Query psy11901
Match_columns 100
No_of_seqs 101 out of 106
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 21:52:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11901hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3476|consensus 100.0 2.5E-58 5.4E-63 320.5 3.0 100 1-100 1-100 (100)
2 PF10235 Cript: Microtubule-as 100.0 1.5E-49 3.3E-54 273.6 3.8 88 11-100 1-90 (90)
3 PF10217 DUF2039: Uncharacteri 94.8 0.0037 8.1E-08 43.6 -1.6 35 54-88 55-90 (92)
4 COG5152 Uncharacterized conser 90.9 0.062 1.3E-06 43.2 -0.3 49 35-89 183-240 (259)
5 PF12773 DZR: Double zinc ribb 90.4 0.18 3.8E-06 29.8 1.5 33 57-90 1-40 (50)
6 KOG3241|consensus 89.6 0.03 6.6E-07 44.2 -2.9 46 46-92 60-106 (227)
7 PF13248 zf-ribbon_3: zinc-rib 79.2 0.87 1.9E-05 24.3 0.6 22 55-77 3-24 (26)
8 PRK14559 putative protein seri 78.2 1.2 2.6E-05 39.7 1.6 35 55-90 2-38 (645)
9 PF14634 zf-RING_5: zinc-RING 74.7 0.79 1.7E-05 26.6 -0.4 20 68-87 21-44 (44)
10 PF13240 zinc_ribbon_2: zinc-r 72.3 1.6 3.4E-05 23.1 0.4 20 56-76 1-20 (23)
11 TIGR00570 cdk7 CDK-activating 68.3 2.1 4.6E-05 35.4 0.6 36 56-91 5-55 (309)
12 PF13920 zf-C3HC4_3: Zinc fing 63.7 1.5 3.3E-05 25.8 -0.8 25 68-92 21-50 (50)
13 KOG1813|consensus 61.8 3.8 8.3E-05 34.2 0.9 36 56-91 243-287 (313)
14 PRK12496 hypothetical protein; 54.1 5.7 0.00012 29.4 0.7 22 69-90 127-154 (164)
15 KOG2272|consensus 51.4 9.3 0.0002 31.9 1.6 52 36-90 148-206 (332)
16 smart00504 Ubox Modified RING 50.5 6.3 0.00014 23.4 0.4 23 68-90 20-46 (63)
17 PF07191 zinc-ribbons_6: zinc- 48.0 4.2 9.1E-05 27.2 -0.8 36 56-91 3-42 (70)
18 PF14471 DUF4428: Domain of un 45.8 9.9 0.00022 23.4 0.7 16 81-96 1-16 (51)
19 TIGR00599 rad18 DNA repair pro 45.3 9.4 0.0002 32.5 0.7 36 55-90 27-71 (397)
20 PF10571 UPF0547: Uncharacteri 44.5 10 0.00022 20.6 0.6 22 56-78 2-23 (26)
21 PF03660 PHF5: PHF5-like prote 41.7 6.3 0.00014 28.4 -0.7 26 50-75 51-76 (106)
22 cd00162 RING RING-finger (Real 40.9 12 0.00025 19.8 0.4 21 68-88 19-44 (45)
23 PF01258 zf-dskA_traR: Prokary 40.0 12 0.00026 20.9 0.4 12 80-91 4-15 (36)
24 PF14446 Prok-RING_1: Prokaryo 39.9 13 0.00029 23.6 0.7 14 77-90 3-16 (54)
25 PF06906 DUF1272: Protein of u 39.2 13 0.00028 24.2 0.5 36 55-90 6-52 (57)
26 PF13894 zf-C2H2_4: C2H2-type 39.0 7.7 0.00017 18.4 -0.4 15 81-95 2-16 (24)
27 PRK11595 DNA utilization prote 37.9 17 0.00038 27.5 1.1 33 56-88 7-43 (227)
28 PF10764 Gin: Inhibitor of sig 37.8 21 0.00046 21.7 1.3 17 2-18 20-36 (46)
29 PF13923 zf-C3HC4_2: Zinc fing 37.1 5 0.00011 22.4 -1.5 10 68-77 18-27 (39)
30 cd04476 RPA1_DBD_C RPA1_DBD_C: 35.2 14 0.00031 26.3 0.3 22 54-75 34-57 (166)
31 KOG3799|consensus 34.6 18 0.00039 27.7 0.8 36 54-91 65-101 (169)
32 KOG0320|consensus 33.1 11 0.00024 29.5 -0.6 37 55-91 132-179 (187)
33 PLN03208 E3 ubiquitin-protein 33.0 15 0.00033 28.6 0.1 36 56-91 20-80 (193)
34 TIGR02420 dksA RNA polymerase- 29.3 23 0.00049 24.3 0.5 11 80-90 81-91 (110)
35 PF05715 zf-piccolo: Piccolo Z 28.8 23 0.0005 23.3 0.4 8 81-88 32-39 (61)
36 smart00746 TRASH metallochaper 26.8 30 0.00066 16.7 0.6 9 82-90 1-9 (39)
37 PRK00420 hypothetical protein; 26.2 30 0.00065 24.7 0.7 22 54-75 23-46 (112)
38 KOG4458|consensus 26.2 24 0.00052 23.9 0.2 33 44-83 4-36 (78)
39 KOG1734|consensus 25.8 23 0.00049 29.8 -0.0 15 79-93 224-238 (328)
40 PHA03096 p28-like protein; Pro 25.1 19 0.00042 29.2 -0.5 25 73-97 135-160 (284)
41 PF11532 HnRNP_M: Heterogeneou 24.4 29 0.00064 19.9 0.3 8 45-52 19-26 (30)
42 COG1996 RPC10 DNA-directed RNA 24.4 29 0.00063 21.7 0.3 28 56-90 8-35 (49)
43 PHA02929 N1R/p28-like protein; 23.9 34 0.00073 27.2 0.6 40 54-93 174-230 (238)
44 PF09706 Cas_CXXC_CXXC: CRISPR 23.8 41 0.00088 21.7 0.9 11 78-88 4-14 (69)
45 PF10367 Vps39_2: Vacuolar sor 23.6 39 0.00084 21.6 0.8 11 81-91 80-90 (109)
46 PF10621 FpoO: F420H2 dehydrog 23.4 36 0.00077 25.0 0.6 35 49-89 29-70 (119)
47 PF11571 Med27: Mediator compl 23.2 43 0.00093 22.3 1.0 20 2-21 56-76 (90)
48 TIGR03826 YvyF flagellar opero 23.0 36 0.00077 25.0 0.6 24 52-77 79-102 (137)
49 PHA02094 hypothetical protein 23.0 42 0.0009 22.9 0.9 11 13-23 65-75 (81)
50 PHA02565 49 recombination endo 22.8 38 0.00083 25.8 0.7 14 77-90 18-31 (157)
51 COG0266 Nei Formamidopyrimidin 22.0 42 0.00092 27.3 0.9 32 45-76 236-272 (273)
52 TIGR00375 conserved hypothetic 22.0 42 0.00091 28.3 0.9 38 46-90 230-269 (374)
53 PF10146 zf-C4H2: Zinc finger- 21.4 50 0.0011 26.0 1.1 21 54-75 194-214 (230)
54 PF10417 1-cysPrx_C: C-termina 20.9 59 0.0013 18.9 1.1 12 12-23 9-20 (40)
55 PF12874 zf-met: Zinc-finger o 20.5 26 0.00055 17.4 -0.5 14 82-95 3-16 (25)
56 PF02945 Endonuclease_7: Recom 20.4 37 0.00081 22.7 0.2 14 77-90 20-33 (81)
57 PRK06393 rpoE DNA-directed RNA 20.3 45 0.00098 21.9 0.6 22 54-88 5-26 (64)
No 1
>KOG3476|consensus
Probab=100.00 E-value=2.5e-58 Score=320.50 Aligned_cols=100 Identities=68% Similarity=1.234 Sum_probs=97.9
Q ss_pred CcchHHHhhhcCccCCCCCCCCCcccccCCCeeccccchhhhhhhhcCCCcccCccchhhhhhhccCCCccCcccccccc
Q psy11901 1 MVCSKCEKKLGKVITPDNWKSGSRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKG 80 (100)
Q Consensus 1 MVC~KCeKKL~kl~tPd~~k~gs~~~~~~g~rkv~eNKlLs~~k~r~~Py~~~~~~C~~CK~~v~q~g~~YCq~CAYkkG 80 (100)
|||++|||||++|++|||||+|+||++++|+|+|+|||.|.+.++||+||+..+.+|+|||+.|||+|+||||.|||+||
T Consensus 1 MVC~kCEkKLskvi~pd~wr~garn~~~sGgrkinenkaL~s~k~r~~p~gt~~~kC~iCk~~vHQ~GshYC~tCAY~Kg 80 (100)
T KOG3476|consen 1 MVCEKCEKKLSKVIGPDPWRDGARNTTESGGRKINENKALISKKKRATPYGTALAKCRICKQLVHQPGSHYCQTCAYKKG 80 (100)
T ss_pred CchhHHHHHhccccccCcccccccccCCCCCeecchhhhhhhhhhhcCccccccchhHHHHHHhcCCcchhHhHhhhhhh
Confidence 99999999999999999999999999999999999999888889999999999999999999999999999999999999
Q ss_pred cccccCcccccccccccccC
Q psy11901 81 ICAMCGKKLLDVKNYKQSAA 100 (100)
Q Consensus 81 iCamCGKki~dt~~ykqS~~ 100 (100)
|||||||+|+||++|+||++
T Consensus 81 iCAMCGKki~nTK~ykQsst 100 (100)
T KOG3476|consen 81 ICAMCGKKILNTKNYKQSST 100 (100)
T ss_pred HHHHhhhHhhccccccccCC
Confidence 99999999999999999986
No 2
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=100.00 E-value=1.5e-49 Score=273.60 Aligned_cols=88 Identities=66% Similarity=1.194 Sum_probs=84.0
Q ss_pred cCccCCCCCCCCC--cccccCCCeeccccchhhhhhhhcCCCcccCccchhhhhhhccCCCccCcccccccccccccCcc
Q psy11901 11 GKVITPDNWKSGS--RNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGICAMCGKK 88 (100)
Q Consensus 11 ~kl~tPd~~k~gs--~~~~~~g~rkv~eNKlLs~~k~r~~Py~~~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKk 88 (100)
++||||||||+|+ +++.++|+|+||||||||+. ++ |||++++++|+|||++|||+|+||||.|||++||||||||+
T Consensus 1 tklatPd~~k~~~~~~~~~~~g~r~i~eNKlLs~~-~~-nPy~~~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKk 78 (90)
T PF10235_consen 1 TKLATPDPWKKGAMYRNTAESGGRKIGENKLLSKK-KK-NPYAPYSSKCKICKTKVHQPGAKYCQTCAYKKGICAMCGKK 78 (90)
T ss_pred CccccCCccccCcccccccCCCCccccceeeeccc-cc-CcccccCccccccccccccCCCccChhhhcccCcccccCCe
Confidence 4799999999999 99999999999999999884 34 99999999999999999999999999999999999999999
Q ss_pred cccccccccccC
Q psy11901 89 LLDVKNYKQSAA 100 (100)
Q Consensus 89 i~dt~~ykqS~~ 100 (100)
|+||++|+||+|
T Consensus 79 i~dtk~ykqs~v 90 (90)
T PF10235_consen 79 ILDTKNYKQSSV 90 (90)
T ss_pred ecccccccccCC
Confidence 999999999987
No 3
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=94.79 E-value=0.0037 Score=43.60 Aligned_cols=35 Identities=34% Similarity=0.768 Sum_probs=31.0
Q ss_pred Cccchhhhh-hhccCCCccCcccccccccccccCcc
Q psy11901 54 FESCKICRQ-KVHQVGSHYCQACAYKKGICAMCGKK 88 (100)
Q Consensus 54 ~~~C~~CK~-~v~q~g~~YCq~CAYkkGiCamCGKk 88 (100)
..+|-.|.+ .|.+.=|..|+.||-..++||.||++
T Consensus 55 p~kC~~C~qktVk~AYh~iC~~Ca~~~~vCaKC~k~ 90 (92)
T PF10217_consen 55 PKKCNKCQQKTVKHAYHVICDPCAKELKVCAKCGKP 90 (92)
T ss_pred CccccccccchHHHHHHHHHHHHHHhhccCcccCCC
Confidence 579999997 66776788999999999999999986
No 4
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=90.87 E-value=0.062 Score=43.15 Aligned_cols=49 Identities=33% Similarity=0.876 Sum_probs=34.5
Q ss_pred cccchhhhhhhhcCCCcccCccchhhhhhh-----ccCCCccCcccc---cccc-cccccCccc
Q psy11901 35 GENKALTASKARFNPYTQKFESCKICRQKV-----HQVGSHYCQACA---YKKG-ICAMCGKKL 89 (100)
Q Consensus 35 ~eNKlLs~~k~r~~Py~~~~~~C~~CK~~v-----~q~g~~YCq~CA---YkkG-iCamCGKki 89 (100)
.|.++++-. .-.-|| .|.|||... ..-||++|..|| |++| .|-.||+..
T Consensus 183 Ee~~v~~~~-~e~IPF-----~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 183 EEAPVISGP-GEKIPF-----LCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred hhcccccCC-CCCCce-----eehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence 345555432 233466 899999743 344999999999 6676 799999864
No 5
>PF12773 DZR: Double zinc ribbon
Probab=90.37 E-value=0.18 Score=29.76 Aligned_cols=33 Identities=24% Similarity=0.673 Sum_probs=18.7
Q ss_pred chhhhhhhccCCCccCcccccccc-------cccccCcccc
Q psy11901 57 CKICRQKVHQVGSHYCQACAYKKG-------ICAMCGKKLL 90 (100)
Q Consensus 57 C~~CK~~v~q~g~~YCq~CAYkkG-------iCamCGKki~ 90 (100)
|..|.+.+.. ++.||..|-..-. +|.-||..+.
T Consensus 1 Cp~Cg~~~~~-~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 1 CPHCGTPNPD-DAKFCPHCGTPLPPPDQSKKICPNCGAENP 40 (50)
T ss_pred CCCcCCcCCc-cccCChhhcCChhhccCCCCCCcCCcCCCc
Confidence 4445555555 4566666655444 5666666654
No 6
>KOG3241|consensus
Probab=89.60 E-value=0.03 Score=44.20 Aligned_cols=46 Identities=28% Similarity=0.755 Sum_probs=37.4
Q ss_pred hcCCCcccCccchhhhh-hhccCCCccCcccccccccccccCcccccc
Q psy11901 46 RFNPYTQKFESCKICRQ-KVHQVGSHYCQACAYKKGICAMCGKKLLDV 92 (100)
Q Consensus 46 r~~Py~~~~~~C~~CK~-~v~q~g~~YCq~CAYkkGiCamCGKki~dt 92 (100)
.|-|.+. ..+|..|+. .|.|.-|..|..||-...+||-|+|.+.++
T Consensus 60 KYKpLt~-akkC~kC~~r~Vk~aYH~~Cr~CA~e~~vCAKC~ks~~~i 106 (227)
T KOG3241|consen 60 KYKPLTE-AKKCQKCTKRNVKQAYHKLCRGCAKEQKVCAKCCKSVDQI 106 (227)
T ss_pred cccccch-hHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHhccHHHh
Confidence 3555554 569999987 778888899999999999999999976543
No 7
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=79.20 E-value=0.87 Score=24.32 Aligned_cols=22 Identities=18% Similarity=0.694 Sum_probs=16.3
Q ss_pred ccchhhhhhhccCCCccCccccc
Q psy11901 55 ESCKICRQKVHQVGSHYCQACAY 77 (100)
Q Consensus 55 ~~C~~CK~~v~q~g~~YCq~CAY 77 (100)
..|..|...+.. ++.||..|-.
T Consensus 3 ~~Cp~Cg~~~~~-~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP-DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc-ccccChhhCC
Confidence 478889886554 7888887743
No 8
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=78.21 E-value=1.2 Score=39.67 Aligned_cols=35 Identities=23% Similarity=0.651 Sum_probs=27.6
Q ss_pred ccchhhhhhhccCCCccCccccccc--ccccccCcccc
Q psy11901 55 ESCKICRQKVHQVGSHYCQACAYKK--GICAMCGKKLL 90 (100)
Q Consensus 55 ~~C~~CK~~v~q~g~~YCq~CAYkk--GiCamCGKki~ 90 (100)
..|..|...+.. +++||+.|-.+- ..|+-||..+.
T Consensus 2 ~~Cp~Cg~~n~~-~akFC~~CG~~l~~~~Cp~CG~~~~ 38 (645)
T PRK14559 2 LICPQCQFENPN-NNRFCQKCGTSLTHKPCPQCGTEVP 38 (645)
T ss_pred CcCCCCCCcCCC-CCccccccCCCCCCCcCCCCCCCCC
Confidence 368889888866 889999998774 36888888765
No 9
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=74.65 E-value=0.79 Score=26.59 Aligned_cols=20 Identities=35% Similarity=0.936 Sum_probs=16.5
Q ss_pred CCccCcccccccc----cccccCc
Q psy11901 68 GSHYCQACAYKKG----ICAMCGK 87 (100)
Q Consensus 68 g~~YCq~CAYkkG----iCamCGK 87 (100)
||.+|+.|+.+.- .|..|++
T Consensus 21 gH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 21 GHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCHHHHHHHHhhcCCCCCCcCCCC
Confidence 7889999988776 8888875
No 10
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=72.29 E-value=1.6 Score=23.07 Aligned_cols=20 Identities=20% Similarity=0.866 Sum_probs=14.2
Q ss_pred cchhhhhhhccCCCccCcccc
Q psy11901 56 SCKICRQKVHQVGSHYCQACA 76 (100)
Q Consensus 56 ~C~~CK~~v~q~g~~YCq~CA 76 (100)
.|..|...+.. ++.+|+.|-
T Consensus 1 ~Cp~CG~~~~~-~~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIED-DAKFCPNCG 20 (23)
T ss_pred CCcccCCCCCC-cCcchhhhC
Confidence 37778888865 678776654
No 11
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=68.34 E-value=2.1 Score=35.39 Aligned_cols=36 Identities=28% Similarity=0.755 Sum_probs=25.3
Q ss_pred cchhhhhh----------hccCCCccCcccccc-----cccccccCccccc
Q psy11901 56 SCKICRQK----------VHQVGSHYCQACAYK-----KGICAMCGKKLLD 91 (100)
Q Consensus 56 ~C~~CK~~----------v~q~g~~YCq~CAYk-----kGiCamCGKki~d 91 (100)
.|.+|++. |+.=||.+|.+|.-. .+.|+.|++.+..
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 57777772 223489999999743 3489999987753
No 12
>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=63.73 E-value=1.5 Score=25.77 Aligned_cols=25 Identities=28% Similarity=0.813 Sum_probs=19.0
Q ss_pred CCc-cCccccccc----ccccccCcccccc
Q psy11901 68 GSH-YCQACAYKK----GICAMCGKKLLDV 92 (100)
Q Consensus 68 g~~-YCq~CAYkk----GiCamCGKki~dt 92 (100)
||. +|..|+..- ..|++|-..|.++
T Consensus 21 gH~~~C~~C~~~~~~~~~~CP~Cr~~i~~V 50 (50)
T PF13920_consen 21 GHLCFCEECAERLLKRKKKCPICRQPIESV 50 (50)
T ss_dssp CEEEEEHHHHHHHHHTTSBBTTTTBB-SEE
T ss_pred CChHHHHHHhHHhcccCCCCCcCChhhcCC
Confidence 566 788888766 8999999988754
No 13
>KOG1813|consensus
Probab=61.78 E-value=3.8 Score=34.20 Aligned_cols=36 Identities=33% Similarity=0.907 Sum_probs=29.2
Q ss_pred cchhhhhhh-----ccCCCccCcccc---ccc-ccccccCccccc
Q psy11901 56 SCKICRQKV-----HQVGSHYCQACA---YKK-GICAMCGKKLLD 91 (100)
Q Consensus 56 ~C~~CK~~v-----~q~g~~YCq~CA---Ykk-GiCamCGKki~d 91 (100)
.|.||+... ..-||++|-.|| |++ -.|-+|++++.-
T Consensus 243 ~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 243 KCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cccccccccccchhhcCCceeehhhhccccccCCcceeccccccc
Confidence 899999853 344899999999 677 589999998864
No 14
>PRK12496 hypothetical protein; Provisional
Probab=54.08 E-value=5.7 Score=29.42 Aligned_cols=22 Identities=27% Similarity=1.001 Sum_probs=16.7
Q ss_pred CccCcccc--c----ccccccccCcccc
Q psy11901 69 SHYCQACA--Y----KKGICAMCGKKLL 90 (100)
Q Consensus 69 ~~YCq~CA--Y----kkGiCamCGKki~ 90 (100)
.++|++|- | ....|.+||-++.
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCChhh
Confidence 35688887 5 4467999998774
No 15
>KOG2272|consensus
Probab=51.44 E-value=9.3 Score=31.90 Aligned_cols=52 Identities=31% Similarity=0.709 Sum_probs=38.5
Q ss_pred ccchhhhhhhhcCCCcccCccchhhhhhhcc-----CCCccCcccccccc--cccccCcccc
Q psy11901 36 ENKALTASKARFNPYTQKFESCKICRQKVHQ-----VGSHYCQACAYKKG--ICAMCGKKLL 90 (100)
Q Consensus 36 eNKlLs~~k~r~~Py~~~~~~C~~CK~~v~q-----~g~~YCq~CAYkkG--iCamCGKki~ 90 (100)
.|-+|.- |-|||-.|.-+|..|+.-+.. .|.-||..|--+-| ||.-|-+.|-
T Consensus 148 D~~~l~f---r~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 148 DEQPLTF---RGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE 206 (332)
T ss_pred ccccccc---cCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchH
Confidence 3477743 568888888899999987743 46789999987655 6766666664
No 16
>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=50.52 E-value=6.3 Score=23.35 Aligned_cols=23 Identities=22% Similarity=0.353 Sum_probs=17.5
Q ss_pred CCccCccccc----ccccccccCcccc
Q psy11901 68 GSHYCQACAY----KKGICAMCGKKLL 90 (100)
Q Consensus 68 g~~YCq~CAY----kkGiCamCGKki~ 90 (100)
|+.||..|.. ..+.|.+||..+.
T Consensus 20 G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 20 GQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred CCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 7778877764 3578999998873
No 17
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=47.99 E-value=4.2 Score=27.18 Aligned_cols=36 Identities=33% Similarity=0.778 Sum_probs=21.3
Q ss_pred cchhhhhhhccCC-CccCcccc---cccccccccCccccc
Q psy11901 56 SCKICRQKVHQVG-SHYCQACA---YKKGICAMCGKKLLD 91 (100)
Q Consensus 56 ~C~~CK~~v~q~g-~~YCq~CA---YkkGiCamCGKki~d 91 (100)
.|..|.+.+...+ ..+|..|. -+.+.|+-||..+--
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEV 42 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EE
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHH
Confidence 6888888885555 66777776 356788888887753
No 18
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=45.75 E-value=9.9 Score=23.39 Aligned_cols=16 Identities=50% Similarity=0.939 Sum_probs=11.3
Q ss_pred cccccCcccccccccc
Q psy11901 81 ICAMCGKKLLDVKNYK 96 (100)
Q Consensus 81 iCamCGKki~dt~~yk 96 (100)
+|++||++|--.+.++
T Consensus 1 ~C~iCg~kigl~~~~k 16 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFK 16 (51)
T ss_pred CCCcccccccccccee
Confidence 5899999886555433
No 19
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=45.31 E-value=9.4 Score=32.48 Aligned_cols=36 Identities=19% Similarity=0.606 Sum_probs=27.4
Q ss_pred ccchhhhhhhccC-----CCccCccccc----ccccccccCcccc
Q psy11901 55 ESCKICRQKVHQV-----GSHYCQACAY----KKGICAMCGKKLL 90 (100)
Q Consensus 55 ~~C~~CK~~v~q~-----g~~YCq~CAY----kkGiCamCGKki~ 90 (100)
-.|.||...+..+ ||.||..|.. ..+.|.+|...+.
T Consensus 27 l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 27 LRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred cCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 3788887655433 9999999986 3468999998765
No 20
>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=44.50 E-value=10 Score=20.58 Aligned_cols=22 Identities=27% Similarity=0.957 Sum_probs=16.4
Q ss_pred cchhhhhhhccCCCccCcccccc
Q psy11901 56 SCKICRQKVHQVGSHYCQACAYK 78 (100)
Q Consensus 56 ~C~~CK~~v~q~g~~YCq~CAYk 78 (100)
.|..|.+.|.. .++.|..|-|.
T Consensus 2 ~CP~C~~~V~~-~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPE-SAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchh-hcCcCCCCCCC
Confidence 58888888876 57777777653
No 21
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=41.66 E-value=6.3 Score=28.38 Aligned_cols=26 Identities=23% Similarity=0.551 Sum_probs=14.3
Q ss_pred CcccCccchhhhhhhccCCCccCccc
Q psy11901 50 YTQKFESCKICRQKVHQVGSHYCQAC 75 (100)
Q Consensus 50 y~~~~~~C~~CK~~v~q~g~~YCq~C 75 (100)
|+.+..+|.||........+.||..|
T Consensus 51 ~G~~~~rCIiCg~~~g~sdAYYC~eC 76 (106)
T PF03660_consen 51 FGSLQGRCIICGSGPGVSDAYYCWEC 76 (106)
T ss_dssp TSSTTSB-TTTSSSB--EE-EE-HHH
T ss_pred CCCcCceEEEecCCCCcccceehhhh
Confidence 33445789999854433468899888
No 22
>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=40.91 E-value=12 Score=19.76 Aligned_cols=21 Identities=29% Similarity=0.920 Sum_probs=13.9
Q ss_pred CCccCccccc-----ccccccccCcc
Q psy11901 68 GSHYCQACAY-----KKGICAMCGKK 88 (100)
Q Consensus 68 g~~YCq~CAY-----kkGiCamCGKk 88 (100)
||.||..|.. ....|.+|...
T Consensus 19 ~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 19 GHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 6677777763 24568888764
No 23
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=39.96 E-value=12 Score=20.95 Aligned_cols=12 Identities=42% Similarity=1.137 Sum_probs=9.1
Q ss_pred ccccccCccccc
Q psy11901 80 GICAMCGKKLLD 91 (100)
Q Consensus 80 GiCamCGKki~d 91 (100)
|+|..||..|.+
T Consensus 4 g~C~~CGe~I~~ 15 (36)
T PF01258_consen 4 GICEDCGEPIPE 15 (36)
T ss_dssp SB-TTTSSBEEH
T ss_pred CCccccCChHHH
Confidence 679999998874
No 24
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=39.87 E-value=13 Score=23.64 Aligned_cols=14 Identities=43% Similarity=0.990 Sum_probs=10.7
Q ss_pred cccccccccCcccc
Q psy11901 77 YKKGICAMCGKKLL 90 (100)
Q Consensus 77 YkkGiCamCGKki~ 90 (100)
|...+|..||+++.
T Consensus 3 ~~~~~C~~Cg~~~~ 16 (54)
T PF14446_consen 3 YEGCKCPVCGKKFK 16 (54)
T ss_pred ccCccChhhCCccc
Confidence 56678888888885
No 25
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=39.20 E-value=13 Score=24.17 Aligned_cols=36 Identities=28% Similarity=0.854 Sum_probs=25.9
Q ss_pred ccchhhhhhhccCC---------CccCccccccc--ccccccCcccc
Q psy11901 55 ESCKICRQKVHQVG---------SHYCQACAYKK--GICAMCGKKLL 90 (100)
Q Consensus 55 ~~C~~CK~~v~q~g---------~~YCq~CAYkk--GiCamCGKki~ 90 (100)
..|..|.+.+.++. -.||..||-.. ++|.-||=-+.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCccc
Confidence 36777877777643 25788888665 99999996543
No 26
>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=39.03 E-value=7.7 Score=18.37 Aligned_cols=15 Identities=27% Similarity=0.742 Sum_probs=8.3
Q ss_pred cccccCccccccccc
Q psy11901 81 ICAMCGKKLLDVKNY 95 (100)
Q Consensus 81 iCamCGKki~dt~~y 95 (100)
.|.+||+...+-..+
T Consensus 2 ~C~~C~~~~~~~~~l 16 (24)
T PF13894_consen 2 QCPICGKSFRSKSEL 16 (24)
T ss_dssp E-SSTS-EESSHHHH
T ss_pred CCcCCCCcCCcHHHH
Confidence 477888877655444
No 27
>PRK11595 DNA utilization protein GntX; Provisional
Probab=37.94 E-value=17 Score=27.49 Aligned_cols=33 Identities=27% Similarity=0.650 Sum_probs=14.4
Q ss_pred cchhhhhhhccCCCccCcccccc----cccccccCcc
Q psy11901 56 SCKICRQKVHQVGSHYCQACAYK----KGICAMCGKK 88 (100)
Q Consensus 56 ~C~~CK~~v~q~g~~YCq~CAYk----kGiCamCGKk 88 (100)
.|-.|...++......|..|.-. ...|..||+.
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~~~~C~~Cg~~ 43 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTLKTCCPQCGLP 43 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcccCcCccCCCc
Confidence 45555554433222345555311 2345555554
No 28
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=37.83 E-value=21 Score=21.68 Aligned_cols=17 Identities=41% Similarity=0.784 Sum_probs=14.4
Q ss_pred cchHHHhhhcCccCCCC
Q psy11901 2 VCSKCEKKLGKVITPDN 18 (100)
Q Consensus 2 VC~KCeKKL~kl~tPd~ 18 (100)
.|..||++|-.+-+-||
T Consensus 20 IC~~CE~~iv~~~~~d~ 36 (46)
T PF10764_consen 20 ICSDCEKEIVNTETDDP 36 (46)
T ss_pred ehHHHHHHhccCCCCCC
Confidence 59999999998877776
No 29
>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=37.15 E-value=5 Score=22.41 Aligned_cols=10 Identities=30% Similarity=1.075 Sum_probs=6.4
Q ss_pred CCccCccccc
Q psy11901 68 GSHYCQACAY 77 (100)
Q Consensus 68 g~~YCq~CAY 77 (100)
||.||..|+.
T Consensus 18 GH~fC~~C~~ 27 (39)
T PF13923_consen 18 GHSFCKECIE 27 (39)
T ss_dssp SEEEEHHHHH
T ss_pred CCchhHHHHH
Confidence 6666766654
No 30
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=35.17 E-value=14 Score=26.28 Aligned_cols=22 Identities=32% Similarity=0.881 Sum_probs=15.3
Q ss_pred CccchhhhhhhccCC--CccCccc
Q psy11901 54 FESCKICRQKVHQVG--SHYCQAC 75 (100)
Q Consensus 54 ~~~C~~CK~~v~q~g--~~YCq~C 75 (100)
-..|..|+.+|.+.+ .-+|..|
T Consensus 34 Y~aC~~C~kkv~~~~~~~~~C~~C 57 (166)
T cd04476 34 YPACPGCNKKVVEEGNGTYRCEKC 57 (166)
T ss_pred EccccccCcccEeCCCCcEECCCC
Confidence 359999999998753 3444443
No 31
>KOG3799|consensus
Probab=34.63 E-value=18 Score=27.69 Aligned_cols=36 Identities=31% Similarity=0.725 Sum_probs=24.3
Q ss_pred Cccchhhhh-hhccCCCccCcccccccccccccCccccc
Q psy11901 54 FESCKICRQ-KVHQVGSHYCQACAYKKGICAMCGKKLLD 91 (100)
Q Consensus 54 ~~~C~~CK~-~v~q~g~~YCq~CAYkkGiCamCGKki~d 91 (100)
-..|-||-. +...--+|-|..|-.+ .||.||=++.-
T Consensus 65 datC~IC~KTKFADG~GH~C~YCq~r--~CARCGGrv~l 101 (169)
T KOG3799|consen 65 DATCGICHKTKFADGCGHNCSYCQTR--FCARCGGRVSL 101 (169)
T ss_pred CcchhhhhhcccccccCcccchhhhh--HHHhcCCeeee
Confidence 468999954 5544334666666544 79999977653
No 32
>KOG0320|consensus
Probab=33.14 E-value=11 Score=29.46 Aligned_cols=37 Identities=32% Similarity=0.818 Sum_probs=27.4
Q ss_pred ccchhhhhhhcc-------CCCccCcccc---cc-cccccccCccccc
Q psy11901 55 ESCKICRQKVHQ-------VGSHYCQACA---YK-KGICAMCGKKLLD 91 (100)
Q Consensus 55 ~~C~~CK~~v~q-------~g~~YCq~CA---Yk-kGiCamCGKki~d 91 (100)
-+|.||--.+.+ =||-||..|+ .+ -..|..|+|+|..
T Consensus 132 ~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred cCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 589999655432 3789999997 33 3489999998863
No 33
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=33.04 E-value=15 Score=28.58 Aligned_cols=36 Identities=28% Similarity=0.799 Sum_probs=27.1
Q ss_pred cchhhhhhhcc-----CCCccCcccccc--------------------cccccccCccccc
Q psy11901 56 SCKICRQKVHQ-----VGSHYCQACAYK--------------------KGICAMCGKKLLD 91 (100)
Q Consensus 56 ~C~~CK~~v~q-----~g~~YCq~CAYk--------------------kGiCamCGKki~d 91 (100)
.|.||...+.. =||.||..|.++ ...|.+|...|..
T Consensus 20 ~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 20 DCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 78888664432 389999999963 2479999998864
No 34
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=29.27 E-value=23 Score=24.29 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=9.0
Q ss_pred ccccccCcccc
Q psy11901 80 GICAMCGKKLL 90 (100)
Q Consensus 80 GiCamCGKki~ 90 (100)
|+|-.||..|-
T Consensus 81 G~C~~Cge~I~ 91 (110)
T TIGR02420 81 GYCEECGEEIG 91 (110)
T ss_pred CchhccCCccc
Confidence 68999998874
No 35
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=28.76 E-value=23 Score=23.30 Aligned_cols=8 Identities=38% Similarity=1.360 Sum_probs=5.0
Q ss_pred cccccCcc
Q psy11901 81 ICAMCGKK 88 (100)
Q Consensus 81 iCamCGKk 88 (100)
+|.+||-.
T Consensus 32 VCnlCGFN 39 (61)
T PF05715_consen 32 VCNLCGFN 39 (61)
T ss_pred hhcccCCC
Confidence 56677743
No 36
>smart00746 TRASH metallochaperone-like domain.
Probab=26.79 E-value=30 Score=16.68 Aligned_cols=9 Identities=44% Similarity=1.435 Sum_probs=7.6
Q ss_pred ccccCcccc
Q psy11901 82 CAMCGKKLL 90 (100)
Q Consensus 82 CamCGKki~ 90 (100)
|+.||..|.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 788999886
No 37
>PRK00420 hypothetical protein; Validated
Probab=26.22 E-value=30 Score=24.73 Aligned_cols=22 Identities=18% Similarity=0.528 Sum_probs=15.6
Q ss_pred Cccchhhhhhhcc--CCCccCccc
Q psy11901 54 FESCKICRQKVHQ--VGSHYCQAC 75 (100)
Q Consensus 54 ~~~C~~CK~~v~q--~g~~YCq~C 75 (100)
...|..|...+-. .|..||+.|
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~C 46 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVH 46 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCC
Confidence 4689999997753 466666654
No 38
>KOG4458|consensus
Probab=26.16 E-value=24 Score=23.94 Aligned_cols=33 Identities=30% Similarity=0.634 Sum_probs=21.8
Q ss_pred hhhcCCCcccCccchhhhhhhccCCCccCccccccccccc
Q psy11901 44 KARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGICA 83 (100)
Q Consensus 44 k~r~~Py~~~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCa 83 (100)
|.+++||.-...-=-.|+-.+|... ||+.|||-
T Consensus 4 k~k~~pydii~dd~~d~riplhne~-------a~qhgi~f 36 (78)
T KOG4458|consen 4 KKKHGPYDIIADDGHDCRIPLHNED-------AFQHGICF 36 (78)
T ss_pred ccccCCcceeecccccceeeccchh-------hhhccceE
Confidence 3567888732222335666888755 99999984
No 39
>KOG1734|consensus
Probab=25.83 E-value=23 Score=29.79 Aligned_cols=15 Identities=27% Similarity=0.751 Sum_probs=12.2
Q ss_pred cccccccCccccccc
Q psy11901 79 KGICAMCGKKLLDVK 93 (100)
Q Consensus 79 kGiCamCGKki~dt~ 93 (100)
.++||.||++|.++-
T Consensus 224 d~vCaVCg~~~~~s~ 238 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSV 238 (328)
T ss_pred cchhHhhcchheeec
Confidence 459999999998653
No 40
>PHA03096 p28-like protein; Provisional
Probab=25.06 E-value=19 Score=29.20 Aligned_cols=25 Identities=44% Similarity=0.897 Sum_probs=19.4
Q ss_pred cccccccc-cccccCccccccccccc
Q psy11901 73 QACAYKKG-ICAMCGKKLLDVKNYKQ 97 (100)
Q Consensus 73 q~CAYkkG-iCamCGKki~dt~~ykq 97 (100)
..|.|-.| +|.|||+..++...+.|
T Consensus 135 ~~c~~lHg~lC~~C~k~~Lhp~d~eq 160 (284)
T PHA03096 135 KYCEYLHGDICDICEKYLLHPTDIKQ 160 (284)
T ss_pred cCcHHHHHHHHHhhcchhcCCcCHHH
Confidence 45667666 69999999998877655
No 41
>PF11532 HnRNP_M: Heterogeneous nuclear ribonucleoprotein M; InterPro: IPR024666 Heterogeneous nuclear ribonucleoproteins (hnRNPs) bind directly to nascent RNA polymerase II transcripts and play an important role in both transcript-specific packaging and alternative splicing of pre-mRNAs []. hnRNP M proteins are an abundant group of hnRNPs that have been shown to bind avidly to poly(G) and poly(U) RNA homopolymers []. hnRNP M family members are able to induce exon skipping and promote exon inclusion, suggesting that the proteins may broadly contribute to the fidelity of splice site recognition and alternative splicing regulation []. This entry represents the N-terminal PY nuclear localisation signal of heterogeneous nuclear ribonucleoprotein M [].; PDB: 2OT8_C.
Probab=24.40 E-value=29 Score=19.91 Aligned_cols=8 Identities=50% Similarity=1.207 Sum_probs=2.0
Q ss_pred hhcCCCcc
Q psy11901 45 ARFNPYTQ 52 (100)
Q Consensus 45 ~r~~Py~~ 52 (100)
+||.||++
T Consensus 19 ~rfEPY~N 26 (30)
T PF11532_consen 19 NRFEPYAN 26 (30)
T ss_dssp ----SS--
T ss_pred cccccccC
Confidence 79999985
No 42
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=24.36 E-value=29 Score=21.69 Aligned_cols=28 Identities=25% Similarity=0.624 Sum_probs=17.4
Q ss_pred cchhhhhhhccCCCccCcccccccccccccCcccc
Q psy11901 56 SCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLL 90 (100)
Q Consensus 56 ~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKki~ 90 (100)
+|..|...+.... ++.--.|.-||-+|+
T Consensus 8 ~C~~Cg~~~~~~~-------~~~~irCp~Cg~rIl 35 (49)
T COG1996 8 KCARCGREVELDQ-------ETRGIRCPYCGSRIL 35 (49)
T ss_pred EhhhcCCeeehhh-------ccCceeCCCCCcEEE
Confidence 6888888776433 444455666666655
No 43
>PHA02929 N1R/p28-like protein; Provisional
Probab=23.85 E-value=34 Score=27.22 Aligned_cols=40 Identities=28% Similarity=0.697 Sum_probs=29.8
Q ss_pred Cccchhhhhhhc-------------cCCCccCccccc----ccccccccCccccccc
Q psy11901 54 FESCKICRQKVH-------------QVGSHYCQACAY----KKGICAMCGKKLLDVK 93 (100)
Q Consensus 54 ~~~C~~CK~~v~-------------q~g~~YCq~CAY----kkGiCamCGKki~dt~ 93 (100)
...|.||-..+. .=+|.||..|-- .+..|+||-..+.-+.
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~v~ 230 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFISVI 230 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeEEe
Confidence 368999987643 237889999972 5678999998877543
No 44
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=23.78 E-value=41 Score=21.68 Aligned_cols=11 Identities=45% Similarity=1.026 Sum_probs=8.3
Q ss_pred ccccccccCcc
Q psy11901 78 KKGICAMCGKK 88 (100)
Q Consensus 78 kkGiCamCGKk 88 (100)
.+++|..||..
T Consensus 4 ~~~~C~~Cg~r 14 (69)
T PF09706_consen 4 KKYNCIFCGER 14 (69)
T ss_pred CCCcCcCCCCc
Confidence 46789999944
No 45
>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=23.57 E-value=39 Score=21.62 Aligned_cols=11 Identities=45% Similarity=1.047 Sum_probs=7.8
Q ss_pred cccccCccccc
Q psy11901 81 ICAMCGKKLLD 91 (100)
Q Consensus 81 iCamCGKki~d 91 (100)
.|+.||++|.+
T Consensus 80 ~C~vC~k~l~~ 90 (109)
T PF10367_consen 80 KCSVCGKPLGN 90 (109)
T ss_pred CccCcCCcCCC
Confidence 57777777765
No 46
>PF10621 FpoO: F420H2 dehydrogenase subunit FpoO ; InterPro: IPR018288 This entry represents the FpoO subunit of membrane-bound multi-subunit F420H2 dehydrogenase, which oxidises the reduced coenzyme F420H2 to coenzyme F420 and feeds the electrons via an FeS cluster into an energy-conserving electron transport chain [, ]. This enzyme plays a role in the methanogenic pathway in methanogenic archaea. Reduced coenzyme F420H2 is the major cytoplasmic electron carrier of methanogens and a reversible hydride donor, much like NADH []. F420H2 + COB-S-S-CoM = F420 + CoM-SH + CoB-SH Where CoB-S-S-CoM (the heterosulphide of 2-mercaptoethanesulphonate and 7-mercaptoheptanoylthreonine phosphate) is the terminal electron acceptor of the methanogenic pathway, and is reduced with the concomitant generation of a transmembrane proton potential and ATP synthesis. The FpoO subunit of F420H2 dehydrogenase probably participates in the reduction of methanophenazine, where it acts as a special mechanism for the reduction of the methanogenic cofactor [].
Probab=23.35 E-value=36 Score=24.99 Aligned_cols=35 Identities=29% Similarity=0.612 Sum_probs=22.4
Q ss_pred CCcccCccchhhhhh-------hccCCCccCcccccccccccccCccc
Q psy11901 49 PYTQKFESCKICRQK-------VHQVGSHYCQACAYKKGICAMCGKKL 89 (100)
Q Consensus 49 Py~~~~~~C~~CK~~-------v~q~g~~YCq~CAYkkGiCamCGKki 89 (100)
|-|.+..-|.+|-.. +.++ .. +-..|.|.|||++-
T Consensus 29 PeGvwKGLC~~CL~sa~~ty~e~~~~-~~-----s~~~gKC~LCG~kt 70 (119)
T PF10621_consen 29 PEGVWKGLCETCLDSAEKTYQEVNEN-ES-----SCRSGKCDLCGKKT 70 (119)
T ss_pred cchHHHhhHHHHHHHHHHHHHHHhcc-cc-----cccccceeccCCcc
Confidence 666666677777532 3332 22 22789999999874
No 47
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=23.20 E-value=43 Score=22.32 Aligned_cols=20 Identities=35% Similarity=0.640 Sum_probs=16.9
Q ss_pred cchHHHhhhc-CccCCCCCCC
Q psy11901 2 VCSKCEKKLG-KVITPDNWKS 21 (100)
Q Consensus 2 VC~KCeKKL~-kl~tPd~~k~ 21 (100)
+|.+|.|-|+ ..--|-+||+
T Consensus 56 pC~~C~klL~~~~~LPP~~r~ 76 (90)
T PF11571_consen 56 PCKKCGKLLSSKAFLPPVRRP 76 (90)
T ss_pred hhhHHHhHhhhcccCCCeeec
Confidence 6999999996 5788889984
No 48
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=22.99 E-value=36 Score=25.00 Aligned_cols=24 Identities=25% Similarity=0.667 Sum_probs=20.0
Q ss_pred ccCccchhhhhhhccCCCccCccccc
Q psy11901 52 QKFESCKICRQKVHQVGSHYCQACAY 77 (100)
Q Consensus 52 ~~~~~C~~CK~~v~q~g~~YCq~CAY 77 (100)
+..-.|..|.+.+.. | .||..|+-
T Consensus 79 nl~~~CE~CG~~I~~-G-r~C~~C~~ 102 (137)
T TIGR03826 79 NLGYPCERCGTSIRE-G-RLCDSCAG 102 (137)
T ss_pred CCcCcccccCCcCCC-C-CccHHHHH
Confidence 345699999999997 5 99999973
No 49
>PHA02094 hypothetical protein
Probab=22.96 E-value=42 Score=22.94 Aligned_cols=11 Identities=27% Similarity=0.727 Sum_probs=9.8
Q ss_pred ccCCCCCCCCC
Q psy11901 13 VITPDNWKSGS 23 (100)
Q Consensus 13 l~tPd~~k~gs 23 (100)
||-|+|||||-
T Consensus 65 vakpnpfrdgv 75 (81)
T PHA02094 65 VAKPNPFRDGV 75 (81)
T ss_pred ccCCCCCccce
Confidence 88999999974
No 50
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=22.84 E-value=38 Score=25.79 Aligned_cols=14 Identities=36% Similarity=0.942 Sum_probs=11.1
Q ss_pred cccccccccCcccc
Q psy11901 77 YKKGICAMCGKKLL 90 (100)
Q Consensus 77 YkkGiCamCGKki~ 90 (100)
-+.|.||+||..+.
T Consensus 18 ~Q~G~CaiC~~~l~ 31 (157)
T PHA02565 18 AQNGICPLCKRELD 31 (157)
T ss_pred HhCCcCCCCCCccC
Confidence 35679999999865
No 51
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=21.99 E-value=42 Score=27.32 Aligned_cols=32 Identities=22% Similarity=0.630 Sum_probs=24.4
Q ss_pred hhcCCCcccCccchhhhhhh-----ccCCCccCcccc
Q psy11901 45 ARFNPYTQKFESCKICRQKV-----HQVGSHYCQACA 76 (100)
Q Consensus 45 ~r~~Py~~~~~~C~~CK~~v-----~q~g~~YCq~CA 76 (100)
.++.-|+.....|+.|.+.+ .+-+.+||..|-
T Consensus 236 ~~l~VYgR~GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 236 QELKVYGRAGEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred eeEEEecCCCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 45667777788999997754 566889999983
No 52
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=21.98 E-value=42 Score=28.30 Aligned_cols=38 Identities=16% Similarity=0.447 Sum_probs=23.0
Q ss_pred hcCCCc-cc-CccchhhhhhhccCCCccCcccccccccccccCcccc
Q psy11901 46 RFNPYT-QK-FESCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLL 90 (100)
Q Consensus 46 r~~Py~-~~-~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKki~ 90 (100)
-|+|-- .| ...|+.|...+....+ =++ .++|+ ||+.|.
T Consensus 230 g~~P~~GKYh~~~c~~C~~~~~~~~~-----~~~-~~~Cp-CG~~i~ 269 (374)
T TIGR00375 230 GLDPLLGKYHQTACEACGEPAVSEDA-----ETA-CANCP-CGGRIK 269 (374)
T ss_pred eECcCCCccchhhhcccCCcCCchhh-----hhc-CCCCC-CCCcce
Confidence 366644 22 5678888776653211 022 58999 999964
No 53
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=21.43 E-value=50 Score=26.02 Aligned_cols=21 Identities=29% Similarity=1.010 Sum_probs=15.9
Q ss_pred CccchhhhhhhccCCCccCccc
Q psy11901 54 FESCKICRQKVHQVGSHYCQAC 75 (100)
Q Consensus 54 ~~~C~~CK~~v~q~g~~YCq~C 75 (100)
...|..|-|++|. .+-.|.-|
T Consensus 194 MK~C~sC~qqIHR-NAPiCPlC 214 (230)
T PF10146_consen 194 MKTCQSCHQQIHR-NAPICPLC 214 (230)
T ss_pred cchhHhHHHHHhc-CCCCCccc
Confidence 4799999999999 45554444
No 54
>PF10417 1-cysPrx_C: C-terminal domain of 1-Cys peroxiredoxin; InterPro: IPR019479 This entry represents the C-terminal domain of 1-Cys peroxiredoxin, a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding alcohols []. The C-terminal domain is crucial for providing the extra cysteine necessary for dimerisation of the whole molecule. Loss of the enzyme's peroxidase activity is associated with oxidation of the catalytic cysteine found upstream of this domain. Glutathionylation, presumably through its disruption of protein structure, facilitates access for GSH, resulting in spontaneous reduction of the mixed disulphide to the sulphydryl and consequent activation of the enzyme []. The domain is associated with IPR000866 from INTERPRO, which carries the catalytic cysteine. ; GO: 0051920 peroxiredoxin activity, 0055114 oxidation-reduction process; PDB: 1ZOF_E 2H01_A 3EMP_D 1YF1_G 1YF0_D 1N8J_C 1YEP_D 1YEX_D 2V41_H 2V32_C ....
Probab=20.91 E-value=59 Score=18.89 Aligned_cols=12 Identities=58% Similarity=1.110 Sum_probs=10.3
Q ss_pred CccCCCCCCCCC
Q psy11901 12 KVITPDNWKSGS 23 (100)
Q Consensus 12 kl~tPd~~k~gs 23 (100)
.++||.-|+.|.
T Consensus 9 ~v~tPanW~pGd 20 (40)
T PF10417_consen 9 GVATPANWKPGD 20 (40)
T ss_dssp SSBBCTTTCTTS
T ss_pred CcccCcCCCCCC
Confidence 489999999875
No 55
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=20.48 E-value=26 Score=17.38 Aligned_cols=14 Identities=21% Similarity=0.693 Sum_probs=8.1
Q ss_pred ccccCccccccccc
Q psy11901 82 CAMCGKKLLDVKNY 95 (100)
Q Consensus 82 CamCGKki~dt~~y 95 (100)
|.+|++...+-..|
T Consensus 3 C~~C~~~f~s~~~~ 16 (25)
T PF12874_consen 3 CDICNKSFSSENSL 16 (25)
T ss_dssp ETTTTEEESSHHHH
T ss_pred CCCCCCCcCCHHHH
Confidence 66666666554444
No 56
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=20.41 E-value=37 Score=22.72 Aligned_cols=14 Identities=50% Similarity=0.968 Sum_probs=7.8
Q ss_pred cccccccccCcccc
Q psy11901 77 YKKGICAMCGKKLL 90 (100)
Q Consensus 77 YkkGiCamCGKki~ 90 (100)
.+.|.|++||....
T Consensus 20 ~q~~~C~iC~~~~~ 33 (81)
T PF02945_consen 20 EQGGRCAICGKPLP 33 (81)
T ss_dssp HTTTE-TTT-SEEE
T ss_pred HhCCcCcCCCCCcc
Confidence 45568999998443
No 57
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=20.33 E-value=45 Score=21.89 Aligned_cols=22 Identities=23% Similarity=0.780 Sum_probs=16.3
Q ss_pred CccchhhhhhhccCCCccCcccccccccccccCcc
Q psy11901 54 FESCKICRQKVHQVGSHYCQACAYKKGICAMCGKK 88 (100)
Q Consensus 54 ~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKk 88 (100)
+..|+.|+.-++.. .|.+||-.
T Consensus 5 ~~AC~~C~~i~~~~-------------~Cp~Cgs~ 26 (64)
T PRK06393 5 YRACKKCKRLTPEK-------------TCPVHGDE 26 (64)
T ss_pred hhhHhhCCcccCCC-------------cCCCCCCC
Confidence 35899999888531 78888875
Done!