Query psy16822
Match_columns 97
No_of_seqs 104 out of 185
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 22:57:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16822.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16822hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0396|consensus 100.0 1E-32 2.2E-37 223.2 -0.7 86 5-97 276-361 (389)
2 KOG2817|consensus 98.6 1.2E-08 2.7E-13 83.8 1.3 41 56-96 324-364 (394)
3 PF13445 zf-RING_UBOX: RING-ty 98.4 5.4E-08 1.2E-12 57.6 -0.1 28 69-96 1-28 (43)
4 COG5109 Uncharacterized conser 98.2 3.9E-07 8.4E-12 74.3 1.2 41 56-96 326-366 (396)
5 smart00504 Ubox Modified RING 98.0 1.4E-06 3E-11 52.6 0.3 27 67-96 2-28 (63)
6 PF04564 U-box: U-box domain; 97.5 1.7E-05 3.6E-10 50.6 -0.8 28 66-96 4-31 (73)
7 PF04641 Rtf2: Rtf2 RING-finge 96.8 0.00048 1E-08 53.1 1.2 35 63-97 110-145 (260)
8 KOG3113|consensus 96.0 0.0022 4.7E-08 51.2 0.3 35 63-97 108-143 (293)
9 PF15227 zf-C3HC4_4: zinc fing 91.3 0.12 2.6E-06 29.8 1.3 15 80-94 9-23 (42)
10 PF11789 zf-Nse: Zinc-finger o 85.6 0.23 5.1E-06 30.6 -0.1 28 66-96 11-39 (57)
11 PF05605 zf-Di19: Drought indu 76.7 1 2.2E-05 26.9 0.4 31 42-72 4-37 (54)
12 COG2835 Uncharacterized conser 76.6 1.4 3.1E-05 28.0 1.1 39 41-87 9-48 (60)
13 PRK11827 hypothetical protein; 75.5 1.3 2.9E-05 27.9 0.8 39 41-87 9-48 (60)
14 PF13639 zf-RING_2: Ring finge 66.5 4.3 9.3E-05 22.7 1.5 26 69-94 3-28 (44)
15 PF10367 Vps39_2: Vacuolar sor 61.7 6 0.00013 25.3 1.7 12 39-50 77-88 (109)
16 PF08271 TF_Zn_Ribbon: TFIIB z 61.2 3.7 8E-05 23.4 0.6 32 42-80 2-33 (43)
17 PF04641 Rtf2: Rtf2 RING-finge 59.1 4.4 9.5E-05 31.2 0.8 26 68-96 36-62 (260)
18 PF08274 PhnA_Zn_Ribbon: PhnA 58.3 6.3 0.00014 21.6 1.2 24 41-73 3-26 (30)
19 PF07282 OrfB_Zn_ribbon: Putat 53.1 8.8 0.00019 23.4 1.3 33 39-79 27-59 (69)
20 PLN03208 E3 ubiquitin-protein 52.0 6.2 0.00013 30.1 0.6 15 80-94 29-43 (193)
21 KOG2177|consensus 50.8 3.5 7.6E-05 29.0 -0.8 12 39-50 12-23 (386)
22 PF09538 FYDLN_acid: Protein o 50.2 9.6 0.00021 26.3 1.3 32 39-79 8-39 (108)
23 PRK00420 hypothetical protein; 45.4 14 0.00029 25.9 1.5 31 39-78 22-52 (112)
24 PF04423 Rad50_zn_hook: Rad50 45.3 7.1 0.00015 23.1 0.0 12 41-52 21-32 (54)
25 PF10571 UPF0547: Uncharacteri 43.3 13 0.00028 19.6 0.9 17 42-58 2-18 (26)
26 PF14634 zf-RING_5: zinc-RING 42.4 15 0.00032 20.7 1.1 18 77-94 10-27 (44)
27 smart00734 ZnF_Rad18 Rad18-lik 41.6 13 0.00027 19.5 0.6 10 41-50 2-11 (26)
28 TIGR02300 FYDLN_acid conserved 38.5 15 0.00033 26.5 0.8 31 39-78 8-38 (129)
29 TIGR01206 lysW lysine biosynth 38.1 25 0.00054 21.6 1.7 31 41-77 3-33 (54)
30 smart00184 RING Ring finger. E 38.0 20 0.00043 17.8 1.1 16 79-94 8-23 (39)
31 PF09986 DUF2225: Uncharacteri 37.0 13 0.00028 28.0 0.3 13 39-51 4-16 (214)
32 TIGR03831 YgiT_finger YgiT-typ 36.9 8.5 0.00019 21.2 -0.5 26 43-68 1-27 (46)
33 PF09866 DUF2093: Uncharacteri 35.3 24 0.00053 21.0 1.2 14 64-77 5-18 (42)
34 TIGR00599 rad18 DNA repair pro 34.4 13 0.00029 31.0 0.0 11 40-50 26-36 (397)
35 PF13923 zf-C3HC4_2: Zinc fing 34.3 35 0.00077 18.5 1.8 13 82-94 11-24 (39)
36 COG0675 Transposase and inacti 33.2 33 0.00071 25.4 2.0 29 38-79 307-335 (364)
37 KOG3039|consensus 32.1 15 0.00033 29.7 0.0 17 80-96 54-70 (303)
38 PF10588 NADH-G_4Fe-4S_3: NADH 31.2 28 0.00062 19.8 1.1 18 39-56 12-33 (41)
39 KOG0883|consensus 30.8 25 0.00055 30.2 1.1 32 55-96 36-67 (518)
40 PF13824 zf-Mss51: Zinc-finger 29.9 23 0.00049 22.1 0.5 11 63-73 11-21 (55)
41 PF05237 MoeZ_MoeB: MoeZ/MoeB 29.7 23 0.0005 22.6 0.6 11 38-48 72-82 (84)
42 PHA02446 hypothetical protein 28.6 13 0.00029 27.2 -0.8 39 39-77 61-99 (166)
43 smart00531 TFIIE Transcription 28.0 25 0.00054 24.8 0.5 40 40-81 99-138 (147)
44 PF05191 ADK_lid: Adenylate ki 27.7 34 0.00073 19.2 0.9 17 66-82 1-18 (36)
45 PF13894 zf-C2H2_4: C2H2-type 27.6 18 0.00039 16.7 -0.2 11 42-52 2-12 (24)
46 PRK10220 hypothetical protein; 27.6 47 0.001 23.5 1.8 11 41-51 21-31 (111)
47 cd00714 GFAT Glutamine amidotr 27.1 18 0.00039 26.7 -0.3 31 63-95 69-107 (215)
48 COG0482 TrmU Predicted tRNA(5- 26.9 64 0.0014 26.8 2.8 46 48-93 172-227 (356)
49 PRK01343 zinc-binding protein; 26.8 30 0.00064 21.7 0.6 12 39-50 8-19 (57)
50 PF00412 LIM: LIM domain; Int 26.1 15 0.00032 21.1 -0.8 26 65-92 25-50 (58)
51 PF12230 PRP21_like_P: Pre-mRN 25.9 23 0.00049 26.6 0.0 15 65-79 167-181 (229)
52 COG3908 Uncharacterized protei 25.9 41 0.00088 22.2 1.2 16 63-78 27-42 (77)
53 PF13522 GATase_6: Glutamine a 24.9 48 0.001 22.7 1.5 44 49-94 2-54 (133)
54 COG1998 RPS31 Ribosomal protei 24.7 54 0.0012 20.3 1.5 23 39-70 18-41 (51)
55 PRK11088 rrmA 23S rRNA methylt 24.4 46 0.001 25.1 1.4 9 42-50 4-12 (272)
56 PF14803 Nudix_N_2: Nudix N-te 24.4 40 0.00086 18.8 0.8 29 43-75 3-31 (34)
57 PF13913 zf-C2HC_2: zinc-finge 24.3 28 0.00061 17.8 0.2 12 41-52 3-14 (25)
58 PRK00807 50S ribosomal protein 24.2 61 0.0013 19.5 1.7 24 68-91 3-27 (52)
59 PF03119 DNA_ligase_ZBD: NAD-d 24.2 24 0.00051 18.7 -0.1 10 42-51 1-10 (28)
60 PF10915 DUF2709: Protein of u 23.7 54 0.0012 25.8 1.7 20 61-80 82-101 (238)
61 KOG4265|consensus 22.6 39 0.00084 28.1 0.8 17 39-55 324-340 (349)
62 PRK07758 hypothetical protein; 22.6 37 0.00081 23.3 0.6 17 30-46 9-25 (95)
63 PF13395 HNH_4: HNH endonuclea 22.5 34 0.00073 20.2 0.3 12 69-80 1-12 (54)
64 PF13920 zf-C3HC4_3: Zinc fing 22.4 28 0.00061 19.9 -0.1 13 39-51 36-48 (50)
65 cd00162 RING RING-finger (Real 21.9 35 0.00075 17.6 0.3 9 42-50 1-9 (45)
66 PF05477 SURF2: Surfeit locus 21.9 46 0.001 26.2 1.0 19 60-78 73-91 (244)
67 TIGR02194 GlrX_NrdH Glutaredox 21.8 35 0.00077 20.5 0.3 24 39-62 5-29 (72)
68 TIGR00686 phnA alkylphosphonat 21.8 70 0.0015 22.5 1.8 12 41-52 20-31 (109)
69 PF13186 SPASM: Iron-sulfur cl 21.3 50 0.0011 18.7 0.9 10 83-92 9-18 (64)
70 PF14169 YdjO: Cold-inducible 20.6 46 0.001 21.0 0.6 21 38-58 37-57 (59)
71 cd02970 PRX_like2 Peroxiredoxi 20.4 35 0.00076 22.3 0.1 18 39-56 32-49 (149)
72 PF12792 CSS-motif: CSS motif 20.3 57 0.0012 22.5 1.2 30 44-73 38-75 (208)
No 1
>KOG0396|consensus
Probab=99.97 E-value=1e-32 Score=223.16 Aligned_cols=86 Identities=45% Similarity=0.860 Sum_probs=79.5
Q ss_pred ccccCcccceeeEEecCccccccCccccccccccCCCCCCCCChhHHHhhhhCCCceecccEEEeccccccccCCCCcee
Q psy16822 5 QPLAHGLDLIKVVSSPPGLSALKTPQCSSEVMETRNKSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFNEYNQPMV 84 (97)
Q Consensus 5 ~pll~~~~~~~~~~l~aGlsaLKTp~C~~~~~~~~~~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmde~N~P~~ 84 (97)
.|+|+ ++++||||++|||.|+.+.+.....+||+|++.|+++|++||||||.||+|||+||||.||++|+|++
T Consensus 276 ~~~L~-------~~l~~GLsalKTp~c~~~~~~~~~~~CpvC~~~f~~ia~~LPfah~~~S~Lvc~isge~md~~N~P~l 348 (389)
T KOG0396|consen 276 NPALT-------IYLQAGLSALKTPRCLNDESDNNPNNCPVCCEAFKPIAQALPFAHHAQSRLVCSISGELMDDDNPPHL 348 (389)
T ss_pred CcHHH-------HHHHhhhhhcccccccccccCCCCCCCCCcccccchhhhcCCchhhhhhHHHhhccccccCCCCCccc
Confidence 56677 99999999999999998865545568999999999999999999999999999999999999999999
Q ss_pred cCCCceecccCCC
Q psy16822 85 LPNGYVYGEQEGK 97 (97)
Q Consensus 85 lPNG~VYs~~aL~ 97 (97)
||||+|||.++|+
T Consensus 349 fpnG~Vyg~~~L~ 361 (389)
T KOG0396|consen 349 FPNGYVYGTKALE 361 (389)
T ss_pred ccCceeehhHHHH
Confidence 9999999999874
No 2
>KOG2817|consensus
Probab=98.61 E-value=1.2e-08 Score=83.85 Aligned_cols=41 Identities=24% Similarity=0.271 Sum_probs=39.1
Q ss_pred hCCCceecccEEEeccccccccCCCCceecCCCceecccCC
Q psy16822 56 SLPYARCNQSRLVCSISGLQFNEYNQPMVLPNGYVYGEQEG 96 (97)
Q Consensus 56 ~LP~ah~~~S~LvC~iSg~vmde~N~P~~lPNG~VYs~~aL 96 (97)
.||...|.||.++|+|+.|+.+|+||||+|..|||.|++||
T Consensus 324 eL~~~~~fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAl 364 (394)
T KOG2817|consen 324 ELGKEYHFHSVFICPVLKEQTSDENPPMMLICGHVISKDAL 364 (394)
T ss_pred eccccccccceeecccchhhccCCCCCeeeeccceecHHHH
Confidence 67888899999999999999999999999999999999886
No 3
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.39 E-value=5.4e-08 Score=57.62 Aligned_cols=28 Identities=39% Similarity=0.506 Sum_probs=18.3
Q ss_pred eccccccccCCCCceecCCCceecccCC
Q psy16822 69 CSISGLQFNEYNQPMVLPNGYVYGEQEG 96 (97)
Q Consensus 69 C~iSg~vmde~N~P~~lPNG~VYs~~aL 96 (97)
|+|+.|..+++|+||+||.||||++++|
T Consensus 1 CpIc~e~~~~~n~P~~L~CGH~~c~~cl 28 (43)
T PF13445_consen 1 CPICKEFSTEENPPMVLPCGHVFCKDCL 28 (43)
T ss_dssp -TTT----TTSS-EEE-SSS-EEEHHHH
T ss_pred CCccccccCCCCCCEEEeCccHHHHHHH
Confidence 7899996679999999999999999876
No 4
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.23 E-value=3.9e-07 Score=74.29 Aligned_cols=41 Identities=24% Similarity=0.374 Sum_probs=39.3
Q ss_pred hCCCceecccEEEeccccccccCCCCceecCCCceecccCC
Q psy16822 56 SLPYARCNQSRLVCSISGLQFNEYNQPMVLPNGYVYGEQEG 96 (97)
Q Consensus 56 ~LP~ah~~~S~LvC~iSg~vmde~N~P~~lPNG~VYs~~aL 96 (97)
.||-..|.||.++|+++.|...++||||||..|||.+++||
T Consensus 326 klp~~~hfHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal 366 (396)
T COG5109 326 KLPKGRHFHSLFICPVLKELCTDENPPVMLECGHVISKEAL 366 (396)
T ss_pred ecCCcccccceeeccccHhhhcccCCCeeeeccceeeHHHH
Confidence 68889999999999999999999999999999999999886
No 5
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.01 E-value=1.4e-06 Score=52.60 Aligned_cols=27 Identities=30% Similarity=0.647 Sum_probs=24.4
Q ss_pred EEeccccccccCCCCceecCCCceecccCC
Q psy16822 67 LVCSISGLQFNEYNQPMVLPNGYVYGEQEG 96 (97)
Q Consensus 67 LvC~iSg~vmde~N~P~~lPNG~VYs~~aL 96 (97)
|+|+||+++|++ |+++|+||||.+++|
T Consensus 2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i 28 (63)
T smart00504 2 FLCPISLEVMKD---PVILPSGQTYERRAI 28 (63)
T ss_pred cCCcCCCCcCCC---CEECCCCCEEeHHHH
Confidence 689999999986 899999999998765
No 6
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=97.49 E-value=1.7e-05 Score=50.59 Aligned_cols=28 Identities=29% Similarity=0.701 Sum_probs=22.8
Q ss_pred EEEeccccccccCCCCceecCCCceecccCC
Q psy16822 66 RLVCSISGLQFNEYNQPMVLPNGYVYGEQEG 96 (97)
Q Consensus 66 ~LvC~iSg~vmde~N~P~~lPNG~VYs~~aL 96 (97)
.|+|+|||++|. .|+.+|.|++|.+.+|
T Consensus 4 ~f~CpIt~~lM~---dPVi~~~G~tyer~~I 31 (73)
T PF04564_consen 4 EFLCPITGELMR---DPVILPSGHTYERSAI 31 (73)
T ss_dssp GGB-TTTSSB-S---SEEEETTSEEEEHHHH
T ss_pred ccCCcCcCcHhh---CceeCCcCCEEcHHHH
Confidence 468999999995 5999999999998765
No 7
>PF04641 Rtf2: Rtf2 RING-finger
Probab=96.81 E-value=0.00048 Score=53.10 Aligned_cols=35 Identities=31% Similarity=0.681 Sum_probs=30.0
Q ss_pred cccEEEeccccccccCCCCceec-CCCceecccCCC
Q psy16822 63 NQSRLVCSISGLQFNEYNQPMVL-PNGYVYGEQEGK 97 (97)
Q Consensus 63 ~~S~LvC~iSg~vmde~N~P~~l-PNG~VYs~~aL~ 97 (97)
..+.++|+||++.|+....-+.| |.|+||++++|+
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alk 145 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALK 145 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHH
Confidence 57899999999999877666666 999999999874
No 8
>KOG3113|consensus
Probab=95.96 E-value=0.0022 Score=51.24 Aligned_cols=35 Identities=26% Similarity=0.493 Sum_probs=29.2
Q ss_pred cccEEEeccccccccCCCCcee-cCCCceecccCCC
Q psy16822 63 NQSRLVCSISGLQFNEYNQPMV-LPNGYVYGEQEGK 97 (97)
Q Consensus 63 ~~S~LvC~iSg~vmde~N~P~~-lPNG~VYs~~aL~ 97 (97)
.+++++|+|||-.||.--.=++ -+.|+|||++||+
T Consensus 108 ~~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlK 143 (293)
T KOG3113|consen 108 QRARFICPVTGLEMNGKYRFCALRCCGCVFSERALK 143 (293)
T ss_pred ccceeecccccceecceEEEEEEeccceeccHHHHH
Confidence 3789999999999997655444 4999999999874
No 9
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=91.28 E-value=0.12 Score=29.78 Aligned_cols=15 Identities=27% Similarity=0.596 Sum_probs=11.8
Q ss_pred CCceecCCCceeccc
Q psy16822 80 NQPMVLPNGYVYGEQ 94 (97)
Q Consensus 80 N~P~~lPNG~VYs~~ 94 (97)
..|+.|+-||+|-+.
T Consensus 9 ~~Pv~l~CGH~FC~~ 23 (42)
T PF15227_consen 9 KDPVSLPCGHSFCRS 23 (42)
T ss_dssp SSEEE-SSSSEEEHH
T ss_pred CCccccCCcCHHHHH
Confidence 889999999999543
No 10
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=85.55 E-value=0.23 Score=30.60 Aligned_cols=28 Identities=21% Similarity=0.385 Sum_probs=17.7
Q ss_pred EEEeccccccccCCCCceec-CCCceecccCC
Q psy16822 66 RLVCSISGLQFNEYNQPMVL-PNGYVYGEQEG 96 (97)
Q Consensus 66 ~LvC~iSg~vmde~N~P~~l-PNG~VYs~~aL 96 (97)
.+.|+||+.++. .|+.- -.||||++++|
T Consensus 11 ~~~CPiT~~~~~---~PV~s~~C~H~fek~aI 39 (57)
T PF11789_consen 11 SLKCPITLQPFE---DPVKSKKCGHTFEKEAI 39 (57)
T ss_dssp -SB-TTTSSB-S---SEEEESSS--EEEHHHH
T ss_pred ccCCCCcCChhh---CCcCcCCCCCeecHHHH
Confidence 367888888875 57765 67999999876
No 11
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=76.74 E-value=1 Score=26.85 Aligned_cols=31 Identities=26% Similarity=0.570 Sum_probs=15.4
Q ss_pred CCCCCChh--HHHhhhhCCCceecccE-EEeccc
Q psy16822 42 SCPVCMEP--FNTLAKSLPYARCNQSR-LVCSIS 72 (97)
Q Consensus 42 ~CPvC~~~--~~~La~~LP~ah~~~S~-LvC~iS 72 (97)
.||.|.+. ...|.+.+-..|...+. .+|+|=
T Consensus 4 ~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC 37 (54)
T PF05605_consen 4 TCPYCGKGFSESSLVEHCEDEHRSESKNVVCPIC 37 (54)
T ss_pred CCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCc
Confidence 45555554 23455555555555432 555553
No 12
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=76.61 E-value=1.4 Score=27.99 Aligned_cols=39 Identities=28% Similarity=0.688 Sum_probs=29.8
Q ss_pred CCCCCCChhHHHhhhhCCCceecccEEEecccccccc-CCCCceecCC
Q psy16822 41 KSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFN-EYNQPMVLPN 87 (97)
Q Consensus 41 ~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmd-e~N~P~~lPN 87 (97)
--||+|.-.+.- ...+..|||+.-|.--. ++..|+|||+
T Consensus 9 LaCP~~kg~L~~--------~~~~~~L~c~~~~~aYpI~dGIPvlL~~ 48 (60)
T COG2835 9 LACPVCKGPLVY--------DEEKQELICPRCKLAYPIRDGIPVLLPD 48 (60)
T ss_pred eeccCcCCcceE--------eccCCEEEecccCceeecccCccccCch
Confidence 358888766432 33445899999999988 8899999986
No 13
>PRK11827 hypothetical protein; Provisional
Probab=75.53 E-value=1.3 Score=27.91 Aligned_cols=39 Identities=26% Similarity=0.572 Sum_probs=29.5
Q ss_pred CCCCCCChhHHHhhhhCCCceecccEEEecccccccc-CCCCceecCC
Q psy16822 41 KSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFN-EYNQPMVLPN 87 (97)
Q Consensus 41 ~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmd-e~N~P~~lPN 87 (97)
-.||+|...+.-- .....|+|...|..-. .|+.|+||++
T Consensus 9 LaCP~ckg~L~~~--------~~~~~Lic~~~~laYPI~dgIPVlL~d 48 (60)
T PRK11827 9 IACPVCNGKLWYN--------QEKQELICKLDNLAFPLRDGIPVLLET 48 (60)
T ss_pred eECCCCCCcCeEc--------CCCCeEECCccCeeccccCCccccCHH
Confidence 4699997765321 1345799999999888 8999999976
No 14
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=66.50 E-value=4.3 Score=22.71 Aligned_cols=26 Identities=27% Similarity=0.507 Sum_probs=17.4
Q ss_pred eccccccccCCCCceecCCCceeccc
Q psy16822 69 CSISGLQFNEYNQPMVLPNGYVYGEQ 94 (97)
Q Consensus 69 C~iSg~vmde~N~P~~lPNG~VYs~~ 94 (97)
|+|--+.+++++..+.+|.|++|-.+
T Consensus 3 C~IC~~~~~~~~~~~~l~C~H~fh~~ 28 (44)
T PF13639_consen 3 CPICLEEFEDGEKVVKLPCGHVFHRS 28 (44)
T ss_dssp ETTTTCBHHTTSCEEEETTSEEEEHH
T ss_pred CcCCChhhcCCCeEEEccCCCeeCHH
Confidence 33334444556778889999998654
No 15
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=61.73 E-value=6 Score=25.30 Aligned_cols=12 Identities=33% Similarity=0.988 Sum_probs=9.2
Q ss_pred CCCCCCCCChhH
Q psy16822 39 RNKSCPVCMEPF 50 (97)
Q Consensus 39 ~~~~CPvC~~~~ 50 (97)
....|++|.+.|
T Consensus 77 ~~~~C~vC~k~l 88 (109)
T PF10367_consen 77 ESTKCSVCGKPL 88 (109)
T ss_pred CCCCccCcCCcC
Confidence 457799998876
No 16
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=61.15 E-value=3.7 Score=23.38 Aligned_cols=32 Identities=28% Similarity=0.500 Sum_probs=21.3
Q ss_pred CCCCCChhHHHhhhhCCCceecccEEEeccccccccCCC
Q psy16822 42 SCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFNEYN 80 (97)
Q Consensus 42 ~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmde~N 80 (97)
.||.|.... + .....+..+||+--|.|++|+.
T Consensus 2 ~Cp~Cg~~~--~-----~~D~~~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 2 KCPNCGSKE--I-----VFDPERGELVCPNCGLVLEENI 33 (43)
T ss_dssp SBTTTSSSE--E-----EEETTTTEEEETTT-BBEE-TT
T ss_pred CCcCCcCCc--e-----EEcCCCCeEECCCCCCEeeccc
Confidence 488887642 2 2235677889999999999875
No 17
>PF04641 Rtf2: Rtf2 RING-finger
Probab=59.07 E-value=4.4 Score=31.23 Aligned_cols=26 Identities=23% Similarity=0.478 Sum_probs=21.5
Q ss_pred EeccccccccCCCCcee-cCCCceecccCC
Q psy16822 68 VCSISGLQFNEYNQPMV-LPNGYVYGEQEG 96 (97)
Q Consensus 68 vC~iSg~vmde~N~P~~-lPNG~VYs~~aL 96 (97)
.|++|++++.. |+| =.-|++|..++|
T Consensus 36 ~CaLS~~pL~~---PiV~d~~G~LynKeai 62 (260)
T PF04641_consen 36 HCALSQQPLED---PIVSDRLGRLYNKEAI 62 (260)
T ss_pred cccCcCCccCC---CeeeCCCCeeEcHHHH
Confidence 48899999987 775 589999998765
No 18
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=58.29 E-value=6.3 Score=21.61 Aligned_cols=24 Identities=33% Similarity=0.753 Sum_probs=11.0
Q ss_pred CCCCCCChhHHHhhhhCCCceecccEEEecccc
Q psy16822 41 KSCPVCMEPFNTLAKSLPYARCNQSRLVCSISG 73 (97)
Q Consensus 41 ~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg 73 (97)
++||.|..+ |+.+.++.+||+--|
T Consensus 3 p~Cp~C~se---------~~y~D~~~~vCp~C~ 26 (30)
T PF08274_consen 3 PKCPLCGSE---------YTYEDGELLVCPECG 26 (30)
T ss_dssp ---TTT--------------EE-SSSEEETTTT
T ss_pred CCCCCCCCc---------ceeccCCEEeCCccc
Confidence 578888766 344778888887544
No 19
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=53.06 E-value=8.8 Score=23.35 Aligned_cols=33 Identities=18% Similarity=0.498 Sum_probs=25.0
Q ss_pred CCCCCCCCChhHHHhhhhCCCceecccEEEeccccccccCC
Q psy16822 39 RNKSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFNEY 79 (97)
Q Consensus 39 ~~~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmde~ 79 (97)
.+..||.|.....+ ....-.++|+--|..+|-|
T Consensus 27 TSq~C~~CG~~~~~--------~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--------RRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred CccCccCccccccc--------ccccceEEcCCCCCEECcH
Confidence 56789999877655 4456678999989888854
No 20
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=52.00 E-value=6.2 Score=30.13 Aligned_cols=15 Identities=20% Similarity=0.295 Sum_probs=11.6
Q ss_pred CCceecCCCceeccc
Q psy16822 80 NQPMVLPNGYVYGEQ 94 (97)
Q Consensus 80 N~P~~lPNG~VYs~~ 94 (97)
..|++.+.||+|-..
T Consensus 29 ~dPVvT~CGH~FC~~ 43 (193)
T PLN03208 29 RDPVVTLCGHLFCWP 43 (193)
T ss_pred CCcEEcCCCchhHHH
Confidence 567888999988654
No 21
>KOG2177|consensus
Probab=50.82 E-value=3.5 Score=28.95 Aligned_cols=12 Identities=42% Similarity=1.240 Sum_probs=8.9
Q ss_pred CCCCCCCCChhH
Q psy16822 39 RNKSCPVCMEPF 50 (97)
Q Consensus 39 ~~~~CPvC~~~~ 50 (97)
....||+|...|
T Consensus 12 ~~~~C~iC~~~~ 23 (386)
T KOG2177|consen 12 EELTCPICLEYF 23 (386)
T ss_pred ccccChhhHHHh
Confidence 346799997776
No 22
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=50.25 E-value=9.6 Score=26.35 Aligned_cols=32 Identities=31% Similarity=0.713 Sum_probs=25.1
Q ss_pred CCCCCCCCChhHHHhhhhCCCceecccEEEeccccccccCC
Q psy16822 39 RNKSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFNEY 79 (97)
Q Consensus 39 ~~~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmde~ 79 (97)
....||.|..=|..|-+ .-+||+.+|+...-.
T Consensus 8 tKR~Cp~CG~kFYDLnk---------~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNK---------DPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCC---------CCccCCCCCCccCcc
Confidence 45789999999988854 447899999887755
No 23
>PRK00420 hypothetical protein; Validated
Probab=45.42 E-value=14 Score=25.95 Aligned_cols=31 Identities=32% Similarity=0.707 Sum_probs=21.6
Q ss_pred CCCCCCCCChhHHHhhhhCCCceecccEEEeccccccccC
Q psy16822 39 RNKSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFNE 78 (97)
Q Consensus 39 ~~~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmde 78 (97)
....||+|.-.|-++ -+...+|+.-|++...
T Consensus 22 l~~~CP~Cg~pLf~l---------k~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 22 LSKHCPVCGLPLFEL---------KDGEVVCPVHGKVYIV 52 (112)
T ss_pred ccCCCCCCCCcceec---------CCCceECCCCCCeeee
Confidence 347799997665333 4677888888887663
No 24
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=45.30 E-value=7.1 Score=23.13 Aligned_cols=12 Identities=33% Similarity=1.110 Sum_probs=6.0
Q ss_pred CCCCCCChhHHH
Q psy16822 41 KSCPVCMEPFNT 52 (97)
Q Consensus 41 ~~CPvC~~~~~~ 52 (97)
..||+|...|.+
T Consensus 21 ~~CPlC~r~l~~ 32 (54)
T PF04423_consen 21 GCCPLCGRPLDE 32 (54)
T ss_dssp EE-TTT--EE-H
T ss_pred CcCCCCCCCCCH
Confidence 389999987643
No 25
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=43.35 E-value=13 Score=19.57 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=8.3
Q ss_pred CCCCCChhHHHhhhhCC
Q psy16822 42 SCPVCMEPFNTLAKSLP 58 (97)
Q Consensus 42 ~CPvC~~~~~~La~~LP 58 (97)
+||.|...+..-++.-|
T Consensus 2 ~CP~C~~~V~~~~~~Cp 18 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCP 18 (26)
T ss_pred cCCCCcCCchhhcCcCC
Confidence 45555555544444333
No 26
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=42.37 E-value=15 Score=20.69 Aligned_cols=18 Identities=22% Similarity=0.451 Sum_probs=14.2
Q ss_pred cCCCCceecCCCceeccc
Q psy16822 77 NEYNQPMVLPNGYVYGEQ 94 (97)
Q Consensus 77 de~N~P~~lPNG~VYs~~ 94 (97)
+++.+|++++-||+|-++
T Consensus 10 ~~~~~~~l~~CgH~~C~~ 27 (44)
T PF14634_consen 10 SEERRPRLTSCGHIFCEK 27 (44)
T ss_pred cCCCCeEEcccCCHHHHH
Confidence 566789999999998543
No 27
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=41.59 E-value=13 Score=19.47 Aligned_cols=10 Identities=40% Similarity=1.135 Sum_probs=7.8
Q ss_pred CCCCCCChhH
Q psy16822 41 KSCPVCMEPF 50 (97)
Q Consensus 41 ~~CPvC~~~~ 50 (97)
..||+|...+
T Consensus 2 v~CPiC~~~v 11 (26)
T smart00734 2 VQCPVCFREV 11 (26)
T ss_pred CcCCCCcCcc
Confidence 4699998775
No 28
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=38.55 E-value=15 Score=26.54 Aligned_cols=31 Identities=26% Similarity=0.436 Sum_probs=22.6
Q ss_pred CCCCCCCCChhHHHhhhhCCCceecccEEEeccccccccC
Q psy16822 39 RNKSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFNE 78 (97)
Q Consensus 39 ~~~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmde 78 (97)
....||.|..-|..|-+ +-+||+.+|+....
T Consensus 8 tKr~Cp~cg~kFYDLnk---------~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNR---------RPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCCCcCccccccCC---------CCccCCCcCCccCc
Confidence 45779999888888844 44678888887653
No 29
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=38.06 E-value=25 Score=21.58 Aligned_cols=31 Identities=19% Similarity=0.478 Sum_probs=20.8
Q ss_pred CCCCCCChhHHHhhhhCCCceecccEEEecccccccc
Q psy16822 41 KSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFN 77 (97)
Q Consensus 41 ~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmd 77 (97)
.+||.|...+ .+|-... .-++.|+..|...-
T Consensus 3 ~~CP~CG~~i-----ev~~~~~-GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEI-----ELENPEL-GELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEE-----ecCCCcc-CCEEeCCCCCCEEE
Confidence 4788888766 4565555 66778887775443
No 30
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=38.00 E-value=20 Score=17.82 Aligned_cols=16 Identities=31% Similarity=0.671 Sum_probs=12.4
Q ss_pred CCCceecCCCceeccc
Q psy16822 79 YNQPMVLPNGYVYGEQ 94 (97)
Q Consensus 79 ~N~P~~lPNG~VYs~~ 94 (97)
...++.+|.|++|-.+
T Consensus 8 ~~~~~~~~C~H~~c~~ 23 (39)
T smart00184 8 LKDPVVLPCGHTFCRS 23 (39)
T ss_pred CCCcEEecCCChHHHH
Confidence 4678889999998543
No 31
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=36.98 E-value=13 Score=28.01 Aligned_cols=13 Identities=38% Similarity=1.073 Sum_probs=10.8
Q ss_pred CCCCCCCCChhHH
Q psy16822 39 RNKSCPVCMEPFN 51 (97)
Q Consensus 39 ~~~~CPvC~~~~~ 51 (97)
+...||+|...|.
T Consensus 4 k~~~CPvC~~~F~ 16 (214)
T PF09986_consen 4 KKITCPVCGKEFK 16 (214)
T ss_pred CceECCCCCCeee
Confidence 5688999999873
No 32
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=36.90 E-value=8.5 Score=21.23 Aligned_cols=26 Identities=19% Similarity=0.501 Sum_probs=16.0
Q ss_pred CCCC-ChhHHHhhhhCCCceecccEEE
Q psy16822 43 CPVC-MEPFNTLAKSLPYARCNQSRLV 68 (97)
Q Consensus 43 CPvC-~~~~~~La~~LP~ah~~~S~Lv 68 (97)
||+| ...+....+..+|....+++++
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~~~~~~i 27 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEYGGELIVI 27 (46)
T ss_pred CCCCCCceecceEEEEEEEeCCEEEEE
Confidence 7777 3556566666666665555555
No 33
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=35.33 E-value=24 Score=20.96 Aligned_cols=14 Identities=21% Similarity=0.475 Sum_probs=11.9
Q ss_pred ccEEEecccccccc
Q psy16822 64 QSRLVCSISGLQFN 77 (97)
Q Consensus 64 ~S~LvC~iSg~vmd 77 (97)
.+..+|.+||+.+.
T Consensus 5 G~~V~CAVTg~~Ip 18 (42)
T PF09866_consen 5 GSFVRCAVTGQPIP 18 (42)
T ss_pred CCEEEEEeeCCccc
Confidence 46789999999876
No 34
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.40 E-value=13 Score=31.02 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=7.6
Q ss_pred CCCCCCCChhH
Q psy16822 40 NKSCPVCMEPF 50 (97)
Q Consensus 40 ~~~CPvC~~~~ 50 (97)
.-.||+|...|
T Consensus 26 ~l~C~IC~d~~ 36 (397)
T TIGR00599 26 SLRCHICKDFF 36 (397)
T ss_pred ccCCCcCchhh
Confidence 46788887665
No 35
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=34.31 E-value=35 Score=18.48 Aligned_cols=13 Identities=31% Similarity=0.680 Sum_probs=10.3
Q ss_pred c-eecCCCceeccc
Q psy16822 82 P-MVLPNGYVYGEQ 94 (97)
Q Consensus 82 P-~~lPNG~VYs~~ 94 (97)
| ++++.||+|-++
T Consensus 11 ~~~~~~CGH~fC~~ 24 (39)
T PF13923_consen 11 PVVVTPCGHSFCKE 24 (39)
T ss_dssp EEEECTTSEEEEHH
T ss_pred cCEECCCCCchhHH
Confidence 6 689999999543
No 36
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.21 E-value=33 Score=25.39 Aligned_cols=29 Identities=21% Similarity=0.503 Sum_probs=22.7
Q ss_pred cCCCCCCCCChhHHHhhhhCCCceecccEEEeccccccccCC
Q psy16822 38 TRNKSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFNEY 79 (97)
Q Consensus 38 ~~~~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmde~ 79 (97)
..+..||.|.. -....+.|+-.|.++|-|
T Consensus 307 ~tS~~C~~cg~-------------~~~r~~~C~~cg~~~~rD 335 (364)
T COG0675 307 YTSKTCPCCGH-------------LSGRLFKCPRCGFVHDRD 335 (364)
T ss_pred CCcccccccCC-------------ccceeEECCCCCCeehhh
Confidence 36688999987 235668999999998855
No 37
>KOG3039|consensus
Probab=32.15 E-value=15 Score=29.72 Aligned_cols=17 Identities=24% Similarity=0.804 Sum_probs=15.1
Q ss_pred CCceecCCCceecccCC
Q psy16822 80 NQPMVLPNGYVYGEQEG 96 (97)
Q Consensus 80 N~P~~lPNG~VYs~~aL 96 (97)
-.||+-|.||+|.+++|
T Consensus 54 ~dPvit~~GylfdrEaI 70 (303)
T KOG3039|consen 54 RDPVITPDGYLFDREAI 70 (303)
T ss_pred cCCccCCCCeeeeHHHH
Confidence 57899999999998875
No 38
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=31.22 E-value=28 Score=19.80 Aligned_cols=18 Identities=28% Similarity=0.615 Sum_probs=10.1
Q ss_pred CCCCCCCCChh----HHHhhhh
Q psy16822 39 RNKSCPVCMEP----FNTLAKS 56 (97)
Q Consensus 39 ~~~~CPvC~~~----~~~La~~ 56 (97)
.+.+|++|... |+++|..
T Consensus 12 H~~dC~~C~~~G~CeLQ~~~~~ 33 (41)
T PF10588_consen 12 HPLDCPTCDKNGNCELQDLAYE 33 (41)
T ss_dssp ----TTT-TTGGG-HHHHHHHH
T ss_pred CCCcCcCCCCCCCCHHHHHHHH
Confidence 56789999876 7777764
No 39
>KOG0883|consensus
Probab=30.77 E-value=25 Score=30.24 Aligned_cols=32 Identities=25% Similarity=0.563 Sum_probs=25.2
Q ss_pred hhCCCceecccEEEeccccccccCCCCceecCCCceecccCC
Q psy16822 55 KSLPYARCNQSRLVCSISGLQFNEYNQPMVLPNGYVYGEQEG 96 (97)
Q Consensus 55 ~~LP~ah~~~S~LvC~iSg~vmde~N~P~~lPNG~VYs~~aL 96 (97)
+.|||.|+.-+.+= -+.|+..+.|.||...+|
T Consensus 36 krLP~~hC~lt~~P----------fe~PvC~~dg~vFd~~~I 67 (518)
T KOG0883|consen 36 KRLPFNHCSLTMLP----------FEDPVCTVDGTVFDLTAI 67 (518)
T ss_pred ccCChhhceecccc----------ccCcccccCCcEEeeehh
Confidence 58999999988863 477888888888876654
No 40
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=29.86 E-value=23 Score=22.08 Aligned_cols=11 Identities=18% Similarity=0.459 Sum_probs=5.2
Q ss_pred cccEEEecccc
Q psy16822 63 NQSRLVCSISG 73 (97)
Q Consensus 63 ~~S~LvC~iSg 73 (97)
.+..+.|+.+|
T Consensus 11 ~~v~~~Cp~cG 21 (55)
T PF13824_consen 11 AHVNFECPDCG 21 (55)
T ss_pred cccCCcCCCCC
Confidence 34444555544
No 41
>PF05237 MoeZ_MoeB: MoeZ/MoeB domain; InterPro: IPR007901 This putative domain is found in the MoeZ protein and the MoeB protein. The domain has two CXXC motifs that are only partly conserved. MoeZ is necessary for the synthesis of pyridine-2,6-bis(thiocarboxylic acid), a small secreted metabolite that has a high affinity for transition metals, increases iron uptake efficiency by 20% in Pseudomonas stutzeri, has the ability to reduce both soluble and mineral forms of iron, and has antimicrobial activity towards several species of bacteria. MoeB is the molybdopterin synthase activating enzyme in the molybdopterin cofactor biosynthesis pathway. Both these enzymes are members of a superfamily consisting of related but structurally distinct proteins that are members of pathways involved in the transfer of sulphur-containing moieties to metabolites [] and both also contain the UBA/THIF-type NAD/FAD binding fold (IPR000594 from INTERPRO). ; PDB: 1JWA_B 1JW9_B 1JWB_B 1ZKM_D 1ZUD_3 1ZFN_D.
Probab=29.74 E-value=23 Score=22.58 Aligned_cols=11 Identities=45% Similarity=1.105 Sum_probs=4.8
Q ss_pred cCCCCCCCCCh
Q psy16822 38 TRNKSCPVCME 48 (97)
Q Consensus 38 ~~~~~CPvC~~ 48 (97)
.++.+||+|.+
T Consensus 72 ~k~~~C~~C~~ 82 (84)
T PF05237_consen 72 KKNPDCPVCGP 82 (84)
T ss_dssp ---TT-TTT--
T ss_pred CCCccCcCcCc
Confidence 37899999975
No 42
>PHA02446 hypothetical protein
Probab=28.58 E-value=13 Score=27.20 Aligned_cols=39 Identities=18% Similarity=0.388 Sum_probs=31.0
Q ss_pred CCCCCCCCChhHHHhhhhCCCceecccEEEecccccccc
Q psy16822 39 RNKSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFN 77 (97)
Q Consensus 39 ~~~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmd 77 (97)
+...||+|..+-+-.....=-||-..-.--|++||+-..
T Consensus 61 ~~q~cp~cg~dawv~~~g~~eahpd~l~qecplsgqsv~ 99 (166)
T PHA02446 61 EQQQCPLCGQDAWVIHTGIVEAHPDKLLQECPLSGQSVA 99 (166)
T ss_pred hhhcCCCcccceeEeecCccccCcHHHHHhCCCCCCccc
Confidence 457899999998888777777887777777899887654
No 43
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=28.05 E-value=25 Score=24.80 Aligned_cols=40 Identities=18% Similarity=0.428 Sum_probs=24.7
Q ss_pred CCCCCCCChhHHHhhhhCCCceecccEEEeccccccccCCCC
Q psy16822 40 NKSCPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQFNEYNQ 81 (97)
Q Consensus 40 ~~~CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~vmde~N~ 81 (97)
.-.||.|...+.-+ +.+=..+ ....+.|+..|+.+-+++.
T Consensus 99 ~Y~Cp~C~~~y~~~-ea~~~~d-~~~~f~Cp~Cg~~l~~~dn 138 (147)
T smart00531 99 YYKCPNCQSKYTFL-EANQLLD-MDGTFTCPRCGEELEEDDN 138 (147)
T ss_pred EEECcCCCCEeeHH-HHHHhcC-CCCcEECCCCCCEEEEcCc
Confidence 35699998775433 2111111 2455999999999875543
No 44
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=27.69 E-value=34 Score=19.19 Aligned_cols=17 Identities=29% Similarity=0.743 Sum_probs=11.3
Q ss_pred EEEeccccccccC-CCCc
Q psy16822 66 RLVCSISGLQFNE-YNQP 82 (97)
Q Consensus 66 ~LvC~iSg~vmde-~N~P 82 (97)
|.+|+-.|++-+. .|||
T Consensus 1 Rr~C~~Cg~~Yh~~~~pP 18 (36)
T PF05191_consen 1 RRICPKCGRIYHIEFNPP 18 (36)
T ss_dssp EEEETTTTEEEETTTB--
T ss_pred CcCcCCCCCccccccCCC
Confidence 5688888888884 4544
No 45
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=27.58 E-value=18 Score=16.66 Aligned_cols=11 Identities=36% Similarity=1.234 Sum_probs=5.9
Q ss_pred CCCCCChhHHH
Q psy16822 42 SCPVCMEPFNT 52 (97)
Q Consensus 42 ~CPvC~~~~~~ 52 (97)
.|+.|...+..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 48888776543
No 46
>PRK10220 hypothetical protein; Provisional
Probab=27.57 E-value=47 Score=23.49 Aligned_cols=11 Identities=36% Similarity=0.951 Sum_probs=5.1
Q ss_pred CCCCCCChhHH
Q psy16822 41 KSCPVCMEPFN 51 (97)
Q Consensus 41 ~~CPvC~~~~~ 51 (97)
-.||-|.-+|+
T Consensus 21 ~vCpeC~hEW~ 31 (111)
T PRK10220 21 YICPECAHEWN 31 (111)
T ss_pred EECCcccCcCC
Confidence 34555544443
No 47
>cd00714 GFAT Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. In humans, GFAT catalyzes the first and rate-limiting step of hexosamine metabolism, the conversion of D-fructose-6P (Fru6P) into D-glucosamine-6P using L-glutamine as a nitrogen source. The end product of this pathway, UDP-N-acetyl glucosamine, is a major building block of the bacterial peptidoglycan and fungal chitin.
Probab=27.09 E-value=18 Score=26.73 Aligned_cols=31 Identities=19% Similarity=0.205 Sum_probs=22.3
Q ss_pred cccEEEeccccccccCCCCceecC--------CCceecccC
Q psy16822 63 NQSRLVCSISGLQFNEYNQPMVLP--------NGYVYGEQE 95 (97)
Q Consensus 63 ~~S~LvC~iSg~vmde~N~P~~lP--------NG~VYs~~a 95 (97)
.|.|+ ++.|.+.+++.+|+... ||.+|..+.
T Consensus 69 gH~R~--at~g~~~~~n~qPf~~~~~~~~~vhNG~I~N~~~ 107 (215)
T cd00714 69 GHTRW--ATHGEPTDVNAHPHRSCDGEIAVVHNGIIENYAE 107 (215)
T ss_pred EEEEc--cCCCCCCccCCCCCCcCCCCEEEEEeEEEcCHHH
Confidence 35555 67787778899999887 677776543
No 48
>COG0482 TrmU Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]
Probab=26.92 E-value=64 Score=26.75 Aligned_cols=46 Identities=24% Similarity=0.319 Sum_probs=33.1
Q ss_pred hhHHHhhh--hCCCceecccEEEeccc-cc---c----ccCCCCceecCCCceecc
Q psy16822 48 EPFNTLAK--SLPYARCNQSRLVCSIS-GL---Q----FNEYNQPMVLPNGYVYGE 93 (97)
Q Consensus 48 ~~~~~La~--~LP~ah~~~S~LvC~iS-g~---v----mde~N~P~~lPNG~VYs~ 93 (97)
++++++|+ .||.|..-.|.-||.|- |. . .....--|+=.+|.||++
T Consensus 172 ~evR~iA~~~gL~~a~KkdS~~ICFi~~~~~~~fl~~~~p~~~G~ii~~~G~v~g~ 227 (356)
T COG0482 172 LEVRPIAAEKGLPTAKKKDSQGICFIGERKFKDFLGRYLPAKPGEIIDKDGKVLGE 227 (356)
T ss_pred HHHHHHHHHcCCCccCcccCCcceecCCCCHHHHHHhhCCCCCceEEecCCcEeee
Confidence 56899998 89999999999999998 21 1 222233456677777765
No 49
>PRK01343 zinc-binding protein; Provisional
Probab=26.81 E-value=30 Score=21.69 Aligned_cols=12 Identities=33% Similarity=0.941 Sum_probs=8.8
Q ss_pred CCCCCCCCChhH
Q psy16822 39 RNKSCPVCMEPF 50 (97)
Q Consensus 39 ~~~~CPvC~~~~ 50 (97)
....||+|.+.+
T Consensus 8 p~~~CP~C~k~~ 19 (57)
T PRK01343 8 PTRPCPECGKPS 19 (57)
T ss_pred CCCcCCCCCCcC
Confidence 346799998765
No 50
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=26.11 E-value=15 Score=21.08 Aligned_cols=26 Identities=23% Similarity=0.370 Sum_probs=18.4
Q ss_pred cEEEeccccccccCCCCceecCCCceec
Q psy16822 65 SRLVCSISGLQFNEYNQPMVLPNGYVYG 92 (97)
Q Consensus 65 S~LvC~iSg~vmde~N~P~~lPNG~VYs 92 (97)
.-+.|..=++.+++.. +..-+|.+|-
T Consensus 25 ~Cf~C~~C~~~l~~~~--~~~~~~~~~C 50 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGD--FYEKDGKPYC 50 (58)
T ss_dssp TTSBETTTTCBTTTSS--EEEETTEEEE
T ss_pred cccccCCCCCccCCCe--eEeECCEEEC
Confidence 3467777777777666 7777778774
No 51
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=25.91 E-value=23 Score=26.58 Aligned_cols=15 Identities=20% Similarity=0.485 Sum_probs=0.0
Q ss_pred cEEEeccccccccCC
Q psy16822 65 SRLVCSISGLQFNEY 79 (97)
Q Consensus 65 S~LvC~iSg~vmde~ 79 (97)
-.++|+|||+.+..+
T Consensus 167 ~~~~cPitGe~IP~~ 181 (229)
T PF12230_consen 167 KMIICPITGEMIPAD 181 (229)
T ss_dssp ---------------
T ss_pred ccccccccccccccc
Confidence 358999999987654
No 52
>COG3908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.87 E-value=41 Score=22.24 Aligned_cols=16 Identities=19% Similarity=0.407 Sum_probs=13.2
Q ss_pred cccEEEeccccccccC
Q psy16822 63 NQSRLVCSISGLQFNE 78 (97)
Q Consensus 63 ~~S~LvC~iSg~vmde 78 (97)
..|..+|.+||+.+.-
T Consensus 27 ~GsfV~CAVtgk~IPl 42 (77)
T COG3908 27 PGSFVLCAVTGKPIPL 42 (77)
T ss_pred CCcEEEEEecCCcccH
Confidence 4688999999998763
No 53
>PF13522 GATase_6: Glutamine amidotransferase domain
Probab=24.89 E-value=48 Score=22.67 Aligned_cols=44 Identities=25% Similarity=0.314 Sum_probs=24.7
Q ss_pred hHHHhhhhCCCce-ecccEEEeccccccccCCCCce--------ecCCCceeccc
Q psy16822 49 PFNTLAKSLPYAR-CNQSRLVCSISGLQFNEYNQPM--------VLPNGYVYGEQ 94 (97)
Q Consensus 49 ~~~~La~~LP~ah-~~~S~LvC~iSg~vmde~N~P~--------~lPNG~VYs~~ 94 (97)
++..+++.+.-.. ..|.|+ ...|..-.++|.|+ +.=||.|+..+
T Consensus 2 d~~~~~~~~~~~~~lgH~R~--AT~G~~~~~~~hPf~~~~g~~~~~HNG~i~n~~ 54 (133)
T PF13522_consen 2 DFEGLASWLDGEAALGHTRY--ATVGSPTEENNHPFSNRDGRIALAHNGNIDNYK 54 (133)
T ss_pred ChHHHHHhcCCCEEEEEeec--CCCCCCCCcCCCCCcCCCCCEEEEECCeecCHH
Confidence 4555555443321 124444 46788877777998 34566666554
No 54
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=24.69 E-value=54 Score=20.25 Aligned_cols=23 Identities=35% Similarity=0.790 Sum_probs=15.2
Q ss_pred CCCCCCCCCh-hHHHhhhhCCCceecccEEEec
Q psy16822 39 RNKSCPVCME-PFNTLAKSLPYARCNQSRLVCS 70 (97)
Q Consensus 39 ~~~~CPvC~~-~~~~La~~LP~ah~~~S~LvC~ 70 (97)
.+..||-|.+ .| +|+|-. |+.|-
T Consensus 18 k~~~CPrCG~gvf--------mA~H~d-R~~CG 41 (51)
T COG1998 18 KNRFCPRCGPGVF--------MADHKD-RWACG 41 (51)
T ss_pred ccccCCCCCCcch--------hhhcCc-eeEec
Confidence 6789999986 33 344544 66664
No 55
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=24.38 E-value=46 Score=25.12 Aligned_cols=9 Identities=44% Similarity=1.575 Sum_probs=6.7
Q ss_pred CCCCCChhH
Q psy16822 42 SCPVCMEPF 50 (97)
Q Consensus 42 ~CPvC~~~~ 50 (97)
.||+|...+
T Consensus 4 ~CP~C~~~l 12 (272)
T PRK11088 4 QCPLCHQPL 12 (272)
T ss_pred cCCCCCcch
Confidence 588887765
No 56
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=24.36 E-value=40 Score=18.79 Aligned_cols=29 Identities=38% Similarity=0.907 Sum_probs=13.5
Q ss_pred CCCCChhHHHhhhhCCCceecccEEEecccccc
Q psy16822 43 CPVCMEPFNTLAKSLPYARCNQSRLVCSISGLQ 75 (97)
Q Consensus 43 CPvC~~~~~~La~~LP~ah~~~S~LvC~iSg~v 75 (97)
||.|... |...+| +--.+.|+||+--|.|
T Consensus 3 C~~CG~~---l~~~ip-~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGP---LERRIP-EGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B----EEE---TT-SS-EEEETTTTEE
T ss_pred cccccCh---hhhhcC-CCCCccceECCCCCCE
Confidence 7778665 344555 4456778888766544
No 57
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=24.28 E-value=28 Score=17.81 Aligned_cols=12 Identities=42% Similarity=1.099 Sum_probs=9.4
Q ss_pred CCCCCCChhHHH
Q psy16822 41 KSCPVCMEPFNT 52 (97)
Q Consensus 41 ~~CPvC~~~~~~ 52 (97)
..||.|...|+.
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 469999988754
No 58
>PRK00807 50S ribosomal protein L24e; Validated
Probab=24.22 E-value=61 Score=19.49 Aligned_cols=24 Identities=21% Similarity=0.397 Sum_probs=18.4
Q ss_pred EeccccccccCCC-CceecCCCcee
Q psy16822 68 VCSISGLQFNEYN-QPMVLPNGYVY 91 (97)
Q Consensus 68 vC~iSg~vmde~N-~P~~lPNG~VY 91 (97)
.|.++|..+.... .-++--+|.||
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~ 27 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTIL 27 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEE
Confidence 5899999999444 44477899998
No 59
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=24.18 E-value=24 Score=18.75 Aligned_cols=10 Identities=40% Similarity=1.045 Sum_probs=4.7
Q ss_pred CCCCCChhHH
Q psy16822 42 SCPVCMEPFN 51 (97)
Q Consensus 42 ~CPvC~~~~~ 51 (97)
.||+|...+.
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4899976653
No 60
>PF10915 DUF2709: Protein of unknown function (DUF2709); InterPro: IPR024484 Members of this family appear restricted to Chlamydiales. Their function is unknown.
Probab=23.72 E-value=54 Score=25.75 Aligned_cols=20 Identities=15% Similarity=0.458 Sum_probs=16.0
Q ss_pred eecccEEEeccccccccCCC
Q psy16822 61 RCNQSRLVCSISGLQFNEYN 80 (97)
Q Consensus 61 h~~~S~LvC~iSg~vmde~N 80 (97)
..+.-+-||++||+|.-+|-
T Consensus 82 E~TkkIYICPFTGKVF~DNt 101 (238)
T PF10915_consen 82 EQTKKIYICPFTGKVFGDNT 101 (238)
T ss_pred cccceEEEcCCcCccccCCC
Confidence 34566789999999998874
No 61
>KOG4265|consensus
Probab=22.64 E-value=39 Score=28.09 Aligned_cols=17 Identities=29% Similarity=0.995 Sum_probs=14.1
Q ss_pred CCCCCCCCChhHHHhhh
Q psy16822 39 RNKSCPVCMEPFNTLAK 55 (97)
Q Consensus 39 ~~~~CPvC~~~~~~La~ 55 (97)
..++||+|...+.+|.+
T Consensus 324 q~n~CPICRqpi~~ll~ 340 (349)
T KOG4265|consen 324 QTNNCPICRQPIEELLE 340 (349)
T ss_pred hhcCCCccccchHhhhe
Confidence 47899999999888754
No 62
>PRK07758 hypothetical protein; Provisional
Probab=22.59 E-value=37 Score=23.31 Aligned_cols=17 Identities=24% Similarity=0.729 Sum_probs=9.9
Q ss_pred cccccccccCCCCCCCC
Q psy16822 30 QCSSEVMETRNKSCPVC 46 (97)
Q Consensus 30 ~C~~~~~~~~~~~CPvC 46 (97)
.|.....+.++.+||.|
T Consensus 9 ~~~~~~~~~~~~~~~~~ 25 (95)
T PRK07758 9 TCEKGHEYYKSSDCPTC 25 (95)
T ss_pred HHhcccceeccCCCCCC
Confidence 46555444566666666
No 63
>PF13395 HNH_4: HNH endonuclease
Probab=22.46 E-value=34 Score=20.23 Aligned_cols=12 Identities=25% Similarity=0.443 Sum_probs=10.1
Q ss_pred eccccccccCCC
Q psy16822 69 CSISGLQFNEYN 80 (97)
Q Consensus 69 C~iSg~vmde~N 80 (97)
|.+||+.|+.++
T Consensus 1 C~Y~g~~i~~~~ 12 (54)
T PF13395_consen 1 CPYCGKPISIEN 12 (54)
T ss_pred CCCCCCCCChhh
Confidence 889999999665
No 64
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=22.37 E-value=28 Score=19.86 Aligned_cols=13 Identities=46% Similarity=1.331 Sum_probs=9.6
Q ss_pred CCCCCCCCChhHH
Q psy16822 39 RNKSCPVCMEPFN 51 (97)
Q Consensus 39 ~~~~CPvC~~~~~ 51 (97)
....||+|...+.
T Consensus 36 ~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 36 RKKKCPICRQPIE 48 (50)
T ss_dssp TTSBBTTTTBB-S
T ss_pred cCCCCCcCChhhc
Confidence 5688999987764
No 65
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=21.95 E-value=35 Score=17.60 Aligned_cols=9 Identities=56% Similarity=1.730 Sum_probs=5.0
Q ss_pred CCCCCChhH
Q psy16822 42 SCPVCMEPF 50 (97)
Q Consensus 42 ~CPvC~~~~ 50 (97)
+|++|...+
T Consensus 1 ~C~iC~~~~ 9 (45)
T cd00162 1 ECPICLEEF 9 (45)
T ss_pred CCCcCchhh
Confidence 366665554
No 66
>PF05477 SURF2: Surfeit locus protein 2 (SURF2); InterPro: IPR008833 Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown [].
Probab=21.94 E-value=46 Score=26.19 Aligned_cols=19 Identities=26% Similarity=0.628 Sum_probs=15.4
Q ss_pred ceecccEEEeccccccccC
Q psy16822 60 ARCNQSRLVCSISGLQFNE 78 (97)
Q Consensus 60 ah~~~S~LvC~iSg~vmde 78 (97)
+....+.|+|.|||..+|-
T Consensus 73 s~~~~~~LfCkLT~~~iNk 91 (244)
T PF05477_consen 73 STKNPHKLFCKLTGRHINK 91 (244)
T ss_pred ccCCCceeEEechHhHhcc
Confidence 3445788999999999984
No 67
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=21.83 E-value=35 Score=20.47 Aligned_cols=24 Identities=13% Similarity=0.416 Sum_probs=18.1
Q ss_pred CCCCCCCCChhHHHhhh-hCCCcee
Q psy16822 39 RNKSCPVCMEPFNTLAK-SLPYARC 62 (97)
Q Consensus 39 ~~~~CPvC~~~~~~La~-~LP~ah~ 62 (97)
....||-|....+-|.+ ++||.-+
T Consensus 5 ~~~~Cp~C~~ak~~L~~~~i~~~~~ 29 (72)
T TIGR02194 5 SKNNCVQCKMTKKALEEHGIAFEEI 29 (72)
T ss_pred eCCCCHHHHHHHHHHHHCCCceEEE
Confidence 45789999888877877 6777543
No 68
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=21.83 E-value=70 Score=22.52 Aligned_cols=12 Identities=33% Similarity=0.905 Sum_probs=6.0
Q ss_pred CCCCCCChhHHH
Q psy16822 41 KSCPVCMEPFNT 52 (97)
Q Consensus 41 ~~CPvC~~~~~~ 52 (97)
--||-|.-+|.+
T Consensus 20 ~iCpeC~~EW~~ 31 (109)
T TIGR00686 20 LICPSCLYEWNE 31 (109)
T ss_pred eECccccccccc
Confidence 445555555443
No 69
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=21.26 E-value=50 Score=18.71 Aligned_cols=10 Identities=40% Similarity=0.737 Sum_probs=7.9
Q ss_pred eecCCCceec
Q psy16822 83 MVLPNGYVYG 92 (97)
Q Consensus 83 ~~lPNG~VYs 92 (97)
.+.|+|.||.
T Consensus 9 ~I~~dG~v~p 18 (64)
T PF13186_consen 9 YIDPDGDVYP 18 (64)
T ss_pred EEeeCccEEe
Confidence 4689999984
No 70
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=20.61 E-value=46 Score=20.96 Aligned_cols=21 Identities=29% Similarity=0.768 Sum_probs=14.3
Q ss_pred cCCCCCCCCChhHHHhhhhCC
Q psy16822 38 TRNKSCPVCMEPFNTLAKSLP 58 (97)
Q Consensus 38 ~~~~~CPvC~~~~~~La~~LP 58 (97)
...+.||.|...+.+=.+.||
T Consensus 37 ~~~p~CPlC~s~M~~~~r~Lp 57 (59)
T PF14169_consen 37 EEEPVCPLCKSPMVSGTRMLP 57 (59)
T ss_pred CCCccCCCcCCccccceeecc
Confidence 356899999887655444444
No 71
>cd02970 PRX_like2 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these proteins do not contain the other two residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. TRXs alter the redox state of target proteins by catalyzing the reduction of their disulfide bonds via the CXXC motif using reducing equivalents derived from either NADPH or ferredoxins.
Probab=20.41 E-value=35 Score=22.35 Aligned_cols=18 Identities=39% Similarity=0.755 Sum_probs=13.8
Q ss_pred CCCCCCCCChhHHHhhhh
Q psy16822 39 RNKSCPVCMEPFNTLAKS 56 (97)
Q Consensus 39 ~~~~CPvC~~~~~~La~~ 56 (97)
...-||.|..++..|++-
T Consensus 32 ~~~~Cp~C~~~~~~l~~~ 49 (149)
T cd02970 32 RGFGCPFCREYLRALSKL 49 (149)
T ss_pred CCCCChhHHHHHHHHHHH
Confidence 457899999887776653
No 72
>PF12792 CSS-motif: CSS motif domain associated with EAL ; InterPro: IPR024744 This domain, with its characteristic highly conserved CSS sequence motif, is found N-terminal to the EAL domain (PF00563 from PFAM), found in many putative cyclic diguanylate phosphodiesterases.
Probab=20.28 E-value=57 Score=22.52 Aligned_cols=30 Identities=20% Similarity=0.311 Sum_probs=18.2
Q ss_pred CCCChh-HHHhhhhCCCceec-------ccEEEecccc
Q psy16822 44 PVCMEP-FNTLAKSLPYARCN-------QSRLVCSISG 73 (97)
Q Consensus 44 PvC~~~-~~~La~~LP~ah~~-------~S~LvC~iSg 73 (97)
.-|++. +.+|.+.+=++.+. +.+++|+--+
T Consensus 38 ~~Cs~~~~~~Lr~~~~~~~~ir~i~~~~~g~i~CSS~~ 75 (208)
T PF12792_consen 38 QPCSPAHLNALRQIVARSPYIRDIGLVRNGRIYCSSLW 75 (208)
T ss_pred CCCCHHHHHHHHHHHHhchhhhheeEEeCCeEEecCCC
Confidence 347777 66666655444444 5667787644
Done!