccCcCHHHHHHHH
Confidence 6788999999999999999999 44568887653
No 43
>cd06472 ACD_ScHsp26_like Alpha crystallin domain (ACD) found in Saccharomyces cerevisiae (Sc) small heat shock protein (Hsp)26 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. ScHsp26 is temperature-regulated, it switches from an inactive to a chaperone-active form upon elevation in temperature. It associates into large 24-mers storage forms which upon heat shock disassociate into dimers. These dimers initiate the interaction with non-native substrate proteins and re-assemble into large globular assemblies having one monomer of substrate bound per dimer. This group also contains Arabidopsis thaliana (Ath) Hsp15.7, a peroxisomal matrix protein which can complement the morphological phenotype of S. cerevisiae mutants deficient in Hsps26. AthHsp15.7 is minimally expressed under normal conditions and is strongly induced by heat and oxidative st
Probab=20.37 E-value=97 Score=19.25 Aligned_cols=31 Identities=13% Similarity=0.108 Sum_probs=23.6
Q ss_pred cCCcEEEEEecCCCCHHHHHHhhC--CceeecC
Q psy5915 49 KERGLTLIEIAEGVEVPEIIVSTG--CDFAVSP 79 (89)
Q Consensus 49 ~~~~l~L~ei~pGvt~eeV~~~Tg--~~l~va~ 79 (89)
.++.+.|.--.||++.++|.=... --|.|+.
T Consensus 7 ~~~~~~i~~~lPGv~~edi~i~v~~~~~L~I~g 39 (92)
T cd06472 7 TPEAHVFKADVPGVKKEDVKVEVEDGRVLRISG 39 (92)
T ss_pred cCCeEEEEEECCCCChHhEEEEEeCCCEEEEEE
Confidence 456899999999999999876653 2366654
No 44
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=20.13 E-value=80 Score=18.72 Aligned_cols=23 Identities=17% Similarity=0.187 Sum_probs=17.9
Q ss_pred EEEecCCCCHHHHHHhhCCceee
Q psy5915 55 LIEIAEGVEVPEIIVSTGCDFAV 77 (89)
Q Consensus 55 L~ei~pGvt~eeV~~~Tg~~l~v 77 (89)
+.+|.+|.|.+||++..|-+...
T Consensus 9 ~~~i~~GmTk~qV~~lLG~P~~~ 31 (71)
T PF04355_consen 9 LAQIKPGMTKDQVRALLGSPSLR 31 (71)
T ss_dssp HTTT-TTSBHHHHHHHHTS-SEE
T ss_pred HHhhcCCCCHHHHHHhcCCCCcc
Confidence 34578999999999999988776
Done!