Query psy12540
Match_columns 79
No_of_seqs 107 out of 168
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 21:55:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12540.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12540hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0891|consensus 99.6 6.9E-16 1.5E-20 139.6 6.3 72 8-79 1745-1816(2341)
2 COG5032 TEL1 Phosphatidylinosi 97.7 3.2E-05 6.9E-10 71.0 4.1 69 10-78 1552-1620(2105)
3 KOG0890|consensus 96.6 0.0055 1.2E-07 57.6 6.6 68 7-74 1894-1961(2382)
4 KOG0892|consensus 87.6 1.9 4.1E-05 42.1 6.7 72 7-78 2295-2380(2806)
5 PF13646 HEAT_2: HEAT repeats; 71.6 8.7 0.00019 22.4 3.7 54 11-67 4-58 (88)
6 KOG0889|consensus 70.9 3.4 7.4E-05 41.3 2.6 26 23-48 2941-2966(3550)
7 PF12830 Nipped-B_C: Sister ch 68.3 26 0.00055 24.6 6.1 62 16-77 18-82 (187)
8 PF13646 HEAT_2: HEAT repeats; 65.3 24 0.00052 20.4 4.7 49 10-61 35-84 (88)
9 PF13880 Acetyltransf_13: ESCO 48.8 18 0.00039 22.6 2.2 21 51-71 14-34 (70)
10 PF00771 FHIPEP: FHIPEP family 48.3 12 0.00027 31.8 1.9 42 24-78 456-497 (658)
11 cd07439 FANCE_c-term Fanconi a 44.5 46 0.001 25.2 4.3 41 10-50 86-126 (254)
12 cd06561 AlkD_like A new struct 43.1 32 0.0007 23.2 3.0 33 10-42 144-177 (197)
13 PF12717 Cnd1: non-SMC mitotic 42.5 1.1E+02 0.0024 20.9 6.1 58 11-68 68-139 (178)
14 KOG2956|consensus 41.7 28 0.0006 29.4 2.9 40 35-74 325-364 (516)
15 PF12717 Cnd1: non-SMC mitotic 41.4 1.1E+02 0.0024 20.9 5.6 66 10-75 29-99 (178)
16 PRK09687 putative lyase; Provi 39.4 1E+02 0.0023 23.0 5.5 20 16-35 64-83 (280)
17 PRK15389 fumarate hydratase; P 38.8 75 0.0016 26.9 5.0 55 15-69 39-95 (536)
18 PRK13800 putative oxidoreducta 38.7 1E+02 0.0022 26.8 5.9 50 10-62 625-675 (897)
19 PRK06012 flhA flagellar biosyn 38.2 29 0.00063 29.9 2.6 20 58-77 507-526 (697)
20 PRK02733 photosystem I reactio 38.0 29 0.00062 20.0 1.8 21 25-45 21-41 (42)
21 PF12830 Nipped-B_C: Sister ch 37.9 34 0.00074 23.9 2.6 30 11-40 50-79 (187)
22 PRK13683 hypothetical protein; 37.9 16 0.00034 24.1 0.8 33 43-76 13-45 (87)
23 PRK09687 putative lyase; Provi 37.2 98 0.0021 23.1 5.1 60 9-68 92-156 (280)
24 PF11510 FA_FANCE: Fanconi Ana 36.8 59 0.0013 24.9 3.8 53 12-64 97-152 (263)
25 TIGR01399 hrcV type III secret 36.2 30 0.00065 29.9 2.4 42 24-78 470-511 (677)
26 PF14123 DUF4290: Domain of un 36.1 31 0.00067 25.3 2.1 30 42-74 24-53 (176)
27 PRK05910 type III secretion sy 36.1 34 0.00073 29.2 2.6 20 58-77 399-418 (584)
28 PF08713 DNA_alkylation: DNA a 35.1 44 0.00096 22.8 2.7 34 14-47 163-196 (213)
29 TIGR01398 FlhA flagellar biosy 33.8 38 0.00083 29.3 2.6 22 57-78 490-511 (678)
30 PF02985 HEAT: HEAT repeat; I 33.6 68 0.0015 15.9 3.1 25 12-36 6-30 (31)
31 PRK12720 secretion system appa 33.1 36 0.00078 29.5 2.4 22 57-78 486-507 (675)
32 PRK12792 flhA flagellar biosyn 33.0 40 0.00087 29.3 2.6 21 57-77 504-524 (694)
33 PRK15337 type III secretion sy 32.7 41 0.00089 29.2 2.6 21 57-77 500-520 (686)
34 CHL00105 psaJ photosystem I su 32.6 39 0.00084 19.5 1.8 21 25-45 21-41 (42)
35 COG4335 DNA alkylation repair 31.8 1.4E+02 0.0029 21.9 4.8 47 19-69 95-141 (167)
36 PF13170 DUF4003: Protein of u 31.7 79 0.0017 24.1 3.8 61 17-77 73-139 (297)
37 PF01603 B56: Protein phosphat 29.0 83 0.0018 24.8 3.6 35 6-40 133-167 (409)
38 PF14561 TPR_20: Tetratricopep 27.4 83 0.0018 19.7 2.8 25 19-43 57-81 (90)
39 PF12841 YvrJ: YvrJ protein fa 26.9 50 0.0011 18.4 1.5 30 2-31 7-36 (38)
40 PF04675 DNA_ligase_A_N: DNA l 26.6 60 0.0013 21.9 2.2 47 1-49 1-49 (177)
41 cd03568 VHS_STAM VHS domain fa 26.5 1.5E+02 0.0032 20.3 4.2 59 10-68 23-86 (144)
42 PRK09330 cell division protein 26.5 49 0.0011 26.5 2.0 46 29-75 118-164 (384)
43 PF12765 Cohesin_HEAT: HEAT re 26.5 63 0.0014 17.7 1.9 23 8-30 20-42 (42)
44 PF02637 GatB_Yqey: GatB domai 25.3 1.8E+02 0.0039 19.4 4.3 61 12-78 52-112 (148)
45 PF08359 TetR_C_4: YsiA-like p 24.4 1.5E+02 0.0032 18.7 3.6 65 11-78 15-80 (133)
46 PF01713 Smr: Smr domain; Int 24.3 89 0.0019 18.6 2.5 25 16-41 39-63 (83)
47 PF14676 FANCI_S2: FANCI solen 23.4 70 0.0015 22.4 2.1 34 9-42 58-91 (158)
48 COG5240 SEC21 Vesicle coat com 23.1 65 0.0014 28.5 2.2 44 33-76 296-339 (898)
49 PF09280 XPC-binding: XPC-bind 23.1 52 0.0011 19.7 1.2 16 25-40 23-38 (59)
50 PF12348 CLASP_N: CLASP N term 22.9 2.6E+02 0.0056 19.2 7.5 63 9-71 97-163 (228)
51 PF01602 Adaptin_N: Adaptin N 22.8 3.3E+02 0.0071 21.0 5.8 53 16-68 52-107 (526)
52 PF05687 DUF822: Plant protein 22.6 87 0.0019 22.5 2.4 19 54-72 20-38 (150)
53 PF10508 Proteasom_PSMB: Prote 22.5 3.4E+02 0.0075 21.9 6.1 63 12-74 83-153 (503)
54 PF14664 RICTOR_N: Rapamycin-i 22.3 1.7E+02 0.0037 23.0 4.3 42 36-77 104-145 (371)
55 PF00273 Serum_albumin: Serum 22.2 77 0.0017 22.1 2.1 19 22-40 131-149 (178)
56 TIGR01446 DnaD_dom DnaD and ph 22.0 1.4E+02 0.0029 17.4 2.9 60 17-78 12-71 (73)
57 cd00280 TRFH Telomeric Repeat 21.8 3.5E+02 0.0076 20.3 5.7 55 2-69 85-139 (200)
58 COG1298 FlhA Flagellar biosynt 21.8 79 0.0017 27.7 2.4 21 58-78 506-526 (696)
59 cd03561 VHS VHS domain family; 21.3 2.2E+02 0.0048 18.7 4.1 50 12-61 25-78 (133)
60 PF09961 DUF2195: Uncharacteri 21.1 1.2E+02 0.0026 21.0 2.8 36 2-40 61-96 (121)
61 PF12603 DUF3770: Protein of u 20.5 90 0.002 24.0 2.3 21 56-76 11-31 (250)
62 PF14046 NR_Repeat: Nuclear re 20.2 27 0.00058 20.5 -0.5 18 34-51 3-22 (46)
63 PF05536 Neurochondrin: Neuroc 20.1 3.1E+02 0.0066 22.7 5.4 68 6-74 23-90 (543)
No 1
>KOG0891|consensus
Probab=99.61 E-value=6.9e-16 Score=139.59 Aligned_cols=72 Identities=47% Similarity=0.596 Sum_probs=69.6
Q ss_pred HHHHHHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhhccC
Q psy12540 8 ALCAFLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVKLER 79 (79)
Q Consensus 8 ~~~~iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~q~~ 79 (79)
--|++||||.|+..+.+++++++.++|++||||++||+|||+||++..|+++|..|+|+|++|+|+||+|++
T Consensus 1745 ipqLiari~~~~~~~~~l~~~ll~dig~~~pqA~iy~ltvas~s~~~~r~~~a~~ile~m~~~~~~Lv~~a~ 1816 (2341)
T KOG0891|consen 1745 IPQLIARIHTPDQLVVQLVLQLLSDIGRAHPQALVYPLTVASKSKSVARQKAALSILEKMREHSPTLVRQAR 1816 (2341)
T ss_pred HHHHHHHHhccchHHHHHHHHHHHHhhhcchhhhhHHHHHHHhcchHHHHHhHHHHHHHHHHhhHhhhhhhh
Confidence 358999999999999999999999999999999999999999999999999999999999999999999974
No 2
>COG5032 TEL1 Phosphatidylinositol kinase and protein kinases of the PI-3 kinase family [Signal transduction mechanisms / Cell division and chromosome partitioning / Chromatin structure and dynamics / DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=97.72 E-value=3.2e-05 Score=71.02 Aligned_cols=69 Identities=33% Similarity=0.294 Sum_probs=64.5
Q ss_pred HHHHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhhcc
Q psy12540 10 CAFLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVKLE 78 (79)
Q Consensus 10 ~~iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~q~ 78 (79)
+...+++.........++.++.++|+.||||++|+|+.+.||....+...+..+..+.+.|.|.+|.++
T Consensus 1552 ~~~~l~~~l~~~~~~~~~~~l~~~~~~~~~a~~~~L~~~~~s~~~~~e~~~~~~~~~~~~~~~~~v~~~ 1620 (2105)
T COG5032 1552 FIPQLLSSLSLLDLNSAQSLLSKIGKEHPQALVFTLRSAIESTALSKESVALSLENKSRTHDPSLVKEA 1620 (2105)
T ss_pred hhhhhhhhcchhHHHHHHHHHHhhhhhchhhhhhhhhHHHHHhhhhhHhHHHHHhhhhhcCChhhHhHH
Confidence 467788888888999999999999999999999999999999999999999999999999999999875
No 3
>KOG0890|consensus
Probab=96.62 E-value=0.0055 Score=57.57 Aligned_cols=68 Identities=16% Similarity=0.131 Sum_probs=62.4
Q ss_pred HHHHHHHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhh
Q psy12540 7 VALCAFLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLL 74 (79)
Q Consensus 7 ~~~~~iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~L 74 (79)
+--|++.||..|+..|-+.|-+++..+--++||--+.-++--+||.++.|++..+.|+++-+.++++.
T Consensus 1894 a~sQLlSRicH~~~dV~~vl~~II~~l~~~YPqq~lW~~~a~~kS~~p~R~~R~keIL~k~~~~~~~~ 1961 (2382)
T KOG0890|consen 1894 AYSQLLSRICHPNQDVARVLKHIIAKLVLAYPQQTLWQSAALSKSNVPSRVERCKEILTKSRRQKPDY 1961 (2382)
T ss_pred HHHHHHHHHcCCchHHHHHHHHHHHHHHHhCchHHHHHHHHHHhcccHHHHHHHHHHHHHHHhcCccH
Confidence 34599999999999999999999999999999999999999999999999999999999777666554
No 4
>KOG0892|consensus
Probab=87.57 E-value=1.9 Score=42.08 Aligned_cols=72 Identities=17% Similarity=0.195 Sum_probs=58.7
Q ss_pred HHHHHHHHhc-CCCchhhHHHHHHHHHHhhhCchhhhhh---hhhccc-------CCC---HHHHHHHHHHHHHHHhhCH
Q psy12540 7 VALCAFLKRK-RKSKLIGGPVQAYLSDIGKRHPQALVYP---LTVASK-------SNS---SSRRNAANKILQSMCDLSP 72 (79)
Q Consensus 7 ~~~~~iaRi~-s~~~~vr~li~~LL~~IGk~HPQALvYP---LtVA~K-------S~s---~~R~~aA~~Il~~mr~hsp 72 (79)
++-|+-||+. ..+....+.+.+|+.++|++||.--+|- |.-+-+ |.+ ..|+-+|+.++.....-.+
T Consensus 2295 ~~yQlAaRl~~~~~~~fq~~L~~Li~r~~~dhPyhtly~L~~L~~~~rd~e~~n~sr~sl~~~rki~a~l~~~~v~~~~~ 2374 (2806)
T KOG0892|consen 2295 LVYQLAARLGNSENNSFQKSLTSLIYRVGRDHPYHTLYQLLSLVNAVRDNEDENRSRGSIDRDRKIAAELDLCDVNQGAG 2374 (2806)
T ss_pred HHHHHHHHhccccCchHHHHHHHHHHHHhccCchHHHHHHHHHHhcCcChhhhhhcccccchhHHHHHHHhhhHhhccch
Confidence 5679999999 6889999999999999999999977664 444545 222 5688889999999998888
Q ss_pred hhhhcc
Q psy12540 73 LLVKLE 78 (79)
Q Consensus 73 ~LV~q~ 78 (79)
+.|.+.
T Consensus 2375 ~~v~~v 2380 (2806)
T KOG0892|consen 2375 NMVRQL 2380 (2806)
T ss_pred hHHHHH
Confidence 888763
No 5
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=71.61 E-value=8.7 Score=22.36 Aligned_cols=54 Identities=15% Similarity=0.153 Sum_probs=33.0
Q ss_pred HHHHh-cCCCchhhHHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHH
Q psy12540 11 AFLKR-KRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSM 67 (79)
Q Consensus 11 ~iaRi-~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~m 67 (79)
++..+ +.+++.+|......|.++|.. ..+-+|.-..++++..=|.+|-.-+.++
T Consensus 4 L~~~l~~~~~~~vr~~a~~~L~~~~~~---~~~~~L~~~l~d~~~~vr~~a~~aL~~i 58 (88)
T PF13646_consen 4 LLQLLQNDPDPQVRAEAARALGELGDP---EAIPALIELLKDEDPMVRRAAARALGRI 58 (88)
T ss_dssp HHHHHHTSSSHHHHHHHHHHHHCCTHH---HHHHHHHHHHTSSSHHHHHHHHHHHHCC
T ss_pred HHHHHhcCCCHHHHHHHHHHHHHcCCH---hHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 45566 677888888888888866533 3345555555776664444444444443
No 6
>KOG0889|consensus
Probab=70.89 E-value=3.4 Score=41.27 Aligned_cols=26 Identities=42% Similarity=0.547 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHhhhCchhhhhhhhhc
Q psy12540 23 GGPVQAYLSDIGKRHPQALVYPLTVA 48 (79)
Q Consensus 23 r~li~~LL~~IGk~HPQALvYPLtVA 48 (79)
...+..+|..||+.|||||-|||-=|
T Consensus 2941 ~~~~~~iL~kia~~yPQal~f~lRta 2966 (3550)
T KOG0889|consen 2941 AKLVRLILIKIAKSYPQALYFPLRTA 2966 (3550)
T ss_pred hhHHHHHHHHHHHhchHHHHHHHHHH
Confidence 45778899999999999999998433
No 7
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=68.33 E-value=26 Score=24.57 Aligned_cols=62 Identities=19% Similarity=0.175 Sum_probs=46.4
Q ss_pred cCCCchhhHHHHHHHH---HHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhhc
Q psy12540 16 KRKSKLIGGPVQAYLS---DIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVKL 77 (79)
Q Consensus 16 ~s~~~~vr~li~~LL~---~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~q 77 (79)
-+++..+|..-.+++. +-|=.||---+=.|.--.-|++..=++.|..++..+-+.+|.+|+.
T Consensus 18 ~~~~~~vr~~Al~~l~~il~qGLvnP~~cvp~lIAL~ts~~~~ir~~A~~~l~~l~eK~~s~v~~ 82 (187)
T PF12830_consen 18 LSSDDSVRLAALQVLELILRQGLVNPKQCVPTLIALETSPNPSIRSRAYQLLKELHEKHESLVES 82 (187)
T ss_pred hCCCHHHHHHHHHHHHHHHhcCCCChHHHHhHhhhhhCCCChHHHHHHHHHHHHHHHHhHHHHHH
Confidence 3567778877666665 4577899886655544455667777888999999999999998863
No 8
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=65.32 E-value=24 Score=20.42 Aligned_cols=49 Identities=20% Similarity=0.247 Sum_probs=31.9
Q ss_pred HHHHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhcccC-CCHHHHHHHH
Q psy12540 10 CAFLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKS-NSSSRRNAAN 61 (79)
Q Consensus 10 ~~iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS-~s~~R~~aA~ 61 (79)
.++..+.++++.||.....-|..+|. |++ +=.|.=..++ ++...|..|.
T Consensus 35 ~L~~~l~d~~~~vr~~a~~aL~~i~~--~~~-~~~L~~~l~~~~~~~vr~~a~ 84 (88)
T PF13646_consen 35 ALIELLKDEDPMVRRAAARALGRIGD--PEA-IPALIKLLQDDDDEVVREAAA 84 (88)
T ss_dssp HHHHHHTSSSHHHHHHHHHHHHCCHH--HHT-HHHHHHHHTC-SSHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHhCC--HHH-HHHHHHHHcCCCcHHHHHHHH
Confidence 45666788999999999999999984 554 3334333444 4444344443
No 9
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=48.81 E-value=18 Score=22.60 Aligned_cols=21 Identities=24% Similarity=0.295 Sum_probs=17.9
Q ss_pred CCCHHHHHHHHHHHHHHHhhC
Q psy12540 51 SNSSSRRNAANKILQSMCDLS 71 (79)
Q Consensus 51 S~s~~R~~aA~~Il~~mr~hs 71 (79)
+++.+|+..|.++||..|++.
T Consensus 14 ~~~~RR~GIAt~Lld~ar~~~ 34 (70)
T PF13880_consen 14 SPSHRRKGIATRLLDAARENF 34 (70)
T ss_pred ChhhhhhhHHHHHHHHHHHhc
Confidence 466789999999999999863
No 10
>PF00771 FHIPEP: FHIPEP family; InterPro: IPR001712 The Flagellar/Hr/Invasion Proteins Export Pore (FHIPEP) family [, ] consists of a number of proteins that constitute the type III secretion (or signal peptide-independent) pathway apparatus [, ]. This mechanism translocates proteins lacking an N-terminal signal peptide across the cell membrane in one step, as it does not require an intermediate periplasmic process to cleave the signal peptide. It is a common pathway amongst Gram-negative bacteria for secreting toxic and flagellar proteins. The pathway apparatus comprises three components: two within the inner membrane and one within the outer []. An FHIPEP protein is located within the inner membrane, although it is unknown which component it constitutes. FHIPEP proteins have all about 700 amino-acid residues. Within the sequence, the N terminus is highly conserved and hydrophobic, suggesting that this terminus is embedded within the membrane, with 6-8 transmembrane (TM) domains, while the C terminus is less conserved and appears to be devoid of TM regions. It is possible that members of the FHIPEP family serve as pores for the export of specific proteins.; GO: 0009306 protein secretion, 0016020 membrane; PDB: 3MIX_A 2X4A_A 3LW9_A 2X49_A 3MYD_A 3A5I_A.
Probab=48.27 E-value=12 Score=31.76 Aligned_cols=42 Identities=24% Similarity=0.327 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhhcc
Q psy12540 24 GPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVKLE 78 (79)
Q Consensus 24 ~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~q~ 78 (79)
..|..-|.++=++|-.-++ =++-.+.++|.++++||+||+|.
T Consensus 456 tvi~tHL~evlr~~a~ell-------------g~QEvq~LLd~l~~~~P~LV~El 497 (658)
T PF00771_consen 456 TVIATHLSEVLRRHAAELL-------------GRQEVQALLDRLEKEYPELVEEL 497 (658)
T ss_dssp HHHHHHHHHHHHHCHHHCH-------------CHHHHHHHHHHHHTTHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHh-------------CHHHHHHHHHHHHhhchHHHHHh
Confidence 4445555555566655543 14567899999999999999985
No 11
>cd07439 FANCE_c-term Fanconi anemia complementation group E protein, C-terminal domain. Fanconi Anemia (FA) is an autosomal recessive disorder associated with increased susceptibility to various cancers, bone marrow failure, cardiac, renal, and limb malformations, and other characteristics. Cells are highly sensitive to DNA damaging agents. A multi-subunit protein complex, the FA core complex, is responsible for ubiquitination of the protein FANCD2 in response to DNA damage. This monoubiquitination results in a downstream effect on homology-directed DNA repair. FANCE is part of the FA core complex and its C-terminal domain, which is modeled here, has been shown to directly interact with FANCD2. The domain contains a five-fold repeat of a structural unit similar to ARM and HEAT repeats. FANCE appears conserved in metazoa and in plants.
Probab=44.47 E-value=46 Score=25.24 Aligned_cols=41 Identities=17% Similarity=0.096 Sum_probs=32.1
Q ss_pred HHHHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhccc
Q psy12540 10 CAFLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASK 50 (79)
Q Consensus 10 ~~iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~K 50 (79)
..+=++.+=++..++.+...+...++.||.+.++.+++..+
T Consensus 86 l~LpKl~~l~~~aSR~L~~al~~f~~r~~~~~ceall~PLl 126 (254)
T cd07439 86 LLLPKLLSLNESASRALVAALASFAKRYPRPFCEALLRPLL 126 (254)
T ss_pred HHhhhhhccCcchhHHHHHHHHHHHHhCChhHHHHHHHHHH
Confidence 34456666667778999999999999999998888877644
No 12
>cd06561 AlkD_like A new structural DNA glycosylase. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity.
Probab=43.15 E-value=32 Score=23.17 Aligned_cols=33 Identities=15% Similarity=0.253 Sum_probs=25.3
Q ss_pred HHHHHhcC-CCchhhHHHHHHHHHHhhhCchhhh
Q psy12540 10 CAFLKRKR-KSKLIGGPVQAYLSDIGKRHPQALV 42 (79)
Q Consensus 10 ~~iaRi~s-~~~~vr~li~~LL~~IGk~HPQALv 42 (79)
..+.++-. ++..|++.+-..|.++|+.+|...+
T Consensus 144 ~~~~~~~~d~~~~Vqkav~w~L~~~~~~~~~~v~ 177 (197)
T cd06561 144 EIIERLLHDEEYFVQKAVGWALREYGKKDPERVI 177 (197)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHHHHHhhCHHHHH
Confidence 34444444 6788999999999999999998754
No 13
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=42.48 E-value=1.1e+02 Score=20.93 Aligned_cols=58 Identities=12% Similarity=0.179 Sum_probs=41.3
Q ss_pred HHHHhcCCCchhhHHHHHHHHHHhhh-Cchhh-------hhhhhhcc------cCCCHHHHHHHHHHHHHHH
Q psy12540 11 AFLKRKRKSKLIGGPVQAYLSDIGKR-HPQAL-------VYPLTVAS------KSNSSSRRNAANKILQSMC 68 (79)
Q Consensus 11 ~iaRi~s~~~~vr~li~~LL~~IGk~-HPQAL-------vYPLtVA~------KS~s~~R~~aA~~Il~~mr 68 (79)
.+.-+..+++.||+.-...+.++.+. +|+.+ ++-|+-.. +.+.+.|++.-+.+++.|.
T Consensus 68 ~l~~l~D~~~~Ir~~A~~~~~e~~~~~~~~~i~~~~~e~i~~l~~~~~~~~~~~~~~~~~~~I~~fll~~i~ 139 (178)
T PF12717_consen 68 ILKLLVDENPEIRSLARSFFSELLKKRNPNIIYNNFPELISSLNNCYEHPVYGPLSREKRKKIYKFLLDFID 139 (178)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHhCccccccccccCHHHHHHHHHHHHHHcC
Confidence 33445777999999999999999999 88863 23333322 2344578888888888887
No 14
>KOG2956|consensus
Probab=41.73 E-value=28 Score=29.35 Aligned_cols=40 Identities=23% Similarity=0.272 Sum_probs=33.4
Q ss_pred hhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhh
Q psy12540 35 KRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLL 74 (79)
Q Consensus 35 k~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~L 74 (79)
+.+-+-|.-=+-|-.+|.+..+++.|.+|+.+|.+++|.-
T Consensus 325 q~f~~iL~~l~EvL~d~~~~~~k~laLrvL~~ml~~Q~~~ 364 (516)
T KOG2956|consen 325 QHFAEILLLLLEVLSDSEDEIIKKLALRVLREMLTNQPAR 364 (516)
T ss_pred HHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHhchHh
Confidence 4456666666778899999999999999999999999863
No 15
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=41.38 E-value=1.1e+02 Score=20.87 Aligned_cols=66 Identities=9% Similarity=0.093 Sum_probs=39.4
Q ss_pred HHHHHhcCCCchhhHHHHHHHHHHhhhC---chhhh-hhhhhcccCCCHHHHHHHHHHHHHHHhh-CHhhh
Q psy12540 10 CAFLKRKRKSKLIGGPVQAYLSDIGKRH---PQALV-YPLTVASKSNSSSRRNAANKILQSMCDL-SPLLV 75 (79)
Q Consensus 10 ~~iaRi~s~~~~vr~li~~LL~~IGk~H---PQALv-YPLtVA~KS~s~~R~~aA~~Il~~mr~h-sp~LV 75 (79)
.+..++..+++.||+--...|+++-.+. +..-+ |-+..+...++..=++.|...+..+-.. +|+.+
T Consensus 29 ~l~~~L~D~~~~VR~~al~~Ls~Li~~d~ik~k~~l~~~~l~~l~D~~~~Ir~~A~~~~~e~~~~~~~~~i 99 (178)
T PF12717_consen 29 NLYKCLRDEDPLVRKTALLVLSHLILEDMIKVKGQLFSRILKLLVDENPEIRSLARSFFSELLKKRNPNII 99 (178)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHcCceeehhhhhHHHHHHHcCCCHHHHHHHHHHHHHHHHhccchHH
Confidence 4566777777777777777776665443 34444 5555555555555556666666665555 55443
No 16
>PRK09687 putative lyase; Provisional
Probab=39.40 E-value=1e+02 Score=22.99 Aligned_cols=20 Identities=20% Similarity=0.179 Sum_probs=11.8
Q ss_pred cCCCchhhHHHHHHHHHHhh
Q psy12540 16 KRKSKLIGGPVQAYLSDIGK 35 (79)
Q Consensus 16 ~s~~~~vr~li~~LL~~IGk 35 (79)
+++++.+|..-...|..+|.
T Consensus 64 ~~~d~~vR~~A~~aLg~lg~ 83 (280)
T PRK09687 64 SSKNPIERDIGADILSQLGM 83 (280)
T ss_pred hCCCHHHHHHHHHHHHhcCC
Confidence 45556666666666666653
No 17
>PRK15389 fumarate hydratase; Provisional
Probab=38.78 E-value=75 Score=26.86 Aligned_cols=55 Identities=15% Similarity=0.052 Sum_probs=44.6
Q ss_pred hcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhcc-c-CCCHHHHHHHHHHHHHHHh
Q psy12540 15 RKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVAS-K-SNSSSRRNAANKILQSMCD 69 (79)
Q Consensus 15 i~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~-K-S~s~~R~~aA~~Il~~mr~ 69 (79)
|+.+.+.+.+.+.++..++...+|.-.+-.|.-|. + -++..-+.+.+.|+++.+.
T Consensus 39 ~~v~~~~i~~~v~~l~~~a~~~lp~Dv~~aL~~a~~~~E~s~~ak~vl~~ileN~~i 95 (536)
T PRK15389 39 LKVEPEALTLLAEEAFHDISHLLRPAHLQQLAKILDDPEASDNDKFVALDLLKNANI 95 (536)
T ss_pred EEECHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHH
Confidence 45566779999999999999999999999998883 5 3456667788888888764
No 18
>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional
Probab=38.74 E-value=1e+02 Score=26.76 Aligned_cols=50 Identities=18% Similarity=0.094 Sum_probs=33.9
Q ss_pred HHHHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhcccCCCHH-HHHHHHH
Q psy12540 10 CAFLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSS-RRNAANK 62 (79)
Q Consensus 10 ~~iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~-R~~aA~~ 62 (79)
.|+..++.+++.||+.-.+.|.++| |...+=+|.-+.+++... |..++..
T Consensus 625 ~L~~~L~D~d~~VR~~Av~~L~~~~---~~~~~~~L~~aL~D~d~~VR~~Aa~a 675 (897)
T PRK13800 625 ELAPYLADPDPGVRRTAVAVLTETT---PPGFGPALVAALGDGAAAVRRAAAEG 675 (897)
T ss_pred HHHHHhcCCCHHHHHHHHHHHhhhc---chhHHHHHHHHHcCCCHHHHHHHHHH
Confidence 5678888888889998888888887 344455666666666553 4444433
No 19
>PRK06012 flhA flagellar biosynthesis protein FlhA; Validated
Probab=38.23 E-value=29 Score=29.93 Aligned_cols=20 Identities=20% Similarity=0.350 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHhhCHhhhhc
Q psy12540 58 NAANKILQSMCDLSPLLVKL 77 (79)
Q Consensus 58 ~aA~~Il~~mr~hsp~LV~q 77 (79)
+-.+.++|.|++.||.||+|
T Consensus 507 QEvq~LLD~L~~~~p~LVeE 526 (697)
T PRK06012 507 QEVQQLLDRLAKEYPKLVEE 526 (697)
T ss_pred HHHHHHHHHHHHhChHHHHH
Confidence 45688999999999999998
No 20
>PRK02733 photosystem I reaction center subunit IX; Provisional
Probab=38.03 E-value=29 Score=20.03 Aligned_cols=21 Identities=19% Similarity=0.360 Sum_probs=18.5
Q ss_pred HHHHHHHHHhhhCchhhhhhh
Q psy12540 25 PVQAYLSDIGKRHPQALVYPL 45 (79)
Q Consensus 25 li~~LL~~IGk~HPQALvYPL 45 (79)
....+|++|-+-+|-+|.+|+
T Consensus 21 ~tag~lIEiNRffPD~L~~p~ 41 (42)
T PRK02733 21 LTAGILIEFNRFFPDLLFHPM 41 (42)
T ss_pred HHHHHHHHHHHhCchHhccCC
Confidence 456789999999999999996
No 21
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=37.91 E-value=34 Score=23.92 Aligned_cols=30 Identities=10% Similarity=0.132 Sum_probs=25.6
Q ss_pred HHHHhcCCCchhhHHHHHHHHHHhhhCchh
Q psy12540 11 AFLKRKRKSKLIGGPVQAYLSDIGKRHPQA 40 (79)
Q Consensus 11 ~iaRi~s~~~~vr~li~~LL~~IGk~HPQA 40 (79)
+||=..+|++.+|..-.++|.++..+||--
T Consensus 50 lIAL~ts~~~~ir~~A~~~l~~l~eK~~s~ 79 (187)
T PF12830_consen 50 LIALETSPNPSIRSRAYQLLKELHEKHESL 79 (187)
T ss_pred hhhhhCCCChHHHHHHHHHHHHHHHHhHHH
Confidence 455567899999999999999999999843
No 22
>PRK13683 hypothetical protein; Provisional
Probab=37.90 E-value=16 Score=24.11 Aligned_cols=33 Identities=24% Similarity=0.344 Sum_probs=24.7
Q ss_pred hhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhh
Q psy12540 43 YPLTVASKSNSSSRRNAANKILQSMCDLSPLLVK 76 (79)
Q Consensus 43 YPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~ 76 (79)
.|++|.=|.... =...=++|.+.|+.-+|+|+|
T Consensus 13 ~P~SVQRKe~ed-A~alYq~I~~am~sg~P~llE 45 (87)
T PRK13683 13 MPISVQRKEAED-AEALYQQIRQAMRSGNPRLLE 45 (87)
T ss_pred cceEEEeccHHH-HHHHHHHHHHHHhcCCCcEEE
Confidence 477888777655 344447799999999999886
No 23
>PRK09687 putative lyase; Provisional
Probab=37.20 E-value=98 Score=23.14 Aligned_cols=60 Identities=15% Similarity=0.113 Sum_probs=36.4
Q ss_pred HHHHHH--hcCCCchhhHHHHHHHHHHhhhCc--h-hhhhhhhhcccCCCHHHHHHHHHHHHHHH
Q psy12540 9 LCAFLK--RKRKSKLIGGPVQAYLSDIGKRHP--Q-ALVYPLTVASKSNSSSRRNAANKILQSMC 68 (79)
Q Consensus 9 ~~~iaR--i~s~~~~vr~li~~LL~~IGk~HP--Q-ALvYPLtVA~KS~s~~R~~aA~~Il~~mr 68 (79)
+.++.. .+.+++.||......|.++|..++ + .++-+|..+.++++..-|.+|-.-|.+++
T Consensus 92 ~~~L~~l~~~D~d~~VR~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~D~~~~VR~~a~~aLg~~~ 156 (280)
T PRK09687 92 FNILNNLALEDKSACVRASAINATGHRCKKNPLYSPKIVEQSQITAFDKSTNVRFAVAFALSVIN 156 (280)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHhcccccccccchHHHHHHHHHhhCCCHHHHHHHHHHHhccC
Confidence 344443 377788999999999999887664 2 23345556666655544444444444443
No 24
>PF11510 FA_FANCE: Fanconi Anaemia group E protein FANCE; InterPro: IPR021025 Fanconi Anaemia (FA) is a cancer predisposition disorder characterised by chromosome fragility and hypersensitivity to genotoxic agents that suggest defects in the molecular mechanisms of DNA damage signalling and repair. In response to DNA damage, the FA core complex monoubiquitinates the FANCD2 protein. This ubiquitination targets FANCD2 to nuclear foci where it interacts with a variety of DNA repair proteins. The FA group E protein (FANCE) has an important role in DNA repair, functioning as the FANCD2-binding protein in the FA core complex []. This entry represents the C-terminal domain of FANCE, which consists predominantly of helices and does not contain any beta-strands. This domain folds in a continuous right-handed solenoidal pattern from its N terminus to its C terminus. ; PDB: 2ILR_A.
Probab=36.81 E-value=59 Score=24.91 Aligned_cols=53 Identities=11% Similarity=0.109 Sum_probs=30.7
Q ss_pred HHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhc---ccCCCHHHHHHHHHHH
Q psy12540 12 FLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVA---SKSNSSSRRNAANKIL 64 (79)
Q Consensus 12 iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA---~KS~s~~R~~aA~~Il 64 (79)
+-|+-+=+....+.+..-++..+++||.+.++.+.+. ...-+..-.+.-.+|+
T Consensus 97 LpkilsL~~~ASR~L~sal~~f~k~~p~~~~~all~PlL~~~~~g~~Q~eLl~rlv 152 (263)
T PF11510_consen 97 LPKILSLEEPASRLLVSALTSFCKKYPRPVCEALLVPLLQAPGLGPPQCELLCRLV 152 (263)
T ss_dssp HHHHHH-SS---HHHHHHHHHHHHHSHHHHHHHHHHHHHHSTT--HHHHHHHHHHH
T ss_pred HHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 3444444555678899999999999998876665555 2233334444555555
No 25
>TIGR01399 hrcV type III secretion protein, HrcV family. Members of this family are closely homologous to the flagellar biosynthesis protein FlhA (TIGR01398) and should all participate in type III secretion systems. Examples include InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc. Type III secretion systems resemble flagellar biogenesis systems, and may share the property of translocating special classes of peptides through the membrane.
Probab=36.23 E-value=30 Score=29.90 Aligned_cols=42 Identities=21% Similarity=0.156 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhhcc
Q psy12540 24 GPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVKLE 78 (79)
Q Consensus 24 ~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~q~ 78 (79)
..+..-|+++=|.|-+-++ =++-.+.++|+++++||.||+|.
T Consensus 470 svi~thl~e~i~~~a~ell-------------grqe~~~Lld~l~~~~p~Lv~El 511 (677)
T TIGR01399 470 QVITHRLKATLLRNAQEFI-------------GIQETRYLLDQMEREYPELVKEV 511 (677)
T ss_pred HHHHHHHHHHHHHHHHHHc-------------CHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555555555555443 13456889999999999999973
No 26
>PF14123 DUF4290: Domain of unknown function (DUF4290)
Probab=36.13 E-value=31 Score=25.26 Aligned_cols=30 Identities=30% Similarity=0.537 Sum_probs=23.9
Q ss_pred hhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhh
Q psy12540 42 VYPLTVASKSNSSSRRNAANKILQSMCDLSPLL 74 (79)
Q Consensus 42 vYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~L 74 (79)
=|-+|+.- ..+|++.|..|++-|..-+|.+
T Consensus 24 d~~~tieD---reeR~~~A~~II~iM~~l~P~l 53 (176)
T PF14123_consen 24 DYAVTIED---REERNRCAETIIEIMGNLNPHL 53 (176)
T ss_pred HHHHhCCC---HHHHHHHHHHHHHHHHhcCCcc
Confidence 35555543 3679999999999999999976
No 27
>PRK05910 type III secretion system protein; Validated
Probab=36.06 E-value=34 Score=29.19 Aligned_cols=20 Identities=0% Similarity=0.227 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHhhCHhhhhc
Q psy12540 58 NAANKILQSMCDLSPLLVKL 77 (79)
Q Consensus 58 ~aA~~Il~~mr~hsp~LV~q 77 (79)
+-.+.++|.+++.+|.||||
T Consensus 399 qevq~Lld~l~~~~p~lVee 418 (584)
T PRK05910 399 RFVKRLVEEFQEVAGISIEE 418 (584)
T ss_pred HHHHHHHHHHHHhChHHHHH
Confidence 34578999999999999998
No 28
>PF08713 DNA_alkylation: DNA alkylation repair enzyme; InterPro: IPR014825 These proteins are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein shows it to adopt a super coiled alpha helical structure. ; PDB: 3JY1_A 3JXY_A 3JX7_A 3JXZ_A 3BVS_A 2B6C_B 1T06_B 3L9T_A.
Probab=35.12 E-value=44 Score=22.78 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=26.8
Q ss_pred HhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhh
Q psy12540 14 KRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTV 47 (79)
Q Consensus 14 Ri~s~~~~vr~li~~LL~~IGk~HPQALvYPLtV 47 (79)
.+++++.-|+.-+--.|.++|+.+|+.+.==|.-
T Consensus 163 ~~~d~~~~vq~ai~w~L~~~~~~~~~~v~~~l~~ 196 (213)
T PF08713_consen 163 LLKDEEYYVQKAIGWALREIGKKDPDEVLEFLQK 196 (213)
T ss_dssp CTTGS-HHHHHHHHHHHHHHCTT-HHHHHHHHHH
T ss_pred HcCCchHHHHHHHHHHHHHHHHhCHHHHHHHHHH
Confidence 4688889999999999999999999987765554
No 29
>TIGR01398 FlhA flagellar biosynthesis protein FlhA. This model describes flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. A separate model describes InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc., all of which score below the noise cutoff for this model.
Probab=33.76 E-value=38 Score=29.29 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHhhCHhhhhcc
Q psy12540 57 RNAANKILQSMCDLSPLLVKLE 78 (79)
Q Consensus 57 ~~aA~~Il~~mr~hsp~LV~q~ 78 (79)
++-.+.++|++++++|.||+|.
T Consensus 490 rqevq~Lld~l~~~~p~lveel 511 (678)
T TIGR01398 490 RQEVQNLLDRLKEEYPKLVEEL 511 (678)
T ss_pred HHHHHHHHHHHHHHChHHHHHh
Confidence 3456889999999999999984
No 30
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=33.62 E-value=68 Score=15.94 Aligned_cols=25 Identities=12% Similarity=0.082 Sum_probs=17.8
Q ss_pred HHHhcCCCchhhHHHHHHHHHHhhh
Q psy12540 12 FLKRKRKSKLIGGPVQAYLSDIGKR 36 (79)
Q Consensus 12 iaRi~s~~~~vr~li~~LL~~IGk~ 36 (79)
+.-+..|++.||+....-|..+++.
T Consensus 6 ~~~l~D~~~~VR~~a~~~l~~i~~~ 30 (31)
T PF02985_consen 6 LQLLNDPSPEVRQAAAECLGAIAEH 30 (31)
T ss_dssp HHHHT-SSHHHHHHHHHHHHHHHHT
T ss_pred HHHcCCCCHHHHHHHHHHHHHHHhh
Confidence 4456678888888888888877753
No 31
>PRK12720 secretion system apparatus protein SsaV; Provisional
Probab=33.08 E-value=36 Score=29.46 Aligned_cols=22 Identities=18% Similarity=0.054 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHhhCHhhhhcc
Q psy12540 57 RNAANKILQSMCDLSPLLVKLE 78 (79)
Q Consensus 57 ~~aA~~Il~~mr~hsp~LV~q~ 78 (79)
++-.+.++|++++.+|.||+|.
T Consensus 486 ~qev~~Lld~l~~~~p~Lv~el 507 (675)
T PRK12720 486 VQETRYLMDAMEKRYGELVKEL 507 (675)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3456889999999999999973
No 32
>PRK12792 flhA flagellar biosynthesis protein FlhA; Reviewed
Probab=32.98 E-value=40 Score=29.26 Aligned_cols=21 Identities=10% Similarity=0.009 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHhhCHhhhhc
Q psy12540 57 RNAANKILQSMCDLSPLLVKL 77 (79)
Q Consensus 57 ~~aA~~Il~~mr~hsp~LV~q 77 (79)
++-.+.++|.+++.||+||+|
T Consensus 504 rqev~~Lld~l~~~~p~Lvee 524 (694)
T PRK12792 504 YKDMRALLDRLDPEYKRLIDD 524 (694)
T ss_pred HHHHHHHHHHHHHhChHHHHH
Confidence 345688999999999999998
No 33
>PRK15337 type III secretion system protein InvA; Provisional
Probab=32.70 E-value=41 Score=29.16 Aligned_cols=21 Identities=19% Similarity=0.229 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHhhCHhhhhc
Q psy12540 57 RNAANKILQSMCDLSPLLVKL 77 (79)
Q Consensus 57 ~~aA~~Il~~mr~hsp~LV~q 77 (79)
++-.+.++|++++.+|.||+|
T Consensus 500 ~qev~~Lld~l~~~~p~Lv~e 520 (686)
T PRK15337 500 IQETKHLLDQLEKKYPDLLKE 520 (686)
T ss_pred HHHHHHHHHHHHHHCHHHHHH
Confidence 345678999999999999997
No 34
>CHL00105 psaJ photosystem I subunit IX
Probab=32.63 E-value=39 Score=19.48 Aligned_cols=21 Identities=29% Similarity=0.581 Sum_probs=18.5
Q ss_pred HHHHHHHHHhhhCchhhhhhh
Q psy12540 25 PVQAYLSDIGKRHPQALVYPL 45 (79)
Q Consensus 25 li~~LL~~IGk~HPQALvYPL 45 (79)
....+|++|-+-+|-+|.+|+
T Consensus 21 ~tag~lIEiNRffPD~L~~p~ 41 (42)
T CHL00105 21 FLAGLLIEINRFFPDALTFPF 41 (42)
T ss_pred HHHHHHHHHHHhCChhhccCC
Confidence 456789999999999999996
No 35
>COG4335 DNA alkylation repair enzyme [DNA replication, recombination, and repair]
Probab=31.77 E-value=1.4e+02 Score=21.86 Aligned_cols=47 Identities=28% Similarity=0.273 Sum_probs=32.2
Q ss_pred CchhhHHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHh
Q psy12540 19 SKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCD 69 (79)
Q Consensus 19 ~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~ 69 (79)
+-.+|+.+.+-|-+|.|.||.-.+--..-=.|-....| -.|+..||+
T Consensus 95 ~lyvrksvan~lndi~k~hp~f~~~~~~aw~kt~~~~~----wiIkq~~R~ 141 (167)
T COG4335 95 ELYVRKSVANNLNDIKKVHPSFDVSAFDAWAKTSNHTR----WIIKQAMRT 141 (167)
T ss_pred HHHHHHHHHHHHHHhhhcChHHHHHHHHhhccccchHH----HHHHHHHHH
Confidence 45689999999999999999875544443345434433 456666664
No 36
>PF13170 DUF4003: Protein of unknown function (DUF4003)
Probab=31.72 E-value=79 Score=24.12 Aligned_cols=61 Identities=16% Similarity=0.209 Sum_probs=41.4
Q ss_pred CCCchhhHH--HHHHHHHHhhhCchhhhhh-hhhcc---cCCCHHHHHHHHHHHHHHHhhCHhhhhc
Q psy12540 17 RKSKLIGGP--VQAYLSDIGKRHPQALVYP-LTVAS---KSNSSSRRNAANKILQSMCDLSPLLVKL 77 (79)
Q Consensus 17 s~~~~vr~l--i~~LL~~IGk~HPQALvYP-LtVA~---KS~s~~R~~aA~~Il~~mr~hsp~LV~q 77 (79)
.|+..+.+. +++.|.+-|.....-+.-. +.++. +.+-..+-+-|..|.+.||+++|-|...
T Consensus 73 ~p~~~~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~ 139 (297)
T PF13170_consen 73 DPEEAFKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSP 139 (297)
T ss_pred CHHHHHHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCc
Confidence 345555554 5788999998888754333 22222 3344567777889999999999988753
No 37
>PF01603 B56: Protein phosphatase 2A regulatory B subunit (B56 family); InterPro: IPR002554 Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family [].; GO: 0008601 protein phosphatase type 2A regulator activity, 0007165 signal transduction, 0000159 protein phosphatase type 2A complex; PDB: 2NYM_B 2NYL_B 2IAE_E 2NPP_B 3FGA_B 2JAK_A.
Probab=28.98 E-value=83 Score=24.83 Aligned_cols=35 Identities=9% Similarity=-0.083 Sum_probs=29.5
Q ss_pred HHHHHHHHHhcCCCchhhHHHHHHHHHHhhhCchh
Q psy12540 6 LVALCAFLKRKRKSKLIGGPVQAYLSDIGKRHPQA 40 (79)
Q Consensus 6 ~~~~~~iaRi~s~~~~vr~li~~LL~~IGk~HPQA 40 (79)
-...+++.+++++|++=|+.+..+|.+|=..+|.-
T Consensus 133 ~fi~~Ll~l~~S~D~rER~~lk~~l~~iy~k~~~~ 167 (409)
T PF01603_consen 133 KFIKKLLELFDSPDPRERDYLKTILHRIYGKFPNL 167 (409)
T ss_dssp HHHHHHHHTTTSSTHHHHHHHHHHHHHHHHH-TTT
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhhh
Confidence 35678999999999999999999999987777653
No 38
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=27.43 E-value=83 Score=19.73 Aligned_cols=25 Identities=12% Similarity=0.155 Sum_probs=19.5
Q ss_pred CchhhHHHHHHHHHHhhhCchhhhh
Q psy12540 19 SKLIGGPVQAYLSDIGKRHPQALVY 43 (79)
Q Consensus 19 ~~~vr~li~~LL~~IGk~HPQALvY 43 (79)
+...|+.+.+++.-+|..||-+.=|
T Consensus 57 ~~~ar~~ll~~f~~lg~~~plv~~~ 81 (90)
T PF14561_consen 57 DDAARKRLLDIFELLGPGDPLVSEY 81 (90)
T ss_dssp CCHHHHHHHHHHHHH-TT-HHHHHH
T ss_pred ccHHHHHHHHHHHHcCCCChHHHHH
Confidence 5889999999999999999966443
No 39
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=26.86 E-value=50 Score=18.39 Aligned_cols=30 Identities=13% Similarity=0.201 Sum_probs=24.4
Q ss_pred hhHHHHHHHHHHHhcCCCchhhHHHHHHHH
Q psy12540 2 LFSALVALCAFLKRKRKSKLIGGPVQAYLS 31 (79)
Q Consensus 2 ~~~~~~~~~~iaRi~s~~~~vr~li~~LL~ 31 (79)
-|...|+.-|+-|+...=+...+.|.+|-.
T Consensus 7 GFPi~va~yLL~R~E~kld~L~~~i~~L~~ 36 (38)
T PF12841_consen 7 GFPIAVAIYLLVRIEKKLDELTESINELSE 36 (38)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 477889999999999987778777777644
No 40
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=26.60 E-value=60 Score=21.86 Aligned_cols=47 Identities=19% Similarity=0.084 Sum_probs=29.4
Q ss_pred ChhHHHHHHHHHHHhcCCC--chhhHHHHHHHHHHhhhCchhhhhhhhhcc
Q psy12540 1 MLFSALVALCAFLKRKRKS--KLIGGPVQAYLSDIGKRHPQALVYPLTVAS 49 (79)
Q Consensus 1 ~~~~~~~~~~~iaRi~s~~--~~vr~li~~LL~~IGk~HPQALvYPLtVA~ 49 (79)
|.|+.++ .++.++...+ ..-.+++.+++..+....+..-+||++=-.
T Consensus 1 m~F~~l~--~l~~~l~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l 49 (177)
T PF04675_consen 1 MPFSDLC--ELFEKLESTSSRLEKIAILSNFFRSWREEDLGPDLYLLLRLL 49 (177)
T ss_dssp GBHHHHH--HHHHHHHT---HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHS
T ss_pred CcHHHHH--HHHHHHHhccCHHHHHHHHHHHHHHcccchhhhHHHHHhccc
Confidence 6788887 5667777543 334556666666665554556789987644
No 41
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=26.52 E-value=1.5e+02 Score=20.27 Aligned_cols=59 Identities=12% Similarity=0.137 Sum_probs=38.7
Q ss_pred HHHHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhc---ccCCCH-HHHHH-HHHHHHHHH
Q psy12540 10 CAFLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVA---SKSNSS-SRRNA-ANKILQSMC 68 (79)
Q Consensus 10 ~~iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA---~KS~s~-~R~~a-A~~Il~~mr 68 (79)
.+.-.|++.....+..+.-|--+++...|+..+|.|++- .|.-.. -.++. ....++.|.
T Consensus 23 ~icD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evask~Fl~eL~ 86 (144)
T cd03568 23 DVCDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVASRDFTQELK 86 (144)
T ss_pred HHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHH
Confidence 334445555667888999999999999999999999874 444332 23333 344555553
No 42
>PRK09330 cell division protein FtsZ; Validated
Probab=26.51 E-value=49 Score=26.48 Aligned_cols=46 Identities=13% Similarity=0.156 Sum_probs=33.5
Q ss_pred HHHHHhhhCchhhhhhhhh-cccCCCHHHHHHHHHHHHHHHhhCHhhh
Q psy12540 29 YLSDIGKRHPQALVYPLTV-ASKSNSSSRRNAANKILQSMCDLSPLLV 75 (79)
Q Consensus 29 LL~~IGk~HPQALvYPLtV-A~KS~s~~R~~aA~~Il~~mr~hsp~LV 75 (79)
++.++.|+.| +++|.+-. ...++...|.+.|..=+++|+++...++
T Consensus 118 vIA~iake~g-~ltvaVvt~PF~fEG~~r~~nA~~gL~~L~~~~D~vI 164 (384)
T PRK09330 118 VVAEIAKELG-ILTVAVVTKPFSFEGKKRMKQAEEGIEELRKHVDTLI 164 (384)
T ss_pred HHHHHHHHcC-CcEEEEEecCccccchhHHHHHHHHHHHHHHHCCEEE
Confidence 4566777777 55555433 4567788899999999999999876543
No 43
>PF12765 Cohesin_HEAT: HEAT repeat associated with sister chromatid cohesion
Probab=26.48 E-value=63 Score=17.70 Aligned_cols=23 Identities=9% Similarity=0.003 Sum_probs=18.2
Q ss_pred HHHHHHHhcCCCchhhHHHHHHH
Q psy12540 8 ALCAFLKRKRKSKLIGGPVQAYL 30 (79)
Q Consensus 8 ~~~~iaRi~s~~~~vr~li~~LL 30 (79)
--.+..|+..+++.||+...++|
T Consensus 20 ~~~i~~rl~D~s~~VR~aav~ll 42 (42)
T PF12765_consen 20 QSAIIRRLSDSSPSVREAAVDLL 42 (42)
T ss_pred HHHHHHHhcCCChHHHHHHHHHC
Confidence 34567889999999999887764
No 44
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=25.34 E-value=1.8e+02 Score=19.35 Aligned_cols=61 Identities=11% Similarity=0.116 Sum_probs=33.4
Q ss_pred HHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhhcc
Q psy12540 12 FLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVKLE 78 (79)
Q Consensus 12 iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~q~ 78 (79)
+.+=.......++++..++.. ...|..+|=-.....-|+... -..+.+.+-..+|..|++.
T Consensus 52 ~~~~~Is~~~ak~ll~~~~~~--~~~~~~ii~~~~l~~i~d~~e----l~~~v~~vi~~n~~~v~~~ 112 (148)
T PF02637_consen 52 LEDGKISKKSAKELLRELLEN--GKSPEEIIEENGLWQISDEEE----LEALVEEVIAENPKEVEDY 112 (148)
T ss_dssp HHTTSSGHHHHHHHHHHHHHH--TS-HHHHHHHTT---B--CCH----HHHHHHHHHHC-HHHHHHH
T ss_pred HHcCCCCHHHHHHHHHHHHHc--CCCHHHHHHHcCCCcCCCHHH----HHHHHHHHHHHCHHHHHHH
Confidence 333333345556666666655 789999998887777776443 3344455555778888764
No 45
>PF08359 TetR_C_4: YsiA-like protein, C-terminal region; InterPro: IPR013570 The members of this family are thought to be TetR-type (tetracycline resistance) transcriptional regulators that bear particular similarity to YsiA (P94548 from SWISSPROT). This entry represents the C-terminal domain.; PDB: 1VI0_B.
Probab=24.36 E-value=1.5e+02 Score=18.69 Aligned_cols=65 Identities=14% Similarity=0.219 Sum_probs=36.0
Q ss_pred HHHHhcCCCchhhHHHHHHHHHHhhhCch-hhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhhcc
Q psy12540 11 AFLKRKRKSKLIGGPVQAYLSDIGKRHPQ-ALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVKLE 78 (79)
Q Consensus 11 ~iaRi~s~~~~vr~li~~LL~~IGk~HPQ-ALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~q~ 78 (79)
.++...+|.+.++.++..-+..+. .||. +.++- +-..+.+...++....+.++....=-.+++++
T Consensus 15 ~~~~~~~~~ekL~~~i~~~~~~~~-~~~~~~~v~~--~e~~~~~~~~~~~~~~~~~~~~~~i~~iI~eG 80 (133)
T PF08359_consen 15 AIADESSPEEKLRALIEAHLDFLE-ENPDLAIVLS--LELRQSNEELRKKINEIRREYLRIIEEIIEEG 80 (133)
T ss_dssp HHCC--SHHHHHHHHHHHHHHHHH-T-HHHHHHHH--CTTS-SSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHccCCCHHHHHHHHHHHHHHHHH-hCCChhhhhH--HHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556667778888888887776 4665 43332 23334445555666666666655555555543
No 46
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=24.26 E-value=89 Score=18.64 Aligned_cols=25 Identities=20% Similarity=0.403 Sum_probs=21.0
Q ss_pred cCCCchhhHHHHHHHHHHhhhCchhh
Q psy12540 16 KRKSKLIGGPVQAYLSDIGKRHPQAL 41 (79)
Q Consensus 16 ~s~~~~vr~li~~LL~~IGk~HPQAL 41 (79)
|+++..+++.+.+.|.+ |..||..+
T Consensus 39 hS~~g~Lk~~V~~~L~~-~~~~~~v~ 63 (83)
T PF01713_consen 39 HSKGGVLKRAVRRWLEE-GYQYEEVL 63 (83)
T ss_dssp TCCTSHHHHHHHHHHHH-THCCTTEE
T ss_pred CCCCCcHHHHHHHHHHh-hhccchhh
Confidence 56677799999999999 99998753
No 47
>PF14676 FANCI_S2: FANCI solenoid 2; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=23.40 E-value=70 Score=22.40 Aligned_cols=34 Identities=15% Similarity=0.123 Sum_probs=21.4
Q ss_pred HHHHHHhcCCCchhhHHHHHHHHHHhhhCchhhh
Q psy12540 9 LCAFLKRKRKSKLIGGPVQAYLSDIGKRHPQALV 42 (79)
Q Consensus 9 ~~~iaRi~s~~~~vr~li~~LL~~IGk~HPQALv 42 (79)
-+++-||-+.++....-..++|.++.+.+|+-+.
T Consensus 58 e~l~~rI~~~s~~~~~~~idlL~~lv~~~p~~vl 91 (158)
T PF14676_consen 58 EQLLNRIVTKSSSPSSQYIDLLSELVRKAPLTVL 91 (158)
T ss_dssp HHHHHHHHH--SS--HHHHHHHHHHHHH-HHHHS
T ss_pred HHHHHHHHhcCccchhHHHHHHHHHHHHChHHHH
Confidence 4566777776655445567999999998887765
No 48
>COG5240 SEC21 Vesicle coat complex COPI, gamma subunit [Intracellular trafficking and secretion]
Probab=23.13 E-value=65 Score=28.54 Aligned_cols=44 Identities=25% Similarity=0.228 Sum_probs=38.9
Q ss_pred HhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhh
Q psy12540 33 IGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVK 76 (79)
Q Consensus 33 IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~ 76 (79)
||-+.=|+.|-.|---.||....=|-+|.+|++.+.+.+|..|.
T Consensus 296 v~~~~~~~~vs~L~~fL~s~rv~~rFsA~Riln~lam~~P~kv~ 339 (898)
T COG5240 296 VGSQFVDQTVSSLRTFLKSTRVVLRFSAMRILNQLAMKYPQKVS 339 (898)
T ss_pred cCHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhCCceee
Confidence 56677778888888889999999999999999999999999874
No 49
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=23.06 E-value=52 Score=19.68 Aligned_cols=16 Identities=25% Similarity=0.536 Sum_probs=10.8
Q ss_pred HHHHHHHHHhhhCchh
Q psy12540 25 PVQAYLSDIGKRHPQA 40 (79)
Q Consensus 25 li~~LL~~IGk~HPQA 40 (79)
++..+|-.||..+|+.
T Consensus 23 lL~~lLqql~~~nP~l 38 (59)
T PF09280_consen 23 LLPPLLQQLGQSNPQL 38 (59)
T ss_dssp GHHHHHHHHHCCSHHH
T ss_pred HHHHHHHHHhccCHHH
Confidence 4566777777777764
No 50
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=22.87 E-value=2.6e+02 Score=19.15 Aligned_cols=63 Identities=16% Similarity=0.080 Sum_probs=39.5
Q ss_pred HHHHHHhcCCCchhhHHHHHHHHHHhhhCc--hhh-hhhhhhcccCCCH-HHHHHHHHHHHHHHhhC
Q psy12540 9 LCAFLKRKRKSKLIGGPVQAYLSDIGKRHP--QAL-VYPLTVASKSNSS-SRRNAANKILQSMCDLS 71 (79)
Q Consensus 9 ~~~iaRi~s~~~~vr~li~~LL~~IGk~HP--QAL-vYPLtVA~KS~s~-~R~~aA~~Il~~mr~hs 71 (79)
-.++-++..++..+++...+.|..+.+.-| .-+ +..+.-+.++.+. .|...++-+..-+..+.
T Consensus 97 ~~Ll~~~~~~~~~i~~~a~~~L~~i~~~~~~~~~~~~~~l~~~~~~Kn~~vR~~~~~~l~~~l~~~~ 163 (228)
T PF12348_consen 97 PPLLKKLGDSKKFIREAANNALDAIIESCSYSPKILLEILSQGLKSKNPQVREECAEWLAIILEKWG 163 (228)
T ss_dssp HHHHHGGG---HHHHHHHHHHHHHHHTTS-H--HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHTT--
T ss_pred HHHHHHHccccHHHHHHHHHHHHHHHHHCCcHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcc
Confidence 468889999999999999999999988776 334 6666767777776 45555555544444444
No 51
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=22.78 E-value=3.3e+02 Score=20.96 Aligned_cols=53 Identities=19% Similarity=0.121 Sum_probs=26.7
Q ss_pred cCCCchhhHHHHHHHHHHhhhCchhhhhhhh---hcccCCCHHHHHHHHHHHHHHH
Q psy12540 16 KRKSKLIGGPVQAYLSDIGKRHPQALVYPLT---VASKSNSSSRRNAANKILQSMC 68 (79)
Q Consensus 16 ~s~~~~vr~li~~LL~~IGk~HPQALvYPLt---VA~KS~s~~R~~aA~~Il~~mr 68 (79)
.+++...+++.+=.+..++...|+.++--.+ =-.+|+++..+-.|.+.+.+++
T Consensus 52 ~s~~~~~Krl~yl~l~~~~~~~~~~~~l~~n~l~kdl~~~n~~~~~lAL~~l~~i~ 107 (526)
T PF01602_consen 52 SSKDLELKRLGYLYLSLYLHEDPELLILIINSLQKDLNSPNPYIRGLALRTLSNIR 107 (526)
T ss_dssp SSSSHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHH-
T ss_pred CCCCHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhhcCCCHHHHHHHHhhhhhhc
Confidence 3555556666666666666666663322111 1234455555555555555554
No 52
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=22.56 E-value=87 Score=22.49 Aligned_cols=19 Identities=26% Similarity=0.305 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHhhCH
Q psy12540 54 SSRRNAANKILQSMCDLSP 72 (79)
Q Consensus 54 ~~R~~aA~~Il~~mr~hsp 72 (79)
-.||.+|.+|+..+|+|-.
T Consensus 20 RrRRAIaakIfaGLR~~Gn 38 (150)
T PF05687_consen 20 RRRRAIAAKIFAGLRAHGN 38 (150)
T ss_pred HHHHHHHHHHHHHHHHhcC
Confidence 3688899999999998743
No 53
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=22.50 E-value=3.4e+02 Score=21.89 Aligned_cols=63 Identities=17% Similarity=0.114 Sum_probs=44.2
Q ss_pred HHHhcCCCchhhHHHHHHHHHHhhhC-------chhhhhhhhh-cccCCCHHHHHHHHHHHHHHHhhCHhh
Q psy12540 12 FLKRKRKSKLIGGPVQAYLSDIGKRH-------PQALVYPLTV-ASKSNSSSRRNAANKILQSMCDLSPLL 74 (79)
Q Consensus 12 iaRi~s~~~~vr~li~~LL~~IGk~H-------PQALvYPLtV-A~KS~s~~R~~aA~~Il~~mr~hsp~L 74 (79)
..=+.+|++.||++....|.++.++. ...-+||+.+ +..+++..=.+.|..++.++..+.+.+
T Consensus 83 ~~gL~h~~~~Vr~l~l~~l~~~~~~~~~~~~~~~~~~l~~~i~~~L~~~d~~Va~~A~~~L~~l~~~~~~~ 153 (503)
T PF10508_consen 83 QRGLTHPSPKVRRLALKQLGRIARHSEGAAQLLVDNELLPLIIQCLRDPDLSVAKAAIKALKKLASHPEGL 153 (503)
T ss_pred HHHhcCCCHHHHHHHHHHHHHHhcCCHHHHHHhcCccHHHHHHHHHcCCcHHHHHHHHHHHHHHhCCchhH
Confidence 34467889999999888777765443 2344666654 455566667888889999998776654
No 54
>PF14664 RICTOR_N: Rapamycin-insensitive companion of mTOR, N-term
Probab=22.30 E-value=1.7e+02 Score=23.03 Aligned_cols=42 Identities=21% Similarity=0.269 Sum_probs=33.3
Q ss_pred hCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhhc
Q psy12540 36 RHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVKL 77 (79)
Q Consensus 36 ~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~q 77 (79)
.-|.+++..+.=..-++.+.-+.++-..+-.+.-.+|.||-.
T Consensus 104 ~~~~~vvralvaiae~~~D~lr~~cletL~El~l~~P~lv~~ 145 (371)
T PF14664_consen 104 EIPRGVVRALVAIAEHEDDRLRRICLETLCELALLNPELVAE 145 (371)
T ss_pred cCCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHhhCHHHHHH
Confidence 448888888865566677778888999999999999988854
No 55
>PF00273 Serum_albumin: Serum albumin family; InterPro: IPR014760 A number of serum transport proteins are known to be evolutionarily related, including albumin, alpha-fetoprotein, vitamin D-binding protein and afamin [, , ]. Albumin is the main protein of plasma; it binds water, cations (such as Ca2+, Na+ and K+), fatty acids, hormones, bilirubin and drugs - its main function is to regulate the colloidal osmotic pressure of blood. Alphafeto- protein (alpha-fetoglobulin) is a foetal plasma protein that binds various cations, fatty acids and bilirubin. Vitamin D-binding protein binds to vitamin D and its metabolites, as well as to fatty acids. The biological role of afamin (alpha-albumin) has not yet been characterised. The 3D structure of human serum albumin has been determined by X-ray crystallography to a resolution of 2.8A []. It comprises three homologous domains that assemble to form a heart-shaped molecule []. Each domain is a product of two subdomains that possess common structural motifs []. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and IIIA, which exhibit similar chemistry. Structurally, the serum albumins are similar, each domain containing five or six internal disulphide bonds, as shown schematically below: +---+ +----+ +-----+ | | | | | | xxCxxxxxxxxxxxxxxxxCCxxCxxxxCxxxxxCCxxxCxxxxxxxxxCxxxxxxxxxxxxxxCCxxxxCxxxx | | | | | | +-----------------+ +-----+ +---------------+ ; GO: 0005615 extracellular space; PDB: 3V09_A 3V03_B 3MRK_P 1MA9_A 1KW2_A 1KXP_D 1J7E_A 1J78_A 1LOT_A 2BXL_A ....
Probab=22.16 E-value=77 Score=22.12 Aligned_cols=19 Identities=26% Similarity=0.527 Sum_probs=15.9
Q ss_pred hhHHHHHHHHHHhhhCchh
Q psy12540 22 IGGPVQAYLSDIGKRHPQA 40 (79)
Q Consensus 22 vr~li~~LL~~IGk~HPQA 40 (79)
-...+..+|.+++|.||++
T Consensus 131 ~~~~~~~~lye~~RrhP~~ 149 (178)
T PF00273_consen 131 PQKFLQRFLYELSRRHPEL 149 (178)
T ss_dssp HHHHHHHHHHHHHHHSTTS
T ss_pred hHHHHHHHHHHHHHhCCCC
Confidence 3456788999999999995
No 56
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=22.00 E-value=1.4e+02 Score=17.37 Aligned_cols=60 Identities=15% Similarity=0.127 Sum_probs=45.7
Q ss_pred CCCchhhHHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhhhhcc
Q psy12540 17 RKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVKLE 78 (79)
Q Consensus 17 s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~LV~q~ 78 (79)
.+++.-.+.|.+++.+.|-. |--+.+.+--|.+. +...-+..++|+.+=+++.-.-++|+
T Consensus 12 ~ls~~e~~~i~~~~~~~~~~-~evI~~ai~~a~~~-~~~~~~Yi~~Il~~W~~~gi~T~e~~ 71 (73)
T TIGR01446 12 MLSPFEMEDLKYWLDEFGNS-PELIKEALKEAVSN-NKANYKYIDAILNNWKNNGIKTVEDV 71 (73)
T ss_pred CCCHHHHHHHHHHHHHhCCC-HHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCCCHHHH
Confidence 35667788899999888854 77788888877764 33346799999999998887777765
No 57
>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.
Probab=21.83 E-value=3.5e+02 Score=20.27 Aligned_cols=55 Identities=16% Similarity=0.233 Sum_probs=39.1
Q ss_pred hhHHHHHHHHHHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHh
Q psy12540 2 LFSALVALCAFLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCD 69 (79)
Q Consensus 2 ~~~~~~~~~~iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~ 69 (79)
|=||+-.+..|.+=.+......+.|++++.. -...|+.|+..- +-|..|++++-+
T Consensus 85 LESAl~v~~~I~~E~~~~~~lhe~i~~lik~----------~aV~VCm~~g~F---k~A~eiLkr~~~ 139 (200)
T cd00280 85 LESALMVLESIEKEFSLPETLHEEIRKLIKE----------QAVAVCMENGEF---KKAEEVLKRLFS 139 (200)
T ss_pred HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHH----------HHHHHHHhcCch---HHHHHHHHHHhc
Confidence 3477777777777777666677777776653 346788898744 678888888766
No 58
>COG1298 FlhA Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=21.83 E-value=79 Score=27.68 Aligned_cols=21 Identities=19% Similarity=0.325 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHhhCHhhhhcc
Q psy12540 58 NAANKILQSMCDLSPLLVKLE 78 (79)
Q Consensus 58 ~aA~~Il~~mr~hsp~LV~q~ 78 (79)
+-.++++|.++++||.|||+.
T Consensus 506 qevq~Lld~l~~~~p~lvEei 526 (696)
T COG1298 506 QEVQQLLDRLAEEYPKLVEEI 526 (696)
T ss_pred HHHHHHHHHHHHHhHHHHHHh
Confidence 345789999999999999974
No 59
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=21.27 E-value=2.2e+02 Score=18.67 Aligned_cols=50 Identities=16% Similarity=0.050 Sum_probs=32.7
Q ss_pred HHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhc---ccCCCH-HHHHHHH
Q psy12540 12 FLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVA---SKSNSS-SRRNAAN 61 (79)
Q Consensus 12 iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA---~KS~s~-~R~~aA~ 61 (79)
.-.|++.+...+..+.-|--++...+|+..++.|++- .|.-.. -+...|.
T Consensus 25 cd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s 78 (133)
T cd03561 25 CDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVAD 78 (133)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhh
Confidence 3344455666777888888888888888888888774 344322 4455554
No 60
>PF09961 DUF2195: Uncharacterized protein conserved in bacteria (DUF2195); InterPro: IPR018696 This family of various bacterial proteins has no known function.
Probab=21.08 E-value=1.2e+02 Score=21.01 Aligned_cols=36 Identities=19% Similarity=0.185 Sum_probs=31.1
Q ss_pred hhHHHHHHHHHHHhcCCCchhhHHHHHHHHHHhhhCchh
Q psy12540 2 LFSALVALCAFLKRKRKSKLIGGPVQAYLSDIGKRHPQA 40 (79)
Q Consensus 2 ~~~~~~~~~~iaRi~s~~~~vr~li~~LL~~IGk~HPQA 40 (79)
-||||+..+.....+ ..++..+++=+.++.+.-|-.
T Consensus 61 C~SAL~~Y~s~v~~~---~g~~~~LQ~G~i~~~~~~~rt 96 (121)
T PF09961_consen 61 CMSALANYTSSVEQD---NGVRQVLQEGLIDLAKSGGRT 96 (121)
T ss_pred hHHHHHHHHHHHHhh---hhHHHHHHHhhhhhhhcCCeE
Confidence 389999999998887 568999999999999988873
No 61
>PF12603 DUF3770: Protein of unknown function (DUF3770); InterPro: IPR022531 This family is found in viruses, and is approximately 250 amino acids in length. It is found N-terminal to PF04196 from PFAM in polyproteins.; GO: 0003968 RNA-directed RNA polymerase activity
Probab=20.51 E-value=90 Score=23.98 Aligned_cols=21 Identities=29% Similarity=0.319 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHhhCHhhhh
Q psy12540 56 RRNAANKILQSMCDLSPLLVK 76 (79)
Q Consensus 56 R~~aA~~Il~~mr~hsp~LV~ 76 (79)
|-..|..|++.|++.+|.|-.
T Consensus 11 RfRlA~~I~ee~k~~~pel~~ 31 (250)
T PF12603_consen 11 RFRLARAIMEEMKKYYPELSD 31 (250)
T ss_pred HHHHHHHHHHHHHHhcccccc
Confidence 788999999999999998743
No 62
>PF14046 NR_Repeat: Nuclear receptor repeat
Probab=20.20 E-value=27 Score=20.51 Aligned_cols=18 Identities=28% Similarity=0.807 Sum_probs=13.6
Q ss_pred hhhCch--hhhhhhhhcccC
Q psy12540 34 GKRHPQ--ALVYPLTVASKS 51 (79)
Q Consensus 34 Gk~HPQ--ALvYPLtVA~KS 51 (79)
|++||+ .++|.+....|-
T Consensus 3 GEdhprqgSIly~~~~SAkQ 22 (46)
T PF14046_consen 3 GEDHPRQGSILYSMLTSAKQ 22 (46)
T ss_pred CCCCCcccceeecCcccccc
Confidence 678888 688887776664
No 63
>PF05536 Neurochondrin: Neurochondrin
Probab=20.07 E-value=3.1e+02 Score=22.74 Aligned_cols=68 Identities=18% Similarity=0.179 Sum_probs=52.4
Q ss_pred HHHHHHHHHhcCCCchhhHHHHHHHHHHhhhCchhhhhhhhhcccCCCHHHHHHHHHHHHHHHhhCHhh
Q psy12540 6 LVALCAFLKRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLL 74 (79)
Q Consensus 6 ~~~~~~iaRi~s~~~~vr~li~~LL~~IGk~HPQALvYPLtVA~KS~s~~R~~aA~~Il~~mr~hsp~L 74 (79)
+|||-++.++-..++.-+..-..+...||-.++.-|+-+-.+....+...-+..|-.|+..... .|++
T Consensus 23 fagL~lvtk~~~~~~~~~~~~~~v~~aig~~Fl~RLL~t~~~~~~~~~~~~~~LavsvL~~f~~-~~~~ 90 (543)
T PF05536_consen 23 FAGLLLVTKLLDADDEDSQTRRRVFEAIGFKFLDRLLRTGSVPSDCPPEEYLSLAVSVLAAFCR-DPEL 90 (543)
T ss_pred HHHHHHHHHcCCCchhhHHHHHHHHHhcChhHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHcC-Chhh
Confidence 6788888888887665554444555899999999999887776666778899999999988776 4443
Done!